title: NK2-Lesion3

first: Hin Ching

last: Lo

address: 1885 El Paseo St, Apt 1033

institute: Baylor College of Medicine

description:
sample name:
XZ20219_17

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DEseq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM read counts, DESeq2 normalized gene expression matrix and annotations

source_name: Lung metastasis

growth_protocol: GFP and mCherry-labelled AT3 cells were injected into the mammary fat pad of Rag1-/-IL2rg-/- mice to generate mammary gland tumors. Tumor cells then spontaneously metastasized to lungs.

extract_protocol:
Lungs were harvested, embedded in OCT and cut into frozen sections on a Leica CM3050 S Research Cryostat equipped with Cryojane. GFP and RFP+ Lung lesions were extracted by laser capture microdissection on a Leica LMD7000 instrument instrument. RNA was purified by RNeasy micro kit (Qiagen). 2ng of total RNA per sample was used to prepare the sequencing libraries.
Libraries were then prepared using QIAseq FX single cell RNA library kit (Qiagen) following standard manufacturer's protocol. The cDNA library was inspected using using Agilent Bioanalyzer High Sensitivity DNA chips and quantitated by PicoGreen dsDNA Assay kit (ThermoFisher).

treatment_protocol: Mice receive intravenous injection of PBS or 60,000 in vitro activated murine NK cells on Day 11.

tag: treatment

value: NK transferred

value: breast cancer lung metastatic lesion


title: NK2-Lesion4

status: Public on Apr 16 2020

type: SRA

city: Houston

state: TX

country: USA

description:
sample name:
XZ20219_18

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: Single Cell P20 IFE Basal GC050904_B07

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description: SmartSEQ2 scRNAseq

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated matrix containing raw transcript counts

source_name: Lrig1-CreERT2/RosaYFP IFE basal epidermal cells FACS sorted for Cd34-/Itga6+/YFP-

growth_protocol: The dermis and epidermis were removed from the tail bone using forceps. The samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight. The next day, the epidermis was separated from the dermis. Epidermis was then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Basal cells were mechanically separated from the epidermis by flushing 10 times under the epidermis. Tissues were then cut in small pieces with a scalpel and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (cFCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in PBS 2% cFCS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Basal IFE and infundibulum cells were stained using PE-conjugated anti-a6-integrin (clone GoH3; 1/200, ebioscience) and bulge cells were stained with biotinylated CD34 (clone RAM34; 1:50, BD Biosciences). Primary antibodies were washed with PBS 2% cFCS and cells incubated for 30 min in APC-conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Secondary antibody was washed with PBS 2% FCS and cells were incubated in Hoechst solution (1:4000 in PBS 2%cFCS) prior FACS analysis. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. For H2BGFP proliferation experiments, K5tTA/TRE-mCMV-H2B-GFP mice chased with doxycycline were used. basal cells were targeted using CD34 negative and α6 integrin positive gating. For P20 basal epidermal cells sorting, Lrig1-CreERT2/RosaYFP mice were used and basal cells from the interfollicular epidermis were targeted using CD34 negative, α6 integrin positive and YFP negative gating. Analysis were perfomed on a FACS Fortessa (BD Bioscience). Cell sorting was performed using a FACS Aria at high pressure (70 psi) and FACS Diva software (BD Biosciences).

extract_protocol:
Single-cell transcriptomes were generated using a modified Smartseq-2 protocol. Lysis buffer (2 µl) in 96-well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer, 2.5 mM dNTPs, 2.5 µM oligo-dT30-VN and ERCC controls at a final dilution of 1:400 million. Reverse transcription and PCR were performed according to the Smartseq-2 protocol: 5,7 µl reverse transcription mix and 15 µl PCR Master mix. cDNA was amplified for 23 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8 × ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 25 µl buffer EB (Qiagen) and transferred to 96_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermo Fisher Scientific) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit.
Next-generation sequencing library preparation was performed using the Illumina Nextera DNA library preparation kit with volumes reduced by one-tenth (Illumina). In brief, 100 pg cDNA in a volume of 500 nl was tagmented by adding 1.5 µl Tn5-buffer mix and incubating for 10 min at 55 °C. Tagmented samples were barcoded with Nextera indexes A-D and amplified with 11 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6 × ratio. Library pools were eluted in buffer EB and quality controlled using an Agilent 2100 BioAnalyser and High Sensitivity DNA kits before adjusting to a concentration of 4 nM. The diluted pools were quantified using the KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before final dilution to 2 nM. Sequencing was performed on a HiSeq4000 on two lanes in high output mode.
scRNAseq

tag: library type

value: Nextera XT


title: Single Cell P20 IFE Basal GC050904_B08

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_B06

description: SmartSEQ2 scRNAseq


title: KO2-Lesion3

description:
sample name:
XZ20219_13

value: Ctrl


title: KO2-Lesion4

description:
sample name:
XZ20219_14


title: Single Cell P20 IFE Basal GC050904_B04

description: SmartSEQ2 scRNAseq


title: KO2-Lesion2

description:
sample name:
XZ20219_12


title: KO2-Lesion1

description:
sample name:
XZ20219_11


title: Single Cell P20 IFE Basal GC050904_B03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_B05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_B01

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_B02

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A12

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A11

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A10

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A09

description: SmartSEQ2 scRNAseq


title: KO1-Lesion3

description:
sample name:
XZ20219_06


title: KO1-Lesion5

description:
sample name:
XZ20219_08


title: Single Cell P20 IFE Basal GC050904_A08

description: SmartSEQ2 scRNAseq


title: KO1-Lesion1

description:
sample name:
XZ20219_04


title: NK1-Lesion2

description:
sample name:
XZ20219_02


title: NK1-Lesion3

description:
sample name:
XZ20219_03


title: KO3-Lesion2

description:
sample name:
XZ20219_16


title: Single Cell P20 IFE Basal GC050904_A07

description: SmartSEQ2 scRNAseq


title: KO3-Lesion1

description:
sample name:
XZ20219_15


title: Single Cell P20 IFE Basal GC050904_A05

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A06

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A03

description: SmartSEQ2 scRNAseq


title: Single Cell P20 IFE Basal GC050904_A04

description: SmartSEQ2 scRNAseq


title: NK2-Lesion1

description:
sample name:
XZ20219_09


title: Single Cell P20 IFE Basal GC050904_A02

description: SmartSEQ2 scRNAseq


title: ATAC-seq; Col2a-eCFP Proximal Femur E15.5

city: Cambridge

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

description: ATAC-seq on growth plate chondrocytes sorted using Col2a1-ECFP

library_source: genomic

data_processing:
alignment to mm10; Bowtie2 version 2.3.2; default parameters for mm10 alignment
filter for duplicates; MACS2 version 2.1.1.2; macs2 filterdup -i file -g hs --keep-dup 1 -o outfile
peak calling; MACS2 version 2.1.1.2; macs2 callpeak -B -t rep1file -n name --nomodel --shift -100 --extsize 200
peak filtering ; IDR https://github.com/nboley/idr; idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 ?plot; MACS2 .narrowPeak output was cut using the number of peaks below the IDR threshold, sorting by MACS2 reported p-value
Genome_build: mm10
Supplementary_files_format_and_content: Distal_femur_Col2a1_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the distal femur Col2a1 experiment;
Supplementary_files_format_and_content: Proximal_femur_Col2a1_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the proximal femur Col2a1 ATAC-seq experiment;
Supplementary_files_format_and_content: PFA_S1_peakcalls_mm10.bed; bed format; contains the coordinates of the peaks called as described for the proximal femur ATAC-seq experiment;
Supplementary_files_format_and_content: DFA_S2_peakcalls_mm10.bed; bed format; contains the coordinates of the peaks called as described for the distal femur ATAC-seq experiment;

molecule: genomic DNA

source_name: Proximal femoral growth plates E15.5

growth_protocol: in vivo collected E59 growth plate chondrocytes

extract_protocol:
The samples were collected in microcentrifuge tubes containing 200ul 5% FBS/DMEM. To generate a single cell chondrocyte suspension, each pooled sample was then subjected to 1% Collagenase II (VWR 80056-222) digestion for 2hrs at 37C rocking, mixing every 30 minutes. After placing on ice, samples were filtered using a micro-centrifuge filter set-up by gently mashing the residual tissues through the filter followed by rinsing with 5% FBS/DMEM. Samples were then spun down at 500g at 4C for 5 min. We next performed cell counting methods using trypan blue and a hemacytometer and performed subsequent ATAC-seq steps on those samples that had cell death rates well below 25%. On average we acquired 500,000-1,000,000 living cells per harvest. Next, cells were resuspended in concentrations of 50,000 cells in 1x PBS.  Cell samples then subjected to the ATAC-seq protocol as described in Buenrostro et al., 2015, modifying the protocol by using 2 ul of transposase per reaction. The transposase reaction product was then purified using the Omega MicroElute DNA Clean Up Kit following manufacturers protocols, eluted in 10 ul of warmed ddH20, and stored at -20C.
Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500

treatment_protocol: All experiments were performed following protocols approved by the Harvard University IACUC committee. Timed matings were established between Col2a-eCFP (as well as FVBNJ) mice, and pregnant females were euthanized at E15.5 in order to acquire embryonic long bone growth plates. Embryos were dissected in PBS1X on ice under a dissection scope and the proximal and distal growth zones of the right and left femur were stripped clear of soft tissues. Each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis and separately pooled from a single litter, consisting on average of 8 animals. Four biological replicates for each bone-end were obtained.

value: Proximal femoral growth plates

tag: cell type

value: chondrocytes

tag: reagent

value: tn5 transposase

tag: developmental stage


title: NK1-Lesion1

description:
sample name:
XZ20219_01


title: ATAC-seq; proximal femur E15.5

description: ATAC-seq on growth plate chondrocytes

value: FVBNJ


title: KO1-Lesion4

description:
sample name:
XZ20219_07


title: NK2-Lesion2

description:
sample name:
XZ20219_10


title: ATAC-seq; distal femur E15.5

description: ATAC-seq on growth plate chondrocytes

source_name: Distal femoral growth plates E15.5

value: Distal femoral growth plates


title: ATAC-seq; Col2a-eCFP Distal Femur E15.5


title: 180221_WT_6DL_UNC2400_S2

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

department: Department of Medicine

country: Canada

institute: University of Montreal

description: Illumina sequencing

data_processing:
Libraries were sequenced with 75 bp single-end reads
Sequences were trimmed to 36 bp and mapped to mm9 using Bowtie 2 (v2.0.5) with default parameters (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
Any sample reads with less than 10M and/or peaks less than 20 M were excluded from further analysis. Poor quality reads (MAPQ<=30, reads mapping to chrM, chrY and patch chromosomes were also removed.
Reads were further filtered to remove PCR duplicates using Picard Tool MarkDuplicates (v2.6.0, https://broadinstitute.github.io/picard/). Accessible chromatin regions (peaks) were called using MACS2 v2.0.10. Default parameters were used except for the following: --keep-dup all -B -- nomodel --SPMR -q 0.05.
The signal intensity was calculated as the fold enrichment of the signal per million reads in a sample over a modelled local background using the bdgcmp function in MACS2. We then calculated the maximum signal intensity over every peak for conditions being compared using mapBed –o max and quantile normalized them across samples.
The average normalized signal intensity across replicates for each condition was then plotted in PCA. All downstream analyses (e.g. Spearman correlation coefficient analysis) were carried out using Bedtools v2.26.0 (https://bedtools.readthedocs.io/en/latest/) and R 3.4.1 (https://www.r-project.org/). Figures were plotted using ggplot2 (https://ggplot2.tidyverse.org/).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: wild-type Embryonic stem cells

growth_protocol: Murine embryonic stem cells were thawed (initial cell passage indicated), cultured in LIF containing media for 2 days (2DL), transferred to media containing 5 micromolar ATRA for a further 6 days (6DA) and transferred to LIF-containing media for a further 6 days (6DL). Where indicated, samples were sorted via FACS for GFP status (positive= pos or plus; negative = neg).

extract_protocol:
Frozen ESC pellets were thawed and assessed for viability followed by nuclei preparation and treatment with Tn5 transposase. The samples were subjected to PCR amplification and DNA purification. Adapted from Buenostro et al., 2015; doi:10.1002/0471142727.mb2129s109
Libraries were generated and optimized by PCR amplification, purified, and verified for proper size selection using a Agilent BioAnalyzer
To determine if the ATAC reactions were successful, an assessment of the overall enrichment of open chromatin regions was assayed by qPCR. Enrichment scores were calculated for each possible open vs closed region (2^(Ct_Open – Ct_Closed)). Scores over 10 were considered to be positively enriched.

treatment_protocol: ESC populations were untreated or treated throughout the 14 day differentiation treatment with the compounds indicated: A395, A395N, UNC1999, UNC2400, GSK343, GSKJ4, GSK5. The compound concentration was 1 micromolar for all compounds except GSK343 (3 micromolar)

tag: sequencing run#

tag: passage numbers

tag: treatment group

tag: sample preparation

value: ATAC-seq


title: 180423_WT_6DL_UNC2400_S3

description: Illumina sequencing


title: Single Cell P20 IFE Basal GC050904_A01

description: SmartSEQ2 scRNAseq


title: 180423_WT_6DL_UNC1999_S2

description: Illumina sequencing


title: KO1-Lesion2

description:
sample name:
XZ20219_05


title: 180221_WT_6DL_UNC1999_S1

description: Illumina sequencing


title: 180424_WT_6DL_GSKJ5_S6

description: Illumina sequencing


title: cost1_Drought_rep3

city: East Lansing

first: Yan

last: Bao

address: 603 Wilson Road

institute: MIchigan State University

data_processing:
All paired end data with read length 250 bp were aligned to Arabidopsis TAIR10 genome, using STAR (version 2.4.0 with parameters “--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.10”)
Subsequently, reads count of each annotated gene was calculated by htseq-count (version 0.6.0 with parameters “-t mRNA -m intersection-nonempty --stranded no”).
Next, significantly differently expressed genes (DEGs) between each two samples were extracted with cutoff FDR (false discovery rate) < 0.01 using DESeq2
Genome_build: TAIR10

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana 10-days Seedlings

growth_protocol: Seeds from WT and cost1 were germinated and vertically grown on 100 mm × 100 mm square plates (Fisher Scientific) with 1/2 MS-0 media for 10 days.

extract_protocol: Samples were harvested and immediately ground into powder in liquid nitrogen. Total RNA extraction was extracted by using RNeasy Plant Mini Kit (QIAGEN, Cat. No. 74904).

treatment_protocol: Seedlings with similar size were picked up and treated with dehydration on petri dish for 6h.

value: seedling

tag: genotype

value: cost1 mutant


title: cost1_Drought_rep2


title: 180222_WT_6DL_GSKJ5_S12

description: Illumina sequencing


title: cost1_Drought_rep1


title: 180424_WT_6DL_GSKJ4_S5

description: Illumina sequencing


title: 180222_WT_6DL_GSKJ4_S11

description: Illumina sequencing


title: cost1_Control_rep2


title: cost1_Control_rep3


title: 181002_WT_6DL_GSK343_S8

description: Illumina sequencing


title: 180423_WT_6DL_GSK343_S4

description: Illumina sequencing


title: cost1_Control_rep1


title: WT_Drought_rep2

value: wild type


title: WT_Drought_rep3


title: 180424_WT_6DL_A395N_S4

description: Illumina sequencing


title: 180221_WT_6DL_GSK343_S3

description: Illumina sequencing


title: WT_Drought_rep1


title: 180221_WT_6DL_A395N_S4

description: Illumina sequencing


title: KPC 4662 Rab27a 3.2 p17

type: RNA

city: Chapel Hill, NC

first: Yuliya

last: Pylayeva-Gupta

state: NC

address: 450 West Drive, CB 7295

department: Lineberger Comprehensive Center

institute: UNC

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridization controls (Affymetrix) were hybridized on the Affymetrix GeneChip Mouse Gene 2.1 ST Array Plate followed by washing and staining in the GeneTitan® Instrument (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneTitan® HT Array Plate Scanner (Affymetrix).

data_processing: The data was analyzed in GeneSpring using Affymetrix default settings.  Data scaled Log2.

label: biotin

source_name: KPC 4662 cell line isolated from pancreatic ductal adenocarcinoma of a mouse

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrix arrays. The Affymetrix GeneChip® WT PLUS Reagent Kit Manual was followed to prepare the samples. Briefly, the GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA. Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with biotin in a terminal labeling reaction.

growth_protocol: KPC 4662 cells were gown in DMEM +10 FBS and PenStrep.

extract_protocol: RNA was isolated using Rneasy Qiagen kit.  RNA was run on Agilent tapestation to verify quality prior to running microarray.

treatment_protocol: Cells were infected with lentiviral pLKO.1 containing either scrambled shRNA or shRab27a.  Cells were selected using puromycin and knockdown was validated by qPCR and western blot.

tag: cell line

value: Rab27a knockdown


title: KPC 4662 Rab27a #3 p16


title: KPC 4662 scramble p17

value: scramble (control)


title: WT_Control_rep2


title: 180222_WT_6DL_A395_S4

description: Illumina sequencing


title: 180424_WT_6DL_A395_S3

description: Illumina sequencing


title: WT_Control_rep1


title: 180222_WT_6DL_S7

description: Illumina sequencing


title: KPC 4662 Rab27a #4 p16


title: 16hrdex_YFP-rep3

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

data_processing:
The first phase of the data analysis pipeline was the quality control step. In this step, the quality of the raw sequencing data was assessed using the tool FastQC
Bases with bad quality (Phred score <20), over-represented PCR primers and bases with fluctuating GC content identified in this step were pruned using a combination of Cutadapt and Seqtk  tools.
The second phase of quality control was the removal of rRNA reads from raw sequencing data.
For aligning the filtered raw data, we used the standard Arabidopsis genome annotation, TAIR10, and used TopHat tool.
we used the python package HTSeq to count the reads that are aligned to each genomic feature (exon) and to generate gene expression read count matrices. For identifying the deferentially expressed genes from the read count data, we used the R package DESeq2, which models read count data following a negative binomial distribution
Genome_build: Arabidopsis genome annotation, TAIR10
Supplementary_files_format_and_content: .csv file having gene ID and number of counts in tab delimited format

source_name: shoot apical meristem

growth_protocol: Plants were grown on soil in short day conditions for 4-5 weeks before harvesting

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all the samples were prepared using ‘NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: Plants were treated with 10 um dexamethasone for 6 or 16hr. About 50 SAMs of 4-5 week old plants were quickly harvested and placed in cell-wall dissolving enzyme solution in 70um cell-strainer in a small petridish. Protoplasts samples were sorted by the EMBL flow cytometry core facility using a special setup MoFlo XDP cell sorter from Beckman Coulter equipped with a Coherent Sabr Argon gas laser emitting at 514.5nm (400mW), a Coherent Innova gas laser emitting at 488nm (300mW), and a Coherent Obis 405nm solid state laser (240mW).

value: Dex

tag: tissue-type

value: epidermis

tag: fluroscence protein

value: Venus


title: 16hrdex_YFP-rep4


title: 16hrdex_YFP-rep2


title: 16hrdex_YFP-rep1


title: 180221_WT_6DA_S5

description: Illumina sequencing


title: 181002_WT_2DL_undifferentiated_S2

description: Illumina sequencing


title: 180222_WT_2DL_undifferentiated_S5

description: Illumina sequencing


title: 180419_WT_2DL_undifferentiated_S1

description: Illumina sequencing


title: 16hrdex_BFP-rep3

value: BFP


title: 16hrdex_BFP-rep2


title: WT_Control_rep3


title: 181002_KO_6DL_unsorted_untreated_S6

description: Illumina sequencing

source_name: mTert-/- Embryonic stem cells


title: 6hr_ML1REV_rep4


title: 180419_WT_6DL_S1

description: Illumina sequencing


title: 16hrdex_BFP-rep1


title: 180222_KO_6DL_unsorted_untreated_S8

description: Illumina sequencing


title: 6hr_ML1BFP_rep4


title: 180419_KO_6DL_UNC2400_S6

description: Illumina sequencing


title: 180221_KO_6DL_UNC1999_S9

description: Illumina sequencing


title: 180221_KO_6DL_UNC2400_S10

description: Illumina sequencing


title: 6hr_ML1REV_rep1


title: 6hr_ML1REV_rep3


title: 180419_WT_6DA_S3

description: Illumina sequencing


title: 6hr_ML1BFP_rep3


title: 180423_KO_6DL_GSKJ5_S1

description: Illumina sequencing


title: 16hrdex_BFP-rep4


title: 6hr_ML1BFP_rep1


title: 180222_KO_6DL_GSKJ5_S3

description: Illumina sequencing


title: 180222_KO_6DL_GSKJ4_S2

description: Illumina sequencing


title: 180424_KO_6DL_GSKJ4_S2

description: Illumina sequencing


title: 16h_GFP_R2

value: GFP


title: 16h_GFP_R4


title: 16h_GFP_R3


title: 180419_KO_6DL_unsorted_untreated_S2

description: Illumina sequencing


title: 181002_KO_6DL_GSK343_7_S7

description: Illumina sequencing


title: 181002_KO_6DL_GSK343_1_S1

description: Illumina sequencing


title: 16h_GFP_R1


title: 180419_KO_6DL_UNC1999_S5

description: Illumina sequencing


title: 180423_KO_6DL_GSK343_S5

description: Illumina sequencing


title: 180221_KO_6DL_GSK343_S11

description: Illumina sequencing


title: 180419_KO_6DL_GFP_plus_S3

description: Illumina sequencing


title: 16h_BFP_R1


title: 16h_BFP_R2


title: 16h_BFP_R4


title: 16h_BFP_R3


title: 6hr_GFP_R2


title: 6hr_GFP_R3


title: 6hr_GFP_R4


title: 180222_KO_6DL_GFP_pos_S9

description: Illumina sequencing


title: 180419_KO_6DL_GFP_S4

description: Illumina sequencing


title: 6hr_GFP_R1


title: 180424_KO_6DL_A395N_S1

description: Illumina sequencing


title: 180222_KO_6DL_GFP_neg_S10

description: Illumina sequencing


title: 180423_KO_6DL_A395_S6

description: Illumina sequencing


title: 180222_KO_6DL_A395N_S1

description: Illumina sequencing


title: 6hr_BFP_R4


title: 6hr_BFP_R3


title: 180221_KO_6DL_A395_S12

description: Illumina sequencing


title: 6hr_BFP_R2


title: mirap_16h_r4

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all the samples were prepared using ‘TruSeq Stranded mRNA Library Prep Kit from Illumina'.

treatment_protocol: Plants were treated with 10 um dexamethasone for 8 or 16hr. About 6 SAM from 6 different T3 plants were quickly harvested and qucik forzen in liquid nitrogen for one biological replicate.

tag: transgenic line

tag: time point

value: 16 hr


title: 180221_KO_6DA_unsorted_S8

description: Illumina sequencing


title: 181002_KO_6DA_GFP_plus_S5

description: Illumina sequencing


title: mirap_8h_r3

value: 8 hr

tag: treatment


title: mirap_16h_r2


title: 180419_KO_6DA_GFP_plus_S5

description: Illumina sequencing

tag: strain


title: 180221_KO_6DA_GFP_pos_S6

description:
Illumina sequencing
processed data not applicable: sample failed QC and was not included in analysis


title: 180419_KO_6DA_GFP_neg_S6

description: Illumina sequencing


title: 180221_KO_6DA_GFP_neg_S7

description: Illumina sequencing


title: 181002_KO_2DL_undifferentiated_S3

description: Illumina sequencing


title: LHGap_16h_r3


title: mirap_8h_r1


title: 180222_KO_2DL_undifferentiated_S6

description: Illumina sequencing


title: LHGap_16h_r2


title: LHGap_8h_r2


title: 181002_KO_6DA_unsorted_S4

description: Illumina sequencing


title: LHGap_8h_r3


title: SureCell_sc_E18_4

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Barcode sequence was corrected by edit distance < 2.
corrected reads were processed using Drop-seq_tools-1.12.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are DigitalExpression generated using Drop-seq_tools, row and column indicate gene and cell barcode, respectively.

source_name: PBC Colony

growth_protocol: Peripheral blood cells were cultured with MesenCult medium.

extract_protocol:
Peripheral blood was collected from the heart and removed red blood cells.
Library was constructed by the SureCell protocol.

value: SureCell

value: Pa-GFP KI

tag: age


title: 180419_KO_2DL_undifferentiated_S2

description: Illumina sequencing


title: 180419_KO_6DA_unsorted_S4

description: Illumina sequencing


title: SureCell_sc_E18_2


title: SureCell_sc_E18_3


title: SureCell_sc_E18_1


title: YFP_rep2

data_processing:
The first phase of the data analysis pipeline was the quality control step. In this step, the quality of the raw sequencing data was assessed using the tool FastQC
Bases with bad quality (Phred score <20), over-represented PCR primers and bases with fluctuating GC content identified in this step were pruned using a combination of Cutadapt [citation] and Seqtk [citation] tools.
The second phase of quality control was the removal of rRNA reads from raw sequencing data.
For aligning the filtered raw data, we used the standard Arabidopsis genome annotation, TAIR10, and used TopHat tool.
we used the python package HTSeq to count the reads that are aligned to each genomic feature (exon) and to generate gene expression read count matrices. For identifying the deferentially expressed genes from the read count data, we used the R package DESeq2, which models read count data following a negative binomial distribution
Genome_build: Arabidopsis genome annotation, TAIR10
Supplementary_files_format_and_content: .csv file having gene ID and number of counts in tab delimited format

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all cell-types were prepared using ‘NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: About 50 SAMs of 4-5 week old plants were quickly harvested and placed in cell-wall dissolving enzyme solution in 70um cell-strainer in a small petridish. Protoplasts samples were sorted by the EMBL flow cytometry core facility using a special setup MoFlo XDP cell sorter from Beckman Coulter equipped with a Coherent Sabr Argon gas laser emitting at 514.5nm (400mW), a Coherent Innova gas laser emitting at 488nm (300mW), and a Coherent Obis 405nm solid state laser (240mW).

value: Only YFP positive cells in FACS sorting triple marker line containing REV-2YFP, KAN1-2GFP, ML1-BFP reporters


title: YFP_rep3


title: ATAC-seq distal radius - E15.5

data_processing:
alignment to mm10; Bowtie2 version 2.3.2; default parameters for mm10 alignment
filter for duplicates; MACS2 version 2.1.1.2; macs2 filterdup -i file -g mm --keep-dup 1 -o outfile;
peak calling; MACS2 version 2.1.1.2; macs2 callpeak -B -t rep1file -n name --nomodel --shift -100 --extsize 200
peak filtering ; IDR https://github.com/nboley/idr; idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 ?plot; MACS2 .narrowPeak output was cut using the number of peaks below the IDR threshold, sorting by MACS2 reported p-value
Genome_build: mm10
Supplementary_files_format_and_content: distal_femur_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the distal femur ATAC-seq experiment
Supplementary_files_format_and_content: distal_humerus_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the distal humerus ATAC-seq experiment
Supplementary_files_format_and_content: distal_radius_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the distal radius ATAC-seq experiment
Supplementary_files_format_and_content: distal_tibia_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the distal tibia ATAC-seq experiment
Supplementary_files_format_and_content: proximal_femur_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the proximal femur ATAC-seq experiment
Supplementary_files_format_and_content: proximal_humerus_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the proximal humerus ATAC-seq experiment
Supplementary_files_format_and_content: proximal_radius_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the proximal radius ATAC-seq experiment
Supplementary_files_format_and_content: proximal_tibia_IDR005_mm10.bed; bed format; contains the coordinates of the peaks called and filtered as described for the proximal tibia ATAC-seq experiment

source_name: Distal radial growth plates E15.5

growth_protocol: in vivo collected E15.5 growth plate chondrocytes

treatment_protocol: All experiments were performed following protocols approved by the Harvard University IACUC committee. Timed matings were established between FVB mice, and pregnant females were euthanized at E15.5 in order to acquire embryonic long bone growth plates. Embryos were dissected in PBS1X on ice under a dissection scope and the proximal and distal growth zones of the right and left femur were stripped clear of soft tissues. Each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis and separately pooled from a single litter, consisting on average of 8 animals. Two biological replicates were collected in line with previous ATAC-seq studies.

tag: tissue

value: Distal radial growth plates

value: chondrocytes

value: FVBNJ

value: tn5 transposase


title: LHGap_8h_r1


title: YFP_rep1

tag: cell type


title: GFP_rep3

value: Only GFP positive cells in FACS sorting triple marker line containing REV-2YFP, KAN1-2GFP, ML1-BFP reporters


title: mirap_16h_r3


title: mirap_8h_r2


title: GFP_rep2


title: ATAC-seq proximal radius - E15.5

source_name: Proximal radial growth plates E15.5

value: Proximal radial growth plates

tag: reagent


title: GFP_rep1


title: ATAC-seq proximal humerus - E15.5

source_name: Proximal humeral growth plates E15.5

value: Proximal humeral growth plates

tag: developmental stage


title: ATAC-seq distal humerus - E15.5

source_name: Distal humeral growth plates E15.5

value: Distal humeral growth plates


title: ATAC-seq distal tibia - E15.5

source_name: Distal tibial growth plates E15.5

value: Distal tibial growth plates


title: LHGap_16h_r1

value: Dex


title: ATAC-seq proximal tibia - E15.5

source_name: Proximal tibial growth plates E15.5

value: Proximal tibial growth plates


title: BFPYFP_rep3

value: BFP YFP double positive cells in FACS sorting triple marker line containing REV-2YFP, KAN1-2GFP, ML1-BFP reporters


title: ATAC-seq distal femur - E15.5

value: Distal femoral growth plates


title: BFPYFP_rep2


title: BFPGFP_rep3

value: BFP GFP double positive cells in FACS sorting triple marker line containing REV-2YFP, KAN1-2GFP, ML1-BFP reporters


title: ATAC-seq proximal femur - E15.5

value: Proximal femoral growth plates


title: BFPYFP_rep1


title: BFPGFP_rep2


title: BFPGFP_rep1


title: BFP_rep3

value: Only BFP positive cells in FACS sorting triple marker line containing REV-2YFP, KAN1-2GFP, ML1-BFP reporters


title: dntrB_3

city: Vancouver

first: Robert

middle: EW

last: Hancock

state: BC

address: 2259 Lower Mall Research Station

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
Quality control using fastqc (v0.11.7) and multiqc (v1.6)
Alignment to the P. aeruginosa PA14 genome using STAR (v2.6.0a)
Read counting using htseq-count (v0.10.0)
Genome_build: Pseudomonas aeruginosa UCBPP-PA14 (GCF_000014625.1)
Supplementary_files_format_and_content: CSV file of raw unfiltered counts from htseq-count

organism: Pseudomonas aeruginosa

source_name: Swarming BM2 plates

growth_protocol: PA14 strains were subcultured to an OD600 = 0.4-0.6 and spot cultured on BM2 swarming plates for 18-24 h at 37°C. Actively swarming cells were harvested from the tips of tendrils in RNA Protect reagent (Qiagen).

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications. Deoxyribonucleases were removed using the TURBO DNA-free kit (Thermo Fisher) and rRNA was depleted using the RiboZero Bacteria Kit (Illumina).
Single-end cDNA libraries were  constructed using a KAPA stranded Total RNA Kit (KAPA Biosystems).

value: dntrB

tag: batch

value: two


title: BFP_rep2


title: dntrB_2

value: one


title: dntrB_1


title: Allneg_rep3

value: Negative cells in FACS sorting triple marker line containing REV-2YFP, KAN1-2GFP, ML1-BFP reporters


title: dntrC_2

value: dntrC


title: Allneg_rep2


title: MCF7_R2

city: Valencia

first: Sara

last: OLTRA SANCHIS

state: Valencia

address: Avda Menéndez Pelayo, 4 accesorio

department: Medical Oncology

country: Spain

institute: INCLIVA

hyb_protocol: Hybridization and scanning were performed according to the Affymetrix standard protocol, using Affymetrix Expression Console software.

data_processing: Data quality of *.CEL sample files was analyzed by affy package from R/Bioconductor

organism: Homo sapiens

label_protocol: not provided

growth_protocol: Cell lines were cultured in RPMI 1640 medium supplemented with 1% L-glutamine and 10% fetal bovine serum (GIBCO, New York, NY).  The culture conditions were identical in all cell lines: 37 ̊C and 5% CO2.

extract_protocol: Total RNA from BC cell lines was isolated in passage 4 using High Pure RNA Isolation Kit from Roche following the manufacturer’s protocol

value: breast cancer cell line

tag: patient age

value: old


title: dntrC_1


title: wt_3

value: wildtype


title: MCF7_R3

scan_protocol: Hybridization and scanning were performed according to the Affymetrix standard protocol, using Affymetrix Expression Console software.


title: wt_2


title: Allneg_rep1


title: wt_1


title: MDA_MB_468_R2


title: MDA_MB_468_R3


title: 76_MF2

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description:
4_MF2 infected versus non-infected 24 hours.xlsx
76_MF2_GCCAAT_L001_R1_001

data_processing:
Base calling was done by the Illumina HCS version 1.15.1
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts
RNA-seq was performed using an Illumina Hi-Seq 2500 as previously described (Marin-Juez R, Jong-Raadsen S, Yang S, Spaink HP. Hyperinsulinemia induces insulin resistance and immune suppression via Ptpn6/Shp1 in zebrafish. The Journal of endocrinology. 2014;222(2):229-41.). The RNA-seq data were mapped versus the human genome (version GRCH38) and tag counts were performed by Bowtie 2 using GeneTiles software (http://www. genetiles.com) (Veneman WJ, de Sonneville J, van der Kolk KJ, Ordas A, Al-Ars Z, Meijer AH, et al. Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics. Immunogenetics. 2015;67(3):135-47.).
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq2 package (Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550).
False discovery rate (FDR)-adjustedPvalues were calculated based on the algorithm ofBenjamini & Hochberg (1995).
Genome_build: GRCH38
Supplementary_files_format_and_content: Microsoft Excel files include non-normalized and normalized (per million reads) values for each sample

source_name: CD14+ monocytes

growth_protocol: CD14+ monocytes were isolated from buffy coats of one single healthy blood bank donor by positive selection using an autoMACS Pro Separator (Miltenyi Biotec BV, Leiden, The Netherlands). Monocytes were differentiated into macrophages using 50 ng/ml macrophage colony-stimulating factor (M-CSF; Miltenyi Biotec) or 5 ng/ml granulocyte-macrophage colony-stimulating factor (GM-CSF; Miltenyi Biotec) for six days at 37°C/5%CO2. Cells were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS), 100 units/ml penicillin and 100 µg/ml streptomycin and GlutaMAX (Gibco, Thermo Fisher, Merelbeke, Belgium). After differentiation macrophages were harvested by trypsinization and seeded in multiwell plates. As a quality control, macrophages were stained for surface expression of CD14 and CD163 and acquired on a BD LSRFortessa flow cytometer (BD Biosciences, Erembodegem, Belgium).

extract_protocol:
RNA was extracted using TRIzol Reagent (Thermo Fisher) at 4 and 24 h post-infection and purified using RNeasy MinElute Cleanup Kit (Qiagen, The Netherlands). The concentration and purity of RNA was evaluated by NanoDrop 2000 (Thermo Fisher).
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina protocols were used for RNA-seq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina,Inc., San Diego, CA, USA). The manufacturer’s instructionswere followed with the exception of two modifications. Inthe adapter ligation step, 1ml, instead of 2.5ml, adaptor was used.

treatment_protocol: Mtb H37Rv cultures were grown to mid-log phase in Middlebrook 7H9 liquid medium (Difco, BD Biosciences) supplemented with albumin/dextrose/catalase (ADC) (BBL, BD Biosciences). Bacterial concentrations were determined by measuring the culture optical density at 600nm. Macrophages were infected with H37Rv at a multiplicity of infection (MOI) of 10:1 for 1 hour at 37°C, after which the cells were washed twice with medium containing 30 µg/ml gentamicin and further cultured for 4 or 24 h in fresh medium containing 5 µg/ml gentamicin. MOI was confirmed by plating a dilution series of the inoculum on 7H10 square agar plates supplemented with oleate/albumin/dextrose/catalase (OADC) (BBL, BD Biosciences).

value: Human macrophages MF2

tag: bacterial infection

value: Uninfected

tag: moi

value: 10:1 for 1 hour at 37°C

value: 24 hours


title: MDA_MB_468_R1


title: MDA_MB_231_R3


title: BFP_rep1


title: 73_MF2

description:
4_MF2 infected versus non-infected 24 hours.xlsx
73_MF2_CGATGT_L001_R1_001


title: dntrC_3

tag: genotype


title: 70_MF2

description:
4_MF2 infected versus non-infected 24 hours.xlsx
70_MF2_GAGTGG_L004_R1_001


title: MDA_MB_231_R1

tag: cell line


title: MCF7_R1


title: 64_MF2

description:
4_MF2 infected versus non-infected 24 hours.xlsx
64_MF2_GATCAG_L002_R1_001

value: Mtb H37Rv


title: 67_MF2

description:
4_MF2 infected versus non-infected 24 hours.xlsx
67_MF2_GTGGCC_L002_R1_001


title: HCC1937_R3

value: young


title: 61_MF2

description:
4_MF2 infected versus non-infected 24 hours.xlsx
61_MF2_ATCACG_L002_R1_001


title: 58_MF1

description:
3_MF1 infected versus non infected 24 hours.xlsx
58_MF1_CCGTCC_L004_R1_001

value: Human macrophages MF1


title: MDA_MB_231_R2


title: 55_MF1

description:
3_MF1 infected versus non infected 24 hours.xlsx
55_MF1_AGTCAA_L008_R1_001


title: metM_Wnt_FA withdrawal_replicate3

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

hyb_protocol: Samples were hybridized to custom two-color 180K Agilent microarrays (BARCODE25503)

scan_protocol: Samples were scanned using an Agilent Technologies Scanner G2505C

data_processing: Data were read and processed using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: metM_Wnt withdrawal

label_protocol: Complementary RNA (cRNA) was generated using a Low Input Quick Amp labeling kit (Agilent, Santa Clara, CA) with NIH3T3 cells as reference RNA.

growth_protocol: E-Wnt, M-Wnt and metM-Wnt cells were cultured in 10-cm plates for 72 hours using either standard RPMI 1640 medium (containing 2.2 µM folic acid) with 10% fetal bovine serum (FBS) or RPMI 1640 medium without folic acid with dialyzed FBS.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's intructions.

value: metM-Wnt

value: folic acid withdrawal

value: liver metastasis

source_name: NIH3T3 cells

tag: type

value: Common reference


title: HCC1937_R2


title: HCC1806_R3


title: metM_Wnt_FA withdrawal_replicate2


title: metM_Wnt_FA withdrawal_replicate1


title: 6hr_BFP_R1

value: Dex

tag: tissue-type

value: epidermis

tag: fluroscence protein

value: BFP


title: metM_Wnt_control_replicate3

source_name: metM_Wnt control

value: control condition


title: metM_Wnt_control_replicate1


title: HCC1937_R1

value: breast cancer cell line


title: M_Wnt_FA withdrawal_replicate2

source_name: M_Wnt withdrawal

value: M-Wnt

value: mammary tumor


title: HCC1500_R3


title: HCC1806_R2

value: old


title: HCC1806_R1


title: M_Wnt_FA withdrawal_replicate3


title: M_Wnt_control_replicate2

source_name: M_Wnt control


title: E_Wnt_FA withdrawal_replicate2

source_name: E_Wnt withdrawal

value: E-Wnt


title: M_Wnt_control_replicate3


title: HCC1500_R2


title: 52_MF1

description:
3_MF1 infected versus non infected 24 hours.xlsx
52_MF1_GCCAAT_L008_R1_001

value: Uninfected

value: 10:1 for 1 hour at 37°C

tag: time point

value: 24 hours


title: E_Wnt_FA withdrawal_replicate3

tag: treatment


title: 49_MF1

description:
3_MF1 infected versus non infected 24 hours.xlsx
49_MF1_CGATGT_L008_R1_001

value: Human macrophages MF1

value: Mtb H37Rv


title: HCC1500_R1

value: young


title: M_Wnt_control_replicate1


title: 46_MF1

description:
3_MF1 infected versus non infected 24 hours.xlsx
46_MF1_GAGTGG_L001_R1_001


title: E_Wnt_FA withdrawal_replicate1

value: folic acid withdrawal


title: 2607: KSHV (-) tumor

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The DNA libraries were sequenced on Illumina HiSeq2000, with HiSeq rapid 100PE.
Data analysis was performed on the Partek flow platform, raw reads were aligned to the mouse genome mm10 (GRCm38/mm10) with BWA
Mapped reads were analyzed with MACS2 to generate peaks and annotate differentially methylated regions. Peaks with False discovery rate (FDR) ≤5% & Fold change (FC) ≥2, were considered differentially methylated.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files includes peak size, chromosome and start end locations, and fold enrichment.

source_name: KSHV-negative mECK36 tumors

growth_protocol: mECK36 cells KSHV (+) were obtained and cultured as previously described (Mutlu et al., 2007). mECK36 KSHV (+) tumors were obteined as previously described (Mutlu et al., 2007). KSHV (-) tumor cells were obtained from mECK36 tumor explants after Bac36 episome loss achieved by growth without hygromycin selection as previously described (Mutlu et al., 2007). KSHV (-) tumors were obteined by subcutaneous injection of KSHV (-) tumor cells in nude mice as previously described (Ma et a., 2013).

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (QIAGEN) and sheared by sonication to fragments of ~500bp.
Methylated DNA enrichment protocol: The sheared DNA (1µg) was added to 10 µl MBD-Bead slurry (MethylMiner DNA Enrichment Kit, Invitrogen, Carlsbad, CA) and incubated on a rotating mixer for 1 hr, as described previously [49]. The DNA fragments were eluted into distinct subpopulations based on the degree of methylation; non-captured fraction (NC, representing un-methylated DNA fragments), 450 mM NaCl (representing partially methylated DNA fragments) and 2000 mM NaCl (representing methylated DNA fragments). The fractions were then ethanol precipitated and re-suspended in H2O.
MBD2 enriched methylated DNA fractions were subjected to library preparation with NEBNext® Ultra™ II DNA library prep kit for Illumina (NEB #E7645) at the next generation genomic center in the Azrieli Faculty of Medicine, Bar-Ilan University.

value: KSHV-negative mECK36 tumors


title: 2608: KSHV (+) tumor

source_name: KSHV-positive mECK36 tumors

value: KSHV-positive mECK36 tumors


title: E_Wnt_control_replicate3

source_name: E_Wnt control

value: Common reference


title: E_Wnt_control_replicate2


title: M_Wnt_FA withdrawal_replicate1


title: 40_MF2

description:
2_MF2 infected versus non-infected 4 hours.xlsx
40_MF2_GATCAG_L007_R1_001

value: Human macrophages MF2

value: 4 hours


title: E_Wnt_control_replicate1

value: control condition


title: 2603: KSHV (+) tumor


title: 2604: KSHV (+) cell

source_name: KSHV-positive mECK36 cells

value: KSHV-positive mECK36 cells


title: 43_MF1

description:
3_MF1 infected versus non infected 24 hours.xlsx
43_MF1_GTGGCC_L007_R1_001


title: 37_MF2

description:
2_MF2 infected versus non-infected 4 hours.xlsx
37_MF2_ATCACG_L007_R1_001


title: 2602: KSHV (-) tumor


title: 2601: KSHV (-) tumor cells

source_name: tumorigenic KSHV-negative mECK36 cells

value: tumorigenic KSHV-negative mECK36 cells


title: 2600: KSHV (-) cell

source_name: KSHV-negative mECK36 cells

value: KSHV-negative mECK36 cells


title: 34_MF2

description:
2_MF2 infected versus non-infected 4 hours.xlsx
34_MF2_CCGTCC_L005_R1_001


title: male_vnc_rep2

city: Oxford

first: Aaron

middle: Munro

last: Allen

address: Tinsley Building, Mansfield Road

department: DPAG

country: United Kingdom

institute: University of Oxford

data_processing:
Drop-seq_tools v2.1.0 to extract cell tag, extract molecule tag, trim polyA (12 bases)
STAR aligner to Drosophila melanogaster genome R6.13, aligned intron max of 200000
Drop-seq_tools v2.1.0 to merge tags and aligned reads, and make digital expression matrix
code available at https://github.com/aaron-allen/VNC_scRNAseq
Genome_build: Drosophila melanogaster genome release 6.13
Supplementary_files_format_and_content: digital expression matrix: rows = cell barcodes, columns = genes

organism: Drosophila melanogaster

source_name: ventral nerve cord

growth_protocol: All flies were reared at 25°C in a 12:12 hr light:dark cycle on standard food at 40-50% relative humidity. Virgin males and females were collected and stored individually. Flies were aged 5 days post-eclosion at 25°C prior to dissection.

extract_protocol:
The VNC dissociation protocol was carried out as described previously (Croset et al., 2018).
Libraries were prepared following the 10x Chromium Single Cell 3’ Reagent Kits v2 User Guide.

tag: Sex

value: male

value: +/Y; {UAS-Stinger}, {13XLexAop2-IVS-tdTomato.nls}/+; dsx[GAL4]/+

value: ventral nerve cord

value: 5-day old adult


title: 31_MF2

description:
2_MF2 infected versus non-infected 4 hours.xlsx
31_MF2_AGTCAA_L005_R1_001

value: 10:1 for 1 hour at 37°C


title: 2599: KSHV (+) cell


title: HFD_caloric_restriction_rep5

city: Boston

first: Qiong

last: Zhou

address: 1 Joslin PLace

institute: Joslin Diabetes Center

hyb_protocol: Approximately 3.5 ug cDNA was hybridized to GeneChip Mouse Gene 2.0 ST arrays for 16 hours at 45°C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with reagents from Affymetrix.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

data_processing: The data were normalized on Expression Console using RMA.

label_protocol: Fragmented and labeled cDNA were prepared according to the WT Plus Affymetrix protocol from 250 ng total RNA.

growth_protocol: 6 weeks old male C57Bl/6J were treated with 60% high fat diet (HFD) ad libitum for 4 weeks to induced obesity

extract_protocol: Total RNA was isolated from mice treated for 4 weeks in each of the 3 experimental groups (n=3-5 per group) using TRIzol (Life Technologies) and choloroform. RNA pellet were washed with propanol and 75% ethanol.

treatment_protocol: Mice were treated with either (1) Continued HFD for additional 4 weeks (2) HFD +canagliflozin (25-30mg/kg) (3) Weight match control to group(2) with 15-30% caloric restriction.

tag: strain

tag: sample group

value: weight-match control with 15-30% caloric restriction


title: HFD_caloric_restriction_rep4


title: male_vnc_rep1

tag: tissue


title: HFD_CANA_rep4

value: HFD +canagliflozin (25-30mg/kg)


title: HFD_rep4

source_name: HFD

value: Continued HFD for additional 4 wks


title: KPC 4662 p12

source_name: KPC 4662 cell line isolated from pancreatic ductal adenocarcinoma of a GEM mouse

value: WT Rab27a (parental control)


title: 28_MF2

description:
2_MF2 infected versus non-infected 4 hours.xlsx
28_MF2_GCCAAT_L003_R1_001

tag: cell type

value: Mtb H37Rv


title: 2598: KSHV (+) tumor

value: KSHV-positive mECK36 tumors


title: female_vnc_rep2

value: female

value: +/w*; {UAS-Stinger}, {13XLexAop2-IVS-tdTomato.nls}/+; dsx[GAL4]/+

tag: developmental stage


title: 2597: KSHV (-) tumor

value: KSHV-negative mECK36 tumors


title: female_vnc_rep1


title: 25_MF2

description:
2_MF2 infected versus non-infected 4 hours.xlsx
25_MF2_CGATGT_L005_R1_001

value: Human macrophages MF2

value: 4 hours


title: 2595: KSHV (-) cell

value: KSHV-negative mECK36 cells


title: HFD_CANA_rep3

value: male


title: HFD_rep3


title: 22_MF1

description:
1_MF1 infected versus non infected 4 hours.xlsx
22_MF1_GAGTGG_L003_R1_001

value: Human macrophages MF1

value: Uninfected


title: 2596: KSHV (-) tumor cells

value: tumorigenic KSHV-negative mECK36 cells


title: HFD_caloric_restriction_rep3


title: 2594: KSHV (+) cell

value: KSHV-positive mECK36 cells


title: 19_MF1

description:
1_MF1 infected versus non infected 4 hours.xlsx
19_MF1_GTGGCC_L002_R1_001

value: 10:1 for 1 hour at 37°C


title: 2606: KSHV (-) tumor cells


title: 587680_47

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads aligned to Danio_rerio.GRCz11 (release 94) and processed using Cell Ranger v2.1.1
Counts extracted using scanpy in python
Genome_build: Danio_rerio.GRCz11 (release 94)
Supplementary_files_format_and_content: Counts: Mapped read counts per gene, per cell

organism: Danio rerio

source_name: Injured runx1 KO

growth_protocol: Adult wild-type (wt) (KCL strain), Tg(kdrl:Hsa.HRAS-mCherry)34 (subsequently referred to as Tg(kdrl:mCherry)) and runx1W84X mutants27, TgBAC(runx1P2:Citrine)29  were housed in a Techniplast aquarium system [28 °C, 14/10 hours light/dark cycle, fed 3x daily with dry food and brine shrimp]. All double transgenic lines on wild-type or mutant background were generated by natural mating.

extract_protocol:
Hearts were extracted and transferred to Ringer solution with heparin sodium salt (50 U/ml) (Ringer composition: 7.2 g NaCl, 0.225g CaCl2.H2O, 0.37 g KCl, 0.2175g Na2HPO4.7H2O, 0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit) and rinsed once with Phosphate buffered saline (PBS) or directly isolated in PBS. Hearts were inspected, cleaned and then fixed with 4% Paraformaldehyde (PFA) overnight (O/N) on nutator at room temperature (RT). Samples were rinsed once in PBS, dehydrated into Ethanol (EtOH) at 70%, 80%, 90%, 96%  for 2 hours each step and 2x100% for 1 hour each step, followed by a 100% 1-butanol step overnight. The samples were then transferred to paraffin (Paraplast Plus, Sigma-Aldrich P3683) wax at 65°C.
Cells were washed in PBS with 0.04% BSA and re-suspended before loading 12,000-12,500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584). Quantification of library construction was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584).

treatment_protocol: A small incision was made through the thorax and the pericardium using forceps and spring scissors. The abdomen was gently squeezed to expose the ventricle and tissue paper was used to dry the heart. A cryo-probe with a copper filament was cooled in liquid nitrogen and placed on the ventricle surface until thawing was observed. Body wall incisions were not sutured, and after surgery, fish were returned to water and stimulated to breathe by pipetting water over the gills until the fish started swimming again. For sham surgery, the thorax and pericardial sac were opened, but the heart was not injured. All operated fish were kept in individual tanks for the first week after surgery, then fish were combined in larger tanks.

value: Heart (Ventricle)  (pool 20 hearts)

value: KCL

value: runx1 KO

value: injured


title: 587680_46

source_name: Injured Wild Type

value: WT


title: HFD_caloric_restriction_rep2

value: weight-match control with 15-30% caloric restriction


title: 16_MF1

description:
1_MF1 infected versus non infected 4 hours.xlsx
16_MF1_GATCAG_L002_R1_001

source_name: CD14+ monocytes


title: 587680_45

source_name: Uninjured Wild Type

value: uninjured


title: 13_MF1

description:
1_MF1 infected versus non infected 4 hours.xlsx
13_MF1_ATCACG_L002_R1_001

value: Mtb H37Rv


title: HFD_rep2

value: Continued HFD for additional 4 wks


title: 10_MF1

description:
1_MF1 infected versus non infected 4 hours.xlsx
10_MF1_CCGTCC_L003_R1_001

value: 4 hours


title: 7_MF1

description:
1_MF1 infected versus non infected 4 hours.xlsx
7_MF1_AGTCAA_L001_R1_001


title: KO_6DL_UNC1999_n_3

description: Illumina sequencing

data_processing:
Libraries were sequenced with 100 bp single-end reads
Sequences were mapped to mm9 using Bowtie 2 (v2.0.5) with default parameters (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
Poor quality reads (MAPQ<=30, reads mapping to chrM, chrY and patch chromosomes were also removed.
Reads were further filtered to remove PCR duplicates using Picard Tool MarkDuplicates (v2.6.0, https://broadinstitute.github.io/picard/). H3K27me3 peaks were called using MACS2 v2.0.10 using the following parameters: --keep-dup all -B -- broad -q 0.05.
The signal intensity was calculated as the fold enrichment of the signal per million reads in a sample over the input sample. We then calculated the maximum signal intensity over every peak for conditions being compared using mapBed –o max and quantile normalized them across samples.
Spearman correlation was then calculated between average normalized signal intensity across replicates for each condition which was then plotted in heatmap. Analysis of downstream peak calling were carried out using Bedtools v2.26.0 (https://bedtools.readthedocs.io/en/latest/) and R 3.4.1 (https://www.r-project.org/). Figures were plotted using ggplot2 (https://ggplot2.tidyverse.org/).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: Tert-/- Embryonic stem cells

growth_protocol: Murine embryonic stem cells were thawed (initial cell passage indicated), cultured in LIF containing media for 2 days (2DL), transferred to media containing 5 micromolar ATRA for a further 6 days (6DA) and transferred to LIF-containing media for a further 6 days (6DL).

extract_protocol:
ESC populations were harvested and crosslinked in formaldehyde. Cell pellets (frozen, or fresh) were subjected to chromatin preparation and immunopreciptiation with an antibody against H3K27me3, followed by extraction of genomic DNA.
DNA samples were quantified, and libraries were generated and amplified by PCR, followed by library size determination using a Agilent BioAnalyzer.
Libraries were then pooled, quantified, and sequenced on an Illumina MiSeq to determine the amount required for deep sequencing. Pooled libraries were then diluted accordingly and loaded on an Illumina NovSeq6000 for sequencing.

treatment_protocol: ESC populations were untreated (DMSO) or treated throughout the 14 day differentiation treatment with the compounds indicated: UNC1999, UNC2400, GSK343. The compound concentration was 1 micromolar for UNC1999 and UNC2400, and 3 micromolar GSK343.

tag: sequencing run#

tag: passage numbers

tag: treatment group

tag: sample preparation

value: ChIP-seq


title: PBS_3

city: San Antonio

first: Chiung-Yu

last: Hung

state: Texas

address: One UTSA Circle

department: Biology

institute: The University of Texas at San Antonio

data_processing:
Illumina HiSeq 3000 platform (50 bp single-read module)
Sequencing reads were preprocessed by Trim Sequences tools in CLC Genomics workbench. Remaining reads were then aligned to mouse GRCm38(mm10) reference genome using RNA-Seq Analysis module in CLC Genomics workbench.
To determine differentially expressed genes, exact test were performed after filtering lowly expressed gene (counts per million < 1 in more than three samples across the dataset) using edgeR package (Robinson, McCarthy et al. 2010).
Gene Ontology (GO) analysis were performed using DAVID (Dennis, Sherman et al. 2003) and then visualized by GOplot (Walter, Sanchez-Cabo et al. 2015).
The causal network analysis was performed using Ingenuity Pathway Analysis (IPA) software (Qiagen, Redwood City, CA) (Ashburner, Ball et al. 2000; Conesa, Madrigal et al. 2016).
Genome_build: Release M15 of GRCm38 downloaded from GENCODE
Supplementary_files_format_and_content: txt file shows raw counts and csv file shows statistics for each sample

growth_protocol: Bone marrow-derived macrophages (BMMs) were prepared from femurs and tibiae of mice as previously described(Campuzano, Castro-Lopez et al. 2017). Briefly, bone marrow cells were washed, counted and plated at a concentration of 4 x 105 cells/ml in RPMI 1640  medium supplemented with 10% heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 U penicillin/ml, 100 µg of streptomycin/ml, 50 mM 2-mercaptoethanol and  20 ng/ml of murine M-CSF (Peprotech).  Cells were incubated at 37oC and 5% CO2, half the medium replaced every three days, and cells harvested on day 7. BMMs were washed and incubated with macrophage detachment solution DXF (PromoCell) for 40 mins at 4oC.

extract_protocol:
RNA was harvested using Qiagen Rneasy kit. Preparation of sequencing libraries and sequencing analysis using Illumina HiSeq 3000 platform (50 bp single-read module)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMMs were either stimulated with GCP-rCpa1 at a ratio of 50:1 (GCP-rCpa1 particle: BMMs) or an equal volume of PBS for 12 hours in 5% CO2. The cells were spun down and RNA was extracted as mentioned in summary.

tag: age

value: 6-8 weeks old

tag: genotype/variation

value: wild type

value: Bone marrow derived macrophages (BMDMs)

value: PBS (control)


title: HFD_caloric_restriction_rep1

value: male


title: PBS_2


title: HFD_CANA_rep1

value: HFD +canagliflozin (25-30mg/kg)


title: KO_6DL_UNC1999_n_3_input

description: Illumina sequencing


title: Small-RNA seq of ERH gRNA2 control cells

first: Wenwen

last: Fang

state: Massachusetts

address: Room 625, 455 Main Street

institute: Whitehead Institute

description: gel purified small RNA

data_processing:
Cut 3' adapter and NNNN at both ends of the read.
Quality filter using fastq_quality_filter, -q 30 -p 100.
Count all the reads that are assigned to a particular miRNA (containing an exact match to the first 18 nt of the miRNA) for all human miRNAs.

source_name: K562-dCas9-KRAB cells

growth_protocol: K562-dCas9-KRAB cells were cultured in RPMI 1640 Media supplemented with 10% FBS at 37°C with 5% CO2.

extract_protocol:
After 5 d of +/- doxycycline induction, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.
A detailed protocol for making small-RNA seq libraries is available at http://bartellab.wi.mit.edu/protocols/Small_RNA_library_prep_2017.pdf.

treatment_protocol: Doxycycline-inducible polyclonal cell lines were made following Gilbert et al. (2014). To induce knockdown, 0.05 µg/ml doxycycline was added the media.

tag: cell line

value: K562-dCas9-KRAB cells

value: control


title: GCP_3

value: GCP-rCpa1 at a ratio of 50:1 for 12 hours with 5% CO2


title: KO_6DL_UNC2400_n_3

description: Illumina sequencing


title: Small-RNA seq of ERH gRNA2 KD cells

description: gel purified small RNA

value: ERH knockdown


title: KO_6DL_GSK343_n_3

description: Illumina sequencing


title: GCP_2


title: GCP_1


title: KO_6DL_UNC2400_n_3_input

description: Illumina sequencing


title: WT-Pd(II) rep2

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2/ASM798v2 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq software
Genome_build: GCF_000007985.2
Supplementary_files_format_and_content: tab-delimited text file include the differential expression results of DESeq and raw and normalized counts  for each sample. First column is the ID gene. Columns from 2 to 8 are the DESeq results including: log2FoldChange (column 6) and padjust  (column 8). Columns 9 and 10 are WT-PdII  raw counts, columns 11 and 12 are WT-NBAF raw counts, columns 13 and 14 are WT-PdII  normalized counts and columns 15 and 16 are WT-NBAF normalized counts.

organism: Geobacter sulfurreducens PCA

source_name: Geobacter sulfurreducens in Pd(II) reduction

growth_protocol: The cells were grown anaerobically at 30 oC in NBAF medium, supplemented with acetate and fumarate. For experiments conducted under “Pd(II)-reducing” conditions, late logarithmic phase cultures of G. sulfurreducens were used.

extract_protocol:
For each biological sample, total RNA samples were extracted using the RNeasy mini kit (Qiagen), then they were examined with an Agilent 2100 Bioanalyzer and quantified using NanoDrop 200c (Thermo Scientific).
Illumina sequencing was performed at the UUSMD (UNAM, Mexico). After removing residual DNA using DNase I (ThermoScientific) and ribosomal RNA with Terminator 5´-Phosphate-dependent exonuclease (Epicentre), the mRNA-enriched RNA was chemically fragmented to 150~200 bp. Based on these cleaved RNA fragments, cDNA was synthesized using a random hexamer primer and reverse transcriptase. After end reparation and ligation of adaptors, the products were amplified by PCR, further purified, and used to create the final cDNA library. Libraries were sequenced on an Illumina Genome Analyzer IIx.

treatment_protocol: RNA Later (Ambion) was added to cultures before harvesting cells

value: PCA

tag: donor /acceptor electrons

value: Acetate/Pd(II)


title: WT-Pd(II) rep1


title: HFD_CANA_rep2


title: HFD_rep1


title: NormalFibroblast_primary_05_rep1

city: Budapest

first: Alexandra

last: Fullár

address: Üllői út 26

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

description: Gene expression of primary fibroblast from tumor free cervix tissue

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffers (Agilent) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Patient 05

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Fresh surgical specimens obtained from radical Wertheim hysterectomy were sent for routine pathology service. Tumorous and normal areas of surgical specimens taken from the same patient and not used for diagnosis were excised and cut into small pieces and placed into sixwell tissue culture dishes containing Cytogen Amnio Grow Plus medium (CytoGen GmbH, Sinn, Germany), optimized for development of primary cell culture.

extract_protocol: Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen). Integrity of RNA was confirmed on Experion Automated Electrophoresis System (Bio-Rad Laboratories GmbH, Münich, Germany).

tag: patient number

value: Patient 05

value: primary fibroblasts from normal regions of uterine cervix

tag: fibroblast type

value: normal fibroblast


title: TumorAssocFibroblast_primary_01_rep1

description: Gene expression of primary fibroblast from tumorous cervix tissue

source_name: Patient 01

value: Patient 01

value: primary fibroblasts from tumorous regions of uterine cervix

value: tumor-associated fibroblast


title: KO_6DL_GSK343_n_3_input

first: Lea

last: Harrington

description: Illumina sequencing

value: ChIP-seq


title: Small-RNA seq of ERH gRNA1 KD cells

city: Cambridge

description: gel purified small RNA


title: NormalFibroblast_primary_02_rep1

source_name: Patient 02

value: Patient 02


title: KO_6DL_DMSO_n_3

city: Montreal

description: Illumina sequencing


title: WT-NBAF rep2

source_name: Geobacter sulfurreducens in NBAF medium

value: Acetate/Fumarate


title: PBS_1

value: 6-8 weeks old

value: wild type

value: Bone marrow derived macrophages (BMDMs)

tag: treatment

value: PBS (control)


title: case12_F-1

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a  75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks ver.2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: leukemic cells from peripheral blood in case 12 patients with acute/chronic type of disease

extract_protocol:
Total RNA samples were prepared by miRNeasy-Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
Library preparation was performed using the Clontech SMARTer Stranded RNA-Seq kit according to the manufacturer’s instructions.

treatment_protocol: PBMCs from ATLL patients were separated into CD4+ CD7- CADM1+ ATLL cells and adjacent CD4+CD7+CADM1- normal T cells using Fluorescence-activated Cell Sorter (FACS Aria, Becton, Dickinson and Company: BD, United States)

tag: case no.

tag: subject status

value: Adult T-cell leukemia/lymphoma (ATLL) patient

tag: gender

value: male

tag: atll type

value: acute/chronic

value: leukemic cells


title: KO_6DL_DMSO_n_3_input

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

institute: University of Montreal

description: Illumina sequencing

tag: strain


title: Small-RNA seq of ERH gRNA1 control cells

description: gel purified small RNA

value: K562-dCas9-KRAB cells

value: control


title: TumorAssocFibroblast_primary_03_rep1

source_name: Patient 03

value: Patient 03

tag: cell type


title: WT_6DL_UNC2400_n_2

description: Illumina sequencing

source_name: wild-type Embryonic stem cells

tag: sequencing run#


title: NormalFibroblast_primary_04_rep1

source_name: Patient 04

value: Patient 04

value: primary fibroblasts from normal regions of uterine cervix

value: normal fibroblast


title: case3_HT-N

source_name: normal cells from peripheral blood in case 3 patients with chronic type of disease

value: female

value: chronic

value: normal CD4+ cells


title: WT_6DL_UNC2400_n_2_input

description: Illumina sequencing

tag: passage numbers

value: ChIP-seq


title: mix60_mrna

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description: Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry) with 60 minute 37C incuabtion prior to RT. A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/rnabioco/rhumba/tree/master/haircut). Single cell RNA-Seq libraries were preprocessed using the 10x genomics software cellranger (3.0.2). The single cell DNA repair libraries were preprocessed to append the read 1 sequence to the paired read 2 read id using umi_tools extract(v 1.0.0 --bc-pattern CCCCCCCCCCCCCCCCNNNNNNNNNN)(Smith et al. 2017) followed by poly(A) tail and template switching oligo removal from read 2 using cutadapt (v. 1.8.3 -a AAAAAAAAAAA -g AAGCAGTGGTATCAACGCAGAGTACATGGG --minimum-length=2)  (Martin 2011). Reads were next aligned with bowtie2 (v 2.3.2 Langmead B, Salzberg S. 2012) to a repair substrate reference.     Following alignment, BAM files were processed to extract the alignment hairpin and position into a tag (XT) within the BAM file (tag_bam). UMI groups were identified and added as a tag (CB) using umi_tools group (--read-length = True --per-cell --output-bam = True --output-unmapped = True). BAM files were then sorted by cell barcode tag using samtools sort (v 1.5-4 -t CB -@ 23) (Li 2009). UMIs per hairpin_position were enumerated per cell using umi-tools count (v 0.5.3) (Smith et al. 2017) using the directional method to disambiguate similar UMI sequences.    Count tables produced by umi_tools are then converted into sparseMatrix format using the scrunchy R package (https://github.com/hesselberthlab/scrunchy, umitools_to_mtx). Matrices are the filtered to include only the cell-associated barcodes using the scrunchy R package (filter_matrix). Cell-associated barcodes are identified from the mRNA data using cellranger (v 3.0.2) from the filtered barcodes.tsv output.
Genome_build: hg38, custom repair substrate reference
Supplementary_files_format_and_content: Text file containing cell barcodes, genes/features, and UMI counts per gene/fetaure per cell are provided

source_name: 1:1 mix of UNGKO Hap1 cell line and RNASEH2CKO Hap1 cell line

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 60 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: case3_HT-P

source_name: leukemic cells from peripheral blood in case 3 patients with chronic type of disease


title: NormalFibroblast_primary_01_rep1

value: Patient 01


title: WT_6DL_UNC1999_n_2

description: Illumina sequencing

tag: treatment group


title: mix15_mrna

description: Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry) with 15 minute 37C incuabtion prior to RT. With A 1:1 mix of Hap1 UNGKO and Hap1 RNASEH2CKO cells were isolated.

extract_protocol:
Hap cells were isolated, resuspended in single cell suspension, and mixed in a 1:1 ratio, and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 15 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.

value: 1:1 mix of UNGKO Hap1 cell line and RNASEH2CKO Hap1 cell line


title: TumorAssocFibroblast_primary_02_rep1

value: Patient 02

value: primary fibroblasts from tumorous regions of uterine cervix

value: tumor-associated fibroblast


title: WT_6DL_GSK343_n_2

description: Illumina sequencing

tag: sample preparation


title: pbmc60_mrna

description: Single cell RNAseq library from the 10X genomics 3´ end kit (v2 chemistry). Fresh PBMCs were isolated from a healthy human donor.

source_name: Human PBMCs

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 60 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.

value: Human PBMCs


title: case4_FS-N

source_name: normal cells from peripheral blood in case 4 patients with chronic type of disease

value: Adult T-cell leukemia/lymphoma (ATLL) patient

tag: age


title: WT-NBAF rep1

value: PCA

value: Acetate/Fumarate


title: metM_Wnt_control_replicate2

institute: UNC

source_name: metM_Wnt control

value: metM-Wnt

value: control condition

tag: tissue

value: liver metastasis

source_name: NIH3T3 cells

tag: type

value: Common reference


title: pbmc30_mrna

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 30 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: case12_F-2

source_name: normal cells from peripheral blood in case 12 patients with acute/chronic type of disease

value: male

value: acute/chronic


title: WT_6DL_GSK343_n_2_input

description: Illumina sequencing


title: pbmc15_mrna

extract_protocol:
PBMCs were isolated from a healthy adult using standard protocols and captured on the 10x genomics single cell RNA-seq platform
10x genomics 3' end single cell RNA-seq kit. Alterations to protocol include, following GEM generation, RT was done at 37C for 15 min, then 53 C for 45 minutes. Following silane purification of RT products, mRNA was isolated using Ampure size selection of 0.6x. Read 1 positions 1-16 contain the 16bp cell barcode, and positions 17-26 contain a 10bp UMI. Read 2 contains the cDNA.


title: PANC1 KLF7 H5 (shRNA#2) replicate 2

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description:
Sample_PC17_008
KLF7 H5 (shRNA#2)

data_processing:
Bases were called using RTA 1.18.64.0
reads were mapped with the STAR aligner (version STAR_2.5.2b) to the GRCH38 genome using overhang of 100 with the following options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate
reads counts were obtained for each gene (gencode.v25.primary_assembly.annotation.gtf) using the R (v3.3.1) bioconductor GenomicAlignments (v1.10.1)
DESeq2(v1.14.1) was used to call differential expressed genes directly from read counts.
Genome_build: GRCH38
Supplementary_files_format_and_content: The read counts per gene are contained in an R binary file (counts.Rdata).  The 'counts' object of type “RangedSummarizedExperiment” contains the read counts. counts.csv is text printout of count data from counts.Rdata

source_name: KLF7 H5 (shRNA#2)

growth_protocol: PANC1 cell lines were grown in DMEM medium with 10% Fetal bovine serum and Penicillin and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: PANC1 cells that expressed shRNA targeting HOXC6 (#1,#2) or shRNA targeting KLF7 (#1,#2) or Non-specific (NS) were used for preparing the total RNA and to perfrom gene expression array.

tag: cell line

tag: shRNA


title: PANC1 KLF7 H5 (shRNA#2) replicate 3

description:
Sample_PC18_009
KLF7 H5 (shRNA#2)


title: WT_6DL_UNC1999_n_2_input

description: Illumina sequencing


title: PANC1 KLF7 H5 (shRNA#2) replicate 1

description:
Sample_PC16_007
KLF7 H5 (shRNA#2)


title: case4_FS-P

source_name: leukemic cells from peripheral blood in case 4 patients with chronic type of disease

value: female

value: chronic

value: leukemic cells


title: S943Nr24

city: Berlin

first: Katrin

last: Kreuzer

address: Max-Dohrn-Str. 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
De-multipltiplexing of sequencing reads was accomplished using Illumina bcl2fastq (version 2.19)
Adapter trimming was performed with Skewer (version 0.2.2)
Alignment to the human genome (hg 19) was performed using STAR (version 2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: Counted reads per gene as raw counts and normalized counts. Normalized counts contain all genes which sum of mapped reads across all samples is greater than one. Normalizing was performed with DESeq2.

source_name: HepaRG cell line

growth_protocol: HepaRG cells were seeded in 6-well-plates (200 00 cells per well) and cultivated and proliferated in Williams E medium with 2 mM glutamine supplemented with 10 % fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, 0.05 % human insulin and 50 µM hydrocortison. After a 2-week proliferation phase, cells were differentiated in the mentioned culture medium additionally containing 1.7 % DMSO, for another 2 weeks.

extract_protocol:
RNA isolation was performed with the RNeasy Mini Kit (Qiagen) according to the manufactures' protocol.
Libraries were prepared from 100 ng of RNA using the TruSeq Stranded Total RNA kit (Illumina)

treatment_protocol: Differentiated HepaRG cells were treated with the non toxic concentrations of 1 µM aflatoxin B1, 5 µM benzo[a]pyrene, 1 µM lasiocarpine, 250 µM methyleugenol or 20 mM nitrosopyrrolidine for 24h.

value: Control

tag: cas number

tag: concentration

value: Medium


title: PANC1 KLF7 H2 (shRNA#1) replicate 3

description:
Sample_PC15_006
KLF7 H2 (shRNA#1)

source_name: KLF7 H2 (shRNA#1)


title: S943Nr23

tag: treatment


title: WT_2DL_n_2

description: Illumina sequencing

value: ChIP-seq


title: WT_6DL_DMSO_n_2_input

description: Illumina sequencing


title: cocultured with KLN205KD withSEMA6A o/e and SEMA3A protein rep1

city: TAIPEI

first: Li-Han

last: Chen

state: Taipei

address: No. 1, Sec. 4, Roosevelt Rd.

country: Taiwan

institute: National Taiwan University

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA6A+3A 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse splenocytes cocultured with KLN205KD with SEMA6A o/e and SEMA3A protein

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Splenocytes of DBA/2 mouse cultured in CM-10 medium for 9 days

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden, Germany) was performed to extract RNA according to the manufacturer's instructions.

treatment_protocol: Splenocytes were stimulated by coculture with  SEMA3A-knockdown KLN-205 (KLN-205KD) cells, SEMA6A-overexpressing KLN-205KD cells, KLN-205KD cells with purified SEMA3A (10 µg/mL), or SEM6A-overexpressing KLN-205KD cells with purified SEMA3A (10 µg/mL) and IL-2 for 9 days

value: Spleen

value: splenocytes

value: 10 weeks


title: PANC1 KLF7 H2 (shRNA#1) replicate 2

description:
Sample_PC14_005
KLF7 H2 (shRNA#1)


title: S943Nr21


title: cocultured with KLN205KD withSEMA6A o/e and SEMA3A protein rep2

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA6A+3A 2

value: cocultured with KLN205KD with SEMA6A o/e and SEMA3A protein


title: cocultured with KLN205KD withSEMA6A o/e and SEMA3A protein rep3

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA6A+3A 3


title: cocultured with KLN205KD with SEMA3A protein rep2

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA3A 2

source_name: mouse splenocytes cocultured with KLN205KD with SEMA3A protein


title: WT_2DL_n_2_input

description: Illumina sequencing


title: PANC1 KLF7 H2 (shRNA#1) replicate 1

description:
Sample_PC13_004
KLF7 H2 (shRNA#1)


title: cocultured with KLN205KD with SEMA3A protein rep3

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA3A 3


title: cocultured with KLN205KD with SEMA6A o/e rep3

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA6A 3

source_name: mouse splenocytes cocultured with KLN205KD with SEMA6A o/e


title: S943Nr22


title: cocultured with KLN205KD with SEMA3A protein rep1

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA3A 1


title: S943Nr20


title: KO_6DL_UNC2400_n_2

description: Illumina sequencing

source_name: Tert-/- Embryonic stem cells


title: KO_6DL_UNC2400_n_2_input

description: Illumina sequencing


title: S943Nr19


title: PANC1 non silencing shRNA replicate 2B

description:
Sample_PC11_002
non silcencing shRNA  (TRC)

source_name: non silencing shRNA  (TRC)

value: non-specific


title: S943Nr18

value: Lasiocarpine

value: 1 uM


title: 2605: KSHV (-) cell

source_name: KSHV-negative mECK36 cells

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (QIAGEN) and sheared by sonication to fragments of ~500bp.
Methylated DNA enrichment protocol: The sheared DNA (1µg) was added to 10 µl MBD-Bead slurry (MethylMiner DNA Enrichment Kit, Invitrogen, Carlsbad, CA) and incubated on a rotating mixer for 1 hr, as described previously [49]. The DNA fragments were eluted into distinct subpopulations based on the degree of methylation; non-captured fraction (NC, representing un-methylated DNA fragments), 450 mM NaCl (representing partially methylated DNA fragments) and 2000 mM NaCl (representing methylated DNA fragments). The fractions were then ethanol precipitated and re-suspended in H2O.
MBD2 enriched methylated DNA fractions were subjected to library preparation with NEBNext® Ultra™ II DNA library prep kit for Illumina (NEB #E7645) at the next generation genomic center in the Azrieli Faculty of Medicine, Bar-Ilan University.

value: KSHV-negative mECK36 cells


title: KO_6DL_UNC1999_n_2

description: Illumina sequencing


title: PANC1 non silencing shRNA replicate 1B

description:
Sample_PC10_001
non silcencing shRNA  (TRC)


title: S943Nr17


title: KO_6DL_UNC1999_n_2_input

description: Illumina sequencing


title: KO_6DL_GSK343_n_2

description: Illumina sequencing


title: cocultured with KLN205KD with SEMA6A o/e rep1

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA6A 1


title: CHLA136

city: Tromso

first: Peter

last: Utnes

address: Hansine Hansens veg 18

country: Norway

institute: UiT - The Arctic University of Norway

data_processing:
BaseCalling was done with Illumina Casava Pipeline 1.8.2.
Initial quality assessment was based on data passing the Illumina Chastity filter.
Quality assessment was based on the reads using the FASTQC quality control.
Reads were mapped with STAR Aligner 2.5 onto the human reference genome GRCh38.
Duplicate removal was done with Picard’s tool MarkDuplicates (http://broadinstitute.github.io/picard).
Read counting was performed with featureCounts v1.5.0-p2 on ENSEMBL gene annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with CPM values for each sample

source_name: Neuroblastoma cell line

growth_protocol: CHLA cells were grown in Iscove’s modified Dulbecco’s medium supplemented with 20% fetal bovine serum, 4 mM L-glutamine, and 1× ITS (5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL selenous acid). The other cell lines were grown in RPMI-1640 supplemented with 10% fetal bovine serum and 2 mM L-glutamine (final concentrations).    All cell lines were cultured at 37°C in a humidified incubator with 95% air and 5% CO2 atmosphere without antibiotics. The identity of all cell lines was authenticated by short tandem repeat (STR) analysis at the Center of Forensic Genetics, The Arctic University of Norway—UiT, Norway. Cells were tested and confirmed negative for mycoplasma contamination.

extract_protocol:
Total RNA was extracted by adding 1 mL of TRIzol (Invitrogen, Carlsbad, USA) to the samples, vortexed for 1 min, and placed at room temperature for 5 min before adding 200 µL chloroform. The phases were mixed and phase separation was done by centrifuging at 12 000×g, 15 min at 4°C. To maximize yields and reducing the risk of phenol contamination, the lower phenol phase was removed and the sample was re-spun at 12 000×g, 15 min at 4°C. The aqueous phase was moved to a new tube with glycogen (Ambion) and 1 volume of 0.2 M NH4OAc isopropanol. The mixture was chilled at −20°C for 15 min and RNA was co-precipitated with glycogen by centrifuging at 12 000×g, 15 min, 4°C. The visible RNA pellet was washed twice in 1 mL 75 % ethanol and re-acquiring of the pellet was done by spinning down at 7500×g, 5 min at 4°C. The pellet was resuspended in Tris-ethylenediaminetetraacetic acid (EDTA) buffer (10 mM Tris-HCl (pH 8.0), 0.1 mM EDTA). RNA concentration and DNA contamination were assessed using NanoDrop 2000 (Thermo Scientific).
RNA concentrations were measured using Agilent’s Eukaryote Total RNA Pico Assay. After fragmentation, a quality control (QC) was done on Agilent 2100 HS DNA chip. Concentration was determined with smear analysis on the Agilent 2100 and checked for degradation. Samples were prepared using the NEBNext Ultra Directional RNA Library Protocol (New England Biolabs). The paired-end, cDNA libraries were consequently sequenced on the Illumina HiSeq 2000 sequencer.

tag: Sex

tag: age (months)


title: CHLA20


title: S943Nr16


title: cocultured with KLN205KD rep2

description:
Gene expression data from cancer cells co-cultured splenocyte
Control 2

source_name: mouse splenocytes cocultured with KLN205KD

value: cocultured with KLN205KD


title: PANC1 non silencing shRNA replicate 3B

description:
Sample_PC12_003
non silcencing shRNA  (TRC)


title: NBLWR

value: NBLWR


title: KO_6DL_GSK343_n_2_input

description: Illumina sequencing


title: S943Nr14

value: Methyleugenol


title: KANR

value: KANR

value: female


title: cocultured with KLN205KD with SEMA6A o/e rep2

description:
Gene expression data from cancer cells co-cultured splenocyte
SEMA6A 2


title: KO_6DL_DMSO_n_2

description: Illumina sequencing


title: KO_6DL_DMSO_n_2_input

description: Illumina sequencing


title: cocultured with KLN205KD rep3

description:
Gene expression data from cancer cells co-cultured splenocyte
Control 3


title: BE2

value: male


title: KO_2DL_n_2

description: Illumina sequencing


title: S943Nr13


title: CHLA15


title: S943Nr9

value: Nitrosopyrrolidine

value: 20 mM


title: S943Nr15


title: NUGC3-PRMT6-KO (2)

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

description: Gene expression profile of NUGC3-PRMT6-KO (2)

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: PRMT6 knockout Human gastric cancer cell line NUGC3

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human gastric cancer cell line NUGC3 was purchased from the Human Science Research Resources Bank, and then grown in RPMI1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting PRMT6 (5'-GACGGTACTGGACGTGGGCG-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). PRMT6-konckout clones were obtained by limiting dilution.

value: Gastric cancer


title: NUGC3-PRMT6-KO (1)

description: Gene expression profile of NUGC3-PRMT6-KO (1)


title: NBLW

value: NBLW


title: NUGC3-control (2)

description: Gene expression profile of NUGC3-control (2)

source_name: PRMT6 wild-type Human gastric cancer cell line NUGC3


title: CHLA122


title: S943Nr7


title: Not4.rep2

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

institute: The University of Tokyo,

description: Ribosome Profiling

data_processing:
Library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming and sorting by sample barcode with FastX-toolkit
random barcode (UMI) triming with UMI-tools v1.0.1
rRNA alignment with bowtie2 v2.2.5
Alignment with TopHat v2.1.1 to Genome
Read quantitation using plastid v0.4.7
Genome_build: sacCer3
Supplementary_files_format_and_content: Not4.IP.rep2.RPM.csv: Comma-separated text files contain following columns: 1. mrna; 2. codon (assigned by Psite); 3. E-site codon; 4. P-site codon; 5. A-site codon; 6. read count (RPM).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted by TRIzol reagent from the IPed ribosome.
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129.

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1 Not4-FTP::natNT2

tag: protocol

value: RNase I footprinting, ribosome IP, RNA extraction


title: cocultured with KLN205KD rep1

description:
Gene expression data from cancer cells co-cultured splenocyte
Control 1

value: Spleen

tag: cell type

value: splenocytes

tag: strain

value: 10 weeks


title: Not4.rep1

description: Ribosome Profiling

data_processing:
Library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming and sorting by sample barcode with FastX-toolkit
random barcode (UMI) triming with UMI-tools v1.0.1
rRNA alignment with bowtie2 v2.2.5
Alignment with TopHat v2.1.1 to Genome
Read quantitation using plastid v0.4.7
Genome_build: sacCer3
Supplementary_files_format_and_content: Not4.IP.rep1.RPM.csv: Comma-separated text files contain following columns: 1. mrna; 2. codon (assigned by Psite); 3. E-site codon; 4. P-site codon; 5. A-site codon; 6. read count (RPM).


title: Input.rep2

description: Ribosome Profiling

data_processing:
Library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming and sorting by sample barcode with FastX-toolkit
random barcode (UMI) triming with UMI-tools v1.0.1
rRNA alignment with bowtie2 v2.2.5
Alignment with TopHat v2.1.1 to Genome
Read quantitation using plastid v0.4.7
Genome_build: sacCer3
Supplementary_files_format_and_content: input.rep2.RPM.csv: Comma-separated text files contain following columns: 1. mrna; 2. codon (assigned by Psite); 3. E-site codon; 4. P-site codon; 5. A-site codon; 6. read count (RPM).

value: RNase I footprinting, Sucrose cushion, RNA extraction