title: sample 17, primary tumor from ERneg BC


title: subjectSLE69_week0

status: Public on Sep 24 2018

type: SRA

city: Cambridge

first: Emma

middle: Elisabeth

last: Davenport

state: Cambridgeshire

address: Hinxton

country: United Kingdom

institute: Wellcome Sanger Institute

library_source: transcriptomic

data_processing:
We aligned reads to the reference genome using Subread
We quantified gene expression using featureCounts
We included genes with at least 10 reads (CPM>0.38) in at least 32 samples (minimum number of subjects with both unexposed and exposed RNA-seq assays in a drug group) prior to normalization.
Following quality control, we removed 4 samples as outliers (SLE103_W0,  SLE106_W0,  SLE100_W12,  SLE36_W24)
We normalized 20,253 transcripts using the trimmed mean of M-values method and the edgeR R package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with normalized expression levels presented as log2(cpm +1) for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
We extracted total RNA from blood samples using the PAXgene Blood RNA kit (Qiagen). We processed an aliquot of 500-1000 ng of each RNA with a GlobinClear-Human kit, (ThermoFisher Scientific) to remove globin mRNA.
RNA samples were converted to cDNA libraries using TruSeq RNA Sample Prep Kit v2 (Illumina)

tag: tissue

value: Whole blood

tag: timepoint

tag: ifn status

value: Low

tag: drug dose

tag: drug exposure

tag: subject age

tag: subject sex

value: Female

tag: recruitment site


title: WT H3K4me3 eSPAN repeat 3

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

library_source: genomic

data_processing:
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To obtain the nucleosome occupancy, DNA fragments from 120 to 170 bp in size determined by the paired-reads were firstly selected for calculation. The length of DNA fragments were then adjusted to half of the nucleosome size (74bp) to increase the signal-to-noise ratio. Finally, the count of adjusted DNA fragments covering each base pair in the genome were used to calculate the nucleosome occupancy.
To identify BrdU-IP-ssSeq peaks, the sequence reads of both Watson and Crick strands were merged and used to call peaks using SICER software with false discovery rate (FDR) cut-off 0.01.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: To synchronize cells at G1, alpha factor was added at cell density OD600=0.4-0.5 to achieve a final concentration of five µg/mL for yeast strains.  After three hours arrest at 25°C, the cells were released to fresh YPD medium with or without 200 mM HU.  For the histone H3 Recombination-induced Tag Exchange (RITE) experiments, yeast cells were grown overnight in YPD in the presence of hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into two fresh YPD flask (one with, the other without hygromycin B) and incubated for 32 hours (G0 state). The cells were centrifuged by 3000 rpm for 10 minutes. The cells cultured with hygromycin B were transferred to another flask containing depleted medium without hygromycin B. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich) and the cells were cultured for additional 16 hours. Subsequently, these cells were diluted 1:25 in fresh YPD media containing 200 mM HU and 400ul/ml BrdU. After incubation at 25 C for 90 minutes, samples were collected for ChIP and eSPAN.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously except that Mnase digestion was used for chromatin fragmentation in order to map nucleosomes. Briefly, the samples were incubated with 1% fresh-made formaldehyde at 25 °C for 20 min, and then quenched with 0.125M glycine for five min.  The cells wer harvested and lysed with glass beads in ChIP lysis buffer (50 mM HEPES, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate). The resulting cell and chromatin pellet was washed with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM β-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine).  Proper amounts of Mnase was added to ensure that majority of chromatin are mono- and di-nucleosomes with incubation at 37 °C for 20 min . The reacation was terminated by adding 5ul 0.5M EDTA. Further, ¼ volume 5X ChIP lysis buffer was added into dilute thedigested chromatin. The lysates was incubated in ice for 30 minutes. After clarification of lysates by centrifugation, soluble chromatin (mainly mononucleosomes) was immunoprecipitated with a specific antibody including anti-H3K4me3 antibody (ab8580), anti-H3K56ac antibody (6), anti-HA antibody (12CA5) or anti-T7 (A190-117A BETHYL)). ChIP DNA was recovered using Chelex-100. The ChIP or total DNA was denatured at 100°C for five min and was immediately transferred to ice bath for five minutes.  The DNA was diluted at least ten times with BrdU IP solution (PBS, 0.0625% Triton X-100(v/v), 6.7 g/mL Escherichia. coli tRNA, 0.67 ul/mL BrdU antibody (BD Bioscience)).  After the samples were incubated at 4°C for two hour, 20 uL protein G beads (GE Healthcare) were added.  After incubation at 4°C for another hour, the protein G beads was washed extensively. DNA were eluted using 100 uL 1XTE buffer plus 1% SDS and incubation at 65 °C for 15 min. Eluted DNA was purified using a Qiagen Mini-elute kit.
We used the ssDNA library preparation kit to prepare library (Cat no. 10096 Swift Bioscience). The ssDNA libraries were sequenced using the paired-end method by different sequencing platform over the years including Hi-seq 2000 or 2500 machine at Mayo Clinic or Columbia University.

tag: media

value: YPD+HU

tag: cell cycle stage

value: S

tag: genotype

value: wild type

tag: strains genetic background

tag: chip antibody

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: subjectSLE68_week0


title: sample 17, second tumor from ERneg BC

type: genomic

city: Amherst

first: Kathleen

last: Arcaro

state: Massachusetts

address: 240 Thatcher Road LSL1 N529, University of Massachusetts

department: Veterinary and Animal Science

institute: University of Massachusetts- Amherst

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader and standard Illumina protocols

data_processing: Illumina GenomeStudio version 1.9.0 methylation module was used to analyze the data, raw data were filtered using a detection p-value < 0.05.

label: biotin

source_name: genomic DNA from FFPE slide

label_protocol: Standard Illumina protocol

extract_protocol: DNA was purified from tumor tissue obtained from 10 μm sections of FFPE blocks. Briefly, a pathologist measured and outlined the breast tumor on an H&E stained slide to estimate the number of sections needed to purify a minimum of 500 ng of DNA. For samples exceeding 4 mm x 4 mm, a single section was sufficient. Tumor cells were collected from the sections by placing an unstained slide on top of the H&E stained slide and carefully removing cells within the parameters defined by H&E slide. Cells collected from multiple sections were combined in a single tube and DNA was purified using the BiOstic FFPE tissue DNA isolation kit (Mo Bio, Carlsbad, CA).

tag: Sex

value: female

value: breast tumor

tag: disease state

value: cancer

tag: estrogen receptor status

value: negative

tag: tumor status

value: second


title: subjectSLE67_week0

tag: tissue

value: High


title: WT H3K56ac eSPAN repeat 3

value: Anti-H3K56ac and Anti-BrdU Antibody


title: subjectSLE66_week0

tag: timepoint


title: subjectSLE65_week0

tag: ifn status

value: Placebo

value: Male


title: WT H3K56ac eSPAN repeat 2


title: subjectSLE64_week0

tag: drug dose


title: subjectSLE63_week0

tag: drug exposure


title: subjectSLE62_week0

tag: subject age


title: WT H3K4me3 ChIP-ssSeq repeat 4

value: Anti-H3K4me3 Antibody (ab8580)


title: subjectSLE61_week0

value: Whole blood

tag: subject sex


title: subjectSLE60_week0

tag: recruitment site


title: WT H3K4me3 ChIP-ssSeq repeat 3

tag: media


title: sample 16, second tumor from ERneg BC


title: subjectSLE58_week0


title: WT H3K56ac ChIP-ssSeq repeat 3

tag: cell cycle stage

value: Anti-H3K56ac antibody


title: subjectSLE57_week0

value: Female


title: sample 16, primary tumor from ERneg BC

value: primary


title: sample 15, primary tumor from ERneg BC


title: WT H3K56ac ChIP-ssSeq repeat 2

value: YPD+HU

value: S

tag: genotype


title: subjectSLE59_week0

value: Low


title: sample 14, primary tumor from ERneg BC

value: female


title: sample 13, second tumor from ERneg BC

value: breast tumor


title: subjectSLE55_week0


title: subjectSLE54_week0


title: WT BrdU-IP-ssSeq repeat 3

value: wild type

tag: strains genetic background

value: Anti-BrdU (BD BioScience, 347580)


title: sample 15, second tumor from ERneg BC

value: cancer

value: negative

value: second


title: subjectSLE56_week0

value: High


title: WT BrdU-IP-ssSeq repeat 2

tag: chip antibody


title: subjectSLE52_week0


title: sample 14, second tumor from ERneg BC

tag: Sex


title: subjectSLE51_week0


title: subjectSLE50_week0


title: subjectSLE53_week0


title: subjectSLE48_week0


title: WT input MNase-ssSeq repeat 2


title: sample 12, second tumor from ERpos BC

tag: disease state

value: positive


title: subjectSLE47_week0

value: Male


title: sample 12, primary tumor from ERpos BC

tag: estrogen receptor status


title: ctf4D without HU 40min H3K4me3 eSPAN

value: YPD

value: ctf4 deletion

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: sample 13, primary tumor from ERneg BC

tag: tumor status

value: primary


title: sample 11, second tumor from ERpos BC

tag: tissue


title: subjectSLE49_week0

value: Whole blood

tag: timepoint

value: Female


title: subjectSLE45_week0

tag: ifn status


title: subjectSLE46_week0

tag: drug dose


title: ctf4D without HU 30min H3K4me3 eSPAN

value: S


title: subjectSLE44_week0

tag: drug exposure


title: subjectSLE43_week0

value: Low

tag: subject age


title: subjectSLE42_week0

tag: subject sex


title: ctf4D without HU 40min H3K56ac eSPAN

value: Anti-H3K56ac and Anti-BrdU Antibody


title: sample 10, primary tumor from ERpos BC

value: female

value: breast tumor


title: subjectSLE41_week0

tag: recruitment site


title: subjectSLE40_week0

value: Placebo


title: subjectSLE39_week0


title: subjectSLE37_week0


title: ctf4D without HU 30min H3K56ac eSPAN

tag: media


title: sample 11, primary tumor from ERpos BC

value: cancer


title: subjectSLE36_week0


title: sample 9, primary tumor from ERpos BC


title: subjectSLE35_week0


title: subjectSLE38_week0


title: sample 9, second tumor from ERpos BC

value: second


title: ctf4D without HU 40min H3K56ac ChIP-ssSeq

tag: cell cycle stage

value: Anti-H3K56ac antibody


title: subjectSLE34_week0

value: High


title: subjectSLE33_week0


title: sample 8, second tumor from ERpos BC

value: positive


title: subjectSLE32_week0

value: Male


title: ctf4D without HU 30min H3K56ac ChIP-ssSeq

value: YPD

tag: genotype

value: ctf4 deletion


title: sample 7, second tumor from ERpos BC


title: sample 8, primary tumor from ERpos BC

value: primary


title: sample 10, second tumor from ERpos BC


title: ctf4D without HU 40min BrdU-IP-ssSeq

tag: strains genetic background

value: Anti-BrdU (BD BioScience, 347580)


title: subjectSLE29_week0

value: Whole blood


title: ctf4D without HU 30min BrdU-IP-ssSeq

value: S

tag: chip antibody


title: ctf4D without HU 40min H3K4me3 ChIP-ssSeq

value: Anti-H3K4me3 Antibody (ab8580)


title: ctf4D without HU 40min input MNase-ssSeq


title: subjectSLE25_week0

value: Female


title: subjectSLE26_week0

value: Low


title: ctf4D without HU 30min input MNase-ssSeq


title: subjectSLE24_week0


title: subjectSLE27_week0


title: subjectSLE28_week0


title: sample 5, primary tumor from ERpos BC

tag: Sex

value: female

value: breast tumor


title: subjectSLE30_week0


title: subjectSLE23_week0


title: sample 6, primary tumor from ERpos BC

tag: disease state

value: cancer


title: subjectSLE21_week0

value: Placebo


title: TF plasmid library gDNA

city: La Jolla

first: Yan

last: Wu

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description:
up-tf_dropout_counts.tsv
ctrl

data_processing:
Align mRNA fastq files to genome and generate gene expression matrices with 10X genomics cellranger 2.0.0 with default parameters
Convert genotype barcode fastq files to unaligned bam, tag each read with cell and molecule barcodes, and assign one of more genotypes to each cell
Process gDNA fastq files with MageCK with default parameters to generate fitness counts matrix
R1 is the barcode and R2 is biological. For R1, bases 1 - 16 correspond to the cell barcode and bases 17 -26 correspond to the unique molecular index (UMI).
Genome_build: hg38
Supplementary_files_format_and_content: Files ending in ".counts.tsv.gz" are counts matrices in tab separated value format.  Column headers are cell barcodes.
Supplementary_files_format_and_content: Files ending in "pheno_dict.csv" are genotype to cell dictionaries. Each line begins with the name of the genotype, followed by the cell barcodes mapped to that genotype separated by commas
Supplementary_files_format_and_content: File up-tf_functional_gene_modules.gmt corresponds to annotated gene clusters that we computed and are essential to our higher level analyses.
Supplementary_files_format_and_content: The Series-level supplementary files correspond to the aggregated data across biological samples.

organism: unidentified plasmid

source_name: DNA Array

growth_protocol: H1 hESC cells were maintained under feeder-free conditions in mTesR1 medium, in growth-factor reduced Matrigel coated tissue coated plates. Cellls were dissociated and passaged using Versene

extract_protocol:
Cells were dissociated to single cell suspensions using Accutase, resuspended in PBS-BSA and loaded onto the 10X Genomics Chromium system as per manufacturer's instructions. Remaining cells were pelleted, lysed, and genomic DNA was extracted for fitness effect quantification
Single cell libraries were constructed with the Single Cell 3' Reagent Kit v2 (10X genomics). TF barcodes were amplified from full length cDNA for genotype deconvolution using primers

treatment_protocol: H1 cells were seeded into 10 cm dishes and transduced with lentivirus added to fresh media mTeSR containing polybrene. On Day 1, medium was replaced with appropriate fresh medium. Hygromycin selection was started on Day 2

tag: culture media

tag: cell sorting

tag: estimated moi


title: Tagging swithching system mcm2-3a T7 eSPAN

value: YPD+HU

value: mcm2-3a mutant

value: Anti-T7 and Anti-BrdU Antibody


title: subjectSLE20_week0

tag: tissue

tag: timepoint


title: sample 4, primary tumor from ERpos BC

tag: estrogen receptor status

value: positive

tag: tumor status


title: ctf4D without HU 30min H3K4me3 ChIP-ssSeq

value: YPD


title: sample 5, second tumor from ERpos BC

value: second


title: subjectSLE19_week0

tag: ifn status

value: High

tag: drug dose

tag: drug exposure

tag: subject age

value: Male


title: mcm2-3a H3K4me3 eSPAN repeat 2

tag: media

tag: cell cycle stage

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: subjectSLE7_week0

value: Whole blood

tag: subject sex

tag: recruitment site


title: subjectSLE19_week12


title: Tagging swithching system mcm2-3a H3K56ac eSPAN

value: S

tag: genotype

tag: strains genetic background

tag: chip antibody

value: Anti-H3K56ac and Anti-BrdU Antibody


title: sample 3, second tumor from ERpos BC

tag: Sex

tag: disease state


title: sample 4, second tumor from ERpos BC

tag: tissue


title: sample 6, second tumor from ERpos BC


title: mcm2-3a H3K4me3 eSPAN repeat 1


title: Tagging swithching system mcm2-3a HA eSPAN

value: Anti-HA and Anti-BrdU Antibody


title: subjectSLE18_week0

tag: timepoint

value: Female


title: subjectSLE17_week0


title: Tagging swithching system mcm2-3a HA ChIP-ssSeq

value: Anti-HA antibody (12CA5)


title: subjectSLE15_week0


title: subjectSLE16_week0

value: Low


title: sample 3, primary tumor from ERpos BC

value: female

value: breast tumor

value: cancer

tag: estrogen receptor status

value: primary


title: sample 7, primary tumor from ERpos BC

value: positive

tag: tumor status


title: sample 2, primary tumor from ERpos BC


title: mcm2-3a H3K4me3 ChIP-ssSeq repeat 2

value: YPD+HU

value: mcm2-3a mutant

value: Anti-H3K4me3 Antibody (ab8580)


title: sample 2, second tumor from ERpos BC

value: second


title: subjectSLE13_week0

tag: ifn status


title: subjectSLE11_week0

value: High

tag: drug dose


title: Tagging swithching system mcm2-3a T7 ChIP-ssSeq

value: Anti-T7 (A190-117A BETHYL)


title: Tagging swithching system mcm2-3a H3K4me3 ChIP-ssSeq

value: S


title: mcm2-3a H3K4me3 ChIP-ssSeq repeat 1


title: sample 1, second tumor from ERpos BC


title: subjectSLE12_week0

value: Whole blood

tag: drug exposure


title: mcm2-3a H3K56ac ChIP-ssSeq repeat 1

value: Anti-H3K56ac antibody


title: mcm2-3a H3K56ac eSPAN repeat 1

value: Anti-H3K56ac and Anti-BrdU Antibody


title: Tagging swithching system mcm2-3a H3K56ac ChIP-ssSeq


title: subjectSLE14_week0

tag: subject age

value: Female


title: subjectSLE9_week0

value: Low


title: WT input MNase-ssSeq repeat 3

tag: media

value: wild type


title: subjectSLE8_week0

value: Placebo


title: Tagging swithching system mcm2-3a BrdU-IP-ssSeq

tag: cell cycle stage

value: Anti-BrdU (BD BioScience, 347580)


title: subjectSLE10_week0

tag: subject sex


title: sample 1, primary tumor from ERpos BC

value: female

value: breast tumor

value: cancer

value: primary


title: Tagging swithching system mcm2-3a input MNase-ssSeq

value: YPD+HU

value: mcm2-3a mutant


title: subjectSLE6_week0

tag: recruitment site


title: mcm2-3a BrdU-IP-ssSeq repeat 1

tag: genotype


title: subjectSLE5_week0

value: Male


title: subjectSLE4_week0

value: High


title: mcm2-3a input MNase-ssSeq repeat 2

value: S

tag: strains genetic background


title: Tagging swithching system WT HA eSPAN

tag: chip antibody

value: Anti-HA and Anti-BrdU Antibody


title: subjectSLE2_week0

value: Whole blood


title: subjectSLE1_week0


title: Tagging swithching system WT T7 eSPAN

value: Anti-T7 and Anti-BrdU Antibody


title: mcm2-3a BrdU-IP-ssSeq repeat 2


title: Tagging swithching system WT H3K4me3 eSPAN

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: WT H3K4me3 eSPAN repeat 2


title: WT H3K56ac eSPAN repeat 1

value: Anti-H3K56ac and Anti-BrdU Antibody


title: WT H3K4me3 ChIP-ssSeq repeat 2

value: wild type

value: Anti-H3K4me3 Antibody (ab8580)


title: Tagging swithching system WT T7 ChIP-ssSeq

value: Anti-T7 (A190-117A BETHYL)


title: WT H3K4me3 eSPAN repeat 1


title: Tagging swithching system WT H3K4me3 ChIP-ssSeq


title: Tagging swithching system WT H3K56ac ChIP-ssSeq

value: Anti-H3K56ac antibody


title: subjectSLE7_week12

value: Female


title: subjectSLE31_week0

value: Low


title: WT H3K4me3 ChIP-ssSeq repeat 1


title: Tagging swithching system WT BrdU-IP-ssSeq

value: Anti-BrdU (BD BioScience, 347580)


title: WT H3K56ac ChIP-ssSeq repeat 1

value: YPD+HU


title: GFP3

city: boston

first: Yuxuan

last: Guo

state: MA

address: 320 Longwood Ave, Enders 1250,

department: Department of Cardiology

institute: Boston childrens hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were aligned to mm10 whole genome by STAR 2.5.3a default setting
Read counts were calculated by featureCounts of Subread 1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: Gene reads counts matrix generated by FeatureCounts

molecule: polyA RNA

organism: Mus musculus

source_name: cardiomyocyte

extract_protocol:
total RNA was extracted from FACS sorted cells using PureLink™ RNA Micro Scale Kit (ThermoFisher)
10ng total RNA was reverse transcribed, cDNA further amplified by 8 PCR cycles using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). 500pg cDNA was next used to generate RNA-seq libraries using Nextera XT DNA Library Preparation Kit (Illumina)

treatment_protocol: 5×10^8 vg/g AAV9-cTNT-SRF-2A-GFP or AAV-GFP virus was injected into P1. Cells were collected at P14through retrograde collagenase perfusion followed by fluorescence activated cell sorting by GFP expression

tag: group

value: AAV9-cTNT-GFP control

value: wildtype

tag: age

value: postnatal day 14

tag: aav injection time

value: postnatal day 1


title: GFP2


title: GFP1


title: Tagging swithching system WT input MNase-ssSeq

value: S


title: subjectSLE3_week0

tag: tissue

value: Whole blood

tag: timepoint

value: Placebo


title: OE3


title: mcm2-3a input MNase-ssSeq repeat 1

value: mcm2-3a mutant


title: WT BrdU-IP-ssSeq repeat 4


title: Tagging swithching system WT H3K56ac eSPAN

value: Anti-H3K56ac and Anti-BrdU Antibody


title: OE1


title: ctf4D  sonication ChIP-ssSeq

value: ctf4 deletion

value: Anti-Ctf4 antibody (Karim Labib)


title: Tagging swithching system mcm2-3a H3K4me3 eSPAN

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: subjectSLE22_week0

value: High


title: Adult_SrfChIP_input

data_processing:
Basecalls performed using CASAVA version 1.8
Aligned fastq file to mm10 genome using bowtie version 1.1.1 using parameter -m 1
Samtools/1.2 for processing sam/bam files
macs2/2.1.0.20140616 for calling peaks(.narrowpeak) and making bedgraph files (.bdg) using parameters: -B , -p 1e-5,  using input files as background
UCSC utility bedGraphToBigWig used to convert .bdg files to .bw
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Heart ventricles were homogenized and fixed by 1% formaldehyde, chromatin isolated and sheared by sonication
SRF bound DNA was pulled down onto Streptavidin beads. Purified DNA released from beads was converted into sequencing libraries by Kapa Hyper Library Kit

tag: genotype/variation

value: Srf-fbio/+;Rosa-birA/+

value: postnatal day 42

value: heart ventricle

tag: chip method

value: strepavidin pull-down of biotinylated SRF


title: Adult_SrfChIP_rep2


title: WT input MNase-ssSeq repeat 4

value: YPD+HU

value: wild type


title: Adult_SrfChIP_rep1


title: P14_SrfChIP_rep2_input

value: postnatal day 14


title: ctf4D  sonication input ssSeq


title: P14_SrfChIP_rep2


title: P14_SrfChIP_rep1_input


title: P14_SrfChIP_rep1


title: ctf4D  sonication BrdU-IP-ssSeq


title: ctf4-4E Ctf4 ChIP-ssSeq repeat 1

value: ctf4-4E mutant


title: spindleTransfer-2C-WW-rep1

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
RRBS sequencing reads were mapped to the mouse genome (mm9) using Bismark v0.10.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics). The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
RNA-Seq data were mapped by TopHat and quantitified by Cufflinks
Genome_build: mm9 / hg19
Supplementary_files_format_and_content: CpG methylation levels were generated with Bismark, and only sites with depth greater than 5 were kept. Methylation levels of 100-bp tiles along the genome (mm9) were calculated as total C / total C+T within each tile. RNA-seq samples includes FPKM values in a text file.

source_name: 2-cell embryos from oocytes (WT spindle transferred to WT cytoplasm) and WT DBA/2 sperm

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
RRBS for oocyte and PGC samples: For oocytes, before MspI digestion, 5 µl of lysis buffer (20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, 1 mg/ml QIAGEN Protease) was directly added to the frozen samples (in < 1µl PBS) followed by 3 hours of incubation at 50 ℃ and 30 minutes of inactivation at 75 ℃. Then to the same tube, 13 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) and 0.5pg unmethylated λ DNA (Thermo Scientific) was added followed by 3 hours of incubation at 37 ℃. For PGCs, the purified genomic DNA was directly digested with MspI in an 18 µl total volume. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 0.2 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 20 minutes of incubation at 30 ℃, 20 min of incubation at 37 ℃ and 15 minutes of inactivation at 80 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5 mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where -s- indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Bisulfite Conversion Kit (QIAGEN) with modified program: 95 C for 5 min, 60 C for 25 min, 95C for 5 min, 60C for 85 min, 95C for 5 min, 60C for 175 min, 3x (95 C for 5 min, 60 C for 90 min). After clean up, the optimal, minimum PCR cycle number required to generate the final libraries was determined using diagnostic PCRs. Remaining bisulfite converted products were PCR amplified with NEBNext Multiplex Oligos (NEB) and KAPA HiFi Hotstart Uracil+ ReadyMix (Kapa Biosystems). Final libraries were obtained by size selection of 150-500 bp DNA fragments using AMPure XP beads (Beckman Coulter).
RRBS for sperm: 100ng genomic DNA was digested with 10 units of MspI in a 18 µl total volume at 37 ℃ overnight. The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment exo- , 0.2 µl of 10x Buffer Tango, 5 mM dATP, and 0.5 mM each of dGTP and dCTP, followed by 20 minutes of incubation at 30 ℃, 20min of incubation at 37 ℃ and 15 minutes of inactivation at 80 ℃. Adaptor ligation was then performed at 20 ℃ for 15min using NEBNext Ultra Ligation Module (NEB) by adding 15 µl of ligase master mix, 1 µl of ligation enhancer, 2.5 µl of 1.5 µM methylated custom adaptor and ddH2O to a total volume of 80 µl. The reaction mix was then size selected of 150-500 bp DNA fragments using AMPure XP beads. The size-selected sample was then subjected to EpiTect Bisulfite Conversion Kit (QIAGEN) with modified program: 95 C for 5 min, 60 C for 25 min, 95C for 5 min, 60C for 85 min, 95C for 5 min, 60C for 175 min, 3x (95 C for 5 min, 60 C for 90 min). After clean up, the optimal, minimum PCR cycle number required to generate the final libraries was determined using diagnostic PCRs. Remaining bisulfite converted products were PCR amplified with NEBNext Multiplex Oligos (NEB) and KAPA HiFi Hotstart Uracil+ ReadyMix (Kapa Biosystems). Final libraries were obtained by AMPure XP beads clean-up of the PCR product.
RNA-seq for oocyte samples: cDNA libraries were synthesized and amplified using SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech) following manufacturer’s instructions. The purified cDNA was fragmented with Covaris M220 sonicator, and then subjected to Illumina sequencing library construction with KAPA Hyper Prep kits (Kapa Biosystems) following manufacturer’s instructions.

tag: strain background

tag: cell line

value: primary cells isolated from mouse

tag: cell type

value: 2-cell embryo

value: WT/WT, WT

value: embryo

tag: developmental stage

value: 2-cell stage


title: spindleTransfer-2C-WW-rep2


title: P90_KO_rep3

description: Adult.txt

treatment_protocol: 5×10^8 vg/g AAV9-cTNT-Cre virus was injected into P1 or P60 animals. Cells were collected at P14 or P90 respectively through retrograde collagenase perfusion followed by fluorescence activated cell sorting using Cre-activated fluorescence protein reporters

value: Srf-flox/flox

value: postnatal day 90

value: postnatal day 60


title: P90_KO_rep2

description: Adult.txt


title: P90_Ctrl_rep3

description: Adult.txt

value: Srf-flox/+


title: OE2

value: wildtype

value: postnatal day 1


title: spindleTransfer-2C-WK-rep2

source_name: 2-cell embryos from oocytes (WT spindle transferred to KO cytoplasm) and WT DBA/2 sperm

value: WT/stella-KO, WT


title: ctf4-4E sonication BrdU-IP-ssSeq repeat 2

tag: media

tag: cell cycle stage

value: S

value: Anti-Ctf4 antibody (Karim Labib)


title: WT BrdU-IP-ssSeq repeat 1

value: YPD+HU

value: wild type

value: Anti-BrdU (BD BioScience, 347580)


title: P90_Ctrl_rep2

description: Adult.txt


title: spindleTransfer-2C-WK-rep1

value: primary cells isolated from mouse


title: ctf4-4E sonication BrdU-IP-ssSeq repeat 1

value: ctf4-4E mutant


title: P90_Ctrl_rep1

description: Adult.txt


title: ctf4-4E Ctf4 ChIP-ssSeq repeat 2


title: spindleTransfer-2C-KW-rep2

source_name: 2-cell embryos from oocytes (KO spindle transferred to WT cytoplasm) and WT DBA/2 sperm

value: 2-cell embryo

value: stella-KO/WT, WT


title: WT input MNase-ssSeq repeat 1


title: ctf4-4E sonication input ssSeq repeat 2


title: P14_KO_rep2

description: Neonatal.txt

value: postnatal day 14


title: ctf4-4E sonication input ssSeq repeat 1


title: pol1-4A Ctf4 eSPAN repeat 2

value: pol1-4A mutant


title: P14_KO_rep1

description: Neonatal.txt

value: Srf-flox/flox


title: P14_Ctrl_rep3

description: Neonatal.txt


title: spindleTransfer-2C-KW-rep1

value: embryo

value: 2-cell stage


title: spindleTransfer-2C-KK-rep2

source_name: 2-cell embryos from oocytes (KO spindle transferred to KO cytoplasm) and WT DBA/2 sperm

value: stella-KO/stella-KO, WT


title: P14_Ctrl_rep2

description: Neonatal.txt

value: Srf-flox/+

value: postnatal day 1


title: P90_KO_rep1

description: Adult.txt

value: postnatal day 90

value: postnatal day 60


title: spindleTransfer-2C-KK-rep1


title: P14_Ctrl_rep1

description: Neonatal.txt


title: sKO-pPN-RRBS.rep1

source_name: Paternal pronucleus from Stella-/- mouse

value: Paternal pronucleus

value: stella-/-

value: zygote

value: PN4-PN5 stage zygotes 11 hours post fertilization (hpf)


title: sKO-mPN-RRBS.rep1

source_name: Maternal pronucleus from Stella-/- mouse

value: primary cells isolated from mouse

value: Maternal pronucleus


title: P14_KO_rep3

description: Neonatal.txt


title: sKO-D20-oocyte-RRBS.rep2

source_name: Dpp 20 oocytes from Stella-/- mouse

value: growing oocyte

value: ovary

value: day 20 postpartum


title: PICMI2

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

description: Day 6 expanded blastocysts were cultured on mouse embryonic fibroblasts and manual dissection was performed on the PICMI outgrowths between post plating day 6 and day 10

data_processing:
Reads were trimmed using cutadapt versin 1.11 to remove the Illumina adaptor sequences
The reads were mapped against the Homo sapiens GRCh37.74 reference genome using CLC genomics workbench version 9.0.1 (CLC)
Count tables were made by counting the reads that mapped against the genes defined by the Ensembl GRCh37.74 Gene Transfer Format file (GTF) and exported from CLC
Genome_build: Homo sapines GRCh37.74
Supplementary_files_format_and_content: comma separated values files including Gene counts, Gene ID and other gene information

source_name: post ICM intermediate, P0

extract_protocol:
The samples were processed directly using the SMARTer Ultra Low Input RNA for Illumina sequencing kit (Clontech Laboratories, Mountain View, CA, USA) to ensure minimum loss of cells. According to the manufacturer's suggested protocol, samples were collected in 2µl of DMEM-F12 + Glutamax (Invitrogen) with 25% bovine serum albumin (Sigma) and transferred to 5µl of pre-prepared reaction buffer. A final volume of 9µl was set up using nuclease-free water. The sample reaction mixture was then mixed with the first primer (3' SMART CDS primer II A) for first strand synthesis. This reaction mixture was placed in a thermocycler for 3 minutes and then incubated on ice. From this step, the first strand cDNA synthesis was set up directly using the SMARTScribe Reverse Transcriptase. Once completed, the first-strand cDNA was purified using SPRI Ampure beads, followed by double stranded (ds) cDNA amplification by long distance PCR. The amplified ds cDNA was then further purified using the Ampure beads.
cDNA was fragmented in the 200-500bp range on a Covaris S2 Focused-ultrasonicator (Brighton, UK), according to the SMARTer Ultra Low Input RNA for Illumina sequencing protocol. A sequencing library was made using the Low Input Library Prep Kit (Clontech Laboratories, Mountain View, CA, USA).

value: pluripotent cell, post ICM plating

tag: Stage

value: peri-implantation stage


title: PICMI4


title: PICMI1


title: ICM3

description: Day 3, frozen-thawed human embryos were cultured up to day 5 blastocyst stage and only good quality blastocysts were subjected to laser-assisted micromanipulation for ICM collection

source_name: day 5 late blastocyst

value: human embryonic preimplantation cells

value: pre-implantation stage


title: ICM2


title: sKO-D1.MII.RRBS.rep1

source_name: MII oocytes from Stella-KO/Dnmt1-KO mouse

value: MII oocyte

value: stella-/-, Dnmt1-/-

value: week 7 postpartum


title: pol1-4A Ctf4 ChIP-ssSeq repeat 2

value: YPD+HU

value: S

tag: genotype

value: pol1-4A mutant

value: Anti-Ctf4 antibody (Karim Labib)


title: pol1-4A Ctf4 eSPAN repeat 1

tag: strains genetic background


title: pol1-4A Ctf4 ChIP-ssSeq repeat 4

tag: chip antibody


title: hESC3

description: Primed hESCs (XX) were maintained in feeder-free culture conditions on Matrigel for two passages and approximately 50 cells were collected

source_name: pluripotent stem cells

value: Pluripotent cell

value: post-implantation stage


title: sKO-3A.MII.RRBS.rep1

source_name: MII oocytes from Stella-KO/Dnmt3a-KO mouse

value: primary cells isolated from mouse

value: stella-/-, Dnmt3a-/-


title: pol1-4A sonication BrdU-IP-ssSeq repeat 3

value: Anti-BrdU (BD BioScience, 347580)


title: ICM1


title: pol1-4A Ctf4 ChIP-ssSeq repeat 1


title: pol1-4A sonication BrdU-IP-ssSeq repeat 1


title: sKO-2C-RNA-rep1

source_name: 2-cell embryos derived from Stella-KO oocytes(C57BL/6) and WT sperm (DBA/2)

value: 2-cell embryo

value: stella-/-, WT

value: embryo

value: 2-cell stage


title: hESC2


title: pol1-4A sonication input ssSeq repeat 2

source_name: whole cell


title: sHet-UKO.MII.RRBS.rep1

source_name: MII oocytes from Stella-Het/Uhrf1-KO mouse

value: stella+/-, Uhrf1-/-

value: ovary


title: pol1-4A sonication input ssSeq repeat 1


title: sKO-UKO.MII.RRBS.rep1

source_name: MII oocytes from Stella-KO/Uhrf1-KO mouse

value: MII oocyte

value: stella-/-, Uhrf1-/-


title: pol1-4A Ctf4 ChIP-ssSeq repeat 3

value: YPD+HU


title: hESC1


title: sHet-pPN-RRBS.rep1

source_name: Paternal pronucleus from Stella+/- mouse

value: Paternal pronucleus

value: stella+/-

value: zygote

value: PN4-PN5 stage zygotes 11 hours post fertilization (hpf)


title: WT Ctf4 eSPAN repeat 2

value: S

value: wild type

value: Anti-Ctf4 antibody (Karim Labib)


title: sHet-mPN-RRBS.rep1

source_name: Maternal pronucleus from Stella+/- mouse

value: primary cells isolated from mouse

value: Maternal pronucleus


title: pol1-4A sonication BrdU-IP-ssSeq repeat 2

value: pol1-4A mutant

value: Anti-BrdU (BD BioScience, 347580)


title: sKO-2C-RNA-rep2

value: 2-cell embryo

value: stella-/-, WT

value: embryo

value: 2-cell stage


title: pol1-4A sonication input ssSeq repeat 3


title: sHet-D20-oocyte-RRBS.rep2

source_name: Dpp 20 oocytes from Stella+/- mouse

value: growing oocyte

value: ovary

value: day 20 postpartum


title: WT Ctf4 ChIP-ssSeq repeat 4

value: YPD+HU


title: WT Ctf4 eSPAN repeat 1


title: sHet-D1.MII.RRBS.rep1

source_name: MII oocytes from Stella-Het/Dnmt1-KO mouse

value: MII oocyte

value: stella+/-, Dnmt1-/-

value: week 7 postpartum


title: sHet-3A.MII.RRBS.rep1

source_name: MII oocytes from Stella-Het/Dnmt3a-KO mouse

value: stella+/-, Dnmt3a-/-


title: WT Ctf4 ChIP-ssSeq repeat 3

value: S

value: wild type

value: Anti-Ctf4 antibody (Karim Labib)


title: WT Ctf4 ChIP-ssSeq repeat 1


title: WT sonication BrdU-IP-ssSeq repeat 3


title: koMII.RNAseq.rep2

source_name: MII oocytes from Stella-/- mouse

value: primary cells isolated from mouse

value: stella-/-


title: WT sonication BrdU-IP-ssSeq repeat 2

value: Anti-BrdU (BD BioScience, 347580)


title: WT Ctf4 ChIP-ssSeq repeat 2


title: 15_CCGTCC_L004/L007

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

description:
Replicate si-hnRNPR-03
15

data_processing:
HiSeq Control Software v2.0.12.0, Basecalls performed with RTA v1.17.21.3
Reads were aligned to the human reference (GRCh38) using BWA-MEM (bwa-0.7.12) with standard parameters.
Only uniquely aligned reads were used for expression profiling
Gene expression was measured based on annotation GRCh38.ensembl_genes_77_all_exons using featureCounts (Subread package 1.4.6).
Raw read counts were converted to CPM values using TMM normalization (edgeR package)
Differential expression analysis was performed using the edgeR package. Features had to have a counts-per-million value of more than 1 in at least 3 samples or were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: File *.profiling-table.txt contains per line: Accession of featue, length of feature, length of exon-covered region, short description, raw read counts per sample, CPM values per sample
Supplementary_files_format_and_content: Files *.DE.tsv contain per line: Accession of featue, short description, log2 fold-change, log2 average CPM value, PValue, FDR

growth_protocol: DMEM+FBS10%+Pen/Strep 1%

extract_protocol:
RNA was obtained using Eurogold Trifast (Euroclone, Milan, Italy), following the manufacturer’s instructions.
The RNA sequencing was performed by Eurofins (https://www.eurofinsgenomics.eu/). RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human neuroblastoma SH-SY-5Y cells were cultured in DMEM–Glutamax-I (Gibco-BRL, Life Technologies Inc., Frederick, MD, USA) supplemented with 10% fetal bovine serum (Gibco-BRL, Life Technologies Inc., Frederick, MD, USA) and Antibiotic-Antimycotic-stabilized suspension (SigmaAldrich, St. Louis, MO, USA) at 37°C incubator with humidified atmosphere of 5% CO2. The siRNA sense sequences used for silencing the different target proteins were the following: luciferase (control): uaaggcuaugaagagauac, hnRNPQ: agacagugaucucucucau, hnRNPR: cauuugggaucuacgucuu. After twice gene silencing by Hyperfectamine (Qiagen Inc, Gaithersburg, Maryland), cells were collected and divided into two aliquots; one half for western blot and the other half for RT–PCR analysis.

value: neuroblastoma

tag: sirna

value: anti-hnRNPR


title: 5_ACAGTG_L004/L007

description:
Replicate si-hnRNPR-01
5


title: 14_ATGTCA_L004/L007

description:
Replicate si-hnRNPQ-03
14

value: anti-hnRNPQ


title: sHet-2C-RNA-rep1

source_name: 2-cell embryos derived from Stella+/- oocytes(C57BL/6) and WT sperm (DBA/2)

value: 2-cell embryo

value: stella+/-, WT

value: embryo

value: 2-cell stage


title: 9_TAGCTT_L004/L007

description:
Replicate si-hnRNPQ-02
9


title: WT sonication BrdU-IP-ssSeq repeat 1

value: YPD+HU


title: ko2C.RRBS.rep1

source_name: 2-cell embryos derived from Stella-/- oocytes(C57BL/6) and WT sperm (DBA/2)

value: stella-/-, WT


title: 4_TGACCA_L004/L007

description:
Replicate si-hnRNPQ-01
4


title: 10_GGCTAC_L004/L007

description:
Replicate si-hnRNPR-02
10


title: koMII.RNAseq.rep1

value: MII oocyte

value: ovary

value: week 7 postpartum


title: Hnf4a mutant kindey rep2

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
sequences (fastq files) were aligned to mm9 using Tophat (v2.0.11) and Bowtie (v1.0.0) with parameters --library-type fr-unstranded -p 3 --no-coverage-search.
BAM files were further processed for sorting and duplicate removal using Samtools (v0.1.19)
FPKM were calculated using cufflinks (v2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Kidney

extract_protocol:
Total RNA was extracted from mouse embryonic kidneys using Qiagen RNeasy Micro (Qiagen 74004). Afterwards, mRNA was isolated from total RNA using  NEBNext® Poly(A) mRNA Magnetic Isolation Module, 24 rxns (NEB, E7490)
Sequencing libraries were generated using ThruPLEX DNA-seq 12S (48) Kit (Rubicon Genomics, Ann Arbor, MI)

tag: strain

value: mixed

value: Kidney

value: Hnf4a c/c ; Six2GFPcre


title: WT sonication input ssSeq repeat 3

value: S

value: wild type


title: Hnf4a mutant kindey rep1


title: hetMII.RNAseq.rep2

source_name: MII oocytes from Stella+/- mouse

value: primary cells isolated from mouse

value: stella+/-


title: Control rep2

value: Hnf4a c/+ ; Six2GFPcre


title: WT sonication input ssSeq repeat 2


title: sHet-2C-RNA-rep2

value: 2-cell embryo


title: hetMII.RNAseq.rep1


title: Control rep1


title: 6_GCCAAT_L004/L007

description:
Replicate siLUC-02
6

value: neuroblastoma

value: anti-Luciferase


title: 11_CTTGTA_L004/L007

description:
Replicate siLUC-03
11


title: 1_ATCACG_L004/L007

description:
Replicate siLUC-01
1


title: WT sonication input ssSeq repeat 1


title: het2C.RRBS.rep1

value: stella+/-, WT

value: embryo

value: 2-cell stage


title: Ca9-22-siDLEU1

status: Public on Sep 23 2018

type: RNA

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: Ca9-22 with DLEU1 siRNA

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: OSCC cell lines (HSC-3, KON and Ca9-22) were cultured in RPMI1640 supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: OSCC cell lines (HSC-3, KON and Ca9-22) were transfected with a control siRNA (Sigma-Aldrich) or a siRNA targeting DLEU1 (Sigma-Aldrich) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h.

tag: cell typeline

value: oral squamous cell carcinoma cells


title: Ca9-22-siCtrl

description: Ca9-22 with control siRNA

value: control


title: KMS12PE-12days-SGC0946-2

description: KMS-12PE treated with SGC0946 for 12 days replicate2

growth_protocol: MM cell lines (RPMI-8226, MM.1S and KMS-12PE) were cultured in RPMI1640 supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: MM cell lines were treated with SGC0946 (Sigma-Aldrich) for 6 days (RPMI-8226 and MM.1S) or 12 days (KMS-12PE).

tag: drug

tag: time point

value: 12 days


title: KMS12PE-12days-SGC0946-1

description: KMS-12PE treated with SGC0946 for 12 days replicate1


title: MM1S-6days-SGC0946-2

description: MM.1S treated with SGC0946 for 6 days replicate2

value: 6 days


title: KON-siCtrl

description: KON with control siRNA

source_name: KON

value: KON


title: HSC-3-siDLEU1

description: HSC-3 with DLEU1 siRNA


title: KON-siDLEU1

description: KON with DLEU1 siRNA


title: HLF miR-199a-3p

description: Gene expression in HLF cells transfected with a miR-199a-3p mimic

source_name: HLF cells with miR-199a-3p mimic

growth_protocol: HLE and HLF cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Thermo Fisher Scientific).

treatment_protocol: HLE and HLF cells (5.0E+5 cells in 6-well plate) were transfected with 30 pmol of a mirVana miR-196a-3p mimic (Thermo Fisher Scientific) or a mirVana miRNA mimic Negative Control #1 (Thermo Fisher Scientific) using a Lipofectamine RNAiMAX according to manufacturer's instruction. Seventy-two hours after transfection, total RNA was extracted.

tag: tissue

value: hepatocellular carcinoma (HCC)

value: HLF

tag: miRNA


title: KMS12PE-12days-DMSO-2

description: KMS-12PE treated with DMSO for 12 days replicate2

value: DMSO


title: HSC-3-siCtrl

description: HSC-3 with control siRNA


title: KMS12PE-12days-DMSO-1

description: KMS-12PE treated with DMSO for 12 days replicate1


title: HLF control

description: Gene expression in HLF cells transfected with a miRNA mimic negative control

source_name: HLF cells with negative control

value: negative control


title: HLE miR-199a-3p

description: Gene expression in HLE cells transfected with a miR-199a-3p mimic

source_name: HLE cells with miR-199a-3p mimic

value: HLE


title: RPMI8226-6days-SGC0946-2

description: RPMI-8226 treated with SGC0946 for 6 days replicate2


title: HLE control

description: Gene expression in HLE cells transfected with a miRNA mimic negative control

source_name: HLE cells with negative control


title: MM1S-6days-DMSO-1

description: MM.1S treated with DMSO for 6 days replicate1


title: MM1S-6days-DMSO-2

description: MM.1S treated with DMSO for 6 days replicate2


title: Nomal4

description:
Normal liver specimen 4
miRNA expression in normal liver

source_name: Normal liver-4

label_protocol: Total RNA (100 ng) was labeled using a miRNA Labeling Reagent & Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

tag: group

value: Normal group

value: Normal liver

tag: time of sampling

value: No treatment


title: HCC10

description:
HCC specimen 10
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-10

value: HCC group

value: Post NA treatment


title: RPMI8226-6days-DMSO-1

description: RPMI-8226 treated with DMSO for 6 days replicate1

tag: cell line


title: Nomal3

description:
Normal liver specimen 3
miRNA expression in normal liver

source_name: Normal liver-3


title: RPMI8226-6days-DMSO-2

description: RPMI-8226 treated with DMSO for 6 days replicate2


title: Nomal2

description:
Normal liver specimen 2
miRNA expression in normal liver

source_name: Normal liver-2


title: Nomal1

description:
Normal liver specimen 1
miRNA expression in normal liver

source_name: Normal liver-1


title: MM1S-6days-SGC0946-1

description: MM.1S treated with SGC0946 for 6 days replicate1


title: HCC9

description:
HCC specimen 9
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-9


title: RPMI8226-6days-SGC0946-1

description: RPMI-8226 treated with SGC0946 for 6 days replicate1


title: HCC7

description:
HCC specimen 7
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-7


title: HCC5

description:
HCC specimen 5
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-5


title: CHB19

description:
CHB specimen 19
miRNA expression in CHB before NA treatment

source_name: HCC group-pre-3

value: Chronic hepatitis B (CHB)

value: Pre NA treatment


title: HCC2

description:
HCC specimen 2
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-2


title: CHB12

description:
CHB specimen 12
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-4

value: non-HCC group


title: CHB28

description:
CHB specimen 28
miRNA expression in CHB after NA treatment

source_name: HCC group-post-9


title: HCC4

description:
HCC specimen 4
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-4


title: HCC1

description:
HCC specimen 1
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-1


title: CHB24

description:
CHB specimen 24
miRNA expression in CHB after NA treatment

source_name: HCC group-post-5


title: HCC3

description:
HCC specimen 3
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-3


title: CHB25

description:
CHB specimen 25
miRNA expression in CHB after NA treatment

source_name: HCC group-post-6


title: CHB17

description:
CHB specimen 17
miRNA expression in CHB before NA treatment

source_name: HCC group-pre-1


title: CHB18

description:
CHB specimen 18
miRNA expression in CHB before NA treatment

source_name: HCC group-pre-2


title: CHB23

description:
CHB specimen 23
miRNA expression in CHB after NA treatment

source_name: HCC group-post-4


title: CHB27

description:
CHB specimen 27
miRNA expression in CHB after NA treatment

source_name: HCC group-post-8


title: CHB11

description:
CHB specimen 11
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-3


title: HCC8

description:
HCC specimen 8
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-8


title: HCC6

description:
HCC specimen 6
miRNA expression in HCC after NA treatment

source_name: HCC group-post-tumor-6


title: CHB21

description:
CHB specimen 21
miRNA expression in CHB after NA treatment

source_name: HCC group-post-2


title: CHB16

description:
CHB specimen 16
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-8


title: CHB14

description:
CHB specimen 14
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-6


title: CHB15

description:
CHB specimen 15
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-7


title: CHB20

description:
CHB specimen 20
miRNA expression in CHB after NA treatment

source_name: HCC group-post-1


title: CHB13

description:
CHB specimen 13
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-5


title: CHB10

description:
CHB specimen 10
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-2


title: CHB22

description:
CHB specimen 22
miRNA expression in CHB after NA treatment

source_name: HCC group-post-3


title: CHB26

description:
CHB specimen 26
miRNA expression in CHB after NA treatment

source_name: HCC group-post-7


title: KO_TAM_15

city: Toronto

first: James

last: Dowling

state: Ontario

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

data_processing:
 base calling was done using bcl2fastq2 v2.17
Alignment was carried out using STAR ver. 2.5.0c
RPKM was calculated using cufflinks ver2.2.1
RNAseq data were with the RNAseq pipeline in GenPipes ver 2.2.0 (https://bitbucket.org/mugqic/genpipes)
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKM or counts

source_name: KO_TAM_Quadriceps Muscle

extract_protocol:
Quadriceps muscle was removed, flash frozen on dry ice, and RNA was harvested using the Qiagen total RNA-seq extraction kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All drug treatments in this study were conducted from 21 days of age until 36 days of age or until animals reached end point (defined as lack of movement, significant weight loss, or hindlimb paralysis). Body weight and food consumption were monitored three times weekly. Tamoxifen-citrate mixture at 40 mg/kg (high-dose) was incorporated to the standard rodent diet premixed with ~5% sucrose as a palatability enhancer (Harlan Laboratories Teklad Diets).

tag: strain background

tag: age

value: post natal day 36

tag: genotype/variation

tag: treatment

value: 40mg/kg tamoxifen/day

value: Quadriceps Muscle


title: KO_TAM_16


title: ILC2_RNA

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

institute: Chiba University

description: Splenic ILC2 cells were culture under  conditions (10 U/ml IL-7, 10 ng/ml IL-25, 10ng/ml IL-33) for 5 days in vitro.

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Five-day cultured ILC2 cells generated from primary splenic Lin-CD127hiThy1.2+TCRb-ST2hi cells

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

tag: cell type

value: BALB/c

value: ILC2 cells


title: Th2_RNA

description: Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro.

source_name: Five-day cultured Th2 cells generated from primary splenic CD4_T cells

value: Th2 cells


title: Tpath2_RNA

description: Splenic memory Th2 cells were culture under conditions (10 U/ml IL-7, 10 ng/ml IL-25, 10ng/ml IL-33) for 5 days in vitro.

source_name: Five-day cultured Tpath2 cells generated from primary splenic ST2hi memory Th2 cells

value: Tpath2 cells


title: KO_TAM_14


title: KO_TAM_13


title: KO_12

source_name: KO_Quadriceps Muscle


title: KO_10


title: KO_9


title: KO_11


title: WT_TAM_7

source_name: WT_TAM_Quadriceps Muscle

value: wild type


title: WT_TAM_8


title: WT_TAM_5


title: CHB9

description:
CHB specimen 9
miRNA expression in CHB after NA treatment

source_name: Non-HCC group-post-1


title: WT_4

source_name: WT_Quadriceps Muscle


title: CHB7

description:
CHB specimen 7
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-7


title: CHB6

description:
CHB specimen 6
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-6


title: WT_3


title: CHB5

description:
CHB specimen 5
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-5


title: siTDRD9-2, biological rep3

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

description: 3' Gene Expression Arrays

hyb_protocol: GeneChip® PrimeView Gene Expression Array oligonucleotide microarray (Affymetrix, Santa Clara, CA) were hybridized for 16 hours in a 45°C oven, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix), and raw data were extracted from the scanned images and analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix)

data_processing:
The raw array data were normalized using the Robust Multichip Average (RMA) method using Expression Console software from Affymetrix. Fold-change and statistic parameters of siControl versus siTDRD9-1 or siTDRD9-2 comparisons were performed using the LIMMA package through oneChannelGUI.
LIMMA signal intensity. Genes differentially expressed more than 2-fold (lineal change) and with FDR < 0.01 were selected

source_name: NCI-H1993, siTDRD9-2

label_protocol: 100 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA), according to manufacturer’s recommendations.

growth_protocol: NCI-H1993 cells were cultured in RPMI medium. Medium was supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 µg/ml streptomycin, and cells were cultivated in a 37°C incubator with 5% CO2.

extract_protocol: Total RNA was isolated in triplicate from HCT-shSLBP cells using RNeasy Mini Kit (Qiagen)

treatment_protocol: Three independent cultures (replicates) were treated with control siRNAs (siControl). Six independent cultures were treated with two different siRNAs (three culture each (replicates)) that target TDRD9 transcript (siTDRD9-1 and siTDRD9-2).

value: TDRD9-depleted (siTDRD9-2)


title: CHB8

description:
CHB specimen 8
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-8


title: WT_2


title: CHB4

description:
CHB specimen 4
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-4


title: siTDRD9-1, biological rep3

description: 3' Gene Expression Arrays

source_name: NCI-H1993, siTDRD9-1

value: TDRD9-depleted (siTDRD9-1)


title: siTDRD9-2, biological rep2

description: 3' Gene Expression Arrays


title: siTDRD9-1, biological rep2

description: 3' Gene Expression Arrays


title: WT_TAM_6


title: CHB3

description:
CHB specimen 3
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-3


title: siTDRD9-1, biological rep1

description: 3' Gene Expression Arrays


title: CHB1

description:
CHB specimen 1
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-1


title: siTDRD9-2, biological rep1

description: 3' Gene Expression Arrays


title: WT_1


title: NORP11

city: Shanghai

first: Lin

last: Liangyu

state: Shanghai

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Science

description: gene expression data from normoxic control for human mesenchymal stem cells cultured under 10% oxygen for six passages

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Normoxic for human mesenchymal stem cells cultured under hypoxia for six passages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: The same strain of mesencymal stem cells were culture under hypoxic and normoxic condition since passage 5.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The gene expression levels of hypoxic and normoxic mesenchymal cells were analysed on passage 8 and passage 11.

value: Human umbilical cord derived MSCs

tag: passage number

tag: oxygen status

value: normoxia


title: HYPP8

description: gene expression data from human mesenchymal stem cells cultured under 10% oxygen for three passages

source_name: Human mesenchymal stem cells cultured under hypoxia for three passages

value: hypoxia


title: NORP8

description: gene expression data from normoxic control for human mesenchymal stem cells cultured under 10% oxygen for three passages

source_name: Normoxic control for human mesenchymal stem cells cultured under hypoxia for three passages


title: CHB2

description:
CHB specimen 2
miRNA expression in CHB before NA treatment

source_name: Non-HCC group-pre-2


title: HYPP11

description: gene expression data from human mesenchymal stem cells cultured under 10% oxygen for six passages

source_name: Human mesenchymal stem cells cultured under hypoxia for six passages


title: 13624928

status: Public on Sep 22 2018

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA

description:
M-MidR3_D
Date:2009/05/27

hyb_protocol: Corning Pronto : 1102.0 ng at 42 degree_C during 14 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Unnormalized, log (base 2) transform of the (Ch1/Ch2) ratio of the medians shown in the data table below. Normalized data [i.e., Log (base 2) transform of the (Ch1/Ch2) ratio of the medians;limma package: normalizeWithinArray(loess, background:subtract) normalizeBetweenArrays (quantile); lmFit ;eBayes] linked as supplementary files on the Series record.

organism: Spodoptera frugiperda

label_protocol: cDNA Pronto Promega/Promega Chipshot labeling

extract_protocol: Trizol

value: midgut

value: stade 6


title: 13624925

description:
M-MidR3_Fip
Date:2009/06/17

hyb_protocol: Corning Pronto : 1261.0 ng at 42 degree_C during 14 hours


title: 13624916

description:
M-MidR1_D
Date:2009/05/27

hyb_protocol: Corning Pronto : 1725.0 ng at 42 degree_C during 14 hours


title: 13624926

description:
M-MidR3_D
Date:2009/05/27

hyb_protocol: Corning Pronto : 1584.0 ng at 42 degree_C during 14 hours


title: siControl, biological rep3

description: 3' Gene Expression Arrays

source_name: NCI-H1993, siControl

value: control


title: siControl, biological rep1

description: 3' Gene Expression Arrays


title: siControl, biological rep2

description: 3' Gene Expression Arrays


title: 13624927

description:
M-MidR2_D
Date:2009/05/27

hyb_protocol: Corning Pronto : 1753.0 ng at 42 degree_C during 14 hours


title: 13624920

description:
M-MidR3_Fip
Date:2009/06/17

hyb_protocol: Corning Pronto : 1313.0 ng at 42 degree_C during 14 hours


title: 13624919

description:
M-MidR1_Fip
Date:2009/06/17

hyb_protocol: Corning Pronto : 1369.0 ng at 42 degree_C during 14 hours


title: 13624921

description:
M-MidR2_Fip
Date:2009/06/17

hyb_protocol: Corning Pronto : 1236.0 ng at 42 degree_C during 14 hours


title: 13624917

description:
M-MidR2_D
Date:2009/05/27

hyb_protocol: Corning Pronto : 1165.0 ng at 42 degree_C during 14 hours


title: 13624918

description:
M-MidR1_Fip
Date:2009/06/17

hyb_protocol: Corning Pronto : 1198.0 ng at 42 degree_C during 14 hours


title: 13624777

description:
M-MidR3_Mtfz
Date:2009/05/19

hyb_protocol: Corning Pronto : 1018.0 ng at 42 degree_C during 14 hours


title: 13904715

description:
M_MidR3_Ind_Cy3 vs M_MidR3_DMSO_Cy5
Date:2010/03/19

hyb_protocol: Corning Pronto : 1293.0 ng at 42 degree_C during 15 hours


title: 13904716

description:
M_MidR3_Pheno_Cy3 vs M_MidR3_DMSO_Cy5
Date:2010/03/19

hyb_protocol: Corning Pronto : 1295.0 ng at 42 degree_C during 15 hours


title: 13904714

description:
M_MidR2_Pheno_Cy3 vs M_MidR2_DMSO_Cy5
Date:2010/03/19


title: 13624774

description:
M-MidR3_Mtfz
Date:2009/05/19

hyb_protocol: Corning Pronto : 1743.0 ng at 42 degree_C during 14 hours


title: 13624779

description:
M-MidR3_MTP
Date:2009/05/27

hyb_protocol: Corning Pronto : 1365.0 ng at 42 degree_C during 15 hours


title: 13904713

description:
M_MidR3_DMSO_Cy3 vs M_MidR3_Pheno_Cy5
Date:2010/03/19

hyb_protocol: Corning Pronto : 1291.0 ng at 42 degree_C during 15 hours


title: 13627412

description:
M-MidR3_MTP
Date:2009/05/27

hyb_protocol: Corning Pronto : 1419.0 ng at 42 degree_C during 15 hours


title: 13627413

description:
M-MidR2_MTP
Date:2009/05/27

hyb_protocol: Corning Pronto : 1470.0 ng at 42 degree_C during 15 hours


title: 13624778

description:
M-MidR2_MTP
Date:2009/05/27

hyb_protocol: Corning Pronto : 1478.0 ng at 42 degree_C during 15 hours


title: 13624903

description:
M-MidR1_MTP
Date:2009/05/27

hyb_protocol: Corning Pronto : 1351.0 ng at 42 degree_C during 15 hours


title: 13624756

description:
M-MidR1_clo
Date:2009/03/10

hyb_protocol: Corning Pronto : 1094.0 ng at 42 degree_C during 12 hours


title: 13624754

description:
M-MidR3_clo
Date:2009/03/11

hyb_protocol: Corning Pronto : 1555.0 ng at 42 degree_C during 12 hours


title: 13624760

description:
M-MidR3_Q
Date:2009/03/26

hyb_protocol: Corning Pronto : 1213.0 ng at 42 degree_C during 12 hours


title: 13624761

description:
M-MidR2_Q
Date:2009/03/26

hyb_protocol: Corning Pronto : 1234.0 ng at 42 degree_C during 12 hours


title: 13904712

description:
M_MidR2_DMSO_Cy3 vs M_MidR2_Pheno_Cy5
Date:2010/03/19

hyb_protocol: Corning Pronto : 1294.0 ng at 42 degree_C during 15 hours


title: 13624902

description:
M-MidR1_MTP
Date:2009/05/27

hyb_protocol: Corning Pronto : 1360.0 ng at 42 degree_C during 15 hours


title: 13624758

description:
M-MidR1_Q
Date:2009/03/26

hyb_protocol: Corning Pronto : 1133.0 ng at 42 degree_C during 12 hours


title: 13624755

description:
M-MidR2_clo
Date:2009/03/10

hyb_protocol: Corning Pronto : 1765.0 ng at 42 degree_C during 12 hours


title: 13624770

description:
M-MidR2_Ind
Date:2009/05/19

hyb_protocol: Corning Pronto : 1308.0 ng at 42 degree_C during 15 hours


title: 13624759

description:
M-MidR1_Q
Date:2009/03/26

hyb_protocol: Corning Pronto : 1177.0 ng at 42 degree_C during 12 hours


title: 13624757

description:
M-MidR1_clo
Date:2009/03/10

hyb_protocol: Corning Pronto : 1490.0 ng at 42 degree_C during 12 hours


title: 13904278

description:
M_MidR1_DMSO_Cy3 vs M_MidR1_Pheno_Cy5
Date:2010/03/19

hyb_protocol: Corning Pronto : 1292.0 ng at 42 degree_C during 15 hours


title: 13624929

description:
M-MidR1_D
Date:2009/05/27

hyb_protocol: Corning Pronto : 1015.0 ng at 42 degree_C during 14 hours


title: 13904279

description:
M_MidR1_Pheno_Cy3 vs M_MidR1_DMSO_Cy5
Date:2010/03/19


title: 13624766

description:
M-MidR2_Ind
Date:2009/05/19

hyb_protocol: Corning Pronto : 1290.0 ng at 42 degree_C during 15 hours


title: 13624771

description:
M-MidR1_Ind
Date:2009/05/19

hyb_protocol: Corning Pronto : 1486.0 ng at 42 degree_C during 15 hours


title: 13624775

description:
M-MidR3_Q
Date:2009/03/26

hyb_protocol: Corning Pronto : 1206.0 ng at 42 degree_C during 12 hours


title: 13624769

description:
M-MidR1_Ind
Date:2009/05/19

hyb_protocol: Corning Pronto : 1399.0 ng at 42 degree_C during 15 hours


title: 13624763

description:
M-MidR2_Q
Date:2009/03/26

hyb_protocol: Corning Pronto : 1289.0 ng at 42 degree_C during 12 hours


title: 13904280

description:
M_MidR3_DMSO_Cy3 vs M_MidR3_Ind_Cy5
Date:2010/03/19


title: 13619534

description:
M-MidR1_2-tri
Date:2008/12/10

hyb_protocol: Corning Pronto : 1476.0 ng at 42 degree_C during 14 hours


title: 13624750

description:
M-MidR2_I3C
Date:2009/03/10

hyb_protocol: Corning Pronto : 1458.0 ng at 42 degree_C during 12 hours


title: 13627644

description:
M-MidR1_I3C
Date:2009/03/10

hyb_protocol: Corning Pronto : 1511.0 ng at 42 degree_C during 12 hours


title: 13624748

description:
M-MidR2_I3C
Date:2009/03/10

hyb_protocol: Corning Pronto : 1640.0 ng at 42 degree_C during 12 hours


title: 13624751

description:
M-MidR1_I3C
Date:2009/03/10

hyb_protocol: Corning Pronto : 1618.0 ng at 42 degree_C during 12 hours


title: 13624765

description:
M-MidR1_Mtfz
Date:2009/05/19

hyb_protocol: Corning Pronto : 2015.0 ng at 42 degree_C during 14 hours


title: 13624767

description:
M-MidR2_Mtfz
Date:2009/05/19

hyb_protocol: Corning Pronto : 1744.0 ng at 42 degree_C during 14 hours


title: 13627646

description:
M-MidR2_clo
Date:2009/03/10

hyb_protocol: Corning Pronto : 1670.0 ng at 42 degree_C during 12 hours


title: 13627645

description:
M-MidR3_clo
Date:2009/03/10

hyb_protocol: Corning Pronto : 1522.0 ng at 42 degree_C during 12 hours


title: 13624740

description:
M-MidR3_2-tri
Date:2009/02/19

hyb_protocol: Corning Pronto : 1748.1 ng at 42 degree_C during 14 hours


title: 13624725

description:
M-MidR2_2-tri
Date:2008/12/10

hyb_protocol: Corning Pronto : 1592.0 ng at 42 degree_C during 14 hours


title: 13619540

description:
M-MidR2_X
Date:2008/12/09

hyb_protocol: Corning Pronto : 1040.0 ng at 42 degree_C during 14 hours


title: 13619542

description:
M-MidR1_X
Date:2008/12/09

hyb_protocol: Corning Pronto : 1236.0 ng at 42 degree_C during 14 hours


title: 13624776

description:
M-MidR2_Mtfz
Date:2009/05/19

hyb_protocol: Corning Pronto : 1021.0 ng at 42 degree_C during 14 hours


title: 13624738

description:
M-MidR3_X
Date:2009/02/19

hyb_protocol: Corning Pronto : 1631.0 ng at 42 degree_C during 14 hours


title: 13619529

description:
M-MidR2_2-tri
Date:2008/12/10

hyb_protocol: Corning Pronto : 1536.5 ng at 42 degree_C during 14 hours


title: 13624749

description:
M-MidR3_I3C
Date:2009/03/10

hyb_protocol: Corning Pronto : 1481.0 ng at 42 degree_C during 12 hours


title: 13624729

description:
M-MidR1_X
Date:2008/12/09

hyb_protocol: Corning Pronto : 1002.0 ng at 42 degree_C during 14 hours


title: 13624735

description:
M-MidR3_X
Date:2009/02/19

hyb_protocol: Corning Pronto : 1677.0 ng at 42 degree_C during 14 hours


title: 13624726

description:
M-MidR2_X
Date:2008/12/09

hyb_protocol: Corning Pronto : 1194.1 ng at 42 degree_C during 14 hours


title: 13624728

description:
M-MidR1_2-tri
Date:2008/12/10

hyb_protocol: Corning Pronto : 1151.0 ng at 42 degree_C during 14 hours


title: 13624746

description:
M-MidR3_I3C
Date:2009/03/10

hyb_protocol: Corning Pronto : 1571.0 ng at 42 degree_C during 12 hours


title: 13624737

description:
M-MidR3_2-tri
Date:2009/02/19

hyb_protocol: Corning Pronto : 1813.0 ng at 42 degree_C during 14 hours


title: 13904543

description:
M-Sf9R3_PB
Date:2010/02/19

hyb_protocol: Corning Pronto : 2006.0 ng at 42 degree_C during 15 hours

data_processing: Unnormalized, log (base 2) transform of the (Ch1/Ch2) ratio of the medians shown in the data table below. Normalized data [i.e., Log (base 2) transform of the (Ch1/Ch2) ratio of the medians;limma package: normalizeWithinArray (loess, background:subtract) normalizeBetweenArrays (quantile); lmFit ;eBayes] linked as supplementary files on the Series record.

label_protocol: Promega Chipshot labeling


title: 13904539

description:
M-Sf9R2_PB
Date:2010/02/19

hyb_protocol: Corning Pronto : 1895.0 ng at 42 degree_C during 15 hours


title: 13904250

description:
M-Sf9R1_PB
Date:2010/02/19

hyb_protocol: Corning Pronto : 1532.0 ng at 42 degree_C during 15 hours


title: 13904541

description:
M-Sf9R3_PB
Date:2010/02/23

hyb_protocol: Corning Pronto : 1594.0 ng at 42 degree_C during 15 hours


title: 13904540

description:
M-Sf9R2_PB
Date:2010/02/19

hyb_protocol: Corning Pronto : 1796.0 ng at 42 degree_C during 15 hours


title: 13904071

description:
M-Sf9R2_Q
Date:2009/12/10

hyb_protocol: Corning Pronto : 1555.0 ng at 42C during 17 hours


title: 13904257

description:
M-Sf9R2_X
Date:2009/10/28

hyb_protocol: Corning Pronto : 1333.0 ng at 42C during 16 hours


title: 13904068

description:
M_Sf9R1_DMSOcy3 vs M_Sf9R1_Clocy5
Date:2009/12/15

hyb_protocol: Corning Pronto : 1200.0 ng at 42C during 15 hours


title: 13904069

description:
M-Sf9R3_Q
Date:2009/12/10

hyb_protocol: Corning Pronto : 1654.0 ng at 42C during 17 hours


title: 13904070

description:
M-Sf9R3_Q
Date:2009/12/10

hyb_protocol: Corning Pronto : 1744.0 ng at 42C during 17 hours


title: 13904055

description:
M-Sf9R1_Fip
Date:2009/12/17

hyb_protocol: Corning Pronto : 1489.0 ng at 42C during 16 hours


title: 13904067

description:
M-Sf9R1_Clo
Date:2009/12/15

hyb_protocol: Corning Pronto : 1466.0 ng at 42C during 15 hours


title: 13904236

description:
M-Sf9R1_Delta
Date:2010/01/12

hyb_protocol: Corning Pronto : 1513.0 ng at 42C during 16 hours


title: 13904263

description:
M-Sf9R3_X
Date:2009/10/29

hyb_protocol: Corning Pronto : 1449.0 ng at 42C during 16 hours


title: 13904057

description:
M-Sf9R3_Clo
Date:2009/12/15

hyb_protocol: Corning Pronto : 1532.0 ng at 42C during 15 hours


title: 13904072

description:
M-Sf9R1_Fip
Date:2009/12/17

hyb_protocol: Corning Pronto : 1493.0 ng at 42C during 16 hours


title: 13904059

description:
M-Sf9R2_Clo
Date:2009/12/15

hyb_protocol: Corning Pronto : 1577.0 ng at 42C during 15 hours


title: 13904061

description:
M-Sf9R3_2Tri
Date:2009/12/02

hyb_protocol: Corning Pronto : 1715.0 ng at 42C during 16 hours


title: 13904258

description:
M-Sf9R2_X
Date:2009/10/28

hyb_protocol: Corning Pronto : 1341.0 ng at 42C during 16 hours


title: 13903677

description:
M-Sf9R3_Ind
Date:2010/01/14

hyb_protocol: Corning Pronto : 1542.0 ng at 42C during 16 hours


title: 13903679

description:
M-Sf9R3_Ind
Date:2010/01/14

hyb_protocol: Corning Pronto : 1318.0 ng at 42C during 16 hours


title: 13904060

description:
M-Sf9R2_Clo
Date:2009/12/15

hyb_protocol: Corning Pronto : 1464.0 ng at 42C during 15 hours


title: 13903678

description:
M-Sf9R3_Fip
Date:2009/12/18

hyb_protocol: Corning Pronto : 1583.0 ng at 42C during 16 hours


title: 13903680

description:
M_Sf9R3_Fipcy3 vs M_Sf9R3_DMSOcy5
Date:2009/12/18

hyb_protocol: Corning Pronto : 1580.0 ng at 42C during 16 hours


title: 13904260

description:
M-Sf9R3_X
Date:2009/10/28

hyb_protocol: Corning Pronto : 1325.0 ng at 42C during 16 hours


title: 13904062

description:
M-Sf9R1_I3C
Date:2009/12/04

hyb_protocol: Corning Pronto : 1405.0 ng at 42C during 16 hours


title: 13904064

description:
M-Sf9R2_I3C
Date:2009/12/04

hyb_protocol: Corning Pronto : 1463.0 ng at 42C during 16 hours


title: 13904054

description:
M-Sf9R3_2Tri
Date:2009/12/02

hyb_protocol: Corning Pronto : 1741.0 ng at 42C during 16 hours


title: 13904058

description:
M-Sf9R3_Clo
Date:2009/12/15

hyb_protocol: Corning Pronto : 1612.0 ng at 42C during 15 hours


title: 13904230

description:
M-Sf9R1_PB
Date:2010/02/19

hyb_protocol: Corning Pronto : 1760.0 ng at 42 degree_C during 15 hours


title: 13903675

description:
M-Sf9R1_X
Date:2009/10/28

hyb_protocol: Corning Pronto : 1437.0 ng at 42C during 16 hours


title: 13624762

description:
M-MidR1_Mtfz
Date:2009/05/19

hyb_protocol: Corning Pronto : 750.0 ng at 42 degree_C during 14 hours


title: Control-5 [beta-cells]

city: HUNTSVILLE

first: NRIPESH

last: PRASAD

state: AL

address: 601 GENOME WAY

department: GENOMIC SERVICES LABORATORY

institute: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY

description:
GSM3242811
3351-ACP-0022

data_processing: Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference hg19 using TopHat v2.0. Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered based on read quality,alignment quality follwed by removing duplicates. Transcript abundance was quantified using Trimmed Means of M-values (TMM) as the normalization method. Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±1.5.0) observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by z test using Benjamini Hochberg corrections of 0.05 for false-discovery rate. Differentially expressed genes were further analyzed through Gene Ontology (GO) analysis using DAVID v6.8. The Normalized expression values are in log2scale in the uploaded worksheet.  Genome_build: hg19  Supplementary_files_format_and_content: Excel file with Normalized expression values for each sample

source_name: cadaveric pancreatic islet tissue

extract_protocol:
RNA was isolated from FACS-sorted β-cells using the RNAqueous®-Micro Total RNA Isolation Kit (Ambion AM1931). Residual genomic DNA was removed with the DNA-free™ system (provided with kit AM1931).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pancreatic beta-cells

tag: gender

value: Male

tag: disease state

value: Non-diabetic


title: 13904063

description:
M-Sf9R1_I3C
Date:2009/12/04

hyb_protocol: Corning Pronto : 1661.0 ng at 42C during 16 hours


title: 13903676

description:
M-Sf9R2_Fip
Date:2009/12/18

hyb_protocol: Corning Pronto : 1525.0 ng at 42C during 16 hours


title: 13624924

description:
M-MidR2_Fip
Date:2009/06/17

hyb_protocol: Corning Pronto : 1424.0 ng at 42 degree_C during 14 hours


title: 13904254

description:
M-Sf9R1_Q
Date:2009/12/10

hyb_protocol: Corning Pronto : 1444.0 ng at 42C during 17 hours


title: Control-4 [beta-cells]

description:
GSM3242810
3351-ACP-0038


title: 13904052

description:
M-Sf9R2_2Tri
Date:2009/12/02

hyb_protocol: Corning Pronto : 1533.0 ng at 42C during 16 hours


title: 13904255

description:
M-Sf9R1_Q
Date:2009/12/10

hyb_protocol: Corning Pronto : 1658.0 ng at 42C during 17 hours


title: 13904065

description:
M-Sf9R2_I3C
Date:2009/12/04

hyb_protocol: Corning Pronto : 1616.0 ng at 42C during 16 hours


title: 13904256

description:
M-Sf9R2_Q
Date:2009/12/10

hyb_protocol: Corning Pronto : 1587.0 ng at 42C during 17 hours


title: 13904049

description:
M-Sf9R1_2Tri
Date:2009/12/02

hyb_protocol: Corning Pronto : 1479.0 ng at 42C during 16 hours


title: Control-2 [beta-cells]

description:
GSM3242808
3351-ACP-0029

value: Female


title: Control-3 [beta-cells]

description:
GSM3242809
3351-ACP-0016


title: Control-1 [beta-cells]

description:
GSM3242807
3351-ACP-0019


title: 13903674

description:
M-Sf9R1_X
Date:2009/10/28

hyb_protocol: Corning Pronto : 1363.0 ng at 42C during 16 hours


title: 13904252

description:
M-Sf9R3_I3C
Date:2009/12/04

hyb_protocol: Corning Pronto : 1403.0 ng at 42C during 16 hours


title: 13904050

description:
M-Sf9R1_2Tri
Date:2009/12/02

hyb_protocol: Corning Pronto : 1391.0 ng at 42C during 16 hours


title: Control-4 [alpha cells]

description:
GSM2830485
3351-ACP-0037

source_name: FACS-purified alpha cells

extract_protocol:
RNAqueous micro-scale phenol-free total RNA isolation kit
RNA concentration and integrity was evaluated (Qubit Fluormeter; Invitrogen, Carlsbad, CA; Agilent 2100 Bioanayzer), and high-integrity total RNA was amplified (Ovation system; NuGen Technologies, San Carlos, CA) per standard protocol as described previously (Brissova et al., 2014). Amplified cDNA was sheared to target 200bp fragment size and libraries were prepared using NEBNext DNA Library Prep (New England BioLabs, Ipswich, MA). Accurate quantification of libraries for sequencing was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). 50bp Paired End (PE) sequencing was performed on an Illumina HiSeq 2500(Illumina Inc., San Diego, CA, USA)  to generate approximately 50 million reads per sample

value: FACS-purified alpha cells

value: Human pancreatic islets

value: Donor:50 years old

value: male

value: non-diabetic control


title: Control-5 [alpha cells]

description:
GSM2830486
3351-ACP-0015

value: Donor:49 years old

value: female


title: 13904245

description:
MSf9R2_Ind
Date:2010/01/14

hyb_protocol: Corning Pronto : 1500.0 ng at 42C during 16 hours


title: 13904253

description:
M-Sf9R3_I3C
Date:2009/12/04

hyb_protocol: Corning Pronto : 1554.0 ng at 42C during 16 hours


title: 13904246

description:
M-Sf9R2_Ind
Date:2010/01/14

hyb_protocol: Corning Pronto : 1537.0 ng at 42C during 16 hours


title: 13904051

description:
M-Sf9R2_2Tri
Date:2009/12/02

hyb_protocol: Corning Pronto : 1591.0 ng at 42C during 16 hours


title: Control-2 [alpha cells]

description:
GSM2830483
3351-ACP-0021

value: Donor:55 years old


title: Control-1 [alpha cells]

description:
GSM2830482
3351-ACP-0028

value: Donor:35 years old


title: HNEPc4_EDN_biological_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description:
HNEPc4_EDN2
HNEpCs upon stimulation with eosinophil-derived neurotoxin (EDN).
mRNA-seq

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKMs.

source_name: HNEpCs stimulated with EDN

growth_protocol: Primary human nasal epithelial cells, HNEpCs (PromoCell, Heidelberg, Germany), were cultured at 37 degrees C, 5% CO2, using an airway epithelial cell growth medium with supplements (PromoCell).

extract_protocol:
Total RNA from HNEpCs stimulated with EDN was extracted using QIAzol (Qiagen, Osaka, Japan) and the RNeasy Mini Kit (Qiagen).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: After the monolayer reached 90% confluence, the cells were treated for 24 hr with rEDN (2 μ g/ml) (Abcam, Tokyo, Japan). Supernatants and cell pellets were collected and preserved at -80 degrees C.

value: nasal epithelial cells (HNEpCs)

value: eosinophil-derived neurotoxin (EDN)


title: HNEPc_Ctrl_biological_rep1

description:
HNEPc_Ctrl1
HNEpCs upon stimulation without eosinophil-derived neurotoxin (EDN).
mRNA-seq

source_name: HNEpCs stimulated without EDN


title: Control-3 [alpha cells]

description:
GSM2830484
3351-ACP-0018

value: Donor:26 years old


title: 13904244

description:
M-Sf9R1_Ind
Date:2010/01/14

hyb_protocol: Corning Pronto : 1311.0 ng at 42C during 16 hours


title: 13904241

description:
M-Sf9R3_Delta
Date:2010/01/12

hyb_protocol: Corning Pronto : 1970.0 ng at 42C during 16 hours


title: 13904238

description:
M-Sf9R2_Delta
Date:2010/01/12

hyb_protocol: Corning Pronto : 1674.0 ng at 42C during 16 hours


title: 13904237

description:
M-Sf9R1_Delta
Date:2010/01/12

hyb_protocol: Corning Pronto : 1536.0 ng at 42C during 16 hours


title: 13904243

description:
M-Sf9R1_Ind
Date:2010/01/14

hyb_protocol: Corning Pronto : 1260.0 ng at 42C during 16 hours


title: HNF1A-2

data_processing:
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference hg19 using TopHat v2.0. Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered based on read quality,alignment quality follwed by  removing duplicates. Transcript abundance was quantified using Trimmed Means of M-values (TMM) as the normalization method. Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±1.5.0) observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by z test using Benjamini Hochberg corrections of 0.05 for false-discovery rate. Differentially expressed genes were further analyzed through Gene Ontology (GO) analysis using DAVID v6.8. The Normalized expression values are in log2scale in the uploaded worksheet.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with Normalized expression values for each sample

source_name: FACS-purified β cells

value: beta cell

tag: donor age

value: Donor:33 years old (33-16yM)

value: human pancreatic islets


title: glia4

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

description: Each sample isolated independently

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2
Reads were filtered for the presence of adapters using Cutadapt version 1.9.1
Reads were aligned to the transcriptome using STAR version 2.5.2b with the option ‘--quantMode TranscriptomeSAM’
Transcript expression per sample, in transcripts per million (TPM), was calculated with Salmon version 0.7.2 in alignment based mode
Gene expression per sample, in transcripts per million (TPM), was calculated by summing the transcript expression for all transcripts of a given gene
Genome_build: FlyBase genome release 6.10
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all isoforms for each sample
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all genes for each sample

organism: Drosophila melanogaster

source_name: central glia

extract_protocol:
Cells were isolated by FACS on an AriaII and snap frozen in lysis buffer. Total RNA was isolated with the RNAqueous Micro Kit (Ambion AM1931), converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

tag: developmental stage

value: third instar

tag: genotype

value: repo-Gal4 > UAS-Red Stinger

value: brain

tag: quantity

value: 100 cells


title: glia2

description: Each sample isolated independently

tag: tissue


title: motorneurons6

description: Each sample isolated independently

source_name: motor neurons

value: ok371-Gal4 > UAS-Red Stinger


title: motorneurons5

description: Each sample isolated independently


title: glia1

description: Each sample isolated independently


title: glia3

description: Each sample isolated independently


title: motorneurons7

description: Each sample isolated independently


title: 13904073

description:
M-Sf9R2_Fip
Date:2009/12/17

hyb_protocol: Corning Pronto : 1486.0 ng at 42C during 16 hours


title: motorneurons4

description: Each sample isolated independently


title: 13904242

description:
M-Sf9R3_Delta
Date:2010/01/12

hyb_protocol: Corning Pronto : 1699.0 ng at 42C during 16 hours


title: 13904240

description:
M-Sf9R2_Delta
Date:2010/01/12

hyb_protocol: Corning Pronto : 1650.0 ng at 42C during 16 hours


title: HNEPc4_EDN_biological_rep1

description:
HNEPc4_EDN1
HNEpCs upon stimulation with eosinophil-derived neurotoxin (EDN).
mRNA-seq


title: motorneurons3

description: Each sample isolated independently


title: muscles4

description: Each sample isolated independently

source_name: bodywall muscles

value: mef-Gal4 > UAS-Red Stinger

value: bodywall


title: HNEPc_Ctrl_biological_rep2

description:
HNEPc_Ctrl2
HNEpCs upon stimulation without eosinophil-derived neurotoxin (EDN).
mRNA-seq

value: control


title: motorneurons2

description: Each sample isolated independently


title: muscles3

description: Each sample isolated independently


title: motorneurons1

description: Each sample isolated independently


title: muscles2

description: Each sample isolated independently


title: HNF1A-1

source_name: FACS-purified α cells

value: alpha cell


title: cns4

description: All five samples isolated together and RNA extraction performed prior to separating into five samples

source_name: central neurons

value: elav-Gal4 > UAS-Red Stinger


title: muscles1

description: Each sample isolated independently


title: cns5


title: cns3


title: epithelia2

description: Each sample isolated independently

source_name: bodywall epidermis

value: A58-Gal4 > UAS-Red Stinger


title: PD2

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

institute: Cardiff University

data_processing:
Salmon version 0.7.2 with default settings was used to quantify transcript expression using ensembl v87 as the human transcriptome reference, which combined cDNA and ncRNA, and for which alternative sequences were removed before mapping.
Gene annotation was obtained from the fasta headers of the ensembl reference used for mapping.
For downstream analyses expression data were summarised on the gene level using the tximport R package.
Genome_build: ensembl GRCh38 release 87
Supplementary_files_format_and_content: TAB-delimited text files contain standard Salmon output providing transcript quantifiaction (Name, ensembl transcript ID; Length, length of transcript; EffectiveLength, effective length of transcript; TPM, Salmon-computed transcripts per million; NumReads, number of mapped reads)

source_name: iPSC-derived astrocytes

extract_protocol:
For each sample 386 ng total RNA was used for library preparation. RNA samples were prepared using standard poly-A isolation protocol (Illumina TruSeq Stranded mRNA kit).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: lrrk2 genotype

tag: reprogramming method

value: Retrovirus

tag: Sex

value: F

tag: percentage astrocytes


title: PD4

tag: cell line

value: Cytotune (Sendai virus)


title: pns2 (peripheral neurons)

description: Each sample isolated independently

source_name: peripheral neurons


title: epithelia3

description: Each sample isolated independently


title: pns4 (peripheral neurons)

description: Each sample isolated independently


title: cns2


title: PD1

value: M


title: epithelia1

description: Each sample isolated independently


title: pns3 (peripheral neurons)

description: Each sample isolated independently


title: PD3

value: Cytotune 2.0 (Sendai virus)


title: MOLT4 Control

city: Shimotsuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg38 genome assembly using EasyAlign version 3.2
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
Peaks were called using either the MACSa or SICERb algorithms. MACS default cutoff is pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist
Genome_build: hg38

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: We cultured MOLT-4 cells  in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Histone-DNA complexes were isolated with anti-histone H3K27ac antibody from purified chromatin lysates.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: MOLT4 cells were cultured with either vehicle (0.01% DMSO) alone or 12 μM LSD1 inhibitor (S2157) for 24 hours.

value: Acute leukemia of T-cell origin

value: Hematopoietic cells

tag: chip antibody

value: H3K27ac (Active Motif 39133)


title: Input DNA


title: MOLT4 S2157


title: CT3


title: CT2


title: CT1