title: Case_49: Second squamous cell carcinoma of the lung 18

source_name: Lung biopsy

value: Female

tag: age

value: Active (20 py)

tag: hnsc site of origin

value: Not applicable


title: S_H32_BR2

status: Public on Sep 10 2019

type: SRA

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

library_source: transcriptomic

data_processing:
Sequencing quality was assessed using FastQC, and Illumina adapter sequences and some low-quality base pairs were removed using cutadapt version 1.9 (Martin, 2011). Reads were further trimmed in 3’ using “sickle” program version 1.33 with option -x and default values for all other parameters (implying Phred quality cut-off of 20).
The cleaned reads were then mapped against the whole repertoire of allelic variants for the 2,867 CDSs annotated in EGDe (GenBank accession No. NC_003210, length 2,944,528 bp) found in the 33 genomes.
Identification of allelic variants used “tblastn” version 2.6.0+ with options ‘-task tblastn -evalue 1e-10 -seg no’ (Camacho et al., 2009) and cut-offs corresponding to 80% identity at the amino-acid sequence and minimum coverage of 80% of the query.
Mapping used "bowtie2" version 2.2.6 (Langmead and Salzberg, 2012) with options ‘-N 1 -L 16 -R 4’ and converted to bam format using “samtools” version 1.9 (Li et al., 2009).
Read counts on each allelic variants were obtained using “htseq-count” version 0.10.0 (Anders et al., 2015) with options ‘-s reverse --nonunique all -a 1’. Read counts associated with all allelic variants were summed up to obtain a single read count per gene per sample. Importantly, “bowtie2” as used here mapped each read on a single allelic variant ensuring that each read could not be counted more than once and “htseq-count” options allowed to retrieve the reads that mapped equally well on several sequences as expected given the redundancy of the repertoire of allelic variants.
Read counts were normalized with the function “estimateSizeFactors” provided in the R package “DESeq2” (Love et al., 2014) version 1.20.0 based on the behaviour of the 2,456 conserved single copy genes (option ‘controlGenes’).
Genome_build: GenBank accession No. NC_003210
Supplementary_files_format_and_content: The file counts_bohyung_virulence_20190314.csv contains normalized read counts for 2867 CDSs of GenBank accession No. NC_003210 in the 66 samples, plus a column indicating which CDSs belong to the set of 2,456 conserved single copy genes.
Supplementary_files_format_and_content: ASCII text, tabulated separated values

molecule: total RNA

organism: Listeria monocytogenes

source_name: cells grown in BHI medium, late exponential phase

growth_protocol: Mother cultures were inoculated into fresh BHI broth and grown at 37°C for 5-6 h to reach exponential phase.

extract_protocol:
The mixtures were pelleted by centrifugation (5,000g, 10 min, room temperature) and pellets were suspended in 5M Guanidine thiocyanate (Roth) lysis buffer with 10 µl/ml 2-Mercaptoethanol (Sigma-Aldrich). To lyse cell walls, 0.5mm glass beads (Roth) were added and bacterial cells were homogenized using Tissulyser (Qiagen) at a frequency of 30-1 for 6 min. After centrifugation (16,000g, 30 s, room temperature) supernatants were collected and RNA was purified using column-based RNA Clean & Concentrator-5 kit (Zymo Research). Quality of extracted RNA was assessed using Labchip GX II bioanalyzer (Perkin Elmer). To remove DNA contamination, total RNA was incubated with Baseline-Zero DNase (Epicentre) in the presence of RiboLock RNase inhibitor (40U/µl) (Thermo Fisher Scientific) for 30 min at 37°C followed by purification using RNA Clean & Concentrator-5 kit. RNA concentration was measured using fluorescence-based Qubit™ RNA HS Assay (Thermo Fisher Scientific).
To enrich mRNA and remove ribosomal RNA (rRNA), total RNA was treated with Ribo-Zero rRNA removal kit (Illumina). Briefly, beads were washed twice and hybridized with probes at 68°C for 10 min. Five hundred ng of total RNA was added to the mixture and incubated at RT and 50°C for 5 min each. rRNA bound to the beads was separated from mRNA using a magnetic stand. Enriched mRNA was then purified with RNA Clean & Concentrator-5 kit and and rRNA depletion was confirmed on Labchip GX II bioanalyzer (Perkin Elmer). Preparation of cDNA fragment libraries was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (Illumina) with slight modifications. Briefly, the enriched mRNA was fragmented for 15 min at 94°C and reverse transcribed to synthesize the first-strand cDNA followed by second strand cDNA synthesis. Double-stranded cDNA (ds cDNA) was purified using NucleoMag (Macherey nagel) SPRI selection. End repair was performed on the ds cDNA library followed by ligation of adapters. High fidelity PCR was performed using KAPA Hifi polymerase (Kapa Biosystems) and NEBNext Multiplex Oligos for Illumina (Dual Index Primers) to selectively enrich library fragments. The PCR products were purified twice using NucleoMag SPRI beads and the quality of the final library was assessed on Labchip GX II bioanalyzer. Indexed and purified libraries were sequenced on Illumina NextSeq 500 platform (paired-end, 2 X 75 bp per read).

treatment_protocol: RNAprotect (Qiagen) was immediately added and cultures were vortexed followed by incubation at room temperature for 5 min.

tag: strain

tag: lineage

value: Lineage 2

tag: growth medium

value: BHI

tag: growth phase

value: exponential phase

tag: growth temperature

tag: biological replicate


title: RE2_lncRNA

city: Yangling District

first: Lei

last: Zhang

state: Province, State or Region

address: No.22 Xinong Road,  Yangling District

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

description: lncRNA

data_processing:
Prior to reference genome mapping, raw reads (raw data) in the fastq format were processed.
Firstly, The RNA-seq clean reads (valid data) were mapped to the goat reference genome (http://www.ncbi.nlm.nih.gov/genome/?term=goat) using a publicly available program TopHat 2 (http://ccb.jhu.edu/software/tophat/index.shtml) , which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Second, Cufflinks was used to assemble the transcripts at first, and then Cuffmerge was used to alignment all transcripts of sample PE and RE to generate known mRNA what were excluded. The remaining transcripts were compared with the known mRNA also using Cuffmerge to gather statistics information of class code and obtained 5 classes as lncRNA candidates: (1) j, Potentially novel isoform (fragment): at least one splice junction is hared with a reference transcript; (2) i, A transfrag falling entirely within a reference intron; (3) o, Generic exonic overlap with a reference transcript; (4) u, Unknown, intergenic transcript; (5) x, Exonic overlap with reference on the opposite strand.
Last, lncRNA candidate filter was a key step in the analysis of lncRNA sequencing data, had the direct relation to the credibility of subsequent functional verification. In this study, lncRNA candidate was filtered using the following parameters to identify reliable lncRNAs: (1) the length of transcript was longer than 200bp, (2) the reads coverage was equaled or more than 3, (3) the exon number was equaled or more than 1, (4) Protein-coding-score test: Both the Coding-Non-Coding Index (CNCI, http://www.bioinfo.org/software/cnci/) and Coding Potential Calculator (CPC, http://cpc.cbi.pku.edu.cn/) were used to evaluate the coding potential of candidate lncRNAs [20,21], the transcript was identified as novel lncRNA simultaneously satisfy: CPC score < -1 and CNCI score <0.
The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The feference GTF annotation file used in Cufflinks was downloaded from the UCSC database. Cufflink was used to de novo assemble the transcripiome at first; the second, Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded UCSC GTF file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with “q value” less than 0.05 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression.

organism: Capra hircus

source_name: receptive endometrium

growth_protocol: A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study.

extract_protocol:
Total RNA was extracted from every sample using the TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 (Agilent, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number> 7.0. Approximately 10 ug of total RNA representing a specic adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). First, ribosomal RNA was removed by using an Epicentre Ribo-zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Subsequently, the high strand-specificity of the libraries was generated using the rRNA-depleted RNA of the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA), following manufacturer’s recommendations. Following purication, the RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 2×125 bp. And then we performed the paired-end sequencing on an Illumina Hiseq2500 at the (LC Sceiences, USA) following the vendor's recommended protocol.
Paired-end sequencing on an Illumina Hiseq2500 (LC Sceiences, USA) following the vendor's recommended protocol.

treatment_protocol: The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium).

tag: tissue

value: endometrium

tag: phenotype

value: receptive

value: at gestational day 15


title: Case_47: Second squamous cell carcinoma of the lung 16

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.1.444 based on the statistical language R version 3.4.2.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction from FFPE samples was performed according the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, AX4920, Promega, Madison, USA).

tag: gender

value: Male

tag: smoking status (pack years)

value: Former smoker (30 py)

tag: hpv genotyping

tag: p16 immunohistochemistry

value: Negative

tag: dna input [ng]

tag: tumor cell content (%)


title: Case_28: Pulmonary metastasis of head and neck squamous cell carcinoma 28

source_name: Resection

value: Former smoker (40 py)

value: Positive

value: Larynx


title: Reference_sample_2: Primary head and neck squamous cell carcinoma 02

value: Oral cavity


title: S_H31_BR2


title: S_H32_BR1


title: HiC_IMR90_EMPTY_GM_Rep1

city: Cambridge

first: Alessandra

last: Dall'Agnese

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

description: processed data file: GSE98509_E_GMvsM_GM_differentials.txt

library_source: genomic

data_processing:
ChIP-Seq - Read quality was determined using FASTQC. Reads were mapped using bowtie2-2.0.5/bowtie2 to the female Homo sapiens hg19 genomes with options: --very-sensitive-local. Peaks were called using macs2 2.1.1.20160309 with qvalue=0.01, macs2 2.1.1.20160309 was also used for differential peak calling among samples.
RNA-Seq - Spike-in were added based on number of nuclei but were not used for the analysis. Read quality was determined using FASTQC. Reads were mapped using TopHat2.1.1 to the female Homo sapiens hg19 genomes with options: -p 8 -g 1 --segment-length 17 --library-type fr-firststrand. HTSeq-0.6.1p1173 with --stranded=reverse option was used to assigned mapped reads to Homo Sapiens GRCh37.75 genes. Differential expression analysis was performed using DESeq2.
Hi-C - Read quality was determined using FASTQC. HiCPro-v2.7.7 was used for read mapping, valid ligation product detection, quality control, and sparse chromosomal interaction maps. HiTC was used to transform sparse matrices to NbyN matrices. Differential interactions 4kb resolution were called by DiffHiC. Requirement for significant differential interaction: Log(Fold Change) lower than -2 or higher than 2, pvalue lower than 0.05. Boundaries were called following a previously described method (Crane et al., 2015)
Genome_build: hg19

growth_protocol: IMR90 cells were cultured in EMEM supplemented with 10% FBS

extract_protocol:
For RNASeq: cells were lyzed with Trizol and RNA was extracted following manufacturer's instruction. For Hi-C, DNA crossliked, digested and ligated, ligation products were isolated with streptavidine beads, Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications
RNASeq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations. Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point. Cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and for 3days in EMEM 2% HS 1%ITS collected for DM time point. Cells were then treated or not with hTNF for 1hr prior collection

tag: cell type

value: Lung fibroblast

tag: ectopic gene expression

value: EMPTY VECTOR

tag: passage from isolation

value: passage 21-28


title: HiC_IMR90_EMPTY_GM_Rep2


title: RNA_Seq_MYOD_DM_Rep2 TNFa

description: processed data file: GSE98509_IMR90_MYOD_DM_T_over_EMPTY_DM_T.csv

value: Lung fibroblast-derived myotube

value: mouse MYOD overexpression


title: S_H31_BR1

tag: strain

value: Lineage 2

value: BHI


title: RNA_Seq_EMPTY_DM_Rep2 TNFa


title: PE1_lncRNA

description: lncRNA

source_name: pre-receptive endometrium

value: endometrium

value: pre-receptive

tag: age

value: at gestational day 5


title: S_H28_BR2

tag: lineage

value: Lineage 1

tag: growth medium

value: exponential phase


title: RNA_Seq_MYOD_GM_Rep2 TNFa

description: processed data file: GSE98509_IMR90_MYOD_GM_T_over_EMPTY_GM_T.csv

value: Lung fibroblast-derived myoblast


title: RE1_lncRNA

description: lncRNA

value: receptive

value: at gestational day 15


title: Rcor1 Treg replicate 3

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

data_processing:
Base calling, aligment, filtering, peak calling, normalized abundance measurements, by Novogene company.
remove adapter, low quality, N reads
Supplementary_files_format_and_content: fq; BAM (mapping)STAR software to alignment for RNA-seq sequencing data analysis, using the MM10 genome
Genome_build: MM10
Supplementary_files_format_and_content: Rcor1_Hancock_normalized_data.xls reports normalized abundance measurements.

organism: Mus musculus

source_name: Foxp3+ YFP-sorted regulatory T cell

growth_protocol: Floxed Rcor1 mice (Jackson Laboratory #025877) were mated with Foxp3YFPcre mice (Rubtsov et al. Immunity 2008) to generate conditional Rcor1-knockout mice lacking Rcor1 in Foxp3+ Treg. Foxp3YFPcre mice were used as control. We used male mice 6-8 weeks of age in this study.

extract_protocol:
RNA was isolated using RNeasy kits (QIAGEN), and RNA integrity and quantity were analyzed by NanoDrop ND-1000 and Nanochip 2100 Bioanalyzer (Agilent Technologies)
NEBNext® Ultra™ II RNA Library Prep was used according to the manufacturers instructions.

treatment_protocol: Foxp3+ regulatory T cells were isolated using FACS sorting via YFP (after CD4+ column enrichment).

tag: genotype

value: Rcor1 deletion

value: Foxp3+ YFP-sorted regulatory T cell


title: RNA_Seq_EMPTY_GM_Rep2 TNFa

value: Lung fibroblast


title: S_H28_BR1

tag: growth phase

tag: growth temperature

tag: biological replicate


title: Rcor1 Treg replicate 2


title: S_H27_BR2


title: Case_48: Second squamous cell carcinoma of the lung 17

tag: gender

value: Female

value: Negative

value: Positive

tag: hnsc site of origin

value: Not applicable


title: Case_45: Second squamous cell carcinoma of the lung 14

source_name: Lung resection

value: Male

tag: smoking status (pack years)

value: Active (NA)

tag: hpv genotyping


title: RNA_Seq_MYOD_DM_Rep1 TNFa

value: Lung fibroblast-derived myotube

value: mouse MYOD overexpression

value: passage 21-28


title: Rcor1 Treg replicate 1


title: Case_44: Second squamous cell carcinoma of the lung 13

value: Active (50 py)

tag: p16 immunohistochemistry

tag: dna input [ng]


title: Case_46: Second squamous cell carcinoma of the lung 15

tag: tumor cell content (%)


title: S_H27_BR1

value: Lineage 1

value: BHI

value: exponential phase


title: WT Treg replicate 3

value: wild type

tag: cell type


title: RNA_Seq_EMPTY_DM_Rep1 TNFa

tag: ectopic gene expression

value: EMPTY VECTOR

tag: passage from isolation


title: S_H19_BR2

tag: strain


title: Case_43: Second squamous cell carcinoma of the lung 12

tag: age

value: Active (60 py)


title: WT Treg replicate 2

value: Foxp3+ YFP-sorted regulatory T cell


title: RNA_Seq_MYOD_GM_Rep1 TNFa

value: Lung fibroblast-derived myoblast


title: RNA_Seq_EMPTY_GM_Rep1 TNFa

value: Lung fibroblast


title: S_H17_BR2

tag: lineage

value: Lineage 2

tag: growth medium


title: IMR90_RNA_Seq_MYOD_DM_Rep2

description:
Cells were lyzed with Trizol and RNA was ectracted following manufacturer's instruction. Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations
IMR90_MYOD_DM_vs_MYOD_GM.csv

data_processing:
ChIP-Seq - Read quality was determined using FASTQC. Reads were mapped using bowtie2-2.0.5/bowtie2 to the female Homo sapiens hg19 genomes with options: --very-sensitive-local. Peaks were called using macs2 2.1.1.20160309 with qvalue=0.01, macs2 2.1.1.20160309 was also used for differential peak calling among samples.
RNA-Seq - Spike-in were added based on number of nuclei but were not used for the analysis. Read quality was determined using FASTQC. Reads were mapped using TopHat2.1.1 to the female Homo sapiens hg19 genomes with options: -p 8 -g 1 --segment-length 17 --library-type fr-firststrand. HTSeq-0.6.1p1173 with --stranded=reverse option was used to assigned mapped reads to Homo Sapiens GRCh37.75 genes. Differential expression analysis was performed using DESeq2.
Genome_build: hg19

extract_protocol:
For RNASeq: cells were lyzed with Trizol and RNA was ectracted following manufacturer's instruction. For ChIPSeq lysates were clarified from sonicated crosslinked nuclei and MYOD-DNA complexes were isolated with antibody.
RNASeq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations . ChIPSeq libraries were prepared as in http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf.

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point. Cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and for 3days in EMEM 2% HS 1%ITS collected for DM time point.


title: WT Treg replicate 1

tag: genotype


title: mouse liver ATAC-seq LKO6

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
atactk (0.1.5) was used for adapator trimming.
bwa (0.7.17-r1188) was used for alignment to generate bam files for ATAC-seq. STAR was used for alignment to generate bam files for RNA-seq.
Duplicates were marked by Picard (v.2.8.14) for ATAC-seq.
Samtools was used to remove duplicates for ATAC-seq.
macs2 (2.1.1.20160309) was used for peak calling at FDR < 0.1 for ATAC-seq.
The treat_pileup.bedgraph files (generated by macs2) from each individual samples were normalized to its own library size and converted to bigwig file by bedGraphToBigWig (v.4).
Broad peaks were filtered against an mm10 blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz).
The master peaks list was generated from the union of all blacklist-filtered broad peaks
Bedtools (v.2.27.1) was used to count reads in each peak for each ATAC-seq sample. HTSeq was used to count reads in gene feature for each RNA-seq sample
HOMER were used to annotate peaks to closest gene for ATAC-seq.
The R package DESeq2 (v.1.20.0) was used to perform the differential peak/gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from RNA-seq, DESeq2-normalized read counts from ATAC-seq, bigwig file of ATAC-seq coverage.

source_name: liver

extract_protocol: Nuclei from frozen mouse liver were isolated by gradient centrifugation. 50000 isolated nuclei were used in each transposase reaction (Illumina). The sequencing libraries were barcoded and amplified by 2-step PCR. DNA sequencing were performed on Illumina NovaSeq 6000 instrument with 50-bp paired-end reads.

tag: tissue

value: liver

tag: phenotype

value: HFD LKO


title: mouse liver ATAC-seq LKO5


title: IMR90_RNA_Seq_EMPTY_DM_Rep2

description: Cells were lyzed with Trizol and RNA was ectracted following manufacturer's instruction. Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations


title: S_H17_BR1

tag: growth phase

tag: growth temperature

tag: biological replicate


title: S_H11_BR2


title: PE2_lncRNA

description: lncRNA

value: endometrium

value: pre-receptive

value: at gestational day 5


title: IMR90_RNA_Seq_MYOD_GM_Rep2

value: mouse MYOD overexpression

value: passage 21-28


title: S_H19_BR1

value: Lineage 1


title: mouse liver ATAC-seq LKO4


title: IMR90_RNA_Seq_EMPTY_GM_Rep2


title: S_H10_BR2

value: BHI


title: S_H11_BR1

value: exponential phase


title: mouse liver ATAC-seq LKO2


title: mouse liver ATAC-seq LKO3


title: IMR90_RNA_Seq_EMPTY_DM_Rep1


title: mouse liver ATAC-seq LKO1


title: S_H10_BR1


title: Case_40: Second squamous cell carcinoma of the lung 09

tag: gender

value: Male

tag: smoking status (pack years)

value: Active (40 py)

tag: hpv genotyping

value: Positive

tag: hnsc site of origin

value: Not applicable


title: S_H8_BR2


title: IMR90_RNA_Seq_MYOD_GM_Rep1

tag: cell type

value: Lung fibroblast-derived myoblast


title: IMR90_RNA_Seq_MYOD_DM_Rep1

value: Lung fibroblast-derived myotube

tag: ectopic gene expression


title: S_H8_BR1

value: Lineage 2


title: Case_42: Second squamous cell carcinoma of the lung 11

value: Active (NA)

tag: p16 immunohistochemistry

tag: dna input [ng]

tag: tumor cell content (%)


title: Case_38: Second squamous cell carcinoma of the lung 07

tag: age

value: Negative


title: mouse liver ATAC-seq Ctrl6

tag: strain

value: liver

value: HFD flox/flox


title: Case_41: Second squamous cell carcinoma of the lung 10

value: Female

value: Negativ


title: mouse liver ATAC-seq Ctrl5


title: IMR90_RNA_Seq_EMPTY_GM_Rep1

value: Lung fibroblast

value: EMPTY VECTOR

tag: passage from isolation

value: passage 21-28


title: S_H7_BR1

tag: lineage

value: Lineage 1

tag: growth medium

value: BHI

value: exponential phase


title: mouse liver ATAC-seq Ctrl3

tag: tissue

tag: phenotype


title: ΔrnhAΔdnaArrnD-rrnC 1

city: Bengaluru

first: Aswin

middle: Sai narain

last: Seshasayee

state: Karnataka

address: GKVK campus Bellary road

department: Bioinformatics

country: India

institute: National Centre for Biological Sciences

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads
BEDTOOLS(2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using EdgeR
Genome_build: Reference genome used : E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: tab delimited .txt file containing raw reads count (raw_data_counts.txt)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria grown in LB Media

growth_protocol: Escherichia coli str K-12 substr MG1655 cells were grown in Luria broth media till exponential phase of growth at 37 degrees Celsius at 200 rpm.

extract_protocol:
Total RNA was extracted from bacteria using Trizol method and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for each mRNA sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Directional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a high throughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads.

treatment_protocol: Escherichia coli str K-12 substr MG1655 cells were grown in Luria broth media till exponential phase of growth at 37 degrees Celsius at 200 rpm were used to isolate total RNA .

tag: growth phase

value: Single colony grown in LB media and sequenced at exponential phase

tag: genotype

value: {delta}rnhA{delta}dnaArrnD-rrnC


title: Case_34: Second squamous cell carcinoma of the lung 03

source_name: Biospy

tag: gender

value: Male

tag: smoking status (pack years)

value: Former smoker (55 py)

value: Positive

value: Not applicable


title: S_H7_BR2

tag: growth temperature

tag: biological replicate


title: Case_39: Second squamous cell carcinoma of the lung 08

value: Active (40 py)

tag: hpv genotyping

value: Negative

tag: hnsc site of origin


title: mouse liver ATAC-seq Ctrl4

value: liver

value: HFD flox/flox


title: Case_35: Second squamous cell carcinoma of the lung 04

value: Former smoker 100 py

value: Negativ

tag: p16 immunohistochemistry

tag: dna input [ng]


title: ΔrnhAΔdnaArrnD-rrnE 1

value: {delta}rnhA{delta}dnaArrnD-rrnE


title: ΔrnhAΔdnaArrnD-rrnC 2


title: S_H5_BR2

value: Lineage 2


title: S_H6_BR2

value: Lineage 1


title: Case_37: Second squamous cell carcinoma of the lung 06

tag: age

value: Active (60 py)

tag: tumor cell content (%)


title: S_H6_BR1

tag: strain

value: BHI

value: exponential phase


title: mouse liver ATAC-seq Ctrl1


title: Case_32: Second squamous cell carcinoma of the lung 01

value: Active (80 py)


title: Case_23: Pulmonary metastasis of head and neck squamous cell carcinoma 23

value: Male

value: HPV16, HPV18

value: Oropharynx


title: ΔrnhAΔdnaA 2

value: Single colony grown in LB media and sequenced at exponential phase

value: {delta}rnhA{delta}dnaA


title: S_H5_BR1

tag: lineage


title: ddk-KR BrdU HU

city: Milan

first: Ivan

last: Psakhye

address: Via Adamello 16

country: Italy

institute: IFOM, the FIRC Institute of Molecular Oncology

description: HY9126 cells were arrested in G1 with alpha-factor for 3 h and then released in media containing 200 μg/ml BrdU and 0.2 M HU for 90 min

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner.

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

label: biotin

organism: Saccharomyces cerevisiae

source_name: HU 90 min

label_protocol: Sample preparation and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YP+Glucose 2% (YPD) media at 25°C in 500 ml flask for a density of 1.2×10^7 cells/ml.

extract_protocol: BrdU IP-on-chip profiles were determined as described in (Katou et al, 2003). Binding profiles by ChIP-on-chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G1 synchronization was performed by alpha−factor treatment (3-5 μg/ml) for 120-180 minutes at 25°C and validated by microscopy. Cells were pelleted, washed once with YP and released into YPD media containing 0.2 M HU for 90 min, and fixed with 1% formaldehyde for 30 min at room temperature for further ChIP. For BrdU incorporation profiles, cells were released from G1 arrest into YPD media containing 0.2 M HU and 200 μg/ml BrdU for 90 min, and fixed with 0.1% sodium azide on ice for 30 minutes.

tag: strain genotype

value: W303 MATa ura3::URA3/GPD-TK(7X) (LEU2)pCDC7-cdc7-K16R (HIS3)pDBF4-dbf4-K6R,K14R,K432R(HphNT1)

tag: antibody

value: Anti-BrdU antibody MBL M1-11-3


title: S_H3_BR2

tag: growth medium


title: Case_26: Pulmonary metastasis of head and neck squamous cell carcinoma 26

value: Active (NA)

value: Negative

value: Oral cavity


title: BD120-Dbf4 Ulp2-PK HU

description: HY7873 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa (NatNT2)pADH1-3HA-gal4DBD120-DBF4 (TRP1)pSMT3-7His-SMT3 Ulp2-9PK::HIS3MX6

value: Anti-PK SV5-Pk1 (AbD Serotech)


title: ΔrnhA 2

tag: growth phase

value: {delta}rnhA


title: S_H3_BR1

value: Lineage 2


title: Case_22: Pulmonary metastasis of head and neck squamous cell carcinoma 22

value: Former smoker (120 py)

value: Positive


title: Case_33: Second squamous cell carcinoma of the lung 02

value: Active (50 py)

value: Negativ

value: Not applicable


title: ΔrnhA 1

tag: genotype


title: Case_19: Pulmonary metastasis of head and neck squamous cell carcinoma 19

tag: gender

value: Male


title: Case_36: Second squamous cell carcinoma of the lung 05

tag: smoking status (pack years)


title: ddk-KR ulp2 BrdU HU

description: HY9128 cells were arrested in G1 with alpha-factor for 3 h and then released in media containing 200 μg/ml BrdU and 0.2 M HU for 90 min

value: W303 MATa ura3::URA3/GPD-TK(7X) (LEU2)pCDC7-cdc7-K16R (HIS3)pDBF4-dbf4-K6R,K14R,K432R(HphNT1) ulp2::KANMX4


title: Dbf4 Ulp2-PK HU

description: HY7805 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa (NatNT2)pADH1-3HA-DBF4 (TRP1)pSMT3-7His-SMT3 Ulp2-9PK::HIS3MX6


title: S_H2_BR2

value: Lineage 1

value: BHI

value: exponential phase

tag: growth temperature


title: ΔrnhAΔdnaA 1

value: Single colony grown in LB media and sequenced at exponential phase

value: {delta}rnhA{delta}dnaA


title: Case_24: Pulmonary metastasis of head and neck squamous cell carcinoma 24

value: Negative

value: Hypopharynx


title: Wild type GJ13519 2

value: Wild type


title: S_H2_BR1

tag: biological replicate


title: ulp2 slx5 BrdU HU

description: HY5822 cells were arrested in G1 with alpha-factor for 3 h and then released in media containing 200 μg/ml BrdU and 0.2 M HU for 90 min

value: W303 MATa ura3::URA3/GPD-TK(7X) ulp2::HIS3MX6 slx5::NatMX4

value: Anti-BrdU antibody MBL M1-11-3


title: ulp2 BrdU HU

description: HY1443 cells were arrested in G1 with alpha-factor for 3 h and then released in media containing 200 μg/ml BrdU and 0.2 M HU for 90 min

value: W303 MATa ura3::URA3/GPD-TK(7X) ulp2::TRP1


title: Wild type GJ13519 1


title: Case_21: Pulmonary metastasis of head and neck squamous cell carcinoma 21

value: Female

value: Former smoker (NA)

tag: hpv genotyping

value: Oral cavity


title: Case_25: Pulmonary metastasis of head and neck squamous cell carcinoma 25

value: Male

value: Positive

tag: hnsc site of origin

value: Larynx


title: S_H1_BR2

value: Lineage 2


title: L16526_NC-wo_09_D06

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

description: no RNA

data_processing:
basecalling: bcl2fastq 2.17.1.14
alignment: alignment of single-end data against mm10 with gsnap version 2017-03-17; splice sites were supported by using Ensembl version 87 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-87.ss.mm10.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.5.2 (-a EnsemblGene-87.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 87 gtf file
quality filtering: qc was done with the scater package and cells removed based on various quality metrics (ERCC content, chrM, total Features, total Counts and cell cycle)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.mm10.e87.tsv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the sequenced single cell libraries
Supplementary_files_format_and_content: tab delimited file (scater.cpmlog10_counts.tsv.gz) created with the scater package; columns are the remaining cells and rows are genes

organism: synthetic construct

source_name: negative control (no source)

extract_protocol:
To isolate Aldh1b1 expressing cells and their progeny, 1 mg of corn oil dissolved tamoxifen (20 mg/ml; Sigma) was injected intraperitoneally in Aldh1b1CreERT2 / ROSA26 LSLtdTomato double heterozygous adult mice for 5 consecutive days. Aldh1b1 expressing cells and their early progeny were isolated one day later from pancreata dissociated into single cells by virtue of their tdTomato (PE-Texas Red channel) expression from the lineage tracing mouse pancreas by FACS.
Pancreata were dissociated into single cells and cells were FACsorted into a 96 well plate containing 2 ul of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. Lysis, reverse transcription of the RNA and cDNA amplification was performed according to the smartseq-2 protocol 6 with few modifications as detailed below. After thawing the samples, 2 ul of a primer mix (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)) was added. After filling up to 10 ul with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II, RNA was denatured for 3 minutes at 72°C and reverse transcription was performed at 42°C for 90 min. The reverse transcriptase was then inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 uM UP primer* under the following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) and the DNA was eluted in 12 ul nuclease free water. The concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium). For library preparation 700 pg cDNA in 2 ul was mixed with 0.5 ul tagment DNA enzyme and 2.5 ul tagment DNA buffer (Nextera, Illumina) and tagmented at 55°C for 5 min. Subsequently, Illumina indices were added during PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.7 uM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina sequencing on a Nextseq500 aiming at an average sequencing depth of 0.5 mio reads per cell. Primers were as follows: dT primer: Aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACT(30)VN; Template Switch Oligo (TSO) primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG; Universal Part (UP) primer: AAGCAGTGGTATCAACGCAGAGT.

value: negative control (no strain)

tag: tissue


title: S_H1_BR1

value: BHI

value: exponential phase


title: Case_15: Pulmonary metastasis of head and neck squamous cell carcinoma 15

value: Active (50 py)

tag: p16 immunohistochemistry

tag: dna input [ng]

value: Oropharynx


title: ulp2-16A-PK HU

description: HY5343 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa ulp2-16A-9PK::HIS3MX6

value: Anti-PK SV5-Pk1 (AbD Serotech)


title: Case_18: Pulmonary metastasis of head and neck squamous cell carcinoma 18

tag: age

value: Active (80 py)

tag: tumor cell content (%)


title: ΔrnhAΔdnaArrnD-rrnE 2

value: Single colony grown in LB media and sequenced at exponential phase

value: {delta}rnhA{delta}dnaArrnD-rrnE


title: mouse liver ATAC-seq Ctrl2

tag: strain

value: liver

tag: phenotype

value: HFD flox/flox


title: clb5 clb6 Ulp2-PK HU

description: HY3886 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

tag: strain genotype

value: W303 MATa clb5::URA3 clb6::LEU2 ULP2-9PK::HIS3MX6

tag: antibody


title: cdc28-as1 Ulp2-PK HU

description: HY1434 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa cdc28-as1::URA3 ULP2-9PK::HIS3MX6


title: Tc-cdc7 Ulp2-PK HU

description: HY2007 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa ULP2-9PK::HIS3MX6 pADH1-tc3-3HA-CDC7::KANMX6


title: PBL4095-d40-9-rxn-B TCR

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

description:
KRAS-9mer tetramer-enriched T cells
single-cell 5' TCR sequencing

data_processing:
Library strategy: TCR sequencing
Fastq files were generated by Cell Ranger pipeline (v2.1.1) from 10X Genomics
Genome_build: hg19
Supplementary_files_format_and_content: with 10X Genomics, Cell Ranger can be performed to generate the data matrix

source_name: Patient's PBL on day 40 after TIL treatment

extract_protocol:
TILs were thawed and cultured overnight. PBLs were thawed and sorted by tetramers.
RNA libraries were prepared for sequencing using standard single-cell VDJ protocol from 10X Genomics

tag: cell type

value: KRAS-9mer tetramer(+) T cells from PBL

tag: description

value: TCR sequencing


title: Case_16: Pulmonary metastasis of head and neck squamous cell carcinoma 16

tag: gender

value: Male

value: Former smoker (60 py)

value: Positive

value: Oral cavity


title: Case_20: Pulmonary metastasis of head and neck squamous cell carcinoma 20

tag: smoking status (pack years)

value: Former smoker (NA)

value: Negative

value: Tounge


title: Case_12: Pulmonary metastasis of head and neck squamous cell carcinoma 12

value: Former smoker (40 py)


title: Col-0 NaCl stress rep. 2

type: RNA

city: Yokohama

first: Minoru

last: Ueda

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

organism: Arabidopsis thaliana

source_name: Col-0 NaCl-stress

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds of Arabidopsis thaliana (hda19, quad, quint, Col-0 ecotype) were grown on liguid MS medium containing 0.1% pure Agar at 22°C under 16-h-light/8-h-dark for 5 days.

extract_protocol: RNA was extracted from at least three biological replicates with the RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: The salt treatment was performed at 5 day after germination in 125 mM NaCl condition. Samples were collected at 2 h after the NaCl treatment.

tag: gentoype/variation

value: wildtype

tag: ecotype

tag: condition

value: salt stress


title: Col-0 NaCl stress rep. 3


title: L15216_NC-wo_04_D06

description: no RNA

value: negative control (no strain)

tag: genotype


title: Case_13: Pulmonary metastasis of head and neck squamous cell carcinoma 13

value: Female

tag: hpv genotyping

tag: hnsc site of origin

value: Oropharynx


title: PBL4095-d40-10-rxn-B TCR

description:
KRAS-10mer tetramer-enriched T cells
single-cell 5' TCR sequencing

value: KRAS-10mer tetramer(+) T cells from PBL

tag: tissue

value: Patient's PBL on day 40 after TIL treatment


title: L15312_NC-wo_05_D06

description: no RNA

tag: age


title: L16430_NC-wo_08_D06

description: no RNA


title: Col-0 NaCl stress rep. 1


title: Ulp2-PK YPD

description: HY1280 cells were arrested in G1 with alpha-factor for 2 h, released in media containing 0.2 M HU for 90 min, then pelleted, washed in YP and released in YPD for 30 min

source_name: HU 90 min, release in YPD for 30 min

value: W303 MATa ULP2-9PK::HIS3MX6

value: Anti-PK SV5-Pk1 (AbD Serotech)


title: Case_17: Pulmonary metastasis of head and neck squamous cell carcinoma 17

value: Male

value: Former smoker (6 py)

tag: p16 immunohistochemistry

tag: dna input [ng]

tag: tumor cell content (%)


title: PBL4095-d12-9-rxn-C TCR

source_name: Patient's PBL on day 12 after TIL treatment

value: KRAS-9mer tetramer(+) T cells from PBL

value: TCR sequencing


title: Case_14: Pulmonary metastasis of head and neck squamous cell carcinoma 14

value: Larynx


title: Case_09: Pulmonary metastasis of head and neck squamous cell carcinoma 09

value: Active (100 py)

value: Negative


title: Flag-SUMO HU

description: HY3030 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

tag: strain

tag: strain genotype

value: W303 MATa pSMT3-6HisFLAG-SMT3(KANMX6)

value: Anti-FLAG M2 F1804 (SIGMA)


title: PBL4095-d12-9-rxn-B TCR

tag: cell type

value: Patient's PBL on day 12 after TIL treatment


title: PBL4095-d12-10 TCR

tag: description


title: L14289_NC-wo_02_D06

description: no RNA

value: negative control (no strain)


title: L14193_NC-wo_01_D06

description: no RNA


title: L16238_NC-wo_06_D06

description: no RNA


title: L16334_NC-wo_07_D06

description: no RNA


title: ars Ulp2-PK HU

description: HY2144 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa ARS603.5-dis ARS604-dis ARS605-dis ARS606-dis ARS607-dis ULP2-9PK::KANMX6

tag: antibody


title: WT BrdU YPD

description: FY1110 cells were arrested in G1 with alpha-factor for 2 h, released in media containing 0.2 M HU for 90 min, then pelleted, washed in YP and released in YPD containing 200 μg/ml BrdU for 30 min

value: W303 MATa ura3::URA3/GPD-TK(7X)

value: Anti-BrdU antibody MBL M1-11-3


title: Col-0 non-stress rep. 1

source_name: Col-0 non-stress

value: wildtype

value: non-stress


title: PBL4095-d12-9-rxn-A TCR


title: WT BrdU HU

description: FY1110 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 200 μg/ml BrdU and 0.2 M HU for 90 min


title: Ulp2-PK HU #2

description: HY1280 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa ULP2-9PK::HIS3MX6

value: Anti-PK SV5-Pk1 (AbD Serotech)


title: IP mock infected RNA A549

city: CHICAGO

first: Zijie

state: IL

department: Chemistry

institute: University of Chicago

description:
m6A enriched mRNA
Ctl.align_hg38-IP
A549_jointPeak_readCount.txt

data_processing:
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Hisat2
m6A peak calling was performed using R package m6Amonster
Genome_build: hg38
Supplementary_files_format_and_content: peak

growth_protocol: HeLa (ATCC CCL-2),A549(ATCC CCL-185) cell lines were purchased from the American Type Culture Collection (Manassas, VA) and were grown in Dulbecco's modified Eagle's medium (DMEM; Life Technologies) supplemented with 10% FBS.

extract_protocol:
TRIzol (Invitrogen) + polyT beads(thermo fisher)
Kapa hyper RNA library kit

treatment_protocol: Recombinant RSV containing a green fluorescence protein (GFP) gene between the leader sequence and NS1 gene (rgRSV) (50) was propagated and titered in HeLa cells or A549 cells. To prepare purified rgRSV, 20 T150 flasks of HeLa cells or A549 cells were infected by rgRSV at an MOI of 0.1, and cell culture supernatants harvested at 48 or 72 h post-infection were clarified by centrifugation at 10,000 ×g for 30 min.

tag: group

value: mock infected

tag: cell line


title: TIL4081 TCR

description:
in vitro culture
single-cell 5' TCR sequencing

source_name: Tumor infiltrating lymphocytes (TILs)

value: Tumor infiltrating lymphocytes (TILs)


title: IP RSV infected RNA2 A549

description:
m6A enriched mRNA
RSVinfect2.align_hg38-IP
A549_jointPeak_readCount.txt

value: RSV infected


title: L14385_NC-wo_03_D06

description: no RNA


title: hda5/14/15/18/19 NaCl stress rep. 3

tag: gentoype/variation

tag: ecotype

value: salt stress


title: Ulp2-FLAG HU

description: HY0645 cells were arrested in G1 with alpha-factor for 2 h and then released in media containing 0.2 M HU for 90 min

value: W303 MATa ULP2-6His-3FLAG::KANMX6


title: TIL4071 TCR

value: TCR sequencing


title: PBL4095-d40-9-rxn-A TCR

value: KRAS-9mer tetramer(+) T cells from PBL

value: Patient's PBL on day 40 after TIL treatment


title: TIL4069 TCR


title: Ulp2-PK G1

description: HY1366 cells were arrested in G1 with alpha-factor for 2 h

source_name: G1 arrest with alpha-factor

value: W303 MATa ULP2-9PK::HIS3MX6 bar1::TRP1


title: IP viral genome RNA2 A549

description: m6A enriched mRNA

value: viral genome


title: hda5/14/15/18/19 NaCl stress rep. 2

tag: condition


title: Case_04: Pulmonary metastasis of head and neck squamous cell carcinoma 04

tag: gender

value: Male

tag: smoking status (pack years)

value: Former smoker (120 py)

tag: hpv genotyping

value: Positive

value: Oropharynx


title: Col-0 non-stress rep. 2

value: wildtype

value: non-stress


title: IP RSV infected RNA1 A549

description:
m6A enriched mRNA
RSVinfect1.align_hg38-IP
A549_jointPeak_readCount.txt


title: TIL4007 TCR

tag: tissue


title: PBL4095-d40-10-rxn-A TCR

value: KRAS-10mer tetramer(+) T cells from PBL


title: IP viral genome RNA1 A549

description: m6A enriched mRNA


title: TIL4095-4-rxn-4 TCR


title: Case_03: Pulmonary metastasis of head and neck squamous cell carcinoma 03

source_name: Lung biopsy

tag: age

value: Active (NA)

tag: p16 immunohistochemistry

value: Negative

tag: hnsc site of origin

value: Hypopharynx


title: IP mock infected RNA2 Hela

description:
m6A enriched mRNA
Hela2.alignTohg38-IP
Hela_jointPeak_readCount.txt

source_name: Hela

value: mock infected

value: HeLa


title: Col-0 non-stress rep. 3


title: Case_11: Pulmonary metastasis of head and neck squamous cell carcinoma 11

tag: dna input [ng]

tag: tumor cell content (%)

value: Oral cavity


title: TIL4095-3-rxn-3 TCR

tag: cell type

value: Tumor infiltrating lymphocytes (TILs)

value: TCR sequencing


title: Case_07: Pulmonary metastasis of head and neck squamous cell carcinoma 07

value: Former smoker (50 py)

value: HPV6, HPV 16


title: hda5/14/15/18/19 non-stress rep. 2


title: hda5/14/15/18/19 non-stress rep. 3


title: IP mock infected RNA1 Hela

description:
m6A enriched mRNA
Hela1.alignTohg38-IP
Hela_jointPeak_readCount.txt


title: Case_08: Pulmonary metastasis of head and neck squamous cell carcinoma 08

value: Male

value: Active (30 py)


title: hda5/14/15/18/19 non-stress rep. 1


title: TIL4095-2-rxn-2 TCR

tag: description


title: IP RSV infected RNA2 Hela

description:
m6A enriched mRNA
Hela.RSVinfect2.alignTohg38-IP
Hela_jointPeak_readCount.txt

value: RSV infected


title: hda5/14/15/18/19 NaCl stress rep. 1

value: salt stress


title: TIL4095-1-rxn-1 TCR


title: IP RSV infected RNA1 Hela

description:
m6A enriched mRNA
Hela.RSVinfect1.alignTohg38-IP
Hela_jointPeak_readCount.txt


title: Ulp2-PK HU

tag: strain

tag: strain genotype

value: W303 MATa ULP2-9PK::HIS3MX6

tag: antibody

value: Anti-PK SV5-Pk1 (AbD Serotech)


title: Case_05: Pulmonary metastasis of head and neck squamous cell carcinoma 05

value: Positive


title: PBL4095-d40-10-rxn-B GEX

description:
KRAS-10mer tetramer-enriched T cells
single-cell 5' mRNA sequencing

data_processing:
Fastq files were generated by Cell Ranger pipeline (v2.1.1) from 10X Genomics
Genome_build: hg19
Supplementary_files_format_and_content: with 10X Genomics, Cell Ranger can be performed to generate the data matrix

value: KRAS-10mer tetramer(+) T cells from PBL

value: transcriptome on gene expression

value: Patient's PBL on day 40 after TIL treatment


title: Case_01: Pulmonary metastasis of head and neck squamous cell carcinoma 01

value: Active (60 py)

value: Negative

value: Larynx


title: Case_10: Pulmonary metastasis of head and neck squamous cell carcinoma 10

value: Oral cavity


title: Input mock infected RNA A549

description:
Ctl.align_hg38-input
A549_jointPeak_readCount.txt

tag: group

value: mock infected

tag: cell line


title: IP viral genome RNA2 Hela

description: m6A enriched mRNA

value: viral genome

value: HeLa


title: PBL4095-d40-10-rxn-A GEX


title: Case_02: Pulmonary metastasis of head and neck squamous cell carcinoma 02

value: Male

value: Active (40 py)

value: Hypopharynx


title: PBL4095-d40-9-rxn-B GEX

description:
KRAS-9mer tetramer-enriched T cells
single-cell 5' mRNA sequencing

value: KRAS-9mer tetramer(+) T cells from PBL


title: IP viral genome RNA1 Hela

description: m6A enriched mRNA


title: hda5/14/15/18 NaCl stress rep. 3

source_name: hda5/14/15/18 NaCl-stress

tag: gentoype/variation

tag: ecotype

tag: condition

value: salt stress


title: PBL4095-d40-9-rxn-A GEX


title: Input RSV infected RNA2 A549

description:
RSVinfect2.align_hg38-input
A549_jointPeak_readCount.txt

value: RSV infected


title: Case_06: Pulmonary metastasis of head and neck squamous cell carcinoma 06

tag: gender

tag: smoking status (pack years)

value: Active (50 py)

tag: hpv genotyping


title: hda5/14/15/18 NaCl stress rep. 1


title: PBL4095-d12-10 GEX

value: KRAS-10mer tetramer(+) T cells from PBL

tag: tissue

value: Patient's PBL on day 12 after TIL treatment


title: hda19 NaCl stress rep. 3

source_name: hda19 NaCl stress

value: hda19 mutant


title: hda5/14/15/18 non-stress rep. 2

source_name: hda5/14/15/18 non-stress

value: non-stress


title: hda5/14/15/18 non-stress rep. 3


title: hda5/14/15/18 non-stress rep. 1


title: hda5/14/15/18 NaCl stress rep. 2


title: Input viral genome RNA2 A549


title: PBL4095-d12-9-rxn-C GEX

value: transcriptome on gene expression


title: Input viral genome RNA1 A549


title: PBL4095-d12-9-rxn-B GEX


title: PBL4095-d12-9-rxn-A GEX


title: Input mock infected RNA2 Hela

description:
Hela2.alignTohg38-input
Hela_jointPeak_readCount.txt


title: Input RSV infected RNA1 A549

description:
RSVinfect1.align_hg38-input
A549_jointPeak_readCount.txt


title: mouse liver RNA-seq LKO3

source_name: liver

extract_protocol: Total RNA from liver tissue was extracted using TRIzol method, library was sequenced by BGI 500 instrument with 50-bp single-ended reads.

value: liver

tag: phenotype

value: HFD LKO


title: hda19 NaCl stress rep. 2


title: TIL4081 GEX

description:
in vitro culture
single-cell 5' mRNA sequencing

value: Tumor infiltrating lymphocytes (TILs)


title: Input mock infected RNA1 Hela

description:
Hela1.alignTohg38-input
Hela_jointPeak_readCount.txt

value: mock infected


title: mouse liver RNA-seq LKO2


title: TIL4071 GEX


title: hda19 non-stress rep. 2

source_name: hda19 non-stress


title: genomic DNA from normotrophic scar fibroblasts from patient 4

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description: Normotrophic Scar Fibroblast DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Methylation data was imported from the raw files using Illumina® GenomeStudio and analysed using R statistics software, using the RnBeads package

label: Cy3 and Cy5

source_name: Patient 4 Scar

growth_protocol: 3mm punch biopsies were taken from the forearm scar site and a matched site on the uninjured forearm by the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and a drop of 100% foetal bovine serum (FBS) added to the surface of each piece. They were then cultured in DMEM with 10% FBS and 5% pen/strep until passage 2, at which point DNA and RNA was extracted.

extract_protocol: Genomic DNA was extracted using either the Promega Wizard SV Genomic DNA system (Patients 1 and 2, Promega, USA) or the QIAamp DNA mini kit system (Patients 3-6, Qiagen, Netherlands) as per manufacturer’s instructions

treatment_protocol: There were no treatments applied to the scar and control cells in vitro. DNA was bisulfite treated prior to processing on the chip

tag: Sex

tag: age (years)

tag: time since injury (years)


title: mouse liver RNA-seq LKO1


title: hda19 non-stress rep. 3


title: genomic DNA from normotrophic scar fibroblasts from patient 3

description: Normotrophic Scar Fibroblast DNA

source_name: Patient 3 Scar


title: hda19 NaCl stress rep. 1


title: mouse liver RNA-seq Ctrl2

value: HFD flox/flox


title: TIL4007 GEX

tag: cell type

tag: description


title: Diabetes Sample 2 (snRNAseq)

city: SAINT LOUIS

first: Parker

middle: C

last: Wilson

state: MO

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

description: snRNAseq

data_processing:
Count matrices were generated with zUMIs v2.0 and saved as .rds files
Seurat objects were created from the count matrices and filtered using min.cells=3 and low.thresholds=500 (Seurat v2.3.4)
Seurat objects from control and diabetic samples were combined using the RunMultiCCA function to generate combined.rds
Genome_build: GRCh38
Supplementary_files_format_and_content: individual rds files were generated from count matrices using zUMIs v2.0 and Seurat v2.3.4

source_name: Human Diabetic Kidney

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 10e6 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Samples were cut into <2-mm pieces and homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and then centrifuged at 500×g for 5 minutes at 4°C. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1× PBS, 0.07% BSA, and 0.1% RNase inhibitor), filtered through a 20-μm cell strainer (43–50020–50; pluriSelect), and counted.
Libraries were prepared according to Illumina's instructions and accompanying 10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit
Single Nucleus RNA Sequencing (snRNAseq)

value: kidney

tag: disease state

value: diabetic

tag: age

tag: gfr

tag: global glomerulosclerosis

tag: ifta

value: M


title: Input viral genome RNA2 Hela

tag: group

value: viral genome

tag: cell line

value: HeLa


title: Diabetes Sample 1 (snRNAseq)

description: snRNAseq

value: Moderate 26-50%

tag: gender


title: mouse liver RNA-seq Ctrl1

tag: strain


title: genomic DNA from normotrophic scar fibroblasts from patient 2

description: Normotrophic Scar Fibroblast DNA

source_name: Patient 2 Scar

value: Male


title: Diabetes Sample 3 (snRNAseq)

description: snRNAseq

value: F


title: TIL4095-4-rxn-4 GEX


title: hda19 non-stress rep. 1

tag: gentoype/variation

tag: ecotype

tag: condition


title: Input RSV infected RNA1 Hela

description:
RSVinfect1.alignTohg38-input
Hela_jointPeak_readCount.txt

value: RSV infected


title: genomic DNA from normotrophic scar fibroblasts from patient 5

description: Normotrophic Scar Fibroblast DNA

source_name: Patient 5 Scar

tag: Sex


title: Input viral genome RNA1 Hela


title: genomic DNA from normotrophic scar fibroblasts from patient 1

description: Normotrophic Scar Fibroblast DNA

source_name: Patient 1 Scar

tag: age (years)


title: Young adult

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

data_processing:
The original raw data from Nanopore MinION are trasformed to sequenced reads by basecailling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using porechop (V0.2.4), then mapped to to C. elegans genome (WS260) using minimap2 (V2.14).
The mapping result are tranformed to bigGenPred format using scripts in TrackCluster package.
The isoform calling and quantification are carried out with TrackCluster.
Genome_build: WS260
Supplementary_files_format_and_content: csv file containing the normalized read count for each isoform and the read track for each stage

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Young adult

extract_protocol:
Animals of different stages, i.e., embryo, L1 larva and young adult, were collected and total RNAs were extracted using TRIzol (Invitrogen) following the manufacturer’s instructions. Approximately 100 µg total RNAs were extracted for each sample. Around 900 ng of poly-A tailed mRNAs was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) based on the user’s manual for each library preparation.
Nanopore sequencing libraries were constructed using Direct RNA sequencing kit (cat# SQK-RNA001). The libraries were loaded onto Nanopore R9.4.1 flow cell (cat# FLO-MIN106) and sequenced on MinION acquired from Oxford Nanopore Technologies. The software used for sequencing was MINKNOW 2.1 with base-caller, Albacore (v2.0.1).

tag: Stage

value: Young adult

tag: tissue

value: Whole worm


title: genomic DNA from control fibroblasts from patient 5

description: Normal Fibroblast DNA

source_name: Patient 5 Control

tag: time since injury (years)


title: L1 larva

source_name: L1 larva

value: L1 larva


title: TIL4095-2-rxn-2 GEX

source_name: Tumor infiltrating lymphocytes (TILs)

tag: cell type

tag: description

value: transcriptome on gene expression


title: genomic DNA from normotrophic scar fibroblasts from patient 6

description: Normotrophic Scar Fibroblast DNA

source_name: Patient 6 Scar


title: TIL4095-1-rxn-1 GEX


title: P3_11

status: Public on Sep 09 2019

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

institute: Helmholtz Zentrum München

description:
384-plate, all 4 cell types
cell IDs were assigned based on FACS gating strategy
single cell RNA

data_processing:
Raw sequencing data for both single cell and bulk experiments were controlled for quality and trimmed.
For scRNA-seq paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
The file GEO_info_cellbarcodes_cellid.txt (available on the series record) contains the cell barcode ID, which is also the processed data column header, cell barcode and cell markers. The same barcodes and IDs were used for each count*P.csv  file.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Bulk RNA-seq data were mapped to the reference mm10 genome using STAR (Dobin et al., 2013).
The identity of reads was identified through FeatureCount (Liao et al., 2014).
For scRNA-seq analyses, the RNA expression matrices from each cell were merged and further analysed with RaceID3 software package (Herman et al., 2018).
For both scRNA-seq and the bulk Brain-FACS RNA-seq analyses, differentially expressed genes between the cell types or cell clusters were identified using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited and csv text files include count matrices for scRNA-seq data and bulk RNA-seq samples

source_name: E14.5 brain

extract_protocol:
Mouse E14.5 brain was dissociated and either mCEL-Seq2 protocol for scRNA-seq or population-based FACS-sorting and bulk RNA-seq was performed.
scRNA-seq libraries were prepared according to mCEL-Seq2 protocol. Libraries were sequenced on an Illumina HiSeq 3000 sequencing system (pair-end multiplexing run, high output mode) at a depth of ~200,000 reads per cell. Population-based FACS-sorting and bulk RNA-seq  from neural cells was isolated using the Qiagen mini kit (#74104), while RNA from mural cells, endothelial cells and microglia was extracted using the Qiagen miRNeasy Micro kit (#1071023). Libraries for RNA-seq of the neural population were prepared using the Illumina TruSeq library preparation kit. For mural cells, endothelial cells and microglia, cDNA was prepared from isolated RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech 634891). Libraries were prepared using the Nextera XT DNA library preparation kit (Illumina FC-131-1096) and sequenced on the HiSeq 2500 instrument.

value: mixture of 4 cell types (non-demultiplexed)

value: brain

tag: developmental stage


title: Mix-stage embryo

source_name: Mix-stage embryo

value: Mix-stage embryo


title: TIL4095-3-rxn-3 GEX

value: Tumor infiltrating lymphocytes (TILs)


title: P3_10


title: genomic DNA from control fibroblasts from patient 4

description: Normal Fibroblast DNA

source_name: Patient 4 Control


title: P2_8


title: P3_9


title: P2_6


title: P2_7


title: P2_5


title: P1_3


title: H3K9ac-input

city: shanghai

first: min

last: liu

address: huashan road

institute: shanghaijiaotong university

data_processing:
Illumina NextSeq 500 used for sequencing
The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 (v2.2.6) software
Peak detection was performed using the MACS (v2.1.1)  peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file obtained by annotating the peak with the ChIPseeker package in the original file KO_peaks.narrowPeak.chr.xlsx after MACS2 search.

source_name: Intestinal epithelial cells

extract_protocol:
Intestinal epithelial cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti- H3K9ac antibodies.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq 500 with single-end 1x75 as the sequencing mode.

tag: age

value: Two-month-old

tag: genotype


title: H3K9ac-WT


title: P1_1


title: H3K9ac-KO


title: P1_2


title: BAT_KO_2 (RNA-seq)

city: Singapore

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

description:
RNA-seq_FPKM.xlsx
KO_BAT_2

data_processing:
Reads were aligned to mm10, using Tophat (version tophat-2.0.11) and genes were quantified using Cufflinks (Version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs of genes

source_name: Brown Adipose

growth_protocol: HuRflox/flox mice were originally purchased from the Jackson Laboratory and subsequently bred in house. HuRflox/floxmice were backcrossed with C57BL/6 mice for 2 generations and then used to cross adiponectin-Cre mice to generate AdipoQ-Cre;HuRf/+ mice. Heterozygous AdipoQ-Cre;HuRf/+ were then crossed with HuRf/f  to produce homozygous AdipoQ-Cre;HuRf/f. AdipoQ-Cre;HuRf/f were further bred with HuRf/f mice to generate AdipoQ-Cre;HuRf/f (HuR-FKO) and littermate HuRf/f controls (Ctrl) for experiments. All mice were kept under specific pathogen–free conditions in the animal vivarium at DUKE-NUS Medical School. All animal experimental protocols were approved by the Singapore SingHealth Research Facilities Institutional Animal Care and Use Committee.

extract_protocol:
Qiagen miRNeasy Mini Kit
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: huR knockout

value: brown fat

value: 12 weeks


title: BAT_WT_1 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_Bat_1

value: control


title: BAT_KO_1 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
KO_BAT_1


title: genomic DNA from control fibroblasts from patient 3

description: Normal Fibroblast DNA

source_name: Patient 3 Control


title: genomic DNA from control fibroblasts from patient 1

description: Normal Fibroblast DNA

source_name: Patient 1 Control


title: genomic DNA from control fibroblasts from patient 6

description: Normal Fibroblast DNA

source_name: Patient 6 Control


title: Epi_KO_1 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
KO_EPI_1

source_name: Epididymal

value: epididymal white fat


title: Epi_KO_3 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
KO_EPI_3


title: Ing_KO_2 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
KO_ING_2

source_name: Inguinal

value: inguinal white fat


title: Ing_WT_3 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_ING3


title: Epi_KO_2 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
KO_EPI_2


title: Epi_WT_1 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_EPI_1


title: Ing_KO_1 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
KO_ING_1


title: Epi_WT (RIP-seq)

description:
Rip-seq_EPI.xlsx
WT_EPI_Rip-seq

extract_protocol:
Qiagen miRNeasy Mini Kit
NEBNext® Ultra™ RNA Library Prep Kit

treatment_protocol: eWATs from 6 weeks old control (HuRf/f) and huR knockout (AdipoQ-Cre; HuRf/f) were harvested. RNA immunoprecipitation (RIP) was performed using HuR antibody (Santa Cruz).

value: 6 weeks old

tag: rip antibody

value: HuR antibody (Santa Cruz)


title: Epi_WT_3 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_EPI3


title: Epi_KO (RIP-seq)

description:
Rip-seq_EPI.xlsx
KO_EPI_Rip-seq


title: genomic DNA from control fibroblasts from patient 2

description: Normal Fibroblast DNA

source_name: Patient 2 Control

value: Male


title: Ing_WT_2 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_ING2


title: Ing_WT_1 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_ING_1


title: BAT_WT_2 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_Bat_2


title: Epi_WT_2 (RNA-seq)

description:
RNA-seq_FPKM.xlsx
WT_EPI2


title: NGN2-48hrs

city: New Haven

first: Albert

middle: E.

last: Ayoub

state: CT

address: 333 Cedar St. SHM C317

department: Neurobiology

institute: Yale University

data_processing:
Tophat 1.42
Samtools 0.1.18; samtools sort -n; samtools view
Samtools 0.1.18
RSEQTools 0.6; sam2mrf; mrfQuantifier
Genome_build: hg19/RheMac2/mm9
Supplementary_files_format_and_content: EnsemblGene/RPKM

source_name: dorsal neocortex

extract_protocol:
Qiagen RNAeasy microkit
standard illumina strand specific protocol

tag: tissue subtype

value: in utero electroporation

tag: sample type

value: Laser-microdissected

tag: time point

value: Neurog2 48hrs survival


title: NGN1-48hrs

tag: strain


title: NGN2-24hrs

value: Neurog2 24hrs survival


title: DNM2-48hrs

value: dnMAML 48hrs survival


title: DNM2-24hrs

value: dnMAML 24hrs survival


title: DNM1-48hrs


title: DNM1-24hrs


title: C1-24hrs

value: control 24hrs survival


title: C1-48hrs

value: control 48hrs survival


title: C2-48hrs


title: E17-2-SVZo

tag: tissue/cell type

value: Occipital cortex

value: Subventricular & Intermediate Zone


title: E17-2-VZf

value: Frontal cortex

value: Ventricular Zone


title: E17-2-CPf

value: Cortical Plate


title: E17-2-VZo


title: E12 replicate 1

value: dorsal neocortex

value: microdissected


title: E12 replicate 2


title: E11 replicate 1


title: E11 replicate 2


title: E17-1-Vzf


title: E17-2-CPo


title: E17-1-SVZf


title: wt_1

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

data_processing:
fastqc tool was used to ensure high data quality (v. 0.11.5)
fastq files were mapped to the Caenorhabditis elegans genome (Ensembl genome version WBcel235) using the STAR algorithm (v. 2.5.2b)
the reads were counted per gene using the featureCounts tool from the SubRead package (v. 1.4.6-p4)
differentail expression analysis was done using DESeq2 (v. 1.18.1)
Genome_build: WBcel235
Supplementary_files_format_and_content: counts

source_name: whole worms

extract_protocol:
Adult animals were hand-picked 24h past the mid-L4 larval stage and total RNA was extracted using Trizol following the standard protocol. mRNA was enriched using Ribo-Zero Gold Kit (human, mouse, rat) from Illumina according to the manufacturer’s instructions.
Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra Directional RNA Library Prep II, NEB).

tag: type

value: total RNA

value: wild-type


title: C2-24hrs

value: in utero electroporation


title: gld2_1

value: KO gld2


title: wt_3


title: gld2_2


title: gld2_3


title: NGN1-24hrs

value: Laser-microdissected


title: E17-2-SVZf


title: gld2-ccr4_1

value: dKO gld2 ccr4


title: gld2-ccr4_2


title: E17-1-Cpf


title: Ing_KO_3 (RNA-seq)

first: Lei

description:
RNA-seq_FPKM.xlsx
KO_ING3

value: huR knockout

value: inguinal white fat

value: 12 weeks


title: gld2-ccr4_3


title: gld2-ccf1_2

value: dKO gld2 ccf1


title: gld2-ccf1_1


title: gld2-parn1_1

value: dKO gld2 parn1


title: gld2-parn1_2


title: gld2-ccf1_3


title: gld2-parn1_3


title: wt_2


title: TIL4069 GEX

value: Tumor infiltrating lymphocytes (TILs)

value: transcriptome on gene expression


title: Input RSV infected RNA2 Hela

last: Zhang

description:
RSVinfect2.alignTohg38-input
Hela_jointPeak_readCount.txt

source_name: Hela

tag: group

value: RSV infected

tag: cell line

value: HeLa


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD012

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: single-nucleus methyl-3C sequencing (sn-m3C)
Raw reads were trimmed first 25bp and last 3bp of both read1 and read2 to remove random primer sequence and adaptase low complexity tails. For the alignment, Bismark is used. C to T converted and G to A converted reference genomes are prepared for hg19 using bismark_genome_preparation. Each read end is mapped separately using Bismark with Bowtie1 with read1 as complementary (always G to A converted) and read2 (always C to T converted) as original strand. After first alignment, unmapped reads are retained and splitted into 3 pieces by 40bp, 32bp, and 40bp after removing 5bp of both ends results in having 6 reads (read1 and read2). Six reads derived from unmapped reads are mapped separately using Bismark Bowtie1. All aligned reads are merged into BAM using picard that is query name sorted. The fragments with all the mapped reads aligned to the same positions are considered as duplicates and removed and DNA methylation tracks are generated. For each fragment, the outermost aligned reads are chosen for the chromatin conformation map generation.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
tab delimited text files of contact.txt files; columns in contact.txt files are: column 1 - Sample_ID; column 2- chromosome_1; column 3 - Position_1; column 4 - Chromosome_2 ; column5 - Position_2; column6 - Strand_1; column 7 - Strand_2

source_name: Human frontal cortex

growth_protocol: Postmortem human brain biospecimens were obtained from brain donors of NIH NeuroBioBank and University of Maryland Brain and Tissue Bank.

extract_protocol: in situ Hi-C was performed as previously described using the NlaIII restriction enzyme. in situ 3C experiments were performed based on the previously described in situ Hi-C protocol with minor modifications. Briefly, prior to fixation, adherent cells were trypsinized, counted, and collected by centrifugation, and suspension cells were counted and collected by centrifugation. Cells were resuspended in culture media at a concentration of 1x106 cells per mL of media and fixed in 1% formaldehyde for 10 minutes at room temperature with shaking. For standard species mixture experiments, equal numbers of mouse and human cells were combined into a single tube prior to fixation. For the 1:10 dilution species mixture experiment, cells were resuspended at a concentration of 1x105 cells per mL of media prior to fixation. For the species mixture experiments where samples were mixed after fixation, each cell type was fixed independently as described above and combined at later stages in the protocol. in situ Hi-C samples were digested with the MboI restriction enzyme and processed as described previously. For in situ 3C experiments, samples were digested with DpnII enzyme overnight at 37ºC with gentle mixing. The following day, the sample was incubated at 62ºC for 10 minutes to inactivate the restriction enzyme. The typical biotin fill in step in the Hi-C protocol is omitted. The sample is then ligated for 4 hours at room temperature with T4 DNA ligase in the same manner as in in situ Hi-C experiments. The sample is then stained with Hoechst (0.1µg/µL) for the final 30 minutes of the ligation step. The sample is then passed through a 40 µM nylon cell strainer (Corning 431750) into a FACS tube prior to sorting. As a quality control step, 10% of the sample is taken for conventional library preparation and sequenced using shallow sequencing on a MiSeq. Libraries for bulk and single-cell methylomes were generated using snmC-seq2. A detailed step-by-step bench protocol for snmC-seq2 is provided as Supplement Methods in Luo et al. (2018) 23. Bulk methylome libraries were prepared manually using individual tubes. Single-cell methylome libraries were prepared using a Tecan Evo 100 robotic platform as described in Luo et al. (2018) 23. Sequencing libraries were sequenced using Illumina MiSeq and HiSeq 4000 instruments in PE150 mode.

value: frontal cortex

tag: Sex

value: Male

tag: donor


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD010

tag: tissue


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H8_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD004


title: P1_4

tag: cell type

value: mixture of 4 cell types (non-demultiplexed)

value: brain


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H8_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H8_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H9_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H8_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H7_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H7_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H7_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H8_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H7_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H8_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H7_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H6_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H6_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H6_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H6_AD001


title: HCT116_WT_Ctrl_3weeks

city: Kitakyushu

first: Masaoki

last: Kohzaki

state: Fukuoka

address: 1-1 Iseigaoka Yahatanishi-ku

department: Institute of Industrial Ecological Sciences

institute: University of Occupational and Environmental Health, Japan

description:
Purified Genomic DNA
1 month culture with no treatment.

hyb_protocol: Samples were prepared and hybridized to Cytoscan HD Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an AGCC (Affymetrix GeneChip Command Console) system according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Analysis Software (Chromosome Analysis Suite/ChAS).
The resulting cychp files are generated by the Affymetrix Analysis Software (Chromosome Analysis Suite/ChAS).

label: Biotin

growth_protocol: HCT116 cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin.

extract_protocol: Genomic DNA was extracted (Qiagen, 69506).

treatment_protocol: Exponentially growing WT and RECQL4ΔC HCT116 clones were treated either with or without 10 uM cisplatin for 2 h and trypsinized to establish single clones using 96-well plates. After 2 weeks of treatment with or without 1 uM EGC, several clones that grew normally were selected and expanded for 3 weeks.

value: HCT116 (RIKEN RCB2979)

tag: genotype/variation

value: WT

tag: treatment

value: Cell expansion


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD004

tag: age


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD007


title: HCT116_WT_Cisplatin_EGC_No.1

description:
Purified Genomic DNA
Cisplatin treatment then 1 month culture with EGC for first 2 weeks.

label_protocol: Samples were prepared and hybridized to Cytoscan HD Array according to Affymetrix specifications.

value: Cisplatin treatment then cell expansion with EGC


title: Genomic DNA from glioma sample; IDHwt_GBM_34

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

hyb_protocol: DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Scanned data files were analyzed with Affymetrix Chromosome Analysis Suite v3.1 (ChAS) (Affymetrix Inc., USA) using the CytoScanHD_Array.na33.annot.db annotation file on hg19 genome. To find copy numbers variations, single sample analysis strategy were done using the reference model file “CytoScanHD_Array.na33.r2.REF_MODEL”. To prevent false positive CNVs detection arising due to inherent microarray “noise”, only alterations that involved at least 50 consecutive probes and spanning more than 100 kbp were considered in the analysis.
Matrix of CNV fragments from single sample analyses

source_name: DNA from Glioma sample

growth_protocol: Immediately after surgery, glioma samples were snap-frozen and stored in liquid nitrogen. non-tumoral control brain samples were cadaveric specimens removed by autopsy 4-16 h following accidental death (Brain and Tissue Bank of Maryland).

extract_protocol: DNA  were isolated from frozen  tissue samples  using the QIAamp DNA Mini Kit (Qiagen, Hamburg, GmbH)

tag: disease

value: glioma

tag: gliomas classification

value: IDH statut:IDHwt

tag: gender


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD008


title: Genomic DNA from glioma sample; IDHmut_GIII_22

label_protocol: DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.

value: grade:Grade IIII

value: IDH statut:IDHmut

value: Female


title: Genomic DNA from glioma sample; IDHwt_GIII_17


title: Genomic DNA from glioma sample; IDHmut_GII_5

value: grade:Grade II


title: HCT116_RecQL4_EGC_No.1

description:
Purified Genomic DNA
1 month culture with EGC for first 2 weeks.

value: RECQL4 KO

value: Cell expansion with EGC


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD002


title: HCT116_RecQL4_Cisplatin_No.3

description:
Purified Genomic DNA
Cisplatin treatment then 1 month culture.

value: Cisplatin treatment then cell expansion


title: Genomic DNA from glioma sample; IDHwt_GIII_11


title: HCT116_RecQL4_Ctrl_3weeks


title: HCT116_WT_EGC_No.2


title: Genomic DNA from glioma sample; IDHwt_GBM_4


title: Genomic DNA from healthy donor 4; frontal cortex

source_name: DNA from  frontal cortex

value: healthy

value: grade:not applicable

value: IDH statut:not applicable


title: HCT116_RecQL4_Cisplatin_EGC_No.1


title: Genomic DNA from glioma sample; IDHwt_GBM_27


title: Genomic DNA from glioma sample; IDHwt_GBM_7


title: Genomic DNA from glioma sample; IDHmut_GIII_24

value: Male


title: Genomic DNA from glioma sample; IDHmut_GII_2


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H5_AD001

value: frontal cortex


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H4_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H4_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H3_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H4_AD002


title: Genomic DNA from healthy donor 4; corpus callosum

source_name: DNA from corpus callosum


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H3_AD006


title: HCT116_RecQL4_original_clone

description:
Purified Genomic DNA
Original control.

value: HCT116 (RIKEN RCB2979)

value: Original control


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H4_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H3_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H3_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H4_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H2_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H2_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H2_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H1_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H1_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H1_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H1_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H2_AD007


title: HCT116_WT_original_clone

description:
Purified Genomic DNA
Original control.

value: WT


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H2_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H4_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H1_AD006


title: Genomic DNA from glioma sample; IDHwt_GIII_4

value: glioma


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD010


title: HCT116_WT_Cisplatin_No.2


title: Genomic DNA from glioma sample; IDHwt_GIII_12

value: IDH statut:IDHwt


title: Genomic DNA from glioma sample; IDHmut_GII_4


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H12_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H2_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H10_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H10_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H10_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G9_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G9_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G9_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G8_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G9_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G8_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G8_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H1_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G8_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G8_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G8_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G7_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G7_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G7_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H11_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H10_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G7_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G6_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G6_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G6_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G6_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_H3_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G5_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G5_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G6_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G5_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G3_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G3_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G4_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G7_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G4_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G5_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G4_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G3_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G3_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G2_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G2_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G2_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G2_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G2_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G2_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G1_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G1_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G1_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G5_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G4_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G3_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G1_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G11_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G11_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G11_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G11_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G11_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G1_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F9_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G12_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F9_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G10_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F9_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F9_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F8_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F8_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F8_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F9_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_G11_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F8_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F8_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F7_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F8_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F6_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F6_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F7_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F7_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F5_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F6_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F5_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F5_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F5_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F6_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F5_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F7_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F4_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F4_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F4_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F4_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F6_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F2_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F3_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F2_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F3_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F3_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F2_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F2_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F3_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F2_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F1_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F11_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F11_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F11_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F11_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F10_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F10_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F10_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F11_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F10_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E9_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F10_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F10_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E9_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E8_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E8_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E8_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E8_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_F12_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E7_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E7_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E7_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E6_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E6_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E7_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E6_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E6_AD012


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E7_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E6_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E9_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E5_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E5_AD002


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E3_AD004


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E5_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E2_AD008


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E2_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E2_AD010


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E2_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E3_AD001


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E1_AD007


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E12_AD006


title: 190315_snm3Cseq_hs_29yr_BA10_UMB5580_5_UMB5580_6_E12_AD008