title: 12560 PDX

source_name: Pancreatic adenocarcinoma mouse xenograft

value: Primary pancreatic adenocarcinoma xenograft


title: 12556 MAT 1

status: Public on Jul 03 2021

type: SRA

city: London

first: David

last: Osuna de la Peña

address: 5 University Street

department: Respiratory Medicine

country: United Kingdom

institute: University College London

library_source: transcriptomic

data_processing:
Base calling done on the NovaSeq 6000 Sequencing System, which runs RTA3.
Filtering of rRNA was performed on the fastq files of tissue samples to reduce GC bias with SortMeRNA 2.1.
Fastq files were pseudoaligned to the GENCODE v30 primary assembly with kallisto v.0.46.0.
Transcript counts were imported into R with tximport and normalised for differential expression analysis at the gene level with DESEq2 3.9.
Genome_build: GENCODE v30 (GRCh38)
Supplementary_files_format_and_content: kallisto_tpm_allsamples.tsv (Kallisto output files (.h5) with transcript abundances in TPM.)
Supplementary_files_format_and_content: DESeqDataSet.tsv (Normalised counts used for differential expression analysis with DESeq2.)

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatic adenocarcinoma cells

extract_protocol:
Total RNA was extracted from disassociated tissues and cultures using a Qiagen RNeasy Mini kit and quantified on a NanoDrop 2000; RNA quality was measured on an Agilent Tapestation 4200.
Illumina TruSeq (done by Oxford Genomics) with polyA selection of mRNA.

tag: tissue

value: Pancreatic adenocarcinoma

tag: material

value: cells

tag: patient

tag: sample type

value: Patient-derived pancreatic cancer organoids cultured in Matrigel for 7 days


title: KO-4wks-R2

type: RNA

city: Taipei city

first: Meng-Ting

last: Yang

state: Nankang

address: 128 Academia Road, Section 2, Nankang, Taipei

department: ABRC

country: Taiwan

institute: Academia Sinica

description: RNA QC checked

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to Affymetrix Gene Expression Service Lab.

scan_protocol: GeneChips were scanned according to Affymetrix Gene Expression Service Lab.

data_processing: The data were analyzed and normalized by Affymetrix Gene Expression Service Lab. The TGT value is 500.

label: biotin

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to Affymetrix Gene Expression Service Lab.

growth_protocol: LLC were subcutaneously inoculated into B6 mice for 4 weeks

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

treatment_protocol: WT or Pdia4 knockout

value: cancer stromata

tag: genotype

tag: Sex

value: male


title: 12d_RNA-seq_rep1

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

country: China

institute: Jiangsu Normal University

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases..
Then sequence quality was verified using fastp. We used HISAT2 to map reads to the genome of Solanum lycopersicum (Version: V3.2) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR.
Genome_build: Excel files include FPKM values for each Sample
Supplementary_files_format_and_content: fastq files are the raw date of RNA-seq and m6A MeRIP-seq

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: All plants were grown in greenhouse under a long day condition (16-h-light/8-h-dark) at 26°C

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately more than 200 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into ~100-nt-long oligonucleotides using divalent cations under elevated temperature. Then the cleaved RNA fragments were subjected to incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) supplemented with BSA (0.5 μg μl−1). The mixture was then incubated with protein-A beads and eluted with elution buffer (1 × IP buffer and 6.7mM m6A). Eluted RNA was precipitated by 75% ethanol. Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was ~100±50 bp.
And then we performed the paired-end 2×150bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

tag: cultivar

value: Micro-Tom

tag: state

value: 12-day-growth tomato fruit

value: The equatorial plate of tomato fruit

tag: time point


title: KO-4wks-R3

description: RNA QC checked


title: 12556 PDX

value: tumour piece


title: 12d_m6A MeRIP-seq_rep2


title: 28d_m6A MeRIP-seq_rep2

value: 28-day-growth tomato fruit


title: 12556 PRI

source_name: Pancreatic adenocarcinoma

value: Primary pancreatic adenocarcinoma tumour


title: 12d_m6A MeRIP-seq-seq_rep1


title: KO-4wks-R1

description: RNA QC checked


title: WT-4wks-R3

description: RNA QC checked

value: WT


title: WT-4wks-R1

description: RNA QC checked


title: Primary Cardiomyocyte_2

status: Public on Jul 02 2021

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

country: South Korea

institute: KRIBB

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed of adapters and sequencing quality lower than 20 (using cutadapt and sickle)
The RNAseq reads were aligned to hg38 whole genome using Hisat2
Fragments Per Kilobase of transcript per Million (FPKM) was calculated using StringTie with gene level and converted to TPM (Transcripts Per Million) by in-house script.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: Heart Cardiomyocytes

extract_protocol:
Illumina TruSeq kit for paired-end reads, poly-A selection, non-strand-specific
The NEBNext RNA first-strand synthesis module and NEBNExt Ultra Directional second strand synthesis kit (New England BioLabs) were used for the preparation of RNA sequencing (RNA-Seq) libraries.

tag: cell type

value: Heart Cardiomyocytes


title: Cardiomyocyte+BMP4

source_name: Cardiomyocytes

value: Cardiomyocytes


title: IPSC-Gastric oganoid_3

source_name: Organoid

value: iPSC-derived organoid


title: Fundic Gastric oganoid_2


title: Cardiomyocyte


title: Human induced pluripotent stem cell_2

source_name: Skin fibroblast

value: Skin fibroblast

value: Male

tag: age

value: newborn


title: Human induced pluripotent stem cell_1


title: ES-Gastric oganoid_2


title: WT-4wks-R2

description: RNA QC checked


title: Posterior-foregut_1


title: Posterior-foregut_2


title: ES-Gastric oganoid_1


title: Lung bud organoid_D59


title: Ventralized anterior foregut endoderm_D21


title: Definitive endoderm_D4


title: Definitive endoderm_2


title: Embryonic Stem Cells_4

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells

value: Female


title: MPR3

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to GENCODE GRCh38.p13 genome assembly using STAR
Counts were generated by Rsubread
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Skin biopsy

extract_protocol:
RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) skin biopsies with a Qiagen® RNeasy FFPE Kit.
Library preparation for RNA-seq was performed by using the TruSeq  Stranded RNA library preparation kit including polyA enrichment (Illumina) from total RNA.

tag: condition

value: MPR


title: Embryonic Stem Cells_3


title: Primary Cardiomyocyte_1


title: Embryonic Stem Cells_2


title: Lung bud organoid_D56


title: Embryonic Stem Cells_1


title: IPSC-Gastric oganoid_4


title: Fundic Gastric oganoid_1


title: UK1393

city: Lexington

first: Joseph

middle: Robert

last: McCorkle

state: KY

address: 760 Press Ave.

country: USA

institute: University of Kentucky

data_processing:
FASTQ files were generated with bcl2fastq software (Illumina)
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from human samples were mapped to Ensembl GRCh38 transcripts annotation (release 82), using RSEM
Gene expression data normalization and differential expression analysis were performed using the R package edgeR
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: primary tumor tissue (omentum)

growth_protocol: Tumor organoids were cultured in growth factor-reduced Matrigel overlaid with Advanced DMEM/F12 media supplemented with 20% R-spondin conditioned media, 50 ng/mL Wnt-3A, 100 ng/mL FGF10, 100 ng/mL noggin, 10 ng/mL EGF, 500nM A83-01, 9uM Y-27632, B27 supplement, N2 supplement, 1mM nicotinamide, 2mM L-glutamine, 10mM HEPES, 50ug/mL primocin. Media was changed 2X per week and organoids were passaged when diameter exceeded 200um or organoids became confluent

extract_protocol:
RNA was harvested using RNEasy Plus Mini Kits (Qiagen) according to the manufacturer's protocol
Isolated RNA quality and quantity was assessed using the Agilent Bioanalyzer 2100 RNA Nano chip. RNA-Seq libraries were prepared using KAPA RNA Hyper + RiboErase HMR (Roche)

value: primary tumor tissue (omentum)

tag: tumor stage

value: IIIC

tag: histotype

value: serous carcinoma

tag: grade


title: UK2238

source_name: primary tumor tissue (fallopian tube)

value: primary tumor tissue (fallopian tube)


title: UK2326


title: UK1254

source_name: primary tumor tissue (ovary)

value: primary tumor tissue (ovary)

value: IVA

value: residual serous adenocarcinoma


title: UK1226

value: serous adenocarcinoma with marked psammoma bodies

value: 1 (low grade)


title: DMSO

city: Göttingen

first: Shiv K.

last: Singh

address: Robert-Koch-Str. 40

department: Gastroenterology and Gastrointestinal Oncology

country: Germany

institute: Univeristy Medical Center

description: PANC1 cells were treated with DMSO for 8h, followed by i4C-seq for cJUN enhancer region

library_source: genomic

data_processing:
Library strategy: i4C-seq
First 36 nucleotides after the enhancer viewpoint were mapped to reference genome
Reads per restriction fragment were quantified using bedtools
Genome_build: hg38
Supplementary_files_format_and_content: mapped read coverage in bedgraph format

molecule: genomic DNA

source_name: Pancreatic cancer

growth_protocol: PANC1 cells were cultured in DMEM medium (supplemented with 10% FCS)

extract_protocol:
Nuclei were isolated in a near-physiological isotonic buffer, followed by primary digestion with NlaIII, in situ ligation of digested chromatin, followed by cell lysis and digestion with DpnII. Finally, DNA was circularized by ligation and re-purified.
The library was amplified by inverse PCR with viewpoints-specific primers containing a 6-nucleotide long barcode (DMSO: AGAGCTCCTTGCAGCTCTCCAACA; JQ1: GAGCTACCTTGCAGCTCTCCAACA) and susequently coupled to Illumina P5 and P7 adapters for sequencing.

treatment_protocol: 10^7 PANC1 cells were treated with either 500 nM JQ1 or equal volume DMSO as control for 8h

tag: cell line

tag: treatment

value: DMSO


title: UK1236

tag: tissue


title: UK1225

value: IA

value: endometrioid adenocarcinoma

value: 1 (well differentiated)


title: TOV21G-PacR_replicate3

source_name: immortalized cell line (TOV-21G)

growth_protocol: OVCAR3 cells were cultured in high-glucose RPMI-1640 supplemented with 20% fetal bovine serum, 10 ug/mL bovine insulin and 2 mM L-glutamine. TOV-21G cells were cultured in 1:1 MCDB105:Medium 199 (v:v) supplemented with 15% fetal bovine serum. Cells were grown at 37o C, 5% CO2 and sub-cultured every 3-4 days. Cells were re-plated and grown 48 hours to ~60-80% confluence before RNA extraction.

extract_protocol:
Cells were lysed in tissue culture dishes and RNA was harvested using RNEasy Plus Mini Kits (Qiagen) according to the manufacturer's protocol
Isolated RNA quality and quantity was assessed using the Agilent Bioanalyzer 2100 RNA Nano chip. RNA-Seq libraries were prepared using KAPA RNA Hyper + RiboErase HMR (Roche)

value: epithelial

tag: disease state

value: grade 3, stage III, primary malignant clear cell carcinoma

value: ovary


title: TOV21G-PacR_replicate1


title: JQ1

description: PANC1 cells were treated with JQ1 [500 nM] for 8h, followed by i4C-seq for cJUN enhancer region


title: TOV21G-control_replicate3


title: TOV21G-PacR_replicate2


title: OVCAR3-PacR_replicate3

source_name: immortalized cell line (NIH: OVCAR3)

value: progressive papillary adenocarcinoma

value: ascites/ovary


title: Definitive endoderm_1

value: iPSC-derived organoid


title: TOV21G-control_replicate1


title: TOV21G-control_replicate2


title: OVCAR3-PacR_replicate1


title: OVCAR3-control_replicate2


title: OVCAR3-PacR_replicate2


title: MeiS_ALL_hsS1_2to4C_SCP3_NA.hg38.RT

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: Whole genome sequencing

data_processing:
Library strategy: DNA-Seq
----------ALIGNMENT----------
BWA mem 0.7.12 (Li, 2013; Li and Durbin, 2009) was used to align to the reference genome (mm10 for mouse; hg38 for human).
-------RT BEDGRAPHS-------
WGS from a non-replicating population was used to calibrate the expected GC-biases from different sequencing instruments (Illumina HiSeq 2500, Illumina HiSeq X, Illumina NextSeq 500). Calibration files were generated by examining a subset of perfectly mappable genomic loci. Each locus is a 101 bp region with the following properties:
1. Full mappability of all bases within the 101 bp window. To determine mappability, we generated a fastq file of pseudoreads of the requisite length from the reference genome fasta file. One pseudo-read was generated per bp; all bases were assigned a q-score of 60. Pseudo-reads were mapped to the reference genome using bwa mem 0.7.12 and the coverage at each base in the genome was assessed.
2. The window does not overlap with sequencing gaps (UCSC Gaps track), segmental duplications (UCSC SegDups track), high copy repeats (UCSC repeatmasker track) or otherwise blacklisted genomic regions (Amemiya et al., 2019; Kent et al., 2002).
The GC content (rounded to 1%) and WGS sequencing coverage of each 101 bp window was assessed. The median coverage for all windows of a given GC content was used as a correction factor. These correction factors vary substantially across the different sequencing platforms used. 2% of all qualifying 101 bp autosomal windows were used to calculate the GC correction coefficients. Coverage in each window was corrected using these coefficients.
Replication timing was calculated as the log2 ratio of corrected sequencing coverage at a locus to the genome-wide median (method was adapted from (Koren et al., 2014)). RT-Seq coverage was smoothed in 500 Kb windows with a 50 Kb step. For compatibility with RT-Sim, each 50Kb window is split into five 10Kb bins with equal RT in the RT BEDGRAPH files.

source_name: Whole genome sequencing for RT-Seq in Meiotic & S/gonia (b) RT_WGS

growth_protocol: All DNA was harvested from organs.

extract_protocol:
Nuclei from mouse or human testes were prepared as described in (Lam et al., 2019). To purify the populations of interest, a combination of intranuclear markers were used (Table 1, Figure 2). Pure nuclei populations were resuspended in 300 ul of lysis buffer (SDS 1%, 10mM EDTA, 50mM, Tris pH=8) and then sonicated in a Bioruptor UCD200 for 20 min 30 sec ON 30 sec OFF, “high” setting. NaCl was added to a final concentration of 0.2M and the sample incubated overnight at 65C to reverse DNA-protein crosslinks. 5U of Proteinase K (NEB Cat. No. P8107S) was added and the sample further incubated for 1h at 45C. DNA was purified with MinElute columns (QIAGEN), as indicated by the instruction manual.
Whole genome sequencing libraries were prepared from 100 ng of purified DNA using the KAPA Hyper Prep Kit (Cat. No. KK8502) following the manufacturer's instructions.

treatment_protocol: Samples were untreated.

value: Sorted nuclei from testis

tag: strain

tag: experiment type

value: Whole genome sequencing for RT-Seq

tag: s-phase sub-stage

tag: cell-type

value: Meiotic S-phase

tag: dna content

tag: positive selection marker

tag: negative selection marker


title: inputSSDS_Human_Prdm9A-A (Sample 2)

description:
GSM1447329: SRR1528832
Input-SSDS
human_AA2.peaks.RC.bedgraph

data_processing:
Library strategy: Input-SSDS
Sequencing reads were aligned to the human hg38 reference genome using bwa 0.7.12 and the single-stranded DNA pipeline (Brick et al. 2018; Khil et al. 2012).

source_name: Control for DSB hotspot capture in PRDM9 A-A homozygous male using input-SSDS in testis (Sample 2)

extract_protocol:
Testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. DMC1 ChIP was performed as described previously (Khil et al., 2012; Brick et al., 2018) with minor modifications.
Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).

value: Testis

value: Control for DSB hotspot mapping using Single Stranded DNA Sequencing of Input DNA (Input-SSDS)

tag: antibody


title: 2C_HSC_NA_2C_NA_NA.RT

description:
Whole genome sequencing
RTseqCorrectionFiles.tar.gz

source_name: Whole genome sequencing for RT-Seq in 2C_HSC_RT_WGS

value: Non-replicating


title: dmc1SSDS_Human_Prdm9A-A (Sample 2)

description:
GSM1447328: SRR1528830,SRR1528831
ChIP-SSDS
human_AA2.peaks.RC.bedgraph

data_processing:
Library strategy: DMC1-SSDS
Sequencing reads were aligned to the human hg38 reference genome using bwa 0.7.12 and the single-stranded DNA pipeline (Brick et al. 2018; Khil et al. 2012). Hotspots were called using the SSDS DSB hotspot calling pipeline (Brick et al. 2018). Hotspot strength was calculated using the method in (Brick et al. 2018). Briefly, each peak is recentred to the midpoint of the Watson and Crick fragment distributions. Signal is estimated as the Crick-strand signal to the left of the origin center + the Watson-strand signal to the right of the center. The background is estimated by counting the remaining fragments at the left and right edges of origins (15%); Watson-strand fragments to the left of the center, Crick-strand fragments to the right. This background is then extrapolated to the entire origin and subtracted from the signal.

source_name: DSB hotspot capture in PRDM9 A-A homozygous male using DMC1-SSDS in testis (Sample 2)

value: DSB hotspot mapping using Dmc1 ChIP followed by Single Stranded DNA Sequencing (Dmc1-SSDS)

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)


title: dmc1SSDS_Human_Prdm9A-A (Sample 1)

description:
GSM1447325: SRR1528821
ChIP-SSDS
human_AA1.peaks.RC.bedgraph

source_name: DSB hotspot capture in PRDM9 A-A homozygous male using DMC1-SSDS in testis (Sample 1)


title: inputSSDS_Human_Prdm9A-A (Sample 1)

description:
GSM1447326: SRR1528822
Input-SSDS
human_AA1.peaks.RC.bedgraph

source_name: Control for DSB hotspot capture in PRDM9 A-A homozygous male using input-SSDS in testis (Sample 1)


title: dmc1SSDS_Human_Prdm9C-L4

description:
ChIP-SSDS
human_CL4.peaks.RC.bedgraph

source_name: DSB hotspot capture in PRDM9 C-L4 heterozygous male using DMC1-SSDS in testis


title: GCDX62-EV_3

description: GCDX62 cell line was transduced with retroviral empty vector pMSCV

data_processing:
Raw reads were quality-checked using FastQC v0.11.5
Alignment against hg19 human reference genome was done by using STAR v2.7.5b
Aligned reads were assigned to genes using HTSeq-count Galaxy version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

growth_protocol: GCDX62-EV and GCDX62-cJUN cells were cultured in puromycin-containing (1 µg/mL) Keratinocyte-SFM medium (supplemented with 2% FCS, 1% P/S, 0,35% BPE, and EGF) plus RPMI 1640 medium (supplemented with 10% FCS and 1% P/S) in a 3:1 ratio

extract_protocol:
RNA was harvested using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Pancreatic cancer

tag: genotype/variation

value: control (pMSCV empty vector)


title: GCDX62-cJUN-OE_2

description: GCDX62 cell line was transduced with retroviral vector pMSCV-cJUN to induce stable cJUN overexpression in the cell line

value: cJUN overexpression (pMSCV-cJUN)


title: GCDX62-cJUN-OE_3


title: GCDX62-cJUN-OE_1


title: MYC_HMEC_SHY1_rep1 [RNA-seq]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
processed data file: featurecounts.txt
MYC_HMEC_R1_SHY-1_1_S3_L007

data_processing:
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner.
Genome_build: hg19
Supplementary_files_format_and_content: Featurecounts

source_name: MYC-ER HMEC

growth_protocol: Standard.

extract_protocol:
Total RNA extraction using Trizol and Zymo's Directzol RNA extraction kit.
1ug total RNA was rRNA depleted and processed using the TruSeq Stranded Total RNA Preparation Kit by Illumina according to manufacturer’s instructions.

treatment_protocol: 4-Hydroxytamoxifen at 15nM for 48 hours

value: MYC-ER HMEC

tag: cell culture

value: Medium 171/ MEGS supplement


title: OVCAR3-control_replicate3

value: epithelial


title: EPCR+ HSC  183

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

institute: DKFZ

data_processing:
Sequencing was set for 3 million 100 bp pair-end reads per cell under Illumina’s kit instructions.
Raw sequencing reads were mapped with STAR
Expression counts estimates and transcripts per million (TPM) were generated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: transcripts per million in txt matrix from

molecule: polyA RNA

source_name: cord blood

extract_protocol:
C1 Fluidigm
Multiplexed Nextera XT; each single cell was barcoded
scRNA-seq 3 million 100 bp pair-end reads per cell

value: CD34+ cells


title: EPCR+ HSC  178


title: EPCR+ HSC  176


title: EPCR+ HSC  182


title: EPCR+ HSC  177


title: GCDX62-EV_1


title: EPCR+ HSC  175


title: MYC_HMEC_SHY2_rep2 [RNA-seq]

description:
processed data file: featurecounts.txt
MYC_HMEC_R2_SHY-2_2_S6_L007

extract_protocol:
Total RNA extraction using Trizol and Zymo's Directzol RNA extraction kit
1ug total RNA was rRNA depleted and processed using the TruSeq Stranded Total RNA Preparation Kit by Illumina according to manufacturer’s instructions.


title: MYC_HMEC_SHY2_rep1 [RNA-seq]

description:
processed data file: featurecounts.txt
MYC_HMEC_R1_SHY-2_1_S5_L007


title: GCDX62-EV_2


title: EPCR+ HSC  180


title: EPCR+ HSC  181


title: OVCAR3-control_replicate1

value: progressive papillary adenocarcinoma

value: ascites/ovary


title: EPCR+ HSC  179


title: EPCR+ HSC  174


title: EPCR+ HSC  173


title: MYC_HMEC_SHY1_rep2 [RNA-seq]

description:
processed data file: featurecounts.txt
MYC_HMEC_R2_SHY-1_2_S4_L007

data_processing:
RNA-seq: Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner.
Genome_build: hg19
Supplementary_files_format_and_content: Featurecounts


title: EPCR+ HSC  172


title: EPCR+ HSC  171


title: EPCR+ HSC  170


title: EPCR+ HSC  168


title: EPCR+ HSC  167


title: EPCR+ HSC  169


title: EPCR+ HSC  164


title: EPCR+ HSC  165


title: EPCR+ HSC  163


title: EPCR+ HSC  166


title: EPCR+ HSC  161


title: EPCR+ HSC  162


title: inputSSDS_Human_Prdm9C-L4

description:
Input-SSDS
human_CL4.peaks.RC.bedgraph

source_name: Control for DSB hotspot capture in PRDM9 C-L4 heterozygous male using input-SSDS in testis


title: EPCR+ HSC  156


title: EPCR+ HSC  160


title: EPCR+ HSC  159


title: EPCR+ HSC  153


title: EPCR+ HSC  152


title: EPCR+ HSC  155


title: EPCR+ HSC  150


title: EPCR+ HSC  151


title: EPCR+ HSC  146


title: EPCR+ HSC  154


title: EPCR+ HSC  148


title: EPCR+ HSC  145


title: EPCR+ HSC  147


title: EPCR+ HSC  149


title: EPCR+ HSC  142


title: EPCR+ HSC  144


title: EPCR+ HSC  138


title: EPCR+ HSC  141


title: EPCR+ HSC  139


title: EPCR+ HSC  140


title: EPCR+ HSC  134


title: EPCR+ HSC  137


title: EPCR+ HSC  143


title: EPCR+ HSC  135


title: EPCR+ HSC  136


title: EPCR+ HSC  157


title: EPCR+ HSC  127


title: EPCR+ HSC  130


title: EPCR+ HSC  132


title: EPCR+ HSC  133


title: EPCR+ HSC  128


title: EPCR+ HSC  126


title: EPCR+ HSC  123


title: EPCR+ HSC  124


title: EPCR+ HSC  120


title: EPCR+ HSC  121


title: EPCR+ HSC  129


title: EPCR+ HSC  125


title: EPCR+ HSC  119


title: EPCR+ HSC  118


title: EPCR+ HSC  117


title: EPCR+ HSC  122


title: EPCR+ HSC  158


title: EPCR+ HSC  112


title: EPCR+ HSC  113


title: EPCR+ HSC  111


title: EPCR+ HSC  110


title: EPCR+ HSC  115


title: EPCR+ HSC  114


title: EPCR+ HSC  106


title: EPCR+ HSC  105


title: EPCR+ HSC  107


title: EPCR+ HSC  104


title: EPCR+ HSC  99


title: EPCR+ HSC  98


title: EPCR+ HSC  101


title: EPCR+ HSC  102


title: EPCR+ HSC  103


title: EPCR+ HSC  116


title: EPCR+ HSC  96


title: EPCR+ HSC  100


title: EPCR+ HSC  95


title: EPCR+ HSC  92


title: EPCR+ HSC  94


title: EPCR+ HSC  91


title: EPCR+ HSC  90


title: EPCR+ HSC  89


title: EPCR+ HSC  109


title: EPCR+ HSC  131


title: EPCR+ HSC  88


title: EPCR+ HSC  85


title: EPCR+ HSC  83


title: EPCR+ HSC  108


title: EPCR+ HSC  84


title: EPCR+ HSC  81


title: EPCR+ HSC  87


title: EPCR+ HSC  82


title: EPCR+ HSC  80


title: EPCR+ HSC  86


title: EPCR+ HSC  93


title: EPCR+ HSC  79


title: EPCR+ HSC  78


title: EPCR+ HSC  77


title: EPCR+ HSC  75


title: EPCR+ HSC  73


title: EPCR+ HSC  97


title: EPCR+ HSC  74


title: EPCR+ HSC  70


title: EPCR+ HSC  72


title: EPCR+ HSC  69


title: EPCR+ HSC  68


title: EPCR+ HSC  64


title: EPCR+ HSC  71


title: EPCR+ HSC  63


title: EPCR+ HSC  65


title: EPCR+ HSC  62


title: EPCR+ HSC  67


title: EPCR+ HSC  66


title: EPCR+ HSC  60


title: EPCR+ HSC  59


title: EPCR+ HSC  61


title: EPCR+ HSC  57


title: EPCR+ HSC  58


title: EPCR+ HSC  55


title: EPCR+ HSC  54


title: EPCR+ HSC  53


title: EPCR+ HSC  56


title: EPCR+ HSC  51


title: EPCR+ HSC  76


title: EPCR+ HSC  49


title: EPCR+ HSC  48


title: EPCR+ HSC  46


title: EPCR+ HSC  44


title: EPCR+ HSC  45


title: EPCR+ HSC  47


title: EPCR+ HSC  43


title: EPCR+ HSC  40


title: EPCR+ HSC  41


title: EPCR+ HSC  42


title: EPCR+ HSC  38


title: EPCR+ HSC  34


title: EPCR+ HSC  36


title: EPCR+ HSC  33


title: EPCR+ HSC  37


title: EPCR+ HSC  39


title: EPCR+ HSC  35


title: EPCR+ HSC  29


title: EPCR+ HSC  32


title: EPCR+ HSC  26


title: EPCR+ HSC  52


title: EPCR+ HSC  24


title: EPCR+ HSC  27


title: EPCR+ HSC  25


title: EPCR+ HSC  28


title: EPCR+ HSC  23


title: EPCR+ HSC  50


title: EPCR+ HSC  22


title: EPCR+ HSC  21


title: EPCR+ HSC  20


title: EPCR+ HSC  19


title: EPCR+ HSC  17


title: EPCR+ HSC  18


title: EPCR+ HSC  16


title: EPCR+ HSC  11


title: EPCR+ HSC  31


title: EPCR+ HSC  30


title: EPCR+ HSC  7


title: EPCR+ HSC  4


title: EPCR+ HSC  10


title: EPCR+ HSC  13


title: EPCR+ HSC  12


title: EPCR+ HSC  14


title: EPCR+ HSC  3


title: EPCR+ HSC  2


title: EPCR+ HSC  1


title: EPCR+ HSC  8


title: MYC_HMEC_TAM_SHY2_rep1 [RNA-seq]

description: featurecounts.txt

growth_protocol: Standard


title: MYC_HMEC_TAM_SHY2_rep2 [RNA-seq]

description: featurecounts.txt


title: MYC_HMEC_TAM_SHY1_rep1 [RNA-seq]

description: featurecounts.txt

data_processing:
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner.
Genome_build: hg19
Supplementary_files_format_and_content: Featurecounts


title: EPCR+ HSC  6


title: EPCR+ HSC  9


title: MYC_HMEC_TAM_NTC_rep2 [RNA-seq]

description: featurecounts.txt


title: SKBR3_INPUT_rep2 [m6A-seq]

data_processing:
Library strategy: m6A-seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs)

extract_protocol: 250 ug RNA was phenol-chloroform extracted, rRNA depleted, and fragmented to ~100 nt. 1 ug fragmented RNA was saved as input and the rest was immunoprecipitated. RNA was precipitated and libraries were prepared with TruSeq Stranded Total RNA Preparation Kit according to manufacturer’s instructions.

value: McCoy's 5A +10% FBS


title: MCF7_INPUT_rep1 [m6A-seq]

data_processing:
Library strategy: m6A-seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).

value: DMEM + 10% FBS


title: MYC_HMEC_TAM_SHY1_rep2 [RNA-seq]

description: featurecounts.txt

data_processing:
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Feature counts were calculated for RNA-seq samples.
Genome_build: hg19
Supplementary_files_format_and_content: Featurecounts


title: EPCR+ HSC  5


title: MYC_HMEC_TAM_NTC_rep1 [RNA-seq]

description: featurecounts.txt


title: MDA_INPUT_rep2 [m6A-seq]

extract_protocol: m6A-seq: 250 ug RNA was phenol-chloroform extracted, rRNA depleted, and fragmented to ~100 nt. 1 ug fragmented RNA was saved as input and the rest was immunoprecipitated. RNA was precipitated and libraries were prepared with TruSeq Stranded Total RNA Preparation Kit according to manufacturer’s instructions.


title: MCF7_M6A_rep1 [m6A-seq]


title: EPCR+ HSC  15


title: SKBR3_M6A_rep1 [m6A-seq]


title: MDA_INPUT_rep1 [m6A-seq]


title: MCF7_INPUT_rep2 [m6A-seq]


title: LM2_M6A_rep2 [m6A-seq]


title: SKBR3_M6A_rep2 [m6A-seq]

data_processing:
Library strategy: m6A-seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: m6A input normalized and filtered peaks in BED format andPeaks files (bigwigs)


title: MYC_HMEC_TAM_INPUT_rep1 [m6A-seq]


title: SKBR3_INPUT_rep1 [m6A-seq]

data_processing:
Library strategy: m6A-seq
Raw sequencing reads were trimmed for adapter sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: m6A input normalized and filtered peaks in BED format and Peaks files (bigwigs).


title: LM2_M6A_rep1 [m6A-seq]

data_processing:
Library strategy: m6A-seq
Raw sequencing reads were trimmed for adapter sequences and using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify m6A peaks using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).


title: MYC_HMEC_INPUT_rep1 [m6A-seq]


title: MYC_HMEC_TAM_M6A_rep1 [m6A-seq]


title: MYC_HMEC_INPUT_rep2 [m6A-seq]


title: MYC_HMEC_TAM_INPUT_rep2 [m6A-seq]


title: MYC_HMEC_TAM_M6A_rep2 [m6A-seq]


title: LM2_INPUT_rep1 [m6A-seq]


title: MYC_HMEC_M6A_rep1 [m6A-seq]

extract_protocol: 250 ug RNA was extracted, rRNA depleted, and fragmented to ~100 nt. 1 ug fragmented RNA was saved as input and the rest was immunoprecipitated. RNA was precipitated and libraries were prepared with TruSeq Stranded Total RNA Preparation Kit according to manufacturer’s instructions.


title: MCF7_M6A_rep2 [m6A-seq]


title: SKBR3_SMINPUT_rep1 [eCLIP-seq]

data_processing:
Library strategy: eCLIP-seq
Raw sequencing reads were trimmed for adapter sequences and barcode sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify eCLIP peaks.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).

extract_protocol: 20M cells were UV-crosslinked, lysed and sonicated. RNA was fragmented and protein-RNA complexes were immunoprecipitated with a YTHDF2 antibody. Inputs (2% of lysate) were saved and run alongside IP samples. IP samples were stringently washed, and for all samples the RNA was dephosphorylated, followed by on-bead ligation of barcoded RNA adapters to the 3’ end. RNA-protein complexes were run on standard protein gels and transferred to nitrocellulose membranes where the RNA in the region 65 kDa – 140kDa was excised off the membrane and proteinase K treated. RNA was then reverse transcribed followed by treatment with ExoSAP-IT to remove excess oligonucleotides. Samples were cleaned up with Dynabeads MyOne Silane and subject to qPCR to determine the appropriate number of PCR cycles.


title: MYC_HMEC_M6A_rep2 [m6A-seq]


title: MDA_M6A_rep2 [m6A-seq]


title: SKBR3_CLIP_rep1 [eCLIP-seq]


title: MCF7_CLIP_rep2 [eCLIP-seq]


title: MDA_M6A_rep1 [m6A-seq]


title: LM2_INPUT_rep2 [m6A-seq]


title: MCF7_SMINPUT_rep1 [eCLIP-seq]

data_processing:
Library strategy: eCLIP-seq
Raw sequencing reads were trimmed for adapter sequences and barcode sequences using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify eCLIP  peaks.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).


title: MCF7_CLIP_rep1 [eCLIP-seq]


title: MDA_CLIP_rep2 [eCLIP-seq]


title: MDA_SMINPUT_rep2 [eCLIP-seq]

extract_protocol: 20M cells were UV-crosslinked, lysed and sonicated. RNA was fragmented and protein-RNA complexes were immunoprecipitated with a YTHDF2 antibody. Inputs (2% of lysate) were saved and run alongside IP samples. IP samples were stringently washed, and for all samples the RNA was dephosphorylated, followed by on-bead ligation of barcoded RNA adapters to the 3’ end.. RNA-protein complexes were run on standard protein gels and transferred to nitrocellulose membranes where the RNA in the region 65 kDa – 140kDa was excised off the membrane and proteinase K treated. RNA was then reverse transcribed followed by treatment with ExoSAP-IT to remove excess oligonucleotides. Samples were cleaned up with Dynabeads MyOne Silane and subject to qPCR to determine the appropriate number of PCR cycles.


title: SKBR3_CLIP_rep2 [eCLIP-seq]


title: SKBR3_SMINPUT_rep2 [eCLIP-seq]


title: LM2_CLIP_rep2 [eCLIP-seq]


title: LM2_SMINPUT_rep1 [eCLIP-seq]


title: LM2_SMINPUT_rep2 [eCLIP-seq]


title: MYC_HMEC_TAM_SMINPUT_rep2 [eCLIP-seq]

description: MYC_HMEC_TAM_1-MYC_HMEC_TAM_2.idr.final.bed


title: LM2_CLIP_rep1 [eCLIP-seq]

data_processing:
Library strategy: eCLIP-seq
Raw sequencing reads were trimmed for adapter sequences and barcode sequences  using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner. Read densities were calculated to identify eCLIP  peaks.
Genome_build: hg19
Supplementary_files_format_and_content: input normalized and filtered peaks in BED format and Peaks files (bigwigs).


title: MCF7_SMINPUT_rep2 [eCLIP-seq]


title: MYC_HMEC_TAM_CLIP_rep2 [eCLIP-seq]


title: Seven days old, FruLexA/Fru440 mutant - replicate 2

city: Chapel Hil

first: Corbin

last: Jones

state: NC

address: 250 Bell Tower Dr

department: Biology

institute: UNC-CH

data_processing:
Sequenced reads were filtered/trimmed with FASTP.
Filtered reads were aligned to the dm6 reference genome (consolidated chromosomes only) using Mapsplice2 with default parameters.
Samtools was used to filter alignments for read duplication ( rmdup -rS) and quality ( view -bh -q 20 -F 0x0200 -F 0x04 -f 0x0002 ).
Mapped reads were counted against the reference gene annotation using featureCounts ( -J —verbose -M -p -B -C ).
Genome_build: dm6
Supplementary_files_format_and_content: new_sequence.vs_dm6main.dm6_genes.mapspliceMulti.MpBC.counts.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Drosophila melanogaster

source_name: Seven days old, FruLexA/Fru440 mutant

growth_protocol: Flies were raised on standard fly food (containing yeast, cornmeal, agar, and molasses) at 25°C in a 12-hour light/12-hour dark cycle in cylindrical plastic vials (diameter, 24 mm and height, 94 mm).

extract_protocol:
KAPA HYPER mRNA , NON stranded.
Illumina NovaSeq 6000.

treatment_protocol: For single housing (SH) condition, 80-100 hour-old pupae were separated by sex and males were placed into individual vials, allowed to eclose alone, and aged to 7 days to deprive flies of pheromone interaction on ORNs. For group housing (GH) condition, 25-30 newly eclosed males were collected and placed into food vials. These were aged to 7 days and 180 antennae were dissected per sample.

tag: replicate

tag: age

value: 7 days

tag: Sex

value: male

tag: housing

value: group

tag: genotype

value: antennae


title: Seven days old, white-eyed social isolation - replicate 3

value: isolated

value: wt

tag: tissue


title: Seven days old, white-eyed group housed - replicate 3

source_name: Seven days old, white-eyed group housed


title: Seven days old, 67d mutant - replicate 3

source_name: Seven days old, 67d mutant


title: Seven days old, white-eyed social isolation - replicate 2


title: Seven days old, white-eyed group housed - replicate 2


title: Seven days old, 67d mutant - replicate 1


title: MYC_HMEC_TAM_SMINPUT_rep1 [eCLIP-seq]

tag: cell line

tag: treatment


title: Seven days old, 67d mutant - replicate 2


title: MYC_HMEC_TAM_CLIP_rep1 [eCLIP-seq]


title: MYC_HMEC_CLIP_rep2 [eCLIP-seq]


title: Seven days old, 47b1 mutant - replicate 1

source_name: Seven days old, 47b1 mutant


title: MYC_HMEC_SMINPUT_rep2 [eCLIP-seq]


title: Seven days old, FruLexA/Fru440 mutant - replicate 3


title: Seven days old, white-eyed group housed - replicate 1


title: Seven days old, 47b1 mutant - replicate 2


title: MDA_SMINPUT_rep1 [eCLIP-seq]


title: MYC_HMEC_CLIP_rep1 [eCLIP-seq]


title: MYC_HMEC_SMINPUT_rep1 [eCLIP-seq]


title: MDA_CLIP_rep1 [eCLIP-seq]


title: T16_Tr_rep1_CRISPR_RBP

description:
all.countsummary.txt
MYC_HMEC_MLE_day16.gene_summary.txt

data_processing:
Library strategy: DNA-seq
CRISPR screening data was aligned and processed using MaGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: MaGeCK processed gene summary

extract_protocol: gDNA was extracted and sonicated to ~1000bp. sgRNA containing fragments were recovered with biotinylated RNA probes targeting the flanking region on the lenticrispr v2 backbone and pulled down with streptavidin beads. gDNA fragments were PCRed first with primers flanking the sgRNA and second with Illumina sequencing adapters.

treatment_protocol: 4-Hydroxytamoxifen at 15nM

tag: timepoint

value: Day 16


title: Seven days old, white-eyed social isolation - replicate 1


title: Seven days old, 47b1 mutant - replicate 3


title: T16_Unt_rep1_CRISPR_RBP


title: T8_Tr_rep2_CRISPR_RBP

description:
all.countsummary.txt
MYC_HMEC_MLE_day8.gene_summary.txt

data_processing:
Library strategy: HEI-seq
CRISPR screening data was aligned and processed using MaGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: MaGeCK processed gene summary

value: Day 8


title: T8_Tr_rep1_CRISPR_RBP


title: T8_Unt_rep1_CRISPR_RBP


title: T0_rep1_CRISPR_RBP

description: all.countsummary.txt

value: Day 0


title: T0_rep2_CRISPR_RBP

description: all.countsummary.txt

value: MYC-ER HMEC


title: T16_Unt_rep2_CRISPR_RBP

value: Medium 171/ MEGS supplement


title: T16_Tr_rep2_CRISPR_RBP

data_processing:
Library strategy: DNA-seq
CRISPR screening data was aligned and processed using MaGeCK.
Genome_build: hg19
Supplementary_files_format_and_content:MaGeCK processed gene summary


title: S.pneum_1dpi_13

city: Tampere

first: Markus

last: Ojanen

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere university

data_processing:
Quality control steps and alignment for sequenced reads was performed with Snakemake 5.6.0 combining the relevant modules (FASTQC, TrimGalore!, STAR) from Snakemake-wrapper release 0.38.0 with in-house scripts.
Differential expression (DE) analysis in gene level was performed with DEseq2 1.24.0. Matrix was prefiltered by rowsum (threshold 10). Dataset was split by treatment and the cases analyzed separately because of variation.
Result tables were annotated with bioMart, ranked by p-value and merged with the DESeq2 abundance measures for samples.
Genome_build: GRCz11 (ENSEMBL release 97 )
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts from STAR for every gene and every sample.
Supplementary_files_format_and_content: *.xlsx: Excel tables containing annotated ranked DEGs and DEseq2 abundance measurements for each treatment.

organism: Danio rerio

source_name: Liver

extract_protocol:
Zebrafish liver was dissected on ice, flash frozen on dry ice and the total RNA was extracted using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: 5 months

tag: gender

value: Female

value: S. pneumoniae 1dpi


title: S.pneum_1dpi_14

value: WT


title: S.pneum_1dpi_15


title: S.pneum_1dpi_12


title: S.pneum_1dpi_16


title: lung,survivor rep 5

city: Baltimore

first: Wanchang

last: Cui

state: Maryland

address: 10 South Pine St

department: Radiation Oncology

institute: University of Maryland Baltimore

hyb_protocol: Fragmented and labeled DNA samples were hybridized to Rhesus Gene 1.1 ST Array strips (catalog # 901799, Affymetrix Inc., Santa Clara, CA) at 48 degree for 16 hours.

scan_protocol: Array images were scanned using a GeneAtlas® Imaging Station (Affymetrix Inc.).

data_processing: Probe set summarization and initial data quality examination was performed using the Expression ConsoleTM software (Affymetrix Inc.). Differentially expressed genes were identified using the Transcriptome Analysis Console (TAC) software (Affymetrix Inc.).

organism: Macaca mulatta

source_name: lung tissue from a survivor NHP exposed to 9 Gy WTLI

label_protocol: 100ng total RNA was used for generating sense-strand cDNA using Ambion® WT Expression Kit (Life Technologies , Carlsbad, CA) and subsequent fragmentation and labeling using the GeneChip® WT Terminal Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted using miRNeasy mini kit from Qiagen according to manufacturer’s instruction.

treatment_protocol: NHP were irradiated to the whole thorax at doses from 9.0 to 12.0 Gy. NHP were followed for 180 days. NHP were euthanized if the pre-dertermined euthanasia criteria were met or past the 180 days post radiation.

tag: stress

value: irradiated

tag: radiation dose

value: lung

tag: outcome

value: survivor group


title: lung,survivor rep 9

value: male


title: lung,survivor rep 7


title: lung,decedent rep 11

source_name: lung tissue from a decedent NHP exposed to 10 Gy WTLI

value: decedent group


title: lung,decedent rep 12


title: lung,decedent rep 10


title: lung,survivor rep 10


title: lung,survivor rep 11


title: lung,decedent rep 14


title: lung,survivor rep 12


title: lung,decedent rep 13


title: T8_Unt_rep2_CRISPR_RBP


title: lung,survivor rep 1

source_name: lung tissue from a survivor NHP exposed to 11 Gy WTLI


title: S.pneum_1dpi_11


title: lung,survivor rep 4


title: lung,survivor rep 3


title: lung,survivor rep 6


title: PBS_1dpi_8

value: PBS 1dpi


title: PBS_1dpi_10


title: lung,survivor rep 8


title: lung,survivor rep 2


title: PBS_1dpi_6


title: lung,decedent rep 9

source_name: lung tissue from a decedent NHP exposed to 11 Gy WTLI


title: PBS_1dpi_7


title: PBS_1dpi_9


title: lung,decedent rep 7


title: Unchallenged_3

value: 7 months

value: Unchallenged


title: Unchallenged_4


title: Unchallenged_2


title: hex-RNAseq-rep-1

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: morc hex RNA-seq replicate 1

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0), allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9). Peaks were called using MACS2 (v2.1.1).
Cleaned short reads were aligned to reference genome tair10 by Bowtie2 (v2.1.0), and expression abundance was calculated by RSEM (v1.3.1) with default parameters.
Genome_build: tair10
Supplementary_files_format_and_content: bigWig, peak, normalized abundance

organism: Arabidopsis thaliana

source_name: hex-RNAseq

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants

extract_protocol:
ChIP seq: Samples were crosslinked in vitro. Nuclei were prepared with Nuclei Isolation Buffer (50 mM HEPES, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 0.6% Triton X-100, 0.4 mM PMSF, 5 mM benzamidine, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)). Chromatin was sheared with Bioruptor Plus (Diagenode) for 20 minutes with 30 s on and 30 s off and incubated with anti-FLAG M2 (Sigma) antibody overnight at 4◦C. Chromatin bound proteins were immunoprecipitated with Protein A and Protein G magnetic Dynabeads (Invitrogen) for 2 hours at 4◦C. DNA fragments were precipitated with EtOH overnight at -20◦C. Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seq: DNA from floral tissues were extracted with cetyl trimethylammonium bromide (CTAB)-based method. RNA was removed with PureLink RNase A (Invitrogen). 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). RNA seq: Floral tissues from 5-6 week old seedlings were used for RNA extraction with Zymo Direct-zol RNA MiniPrep kit (Zymo Research) following manufacturer’s instructions.
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
RNA seq: Leaf tissues from three-week-old seedlings were used for RNA extraction with Zymo Direct-zol RNA MiniPrep kit (Zymo Research) following manufacturer’s instructions. 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).

tag: ecotype background

tag: developmental stage

value: 5-6 weeks

value: hex

value: floral tissue


title: hex-RNAseq-rep-2

description: morc hex RNA-seq replicate 2

tag: genotype/variation


title: hex-RNAseq-rep-3

description: morc hex RNA-seq replicate 3


title: nrpe1-RNAseq-rep-2

description: nrpe1 RNA-seq replicate 2


title: nrpe1-RNAseq-rep-3

description: nrpe1 RNA-seq replicate 3


title: nrpe1-RNAseq-rep-1

description: nrpe1 RNA-seq replicate 1


title: NF702

city: Shanghai

first: Weijun

last: Ou

state: Shanghai

address: 1665, Kongjiang Road

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GR38p7
Supplementary_files_format_and_content: NF-CF expression.txt reports FPKMs.

source_name: normal fibroblast

extract_protocol:
Total RNA was extracted from primary human intestinal fibroblasts isolated from the normal and stenotic intestines of CD patients using TRIzol reagent. Purify and fragment mRNA, synthesize first strand cDNA, synthesize second strand cDNA,  purification, adenylate 3' ends, ligate adapters, purification, enrich DNA fragments and purification in turns.
RNA libraries were prepared for sequencing using standard illumina protocols

tag: individual id

tag: disease state

value: Crohn's disease

tag: cell type

value: normal fibroblast

value: small intestine

value: untreated


title: Unchallenged_1

value: liver

tag: age

value: Female


title: lung,decedent rep 5

value: irradiated


title: lung,decedent rep 2

source_name: lung tissue from a decedent NHP exposed to 12 Gy WTLI

value: lung


title: CF627

source_name: Stenotic fibroblast

value: Stenotic fibroblast


title: lung,0 Gy rep 5

source_name: lung tissue from non-irradiated NHP

value: male

value: non-irradiated

value: 0 Gy

value: control group


title: CF702


title: lung,0 Gy rep 2


title: 48h_2

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts.

source_name: Spleen_Lymph nodes_37 degrees_48h

growth_protocol: Naive CD8+ T cells were isolated from spleen and lymph nodes from 6-12 week old mice using a negative selection naive CD8 T cell kit (Stem Cell technologies) according to the manufacturer´s protocol. Unless otherwise stated isolated T cells (1x10^6/ml) were activated using plate bound αCD3 (5 μg/ml) and soluble αCD28 (0.5 μg/ml) in T cell media (TCM; 1640 RPMI with 10% fatal calf serum, 4mM L-glutamine, 1% penicillin/streptomycin, 55μM beta-mercaptoethanol) supplemented with 100 U/ml hrIL-2 (Peprotech).

extract_protocol:
RNA was extracted using RNeasy Kit (QIAGEN) following the manufacturer’s instructions with an additional on-column DNase treatment using the RNAse-Free DNase set (Qiagen). RNA was quantified using Qubit 2.0 (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)

treatment_protocol: Cells were cultured a 37°C or 39°C as indicated in humidified incubators with 5% CO2 and atmospheric oxygen for 24 or 48h hours following activation.

tag: strain

value: 6-12 week old

value: WT

tag: condition

value: 37 degrees

tag: time point

value: Spleen and Lymph nodes

value: CD8 T cell


title: lung,0 Gy rep 1

tag: tissue


title: 48h_1

tag: genotype


title: 48h_3


title: lung,0 Gy rep 4


title: 39_3

source_name: Spleen_Lymph nodes_39 degrees_24h

value: 39 degrees


title: lung,decedent rep 6

value: decedent group


title: WT-RNAseq-rep-3

description: wild type RNA-seq replicate 3

source_name: WT-RNAseq

value: 5-6 weeks

value: floral tissue


title: lung,0 Gy rep 3


title: lung,decedent rep 4


title: lung,decedent rep 3


title: lung,decedent rep 1


title: 39_2


title: WT-RNAseq-rep-1

description: wild type RNA-seq replicate 1


title: 39_1


title: 37_3

source_name: Spleen_Lymph nodes_37 degrees_24h


title: NF627

value: Crohn's disease

value: normal fibroblast

value: small intestine

tag: treatment

value: untreated


title: lung,decedent rep 8

tag: gender

value: male

value: irradiated

value: lung


title: MeiS_ALL_S2_2to4C_SCP3_DMRT1.hg38.RT

description: Whole genome sequencing

data_processing:
Library strategy: DNA-Seq
----------ALIGNMENT----------
BWA mem 0.7.12 (Li, 2013; Li and Durbin, 2009) was used to align to the reference genome (mm10 for mouse; hg38 for human).
-------RT BEDGRAPHS-------
WGS from a non-replicating population was used to calibrate the expected GC-biases from different sequencing instruments (Illumina HiSeq 2500, Illumina HiSeq X, Illumina NextSeq 500). Calibration files were generated by examining a subset of perfectly mappable genomic loci. Each locus is a 101 bp region with the following properties:
1. Full mappability of all bases within the 101 bp window. To determine mappability, we generated a fastq file of pseudoreads of the requisite length from the reference genome fasta file. One pseudo-read was generated per bp; all bases were assigned a q-score of 60. Pseudo-reads were mapped to the reference genome using bwa mem 0.7.12 and the coverage at each base in the genome was assessed.
2. The window does not overlap with sequencing gaps (UCSC Gaps track), segmental duplications (UCSC SegDups track), high copy repeats (UCSC repeatmasker track) or otherwise blacklisted genomic regions (Amemiya et al., 2019; Kent et al., 2002).
The GC content (rounded to 1%) and WGS sequencing coverage of each 101 bp window was assessed. The median coverage for all windows of a given GC content was used as a correction factor. These correction factors vary substantially across the different sequencing platforms used. 2% of all qualifying 101 bp autosomal windows were used to calculate the GC correction coefficients. Coverage in each window was corrected using these coefficients.
Replication timing was calculated as the log2 ratio of corrected sequencing coverage at a locus to the genome-wide median (method was adapted from (Koren et al., 2014)). RT-Seq coverage was smoothed in 500 Kb windows with a 50 Kb step. For compatibility with RT-Sim, each 50Kb window is split into five 10Kb bins with equal RT in the RT BEDGRAPH files.

source_name: Whole genome sequencing for RT-Seq in MeiS_RT_WGS

extract_protocol:
Nuclei from mouse or human testes were prepared as described in (Lam et al., 2019). To purify the populations of interest, a combination of intranuclear markers were used (Table 1, Figure 2). Pure nuclei populations were resuspended in 300 ul of lysis buffer (SDS 1%, 10mM EDTA, 50mM, Tris pH=8) and then sonicated in a Bioruptor UCD200 for 20 min 30 sec ON 30 sec OFF, “high” setting. NaCl was added to a final concentration of 0.2M and the sample incubated overnight at 65C to reverse DNA-protein crosslinks. 5U of Proteinase K (NEB Cat. No. P8107S) was added and the sample further incubated for 1h at 45C. DNA was purified with MinElute columns (QIAGEN), as indicated by the instruction manual.
Whole genome sequencing libraries were prepared from 100 ng of purified DNA using the KAPA Hyper Prep Kit (Cat. No. KK8502) following the manufacturer's instructions.

value: Sorted nuclei from testis

tag: experiment type

value: Whole genome sequencing for RT-Seq

tag: s-phase sub-stage

tag: cell-type

value: Meiotic S-phase

tag: dna content

tag: positive selection marker

tag: negative selection marker


title: 37_2

value: 6-12 week old

value: WT

value: 37 degrees


title: 37_1

value: Spleen and Lymph nodes

value: CD8 T cell


title: MeiS_ALL_hsS1_2to4C_HORMAD1DMRT1_NA.hg38.RT

description: Whole genome sequencing

source_name: Whole genome sequencing for RT-Seq in Meiotic & S/gonia (b) RT_WGS

value: Hormad1 and weak Dmrt1


title: 0h_3

source_name: Spleen_Lymph nodes_37 degrees_0h


title: Germline_ALL_S2_2to4C_SCP3_DMRT1w.hg38.RT

description: Whole genome sequencing

source_name: Whole genome sequencing for RT-Seq in Meiotic & S/gonia (a) RT_WGS

value: Sycp3 and weak Dmrt1


title: 0h_1


title: 2C_ALL_hsP4_2C_NA_REC8.hg38.RT

description: Whole genome sequencing

source_name: Whole genome sequencing for RT-Seq in 2C_HS_RT_WGS

value: Non-replicating


title: dms3MORC7-FLAG_ChIPseq_rep-3

tag: ecotype background

tag: developmental stage

value: 5-6 weeks

tag: genotype/variation

value: floral tissue

tag: antibody

value: anti-FLAG M2 (Sigma)

tag: target protein


title: AC2P20_2: WT treated with AC2P20, pH 5.7 rep 2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplexe and converte reads to FASTQ format
Trimmomatic (v0.30)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie  was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
SAMtools was used to calculate coverage depth (>98% coverage acrosss the genome for all samples).
HTSeq software suite was used to analyze aligned and determin counts per gene feature in the M. tuberculosis CDC1551 genome
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the edgeR package
Qualimap was used to analyze coverage against the reference genome, sequence depth and pearson's correlation coefficient between replicates
Genome_build: M. tuberculosis CDC1551 genome (NCBI accession AE000516)
Supplementary_files_format_and_content: Processed files are presented as .csv spreadsheets and represents the average of 2 biological replicates

organism: Mycobacterium tuberculosis CDC1551

source_name: Bacterial cell

growth_protocol: Mtb cultures were grown to an OD600 of 0.5 in 8 mL of 7H9 OADC buffered media (pH 5.7)  at 37°C and 5% CO2 in standing T-25 culture flasks.

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Mtb cultures were subsequently treated with 20 µM AC2P20. For the control, cultures treated with an equal amount of DMSO.  Following a 24 h incubation period, RNA was isolated from the bacterial cultures and used for RNA-seq. For each condition, 2 biological replicates were performed.

tag: strain

tag: acidity


title: AC2P20_1: WT treated with AC2P20, pH 5.7 rep 1


title: 0h_2

tag: age

tag: condition

tag: time point

tag: tissue

tag: cell type


title: DMSO_2: WT treated with DMSO, pH 5.7 rep 2

tag: treatment

value: DMSO


title: IMP2_R3

city: Pittsburgh

first: Anita

last: Bansal

state: PA

address: Biomedical Science Tower

department: Immunology

institute: University of Pittsburgh

description:
processed data file: RIP.xlsx
IP_IMP2_IL17_3_S11

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq data was aligned using STAR followed by DESeq2 analysis
RIP-seq data was aligned using STAR followed by idientification of iMP2 binding using Piranha and then DESeq2 analysis
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

extract_protocol: RNA-seq libraries were prepared using standard Nextera XT Kit and RIP-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA kit

tag: antibody vendor

value: MBL international

tag: antibody catalog number

value: Cat# RN008P,

tag: antibody rrid

tag: antibody lot used


title: met1MORC7_BSseq-2_CG

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Genome_build: tair10
Supplementary_files_format_and_content: bigWig

extract_protocol:
ChIP seq: Samples were crosslinked in vitro. Nuclei were prepared with Nuclei Isolation Buffer (50 mM HEPES, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 0.6% Triton X-100, 0.4 mM PMSF, 5 mM benzamidine, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)). Chromatin was sheared with Bioruptor Plus (Diagenode) for 20 minutes with 30 s on and 30 s off and incubated with anti-FLAG M2 (Sigma) antibody overnight at 4◦C. Chromatin bound proteins were immunoprecipitated with Protein A and Protein G magnetic Dynabeads (Invitrogen) for 2 hours at 4◦C. DNA fragments were precipitated with EtOH overnight at -20◦C. Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seq: DNA from floral tissues were extracted with cetyl trimethylammonium bromide (CTAB)-based method. RNA was removed with PureLink RNase A (Invitrogen). 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). RNA seq: Floral tissues from 5-6 week old seedlings were used for RNA extraction with Zymo Direct-zol RNA MiniPrep kit (Zymo Research) following manufacturer’s instructions.
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).


title: dms3MORC7-FLAG_ChIPseq_rep-2

tag: ecotype background


title: met1MORC7_BSseq-1_CG

tag: developmental stage


title: IMP2_R2

description:
processed data file: RIP.xlsx
IP_IMP2_IL17_2_S9


title: DMSO_1: WT treated with DMSO, pH 5.7 rep 1


title: MORC7_BSseq-3_CG


title: IMP2_R1

description:
processed data file: RIP.xlsx
IP_IMP2_IL17_1_S7


title: RJG_m6

type: genomic

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned  on iScan

data_processing: Theta values from unprocessed file

source_name: blood

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA).

extract_protocol: Genomic DNA was extracted from whole blood treated with EDTA using a QIAamp DNA Mini Kit

tag: clinical condition

value: colorectal cancer

tag: Sex

value: male


title: HL8

value: Hodgkin lymphoma

value: female


title: K_m_13

value: control


title: K_k_1


title: WT-RNAseq-rep-2

description: wild type RNA-seq replicate 2

tag: genotype/variation

value: WT


title: MORC7_BSseq-2_CG

tag: strain


title: T1D p8

value: type 1 diabetes


title: IgG_R3

description:
processed data file: RIP.xlsx
IP_IgG_IL17_3_S10

tag: antibody

value: normal rabbit IgG

value: Cat# PM035,


title: met1MORC7_BSseq-3_CG


title: K_k_13


title: K_m_9


title: HL7


title: DL8

value: Diffuse large B-cell lymphoma


title: MORC7_BSseq-1_CG


title: IgG_R2

description:
processed data file: RIP.xlsx
IP_IgG_IL17_2_S8


title: RJG_k7


title: T1D p7


title: MORC7-FLAG_ChIPseq_rep-1

tag: target protein


title: RJG_m11


title: IgG_R1

description:
processed data file: RIP.xlsx
IP_IgG_IL17_1_S6


title: K_m_8


title: Petro_MC_DOM

city: atlanta

first: Jeffery

last: Streelman

address: 950 atlantic drive

institute: georgia institute of technology

description: Petrotilapia nigra (tax_id 526958) (rock) ♂ x Mchenga conophoros (tax_id 35575) (sand)♀ F1

data_processing:
Raw sequence reads from “Social Rock” and “Social Sand” samples were quality controlled using the NGS QC Toolkit
Raw reads with an average PHRED quality score below 20 were filtered out. The remaining reads were further trimmed of low-quality bases at the 3’ end. High quality sequence reads were aligned to the M.zebra reference genome MZ_UMD2a using TopHat v2.0.9
TopHat2 output bam files were sorted and converted to sam files using samtools v0.19
Sorted sam files were used as input for the HTSeq-count v0.6.1 program to obtain fragment counts for each locus. Fragment counts were scale-normalized across all samples using the calcNormFactors function in the edgeR package v3.6.8
Genome_build: MZ_UMD2a
Supplementary_files_format_and_content: Text file with matrix of raw transcript counts

organism: Petrotilapia nigra x Mchenga conophoros

source_name: Petrotilapia nigra (rock) ♂ x Mchenga conophoros (sand)♀ F1

extract_protocol:
Tissues were frozen in liquid nitrogen, homogenized using a mortar and pestle and placed in trizol. Following standard chloroform extraction RNeasy mini columns (Qiagen)
TruSeq Stranded mRNA Sample Prep Kit (Illumina- Kit A)

tag: parental species

value: Petrotilapia nigra (male) x Mchenga conophoros (female)

tag: generation

tag: social context

value: rock-like behavior

value: whole brain


title: NA_8

description:
processed data file: GeneExpression.xlsx
NA_8_S8

source_name: C57BL/6_Imp2 siRNA+ IL-17

value: Imp2 siRNA+ IL-17


title: HL6


title: DL7


title: K_k_14


title: NA_7

description:
processed data file: GeneExpression.xlsx
NA_7_S7

source_name: C57BL/6_Imp2 siRNA

value: Imp2 siRNA


title: NA_6

description:
processed data file: GeneExpression.xlsx
NA_6_S6


title: Petro_MC_SUB

value: sand-like behavior

tag: tissue


title: RJG_m5


title: NA_5

description:
processed data file: GeneExpression.xlsx
NA_5_S5

tag: treatment

value: Mock


title: RJG_m10

value: colorectal cancer


title: NA_4

description:
processed data file: GeneExpression.xlsx
NA_4_S4


title: K_m_3

value: male


title: T1D p6


title: K_k_4


title: NA_2

description:
processed data file: GeneExpression.xlsx
NA_2_S2


title: K_k_9


title: NA_3

description:
processed data file: GeneExpression.xlsx
NA_3_S3


title: RJG_k5


title: RJG_m4


title: NA_1

description:
processed data file: GeneExpression.xlsx
NA_1_S1


title: DL6


title: T1D p5


title: RB160_6

description:
processed data file: GeneExpression.xlsx
RB160_6_S12


title: K_k_3


title: K_k_8


title: RJG_k6


title: RB160_3

description:
processed data file: GeneExpression.xlsx
RB160_3_S10


title: K_m_10


title: K_m_7


title: RB160_4

description:
processed data file: GeneExpression.xlsx
RB160_4_S11

source_name: C57BL/6 _Mock+IL-17


title: HL5

value: Hodgkin lymphoma


title: HDFn-DH-3

city: Montevideo

first: Tatiana

last: Basika

state: Montevideo

address: Mataojo 2020

country: Uruguay

institute: Institut Pasteur de Montevideo

hyb_protocol: Hybridization, washing and scanning were performed according to the protocol specified by Agilent

scan_protocol: The slides were scanned using an Agilent microarray scanner G2505C. Feature Extraction software (version 9.5.1) was used to extract data, quality control, filtering, and data normalization.

data_processing: Differential gene expression analysis was performed with Genespring software (Agilent, v 14.9). Genes significantly up- and down-regulated were identified by t-test with a p-value of 0.05 (Benjamini–Hochberg false discovery rate correction). Functional annotation, gene ontology terms assignment and clustering analysis was performed using DAVID database (v 6.8, https://david.ncifcrf.gov/ ). The resulting GO lists were summarized using the REVIGO online tool (http://revigo.irb.hr/revigo.jsp)

source_name: HDFn cell line, DH treatment, replicate 3

label_protocol: 100 ng of total RNA were reverse-transcribed into cDNA, and this was transcribed into cRNA and Cy-3 labeled using the Low Input Quick Amp Labeling Kit, One-color (Agilent Technologies). The labeled cRNA was purified with Illustra RNAspin Mini Isolation kit (GE Healthcare, USA). cRNA quality was verified by total yield and specificity calculated based on NanoDrop ND-1000 spectrophotometer measurements (Thermo, USA).

growth_protocol: according to cell line specification

extract_protocol: Cellular pellet was resuspended in RNA protection reagent (NEB) and storage at -80°C until use. RNA extraction was done using RNA Monarch miniprep (NEB) according to manufacturers instructions. RNA quantification and integrity were assessed with Nandrop ND-1000 (Thermo) y en el Agilent 2100 Bioanalyzer  (Agilent Technologies), respectively.

treatment_protocol: Cells were seeded in 6 well plates and cultivated until 70-80% confluence was reached. Then a gap was created in the monolayer using a 200 µL tip. Cells were washed with PBS to remove cell debris. Then, cells were incubated with DHA, DHA, SA 0,625% w/v in DMEM-tween20 0,01% or culture media as control during 12h.

tag: cell type

value: fibroblasts

tag: cell line

value: HDFn

value: dersani hydrogel with alginate treatment after scratch


title: HDFn-DH-2

source_name: HDFn cell line, DH treatment, replicate 2


title: HDFn-DH-1

source_name: HDFn cell line, DH treatment, replicate 1


title: DL5

value: female


title: HDFn-DHA-1

source_name: HDFn cell line, DHA treatment, replicate 1


title: HDFn-DHA-2

source_name: HDFn cell line, DHA treatment, replicate 2


title: HDFn-CTRL-3

source_name: HDFn cell line, CTRL treatment, replicate 3

value: culture media treatment after scratch


title: HDFn-CTRL-2

source_name: HDFn cell line, CTRL treatment, replicate 2


title: HDFn-DHA-3

source_name: HDFn cell line, DHA treatment, replicate 3


title: HDFn-CTRL-1

source_name: HDFn cell line, CTRL treatment, replicate 1


title: RJG_m9


title: Lactation (D6)

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Read alignment and count summarization were performed using CellRanger v3.1.0 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format. Cells with at least 500 reads are included. The supplementary file features.tsv.gz contains the corresponding Ensembl IDs and gene symbols as tab-delimited text. The barcode.tsv files contain the 10X barcodes used to identify cells. Each matrix market file can be read into R, together with features.tsv.gz, using the read10X function of the edgeR software package.

source_name: Mammary gland

extract_protocol:
A 10x Genomics Chromium machine was used for single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10x Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of about 750,000 barcodes to separately index each cell’s transcriptome. The R1 primers were added during the GEM incubation and the P5, P7, a sample index and R2 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina NextSeq 500.

value: FVB/NJ

tag: cell population

value: epithelium

value: lactating (10 days post birth)

tag: number of cells with at least 500 sequence reads


title: K_m_6

value: control


title: K_m_12


title: RB160_1

description:
processed data file: GeneExpression.xlsx
RB160_1_S9

source_name: C57BL/6 _Mock


title: K_k_11


title: K_m_4


title: Late-pregnancy (B4)

value: pregnant (18.5 days)


title: DL4

value: Diffuse large B-cell lymphoma


title: Mid-pregnancy (G)

value: pregnant (12.5 days)


title: RJG_m3


title: Adult FVB/NJ (D12)

value: adult virgin (10 weeks)


title: RJG_k4


title: K_m_5


title: HL4


title: PBS_1dpi_5

source_name: Liver

tag: genotype

value: WT

value: liver

tag: age

value: 5 months

tag: gender

value: Female

value: PBS 1dpi


title: Adult FVB/NJ (P7)

tag: developmental stage


title: T1D p3

source_name: blood

tag: clinical condition

value: type 1 diabetes

tag: Sex


title: K_m_2

value: male


title: RNA-seq Luminal terminal endbuds replicate 3

data_processing:
Libraries were sequenced on an Illumina NextSeq 500 to generate 75bp paired-end reads.
Reads were aligned to the mosue genome mm10 by Rsubread version 1.34.4
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

extract_protocol: Total RNA was extracted to generate libraries for whole transcriptome analysis.

tag: mouse strain

tag: organ

value: Mammary gland

value: terminal end buds

value: luminal epithelium


title: RNA-seq Luminal terminal endbuds replicate 2


title: HaCaT-DH-3

source_name: HaCaT-SF cell line, DH treatment, replicate 3

value: keratinocytes

value: HaCaT-SF

value: dersani hydrogel with alginate treatment after scratch


title: HDFn-SA-3

source_name: HDFn cell line, SA treatment, replicate 3

value: fibroblasts

value: HDFn

value: sodium alginate treatment after scratch


title: HDFn-SA-2

source_name: HDFn cell line, SA treatment, replicate 2


title: K_k_10

value: control

value: female


title: HDFn-SA-1

source_name: HDFn cell line, SA treatment, replicate 1


title: HaCaT-DH-2

source_name: HaCaT-SF cell line, DH treatment, replicate 2


title: HaCaT-DH-1

source_name: HaCaT-SF cell line, DH treatment, replicate 1


title: K_k_7


title: RNA-seq Luminal terminal endbuds replicate 1


title: RJG_m2

value: colorectal cancer


title: K_m_1


title: HL3

value: Hodgkin lymphoma


title: K_m_11


title: RNA-seq Luminal ducts replicate 1

value: ducts


title: RNA-seq Luminal ducts replicate 3


title: K_k_12


title: HaCaT-DHA-2

source_name: HaCaT-SF cell line, DHA treatment, replicate 2


title: HaCaT-DHA-3

source_name: HaCaT-SF cell line, DHA treatment, replicate 3


title: T1D p10


title: RJG_k3


title: RNA-seq Basal terminal endbuds replicate 3

value: basal epithelium


title: HaCaT-DHA-1

source_name: HaCaT-SF cell line, DHA treatment, replicate 1


title: RJG_m8


title: HaCaT-CTRL-2

source_name: HaCaT-SF cell line, CTRL treatment, replicate 2

value: culture media treatment after scratch


title: HaCaT-CTRL-3

source_name: HaCaT-SF cell line, CTRL treatment, replicate 3


title: HaCaT-CTRL-1

source_name: HaCaT-SF cell line, CTRL treatment, replicate 1


title: RNA-seq Basal terminal endbuds replicate 1


title: K_k_6


title: DL3

value: Diffuse large B-cell lymphoma

value: male


title: K_k_2


title: RNA-seq Basal terminal endbuds replicate 2

value: Mammary gland

value: terminal end buds


title: T1D p2

value: type 1 diabetes


title: RJG_k2


title: RJG_m7


title: RJG_m1


title: RNA-seq Basal ducts replicate 3


title: RNA-seq Basal ducts replicate 2


title: HL2


title: p53-6h_K17KO_rep2

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 v2.2.5 and using samtools v1.7 to sorting bam
peaks were called using MACS2 version 2.1.2 with the following setting: band width = 300 model fold = [5, 50] pvalue cutoff = 1.00e-03
Genome_build: mm10

source_name: back skin

growth_protocol: the skin isolate from 8-10 weeks mouse

extract_protocol:
Lysates were clarified from sonicated nuclei and p53-DNA  histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: treat by radition with 5Gy

value: ionizing radiation


title: p53-T0_K17KO_rep2


title: RNA-seq Basal ducts replicate 1

source_name: Mammary gland


title: p53-T0_WT_rep2

value: Wild type


title: T1D p1


title: HaCaT-SA-2

source_name: HaCaT-SF cell line, SA treatment, replicate 2

value: keratinocytes

value: HaCaT-SF


title: HaCaT-SA-3

source_name: HaCaT-SF cell line, SA treatment, replicate 3

value: sodium alginate treatment after scratch


title: Post-involution

tag: strain

value: FVB/NJ

value: epithelium

value: post-involution (3 weeks post birth)


title: HaCaT-SA-1

source_name: HaCaT-SF cell line, SA treatment, replicate 1


title: RJG_k1

source_name: blood

value: colorectal cancer

value: female


title: T1D p9


title: K_k_5

value: control


title: p53-6h_WT_rep2


title: Lactation (F11)

value: lactating (10 days post birth)


title: HL9

value: Hodgkin lymphoma


title: H3K4me3-6h_WT_rep2


title: HL1

value: male


title: DL1

value: Diffuse large B-cell lymphoma


title: H3K4me3-T0_WT_rep2


title: Mid-pregnancy (H)

value: pregnant (12.5 days)


title: DL2


title: K_k_15


title: Late-pregnancy (F4)

value: pregnant (18.5 days)


title: Adult C57BL/6

value: adult virgin (10 weeks)


title: RRBS_3W4

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the bowtie2 sequence analysis programs. Reads were mapped to the ensembl reference human genome.
To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.
Methylation percentage for each CpG sites were calcualted by methylKit
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files including methylation percentage for each sample in the matrix for 3 and 13-month old animal.

source_name: Microglia Enriched Brain homogenate

growth_protocol: Mice were provided with food and water ad libitum and housed in a 12-hour light/dark cycle.

extract_protocol:
The AllPrep DNA/RNA MiniKit (Qiagen; Germantown, MD; Product ID: 80204) was used to individually extract RNA and DNA from each flash-frozen lysate sample. All RNA and DNA samples were stored at -80°C for later use.
RRBS samples were prepared at the University of Michigan Epigenetics Core facility (PMID: 25742437)

treatment_protocol: Microglia extraction was performed on brains dissected from the mice involved in this study. This protocol was adapted from Lee and Tansey (PMID:23813365).

tag: background strain

value: microglia enriched brain homogenate

value: WT

value: 3 months

tag: group


title: RRBS_3W5

tag: tissue


title: RRBS_3W3


title: RRBS_3W1


title: Adult FVB/NJ (A10)


title: RRBS_3H7

value: HEM


title: Puberty terminal endbuds

value: terminal endbud epithelium

value: puberty (5 weeks)


title: RRBS_3H3


title: Bone Marrow B220+ cells from WT mouse, biological replicate 5

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from Wild-type B220+ bone marrow cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

source_name: WT 6

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were bred and maintained in the SPF (specific pathogen-free) area of the animal house until the start of the ruxolitinib treatment where they were moved to a conventional facility and they have been exposed to common pathogens.

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

treatment_protocol: Pax5+/-  and WT mice were treated with Ruxolitinib in the chow for 2 weeks at a dose of 120 mg/kg/day (0.375 g/kg of food).

value: Bone marrow:MACS-sorted B220+ cells

tag: treatment


title: Bone Marrow B220+ cells from WT mouse, biological replicate 1

source_name: WT 1


title: Adult SWISS

value: SWISS

value: epithelium


title: RRBS_3H2


title: Pre-puberty

value: pre-puberty (2.5 weeks)


title: Bone Marrow B220+ cells from WT mouse, biological replicate 4

source_name: WT 5


title: Bone Marrow B220+ cells from WT mouse, biological replicate 3

source_name: WT 4


title: Bone Marrow B220+ cells from WT mouse, biological replicate 2

source_name: WT 3


title: Bone Marrow B220+ cells from WT mouse treated with ruxolitinib, biological replicate 5

description: Gene expression data from Wild-type B220+ bone marrow cells after ruxolitinib treatment

source_name: WT 24_RUXO

value: RUXO


title: Early postnatal

value: early postnatal (5 days)


title: RRBS_3H1


title: Embryonic adjacent skin

value: adjacent epidermis

value: embryo (E18.5)


title: Bone Marrow B220+ cells from WT mouse treated with ruxolitinib, biological replicate 4

source_name: WT 23_RUXO


title: Puberty ducts

value: ductal epithelium


title: RRBS_13W7

value: 13 months


title: Bone Marrow B220+ cells from WT mouse treated with ruxolitinib, biological replicate 3

source_name: WT 22_RUXO


title: Bone Marrow B220+ cells from WT mouse treated with ruxolitinib, biological replicate 1

source_name: WT 20_RUXO


title: Bone Marrow B220+ cells from Pax5+/- mouse, biological replicate 4

description: Gene expression data from Pax5+/- B220+ bone marrow cells


title: Bone Marrow B220+ cells from WT mouse treated with ruxolitinib, biological replicate 2

source_name: WT 21_RUXO


title: Embryonic mammary


title: Bone Marrow B220+ cells from Pax5+/- mouse treated with ruxolitinib, biological replicate 2

description: Gene expression data from Pax5+/- B220+ bone marrow cells after ruxolitinib treatment


title: Bone Marrow B220+ cells from Pax5+/- mouse treated with ruxolitinib, biological replicate 4


title: Bone Marrow B220+ cells from Pax5+/- mouse, biological replicate 3


title: Bone Marrow B220+ cells from Pax5+/- mouse, biological replicate 1


title: Bone Marrow B220+ cells from Pax5+/- mouse treated with ruxolitinib, biological replicate 3


title: RRBS_13W6


title: Bone Marrow B220+ cells from Pax5+/- mouse treated with ruxolitinib, biological replicate 1


title: Bone Marrow B220+ cells from Pax5+/- mouse, biological replicate 2


title: RRBS_13W2


title: Orc4_V1_LRY3138

city: Buffalo

first: Laura

middle: N

last: Rusche

state: NY

address: 109 Cooke Hall, UB North/Amherst Campus

department: Biological Sciences

institute: State University of New York at Buffalo

data_processing:
Paired-end sequence reads were processed to remove 3’ adapter sequences using Cutadapt 2.10 with the parameters --nextseq-trim=20 and -m 10.
T. delbrueckii genome index was built using Bowtie2/2.3.4.1.
ChIP- seq reads for both single-end and paired-end sequencing were aligned to the T. delbrueckii genome index using Bowtie2/2.3.4.1.
ChIP peaks were called using MACS2/2.2.7.1 with the parameters: --nomodel was used for both, --extsize 200 was used for single-end reads only, -f BEDPE was used for paired end reads
Genome_build: CBS1146 (GCA_000243375.1)
Supplementary_files_format_and_content: bigWig

organism: Torulaspora delbrueckii

source_name: Yeast

growth_protocol: Yeast cells were grown at 30˚C in YPD medium containing 1% yeast extract, 2% peptone, and 2% glucose.

extract_protocol:
Cells were grown in YPD overnight. Following day, cells were diluted at OD600 0.3, grown at 30˚C, and harvested at an OD600 of ∼1.
Libraries were prepared using Takara Bio SMARTer ThruPlex DNA seq kit

treatment_protocol: Cells were cross-linked for 1 hour in 1% formaldehyde. After cell lysis, chromatin was sonicated. Immunoprecipitation was conducted with 10μL Protein A agarose beads and 4 µl of anti MYC (Millipore 06-549) or anti V5 antibody (Millipore AB3792) antibody.

tag: epitope tag

tag: chip antibody

value: V5 (Millipore AB3792)


title: Subject 33 G3-29M

city: Kansas City

first: Zohreh

last: Talebizadeh

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Hospital

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: blood microRNA

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.

value: maternal blood

value: Female

tag: sert genotype

value: LL

tag: prenatal stress level

value: Low


title: Plasmid_rep1_CRISPR_RBP

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: all.countsummary.txt

data_processing:
Library strategy: DNA-seq
CRISPR screening data was aligned and processed using MaGeCK.
Genome_build: hg19
Supplementary_files_format_and_content: MaGeCK processed gene summary

organism: synthetic construct

source_name: plasmid

extract_protocol: Plasmid was PCRed first with primers flanking the sgRNA and second with Illumina sequencing adapters.

tag: cell line

value: plasmid


title: Subject 32 G3-59M


title: MZ_MC_LONE

description: Maylandia zebra (tax_id 106582) (rock) ♂ x Mchenga conophoros (tax_id 35575) (sand)♀ F1

organism: Maylandia zebra x Mchenga conophoros

source_name: Maylandia zebra (rock) ♂ x Mchenga conophoros (sand)♀ F1

tag: parental species

value: Maylandia zebra (male) x Mchenga conophoros (female)

tag: generation

tag: social context

value: rock-like behavior

value: whole brain


title: Orc2_V2_LRY3143


title: MZ_TI_DOM

description: Maylandia zebra (tax_id 106582) (rock) ♂ x Tramitichromis intermedius (tax_id 323801) (sand)♀

organism: Maylandia zebra x Tramitichromis intermedius

source_name: Maylandia zebra (rock) ♂ x Tramitichromis intermedius (sand)♀ F1

value: Maylandia zebra (male) x Tramitichromis intermedius (female)


title: Subject 31 G3-52M


title: Subject 34 G3-36M


title: Subject 30 G3-06M


title: Orc2_V1_LRY3142


title: RRBS_13H11

value: microglia enriched brain homogenate

tag: genotype

value: HEM

tag: age


title: RRBS_13H10


title: Orc4_V2_LRY3139


title: Plasmid_rep2_CRISPR_RBP

description: all.countsummary.txt


title: LF_MC_SUB

description: Labeotropheus fuelleborni (tax_id 57307 ) (rock) ♂ x Mchenga conophoros (tax_id 35575) (sand)♀ F1

organism: Labeotropheus fuelleborni x Mchenga conophoros

source_name: Labeotropheus fuelleborni (rock) ♂ x Mchenga conophoros (sand)♀ F1

value: Labeotropheus fuelleborni (male) x Mchenga conophoros (female)

value: sand-like behavior


title: Mock_V_JRY10156


title: RRBS_13H8

source_name: Microglia Enriched Brain homogenate


title: Orc1_M2_LRY3211

value: MYC

value: MYC (Millipore 06-549)


title: Subject 29 G3-15M

tag: Sex


title: LF_MC_LONE


title: RRBS_13W1

value: WT

value: 13 months


title: RRBS_13H7


title: MZ_TI_SUB

description: Maylandia zebra (tax_id 106582) (rock) ♂ x Tramitichromis intermedius (tax_id 323801) (sand)♀ F1


title: Subject 27 G2b-55M

value: maternal blood

value: SS


title: RRBS_13H6


title: Petro_AB_DOM

description: Petrotilapia nigra (tax_id 526958) (rock) ♂ x Aulonocara baenschi (tax_id 143496 ) (sand)♀ F1

organism: Petrotilapia nigra x Aulonocara baenschi

source_name: Petrotilapia nigra (rock) ♂ x Aulonocara baenschi (sand)♀ F1

value: Petrotilapia nigra (male) x Aulonocara baenschi (female)


title: Orc1_M1_LRY3204


title: Petro_AB_SUB


title: RRBS_13H3


title: Input2_JRY10156


title: Subject 26 G2b-49M

value: Female

value: Low


title: LF_MC_DOM


title: Subject 28 G2b-21M


title: T3

city: Göttingen

first: Shiv K.

last: Singh

address: Robert-Koch-Str. 40

institute: Univeristy Medical Center

description: 10 ng/ul TNFα (18h)

data_processing:
Raw reads were quality-checked using FastQC v0.11.5
Alignment against hg38 human reference genome was done by using STAR v2.5.2b
Aligned reads were assigned to genes using HTSeq-count version 0.10.0
DESeq2 was utilized for differential gene expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreatic cancer

growth_protocol: CAPAN1 cells were cultured in RPMI 1640 supplemented with 10% FCS and 1% P/S.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded in 6-well plate 24 h prior to treatment. Next day cells were exposed to 10 ng/ul TNFα for 18 h, aqua dest was used as a control.

value: 10 ng/ul TNFalpha

tag: time point


title: RNA-seq_3W5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence and low-quality sequence using Trimmomatic
Reads were mapped to the mm10 reference genome using Hisat2 sequence analysis program to identify transcripts.
Count values were calculated using featureCounts
Counts were normalized by DESeq2 and rlogTransformed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include rlogTransformed values for each sample in the matrix

extract_protocol:
The AllPrep DNA/RNA MiniKit (Qiagen; Germantown, MD; Product ID: 80204) was used to individually extract RNA and DNA from each flash-frozen lysate sample. All RNA and DNA samples were stored at -80°C for later use.
RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

value: 3 months

value: Microglia Enriched Brain homogenate


title: RRBS_13H1