title: 631-GFP+

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: tumor dissociation and cell sorting

hyb_protocol: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray  were scanned on an Agilent G2505C scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: mammary tumor

label_protocol: manufacturer's instructions

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Mammry tumor were dissociated by Mouse Tumor Dissociation Kit (Miltenyi Biotec) and single cell suspension were sored by FACSAria flow cytometer (BD Biosciences) using GFP and CD49f as sorting criteria.

tag: sorted cells


title: 567-GFP-

status: Public on May 02 2019

type: RNA

description: tumor dissociation and cell sorting

molecule: total RNA

organism: Mus musculus


title: 566-GFP-

description: tumor dissociation and cell sorting


title: E10_5_CTRL_OFT_RV_RNA_seq_rep4

type: SRA

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description:
E10_5_CTRL_OFT_RV_RNA_seq.bw
E10_5_Isl1_hypo_OFT_RV_quanty_transcripts_diff_expr.txt

library_source: transcriptomic

data_processing:
RNA-Seq reads were mapped to the mm9 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000). Samples were quantified using analyzeRepeats.pl (mm9 –count exons –strand both –noadj). Differential expression (fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR. The KNIME 2.9.1 platform (Konstanz, Germany) was used to filter differentially regulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: bw, differential expressed DESEq2 file

molecule: polyA RNA

extract_protocol: Outflow tract and right ventricle of E10.5 control and Isl1 hypomorphic embryos were dissected and stored at −80 °C in Qiazol. After genotyping, total RNA from single embryos was extracted using Rneasy Microarray Tissue Kit (Qiagen #73304). The integrity of RNA was assessed on Bioanalyzer 2100 (Agilent). For RNA-Seq of control and Isl1 hypomorphic tissue samples, 100 ng of total RNAs was used for library preparation and sequenced on BGISEQ-500.

tag: embryonic stage

tag: tissue

value: dissected outflow tract and right ventricle

tag: strain

tag: genotype

value: wild type


title: training cohort patient 05

city: Berlin

first: Ingeborg

last: Tinhofer

address: Chariteplatz 1

department: Dept of Radiooncology and Radiotherapy

institute: Charite University Hospital

hyb_protocol: Hybridization was carried out according to the standard NanoString nCounter® XT Assay protocol.

scan_protocol: Data Collection was carried out in the nCounter® Digital Analyzer. Digital images were processed on the nCounter Digital Analyzer and the barcode counts were tabulated in a comma separated value (CSV) format.

data_processing:
Raw expression data were analyzed with the nSolver Analysis Software version 4.0 using the Advanced Analysis Module (NanoString Technologies).
For background correction, the geometric mean of negative controls was subtracted from the counts of each gene. The geometric mean of the housekeeping genes was used to calculate a normalization factor for each sample.

label: biotin

organism: Homo sapiens

source_name: primary oropharyngeal carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard NanoString nCounter® XT Assay protocol from 100 ng total RNA.

extract_protocol: FFPE tissue slides (5-µm) were stained with hematoxylin and eosin (HE) and reviewed by a pathologist to delineate tumor areas. RNA was isolated from macrodissected tumor areas using the High Pure FFPE RNA Micro Kit (Roche) according to the manufacturer’s protocol.

tag: cohort

value: training

tag: disease status

value: oropharyngeal squamous cell carcinoma (OPSCC)

value: primary oropharyngeal carcinoma

tag: 3-year os status

value: alive

tag: hpv status


title: 566-GFP+

description: tumor dissociation and cell sorting


title: 567-GFP+

description: tumor dissociation and cell sorting


title: training cohort patient 04

value: deceased

value: not available


title: 573-GFP-

description: tumor dissociation and cell sorting


title: 631-GFP-

description: tumor dissociation and cell sorting


title: 573-GFP+

description: tumor dissociation and cell sorting


title: VDHG_Glc2

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

country: USA

institute: University of California, San Diego

description:
RNA sample 2 of V. sp. dhg which was grown in glucose medium
Total RNA without ribosomal RNA

data_processing:
The quality of the sequence reads obtained from RNA-seq was checked by FastQC.
The sequence reads were aligned to the reference genome using bowtie2.
The Cufflink package (http://cufflinks.cbcb.umd.edu/) was run to obtain transcriptomic data.
Genome_build: The genome sequence of V. sp. dhg has been uploaded to Genbank (accession number: CP028943, CP028944, and CP028945).
Supplementary_files_format_and_content: gtf, FPKM values for each gene
*_1_transcripts.gtf corresponds to CP028943
*_2_transcripts.gtf corresponds to CP028944
*_3_transcripts.gtf corresponds to CP028945

organism: Vibrio sp. dhg

source_name: KCTC 13229BP

growth_protocol: For expression profiling, V. sp. dhg was cultured in buffered minimal medium supplemented with alginate, mannitol, or glucose as a sole carbon source, and harvested at early exponential phase (OD600=0.6).

extract_protocol:
Total RNA including small RNAs was extracted by using an RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Then, the ribosomal RNAs were removed from the total RNA using the Ribo-Zero rRNA Removal Kit for Gram-negative bacteria (Illumina, San Diego, USA).
The strand-specific RNA-seq library was constructed using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina platforms according to the manufacturer’s instructions.

treatment_protocol: The cells were treated with RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany).

value: sp. dhg

value: wildtype

tag: carbon source

value: glucose


title: E10_5_CTRL_OFT_RV_RNA_seq_rep3


title: E10_5_CTRL_OFT_RV_RNA_seq_rep2


title: VDHG_Alg1

description:
RNA sample 1 of V. sp. dhg which was grown in alginate medium
Total RNA without ribosomal RNA

value: alginate


title: training cohort patient 02


title: VDHG_Glc1

description:
RNA sample 1 of V. sp. dhg which was grown in glucose medium
Total RNA without ribosomal RNA


title: training cohort patient 03


title: E10_5_CTRL_OFT_RV_RNA_seq_rep1


title: VDHG_Alg2

description:
RNA sample 2 of V. sp. dhg which was grown in alginate medium
Total RNA without ribosomal RNA


title: dsEGFP-S2 (small RNA-seq)

status: Public on May 01 2019

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

country: China

institute: Wuhan University

data_processing:
For the analysis of small RNA sequencing data, we followed a workflow that was described previously (M.Lee, V.N.Kim et al., Mol cell,56(2014) 696-707).
Briefly, for the annotation of Drosophila miRNAs, abundance collapsed reads, after read quality control and adapter trimming, were mapped to mature miRNA sequences annotated in miRBase (www.mirbase.org, version 21) with no mismatch allowed.
Sample-wise normalization of miRNA reads by mapped reads was done with reads per million (RPM) normalization.
Genome_build: Dm3
Supplementary_files_format_and_content: txt files report count reads in number for each miRNA

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: S2 cells, obtained from the China Center for Type Culture Collection (CCTCC), were cultured and maintained in Schneider’s Insect Medium (Sigma) containing 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin solution (Hyclone).

extract_protocol:
Total RNAs from S2 cells were extracted by Trizol (RNAiso plus, Takara) and DNA was removed by DNase I (Thermo Fisher) treatment.
TruSeq Small RNA Library Preparation Kits (Illumina)

treatment_protocol: The cells were transfected by purified dsRNA using Fugene HD tranfection reagent (Promega).

tag: cell line

tag: transfection

value: EGFP dsRNA

value: control


title: dsTrf4-1-S2 (small RNA-seq)

value: Trf4-1 dsRNA

value: Trf4-1 knockdown


title: xct2_RNA_2

city: Davis

first: Stacey

last: Harmer

state: CA

address: 1002 Green Hall, One Shields Ave.

department: Plant Biology

institute: UC Davis

data_processing:
For RNA sequencing, reads were mapped to Arabidopsis TAIR10 representative gene models with BWA [Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler   transform. Bioinformatics 25: 1754-1760. ]   using the parameters –k 1 –l 25 –n 0.1 –e 12 –i 100. Reads were quality filtered such that only those   with a quality cut-off score of 20 or greater over 85% or more of the 100-nucleotide   sequence were retained.  Reads were separated by their barcodes and Illumina adapter   contamination was removed, resulting in a total of 58.0, 53.3, 48.7, and 55.7 million   high-quality reads for the Col, xct-1, xct-2, and xct-2 xap5 genotypes, respectively. 80.1% of the Col, 80.1% of the xct- 1, 77.2% of the xct-2, and 80.6% of the xct-2 xap5 reads mapped to the TAIR10 gene   models.
For Bisulfite Sequencing, we used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  reference scaffold, allowing up to two mismatches per read. 100 base reads were divided in half and 50 base reads were processed as single reads.  Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR8 for bisulfite sequencing analysis, TAIR10 for RNA-se analysis
Supplementary_files_format_and_content: Differential expression analysis of the three experimental genotypes (xct-2, xct-1, and xct-2 Xap5) compared to wild type (Col) is provided in .csv format.  The log2 fold-change, log2 counts per million, p-value, and false discovery rate (multiple-measure corrected p-values) are included for each mutant compared to wild type.  All expressed genes (including those regulated by the circadian clock) are included in this analysis.

organism: Arabidopsis thaliana

source_name: seedlings 12days old

growth_protocol: For both the bisulfite sequencing and RNA-seq experiments, seeds were ethanol sterilized.  Arabidopsis genotypes used included Col, xct-1, xct-2,   and xct-2 xap5 (line S2X5-1).  Seeds were sown onto 1X MS media containing 1.5%   (w/v) sucrose.  Following cold stratification, seed plates were transferred to 12 hour   light/12 hour dark (12:12 L/D) cycles under 55 umol m-2 s-1 white light at constant 22 degrees C.    Plants were grown in this condition for 11 days and on the 12th day of growth at three   hours after dawn plant tissue from each genotype was harvested and flash frozen in liquid   nitrogen.

extract_protocol:
For RNA-seq library construction, total RNA was isolated from frozen plants   using the TRIzol reagent and protocol (Invitrogen) according to manufacturer   instructions.  The Ribo-Zero rRNA Removal Kit-Plant Leaf (Epicentre) was used   according to manufacturer instructions to remove rRNAs from the total RNA population.  For bisulfite sequencing, genomic DNA was extracted (Qiagen DNeasy plant tissue mini   protocol) using 10 seedlings for each sample.
For RNA-seq, 100 ng of RNA from the rRNA-depleted total RNA samples were used to construct   strand-specific libraries for RNA sequencing according to the protocol described in Wang L et al. (2011) PLoS One 6: e26426.  Twelve libraries (three each generated from Col, xct-1, xct-1, and xct-2 xap5 line S2X5-   1) were multiplexed and sequenced on two lanes of an Illumina HiSeq.  100 cycle runs   were used to generate single-end reads.    For bisulfite sequencing, the library construction protocol was adapted from Zemach A et al. (2013) Cell 153: 193-205. In brief, for adapter preparation, Illumina adapters   in which cytosines were replaced by 5-methylcytosines were synthesized and annealed   before use.  For library construction, genomic DNA (2 ug) was sheared by sonication for   4 min to fragments of around 150 bp.  1 ug of sheared DNA was used for the following   step. The adapters were ligated following the Illumina protocol.  The libraries were   treated twice with sodium bisulfite using the Qiagen EpiTect Kit following the   manufacturer`s instructions. The libraries were then amplified by 18 cycles of PCR   performed with the PfuTurboC  polymerase (Stratagene). The amplified libraries were   run on 2% agarose gels and a band corresponding to 300bp was gel purified for each   library. The libraries were then sequenced using the Illumina HiSeq DNA sequencing   platform at the Vincent J. Coates Genomic Sequencing Laboratory at the University of   California, Berkeley, USA (UC Berkeley).

value: seedlings

tag: ecotype


title: xct2_xap5_RNA_2


title: xct2_xap5_RNA_1


title: xct2_xap5_RNA_3


title: xct1_RNA_3


title: xct2_RNA_1


title: xct1_RNA_2


title: xct1_RNA_1


title: col_RNA_3

value: Col


title: col_RNA_1


title: col_RNA_2


title: xct2_BS_1

library_source: genomic

molecule: genomic DNA


title: xct1_BS_1


title: col_BS_1


title: scRNA-seq_Human: Single cell human subcutaneous SVF

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: Smilow Center 3400 Civic Center Blvd. 1

institute: University of Pennsylvania

description: 10X Genomics Single Cell RNA-Seq

data_processing:
Basecalling via illumina software after
The Cell Ranger Single Cell Software Suite v.2.0.1 (mouse studies) or v.3.0.1 (human studies) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Data were analyzed with the default settings for these pipelines.
Clustering and gene expression were visualized with the Seurat package (version 3.0, https://satijalab.org/seurat/) on R Studio (https://www.rstudio.com).  Cells were first filtered to have > 500 detected genes and less than 5% of total UMIs mapping to the mitochondrial genome
Clusters with very few cells were filtered before downstream analysis.   Data was scaled to mitigate the effects of the following variables number of genes detected per cell, percent mitochondrial reads and cell cycle phase.
Dimensionality reduction was performed using the T-stochastic Neighboring Embedding method (t-SNE) using Seurat. Differential gene expression analysis between clusters was performed using the Seurat function FindMarkers using the wilcox test.  Violin plots, heatmap and individual tSNE plots for the given genes were generated using the Seurat toolkit ‘VlnPlot’, ‘DoHeatmap’ and ‘FeaturePlot’ functions respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger barcodes and gene count matrices

source_name: Human

extract_protocol:
Tissues were manually minced, digested with Collagenase D and Dispase II at 37C for 45 min. For both mouse and human studies stromal vascular cells were isolated and flow sorted with gating to isolate single cells away from debris, doublets, and dead cells.  For the p12 pups (pooled male and female C57BL/6) and human single cell study, the cells were further gated against CD45 to exclude leukocytes.  For the adult mouse thermoneutral (pooled male 129S6/SvEvTac) sample CD45 cells were segregated and remixed with the SVC cells at a ratio of approximately 20% of the total cells.
The sorted cells were loaded onto a GemCode instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell barcoded droplets (GEMs) according to the manufacture’s protocol using the 10x Single Cell 3’ v2 chemistry.

tag: gender

value: Female

value: Subcutaneous WAT (abdominal)

tag: developmental stage

value: 31 Years


title: MDA-MB-436-shQa / ON-d5-r1

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

address: 5117 Centre Ave

institute: University of Pittsburgh

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al 2014).
RNA-seq reads were then aligned to GRCh37.75(hg19) with STAR (Dobin et. al 2012)
genome-wide transcript counting was performed by HTSeq (Anders et al. 2015) to generate a matrix of raw counts.
Genome_build: hg19
Supplementary_files_format_and_content: count files

source_name: knockdown of MITF (shQa)

growth_protocol: MDA-MB-436 cells were maintained in RPMI 1640, supplemented with 10% FBS (Gemini, Cat. 900-208), 1X Glutamax (Gibco, Cat. 35050061) and Penicillin-Streptomycin (1%).

extract_protocol:
RNA was extracted using TRIzol (Thermal Fisher Scientific, Cat. 15596018), according to manufacturer’s instructions.
Poly-A RNA-Seq / single-end 50.

treatment_protocol: MDA-MB-436 cells were transduced with a lentiviral construct (LT3GEPIR, Fellmann et al Cell Rep. 2013) encoding a doxycycline-inducible shRNA targeting MITF or Renilla Lucifease (control). Infected cells were selected with puromycin (1ug/mL), and harvested 17 days after culture in growth media containing 1 ug/ml doxycycline. Two independent shRNA against MITF were used (sh962 or shQa).


title: MDA-MB-436-shQa / ON-d5-r2


title: MDA-MB-436-shRen / ON-d5-r1

source_name: control cells (shRen)


title: MDA-MB-436-shRen / ON-d5-r2


title: MDA-MB-436-sh962 / ON-d5-r2

source_name: knockdown of MITF (sh962)


title: MDA-MB-436-sh962 / ON-d5-r1


title: xct2_RNA_3


title: First-round cell sort

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

source_name: Human HAP1 cells

growth_protocol: HAP1 and HAP1-derived cell lines and pools were maintained in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% FBS and 100 units/mL penicillin, 100 µg/mL streptomycin (Invitrogen).

extract_protocol:
Genomic DNA was prepared using the Gentra Puregene kit (Qiagen #158767)
Integrated sgRNAs were amplified by PCR for 24 cycles. For sgRNA sequencing, 2 ug of gDNA per PCR reaction was used as template, and four reactions were pooled per sample to ensure sufficient representation of integrated sgRNAs. The resulting amplicon was diluted and further amplified in a second-round PCR to add Illumina adaptor sequences and sample-specific index barcodes.

treatment_protocol: HAP1 cells were transduced with the GECKOv2 lentiviral library, and at 24-hours post infection, puromycin (2.5 ug/ml final concentration) was added to the media to select for transduced cells.


title: Transduced cell population


title: training cohort patient 01

value: training

value: oropharyngeal squamous cell carcinoma (OPSCC)

value: primary oropharyngeal carcinoma


title: Pt18 - L002

city: Seattle

first: Kelly

last: Paulson

state: WA

address: 1100 Fairview Ave N

institute: University of Washington/Fred Hutch Cancer Research Center

data_processing:
Alignment and quantification have been done following the Cell Ranger Software Suite (2.1.0). The Cell Ranger Single-Cell Software Suite (version 2.1.0) was used to perform sample demultiplexing, barcode processing and single-cell 5' gene counting (http://10xgenomics.com/). First, raw base BCL files were demultiplexed using the cellranger mkfastq pipeline into sample-specific FASTQ files. Second, these FASTQ files were processed with the cellranger count pipeline. Each sample was analyzed separately. The Cell Ranger pipeline uses the STAR alignment software (Dobin et al., 2013) to align cDNA reads to the GRCh38 human reference genome. Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads. cellranger aggr was then used to aggregate the two samples together. A correction for sequencing depth was performed during the aggregation.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv-delimited table

source_name: leukemia patient in remission

extract_protocol:
PBMC were extracted with FICOLL
10x genomics 3' chromium gene expression per manufacter's protocol

tag: patient id

value: peripheral blood mononuclear cells

tag: diagnosis

value: leukemia

tag: lane


title: Pt10 - L002


title: Pt18 - L001


title: Patient5_Relapse_91

city: Cleveland

first: David

last: Wald

state: OH

address: Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road

department: Pathology

institute: Case Western Reserve University

data_processing:
Raw reads were preprocessed and aligned to the hg19 human reference genome using the STAR aligner.
Resulting bam files were processed using featureCounts (R package) and hg19 gtf file.
featureCounts() parameters: largestOverlap=T, isPairedEnd=T, isGTFAnnotationFile=TRUE, useMetaFeatures=TRUE
Resulting count files appended into csv file. One csv file per patient that includes untreated diagnosis and post-treatment relapse cells.
Genome_build: hg19
Supplementary_files_format_and_content: csv files represent raw un-normalized counts. One csv file per patient with each column representing an individual cell.

source_name: Acute myeloid leukemia intiating cell

extract_protocol:
Bone marrow samples were thawed and processed rapidly. Cells were washed in PBS twice, then stained with antibodies (BD Pharmingen, Franklin Lakes, New Jersey) for leukemic stem cell markers (CD34, CD38, CD90, CD45RA, Lin) and viability (7-AAD) and incubated in the dark for 20 minutes at room temperature. Cells were washed once and resuspended in 3%FBS/PBS. 2μL of RiboLock RNase inhibitor (40U/μL; Thermo Scientific, Waltham, Massachusetts) was added to the cells to be sorted.
The protocol for single cell RNA sequencing was performed as per Picelli et al (SmartSeq2; Nature Methods 2013). Briefly, 4 ul of lysis buffer containing 0.2% Triton X-100 solution, 1 ul of dNTP mix (KAPA Biosystems, Wilmington, Massachusetts), 1ul of 10uM 5’ anchored oligo-dT oligonucleotide (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′; Sigma Life Science, St. Louis, Missouri) and 1ul RNase inhibitor were added to each well of the 96-well plates.
Using a BD FACSAria cell sorter the AML stem cells were identified as the population that was CD34+, CD38 dim, CD90-, CD45RA+, lineage-, and 7-AAD-. Samples were the incubated at 72°C for 3 min in a thermocycler and immediately placed on ice. Samples were then spun down and 5.7ul of RT mix (100U PrimeScript (Takara Biosciences), 10U RNase inhibitor, 1X Primerscript first strand buffer (5X), 5mM DTT, 1M Betaine, 1uM template switching oligo (5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′)) was added to each well.
The 96-well plate was spun down and incubated at 42°C for 90 min, followed by an additional 10 cycles of 4 min at 42 °C. 1X KAPA HiFi Hotstart ReadyMix was then added along with 0.1 uM PCR primers (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and the PCR was performed for 22 cycles. PCR purification was performed using Sera-mag SpeedBeads (1:1 ratio of beads: cDNA mixture; Thermo Scientific, Fremont, California). PCR product size distribution is checked using an Agilent high-sensitivity DNA chip, with a good library classified as being devoid of fragments <500bp and with a peak around 1.5-2kb.
Library preparation was performed as per manufacturer instructions by Illumina Nextera XT DNA sample preparation kit (Illumina, San Diego, California). Briefly, the tagmentation reaction was carried out on 1 ng of cDNA at 55 °C for 10 min. The amplification of adapter-ligated fragments was performed using Nextera PCR master mix, index primers and barcodes were added to identify each cell for 15 cycles. The PCR products from each cell were then pooled together and purified using Sera-mag SpeedBeads (0.6:1 ratio). A final quality check of the cDNA library was performed using an Agilent high-sensitivity DNA chip, obtaining a broad peak between 300-800bp.  Single cells were sequenced using 100bp paired end sequencing on the Illumina HiSeq 2500.

value: Single acute myeloid leukemia intitiating cell

tag: state

value: Post-treatment relapse

value: Patient 5

tag: surface markers


title: Patient5_Relapse_92

tag: tissue


title: xct2_xap5_BS_1


title: Patient5_Relapse_87


title: Patient5_Relapse_9


title: Patient5_Relapse_86


title: Patient5_Relapse_90


title: Patient5_Relapse_88


title: Patient5_Relapse_83


title: Patient5_Relapse_85


title: Patient5_Relapse_84


title: Patient5_Relapse_93


title: Patient5_Relapse_81


title: Pt10 - L001


title: Patient5_Relapse_80


title: Patient5_Relapse_82


title: Patient5_Relapse_8


title: Patient5_Relapse_79


title: Patient5_Relapse_76


title: Patient5_Relapse_77


title: Patient5_Relapse_75


title: Patient5_Relapse_74


title: Patient5_Relapse_72


title: Patient5_Relapse_71


title: Patient5_Relapse_73


title: Patient5_Relapse_7


title: Patient5_Relapse_70


title: Patient5_Relapse_89


title: Patient5_Relapse_69


title: Patient5_Relapse_68


title: Patient5_Relapse_66


title: Patient5_Relapse_67


title: Patient5_Relapse_64


title: Patient5_Relapse_65


title: Patient5_Relapse_63


title: Patient5_Relapse_62


title: Patient5_Relapse_60


title: Patient5_Relapse_59


title: Patient5_Relapse_78


title: Patient5_Relapse_56


title: Patient5_Relapse_57


title: Patient5_Relapse_6


title: Patient5_Relapse_55


title: Patient5_Relapse_53


title: Patient5_Relapse_52


title: Patient5_Relapse_54


title: Patient5_Relapse_50


title: Patient5_Relapse_49


title: Patient5_Relapse_61


title: Patient5_Relapse_5


title: Patient5_Relapse_48


title: Patient5_Relapse_51


title: Patient5_Relapse_47


title: Patient5_Relapse_45


title: Patient5_Relapse_58


title: Patient5_Relapse_44


title: Patient5_Relapse_42


title: Patient5_Relapse_43


title: Patient5_Relapse_41


title: Patient5_Relapse_46


title: Patient5_Relapse_40


title: Patient5_Relapse_4


title: Patient5_Relapse_36


title: Patient5_Relapse_35


title: Patient5_Relapse_34


title: Patient5_Relapse_33


title: Patient5_Relapse_32


title: Patient5_Relapse_31


title: Patient5_Relapse_3


title: Patient5_Relapse_39


title: Patient5_Relapse_28


title: Patient5_Relapse_37


title: Patient5_Relapse_38


title: Patient5_Relapse_25


title: Patient5_Relapse_26


title: Patient5_Relapse_23


title: Patient5_Relapse_24


title: Patient5_Relapse_16


title: Patient5_Relapse_2


title: Patient5_Relapse_13


title: Patient5_Relapse_14


title: Patient5_Relapse_17


title: Patient5_Relapse_22


title: Patient5_Relapse_15


title: Patient5_Relapse_18


title: Patient5_Relapse_10


title: Patient5_Relapse_12


title: Patient5_Relapse_20


title: Patient5_Relapse_1


title: Patient5_Diagnosis_96

value: Pre-treatment diagnosis


title: Patient5_Relapse_29


title: Patient5_Relapse_19


title: Patient5_Relapse_27


title: Patient5_Diagnosis_93


title: Patient5_Diagnosis_92


title: Patient5_Relapse_30


title: Patient5_Diagnosis_95


title: Patient5_Diagnosis_94


title: Patient5_Relapse_21


title: Patient5_Diagnosis_90


title: Patient5_Diagnosis_88


title: Patient5_Relapse_11


title: Patient5_Diagnosis_85


title: Patient5_Diagnosis_9


title: Patient5_Diagnosis_83


title: Patient5_Diagnosis_86


title: Patient5_Diagnosis_84


title: Patient5_Diagnosis_79


title: Patient5_Diagnosis_80


title: Patient5_Diagnosis_82


title: Patient5_Diagnosis_8


title: Patient5_Diagnosis_77


title: Patient5_Diagnosis_73


title: Patient5_Diagnosis_74


title: Patient5_Diagnosis_75


title: Patient5_Diagnosis_81


title: Patient5_Diagnosis_72


title: Patient5_Diagnosis_70


title: Patient5_Diagnosis_91


title: Patient5_Diagnosis_76


title: Patient5_Diagnosis_71


title: Patient5_Diagnosis_68


title: Patient5_Diagnosis_69


title: Patient5_Diagnosis_67


title: Patient5_Diagnosis_66


title: Patient5_Diagnosis_87


title: Patient5_Diagnosis_65


title: Patient5_Diagnosis_63


title: Patient5_Diagnosis_78


title: Patient5_Diagnosis_62


title: Patient5_Diagnosis_64


title: Patient5_Diagnosis_60


title: Patient5_Diagnosis_61


title: Patient5_Diagnosis_59


title: Patient5_Diagnosis_6


title: Patient5_Diagnosis_58


title: Patient5_Diagnosis_57


title: Patient5_Diagnosis_7


title: Patient5_Diagnosis_56


title: Patient5_Diagnosis_55


title: Patient5_Diagnosis_54


title: Patient5_Diagnosis_5


title: Patient5_Diagnosis_49


title: Patient5_Diagnosis_48


title: Patient5_Diagnosis_50


title: Patient5_Diagnosis_52


title: Patient5_Diagnosis_47


title: Patient5_Diagnosis_53


title: Patient5_Diagnosis_46


title: Patient5_Diagnosis_45


title: Patient5_Diagnosis_44


title: Patient5_Diagnosis_43


title: Patient5_Diagnosis_42


title: Patient5_Diagnosis_41


title: Patient5_Diagnosis_40


title: Patient5_Diagnosis_4


title: Patient5_Diagnosis_37


title: Patient5_Diagnosis_38


title: Patient5_Diagnosis_39


title: Patient5_Diagnosis_35


title: Patient5_Diagnosis_36


title: Patient5_Diagnosis_51


title: Patient5_Diagnosis_31


title: Patient5_Diagnosis_32


title: Patient5_Diagnosis_34


title: Patient5_Diagnosis_30


title: Patient5_Diagnosis_33


title: Patient5_Diagnosis_3


title: Patient5_Diagnosis_28


title: Patient5_Diagnosis_24


title: Patient5_Diagnosis_27


title: Patient5_Diagnosis_25


title: Patient5_Diagnosis_23


title: Patient5_Diagnosis_22


title: Patient5_Diagnosis_26


title: Patient5_Diagnosis_29


title: Patient5_Diagnosis_21


title: Patient5_Diagnosis_20


title: Patient5_Diagnosis_17


title: Patient5_Diagnosis_19


title: Patient5_Diagnosis_16


title: Patient5_Diagnosis_15


title: Patient5_Diagnosis_13


title: Patient5_Diagnosis_14


title: Patient5_Diagnosis_2


title: Patient5_Diagnosis_18


title: Patient5_Diagnosis_10


title: Patient5_Diagnosis_12


title: Patient4_Relapse_96

value: Patient 4


title: Patient5_Diagnosis_1


title: Patient4_Relapse_93


title: Patient4_Relapse_92


title: Patient4_Relapse_91


title: Patient4_Relapse_90


title: Patient4_Relapse_88


title: Patient4_Relapse_87


title: Patient4_Relapse_84


title: Patient4_Relapse_85


title: Patient5_Diagnosis_11


title: Patient4_Relapse_86


title: Patient4_Relapse_80


title: Patient4_Relapse_83


title: Patient4_Relapse_82


title: Patient4_Relapse_81


title: Patient4_Relapse_89


title: Patient4_Relapse_76


title: Patient4_Relapse_73


title: Patient4_Relapse_79


title: Patient4_Relapse_77


title: Patient4_Relapse_8


title: Patient4_Relapse_78


title: Patient4_Relapse_71


title: Patient4_Relapse_74


title: Patient4_Relapse_69


title: Patient4_Relapse_68


title: Patient4_Relapse_9


title: Patient4_Relapse_67


title: Patient4_Relapse_70


title: Patient4_Relapse_7


title: Patient4_Relapse_66


title: Patient4_Relapse_75


title: Patient4_Relapse_64


title: Patient4_Relapse_63


title: Patient4_Relapse_61


title: Patient4_Relapse_72


title: Patient4_Relapse_62


title: Patient4_Relapse_58


title: Patient4_Relapse_57


title: Patient4_Relapse_55


title: Patient4_Relapse_54


title: Patient4_Relapse_56


title: Patient4_Relapse_6


title: Patient4_Relapse_52


title: Patient4_Relapse_50


title: Patient4_Relapse_5


title: Patient4_Relapse_65


title: Patient4_Relapse_48


title: Patient4_Relapse_46


title: Patient4_Relapse_45


title: Patient4_Relapse_44


title: Patient4_Relapse_42


title: Patient4_Relapse_43


title: Patient4_Relapse_60


title: Patient4_Relapse_41


title: Patient4_Relapse_53


title: Patient4_Relapse_47


title: Patient4_Relapse_40


title: Patient4_Relapse_39


title: Patient4_Relapse_4


title: Patient4_Relapse_38


title: Patient4_Relapse_51


title: Patient4_Relapse_49


title: Patient4_Relapse_37


title: Patient4_Relapse_35


title: Patient4_Relapse_34


title: Patient4_Relapse_33


title: Patient4_Relapse_36


title: Patient4_Relapse_30


title: Patient4_Relapse_28


title: Patient4_Relapse_3


title: Patient4_Relapse_29


title: Patient4_Relapse_26


title: Patient4_Relapse_27


title: Patient4_Relapse_25


title: Patient4_Relapse_24


title: Patient4_Relapse_23


title: Patient4_Relapse_22


title: Patient4_Relapse_2


title: Patient4_Relapse_19


title: Patient4_Relapse_20


title: Patient4_Relapse_21


title: Patient4_Relapse_17


title: Patient4_Relapse_18


title: Patient4_Relapse_16


title: Patient4_Relapse_14


title: Patient4_Relapse_32


title: Patient4_Relapse_31


title: Patient4_Relapse_12


title: Patient4_Relapse_11


title: Patient4_Relapse_13


title: Patient4_Relapse_10


title: Patient4_Relapse_1


title: Patient4_Relapse_15


title: Patient4_Diagnosis_88


title: Patient4_Relapse_59


title: Patient4_Diagnosis_87


title: Patient4_Diagnosis_82


title: Patient4_Diagnosis_86


title: Patient4_Diagnosis_84


title: Patient4_Diagnosis_83


title: Patient4_Diagnosis_81


title: Patient4_Diagnosis_8


title: Patient4_Diagnosis_79


title: Patient4_Diagnosis_77


title: Patient4_Diagnosis_85


title: Patient4_Diagnosis_76


title: PAO1RpoN(DK2)_ChIP_replicate 1

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

description: ChIP-seq RpoN-DK2 rep 1

data_processing:
Sequenced ChIP-seq reads were trimmed for adaptor sequence allowing for a minimal quality of 10 at their ends, then mapped to the PAO1 genome using stampy with default parameters
RNA-seq reads were mapped to the PAO1 genome using the stampy aligner with default settings.
ChIP-seq peaks were called using the MACS algorithm with the following options: -g 5200000 –nomodel --shiftsize=30 -p 0.05
Differential expression was estimated using the DESeq2 R library.
For detection of the differentially expressed genes, both replicates for each condition were used, thus the corresponding processed data files were generated on the basis of 4 samples each. The ChIP-seq peaks were detected superposing the treated against the control sample.
Genome_build: gi|110645304|ref|NC_002516|
Supplementary_files_format_and_content: Artemis browser files containing the read pileup at each genomic position covered in the ChIP-seq experiments. Processed RNA-seq data includes the raw read counts for each gene.

organism: Pseudomonas aeruginosa

growth_protocol: PAO1RpoN(WT) and PAO1rpoN(DK2) strains in LB medium at 37°C and 180 r.p.m. Sigma factor expression induced with l-arabinose at OD600 = 0.1, cells harvested at OD600=2.0.

extract_protocol:
Polyhistidine-tagged sample was isolated by using anti6Xhis-antibodies (abcam) and magnetic beads coupled with protein-G (Invitrogen) on a rotator.
Immunoprecipitated DNA was linear amplified similar to the LinDA-ChIP-seq protocol published by Shankaranarayanan et al., Nature potocols, 2012. Library was constructed using the TruSeq DNA sample preparation kit according to the low-throughput protocol (Illumina).

treatment_protocol: DNA-protein crosslinking was performed by addition of formaldehyde to a final concentration of 0.5% for 5 minutes at ambient temperature. Reaction was quenched by addition of glycine to a final concentration of 137 mM. Cells were lysed in lysis buffer containing EDTA and lysozyme. Cells were disrupted and DNA was sheared by sonication.

tag: strain background

tag: genotype/variation


title: PAO1RpoN(WT)_ChIP_replicate 2

description: ChIP-seq RpoN-WT rep 2

value: RpoN(WT)


title: Patient4_Diagnosis_74


title: Patient4_Diagnosis_78


title: PAO1RpoN(DK2)_ChIP_replicate 2

description: ChIP-seq RpoN-DK2 rep 2


title: Patient4_Diagnosis_75


title: Patient4_Diagnosis_73


title: Patient4_Diagnosis_71


title: Patient4_Diagnosis_9


title: Patient4_Diagnosis_69


title: Patient4_Diagnosis_67


title: Patient4_Diagnosis_66


title: Patient4_Diagnosis_68


title: PAO1RpoN(WT)_ChIP_replicate 1

description: ChIP-seq RpoN-WT rep 1


title: Patient4_Diagnosis_65


title: Patient4_Diagnosis_63


title: Patient4_Diagnosis_64


title: Patient4_Diagnosis_62


title: Patient4_Diagnosis_7


title: Patient4_Diagnosis_70


title: erythroid cells: WT4

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: rRNA-depleted RNA

data_processing:
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM, Cufflinks (version 2.2.1) was used.
Genome_build: GRcz10
Supplementary_files_format_and_content: tab-delimited text file includeS FPKM values for each Sample

organism: Danio rerio

source_name: erythroid cells

extract_protocol:
Gata1-positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep (Zymo). Ribosomal RNA was depleted with Ribogone (Clontech).
Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA-Seq Kit (Clontech).

tag: age

value: 24 hours post fertilization

tag: cell type

value: gata1-positive erythroid cells

value: wild type


title: erythroid cells: WT5

description: rRNA-depleted RNA


title: erythroid cells: WT6

description: rRNA-depleted RNA


title: VCF_1mo_rep1

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

country: Japan

institute: Gifu University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 μl containing 1x Blocking Agent and 1x Fragmentation Buffer. On completion of the fragmentation reaction, 2x Hybridization Buffer HI-RPM solution was added to the fragmentation mixture containing 0.6 μg of Cy3-labelled cRNA and hybridized for 17 h, at 65C and 10 rpm. After hybridization, microarrays were washed according to Quick Amp Labeling Kit Protocol (Agilent).

scan_protocol: The hybridized microarray slides were washed according to the manufacturer’s instructions and were scanned with an Agilent DNA Microarray Scanner (#G2565CA, Agilent Technologies, CA, USA) at a resolution of 5 μm.

data_processing: These data were normalized by the percentile shift 75% using GeneSpring GX version 11.5.1 software (Agilent Technologies).

label_protocol: The cDNA was synthesized by Quick Amp Labeling Kit (Agilent) using 0.5 μg total RNA as a template. Cyanine-3 (Cy3) labeled cRNA was prepared from cDNA using the T7 RNA polymerase. Cy3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN, Hilden, Germany), and checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the lung by phenol-chloroform method using a Fast RNA Pro Red Kit (MP Biomedicals, California, USA) following the manufacturer's instructions. Total RNA was purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. The concentration and purity of the resulting RNA were evaluated by absorbance at 260 nm using an Agilent 2100 BioanalyzerTM (Agilent Technologies, California, USA).

treatment_protocol: After the mice were sacrificed, their lungs were rapidly removed and processed for DNA microarray analysis.

tag: strain

value: lung

value: male


title: Patient4_Diagnosis_60


title: CCF_1mo_rep2


title: erythroid cells: WT3

description: rRNA-depleted RNA


title: VCF_1mo_rep2


title: Patient4_Diagnosis_6


title: Ctrl_1mo_rep1


title: Patient4_Diagnosis_58


title: Ctrl_1mo_rep3


title: RCF_1mo_rep2


title: CCF_1mo_rep1


title: erythroid cells: Mut6

description: rRNA-depleted RNA

value: sf3b1 mutant


title: Patient4_Diagnosis_57


title: Patient4_Diagnosis_61


title: Ctrl_1mo_rep4


title: VCF_1mo_rep3


title: Patient4_Diagnosis_56


title: RCF_1mo_rep1


title: erythroid cells: Mut5

description: rRNA-depleted RNA


title: CCF_1mo_rep3


title: RCF_1mo_rep3


title: Ctrl_1mo_rep5


title: Ctrl_1mo_rep2


title: Patient4_Diagnosis_55


title: erythroid cells: Mut3

description: rRNA-depleted RNA


title: erythroid cells: Mut4

description: rRNA-depleted RNA


title: erythroid cells: Mut1

description: rRNA-depleted RNA


title: Patient4_Diagnosis_53


title: Patient4_Diagnosis_54


title: erythroid cells: WT2

description: rRNA-depleted RNA


title: Patient4_Diagnosis_52


title: Patient4_Diagnosis_50


title: WGBS_THP1_0hrPMA_rep1

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2212 Garland Ave.

department: Biochemistry

institute: Vanderbilt University

description: Whole genome bisulfite-seq of THP1 Monocytes: 0hrs 162nM PMA treatment

data_processing:
Trimming: All sequencing library reads were trimmed of adapters using TrimGalore script wrapper for Cutadapt (Martin, 2011) and FastQC. Version: trim_galore 0.4.0. Command: trim_galore --fastqc --fastqc_args "--outdir ${FASTQC_DIR}" --clip_R1 9 --clip_R2 9 --paired --retain_unpaired --output_dir ${TRIM_DIR} ${R1} ${R2}
Mapping: Standard ATAC reads were mapped with bowtie2. Version: bowtie2 2.2.6. Command: bowtie2 -p 8 --no-discordant --no-mixed -X 1000 -x ${INDEX} -1 ${R1} -2 ${R2} -S ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All bisulfite converted samples were mapped with WALT. Version: WALT v1.0. Command: walt -m 8 -t 6 -i ${INDEX} -1 ${R1} -2 ${R2} -o ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All RNA-seq reads were mapped with STAR. Version: STAR_2.6.1a. Command: STAR --runThreadN 4 --genomeDir /data/hodges_lab/human_genome/GRCh38_Gencode24 --sjdbGTFfile /data/hodges_lab/human_genome/GRCh38_Gencode24/gencode.v24.primary_assembly.annotation.gtf --readFilesCommand zcat --readFilesIn --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
ATAC peak calling: All peak calling was done with MACS2. Version: MACS2 2.1.1. Command: macs2 callpeak -t ${MAPPED_DIR}/${MAPPED}.shifted.bam -f BAMPE -n ${MACS_DIR}/${MAPPED} -g hs -q 0.005 -B --SPMR --keep-dup all --broad --broad-cutoff 0.005
DNA methylation analysis: The Methpipe suite of tools was used for all CpG methylation analysis. Version: Methpipe 3.4.3
Differential RNA-seq analysis: DESeq2 was use to calculate differential RNA expression across the time course. Version: DESeq2 1.18.1. R-Version: 3.4.3
Differential ATAC-seq analysis: TCseq was used to calculate differential chromatin accessibility across the time course. Version: 1.6.1. R-version: 3.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are broadPeak output bed files from MACS2, meth files are a tab delimited text file of CpG methylation values for all symmetic CpGs in hg19, meth files are generated as output from Methpipe
Supplementary_files_format_and_content: DEseq2 normalized transcript abundance table

source_name: THP-1 Monocyte

growth_protocol: THP1 monocytes were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 units penicillin/streptomycin and 1mM sodium pyruvate. During routine culture THP1 cells were maintained at a density of 0.5-2E6 cells/mL. All cells were regularly screened for mycoplasma contamination using the Lonza MycoAlert kit.

extract_protocol: Whole genome bisulfie libraries were prepared fron 50ng DNA as described in "Adey, A. & Shendure, J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research 22, 1139-1143 (2012)"

treatment_protocol: Differentiation of THP1 monocytes was induced with RPMI medium carrying PMA at a concentration of 100ng/mL (162nM). THP1 monocyte PMA stimulation time points were harvested with a combination of aspiration (for suspended cells) and trypsin (for adherent cells). The final collection of each time point was pelleted at 4°C, 500 R.C.F for 5 minutes. After pelleting cells were resuspended in ice cold PBS and cell counted using an automated cell counter (Biorad). This cell suspension was divided as input material for RNA extraction, genomic DNA extraction and ATAC reactions.

tag: pma stimulation time point

value: 0 hr


title: WGBS_THP1_24hrPMA_rep1

description: Whole genome bisulfite-seq of THP1 Monocytes: 24hrs 162nM PMA treatment

value: 24 hr


title: Patient4_Diagnosis_51


title: Patient4_Diagnosis_5


title: Patient4_Diagnosis_49


title: Patient4_Diagnosis_48


title: Patient4_Diagnosis_47


title: GT28 Week 8 Control [GT28_8_C]

city: Manchester

first: Ardeshir

last: Bayat

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description: processed data file: G8_TvsG8_C.Differential_analysis_results.txt

data_processing:
Raw image data file from high-throughput sequencing (Illumina PE150 HiSeqX-ten) was transformed to Sequenced Reads by CASAVA v1.8 base recognition (Base Calling)
TopHat v2 was used for alignment. TopHat v2 mapping was divided into three steps: (1) Align reads to trancrtiptome (optional). (2) Align the whole read to exon,disallowing large gaps. (3) Unmapped reads are split into shorter segments and aligned independently. The genomic regions surrounding the mapped read segments are then searched for possible spliced connections.
Raw reads filtering as follows: (1) Remove reads containing adaptors;(2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5. RNA-seq Adapter information:NEBNext® UltraTM RNA Library Prep Kit,
For samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package providing statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genome_build: Ensembl version Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: readcount and differential expression analysis data

source_name: human skin_Week 8_Placebo

extract_protocol:
Tissue biopsies were homogenised in 300μL of RLT buffer (Qiagen, GmbH, Helden, Germany) mixed with β-mercaptoethanol (Sigma-Aldrich, St Louis, MO) (10μl β-mercaptoethanol/ml RLT buffer) using 5-mm stainless steel beads and a Qiagen TissueLyser II (Qiagen GmbH) at 30 oscillations/second for 10 minutes. RNA was extracted using RNeasy Tissue Mini Kits (Qiagen GmbH). Eluted RNA quantity and purity was assessed using NanoDrop ND-100 v3.0.1 spectrophotometer (NanoDrop Technologies, Wilmington, DE), Agarose gel electrophoresis and Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human skin

tag: wound/scar time point

value: Week 8

tag: treatment

value: Placebo


title: GT29 Week 8 Treated [GT29_8_T]

source_name: human skin_Week 8_EGCG Treated

value: EGCG Treated


title: Patient4_Diagnosis_45

value: Single acute myeloid leukemia intitiating cell


title: GT28 Week 8 Treated [GT28_8_T]


title: Patient4_Diagnosis_44


title: GT27 Week 8 Control [GT27_8_C]


title: GT29 Week 8 Control [GT29_8_C]


title: Patient4_Diagnosis_42


title: GT35 Week 6 Control [GT35_6_C]

description: processed data file: G6_TvsG6_C.Differential_analysis_results.txt

source_name: human skin_Week 6_Placebo

value: Week 6


title: GT37 Week 6 Treated [GT37_6_T]

source_name: human skin_Week 6_EGCG Treated


title: Patient4_Diagnosis_46

value: Pre-treatment diagnosis


title: Patient4_Diagnosis_41

value: Patient 4


title: GT34 Week 6 Control [GT34_6_C]


title: GT37 Week 6 Control [GT37_6_C]


title: GT27 Week 8 Treated [GT27_8_T]


title: GT35 Week 6 Treated [GT35_6_T]


title: GT34 Week 6 Treated [GT34_6_T]


title: Patient4_Diagnosis_4


title: GT41 Week 5 Control [GT41_5_C]

description: processed data file: G5_TvsG5_C.Differential_analysis_results.txt

source_name: human skin_Week 5_Placebo

value: Week 5


title: GT41 Week 5 Treated [GT41_5_T]

source_name: human skin_Week 5_EGCG Treated


title: Patient4_Diagnosis_39


title: Patient4_Diagnosis_38


title: GT40 Week 5 Control [GT40_5_C]


title: Patient4_Diagnosis_37


title: GT40 Week 5 Treated [GT40_5_T]


title: Patient4_Diagnosis_43


title: Patient4_Diagnosis_35


title: Patient4_Diagnosis_40


title: GT39 Week 5 Treated [GT39_5_T]


title: Patient4_Diagnosis_32


title: Patient4_Diagnosis_30


title: Patient4_Diagnosis_33


title: Patient4_Diagnosis_31


title: Patient4_Diagnosis_3


title: GT47 Week 3 Control [GT47_3_C]

description: processed data file: G3_TvsG3_C.Differential_analysis_results.txt

source_name: human skin_Week 3_Placebo

value: Week 3


title: GT17 Week 4 Treated [GT17_4_T]

description: processed data file: G4_TvsG4_C.Differential_analysis_results.txt

source_name: human skin_Week 4_EGCG Treated

value: Week 4


title: GT18 Week 4 Control [GT18_4_C]

source_name: human skin_Week 4_Placebo


title: GT18 Week 4 Treated [GT18_4_T]


title: Patient4_Diagnosis_28


title: Patient4_Diagnosis_29


title: Patient4_Diagnosis_26


title: GT46 Week 3 Control [GT46_3_C]


title: GT47 Week 3 Treated [GT47_3_T]

source_name: human skin_Week 3_EGCG Treated


title: Patient4_Diagnosis_25


title: Patient4_Diagnosis_36


title: GT45 Week 3 Control [GT45_3_C]


title: GT46 Week 3 Treated [GT46_3_T]


title: GT39 Week 5 Control [GT39_5_C]


title: GT45 Week 3 Treated [GT45_3_T]


title: Patient4_Diagnosis_34


title: Patient4_Diagnosis_22


title: GT53 Week 2 Control [GT53_2_C ]

description: processed data file: G2_TvsG2_C.Differential_analysis_results.txt

source_name: human skin_Week 2_Placebo

value: Week 2


title: GT19 Week 4 Treated [GT19_4_T]


title: Patient4_Diagnosis_21


title: GT19 Week 4 Control [GT19_4_C]


title: GT53 Week 2 Treated [GT53_2_T]

source_name: human skin_Week 2_EGCG Treated


title: GT17 Week 4 Control [GT17_4_C]


title: GT52 Week 2 Control [GT52_2_C]


title: Patient4_Diagnosis_20


title: GT52 Week 2 Treated [GT52_2_T]


title: Patient4_Diagnosis_19


title: Patient4_Diagnosis_2


title: Patient4_Diagnosis_17


title: Patient4_Diagnosis_18


title: GT51 Week 2 Control [GT51_2_C]


title: Patient4_Diagnosis_16


title: Patient4_Diagnosis_15


title: GT51 Week 2 Treated [GT51_2_T]


title: GT59 Week 1 Control [GT59_1_C]

description: processed data file: G1_TvsG1_C.Differential_analysis_results.txt

source_name: human skin_Week 1_Placebo

value: Week 1


title: GT59 Week 1 Treated [GT59_1_T ]

source_name: human skin_Week 1_EGCG Treated


title: Patient4_Diagnosis_23

source_name: Acute myeloid leukemia intiating cell


title: GT58 Week 1 Treated [GT58_1_T]


title: GT58 Week 1 Control [GT58_1_C ]


title: Patient4_Diagnosis_24


title: Patient4_Diagnosis_14


title: GT57 Week 1 Control  [GT57_1_C ]


title: Patient4_Diagnosis_12


title: Patient4_Diagnosis_11


title: GT19 D0

source_name: human skin_Day 0 uninjured skin

value: Day 0 uninjured skin

value: No treatment or placebo


title: GT57 Week 1 Treated [GT57_1_T]


title: GT01 D0


title: GT09 D0


title: Patient4_Diagnosis_1


title: Patient4_Diagnosis_10


title: Patient3_Relapse_96

value: Post-treatment relapse

value: Patient 3


title: HEK293T Chtopl Knockdown RNAseq replicate 3

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

data_processing:
Reads were trimmed using Trimmomatic with parameters 'PE   -phred33   ILLUMINACLIP:TruSeq_all.fa:1:30:10:1:true LEADING:15 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36'
Reads were mapped to the hg19 using STAR v2.4.2a and a junction database built from ensembl 75. The options to STAR were ‘--outFilterType BySJout  --outFilterMismatchNmax 5’
Alignments were converted to bedGraph and biWig using bedtools and bedGraphToBigWig
Gene expression was quantified using Salmon 0.8.3 against a combined coding and noncoding transcriptome annotation from ensembl 75
Alternative polyadenylation was identified using DaPars
Genome_build: hg19
Supplementary_files_format_and_content: quant.sf.txt files are output from salmon. Bw files are bigWigs and represent read depth across the genome. dapars_outputs.tsv  is the tab seperated output from the dapars tool (http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html)

source_name: HEK293T Chtopl Knockdown

growth_protocol: FlpIn-293 cells were maintained in DMEM with 10% FBS.

extract_protocol:
Total RNA extraction was performed using TRIzol following the manufacturer instructions. Samples were resuspended in 50 µL of RNases-free water (Sigma), DNase-treated with 4 U of Turbo DNase (Ambion) for 1 hour at 37°C, phenol-extracted, ethanol-precipitated overnight at -20°C and resuspended in 40 µL of RNases-free water
cDNA was synthesised, poly-A enriched and strand-specific libraries constructed by Novogene(Beijing, china) using standard illumina protocols.

treatment_protocol: Cells were transfected on the day of seeding with 7.5 nM of siRNAs (30 nM for HeLa cells) using RNAiMAX (Life technologies) according to the manufacturer’s instructions. The transfection was repeated at 48 hours and the cells were harvested between 68 and 72 hours after the first transfection.

tag: cell line

tag: sirna

value: siChtop (GACAACCAAUUGGAUGCAUAU)


title: Patient3_Relapse_95


title: HEK293T Chtopl Knockdown RNAseq replicate 2


title: HEK293T Chtopl Knockdown RNAseq replicate 1


title: Patient3_Relapse_94


title: Patient3_Relapse_92


title: Patient3_Relapse_91


title: HEK293T Control Knockdown RNAseq replicate 2

source_name: HEK293T Control Knockdown

value: siControl (CACCGUGAAGCUGAAGGUG)


title: Patient3_Relapse_90


title: Patient3_Relapse_88


title: Patient3_Relapse_9


title: Patient3_Relapse_87


title: Patient4_Diagnosis_13


title: HEK293T Control Knockdown RNAseq replicate 1


title: Patient3_Relapse_83


title: Patient3_Relapse_85


title: Patient3_Relapse_81


title: Patient3_Relapse_93


title: Patient3_Relapse_82


title: Patient3_Relapse_80


title: HEK293T Control Knockdown RNAseq replicate 3


title: Patient3_Relapse_8


title: Patient3_Relapse_79


title: Patient3_Relapse_86


title: Patient3_Relapse_78


title: Patient3_Relapse_76


title: Patient3_Relapse_77


title: Patient3_Relapse_74


title: Patient3_Relapse_73


title: TG_normoxia_rep4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

description: SAMPLE 8

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: TG_20% oxygen_lung

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

extract_protocol: RNA was isolated by using miRNeasy Mini Kit (Qiagen, Cat. No. 217004), RNA was eluted with RNAse-free water at the last step of the protocol, concentration was measured by nanodrop, RNA was stored at -80°C

treatment_protocol: WT vs Fgf10+/- pups were be treated from P0-P3 with 20% oxygen in a chamber

tag: age (during the treatment)

tag: treated with

value: 20% oxygen in a chamber

value: lung


title: spleen organization 45d 800 mg/kg/d replicate 2

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

description: Gene expression after 45d in mouse spleen

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: spleen organization,45d,800 mg/kg/d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 700μL RNA using the RNeasy Mini Kit (Qiagen p/n 74104) according to the manufacturer's instructions, followed by RNAeasy column purification. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Briefly, the liver tissue was ground into powders under the frozen condition with liquid nitrogen, and before the liquid nitrogen was volatilized, the liver powder was transferred into a 1.5ml microcentrifuge tube containing Trizol reagent (500mg of the liver tissue per 0.5 ml Trizol reagent). The liver powder in the microcentrifuge tube was drawn and re-injected vigorously several times with a 5 ml disposable syringe until the tissue homogenate was no longer sticky, in favor of the full breaking down of the cells and genomic DNA. The tissue homogenate was left to stand at room temperature for use. According to the ratio of 200ul chloroform per 1mlTrizol reagent, chloroform was added to the homogenate. The mixed solution was oscillated violently for 30sec for evenly mixing and then left to stand at room temperature for 5min. The mixed sample solution was centrifuged at 12000r/m for 15min to obtain the supernatant and the obtained supernatant was carefully transferred to another centrifuge tube, in which it was noticeable not to draw the intermediate phase. 500ul isopropanol was added to the supernatant, which was left to stand at the room temperature for 10min for its precipitation, and then centrifuged at 12000r/m for 15min and the supernatant was discarded to obtain the precipitation. 1Ml of 75% ethanol was added to the precipitation for the wash of RNA by oscillating it with a vortex, which was left to stand at room temperature for 5min and then centrifuged at 7500r/m for 5min to discard the supernatant. Finally, 75% ethanol was added to the precipitation to wash the RNA again, the precipitation solution was centrifuged at 7500r/m for 5min, the supernatant was removed, and the final precipitation was dried at room temperature, in which the RNA precipitation should not be too dried, otherwise it was not easy to dissolve.

treatment_protocol: The experimental animals were fed under the conditions with a relative humidity of 40-70%, at 20±1℃ and in a sterile environment, with ad libitum access to water and food. After they adapted to the environment for one week, the mice were randomly divided into blank control group, model group, and low-, medium- and high-dose Cordyceps militaris polypeptide (CMP) groups. Mice in low-, medium- and high-dose Cordyceps militaris polypeptide were orally given 32, 160and 800 mg/kg once daily continuously for 45 days, respectively, and those in the blank control group and model group were given equal volume of distilled water in the same way. In addition to those in the blank control group, mice in the other groups were injected with 40 mg/kg of cyclophosphamide intraperitoneally once daily, successively for 2 day for the establishment of mice immunodeficiency model. The mice’s body weights were measured every week regularly for the observation on changes in their body weights and their general states were also observed at the same time.

value: spleen

tag: gender

value: male

value: Cordyceps militaris polypeptide at 800 mg/kg once daily continuously for 45 days


title: spleen organization 45d 800 mg/kg/d replicate 3


title: spleen organization 2d 40 mg/kg replicate 3

description: Gene expression after 2d in mouse spleen

source_name: spleen organization,2d,40 mg/kg

value: 40 mg/kg of cyclophosphamide


title: spleen organization 2d 40 mg/kg replicate 1


title: spleen organization 2d 40 mg/kg replicate 2


title: TG_normoxia_rep2

description: SAMPLE 4


title: spleen organization 45d 800 mg/kg/d replicate 1


title: WT_normoxia_rep2

description: SAMPLE 3

source_name: WT_20% oxygen_lung

value: wild-type


title: WT_normoxia_rep4

description: SAMPLE 7


title: Patient3_Relapse_7

value: Single acute myeloid leukemia intitiating cell

tag: patient id


title: Patient3_Relapse_71

tag: state


title: Patient3_Relapse_70

tag: surface markers


title: Patient3_Relapse_72

tag: tissue


title: TG_normoxia_rep1

description: SAMPLE 1

tag: strain background


title: WT_normoxia_rep3

description: SAMPLE 6

tag: genotype/variation


title: Patient3_Relapse_69


title: Patient3_Relapse_68


title: TG_hyperoxia_rep4

description: SAMPLE 8

source_name: TG_85% oxygen_lung

treatment_protocol: WT vs Fgf10+/- pups were be treated from P0-P3 with 85% oxygen in a chamber

value: 85% oxygen in a chamber


title: TG_normoxia_rep3

description: SAMPLE 5


title: WT_hyperoxia_rep4

description: SAMPLE 7

source_name: WT_85% oxygen_lung


title: WT_hyperoxia_rep3

description: SAMPLE 6


title: TG_hyperoxia_rep2

description: SAMPLE 4


title: WT_hyperoxia_rep2

description: SAMPLE 3


title: Patient3_Relapse_67


title: TG_hyperoxia_rep3

description: SAMPLE 5


title: Patient3_Relapse_66


title: WT_normoxia_rep1

description: SAMPLE 2


title: Patient3_Relapse_65


title: TG_hyperoxia_rep1

description: SAMPLE 1


title: C114Rd

city: Heidelberg

last: Musser

address: Meyerhofstrasse 1

institute: European Molecular Biology Laboratory

data_processing:
Basecalls performed using CASAVA
reads mapped to chicken, emu, or alligator genomes using Tophat2 version 2.0.6. using default parameters and setting the -GTF option
read counts generated using HTSEQ version 0.5.3p9 implemented in python version 2.7.2. We set the option requiring reads to map to the correct strand, and resolved issues with multiple mappings using the option "intersection-nonempty".
TPM (transcript per million) relative expression values were calculated for all genes using the following method: Wagner GP, Kin K, Lynch VJ. 2012. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theor Biosci. 131:281-285.
We applied a scaling factor to all emu TPM values (.55x) and alligagtor TPM values (.62) to account for differences in the number of annotated genes. This value was calculated using the method outlined here: Musser, J. M. & Wagner, G. P. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called ‘species signal’. J Exp Zool (Mol Dev Evol) 324, 588–604 (2015).
Genome_build: Chicken reads were mapped to ensembl WASHUC2 release version 68. Emu reads were mapped to a preliminary version of the Emu genome generated by the Alan Baker Lab at the University of Toronto. Alligator reads were mapped to american alligator genome allmis1.
Genome_build: Chicken:  WASHUC2 (https://may2012.archive.ensembl.org/Gallus_gallus/Info/Index)
Genome_build: Alligator: Allmis1 (https://hgdownload-test.gi.ucsc.edu/goldenPath/allMis1/bigZips/)
Genome_build: Emu:  preliminary version from Allan Baker's Lab is not available publicly
Supplementary_files_format_and_content: the final scaled TPM values for all chicken, emu, and alligator one-to-one orthologs that were used for analyses. The matrix uses chicken gene identifiers from the WASHUC2 version of the chicken genome (the data from Emu and Alligator are only for the 1-1 orthologs to chicken).

organism: Gallus gallus

source_name: reticulate scale morphogenesis tract dermis

growth_protocol: Bird eggs were incubated with rotation in a G.Q.F 1502 Sportsmen Incubator at 37.8 degrees celsius (chicken) or 35.5 degrees celsius (emu). Alligator egg incubation is described in detail in Musser et al. 2015.

extract_protocol:
Total RNA was extracted using a Qiagen Rneasy kit.
polyA enriched strand-specific library was constructed using a proprietary method developed by the Yale Center for Genome Analysis

treatment_protocol: Skin samples were dissected and placed in a minimal amount of 10 mg/mL dispase and incubated at 4 degrees celsius for 13 hours to permit clean separation of epidermis.

tag: developmental stage

value: Hamburger and Hamilton stage 40


title: C95Sd

description:
C95Sd_005_ACAGTG_L008
C95Sd

source_name: scutate scale morphogenesis tract dermis


title: C56C

description:
C56C_GCCAAT_L008_CAT
C56C

source_name: claw morphogenesis epidermis

value: Hamburger and Hamilton stage 38

value: claw morphogenesis epidermis


title: WT_hyperoxia_rep1

description: SAMPLE 2


title: C97Fd

source_name: feather morpogenesis femoral tract dermis

value: Hamburger and Hamilton Stage 36


title: Patient3_Relapse_61

value: Post-treatment relapse


title: C56Cd

description:
C56Cd_CTTGTA_L008_001
C56Cd

source_name: claw morphogenesis dermis

value: claw morphogenesis dermis


title: Patient3_Relapse_6

value: Patient 3


title: Patient3_Relapse_60


title: Patient3_Relapse_63


title: C114R

description:
C114R_CTTGTA_L008_CAT
C114R

source_name: reticulate scale morphogenesis tract epidermis


title: C122R

description:
C122R_CTTGTA_L001
C122R

value: reticulate scale morphogenesis tract epidermis


title: Bcl-2 overepxression in rat NPCs

city: Seoul

first: Yun Young

last: Lee

address: 222, Wangsimni-ro, Seongdong-gu

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: Hanyang University

description: Bcl-2 overexpression (Bcl-2 overexpression vs Proliferation)

hyb_protocol: It was hybridized using Agilent's Gene Expression Hybridization Kit.

scan_protocol: Images were scanned on Agilent's DNA microarray scanner and quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: Rat neural stem cells overexpreesed by rBcl-2 gene (with bFGF)

label_protocol: Total RNA was amplifed and labed with Cy3/Cy5 using Agilent's Low RNA Input Linear Amplification kit PLUS.

growth_protocol: Rat neural precurosr cells (NPCs) derived from E14 rat embryos were cultured in N2 medium supplemeted with 10 ng/mL bFGF.

extract_protocol: Total RNA was isolated using Trizol following manufacturer's instructions. Its quality was analyzed using Agilent's 2100 Bioanalyzer system.

treatment_protocol: Rat NPCs were transiently tranfected with 4 μg of either MSCV-IRES-EGFP (Empty vector) or rBcl-2-MSCV-IRES-EGFP (for Bcl-2 overexpression) using an Nucleofector™ kit (Lonza, Walkersville, MD, USA). Then, the cells were proliferated by N2+bFGF or differentiated by withdrwing bFGF and incubating them NB medium for 2 days.

value: SD Rat

tag: tissue source

value: Embryonic brain cortex derived from E14

tag: cell type

value: Primary neural stem cells

value: with bFGF

source_name: Rat neral stem cells transfected by empty vector (with bFGF)

value: MSCV-IRES-EGFP (Empty vector)

value: N2+bFGF (control; proliferation)


title: Stimulation of neuronal differnetiation

description: Neuronal differentation (Differentiation vs Proliferation)

source_name: Rat neral stem cells transfected by empty vector (without bFGF)

tag: strain

value: withdrawing bFGF (differentiation)


title: C94S

description:
C94S_ACAGTG_L008_CAT
C94S

source_name: scutate scale morphogenesis tact epidermis


title: Patient3_Relapse_62

source_name: Acute myeloid leukemia intiating cell

value: Single acute myeloid leukemia intitiating cell


title: Patient3_Relapse_57


title: C49C


title: C95S

value: scutate scale morphogenesis tact epidermis


title: Patient3_Relapse_56


title: Patient3_Relapse_58


title: C99F

source_name: feather morphogenesis femoral tract epidermis


title: Patient3_Relapse_55


title: C97F

value: feather morphogenesis femoral tract epidermis


title: Patient3_Relapse_64


title: Patient3_Relapse_54


title: C97Bd

description:
C97Bd_TGACCA_L008
C97Bd

source_name: feather morphogenesis dorsal tract dermis


title: C99B

source_name: feather morphogenesis dorsal tract epidermis


title: Patient3_Relapse_59


title: Patient3_Relapse_53


title: Patient3_Relapse_51


title: C97B

description:
C97B_TGACCA_L008_CAT
C97B

value: feather morphogenesis dorsal tract epidermis


title: C100Cd

description:
C100Cd_GCCAAT_L008
C100Cd

source_name: claw placode dermis

value: claw placode dermis


title: Patient3_Relapse_49


title: Patient3_Relapse_5


title: Patient3_Relapse_50


title: Patient3_Relapse_48


title: C126C

source_name: claw placode epidermis

value: Hamburger and Hamilton Stage 36

value: claw placode epidermis


title: C113Rd

source_name: reticulate scale placode tract dermis

value: Hamburger and Hamilton Stage 39

value: reticulate scale placode tract dermis


title: Patient3_Relapse_47

value: Post-treatment relapse

value: Patient 3


title: C103Sd

description:
C103Sd_ACAGTG_L008
C103Sd

source_name: scutate scale placode tract dermis

value: Hamburger and Hamilton Stage 37

value: scutate scale placode tract dermis


title: Patient3_Relapse_46


title: C17Fd

source_name: feather placode femoral tract dermis

value: Hamburger and Hamilton Stage 33/34

value: feather placode femoral tract dermis


title: C17Bd

description:
C17Bd_CTTGTA_L007
C17Bd

source_name: feather placode dorsal tract dermis

value: feather placode dorsal tract dermis


title: C99C


title: C113R

source_name: reticulate scale placode tract epidermis


title: Patient3_Relapse_43


title: C91R

value: reticulate scale placode tract epidermis


title: Patient3_Relapse_42

value: Single acute myeloid leukemia intitiating cell


title: C116S

source_name: scutate scale placode tract epidermis

value: scutate scale placode tract epidermis


title: Patient3_Relapse_45


title: C103S


title: C14F

source_name: feather placode femoral tract epidermis

value: feather placode femoral tract epidermis


title: Patient3_Relapse_40


title: C17F


title: Patient3_Relapse_4


title: C14B

source_name: feather placode dorsal tract epidermis

value: feather placode dorsal tract epidermis


title: C17B


title: Patient3_Relapse_38


title: Patient3_Relapse_36


title: Patient3_Relapse_34


title: Patient3_Relapse_33


title: Patient3_Relapse_31


title: Patient3_Relapse_32


title: Patient3_Relapse_30


title: Patient3_Relapse_3


title: Patient3_Relapse_29


title: Patient3_Relapse_26


title: Patient3_Relapse_41


title: Patient3_Relapse_39


title: Patient3_Relapse_27


title: Patient3_Relapse_25


title: Patient3_Relapse_24


title: Patient3_Relapse_35


title: Patient3_Relapse_22


title: NPC (3) exposed to 1µM BDE-47 for 24h Exp3

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
BDE47_1μM_24h_Exp3

hyb_protocol: Labeled cRNA was purified with an RNeasy column (QIAGEN). Quality was evaluated by using the Agilent Bioanalyzer 2100 system. cRNA was fragmented at 94 C for 35 min.

scan_protocol: Hybridized with 15ug of cRNA and then washed, stained, and imaged at the Gladstone Genomics Core Facility by using standard Affymetrix protocols.

data_processing: Affymetrix CEL files were processed using the Affymetrix Expression Console and Transcriptome Analysis Console (TAC) software packages. Raw values were normalized via the Robust Multi-array Average (RMA) algorithm.

label: Biotin

source_name: UCSF4 human embryonic stem cell line (hESC) derived human neural progenitor cells (NPCs)

label_protocol: Hybridization and labeling was accomplished by using the protocol devised by the UCSF Gladstone Genomics Core Facility. Double-stranded cDNAs were generated from total RNA samples by using SuperScript II reverse transcriptase (Invitrogen) and a T7-oligo primer (QIAGEN). Biotin-labeled cRNA was synthesized by in vitro transcription using an Enzo Bioassay RNA labeling kit (Enzo Diagnostics).

growth_protocol: Neural precursor cells (NPCs) were derived from hESCs (UCSF4, NIH registry code 0044) using a protocol developed by Swistowski et al., 2009 at the Buck Institute for Age Research,. NPCs were grown in Neurobasal Medium (Gibco), NEAA (2mM), L-Glutamine (2mM), penicillin/ streptomycin, B27, FGF2 (20ng/mL) and LIF (10ng/mL; Millipore) at 8% O2 and 5%CO2,  and passaged every 3-5 days in culture. For transcriptomic experiments, NPCs (passages <15) were plated at 500,000 cells/well (6-well plate).

extract_protocol: Immediately following a 24h exposure duration, NPCs were washed once with PBS and RLT Lysis Buffer (Qiagen) was directly added to the culture dish well. The lysate was collected and stored at -80oC. We isolated and purified RNA using the RNeasy Micro Kit (Qiagen). The RNA concentration and quality were estimated (Absorbance 260nm/280nm = 1.9 - 2.1) by using a Nanodrop spectrometer (Thermo Scientific) and the Agilent RNA 6000 Nano LabChip Kit and Bioanalyzer 2100 system (RIN ≥ 9).

treatment_protocol: After 2 days of culture (~60-70% confluency) fresh media was supplied and NPCs were exposed to vehicle control (0.1% DMSO), 1µM BDE-47 or 10µM BDE-47 at a 1:1000 dilution.

tag: experiment date

tag: passage

tag: exposure duration


title: NPC (2) exposed to 0.1% DMSO for 24h Exp2

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
DMSO_24h_Exp2

tag: cell line


title: NPC (3) exposed to 10µM BDE-47 for 24h Exp3

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
BDE47_10μM_24h_Exp3


title: NPC (1) exposed to 10µM BDE-47 for 24h Exp1

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
BDE47_10μM_24h_Exp1


title: NPC (2) exposed to 10µM BDE-47 for 24h Exp2

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
BDE47_10μM_24h_Exp2


title: NPC (1) exposed to 0.1% DMSO for 24h Exp1

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
DMSO_24h_Exp1


title: Patient3_Relapse_21


title: Patient3_Relapse_2


title: Patient3_Relapse_19


title: NPC (1) exposed to 1µM BDE-47 for 24h Exp1

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
BDE47_1μM_24h_Exp1


title: NPC (3) exposed to 0.1% DMSO for 24h Exp3

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
DMSO_24h_Exp3


title: NPC (2) exposed to 1µM BDE-47 for 24h Exp2

description:
Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)
BDE47_1μM_24h_Exp2


title: AML#4 leukemic xenograft_TDZ_Recipient mouse 2

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and batch corrected to account for technical variation of isolation of human cells from patients versus xenografts using Partek Genomics Suite 6.6 software.

source_name: Xenografted human AML

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: Xenografted animals were treated with intraperitoneal injections of TDZ (22.5 mg/kg/day) or Captisol 30% control for 21 consecutive days

value: Xenografted human leukemic cells (CD45+CD33+)

tag: treatment

value: PB


title: Patient3_Relapse_18


title: AML#5 leukemic xenograft_TDZ

label_protocol: In accordance with manufacturer's protocols


title: AML#5 leukemic xenograft_Control


title: AML#4 leukemic xenograft_TDZ_Recipient mouse 1


title: AML#1 leukemic xenograft_Control_Recipient mouse 1


title: AML#1 leukemic xenograft_TDZ


title: Patient3_Relapse_17


title: AML#4 leukemic xenograft_Control


title: Patient3_Relapse_23


title: Patient3_Relapse_16


title: Patient3_Relapse_20


title: Patient3_Relapse_15


title: Patient3_Relapse_14


title: Patient3_Relapse_13


title: Patient3_Relapse_12


title: Patient3_Relapse_11


title: Patient3_Relapse_10


title: Patient3_Relapse_1


title: Patient3_Diagnosis_97

value: Pre-treatment diagnosis


title: Patient3_Diagnosis_98


title: Patient3_Diagnosis_99


title: Patient3_Diagnosis_92


title: Choroid plexus papilloma, biological rep1

city: La Jolla

first: Jun

last: Wang

address: 2880 Torrey Pines Scenic Drive

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Gene expression data from choroid plexus papilloma

hyb_protocol: The labeled sscDNA was hybridized onto GeneChip Mouse Gene 2.0 ST Array (Affymetrix).

scan_protocol: The arrays were scanned using Affymetrix GeneChip Command Console Software (AGCC) and GeneChip® Scanner 3000 7G.

data_processing: QC was performed using Affymetrix Expression Console and RMA was used as normalization method.

source_name: Choroid plexus papilloma

label_protocol: The single-stranded cDNA was generated according to Whole Transcript (WT) Sense Target Labeling Assay protocol using Ambion’s WT Expression kit (p/n 4411974). The sscDNA was  then fragmented and labeled using GeneChip WT Terminal Labeling kit (PN 900671).

growth_protocol: Transgenic mice were monitored for tumor growth. Animals were sacrificed and tumor tissues were collected when mice show sign of tumor development including weight loss, ataxia, hydrocephalus.

extract_protocol: Qiagen RNeasy plus mini kit was used to extract total RNA from all tissues.

treatment_protocol: Tissues were isolated from animals and immediately snap-frozen. Tissues were then stored at -80C until ready for RNA extraction.

tag: background strain

value: C57Bl/6 and 129 mix

tag: genotype

value: Atoh1-Cre; Myc/Myc

value: Choroid plexus papilloma

tag: disease state

value: Tumor


title: Choroid plexus papilloma, biological rep5


title: Choroid plexus papilloma, biological rep2


title: Patient3_Diagnosis_91

source_name: Acute myeloid leukemia intiating cell

tag: state

tag: patient id

value: Patient 3


title: Choroid plexus carcinoma, biological rep2

description: Gene expression data from choroid plexus carcinoma

source_name: Choroid plexus carcinoma

value: Atoh1-Cre; Myc/Myc; p53fl/fl

tag: tissue

value: Choroid plexus carcinoma


title: Choroid plexus papilloma, biological rep4


title: Normal choroid plexus, biological rep3

description: Gene expression data from normal choroid plexus

source_name: Normal choroid plexus

value: Myc/Myc; p53fl/fl

value: choroid plexus

value: Normal


title: Choroid plexus papilloma, biological rep3


title: Choroid plexus carcinoma, biological rep4


title: Normal choroid plexus, biological rep5


title: Choroid plexus carcinoma, biological rep3


title: Patient3_Diagnosis_93

value: Single acute myeloid leukemia intitiating cell

tag: surface markers


title: Choroid plexus carcinoma, biological rep5


title: Choroid plexus carcinoma, biological rep1


title: Normal choroid plexus, biological rep2


title: Normal choroid plexus, biological rep1


title: Sash1-ko embryonic mouse lung endothelium, replicate 3

city: Vancouver

first: Aly

last: Karsan

state: BC

address: W10th Ave

department: Genome Sciences Centre

institute: BC Cancer Agency

hyb_protocol: Hybridization on the Affymetrix Fluidics 450 system was performed with the standard protocol #FS450_0002 as detailed in the program software.

scan_protocol: Scanning was performed on the GeneChip ® Scanner 3000 using the preset pixel value and resolution parameters defined in the scanner.

data_processing:
RMA was performed using Affymetrix Expression Console (version 1.1)
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

label_protocol: labelled using the Nugen Pico WTA kit.

growth_protocol: Mouse embryonic lungs collected at E18.5 from Sash1-/- or wild-type littermates (C57BL/6 background)

extract_protocol: RNA was extracted using Qiagen RNeasy kits and analyzed by Agilent 2100 Bioanalyzer; samples with RIN > 7 were amplified

treatment_protocol: Embryos were genotyped by PCR; embryonic lungs (E18.5) were dissected  and endothelial cells were separately sorted as viable CD31+/CD45-/CD326- cells, and snap-frozen.

value: C57BL/6 background

tag: age

value: lung

value: endothelial cells


title: Normal choroid plexus, biological rep4


title: Patient3_Diagnosis_9


title: Patient3_Diagnosis_89


title: Patient3_Diagnosis_86


title: Sash1-ko embryonic mouse lung endothelium, replicate 4


title: wild-type embryonic mouse lung endothelium, replicate 3

value: wild-type


title: Sash1-ko embryonic mouse lung endothelium, replicate 2


title: Patient3_Diagnosis_84


title: Patient3_Diagnosis_90


title: Patient3_Diagnosis_83


title: Patient3_Diagnosis_82


title: Patient3_Diagnosis_81


title: wild-type embryonic mouse lung endothelium, replicate 1


title: Patient3_Diagnosis_80


title: Patient3_Diagnosis_8


title: Sash1-ko embryonic mouse lung endothelium, replicate 1


title: wild-type embryonic mouse lung endothelium, replicate 2


title: Input3

city: Berkeley

first: Zhe

last: Zhang

address: University of California Berkeley

department: MCB

institute: University of California, Berkeley

data_processing:
Sequenced reads were trimmed for adaptor sequences and index sequences
Alignment and abundance calculation were done using RSEM (RNA-Seq by Expectation-Maximization) software.
Gene expression analysis was performed with DESeq software.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes gene ID, TPM values fore each sample.

source_name: brain pIII region

extract_protocol:
pIII was rapidly dissected on ice. For each repeat, tissues from 4-5 mice were pooled, homogenized, and immunoprecipitation with eGFP antibodies
RNA libraries were prepared for sequencing using Illumina Nextera Library Prep Kits

treatment_protocol: Mice expressing CreER under the Fos promoter are crossed with Cre-inducible reporter mice expressing eGFP-L10a. Each mouse undergoes 6 hr of sleep deprivation (SD) and 3 hr of recovery sleep (RS); 4-OHT was injected immediately before SD or RS to label wake- or sleep-active neurons, respectively.

value: brain

tag: brain region

value: perioculomotor (pIII) region


title: Patient3_Diagnosis_77

value: Pre-treatment diagnosis


title: Patient3_Diagnosis_79


title: Patient3_Diagnosis_75


title: Patient3_Diagnosis_74


title: AML#1 leukemic xenograft_Control_Recipient mouse 2

value: Xenografted human leukemic cells (CD45+CD33+)

value: PB


title: Patient3_Diagnosis_76


title: 15q13.248.hippocampus.wt

city: Los Angeles

first: Aaron

last: Gordon

address: Gonda Building, 695 Charles E. Young Drive South

department: Neurology

institute: UCLA

data_processing:
Reads were mapped to GRCm38 using Gencode v11 via STAR (v2.5.2b)
Gene expression levels were quantified using featureCounts (v1.5.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files conating raw counts

source_name: hippocampus

extract_protocol:
Samples were lysed and homogenized in RA1 lysis buffer with 1% β-mercaptoethanol (Macherey-Nagel, Düren, Germany) using a PT 1200 E Polytron® (Kinematica, Luzern, Switzerland). Total RNA was purified using TruSeq® Stranded mRNA Sample Preparation kit according to manufacturer’s instructions (Illumina, San Diego, Ca, USA).
3’ poly-adenylation purification, adapter ligation, and PCR amplification was carried out using the TruSeq® Stranded mRNA Sample Preparation kit per manufacturer’s instructions, with a minimum amount of 160 ng RNA per sample (Illumina)

tag: sequencing study

value: Study 1

tag: library preparation kit

value: TruSeq stranded mRNA sample preparation kit

tag: sample id

tag: cnv

value: wt

tag: Sex

value: M

tag: sequencing protocol

value: Paired reads, 100 bp


title: Patient3_Diagnosis_78

city: Cleveland

last: Wald

address: Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road

institute: Case Western Reserve University

data_processing:
Raw reads were preprocessed and aligned to the hg19 human reference genome using the STAR aligner.
Resulting bam files were processed using featureCounts (R package) and hg19 gtf file.
featureCounts() parameters: largestOverlap=T, isPairedEnd=T, isGTFAnnotationFile=TRUE, useMetaFeatures=TRUE
Resulting count files appended into csv file. One csv file per patient that includes untreated diagnosis and post-treatment relapse cells.
Genome_build: hg19
Supplementary_files_format_and_content: csv files represent raw un-normalized counts. One csv file per patient with each column representing an individual cell.

extract_protocol:
Bone marrow samples were thawed and processed rapidly. Cells were washed in PBS twice, then stained with antibodies (BD Pharmingen, Franklin Lakes, New Jersey) for leukemic stem cell markers (CD34, CD38, CD90, CD45RA, Lin) and viability (7-AAD) and incubated in the dark for 20 minutes at room temperature. Cells were washed once and resuspended in 3%FBS/PBS. 2μL of RiboLock RNase inhibitor (40U/μL; Thermo Scientific, Waltham, Massachusetts) was added to the cells to be sorted.
The protocol for single cell RNA sequencing was performed as per Picelli et al (SmartSeq2; Nature Methods 2013). Briefly, 4 ul of lysis buffer containing 0.2% Triton X-100 solution, 1 ul of dNTP mix (KAPA Biosystems, Wilmington, Massachusetts), 1ul of 10uM 5’ anchored oligo-dT oligonucleotide (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′; Sigma Life Science, St. Louis, Missouri) and 1ul RNase inhibitor were added to each well of the 96-well plates.
Using a BD FACSAria cell sorter the AML stem cells were identified as the population that was CD34+, CD38 dim, CD90-, CD45RA+, lineage-, and 7-AAD-. Samples were the incubated at 72°C for 3 min in a thermocycler and immediately placed on ice. Samples were then spun down and 5.7ul of RT mix (100U PrimeScript (Takara Biosciences), 10U RNase inhibitor, 1X Primerscript first strand buffer (5X), 5mM DTT, 1M Betaine, 1uM template switching oligo (5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′)) was added to each well.
The 96-well plate was spun down and incubated at 42°C for 90 min, followed by an additional 10 cycles of 4 min at 42 °C. 1X KAPA HiFi Hotstart ReadyMix was then added along with 0.1 uM PCR primers (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and the PCR was performed for 22 cycles. PCR purification was performed using Sera-mag SpeedBeads (1:1 ratio of beads: cDNA mixture; Thermo Scientific, Fremont, California). PCR product size distribution is checked using an Agilent high-sensitivity DNA chip, with a good library classified as being devoid of fragments <500bp and with a peak around 1.5-2kb.
Library preparation was performed as per manufacturer instructions by Illumina Nextera XT DNA sample preparation kit (Illumina, San Diego, California). Briefly, the tagmentation reaction was carried out on 1 ng of cDNA at 55 °C for 10 min. The amplification of adapter-ligated fragments was performed using Nextera PCR master mix, index primers and barcodes were added to identify each cell for 15 cycles. The PCR products from each cell were then pooled together and purified using Sera-mag SpeedBeads (0.6:1 ratio). A final quality check of the cDNA library was performed using an Agilent high-sensitivity DNA chip, obtaining a broad peak between 300-800bp.  Single cells were sequenced using 100bp paired end sequencing on the Illumina HiSeq 2500.

value: Patient 3


title: 15q13.249.hippocampus.homo

value: homo


title: 15q13.247.hippocampus.wt


title: CD19_tamoxifen Tx_rep2.

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

institute: Konyang university

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip mouse Array at 45°C for 16 h. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on a GCS3000 Scanner (Affymetrix)

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software. The data was summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

source_name: CD19 deletion of resting B cell in spleen of sirt1 conditional knockout mouse

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Resting B cells of spleen were prepared using Magnetic-activated cell sorting (MACS).

extract_protocol: Total RNA from the cells was extracted using TRI reagent® (Ambion).

treatment_protocol: For preparation of CD19 deleted resting B cells, we treated tamoxifen for 5 days in sirt1 conditional knockout mouse.

tag: genotype/variation

value: sirt1 conditional knockout mouse

value: spleen

tag: cell type

value: resting B cell

value: tamoxifen


title: 15q13.246.hippocampus.homo


title: 15q13.244.hippocampus.wt

value: F


title: 15q13.245.hippocampus.wt


title: Patient3_Diagnosis_73

first: David

value: Single acute myeloid leukemia intitiating cell


title: CD19_tamoxifen Tx_rep3.

tag: treatment


title: CD19_tamoxifen Tx_rep1.


title: Patient3_Diagnosis_72


title: CD19_control_rep3.

source_name: CD19 control of resting B cell in spleen of sirt1 conditional knockout mouse

value: control


title: CD19_control_rep2.


title: Patient3_Diagnosis_71

value: Pre-treatment diagnosis


title: Patient3_Diagnosis_70


title: Patient3_Diagnosis_7


title: 15q13.238.hippocampus.wt

tag: genotype


title: 15q13.242.hippocampus.wt


title: Patient3_Diagnosis_69


title: 15q13.241.hippocampus.homo


title: 15q13.237.hippocampus.wt


title: 15q13.236.hippocampus.wt


title: Patient3_Diagnosis_67


title: Patient3_Diagnosis_68


title: Patient3_Diagnosis_66


title: 15q13.243.hippocampus.homo


title: Patient3_Diagnosis_65


title: 15q13.235.hippocampus.homo


title: Patient3_Diagnosis_64


title: Patient3_Diagnosis_63


title: 15q13.230.hippocampus.homo


title: Patient3_Diagnosis_62


title: 15q13.233.hippocampus.wt


title: 15q13.234.hippocampus.wt


title: 15q13.231.hippocampus.homo


title: 15q13.229.cortex.wt

source_name: cortex


title: 15q13.227.cortex.wt


title: 15q13.228.cortex.homo


title: 15q13.232.hippocampus.homo


title: Patient3_Diagnosis_59


title: Patient3_Diagnosis_60


title: Patient3_Diagnosis_61


title: CD19_control_rep1.


title: 15q13.226.cortex.wt


title: Patient3_Diagnosis_57


title: Patient3_Diagnosis_56


title: 15q13.225.cortex.homo


title: 15q13.224.cortex.wt


title: 15q13.223.cortex.wt


title: 15q13.222.cortex.homo


title: Patient3_Diagnosis_53


title: Patient3_Diagnosis_54


title: 15q13.221.cortex.wt


title: 15q13.220.cortex.homo


title: Patient3_Diagnosis_52


title: Patient3_Diagnosis_51


title: 15q13.219.cortex.wt


title: 15q13.217.cortex.wt


title: Patient3_Diagnosis_5


title: 15q13.215.cortex.wt


title: Patient3_Diagnosis_50


title: Patient3_Diagnosis_49


title: 15q13.214.cortex.homo


title: Patient3_Diagnosis_48


title: 15q13.213.cortex.wt


title: 15q13.212.cortex.wt


title: Patient3_Diagnosis_46


title: Patient3_Diagnosis_45


title: Patient3_Diagnosis_58


title: Patient3_Diagnosis_44


title: 15q13.210.cortex.homo


title: 15q13.209.cortex.homo


title: Patient3_Diagnosis_41


title: Patient3_Diagnosis_42


title: scRNA-seq_Adult: Single cell murine 10w inginal WAT SVF

city: Philadelphia

first: Patrick

last: Seale

address: Smilow Center 3400 Civic Center Blvd. 1

institute: University of Pennsylvania

description: 10X Genomics Single Cell RNA-Seq

data_processing:
Basecalling via illumina software after
The Cell Ranger Single Cell Software Suite v.2.0.1 (mouse studies) or v.3.0.1 (human studies) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Data were analyzed with the default settings for these pipelines.
Clustering and gene expression were visualized with the Seurat package (version 3.0, https://satijalab.org/seurat/) on R Studio (https://www.rstudio.com).  Cells were first filtered to have > 500 detected genes and less than 5% of total UMIs mapping to the mitochondrial genome
Clusters with very few cells were filtered before downstream analysis.   Data was scaled to mitigate the effects of the following variables number of genes detected per cell, percent mitochondrial reads and cell cycle phase.
Dimensionality reduction was performed using the T-stochastic Neighboring Embedding method (t-SNE) using Seurat. Differential gene expression analysis between clusters was performed using the Seurat function FindMarkers using the wilcox test.  Violin plots, heatmap and individual tSNE plots for the given genes were generated using the Seurat toolkit ‘VlnPlot’, ‘DoHeatmap’ and ‘FeaturePlot’ functions respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger barcodes and gene count matrices

source_name: 129SVE mice

extract_protocol:
Tissues were manually minced, digested with Collagenase D and Dispase II at 37C for 45 min. For both mouse and human studies stromal vascular cells were isolated and flow sorted with gating to isolate single cells away from debris, doublets, and dead cells.  For the p12 pups (pooled male and female C57BL/6) and human single cell study, the cells were further gated against CD45 to exclude leukocytes.  For the adult mouse thermoneutral (pooled male 129S6/SvEvTac) sample CD45 cells were segregated and remixed with the SVC cells at a ratio of approximately 20% of the total cells.
The sorted cells were loaded onto a GemCode instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell barcoded droplets (GEMs) according to the manufacture’s protocol using the 10x Single Cell 3’ v2 chemistry.

tag: gender

value: Male

value: Subcutaneous WAT (inguinal)

tag: developmental stage

value: 8-10 weeks


title: scRNA-seq_p12: Single cell murine p12 subcutaneous WAT SVF

description: 10X Genomics Single Cell RNA-Seq

source_name: C57BL/6 mice

value: pooled male and female

value: Subcutaneous WAT (inguinal + axillary)


title: Patient3_Diagnosis_40

tag: state

tag: patient id


title: Patient3_Diagnosis_4

tag: tissue

tag: surface markers