title: mouse, normal control, male, rep3

value: normal control


title: Hippocampal neuron culture, HH_rep1

status: Public on Sep 01 2024

type: SRA

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
confirming the quality of sequencing data by FastQC
reads were mapped to rn6 reference genome using Bowtie2
and annotated with Tophat 2
Adaptors were trimmed using BBDUK
Bru-seq signals of genes were quantified by FeatureCounts
Genome_build: RN6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Hippocampal neuron culture

growth_protocol: To achieve enough neurons, both cortical and hippocampal tissue were isolated as described. Neurons were plated onto poly-D-lysine-coated 6-well cell culture plates at a density of ~3 million cells/well. Cells were plated with ~1mL NGM per well and then supplemented with ~1mL of NGM-GC 2hrs after plating. Prior to experimental treatments, neurons were maintained at 5% CO2 and 37°C and fed NGM-GC every 4 days until DIV14.

extract_protocol:
RNA was purified using phenol-chloroform extraction and isopropanol precipitation, treated with DNase-I (NEB, M0303) then fragmented by high-magnesium, high temperature incubation.
Enrichment of BrU-containing RNA and library preparation were performed as previously described (PMID: 32783930).

treatment_protocol: At the start of the experiment, each well contained ~3mL of media. Similarly, to our electrophysiology experiments, 1mL of initial conditioned media is removed and saved for the drug-washout period. After removal, neurons were treated with either TTX or Veh (1:1000; 1µM TTX) for 24hrs. The initial TTX/Veh treatment was thoroughly removed via 2x washes (leaving ~500µL of media to cover the cells each wash) and lastly maintained with a final 50:50 saved media and fresh NGM solution for 48hrs before secondary treatment. On DIV17, cells were treated with TTX or Veh. 3.5hrs post-treatment, bromouridine (BrU, Sigma, 18670, dissolved in PBS) was added to cultures at 2mM final concentration and incubated at 5% CO2 and 37°C for the final .5hrs. Cultures were harvested in Tri-reagent BD (Sigma, T3809) and frozen immediately.

tag: cell type

value: Cultured neurons from newborn rat pups

tag: age

tag: strain

value: Sprague Dawley

tag: treatment

tag: fraction

value: Nascent RNA


title: Integument of 18DAP in WT rep2

city: Wuhan

first: Liqing

last: Lu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
Cutadapt was used to remove the 3’ sequencing adapters (at least 10bp overlap) and allow 20% mismatches
The full-length isoform produced by pacbio sequencing were used to establish index using bowtie2 with default parameters
The software RSEM were used to calculate readcount of each transcript and transform into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value
The differential expression analysis was performed by DESeq R package with a criterion of |log2FoldChange| > 1 and P value < 0.05
Supplementary_files_format_and_content: Tab-delimited text files include read count and FPKM values for each sample

organism: Citrus reticulata

source_name: Integument

extract_protocol:
RNA was extracted from cell mass captured by laser capture microdissection following the manufacturer’s suggested protocol (Arcturus Picopure kit, Kit0204). About 10-20ng total RNA of 36 samples (contained three biological replications) was used for cDNA synthesis and amplification using an Ovation RNA-seq System V2 Kit (Nugen Technologies).
The first strand cDNA were synthesized using random hexamer primers and dNTPs, and the second strand cDNA were synthesized using the first strand cDNA as a template with same reaction mix as above. The purification steps were carried out in accordance with the protocol. The product was used to SPIA cDNA amplification following by the purification again with QIAGEN MinElute Reaction Cleanup Kit to guarantee no primer and dNTP remains. The cDNA libraries were sequenced with the paired-end (PE, 2 x 150bp) strategy on the Hiseq X ten platform / NovaSeq 6000 (Illumina)

tag: development stage

value: 18 day after pollening

tag: cultivar

value: Egan No.1 ponkan


title: mouse, normal control, male, rep2

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

data_processing:
fastp 0.20.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp 0.20.1 with default parameters
Clean read were aligned to reference genome with hisat2 version 2.1.0 (--rna-strandness rf --fr)
htseq-count (version 0.11.2;-s reverse) was used to analysis FPKM values
DESeq2 (Version 1.22.2)was used to analyze differentially expressed genes (cutoff qvalue(pvalue)<0.05, |log2FoldChange|>1)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: placenta

extract_protocol:
Three male and three female placenta samples per group were randomly selected for RNA isolation, which was performed by using TRIzol Reagent (Invitrogen) under the manufacturer’s instructions. Extracted RNA was dissolved in RNase-free water and quantified using Qubit○R RNA Assay Kit in Qubit○R 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using NEBXext○R UltraTM RNA Library Prep Kit for Illumina○R (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNest First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37℃ for 15 min followed by 5 min at 95℃ before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent bioanalyzer 2100 system.

tag: tissue

value: placenta

tag: Sex

value: male


title: Integument of 18DAP in WT rep1


title: mouse, normal control, male, rep1


title: miR-26a KO mice cells transfected with Silencer Negative Control  [Control_26KO]

city: Hiroshima

first: Shigeru

last: Miyaki

state: Hiroshima

address: 1-2-3, kasumi Minami-ku

department: Medical Center for Translational and Clinical Research

country: Japan

institute: Hiroshima University

data_processing:
Raw data were assesed for quality using FastQC
using HISAT to align the clean reads to the reference genome
using Bowtie2 to align the clean reads to the reference genes
Reference Genome Version: GCF_000001635.26_GRCm38.p6
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for all samples

source_name: shoulder joint capsule tissue derived synovial fibroblasts

growth_protocol: Synovial fibroblasts (SFBs) derived from shoulder joint capsule tissue of WT and miR-26a KO mice one week after immobilization were isolated by outgrowth method in Dulbecco’s modified Eagle’s medium (DMEM) . Isolated SFBs were cultured in DMEM with 10 % fetal bovine serum. Experiments were carried out at passage 2.

extract_protocol:
Total RNA of wild-type and, miR-26a KO SFBs were extracted using Direct-zol RNA Microprep Kit (ZYMO RESEARCH) and underwent RNA-sequencing (RNA-seq) analysis (BGI Genomics, China).
RNA libraries were constructed by BGI Genomics, China.

treatment_protocol: Double-stranded RNA oligonucleotides representing mature sequences that 10 nM miR-26a mimic (sense: 5’-UUCAAGUAAUCCAGGAUAGGCU-3’ and anti-sense: 5’-CCUAUUCUUGGUUCCUUGCACG-3’) or Silencer Negative Control siRNA#1 (Themo Fisher Scientific) were transfected into miR-26a KO SFBs using Lipofectamine RNAiMax Reagent (Themo Fisher Scientific) for 24 hours according to the manufacturers’ instructions.

tag: genotype

value: transfected with 10nM Silencer Negative Control


title: miR-26a KO mice cells transfected with miR-26a mimic [TF26]

value: shoulder joint capsule tissue derived synovial fibroblasts

value: transfected with 10nM miR-26a mimic


title: miR-26a KO mice cells [KO26]


title: Integument of 32DAP in MT rep2

value: 32 day after pollening

value: Huagan No.4 ponkan


title: BN03

city: Yangling

first: Zehui

last: Wei

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
The quality of the RNA samples was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After the quality control, the library preparations were sequenced on an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) and paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Bos_taurus.ARS-UCD1.2 whole genome using HISAT2 v2.0.4 with parameters -p 8 --dta -x -S
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: The longissimus dorsi muscle

extract_protocol:
All the samples were frozen in liquid nitrogen immediately and stored at -80℃ until further processing.Total RNA of each muscle sample was extracted from approximately 50 mg of frozen tissue using TRIzol Reagent (Invitrogen Corporation, Carlsbad, CA, USA) according to manufacturer recommendations. The quality of the RNA samples was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After the quality control, the library preparations were sequenced on an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) and paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 3.5 ± 0.5-year-old

value: m. longissimus dorsi

tag: species

value: Banna


title: mouse, normal control, female, rep2

value: female


title: Integument of 32DAP in MT rep3


title: Hippocampal neuron culture, TH_rep1


title: Integument of 32DAP in MT rep1


title: mouse, high E2 prenatal exposure, female, rep1

value: high E2 prenatal exposure


title: C_2_V

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38_91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38_91
Supplementary files format and content: TMM-normalized counts for 14549 expressed genes (at least 1 CPM, in at least 3 samples), in each sample.

molecule: polyA RNA

source_name: Epicardium+Subepicardium

growth_protocol: Conditional Meis1 and Meis2 double-deficient  recombined with WT1-Cre (Meis1fl/fl;Meis2fl/fl;WT1-Cre) were retrieved at E16.5

extract_protocol:
RNA was then purified from each pool using RNeasy Micro kit (Qiagen 74004).
40 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies).

treatment_protocol: The epicardium/subepicardium was dissected as previously described (Lioux et al., 2020) and quickly frozen in separate 1.5 ml Eppendorf tubes on dry ice. For mRNA isolation, samples from at least three different litters were used. As low RNA amount from one single epicardial layer was expected, two dissected epicardia of the same genotype were pooled together. Therefore, the three biological replicates per genotype represent six different hearts pooled by pairs.

value: Epicardium+Subepicardium

tag: organ

value: Heart

value: Epicardial+Subepicardial cells

value: Wild-type


title: C57BL6/J mice cells [Control_B6]

value: Wild type


title: Integument of 28DAP in MT rep3

value: 28 day after pollening


title: BN01


title: mouse, normal control, female, rep1

value: placenta

value: normal control


title: Pfalciparum_Day11_Input4

city: Silver Spring

first: Riette

last: Van Biljon

state: MD

address: 10903 New Hampshire Avenue

institute: US FDA

data_processing:
Fastq files generated from Illumina Miseq software were subject to adaptor trimming using Trimmomatic v 0.39 to a final quality score >20 and adding an adaptor trimming step (Illuminaclip)
Reads were mapped to Plasmodium falciparum genome v 59.0 using BWA-MEM2 v2.2.1 with minimum insert length >50 bp, BAM files were filtered for a minimum MAPQ quality score of 1 to remove most multiply mapped sequences
Bigwig files were generated by using bamcompare v 3.5.4 to subtract input sample readcounts from IgG and IP samples respectively.
Bound mRNA were identified using Piranha v 0.1.0 which called peaks with P-values <0.01 on input substracted bigwig files for the IP conditions with the IgG bigwig files were specified as covariate
Additional bound mRNA were identified using PureCLIP v 1.0.4 using filtered bam files to call mRNA enriched in either the IgG or IP samples against the input samples
Assembly: PlasmoDB-59_Pfalciparum3D7_Genome
Supplementary files format and content: bigwigs containing input subtracted IgG and IP samples

organism: Plasmodium falciparum

growth_protocol: P. falciparum NF54e with PfMD3 C-terminal 3xHA tag was grown in under stationary conditions and heparin was added following appearance of gametocyte to deplete asexual parasites.

extract_protocol:
RNA-protein complexes were crosslinked with UV at 254nm to a final exposure of 400 mJ. Following cell lysis, immunoprecipitation with HA-tag antibody was performed prior to proteinase K digestion and RNA purification with RNA clean and concentrator kit from Zymo Research
RNA libraries for CLIP-seq were prepared using Illumina Truseq total RNA library preparation kit according to manufacturer's instructions

tag: cell line

value: Stage V gametocytes

value: Input (no antibody)


title: Integument of 28DAP in MT rep2


title: Huh751_HCVcc_72h

type: RNA

city: Hamamatsu

first: Tetsuro

last: Suzuki

address: 1-20-1 Handayama, Chuou-ku,

department: Department of Microbiology and Immunology

institute: Hamamatsu University School of Medicine

hyb_protocol: Hybridized for 16 h at 37 ˚C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Homo sapiens

source_name: mock infected cells_72h

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: Huh7.5.1  cells were maintained in DMEM containing 10% fetal bovine serum at 37 ˚C in a fully-humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

treatment_protocol: The subconfluent cells were exposed to 1μg/mL tunicamycin for 48 hours or infected with HCVcc for 48 hours  or 72 hours at 37 ˚C in a fully-humidified 5% CO2 atmosphere.

value: mock infection

tag: time

source_name: HCVcc infected cells_72h

value: HCVcc infection


title: Huh751_tunicamycin_48h

source_name: DMSO treated cells_48h

value: DMSO treatment

source_name: tunicamycin treated cells_48h

value: Tunicamycin treatment


title: Pfalciparum_Day11_IgG4

value: Rat IgG antibody IP (PP68)


title: Huh751_HCVcc_48h

source_name: mock infected cells_48h

source_name: HCVcc infected cells_48h


title: Integument of 28DAP in MT rep1

value: Huagan No.4 ponkan


title: mouse, normal control, female, rep3

value: female


title: sALS_4

city: Pavia

first: Jessica

last: Garau

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated using the llumina bcl2fastq2 software (Version 2.17.1.14 -http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html) from raw sequencing reads gener-ated by the Illumina NextSeq 500 sequencer (Illumina, California, USA). STAR/RSEM software was used to cal-culate gene and transcript intensities using Gencode Release 19 (GRCh37.p13) as a reference and the "stranded" op-tion. The mRNA differential expression analysis was carried out using the R package EBSeq. The R package DESeq2 was used to perform differential expression analysis on lncRNAs. With |log2(disease sample/healthy con-trol)|1 and an FDR of 0.1, genes were considered differentially expressed and retained for further analysis.
Assembly: Hg19
Supplementary files format and content: fastq.gz

source_name: Blood

growth_protocol: PBMCs were isolated from peripheral venous blood samples. Lymphocytes B were isolated from an aliquot of PBMCs and were immortalized into LCLs via Epstein-Barr Virus (EBV) infection.

extract_protocol:
Samples were homogenized and total RNA was isolated by Trizol® reagent.
Sequencing libraries were prepared by the Illumina TruSeq RNA Library Prep, version 2, Protocol D, using 500-ng total RNA (Illumina, California, USA).

value: Blood

value: Lymphoblastoid cell line


title: sALS_3


title: Integument of 18DAP in MT rep3

value: 18 day after pollening


title: BN02

value: 3.5 ± 0.5-year-old

value: m. longissimus dorsi

value: Banna


title: Pfalciparum_Day11_Input3


title: sALS_2


title: Pfalciparum_Day11_IgG3


title: sALS_1


title: fALS_SOD1_3


title: P3jerboa_forelimb_1

city: Salt Lake City

first: Mai

last: Tran

state: UT

address: 201 President Circle

institute: University of Utah

description: raw original fastq files

data_processing:
Sequenced were trimmed for low quality sequence
trimmed sequence were mapped as described in the method section
normalized readcount were extracted for further differential gene expression analysis
Assembly: custom
Supplementary files format and content: tab-delimited read-count output of STAR

organism: Jaculus jaculus

source_name: forelimb muscle

extract_protocol: NOT PROVIDED

value: forelimb muscle

value: normal


title: Pfalciparum_Day11_IP3

value: Stage V gametocytes

value: HA antibody IP (Roche 3F10)


title: Integument of 18DAP in MT rep1


title: Integument of 18DAP in MT rep2


title: P3jerboa_forelimb_2

description: raw original fastq files


title: fALS_SOD1_2


title: Pfalciparum_Day11_Input2

value: Input (no antibody)


title: Nucellus of 32DAP in WT rep2

source_name: Nucellus

value: 32 day after pollening

value: Egan No.1 ponkan


title: Nucellus of 32DAP in WT rep3


title: P3jerboa_foot_2

description: raw original fastq files

source_name: hindfoot muscle

value: hindfoot muscle


title: fALS_SOD1_1


title: P3jerboa_foot_3

description: raw original fastq files


title: Pfalciparum_Day11_IgG2

value: Rat IgG antibody IP (PP68)


title: DU145_C30-2

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from  DU145 cells  treated with C-30 (2 μM)

hyb_protocol: The samples were hybridized to Human Clariom S-arrays according to standardized protocols from Applied Biosystems.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G ( Applied Biosystems).

data_processing: The microarray data were preprocessed with Applied Biosystems GeneChip Expression Console software ver.1.3.0 using SST-RMA algorithm workflow.

label: biotin

source_name: prostate cancer

label_protocol: Total RNA was labeled employing Applied Biosystems Gene Chip WT PLUS Reagent kit according to the manufacturer’s instructions

growth_protocol: DU145 cells were cultures in RPMI 1640 containing 10% FBS.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were treated with vehicle, No.10-3 or C-30 for 48 h.


title: Nucellus of 32DAP in WT rep1


title: DU145_Control

description: Gene expression data from DU145 cells treated with vehicle

value: Control


title: Pfalciparum_Day11_IP4


title: fALS_c9orf72_4


title: Pfalciparum_Day11_IP2


title: P3jerboa_forelimb_3

description: raw original fastq files


title: DU145_C30-1

description: Gene expression data from  DU145 cells treated with C-30 (0.5 μM)


title: DU145 10-3

description: Gene expression data from  DU145 cells treated with No.10-3 (5 μM)


title: Pfalciparum_Day11_Input1


title: fALS_c9orf72_3


title: Nucellus of 28DAP in WT rep3

value: 28 day after pollening


title: Nucellus of 28DAP in WT rep2


title: P0jerboa_forelimb_3

description: trimmed fastq files


title: P3jerboa_foot_1

description: raw original fastq files


title: Nucellus of 28DAP in WT rep1


title: Pfalciparum_Day11_IP1


title: fALS_c9orf72_2

value: Blood


title: Nucellus of 18DAP in WT rep3


title: P0jerboa_forelimb_2

description: trimmed fastq files


title: fALS_c9orf72_1

value: Lymphoblastoid cell line


title: Pfalciparum_Day11_IgG1


title: fALS_FUS_2


title: Nucellus of 18DAP in WT rep2

value: 18 day after pollening


title: P0jerboa_foot_2

description: trimmed fastq files


title: Nucellus of 18DAP in WT rep1


title: P0jerboa_foot_3

description: trimmed fastq files


title: Pfalciparum_Day5_IP4

value: Stage II gametocytes


title: fALS_TARDBP_3


title: Pfalciparum_Day5_IgG4


title: Nucellus of 32DAP in MT rep3

value: Huagan No.4 ponkan


title: P0jerboa_foot_1

description: trimmed fastq files


title: fALS_TARDBP_2


title: Filamentous haploid M10

city: Nanning

first: Shan

state: --- Select One ---

address: No.100,Daxue East Road

institute: Guangxi University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Supplementary files format and content: fpkm

organism: Sporisorium scitamineum

source_name: filamentous growth

extract_protocol:
RNA was iextracted using an RNA Extraction Kit (TaKaRa, Beijing, No. 9769) following the manufacturer’s protocol
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: filamentous growth

value: haploid mutant


title: Pfalciparum_Day5_Input3


title: Nucellus of 32DAP in MT rep2


title: Pfalciparum_Day5_IgG3


title: Filamentous haploid M9


title: Pfalciparum_Day5_Input4


title: Nucellus of 32DAP in MT rep1


title: fALS_TARDBP_1


title: Pfalciparum_Day5_IP3


title: Filamentous haploid M8


title: Control_4


title: Nucellus of 28DAP in MT rep3


title: fALS_FUS_1


title: Control_3


title: P0jerboa_forelimb_1

description: trimmed fastq files

value: forelimb muscle

value: normal


title: Pfalciparum_Day5_IgG2


title: Nucellus of 28DAP in MT rep2


title: Filamentous haploid M6


title: Control_2


title: Pfalciparum_Day5_IP2

value: HA antibody IP (Roche 3F10)


title: Control_1


title: Pfalciparum_Day5_Input1

value: Input (no antibody)


title: Nucellus of 18DAP in MT rep3


title: Nucellus of 28DAP in MT rep1


title: Nucellus of 18DAP in MT rep2


title: Pfalciparum_Day5_IgG1


title: ABTr_2

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

description: clone #1

library_source: genomic

data_processing:
Fastq files of pair-end WES reads were aligned with bwa-mem v0.7.12  to the reference genome UCSC hg38 using default parameters.
Assembly: hg38
Supplementary files format and content: vcf

molecule: genomic DNA

source_name: Ovary

growth_protocol: PEO1 and ABTR clones were grown in DMEM with 10% heat-inactivated Fetal Bovine Serum (FBS), 100 𝜇M nonessential amino acids, 10 𝜇g/mL insulin, 100 units/mL penicillin G, 100 𝜇g/mL streptomycin, and 2 mM glutamine

extract_protocol:
DNA was column-extracted using Qiagen DNeasy Blood and Tissue kit (qiagen)
WES libraries were prepared from prepared from 750 ng high-quality DNA using Agilent’s SureSelect Human All Exon v5 + UTRs 75 MB kit (Agilent).

treatment_protocol: ABTR clones were treated continuously with 40 𝜇M veliparib for 6 months and removed from drug 4-5 days before RNA collection

value: Ovary

value: epithelial

value: Veliparib resistant


title: IT4var01-BirA*Pos1endo + TryThrA-TGD

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

country: Germany

institute: Bernhard Nocht Institute for Tropical Medicine

data_processing:
SOAPnuke (v2.2.6) was used for filtering raw reads and performing quality control (QC) with the parameters -n 0.001, -l 10, -q 0.5, and -Q 2. Clean reads obtained after filtering were aligned to the reference genome using BWA (v0.7.17) with the bwa mem -M -Y algorithm. SAM files generated by BWA were converted to BAM format using Samtools (v1.9) with the command samtools view -Sb. The BAM files were then sorted using samtools sort, mates were fixed using samtools fixmate, duplicates were marked using samtools markdup, and the files were indexed with samtools index.  SNPs and Indels were called using GATK (v4.2.6.1) with HaplotypeCaller to generate GVCF files, followed by CombineGVCFs, and GenotypeGVCFs for variant calling. Variants were filtered using SelectVariants and VariantFiltration with specific criteria: SNPs were filtered with "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0", and Indels were filtered with "QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0". Annotation of SNPs and Indels was performed using SnpEff (v4.3.1).  Structural variations (SVs) were identified using Manta (v1.6.0) with default parameters, and the resulting variants were annotated using SnpEff. Copy number variations (CNVs) were detected using Control-FREEC (v11.5) with a window size of 50,000 bp, step size of 10,000 bp, and chromosome ploidy set to 2. CNVs were then annotated using SnpEff..
Assembly: IT4: Release 68
Supplementary files format and content: BioIDPos1_processed.xlsx; variation annotation (cnv, indel, snp, sv)
Supplementary files format and content: TryThrA_processed.xlsx; variation annotation (cnv, indel, snp, sv)
Supplementary files format and content: EMPIC3_processed.xlsx; variation annotation (cnv, indel, snp, sv)
Library strategy: Whole genome sequencing

source_name: P. f. infected human erythrocytes

growth_protocol: P. falciparum parasites (3D7 (Walliker et al., 1987) and IT4 (Jensen and Trager, 1978) were cultured using standard procedures (Trager and Jensen, 1976). The parasites were maintained in RPMI1640 supplemented with 0.5% Albumax and human 0+ erythrocytes, at a haematocrit of 5% at 37°C under an atmosphere consisting of 1% O2, 5% CO2, and 94% N2.

extract_protocol:
10 ml P. falciparum parasites culture with a parasitemia of 5-10% was pelleted abd genomic DANN was isolated using the Monarch Genomic DNA Purification Kit (NEB). Genomic DNA was froozen at -20°C until sent of to BGI for sequencing.
After quality control (QC) of DNA samples, the qualified DNA samples were randomly fragmented using a Covaris instrument. The fragmented DNA was then collected using magnetic beads.  The next step involved end-repair of the DNA fragments, where adenine bases were added to the 3’ ends to facilitate adaptor ligation. Adaptors were ligated to the prepared DNA fragments.  Following ligation, the products were cyclized and subjected to amplification using linear isothermal Rolling-Circle Replication (RCR). The amplified products were then processed using DNA NanoBall (DNB) technology to generate highly dense DNA nanoballs.  Finally, sequencing of these DNA libraries was performed using the DNBSEQ sequencing platform.

value: P. f. infected human erythrocytes

value: SLI/SLI2 double integrant


title: IT4var01-BirA*Pos1endo + EMPIC3-TGD

value: SLI/SLI2 double Integrant


title: IT4var01-BirA*Pos1endo

value: SLI integrant parent


title: Nucellus of 18DAP in MT rep1


title: ovarian cancer P0996

status: Public on Aug 31 2024

type: genomic

city: Kyoto

first: Shiro

last: Takamatsu

address: 54 Shogoin Kawahara, Sakyo, Kyoto

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Using EZ DNA Methylation Kit (Zymo Research Inc.), bisulfite conversion was performed on each 250ng genomic sample followed by purification and recovery. Bisulfite-converted DNA was alkaline-denatured and subjected to enzymatic whole-genome amplification. The amplified genomic DNA was fragmented by enzyme, purified by isopropanol precipitation, and resuspended in buffer. The resuspended DNA was heat-denatured and applied to the Infinium MethylationEPIC BeadChip for hybridization at 48 °C in an oven for approximately 23 hours.

scan_protocol: After hybridization, the BeadChip was washed with buffer, and a single nucleotide labeled at the end of the probe was incorporated by single nucleotide extension reaction. The hybridized genomic DNA was then denatured and removed, and stained with a fluorescent dye-labeled antibody against the incorporated labeled nucleotide. The stained BeadChip was washed, coated, and dried, and then the fluorescent image was acquired using iScan.

data_processing:
Background Subtraction and Normalization by Internal Controls were performed using GenomeStudio (V2011.1) and Methylation Module (1.9.0) to analyze the acquired fluorescence image data.
Matrix_processed_normalized_beta_values.txt:  Normalized average beta values (GenomeStudio V2011.1 and Methylation Module 1.9.0)

label: Cy3, Cy5

source_name: Primary tumor

label_protocol: Bead array analysis was performed with iScan (Illumina) according to the Infinium HD Methylation Protocol Guide, Manual Protocol (15019519 v01).

extract_protocol: genomic DNA was extracted from fresh frozen tumor samples

value: HGSC

value: Serous carcinoma


title: ovarian cancer P0991


title: Pfalciparum_Day5_IP1

value: Stage II gametocytes


title: ovarian cancer P0993


title: Pfalciparum_Day5_Input2


title: PE01

description: Parental

value: WT

value: no treatment


title: ovarian cancer P0978


title: ovarian cancer P0973


title: ovarian cancer P0966


title: ovarian cancer P0968


title: ovarian cancer P0956

value: Endometrioid carcinoma


title: Wild type strain JG36

source_name: yeast list

value: yeast list

value: wild type


title: ovarian cancer P0954


title: ovarian cancer P0946


title: ovarian cancer P0952


title: ABTr_3

description: clone #2

value: clones were treated continuously with 40 𝜇M veliparib for 6 months and removed from drug 4-5 days before RNA collection


title: ovarian cancer P0927


title: ovarian cancer P0941


title: ovarian cancer P0920


title: ovarian cancer P0919


title: ovarian cancer P0916


title: ovarian cancer P0917


title: ovarian cancer P0915


title: ovarian cancer P0912


title: ovarian cancer P0909


title: ovarian cancer P0970

value: Other


title: ovarian cancer P0893


title: ovarian cancer P0888


title: ovarian cancer P0892


title: ovarian cancer P0906


title: ovarian cancer P0884


title: ovarian cancer P0882


title: ovarian cancer P0901


title: ovarian cancer P0895


title: ovarian cancer P0880


title: ovarian cancer P0879


title: ovarian cancer P0873


title: ovarian cancer P0934


title: ovarian cancer P0867


title: ovarian cancer P0868


title: ovarian cancer P0859


title: ovarian cancer P0854


title: ovarian cancer P0861


title: ovarian cancer P0853


title: ovarian cancer P0850


title: ovarian cancer P0846


title: ovarian cancer P0847


title: ovarian cancer P0837


title: ovarian cancer P0830


title: ovarian cancer P0831


title: ovarian cancer P0834


title: ovarian cancer P0908


title: ovarian cancer P0844


title: ovarian cancer P0827


title: ovarian cancer P0821


title: ovarian cancer P0825


title: ovarian cancer P0818


title: ovarian cancer P0796


title: ovarian cancer P0786


title: ovarian cancer P0808


title: ovarian cancer P0809


title: ovarian cancer P0793


title: ovarian cancer P0781


title: ovarian cancer P0791


title: ovarian cancer P0775


title: ovarian cancer P0770


title: ovarian cancer P0766


title: ovarian cancer P0777


title: ovarian cancer P0771


title: ovarian cancer P0802


title: ovarian cancer P0758


title: ovarian cancer P0760


title: ovarian cancer P0773


title: ovarian cancer P0754


title: ovarian cancer P0750


title: ovarian cancer P0774


title: ovarian cancer P0740


title: ovarian cancer P0753


title: ovarian cancer P0725


title: ovarian cancer P0738


title: ovarian cancer P0721


title: ovarian cancer P0737


title: ovarian cancer P0719


title: ovarian cancer P0756

value: Clear cell carcinoma


title: ovarian cancer P0713


title: ovarian cancer P0706


title: ovarian cancer P0698


title: ovarian cancer P0690


title: ovarian cancer P0696


title: ovarian cancer P0687


title: ovarian cancer P0683


title: ovarian cancer P0679


title: ovarian cancer P0676


title: ovarian cancer P0678


title: ovarian cancer P0671


title: ovarian cancer P0669


title: ovarian cancer P0661


title: ovarian cancer P0670


title: ovarian cancer P0657


title: ovarian cancer P0638


title: ovarian cancer P0642


title: ovarian cancer P0652


title: ovarian cancer P0635


title: ovarian cancer P0624


title: ovarian cancer P0626


title: ovarian cancer P0641


title: ovarian cancer P0619


title: ovarian cancer P0615


title: ovarian cancer P0621


title: ovarian cancer P0700


title: ovarian cancer P0689


title: ovarian cancer P0606


title: ovarian cancer P0607


title: ovarian cancer P0613


title: ovarian cancer P0684


title: ovarian cancer P0675


title: ovarian cancer P0594


title: ovarian cancer P0602


title: ovarian cancer P0592


title: ovarian cancer P0593


title: ovarian cancer P0599


title: ovarian cancer P0587


title: ovarian cancer P0580


title: ovarian cancer P0581


title: ovarian cancer P0577


title: ovarian cancer P0620


title: ovarian cancer P0573


title: ovarian cancer P0560


title: ovarian cancer P0556


title: ovarian cancer P0567


title: ovarian cancer P0553


title: ovarian cancer P0563


title: ovarian cancer P0541


title: ovarian cancer P0550


title: ovarian cancer P0543


title: ovarian cancer P0527


title: ovarian cancer P0549


title: ovarian cancer P0539


title: ovarian cancer P0538


title: ovarian cancer P0524


title: ovarian cancer P0588


title: ovarian cancer P0536


title: ovarian cancer P0528


title: ovarian cancer P0589


title: ovarian cancer P0533


title: ovarian cancer P0531


title: ovarian cancer P0510


title: ovarian cancer P0518


title: ovarian cancer P0514


title: ovarian cancer P0517


title: ovarian cancer P0516


title: ovarian cancer P0513


title: ovarian cancer P0456


title: ovarian cancer P0488


title: ovarian cancer P0480


title: ovarian cancer P0504


title: ovarian cancer P0466


title: ovarian cancer P0451


title: ovarian cancer P0525


title: ovarian cancer P0445


title: ovarian cancer P0434


title: ovarian cancer P0447


title: ovarian cancer P0446


title: ovarian cancer P0519


title: ovarian cancer P0431


title: ovarian cancer P0438


title: ovarian cancer P0422


title: ovarian cancer P0413


title: ovarian cancer P0415


title: ovarian cancer P0411


title: ovarian cancer P0407


title: ovarian cancer P0404


title: ovarian cancer P0414


title: ovarian cancer P0401


title: ovarian cancer P0468


title: ovarian cancer P0406


title: ovarian cancer P0400


title: ovarian cancer P0398


title: ovarian cancer P0395


title: ovarian cancer P0387


title: ovarian cancer P0385


title: ovarian cancer P0383


title: ovarian cancer P0394


title: ovarian cancer P0380


title: ovarian cancer P0375


title: ovarian cancer P0369


title: ovarian cancer P0378


title: ovarian cancer P0371


title: ovarian cancer P0356


title: ovarian cancer P0357


title: ovarian cancer P0361


title: ovarian cancer P0372


title: ovarian cancer P0363


title: ovarian cancer P0349


title: ovarian cancer P0347


title: ovarian cancer P0326


title: ovarian cancer P0339


title: ovarian cancer P0322


title: ovarian cancer P0327


title: ovarian cancer P0332


title: ovarian cancer P0337


title: ovarian cancer P0320


title: ovarian cancer P0314


title: ovarian cancer P0324


title: ovarian cancer P0318


title: ovarian cancer P0298


title: ovarian cancer P0294


title: ovarian cancer P0299


title: ovarian cancer P0284


title: ovarian cancer P0300


title: ovarian cancer P0279


title: ovarian cancer P0278


title: ovarian cancer P0262


title: ovarian cancer P0264


title: ovarian cancer P0250


title: ovarian cancer P0256


title: ovarian cancer P0252


title: ovarian cancer P0429


title: ovarian cancer P0230


title: ovarian cancer P0220


title: ovarian cancer P0313


title: ovarian cancer P0211


title: ovarian cancer P0215


title: ovarian cancer P0205


title: ovarian cancer P0197


title: ovarian cancer P0286


title: ovarian cancer P0196


title: ovarian cancer P0283


title: ovarian cancer P0193


title: ovarian cancer P0184


title: ovarian cancer P0194


title: ovarian cancer P0177


title: ovarian cancer P0189


title: ovarian cancer P0174


title: ovarian cancer P0183


title: ovarian cancer P0166


title: ovarian cancer P0242


title: ovarian cancer P0160


title: ovarian cancer P0154


title: ovarian cancer P0159


title: ovarian cancer P0151


title: ovarian cancer P0152


title: ovarian cancer P0147


title: ovarian cancer P0142


title: ovarian cancer P0144


title: ovarian cancer P0210


title: ovarian cancer P0127


title: ovarian cancer P0133


title: ovarian cancer P0110


title: ovarian cancer P0107


title: ovarian cancer P0099


title: ovarian cancer P0102


title: ovarian cancer P0111


title: ovarian cancer P0105


title: ovarian cancer P0179


title: ovarian cancer P0164


title: ovarian cancer P0080


title: ovarian cancer P0094


title: ovarian cancer P0163


title: ovarian cancer P0079


title: ovarian cancer P0085


title: ovarian cancer P0076


title: ovarian cancer P0073


title: ovarian cancer P0068


title: ovarian cancer P0075


title: ovarian cancer P0063


title: ovarian cancer P0065


title: ovarian cancer P0057


title: ovarian cancer P0124


title: ovarian cancer P0055


title: ovarian cancer P0112


title: ovarian cancer P0050


title: ovarian cancer P0046


title: ovarian cancer P0042


title: ovarian cancer P0030


title: ovarian cancer P0038


title: ovarian cancer P0033


title: ovarian cancer P0029


title: ovarian cancer P0037


title: ovarian cancer P0023


title: ovarian cancer P0019


title: ovarian cancer P0013


title: ovarian cancer P0006


title: ovarian cancer P0005


title: ovarian cancer P0016


title: ovarian cancer P0007


title: AJ_BSF_wt_1

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

data_processing:
Reads were mapped with STAR v2.7.10b
Featurecounts were done with FeatureCounts from the package Subread v2.0.4
Assembly: TriTrypDB-63_TbruceiLister427_2018 from https://tritrypdb.org/
Supplementary files format and content: Tab delimited tables with Read Count data

organism: Trypanosoma brucei

source_name: Lister 427

growth_protocol: Bloodstream forms of T. brucei brucei “single marker” S427 (S16) (Lister 427, antigenic type MiTat 1.2, clone 221a) were grown at 37 °C, 5% CO2 in HMI-9 medium supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen, EEUU); Procyclic forms of T. brucei 449 were cultured at 28°C, 5% CO2 in SDM-79 medium containing 10% hiFBS (Invitrogen, EEUU) and 7.5 μg ml−1 hemin (Sigma-Aldrich, EEUU).

extract_protocol:
Total RNA was purified using a total RNA isolation kit (Qiagen, Germany)
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: T. brucei parasites in logarithmic phase were incubated with 2X of the half-maximal inhibitory concentration of AQ1 (BSF: 0,24 uM and PCF: 9), Pt-TTPY (BSF: 0,26 uM and PCF: 48,46 uM) and pyridostatin (BSF: 11,04 uM and PCF: 18,18 uM) for 18 h at 37ºC or 28 ºC,  5% CO2 and 100% of humidity

value: BCF

value: wt


title: ovarian cancer P0053


title: ovarian cancer P0956

hyb_protocol: Target preparation was performed based on Molecular Inversion Probe (MIP) technology using  genomic DNA extracted from the tumor samples according to the Thermo Fisher Scientific recommended protocol. After annealing of MIP linear probe and genomic DNA, cyclic DNA probes were formed by Gap fill reaction with A/T or G/C bases. For both the A/T and G/C reaction solutions, DNA strands other than the cyclic DNA probe were cleaved by Exonuclease, and the cyclic DNA was relinearized by cleavage at the cleavage site.A/T and G/C reaction solutions were mixed with Hybridization Mix and hybridized with the OncoScan CNV Array at 49 °C for 16 to 18 hours. The

scan_protocol: The OncoScan CNV Array was cleaned and stained, followed by fluorescence intensity reading using GeneChip Scanner 3000 7G. Signal data from the image files of the reaction solution of each sample were output numerically as CEL files using Affymetrix GeneChip Command Console Software.

data_processing:
Signal normalization and copy number change analysis were performed on the CEL files using Chromosome Analysis Suite and OSCHP, logR ratio, B-Allele Frequency files were created.
Primary data description: CEL, OSCHP, logR ratio, B-Allele Frequency files

label: Biotin

label_protocol: As per manufacturer (Affymetrix/Thermo Fisher Scientific)

value: Primary tumor


title: ovarian cancer P0968


title: ovarian cancer P0962


title: ovarian cancer P0996


title: ovarian cancer P0978


title: ovarian cancer P0973


title: ovarian cancer P0074


title: ovarian cancer P0970


title: ovarian cancer P0952


title: ovarian cancer P0954


title: ovarian cancer P0941


title: ovarian cancer P0934


title: ovarian cancer P0927


title: ovarian cancer P0993


title: ovarian cancer P0966


title: ovarian cancer P0917


title: ovarian cancer P0919


title: AJ_PCF_wt_1

value: PCF


title: ovarian cancer P0915


title: ovarian cancer P0920


title: ovarian cancer P0912


title: ovarian cancer P0908


title: ovarian cancer P0909


title: ovarian cancer P0906


title: ovarian cancer P0884


title: ovarian cancer P0895


title: ovarian cancer P0893


title: ovarian cancer P0901


title: ovarian cancer P0873


title: ovarian cancer P0888


title: ovarian cancer P0868


title: ovarian cancer P0880


title: ovarian cancer P0892


title: ovarian cancer P0879


title: ovarian cancer P0946


title: ovarian cancer P0853


title: ovarian cancer P0867


title: ovarian cancer P0859


title: ovarian cancer P0854


title: ovarian cancer P0916


title: ovarian cancer P0850


title: ovarian cancer P0844


title: ovarian cancer P0834


title: ovarian cancer P0837


title: ovarian cancer P0831


title: ovarian cancer P0830


title: ovarian cancer P0846


title: ovarian cancer P0882


title: ovarian cancer P0821


title: ovarian cancer P0818


title: ovarian cancer P0802


title: ovarian cancer P0793


title: ovarian cancer P0808


title: ovarian cancer P0809


title: ovarian cancer P0796


title: ovarian cancer P0786


title: ovarian cancer P0791


title: ovarian cancer P0781


title: ovarian cancer P0847


title: ovarian cancer P0777


title: ovarian cancer P0775


title: ovarian cancer P0771


title: ovarian cancer P0774


title: ovarian cancer P0770


title: ovarian cancer P0773


title: ovarian cancer P0827


title: ovarian cancer P0754


title: ovarian cancer P0753


title: ovarian cancer P0750


title: ovarian cancer P0766


title: ovarian cancer P0756


title: ovarian cancer P0861


title: ovarian cancer P0738


title: ovarian cancer P0760


title: ovarian cancer P0758


title: ovarian cancer P0825


title: ovarian cancer P0725


title: ovarian cancer P0721


title: ovarian cancer P0713


title: ovarian cancer P0719


title: ovarian cancer P0690


title: ovarian cancer P0698


title: ovarian cancer P0564


title: ovarian cancer P0740


title: ovarian cancer P0700


title: ovarian cancer P0679


title: ovarian cancer P0683


title: ovarian cancer P0737


title: ovarian cancer P0706


title: ovarian cancer P0696


title: ovarian cancer P0991


title: ovarian cancer P0689


title: ovarian cancer P0687


title: ovarian cancer P0684


title: ovarian cancer P0678


title: ovarian cancer P0670


title: ovarian cancer P0661


title: ovarian cancer P0671


title: ovarian cancer P0676


title: ovarian cancer P0675


title: ovarian cancer P0657


title: ovarian cancer P0642


title: ovarian cancer P0641


title: ovarian cancer P0669


title: ovarian cancer P0652


title: ovarian cancer P0044


title: ovarian cancer P0635


title: ovarian cancer P0638


title: ovarian cancer P0626


title: ovarian cancer P0624


title: ovarian cancer P0620


title: ovarian cancer P0621


title: ovarian cancer P0619


title: ovarian cancer P0613


title: ovarian cancer P0607


title: ovarian cancer P0606


title: ovarian cancer P0594


title: ovarian cancer P0589


title: ovarian cancer P0593


title: ovarian cancer P0592


title: ovarian cancer P0588


title: ovarian cancer P0599


title: ovarian cancer P0580


title: ovarian cancer P0581


title: ovarian cancer P0577


title: ovarian cancer P0573


title: ovarian cancer P0560


title: ovarian cancer P0556


title: ovarian cancer P0563


title: ovarian cancer P0564


title: ovarian cancer P0550


title: ovarian cancer P0549


title: ovarian cancer P0543


title: ovarian cancer P0615


title: ovarian cancer P0541


title: ovarian cancer P0587


title: ovarian cancer P0539


title: ovarian cancer P0538


title: ovarian cancer P0536


title: ovarian cancer P0602


title: ovarian cancer P0528


title: ovarian cancer P0533


title: ovarian cancer P0527


title: ovarian cancer P0531


title: ovarian cancer P0567


title: ovarian cancer P0525


title: ovarian cancer P0519


title: ovarian cancer P0524


title: ovarian cancer P0518


title: ovarian cancer P0516


title: ovarian cancer P0513


title: ovarian cancer P0510


title: ovarian cancer P0514


title: ovarian cancer P0553


title: ovarian cancer P0488


title: ovarian cancer P0504


title: ovarian cancer P0480


title: ovarian cancer P0466


title: ovarian cancer P0451


title: ovarian cancer P0456


title: ovarian cancer P0447


title: ovarian cancer P0446


title: ovarian cancer P0434


title: ovarian cancer P0431


title: ovarian cancer P0438


title: ovarian cancer P0422


title: ovarian cancer P0445


title: ovarian cancer P0414


title: ovarian cancer P0411


title: ovarian cancer P0413


title: ovarian cancer P0404


title: ovarian cancer P0517


title: ovarian cancer P0401


title: ovarian cancer P0400


title: ovarian cancer P0406


title: ovarian cancer P0407


title: ovarian cancer P0395


title: ovarian cancer P0468


title: ovarian cancer P0387


title: ovarian cancer P0385


title: ovarian cancer P0394


title: ovarian cancer P0383


title: ovarian cancer P0380


title: ovarian cancer P0375


title: ovarian cancer P0371


title: ovarian cancer P0372


title: ovarian cancer P0369


title: ovarian cancer P0429


title: ovarian cancer P0415


title: ovarian cancer P0357


title: ovarian cancer P0363


title: ovarian cancer P0361


title: ovarian cancer P0356


title: ovarian cancer P0349


title: ovarian cancer P0337


title: ovarian cancer P0347


title: ovarian cancer P0332


title: ovarian cancer P0339


title: ovarian cancer P0324


title: ovarian cancer P0327


title: ovarian cancer P0326


title: ovarian cancer P0320


title: ovarian cancer P0318


title: ovarian cancer P0322


title: ovarian cancer P0398


title: ovarian cancer P0314


title: ovarian cancer P0313


title: ovarian cancer P0299


title: ovarian cancer P0298


title: ovarian cancer P0300


title: ovarian cancer P0294


title: ovarian cancer P0378


title: ovarian cancer P0286


title: ovarian cancer P0284


title: ovarian cancer P0283


title: ovarian cancer P0264


title: ovarian cancer P0252


title: ovarian cancer P0256


title: ovarian cancer P0242


title: ovarian cancer P0278


title: ovarian cancer P0262


title: ovarian cancer P0250


title: ovarian cancer P0230


title: ovarian cancer P0220


title: ovarian cancer P0211


title: ovarian cancer P0210


title: ovarian cancer P0193


title: ovarian cancer P0205


title: ovarian cancer P0194


title: ovarian cancer P0215


title: ovarian cancer P0197


title: ovarian cancer P0184


title: ovarian cancer P0196


title: ovarian cancer P0179


title: ovarian cancer P0183


title: ovarian cancer P0164


title: ovarian cancer P0163


title: ovarian cancer P0177


title: ovarian cancer P0166


title: ovarian cancer P0174


title: ovarian cancer P0279


title: ovarian cancer P0160


title: ovarian cancer P0159


title: ovarian cancer P0152


title: ovarian cancer P0151


title: ovarian cancer P0147


title: ovarian cancer P0144


title: ovarian cancer P0133


title: ovarian cancer P0127


title: ovarian cancer P0142


title: ovarian cancer P0189


title: ovarian cancer P0114


title: ovarian cancer P0124


title: ovarian cancer P0110


title: ovarian cancer P0111


title: ovarian cancer P0085


title: ovarian cancer P0099


title: ovarian cancer P0094


title: ovarian cancer P0107


title: ovarian cancer P0080


title: ovarian cancer P0075


title: ovarian cancer P0073


title: ovarian cancer P0074


title: ovarian cancer P0076


title: ovarian cancer P0154


title: ovarian cancer P0068


title: ovarian cancer P0065


title: ovarian cancer P0050


title: ovarian cancer P0053


title: ovarian cancer P0046


title: ovarian cancer P0055


title: ovarian cancer P0044


title: ovarian cancer P0102


title: ovarian cancer P0112


title: ovarian cancer P0105


title: ovarian cancer P0042


title: ovarian cancer P0029


title: ovarian cancer P0013


title: ovarian cancer P0023


title: ovarian cancer P0079


title: ovarian cancer P0007


title: ovarian cancer P0030


title: ovarian cancer P0037


title: ovarian cancer P0019


title: ovarian cancer P0016


title: ovarian cancer P0006


title: ovarian cancer P0063


title: ovarian cancer P0057


title: ovarian cancer P0005


title: Control_Mo_rep2

status: Public on Aug 29 2024

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: control Morpholino injected embryos, replicate 2

data_processing:
Sample demultiplexing was performed using Illumina's bcl2fastq Conversion Software v.2.18.0.12 and read quality was checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads were aligned to the Xenopus tropicalis genome assembly version 7.1 with gene annotation from Xenbase (https://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1) using STAR v.2.5.4b (https://github.com/alexdobin/STAR) and secondary alignments were removed with Samtools v.1.3.1 (http://www.htslib.org).
Read counts were summarised on the gene level using Subread featureCounts v.1.5.1 (https://subread.sourceforge.net) with stranded parameter “-s 2”.
Assembly: Xenopus tropicalis v.7.1 (JGI7.1)
Supplementary files format and content: tab-delimited text file with summarized read counts per gene

organism: Xenopus tropicalis

source_name: blastula stage 9 embryos

extract_protocol:
Biological triplicates with 50 embryos per sample at blastula stage 9 were homogenized in 1 ml of QIAzol. RNA was extracted using the miRNeasy kit (QIAGEN) following manufacturer’s instructions with on-column DNAse digestion. RNA integrity (RIN) values were checked using an RNA 6000 Nano kit on a 2100 Bioanalyzer (Agilent) and were consistently above 9.0.
NGS libraries were prepared using Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part #15031047 Rev.E) with a starting amount of 1 μg and amplified in 10 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). All samples were pooled in equimolar ratio and sequenced on a NextSeq 500 High Output Flowcell, SR mode with 84 cycles plus 7 cycles for the index read.

treatment_protocol: ATG-blocking Morpholino antisense oligonucleotides (Gene Tools) were injected into the animal hemisphere of one-cell stage Xenopus tropicalis embryos in a 5 nl volume. Total amount of Morpholinos injected per embryo was 30 ng Tet2 and 30 ng Tet3 or 60 ng standard control Morpholino.

value: blastula stage 9 embryos

value: control Morpholino


title: Tet2_Tet3_Mo_rep3

description: Tet2 and Tet3 Morpholino injected embryos, replicate 3

value: Tet2 and Tet3 Morpholino


title: Control_Mo_rep3

description: control Morpholino injected embryos, replicate 3


title: Tet2_Tet3_Mo_rep1

description: Tet2 and Tet3 Morpholino injected embryos, replicate 1


title: Control_Mo_rep1

description: control Morpholino injected embryos, replicate 1


title: Tet2_Tet3_Mo_rep2

description: Tet2 and Tet3 Morpholino injected embryos, replicate 2


title: ovarian cancer P0033

value: HGSC


title: SJNBL012407_X1, FBS_ACBI1_d4, scRNAseq

status: Public on Aug 28 2024

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.

extract_protocol:
To get single cell suspension, SJNBL012407_X1 cells cultured in SCM or FBS-containing media were treated with TrypLE Express for 8 minutes at 37˚C. After 2 times washing with PBS+0.04% BSA, the cells were filtered using 40 µM pluri-strainer.
Library was performed according to the manufacter's instructions (single cell 3' v3.1 protocol, 10x Genomics). Briefly, SJNBL012407_X1 cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropicated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Human neuroblastoma

tag: culture media

value: FBA containing media


title: SJNBL012407_X1, FBS_DMSO_d4, scRNAseq

description: 10x Genomics

value: FBS containing media

value: DMSO


title: SJNBL012407_X1, SCM, scRNAseq

description: 10x Genomics

value: SCM

value: no treatment


title: 20A042628 Thyroid carcinoma

status: Public on Aug 23 2024

first: Leiqin

last: Liu

address: 320 Yueyang Road

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

description: Thyroid carcinoma

data_processing:
Sequence adapters were trimmed by trim_galore (version 0.6.2) in paired-end mode with default parameters.
Trimmed sequences were aligned to the human genome version hg19 using BSMAP, with options “-q 20 -f 5 -r 0 -v 0.05 -s 16 -S 1”.
Duplicate reads were marked by Sambamba (version 0.7.1).
Mean CpG methylation levels were extracted using MethylDackel (https://github.com/dpryan79/MethylDackel) (version 0.5.0).
genome build/assembly: hg19
processed data files format and content: The bedGraph contains the following 6 columns: 1) The chromosome. 2) The start coordinate. 3) The end coordinate. 4) The methylation percentage rounded to an integer. 5) The number of alignments/pairs reporting methylated bases. 6) The number of alignments/pairs reporting unmethylated bases.
processed data files format and content: The mhap contains the following 6 columns: 1) The chromosome. 2) The start coordinate, also the first CpG site position. 3) The end coordinate, also the last CpG site position. 4) The haplotype status with 1 for methylated sites, 0 for unmethylated ones. 5) Number of DNA methylation haplotypes. 6) Strand.

source_name: thyroid

extract_protocol:
Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (QIAGEN, Cat. No. 69504; Hilden, Germany) per the manufacturer’s instructions. Then, 200 ng of purified genomic DNA were sheared to 100-500 bp using a Covaris S2 (Covaris; Woburn, MA, USA) sonicator. Next, we treated the fragmented DNA using the EpiTect Fast Bisulfite Conversion Kit (QIAGEN, Cat. No. 59824; Hilden, Germany) with a modified protocol--two cycles of 98°C for 5 min and 60°C for 25 min, followed by a hold at 25°.
The bisulfite-converted DNA was subjected to WGBS construction using the Accel-NGS Methyl-seq DNA Library Kit (Swift Biosciences, Cat. No. 51002025P; Ann Arbor, MI, USA) as recommended by the manufacturer. WGBS libraries were sequenced for 2x150 cycles in an Illumina NovaSeq 6000 sequencer.

tag: clinical prognosis

value: THCA

tag: gender

value: male

value: thyroid


title: 20A042625 Breast carcinoma

description: Breast carcinoma

source_name: breast

value: BRCA

value: female

value: breast


title: 20A042612 Cervical and endocervical cancers

description: Cervical and endocervical cancers

source_name: cervix

value: CESC

value: cervix


title: 20A042615 Breast carcinoma

description: Breast carcinoma


title: 20A042599 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042591 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042590 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042571 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042553  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma

source_name: ovary

value: OV

value: ovary


title: 20A042566 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma

value: HNSC


title: 20A042539 Breast carcinoma

description: Breast carcinoma


title: 20A042496 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042450 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A042453 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: ovarian cancer P0038

value: Primary tumor

value: HGSC

value: Serous carcinoma


title: 20A042565 Breast carcinoma

description: Breast carcinoma


title: 20A042540 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042558 Non-small cell lung cancer

description: Non-small cell lung cancer

source_name: lung

value: NSCLC

value: lung


title: 20A042440 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A042444 Breast carcinoma

description: Breast carcinoma


title: 20A042462 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042592 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A042438 Stomach adenocarcinoma

description: Stomach adenocarcinoma

source_name: stomach

value: STAD

value: stomach


title: 20A042490 Colon adenocarcinoma

description: Colon adenocarcinoma

source_name: colon

value: COAD

value: colon


title: 20A042504 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042527 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A042433 Colon adenocarcinoma

description: Colon adenocarcinoma

value: male


title: 20A042405 Colon adenocarcinoma

description: Colon adenocarcinoma

value: female


title: 20A042420 Thyroid carcinoma

description: Thyroid carcinoma

value: THCA

value: thyroid


title: 20A042394 Breast carcinoma

description: Breast carcinoma

value: BRCA

value: breast


title: 20A042406 Cervical and endocervical cancers

description: Cervical and endocervical cancers

value: CESC

value: cervix


title: 20A042401  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma

value: OV

value: ovary


title: 20A042381 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042377 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A042360 Breast carcinoma

description: Breast carcinoma


title: 20A042352 Breast carcinoma

description: Breast carcinoma


title: 20A042346 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042344 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042343 Breast carcinoma

description: Breast carcinoma


title: 20A042339  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042333 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma

value: HNSC


title: 20A042336  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042337  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042330 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042317 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A042300 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042328  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042296 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042288 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042306 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042421 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A042287 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042279 Cervical and endocervical cancers

description: Cervical and endocervical cancers


title: 20A042270  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042245 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A042221 Non-small cell lung cancer

description: Non-small cell lung cancer

value: NSCLC


title: 20A042263 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A042217 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A042200 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A042368 Breast carcinoma

description: Breast carcinoma


title: 20A042220 Non-small cell lung cancer

description: Non-small cell lung cancer

value: lung


title: 20A042216  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042183 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042331 Stomach adenocarcinoma

description: Stomach adenocarcinoma

value: STAD


title: 20A042185 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A042191 Thyroid carcinoma

description: Thyroid carcinoma


title: 20A042178  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042175  Ovarian serous adenocarcinoma

description: Ovarian serous adenocarcinoma


title: 20A042174 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042302 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042150 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A042161 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A042301 Colon adenocarcinoma

description: Colon adenocarcinoma


title: 20A042149 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A042147 Stomach adenocarcinoma

description: Stomach adenocarcinoma

value: stomach


title: 20A042143 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A042139 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A042137 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A041614 Esophageal carcinoma

description: Esophageal carcinoma

source_name: esophagus

value: ESCA

value: esophagus


title: 20A042130 Stomach adenocarcinoma

description: Stomach adenocarcinoma


title: 20A041686 Pancreatic carcinoma

description: Pancreatic carcinoma

source_name: pancreas

value: PACA

value: male

value: pancreas


title: 20A041605 Pancreatic carcinoma

description: Pancreatic carcinoma

value: female


title: 20A041609 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041685 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041597 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041594 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A042163 Non-small cell lung cancer

description: Non-small cell lung cancer


title: 20A041603 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041593 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041573 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma

source_name: liver

value: LIHC

value: liver


title: 20A041583 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041567 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041544 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041566 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041556 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041547 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041543 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041537 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041529 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041523 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A042135 Head and neck squamous  cell carcinoma

description: Head and neck squamous  cell carcinoma


title: 20A041519 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041508 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041606 Pancreatic carcinoma

description: Pancreatic carcinoma


title: 20A041517 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041505 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041510 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041498 Esophageal carcinoma

description: Esophageal carcinoma


title: 20A041558 Liver hepatocellular carcinoma

description: Liver hepatocellular carcinoma


title: 20A041506 Esophageal carcinoma

description: Esophageal carcinoma


title: opossum_scRNAseq_3

status: Public on Aug 16 2024

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: 10x genomics scRNA-seq

data_processing:
Single cell RNA-seq library alignment to Ensembl GRCm39 (mouse) or ASM229v1 (opossum) and quality control was performed using 10x Genomics Cell Ranger 6.0.1 with default parameters (Zheng et al., 2017). CellRanger filtered matrices were then used for further filtering with SoupX (Young and Behjati, 2020) using the standard settings and no additional clustering data. Strained SoupX count matrices were used for all downstream analyses.
see data processing associated with each sample
Assembly: see information associated with each sample
Supplementary files format and content: filtered index (.tsv), feature (.tsv), and matrix (.mtx) files

organism: Monodelphis domestica

source_name: testis

growth_protocol: Animals were grown under standard laboratory conditions and euthanized at the indicated developmental time points.

extract_protocol:
Whole testis single cell suspension was diluted to 10,000 cells/mL and single cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM Library Kit. Libraries were sequenced on an Illumina NovaSeq.
Testes from gray short-tailed opossums at Yale or adult (8-16 week old) male C57BL6/J mice purchased from Jackson Laboratories were harvested and dissociated into single-cell suspension for RNA isolation using collagenase and trypsin. Briefly, testes were removed from the scrotum, decapsulated from the tunica albuginea, and incubated in 0.75mg/mL collagenase in Dulbecco’s Modified Eagle Medium (Gibco 11965-09L; Thermo Fisher Scientific, Inc.) at 37oC. DMEM was added to dilute collagenase and samples were centrifuged for 5 minutes at 400 x g at room temperature. Supernatant was discarded and samples were washed in DMEM. Samples were resuspended in 0.05% trypsin-EDTA (Gibco 25300-054; Thermo Fisher Scientific Inc.) with DNAse (1:10,000; Stem Cell Technologies #07900, Vancouver BC, Canada). The reaction was quenched with 10% Cosmic Calf Serum (Sigma-Aldrich #C8056, Burlington, MA, USA) in DMEM (CCS-DMEM) and centrifuged. Samples were resuspended in CCS-DMEM and filtered through a 100-micron filter. Cell concentration was determined by hemocytometer.
See protocols associated with each sample

value: testis

tag: cell type

value: adult

tag: genome build


title: Sample10_LRRK2

status: Public on Jul 31 2024

city: Tuebingen

first: Mo

last: Dehestani

address: Otfried-Müller-Straße 23

institute: DZNE

description:
poly-adenylated mRNA
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A (introns included)
Supplementary files format and content: all_new_SCT_harmony_res0.1_v1.rds

source_name: ACC

extract_protocol:
The process of isolating nuclei involves breaking down cellular membranes using a detergent lysis technique, followed by centrifugal separation. Specifically, 300 mg of post-mortem brain tissue is homogenized in 2 ml of Nuclei EZ Prep Lysis Buffer with RNase inhibitor, DTT, and Triton X100. After a brief incubation on ice, the tissue is washed with PBSB, filtered, and combined with an ice-cold sucrose cushion solution. The mixture is centrifuged, and the supernatant and debris are discarded. The nuclei are resuspended in PBS buffer and a nuclei suspension buffer, then centrifuged again. DAPI is added to stain the nuclei, which are incubated and then resuspended in sorting buffer for quality inspection. Finally, fluorescence-activated cell sorting (FACS) is used to assess the quality, ensuring that over 95% of the events are DAPI-positive individual nuclei.
Single-nuclei suspension concentration was determined by automatic cell counting (DeNovix CellDrop, DE, USA) using an AO/PI viability assay (DeNovix, DE, USA) and counting nuclei as dead cells. Single-nucleus gene expression libraries were generated using the 10x Chromium Next gel beads-in-emulsion (GEM) Single Cell 3’ Reagent Kit v3.1 (10x Genomics, CA, USA) according to manufacturer’s instructions. In brief, cells were loaded on the Chromium Next GEM Chip G, which was subsequently run on the Chromium Controller (10x Genomics, CA, USA) to partition cells into GEMs. Cell lysis and reverse transcription of poly-adenylated mRNA occurred within the GEMs and resulted in cDNA with GEM-specific barcodes and transcript-specific unique molecular identifiers (UMIs). After breaking the emulsion, cDNA was amplified by PCR, enzymatically fragmented, end-repaired, extended with 3′ A-overhangs, and ligated to adapters. P5 and P7 sequences, as well as sample indices (Chromium i7 Multiplex kit, 10x Genomics, CA, USA), were added during the final PCR amplification step. The fragment size of the final libraries was determined using the Bioanalyzer High-Sensitivity DNA Kit (Agilent, CA, USA). Library concentration was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, MA, USA). snRNA libraries were pooled and paired-end-sequenced on the Illumina NovaSeq 6000 platform (Illumina, CA, USA).

tag: seq name

value: Brain cells

value: ACC

tag: subject status

value: Parkinson's disease (PD) patient

tag: mutation


title: Sample3_LRRK2

description:
poly-adenylated mRNA
10x Genomics

source_name: PFC

value: PFC


title: Sample2_GBA1

description:
poly-adenylated mRNA
10x Genomics


title: Sample12_HC

description:
poly-adenylated mRNA
10x Genomics

value: healthy control


title: Sample1_GBA1

description:
poly-adenylated mRNA
10x Genomics


title: Sample11_HC

description:
poly-adenylated mRNA
10x Genomics


title: Sample9_LRRK2

description:
poly-adenylated mRNA
10x Genomics


title: Sample7_HC

description:
poly-adenylated mRNA
10x Genomics


title: Sample8_HC

description:
poly-adenylated mRNA
10x Genomics


title: Sample6_GBA1

description:
poly-adenylated mRNA
10x Genomics


title: CLSY3_GFP_Panicle_Rep2

status: Public on Jul 27 2024

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adaptor trimming by cutadapt.
The reads obtained were trimmed using cutadapt and aligned to IRGSP1 rice genome with parameters -q -v 3 -k 1 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 5bp bin size.
Assembly: Oryza sativa japonica Nipponbare genome – IRGSP1
Supplementary files format and content: The coverage files of the ChIP-seq alignments were provided in bigwig format.

organism: Oryza sativa

source_name: Panicle (before anthesis)

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Sheared chromatin from the equally developed pre emerged panicle of WT and kd plants were incubated with appropriate antibodies bound to Protein G Dynabeads (Thermo Fisher, catalog number 10003D).  Washes, elution, de-crosslinking and DNA.  purification was done as described. The purified DNA was taken for library preparation. Antibody used (GFP-Sigma G1544) and (myc-Abcam ab9106).
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: Panicle tissues were handled in the same manner.

value: Panicle (before anthesis)

tag: subspecies

value: Indica

value: Pusa Basmati1 (PB1)


title: CLSY3_MYC_Panicle_Rep1

tag: cultivar


title: 20A041564 Liver hepatocellular carcinoma

city: Shanghai

description: Liver hepatocellular carcinoma

tag: tissue


title: Sample5_GBA1

description:
poly-adenylated mRNA
10x Genomics


title: Sample4_LRRK2

description:
poly-adenylated mRNA
10x Genomics


title: DfJ5KO mbt female C

status: Public on Jul 17 2024

city: Barcelona

first: Cayetano

last: Gonzalez

address: baldiri Reixac 10

institute: IRB Barcelona

data_processing:
Data were processed with the Grape RNA-seq pipeline. Raw reads were aligned to the fly genome and transcriptome uding STAR. Genes and transcripts were quantified using RNA-seq by Expectation Maximization (RSEM).
The library size for each sample was scaled according to the TMM (trimmed mean of M values) normalization method.
Expression coverage files in BAM format were generated using STAR (v2.4.0j) and later normalized according to the scaling factors obtained by the TMM normalization method
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Drosophila melanogaster

source_name: larval brain

extract_protocol:
RNA was isolated using magnetic beads (RNAClean XP, Beckman Coulter, A63987) from 10 Drosophila larval brains per sample.
Library preparation were done with NEBNext Ultra RNA II Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina Set 1, 2, and 3 followingthe manufacturer's instructions.

value: larval brain

tag: treatment


title: DfJ5KO mbt male C

tag: genotype


title: DfJ5KO mbt male B


title: DfJ5KO mbt female B


title: DfJ5KO mbt male A


title: INPUT_Rep1


title: INPUT_Rep2


title: dhdKO mbt female A


title: CLSY3_MYC_Panicle_Rep2


title: CLSY3_GFP_Panicle_Rep1


title: DfJ5KO mbt female A


title: dhdKO mbt female C


title: dhdKO mbt female B


title: TrxTKO mbt female C


title: TrxTKO mbt male B


title: TrxTKO mbt female A


title: TrxTKO mbt male A


title: dhdKO mbt male C


title: wt male C

value: wt


title: dhdKO mbt male A

value: male


title: TrxTKO mbt female B


title: TrxTKO mbt male C


title: mbt female C


title: mbt female B


title: mbt female A


title: mbt male C


title: in-situ Hi-C library WG_88GZ

status: Public on Jul 05 2024

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

description:
WG_88GZ
in-situ Hi-C library

data_processing:
Juicer Tools (v1.19.02) Arrowhead with parameters ‘--ignore-sparsity -k SCALE’ for the following data resolutions (kb): 10, 25
RobusTAD (v1.0) was run with parameters ‘--norm=norm’ on 50-kb Hi-C contact matrices generated by Juicer Tools dump with parameters ‘-d observed SCALE BP 50000’.
Loops were called using Chromosight v1.6.1 with default parameters.
Loops were called using Mustache v1.0.1 with default parameters.
Loop interactions were quantified using hicdcdiff function from the package HiC-DC+ v0.99.14
Loop interactions were quantified using Chromosight’s quantify module at 10kb resolution. Significance was determined using a two-sided t-test.
HiCRep was used to calculate the Stratum-adjusted Correlation Coefficient (SCC)
Insulation scores were computed for mcool files at 10-kb resolution with a window size of 100 kb using the diamond-insulation module of cooltools v0.4.0
RNA-seq reads were aligned to hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) using HISAT2 (v2.1.0). A counts table was prepared using the count function of HTSeq (v0.13) and differential expression testing was performed using Limma with Voom transformation (v3.44)
StringTie (v2.0) was used to annotate transcripts present in each sample using parameters ‘-m 150’, then ‘stringtie --merge' was used to generate a unified annotation GTF. GffCompare (v 0.11.7) was run to determine how each of our de novo annotations compared to the GENCODE reference (v34). RNA-seq reads were pseudoaligned and quantified using kallisto (v 0.45.1)
TADpole was used to partition the genome into domains.
Assembly: GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set (hg38)
Assembly: GENCODEv34 transcripts
Supplementary files format and content: arrowhead.contact_domains.10kb.bed: BED format. Arrowhead contact domain calls at 10-kb resolution.
Supplementary files format and content: arrowhead.contact_domains.25kb.bed: BED format. Arrowhead contact domain calls at 25-kb resolution
Supplementary files format and content: chromosight.loops.bedpe: BEDPE format. Loops calls generated by Chromosight
Supplementary files format and content: chromosight_scores.tsv: Table of values. Chromosight scores at each loop position across all samples
Supplementary files format and content: diff_loops.chromosight.chromosight.tsv: Table of differential loop contacts. Loop positions identified by Chromosight, quantified by Chromosight.
Supplementary files format and content: diff_loops.hiccups.chromosight.tsv: Table of differential loop contacts. Loop positions identified by HiCCUPS, quantified by Chromosight.
Supplementary files format and content: diff_loops.mustache.chromosight.tsv: Table of differential loop contacts. Loop positions identified by Mustache, quantified by Chromosight.
Supplementary files format and content: hicrep.scc.tsv: Table of Stratum-adjusted Correlation Coefficient between samples.
Supplementary files format and content: insulationScore.10kbBin.100kbwindow.bw: BigWig format. Insulation Score as implemented by cooltools.
Supplementary files format and content: insulationScores.cooltools.tsv: Table of Insulation Score values across samples.
Supplementary files format and content: mustache_loops.count_table.tsv: Table of loop counts. Loop positions identified by Mustache, quantified by HiCDCPlus.
Supplementary files format and content: rna.htseq_count_table.tsv: Table of bulk RNA-seq counts. Quantified by HTseq with GENCODE v34 reference.
Supplementary files format and content: rna.limma.PFA.wrt.nonPFA.tsv: Table of differential expression calls generated by Limma with Voom transformation.
Supplementary files format and content: BoundaryScores.left.50kb.bdg: Bedgraph format. RobusTAD left boundary score.
Supplementary files format and content: BoundaryScores.right.50kb.bdg: Bedgraph format. RobusTAD right boundary score.
Supplementary files format and content: BoundaryScores.left.50kb.wig: Wiggle format. RobusTAD left boundary score.
Supplementary files format and content: BoundaryScores.right.50kb.wig: Wiggle format. RobusTAD right boundary score.
Supplementary files format and content: stringTie.pedBrainTx.annotated.sorted.gtf: GTF format. Transcript annotation generated from bulk RNA-seq using StringTie, referencing GENCODEv34.
Supplementary files format and content: tadpole.bed: BED format. TADpole calls for partitioning genome into domains.
Supplementary files format and content: union_eigenvalues.tsv: Table of compartment eigenvalues across all samples.

source_name: Fetal brain

growth_protocol: The majority of samples were uncultured, primary tissue. Cultured samples (with biotype==culture) were grown as described previously (Michealraj et al. Cell. 2020; PMID: 32445698).

extract_protocol: Approximately 2.5M cells were used for In-situ Hi-C library approach (Rao et al. Cell. 2014; PMID: 25497547) with library preparation performed as described previously (Johnston et al. Genome Research. PMID: 31249064). Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).

value: Fetal brain

tag: tumor type

value: nonTumor

tag: subgroup

value: GZ

tag: biotype


title: in-situ Hi-C library WG_119GZ

description:
WG_119GZ
in-situ Hi-C library


title: mbt male B


title: in-situ Hi-C library ST4

description:
ST4
in-situ Hi-C library

source_name: Pediatric brain tumor derived cell culture

value: EP

value: STE

value: culture


title: mbt male A


title: in-situ Hi-C library WG_119CP

description:
WG_119CP
in-situ Hi-C library

value: CP


title: in-situ Hi-C library RTL

description:
RTL
in-situ Hi-C library

source_name: Pediatric brain

value: Pediatric brain


title: wt female A

value: female


title: wt female B


title: wt female C


title: in-situ Hi-C library WG_126GZ

description:
WG_126GZ
in-situ Hi-C library


title: in-situ Hi-C library WG_88CP

description:
WG_88CP
in-situ Hi-C library


title: in-situ Hi-C library WG_126CP

description:
WG_126CP
in-situ Hi-C library


title: in-situ Hi-C library MB4143

description:
MB4143
in-situ Hi-C library

value: MB

value: SHH


title: wt male A


title: in-situ Hi-C library MB3807

description:
MB3807
in-situ Hi-C library


title: dhdKO mbt male B


title: in-situ Hi-C library MB3716

description:
MB3716
in-situ Hi-C library


title: in-situ Hi-C library MB3693

description:
MB3693
in-situ Hi-C library


title: in-situ Hi-C library PS10801

description:
PS10801
in-situ Hi-C library

value: Pediatric brain tumor derived cell culture

value: HGG


title: in-situ Hi-C library PFA4

description:
PFA4
in-situ Hi-C library

value: PFA


title: in-situ Hi-C library PCGMB2

description:
PCGMB2
in-situ Hi-C library

value: Histone WT


title: in-situ Hi-C library MB3662

description:
MB3662
in-situ Hi-C library


title: wt male B

value: larval brain

value: wt


title: in-situ Hi-C library PFA9N

description:
PFA9N
in-situ Hi-C library


title: in-situ Hi-C library KNS42

description:
KNS42
in-situ Hi-C library


title: in-situ Hi-C library HSJ050T

description:
HSJ050T
in-situ Hi-C library


title: in-situ Hi-C library MB3690

description:
MB3690
in-situ Hi-C library


title: in-situ Hi-C library LTL

description:
LTL
in-situ Hi-C library


title: in-situ Hi-C library E851

description:
E851
in-situ Hi-C library


title: in-situ Hi-C library HSJ051T

description:
HSJ051T
in-situ Hi-C library


title: in-situ Hi-C library E840

description:
E840
in-situ Hi-C library


title: in-situ Hi-C library E833

description:
E833
in-situ Hi-C library


title: in-situ Hi-C library HSJ019

description:
HSJ019
in-situ Hi-C library


title: in-situ Hi-C library HSJ031T

description:
HSJ031T
in-situ Hi-C library


title: in-situ Hi-C library G477

description:
G477
in-situ Hi-C library


title: in-situ Hi-C library HSJ002

description:
HSJ002
in-situ Hi-C library

value: JPA


title: in-situ Hi-C library E835

description:
E835
in-situ Hi-C library


title: in-situ Hi-C library GBM002

description:
GBM002
in-situ Hi-C library


title: in-situ Hi-C library HSJ009

description:
HSJ009
in-situ Hi-C library

value: PFB


title: in-situ Hi-C library E783

description:
E783
in-situ Hi-C library


title: in-situ Hi-C library E838

description:
E838
in-situ Hi-C library


title: in-situ Hi-C library E823

description:
E823
in-situ Hi-C library


title: in-situ Hi-C library E820

description:
E820
in-situ Hi-C library


title: in-situ Hi-C library E2181

description:
E2181
in-situ Hi-C library


title: in-situ Hi-C library E2115

description:
E2115
in-situ Hi-C library

value: spinal


title: in-situ Hi-C library E2112

description:
E2112
in-situ Hi-C library

value: EP


title: in-situ Hi-C library E809

description:
E809
in-situ Hi-C library


title: in-situ Hi-C library E2105

description:
E2105
in-situ Hi-C library


title: in-situ Hi-C library E805

description:
E805
in-situ Hi-C library


title: in-situ Hi-C library E2061

description:
E2061
in-situ Hi-C library


title: in-situ Hi-C library E782

description:
E782
in-situ Hi-C library


title: in-situ Hi-C library E2223

description:
E2223
in-situ Hi-C library


title: in-situ Hi-C library E519

description:
E519
in-situ Hi-C library


title: in-situ Hi-C library HSJ022

description:
HSJ022
in-situ Hi-C library

value: nonTumor


title: in-situ Hi-C library E1859

description:
E1859
in-situ Hi-C library


title: in-situ Hi-C library E2113

description:
E2113
in-situ Hi-C library


title: in-situ Hi-C library E1858

description:
E1858
in-situ Hi-C library

value: STE


title: in-situ Hi-C library DIPG6

description:
DIPG6
in-situ Hi-C library

value: culture


title: in-situ Hi-C library BT245_parental_K27M

description:
BT245_parental_K27M
in-situ Hi-C library


title: in-situ Hi-C library DIPG13_parental_K27M

description:
DIPG13_parental_K27M
in-situ Hi-C library


title: in-situ Hi-C library E2074

description:
E2074
in-situ Hi-C library

value: Pediatric brain


title: in-situ Hi-C library E2053

description:
E2053
in-situ Hi-C library


title: in-situ Hi-C library E1864

description:
E1864
in-situ Hi-C library


title: in-situ Hi-C library 3004

description:
3004
in-situ Hi-C library

value: PFA K27M


title: in-situ Hi-C library E767

description:
E767
in-situ Hi-C library


title: in-situ Hi-C library E1816

description:
E1816
in-situ Hi-C library


title: in-situ Hi-C library DIPG13_C8_K27M

description:
DIPG13_C8_K27M
in-situ Hi-C library


title: in-situ Hi-C library E562

description:
E562
in-situ Hi-C library


title: WG_88CP

data_processing:
Fastqs were processed to hic files using Juicer v1.6.
Contact domains were annotated from hic files using Arrowhead from Juicer Tools v1.19.02
Loops were annotated from hic files using HiCCUPS from Juicer Tools v1.19.02
Compartments were annotated from hic files using the leading eigenvectors of the Pearson correlation matrix.
Boundary scores were annotated from 50-kb contact matrices using Robustad v1.0
Multi-resolution cooler (.mcool) files were generated from hic files using hic2cool v0.8.3.
Significant long-range interactions were identified using Mustache v1.0.1 (https://github.com/ay-lab/mustache, PMID:  32998764) from 10kb contact matrices with default parameters.
Insulation scores were computed at 10-kb resolution with a window size of 100 kb using the diamond-insulation module of cooltools v0.4.0.
TULIP calls were generated by identifying 50-kb bins separated by > 10 Mb that exhibited unusually high interaction frequency. HiC contact signal was thresholded, B-B compartment interactions were isolated, then the pixels of the resulting Hi-C contact matrix were smoothed using ImageMagick v7.0.10_28.  Only bins covered by >10 interactions were maintained in final TULIP calls.
Transcriptome assembly was accomplished using HISAT2 alignment (v2.1.0), StringTie assembly (v2.0), and GffCompare (v 0.11.7) merging of transcripts with GenCode v34 annotation.
Transcript quantification was performed using kallisto (v 0.45.1)
Differential expression calling was performed using sleuth (v0.30.0)
Genome_build: GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set
Supplementary_files_format_and_content: TSV: BoundaryScores_chrAll_50kb.tsv; RobusTAD output containing genomic bin, Left Score, Right Score, and Max Score for each bin in the genome.
Supplementary_files_format_and_content: TSV: TADBoundaryCalls_chrAll_50kb.tsv; RobusTAD output containing genomic bin, Left Score, Right Score, and Max Score for likely boundary regions only.
Supplementary_files_format_and_content: BED: TADBoundaryCalls.50kb.bed; Boundary regions called by RobusTAD in BED format.
Supplementary_files_format_and_content: BED: eigenvalue_allChr_50kb.bed; Compartment status based on eigenvector of Pearson correlation matrix.
Supplementary_files_format_and_content: WIG: eigenvalue_allChr_50kb.wig; Eigenvalues for each big of leading eigenvector of the Pearson correlation matrix. Positive values should associate with Type A compartments with open chromatin.
Supplementary_files_format_and_content: HIC: .hic; Juicebox-formatted Hi-C contact map
Supplementary_files_format_and_content: MCOOL: .mcool; multi-resolution cooler formatted Hi-C contact map
Supplementary_files_format_and_content: TSV: PFA-wrt-nonPFA_LRT_byGene_w_FC_noNA.wGenomePos.tsv; Differential expression output from Sleuth either by gene or by transcript
Supplementary_files_format_and_content: Rdata: union.abundance.gene.Rdata; Binary R format of Kallisto-quantified abundance for each sample, either by gene or by transcript
Supplementary_files_format_and_content: TSV: union.abundance.gene.tsv; Tab-separated format of Kallisto-quantified abundance for each sample, either by gene or by transcript
Supplementary_files_format_and_content: TSV: union_arrowhead_scores.tsv; Arrowhead scores for each sample for the union of all Arrowhead domains called. First column contains the position as an underscore-delimited BEDPE entry with the resolution of the original call trailing the @ symbol
Supplementary_files_format_and_content: RDS: mustache.ep_union.dds.rds; Union of Mustache-called loop scores for all Ependymoma (subgroup==EP) samples.
Supplementary_files_format_and_content: TSV: insulation_scores; Output of cooltools insulation score metrics.
Supplementary_files_format_and_content: TSV: merged_loops.bedpe; Output of HiCCUPS loop calls
Supplementary_files_format_and_content: TSV: ; Output of Mustache loop calls
Supplementary_files_format_and_content: BED: tulips.bed; BED-format genome positions of TULIP calls for each sample.

value: CP


title: in-situ Hi-C library BT2018078

description:
BT2018078
in-situ Hi-C library

value: LGG

value: Unspecified


title: WG_119GZ

value: GZ


title: ST4


title: in-situ Hi-C library 190109

description:
190109
in-situ Hi-C library

value: ATRT


title: in-situ Hi-C library BT2018011

description:
BT2018011
in-situ Hi-C library


title: RTL


title: in-situ Hi-C library BT2018110

description:
BT2018110
in-situ Hi-C library

value: HGG

value: Histone WT


title: PS10801


title: PFA4

value: PFA


title: PCGMB2


title: MB4143

value: MB

value: SHH


title: in-situ Hi-C library 180509

description:
180509
in-situ Hi-C library


title: in-situ Hi-C library 180618

description:
180618
in-situ Hi-C library

value: CPP


title: MB3807


title: in-situ Hi-C library 170922

description:
170922
in-situ Hi-C library

value: JPA


title: in-situ Hi-C library E2051

description:
E2051
in-situ Hi-C library

value: EP


title: WG_88GZ

value: nonTumor


title: in-situ Hi-C library E1697

description:
E1697
in-situ Hi-C library


title: MB3693


title: WG_126GZ


title: MB3662


title: LTL


title: WG_126CP


title: PFA9N

value: culture


title: WG_119CP


title: HSJ051T


title: HSJ031T


title: MB3690


title: HSJ050T


title: MB3716


title: HSJ022


title: HSJ019


title: HSJ009

value: PFB


title: E851


title: GBM002


title: HSJ002


title: G477


title: E840


title: E838


title: E835


title: E809


title: E820


title: E833


title: E805


title: KNS42


title: E783


title: E782


title: E2112


title: E767


title: E2074


title: E2223


title: E562


title: E519


title: E2105

value: spinal


title: E2061


title: E2113


title: PFA4, H3K9me3

data_processing:
Reads were aligned to hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) using bwa mem
Alignments were filtered out if (1) the chromosome name contained “chrUn”, “random”, or “_alt” (2) the alignment MAPQ was lower than 30 or (3) the alignment overlapped the ENCODE Unified GRCh38 Exclusion List (https://www.encodeproject.org/files/ENCFF356LFX/).
Peak calling was performed using MACS2 (v 2.1.2) including input control BAMs. Additional parameters to the MACS2 callpeak function include: “-f BAMPE -g hs --broad --bdg --SPMR”.
Fold enrichment traces were generated using MACS2 bdgcmp with the parameter “-m FE”.
TDF files generated using "igvtools toTDF -z 10"
Assembly: hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set)
Supplementary files format and content: broadPeaks: Output of MACS2 peak calling.
Supplementary files format and content: FE.sorted.bdg: Bedgraph fold-enrichment trace generated by MACS2 bdgcmp.
Supplementary files format and content: FE.tdf: Compressed Bedgraph for IGV viewing.

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma), followed by reverse crosslinking with glycine. Fixed cell preparations were washed in PBS, pelleted and stored at −80 °C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a Diagenode BioRuptor for 15 cycles, 30s on 30s off. After sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated Drosophila S2 cell chromatin was spiked-in the samples.
ChIP-seq was performed as previously described for primary cultures (PMID 30890717).
ChIP-seq was performed as previously described for tumor tissue (PMID 29258295)
Library construction used Kapa HTP Illumina library preparation reagents, following manufacturer’s instructions

value: Pediatric brain tumor derived cell culture

tag: chip antibody

value: H3K9me3, Active Motif, 39161


title: E2181


title: E823


title: E2051

value: STE


title: E1864


title: E809, H3K9me3

value: Pediatric brain


title: E805, H3K9me3


title: E1859


title: PFA9N, H3K9me3


title: E823, H3K9me3


title: E1697


title: E2115


title: E782, H3K9me3


title: E2053


title: E767, H3K9me3


title: E562, H3K9me3


title: E1816


title: DIPG13_parental_K27M


title: DIPG6


title: E519, H3K9me3


title: PFA9N, H3K27me3


title: E783, H3K9me3


title: BT245_parental_K27M


title: BT2018110


title: E805, H3K27me3

value: H3K27me3, Diagenode, C15410069


title: E809, H3K27me3


title: E1858


title: BT2018078

value: LGG

value: Unspecified


title: 190109

value: ATRT


title: BT2018011


title: E782, H3K27me3

value: PFA


title: E783, H3K27me3


title: E767, H3K27me3


title: 180509

value: HGG

value: Histone WT


title: 170922

value: JPA