title: L1210-Fbxw11c

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

description:
4C
Gene expression after Fbxw11 variant overexpression.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: L1210 cells, Fbxw11c

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with 10% FBS, glutamine (2 mM), penicillin (100 U/ml), and streptomycin (100μg/ml), at 37℃ in 5% CO2 atmosphere.

extract_protocol: Extract total RNA by Trizol following the manufacturer's protocol.

treatment_protocol: L1210 cells were infected with lentivirus carrying Fbxw11 variants. The GFP+ stably transfected cells were sorted by FACS, then lysis in Trizol agent.

tag: strain/background

value: DBA subline 212

tag: stable transfection


title: 818-CRIS-AR-6A

status: Public on Mar 29 2018

type: SRA

city: New York

first: Brett

last: Carver

state: NY

address: 1275 York Ave

country: USA

institute: MSKCC

library_source: transcriptomic

data_processing:
Steps in the NYGC RNA analysis pipeline include:
- Alignment of raw reads to mm9 using STAR aligner
- Quality control using RSeQC and Picard (%GC, %duplicates, gene body coverage, unsupervised
clustering, library complexity, etc.)
- Picard MarkDuplicates
- Gene quantification using featureCounts
- Gene annotation using Gencode
- Normalize count matrix with DESeq2
- Differential expression with DESeq2
- Transcript quantification with Kallisto and differential isoform expression with Sleuth
- Fusion gene discovery with FusionCatcher (for somatic studies)
RNAseq data was analyzed for differential expression by genotype and treatment (n=3 per condition) using DESEq2.  Adjusted P-values less than 0.05 were considered significant at a fold change threshold of 1.5.
Genome_build: NCBI genome build mm9
Supplementary_files_format_and_content: Normalized counts

molecule: total RNA

organism: Mus musculus

source_name: Prostate cancer

growth_protocol: Cells (triplicate individual clones of each genotype/condition) were grown in prostate epithelial organoid media as 2d layer in vitro and split at 70% confluency.

extract_protocol:
QIAshredder (Qiagen; 79656) and RNeasy Mini kit (Qiagen; 74106) were used to isolate RNA from cell lines. The standard protocol of the kit was followed.
RNA-seq was performed by New York genome center.  RNA sequencing libraries were prepared using the TruSeq Stranded mRNA sample preparation kit in accordance with the manufacturer’s instructions.  Briefly, 500ng of total RNA was used for purification and fragmentation of mRNA.  Following conversion of mRNA to cDNA, DNA was adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 10 cycles).  Final libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems), Qubit Fluorometer (Life Technologies) and Agilent 2100 BioAnalyzer, and were sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 2 x 50bp cycles targeting 35M single-end reads per sample.

treatment_protocol: A subset of cells were treated with 10uM MDV3100 for 24 hours prior to harvesting.

tag: strain

tag: genotype

value: Pten-/- Rosa26-Tmprss2-ERG

tag: manipulation

value: CRISPR-AR

tag: tissue

value: Prostate cancer


title: 818-12A


title: 818-CRIS-E-5F

value: CRISPR-ERG


title: 218-5A

value: Pten-/-


title: 218-3H


title: 818-CRIS-E-7F-MDV

value: CRISPR-ERG + 10uM MDV3100 treatment


title: 818-11G


title: 818-CRIS-E-12C-MDV


title: L1210-Control

type: RNA

city: Tianjin

country: China

description:
4B
Gene expression after control overexpression.

source_name: L1210 cells, Control

tag: cell line

value: Control


title: 818-CRIS-E-5F-MDV


title: 218-4G


title: 818-CRIS-E-12C


title: L1210-Fbxw11a

description:
4A
Gene expression after Fbxw11 variant overexpression.

source_name: L1210 cells, Fbxw11a


title: 3052

city: Montreal

first: Corine

last: Martineau

state: Quebec

address: 1003 Decarie Boulevard

department: Research Centre

country: Canada

institute: Shriners Hospital for Children - Canada

hyb_protocol: Samples were prepared and hybridized to GeneChip Mouse 430_2 Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Applied Biosystem Transcriptome Analysis Suite (v. 4.0.1) considering at least a 2-fold increased expression with a significance threshold set at p < 0,05 and a FDR of < 0.05.
The resulting CHP files are with the Applied Biosystem Transcriptome Analysis Suite (v. 4.0.1) considering at least a 2-fold increased expression with a significance threshold set at p < 0,05 and a FDR of < 0.05.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: biotin

source_name: Cyp24a1 (-/-)_Bone callus tissue, D14 post-OT

extract_protocol: Total RNA was extracted using Trizol and RNAeasy (QIAGEN) as indicated in manufacturer's protocols.

treatment_protocol: 12-week-old mice were used for tibial intramedullary rod-stabilized osteotomy and left to heal for 14 days. On day 14 post-OT, mice were sacrificed, callus tissue was harvested in RNAlater until analysis.

tag: strain background

value: C57BL6J x 129SV mixed

tag: age

value: 12 weeks

tag: treatment

tag: time point

value: 14 post-OT

value: bone callus


title: L1210-Fbxw11d

description:
4D
Gene expression after Fbxw11 variant overexpression.

source_name: L1210 cells, Fbxw11d


title: 3008

label_protocol: Samples were prepared and hybridized to GeneChip Mouse 430_2 Array according to Affymetrix specifications.

value: tibial intramedullary rod-stabilized osteotomy


title: 818-CRIS-AR-1E


title: 818-CRIS-AR-10B


title: 818-CRIS-E-7F


title: 818-8E


title: 218-CRIS-AR-3A


title: 218-CRIS-AR-2G


title: 218-CRIS-AR-1H


title: aPD-L1 rep 3

city: Buffalo

first: John

last: Ebos

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

institute: Roswell Park Cancer Institute

description: SAMPLE 9

hyb_protocol: Seven hundred and fifty nanograms of the labeled probes were mixed with hybridization reagents and hybridized overnight at 58oC to the MouseWG-6v2 whole genome BeadChip (Illumina; BD-201-0202).

scan_protocol: After Cy3-streptavidin conjugation the BeadChips were imaged using the Illumina iScan Reader.

data_processing: The background corrected gene expression levels were extracted from BeadChip using Illumina's Genome Studio (v2011.1) gene expression module (v1.9.0). Gene expression levels were log2 transformed and quantile normalized using lumi in the R-base Bioconductor package.

source_name: mouse lung

label_protocol: Five hundred nanograms total RNA was converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer's instructions.

extract_protocol: Total RNA from individual lungs was extracted using the RNeasy mini kit (QIAGEN; 74104). Genomic DNA wa digested using DNase I (QIAGEN; 79254) as described in the on-column DNase digestion protocol from QIAGEN.

value: Balb/c

value: 8 weeks

tag: treatment 1

tag: dose 1

value: 250ug/mouse/3 days

tag: duration

value: 7 days

value: Lung


title: aPD-1 rep 3

description: SAMPLE 12


title: aPD-L1 rep 2

description: SAMPLE 8


title: aPD-1 rep 2

description: SAMPLE 11


title: aPD-1 rep 1

description: SAMPLE 10


title: PBS control rep 3

description: SAMPLE 3

source_name: PBS

value: PBS


title: aPD-L1 rep 1

description: SAMPLE 7


title: IgG rep 3

description: SAMPLE 6

value: IgG


title: PBS rep 1

description: SAMPLE 1


title: Sunitinib 120mg/kg/day rep 3

source_name: Sunitinib 120mg/kg/day

value: Sunitinib

value: 120 mg/kg/day


title: IgG rep 2

description: SAMPLE 5


title: DC101 800ug/mouse/3 days rep 1

description: SAMPLE 4

source_name: DC101 800ug/mouse/3 days

value: 800ug/mouse/3 days


title: IgG rep 1

description: SAMPLE 4


title: DC101 800ug/mouse/3 days rep 3

description: SAMPLE 6


title: Sunitinib 120mg/kg/day rep 2


title: Sunitinib 60mg/kg/day + Crizotinib 50mg/kg/day rep 1

tag: treatment 2

value: Crizotinib

value: 60 mg/kg/day

tag: dose 2

value: 50 mg/kg/day


title: Axitinib 100mg/kg/day rep 1

source_name: Axitinib 100mg/kg/day

value: Axitinib

value: 100 mg/kg/day


title: Crizotinib 50mg/kg/day rep 3

source_name: Crizotinib 50mg/kg/day


title: PBS rep 3

description: SAMPLE 3


title: PBS rep 2

description: SAMPLE 2


title: Crizotinib 50mg/kg/day rep 2


title: Axitinib 100mg/kg/day rep 3


title: DC101 800ug/mouse/3 days rep 2

description: SAMPLE 5


title: Axitinib 100mg/kg/day rep 2


title: PBS control rep 1

description: SAMPLE 1


title: Sunitinib 60mg/kg/day + Crizotinib 50mg/kg/day rep 3


title: Crizotinib 50mg/kg/day rep 1


title: PBS control rep 2

description: SAMPLE 2


title: Sunitinib 60mg/kg/day + Crizotinib 50mg/kg/day rep 2


title: Sunitinib 120mg/kg/day rep 1


title: Sunitinib 60mg/kg/day rep 3

source_name: Sunitinib 60mg/kg/day


title: Sunitinib 60mg/kg/day rep 2


title: Vehivle rep 3

source_name: Vehivle

value: Vehicle


title: Vehicle rep 2

source_name: Vehicle


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_EpiLC_48H_cESC

city: Boston

first: Peng

last: Du

state: MA

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_EpiLC_48H-cESC

data_processing:
Bowtie software was used to align sequencing reads to reference mRNA and miRNA database
For polyA(+) RNA-seq, mouse cDNA database (Ensembl, GRCm38) was use for alignment
For small RNA-seq, homemade PERL software was used to remove adaptor sequences, and 20-25nt small RNAs was aligned to known  mature miRNA sequences (miRBase)
both polyA(+) and small RNA-seq, Reads per Million was culculated for the normaliztion
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

molecule: polyA RNA

source_name: ESCs

extract_protocol:
total RNA was extracted using Trizol reagent.  TruSeq Stranded mRNA LT Sample Prep Kit (Cat# RS-122-2101) was used for polyA (+) RNA-seq sample preparation with 3 ug of total RNA. NBE Mutiple small RNA librariry prep set (Cat# E7580S) was used for small RNA-seq sample preparation.
RNA libraries for polyA(+) RNA-seq and small RNA-seq were prepared following the manufacturer's  protocols, respectively

value: Dox-inducible Flag-ISY1 KH2 ESC line

tag: cell type

value: ESCs

tag: culture condition

value: 48 hour EpiLCs (+Dox) replated into 2i/Lif medium to convert to ESCs (cESCs)

value: without Dox


title: Small_RNA-seq_KH2-ISY1 (+Dox)_SL_Day0

description:
Small RNA
with Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_KH2-ISY1_+Dox_SL_Day0

value: cultured in Serum/Lif medium

value: with Dox


title: Small_RNA-seq_KH2-ISY1 (-Dox)_SL_Day0

description:
Small RNA
without Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_KH2-ISY1_-Dox_SL_Day0


title: PolyA(+)_RNA-seq_DGCR8ko_EpiLC_72H

description:
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_EpiLC_72H

value: DGCR8 knockout ESC line

value: cultured in Differentiation medium for EpiLC induction for 72 hours


title: Small_RNA-seq_V6.5_siISY1-2

description:
Small RNA
transfected with siRNAs targeting ISY1
V6.5_siRNAs treatment.txt
Small_RNA-seq_siISY1-2

value: V6.5 ESC line

value: transfected with siRNAs targeting ISY1


title: PolyA(+)_RNA-seq_DGCR8ko_EpiLC_24H

description:
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_EpiLC_24H

value: cultured in Differentiation medium for EpiLC induction for 24 hours


title: PolyA(+)_RNA-seq_DGCR8ko_EpiLC_48H

description:
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_EpiLC_48H

value: cultured in Differentiation medium for EpiLC induction for 48 hours


title: PolyA(+)_RNA-seq_DGCR8ko_EpiLC_6H

description:
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_EpiLC_6H

value: cultured in Differentiation medium for EpiLC induction for 6 hours


title: Small_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_48H

description:
Small RNA
without Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_KH2-ISY1_-Dox_EpiLC_48H


title: Small_RNA-seq_V6.5_siCTRL

description:
Small RNA
transfected with Control siRNAs
V6.5_siRNAs treatment.txt
Small_RNA-seq_siCTRL

value: transfected with Control siRNAs


title: Small_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_6H

description:
Small RNA
without Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_KH2-ISY1_-Dox_EpiLC_6H


title: PolyA(+)_RNA-seq_DGCR8ko_EpiLC_96H

description:
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_EpiLC_96H

value: cultured in Differentiation medium for EpiLC induction for 96 hours


title: PolyA(+)_RNA-seq_DGCR8ko_2iL_0H

description:
DGCR8 knock-out
EpiLC_differentiation.txt
PolyA_+_RNA-seq_DGCR8ko_2iL_0H

value: cultured in 2i/Lif medium


title: Small_RNA-seq_V6.5_siISY1-1

description:
Small RNA
transfected with siRNAs targeting ISY1
V6.5_siRNAs treatment.txt
Small_RNA-seq_siISY1-1


title: Small_RNA-seq_EB (-Dox)_D1

description:
Small RNA
without Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_EB_-Dox_D1

value: cultured in Differentiation medium for EB induction for 1 day


title: Small_RNA-seq_KH2-ISY1 (-Dox)_2iL_0H

description:
Small RNA
without Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_KH2-ISY1_-Dox_2iL_0H

value: Dox-inducible Flag-ISY1 KH2 ESC line


title: 1223

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

description: gene expression

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays containing 41,000 human transcripts (Agilent Technologies) following the manufacture's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned by Agilent G2565BA scanner and images were processed by Feature Extraction software v.9.5.3.1 (Agilent Technologies)

data_processing: Tab-delimited text files containing FE results were acquired and analyzed with Rv3.2.1 software using the limma package of Bioconductor. Data were preliminarily corrected for background and normalized in order to have similar distributions across the set of arrays. Ranking of genes by their evidence for differential expression was made using the paired moderated t-statistics based on empirical Bayes moderation of the standard errors

organism: Homo sapiens

source_name: primary NB tumors from localized NB

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com).  Dye incorporation and cRNA yield were checked with Nanodrop (Thermo Scientific).

growth_protocol: BM and primary NB tumors were directly subjected to total RNA extraction

extract_protocol: Total RNA extraction was performed by the RNeasy Mini kit (qiagen) according to the manufacturer's instructions, including an Rnase-free DNAse digestion. Total RNA was quantified and the quality assessed by RNA 6000 Nano chip on the 2100 Bioanalyzer (Agilent technologies). only samples with RNA integrity number greater than 6 were included in the study.

treatment_protocol: To isolate GD2+ cells from BM of metastatic NB, the BM samples from patients with  metastatic NB were subjected to immunomagnetic separation,after lysis of erythrocytes, cells were incubated for 30 minutes at 4°C with the anti-GD2 mAb in the presence of human Fc blocking reagent. After washing, the cell pellet was incubated for 15 minutes at 4°C with goat anti-mouse IgG2a microbeads (Miltenyi). Cells were then washed twice, suspended in 500 L of sterile ice-cold PBS and loaded onto a MS column (Miltenyi).The GD2 positive fractions were then subjected to RNA extraction.

tag: age (months)

tag: Sex

value: M

tag: inss stage

tag: mycn status

value: single copy

tag: date of sampling/diagnosis

tag: patient's id


title: 1456

description: gene expression


title: 2404

description: gene expression


title: 1181

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_EpiLC_24H_cESC

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_EpiLC_24H-cESC

tag: cell line

value: ESCs

value: 24 hour EpiLCs (+Dox) replated into 2i/Lif medium to convert to ESCs (cESCs)

value: without Dox


title: Vehicle rep 1

tag: strain

value: Balb/c

tag: age

value: 8 weeks

value: Vehicle

value: 7 days

tag: tissue

value: Lung


title: 1338

description: gene expression

value: F


title: 1460

description: gene expression


title: 1548

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_24H_cESC

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_24H-cESC

value: 24 hour EpiLCs (-Dox) replated into 2i/Lif medium to convert to ESCs (cESCs)

tag: treatment


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_EpiLC_96H

description:
cells with ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_EpiLC_96H

value: with Dox


title: Sunitinib 60mg/kg/day rep 1

tag: treatment 1

value: Sunitinib

tag: dose 1

value: 60 mg/kg/day


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_48H_cESC

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_48H-cESC

value: 48 hour EpiLCs (-Dox) replated into 2i/Lif medium to convert to ESCs (cESCs)


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_EpiLC_72H

description:
cells with ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_EpiLC_72H

value: Dox-inducible Flag-ISY1 KH2 ESC line

value: cultured in Differentiation medium for EpiLC induction for 72 hours


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_EpiLC_24H

description:
cells with ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_EpiLC_24H

value: cultured in Differentiation medium for EpiLC induction for 24 hours


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_96H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_96H

value: ESCs

value: cultured in Differentiation medium for EpiLC induction for 96 hours


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_72H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_72H

value: without Dox


title: 2008

description: gene expression

value: M

value: unknown


title: 1243

description: gene expression

source_name: primary NB tumors from stage 4 NB (patient DEAD at 5 years )

value: single copy


title: 535

description: gene expression


title: 1544

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_EpiLC_48H

description:
cells with ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_EpiLC_48H

value: cultured in Differentiation medium for EpiLC induction for 48 hours


title: 806

description: gene expression


title: 2144

description: gene expression


title: 1439

description: gene expression


title: 2003

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_48H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_48H


title: 984

description: gene expression


title: 2368

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_36H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_36H

value: cultured in Differentiation medium for EpiLC induction for 36 hours


title: 2100

description: gene expression


title: 1965

description: gene expression


title: 1641

description: gene expression

source_name: primary NB tumors from stage 4 NB (patient ALIVE at 5 years)


title: 1558

description: gene expression

value: F

value: amplified


title: 2056 (2nd)

description: gene expression


title: 2035

description: gene expression


title: 2362

description: gene expression


title: 1995

description: gene expression


title: 1905

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_30H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_30H

value: cultured in Differentiation medium for EpiLC induction for 30 hours


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_24H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_24H


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_18H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_18H

value: cultured in Differentiation medium for EpiLC induction for 18 hours


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_12H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_12H

value: cultured in Differentiation medium for EpiLC induction for 12 hours


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_EpiLC_6H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_EpiLC_6H

value: cultured in Differentiation medium for EpiLC induction for 6 hours


title: 1889

description: gene expression


title: 1045

description: gene expression


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_2iL_0H

description:
cells without ISY1 overexpression
EpiLC_differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_2iL_0H

value: Dox-inducible Flag-ISY1 KH2 ESC line

value: cultured in 2i/Lif medium


title: 27_11_GLIO

city: Columbus

first: Alessandra

last: Drusco

address: 460 W. 12th Ave.  Biological Research Tower 1094

department: Department of Cancer Biology and Genetics

institute: The Ohio State University

description: MIRNA EXPRESSION FROM SEV

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Hybridization reactions were performed with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies) following the manufacturer’s instructions

scan_protocol: For each assay, a high density scan (600 fields of view) was performed.

data_processing: Nanostring data were normalized by using the Top-100 expressed miRNA normalization as implemented by the Nanostring nSolver software. P-values were calculated using the LIMMA package (Linear Models for Microarray Data) from the Bioconductor R project.

label: Refer to the NanoString nCounter Assay System Manual

source_name: GLIOBLASTOMA

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

extract_protocol: Extracellular vesicles were extracted from 250μl of serum using Exoquick plus (System Bioscience cat#EXOQ5TM-1) and following manufacturer instructions. The exosomal pellet resuspended in  1,5 ml of TRIReagent (SIGMA-ALDRICH cat#T9424-200ml), and  2μl of 33.3 attoMole solution of spike-ins (cel-miR-248 and ath-miR159a) were added to each sample. Manufacturer instructions were followed up to the isolation of the acqueous phase. An equal volume of 70% ETOH was added to the acqueous phase, and loaded to the columns of the NORGEN RNA Clean-up and Concentration kit (cat#23600) and RNA was isolated following manufacturer instructions.

value: GLIOBLASTOMA

value: serum extracellular vescicles (SEV)


title: 28_12_GLIO

description: MIRNA EXPRESSION FROM SEV


title: 26_10_GLIO

description: MIRNA EXPRESSION FROM SEV


title: PolyA(+)_RNA-seq_EB (-Dox)_D10

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_EB_-Dox_D10

value: ESCs

value: cultured in Differentiation medium for EB induction for 10 day


title: PolyA(+)_RNA-seq_EB (-Dox)_D13

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_EB_-Dox_D13

value: cultured in Differentiation medium for EB induction for 13 day

value: without Dox


title: PolyA(+)_RNA-seq_EB (-Dox)_D8

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_EB_-Dox_D8

value: cultured in Differentiation medium for EB induction for 8 day


title: 22_09_GLIO

description: MIRNA EXPRESSION FROM SEV


title: 25_12_GLIO

description: MIRNA EXPRESSION FROM SEV


title: 24_11_GLIO

description: MIRNA EXPRESSION FROM SEV


title: PolyA(+)_RNA-seq_EB (-Dox)_D4

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_EB_-Dox_D4

value: cultured in Differentiation medium for EB induction for 4 day


title: 23_10_GLIO

description: MIRNA EXPRESSION FROM SEV


title: PolyA(+)_RNA-seq_EB (-Dox)_D2

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_EB_-Dox_D2

value: cultured in Differentiation medium for EB induction for 2 day


title: 21_12_GLIO

description: MIRNA EXPRESSION FROM SEV


title: PolyA(+)_RNA-seq_EB (-Dox)_D1

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_EB_-Dox_D1

value: cultured in Differentiation medium for EB induction for 1 day


title: PolyA(+)_RNA-seq_KH2-ISY1 (+Dox)_SL_Day0

description:
cells with ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_+Dox_SL_Day0

value: cultured in Serum/Lif medium

value: with Dox


title: 20_11_GLIO

description: MIRNA EXPRESSION FROM SEV


title: 19_10_GLIO

description: MIRNA EXPRESSION FROM SEV


title: PolyA(+)_RNA-seq_KH2-ISY1 (-Dox)_SL_Day0

description:
cells without ISY1 overexpression
EB_Differentiation.txt
PolyA_+_RNA-seq_KH2-ISY1_-Dox_SL_Day0


title: 8_04_OLIGO

description: MIRNA EXPRESSION FROM SEV

source_name: OLIGODENDROGLIOMA

value: OLIGODENDROGLIOMA


title: 1684

description: gene expression

value: M

value: amplified


title: 1236

description: gene expression

source_name: BM from metastatic NB

value: F

value: single copy


title: 1864

description: gene expression


title: 2010

description: gene expression

value: gain


title: 1401

description: gene expression


title: Serum, WNT1 mutation negative, rep12

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: CONTROL

data_processing: Cq-values were normalized to the mean Cq-value in each sample (global mean normalization) by subtracting the individual miRNA Cq-value from the Cq average calculated for that sample.

label: SYBR Green

source_name: serum

label_protocol: Starting from total RNA samples, we synthesized cDNA using the Universal cDNA Synthesis Kit II (Exiqon, Denmark). We chose reaction conditions according to recommendations by the manufacturer. The protocol was modified in that 4µL of total RNA were used per 10 µl reverse transcription (RT) reaction. To monitor RT efficiency and presence of impurities with inhibitory activity, a synthetic RNA spike-in (cel-miR-39-3p) was added to the RT reaction. PCR amplification was performed in a 384-well plate format using custom pick&mix plates (Exiqon, Denmark) in a Roche LC480 II instrument (Roche, Germany) and EXiLENT SYBR Green mastermix (Exiqon, Denmark) with the following settings: 95°C for 10 min, 45 cycles of 95°C for 10 s and 60°C for 60s, followed by melting curve analysis. To calculate the cycle of quantification values (Cq-values), the second derivative method was used.

growth_protocol: We collected all serum samples during the spring (January-April) in 2017 to avoid bias from natural sunlight. All samples were taken after a 12-hour fast, in the morning between 8 and 9 am. First venous blood was collected into normal serum tubes and left to stand in room temperature for 30-60 minutes to allow clotting. To separate the serum, the tubes were then centrifuged at 2500 x g for 10 minutes in room temperature. The supernatant was then transferred to 250 µl aliquots in 1.5 ml tubes. The serum was then immediately stored at -80°C.

extract_protocol: We isolated RNA was isolated using the miRNeasy Mini Kit (Qiagen, Germany). Serum samples were thawed on ice and centrifuged at 12,000g for 5 minutes to remove any cellular debris. For each sample, 200 µL of serum was mixed with 1000 µL Qiazol and 1µL synthetic Spike-Ins (Exiqon, Denmark). After a 10-minute incubation at room temperature, 200 µL chloroform were added to the lysates followed by cooled centrifugation at 12,000g for 15 minutes at 4°C. Precisely 650 µL of the upper aqueous phase were mixed with 7 µL glycogen (50mg/mL) to enhance precipitation. Samples were transferred to a miRNeasy mini column, RNA was precipitated with 750 µL ethanol followed by washing with RPE and RWT buffer. RNA as eluted in 30 µL nuclease free water and stored at -80°C until further analysis.

value: male

tag: subfamily

value: serum

tag: genotype

value: wildtype WNT1


title: 1108

description: gene expression


title: 789

description: gene expression


title: 1127

description: gene expression


title: 1893

description: gene expression


title: 1928

description: gene expression


title: 1305

description: gene expression


title: 20GD2+

description: gene expression

source_name: GD2 positive cells from metastatic NB


title: 6_06_OLIGO

description: MIRNA EXPRESSION FROM SEV

tag: cell type

value: serum extracellular vescicles (SEV)


title: Serum, WNT1 mutation negative, rep11

description: CONTROL

value: female


title: Small_RNA-seq_EB (-Dox)_D4

description:
Small RNA
without Dox treatment
KH2-ISY1_miRNA.txt
Small_RNA-seq_EB_-Dox_D4

value: Dox-inducible Flag-ISY1 KH2 ESC line

value: ESCs

tag: culture condition

value: without Dox


title: 7_03_OLIGO

description: MIRNA EXPRESSION FROM SEV


title: 1198

description: gene expression

tag: age (months)


title: 5_05_OLIGO

description: MIRNA EXPRESSION FROM SEV


title: 1386

description: gene expression

tag: Sex


title: 1051

description: gene expression

tag: inss stage


title: 17GD2+

description: gene expression

tag: mycn status


title: 2092

description: gene expression

tag: date of sampling/diagnosis


title: 1445

description: gene expression

tag: patient's id


title: 3917GD2+

description: gene expression


title: 15GD2+

description: gene expression


title: Serum, WNT1 mutation negative, rep9

description: CONTROL


title: Serum, WNT1 mutation negative, rep10

description: CONTROL


title: Serum, WNT1 mutation negative, rep8

description: CONTROL


title: 4_04_OLIGO

description: MIRNA EXPRESSION FROM SEV


title: 3_06_OLIGO

description: MIRNA EXPRESSION FROM SEV


title: Serum, WNT1 mutation negative, rep7

description: CONTROL


title: Serum, WNT1 mutation negative, rep6

description: CONTROL


title: 13GD2+

description: gene expression


title: 2_05_OLIGO

description: MIRNA EXPRESSION FROM SEV


title: 3GD2+

description: gene expression


title: 2GD2+

description: gene expression


title: Serum, WNT1 mutation negative, rep5

description: CONTROL


title: 1_04_OLIGO

description: MIRNA EXPRESSION FROM SEV


title: Serum, WNT1 mutation negative, rep4

description: CONTROL


title: 14GD2+

description: gene expression


title: Serum, WNT1 mutation negative, rep3

description: CONTROL


title: Serum, WNT1 mutation negative, rep2

description: CONTROL


title: Serum, WNT1 mutation negative, rep1

description: CONTROL


title: Serum, WNT1 mutation positive, rep12

description: CASE

value: heterozygous missense mutation p.C218G in WNT1


title: 15_09_ASTRO

description: MIRNA EXPRESSION FROM SEV

source_name: ASTROCYTOMAS

value: ASTROCYTOMAS


title: 16_06_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: 14_08_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: 13_07_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: 18_08_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: 12_09_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: Serum, WNT1 mutation positive, rep11

description: CASE


title: Serum, WNT1 mutation positive, rep10

description: CASE


title: 17_07_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: 6GD2+

description: gene expression


title: 7GD2+

description: gene expression


title: Serum, WNT1 mutation positive, rep9

description: CASE


title: 5GD2+

description: gene expression


title: 1506

description: gene expression


title: 11_08_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: 1276

description: gene expression


title: Serum, WNT1 mutation positive, rep7

description: CASE


title: Liver from Bmi1 KO C57 mice,biological rep1

city: Wuhan

first: Yuyuan

last: Chen

address: Hangkong Road

institute: School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: liver, gene knockout

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Both wild type and Bmi1 KO mice were fed with normal chow.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Gene knockout.

value: liver

tag: genotype/variation

value: Bmi1 KO


title: Liver from Bmi1 KO C57 mice,biological rep2


title: Liver from Bmi1 KO C57 mice,biological rep3


title: Serum, WNT1 mutation positive, rep6

description: CASE


title: C8_02_CTRL

description: MIRNA EXPRESSION FROM SEV

source_name: NORMAL/NONDISEASED

value: NORMAL/NONDISEASED


title: C7_01_CTRL

description: MIRNA EXPRESSION FROM SEV


title: C6_03_CTRL

description: MIRNA EXPRESSION FROM SEV


title: Liver from wildtype C57 mice, biological rep2

source_name: liver

value: control


title: Serum, WNT1 mutation positive, rep8

description: CASE


title: C5_02_CTRL

description: MIRNA EXPRESSION FROM SEV


title: 10_07_ASTRO

description: MIRNA EXPRESSION FROM SEV


title: C4_01_CTRL

description: MIRNA EXPRESSION FROM SEV


title: Serum, WNT1 mutation positive, rep4

description: CASE


title: Serum, WNT1 mutation positive, rep5

description: CASE


title: Hep3B Bmi1 KO

source_name: HCC cell, gene knockout

growth_protocol: Cell lines were grown under standard cell culture conditions in a 5% CO2-humidified chamber

treatment_protocol: shRNA interference.

tag: cell line


title: TUV-2

city: Shanghai

first: ruixue

last: zhou

address: Dong'an Road

institute: Fudan University

data_processing:
Illumina Hiseq sequencing platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT
The exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Expression of genes in all samples

source_name: EHEC（the strain of EHEC）

growth_protocol: Mouse peritoneal macrophages were cultured with10% DMEM complete medium.

extract_protocol:
Total RNA was harvested from primary macrophages using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: Primary macrophages were infected with the bacterial strains of EHEC or EHEC∆Tir for 6 hours.

tag: strain

tag: age

value: peritoneal macrophages


title: delta Tir-2

source_name: EHEC△Tir (an EHEC strain in which the Tir protein is deleted)

tag: tissue


title: delta Tir-1


title: Hep3B control

source_name: HCC cell


title: C3_03_CTRL

description: MIRNA EXPRESSION FROM SEV


title: Serum, WNT1 mutation positive, rep3

description: CASE


title: Serum, WNT1 mutation positive, rep2

description: CASE


title: Liver from wildtype C57 mice, biological rep1


title: C2_02_CTRL

description: MIRNA EXPRESSION FROM SEV


title: Huh7 Bmi1 KO


title: Liver from wildtype C57 mice, biological rep3


title: TUV-1


title: Huh7 control


title: Serum, WNT1 mutation positive, rep1

description: CASE


title: C1_01_CTRL

description: MIRNA EXPRESSION FROM SEV


title: Escherichia_coli_pnp_Rend_seq_MOPS_comp_25s_frag

status: Public on Mar 28 2018

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

institute: University of Montreal

description: mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000913.2 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
NC_000913.2
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

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

source_name: Bacteria

growth_protocol: Overnight cultures were diluted to OD590 0.0003 in 20 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (200 rpm) until OD590 reached 0.3.

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

tag: growth medium

value: MOPS complete (Teknova) with full supplement (Neidhart et al., 1974).


title: 1394_48hr_1

first: Ryan

middle: D

last: Fine

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

data_processing:
Barcoded cDNA was sequenced on an Illumina Nextseq 500. Fastq files from all 4 lanes were pooled together for individual samples.
Reads were then mapped to the sacCer3 genome using bowtie2 with default options.
The resulting bam files were then converted into counts of reads overlapping sacCer3 annotated ORFs using bedtools.
The resulting matrix of read counts was manually annoated with sample names and further analyzed in edgeR to produce the figures in the paper.
Genome_build: sacCer3
Supplementary_files_format_and_content: Text file containing a matrix of sample read counts for the ~6700 genes in the yeast genome.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30C in YPD medium with 2% Glucose as the Carbon source.

extract_protocol:
Cells were grown in 50mL volumes to the indicated time point. 3mL of cells was taken and spun down for RNA acid-phenol extraction followed by standard etOH precipitation.
A minimum of 5 ug of RNA was used as input for NEBNext® Poly-A enrichment and Ultra Directional II cDNA library construction.
Poly-A enrichment coupled with directional cDNA dUTP second strand synthesis.

tag: time

value: snf1 null


title: 1394_48hr_2


title: 1416_48hr_1

value: snf1 suppressor


title: 1416_48hr_3


title: 1416_48hr_2


title: 1256_48hr_2

value: WT


title: 1256_48hr_3


title: 1416_24hr_2


title: 1394_48hr_3


title: 1416_24hr_1


title: 1256_48hr_1


title: 1394_24hr_1


title: 1394_24hr_3


title: 1256_24hr_3


title: 1394_24hr_2


title: 1256_24hr_2


title: 1256_24hr_1


title: 1394_5hr_3


title: 1416_5hr_1


title: 1394_5hr_2


title: 1256_5hr_3


title: 1256_5hr_2


title: 1394_5hr_1


title: Escherichia_coli_rnb_Rend_seq_MOPS_comp_25s_frag

description: mRNA

growth_protocol: Overnight cultures were diluted to OD590 0.0003 in 20 mL fresh media. The culture was kept in a 125 mL flask at 30C with aeration (200 rpm) until OD590 reached 0.3.


title: 9_05_OLIGO

description: MIRNA EXPRESSION FROM SEV

value: OLIGODENDROGLIOMA


title: 1256_5hr_1


title: Escherichia_coli_WT_Rend_seq_5_exo_MOPS_comp_25s_frag

description: 5' monophosphate sensitive exonuclease treated mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000913.2 using Bowtie v1.0.1 with options -v 1 -k 2 m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
NC_000913.2
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Total extracted RNA was treated with 5' monophosphate dependent exonuclease (Epicentre). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: Xnr2-animal_caps st14 (NR2_st14_1)

city: La Jolla

first: Chris

last: Kintner

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular Neurobiology Lab

institute: Salk Institute for Biological Studies

description: diff.txt

data_processing:
Sequenced reads were quality-tested using FASTQC (Andrew, 2010) and aligned to the Xenopus laevis (V9.1) genome using the STAR aligner (Dobin et al., 2013) version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
The genome index was constructed using the gene annotation provided by the Mayball models. Uniquely mapped reads were quantified across all gene exons using the top-expressed isoform as proxy for gene expression with the HOMER (Heinz et al., 2010) analysis suite, and differential gene expression was carried out with edger (Robinson et al., 2010) using duplicates to compute within-group dispersion.
Genome_build: XL9.1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

organism: Xenopus laevis

source_name: Xenopus laevis animal cap

growth_protocol: XenoThe animal caps were excised at st10, the blastula stage. Tissues are cultured at DFA and harvested at stage 14 for RNA extraction.

extract_protocol:
A total of ten explants were pooled and extracted for total RNA, using the proteinase-K approach, followed by phenol/Chloroform extraction, followed by LiCl precipitation.
RNA was subjected to polyA selection and then converted into RNAseq libraries, using the Illumina Truseq RNA Sample Preparation kit v2 according to the manufacturer’s instructions, and sequenced on a HiSeq 2000 or 2500 at 1x50 or 1x100 base pairs to a depth of 20-40 million reads.

tag: Stage

value: exogenous xnr2 expression


title: Xnr2-animal_caps st14 (NR2_st14_3)

description: diff.txt

tag: genotype


title: Escherichia_coli_WT_Rend_seq_MOPS_comp_25s_frag_pooled

description: mRNA

data_processing:
Base calls performed using Casava version 1.7.
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000913.2 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_000913.2
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

growth_protocol:
growth medium: MOPS complete (Teknova) with full supplement (Neidhart et al., 1974).
Overnight cultures were diluted 10 000 fold in 20 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.


title: H3K36me3-0hour

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

description: H3K36me3 ChiP-seq after VEGF stimulation for 0hour

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using bowtie2 with the following configurations: -p 1
ChiP-seq Peaks were called using MACS with the following setting: -f BAM -g 2.45e9, and then peaks fall inside the blacklist of ChIP-seq regions were trimmed.
The reads density was calculated using Homer and displayed in tag heat map using JAVA Tree.
RNA-seq reads were aligned to the hg19 genome assembly using tophat2.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al. , Nature protocols 7.3 (2012): 562-578. In short, cufflinks was used for transcript assembly supplying a set of gene model annotation from GENCODE 19, cuffmerge for assemblies merge, cuffdiff for differnetial analysis and CummeRbund for the following analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

growth_protocol: Primary HUVEC cells purchased from Lonza  within 3-6 passages were grown  in EBM2+1% FBS or EGM2 medium (Lonza)

extract_protocol:
ChiP-seq: Chromatin DNA was extracted from sonicated nuclei and further selectively accumulated by ChiP-specific antibody.  RNA-seq: total RNA were purified by Qiagen RNeasy column.
Illumina multiplex library protocol for ChiP-seq and mRNA seq of VEGF stimualtion is as described (Bing Zhang, et al. , 2013,Genome Res. 2013 Jun;23(6):917-27); Spike-in mRNA-seq protocol followed ScriptSeq v2 RNA-seq kit (Illumina)

treatment_protocol: 50ng/ml VEGFa was used to treat serum-starved HUVEC cells. For modified RNA experiments, 0.5ug/ml modified RNA expressing GFP and ETS1 was used. For siRNA experiment, 10ng/ml siRNA was used.

value: HUVEC

tag: cell type

value: Primary Human Umbilical Vein Endothelial Cell line

tag: passage

tag: chip antibody

value: H3K36me3, Abcam


title: H3K36me3-4hour

description: H3K36me3 ChiP-seq after VEGF stimulation for 4hour

tag: stimulated with

value: 50ng/ml VEGFa for 4hr


title: lt-NES_201B7_input_rep1

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Adaptor was removed and low quality reads were trimmed using Trimmomatic version 0.33.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.1.0 with default settings.
Peaks were called using MACS version 2.1.0.20150731.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using Deeptools version 1.5.1 (bamCoverage) with the following option --binSize 50 --fragmentLength 200.

source_name: hiPSC-derived lt-NES

extract_protocol:
For single fixation with formaldehyde, cells were fixed with 1% formaldehyde-containing medium for 10 min. For double fixation, the cells were first fixed with 2 mM EGS for 30 min followed by with 1% formaldehyde-containing medium for 10 min.
Libraries were prepared using KAPA Hyperprep Kit.

value: hiPSC-derived lt-NES

value: wild type

tag: chip-antibody


title: lt-NES_201B7_input_rep2


title: lt-NES_201B7_H3K27ac_rep2

value: H3K27ac (MBL, MABI0309)


title: NCC_CHD7_CST_rep2

source_name: hiPSC-derived neural crest cell

value: hiPSC-derived neural crest cell

value: CHD7 (CST, #6505,  clone D3F5)


title: lt-NES_201B7_H3K27ac_rep1


title: VEGF-0hour

description: RNA-seq after VEGF stimulation for 0hour

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using bowtie2 with the following configurations: -p 1
ChiP-seq Peaks were called using MACS with the following setting: -f BAM -g 2.45e9, and then peaks fall inside the blacklist of ChIP-seq regions were trimmed.
The reads density was calculated using Homer and displayed in tag heat map using JAVA Tree.
RNA-seq reads were aligned to the hg19 genome assembly using tophat2.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell, Cole, et al. , Nature protocols 7.3 (2012): 562-578. In short, cufflinks was used for transcript assembly supplying a set of gene model annotation from GENCODE 19, cuffmerge for assemblies merge, cuffdiff for differnetial analysis and CummeRbund for the following analysis.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm, peaks.bed

source_name: Human Endothlial cell line

value: Primary Human Umbilical Vein Endothelial Cells

tag: agent

value: VEGF

tag: time point


title: VEGF-4hour

description: RNA-seq after VEGF stimulation for 4hour


title: NCC_input_rep2


title: H3K36me3-12hour

description: H3K36me3 ChiP-seq after VEGF stimulation for 12hour

value: 50ng/ml VEGFa for 12hr


title: lt-NES_1210B2_H3K27ac_rep1


title: NE_input_rep2


title: NE_CHD7_CST_rep1


title: NE_input_rep1


title: H3K36me3-1hour

description: H3K36me3 ChiP-seq after VEGF stimulation for 1hour

value: 50ng/ml VEGFa for 1hr


title: lt-NES_1210B2_input


title: iPSC_CHD7_CST_rep2

source_name: hiPSC

value: hiPSC


title: NCC_input_rep1


title: NE_CHD7_CST_rep2


title: iPSC_input_rep2


title: NCC_CHD7_CST_rep1


title: iPSC_CHD7_CST_rep1


title: VEGF-12hour

description: RNA-seq after VEGF stimulation for 12hour


title: VEGF-1hour

description: RNA-seq after VEGF stimulation for 1hour


title: lt-NES_1210B2_H3K27ac_rep2


title: AF22_p300_input


title: AF22_p300

value: P300 (Santa Cruz,  sc-48343)


title: AF22_shMix_H3K27Ac_rep2

value: shMix (CHD7-KD)


title: AF22_shMix_input_rep1


title: AF22_shMix_input_rep2


title: AF22_sh411_H3K27Ac_rep1

value: sh411 (CHD7-KD)


title: AF22_sh410_H3K27Ac_rep1

value: sh410 (CHD7-KD)


title: AF22_sh411_H3K27Ac_rep2


title: AF22_sh411_input_rep2


title: AF22_sh410_input_rep2


title: CB1_HA (CHD7)

value: HA-tag knockin cell

value: HA (Roche, clone 3F10)


title: AF22_shCTRL_input_rep1

value: shCTRL


title: AF22_shMix_H3K27Ac_rep1

value: hiPSC-derived lt-NES


title: F10_HA (CHD7)


title: AF22_sh411_input_rep1


title: AF22_HA_input

value: wild type


title: AF22_sh410_H3K27Ac_rep2

value: H3K27ac (MBL, MABI0309)


title: AF22_shCTRL_H3K27Ac_rep1


title: AF22_shCTRL_H3K27Ac_rep2


title: AF22_shCTRL_input_rep2


title: AF22_sh410_input_rep1


title: iPSC_input_rep1


title: AF22_CHD7_CST_D3F5


title: AF22_HA (non-HA knockin cells)_rep1


title: AF22_CHD7_Bethyl_input


title: AF22_CHD7_CST_input


title: AF22_H3K36me3

value: H3K36me3 (MBL, MABI0333)


title: AF22_H3K27ac


title: F10_input


title: AF22_H3K27me3

value: H3K27me3 (MBL, MABI0323)


title: AF22_HA (non-HA knockin cells)_rep2


title: CB1_input


title: AF22_H3K9me3

value: H3K9me3 (MBL, MABI0308)


title: sh411_H10

description:
PolyA RNA
processed data file: SF_Gene_TPM_matrix.txt

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
The resulting reads were mapped to the UCSC human genome 19 using sailfish version 0.7.6 with default setting.
Low quality samples (CTRL_F01 and sh410_D05) were removed from data set based on mapping rate and detected gene number.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SF_Gene_TPM_matrix.txt: Tab-delimited text file includes TPM values for each Sample.

extract_protocol:
Control and CHD7-knockdown NE cells were sorted into 96 well plate with a flow cytometer SH800 (SONY) and dissolved with single cell lysis buffer (0.5% NP40).
Whole-transcript amplification was performed as previously described (Sasagawa et al. 2013; Sasagawa et al. 2017). Amplified cDNA from single cell was processed for library preparation using Nextera XT Library Prep Kit (Illumina).

tag: condition


title: sh411_H11


title: sh411_F09


title: sh411_H09


title: sh411_F11


title: sh411_F10


title: sh411_E10


title: sh411_F12


title: sh411_G11


title: sh411_G10


title: sh411_G12


title: AF22_CHD7_Bethyl_223A

tag: genotype/variation

value: CHD7 (Bethyl, A301-223A)


title: sh411_G09

tag: cell line


title: sh411_E11


title: AF22_input


title: AF22_H3K4me1

value: H3K4me1 (MBL, MABI0302)


title: AF22_H3K4me3

value: H3K4me3 (MBL, MABI0304)


title: sh411_D12


title: sh411_E09


title: sh411_D11


title: PrrX1_KO-rep2

city: shenzhen

first: Xiaolong

last: Tang

address: 3688 Nanhai Ave, Nanshan District

institute: shenzhen university

description:
all_samples_rpkm&RC.txt
PrrX1_KO2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: text files include RPKM and read count (RC)  values for each Sample

source_name: breast cancer cells

growth_protocol: BT549 cells were cultured in RPMI-1640 (Gibco®) with 10% FBS.

extract_protocol:
Total RNA extracts are first treated with DNase I to degrade DNA contamination. Next, by using the oligo (dT) magnetic beads the mRNA is enriched . Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. The first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with AMPure XP beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SIRT1 and PRRX1 were knocked out by CRISPR-Cas9 procedure in BT549 cells.

value: breast cancer

value: PRRX1 KO


title: sh411_D10


title: PrrX1_KO-rep1

description:
all_samples_rpkm&RC.txt
PrrX1_KO1


title: PrrX1_KO-rep3

description:
all_samples_rpkm&RC.txt
PrrX1_KO3


title: sh411_D09


title: Sirt1_KO-rep3

description:
all_samples_rpkm&RC.txt
Sirt1_KO3

value: Sirt1 KO


title: sh411_C12


title: Sirt1_KO-rep2

description:
all_samples_rpkm&RC.txt
Sirt1_KO2


title: sh411_E12


title: sh411_C11


title: Sirt1_KO-rep1

description:
all_samples_rpkm&RC.txt
Sirt1_KO1


title: WT-rep3

description:
all_samples_rpkm&RC.txt
WT_BT3

value: wildtype


title: sh411_B10


title: sh411_C09


title: sh411_A10


title: sh410_H07


title: sh410_H08


title: WT-rep2

description:
all_samples_rpkm&RC.txt
WT_BT2


title: WT-rep1

description:
all_samples_rpkm&RC.txt
WT_BT1


title: sh411_A09


title: sh410_G08


title: sh411_B11


title: sh411_A11


title: sh410_G07


title: sh410_H05


title: sh410_G05


title: HCT116_H3K9me3_5-aza-CdR

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: Z-score (H3K9me3_5-aza-CdR)

data_processing:
Sequencing reads were aligned against the human hg19 reference genome using Bowtie2
The number of overlapping mapped reads with ERV elements were obtained using Bedtool
The definitions of ERV elements were based on RepeatMasker
Genome_build: hg19
Supplementary_files_format_and_content: csv file. Z-score of H3K9 ChIP-seq for ERVs in each evolutionary age

growth_protocol: HCT116 cells were maintained in McCoy's 5A medium and cultured according to strandard mammalian tissue culture protocol and sterile technique.

extract_protocol:
All cells were harvested at 5 days post-treatments.
Single nucleosome preparation was performed according to the Dilworth lab native ChIP protocol.

treatment_protocol: HCT116 cells were treated with PBS or 300 nM 5-aza-CdR for 24 h.

value: colorectal carcinoma

tag: treatment

value: H3K9me3 (Active Motif AM39161)


title: HCT116_H3K9me2_5-aza-CdR

description: Z-score (H3K9me2_5-aza-CdR)

value: H3K9me2 (Abcam ab1220)


title: HCT116_H3K9me3_PBS

description: Z-score (H3K9me3_PBS)

value: PBS


title: sh410_G06

value: hiPSC-derived lt-NES


title: sh410_F08


title: sh410_F07


title: sh410_F06


title: sh410_F05


title: sh411_C10


title: sh410_E08


title: sh411_B12


title: sh411_B09


title: sh410_E07


title: sh410_H06


title: sh410_D08


title: sh410_C06


title: sh410_B07


title: sh410_C05


title: sh410_D07


title: sh410_B05


title: sh410_B08


title: sh410_E06


title: sh410_A08


title: sh410_D06


title: sh410_A07


title: HCT116_H3K9me2_PBS

description: Z-score (H3K9me2_PBS)


title: sh410_B06


title: sh410_A06


title: CTRL_H03

value: shCTRL


title: CTRL_H04


title: sh410_C08


title: CTRL_H01


title: sh410_C07


title: CTRL_G04


title: sh410_E05


title: CTRL_G03


title: 3dp MPLA 2

city: Nashville

first: Benjamin

middle: Ari

last: Fensterheim

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University

description:
Sample 11
MultiRankSeq_123_vs_101112.html.diff.csv

data_processing:
Pooled libraries were subjected to 75 bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.created by a polyA-selected build. The RNA-seq data was quality controlled following the multi-perspective guideline(24). Quality control metrics were computed from software QC3(25). No quality issues were observed.
Alignment was performed by TopHat 2(26) on MM10 reference genome. Read count per gene was generated using HTSeq(27). Differential expression analyses were performed using MultiRankSeq(28) which combines results from DEGseq(29), edgeR(30), and baySeq(31). Log2 fold change values shown are derived from DEGseq with an adjusted p<.05.
Differential expression analyses were performed using MultiRankSeq which combines results from DEGseq, edgeR, and baySeq. Log2 fold change values shown are derived from DEGseq with an adjusted p<.05.
Genome_build: MM10
Supplementary_files_format_and_content: .csv that includes geneID, log2FoldChange(DESeq2), pValue(DESeq2,) pAdj(DESeq2), log2FoldChange(edgeR), pValue(edgeR), pAdj(edgeR), log2FoldChange(raw), 1-Likelihood(baySeq), AdjLikelihood(baySeq), rank(DESeq), rank(edgeR), rank(baySeq), rankMethod1 (combined rank).

source_name: Bone Marrow Derived Macrophages

growth_protocol: WT bone marrow derived macrophages were derived from 8-16 week old C57/BL6 male mice purchased from the Jackson Laboratories. Male MyD88-/- and TRIF-/- mice were purchased from the Jackson Laboratories. For macrophage generation, femurs were flushed with 5mL cold PBS and bone marrow was incubated on Falcon petri dishes in RPMI 1640 with glutamine and 25mM HEPES (Gibco, Carlsbad, CA) containing 10% certified FBS (Gibco, Carlsbad, CA), 1% antibiotic-antimycotic (Gibco, Carlsbad, CA), and 10ng/mL mouse recombinant macrophage colony stimulating factor (M-CSF, R&D Systems, Minneapolis, MN) for 7 days. At the initiation of the growth period, bone marrow cell concentration was 4x104/ml, as this density has been found to yield mature macrophages. M-CSF remained in the culture throughout experimentation. After 7 days of incubation, macrophages were washed with PBS and incubated with media containing MPLA.

extract_protocol:
Total RNA was isolated under an RNase-free environment, using the RNeasy Mini Kit (Qiagen). RNA concentration and quality were verified with a Thermo Scientific NanoDrop 2000 spectrophotometer. Total RNA quality was then re-assessed using the 2100 Bioanalyzer (Agilent Technologies).
At least 200ng of DNase-treated total RNA with a RNA integrity number greater than 6 was used to generate polyA (mRNA) enriched libraries using TruSeq Stranded mRNA sample kits with indexed adaptors (Illumina). Library quality was assessed using the 2100 Bioanalyzer (Agilent Technologies) and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems).

treatment_protocol: Bone marrow derived macrophages were harvested for RNA after 4hrs of monophosphoryl lipid A (MPLA) priming, 24hrs of MPLA priming, 3 days following the end of MPLA priming, or a control group not exposed to MPLA

tag: strain

tag: growth media

value: M-CSF


title: 3dp MPLA 3

description:
Sample 12
MultiRankSeq_123_vs_101112.html.diff.csv


title: 3dp MPLA 1

description:
Sample 10
MultiRankSeq_123_vs_101112.html.diff.csv


title: 24hrs MPLA 1

description:
Sample 7
MultiRankSeq_123_vs_789.html.diff.csv


title: 24hrs MPLA 2

description:
Sample 8
MultiRankSeq_123_vs_789.html.diff.csv


title: 24hrs MPLA 3

description:
Sample 9
MultiRankSeq_123_vs_789.html.diff.csv


title: 4hrs MPLA 3

description:
Sample 6
MultiRankSeq_123_vs_456.html.diff.csv


title: 4hrs MPLA 2

description:
Sample 5
MultiRankSeq_123_vs_456.html.diff.csv


title: sh410_A05


title: Control 3

description:
Sample 3
MultiRankSeq_123_vs_456.html.diff.csv
MultiRankSeq_123_vs_789.html.diff.csv
MultiRankSeq_123_vs_101112.html.diff.csv


title: CTRL_G01


title: CTRL_H02


title: 4hrs MPLA 1

description:
Sample 4
MultiRankSeq_123_vs_456.html.diff.csv


title: CTRL_E04


title: CTRL_G02


title: Control 2

description:
Sample 2
MultiRankSeq_123_vs_456.html.diff.csv
MultiRankSeq_123_vs_789.html.diff.csv
MultiRankSeq_123_vs_101112.html.diff.csv


title: CTRL_E03


title: CTRL_F02


title: CTRL_F03


title: CTRL_F04


title: CTRL_E02


title: Patient_CODE38 - CTRL

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

institute: IRCCS Ospedale Oncologico di Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <700 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.

source_name: PBMCs

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the QIAzol® Lysis Reagent, according to the manufacturer’s instructions. Quality control was performed with Biorad Experion.

tag: disease state

value: control

tag: age

tag: tissue

value: PBMCs


title: Patient_CODE37 - CTRL


title: Patient_CODE40 - CTRL


title: Patient_CODE34 - CTRL


title: Patient_CODE36 - CTRL


title: Patient_CODE35 - CTRL


title: Control 1

description:
Sample 1
MultiRankSeq_123_vs_456.html.diff.csv
MultiRankSeq_123_vs_789.html.diff.csv
MultiRankSeq_123_vs_101112.html.diff.csv


title: CTRL_D04


title: Patient_CODE33 - CTRL


title: CTRL_D01


title: CTRL_D02


title: Patient_CODE32 - CTRL


title: CTRL_C04


title: CTRL_C03


title: Patient_CODE39 - CTRL


title: Patient_CODE31 - CTRL


title: Patient_CODE30 - CTRL


title: Patient_CODE29 - CTRL


title: Patient_CODE28 - CTRL


title: Patient_CODE27 - CTRL


title: CTRL_D03


title: CTRL_E01


title: arota_diabetes_rep2

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: gene expression data from adipose from control

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

organism: Rattus norvegicus

source_name: diabetic, 17 weeks

label_protocol: Affymetrix protocol

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

value: cardiac muscle

value: 17 week


title: arota_diabetes_rep3


title: arota_diabetes_rep1


title: arota_liraglutide-treated_rep3

description: gene expression data from adipose from maternal chromium restriction

source_name: liraglutide-treated, 17 weeks


title: arota_liraglutide-treated_rep2


title: arota_liraglutide-treated_rep1


title: CTRL_C01


title: CTRL_B04


title: CTRL_B03


title: CTRL_C02


title: Patient_CODE25 - CTRL


title: Patient_CODE24 - CTRL


title: CTRL_B02


title: CTRL_B01


title: Patient_CODE23 - CTRL


title: Patient_CODE22 - CTRL


title: Patient_CODE26 - CTRL


title: Patient_CODE21 - CTRL


title: CTRL_A03


title: Patient_CODE20- MS

value: Metabolic Syndrome


title: CTRL_A02


title: Patient_CODE19 - MS


title: CTRL_A01


title: CTRL_A04


title: PEO1R_SI+MI-3

city: Philadelphia

first: Gao

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: human ovarian cancer cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Human ovarian cancer cells were grown in 10% RPMI 1640 medium before they reach the 70% confluency.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

treatment_protocol: Human melanoma cells were treated with the control, Src inhibitor, MEK inhibitor, respectively or in combination.

value: PEO1R ovarian cancer cells

value: MEK inhibition plus Src inhibition


title: Patient_CODE18 - MS


title: PEO1R_SI-1

value: Src inhibition


title: Patient_CODE16 - MS


title: Bacillus_subtilis_yhaM_Rend_seq_LB_105s_frag

city: Montreal

description: mRNA

data_processing:
Base calls performed using Casava version 1.7.
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse).
genome build: NC_000964.3
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol:
growth medium: LB
Overnight cultures were diluted to OD590 0.001 in 20 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 105 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: subspecies 168, yhaM::lox72


title: PEO1R_SI+MI-1


title: PEO1R_S3-1


title: Bacillus_subtilis_rnr_Rend_seq_LB_105s_frag

description: mRNA

value: subspecies 168, rnr::lox72


title: Patient_CODE15 - SM


title: PEO1R_M2-1

value: MEK inhibition


title: Patient_CODE14 - SM


title: Patient_CODE17 - SM


title: Bacillus_subtilis_pnpA_Rend_seq_LB_25s_frag

description: mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse).
NC_000964.3
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

value: subspecies 168, pnpA::lox72

tag: growth medium

value: LB


title: PEO1R_Ctrl-2


title: PEO1R_Ctrl-3


title: PEO1R_MI-1


title: Bacillus_subtilis_WT_Rend_seq_5_exo_LB_25s_frag_pooled

description: 5' monophosphate sensitive exonuclease treated mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 2 -m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
NC_000964.3
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

growth_protocol: Overnight cultures were diluted to OD590 0.0003 20 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (200 rpm) until OD590 reached 0.3.

value: subspecies 168


title: PEO1R_SI+MI-2


title: PEO1R_M3-1


title: Bacillus_subtilis_rph_Rend_seq_LB_105s_frag

description: mRNA

value: subspecies 168, rph::lox72


title: Patient_CODE13 - SM


title: Patient_CODE40 - CTRL

description: 5141769075 I

data_processing: The data were normalised using quantile normalization (background was not subtracted) with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <100 in more than 1 group were excluded. Data were analyzed with non parametric analysis plus False Discovery Rate, FDR.


title: Bacillus_subtilis_pnpA_Rend_seq_LB_105s_frag_2

description: mRNA


title: CH2-rep2

description:
SAMPLE 12
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were loaded into R for background correction, quantile normalization and log (base 2) conversion with the limma package.

source_name: iPS-derived ltNES

label_protocol: Total RNA was reverse-transcribed, labeled with biotin using the Target Amp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre).

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

value: CHARGE

tag: cell type

value: iPSC-derived neural stem/progenitor cells


title: Bacillus_subtilis_pnpA_Rend_seq_LB_105s_frag_1

description: mRNA

value: subspecies 168, pnpA::kan


title: Bacillus_subtilis_rho_Rend_seq_LB_25s_frag_pooled

description: mRNA

growth_protocol:
growth medium: LB
The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

value: subspecies 168, rho::lox72


title: Bacillus_subtilis_WT_Rend_seq_LB_200s_frag

description: mRNA

growth_protocol:
growth medium: LB
Overnight cultures were diluted to OD590 0.0003 in 20 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 200 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: CH2-rep1

description:
SAMPLE 11
Replicate 1


title: Bacillus_subtilis_WT_Rend_seq_LB_100s_frag

description: mRNA

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 100 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: PEO1R_S2-1


title: Patient_CODE6 - MS

value: PBMCs


title: Patient_CODE7 - MS


title: Bacillus_subtilis_WT_Rend_seq_LB_25s_frag_pooled

description: mRNA

data_processing:
Base calls performed using Casava version 1.7.
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position.The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peaks shadows were removed as described in the publication.
genome build: NC_000964.3
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

growth_protocol:
growth medium: LB
Overnight cultures were diluted to OD590 0.0003 20 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: Bacillus_subtilis_WT_Rend_seq_LB_50s_frag

description: mRNA

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 50 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: Patient_CODE8 - MS


title: Patient_CODE9 - MS


title: Patient_CODE10 - SM


title: Patient_CODE12 - SM


title: Patient_CODE11 - SM


title: Patient_CODE38 - CTRL

description: 5141769075 E

value: control


title: AF22+CHD7(R1494X)-rep2

description:
SAMPLE 8
Replicate 2

value: WT + mutant CHD7


title: Patient_CODE36 - CTRL

description: 5141769075 A


title: Patient_CODE39 - CTRL

description: 5141769075 G


title: CH1-rep2

description:
SAMPLE 10
Replicate 2


title: Bacillus_subtilis_ribosome_profiling_LB

description: ribosome protected mRNA

data_processing:
Base calls performed using Casava version 1.7.
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The footprint reads with size between 20 to 42 nucleotides in length were mapped to the genome using the center-weighted approach; for each footprint read, the center residues that are at least 10 nucleotides away from either ends were given a weight of one over the length of the fragment (minus the 10 nucleotides on both ends) to generate the wig file.
genome build: NC_000964.3
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

growth_protocol:
growth medium: LB
Overnight cultures were diluted to OD590 0.0003 in 250 mL fresh media. The culture was kept in a 2.8 L flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., Cell 2014). 250 mL of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
Ribosome protected mRNA fragments were size selected via gel purification, dephosphorylated at the 3’ end and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.


title: AF22+CHD7(G1391fs)-rep1

description:
SAMPLE 5
Replicate 1


title: Patient_CODE5 - MS

value: Metabolic Syndrome


title: PEO1R_Ctrl-1

value: PEO1R ovarian cancer cells


title: CH1-rep1

description:
SAMPLE 9
Replicate 1


title: Patient_CODE37 - CTRL

description: 5141769075 C


title: Patient_CODE3 - MS


title: Patient_CODE2 - MS


title: Patient_CODE4 - MS


title: Patient_CODE34 - CTRL

description: 5141769053 I


title: AF22-rep2

description:
SAMPLE 4
Replicate 2

value: WT


title: Patient_CODE1 - MS


title: AF22+CHD7(R1494X)-rep1

description:
SAMPLE 7
Replicate 1


title: AF22-rep1

description:
SAMPLE 3
Replicate 1


title: Patient_CODE35 - CTRL

description: 5141769053 K


title: AF22+CHD7(G1391fs)-rep2

description:
SAMPLE 6
Replicate 2


title: Patient_CODE33 - CTRL

description: 5141769053 G


title: Patient_CODE31 - CTRL

description: 5141769053 E


title: Patient_CODE29 - CTRL

description: 5141769075 K


title: 1210B2-rep1

description:
SAMPLE 1
Replicate 1


title: Patient_CODE27 - CTRL

description: 5141769038 J


title: Patient_CODE32 - CTRL

description: 5141769044 B


title: Patient_CODE30 - CTRL

description: 5141769053 C


title: Patient_CODE25 - CTRL

description: 5141751019 J


title: Patient_CODE23 - CTRL

description: 5141751084 J


title: T3_wt_3

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

data_processing:
Primary data analysis was done using Illumina’s real-time analysis software (RTA)
Sequenced reads containing adaptor sequences were discarded, remaining reads were trimmed, then mapped to the dm3 genome assembly and Ensembl gene-annotation version 78 using STAR aligner (using ENCODE settings)
Gene-level exon read counts were quantified using featurecounts (using ensembl78) and differential expression calculated using the limma voom pipeline
Replicate expression levels were quantified using rsem (using ensembl version 78)
Genome_build: dm3
Supplementary_files_format_and_content: Table (as tab separated values) with replicate expression levels [TPM], fold changes and p-values (Ash1-/- over wild type) for all quantifiable genes as output by the limma voom pipeline for T3 and T2 disks

organism: Drosophila melanogaster

source_name: T3 discs wt larvae replicate 3

growth_protocol: Drosophila were grown on standard medium at 25˚C

extract_protocol:
RNA was isolated from independently prepared batches of hand-dissected haltere and third-leg imaginal discs (T3 discs) or wing discs (T2 discs) from wild-type or ash122 homozygous larvae, using the Direct-zol RNA mini Prep Kit (Zymo Research). After additional Agencourt AMPure XP purification (Beckman Coulter) isolated RNA was analyzed on a Bioanalyzer (Agilent) using an RNA 6000 Nano Chip (Agilent).
Non-degraded RNA from independent biological replicates of each type of sample was used to construct sequencing libraries with the sense mRNA-Seq Library Prep Kit (Lexogen).
Quality-controlled and quantified libraries were sequenced on an HiSeq1500 system (Illumina) in the single-end mode (100 nt reading length).

value: haltere imaginal discs (T3 discs)

tag: genotype

value: wild type


title: T3_ASH1ko_5

source_name: T3 discs ash1[22] homozygous larvae replicate 5

value: ash1[22] null mutation


title: T3_wt_2

source_name: T3 discs wt larvae replicate 2


title: Patient_CODE28 - CTRL

description: 5141769053 A


title: 1210B2-rep2

description:
SAMPLE 2
Replicate 2


title: miRNA-12H2

description: VEGF treat 12hour

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed

data_processing: The NanoString nCounter assay measures 818 endogenous miRNAs. In addition there are 6 positive controls probes, 6 negative control probes, 5 housekeeping control probes, and 5 spike-in control probes. Data was processed with the NanoStringNorm R library. DESeq2 was used for data normalization and analysis of differential expression. Endogenous miRNAs with a count value smaller than the average count of the negative controls at any time point were removed. miRDB v5 was used for target predictions with a cut-off of > 80 for the prediction score.

source_name: VEGF treat 12hour

label_protocol: 100 ng of total RNA was used in 5 µl with specific miRNA tag probes from Nanostring using nCounter Human miRNA Expression Assay Kit

growth_protocol: Primary HUVEC cells purchased from Lonza (CC-2519) were grown in EGM2 full medium (CC-3162, Lonza). For VEGFA stimulation, HUVEC cells at 3-6 passages were grown overnight in low seum (EBM2 with 1% FBS) and then treated with 50 ng/ml VEGFA.

extract_protocol: miRNA was recovered from HUVECs using the PurelinkTM miRNA Kit (Life Technologies) with on-column DNaseI digestion.

treatment_protocol: After the starvation for overnight, HUVECs were treated with VEGF at 0-12hours.

value: VEGF

value: Primary Human Umbilical Vein Endothelial Cells


title: Patient_CODE26 - CTRL

description: 5141751019 K


title: Patient_CODE19 - MS

description: 5141769013 F


title: miRNA-12H1

description: VEGF treat 12hour


title: Vibrio_natriegens_ribosome_profiling_MOPS_comp_3NaCl

description: ribosome protected mRNA

data_processing:
Base calls performed using Casava version 1.7.
Sequence reads were trimmed for poly A stretches at the 3’ ends.
Trimmed reads were aligned to CP009977.1 and CP009978.1 (chromosome 1 and 2 respectively) using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The 5’ end of footprint reads with size between 20 to 42 nucleotides in length were mapped to the genome. Read counts were added 11 nt downstream of the 5’ end to generate the wig file.
genome build: CP009977.1, CP009978.1
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

source_name: Bacteria

growth_protocol:
growth medium: MOPS complete (Teknova) with full supplement (Neidhart et al., 1974), with added 3% NaCl
Overnight cultures were diluted to OD590 0.0003 in 100 mL fresh media. The culture was kept in a 2.8 L flask at 37C with aeration (180 rpm) until OD590 reached 0.3.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., Cell 2014). 100 mL of cell cultures was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
Ribosome protected mRNA fragments were size selected via gel purification and dephosphorylated at the 3’ end. cDNA library preparation then proceeded using the SMARTer smRNA-seq kit from Clontech following the manufacturer’s instructions.


title: Patient_CODE24 - CTRL

description: 5141769013 J


title: Patient_CODE22 - CTRL

description: 5141751019 I


title: lt-NES_CH2_H3K27ac_rep2

description: CHARGE patient require controlled access. Raw data is being registered at JGA (Japanese Genotype-Phenotype Archive).

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Adaptor was removed and low quality reads were trimmed using Trimmomatic version 0.33.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.1.0 with default settings.
Peaks were called using MACS version 2.1.0.20150731.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using Deeptools version 1.5.1 (bamCoverage) with the following option --binSize 50 --fragmentLength 200.

extract_protocol:
For single fixation with formaldehyde, cells were fixed with 1% formaldehyde-containing medium for 10 min. For double fixation, the cells were first fixed with 2 mM EGS for 30 min followed by with 1% formaldehyde-containing medium for 10 min.
Libraries were prepared using KAPA Hyperprep Kit.

value: hiPSC-derived lt-NES

value: CHARGE patient

value: H3K27ac (MBL, MABI0309)


title: Patient_CODE15 - SM

description: 5141769013 I


title: miRNA-4H2

description: VEGF treat 4hour

source_name: VEGF treat 4hour


title: Patient_CODE20- MS

description: 5141769013 H


title: lt-NES_CH2_input_rep2

source_name: hiPSC-derived lt-NES


title: Patient_CODE17 - SM

description: 5141769013 B


title: miRNA-4H1

description: VEGF treat 4hour


title: Patient_CODE16 - MS

description: 5141769013 K


title: miRNA-1H2

description: VEGF treat 1hour

source_name: VEGF treat 1hour


title: lt-NES_CH2_H3K27ac_rep1


title: Patient_CODE14 - SM

description: 5141769013 G


title: Patient_CODE21 - CTRL

description: 5141769057 J


title: WT-3

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
The purified cDNA template library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on Genome Analyzer IIx (GAIIx) with SBS TruSeq v5 reagents following the manufacturer's instructions (SingleRead 1 × 40 bases).
Image analysis and per-cycle base calling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ was performed with CASAVA-1.8 (Illumina). These files contain only reads that passed “chastity” filtering (flagged with a N, for *NOT filtered* in the sequence identifier line). “Chastity” parameter measures signal contamination in raw data and allows flagging unreliable reads.
Quality check was done via fastqc (v0.9.4, Babraham Bioinformatics). Raw reads were aligned to the reference genome hg19/GRCh37 with tophat1 (version 2.0.4) using the following parameters: –bowtie1, –max-multihits 5, –genome-read-mismatches 1, –segment-mismatches 1, –segment-length 19, –splice-mismatches 0, and –library-type fr-firststrand.
Gene expression levels (fragments per kilobase of exon per million fragments, FPKM) were quantified with cufflinks2 (version 2.0.2), as annotated in Ensembl version GRCh37.65, with the following parameters: -N, –library-type fr-firststrand, -u.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files or visualization in UCSC genome browser; txt files with cuantification from cufflinks

source_name: Pancreatic ductal adenocarcinoma

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 1% Na pyruvate, and 1% penicillin/streptomycin. All cells were free of mycoplasma contamination.

extract_protocol:
RNA from parental and MN58b-resistant cells was purified using TRIzol. Integrity was assayed on an Agilent 2100 Bioanalyzer
PolyA+ fractions were purified and randomly fragmented, converted to double-stranded cDNA, and processed by end-repair, dA-tailing, and adapter ligation (Illumina “TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D”). Adapter-ligated library was completed by 10 PCR cycles with Illumina PE primers. The purified cDNA template library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on Genome Analyzer IIx (GAIIx) with SBS TruSeq v5 reagents following the manufacturer's instructions (SingleRead 1 × 40 bases)

treatment_protocol: To generate MN58b-resistant IMIM-PC-2 cells, MN58b was added starting at 0.1 μmol/L. Control IMIM-PC-2 cells were cultured without drug. MN58b concentration was increased by 50% weekly at each passage of the cells (split 1:3 when confluent); final concentration was 8 μmol/L.

value: Parental

tag: Sex

value: Male


title: Patient_CODE13 - SM

description: 5050509010 K


title: WT-2


title: Patient_CODE11 - SM

description: 5141769013 A


title: Patient_CODE18 - MS

description: 5141769013 D


title: lt-NES_CH2_input_rep1


title: miRNA-1H1

description: VEGF treat 1hour


title: WT-1


title: lt-NES_CH1_H3K27ac_rep2


title: Patient_CODE12 - SM

description: 5141769013 C


title: R-3

description: we generated an MN58b-resistant line from parental IMIM-PC-2 cells by continuous culture with increasing drug concentrations. After 9 months of treatment, IMIM-PC-2-R cells were established


title: miRNA-0H2

description: VEGF treat 0hour

source_name: VEGF treat 0hour


title: Patient_CODE10 - SM

description: 5141769057 H


title: lt-NES_CH1_input_rep2


title: lt-NES_CH1_H3K27ac_rep1


title: miRNA-0H1

description: VEGF treat 0hour


title: R-2


title: R-1


title: Bacillus_subtilis_Delta_sU_ylqC_yqlD_ribosome_profiling_LB

description: ribosome protected mRNA

data_processing:
Sequence reads were trimmed for adaptor sequences.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The footprint reads with size between 20 to 42 nucleotides in length were mapped to the genome using the center-weighted approach; for each footprint read, the center residues that are at least 10 nucleotides away from either ends were given a weight of one over the length of the fragment (minus the 10 nucleotides on both ends) to generate the wig file.
NC_000964.3
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

growth_protocol: Overnight cultures were diluted to OD590 0.0003 in 250 mL fresh media. The culture was kept in a 2.8 L flask at 37C with aeration (200 rpm) until OD590 reached 0.3.

value: subspecies 168, Delta sU ylqD/ylqD (disrupted terminator between ylqC and ylqD), spec resistant

value: LB