title: CD8+ CAR-T cell, Blimp-1 KO, Donor 31

city: Barcelona

first: David

middle: F.

last: Moreno

state: Barcelona

address: Villarroel 170

department: Hematology

country: Spain

institute: IDIBAPS - Hospital Clínic de Barcelona

data_processing:
fastqc (v.0.12.1) and trim-galore (v.0.6.10) were used to perform quality control and adaptor trimming of the FASTQ files.
Trimmed reads were then mapped to the human reference genome (GRCh38) using kallisto (v0.48.0) with standard parameters.
DESeq2 (v.1.42.0) was used to perform normalisation and differential expression analyses between Blimp-1 KO and Mock gene sets.
Assembly: GRCh38
Supplementary files format and content: Raw read counts for each sample and gene are included in a tab-delimited text file.

source_name: CD8+ T cells

growth_protocol: Human T cells activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher Scientific) for 24 hours were transduced with a lentivirus containing an anti-BCMA CAR gene (ARI0002h). Three days later (day 4),     cells were electroporated to introduce Cas9 alone (Mock cells) or an RNP complex containing Cas9 and a Prdm1-targeting single guide RNA. Cells were cultured in T cell media (47.5% Click’s media (Irving Scientific), 47.5% RPMI-1640, 5% human serum, 2 mM L-glutamine, 100 IU/ml penicillin and 100 µg/ml streptomycin) supplemented with 10 ng/ml IL-15 (Miltenyi Biotech).

extract_protocol:
CD8+ cells were purified following the 4 co-cultures of Mock or Blimp-1 KO CAR-T cells and ARP-1-GFP-ffLuc cells using an EasySep Human CD8 Positive Selection kit (STEMCELL Technologies). Cell pellets were frozen and stored at -80ºC and isolation efficiency was confirmed by flow cytometry. Total RNA was extracted from the cell pellets using an RNeasy Mini kit (Qiagen) and subject to paired-end mRNA sequencing using the NovaSeq 6000 platform (Illumina) at a minimum of 30 million reads per sample.
Libraries were prepared according to Illumina instructions.

treatment_protocol: CAR-T cells were stimulated with the multiple myeloma cell line ARP-1 for a total of four times. Each stimulation was 48 hours.

value: CD8+ T cells

value: Prdm1 knockout

value: ARP-1 stimulated

tag: biological replicate

value: Donor 31


title: Hfx. mediterranei cells, rosR deletion strain, immunoprecipitation, rep2

status: Public on Nov 20 2024

type: SRA

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

country: USA

institute: Duke University

library_source: genomic

data_processing:
50 bp reads were assessed for quality using FastQC and adapter sequences trimmed using Trim Galore and Cutadapt. Resultant reads were mapped to the Hfx. mediterranei ATCC3500 (assembly ASM30676v2; NCBI accession GCF_000306765.2) or Hfx. volcanii DS2 genome (ASM2568v1; GCF_000025685.1) using Bowtie2.
Sorting of mapped sequences was conducted using samtools. Sites of significant RosR binding enrichment were called using the MOSAiCS peak-calling package [REF] with sorted bam files as input. MOSAiCS parameters included fragment length (fragLen) 200, cap 0, PET false, analysis type IO, background estimate rMOM, FDR 0.01.
Using the DiffBind R package, peaks were considered reproducible if 100 bp of the reads in the peak overlapped across three of four biological replicate experiments. Using the GenomicRanges and IRanges R packages, a given peak was associated with a given genomic feature (gene or promoter region) if the they overlapped by 100 bp. Peaks that fell entirely inside promoter regions were associated with the nearest gene within 500 bp.
Peak-to-gene associations were then annotated using the corresponding NCBI genome annotation within the GenomicFeatures R package.
Assembly: Hfx. mediterranei ATCC3500 (assembly ASM30676v2; NCBI accession GCF_000306765.2); Hfx. volcanii DS2 genome (ASM2568v1; GCF_000025685.1)
Supplementary files format and content: sorted bam files

molecule: genomic DNA

organism: Haloferax mediterranei ATCC 33500

source_name: archaeal cells

growth_protocol: Each Hfx. strain (parental ΔpyrE and RosR::HA tagged) was grown in quadruplicate (ChIP-seq) in 50 mL rich medium until mid- to late-exponential phase (OD600 ~0.5-1.0).

extract_protocol:
chromatin immunoprecipitation (ChIP) and DNA extraction was conducted as previously described (Martinez Pastor M. et al., 2017).
For ChIP-seq, Libraries were constructed using the KAPA Hyper Prep kit using Illumina TruSeq adapters. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent).
Samples for each species were multiplexed according to the adapter mixtures and pooled. Each pool was run on a single lane on an Illumina HiSeq 4000 instrument by the Duke Sequencing and Genomics Techonology core facility

treatment_protocol: Crosslinking was performed by adding 37% formaldehyde (CH2O) for 20 min at room temperature.

tag: tissue

value: archaeal cells

tag: cell line

tag: cell type

tag: genotype

value: {delta}pyrE HMErosR::HA

tag: treatment

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: 176, S, day 120, biol repl 1, run 1

city: Vienna

first: Julia

last: Naas

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: 10x Genomics

library_source: transcriptomic

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

molecule: total RNA

organism: Homo sapiens

source_name: brain organoid tissue

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

tag: Sex

value: female

tag: time

value: day 120

value: striatum protocol (S)


title: Sf3b4 homozygous null embryo (rep 1)

city: Montreal

first: Loydie

last: Jerome-Majewska

state: QC

address: 1001 Decarie Blvd EM0.2210

department: Pediatrics

country: Canada

institute: McGill University Health Centre Glen Site

data_processing:
bcbio nextgen 1.2.9
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: embryo head

extract_protocol:
RNA was extracted using RNAesay micro kit (Qiagen) according to manufacturer's protocol
libraries were constructed using TruSeq Standard Total RNA sample preparation kit (Illumina) according to manufacturer's protocol

value: embryo head

value: Sf3b4 NCC mutant

tag: age


title: 176, M, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16

value: midbrain protocol (M)


title: Hfx. mediterranei cells, rosR deletion strain, whole cell extract control, rep2.


title: CD8+ CAR-T cell, WT, Donor 31

value: WT


title: 176, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: dorsal protocol (D)


title: CD8+ CAR-T cell, WT, Donor 30

value: CD8+ T cells

value: Donor 30


title: CD8+ CAR-T cell, Blimp-1 KO, Donor 30

value: Prdm1 knockout

value: ARP-1 stimulated


title: Sf3b4 wild type embryo (rep 3)


title: Hfx. mediterranei cells, rosR deletion strain, immunoprecipitation, rep1

value: archaeal cells

value: {delta}pyrE HMErosR::HA


title: Hfx. mediterranei cells, rosR deletion strain, whole cell extract control, rep1.

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: CD8+ CAR-T cell, Blimp-1 KO, Donor 29

value: Donor 29


title: 176, D, day 80, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 80


title: Hfx. mediterranei cells, pyrE control, immunoprecipitation.

value: {delta}pyrE


title: CD8+ CAR-T cell, WT, Donor 29


title: Sf3b4 wild type embryo (rep 2)

value: embryo head


title: CD8+ CAR-T cell, Blimp-1 KO, Donor 28

value: Donor 28


title: 176, D, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: Sf3b4 wild type embryo (rep 1)

value: WT


title: IgG REP

city: BEIJING

address: Malianwa street

country: China

institute: China Agriculture University

data_processing:
After the raw data is obtained, the raw data is filtered first to obtain high-quality clean data, and the clean data is compared to the reference genome of the project species, and then the whole-genome peak calling is performed on the results. The binding preference of proteins on RNA was studied, and the binding sites were analyzed by motif.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: LACE-seq

source_name: islet

extract_protocol: Explore RNA directly bound by PARN

value: islet

tag: lace antibody


title: 176, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: day 25

value: dorsal protocol (D)


title: Hfx. mediterranei cells, pyrE control, whole cell extract control.


title: PARN REP2


title: 176, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: PARN REP1


title: Haloferax mediterranei cells, rosR deletion strain, rep4

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hfx_rosR_4

data_processing:
RNA-seq data were processed using the fastp toolkit (Chen et al., 2018) to trim low-quality bases and sequencing adapters from the 3’ end of reads.
STAR (Dobin et al., 2013) RNA-seq alignment tool was used to map trimmed reads to the genome of Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively). Reads aligning to a single genomic location were summarized across genes.
For genes having an overlap of at least 10 reads, gene counts were normalized and differential expression was carried out using the DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package implemented for the R programming environment. Consistent with the recommendation of the DESeq authors, independent filtering (Ignatiadis et al., 2016) was utilized prior to calculating adjusted p-values (Benjamini Y, 1995) and moderated log2 fold-changes were derived using the ashr package (Stephens, 2017). Genes were considered significantly differentially expressed if the log2 fold change ratio (∆rosR : parent) was >= |1| and adjusted p-value < 0.05.
Assembly: Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively).
Supplementary files format and content: Hfx. mediterranei assembly ASM540632v1 refseq ID = GCF_005406325.1; Hfx. volcanii assembly ASM2568v1 refseq ID = GCF_000025685.1

molecule: polyA RNA

growth_protocol: Hm∆rosR, Hv∆rosR, and corresponding parent strain cultures were grown in biological triplicate in rich medium to mid-exponential phase.

extract_protocol:
RNA was extracted using an Absolutely RNA Miniprep kit according to manufacturer instructions (Agilent, Santa Clara, CA). RNA quality was measured using RNA 6000 Nano kit on a 2100 Bioanalyzer (Aglient, Santa Clara, CA). PCR to verify lack of DNA contamination was  conducted on 300 ng of RNA sample using species-specific primers listed in Supplementary Table S2. Ribosomal RNA depletion was performed from 300 ng of each sample using NEBNextR RNA Depletion Core Reagent (#E7870 New England Biolabs) according to the manufacturer instructions. The resultant mRNA was purified using NEBNext RNA sample purification beads and eluted in 7 l of nuclease-free water. 1l of each sample was used for quantification and quality verification (free of rRNA) in a second round of Agilent Bioanalyzer analysis using 2100 Prokaryote Total RNA Nano kit (Aglient, Santa Clara, CA).
Libraries were constructed using 5 ml of mRNA using the Ultra II Directional RNA Library Preparation Kit (Agilent, Santa Clara. CA). Indexes were designed according to the kit specifications and obtained from Integrated DNA Technologies. Resultant libraries were tested for quality and quantity by Bioanalyzer using the 2100 expert High Sensitivity DNA Assay chip (Agilent Technologies)

value: archaeal cells

value: deltapyrEdeltaHFXrosR

value: standard growth medium, knockout strain


title: Haloferax mediterranei cells, rosR deletion strain, rep3

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hfx_rosR_3


city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

data_processing:
*library strategy: iCLIP2
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcodes.fasta (using sample barcodes: YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep1: NNNNNCGTGATNNNN, YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep2: NNNNNACATCGNNNN, YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep3: NNNNNGCCTAANNNN, YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep4: NNNNNTGGTCANNNN, YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep1: NNNNNCACTGTNNNN, YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep2: NNNNNATTGGCNNNN, YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep3: NNNNNGATCTGNNNN, YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep4: NNNNNCGAAACNNNN)
Mapping: STAR (v2.7.3a) with non-default parameters: --genomeDir Gencode_release31_GRCh38.p12 --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with non-default parameter: umi_tools dedup --method unique
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Peak calling was done on merged samples from STM2457 treatment and control using PureCLIP (v1.3.1, refxx) with default parameters.
Assembly: GRCh38.p12
Supplementary files format and content: bigWig (crosslink events per nucleotide)
Supplementary files format and content: bed (binding sites)

growth_protocol: HEK293T cells were grown and cultured in DMEM supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin and were incubated at 37 °C with 5% CO2.

extract_protocol:
In vivo iCLIP2 for YTHDF2 was performed as described before (Buchbender, A. et al 2020). Briefly, HEK293T cells treated with DMSO or STM2457 for 12 h were irradiated with 150 mJ/cm2 in a UV-C crosslinker (CL‑1000 Ultraviolet Crosslinker, UVP) at 254 nm. Crosslinked cells were lysed and RNA was digested to create 50–200 nt long fragments. YTHDF2 protein immunoprecipitation was performed with an YTHDF2-specific antibody (AVIVA SYSTEMS BIOLOGY, ARP67917_P050) conjugated to protein A beads. Protein-RNA complexes were visualized using 5' end radioactive labelling of the precipitated RNA, followed by SDS-PAGE and transfer to a nitrocellulose membrane. Protein-RNA complexes were recovered from the membrane and treated by proteinase K to get protein-free RNA.
cDNA was generated by reverse transcription, with termination occurring at the crosslinked site, thereby generating truncated cDNAs. MyONE beads were used to clean cDNA twice and the library was subsequently subjected to PCR amplification and ProNex size selection for amplification and purification, respectively. iCLIP libraries were sequenced on an Illumina NextSeq 500 sequencing device with 77 nt single-end reads

treatment_protocol: m6A depletion was performed by adding medium supplemented with 20 µM STM2457 in DMSO 0.2% (v/v) or with DMSO 0.2% (v/v) alone as control for 12 h.

tag: chip antibody

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P057

value: Human embryonic kidney 293T cell line


title: Cko3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Trizol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: CKO


title: Haloferax mediterranei cells, rosR deletion strain, rep2

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hfx_rosR_2


title: Haloferax mediterranei cells, rosR deletion strain, rep1

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hfx_rosR_1


title: Cko2


title: Input_AML2_sgPCGF1_DMSO

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

data_processing:
All sequencing reads were mapped to the human genome (hg38) using the Bowtie2 (v2.2.3), and reads with a mapping score > 20 were selected for data analysis with PCR duplicated reads removed by Picardtools (v2.27.0). MACS2 (v2.2.7.0) was used to call ChIP-seq peaks with input as controls using default parameters in paired-end mode. Bigwig files were generated by bamCoverage and used for visualization in Integrative Genomics Viewer (IGV).
Assembly: hg38
Supplementary files format and content: bw

source_name: cell line

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Briefly, 20-50 million cells were cross-linked by formaldehyde (1%) and then quenched with 0.125 M glycine. After washing with cold PBS, cells were suspended in lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor cocktail) and subjected to sonication to shear the chromatin DNA into sizes ranging from 200 to 500 bp. After centrifugation, the supernatant was incubated with primary antibody and Protein A/G Dynabeads magnetic beads (Invitrogen) at 4°C overnight. After six times wash with RIPA wash buffer (50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-Deoxycholate) and one time wash with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, and 50 mM NaCl), chromatin was eluted from beads in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After reverse crosslinking, ChIP DNA was purified using a DNA clean-up kit (Zymo Research).
NEBNext Ultra II Library Prep kit was used for library preparation. ChIP libraries were sequenced on the NovaSeq PE150 platform.

treatment_protocol: Cells were treated with DMSO or VTP50469 (1µM) for 6 days.

value: cell line

value: Acute myeloid leukemia cells


title: YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep2

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P055


title: Cko1


title: Input_AML2_sgLuc_VTP50469


title: YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep3

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P056


title: Haloferax mediterranei cells, pyrE parent control strain, rep2

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hfx_pyrE_2

value: deltapyrE

value: standard growth medium, control strain


title: Ctrl3

value: Ctrl


title: AML2_sgPCGF1_VTP50469_Menin

value: anti-Menin(BETHYL, A300-105A)


title: YTHDF2 iCLIP2, HEK293T, STM2457, 12h, rep1

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P054

value: WT


title: Input_AML2_sgLuc_DMSO


title: YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep4

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P053

value: DMSO 12h


title: 176, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 13

value: dorsal protocol (D)


title: AML2_sgPCGF1_VTP50469_H2AK119ub

value: cell line

value: anti-H2AK119ub(Proteintech, 8240S)


title: CD8+ CAR-T cell, WT, Donor 28

value: CD8+ T cells

value: ARP-1 stimulated

value: Donor 28


title: dcm-/dam- lambda phage DNA, M.SssI, bisulfite treated

city: Munich

first: Raheleh

last: Salehi

state: Bavaria

address: Würmtalstraße 201

department: Chemisty

institute: LMU

data_processing:
Paired-end reads from bisulfite sequencing were processed using Bismark(v0.24.2). Briefly, the reference genome was prepared with bismark_genome_preparation, read were trimmed, and aligned to create methylation bam files. The methylation frequency of each CpG was extracted using bismark_methylation_extractor. Refer to the manuscript for further details.
Assembly: GCF_000840245.1_ViralProj14204_genomic
Supplementary files format and content: BS_LMD.txt and BS_LMD_mdC.txt files represent Bismark methylation text providing the methylation frequency of individual CpG positions, tab delimited, 1-based coords.
Supplementary files format and content: BS_LMD.bedGraph and BS_LMD_mdC.bedGraph provide DNA methylation levels of individual CpG positions in common bedGraph format, tab-delimited, 0-based start, 1-based end coords.

organism: Escherichia phage Lambda

source_name: phage

extract_protocol: The Whole-genome Bisulfite Sequencing (WGBS) libraries were prepared as follows. For A-tailing, 200 ng sheared DNA (~ 300 bp) in 25 µl ddH2O (MilliQ), 3.5 µl NEBNext Ultra II End Prep Reaction Buffer (NEB, cat. no. E7546L) and 1.5 µl NEBNext Ultra II End Prep Enzyme Mix (NEB, cat. no. E7546L) were mixed by pipetting and incubated at 20°C for 30 min. The reaction was inactivated by incubating at 65°C for 30 min. Subsequently, the DNA was purified with 1.8x MagMAX™ Pure Bind beads (ThermoFisher, cat. no. A58522) and the DNA was eluted at 37°C in 16 µl prewarmed (at 50°C) ddH2O (MilliQ) for 5 min. For adapter ligation, 15 µl A-tailed DNA, 2 µl 10x T4 DNA Ligase Buffer (NEB, cat. no. B0202S), 1.5 µl T4 DNA Ligase 2,000 units/µl (NEB, cat. no. M0202M), 1 µl 10 mM ATP (NEB, cat. no. P0756S) and 0.5 µl 50 mM TruSeq Adapter (Microsynth) were mixed by pipetting and incubated at 16°C overnight. The finished ligation reaction was directly subjected to bisulfite treatment according to the manufacturer’s protocol using the EZ DNA Methylation-Gold™ Kit (Zymo Research, cat. no. D5005). The DNA was eluted on the bench in 15 µl prewarmed (55°C) M-Elution Buffer (Zymo Research) for 5 min.

value: phage


title: dcm-/dam- lambda phage DANN, bisulfite treated

value: Control


title: Haloferax mediterranei cells, pyrE parent control strain, rep1

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hfx_pyrE_1

value: archaeal cells

value: deltapyrE

value: standard growth medium, control strain


title: YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep3

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P052

value: Human embryonic kidney 293T cell line

value: WT


title: AML2_sgPCGF1_DMSO_Menin

value: Acute myeloid leukemia cells

value: anti-Menin(BETHYL, A300-105A)


title: Ctrl1

value: islet

value: Ctrl


title: YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep2

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P051

value: DMSO 12h


title: Input_AML2_sgPCGF1_VTP50469

value: cell line


title: KO-2

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent. 2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: strain

tag: developmental stage


title: AML2_sgPCGF1_DMSO_H2AK119ub

value: anti-H2AK119ub(Proteintech, 8240S)


title: YTHDF2 iCLIP2, HEK293T, DMSO, 12h, rep1

value: AVIVA SYSTEMS BIOLOGY, ARP67917_P050


title: KJ074_6420

type: RNA

city: Richmond

first: Kaitlyn

middle: G

last: Jackson

state: Virginia

address: 7414 Seminary Ave

department: Immunology

institute: VCU

description: WDSW-SphK2 KO

hyb_protocol: hybridization of sample to NanoString probes for 16h at 65C in hybridization buffer, according to the manufacturer instructions

scan_protocol: scanning completed by NanoString nCounter Digital Analyzer

data_processing: Raw counts processed using nSolver Analysis Software; data normalization to internal reference probes and background subtraction performed using Rosalind Software> partner recommended analysis, gene expression RCC (mRNA)

label: Nanostring metabolic panel barcode

source_name: Constitutive SphK2 KO

label_protocol: RNA target-specific barcoded probes

growth_protocol: Mice aged 12-18 weeks old were fed diet for 16 weeks prior to sacrifice

extract_protocol: Trizole method; total RNA diluted to 40ng/uL

treatment_protocol: diet feeding, ad libitum; see characteristics: Tag_ diet

tag: position

value: male

tag: diet

value: Western diet and sugar water

value: SphK2 KO

tag: genetic background

tag: age (days)

tag: diet duration (weeks)


title: KO-1


title: WT-1


title: AML2_sgLuc_VTP50469_H2AK119ub

tag: tissue


title: Ctrl2


title: KJ074_6407

description: CDNW-SphK2 KO

value: control diet and normal water


title: AML2_sgLuc_VTP50469_Menin

tag: cell line


title: AML2_sgLuc_DMSO_H2AK119ub

tag: cell type


title: KJ074_6551

description: WDSW-WT

source_name: Wild type control

tag: genotype


title: WT-2


title: RKO AVEN OE

city: Nanjing

first: liu

last: xin

address: Xianlin Road

institute: Nanjing University of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Colorectal cancer cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer cell

value: AVEN overexpression

value: RKO


title: HCT116 AVEN OE


title: 115_KO (NULL)

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCm38
Supplementary files format and content: Tab delimited file for raw hit counts per sample

source_name: hypothalamus

extract_protocol: The hypothalami were extracted from WT or NULL mice brains similarly to as described. The tissue was homogenized with a plastic tissue grinder in TRI Reagent RT (50-100 mg tissue per 1.0 ml TRI Reagent RT. Molecular Research Center Inc. Cincinnati OH). The homogenate was supplemented with 25 ml bromoanisole, covered and shook vigorously for 15 seconds; and centrifuged at 12,000g for 15 minutes at 4 C. The RNA was collected from the aqueous phase and transferred into a new centrifuge tube, precipitated with isopropanol, stored at room temperature for 10 minutes and then centrifuged for 12,000 g for 5 minutes at room temperature. The RNA white pellet was first washed with 75% ethanol and centrifuged at 6,000g for 5 minutes at room temperature; afterwards it was resuspended in dH2O. The RNA concentration was measured with a nanodrop and adjusted to a ~300ng/ml final concentration.

treatment_protocol: All experiments with mice performed in this study were approved by our institution's Animal Care and Use Committee (IACUC). Littermates of either sexes were randomly assigned (by flipping of a coin) to experimental groups. The animals were housed in an Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC)-approved vivarium, under the care of a veterinarian. The mice lived in large cages, with a 12 h light-dark cycle, and were fed ad libitum.

value: hypothalamus

value: post-mitotic


title: KJ074_6401

description: CDNW-SphK2 KO


title: AML2_sgLuc_DMSO_Menin

value: Acute myeloid leukemia cells

value: anti-Menin(BETHYL, A300-105A)


title: 11_NTG (WT)


title: 173_NTG (WT)


title: 14_KO (NULL)


title: HCT116 AVEN WT

value: AVEN wildtype


title: 15_KO (NULL)


title: KJ074_6123

description: WDSW-SphK2 KO


title: KJ074_6122

description: WDSW-SphK2 KO


title: KO_J_N

city: Jinan

first: bei

middle: Bei

last: Guo

address: Wenhua XiRoad No.44

institute: Shandong University

data_processing:
Raw data of fastq format were processed throuth in-house perlscripts
the mapped reads of each sample were assembled by StringTie in a reference-based approach
FeatureCounts v1.5.0-p3 was used to count the reas numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
differential expression analysis was performed using the DESeq2 R package
GO and KEGG were implemented by the clusterProfiler R package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: colon

extract_protocol:
colon adenoma and adjacent normal tissue were isolated from colon carefully and total RNA was harvested using Trizol reagent. NEBNextⓇ UltraTM RNA Library Prep KIT for IlluminaⓇ(NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNextⓇ UltraTM RNA Library Prep KIT for IlluminaⓇ(NEB, USA) following manufacturer's recommendations and index codes were added to attribure sequences to each sample

value: colon

value: 5 months

value: ApcMin/+; Cul4bdeltaIEC


title: A5NC

city: Zhengzhou

first: Liping

last: Dai

state: Henan

address: 40 Daxue Road

institute: Zhengzhou University

data_processing:
Basecalls performed using data collection software from Illumina
Purified libraries were quantified and validated by Qubit® 2.0 Fluorometer and Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration.
Cluster was generated by cBot after the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM).
Differential expression analysis for mRNA/lncRNA was performed using R package edgeR.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Tissue

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit（50）Qiagen
Following "TruSeq RNA Sample Preparation Guide".

value: lung

tag: patient diagnosis

value: Non-Small Cell Lung Cancer


title: KJ074_6501

description: WDSW-WT

tag: Sex

value: male

value: WT


title: KJ074_6503

description: WDSW-WT

value: Western diet and sugar water


title: A2NC


title: 10_NTG (WT)


title: KJ074_6398

description: CDNW-SphK2 KO

value: control diet and normal water

value: SphK2 KO


title: KJ074_6543

description: CDNW-WT


title: KJ074_6552

description: CDNW-WT


title: WT_J_N

value: ApcMin/+; Cul4bWT


title: A1NC


title: KO_4_N

value: 4 months


title: Haloferax volcanii cells, rosR deletion strain, rep4

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_4

organism: Haloferax volcanii DS2

value: archaeal cells

value: deltapyrEdeltaHVOrosR

tag: treatment

value: standard growth medium, knockout strain


title: Haloferax volcanii cells, rosR deletion strain, rep3

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_3


title: A5CA


title: Haloferax volcanii cells, pyrE parent control strain, rep4

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_4

value: deltapyrE

value: standard growth medium, control strain


title: A1CA


title: KO_3_N

value: colon

tag: age

value: 3 months


title: B4NC


title: B7NC


title: Haloferax volcanii cells, rosR deletion strain, rep1

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_1


title: A2CA


title: B7CA


title: WT_4_N


title: KO_4_T

value: ApcMin/+; Cul4bdeltaIEC


title: WT_J_T

value: 5 months


title: Haloferax volcanii cells, pyrE parent control strain, rep2

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_2


title: Haloferax volcanii cells, pyrE parent control strain, rep3

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_3


title: B4CA

value: lung

value: Non-Small Cell Lung Cancer


title: WT_4_T


title: KO_J_T


title: HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq rep2

description: imb_koenig_2022_10_17_HEK293T_YTHDF2_KD_STM_2

data_processing:
Quality control: FastQC (v0.11.8 [HEK293T 9h treatment], v0.11.9 [HEK293T 6h treatment, HEK293T YTHDF2 KD, HEK293T 2h DMSO/Emetine treatment])
Trimming [HEK293T 9h treatment]: Cutadapt (v1.18) with parameters: cutadapt -a file:NexteraPE-PE.fa --overlap=3 --minimum-length 50 --error-rate 0.1 (NexteraPE-PE.fa was used as provided here: https://github.com/timflutre/trimmomatic/blob/master/adapters/NexteraPE-PE.fa)
Trimming [HEK293T 2h DMSO/Emetine treatment]: Cutadapt (v4.0) with parameters: cutadapt --adapter Nextera=ACTGTCTCTTATACACATCT --overlap=5 --minimum-length 30 --nextseq-trim=20 --error-rate 0.1
Mapping [HEK293T 9h treatment]: STAR (v2.7.3a) with parameters: STAR --runMode alignReads --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --outStd SAM --readFilesCommand zcat --sjdbOverhang 78 --genomeDir Gencode_release-31_GRCh38.p12.starindex --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --runThreadN 4
Mapping [HEK293T 6h treatment, HEK293T YTHDF2 KD]: STAR (v2.7.3a) with parameters: STAR --runMode alignReads --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --outStd SAM --readFilesCommand zcat --sjdbOverhang 78 --genomeDir Gencode_release-31_GRCh38.p12_ERCC.starindex --sjdbGTFfile gencode.v31.primary_assembly.annotation_ERCC.gtf --runThreadN 1 --outMultimapperOrder Random
Mapping [HEK293T 2h DMSO/Emetine treatment]: STAR (v2.7.3a) with parameters: STAR --runMode alignReads --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --outStd SAM --readFilesCommand zcat --sjdbOverhang 115 --genomeDir Gencode_release-31_GRCh38.p12_ERCC.starindex --sjdbGTFfile gencode.v31.primary_assembly.annotation_ERCC.gtf --runThreadN 1 --outMultimapperOrder Random
Filter/remove secondary hits: Samtools (v1.9 [HEK293T 9h treatment], v1.10 [HEK293T 6h treatment, HEK293T YTHDF2 KD, HEK293T 2h DMSO/Emetine treatment]) with parameters: samtools view -F 256
Counts per gene: Subread (v2.0.0) with non-default parameters: featureCounts --donotsort -s 2 -T 4 (defaults used for -t exon -g gene_id)
Assembly: GRCh38.p12
Supplementary files format and content: tsv count tables (read count per gene)

extract_protocol:
RNA was purified using Rneasy PLUS Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq Strand-Specific mRNA Library Prep with PolyA-Selection

treatment_protocol:
m6A depletion was performed by adding medium supplemented with 20 µM STM2457 in DMSO 0.2% (v/v) or with DMSO 0.2% (v/v) alone as control for 6-24 h.
Small interfering RNAs targeting YTHDF2 or a non-targeting control siRNA were transfected into the cells 24 h after seeding using RNAiMAX following the manufacturer's instructions at a final concentration of 20 nM. Cells were harvested 48 h after transfection for further analysis.
To combine the siRNA knockdown with m6A depletion, 42 h after transfection, cells were treated with 20 µM STM2457 or DMSO for additional 6 h.

value: Human embryonic kidney 293T cell line

value: YTHDF2 KD


title: HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq rep3

description: imb_koenig_2022_10_18_HEK293T_YTHDF2_KD_STM_3


title: Haloferax volcanii cells, pyrE parent control strain, rep1

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_1


title: rsks-1, Fed, 3

city: Higashihiroshima

first: Takafumi

last: Ogawa

state: Hiroshima

address: 1-3-1 Kagamiyama

country: Japan

institute: Hiroshima University

data_processing:
The annotated genes (Aligned.sortedByCoord.out.bam file from STAR outputs) were quantified using RSEM.
Assembly: Differential expression analysis of genes and transcripts was performed in R using the Bioconductor package DESeq2.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Nematode strains were maintained on nematode growth medium (NGM) plates seeded with Escherichia coli strain OP50-1 as a food source using standard techniques at 20ºC

extract_protocol:
Samples were snap-frozen in liquid nitrogen and stored at −80°C until needed. After five freeze-thaw steps in a 37°C water bath and liquid nitrogen, total RNA was extracted using TRIzol, then purified with the Direct-zol™ RNA Kit and treated with DNase I to remove possible DNA contamination.
FASTQ output files were aligned to C. elegans WBcel269 reference genomes using STAR with a 2-pass procedure.

treatment_protocol: All worms were passaged on NGM with OP50 bacteria for at least two generations before the assay. Adult stage worms were bleached and the collected eggs were incubated in M9 buffer for 24hr for synchronization and induction of starvation-induced arrest. Hatched and starved larvae were placed on NGM plates with OP50 for 4h, then harvested after washing in M9 buffer.

value: whole body

tag: line

value: 4h feeding


title: HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq rep1

description: imb_koenig_2022_10_16_HEK293T_YTHDF2_KD_STM_1


title: Haloferax volcanii cells, rosR deletion strain, rep2

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_2


title: WT_3_N

value: ApcMin/+; Cul4bWT


title: KJ074_6542

description: CDNW-WT

value: male

value: control diet and normal water

value: WT


title: rsks-1, Fed, 2


title: KO_3_T


title: WT_3_T


title: HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq rep3

description: imb_koenig_2022_10_15_HEK293T_YTHDF2_KD_DMSO_3

value: DMSO 6h


title: CUTandRUN_K27M_in_K27Mubc20_L2_Rep2

city: Oxford

first: Alan

state: MA

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

data_processing:
Reads were aligned to the C. elegans ce11 (target genome) and Saccharomyces cerevisiae sacCer3 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: ce11, sacCer3
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: worm

growth_protocol: C. elegans were grown on NA22-seeded agar plates at 20C.

extract_protocol:
CUT&RUN (Cleavage under targets and release using nuclease). Enriched genomic DNA fragments were extracted using Monarch PCR & DNA Cleanup columns (NEB T1030S).
3-15ng of genomic DNA was used for library construction. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

tag: larval stage

value: worm

tag: cut&run antibody


title: HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq rep2

description: imb_koenig_2022_10_14_HEK293T_YTHDF2_KD_DMSO_2


title: rsks-1, Stv, 3

value: starvation


title: CUTandRUN_K27M_in_K27Mubc20_L2_Rep1


title: rsks-1, Fed, 1


title: HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq rep1

description: imb_koenig_2022_10_13_HEK293T_YTHDF2_KD_DMSO_1


title: VT055068-A

city: Waltham

first: Michael

last: Rosbash

address: 415 South street

institute: HHMI/Brandeis University

description:
ZT02 Repeat A
normalized_bulk_seq_data.csv

data_processing:
sequenging data were mapped to the genome by cellranger or STAR (bulk)
Assembly: dm6
Supplementary files format and content: mapped read counts or nomalized bulk seq data were included

organism: Drosophila melanogaster

extract_protocol:
Dynabeads Magnetic Beads were used to extract RNA for bulk sequencing
10X Chromium and smart-seq3

value: Brain

value: clock neuron

value: R11B03-AD;VT055068-DBD > UAS-EGFP


title: rsks-1, Stv, 2


title: HEK293T, STM2457, 9h, RNA-seq rep3

description: imb_koenig_2022_06_13_HEK293T_9h_STM2457_3


title: VT055068-B

description:
ZT02 Repeat B
normalized_bulk_seq_data.csv


title: rsks-1, Stv, 1


title: CUTandRUN_K27M_in_K27M_L2_Rep2

value: his-72(bm3[K27M]) III


title: 0367-A

value: split-0367 > UAS-EGFP


title: 0367-B


title: CUTandRUN_K27M_in_K27M_L2_Rep1


title: raga-1, Fed, 3


title: HEK293T, STM2457, 9h, RNA-seq rep2

description: imb_koenig_2022_06_12_HEK293T_9h_STM2457_2


title: CUTandRUN_IgG_in_N2_L2


title: CUTandRUN_K27M_in_K27Mubc20_L2_Rep3


title: raga-1, Fed, 2


title: R77H08-B

value: R11B03-AD;R77H08-DBD > UAS-EGFP


title: CUTandRUN_IgG_in_K27Mubc20_L2


title: HEK293T, STM2457, 9h, RNA-seq rep1

description: imb_koenig_2022_06_11_HEK293T_9h_STM2457_1

value: Human embryonic kidney 293T cell line


title: R77H08-A


title: HEK293T, DMSO, 9h, RNA-seq rep4

value: DMSO 9h


title: ZT22_0805

description:
ZT22 collected on 20220805
single_cell_read_count.csv

library_source: transcriptomic single cell

value: Clk856-GAL4 R11B03-AD;VT002670-DBD > UAS-EGFP


title: raga-1, Fed, 1

value: whole body

value: 4h feeding


title: CUTandRUN_K27M_in_K27M_L2_Rep3


title: CUTandRUN_IgG_in_K27M_L2


title: HEK293T, STM2457, 9h, RNA-seq rep4

description: imb_koenig_2022_06_14_HEK293T_9h_STM2457_4


title: ZT06_0805

description:
ZT06 collected on 20220805
single_cell_read_count.csv


title: HEK293T, DMSO, 9h, RNA-seq rep3


title: raga-1, Stv, 2


title: raga-1, Stv, 1


title: HEK293T, DMSO, 9h, RNA-seq rep2


title: CUTandRUN_H3K27me3_in_N2_L2_Rep3


title: HEK293T, DMSO, 9h, RNA-seq rep1


title: ZT22_0624

description:
ZT22 collected on 20220624
single_cell_read_count.csv


title: CUTandRUN_H3K27me3_in_N2_L2_Rep2


title: N2, Fed, 3


title: CUTandRUN_H3K27me3_in_N2_L2_Rep1


title: ZT14_0307

description:
ZT14 collected on 20220307
single_cell_read_count.csv


title: CUTandRUN_H3K27me3_in_K27Mubc20_L2_Rep3


title: N2, Fed, 2


title: HEK293T, STM2457, 6h, RNA-seq rep3

description: imb_koenig_2022_10_06_HEK293T_sR18_STM_3


title: HEK293T, STM2457, 6h, RNA-seq rep2

description: imb_koenig_2022_10_05_HEK293T_sR18_STM_2


title: ZT02_0307

description:
ZT02 collected on 20220307
single_cell_read_count.csv


title: CUTandRUN_H3K27me3_in_K27Mubc20_L2_Rep2


title: HEK293T, STM2457, 6h, RNA-seq rep1

description: imb_koenig_2022_10_04_HEK293T_sR18_STM_1


title: CUTandRUN_H3K27me3_in_K27Mubc20_L2_Rep1


title: raga-1, Stv, 3


title: HEK293T, DMSO, 6h, RNA-seq rep3

description: imb_koenig_2022_10_03_HEK293T_sR18_DMSO_3


title: ZT18_0623

description:
ZT18 collected on 20220623
single_cell_read_count.csv


title: ZT06_0623

description:
ZT06 collected on 20220623
single_cell_read_count.csv


title: CUTandRUN_H3K27me3_in_K27M_L2_Rep3


title: N2, Stv, 2


title: ZT14_1209

description:
ZT14 collected on 20211209
single_cell_read_count.csv


title: ZT10_0624

description:
ZT10 collected on 20220624
single_cell_read_count.csv


title: RKO AVEN WT

value: Colorectal cancer cell

value: AVEN wildtype

value: RKO


title: CUTandRUN_H3K27me3_in_K27M_L2_Rep2


title: N2, Stv, 1

value: WT


title: HEK293T, DMSO, 6h, RNA-seq rep2

description: imb_koenig_2022_10_02_HEK293T_sR18_DMSO_2

value: DMSO 6h


title: ZT02_1209

description:
ZT02 collected on 20211209
single_cell_read_count.csv


title: UCSF IDH-wildtype glioblastoma 116 recurrent

status: Public on Nov 19 2024

type: genomic

city: Stanford

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description:
IDH-wildtype glioblastoma tumor
205437190144_R01C01

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k version 1.0 Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing:
Methylation data were preprocessed using the minfi package (v.1.40.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.
Normalized DNA methylation beta-values and detection p-values

label: Cy3 and Cy5

source_name: Primary human tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using disposable biopsy punches.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients. 99 tumors were from the initial diagnostic surgical procedure prior to any radiation or chemotherapy treatment, and 127 tumors were from a subsequent surgery for recurrence/progressive disease usually following radiation and/or chemotherapy.

value: Primary human tumor tissue

tag: patient id

tag: tumor category

value: recurrent


title: CUTandRUN_H3K27me3_in_K27M_L2_Rep1

value: worm


title: UCSF IDH-wildtype glioblastoma 116 initial

description:
IDH-wildtype glioblastoma tumor
205437190167_R01C01

value: initial


title: N2, Fed, 1


title: UCSF IDH-wildtype glioblastoma 114 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150116_R07C01


title: UCSF IDH-wildtype glioblastoma 114 initial

description:
IDH-wildtype glioblastoma tumor
205854150116_R06C01


title: UCSF IDH-wildtype glioblastoma 113 initial

description:
IDH-wildtype glioblastoma tumor
205854150116_R04C01


title: HEK293T, DMSO, 6h, RNA-seq rep1

description: imb_koenig_2022_10_01_HEK293T_sR18_DMSO_1


title: UCSF IDH-wildtype glioblastoma 112 initial

description:
IDH-wildtype glioblastoma tumor
205854150116_R02C01


title: UCSF IDH-wildtype glioblastoma 110 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150105_R07C01


title: N2, Stv, 3

value: starvation


title: UCSF IDH-wildtype glioblastoma 111 initial

description:
IDH-wildtype glioblastoma tumor
205854150105_R08C01


title: UCSF IDH-wildtype glioblastoma 111 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150116_R01C01


title: UCSF IDH-wildtype glioblastoma 109 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150105_R05C01


title: UCSF IDH-wildtype glioblastoma 108 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150105_R03C01


title: UCSF IDH-wildtype glioblastoma 108 initial

description:
IDH-wildtype glioblastoma tumor
205854150105_R02C01


title: UCSF IDH-wildtype glioblastoma 107 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150105_R01C01


title: UCSF IDH-wildtype glioblastoma 110 initial

description:
IDH-wildtype glioblastoma tumor
205854150105_R06C01


title: UCSF IDH-wildtype glioblastoma 107 initial

description:
IDH-wildtype glioblastoma tumor
205854150104_R08C01


title: UCSF IDH-wildtype glioblastoma 112 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150116_R03C01


title: UCSF IDH-wildtype glioblastoma 106 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150104_R07C01


title: UCSF IDH-wildtype glioblastoma 115 initial

description:
IDH-wildtype glioblastoma tumor
205854150116_R08C01


title: UCSF IDH-wildtype glioblastoma 109 initial

description:
IDH-wildtype glioblastoma tumor
205854150105_R04C01


title: UCSF IDH-wildtype glioblastoma 113 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150116_R05C01


title: UCSF IDH-wildtype glioblastoma 103 initial

description:
IDH-wildtype glioblastoma tumor
205437190144_R08C01


title: UCSF IDH-wildtype glioblastoma 115 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150104_R04C01


title: UCSF IDH-wildtype glioblastoma 102 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150104_R02C01


title: UCSF IDH-wildtype glioblastoma 102 initial

description:
IDH-wildtype glioblastoma tumor
205854150104_R01C01


title: UCSF IDH-wildtype glioblastoma 101 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150042_R08C01


title: UCSF IDH-wildtype glioblastoma 100 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150042_R06C01


title: UCSF IDH-wildtype glioblastoma 104 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150104_R05C01


title: UCSF IDH-wildtype glioblastoma 101 initial

description:
IDH-wildtype glioblastoma tumor
205854150042_R07C01


title: UCSF IDH-wildtype glioblastoma 98 initial

description:
IDH-wildtype glioblastoma tumor
205437180023_R04C01


title: UCSF IDH-wildtype glioblastoma 100 initial

description:
IDH-wildtype glioblastoma tumor
205854150042_R05C01


title: UCSF IDH-wildtype glioblastoma 98 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180023_R05C01


title: UCSF IDH-wildtype glioblastoma 97 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180023_R03C01


title: UCSF IDH-wildtype glioblastoma 97 initial

description:
IDH-wildtype glioblastoma tumor
205437180033_R05C01


title: UCSF IDH-wildtype glioblastoma 96 initial

description:
IDH-wildtype glioblastoma tumor
205437180033_R03C01


title: UCSF IDH-wildtype glioblastoma 96 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180033_R04C01


title: UCSF IDH-wildtype glioblastoma 95 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180033_R02C01


title: UCSF IDH-wildtype glioblastoma 95 initial

description:
IDH-wildtype glioblastoma tumor
205854120054_R04C01


title: UCSF IDH-wildtype glioblastoma 94 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180033_R01C01


title: UCSF IDH-wildtype glioblastoma 92 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180030_R07C01


title: UCSF IDH-wildtype glioblastoma 106 initial

description:
IDH-wildtype glioblastoma tumor
205854150104_R06C01


title: UCSF IDH-wildtype glioblastoma 93 recurrent

description:
IDH-wildtype glioblastoma tumor
205854120054_R05C01


title: UCSF IDH-wildtype glioblastoma 93 initial

description:
IDH-wildtype glioblastoma tumor
205437180030_R08C01


title: UCSF IDH-wildtype glioblastoma 103 recurrent

description:
IDH-wildtype glioblastoma tumor
205854150104_R03C01


title: UCSF IDH-wildtype glioblastoma 92 initial

description:
IDH-wildtype glioblastoma tumor
205437180030_R06C01


title: UCSF IDH-wildtype glioblastoma 91 recurrent

description:
IDH-wildtype glioblastoma tumor
205437190142_R08C01


title: UCSF IDH-wildtype glioblastoma 89 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180030_R02C01


title: UCSF IDH-wildtype glioblastoma 88 recurrent

description:
IDH-wildtype glioblastoma tumor
205854120054_R03C01


title: UCSF IDH-wildtype glioblastoma 87 recurrent2

description:
IDH-wildtype glioblastoma tumor
205854150042_R02C01


title: UCSF IDH-wildtype glioblastoma 89 recurrent2

description:
IDH-wildtype glioblastoma tumor
205437180030_R03C01


title: UCSF IDH-wildtype glioblastoma 87 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180028_R08C01


title: UCSF IDH-wildtype glioblastoma 87 initial

description:
IDH-wildtype glioblastoma tumor
205437180028_R07C01


title: UCSF IDH-wildtype glioblastoma 84 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180028_R03C01


title: UCSF IDH-wildtype glioblastoma 83 initial

description:
IDH-wildtype glioblastoma tumor
205437180168_R08C01


title: UCSF IDH-wildtype glioblastoma 91 initial

description:
IDH-wildtype glioblastoma tumor
205437190142_R02C01


title: UCSF IDH-wildtype glioblastoma 86 recurrent

description:
IDH-wildtype glioblastoma tumor
205854120054_R02C01


title: UCSF IDH-wildtype glioblastoma 82 recurrent2

description:
IDH-wildtype glioblastoma tumor
205437180168_R07C01


title: UCSF IDH-wildtype glioblastoma 84 initial

description:
IDH-wildtype glioblastoma tumor
205437180028_R02C01


title: UCSF IDH-wildtype glioblastoma 82 initial

description:
IDH-wildtype glioblastoma tumor
205437180168_R06C01


title: UCSF IDH-wildtype glioblastoma 81 recurrent2

description:
IDH-wildtype glioblastoma tumor
205437180168_R05C01


title: UCSF IDH-wildtype glioblastoma 81 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180168_R04C01


title: UCSF IDH-wildtype glioblastoma 80 recurrent2

description:
IDH-wildtype glioblastoma tumor
205841310100_R05C01


title: UCSF IDH-wildtype glioblastoma 80 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180168_R03C01


title: UCSF IDH-wildtype glioblastoma 79 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180168_R02C01


title: UCSF IDH-wildtype glioblastoma 79 initial

description:
IDH-wildtype glioblastoma tumor
205841310100_R04C01


title: UCSF IDH-wildtype glioblastoma 78 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180168_R01C01


title: UCSF IDH-wildtype glioblastoma 78 recurrent2

description:
IDH-wildtype glioblastoma tumor
205437190144_R07C01


title: UCSF IDH-wildtype glioblastoma 78 initial

description:
IDH-wildtype glioblastoma tumor
205437180141_R08C01


title: UCSF IDH-wildtype glioblastoma 77 recurrent2

description:
IDH-wildtype glioblastoma tumor
205437180141_R07C01


title: UCSF IDH-wildtype glioblastoma 88 initial

description:
IDH-wildtype glioblastoma tumor
205437180030_R01C01


title: UCSF IDH-wildtype glioblastoma 74 initial

description:
IDH-wildtype glioblastoma tumor
205437180141_R01C01


title: UCSF IDH-wildtype glioblastoma 77 initial

description:
IDH-wildtype glioblastoma tumor
205437180141_R05C01


title: UCSF IDH-wildtype glioblastoma 70 initial

description:
IDH-wildtype glioblastoma tumor
205437180137_R02C01


title: UCSF IDH-wildtype glioblastoma 73 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180137_R07C01


title: UCSF IDH-wildtype glioblastoma 76 recurrent

description:
IDH-wildtype glioblastoma tumor
205841310100_R03C01


title: UCSF IDH-wildtype glioblastoma 76 initial

description:
IDH-wildtype glioblastoma tumor
205437180141_R04C01


title: UCSF IDH-wildtype glioblastoma 77 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180141_R06C01


title: UCSF IDH-wildtype glioblastoma 82 recurrent

description:
IDH-wildtype glioblastoma tumor
205841310100_R06C01


title: UCSF IDH-wildtype glioblastoma 73 initial

description:
IDH-wildtype glioblastoma tumor
205854150042_R01C01


title: UCSF IDH-wildtype glioblastoma 75 initial

description:
IDH-wildtype glioblastoma tumor
205437180141_R03C01


title: UCSF IDH-wildtype glioblastoma 83 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180028_R01C01


title: UCSF IDH-wildtype glioblastoma 71 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180137_R04C01


title: UCSF IDH-wildtype glioblastoma 74 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180141_R02C01


title: UCSF IDH-wildtype glioblastoma 86 initial

description:
IDH-wildtype glioblastoma tumor
205437180028_R06C01


title: UCSF IDH-wildtype glioblastoma 71 initial

description:
IDH-wildtype glioblastoma tumor
205841310100_R02C01


title: UCSF IDH-wildtype glioblastoma 75 recurrent

description:
IDH-wildtype glioblastoma tumor
205854120054_R06C01


title: UCSF IDH-wildtype glioblastoma 72 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180137_R06C01


title: UCSF IDH-wildtype glioblastoma 73 recurrent2

description:
IDH-wildtype glioblastoma tumor
205437180137_R08C01


title: UCSF IDH-wildtype glioblastoma 66 initial

description:
IDH-wildtype glioblastoma tumor
205437180133_R02C01


title: UCSF IDH-wildtype glioblastoma 68 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180133_R07C01


title: UCSF IDH-wildtype glioblastoma 68 initial

description:
IDH-wildtype glioblastoma tumor
205437180133_R06C01


title: UCSF IDH-wildtype glioblastoma 67 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180133_R05C01


title: UCSF IDH-wildtype glioblastoma 67 initial

description:
IDH-wildtype glioblastoma tumor
205437180133_R04C01


title: UCSF IDH-wildtype glioblastoma 69 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180133_R08C01


title: UCSF IDH-wildtype glioblastoma 65 initial

description:
IDH-wildtype glioblastoma tumor
205118950055_R08C01


title: UCSF IDH-wildtype glioblastoma 66 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180133_R03C01


title: UCSF IDH-wildtype glioblastoma 72 initial

description:
IDH-wildtype glioblastoma tumor
205437180137_R05C01


title: UCSF IDH-wildtype glioblastoma 69 initial

description:
IDH-wildtype glioblastoma tumor
205437180137_R01C01


title: UCSF IDH-wildtype glioblastoma 70 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180137_R03C01


title: UCSF IDH-wildtype glioblastoma 63 initial

description:
IDH-wildtype glioblastoma tumor
205118950055_R04C01


title: UCSF IDH-wildtype glioblastoma 59 recurrent2

description:
IDH-wildtype glioblastoma tumor
205118950054_R06C01


title: UCSF IDH-wildtype glioblastoma 62 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950055_R03C01


title: UCSF IDH-wildtype glioblastoma 64 initial

description:
IDH-wildtype glioblastoma tumor
205118950055_R06C01


title: UCSF IDH-wildtype glioblastoma 64 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950055_R07C01


title: UCSF IDH-wildtype glioblastoma 57 initial

description:
IDH-wildtype glioblastoma tumor
205841310002_R07C01


title: UCSF IDH-wildtype glioblastoma 63 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950055_R05C01


title: UCSF IDH-wildtype glioblastoma 56 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950054_R02C01


title: UCSF IDH-wildtype glioblastoma 59 initial

description:
IDH-wildtype glioblastoma tumor
205118950054_R05C01


title: UCSF IDH-wildtype glioblastoma 57 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950054_R03C01


title: UCSF IDH-wildtype glioblastoma 60 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950054_R08C01


title: UCSF IDH-wildtype glioblastoma 55 recurrent2

description:
IDH-wildtype glioblastoma tumor
205118950025_R07C01


title: UCSF IDH-wildtype glioblastoma 55 recurrent

description:
IDH-wildtype glioblastoma tumor
205841310002_R06C01


title: UCSF IDH-wildtype glioblastoma 62 initial

description:
IDH-wildtype glioblastoma tumor
205841310100_R01C01


title: UCSF IDH-wildtype glioblastoma 56 initial

description:
IDH-wildtype glioblastoma tumor
205118950054_R01C01


title: UCSF IDH-wildtype glioblastoma 58 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950054_R04C01


title: UCSF IDH-wildtype glioblastoma 65 recurrent

description:
IDH-wildtype glioblastoma tumor
205437180133_R01C01


title: UCSF IDH-wildtype glioblastoma 55 recurrent3

description:
IDH-wildtype glioblastoma tumor
205118950025_R08C01


title: UCSF IDH-wildtype glioblastoma 53 initial

description:
IDH-wildtype glioblastoma tumor
205118950025_R03C01


title: UCSF IDH-wildtype glioblastoma 60 initial

description:
IDH-wildtype glioblastoma tumor
205118950054_R07C01


title: UCSF IDH-wildtype glioblastoma 54 initial

description:
IDH-wildtype glioblastoma tumor
205841310002_R05C01


title: UCSF IDH-wildtype glioblastoma 54 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950025_R05C01


title: UCSF IDH-wildtype glioblastoma 53 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950025_R04C01


title: UCSF IDH-wildtype glioblastoma 58 initial

description:
IDH-wildtype glioblastoma tumor
205841310002_R08C01


title: UCSF IDH-wildtype glioblastoma 52 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950025_R02C01


title: UCSF IDH-wildtype glioblastoma 54 recurrent2

description:
IDH-wildtype glioblastoma tumor
205118950025_R06C01


title: UCSF IDH-wildtype glioblastoma 59 recurrent

description:
IDH-wildtype glioblastoma tumor
205841310100_R07C01


title: UCSF IDH-wildtype glioblastoma 52 initial

description:
IDH-wildtype glioblastoma tumor
205118950025_R01C01


title: UCSF IDH-wildtype glioblastoma 51 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950008_R08C01


title: UCSF IDH-wildtype glioblastoma 58 recurrent2

description:
IDH-wildtype glioblastoma tumor
205854130060_R02C01


title: UCSF IDH-wildtype glioblastoma 51 initial

description:
IDH-wildtype glioblastoma tumor
205118950008_R07C01


title: UCSF IDH-wildtype glioblastoma 50 recurrent2

description:
IDH-wildtype glioblastoma tumor
205841310002_R04C01


title: UCSF IDH-wildtype glioblastoma 48 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950008_R05C01


title: UCSF IDH-wildtype glioblastoma 48 initial

description:
IDH-wildtype glioblastoma tumor
205841310002_R03C01


title: UCSF IDH-wildtype glioblastoma 47 recurrent

description:
IDH-wildtype glioblastoma tumor
205854130060_R03C01


title: UCSF IDH-wildtype glioblastoma 45 recurrent

description:
IDH-wildtype glioblastoma tumor
203490650090_R08C01


title: UCSF IDH-wildtype glioblastoma 46 recurrent

description:
IDH-wildtype glioblastoma tumor
205841310002_R01C01


title: UCSF IDH-wildtype glioblastoma 46 initial

description:
IDH-wildtype glioblastoma tumor
205118950008_R04C01


title: UCSF IDH-wildtype glioblastoma 44 recurrentB

description:
IDH-wildtype glioblastoma tumor
205854120054_R01C01


title: UCSF IDH-wildtype glioblastoma 47 initial

description:
IDH-wildtype glioblastoma tumor
205841310002_R02C01


title: UCSF IDH-wildtype glioblastoma 44 initial

description:
IDH-wildtype glioblastoma tumor
204667540041_R05C01


title: UCSF IDH-wildtype glioblastoma 44 recurrentA

description:
IDH-wildtype glioblastoma tumor
205854120054_R07C01


title: UCSF IDH-wildtype glioblastoma 43 initial

description:
IDH-wildtype glioblastoma tumor
204667540082_R08C01


title: UCSF IDH-wildtype glioblastoma 43 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550101_R06C01


title: UCSF IDH-wildtype glioblastoma 42 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550061_R05C01


title: UCSF IDH-wildtype glioblastoma 42 initial

description:
IDH-wildtype glioblastoma tumor
204667550061_R04C01


title: UCSF IDH-wildtype glioblastoma 45 initial

description:
IDH-wildtype glioblastoma tumor
203490650090_R07C01


title: UCSF IDH-wildtype glioblastoma 41 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540099_R03C01


title: UCSF IDH-wildtype glioblastoma 41 initial

description:
IDH-wildtype glioblastoma tumor
204667550101_R07C01


title: UCSF IDH-wildtype glioblastoma 40 initial

description:
IDH-wildtype glioblastoma tumor
204667550061_R03C01


title: UCSF IDH-wildtype glioblastoma 39 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550061_R02C01


title: UCSF IDH-wildtype glioblastoma 39 initial

description:
IDH-wildtype glioblastoma tumor
204667540099_R01C01


title: UCSF IDH-wildtype glioblastoma 40 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540099_R02C01


title: UCSF IDH-wildtype glioblastoma 38 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550061_R01C01


title: UCSF IDH-wildtype glioblastoma 38 initial

description:
IDH-wildtype glioblastoma tumor
204667550034_R08C01


title: UCSF IDH-wildtype glioblastoma 37 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550034_R07C01


title: UCSF IDH-wildtype glioblastoma 37 initial

description:
IDH-wildtype glioblastoma tumor
204667550034_R06C01


title: UCSF IDH-wildtype glioblastoma 36 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550034_R05C01


title: UCSF IDH-wildtype glioblastoma 50 recurrent

description:
IDH-wildtype glioblastoma tumor
205118950008_R06C01


title: UCSF IDH-wildtype glioblastoma 36 initial

description:
IDH-wildtype glioblastoma tumor
204667550034_R04C01


title: UCSF IDH-wildtype glioblastoma 35 initial

description:
IDH-wildtype glioblastoma tumor
204667550101_R05C01


title: UCSF IDH-wildtype glioblastoma 33 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550034_R01C01


title: UCSF IDH-wildtype glioblastoma 34 initial

description:
IDH-wildtype glioblastoma tumor
204667550034_R02C01


title: UCSF IDH-wildtype glioblastoma 32 recurrent2

description:
IDH-wildtype glioblastoma tumor
204667550101_R03C01


title: UCSF IDH-wildtype glioblastoma 33 initial

description:
IDH-wildtype glioblastoma tumor
204667540108_R08C01


title: UCSF IDH-wildtype glioblastoma 31 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550101_R02C01


title: UCSF IDH-wildtype glioblastoma 32 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540082_R07C01


title: UCSF IDH-wildtype glioblastoma 32 initial

description:
IDH-wildtype glioblastoma tumor
204667540082_R06C01


title: UCSF IDH-wildtype glioblastoma 30 initial

description:
IDH-wildtype glioblastoma tumor
204667540039_R04C01


title: UCSF IDH-wildtype glioblastoma 28 recurrent2

description:
IDH-wildtype glioblastoma tumor
204667540039_R02C01


title: UCSF IDH-wildtype glioblastoma 28 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540039_R01C01


title: UCSF IDH-wildtype glioblastoma 29 initial

description:
IDH-wildtype glioblastoma tumor
204667540039_R03C01


title: UCSF IDH-wildtype glioblastoma 30 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540039_R05C01


title: UCSF IDH-wildtype glioblastoma 26 recurrent2

description:
IDH-wildtype glioblastoma tumor
204667540082_R05C01


title: UCSF IDH-wildtype glioblastoma 31 initial

description:
IDH-wildtype glioblastoma tumor
204667540039_R06C01


title: UCSF IDH-wildtype glioblastoma 28 initial

description:
IDH-wildtype glioblastoma tumor
204667540038_R08C01


title: UCSF IDH-wildtype glioblastoma 27 initial

description:
IDH-wildtype glioblastoma tumor
204667550104_R07C01


title: UCSF IDH-wildtype glioblastoma 27 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550104_R08C01


title: UCSF IDH-wildtype glioblastoma 26 initial

description:
IDH-wildtype glioblastoma tumor
204667540082_R04C01


title: UCSF IDH-wildtype glioblastoma 25 recurrent2

description:
IDH-wildtype glioblastoma tumor
204667550061_R07C01


title: UCSF IDH-wildtype glioblastoma 26 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550061_R08C01


title: UCSF IDH-wildtype glioblastoma 25 initial

description:
IDH-wildtype glioblastoma tumor
204667550061_R06C01


title: UCSF IDH-wildtype glioblastoma 24 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550104_R06C01


title: UCSF IDH-wildtype glioblastoma 34 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550034_R03C01


title: UCSF IDH-wildtype glioblastoma 24 initial

description:
IDH-wildtype glioblastoma tumor
204667550104_R05C01


title: UCSF IDH-wildtype glioblastoma 23 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550104_R04C01


title: UCSF IDH-wildtype glioblastoma 23 initial

description:
IDH-wildtype glioblastoma tumor
204667550104_R03C01


title: UCSF IDH-wildtype glioblastoma 21 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540121_R06C01


title: UCSF IDH-wildtype glioblastoma 29 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550101_R01C01


title: UCSF IDH-wildtype glioblastoma 20 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540038_R07C01


title: UCSF IDH-wildtype glioblastoma 21 initial

description:
IDH-wildtype glioblastoma tumor
204667540121_R05C01


title: UCSF IDH-wildtype glioblastoma 32 recurrent3

description:
IDH-wildtype glioblastoma tumor
204667550101_R04C01


title: UCSF IDH-wildtype glioblastoma 19 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550041_R08C01


title: UCSF IDH-wildtype glioblastoma 20 initial

description:
IDH-wildtype glioblastoma tumor
204667550101_R08C01


title: UCSF IDH-wildtype glioblastoma 17 recurrent2

description:
IDH-wildtype glioblastoma tumor
204667550102_R08C01


title: UCSF IDH-wildtype glioblastoma 17 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550102_R07C01


title: UCSF IDH-wildtype glioblastoma 19 initial

description:
IDH-wildtype glioblastoma tumor
204667550041_R07C01


title: UCSF IDH-wildtype glioblastoma 14 initial

description:
IDH-wildtype glioblastoma tumor
204667550035_R06C01


title: UCSF IDH-wildtype glioblastoma 17 initial

description:
IDH-wildtype glioblastoma tumor
204667550102_R06C01


title: UCSF IDH-wildtype glioblastoma 14 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550035_R07C01


title: UCSF IDH-wildtype glioblastoma 12 initial

description:
IDH-wildtype glioblastoma tumor
204667540038_R03C01


title: UCSF IDH-wildtype glioblastoma 25 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540082_R03C01


title: UCSF IDH-wildtype glioblastoma 10 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550035_R05C01


title: UCSF IDH-wildtype glioblastoma 11 initial

description:
IDH-wildtype glioblastoma tumor
204667540038_R01C01


title: UCSF IDH-wildtype glioblastoma 12 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540038_R04C01


title: UCSF IDH-wildtype glioblastoma 8 recurrent2

description:
IDH-wildtype glioblastoma tumor
204667550035_R01C01


title: UCSF IDH-wildtype glioblastoma 8 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540121_R08C01


title: UCSF IDH-wildtype glioblastoma 9 initial

description:
IDH-wildtype glioblastoma tumor
204667550035_R02C01


title: UCSF IDH-wildtype glioblastoma 11 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540038_R02C01


title: UCSF IDH-wildtype glioblastoma 13 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540038_R06C01


title: UCSF IDH-wildtype glioblastoma 10 initial

description:
IDH-wildtype glioblastoma tumor
204667550035_R04C01


title: UCSF IDH-wildtype glioblastoma 8 initial

description:
IDH-wildtype glioblastoma tumor
204667540121_R07C01


title: UCSF IDH-wildtype glioblastoma 7 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540082_R02C01


title: UCSF IDH-wildtype glioblastoma 9 recurrent

description:
IDH-wildtype glioblastoma tumor
204667550035_R03C01


title: UCSF IDH-wildtype glioblastoma 7 initial

description:
IDH-wildtype glioblastoma tumor
204667540039_R07C01


title: UCSF IDH-wildtype glioblastoma 6 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540121_R04C01


title: UCSF IDH-wildtype glioblastoma 6 initial

description:
IDH-wildtype glioblastoma tumor
204667540121_R03C01


title: UCSF IDH-wildtype glioblastoma 4 initial

description:
IDH-wildtype glioblastoma tumor
204667540111_R07C01


title: UCSF IDH-wildtype glioblastoma 3 initial

description:
IDH-wildtype glioblastoma tumor
204667540111_R05C01


title: UCSF IDH-wildtype glioblastoma 5 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540121_R02C01


title: UCSF IDH-wildtype glioblastoma 4 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540111_R08C01


title: UCSF IDH-wildtype glioblastoma 5 initial

description:
IDH-wildtype glioblastoma tumor
204667540121_R01C01


title: UCSF IDH-wildtype glioblastoma 3 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540111_R06C01


title: UCSF IDH-wildtype glioblastoma 13 initial

description:
IDH-wildtype glioblastoma tumor
204667540038_R05C01


title: UCSF IDH-wildtype glioblastoma 2 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540111_R04C01


title: UCSF IDH-wildtype glioblastoma 1 initial

description:
IDH-wildtype glioblastoma tumor
204667540111_R01C01


title: UCSF IDH-wildtype glioblastoma 2 initial

description:
IDH-wildtype glioblastoma tumor
204667540111_R03C01


title: UCSF IDH-wildtype glioblastoma 1 recurrent

description:
IDH-wildtype glioblastoma tumor
204667540111_R02C01


title: UCSF IDH-mutant astrocytoma #204 recurrent

description: IDH-mutant astrocytoma tumor

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: Astrocytoma, IDH-mutant

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using disposable biopsy punches.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients. 14 tumors were from the initial diagnostic surgical procedure prior to any radiation or chemotherapy treatment, and 17 tumors were from a subsequent surgery for recurrence/progressive disease usually following radiation and/or chemotherapy.

tag: tumor status

value: paired


title: UCSF IDH-mutant astrocytoma #209 initial

description: IDH-mutant astrocytoma tumor

value: unpaired


title: UCSF IDH-mutant astrocytoma #211 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #207 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #216 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #207 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #202 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #213 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #205 initial

description: IDH-mutant astrocytoma tumor


title: BAC ham silencer-seq, input

last: Stark

address: Campus-Vienna-Biocenter 1

institute: The Research Institute of Molecular Pathology (IMP)

library_source: other

data_processing:
Paired-end sequencing reads were aligned to the D. melanogaster reference genome BDGP R5/dm3 using Bowtie (version 1.2.2, (Langmead et al., 2009)) allowing 3 mismatches with the options: “‐v 3 ‐m 1 –best –strata –X 2000”. Mapped read pairs were collapsed by coordinates (start, end, strand) and by unique molecular identifiers (UMI) to distinguish PCR duplicates from reads originating from distinct RNA molecules with identical sequence. Fragments with identical coordinates were considered as duplicates if their UMIs differed by < 3 out of the 10 nucleotides. Genome coverage per sample was calculated using genomeCoverageBed from bedtools (version 2.27.1, Quinlan and Hall, 2010). BigWig files were created using the wigToBigWig utility from KentUtils (Kent et al., 2010).
To identify silencer-seq depleted regions in the genome (“dips” instead of peaks), first position-specific coverage for each sample and each strand were calculated separately using the coverage() function of the GenomicRanges R package (version 1.34.0, (Lawrence et al., 2013)). Afterwards, the log2 fold change and hypergeometric p‐value between coverage in experiment and input samples were determined. Loci with log2 fold change ≤ (-1.58) – corresponding to a 3-fold depletion over input – and hypergeometric p‐value ≤ 0.001 were collapsed into continuous depleted regions using the reduce() function.
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage of silencer-seq screen or input samples in bigWig format
Supplementary files format and content: silencer-seq dip calls as tsv files containing genomic regions of significant coverage depletion relative to input (collapsed regions with ≥ 3-fold depletion and hypergeometric p‐value ≤ 0.001)
Library strategy: STARR-seq

molecule: other

source_name: Schneider S2

growth_protocol: D. melanogaster Schneider S2 cells were cultured in Schneider’s Medium (Gibco, cat. no. 21720-024) supplemented with 10% heat-inactivated fetal bovine serum (Sigma-Aldrich, cat. no. F7524) at 27°C and 0.4% CO2.

extract_protocol:
Total RNA was isolated after cell lysis (Qiagen Tissue Ruptor) using the Qiagen RNeasy Maxi Kit. The entire total RNA samples were subjected to mRNA isolation by Dynabeads Oligo-dT25 beads (Invitrogen).
UMI-STARR-Seq libraries were UMI-tagged and prepared for NGS as previously described (Arnold et al., 2013, Neumayr et al., 2019).

treatment_protocol:
The sugarless (sgl) or hamlet (ham) S2 cell developmental enhancer (Zabidi et al., 2015) as 599bp sequences was introduced directly upstream of the Drosophila synthetic core promoter (DSCP) in the original STARR-seq vector (pSTARR-seq_fly Addgene #71499, Arnold et al., 2013) to obtain two different silencer-seq vectors.
A D. melanogaster genome-wide silencer-seq library in the sgl enhancer vector and two focused silencer-seq libraries (containing approximately 10Mb D. melanogaster genomic DNA from bacterial artificial chromosomes (BACs) covering ≈6% of the genome) in the sgl and ham vectors were produced by cloning roughly 500-800bp sheared genomic DNA or BAC fragments downstream of the reporter open reading frame, as described previously (Arnold et al., 2013).
For genome-wide and BAC-scale silencer-seq screens, the libraries were electroporated (MaxCyte STX Scalable Transfection System, 0.1ug DNA per one million cells) into exponentially growing S2 cells (80-90% confluency) in two biological replicates (200 million cells per BAC library replicate; 800-1600 million cells per genome-wide library replicate) after one cell washing step in a 1:1 mix of HyClone MaxCyte Electroporation Buffer with Schneider’s Medium (with no supplements).
Twenty-four hours after library transfection, cells were havested and the samples processed like regular UMI-STARR-seq (Arnold et al., 2013, Neumayr et al., 2019).

value: Schneider S2

tag: fraction

value: input

value: PCR amplified inserts of focused BAC ham silencer-seq library


title: UCSF IDH-mutant astrocytoma #215 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #205 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #203 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #218 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #223 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #212 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #201 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #203 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #206 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #224 recurrent

description: IDH-mutant astrocytoma tumor


title: BAC ham silencer-seq, rep1

value: screen

value: cells electroporated with focused BAC ham silencer-seq library


title: UCSF IDH-mutant astrocytoma #219 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #221 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #202 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #220 recurrent

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #210 initial

description: IDH-mutant astrocytoma tumor


title: BAC ham silencer-seq, rep2


title: CG11247 (Saft)-mut2 RNA-seq ovary, rep1

description:
w;; CG11247[indel2]/TM3,Sb;
clone2_ovary_rep1
ovary_raw_counts.txt

data_processing:
Reads of the fly tissue RNA-seq experiments were trimmed using TrimGalore (version 0.6.2) with default options and subsequently mapped to and quantified over the D. melanogaster reference protein-coding genes (Flybase version 5.57) with the Salmon aligner (version 1.2.1) in quasi-mapping mode. The resulting Salmon quantification files of each replicate and condition were imported into R using the tximport R package (version 1.30.0) and Salmon calculated raw counts per gene were extracted.
Assembly: BDGP R5/dm3
Supplementary files format and content: tab-delimited text files with raw counts for all samples per tissue or cell line

source_name: ovary

growth_protocol: D. melanogaster flies were maintained at 25°C with 60% humidity under 12h light/dark cycles. For brain and ovary dissections, female flies were aged for 1-2 days and mated on apple juice plates with yeast paste for 2 days. Dissected tissues of 3-4–day old females were snap-frozen in liquid N2 and stored at -70°C before processing for RNA-seq.

extract_protocol:
RNA was prepared as described in ElMaghraby et al. 2019. In brief, per replicate five ovary pairs or forty brains from 3-4-day old female flies were homogenized in TRIzol (Invitrogen) with a plastic pestle. Total RNA was TRIzol-extracted and purified using the RNA Clean & Concentrator kit (Zymo research) with on-column DNase I digest according to the manufacturer’s instructions. Ribosomal RNA was depleted starting with 1ug (ovary) or 0.5ug (brain) total RNA using custom oligonucleotides complementary to D. melanogaster rRNAs (listed in ElMaghraby et al. 2019) and Hybridase Thermostable RNase H (LGC Biosearch Technologies).
Libraries of rRNA depleted samples were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

treatment_protocol: CRISPR-Cas9 was applied to generate two independent Saft frame-shift mutant alleles in isogenised white flies: mutant 1 (single nucleotide deletion in exon 1, GATTACGTGCAACCGCAG-TTAAGAAGTCTGCCCGAA) and mutant 2 (2bp deletion in exon 2, GCCAGCTTCTCAACCAAC--CAATTTACGGGTGCACA).

value: ovary

value: Saft mutant 2


title: UCSF IDH-mutant astrocytoma #214 initial

description: IDH-mutant astrocytoma tumor


title: UCSF IDH-mutant astrocytoma #222 recurrent

description: IDH-mutant astrocytoma tumor


title: BAC sgl silencer-seq, rep2

value: cells electroporated with focused BAC sgl silencer-seq library


title: CG11247 (Saft)-wt RNA-seq ovary, rep1

description:
w;;;
w11_ovary_rep1
ovary_raw_counts.txt

value: wt


title: CG11247 (Saft)-wt RNA-seq ovary, rep3

description:
w;;;
w11_ovary_rep3
ovary_raw_counts.txt


title: CG11247 (Saft)-mut1 RNA-seq ovary, rep2

description:
w;; CG11247[indel1]/TM3,Sb;
clone1_ovary_rep2
ovary_raw_counts.txt

value: Saft mutant 1


title: CG11247 (Saft)-mut1 RNA-seq ovary, rep3

description:
w;; CG11247[indel1]/TM3,Sb;
clone1_ovary_rep3
ovary_raw_counts.txt


title: CG11247 (Saft)-mut2 RNA-seq ovary, rep2

description:
w;; CG11247[indel2]/TM3,Sb;
clone2_ovary_rep2
ovary_raw_counts.txt


title: CG11247 (Saft)-mut2 RNA-seq brain, rep1

description:
w;; CG11247[indel2]/TM3,Sb;
clone2_brain_rep1
brain_raw_counts.txt

source_name: brain

value: brain


title: CG11247 (Saft)-mut2 RNA-seq brain, rep2

description:
w;; CG11247[indel2]/TM3,Sb;
clone2_brain_rep2
brain_raw_counts.txt


title: CG11247 (Saft)-wt RNA-seq brain, rep1

description:
w;;;
w11_brain_rep1
brain_raw_counts.txt


title: CG11247 (Saft)-mut1 RNA-seq brain, rep1

description:
w;; CG11247[indel1]/TM3,Sb;
clone1_brain_rep1
brain_raw_counts.txt


title: UCSF IDH-mutant astrocytoma #204 initial

description: IDH-mutant astrocytoma tumor


title: CG11247 (Saft)-mut1 RNA-seq ovary, rep1

description:
w;; CG11247[indel1]/TM3,Sb;
clone1_ovary_rep1
ovary_raw_counts.txt


title: BAC STARR-seq, DLM3, rep2

data_processing:
Paired-end sequencing reads were aligned to the D. melanogaster reference genome BDGP R5/dm3 and the artificial D. pseudoobscura BAC region genome using Bowtie (version 1.2.2, (Langmead et al., 2009)) allowing 3 mismatches with the options: “‐v 3 ‐m 1 –best –strata –X 2000”. Mapped read pairs were collapsed by coordinates (start, end, strand) and by unique molecular identifiers (UMI) to distinguish PCR duplicates from reads originating from distinct RNA molecules with identical sequence. Fragments with identical coordinates were considered as duplicates if their UMIs differed by < 3 out of the 10 nucleotides. Genome coverage per sample was calculated using genomeCoverageBed from bedtools (version 2.27.1, Quinlan and Hall, 2010). BigWig files were created using the wigToBigWig utility from KentUtils (Kent et al., 2010).
For spike-in normalization of sample reads, a scaling factor per sample (BAC STARR-seq, ctrl, rep1 = 1.409819401; BAC STARR-seq, ctrl, rep2 = 1.667366961; BAC STARR-seq, DLM3, rep1 = 0.779454999; BAC STARR-seq, DLM3, rep2 = 0.848202481) was calculated by normalizing the ratio of total unique spike-in reads to total unique sample reads by the minimum ratio among all samples and adjusting for sample library size.
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage of STARR-seq input and spike-in normalized screen samples in bigWig format
Library strategy: STARR-seq

treatment_protocol:
The spz4 DLM3 silencer (530bp sequence) was cloned into the two original DSCP and RpS12 STARR-seq vectors (pSTARR-seq_fly Addgene #71499 and pSTARR-seq_fly-RpS12 Addgene #71504) downstream of the reporter polyA site (using PciI).
Focused STARR-seq libraries from 500-800bp BAC fragments (covering approximately 8Mb or 5% of the D. melanogaster genome) were created in the pSTARR-seq-DSCP-DLM3 and pSTARR-seq-RpS12-DLM3 vectors, as well as in the two corresponding original STARR-seq plasmids without the silencer (Addgene #71499 and #71504), as described previously (Arnold et al., 2013). Additionally, two focused spike-in libraries were derived by cloning sheared BACs containing D. pseudoobscura genomic sequences into the DSCP and RpS12 STARR-seq vectors.
For each condition (+/– silencer) and replicate, 20ug of focused pre-mixed STARR-seq libraries (equimolar dm3 BAC DSCP/RpS12  library mix spiked with 1% equimolar dp3 BAC DSCP/RpS12 library mix) were electroporated into 200 million exponentially growing S2 cells (80-90% confluency; MaxCyte STX Scalable Transfection System) after one cell washing step in a 1:1 mix of HyClone MaxCyte Electroporation Buffer with Schneider’s Medium (with no supplements).
Twenty-four hours after library transfection, cells were havested and the samples processed like regular UMI-STARR-seq (Arnold et al., 2013, Neumayr et al., 2019).

tag: core promoter

value: Mixed DSCP and RpS12

value: cells electroporated with mixed DLM3 STARR-seq libraries + spike-in


title: UCSF IDH-mutant astrocytoma #217 recurrent

description: IDH-mutant astrocytoma tumor

value: recurrent


title: CG11247 (Saft)-mut1 RNA-seq brain, rep2

description:
w;; CG11247[indel1]/TM3,Sb;
clone1_brain_rep2
brain_raw_counts.txt


title: CG11247 (Saft)-mut2 RNA-seq ovary, rep3

description:
w;; CG11247[indel2]/TM3,Sb;
clone2_ovary_rep3
ovary_raw_counts.txt


title: BAC STARR-seq, DLM3, RpS12, input

description:
36bp
LibLOH010_DSCP_libLOH011_Rps12.merged.input.bw

value: PCR amplified inserts of input library


title: BAC sgl silencer-seq, rep1


title: UCSF IDH-mutant astrocytoma #206 recurrent

description: IDH-mutant astrocytoma tumor

value: paired


title: UCSF IDH-mutant astrocytoma #208 initial

description: IDH-mutant astrocytoma tumor

value: unpaired

value: initial


title: CG11247 (Saft)-wt RNA-seq brain, rep2

description:
w;;;
w11_brain_rep2
brain_raw_counts.txt


title: BAC STARR-seq, ctrl, rep1

value: Schneider S2

value: cells electroporated with mixed standard STARR-seq libraries + spike-in


title: BAC STARR-seq, ctrl, rep2

value: screen


title: CG11247 (Saft)-wt RNA-seq ovary, rep2

description:
w;;;
w11_ovary_rep2
ovary_raw_counts.txt


title: BAC STARR-seq, ctrl, DSCP, input

description:
36bp
DSCP_merged_RpS12_BAC32_input.bw

value: input

value: DSCP


title: BAC STARR-seq, DLM3, rep1


title: CG11247 (Saft)-AID RNA-seq S2, untreated, rep2

description:
75bp
CG9C_raw_counts.tsv

data_processing:
Reads of the Schneider S2 cell Saft-AID RNA-seq experiment were processed and aligned to the D. melanogaster reference genome BDGP R5/dm3 using the nf-core/slamseq pipeline (version 1.0.0, (Neumann et al., 2019; Ewels et al., 2020)) with options '--quantseq 1 --multimappers 1’.
genome build/assembly: BDGP R5/dm3
processed data files format and content: tab-delimited text files with raw counts for all samples per tissue or cell line

extract_protocol:
Following auxin-mediated Saft protein depletion for the specified durations, 2 million cells were harvested per sample by centrifugation at 300 g for 5 min and washed once with PBS. Total RNA was isolated and DNase I treated after cell lysis with the RNA isolation kit provided by the VBC core facilities, which uses a lysis step based on guanidine thiocyanate (adapted from (Boom et al., 1990)) and SpeedBeads magnetic carboxylate modified particles (Merck) and eluted in 50ul water.
cDNA libraries from 500ng total RNA were prepared with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer's protocol.

treatment_protocol: The endogenous CG11247/Saft ORF was homozygously tagged with a FLAG-AID peptide in OsTir1 S2 cells as previously described (Hendy et al., 2022; Serebreni et al., 2023). Cells were treated with 500µM auxin (indole-3-acetic acid, IAA) for 24h or 48h or left untreated (solvent only). Cells were treated with 500µM auxin (indole-3-acetic acid, IAA) for 24h or 48h or left untreated (solvent only).

value: OsTir1, Saft_FLAG-AID

tag: clone

value: mock


title: BAC STARR-seq, DLM3, DSCP, input


title: CG11247 (Saft) ChIP-seq, cl.2, rep1, input

data_processing:
Reads from S2 cell ChIP-seq experiments were trimmed to a uniform length of 36 nucleotides, applying a standard quality setting (-Q33) using TrimGalore (version 0.6.2, (Krueger, n.d.)) and FASTX-Toolkit (version 0.0.14, (Hannon, 2010)). Trimmed reads were then aligned to the D. melanogaster reference genome BDGP R5/dm3 using Bowtie (version 1.2.2, (Langmead et al., 2009)). Following alignment, the read counts were normalized on a per million basis and bigwig files were generated with an extended read length setting of 150 nucleotides using bedtools (version 2.27.1, (Quinlan and Hall, 2010)).
Peak calling was performed with MACS2 (version 2.1.2.1, (Zhang et al., 2008)) separately in both replicates and per clonal cell line.
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage in FLAG-ChIP or input samples (either separately for each replicate or both replicates merged in one file) in bigWig format
Supplementary files format and content: narrowPeak files of MACS2 called peaks for each replicate

extract_protocol:
For each sample and replicate, 50 million 80-90% confluent S2 cells were harvested, washed with PBS, cross-linked in 1% formaldehyde at room temperature for 10 min and quenched with 125mM glycine. For nuclei isolation, cells were incubated in cell lysis buffer (50mM Tris pH8, 2mM EDTA, 0.5% NP-40, 10% glycerol, cOmplete Protease Inhibitor Cocktail (Roche)) for 10min at 4°C. After pelleting, nuclei were lysed in 50mM Tris pH8, 10mM EDTA, 1% SDS and cOmplete Protease Inhibitor Cocktail (Roche) for 15min. Chromatin fragments between 200-1000bp were obtained through sonication (E220 Focused-ultrasonicator, Covaris). Chromatin from approximately 30 million cells was immunoprecipitated overnight at 4°C with the anti-FLAG M2 (Merck, F1804) antibody. Antibody-bound chromatin was loaded on 40ul magnetic Dynabeads (1:1 mix of Protein G and A beads, Invitrogen) for 1h 4°C, washed twice in low-salt, high-salt, LiCl and TE buffer and eluted with 1% SDS, 100mM NaHCO3, 5mM DTT in water. Subsequently, samples were decrosslinked overnight at 65°C and treated with RNase A and proteinase K.
DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo Research), according to manufacturer’s instructions. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

treatment_protocol:
The endogenous CG7372/Phaser or CG11247/Saft ORF was homozygously tagged with a FLAG-AID peptide in OsTir1 S2 cells as previously described (Hendy et al., 2022; Serebreni et al., 2023).
cells were left untreated (i.e. no protein depletion)

value: 4H (clone 2)

tag: chip antibody


title: CG11247 (Saft)-AID RNA-seq S2, 48h auxin, rep2

description:
75bp
CG9C_raw_counts.tsv

tag: cell line

value: 48h auxin (IAA)