title: Cochleae explants cultured in vitro, neomycin 3

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

data_processing:
Preliminary processing of raw reads was performed using Casava 1.8 (Illumina)
Adapters and low-quality bases were trimmed using trimmomatic (version 0.23)
Trimmed reads for each sample were aligned to the Mus musculus UCSC mm10 genome using Hisat2
Aligned reads were counted with HTseq according to UCSC mm10 annotation
Differential expression analysis between conditions was performed using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: comma-delimmated file of raw counts

source_name: Cochleae explants

growth_protocol: Cochleae of P2 neonatal mice were isolated and cultured for 12 h, then damaged with 1 mM neomycin for 6 h and cultured for another 5 days with 10 μM EdU

extract_protocol:
Six to eight cultured cochleae were collected to isolate the total RNA using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN).
Libraries for RNA-seq were prepared using Illumina mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Cochleae explants

tag: treatment

value: neomycin


title: ADC1

status: Public on Sep 25 2022

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using the minfi package running on RStudio version 1.3.1093 based on the statistical language R version 3.5.1
Average beta-Values after normalization using the Noob method

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: methylation class

value: ADC

tag: conventional class

tag: initial diagnosis

value: Adenocarcinoma

tag: gender

value: male

tag: age

tag: localization

value: Nasal cavity

tag: tissue source

value: Others

tag: related publication

value: Capper, Acta Neuropathol 2018


title: Cochleae explants cultured in vitro, neomycin 1

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

value: WT


title: HuH-7 cells, sgKLB, biol rep 1

city: Beijing

first: yue

last: cui

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences，Beijing

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence.
Trimmed sequence were mapped to GRCh38/hg38 whole genome using Botwie2.
Read count extraction and normalization were performed using RSEM.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files with matrix table including FPKM values for every gene and every sample.

growth_protocol: HuH-7 and JHH-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated from in vitro cultured cells using TRNzol (Tiangen).
RNA-seq library construction and sequencing were performed by Berry Genomics (Berry Genomics, Beijing, China).

tag: cell line

value: liver cancer cells

tag: genotype

value: KLB knockout


title: MC011KO RNA-seq, rep2

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

country: USA

institute: Augusta University

data_processing:
Alignment was performed using STAR (v2.7.3a) aligner. Reads mapping to ribosomal and mitochondrial genome were removed before performing alignment. The raw read counts were estimated using HTSeq (v0.11.2). Read counts were normalized using DESeq2 to get the normalized counts.
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: DEseq2 output file including differential analysis results and normalized count table as well as raw count files generated by HTSeq

source_name: Stable cell line from IRF8KO fibrosarcoma

growth_protocol:
[stable cell line protocol] Tumors were dissected from mice approximately 3 months later and digested with collagenase solution [Collagenase, Sigma-Aldrich cat#C0130: 1 mg/mL, Hyaluronidase, Sigma-Aldrich, Cat#H3506: 0.1 mg/mL, and DNase I: 30 U/mL). The tumor cell mixture was then cultured for at least 10 passages to establish stable tumor cell line
The stable cell lines were grown in RPMI 1640 +FBS+ antibiotics

extract_protocol:
Total RNA was purified from tumor cells using the Direct-zol RNA microprep kit according to manufacturer’s instructions (Zymo Research, Irvine CA)
MedGenome Inc Custome library construction
Stranded mRNA-Seq

treatment_protocol: WT and IRF8 KO mice were injected subcutaneously with methylcholanthrene (MCA, Sigma-Aldrich, St Luis, MO) at 100 ug in 100 ul peanut oil per mouse

value: Tumor cell

value: KO

value: soft tissue sarcoma

tag: replicate

value: Replicate 2


title: HuH-7 cells, sgFGFR4, biol rep 2

value: FGFR4 knockout


title: Cochleae explants cultured in vitro, neomycin 2


title: ACC1

value: ACC

value: Adenoid cystic carcinoma

value: female

value: Paranasal sinus


title: Cochleae explants cultured in vitro, control 3

value: Cochleae explants

value: control


title: HuH-7 cells, sgNTC, biol rep 3


title: ALV_RMS1

value: ALV RMS

value: Alveolar rhabdomyosarcoma

value: male

value: Neuropathology, Heidelberg


title: MC011KO RNA-seq, rep1

value: Replicate 1


title: Cochleae explants cultured in vitro, control 2

value: WT


title: NEC1

value: NEC

value: Neuroendocrine carcinoma

value: Nasal cavity


title: SNUC1

value: NEC-like SMARCA4 ARID1A

value: SNUC


title: Mixed worms, whole worm, biol rep 2

status: Public on Sep 24 2022

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

data_processing:
Ribosomal RNA reads were filtered out using Bowtie2 (v2.4.2). The non-rRNA reads from each sample were mapped to the O. tipulae genome with STAR (v2.7.10).
The transcripts for each sample were assembled separately using the StringTie (v2.2.0) and merged into a non-redundant set of transcripts. The predicted coding regions (https://github.com/TransDecoder) from the transcripts were used to further evaluated and to remove artifacts, cryptic transcripts, and transcriptional noises based on their coding capacity (< 50%), the lack of splicing, and/or low expression.
For expression analysis, we used the HTSeq (v2.0.2) to get the read count for all transcripts.
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: tab deliminated file containing normalized expression data

organism: Oscheius tipulae

source_name: whole worm

extract_protocol:
Egg-laying worms were washed off plates and passed through a 70-µm mesh. This step allows existing eggs to fall through the mesh, leaving the mature worms on the top. These worms were then bleached with sodium hypochlorite solution (Sigma Cat# 425044-250ML, 0.5 M NaOH, 3% bleach) to collect embryos (largely 2-4 cell stage, Fig. S1). Early embryos were further developed in Virgin S Basal (VSB) medium (100 mM NaCl, 5.7 mM K2HPO4, 44.1 mM KH2PO4) at 25°C to reach to the desired embryonic stages. To prepare larval stages, the flow-through of the 70-µm mesh was further passed through a 25-µm mesh to separate mixed embryos from various stages of worms. These mixed embryos were developed in the VSB medium until all embryos reach to L1. The arrested L1s were plated on NGM with a robust OP50 lawn to develop at 20°C to synchronous stages of larvae, young adults, and mature adults. Alternatively, post-dauer larvae and worm samples were collected starting from the dauer harvested from the liquid culture. For adult males, we handpicked 200 males from the HIM-1 mutant for RNA-seq library replicate.
Total RNA was prepared using TRIzol (Invitrogen Cat# 15596026) protocol. The quality of the RNA was evaluated with the TapeStation 4200 (Agilent) and quantified with the Qubit™ 4 Fluorometer (Thermo Fisher). The ribosomal RNAs were removed using the RiboCop rRNA Depletion Kit (LEXOGEN Cat# No 144). The RNA-seq libraries were constructed using the CORALL Total RNA-Seq Library Prep Kit (LEXOGEN Cat# No 146)

tag: strain

value: whole worm

tag: developmental stage

value: Mixed worms


title: MC010KO RNA-seq, rep2

value: Tumor cell

value: KO

value: soft tissue sarcoma

value: Replicate 2


title: Dauer, whole worm, biol rep 1

value: Dauer


title: Post-dauer young adult, whole worm, biol rep 1

value: Post-dauer young adult


title: Mature Adult, whole worm, biol rep 2

value: Mature Adult


title: L4 Larvae, whole worm, biol rep 3

value: L4 Larvae


title: Mature Adult, whole worm, biol rep 1


title: Young Adult, whole worm, biol rep 2

value: Young Adult


title: Young Adult, whole worm, biol rep 1


title: L4 Larvae, whole worm, biol rep 2


title: L3 Larvae, whole worm, biol rep 3

value: L3 Larvae


title: L3 Larvae, whole worm, biol rep 2


title: Dauer, whole worm, biol rep 2


title: L2 Larvae, whole worm, biol rep 2

value: L2 Larvae


title: L1 Larvae, whole worm, biol rep 3

value: L1 Larvae


title: L1 Larvae, whole worm, biol rep 2


title: 150-200 cell, embryo, biol rep 1

source_name: embryo

value: embryo


title: L1 Larvae, whole worm, biol rep 1


title: 32-64 cell, embryo, biol rep 3


title: 64-128 cell, embryo, biol rep 2


title: 64-128 cell, embryo, biol rep 1


title: 100-150 cell, embryo, biol rep 1


title: Cochleae explants cultured in vitro, control 1

value: Cochleae explants

value: WT

value: control


title: 32-64 cell, embryo, biol rep 2


title: Post-dauer L3, whole worm, biol rep 2

value: whole worm

value: Post-dauer L3


title: MC010KO RNA-seq, rep1

value: Tumor cell

value: KO

value: Replicate 1


title: Post-dauer mature adult, whole worm, biol rep 2

value: Post-dauer mature adult


title: HuH-7 cells, sgNTC, biol rep 2

value: liver cancer cells


title: 32-64 cell, embryo, biol rep 1


title: Post-dauer mature adult, whole worm, biol rep 1


title: HuH-7 cells, sgNTC, biol rep 1


title: L2 Larvae, whole worm, biol rep 3


title: 16-32 cell, embryo, biol rep 3


title: Post-dauer young adult, whole worm, biol rep 2

value: Post-dauer young adult


title: Post-dauer L4, whole worm, biol rep 2

value: Post-dauer L4


title: Mixed worms, whole worm, biol rep 1

value: Mixed worms


title: 16-32 cell, embryo, biol rep 2


title: 8-16 cell, embryo, biol rep 3

value: 8-16 cell


title: 8-16 cell, embryo, biol rep 2


title: 4-8 cell, embryo, biol rep 3

value: 4-8 cell


title: 16-32 cell, embryo, biol rep 1


title: 8-16 cell, embryo, biol rep 1


title: Post-dauer L4, whole worm, biol rep 1


title: 2-4 cell, embryo, biol rep 2

value: 2-4 cell


title: 4-8 cell, embryo, biol rep 1

value: embryo


title: 2-4 cell, embryo, biol rep 3


title: 2-4 cell, embryo, biol rep 1


title: 2 cell, embryo, biol rep 1

value: 2 cell


title: embryo, 120min, biol rep2

library_source: genomic

data_processing:
Reads (R1 files only) were mapped to the genome with Bowtie2 v2.4.2
Mapped reads were processed with SAMtools v1.14
The 5’ position of each read was mapped, and its strand was determined with BEDTools v2.30.0 genomecov
For comparison between libraries reads were normalized to 1 million genome-mapped reads
Reads (R1 and R2 files) with two sequential telomeric sequences (TTAGGCTTAGGC) were obtained with grep v3.8. Reads were converted to the G-rich strand (TTAGGC)
Cutadapt v3.7 (-j 0 -m 20 -b TTAGGCTTAGGC) was used to trim the telomeric sequences
Reads were mapped to the genome and processed as previously described except 3' ends of the read were mapped
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: bigWig file containing the 5' end of reads
Supplementary files format and content: bigWig file containing telomere additon site
Library strategy: END-seq

extract_protocol:
Egg-laying worms were washed off plates and passed through a 70-µm mesh. This step allows existing eggs to fall through the mesh, leaving the mature worms on the top. These worms were then bleached with sodium hypochlorite solution (Sigma Cat# 425044-250ML, 0.5 M NaOH, 3% bleach) to collect embryos (largely 2-4 cell stage, Fig. S1). Early embryos were further developed in Virgin S Basal (VSB) medium (100 mM NaCl, 5.7 mM K2HPO4, 44.1 mM KH2PO4) at 25°C to reach to the desired embryonic stages
An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Briefly, embryos were embedded in agarose plugs to protect the DNA from exogenous breaks. Some plugs were digested with the restriction enzyme AsiSI (NEB, catalog # R0630) or FseI (NEB, catalog # R0588) to generate DSBs as an internal control. DSBs were blunted with exonuclease VII (NEB, catalog # R0630) and exonuclease T (NEB, catalog # M0625). Blunt ends were A-tailed and capped with END-seq adaptor 1, a biotinylated hairpin adaptor. DNA was liberated from the plugs and sheared to ~200-300 bp with a Covaris M220 focused-ultrasonicator (130 L tube, peak power 50, duty 16, cycles/burst 200 for 420 seconds). DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen, catalog # 65001). The other ends broken by sonication were repaired and A-tailed with END-seq adaptor 2. Hairpins were digested with USER (NEB, catalog # M5505), and the DNA was amplified with Illumina TruSeq primers and barcodes.

tag: time after_harvest

value: embryos were developed for embryo, 120min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)

value: FseI


title: embryo, 120min, biol rep1

value: embryos were developed for embryo, 120min, biol rep1 after harvest (a typical harvest is between the 2-4 cell stages)


title: 4-8 cell, embryo, biol rep 2


title: embryo, 60min, biol rep2

value: embryos were developed for embryo, 60min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)

tag: treatment


title: embryo, 90min, biol rep1

value: embryos were developed for embryo, 90min, biol rep1 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 30min, biol rep3

value: embryos were developed for embryo, 30min, biol rep3 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 30min, biol rep2

value: embryos were developed for embryo, 30min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 60min, biol rep1

value: embryos were developed for embryo, 60min, biol rep1 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 30min, biol rep1

value: embryos were developed for embryo, 30min, biol rep1 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 15min, biol rep2

value: embryos were developed for embryo, 15min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)


title: Male Adult, whole worm, biol rep 1

value: whole worm

value: Male Adult


title: embryo, 0min, biol rep4

value: embryos were developed for embryo, 0min, biol rep4 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 0min, biol rep2

value: embryos were developed for embryo, 0min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 15min, biol rep1

value: embryos were developed for embryo, 15min, biol rep1 after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 0min, biol rep3

value: embryo

value: embryos were developed for embryo, 0min, biol rep3 after harvest (a typical harvest is between the 2-4 cell stages)


title: Post-dauer L3, whole worm, biol rep 1

value: Post-dauer L3


title: embryo, 0min, atac

data_processing:
Reads were mapped to the genome with Bowtie2 v2.4.2
Mapped reads were processed with SAMtools (v1.14) and BEDtools (v2.30.0). Reads were normalized based on the genome-mapped reads
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: bigWig

extract_protocol:
Egg-laying worms were washed off plates and passed through a 70-µm mesh. This step allows existing eggs to fall through the mesh, leaving the mature worms on the top. These worms were then bleached with sodium hypochlorite solution (Sigma Cat# 425044-250ML, 0.5 M NaOH, 3% bleach) to collect embryos (largely 2-4 cell stage, Fig. S1). Early embryos were further developed in Virgin S Basal (VSB) medium (100 mM NaCl, 5.7 mM K2HPO4, 44.1 mM KH2PO4) at 25°C to reach to the desired embryonic stages. Embryos were resuspended in 5 mL of cold ATAC-seq lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Triton-X 100, 0.1% NP40 alternative) and transferred to a dounce homogenizer kept cold on ice.  Embryos were dounced ten times before being transferred to a 15 mL Eppendorf tube and spun down at 500 x g for 5 minutes at 4°C.
Samples were tagmented and subsequently purified using an ATAC-seq kit (Active Motif, 53150) according to the cell sample protocol. Libraries were amplified through ten rounds of PCR

value: embryos were developed for 0min after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 90min, atac

value: embryos were developed for 90min after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 30min, atac

source_name: embyro

value: embyro

value: embryos were developed for 30min after harvest (a typical harvest is between the 2-4 cell stages)


title: embryo, 0min, biol rep1

value: embryos were developed for embryo, 0min, biol rep1 after harvest (a typical harvest is between the 2-4 cell stages)

value: AsiSI


title: embryo, 210min, atac

value: embryos were developed for 210min after harvest (a typical harvest is between the 2-4 cell stages)


title: Patient 35

type: RNA

city: Fort Collins

first: Daniel

last: Regan

address: 1678 Campus Delivery

institute: Colorado State University

hyb_protocol: Sequence specific flurorescent reporter probes and biotinlyated capture probes were hybridized to target nucleic acid transcript sequences overnight at 65c for 19 h, followed by a a series of automated washes and immobilization onto a strepavidin lined cartridge for data collection

scan_protocol: Digital images from the cartridges were obtained over 4 h using the nCounter Digital Analyzer (CCD camera and microscope objective lens) using 555 FOV data resolution. Digital counts were tabulated and exported as comma separated values (CSV).

data_processing: Raw count data underwent positive contorl and housekeeping gene normalization and normalization quality control using the nSolver software.

organism: Canis lupus familiaris

source_name: tumor

label_protocol: Depending on RNA qualities, up to 600ng total RNA was used in a multiplexed probeset hybridization reaction following manufacturer protocol

extract_protocol: RNA was extracted from archived frozen and FFPE tumor and normal tissues using Qiagen RNeasy and Qiagen RNeasy FFPE kits, respectively. For the FFPE samples, five to seven tissue sections (5-10 µm thick) were cut from each block and pooled for RNA extraction. RNA was extracted from flash-frozen lymph node tumor tissues using the RNeasy Plus Mini Kit (QIAGEN) following manufacturer protocol. Depending on starting material, samples were eluted in 30-50uL and were initially checked for quantity and purity on a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher) prior to being stored at -80c until further processing. Samples were additionally quantity and quality checked using the RNA High Sensitivity assays on the Qubit 2.0 Fluorometer (Invitrogen/LifeTechnologies) and 5200 Fragment Analyzer Automated CE System (Agilent), respectively.

value: tumor


title: Patient 34


title: Patient 31


title: Patient 32


title: Patient 36


title: Patient 33


title: Patient 30


title: Patient 29


title: HeLa, MMS 5.9 mM 1h treated, spMag1/C1/C3 enriched alkylation damage

city: Riverside

first: Chaoxing

last: Liu

state: CA

address: 900 University Ave

institute: University of California, Riverside

description: Mitochondrial DNA

data_processing:
FastQC v0.11.3 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check the quality of raw sequencing reads. Raw reads were trimmed using Trim_Galore (v0.6.5). PCR duplicates were removed using Fastuniq (v1.1) with default settings. The reads were aligned to the hg38 reference genome using Bowtie2 (v2.4.2) 10 with parameters -L 20 -N 1. Furthermore, alignment files were sorted by position and indexed using Samtools (v1.14). Finally, VarScan2 (v2.4.4) was used for variant calling.
Assembly: hg38
Supplementary files format and content: Microsoft Excel files include DNA modification position sites values for each sample

source_name: HeLa Tet-On 3G Cell Line

growth_protocol: HeLa cells were cultured in DMEM containing 4.5 g/L glucose (Life Technologies, 12100046), 10% (v/v) tetracycline-free FBS (Takara, 631106), 2 µg/mL of puromycin, and 100 mg/L G418 at 37 °C and 5% CO2.

extract_protocol:
Mitochondria were purified using an mtDNA isolation kit (BioVision, K280) along with custom procedures. Around 3 × 107 cells were resuspended in 5 mL of 1X cytosol extraction buffer, and the suspension was kept on ice for 15 min. Cells were homogenized using an ice-cold Dounce tissue grinder (90 passes). The homogenate was centrifuged at 1200 g for 5 min at 4 °C. Afterward, the supernatant was transferred to a new tube and spun at 1200 g for another 4 min at 4 °C. The supernatant was aspirated and centrifuged at 15000 g for 10 min at 4 °C. The pelleted mitochondria were resuspended in 200 µL of DNase reaction buffer (5 mM HEPES buffer pH 7.4, 210 mM mannitol, 70 mM sucrose, 10 mM MgCl2, 5 mM CaCl2, 0.2% (w/v) BSA, 1X proteinase inhibitor cocktails (Thermo Fisher Scientific, A32955) and 200 U of turbo nuclease (Millipore Sigma, T4330) at 37 °C for 15 min to remove nDNA contaminants. The suspension was added by 1 mL of fresh 1X cytosol extraction buffer followed by centrifugation at 15000 g for 10 min at 4 °C. Finally, the purified mitochondria pellet was washed with 1 mL of fresh 1X cytosol extraction buffer before mtDNA extraction using the Monarch genomic DNA purification kit (NEB, T3010L) to obtain purified mtDNA for the TruAP-seq workflow.
Purified mtDNA (50 μL) were broken into 250-500 bp fragments using Covaris M220 system according to manufacturer-recommended procedures, followed by quantification using a Qubit fluorometer. The DNA fragments were end repaired and dA-tailed using NEBNext® Ultra™ II DNA library prep kit for Illumina (E7645S). Custom adapters (ODN-24/25, at a 15 μM final concentration) were incubated with the mtDNA sample at 20 °C for 40 min on a dry bath incubator without heating lids. If DNA input is ≤ 100 ng, use a final concentration of 1.5 μM for adapters. Sera-Mag Select beads (1.5 X) were used for purification, followed by elution with milli-Q water (30 μL). C1 and DBCO-PEG4-biotin were conjugated (80 nmol, 1 eq. C1 and 1.3 eq. DBCO-PEG4-biotin at 37 °C for 2 h) and stored at -20 °C as an aliquot for further use. Ligated mtDNA fragments were incubated with an aliquot of C1-DBCO-PEG4-biotin in a 50 µL reaction mixture containing 100 mM MES buffer, pH 6.5 at 37 °C for 1 h with shaking at 850 rpm. Products were purified with a BioRad P6 column with the packaging buffer replaced with Milli-Q water before purification. Hydrophilic streptavidin magnetic beads (50 μL, S1421S, NEB) were washed with 1X binding and washing buffer (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) (3 x 500 μL) and resuspended in 50 μL 2X binding and washing buffer (10 mM Tris pH 7.5, 1 mM EDTA, 2 M NaCl, 0.1 % Tween 20). The purified mtDNA fragments containing AP-C1-DBCO-PEG4-biotin conjugates (50 μL) were mixed with the magnetic beads and incubated for 15 min at room temperature with gentle rotation. Beads were washed with 1X binding buffer (6 X 500 μL) and incubated with 50 μL C3 elution solution (100 mM MES buffer, pH 6.5, 1 mM C3) at 37 °C for 1 h with shaking at 850 rpm. Lastly, the solution was placed on a magnetic stand, and the supernatant containing enriched AP-DNA fragments was collected. The enriched sample was amplified via PCR using i5 and i7 index primers and Terra PCR Direct polymerase. The PCR condition was as follows, denaturation at 98°C for 2 min, N cycles of 98°C for 10 s, annealing 60°C for 15 s, extension 68°C for 50 s; and final extension 68 °C 5 min. The number of PCR cycles (N) was determined empirically based on the Ct value of the sample in qPCR plus three. The condition strikes a balance between providing sufficient library fragments for successful sequencing experiments and avoiding PCR artifacts and over-cycling. Sera-Mag Select beads (1.5 X) were used for further purification, followed by elution with milli-Q water (30 μL). For mtDNA samples from MMS-treated or untreated cells, freshly purified mtDNA was fragmented, ligated, and purified as described above. Background AP sites were masked via reactions with EtONH2 (1 mM EtONH2 at 37 °C for 30 min with shaking at 850 rpm). Afterward, N7mG and N3mA were converted to AP sites via a reaction with SpMag1 (137 pmol) at 25 °C for 30 min. The resulting sample was processed via the TruAP-seq workflow as described above.
TruAP-seq or EtONH2-SpMag1 assisted TruAP-seq

treatment_protocol: Untreated, doxycycline and apurinic/apyrimidinic endonuclease 1 (APE1) inhibitor (C52) treated, MMS (0.1 mM) 24h treated,  MMS (5.9 mM) 1h treated

value: HeLa Tet-On 3G Cell Line

value: MMS 5.9 mM 1h treated Cells, spMag1/C1/C3 enriched alkylation damage


title: HeLa, MMS 5.9 mM 1h treated, unenriched alkylation damage

description: Mitochondrial DNA

value: MMS 5.9 mM 1h treated Cells, unenriched alkylation damage


title: Male Adult, whole worm, biol rep 2

value: whole worm

value: Male Adult


title: HeLa, untreated, unenriched alkylation damage, rep2

description: Mitochondrial DNA

value: untreated Cells, unenriched alkylation damage


title: Patient 28


title: Patient 27


title: Patient 25


title: Patient 26


title: embryo, 90min, biol rep2

value: embryo

value: embryos were developed for embryo, 90min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)

value: FseI


title: HeLa, untreated, spMag1/C1/C3 enriched alkylation damage, rep2

description: Mitochondrial DNA

value: untreated Cells, spMag1/C1/C3 enriched alkylation damage


title: Patient 24


title: HeLa, MMS 0.1 mM 24h treated, unenriched alkylation damage

description: Mitochondrial DNA

value: MMS 0.1 mM 24h treated Cells, unenriched alkylation damage


title: Patient 23


title: Patient 22


title: HeLa, MMS 0.1 mM 24h treated, spMag1/C1/C3 enriched alkylation damage

description: Mitochondrial DNA

value: MMS 0.1 mM 24h treated Cells, spMag1/C1/C3 enriched alkylation damage


title: Patient 21


title: Patient 19


title: HeLa, untreated, spMag1/C1/C3 enriched alkylation damage, rep1

description: Mitochondrial DNA


title: Mixed embryos, embryo, biol rep 1

value: Mixed embryos


title: HeLa, doxycycline and C52 treated, unenriched AP

description: Mitochondrial DNA

value: doxycycline and C52 treated Cells, unenriched AP


title: Patient 18


title: HeLa, untreated, unenriched alkylation damage, rep1

description: Mitochondrial DNA


title: HeLa, untreated, C1/C3 enriched AP

description: Mitochondrial DNA

value: untreated Cells, C1/C3 enriched AP


title: HeLa, doxycycline and C52 treated, C1/C3 enriched AP

description: Mitochondrial DNA

value: doxycycline and C52 treated Cells, C1/C3 enriched AP


title: HeLa, untreated, unenriched AP

description: Mitochondrial DNA

value: untreated Cells, unenriched AP


title: Patient 17

value: tumor


title: Patient 20


title: Patient 11


title: Patient 14


title: Patient 16


title: Patient 15


title: Patient 13


title: Patient 12


title: MRC5

city: Miyazaki

first: Koichiro

last: Nishino

state: Miyazaki

address: 1-1 Gakuen-Kibanadai-Nishi

department: Veterinary Medicine

country: Japan

institute: University of Miyazaki

description: Fetal lung fibroblast-derived cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

source_name: Fetal lung fibroblast-derived cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: Male

value: Somatic cells

tag: disease state

value: normal


title: IMR90

description: Fetal lung fibroblast-derived cells

value: Female


title: Patient 10


title: Patient 9

source_name: mucosal stroma

value: mucosal stroma


title: Patient 8


title: Patient 7


title: Patient 6


title: Control Sample

city: Fukui

first: Masaya

last: Nagaya

address: 3-9-1 Bunkyo

institute: University of Fukui

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
RaGene-2_0-st.pgf
RaGene-2_0-st.mps

label: biotin

organism: Rattus norvegicus

source_name: Rat lense, without galactose

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

value: Sprague Dawley

value: lens


title: Galactose-2

source_name: Rat lense, 30mM galactose, replicate2


title: KU55933

source_name: Rat lense, 30mM galactose, 20µM KU55933 added


title: Patient 5


title: Galactose-1

source_name: Rat lense, 30mM galactose, replicate1


title: DFM2

description: Dermal Fibroblast-derived cells

source_name: Dermal Fibroblast-derived cells


title: AZD0156

source_name: Rat lense, 30mM galactose, 20µM AZD0156 added


title: Galactose-3

source_name: Rat lense, 30mM galactose, replicate3


title: DFM1

description: Dermal Fibroblast-derived cells


title: UtE1104

description: Endometrium-derived cells

source_name: Endometrium-derived cells


title: Patient 4


title: Edom22

description: Menstrual Blood-derived cells

source_name: Menstrual Blood-derived cells


title: DFMF1

description: Fetal dermal Fibroblast-derived cells

source_name: Fetal dermal Fibroblast-derived cells


title: RNA-MRC-iPS-7

description: MRC5-derived iPS cells

source_name: MRC5-derived iPS cells

value: inducible pluripotent stem cells


title: Patient 3


title: Patient 1


title: RNA-MRC-iPS-6-2

description: MRC5-derived iPS cells


title: Patient 2


title: RNA-MRC-iPS-23

description: MRC5-derived iPS cells


title: Cortex, KO, 959

city: Toronto

first: Karun

last: Singh

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Krembil Research Institute

data_processing:
Qaulity checked with the FastQC tool
Adaptor sequences were trimmed with the trimmomatic tool
Alignment to the mouse genome was done using the HISAT2 alignment program
The featureCounts tool was used to count read per gene
DESEQ2 was used to determine significant differentially expressed genes between Taok2 WT and KO samples
Assembly: GCRm38 (NCBI)
Supplementary files format and content: Total_Male_KO_DESEQ.xlsx
Supplementary files format and content: DESEQ2 output file with adjusted significance values
Supplementary files format and content: Taok2_KO_Male_Normalized_Counts_tabular.xlsx
Supplementary files format and content: Normalized gene counts for each sample

source_name: Brain

extract_protocol:
RNA was extracted using Trizol and mRNA was purified using poly(A) selection
RNA libraries for RNA-seq were prepared by the Center of Applied Genomics using the mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Brain

value: Cortex

value: Taok2 -/-


title: Cortex, WT, 911

value: Wildtype


title: Cortex, KO, 968


title: Cortex, KO, 920


title: RNA-MRC-iPS-21

description: MRC5-derived iPS cells


title: RNA-MRC-iPS-18

description: MRC5-derived iPS cells


title: Cortex, WT, 909


title: RNA-MRC-iPS-10

description: MRC5-derived iPS cells


title: RNA-MRC-iPS-1

description: MRC5-derived iPS cells


title: RNA-IMR-iPS-4

description: IMR90-derived iPS cells

source_name: IMR90-derived iPS cells


title: RNA-IMR-iPS-18

description: IMR90-derived iPS cells


title: OMM1_GDC-0349_SAMMSON ASO #3

city: Ghent

first: Shanna

last: Dewaele

address: Corneel Heymanslaan

country: Belgium

institute: Ghent University

description: 3' end RNA

data_processing:
raw reads were evaluated using FastQC (v0.11.3)
Adapter content and polyA tails were removed using bbmap (v38.23)
reads were mapped to hg38 whole human genome using bowtie v2.2.3, followed by splice junction identification using TopHat and quality after mapping is performed with QoRTs (v1.0.7)
Gene expression was quantified based on the Ensemble transcriptome annotation using HTSeq (v0.6.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: uveal melanoma cells

growth_protocol: Uveal melanoma cells were cultured in DMEM F12:RPMI 1640 (1:1) + 10% FBS

extract_protocol:
After 24h of treatment, RNA was obtained by singleshot lysis. Illumina Quant Seq 3'end library prep was used with 2.5 µl of RNA lysates for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected using lipofectamine 2000 (for ASO treatment (50 nM)) and subsequently GDC-0349 (0.625 µM) or 0.006% DMSO was added in 96 well plates

value: GDC-0349 (0.625 microM) + SAMMSON ASO (50 nM)


title: OMM1_GDC-0349_SAMMSON ASO #2

description: 3' end RNA


title: OMM1_SAMMSON ASO#4

description: 3' end RNA

value: SAMMSON ASO (50 nM)


title: RNA-MRC-iPS-15

description: MRC5-derived iPS cells


title: RNA-DFM2-iPS-5

description: DFM2-derived iPS cells

source_name: DFM2-derived iPS cells


title: PEC_untreated [PEC_ctl]

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

source_name: primary cell culture

growth_protocol: Human PEC derived from whole glomeruli culture prepared by standard sieving technique through graded mesh screens (60, 80 and 150 mesh) and plated in EGM-MV media (Lonza) supplemented with 20% FBS (Hyclone).

extract_protocol:
The single cell suspension with 98% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions

treatment_protocol: For panobinostat treatment, cells were stimulated with 0.2 µM panobinostat (LBH-589, MedChemExpress) at passage 1 for 48 hours

value: parietal epithelial cells

value: adult

tag: passage

value: untreated


title: OMM1_GDC-0349_SAMMSON ASO #1

description: 3' end RNA


title: OMM1_GDC-0349_SAMMSON ASO #4

description: 3' end RNA


title: RNA-IMR-iPS-17-2

description: IMR90-derived iPS cells


title: 606A1

description: Cord Blood-derived iPS cells

source_name: Cord Blood-derived iPS cells


title: RNA-IMR-iPS-17-1

description: IMR90-derived iPS cells


title: RNA-IMR-iPS-1

description: IMR90-derived iPS cells


title: 585A1

description: Peripheral Blood-derived iPS cells

source_name: Peripheral Blood-derived iPS cells

value: Male


title: OMM1_SAMMSON ASO#1

description: 3' end RNA


title: Cortex, WT, 910


title: RNA-DFMF1-iPS-11-2

description: DFMF1-derived iPS cells

source_name: DFMF1-derived iPS cells


title: OMM1_GDC-0349#1

description: 3' end RNA


title: OMM1_GDC-0349#3

description: 3' end RNA


title: RNA-DFMF1-iPS-11-1

description: DFMF1-derived iPS cells


title: OMM1_GDC-0349#2

description: 3' end RNA


title: OMM1_DMSO#4

description: 3' end RNA

value: DMSO (0.006 percent)


title: OMM1_GDC-0349#4

description: 3' end RNA


title: RNA-DFMF1-iPS-3

description: DFMF1-derived iPS cells

value: normal


title: Retro-UtE-iPS-11

description: UtE1104-derived iPS cells

source_name: UtE1104-derived iPS cells

value: Female


title: OMM1_DMSO#3

description: 3' end RNA


title: RNA-DFMF1-iPS-7-1

description: DFMF1-derived iPS cells


title: OMM1_NTC #3

description: 3' end RNA

value: NTC ASO (50 nM)


title: RNA-DFM1-iPS-1

description: DFM1-derived iPS cells

source_name: DFM1-derived iPS cells


title: PEC_panobinostat [PEC_tr]

value: 0.2 uM panobinostat (LBH-589) 48h


title: OMM1_NTC #4

description: 3' end RNA


title: OMM1_SAMMSON ASO#2

description: 3' end RNA


title: Retro-Mim-iPS-9

description: Auricular Cartilage-derived iPS cells

source_name: Auricular Cartilage-derived iPS cells


title: Retro-MRC-iPS-25

description: MRC5-derived iPS cells


title: OMM1_DMSO#1

description: 3' end RNA


title: OMM1_NTC #2

description: 3' end RNA


title: LCS8269_DR_WT04

city: Chicago

first: David

middle: A

last: Reed

state: IL

address: 801 South Paulina Street

department: Department of Oral Biology

institute: University of Illinois at Chicago

data_processing:
Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system
For bioinformatics analysis, in house scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases (56). Then sequence quality was verified using FastQC
HISAT2 (57) was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie (58). Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie (58) and edgeR (59) was used to estimate the expression levels of all transcripts
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/
Supplementary files format and content: FPKMs and counts

source_name: mandibular condular cartilage

growth_protocol: Primary cells isolated from mandibular condylar cartilage of 10-14 day old pups, digested overnight in collagenase, and plated. RNA collected at passage 4

extract_protocol:
QIAGEN RNEasy kit
RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification
After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip
a Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation proto

treatment_protocol: None, normal growth conditions in AMEM, heat inactivated FBS, L-Glut, Pen, and Plasmocin

value: 10-14 day old pups

value: mandibular condular cartilage

value: primary mandibular fibrochondrocytes

value: WT

value: Norm AMEM growth conditions


title: OMM1_NTC #1

description: 3' end RNA


title: LCS8269_DR_WT03


title: Retro-Mim-iPS-6

description: Auricular Cartilage-derived iPS cells

value: inducible pluripotent stem cells


title: OMM1_SAMMSON ASO#3

description: 3' end RNA


title: 92.1_GDC-0349_SAMMSON ASO #3

description: 3' end RNA

value: GDC-0349 (0.625 microM) + SAMMSON ASO (50 nM)


title: LCS8269_DR_WT02


title: Episomal-Edom-iPS-9-2

description: Edom22-derived iPS cells

source_name: Edom22-derived iPS cells


title: RNA-IMR-iPS-15

description: IMR90-derived iPS cells


title: 92.1_GDC-0349_SAMMSON ASO #2

description: 3' end RNA


title: LCS8269_DR_WT01


title: OMM1_DMSO#2

description: 3' end RNA


title: 92.1_SAMMSON ASO#3

description: 3' end RNA

value: SAMMSON ASO (50 nM)


title: Retro-Edom-iPS-K3

description: Edom22-derived iPS cells


title: LCS8269_DR_NG2ko04

value: NG2/CSPG4 -/-


title: Episomal-Edom-iPS-9-1

description: Edom22-derived iPS cells


title: 92.1_GDC-0349_SAMMSON ASO #1

description: 3' end RNA


title: LCS8269_DR_NG2ko03


title: Episomal-Edom-iPS-8

description: Edom22-derived iPS cells


title: 92.1_SAMMSON ASO#4

description: 3' end RNA


title: 92.1_SAMMSON ASO#1

description: 3' end RNA


title: 92.1_SAMMSON ASO#2

description: 3' end RNA


title: 92.1_GDC-0349_SAMMSON ASO #4

description: 3' end RNA


title: 92.1_GDC-0349#4

description: 3' end RNA


title: LCS8269_DR_NG2ko02


title: POW3

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Genome_build: Data were aligned to GRCm39 (GCA_000001635.9) mouse reference genome assembly.
Supplementary_files_format_and_content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

source_name: Soleus muscle

extract_protocol:
DNA was isolated from the soleus myonuclei using the Qiagen DNA Micro Kit, using carrier RNA, according to the manufacturer protocol.
“Classic” RRBS library preparation was performed by digesting 10 ng of genomic DNA with 30 units of MspI enzyme (New England BioLabs), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 bp were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Zymo Research, D5030). Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.

treatment_protocol: Soleus muscle myonuclei from sedentary and PoWeR micei were isolated by fluorescent activated myonuclear sorting, DNA were extracted, and reduced representation bisulfite sequencing (RRBS) for methylation analysis

value: Myonuclei

value: 22-24 months

tag: condition

value: Progressive weighted wheel run (PoWeR)


title: RNA-MRC-iPS-6-1

description: MRC5-derived iPS cells

tag: gender

value: Male


title: POW2

tag: age


title: 92.1_GDC-0349#3

description: 3' end RNA


title: Liproxstatin-treated, replicate 2, scRNAseq

city: Cambridge

first: Gozde

last: Kar

address: Cambridge

country: United Kingdom

institute: AstraZeneca

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CT26 mouse model

extract_protocol:
Protocol of Miltenyi technology's beads (CD45 microbeads, positive selection) were used. CD45+ cells were isolated in tumors and freshly sent to be sequenced.
Library construction protocol of 10X guide CG000315 was followed.

value: CD45+ cells

value: Liproxstatin

value: CT26 mouse model

value: Balb/c

value: 9 weeks old


title: Liproxstatin-treated, replicate 1, scRNAseq

description: 10x Genomics


title: KSL0608-Se + irradiation rep5

city: Haikou

first: Wenwen

address: 58 People's Avenue

department: College of Pharmacy

institute: Hainan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Liver

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: group

value: KSL0608-Se + irradiation


title: Ctrl, replicate 2, scRNAseq

description: 10x Genomics

value: control


title: RNA-DFMF1-iPS-6

description: DFMF1-derived iPS cells

value: normal


title: Ctrl, replicate 1, scRNAseq

description: 10x Genomics


title: CON3

value: Sedentary


title: KSL0608-Se + irradiation rep3


title: KSL0608-Se + irradiation rep4


title: KSL0608-Se + irradiation rep2


title: 92.1_GDC-0349#2

description: 3' end RNA


title: CON2


title: 92.1_GDC-0349#1

description: 3' end RNA


title: 92.1_DMSO#4

description: 3' end RNA

value: DMSO (0.006 percent)


title: CON1


title: Aged control rep5

value: Aged control


title: KSL0608-Se + irradiation rep1


title: LCS8269_DR_NG2ko01

value: 10-14 day old pups

value: mandibular condular cartilage

value: primary mandibular fibrochondrocytes

value: NG2/CSPG4 -/-

value: Norm AMEM growth conditions


title: iPSC

city: Kashihara

first: Tsutomu

last: Nakazawa

state: Nara

address: 840, Shijo-cho

institute: Nara medical university

hyb_protocol: TAKARA bio standard protocol (Japan)

scan_protocol: TAKARA bio standard protocol (Japan)

data_processing: Affymetrix Gene Console -ExpressionStat

source_name: human iPSC

label_protocol: TAKARA bio standard protocol (Japan)

growth_protocol: Episomal vectors (OCT3/4, KLF4, SOX2, L-MYC, LIN28, mouse p53 dominant negative form) were electroporated to 2 × 105 of PBMCs using a Human T cell Nucleofector Kit (Lonza, Basel, Switzerland). The electroporation was performed by Nucleofector 2B (LONZA), program number V-024. The electroporated cells were cultured in AIM-V medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 200 IU/ml of recombinant human interleukin-2 (rhIL-2; Primmune Inc.) at 6 well plate coated by human laminin 511E8 fragment (iMatrix-511; Nippi, Tokyo, Japan). Then, Human T-Activator CD3/CD28 (Themo) were added for T cell activation. StemFitAK02N (AJINOMO, Tokyo, Japan) was charged day 2, 4, 6, and culture medium was completely changed to StemFitAK02N on day 8. The medium was changed following every 2 days.  The colonies were appeared on over 20 days and were picked up by pipette under stereo microscope (SZ61, Olympus, Tokyo, Japan). The colony-derived cells were in-cubated for 10 min in TrypLE select (Thermo) to prepare for single cells. The cells were cultured in StemFitAK02N supplemented with 10 µM Rock inhibitor (Y-27632; FUJI-FILM WAKO, Tokyo, Japan) in 6 well plate coated by human laminin 511E8 fragment. Next day, medium was changed to fresh StemfitAK02N without Rock inhibitor. Me-dium was changed to every 2 days until confluent well. The cellular characterization was performed after over 10 passages.

extract_protocol: The total RNA of the cells was extracted with NucleoSpin RNA (MA-CHEREY-NAGEL, Düren, Germany).

treatment_protocol: Embryoid bodies were induced from iPSCs in Primate ES Cell Medium (Repro-CELL) supplemented with KnockOut™ Serum Replacement (Thermo) for 7 days.

value: iPSC


title: EB

source_name: huamn EB

value: EB


title: 92.1_DMSO#2

description: 3' end RNA


title: RCC XEN [XEN093-218 P2]

city: STANFORD

first: James

last: Brooks

address: 300 PASTEUR DR

institute: STANFORD UNIVERSITY

description: XEN093-218 P2

data_processing:
NovaSeq PE150
Raw sequencing reads were aligned to the Ensembl GRCm38.p6 reference genome using STAR and gene counts were calculated using HTSeq. Transcript counts were normalized to the total of all transcripts detected in each sample, of which 98% corresponded to protein coding genes.
Assembly: GRCm38.p6
Supplementary files format and content: RCC_PDXs_Xens_RNAseq_Gene_Counts.tsv: Tab-delimited text file

source_name: Tumor

growth_protocol: Different RCC Tissues are implanted into the RAG2-/- mice through the subrenal or subcutaneous methods. The tumors were harvested for the RNAseq.

extract_protocol:
Total RNA was isolated from fresh frozen kidney tissues using an Allprep DNA/RNA mini kit (Qiagen).
Libraries were constructed with PrepX mRNA library kit (WaferGen) and sequenced to 50 bp using TruSeq SBS kit on Illumina Hiseq system.

value: Tumor

tag: type

value: RCC XEN


title: POW1

value: Myonuclei

value: 22-24 months

value: Progressive weighted wheel run (PoWeR)


title: Aged control rep4

value: Liver


title: 92.1_DMSO#1

description: 3' end RNA

source_name: uveal melanoma cells


title: MRC5

description: Fetal lung fibroblast-derived cells

hyb_protocol: Cy3-labeled cRNA was fragmented, hybridized onto the SurePrint G3 human GE microarrays 8x60K slide using standard Agilent protocol

scan_protocol: The array were canned by the Agilent Microarray scanner system

data_processing: Backgroud correction and quantile normalization between arrays were performed limma package for R

source_name: Fetal lung fibroblast-derived cells

label_protocol: Agilent Low-Input QuickAmp labeling kit

extract_protocol: Total RNA was extracted and purified from samples using Qiagen Rneasy kit according to standard instructions

value: Male

value: Somatic cells


title: RCC XEN [XEN093-216 P2]

description: XEN093-216 P2


title: 92.1_NTC #4

description: 3' end RNA

value: NTC ASO (50 nM)


title: IMR90

description: Fetal lung fibroblast-derived cells

value: Female


title: DFMF1

description: Fetal dermal Fibroblast-derived cells

source_name: Fetal dermal Fibroblast-derived cells


title: DFM2

description: Dermal Fibroblast-derived cells

source_name: Dermal Fibroblast-derived cells


title: Aged control rep3

value: Aged control


title: 92.1_DMSO#3

description: 3' end RNA

value: DMSO (0.006 percent)


title: RCC XEN [XEN072-160 P2]

description: XEN072-160 P2


title: 92.1_NTC #3

description: 3' end RNA


title: 92.1_NTC #2

description: 3' end RNA


title: RCC XEN [XEN072-159 P2]

description: XEN072-159 P2


title: Aged control rep2


title: RCC XEN [XEN072-158 P2]

description: XEN072-158 P2


title: Aged control rep1


title: RCC XEN [XEN093-217 P2]

description: XEN093-217 P2


title: RCC XEN [XEN072-153 P2]

description: XEN072-153 P2


title: Young control rep5

value: Young control


title: Young control rep4


title: UtE1104

description: Endometrium-derived cells

source_name: Endometrium-derived cells


title: 92.1_NTC #1

description: 3' end RNA


title: RNA-MRC-iPS-7

description: MRC5-derived iPS cells

source_name: MRC5-derived iPS cells

value: inducible pluripotent stem cells


title: RCC XEN [XEN054-175 P2]

description: XEN054-175 P2


title: Young control rep3


title: Young control rep2


title: RCC XEN [XEN054-171 P2]

description: XEN054-171 P2


title: RCC XEN [XEN054-170 P2]

description: XEN054-170 P2


title: Young control rep1


title: RNA-MRC-iPS-23

description: MRC5-derived iPS cells


title: Edom22

description: Menstrual Blood-derived cells

source_name: Menstrual Blood-derived cells


title: RCC XEN [XEN054-167 P2]

description: XEN054-167 P2


title: RNA-MRC-iPS-6-1

description: MRC5-derived iPS cells


title: RCC XEN [XEN054-169 P2]

description: XEN054-169 P2


title: P2: Control Day 2

city: Bronx

first: Ana

middle: Maria

last: Cuervo

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: day 2 of adipogenesis

hyb_protocol: Amount used was 0.6 μg Cy3-labeled aRNA. Agilent Hybridization Protocol

scan_protocol: Not provided

data_processing: Not provided

label_protocol: Not provided

extract_protocol: Total RNA was isolated with RLT buffer (Qiagen) and by using the RNeasy Plus mini kit (Qiagen, 74134) according to manufacturer’s instructions. RNA was quantified using a NanoDrop ND-1000 and quality was monitored with Agilent RNA 6000 Nano Assay Bioanalyzer.

treatment_protocol: 3T3L1 preadipocytes were cultured to confluency (Day 0) in DMEM supplemented with 10% heat-inactivated fetal bovine serum and 1% antibiotics. Adipocyte differentiation was initiated at Day 0 by culturing confluent cells in adipogenic induction medium consisting of the growth medium supplemented with 160nM insulin, 250nM dexamethasone, and 0.5mM 1-methyl-3-isobutylxanthine. The cultures were maintained at 37 ºC in a humidified incubator with 5% CO2. Cells were collected at Day 0 and Day 2.

value: 3T3L1 preadipocytes

value: control

value: Day 2 of adipogenesis


title: RNA-MRC-iPS-18

description: MRC5-derived iPS cells


title: DFM1

description: Dermal Fibroblast-derived cells


title: RCC XEN [XEN054-168 P2]

description: XEN054-168 P2

value: Tumor


title: RNA-MRC-iPS-10

description: MRC5-derived iPS cells


title: P5_2iL_F, teratoma

city: Tianjin

first: chen

last: jiyu

address: Nankai university

institute: Nankai university

description: P5_2iL_F, teratoma, bisulfite-seq (reduced representation)

data_processing:
Reads were trimmed to remove low quality bases and adaptor sequences with trim_galore (version 0.6.4)
clean reads were aligned to the mm10 genome from UCSC using Bismark with paired-end alignment mode (version 0.19.1)
Methylation calls were extracted using the Bismark methylation extractor
Quantification of methylation levels of CpGs was referred to previously published: the methylation level is estimated as the number of reads showing methylation over position /total reads (methylated and unmethylated)
Assembly: mm10
Supplementary files format and content: bed files, including colums: <chromosome> <start position> <end position> <methylation percentage>

source_name: teratoma

extract_protocol:
DNA was harvested using DNeasy Blood & Tissue Kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: teratoma

tag: culture condition


title: P5_LCDM_1, teratoma

description: P5_LCDM_1, teratoma, bisulfite-seq (reduced representation)

tag: tissue


title: P5_a2iL_1, teratoma

description: P5_a2iL_1, teratoma, bisulfite-seq (reduced representation)


title: P5_2iL, teratoma

description: P5_2iL, teratoma, bisulfite-seq (reduced representation)


title: L0: LAMP2A- Day 0

description: day 0 of adipogenesis

tag: cell type

value: Day 0 of adipogenesis


title: RNA-MRC-iPS-1

description: MRC5-derived iPS cells


title: RNA-MRC-iPS-15

description: MRC5-derived iPS cells


title: L2: LAMP2A- Day2

description: day 2 of adipogenesis


title: muscle, control

description: muscle, control, bisulfite-seq (reduced representation)

source_name: muscle

value: muscle


title: RCC XEN [XEN047-164 P2]

description: XEN047-164 P2

value: RCC XEN


title: RNA-IMR-iPS-4

description: IMR90-derived iPS cells

source_name: IMR90-derived iPS cells


title: RCC XEN [XEN047-162 P2]

description: XEN047-162 P2


title: RNA-MRC-iPS-21

description: MRC5-derived iPS cells


title: RNA-IMR-iPS-18

description: IMR90-derived iPS cells


title: M442

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

hyb_protocol: The OncoScan platform uses molecular inversion probe (MIP) technology, optimized for FFPE samples, to query over 220,000 SNPs at carefully selected genomic locations, evenly distributed across the genome and with increased density within approximately 900 cancer or cancer related genes. Molecular inversion probes were annealed to the DNA overnight at 58°C.  Each sample was then divided into 2 reactions and gap fill and ligation was performed at 58°C with either A and T deoxynucleotides in one reaction or G and C in the second reaction. Circular probe DNA was then linearized by cleavage at site #1 at 37°C, followed by two consecutive PCR amplifications performed on an ABI 9700 Gold-block thermal cycler.  Digestion with restriction enzyme HaeIII at cleavage site #2 at 37°C was then performed. The digested products along with biotinylated oligos were loaded onto the arrays and hybridized overnight at 49°C and 60 rpm.   The arrays were then washed, stained and scanned.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing:
CEL files containing the raw array data were analyzed using the OncoScan Console 1.3 software to create OSCHP files containing copy number calls.  The data were aligned to the National Center for Biotechnology Information (NCBI) human build GRCh37/hg19 assembly and viewed using the Chromosome Analysis Suite 3.1 (ChAS 3.1) and the OncoScan Nexus Copy Number 7.5 software.
Upon review of the copy number data, if necessary, re-centering of the copy number calls was done using the TuScan algorithm in the ChAS 3.1 software.

source_name: pediatric liver cancer

label_protocol: standard Affymetrix protocol

extract_protocol: 25-50 mg fresh frozen tissue or FFPE tumor blocks cut in 10-20 micron sections (5-10 slides per sample) and one H&E slide are utilized for DNA extraction. These specimens were prepared for genomic DNA extraction from tumor cell-rich areas, which were identified by a surgical pathologist (Dr. Terrada, Dr. Peters). DNA was isolated using the QIAamp DNA FFPE Tissue Kit (Qiagen) or QIAamp DNA Mini Kit for frozen tissue (Qiagen).

value: Tumor FFPE

tag: ctnnb1 mutation

tag: tert promoter mutation

value: WT

tag: Sex

value: M

tag: stage (pretext)

tag: status

value: DOD

tag: histology

value: HB FPA


title: P0: Control Day 0

description: day 0 of adipogenesis

tag: genotype

tag: treatment


title: RCC XEN [XEN047-163 P2]

description: XEN047-163 P2


title: RNA-IMR-iPS-17-2

description: IMR90-derived iPS cells

value: Female


title: RCC XEN [XEN047-112 P2]

description: XEN047-112 P2


title: RCC PDX [PDX093-11221904 P3]

description: PDX093-11221904 P3

value: RCC PDX


title: #5 PRP+Decidulization

city: Tokyo

first: Keiji

last: Kuroda

address: Nishi-shinjuku, 1-19-6, Shinjuku-ku

department: Center for Reproductive Medicine and Implantation Research

institute: Sugiyama Clinic Shinjuku

description: Human endometrial stromal cells were treated with PRP and decidualized.

hyb_protocol: Using the proprietary DNA-labeling reagent, the fragmented cDNA was labeled by terminal deoxynucleotidyl transferase and hybridized to GeneChip Human Gene 2.0 ST Array (Thermo Fisher Scientific). The array was incubated for 16 h at 45°C and then automatically washed and stained with GeneChip Hybridization, Wash and Stain Kit (Thermo Fisher Scientific).

scan_protocol: The array was scanned using a GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using GeneChip Command Console Software and Expression Console. Data were summarized according to the robust multichip analysis (RMA) algorithm.

source_name: Decidualized endometrial stromal cells with PRP treatment

label_protocol: Isolated total RNA was amplified and labeled using the GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer’s manual.

growth_protocol: The endometrial cells were cultured until they achieved confluency in 75-cm2 culture flasks at 37°C in 5% carbon dioxide and then passaged equally into four 1-well cell-culture dishes.

extract_protocol: Total RNA was extracted from primary HESC cultures using the RNeasy plus mini kit (QIAGEN, Tokyo, Japan).

treatment_protocol: Two cell-culture dishes were treated and cultured with 1 mL of PRP each for 24 h on 1 and 3 days after endometrial scratching. The other two dishes were cultured with media without PRP. Four days after scratching, two culture dishes with and without PRP treatment were maintained in DMEM/F12 without phenol red containing 2% DCC-FBS and treated with 0.5 mM cAMP and 1 μM P4 for decidualization. The other two culture dishes were cultured in media without cAMP and P4. All culture samples were harvested 9 days after scratching (5 days of decidualization).

value: Human endometrial stromal cells

value: PRP+Decidulization


title: RCC PDX [PDX093-053 P3]

description: PDX093-053 P3


title: M432

value: F


title: RCC PDX [PDX093-052 P3]

description: PDX093-052 P3


title: M415


title: M425

value: Biphasic NOS


title: RNA-IMR-iPS-17-1

description: IMR90-derived iPS cells

value: inducible pluripotent stem cells


title: M412

value: Equivocal NOS


title: RCC PDX [PDX072-105 P4]

description: PDX072-105 P4

value: Tumor


title: M433

value: DOD after Transplant

value: Older HB (age>8)


title: #5 Decidulization

description: Human endometrial stromal cells without PRP treatment were decidualized

source_name: Decidualized endometrial stromal cells without PRP treatment

value: Decidulization


title: #4 PRP

description: Human endometrial stromal cells were treated with PRP

source_name: Undifferentiated endometrial stromal cells with PRP treatment

value: PRP


title: RCC PDX [PDX072-104 P4]

description: PDX072-104 P4


title: RNA-IMR-iPS-15

description: IMR90-derived iPS cells


title: #5 PRP


title: M381

description: Copy number testing of both HB and HCC components

value: Tumor FFPE

value: WT

value: Alive


title: #3 PRP+Decidulization


title: #4 Decidulization


title: RNA-DFMF1-iPS-7-1

description: DFMF1-derived iPS cells

source_name: DFMF1-derived iPS cells

value: Male


title: #5 Control

description: Human endometrial stromal cells without PRP treatment

source_name: Undifferentiated endometrial stromal cells without PRP treatment

value: Control


title: #3 PRP


title: RNA-IMR-iPS-1

description: IMR90-derived iPS cells

value: Female


title: M342

value: M

value: Alive after Transplant


title: #4 PRP+Decidulization

value: Human endometrial stromal cells

value: PRP+Decidulization


title: #4 Control


title: RNA-DFMF1-iPS-3

description: DFMF1-derived iPS cells

value: inducible pluripotent stem cells


title: #3 Control


title: RCC PDX [PDX072-102 P4]

description: PDX072-102 P4

source_name: Tumor

value: RCC PDX


title: RNA-DFMF1-iPS-11-1

description: DFMF1-derived iPS cells


title: M341

value: Relapsed

value: Biphasic NOS


title: #3 Decidulization


title: M340


title: RCC PDX [PDX072-043 P4]

description: PDX072-043 P4

value: Tumor


title: RCC PDX [PDX072-103 P4]

description: PDX072-103 P4


title: #1 PRP+Decidulization


title: M339


title: RCC PDX [PDX072-042 P4]

description: PDX072-042 P4


title: RNA-DFM2-iPS-5

description: DFM2-derived iPS cells

source_name: DFM2-derived iPS cells


title: M333

value: Older HB (age>8)


title: M334

value: Equivocal NOS


title: RNA-DFMF1-iPS-6

description: DFMF1-derived iPS cells


title: RNA-DFM1-iPS-1

description: DFM1-derived iPS cells

source_name: DFM1-derived iPS cells


title: RCC PDX [PDX068-182 P6]

description: PDX068-182 P6


title: #1 PRP

value: PRP


title: RCC PDX [PDX068-063 P6]

description: PDX068-063 P6


title: Retro-UtE-iPS-11

description: UtE1104-derived iPS cells

source_name: UtE1104-derived iPS cells


title: #1 Decidulization

value: Decidulization


title: #1 Control


title: Retro-Mim-iPS-9

description: Auricular Cartilage-derived iPS cells

source_name: Auricular Cartilage-derived iPS cells


title: RCC PDX [PDX068-062 P6]

description: PDX068-062 P6


title: RCC PDX [PDX068-059 P6]

description: PDX068-059 P6


title: M332

value: Tumor FFPE

value: WT

value: F


title: Rat dermal fibroblast,  48h,  lnc-URIDS shRNA lentivirus, replicate2

city: guangzhou

first: Meng

last: Ren

address: 107 Yanjiang West Road

department: endocrinology department

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: Gene expression after 48hr lnc-URIDS shRNA lentivirus

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene 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 G2505C).

data_processing:
the scanned images were analysed using Agilent Feature Extraction software (v11.0.0.1).
Normalization of signal intensity using Agligent GeneSpring GX v12.1 software

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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: Dermal fibroblasts  were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 1,000 mg/L glucose (Gibco, Gaithersburg, MD) and 10%FBS.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (AGbio, China) following the manufacturer’s instructions.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: A lnc-URIDS shRNA lentivirus and a control lentivirus (GenePharma, Shanghai, China) were transfected into rat dermal fibroblasts at a multiplicity of infection (MOI) of 10, and 2 µg/mL puromycin (Thermo Fisher Scientific) for 48h was added to the medium of the cells.

value: fibroblast

value: lnc-URIDS shRNA lentivirus

value: lnc-URIDS knockdown


title: Rat dermal fibroblast,  48h,  lnc-URIDS shRNA lentivirus, replicate3


title: M329

value: M

value: DOD

value: HB FPA


title: RCC PDX [PDX068-058 P6]

description: PDX068-058 P6

value: RCC PDX


title: Retro-Mim-iPS-6

description: Auricular Cartilage-derived iPS cells

value: Female

value: inducible pluripotent stem cells


title: Retro-Edom-iPS-K3

description: Edom22-derived iPS cells

source_name: Edom22-derived iPS cells


title: Retro-MRC-iPS-25

description: MRC5-derived iPS cells

source_name: MRC5-derived iPS cells

value: Male


title: Rat dermal fibroblast,  48h,  lnc-URIDS shRNA lentivirus, replicate1


title: RCC PDX [PDX068-055 P6]

description: PDX068-055 P6

value: Tumor


title: Rat dermal fibroblast,  48h,  control lentivirus, replicate3

description: Gene expression after 48hr trasfected control lentivirus

value: control lentivirus

value: control


title: RCC PDX [PDX054-010 P5]

description: PDX054-010 P5


title: M327

value: Alive after Transplant


title: Episomal-Edom-iPS-9-2

description: Edom22-derived iPS cells


title: M326

value: Tumor FFPE

value: Alive


title: RCC PDX [PDX054-009 P5]

description: PDX054-009 P5


title: M331

value: Fresh Frozen Tumor

value: WT


title: Episomal-Edom-iPS-9-1

description: Edom22-derived iPS cells


title: Rat dermal fibroblast,  48h,  control lentivirus, replicate2

value: fibroblast


title: M325

value: F


title: M324

value: M

value: DOD after Transplant


title: Episomal-Edom-iPS-8

description: Edom22-derived iPS cells


title: Rat dermal fibroblast,  48h,  control lentivirus, replicate1


title: RCC PDX [PDX054-005 P5]

description: PDX054-005 P5


title: RCC PDX [PDX054-007 P5]

description: PDX054-007 P5


title: RCC PDX [PDX047-118 P4]

description: PDX047-118 P4


title: Cx30KO mSOD1

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

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

department: Neurology

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Cx30 deficient mutant SOD1 transgenic mice,  spinal cord, 8w old

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: spinal cord


title: M322

value: Biphasic NOS


title: P1 lens H3.3 ChIP-seq, control

first: William

last: Chang

address: 1301 Morris Park Ave

department: Ophthalmology

data_processing:
WGBS data were aligned and methylation called with Bismark and bowtie2
histone 3.3 ChIP-seq was aligned to the mm10 mouse genome using BWA
histone 3.3 profiles were calculated as bigWigs using deeptools (bamCoverage)
histone 3.3 peaks were called using SICER2
Assembly: mm10
Supplementary files format and content: bigWig, bed

source_name: lens

extract_protocol:
WGBS: genomic DNA was isolated from all samples using QIAamp DNA Mini Kits (Cat. ID 51304) followed by isopropanol precipitation (-80C, one hour incubation).
Histone 3.3 ChIP-seq: Mouse lenses from P0.5 CD1 mice (Charles River) were micro dissected into epithelium and fiber as previously described (Zhao et al. Epigenetics & Chromatin (2019). 150 lenses were used per sample duplicate (total 300 lenses) and stored at -80C prior to the use.  Preparation of samples for ChIP-seq was provided by ActiveMotif (Carlsbad, CA, USA).
WGBS: identical to GEO sample GSM2772524.
Histone 3.3 ChIP-seq: Immunoprecipitation was performed on 12 µg chromatin from microdissected lens cells with 5 µl anti-H3.3 antibody (Millipore, cat. # 17-10245), n=2 biological replicates, at ActiveMotif.

value: lens

tag: antibody


title: P1 lens fiber, H3.3 ChIP-seq, rep2

value: newborn lens fiber


title: WT

source_name: wild type mice, spinal cord,v8w old


title: mSOD1

source_name: mutant SOD1 transgenic mice spinal cord, 8w old


title: RCC PDX [PDX047-067 P4]

description: PDX047-067 P4

value: RCC PDX


title: RCC PDX [PDX047-066 P4]

description: PDX047-066 P4

value: Tumor


title: M320

source_name: pediatric liver cancer

value: DOD

value: Equivocal NOS


title: M319


title: P1 lens fiber, H3.3 ChIP-seq, rep1


title: M323

value: HB FPA


title: P1 lens epithelium, H3.3 ChIP-seq, rep2

value: newborn lens epithelium


title: RCC PDX [PDX047-065 P4]

description: PDX047-065 P4


title: P0.5 lens fiber, WGBS, rep3

value: embryonic lens fiber


title: RCC PDX [PDX047-064 P4]

description: PDX047-064 P4


title: M318

value: Tumor FFPE

value: Relapsed


title: RCC PDX [PDX047-087 P3]

description: PDX047-087 P3


title: P1 lens epithelium, H3.3 ChIP-seq, rep1


title: M315

value: Alive after Transplant

value: Older HB (age>8)


title: RCC PDX [PDX047-037 P3]

description: PDX047-037 P3


title: M317

value: M


title: RCC PDX [PDX047-035 P3]

description: PDX047-035 P3


title: M311

value: Fresh Frozen Tumor

value: F

value: COG 1


title: RCC PDX [PDX047-028 P3]

description: PDX047-028 P3


title: M310

value: WT

value: Biphasic NOS


title: RCC PDX [PDX047-027 P3]

description: PDX047-027 P3

value: RCC PDX


title: M309


title: M313


title: RCC PDX [PDX047-024 P3]

description: PDX047-024 P3

value: Tumor


title: M308

value: DOD


title: M307


title: 24 hour after drought treatment

city: taian

first: Zhiwen

last: Qiao

state: China

address: shandongtaian

institute: Shandong Agricultural University

description:
Test
SAMPLE 6

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.thermofisher.cn/cn/zh/home.html
The housekeeping gene MdActin (GenBank accession number CN938024) was used as the internal control.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

organism: Malus domestica

source_name: apple seedling

label_protocol: Reverse transcription of total RNA to cDNA using the kit (MonScript™ RTIII All-in-One Mix with dsDNase by Monad, REF: MR05101). The panel of PCR assays (StepOnePlus, Applied Biosystems by Thermo Fisher Scientific) following the Manufacturer’s instructions. Quantitative real-time PCR were performed with 40 cycles at 95°C for 15 seconds and 60°C for 60 seconds.

extract_protocol: Total RNAs of apple plantlets and Arabidopsis seedlings were isolated using an RNA extraction kit (Tiangen, Beijing, China)

value: cells from root, stem and leaves

tag: treatment time


title: oid_End rep2

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

description: blastoid-derived

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed RNA-Seq reads were mapped to hg38 genome using STAR (v2.5.2b). Refseq genes were quantified to FPKM using Stringtie.
Assembly: hg38
Supplementary files format and content: text files of FPKM values

molecule: polyA RNA

source_name: pluripotent stem cells

extract_protocol:
total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions.
mRNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: cell line

value: pluripotent stem cells

value: endoderm stem cell

tag: passage

value: passage 10


title: oid_End rep1

description: blastoid-derived


title: blastoid

description: 10X single cell RNA-seq

data_processing:
10× Genomics single-cell data were pre-processed using the Cell Ranger pipeline (v.4.0.0) with default parameters.
Integration, Dimensionality reduction,clusering and visualization were done by Seurat (v.3.2.3)
Assembly: hg38
Supplementary files format and content: rawcount.tab: Tab-delimited file of raw counts.

extract_protocol:
Standard 10× genomics scRNA-seq protocol
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) , according to the manufacturer’s instructions. Briefly,  cells were washed with 0.04% BSA DPBS for three times and were resuscitated to a concentration of 700~1200 cells/ul (viability≥85%). Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification. Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads.

value: blastoid


title: P0.5 lens epithelium, WGBS, rep3

value: lens

value: embryonic lens epithelium


title: P0.5 lens fiber, WGBS, rep1

value: embryonic lens fiber


title: E14.5 lens fiber, WGBS, rep3


title: E14.5 lens fiber, WGBS, rep1


title: E14.5 lens fiber, WGBS, rep2


title: P0.5 lens fiber, WGBS, rep2


title: P0.5 lens epithelium, WGBS, rep1


title: P0.5 lens epithelium, WGBS, rep2


title: E14.5 lens epithelium, WGBS, rep3


title: M306

value: Fresh Frozen Tumor

tag: age

value: M

value: Alive

value: Equivocal NOS


title: oid_TSC rep2

description: blastoid-derived

value: trophoblast stem cell


title: M305

tag: tissue

value: WT

value: F

value: Alive after Transplant


title: E14.5 lens epithelium, WGBS, rep2

tag: cell type


title: M304

value: Tumor FFPE

tag: ctnnb1 mutation

value: DOD


title: oid_TSC rep1

description: blastoid-derived

value: male

value: pluripotent stem cells


title: M303

tag: tert promoter mutation

value: Biphasic NOS


title: oid_pESC rep2

description: blastoid-derived

value: primed ESC

value: passage 10


title: 0 hour after drought treatment

description:
Control
SAMPLE 1

value: cells from root, stem and leaves

value: control


title: 1 hour after drought treatment

description:
Test
SAMPLE 2


title: 12 hour after drought treatment

description:
Test
SAMPLE 5


title: 6 hour after drought treatment

description:
Test
SAMPLE 4


title: 3 hour after drought treatment

description:
Test
SAMPLE 3


title: M301

tag: Sex


title: oid_pESC rep1

description: blastoid-derived


title: E14.5 lens epithelium, WGBS, rep1

value: lens

value: embryonic lens epithelium


title: SB+Dyrk2_3

city: Nishi-Shimbashi

first: Hiroshi

last: Kamioka

state: Tokyo

department: Gastroenterology and Hepatology

institute: Jikei University School of Medicine

description: co-indutroduced with myrAkt, Myc and mutant Hras

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: Biotin

source_name: Dyrk2-expressed liver tumor, Dyrk2 LKO mice, replicate 3

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: liver cancer


title: oid_nESC rep2

description: blastoid-derived

value: naive ESC


title: SB+HA_2

source_name: HA-expressed liver tumor, Dyrk2 LKO mice, replicate 2


title: oid_nESC rep1

description: blastoid-derived


title: anti-GBM-Mice_Ruxolitinib

first: Roberto

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

source_name: kidney

extract_protocol:
The single cell suspension with 98% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions
Libraries were sequenced on an Illumina NextSeq500 (Illumina Inc., San Diego, CA).

treatment_protocol: Male mice were injected anti-GBM serum (PTX-001; Probetex). Following 1 day, different groups of animals (n=2 for each group) received vehicle (distilled water) or 15 mg/kg panobinostat (LBH-589, MedChemExpress); or 10 mg/kg givinostat (ITF2357, Selleckchem); or 60 mg/kg ruxolitinib (INCB18424, MedChemExpress). Animals were sacrificed 7 days after anti-GBM serum injection.

value: Total cells from mouse kidney

tag: developmental stage

value: 9 weeks

value: anti-GBM + Ruxolitinib


title: anti-GBM-Mice_Panobinostat

value: anti-GBM + Panobinostat


title: anti-GBM-Mice_Givinostat

value: anti-GBM + Givinostat


title: anti-GBM-Mice

value: anti-GBM


title: SB+HA_3

source_name: HA-expressed liver tumor, Dyrk2 LKO mice, replicate 3

value: male


title: SB+Dyrk2_1

source_name: Dyrk2-expressed liver tumor, Dyrk2 LKO mice, replicate 1


title: D14, Eprs+/+, replicate 1

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

country: South Korea

institute: Seoul National University Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: h5 format

source_name: Kidney

extract_protocol:
After digesting kidneys with 0.2 mg/ml liberase (Roche, Basel, Switzerland) at 37°C for 30 min, libraries were prepared using the chromium controller according to the 10× Chromium Next GEM Single Cell 3′ protocol (version 3.1; 10× Genomics, Pleasanton, CA, USA). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a target count of 10,000. The cell suspension was mixed with master mix and loaded with gel beads and partitioning oil into a Chromium Next GEM chip G. The RNA transcripts were uniquely barcoded and reverse-transcribed within droplets. The cDNA molecules were pooled and subjected to an end repair process, the addition of a single A base, and ligation of the adapters. The products were purified and enriched using PCR to produce the final cDNA library.
The purified libraries were quantified using qPCR according to the protocol (Sigma Aldrich) and were qualified using the Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA), and sequenced using HiSeqX (Illumina, San Diego, CA, USA) with a read length of 28 bp for read 1 (cell barcode and UMI), an 8-bp index read (sample barcode), and a read length of 91 bp for read 2 (RNA read). The Cell Ranger pipeline (version 3.1.0; 10× Genomics) was used to process the raw dataset.

treatment_protocol: For a toxin-induced TIN model, mice were treated with AD and harvested at the indicated time points after reperfusion.

value: Kidney

value: 8 weeks

value: toxin-induced TIN


title: D14, Eprs+/-, replicate 1

description: 10x Genomics


title: D14, Eprs+/-, replicate 2

description: 10x Genomics


title: SB+Dyrk2_2

source_name: Dyrk2-expressed liver tumor, Dyrk2 LKO mice, replicate 2


title: LOXL2 positive rep 2

status: Public on Sep 23 2022

city: Wenzhou

first: Xufeng

last: Lu

state: Zhejiang

address: Caolong Road

institute: Wenzhou Medical University

description: Gene expression in LOXL2 positive uterine carcinoma sample rep 2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Gene Expression Microarray 4×44K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with at room temperature GE Wash buffer 2 , then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The algorithm used to normalize data: Threshold raw signals to 1.0. Normalization algorithm 75% Percentile shift. Baseline to median of all samples.

source_name: LOXL2 positive

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color One-Color Quick Amp Labering kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And RNA was prepared using the RNeasy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: uterine carcinoma

value: female

value: LOXL2 positive


title: LOXL2 positive rep 1

description: Gene expression in LOXL2 positive uterine carcinoma sample rep 1


title: LOXL2 negative rep 1

description: Gene expression in LOXL2 negative uterine carcinoma sample rep 1

source_name: LOXL2 negative

value: LOXL2 negative


title: LOXL2 positive rep 3

description: Gene expression in LOXL2 positive uterine carcinoma sample rep 3


title: LOXL2 negative rep 3

description: Gene expression in LOXL2 negative uterine carcinoma sample rep 3


title: SB+HA_1

source_name: HA-expressed liver tumor, Dyrk2 LKO mice, replicate 1


title: MNase-Seq_SSDDCS-50

first: Philip

last: Zegerman

address: 80, Tennis Court Road

department: Department of Biochemistry

institute: University of Cambridge

description: MNase-Seq

data_processing:
fastq files were mapped using Bowtie2 (version 2.2.6).
SAM files were converted to BAM files using samtools view (samtools version 0.1.19)
BAM files were sorted and indexes using samtools sort and samtools index, respectively (samtools version 0.1.19)
Identification of high confidence sub-nucleosomal peaks was performed following the analysis from Gutiérrez et al. (G&D 2019)
Assembly: sacCer3
Supplementary files format and content: txt file containing the location of each sub-nucleosomal peak and the corresponding signal in each sample

organism: Saccharomyces cerevisiae

source_name: S-phase yeast cells - 50 min after G1 release

growth_protocol: Mid log phase yeast culture grown in standard media (YPRaff ) and arrested in G1. Released into synchronous S-phase in media with galactose (YPGal)

extract_protocol:
DNA was crosslinked, digested with MNase (5U for 20min at room temperature) and extracted using phenol-chloroform to isolate sub-nucleosomal sized fragments. Protocol adapted from Gutiérrez et al. (G&D 2019)
Library preparation was carried out according to Illumina TruSeq Nano instructions, with the following modifications: after end-repair and before A-tailing, samples were cleaned by performing a phenol-chloroform precipitation, in order to reduce the volume of the samples without using AMPure XP beads.  20% of the amount of adapters recommended by Illumina was used, to reduce adpater dimer formation. After ligation, samples were cleaned using 1.8x AMPure XP beads

treatment_protocol: Induction of SSDDCS overexpression by adding galactose to the media to the G1 arrested population.

value: sml1_delta SSDDCS

value: W303a MATa ade2-1 ura3-1 his3-11, 15 trp1-1 leu2-3, 112 can1-100 rad5-535 leu2::Sld7-PGAL1-10-Cdc45::LEU2 his3::SLD3-A-PGAL1-10-Dbf4-A::HIS3 trp1::Sld2-PGAL1-10-Dpb11::TRP1 sml1_delta::HphNT

tag: strain background


title: MNase-Seq_SSDDCS-60

description: MNase-Seq

source_name: S-phase yeast cells - 60 min after G1 release


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_11]

city: moroyama-machi

first: Tomoyuki

last: Araki

institute: Saitama medical university

description: pancreatic exocrine cells from high-fat diet fed mouse

hyb_protocol: Illumina Infinium HD methylation assay, Manual protocol

scan_protocol: Scan was performed using iScan (version 4.0.0.147) and library (version 3.8.117)

data_processing: Data was processed by GenomeStudio (v2011.1) and methylation module (1.9.0)

label: Dinitrophenol and Biotin

source_name: pancreatic exocrine cells

extract_protocol: Genomic DNA was prepared according to a standard protocol using commercially available kit (NucleoSpin, Takara Bio.)

tag: weight

value: overweight


title: MNase-Seq_SSDDCS-45

description: MNase-Seq

source_name: S-phase yeast cells - 45 min after G1 release

tag: genotype


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_03]

description: pancreatic exocrine cells from normal-fat diet fed mouse

label_protocol: Illumina Infinium HD methylation assay, Manual protocol

value: normal weight


title: MNase-Seq_SSDDCS-35

description: MNase-Seq

source_name: S-phase yeast cells - 35 min after G1 release


title: MNase-Seq_SSDDCS-30

description: MNase-Seq

source_name: S-phase yeast cells - 30 min after G1 release


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_05]


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_08]


title: LOXL2 negative rep 2

description: Gene expression in LOXL2 negative uterine carcinoma sample rep 2


title: MNase-Seq_SSDDCS-40

description: MNase-Seq

source_name: S-phase yeast cells - 40 min after G1 release


title: MNase-Seq_SSDDCS-25

description: MNase-Seq

source_name: S-phase yeast cells - 25 min after G1 release


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_09]


title: MNase-Seq_SSDDCS-15

description: MNase-Seq

source_name: S-phase yeast cells - 15 min after G1 release


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_12]


title: MNase-Seq_SSDDCS-10

description: MNase-Seq

source_name: S-phase yeast cells - 10min after G1 release


title: MNase-Seq_SSDDCS-5

description: MNase-Seq

source_name: S-phase yeast cells - 5 min after G1 release


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_10]


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_06]


title: MNase-Seq_SSDDCS-G1

description: MNase-Seq

source_name: Synchronised G1 phase yeast cells


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_02]


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_04]


title: MNase-Seq_sml1-40

description: MNase-Seq


title: MNase-Seq_sml1-35

description: MNase-Seq


title: MNase-Seq_sml1-30

description: MNase-Seq


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_01]


title: MNase-Seq_sml1-25

description: MNase-Seq


title: MNase-Seq_sml1-20

description: MNase-Seq

source_name: S-phase yeast cells - 20 min after G1 release


title: MNase-Seq_sml1-45

description: MNase-Seq


title: MNase-Seq_sml1-15

description: MNase-Seq


title: MNase-Seq_sml1-10

description: MNase-Seq


title: MNase-Seq_sml1-G1

description: MNase-Seq


title: Ori∆_sml1_NDT80_60

description: Repli-Seq

data_processing:
Library strategy: Repli-Seq
Sequence reads were mapped using Bowtie2 (version 2.3.4).
Unique reads mapping to a single genomic location were summed in 1 kb bins, using Samtools (version 1.7.2) and Bedtools (version 2.26.0).
Assembly: sacCer3
Supplementary files format and content: csv files containing number of unique reads in 1 kb bins normalised to G1 controls.

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation was carried out according to Illumina TruSeq Nano instructions.

value: sml1_delta ARS816_delta ARS818_delta

value: W303a MATa ade2-1 ura3-1 his3-11, 15 trp1-1 leu2-3, 112 can1-100 rad5-535 sml1_delta::URA3 ARS816_delta ARS818_delta


title: Genomic DNA from cultured pancreatic exocrine cells [BA0412_07]


title: Ori∆_sml1_NDT80_50

description: Repli-Seq


title: Genomic DNA from EGL 6

city: Memphis

first: Kyle

middle: S

last: Smith

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description: Normal fetal cerebellum

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using standard Illumina protocol

data_processing: Minfi

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: fetal cerebellum

tag: brain region

value: EGL

value: Unknown


title: Ori∆_sml1_NDT80_45

city: Cambridge

description: Repli-Seq

tag: strain


title: Ori∆_sml1_NDT80_35

description: Repli-Seq


title: Ori∆_sml1_NDT80_25

description: Repli-Seq


title: Ori∆_sml1_NDT80_20

description: Repli-Seq


title: Ori∆_sml1_NDT80_15

description: Repli-Seq


title: Ori∆_sml1_NDT80_10

description: Repli-Seq


title: Ori∆_sml1_NDT80_5

description: Repli-Seq


title: Ori∆_sml1_NDT80_GI

description: Repli-Seq


title: Ori∆_sml1_NDT80_30

description: Repli-Seq


title: Genomic DNA from EGL 2

description: Normal fetal cerebellum


title: Ori∆_SSDDCS_NDT80_60

description: Repli-Seq

value: sml1_delta SSDDCS ARS816_delta ARS818_delta

value: W303a MATa ade2-1 ura3-1 his3-11, 15 trp1-1 leu2-3, 112 can1-100 rad5-535 leu2::Sld7-PGAL1-10-Cdc45::LEU2 his3::SLD3-A-PGAL1-10-Dbf4-A::HIS3 trp1::Sld2-PGAL1-10-Dpb11::TRP1 sml1_delta::HphNT ARS816_delta ARS818_delta


title: MNase-Seq_SSDDCS-20

description: MNase-Seq


title: Ori∆_SSDDCS_NDT80_50

description: Repli-Seq


title: Ori∆_sml1_NDT80_40

description: Repli-Seq


title: Genomic DNA from EGL 7

description: Normal fetal cerebellum


title: Genomic DNA from Rhombic Lip 5

description: Normal fetal cerebellum

value: RL


title: Genomic DNA from EGL 5

description: Normal fetal cerebellum


title: Genomic DNA from Rhombic Lip 7

description: Normal fetal cerebellum


title: Ori∆_SSDDCS_NDT80_45

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_40

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_35

description: Repli-Seq


title: Genomic DNA from EGL 4

description: Normal fetal cerebellum


title: Ori∆_SSDDCS_NDT80_15

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_10

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_30

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_GI

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_25

description: Repli-Seq


title: Genomic DNA from Rhombic Lip 2

description: Normal fetal cerebellum


title: Genomic DNA from EGL 3

description: Normal fetal cerebellum


title: Ori∆_sml1_IME2_50

description: Repli-Seq

value: sml1_delta ARS1008_delta ARS1009_delta

value: W303a MATa ade2-1 ura3-1 his3-11, 15 trp1-1 leu2-3, 112 can1-100 rad5-535 sml1_delta::URA3 ARS1008_delta ARS1009_delta


title: Genomic DNA from Rhombic Lip 1

description: Normal fetal cerebellum


title: Genomic DNA from Rhombic Lip 6

description: Normal fetal cerebellum


title: Ori∆_sml1_IME2_35

description: Repli-Seq


title: Ori∆_sml1_IME2_40

description: Repli-Seq


title: Genomic DNA from Rhombic Lip 4

description: Normal fetal cerebellum


title: Ori∆_SSDDCS_NDT80_5

description: Repli-Seq


title: Ori∆_sml1_IME2_60

description: Repli-Seq


title: Ori∆_sml1_IME2_25

description: Repli-Seq


title: Ori∆_sml1_IME2_15

description: Repli-Seq


title: MNase-Seq_sml1-50

description: MNase-Seq


title: Ori∆_sml1_IME2_10

description: Repli-Seq


title: Ori∆_sml1_IME2_GI

description: Repli-Seq


title: Genomic DNA from EGL 1

description: Normal fetal cerebellum


title: Ori∆_SSDDCS_IME2_50

description: Repli-Seq

value: sml1_delta SSDDCS ARS1008_delta ARS1009_delta

value: W303a MATa ade2-1 ura3-1 his3-11, 15 trp1-1 leu2-3, 112 can1-100 rad5-535 leu2::Sld7-PGAL1-10-Cdc45::LEU2 his3::SLD3-A-PGAL1-10-Dbf4-A::HIS3 trp1::Sld2-PGAL1-10-Dpb11::TRP1 sml1_delta::HphNT ARS1008_delta ARS1009_delta


title: Ori∆_SSDDCS_IME2_60

description: Repli-Seq


title: Ori∆_SSDDCS_IME2_40

description: Repli-Seq


title: Ori∆_SSDDCS_IME2_45

description: Repli-Seq


title: Ori∆_SSDDCS_IME2_35

description: Repli-Seq


title: MNase-Seq_sml1-5

description: MNase-Seq


title: Ori∆_sml1_IME2_5

description: Repli-Seq


title: Ori∆_SSDDCS_IME2_30

description: Repli-Seq


title: Ori∆_SSDDCS_NDT80_20

description: Repli-Seq


title: Genomic DNA from Rhombic Lip 3

description: Normal fetal cerebellum


title: Ori∆_SSDDCS_IME2_25

description: Repli-Seq


title: Ori∆_sml1_IME2_20

description: Repli-Seq