title: lung210 biopsy


title: lung146 biopsy

status: Public on Aug 16 2019

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: tissue

value: lung transplant transbronchial biopsy (TBB)

tag: high surfactant (yes or no)

value: yes


title: lung242 biopsy

value: no


title: lung186 biopsy


title: lung209 biopsy


title: lung80 biopsy


title: lung10 biopsy


title: lung53 biopsy


title: lung174 biopsy


title: lung222 biopsy


title: lung135 biopsy


title: lung31 biopsy


title: lung240 biopsy


title: lung47 biopsy


title: lung238 biopsy


title: lung44 biopsy


title: lung213 biopsy


title: lung191 biopsy


title: lung184 biopsy


title: lung166 biopsy


title: lung157 biopsy


title: lung130 biopsy


title: lung42 biopsy


title: lung86 biopsy


title: lung116 biopsy


title: lung61 biopsy


title: lung93 biopsy


title: lung37 biopsy


title: lung204 biopsy


title: lung108 biopsy


title: lung176 biopsy


title: lung182 biopsy


title: lung43 biopsy


title: lung162 biopsy


title: heart biopsy_heart163

hyb_protocol: Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: heart biopsy_corhort558_3AA group1_4AA group1

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array  (Affymetrix, Santa Clara, CA).

growth_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: sample type

value: heart biopsy; endomyocardial biopsies (EMBs)

tag: cohort (331 or 558)


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title: heart biopsy_heart263


title: lung23 biopsy


title: lung152 biopsy


title: heart biopsy_heart499


title: lung216 biopsy


title: heart biopsy_heart429

source_name: heart biopsy_corhort558_3AA group3_4AA group3


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title: heart biopsy_heart448


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source_name: heart biopsy_corhort558_3AA group2_4AA group2


title: heart biopsy_heart618


title: heart biopsy_heart112

source_name: heart biopsy_corhort558_3AA group3_4AA group4


title: heart biopsy_heart720


title: lung160 biopsy


title: heart biopsy_heart449


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title: heart biopsy_heart441


title: heart biopsy_heart648


title: heart biopsy_heart526


title: heart biopsy_heart402


title: heart biopsy_heart606


title: heart biopsy_heart231

source_name: heart biopsy_corhort558_3AA group1_4AA group1


title: heart biopsy_heart422


title: heart biopsy_heart359


title: heart biopsy_heart869


title: heart biopsy_heart871


title: heart biopsy_heart685


title: heart biopsy_heart718


title: heart biopsy_heart269


title: heart biopsy_heart155


title: heart biopsy_heart76


title: heart biopsy_heart353


title: heart biopsy_heart834


title: heart biopsy_heart73


title: heart biopsy_heart693


title: heart biopsy_heart303


title: heart biopsy_heart781


title: heart biopsy_heart447


title: heart biopsy_heart504


title: heart biopsy_heart223


title: heart biopsy_heart599


title: heart biopsy_heart335


title: heart biopsy_heart677


title: heart biopsy_heart483


title: heart biopsy_heart529


title: heart biopsy_heart317


title: heart biopsy_heart452


title: heart biopsy_heart90


title: heart biopsy_heart543


title: heart biopsy_heart787


title: heart biopsy_heart148


title: heart biopsy_heart331


title: heart biopsy_heart162


title: heart biopsy_heart881


title: heart biopsy_heart856


title: heart biopsy_heart831


title: heart biopsy_heart885


title: heart biopsy_heart261


title: heart biopsy_heart405


title: heart biopsy_heart420


title: heart biopsy_heart46


title: heart biopsy_heart635


title: heart biopsy_heart194


title: heart biopsy_heart695


title: heart biopsy_heart425


title: heart biopsy_heart771


title: heart biopsy_heart288


title: heart biopsy_heart347


title: heart biopsy_heart412


title: heart biopsy_heart431


title: heart biopsy_heart473

source_name: heart biopsy_corhort331_3AA group1_4AA group3


title: heart biopsy_heart799


title: heart biopsy_heart700


title: heart biopsy_heart561


title: heart biopsy_heart275


title: heart biopsy_heart382


title: heart biopsy_heart492


title: heart biopsy_heart836


title: heart biopsy_heart442


title: heart biopsy_heart265


title: heart biopsy_heart54


title: heart biopsy_heart495


title: ERY3

type: SRA

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

country: USA

institute: FHCRC

description: Total RNA with rRNA removal

library_source: transcriptomic

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2
Custom R scripts were written for identification of peaks based on Meyer et al(https://www.ncbi.nlm.nih.gov/pubmed/22608085) and for visualization of peaks. The Human transcriptome (from hg19) was broken into 25nt wide discrete non-overlapping reads. Using bedtools 84 the 50bp reads were mapped to 25nt windows and windows with fewer than 5 aligned reads were dropped. We used one sided Fisher’s exact test to compare the number of reads that mapped to a given window for the MeRIP sample and the non-IP sample to the total number of reads in each. The Benjamini-Hochberg procedure was used to adjust the p-values from the Fisher's exact test to reduce our false discovery rate to 5%. To find a final p-value for each window, Fisher's Method was used to combine p-values across replicates. To find distinct m6A peaks, we combined consecutive significant 25nt windows across the transcriptome. Consecutive significant windows less than 100bp were discarded. Gene region annotations for the peaks were found from UCSC RefSeq Table for Hg19
Genome_build: hg19
Supplementary_files_format_and_content: Peaks identified for each IP and input pair are reported.

source_name: HEL

growth_protocol: Cells were cultured in RPMI+10% FBS at 37C 5% CO2

extract_protocol:
RNA was extracted from bulk cells or the indicated hematopoietic progenitor population using the Direct-zol RNA kit  (Zymo Research). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
The  RNA libraries were prepared for sequencing using standard KAPA Biosystems Stranded RNA-Seq Kit protocols. All other libraries were prepared for sequencing using standard SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) kit protocols.

tag: cell type

tag: group

value: non-ip sample


title: GMP_IP

description: Total RNA with rRNA removal

value: GMP

value: ip sample


title: HSC

description: Total RNA with rRNA removal

value: HSC


title: GMP

description: Total RNA with rRNA removal


title: MEP_IP

description: Total RNA with rRNA removal

value: MEP


title: ERY3_IP

description: Total RNA with rRNA removal


title: MEP

description: Total RNA with rRNA removal


title: heart biopsy_heart278


title: heart biopsy_heart273


title: HSC_IP

description: Total RNA with rRNA removal


title: heart biopsy_heart458


title: heart biopsy_heart879


title: heart biopsy_heart374


title: CMP_IP

description: Total RNA with rRNA removal

value: CMP


title: heart biopsy_heart67


title: heart biopsy_heart77


title: heart biopsy_heart637


title: heart biopsy_heart95


title: heart biopsy_heart807


title: heart biopsy_heart256


title: CMP

description: Total RNA with rRNA removal


title: heart biopsy_heart474


title: ERY1_IP

description: Total RNA with rRNA removal


title: ERY1

description: Total RNA with rRNA removal


title: CD14_IP

description: Total RNA with rRNA removal


title: MEG_IP

description: Total RNA with rRNA removal

value: MEG


title: MEG

description: Total RNA with rRNA removal


title: CD14

description: Total RNA with rRNA removal


title: ERY2_IP

description: Total RNA with rRNA removal


title: HEL_3ug_3_IP

description: Total RNA with rRNA removal

value: HEL cells


title: heart biopsy_heart882


title: heart biopsy_heart439

source_name: heart biopsy_corhort331_3AA group1_4AA group4


title: ERY2

description: Total RNA with rRNA removal


title: HEL_3ug_1_IP

description: Total RNA with rRNA removal


title: HEL_3ug_3

description: Total RNA with rRNA removal


title: HEL_3ug_2_IP

description: Total RNA with rRNA removal


title: heart biopsy_heart714


title: HEL_3ug_2

description: Total RNA with rRNA removal


title: HEL_3ug_1

description: Total RNA with rRNA removal


title: heart biopsy_heart47


title: heart biopsy_heart486


title: heart biopsy_heart251


title: heart biopsy_heart788


title: heart biopsy_heart117


title: heart biopsy_heart751


title: heart biopsy_heart421


title: heart biopsy_heart138


title: heart biopsy_heart555


title: heart biopsy_heart880


title: heart biopsy_heart576


title: heart biopsy_heart668


title: heart biopsy_heart266


title: HBandArch1-4_fbln1null_5

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Mouse 430A GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files were analyzed with ArrayQuest webtool (PMID: 16321157) by gcRMA algorithm to obtain log2 normalized probe set expression values

organism: Mus musculus

source_name: Hindbrain and pharyngeal arches 1-4, E10.5 mouse embryo, Fbln1 knockout

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: The Fbln1 gene trap insertion mouse strain was housed at the Animal Research Facility of the Medical University of South Carolina (MUSC). All procedures and protocols were done in accordance with a Medical University of South Carolina IACUC approved protocol.

extract_protocol: Microdissected tissues were transferred into RNA Stat 60 (Tel-Test, Friendswood, TX), homogenized, and total RNA purified using a hybrid method involving organic extraction followed by processing with the Qiagen RNeasy Mini Kit (Germantown, MD). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Embryos were harvested from pregnant females following matings of mice heterozygous for the Fbln1 gene trap insertion. E10.5 embryos were removed and submerged in sterile PBS. A piece of the yolk sac was isolated for genotyping. Tissue containing pharyngeal arches 1-4 and hindbrain was isolated by microdissection.

value: Hindbrain and pharyngeal arches 1-4

tag: genotype

value: Fbln1 homozygous gene trap

tag: developmental stage


title: HBandArch1-4_fbln1null_8


title: heart biopsy_heart337


title: HBandArch1-4_fbln1null_7


title: heart biopsy_heart698


title: heart biopsy_heart887


title: HBandArch1-4_wildtype_3

source_name: Hindbrain and pharyngeal arches 1-4, E10.5 mouse embryo, wildtype

value: wildtype


title: heart biopsy_heart233


title: heart biopsy_heart762


title: HBandArch1-4_wildtype_4


title: HBandArch1-4_fbln1null_4


title: HBandArch1-4_wildtype_5


title: heart biopsy_heart234


title: heart biopsy_heart607


title: heart biopsy_heart383


title: HBandArch1-4_wildtype_2


title: heart biopsy_heart123


title: heart biopsy_heart862


title: HBandArch1-4_wildtype_1


title: heart biopsy_heart371


title: heart biopsy_heart87


title: heart biopsy_heart715


title: heart biopsy_heart26


title: TE-ventral, biological rep2

city: Nagoya

first: Atsushi

last: Kuroiwa

state: Aichi

address: Furo-cho, Chkusa-ku

department: Graduate School of Science

country: Japan

institute: Nagoya University

description: Gene expression data from the ventral half of tracheoesophageal anlagen isolated from E9.75 embryos

hyb_protocol: 15ug of phycoerythrin labled cRNA was used for hybridization with Mouse Genome 430 2.0 Array according to Affimetrix protocole.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000 (Applied Biosystems) using Genechip Operation Software Ver1.2.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mouse embryos around E9.75

label_protocol: Biotinylated cRNA was prepared from 100ng of total RNA by Two-Cycle Target Labeling (Affymetrix) according to manufacturer's protocol.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions. Contanimating DNA wad removed using Massage Clean (GenHunter Corporation).

treatment_protocol: The embryos were isolated by caesarean incision and tracheoesophageal anlage were dissected in ice-cold PBS(-) then stored in the RNA later (Ambion). Tissue was separated into the dorsal and ventral halves manually under the microscope.

value: Ventral half of the tracheoesophageal region

tag: strain

value: BALB/c


title: heart biopsy_heart160


title: iWAT_WT#3-HFD_1

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The data were analyzed with GeneSpring GX (Agilent) using cutoffs of fold change > 2 and p value < 0.05.

source_name: Inguinal WAT, WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: WT and Naa10-KO male mice aged at 6 weeks were fed with high fat diet 60% of calories from fat for 15 weeks.

extract_protocol: Total RNAs from tissues were purified using TRIzolTM Reagent (Thermo Fisher Scientific) and TissueLyser II homogenizer (Qiagen). Chloroform extraction of RNA was performed with tissue lysates depleted of lipid. RNAs in the aqueous phase were purified using RNeasy® Plus Mini Kit according to manufacturer’s instructions.

treatment_protocol: Before adipose tissue isolation, mice treated with HFD were exposed to 4°C for 4 hrs.

tag: gender

value: Male

value: iWAT

tag: diet

value: HFD for 15 weeks


title: iWAT_KO#4-HFD_1

source_name: Inguinal WAT, Naa10-KO


title: iWAT_WT#6-HFD_2


title: TE-dorsal, biological rep2

description: Gene expression data from the dorsal half of tracheoesophageal anlagen isolated from E9.75 embryos

value: Dorsal half of the tracheoesophageal region


title: TE-dorsal, biological rep1


title: heart biopsy_heart664

value: heart biopsy; endomyocardial biopsies (EMBs)


title: I_3

city: Guangzhou

first: Wei

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University

description: lncRNA expression

hyb_protocol: 0.6 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  the Human LncRNA Array v2.0 (8 x 60K, Arraystar) 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 Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to10%~ 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs  that at least 8 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis

source_name: para-carcinoma tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Cryopulverization of tissue using the Biopulverizer and  Homogenization using the Mini-Bead-Beater-16 following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer,RNA Integrity and gDNA contamination test by Denaturing Agarose Gel Electrophoresis.

value: para-carcinoma tissues


title: I_4

description: lncRNA expression


title: TE-ventral, biological rep1


title: I_1

description: lncRNA expression


title: iWAT_KO#52-HFD_3


title: iWAT_WT#42-HFD_3


title: heart biopsy_heart365

source_name: heart biopsy_corhort558_3AA group3_4AA group3


title: heart biopsy_heart336


title: heart biopsy_heart395

source_name: heart biopsy_corhort331_3AA group1_4AA group1


title: heart biopsy_heart172


title: iWAT_KO#45-HFD_2


title: heart biopsy_heart304


title: heart biopsy_heart783


title: Raji_unfixed

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Raji.detected.genes.RPKM.csv

data_processing:
Raw sequencing reads were mapped to the mm10 or hg38 genome using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to reads per kilobase per million (RPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 3 reads per million (Raji B cells) or 10 reads per million (mouse ASC) in all samples.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes for each sample.

molecule: polyA RNA

source_name: Raji (ATCC, CCL-86)

growth_protocol: Raji B cells were cultured in RPMI supplemented with 10% FCS and 100 U/ml Penecillin/Streptomycin

extract_protocol:
RNA lysates were incubated at 65 degrees C for the indicated time and total RNA extracted using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMARTer Stranded Total RNA-seq kit v2 (Takara).

treatment_protocol: Splenocytes were intracellulary stained using the BD Cytofix/Cytoperm kit (Cat# 554714) according to the manufacturers instructions and sorted directly into RLT +1% Bme lysis buffer (Qiagen).

value: Raji B cells

value: male

tag: cell line

value: Raji (ATCC, CCL-86)

tag: decrosslinking time at 65 degrees c

value: 5 min

tag: genome build


title: heart biopsy_heart287

source_name: heart biopsy_corhort331_3AA group3_4AA group3


title: I_2

description: lncRNA expression


title: HBandArch1-4_fbln1null_3


title: heart biopsy_heart541

source_name: heart biopsy_corhort331_3AA group2_4AA group4


title: heart biopsy_heart553


title: Liver, 131KO, Vehicle

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

description: Index: GAATCT

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Trimmed reads were then aligned with TopHat version 2.0.12 (Bowtie2 version 2.2.3) to UCSC hg19 reference genome with parameters: -r 150, --library-type fr-firststrand, --keep-fasta-order, --transcriptome-index, --rg-id, --rg-sample, --rg-library, --rg-platform-unit, --rg-platform, -o
Cufflinks version 2.2.1 estimated transcript abundances with parameters: --library-type fr-firststrand, -o, -g, -L, -b, -u
Cuffmerge, Cuffquant, Cuffdiff, and Cuffquant were then run to get to final differential expression results
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs, differential expression

source_name: Liver

extract_protocol:
Livers were removed at time of sacrifice, flash frozen on dry ice, and RNA was harvested 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: Liver RNA was isolated from 2h fasted mice fed either high fat-fed or standard chow-fed diets.

tag: background strain

tag: treatment

value: Vehicle

value: KO

value: Liver


title: Liver, 102WT, IUB288

description: Index: ACAAGC

value: WT


title: Liver, 98WT, Vehicle

description: Index: GAACAG


title: Liver, 122KO, IUB288

description: Index: AACGTG


title: Liver, 141WT, Vehicle

description: Index: ACACAG


title: Liver, 135KO, Vehicle

description: Index: ATGCCT


title: Liver, 156WT, IUB288

description: Index: AACCGA


title: Liver, 106KO, IUB288

description: Index: CACTTC


title: heart biopsy_heart510


title: heart biopsy_heart472


title: T_4

description: lncRNA expression

source_name: nasopharyngeal carcinoma tissue

value: nasopharyngeal carcinoma tissue


title: heart biopsy_heart863


title: heart biopsy_heart79


title: JunD-3

city: Philadelphia

first: Austin

middle: Lewis

last: Good

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Illumina used for basecalling
Data was aligned to mm10 using TopHat2
Read counts per gene were determined using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of raw counts

source_name: Mouse insulinoma cell line

growth_protocol: Min6 cells were grown in high glucose DMEM

extract_protocol:
RNA was isolated from Min6 cells using the RNeasy Mini kit (Qiagen) as per manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Min6 cells were transduced with lentiCRISPR v2 containing gRNAs targeting Rosa26 locus or JunD. Cells harvested 8 days post-transduction following 30hr treatment with glucolipotoxic conditions.

tag: cell-type

value: Min6 cells

tag: passage

tag: grna

value: JunD


title: JunD-2


title: T_1

description: lncRNA expression

tag: tissue


title: Rosa26-2


title: JunD-1


title: heart biopsy_heart519

source_name: heart biopsy_corhort331_3AA group2_4AA group2

tag: sample type

tag: cohort (331 or 558)


title: heart biopsy_heart548


title: heart biopsy_heart170

source_name: heart biopsy_corhort331_3AA group3_4AA group1


title: heart biopsy_heart600

source_name: heart biopsy_corhort331_3AA group3_4AA group4


title: heart biopsy_heart133


title: Rosa26-3


title: heart biopsy_heart482


title: T_2

description: lncRNA expression


title: Th17_input_control

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained using the Illumina CASAVA v1.8.2. Reads were aligned against the mouse mm9 reference genome using the Bowtie aligner. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection and Superenhancer identification were performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: mm9
Supplementary_files_format_and_content: bowtie files are alignments made from fastq files with the Bowtie aligner; bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak and superenhancer files were generated using Homer.

molecule: genomic DNA

source_name: wild-type primary Th17 cells

growth_protocol: Th17 cells were cultured as described by Ivanov et al, Cell 126, 1121-1133, 2006

extract_protocol: Standard Illumina DNA library construction

tag: cell type

value: primary cultured T helper 17 (Th17) cells

tag: chip antibody

value: input DNA


title: T_3

description: lncRNA expression


title: Th17_REV-ERBa_ChIP

value: Reverb-alpha


title: Rosa26-1


title: m3_Flu_IgG

description: Flu.ASC.detected.genes.RPKM.csv

source_name: Spleen and Mediastinal Lymph node

value: Antibody Secreting Cell

tag: sorting markers

value: Spleen and Mediastinal Lymph node

tag: tetramer staining

value: NP+ HA+

tag: bcr isotype

value: IgG

tag: infection

value: Influenza A/PR8/34

tag: day post infection

value: Day 14

value: 15 min


title: UNC_B_2

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Hisat2 (version 2.1.0) to map reads to human genome GRCh37
bedtools to assemble transcripts
edgeR to identify differenentially expressed genes
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized expression

source_name: RNA-Seq UNC0642 treated PEO1-OR cells (B2)

extract_protocol:
RNeasy kit (Qiagen)/Quick DNA Mini-Prep protocol (Zymo Research)
RNAlibraries were prepared for sequencing using TruSEQ RNA Sample Prep v4 using standard Illumina protocols.

tag: cell line background

value: Olaparib resistant high grade serous ovarian cancer clonal 4 cell line PEO1-OR

tag: culture condition

value: complete growth media + UNC0642 for 72 hrs


title: UNC_B_1

source_name: RNA-Seq UNC0642 treated PEO1-OR cells (B1)


title: m3_Flu_IgA

description: Flu.ASC.detected.genes.RPKM.csv

tag: gender

value: male

tag: strain

value: IgA

tag: decrosslinking time at 65 degrees c

tag: genome build


title: UNC_A_2

source_name: RNA-Seq UNC0642 treated PEO1-OR cells (A2)


title: m3_Flu_IgM

description: Flu.ASC.detected.genes.RPKM.csv

value: IgM


title: PEO1_Clone4 [re-analysis]

source_name: PEO1 olaparib-resistant C4 cells

value: complete growth media


title: PEO1_Clone5 [re-analysis]

source_name: PEO1 olaparib-resistant C5 cells

value: Olaparib resistant high grade serous ovarian cancer clonal 5 cell line PEO1-OR


title: PEO1_Clone18 [re-analysis]

source_name: PEO1 olaparib-resistant C18 cells

value: Olaparib resistant high grade serous ovarian cancer clonal 18 cell line PEO1-OR


title: PEO1_Clone10 [re-analysis]

source_name: PEO1 olaparib-resistant C10 cells

value: Olaparib resistant high grade serous ovarian cancer clonal 10 cell line PEO1-OR


title: m2_Flu_IgM

description: Flu.ASC.detected.genes.RPKM.csv


title: heart biopsy_heart136

value: heart biopsy; endomyocardial biopsies (EMBs)


title: ZIKV_TEC

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using tophat v2.0.11.
For RNA-seq data of HuES8, trophoblasts differentiation to day4 and day9, read counts were calculated using HTSeq-count v0.6.1, and were further normalized using DESeq2 package v1.6.3.
For RNA-seq data of day 4 trophoblast cells infected with MOCK and ZIKV, transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file,  normalized expression

source_name: day 4 trophoblast cells infected by ZIKV

growth_protocol: human ESCs were cultured with mTeSR medium and induced to differentiation with BMP4 plus conditioned medium.

extract_protocol:
total RNA samples were prepared with Rneasy plus kit and QC was performed with nanodrop.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation (Non-stranded and Poly-A selection).

treatment_protocol: differentiated day 4 trophoblast cells were infected by MOCK or ZIKV for 2 hours at 37 degree temperature.

value: day 4 trophoblast cells

tag: developmental stage

value: differentiated

tag: treatment

value: infected by ZIKV


title: m2_Flu_IgG

description: Flu.ASC.detected.genes.RPKM.csv

value: Antibody Secreting Cell

tag: tissue

value: Spleen and Mediastinal Lymph node

value: NP+ HA+

value: IgG


title: Trophoblast_D9

source_name: day 9 trophoblast cells

value: day 9 trophoblast cells


title: heart biopsy_heart701

source_name: heart biopsy_corhort331_3AA group3_4AA group3

tag: sample type

tag: cohort (331 or 558)


title: m2_Flu_IgA

description: Flu.ASC.detected.genes.RPKM.csv

tag: cell type

value: Influenza A/PR8/34

value: Day 14

value: 15 min


title: TEC_D4

source_name: day 4 trophoblast cells


title: MOCK_TEC

source_name: day 4 trophoblast cells infected by MOCK

value: infected by MOCK


title: heart biopsy_heart525


title: Combo treated sample 3 ip MBH [F06_S8]

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq reads were mapped to the Mouse GRCm38 genome using Tophat V2.0.11
Gene counts were determined using htseq-count 0.6.1p1.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_count.tsv contain raw gene-level counts in tab-delimited text

source_name: Combo treated ip MBH

growth_protocol: 9 weeks old C57/Bl6 male mice were maintained on standard chow and fasted for 6h before treatment administration

extract_protocol:
Samples were homogenised in a homogenisation buffer containing 10 mM HEPES (pH 7.4), 150 mM KCl, 5 mM MgCl2, 100 nM calyculin A, 2 mM DTT, 100 U/mL RNasin, 100 mg/mL cycloheximide and Roche protease and phosphatase inhibitor cocktails and clarified by centrifugation at 2,000g at 4  C for 10 min. Supernatants were resuspended in 1 ml of 10% NP40 and 10   L of 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC) and centrifuged at 16,100 g at 4  C for 10 min. 25   L of the sample was used for RNA extraction (input sample) using Qiagen RNeasy Micro kit. The rest of the supernatant was used for ribosome immunoprecipitation by incubation with an antibody-beads conjugate containing anti-pS6 240/244 antibody (#2215, Cell Signalling Technology)  and protein A dynabeads resuspended in the homogenization buffer supplemented with 50   L of 10% NP40 and 10   L of DHPC for 1 mL of buffer C, and 1   M ZK10 for 10 min at 4  C.  The beads were washed twice with wash buffer (10 mM HEPES, 350 mM KCl, 5 mM MgCl2, 2 mM DTT, 1% NP40, 100 U/mL RNasin, 100 mg/mL cycloheximide, and Roche protease and phosphatase inhibitor cocktails) and resuspended in RLT for subsequent RNA extraction using Qiagen RNeasy Micro kit.
RNA was amplified using Clontech Smartseq V4 Ultra Low-input RNA kit and the amplified cDNA was used for library preparation with Illumina Nextera XT kit.

treatment_protocol: Mice were randomized into treatment groups and received an ip injection (10 µL/g of body weight) of either saline , AC710222 (2.5 or 10 µg/kg), exenatide (1 µg/kg, n=8), AC3174 (1 µg/kg), AC170222 (2.5 µg/kg) or a combination of these drugs

tag: age

value: 9 weeks

tag: Sex

value: male

value: COMBO

tag: brain site/tissue

value: mouse mediobasal hypothalamus (MBH)

tag: ip antibody

tag: rna sample type

value: ip

tag: molecule subtype

value: ribosomal RNA


title: heart biopsy_heart154

source_name: heart biopsy_corhort331_3AA group1_4AA group1

value: heart biopsy; endomyocardial biopsies (EMBs)


title: heart biopsy_heart520


title: heart biopsy_heart407


title: Combo treated sample 1 ip MBH [F04_S7]

value: anti-pS6 240/244 antibody (#2215, Cell Signalling Technology)


title: UNC_A_1

source_name: RNA-Seq UNC0642 treated PEO1-OR cells (A1)

tag: cell line background

value: Olaparib resistant high grade serous ovarian cancer clonal 4 cell line PEO1-OR

tag: culture condition

value: complete growth media + UNC0642 for 72 hrs


title: HuES8

source_name: huaman ESCs

value: huaman ESCs

value: undifferentiated


title: heart biopsy_heart717


title: AC170222 treated sample 3 ip MBH [F03_S7]

source_name: AC170222 treated ip MBH

tag: strain


title: A673_WT_input_A350C18

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
ChIP-seq reads were aligned to the human genome (hg19 version) with Bowtie2  (Langmead & Salzberg, Nat Methods, 2012). Peaks were called with MACS2 with option narrow (Zhang et al., Genome Biol, 2008). To normalize, we took the input dataset from the same cell line. PAVIS was used for peak annotation and visualization (Huang et al., Bioinformatics, 2013).
Reads mapped with bowtie2 version 2.1.10 against human genome (hg19)
Peaks called with MACS2 version 2.0.10 with option narrow (default option) with input DNA as control
Genome_build: hg19
Supplementary_files_format_and_content: peaks called by MACS2

source_name: A673 Ewing sarcoma cells

growth_protocol: All cell lines were grown at 37°C and 5% CO2 in humidified atmosphere. RPMI 1640 medium with stable glutamine (Biochrom) with 10% tetracycline-free FCS (Biochrom), 100 U/ml penicillin (Biochrom), and 100 µg/ml streptomycin (Biochrom) was used to grow the cells.

extract_protocol: DNA-protein cross-linking was done in presence of 1% of paraformaldehyde on 12 × 10^6 cells for each condition for 10 minutes. Cell lysis, chromatin shearing, immunoprecipitation and DNA purification was performed with reagents from iDeal ChIP-seq kit for Transcription Factors (Diagenode, ref: C01010054). Chromatin shearing was carried out in a Bioruptor (Diagenode) using 20 cycles of sonication (30sec high, 30sec off) in TPX tubes (Diagenode, ref: 50001). For immunoprecipitation of MYBL2, 2 µg of a monoclonal ChIP-grade rabbit anti-MYBL2 antibody (Abcam, ab76009) were used. MYBL2 ChIP and input were sequenced on a HiSeq2500 instrument (Illumina) using 100bp single-end sequencing.

tag: cell line

value: Ewing sarcoma cells

tag: chip-antibody

value: none (input DNA)


title: AC170222 treated sample 2 ip MBH [F02_S8]


title: AC3174 treated sample 1 ip MBH [E04_S6]

source_name: AC3174 treated ip MBH


title: AC3174 treated sample 2 ip MBH [E05_S5]


title: AC170222 treated sample 1 ip MBH [F01_S7]


title: heart biopsy_heart876

source_name: heart biopsy_corhort331_3AA group2_4AA group2


title: Combo treated sample 2 ip MBH [F05_S8]


title: AC3174 treated sample 3 ip MBH [E06_S6]


title: RDES-siMYBL2_1-3

data_processing:
Reads from fastq were aligned on the human genome (v. hg19) using TopHat (version 2.0.6)
Counting of reads on annotated genes from the GRCh37 gene build was done using htseq-count (v. HTSeq-0.5.3p9) with the following parameters: htseq-count -a 10 -q -s no -m union
Sample-to-sample normalization was performed by rescaling using DESeq size factors.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
RNA was extracted with the Nucleospin II kit (Macherey-Nagel) and reverse-transcribed using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For siRNA transfection, cells were seeded in a six-well plate at a density of 1.5 × 10^5 per well in 1.6 ml of growth medium. The cells were transfected with either a negative control non-targeting siRNA (Sigma-Aldrich MISSION siRNA Universal Negative Control #1) or a specific siRNA directed against MYBL2 (25 to 65 nM, depending on the cell line) and HiPerfect (Qiagen). Cells were retransfected 48h after the first transfection and harvested 96h after the first transfection.

value: RDES

tag: sirna used


title: 22Rv1-Control-RNA-seq

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

data_processing:
Standard RNA-seq workflow from DNASTAR Genomics Suite (Madison, WI) was used to map RNA-seq data.
Total raw read count for each gene was reported.
Genome_build: hg19
Supplementary_files_format_and_content: one txt file containing all three RNA-seq read counts

source_name: Prostate

growth_protocol: Prostate cancer cell line 22Rv1 was purchased from American Type Culture Collection (Manassas, VA, USA) and was cultured in RPMI 1640 media with 10% fetal bovine and 1% penicillin and streptomycin (Gibco, Carlsbad, CA, USA).

extract_protocol:
Total RNA was isolated using total RNA extraction kit (Zymo Research). The RNA concentration was determined by measuring the absorbance at 260 nm using a NanoDrop.
High quality RNA samples (1 μg each) were used to enrich poly A mRNA and then subjected to RNA-seq library preparation by Novogene (Chula Vista, CA, USA). 150bp single-end sequencing was performed in a HiSeq2500.

treatment_protocol: 22Rv1 cells was treated with 20 μg MLPH transcripts V1 or V4 plasmid for 48 h.

value: Prostate cancer cell line

tag: transfection

value: Empty vector


title: 22Rv1-V1-RNA-seq

value: MLPH-transcript V1 transfection


title: RDES-siMYBL2_1-2


title: RDES-siMYBL2_1-1


title: 22Rv1-V4-RNA-seq

value: MLPH-transcript V4 transfection


title: Combo treated sample 3 input MBH [B06_S4]

source_name: Combo treated input MBH

value: 9 weeks

value: male

tag: treatment

value: COMBO

value: input

value: total RNA


title: Saline treated sample 2 ip MBH [E02_S6]

source_name: Saline treated ip MBH

value: saline

value: mouse mediobasal hypothalamus (MBH)

value: anti-pS6 240/244 antibody (#2215, Cell Signalling Technology)

value: ip

value: ribosomal RNA


title: Combo treated sample 2 input MBH [B05_S3]


title: WT3 MDA

city: University of Melbourne

first: Charles

last: Pagel

state: Victoria

address: Grattan Street

department: Faculty of Veterinary and Agricultural Sciences

country: Australia

institute: University of Melbourne

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence,
Reads were mapped to mm10 whole genome using using TopHat version 2.0.9  with default parameters and mean inner distance of 40 between mate pairs.
Mapped reads were assembled into transcripts, their abundances were estimated and reported as fragments per kilo base of transcript per million fragments sequenced (FPKM) by Cufflinks version 2.1.1 . Confidence intervals for FPKM values were generated using the Bayesian inference method.
A single reference annotation-based transcript assembly was prepared by merging all the assembled transcripts from Cufflinks and the corresponding reference annotation  (build GRCm38/mm10) into the merged transcript using Cuffmerge utility version 1.0.0. Differential gene expression between experimental groups was compared using Cuffdiff version 2.1.1 .
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deliminated text files include FPKM values for each sample.

source_name: Calvarial digestion

growth_protocol: Primary osteoblasts were isolated by sequential collagenase digestion from the calvariae of neonatal wild type and PAR2 KO mice as described (45), and cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) FCS, L-glutamine (2 mM) and gentamicin (50 μg/ml).

extract_protocol:
Total RNA was isolated using the Total RNA Isolation mini columns according to the manufacturer’s instructions (Promega, Madison, Wisconsin, USA). RNA was eluted in 50-100 μL nuclease free water and stored at -80°C i
Samples with a high RNA integrity number (RIN; RIN>7.5) were processed for sequencing. Total RNA (5 μg) was used for cDNA library preparation using TruSeq RNA v2 (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. Next generation sequencing was performed using the high throughput IlluminaHiSeq2000 platform.

treatment_protocol: After inncubating cell isolates for 48 h, medium was replaced with complete unconditioned complete BRFF-HPC1 medium supplemented with 20% FCS L-Glu (2 mM), genatmicin (50 ml/ml) (Control) or complete medium conditioned by 60-80% confluent cultures of MDA-PCa-2b cells for 48 hours (MDA). medium and cells were incubated for an additional 4 days prior to RNA

value: Osteoblast-like

tag: genotype

value: Wildtype

value: MDA PCa 2b-conditioned medium


title: Saline treated sample 3 ip MBH [E03_S5]


title: RDES-sictrl-1

value: RDES

value: Ewing sarcoma cells

value: siControl


title: WT3 Control

value: Unconditioned medium


title: SK-N-MC-siMYBL2_1-3

value: SK-N-MC


title: RDES-sictrl-3


title: WT1 MDA


title: Combo treated sample 1 input MBH [B04_S4]

value: 9 weeks

value: male


title: AC170222 treated sample 3 input MBH [B03_S3]

source_name: AC170222 treated input MBH

value: input


title: SK-N-MC-siMYBL2_1-2


title: SK-N-MC-siMYBL2_1-1


title: AC170222 treated sample 2 input MBH [B02_S4]

value: total RNA


title: WT2 MDA


title: AC170222 treated sample 1 input MBH [B01_S3]


title: KO3 Control


title: Control

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

hyb_protocol: For microarray analysis, 100ng of total RNA was amplified and hybridized to the Mouse Gene 1.0 ST array.

scan_protocol: According to the standard Affymetrix protocol using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA normalized data was generated from the CEL files using the Affymetrix Transriptome Analysis Console.

source_name: Rosa-CreER / MLL1 fl/fl myoblasts

label_protocol: According to the Affymetrix protocol.

growth_protocol: Myoblasts were grown in Ham's F10 medium with 20% FBS and 5 ng/ml FGF

extract_protocol: Nucleospin RNA kit, Macherey-Nagel, 740955

treatment_protocol:
Grown  with 0.01% EtOH for 7 days followed by 3 days in media without EtOH
Treated or mock-treated with 4-OHT in induce MLL1 KO harvested after 1 week treatment and 3 days washout

value: myoblasts

value: Rosa-CreER / MLL1 fl/fl

tag: phenotype

value: Control


title: WT1 Control

tag: cell type


title: RDES-sictrl-2


title: Saline treated sample 1 ip MBH [E01_S5]

tag: age

value: saline

value: mouse mediobasal hypothalamus (MBH)

value: anti-pS6 240/244 antibody (#2215, Cell Signalling Technology)

value: ip


title: SK-N-MC-sictrl-3


title: KO3 MDA

value: Osteoblast-like

value: MDA PCa 2b-conditioned medium


title: MLL1 KO

treatment_protocol:
Grown  with 500nM 4-OHT with 0.01% EtOH for 7 days followed by 3 days in media without 4-OHT and EtOH
Treated or mock-treated with 4-OHT in induce MLL1 KO harvested after 1 week treatment and 3 days washout

value: MLL1 KO


title: KO2 MDA


title: AC3174 treated sample 3 input MBH [A06_S2]

source_name: AC3174 treated input MBH

tag: Sex


title: AC3174 treated sample 2 input MBH [A05_S1]

tag: brain site/tissue


title: AC3174 treated sample 1 input MBH [A04_S2]


title: SK-N-MC-sictrl-1

value: Ewing sarcoma cells

value: siControl


title: WT2 Control

value: Wildtype

value: Unconditioned medium


title: A673-siMYBL2_1-3


title: KO2 Control


title: Saline treated sample 3 input MBH [A03_S1]

source_name: Saline treated input MBH

value: 9 weeks

value: male


title: A673-siMYBL2_1-2


title: Saline treated sample 2 input MBH [A02_S2]

value: input

value: total RNA


title: A673-siMYBL2_1-1


title: Saline treated sample 1 input MBH [A01_S1]


title: A673-sictrl-3


title: KO1 Control


title: Pdx1 Total 3

source_name: Mouse insulinoma cell line

extract_protocol:
RNA was isolated as per TRAP protocol (see Doyle et al. Cell. 2008) to obtain IP and Total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Min6 cells were transfected with siRNA via AMAXA nucleofection and harvested 72 hours post-transfection

tag: cell-type

value: Min6 cells

tag: passage

tag: sirna


title: SK-N-MC-sictrl-2

value: SK-N-MC


title: Combo treated sample 3 ip DVC [H06_S8]

source_name: Combo treated ip DVC

value: COMBO

value: mouse dorsovagal complex (DVC)

tag: ip antibody

tag: rna sample type

tag: molecule subtype

value: ribosomal RNA


title: A673-sictrl-2

tag: cell line


title: Pdx1 Total 2


title: Pdx1 Total 1


title: Pdx1 IP 3


title: A673-sictrl-1


title: KO1 MDA

tag: strain


title: CD49f-high 2

city: Beijing

first: Zhigang

last: Yang

address: 33 Ba-Da-Chu Rd.

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

description: processed data file: genes.fpkm.anno.txt

data_processing:
The sequencing quality of the raw data of the FASTQ format was assessed with FastQC and then low quality data were filtered using NGSQC.
The clean reads with high quality were then aligned to the reference genome using Tophat2 with default parameters.
Transcriptomes were assembled and fragments per kilobase per million reads (FPKM) for each gene were computed with StringTie software.
Genome_build: ENSEMBL release-84/GRCm38
Supplementary_files_format_and_content: genes.fpkm.anno.txt file includes FPKM values for each Sample.

source_name: CD49f-high subpopulation

extract_protocol:
FACS sorted CD49f-neg, CD49f-low and CD49f-high cells were immediately lysed with Trizol reagent and RNA was harvested as the protocol indicated.
The NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: Krt14 cre;Rosa26-mTmG

value: Dermal cells of newborn mice

tag: subpopulation

value: CD49f-high mesenchymal cells

value: Directly isolated primary cells


title: CD49f-high 3


title: CD49f-high 1


title: AC170222 treated sample 1 ip DVC [H01_S7]

source_name: AC170222 treated ip DVC

value: anti-pS6 240/244 antibody (#2215, Cell Signalling Technology)

value: ip


title: AC170222 treated sample 2 ip DVC [H02_S8]


title: CD49f-low 3

source_name: CD49f-low subpopulation

value: CD49f-low mesenchymal cells


title: Pdx1 IP 1


title: Combo treated sample 1 ip DVC [H04_S8]


title: CD49f-low 2


title: AC3174 treated sample 3 ip DVC [G06_S6]

source_name: AC3174 treated ip DVC


title: Control Total 2

value: NT


title: CD49f-low 1


title: AC3174 treated sample 1 ip DVC [G04_S6]

value: 9 weeks


title: Saline treated sample 3 ip DVC [G03_S5]

source_name: Saline treated ip DVC

value: male

value: saline


title: Combo treated sample 2 ip DVC [H05_S7]


title: Control IP 3


title: AC170222 treated sample 3 ip DVC [H03_S7]


title: Control IP 2


title: Pdx1 IP 2


title: Control IP 1


title: CD49f-neg 1

source_name: CD49f-neg subpopulation

value: CD49f-neg mesenchymal cells


title: Saline treated sample 1 ip DVC [G01_S5]


title: Control Total 3

value: Min6 cells


title: Combo treated sample 3 input DVC [D06_S4]

source_name: Combo treated input DVC

value: input

value: total RNA


title: Combo treated sample 2 input DVC [D05_S3]

value: COMBO

value: mouse dorsovagal complex (DVC)


title: Control Total 1


title: zikv6

data_processing:
Illumina bcl2fastq2 v2.19 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse mm10 reference genome using STAR v2.5.2b.
Read counts were calculated using HTSeq-count v0.6.1. Differential expression analysis was performed using DESeq2 package v1.6.3.
Genome_build: mm10
Supplementary_files_format_and_content: excel file including gene name, Ensembl id and normalized expression (regularized-logarithm transformation) of each gene in each sample

source_name: blastocyst

growth_protocol: C57BL/6 females were plugged by C57BL/6 males

extract_protocol:
Embryos were washed with several drops of media and PBS, and processed as in Poulain, S. et al., . Methods Mol Biol, 2017 PMID: 28349422. In short, embryos were lysed in 5 ul lysis buffer containing an RT primer (TCGTCGGCAGCGTCAGATGTGNNNNNN).
Samples were then reverse transcribed in a 20 ul RT reaction containing a template-switching oligo (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNNTATA(rG)(rG)(rG)). Pre-amplification PCR was performed using a PCR primer (TCGTCGGCAGCGTCAGATGTG). The concentration of the resulting cDNA libraries was measured with Qubit® 2.0 Fluorometer (ThermoFisher Scientific) and library preparation was performed with the Nextera XT Library Preparation Kit (Illumina, Cat. FC-131-1096), followed by library fragment size validation with BioAnalyzer (Agilent Technologies).

treatment_protocol: E3.5 embryos were flushed, zona pellucidas were removed, and blastocysts were treated with MOCK or Zika virus (MR766) for 24 hours in hanging drops

tag: tissue

value: single blastocyst

tag: developmental stage

value: ZIKV, MR766


title: zikv4

tag: treatment


title: zikv7


title: zikv5


title: Combo treated sample 1 input DVC [D04_S4]


title: AC170222 treated sample 3 input DVC [D03_S3]

source_name: AC170222 treated input DVC


title: CD49f-neg 3

value: Krt14 cre;Rosa26-mTmG

value: Dermal cells of newborn mice


title: CD49f-neg 2

value: Directly isolated primary cells


title: Saline treated sample 2 ip DVC [G02_S6]

value: anti-pS6 240/244 antibody (#2215, Cell Signalling Technology)

value: ip

value: ribosomal RNA


title: AC170222 treated sample 1 input DVC [D01_S3]

value: 9 weeks


title: AC170222 treated sample 2 input DVC [D02_S4]

value: male


title: zikv2


title: zikv3


title: mock5

value: MOCK


title: AC3174 treated sample 2 input DVC [C05_S1]

source_name: AC3174 treated input DVC


title: mock4


title: MCF7 cells ESR1 siRNA, replicate 3

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and analyzed by Genome Studio (Illumina)

label: Biotin

source_name: MCF7 breast cancer cell line

label_protocol: After RNA was converted to cDNA, biotinylated cRNA was prepared by the standard protocol

growth_protocol: MCF7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin/streptomycin

extract_protocol: Total RNA samples from three independent biological replicates were extracted using RNA Extraction kit (Invitrogen)

treatment_protocol: Small interfering RNA (siRNA) (Human GATA3 or LSD1 or ESR1 SMARTpool, Dharmacon) and nonspecific control siRNA were obtained from Invitrogen (California, USA) and transfected into MCF7 cells using Lipofectamine RNAiMAX (Invitrogen)

value: ESR1 siRNA

value: ER+ luminal breast cancer cell


title: Saline treated sample 3 input DVC [C03_S1]

source_name: Saline treated input DVC

value: saline

value: input


title: MCF7 cells ESR1 siRNA, replicate 2

description: replicate 2


title: mock3


title: mock1


title: mock2


title: Saline treated sample 2 input DVC [C02_S2]

value: total RNA


title: AC3174 treated sample 2 ip DVC [G05_S5]

value: mouse dorsovagal complex (DVC)


title: Saline treated sample 1 input DVC [C01_S1]


title: AC3174 treated sample 3 input DVC [C06_S2]


title: KOstroma_CLL_C

status: Public on Aug 15 2019

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
Basecalls performed using HiSeq Control Software X, RTA X and CASAVA version X
Quality control of reads were performed using RSeQC v2.6, adapters and low quality reads were removed using using TrimGalore v0.4
Filtered reads were aligned to a mm10 reference index based off of GENCODE Release M14 (GRCm38.p5) using RNA-STAR aligner with the following parameters: --outSAMtype BAM SortedByCoordinate --sjdbGTFfile gencode.m14.annotation.gtf  --outFilterType BySJout --outFilterMultimapNmax 50 --alignSJoverhangMin 1  --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif
Quantification of gene expression was performed with HTSeq-0.11.0 using the aligned bam files and the GENCODE Release M14 comprehensive GTF annotation file
Genome_build: mm10 GRCm38.p5
Supplementary_files_format_and_content: Raw HTSeq-counts for all files are merged in the stroma_rawcounts.matrix.txt file

source_name: bone marrow derived mesenchymal stromal cells

growth_protocol: Bone marrow derived mesenchymal stromal cells (BMSCs) from either Wild Type or prkcb-/- mice were mono-cultured or co-cultured with primary CLL cells in vitro in RPMI 1640 medium for totally 48 hours.

extract_protocol:
Purified BMSCs were harvested after incubating with Dynabeads® CD19 pan B to deplete CLL cells. Total RNA was extracted using the standard protocol from GenElute Mammalian Total RNA Miniprep Kit (Sigma#RTN70-1KT).
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB #7420) was used with 100ng-200ng of total RNA for the construction of sequencing libraries. mRNA was isolated and purified by using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #7490) before cDNA synthesis.

value: mesenchymal stromal cells

tag: genotype

value: Prkcb-/-

value: co-cultured with primary CLL cells (patient 3) in vitro


title: WTstroma_CLL_A

tag: cell type

value: wild type

value: mono-cultured in vitro


title: KOstroma_CLL_A

value: co-cultured with primary CLL cells (patient 1) in vitro


title: WTstroma_rep1


title: CLIP18: Ref, 72h, Rep#2

city: Seoul

first: Jaewon

last: Song

state: Seoul

address: 504-407, School of Biological Sciences, College of Natural Sciences, 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National  University

data_processing:
Library strategy: CLIP-seq
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdapt version 1.10, in-house python program, and FASTX-Toolkit version 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to human tRNA and rRNA sequences by Bowtie2 version 2.2.7 (-t -k 2 --very-sensitive)
Tophat version 2.1.1 [command-line parameters: with–no-coverage-search–b2-very-sensitive (−b2- score-min L, −0.6, −0.9 only for CLIP-seq due to the high error rate)] was used to align the reads against human and viral genome.
RSEM version 1.2.30 was used to estimate transcript abundance. Differentially expressed genes were assessed using the limma package in R, and voom transformation was applied.
We applied Fisher’s exact test to detect significant peaks (CLIP-seq enriched regions over reference seq) and p-values were calculated for every genomic position in the whole genome background, then adjusted using qvalue package in R.
Genome_build: human (GRCh37.p13), HCMV Toledo (GU937742.2)
Supplementary_files_format_and_content: Files starting with "KD_": tab-delimited text files include genes, transcripts, fold change values and differential expression probabilities, which were made using RSEM.
Supplementary_files_format_and_content: Files starting with "514A_", "515A_", or "Overlap_": CLIP peaks identified using Roquin antibodies. tab-delimited text files include genomic loci of peaks and adjusted p-values. "Overlap" peaks were built by overlapping (by one nucleotide) the libraries derived from the two different antibodies.

source_name: Fibroblast, infected

growth_protocol: Human foreskin fibroblasts (HFFs) (ATCC, passages 10–15) were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin, and 50 µg/mL streptomycin.

extract_protocol:
Total RNAs from HFFs were isolated using the Trizol reagent. For CLIP-seq samples, Roquin-RNA complexes were isolated using antibodies.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: primary cell

value: Human foreskin fibroblast

tag: virus strain

value: HCMV Toledo strain

tag: clip antibody


title: CLIP17: Ref, 24h, Rep#2


title: KOstroma_rep3


title: KOstroma_rep2

value: co-cultured with primary CLL cells (patient 2) in vitro


title: WTstroma_rep3


title: KOstroma_CLL_B


title: WTstroma_CLL_B


title: WTstroma_rep2


title: CLIP16: Ref, NI, Rep#2

source_name: Fibroblast, uninfected


title: WTstroma_CLL_C


title: KOstroma_rep1


title: CM_4C

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

institute: Georg-Speyer-Haus

data_processing:
Library strategy: 4C
Single-end FASTQ files were preprocessed by removing the view point from all reads then the FASTQ files were aligned to mm10 with BWA aligner. The output Sam files were converted to binary Bam files with samtools. Bam files were indexed and reads were counted and converted to bedgraph.
Genome_build: mm10
Supplementary_files_format_and_content: Data are represented as BAM files

growth_protocol: mESC cells were grown in 2i media feeder free. E11.5 embryos were harvested in HBSS and the hearts isolated. Cardiomyocytes (CMs) were isolated from the heart using the Heart Dissociation Kit from Miltenyi.

extract_protocol:
4C experiment was carried out as previously described (Brouwer et al., 2017; van de Werken et al., 2012). Briefly, 10 million mESCs and cardiomyocytes and 120 embryonic Hearts (E11.5) were crosslinked in 1% methanol-free formaldehyde in PBS for 10 minutes at room temperature. Then the formaldehyde is quenched with 0.125M Glycine for 5 minutes at room temperature. The samples were washed two times with ice-cold PBS to remove any residual formaldehyde. Samples were lysed in 5ml lysis buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM EDTA, 0.5% Igepal CA-630, 1% Triton X-100, and complete protease inhibitors) on ice for 30 minutes. In case of E11.5 hearts, the sample were further lysed mechanically by Dounce homogenizer to create single cell suspension then the nuclei were applied to 70 μM cell strainer (BD Bioscience) to remove the non-digested tissue.  For all samples, nuclei were collected by centrifugation at 1000 rpm for 5 min at 4 °C. then the nuclei were washed once with a total volume of 500 μl 1.2X Cutsmart (NEB). centrifuge the nuclei for 1 min at 1000 rpm at 4 °C and remove the supernatant. The nuclei were taken up in 500 μl 1.2X Cutsmart (NEB), placed at 55 °C in a shaker at 900 rpm and immediately 7.5 μl of a 20% SDS solution (final concentration 0.3 %) is added. Nuclei were incubated for 10 min at 60 °C, followed by another 50 min at 37 °C in a shaker at 900 rpm. The SDS was sequestered by adding 50 μl of a 20% Triton X-100 solution (final concentration 2 %) and incubated for 1 h at 37 °C in a shaker at 750 rpm.   The nuclei were digested by adding 400 Units of MboI (NEB, 25 U/ μl) restriction enzyme at 37 °C for 6 h in a shaker at 900 rpm then another 400 Units of the restriction enzyme was added for overnight digestion. The primary ligation was done according to (Rao et al., 2014)in small volume (1200 μl). After de-crosslinking the samples at 65 °C overnight, the DNA was purified with phenol–chloroform–IAA solution and ethanol precipitation.  The 3C libraries were then digested using another 4-base cutter MseI (NEB) overnight. After the digestion the DNA was purified with phenol–chloroform–IAA solution and ethanol precipitation. The second ligation was performed under extreme dilution (15 ml reaction volume) to provoke circularization at 16 °C for 6 hrs followed by 1 hr at room temperature. The ligated products were precipitated by phenol–chloroform–IAA solution and ethanol and further cleaned using Qiagen PCR purification kit.
Library was constructed using viewpoint specific primers as indicated in the publication.

value: cardiomyocytes


title: mESC_4C

source_name: mESC

value: mESC


title: Heart_4C

value: whole heart


title: CLIP15: Ref, 72h, Rep#1


title: AC3174 treated sample 1 input DVC [C04_S2]

tag: age

value: 9 weeks

tag: Sex

value: male

tag: brain site/tissue


title: A673_WT_MYBL2_A763C13

source_name: A673 Ewing sarcoma cells

extract_protocol:
DNA-protein cross-linking was done in presence of 1% of paraformaldehyde on 12 × 10^6 cells for each condition for 10 minutes. Cell lysis, chromatin shearing, immunoprecipitation and DNA purification was performed with reagents from iDeal ChIP-seq kit for Transcription Factors (Diagenode, ref: C01010054). Chromatin shearing was carried out in a Bioruptor (Diagenode) using 20 cycles of sonication (30sec high, 30sec off) in TPX tubes (Diagenode, ref: 50001). For immunoprecipitation of MYBL2, 2 µg of a monoclonal ChIP-grade rabbit anti-MYBL2 antibody (Abcam, ab76009) were used.
MYBL2 ChIP and input were sequenced on a HiSeq2500 instrument (Illumina) using 100bp single-end sequencing.

value: Ewing sarcoma cells

tag: chip-antibody

value: monoclonal ChIP-grade rabbit anti-MYBL2 antibody (Abcam, ref:76009)


title: KD23: siRoq#2, 24h, Rep#2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence by using CutAdapt version 1.10, in-house python program, and FASTX-Toolkit version 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/).
After preprocessing, the sequenced reads were mapped to human tRNA and rRNA sequences by Bowtie2 version 2.2.7 (-t -k 2 --very-sensitive)
Tophat version 2.1.1 [command-line parameters: with–no-coverage-search–b2-very-sensitive (−b2- score-min L, −0.6, −0.9 only for CLIP-seq due to the high error rate)] was used to align the reads against human and viral genome.
RSEM version 1.2.30 was used to estimate transcript abundance. Differentially expressed genes were assessed using the limma package in R, and voom transformation was applied.
We applied Fisher’s exact test to detect significant peaks (CLIP-seq enriched regions over reference seq) and p-values were calculated for every genomic position in the whole genome background, then adjusted using qvalue package in R.
Genome_build: human (GRCh37.p13), HCMV Toledo (GU937742.2)
Supplementary_files_format_and_content: Files starting with "KD_": tab-delimited text files include genes, transcripts, fold change values and differential expression probabilities, which were made using RSEM.
Supplementary_files_format_and_content: Files starting with "514A_", "515A_", or "Overlap_": CLIP peaks identified using Roquin antibodies. tab-delimited text files include genomic loci of peaks and adjusted p-values. "Overlap" peaks were built by overlapping (by one nucleotide) the libraries derived from the two different antibodies.


title: CLIP01: 514a, NI, Rep#1

value: Roquin (A300-514A; Bethyl Laboratories)


title: CLIP08: 514a, 24h, Rep#2


title: CLIP09: 514a, 72h, Rep#2


title: CLIP13: Ref, NI, Rep#1


title: CLIP12: 515a, 72h, Rep#2

value: Roquin (A300-515A; Bethyl Laboratories)


title: CLIP02: 514a, 24h, Rep#1


title: CLIP10: 515a, NI, Rep#2


title: CLIP11: 515a, 24h, Rep#2


title: CLIP14: Ref, 24h, Rep#1


title: CLIP07: 514a, NI, Rep#2


title: CLIP05: 515a, 24h, Rep#1


title: CLIP06: 515a, 72h, Rep#1


title: MCF7 cells ESR1 siRNA, replicate 1

description: replicate 1

tag: sirna

value: ESR1 siRNA

value: ER+ luminal breast cancer cell


title: CLIP03: 514a, 72h, Rep#1


title: KD24: siRoq#2, 72h, Rep#2


title: zikv1

value: single blastocyst

value: ZIKV, MR766


title: CLIP04: 515a, NI, Rep#1


title: KD21: siRoq#2, NI, Rep#2


title: KD20: siRoq#1, 72h, Rep#2


title: KD13: siCon, NI, Rep#2


title: KD10: siRoq#2, 06h, Rep#1


title: KD18: siRoq#1, 06h, Rep#2


title: KD14: siCon, 06h, Rep#2


title: KD15: siCon, 24h, Rep#2


title: KD11: siRoq#2, 24h, Rep#1


title: KD12: siRoq#2, 72h, Rep#1


title: KD09: siRoq#2, NI, Rep#1


title: KD17: siRoq#1, NI, Rep#2


title: KD07: siRoq#1, 24h, Rep#1


title: MCF7 cells GATA3 siRNA, replicate 3

description: replicate 3

value: GATA3 siRNA


title: KD08: siRoq#1, 72h, Rep#1

value: Human foreskin fibroblast


title: KD16: siCon, 72h, Rep#2

value: HCMV Toledo strain


title: MCF7 cells GATA3 siRNA, replicate 2

description: replicate 2


title: MCF7 cells GATA3 siRNA, replicate 1

description: replicate 1


title: KD19: siRoq#1, 24h, Rep#2


title: MCF7 cells LSD1 siRNA, replicate 3

description: replicate 3

value: LSD1 siRNA


title: KD04: siCon, 72h, Rep#1


title: KD06: siRoq#1, 06h, Rep#1


title: KD03: siCon, 24h, Rep#1


title: MCF7 cells LSD1 siRNA, replicate 1

description: replicate 1


title: KD05: siRoq#1, NI, Rep#1


title: KD02: siCon, 06h, Rep#1


title: KD01: siCon, NI, Rep#1


title: MCF7 cells control siRNA, replicate 1

description: replicate 1

value: control siRNA


title: PANC03.27_MTAP_KO_Combo_N2

city: Collegeville

first: Satyajit

last: Rajapurkar

address: 1250S. Collegeville Rd.

institute: GlaxoSmithKline LLC

description: processed data file: PANC0327_MTAP_KO_Combo.rMATS.concat.JC.txt

data_processing:
QC of the Fastq files was performed using FastQC.
Fastq files were aligned to GRCh38 version 23 using STAR 2.5.2b.
The BAM files obtained from STAR were filtered, sorted, and indexed using RSeQC and SAMtools.
rMATS was used to identify differential alternative splicing events from the relevant BAM files.
Custom scripts were used to filter the output and generate relevant plots.
Genome_build: GRCh38.v23
Supplementary_files_format_and_content: *.rMATS.concat.JC.txt: Tab-delimited text files containing concatenated rMATS output. The concatenation order is A3SS, A5SS, MXE, RI and SE respectively. Each set contains the list of events given by rMATS with statistics, co-ordinates, counts and inclusion levels for each. SAMPLE_1 is the treated sample, and SAMPLE_2 is the corresponding control (DMSO) sample.

source_name: Pancreatic cancer cell line

extract_protocol:
Total RNA, including miRNA, was isolated from cell pellet using the Qiagen miRNeasy Mini Kit.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina). Samples were sequenced at a depth of 100 million paired-end reads per sample, 100base-pair read length.

tag: replicate

value: Replicate #2

value: Treated (Combination)

tag: mtap status

value: Knock out


title: PANC03.27_MTAP_KO_Combo_N1

tag: cell line

value: Replicate #1


title: PANC03.27_MTAP_KO_GSK591_N2

description: processed data file: PANC0327_MTAP_KO_591.rMATS.concat.JC.txt

value: Treated (GSK3203591)


title: PANC03.27_MTAP_KO_GSK591_N1


title: MCF7 cells LSD1 siRNA, replicate 2

description: replicate 2


title: MCF7 cells control siRNA, replicate 2

description: replicate 2


title: PANC03.27_MTAP_WT_GSK712_N1

description: processed data file: PANC0327_MTAP_WT_712.rMATS.concat.JC.txt

value: Treated (GSK3368712)

value: Parental


title: PANC03.27_MTAP_WT_DMSO_N2

description:
Control samples for PANC03.27 WT comparisons.
processed data file: PANC0327_MTAP_WT_*.rMATS.concat.JC.txt

value: Control (DMSO)


title: PANC03.27_MTAP_KO_GSK712_N1

description: processed data file: PANC0327_MTAP_KO_712.rMATS.concat.JC.txt


title: PANC03.27_MTAP_KO_DMSO_N2

description:
Control samples for PANC03.27 KO comparisons.
processed data file: PANC0327_MTAP_KO_*.rMATS.concat.JC.txt


title: PANC03.27_MTAP_WT_Combo_N2

description: processed data file: PANC0327_MTAP_WT_Combo.rMATS.concat.JC.txt


title: PANC03.27_MTAP_KO_GSK712_N2


title: PANC08.13_N2_GSK712

description: processed data file: PANC08_712_DMSO.rMATS.concat.JC.txt


title: PANC03.27_MTAP_WT_GSK712_N2


title: PANC03.27_MTAP_WT_GSK591_N1

description: processed data file: PANC0327_MTAP_WT_591.rMATS.concat.JC.txt


title: PANC03.27_MTAP_WT_Combo_N1


title: PANC08.13_N2_DMSO


title: PANC08.13_N1_GSK712


title: PANC08.13_N1_DMSO


title: HupT4_N2_GSK712

description: processed data file: HuPT4_712_DMSO.rMATS.concat.JC.txt


title: MCF7 cells control siRNA, replicate 3

description: replicate 3


title: HupT4_N1_GSK712


title: CAPAN-2_N2_GSK712

description: processed data file: CAPAN2_712_DMSO.rMATS.concat.JC.txt


title: PANC03.27_MTAP_WT_GSK591_N2


title: HupT4_N2_DMSO


title: PANC03.27_MTAP_KO_DMSO_N1


title: CAPAN-2_N1_DMSO


title: CAPAN-2_N2_DMSO


title: PANC03.27_MTAP_WT_DMSO_N1


title: BxPC3_N2_DMSO

description: processed data file: BxPC3_712_DMSO.rMATS.concat.JC.txt


title: BxPC3_N2_GSK712


title: BxPC3_N1_DMSO


title: BxPC3_N1_GSK712


title: OTX_rep_3

city: Guangzhou

first: Lingyun

last: Zheng

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

data_processing:
Basecalls performed using bcl2fastq version 2.18
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat 2.1.1
Use Cufflinks version 2.1.1 compute the FPKM, use Refseq GTF file to transcript annotations
RNA-seq data analysis using Excel to compute the Fold change and p-value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample processed by cufflinks

extract_protocol:
mRNA was extracted from DMSO and OTX015 treated cells
mRNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Library Prep Kit for Illumina according to the manusfacture's protocol


title: DMSO_rep_1

value: DMSO


title: OTX_rep_1


title: DMSO_rep_3


title: DMSO_rep_2


title: CMT1A iNC 05148 Schwann-2

first: Macrogen

last: Inc.

address: 12F, World Meridian Venture Center #254 Beotkkot-ro, Geumcheon-gu

institute: Macrogen Inc.

description:
CMT1A disease hiNC derived Schwann cell
25

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.2 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 19 samples.

source_name: CD34+ CMT1A iNC 05148 derived Schwann

growth_protocol: We cultured undifferentiated hESC and hiPSC lines on mitotically inactivated mouse embryonic fibroblasts, in a medium containing DMEM/F12, 20% knockout serum replacement, 0.1 mM MEM-NEAA, 1 mM L-glutamine, 55 μM β-mercaptoethanol and 4 ng/mL FGF2. For the Fibroblast culture, MEM containing 10% FBS was used. All cells were maintained at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Lysed cells by adding TRIzol
Libraries were constructed from mRNA using the Illumina TruSeq RNA Access Library Prep Kit following  manufacturer's protocols.

treatment_protocol: We differentiated human Schwann cell precursors from hESCs (H9 or PGD CMT1A hESCs) and hiPSCs (healthy donor 00024, 02623, and CMT1A disease line 05148, 05165) by using 2i protocol, and WNT was activated for iNC differentiation.

tag: disease state

value: CMT1A disease

value: hiNC derived Schwann cell


title: CMT1A iNC 05165 Schwann-1

description:
CMT1A disease hiNC derived Schwann cell
26

source_name: CD34+ CMT1A iNC 05165 derived Schwann


title: Control iNC 02623 Schwann-2

description:
healthy hiNC derived Schwann cell
22

source_name: CD34+ Control iNC 02623 derived Schwann

value: healthy


title: CMT1A iNC 05148 Schwann-1

description:
CMT1A disease hiNC derived Schwann cell
Re24


title: HupT4_N1_DMSO


title: Control iNC 02623 Schwann-1

description:
healthy hiNC derived Schwann cell
21


title: CMT1A iPSC 05165 Schwann-2

description:
CMT1A disease hiPSC derived Schwann cell
14

source_name: CD49d+ CMT1A iPSC 05165 Schwann

value: hiPSC derived Schwann cell


title: Control iNC 00024 Schwann-2

description:
healthy hiNC derived Schwann cell
20

source_name: CD34+ Control iNC 00024 derived Schwann


title: Control iNC 00024 Schwann-1

description:
healthy hiNC derived Schwann cell
19


title: CMT1A iPSC 05165 Schwann-1

description:
CMT1A disease hiPSC derived Schwann cell
13


title: Control iPSC 00024 Schwann-1

description:
healthy hiPSC derived Schwann cell
7

source_name: CD49d+ Control iPSC 00024 Schwann


title: Control iPSC 02623 Schwann-1

description:
healthy hiPSC derived Schwann cell
9

source_name: CD49d+ Control iPSC 02623 Schwann


title: Control iPSC 02623 Schwann-2

description:
healthy hiPSC derived Schwann cell
10