title: Doped library with SF3B1 siRNA 3

city: Barcelona

first: Pablo

last: Baeza

address: Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

description:
Reads were amplified from the mature mRNA extracted from the cells that contained FAS exon 6.
Processed_Data_File_02.xlsx

data_processing:
Library strategy: DNA-seq of PCR amplicon
Demultiplex sample replicates (Sabre https://github.com/najoshi/sabre)
Paired end read merging (PEAR https://sco.h-its.org/exelixis/web/software/pear/)
Base-calling (custom python scripts)
Supplementary_files_format_and_content: Excel format. File 01. Headers: Sequence=exon genotype; Genotype.ID=Nucleotide substitutions relative to the ancestral exon sequence; Number.Mutations=Number of mutations compared to the ancestral exon genotype; ES.1-9=Genotype enrichment score in each of the nine replicates; Mean.ES=Mean enrichment score across the nine replicates;PSI.1-9=Estimated percent spliced-in (PSI) in each of the nine replicates; Mean.PSI=Mean PSI value across the nine replicates; PSI.Standard.Deviation=Standard deviation of the PSI value across the nine replicates. File 02. Headers: Sequence=exon genotype; Genotype.ID=Nucleotide substitutions relative to the human wild-type sequence; Number.Mutations=Number of mutations compared to the human wild-type sequence; siControl.ES.1-3=Genotype enrichment score in the control siRNA experiment; siControl.Median.ES=Median enrichment score across the three replicates in the control siRNA experiment; siControl.ES.Standard.Deviation=Standard deviation of the enrichment scores across the three replicates in the control siRNA experiment; siControl.PSI=Estimated PSI value for each genotype in the control siRNA experiment; siSF3B1.ES.1-3=Genotype enrichment score in the SF3B1 siRNA experiment; siSF3B1.Median.ES=Median enrichment score across the three replicates in the SF3B1 siRNA experiment; siSF3B1.ES.Standard.Deviation=Standard deviation of the enrichment scores across the three replicates in the SF3B1 siRNA experiment; siSF3B1.PSI=Estimated PSI value for each genotype in the SF3B1 siRNA experiment.

source_name: cell culture

growth_protocol: Mycoplasma-free tested HEK293 cells (ATCC, CRL-1573) were sub-cultured in DMEM Glutamax (Thermo scientific, 61965059) containing 2.5mM glutamine, 15mM HEPES, 10% FBS (Thermo scientific, 10270) and Pen-Strep (Thermo scientific, 15070063). 250,000 HEK293 cells were plated in 6-well plates (NUNC, 140675).

extract_protocol:
For each of the experimental replicates, 10 ng of the library were transfected into 250 000 HEK293 cells in one well of a 6-well plate using Lipofectamine 2000 (11668027, Thermo scientific) and OPTIMEM I Reduced Serum Medium (31985-047, Thermo scientific). Six hours post-transfection, the cell culture medium was replaced with DMEM Glutamax (61965059, Life Technologies) containing 10% FBS and Pen/Strep antibiotics. 48 hours post-transfection (72 in the case of the siRNA experiments), total RNA was isolated using the automated Maxwell LEV 16 simplyRNA tissue kit (AS1280, Promega).
Accuprime Pfx (12344024, Thermo scientific) was used following the manufacturer’s instructions to amplify 20 ng of single-stranded library DNA for 25 cycles with the following flanking intronic primers: FAS_i5_GC_F and FAS_i6_GC_R (“Primers used for library amplification” in Table S5). The amplified library was recombined with pCMV FAS wt minigene exon 5-6-7 (Förch et al., 2000) using the In-Fusion HD Cloning kit (639649, Clontech) in a 1:8 vector:insert optimized ratio and transformed into Stellar competent cells (636766, Clontech) to maximise the number of individual transformants, which was around 800,000 individual clones per library. The library was amplified by growing for 18 hours in LM medium containing ampicillin and the final plasmid library was purified using the Quiagen plasmid maxi kit (50912163, Quiagen) and quantified with a NanoDrop spectrophotometre. 20 ng of the library was amplified in triplicates using GoTaq flexi DNA polymerase (M7806, Promega) for 25 cycles with three pairs of intronic primers FAS_i5_BR_F and FAS_i6_BR_R (“Primers used for Ampliseq sequencing” in Table S5), leading to a 135 nucleotide PCR band that was gel-purified and sequenced. Each pair of primers had a distinct 8-mer barcode sequence to discriminate between technical replicates (“Primers used for Ampliseq sequencing” in Table S5). For the output libraries, cDNA was synthetized from 500 ng total RNA using Superscript III (18080085, Life Technologies), and amplified with one of the pairs of barcoded FAS_e5_BR_F and FAS_e5_BR_R primers (“Primers used for Ampliseq sequencing” in Table S5) and GoTaq flexi DNA polymerase (M7806, Promega). Each pair of primers had a distinct 8-mer barcode sequence to distinguish the nine experimental replicates (“Primers used for Ampliseq sequencing” in Table S5). PCR products were run on a 2% agarose gel and the band corresponding in size to the amplification product of splicing inclusion was excised, purified using the Quiaquick Gel extraction kit (Quiagen, 50928704) and quantified with a NanoDrop spectrophotometre. Equimolar quantities of three independent amplifications of the input library and equimolar quantities of the purified inclusion band (output library) of each of the nine replicates were pooled and sequenced at the EMBL Genomics Core Facility where Illumina Ampliseq PCR-free libraries were prepared and run on a single lane of an Illumina HiSeq3000. In total, 191.6 million paired-end reads were obtained. The median sequencing coverage for all 3072 genotypes in the input was between 657 and 2069 reads. In the output, the median sequencing coverage was between 389 and 1447 reads depending on the replicate.

treatment_protocol: 10 ng of a FAS exon 6 doped library (Julien et al., 2016) were co-transfected in triplicates with 100nM On-TARGETplus SMARTpool siRNA against SF3B1 L-020061-0005 (Dharmacon) using 2μl Lipofectamine 2000 (Thermo scientific, 11668027) per 1ml of total volume of transfection in OPTIMEM (Thermo scientific, 13778150). Five hours after treatment, the medium was replaced with DMEM-F12 containing 10% FBS and Pen-Strep.

tag: sample type

value: PCR amplicon


title: BAB2492

status: Public on Jan 17 2019

type: genomic

city: Houston

first: James

middle: R

last: Lupski

state: TX

address: One Baylor Plaza Room #604B

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description:
17p11.2 interrogation
aCGH experiment of trios for capture and sequencing

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner- Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA extracted from whole blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP, PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: tissue

value: whole blood

tag: proband or parent

value: Proband

tag: tag

value: Reference sample


title: BAB1931

tag: lymphoblastoid dna reference


title: Doxorubicin-resistant 834 hepatoma cells

type: RNA

city: Taoyuan

first: Tse-Ching

last: Chen

address: 5. Fu-Hsing Street

department: Anatomic Pathology

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Gene expression data from doxorubicin-resistant 834 hepatoma cells.

hyb_protocol: Hybridization protocols follows the Affymetrix's instructions

scan_protocol: Following a quantitative scan of the chip, a grid was aligned to the image using the dimension of the microarray chips and the corner control regions as markers.

data_processing:
The images were transformed into text files containing the intensity information using GeneChip Operating Software (GCOS), developed by Affymetrix. The microarray data were analyzed using the GeneSpring 7.0 software (Silicon Genetics, Redwood City, CA, USA).
The absolute intensity statistics were based on the feature intensities and corresponding standard deviations provided in the microarray chip-generated CEL files. In addition, normalization between different arrays was performed for all regions, and each gene expression signal was normalized to the median value of all genes in each chip.

label: biotin

molecule: total RNA

label_protocol: Labeled cRNA was synthesized from the cDNA using the Bioarray High Yield RNA Transcript Labeling Kit (Affymetrix, Cat# 900182) according to the manufacturer's instructions. Fragmentation of biotinylated cRNA (15 μg) was performed by employing the GeneChip Sample Cleanup Module (Affymetrix, Cat# 900371).

growth_protocol: We generated three hepatoma cell lines, designated 834, LC413T-1 and P15, that isolated from three individual HCC patients. Briefly, fresh liver tumor tissues from HCC patients were collected for primary culture. After cleaning with HBSS containing penicillin (50 units/ml) and streptomycin (50 μg/ml), the liver tumor tissues were minced; followed by enzymatic digestion with type IV collagenase (20-30 min at 37˚C) and passed through an 18 mm needle (4-5 times). The collagenase activity was stopped by immediate addition of 4 mM EDTA in HBSS and then disaggregated cells were collected after centrifugation (1000 × g for 5 min, 2 times).  The 834 and LC413T-1 hepatoma cells were cultured in DMEM medium (pH 7.2) supplemented with 10% heat inactivated fetal bovine serum (FBS), penicillin (50 units/ml), streptomycin (50μg/ml) and non-essential amino acid (1 μg/ml). The P15 hepatoma cells were cultured in DMEM/F12 medium supplemented with Insulin, hepatocyte growth factor, 10% FBS, penicillin, streptomycin and non-essential amino acid. After 24 h of incubation at 37˚C in a humidified incubator containing 5% CO2, the floating cells were discarded and replacement with fresh growth medium.

extract_protocol: From primary HCC cells and their drug-resistant counterpart, total RNA was isolated with Trizol reagent according to the manufacturer's instructions and the quality of RNA was determined using Spectra Max Plus spectrophotometer (Molecular Devices, Sunnyvale, California, USA).

treatment_protocol: For establishment of doxorubicin resistant sub-lines, primary HCC cells (5 × 105) were repeatedly treated with sub lethal concentrations of doxorubicin. The starting concentration was (1 μM), until the recovery rate was maintained in a stable state (~80%) at 10 μM, and that was defined as drug-resistant cells.

value: Primary hepatoma cells isolated from liver


title: BAB1958

value: Parent


title: Doped library with SF3B1 siRNA 2

type: SRA

library_source: genomic

tag: cell line


title: BAB1354


title: BAB1957


title: BAB2993


title: BAB2994


title: BAB2552


title: Doped library with SF3B1 siRNA 1


title: BAB2310


title: BAB1604


title: BAB8326


title: BAB2540


title: BAB429


title: Doped library with control siRNA 3

treatment_protocol: 10 ng of a FAS exon 6 doped library (Julien et al., 2016) were co-transfected in triplicates with control siRNA ordered from SIGMA (sequence: AAGGUCCGGCUCCCCCAAAUG) using 2μl Lipofectamine 2000 (Thermo scientific, 11668027) per 1ml of total volume of transfection in OPTIMEM (Thermo scientific, 13778150). Five hours after treatment, the medium was replaced with DMEM-F12 containing 10% FBS and Pen-Strep.


title: Doped library with control siRNA 2


title: Doped library with control siRNA 1


title: BAB2992


title: BAB279


title: BAB243


title: BAB251


title: BAB2986


title: BAB530


title: BAB2386


title: BAB6094/BAB3988


title: Combinatorially Complete Library Output 9

description:
Output reads were amplified from the mature mRNA extracted from the cells that contained FAS exon 6.
Processed_Data_File_01.xlsx


title: Combinatorially Complete Library Output 8


title: BAB2967


title: BAB247


title: BAB3144


title: BAB3143


title: BAB3142


title: BAB2987


title: BAB2966


title: BAB241


title: BAB2988


title: BAB242


title: BAB8634


title: BAB2965


title: Combinatorially Complete Library Output 6


title: BAB8125


title: BAB8124


title: Combinatorially Complete Library Output 7


title: Combinatorially Complete Library Output 5


title: Combinatorially Complete Library Output 4


title: Combinatorially Complete Library Output 3


title: Combinatorially Complete Library Output 2


title: BAB8633


title: Combinatorially Complete Library Output 1


title: BAB2811


title: BAB6312


title: BAB8123


title: BAB6313


title: BAB2695


title: BAB6919


title: BAB1616


title: BAB1617


title: BAB2696


title: BAB2543


title: BAB767


title: BAB2697


title: BAB6918


title: BAB1231


title: Combinatorially Complete Library Input 3

description:
Input reads were amplified from the plasmid library.
Processed_Data_File_01.xlsx

source_name: plasmid library


title: BAB3795


title: BAB2337


title: BAB6917


title: BAB3810


title: BAB1456


title: BAB766


title: Combinatorially Complete Library Input 2


title: Combinatorially Complete Library Input 1


title: Ep_2

city: WuHan

first: Qing

last: Ye

state: HuBei

address: Shizishan street

department: state key laboratory of agricultural microbiology

country: China

institute: Huazhong Agricultural University

library_source: transcriptomic

data_processing:
Illumina Casava HiSeqX HD 3.4.0.38 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the cleandata were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.L. Salzberg, 2012)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: S. islandicus REY15A (accession no. NC_017276)
Supplementary_files_format_and_content: fpkm, Differential expression analysis of two groups

organism: Saccharolobus islandicus REY15A

growth_protocol: Strains were cultured in ACVy medium at 75°C to log phase (OD600=0.2)

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA), NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. rRNA is removed using a specialized kit that leaves the mRNA. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 μl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

tag: genotype/variation

value: wild type with pSeSD plasmid

tag: growth phase

value: log phase


title: Ep_1


title: CENH3_InputSeq_Gossypium_barbadense

city: Fuzhou

first: Zhiliang

last: Zhang

address: Shangxiadian

institute: Fujian Agriculture and Forestry University

description: processed data file: Hai7124_CHIp.uniq.sort-W200-G400-islands-summary-FDR0.01.txt

data_processing:
Remove PCR duplication and low quality reads using FastUniq and Trimmomatic.
Read mapping using Bowtie2 (reads with mapping quality ≥ 30 and uniquely mapped locus were retained and used for further analysis).
Map the position of centromere regions (the CenH3 binding sites) using SICER (200-bp windows, a required fold change/control ≥5, FDR<0.01, and allowed 400-bp gaps).
Genome_build: TM-1 V2.1; Hai7124 V1.1
Supplementary_files_format_and_content: *_CHIp.uniq.sort-W200-G400-islands-summary-FDR0.01.txt: Tab-delimited text files were generated using SICER include regions and its FDR.

organism: Gossypium barbadense

source_name: leaf

extract_protocol:
Lysates were clarified from enzyme (MNase) nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: leaf

tag: age

value: 4 weeks after planting

tag: chip antibody


title: OE3b_2

value: wild type with pCsa3b plasmid


title: CENH3_ChIPSeq_Gossypium_barbadense

value: CENH3 (AbMax Biotechnology Co., Ltd.)


title: OE3b_1


title: BAB650


title: BAB1190


title: BAB644


title: BAB200


title: BAB1153


title: BAB3133


title: BAB3794


title: BAB1357


title: BAB3344


title: BAB2564


title: BAB642


title: BAB8501


title: non-photo-responisve_gel_740nm(48h)_Rep6

status: Public on Jan 16 2019

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: ReadCounts_control1_non-photo_responisve_hydrogel.txt

data_processing:
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Ensembl (release: 75) annotation using TopHat2 (v2.0.13) with the options mate-inner-dist, mate-std-dev and library-type (fr- firststrand).
The distance between read mates (mate-inner-dist and mate-std-dev) were assessed individually using RSeQC (v2.6.1).
After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Homo sapiens gtf file from the Ensembl release 75 were used as reference for counting.
DESeq2 was used for differential expression analysis of all replicates for each condition. In this analysis, all libraries were compared in a pairwise manner.
Genome_build: hg19

source_name: hMSC

growth_protocol: hMSCs were cultivated on the indicated substrates.

extract_protocol: The cells were lysed using 1 ml peqGOLD Trifast (VWR International, Erlangen, Germany, cat. no. 30-2020) per hydrogel and RNA was extracted from the aqueous phase using the RNA purification kit R1013 (Zymo Research, Irvine, CA) according to the manufacturer’s protocol.

treatment_protocol: Samples were exposed to the indicated illumination.

tag: condition

value: non-photo-responsive hydrogels

tag: illumination


title: non-photo-responisve_gel_740nm(48h)_Rep5


title: Microdissected PTS2, Single-tubule RNA-Seq, transcriptome 10

city: Bethesda

first: Lihe

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm38.p5) using STAR v2.5.1b
Transcript abundances in TPM were caculated by  RSEM/1.2.31
GRCm38.p5 (Ensembl)
Genome_build: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: microdissected proximal tubule

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male mice were grown and maintained in the Animal Facility of the NHLBI. 2 month-old mice were used in the experiments.

tag: strain

value: Kidney

tag: gender

value: male

value: 2 month-old


title: BAB3031


title: BAB651


title: non-photo-responisve_gel_740nm(48h)_Rep4


title: BAB1615


title: BAB1358


title: non-photo-responisve_gel_740nm(48h)_Rep3


title: BAB574


title: BAB3793


title: non-photo-responisve_gel_740nm(48h)_Rep2


title: non-photo-responisve_gel_740nm(48h)_Rep1


title: non-photo-responisve_gel_660nm(48h)_Rep4


title: non-photo-responisve_gel_660nm(48h)_Rep3


title: non-photo-responisve_gel_660nm(48h)_Rep2


title: non-photo-responisve_gel_660nm(48h)_Rep1


title: OPA1 F38D mutant cells 75_1

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

description:
OPA1 F38D mutant cells 75_1
F38D_75_1

data_processing:
Fastq files were adapter-trimmed and wuality-filtered with Trimmomatic.
High quality fastq files were aligned to the human genome by using STAR.
Gene read counts were calculated with featureCounts.
Differential gene expression was performed with DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tabular gene counts

source_name: OPA1 F38D mutant cells 75

growth_protocol: iPSC cell lines were maintained in feeder-free conditions in mTeSR1 (Stem Cell Technologies) and seeded in HESC qualified Matrigel (Corning)-coated 6-well plates.

extract_protocol:
Total RNA isolation was performed with RNeasy Mini Kit (QIAGEN).
RNA libraries were generated starting from 1 µg of total RNA extracted using TRIzol (Invitrogen, Life Technologies). RNA quality was assessed by using a Tape Station instrument (Agilent). To avoid over-representation of 3’ends, only high-quality RNA with RNA Integrity Number (RIN) ≥ 8 was used.

treatment_protocol: NPCs were generated as previously described with appropriated optimization (Marchetto et al., 2010).

tag: cell type

value: induced Pluripotent Stem Cell-derived Neural Precursor Cells

tag: genotype

value: OPA1 F38D mutant


title: non-photo-responisve_gel_660nm(48h)_Rep5


title: BAB6311

value: whole blood


title: Control cells 37_2

description:
Control cells 37_2
DIGI_37_2

source_name: Control cells 37

value: control


title: Control cells 37_1

description:
Control cells 37_1
DIGI_37_1


title: Control cells 68_1

description:
Control cells 68_1
DIGI_68_1

source_name: Control cells 68


title: OPA1 F38D mutant cells 75_3

description:
OPA1 F38D mutant cells 75_3
F38D_75_3


title: RFPHigh-Repl.1

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
Raw reads were trimmed using trim_galore v0.4.2
Trimmed reads were mapped to mm10 whole genome using STAR v2.3.0
Fragments Per Kilobase of Transcript Per Million Mragments (FPKM) were calculated by cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: embryonic stem cells

growth_protocol: ESCs were cultured on gelatin  in ES cell medium (DMEM plus 15% FBS, nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor).

extract_protocol:
Cells were treated with TRIzol and followed with phase seperation,  RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.
Library was constructed with NEBNext® Ultra™ Directional RNA Library Prep Kit. Briefly, total RNA was subjected to two rounds of purification using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds cDNA was ligated to adaptors and sequenced with illumina HiseqXten platform.

treatment_protocol: ESCs were sorted by Flow cytometry based on RFP intensity. Lower 5% and Top 5% subpopulations were sorted.

tag: developmental stage

value: 3.5 days

value: embryonic stem cells

tag: subpopulation

value: sorted RFP high


title: RFPHigh-Repl.2


title: RFPLow-Repl.2

value: sorted RFP low


title: Wild type cells, 25U MNase, Experiment 2

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

data_processing:
Sequences were aligned to the yeast genome (sacCer3) using Bowtie2 with default settings.
Reads were size selected, and we kept all reads with the lengths between 120-180 bp (mono-nucleosomes) and 250-350 bp (di-nucleosomes).
Genome-wide coverage profiles were computed in MATLAB, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in Synthetic Complete (SC) medium, harvested by filtration and cell pellets were stored at -80C.

extract_protocol:
Nuclei were prepared and digested with different amounts of MNase (units given in filenames, see paper for details).
The DNA was repaired using the DNA PreCR kit from New England Biolabs. Paired-end libraries were constructed and indexed using Illumina kits from NEB (E7370 and E7335).

tag: strain name


title: isw1∆ chd1∆ cells, 50U MNase, Experiment 1

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 chd1-delta::HIS5


title: Wild type cells, 50U MNase, Experiment 2


title: isw1∆ chd1∆ cells, 25U MNase, Experiment 2


title: Trm13_pulldown_A

city: New Haven

first: Wendy

last: Gilbert

state: CT

address: 333 Cedar Street, P.O. Box 208024

institute: Yale University

description:
UV-crosslinked RNA
TableS7.Trm13_eCLIP.csv
Trm13_A

data_processing:
Read demultiplexing: removed the first 10-nt of the forward reads, and adding them to the sequence name for later use
Use cutadapt (version 1.7.1) to trim 3’ adapter, requiring a minimum trimmed read length of 18-nt.
Map reads using STAR(version 2.5.1b) to a repeat-masked yeast genome.
Collapse PCR duplicates: use the 10-nt barcode from step 1 to merge reads that map to the same position and share the same barcode.
Call peaks using CLIPper
Normalize peaks from pulldown libraries by peaks in size-matched input library
Genome_build: sacCer3
Supplementary_files_format_and_content: *.csv files are tables of normalized peak heights
*.bed files represent raw peaks

growth_protocol: For ePAR-CLIP assays yeast were grown at 30°C in minimal media with reduced uracil (SCUra120uM) to an A600nm=0.4-0.5, supplemented with 4-thiouracil to a final concentration of 500uM and cultured for 3 more hours before harvest.

extract_protocol:
Cells were resuspened in 1.5 mL iCLIP lysis buffer (50 mM Tris-HCl pH7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1X protease inhibitor cocktail (Millipore), 400U/mL Murine RNase inhibitor (NEB)) per g of cell pellet and lysed by vortexing with glass beads (Manufacturer). Lysates were clarified by centrifugation, flash frozen in liquid N2 and stored at -80°C.
Lysates were diluted in iCLIP lysis buffer to 26 ODU/2 mL and treated with Turbo DNase (Lifetech) and RNase I (Lifetech) for 15min at 22°C before placing on ice. Treated lysates were centrifuged (15,000 x g 15min) and added to Protein G magnetic beads (Dynabeads) pre-bound with 10 µg of antibody (anti-Myc or anti-FLAG, Sigma) and rotated for 2.5hr at 4°C. 4% of the binding reaction was saved as input before extensive washing of bead-bound protein-RNA complexes. Bound RNA 3′ ends were dephosphorylated with FastAP (Lifetech) and PNK (NEB) before on-bead ligation of a 3′ RNA linker with T4 Rnl (NEB) at 16°C overnight. After washing, 10% of bound RNA was labeled by PNK with 32P ATP for diagnostic gels. The remainder was eluted from the beads by incubation in 1X NuPAGE loading buffer with 0.1M DTT at 70°C for 10min. CLIP eluates and paired inputs were electrophoresed on 4-12% Bis-Tris NuPAGE and transferred to nitrocellulose membranes. Tagged protein MW was determined by western blot of 2% input before CLIP and size-matched input (SMI) membranes were cut, taking a 75kDa region just above the target protein size. RNA was released with proteinase K, extracted with phenol:chloroform:isoamy alcohol, and purified on RNA Clean & Concentrator-5 columns (Zymo). SMI RNA was dephosphorylated, a 3′ linker ligated, and purified on silane beads (Dynabeads). CLIP and SMI RNA was reverse transcribed with SuperScript IV, hydrolyzed with NaOH, neutralized with HCl, and cDNA was purified on silane beads. A 5′ linker was ligated with T4 Rnl (NEB) overnight at 16°C. Linker-ligated cDNA was purified on silane beads before diagnostic PCRs to determine the minimum number of cycles. Final PCR products were gel-purified, precipitated and sequenced on an Illumina HiSeq 2000.

treatment_protocol: Cells were harvested by centrifugation, resuspended in ice cold water, and UV irradiated on ice in a Stratalinker (365 nm, energy = 7.2J/cm2). Crosslinked cells were washed in ice water, flash frozen in liquid N2, and stored at -80°C until lysis.

tag: pulldown

value: pulldown

tag: affinity tag

value: HPM

tag: rip antibody

value: anti-myc, Sigma, catalog # M4439, lot # 026M-4825V


title: Trm7_pulldown_B

description:
UV-crosslinked RNA
TableS6.Trm7_eCLIP.csv
Trm7_B


title: Trm13_input_A

description:
UV-crosslinked RNA
TableS7.Trm13_eCLIP.csv
Trm13_Ai

value: size-matched input


title: Trm13_pulldown_B

description:
UV-crosslinked RNA
TableS7.Trm13_eCLIP.csv
Trm13_B


title: Trm7_input_A

description:
UV-crosslinked RNA
TableS6.Trm7_eCLIP.csv
Trm7_Ai


title: Spb1_input_A

description:
UV-crosslinked RNA
TableS14.Spb1_eCLIP.csv
Spb1_Ai

value: FLAG


title: Trm13_input_B

description:
UV-crosslinked RNA
TableS7.Trm13_eCLIP.csv
Trm13_Bi


title: Wild type cells, 200U MNase, Experiment 1


title: Trm3_input_B

description:
UV-crosslinked RNA
TableS5.Trm3_eCLIP.csv
Trm3_Bi


title: Trm7_pulldown_A

description:
UV-crosslinked RNA
TableS6.Trm7_eCLIP.csv
Trm7_A


title: Trm3_input_A

description:
UV-crosslinked RNA
TableS5.Trm3_eCLIP.csv
Trm3_Ai


title: Trm44_pulldown_A

description:
UV-crosslinked RNA
TableS3.Trm44_eCLIP.csv
Trm44_A


title: RFPLow-Repl.1


title: Trm3_pulldown_B

description:
UV-crosslinked RNA
TableS5.Trm3_eCLIP.csv
Trm3_B


title: isw1∆ chd1∆ cells, 50U MNase, Experiment 2


title: Trm3_pulldown_A

description:
UV-crosslinked RNA
TableS5.Trm3_eCLIP.csv
Trm3_A


title: Pus1_pulldown_B

description:
UV-crosslinked RNA
TableS4.Pus1_eCLIP.csv
Pus1_B


title: Pus1_input_B

description:
UV-crosslinked RNA
TableS4.Pus1_eCLIP.csv
Pus1_Bi


title: Pus1_input_A

description:
UV-crosslinked RNA
TableS4.Pus1_eCLIP.csv
Pus1_Ai


title: Trm44_pulldown_B

description:
UV-crosslinked RNA
TableS3.Trm44_eCLIP.csv
Trm44_B


title: Trm7_input_B

description:
UV-crosslinked RNA
TableS6.Trm7_eCLIP.csv
Trm7_Bi


title: pGAL-spb1_RepB_OD12

description:
OD12_Spb1_B
Spb1_OD12.MeTH_peaks.csv

data_processing:
Trim reads using cutadapt
Map to yeast genome using Tophat2, using defined splice junctions
Use SAMtools to exclude multiply-mapping reads
Use read 5’ ends in permissive and restrictive conditions to call peaks.
Genome_build: sacCer3
Supplementary_files_format_and_content: *MeTH_peaks.csv files are tables of peak heights >= 2

growth_protocol: All strains, with the exception of pGAL-HA-SPB1, were grown at 30°C in YPAD (1% yeast extract, 2% peptone, 0.01% adenine hemisulphate, 2% glucose). Cultures for MeTH-seq were harvested by centrifugation in log phase (A600nm≈1.0) or at high density (A600nm≈12.0). High density trm7∆ cells were grown to A600nm≈8.0.

extract_protocol:
Total yeast RNA was isolated by hot acid phenol extraction followed by isopropanol precipitation. PolyA+ mRNA was isolated from 10-15mg of yeast total RNA by two rounds of selection on oligo-dT cellulose beads according to the manufacturer’s instructions (NEB).
RNA fragmentation was performed in 10mM ZnCl2 at 95C for 55s. RNA fragments were precipitated, dephosphorylated with CIP and PNK, and separated by denaturing (8% urea-TBE) polyacrylamide gel electrophoresis. Gel-purified RNA fragments (60-70nt, 70-80nt, 80-90nt) were eluted overnight with rocking in RNA elution buffer (300mM NAOAc pH 5.5, 1mM EDTA, 100 U/ml RNasin (Promega) and ligated to a pre-adenylated adaptor using T4 RNA ligase (NEB) at 22°C for 2.5h, followed by precipitation. Reverse transcription was completed using AMV-RT (Promega) and the reverse transcription primer using the following conditions. RNA and RT primer were denatured and annealed in reverse transcription buffer (50 mM Tris-Cl pH 8.6, 60mM NaCl, 10mM DTT). After annealing, the reverse transcription reaction was split in equal halves for the restrictive and permissive conditions. The restrictive reaction received a final concentration of 2.5mM dNTPs, 6mM MgCl2 and 7.1% DMSO, whereas the permissive reaction received a final concentration of 4mM dNTPs, 20mM MgCl2 and 7.1% DMSO. Reactions were carried out at 42°C for 1h, prior to degradation of RNA with the addition of NaOH at 85°C. Truncated cDNAs were size-selected and purified on an 8% urea-TBE PAGE gel, followed by elution from gel slices in DNA elution buffer (300mM NaCl, 10mM Tris-HCl, pH 8.0) overnight at room temperature. cDNAs were circularized with circLigase (Epicentre) and amplified by PCR (Phusion; NEB) with the forward primer  and a barcoded reverse primer . PCR products were gel-purified, precipitated and sequenced on an Illumina HiSeq 2000.

tag: culture od_600

value: spb1 knockdown

tag: restrictive mg2+ concentration

tag: permissive mg2+ concentration


title: Pus1_pulldown_A

description:
UV-crosslinked RNA
TableS4.Pus1_eCLIP.csv
Pus1_A


title: rtt10_RepB_OD12

description:
OD12_Rtt10_B
OD12.MeTH_peaks.csv

value: rtt10 knockout


title: trm732_RepA_OD12

description:
OD12_Trm732_A
OD12.MeTH_peaks.csv

value: trm732 knockout


title: rtt10_RepA_OD12

description:
OD12_Rtt10_A
OD12.MeTH_peaks.csv


title: trm732_RepB_OD12

description:
OD12_Trm732_B
OD12.MeTH_peaks.csv


title: pGAL-spb1_RepA_OD12

description:
OD12_Spb1_A
Spb1_OD12.MeTH_peaks.csv


title: trm44_RepB_OD12

description:
OD12_Trm44_B
OD12.MeTH_peaks.csv

value: trm44 knockout


title: trm44_RepA_OD12

description:
OD12_Trm44_A
OD12.MeTH_peaks.csv


title: trm3_RepB_OD12

description:
OD12_Trm3_B
OD12.MeTH_peaks.csv

value: trm3 knockout


title: trm7_RepB_OD12

description:
OD8_Trm7_B
OD12.MeTH_peaks.csv

value: trm7 knockout


title: trm3_RepA_OD12

description:
OD12_Trm3_A
OD12.MeTH_peaks.csv


title: trm7_RepA_OD12

description:
OD8_Trm7_A
OD12.MeTH_peaks.csv


title: trm13_RepA_OD12

description:
OD12_Trm13_A
OD12.MeTH_peaks.csv

value: trm13 knockout


title: snoRNA72-78_repB_OD12

description:
OD12_YWG318
OD12.MeTH_peaks.csv

value: Snr72-78 knockout


title: WT_RepD_OD12

description:
OD12_WT_D
OD12.MeTH_peaks.csv

value: Wild-type


title: WT_RepB_OD12

description:
OD12_WT_B
OD12.MeTH_peaks.csv


title: snoRNA72-78_repA_OD12

description:
OD12_YWG372
OD12.MeTH_peaks.csv


title: WT_RepC_OD12

description:
OD12_WT_C
OD12.MeTH_peaks.csv


title: WT_RepA_OD8

description:
OD8_WT_A
OD12.MeTH_peaks.csv


title: WT_RepA_OD12

description:
OD12_WT_A
OD12.MeTH_peaks.csv


title: WT_RepB_OD8

description:
OD8_WT_B
OD12.MeTH_peaks.csv


title: PGAL-spb1_RepB_OD1

description:
OD1_Spb1_B
Spb1_OD1.MeTH_peaks.csv


title: Trm732_RepB_OD1

description:
OD1_Trm732_B
OD1.MeTH_peaks.csv


title: Trm44_RepA_OD1

description:
OD1_Trm44_A
OD1.MeTH_peaks.csv


title: Trm13_RepB_OD1

description:
OD1_Trm13_B
OD1.MeTH_peaks.csv


title: Trm44_RepB_OD1

description:
OD1_Trm44_B
OD1.MeTH_peaks.csv


title: Trm13_RepA_OD1

description:
OD1_Trm13_A
OD1.MeTH_peaks.csv


title: Trm3_RepB_OD1

description:
OD1_Trm3_B
OD1.MeTH_peaks.csv


title: WT_RepF_OD1

description:
OD1_WT_F
OD1.MeTH_peaks.csv


title: Trm7_RepB_OD1

description:
OD1_Trm7_B
OD1.MeTH_peaks.csv


title: Trm7_RepA_OD1

description:
OD1_Trm7_A
OD1.MeTH_peaks.csv


title: trm13_RepB_OD12

description:
OD12_Trm13_B
OD12.MeTH_peaks.csv


title: WT_RepE_OD1

description:
OD1_WT_E
OD1.MeTH_peaks.csv


title: WT_RepD_OD1

description:
OD1_WT_D
OD1.MeTH_peaks.csv


title: WT_RepC_OD1

description:
OD1_WT_C
OD1.MeTH_peaks.csv


title: WT_RepB_OD1

description:
OD1_WT_B
OD1.MeTH_peaks.csv


title: WT_RepA_OD1

description:
OD1_WT_A
OD1.MeTH_peaks.csv


title: Rtt10_RepB_OD1

description:
OD1_Rtt10_B
OD1.MeTH_peaks.csv


title: pGAL-spb1_RepA_OD1

description:
OD1_Spb1_A
Spb1_OD1.MeTH_peaks.csv


title: Cx3cr1_2

city: Durham

first: Yasuhito

last: Yahara

state: NC

address: Duke Hospital South, 200 Trent Drive, Orange Zone 5th floor

institute: Duke Univ

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of samples: Csf1r_1, Csf1r_2, Cx3cr1_1, and Cx3cr1_2, using 10X Cellranger v2.1.1 with default parameters.
Alignment, counting, filtering, of single cell RNA-Seq of 2_mo_BMC_1 and 2_mo_BMC_2, using 10X Cellranger v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BMC.matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus 2_mo_BMC_1 and Mus musculus 2_mo_BMC_1 total bone marrow cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: BMC.genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: BMC.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.
Supplementary_files_format_and_content: Cx3cr1_Csf1r.matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus Csf1r_1, Csf1r_2, Cx3cr1_1, and Cx3cr1_2 total bone marrow cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: Cx3cr1_Csf1r.genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: Cx3cr1_Csf1rbarcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: Macrophage from E14.5 body lysate

growth_protocol: Macrophage/ monocyte lineage cells were isolated from E14.5 whole body cell suspensions. Total bone marrow cells were isolated from 2-month-old C57BL6 mice.

extract_protocol:
Cell were prepared for 10X Genomics Single Cell RNA-Seq using Chromium Single Cell 3′ Library & Gel Bead Kit v1.
10X Single Cell 3'

treatment_protocol: Pregnant female carrying Cx3cr1CreER; R26tdTomato or Csf1r-Mer-iCre-Mer; Csf1r-EGFP; R26tdTomato pups were injected with 4 hydroxytamoxifen at either E8.5 or 9.5.

value: Cx3cr1CreER; R26tdTomato

tag: 4 hydroxytamoxifen


title: Csf1r_2


title: Csf1r_1


title: Cx3cr1_1


title: genomic DNA from sample614

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples, resultng in 249874 data rows out of a possible 485577 (provided in the matrix_normalized.txt)

label: Cy5 and Cy3

source_name: case_whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: age

tag: Sex

value: M

tag: tissue

value: whole blood

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample559

description: whole blood control sample

source_name: control_whole blood

value: control

value: F


title: genomic DNA from sample666

description: whole blood case sample


title: genomic DNA from sample643

description: whole blood case sample


title: genomic DNA from sample694

description: whole blood case sample


title: genomic DNA from sample647

description: whole blood case sample


title: genomic DNA from sample688

description: whole blood case sample


title: genomic DNA from sample599

description: whole blood case sample


title: genomic DNA from sample564

description: whole blood control sample


title: genomic DNA from sample690

description: whole blood case sample


title: genomic DNA from sample699

description: whole blood case sample


title: Trm3_RepA_OD1

description:
OD1_Trm3_A
OD1.MeTH_peaks.csv

tag: strain

tag: genotype


title: genomic DNA from sample681

description: whole blood case sample


title: genomic DNA from sample568

description: whole blood control sample


title: genomic DNA from sample692

description: whole blood case sample


title: genomic DNA from sample588

description: whole blood case sample


title: genomic DNA from sample539

description: whole blood case sample


title: genomic DNA from sample653

description: whole blood case sample


title: genomic DNA from sample662

description: whole blood case sample


title: genomic DNA from sample641

description: whole blood case sample


title: genomic DNA from sample590

description: whole blood case sample


title: genomic DNA from sample639

description: whole blood case sample


title: genomic DNA from sample697

description: whole blood case sample


title: genomic DNA from sample628

description: whole blood case sample


title: genomic DNA from sample655

description: whole blood case sample


title: genomic DNA from sample561

description: whole blood control sample


title: genomic DNA from sample679

description: whole blood case sample


title: genomic DNA from sample645

description: whole blood case sample


title: genomic DNA from sample576

description: whole blood case sample


title: genomic DNA from sample566

description: whole blood control sample


title: genomic DNA from sample556

description: whole blood case sample


title: genomic DNA from sample680

description: whole blood case sample


title: genomic DNA from sample565

description: whole blood control sample


title: genomic DNA from sample554

description: whole blood case sample


title: genomic DNA from sample673

description: whole blood case sample


title: genomic DNA from sample595

description: whole blood case sample


title: genomic DNA from sample586

description: whole blood case sample


title: genomic DNA from sample665

description: whole blood case sample


title: genomic DNA from sample649

description: whole blood case sample


title: genomic DNA from sample651

description: whole blood case sample


title: genomic DNA from sample656

description: whole blood case sample


title: genomic DNA from sample567

description: whole blood control sample


title: genomic DNA from sample605

description: whole blood case sample


title: genomic DNA from sample573

description: whole blood case sample


title: genomic DNA from sample607

description: whole blood case sample


title: genomic DNA from sample547

description: whole blood case sample


title: genomic DNA from sample621

description: whole blood case sample


title: genomic DNA from sample657

description: whole blood case sample


title: genomic DNA from sample637

description: whole blood case sample


title: genomic DNA from sample671

description: whole blood case sample


title: genomic DNA from sample548

description: whole blood case sample


title: genomic DNA from sample624

description: whole blood case sample


title: genomic DNA from sample583

description: whole blood case sample


title: genomic DNA from sample636

description: whole blood case sample


title: genomic DNA from sample555

description: whole blood case sample


title: genomic DNA from sample625

description: whole blood case sample


title: genomic DNA from sample579

description: whole blood control sample


title: genomic DNA from sample563

description: whole blood control sample


title: genomic DNA from sample585

description: whole blood case sample


title: genomic DNA from sample661

description: whole blood case sample


title: genomic DNA from sample578

description: whole blood control sample


title: genomic DNA from sample634

description: whole blood case sample


title: genomic DNA from sample582

description: whole blood case sample


title: genomic DNA from sample616

description: whole blood case sample


title: genomic DNA from sample698

description: whole blood case sample


title: genomic DNA from sample615

description: whole blood case sample


title: genomic DNA from sample650

description: whole blood case sample


title: genomic DNA from sample670

description: whole blood case sample


title: genomic DNA from sample580

description: whole blood control sample


title: genomic DNA from sample629

description: whole blood case sample


title: genomic DNA from sample602

description: whole blood case sample


title: genomic DNA from sample689

description: whole blood case sample


title: OPA1 F38D mutant cells 75_2

description:
OPA1 F38D mutant cells 75_2
F38D_75_2

tag: cell type

value: induced Pluripotent Stem Cell-derived Neural Precursor Cells

value: OPA1 F38D mutant


title: genomic DNA from sample572

description: whole blood control sample


title: genomic DNA from sample672

description: whole blood case sample


title: genomic DNA from sample598

description: whole blood case sample


title: genomic DNA from sample549

description: whole blood case sample


title: genomic DNA from sample626

description: whole blood case sample


title: genomic DNA from sample600

description: whole blood case sample


title: genomic DNA from sample683

description: whole blood case sample


title: genomic DNA from sample667

description: whole blood case sample


title: genomic DNA from sample684

description: whole blood case sample


title: genomic DNA from sample663

description: whole blood case sample


title: genomic DNA from sample542

description: whole blood case sample


title: genomic DNA from sample654

description: whole blood case sample


title: genomic DNA from sample633

description: whole blood case sample


title: genomic DNA from sample609

description: whole blood case sample


title: genomic DNA from sample669

description: whole blood case sample


title: genomic DNA from sample617

description: whole blood case sample


title: genomic DNA from sample552

description: whole blood case sample


title: genomic DNA from sample644

description: whole blood case sample


title: Islet Replicate 5

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

description: Islet Replicate 5

data_processing:
Cutadapt was used to remove adapters and reads >16 nts in length were aligned to the human (Hg18) genome with 1 mismatch allowance by Bowtie1(v1.1.2) and DEseq2 (v1.18.1)
Reads per million (RPM)  values are shown in the data processing file.
Genome_build: Hg18
Supplementary_files_format_and_content: csv files include DEseq values for each Sample

source_name: islet RNA

extract_protocol:
Primary human islets were treated with HDL. RNA was isolated using the Qiagen miRNeasy isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: homo sapiens

value: primary islets


title: Islet Replicate 4

description: Islet Replicate 4


title: Islet Replicate 3

description: Islet Replicate 3


title: Islet Replicate 1

description: Islet Replicate 1


description:
X3187.KCV.1.i7
miRNAs on HDL from islets (islet-nHDL) Sample 3

data_processing:
Cutadapt was used to remove adapters and reads >16 nts in length were aligned to the rat (Hg18) genome with 1 mismatch allowance by Bowtie1(v1.1.2) and DEseq2 (v1.18.1)
Deseq values are shown in the data processing file.
Genome_build: Hg18
Supplementary_files_format_and_content: csv files include DEseq values for each Sample

source_name: HDL

extract_protocol:
Primary human islets were treated with HDL. HDL was isolated from media by immunoprecipitation for ApoAI from cell-free media (cf-nHDL) or media with islet-cells (islet-nHDL). RNA was isolated using the Qiagen miRNeasy isolation kit. 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

value: HDL


title: Islet Replicate 2

description: Islet Replicate 2


description:
X3187.KCV.1.i6
miRNAs on HDL from islets (islet-nHDL) Sample 2


description:
X3187.KCV.1.i8
miRNAs on HDL from islets (islet-nHDL) Sample 4


title: Islet Replicate 6

description: Islet Replicate 6


title: TGFbeta

city: Stony Brook

first: John

middle: D

last: Haley

state: NY

address: BST 9-168, SB Medical

institute: Stony Brook University

hyb_protocol: U133 Plus2 Affymetrix standard protocol

scan_protocol: Affy scanner

data_processing: Affymetrix default settings

source_name: H358 isogenic dox-inducible

label_protocol: Biotinylated cRNA

extract_protocol: Qiagen RNA Easy, QC on Agilent bioanalyzer

treatment_protocol: 0.5ug/ml doxycycline

tag: sample type

value: H358 harbors mutant Kras

tag: transcription factors

value: Dox-inducible TGFbeta


title: Vector Dox

tag: treatment

value: doxycycline

value: DNA vector control


title: Snail

value: Dox-inducible Snail


title: Zeb1 Dox

value: Dox-inducible Zeb1


title: Zeb1


title: Snail Dox


title: Vector


title: TGFbeta Dox


description:
X3187.KCV.1.i5
miRNAs on HDL from islets (islet-nHDL) Sample 1


description:
X3187.KCV.1.i2
miRNAs on baseline HDL (cellfree(cf)-nHDL) - Sample 2


description:
X3187.KCV.1.i4
miRNAs on baseline HDL (cellfree(cf)-nHDL) - Sample 4


description:
X3187.KCV.1.i3
miRNAs on baseline HDL (cellfree(cf)-nHDL) - Sample 3


description:
X3187.KCV.1.i1
miRNAs on baseline HDL (cellfree(cf)-nHDL) - Sample 1


title: ANRIL-specific siRNA, Rep 1

city: Cleveland

first: QING

middle: K

last: WANG

state: Ohio

address: 9500 Euclid Ave

department: Molecular Cardiology

institute: Cleveland Clinic

hyb_protocol: After fragmentation, biotinylated cRNA was hybridized to the microarray during a 16-hour incubation, and then washed and stained with Fluidics Station 400 followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings.

data_processing: Raw intensities of 54,675 probes were quantified and normalized by the robust multi-array average (RMA) algorithm in R package affy. Low-quality probes were filtered out using the shorth function built-in R package genefilter. Linear regression models were used to identify expression probes showing differential expression in ANRIL siANRIL-treated cells compared to siNC-treated cells. An empirical Bayes method implemented in R package limma was applied to shrink the probe-wise sample variances towards a common value and to augment the degrees of freedom for the individual variances. To control the false discovery rate (FDR) in multiple testing, the q values were calculated using Benjamini-Hochberg FDR procedure. Significant probes were defined as those with q<0.05.

source_name: HUVECs treated with ANRIL-specific siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from above 150ng of total RNA in 3ul of DEPC water.  Microarray experiments were carried out at the CWRU Gene Expression Core.

growth_protocol: HUVECs (Lonza, USA) were cultured in a phenol-red-free endothelial growth medium (ATCC, USA) supplemented with 2% fetal bovine serum (FBS), 0.4% human fibroblast growth factor, 0.1% human epidermal growth factor, 0.1% vascular endothelial growth factor, 0.1% insulin-like growth factor, 0.1% ascorbic acid, 0.1% heparin, 0.1% gentamicin/amphotericin-B and 0.04% hydrocortisone (all from ATCC, USA). All cultures were maintained at 37°C in a humidified atmosphere with 5% CO2.

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

treatment_protocol: Transient transfection of siRNAs (purchased from Integrated DNA Technologies, Skokie, IL) was performed using non-liposomal TransIT-X2 Dynamic Delivery System (Mirus Bio, Madison, WI) according to the manufacturer’s instructions.   The sequences of ANRIL-specific siRNA were 5’-GGA UAU GUG CCA UGA GUA AGA AUA A-3’ and 3’-UAC CUA UAC ACG GUA CUC AUU CUU AUU-5’.

value: ANRIL-specific siRNA

tag: cell line

value: HUVEC


title: genomic DNA from sample660

description: whole blood case sample

value: case


title: Control scrambled siRNA, Rep 3

source_name: HUVECs treated with control scrambled siRNA

value: control scrambled siRNA


title: ANRIL-specific siRNA, Rep 3


title: genomic DNA from sample597

description: whole blood case sample

value: whole blood


title: ANRIL-specific siRNA, Rep 2


title: Control scrambled siRNA, Rep 1


title: Control scrambled siRNA, Rep 2


title: 660nm(1-24h)_740nm(25-48h)_Rep4

tag: condition

value: phytochrome-based hydrogels

tag: illumination


title: 660nm(1-24h)_740nm(25-48h)_Rep1


title: 660nm(1-24h)_740nm(25-48h)_Rep3


title: 660nm(1-24h)_740nm(25-48h)_660nm(40min)_Rep4


title: 660nm(1-24h)_740nm(25-48h)_Rep5


title: 660nm(1-24h)_740nm(25-48h)_Rep2


title: 660nm(1-24h)_740nm(25-48h)_660nm(40min)_Rep5


title: 660nm(1-24h)_740nm(25-48h)_660nm(160min)_Rep3


title: 660nm(1-24h)_740nm(25-48h)_660nm(40min)_Rep2


title: 660nm(1-24h)_740nm(25-48h)_660nm(160min)_Rep4


title: genomic DNA from sample659

description: whole blood case sample

tag: diagnosis

value: F


title: 660nm(1-24h)_740nm(25-48h)_660nm(40min)_Rep1


title: 660nm(1-24h)_740nm(25-48h)_660nm(160min)_Rep1


title: genomic DNA from sample603

description: whole blood case sample

tag: age


title: genomic DNA from sample677

description: whole blood case sample

tag: Sex

value: M


title: 660nm(1-24h)_740nm(25-48h)_660nm(160min)_Rep2


title: 660nm(1-24h)_740nm(25-48h)_660nm(160min)_Rep5


title: genomic DNA from sample632

description: whole blood case sample

tag: tissue


title: 660nm(1-24h)_740nm(25-48h)_660nm(10min)_Rep5


title: 660nm(1-24h)_740nm(25-48h)_660nm(10min)_Rep4


title: 660nm(1-24h)_740nm(25-48h)_660nm(40min)_Rep3


title: genomic DNA from sample562

description: whole blood control sample

value: control

tag: cellcount-nk


title: 660nm(1-24h)_660nm(25-48h)_Rep4


title: 660nm(1-24h)_740nm(25-48h)_660nm(10min)_Rep2


title: 660nm(1-24h)_740nm(25-48h)_660nm(10min)_Rep1


title: 660nm(1-24h)_740nm(25-48h)_660nm(10min)_Rep3


title: 660nm(1-24h)_660nm(25-48h)_Rep2


title: 660nm(1-24h)_660nm(25-48h)_Rep1


title: 660nm(1-24h)_660nm(25-48h)_Rep3


title: 660nm(1-24h)_660nm(25-48h)_Rep5


title: genomic DNA from sample652

description: whole blood case sample

tag: cellcount-bcell


title: THP1_DMSO_Day2_n1

city: Amsterdam

first: Tesa

last: Severson

address: 121 Plesmanlaan

department: Molecular Carcinogensis

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Libraries were sequenced on an Illumina HiSeq2500 to in paired-end configuration (101 bp reads).
Reads were trimmed for adapters using Trimmomatic version 0.36 and aligned to the Human Reference Transcriptome (GRCh38) using STAR version 2.4.2a
RSeQC version.2.6.4 was used to remove rRNA features (identified by gencode.v24.annotation.gtf)
HTSeq was used to count reads for all genes using the htseq-count version 0.6.0 with intersection strict mode for exon feature type setting (gencode.v24.annotation.gtf).
Feature "ENSG00000202198.1" was removed from the count matrix due to disproportionately high read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression matrix of samples (columns) by transcript (rows).

growth_protocol: Cells were seeded in flasks.

extract_protocol:
After treatment, a minimum of 10 million cells were harvested, centrifuged, and resuspended in TRIzol (Invitrogen), then snap frozen on dry ice and stored at -80 degrees C. RNA was purified from cells stored in TRIzol using the RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit   (Illumina).

treatment_protocol: Cell were treated with 0.1% DMSO, 1 μM G  SK2879552, 100 nM   ATRA, or the combination of 1 μM G  SK2879552 and 100 nM ATRA for 2 or 4 days.


title: THP1_DMSO_Day4_n1


title: THP1_DMSO_Day2_n2


title: THP1_Combo_Day4_n2


title: THP1_DMSO_Day4_n2


title: THP1_Combo_Day4_n1


title: THP1_ATRA_Day2_n2


title: THP1_ATRA_Day4_n2


title: THP1_ATRA_Day4_n1


title: THP1_Combo_Day2_n2


title: genomic DNA from sample593

description: whole blood case sample

tag: cellcount-mono


title: THP1_552A_Day4_n1


title: THP1_552A_Day4_n2


title: THP1_552A_Day2_n2


title: OCIAML3_DMSO_Day4_n1


title: THP1_552A_Day2_n1


title: OCIAML3_DMSO_Day2_n2


title: OCIAML3_DMSO_Day2_n1


title: OCIAML3_Combo_Day4_n2


title: OCIAML3_Combo_Day2_n1


title: OCIAML3_Combo_Day2_n2


title: genomic DNA from sample685

description: whole blood case sample

tag: cellcount-gran


title: THP1_Combo_Day2_n1


title: OCIAML3_ATRA_Day4_n1


title: THP1_ATRA_Day2_n1


title: OCIAML3_ATRA_Day4_n2


title: genomic DNA from sample581

description: whole blood control sample


title: OCIAML3_ATRA_Day2_n1


title: OCIAML3_552A_Day4_n1


title: MV411_DMSO_Day2_n2


title: OCIAML3_552A_Day2_n1


title: MV411_DMSO_Day2_n1


title: genomic DNA from sample658

description: whole blood case sample


title: genomic DNA from sample587

description: whole blood case sample


title: genomic DNA from sample577

description: whole blood control sample


title: MV411_Combo_Day4_n1


title: MV411_Combo_Day4_n2


title: OCIAML3_ATRA_Day2_n2


title: MV411_Combo_Day2_n2


title: MV411_DMSO_Day4_n2


title: OCIAML3_552A_Day4_n2


title: MV411_DMSO_Day4_n1


title: OCIAML3_DMSO_Day4_n2


title: MV411_Combo_Day2_n1


title: MV411_ATRA_Day4_n2


title: OCIAML3_Combo_Day4_n1


title: MV411_ATRA_Day2_n2


title: OCIAML3_552A_Day2_n2


title: Tumor from high fat diet fed animals, biological rep 3

city: Cologne

first: thomas

last: wunderlich

state: NRW

address: Gleueler Str. 50

institute: MPI for Metabolism Research

description:
Gene expression data from colitis-associated colon tumor from 17 weeks old high fat diet fed mouse
HFD_wt_3

hyb_protocol: RNA was processed to be hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) according to the manufacture`s instruction.

scan_protocol: scanning was performed on a Gene Chip scanner 3000 7G affimetrix

data_processing: Affymetrix Powertools and the robust multiarray average method were used forbackground correction, quantile normalization and summerization of the raw intensity values. R software (version 2.13.1) along with the Bioconducter software package were used for robust multiarray average method, statistical analysis (Student`s t-test), calculation of the change in intensity and illustration. Genes were considered significantly deregulated when they had difference in expresion with a P value of <0.025. Genes with a fold change of <1.5 were removed from the data.

source_name: Tumor from high fat diet fed animals

label_protocol: Biotin labeled cDNA was synthezied with a Gene Chip whole Transcript Sense Target Labeling Assay according to the manufacture s guidelines (affimetrix)

growth_protocol: Mice were housed in groups of three to five in single ventilated cages at 22-24 °C

extract_protocol: RNA was isolated with an Rneasy Kit from Qiagen according to the manufacture`s instruction.

treatment_protocol: Mice were fed a normal chow or a high fat diet from weaning on. 8-week-old animals were i.p. injected with 10 mg/kg body weight azoxymethane. 4 days later animals were exposed to 1,5% dextrane sodium sulfate (MW=36000-50000) in the drinking water for 5 days and then provided with normal drinking water until the end of the experiment with 17 weeks of age.

tag: strain

tag: diet

value: high fat diet

value: 17 weeks old mouse

value: colitis-associated colon tumor

tag: gender

value: female


title: MV411_ATRA_Day2_n1


title: MV411_552A_Day4_n2


title: MV411_552A_Day4_n1


title: MV411_552A_Day2_n2


title: MV411_552A_Day2_n1


title: MOLM13_DMSO_Day4_n2


title: Tumor from high fat diet fed animals, biological rep 2

description:
Gene expression data from colitis-associated colon tumor from 17 weeks old high fat diet fed mouse
HFD_wt_2

tag: genotype


title: MOLM13_DMSO_Day4_n1


title: MOLM13_DMSO_Day2_n2


title: genomic DNA from sample551

description: whole blood case sample


title: MOLM13_Combo_Day4_n1


title: MOLM13_Combo_Day4_n2


title: MOLM13_DMSO_Day2_n1


title: day7_R2

city: Tianjin

first: Shaohui

address: NO.38 Tongyan Road

institute: Nankai University

data_processing:
Clean reads were mapped to mouse genome mm10 using HISAT2 (2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2 (1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values for each Sample. Normalized_Counts.xlsx.

source_name: Differential E14 cell-replicate-2 cultured in medium lacking 2i and LIF for 7 days

growth_protocol: Mouse E14 cell line was cultured in stem cell medium containing Dulbecco’s modified Eagles medium supplemented with 15% ES qualified fetal bovine serum (FBS), 100 μM non-essential amino acids (NEAA), 5,000 U/mL antibiotics, 2 mM L-Glutamine, 0.1mM β-mercaptoethanol, 1000 U/mL LIF and 2i.

extract_protocol:
Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit following the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: ESCs


title: day7_R3

source_name: Differential E14 cell-replicate-3 cultured in medium lacking 2i and LIF for 7 days

tag: treatment


title: day7_R1

source_name: Differential E14 cell-replicate-1 cultured in medium lacking 2i and LIF for 7 days

tag: cell line


title: day0_R3

source_name: WT E14 cell -replicate-3 cultured in 2i and LIF medium

value: cultured in 2i and LIF medium


title: MV411_ATRA_Day4_n1


title: MOLM13_ATRA_Day2_n2


title: MOLM13_ATRA_Day4_n1


title: MOLM13_ATRA_Day4_n2


title: MOLM13_Combo_Day2_n1


title: day0_R2

source_name: WT E14 cell -replicate-2 cultured in 2i and LIF medium


title: Tumor from normal chow diet fed animals, biological rep 3

description:
Gene expression data from colitis-associated colon tumor from 17 weeks old normal chow diet fed mouse
NCD_wt_3

source_name: Tumor from normal chow diet fed animals

value: normal chow diet


title: MOLM13_ATRA_Day2_n1


title: Tumor from normal chow diet fed animals, biological rep 2

description:
Gene expression data from colitis-associated colon tumor from 17 weeks old normal chow diet fed mouse
NCD_wt_2


title: day0_R1

source_name: WT E14 cell -replicate-1 cultured in 2i and LIF medium


title: MOLM13_552A_Day4_n2


title: MOLM13_552A_Day4_n1


title: MOLM13_552A_Day2_n2


title: genomic DNA from sample604

description: whole blood case sample


title: MOLM13_552A_Day2_n1


title: MOLM13_Combo_Day2_n2


title: Kasumi1_DMSO_Day4_n2


title: Kasumi1_DMSO_Day4_n1


title: E14_Bcat1_KO2_Replicate_1

source_name: Bcat1-KO_Clone 2#-replicate 1


title: Tumor from high fat diet fed animals, biological rep 1

description:
Gene expression data from colitis-associated colon tumor from 17 weeks old high fat diet fed mouse
HFD_wt_1


title: Kasumi1_DMSO_Day2_n2


title: E14_Bcat1_KO1_Replicate_2

source_name: Bcat1-KO_Clone 1#-replicate 2


title: Kasumi1_Combo_Day4_n2


title: E14_Bcat1_KO1_Replicate_1

source_name: Bcat1-KO_Clone 1#-replicate 1


title: Kasumi1_Combo_Day2_n2


title: E14_WT_Replicate_2

source_name: WT -replicate-2 for Bcat1-KO

value: WT


title: Tumor from normal chow diet fed animals, biological rep 1

description:
Gene expression data from colitis-associated colon tumor from 17 weeks old normal chow diet fed mouse
NCD_wt_1


title: Kasumi1_ATRA_Day4_n1


title: Kasumi1_ATRA_Day4_n2


title: genomic DNA from sample620

description: whole blood case sample

source_name: case_whole blood


title: E14_WT_Replicate_1

source_name: WT -replicate-1 for Bcat1-KO


title: Kasumi1_Combo_Day4_n1


title: Kasumi1_Combo_Day2_n1


title: Kasumi1_ATRA_Day2_n2


title: Etv6_Input3

city: Oxford

first: Lei

last: Li

address: University of Oxford

department: Radcliffe Department of Medicine

country: United Kingdom

institute: WIMM

data_processing:
Base calling performed on illumina 1.9 platform
Raw sequence reads were checked for base quality, trimmed and filtered to exclude adapters using Trimmomatic (Version 0.32)
Filtered read were aligned to the X. Laevis V9.1 with BWA version 0.7.12
Peaks were analyzed using MACS2 peak calling software at default thresholds, with the input samples as control for each replicate.
Peaks consistent between replicates were identified using DiffBind (Bioconductor package)
Peaks located in TSS regions were identified using Homer software and used to perform Transcription factors binding site analysis with Homer software (findMotifsGenome.pl)
Genome_build: Xenopus Laevis V9.1
Supplementary_files_format_and_content: xlsx file contains Etv6 ChIP consistent peaks in triple biological replicates; bam files include RPKM value of each sample.

organism: Xenopus laevis

source_name: Somitic cells

growth_protocol: Xenopus embryos were obtained by artificial fertilisation. They were cultured at 19 degree in 0.1x MMR (1xMarc’s Modified Ringer: 100 mM NaCl, 2 mM KCl, 1 mM MgCl2, 2 mM CaCl2, 5 mM HEPES, pH 7.5) after being dejellied in 2% cysteine (PH 7.8-8.0).

extract_protocol:
Etv6 immunoprecipitated DNA was eluted from beads in a thermomixer at 65 degres for 15 min and the eluates and reserved inputs were reverse cross-linked overnight at 65C. The samples were then treated with RNaseA, proteinase K and phenol/chloroform purified, and quantified using Qubit Fluorometer
Sequencing libraries were constructed with 1 ng of DNA using NEBNext Ultra DNA Library Prep Kit (NEB#E7370) according to manufacturer’s protocol

treatment_protocol: The somites of stage 22 Xenopus embryos were manually dissected in 0.35x MMR using forceps. Crosslinker EGS was added into cell homogenates (EGS final concentration: 2 mM) before fixation (10 minutes) . Sonication was performed using Covaris S220 (Duty factor: 10%; cycle per burst: 200; intensity: 5; duration time: 300 seconds; cycle: 3).

value: somites

tag: Stage

value: stage 22

value: J-strain

tag: chip antibody


title: Etv6_Input2


title: Kasumi1_ATRA_Day2_n1


title: Etv6_Input1


title: Kasumi1_552A_Day4_n2


title: Etv6_ChIP3

value: Etv6 (custom made by NovoPro Bioscience Inc, Shanghai, China)


title: E14_Bcat1_KO2_Replicate_2

source_name: Bcat1-KO_Clone 2#-replicate 2


title: Kasumi1_552A_Day4_n1


title: Kasumi1_DMSO_Day2_n1


title: Etv6_ChIP2


title: Kasumi1_552A_Day2_n2


title: Etv6_ChIP1


title: Kasumi1_552A_Day2_n1


title: Mo_3

data_processing:
Raw sequence reads were checked for base quality, trimmed and filtered to exclude adapters using Trimmomatic (Version 0.32)
Filtered read were aligned to the X. Laevis V9.1 using STAR with default parameters.
Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
Differential gene expression analysis was carried out using EdgR (Bioconductor Package)
An ANOVA-like test analysis was performed between WT and MO samples, using the generalized linear model followed by Estimates “Dispersion”, fitted with “negative binomial model” and estimates “Generalized linear model likelihood ratio”. Genes with a False Discovery Rate (FDR) above 0.05 were filtered out.
Genome_build: Xenopus Laevis V9.1
Supplementary_files_format_and_content: xlsx file contains gene_id, gene_name, RPKM value of each sample, log FC (wt/mo), P value and FDR value.

extract_protocol:
Total RNA was extracted from somites dissected from 20 WT or etv6-deficient embryos at stage 22. Triple biological replicates were generated.
Indexed libraries were constructed with 1 µg of total RNA using the KAPA Stranded RNA-seq Kit with RoboErase (KK8483) and NEBNext Mutiplex Oligos (NEB#E7500S) for Illumina sequencing, and sequenced using NextSeq 500.

treatment_protocol: The somites of stage 22 Xenopus embryos were manually dissected in 0.35x MMR using forceps.

tag: genotype/variation

value: etv6 morpholino injected


title: HepG2 MC3 1 h

city: Frankfurt am Main

first: Xinlai

last: Cheng

state: Hessen

address: Max-von-Laue-Strasse 15. R. 3.652

department: Chemical Biology

institute: Goethe Frankfurt University. BMLS

description: Not applicable

hyb_protocol: No modifications were made to the recommended manufacturer's protocol for BeadChips

scan_protocol: Standard protocol for a BeadArray Reader

data_processing: The data were obtained from Beadstudio Software and transferred to R Software

label: Biotin

source_name: HepG2 cells treated for 1 h with MC3 1 µM

label_protocol: The Illumina Totalprep RNA Amplification Kit was used to synthesize cDNA as well as to amplify biotinylated cRNA.

growth_protocol: HepG2 cells were culturted on standard well-plate, with DMEM medium enriched with FCS 10% and with Penicillin/Streptomycin added.

extract_protocol: Total RNA was extracted and purified by means of the Guanadine thyocyanate-phenol-chloroform extraction method using QIAzol Lysis Reagent.

treatment_protocol: Non-treated cells were kept in unaltered medium, while the other two samples were treated MC3 1µM for 1 and 24 hours.

value: Wild type


title: HepG2 MC3 24 h

description: Not applicable

source_name: HepG2 cells treated for 24 h with MC3 1 µM


title: HepG2 NT

description: Not applicable

source_name: Non treated HepG2 cells


title: BJ142; biological rep 3

city: Aachen

first: Bernd

last: Denecke

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 18 hours at 60 rpm; Fluidics Station Program FS_450_0002

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with robust multiarray average algorithm (Affymetrix): RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

organism: Caenorhabditis elegans

source_name: Intestine of C.elegans strain BJ142 carrying the mutant allele ifo-1(kc2)

label_protocol: Fragmented, biotinylated cDNAs were prepared from 20 ng total RNA using  the Nugen Ovation Pico  WTA System V2+ Encore Biotin Module according to the manufacturers instructions.

growth_protocol: Transcriptome analyses were performed on dissected intestines of wild-type and ifo-1(kc2)-mutant worms that were grown on OP50 bacteria.

extract_protocol: L4 larvae were suspended in ddH2O containing 1% (w/v) levamisole (Sigma-Aldrich), incised either at their anterior or posterior end to extrude intestines. Intestines were cut off, collected with a capillary and transferred directly into an excess of RNA extraction buffer (Arcturus PicoPure RNA Isolation Kit, Thermo Fisher Scientific). For each wild-type pool, 40 intestines were collected, and 80 were collected for each pool of the smaller ifo-1(kc2) mutants, before processing them according to the protocol provided by the manufacturer. The purification included an on-column DNAse digest using the peqGOLD DNase I Digest Kit (Peqlab). For gene chip analysis, three independent RNA isolates were used.

treatment_protocol: not applicable

tag: age

value: intestine minus pharynx minus tail

value: ifo(kc)ko


title: HL60_DMSO_Day4_n2


title: genomic DNA from sample695

description: whole blood case sample

tag: diagnosis

value: case

tag: Sex

value: M

value: whole blood


title: HL60_DMSO_Day4_n1


title: Mo_1

tag: tissue


title: Mo_2


title: HL60_DMSO_Day2_n2


title: WT_3

value: wild type


title: HL60_DMSO_Day2_n1


title: HL60_Combo_Day4_n2


title: BJ142; biological rep 1


title: WT_1


title: N2; biological rep 3

source_name: Intestine of C.elegans wild-type N2 strain

value: wt


title: WT_2


title: HL60_Combo_Day4_n1


title: N2; biological rep 2


title: HL60_Combo_Day2_n2


title: N2 control, biological rep 1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

source_name: whole animal

label_protocol: Fragmented, biotinylated cDNAs were prepared from 100 ng total RNA using  the WT Plus Reagent Kit of Affymetrix according to the manufacturers instructions.

growth_protocol: For Cry5B intoxication experiments, control JM103 or Cry5B-producing JM103 were grown overnight in Luria broth (LB) with 100 μg/ml ampicillin and 7 μl/ml 1 M isopropyl β-d-1-thiogalactopyranoside (IPTG) and 300 μl aliquots were placed on nematode growth medium (NGM) plates containing 100 μg/ml ampicillin and 2 mM IPTG. The inoculated plates were incubated overnight at room temperature and plates were stored at 4°C for up to two weeks without detectable loss of bacterial and toxin activity. Intoxication and infection experiments were started by transferring adult worms into 70 μl bleaching solution containing 1 ml PBS, 150 μl 13% NaOCl and 100 μl 4 M NaOH next to the bacterial lawn. Mother animals dissolved, releasing embryos that survived owing to their crude eggshell. Plates were incubated at 18°C during the entire experimental period and animals were transferred at least every 3 days onto new plates.

extract_protocol: Worms were then washed three times in ice-cold M9 medium to remove remaining bacteria. Pelleted worms were ground thoroughly with mortar and pestle under liquid nitrogen. A maximum of 100 mg tissue powder was then transferred into an RNase-free, liquid nitrogen-cooled, 2 ml microcentrifuge tube and the following steps were performed according to the RNeasy Plant Mini Kit (Qiagen) including an on-column DNAse digest using the peqGOLD DNase I Digest Kit. For gene chip analysis three independent RNA isolates were used.

treatment_protocol: To assess transcriptional effects of Cry5B intoxication, mRNA levels were analyzed after growing wild-type worms either on control JM103 or Cry5B-producing JM103 bacteria. This was done by transferring adult wildtype animals into 70 μl of bleaching solution, which was pipetted next to the bacterial lawn of the culture plate. Plates were incubated for 4 days at 18°C when worms had reached L4 or young adult stage

value: 4 days adult

tag: cultivated on

value: E. coli JM103


title: BJ142; biological rep 2


title: ProliHH P8 Rep2 in hypoxia

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Trimmed reads were aligned to the human genome (hg38, Genome Reference Consortium GRCh38) using Hisat2-2.0.0-beta
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The counts expression profiles were normalized  by Deseq2 using rlog function
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2 tranformed counts for each Sample

source_name: Proliferating Human Hepatocytes at P8 cultured for 48day in hypoxia

growth_protocol: Primary human hepatocytes or proliferating human hepatocytes were seeded at 2 x 104 cells/cm2 on 6-wells collagen-coated plates (Corning) in hypoxia . The medium was changed every 3 days. At day 6 of the primary culture, cells cultured in the presence of HM were harvested via trypsinization

extract_protocol:
Proliferaitng human hepatocyte or mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Proliferating Human Hepatocytes at P8 in hypoxia

value: liver

tag: passages

tag: condition

value: hypoxia


title: ProliHH P8 Rep1 in hypoxia


title: N2 control, biological rep 2


title: HL60_ATRA_Day4_n2


title: ProliHH P6 Rep1 in hypoxia

source_name: Proliferating Human Hepatocytes at P6 cultured for 36day in hypoxia

value: Proliferating Human Hepatocytes at P6 in hypoxia


title: N2 control, biological rep 3


title: Cry5B, biological rep 3

value: 4 days L3

value: Cry5B pore-forming toxin producing JM103


title: HL60_Combo_Day2_n1


title: ProliHH P6 Rep2 in hypoxia


title: ProliHH P4 Rep1 in hypoxia

source_name: Proliferating Human Hepatocytes at P4 cultured for 24day in hypoxia

value: Proliferating Human Hepatocytes at P4 in hypoxia


title: ProliHH P4 Rep2 in hypoxia


title: HL60_ATRA_Day2_n2


title: N2; biological rep 1


title: ProliHH P2 Rep2 in hypoxia

source_name: Proliferating Human Hepatocytes at P2 cultured for 12day in hypoxia

value: Proliferating Human Hepatocytes at P2 in hypoxia


title: HL60_ATRA_Day2_n1


title: HL60_ATRA_Day4_n1


title: S10978-24H-03

first: Xiaozhen

last: Huang

address: 800 Dongchuan RD. Minhang District.

department: School of Agriculture & Biology

institute: Shanghai Jiao Tong University

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 to get clean reads,the clean reads was compared to reference genomic sequences using HISAT, and the average ratio of each sample reached 97.51%.
Prediction of New transcript.The new transcription product was predicted by comparing the sequence alignment results with the reference gene sequences.We first selected potential regions with a length greater than 100 bp, an average coverage greater than 8 bp, and 60 bp away from upstream and downstream genes as candidate new transcripts. The genomic annotation information together with the new transcription products made up the integral reference genes that were used in the subsequent analyses.
The clean reads were mapped to the integral reference genes with Bowtie2 v2.2.5(Parameter: ：-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200) and the gene expression level was calculated by RSEM v1.2.12(Parameter：--forward-prob=0.0)
The fragments per kilobase of transcript per million mapped fragments (FPKM) incorporate normalization steps to ensure that expression levels for different genes and transcripts can be compared across runs. The DESeq2 method(parameter: abs log2(FoldChange) >= 1 && Adjusted Pvalue <= 0.05) was used to calculate the differentially expressed genes (DEG). Genes with fold change ≥ 2, Bonferroni-corrected P value (Padj) ≤0.05 and FPKM≥30 in at least one sample were determined to be DGEs.
Genome_build: Salmonella enterica serovar Enteritidis SJTUF 10978 genome, the accession number is CP015524.1
Supplementary_files_format_and_content: Excel files include GeneID, gene Length, Normalized FPKM value of S10978-0H-Expression and S10978-6H-Expression, log2FoldChange(S10978-6H/S10978-0H), Up-Down-Regulation(S10978-6H/S10978-0H), Padj Pvalue type , KEGG Orthology, GO Component, GO Function, GO Process, Blast nr

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Salmonella strain isolated from chicken

growth_protocol: The mid-log phase bacteria cultures that grown in M9FeS medium at 37°C with shaking at 200 rpm, was harvest. And then 10 mL samples were centrifuged at 5000 × g for 3 min, washed twice and suspended in PBS. The cell concentration was adjusted to 5 × 108 CFU/mL and 0.5 mL cell suspension solution was added to 9.5 mL PBS, mixed and transferred to 40 mL egg white in a 250 mL cone bottle that had been preheated to 37°C. This achieved a final inoculum concentration of 5×106 CFU/mL and a final egg white concentration of 80% (V/V).These solutions were mixed and incubated at 37°C under a 65% humidified atmosphere.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen, CAS 15596026) according to the manual.RNA quality and integrity was verified by electrophoretic analysis and UV spectroscopy using NanoDrop and Agilent 2100 instruments. The RNA integrity number for all samples were between 8.2 and 9.7.
The Strand-specific transcriptome library construction and RNA sequencing was done as follow. Briefly, 1 µg total RNA was digested with DNase I (Thermo Scientific) and treated with Ribo-Zero Magnetic Gold Kit (Epicenter) to deplete rRNA. The protocol of TruSeq RNA Sample Prep Kit v2 (Illumina) was used to construct the libraries. The RNA was fragmented into small pieces and first-strand cDNA was generated using Super Script II (Invitrogen). The products were purified and used in a Second Strand Master Mix containing dATP, dGTP, dCTP and dUTP. The purified fragmented cDNA was end-repaired and purified and A-tailed and adapters were attached. The purified product was digested with uracil-N-glycosylase to remove the dUTP containing second strand cDNA, followed by several rounds of PCR amplification to enrich the cDNA fragments. The PCR products were purified and the libraries were assessed using the Agilent 2100 Bioanalyzer and qPCR.

treatment_protocol: Mid-log phase bacteria cultures that grown in M9FeS medium was added 2/5 of the culture volume ) ice-cold RNA-stabilizing solution (5% (v/v) water-saturated phenol pH 4.3 in 95% (v/v) ethanol), and immediately after harvest. The mixture was incubated on ice for 40 min, transferred to 2 mL RNase free ice-cold centrifuge tubes, and centrifuged at 3000 × g for 10 min at 4°C to pellet the bacteria. The cell pellets were then immediatelyfrozen in liquid nitrogen and stored at -70°C. This sample was defined as the 0 h sample for the RNAseq experiments. Four culture bottles of egg whites incubation samples (50 mL/bottle) were harvested for RNA extraction by centrifuging at 12857× g for 2 min at 4°C in 50 mL Falcon tubes to pellet the bacteria, the supernatant was discarded and tubes were inverted the on paper for 15 s to remove the residual liquid as completely as possible. . The tubes were placed on ice and immediately added 1 mL diluted ice-cold RNA-stabilizing solution (1.5% (v/v) water-saturated phenol pH 4.3, 19% (v/v) ethanol in water) to scatter the pellet, and the pellets were transferred to 2 mL RNase free centrifuge tubes and kept on ice for 40 min to inhibits the degradation of mRNA, then centrifuged,. The centrifugation step was repeated and the samples were frozen in liquid nitrogen and stored at -70°C. At each time point, RNA from 4 parallel samples were pooled and taken as an independent biological replicate. Three independent biologically repeated experiments were done at different times with different batches of SPF eggs.

tag: strain

value: SJTUF 10978


title: S10978-24H-02


title: genomic DNA from sample640

description: whole blood case sample

value: F

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: HL60_552A_Day4_n1

tag: treatment


title: S10978-24H-01

tag: genotype


title: glass_surface_660nm(48h)_Rep5

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: ReadCounts_control2_PEG_Cph1_coated_glass_surface.txt

data_processing:
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Ensembl (release: 75) annotation using TopHat2 (v2.0.13) with the options mate-inner-dist, mate-std-dev and library-type (fr- firststrand).
The distance between read mates (mate-inner-dist and mate-std-dev) were assessed individually using RSeQC (v2.6.1).
After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Homo sapiens gtf file from the Ensembl release 75 were used as reference for counting.
DESeq2 was used for differential expression analysis of all replicates for each condition. In this analysis, all libraries were compared in a pairwise manner.
Genome_build: hg19

source_name: hMSC

growth_protocol: hMSCs were cultivated on the indicated substrates.

extract_protocol: The cells were lysed using 1 ml peqGOLD Trifast (VWR International, Erlangen, Germany, cat. no. 30-2020) per hydrogel and RNA was extracted from the aqueous phase using the RNA purification kit R1013 (Zymo Research, Irvine, CA) according to the manufacturer’s protocol.

value: PEG-Cph1-coated glass surface

tag: illumination


title: ProliHH P2 Rep1 in hypoxia

tag: cell type


title: Cry5B, biological rep 1


title: Cry5B, biological rep 2


title: HL60_552A_Day2_n2

tag: cell line


title: glass_surface_660nm(48h)_Rep4


title: S10978-12H-01


title: S10978-6H-02


title: HL60_552A_Day4_n2


title: S10978-12H-03


title: glass_surface_660nm(1-24h)_740nm(25-48h)_Rep5


title: S10978-6H-01


title: glass_surface_660nm(48h)_Rep1


title: S10978-0H-03


title: S10978-12H-02


title: MRA9 mRNA-seq

city: MADISON

first: Vijayasaradhi

last: Setaluri

address: 1300 University Avenue

department: Dermatology

institute: University of Wisconsin-Madison

data_processing:
Raw FASTQ files were analyzed for quality using FASTQC, and low quality reads and adaptors were filtered and trimmed using cut-adapt. RSEM was used to map the reads to transcripts from human genome version hg19 and call isoform level expression.
Genome_build: hg19
Supplementary_files_format_and_content: Gene transfer format files that holds gene transcripts data
Supplementary_files_format_and_content: Fragments Per Kilobase of sequence per Million mapped reads files that normalizes the number of aligned reads by the size of the sequence feature and the total number of mapped reads
Supplementary_files_format_and_content: Comma Separated Values file for log2-transformed data for all samples

source_name: Metastatic tumor

growth_protocol: Cells were maintained and passaged in DMEM, high glucose, pyruvate medium supplemented with 10% FBS and 1% penicillin-streptomycin. BRAF and NRAS mutations were confirmed by genomic DNA PCR and western blotting for expression of BRAF(V600E) protein (36). The cell cultures were maintained in a CO2 (5%) incubator at 37oC. Normal human melanocytes were obtained from human neonatal foreskin tissue processed in the Cell Culture Core of the UW Skin Disease Research Center. Melanocytes were cultured in Ham’s F10 medium supplemented with 5% FBS, 85nM phorbol 12-myrisate 13-acetate, 2.5nM cholera toxin, 0.1mM 3-isobutyl-1-methylxanthine and 1% penicillin/ streptomycin

extract_protocol:
Total RNA was isolated using miRNeasy kit from Qiagen. RNA quality was verified using a 1% TBE gel as well as a Bioanalyzer. RNA concentration was estimated using the Bioanalyzer.
Total RNA was processed as per manufacturer’s instructions using the Illumina TruSeq Stranded mRNA kit for RNA-seq and TruSeq Small Library kit for miRNA-seq and sequenced using Illumina’s HiSeq 2500 platform. Raw reads were analyzed for quality using FASTQC and mapped to known transcripts in human genome version hg19 using Salmon. The Salmon index for mapping was built using a k value of 25 and the UCSC genome browser CDS data hg19.RNA libraries were prepared for sequencing using standard Illumina protocols

value: Metastatic tumor

value: WT BRAF/ NRAS(Q61K)


title: MRA6 mRNA-seq

value: BRAF(V600E)/WT NRAS


title: glass_surface_660nm(1-24h)_740nm(25-48h)_Rep3


description:
X3187.KCV.2.i11
miRNAs export to HDL from INS-1 cells (INS-1-nHDL)

data_processing:
Cutadapt was used to remove adapters and reads >16 nts in length were aligned to the rat (Rnor5.0) genome with 1 mismatch allowance by Bowtie1(v1.1.2) and DEseq2 (v1.18.1)
Deseq values are shown in the data processing file.
Genome_build: Rnor5.0
Supplementary_files_format_and_content: csv files include DEseq values for each Sample

organism: Rattus norvegicus

source_name: HDL

extract_protocol:
INS-1 832/13 cells were treated with HDL. HDL was isolated from media by immunoprecipitation for ApoAI from cell-free media (cf-nHDL) or media with INS-1 cells (INS-1-nHDL). RNA was isolated using the Qiagen miRNeasy isolation kit. 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

value: HDL


title: MRA4 mRNA-seq

value: WT BRAF/ WT NRAS


title: MRA5 mRNA-seq


title: glass_surface_660nm(1-24h)_740nm(25-48h)_Rep4


title: MRA2  mRNA-seq


title: glass_surface_660nm(1-24h)_740nm(25-48h)_Rep2


description:
X3187.KCV.2.i9
miRNAs on baseline HDL (cellfree(cf)-nHDL)


title: Melanocyte in F10 Media miRNA-seq

data_processing:
Raw FASTQ files were analyzed for quality using FASTQC, and low quality reads and adaptors were filtered and trimmed using cut-adapt. The trimmed reads were mapped to the human genome version hg19 using bowtie2. The reads were counted at all miRNA genes using coordinates from miRBase v19, and bedtools. The counts were normalized by library size for each library.
Genome_build: hg19

source_name: Human neonatal foreskin

extract_protocol:
Total RNA was isolated using miRNeasy kit from Qiagen. RNA quality was verified using a 1% TBE gel as well as a Bioanalyzer. RNA concentration was estimated using the Bioanalyzer.
Total RNA was processed as per manufacturer’s instructions using the Illumina TruSeq Stranded mRNA kit for miRNA-seq and TruSeq Small Library kit for miRNA-seq and sequenced using Illumina’s HiSeq 2500 platform. Raw reads were analyzed for quality using FASTQC and mapped to known transcripts in human genome version hg19 using Salmon. The Salmon index for mapping was built using a k value of 25 and the UCSC genome browser CDS data hg19.RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human neonatal foreskin

value: WT BRAF/WT NRAS


title: glass_surface_660nm(1-24h)_740nm(25-48h)_Rep1


title: S10978-6H-03

value: wild type


title: S10978-0H-01


title: HL60_552A_Day2_n1


title: Ufo1_3_pericarp_2_sRNA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA
18 Day-after-pollination pericarp

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: maize AGPv3 genome
Supplementary_files_format_and_content: tag count file

organism: Zea mays

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 3, batch 2

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed with Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNAseq libraries were constructed with Illumina Truseq RNA sample preparation kit (RS-122-2001) . Script-Seq libraries (strand-specific RNAseq) were constructed with Illumina ScriptSeq RNA-seq library preparation kit (SSV21106).

value: pericarp

value: Ufo1-1 expresser

tag: developmental stage

value: 18 days after pollination


title: glass_surface_660nm(48h)_Rep3


title: Melanocyte in M254 Media miRNA-seq


title: glass_surface_660nm(48h)_Rep2


title: Melanocyte in F10 Media mRNA-seq


title: 740nm(48h)_Rep7

value: phytochrome-based hydrogels


title: S10978-0H-02


title: Ufo1_1_pericarp_2_sRNA

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 1, batch 2


title: MRA9 miRNA-seq


title: 740nm(48h)_Rep6


title: sil_3_pericarp_2_sRNA

source_name: Ufo1-1 silent, 18 Day-after-pollination pericarp  sample 3, batch 2

value: Ufo1-1 silent


title: Ufo1_2_pericarp_2_sRNA

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 2, batch 2


title: 740nm(48h)_Rep4


title: MRA5 miRNA-seq


title: 740nm(48h)_Rep3


title: 740nm(48h)_Rep5


title: sil_2_pericarp_2_sRNA

source_name: Ufo1-1 silent, 18 Day-after-pollination pericarp  sample 2, batch 2


title: genomic DNA from sample678

description: whole blood case sample

data_processing: Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples, resultng in 249874 data rows out of a possible 485577 (provided in the matrix_normalized.txt)

source_name: case_whole blood

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: age

value: M

value: whole blood


title: genomic DNA from sample592

description: whole blood case sample

tag: Sex

value: F

tag: tissue


title: MRA6 miRNA-seq

value: Metastatic tumor


title: sil_1_pericarp_2_sRNA

source_name: Ufo1-1 silent, 18 Day-after-pollination pericarp  sample 1, batch 2


title: genomic DNA from sample638

description: whole blood case sample


title: MRA2  miRNA-seq


title: Ufo1_1_pericarp_1

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 1, batch 1


title: 740nm(48h)_Rep2


title: MRA4 miRNA-seq


title: Ufo1_2_pericarp_1

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 2, batch 1


title: 740nm(1-24h)_alternating_160min(25-48h)_Rep5


title: 740nm(48h)_Rep1


title: Ufo1_1_leaf

description: mature leaf

source_name: Ufo1-1 expressser, mature leaf sample 1

value: leaf

value: mature


title: B73_2_pericarp_1

description: 18 Day-after-pollination pericarp

source_name: B73, 18 Day-after-pollination pericarp  sample 2, batch 1


title: 740nm(1-24h)_alternating_160min(25-48h)_Rep4


title: B73_1_pericarp_1

description: 18 Day-after-pollination pericarp

source_name: B73, 18 Day-after-pollination pericarp  sample 1, batch 1


title: 740nm(1-24h)_alternating_160min(25-48h)_Rep1


title: genomic DNA from sample610

description: whole blood case sample


title: B73_1_leaf

description: mature leaf

source_name: B73 mature leaf sample 1


title: B73_2_leaf

description: mature leaf

source_name: B73 mature leaf sample 2


title: 740nm(1-24h)_alternating_160min(25-48h)_Rep3

source_name: hMSC


title: 740nm(1-24h)_alternating_160min(25-48h)_Rep2


title: Ufo1_2_leaf

description: mature leaf

source_name: Ufo1-1 expressser, mature leaf sample 2


title: 740nm(1-24h)_alternating_10min(25-48h)_Rep4


title: 740nm(1-24h)_alternating_10min(25-48h)_Rep3


title: wt_3_seedling

description: aboveground tissue of V2 stage seedling

source_name: wildtype segregate, seedling  sample 3

value: aboveground seedling tissue

value: wt


title: wt_5_seedling

description: aboveground tissue of V2 stage seedling

source_name: wildtype segregate, seedling  sample 5