title: Weeping peach tree #3 branch #5 Internode 2 tissue from top (upper / adaxial) side of branch

city: East Lansing

first: Courtney

last: Hollender

address: 1066 Bogue St

department: Horticulture

institute: Michigan State University

data_processing:
FastQ files were processed in CLC Genomics workbench v22. For each library, the data from all three lanes was merged into a single file prior to adapter and quality trimming. Using the trim reads tool set to remove adaptor and following sequence (3’ trim), all files were trimmed for the Illumina Stranded mRNA Prep adaptor (CTGTCTCTTATACACATCT). The mismatch cost =2, gap cost=3, minimal internal match score=10, minimum end match score=4. No homopolymer trimming or filtering based on length. Following adaptor trimming, the trim reads tool was run again to perform quality trimming, with a quality score limit of 0.001 and maximum of 2 ambiguous nucleotides.
Trimmed reads were aligned to the peach genome v. 2.0 (Verde et al., 2017). For RNAseq alignment, CLC Genomics v22.0 the RNA-Seq Analysis (GE) tool was used with parameters as follows: reverse strand specificity, library type= no 3’ bias, mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.9, similarity fraction=0.8, with a maximum number of hits=6, expression value=RPKM.
Assembly: Prunus persica (peach) genome v. 2.0
Supplementary files format and content: xlsx files including read counts, RPKM, and exon/intron mapping counts for each gene

organism: Prunus persica

source_name: Weeping Peach Tree Branch Internode 2 tissue from top (upper / adaxial) side of branch

growth_protocol: Trees were grown in pots ranging in size from 1- to 15-gallons in standard greenhouse conditions, with supplemental lighting to maintain an approximately 16-hour photoperiod.

extract_protocol:
EZNA SQ Total RNA kit, followed by Zymo RNA clean-up wi\th DNA digestion step.
Library preparation and sequencing were performed by the Michigan State University Genomics Core. Libraries were created using Illumina Stranded mRNA Prep and indexed with IDT for Illumina RNA UD Indexes. Quality control and quantification for the libraries were performed using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays.
A single pool, with equimolar proportions of each library, was quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit. The pool was loaded onto three lanes of an Illumina HiSeq 4000 single read flow cell and single end 50 bp sequencing was performed using HiSeq 4000 SBS reagents. Base calling was performed using Illumina Real Time Analysis (RTA) v2.7.7 and the output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.

treatment_protocol: No treatments

value: Weeping architecture peach tree


title: glioma_Recurrence 1 [TCGA-06-0211-R1-02M-450-PML9WT]

status: Public on Dec 13 2023

type: genomic

city: Detroit

first: Laila

middle: M

last: Poisson

state: MI

address: 2799 W Grand Blvd

country: USA

institute: Henry Ford Health

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

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

data_processing:
The raw DNA methylation intensity data files (IDAT) were processed with the minfi package. We performed noob (Normal-exponential convolution using out-of-band probes) background correction and dye bias correction using the minfi package (v 1.36.0). The DNA methylation value for each locus is presented as a beta (β) value (β = (M/(M+U)) in which M and U indicate the mean methylated and unmethylated signal intensities for each locus, respectively. β-values range from zero to one, with scores of zero indicating no DNA methylation and scores of one indicating complete DNA methylation. A detection p-value also accompanies each data point and compares the signal intensity difference between the analytical probes and a set of negative control probes on the array. Any data point with a corresponding p-value greater than 1E-4 is deemed not to be statistically significantly different from background and was thus masked as “NA”.
matrix processed value definition: Average Beta

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified at each institution following standard protocols that ensure high quality DNA.

tag: gender

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence

value: IDHwt

value: noncodel

value: Classic-like

value: RTK II


title: Weeping peach tree #3 branch #5 Internode 1 tissue from top (upper / adaxial) side of branch

type: SRA

library_source: transcriptomic

molecule: total RNA

source_name: Weeping Peach Tree Branch Internode 1 tissue from top (upper / adaxial) side of branch

tag: tissue

tag: genotype


title: 3543_OF1A_1-1-I1-I14

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

source_name: OF1A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: BS_9_2

city: Beijing

first: SUN

last: WAN

state: Beijing

address: o. 2 Yuanmingyuan West Road, Haidian District

country: China

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Triticum aestivum

source_name: wheat spikelet

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wheat spikelet

tag: time

value: 9 days after terminal spikelet

tag: position

value: basal spikelet

tag: treatment

value: untreated


title: Weeping peach tree #3 branch #5 Internode 2 tissue from bottom (lower / abaxial) side of branch

source_name: Weeping Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch


title: 3543_OF1A_1-1-I1-I13


title: Weeping peach tree #3 branch #5 Internode 1 tissue from bottom (lower / abaxial) side of branch

source_name: Weeping Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: 3543_OF1A_1-1-I1-H2


title: MS_6_3

value: 6 days after terminal spikelet

value: central spikelet


title: glioma_Primary [TCGA-06-0210-TP-01M-450-IST5AV]

value: female

value: Primary

value: Mesenchymal-like


title: glioma_Recurrence 1 [TCGA-06-0210-R1-01M-450-DNWLII]

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence

value: RTK I


title: BS_9_1


title: 3543_OF1A_1-1-I1-H1


title: glioma_Primary [TCGA-06-0190-TP-01M-450-YDSMF9]

value: male

value: IDHwt

value: noncodel

value: mesenchymal


title: 3543_OF1A_1-1-I1-H14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-1-I1-H13


title: BS_6_3

value: wheat spikelet

value: basal spikelet


title: MS_6_1

value: 6 days after terminal spikelet

value: untreated


title: glioma_Primary [TCGA-06-0171-TP-02M-450-LMVVPP]

value: Classic-like

value: RTK II


title: Weeping peach tree #3 branch #2 Internode 1 tissue from top (upper / adaxial) side of branch

value: Weeping Peach Tree Branch Internode 1 tissue from top (upper / adaxial) side of branch

value: Weeping architecture peach tree


title: Weeping peach tree #3 branch #2 Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Weeping Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch


title: BS_6_2


title: Weeping peach tree #3 branch #2 Internode 1 tissue from bottom (lower / abaxial) side of branch

value: Weeping Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: glioma_Recurrence 1 [TCGA-06-0171-R1-11M-450-KRJEHO]

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence

value: Mesenchymal-like


title: 3543_OF1A_1-1-I1-G2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: MS_9_3

value: 9 days after terminal spikelet

value: central spikelet


title: 3543_OF1A_1-1-I1-G1

value: Female

value: nuclear RNA + genomic DNA


title: glioma_Primary [TCGA-06-0152-TP-02M-450-GGWYUC]

value: Primary

value: IDHwt

value: noncodel


title: BS_6_1

value: wheat spikelet

value: 6 days after terminal spikelet

value: basal spikelet

value: untreated


title: 3543_OF1A_1-1-I1-G14


title: Weeping peach tree #1 branch #5 Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Weeping Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Weeping architecture peach tree


title: glioma_Recurrence 1 [TCGA-06-0152-R1-01M-450-OWMIQB]

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Classic-like

value: RTK II


title: Weeping peach tree #3 branch #2 Internode 2 tissue from top (upper / adaxial) side of branch

value: Weeping Peach Tree Branch Internode 2 tissue from top (upper / adaxial) side of branch


title: KPK2_t1_CB839_rep2

city: New York

first: Dimitris

last: Karagiannis

state: NY

institute: Columbia University

data_processing:
Computational analysis was done using MAGeCK. Briefly, the sequencing data were de-barcoded and the 20 bp sgRNA sequence was mapped to the reference sgRNA library without allowing for any mismatches.
The read counts were calculated for each individual sgRNA and normalized, and differential analysis was done between KP and KPK samples
Quality control, gene hit identification and graphs were generated using MAGeCKFlute.
Assembly: sgRNA library
Supplementary files format and content: sgRNA raw counts txt: sgRNA raw counts for each sample
Supplementary files format and content: 2 sgrna_summary.txt; sgRNA - gene correspondence
Supplementary files format and content: 2 gene_summary.txt files: Comparative analysis between KP and KPK cells (DMSO or CB-839 treated) in sgRNA enrichment for each gene

organism: Mus musculus

source_name: cell line

growth_protocol: KP and KPK cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA from collected cell pellets were prepared with purelink mini kit (ThermoFisher) according to the manufacturer’s suggested protocol.
Libraries were generated by amplification from genomic DNA using a modified 2-step PCR version of the protocol published by Doench et al. Briefly, we perform an initial “enrichment” PCR, whereby the integrated sgRNA cassettes are amplified from gDNA, followed by a second PCR to append Illumina sequencing adapters on the 5’- and 3’-ends of the amplicon, as well as a random nucleotide stagger and unique demultiplexing barcode on the 5’ end. Each “PCR1” reaction contains 25µL of Q5 High-Fidelity 2X Master Mix (NEB), 2.5µL of Nuc PCR#1 Fwd Primer (10µM), 2.5µL of Nuc PCR#1 Rev Primer (10µM), and 5µg of gDNA in 20µL of water (for a total volume of 50µL per reaction). The number of PCR1 reactions is scaled accordingly; therefore, we performed six PCR1 reactions per technical replicate, per time point (T0 or TF), and per condition. PCR1 amplicons were purified using the QIAquick PCR Purification Kit (Qiagen) and used as template for “PCR2” reactions. Each PCR2 reaction contains 25µL of Q5 High-Fidelity 2X Master Mix (NEB), 2.5µL of a unique Nuc PCR#2 Fwd Primer (10µM), 2.5µL of Nuc PCR#2 Rev Primer (10µM), and 300ng of PCR1 product in 20µL of water (for a total volume of 50µL per reaction). We performed two PCR2 reactions per PCR1 product.   PCR Program for PCR1 and PCR2: 1) 98°C x 30s; 2) 98°C x 10s; 3) 65°C x 30s; 4) 72°C x 30s; 5) Go to step 2 x 24 cycles; 6) 72°C x 2 min; 7) 4°C forever. Library amplicons were size-selected on a 2.5% agarose gel, purified using the QIAquick Gel Extraction Kit (Qiagen), and sequenced on an Illumina NextSeq500 instrument (75nt single end reads). Files resulting from 4 sequencing lanes were concatenated into a single file for each condition.

treatment_protocol: Derivatives of KP and KPK cells were generated by stable lentiviral transduction of Cas9 with blasticidin resistance (Addgene#52962). Cells were maintained with blasticidin selection throughout the experiment. Transduction of Cas9-expressing KP/KPK cells was performed at an MOI of approximately 0.2 by incubating cell suspension in lentiviral supernatant and centrifugation at 1500 rpm for 1.5 hours at room temperature before being returned to a humidified incubator. An initial population was infected to represent a 2500x representation of the epigenetic library; 36 hours post-transduction cells were resuspended and replated in 10 ug/mL puromycin and selected for another 48 hours. After complete puromycin selection cells were trypsinized, pooled, a cell sample representing time-0hr (t0) of the screen was reserved and stored at -20C. The remaining cells from each line were then passaged into Vehicle (DMSO) or CB839 250nM conditions. CB839 treatment was initially started when cells had initially attached after initially being plated at a concentration of 125nM. This was then increased to 250nM and maintained constantly during the subsequent passage. Each condition was performed in technical triplicate for the entire screen and maintained in 15 cm tissue culture dishes (Corning) with at least 2500x library representation maintained throughout all culture and library preparation steps. Population doublings for each cell line and condition were recorded and a sample was collected when a particular condition had reached 14 cumulative population doublings(t1) and stored at -20o C. 3 biological replicates per condition are included.

value: cell line

tag: cell line

tag: cell type

value: Mouse LUAD

value: 14 doublings


title: MS_6_2

value: central spikelet


title: 3543_OF1A_1-1-I1-G13

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: glioma_Primary [TCGA-06-0125-TP-01M-450-XC6ZJF]

value: female

value: Primary

value: IDHwt

value: noncodel


title: Weeping peach tree #1 branch #5 Internode 1 tissue from top (upper / adaxial) side of branch

value: Weeping Peach Tree Branch Internode 1 tissue from top (upper / adaxial) side of branch

value: Weeping architecture peach tree


title: KPK2_t1_CB839_rep3


title: glioma_Recurrence 1 [TCGA-06-0190-R1-01M-450-BR0QI9]

value: male

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence

value: Mesenchymal-like

value: mesenchymal


title: Weeping peach tree #1 branch #5 Internode 1 tissue from bottom (lower / abaxial) side of branch

value: Weeping Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: 3543_OF1A_1-1-I1-F2


title: glioma_Primary [GLSS-LU-0B13-TP-01M-450-F3AA51]


title: Weeping peach tree #1 branch #4 Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Weeping Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch


title: KPK1_t1_CB839_rep3

value: cell line

value: Mouse LUAD

value: 14 doublings


title: 3543_OF1A_1-1-I1-F1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: Weeping peach tree #1 branch #4 Internode 2 tissue from top (upper / adaxial) side of branch

value: Weeping Peach Tree Branch Internode 2 tissue from top (upper / adaxial) side of branch


title: KPK1_t1_CB839_rep2


title: 3543_OF1A_1-1-I1-F14


title: Weeping peach tree #1 branch #4 Internode 1 tissue from top (upper / adaxial) side of branch


title: KPK1_t1_CB839_rep1


title: glioma_Primary [GLSS-LU-00C7-TP-01M-450-9EDFD9]

value: Primary

value: IDHwt

value: noncodel

value: midline


title: 3543_OF1A_1-1-I1-F13


title: Weeping peach tree #1 branch #5 Internode 2 tissue from top (upper / adaxial) side of branch

value: Weeping architecture peach tree


title: glioma_Recurrence 1 [GLSS-LU-0B13-R1-01M-450-2D305E]

value: female

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Recurrence


title: glioma_Recurrence 1 [GLSS-LU-00C7-R1-01M-450-AC08D4]

value: male


title: Weeping peach tree #1 branch #4 Internode 1 tissue from bottom (lower / abaxial) side of branch

value: Weeping Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: 3543_OF1A_1-1-I1-E1


title: Standard peach tree #3 branch #2 Internode 2 tissue from top (upper / adaxial) side of branch

source_name: Standard Peach Tree Branch Internode 2 tissue from top (upper / adaxial) side of branch

value: Standard architecture peach tree


title: Standard peach tree #3 branch #2 Internode 2 tissue from bottom (lower / abaxial) side of branch

source_name: Standard Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch


title: glioma_Primary [GLSS-LU-00C4-TP-01M-450-73E71B]

value: Mesenchymal-like

value: RTK I


title: KP2_t1_CB839_rep3

value: cell line

value: Mouse LUAD

value: 14 doublings


title: 3543_OF1A_1-1-I1-E14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-1-I1-E13


title: KP2_t1_CB839_rep1


title: KPK2_t1_CB839_rep1


title: glioma_Recurrence 1 [GLSS-LU-00C4-R1-01M-450-F506FB]

value: IDHwt

value: noncodel

value: mesenchymal


title: glioma_Primary [GLSS-LU-00B9-TP-01M-450-8488BF]

value: Primary


title: glioma_Recurrence 1 [TCGA-06-0125-R1-11M-450-7VHZXA]

value: female

value: Glioblastoma, IDH-wildtype (WHO grade 4)

value: Classic-like


title: Standard peach tree #3 branch #2 Internode 1 tissue from bottom (lower / abaxial) side of branch

source_name: Standard Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: KP1_t1_CB839_rep3


title: Standard peach tree #3 branch #2 Internode 1 tissue from top (upper / adaxial) side of branch

source_name: Standard Peach Tree Branch Internode 1 tissue from top (upper / adaxial) side of branch


title: 3543_OF1A_1-1-I1-D2


title: KP2_t1_CB839_rep2


title: glioma_Recurrence 1 [GLSS-LU-00B9-R1-01M-450-2D8DD7]

value: male

value: Recurrence


title: 3543_OF1A_1-1-I1-D14


title: Standard peach tree #3 branch #1 Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Standard Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Standard architecture peach tree


title: 3543_OF1A_1-1-I1-D13


title: 3543_OF1A_1-1-I1-D1


title: KP1_t1_CB839_rep1

value: cell line


title: glioma_Recurrence 1 [GLSS-FG-0003-R1-01M-450-FE0A32]

value: Mesenchymal-like

value: no class


title: glioma_Primary [GLSS-FG-0003-TP-01M-450-1B5F61]


title: 3543_OF1A_1-1-I1-C2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Standard peach tree #3 branch #1 Internode 1 tissue from bottom (lower / abaxial) side of branch

value: Standard Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: glioma_Primary [GLSS-FG-0002-TP-01M-450-12EF91]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 2)

value: IDHmut

value: codel

value: G-CIMP-high

value: 1p/19q codeleted oligodendroglioma


title: glioma_Primary [GLSS-FG-0002-TP-02M-450-948D90]

value: female

value: Primary


title: lineage-traced cells after (1) light-damage (2) Ascl1 expression in MG

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

institute: University of Washington

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Read demutliplexing and intensity to fastq conversion done using cellranger mkfastq
Gene by cell matricies were created using cellranger count
Downstream processing was preformed in R using Seurat
Assembly: mm10
Supplementary files format and content: CellRanger outputs: filtered feature bc matrices in h5 format

source_name: retina

extract_protocol:
Tissue was dissociated according to the Worthington Papain Dissociation System and the cell suspension was sorted on a BD FACSAria III cell sorter to collect GFP+ cells. The sorted cells were centrifuged at 400 rcf for 10 minutes (4 C) and then resuspended in PBS/glucose for a concentration of 1000 cells/uL.
10x Chromium Single Cell 3' V3.1 (scRNA-seq)

value: retina

tag: cellranger version


title: lineage-traced cells after (1) light-damage (2) Ascl1-Atoh1 expression in MG

description: 10x Genomics


title: lineage-traced cells after (1) Ascl1-Atoh1 expression in MG (2) light-damage

description: 10x Genomics


title: 3543_OF1A_1-1-I1-C1

value: Female

value: nuclear RNA + genomic DNA


title: KP1_t1_CB839_rep2

value: Mouse LUAD

value: 14 doublings


title: glioma_Recurrence 1 [GLSS-FG-0002-R1-01M-450-70581A]

value: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted (WHO grade 3)

value: Recurrence

value: G-CIMP-low

value: high grade astrocytoma


title: lineage-traced cells after (1) Ascl1-Atoh1 expression in MG (2) NMDA injury

description: 10x Genomics


title: Standard peach tree #1 branch #7 Internode 2 tissue from top (upper / adaxial) side of branch

value: Standard Peach Tree Branch Internode 2 tissue from top (upper / adaxial) side of branch

value: Standard architecture peach tree


title: glioma_Recurrence 2 [GLSS-FG-0002-R2-01M-450-515BA3]

value: IDHmut

value: Codel


title: 3543_OF1A_1-1-I1-C14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Standard peach tree #1 branch #7 Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Standard Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch


title: Standard peach tree #1 branch #7 Internode 1 tissue from top (upper / adaxial) side of branch

value: Standard Peach Tree Branch Internode 1 tissue from top (upper / adaxial) side of branch


title: 3543_OF1A_1-1-I1-B2


title: 3543_OF1A_1-1-I1-C13


title: 3543_OF1A_1-1-I1-B1


title: lineage-traced cells after (1) Ascl1-Atoh1 expression in MG without injury

description: 10x Genomics


title: Standard peach tree #3 branch #1 Internode 1 tissue from top (upper / adaxial) side of branch


title: Standard peach tree #3 branch #1 Internode 2 tissue from top (upper / adaxial) side of branch


title: glioma_Recurrence 1 [GLSS-FG-0001-R1-01M-450-AED962]

value: male

value: Astrocytoma, IDH-mutant (WHO grade 3)

value: noncodel

value: G-CIMP-high

value: astrocytoma


title: lineage-traced cells after (1) Ascl1 expression in MG (2) NMDA injury

description: 10x Genomics

value: retina


title: Standard peach tree #1 branch #7 Internode 1 tissue from bottom (lower / abaxial) side of branch

value: Standard Peach Tree Branch Internode 1 tissue from bottom (lower / abaxial) side of branch


title: AAV8-p21_dpc16_ex3

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.1.0) with the GENCODE vM25 annotation gtf file after trimming the adaptor sequences and low-quality bases using cutadapt 1.14.
The uniquely mapped reads were counted at the gene level (protein coding) using HTSeq-count v0.12.4 and the GENCODE vM25 annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene count values for each Sample

source_name: liver from AAV8-p21-infected pregnant mice at dpc16

extract_protocol:
Liver pieces digested in ISOGEN (NIPPON GENE). RNA was extracted from liver samples using an RNeasy Micro Kit (Qiagen), in accordance with the manufacturer’s instructions. Quality RNA samples were selected (RIN>7).
200 ng Total RNA was used to generate RNA-seq libraries using a TruSeq Stranded mRNA library prep kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For p21 expression, mouse p21 cDNA was amplified from a mouse liver mRNA library using the primer pairs 5'-ACCATGTCCAATCCTGGTGATG-3' and 5'-TCAGGGTTTTCTCTTGCAGAAG-3' and subcloned between the BamHI and HindIII sites of the AAV8.TBG.PI.Null.bGH plasmid. Viral particle solutions (100 µl, 5.0 × 1012 genome copies per millilitre) were administered to wild-type (WT) mice by tail vein injection.

tag: strain

value: WT

value: female


title: AAV8-p21_dpc16_ex2


title: 3543_OF1A_1-1-I1-A2

value: Female

value: nuclear RNA + genomic DNA


title: Standard peach tree #1 branch #1 Internode 1 tissue from top (upper / adaxial) side of branch

value: Standard architecture peach tree


title: Standard peach tree #1 branch #1 Internode 1 tissue from bottom (lower / abaxial) side of branch


title: 3543_OF1A_1-1-I1-B13


title: AAV8-p21_dpc16_ex1


title: AAV8-p21_dpc8_ex3

source_name: liver from AAV8-p21-infected pregnant mice at dpc8


title: KO B cells stimulated 4

city: Madrid

first: Nuria

last: Martínez-Martín

address: Nicolás Cabrera 1

country: Spain

institute: CBMSO-CSIC

data_processing:
Quantified libraries were pooled and sequenced by paired-end read on Illumina platform. Raw data on fastq format were processed to remove reads containing adapter poly-N and low-quality sequences. All the downstream analyses were based on clean data with high quality. Index of the reference genome was built using Hisat2 v2.0.5, paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file and, thus, a better mapping result than other non-splice mapping tools. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and the reads count mapped to this gene. Downstream analysis was performed in the R environment (version 4.2.2) using the Bioconductor package DESeq2 (V1.38.2) for gene count normalisation (size factor normalisation method). For differential gene expression analysis, the "apeglm" method was used to obtain unbiased logFC estimates, specifically targeting accurate identification of significant differences in the dataset. Genes with adjusted p-values < 0.05 after Benjamini–Hochberg correction were identified as differentially expressed genes (DEGs).
Assembly: mm39
Supplementary files format and content: Excel file contains raw counts for each sample

source_name: B lymphocytes

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini KIT
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: B lymphocytes

value: TFAM KO


title: KO B cells stimulated 3


title: KO B cells stimulated 2


title: glioma_Primary [GLSS-FG-0001-TP-02M-450-D60E26]

value: Astrocytoma, IDH-mutant (WHO grade 2)

value: Primary

value: IDHmut


title: METTL3KD_U2OS_ONT

city: Gothenburg

first: Tanmoy

last: Mondal

state: Västra Götaland

address: Bruna Stråket 16

department: Department of Clinical Chemistry and Transfusion Medicine

country: Sweden

institute: University of Gothenburg

description:
direct RNA Oxford Nanopore sequencing
featureCounts_matrix.tsv

data_processing:
Raw Illumina short-reads data obtained from SMARTER-Stranded Total RNA-Seq Kit v2 sequencing was processed using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a minimal length threshold of 20bp. Quality control of Illumina short-reads was performed using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with default parameters (-q 20). Trimmed reads were mapped with HISAT2 v2.2.1 (Kim et al. 2019) preserving strand information (-U –rna-strandness R) using the Telomere-to-Telomere (T2T) human reference genome assembly (T2T-CHM13 v1.1) (Nurk et al. 2022) . The Escherichia coli K12 genome was concatenated to the T2T reference assembly for further spike-in normalization. To control the systematic variation across m6A-RIP experiments, the amount of spiked-in bacterial RNA was estimated by counting the total number of reads uniquely mapping to the E. coli K-12 reference genome using Sambamba v0.7.1 (Tarasov et al. 2015). The E. coli spike-in Bacterial counts were further used to calculate scaling factors for each batch of m6A-RIP-seq samples. Duplicate reads were labeled using MarkDuplicates from Picard v2.23.4 (http://broadinstitute.github.io/picard/). Alignments were downsampled according to calculated spike-in scaling factors using DownsampleSam from Picard (--strategy HighAccuracy). Mapping files were separated by strand after duplicate removal using Sambamba v0.7.1.
Direct RNA Oxford Nanopore Technology (ONT) sequencing data was base-called using Guppy v5.0.16 (flowcell FLO-MIN106, kit SQK-RNA002). Quality control was performed with PycoQC (https://github.com/a-slide/pycoQC) and NanoPlot (https://github.com/wdecoster/NanoPlot) on base-called data. ONT reads were mapped to the T2T-CHM13 v1.1 reference genome using Minimap v2.24 (-map-ont -uf -k14)
Assembly: T2T CHM13 v1.1 (Homo sapiens)
Assembly: U00096.2 (Escherichia coli K-12, substr. MG1655)
Supplementary files format and content: bigwig files for coverage on input RNA and m6A-RIP

molecule: polyA RNA

growth_protocol: U2OS cells were procured from Sigma and cultured in DMEM media. Two Mettl3 KD and one control U2OS stable cell line were generated using lentivirus expressing shRNA against METTL3 or non-targeted genomic region. Here known as Control-sh and METTL3sh-1, METTLsh-2. CHLA-90 (CCOG) and SK-N-F1 (Sigma Aldrich) cells were cultured in DMEM media supplemented with 20% and 10% FBS respectively.

extract_protocol:
Nuclear fractionation of Control-sh and METTL3sh-2 cells was carried out by washing the trypsinized cells in ice-cold PBS and resuspending them in ice-cold RLN1 buffer (50 mM Tris pH 8.0, NaCl 500 mM, MgCl2 1.5 mM and 0.5% NP-40) and after 5 min incubation for on ice, the samples were spun at 300g for 2 min at 4°C. The supernatant containing cytoplasmic fraction was discarded and RNA from the nuclear pellet was isolated using TRIzol reagent (Invitrogen).  RNA fragmentation followed by m6A RIP was performed with 15 µg of RNA spiked in with 9 ng of Bacterial RNA as previously described by Zeng et al 2018.
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit V2 (Pico Input Mammalian) from Takara and single end sequenced (1X 75 bp) on illumina NextSeq 550 platform.  Total RNA isolated from Control-sh and METTL3 KD cells, 20-25 ug was directly sequenced on the Oxford nanopore platform. In brief Total RNA quantification and quality control was performed on Fragment Analyzer 5300 system and showed RNA integrity number (RIN) of 10 for both samples. Poly(A) RNA Selection Kit V1.5 (Lexogen) was used to enrich for polyadenylated transcripts with minor changes to the protocol. All the processing volumes were doubled, and 4ug of Control-sh or METTL3-KD RNA was used as an input in a single reaction. Each sample was batch-processed in 5 separate reactions that were combined at the final elution step. Control-sh and METTL3-KD poly(A)-enriched RNA was analyzed on Fragment Analyzer showing remaining rRNA contamination to be 11% and 21% of mass for each sample respectively. Enriched poly(A)-RNA was then purified using 1x of RNAClean XP (Beckman Coulter) beads to concentrate the sample and remove very short RNA fragments and eluted into 11ul of water. Qubit™ RNA High Sensitivity kit (Invitrogen) was used to quantify the RNA before direct RNA sequencing. SQK-RNA002 (ONT) kit was used for library preparation and followed according to the manufacturer’s protocol. Briefly, 400ng of poly(A)-enriched RNA was used as an input, and recommended reverse-transcription step was performed. Control-sh and METTL3-KD libraries were loaded on individual FLO-MIN106 (ONT) flowcells and sequenced on GridION Mk1 device (ONT) for 72 hours yielding 1.65 and 1.35 million long-reads respectively.
direct-RNA Nanopore sequencing

value: Human Bone Osteosarcoma Epithelial Cells

value: METTL3 knockdown

tag: antibody

tag: spike-in organism

tag: rna fraction

value: Poly-A RNA


title: KO B cells stimulated 1


title: AAV8-p21_dpc8_ex2


title: AAV8-p21_dpc8_ex1


title: 3543_OF1A_1-1-I1-A13

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-1-I1-A1


title: 3543_OF1A_1-1-I1-A14


title: Standard peach tree #1 branch #1 Internode 2 tissue from top (upper / adaxial) side of branch

value: Standard Peach Tree Branch Internode 2 tissue from top (upper / adaxial) side of branch


title: 3543_OF1A_1-1-I1-B14


title: AAV8-Null_dpc16_ex3

source_name: liver from mock-infected pregnant mice at dpc16

value: AAV-Null


title: Standard peach tree #1 branch #1 Internode 2 tissue from bottom (lower / abaxial) side of branch

value: Standard Peach Tree Branch Internode 2 tissue from bottom (lower / abaxial) side of branch


title: AAV8-Null_dpc16_ex2

value: WT


title: Controlsh_U2OS_ONT


title: WT B cells stimulated 4


title: glioma_Primary [GLSS-FG-0001-TP-01M-450-754721]

tag: gender

value: male

value: noncodel

value: G-CIMP-high

value: astrocytoma


title: WT B cells stimulated 3

value: B lymphocytes


title: si-DRAIC no2

type: RNA

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

description: DRAIC knockdown-VMRC-LCD

hyb_protocol: 2.3 ug fragmented and labeled cDNA was hybridized for 16 h at 45 °C on Human Clariom S Array. The GeneChip was washd using the GeneChip Fluidics Station 450.

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

data_processing: The data were processed with SST-RMA using the Transcriptome Analysis Console (TAC) software.

label: biotin

source_name: VMRC-LCD

label_protocol: Biotinylated cDNA was prepared according to the protocol starting from 250 ng of total RNA using the GeneChip WT PLUS Reagent Kit.

growth_protocol: VMRC-LCD cells were cultured in Dulbecco's modified Eagle's medium containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using NucleoSpin RNA reagent according to the manufacturer's instruction.

treatment_protocol: VMRC-LCD cells were transfected with si-NC (20 nmol/L) or si-DRAIC2 (20 nmol/L), and incubated for 72 h.

value: VMRC-LCD

value: lung cancer cell

value: siRNA no2 against DRAIC (si-DRAIC2)


title: AAV8-Null_dpc16_ex1

value: female


title: IgAN_24

city: Bengaluru

last: Shankar

address: Mysore Rd, near City Market, New Tharagupet

department: Nephrology

country: India

institute: Institute of Nephrourology, Victoria Hospital Campus, Bengaluru

hyb_protocol: Ligated product was diluted with 15 µl of nuclease free water and denatured at 85degC for 5 minutes. 5 µl of this was hybridized overnight at 65degC with Reporter and Capture probes. Protocol followed as per Manual (nCounter miRNA Expression Assay User Manual, MAN-C0009-07).

scan_protocol: Hybridized molecules are loaded to Nanostring sprint catridge and loaded onto nCounter SPRINT machine for scanning the barcodes. Raw counts data (.RCC) was retrieved from the machine after the scanning completes.

data_processing: Raw data were normalized using nSolver 4.0 software. Normalization were carried out using the geometrical mean of Positive control probes and the Top 100 highly expressing miRNA approach as guided by the NanoString data analysis manual.

label: NanoString

source_name: Urinary Exosome

label_protocol: With NanoString nCounter Human v3 miRNA Expression Assay (NS_H_miR_v3b)  kit (CSO-MIR3-12), miRNA (3ul) was ligated to mir-Tag  with ligation buffer and Ligase supplied with the kit.

extract_protocol: Exosomal RNA was isolated from human urine samples using Norgen’s Urine Exosome RNA isolation kit (Cat#47200). 2ml urine from 5 subjects was pooled to obtain 10ml pooled urine samples for Control. Similarly, 5ml urine from 2 subjects was pooled for IgA Nephrophathy (IgN). Urine samples were completely thawed and incubated for 5 minutes at 37 degC to dissolve sediments if any. After pooling protocol was followed as per manufacturer’s guidelines. RNA was eluted in 0.1ml of Elution Buffer. Eluted RNA was concentrated using Zymo’s RNA Clean & concentrator-5(Cat#R1015). Exosomal RNA was eluted from Zymo column in 15µl of Elution buffer provided in the kit.

tag: disease state

value: IgAN


title: IgAN_25


title: WT B cells stimulated 1

tag: genotype


title: pEF-2-H

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

data_processing:
Hi-C datasets were processed using a Juicer pipeline (version 1.8.9).
The high-quality Hi-C reads was aligned against the pig reference genome (Sscrofa11.1) using BWA software (version 0.7.8) with default parameters. The alignable reads were then followed duplicated read removal step provided in Juicer and remained were unique reads. Low-quality alignments (defined as MAPQ < 30) and intra-fragment reads were filtered from unique reads thus generated valid Hi-C contacts which were used for later analysis. Intra-chromosomal contract matrices were separately generated at two resolutions (100kb and 20 kb) after normalized intrinsic biases (KR algorithm) and sequencing depth (quantile algorithm) for each Hi-C library.Inter-chromosomal contact matrices were generated after normalized intrinsic biases (KR algorithm) by using Juicer tool.
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: The .hic file is a highly compressed binary file that stores contact matrices from multiple resolutions in a clever way, allowing random access.

organism: Sus scrofa

source_name: Porcine embryonic fibroblast

extract_protocol:
The 1×10^6 cells were cross-linked with a final concentration of 4% formaldehyde for 30min at room temperature and followed by quenching with glycine in a final concentration of 0.25 mol/L. Mixtures were next centrifuged at 1,500×g for 10min at room temperature, and separated supernatant were added lysis buffer and incubate 15 min on ice. The mixture was then centrifuged at 5,000×g for 10 min in room temperature. The sediment was washed with 100μL 1×NEBuffer 2. The mixture was added with SDS in a final concentration of 0.1% and incubate 10min at 65°C, then added with TritonX-100 in a final concentration of 1% and incubate 15min at 37°C, thus nuclei of cells were permeabilized.
DNA was digested with 200 units of DpnII (a 4-cutter restriction enzyme) for one hour at 37°C. The restriction fragment overhangs were filled and labeled by biotinylated nucleotides and then ligated in a small volume. After crosslink reversal,  DNA were purified and sonicated to fragments about 300-500 bp by applying Covaris S220 sonicator, at which point ligated fragments were pulled down with Dynabeads™ M-280 Streptavidin (Invitrogen, Cat.N: 11206D) and also were end repaired and A-tailed. Adaptors were next ligated and DNA fragments were PCR amplified using KAPA Hyper Prep Kit (Roche, Cat.N: KK8504) for 8-10 cycles. These fragments were then performed double-size selected using AMPure XP Beads (Beckman, Cat.N: A63882) in order to isolate fragments between 300 and 800bp, which were prepped for sequencing at BGISEQ-500 platform to provided 100 bp paired-end reads. Consequently, we generated a total of ~10.91-billion valid contacts of 16 Hi-C libraries (~681.95 M contacts per library) for pgEpiSCs, and a total of ~14.34-billion valid contacts of 16 Hi-C libraries (~895.96 M contacts per library) for pEFs.

tag: developmental stage

value: E30 fetal

tag: tissue

value: Embryonic fibroblast


title: si-NC

description: negative control-VMRC-LCD

value: si-negative control (si-NC)


title: AAV8-Null_dpc8_ex2

source_name: liver from mock-infected pregnant mice at dpc8

tag: Sex


title: IgAN_22


title: IgAN_23


title: pEF-2-G


title: AAV8-Null_dpc8_ex1


title: AAV8-Null_non-pregnant_ex3

source_name: liver from mock-infected non-pregnant mice


title: AAV8-Null_non-pregnant_ex2


title: pEF-2-E


title: pEF-2-F


title: K3_33

city: Bunkyo-ku,

first: Mamiko

last: Tosa

state: Tokyo-to

address: 1-1-5, Sendagi

department: Plastic and Reconstructive Surgery

institute: Nippon Medical School Hospital

description:
EA1488_24.a
keloid center fibroblast 3

hyb_protocol: Following fragmentation, 5.5 ug of Single Stranded cDNA was hybridized for 16 hr at 45˚C on Clariom S Human Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console Software 1.4.1 offered SST-RMA and SST-Alt. Splice Analysis for gene and exon level analysis using Affymetrix default analysis settings.

source_name: Human Skin

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit (Affymetrix) following the manufacturer's instructions.

extract_protocol: Total RNA was isolated using Nucleospin RNA (TAKARA Bio) according to the manufacturer's instructions.

value: keloid center fibroblasts


title: IgAN_20


title: IgAN_21


title: AAV8-Null_non-pregnant_ex1

value: AAV-Null


title: K3_22

description:
EA1488_23.a
keloid margin fibroblast 3

value: keloid margin fibroblasts


title: IgAN_18


title: pEF-2-D


title: K3_2

description:
EA1488_20.a
keloid margin stem cell 3

value: keloid margin stem cells


title: K3_1

description:
EA1488_19.a
keloid normal stem cell 3

value: keloid normal stem cells


title: K3_11

description:
EA1488_22.a
keloid normal fibroblast 3

value: keloid normal fibroblasts


title: WT B cells stimulated 2

value: WT


title: RNA_seq_WT_dpc16_Zone3_ex3

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2  (version 2.1.0) with the GENCODE  vM22 annotation gtf file after trimming the adaptor sequences and low-quality bases using cutadapt- 1.18. Uniquely mapped reads were used for further analyses.
The expression levels were caluculated as FPKM usign Cuffdiff within Cufflinks  v.2.2.1 package and GENCODE vM22 annotation file (protein-coding).
Genome_build: mm10
Supplementary_files_format_and_content: A tsv file includes FPKM values for each sample.

source_name: zone3 in liver from pregnant mice at dpc16

extract_protocol:
Liver samples were embedded in OCT compound and 5-µm-thick sections were prepared, mounted on polyethylene naphthalate membrane-coated slides (Leica, 11505158), dried for 5 sec at room temperature, fixed in acetone for 2 min, and then stored at -80℃. The fixed tissue sections were microdissected using a LMD7000 (Leica) and the tissue fragments were captured and collected in sampling tubes (BMBio, BMC-06) containing buffer RLT (Qiagen). Areas of 2 mm2 from each zone were subjected to RNA extract by using the RNeasy Micro Kit (Qiagen). Quality RNA samples were selected (RIN>7).
50 ng Total RNA was used to generate RNA-seq libraries using KAPA RNA HyperPrep Kit with RiboErase (Roche).


title: AAV8-Null_dpc8_ex3


title: pEF-2-C


title: RNA_seq_WT_dpc16_Zone3_ex2


title: RNA_seq_WT_dpc16_Zone3_ex1


title: RNA_seq_WT_dpc16_Zone2_ex3

source_name: zone2 in liver from pregnant mice at dpc16


title: pEF-1-H


title: IgAN_17


title: pEF-2-B


title: IgAN_19


title: K3_3

description:
EA1488_21.a
keloid center stem cell 3

value: keloid center stem cells


title: pEF-1-G


title: K2_33

description:
EA1488_18.a
keloid center fibroblast 2


title: K2_11

description:
EA1488_16.a
keloid normal fibroblast 2


title: IgAN_16


title: IgAN_15


title: IgAN_14


title: K2_22

description:
EA1488_17.a
keloid margin fibroblast 2


title: RNA_seq_WT_dpc16_Zone2_ex2


title: pEF-1-F


title: IgAN_13


title: pEF-2-A


title: RNA_seq_WT_dpc16_Zone1_ex3

source_name: zone1 in liver from pregnant mice at dpc16


title: K2_3

description:
EA1488_15.a
keloid center stem cell 2


title: K2_2

description:
EA1488_14.a
keloid margin stem cell 2


title: RNA_seq_WT_dpc16_Zone1_ex2


title: RNA_seq_WT_dpc16_Zone2_ex1


title: K1_22

description:
EA1488_11.a
keloid margin fibroblast 1


title: RNA_seq_WT_dpc16_Zone1_ex1


title: IgAN_12


title: RNA_seq_WT_dpc8_Zone3_ex3

source_name: zone3 in liver from pregnant mice at dpc8


title: IgAN_11


title: IgAN_10


title: K1_33

description:
EA1488_12.a
keloid center fibroblast 1


title: IgAN_9


title: pEF-1-C


title: K2_1

description:
EA1488_13.a
keloid normal stem cell 2


title: pEF-1-D


title: pEF-1-E


title: RNA_seq_WT_dpc8_Zone3_ex2


title: pEF-1-B


title: pgEpiSC-4-D

source_name: Pig pre-gastrulation epiblast stem cells (pig pgEpiSCs)

value: E10 embryonic epiblast

value: Embryonic epiblast


title: pEF-1-A


title: RNA_seq_WT_dpc8_Zone3_ex1


title: IgAN_8


title: RNA_seq_WT_dpc8_Zone2_ex3

source_name: zone2 in liver from pregnant mice at dpc8


title: K1_3

description:
EA1488_09.a
keloid center stem cell 1


title: IgAN_6


title: IgAN_5


title: K1_2

description:
EA1488_08.a
keloid margin stem cell 1


title: pgEpiSC-4-B


title: IgAN_7


title: RNA_seq_WT_dpc8_Zone2_ex2


title: RNA_seq_WT_dpc8_Zone1_ex3

source_name: zone1 in liver from pregnant mice at dpc8


title: K1_1

description:
EA1488_07.a
keloid normal stem cell 1


title: pgEpiSC-4-A


title: pgEpiSC-3-D


title: K1_11

description:
EA1488_10.a
keloid normal fibroblast 1


title: pgEpiSC-3-C


title: WS_S

description:
EA1488_05.a
normal scar dermal stem cell

value: normal scar dermal stem cells


title: RNA_seq_WT_dpc8_Zone1_ex1


title: pgEpiSC-3-B


title: RNA_seq_WT_dpc8_Zone1_ex2


title: N2_F

description:
EA1488_04.a
normal fibroblast 2

value: normal fibroblasts


title: IgAN_2


title: IgAN_1


title: IgAN_3


title: IgAN_4


title: WS_F

description:
EA1488_06.a
normal scar fibroblast

value: normal scar fibroblasts


title: pgEpiSC-4-C


title: N1_F

description:
EA1488_02.a
normal fibroblast 1


title: RNA_seq_WT_non-pregnant_Zone3_ex3

source_name: zone3 in liver from non-pregnant mice

value: female


title: Control_9

value: Control


title: Control_10


title: RNA_seq_WT_non-pregnant_Zone3_ex2


title: pgEpiSC-2-D


title: pgEpiSC-3-A


title: RNA_seq_WT_non-pregnant_Zone3_ex1


title: N1_S

description:
EA1488_01.a
normal dermal stem cell 1

value: normal dermal stem cells


title: Control_8


title: pgEpiSC-2-C


title: RNA_seq_WT_dpc8_Zone2_ex1


title: RNA_seq_WT_non-pregnant_Zone2_ex3

source_name: zone2 in liver from non-pregnant mice


title: Control_7


title: pgEpiSC-2-B


title: pgEpiSC-2-A


title: RNA_seq_WT_non-pregnant_Zone2_ex2


title: pgEpiSC-1-D


title: Control_6


title: RNA_seq_WT_non-pregnant_Zone2_ex1


title: Control_5


title: Control_4


title: AT

description: EA1874 08 a

treatment_protocol: KMF-transplanted mice were treated with vehicle or vismodegib by intraperitoneal injection once a day.

tag: treatment of kmf-transplanted mice

value: Vehicle

value: Transplant-derived cells


title: RNA_seq_WT_non-pregnant_Zone1_ex3

source_name: zone1 in liver from non-pregnant mice


title: pgEpiSC-1-C


title: RNA_seq_WT_non-pregnant_Zone1_ex2


title: BH

description: EA1874 03 a

value: Vismodegib


title: RNA_seq_WT_non-pregnant_Zone1_ex1


title: N2_S

description:
EA1488_03.a
normal dermal stem cell 2


title: BT

description: EA1874 09 a


title: AI

description: EA1874 05 a


title: pgEpiSC-1-B


title: AH

description: EA1874 02 a


title: BI

description: EA1874 06 a


title: Control_1


title: T-ALL_CCRF-CEM_3D_biological rep2

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

institute: CIB-CSIC

description: Gene expression data from T-ALL cells cultured in 3D conditions for 3 hours

hyb_protocol: RNA was hybridized to Clariom™ S Human Array following manufacturer’s instructions in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC)

label: Biotin

source_name: CCRF-CEM cells cultured in 3D conditions for 1 hour

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit

growth_protocol: CCRF-CEM cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol: RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.

treatment_protocol: CCRF-CEM cells were cultured in suspension or 3D conditions for 1 hour. For 3D matrix, type I collagen solution from bovine were reconstituted at 1.7 mg/mL in RPMI and neutralized with 7.5% NaHCO3 and 25 mM Hepes. Cells were added to the collagen solution before polymerization at 37 °C for 1 h.

value: CCRF-CEM

value: T-ALL

value: cultured in 3D conditions for 1 hour


title: DM2_5

status: Public on Dec 12 2023

city: Dresden

first: Sarah

last: Rösing

address: Fetscherstr. 74

country: Germany

institute: University hospital Carl Gustav Carus, TU Dresden

data_processing:
raw reads were inspected using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/),
trimmed using trimmomatic (https://academic.oup.com/bioinformatics/article/30/15/2114/2390096?login=true) and
aligned using STAR (https://academic.oup.com/bioinformatics/article/29/1/15/272537?login=true).
Read counts were extracted from the alignments using the featureCounts method of the subread package (https://academic.oup.com/bioinformatics/article/30/7/923/232889).
Afterwards DESeq2 was applied to identify differentially expressed genes (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8).
Assembly: GRCh37
Supplementary files format and content: unicode text files include FPKM values for each sample

source_name: skin

growth_protocol: human fibroblasts were cultured in DMEM (Gibco) supplemented with 10 % FCS, 1 % antibiotics and 1 mM sodium pyruvate

extract_protocol:
Total RNA from fibroblasts was extracted with the RNeasy Mini Kit (Qiagen)
non-stranded mRNA

value: skin

value: fibroblasts

value: myotonic dystrophy type 2


title: DM2_1


title: DM2_3


title: DM2_2


title: pgEpiSC-1-A

value: E10 embryonic epiblast


title: DM1_4

value: myotonic dystrophy type 1


title: DM2_4


title: T-ALL_CCRF-CEM_control_biological rep1

description: Gene expression data from T-ALL cells control

source_name: CCRF-CEM cells control

value: control


title: DM1_3


title: Control_3

source_name: Urinary Exosome


title: DM1_1


title: HC_4

value: healthy control


title: DM2_7


title: HC_1


title: HC_2


title: HC_3


title: OVCAR8_Ctrl_3

city: 武汉

first: Hu

last: Xingyuan

state: Hubei

address: 湖北武汉

institute: 同济医院

data_processing:
Sequence reads were trimmed for adaptor sequence  using Trim Galore 3.5
Trimmed sequence reads were mapped to hg38 using STAR (020201)
read counts definded unsing SUBREAD
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Ovary

growth_protocol: OVCAR8 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
>2 × 106 cells were collected and resolved in TRIzol (Takara, 9109) for RNA extraction
RNA was harvested using QIAGEN’s AllPrep RNA Mini Kit. 2ug of total RNA was used for the construction of sequencing libraries.
VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer's recommendations.

treatment_protocol: OVCAR8 was exposed cells to hyperthemia (42℃) for 90 mins

value: Ovary

value: ovarian cancer cell


title: OVCAR8_HT_3

value: hyperthermia stimulation


title: OVCAR8_Ctrl_2


title: T-ALL_CCRF-CEM_3D_biological rep1


title: OVCAR8_HT_2


title: T-ALL_CCRF-CEM_control_biological rep2


title: M01757EN_IDPN

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

institute: Universitat de Barcelona

data_processing:
Reads were mapped against the Mus musculus (GRCm38) reference genome with STAR 2.5.3a and ENCODE parameters
Genes were quantified with RSEM 2.3.0 with default parameters using the gencodeM15 annotation
Assembly: GRCm38
Supplementary files format and content: Raw counts matrix (text file)

source_name: Vestibular ganglion

extract_protocol:
Vestibular ganglia were quickly dissected in ice-cold PBS. Both ganglia from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.

treatment_protocol: Subchronic ototoxicity mice were given 30 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 8 weeks; control mice received plain drinking water.

value: Vestibular ganglion

value: male 129S1/SvImJ

value: Subchronic ototoxicity


title: M01757NN_IDPN


title: DM1_2


title: M01743EN_Control

value: Control


title: Control_2


title: M01743ND_Control


title: HC_5


title: M01743NN_Control


title: WT P+T biol rep 3

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

description: WT P+T (priming and heat stress treatment) biol rep 3

data_processing:
Paired-end reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using STAR version 2.7.10a.
Quantification at gene level was also done using STAR with the –quantMode GeneCounts option.
Assembly: TAIR10
Supplementary files format and content: Raw gene read counts for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
RNA was extracted using the RNeasy Plant Mini kit (Qiagen). Genomic DNA was degraded using TURBO™ DNAse, and RNA quality checked using RNA ScreenTape (TapeStation 4200, Agilent).
Library preparation using oligo-dT enrichment of mRNAs, and RNA sequencing were performed by BGI Genomics (http://www.bgi.com) with the DNBseq platform, generating 2 x 150 bp paired-end sequencing reads (~67 million reads per sample).

treatment_protocol: Heat stress (HS) treatments consisted of 1 h at 37°C in a waterbath. Seedlings were exposed to one of the following regimes: HS on day 5 only (P); HS on day 7  only (T); HS on both day 5 and day 7 (P+T); or no HS (NHS). Seedlings were harvested from all plates at the same time on day 7.

value: seedlings

value: WT

value: P+T


title: hsfa2 P+T biol rep 3

description: hsfa2 P+T (priming and heat stress treatment) biol rep 3


title: cdk8 P+T biol rep 3

description: cdk8 P+T (priming and heat stress treatment) biol rep 3


title: M01741EN_IDPN


title: OVCAR8_Ctrl_1

extract_protocol:
>2 × 10^6 cells were collected and resolved in TRIzol (Takara, 9109) for RNA extraction
RNA was harvested using QIAGEN’s AllPrep RNA Mini Kit. 2ug of total RNA was used for the construction of sequencing libraries.
VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer's recommendations.


title: WT T biol rep 3

description: WT T (heat stress treatment) biol rep 3

value: T


title: cdk8 T biol rep 3

description: cdk8 T (heat stress treatment) biol rep 3


title: WT P biol rep 3

description: WT P (priming) biol rep 3

value: P


title: hsfa2 T biol rep 3

description: hsfa2 T (heat stress treatment) biol rep 3


title: hsfa2 NHS biol rep 3

description: hsfa2 NHS (no heat stress) biol rep 3

value: NHS


title: cdk8 P biol rep 3

description: cdk8 P (priming) biol rep 3


title: hsfa2 P biol rep 3

description: hsfa2 P (priming) biol rep 3


title: cdk8 NHS biol rep 3

description: cdk8 NHS (no heat stress) biol rep 3


title: OVCAR8_HT_1


title: hsfa2 T biol rep 2

description: hsfa2 T (heat stress treatment) biol rep 2


title: cdk8 T biol rep 2

description: cdk8 T (heat stress treatment) biol rep 2


title: WT T biol rep 2

description: WT T (heat stress treatment) biol rep 2


title: cdk8 P+T biol rep 2

description: cdk8 P+T (priming and heat stress treatment) biol rep 2


title: WT NHS biol rep 3

description: WT NHS (no heat stress) biol rep 3


title: hsfa2 P+T biol rep 2

description: hsfa2 P+T (priming and heat stress treatment) biol rep 2


title: hsfa2 P biol rep 2

description: hsfa2 P (priming) biol rep 2


title: cdk8 P biol rep 2

description: cdk8 P (priming) biol rep 2


title: WT P+T biol rep 2

description: WT P+T (priming and heat stress treatment) biol rep 2


title: WT P biol rep 2

description: WT P (priming) biol rep 2


title: hsfa2 NHS biol rep 2

description: hsfa2 NHS (no heat stress) biol rep 2


title: cdk8 NHS biol rep 2

description: cdk8 NHS (no heat stress) biol rep 2


title: cdk8 T biol rep 1

description: cdk8 T (heat stress treatment) biol rep 1


title: WT P+T biol rep 1

description: WT P+T (priming and heat stress treatment) biol rep 1


title: hsfa2 T biol rep 1

description: hsfa2 T (heat stress treatment) biol rep 1


title: cdk8 NHS biol rep 1

description: cdk8 NHS (no heat stress) biol rep 1


title: WT T biol rep 1

description: WT T (heat stress treatment) biol rep 1


title: hsfa2 P+T biol rep 1

description: hsfa2 P+T (priming and heat stress treatment) biol rep 1


title: cdk8 P+T biol rep 1

description: cdk8 P+T (priming and heat stress treatment) biol rep 1


title: WT NHS biol rep 1

description: WT NHS (no heat stress) biol rep 1


title: hsfa2 P biol rep 1

description: hsfa2 P (priming) biol rep 1


title: cdk8 P biol rep 1

description: cdk8 P (priming) biol rep 1


title: WT P biol rep 1

description: WT P (priming) biol rep 1


title: pbrm-1(control), L1 larvae, rep 6 [RA685-6]

city: Richmond

first: Laura

last: Mathies

state: VA

address: 1220 East Broad St.

institute: Virginia Commonwealth University

data_processing:
Sequencing reads were trimmed to remove adapter sequences and low-quality bases.
Trimmed reads were mapped to the C. elegans genome using the STAR aligner version 2.5.2b
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: Ensembl genome assembly release WBcel325
Supplementary files format and content: Csv file contains raw read counts for each sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Populations were grown to adulthood at 20°C, harvested, and treated with hypochlorite to obtain embryos. Embryos were hatched overnight in sterile M9 medium on a rotating platform to obtain a synchronous population of early L1 larvae.

extract_protocol:
Total RNA was isolated using the miRNeasy kit with DNase I digestion performed on the column.
RNA was polyA selected and sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Worms were washed from the plate, purified by sucrose floatation, rinsed once with M9 medium, and stored in Trizol at -80°C until RNA preparation.

value: whole animal

value: hermaphrodite

tag: Stage

value: L1 larvae


title: pbrm-1(control), L1 larvae, rep 7 [RA685-7]


title: pbrm-1(control), L1 larvae, rep 4 [RA685-4]


title: pbrm-1(control), L1 larvae, rep 1 [RA685-1]


title: pbrm-1(TS-KO), L1 larvae, rep 7 [RA678-7]


title: pbrm-1(TS-KO), L1 larvae, rep 5 [RA678-5]


title: pbrm-1(TS-KO), L1 larvae, rep 1 [RA678-1]


title: pbrm-1(TS-KO), L1 larvae, rep 6 [RA678-6]


title: Lg7742a WGS HiSeq

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Offline base calling of ONT reads was performed with Guppy 5.0.7 and the R9.4.1 450bps SUP model on NVIDIA Tesla V100 GPUs.
Direct 5-methylcytosine modification calling in all contexts from the ONT WGS reads was performed with Megalodon v2.5.0 with the dna_r9.4.1_450bps_modbases_5mc_hac model and Guppy v5.0.7 on NVIDIA Tesla V100 GPUs. Calls for Cs with fewer than 5 supporting reads were discarded, and the resulting bedMethyl files were split by cytosine context (CpG, CHG, CHH) using bedtools v2.30.0 intersect. Fractional methylation calls at each cytosine were adjusted to a [0..1] scale, and the bedMethyl files were converted to bigWig format. Profiles over genomic regions were calculated as for the WGBS libraries.
ONT reads were aligned to their respective reference assemblies with minimap2 v2.24-r1122 “-x map-ont --MD”. Single nucleotide variants and indels shorter than 50 bp (SNVs) were called using Clair3 v0.1-r12 with options “--min_contig_size=1000000 --platform ont --model_path /opt/models/r941_prom_sup_g5014”. Structural variants (SVs) were called with Sniffles2 v2.0.7 with default options. SNVs and SVs were filtered using RTG Tools v3.12.1 (https://github.com/RealTimeGenomics/rtg-tools) with options “vcffilter --min-read-depth=10 --min-genotype-quality=20”, and homozygous calls were removed with “vcffilter --remove-hom”.
Illumina gDNA reads were aligned to the reference assemblies with bwa-mem2 v2.2.1 and coverage was calculated over 1bp bins with deeptools v3.5.2 “bamCoverage --samFlagExclude 2304 --ignoreDuplicates --binSize 1 --normalizeUsing CPM”.
Supplementary files format and content: ONT 5mC BigWigs: Consensus 5mC calls from Megalodon split by context. In the bigwig coverage tracks (1bp bins), positive values are used for cytosines on the top reference strand, negative for the bottom strand.
Supplementary files format and content: VCFs: heterozygous variant calls made with the same reads used for assembly aligned to their respective assembled references.

organism: Lemna gibba

source_name: whole frond

growth_protocol: Sterile cultures were obtained from the Rutgers Duckweed Stock Cooperative and cultivated in 50 mL Schenk and Hildebrandt (SH) medium with 1% sucrose at pH 5.6 at 23°C under a 16 hour photoperiod of approximately 30 μmol/m2/s per second of white fluorescent light. For HMW DNA extraction, culture flasks were covered in foil and grown in the dark for up to 2 weeks prior to harvest to deplete excess carbohydrates. Cultures were then flash frozen in liquid N2 and stored at -80ºC.

extract_protocol:
High molecular weight (HMW) DNA extractions were performed using either a modified CTAB prep followed by a high-salt low-ethanol starch cleanup (Pacific Biosciences), or nuclear extraction as follows:  CTAB prep (Lg7742a, Lj8627, Wa8730): 4 g frozen tissue was ground three times under liquid N2 with a mortar and pestle and transferred to 20 mL pre-warmed lysis buffer (100 mM Tris-HCl pH 9.0, 2% w/v CTAB, 1.4 M NaCl, 20 mM EDTA, 2% PVP-10, 1% 2-mercaptoethanol, 0.1% sarkosyl, 100ug/mL Proteinase K), briefly vortexed, and then incubated at 65ºC for 1 hour with periodic mixing by gentle inversion. The lysate was extracted with 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) and then 1 vol. of chloroform:isoamyl alcohol in phase-lock gel tubes. HMW DNA was precipitated from the aqueous phase in a 50 mL falcon tube by the addition of 0.1 vol. 3M NaOAc pH 5.2 followed by 0.7 vol. Isopropanol. After gentle swirling but no inversion mixing, precipitated salt in the upper phase was pipetted off and HMW DNA was hooked out with a bent pasteur pipette, washed by dipping in 70% EtOH, air-dried for 2 minutes, and resuspended in 200 uL Tris-Cl pH 8.5 (EB). The DNA solution was treated with 2 uL 20 mg/mL RNase A at 37ºC for 20 minutes followed by 2 uL 50 mg/mL Proteinase K at 50ºC for 30 minutes. 194 uL EB, 100 uL 5M NaCl, and 2 uL 0.5 M EDTA were added and organic solvent extractions were performed as before (1x P:C:IA and 1x C:IA). 0.3 vol. EtOH was added followed by centrifugation at 16,000 x g for 15 minutes to precipitate carbohydrates. The supernatant was poured into a new tube and 1.7 vol. of EtOH was added to precipitate HMW DNA, followed by hooking with a pasteur pipette, a 70% EtOH wash, drying, and resuspension in 50 uL EB.  Nuclear prep (Lm7210, Lm9252, Lj7182, Lj9421, Lt9434): as previously described with modifications.
Long-read data for Lg7742a, Lj8627, and Wa8730 were collected over multiple years as the MinION sequencing platform matured. Various protocols and both the SQK-LSK108 and SQK-LSK109 kits were used to prepare libraries for sequencing on multiple flow cell revisions. Here we describe the method used to produce the most recent runs in this study: 2 µg HMW DNA was sheared by 20 passes through a P1000 pipette tip and size-selected using 0.8 vol of custom SPRI beads. The SQK-LSK109 1D Genomic DNA Protocol was followed with the following modifications: Incubation times for all enzymatic reactions were extended to 20 minutes; cleanups following the repair reaction and adapter ligation were performed with 1 vol and 0.8 vol, respectively, of custom SPRI beads rather than Ampure XP; bead elutions were carried out at 37ºC until evenly resuspended; completed libraries were eluted in 24 uL Oxford EB, and half of this volume was mixed with LB and SQB and loaded onto an R9.4.1 rev. D flow cell. After about 20 hours the run was stopped, the Nuclease Flush protocol was performed, and the flow cell re-primed. 6 uL of the remaining library was mixed with 6 uL EB and the loading reagents, loaded onto the flow cell, and the run restarted.  Libraries for Lj7182, Lj9421, Lm7210, Lm9252, and Lt9434 were prepared as previously described and sequenced on R9.4.1 flow cells on the PromethION platform. Short read WGS libraries for Lg7742a and Lj8627 were prepared from 2µg of HMW gDNA using the Illumina TruSeq DNA PCR-Free kit (Illumina, cat#20015962) and sequenced on an Illumina MiSeq (PE 250bp, PE 300bp) or HiSeq 2500 instrument (PE 150bp). Libraries for other Lemna accessions were prepared as described for the NCBI SRA experiment SRX7624904, and previously published libraries were used for Wa8730 (SRX8008794, SRX8008795).

value: whole frond


title: WT NHS biol rep 2

description: WT NHS (no heat stress) biol rep 2


title: hsfa2 NHS biol rep 1

description: hsfa2 NHS (no heat stress) biol rep 1


title: pbrm-1(TS-KO), L1 larvae, rep 4 [RA678-4]


title: pbrm-1(control), L1 larvae, rep 5 [RA685-5]


title: SC02299A

city: Oxford

first: Andrew

last: Blake

state: Oxfordshire, UK

address: Old Road Campus

country: United Kingdom

institute: Department of Oncology

hyb_protocol: The amplified product was hybridised to the Almac Diagnostics XCEL array (Almac, Craigavon, UK), a cDNA microarray-based technology optimised for archival FFPE tissue, and analysed using the Affymetrix Genechip 3000 7G scanner (Affymetrix, Santa Clara, California, USA) as previously described (12).

scan_protocol: Affymetrix protocol

data_processing: Microarray data were quality checked (see Supplementary methods) then pre-processed where raw CEL files underwent the Robust Multiarray Average (RMA) normalisation for the Almac Diagnostic XCEL array with the affy package (v1.56.0) (17).

source_name: Primary Colorectal Cancer

label_protocol: Affymetrix protocol

extract_protocol: All the archival formalin-fixed paraffin-embedded (FFPE) tumour tissue samples were tested at Almac’s Diagnostic CLIA Laboratories. Samples were reviewed and tumour material identified on an adjacent H&E stained slide for microdissection. Total RNA was extracted from two sequential 5µm sections using the Roche High Pure FFPE Extraction Kit (Roche Life Sciences, Penzberg, Germany) and amplified using the NuGen Ovation FFPE Amplification System v3 (NuGen San Carlos, California, USA). All the archival formalin-fixed paraffin-embedded (FFPE) tumour tissue samples were tested at Almac’s Diagnostic CLIA Laboratories. Samples were reviewed and tumour material identified on an adjacent H&E stained slide for microdissection. Total RNA was extracted from two sequential 5µm sections using the Roche High Pure FFPE Extraction Kit (Roche Life Sciences, Penzberg, Germany) and amplified using the NuGen Ovation FFPE Amplification System v3 (NuGen San Carlos, California, USA).

tag: condition

value: colorectal cancer


title: SC02303A

description: Almac Diagnostics XCEL array (Almac, Craigavon, UK)


title: SC02301A


title: SC02281A


title: SC02287A


title: SC02297A


title: SC01773A


title: SC02295A


title: SC01759A


title: SC02279A


title: SC02293A


title: SC01771A


title: SC01735A


title: SC01763A


title: SC01783A


title: SC01769A


title: SC01781A


title: SC02283A


title: SC01765A


title: DM2_6

value: skin

value: fibroblasts

value: myotonic dystrophy type 2


title: SC02285A


title: SC01743A


title: SC01761A


title: SC01757A


title: SC01747A


title: SC01753A


title: SC01755A


title: SC01745A


title: SC01727A


title: SC01737A


title: SC01707A


title: SC01777A


title: SC01715A


title: SC01714A


title: SC01719A


title: SC01701A


title: SC01733A


title: SC01708A


title: SC01709A


title: SC01720A


title: SC01700A


title: SC01680A


title: SC01706A


title: SC01679A


title: SC01675A


title: SC01731A


title: SC01667A


title: SC01658A


title: SC01690A


title: SC01695A


title: SC01688A


title: SC01689A


title: SC01699A


title: SC01654A


title: SC01710A


title: SC01668A


title: SC01656A


title: SC01664A


title: SC01641A


title: SC01642A


title: SC01653A


title: SC01625A


title: SC01623A


title: SC01712A


title: SC01631A


title: SC01637A


title: SC01629A


title: SC01609A


title: SC01601A


title: SC01635A


title: SC01611A


title: SC01603A


title: SC01655A


title: SC01613A


title: SC01621A


title: SC01627A


title: SC01597A


title: SC01589A


title: SC01605A


title: SC01640A


title: SC01585A


title: SC01577A


title: SC01617A


title: SC01587A


title: SC01591A


title: SC01593A


title: SC01579A


title: SC01575A


title: SC01573A


title: SC01563A


title: SC01561A


title: SC01537A


title: SC01567A


title: SC01547A


title: SC01543A


title: SC01545A


title: SC01517A


title: SC01541A


title: SC01559A


title: SC01571A


title: SC01553A


title: SC01512A


title: SC01529A


title: SC01551A


title: SC01555A


title: SC01525A


title: SC01527A


title: SC01511A


title: SC01515A


title: SC01565A


title: SC01535A


title: SC01569A


title: SC01607A


title: SC01519A


title: SC01514A


title: SC01549A


title: SC01505A


title: SC01509A


title: SC01531A


title: SC01533A


title: SC01502A


title: SC01521A


title: SC01499A


title: SC01498A


title: SC01494A


title: SC01495A


title: SC01493A


title: SC01491A


title: SC01484A


title: SC01483A


title: SC01486A


title: SC01476A


title: SC01426A


title: SC01477A


title: SC01482A


title: SC01479A


title: SC01481A


title: SC01427A


title: SC01488A


title: SC01467A


title: SC01485A


title: SC01472A


title: SC01497A


title: SC01471A


title: SC01489A


title: SC01419A


title: SC01429A


title: SC01428A


title: SC01424A


title: SC01422A


title: SC01425A


title: SC01474A


title: SC01415A


title: SC01414A


title: SC01421A


title: SC01412A


title: SC01411A


title: SC01409A


title: SC01408A


title: SC01405A


title: SC01403A


title: SC01404A


title: SC01125A


title: SC01116A


title: SC01124A


title: SC01117A


title: SC01119A


title: SC01115A


title: SC01107A


title: SC01130A


title: SC01131A


title: SC01121A


title: SC01112A


title: SC01108A


title: SC01111A


title: SC01401A


title: SC01110A


title: SC01104A


title: SC01096A


title: SC01105A


title: SC01095A


title: SC01102A


title: SC01097A


title: SC01094A


title: SC01114A


title: SC01099A


title: SC01088A


title: SC01087A


title: SC01101A


title: SC01091A


title: SC01085A


title: SC01084A


title: SC01078A


title: SC01077A


title: SC01075A


title: SC01074A


title: SC01076A


title: SC01082A


title: SC01067A


title: SC01072A


title: SC01049A


title: SC01061A


title: SC01060A


title: SC01073A


title: SC01064A


title: SC01056A


title: SC01057A


title: SC01059A


title: SC00750A


title: SC01070A


title: SC01051A


title: SC01063A


title: SC00752A


title: SC01086A


title: SC01055A


title: SC00753A


title: SC01052A


title: SC01083A


title: SC00748A


title: SC01048A


title: SC00747A


title: SC00745A


title: SC00743A


title: SC00739A


title: SC00737A


title: SC00734A


title: SC00731A


title: SC00729A


title: SC00730A


title: SC00744A


title: SC00718A


title: SC00712A


title: SC00716A


title: SC00643A


title: SC00721A


title: SC00642A


title: SC00733A


title: SC00639A


title: SC00640A


title: SC01093A


title: SC00610A


title: SC00720A


title: SC00628A


title: SC00728A


title: 5730_YM2B_7-3-H6-P5

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

source_name: YM2B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

value: Male

tag: molecule subtype

value: nuclear RNA + genomic DNA


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