title: F112954

description:
38013-OCT-1_Per-Site-Unphased-Methylation, 38013-OCT-1_Per-Read-Unphased-Methylation, 38013-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 38013-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 38013-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 38013-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2

data_processing:
Per-site and per-read unphased methylation data detected from nanopore sequencing raw signals using nanopolish. Phased methylation data were obtained using NanoMethPhase.
Assembly: GRCh38
Supplementary files format and content: Phased and Unphased CpG methylation data in tsv.gz format.
Library strategy: NanoMethPhase

extract_protocol:
Frozen tissue sections were immersed in 420 μL of RLT Plus buffer (QIAGEN) containing tris(2-carboxyethyl)phosphine (a reducing agent; TCEP) and a unique sample tracking DNA plasmid, and gently agitated overnight at room temperature. Lysates were transferred from 2 mL tubes to wells of a 1.2 mL plate (Thermo Scientific, AB1127) to which was added 400 mL of 5x bind buffer (80 mL beads in 320 mL isopropyl alcohol). Following a 5 minute incubation at room temperature lysates were cleared on a Magnum FLX magnet place (Alpaqua Inc) for 6 minutes and the protein-containing supernatant removed. The beads, with bound nucleic acids, were washed by pipetting 10 times in wash buffer and returned to the magnet. Beads were washed three times in 70% ethanol then dried for 10 minutes. 40 mL nuclease-free water was added to the dried beads and returned to the magnet. The eluted total nucleic acids were transferred to a 96-well storage plate and aliquots taken for quantification using Invitrogen Qubit 4 Fluorometer (Thermo Fisher Q33226)  For samples with concentrations below 166 ng/µL or in volumes greater than 30 µL, 5000 ng of Total Nucleic Acid (TNA) was transferred to a 1.5 mL DNase/RNase free tube and concentrated without heat on the Savant SpeedVac Plus (SC210A) to a maximum volume of 30 µL. This 5000 ng sample in 30 µL was topped up with 10 µL of Qiagen Buffer EB (Cat.19086). The samples were then run on the SAGE Science Blue Pippin instrument using the High Pass Plus Cassette (BPPLUS 10) with a maximum of 4 samples per run. The start range was selected at 15,000 base pairs and the end range was selected at 150,000 base pairs yielding a targeted size of 82,500 base pairs. Following the run completion, each sample was eluted in 80 µL and each sample elution well was then washed with 80 µL of 10 mM Tris, 1mM EDTA containing 0.1% Tween to maximize sample recovery. The total volume of 160µL was then concentrated without heat to 50 µL using the SpeedVac Plus. Each sample was then quantified using the Invitrogen Qubit 4 Fluorometer (Q33226) and normalized to 2000 ng in 47.5 µL for PromethION genome sequencing.
Library construction and sequencing followed the Oxford Nanopore Technologies Genomic DNA by Ligation (SQK-LSK110) protocol. DNA libraries starting with 2 µg of sample per library. No shearing was performed. The NEBUltra-II kit, (New England Biolabs, Ipswich, MA, USA, cat. no. E7646A) was used for end-repair and A-tailing. NEBNext quick ligase (E6056S) was used to ligate the Oxford Nanopore sequencing adapter. A final size selection of 0.4:1 ratio beads:library (PCRClean – DX Aline Biosciences L/N 06180316) was done to select against smaller molecules. These library preparation steps were performed on Hamilton Nimbus96 liquid handlers. An example deck layout, in this case for the bead purification step, is shown in Extended Data Figure 1c. DNA libraries were loaded in R9.4.1 pore flow cells on PromethION 24 instrument running software version 19.06.9 (MinKNOW GUI v4.0.23). Sequencing was carried out for 72 hours. DNase I (Invitrogen cat no. AM2222) nuclease flush was performed after 24-48 hours by reloading the flow cell with the same library mix.


title: Leaf sample from plants treated with the combination of calbio and bacteria under normal conditions, replicate 1

status: Public on Oct 15 2024

type: SRA

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

library_source: transcriptomic

data_processing:
Sequencing data were filtered using SOAPnuke. Clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (0.5.5-5) and rMATS (v4.1.1) were used to detect fusion genes and differential splicing genes (DSG), respectively.
Assembly: Reference Genome Version: GCF_002870075.4_Lsat_Salinas_v11
Supplementary files format and content: Tab-separated read counts per gene (gene_expression_read_counts.tsv) and transcript (rna_expression_read_counts.tsv) per sample

molecule: total RNA

organism: Lactuca sativa

source_name: Leaf

growth_protocol: Lettuce plants were grown in a greenhouse under normal and salt stress conditions.

extract_protocol:
NucleoSpin® RNA Plant kit (Macherey–Nagel GmbH & Co. KG, Düren, Germany) according to the manufacturer's instructions
Eukaryotes stranded transcriptome library
RNA-seq was performed on the DNBseq™ platform by sequencing 150 bp read lengths.

treatment_protocol: control (without product), Calbio (BS), Bacteria (PGPB), mycorrhizal fungus (AMF), Calbio with bacteria (BS+PGPB) and Valbio with mycorrhizal fungus (BS+AMF)

tag: tissue

value: Leaf

tag: treatment

value: Combination of calbio and bacteria (BS+PGPB)

tag: condition

value: Normal conditions


title: CPSF6-RARG-1

city: Beijing

first: Feng

last: Wang

address: 1 Tian Tan Xi Li

country: China

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
Bowtie v1.0.1  was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 V2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq V0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq2 V1.20.0  was used for differential gene expression analysis between two samples with  biological replicates.
Assembly: Homo_sapiens.GRCh38.94.chr
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: mobilized peripheral blood

growth_protocol: The hCD34+ cells were cultured with StemSpanTM SFEM IImedium supplemented with 2mM Glutamine, 100 units/ml Penicillin/Streptomycin, 100 ng/mL for human SCF, 100 ng/mL human TPO, 20 ng/mL human GM-CSF, 100 ng/mL human Flt3L, 50 ng/mL human IL-6, and 50 ng/mL human IL-3.

extract_protocol:
cells were collected , flash frozen on dry ice, and the total RNA was extracted from hCD34+ cells with or without RARG fusions overexpression by using RNA-QuickTM MicroPrep Kit (ZYMO RESEARCH, R1055).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA).

treatment_protocol: Human CD34+ cells infected with control, RARG fusions or PML-RARA retrovirus for 48 hours and then GFP positive cells were sorted and cultured for RNA-seq.

value: mobilized peripheral blood

tag: cell line

value: primary hCD34+ cells

tag: cell type

value: human hemopoietic stemcells

tag: genotype


title: Leaf sample from plants treated with the combination of calbio and mycorrhiza under normal conditions, replicate 1

value: Combination of calbio and mycorrhiza (BS+AMF)


title: WI-38-hTERT, 40°C, H3, ChIP

city: Kyoto-shi

first: Yoshikazu

last: Nagagaki

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University

library_source: genomic

data_processing:
The overall read quality was checked using FastQC v0.11.3.
DROMPA2 v2.6.4 software with its default settings (p < 0.001 and FDR < 0.01 for ChIP/Input enrichment for each 100-bp bin) was used to call peaks representing enriched binding sites.
A total of approximately 45 million sequenced reads were mapped to the human genome (UCSC, hg19) using Bowtie v1.1.1 alignment software, allowing only unique reads mapped to a single location with no more than two mismatches.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: lung

growth_protocol: Cells were grown at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Nissui) supplemented with 10% FBS (GIBCO), L-glutamine, and antibiotics.

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 min at room temperature and quenched with 125 mM glycine for 3 min. After cell lysis, chromatin was sonicated using a Branson Sonifier 250 at 4°C to generate DNA fragments of 100 – 500 bp.
ChIP-seq libraries were prepared from ChIP-DNA or input DNA using a NEBNext ChIP-seq Library kit (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: For heat stress treatment, cells were cultured in an incubator at 40°C (± 0.5°C) and 5% CO2 for 2 hours. Control cells were cultured in an incubator at 37°C (± 0.5°C) and 5% CO2 for 2 hours.

value: lung

value: immortalized human fibroblast cells

value: WT

value: heat stress treatment (40°C, 2 hours)


title: F112953

city: Vancouver

first: Marco

last: Marra

state: BC

address: 570 W 7th Ave

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description:
33033-OCT-1_Per-Site-Unphased-Methylation, 33033-OCT-1_Per-Read-Unphased-Methylation, 33033-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33033-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33033-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33033-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WI-38-hTERT, 40°C, control IgG, ChIP


title: PML-RARA

data_processing:
Trimmomatic software were used to remove adapter and low quality reads
Quality distribution plot and base content distribution were generated by FASTQC
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing.
Using MACS2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Homo_sapiens.GRCh38.89.chr
Supplementary files format and content: bw files were generated using …; Scores represent …
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested, counted and  were washed with  Wash Buffer . Concanavalin A Beads were prepared with Binding buffer and 10 µL of activated beads were added per sample, invert to mix and incubate at room temperature .
The primary antibody incubation was performed on a rotating platform overnight at 4 °C. Beads were washed and incubated with secondary antibody . After incubation, the beads were washed and incubated with hyperactive pA/G-transposon (pA/G-Tnp) at RT. Next, cells were re-suspended in  Trueprep Tagment Buffer L and  the DNA fragments were extracted with  DNA Extract Beads .  Beads were washed twice with Buffer WA and Buffer WB. After drying ~ 5 min, 20 µL ddH2O was added. To amplify libraries, 15 µL DNA was mixed with 25 µL 2×CUT&Tag amplification mix, 5 µL N5, and 5 µL N7 primer, using a different barcode for each sample. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min; 95 °C for 30 min; 14 cycles of 98 °C for 10 s and 60 °C for 5 s; final extension at 72 °C for 1 min and hold at 4 °C. Post-PCR clean-up was performed by adding 100 µL VAHTS DNA Clean Beads (Vazyme, #N411), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 µL ddH2O.

treatment_protocol: Human CD34+ cells infected with control, RARG fusions or PML-RARA retrovirus for 48 hours and then GFP positive cells were sorted and cultured for CUT & Tag.

value: PML-RARA

tag: chip antibody

value: HA tag antibody (CST, #3724）


title: CON-2

value: CON


title: Leaf sample from plants treated with Calbio under normal conditions, replicate 1

value: Calbio(BS)


title: WI-38-hTERT, 37°C, RNA-seq, rep2

description:
37C_RNA-seq_rep2
2019_005A_37C_RNA-seq_rep2

data_processing:
mapping: STAR v2.7.0d
Expression estimation: RSEM v1.3.1
DEG analysis: edgeR
Assembly: UCSC hg19
Supplementary files format and content: excel file includes CPM values for each sample

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit following the manufacture’s protocol.1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat following manufacture's protocol.

treatment_protocol: Cells were seeded at a density of 1.1 × 104 or 1.7 × 104 cells/cm2 in 35 mm dishes for immortalized cells and primary cells, respectively, and incubated for 24 hr at 37°C before heat shock treatment. For priming stress treatment, culture media was replaced with fresh media pre-heated at 40°C, and cells were cultured in an incubator at 40°C (± 0.5°C) and 5% CO2 for 2 hr.

value: control


title: WI-38-hTERT, 37°C, input


title: WI-38-hTERT, 40°C, H3.3, ChIP


title: Leaf sample from plants treated with mycorrhizae under normal conditions, replicate 1

value: Mycorrhizal fungus (AMF)


title: NUP98-RARG


title: F112951

description:
19512-OCT-1_Per-Site-Unphased-Methylation, 19512-OCT-1_Per-Read-Unphased-Methylation, 19512-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 19512-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 19512-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 19512-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112949

description:
25593-OCT-3_Per-Site-Unphased-Methylation, 25593-OCT-3_Per-Read-Unphased-Methylation, 25593-OCT-3_Per-Read-Phased-Methylation-Haplotype1, 25593-OCT-3_Per-Site-Phased-Methylation-Haplotype1, 25593-OCT-3_Per-Read-Phased-Methylation-Haplotype2 and 25593-OCT-3_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: NPM1-RARG


title: F112950

description:
30807-OCT-1_Per-Site-Unphased-Methylation, 30807-OCT-1_Per-Read-Unphased-Methylation, 30807-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30807-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30807-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30807-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WI-38-hTERT, 37°C, H3, ChIP


title: WI-38-hTERT, 37°C, control IgG, ChIP


title: HNRNPC-RARG

value: HNRNPC-RARG


title: F112948

description:
25604-OCT-1_Per-Site-Unphased-Methylation, 25604-OCT-1_Per-Read-Unphased-Methylation, 25604-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25604-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25604-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25604-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WI-38-hTERT, 37°C, H3.3, ChIP


title: F112947

description:
27034-OCT-1_Per-Site-Unphased-Methylation, 27034-OCT-1_Per-Read-Unphased-Methylation, 27034-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27034-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27034-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27034-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: PML-RARG

value: PML-RARG


title: CPSF6-RARG


title: F112952

description:
24423-OCT-1_Per-Site-Unphased-Methylation, 24423-OCT-1_Per-Read-Unphased-Methylation, 24423-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 24423-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 24423-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 24423-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112946

description:
24177-OCT-1_Per-Site-Unphased-Methylation, 24177-OCT-1_Per-Read-Unphased-Methylation, 24177-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 24177-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 24177-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 24177-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: CON-1


title: F112945

description:
18880-OCT-1_Per-Site-Unphased-Methylation, 18880-OCT-1_Per-Read-Unphased-Methylation, 18880-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 18880-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 18880-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 18880-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: LU28-CTRLgliacells-1A

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

library_source: transcriptomic single cell

data_processing:
Basecalling using bcl2fastq 2.20
Cell Ranger pipeline (10x Genomics, Cellranger count v6) with default parameters  and a combined GrCh38/transgene reference genome
Seurat (v 4.3 and R version 4.2.1) was applied to the scRNA-data for downstream analysis of matrix files.
Assembly: GrCH38

source_name: Glial progenitors

growth_protocol: hGPCs were derived from hESCs (RC17 Roslin Cells, cat.no. hPSCreg RCe021-A, p26–30). hESCs were cultured in IPS-Brew XF medium (StemMACS, Miltenyi) on LN521 (0.5 g/cm2, Biolamina)-coated tissue plates and passaged weekly with EDTA (0.5 mM, Gibco, Thermo Fisher). We refer to (Nolbrant et al. 2020) for detailed in-formation on glial differentiation and cryopreservation protocols.

extract_protocol:
Spheroids were collected at different timepoints during direct neuronal conversion, snap-frozen on dry ice and stored at -80°C. The nuclei isolation was performed according to (Sodersten et al. 2018) with modifications.
According to 10X protocols.

tag: culture condition

value: General media

tag: days in culture


title: LU28-CTRLgliacells-1B


title: WT bud (10 hpf) tRNA-seq rep1

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.2) using the parameters --species Drer --cluster-id 0.93 --min-cov 0.001 --max-mismatches 0.075 --control-condition Egg --deconv-cov-ratio 0.4 --remap-mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters, and on read counts summed by isotype.
Assembly: GRCz11
Supplementary files format and content: csv; mim-tRNAseq generated tRNA transcript resad counts

organism: Danio rerio

source_name: Gastrula

growth_protocol: Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.

extract_protocol:
50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer(5% Lithium dodecyl sulfate in 20 mM Tris-HCl pH=7.4, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH 7.4).
tRNA-seq libraries were prepared using the mim-tRNAseq workflow (Behrens 2021, 2022) and sequenced on an Illumina NextSeq 500 platform.
mim-tRNAseq

treatment_protocol: unperturbed growth conditions in E3 medium for zebrafish embryos.

tag: strain

value: TLAB strain

value: Gastrula

tag: developmental stage

value: Bud (10 hpf)


title: F112943

description:
27647-OCT-1_Per-Site-Unphased-Methylation, 27647-OCT-1_Per-Read-Unphased-Methylation, 27647-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27647-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27647-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27647-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WT shield (6 hpf) tRNA-seq rep2

value: Shield (6 hpf)


title: F112944

description:
27503-FF-1_Per-Site-Unphased-Methylation, 27503-FF-1_Per-Read-Unphased-Methylation, 27503-FF-1_Per-Read-Phased-Methylation-Haplotype1, 27503-FF-1_Per-Site-Phased-Methylation-Haplotype1, 27503-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 27503-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG053-LU28-GM-D21


title: F112942

description:
27078-FF-1_Per-Site-Unphased-Methylation, 27078-FF-1_Per-Read-Unphased-Methylation, 27078-FF-1_Per-Read-Phased-Methylation-Haplotype1, 27078-FF-1_Per-Site-Phased-Methylation-Haplotype1, 27078-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 27078-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WT shield (6 hpf) tRNA-seq rep1


title: Drosophila_bipectinata_testes_G_z10_131017_I1125

city: Davis

first: Ben

last: Hopkins

state: CA

address: One Shields Avenue

department: Evolution & Ecology

country: USA

institute: UC Davis

data_processing:
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05  NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate

molecule: polyA RNA

organism: Drosophila bipectinata

source_name: testes

extract_protocol:
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)

value: testes

tag: sample id

tag: library name

tag: strain information


title: WI-38-hTERT cells transfected with shLuciferase

type: RNA

description: WI-38-hTERT cells are WI-38 human lung fibroblast cells immortalized by expressing human TERT.

hyb_protocol: According to Affymetrix protocol

scan_protocol: Scan was done on GeneChip Scanner 3000 7G

data_processing: After using the RMA algorithm to obtain the summarized probeset-level expression data, the array data were transferred to GeneSpring microarray analysis software (Agilent Technologies) for normalization and entities in the lowest 20 percentile were removed.

label: biotin

source_name: WI-38-hTERT cells, shLuciferase

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Affymetrix, Cat #4411973) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling kit (Affymetrix, Cat #900670) and Controls Kit (Affymetrix, Cat #901525).

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit following the manufacture’s protocol.

treatment_protocol: shHIRA#2 (5’-GGAGATGACAAACTGATTA-3’) and shLuciferase (5’- TAAGGCTATGAAGAGATAC-3’) cassettes were cloned into a conventional lentiviral RNAi vector, pCSII-RNAi-MCS-CMV-puro. These lentiviral vectors were a generous gift from Dr. Shin Yonehara, Kyoto University. For packaging, 293T cells were transfected with lentiviral vectors using the calcium phosphate method. Culture supernatants were supplemented with 5 μg/ml polybrene (Sigma-Aldrich) and incubated with target cells. Infected cells were selected by incubating with 2.5 μg/ml puromycin (Sigma-Aldrich) for 3 days.

value: shLuciferase


title: JG053-LU28-ALN-D50

source_name: Glial progenitors after ALN transduction

value: ALN


title: WT sphere (4 hpf) tRNA-seq rep2

source_name: Blastula

value: Blastula

value: Sphere (4 hpf)

value: WT


title: WI-38-hTERT cells transfected with shHIRA

source_name: WI-38-hTERT cells, shHIRA

value: shHIRA


title: F112941

description:
27078-OCT-1_Per-Site-Unphased-Methylation, 27078-OCT-1_Per-Read-Unphased-Methylation, 27078-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27078-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27078-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27078-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Drosophila_bipectinata_ag_G_z9_131220_I433

source_name: accessory glands

value: accessory glands


title: WT sphere (4 hpf) tRNA-seq rep1


title: JG053-LU28-ALN-D21


title: Drosophila_bipectinata_ag_G_z9_131017_I1125


title: JG053-LU28-ALN-D14


title: WT 1000-cell (3 hpf) tRNA-seq rep2


title: JG053-LU28-ALN-D07


title: F112938

description:
23674-FF-1_Per-Site-Unphased-Methylation, 23674-FF-1_Per-Read-Unphased-Methylation, 23674-FF-1_Per-Read-Phased-Methylation-Haplotype1, 23674-FF-1_Per-Site-Phased-Methylation-Haplotype1, 23674-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 23674-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112341_F94404

description:
25134-FF-1_Per-Site-Unphased-Methylation, 25134-FF-1_Per-Read-Unphased-Methylation, 25134-FF-1_Per-Read-Phased-Methylation-Haplotype1, 25134-FF-1_Per-Site-Phased-Methylation-Haplotype1, 25134-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 25134-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112342_F94419

description:
31190-OCT-2_Per-Site-Unphased-Methylation, 31190-OCT-2_Per-Read-Unphased-Methylation, 31190-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 31190-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 31190-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 31190-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG053-LU28-NDiff-D21

value: Neural differentiation media


title: JG053-LU28-GM-D0


title: JG048-J4-NDiff-D21


title: WT 1000-cell (3 hpf) tRNA-seq rep1


title: Drosophila_elegans_testes_G_z6_131220_I433

organism: Drosophila elegans


title: WT 256-cell (2.5 hpf) tRNA-seq rep2


title: Drosophila_elegans_ag_G_z5_131220_I433


title: WT bud (10 hpf) tRNA-seq rep2


title: Drosophila_bipectinata_testes_G_z10_130917_I1135


title: F112939

description:
23674-FF-3_Per-Site-Unphased-Methylation, 23674-FF-3_Per-Read-Unphased-Methylation, 23674-FF-3_Per-Read-Phased-Methylation-Haplotype1, 23674-FF-3_Per-Site-Phased-Methylation-Haplotype1, 23674-FF-3_Per-Read-Phased-Methylation-Haplotype2 and 23674-FF-3_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-J4-GM-D21


title: Drosophila_elegans_ag_G_z5_131017_I1125


title: F112339_F94410

description:
27327-OCT-1_Per-Site-Unphased-Methylation, 27327-OCT-1_Per-Read-Unphased-Methylation, 27327-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27327-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27327-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27327-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WT 256-cell (2.5 hpf) tRNA-seq rep1


title: WT egg (0 hpf) tRNA-seq rep2

source_name: Unfertilized egg

value: Unfertilized egg

value: unfertilized egg (0 hpf)


title: JG048-J4-GM-D0


title: Drosophila_biarmipes_testes_G_z4_131017_I1125

organism: Drosophila biarmipes


title: F112338_F94429

description:
36069-OCT-1_Per-Site-Unphased-Methylation, 36069-OCT-1_Per-Read-Unphased-Methylation, 36069-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36069-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36069-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36069-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-J4-ALN-D50


title: WT egg (0 hpf) tRNA-seq rep1


title: F112340_F94432

description:
37970-OCT-1_Per-Site-Unphased-Methylation, 37970-OCT-1_Per-Read-Unphased-Methylation, 37970-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37970-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37970-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37970-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112337_F94420

description:
30822-OCT-2_Per-Site-Unphased-Methylation, 30822-OCT-2_Per-Read-Unphased-Methylation, 30822-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 30822-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 30822-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 30822-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-J4-ALN-D14


title: WT bud (10 hpf) Ribo-seq rep1

description:
bud_1
codonDT_all.csv
allRPF_TPM.csv

data_processing:
We identified the A site location in each mapped read with Scikit-ribo [Fang et al. 2018], which uses a random forest with recursive feature selection and a generalized linear model for accurate A-site prediction based on matched ribosome profiling and RNA-Seq datasets. Kallisto 0.44.0 with parameters -b 100 --single -l 180 -s 20 -t 40 was used to quantify transcript abundances in Transcripts Per Million (TPM) from RNA-Seq data based on the reference set of MANE-annotated transcripts (see Codon usage analysis for description of this annotation). To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms, all RNAfold dependencies in Scikit-ribo were omitted, and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit-ribo, transcript/UTR annotations were removed. For each transcript, the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates, taking into account the gene strand. To estimate codon dwell times, short (20-23 nt) and long (28-33 nt) ribosome footprints were analyzed separately.
rRNA-filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al., 2013] the following options: --outFilterMultimapNmax 1 --seedSearchStartLmax 15 --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 2 --alignEndsType EndToEnd --quantMode TranscriptomeSAM --outSAMattributes NH HI AS nM NM MD
We identified the A site location in each mapped read with Scikit-ribo [Fang et al. 2018], which uses a random forest with recursive feature selection and a generalized linear model for accurate A-site prediction based on matched ribosome profiling and RNA-Seq datasets. Kallisto 0.44.0 with parameters -b 100 --single -l 180 -s 20 -t 40 was used to quantify transcript abundances in Transcripts Per Million (TPM) from RNA-Seq data based on the reference set of MANE-annotated transcripts (see Codon usage analysis for description of this annotation). To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms, all RNAfold dependencies in Scikit-ribo were omitted, and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit-ribo, transcript/UTR annotations were removed. For each transcript, the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates, taking into account the gene strand. To estimate codon dwell times, we utilised ribosome footprints with length 30-34 nt.
Assembly: GRCz11
Supplementary files format and content: csv; codon dwell times from scikit-ribo for all samples
Supplementary files format and content: csv; transcript-per-million (TPM) counts per transcript in MANE annotation
Library strategy: Ribo-Seq

extract_protocol:
200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 µg/ml CHX and 100 µg/ml TIG, 0.1% NP-40, 10 µg/ml aprotinin, 20 µM leupeptin, 2.5 µM pepstatin A, 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously, triturated through a 26G gauge needle, and spun down for 7 minutes at 16,000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2,000 rpm/22°C. After incubation on ice for 5 minutes, extracts were pre-cleared by centrifugation for 5 minutes at 3,000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion (1 M sucrose, 20 mM Tris pH=8.0, 140 mM KCl, 5 mM MgCl2, 1 mM DTT) by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50,000 rpm/ 4°C. Ribosome pellets were rinsed once, dissolved in 200 µl drug-free polysome lysis buffer, and incubated with 200 U (hiPSC) or 300 U (NPC) RNase I for 45 minutes at 2,000 rpm/22°C.
Ribosome footprint libraries were prepared essentially as described (McGlincy and Ingolia, 2017; Wu 2019) with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection, with T4 PNK and ligated to pre-adenylated adapters containing 5 random nucleotides at their 5’ ends (McGlinzy 2017) with T4 RNA Ligase 2, truncated KQ. Adapter-ligated RNA was subjected to rRNA depletion using the Ribo-Seq riboPOOL h/m/r depletion kit (siTOOLs) for CHX-only samples, and legacy RiboZero Gold kit (Illumina) for CHX+TIG samples The rRNA-depleted footprints were reverse-transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 (commercially available as CircLigase). Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single-end sequencing was performed on a NextSeq 500 platform (Illumina).

value: 100 µg/ml CHX, 100 µg/ml TIG


title: Drosophila_biarmipes_ag_G_z3_131017_I1125


title: Drosophila_takahashii_testes_G_z14_130917_I1135

organism: Drosophila takahashii


title: F112334_F94482

description:
37146-OCT-1_Per-Site-Unphased-Methylation, 37146-OCT-1_Per-Read-Unphased-Methylation, 37146-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37146-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37146-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37146-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-J4-ALN-D07


title: JG048-J4-ALN-D21


title: WT bud (10 hpf) RNA-seq rep2

description:
bud_2
allRNA_TPM.csv

data_processing:
3’ adapters were trimmed using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Reads were aligned to the GRCz11 zebrafish genome using STAR v2.6.1c with the following parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode TranscriptomeSAM GeneCounts --alignEndsType Local --seedSearchStartLmax 14 --alignIntronMax 10000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts.
Assembly: GRCz11
Supplementary files format and content: csv; transcripts-per-million (TPM) counts per transcript in MANE annotation

extract_protocol:
50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer(5% Lithium dodecyl sulfate in 20 mM Tris-HCl pH=7.4, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH 7.4).
250 ng of the same total RNA used for mim-tRNAseq library preparation were used for mRNA-Seq library construction with the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, #R3000). Libraries were sequenced on a NextSeq 500 platform.


title: Drosophila_biarmipes_testes_G_z4_130917_I1135


title: Drosophila_biarmipes_ag_G_z3_130917_I1135


title: JG048-GlialOrganoids-Ndiff-D21

value: General media


title: Drosophila_takahashii_testes_G_z14_131017_I1125


title: F112335_F94471

description:
25721-OCT-1_Per-Site-Unphased-Methylation, 25721-OCT-1_Per-Read-Unphased-Methylation, 25721-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25721-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25721-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25721-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112333_F94468

description:
38119-OCT-1_Per-Site-Unphased-Methylation, 38119-OCT-1_Per-Read-Unphased-Methylation, 38119-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 38119-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 38119-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 38119-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-GlialOrganoids-GM-D21


title: WT bud (10 hpf) RNA-seq rep1

description:
bud_1
allRNA_TPM.csv

value: TLAB strain


title: WT sphere (4 hpf) Ribo-seq rep1

description:
sphere_1
codonDT_all.csv
allRPF_TPM.csv


title: F112332_F94491

description:
31980-OCT-1_Per-Site-Unphased-Methylation, 31980-OCT-1_Per-Read-Unphased-Methylation, 31980-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31980-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31980-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31980-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Drosophila_takahashii_ag_G_z13_131220_I433


title: WT sphere (4 hpf) RNA-seq rep2

description:
sphere_2
allRNA_TPM.csv


title: F112331_F94490

description:
32395-OCT-1_Per-Site-Unphased-Methylation, 32395-OCT-1_Per-Read-Unphased-Methylation, 32395-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32395-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32395-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32395-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-GlialOrganoids-GM-D0


title: JG048-GlialOrganoids-ALN-D50


title: WT sphere (4 hpf) RNA-seq rep1

description:
sphere_1
allRNA_TPM.csv


title: JG048-GlialOrganoids-ALN-D21


title: Drosophila_biarmipes_testes_NG_52_52b_S15


title: Drosophila_biarmipes_testes_NG_52_52_S95


title: F112330_F94467

description:
37917-OCT-1_Per-Site-Unphased-Methylation, 37917-OCT-1_Per-Read-Unphased-Methylation, 37917-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37917-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37917-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37917-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: G120_N.1, ATAC

city: Campinas

first: Diogo

middle: Fernando Troggian

last: Veiga

state: SP

address: Rua Vital Brasil, 80

department: Department of Translational Medicine

country: Brazil

institute: Universidade Estadual de Campinas

description:
G120_F1_N_barcodes.tsv.gz
G120_F1_N_features.tsv.gz
G120_F1_N_matrix.mtx.gz

data_processing:
CellRanger-arc 2.0.2 count was used to generate barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files for each sample
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: 10x Multiome single-cell

extract_protocol:
The nuclei extraction protocol for human brain tissue was adapted from Jessa et al, 2019. Briefly, frozen tissue was dounce homogenized and incubated for 2 minutes in lysis buffer containing 0.1% NP-40. Then, suspension was filtered through a 30 m cell strainer (MACS), and washed in buffer containing 10% BSA to remove debris, followed by a centrifugation at 500g and 4oC for 5 minutes. Next, suspension was carefully layered on a double 29% and 50% iodixanol (Sigma) cushion layers, and centrifuged at 10,000g and 4oC for 30 minutes for additional removal of debris and cell aggregates. Retrieved nuclei was resuspended and counted. Nuclei were stained with Trypan blue and counted using a hemocytometer. Nuclei integrity was evaluated under microscope using 40X or 60X magnifications, and nuclei was considered viable if they were roundish and with an intact membrane.
Libraries were prepared using the Multiome ATAC + Gene Expression kit (10X Genomics) in accordance with the manufacture’s protocol CG000338 revision E.

value: cerebral cortex

tag: donor

tag: disease

value: focal cortical dysplasia

tag: library type

value: ATAC

tag: Sex

value: Female

tag: age at_surgery

tag: age at_onset

tag: duration

tag: lobe

value: Frontal

tag: lateralization

value: L

tag: histological assessment

value: Normal

tag: surgery reason

value: FCD

tag: seq batch


title: Drosophila_biarmipes_ag_NG_8_8_S90

tag: tissue


title: ACT treated

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
ACT
10X genomics visium

data_processing:
*library strategy: Spatial Transciptomics
The demultiplexing, bardoded processing,  gene count and aggregation were make with CellRanger v6.1.2
The downstream data analyses were done using Seurat.
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files.
Supplementary files format and content: Images and position of spots

organism: Mus musculus

source_name: ovarian cancer

extract_protocol:
FFPE sections prepared from omental tumors of MOVCAR 5009-bearing SCID mice 10 days after OV treatments
Tissues were sectioned at 5 µm and trimmed to fit in the capture area (6.5 mm x 6.5 mm) of the 10x Genomics Visium Spatial slides and hybridized with whole transcriptome probe panel. Final libraries were prepared using 10x genomic recommended protocol.

value: ovarian cancer

tag: treatment

value: ACT


title: F111748

description:
25981-PB_Per-Site-Unphased-Methylation, 25981-PB_Per-Read-Unphased-Methylation, 25981-PB_Per-Read-Phased-Methylation-Haplotype1, 25981-PB_Per-Site-Phased-Methylation-Haplotype1, 25981-PB_Per-Read-Phased-Methylation-Haplotype2 and 25981-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: G120_N.1, GEX

value: mRNA


title: F111745

description:
31190-PB_Per-Site-Unphased-Methylation, 31190-PB_Per-Read-Unphased-Methylation, 31190-PB_Per-Read-Phased-Methylation-Haplotype1, 31190-PB_Per-Site-Phased-Methylation-Haplotype1, 31190-PB_Per-Read-Phased-Methylation-Haplotype2 and 31190-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Drosophila_biarmipes_testes_G_48_48b_S12

value: testes

tag: sample id


title: F112329_F94465

description:
37013-OCT-1_Per-Site-Unphased-Methylation, 37013-OCT-1_Per-Read-Unphased-Methylation, 37013-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37013-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37013-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37013-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: OV-FC + ACT treated

description:
OV_FC_ACT
10X genomics visium

value: OV-FC + ACT


title: JG048-GlialOrganoids-ALN-D14

tag: culture condition

value: ALN

tag: days in culture


title: Drosophila_biarmipes_ag_NG_37_37_S93

value: accessory glands

tag: library name

tag: strain information


title: ALN-D07


title: Drosophila_biarmipes_testes_G_48_48_S89


title: OV-CXCR4 + ACT treated

description:
OV_CXCR4_ACT
10X genomics visium

value: OV-CXCR4 + ACT


title: ALN-D05


title: F111744

description:
18843-PB_Per-Site-Unphased-Methylation, 18843-PB_Per-Read-Unphased-Methylation, 18843-PB_Per-Read-Phased-Methylation-Haplotype1, 18843-PB_Per-Site-Phased-Methylation-Haplotype1, 18843-PB_Per-Read-Phased-Methylation-Haplotype2 and 18843-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111746

description:
27981-PB_Per-Site-Unphased-Methylation, 27981-PB_Per-Read-Unphased-Methylation, 27981-PB_Per-Read-Phased-Methylation-Haplotype1, 27981-PB_Per-Site-Phased-Methylation-Haplotype1, 27981-PB_Per-Read-Phased-Methylation-Haplotype2 and 27981-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: JG048-GlialOrganoids-ALN-D07


title: Drosophila_biarmipes_ag_NG_37_37b_S143


title: OV-FC + ACT treated [scRNA-seq]

description:
OV_FC_ACT
10X genomics

data_processing:
The demultiplexing, bardoded processing,  gene count and aggregation were make with CellRanger v6.1.2
The downstream data analyses were done using Seurat.
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files.

source_name: tumor draining lymph node

extract_protocol:
Tumor-draining lymph nodes (tdLN) were harvested, homogenized, and obtained cells were resuspended in 0.04% BSA in phosphate-buffered saline without calcium and magnesium, passed through a 70 μm cell strainer to receive single-cell suspension and washed three times in pre-chilled 1% BSA in PBS.
Single-cell gene expression libraries were created using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v.3.1 (10x Genomics) as per manufacturer recommendations.

value: tumor draining lymph node

tag: cell type

value: immune cells


title: F111747

description:
23315-PB_Per-Site-Unphased-Methylation, 23315-PB_Per-Read-Unphased-Methylation, 23315-PB_Per-Read-Phased-Methylation-Haplotype1, 23315-PB_Per-Site-Phased-Methylation-Haplotype1, 23315-PB_Per-Read-Phased-Methylation-Haplotype2 and 23315-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111741

description:
30221-PB_Per-Site-Unphased-Methylation, 30221-PB_Per-Read-Unphased-Methylation, 30221-PB_Per-Read-Phased-Methylation-Haplotype1, 30221-PB_Per-Site-Phased-Methylation-Haplotype1, 30221-PB_Per-Read-Phased-Methylation-Haplotype2 and 30221-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GM-D0

value: General media


title: Drosophila_biarmipes_ag_NG_8_8b_S142


title: Drosophila_biarmipes_ag_G_106_106_S19


title: Drosophila_biarmipes_testes_NG_78_78_S5


title: ALN-D02


title: Untreated

description:
Untreated
10X genomics visium

value: Untreated


title: OV-CXCR4 + ACT treated [scRNA-seq]

description:
OV_CXCR4_ACT
10X genomics


title: Drosophila_eugracilis_testes_NG_56_56_S21

organism: Drosophila eugracilis


title: H007-NileF [RNA-seq]

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

institute: The University of Hong Kong

data_processing:
The RNAseq reads in FASTA format were aligned to the Genome Reference Consortium human build 37 (hg19) by STAR (version 2.5.2b).
Duplicate reads were removed from the BAM files and the transcript abundances were quantified by RSEM to calculate the transcripts per million (TPM) value for each gene.
Assembly: GRCh37
Supplementary files format and content: Log-normalized expression data for each sample in a tab-delimited text format.

source_name: Human nomal ileum tissue

growth_protocol: IM and normal gastric organoids were cultured in a standard gastric organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and FGF10. Normal colon and ileum organoids were cultured in a standard intestinal organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and SB202190.

extract_protocol:
RNA of organoids and frozen tissues were extracted using AllPrep® DNA/RNA/miRNA Universal Kit (Qiagen). following the manufacturers’ protocol.
Four micrograms of total RNA were used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), according to the manufacturer’s protocol. The library was amplified by 6 PCR cycles and sequenced using either the NovaSeq6000/HiSeqX Ten with paired end 151bp reads or the HiSeq1500 with paired end 101bp reads.

tag: tissue/cell type

value: Human nomal ileum tissue


title: ACT treated [scRNA-seq]

description:
ACT
10X genomics


title: Drosophila_eugracilis_testes_NG_25_25_S98


title: F111739

description:
32395-PB_Per-Site-Unphased-Methylation, 32395-PB_Per-Read-Unphased-Methylation, 32395-PB_Per-Read-Phased-Methylation-Haplotype1, 32395-PB_Per-Site-Phased-Methylation-Haplotype1, 32395-PB_Per-Read-Phased-Methylation-Haplotype2 and 32395-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX094-BfF [RNA-seq]

source_name: Human normal gastric frozen tissue

value: Human normal gastric frozen tissue


title: MPL512, Adeno-CRE

city: Madrid

first: Vasiliki

last: Liaki

address: Melchor Fernandez Almagro 3

institute: CNIO

data_processing:
Cluster_rnaseq pipeline developed by the Bioinformatic Unit of CNIO (https://github.com/cnio-bu/cluster_rnaseq)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: pancreas

growth_protocol: PDAC cells were maintained in DMEM supplemented with 10% of fetal bovine serum (FBS) and antibiotics at 37C in humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from mouse PDAC cells using the RNeasy Mini Kit (Qiagen) and 1 μg of total RNA  was converted into sequencing libraries.
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs E7760), as recommended by the manufacturer.

treatment_protocol: Cells were infected with Adeno-GFP or Adeno-CRE viral particles.

value: pancreas

tag: cell line

value: adenocarcinoma

tag: genotype

value: Adeno-CRE


title: GX093-IM2F [RNA-seq]


title: MXD2840, Adeno-CRE


title: F111738

description:
23737-PB_Per-Site-Unphased-Methylation, 23737-PB_Per-Read-Unphased-Methylation, 23737-PB_Per-Read-Phased-Methylation-Haplotype1, 23737-PB_Per-Site-Phased-Methylation-Haplotype1, 23737-PB_Per-Read-Phased-Methylation-Haplotype2 and 23737-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2

data_processing:
Per-site and per-read unphased methylation data detected from nanopore sequencing raw signals using nanopolish. Phased methylation data were obtained using NanoMethPhase.
Assembly: GRCh38
Supplementary files format and content: Phased and Unphased CpG methylation data in tsv.gz format.
Library strategy: NanoMethPhase

extract_protocol:
Frozen tissue sections were immersed in 420 μL of RLT Plus buffer (QIAGEN) containing tris(2-carboxyethyl)phosphine (a reducing agent; TCEP) and a unique sample tracking DNA plasmid, and gently agitated overnight at room temperature. Lysates were transferred from 2 mL tubes to wells of a 1.2 mL plate (Thermo Scientific, AB1127) to which was added 400 mL of 5x bind buffer (80 mL beads in 320 mL isopropyl alcohol). Following a 5 minute incubation at room temperature lysates were cleared on a Magnum FLX magnet place (Alpaqua Inc) for 6 minutes and the protein-containing supernatant removed. The beads, with bound nucleic acids, were washed by pipetting 10 times in wash buffer and returned to the magnet. Beads were washed three times in 70% ethanol then dried for 10 minutes. 40 mL nuclease-free water was added to the dried beads and returned to the magnet. The eluted total nucleic acids were transferred to a 96-well storage plate and aliquots taken for quantification using Invitrogen Qubit 4 Fluorometer (Thermo Fisher Q33226)  For samples with concentrations below 166 ng/µL or in volumes greater than 30 µL, 5000 ng of Total Nucleic Acid (TNA) was transferred to a 1.5 mL DNase/RNase free tube and concentrated without heat on the Savant SpeedVac Plus (SC210A) to a maximum volume of 30 µL. This 5000 ng sample in 30 µL was topped up with 10 µL of Qiagen Buffer EB (Cat.19086). The samples were then run on the SAGE Science Blue Pippin instrument using the High Pass Plus Cassette (BPPLUS 10) with a maximum of 4 samples per run. The start range was selected at 15,000 base pairs and the end range was selected at 150,000 base pairs yielding a targeted size of 82,500 base pairs. Following the run completion, each sample was eluted in 80 µL and each sample elution well was then washed with 80 µL of 10 mM Tris, 1mM EDTA containing 0.1% Tween to maximize sample recovery. The total volume of 160µL was then concentrated without heat to 50 µL using the SpeedVac Plus. Each sample was then quantified using the Invitrogen Qubit 4 Fluorometer (Q33226) and normalized to 2000 ng in 47.5 µL for PromethION genome sequencing.
Library construction and sequencing followed the Oxford Nanopore Technologies Genomic DNA by Ligation (SQK-LSK110) protocol. DNA libraries starting with 2 µg of sample per library. No shearing was performed. The NEBUltra-II kit, (New England Biolabs, Ipswich, MA, USA, cat. no. E7646A) was used for end-repair and A-tailing. NEBNext quick ligase (E6056S) was used to ligate the Oxford Nanopore sequencing adapter. A final size selection of 0.4:1 ratio beads:library (PCRClean – DX Aline Biosciences L/N 06180316) was done to select against smaller molecules. These library preparation steps were performed on Hamilton Nimbus96 liquid handlers. An example deck layout, in this case for the bead purification step, is shown in Extended Data Figure 1c. DNA libraries were loaded in R9.4.1 pore flow cells on PromethION 24 instrument running software version 19.06.9 (MinKNOW GUI v4.0.23). Sequencing was carried out for 72 hours. DNase I (Invitrogen cat no. AM2222) nuclease flush was performed after 24-48 hours by reloading the flow cell with the same library mix.


title: F111740

description:
31189-PB_Per-Site-Unphased-Methylation, 31189-PB_Per-Read-Unphased-Methylation, 31189-PB_Per-Read-Phased-Methylation-Haplotype1, 31189-PB_Per-Site-Phased-Methylation-Haplotype1, 31189-PB_Per-Read-Phased-Methylation-Haplotype2 and 31189-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111737

description:
25426-PB_Per-Site-Unphased-Methylation, 25426-PB_Per-Read-Unphased-Methylation, 25426-PB_Per-Read-Phased-Methylation-Haplotype1, 25426-PB_Per-Site-Phased-Methylation-Haplotype1, 25426-PB_Per-Read-Phased-Methylation-Haplotype2 and 25426-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Drosophila_eugracilis_testes_NG_25_25b_S148


title: ALN-D03


title: GX092-AF [RNA-seq]


title: Drosophila_eugracilis_testes_G_7_7_S97


title: MPL1071, Adeno-CRE


title: MTL382, Adeno-CRE


title: Drosophila_eugracilis_testes_G_7_7b_S147


title: Drosophila_eugracilis_ag_NG_39_39b_S8


title: MPL2215, Adeno-CRE


title: MPL1239, Adeno-CRE


title: F111736

description:
25721-PB_Per-Site-Unphased-Methylation, 25721-PB_Per-Read-Unphased-Methylation, 25721-PB_Per-Read-Phased-Methylation-Haplotype1, 25721-PB_Per-Site-Phased-Methylation-Haplotype1, 25721-PB_Per-Read-Phased-Methylation-Haplotype2 and 25721-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX090-BF [RNA-seq]


title: F111734

description:
27329-PB_Per-Site-Unphased-Methylation, 27329-PB_Per-Read-Unphased-Methylation, 27329-PB_Per-Read-Phased-Methylation-Haplotype1, 27329-PB_Per-Site-Phased-Methylation-Haplotype1, 27329-PB_Per-Read-Phased-Methylation-Haplotype2 and 27329-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX090-AF [RNA-seq]


title: Drosophila_eugracilis_ag_NG_34_34b_S7


title: Drosophila_eugracilis_ag_NG_39_39_S84


title: MPL660, Adeno-CRE


title: F111732

description:
28126-PB_Per-Site-Unphased-Methylation, 28126-PB_Per-Read-Unphased-Methylation, 28126-PB_Per-Read-Phased-Methylation-Haplotype1, 28126-PB_Per-Site-Phased-Methylation-Haplotype1, 28126-PB_Per-Read-Phased-Methylation-Haplotype2 and 28126-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL60, Adeno-CRE


title: GX089-BlF [RNA-seq]


title: Drosophila_eugracilis_ag_NG_34_34_S83


title: F111742

description:
23808-PB_Per-Site-Unphased-Methylation, 23808-PB_Per-Read-Unphased-Methylation, 23808-PB_Per-Read-Phased-Methylation-Haplotype1, 23808-PB_Per-Site-Phased-Methylation-Haplotype1, 23808-PB_Per-Read-Phased-Methylation-Haplotype2 and 23808-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL1540, Adeno-CRE


title: F111731

description:
31042-PB_Per-Site-Unphased-Methylation, 31042-PB_Per-Read-Unphased-Methylation, 31042-PB_Per-Read-Phased-Methylation-Haplotype1, 31042-PB_Per-Site-Phased-Methylation-Haplotype1, 31042-PB_Per-Read-Phased-Methylation-Haplotype2 and 31042-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Drosophila_eugracilis_ag_G_102_102_S22


title: GX089-AlF [RNA-seq]


title: F111730

description:
32971-PB_Per-Site-Unphased-Methylation, 32971-PB_Per-Read-Unphased-Methylation, 32971-PB_Per-Read-Phased-Methylation-Haplotype1, 32971-PB_Per-Site-Phased-Methylation-Haplotype1, 32971-PB_Per-Read-Phased-Methylation-Haplotype2 and 32971-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX091-BgF [RNA-seq]


title: F111733

description:
additional 25990-PB_Per-Site-Unphased-Methylation, 25990-PB_Per-Read-Unphased-Methylation, 25990-PB_Per-Read-Phased-Methylation-Haplotype1, 25990-PB_Per-Site-Phased-Methylation-Haplotype1, 25990-PB_Per-Read-Phased-Methylation-Haplotype2 and 25990-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX087-IM2F [RNA-seq]


title: MXD3562, Adeno-CRE


title: MPL195, Adeno-CRE


title: Drosophila_eugracilis_testes_G_114_114_S24


title: Drosophila_eugracilis_ag_G_102_102b_S26


title: F111729

description:
34120-PB_Per-Site-Unphased-Methylation, 34120-PB_Per-Read-Unphased-Methylation, 34120-PB_Per-Read-Phased-Methylation-Haplotype1, 34120-PB_Per-Site-Phased-Methylation-Haplotype1, 34120-PB_Per-Read-Phased-Methylation-Haplotype2 and 34120-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111728

description:
37146-PB_Per-Site-Unphased-Methylation, 37146-PB_Per-Read-Unphased-Methylation, 37146-PB_Per-Read-Phased-Methylation-Haplotype1, 37146-PB_Per-Site-Phased-Methylation-Haplotype1, 37146-PB_Per-Read-Phased-Methylation-Haplotype2 and 37146-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX080-IMF [RNA-seq]


title: R60 3

city: Turku

first: Mehmet

last: Kilic

address: FI-20014 TURUN YLIOPISTO

department: Molecular Plant Biology

country: Finland

institute: University of Turku

description: Treated with HL for 60 min followed by recovery for 60 min at GL 3

data_processing:
Salmon (v0.12; Patro et al., 2017) for quantification.
Transcripts were aggregated to the gene level using tximport R package.
Raw counts were obtained with DESeq2 R package.
Assembly: TAIR10.49
Supplementary files format and content: Tab-limited text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis thaliana plants were grown in 8 h photoperiod under 100 µmol photons m-2 s-1 for 6-7 weeks.

extract_protocol:
RNA was isolated with innuPREP plant RNA isolation kit (Analytik Jena) according to manufacturers instructions.
RNA was converted to cDNA and sent to BGI Europe Genomic Center for sequencing.

treatment_protocol: GL plants were illuminated at 100 µmol photons m-2 s-1. HL plants were harvested after 15 min (HL15) or 60 min (HL60) exposure to  HL (1000 µmol photons m-2 s-1). Recovery plants were first exposed to HL for 60 min followed by the recovery for 15 min (R15) or 60 min (R60) at GL.

value: Leaf

tag: ecotype

value: High Light 60 min followed by growth light (Recovery) 60 min


title: MXD2365, Adeno-CRE


title: F111727

description:
20794-PB_Per-Site-Unphased-Methylation, 20794-PB_Per-Read-Unphased-Methylation, 20794-PB_Per-Read-Phased-Methylation-Haplotype1, 20794-PB_Per-Site-Phased-Methylation-Haplotype1, 20794-PB_Per-Read-Phased-Methylation-Haplotype2 and 20794-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX077-BF [RNA-seq]


title: R60 2

description: Treated with HL for 60 min followed by recovery for 60 min at GL 2


title: MXD1803, Adeno-CRE


title: GX059-BF [RNA-seq]


title: F111726

description:
25902-PB_Per-Site-Unphased-Methylation, 25902-PB_Per-Read-Unphased-Methylation, 25902-PB_Per-Read-Phased-Methylation-Haplotype1, 25902-PB_Per-Site-Phased-Methylation-Haplotype1, 25902-PB_Per-Read-Phased-Methylation-Haplotype2 and 25902-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111725

description:
25990-PB_Per-Site-Unphased-Methylation, 25990-PB_Per-Read-Unphased-Methylation, 25990-PB_Per-Read-Phased-Methylation-Haplotype1, 25990-PB_Per-Site-Phased-Methylation-Haplotype1, 25990-PB_Per-Read-Phased-Methylation-Haplotype2 and 25990-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX089-AgF [RNA-seq]


title: MPL512, Adeno-GFP

value: Adeno-GFP


title: GX052-AF [RNA-seq]


title: R15 3

description: Treated with HL for 60 min followed by recovery for 15 min at GL 3

value: High Light 60 min followed by growth light (Recovery) 15 min


title: F111724

description:
32034-PB_Per-Site-Unphased-Methylation, 32034-PB_Per-Read-Unphased-Methylation, 32034-PB_Per-Read-Phased-Methylation-Haplotype1, 32034-PB_Per-Site-Phased-Methylation-Haplotype1, 32034-PB_Per-Read-Phased-Methylation-Haplotype2 and 32034-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MTL382, Adeno-GFP


title: MXD2840, Adeno-GFP


title: GX035-BF [RNA-seq]


title: MXD1078, Adeno-CRE


title: HL60 3

description: HL treated for 60 min 3

value: High Light 60 min


title: MPL1071, Adeno-GFP


title: F111720

description:
37076-PB_Per-Site-Unphased-Methylation, 37076-PB_Per-Read-Unphased-Methylation, 37076-PB_Per-Read-Phased-Methylation-Haplotype1, 37076-PB_Per-Site-Phased-Methylation-Haplotype1, 37076-PB_Per-Read-Phased-Methylation-Haplotype2 and 37076-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111722

description:
36684-PB_Per-Site-Unphased-Methylation, 36684-PB_Per-Read-Unphased-Methylation, 36684-PB_Per-Read-Phased-Methylation-Haplotype1, 36684-PB_Per-Site-Phased-Methylation-Haplotype1, 36684-PB_Per-Read-Phased-Methylation-Haplotype2 and 36684-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL1239, Adeno-GFP


title: F111723

description:
32973-PB_Per-Site-Unphased-Methylation, 32973-PB_Per-Read-Unphased-Methylation, 32973-PB_Per-Read-Phased-Methylation-Haplotype1, 32973-PB_Per-Site-Phased-Methylation-Haplotype1, 32973-PB_Per-Read-Phased-Methylation-Haplotype2 and 32973-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX099-IM2F [RNA-seq]

source_name: Human IM frozen tissue

value: Human IM frozen tissue


title: GX099-IMF [RNA-seq]


title: R15 1

description: Treated with HL for 60 min followed by recovery for 15 min at GL 1


title: GX098-IMF [RNA-seq]


title: R60 1

description: Treated with HL for 60 min followed by recovery for 60 min at GL 1


title: F111719

description:
37917-PB_Per-Site-Unphased-Methylation, 37917-PB_Per-Read-Unphased-Methylation, 37917-PB_Per-Read-Phased-Methylation-Haplotype1, 37917-PB_Per-Site-Phased-Methylation-Haplotype1, 37917-PB_Per-Read-Phased-Methylation-Haplotype2 and 37917-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: HL60 1

description: HL treated for 60 min 1


title: F111717

description:
28131-PB_Per-Site-Unphased-Methylation, 28131-PB_Per-Read-Unphased-Methylation, 28131-PB_Per-Read-Phased-Methylation-Haplotype1, 28131-PB_Per-Site-Phased-Methylation-Haplotype1, 28131-PB_Per-Read-Phased-Methylation-Haplotype2 and 28131-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL2215, Adeno-GFP


title: GX094-IMF [RNA-seq]


title: HL60 2

description: HL treated for 60 min 2


title: F111718

description:
40723-PB_Per-Site-Unphased-Methylation, 40723-PB_Per-Read-Unphased-Methylation, 40723-PB_Per-Read-Phased-Methylation-Haplotype1, 40723-PB_Per-Site-Phased-Methylation-Haplotype1, 40723-PB_Per-Read-Phased-Methylation-Haplotype2 and 40723-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R15 2

description: Treated with HL for 60 min followed by recovery for 15 min at GL 2


title: MPL60, Adeno-GFP


title: GX039-BF [RNA-seq]


title: HL15 3

description: HL treated for 15 min 3

value: High Light 15 min


title: MPL660, Adeno-GFP


title: F111716

description:
34117-PB_Per-Site-Unphased-Methylation, 34117-PB_Per-Read-Unphased-Methylation, 34117-PB_Per-Read-Phased-Methylation-Haplotype1, 34117-PB_Per-Site-Phased-Methylation-Haplotype1, 34117-PB_Per-Read-Phased-Methylation-Haplotype2 and 34117-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX091-AgF [RNA-seq]


title: F111715

description:
36686-PB_Per-Site-Unphased-Methylation, 36686-PB_Per-Read-Unphased-Methylation, 36686-PB_Per-Read-Phased-Methylation-Haplotype1, 36686-PB_Per-Site-Phased-Methylation-Haplotype1, 36686-PB_Per-Read-Phased-Methylation-Haplotype2 and 36686-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL195, Adeno-GFP


title: GX085-IMF [RNA-seq]


title: GL 3

description: Sample taken before HL treatment 3

value: Growth light


title: HL15 1

description: HL treated for 15 min 1


title: GX088-IMF [RNA-seq]


title: MXD3562, Adeno-GFP


title: GL 1

description: Sample taken before HL treatment 1


title: GL 2

description: Sample taken before HL treatment 2


title: F111713

description:
30784-PB_Per-Site-Unphased-Methylation, 30784-PB_Per-Read-Unphased-Methylation, 30784-PB_Per-Read-Phased-Methylation-Haplotype1, 30784-PB_Per-Site-Phased-Methylation-Haplotype1, 30784-PB_Per-Read-Phased-Methylation-Haplotype2 and 30784-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX092-BF [RNA-seq]


title: MPL1540, Adeno-GFP


title: GX072-IMF [RNA-seq]


title: F111565

description:
33987-OCT-1_Per-Site-Unphased-Methylation, 33987-OCT-1_Per-Read-Unphased-Methylation, 33987-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33987-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33987-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33987-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MXD2758, Adeno-GFP


title: F111712

description:
18153-PB_Per-Site-Unphased-Methylation, 18153-PB_Per-Read-Unphased-Methylation, 18153-PB_Per-Read-Phased-Methylation-Haplotype1, 18153-PB_Per-Site-Phased-Methylation-Haplotype1, 18153-PB_Per-Read-Phased-Methylation-Haplotype2 and 18153-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MXD2365, Adeno-GFP


title: F111714

description:
25980-PB_Per-Site-Unphased-Methylation, 25980-PB_Per-Read-Unphased-Methylation, 25980-PB_Per-Read-Phased-Methylation-Haplotype1, 25980-PB_Per-Site-Phased-Methylation-Haplotype1, 25980-PB_Per-Read-Phased-Methylation-Haplotype2 and 25980-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX072-IM3F [RNA-seq]


title: GX062-IMF [RNA-seq]


title: F111564

description:
32015-OCT-1_Per-Site-Unphased-Methylation, 32015-OCT-1_Per-Read-Unphased-Methylation, 32015-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32015-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32015-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32015-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX091-BlF [RNA-seq]


title: F111566

description:
25981-OCT-1_Per-Site-Unphased-Methylation, 25981-OCT-1_Per-Read-Unphased-Methylation, 25981-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25981-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25981-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25981-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: HL15 2

description: HL treated for 15 min 2


title: MPL508, Adeno-GFP


title: F111562

description:
25720-OCT-1_Per-Site-Unphased-Methylation, 25720-OCT-1_Per-Read-Unphased-Methylation, 25720-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25720-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25720-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25720-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX062-IM2F [RNA-seq]


title: MXD1803, Adeno-GFP


title: F111560

description:
25435-OCT-1_Per-Site-Unphased-Methylation, 25435-OCT-1_Per-Read-Unphased-Methylation, 25435-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25435-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25435-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25435-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX054-IM2F [RNA-seq]


title: GX076-IMF [RNA-seq]


title: MXD3809, Adeno-GFP


title: MPL1539, Adeno-GFP


title: GX049-IMF [RNA-seq]


title: F111563

description:
30606-OCT-1_Per-Site-Unphased-Methylation, 30606-OCT-1_Per-Read-Unphased-Methylation, 30606-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30606-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30606-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30606-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX060-IMF [RNA-seq]


title: GX040-IMF [RNA-seq]


title: F111557

description:
36963-OCT-1_Per-Site-Unphased-Methylation, 36963-OCT-1_Per-Read-Unphased-Methylation, 36963-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36963-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36963-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36963-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL1380, Adeno-GFP


title: MPL337, Adeno-GFP


title: MPL474, Adeno-GFP


title: F111561

description:
25437-OCT-1_Per-Site-Unphased-Methylation, 25437-OCT-1_Per-Read-Unphased-Methylation, 25437-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25437-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25437-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25437-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111559

description:
25589-OCT-2_Per-Site-Unphased-Methylation, 25589-OCT-2_Per-Read-Unphased-Methylation, 25589-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 25589-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 25589-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 25589-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MPL1621, Adeno-GFP


title: MPL789, Adeno-GFP


title: F111558

description:
14891-OCT-2_Per-Site-Unphased-Methylation, 14891-OCT-2_Per-Read-Unphased-Methylation, 14891-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 14891-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 14891-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 14891-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: MXD1078, Adeno-GFP


title: F111555

description:
27338-OCT-1_Per-Site-Unphased-Methylation, 27338-OCT-1_Per-Read-Unphased-Methylation, 27338-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27338-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27338-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27338-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX014-IM2F [RNA-seq]


title: GX059-IMF [RNA-seq]


title: F111553

description:
26416-OCT-1_Per-Site-Unphased-Methylation, 26416-OCT-1_Per-Read-Unphased-Methylation, 26416-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 26416-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 26416-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 26416-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: DCD2257, Adeno-GFP


title: F111552

description:
25977-OCT-1_Per-Site-Unphased-Methylation, 25977-OCT-1_Per-Read-Unphased-Methylation, 25977-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25977-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25977-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25977-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX031-IMF [RNA-seq]


title: F111556

description:
34071-OCT-1_Per-Site-Unphased-Methylation, 34071-OCT-1_Per-Read-Unphased-Methylation, 34071-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 34071-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 34071-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 34071-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_32_R (methylation)

type: genomic

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation chip using standard Illumina protocol

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

data_processing: The raw signal data were normalized to control by GenomeStudio v2011.1 software.

label: Cy5 and Cy3

source_name: PBMC at Removal

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and then applied on bisulfite treatment by EZ DNA Methylation Kit (ZYMO RESERCH) according to manufacturer's protocol.

tag: disease state

value: Acute myocardial infarction

tag: age

tag: gender

value: M

tag: outcome

value: Success

value: PBMC

tag: time

value: Removal


title: N173

city: Stanford

first: Yin

last: Liu

address: 279 Campus Dr.

institute: Stanford University

description: Low quality

data_processing:
Nextseq 500 was used for sequecing and de-multiplexed to generate a fastq file.
Raw reads were aligned to the NCBI RefSeq mouse transcriptome (modified to exclude model XR_/XM_ sequences and include the tdTomato sequence) using kallisto with default settings (Bray et al., 2016). Read count and transcripts per million (TPM) values from splice isoforms of the same genes were collapsed, and for quality control cells with less than 2,000,000 paired-end reads that mapped to endogenous genes or less than 10,000 endogenous genes with mapped paired-end reads were excluded from the following analysis.
The TPM table was log-transformed (log2(TPM+1)) and scaled, and PCA was performed using 305 glial cell-enriched genes (Li et al., 2016). Cells were plotted along the first two PCs and 7 cells clearly separated from the rest, which were considered glial contaminated.
Subtype identification was performed using an iterative cluster analysis described in the paper
Genome_build: Genome_build: NCBI RefSeq mouse transcriptome (mouse.rna.fna.gz downloaded from ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot on April 7, 2014)
Supplementary_files_format_and_content: tab-delimited table of TPM value for each gene and each sample
Supplementary_files_format_and_content: tab-delimited table of subtype identity of each high-quality sample

source_name: vagal pulmonary sensory neurons

extract_protocol:
Mice were euthanized with CO2 and transcardially perfused with cold Hank's balanced salt solution (HBSS) (without Ca2+ and Mg2+). Vagal ganglia were quickly dissected after perfusion in cold buffered HBSS (10 mM HEPES, pH7.2-7.5) and each was cut into 2~3 pieces. Ganglion tissue was then digested with papain solution at 20 U/ml (Worthington LS003124, in buffered HBSS containing 0.5 mM EDTA, 1.5 mM CaCl2, 0.4 mg/ml L-cysteine, pre-warmed for 30 min for activation) for 10 min at 37°C, and then collagenase/dispase solution (collagenase IV, 300 U/ml, Worthington LS004186; dispase, 1mg/ml, Thermo Fisher Scientific 17105-041, in HBSS, pre-warmed) for 30 min at 37°C with tube inversion to agitate every 10 min. After centrifuging at 400 g for 4 min, tissue pellet was resuspended in 1 ml L15 medium (with 10mM HEPES pH 7.2-7.5 and 10% fetal bovine serum) and triturated using fire-polished Pasteur pipettes. A Percoll gradient spin was used to clear axonal debris and glial cells by layering the cell suspension onto a buffered L15 medium (10 mM HEPES)/Percoll (4:1) solution and then centrifuging for 9 min at 400 g. The cell pellet was resuspended in 2 ml buffered L15 medium, centrifuged again for 3 min at 750 g, and resuspended in 200 µl suspension medium (L15 medium, 10mM HEPES pH 7.2-7.5, 1mg/ml BSA, and 0.1% Pluronic F-68).
cDNA samples were prepared using SMART-Seq v3 Ultra Low Input RNA Kit (Clontech), and sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina FC-131-1096) and Index Adapters (Illumina, FC-131-1002), following the C1 system for mRNA Seq Protocol (Fluidigm).

value: Wildtype

value: post natal 6-12 weeks


title: MPL1658, Adeno-GFP

tag: tissue

value: pancreas

value: adenocarcinoma


title: ECMO_28_R (methylation)

value: Dilated cardiomyopathy


title: GX006-IM3F [RNA-seq]


title: MXD1439, Adeno-GFP

tag: treatment


title: MPL500, Adeno-GFP


title: GX023-IM3dysF [RNA-seq]


title: GX001-IM3F [RNA-seq]


title: F111554

description:
27028-OCT-2_Per-Site-Unphased-Methylation, 27028-OCT-2_Per-Read-Unphased-Methylation, 27028-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 27028-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 27028-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 27028-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_38_R (methylation)


title: ECMO_42_R (methylation)

value: Congestive heart failure


title: ECMO_27_R (methylation)

value: Arrhythmia


title: N139

description: Low quality


title: H011-NileO [RNA-seq]

source_name: Human nomal ileum organoid

value: Human nomal ileum organoid

value: Culture condition:Standard colon organoid medium


title: ECMO_22_R (methylation)

value: Acute myocarditis

value: F


title: F111548

description:
42298-FF-1_Per-Site-Unphased-Methylation, 42298-FF-1_Per-Read-Unphased-Methylation, 42298-FF-1_Per-Read-Phased-Methylation-Haplotype1, 42298-FF-1_Per-Site-Phased-Methylation-Haplotype1, 42298-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 42298-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111551

description:
26066-OCT-1_Per-Site-Unphased-Methylation, 26066-OCT-1_Per-Read-Unphased-Methylation, 26066-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 26066-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 26066-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 26066-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_39_R (methylation)


title: ECMO_19_R (methylation)


title: ECMO_33_R (methylation)


title: N147

description: Low quality


title: ECMO_14_R (methylation)


title: GX099-BO [RNA-seq]

source_name: Human normal gastric organoid

value: Human normal gastric organoid

value: Culture condition:Standard gastric organoid medium


title: F111547

description:
39279-OCT-1_Per-Site-Unphased-Methylation, 39279-OCT-1_Per-Read-Unphased-Methylation, 39279-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 39279-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 39279-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 39279-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX098-BO [RNA-seq]


title: ECMO_10_R (methylation)

value: Acute myocardial infarction

value: M


title: F111550

description:
23411-OCT-2_Per-Site-Unphased-Methylation, 23411-OCT-2_Per-Read-Unphased-Methylation, 23411-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 23411-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 23411-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 23411-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GX094-BfO [RNA-seq]


title: H007-NileO [RNA-seq]


title: N41

description: Glial contaminated


title: F111545

description:
32559-OCT-3_Per-Site-Unphased-Methylation, 32559-OCT-3_Per-Read-Unphased-Methylation, 32559-OCT-3_Per-Read-Phased-Methylation-Haplotype1, 32559-OCT-3_Per-Site-Phased-Methylation-Haplotype1, 32559-OCT-3_Per-Read-Phased-Methylation-Haplotype2 and 32559-OCT-3_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: ECMO_6_R (methylation)

value: Success

value: PBMC


title: ECMO_41_2 (methylation)

source_name: PBMC at 2hr


title: N32

description: Glial contaminated

value: Wildtype


title: GX090-BO [RNA-seq]


title: N26

description: Low quality

value: post natal 6-12 weeks


title: GX089-BlO [RNA-seq]


title: ECMO_42_2 (methylation)


title: N19

description: Glial contaminated


title: F111542

description:
28384-FF-1_Per-Site-Unphased-Methylation, 28384-FF-1_Per-Read-Unphased-Methylation, 28384-FF-1_Per-Read-Phased-Methylation-Haplotype1, 28384-FF-1_Per-Site-Phased-Methylation-Haplotype1, 28384-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 28384-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111549

description:
44955-OCT-1_Per-Site-Unphased-Methylation, 44955-OCT-1_Per-Read-Unphased-Methylation, 44955-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 44955-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 44955-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 44955-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F111541

description:
32353-OCT-1_Per-Site-Unphased-Methylation, 32353-OCT-1_Per-Read-Unphased-Methylation, 32353-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32353-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32353-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32353-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: H007-NAsCO [RNA-seq]

source_name: Human normal colon organoid

value: Human normal colon organoid


title: ECMO_7_R (methylation)

value: Removal


title: N44

description: Glial contaminated

value: CGRPalphaCreER/+; Ai14

tag: trreatment

value: 3mg Tamoxifen oral gavage


title: H007-NCaeO [RNA-seq]

tag: culture condition


title: N108

description: Low quality

value: Phox2b-Cre; Ai14


title: ECMO_8_R (methylation)

value: Failure


title: N42

description: Glial contaminated


title: ECMO_38_2 (methylation)


title: N15

description: Glial contaminated


title: ECMO_37_2 (methylation)

value: Dilated cardiomyopathy, DCMP


title: GX091-BgO [RNA-seq]


title: F111546

description:
32572-OCT-1_Per-Site-Unphased-Methylation, 32572-OCT-1_Per-Read-Unphased-Methylation, 32572-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32572-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32572-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32572-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2