title: CIA_replicate_3

city: Aurora

first: Eric

middle: M

last: Pietras

state: CO

address: 12700 E. 19th Avenue, Research Complex 2 Room 10014

department: Medicine

institute: University of Colorado Anschutz Medical Campus

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: Bone marrow

growth_protocol: 6-12 week-old male C57BL/6J (Strain #000664) mice were from The Jackson Laboratory (Bar Harbor, ME) and maintained in a temperature- and light-controlled environment with irradiated chow and water ad libitum for all experiments.

extract_protocol:
Cells were pelleted and Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) or Arcturus Pico Pure kit (Life Technnologies, Carlsbad, CA) per manufacturer’s recommendations. RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample using an Illumina HiSeq2500v4 high-throughput sequencer.

treatment_protocol: Arthritis was induced by intradermally injecting type II chicken (C57BL/6J mice) collagen (Sigma-Aldrich) emulsified in Complete Freund’s Adjuvant (Sigma-Aldrich).  All animal procedures were approved by the University of Colorado Denver Anschutz Medical Campus Institutional Animal Care and Use Committee (IACUC).

value: Hematopoietic Stem Cells

tag: strain

value: Bone marrow

tag: age

value: Adult 6-12 weeks

tag: condition

value: collagen-induced arthritis


title: CIA_replicate_2

status: Public on May 01 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: tissue

tag: Sex

value: Male


title: Patient3_Diagnosis_39

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.

organism: Homo sapiens

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: Pre-treatment diagnosis

tag: patient id

value: Patient 3

tag: surface markers


title: Patient3_Diagnosis_38


title: Patient3_Diagnosis_47


title: Patient3_Diagnosis_35


title: 15q13.211.cortex.homo

city: Los Angeles

first: Aaron

last: Gordon

state: CA

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: cortex

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

tag: genotype

value: homo

value: F

tag: sequencing protocol

value: Paired reads, 100 bp


title: Control_replicate_1

value: control


title: Control_replicate_2


title: Patient3_Diagnosis_32


title: Patient3_Diagnosis_33


title: Patient3_Diagnosis_30


title: KO5: Hb9:Gfp+ p190 KO 5

city: La Jolla

first: Samuel

middle: L

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Illumina adapters were trimmed down to minimum of 50bp with BBTools
Reads were filtered selecting reads with average base quality of > 15 using BBTools
Reads were aligned to the mouse genome, mm10, to filter out unalignable reads prior to Kallisto
Aligned reads were quantified against the Gencode mouse gene annotation using Kallisto with default settings
Genome_build: mm10
Supplementary_files_format_and_content: CSV formatted raw read counts and TPM gene expressions (two files)

molecule: polyA RNA

source_name: Ventral spinal cord

extract_protocol:
Ventral spinal cord regions micro-dissected from E12.5 Arhgap35 (aka, p190) knockout embryos or control littermates (wild-type or p190+/-) were pulled and dissociated with papain (Worthington Biochemical Cat# LK003153) according to the manufacturer’s instructions. Cells were sorted on a Becton Dickinson FACS Vantage SE DiVa using Coherent Sapphire 488 nm solid state laser and collected directly into RLT lysis buffer containing β-mercaptoethanol (Qiagen). RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion (Qiagen RNase-Free DNase Set). RNA samples were quantified with Agilent 2200 TapeStation system prior to preparation of mRNA-sequencing libraries (50 bp single-end) using the Illumina TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions. Libraries were sequenced with Illumina HiSeq 2500 platform.
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit (v2) (Illumina) according to the manufacturer’s instructions.

tag: genotype/variation

value: Arhgap35 knockout

value: Ventral spinal cord

value: motor neuron


title: WT5: Hb9:Gfp+ wild type 5

value: Wild type


title: Patient3_Diagnosis_43


title: KO4: Hb9:Gfp+ p190 KO 4


title: Patient3_Diagnosis_29


title: Patient3_Diagnosis_28


title: WT4: Hb9:Gfp+ wild type 4


title: KOneg1: Hb9:Gfp- p190 KO 1


title: Patient3_Diagnosis_27


title: KO3: Hb9:Gfp+ p190 KO 3


title: WT3: Hb9:Gfp+ wild type 3


title: CIA_replicate_1

value: Hematopoietic Stem Cells

value: Bone marrow


title: Patient3_Diagnosis_26


title: Control_replicate_3

value: Adult 6-12 weeks


title: Patient3_Diagnosis_34


title: WTneg1: Hb9:Gfp- wild type 1


title: Patient3_Diagnosis_25


title: KO1: Hb9:Gfp+ p190 KO 1


title: KO2: Hb9:Gfp+ p190 KO 2


title: WT2: Hb9:Gfp+ wild type 2


title: Patient3_Diagnosis_24


title: WT1: Hb9:Gfp+ wild type 1


title: Patient3_Diagnosis_21


title: Patient3_Diagnosis_3


title: Patient3_Diagnosis_22


title: Patient3_Diagnosis_2


title: IP2

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: Input2

tag: strain


title: Input1


title: IP3


title: Patient3_Diagnosis_19

value: Single acute myeloid leukemia intitiating cell

value: Pre-treatment diagnosis


title: Patient3_Diagnosis_17

value: Patient 3


title: Patient3_Diagnosis_18


title: Patient3_Diagnosis_16


title: MEFs KL001 siCop1_3

city: New York

first: Luca

last: Rizzini

state: NY

address: 522 1st Ave

department: Department of Pharmacology

institute: NYU Langone

data_processing:
Base calling and demultiplexing were performed using the Illumina bcl2fastq software v1.8.4
Sequencing reads were mapped to the mouse reference genome (GRCm38/mm10) using the STAR aligner (v2.4.5a)
Alignments were guided by a Gene Transfer Format file (Ensembl GTF version GRCm38/mm10)
featureCounts (Subread package v1.4.6-p3) was used to generate the matrix of read counts for annotated genomic features
The DESeq2 package (Bioconductor v3.3.0) in the R statistical programming environment was utilized to calculate differential gene statistical comparisons
The mean read insert sizes and their standard deviations were calculated using Picard tools (v1.126)
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing normalized matrix of read counts which includes values for all features and all samples
Supplementary_files_format_and_content: Counts.raw.csv: The raw read count table were generated using featureCounts (Subread package v1.4.6-p3)
Supplementary_files_format_and_content: Counts.normalized.csv: The normalized based on their library size factors using DEseq2

source_name: mouse embryonic fibroblasts

extract_protocol:
Qiagen RNeasy Mini Kit
Libraries were prepared with the Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101). Input was 500 nanogram for all samples, per cycles x10. Libraries were normalized, pool, and run on 3 lanes of single-read 50 Illumina HiSeq 2500.

value: wild type


title: MEFs Dexa KL001 siCop1_2


title: MEFs Dexa KL001 siCop1_1


title: Patient3_Diagnosis_15


title: Patient3_Diagnosis_14


title: Patient3_Diagnosis_23


title: Patient3_Diagnosis_13


title: MEFs KL001 siCop1_2


title: IP1


title: Patient3_Diagnosis_12


title: Patient3_Diagnosis_20


title: MEFs siCop1 control (DMSO)_3


title: MEFs Dexa siCop1 control (DMSO)_3


title: MEFs Dexa siCop1 control (DMSO)_1


title: MEFs Dexa siCop1 control (DMSO)_2


title: Patient3_Diagnosis_103


title: Patient3_Diagnosis_11


title: Patient3_Diagnosis_104


title: Patient3_Diagnosis_101


title: Patient3_Diagnosis_102


title: MEFs siCop1 control (DMSO)_2


title: MEFs siCop1 control (DMSO)_1


title: Patient3_Diagnosis_100


title: MEFs Dexa KL001 control (siCTRL)_3


title: MEFs Dexa KL001 siCop1_3


title: Patient3_Diagnosis_10


title: Patient3_Diagnosis_1


title: MEFs Dexa KL001 control (siCTRL)_2


title: MEFs Dexa KL001 control (siCTRL)_1


title: Patient2_Relapse_9

value: Post-treatment relapse

value: Patient 2


title: MEFs KL001 siCop1_1


title: Patient2_Relapse_88


title: Patient2_Relapse_87


title: MEFs KL001 control (siCTRL)_2


title: MEFs KL001 control (siCTRL)_1


title: Patient2_Relapse_86


title: MEFs Dexa control (DMSO, siCTRL)_3


title: MEFs Dexa control (DMSO, siCTRL)_2


title: Patient2_Relapse_85


title: Patient2_Relapse_82


title: MEFs Dexa control (DMSO, siCTRL)_1


title: Patient2_Relapse_84


title: MEFs control (DMSO, siCTRL)_2


title: Patient2_Relapse_81


title: Patient3_Diagnosis_31


title: MEFs control (DMSO, siCTRL)_3


title: Patient2_Relapse_80


title: Patient2_Relapse_79


title: Patient2_Relapse_8


title: Patient2_Relapse_77


title: MEFs KL001 control (siCTRL)_3


title: Patient2_Relapse_83


title: Rx1698

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: run1954_lane12_read*_indexN705-S505=Rx1698

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq paired reads were aligned to the mm10 genome assembly using TopHat
Raw read counts were calculated using featureCounts
Differential expression were predicted using limma/voom
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Runx1/Runx3 double kockout neurofibroma tumors

extract_protocol:
Total RNAs isolated from Nf1fl/fl;DhhCre and Rx1fl/fl;Rx3fl/fl;Nf1fl/fl;DhhCre mouse DRG/tumors was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol.
The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies).

tag: strain background

value: Neurofibroma tumor


title: Nf1fl/fl;DhhCre neurofibroma cells_RUNX1 antibody

description:
RUNX1 treated
run2116_lane1_read1_indexA002=mouse-Runx1-JQ

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 v2.2.6
Peaks were called using HOMER v4.9
Genome_build: mm10
Supplementary_files_format_and_content: A peak calling file was generated and annotated using HOMER, TDF file were generated using IGV.

molecule: genomic DNA

growth_protocol: Primary Nf1fl/fl;DhhCre mouse neurofibroma cells were used for the Chromatin immunoprecipitation (CHIP) assay according to Magna CHIP TM instruction (Millipore, Billerica, MA)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303)

treatment_protocol: The Runx1 in-house Antibody was obtained from Yoram Groner (PLoS Genet. 2015 Aug 14;11(8):e1005457. doi: 10.1371/journal.pgen.1005457. eCollection 2015 Aug.)

tag: stain

value: primary neurofibroma cells

tag: chip antibody

value: Runx1 in-house Antibody


title: MEFs control (DMSO, siCTRL)_1


title: Patient2_Relapse_75

tag: tissue


title: Nf1fl/fl;DhhCre neurofibroma cells_Input DNA

description:
Input DNA as control
run2116_lane1_read1_indexA011=mouse-IgG-JQ

source_name: Primary Nf1fl/fl;DhhCre mouse neurofibroma cells

tag: cell type


title: Patient2_Relapse_76

tag: state


title: Rx1692

description: run1980_lane12_read*_indexN706-S506=Rx1692


title: NF1-Runx1-Runx3-KO [ATAC-seq]

description:
Nf1/ Runx1 / Runx3 triple knock-out
run2280_lane1_read1_index6-1=Ad2.6

data_processing:
We targeted 25-30 million reads for ATAC-seq.
Sequencing reads in Fastq files were examined by FastQC (v0.11.5) and trimmed using TrimGalore  (v0.4.4).
Reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.2.6)
HOMER (v4.9) was used to predict and annotate differential peaks with default parameters. We considered differential peaks with FDR < 0.01 (RNA-seq) or FDR<0.001 (CHIP-seq and ATAC-seq) as statistically significant.
Supplementary_files_format_and_content: Differential peaks were calling using HOMER and TDF files were generated using IGV

source_name: Neurofibroma tumor

value: EGFP+ Rx1fl/fl;Rx3fl/fl;Nf1fl/fl;DhhCre


title: Patient2_Relapse_74

tag: patient id


title: Rx1677

description: run1954_lane12_read*_indexN704-S504=Rx1677


title: Nf827

description: run1954_lane12_read*_indexN703-S503=Nf827

source_name: Nf1-/- mouse nerve tissues

value: Dorsal root ganglion (DRG)


title: Nf809

description: run1954_lane12_read*_indexN701-S517=Nf809


title: Patient2_Relapse_73

tag: surface markers


title: Nf803

description: run1954_lane12_read*_indexN702-S502=Nf803


title: Patient2_Relapse_72


title: Patient2_Relapse_71


title: Patient2_Relapse_70


title: Patient2_Relapse_7


title: Patient2_Relapse_69


title: Nf1-KO [ATAC-seq]

description:
Nf1 single knock-out
run2280_lane1_read1_index4-1=Ad2.4

source_name: DRG

value: EGFP+ Nf1fl/fl;DhhCre DRG


title: KPC-Par1-KO8_Thrombin_Rep4

city: West Lafayette

first: Stephen

last: Konieczny

state: Indiana

address: 1203 W. State Street

department: Biological Sciences

institute: Purdue University

data_processing:
Reads were quality trimmed and Illumina TruSeq adapter sequences were removed using Trimmomatic v. 0.32
Reads were further trimmed using FastX-Toolkit v. 0.0.13.2 with a minimume quality score of 30 and a maximum length set to 101 bases.
Reads were aligned to mus musculus genome assembly (build mm10) using tophat2 under default setting but allowing only 1 mismatch.
HTSeq v.0.6.1 was used along with the htseq-count script to determine gene counts based on aligned reads. HTSeq was rung using the GTF file on "intersection-nonempty" mode with feature set to "exon" and atribute set to "gene_id" which specified the Ensembl gene IDs. The --stranded=reverse option was set for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing gene counts for each sample

source_name: Pancreatic ductal adenocarcinoma cell line

growth_protocol: Cells were plated in 6cm dishes at 1x10^6 cells/dish in RPMI supplemented 10% FBS 1X Penicillin/Streptomycin. 24h post plating media was replaced with low serum (1% FBS) RPMI. The next day cells were stimulated with either 1U/mL thrombin or an equivilant volume of vehicle and RNA was harvested 24h post treatment.

extract_protocol:
Total RNA was islated using the miRNAeasy isolation kit (Qiagen, 217004) per the manufacterurs instructions.
Libraries were constructed by the Purdue Genomics Facility using the TrueSeq Stranded Total RNA with Ribo-Zero Globin kit (Illimina, San Diego, CA). Paired-end, 2x100 bp reads were sequenced using the HiSeq2500 on high-throughput mode.  Before library preparation the dscDNA quality was checked using an Agilent Bioanalyzer with the High Sensitivity DNA Chip.

value: KRas-G12D; Trp53-R172H; Elas-CreER; F2R-KO

tag: treatment

value: 24h 1U/mL thrombin


title: KPC-Par1-KO8_Thrombin_Rep2


title: KPC-Par1-KO8_Thrombin_Rep3


title: Patient2_Relapse_68


title: KPC-Par1-KO8_Control_Rep4

value: 24h vehicle


title: Patient2_Relapse_67


title: Patient2_Relapse_66


title: KPC-Par1-KO8_Control_Rep3


title: KPC-Par1-KO8_Control_Rep2


title: Patient2_Relapse_65


title: KPC-Par1-KO8_Thrombin_Rep1


title: Patient2_Relapse_78


title: Patient2_Relapse_63


title: Patient2_Relapse_62


title: KPC-Par1-KO1_Thrombin_Rep3


title: KPC-Par1-KO1_Thrombin_Rep4


title: Patient2_Relapse_64


title: Patient2_Relapse_61


title: KPC-Par1-KO1_Thrombin_Rep2


title: KPC-Par1-KO1_Thrombin_Rep1


title: KPC-Par1-KO1_Control_Rep4


title: Patient2_Relapse_60


title: KPC-Par1-KO1_Control_Rep3


title: Patient2_Relapse_6


title: Patient2_Relapse_59


title: KPC-Par1-KO1_Control_Rep1


title: Patient2_Relapse_58


title: KPC-Par1-KO1_Control_Rep2


title: Patient2_Relapse_57


title: Patient2_Relapse_56


title: KPC_Thrombin_Rep3

value: KRas-G12D; Trp53-R172H; Elas-CreER


title: KPC_Thrombin_Rep4


title: Patient2_Relapse_55


title: KPC_Thrombin_Rep2


title: KPC-Par1-KO8_Control_Rep1


title: Patient2_Relapse_53


title: Patient2_Relapse_51


title: KPC_Control_Rep4


title: Patient2_Relapse_52


title: KPC_Control_Rep3


title: KPC_Control_Rep2


title: KPC_Control_Rep1


title: Patient2_Relapse_50


title: mouse_hindbrain_postnatal_day_14

city: Toronto

first: Maria

last: Vladoiu

state: Ontarion

address: 555 University Ave

department: DSCB

country: Canada

institute: Hospital for Sick Children

data_processing:
Cell Ranger v1.2.1 default pipeline
Genome_build: mm10
Supplementary_files_format_and_content: filtered gene matrix

source_name: hindbrain

extract_protocol:
Hindbrain were dissected from mice, dissociated into a single cell suspension suing Papain and the ran on the 10X instrument using 10x Genomics Chromium Single Cell 3' Solution V2. protocol
10x Genomics Chromium Single Cell 3' Solution V2 protocol.

tag: developmental stage

value: Post natal day 14

value: hindbrain

tag: 10x library index


title: Patient2_Relapse_49

value: Single acute myeloid leukemia intitiating cell


title: Patient2_Relapse_48


title: mouse_hindbrain_postnatal_day_7

value: Post natal day 7


title: Patient2_Relapse_47


title: mouse_hindbrain_postnatal_day_0

value: Post natal day 0

value: wild type


title: mouse_hindbrain_embryonic_day_18

value: Embryonic day 18


title: mouse_hindbrain_postnatal_day_5

value: Post natal day 5


title: Patient2_Relapse_45

value: Post-treatment relapse

value: Patient 2


title: mouse_hindbrain_embryonic_day_16

value: Embryonic day 16


title: Patient2_Relapse_43


title: mouse_hindbrain_embryonic_day_14

value: Embryonic day 14


title: Patient2_Relapse_54


title: Patient2_Relapse_42


title: KPC_Thrombin_Rep1


title: mouse_hindbrain_embryonic_day_10

value: Embryonic day 10


title: Patient2_Relapse_41


title: Patient2_Relapse_5


title: Patient2_Relapse_40


title: AD-IL1b MX04 Pos 2

city: Rochester

first: M. Kerry

last: O'Banion

address: 601 Elmwood Avenue

department: Neuroscience

institute: University of Rochester

data_processing:
Demultiplexing - bcltofastq-1.8.4
Cleaning - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
RNA-Seq bam file was mapped to mm10 reference genome obtained from Ensemble.
The data was analyzed using Rsamtools and GenomicAlignments
GenomicAlignments count function summarizeOverlaps was used to generate the raw count data.
Genome_build: mm10
Supplementary_files_format_and_content: text file include raw expression counts

source_name: hippocampus

growth_protocol: Heterozygous APPswe/PS1dE9 (APP/PS1) mice on a congenic C57BL/6 background were purchased from the Jackson Laboratory and bred in house under standard group housing conditions.

extract_protocol:
Sorted microglia were collected in 500 μl RLT Buffer (Qiagen) and total RNA was isolated using the RNeasy Mini Plus Kit (Qiagen). 1 ng of total RNA was preamplified with the SMARter Ultra Low Input kit V2 (Clontech, Mountain View, CA).
Libraries were constructed using the NexteraXT library kit (Illumina, San Diego, CA) and sequenced on the Illumina HiSeq2500 to generate approximately 20 million 100-bp single end-reads per sample.

treatment_protocol: APP/PS1 mice at 7.5 months of age were bilaterally transduced in the hippocampus with rAAV2-IL-1β (APP/PS1-IL-1β) or a control viral vector, rAAV2-Phe (APP/PS1-Phe), and sacrificed three to four weeks post-injection. Three days prior to sacrifice, mice received an i.p. injection of methoxy-X04 (MX04) to label fibrillar amyloid beta plaques

value: hippocampus

value: microglia

tag: age


title: Patient2_Relapse_4


title: AD-IL1b MX04 Pos 1


title: AD-IL1b MX04 Neg 2


title: Patient2_Relapse_39


title: AD-Phe MX04 Pos 2

value: Phe


title: Patient2_Relapse_37


title: Patient2_Relapse_46


title: AD-Phe MX04 Pos 1


title: AD-Phe MX04 Neg 2


title: Patient2_Relapse_36


title: Patient2_Relapse_35


title: AD-Phe MX04 Neg 1


title: Patient2_Relapse_44


title: Patient2_Relapse_34


title: mouse_hindbrain_embryonic_day_12

value: Embryonic day 12

tag: genotype


title: Patient2_Relapse_33


title: Patient2_Relapse_32


title: Patient2_Relapse_31


title: ChIP_FGO_Dnmt3l_KO_H3K27me3_rep1

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

description:
processed data file:
FGO_Dnmt3l_KO_H3K27me3.bed.gz

data_processing:
STAR ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 (version 2.2.2) with the parameter:–t –q –N 1 –L 25. Multiple mapped reads and PCR duplicates were removed. After validating the reproducibility, replicates were pooled for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files for STAR ChIP-seq contains the RPKM value in 100bp bin across the mm9 genome.

source_name: oocyte

extract_protocol:
The DNA extraction follows STAR ChIP-seq protocol
The STAR ChIP-seq libraries were generated following the protocol as described previously(Zhang et al., 2016).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h.

value: oocyte

value: FGO

value: H3K27me3 (Diagenode,Cat.C15410069)


title: ChIP_FGO_Setd2_Con_H3K4me3_rep3

description:
processed data file:
FGO_Setd2_Con_H3K4me3.bed.gz

value: H3K4me3 (home made)


title: ChIP_FGO_Setd2_KO_H3K4me3_rep3

description:
processed data file:
FGO_Setd2_KO_H3K4me3.bed.gz


title: Patient2_Relapse_30

value: Single acute myeloid leukemia intitiating cell


title: RNA_FGO_Dnmt3l_Con_RNA

description:
processed data file:
Dnmt3l_KO_RNA_FPKM.txt.gz

data_processing:
RNA-seq datasets were mapped to the mouse mm9 reference genome by Tophat 2.0.11. Gene expression was then calculated according to refFlat database by cufflinks 2.0.2.
Genome_build: mm9
Supplementary_files_format_and_content: The RNA FPKM txt file contains FPKM value for each sample.

extract_protocol: The RNA-seq libraries were generated following the Smart-seq2 protocol with minor modification (Picelli et al., 2014).

treatment_protocol: 8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyst, 98 h. Germinal versicle stage (GV) oocytes were harvested at 48 h after PMSG. For D7, D10, D14 oocytes, corresponding postnatal female mouse were sacrificed and oocytes were harvested in M2.


title: Patient2_Relapse_38


title: Patient2_Relapse_3


title: Patient2_Relapse_29


title: AD-IL1b MX04 Neg 1


title: Patient2_Relapse_28


title: Patient2_Relapse_27


title: Patient2_Relapse_25


title: Patient2_Relapse_24


title: Patient2_Relapse_22


title: Patient2_Relapse_23


title: Patient2_Relapse_21


title: RNA_FGO_Dnmt3l_KO_RNA


title: Patient2_Relapse_20


title: Patient2_Relapse_19


title: Patient2_Relapse_2


title: Patient2_Relapse_18


title: Patient2_Relapse_26


title: Patient2_Relapse_17


title: E10 GFP-EC_5: E10 EC, biological rep5

type: RNA

city: Kumamoto

first: Tomomasa

last: Yokomizo

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: single-cell gene expression data

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GneneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrics GeneChip Scanner 3000 7G.

data_processing: Microarray data processing was performed using the GCRMA algorithm implemented in the R/Bioconductor package affy.

label: biotin

source_name: E10.5 mouse embryo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mice were housed in a specific-pathogen free animal facility.

extract_protocol: Lysis buffer containing single cell was directly used for cDNA synthesis.

treatment_protocol: Single-cell suspensions were prepared by treating tissues with collagenase [0.125% in PBS/10% fetal calf serum (FCS)/1% penicillin/streptomycin] for 1 h at 37°C. Hematopoietic and endothelial fractions were isolated by cell sorter.

value: caudal half

tag: cell population

value: E10.5 endothelial cells

tag: Stage

value: Embryonic day 10.5

tag: markers


title: Patient2_Relapse_16

value: Post-treatment relapse


title: E10 GFP-EC_6: E10 EC, biological rep6

description: single-cell gene expression data


title: Patient2_Relapse_15

value: Patient 2


title: Patient2_Relapse_14


title: E10 GFP+EC_3: E10 hemogenic EC, biological rep3

description: single-cell gene expression data

value: E10.5 hemogenic endothelial cells


title: Patient2_Relapse_13


title: E10 GFP-EC_2: E10 EC, biological rep2

description: single-cell gene expression data


title: Patient2_Relapse_12


title: E10 GFP-EC_7: E10 EC, biological rep7

description: single-cell gene expression data


title: E10 GFP+EC_4: E10 hemogenic EC, biological rep4

description: single-cell gene expression data


title: E10 GFP-EC_4: E10 EC, biological rep4

description: single-cell gene expression data


title: E10 GFP+EC_6: E10 hemogenic EC, biological rep6

description: single-cell gene expression data


title: E10 GFP+EC_5: E10 hemogenic EC, biological rep5

description: single-cell gene expression data


title: E14_26: E14 HSC, biological rep26

description: single-cell gene expression data

source_name: E14.5 mouse embryo

value: fetal liver

value: E14.5 fetal liver HSCs

value: Embryonic day 14.5

value: wild type


title: E10 GFP+EC_1: E10 hemogenic EC, biological rep1

description: single-cell gene expression data


title: Patient2_Relapse_11


title: E14_24: E14 HSC, biological rep24

description: single-cell gene expression data


title: E10 GFP+EC_7: E10 hemogenic EC, biological rep7

description: single-cell gene expression data


title: E14_25: E14 HSC, biological rep25

description: single-cell gene expression data


title: E14_23: E14 HSC, biological rep23

description: single-cell gene expression data


title: E10 GFP+EC_2: E10 hemogenic EC, biological rep2

description: single-cell gene expression data


title: E10 GFP-EC_3: E10 EC, biological rep3

description: single-cell gene expression data


title: E10 GFP-EC_1: E10 EC, biological rep1

description: single-cell gene expression data


title: E14_27: E14 HSC, biological rep27

description: single-cell gene expression data


title: Patient2_Relapse_1


title: E14_22: E14 HSC, biological rep22

description: single-cell gene expression data


title: Patient2_Diagnosis_9

value: Pre-treatment diagnosis


title: Patient2_Diagnosis_80


title: E14_21: E14 HSC, biological rep21

description: single-cell gene expression data


title: Patient2_Diagnosis_79


title: E14_20: E14 HSC, biological rep20

description: single-cell gene expression data


title: Patient2_Relapse_10


title: Patient2_Diagnosis_8


title: Patient2_Diagnosis_78


title: Patient2_Diagnosis_77


title: Patient2_Diagnosis_74


title: Patient2_Diagnosis_75


title: E14_19: E14 HSC, biological rep19

description: single-cell gene expression data


title: Patient2_Diagnosis_72


title: Patient2_Diagnosis_73


title: Patient2_Diagnosis_71


title: Patient2_Diagnosis_70


title: E14_18: E14 HSC, biological rep18

description: single-cell gene expression data


title: Patient2_Diagnosis_7


title: Patient2_Diagnosis_69


title: E14_17: E14 HSC, biological rep17

description: single-cell gene expression data


title: Patient2_Diagnosis_68


title: Patient2_Diagnosis_76


title: Patient2_Diagnosis_67


title: E14_11: E14 HSC, biological rep11

description: single-cell gene expression data


title: E14_14: E14 HSC, biological rep14

description: single-cell gene expression data


title: E14_10: E14 HSC, biological rep10

description: single-cell gene expression data


title: E14_16: E14 HSC, biological rep16

description: single-cell gene expression data


title: E14_15: E14 HSC, biological rep15

description: single-cell gene expression data


title: E14_7: E14 HSC, biological rep7

description: single-cell gene expression data


title: E14_4: E14 HSC, biological rep4

description: single-cell gene expression data


title: E14_12: E14 HSC, biological rep12

description: single-cell gene expression data


title: E14_5: E14 HSC, biological rep5

description: single-cell gene expression data


title: Patient2_Diagnosis_66


title: E14_6: E14 HSC, biological rep6

description: single-cell gene expression data


title: Patient2_Diagnosis_65


title: E14_9: E14 HSC, biological rep9

description: single-cell gene expression data


title: E14_8: E14 HSC, biological rep8

description: single-cell gene expression data


title: E14_13: E14 HSC, biological rep13

description: single-cell gene expression data


title: E14_3: E14 HSC, biological rep3

description: single-cell gene expression data


title: E14_2: E14 HSC, biological rep2

description: single-cell gene expression data


title: Patient2_Diagnosis_64


title: Patient2_Diagnosis_63


title: Patient2_Diagnosis_62


title: Patient2_Diagnosis_61


title: Patient2_Diagnosis_60


title: Patient2_Diagnosis_59


title: Patient2_Diagnosis_57


title: E14_1: E14 HSC, biological rep1

description: single-cell gene expression data


title: E12_13: E12 cluster cell, biological rep13

description: single-cell gene expression data

source_name: E12.5 mouse embryo

value: aorta-gonad-mesonephros

value: E12.5 hematopoietic clusters

value: Embryonic day 12.5


title: E12_16: E12 cluster cell, biological rep16

description: single-cell gene expression data


title: Patient2_Diagnosis_54

source_name: Acute myeloid leukemia intiating cell


title: Patient2_Diagnosis_56


title: Patient2_Diagnosis_52


title: E12_12: E12 cluster cell, biological rep12

description: single-cell gene expression data


title: E12_15: E12 cluster cell, biological rep15

description: single-cell gene expression data


title: Patient2_Diagnosis_53


title: E12_11: E12 cluster cell, biological rep11

description: single-cell gene expression data


title: E12_14: E12 cluster cell, biological rep14

description: single-cell gene expression data


title: Patient2_Diagnosis_50


title: E12_10: E12 cluster cell, biological rep10

description: single-cell gene expression data


title: Patient2_Diagnosis_51


title: E12_9: E12 cluster cell, biological rep9

description: single-cell gene expression data


title: Patient2_Diagnosis_6


title: Patient2_Diagnosis_5


title: Patient2_Diagnosis_58


title: Patient2_Diagnosis_55


title: Patient2_Diagnosis_49


title: Patient2_Diagnosis_48


title: E12_6: E12 cluster cell, biological rep6

description: single-cell gene expression data


title: E10_27: E10 cluster cell, biological rep27

description: single-cell gene expression data

value: E10.5 hematopoietic clusters


title: E12_1: E12 cluster cell, biological rep1

description: single-cell gene expression data


title: E10_28: E10 cluster cell, biological rep28

description: single-cell gene expression data


title: Patient2_Diagnosis_47


title: E12_8: E12 cluster cell, biological rep8

description: single-cell gene expression data


title: E10_26: E10 cluster cell, biological rep26

description: single-cell gene expression data


title: Patient2_Diagnosis_44


title: Patient2_Diagnosis_46


title: Patient2_Diagnosis_45


title: E12_3: E12 cluster cell, biological rep3

description: single-cell gene expression data


title: E12_5: E12 cluster cell, biological rep5

description: single-cell gene expression data


title: E12_4: E12 cluster cell, biological rep4

description: single-cell gene expression data


title: Patient2_Diagnosis_43


title: E12_2: E12 cluster cell, biological rep2

description: single-cell gene expression data


title: E12_7: E12 cluster cell, biological rep7

description: single-cell gene expression data


title: E10_25: E10 cluster cell, biological rep25

description: single-cell gene expression data


title: Patient2_Diagnosis_41


title: Patient2_Diagnosis_42


title: Patient2_Diagnosis_40


title: E10_24: E10 cluster cell, biological rep24

description: single-cell gene expression data


title: E10_21: E10 cluster cell, biological rep21

description: single-cell gene expression data


title: E10_22: E10 cluster cell, biological rep22

description: single-cell gene expression data


title: Patient2_Diagnosis_4


title: Patient2_Diagnosis_39


title: E10_18: E10 cluster cell, biological rep18

description: single-cell gene expression data


title: E10_17: E10 cluster cell, biological rep17

description: single-cell gene expression data


title: E10_19: E10 cluster cell, biological rep19

description: single-cell gene expression data


title: Patient2_Diagnosis_37


title: Patient2_Diagnosis_35


title: Patient2_Diagnosis_34


title: Patient2_Diagnosis_33


title: Patient2_Diagnosis_31


title: E10_20: E10 cluster cell, biological rep20

description: single-cell gene expression data


title: Patient2_Diagnosis_36


title: Patient2_Diagnosis_3


title: E10_23: E10 cluster cell, biological rep23

description: single-cell gene expression data


title: E10_16: E10 cluster cell, biological rep16

description: single-cell gene expression data


title: Patient2_Diagnosis_32


title: Patient2_Diagnosis_30


title: Patient2_Diagnosis_38


title: E10_14: E10 cluster cell, biological rep14

description: single-cell gene expression data


title: E10_13: E10 cluster cell, biological rep13

description: single-cell gene expression data


title: E10_11: E10 cluster cell, biological rep11

description: single-cell gene expression data


title: Patient2_Diagnosis_27


title: Patient2_Diagnosis_26


title: E10_8: E10 cluster cell, biological rep8

description: single-cell gene expression data


title: E10_7: E10 cluster cell, biological rep7

description: single-cell gene expression data


title: E10_15: E10 cluster cell, biological rep15

description: single-cell gene expression data


title: E10_10: E10 cluster cell, biological rep10

description: single-cell gene expression data


title: E10_9: E10 cluster cell, biological rep9

description: single-cell gene expression data


title: E10_6: E10 cluster cell, biological rep6

description: single-cell gene expression data


title: E10_12: E10 cluster cell, biological rep12

description: single-cell gene expression data


title: E10_5: E10 cluster cell, biological rep5

description: single-cell gene expression data


title: E10_4: E10 cluster cell, biological rep4

description: single-cell gene expression data


title: Patient2_Diagnosis_24


title: Patient2_Diagnosis_23


title: E10_3: E10 cluster cell, biological rep3

description: single-cell gene expression data


title: Patient2_Diagnosis_22


title: Patient2_Diagnosis_21


title: Patient2_Diagnosis_28


title: Patient2_Diagnosis_29


title: Patient2_Diagnosis_20


title: Patient2_Diagnosis_2


title: E10_1: E10 cluster cell, biological rep1

description: single-cell gene expression data


title: E10_2: E10 cluster cell, biological rep2

description: single-cell gene expression data


title: Patient2_Diagnosis_25


title: Patient2_Diagnosis_19


title: Patient2_Diagnosis_15


title: Patient2_Diagnosis_17


title: BAL Cells severe biological rep41

city: Pittsburgh

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

institute: University of Pittsburgh

description:
2288G
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4X44K array slides

data_processing:
The data was extracted using the Agilent Feature Extraction software 10.7.3.1 (Agilent Technologies)
The data set was normalized by cyclic-LOESS with use of Bioconductor package as described previously (Wu W et. al. 2005). Probes which did not map to an Entrez ID were excluded

source_name: Human BAL cells

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.  Labeled RNA   was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays.

extract_protocol: Total RNA was extracted from BALF cells the suspended in Trizol solution using the QIACube system (Qiagen, Valencia, CA). RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only samples with an RIN higher than 7 used for microarray experiments.

tag: condition

value: severe asthmatic

tag: cells

value: BAL cells


title: Patient2_Diagnosis_16

value: Single acute myeloid leukemia intitiating cell


title: BAL Cells severe biological rep43

description:
1921X
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

hyb_protocol: RNA  was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays


title: Patient2_Diagnosis_13


title: Patient2_Diagnosis_10


title: Patient2_Diagnosis_1


title: Patient2_Diagnosis_12


title: BAL Cells severe biological rep40

description:
2280Q
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep39

description:
2278D
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient2_Diagnosis_18


title: BAL Cells severe biological rep44

description:
2254P
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient2_Diagnosis_11


title: Patient1_Relapse_9

value: Patient 1


title: BAL Cells severe biological rep37

description:
2261M
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep34

description:
0996X
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep35

description:
1389H
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient2_Diagnosis_14


title: BAL Cells severe biological rep36

description:
1726Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep33

description:
0565W
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep32

description:
0053P
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep42

description:
2293Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep38

description:
2276Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep28

description:
2184U
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep31

description:
0283B
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_8


title: BAL Cells severe biological rep29

description:
0144P
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep30

description:
0029T
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_7


title: Patient1_Relapse_6


title: Patient1_Relapse_5


title: Patient1_Relapse_47


title: BAL Cells severe biological rep26

description:
2136J
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_45


title: BAL Cells severe biological rep24

description:
2102S
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep25

description:
2111T
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep23

description:
2040W
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_44


title: Patient1_Relapse_43


title: BAL Cells severe biological rep27

description:
2166S
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_41


title: Patient1_Relapse_40


title: Patient1_Relapse_42


title: BAL Cells severe biological rep22

description:
2030T
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_4


title: Patient1_Relapse_38


title: Patient1_Relapse_39


title: Patient1_Relapse_37


title: BAL Cells severe biological rep21

description:
2016Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_36


title: BAL Cells severe biological rep20

description:
1986Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep18

description:
1975U
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep13

description:
1814W
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep12

description:
1661X
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep16

description:
1969Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep19

description:
1977Y
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep11

description:
1628Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep15

description:
1946N
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep14

description:
1941D
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_35


title: Patient1_Relapse_34


title: Patient1_Relapse_33


title: Patient1_Relapse_32


title: P1-5_RA-Replicate1

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

description: single-cell

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq. Trimmed FASTQ files (26bp Cell barcode and UMI Read1, 8bp i7 index, and 100bp Read2), were generated using the CellRanger mkfastq command (a 10X Genomics wrapper around BCL2Fastq).
Paired FASTQ files from each sample trimmed and the quality confirmed using FASTQC
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger count (10X Genomics) and the mm10 (mouse) genome assembly/annotation references
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10X Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Mouse reference genome NCBI build 38, GRCm38 (mm10)
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

source_name: Post-natal day 1.5 testis

growth_protocol: Normal mouse husbandry with ad libitum food and water.

extract_protocol:
Testes from postnatal day 1.5 (P1.5) mice (12hr after treatment at midnight on P1) were used to generate suspensions of cells following enzymatic digestion as described previously (Ogawa et al., 1997; Nagano et al., 2003; Oatley and Brinster, 2006). Briefly, testicular parenchyma from at least two pups were pooled and digested with 0.25% trypsin/EDTA (ThermoFisher Scientific) for ~6-8 minutes at 37oC, quenched with 10% FBS (v/v, Sigma). Testis cell suspensions were used directly for single-cell RNA-seq facilitated by the 10X Genomics Chromium Drop-Seq approach. Briefly, Cell suspensions were loaded into Chromium microfluidic chips with 3’ v2 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10X Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~17400 cells were loaded on the instrument with the expectation of collecting up to 10,000 GEMs containing single cells.
Single-cell 3' libraries were prepared according to manufacturer recommendations (10X Genomics v2 chemistry).

treatment_protocol: Single subcutaneous injection of DMSO or 100ug all-trans RA.

tag: number of cells

value: Mixed

tag: agent

value: 100ug all-trans RA


title: P1-5_RA-Replicate2

description: single-cell


title: P1-5_DMSO-Replicate2

description: single-cell

value: DMSO


title: P1-5_DMSO-Replicate1

description: single-cell


title: SMB56-shSufu-DMSO-1

city: Shanghai

first: Yujie

last: Tang

address: 280 South Chong-qing Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The RNAseq reads were mapped to the hg19 reference  genome using STAR (v2.5.3a)
FPKM was calculated using Cufflinks (v2.2.1)
Differential expression analysis was carried  out using R package DESeq2 (v1.20.0)

source_name: medulloblastoma

growth_protocol: SMB56 and SMB56-shSufu cell lines were cultured (typically 1 × 10E6 cells into a well of 6-well plate) as neurospheres in DMEM/F12 media (Gibco, 11330-032) containing 1×B27(-A) (Gibco, 12587-010) and 1×Antibiotic-Antimycotic (Gibco, 15240-062).

extract_protocol:
Cells were harvested in Trizol and extracted by using mirVana miRNA isolation kit.
RNA libraries were prepared for sequencing by service provider using standard Illumina protocols with Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

treatment_protocol: SMB56 cells were treated with DMSO, 0.1 uM THZ1 or 1 uM GDC-0449 for 8 hours, SMB56-shSufu cells were treated with DMSO or 0.1 uM THZ1 for 8 hours

tag: cell line

value: spontaneous medulloblastoma cells from Ptch+/ mice engineered to stably expressing shRNA against Sufu

tag: passages

value: Ptch+/-

value: Treated with DMSO for 8hr


title: SMB56-shSufu-DMSO-2

tag: cell type


title: SMB56-shSufu-THZ1-1

value: Treated with 0.1uM THZ1 for 8hr


title: BAL Cells severe biological rep9

description:
0667E
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep8

description:
0828C
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep6

description:
1841Z
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep17

description:
1970K
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: SMB56-shSufu-THZ1-2


title: Patient1_Relapse_30

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.

tag: tissue

tag: state

value: Post-treatment relapse

tag: patient id


title: BAL Cells severe biological rep7

description:
1870G
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_3

tag: surface markers


title: Patient1_Relapse_29


title: Patient1_Relapse_31


title: 22q11.123.hippocampus

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

tag: sequencing study

value: Study 6

tag: library preparation kit

value: TruSeq stranded mRNA sample preparation kit

tag: sample id

tag: cnv

value: hemi

tag: Sex

value: M

tag: sequencing protocol

value: single read, 50 bp


title: 22q11.124.hippocampus

tag: genotype


title: BAL Cells severe biological rep10

description:
1578K
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

tag: condition

value: severe asthmatic

tag: cells


title: Patient1_Relapse_46


title: 22q11.119.hippocampus


title: Patient1_Relapse_28


title: BAL Cells severe biological rep5

description:
1738G
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: BAL cells


title: 22q11.117.hippocampus


title: 22q11.118.hippocampus


title: Patient1_Relapse_27

value: Single acute myeloid leukemia intitiating cell


title: BAL Cells severe biological rep4

description:
1683H
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 22q11.115.hippocampus


title: 22q11.116.hippocampus


title: BAL Cells severe biological rep3

description:
1568H
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep1

description:
0658D
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells severe biological rep2

description:
1566D
BAL
SA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 22q11.113.hippocampus

value: wt


title: 22q11.121.hippocampus


title: Patient1_Relapse_25

value: Patient 1


title: BAL Cells not severe biological rep72

description:
0423C
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: mild-moderate asmathic


title: 22q11.120.hippocampus


title: 22q11.110.hippocampus


title: 22q11.111.hippocampus


title: BAL Cells not severe biological rep71

description:
GSK082
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_23


title: Patient1_Relapse_26


title: Patient1_Relapse_24


title: 22q11.109.hippocampus


title: BAL Cells not severe biological rep70

description:
GSK081
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 22q11.108.hippocampus


title: 22q11.105.hippocampus


title: Patient1_Relapse_21


title: Patient1_Relapse_20


title: 22q11.114.hippocampus


title: 22q11.112.hippocampus


title: BAL Cells not severe biological rep68

description:
EFI12
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 22q11.191.cortex

source_name: cortex

value: Study 5

value: TruSeq mRNA sample preparation kit


title: BAL Cells not severe biological rep69

description:
EFI13
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep67

description:
EFA16
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep66

description:
EFA09
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep65

description:
EFA08
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep64

description:
2307K
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 22q11.184.cortex


title: 22q11.187.cortex


title: Patient1_Relapse_2


title: 22q11.186.cortex


title: 22q11.189.cortex


title: 22q11.185.cortex


title: Patient1_Relapse_19


title: 22q11.188.cortex


title: 22q11.183.cortex


title: 22q11.182.cortex


title: 22q11.181.cortex


title: 22q11.192.cortex


title: 22q11.190.cortex


title: Patient1_Relapse_22


title: Patient1_Relapse_17


title: 22q11.106.hippocampus


title: BAL Cells not severe biological rep63

description:
2306I
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep62

description:
2305G
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep61

description:
2303C
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 22q11.179.cortex


title: Patient1_Relapse_16


title: 22q11.180.cortex


title: Patient1_Relapse_15


title: Patient1_Relapse_18


title: 22q11.107.hippocampus


title: 22q11.177.cortex


title: BAL Cells not severe biological rep60

description:
2301Y
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_14


title: Patient1_Relapse_13


title: 22q11.176.cortex


title: 22q11.175.cortex


title: 22q11.174.cortex


title: 22q11.173.cortex


title: Patient1_Relapse_12


title: 1q21.104.hippocampus


title: BAL Cells not severe biological rep58

description:
2291J
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Relapse_11


title: 1q21.103.hippocampus


title: Patient1_Relapse_10


title: 1q21.102.hippocampus


title: 22q11.178.cortex


title: 1q21.101.hippocampus


title: 1q21.100.hippocampus


title: BAL Cells not severe biological rep56

description:
2253N
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.99.hippocampus


title: Patient1_Relapse_1


title: 1q21.96.hippocampus


title: 1q21.98.hippocampus


title: BAL Cells not severe biological rep59

description:
2292X
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_9

value: Pre-treatment diagnosis


title: BAL Cells not severe biological rep54

description:
2223E
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.97.hippocampus


title: BAL Cells not severe biological rep55

description:
2237P
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.95.hippocampus


title: Patient1_Diagnosis_7


title: 1q21.94.hippocampus


title: Patient1_Diagnosis_8


title: 1q21.92.hippocampus


title: BAL Cells not severe biological rep52

description:
1523L
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.93.hippocampus


title: 1q21.89.hippocampus


title: Patient1_Diagnosis_6


title: 1q21.90.hippocampus


title: BAL Cells not severe biological rep57

description:
2284Y
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.88.hippocampus


title: Patient1_Diagnosis_5


title: 1q21.87.hippocampus


title: 1q21.86.hippocampus


title: 1q21.91.hippocampus


title: BAL Cells not severe biological rep51

description:
1352K
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_49


title: Patient1_Diagnosis_48


title: BAL Cells not severe biological rep53

description:
2168W
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.85.hippocampus


title: BAL Cells not severe biological rep49

description:
1273O
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_47


title: 1q21.15.cortex

value: Study 3


title: 1q21.14.cortex


title: 1q21.16.cortex


title: BAL Cells not severe biological rep47

description:
0329K
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep46

description:
0311B
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_46


title: BAL Cells not severe biological rep48

description:
1005P
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.12.cortex


title: BAL Cells not severe biological rep50

description:
1341F
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.11.cortex


title: Patient1_Diagnosis_45


title: BAL Cells not severe biological rep44

description:
0112F
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.9.cortex


title: BAL Cells not severe biological rep45

description:
0308V
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.7.cortex


title: Patient1_Diagnosis_44


title: BAL Cells not severe biological rep42

description:
GSK069V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.8.cortex


title: BAL Cells not severe biological rep43

description:
1682F
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_42


title: Patient1_Diagnosis_43


title: 1q21.6.cortex


title: 1q21.5.cortex


title: 1q21.17.cortex


title: Patient1_Diagnosis_41


title: BAL Cells not severe biological rep41

description:
GSK068V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.1.cortex


title: BAL Cells not severe biological rep40

description:
GSK067V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 1q21.2.cortex


title: Patient1_Diagnosis_40


title: Patient1_Diagnosis_4


title: 1q21.4.cortex


title: 15q13.S25.hippocampus.hemi

value: Study 2


title: BAL Cells not severe biological rep37

description:
2183S
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep38

description:
2198F
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_39


title: 1q21.13.cortex


title: 15q13.S24.hippocampus.hemi


title: 15q13.S23.hippocampus.wt


title: Patient1_Diagnosis_38


title: 15q13.S22.hippocampus.wt


title: Patient1_Diagnosis_37


title: 15q13.152.cortex.hemi


title: 15q13.S21.hippocampus.wt


title: 15q13.151.cortex.hemi


title: 15q13.150.cortex.hemi


title: 1q21.3.cortex


title: 15q13.S26.hippocampus.hemi


title: 15q13.146.cortex.hemi


title: 15q13.147.cortex.hemi


title: BAL Cells not severe biological rep39

description:
2230B
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep36

description:
2163M
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_35


title: BAL Cells not severe biological rep33

description:
2150D
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_36


title: 15q13.145.cortex.hemi


title: 15q13.144.cortex.hemi


title: BAL Cells not severe biological rep34

description:
2154L
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 15q13.143.cortex.hemi


title: BAL Cells not severe biological rep32

description:
2139P
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_34


title: 15q13.149.cortex.hemi


title: BAL Cells not severe biological rep35

description:
2156P
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 15q13.142.cortex.wt


title: Patient1_Diagnosis_33


title: 15q13.139.cortex.wt


title: BAL Cells not severe biological rep30

description:
2131Z
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 15q13.141.cortex.wt


title: 15q13.140.cortex.wt


title: 15q13.138.cortex.wt


title: Patient1_Diagnosis_32


title: 15q13.148.cortex.hemi


title: 15q13.137.cortex.wt


title: Patient1_Diagnosis_30


title: Patient1_Diagnosis_31


title: 15q13.135.cortex.wt


title: 15q13.136.cortex.wt


title: 15q13.134.cortex.wt


title: 15q13.133.cortex.wt


title: Patient1_Diagnosis_29


title: 3T3 NNMT Replicate 2

city: Chicago

first: Mark

middle: Adam

last: Eckert

state: IL

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

description:
NNMTvsCtrl_DEG_all.txt
NNMT2

data_processing:
Illumina CASAVA used for base calling
Sequenced reads were trimmed for adaptor sequence, reads with N>10% removed, and reads with less than 50% of reads with Qscore>5 removed, then mapped to mm10 whole genome using STAR v2.5 with parameter mismatch=2
FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)  was estimated using methods described by Mortazavi et al. 2008.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing FPKM values for each gene across all samples

source_name: mouse 3T3 fibroblasts expressing NNMT overexpression construct

growth_protocol: Cells were grown in methionine-free DMEM supplemented to 10 micromolar methionine and 10% dialyzed FBS

extract_protocol:
RNA was extracted using the Qiagen Rneasy Mini Kit.
Libraries were constructed using standard NEB library preparation protocols.

treatment_protocol: Cells were grown for 48 hrs before collection of RNA.

value: 3T3 fibroblast cell line

value: NNMT overexpression


title: 3T3 NNMT Replicate 1

description:
NNMTvsCtrl_DEG_all.txt
NNMT1


title: Patient1_Diagnosis_28

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.


title: BAL Cells not severe biological rep27

description:
2073L
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 3T3 NNMT Replicate 3

description:
NNMTvsCtrl_DEG_all.txt
NNMT3


title: BAL Cells not severe biological rep28

description:
2079X
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep29

description:
2122Y
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: 3T3 Ctrl Replicate 2

description:
NNMTvsCtrl_DEG_all.txt
Ctrl2

source_name: mouse 3T3 fibroblasts expressing control construct

value: Control


title: 3T3 Ctrl Replicate 3

description:
NNMTvsCtrl_DEG_all.txt
Ctrl3


title: Patient1_Diagnosis_27


title: BAL Cells not severe biological rep24

description:
2063I
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep26

description:
2070F
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_3


title: Endocardial_G

city: London

first: Rebecca

middle: J

last: Oakey

address: Great Maze Pond

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

description: raw.counts.csv

data_processing:
quantify with salmon
import and merge into a single table with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: csv; raw counts

source_name: Embryoid body culture

extract_protocol:
Qiagen RNeasy Mini Kit
Illumina stranded mRNA LT Kit

value: endocardial


title: Endothelial_H

description: raw.counts.csv

value: endothelial


title: 3T3 Ctrl Replicate 1

description:
NNMTvsCtrl_DEG_all.txt
Ctrl1


title: Patient1_Diagnosis_26


title: Patient1_Diagnosis_25


title: BAL Cells not severe biological rep23

description:
2048M
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Endocardial_E

description: raw.counts.csv


title: Endothelial_D

description: raw.counts.csv


title: Endothelial_B

description: raw.counts.csv


title: Endocardial_C

description: raw.counts.csv


title: Patient1_Diagnosis_24


title: Endocardial_A

description: raw.counts.csv


title: Patient1_Diagnosis_23


title: Patient1_Diagnosis_22


title: Patient1_Diagnosis_21


title: xct2_BS_2

city: Davis

first: Stacey

last: Harmer

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: BAL Cells not severe biological rep22

description:
2014V
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep21

description:
2012R
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep25

description:
2065M
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Endothelial_F

description: raw.counts.csv


title: col_BS_2

value: Col


title: BAL Cells not severe biological rep20

description:
2003Q
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: BAL cells


title: Patient1_Diagnosis_20

city: Cleveland

first: David

last: Wald

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

institute: Case Western Reserve University

value: Single acute myeloid leukemia intitiating cell


title: BAL Cells not severe biological rep17

description:
0202D
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep19

description:
1958U
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep18

description:
1753C
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Patient1_Diagnosis_19


title: BAL Cells not severe biological rep15

description:
GSK058V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep14

description:
GSK039V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: IFN-treated rep 1

first: Andrew

last: Gravett

address: Cranmer Terrace

institute: SGUL

description: replicate 1

hyb_protocol: Arrays were washed and stained with Streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) according to the Illumina Whole Genome Gene Expression Direct Hybridisation manual.

scan_protocol: Arrays were scanned using  BeadArray Reader (Illumina, San Diego, CA) according to the manufacturer's instructions.

data_processing:
Image data were imported into GenomeStudio (Illumina, San Diego, CA) without normalisation. Non-normalised data were exported from GenomeStudio using the ArrayExpress Data Submission Report Plug-in v1.0. Data were quantile normalized in BeadStudio.
The file processed_data.xls includes hierarchical clustering data, normalized data (All Data tab) and averaged replicate data.

source_name: HCT116 colorectal cancer cell

label_protocol: RNA was labelled using Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX) according to the manufacturer's instructions.

growth_protocol: HCT116 cells were obtained from Public Health England and maintained in Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) foetal bovine serum (FBS), 2mM L-glutamine and 1x penicillin/streptomycin (basal culture medium). Cells were incubated in a humidified atmosphere with 5% CO2 in air at 37°C, and discarded at when the passage number exceeded 15.

extract_protocol: RNA was purified using the Qiagen RNA extraction mini-prep kit using manufacturer's instructions.

treatment_protocol: Cells were cultured in media supplemented with 1uM Interferon-γ (IFN) dissolved in PBS for 4 hours.

tag: cell line

value: colorectal cancer


title: Patient1_Diagnosis_18

value: Patient 1


title: IFN-treated rep 2

description: replicate 2


title: IFN-treated rep 3

description: replicate 3


title: Patient1_Diagnosis_16


title: Patient1_Diagnosis_15


title: CAM-treated rep 2

description: replicate 2

treatment_protocol: Cells were cultured in media supplemented with 1uM camptothecin (CAM) dissolved in PBS for 4 hours.


title: BAL Cells not severe biological rep16

description:
GSK053V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).

value: mild-moderate asmathic


title: CAM-treated rep 3

description: replicate 3


title: 1q21.10.cortex

city: Los Angeles

first: Aaron

last: Gordon

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

institute: UCLA

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)

value: hemi

value: M

value: single read, 50 bp


title: Patient1_Diagnosis_14

value: Pre-treatment diagnosis


title: BAL Cells not severe biological rep13

description:
GSK038V4
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep11

description:
1927J
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: LEN-treated rep 1

description: replicate 1

treatment_protocol: Cells were cultured in media supplemented with 1uM lenalidomide (LEN) dissolved in PBS for 4 hours.


title: BAL Cells not severe biological rep10

description:
1863J
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: LEN-treated rep 3

description: replicate 3


title: ARS-treated rep 2

description: replicate 2

treatment_protocol: Cells were cultured in media supplemented with 1uM Artesunate (ARS) dissolved in PBS for 4 hours.


title: CAM-treated rep 1

description: replicate 1


title: Patient1_Diagnosis_17


title: ARS-treated rep 3

description: replicate 3


title: ARS-treated rep 1

description: replicate 1


title: Patient1_Diagnosis_2


title: Patient1_Diagnosis_13


title: BAL Cells not severe biological rep9

description:
1830U
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep8

description:
1821T
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: DOC-treated rep 3

description: replicate 3

treatment_protocol: Cells were cultured in media supplemented with 1uM docetaxel (DOC) dissolved in PBS for 4 hours.


title: DOC-treated rep 1

description: replicate 1


title: OXP-treated rep 2

description: replicate 2

treatment_protocol: Cells were cultured in media supplemented with 1uM oxaliplatin (OXP) dissolved in PBS for 4 hours.


title: Patient1_Diagnosis_12


title: Patient1_Diagnosis_11


title: OXP-treated rep 3

description: replicate 3


title: OXP-treated rep 1

description: replicate 1


title: Patient1_Diagnosis_1


title: Patient1_Diagnosis_10


title: DOC-treated rep 2

description: replicate 2


title: iHepLPCs-Hep-3D rep2

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Raw data were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks
Read counts of each gene were obtained by htseq-count.
Differentially expressed genes were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: 3D cell spheroids of the iHepLPCs-Hep

growth_protocol: For iHepLPCs, cells  were seeded and kept 2–4 days in TEM until full confluence. For iHepLPCs-Hep, iHepLPCs were seeded and kept 2–4 days in TEM until full confluence. Then the medium was changed to modified Hepatocyte Maturation Medium (mHMM) for another 7-10 days for further maturation; medium was changed every other day. For iHepLPCs-Hep-3D, 1x10^6 iHepLPCs  cells were seeded in the low-attachment 6-well plate. iHepLPCs  formed cellular spheres after 24 hours in TEM. Then the medium was changed to mHMM, and cultured another 7-10 days for further maturation.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following  the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: 3D differentiated human hepatocyte-derived liver progenitor-like cells

tag: immortal gene

value: HPV16 E6/E7

tag: passages


title: BAL Cells not severe biological rep5

description:
1765J
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: GEM-treated rep 1

description: replicate 1

treatment_protocol: Cells were cultured in media supplemented with 1uM gemcitabine (GEM) dissolved in PBS for 4 hours.

tag: cell type


title: iHepLPCs-Hep-3D rep1


title: GEM-treated rep 2

description: replicate 2


title: Untreated control rep 3

description: replicate 3

treatment_protocol: Cells were cultured in media supplemented with phosphate buffered saline (PBS) for 4 hours.


title: GEM-treated rep 3

description: replicate 3


title: BAL Cells not severe biological rep31

description:
2134F
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: BAL Cells not severe biological rep4

description:
1752A
BAL
notSA
Bronchial alveolar lavage cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).


title: Untreated control rep 1

description: replicate 1


title: iHepLPCs-Hep rep2

source_name: Hepatocyte-like cells differentiated from iHepLPCs

value: Monolayer differentiated human hepatocyte-derived liver progenitor-like cells