title: sample14 URE+/+;Tet2-/-

city: Bronx

first: Britta

last: Will

address: 1300 Morris Park Avenue, Chanin Bldg., Rm. #401

institute: Albert Einstein College of Medicine

data_processing:
Low quality reads (more than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get clean reads.
Those reads were mapped with RNA-STAR with default settings and --twopassMode Basic to the GRCm38 (primary assembly) genome using the gencode (vM9) transcript model.
Reads mapped to cis-regulatory elements predicted for genes in hematopoietic cell types (http://usevision.org/) were included in the count data
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
Total bone marrow cells were isolated from the femurs, tibiae, pelvic bones and spines of mice and were treated with 1x ACK lysing buffer pH 7.4 to lyse the red blood cells. cKit+ Lymph- Ery- cells were  FACS-purified and RNA was extracted  using the RNeasy Micro kit (Qiagen)
according to BGI group's procedures (low input, standard illumina protocols)

value: cKit+ Lymph- Ery- HSPC

tag: disease state

value: Normal

tag: ure

value: WT

value: KO


title: KH2 Embryonic Stem Cells in 2iLIF, replicate 3

status: Public on Jul 31 2022

type: SRA

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: KH2 Embryonic Stem Cells, replicate 3

library_source: transcriptomic

data_processing:
Samples were analyzed using UTAP software (Kohen et al. 2019). Reads were trimmed using CutAdapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic - alignSoftClipAtReferenceEnds No).
Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes. Further analysis was done for genes having a minimum of five reads in at least one sample. Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al. 2014) with the parameters betaPrior = true, cooksCutoff = false, and independentFiltering = false.
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: KH2 ESCs

growth_protocol: Cell were cultured on MEFs in humdified 5%Co2 , 21% O2 incubator

extract_protocol:
RNeasy mini RNA kit
Bulk MARS-seq
3 primed library

treatment_protocol: Doxycycline treatment for different time points decribed in each sample. Some samples were treated with LPA as indicated.

tag: cell line

value: Mixed


title: BVDV_negative_rep3

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

description:
CapZyme-seq protocol
FeatureCount_BVDV_output.txt

data_processing:
Library strategy: CapZyme-seq
Illumina bcl2fastq was used to create fastq files
Sequenced reads were trimmed for adaptor sequence (cutadapt -a AGATCGGAAGAGCACACGTCT -q 20 -m 15) and mapped to RNA sequences (viral RNA, rRNA, snoRNA, tRNA and mRNA (TPM>2) using  (bowtie2 --norc --very-sensitive)
Counts for the 5' end of different RNA were obtained using the featureCounts function from the Subread package using a SAF file specifing the first 100 nts of each RNA.
Example code for the processing of the sequencing data is available at https://github.com/jeppevinther/CapZyme
Supplementary files format and content: Tab-delimited text files include FeatureCounts output, raw counts
Supplementary files format and content: Matrix table with raw 5'  counts for every RNA (first 100nt) and every sample in experiment

organism:
Bos taurus
Bovine viral diarrhea virus 1-NADL

source_name: MDBK cell line bovine

extract_protocol:
RNA extraction was performed by Trizol treatment followed on-column DNase I digestion and RNA purification using RNA Clean & Concentrator kit-5
RNA was enzymatically treated with de-capping enzymes that specifically convert different 5’ cap structures to 5’ monophosphates. 5’-phosphate dependent adapter ligation was performed followed by reverse transcription. Libraries were generated using PCR with custom Illumina compatible primers.

tag: cell type

value: MDBK cell line bovine

tag: enzymatic treatment

value: negative

tag: virus

value: Bovine viral diarrhea virus

tag: molecule subtype

value: Total RNA


title: BVDV_Rpp_rep3

value: Rpp


title: 3-1Mo-m1-S3-all-R1-001

city: Nouzilly

first: joelle

last: dupont

address: Centre Val de Loire

country: France

institute: INRA

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.4.6 and bcl2fastq 2.15.0
Adapter sequences were trimmed with Cutadapt-1.3, only reads longer than 10 bp were kept for analysis
Sequences were aligned to the cow genome (bosTau8.fa) with TopHat2 using default parameters
Mapped reads were assigned to features with htseq-count (intersection-nonempty mode)
Differential expression analysis was performed with DESeq2,
Genome_build: bosTau8.fa
Supplementary_files_format_and_content: tabulated .txt file containing DESeq2 results

organism: Bos taurus

source_name: dairy cows one month before calving before diet experiment

extract_protocol:
Total RNA from the fat tissue of three cows per group was extracted using a RNeasy Midi kit (Qiagen®, Courtaboeuf, France) and purified using a DNAfree kit (Invitrogen by Life Technologies), according to the manufacturer’s recommendations.
Directional RNA-Seq libraries were constructed using the TruSeq Stranded Total RNA library prep kit (Illumina), following the manufacturer’s instructions, using 750 ng of total RNA.

tag: breed

value: Prim Holstein

tag: cow status

value: primiparous

tag: time point

tag: tissue

value: subcutaneous adipose tissue


title: sample16 UREΔ/+;Tet2-/-

state: NY

department: Cell Biology

country: USA

molecule: polyA RNA

value: AML

tag: genotype

value: HET


title: 1-1Mo-m1-S1-all-R1-001

value: one month before calving before diet experiment


title: sample12 URE+/+;Tet2+/-


title: BVDV_negative_rep2


title: sample15 UREΔ/+;Tet2+/-


title: BVDV_AtNUDX23_rep3


title: Extra-embryonic Endoderm Stem Cells, replicate 2

source_name: Extra-embryonic Endoderm Stem Cells (XEN)

value: ICR


title: KH2 Embryonic Stem Cells in 2iLIF, replicate 2

description: KH2 Embryonic Stem Cells, replicate 2


title: sample11 URE+/+;Tet2+/-

value: cKit+ Lymph- Ery- HSPC


title: sample13 URE+/+;Tet2-/-

value: Normal


title: BVDV_AtNUDX23_rep2


title: KH2 Embryonic Stem Cells in 2iLIF, replicate 1

description: KH2 Embryonic Stem Cells, replicate 1


title: Established Trophoblast Stem Cells from blastocyst, replicate 3

source_name: Trophoblast Stem Cells


title: BVDV_Rpp_rep2


title: sample10 UREΔ/+;Tet2+/+

value: WT


title: sample17 UREΔ/+;Tet2-/-

value: KO


title: Established Trophoblast Stem Cells from blastocyst, replicate 1


title: sample9 UREΔ/+;Tet2+/+


title: sample8 URE+/+;Tet2+/+


title: Established Trophoblast Stem Cells from blastocyst, replicate 2


title: Established Trophoblast Stem Cells, clone 5, replicate 3


title: sample6 UREΔ/+;Tet2-/-


title: BVDV_Rpp_rep1


title: sample7 UREΔ/+;Tet2+/-


title: BVDV_AtNUDX23_rep1


title: Established Trophoblast Stem Cells, clone 2, replicate 3


title: sample5 URE+/+;Tet2+/-


title: lung cancer cell line VL310

type: genomic

city: Taipei

first: yi-chiung

last: hsu

address: 128 Academia Road, Section 2

country: Taiwan

institute: academia sinica

hyb_protocol: in situ oligonucleotide

scan_protocol: The array scanning and image generation were performed by the GenePixTM Reader (Personal 4000B, Axon Instruments, Molecular Devices, Sunnyvale, CA) and GenePix® Pro 6.0 software.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Generation of log intensity ratio data with normalization was performed by NimbleScanTM version 2.4, SignalMapTM version 1.9 software
normalized log2 ratio (Cy5/Cy3)

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA from lung cancer cells

label_protocol: Labeling, hybridization and washing were processed according to the manufacturer's protocol.

extract_protocol: DNA from frozen cancer tissue of each sample, with quality checked by agarose electrophoresis, against the normal DNA extracted from the PBMC of one male and one female in a community cohort.

value: lung

tag: ethnicity

value: Asian

tag: gender

value: male

tag: source

tag: clinical response

tag: egfr

tag: kras

value: wild type

source_name: Input DNA extracted from the PBMC of one male and one female in a community cohort.

value: PBMC


title: lung cancer cell line HCC827

value: Caucasian

value: female

value: Exon19deletion (type2)


title: lung cancer cell line VL307


title: lung cancer cell line HCC827-IR


title: sample4 URE+/+;Tet2-/-

tag: disease state

tag: ure


title: lung cancer cell line VL301

tag: cell line

tag: cell type


title: sample3 UREΔ/+;Tet2+/+


title: Established Trophoblast Stem Cells, clone 2, replicate 2


title: Established Trophoblast Stem Cells, clone 2, replicate 1


title: sample2 URE+/+;Tet2+/+


title: BVDV_negative_rep1

value: MDBK cell line bovine

tag: enzymatic treatment

value: negative

tag: virus

value: Bovine viral diarrhea virus

value: Total RNA


title: iCdx2 Cells, clone 3,8 days with LPA, replicate 3

source_name: iCdx2 ESCs

value: Mixed + induced Cdx2

tag: treatment

value: DOX+LPA, 8 days


title: lung cancer cell line VL107


title: lung cancer cell line VL080


title: 7250-1_KitSP_AML

city: Philadelphia

first: Sara

middle: E

last: Meyer

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

description: cKit+ AML

data_processing:
Fastq files were processed by Oasis2.0 (1/27/16 release https://oasis.dzne.de/) using the sRNA DETECTION platform with the following options selected: “unknown adapter” sequence, mismatches 5% of the read length, length of reads 15MIN, 50MAX. All species counts were combined into a single text file for expression analysis in AltAnalyze using EnsMart72 Mm38 index.
Differential expression analysis was performed in Oasis2.0. Independently, AltAnalyze 2.1.1 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). was used to generate a different expression analysis using merged count files from Oasis2.0 fastq analysis. A Venn analysis of those differentially expressed ncRNA called by AltAnalyze vs. those with adjp<0.05 by Oasis2.0. The overlap of these was used to compile the final differential expression list of 112 non-coding RNA genes, which were filtered for mouse miRNA.
Heatmap from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005).
Genome_build: mouse GRCm38 ncRNA
Supplementary_files_format_and_content: tab-delimited text files

extract_protocol:
c-Kit+ splenocytes were harvested from three independent mice per each genotype Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (AML) and Flt3ITD/ITD (control). Red blood cells were lysed, and RNA was extracted by TriZol according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant Bioanalyzer. Then samples with a RIN>8.0 were processed. A size range of 120 bp to 165 bp was isolated to select small RNA libraries on the Pippin Prep (Sage). Size selected libraries were each sequenced at 20 million reads.
small RNAs were detected by RNAseq analysis using single-read 75 nucleotide (nt) sequencing and 20 million reads for all samples. RNA Seq libraries were generated with Pippin Prep kits and size selected for small RNA fragements.

value: leukemic splenocytes

value: acute myeloid leukemia


title: sample1 URE+/+;Tet2+/+

value: cKit+ Lymph- Ery- HSPC

value: Normal

value: WT


title: Established Trophoblast Stem Cells, clone 5, replicate 2


title: Established Trophoblast Stem Cells, clone 5, replicate 1


title: iCdx2 Cells, clone 3,8 days with LPA, replicate 2


title: 7209-2_KitSP_AML

description: cKit+ AML


title: iCdx2 Cells, clone 3,8 days with LPA, replicate 1


title: 7207-1_KitSP_AML

description: cKit+ AML


title: iCdx2 Cells, clone 3, 96hr with LPA, replicate 3

value: DOX+LPA, 96hr


title: lung cancer cell line VL036

value: lung

value: Asian

value: wild type


title: lung cancer cell line PE089-IR

value: female

value: Exon19deletion (DEL5)

value: PBMC


title: 6649_KitSP_MPN

description: cKit+ MPN

source_name: Flt3ITD/ITD primary age-matched control


title: lung cancer cell line PE089


title: iCdx2 Cells, clone 3, 96hr with LPA, replicate 1


title: iCdx2 Cells, clone 3, 48hr with LPA, replicate 3

value: DOX+LPA, 48hr


title: lung cancer cell line CL309

value: male

value: Sinica


title: JFH1-SGR-Feo_48hrs_neg_rep2

description:
CapZyme-seq protocol
FeatureCount_JFH1_SGR-Feo_output.txt

organism:
Homo sapiens
Hepacivirus hominis

source_name: Huh7.5 hepatoma cells

value: Huh7.5 hepatoma cells

value: negative

value: JFH1-SGR-Feo replicon

tag: molecule subtype

value: TEX treated total RNA


title: iCdx2 Cells, clone 3, 48hr with LPA, replicate 2

value: Mixed + induced Cdx2


title: JFH1-SGR-Feo_48hrs_AtNUDX23_rep2


title: lung cancer cell line CL68

value: Exon19deletion (type1)/T790M


title: 6650_KitSP_MPN

description: cKit+ MPN

value: leukemic splenocytes

value: acute myeloid leukemia


title: lung cancer cell line CL298

value: lung


title: iCdx2 Cells, clone 3, 48hr with LPA, replicate 1


title: iCdx2 Trophoblast Stem Cells, clone 3, passage 3, replicate 3

source_name: iCdx2 Trophoblast Stem Cells

value: DOX, passage 3 (12 days)


title: JFH1-SGR-Feo_48hrs_Rpp_rep2

value: Rpp


title: iCdx2 Trophoblast Stem Cells, clone 3, passage 3, replicate 2


title: iCdx2 Cells, clone 3, 96hr with LPA, replicate 2

value: DOX+LPA, 96hr


title: lung cancer cell line CL267

value: Asian

value: female

value: PE/NTU

value: No chemotherapy

value: wild type


title: JFH1-SGR-Feo_48hrs_AtNUDX23_rep1

value: Huh7.5 hepatoma cells


title: 7208-2_KitSP_MPN

description: cKit+ MPN


title: JFH1-SGR-Feo_48hrs_Rpp_rep1


title: JFH1-SGR-Feo_24hrs_neg_rep2

value: negative


title: iCdx2 Trophoblast Stem Cells, clone 3, passage 3, replicate 1


title: lung cancer cell line CL241

value: Tarceva over 1 year, reisitant; Navelbine treatment and collect

value: PBMC


title: lung cancer cell line CL237

value: male


title: lung cancer cell line CL239

value: Alimta+Cisplatin for 3 months, PD.


title: JFH1-SGR-Feo_48hrs_neg_rep1

value: JFH1-SGR-Feo replicon

value: TEX treated total RNA


title: iCdx2 Trophoblast Stem Cells, clone 2, passage 3, replicate 2

value: Mixed + induced Cdx2


title: iCdx2 Trophoblast Stem Cells, clone 2, passage 3, replicate 1

value: DOX, passage 3 (12 days)


title: iCdx2 Cells, clone 3, 4 days DOX + 4days wo DOX , replicate 3

description: iCdx2 Cells, clone 3, 8 days, replicate 3

value: DOX, 4 days- 4Days TSC


title: lung cancer cell line CL272

value: lung


title: lung cancer cell line CL83

value: Asian

value: Clinically no response

value: undetectable


title: iCdx2 Cells, clone 3, 4 days DOX + 4days wo DOX , replicate 2

description: iCdx2 Cells, clone 3, 8 days, replicate 2


title: lung cancer cell line CL100

value: female

value: PE/NTU

value: No chemotreappy

value: Exon19deletion (DEL5)


title: JFH1-SGR-Feo_24hrs_Rpp_rep2

value: Huh7.5 hepatoma cells

value: Rpp


title: JFH1-SGR-Feo_24hrs_neg_rep1

value: negative


title: iCdx2 Cells, clone 3, 4 days DOX + 4days wo DOX , replicate 1

description: iCdx2 Cells, clone 3, 8 days, replicate 1


title: JFH1-SGR-Feo_24hrs_Rpp_rep1


title: lung cancer cell line CL182

value: male

value: No chemotherapy

value: wild type

value: PBMC


title: iCdx2 Trophoblast Stem Cells, clone 2, passage 3, replicate 3

value: Mixed + induced Cdx2

value: DOX, passage 3 (12 days)


title: lung cancer cell line CL152

value: lung


title: JFH1-SGR-Feo_24hrs_AtNUDX23_rep2

value: JFH1-SGR-Feo replicon

value: TEX treated total RNA


title: lung cancer cell line PC9-IR

value: Asian

value: Exon19deletion (DEL1)


title: lung cancer cell line CL141

value: PE/NTU


title: iCdx2 Cells, clone 3, 7 days, replicate 3

value: DOX, 7 days


title: JFH1-SGR-Feo_12hrs_AtNUDX23_rep2


title: JFH1-SGR-Feo_12hrs_neg_rep2


title: JFH1-SGR-Feo_24hrs_AtNUDX23_rep1


title: iCdx2 Cells, clone 3, 6 days, replicate 3

value: DOX, 6 days


title: iCdx2 Cells, clone 3, 7 days, replicate 1


title: lung cancer cell line CL97

value: Resistant to Tarceva


title: iCdx2 Cells, clone 3, 6 days, replicate 2


title: iCdx2 Cells, clone 3, 7 days, replicate 2


title: lung cancer cell line CL25

value: Before Tarceva treatment

value: Exon19deletion (DEL5)


title: JFH1-SGR-Feo_12hrs_neg_rep1

value: Huh7.5 hepatoma cells

value: negative


title: lung cancer cell line PC9

value: male

value: wild type


title: JFH1-SGR-Feo_12hrs_AtNUDX23_rep1


title: lung cancer cell line H1975

value: Caucasian

value: female

value: PBMC


title: iCdx2 Cells, clone 3, 6 days, replicate 1

value: Mixed + induced Cdx2


title: JFH1-SGR-Feo_12hrs_Rpp_rep2

value: Rpp

value: JFH1-SGR-Feo replicon

value: TEX treated total RNA


title: lung cancer cell line H1755

value: lung

value: wild type (BRAF-G469A)


title: iCdx2 Cells, clone 3, 5 days, replicate 3

value: DOX, 5 days


title: JFH1-SGR-Feo_12hrs_Rpp_rep1


title: iCdx2 Cells, clone 3, 5 days, replicate 2


title: lung cancer cell line H1437


title: lung cancer cell line H1650

value: Exon19deletion type1 (wild type)


title: JFH1-SGR-Feo_4hrs_AtNUDX23_rep2


title: iCdx2 Cells, clone 3, 5 days, replicate 1


title: lung cancer cell line H1568


title: JFH1-SGR-Feo_4hrs_Rpp_rep2


title: lung cancer cell line H358

value: NCI

value: mutation


title: iCdx2 Cells, clone 3, 96hr, replicate 3

description: iCdx2 Cells, clone 3, 96hr, replicate 3

value: DOX, 96hr


title: lung cancer cell line CL1-5

value: Asian


title: JFH1-SGR-Feo_4hrs_neg_rep1

value: Huh7.5 hepatoma cells

value: negative


title: iCdx2 Cells, clone 3, 96hr, replicate 2

description: iCdx2 Cells, clone 3, 96hr, replicate 2


title: JFH1-SGR-Feo_4hrs_AtNUDX23_rep1


title: iCdx2 Cells, clone 3, 72hr, replicate 3

description: iCdx2 Cells, clone 3, 72hr, replicate 3

value: DOX, 72hr


title: iCdx2 Cells, clone 3, 72hr, replicate 1

description: iCdx2 Cells, clone 3, 72hr, replicate 1


title: lung cancer cell line CL1-0

value: male

value: wild type


title: iCdx2 Cells, clone 3, 72hr, replicate 2

description: iCdx2 Cells, clone 3, 72hr, replicate 2

value: Mixed + induced Cdx2


title: HK6acc_AtNUDX23

description:
CapZyme-seq protocol
FeatureCount_HK6acc_output.txt

value: HCV genotype 6a:HK6acc


title: lung cancer cell line H522

value: Caucasian

value: PBMC


title: JFH1-SGR-Feo_4hrs_neg_rep2

value: JFH1-SGR-Feo replicon

value: TEX treated total RNA


title: lung cancer cell line H23

value: lung

value: Black


title: HK6acc_neg


title: HK6acc_Rpp

value: Rpp


title: lung cancer cell line H460

value: NCI

value: mutation


title: iCdx2 Cells, clone 3, 48hr, replicate 3

description: iCdx2 Cells, clone 3, 48hr, replicate 3

value: DOX, 48hr


title: lung cancer cell line A549


title: iCdx2 Cells, clone 3, 48hr, replicate 1

description: iCdx2 Cells, clone 3, 48hr, replicate 1


title: iCdx2 Cells, clone 3, 48hr, replicate 2

description: iCdx2 Cells, clone 3, 48hr, replicate 2


title: lung cancer cell line HOP62

value: female


title: T_cell_LCMV_KO-4

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

data_processing:
Qubit fluorometer and Agilent TapeStation 4200
Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance.
The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 150bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)
Differential gene expression testing was performed by DESeq2 (v1.22.1) and RNAseq analysis was performed using the VIPER snakemake pipeline
Assembly: mm10
Supplementary files format and content: STAR_Gene_Counts.csv : raw read counts

source_name: T cells

growth_protocol: Total T cells were isolated from spleens by magnetic assisted cell sorting (MACS), using the Pan T cell isolation kit (Miltenyi Biotech).

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen) and submitted for RNA sequencing to the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute (DFCI)
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7

treatment_protocol: Mice were infected via intraperitoneal injection (i.p.) with 105 PFU and maintained for 8 days in the Animal Research facility at BIDMC. On day 8 post infection, mice were euthanized, and tissues were collected for downstream procedures

value: T cells

value: SRSF-1 KO

value: LCMV acute infection 8 days


title: iCdx2 Cells, clone 3, 96hr, replicate 1

description: iCdx2 Cells, clone 3, 96hr, replicate 1

value: DOX, 96hr


title: JFH1-SGR-Feo_4hrs_Rpp_rep1

value: Huh7.5 hepatoma cells


title: SA13cc_Rpp

description:
CapZyme-seq protocol
FeatureCount_SA13_JF470-510cc_output.txt

value: HCV genotype 5a:SA13cc_JF470-510cc


title: T_cell_LCMV_KO-3


title: lung cancer cell line HOP92

value: Caucasian

value: male

value: wild type


title: T_cell_LCMV_KO-2


title: ED43cc_AtNUDX23

description:
CapZyme-seq protocol
FeatureCount_ED43cc_output.txt

value: HCV genotype 4a:ED43cc

value: TEX treated total RNA


title: T_cell_LCMV_KO-1


title: T_cell_LCMV_WT-4

value: WT


title: ED43cc_Rpp

value: Rpp


title: SA13cc_neg

value: negative


title: DBN3acc_neg

description:
CapZyme-seq protocol
FeatureCount_DBN3acc_output.txt

value: HCV genotype 3a:DBN3acc


title: SA13cc_AtNUDX23


title: lung cancer cell line EKVX

value: lung

value: EKVX

value: NCI

value: mutation

value: PBMC


title: DBN3acc_AtNUDX23


title: T_cell_LCMV_WT-3

value: T cells

value: LCMV acute infection 8 days


title: 4n_Na_shoot_2

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Raw data were filtered, removing adapters, reads in which unknown bases are more than 10% and low quality reads. Resulting data are called "clean reads" and constitute the raw files.
Reads were mapped to the A. thaliana genome using Bowtie and HISAT.
Gene expression was quantified using RSEM a tool which computes the Maximum likelihood abundance and calculates FPKM values. The FPKM values accounts for the gene length and sequencing discrepancies.
Differentially expressed genes were quantified and an enrichment expression (EE) above 5 and a p-value below 0.001 used as a cutoff.
Genome_build: https://www.arabidopsis.org/download/index-auto.jsp%3Fdir%3D%252Fdownload_files%252FGenes%252FTAIR10_genome_release

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Plants were grown for 2 weeks on 1/4 hoagland medium solidifid with 1% Agar and containing 1% Sucrose. More information to be found in Fischer et al. DOI to be added.

extract_protocol:
RNA was extracted from frozen tissues using TRIzol® and chloroform and cleand using the RNAeasy Kit from Quiagen. More information to be found in Fischer et al. DOI to be added.
Librarys were generated from mRNA by BGI Hong Kong. More information to be found in Fischer et al. DOI to be added.

treatment_protocol: Plants were grown on control medium containing no NaCl and 35mM NaCl. More information to be found in Fischer et al. DOI to be added.

value: shoot

tag: ploidy

value: tetraploid

tag: replicate


title: T_cell_LCMV_WT-1

tag: tissue

tag: genotype


title: S83cc_AtNUDX23

description:
CapZyme-seq protocol
FeatureCount_S83cc_output.txt

value: Huh7.5 hepatoma cells

value: HCV genotype 2c:S83cc


title: T_cell_LCMV_WT-2


title: lung cancer cell line H322M

tag: ethnicity

value: Caucasian

tag: gender

value: male

value: wild type


title: 4n_Na_root_3

source_name: root

value: root


title: S83cc_neg

value: negative

value: TEX treated total RNA


title: 4n_Na_shoot_1


title: ED43cc_neg

value: HCV genotype 4a:ED43cc


title: hiPSC-derived beta cells - HNF1A wt/R272C_rep3

city: Vanløse

first: Florian

middle: Malte

last: Hermann

address: Dybendalsvej 61, 1.tv

data_processing:
Base calling was done using RTA 2.0 (Illumina). Binary base call files were converted to fastq using bcl2Fastq (Illumnia)
Reads were mapped to GRCh38.p13 release 35 using Kallisto 0.46.0 with parameters "kallisto quant -i [reference] -o [output] -t 40 --single -l 400 -s 20 [input]"
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tsv with tpm for each gene (ESNG) in the rows, for each sample in the columns

source_name: beta cells

growth_protocol: hiPSCs were maintained in 2D the mTESR1 culture system on matrigel and differentiated in 2D to beta cells (stage 7) with a protocol adapted from Kieffer et al. (2014).

extract_protocol:
To purify beta cells from the heterogeneous cultures, the MARIS (method for analyzing RNA following intracellular sorting) protocol was adapted from Hrvatin et al. (2014) to sort NKX6-1 and c-peptide double positive cells by flow cytometry. In brief, S7 cells were harvested as single cells using TrypLE and kept on ice during all steps after dissociation. The cells were stained for viability using LIVE/DEAD Fixable Violet Dead Cell Stain Kit according to manufacturer’s recommendation (Thermo Fisher, Cat# L34955). Cells were fixed and permeabilized with 4 % PFA containing 0.1 % saponin (Sigma, Cat# 47036) and 1 % RNasin Plus RNase Inhibitor (Promega, Cat# N2615) for 30 min at 4° C. 0.1 % saponin and either 1 % or 0.5 % RNasin Plus RNase Inhibitor was maintained in all subsequent incubation or washing steps, respectively. The cells were incubated with primary antibodies and subsequently with secondary antibodies in staining buffer supplemented with 1% BSA for 1 hour or 45 minutes, respectively. The sorting was carried out on a FACS Aria III (BD Biosciences) or on a Sony SH800. Between 200 k and 1.2 million CPEP+/NKX6-1+ cells were sorted per experiment and RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, Cat# AM1975) according to the manufacturer’s protocol. However, the initial protein digestion was prolonged from 15 min to 1 hr at 50°C. Quality of RNA was checked using the Agilent Bioanalyzer 2100. The RIN values were between 4 and 5.4.
100 ng total RNA was subjected to cDNA synthesis and library construction using the Ovation ® Human FFPE RNA seq library system (Nugen, cat no# 0340 and 0341). Fragmentation was not carried out upon recommendation from the manufacturer, otherwise the standard protocol was followed. The quality of the library was assessed using Agilent Bioanalyzer dsDNA 1000 chip, and the library concentration was quantified using QubitTM dsDNA HS assay kit (ThermoFisher Scientific).
The library was loaded onto a high output flowcell FC-404-2005, and 75 base pairs single end RNA sequencing was performed using Illumina NextSeq 500.

tag: purification

value: NKX6.1+/Cpep+ FACS sorted

value: beta cells differentiatied in vitro from hiPSCs

value: HNF1A wt/R272C


title: 4n_Na_root_2


title: lung cancer cell line H226

value: lung

tag: source

value: NCI

tag: clinical response

value: mutation

tag: egfr

value: PBMC


title: 4n_Na_shoot_3

value: shoot

value: tetraploid


title: 4n_Na_root_1


title: Somites_bulk ATAC_rep2

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

description: bulk ATAC-seq

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the mm10 genome assembly using Bowtie version 1.1.1,allowing two mismatches, after adapter sequences were removed using trimgalore version0.6.6.
RNA-seq reads were mapped to the mm10 genome assembly using TopHat version 2.1.1 with the default configurations after adapter sequences were removed using trimgalore version 0.6.6.
peaks were called using MACS 1.4.2 (Zhang et al., 2008)  with the following setting: a p value (1.0E-05).
Gene expression values (RPKM: Reads Per Kilobase exon per Million mapped reads) were calculated using Partek Genomics Suite 7.18.
scRNA-seq reads were processed with CellRanger ver. 3.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
scATAC-seq reads were processed with Cellranger-atac ver. 1.1.0  and bcl2fastq/2.20.0 to generate fastq files with default parameters.
omics reads were processed with cellranger-arc/2.0.0 and bcl2fastq/2.20.0 to generate fastq files with default parameters.
For clustering, filtering, variable gene selection, dimensionality reduction of scRNA(single cell RNA) are performed using the Seurat ver.4.1.0 (Butler et al., 2018).
For clustering, filtering, variable gene selection, dimensionality reduction of scATAC(single cell ATAC) are performed using the Signac ver.1.5.0 (Stuart et al., 2019).
The pseudotemporal Analyses of scRNA(single cell RNA) was performed using Monocle v.3.0.0, Slingshot(ver 2.2.0) (Street et al., 2018)  and tradeSeq(ver 1.8.0) (Van den Berge et al., 2020).
Hi-C  reads were mapped to the mm10 genome assembly using BWA (Li and Durbin, 2010),filtering reads that aligned to more than two places in the genome and low mapping quality score (MAPQ <30).
Hi-C downstream analysis was performed with HOMER (Heinz et al., 2010)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include barcodes,gene names, and UMI counts  for each Sample.

source_name: Somites

growth_protocol: ESCs were plated on 0.1% gelatin and cultured in DMEM supplemented with 15% FBS, 1% penicillin-streptomycin,2 mM L-glutamine, 0.1 mM non-essential amino acids, 0.1% β-mercaptoethanol, 1,500 U/ml LIF and 2i inhibitors. Somites were dissected from embryoes, sorted and processed for RNAseq and ATACseq assays.

extract_protocol:
RNA was extracted using Trizol. For ChIP cells were  lysed in RIPA buffer as described in Mousavi et al., 2012. ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013)
For RNA-seq, poly (A)+ mRNA libraries were generated  using NEBNext Ultra II RNA library preparation kit for Illumina (NEB #E7490). Single-cell RNA-seq libraries were prepared using a Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (P/N 1000121, 10x Genomics) and scATAC seq performed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10x genomics, 1000175). Single Cell Multiome ATAC+ Gene Expression (10x Genomics kit, CG000338). Hi-C experiments were performed using the Arima-HiC kit (A510008GFP)
Bulk RNAseq, Bulk ATAC seq, ChIPseq, scRNA, scATAC, snRNA and scATAC from the same cell (multiomeic) and HiC

treatment_protocol: ESCs differentiation was induced as described inChalet al., 2015. ESC were plated on gelatin-coated plates in serum-free N2B27 medium and BMP4 10ng/ml for 2 days. cells were shifted to MEM, 1%FBS, 14% KSR,10ng/ml Rspo3, 0.5% DMSO and 0.1 μM LDN19318 for 4 days. Subsequently, medium was changed to DMEM, 1%FBS, 14% KSR,  10 ng/ml Rspo3, 10 ng/ml HGF,2 ng/ml IGF-1,20 ng/ml FGF-2  and 0.1 μM LDN193189 for additional 2 days..

tag: sample type

value: from Embryos


title: hiPSC-derived beta cells - HNF1A wt/R272C_rep2

tag: cell line


title: DBN3acc_Rpp

tag: cell type

value: Huh7.5 hepatoma cells

value: Rpp

value: HCV genotype 3a:DBN3acc


title: 4n_Control_shoot_3

value: Control


title: S83cc_Rpp

tag: enzymatic treatment

value: HCV genotype 2c:S83cc


title: DH8cc_neg

description:
CapZyme-seq protocol
FeatureCount_DH8cc_output.txt

value: negative

tag: virus

value: HCV genotype 2b:DH8cc

value: TEX treated total RNA


title: hiPSC-derived beta cells - HNF1A wt/R272C_rep1

value: NKX6.1+/Cpep+ FACS sorted

value: beta cells differentiatied in vitro from hiPSCs


title: DH8cc_AtNUDX23


title: Somites_bulk RNAseq_rep2

description: bulk RNA-seq


title: hiPSC-derived beta cells - HNF1A wt/wt_rep4

value: HNF1A wt/wt


title: Somites_bulk RNAseq_rep1

description: bulk RNA-seq


title: Somites_bulk ATAC_rep1

description: bulk ATAC-seq


title: 4n_Control_shoot_1

tag: treatment


title: 4n_Control_shoot_2


title: hiPSC-derived beta cells - HNF1A wt/R272C_rep4

value: HNF1A wt/R272C


title: T9cc_neg

description:
CapZyme-seq protocol
FeatureCount_T9cc_output.txt

value: HCV genotype 2a:T9cc

tag: molecule subtype


title: 4n_Control_root_2

value: root

tag: ploidy


title: aPSM- scRNAseq_rep1

description: scRNAseq

source_name: aPSM

value: Differentiated ESC


title: hiPSC-derived beta cells - HNF1A wt/wt_rep2


title: DH8cc_Rpp


title: H358-CDDP

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

description: replicate 1

data_processing:
Library strategy: ISO-seq
Subreads coming from PacBio SEQUEL SMRTcells were processed via the SMRTLink’s IsoSeq v3.0 pipeline with default parameters (https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md). This pipeline is composed of the following 6 steps: Circular Consensus Sequence (CCS) calling, primer removal/demultiplexing, refining, merging, clustering and polishing. Resulting CCS reads and HQ transcripts were mapped with minimap2 (v2.17-r941) against hg19 genome with the following parameters : -ax splice -uf --secondary=no -C5 -O6,24 -B4.
Then, CCS reads were classified into 'last exon (LE)' and 'intronic polyadenylation (IPA)' isoforms, depending on whether the 3'-end of the read was located in the last exon of a gene or within a gene but upstream of the last exon ('ELE' region).
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx

source_name: Non-small cell lung cancer cell line

growth_protocol: Cells were cultured in RPMI-1640-Glutamax medium (GibcoBRL, Life Technologies, Cergy Pontoise, France), supplemented with 10% (v/v) heat-inactivated fetal calf serum (GibcoBRL), in 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from total cells.
A starting amount of 1 µg was used for long read library preparation. The first step of cDNA synthesis was done using the SMARTer PCR cDNA Synthesis Kit (Takara). Then, cDNA was amplified by 14 PCR cycles and divided in two fractions to be purified with different AMPure PB beads (Pacific Biosciences) ratio. In order to enrich for larger transcripts, a ratio of 0.4x was applied to a fraction (corresponding to 5 out of 8 of the initial volume), while the other fraction was purified with 1x ratio. For each sample, both fractions were quantified with Qubit dsDNA high-sensitivity kit (ThermoFisher Scientific), qualified by capillary electrophoresis (Bioanalyzer High Sensitivity DNA kit - Agilent), pooled equimolarly, and subjected to the SMRTbell Template Prep Kit 1.0 (Pacific Biosciences). The first DNA damage and end repair steps were applied according to the manufacturers’ recommendations. The following ligation was extended to 16 hours to improve efficiency. The final exonuclease treatment was applied to digest unwanted molecules. The SMRTbells were quantified with Qubit dsDNA high-sensitivity kit (ThermoFisher Scientific) and qualified by capillary electrophoresis as above. Complexes were prepared following the manufacturer’s recommendations using the Sequel Binding Kit 3.0 and the sequencing Primer v3 (Pacific Biosciences). Each sample was sequenced on 4 SMRTcells 1M, on the Sequel I system (Pacific Biosciences) using a loading molarity of 5 pM. For each SMRTcell, 10 hours of movie, 2 hours of immobilization, and 4 hours of pre-extension were set up.

treatment_protocol: Treatment with cisplatin (Selleckchem, Euromedex, Souffelweyersheim, France) was done at 100 µM. Treatment with vehicle (DMSO) was done in parallel.

value: Cisplatin

tag: extract

value: Total cells


title: hiPSC-derived beta cells - HNF1A wt/wt_rep1


title: 4n_Control_root_3

tag: tissue

value: tetraploid

tag: replicate


title: 2n_Na_shoot_3

value: shoot

value: diploid


title: HIFLR-snRNA(omics)

description: Multiomics

source_name: HIFLR


title: H77cc_neg

description:
CapZyme-seq protocol
FeatureCount_H77Ccc_output.txt

value: Huh7.5 hepatoma cells

value: HCV genotype 1a:H77Ccc


title: 2n_Na_shoot_2


title: Instructed ESC- scRNAseq_rep1

description: scRNAseq

source_name: Instructed ESC


title: H358-DMSO

description: replicate 1

value: Vehicle (DMSO)


title: 4n_Control_root_1

value: Control


title: Myoblast - Block-3

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

data_processing:
Quality control was performed with FASTQC (version 0.11.8)
Aligment was performed with STAR (version 2.6.1a_08-27)
Quantification was performed with RSEM
Splicing analysis was perform using Vast-tools
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include gene count without normalization.

source_name: Total RNA from Myoblast

growth_protocol: Healthy immortalized control-derived fibroblasts (CNT) and immortalized patient-derived fibroblasts carrying 1300 CTG repeats (DM1) were provided by Dr. Furling (Institute of Myology, Paris) and were transdifferentiated into myotubes by inducing MyoD expression. The fibroblasts were grown in DMEM with 4.5 g/L glucose, 1% penicillin and streptomycin (P/S), and 10% FBS (Sigma). Transdifferentiation was prompted by muscle differentiation medium (MDM) containing DMEM with 4.5 g/L glucose, 1% P/S, 2% horse serum, 1% apo-transferrin (10 mg/mL), 0.1% insulin (10 mg/mL), and 0.02% doxycycline (10 mg/mL). All cells were grown at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cells were plated at 1.0x105 cells per mL in 10 mL petri dishes (Falcon). Total RNA from transdifferentiated myotubes was isolated using QIAzol Lysis Reagent and RNeasy Mini Kit (Qiagen) following manufacturer’s recommendations. One microgram of RNA was digested with DNase (Zymo) and reverse-transcribed with SuperScript II Reverse Transcriptase (Invitrogen) using random hexanucleotides (Roche).
Library preparation was performed using TruSeq Stranded mRNA Library prep kit from Illumina without any change

treatment_protocol: For RNA extractions as well as immunofluorescence, blockmiRs targeting miR-23b were transfected at 50 nM while blockmiRs targeting miR-218 were transfected at 200 nM. A scrambled control (Scramble) was transfected at 50 nM and 200 nM. Cell  transfection was carried out with XtremeGENE™ HP (Roche) and treated with MDM to promote transdifferentiation. After 4 days, cells were extracted for RNA.

value: normal (iCDF) skin fibroblasts trans-differentiated into myoblast

tag: treatment group

value: DM1 + BlockmiR


title: Instructed ESC- H3K4me1_rep1

description: ChIP-seq


title: H77cc_Rpp

value: Rpp

value: TEX treated total RNA


title: 2n_Na_shoot_1


title: H77cc_AtNUDX23


title: Instructed ESC- H3k4me1_rep2

description: ChIP-seq


title: Instructed ESC- H3k4me1_input_rep2

description: CHIP-seq


title: T9cc_Rpp


title: 2n_Na_root_3


title: Instructed ESC- H3K4me1_input_rep1

description: CHIP-seq


title: T9cc_AtNUDX23


title: TNcc_neg

description:
CapZyme-seq protocol
FeatureCount_TNcc_output.txt

value: negative

value: HCV genotype 1a:TNcc


title: Myoblast - Block-1


title: Myoblast - Block-2


title: Instructed ESC- H3k27Ac_rep2

description: ChIP-seq


title: TNcc_AtNUDX23


title: 2n_Na_root_2

value: root


title: Myoblast - 23b-3

value: DM1 + antagomiR23b


title: 2n_Na_root_1


title: TNcc_Rpp


title: Instructed ESC- H3K27Ac_input_rep2

description: CHIP-seq

value: Differentiated ESC


title: J6JFH1_neg_rep5_2

description:
CapZyme-seq protocol
FeatureCount_J6-JFH_output.txt

value: HCV genotype 2a J6/JFH1-clone2

value: Total RNA


title: Myoblast - 23b-2


title: Myoblast - 23b-1


title: Instructed ESC- bulk RNAseq_rep2

description: bulk RNA-seq


title: 2n_Control_shoot_1

value: shoot


title: Instructed ESC- H3K27Ac_input_rep1

description: CHIP-seq


title: Instructed ESC- bulk RNAseq_rep1

description: bulk RNA-seq


title: J6JFH1_Rpp_rep5_2


title: 2n_Control_shoot_2

value: diploid


title: 2n_Control_root_3


title: Myoblast - DM1-2


title: J6JFH1_neg_rep4_2

value: Huh7.5 hepatoma cells


title: 2n_Control_root_2


title: Myoblast - Control-3


title: Naïve ESC- scRNAseq_rep1

description: scRNAseq

source_name: Naïve ESC

value: ESC-Naive


title: Myoblast - DM1-1


title: J6JFH1_Rpp_rep4_2


title: Naïve ESC- H3k4me1_rep2

description: ChIP-seq


title: Myoblast - Control-2


title: J6JFH1_AtNUDX23_rep4_2


title: 2n_Control_shoot_3


title: Naïve ESC- H3K4me1_rep1

description: ChIP-seq


title: Naïve ESC- H3K4me1_input_rep2

description: CHIP-seq


title: Myoblast - DM1-3


title: Instructed ESC- H3K27Ac_rep1

description: ChIP-seq


title: RC3 MethylC-seq

city: Toledo

first: Carolina

last: Escobar

address: Avenida Carlos III, s/n

institute: University of Castilla-La Mancha

description: Control (non-infected roots)

data_processing:
MethylC-seq data was processed using the pipeline available at https://github.com/seb-mueller/snakemake-bisulfite (commit f12bb6) in GitHub.
The pipeline performed quality control using FastQC (version 0.11.8). Raw reads were trimmed for adapters, quality-trimmed and filtered using Trim Galore (version 0.5.0).
A combined genome was constructed by concatenation the genomes (in fasta format) of A. thaliana (TAIR10, including the chloroplast and mitochondrial genome), M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) and Lambda phage into a single fasta format reference. Reads were then mapped to the constructed reference with Bismark (version 0.20.0; Krueger and Andrews, 2011), using the following parameters: L,0,-0.4.
The SAM alignment generated by Bismark were further processed into BAM format and subsequently imported for further processing into the R package methylKit version 0.99.2 (Akalin et al., 2012).
To identify differential methylated regions (DMRs), we  defined various regions in form of adjacent non-overlapping window of 200 base pairs (referred to as bins), which were posteriorly checked for overlapping different genomic regions, including genes, promoters and transposable elements as specified in Araport11 (06/2016; Cheng et al., 2017). Promoters were considered as 1000 base pairs (bp) upstream until 200 bp downstream of the transcription start site.
For each region, the containing methylated and unmethylated cytosines were counted (separately for each library, each region and each context [CHH, CHG, CG]) and tested for differential methylation using a logistic regression approach using the “MN” over-dispersion correction as implemented in MethylKit. DMRs are then defined if the difference of methylation proportion between the gall samples and the controls was higher than 15% and a FDR (q-value) of less than 0.05 and covered by at least two biological replicates of the treatment or control.
Genome_build: A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017)
Supplementary_files_format_and_content: File with DMRs (in different DNA methylation contexts); .csv

source_name: Roots

growth_protocol: Arabidopsis thaliana plants were were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC

extract_protocol:
Galls and control roots were collected at 14 days post infection and frozen on liquid nitrogen. Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657)
The libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit EZ DNA Methylation-Gold Kit (Zymo Research) following the library protocol Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms. The fragment size distribution of the libraries were checked in an Agilent® 2100 Bioanalyzer using DNA 1000 chip (Agilent® Technologies, Inc., Santa Clara, CA, USA). The libraries were quantified using using qPCR according to the Illumina qPCR Quantification Protocol Guide (Bioanalyzer DNA High Sensitivity chip & LightCycle qPCR). The libraries were sequenced using an Illumina® HiSeq X PE150 (San Diego, California, USA).

treatment_protocol: Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days. During the first 48 hours, the infections and control roots growth were accessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5).

tag: ecotype

tag: age

value: Aprox. 20-days-old plants (14 days post infection)

value: Non-infected


title: hiPSC-derived beta cells - HNF1A wt/wt_rep3

tag: purification

value: NKX6.1+/Cpep+ FACS sorted

value: beta cells differentiatied in vitro from hiPSCs

tag: genotype

value: HNF1A wt/wt


title: 2n_Control_root_1

value: Control


title: J6JFH1_AtNUDX23_rep3_2


title: Myoblast - Control-1

value: normal (iCDF) skin fibroblasts trans-differentiated into myoblast


title: J6JFH1_AtNUDX23_rep5_2


title: RC2 MethylC-seq

description: Control (non-infected roots)


title: Naïve ESC- H3k27Ac_rep2

description: ChIP-seq


title: G3 MethylC-seq

description: Treatment (infected roots)

value: Infected with Meloidogyne javanica


title: G2 MethylC-seq

description: Treatment (infected roots)


title: G1 MethylC-seq

description: Treatment (infected roots)


title: Naïve ESC- H3K27Ac_input_rep2

description: CHIP-seq


title: J6JFH1_neg_rep3_2

value: negative


title: J6JFH1_Rpp_rep3_2

value: Rpp


title: RC3 Roots

description: Control (non-infected roots)

extract_protocol:
Galls and control roots were collected at 3 days post infection and frozen on liquid nitrogen. Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657)
The libraries were prepared using the NEXTflex Bisulfite-Seq Library Prep Kit (BiooScientific), following the manufacturer's instructions. The fragment size distribution of the libraries were checked in the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit. The libraries were then sequenced in one lane of an Illumina HiSeq 4000 PE100 platform. Two of the libraries (RC2 and RC3) were sequenced in an Illumina® HiSeq X PE150 (San Diego, California, USA). Both steps were performed by the company AllGenetics & Biology SL.

tag: developmental stage

value: Aprox. 9-days-old plants (3 days post infection)

tag: agent


title: MCU-KO mouse 8

city: Chicago

first: Enrico

last: Zampese

state: IL

address: 303 E Superior st

department: Neuroscience

institute: Northwestern University

data_processing:
Reads were trimmed using trimgalore
trimmed reads were aligned using star
aligned reads were counted using htseq-count
Assembly: mm10

source_name: Substania nigra

extract_protocol: DAT-Cre+/- and DAT-Cre+/-MCU fl/fl  mice were stereotactically injected with AAV carrying a cre-depended construct to express RiboTag selectively in dopaminergic neurons. After 30 days substantia nigra tissue was dissected, the tissue was homogenized and RiboTag was immunoprecipitated with magnetic beads. RNA was extracted using RNeasy Micro RNA extraction kit (QIAGEN).

value: Substania nigra

tag: cell line

value: dopaminergic neurons

value: DAT-Cre+/- MCU fl/fl


title: MCU-KO mouse 5

tag: cell type


title: J6JFH1_AtNUDX23_rep2_2

tag: enzymatic treatment

value: HCV genotype 2a J6/JFH1-clone2

value: Total RNA


title: Naïve ESC- H3K4me1_input_rep1

description: CHIP-seq

tag: sample type

value: ESC-Naive


title: Naïve ESC- H3K27Ac_rep1

description: ChIP-seq


title: Naïve ESC- bulk RNAseq_rep3

description: bulk RNA-seq


title: MCU-KO mouse 7


title: J6JFH1_Rpp_rep1_2

value: Huh7.5 hepatoma cells

tag: virus


title: J6JFH1_AtNUDX23_rep1_2

tag: molecule subtype


title: RC1 MethylC-seq

description: Control (non-infected roots)

value: Aprox. 20-days-old plants (14 days post infection)

tag: treatment

value: Non-infected


title: MCU-KO mouse 4


title: Naïve ESC- H3K27Ac_input_rep1

description: CHIP-seq


title: J6JFH1_neg_rep1_2


title: J6JFH1_Rpp_rep2_2


title: MCU-KO mouse 6


title: J6JFH1_neg_rep2_2


title: RC2 Roots

description: Control (non-infected roots)


title: Naïve ESC- bulk RNAseq_rep2

description: bulk RNA-seq


title: MCU-KO mouse 2


title: J6JFH1_neg_rep5


title: MCU-KO mouse 3


title: J6JFH1_AtNUDX23_rep5


title: P6_mousecontrol_E7

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

description: single cell

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM with default parameters. Reads aligning to features were counted from the alignment bam files with the htseq-count script from HTSeq(17) with parameters: -r pos -m union -s no. Counts were aggregated accross the 2 lanes for each cell to give the raw counts matrix
Genome_build: hg38
Supplementary_files_format_and_content: Counts matrix with raw feature counts for each cell

source_name: single cell

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation and frozen in FCS containing 10% DMSO and stored at –80°C for later use. T cells were sorted on the FACS Aria fusion (BD, USA) using CD3-PERCPCy5.5 (Biolegend, clone HIT3A), CD4-APC/Cy7 (BD Biosciences, clone RPA-T4), and CD8-Viogreen (Miltneyi Biotec, clone BW135/80). CD56-FITC (Biolegend, clone 5.1H11) was used to gate out NK cells and propidium iodide to exclude dead cells (Miltenyi Biotec).
Single cells were sorted into a 96 well plate directly into 3ul of lysis buffer. Library preparation and sequencing was performed by Oxford Genomics Centre (Oxford University, United Kingdom)
Paired end single cell sequencing using Smartseq2

treatment_protocol: Single cell RNA sequencing was performed in 3 patients on T cells isolated from 30–50 ml peripheral blood collected at two weeks after transplantation

value: mouse cells


title: Naïve ESC- bulk RNAseq_rep1

description: bulk RNA-seq


title: 5_6_monocytes

type: RNA

city: fukuoka

first: Naoya

last: Matsunaga

address: maidashi 3-1-1, higashi-ku

country: Japan

institute: kyushu university

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

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

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

source_name: 5/6 monocytes

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

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

treatment_protocol: The monocytes was prepared from mouse spleen at 8 weeks after operation by flowcytemetry. Cells labeled anti-CD11b antibody and ant-Ly6c antibody.

tag: strain

value: icr

value: monocytes

tag: conditon

value: 5/6 nephrectomized


title: P5_mousecontrol_E8

description: single cell


title: MSCs #6+IFN-γlow AML [339]

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Gene expression data from MSCs after 24h of culture with IFN-γlow AML cells

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on an Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (Thermo Fisher Scientific). Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (sst-RMA).

label: biotin

source_name: MSCs after 24h of culture with IFN-γlow AML cells (on a transwell)

label_protocol: ss-cDNA was prepared according to the standard Thermo Fisher Scientific protocol from 100 ng total RNA (GeneChip® WT PLUS Reagent Kit User Guide, 2018, Thermo Fisher Scientific).

growth_protocol: MSCs were cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1% antibiotics (penicillin/streptomycin). RPMI medium (same supplement as DMEM) was used for co-culture with AML cells.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MSCs were seeded at 2 x 104 cells/cm2. After 24 hours, AML cells (1x106 cells/ml) were seeded with transwells on MSC layers. After 24 hours, AML cells were removed and MSCs were harvested.

value: mesenchymal stromal cell (MSC)

value: IFN-γIFN-γlow AML cells


title: sham_monocytes

source_name: sham monocytes

value: sham


title: MSCs #5+IFN-γlow AML [337]


title: J6JFH1_Rpp_rep5

source_name: Huh7.5 hepatoma cells

value: Rpp


title: MCU-KO mouse 1

tag: tissue

value: Substania nigra


title: P3_mousecontrol_E10

description: single cell


title: P1_mousecontrol_E12

description: single cell


title: J6JFH1_AtNUDX23_rep4


title: control mouse 7

value: dopaminergic neurons

value: DAT-Cre +/-


title: control mouse 8


title: control mouse 5


title: control mouse 6


title: P2_mousecontrol_E11

description: single cell


title: J6JFH1_neg_rep4

value: negative

value: HCV genotype 2a J6/JFH1-clone2


title: MSCs #4+IFN-γlow AML [335]


title: J6JFH1_Rpp_rep4

value: Total RNA


title: control mouse 4


title: P4_mousecontrol_E9

description: single cell


title: J6JFH1_neg_rep3

value: Huh7.5 hepatoma cells


title: IL-10- B cells rep4

city: guangzhou

first: Yinhong

last: Zhu

state: guangdong

address: zhongshan Second Road

country: China

institute: 无

description:
gene_expression_FPKM.txt
N4

data_processing:
The useful Perl script was used to filter the original data.Trim Smart-seq2 public primer sequence from the Reads.Then Remove the contaminated reads for adapters, the low quality reads and the reads whose N base more than 5% for total bases.
The reference genomes and the annotation file were downloaded from ENSEMBL database.Clean Data was then aligned to the reference genome mm10 using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: B cells

growth_protocol: The purified B cells were cultured in RPMI 1640 supplemented with 10% FBS, glutamine, and 2-mercaptoethanol.

extract_protocol:
After splenic B cells from IL-10-eGFP Tiger mice were stimulated with 3 µg/ml LPS for 48 h, IL-10+ B cells and IL-10- B cells were sorted and RNA was harvested using Trizol reagent.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® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B cells from spleen

value: IL-10-GFP Tiger mice

value: untreated


title: MSCs #2+IFN-γlow AML [330]


title: MSCs #3+IFN-γhigh AML [333]

description: Gene expression data from MSCs after 24h of culture with IFN-γhigh AML cells

source_name: MSCs after 24h of culture with IFN-γhigh AML cells (on a transwell)

value: IFN-γIFN-γhigh AML cells


title: MSCs #1+IFN-γlow AML [325]


title: J6JFH1_Rpp_rep3

extract_protocol:
RNA extraction was performed by Trizol treatment followed on-column DNase I digestion and RNA purification using RNA Clean & Concentrator kit-5
RNA was enzymatically treated with de-capping enzymes that specifically convert different 5’ cap structures to 5’ monophosphates. 5’-phosphate dependent adapter ligation was performed followed by reverse transcription. Libraries were generated using PCR with custom Illumina compatible primers.


title: IL-10+ B cells rep4

description:
gene_expression_FPKM.txt
P4


title: J6JFH1_AtNUDX23_rep3


title: control mouse 2


title: J6JFH1_neg_rep2


title: control mouse 3


title: 4050-10-R848

description:
AML R848
R848 treated Dnmt3a/Flt3-mutant leukemia, mouse 4050

data_processing:
FASTQ sequence files were aligned to the mouse genome version 10 using Kallisto with de novo junction discovery in AltAnalyze.
The fastq files were aligned to mouse genome Mm10 Kallisto and gene level FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were obtained using AltAnalyze 2.1.1 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005).
Genome_build: mouse genome mm10
Supplementary_files_format_and_content: tab-delimited text files

growth_protocol: Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (Dnmt3a+/-Flt3ITD AML) leukemic splenocytes were thawed from liquid nitrogen (n=2 mice/genotype) and allowed to recover for 24 hours in standard growth medium RPMI 1640 (Thermo Fisher Scientific) containing 20% FBS (HyClone) supplemented with mouse recombinant SCF (60ng/ml), IL6 (20ng/ml), and IL3 (20ng/ml) (Miltenyi Biotech).

extract_protocol:
Leukemic splenocytes were harvested from two independent Dnmt3afl/fl,Flt3ITD/ITD,Mx1Cre (Dnmt3a+/-Flt3ITD AML) mice. Red blood cells were lysed, and 100x106 leukemia cells were frozen. Frozen cells were thawed and the treatment protocol was performed. At the end of the treatment protocol cells were lysed with Trizol. RNA was extracted according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant 2200 Tape Station. Then samples with a RIN>8.0 were processed by ribosome depletion, stranded True-seq, paired-end 150 base pair (bp), 30 million reads.
RNAs were detected by RNAseq analysis using paired-end 150 nucleotide (nt) sequencing and 30 million reads for all samples. RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits.

treatment_protocol: Equal numbers of 0.5x106 leukemia cells from each mouse in 1ml standard growth medium were mixed with either 10ug/ml R848 or equivalent volume of vehicle control. Cells were incubated with R848 or vehicle for 3 days at 37°C with 5% CO2. Then cells were washed and snap fozen in TriZol.

value: leukemic splenocytes

tag: disease state

value: acute myeloid leukemia

value: Dnmt3a/Flt3-mutant leukemia

value: Resiquimod


title: IL-10- B cells rep2

description:
gene_expression_FPKM.txt
N2


title: IL-10+ B cells rep2

description:
gene_expression_FPKM.txt
P2


title: control mouse 1


title: J6JFH1_AtNUDX23_rep2

data_processing:
Library strategy: CapZyme-seq
Illumina bcl2fastq was used to create fastq files
Sequenced reads were trimmed for adaptor sequence (cutadapt -a AGATCGGAAGAGCACACGTCT -q 20 -m 15) and mapped to RNA sequences (viral RNA, rRNA, snoRNA, tRNA and mRNA (TPM>2) using  (bowtie2 --norc --very-sensitive)
Counts for the 5' end of different RNA were obtained using the featureCounts function from the Subread package using a SAF file specifing the first 100 nts of each RNA.
Example code for the processing of the sequencing data is available at https://github.com/jeppevinther/CapZyme
Supplementary files format and content: Tab-delimited text files include FeatureCounts output, raw counts
Supplementary files format and content: Matrix table with raw 5'  counts for every RNA (first 100nt) and every sample in experiment


title: IL-10+ B cells rep3

description:
gene_expression_FPKM.txt
P3


title: 4182-Control

description:
AML Control
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 4182

value: control


title: IL-10- B cells rep1

description:
gene_expression_FPKM.txt
N1


title: 4182-10-R848

description:
AML R848
R848 treated Dnmt3a/Flt3-mutant leukemia, mouse 4182


title: J6JFH1_neg_rep1


title: 4050-Control

description:
AML Control
vehicle control treated Dnmt3a/Flt3-mutant leukemia, mouse 4050


title: J6JFH1_Rpp_rep2

value: Rpp


title: J6JFH1_AtNUDX23_rep1


title: IL-10- B cells rep3

description:
gene_expression_FPKM.txt
N3


title: IL-10+ B cells rep1

description:
gene_expression_FPKM.txt
P1


title: MSCs #1+IFN-γhigh AML [327]

value: mesenchymal stromal cell (MSC)


title: MSCs #1+IFN-γhigh AML [326]


title: MSCs #2+IFN-γhigh AML [329]


title: MSCs #5 [336]

description: Gene expression data from MSCs control cells after 24h of culture

source_name: MSCs control after 24h of culture


title: 3427T

status: Public on Jul 30 2022

city: Berlin

first: Luis

middle: Philipp

last: Kuschel

address: Robert-Koch-Platz 4

department: Abteilung für experimentelle Neurologie

country: Germany

institute: Charité Universitätsmedizin Berlin

description:
3427T
Oxford Nanopore Technologies MinION Mk 1B

data_processing:
Basecalling was performed using guppy (Oxford Nanopore Technologies, UK) v3.1.5 (CPU-based, fast mode) or v3.4.3 (GPU-based)
Alignment to the hg19 human reference genome using minimap2 v.2.15
Methylation status of CpG sites (5mC) was called using nanopolish v0.13.2 and binarized using 0.6 as a cut-off value
Individual RData files containing binarized methylation status for CpG sites which overlap with the probeset of the 450k microarray are generated using R v4.0.2.
Individual BED files with genomic hg19 coordinates, binary methylation call and Illumina probe ID were generated and merged into a sparse table with sample ID as row header and Illumina probe IDs as column header
Assembly: hg19
Supplementary files format and content: .Rdata files containing binarized methylation status for CpG sites.
Supplementary files format and content: .bed files with hg19 coordinates and binary methylation status (cut-off 0.6)

source_name: brain tumor tissue

extract_protocol:
DNA was extraced either using spin columns (DNeasy Blood & Tissue Kit, Qiagen, NL) or using phenol chloroform procedure.
Library preparation was performed using the Rapid Barcoding Kit (RBK004, Oxford Nanopore Technologies, UK) according to manufacturers instructions.

value: brain tumor tissue

tag: reference diagnosis

value: Glioblastoma, IDH-wildtype

tag: nanopore methylation_call

value: GBM, RTK II

tag: nanopore methylation_class_family_call

value: MCF GBM


title: 2965T

description:
2965T
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: O IDH

value: MCF IDH GLM


title: 2483T

description:
2483T
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH


title: 2922T

description:
2922T
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse astrocytoma, IDH-mutant


title: MSCs #6 [338]


title: MSCs #4 [334]


title: MSCs #2 [328]


title: 2197T

description:
2197T
Oxford Nanopore Technologies MinION Mk 1B


title: 2402T

description:
2402T
Oxford Nanopore Technologies MinION Mk 1B


title: 3523T

description:
3523T
Oxford Nanopore Technologies MinION Mk 1B


title: J6JFH1_Rpp_rep1

city: Copenhagen N

first: Jeppe

last: Vinther

value: Huh7.5 hepatoma cells

value: HCV genotype 2a J6/JFH1-clone2

value: Total RNA


title: MSCs #1 [324]


title: MSCs #3 [332]


title: WT_8_rep1

city: Freiburg im Breisgau

first: Loubna

last: Youssar

state: Baden-Wurttemberg

address: Schänzlestraße 1

institute: University of Freiburg

description: Sample taken at time=8min after Rifampicin addition

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocol GE1_107_Sep09  for one-color arrays

data_processing: The R/Bioconductor Limma package was used for all preprocessing and statistical analysis. Subtraction of background was not implemented as it did not show any positive impact in our data. Cyclic loess (cLOESS) was implemented by using quality weight probes for normalisation

organism: Synechocystis sp. PCC 6803

label_protocol: The RNA was labeled directly, without cDNA synthesis with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis strain PCC-M (Trautmann et al, 2012) used in this work was originally obtained from S. Shestakov, (Moscow State University, Russia). Liquid cultures were cultivated at 30 °C in standard BG11 medium (Rippka et al, 1979) with constant shaking and illuminated with white light of 50 μmol of photons m-2s-1. In order to induce iron limitation, cultures were grown to the same OD750 and the iron chelator Deferoxamine mesylate salt B (DFB) was added to the liquid cultures to a final concentration of 100 μM.  Triplicate liquid cultures with 250 mL volume of Synechocystis wild type were grown at standard conditions until they reached exponential growth with OD750nm of approximately 0.7. Samples for RNA extraction (25 mL each) were taken at time points 0 min (before the addition of rifampicin) and in a time series of 2 min, 4 min, 8 min, 16 min, 32 min and 64 min after the addition of 300 μg/mL rifampicin. The function of rifampicin is to prevent initiation of new transcripts by binding to the β subunit of RNA polymerase (Campbell et al, 2001). The addition of this chemical enabled us to monitor the rate of RNA degradation in the absence of new transcription initiation. The same experiment was performed with Synechocystis cultures, which were treated for 24 hours with 100 μM DFB before the addition of rifampicin.

extract_protocol: Cells were harvested on Supor 800 membranes via vacuum filtration. The folded membrane was transferred in a Sarstedt tube with 1 mL PGTX solution (Pinto et al, 2009), snap frozen in liquid nitrogen and stored at -80 °C until extraction. The RNA extraction process started with 15 minutes incubation at 65 oC with vortexing several times in between. Then, 700 μL chloroform/IAA (isoamyl alcohol) 24:1 mixture was added to the samples, they were mixed well and incubated for 10 min at room temperature with gentle mixing several times. Afterwards, the samples were centrifuged for 3 min at 6000 g and the upper phase was transferred to a new tube. The next step was adding 1 volume phenol/chloroform/IAA mixture, centrifuging and transferring the upper phase to the new tube. Next, one volume chloroform/IAA was added, samples were centrifuged and the upper phase was transferred to a new 2 mL RNase free tube. One volume isopropanol was added and mixed to the samples and RNA was precipitated overnight at -20 oC. The next day samples were centrifuged at 4 oC at 12000 g for 30 minutes, the supernatant was removed and the transparent RNA pellet was washed with 200 μL 70% ethanol (without mixing). The samples were centrifuged for 10 min, 12000g at 4 oC, the ethanol was removed, and the RNA pellet was air dried and dissolved in 20 μL RNase free H2O. RNA samples were stored at -80 oC.  The RNA samples (10 μg) were DNase treated and precipitated by ethanol overnight, the quality was checked on an agarose gel and concentration was measured by Nanodrop. The RNA was labelled with the ULS labelling Kit (Kreatech). 2 μg of RNA was mixed with 0.8 μl Cy3-ULS solution per 1μg of nucleic acid in a volume of 20 μl with 2 μL 10x labelling solution. The samples were incubated at 85°C for 15 min in the dark (the fluorescent dye is light sensitive) and residual unused dye was removed with KREApure columns. The efficiency of labelling was controlled photometrically with the Nanodrop spectrophotometer (microarray mode), which measured simultaneously the absorption at 260 nm (nucleic acid) and 550 nm (Cy3). Agilent custom microarray 8X60k with one colour technique were used. The hybridisation, washing and scanning procedure was done according to the Agilent protocol for one-color microarray-based gene expression analysis. Shortly, labelled RNA samples were mixed with 10X blocking solution, RNase free water and 25X fragmentation buffer and incubated for 30 min at 60 oC in the dark. Subsequently, 2X Hybridisation buffer was carefully mixed with the samples and after short centrifugation they were loaded on the microarray. Hybridisation was performed for 17 hours at 65 oC with constant rotation. Subsequent washing was performed with washing buffer 1 and 2 and with acetonitrile for 1 min each. The scanner Agilent Technologies Scanner G2505B was used for the detection of the signals and the feature extraction was done with the Agilent Feature extraction software.

treatment_protocol: No special treatment was applied

tag: genotype

value: WT

tag: stress

value: Standard conditions


title: WT_64_rep1

description: Sample taken at time=64min after Rifampicin addition


title: WT_16_rep1

description: Sample taken at time=16min after Rifampicin addition


title: WT_2_rep2

description: Sample taken at time=2min after Rifampicin addition


title: WT_4_rep2

description: Sample taken at time=4min after Rifampicin addition


title: WT_32_rep1

description: Sample taken at time=32min after Rifampicin addition


title: WT_16_rep2


title: WT_4_rep1


title: WT_32_rep2


title: FB24_64_rep2

value: iron stress


title: WT_0_rep1

description: Sample taken at time=0min before Rifampicin addition


title: WT_2_rep1


title: FB24_32_rep2


title: FB24_16_rep2


title: FB24_0_rep1


title: WT_0_rep2

description: Sample taken at time=0 before Rifampicin addition


title: FB24_32_rep1


title: FB24_8_rep2


title: FB24_8_rep1


title: WT_8_rep2


title: WT_4_rep3


title: FB24_64_rep1


title: FB24_2_rep2


title: FB24_4_rep2


title: FB24_16_rep1


title: UGS-632-D

description:
UGS-632
Oxford Nanopore Technologies MinION Mk 1B

value: CNS embryonal tumour, NOS

value: PLEX, PED B

value: MCF PLEX T


title: UGS-636-B

description:
UGS-636
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: CNS Ewing sarcoma family tumor with CIC alteration

value: EFT, CIC


title: FB24_2_rep1


title: WT_8_rep3


title: UGS-636-C


title: UGS-619-D

description:
UGS-619
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, WNT-activated

value: MB, WNT


title: UGS-632-A


title: UGS-636-D


title: UGS-636-A


title: UGS-619-C


title: UGS-632-C


title: UGS-619-A


title: UGS-632-B


title: UGS-618-C

description:
UGS-618
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, non-WNT/non-SHH

value: MB, G4

value: MCF MB G3G4


title: WT_2_rep3


title: WT_64_rep2


title: UGS-616-C

description:
UGS-616
Oxford Nanopore Technologies MinION Mk 1B

value: Atypical teratoid/rhabdoid tumour

value: ATRT, SHH

value: MCF ATRT


title: WT_0_rep3

value: WT


title: UGS-618-B


title: UGS-604-D

description:
UGS-604
Oxford Nanopore Technologies MinION Mk 1B

value: CNS neuroblastoma with FOXR2 activation

value: CNS NB, FOXR2


title: UGS-618-A


title: UGS-618-D


title: UGS-604-B


title: UGS-603-C

description:
UGS-603
Oxford Nanopore Technologies MinION Mk 1B


title: UGS-619-B


title: UGS-603-B


title: UGS-616-D


title: UGS-616-A


title: UGS-603-D


title: UGS-604-A


title: UGS-195-T2-A

description:
UGS-195-T2
Oxford Nanopore Technologies MinION Mk 1B

value: ATRT, MYC


title: UGS-603-A


title: UGS-096-A

description:
UGS-096
Oxford Nanopore Technologies MinION Mk 1B

value: Embryonal tumour with multilayered rosettes, C19MC-altered

value: ETMR


title: UGS-096-C

value: brain tumor tissue


title: UGS-195-T2-D


title: UGS-096-B


title: MB-680-D

description:
MB-680
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, NOS

value: MB, SHH INF

value: MCF MB SHH


title: UGS-195-T2-C


title: UGS-604-C


title: MB-680-A


title: MSCs #2+IFN-γhigh AML [331]

description: Gene expression data from MSCs after 24h of culture with IFN-γhigh AML cells

value: mesenchymal stromal cell (MSC)

value: IFN-γIFN-γhigh AML cells


title: MB-683

description:
MB-683
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, WNT-activated

value: MB, WNT


title: UGS-096-D


title: MB-680-B

value: MCF GBM


title: UGS-616-B

value: Atypical teratoid/rhabdoid tumour

value: ATRT, SHH


title: MB-680-C

value: MB, SHH CHL AD


title: MB-416-A

description:
MB-416
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, SHH-activated


title: INI-205-A

description:
INI-205
Oxford Nanopore Technologies MinION Mk 1B

value: ATRT, TYR

value: MCF ATRT


title: UGS-234-A

description:
UGS-234
Oxford Nanopore Technologies MinION Mk 1B

value: Pleomorphic xanthoastrocytoma

value: PXA


title: MB-585-A

description:
MB-585
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Medulloblastoma, genetically defined, non-WNT/non-SHH

value: MB, G3

value: MCF MB G3G4


title: FB24_4_rep1

description: Sample taken at time=4min after Rifampicin addition

value: WT

value: iron stress


title: INI-205-C


title: INI-205-B


title: INI-205-D


title: DX-BLN-039

description:
DX-BLN-039
Oxford Nanopore Technologies MinION Mk 1B

value: Meningothelial meningioma

value: MNG


title: DX-BLN-032

description:
DX-BLN-032
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK II

value: MCF GBM


title: DX-BLN-035

description:
DX-BLN-035
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-022

description:
DX-BLN-022
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: UGS-195-T2-B

value: Atypical teratoid/rhabdoid tumour

value: ATRT, MYC


title: DX-BLN-033

description:
DX-BLN-033
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse astrocytoma, IDH-mutant

value: A IDH

value: MCF IDH GLM


title: DX-BLN-013

description:
DX-BLN-013
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: GBM, MES


title: DX-BLN-023

description:
DX-BLN-023
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-008

description:
DX-BLN-008
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-mutant

value: A IDH, HG


title: DX-BLN-038

description:
DX-BLN-038
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-001

description:
DX-BLN-001
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_8764_20210302_BC02

description:
B2021_8764
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma


title: DX-BLN-003

description:
DX-BLN-003
Oxford Nanopore Technologies MinION Mk 1B

value: Angiomatous meningioma


title: DX-BLN-012

description:
DX-BLN-012
Oxford Nanopore Technologies MinION Mk 1B

value: Meningothelial meningioma


title: B2021_8598_20210301_BC01

description:
B2021_8598
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma TSH producing

value: MNG


title: DX-BLN-010

description:
DX-BLN-010
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype


title: B2021_861_20210111_BC05

description:
B2021_861
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II

value: MCF GBM


title: B2021_8694_20210302_BC07

description:
B2021_8694
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_7824_20210223_BC04

description:
B2021_7824
Oxford Nanopore Technologies MinION Mk 1B

value: Pleomorphic xanthoastrocytoma


title: B2021_8457_20210301_BC06

description:
B2021_8457
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_7196_20210219_BC04

description:
B2021_7196
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_8105_20210225_BC05

description:
B2021_8105
Oxford Nanopore Technologies MinION Mk 1B

value: Adamantinomatous Craniopharyngioma

value: CPH, ADM


title: B2021_8178_20210225_BC05

description:
B2021_8178
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Rosette-forming glioneuronal tumor

value: LGG, RGNT


title: B2021_5831_20210210_BC12

description:
B2021_5831
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_571_20210107_BC12

description:
B2021_571
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_5317_20210205_BC03

description:
B2021_5317
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_5951_20210211_BC01

description:
B2021_5951
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_5184_20210205_BC11

description:
B2021_5184
Oxford Nanopore Technologies MinION Mk 1B

value: Subependymoma

value: SUBEPN, ST


title: DX-BLN-015

description:
DX-BLN-015
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: B2021_52000_20211202_BC07

description:
B2021_52000
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma


title: DX-BLN-006

description:
DX-BLN-006
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_51258_20211129_BC08

description:
B2021_51258
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_50496_20211123_BC11

description:
B2021_50496
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_50078_20211122_BC05

description:
B2021_50078
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_49812_20211118_BC07

description:
B2021_49812
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_49460_20211117_BC08

description:
B2021_49460
Oxford Nanopore Technologies MinION Mk 1B

value: Ependymoma

value: EPN, PF B


title: B2021_48700_20211112_BC11

description:
B2021_48700
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype


title: B2021_4815_20210203_BC10

description:
B2021_4815
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2021_48459_20211112_BC10

description:
B2021_48459
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_47909_20211109_BC08

description:
B2021_47909
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II

value: MCF GBM


title: B2021_47653_20211108_BC07

description:
B2021_47653
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_6762_20210217_BC03

description:
B2021_6762
Oxford Nanopore Technologies MinION Mk 1B

value: MNG


title: B2021_46850_20211103_BC05

description:
B2021_46850
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2021_46408_20211101_BC04

description:
B2021_46408
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_46134_20211029_BC08

description:
B2021_46134
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_50803_20211124_BC10

description:
B2021_50803
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_45299_20211026_BC02

description:
B2021_45299
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2021_4639_20210202_BC01

description:
B2021_4639
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-018

description:
DX-BLN-018
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH

value: MCF IDH GLM


title: B2021_45073_20211025_BC08

description:
B2021_45073
Oxford Nanopore Technologies MinION Mk 1B

value: PITAD, ACTH


title: B2021_450_20210107_BC03

description:
B2021_450
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma ACTH producing


title: B2021_45027_20211022_BC04

description:
B2021_45027
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: B2021_44634_20211021_BC07

description:
B2021_44634
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_45490_20211027_BC07

description:
B2021_45490
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma


title: B2021_48744_20211115_BC10

description:
B2021_48744
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma


title: B2021_46157_20211029_BC01

description:
B2021_46157
Oxford Nanopore Technologies MinION Mk 1B

value: Adamantinomatous Craniopharyngioma


title: B2021_44422_20211020_BC02

description:
B2021_44422
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype


title: B2021_44807_20211021_BC03

description:
B2021_44807
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_43926_20211018_BC09

description:
B2021_43926
Oxford Nanopore Technologies MinION Mk 1B

value: Haemangioblastoma

value: EFT, CIC


title: B2021_43912_20211018_BC03

description:
B2021_43912
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_48294_20211111_BC02

description:
B2021_48294
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II

value: MCF GBM


title: B2021_42775_20211011_BC06

description:
B2021_42775
Oxford Nanopore Technologies MinION Mk 1B

value: MNG


title: B2021_4325_20210202_BC09

description:
B2021_4325
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: A IDH, HG


title: B2021_47316_20211105_BC12

description:
B2021_47316
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_48189_20211110_BC09

description:
B2021_48189
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_47329_20211105_BC06

description:
B2021_47329
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_42311_20211006_BC12

description:
B2021_42311
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_41351_20210929_BC04

description:
B2021_41351
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_41975_20211003_BC05

description:
B2021_41975
Oxford Nanopore Technologies MinION Mk 1B

value: Chordoma

value: CHORDM


title: B2021_42579_20211008_BC02

description:
B2021_42579
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2021_41958_20211003_BC09

description:
B2021_41958
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: O IDH

value: MCF IDH GLM


title: FB24_0_rep2

description: Sample taken at time=0 before Rifampicin addition

value: WT

value: iron stress


title: B2021_41094_20210928_BC06

description:
B2021_41094
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: B2021_41182_20210929_BC03

description:
B2021_41182
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH


title: B2021_3989_20210203_BC02

description:
B2021_3989
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK II


title: B2021_40803_20210927_BC05

description:
B2021_40803
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_38521_20210913_BC09

description:
B2021_38521
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Schwannoma

value: SCHW


title: B2021_40820_20210927_BC01

description:
B2021_40820
Oxford Nanopore Technologies MinION Mk 1B

value: MCF GBM


title: B2021_3913_20210128_BC12

description:
B2021_3913
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2021_38668_20210913_BC07

description:
B2021_38668
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_37917_20210908_BC08

description:
B2021_37917
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_37918_20210907_BC02

description:
B2021_37918
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_38888_20210914_BC04

description:
B2021_38888
Oxford Nanopore Technologies MinION Mk 1B

value: MCF IDH GLM


title: B2021_39160_20210916_BC03

description:
B2021_39160
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_38879_20210914_BC08

description:
B2021_38879
Oxford Nanopore Technologies MinION Mk 1B

value: Central neurocytoma

value: CN


title: B2021_37457_20210906_BC09

description:
B2021_37457
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma densely granulated GH/STH producing

value: PITAD, STH DNS B


title: B2021_37013_20210902_BC04

description:
B2021_37013
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_36444_20210830_BC05

description:
B2021_36444
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_37639_20210906_BC07

description:
B2021_37639
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_3470_20210127_BC02

description:
B2021_3470
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_37405_20210903_BC03

description:
B2021_37405
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma

value: LGG, PA/GG ST


title: B2021_34009_20210811_BC01

description:
B2021_34009
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: B2021_36326_20210827_BC04

description:
B2021_36326
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK II


title: B2021_36070_20210826_BC06

description:
B2021_36070
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2021_36882_20210901_BC06

description:
B2021_36882
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_35699_20210825_BC05

description:
B2021_35699
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_3354_20210126_BC06

description:
B2021_3354
Oxford Nanopore Technologies MinION Mk 1B

value: Adamantinomatous Craniopharyngioma

value: PLEX, PED B

value: MCF PLEX T


title: B2021_30640_20210720_BC07

description:
B2021_30640
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I

value: MCF GBM


title: B2021_29912_20210715_BC11

description:
B2021_29912
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2021_30398_20210719_BC06

description:
B2021_30398
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_29729_20210714_BC04

description:
B2021_29729
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2021_29313_20210712_BC02

description:
B2021_29313
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2021_29484_20210716_BC05

description:
B2021_29484
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_38135_20210909_BC07

description:
B2021_38135
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_29659_20210714_BC07

description:
B2021_29659
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_28027_20210701_BC07

description:
B2021_28027
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma

value: LGG, PA MID

value: MCF PA


title: B2021_28885_20210707_BC12

description:
B2021_28885
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_27818_20210630_BC09

description:
B2021_27818
Oxford Nanopore Technologies MinION Mk 1B

value: Subependymal giant cell astrocytoma

value: GBM, RTK II


title: B2021_28670_20210706_BC11

description:
B2021_28670
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Glioblastoma, IDH-wildtype


title: B2021_24695_20210614_BC05

description:
B2021_24695
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_27611_20210630_BC08

description:
B2021_27611
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma densely granulated GH/STH producing

value: PITAD, STH DNS B


title: B2021_29312_20210712_BC09

description:
B2021_29312
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma ACTH producing

value: PITAD, ACTH


title: B2021_21552_20210525_BC05

description:
B2021_21552
Oxford Nanopore Technologies MinION Mk 1B

value: MCF GBM


title: B2021_21450_20210521_BC06

description:
B2021_21450
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: B2021_22205_20210528_BC07

description:
B2021_22205
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: O IDH

value: MCF IDH GLM


title: B2021_20295_20210517_BC08

description:
B2021_20295
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2021_26685_20210623_BC03

description:
B2021_26685
Oxford Nanopore Technologies MinION Mk 1B

value: Ependymoma

value: EPN, PF A


title: B2021_2548_20210121_BC05

description:
B2021_2548
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_20790_20210519_BC07

description:
B2021_20790
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_24561_20210611_BC04

description:
B2021_24561
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_20143_20210514_BC09

description:
B2021_20143
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2021_23956_20210609_BC02

description:
B2021_23956
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2021_21728_20210528_BC04

description:
B2021_21728
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype


title: B2021_19139_20210507_BC08

description:
B2021_19139
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_1901_20210115_BC03

description:
B2021_1901
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse leptomeningeal glioneuronal tumour

value: DLGNT


title: B2021_27536_20210824_BC12

description:
B2021_27536
Oxford Nanopore Technologies MinION Mk 1B

value: PXA


title: B2021_19285_20210510_BC12

description:
B2021_19285
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_2123_20210118_BC04

description:
B2021_2123
Oxford Nanopore Technologies MinION Mk 1B

value: Medulloblastoma, genetically defined, group 3

value: MB, G3

value: MCF MB G3G4


title: B2021_28275_20210702_BC01

description:
B2021_28275
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_17585_20210428_BC01

description:
B2021_17585
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted

value: O IDH

value: MCF IDH GLM


title: B2021_16905_20210426_BC06

description:
B2021_16905
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma sparsely granulated GH/STH producing

value: PITAD, STH SPA


title: B2021_16667_20210422_BC05

description:
B2021_16667
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II

value: MCF GBM


title: B2021_23493_20210607_BC01

description:
B2021_23493
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2021_26903_20210624_BC02

description:
B2021_26903
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK I


title: B2021_1658_20210114_BC10

description:
B2021_1658
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2021_16307_20210421_BC11

description:
B2021_16307
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_15570_20210416_BC08

description:
B2021_15570
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_24089_20210609_BC03

description:
B2021_24089
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_17506_20210428_BC09

description:
B2021_17506
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_16412_20210421_BC10

description:
B2021_16412
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_1269_20210113_BC09

description:
B2021_1269
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2021_14738_n2_20210412_BC02

description:
B2021_14738
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_13523_20210330_BC03

description:
B2021_13523
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_15916_20210419_BC09

description:
B2021_15916
Oxford Nanopore Technologies MinION Mk 1B

value: Adamantinomatous Craniopharyngioma

value: CPH, PAP


title: B2021_15024_20210413_BC03

description:
B2021_15024
Oxford Nanopore Technologies MinION Mk 1B

value: Anaplastic astrocytoma, IDH-mutant

value: A IDH


title: B2021_14664_n_20210412_BC07

description:
B2021_14664
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_13049_20210329_BC04

description:
B2021_13049
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma ACTH producing

value: PITAD, ACTH


title: B2021_1205_20210112_BC11

description:
B2021_1205
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, MES


title: B2021_11239_20210317_BC09

description:
B2021_11239
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_10847_20210315_BC08

description:
B2021_10847
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_19783_20210511_BC05

description:
B2021_19783
Oxford Nanopore Technologies MinION Mk 1B

value: A IDH, HG

value: MCF IDH GLM


title: B2021_14095_20210407_BC05

description:
B2021_14095
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2021_14259_20210408_BC01

description:
B2021_14259
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, RTK II

value: MCF GBM


title: B2021_10206_20210310_BC12

description:
B2021_10206
Oxford Nanopore Technologies MinION Mk 1B

value: Pilocytic astrocytoma

value: LGG, PA/GG ST


title: B2021_10204_20210310_BC01

description:
B2021_10204
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma densely granulated GH/STH producing

value: PITAD, STH DNS B


title: B2021_14258_20210408_BC06

description:
B2021_14258
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_980_20200113_BC07

description:
B2020_980
Oxford Nanopore Technologies MinION Mk 1B

value: Haemangioblastoma

value: HMB


title: B2020_9037_20200304_BC05

description:
B2020_9037
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2021_11830_20210322_BC12

description:
B2021_11830
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma gonadotropin producing

value: PITAD, FSH LH


title: B2021_13763_20210401_BC04

description:
B2021_13763
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2021_10463_20210311_BC06

description:
B2021_10463
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_10710_20210312_BC01

description:
B2021_10710
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: B2021_10368_20210311_BC05

description:
B2021_10368
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue


title: B2020_8129_20200227_BC12

description:
B2020_8129
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_10681_20210312_BC07

description:
B2021_10681
Oxford Nanopore Technologies MinION Mk 1B


title: B2021_11767_20210319_BC11

description:
B2021_11767
Oxford Nanopore Technologies MinION Mk 1B

value: Chordoma

value: CHORDM


title: B2021_10052_20210310_BC04

description:
B2021_10052
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_7057_20200220_BC03

description:
B2020_7057
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_6827_20200219_BC01

description:
B2020_6827
Oxford Nanopore Technologies MinION Mk 1B

value: Embryonal tumour with multilayered rosettes, C19MC-altered

value: ETMR


title: B2020_7005_20200219_BC02

description:
B2020_7005
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_8101_20200228_BC02

description:
B2020_8101
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-wildtype

value: GBM, MES

value: MCF GBM


title: B2020_8347_20200227_BC01

description:
B2020_8347
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_4916_20200205_BC04

description:
B2020_4916
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_6437_20200218_BC09

description:
B2020_6437
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK II


title: B2020_7605_20200221_BC04

description:
B2020_7605
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse astrocytoma, IDH-mutant

value: A IDH

value: MCF IDH GLM


title: B2020_6589_20200218_BC10

description:
B2020_6589
Oxford Nanopore Technologies MinION Mk 1B

value: GBM, RTK I


title: B2020_537_20200109_BC06

description:
B2020_537
Oxford Nanopore Technologies MinION Mk 1B

value: Glioblastoma, IDH-mutant

value: A IDH, HG


title: B2020_48360_20201214_BC10

description:
B2020_48360
Oxford Nanopore Technologies MinION Mk 1B

value: Meningioma

value: MNG


title: B2020_49334_20201221_BC11

description:
B2020_49334
Oxford Nanopore Technologies MinION Mk 1B

value: brain tumor tissue

value: Pituitary adenoma densely granulated GH/STH producing

value: PITAD, TSH


title: B2020_46487_20201201_BC03

description:
B2020_46487
Oxford Nanopore Technologies MinION Mk 1B

value: Diffuse large B cell lymphoma (DLBCL)

value: LYMPHO


title: B2020_48957_20201217_BC03

description:
B2020_48957
Oxford Nanopore Technologies MinION Mk 1B

value: Pituitary adenoma ACTH producing

value: PITAD, ACTH


title: B2020_48011_20201211_BC10

description:
B2020_48011
Oxford Nanopore Technologies MinION Mk 1B


title: B2020_46582_20201202_BC08

description:
B2020_46582
Oxford Nanopore Technologies MinION Mk 1B

value: Schwannoma

value: SCHW


title: B2020_45551_20201125_BC05

description:
B2020_45551
Oxford Nanopore Technologies MinION Mk 1B

value: Ependymoma

value: EPN, MPE


title: B2020_4661_20200204_BC02_FLO

description:
B2020_4661
Oxford Nanopore Technologies MinION Mk 1B