title: MUC5849_98578h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2D6]

status: Public on Jan 27 2022

type: SRA

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

library_source: transcriptomic

data_processing:
Mapped to GRCh38 using STAR.
Gene counts using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: pclamp_v2_counts.tab: Tab-delimited text file includes gene counts.

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic islets

extract_protocol: SmartSeq2 (21X-23X PCR cycles).

tag: diagnosis

value: Nondiabetic

tag: tissue

value: Pancreatic islets

tag: Sex

value: Male

tag: patched

value: Yes


title: NAD5_Enrich_rep1

city: Shanghai

first: Dean

last: Li

address: Haike Road 100

country: China

institute: Chinese Academy of Science

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to human with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

molecule: polyA RNA

organism: Mus musculus

source_name: Liver tissue

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)

value: Liver

tag: strain

tag: condition

value: 5% NAD-RNA spike-in

tag: assay

value: Enrich


title: pancreatic cells for patch-seq [H2D5]


title: MUC5842_9870_24h_fast_HEP

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: IP'ed nuclei from HEP-INTACT mice

library_source: genomic

data_processing:
Sequence tags from ATAC-seq libraries were aligned to the mm10 using the BWA aligner (version 0.7.5a-r405) (Li and Durbin, 2009).
Post-alignment processing of reads was performed with Samtools (0.1.19-44428cd) (Li et al., 2009) by removing duplicate reads and filtering for high quality reads using Samtools view using the following settings ”-b -h -f 1 -F 4 -F 8 -F 256 -F 2048 -q 30”. Furthermore, only reads with a fragment length<100bp was used corresponding to the reads located in nucleosome-free regions.
ATAC seq peaks were identified, annotated and tags in peaks were counted using HOMER (Heinz et al., 2010). Tag directories from conditions with technical duplicates were combined into one before further analyses. Peaks were called in each library with HOMER findPeaks using the following settings: ‘peaks’, ‘-fragLength 70’, ‘-style factor’, ‘-minDist 140’, ‘-size 70’.
For all peak files, overlapping peaks were merged and collected in one master peak file. Tags were then counted in a 200bp window around the peak centers for each individual library in the resulting master peak file.
Differential accessible sites (fed vs fasted) were determined using DESeq2 using default parameters.
Bedgraph files for individual libraries were generated using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Bedgraph files for each condition were generated by merging the individual tag directories of one condition into one and using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text with norm counts and log2FC (fed vs fasted) (output from DESeq2)
Supplementary_files_format_and_content: Bedgraph files for individual libraries
Supplementary_files_format_and_content: Bedgraph files (merged) - one from each condition

molecule: genomic DNA

source_name: Hepatocyte Nuclei

extract_protocol:
Approximately 25,000 bead-bound nuclei from INTACT reactions were transposed in a 50 μL volume of 1X TTBL buffer and 3.5 μL TTE Mix V50 (from TruePrep™ DNA Library Prep Kit V2 for Illumina, Vazyme TD501) for 30 minutes at 37°C. Fragmented genomic DNA was recovered using Buffer ERC coupled with MinElute spin column purification (Qiagen). Samples originating from MAC INTACT mice were run in technical duplicates.
Transposed genomic DNA was amplified by 12 cycles of quantitative PCR. Amplified DNA was purified and size-selected on AMPure XP beads (Beckman A63881), analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 4000 platform.

value: Hepatocyte Nuclei

tag: feeding state


title: pancreatic cells for patch-seq [H2D7]


title: MUC5841_9898_16h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: 143B kidney

type: RNA

city: Akita City

first: Sei

last: Kuriyama

department: Molecular Medicine & Biochemistry

country: Japan

institute: Akita University

description: Stable gene expression in normal culture condition

hyb_protocol: Biotinylated fragments were hybridized with GeneChip Human Gene 2.0ST array, washed, and stained in Affmetryx Fluidics station 450.

scan_protocol: GeneChips were scanned with Affimetryx Scanner 3000 7G.

data_processing: The data was analyzed using Affimetryx Expression Console.

label: biotin

source_name: 143B-kidney cells

label_protocol: The 1st strand DNA was digested using Uracyl DNA glycosilase with thermal cycler( Vertiti 200, Lifetechnologies Inc.). Using 5.5µg cDNA, 40-70nt fragment was biotinylated.

growth_protocol: Essential Medium Eagle Modification (EMEM) +10% FBS+sodium pyruvate+penicillin/streptomycin

extract_protocol: PureLink RNA Mini Kit was used for RNA preparation

treatment_protocol: 4 x 10exp5 cells/ 100µLHBSS were injected into left ventricule of Balb/c nude mice, and metastasis was monitored using aLuciferin (artificial luciferin substrates) and IVIS imaging system

tag: cell line

tag: disease state

value: osteosarcoma

value: kidney


title: GCB_A

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

country: USA

institute: Rutgers

description:
targeted RNA
GC_A

data_processing:
Library strategy: BCR-seq
Base calling (bcl2fastq v2.20.0.422)
QC, read assembly, alignment, clonal assignment (Immcantation v3.0.0)
Genome_build: Immcantation mouse reference
Supplementary_files_format_and_content: tab delimited file

source_name: Spleen

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
BCR library prepreration was perfromed NEBNext Immune-seq library preparation kit for Mouse IG

tag: cell type

value: GCB

value: Spleen

tag: infected with

value: LCMV Armsttrong

tag: timepoint

value: Day 12 post LCMV infection


title: GCB_D

description:
targeted RNA
GC_D


title: GCB_B

description:
targeted RNA
GC_B


title: NAD1_Enrich_rep2

value: 1% NAD-RNA spike-in


title: pancreatic cells for patch-seq [H2D2]


title: MUC5839_10099_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: 143B parent

source_name: 143B cells

value: adrenal gland


title: pancreatic cells for patch-seq [H2D4]


title: 143B lymph

source_name: 143B-lymph cells

value: lymph node


title: pancreatic cells for patch-seq [H2D3]

value: Nondiabetic


title: 11cB_A

description:
targeted RNA
TbetCD11c_A


title: NAD0_Enrich_rep3

value: 0% NAD-RNA spike-in


title: 11cB_D

description:
targeted RNA
TbetCD11c_D


title: pancreatic cells for patch-seq [H2D12]

value: Pancreatic islets

value: Male


title: 11cB_B

description:
targeted RNA
TbetCD11c_B


title: NAD0_Enrich_rep2

value: Liver


title: MUC5838_10101_16h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC5837_9901_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC5836_9851_8h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD0_Enrich_rep1


title: pancreatic cells for patch-seq [H2D10]

value: Yes


title: pancreatic cells for patch-seq [H2D11]


title: NAD1_Enrich_rep3

value: Enrich


title: NAD10_Input_rep3

value: 10% NAD-RNA spike-in

value: Input


title: NaiveB_D

description:
targeted RNA
Naïve_D

value: naive


title: NAD10_Input_rep2


title: pancreatic cells for patch-seq [H2D1]


title: NAD1_Enrich_rep1


title: MUC5835_9897_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice

value: Hepatocyte Nuclei


title: NAD10_Input_rep1


title: NaiveB_A

description:
targeted RNA
Naïve_A

value: Spleen


title: NAD5_Input_rep3

value: 5% NAD-RNA spike-in


title: MUC5843_9869_16_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC5840_10096_24h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NaiveB_B

description:
targeted RNA
Naïve_B

value: LCMV Armsttrong

value: Day 12 post LCMV infection


title: MUC5834_10108_8h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: MUC5833_9595_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2C9]


title: pancreatic cells for patch-seq [H2C8]


title: pancreatic cells for patch-seq [H2C7]


title: MUC5832_9594_3h_Ad_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD5_Input_rep1


title: miRNA-lung-normal-2(Cap2)

city: 上海

first: Yani

last: Kang

address: 东川路800号

institute: Shanghai Jiaotong University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, the clean reads were mapped onto the reference human genome hg38 using the bowtie2 (version 2.1.0)
The mapped tags were then aligned against miRBase (version 22.1), and read counts were calculated through customized script.
Reads per million mapped reads (RPM) were calculated.
The target genes of DEmiRs were predicted through miRTarbase database
Genome_build: hg38
Supplementary_files_format_and_content: Xlsx file includes matrix table with raw miRNA reads count and RPM values for every miRNA and every sample

source_name: human lung

extract_protocol:
Total RNA was extracted from human lung tissue samples by using TRIzol reagents (Invitrogen, Waltham, Massachusetts, USA) as recommended by the manufacturer. The total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running 1.5% agarose gel electrophoresis and staining with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
1μg of total RNA was used to construct the small RNA-seq libraries by TruSeq® Small RNA Library Prep Kit (NEB, San Diego, California, USA) following the manufacturer’s protocol. The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).

value: lung

value: normal


title: miRNA-lung-normal-3(Cap3)


title: miRNA-lung-normal-1(Cap1)


title: pancreatic cells for patch-seq [H2C6]

value: Nondiabetic


title: miRNA-ung-cancer-3(Ca3)

value: cancer


title: MUC5830_10115_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: pancreatic cells for patch-seq [H2C5]

value: Pancreatic islets


title: NAD1_Input_rep2

value: 1% NAD-RNA spike-in


title: MUC5831_9860_3h_fast_HEP

description: IP'ed nuclei from HEP-INTACT mice


title: NAD5_Input_rep2

value: Liver


title: miRNA-lung-cancer-2(Ca2)


title: NAD1_Input_rep3


title: NAD1_Input_rep1


title: hiPSCNeuron_PSEN1A246E_Semagacestat_rep3

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
Raw RNA-Seq data was uploaded into Illumina’s BaseSpace Sequence Hub, a cloud-based computing environment, for data processing.
Read mapping to the human genome (UCSC hg19) was performed using TopHat v2.0.7 and BowTie v0.12.9 within the TopHat Alignment v1.0 app on the Basespace platform, selecting the stranded and fusion calling features with the default parameters.
Transcripts were assembled and abundances estimated using Cufflinks v.2.1.1 within the Cufflinks Assembly & DE v1.1 app on the Basespace platform, using the novel transcript assembly and adjusting transcript assembly for non-polyA selection.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Processed data file contains expression values for each gene and sample are presented in FPKM as calculated by the TopHat/Cufflinks/Cuffdiff pipeline.

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation, Semagacestat treated

growth_protocol: Non-Demented Control (NDC) fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval, whereas psen1A246E fibroblasts were obtained commercially (Coriell Cat. AG06840). The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors oct4, sox2, klf4, and c-myc. Neural stem cells (NSCs) were expanded in NSC growth medium (DMEM /F12, GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neural differentiation medium (DMEM /F12, GlutamaxTM, 1x B-27, 1x N-2, and 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of IMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with IMag buffer and subsequently incubated with magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences).  The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for downstream applications.

extract_protocol:
Total RNA from magnetically purified human hiPSC-derived neurons was prepared using RNeasy Plus Micro Kit (Qiagen Cat. 74034) according to the manufacturer’s protocol.
Libraries were prepared for RNA-Seq using the TruSeq Stranded Total RNA Library prep kit, using the Ribo-Zero ribosomal RNA reduction method (Illumina).

value: EOFAD patient

value: hiPSC-derived neuron

tag: treatment

value: Semagacestat


title: NAD0_Input_rep3

value: 0% NAD-RNA spike-in

value: Input


title: miRNA-lung-cancer-1(Ca1)


title: hiPSCNeuron_PSEN1A246E_Semagacestat_rep2


title: pancreatic cells for patch-seq [H2C3]

value: Male

value: Yes


title: hiPSCNeuron_PSEN1A246E_Semagacestat_rep1


title: lung-normal-2(Cap2)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Raw counts were derived using stringtie v1.3.3.
Genome_build: hg38
Supplementary_files_format_and_content: Xlsx file includes matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from human lung tissue samples by using TRIzol reagents (Invitrogen, Waltham, Massachusetts, USA) as recommended by the manufacturer. The total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running 1.5% agarose gel electrophoresis and staining with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
1μg of total RNA was used to construct the lncRNA-seq libraries by the ABclonal Whole RNA-seq Lib Prep kit (ABclonal Technology Co.,Ltd.). The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).


title: lung-normal-3(Cap3)


title: pancreatic cells for patch-seq [H2C2]


title: NAD0_Input_rep2


title: hiPSCNeuron_PSEN1A246E_BPN15606_rep3

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation, BPN15606 treated


title: NAD0_Input_rep1


title: Thymus, Cd226KO

city: Xi'an

first: Yitian

last: Liu

state: Shannxi

institute: Fourth Military University

data_processing:
Quality control
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.7.5a
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Thymus

extract_protocol:
Tissues were digested in GEXSCOPE Tissue Dissociation Solution (Singleron Biotechnologies, Nanjing, China) and were passed through 40-μm nylon sterile strainer to obtain single-cell suspensions. Single-cell suspensions with 1 × 10^5 cells/ml in PBS (HyClone) were prepared. The suspensions were then loaded onto microfluidic devices.
scRNA-seq libraries were constructed according to the Singleron GEXSCOPETM protocol using the GEXSCOPE™ Single-Cell RNA Library Kit (Singleron,1110011 )

value: Thymus

tag: age

value: 5 weeks

tag: genotype


title: hiPSCNeuron_PSEN1A246E_BPN15606_rep2


title: lung-normal-1(Cap1)


title: pancreatic cells for patch-seq [H2C11]


title: pancreatic cells for patch-seq [H2C10]


title: lung-cancer-2(Ca2)


title: lung-cancer-3(Ca3)


title: Thymus, WT

value: WT


title: hiPSCNeuron_PSEN1A246E_DMSO_rep3

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation, DMSO treated

value: DMSO


title: hiPSCNeuron_PSEN1A246E_BPN15606_rep1


title: Gpr_nipple rep 2

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to mm10 whole genome using STAR aligner (v2.7.3) following sns rna-star (https://igordot.github.io/sns/routes/rna-star.html) pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mammary gland

extract_protocol:
FACS-sorted Gpr125+ CD49fhi and Gpr125‒ CD49fhi cells isolated from TEB-distal and nipple-proximal regions of pubertal Adgra3lz/+ mammary glands.Total RNA was extracted from centrifugated cell pellets using RNeasy Plus MiniKit (cat, #74136, Qiagen) according to the manufacturer's instructions. RNA quantity and quality was determined using Bioanalyzer RNA Quality and Quantity Assay NANO (Agilent Technologies, Santa Cruz, CA)
Low input Clontech SMART-Seq HT

value: 6 weeks old

value: mammary gland


title: lung-cancer-1(Ca1)

value: lung

value: cancer


title: Gpr_nipple rep 1


title: pancreatic cells for patch-seq [H2B7]

value: Nondiabetic

value: Pancreatic islets


title: hiPSCNeuron_PSEN1A246E_DMSO_rep2

value: EOFAD patient


title: hiPSCNeuron_PSEN1A246E_DMSO_rep1

value: hiPSC-derived neuron


title: Gpr_TEB rep 2


title: hiPSCNeuron_NDC_DMSO_rep2

source_name: hiPSC-derived neurons from human Non-Demented Control patient, DMSO treated

value: Non-Demented Control patient


title: Subject 078 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

description:
IMRAS078.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

data_processing:
a. Reads were aligned to the UCSC hg38 genome using Kallisto alignment tool.
b. Reads were quantified with RSEM.
c. Raw counts from two separate batches were combined into one matrix.
d. Original sample names used during processing were mapped to standardized sample names to include subjectId and visit day.
e. Four samples that could not be mapped to standardized subject-visit day format were excluded.
Genome_build: UCSC hg38 (GRCh38)
Supplementary_files_format_and_content: GEO_IMRAS_mapped_rawCounts.tsv: Tab-delimited file with raw counts for 265 samples.

source_name: Whole Blood

extract_protocol:
Whole blood samples taken from participants via venipuncture and collected into PaxGene tubes. Total RNA was extracted using PAXgene Blood Kit (PreAnalytiX) and globin mRNA removed using GLOBINclear Human Kit (Ambion).
RNA libraries were generated using standard manufacturers’ protocols for the two platforms (BGI’s BGIseq500 and Illumina’s HiSeq2000).

tag: cohort

value: Cohort 1

tag: subject

value: Whole Blood

value: True Immunized

tag: visit day


title: Gpr_TEB rep 1

tag: tissue


title: Gpr_neg rep 2


title: Subject 071 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS071.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 062 VisitDay 000 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS062.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

value: Mock Immunized


title: pancreatic cells for patch-seq [H2B6]

tag: diagnosis

tag: Sex

value: Male

tag: patched

value: Yes


title: hiPSCNeuron_NDC_DMSO_rep1


title: pancreatic cells for patch-seq [H2B5]


title: pancreatic cells for patch-seq [H2C12]


title: Gpr_neg rep 1


title: PVM_8W_6_1

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into fastq files with either the CASAVA1.8.2 software or with the bcl2fastq v2.18 software.
The RNA-seq data was aligned with STAR v2.7.8a to the mouse reference genome Gencode M26. Counts were obtained using FeatureCounts v2.0.2.
Genome_build: Gencode M26
Supplementary_files_format_and_content: counts

source_name: pvMΦ

growth_protocol: SPF breeding facility

extract_protocol:
Cells were sorted into RNAprotect Cell Reagend (QIAGEN) according to the manufacturers recommendations. RNA was extracted using Picopure RNA extraction kit (Life Technologies) according to manufacturer’s protocol. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3.

tag: strain

tag: batch


title: Subject 060 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS060.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2B4]


title: PVM_8W_6_2


title: TNF 3

data_processing:
Paired-end reads were mapped to the mouse genome assembly mm10 using the STAR aligner (v2.6.1a) (Dobin et al., 2013)
Quantification of the number of mapped reads of each gene and differential expression analyses were carried out using iRNA-seq (v 1.1) in 'DE-mode' specifying the "-count gene" option (Madsen et al., 2015)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text with log2FC, differential gene expression analyses and normalized counts (output from iRNA.pl)

source_name: Primary hepatocytes

growth_protocol: For primary hepatocyte culture experiments, 400.000 cells per well were plated in collagen-coated 12-well plates (Thermo Fisher Scientific) in plating medium (William’s Medium E (WME) (PAN-Biotech) containing 5% FCS (PAN-Biotech), 1x Thawing/Plating Cocktail (minus Dexamethasone) (Thermo Fisher Scientific) and 1uM corticosterone) and maintained at 37 °C and 5% CO2. After 1h, cells were washed with PBS (Thermo Fisher Scientific) and medium was changed to maintenance medium (WME, containing 1x Maintenance Cocktail (minus Dexamethasone) (Thermo Fisher Scientific) and 0.1uM corticosterone. After 6 h, medium was changed to starvation medium (DMEM w/o glucose, 1% P/S, 1% FBS, and 5mM glucose) and incubated 16 h.

extract_protocol:
Primary hepatocytes were harvested in Trizol using a Tissuelyzer II (Qiagen) and RNA purification was performed using EconoSpin columns (Epoch).
A total amount of 500 ng of total RNA was used and sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The prepared libraries were sequenced (paired-end) on a Illumina platform.

treatment_protocol: Primary hepatocytes were treated for 8 h with 1uM Corticosterone and 10uM WY-14643, and co-treated with vehicle or 1 ng/ml TNF.

value: 1 ng/ml TNF


title: PVM_8W_6_4


title: Subject 054 VisitDay 000 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS054.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: PVM_8W_6_3


title: Subject 057 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS057.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: TNF 1


title: TNF 2


title: pancreatic cells for patch-seq [H2B3]

source_name: pancreatic islets


title: pancreatic cells for patch-seq [H2B12]


title: Subject 049 VisitDay 000 Cohort IMRAS_Cohort 1_Mock Immunized

description:
IMRAS049.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: PVM_3W_7_3


title: Control 3

value: Vehicle


title: pancreatic cells for patch-seq [H2B11]


title: PVM_3W_7_1


title: Control 2


title: Subject 039 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS039.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2B10]


title: PVM_3W_7_4


title: Control 1


title: Subject 033 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS033.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2B1]


title: PVM_3W_7_2


title: Subject 061 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS061.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: Subject 021 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS021.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2A9]


title: PVM_d10_8_2


title: Subject 005 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS005.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: ImmunoMPRA E15.5 TUBB3+ rep2

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

description: processed data: Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.

data_processing:
library strategy: Targeted barcode amplification from RNA/DNA
50xbp paired-end reads from the DNA or RNA libraries were trimmed using cutadapt with the following parameters: -u 1 -a GAATTCTCATTAC -A TCGACCGCAAGTTGG --discard-untrimmed. Count tables for RNA and DNA reads were generated using MPRAflow (--bc-length 12 and –mpranalyze).
Genome_build: mm10
Supplementary_files_format_and_content: Compressed text file, containing pair-wise contact infomration in the medium juicer format (https://github.com/aidenlab/juicer/wiki/Pre) but omitting the read name: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>.
Supplementary_files_format_and_content: Bigwig files with CpG or GpC methylation levels of all cytosines covered by at last 5 reads (5x coverage).
Supplementary_files_format_and_content: Tab seperated table containing read counts per gene.
Supplementary_files_format_and_content: Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz).
Supplementary_files_format_and_content: Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.

source_name: Electroporated Tubb3+ from E15.5 somatosensory cortex

extract_protocol:
The somatosensory cortex of in utero electroporated E15.5 mouse embryos was isolated and the electroporated area dissected. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen). Dissociated cells were and immediately FAC-sorted at a BD FACSAria Fusion (BD Bioscience) with four lasers (405, 488, 561, 640) using a 100µm nozzle. Fixed sorted cells were digested with Proteinase K (Proteinase K (New England Biolabs, Cat. N: P8107S) at 55˚C for 1 h and decrosslinked at 65 ˚C for 15 min. RNA and DNA were extracted using the Quick-DNA/RNA Microprep Plus Kit (Zymo Research; Cat. N: D7005). Purified RNA was treated with TURBO DNase (Thermo Fisher; Cat. N: AM1907) and reverse transcribed with Maxima H Minus RT (Thermo Fisher; Cat. N: EP0753) using Oligo(dT)18 Primer (Thermo Fisher; Cat. N: SO131). cDNA was purified with 1.5X vol. AMPure XP magnetic beads (Agencourt, Cat. N: A63881) and stored at -20 °C for later use.
Libraries from DNA and cDNA were prepared in the same way. Briefly, UMIs were added (98°C 30s; {98°C 10s, 65°C 30s, 72°C 1min} x3; 72°C 3min; Hold at 4°C) using the primers RV_univ_MPRA (CGACGCTCTTCCGATCT) and FWD_mScar_Tn7_10UMI_3 (0.5 µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG NNNNNNNNNN TCGACCGCAAGTTGGAC). P7 and P5 sequencing adapters were attached in two separate PCRs (98°C 30s; {98°C 10s, 65°C 90s} x(10+X); 72°C 5min; Hold at 4°C) using indexed Ad2.X(CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT) and P5NEXTPT5 primers (0.1 µM each; AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T). Required PCR cycle numbers were estimated by qPCR and using 1/10 of the second PCR product as input. All PCRs were performed in 1X NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544), and PCR products were purified with 0.8X - 1.2X vol. of AMPure XP magnetic beads.

tag: celltype

value: PN (Tubb3+)

tag: technique

value: ImmunoMPRA

tag: molecule subtype

value: RNA and DNA


title: pancreatic cells for patch-seq [H2A8]


title: Subject 002 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS002.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv


title: pancreatic cells for patch-seq [H2A7]


title: PVM_d10_8_1


title: PVM_d10_8_3


title: ImmunoMPRA E15.5 Eomes+ rep2

source_name: Electroporated Eomes+ from E15.5 somatosensory cortex

value: IPC (Eomes+)


title: ImmunoMPRA E15.5 Eomes+ rep1


title: MnM_8W_9_1

source_name: mMΦ


title: KD_4hr

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.0.0 was used with default settings to generate mapped bam files and then to generate filtered feature count (gene-by-cell) matrices
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered feature-barcode matrices in MEX format, that is, a genes-by-cells matrix market file along with cell barcode and gene name tab-delimited text files.

source_name: primary resting memory CD4+ T cells generated from PBMC of healthy donors

growth_protocol: PBMCs were isolated from 50 mL leukopaks of healthy donor blood samples using Lymphoprep density gradient. Naïve CD4+ T cells were isolated from PBMCs following the instruction of EasySep™ Human Naïve CD4+ T Cell Isolation Kit (STEMCELL, 558521). Cells were then activated by culturing with RPMI/10%FBS/1%Penicillin/streptomycin containing 1 mg/ml anti-IL-4, 2 mg/ml anti-IL-12, 10 ng/ml TGF-b1 and Dynabeads human T-activator anti-CD3/anti-CD28 (Gibco, 11132) (1 bead/cell). Cells were cultured at 37°C in 5% CO2 at 1 x 106/mL confluency. After 3 days, beads were removed by a magnetic column. Pre-assembled Cas9-gRNA RNPs were electroporated into cells. Depletion of target protein was monitored by western blotting. Cells were cultured in complete media with 30 IU/ml IL-2. Media containing IL-2 was replenished daily for 10 days, followed by every other day and maintaining cells at 1 x 106/mL until cells transitioned to resting memory phenotype monitored by intracellular Ki67 proliferation marker and CD45Ra-/CD45Ro+ surface markers.

extract_protocol:
Samples were prepared for scRNAseq using the 10X Genomics Next GEM Single cell 3’ Reagent Kit v3.1. Single cell suspensions were washed in 1X PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 μg/mL) and brought to a concentration of ~700-1200 cells/μL. This was accomplished by staining 10 μL of the single cell suspension with Trypan blue and reading on the Countess™ II Automated Cell Counter (ThermoFisher). The appropriate volume of cells was loaded with Single Cell 3’ Gel Beads into a Next GEM Chip G and run on the Chromium™ Controller. GEM emulsions are incubated and then broken. Silane magnetic beads were used to clean up GEM reaction mixture. Read one primer sequence was added during incubation and full-length, barcoded cDNA is then amplified by PCR after cleanup. Sample size was checked on a Tapestation 4200 (Agilent) using the DNAHS 5000 tape and concentration determined by the Qubit 4.0 Fluorimeter (ThermoFisher) using the DNA HS assay.
Samples were enzymatically fragmented and underwent size selection before proceeding to library construction. During library preparation, Read 2 primer sequence, sample index and both Illumina adapter sequences were added. Subsequently, samples were cleaned up using Ampure XP beads (Beckman Coulter) and post library preparation quality control was performed using the DNA 1000 tape on the Agilent Tapestation 4200. Final concentration was ascertained using the Qubit DNA HS assay. Samples are loaded at 1.6 pM and run on the Illumina NextSeq500 High Output FlowCell using V2.5 chemistry. Run configuration is 28x98x8.

treatment_protocol: Once cells were resting, cells were left resting or treated with anti-CD3/anti-CD28 Dynabeads (1 bead/cell) for 4 hrs at 37°C in 5% CO2 at 1 x 106/mL confluency.

tag: cell type

value: primary resting memory CD4+ T cell (30 days post isolation and differentiation)

tag: genotype/variation

value: ADAP1 CRISPR/Cas9 (KD)


title: ImmunoMPRA E15.5 Pax6+ rep2

source_name: Electroporated Pax6+ from E15.5 somatosensory cortex

value: NSC (Pax6+)


title: KD_0hr

tag: treatment

value: no treatment


title: pancreatic cells for patch-seq [H2B2]

value: Nondiabetic

value: Pancreatic islets


title: MnM_8W_9_3

tag: timepoint


title: ImmunoMPRA E15.5 Pax6+ rep1

tag: age


title: Ctrl_4hr

value: WT (Ctl)

value: anti-CD3/anti-CD28 Dynabeads (1 bead/cell) for 4 hrs


title: MnM_8W_9_2

tag: genotype


title: MPRA E15.5 rep2

source_name: Electroporated cells E15.5 somatosensory cortex

extract_protocol:
The somatosensory cortex of in utero electroporated E15.5 mouse embryos was isolated and the electroporated area dissected. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen). Dissociated cells were and immediately FAC-sorted at a BD FACSAria Fusion (BD Bioscience) with four lasers (405, 488, 561, 640) using a 100µm nozzle. RNA and DNA were extracted from sorted cells using the Quick-DNA/RNA Microprep Plus Kit (Zymo Research; Cat. N: D7005). Purified RNA was treated with TURBO DNase (Thermo Fisher; Cat. N: AM1907) and reverse transcribed with Maxima H Minus RT (Thermo Fisher; Cat. N: EP0753) using Oligo(dT)18 Primer (Thermo Fisher; Cat. N: SO131). cDNA was purified with 1.5X vol. AMPure XP magnetic beads (Agencourt, Cat. N: A63881) and stored at -20 °C for later use.
Libraries from DNA and cDNA were prepared in the same way. Briefly, UMIs were added (98°C 30s; {98°C 10s, 65°C 30s, 72°C 1min} x3; 72°C 3min; Hold at 4°C) using the primers RV_univ_MPRA (CGACGCTCTTCCGATCT) and FWD_mScar_Tn7_10UMI_3 (0.5 µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG NNNNNNNNNN TCGACCGCAAGTTGGAC). P7 and P5 sequencing adapters were attached in two separate PCRs (98°C 30s; {98°C 10s, 65°C 90s} x(10+X); 72°C 5min; Hold at 4°C) using indexed Ad2.X(CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT) and P5NEXTPT5 primers (0.1 µM each; AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T). Required PCR cycle numbers were estimated by qPCR and using 1/10 of the second PCR product as input. All PCRs were performed in 1X NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544), and PCR products were purified with 0.8X - 1.2X vol. of AMPure XP magnetic beads.

value: mScarlet-I+

value: MPRA


title: Ctrl_0hr


title: Subject 045 VisitDay 000 Cohort IMRAS_Cohort 1_True Immunized

description:
IMRAS045.000
processed data file: GEO_IMRAS_mapped_rawCounts.tsv

tag: cohort

value: Cohort 1

tag: subject

value: Whole Blood

value: True Immunized


title: pancreatic cells for patch-seq [H2A3]

tag: tissue

value: Male

value: Yes


title: MnM_3W_10_2


title: MPRA E15.5 rep1

value: RNA and DNA


title: H3.3 ChIP-Seq EtOH

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.63
chromosome ideagrams were drawn with RIdeogram v0.2.2
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: neuroblastoma cell line

growth_protocol: S phase synchronized IMR-5 cells with inducible RNaseH1 by double Thymidine block

extract_protocol:
crosslink (5 min), harvest, spike-in with 10 % NIH-3T3, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol:
24 h treatment with 1 µg/ml Doxycycline
Where indicated in the file names, the input samples were obtained from cells that had been incubated for 4 h with 1 µM MLN8237 or 1 µM MK5108 before harvest.

tag: cell line

value: neuroblastoma cell line

tag: chip antibody

value: rabbit monoclonal H3.3 (EPR17899, lot #GR3263393-3)

tag: input file


title: RNA-seq of Nng2 overexpressing cells rep2

description: processed data: Tab seperated table containing read counts per gene.

data_processing:
Reads were aligned using the STAR and FPKM calculated using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed text file, containing pair-wise contact infomration in the medium juicer format (https://github.com/aidenlab/juicer/wiki/Pre) but omitting the read name: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>.
Supplementary_files_format_and_content: Bigwig files with CpG or GpC methylation levels of all cytosines covered by at last 5 reads (5x coverage).
Supplementary_files_format_and_content: Tab seperated table containing read counts per gene.
Supplementary_files_format_and_content: Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz).
Supplementary_files_format_and_content: Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.

extract_protocol:
The somatosensory cortex of in utero electroporated E14.5 mouse embryos was isolated and the electroporated area dissected. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen). Dissociated cells were and immediately FAC-sorted at a BD FACSAria Fusion (BD Bioscience) with four lasers (405, 488, 561, 640) using a 100µm nozzle. RNA from sorted cells were isolated using TRIzol (ThermoFisher, Cat. N.: 15596026) according to the manufacturer instructions.
RNA-seq libraries were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England Biolabs, Cat. N.: E6420) according the manufacturer’s instruction.

tag: strain

value: GFP+

value: RNA-seq


title: MnM_3W_10_1

tag: batch


title: pancreatic cells for patch-seq [H2A12]

data_processing:
Mapped to GRCh38 using STAR.
Gene counts using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: pclamp_v2_counts.tab: Tab-delimited text file includes gene counts.

extract_protocol: SmartSeq2 (21X-23X PCR cycles).

tag: diagnosis

tag: Sex

tag: patched


title: H3.3 ChIP-Seq Dox

tag: cell type


title: ImmunoMPRA E15.5 TUBB3+ rep1

tag: celltype

value: PN (Tubb3+)

tag: technique

value: ImmunoMPRA

tag: molecule subtype


title: IR181_Input_EtOH_MLN [Input H3.3]


title: NOME-seq of Nng2 overexpressing cells rep2

description: processed data: Bigwig files with CpG or GpC methylation levels of all cytosines covered by at last 5 reads (5x coverage).

data_processing:
library strategy: Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
Nome-seq reads were first trimmed using trim galore in a paired-end mode with –clip_R1=1 and –clip_R2=15 to account for the A-tail deposited by adaptase. Reads were then mapped using bismark in paired end mode, deduplicated and methylation calls were extracted (--ignore 6 and --CX). Coverage files were then produced using coverage2cytosine in a --nome-seq mode. Only calls with at least 5x coverage per replicate retained.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed text file, containing pair-wise contact infomration in the medium juicer format (https://github.com/aidenlab/juicer/wiki/Pre) but omitting the read name: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>.
Supplementary_files_format_and_content: Bigwig files with CpG or GpC methylation levels of all cytosines covered by at last 5 reads (5x coverage).
Supplementary_files_format_and_content: Tab seperated table containing read counts per gene.
Supplementary_files_format_and_content: Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz).
Supplementary_files_format_and_content: Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.

extract_protocol:
The somatosensory cortex of in utero electroporated E14.5 mouse embryos was isolated and the electroporated area dissected. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen). Dissociated cells were fixed for 10 min. in 1% Formaldehyde (ThermoFisher, Cat. N: 28908), quenched by addition of Glycine (Invitrogen, Cat. N: 15527013) to a final concentration of 0.2M, washed in PBS with 0.1% BSA, passed through a 40µM cell strainer (ThermoFisher, Cat. N: 15342931) and immediately FAC-sorted at a BD FACSAria Fusion (BD Bioscience) with four lasers (405, 488, 561, 640) using a 100µm nozzle. Sorted cells were lysed with 0.2% Igepal-CA630 (Sigma-Aldrich, Cat. N: I3021) and incubated for 3h at 37˚C in a reaction mix containing 4.5U/µl M.CviPI (New England Biolabs, Cat. N.: M0227S) and 0.6mM SAM (New England Biolabs, Cat. N.: B9003). During the incubation the reaction was substitution with 4U M.CviPI and 0.5µl of 32mM SAM every hour. Thereafter nuclei were lysed and reverse-crosslinked overnight at 68˚C, purified by ethanol precipitation and sheared to ~550 bp fragments using a Covaris S220 sonicator. Methylated and unmethylated spike in controls were added to the samples (~ 0.05%) prior bisulfite conversion using the the EZ DNA Methylation-Gold kit (Zymo Research, Cat. N: D5005).
Final libraries were constructed using the Accel-NGS® Methyl-Seq DNA Library kit (Swift Bioscience, Cat. N: 30024) according to the manufacturer’s instructions until the final library amplification step. To increase the complexity of the samples, library amplification was performed in 5 separate reaction using the EpiMark Hot Start Taq (New England Biolabs, Cat. N: M0490S) with Methyl-Seq Indexing Primers (Swift Bioscience, Cat. N: 36024) using the following PCR program: 95˚C 30s; {95˚C 15s, 61˚C 30s, 68 ˚C 60s} x11; 68˚C 5min; Hold at 10˚C. Different PCR reactions of a sample were pooled and purified using 0.8x AMPure XP beads (Agencourt, Cat. N: A63881).

tag: age

value: NOME-seq


title: MnM_d10_11_2

tag: genotype

tag: timepoint


title: pancreatic cells for patch-seq [H2A10]

value: Nondiabetic

value: Pancreatic islets


title: MnM_d10_11_1


title: RNA-seq of Nng2 overexpressing cells rep1


title: MnM_d10_11_3


title: MnM_3W_10_3


title: MnM_d3_12_1


title: pancreatic cells for patch-seq [H2A6]


title: pancreatic cells for patch-seq [H2A11]


title: Surgery_after_NACT_19

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Hybridization was performed according to manufacturer's instructions. nCounter uses a molecular barcode technology, where the RNA is directly tagged with a target-specific capture probe and target-specific reporter probe containing a labeled barcode. We used the PanCancer IO 360 gene expression panel which includes 770 immune-related genes and associated controls.

scan_protocol: Scanning and image acquisition using the nanoString Digital Analyzer.

data_processing: nanoString data were analyzed and normalized in nSolver software, correcting for the expression of technical controls and 30 housekeeping genes included in the panel.

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_19

label_protocol: Labeling was performed according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from cells using RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions and DNA was eliminated by means of Rnase-Free Dnase Set (Qiagen).

treatment_protocol: Biopsy samples were collected from primary lesions before EOC patients underwent carboplatin/paclitaxel-based neoadjuvant chemotherapy, according to availability. Surgery samples were extracted from residual lesions after treatment with chemotherapy, according to availability.

value: Epithelial Ovarian Cancer

tag: sample type

value: Surgery sample

tag: response to nact

value: Non-responder

tag: crs score


title: IR181_Input_EtOH_DMSO [Input H3.3]

tag: cell line

tag: chip antibody


title: IR181_Input_Dox_MLN [Input H3.3]


title: pancreatic cells for patch-seq [H2A5]

tag: tissue


title: Surgery_after_NACT_18

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_18


title: HiC of Nng2 overexpressing cells rep2

description: processed data: Compressed text file, containing pair-wise contact infomration in the medium juicer format (https://github.com/aidenlab/juicer/wiki/Pre) but omitting the read name: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>.

data_processing:
Hi-C data were mapped to the mm10 genome using Juicer (Rao et al., 2014). Only uniquely mapping reads (mapq>30) were retained for further analysis. After removal of PCR duplicates, reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed text file, containing pair-wise contact infomration in the medium juicer format (https://github.com/aidenlab/juicer/wiki/Pre) but omitting the read name: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>.
Supplementary_files_format_and_content: Bigwig files with CpG or GpC methylation levels of all cytosines covered by at last 5 reads (5x coverage).
Supplementary_files_format_and_content: Tab seperated table containing read counts per gene.
Supplementary_files_format_and_content: Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz).
Supplementary_files_format_and_content: Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.

extract_protocol:
The somatosensory cortex of in utero electroporated E14.5 mouse embryos was isolated and the electroporated area dissected. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen). Dissociated cells were fixed for 10 min. in 1% Formaldehyde (ThermoFisher, Cat. N: 28908), quenched by addition of Glycine (Invitrogen, Cat. N: 15527013) to a final concentration of 0.2M, washed in PBS with 0.1% BSA, passed through a 40µM cell strainer (ThermoFisher, Cat. N: 15342931) and immediately FAC-sorted at a BD FACSAria Fusion (BD Bioscience) with four lasers (405, 488, 561, 640) using a 100µm nozzle. Sorted cells were lysed with 0.2% Igepal-CA630 (Sigma-Aldrich, Cat. N: I3021), permeabilized with 0.5% SDS (Invitrogen, Cat. N:AM9823) and digested with 200U DpnII (New England Biolabs, Cat. N: R0543) overnight at 37˚C. Subsequently, sticky ends were filled by incubating the nuclei for 4h at RT with DNA Polymerase I (New England Biolabs, Cat. N: M0210) and a biotin-14-dATP (Life Technologies, Cat. N: 195245016) containing nucleotide mix in DpnII buffer followed by proximity ligation for at least 6h at 16°C. Thereafter nuclei were lysed, proximity ligated DNA was reverse-crosslinked overnight at 68˚C followed by a purification by ethanol precipitation and shearing to ~550 bp DNA fragments using a Covaris S220 sonicator.
Biotin pulldown was performed by incubation the sheared DNA with MyOne Streptavidin T1 beads (ThermoFisher, Cat. N: 65602) for 30min. at RT followed by on-bead biotin removal and end-repair by incubating the samples for 30 min. at RT in a reacting mix consisting of T4 DNA Polymerase, T4 Polynucleotide Kinase and DNA Polymerase I, Large (Klenow) Fragment (New England Biolabs, Cat. N: M0203, M0201, M0210). Thereafter A-tailing using Klenow Fragment exo-minus (New England Biolabs, Cat.N.: M0212) was performed for 30 min. at 37˚C followed by ligation of NextFlex DNA barcodes (Perkin Elmer, Cat. N.: NOVA-514101) using the NEB Quick Ligase (New England Biolabs, Cat. N: M2200). Between each of the incubation steps the samples bound to the streptavidin beads were washed twice with washing buffer containing 0.05% Tween-20 (Sigma-Aldrich, Cat. N: P9416) and once with the respective buffer of the following reaction. Libraries were amplified on the streptavidin beads using the NEBNext Ultra Q5 II Master mix (New England Biolabs, Cat. N.: M0544) using following program: 98˚C 30s; {98˚C 10s, 65˚C 75s} x10; 65˚C 5min; Hold at 10˚C. After the amplification the streptavidin beads were pelleted and the supernatant was purified twice using 0.7x AMPure XP beads (Agencourt, Cat. N: A63881) to reach an average fragment size of approximately 500bp.

tag: strain

value: HiC


title: pS2 ChIP-Seq EtOH

tag: input file


title: IR181_Input_Dox_DMSO [Input H3.3]


title: MnM_d3_12_2

tag: batch


title: HiC of Nng2 overexpressing cells rep1


title: MnM_d3_12_3


title: RNA-seq of GFP overexpressing cells rep2


title: Surgery_after_NACT_17

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_17


title: Surgery_after_NACT_16

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_16

value: Responder


title: A10 ChIP-Seq EtOH

value: A10 Antibody, Santa Cruz Lot No:J2219


title: RNA-seq of GFP overexpressing cells rep1


title: A10 ChIP-Seq Dox


title: MnM_E14.5_13_3


title: MnM_E14.5_13_1


title: Surgery_after_NACT_15

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_15


title: Surgery_after_NACT_14

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_14


title: INPUT_IMR5_RnaseH_EtOH_MLN [input A10, S2P]


title: Surgery_after_NACT_13

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_13


title: MnM_E14.5_13_2


title: HiC of GFP overexpressing cells rep3


title: INPUT_IMR5_RnaseH_EtOH_MK [input A10, S2P]


title: NOME-seq of GFP overexpressing cells rep1


title: INPUT_IMR5_RnaseH_EtOH_DMSO [input A10, S2P]


title: NOME-seq of Nng2 overexpressing cells rep1


title: MG_8W_1_4

source_name: microglia


title: HiC of Nng2 overexpressing cells rep3


title: MG_8W_1_2


title: MG_8W_1_5


title: Surgery_after_NACT_11

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_11


title: HiC of GFP overexpressing cells rep2


title: Surgery_after_NACT_12

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_12


title: INPUT_IMR5_RnaseH_Dox_MLN [input A10, S2P]


title: Surgery_after_NACT_10

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_10


title: d0d4_earlydiff

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
Sequencing alignment to the mm10 reference genome was performed using CellRanger (version 3.1), and spliced, unspliced, and ambiguous read counts were extracted using Velocyto.
Sample barcode classification was performed using the deMULTIplex R package, and doublets and negatives were removed.
Normalization, log transformation, and other data processing carried out in Scanpy (version 1.4.5; Wolf et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data, including cluster assignments, provided in h5ad format. Cell metadata (names, timepoint, treatment, cluster, etc.) are stored in .obs. Raw counts data is stored in .raw. Normalized and log-transformed data is stored in .X.

source_name: differentiating embryonic stem cells

growth_protocol: GFP-Bracyury mESC cells were maintained on mouse embryonic feeder (mEF) cells in Dulbecco's Modified Eagles' Medium (DMEM; Gibco) containing 15% FBS (Sigmal-Aldrich), 1% PSG (Gibco), LIF (MTI Global Stem; 1,000 U/mL), and 2-mercaptoethanol (Sigma; 0.1mM).

extract_protocol:
Single-cell samples were prepared by dissocaiting cells in TrypLE before strained through a 40 uM cell strainer.
Sample barcoding and library preparation was carried out using the MULTI-seq protocol (McGinnis et al. 2019).

treatment_protocol: mESCs were removed from feeder cells and cultured in suspension in serum-free differentiation media (SFD) from day0 to day 2. At day 2, four different primitive streak induction treatments were established by adding growth factors Wnt3a (25 ng/mL) and Activin A (9 ng/mL) alone or with one of the following additional growth factors: Noggin (150 ng/mL) Gsk3 inhibitor (10 mM), or Bmp4 (0.5 ng/mL).

tag: time

value: day 0 through day 4

tag: developmental stage

value: embryonic stem cells undergoing differentiation to early gastrulation


title: INPUT_IMR5_RnaseH_Dox_MK [input A10, S2P]

tag: cell type

value: neuroblastoma cell line


title: pS2 ChIP-Seq Dox


title: INPUT_IMR5_RnaseH_Dox_DMSO [input A10, S2P]


title: MG_8W_1_3


title: Surgery_after_NACT_9

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_9


title: IR180_Input_MLN

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.63
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

growth_protocol: S phase synchronized IMR-5 cells by double Thymidine block

extract_protocol:
For spike-in experiments (ChIP-Rx) 10% of fixed NIH-3T3 mouse cell lines were added before lysis. Cells were treated with 1% formaldehyde for 5 min at RT following 5 min of incubation with glycine. After cell lysis (5 mM PIPES pH 8.8, 5 mM KCl, 0.5% NP40), nuclei were resuspended in RIPA buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1% Triton-X-100, 0.1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA containing protease and phosphatase inhibitor cocktail) and DNA was fragmented to a size <500 bp using a Covaris M220 sonifier. Antibodies were bound to Protein A/G-Dynabeads® (Invitrogen) and immunoprecipitated. After extensive washing, chromatin was eluted with 1% SDS and crosslinking was reverted overnight. Chloroform/phenol extraction was used for DNA purification. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with a gel extraction kit. DNA fragments were amplified by 16 cycles of PCR and library size and amount of library was specified with the Fragment Analyzer (Agilent). The library was subjected to Illumina NextSeq 500 sequencing according to the manufacturer’s instructions. After base calling with Illumina’s FASTQ Generation software v1.0.0 (NextSeq 500 sequencing), high quality PF-clusters were selected for further analyses.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
spike normalized ChIP-Sequencing (ChIP-rx)

treatment_protocol: 4 h treatment with 1 µM MLN8237 or DMSO

value: neuroblastoma cells


title: Surgery_after_NACT_8

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_8


title: MethylHiC E14.5 Tubb3+ rep3

data_processing:
Library strategy: MethylHiC
Joint Hi-C / DNA methylation data were mapped to the mm10 genome using JuiceMe (Durand et al., 2016). Only uniquely mapping reads (mapq>30) were retained for further analysis. After removal of PCR duplicates, reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. CpG methylation was assessed using MethylDackel (https://github.com/dpryan79/MethylDackel), in a “mergeContext” mode with the first 6 nucleotides omitted from further analysis.
genome build: mm10
supplementary_files_format_and_content: The bedGraph file contains genome-wide CpG methylation levels (1x coverage) with the number of methylated and non-methylated reads per cytosine. A detailed description of the file format can be found under https://github.com/dpryan79/MethylDackel. Compressed text file contains the mapped paired reads with mapq>=30 and belonging to different DpnII fragments in the Juicer short format which can be further analysed using Juicer Pre (https://github.com/aidenlab/juicer/wiki/Pre).

source_name: Tubb3+ from E14.5 somatosensory cortex

extract_protocol:
The somatosensory cortex of E14.5 mouse embryos was isolated and meninges removed. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen). For ImmunoFACS the dissociated cells were fixed for 10min. at RT in 1% freshly prepared Formaldehyde in PBS (ThermoFisher, Cat. N: 28908) under slow rotation and quenched by addition of Glycine (Invitrogen, Cat. N: 15527013) to a final concentration of 0.2M. The fixated cells were spun down with 500g for 5min. at 4˚C, washed once with 1% BSA (ThermoFisher, Cat. N: AM2618) in PBS and subsequently incubated for 10min. at 4°C in permeabilization buffer consistent of 0.1% freshly prepared Saponin (Sigma-Aldrich, Cat. N: SAE0073), 0.2% BSA and 1% RNAsin plus RNase inhibitor (Promega, Cat. N: N261A) in PBS. The permeabilization buffer was removed by centrifuging the cells with 2500g for 5min. at 4˚C followed by staining against Pax6 (1:40, BD 561664), Eomes (1:33, BD 566749) and Tubb3 (1:14, BD 560394) in staining buffer (0.1% saponin, 1% BSA, 0.1% RNAsin plus RNase inhibitor in PBS) for 1h at 4˚C under slow rotation. Cells were washed twice with permeabilization buffer, once with PBS with DAPI (1:1000; ThermoFisher, Cat. N: 62248) and a final wash with PBS containing 0.5% BSA. Between each washing step, the cells were incubated for 5min. at 4˚C with the respected buffer under slow rotation and spun down with 2500g for 5min. at 4˚C. After the last wash the cells were resuspended in PBS with 1% BSA and 1% RNAsin plus RNase inhibitor, passed through a 40µM cell strainer (ThermoFisher, Cat. N: 15342931) and immediately FAC-sorted.
For Methyl-Hi-C we adapted current protocols (Lee et al., 2019; Li et al., 2019). Briefly, frozen pellets of the fixed and sorted cells were thawed on ice, lysed with 0.2% Igepal-CA630 (Sigma-Aldrich, Cat. N: I3021), permeabilized with 0.5% SDS (Invitrogen, Cat. N:AM9823) and digested with 200U DpnII (New England Biolabs, Cat. N: R0543) overnight at 37˚C. Subsequently, sticky ends were filled by incubating the nuclei for 4h at RT with DNA Polymerase I (New England Biolabs, Cat. N: M0210) and a biotin-14-dATP (Life Technologies, Cat. N: 195245016) containing nucleotide mix in DpnII buffer followed by proximity ligation for at least 6h at 16 °C. Thereafter nuclei were lysed, proximity ligated DNA was reverse-crosslinked overnight at 68˚C followed by a purification by ethanol precipitation. DNA was sheared to ~550 bp fragments using a Covaris S220 sonicator and end-repaired by incubation the samples with the T4 DNA Polymerase (New England Biolabs, Cat. N: M0203) for 4h at 20˚C. Prior the bisulfite conversion, sheared and biotinylated fully methylated pUC19 (Zymo Research, Cat. N: D5017) and unmethylated lambda DNA (Promega, Cat. N: D1521) was added to the samples (~ 0.01%). Bisulfite conversion was performed using the EZ DNA Methylation-Gold Kit (Zymo Research, Cat. N: D5005) followed by library construction using the Accel-NGS® Methyl-Seq DNA Library Kit (Swift Bioscience, Cat. N: 30024) according to the manufactory instructions until the adapter ligation step. After this step, biotin pulldown was performed using MyOne Streptavidin T1 beads (ThermoFisher, Cat. N: 65602) followed by 5 washes with washing buffer containing 0.05% Tween-20 (Sigma-Aldrich, Cat. N: P9416) and two additional washes with low-TE water. Libraries were amplified on the streptavidin beads using the EpiMark Hot Start Taq (New England Biolabs, Cat. N: M0490) using following program: 95˚C 30s; {95˚C 15s, 61˚C 30s, 68 ˚C 60s} x14; 68˚C 5min; Hold at 10˚C. Streptavidin T1 beads were pelleted on a magnetic rack and the prepared libraries within the supernatant were purified using 0.6x AMPure XP beads (Agencourt, Cat. N: A63881) to reach an average fragment size of approximately 500bp. Before sequencing, libraries were quantified by qPCR using the NEBNext® Library Quant Kit (New England Biolabs, Cat. N: E7630S). The size distribution of the obtained libraries was assessed using Agilent 2100 Bioanalyzer.

tag: technique

value: MethylHiC


title: Surgery_after_NACT_7

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_7


title: IR180_Input_DMSO


title: MG_3W_2_1


title: MethylHiC E14.5 Tubb3+ rep2


title: histone H3.3 ChIP-Seq MLN

tag: treatment

value: 4 h with 1 µM MLN8237

value: rabbit monoclonal H3.3 (EPR17899) Lot N° GR3263393-3)


title: Surgery_after_NACT_6

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_6


title: MethylHiC E14.5 Tubb3+ rep1

tag: age

value: PN (Tubb3+)


title: MG_3W_2_4

tag: genotype


title: histone H3.3 ChIP-Seq DMSO

value: DMSO


title: Surgery_after_NACT_5

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_5


title: MethylHiC E14.5 Eomes+ rep3

source_name: Eomes+ from E14.5 somatosensory cortex

value: IPC (Eomes+)


title: NOME-seq of GFP overexpressing cells rep2

source_name: Electroporated cells E15.5 somatosensory cortex

tag: celltype

value: GFP+

value: NOME-seq


title: Surgery_after_NACT_4

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_4

value: Epithelial Ovarian Cancer

tag: sample type

value: Surgery sample


title: MethylHiC E14.5 Eomes+ rep2


title: MG_3W_2_3

tag: timepoint


title: Br16_lymphnode_4

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: BSSE_QGF_110901_HHY75BGX7_1_Br16_lymphnode_4_TAGCGCTC_TCTCTCCG_S56_R1_001_MM

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.4.2; parameters : --phred33 --length 36 --clip_R1 9).
To eliminate any residual contamination from mouse RNA, trimmed reads were aligned to human (GRCh38) and mouse (GRCm38) genome references using STAR (v.2.5.2a) and ambiguous reads were removed using Disambiguate
Gene level expression was quantified with Salmon using Ensembl transcripts (release 89).
To normalize gene counts for cell-specific biases, we used size factors computed utilizing the deconvolution strategy developed by Lun et al. (2016) implemented in the scran (v1.6.5) package available on R/Bioconductor
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing the gene count-scale length-scaled TPMs as obtained from Salmon; processed_tmm_normalized_counts_matrix.txt.gz contains normalized counts using TMM normalization

source_name: Lymphnode metastasis from Br16 CDX model

extract_protocol:
Cells were isolated and immediately transferred into individual tubes (#321-032-501, Axygen) containing 2.5 μl RLT Plus lysis buffer (#1053393, Qiagen) and 1U/μl SUPERase In RNase Inhibitor (#AM2694, Invitrogen). Samples were immediately frozen on dry ice and kept at -80°C until further processing
Libraries were prepared with Smart -Seq2 protocol

value: Lymphnode


title: MG_3W_2_2


title: Br16_lymphnode_3

description: BSSE_QGF_110900_HHY75BGX7_1_Br16_lymphnode_3_TAGCGCTC_CGTCTAAT_S55_R1_001_MM


title: HiC of GFP overexpressing cells rep1

value: HiC


title: MG_8W_1_1


title: Surgery_after_NACT_2

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_2

tag: response to nact

value: Non-responder

tag: crs score


title: Br16_lymphnode_2

description: BSSE_QGF_110899_HHY75BGX7_1_Br16_lymphnode_2_TAGCGCTC_CTAAGCCT_S54_R1_001_MM


title: MethylHiC E14.5 Pax6+ rep3

source_name: Pax6+ from E14.5 somatosensory cortex

value: NSC (Pax6+)


title: Surgery_after_NACT_1

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_1

value: Responder


title: Br16_lymphnode_1

description: BSSE_QGF_110898_HHY75BGX7_1_Br16_lymphnode_1_TAGCGCTC_AAGGAGTA_S53_R1_001_MM


title: MG_d10_3_1

source_name: microglia


title: Biopsy_before_NACT_25

description: Paired with surgery sample 19

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_25

value: Biopsy sample


title: Br16_liver_2

description: BSSE_QGF_110907_HHY75BGX7_1_Br16_liver_2_ACTGAGCG_CTAAGCCT_S62_R1_001_MM

source_name: Liver metastasis from Br16 CDX model

value: Liver


title: MG_3W_2_5


title: Br16_liver_1

description: BSSE_QGF_110906_HHY75BGX7_1_Br16_liver_1_ACTGAGCG_AAGGAGTA_S61_R1_001_MM


title: MG_d3_4_4


title: MG_d3_4_3


title: MethylHiC E14.5 Pax6+ rep1

value: MethylHiC


title: scATAC-seq E14.5 somatosensory cortex rep2

data_processing:
Raw sequencing data was converted to fastqs using cellranger-atac mkfastq (10x Genomics, v1.2.0). Reads were aligned to the GRCm38 reference genome (mm10) and quantified using cellranger-atac count (10x Genomics v1.2.0) using integrated doublet removal.
genome build: mm10
supplementary_files_format_and_content: Processed data files represent filtered peak-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as a BED file with peak. Furthermore the gzipped TSV files cotian barcode sequences as well as the genomic position of the obtained fragments, their barcodes and duplication count.  A detailed described of the content of the processed data files can be found at https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/matrices and https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments

source_name: whole E14.5 somatosensory cortex

extract_protocol:
The somatosensory cortex of E14.5 mouse embryos was isolated and meninges removed. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen).
Directly after tissue dissociation scATAC-seq (10x Genomics, Cat. N: PN-1000110, PN-1000086, PN-1000084) libraries were generated according to the manual instructions with a targeted recovery of 6000 cells/nuclei per sample. Before sequencing, libraries were quantified by qPCR using the NEBNext® Library Quant Kit (New England Biolabs, Cat. N: E7630S). The size distribution of the obtained libraries was assessed using Agilent 2100 Bioanalyzer.

value: whole tissue

value: scATAC-seq


title: MG_d3_4_2


title: Br16_brain_4

description: BSSE_QGF_110911_HHY75BGX7_1_Br16_brain_4_CCTAAGAC_TATCCTCT_S66_R1_001_MM

source_name: Brain metastasis from Br16 CDX model

value: Brain


title: scATAC-seq E14.5 somatosensory cortex rep1


title: Br16_brain_3

description: BSSE_QGF_110910_HHY75BGX7_1_Br16_brain_3_CCTAAGAC_CTCTCTAT_S65_R1_001_MM


title: Biopsy_before_NACT_23

description: Paired with surgery sample 17

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_23


title: scRNA-seq E14.5 somatosensory cortex rep2

data_processing:
Raw sequencing data was converted to fastqs using cellranger mkfastq (10x Genomics, v3.1.0). scRNA reads were aligned to the GRCm38 reference genome (mm10) and quantified using cellranger count (10x Genomics v3.1.0).
genome build: mm10
supplementary_files_format_and_content: Processed data files represent filtered feature-barcode matrix (*mtx.gz) stored in the Market Exchange Format (MEX) for sparse matrices as well as gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively. A detailed described of the content of the processed data files can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

extract_protocol:
The somatosensory cortex of E14.5 mouse embryos was isolated and meninges removed. Single cell suspension was prepared using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) according to the manufacturer protocol with reduced dissociation times (5 min. instead of 15 min. at 37˚C). Cell number as well as the viability was assessed using the Countess™ II Automated Cell Counter (Invitrogen).
Directly after tissue dissociation scRNA-seq (v3, 10x Genomics, Cat. N: PN-1000075, PN-1000074, PN-120262) libraries were generated according to the manual instructions with a targeted recovery of 6000 cells/nuclei per sample. Before sequencing, scRNA-seq libraries were quantified by qPCR using KAPA Library Quantification Kit  (Roche, Cat. N: 07960298001). The size distribution of the obtained libraries was assessed using Agilent 2100 Bioanalyzer.

value: scRNA-seq


title: Biopsy_before_NACT_22

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_22


title: MG_E14.5_5_3

extract_protocol:
Cells were sorted into RNAprotect Cell Reagend (QIAGEN) according to the manufacturers recommendations. RNA was extracted using Picopure RNA extraction kit (Life Technologies) according to manufacturer’s protocol. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA.
Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3.


title: Biopsy_before_NACT_21

description: Paired with surgery sample 16

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_21


title: Surgery_after_NACT_3

source_name: Surgery sample from Epithelial Ovarian Carcinoma after carboplatin/paclitaxel-based NACT_3


title: scRNA-seq E14.5 somatosensory cortex rep1


title: Br16_brain_2

description: BSSE_QGF_110909_HHY75BGX7_1_Br16_brain_2_ACTGAGCG_TCTCTCCG_S64_R1_001_MM


title: MethylHiC E14.5 Eomes+ rep1

value: IPC (Eomes+)


title: MG_E14.5_5_1


title: Br16_brain_1

description: BSSE_QGF_110908_HHY75BGX7_1_Br16_brain_1_ACTGAGCG_CGTCTAAT_S63_R1_001_MM


title: MG_d10_3_3


title: Biopsy_before_NACT_20

description: Paired with surgery sample 15

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_20


title: MG_E14.5_5_2


title: MethylHiC E14.5 Pax6+ rep2


title: Br16_2_lymph_node_4

description: BSSE_QGF_75515_HVJJCBGX3_1_Br16_2_lymph_node_1_TAGGCATG_TCTCTCCG_S48_R1_001_MM


title: MG_d10_3_2


title: Br16_2_lymph_node_3

description: BSSE_QGF_75507_HVJJCBGX3_1_Br16_2_lymph_node_1_GGACTCCT_TCTCTCCG_S40_R1_001_MM


title: CT_C

city: Houston

first: Ana

last: Santos

state: Texas

address: 6500 Main St, APT 892

institute: BioScience Research Collaborative

data_processing:
Illumina bcl2fastq  v2.20.0.422 software used for basecalling.
Raw sequence reads are aligned to a reference genome using EDGE-pro(v1.3.1) algorithm
Additional rRNA –depletion, RPKM calculation using EDGE-pro
Differential expression of reference transcripts with DESeq2(3.14), Bioconductor
Gene annotation using in-house script.
Genome_build: MG1655

organism: Escherichia coli

source_name: Bacterial cells_with DMSO (control)

growth_protocol: Mueller-Hinton Broth, 37°C

extract_protocol:
Bacterial cells were collected onto a 0.2 µm PES filter by low vacuum filtration. Two volumes of RNAprotect (Qiagen, Valencia, CA) were added to the cells, and the samples were then centrifuged at 5000 g for 25 min at 4 °C to pellet cells. RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) per the manufacturer’s instructions.
RNA libraries were prepared for sequencing according to Illumina's protocols using the Truseq Stranded mRNA Prep Kit.

treatment_protocol: Cells were treated with 0.5x MIC of MM 1, or 1% DMSO in the dark for 30 min. Cells were then irradiated for 5 min at 146 mW cm-2  (43.8 J cm-2) with 405 nm light.


title: CT_B


title: CT_A


title: Br16_2_lymph_node_2

description: BSSE_QGF_75499_HVJJCBGX3_1_Br16_2_lymph_node_1_TCCTGAGC_TCTCTCCG_S32_R1_001_MM


title: Biopsy_before_NACT_18

description: Paired with surgery sample 14

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_18


title: IP_NS5_rep2

city: Shenzhen

first: Ping

last: Li

address: Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2
Data were filtered after alignment
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg38
Supplementary_files_format_and_content: peak, FC files

growth_protocol: hNPCs were cultured in ReNcell NSC maintenance medium.

extract_protocol:
Chromatin Immunoprecipitation were performed according to  instructions of EZ-Magna ChIP A/G kit (Millipore).
The end of the IP DNA was repaired and added A and connector. Performed the PCR amplification and purified the DNA as the library.

treatment_protocol: hNPCs expreesing NS5 were lysed 48 hours post infection by lentivirus.

value: human neural progenitor cells (hNPCs)

value: Overexpressed ZIKV-NS5

tag: chip antibody

value: Rabbit anti-GFP antibody ( Sigma-Aldrich, G1544)


title: input_NS5


title: Br16_2_liver

description: BSSE_QGF_75498_HVJJCBGX3_1_Br16_2_liver_TCCTGAGC_CGTCTAAT_S31_R1_001_MM

tag: tissue


title: MNM_C

source_name: Bacterial cells treated with MNM

tag: strain


title: Biopsy_before_NACT_24

description: Paired with surgery sample 18

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_24

value: Epithelial Ovarian Cancer


title: Biopsy_before_NACT_17

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_17


title: Biopsy_before_NACT_16

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_16


title: 21 mo/O304-3

city: Guangzhou

first: Mingsheng

last: Zhu

address: 1838 North Guangzhou Avenue

institute: Nanfang hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In   this step, clean data (clean reads) were obtained by removing reads containing adapter, reads   0 containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC   content the clean data were calculated. All the downstream analyses were based on the clean   data with high quality
Reference genome and gene model annotation files were downloaded from genome website   directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the   mapping tool for that Hisat2 can generate a database of splice junctions based on the gene   model annotation file and thus a better mapping result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then   FPKM of each gene was calculated based on the length of the gene and reads count mapped   to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per   Millions base pairs sequenced, considers the effect of sequencing depth and gene length for   the reads count at the same time, and is currently the most commonly used method for   estimating gene expression levels
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2   R package (1.20.0). DESeq2 provide statistical routines for determining differential expression   in digital gene expression data using a model based on the negative binomial distribution. The   resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling   the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were   assigned as differentially expressed
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample

organism: Mus

source_name: Kidney

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mus kidney


title: Biopsy_before_NACT_15

description: Paired with surgery sample 13

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_15


title: 21 mo/O304-2


title: Br16_2_brain_3

description: BSSE_QGF_75645_HVJJCBGX3_1_Br16_2_brain_1_TGCAGCTA_GTAAGGAG_S178_R1_001_MM


title: MNM_A


title: Br16_2_brain_2

description: BSSE_QGF_75637_HVJJCBGX3_1_Br16_2_brain_1_CGATCAGT_GTAAGGAG_S170_R1_001_MM


title: Biopsy_before_NACT_14

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_14


title: CREs to Barcode association

description: processed data: Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz).

data_processing:
library strategy: Targeted barcode amplification from plasmid DNA
50xbp paired-end reads were trimmed using cutadapt with following parameters:  -m 12 -a GAATTCATCTGGTA -G GACCGGATCAACT -u 1 discard-untrimmed. In case of 2x150bp PE, reads were first filtered using cutadapt (-m 12 -a GAATTCATCTGGTACCTCGGTTCACGCAATG -G ^CCAGGACCGGATCAACT -u 1 --discard-untrimmed --action=none --interleaved | cutadapt -g GAATTCATCTGGTACCTCGGTTCACGCAATG -G ^CCAGGACCGGATCAACT --discard-untrimmed --action=none –interleaved) and subsequently forward as well as reverse read were trimmed individually using -l 12 for the barcode, -g ^CCAGGACCGGATCAACT --discard-untrimmed (forward CRE reads) or -g GAATTCATCTGGTACCTCGGTTCACGCAATG -- discard-untrimmed (reverse CRE read). Trimmed fastq reads for both, 50xbp PE and 150xbp PE were separated based on a 5’-four-basepair identifier and CRE-Barcode-association was performed separately on wildtype, mutant sequences using the MPRAflow association pipeline. The resulting pickle libraries were merged to increase the number of recovered CREs and filtered for promiscuous barcodes.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed text file, containing pair-wise contact infomration in the medium juicer format (https://github.com/aidenlab/juicer/wiki/Pre) but omitting the read name: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>.
Supplementary_files_format_and_content: Bigwig files with CpG or GpC methylation levels of all cytosines covered by at last 5 reads (5x coverage).
Supplementary_files_format_and_content: Tab seperated table containing read counts per gene.
Supplementary_files_format_and_content: Compressed files contain sequences of selecred CREs (design.fa.gz), their annotation (labels.tsv.gz) and a pickle library with filtered CRE - Barcode associations (CRE_BC_association.pickle.gz).
Supplementary_files_format_and_content: Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.

source_name: Plasmid DNA

extract_protocol:
Plasmid DNA was purified from approximatly 1.2 million colonies using QIAprep Spin Miniprep Kit (Qiagen; Cat. N: 27106) according to the manufacturer instructions.
5 ng of the plasmid pool was used to attach P5 and P7 sequencing adapters in two separated PCRs. Bother PCRs were performed using the NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544) with RV_univ_MPRA (CGACGCTCTTCCGATCT) + FWD_CRS_Tn7 (0.5µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCAGGACCGGATCAACT; PCR conditions: (98°C 30s; {98°C 10s, 65°C 30s, 72°C 3min} x3; 72°C 3min; Hold at 4°C) and P5NEXTPT5 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T) + indexed Ad2.X (0.1 µM each; CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT; PCR conditions: 98°C 30s; {98°C 10s, 65°C 90s} x10; 72°C 5min; Hold at 4°C), respectively.

value: MPRA and ImmunoMPRA

value: Plasmid DNA


title: 21 mo/O304-1


title: 21 mo-3


title: Biopsy_before_NACT_13

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_13


title: crh-1_KO_Rep4

city: Reno

first: Pedro

last: Miura

state: Nevada

address: 1664 N VIRGINIA ST MS 0314

department: Biology

institute: University of Nevada, Reno

data_processing:
Illumina’s bcl2fastq_v2.19 software
Sequenced reads were trimmed for adaptor sequence, then mapped to WBcel235 whole genome using STAR v2.7.5a
read counts for each gene per exon were obtained using featurecounts v1.5.0 (options: -t exon -g gene_id)
normalized abundance measurements and differential expression analysis were obtained using DESeq2 v1.26.0 with default parameters
Genome_build: WBcel235
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were age-synchronized by hypochlorite treatment and collected eggs were hatched overnight at 20°C in 1x M9 buffer. L1 larvae were then plated onto NGM plates seeded with 10x concentrated E. coli OP50 bacteria and allowed to develop to the L4 larval stage at 20°C. L4 larvae were then collected, washed, and re-plated onto NGM plates and seeded with 10x E. coli OP50 bacteria. Day-1 adult worms were collected by filtering through a 30 µM nylon mesh to remove bacteria

extract_protocol:
RNA-seq analysis, 1-day adult worms were collected in Lysis/Binding Buffer from the mirVana miRNA isolation kit (Ambion, Cat #AM1560). Worms were immediately lysed by bead beating them for 5 min using a Bullet Blender Pro Storm (Next Advance). Total RNA was then extracted following mirVana manufacturers protocol and treated with DNAse I (Invitrogen, Cat #AM1907). RNA were assessed by a Bioanalyzer (Agilent), and quantified using Quant-iT RiboGreen RNA Assay kit (ThermoFisher Scientific, Cat #R11490)
poly(A)-selected libraries were prepared by Novogene LTD., (Beijing, China) at UC Davis genomics center

value: whole worm

value: day-1 adult


title: Biopsy_before_NACT_12

description: Paired with surgery sample 12

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_12

value: Biopsy sample

value: Non-responder


title: Br16_2_bone_1

description: BSSE_QGF_75538_HVJJCBGX3_1_Br16_2_bone_1_AAGAGGCA_CGTCTAAT_S71_R1_001_MM

source_name: Bone metastasis from Br16 CDX model

value: Bone


title: Biopsy_before_NACT_19

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_19

value: Responder


title: 21 mo-2


title: crh-1_KO_Rep3


title: Biopsy_before_NACT_11

description: Paired with surgery sample 11

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_11


title: crh-1_KO_Rep2


title: 21 mo-1


title: Biopsy_before_NACT_10

description: Paired with surgery sample 10

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_10


title: Br16_1_lymph_node_3

description: BSSE_QGF_75620_HVJJCBGX3_1_Br16_1_lymph_node_3_ACTGAGCG_TATCCTCT_S153_R1_001_MM

source_name: Lymphnode metastasis from Br16 CDX model

value: Lymphnode


title: IP_NS5_rep1


title: Br16_1_lymph_node_2

description: BSSE_QGF_75612_HVJJCBGX3_1_Br16_1_lymph_node_2_TAGCGCTC_TATCCTCT_S145_R1_001_MM


title: Biopsy_before_NACT_9

description: Paired with surgery sample 9

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_9


title: 18 mo-2


title: Br16_1_lymph_node_1

description: BSSE_QGF_75604_HVJJCBGX3_1_Br16_1_lymph_node_1_ATGCGCAG_TATCCTCT_S137_R1_001_MM


title: 18 mo-3


title: circ-crh-1_KO_Rep4


title: MNM_B

source_name: Bacterial cells treated with MNM


title: Biopsy_before_NACT_8

description: Paired with surgery sample 8

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_8


title: Biopsy_before_NACT_7

description: Paired with surgery sample 6

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_7


title: circ-crh-1_KO_Rep3


title: circ-crh-1_KO_Rep2


title: Br16_1_brain_4

description: BSSE_QGF_75564_HVJJCBGX3_1_Br16_1_brain_4_ACTCGCTA_TATCCTCT_S97_R1_001_MM

source_name: Brain metastasis from Br16 CDX model

value: Brain


title: Br16_1_brain_1

description: BSSE_QGF_75635_HVJJCBGX3_1_Br16_1_brain_1_CGATCAGT_CTCTCTAT_S168_R1_001_MM


title: Biopsy_before_NACT_5

description: Paired with surgery sample 4

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_5


title: Biopsy_before_NACT_6

description: Paired with surgery sample 5

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_6


title: Br16_1_bone

description: BSSE_QGF_75627_HVJJCBGX3_1_Br16_1_bone_CCTAAGAC_CTCTCTAT_S160_R1_001_MM


title: Br16_1_brain_2

description: BSSE_QGF_75643_HVJJCBGX3_1_Br16_1_brain_2_TGCAGCTA_CTCTCTAT_S176_R1_001_MM


title: miR215_small

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: miR-215−/− small intestinal epithelial cells

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: miR-215-/- small intestinal epithelial cells

extract_protocol:
The total RNAs were extracted from these cells using RNeasy Mini Kit (Qiagen)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: small intestinal epithelia


title: Br16_1_lymph_node_4

description: BSSE_QGF_75628_HVJJCBGX3_1_Br16_1_lymph_node_4_CCTAAGAC_TATCCTCT_S161_R1_001_MM


title: circ-crh-1_KO_Rep1


title: Br16_2_bone_2

description: BSSE_QGF_75483_HVJJCBGX3_1_Br16_2_bone_2_CGTACTAG_TCTCTCCG_S16_R1_001_MM


title: WT_Rep2

value: wild type


title: Biopsy_before_NACT_2

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_2


title: WT_small

description: WT small intestinal epithelial cells

source_name: WT small intestinal epithelial cells


title: WT_Rep4

source_name: Whole worm


title: WT_Rep3


title: Biopsy_before_NACT_1

description: Paired with surgery sample 1

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_1


title: siCKB_2

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

institute: Karolinska Institutet

hyb_protocol: 5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45C to Affymetrix Clariom S human arrays according to standard protocol. Washing and staining were performed using Affymetrix Fluidics Station 450.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were analyzed with packages available from Bioconductor (http://www.bioconductor.org). Normalization and calculation of gene expression was performed with the Robust Multichip Average expression measure using the oligo package.

source_name: hADSC

label_protocol: Biotinylated cRNA was prepared using the GeneChip WT Plus Reagent Kit according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: hADSC cells were plated at a cell density of 20 000 cells/cm2 and incubated at 37°C with 5% CO2. Adipogenesis was induced two days post confluence using DMEM/F12  as well as the adipogenic cocktail; 5 mg/mL insulin, 0.25 mmol/l dexamethasone, 0.5 mmol/l 3-isobutyl-1-methylxanthine (IBMX) and 10 mmol/l rosiglitazone for two days after which the dexamethasone and IBMX were removed and the cells were allowed to undergo full adipogenic differentiation.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, cat. 740955.250) according to the manufacture's instructions. The concentration, purity and quality were measured using Nanodrop 2000 (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Short interfering oligonucleotides (siRNAs) were introduced by electroporation using a Neon Transfection System (1300 V, 20 ms, 2 pulses) 100 µL Kit (Invitrogen) in human in vitro differentiated hADSCs at day eight of differentiation. All transfections were performed using a final concentration of 20 nmol/L siRNA oligonucleotides and were compared with non-silencing control RNAi.

value: Adipose Derived Stem Cells (hADSC)

value: siCKB


title: siCKB_3


title: Biopsy_before_NACT_3

source_name: Biopsy sample from Epithelial Ovarian Carcinoma before carboplatin/paclitaxel-based NACT_3


title: crh-1_KO_Rep1


title: RNAseq_TX1072_XO_d4_r3

status: Public on Jan 26 2022

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

data_processing:
An “N-Masked” genome of the mouse reference genome mm10 was generated using SNPsplit (0.3.4). For this, all the polymorphic sites of the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 were masked by ambiguity nucleobase ‘N’.
The reads were aligned using STAR (2.7.5a) with options [–outSAMattributes NH HI NM MD] to the N-masked mm10 genome (Dobin et al. 2013).
SAM files were translated into BAM files, filtered for properly paired reads and sorted using samtools (1.10) with options [view -b -h -f 3 -q 7] and [sort] (Li et al. 2009)
RNA-seq counts were quantified on exons only with the options [featureCounts(isPairedEnd = TRUE, GTF.featureType = “exon”, strandSpecific = 2, allowMultiOverlap = FALSE)].  Transcripts Per Million (TPM) was then calculated as Fragments Per Kilobase (FPK) divided by the scaling factor. The scaling factor was calculated as the sum of all FPK values divided by a million.
Genome_build: mm10

source_name: Mouse embryonic stem cells

growth_protocol: TX1072 XO Cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% ESC-grade FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901, Axon).

extract_protocol:
RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions.
RNA-seq libraries were generated using the Tru-Seq Stranded Total RNA library preparation kit (Illumina) with 1 μg starting material for rRNA-depletion and amplified with 15 Cycles of PCR.

treatment_protocol: Differentiation was induced for 0, 1, 2, 3 or 4 days by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol at a density of 1.56*10^4 cells/cm2 in fibronectin-coated (10 μg/ml) tissue culture plates.

tag: cell line

value: TX1072 XO

tag: condition

value: Day 4

tag: replicate

tag: strain background

value: CAST / C57BL/6

tag: assay

value: RNAseq