title: 27_KO_M_STR

data_processing:
Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Single-end 75 bp reads were generated for the RNA-seq experiment. Trimgalore v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low-quality bases. STAR (Dobin et al. (2013).Bioinformatics. 29:15-21; PMC3530905) was used to align the reads to the genome. The genome index was generated using STAR using GRCm38.primary_assembly.genome.fa as the reference sequence and gencode.vM15.primary_assembly.annotation.gtf as the gene definition file. The genome fasta sequence was downloaded from ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M15/GRCm38.primary_assembly.genome.fa.gz and gene definitions from ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M15/gencode.vM15.primary_assembly.annotation.gtf.gz.
Genome_build: GRCm38
Supplementary_files_format_and_content: SCZ_RNAseq_STAR_counts.csv - raw gene-level transcript counts per sample. CSV format

growth_protocol: Mice were bred and housed in ventilated polycarbonate cages, and given ad libitum sterile food (LabDiet 5021) and water. Adult mice were housed by sex in groups of 2-5 littermates. The vivarium was maintained under controlled temperature (21°C±1°C) and humidity (50-60%), with a 12-h diurnal cycle (lights on: 0700-1900). Approximately equal numbers of male and female were tested, and no sex differences were detected (in all Western blotting, HPLC, and transcriptomic experiments). No animals were excluded from the study. Wild-type (+/+) and homozygous knock-out (Igf2 enh-/-) adult mice (~2.5 months old) were tested, and sample sizes were comparable to other studies of Igf2 mutant mice40, 41. All animal procedures were approved by the Institutional Animal Care Committee of the Van Andel Research Institute and complied with the requirements of the Institutional Animal Care and Use Committee (AUP # PIL-17-10-010).

extract_protocol:
Brain tissue (~25 mg) was homogenized with a ceramic bead-based homogenizer (Precellys, Bertin Instruments) in 1 mL of Trizol (Life Technologies). Total RNA was isolated according to the Trizol manufacturer’s instructions, treated with RNase-free DNase I (Qiagen) at room temperature for 30 min, and cleaned up with the RNeasy Mini Kit (Qiagen). RNA yield was quantified using a NanoDrop ND-1000 (Thermo Fisher Scientific), and RNA integrity was verified via the Agilent Bioanalyzer 2100 system (Agilent Technologies).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA, using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp.), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).  Individually indexed libraries were pooled, and 75 bp single-end sequencing was performed on an Illumina NextSeq 500 sequencer, with all libraries run across 3 flow cells.  Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: A 4.9 kb-long DNA fragment (chr7: 149,796,331-149,801,250 in mm9) was deleted from the intergenic region of H19 and Igf2 by classical ES cell gene targeting and blastocyst injection in the mouse on the 129S1 genetic background. One loxP site remained at the site of the deletion mutation after the excision of the Pgkneo positive selection cassette by crossing the targeted mutant male mouse to an Hprt-CRE transgenic female39. Three oligonucleotide primers, IGKOCrerecU: CGGAATGTTTGTGTGGAGAGCA; IGKOwtU: TAGGGGTCCTGAAGACGTCAG; and IGKOCreWTL: TTGGTGTAGCACCCTGTAACCC are combined in one PCR reaction to distinguish the mutant from the wild type allele, as visualized by a 450 bp or a 350 bp long PCR product, respectively.

tag: strain background

value: KO; Igf2enh-/-

value: M

tag: tissue region

value: Striatum of the mouse brain [STR]

tag: nucleic acid (ng/ul)


title: Untreated_Control_ULMC134_1

status: Public on May 03 2019

type: SRA

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

country: USA

institute: University of Michigan

description: ULMCControls_Control134plasmaUntreatedRep1

library_source: transcriptomic

data_processing:
TruSeq sRNA adapter and STP oligo sequences were trimmed from reads using cutadapt (v1.91), filtering reads <15 nt.
Trimmed reads were aligned to several sequence databases provided with the sRNAnalyzer pipeline, including univec contaminates, small structural RNAs, microRNAs and bacterial sequences. Additional bowtie libraries were added to include RepeatMasker and SILVA rRNA libraries. sRNAnalyzer was thenrun using default parameters (allowing up to 2 mismatches), sequentially aligning to the sequence libraries using bowtie 1.
Reads not aligned during the previous stage were aligned to the human genome (GRCh38) using STAR. Parameters were altered to allow multi-mapping, disallow spliced alignments, and limit the extent of soft-clipped ends.
RepeatMasker coordinates (UCSC) and gencode small RNA coordinates (v27) were used to filter the genomic alignments. All alignments were removed for any read overlapping at least one RMSK or sRNA-annotated coordinate in either orientation.
Multi-mapping reads were weighted using a strategy similar to CSEM, and weighted reads aligning to mRNA or ncRNA exons were used to calcualte fragment abundances at the gene level.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delmited gene counts file contains multi-mapping-scaled read counts for Gencode (v27) mRNA and lncRNA genes, calculated from exon-aligning exRNA fragments after filtering repeat and structural small RNA reads.

molecule: total RNA

organism: Homo sapiens

source_name: platelet-poor blood plasma

extract_protocol:
Plasma samples from 5 healthy donors and serial plasma sample from 2 patients undergoing allogeneic bone marrow transplantation were collected in 10-mL K2EDTA plasma tubes (Vacutainer 366643; Becton Dickinson) and processed within one hour of blood draw following a two centrifugation protocol to obtain platelet-poor plasma as previously described38: (i) 3,400 xg at room temperature for 10 minutes with high brake; and (ii) 1940 xg at room temperature for 10 minutes without brake. Plasma was stored at -80C until RNA isolation. RNA was isolated from 200 ul of plasma using the miRNeasy mini kit (Qiagen, Hilden, Germany)  according to the manufacturer’s protocol with the following modifications. Plasma samples were mixed with five sample volumes of QIAzol reagent and vortexed for 10 s. Samples in QIAzol were incubated at room temperature for 5 min to inactivate RNases. Next 0.2 volumes of chloroform were added to each sample. At that point, the manufacturer’s protocol was followed.
Untreated plasma sample libraries were prepared using 5 μl of  RNA.  RNA for Phospho-sRNA-seq plasma sample libraries were pretreated with T4 polynucleotide kinase (NEB, Ipswich, MA, US) using an RNA input of 7 ul in a final reaction volume reaction of 10 ul and following the manufacturer’s instructions. After the enzymatic treatment, biological RNA samples were purified by performing sequential washes in silica columns (Zymo, Irvine, CA, US): (i) 900 ul of buffer RWT (Qiagen, Hilden, Germany); (ii) 900 ul of buffer RPE (Qiagen, Hilden, Germany); (iii) 900 ul of ethanol 200 proof, molecular biology grade (Fisher Scientific, Waltham, MA, US) and; (iv) 900 ul of 80% ethanol. Standard ligation-based small RNA libraries were prepared from both untreated and PNK-treated RNA samples using the TruSeq small RNA kit (Illumina, San Diego, CA, US) according to the manufacturer’s instructions. Size selection was performed using pre-cast 6% acrylamide gels (Invitrogen, CarlsbadWaltham, CMA, US) including all products from 140-200 bp plus any additional visible bands of greater size

tag: Sex

value: Female

tag: age

tag: treatment


title: 26_WT_M_STR

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

organism: Mus musculus

tag: genotype/variation

value: WT


title: 25_KO_F_STR

value: F


title: 23_KO_M_STR


title: Untreated_Control_ULMC123_3

description: ULMCControls_Control123plasmaUntreatedRep3

value: Male


title: Untreated_Control_ULMC123_1

description: ULMCControls_Control123plasmaUntreatedRep1


title: TG_FUS_9wk, 3

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Read trimming were performed by Trimmomatic
Reads obtained were aligned to rererence genome (GRCm38) using STAR genome aligner (v 2.5.0a)
Read counting were preformed by featureCounts (v1.5.0-p1)
Genome_build: GRCm38
Supplementary_files_format_and_content: text files generated by featureCounts: GeneID; count number per gene

source_name: Spinal cord

extract_protocol:
Total RNA was extracted from thoracic spinal cord of 9 weeks old male mice using RNeasy Plus Mini Kit with genomic DNA eliminator columns (Qiagen).
cDNA libraries for the dual indexed single-end sequence analysis were prepared from equal amounts (270 ng) of each total RNA sample using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. Following libraries’ quality checks and normalisation, cDNA libraries were sequenced on Illumina NextSeq 500 to generate single end 75 bp reads.

tag: strain

value: 9 weeks

value: transgenic FUS

value: male


title: 22_WT_M_STR


title: 21_KO_M_STR


title: 20_WT_M_STR


title: 18_WT_F_STR


title: 9Redopos

library_source: genomic

data_processing:
Trimmomatic v0.36 was used to trim read adapter sequences and BSMAP 2.74 was used to align reads to the GRCh38/hg38 genome build. The genome index consisted of reference chromosome sequences and the lambda phage genome (https://www.ncbi.nlm.nih.gov/nuccore/215104).
Reads was separated into those aligning to top and bottom strand, duplicates were removed with Picard (2.9.4 SNAPSHOT) , and then matching read pairs were merged.
Samtools v1.5 was used to exclude reads that were not properly paired or were unmapped. Bamutils were used to clip overhanging reads that distort methylation estimates. Methratio.py in BSMAP computed the percent methylation at the base level.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited file with base-level calls of methylated/unmethylated reads at a Cytosine. Output of methratio.py in BSMap software

molecule: genomic DNA

source_name: frontal cortex of the human brain

growth_protocol: DNA was extracted from post-mortem brain samples. No growth protocols were used.

extract_protocol:
Genomic DNA from each NeuN+ and NeuN- fraction of each sample was isolated using standard phenol-chloroform extraction methods.
DNA methylation was captured using the SeqCap Epi Enrichment System (Roche). Biotinylated long oligonucleotide probes were customed designed by Roche NimbleGen. Library preparation was performed following manufacturer instructions. Briefly, gDNA (500 ng) of each sample (n= 4 cases and 4 controls, in addition 4 technical replicate samples) were fragmented (~ 200 bp), end repaired and ligated to barcoded adapters using the KAPA Library Preparation kit (Kapa Biosystems) and SeqCap Adapter Kit A and B (Roche). Bisulfite conversion of the adapter ligated DNA followed by column purification was performed with the EZ DNA Methylation Lightning kit (Zymo). The bisulfite converted DNA for each sample was then amplified by ligation mediated PCR (95°C 2 min, 10 cycles of [98°C 30 sec, 60°C 30 sec, 72°C 4 min], 72°C 10 min, 4°C hold) followed by purification with Agencourt AMPure XP beads (Beckman Coulter). Sample quality was verified on Bioanalyzer (Agilent) and quantity was determined with a NanoDrop spectrophotometer (Thermo Fisher Scientific). Equimolar amounts of each sample were then combined into a single pool. Target regions were captured by hybridizing the amplified bisulfite converted DNA pool (1 μg) to the probe library (Roche), as directed by manufacturer. Enrichment and recovery of captured bisulfite-converted DNA was completed by binding to magnetic beads and subsequent wash steps using the SeqCap Pure Capture Bead kit and the SeqCap Hybridization and Wash kit (Roche). The captured DNA was then amplified by ligation mediated PCR (98°C 45 sec, 11 cycles of [98°C 15 sec, 60°C 30 sec, 72°C 30 sec], 72°C 1 min) followed by purification with Agencourt AMPure XP beads (Beckman Coulter). Library quality and quantity was assessed using a combination of Agilent DNA High Sensitivity chip on a Bioanalyzer (Agilent Technologies), Qubit dsDNA HS Assay kit on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). DNA sequencing was performed on an Illumina HiSeq 2500with all samples run on both sequencing lanes.

treatment_protocol: Neuronal nuclei were separated using a flow cytometry-based approach, similar to as previously described (PMID: 25369517,PMID: 19078943). Human brain tissue (250 mg) for each sample was minced in 2 mL PBSTA (0.3 M sucrose, 1X phosphate buffered saline (PBS), 0.1% Triton X-100). Samples were then homogenized in PreCellys CKMix tubes with a Minilys (Bertin Instruments) set at 3,000 rpm for three 5 sec intervals, 5 min on ice between intervals. Samples homogenates were filtered through Miracloth (EMD Millipore), followed by a rinse with an additional 2 mL of PBSTA. Samples were then place on a sucrose cushion (1.4 M sucrose) and nuclei were pelleted by centrifugation at 4,000 × g for 30 min 4°C using a swinging bucket rotor. For each sample, the supernatant was removed and the pellet was incubated in 700 μl of 1X PBS on ice for 20 min. The nuclei were then gently resuspended and blocking mix (100 μl of 1X PBS with 0.5% BSA (Thermo Fisher Scientific) and 10% normal goat serum (Gibco) was added to each sample. NeuN-488 (1:500; Abcam) was added and samples were incubated 45 min at 4°C with gentle mixing. Immediately prior to flow cytometry sorting, nuclei were stained with 7-AAD (Thermo Fisher Scientific) and passed through a 30 μM filter (SystemX). Nuclei positive for 7-AAD and either NeuN+ (neuronal) or NeuN- (non-neuronal) were sorted using an Influx (BD Biosciences) at the Faculty of Medicine Flow Cytometry Facility at the University of Toronto (Toronto, ON, Canada). Approximately 1 million NeuN+ nuclei were sorted for each sample. Immediately, after sorting nuclei were placed on ice and then precipitated by raising the volume to 10 mL with 1X PBS and adding 2 mL 1.8 M sucrose, 50 μl 1M CaCl2 and 30 μl Mg(Ace)2 and centrifugation at 1,786 × g for 15 min at 4°C. The supernatant was removed from NeuN+ and NeuN- samples and pellets were stored at -80°C.

tag: race

value: White

value: Schizophrenia

tag: tissuebank

value: Sepulveda

tag: tissue

value: brain frontal cortex

tag: cell type

value: NeuN+

tag: pmi

tag: molecule subtype

value: Bisulfite converted DNA from NeuN+ cells


title: 19_KO_M_STR


title: WT_9wk,1

value: wild-type


title: 16_WT_F_STR


title: 87pos

value: HBDL

value: Bipolar Disorder

value: UM Brain Endowment Bank


title: 15_KO_F_STR

value: KO; Igf2enh-/-

value: Striatum of the mouse brain [STR]


title: 92pos

value: HCTYZ

value: Control


title: 17_KO_F_STR

value: F


title: 9Redoneg

value: Male

value: NeuN-

value: Bisulfite converted DNA from NeuN- cells


title: 81pos

value: HCtLI

value: Black


title: 92neg

value: White

value: brain frontal cortex


title: 14_WT_F_STR

value: WT


title: 81neg


title: 80pos

value: HCtRP

value: NeuN+

value: Bisulfite converted DNA from NeuN+ cells


title: 87neg

value: HBDL

value: Female

value: Bipolar Disorder

value: UM Brain Endowment Bank


title: 80neg

value: Control


title: Untreated_Control_ULMC123_2

description: ULMCControls_Control123plasmaUntreatedRep2


title: 13_KO_F_STR

value: KO; Igf2enh-/-

value: F

value: Striatum of the mouse brain [STR]


title: 12_WT_M_FX

value: M

value: Frontal cortex of the mouse brain [FX]


title: 79pos

value: HCtQX

value: Male


title: 11_KO_M_FX


title: 10_WT_M_FX


title: 24_WT_M_STR


title: 9_KO_M_FX


title: 8_WT_M_FX


title: 75neg

value: HCcFH

value: White

value: brain frontal cortex

value: NeuN-

value: Bisulfite converted DNA from NeuN- cells


title: 74pos

value: HCtWI

value: NeuN+

value: Bisulfite converted DNA from NeuN+ cells


title: 74neg

value: Female

value: UM Brain Endowment Bank


title: 7_KO_M_FX

value: KO; Igf2enh-/-


title: 70pos

value: HQQ

value: Bipolar Disorder


title: 70neg


title: 69neg

value: HCtDM

value: Control


title: 4_WT_F_FX

value: WT

value: F

value: Frontal cortex of the mouse brain [FX]


title: 3_KO_F_FX


title: 69pos

value: Male

value: White


title: 1_KO_F_FX


title: 66Redopos

value: HCtVB

value: brain frontal cortex


title: Hlf-positive_3

city: Kumamoto

first: Tomomasa

last: Yokomizo

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

country: Japan

institute: Kumamoto University

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v.11.0.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC genomic workbench v.11.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read number and RPKM values for each Sample.

source_name: Hlf-positive

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

extract_protocol:
Lysis buffer containing 100 cells was directly used for cDNA synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

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 fractions were isolated by cell sorter.

tag: developemental stage

value: Embryonic day 10.5

value: Hlf-tdTomato knock-in

value: caudal half

tag: markers

value: nascent hematopoietic cells


title: 5_KO_F_FX


title: 58pos

value: HXN

value: Schizophrenia

value: UM Brain Endowment Bank

value: NeuN+

value: Bisulfite converted DNA from NeuN+ cells


title: Hlf-positive_2


title: 79neg

value: HCtQX

value: Control

value: NeuN-

value: Bisulfite converted DNA from NeuN- cells


title: Hlf-positive_1


title: 4pos

value: Female

value: Bipolar

value: Sepulveda


title: Hlf-negative_3

source_name: Hlf-negative

value: Embryonic day 9.5

value: yolk sac


title: 58neg

value: Male

value: White

value: brain frontal cortex


title: 4neg


title: 66Redoneg

value: HCtVB


title: 75pos

value: HCcFH


title: Hlf-negative_1

value: Hlf-tdTomato knock-in

value: nascent hematopoietic cells


title: 37pos

value: Schizophrenia

value: Harvard HBTRC

value: NeuN+

value: Bisulfite converted DNA from NeuN+ cells


title: 6_WT_F_FX

value: WT

value: F

value: Frontal cortex of the mouse brain [FX]


title: 37neg

value: NeuN-

value: Bisulfite converted DNA from NeuN- cells


title: Hlf-negative_2

value: Embryonic day 9.5

value: yolk sac


title: 33neg

value: Male

value: White

value: Control


title: 33pos

value: brain frontal cortex


title: 2_WT_F_FX


title: P10-2-Qia-FFPE

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
Patient 10 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 23

data_processing:
Samples were analysed in an Illumina NextSeq 550 instrument.
Data were generated using the AmpliSeq RNA plugin in the Torrent Suite Software and normalised using RPM (reads assigned per million mapped reads) method.
Probes were mapped to Ensembl gene annotations using BioMart.
Data were log2 transformed and quantile normalised using R/Bioconductor software and packages.
Genome_build: Human genome version GRCh38.77
Supplementary_files_format_and_content: The processed data files contain expression data for each sample mapped to Ensemble gene IDS.

source_name: breast cancer tissue

extract_protocol:
RNA was extracted from 2x20µm FFPE tissue sections using the RNeasy FFPE kit.
All samples were processed and libraries constructed following the manufacturer's guidelines in the Edinburgh Clinical Research Facility.

value: breast cancer

tag: time point

value: early on-treatment biopsy


title: P11-1-Qia-FFPE

description:
Patient 11 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 24

value: pre-treatment biopsy


title: P11-3-Qia-FFPE

description:
Patient 11 late on-treatment biopsy (part 1A) sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 25

value: late on-treatment biopsy


title: 2Redopos

value: Female

value: Bipolar

value: Sepulveda

value: NeuN+


title: P10-1-Qia-FFPE

description:
Patient 10 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 22


title: P9-3-Qia-FFPE

description:
Patient 9 late on-treatment biopsy (part 1A) sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 21


title: 2Redoneg


title: P9-2-Qia-FFPE

description:
Patient 9 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 20


title: P8-3-Qia-FFPE

description:
Patient 8 late on-treatment biopsy (part 1A) sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 19


title: P8-2-Qia-FFPE

description:
Patient 8 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 18


title: 25Redoneg

value: Schizophrenia

value: Harvard HBTRC


title: 24Redopos

value: Bisulfite converted DNA from NeuN+ cells


title: P8-1-Qia-FFPE

description:
Patient 8 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 17


title: 25Redopos


title: P7-2-Qia-FFPE

description:
Patient 7 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 16


title: P7-1-Qia-FFPE

description:
Patient 7 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 15


title: P6-4-Qia-FFPE

description:
Patient 6 later on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 14

value: later on-treatment biopsy


title: 24Redoneg

value: NeuN-

value: Bisulfite converted DNA from NeuN- cells


title: P6-3-Qia-FFPE

description:
Patient 6 late on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 13


title: 23Redoneg

value: Male

value: White


title: 23Redopos

value: Control

value: brain frontal cortex


title: 20Redopos


title: 20Redoneg


title: P5-2-Qia-FFPE

description:
Patient 5 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 11

value: breast cancer

value: early on-treatment biopsy


title: P6-1-Qia-FFPE

description:
Patient 6 late on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 12

value: late on-treatment biopsy


title: P5-1-Qia-FFPE

description:
Patient 5 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 10

value: pre-treatment biopsy


title: 10Redopos

value: Female


title: 27pos

value: unknown


title: 27neg


title: P4-2-Qia-FFPE

description:
Patient 4 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 9


title: P3-3-Qia-FFPE

description:
Patient 3 late on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 7


title: P4-1-Qia-FFPE

description:
Patient 4 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 8


title: 10Redoneg

value: Sepulveda


title: 95re_S5_L002

description:
Bisulfite converted DNA from NeuN+ cells
95re.methylation_results.txt.gz

data_processing:
Trimmomatic v0.36 was used to trim read adapter sequences and BSMAP 2.74 was used to align reads to the GRCh38/hg38 genome build. The genome index consisted of reference chromosome sequences and the lambda phage genome (https://www.ncbi.nlm.nih.gov/nuccore/215104).
Following alignment, reads were pooled across the two lanes. The merged set of reads was separated into those aligning to top and bottom strand, duplicates were removed with Picard (2.9.4 SNAPSHOT) , and then matching read pairs were merged.
Samtools v1.5 was used to exclude reads that were not properly paired or were unmapped. Bamutils were used to clip overhanging reads that distort methylation estimates. Methratio.py in BSMAP computed the percent methylation at the base level.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited file with base-level calls of methylated/unmethylated reads at a Cytosine. Output of methratio.py in BSMap software

extract_protocol:
Genomic DNA from each NeuN+ and NeuN- fraction of each sample was isolated using standard phenol-chloroform extraction methods.
DNA methylation was captured using the SeqCap Epi Enrichment System (Roche). Biotinylated long oligonucleotide probes were customed designed by Roche NimbleGen. Library preparation was performed following manufacturer instructions. Briefly, gDNA (500 ng) of each sample (n= 4 cases and 4 controls, in addition 4 technical replicate samples) were fragmented (~ 200 bp), end repaired and ligated to barcoded adapters using the KAPA Library Preparation kit (Kapa Biosystems) and SeqCap Adapter Kit A and B (Roche). Bisulfite conversion of the adapter ligated DNA followed by column purification was performed with the EZ DNA Methylation Lightning kit (Zymo). The bisulfite converted DNA for each sample was then amplified by ligation mediated PCR (95°C 2 min, 10 cycles of [98°C 30 sec, 60°C 30 sec, 72°C 4 min], 72°C 10 min, 4°C hold) followed by purification with Agencourt AMPure XP beads (Beckman Coulter). Sample quality was verified on Bioanalyzer (Agilent) and quantity was determined with a NanoDrop spectrophotometer (Thermo Fisher Scientific). Equimolar amounts of each sample were then combined into a single pool. Target regions were captured by hybridizing the amplified bisulfite converted DNA pool (1 μg) to the probe library (Roche), as directed by manufacturer. Enrichment and recovery of captured bisulfite-converted DNA was completed by binding to magnetic beads and subsequent wash steps using the SeqCap Pure Capture Bead kit and the SeqCap Hybridization and Wash kit (Roche). The captured DNA was then amplified by ligation mediated PCR (98°C 45 sec, 11 cycles of [98°C 15 sec, 60°C 30 sec, 72°C 30 sec], 72°C 1 min) followed by purification with Agencourt AMPure XP beads (Beckman Coulter). Library quality and quantity was assessed using a combination of Agilent DNA High Sensitivity chip on a Bioanalyzer (Agilent Technologies), Qubit dsDNA HS Assay kit on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). DNA sequencing was performed on an Illumina HiSeq 2500 on Rapid Run mode with all samples run on both sequencing lanes.

tag: replicate

tag: sequencing lane

value: HCtYT

value: UM Brain Endowment Bank


title: 95re_S5_L001


title: 90re_S4_L002

description:
Bisulfite converted DNA from NeuN+ cells
90re.methylation_results.txt.gz


title: P2-3-Qia-FFPE

description:
Patient 2 late on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 5


title: 90re_S4_L001


title: P2-2-Qia-FFPE

description:
Patient 2 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 4


title: P1-3-Qia-FFPE

description:
Patient 1 late on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 3


title: 88re_S6_L002

description:
Bisulfite converted DNA from NeuN+ cells
88re.methylation_results.txt.gz

value: HCtKN


title: 88re_S6_L001


title: P1-1-Qia-FFPE

description:
Patient 1 pre-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 1


title: P1-2-Qia-FFPE

description:
Patient 1 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 2


title: 77re_S11_L001

description:
Bisulfite converted DNA from NeuN+ cells
77re.methylation_results.txt.gz

value: HSQ

value: Schizophrenia


title: 77re_S11_L002


title: P11-1-Bio-FFPE

description:
Patient 11 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 24


title: P11-3-Bio-FFPE

description:
Patient 11 late on-treatment biopsy using BioSpyder TempoSeq technology from FFPE.
Sample 25


title: 76-3re_S9_L002

description:
Bisulfite converted DNA from NeuN+ cells
76-3re.methylation_results.txt.gz

value: HYF

value: Bipolar


title: 76-2re_S8_L002

description:
Bisulfite converted DNA from NeuN+ cells
76-2re.methylation_results.txt.gz

value: Male

value: White


title: P10-2-Bio-FFPE

description:
Patient 10 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 23


title: P10-1-Bio-FFPE

description:
Patient 10 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 22


title: 76-3re_S9_L001


title: 76-2re_S8_L001


title: P9-3-Bio-FFPE

description:
Patient 9 late on-treatment biopsy (part 1A) sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 21


title: 76-1re_S7_L002

description:
Bisulfite converted DNA from NeuN+ cells
76-1re.methylation_results.txt.gz


title: P9-2-Bio-FFPE

description:
Patient 9 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 20


title: 41re_S12_L002

description:
Bisulfite converted DNA from NeuN+ cells
41re.methylation_results.txt.gz

value: Harvard HBTRC


title: P9-1-Bio-FFPE

description:
Patient 9 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 19

value: breast cancer


title: 76-1re_S7_L001


title: P3-2-Qia-FFPE

description:
Patient 3 early on-treatment biopsy sequenced using Qiagen Qiaseq UPX 3' technology from FFPE.
Sample 6

value: early on-treatment biopsy


title: 36re_S10_L002

description:
Bisulfite converted DNA from NeuN+ cells
36re.methylation_results.txt.gz


title: P8-2-Bio-FFPE

description:
Patient 8 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 17


title: P8-3-Bio-FFPE

description:
Patient 8 late on-treatment biopsy (part 1B) sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 18

value: late on-treatment biopsy


title: 41re_S12_L001


title: 36re_S10_L001


title: P7-3-Bio-FFPE

description:
Patient 7 late on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 16


title: 31-3re_S3_L001

description:
Bisulfite converted DNA from NeuN+ cells
31-3re.methylation_results.txt.gz

value: Control


title: P6-4-Bio-FFPE

description:
Patient 6 later on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 14

value: later on-treatment biopsy


title: P6-2-Bio-FFPE

description:
Patient 6 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 12


title: P6-1-Bio-FFPE

description:
Patient 6 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 11

value: pre-treatment biopsy


title: 31-2re_S2_L001

description:
Bisulfite converted DNA from NeuN+ cells
31-2re.methylation_results.txt.gz


title: 31-1re_S1_L002

description:
Bisulfite converted DNA from NeuN+ cells
31-1re.methylation_results.txt.gz


title: 31-1re_S1_L001


title: P5-2-Bio-FFPE

description:
Patient 5 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 10


title: P5-1-Bio-FFPE

description:
Patient 5 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 9


title: P4-2-Bio-FFPE

description:
Patient 4 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 8


title: P4-1-Bio-FFPE

description:
Patient 4 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 7


title: iLSD1-2

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to GRCh38.p5 whole genome using STAR-2.5.0c using --outSAMunmapped within and otherwise default parameters
Raw counts were generated for each sample using htseq-count with -t exon -i gene -r pos
Normalized counts were generated using default settings and blind = TRUE in the rlog package of DESeq2.
Differentially expressed features were calculated using DESeq2
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: csv, gene symbol, location, length, average count, fold change (iLSD1/iLuc) and normalized count data

source_name: A673 cells

growth_protocol: A673 Ewing sarcoma cells were grown as described previously (Lessnick et al., 2002)

extract_protocol:
Cells were trypsinized, counted, and 5 million cells were washed with PBS, pelleted, and flash-frozen. RNA was extracted using an Rneasy kit with on-column DNA digestion per kit instructions (Qiagen). 2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

treatment_protocol: A673 cells were stably infected with retroviral vector pMSCV-puro expressing Luciferase shRNA (iLuc) or KDM1A shRNA (iLSD1) and selected for 4 days, followed by total RNA extraction.

tag: shRNA

value: LSD1 (KDM1A)


title: iLSD1-4


title: P3-2-Bio-FFPE

description:
Patient 3 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 6


title: iLuc-4

value: Luciferase


title: iLSD1-1


title: P2-2-Bio-FFPE

description:
Patient 2 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 5


title: P2-1-Bio-FFPE

description:
Patient 2 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 4


title: iLSD1-3


title: P7-2-Bio-FFPE

description:
Patient 7 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 15


title: P1-3-Bio-FFPE

description:
Patient 1 late on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 3


title: iLuc-3


title: 31-3re_S3_L002

tag: Sex


title: P1-2-Bio-FFPE

description:
Patient 1 early on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 2


title: P1-1-Bio-FFPE

description:
Patient 1 pre-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 1


title: iLuc-1


title: 31-2re_S2_L002

tag: age


title: h358_dmso_rep2

city: San Francisco

first: Kevin

last: Lou

state: CA

address: 600 16th Street

institute: University of California, San Francisco

data_processing:
Sequencing and demultiplexing were performed by the UCSF Center for Advanced Technology
The leading 12 bp of all sequencing reads were trimmed with Trimmomatic (Galaxy version 0.36.5) using the HEADCROP step
Trimmed reads were aligned to the hg19 reference genome with STAR (Galaxy version 2.6.0b-1) using default settings and the GENCODE v19 comprehensive gene annotation GTF
Aligned reads were mapped with featureCounts (Galaxy version 1.6.2) using the default settings and the GENCODE v19 comprehensive gene annotation GTF
Read count normalization and differential expression analysis were conducted with DESeq2 (version 1.20.0)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files which include mapped reads for each Entrez Gene ID

source_name: H358 cells

growth_protocol: Cells (500,000 cells/well) were seeded into 6-well ultra-low attachment plates (Corning Costar #3471) and allowed to incubate at 37 °C overnight.

extract_protocol:
Cells were lysed and total RNA was immediately extracted with the RNeasy Mini Kit (Qiagen) according to manufacturer’s recommendations.
RNA-seq libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and assessed on a BioAnalyzer 2100 (Agilent) for quantification and quality control.
RNA-seq libraries from total RNA using poly(A) enrichment to deplete rRNA

treatment_protocol: Cells were treated with DMSO, palbociclib (1 μM, CDK4/6i), ARS-1620 (1 μM), or the combination in duplicate then incubated at 37 °C for 24 hours.

tag: cell line

tag: culture condition

tag: media

value: DMEM +10% FBS +pen/strep

tag: treatment

value: dmso


title: h358_combo_rep2

value: combo


title: P6-3-Bio-FFPE

description:
Patient 6 late on-treatment biopsy sequenced using BioSpyder TempoSeq technology from FFPE.
Sample 13


title: h358_palbo_rep2

value: palbo


title: h358_dmso_rep1


title: P11-3_(1C)-Quant-FFPE

description:
Patient 11 late on-treatment biopsy (part 1C) sequenced using Lexogen QuantSeq technology from FFPE.
Sample 20

data_processing:
Samples were analysed in an Illumina NextSeq 550 instrument.
Lexogen QuantSeq data were generated using the AmpliSeq RNA plugin in the Torrent Suite Software and normalised using RPM (reads assigned per million mapped reads) method.
Probes were mapped to Ensembl gene annotations using BioMart.
Data were log2 transformed and quantile normalised using R/Bioconductor software and packages.
Genome_build: Human genome version GRCh38.77
Supplementary_files_format_and_content: The processed data files contain expression data for each sample mapped to Ensemble gene IDS.

source_name: Breast cancer tissue.

tag: tissue type

value: FFPE

tag: sequencing platform

value: Lexogen QuantSeq


title: P9-3-Quant-FFPE

description:
Patient 9 late on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 17

tag: tissue


title: P11-1-Quant-FFPE

description:
Patient 11 pre-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 19


title: P9-2-Quant-FFPE

description:
Patient 9 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 16


title: h358_ars_rep1

value: ars


title: h358_ars_rep2


title: h358_combo_rep1


title: P9-1-Quant-FFPE

description:
Patient 9 pre-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 15


title: P8-3_(1D)-Quant-FFPE

description:
Patient 8 late on-treatment biopsy (part 1D) sequenced using Lexogen QuantSeq technology from FFPE.
Sample 14


title: h358_palbo_rep1


title: P8-2-Quant-FFPE

description:
Patient 8 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 13


title: P7-2-Quant-FFPE

description:
Patient 7 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 11


title: MV4-11_Par_RNA-seq_rep1

city: new york

first: Xufeng

last: Chen

state: NY

address: 550 First Avenue, Smilow 1307

institute: NYU Langone Medical Center

description: NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific (Catalog no: 5138-07)

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM table

source_name: MV4-11 parental cells

growth_protocol: MOLM-13 human leukemia cells were cultured in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
MOLM-13 cells were harvested at indicated time points and washed with 1x PBS. Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and QIAshredder (Qiagen). We isolated poly(A) mRNA using magnetic isolation method (NEXTFLEX, Bioo Scientific) using ~1 ug of total mRNA.
To generate RNA-Sequencing libraries, we used NEXTFLEX Rapid Directional RNA-Seq Library Prep Kit (Bioo Scientific) and NEXTFLEX RNA-Seq barcodes (Bioo Scientific), which were carried out according to manufacturer’s protocol.
RNA-Seq barcoded libraries were then sequenced using Hi-Seq 4000 (single end, 50 cycles).

treatment_protocol: For samples 1 and 2, MOLM-13 cells were cultured in DMSO or increasing doses of Venetoclax (from 5nM to 1000nM) for over eight weeks. For samples 3-8, sgRNAs targeting CLPB or control (Rosa) were transduced into MOLM-13-Cas9-dBSD cells by spin infection. Media were replenished every other day for 6 or 8 day during which puromycin (1ng/ml) selection was performed.

tag: cell type

value: human acute myeloid leukemia (AML) cells

tag: genotype/variation

value: parental cells


title: MV4-11_VR_RNA-seq_rep2

source_name: MV4-11 venetoclax resistant cells

value: increasing dose of venetoclax for 8 weeks

value: venetoclax resistant cells


title: iLuc-2


title: MV4-11_VR_RNA-seq_rep1


title: MV4-11_Par_RNA-seq_rep2


title: P7-3_(2D)-Quant-FFPE

description:
Patient 7 late on-treatment biopsy (part 2D) sequenced using Lexogen QuantSeq technology from FFPE.
Sample 12

value: breast cancer

value: late on-treatment biopsy


title: HTH045_mTEClo_3

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
QC performed using FastQC
Reads trimmed using Trimmomatic to remove Nextera adapters
Reads aligned using STAR 2-pass mapping (version 2.5.3a)
Read assignment using HTSeq (version 0.5.4)
Genome_build: mm10
Supplementary_files_format_and_content: counts matrix

source_name: mTEClo

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro Kit
SMARTer-seq with inclusion of ERCC spike-ins

value: human thymic epithelial cell subset


title: P5-1-Quant-FFPE

description:
Patient 5 pre-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 8

value: pre-treatment biopsy


title: P6-4_(2C)-Quant-FFPE

description:
Patient 6 later on-treatment biopsy (part 2C) sequenced using Lexogen QuantSeq technology from FFPE.
Sample 10

value: later on-treatment biopsy


title: HTH045_mTEClo_1


title: HTH045_mTEClo_2


title: P5-2-Quant-FFPE

description:
Patient 5 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 9

value: early on-treatment biopsy


title: P4-2-Quant-FFPE

description:
Patient 4 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 7


title: HTH045_cTEC_3

source_name: cTEC


title: P3-3-Quant-FFPE

description:
Patient 3 late on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 5


title: HTH045_mTEChi_1


title: HTH045_mTEChi_2

source_name: mTEChi


title: P4-1-Quant-FFPE

description:
Patient 4 pre-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 6


title: P3-2-Quant-FFPE

description:
Patient 3 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 4


title: HTH044_mTEClo


title: P1-3-Quant-FFPE

description:
Patient 1 late on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 2


title: HTH045_cTEC_1


title: 95-R2 Frontal cortex of the human brain

type: genomic

description: Frontal cortex of the human brain

hyb_protocol: Reagent/array were purchased from Illumina. The experiment was carried out in Sickkids TCAG Microarray facility according to the recommended protocol by Illumina.

data_processing: Genome Studio was used to process raw intensities, following manufacturer's suggestions

label: Cy3 and Cy5

source_name: Frontal cortex of the human brain

extract_protocol: DNA was extracted using standard phenol-chloroform extract methods

treatment_protocol: No treatment was applied to these samples.

tag: index

value: HCTYT

value: Male

tag: race

value: White

value: Control

tag: tissuebank

value: UM Brain Endowment Bank

tag: pmi

tag: sampleID


title: HTH044_mTEChi


title: P1-2-Quant-FFPE

description:
Patient 1 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 1

tag: time point

value: FFPE

value: Lexogen QuantSeq


title: HTH045_mTEChi_3


title: 95-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain

scan_protocol: Reagent/array were purchased from Illumina. The experiment was carried out in Sickkids TCAG Microarray facility according to the recommended protocol by Illumina.

tag: Sex


title: P2-2-Quant-FFPE

description:
Patient 2 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 3


title: HTH042_cTEC


title: HTH042_mTEChi


title: 90-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain

label_protocol: Reagent/array were purchased from Illumina. The experiment was carried out in Sickkids TCAG Microarray facility according to the recommended protocol by Illumina.

tag: age


title: HTH042_mTEClo


title: HTH041_mTEClo


title: 76-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HYF

value: Bipolar


title: 76-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: HTH041_cTEC


title: 90-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 70-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HQQ


title: 70-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: HTH041_mTEChi


title: 76-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 90-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: P10-2-Quant-FFPE

description:
Patient 10 early on-treatment biopsy sequenced using Lexogen QuantSeq technology from FFPE.
Sample 18


title: MOLM-13_sgCLPB#2_D8_RNA-seq_rep2

source_name: MOLM-13-Cas9-dBSD cells

tag: cell line

value: human acute myeloid leukemia (AML) cells

value: Day 8 post sgCLPB#2 transduction

value: CLPB Knockout


title: MOLM-13_sgCLPB#2_D8_RNA-seq_rep1


title: MOLM-13_sgCLPB#2_D8_RNA-seq_rep3


title: 95-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: HTH045_cTEC_2

value: human thymic epithelial cell subset


title: 70-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 67-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HIJ

value: Schizophrenia


title: HTH044_cTEC


title: MOLM-13_sgCLPB#2_D6_RNA-seq_rep3

value: Day 6 post sgCLPB#2 transduction


title: MOLM-13_sgCLPB#2_D6_RNA-seq_rep2


title: 67-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 67-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: MOLM-13_sgCLPB#1_D8_RNA-seq_rep3

value: Day 8 post sgCLPB#1 transduction


title: MOLM-13_sgCLPB#1_D8_RNA-seq_rep2


title: 55-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HGR

value: Female


title: 55-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: White


title: 42-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Harvard HBTRC


title: 42-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: MOLM-13_sgCLPB#1_D6_RNA-seq_rep2

value: Day 6 post sgCLPB#1 transduction


title: 31-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Male

value: Control


title: MOLM-13_sgRosa_D8_RNA-seq_rep3

value: Day 8 post sgRosa transduction

value: CLPB Wild Type


title: MOLM-13_sgRosa_D8_RNA-seq_rep2

value: human acute myeloid leukemia (AML) cells


title: MOLM-13_sgCLPB#2_D6_RNA-seq_rep1


title: MOLM-13_sgCLPB#1_D8_RNA-seq_rep1


title: MOLM-13_sgCLPB#1_D6_RNA-seq_rep3


title: 31-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: MOLM-13_sgRosa_D8_RNA-seq_rep1


title: P5-2-Illu-FF

type: RNA

description:
Patient 5 early on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 14

hyb_protocol: Labelled cDNA was hybridised to Human HT-12v4 whole-genome expression beadarrays (Illumina) according to the standard protocol for NuGEN amplified samples.

scan_protocol: Scanning was performed on a Illumina scanner using the manufacturers protocol

data_processing: Illumina probe profiles were quantile normalised using the lumi package

label: biotin

label_protocol: RNA was reverse transcribed and amplified using the WT-Ovation FFPE System Version 2 (NuGEN), purified using the Qiaquick PCR Purification Kit (Qiagen), biotinylated using the IL Encore Biotin Module (NuGEN), purified using minElute Reaction Cleanup Kit (Qiagen) and quantified once again using the Nanodrop 2000c (Thermo Scientific).

extract_protocol: RNA was extracted from fresh frozen tissue using the Qiagen miRNeasy kit.

value: breast cancer

value: early on-treatment biopsy


title: P4-3-Illu-FF

description:
Patient 4 late on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 12

value: late on-treatment biopsy


title: P4-1-Illu-FF

description:
Patient 4 pre-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 10

value: pre-treatment biopsy


title: P5-1-Illu-FF

description:
Patient 5 pre-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 13


title: P7-1-Illu-FF

description:
Patient 7 pre-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 16


title: 31-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: P5-3-Illu-FF

description:
Patient 5 late on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 15


title: P3-2-Illu-FF

description:
Patient 3 early on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 8


title: P7-2-Illu-FF

description:
Patient 7 early on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 17


title: P7-3-Illu-FF

description:
Patient 7 late on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 18


title: P3-1-Illu-FF

description:
Patient 3 pre-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 7


title: P2-3-Illu-FF

description:
Patient 2 late on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 6


title: P4-2-Illu-FF

description:
Patient 4 early on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 11


title: P2-1-Illu-FF

description:
Patient 2 pre-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 4


title: P2-2-Illu-FF

description:
Patient 2 early on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 5


title: P1-3-Illu-FF

description:
Patient 1 late on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 3


title: P1-2-Illu-FF

description:
Patient 1 early on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 2


title: MOLM-13_sgRosa_D6_RNA-seq_rep3

description: NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific (Catalog no: 5138-07)

value: Day 6 post sgRosa transduction


title: P1-1-Illu-FF

description:
Patient 1 pre-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 1


title: MOLM-13_sgRosa_D6_RNA-seq_rep2


title: 26-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Schizophrenia


title: MOLM-13_VR_RNA-seq_rep2

source_name: MOLM-13 venetoclax resistant cells

value: increasing dose of venetoclax for 8 weeks

value: venetoclax resistant cells


title: MOLM-13_sgRosa_D6_RNA-seq_rep1


title: P7-2-Affy-FF

description:
Patient 7 early on-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 5

hyb_protocol: As per standard Affymetrix protocol.

scan_protocol: As per standard Affymetrix protocol, using a GCS2500 scanner.

data_processing: All statistical analyses were performed using the R/Bioconductor software (http://www.bioconductor.org/) unless stated otherwise. Preprocessing—the raw CEL files were preprocessed using robust multichip average methodology, which encompasses background correction, normalization, and summarization. Nonspecific filtering—using Affymetrix’ absolute call data, genes with “present” calls in fewer than 80% of arrays were discarded so reducing genes whose expression were largely in the noise range.

label: Biotin

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets.


title: MOLM-13_VR_RNA-seq_rep1


title: 100 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 99 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 98 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: MOLM-13_Par_RNA-seq_rep2

source_name: MOLM-13 parental cells

value: parental cells


title: P6-3-Affy-FF

description:
Patient 6 late on-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 3


title: P7-1-Affy-FF

description:
Patient 7 pre-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 4


title: 26-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: White


title: P6-1-Affy-FF

description:
Patient 6 pre-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 1


title: 26-R2 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Harvard HBTRC


title: MOLM-13_Par_RNA-seq_rep1


title: 97 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Female

value: Bipolar


title: 96 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTYF

value: Male

value: Control

value: UM Brain Endowment Bank


title: 94 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HBDB


title: 93 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HBGR

value: Hispanic


title: 79_TC71_DMSO

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to GRCh38.p6 whole genome using STAR-2.5.1b using --outSAMunmapped within and otherwise default
Raw counts were generated for each sample using htseq-count with -t exon -i gene -r pos
Normalized counts were generated using default settings and blind = TRUE in the rlog package of DESeq2.
Genome_build: GRCh38.p6
Supplementary_files_format_and_content: csv, gene symbol and rlog (using DESeq2) normalized count data

source_name: TC71 cells

growth_protocol: Ewing sarcoma cell lines were seeded at 20-25% confluency and left to adhere overnight. The following morning cells were treated with either DMSO or SP-2509 (2uM), and collected  48hrs post treament.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase digestion.  2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

value: DMSO

tag: replicate

tag: sp-2509 sensitivity

value: Sensitive


title: 80_TC71_HCI_2509

treatment_protocol: Ewing sarcoma cell lines were seeded at 20-25% confluency and left to adhere overnight. The following morning cells were treated with either DMSO or SP-2509 (2uM), and collected  48hrs post treament.

tag: treatment


title: 74_TC71_HCI_2509


title: 73_TC71_DMSO


title: 92 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTYZ


title: P6-2-Affy-FF

description:
Patient 6 early on-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 2

value: breast cancer

value: early on-treatment biopsy


title: P7-3-Affy-FF

description:
Patient 7 late on-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 6

value: late on-treatment biopsy


title: P3-3-Illu-FF

description:
Patient 3 late on-treatment biopsy sequenced using Illumina HT12-V4 technology from fresh frozen.
SAMPLE 9


title: 91 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTQC

value: White


title: 89 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTPF


title: 69_TC71_DMSO


title: 68_EWS502_HCI_2509

source_name: EWS-502 cells


title: 55-R3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HGR

value: Female

value: Schizophrenia


title: 70_TC71_HCI_2509


title: 87 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HBDL

value: Bipolar


title: 42-R1 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Harvard HBTRC


title: 67_EWS502_DMSO


title: 88 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTKN

value: Male

value: Control

value: UM Brain Endowment Bank


title: 64_EWS502_HCI_2509

value: Sensitive


title: MOLM-13_sgCLPB#1_D6_RNA-seq_rep1

value: human acute myeloid leukemia (AML) cells

value: Day 6 post sgCLPB#1 transduction

value: CLPB Knockout


title: 86 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTWL


title: 85 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HBCR

value: White


title: 63_EWS502_DMSO

value: DMSO


title: Sample 99

description: neurons from post-mortem human brain

data_processing: Data generated from the microarrays were preprocessed with Minfi v1.19.12. Normalization was performed with noob, followed by quantile normalization. All samples had sex matching that predicted from the methylome.  Probes that overlapping SNPs (MAF > 5%) on the CpG or single-base extension were excluded (11,812 probes), as were probes known to be cross-reactive (42,558 probes; PMID: 27330998) and those that failed detectability (P>0.01) in >20% samples (1,170 probes). After processing, 812,663 probes were left. Based on principal component analysis (PCA) co-clustering, one sample, despite being labeled NeuN+, clustered with NeuN- samples and was excluded from downstream analyses. Downstream analyses were performed using beta values ; only samples that were also genotyped were used in differential methylation analyses.

label: Cy5 and Cy3

source_name: FACS-sorted neurons from the frontal cortex of the human brain

extract_protocol: Genomic DNA from each NeuN+ and NeuN- fraction of each sample was isolated using standard phenol-chloroform extraction methods.

value: frontal cortex of the brain

value: NeuN+


title: Sample 95

description: neurons from post-mortem human brain

value: HCTYT


title: 60_EWS502_HCI_2509


title: Sample 98

description: neurons from post-mortem human brain

value: Female

value: Bipolar


title: Sample 96

description: neurons from post-mortem human brain


title: 84 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HEJ

value: Schizophrenia


title: Sample 94

description: neurons from post-mortem human brain

value: Male

value: Control


title: Sample 87

description: neurons from post-mortem human brain

value: Sepulveda


title: Sample 91

description: neurons from post-mortem human brain

value: HCTYZ

value: UM Brain Endowment Bank


title: Sample 97

description: neurons from post-mortem human brain

value: HCTYF


title: Sample 88

description: neurons from post-mortem human brain

value: HCtYT


title: Sample 89

description: neurons from post-mortem human brain


title: Sample 81

description: neurons from post-mortem human brain


title: Sample 92

description: neurons from post-mortem human brain

value: HBGR

value: Hispanic


title: Sample 86

description: neurons from post-mortem human brain

value: HCtPF

value: White


title: Sample 100

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: Harvard HBTRC

value: NeuN+


title: Sample 79

description: neurons from post-mortem human brain

value: HCcPL


title: 83 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCCAD

value: Female

value: Black


title: Sample 80

description: neurons from post-mortem human brain

value: HCcAD

value: Schizophrenia


title: Sample 83

description: neurons from post-mortem human brain

value: HCtWL

value: Male

value: Control


title: 82 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCCPL

value: UM Brain Endowment Bank


title: 54_TC32_HCI_2509

source_name: TC32 cells

value: Hypersensitive


title: Sample 85

description: neurons from post-mortem human brain

value: HCtKN


title: 53_TC32_DMSO

value: DMSO


title: Sample 90

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: HCtQC

value: White


title: Sample 75

description: neurons from post-mortem human brain

value: HCtQX

value: NeuN+


title: Sample 78

description: neurons from post-mortem human brain

value: HCtLI


title: Sample 93

description: neurons from post-mortem human brain

value: HBDB

value: Bipolar


title: 80 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTRP


title: 81 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTLI

value: Black


title: Sample 84

description: neurons from post-mortem human brain

value: HBDL

value: Female


title: 49_TC32_DMSO


title: 48_TC32_HCI_2509


title: 50_TC32_HCI_2509


title: Sample 76

description: neurons from post-mortem human brain

value: Male

value: Sepulveda


title: Sample 82

description: neurons from post-mortem human brain

value: HBCR

value: UM Brain Endowment Bank


title: 59_EWS502_DMSO

value: DMSO

value: Sensitive


title: 77 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HSQ

value: White

value: Schizophrenia


title: 47_TC32_DMSO

value: Hypersensitive


title: 22_ES2_HCI_2509

source_name: ES-2 cells


title: Sample 74

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: NeuN+


title: 21_ES2_DMSO


title: Sample 71

description: neurons from post-mortem human brain

value: HYF

value: Bipolar


title: 20_ES2_HCI_2509


title: Sample 73

description: neurons from post-mortem human brain


title: Sample 72

description: neurons from post-mortem human brain


title: 73 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTCR

value: Control


title: 75 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCCFH


title: Sample 77

description: neurons from post-mortem human brain

value: HCtRP

value: Male


title: Sample 69

description: neurons from post-mortem human brain

value: HCtWI

value: Female


title: 79 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTQX

value: UM Brain Endowment Bank


title: 74 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTWI


title: Sample 70

description: neurons from post-mortem human brain

value: HCcFH

value: White


title: 78 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTLN

value: Black


title: 19_ES2_DMSO

value: DMSO

value: Sensitive


title: Sample 64

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: HQQ

value: Bipolar

value: NeuN+


title: Sample 68

description: neurons from post-mortem human brain

value: HCtCR

value: Control


title: 72 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCCKT

value: Male


title: 69 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTDM


title: 18_ES2_HCI_2509


title: Sample 66

description: neurons from post-mortem human brain

value: HCtYV

value: UM Brain Endowment Bank


title: 68 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HHG


title: Sample 67

description: neurons from post-mortem human brain

value: HCcKT

value: White


title: 16_TC252_HCI_2509

source_name: TC252 cells

value: Hypersensitive


title: 17_ES2_DMSO

value: DMSO


title: Sample 62

description: neurons from post-mortem human brain

value: Female

value: Sepulveda


title: Sample 61

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: HCtDM


title: Sample 59

description: neurons from post-mortem human brain

value: HIJ

value: Schizophrenia

value: NeuN+


title: Sample 63

description: neurons from post-mortem human brain

value: HQQ

value: Bipolar


title: 15_TC252_DMSO


title: 66 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTVB

value: Male

value: Control


title: 71 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTYV

value: UM Brain Endowment Bank


title: Sample 55

description: neurons from post-mortem human brain

value: White


title: 59 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HTO

value: Hispanic


title: Sample 58

description: neurons from post-mortem human brain


title: tumor-fasting-chemo-S404

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

description:
TUM6_S404
three days fasting, chemotherapy treatment

hyb_protocol: Gene chip hybridization, washing and scanning were carried out according to Affymetrix protocols.

scan_protocol: Scanning was carried out according to Affymetrix protocols

data_processing: Normalization was done via the Robust Multichip Average (RMA) algorithm.

source_name: tumor

label_protocol: RNA was further processed for hybridization to Affymetrix HT MG-430 PM Array Plates at the Microarray Department of the University of Amsterdam, the Netherlands. RNA amplication and labeling were carried out according to Affymetrix protocols

growth_protocol: Animals were allowed to acclimatize for one week before the start of the experiments. Standard laboratory conditions were maintained, i.e. temperature 22ºC, humidity 50%, and a 12 h light/12 h dark cycle. All mice had free access to water and food unless mentioned otherwise. The experimental protocol was approved by the Animal Experiments Committee under the Dutch National Experiments on Animals Act, and complied with the 1986 directive 86/609/EC of the Council of Europe.

extract_protocol: The median liver lobe was isolated for array analysis and directly stored in RNAlater Solution and stored at 4ºC until further analysis.  For gene expression analysis, total RNA was extracted from frozen liver tissue using the QIAzol lysis Reagent and miRNAeasy Mini Kit (QIAGEN, Hilden, Germany), as described in the Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program; animal tissues; aqueous phase. RNA was eluted in RNase free water and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Scientific). Subsequently, quality assessment of the RNA was done using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) and RNA kits and reagents belonging to the same manufacturer.

treatment_protocol:
For tumor growth: mice were anaesthetized (isoflurane inhalation, 5% isoflurane inhalation initially and then 2% isoflurane with a 1:1 air:oxygen mixture for maintenance of anesthesia). Both lateral flanks were shaved for precise injection. 2.5 x 10^5 cells of the murine colon carcinoma cell line C26 were injected on both sides in a volume of 100 µL suspension, using a 21G needle. Tumors were allowed to grow for 12 days before start of the experiment.
Fasting: mice were either fasted for 3 days or fed ad libitum (adlib). After the fasting period, mice were fed adlib again.
Chemotherapy: mice were treated with a single weight-adjusted dose of 133 mg/kg of irinotecan intraperitoneally. The control groups received vehicle treatment (sodium chloride 0.9%). Two hours after injection, the fasted groups received a weighed amount of adlib food. Mice were sacrificed 12 hours after injection by exsanguination.

tag: strain

value: BALB/c

tag: gender

value: male

value: tumor

tag: feeding protocol

value: three days fasting

value: irinotecan chemotherapy


title: Sample 65

description: neurons from post-mortem human brain

tag: tissue

value: frontal cortex of the brain


title: Sample 57

description: neurons from post-mortem human brain

value: HIJ

value: Schizophrenia

value: NeuN+


title: Sample 60

description: neurons from post-mortem human brain

value: HHG

value: Bipolar


title: 12_TC252_HCI_2509

value: Hypersensitive


title: Sample 52

description: neurons from post-mortem human brain

value: Male


title: Sample 53

description: neurons from post-mortem human brain

value: UM Brain Endowment Bank


title: tumor-fasting-chemo-S402

description:
TUM6_S402
three days fasting, chemotherapy treatment


title: Sample 48

description: neurons from post-mortem human brain

value: HGR

value: Female

value: White


title: Sample 49

description: neurons from post-mortem human brain

value: HCtTA

value: Black

value: Control


title: Sample 51

description: neurons from post-mortem human brain

value: HXN


title: Sample 45

description: neurons from post-mortem human brain

value: U Pittsburgh


title: Sample 46

description: neurons from post-mortem human brain

value: frontal cortex of the brain


title: Sample 47

description: neurons from post-mortem human brain


title: Sample 43

description: neurons from post-mortem human brain

value: Harvard HBTRC


title: 11_TC252_DMSO

value: DMSO


title: Sample 54

description: neurons from post-mortem human brain

value: HTO

value: Hispanic

value: Schizophrenia

value: NeuN+


title: Sample 42

description: neurons from post-mortem human brain

value: Bipolar


title: 58 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Male

value: UM Brain Endowment Bank


title: Sample 41

description: neurons from post-mortem human brain

value: Female


title: Sample 56

description: neurons from post-mortem human brain

value: HCtVB

value: White


title: 57 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HTA

value: Black


title: Sample 44

description: neurons from post-mortem human brain

value: Sepulveda


title: Sample 50

description: neurons from post-mortem human brain


title: tumor-fasting-chemo-S399

description:
TUM6_S399
three days fasting, chemotherapy treatment

value: BALB/c

value: male

value: tumor

value: three days fasting

value: irinotecan chemotherapy


title: 10_TC252_HCI_2509

value: Hypersensitive


title: Sample 38

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: Harvard HBTRC


title: Sample 40

description: neurons from post-mortem human brain

value: Bipolar

value: NeuN+


title: tumor-fasting-chemo-S400

description:
TUM6_S400
three days fasting, chemotherapy treatment


title: 9_TC252_DMSO

value: DMSO


title: Sample 39

description: neurons from post-mortem human brain

value: Male


title: 43 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Female


title: 39 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: White


title: 37 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Schizophrenia


title: tumor-fasting-vehicle-S391

description:
TUM4_S391
three days fasting, vehicle treatment

value: vehicle


title: tumor-adlib-chemo-S398

description:
TUM5_S398
adlib food, chemotherapy treatment

value: ad libitum food


title: tumor-adlib-vehicle-S385

description:
TUM3_S385
adlib food, vehicle treatment

value: BALB/c


title: tumor-adlib-chemo-S397

description:
TUM5_S397
adlib food, chemotherapy treatment

value: male


title: 54 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: U Pittsburgh


title: 41 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 38 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: Saline_2

city: Guangzhou

first: Meijun

last: Si

state: Guangdong

address: 600 Tianhe Ave.

department: Nephrology

country: China

institute: The 3rd Affiliated Hospital of Sun Yat-sen University

description: Total RNA

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.

source_name: Peritoneal tissue

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: 8-10 weeks old male C57BL/6 mice were daily intraperitoneally injected with 4.25% peritoneal dialysis fluid (DIANEAL containing 4.25% glucose, Baxter Healthcare) at 0.1 ml/g body weight for 6 weeks. Mice in control group were treated with 0.9% saline at 0.1 ml/g body weight for 6 weeks.

value: Peritoneal tissue

value: Saline for 6 weeks


title: Saline_3

description: Total RNA


title: PD_3

description: Total RNA

value: PD for 6 weeks


title: 56 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: HCTTA

value: Black

value: Control

value: UM Brain Endowment Bank


title: Saline_1

description: Total RNA


title: 40 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Bipolar

value: Harvard HBTRC


title: 44 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Male


title: 36 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: White


title: 35 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Schizophrenia


title: PD_2

description: Total RNA


title: tumor-fasting-vehicle-S392

description:
TUM4_S392
three days fasting, vehicle treatment

value: tumor

value: three days fasting

value: vehicle


title: tumor-adlib-chemo-S395

description:
TUM5_S395
adlib food, chemotherapy treatment

value: BALB/c

value: male

value: ad libitum food

value: irinotecan chemotherapy


title: tumor-adlib-chemo-S396

description:
TUM5_S396
adlib food, chemotherapy treatment


title: tumor-fasting-vehicle-S388

description:
TUM4_S388
three days fasting, vehicle treatment


title: PD_1

description: Total RNA

value: Peritoneal tissue

value: PD for 6 weeks


title: tumor-adlib-vehicle-S383

description:
TUM3_S383
adlib food, vehicle treatment


title: tumor-adlib-vehicle-S384

description:
TUM3_S384
adlib food, vehicle treatment


title: 32 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 34 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: tumor-fasting-vehicle-S389

description:
TUM4_S389
three days fasting, vehicle treatment


title: Breast cancer cell line, cSrcKO, m9327_1 RNA-seq

city: Montreal

first: Harvey

middle: Wilmore

last: Smith

state: Quebec

address: Life Sciences Complex, Room 602, 1160 Pine Avenue West

department: Goodman Cancer Research Centre

institute: McGill University

data_processing:
Raw data (raw reads) in fastq format were processed through in-house perl scripts to remove reads containing adapter or poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Cleaned data were mapped to the genome of the mouse strain FVB/N. An index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene, with FPKM of each gene calculated based gene length and read counts (FPKM - expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) were calculated to estimate gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis was performed using the DESeqR package (1.18.0) and the resulting P-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: FVB_NJ_R, Wellcome Sanger Institue Mouse Genomes Project -  https://mice-geval.sanger.ac.uk/FVB_NJ_R20150819/Info/Index
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values for all samples

source_name: Breast cancer cell line

growth_protocol: Breast cancer cell lines were established from the MMTV-NIC (ErbB2-IRES-Cre) model (PMID: 18273058, Ursini-Siegel et al.) and routinely cultured in DMEM supplemented with 5% FBS, EGF (5 ng/ml), Hydrocortisone (1 μg/ml), Insulin (5 μg/ml) and Bovine Pituitary Extract (BPE) (35μg/ml)). Cells were grown in a humidified, 5% CO2, 37°C incubator.

extract_protocol:
RNA was isolated from two independent control and two independent c-Src knockout cell lines, each in biological duplicate, using an RNEasy mini kit (Qiagen) according to the manufacturer's instructions. RNA concentration was measured using a Qubit® 2.0 Flurometer (Life Technologies, CA, USA) according to the manufacturer's instructions. Degradation and contamination were initially assessed on 1% agarose gels and purity was determined using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity was then assessed using the Bioanalyzer 2100 system (Agilent).
3 μg of RNA per sample was used to generate sequencing libraries using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends, NEBNext Adaptors with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter). Then 3 μl USER Enzyme (NEB) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the HiSeq PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.

value: FVB/N

value: Breast cancer cell line

tag: genotype

value: MMTV-NIC/c-Src LoxP/LoxP

tag: passages

value: mammary gland


title: 33 Frontal cortex of the human brain

description: Frontal cortex of the human brain

tag: index

tag: race

value: Control

value: Harvard HBTRC


title: 29 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Male

value: White

tag: tissuebank

tag: pmi


title: tumor-adlib-vehicle-S382

description:
TUM3_S382
adlib food, vehicle treatment

value: tumor


title: Breast cancer cell line, cSrcKO, m4447_2 RNA-seq


title: Breast cancer cell line, cSrcKO, m4447_1 RNA-seq


title: liver-fasting-chemo-S402

description:
LIV6_S402
three days fasting, chemotherapy treatment

source_name: liver

value: liver

value: three days fasting


title: liver-fasting-chemo-S404

description:
LIV6_S404
three days fasting, chemotherapy treatment


title: Breast cancer cell line, WT, m8905_2 RNA-seq

value: MMTV-NIC/c-Src WT/WT


title: liver-fasting-chemo-S400

description:
LIV6_S400
three days fasting, chemotherapy treatment

value: male


title: Sample 31

description: neurons from post-mortem human brain

value: frontal cortex of the brain

tag: sampleID

value: NeuN+


title: Breast cancer cell line, cSrcKO, m9327_2 RNA-seq


title: 27 Frontal cortex of the human brain

description: Frontal cortex of the human brain

tag: Sex

value: Schizophrenia


title: 28 Frontal cortex of the human brain

description: Frontal cortex of the human brain

tag: age


title: Sample 33

description: neurons from post-mortem human brain


title: liver-fasting-chemo-S399

description:
LIV6_S399
three days fasting, chemotherapy treatment

value: irinotecan chemotherapy


title: Sample 37

description: neurons from post-mortem human brain

value: Female

value: Bipolar

value: Sepulveda


title: 30 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: Sample 35

description: neurons from post-mortem human brain


title: liver-adlib-chemo-S398

description:
LIV5_S398
adlib food, chemotherapy treatment

value: ad libitum food


title: Breast cancer cell line, WT, m8905_1 RNA-seq

value: FVB/N

tag: cell line

value: Breast cancer cell line

value: mammary gland


title: liver-adlib-chemo-S397

description:
LIV5_S397
adlib food, chemotherapy treatment


title: 25 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Male

value: White

value: Harvard HBTRC


title: Breast cancer cell line, WT, m5567_2 RNA-seq


title: 24 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Control


title: 22 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: liver-adlib-chemo-S396

description:
LIV5_S396
adlib food, chemotherapy treatment

value: liver


title: 23 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: liver-fasting-vehicle-S392

description:
LIV4_S392
three days fasting, vehicle treatment

value: male

value: three days fasting

value: vehicle


title: Breast cancer cell line, WT, m5567_1 RNA-seq

value: MMTV-NIC/c-Src WT/WT


title: liver-adlib-chemo-S395

description:
LIV5_S395
adlib food, chemotherapy treatment

value: irinotecan chemotherapy


title: 21 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: liver-fasting-vehicle-S391

description:
LIV4_S391
three days fasting, vehicle treatment


title: liver-fasting-vehicle-S388

description:
LIV4_S388
three days fasting, vehicle treatment


title: 20 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Schizophrenia


title: 19 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 18 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: Sample 29

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: NeuN+


title: liver-fasting-vehicle-S389

description:
LIV4_S389
three days fasting, vehicle treatment


title: Sample 34

description: neurons from post-mortem human brain


title: 17 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Female

value: Sepulveda


title: liver-adlib-vehicle-S386

description:
LIV3_S386
adlib food, vehicle treatment

value: ad libitum food


title: 16 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Bipolar


title: Sample 32

description: neurons from post-mortem human brain

value: Male


title: 15 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: White


title: Sample 30

description: neurons from post-mortem human brain

value: Harvard HBTRC


title: Sample 27

description: neurons from post-mortem human brain

value: Control


title: Sample 36

description: neurons from post-mortem human brain


title: liver-adlib-vehicle-S383

description:
LIV3_S383
adlib food, vehicle treatment

value: liver


title: Sample 28

description: neurons from post-mortem human brain


title: liver-adlib-vehicle-S381

description:
LIV3_S381
adlib food, vehicle treatment

value: male


title: liver-adlib-vehicle-S385

description:
LIV3_S385
adlib food, vehicle treatment


title: Sample 22

description: neurons from post-mortem human brain


title: 14 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: liver-fasting-untreated-S344

description:
LIV2_S344
three days fasting, no treatment

value: three days fasting


title: Sample 24

description: neurons from post-mortem human brain


title: 13 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: FASN Mutant 2 ON P14

city: Zürich

first: Laura

last: Montani

state: ZH

address: Otto Stern Weg 7

country: Switzerland

institute: IMHS - ETH Zürich

description:
P14_Fasn_ON_MU2 [FPKM]
20160726.X-P14_Fasn_ON_MU2

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20).
Read-alignment was done with STAR (v2.5.1b).
Ensembl genome build GRCm38 was used as reference and gene annotations downloaded on 2015-06-25 from Ensembl.
Applied STAR alignment options were: OutFilterType BySJout, outFilter MatchNmin30, outFilter Mismatch Nmax10, outFilter MismatchNoverLmax0.05, alignSJDB overhangMin1, aligns overhangMin8, alignIntron Max1000000, alignMatesGap Max1000000, outFilterMultimapN max50.
Quantification of gene level expression was carried out using RSEM (v1.2.22)
Differential expression was computed using the generalized linear model implemented in the Bioconductor package EdgeR
To correct for multiple testing, the Benjamini-Hochberg algorithm was applied and adjusted p-values computed
Genome_build: Ensembl genome build GRCm38
Supplementary_files_format_and_content: Differential expression results including normalized counts and FPKM data per sample

source_name: FASN Mutant ON P14

extract_protocol:
Optic nerves were dissected and immediately frozen in liquid nitrogen. Samples were stored at -80° C until processed for RNA extraction. Total RNA was isolated with a Qiagen MiniKit according to manufacturer’s protocols, quantity and quality determined with Nanodrop Lite (NanoDrop Technologies, Thermo Fisher Scientific), Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and Bioanalyzer 2100 (Agilent, Santa Clara, CA).
The TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) was used in the succeeding steps. Briefly,poly-A containing RNA molecules were purified from the total RNA samples (100 ng) using oligo-dT attached magnetic beads. Isolated RNA was reverse-transcribed into double-stranded cDNA, with actinomycin added during first-strand synthesis. The cDNA samples were fragmented, end repaired and polyadenylated before ligation of TruSeq adapters. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit 2.0 Fluorometer and Bioanalyzer 2100. The product is a smear with an average fragment size of approximately 360 bp. The libraries were normalized to 10 nM in Tris-Cl 10 mM, pH 8.5 with 0.1% Tween-20. Sequencing was performed on an Illumina HiSeq 4000 in single end 125 bp mode.

tag: strain background

tag: genotype/variation

value: olig2cre FASN lox/lox

value: Optic nerve (ON)


title: FASN Mutant 3 ON P14

description:
P14_Fasn_ON_MU3 [FPKM]
20160726.X-P14_Fasn_ON_MU3


title: 12 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: 11 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: Sample 26

description: neurons from post-mortem human brain


title: FASN Mutant 1 ON P14

description:
P14_Fasn_ON_MU1 [FPKM]
20160726.X-P14_Fasn_ON_MU1


title: FASN Control 4 ON P14

description:
P14_Fasn_ON_CT4 [FPKM]
20160726.X-P14_Fasn_ON_CT4

source_name: FASN Control ON P14

value: FASN lox/lox


title: Sample 25

description: neurons from post-mortem human brain

value: Schizophrenia


title: Sample 23

description: neurons from post-mortem human brain

value: frontal cortex of the brain


title: FASN Control 3 ON P14

description:
P14_Fasn_ON_CT3 [FPKM]
20160726.X-P14_Fasn_ON_CT3


title: 9 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: liver-fasting-untreated-S340

description:
LIV2_S340
three days fasting, no treatment

tag: treatment


title: FASN Control 2 ON P14

description:
P14_Fasn_ON_CT2 [FPKM]
20160726.X-P14_Fasn_ON_CT2


title: 10 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: liver-fasting-untreated-S343

description:
LIV2_S343
three days fasting, no treatment

tag: strain


title: Sample 20

description: neurons from post-mortem human brain

value: NeuN+


title: liver-fasting-untreated-S339

description:
LIV2_S339
three days fasting, no treatment

tag: gender


title: FASN Control 1 ON P14

description:
P14_Fasn_ON_CT1 [FPKM]
20160726.X-P14_Fasn_ON_CT1


title: Sample 16

description: neurons from post-mortem human brain


title: Sample 21

description: neurons from post-mortem human brain

value: unknown


title: 7 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Female

value: Sepulveda


title: Sample 17

description: neurons from post-mortem human brain


title: liver-adlib-untreated-S349

description:
LIV1_S349
adlib food, no treatment

tag: feeding protocol

value: ad libitum food


title: liver-adlib-untreated-S350

description:
LIV1_S350
adlib food, no treatment

tag: tissue


title: Sample 15

description: neurons from post-mortem human brain

value: Male


title: liver-adlib-untreated-S348

description:
LIV1_S348
adlib food, no treatment


title: liver-adlib-untreated-S347

description:
LIV1_S347
adlib food, no treatment


title: 6 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: White

value: Bipolar


title: TruSeq_PNK

data_processing:
TruSeq sRNA adapter and STP oligo sequences were trimmed from reads using cutadapt (v1.91), filtering reads <15 nt.
Trimmed reads were aligned to the sequences of the synthetic RNA pool using the sRNAnalyzer pipeline. A bowtie library containing the sRNAnalyzer sequences was prepared and added to the manifest required as input. sRNAnalyzer was run using default parameters (allowing up to 2 mismatches), sequentially aligning to Univec contaminates and then the sRNA pipeline.
Read counts from sRNAnalyzer ".profile" files were loaded into R for processing
Alignment strand and mismatch information are used to assign sequences to best alignment between Univec contaminates and sRNA pool. The alignment with the fewest mismatches is identified for each read, and kept for analysis only if it matches the + strand of the sRNA pool.
Read counts are combined (sum) for all sequences in the pool, allowing 0-2 mismatches on the + strand. Ambiguous alignments are divided among the respective sequences.
Read counts-per-million (CPM) are calculated using the total number of filtered reads aligned to the synthetic pool.
Genome_build: NA
Supplementary_files_format_and_content: Tab-delimited "profile" files contain all alignments to Univec and sRNA synthetic pool sequences reported by sRNAnalyzer. The columns include: 1) Alignment database ID with # mismatched and alignment orientation; 2) Unique sequence id with count (format: ID-count); 3) read sequence; 4) ID of aligned sRNA database subject; 5) Start position of alignment in subject. Relative position and base difference of mismatch, if applicable. (format: alignStart,mmPos:OldBase>NewBase). 6) read count, 7) n/a. Supplementary .txt file contains CPM values calculated from processing and filtering the .profile files.

organism: synthetic construct

source_name: Synthetic sRNA equimolar pool (SynthRNA476v1)

extract_protocol:
10 femtomoles of the synthetic, equimolar pool were taken from previously-frozen aliquots for each library. The aliquots were either directly used in library construction, or pre-treated with T4 PNK. To perform phospho-small RNA-seq, synthetic and plasma RNA samples were pretreated with T4 polynucleotide kinase (NEB, Ipswich, MA, US) using an RNA input of 7 ul in a final volume reaction of 10 ul and following the manufacturer’s instructions. After the enzymatic treatment, biological RNA samples were purified by performing sequential washes in silica columns (Zymo, Irvine, CA, US): (i) 900 ul of buffer RWT (Qiagen, Hilden, Germany); (ii) 900 ul of buffer RPE (Qiagen, Hilden, Germany); (iii) 900 ul of ethanol 200 proof, molecular biology grade (Fisher Scientific, Waltham, MA, US) and; (iv) 900 ul of 80% ethanol.
Standard ligation-based small RNA libraries were prepared using the TruSeq small RNA kit (Illumina, San Diego, CA, US) according to the manufacturer instructions. Size selection was performed using pre-cast 6% acrylamide gels (Invitrogen, Waltham, MA, US) including all products from 140-200 bp plus any additional visible bands of greater size.

treatment_protocol: The synthetic, equimolar pools were synthezised, HPLC purified and quantified spectrophotometrically by IDT (Coralville, IA), ndwere pooled and aliquoted upon receipt in prelabeled DNA-, DNase-, RNase-, and pyrogen-free screw cap tubes with low adhesion surface and stored immediately at −80 C.


title: Sample 14

description: neurons from post-mortem human brain


title: 5 Frontal cortex of the human brain

description: Frontal cortex of the human brain

source_name: Frontal cortex of the human brain


title: Sample 13

description: neurons from post-mortem human brain


title: 4 Frontal cortex of the human brain

description: Frontal cortex of the human brain


title: B16-F10 CD133+ cells

city: Nashville

first: Chris

middle: P

last: Shidal

state: TN

address: 2525 West End Ave 6th Floor

department: Medicine

institute: Vanderbilt University Medical Center

description: miR expression data from CD133+ B16-F10 murine melanoma cells

hyb_protocol: Hybridizations were performed at 48C for 16 hours at 60 rpm in a hybridization oven per the manufacturers recommendations.

scan_protocol: Following washing and staining procedures, array microchips  were scanned using a GeneChip Scanner (Affymetrix).

data_processing:
Image data were analyzed using Affymetrix Power Tools and subsequently by Transcriptome Analysis Console (TAC, Affymetrix).
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: B16-F10 skin melanoma from C57BL/6J mouse

label_protocol: Biotin labelling and hybridizations were performed using the FlashTag Biotin HSR RNA labeling kit (Applied Biosystems) according to the manuscfacturers protocol using an input of 500 micrograms of total RNA.

growth_protocol: B16-F10 cells were grown as oncospheres in DMEM/F-12 serum free media containing 1x N-2 supplement (Gibco), 10 ng/mL epidermal growth factor (EGF), and 10 ng/mL basic fibroblast growth factor (bFGF) in low cluster 6 well plates prior to dissociation, labelling, and sorting.

extract_protocol: Triazol extractions were performed using the Qiagen miRNeasy kit and used according to the manufacturers recommendation.

treatment_protocol: Spheres were collected by centrifugation at 300g for 10 minutes. The pellet was briefly dissociated into a single cell suspension using TrypLE (Gibco) enzyme-free dissociation buffer, and cells were subsequently labelled with a PE conjugated anti-CD133 antibody. FACS was performed to collect CD133+ and CD133- samples. Cells were stored in Triazol extraction reagent at -80C until total RNA isolation was performed.

tag: cell type

value: melanotic skin melanoma

tag: cell population

value: CD133+ FACS