title: Experiment 2, 2xmRNA vaccinated animal 1, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung24
reads2d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 3, 2dpi, lung sample for bulk RNA-seq

status: Public on May 16 2022

type: SRA

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
2d_lung38
reads2d_counts.txt.gz

library_source: transcriptomic

data_processing:
The Mesocricetus auratus genome MesAur 2.0 was downloaded from https://www.ncbi.nlm.nih.gov/genome/11998. The GFF file was converted to GTF, the generic gene names (LOCxxx) replaced with mouse-derived official gene symbols for several key genes, and 3'-UTRs extended as described previously (doi: 10.1101/2021.10.02.462569). Then, the SARS-CoV-2 genome annotation was merged.
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
For single-cell RNA-sequencing data, fastq files were processed using a the mergend MesAur2.0/SARS-CoV-2 genome with the GTF file provided here by applying CellRanger 6.0.2 with standard parameters
For single-cell RNA-sequencing data, fastq files were processed using a merged Roborvski hamster/SARS-CoV-2 genome by applying CellRanger 6.0.2 with standard parameters
Assembly: MesAur 2.0
Assembly: SARS-CoV-2 MN908947
Supplementary files format and content: GTF file
Supplementary files format and content: tab-separated values
Supplementary files format and content: h5 matrix

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: Lung

growth_protocol:
Hamsters were vaccinated intramuscularly with either an experimental adenovirus vector vaccine containing the whole SARS-CoV-2 spike (5 _ 108 infectious units (IFU) per animal) (PMID: 34835096), or BNT162b2 (5 ug per animal) or intranasally with 1x105 pfu of the live-attenuated SARS-CoV-2 vaccine candidate sCPD9 (PMID: 34320400, PMID: 34851677). For the prime-boost experiment, immunity was boosted by a second vaccination with the respective vaccines at the same dose 21 days after primary vaccination. In, one group, animals were primed with BNT162b2 and boosted with sCPD9, all other groups received a homologues boost.
Hamsters were weighted daily and monitored for signs of disease twice-daily. Hamsters were selected randomly for all scheduled take-out time points (day 2 and 5).
Euthanasia prior analysis occurred by cervical dislocation exsanguination under anesthesia as previously described (PMID 32698441, 33271063). Peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial as backup to repeat virological analyses as needed.

extract_protocol:
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
For isolation of single cells, the caudal lobe of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA) and counted via hemocytometer and trypan blue.
Then, 1,000,000 lung cells per sample were subjected to Cell Multiplexing Oligo (CMO) labeling according to the manufacturers’ instructions (3ʹ-CellPlex-Kit-Set-A, 10x Genomics). Labelled cells from 12 samples were pooled, filtered (40 µm) and counted. Pooled cells were adjusted to a final concentration of ~1,600 cells / μL and filtered with 40 µm FloMi filters (Merck) suitable for low volumes prior subjection to scRNA sequencing.
For Lung RNA Bulk sequencing the lobus medialis of the right lung lobe was removed carefully and homogenzied in Trizol reagent using a bead mill procedure (Speedmill, Analytic Jena), RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: 21 days following primary vaccination or 14 days following booster vaccination, hamsters were infected intranasally as previously described (PMID 32698441, 33271063). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 Variant Delta. [SARS-CoV-2, Human, 2021, Germany ex India, 20A/452R (B.1.617)] intranasally under anesthesia.

tag: first vaccination

value: adenovirus

tag: second vaccination

tag: sampling timepoint

tag: adapter sequence

value: GATCGGAAGAGCACACGT


title: Experiment 2, 2xAdenovirus vaccinated animal 4, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung39
reads2d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 1, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung34
reads2d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 2, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung35
reads2d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 5, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung10
reads2d_counts.txt.gz

value: attenuated


title: Experiment 2, 2xattenuated vaccinated animal 4, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung08
reads2d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 1, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung04
reads2d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 4, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung46
reads2d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 3, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung09
reads2d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 3, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung41
reads2d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 1, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung45
reads2d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 5, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung50
reads2d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 4, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung19
reads2d_counts.txt.gz

value: mRNA


title: Subject 56 before Mifepristone treatment

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA).
Sequenced raw FASTQ files were trimmed for adapters and contaminants such as ribosomal DNA, mitochondrial DNA, unclassified sequences using Bowtie 2 aligner and kraken database, respectively.
Trimmed reads were mapped to the reference genome hg38 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using hg38 assembly and Ensemble transcripts release 99
Genome_build: hg38
Supplementary_files_format_and_content: Filtered Gene Counts in a txt format

molecule: total RNA

organism: Homo sapiens

source_name: Core Needle Breast Biopsy

extract_protocol:
Total RNA is extracted using trizol reagent with Purelink RNA miniprep Kit as per the manufacturers protocol
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014), tagmentation step was accomplished using Nextera XT kit (Illumina) and sequencing was done in Illumina NextSeq 550® at the bioinformatics expression analysis facility at Karolinska University hospital, Sweden.

treatment_protocol: Core needle breast biopsies collected at baseline and after two months of 50 mg mifepristone treatment every other day from healthy women (n=16), aged 18-35 years, with regular menstrual cycles and with no hormonal treatment.

tag: tissue

value: Breast Biopsy

tag: disease state

value: healthy

tag: subject id

value: Subject 56

tag: treatment

value: before Mifepristone treatment


title: Subject 49 After Mifepristone treatment

value: Subject 49

value: After Mifepristone treatment


title: HEK293T tRF-3004b overexpression

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

country: USA

institute: University of Alabama

data_processing:
kallisto v0.46.1 was used with paired-end and stranded mode to quantify reads to human GRCh38 Refseq Transcripts (from NCBI Human Genome Resources).
Genome_build: hg38
Supplementary_files_format_and_content: Kallisto generated abundance output on refseq (GRCh38)

source_name: HEK293T tRF-3004b overexpression

growth_protocol: Cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles medium with L-glutamine (GE #SH30081.01) plus 10% fetal bovine serum (Gibco #10437028) and 1% penicillin/streptomycin (Gibco #15140122).

extract_protocol:
Total RNAs was extracted from cell lines by TRIzol Reagent (Invitrogen #15596018) and Direct-zol RNA Miniprep Plus Kit with on-column DNase treatment (ZYMO #R2071).
Total RNAs (0.1-1 μg) were poly-A selected by NEBNext poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and followed by NEBNext UltraII Directional RNA Kit (NEB #7765).

treatment_protocol: 500 nM final total concentration of RNA mimetic (human tRF-3004b: /5Phos/-rUrCrArArArUrCrUrCrGrGrUrGrGrArArCrCrUrCrCrA-/3OH/) was reverse transfected with Lipofectamine RNAiMax (Thermo Fisher #13778150) and collected 120 hrs post transfection.

tag: cell line


title: HEK293T Ctrl non-targeting RNA

source_name: HEK293T Ctrl non-targeting RNA

treatment_protocol: 500 nM final total concentration of RNA mimetic (non-targeting GL2: /5Phos/-rCrGrUrArCrGrCrGrGrArArUrArCrUrUrCrGrArUrU-/3OH/) was reverse transfected with Lipofectamine RNAiMax (Thermo Fisher #13778150) and collected 120 hrs post transfection.


title: Subject 41 After Mifepristone treatment

value: Subject 41


title: Subject 49 before Mifepristone treatment


title: Experiment 2, Non-vaccinated animal 2, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung49
reads2d_counts.txt.gz


title: Subject 56 After Mifepristone treatment


title: Subject 38 After Mifepristone treatment

value: Subject 38


title: Subject 38 before Mifepristone treatment


title: Subject 41 before Mifepristone treatment


title: Subject 31 After Mifepristone treatment

value: Subject 31


title: Subject 24 before Mifepristone treatment

value: Subject 24


title: Experiment 2, 2xattenuated vaccinated animal 2, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung05
reads2d_counts.txt.gz


title: Subject 24 After Mifepristone treatment


title: Subject 31 before Mifepristone treatment


title: Subject 15 After Mifepristone treatment

value: Subject 15


title: Subject 20 before Mifepristone treatment

value: Subject 20


title: Subject 16 After Mifepristone treatment

value: Subject 16


title: Subject 20 After Mifepristone treatment


title: Subject 16 before Mifepristone treatment


title: Subject 14 After Mifepristone treatment

value: Subject 14


title: Subject 15 before Mifepristone treatment


title: Subject 8 After Mifepristone treatment

value: Subject 8


title: Subject 8 before Mifepristone treatment


title: Subject 7 After Mifepristone treatment

value: Subject 7


title: Subject 7 before Mifepristone treatment


title: Subject 4 After Mifepristone treatment

value: Subject 4


title: Subject 2 After Mifepristone treatment

value: Breast Biopsy

value: Subject 2


title: Subject 4 before Mifepristone treatment

value: healthy


title: Subject 2 before Mifepristone treatment

value: before Mifepristone treatment


title: Subject 14 before Mifepristone treatment


title: Subject 1 After Mifepristone treatment

value: Subject 1


title: Subject 23 before Mifepristone treatment

value: Subject 23


title: Subject 23 After Mifepristone treatment

value: After Mifepristone treatment


title: polysome_seq_KD_Ctrl_P2

city: Beijing

first: Yufeng

last: Gao

state: Beijing

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
For the RNA-seq and polysome-seq data, all samples were sequenced using an Illumina HiSeq X Ten platform with a paired-end 150 base-pair (bp) read length. All reads were mapped to the Homo sapiens genome (Ensembl GRCh38.p5) by TopHat2 (v2.1.1) using default settings. Read counts were normalized using Cufflinks (v2.2.1) 'cuffnorm'. The translational efficiency (TE) value was calculated by taking the ratio of polysome-seq reads over RNA-seq counts with R.
For the RIP-seq experiment, we performed two replicates sequenced using Illumina HiSeq X Ten platform with a paired-end 150 base-pair (bp) read length. All reads were mapped to the Homo sapiens genome (Ensembl GRCh38.p5) by TopHat2 (v2.1.1) using default settings. The protein bound transcripts were identified by Cufflinks (v2.2.1) 'cuffdiff’ software with p value<0.05 and fold-change (IP vs. Input) > 1.2.
For the MeRIP-seq experiment, we performed two replicates for m6A immunoprecipitation (IP) group and input control in MGC-803 cells, and libraries sequenced by using Illumina HiSeq X Ten with pair end 150bp. Low quality reads were removed by Trimmomatic (v0.36) tool. Clean reads were aligned to the Homo sapiens genome (Ensembl GRCh38.p5) using TopHat2 (v2.1.1) with default settings. m6A peaks were detected by R packages with 'MeTPeak' and filtered by log10(p value) < -4 and Log2(fold-change) >3.
Supplementary_files_format_and_content: peaks bed file for MeRIP-seq data; expression matix for RNA-seq, polysome-seq and RIP-seq data

source_name: Gastric cancer cells

growth_protocol: Gastric cancer cell line, MGC-803(DMEM), was obtained from the ATCC and grown in corresponding medium with 10% FBS (Hyclone, Logan, Utah) at 37 ºC in 5% CO2 cell culture incubator. Cell line was tested for mycoplasma detection according to the ATCC cell line verification test recommendations.

extract_protocol:
Total RNA was extracted from cells and tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) and protein-RNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit  (E7530L). Briefly, to deplete rRNA(MeRIP-seq and RIP-seq), we used 1,000 ng of fragmented  RNA , with the NEBNext rRNA remove kit(E6310X) following the manufacturer’s instructions  and to isolate poly(A)+ mRNA(RNA-seq and polysome-seq), we used 5 μg of polysome total RNA with the PolyATtract®mRNA Isolation Systems (Promega) following manufacturer’s standard protocol.

treatment_protocol: MGC-803 was treated with lentivirus for 48 hours.

value: stomach

tag: antibody

value: treated with METTL3/PABPC1 knock down control  for 48 hours


title: polysome_seq_OE_Ctrl_P2

value: treated with METTL3_wt/mut overexpression control for 48 hours


title: polysome_seq_KD_Ctrl_P1


title: polysome_seq_shPABPC1_P2

value: treated with shPABPC1  for 48 hours


title: polysome_seq_OE_Ctrl_P1


title: polysome_seq_shPABPC1_P1


title: polysome_seq_METTL3_wt_Pm

value: treated with METTL3_wt  for 48 hours


title: polysome_seq_METTL3_wt_P1


title: polysome_seq_KD_Ctrl_Pm


title: polysome_seq_shPABPC1_Pm


title: polysome_seq_shMETTL3_Pm

value: treated with shMETTL3  for 48 hours


title: polysome_seq_METTL3_wt_P2


title: polysome_seq_shMETTL3_P1


title: polysome_seq_shMETTL3_P2


title: polysome_seq_METTL3_mut_Pm

value: treated with METTL3_mut  for 48 hours


title: polysome_seq_METTL3_mut_P1


title: RNA_seq_KD_Ctrl_input


title: polysome_seq_METTL3_mut_P2


title: RNA_seq_OE_Ctrl_input


title: Subject 1 before Mifepristone treatment


title: polysome_seq_OE_Ctrl_Pm


title: RNA_seq_shMETTL3_input


title: RNA_seq_METTL3_wt_input


title: RNA_seq_shPABPC1_input


title: MeRIP_IP_rep1

description: IP_MeRIP_MeTPeak_peaks.bed.gz,IP_MeRIP_exomePeak_peaks.bed.gz

data_processing:
Library strategy: Me-RIP-seq
For RIP-seq data: samples were sequenced by Illumina HiSeq X-ten with pair-end 150-base pair (bp) read length. The RIP–seq reads were mapped to human genome version hg19 by Tophat2 version 2.1.1 with default settings. The RIP targets were defined as genes with Log2(immunoprecipitation/input)>0, and P<0.05.
For RNA-seq data: all RNA-seq samples were sequenced by Illumina HiSeq X-ten with pair-end 150-base pair (bp) read length. All reads were mapped to human genome version hg19 by Tophat2 version 2.1.1 with default settings (32). Read counts were calculated using HTSeq (32). Differential gene expression was calculated by DESeq2 (Log2 KD/NC>1, P<0.05).
For m6A-seq data: MeRIP and Input sequencing data were sequenced by Illumina HiSeq X-ten with pair-end 150-base pair (bp) read length transcriptome annotation using TopHat2 version 2.1.1 with default settings (32). The m6A level changes for immunoprecipitation/input were calculated by using MACS (33) (Q value < 0.05).
Genome_build: Ensembl GRCh37.p5
Supplementary_files_format_and_content: peaks bed file for m6A-seq data; expression matix for RNA-seq,polysome-seq and RIP-seq data

value: Anti-N6-methyladenosine (m6A)(Millipore, clone 17-3-4-1, lot 2913860)

value: untreated


title: MeRIP_input_rep2


title: RNA_seq_METTL3_mut_input


title: MeRIP_input_rep1


title: RIP_PABPC1_rep2


title: RIP_PABPC1_rep1


title: RIP_input_rep1


title: RIP_IgG_rep1

value: IgG(Cell Signaling Technology, #2729)


title: RIP_METTL3_rep2


title: RIP_IgG_rep2


title: RIP_METTL3_rep1


title: RIP_input_rep2


title: Input_KO2

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
Library strategy: Nano-TRAP
Basecalling: guppy (v.3.6.1)
Demultiplexing: guppy (v.3.6.1)
Alignment to genome: minimap2 (v.2.14)
Counting at per-gene level: bambu (v.0.3.0) + DESeq2 (v.1.34.0)
Genome_build: GRCm38.primary_assembly.genome.fa
Supplementary_files_format_and_content: Tab delimited file with counts at per-gene level

organism: Mus musculus

source_name: Adult heart

growth_protocol: For the IP experiment, hearts were homogenized using the homogenization buffer (50 mM Tris-HCl, pH 7.5; 100 mM KCl; 12 mM MgCl2; 1% Nonidet P-40 substitute; 1 mM DTT; 200 U/ml RNasin; 1 mg/ml heparin; 100 μg/ml cycloheximide; 1× protease inhibitor mixture). For the input experiment, total RNA was extracted from heart homogenates using TRIzol.

extract_protocol:
For the IP experiment, translating ribosomes were pulled down using anti-HA antibodies (BioLegend, 901513) and Pierce™ Protein A/G Magnetic Beads. Total RNA was extracted from immunoprecipitates using the Qiagen RNeasy extraction kit supplemented with β-mercaptoethanol. For both the IP and Input experiments, Poly(A) enrichment was done using Dynabeads Oligo(dT)25 beads.
Both the IP and Input libraries were prepared using the ONT's sequncing kit SQK-DCS109, and barcoding expansion kit: EXP-NBD104.
Libraries were multiplexed using the barcoding expansion kit and sequenced in a MinION flowcell (FLO-MIN106).

treatment_protocol: For the IP experiment, hearts were treated with 100 µg/mL cycloheximide upon excision.

tag: genotype


title: MeRIP_IP_rep2


title: IP_KO2


title: IP_KO3


title: Input_KO3


title: IP_WT3

value: WT


title: IP_WT1


title: IP_WT2


title: Input_WT3


title: Input_KO1


title: Input_WT2


title: Input_WT1


title: IP_KO1


title: Stage 14, Lane 2, scRNAseq

city: Eugene

first: Austin

last: Seroka

state: Oregon

address: 1440 Franklin Blvd

department: Institute of Neuroscience

institute: University of Oregon

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 v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Drosophila BDGP6.22
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: whole embryo

extract_protocol:
Cell dissociates were prepared from 8-9 hr (stage 12), 10-11 hr (stage 14) and 15-16 hr (stage 16) embryos respectively. Embryos were washed in DI water, before surface sterilization in 100% bleach for 5 minutes. Embryos were homogenized in Chan-Gehring (C+G) media by six to eight strokes of a loose-fitting dounce. The cell suspension was filtered through a 40 μm Nitex mesh, and cells were pelleted in a clinical centrifuge at 4°C (setting 5, IEC). The cell pellet was washed twice by pouring off the supernatant and gently triturating the pellet in fresh C+G. Percent cell-survival was determined for each dissociate by BioRad TC-20 trypan-blue assay.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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 Ilumina 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 apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: whole embryo

tag: strain

value: NB7-1 Gal4, UAS-RedstingerNLS

tag: age


title: Stage 14, Lane 1, scRNAseq

description: 10x Genomics


title: Stage 12, Lane 2, scRNAseq

description: 10x Genomics

value: 8-9 hours @ 25C


title: Stage 16, Lane 2, scRNAseq

description: 10x Genomics


title: Stage 16, Lane 1, scRNAseq

description: 10x Genomics


title: Stage 12, Lane 1, scRNAseq

description: 10x Genomics


title: P1 ctrl (biological replicate 3)

city: Bologna

first: Gabriele

last: D'Uva

address: via Massarenti 9

country: Italy

institute: University of Bologna

data_processing:
The softwares used for data analysis are the following (in order):
NextSeq Control Software v2.2.0.4 (base-calling)
BCL to FASTQ file converter bcl2fastq (demultiplexing)
cutadapt v1.16 (Trimming)
FastQC v0.11.7
multiqc v1.5
STAR v2.5.4a (Alignment)
featureCounts v1.6.2 (Counting)
DESeq2 v1.18.1 (Differential expression)
Assembly: mmu_GRCm38.90_ERCC_SIRV
Supplementary files format and content: tab-delimited text files include raw gene counts

source_name: neonatal cardiomyocytes

growth_protocol: Cardiac cells were isolated by multiple enzymatic digestion of postnatal-day 1 (P1) mouse hearts with pancreatin and collagenase. Cardiomyocyte were purified using the immuno-magnetic cell sorting MACS Neonatal Isolation System (130-100-825, Miltenyi biotech) and cultured in gelatine-coated (0.1%, G1393, Sigma) wells with DMEM/F12 (Aurogene) supplemented with L-glutamine, sodium pyruvate, non- essential amino acids, penicillin, streptomycin, 5% horse serum and 10% FBS  at 37°C and 5% CO2

extract_protocol:
RNA extraction was performed with NucleoSpin RNA II kit (Macherey Nagel); 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.

treatment_protocol: 48 hours later, medium was replaced and cells were starved with medium without serum for 24h

tag: developmental stage

value: postnatal-day-1 (P1)

value: ctrl

tag: cell type

value: neonatal cardiomyocytes


title: P1 GR-cKO (biological replicate 3)

value: GR-cKO


title: P7 GRcKO (biological replicate 2)

source_name: heart tissue

growth_protocol: The hearts were extracted from postnatal-day 7 (P7) mouse models and homogeneized.

extract_protocol:
RNA extraction was performed with NucleoSpin RNA II kit (Macherey Nagel). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.

value: heart tissue


title: P7 ctrl (biological replicate 1)


title: P7 GRcKO (biological replicate 3)


title: P7 GRcKO (biological replicate 1)


title: P1 GR-cKO (biological replicate 1)


title: P1 ctrl (biological replicate 2)


title: P1 ctrl (biological replicate 1)


title: P7 ctrl (biological replicate 3)


title: P7 ctrl (biological replicate 2)


title: C3

city: La Jolla

first: Fotis

last: Asimakopoulos

state: CA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UCSD

description:
Fig.4.processeddata
EV + LPS

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d). FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped of each gene. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package (v1.20.0).
The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38

source_name: MutuDC

extract_protocol:
RNA was isolated using QIAGEN RNeasy Mini Kit and cDNA was synthesized using the iScript Reverse Transcription Supermix (Biorad)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: sample type

value: EV + LPS


title: B2

description:
Fig.4.processeddata
Vkine

value: Vkine


title: B3

description:
Fig.4.processeddata
Vkine


title: D1

description:
Fig.4.processeddata
Vkine + LPS

value: Vkine + LPS


title: D2

description:
Fig.4.processeddata
Vkine + LPS


title: C1

description:
Fig.4.processeddata
EV + LPS


title: D3

description:
Fig.4.processeddata
Vkine + LPS


title: B1

description:
Fig.4.processeddata
Vkine


title: A2

description:
Fig.4.processeddata
EV

value: EV


title: Vk_L3_CD45

description:
Fig.3.processeddata
Vkine tumor CD45

source_name: Bone marrow CD45

value: Vkine tumor CD45


title: Vk_L1_CD45

description:
Fig.3.processeddata
Vkine tumor CD45


title: EV_R1L1_CD45

description:
Fig.3.processeddata
EV tumor CD45

value: EV tumor CD45


title: A1

description:
Fig.4.processeddata
EV


title: P1 GR-cKO (biological replicate 2)


title: EV_R2_CD45

description:
Fig.3.processeddata
EV tumor CD45


title: Vk_L2_CD45

description:
Fig.3.processeddata
Vkine tumor CD45


title: C2

description:
Fig.4.processeddata
EV + LPS


title: snRNA_hippocampus_HDACi-CFC_rep1

city: Lausanne

first: Johannes

last: Gräff

state: Vaud

address: Rte Cantonale

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Animals were i.p. injected with HDACi 1 hour before exposure to novel context + mild shock, then sacrificed 1 hour after context exposure

data_processing:
To generate single cell feature counts cellranger count (CellRanger v3.0.1) was run to align FASTQ files to the mm10 pre-mRNA genome (created using cellranger mkref (CellRanger v3.0.1)) using the following settings: expect-cells=4000, chemistry = SC3Pv3, r2-length = 56.
Seurat (v4.0.3) was used to calculate quality control metrics
DoubletFinder was used to find and remove doublets
Normalization and variance stabilization was done using SCTransform.
Seurat was then used to perform UMAP and TSNE clustering, to define clusters using molecular identifiers and to run the differential expression analysis for each cluster
Genome_build: mm10
Supplementary_files_format_and_content: matrix of raw gene counts for all nuclei

molecule: nuclear RNA

source_name: single nuclei from hippocampus

growth_protocol: Ten-week-old C57BL/6J male mice were  allowed an acclimatization and handling period for two weeks before experimentation. All animals were housed in groups of 4-5 animals at 22-25° C on a 12-hour light-dark cycle with food and water ad libitum. Mice were randomly assigned a drug treatment, and experimental conditions were randomly split by cage so that all mice in one cage underwent the same fear conditioning protocol.

extract_protocol:
To collect nuclei, frozen brain tissue was homogenized in a douncer filled with 6ml Solution D (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tris-HCl, pH 7.5, 5µg/mL actinomycin D (Sigma, Cat# A4262)). Samples were centrifuged for 1 min at max speed and pellets were resuspended in 4ml Solution D and 2ml Optiprep (Serumwerk Bernburg). Samples were  pelleted by centrifugation for 10 min at 3,200g, and the supernatant was discarded. Optiprep purification was performed 2 times. After  final centrifugation, pellets were resuspended in N-PBS (PBS, 5% BSA, 5µg/mL actinomycinD and 0.2U/µl RNAse inhibitor (Thermo Fisher Scientific, Cat#N8080119)) and filtered into 5ml polysterene tubes with filter (75mm) snap-caps (Corning, Cat# 352235).
Library constructions were performed using Chromium SingleCell 3’Reagent Kit v3 chemistry (10x Genomics) according to the manufacturers protocol (CG000183 - Rev A). All 4 libraries were pooled and sequenced across 2 NextSeq 500 (v2.5) chips for 75 cycles. FASTQ files were generated using cellranger mkfastq (CellRanger v3.0.1), yielding an R1 length of 28nt and an R2 length of 56 nucleotides and one information file (I).
single nuclear RNA-seq (10x)

treatment_protocol: The class I HDAC inhibitor, CI-994, was dissolved in 10% dimethyl sulfoxide (Sigma-Aldrich, D2438), 30% Kolliphor (Sigma-Aldrich, C5135), and 60% 0.9% saline (Braun, 395158). Vehicle (VEH) solution consisted of all of the above, without CI-994. One hour before contextual fear conditioning, each animal was interperitoneally (i.p.) injected with either 30mg/kg of CI-994 or a corresponding volume of VEH pre-heated to 37˚C on a thermomixer.  CFC consisted of a 3 min habituation to the conditioning chamber (TSE Systems GmbH) followed by two 1 s foot shocks (0.2mA) with an interval of 29 s and a final 15 s in the chamber. The context groups in all experiments were exposed to the conditioning chamber for the same amount of time with no shocks.

value: hippocampus (DG)

value: 12 weeks

value: HDACi - CFC


title: EV_R1_CD45

description:
Fig.3.processeddata
EV tumor CD45


title: ChIP_hippocampus_HDACi-CFC_rep2_input

library_source: genomic

data_processing:
MID sequence from R2 was appended to the FASTQ header in R1 using a custom R-script.
Adapter sequences and low quality regions from R1 were removed using Trimmomatic (v0.38) with the following parameters: ILLUMINACLIP:Y2_adapter_seq.fa:0:6:6 SLIDINGWINDOW:10:20 MINLEN:36.
The processed FASTQ file (R1) was then aligned to the mm10 genome using Bowtie2 (v2.3.5) in single-end mode and using default parameters.
SAMtools (v1.9) was used to convert SAM files to BAM format and then to sort BAM files. PCR duplicated alignments were removed from the BAM files using a perl script by Active Motif.
multi-mapping and low-quality reads (³ 40) were removed and BAM files were re-indexed using SAMtools.
peaks were defined using MACS2(94) in broad peak mode
Differentially acetylated regions (DARs) were identified using Diffbind (v2.16.2) and DEseq2(v 1.28.1). Peaks were considered differentially enriched if they had a false discover rate (FDR) £ 0.05 and ½log2FoldChange½ ³ 1.
ChromHMM (v1.22) was used to define enhancers and promoters. The program was run, allowing for 8 states, on independently published ChIP-sequencing data (Halder et al., 2016)
Peaks were annotated to genes using HOMER (v4.11) annotatePeaks.pl
Genome_build: mm10
Supplementary_files_format_and_content: matrix of raw peak counts

molecule: genomic DNA

source_name: sorted neuronal nuclei - Dentate Gyrus

extract_protocol:
Frozen brain tissue was homogenized in 6ml Solution D (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tris-HCl, pH 7.5). Samples were purified twice with Optiprep (Serumwerk Bernburg) and centrifuged for 10min at 3,200g. Pellets were resuspended in PBS-T then filtered into 5ml polysterene tubes with filter (75mm) snap-caps (Corning).  Extracted nuclei were cross-linked in 1% formaldehyde (AppliChem) for 5-min and quenched with 125mM glycine (VWR). Approximately 750,000 nuclei/sample were resuspended in 500µl PBS-T. Nuclei were stained with 1:50 Alexa Fluor488 conjugated anti-NeuN (Millipore, MAB377X) for 30min, then washed in PBS-T. Nuclei were stored in 200µl PBS-T, passed through a 26G needle and incubated with Hoechst (1:1000) before sorting on the FACSAriaIII (BD Bioscience). Sorted NeuN+ nuclei were pelleted (4˚C, 1250g, 5min) and lysed in 750µl RIPA buffer for 10min. Samples were sonicated on an E220 Focused-ultra-sonicator (Covaris) for 20min (Peak power = 140W, Duty = 5, Cycle/Burst = 200). Low input ChIP was carried out using the Low Cell ChIP-Seq Kit (Active Motif) using H3K27ac (Abcam, ab4729).
To prepare libraries for both input and IP samples, the Next Gen DNA Library Kit (Active Motif, Cat# 53216) and Next Gen Indexing Kit (Active Motif, Cat# 53264) were used according to the manufacturer’s instructions. After adaptor ligation, fragments were amplified (1 cycle, 30s at 98˚C; 14 cycles, 10s at 98˚C, 30s at 60˚C and 60s at 68˚C) and DNA was cleaned and purified using magnetic SPRI beads (Beckman Coulter, Ca# B23317). Libraries were resuspended in 25µl Low EDTA TE buffer. DNA fragments size was determined using a Fragment analyzer (NGS High Sensitivity kit (DNF-474), Agilent). Libraries were sequenced, paired-end, on the Illumina NextSeq 500 at EPFL’s gene expression core facility.

value: HDACi-CFC

tag: chip antibody


title: ChIP_hippocampus_HDACi-CFC_rep1_input


title: ChIP_hippocampus_HDACi-CFC_rep1_H3K27ac


title: ChIP_hippocampus_HDACi-Context_rep3_input

description: Animals were i.p. injected with HDACi 1 hour before exposure to novel context, then sacrificed 1 hour after context exposure

value: HDACi-Context


title: ChIP_hippocampus_HDACi-CFC_rep3_input


title: ChIP_hippocampus_HDACi-Context_rep2_input


title: ChIP_hippocampus_HDACi-Context_rep1_H3K27ac


title: ChIP_hippocampus_HDACi-Context_rep1_input


title: snRNA_hippocampus_Veh-CFC_rep2

description: Animals were i.p. injected with vehicle 1 hour before exposure to novel context + mild shock, then sacrificed 1 hour after context exposure

value: Veh - CFC


title: snRNA_hippocampus_Veh-CFC_rep1


title: ChIP_hippocampus_HDACi-CFC_rep2_H3K27ac


title: ChIP_hippocampus_HDACi-CFC_rep3_H3K27ac


title: ChIP_hippocampus_Veh-CFC_rep3_H3K27ac


title: snRNA_hippocampus_VEH-CON_rep1

data_processing:
To generate single cell feature counts cellranger count (CellRanger v3.0.1) was run to align FASTQ files to the mm10 pre-mRNA genome (created using cellranger mkref (CellRanger v3.0.1)) using the following settings: expect-cells=4000, chemistry = SC3Pv3, r2-length = 56.
Seurat (v4.0.3) was used to calculate quality control metrics
DoubletFinder was used to find and remove doublets
Normalization and variance stabilization was done using SCTransform.
Seurat was then used to perform UMAP and TSNE clustering, to define clusters using molecular identifiers and to run the differential expression analysis for each cluster
Genome_build: mm10
Supplementary_files_format_and_content: html files of alignment report; 3 matrices of features, barcodes and counts for all nuclei

growth_protocol: Ten-week-old C57BL/6J male mice were allowed an acclimatization and handling period for two weeks before experimentation. All animals were housed in groups of 4-5 animals at 22-25° C on a 12-hour light-dark cycle with food and water ad libitum. Mice were randomly assigned a drug treatment, and experimental conditions were randomly split by cage so that all mice in one cage underwent the same fear conditioning protocol.

extract_protocol:
To collect nuclei, frozen brain tissue was homogenized in a douncer filled with 6ml Solution D (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tris-HCl, pH 7.5, 5µg/mL actinomycin D (Sigma, Cat# A4262)). Samples were centrifuged for 1 min at max speed and pellets were resuspended in 4ml Solution D and 2ml Optiprep (Serumwerk Bernburg). Samples were pelleted by centrifugation for 10 min at 3,200g, and the supernatant was discarded. Optiprep purification was performed 2 times. After final centrifugation, pellets were resuspended in N-PBS (PBS, 5% BSA, 5µg/mL actinomycinD and 0.2U/µl RNAse inhibitor (Thermo Fisher Scientific, Cat#N8080119)) and filtered into 5ml polysterene tubes with filter (75mm) snap-caps (Corning, Cat# 352235).
Library constructions were performed using Chromium SingleCell 3’Reagent Kit v3 chemistry (10x Genomics) according to the manufacturers protocol (CG000183 - Rev A). All 4 libraries were pooled and sequenced across 2 NextSeq 500 (v2.5) chips for 75 cycles. FASTQ files were generated using cellranger mkfastq (CellRanger v3.0.1), yielding an R1 length of 28nt and an R2 length of 56 nucleotides and one information file (I).
single nuclear RNA-seq (10x)

treatment_protocol: The class I HDAC inhibitor, CI-994, was dissolved in 10% dimethyl sulfoxide (Sigma-Aldrich, D2438), 30% Kolliphor (Sigma-Aldrich, C5135), and 60% 0.9% saline (Braun, 395158). Vehicle (VEH) solution consisted of all of the above, without CI-994. One hour before contextual fear conditioning, each animal was interperitoneally (i.p.) injected with either 30mg/kg of CI-994 or a corresponding volume of VEH pre-heated to 37˚C on a thermomixer. CFC consisted of a 3 min habituation to the conditioning chamber (TSE Systems GmbH) followed by two 1 s foot shocks (0.2mA) with an interval of 29 s and a final 15 s in the chamber. The context groups in all experiments were exposed to the conditioning chamber for the same amount of time with no shocks.

value: Veh - Context


title: snRNA_hippocampus_HDACi-CON_rep1

value: HDACi - Context


title: ChIP_hippocampus_HDACi-Context_rep2_H3K27ac


title: snRNA_hippocampus_HDACi-CFC_rep2


title: ChIP_hippocampus_Veh-CFC_rep2_H3K27ac


title: ChIP_hippocampus_Veh-CFC_rep3_input


title: ChIP_hippocampus_Veh-CFC_rep2_input


title: ChIP_hippocampus_HDACi-Context_rep3_H3K27ac


title: ChIP_hippocampus_Veh-Context_rep3_H3K27ac

description: Animals were i.p. injected with vehicle 1 hour before exposure to novel context, then sacrificed 1 hour after context exposure


title: ChIP_hippocampus_Veh-CFC_rep1_input


title: ChIP_hippocampus_Veh-Context_rep2_input


title: ChIP_hippocampus_Veh-Context_rep2_H3K27ac


title: ChIP_hippocampus_Veh-CFC_rep1_H3K27ac


title: ChIP_hippocampus_Veh-Context_rep3_input


title: ChIP_hippocampus_Veh-Context_rep1_input


title: ChIP_hippocampus_Veh-Context_rep1_H3K27ac


title: NOD-AI4-60A-5

city: Bar Harbor

first: David

middle: V

last: Serreze

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description:
LS00119-TG
LS00119-TG_GT19-04483_CAACAATG-CCGTGAAG_S5

data_processing:
KAPA stranded mRNA libraries were constructed and sequenced on an Illumina NextSeq instrument yielding ~30 million single end 75bp reads per sample.
The conda package emase 0.10.16 (EMASE: Expectation-Maximization algorithm for Allele Specific Expression) was used to determine expected counts. EMASE model 4 was run with bowtie 1.0.0 and samtools 0.1.18.
The Bioconductor R package edgeR 3.24.3 was used to analyze differential expression.
Genome_build: GRCm38/mm10 reference genome and NOD/ShiLtJ-specific variants
Supplementary_files_format_and_content: tab-delimited text files include expected counts and tpm values for each sample

extract_protocol:
Thymi were dissected, mashed and passed through nytex to create single cell suspensions.  Live gated CD4+CD8+ cells were sorted by flow cytometry and collected into FBS.  Cell pellets were resuspended in TRIzol and frozen.  Total RNA was extracted according to Thermo Fisher Scientific's TRIzol  protocol and  Qiagen RNeasy MiniElute Cleanup to RIN >9.
KAPA stranded RNA libraries

tag: strain/genotype

tag: Sex

value: Male

value: Thymus


title: NOD-AI4-60A-2

description:
LS00115-TG
LS00115-TG_GT19-04479_ATATCTCG-ACTAAGAT_S16

value: Female


title: NOD-AI4-KO-5

description:
LS00123-KO
LS00123-KO_GT19-04487_GAATGAGA-AATGCCTC_S4


title: NOD-AI4-4

description:
AT12349-CTL
AT12349-CTL_GT19-04474_GGAGCGTC-GCACGGAC_S1


title: NOD-AI4-KO-2

description:
LS00117-KO
LS00117-KO_GT19-04481_AACAGGTT-CTTGGTAT_S14


title: GPR174_KO1-4h

city: San Francisco

first: Lihui

last: Duan

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

data_processing:
Sequences were aligned to the mm10 genome with STAR
HTseq was used to count the mapped reads of each gene .
DESeq2 was used for the gene differential expression analysis.
Assembly: mm10
Supplementary files format and content: csv table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: follicular B cell CD21/35- CD23+

tag: hours of_culture


title: GPR174_WT3-4h


title: NOD-AI4-6

description:
AT12351-CTL
AT12351-CTL_GT19-04476_GCAATGCA-AACGTTCC_S12


title: NOD-AI4-KO-3

description:
LS00120-KO
LS00120-KO_GT19-04484_TGGTGGCA-TTACAGGA_S2


title: GPR174_WT2-4h


title: GPR174_KO3-0h


title: NOD-AI4-2

description:
AT12347-CTL
AT12347-CTL_GT19-04472_GCGCAAGC-CGGCGTGA_S9


title: NOD-AI4-1

description:
AT12346-CTL
AT12346-CTL_GT19-04471_ATATGGAT-TAATACAG_S3


title: GPR174_KO2-4h


title: NOD-AI4-3

description:
AT12348-CTL
AT12348-CTL_GT19-04473_AAGATACT-ATGTAAGT_S7


title: NOD-AI4-5

description:
AT12350-CTL
AT12350-CTL_GT19-04475_ATGGCATG-GGTACCTT_S6


title: NOD-AI4-60A-3

description:
LS00116-TG
LS00116-TG_GT19-04480_GCGCTCTA-GTCGGAGC_S13


title: NOD-AI4-KO-4

description:
LS00122-KO
LS00122-KO_GT19-04486_AGGCAGAG-GGCATTCT_S15


title: GPR174_WT3-0h


title: GPR174_WT1-0h


title: GPR174_KO1-0h


title: GPR174_WT1-4h


title: GPR174_KO3-4h


title: GPR174_KO2-0h


title: NOD-AI4-60A-4

description:
LS00118-TG
LS00118-TG_GT19-04482_GGTGAACC-TCCAACGC_S10


title: RNASeq_KO3

description: RNA-Seq

data_processing:
Trimming and quality filtering: cutadapt (v.1.18)
Filtering rRNA and tRNA reads: bowtie2 (v.2.4.2)
Alignment to transcriptome: bowtie2 (v.2.4.2)
Generating ribo objects: RiboFlow (initial release)
Extracting counts: RiboR
Genome_build: gencode.vM23.transcripts
Supplementary_files_format_and_content: Tab delimited file with counts at per-gene level

growth_protocol: For both the RiboSeq and the RNA-Seq experiments, left ventricular tissues were homogenized using a tissue homogenizer in 5 volumes of ice-cold polysome buffer (20 mM Tris pH 7.4, 10 mM MgCl, 200 mM KCl, 2 mM DTT, 1% Triton X-100, 1U DNAse/μl) containing 100 μg/ml cycloheximide, and further homogenized using a 25G needle.

extract_protocol:
For the RiboSeq experiment, ribosome protected fragments (RPFs) were generated using RNAse I treatment and isolated using MicroSpin S-400 columns (Cytiva). For the RNA-Seq experiment, total RNA was isolated from the lysate using TRIzol.
For the RiboSeq experiment, purified RPFs were used for the library preparation using the NEXTFLEX small-RNAseq V3 kit (Perkin-Elmer). For the RNA-Seq experiment, libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (ref. e7490) and NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (24 reactions ref. e7760 or 96 reactions ref. e7765) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.

treatment_protocol: For the RiboSeq experiment, the lysate was treated with RNAse I for 45 minutes at room temperature. Non-treated lysate was used for the RNA-Seq experiment.


title: NOD-AI4-60A-1

description:
LS00114-TG
LS00114-TG_GT19-04478_ACCTTGGC-ATGAGGCC_S11


title: RNASeq_WT2

description: RNA-Seq

value: WT


title: RNASeq_WT1

description: RNA-Seq


title: RiboSeq_KO3

description: RiboSeq


title: NOD-AI4-KO-1

description:
LS00113-KO
LS00113-KO_GT19-04477_GTTCCAAT-GCAGAATT_S8


title: RiboSeq_KO2

description: RiboSeq


title: RiboSeq_KO1

description: RiboSeq


title: RiboSeq_WT3

description: RiboSeq


title: RNASeq_KO2

description: RNA-Seq


title: RiboSeq_WT2

description: RiboSeq


title: RNASeq_KO1

description: RNA-Seq


title: KAT6A-NCOA2_2 [2_MT2]

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description:
2-MT2_S5_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-KAT6A-NCOA2-IRES-GFP expression.

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: BM progenitor cells_KAT6A-NCOA2

growth_protocol: The cells were cultured for five days in-vitro (IL3, IL6, SCF), sorted for GFP positive cells and sent for bulk RNA-sequencing.

extract_protocol:
Lineage negative cells were isolated using magnetic beads from fresh bone marrow of 6 weeks C57B/6 female. The cell were retrovirally infected with ETV6-NCOA2, KAT6A-NCOA2 or empty vector and cultured in RPMI supplemented with IL-3, IL-6 and SCF for 5 days. The positive cells were sorted (GFP). We extracted RNA from the samples and performed bulk RNA-sequencing.
Inhouse poly A based RNA seq

treatment_protocol: The mice were not treted prior to the bone marrow isolation

tag: strain background

value: Lineage negative bone marrow cells

tag: genotype/variation

tag: sort

value: GFP+


title: Empty vector_2 [2_BB]

description:
2-BB_S4_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-IRES-GFP expression.

source_name: BM progenitor cells_Empty vector

value: Empty vector


title: GPR174_WT2-0h

tag: tissue


title: KAT6A-NCOA2_3 [3_MT2]

description:
3-MT2_S8_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-KAT6A-NCOA2-IRES-GFP expression.


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N712_S517]

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description:
SLX-9714
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

data_processing:
Single-cell RNA-seq reads were quantified using the GRCm38 transcriptome and Kallisto version 0.43.1.
Data were filtered to remove poor quality cells & genes with low abundances.
Normalised using Scater ComputeSumFactors.
Genome_build: Ensembl 87
Supplementary_files_format_and_content: Kapeni_etal_rawcounts.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: Kapeni_etal_logcounts.txt: Tab-delimited text file includes normalised expression measurements.

source_name: subaortic mesenchymal cells

extract_protocol:
Cells were sorted from freshly isolated mouse embryos; dissected tissues were treated with collagenase and then stained with cell surface markers and directly sorted into lysis buffer.
SmartSeq2

value: Wild-type

value: aorta-gonads-mesonephros (AGM)

tag: cell type/region

value: Mesenchymal


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N712_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N712_S505]


title: ETV6-NCOA2_2 [2_TT2]

description:
2-TT2_S6_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-ETV6-NCOA2-IRES-GFP expression.

source_name: BM progenitor cells_ETV6-NCOA2


title: RiboSeq_WT1

description: RiboSeq


title: ETV6-NCOA2_1 [1_TT2]

description:
1-TT2_S3_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-ETV6-NCOA2-IRES-GFP expression.


title: ETV6-NCOA2_3 [3_TT2]

description:
3-TT2_S9_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-ETV6-NCOA2-IRES-GFP expression.


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N712_S502]


title: RNASeq_WT3

description: RNA-Seq


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S502]


title: Empty vector_3 [3_BB]

description:
3-BB_S7_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-IRES-GFP expression.


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S517]


title: KAT6A-NCOA2_1 [1_MT2]

description:
1-MT2_S2_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-KAT6A-NCOA2-IRES-GFP expression.


title: Empty vector_1 [1_BB]

description:
1-BB_S1_L003
Murine lineage negative bone marrow cells were retroviraly infected  with MigR1-IRES-GFP expression.


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N712_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N712_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N711_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N710_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N707_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N709_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N706_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N708_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N704_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N705_S506]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S503]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S502]


title: ctrtac7d3

city: Dallas

first: GUANGYU

last: ZHANG

state: TX

address: 5323 Harry Hines Blvd

department: Cardiology

institute: UTsouthwestern Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: heart

growth_protocol: mice were breed and growth in ARC of Utsouthwestern Meducal Center

extract_protocol:
RNA was harvested using with the Quick-RNA MicroPrep kit (Zymo research). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were treat with sham or TAC surgery

tag: treatment

value: tac

value: heart

tag: overexpression

value: control


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N703_S504]


title: ctrtac7d2


title: ctrtac7d1


title: cKOtac7d2

value: ATF4 overexpression


title: cKOtac7d3


title: cKOtac7d1


title: cKOtac3d3


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S507]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S505]


title: ctrtac3d3


title: cKOtac3d1


title: cKOtac3d2


title: ctrtac3d2


title: ctrtac3d1


title: cKOsham3

value: sham


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S517]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S502]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S507]


title: cKOsham2


title: cKOsham1


title: ctrlsham3


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S505]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S506]


title: ctrlsham2


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S504]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S503]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S517]

description:
SLX-9713
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

source_name: sympathoadrenal cells

value: Ventral


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S508]


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N702_S503]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S506]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S507]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S505]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S503]


title: ctrlsham1


title: ventral Pdgfrb+Ngfr- cells [SLX-9714.N701_S502]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S508]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S517]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S507]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S506]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S505]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S503]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S504]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N711_S502]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N712_S502]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S517]


title: GBM-F3T3-O [BO45]

type: genomic

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

description: Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
R package minfi v1.40.0
Normalized (preprocessFunnorm) Average Beta

label: Cy5 and Cy3

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

tag: gender

value: Male

tag: material

value: FFPE


title: Ganglioglioma [Z950]

description: Tumor

source_name: Ganglioglioma

value: Female

tag: age

value: Ganglioglioma


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S508]

tag: developmental stage


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S507]


title: Ganglioglioma [BN52]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S506]


title: Ganglioglioma [BI84]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S505]


title: Ganglioglioma [BH56]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S504]


title: Ganglioglioma [BE61]

description: Tumor


title: Ganglioglioma [BC10]

description: Tumor


title: Ganglioglioma [BB16]

description: Tumor


title: Ganglioglioma [AV70]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S517]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S508]


title: Ganglioglioma [Y002]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S503]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S507]


title: Ganglioglioma [AR67]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N710_S502]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S506]


title: Ganglioglioma [AO17]

description: Tumor


title: Ganglioglioma [AN13]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S505]


title: GBM [Z476]

description: Tumor

source_name: GBM

value: GBM


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S504]


title: Ganglioglioma [AM46]

description: Tumor


title: CBS_37_2 [AC-9_S12]

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.5 (Andrews, 2010).
First, these reads were trimmed using cutadapt version 1.11 to remove the “QuantSEQ FWD” adaptor sequence.
The trimmed reads were mapped to the genome of CBS339.90 using the STAR aligning software version 2.5.3a
The RSEM software, version v1.2.31, was used to generate count tables.  Only genes with a ccounts per million (cpm) above 1 in at least 3 samples were retained.
Genome_build: L. Hormozganensis (SUB5546006,PRJNA470903)
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

organism: Lasiodiplodia hormozganensis

extract_protocol:
The mycelium of each replicate (three replicates per condition) was ground in liquid nitrogen and total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma), according to the manufacturer’s instructions. Samples were incubated for 15 min with the DNase I digestion set (RNase-Free DNase Set, Qiagen). Integrity and quality analysis were carried on a 2100 Bioanalyzer RNA (Agilent Technologies).
Illumina mRNA sequencing libraries were made from 500 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol. Fourteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

tag: strain

tag: temperature

value: 37 ºC

value: 4 days

value: Mycelium


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S503]

value: Wild-type


title: GBM [Z435]

description: Tumor


title: CBS_37_3 [AC-11_S2]


title: Ganglioglioma [AK38]

description: Tumor


title: GBM [Z432]

description: Tumor


title: Ganglioglioma [AM23]

description: Tumor


title: CBS_37_1 [AC-7_S11]


title: CBS_25_3 [AC-5_S10]

value: 25 ºC


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S508]

value: aorta-gonads-mesonephros (AGM)


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N709_S502]


title: CBS_25_2 [AC-3_S9]


title: GBM [Z268]

description: Tumor


title: Ganglioglioma [Z382]

description: Tumor


title: GBM [Z379]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S505]


title: GBM [Z328]

description: Tumor


title: GBM [Z225]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S507]


title: GBM [Z170]

description: Tumor


title: GBM [Z222]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S517]


title: Pole4 knockout splenic B cells

city: Shanghai

first: Wei

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

description: HU-EdU-seq

data_processing:
Reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.15) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Assembly: mm10

source_name: Spleen

growth_protocol: Resting B cells from Pole4+/+ and -/- spleens were activated with LPS, IL-4, and RP105.

extract_protocol:
Genomic DNA was isolated by phenol:chloroform extraction
Libraries were prepared as described in (Tubbs et al, Cell. 2018)
HU-EdU-seq

treatment_protocol: Cells were incubated with EdU and HU for 28 hours.

value: LPS, IL-4, RP105, HU

tag: genotype


title: t=0mo:patient 9

city: Manchester

first: Sacha

last: Howell

address: Oglesby Cancer Research Centre

department: Faculty of Biology, Medicine and Health

institute: The University of Manchester

description:
DNA samples were normalised to 25 ng/¬µl. We bisulfite-modified 500 ng of tissue DNA using the DNA methylation Lightning Mag Prep Kit from Zymo Research (cat number D5047) on a Hamilton Star liquid handling platform. We eluted 15 ¬µl of the bisulfite-converted DNA, which was then subjected to methylation analysis on the Illumina InfiniumMethylation EPIC BeadChip (Illumina, CA, USA) at UCL Genomics, according to the manufacturer‚Äôs standard protocol.
All DNAme data were background-corrected and normalised with BMIQ. Probes were removed if they had < 95% coverage across samples and any remaining probes with detection p-value > 0.05 were replaced by k-NN imputation, with k=5.
ullipristal acetate 5mg every other day

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Epic Beadchip using standard Illumina protocol.

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

data_processing: Preprocessing with BMIQ

source_name: Breast

label_protocol: Standard Illumina Protocol for Ilumina Epic Chip

growth_protocol: Human tissue

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions.

treatment_protocol: Human tissue

tag: time (months)

tag: patentid

value: patient 9

tag: age (years) at enrolment


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S503]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S504]


title: t=0mo:patient 8

value: patient 8


title: t=3mo:patient 5

value: patient 5


title: GBM [Z218]

description: Tumor


title: t=0mo:patient 6

value: patient 6


title: CBS_25_1 [AC-1_S1]


title: GBM [Z114]

description: Tumor


title: t=3mo:patient 6


title: t=3mo:patient 9


title: t=0mo:patient 1

value: patient 1


title: GBM [Z100]

description: Tumor


title: Wildtype splenic B cells

institute: Center for Excellence in Molecular Cell Science

description: HU-EdU-seq

value: WT


title: GBM [Z109]

description: Tumor

value: FFPE


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N708_S502]

value: Ventral


title: GBM [Z099]

description: Tumor

value: Female


title: GBM [Z007]

description: Tumor

value: Male

value: GBM


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S517]


title: t=3mo:patient 8


title: t=3mo:patient 4

value: patient 4


title: Abl-Lig4-STI-AsisI-NT-4h-RPA-ChIPseq

data_processing:
END-seq and RPA ChIP-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Abelson-transformed pre-B cell

growth_protocol: Abelson-transformed murine pre-B cells were grown in DMEM supplemented by 5% FBS, 1% pen/strep, 1% glutamine, 1% sodium pyruvate, 1% nonessential amino acids, and 55 μM β-mercaptoethanol

extract_protocol:
Cells were fixed in 1% formaldehyde. Cells were sonicated, lysates clarified, and protein-DNA complexes immunoprecipitated.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

treatment_protocol: For G0/G1 cell cycle arrest, asynchronously cycling cells were treated with 3 μM imatinib/STI (Selleckchem, S2475) for 48 hr at 1x106 cells/mL. To induce AsiSI-ER cutting, cells were treated with 3 μg/mL doxycycline for 24 hr, followed by 1 μM 4-hydroxytamoxifen for an additional 18 hr

value: NT

tag: antibody

value: RPA

tag: asisi induction


title: GBM [Z006]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S508]

tag: genotype/variation

value: Wild-type


title: GBM [Z101]

description: Tumor

tag: tissue


title: t=0mo:patient 4


title: t=0mo:patient 5


title: t=0mo:patient 2

value: patient 2


title: GBM [Y974]

description: Tumor


title: t=3mo:patient 7

value: patient 7


title: Abl-Lig4-STI-AsisI-NT-8h-RPA-ChIPseq


title: GBM [Y973]

description: Tumor


title: Abl-Lig4-STI-AsisI-NT-8h-ENDseq_rep2

data_processing:
Library strategy: END-seq
SAR-seq, END-seq, ChIP-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S507]

value: aorta-gonads-mesonephros (AGM)

tag: cell type/region


title: GBM [Y868]

description: Tumor


title: Abl-Lig4-STI-AsisI-NT-4h-ENDseq_rep2

tag: treatment


title: t=3mo:patient 2


title: t=3mo:patient 3

value: patient 3


title: t=0mo:patient 7


title: t=0mo:patient 3


title: GBM [Y700]

description: Tumor


title: Abl-Lig4-STI-AsisI-NT-4h-ENDseq_rep1


title: Abl-Lig4-STI-AsisI-DNAPKi-8h-ENDseq_rep2

value: DNAPKi


title: t=3mo:patient 1


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S504]


title: Abl-Lig4-STI-AsisI-DNAPKi-8h-ENDseq_rep1


title: GBM [Y743]

description: Tumor


title: Ganglioglioma [Y466]

description: Tumor

value: Ganglioglioma


title: GBM-G34 [Y632]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S506]


title: GBM [Y896]

description: Tumor


title: Abl-Lig4-STI-AsisI-NT-8h-ENDseq_rep1


title: Ganglioglioma [Y849]

description: Tumor


title: GBM [Z264]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S508]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S505]


title: GBM [Y795]

description: Tumor


title: GBM [Y421]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S507]


title: GBM [Y430]

description: Tumor


title: GBM [Y640]

description: Tumor


title: Abl-Lig4-STI-AsisI-DNAPKi-4h-ENDseq_rep2


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S502]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N707_S503]


title: Ganglioglioma [Y282]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S517]


title: GBM [Y427]

description: Tumor


title: GBM [Y867]

description: Tumor


title: Abl-Lig4-G2-AsisI-NT-4h-ENDseq_rep2


title: Abl-Lig4-STI-AsisI-DNAPKi-4h-ENDseq_rep1


title: GBM [Y413]

description: Tumor


title: GBM [Y131]

description: Tumor


title: GBM [Y130]

description: Tumor


title: GBM [Y402]

description: Tumor


title: Abl-Lig4-G2-AsisI-NT-8h-ENDseq_rep1


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S506]


title: Abl-Lig4-G2-AsisI-NT-8h-ENDseq_rep2


title: GBM [Y289]

description: Tumor


title: GBM [Y174]

description: Tumor


title: GBM [Y183]

description: Tumor


title: Abl-Lig4-G2-AsisI-NT-4h-ENDseq_rep1


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S505]


title: GBM [Y008]

description: Tumor


title: GBM [X955]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S503]


title: adATF4-3

organism: Rattus norvegicus

source_name: Heart

growth_protocol: NRVM cells were isolatd from neonatal rat heart ventricular and cultured in plating medium (DMEM/M199=3:1) containing 5% FBS, 10% horse serum, 1% penicillin/streptomycin, and bromodeoxyuridine (BrdU, 100 μM). After another 24 hours of plating, NRVMs were washed with PBS and cultured in serum-reduced medium (DMEM/M199=3:1, 1% FBS, 1% penicillin/streptomycin, 100 μM BrdU). Twenty-four hours later, NRVMs were incubated in serum-free medium (DMEM/M199=3:1).

treatment_protocol: Cells were treat with GFP or ATF4 adenovirus in serum free medium.

value: adenovirus

tag: cell type

value: NRVM

tag: adenovirus


title: Abl-Lig4-G2-AsisI-DNAPKi-8h-ENDseq_rep2

value: WT


title: GBM [Y128]

description: Tumor

tag: gender

tag: material

value: FFPE


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S504]

tag: developmental stage

value: Ventral


title: Abl-Lig4-G2-AsisI-DNAPKi-8h-ENDseq_rep1


title: GBM [Y105]

description: Tumor

tag: age


title: GBM-G34 [X921]

description: Tumor

value: Male


title: GBM [X958]

description: Tumor

value: GBM


title: GBM [Y124]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S517]


title: adATF4-2


title: GBM [Y188]

description: Tumor


title: GBM [X884]

description: Tumor

value: Female


title: GBM [Y108]

description: Tumor


title: Abl-Lig4-G2-AsisI-DNAPKi-4h-ENDseq_rep2


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N706_S502]


title: Abl-Lig4-G2-AsisI-DNAPKi-4h-ENDseq_rep1


title: GBM [X851]

description: Tumor


title: adGFP-3

value: adGFP


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S508]


title: GBM [X954]

description: Tumor


title: GBM [X886]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S503]


title: GBM [X881]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S507]


title: Ganglioglioma [X853]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S505]


title: GBM [X617]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S502]


title: GBM [X616]

description: Tumor


title: GBM [X464]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S517]


title: GBM [X649]

description: Tumor


title: GBM [X618]

description: Tumor


title: adATF4-1


title: adGFP-2


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S507]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N705_S506]


title: GBM [X388]

description: Tumor


title: GBM [X248]

description: Tumor


title: GBM [X502]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S508]


title: GBM [X442]

description: Tumor


title: adGFP-1


title: ChIP-seq input DNA: set2D Spn1-AID + IAA 4

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

institute: Harvard Medical School

description: ChIP-seq input library with Spn1 depleted, in set2D background.

data_processing:
Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence and A-tail.
Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read.
Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools.
Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools.
For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental).
Assembly: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor.

organism: Saccharomyces cerevisiae

growth_protocol: Strains FLR196 and FLR142 were grown in triplicate as 170 ml YPD cultures at 30°C to OD600≈0.6. The S. pombestrain FWP10 was grown in YES at 32°Cuntil an OD600≈0.6 was obtained. The FLR196 and FLR142 cultures were diluted two-fold with YPD and divided into two equal volumes with OD600≈0.3.

extract_protocol:
150 mL of each culture was transferred to a flask that was at room temperature, and 36 mL of 4°C YPD was added to each. These cultures were then fixed with 1% formaldehyde for 30 minutes while shaking at room temperature. The crosslinking was quenched by adding glycine to each culture to a final concentration of 125 mM and by shaking for 10 minutes at room temperature. The cells were pelleted, washed twice with cold 1x TBS (100 mM Tris, 150 mM NaCl pH 7.5), and flash frozen. FLR196 and FLR142 cell pellets were resuspended in 800 μL of LB140 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1%. Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 100 μg of leupeptin, 100 μg of pepstatin A, 8.71 mg of PMSF, 3.08 mg of 1M DTT), and lysed by bead-beating at 4°Cfor 8 minutes with 4-minute incubations on ice after every minute of bead-beating. The FWP10 pellets were treated similarly, but they were lysed by bead-beating at 4°C for 11 minutes. The lysate was collected by centrifuging the samples at 14,000 rpm for 5 minutes at 4°C. After  discarding the supernatant, the pellet was washed with LB140. The final pellet was washed in 580 μL of LB140 and sonicated in a QSonica Q800R machine for 10 minutes (30 seconds on, 30 seconds off, 70% amplitude) to obtain fragments of about 100-500 bp. The protein concentrations of all samples were measured by Bradford (Bradford 1976). To prepare the IP reactions, about 250 μg of S. cerevisiaechromatin was used as starting material, and we added 10% the mass of chromatin as spike-in from S. pombe to each sample. We added to each sample 250 μL of WB140 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and the volume was brought up to 500 μL with LB140. Then, 40 μL of each sample were set aside as input for later processing at the reverse crosslinking step, described later. Two sets of IPs were prepared per sample with the following antisera: 3 μL of anti-H4 (AV94), kindly provided by Dr. Alain Verreault, and 16.7 μL of anti-H4ac (Millipore Sigma, 06-866, which targets histone H4ac on lysines 5, 8, 12, and 16), volumes that were optimized by ChIP-qPCR. The immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (∼14-16 hours). Aliquots of Dynabeads Protein G for Immunoprecipitation (Invitrogen) and Dynabeads Protein A for Immunoprecipitation (Invitrogen) were transferred to Eppendorf tubes, and the buffer was removed. A volume of WB140 equivalent to the initial volume of beads was used to wash the beads twice with WB140, and the beads were kept in the second wash to make a slurry. Fifty μL of the Protein G slurry were added to each of the H4 IPs, 278 μL of the Protein A slurry were added to the H4ac IPs, and the reactions were incubated at 4°C with end-over-end rotation for four hours. The beads were washed twice (first wash for one minute and second wash for 5 minutes with nutation) with WB140, twice with WB500 (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with WBLiCl (10 mM Tis-HCl pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE (10 mM Tris-HCl pH 7.4, 1 mM EDTA) for 5 minutes. The IP material was eluted from the beads twice with 100 μL of TES (50 mM Tris-HCl pH 7.4, 10mM EDTA, 1% SDS) at 65°C for 30 minutes first and then for 15 minutes. The saved inputs were thawed, and 60 μL of LB140 and 100 μL of TES were added. To reverse crosslinking, the eluates and the inputs were incubated at 65°C overnight. To degrade RNA, 2 μL of RNAse A/T1 (Thermo Fisher, EN0551) were added to each sample, and the samples were incubated at 37°C for one hour. To degrade protein, a mix of 7 μL of proteinase K (Roche), 1 μL of glycogen (Sigma G1767-1VL, 20 mg/mL), and 250 μL of TE was added to each sample, and the samples were incubated at 50°C for two hours. The DCC-5 kit (Zymo Research, D4014) was used to purify DNA (20-μL elution).
The libraries were built with 10.25 μL of DNA as starting material and using the GeneRead DNA Library I Core Kit (Qiagen, half of the volumes suggested by the manufacturer instructions were used) and custom barcodes (Wong, Jin, and Moqtaderi 2013). The samples were purified twice using 0.7x volume SPRI beads (A63881). PCRs were performed to determine number of amplification cycles, which ranged from 11 to 19, and to perform final library amplifications. Double-sided selection was performed to purify the samples a second time using 0.56x volume SPRI beads first and 0.7x volume SPRI beads second. The size distribution, quality, and concentration of the samples was assessed by running them in an Agilent Bioanalyzer.

treatment_protocol: For Spn1 depletion, one of the cultures from each strain was treated with 25 μM indole-3-acetic acid (IAA) auxin (dissolved in DMSO) for 90 minutes, and for non-depletion, DMSO was added to the other culture (Reim et al. 2020).

tag: strain

value: MATa ura3-52 lys2-128-delta- leu2-delta-1 LEU2::TIR1 SPN1-V5-AID2:KanMX6 set2-delta-0::NatMX

value: 25 μM IAA


title: ChIP-seq input DNA: set2D Spn1-AID + IAA 6

tag: genotype


title: ChIP-seq input DNA: set2D Spn1-AID + IAA 5


title: GBM [X379]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S505]

value: Wild-type


title: GBM [X363]

description: Tumor


title: GBM-G34 [X161]

description: Tumor


title: GBM [X233]

description: Tumor


title: ChIP-seq input DNA: set2D Spn1-AID + DMSO 6

description: ChIP-seq input library with Spn1 non-depleted, in set2D background.

value: DMSO


title: GBM [X160]

description: Tumor


title: GBM [X455]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S504]

value: aorta-gonads-mesonephros (AGM)


title: ChIP-seq input DNA: Spn1-AID + IAA 6

description: ChIP-seq input library with Spn1 depleted.

value: MATa ura3-52 lys2-128-delta- leu2-delta-1 LEU2::TIR1 SPN1-V5-AID2:KanMX6


title: ChIP-seq input DNA: set2D Spn1-AID + DMSO 5


title: ChIP-seq input DNA: set2D Spn1-AID + DMSO 4


title: GBM [X178]

description: Tumor


title: GBM [X093]

description: Tumor


title: GBM [X083]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S503]


title: GBM [W950]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N704_S506]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S507]


title: GBM [X026]

description: Tumor


title: GBM [W994]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S506]


title: GBM [W928]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S517]


title: ChIP-seq input DNA: Spn1-AID + DMSO 5

description: ChIP-seq input library with Spn1 non-depleted.


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S508]


title: ChIP-seq input DNA: Spn1-AID + IAA 5


title: ChIP-seq input DNA: Spn1-AID + IAA 4


title: GBM [W944]

description: Tumor


title: ChIP-seq input DNA: Spn1-AID + DMSO 6


title: GBM [W777]

description: Tumor


title: GBM [W816]

description: Tumor


title: GBM [W945]

description: Tumor


title: GBM [W934]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S505]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S502]


title: GBM [W819]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N702_S517]


title: GBM [W657]

description: Tumor


title: GBM [W947]

description: Tumor


title: Ganglioglioma [W820]

description: Tumor


title: GBM [W761]

description: Tumor


title: ChIP-seq input DNA: Spn1-AID + DMSO 4


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N703_S504]


title: H4ac ChIP-seq, ChIP DNA: set2D Spn1-AID + IAA 5

description: ChIP library from H4ac ChIP-seq with Spn1 depleted, in set2D background.


title: GBM [W637]

description: Tumor


title: GBM [W883]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N702_S506]


title: GBM [W549]

description: Tumor


title: GBM [W551]

description: Tumor


title: GBM-G34 [W760]

description: Tumor


title: H4ac ChIP-seq, ChIP DNA: set2D Spn1-AID + DMSO 6

description: ChIP library from H4ac ChIP-seq with Spn1 non-depleted, in set2D background.


title: GBM [W622]

description: Tumor


title: H4ac ChIP-seq, ChIP DNA: set2D Spn1-AID + IAA 6


title: GBM [W448]

description: Tumor


title: GBM [W269]

description: Tumor


title: H4ac ChIP-seq, ChIP DNA: Spn1-AID + IAA 6

description: ChIP library from H4ac ChIP-seq with Spn1 depleted.


title: H4ac ChIP-seq, ChIP DNA: set2D Spn1-AID + DMSO 5


title: GBM [W167]

description: Tumor


title: GBM [W365]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N702_S502]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N702_S505]


title: H4ac ChIP-seq, ChIP DNA: set2D Spn1-AID + IAA 4


title: GBM [W328]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S508]


title: H4ac ChIP-seq, ChIP DNA: Spn1-AID + IAA 5


title: H4ac ChIP-seq, ChIP DNA: set2D Spn1-AID + DMSO 4


title: GBM [V998]

description: Tumor


title: GBM [W631]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S517]


title: GBM [W165]

description: Tumor


title: H4ac ChIP-seq, ChIP DNA: Spn1-AID + DMSO 6

description: ChIP library from H4ac ChIP-seq with Spn1 non-depleted.


title: H4ac ChIP-seq, ChIP DNA: Spn1-AID + IAA 4


title: GBM [W367]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N702_S504]


title: GBM [W046]

description: Tumor


title: GBM [V964]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S507]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N702_S503]


title: GBM [V918]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S504]


title: H4ac ChIP-seq, ChIP DNA: Spn1-AID + DMSO 5


title: GBM [V800]

description: Tumor


title: GBM [V671]

description: Tumor


title: GBM [V917]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S506]


title: GBM [V773]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S505]


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S502]


title: GBM [V769]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: set2D Spn1-AID + DMSO 6

description: ChIP library from H4 ChIP-seq with Spn1 non-depleted, in set2D background.


title: GBM [V586]

description: Tumor


title: GBM [V706]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: set2D Spn1-AID + IAA 6

description: ChIP library from H4 ChIP-seq with Spn1 depleted, in set2D background.


title: H4ac ChIP-seq, ChIP DNA: Spn1-AID + DMSO 4


title: histone H4 ChIP-seq, ChIP DNA: set2D Spn1-AID + DMSO 4


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N712_S508]

description:
SLX-9712
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

value: Dorsal


title: GBM [V672]

description: Tumor


title: GBM [V587]

description: Tumor


title: GBM [V600]

description: Tumor


title: GBM [V610]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N712_S506]


title: GBM [V327]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: Spn1-AID + IAA 6

description: ChIP library from H4 ChIP-seq with Spn1 depleted.


title: histone H4 ChIP-seq, ChIP DNA: set2D Spn1-AID + DMSO 5


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N712_S517]


title: GBM [V247]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: set2D Spn1-AID + IAA 4


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N712_S504]


title: GBM [V584]

description: Tumor


title: ventral Ngfr+Pdgfrb- cells (Ventral) [SLX-9713.N701_S503]


title: histone H4 ChIP-seq, ChIP DNA: Spn1-AID + IAA 5


title: histone H4 ChIP-seq, ChIP DNA: set2D Spn1-AID + IAA 5


title: Ganglioglioma [V153]

description: Tumor

value: Ganglioglioma


title: GBM [V105]

description: Tumor


title: GBM [V585]

description: Tumor


title: GBM [U941]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S517]


title: histone H4 ChIP-seq, ChIP DNA: Spn1-AID + IAA 4


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N712_S503]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N712_S505]


title: GBM [V194]

description: Tumor


title: GBM [V461]

description: Tumor


title: GBM [V288]

description: Tumor


title: GBM-G34 [U935]

description: Tumor


title: GBM [U867]

description: Tumor


title: GBM [V403]

description: Tumor


title: GBM [V522]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S507]


title: 6289_36_36_TAGCTTA_S99

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

description:
A2780 cis SSP -SG carbo
A2780 cis SSP cell line without serine/glycine + 6 M carboplatin
Total RNAseq
RNAseq_readscounts.txt

data_processing:
RNA-seq: Data, as FASTQ file, were aligned with STAR to the human genome GRCh37.p13. HTSEQ with gencode.v19 annotation was used to count reads at exons of genes. Normalization of read counts was done using DEseq and DEseq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNAseq_readscounts.txt: Tab-delimited text file containing raw read counts (HTSeq).

growth_protocol: A2780 wt and its cisplatin resistant analogue A2780 cis cells were obtained from the ECACC (Sigma Aldrich ECACC 93112519 and Sigma Aldrich ECACC 93112517, respectively) and were maintained in RPMI medium containing 10% FBS (Gibco), 2 mM glutamine (L-Glutamine, Gibco), 100 IU penicillin and 100 μg/mL streptomycin (PenStrep, Gibco).

extract_protocol:
5x10^6 cells per condition per replicate were lysed using RLT buffer (Qiagen) and stored at -80°C. For the generation of total RNA libraries, total RNA was extracted using TRI Reagent (SIGMA), and mRNA was purified using Dynabeads mRNA DIRECT Purification Kit (Invitrogen), according to the manufacturers’ protocol.
Total RNA libraries were constructed using SENSE Total RNA-Seq Library Prep Kit for Illumina (LEXOGEN).

treatment_protocol: For experiments under serine/glycine deprivation conditions, cells were fed homemade medium (homemade RPMI with the same formulation as commercial RPMI from Gibco, supplemented with 10% dialyzed FBS (Gibco) and standard concentrations of penicillin-streptomycin and glutamine) with or without serine and/or glycine (Sigma Aldrich). Isogenic resistant A2780cis were obtained by chronically exposing parental cells to cisplatin.

tag: cell line

value: A2780 cis

value: ovarian cancer cells

value: SSP -SG carbo


title: GBM [U590]

description: Tumor

value: FFPE


title: GBM [U831]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S508]


title: GBM [U775]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 5

description: ChIP library from H4 ChIP-seq with Spn1 non-depleted.


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S505]


title: GBM [U583]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 4


title: GBM [U592]

description: Tumor


title: GBM [U480]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S504]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S506]


title: GBM [U200]

description: Tumor


title: histone H4 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 6


title: GBM [U197]

description: Tumor


title: 6289_35_35_GATCAGA_S98


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S503]


title: GBM [U093]

description: Tumor


title: GBM [U764]

description: Tumor


title: 6289_32_32_ATCACGA_S95

description:
A2780 cis SSP -SG
A2780 cis SSP cell line without serine/glycine
Total RNAseq
RNAseq_readscounts.txt

value: SSP -SG


title: 6289_33_33_TTAGGCA_S96


title: GBM [U528]

description: Tumor


title: GBM [T964]

description: Tumor


title: 6289_34_34_ACTTGAA_S97


title: GBM [T998]

description: Tumor

value: Male


title: GBM [T877]

description: Tumor

value: GBM


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N711_S502]


title: 6289_30_30_GTCCGCA_S94

description:
A2780 cis SSP carbo
A2780 cis SSP cell line + 6  M carboplatin
Total RNAseq
RNAseq_readscounts.txt

value: SSP carbo


title: 6289_29_29_CCGTCCC_S93


title: 6289_31_31_GTGAAAC_S88


title: GBM [T933]

description: Tumor

value: Female


title: GBM [T932]

description: Tumor


title: GBM [T735]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S517]


title: GBM [T675]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S508]


title: GBM [T757]

description: Tumor


title: GBM [T674]

description: Tumor


title: GBM-G34 [T629]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S505]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S506]


title: GBM [T535]

description: Tumor


title: GBM-G34 [T599]

description: Tumor


title: GBM [S914]

description: Tumor


title: GBM [T211]

description: Tumor


title: 6289_26_26_AGTCAAC_S90

description:
A2780 cis SSP
A2780 cis cells with regained activity of serine synthesis pathway (SSP)
Total RNAseq
RNAseq_readscounts.txt

value: SSP


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S504]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S507]


title: GBM [T212]

description: Tumor


title: GBM-G34 [T147]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S502]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N710_S503]


title: GBM [S607]

description: Tumor


title: GBM [S608]

description: Tumor


title: 6289_27_27_AGTTCCG_S91


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S517]


title: 6289_23_23_GCCAATA_S86

description:
A2780 cis -SG carbo
A2780 cis cell line without serine/glycine + 6 M carboplatin
Total RNAseq
RNAseq_readscounts.txt

value: -SG carbo


title: GBM [S149]

description: Tumor


title: GBM [S849]

description: Tumor


title: 6289_24_24_CAGATCA_S87


title: 6289_22_22_ACAGTGA_S85


title: GBM [S687]

description: Tumor


title: GBM [S013]

description: Tumor


title: 6289_28_28_ATGTCAG_S92


title: 6289_21_21_TGACCAA_S84

description:
A2780 cis -SG
A2780 cis cell line without serine/glycine
Total RNAseq
RNAseq_readscounts.txt

value: -SG


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S507]

value: Wild-type


title: GBM [S011]

description: Tumor


title: GBM [R842]

description: Tumor


title: GBM [R803]

description: Tumor


title: 6289_20_20_CGATGTA_S83


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S505]

value: aorta-gonads-mesonephros (AGM)


title: 6289_25_25_CTTGTAA_S89


title: GBM [R754]

description: Tumor


title: GBM [R423]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S504]


title: Ganglioglioma [R707]

description: Tumor


title: 6289_18_18_ACTGATA_S82

description:
A2780 cis carbo
A2780 cis cell line + 6 M carboplatin
Total RNAseq
RNAseq_readscounts.txt

value: carbo


title: GBM-G34 [R355]

description: Tumor


title: 6289_19_19_ATTCCTT_S76


title: GBM [Q910]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S508]

value: Dorsal


title: GBM [R352]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S503]


title: GBM [Q781]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N709_S502]


title: 6289_17_17_GAGTGGA_S81


title: GBM [Q728]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S517]


title: 6289_15_15_GTTTCGG_S79

description:
A2780 cis
cisplatin resistant isogenic analogue of A2780 wt
Total RNAseq
RNAseq_readscounts.txt


title: GBM [Q780]

description: Tumor


title: 6289_16_16_CGTACGT_S80


title: 6289_14_14_GTGGCCT_S78


title: GBM [P9b]

description: Tumor


title: GBM [Q210]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S508]


title: GBM [P9a]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S507]


title: GBM [P8c]

description: Tumor


title: 6289_12_12_TAGCTTA_S75

description:
A2780 WT -SG carbo
A2780 wild type cell line without serine/glycine + 6 M carboplatin
Total RNAseq
RNAseq_readscounts.txt


title: GBM [P7]

description: Tumor


title: GBM [P8a]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S505]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S506]


title: GBM [P6]

description: Tumor


title: GBM [P15]

description: Tumor


title: GBM [P8b]

description: Tumor


title: 6289_10_10_ACTTGAA_S73


title: GBM [P586]

description: Tumor


title: 6289_11_11_GATCAGA_S74


title: 6289_13_13_GGCTACA_S77


title: 6289_9_9_TTAGGCA_S72

description:
A2780 WT -SG
A2780 wild type cell line without serine/glycine
Total RNAseq
RNAseq_readscounts.txt


title: GBM [P5a]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S504]


title: GBM [P4]

description: Tumor


title: GBM-F3T3-O [P2a]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S503]


title: 6289_7_7_GTGAAAC_S64


title: GBM [P5b]

description: Tumor


title: GBM [P3]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N708_S502]


title: GBM-F3T3-O [P2b]

description: Tumor


title: 6289_8_8_ATCACGA_S71


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S517]


title: GBM [P14b]

description: Tumor