title: Myo-DDX6-2-IP

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

description: Myoblast

data_processing:
library strategy: CLIP-seq
Reads were adapter-trimmed and mapped to human-specific repetitive elements from RepBase (version 18.04) by STAR. Repeat-mapping reads were removed and remaining reads mapped to the human genome assembly hg19 with STAR. PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5’ adapter and remaining reads retained as ‘usable reads’.
Peaks were called on the usable reads by CLIPper ,and assigned to gene regions annotated in Gencode (v19)
Each peak was normalized to the size-matched input (SMInput)
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Each bed file was gernated by read normalization between IP over SMInput. The columns in the bed files represent (chr, start, stop,-log10(pvalue),log2(fold change), strand). The CSV files contain the log2 fold change of reads upon IP over SMInput in annotated regions of each transcripts. Each bigwig file contains read distribution of each RBP, and bigbed contains clusters of predicted RBP binding.

source_name: Human Skeletal Myoblasts_DDX6 IP

extract_protocol:
Cell lysates were prepared by sonication in 1 ml iCLIP lysis buffer, treated with RNase I (40 U, LifeTech).
Enhanced crosslinking and immunoprecipitation (eCLIP) was performed on Human Skeletal Myoblast cells, and immunoprecipitated overnight at 4 °C with 10 µg affinity-purified antibody pre-coupled to Dynabeads sheep M-280 anti-IgG beads (LifeTech). Prior to IP, a 20 µl aliquot of extract was removed and stored at 4 °C for preparation of the size-matched input (SMInput) control. After washing, immunoprecipitated protein-RNA complexes were dephosphorylated and 3’-linker ligated on-bead to a custom oligonucleotide adapter. All samples (IPs and SMInputs) were heated in LDS Sample Buffer (LifeTech) containing 0.1 M DTT for 10 min at 70° and run on 4-12% NuPAGE Bis-Tris polyacrylamide gels in MOPS running buffer (LifeTech). Complexes were wet-transferred to iBLOT nitrocellulose membranes in NuPAGE transfer buffer (all LifeTech) containing 10% methanol (overnight, 4 °C, 30V). Successful immunoprecipitation was confirmed by performing standard western blotting on fractions (10%) of each sample. RNA-protein complexes in the range from expected molecular mass to 75 kDa above expected molecular mass (corresponding to the RBP crosslinked to RNAs of ~220 nucleotides in length) were excised from the membrane. RNAs were released by proteinase K treatment in the presence of urea and recovered by phenol/chloroform extraction and column purification (RNA Clean-Up kit; Zymo Research). Input samples were dephosphorylated and 3’-linker ligated to a custom oligonucleotide primer. All samples (IPs and SMInputs) were then reverse transcribed using AffinityScript reverse transcriptase (Agilent). After treatment with ExoSAP-IT (Affymetrix) and alkali, cDNAs were recovered by purification on Dynabeads MyONE Silane beads (LifeTech), 5’-linker ligated on-bead to a custom oligonucleotide primer, and again purified. cDNAs were quantified by qPCR analysis of a fraction of each sample using custom oligonucleotide primers specific to the 5’ and 3’ adapters. Half of the recovered cDNA was PCR-amplified (Q5 polymerase, NEB) using custom sequence-indexed oligonucleotide primers. PCR products were purified (Agencourt AMPure XP beads; Beckman Coulter), size-selected to 175-350 bp on 2% agarose gels, extracted (MinElute Gel Extraction kit; Qiagen), and quantified on a TapeStation using D1000 ScreenTape (Agilent). Libraries were sequenced on a HiSeq 4000 instrument (Illumina) in paired-end 55 bp mode.

treatment_protocol: 10 million cells were UV-crosslinked (254 nm, 400 mJ/cm2)

value: Skeletal Muscle Cells

tag: clip-seq antibody

value: DDX6 antibody; Genetex; GTX102795


title: IGR37_NLS-CTNNB1-0h_dox_R3.gz

status: Public on Oct 16 2019

type: SRA

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

description: Negative control, no Doxycycline replicate 3

library_source: transcriptomic

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR {Robinson, 2010 }.
Reads for each sample set were first filtered for genes whose expression is count-per-million prior to glmQLFTest.
Genome_build: hg38
Supplementary_files_format_and_content: edgeR normalised, differential gene expression using glmQLFTest

molecule: total RNA

organism: Homo sapiens

growth_protocol: IGR37 were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with 100U/ml penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

treatment_protocol: CTNNB1 inducible cell line was treated with 20ng/ml Doxycycline for 24h before harvest.

tag: cell type

value: melanoma

tag: cell line

tag: treatment

value: Negative control, no Doxycycline


title: Elf4-KO rep2

city: beijing

first: Fuping

last: You

address: haidian district xueyuan road 38

department: department of immunology

country: China

institute: peking university health science center

description:
DSSwvsDSSk.DiffExpGeneFilter.anno.txt
DSSk

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM（expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced） were calculated using a cufflinks-2.2.1
Genome_build: mm8
Supplementary_files_format_and_content: text file with FPKM, log2 fold-change, p-values for differentially expressed genes.

organism: Mus musculus

source_name: colon

extract_protocol:
colons were removed, washed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer's recommendations.

tag: strain

tag: genotype

tag: tissue

value: colon

tag: disease state

value: colitis

tag: age


title: Hap1-AS2LV/LV

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
TruSeq libraries prepared from 3C template
5526_10_A3_mit_HiC_Smc4_CCGTCC_S10

library_source: genomic

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

molecule: genomic DNA

growth_protocol: Hap1 cells were cultered in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptomycin (Invitrogen) and 0.5% UltraGlutamin (Lonza). NMuMG cells (Gift of J. Jonkers) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptocmycin (Invitrogen) and 0.5% UltraGlutamin (Lonza).

extract_protocol:
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

tag: genotype/variation


title: Hap1-AS1LV

description:
TruSeq libraries prepared from 3C template
4556_6_mitSmc2A_TAGCTT_S6_L001
4556_7_mitSmc2B_GCCAAT_S7_L001


title: M784_1407_S_T2

city: Boston

first: Jiantao

last: Shi

address: 3 Blackfan Circle

country: USA

institute: dana farber cancer institute

data_processing:
RNA-seq data was processed by Bcbio_nextgen pipeline (https://github.com/bcbio/bcbio-nextgen). Briefly, alignment was performed using TopHat2 against mouse genome assembly mm10 with default settings. Bioconductor package ‘Rsubread’ was used to generate gene-level read counts, which were further used for differential expression analysis by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: text file contains gene-level read counts.

source_name: leukemia stem cells

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy plus Mini or Micro kit (Qiagen). Quality of the RNA was checked by an Agilent 2100 Bioanalyzer. Genomic DNA was extracted using QIAamp DNA Mini or Micro kit (Qiagen) according to manufacturer’s instruction.
For RNA sequencing, poly-A selection and cDNA synthesis were performed, followed by library preparation using Illumina TruSeq RNA Sample Prep Kit, sequencing (75-bp paired reads), and sample identification for quality control.

value: leukemia stem cells

tag: leukemic burden

tag: mouse id

tag: color

value: Sapphire

tag: time point

tag: infection


title: M784_1414_S_T3


title: Tg-A1

type: RNA

city: Nagoya

first: Ian

last: Baudi

state: Aichi

address: Kawasumi, Mizuho

department: Virology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression in non treated liver

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes .Cy3-labelled cRNA were then hybridized on Mouse SurePrint 3 v2.0 chips for 17 hours at 65°C in a rotating Agilent hybridization oven at 10rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with Buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Detection, data extraction, and pre-analysis were performed using a G2505C Agilent microarray scanner, Feature Extraction v10.10.1.1. and GeneSpring GX v14.8.0 software.

source_name: Liver Interferon-alpha- 0hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick-Amp Labeling Kit, one color Cy3 protocol (Agilent Technologies, Santa Clara, CA, USA)

extract_protocol: RNA was isolated from snap-frozen liver tissue obtained at selected time points using Isogen (Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: HBsAg transgenic and control mice were intravenously injected with 5MU/kg recombinant mouse IFN alpha and then sacrificed  2,4,8 and 24 hours later. Non treated mice were sacrificed as time point 0hr. Liver samples were snap frozen in liquid nitrogen at sacrifice for RNA extraction at a later time point.

value: Liver

value: HBsAg transgenic

tag: gender

value: Male

tag: time (hr)


title: Tg-A2

description: Gene expression in non treated liver


title: Hap1-CAPH2KO-AS2LV

description: TruSeq libraries prepared from 3C template

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 1% Ultraglutamin (Lonza).

treatment_protocol: For CRISPR/Cas9 genome-editing gRNAs targeting and SMC4 Forward CACCGAAGATCTTCAACCTTTCGGG and Reverse AAACCCCGAAAGGTTGAAGATCTTC. Phosphorylated and annealed oligo’s were ligated into pX330 (Addgene plasmid #42230). For SMC4 L1191V mutation we used a donor oligo: CAGTGTTCGACCACCTAAGAAAAGTTGGAAAAAGATC  TTCAACGTTTCGGGAGGAGAGAAAACACTTAGTTCATTGGCTTTAGTATTTGC. To obtain CAP-H2 knockout cells, Forward CACCGTTCTTGGTGAGGTCGCGGA and Reverse AAACTCCGCGACCTCACCAAGAAC sgRNAs were cloned into px330. HAP1 clones were generated by insertion of a Blasticidine cassette. 0.1 µg pBabe-Puro was co-transfected (1:10 ratio to CRISPRs) to select for transfected cells by puromycin (2 µg/ml, Sigma-Aldrich). Genomic DNA was isolated from picked clones and the desired mutations were scored for by Sanger sequencing


title: Myo-DDX6-1-Input

description: Myoblast

source_name: Human Skeletal Myoblasts_input

growth_protocol: Enhanced crosslinking and immunoprecipitation (eCLIP) was performed on Human Skeletal Myoblast cells, and immunoprecipitated overnight at 4 °C with 10 µg affinity-purified antibody pre-coupled to Dynabeads sheep M-280 anti-IgG beads (LifeTech).


title: Myo-DDX6-2-Input

description: Myoblast


title: WT rep2

description:
DSSwvsDSSk.DiffExpGeneFilter.anno.txt
DSSw

value: WT


title: WT rep1


title: Hap1-SMC2WT/∆

description:
TruSeq libraries prepared from 3C template
5526_9_A2_mit_HiC_Smc2_ATGTCA_S9


title: LN KO_4

city: New York

first: Theodoros

last: Sakellaropoulos

address: 550 1st Ave

institute: NYU Langone

data_processing:
Reads were aligned to mm10 using bowtie2 (v2.3.1) with parameters --local --minins 50 --maxins 2000 --no-mixed --no-discordant
Duplicates were removed using picard (v 1.88) with LENIENT strigency option
Peaks were called using macs (v 2.1.1.20160309) with parameters: --nomodel --extsize=200 --shift -100 --bdg --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with peaks and their attributes per Sample as called by macs

source_name: tumour-draining lymph nodes

extract_protocol:
14 days upon tumour inoculation tumour-draining lymph nodes were isolated and Tregs were sorted (CD4+CD25+GITR+). Cells were lysed. Transposition reaction was performed with in-house Tn5 Transposase and DNA purification was effectuated by Qiagen MinElute kit and amplified using the NEBNext High-Fidelity PCR Master Mix
Transposition reaction was performed with in-house Tn5 Transposase and DNA purification was effectuated by Qiagen MinElute kit and amplified using the NEBNext High-Fidelity PCR Master Mix

treatment_protocol: Mice were inoculateds.c. with 300000 B16.F10 cells

value: tumour-draining lymph nodes

tag: tumour

value: B16.F10 melanoma day 14

value: CD4+CD25+GITR+Foxp3+ T regulatory cells

tag: strain/genotype

value: il33-/- in C57BL6 background


title: sgDDX6_3_MID

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA16_sgRNA_3_MEDIUM_S30_L002

data_processing:
RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i). Reads did not map to repetitive elements were then mapped to the human genome (hg19). Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: RPKM

source_name: primed hESCs_sgDDX6_MID

growth_protocol: Primed pluripotent stem cells were maintained on Matrigel (Corning) coated dishes in mTeSR edium (Stem Cell Technologies) and passaged using gentle cell dissociation reagent (Stem Cell Technologies). For maintenance, cells were passaged every 4-5 days.

extract_protocol:
Each polysome fraction pools and total input RNA (INPUT) were extracted using Trizol reagent
Strand-specific RNA sequencing libraries were prepared from 0.5-3 µg total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina).

treatment_protocol: Polysome cells were treated with cycloheximide (CHX) at 100 µg/ml for 5 min at 37°C. And then resuspend in polysome lysis buffer(20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5mM MgCl2,  protease inhibitor cocktail (EMD Millipore), CHX 100 µg/ml, 1 mM DTT, and 20 U/ml RNase inhibitor (RNaseOUT, Thermo Fisher)). Sample were loaded on the sucrose gradient and centrifuged at 35,000 x g (Beckman, rotor SW41) at 4 °C for 3 h. Fractions were collected from the top and UV absorbance monitored using a Gradient Station (BioCamp) equipped with ECONO UV monitor (BioRad). 500 µl fraction were collected using a FC203B (Gilson) fraction collector. Fractions containing monosome(MONO), light polysome (LITE), medium polysome (MID), heavy polysome (HEAVY), and total polsome (POLY) were pooled.

tag: cell type

value: primed hESCs


title: sgDDX6_3_HEAVY

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA17_sgRNA_3_HEAVY_S31_L002

source_name: primed hESCs_sgDDX6_HEAVY


title: M784_1402_S_T2


title: M_4826_GMP_T0

source_name: GMP

value: GMP

value: M


title: Hap1-CAPH2KO


title: M784_1405_S_T2


title: Elf4-KO rep1


title: scRNA-Seq_WTC /Colon  (1)

city: Tianjin

first: Ming

last: Wei

address: 94 Weijin road

department: Department of Immunology, Nankai University School of Medicine

institute: Nankai University

data_processing:
Initially, raw base call (BCL) files generated by Illumina sequencers was demultiplexed into FASTQ files
After barcode processing, sequencing reads per cell barcode were then aligned to the UCSC mm10 transcriptome with STAR (version 2.5.1b).
Prior to single-cell 3ʹgene counting, duplicates were filtered based on unique molecular identifiers (UMIs), and finally single cell information (gene expression matrix) of each individual sample was generated.
In this study, outputs of samples from different runs of cellranger count were merged together, facilitated by cellranger aggr pipeline which normalized those runs to the same sequencing depth among libraries.As calculated by Cell Ranger, the post-normalization mean reads per cell from all libraries was >70,000.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

molecule: polyA RNA

source_name: colonic LP tissues of SPF mice (8 weeks old, male)

extract_protocol:
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad)  at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: Dextran sodium sulfate (DSS) induced colitis was performed according to the previous method (Cell Rep 14, 695-707). Briefly, mice (7-8 weeks old, male) received 2.5% (wt/vol) DSS (40,000 kDa; ICN Biochemicals) or indicated doses in their drinking water for 7 days, then switched to regular drinking water.For pan-antibotics treated mice, C57BL/6 mice (7-8 weeks old, male) were with pan-antibiotics (ampicillin (A, 1 g/L, Sigma), vancomycine (V, 0.5g/L, Sigma), neomycin sulfate (N, 1 g/L, Sigma), and metronidazole (M, 1g/L, Sigma) via the drinking water for one week (sometime longer than one week).

value: colonic LP cells

tag: cell population

tag: background strain

value: wildtype

value: 7-8 weeks

tag: Sex

value: male


title: Myo-DDX6-1-IP

description: Myoblast

value: Skeletal Muscle Cells

tag: clip-seq antibody

value: DDX6 antibody; Genetex; GTX102795


title: Hap1-A Hi-C

source_name: Hap1-A Hi-C


title: mutant463_inf_rep4

city: Tampere

first: Sanna-Kaisa

middle: Emilia

last: Harjula

address: Arvo Ylpön katu 34

country: Finland

institute: University of Tampere

description:
raw_expressions.tsv
normalized_expressions.tsv

data_processing:
Read alignment to reference genome was done using STAR
Raw expression estimates (raw read counts) for genes (Danio_rerio.GRCz10.91) were counted using FeatureCounts
Raw expression estimates were normalized using median of rations implemented in R-packages DESeq2
Genome_build: Danio_rerio.GRCz10
Supplementary_files_format_and_content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab-delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample.

organism: Danio rerio

source_name: zebrafish kidney

growth_protocol: The zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene-breaking transposon based mutagenesis using the RP2 construct.

extract_protocol:
Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit (ID: 74104) according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit (K2981).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5 to 6 months old zebrafish were infected with 5 - 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection.

tag: strain


title: sgDDX6_3_LITE

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA15_sgRNA_3_LITE_S29_L002

source_name: primed hiPSCs_sgDDX6_LITE

value: primed hiPSCs


title: sgDDX6_3_MONO

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA14_sgRNA_3_MONO_S28_L002

source_name: primed hiPSCs_sgDDX6_MONO


title: LN KO_1

tag: tissue


title: LN KO_2


title: mutant463_inf_rep3


title: M_1394_S_T1

value: leukemia stem cells

value: Sapphire


title: M_4825_GMP_T0


title: Hap1-AS2LV


title: LN WT b6_6


title: M784_1406_S_T2


title: sgDDX6_3_POLY

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA18_sgRNA_3_POLY_S32_L002

source_name: primed hiPSCs_sgDDX6_POLY

tag: genotype/variation


title: M_1393_S_T1

tag: leukemic burden


title: mutant463_inf_rep2


title: sgDDX6_3_INPUT

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA13_sgRNA_3_INPUT_S27_L002

source_name: primed hiPSCs_sgDDX6_INPUT


title: LN WT b6_4


title: M_1392_S_T1

tag: mouse id


title: mutant463_inf_rep1


title: sgDDX6_2_HEAVY

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA11_sgRNA_2_HEAVY_S25_L002


title: TS603_3

city: Bethesda

first: Mioara

last: Larion

state: Maryland

address: 37 Convent Drive, Building 37

department: NCI, CCR

institute: National Institutes of Health

data_processing:
Strand-specific RNA-seq reads were analyzed using CCBR Pipeliner
Sequencing reads that passed QC thresholds were trimmed of adaptor sequences and aligned to the human genome (hg19) and STAR was then used for genomic alignment
The transcripts were quantified using salmon and rsem, and differentially-expressed genes were determined using edgeR, DESeq2 and limma/voom.
Derived differentially-expressed genes using thresholds of FDR ≤ 0.05 and fold changes ≥ 1.5 or ≤ -1.5 across all three methods (for some contrasts p ≤ 0.05 and fold change 1.3 or ≤ -1.3).
The functional annotation was carried out using Ingenuity Pathway Analysis (IPA, www.qiagenbioinformatics.com) software.

source_name: grade III oligodendroglioma

growth_protocol: Cells were seeded in DMEM F12 media supplemented with N2, EGF, FGF and Heparan sulphate for 3 days.

extract_protocol:
RNA was extracted using PureLink RNA Mini kit (Thermo Fisher Scientific) and RNA quality was measured on an Agilent 2100 Bioanalyzer using the RNA 6000 Pico kit (Agilent Technologies).
The transcriptome library was prepared using Illumina TruSeq Stranded mRNA Library Prep kit following the manufacturer’s instructions.
The library was sequenced on Illumina HiSeq 3000 using 150 bp paired-end reads targeting an average coverage of 25 million reads per sample.

treatment_protocol: Untreated

tag: cell line

value: Glioma stem cells

tag: idh1 status

value: IDH1 mutant


title: ABc_4: WT_control_rep4

growth_protocol: The zebrafish were maintained according to the standard protocols.

treatment_protocol: 5 to 6 months old zebrafish were infected with 5 - 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections.

tag: genotype

value: wild type AB

tag: agent

value: none (control)

value: zebrafish kidney


title: TS603_2


title: sgDDX6_2_LITE

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA9_sgRNA_2_LITE_S9_L001

source_name: primed hESCs_sgDDX6_LITE

value: primed hESCs


title: ABc_3: WT_control_rep3


title: M_1180_G_T1

tag: color

value: GFP

tag: time point

tag: infection


title: TS603_1

tag: cell type


title: ABc_2: WT_control_rep2


title: sgDDX6_2_MONO

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA8_sgRNA_2_MONO_S8_L001

source_name: primed hESCs_sgDDX6_MONO


title: M_1179_G_T1

source_name: leukemia stem cells

value: M


title: ABc_1: WT_control_rep1


title: M_1070_R_T1

value: iRFP


title: BT142_2

source_name: grade III oligoastrocytoma


title: sgDDX6_2_INPUT

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA7_sgRNA_2_INPUT_S7_L001

source_name: primed hESCs_sgDDX6_INPUT


title: M_1069_R_T1


title: BT142_3


title: AB_4: WT_inf_rep4

value: Mycobacterium marinum


title: AB_3: WT_inf_rep3


title: M_1068_R_T1


title: LN WT b6_2

source_name: tumour-draining lymph nodes

value: tumour-draining lymph nodes

tag: tumour

value: B16.F10 melanoma day 14

value: CD4+CD25+GITR+Foxp3+ T regulatory cells

tag: strain/genotype


title: BT142_1


title: M_1391_S_T1


title: AB_2: WT_inf_rep2


title: sgDDX6_1_HEAVY

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA5_sgRNA_1_HEAVY_S5_L001


title: sgDDX6_2_MID

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA10_sgRNA_2_MEDIUM_S10_L001

source_name: primed hESCs_sgDDX6_MID


title: M_1182_G_T1


title: sgDDX6_1_MID

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA4_sgRNA_1_MED_S4_L001

source_name: primed hiPSCs_sgDDX6_MID


title: AB_1: WT_inf_rep1


title: sgDDX6_2_POLY

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA12_sgRNA_2_POLY_S26_L002

source_name: primed hESCs_sgDDX6_POLY


title: sgDDX6_1_LITE

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA3_sgRNA_1_LITE_S3_L001


title: sgDDX6_1_POLY

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA6_sgRNA_1_POLY_S6_L001


title: DMCPD24hrR1

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: replicate 1

data_processing:
Library strategy: XR-seq
adaptor trimming
filtering reads based on length
random sampling
alignment with Bowtie2
read filtering based on nucleotide composition
strand separation
gene coverage count with samtools and bedtools.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig

organism: Drosophila melanogaster

source_name: S2-DGRC cells

extract_protocol: S2-DGRC cells were obtained from the Drosophila Genetic Resources Center. Cells were cultured in Schneider’s medium at 27 degrees with heat inactivated FBS at 10% (v/v).  For UV treatments, cells were inoculated into R-150 plates and grown to about 25 to 80 percent confluence.  Media was gently removed from the semi-adherent monolayer, cells were irradiated with UV-C, and then fresh media containing sterilized, conditioned media was added to cells, and cells were incubated at 27 degrees.  XR-seq assays employed 20 Jm-2.    Following predetermined repair times, plates were placed on ice and cooled cells were harvested by scraping and rinsing with ice-cold PBS. Cells were pelleted, transferred to Eppendorf tubes, washed with cold PBS, and resuspended in 320 to 340 ul of cold TE.  Samples were processed using 5 ul RNase A and proteinase K. Samples were immunoprecipitated with anti-CPD antibody, and then ligated to adapters and processed for sequencing (XR-seq).  One plate of S2 cells per repair time point was sufficient for XR-seq assay.  Drosophila possesses photolyases, so cells were kept in the dark or under dim yellow illumination from the time of irradiation to the time of addition of NaCl to cell lysates. After PCR amplification, libraries wrere sequencing on HS4000.

tag: treatment

value: UV

value: wild type

tag: repair time

value: 24 hours


title: sgDDX6_1_INPUT

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA1_sgRNA_1_INPUT_S1_L001


title: UT-SCC59A_negative control siRNA

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

institute: University of Turku

description: RNA sequencing data from cSCC

data_processing:
The samples were sequenced with the HiSeq3000 instrument using single-end sequencing with 50bp read length. All sample libraries were pooled in one sequencing lane.
The reads obtained from the instrument were base called using instrument manufacturer’s Bcl2fastq2 version 2.17 base calling software and aligned against the human reference genome (GRCh37 assembly).
The reads were aligned against the reference genome using Star version 2.5.2b. Then the reads were associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.1).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.3, Bioconductor version 3.3).
Genome_build: GRCh37
Supplementary_files_format_and_content: For statistical testing the data were further log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values.

source_name: Cutaneous squamous cell carcinoma 59A

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile RNAse-free water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
RNA libraries were prepared for sequencing using  Illumina TruSeq Stranded total RNA Sample Preparation Kit according to the manufacturer's instructions.

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starvated 24 hours before harvesting.

tag: disease state

value: Cutaneous SCC

tag: cell source

value: Derived from cSCC tumors

value: Metastatic cSCC cells

value: Negative control siRNA


title: UT-SCC105_PRECSIT siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 105

value: Primary cSCC cells

value: PRECSIT siRNA


title: UT-SCC59A_PRECSIT siRNA

description: RNA sequencing data from cSCC


title: WholeRoot_100µM_Ni_4d_rep2

city: Bratislava

first: Milan

last: Zvarik

address: Mlynska dolina

country: Slovakia

institute: Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava

description: Gene expression after 4 days of 100 µM nickel treatment

hyb_protocol: RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 021169_D_F_20140929) to obtain background subtracted and spatially detrended Processed Signal intensities. Analysis of microarray data was performed with the R package limma. Raw feature intensities were background corrected using “normexp”, and “quantile” normalization method was used to normalize between arrays.

organism: Arabidopsis thaliana

source_name: Whole root, 100 µM added nickel, 4 days, replicate 1

growth_protocol: Arabidopsis thaliana seedlings (accession Col) were pre-cultured for seven days on solid half-strength MS agar media without added nickel (Ni) were then transferred to fresh media containing no added Ni (control) or 100 µM NiSO4 (+nickel).

extract_protocol: RNA was extracted from whole roots using an RNeasy plant mini kit (Qiagen) with on-column DNase treatment according to the manufacturer’s instructions. cDNA was prepared using random hexamer primers and SuperScript II reverse transcriptase (Life Technologies) according to the manufacturer’s protocol.

treatment_protocol: Seven-day-old plants were transferred to solid half-strength MS agar media containing no added nickel (control) or 100 µM NiSO4 (+nickel) for 4 days.

tag: tissue

value: whole root

tag: plant age

value: 11 days


title: UT-SCC7_negative control siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 7


title: WholeRoot_100µM_Ni_4d_rep1

label_protocol: RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).


title: WholeRoot_control_4d_rep4

description: Gene expression after 4 days of no added nickel (control) treatment

source_name: Whole root, 0 µM added nickel, 4 days, replicate 1


title: DMCPD16hrR1

description: replicate 1

value: 16 hours


title: UT-SCC7_PRECSIT siRNA

description: RNA sequencing data from cSCC


title: UT-SCC105_negative control siRNA

description: RNA sequencing data from cSCC


title: WholeRoot_100µM_Ni_4d_rep4


title: WholeRoot_control_4d_rep3


title: control_3_MONO

description:
GEN1C
processed data file: control_RPKM.csv
SA32_control_3_MONO_S74_L004

source_name: primed hESCs_control_MONO

value: primed hESCs

tag: genotype/variation

value: control


title: control_3_MID

description:
GEN1C
processed data file: control_RPKM.csv
SA34_control_3_MEDIUM_S76_L004

source_name: primed hESCs_control_MID


title: DMCPD8hrR2

description: replicate 2

tag: cell line

value: 8 hours


title: control_3_LITE

description:
GEN1C
processed data file: control_RPKM.csv
SA33_control_3_LITE_S75_L004

source_name: primed hESCs_control_LITE


title: sgDDX6_1_MONO

description:
GEN1C
processed data file: sgRNA_RPKM.csv
SA2_sgRNA_1_MONO_S2_L001

source_name: primed hiPSCs_sgDDX6_MONO

value: primed hiPSCs


title: control_3_POLY

description:
GEN1C
processed data file: control_RPKM.csv
SA36_control_3_POLY_S78_L004

source_name: primed hiPSCs_control_POLY


title: DMCPD8hrR1

description: replicate 1


title: S1-3D TC

city: Taipei City

first: Kelvin

middle: Kun-Chih

last: Tsai

address: 7F, 250 Wuxing St, Xinyi Dist

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Taipei Medical University

description: S1 cells were embedded in 3D rBM and treated with TRAIL (1ug/ml) for 8 hours, replication 3.

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

scan_protocol: Arrays were scanned by a confocal scanner.

data_processing: Affymetrix .cel files were processed with ArrayAssist Lite (v3.4, Stratagene). The files were imported and processed with the GC-RMA algorithm to yield probe set intensities and additionally, Affymetrix Preset, Absent, Marginal flags were computed. These values were exported in .chp files, which were subsequently imported into the Partek Genomics Suite software (v6.2).

label: biotin

source_name: S1 cells embedded and grown in 3D rBM and treated with TRAIL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HMT-3522 S1 cells were propagated as monolayers on rBM-coated tissue culture plastics in chemically defined medium comprising of DMEM/F12, prolactin (0.15 IU/ml), insulin (250 ng/ml), hydrocortisone (1.4 μM), sodium selenite (2.6 ng/ml), β-Estradiol (0.1 nM), Apo-transferrin (10 μg/ml), and EGF (10 ng/ml). For 3D culture, S1 cells were embedded in 3D rBM (Matrigel, BD Bioscience) and grown for 12 days to form 3D acini organoids before the subsequent treatment.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions. The resulted RNA samples were further purified by Rneasy Mini Kit (Qiagen).

treatment_protocol: Cells were pre-treated with caspase inhibitors DEVD-CHO and Ac-IETD-CHO (1μM, respectively) at least 2 hours before TRAIL treatment (1 ug/ml) for 8hrs.

value: breast epithelium


title: WholeRoot_control_4d_rep2


title: DMCPD30mR1

description: replicate 1

value: UV

value: 30 minutes


title: control_3_INPUT

description:
GEN1C
processed data file: control_RPKM.csv
SA31_control_3_INPUT_S73_L004

source_name: primed hiPSCs_control_INPUT


title: control_3_HEAVY

description:
GEN1C
processed data file: control_RPKM.csv
SA35_control_3_HEAVY_S77_L004

source_name: primed hESCs_control_HEAVY


title: WholeRoot_100µM_Ni_4d_rep3


title: S1-3D TB

description: S1 cells were embedded in 3D rBM and treated with TRAIL (1ug/ml) for 8 hours, replication 2.


title: WholeRoot_control_4d_rep1


title: 501mel_DMSO_t48h_R3

description: processed data file: edgeR_SCD_normalised_count_Log.txt

growth_protocol: IGR37 and 501mel were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with 100U/ml penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Libraries were prepared using recommended Illumina protocols
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

treatment_protocol:
For siRNA treatment, cells were treated with 20nM of the indicated siRNA for 48h
For  SCD inhibitor treatment, cells were treated with A939372 at 1 uM for 48 h.

value: melanoma cell line

value: DMSO


title: control_2_LITE

description:
GEN1C
processed data file: control_RPKM.csv
SA27_control_2_LITE_S70_L004


title: pH6_T8_2

city: Birmingham

first: Rebecca

last: Hall

address: University of Birmingham, School of Biosciences

department: IMI

institute: University of Birmingham

description: TPM summary.xlsx

data_processing:
Trim reads, CLC Genomics Workbench 11.0.1
Reads alignement, CLC Genomics Workbench 11.0.1
Genome_build: A21-s02-m09-r10
Supplementary_files_format_and_content: TPM

organism: Candida albicans

source_name: Liquid culture

growth_protocol: Cells were grown in YPD buffered at pH4 or pH6 at 37c, 200 rpm.

extract_protocol:
RNeasy kit (Qiagen)
RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S)

tag: ph

tag: time

tag: replicate


title: control_2_MONO

description:
GEN1C
processed data file: control_RPKM.csv
SA26_control_2_MONO_S69_L004


title: pH6_T8_3

description: TPM summary.xlsx


title: DMCPD10mR2

description: replicate 2

tag: genotype

value: wild type

value: 10 minutes


title: pH6_T8_1

description: TPM summary.xlsx


title: pH4_T8_3

description: TPM summary.xlsx


title: control_2_MID

description:
GEN1C
processed data file: control_RPKM.csv
SA28_control_2_MEDIUM_S71_L004

source_name: primed hiPSCs_control_MID


title: DMCPD10mR1

description: replicate 1


title: control_2_POLY

description:
GEN1C
processed data file: control_RPKM.csv
SA30_control_2_POLY_S72_L004

source_name: primed hESCs_control_POLY


title: control_2_INPUT

description:
GEN1C
processed data file: control_RPKM.csv
SA25_control_2_INPUT_S68_L004

source_name: primed hESCs_control_INPUT


title: S1-3D TA

description: S1 cells were embedded in 3D rBM and treated with TRAIL (1ug/ml) for 8 hours, replication 1.


title: S1-3D CB

description: S1 cells were embedded in 3D rBM,replication 2.

source_name: S1 cells embedded and grown in 3D rBM


title: control_1_HEAVY

description:
GEN1C
processed data file: control_RPKM.csv
SA23_control_1_HEAVY_S48_L003


title: S1-3D CA

description: S1 cells were embedded in 3D rBM,replication 1.


title: S1-3D CC

description: S1 cells were embedded in 3D rBM,replication 3.


title: pH4_T8_1

description: TPM summary.xlsx


title: control_1_MID

description:
GEN1C
processed data file: control_RPKM.csv
SA22_control_1_MEDIUM_S47_L003


title: pH4_T8_2

description: TPM summary.xlsx


title: pH6_T6_3

description: TPM summary.xlsx

value: 6 hours


title: S1-2D TB

description: S1 cells grown on 2D plastic plate and treated with TRAIL (1ug/ml) for 8 hours, replication 2.

source_name: S1 cells grown as monolayer and treated with TRAIL


title: control_1_LITE

description:
GEN1C
processed data file: control_RPKM.csv
SA21_control_1_LITE_S46_L003

source_name: primed hiPSCs_control_LITE


title: S1-2D TC

description: S1 cells grown on 2D plastic plate and treated with TRAIL (1ug/ml) for 8 hours, replication 3.


title: S1-2D CC

description: S1 cells grown on 2D plastic plate,replication 3.

source_name: S1 cells grown as monolayer


title: control_2_HEAVY

description:
GEN1C
processed data file: control_RPKM.csv
SA29_control_2_HEAVY_S35_L002

source_name: primed hiPSCs_control_HEAVY


title: S1-2D TA

description: S1 cells grown on 2D plastic plate and treated with TRAIL (1ug/ml) for 8 hours, replication 1.


title: control_1_MONO

description:
GEN1C
processed data file: control_RPKM.csv
SA20_control_1_MONO_S34_L002

source_name: primed hiPSCs_control_MONO


title: pH6_T6_1

description: TPM summary.xlsx


title: Blank rep3 [RH_Blank_03]

city: Chongqing

first: Gao

last: Guangliang

address: Street Address, No. 51 Changlong Avenue Rongchang County

institute: Chongqing Academy of Animal Sciences

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of six strand-specific libraries were mapped to the pig reference genome (Suscrofa.10.2 from Ensemble) with TopHat (v.2.1.0)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Cufflinks (v.2.2.1).
Cuffquant (part of Cufflinks) was used to generate abundance files, which were applied to Cuffdiff (part of Cufflinks) to detect DE mRNAs/genes between the two groups.
Transcripts were assembled by Stringtie version 1.2.2.
AssemblyLine (http://assemblyline.googlecode.com) was used to characterize and filter background noise and to perform meta-assembly by merging the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
To obtain genomic characterizations for all identified lncRNA transcripts, we ran FEELnc_classifier.pl (a Perl script in FEELnc).
Genome_build: Gallus gallus.10.2 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Anser cygnoides

source_name: Blank

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent  (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Illumina NEBNext® UltraTM RNA Library Prep kits (New England Biolabs, NEB, Ipswich, MA, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: breed

value: Sichuan white goose

tag: age

value: 40 weeks

value: small and large yellow follicles

value: ovarian granulosa cells (GCs)


title: pH4_T6_2

description: TPM summary.xlsx


title: Blank rep2 [RH_Blank_02]

tag: cell type


title: Blank rep1 [RH_Blank_01]


title: pH4_T6_3

description: TPM summary.xlsx


title: Antagonist treatment group rep3 [RH_Ant_03]

source_name: Antagonist treatment group

value: Antagonist treatment


title: S1-2D CB

description: S1 cells grown on 2D plastic plate,replication 2.


title: Antagonist treatment group rep2 [RH_Ant_02]


title: pH4_T6_1

description: TPM summary.xlsx


title: control_1_POLY

description:
GEN1C
processed data file: control_RPKM.csv
SA24_control_1_POLY_S49_L003


title: control_1_INPUT

description:
GEN1C
processed data file: control_RPKM.csv
SA19_control_1_INPUT_S33_L002


title: pH6_T4_2

description: TPM summary.xlsx

value: 4 hours


title: pH6_T6_2

description: TPM summary.xlsx


title: pH6_T4_1

description: TPM summary.xlsx


title: pH4_T4_3

description: TPM summary.xlsx


title: pH4_T4_2

description: TPM summary.xlsx


title: pH6_T4_3

description: TPM summary.xlsx


title: pH4_T4_1

description: TPM summary.xlsx


title: pH6_T2_3

description: TPM summary.xlsx

value: 2 hours


title: pH6_T2_2

description: TPM summary.xlsx


title: pH6_T2_1

description: TPM summary.xlsx


title: Agonist treatment group rep2 [RH_Ag_02]

source_name: Agonist treatment group

value: Agonist treatment


title: Agonist treatment group rep1 [RH_Ag_01]


title: pH4_T2_2

description: TPM summary.xlsx


title: Agonist treatment group rep3 [RH_Ag_03]


title: Antagonist treatment group rep1 [RH_Ant_01]


title: GEN1C-eCLIP-DDX6-1-Input

data_processing:
Reads were adapter-trimmed and mapped to human-specific repetitive elements from RepBase (version 18.04) by STAR. Repeat-mapping reads were removed and remaining reads mapped to the human genome assembly hg19 with STAR. PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5’ adapter and remaining reads retained as ‘usable reads’.
Peaks were called on the usable reads by CLIPper ,and assigned to gene regions annotated in Gencode (v19)
Each peak was normalized to the size-matched input (SMInput)
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Each bed file was generated by read normalization between IP over SMInput. The columns in the bed files represent (chr, start, stop,-log10(pvalue),log2(fold change), strand). The CSV files contain the log2 fold change of reads upon IP over SMInput in annotated regions of each transcripts. Each bigwig file contains read distribution of each RBP, and bigbed contains clusters of predicted RBP binding.

source_name: human induced pluripotent stem cells

extract_protocol:
Cell lysates were prepared by sonication in 1 ml iCLIP lysis buffer, treated with RNase I (40 U, LifeTech).
Enhanced crosslinking and immunoprecipitation (eCLIP) was performed on GENC1 and H1 cells, and immunoprecipitated overnight at 4 °C with 10 µg affinity-purified antibody pre-coupled to Dynabeads sheep M-280 anti-IgG beads (LifeTech). Prior to IP, a 20 µl aliquot of extract was removed and stored at 4 °C for preparation of the size-matched input (SMInput) control. After washing, immunoprecipitated protein-RNA complexes were dephosphorylated and 3’-linker ligated on-bead to a custom oligonucleotide adapter. All samples (IPs and SMInputs) were heated in LDS Sample Buffer (LifeTech) containing 0.1 M DTT for 10 min at 70° and run on 4-12% NuPAGE Bis-Tris polyacrylamide gels in MOPS running buffer (LifeTech). Complexes were wet-transferred to iBLOT nitrocellulose membranes in NuPAGE transfer buffer (all LifeTech) containing 10% methanol (overnight, 4 °C, 30V). Successful immunoprecipitation was confirmed by performing standard western blotting on fractions (10%) of each sample. RNA-protein complexes in the range from expected molecular mass to 75 kDa above expected molecular mass (corresponding to the RBP crosslinked to RNAs of ~220 nucleotides in length) were excised from the membrane. RNAs were released by proteinase K treatment in the presence of urea and recovered by phenol/chloroform extraction and column purification (RNA Clean-Up kit; Zymo Research). Input samples were dephosphorylated and 3’-linker ligated to a custom oligonucleotide primer. All samples (IPs and SMInputs) were then reverse transcribed using AffinityScript reverse transcriptase (Agilent). After treatment with ExoSAP-IT (Affymetrix) and alkali, cDNAs were recovered by purification on Dynabeads MyONE Silane beads (LifeTech), 5’-linker ligated on-bead to a custom oligonucleotide primer, and again purified. cDNAs were quantified by qPCR analysis of a fraction of each sample using custom oligonucleotide primers specific to the 5’ and 3’ adapters. Half of the recovered cDNA was PCR-amplified (Q5 polymerase, NEB) using custom sequence-indexed oligonucleotide primers. PCR products were purified (Agencourt AMPure XP beads; Beckman Coulter), size-selected to 175-350 bp on 2% agarose gels, extracted (MinElute Gel Extraction kit; Qiagen), and quantified on a TapeStation using D1000 ScreenTape (Agilent). Libraries were sequenced on a HiSeq 4000 instrument (Illumina) in paired-end 55 bp mode.

tag: clip-seq antibody

value: primed hiPSCs


title: H1-eCLIP-ILF2-Input

source_name: human embryonic stem cells

value: primed hESCs


title: H1-eCLIP-DCP1B-Input


title: H1-eCLIP-FUS-Input


title: GEN1C-eCLIP-DDX6-1-IP


title: GEN1C-eCLIP-DDX6-2-Input


title: H1-eCLIP-FUS-IP


title: H1-eCLIP-ILF2-IP


title: Mouse microglia + H9 human microglia + abeta

city: Leuven

first: Mark

last: Fiers

address: Herestraat 49

department: Center for Brain and Disease

country: Belgium

institute: VIB

description:
RM49 and RM60
Mice grafted with human microglia.
Rag2-/- IL2rγ-/- hCSF1KI mice were purchased from Jacksons Labs (strain 017708).
processed data file: chimera_mouse.tsv.gz
processed data file: chimera_human_h9.tsv.gz

data_processing:
Cellranger (version 2.1.1).
Genome_build: Human hg38 (GRCh38), Ensembl version 84; mouse mm10 (GRCm38), Ensembl version 84.
Supplementary_files_format_and_content: *.tsv.gz: Raw gene expression counts per cell in a gzipped tab-separated values file.

organism:
Homo sapiens
Mus musculus

source_name: Whole mouse brain microglia + H9 (WiCell Research Institute WA09) Transplanted ESC derived microglia

extract_protocol:
Flow Cytometry or MACS.
10X Genomics V2 chemistry.

value: Microglia

value: Oligomeric amyloid beta

tag: mouse strain

value: Rag2-/- IL2r<gamma>-/- hCSF1KI

tag: mouse age

value: 8-12 weeks

tag: mouse gender

value: Pooled male and female

tag: human gender

value: Female


title: H1-eCLIP-DCP1B-IP

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

value: MBL, #RN112PW


title: GEN1C-eCLIP-DDX6-2-IP


title: pH4_T2_1

description: TPM summary.xlsx


title: Mouse microglia + H9 human microglia + scrambled

description:
RM38 and RM56
Mice grafted with human microglia.
Rag2-/- IL2rγ-/- hCSF1KI mice were purchased from Jacksons Labs (strain 017708).
processed data file: chimera_mouse.tsv.gz
processed data file: chimera_human_h9.tsv.gz

tag: treatment

value: Scrambled


title: pH4_T2_3

description: TPM summary.xlsx


title: Ribo_E1

city: Daejeon

first: Namil

last: Lee

address: Daehakro

department: Biological science

country: South Korea

institute: KAIST

description: ribosome bound RNA

data_processing:
Library strategy: ribosome profiling
Adaptor sequence was trimmed from reads of the RNA-seq, dRNA-seq, and Ribo-seq data. Low quality reads (Phred quality score < 0.05) were discarded. In case of RNA-seq, reads shorter than 25 nucleotides were removed. Remained reads were mapped to the completed genome of S. tsukubaensis using CLC genomics workbench (CLC Bio) with following parameters (mismatch costs = 2, length fraction = 0.9, and similarity fraction = 0.9).
Only uniquely mapped reads were retained and the mapped reads of genes were normalized by DESeq2 package in R 27
Genome_build: Streptomyces tsukubaensis NRRL 18488. The FASTA file with transcript sequences is available on the series record (GSE97637_Stsu_CDS_seq_2.txt).
Supplementary_files_format_and_content: tab-delimited text files with mapped reads on genes

organism: Streptomyces tsukubensis

source_name: Cell culture

growth_protocol: A stock of S.tsukubaensis (NBRC 108819) in 20% glycerol was inoculated in R5(-) liquid complex media composed of 25 mM TES (pH 7.2), 103 g/L sucrose, 1% (w/v) glucose, 5 g/L yeast extract, 10.12 g/L MgCl2∙6H2O, 0.25 g/L K2SO4, 0.1 g/L casamino acids, 0.08 g/L ZnCl2, 0.4 mg/L FeCl3, 0.02 mg/L CuCl2∙2H2O, 0.02 mg/L MnCl2∙4H2O, 0.02 mg/L Na2B4O7∙10H2O, and 0.02 mg/L (NH4)6Mo7O24∙4H2O with 0.16 g/mL glass beads (3 mm ± 0.3 mm) diameter at 30 oC 200 RPM orbital shaker. The inoculated mycelium was diluted 1:100 to fresh R5 liquid complex medium after the inoculated cells reached mid-exponential phase (OD600: 1.325), and cultivated at 30 oC to appropriate cell density.

extract_protocol:
For the Ribo-seq experiment, the cells were harvested in the same manner with a translation elongation inhibitor thiostrepton (Sigma) added to the cultures to a final concentration of 20 mM. Thiostrepton treated cell cultures were then subsequently incubated for 5 min at 30 oC, and then harvested. Cell growth was monitored by measuring the OD600 nm.
Collected mycelium culture was at 3,000 x g for 10 min at 4 oC. The cell pellets were resuspended in 2 mL Polysome buffer (20 mM Tris-HCl (pH 7.4), 140 mM NaCl, and 5 mM MgCl2). The resuspended cells were centrifuged at 3000g for 10 min. The cell pellets were then resuspended in 1 mL lysis buffer (20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM MgCl2, and 1% Triton X-100). The cells resuspended in the lysis buffer were dripped into a mortar filled with liquid nitrogen, and grinded by pestle. The grinded cells were thawed, and centrifuged at 3,000g for 10 min at 4 oC for removal of cell debris. The supernatants were further cleaned by centrifugation at 16,000g for 10 min at 4 oC.
For Ribo-seq,Concentration of the lysate was measured with a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). To digest RNA, 50 µg of lysate was incubated at 37 oC for 45 min with 750 U of RNaseI (Invitrogen). The digested samples loaded on equilibrated Sephacryl S 400 MicroSpin column (GE Healthcare) with 500 µL polysome buffer three times. Column was centrifugated at 4 oC for 2 min at 400g. Flow through were gathered and further purified by phenol-chloroform extraction and ethanol precipitation. Ribosomal RNA was removed by using Ribo-ZeroTM kit. The ribosome-protected RNA fragments were separated by gel electrophoresis for 60 min at 200 V on 15% polyacrylamide TBE-urea gel (Invitrogen). RNA fragments between 26 bp and 34 bp were size-selected and eluted in 400 µL of RNA gel extraction buffer (300 mM sodium acetate (pH5.5), 1 mM EDTA, and 0.25% (w/v) SDS). Samples were frozen at -80 oC for 30 min, followed by incubated at RT for overnight with gentle mixing. RNA fragments were purified by ethanol precipitation and phosphorylated as follows: samples were denatured at 80 oC for 90 sec, followed by equilibrated to 37 oC and incubated at 37 oC for 1 h with 10X T4 PNK buffer (New England Biolabs), 20 U of SUPERase InTM (Invitrogen), and 10 U of T4 PNK (NEB).

tag: strain

tag: growth phase

value: early exponential


title: RNA_S2

description: total RNA

data_processing:
Adaptor sequence was trimmed from reads of the RNA-seq, dRNA-seq, and Ribo-seq data. Low quality reads (Phred quality score < 0.05) were discarded. In case of RNA-seq, reads shorter than 25 nucleotides were removed. Remained reads were mapped to the completed genome of S. tsukubaensis using CLC genomics workbench (CLC Bio) with following parameters (mismatch costs = 2, length fraction = 0.9, and similarity fraction = 0.9).
Only uniquely mapped reads were retained and the mapped reads of genes were normalized by DESeq2 package in R 27
Genome_build: Streptomyces tsukubaensis NRRL 18488. The FASTA file with transcript sequences is available on the series record (GSE97637_Stsu_CDS_seq_2.txt).
Supplementary_files_format_and_content: tab-delimited text files with mapped reads on genes

extract_protocol:
For RNA-seq experiments, cells were harvested in early-exponential phase (15 h), transition phase (18.5 h), late-exponential phase (28 h), and stationary phase (48 h).
Total RNA was isolated from obtained cell lysate by phenol-chloroform extraction and ethanol precipitation. Isolated total RNA was incubated at 37oC for 1 h with DNase I (New England Biolabs) to remove genomic DNA. Total RNA was further purified by phenol-chloroform extraction and ethanol precipitation. Quality of the isolated total RNA was checked by visualization using 2% agarose gel electrophoresis.
Ribosomal RNA was specifically removed using Ribo-ZeroTM kit (Epicentre). Strand-specific RNA sequencing libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc) according to manufacturer’s instructions. Briefly, mRNA samples were chemically fragmented into small pieces and reverse transcribed into cDNA using reverse transcriptase and random primer. The cDNA samples’ ends were repaired and A-tailed to both ends of the cDNA. Illumina adaptors were ligated to A-tailed cDNA and the ligated products were PCR-amplified.

value: stationary


title: Drought stress for 3 day_mRNA [3-2]

city: Pyeongchang

first: Choonkyun

last: Jung

state: Gangwon

address: 1447 Pyeongchang-ro, Daehwa

department: Department of International Agricultural Biotechnology

institute: Seoul National University

data_processing:
The qualities of raw sequencing data were checked by FastQC v0.10.0.
Paired-end reads were trimmed to remove adaptor sequence, and those with a quality lower than Q30 were removed using Trimmomatic 0.32.
Trimmed reads were mapped to reference genome by HISAT2 v2.0.5 and Bowtie2 v2.2.6.
All reads were assembled into transcripts by StringTie v1.3.3b.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Excel file with fold-changes and FPKM

organism: Oryza sativa Japonica Group

source_name: Rice plants

growth_protocol: Rice seeds were germinated on MS media at 28℃ for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.

extract_protocol:
Total RNAs were extracted from rice leaves using Trizol reagent, purified with RNeasy Mini Kit and treated with DNase I.
Strand-specific total RNA- and mRNA-seq libraries were prepared by TruSeq Stranded Total RNA Sample Preparation Guide and TruSeq Stranded mRNA Sample Preparation Guide, respectively.

treatment_protocol: Watering was withheld at 5 weeks after transplanting to soil and the soil water content in each pot was adjusted to approximately 75%. Soil moisture was monitored during the drought treatment using a Soil Moisture Sensor SM150.

tag: tissue

value: Leaves

value: Five-week-old

tag: ecotype

value: Ilmi variety


title: Ribo_E2

description: ribosome bound RNA


title: TSS_TAP+

description:
RNA 5'-polyphosphatase treated total RNA
processed data file: tsukubaensis_TSS.gff

data_processing:
Library strategy: differential RNA-seq (dRNA-seq)
Adaptor sequence was trimmed from reads of the RNA-seq, dRNA-seq, and Ribo-seq data. Low quality reads (Phred quality score < 0.05) were discarded. In case of RNA-seq, reads shorter than 25 nucleotides were removed. Remained reads were mapped to the completed genome of S. tsukubaensis using CLC genomics workbench (CLC Bio) with following parameters (mismatch costs = 2, length fraction = 0.9, and similarity fraction = 0.9).
Only uniquely mapped reads were retained and the mapped reads of genes were normalized by DESeq2 package in R 27
Genome_build: Streptomyces tsukubaensis NRRL 18488. The FASTA file with transcript sequences is available on the series record (GSE97637_Stsu_CDS_seq_2.txt).
Supplementary_files_format_and_content: gff file (on series record).

extract_protocol:
Total RNA was isolated from obtained cell lysate by phenol-chloroform extraction and ethanol precipitation. Isolated total RNA was incubated at 37oC for 1 h with DNase I (New England Biolabs) to remove genomic DNA. Total RNA was further purified by phenol-chloroform extraction and ethanol precipitation. Quality of the isolated total RNA was checked by visualization using 2% agarose gel electrophoresis.
Phosphorylated RNA fragments were purified using RNeasy MinElute Cleanup Kit (Qiagen). Final library construction was performed using NEBNext Multiplex Small RNA Sample Prep Set for Illumina (New England Biolabs) according to manufacturer’s instructions. The amplified library was separated by gel electrophoresis for 120 min at 100 V on 2% SYBR gold (Bio-rad) agarose gel. Final library around 150 bp was size-selected and purified using MinElute Gel extraction kit (Qiagen).


title: TSS_TAP-

description:
total RNA
processed data file: tsukubaensis_TSS.gff


title: Ribo_T2

description: ribosome bound RNA

value: transitional


title: Ribo_S2

description: ribosome bound RNA


title: Ribo_S1

description: ribosome bound RNA


title: Ribo_L1

description: ribosome bound RNA

value: late exponential


title: Ribo_L2

description: ribosome bound RNA


title: Ribo_T1

description: ribosome bound RNA


title: pH4_T30_3

description: TPM summary.xlsx

source_name: Liquid culture

tag: ph

value: 30 min


title: Drought stress for 1 day_mRNA [1-2]


title: pH6_T30_3

description: TPM summary.xlsx

tag: time


title: pH4_T30_1

description: TPM summary.xlsx

tag: replicate


title: RNA_T2

description: total RNA


title: RNA_L1

description: total RNA


title: pH6_T30_1

description: TPM summary.xlsx


title: RNA_S1

description: total RNA


title: Well-watered control_mRNA [C-2]


title: Drought stress for 3 day_totalRNA [3-1]


title: Drought stress for 2 day_mRNA [2-2]


title: pH4_T30_2

description: TPM summary.xlsx


title: RNA_L2

description: total RNA


title: Drought stress for 2 day_totalRNA [2-1]


title: RNA_T1

description: total RNA


title: T0_3

description: TPM summary.xlsx

value: Over-night


title: pH6_T30_2

description: TPM summary.xlsx


title: RNA_E2

description: total RNA


title: Drought stress for 1 day_totalRNA [1-1]


title: T0_2

description: TPM summary.xlsx


title: S1-2D CA

description: S1 cells grown on 2D plastic plate,replication 1.

value: breast epithelium


title: Well-watered control_totalRNA [C-1]


title: T0_1

description: TPM summary.xlsx


title: RNA_E1

description: total RNA


title: wt rep2

status: Public on Oct 15 2019

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

country: Spain

institute: Universitat Politècnica de València

data_processing:
Filtering and trimming of raw sequences using Trimmomatic version 0.36 (Bolger et al., 2014)  with the following options: -threads 4 -phred33 ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:15 MINLEN:36.
Aligment with Arabidopsis genome using Hisat2 version 2.1.0 (Kim et al., 2015) with the following options: -p 4 (number of threads) --phred33 --rna-strandness R --dta-cufflinks --no-discordant and default values for all other parameters.
Transcript quantification was done with cuffdiff program of the Cufflinks version 2.2.1 package (Trapnell et al., 2012) with the following options: -p 4 --library-type fr-firststrand and default values for the rest of the parameters. Three biological replicates were used for each genotype.
Genome_build: TAIR10
Supplementary_files_format_and_content: .read_group_tracking file is a plain text file with tab-delimited columns from the cutdiff program. It shows raw fragments counts for each Arabidopsis gene, their normailzation and FPKM for each replicate and template separately.
Supplementary_files_format_and_content: The xls file is the final data file on which conclusions are made. Data is from the gene_exp.diff file generated by the CutDiff program. Non-significant genes were removed. The first sheet (gene_exp_yes.diff) are all singnificant results, the second (FC>1 UP) is the gene list induced two or more times in the cog-2D mutant vs WT plants and the third sheet (FC<1 DOWN) is the gene list represed two or more times in the COG1-2D mutant vs WT plants. Genes are ordered by differential expression (log2(fold_change)) values. Genes are annotated in the last two sheets. (inf = infinite)

source_name: Seedlings

growth_protocol: 7-days old Arabidopsis seedlings were incubated in MS media in long day conditions at 23ªC.

extract_protocol:
RNA was extreacted using the commercial kit "NuecleoSpin RNA II" from Macherey-Nagel
TruSeq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: non treated plants

tag: genotype

value: No mutant


title: wt rep1


title: cog1-2D rep0

value: Activation tagging cog1-2D mutant


title: cog1-2D rep1


title: wt rep0


title: RGF1 rep1

city: Durham

first: Philip

middle: Norman

last: Benfey

address: Science Drive, Biology Department, Box 90338

department: Biology

institute: Duke University & HHMI

data_processing:
Illumina sequencing reads were mapped to TAIR10 Arabidopsis genome using Tophat V2.1.1. The parameters used for mapping are as follows :“-N 5 --read-gap-length 5 --read-edit-dist 5 --b2-sensitive -r 100 --mate-std-dev 150 -p 5 -i 5 -I 15000 --min-segment-intron 5 --max-segment-intron 15000 --library-type fr-unstranded”.
To select properly mapped reads with unique mapping positions, only alignments with flag of 83, 99, 147 or 163 and a mapping quality score of 50 were kept for further analysis. Mapping positions of these reads were compared with the Araport11 genome annotation (https://www.araport.org/downloads/Araport11_Release_201606/annotation) using HTseq-count generated read count per gene with parameters “--stranded=no --mode=intersection-nonempty”. The raw read counts of miRNA, lncRNA and protein coding genes were then used as input into DESeq2 for differential gene expression analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read counts for each sample.

source_name: root meristem

extract_protocol:
Using an ophthalmic scalpel (Feather), the meristematic zone of the seedlings was precisely dissected based on HYP2-GFP fluorescence as detected under a dissecting microscope (Axio Zoom, Zeiss). Total RNA was extracted from 20 root sections treated with mock or 100nM RGF1 using the RNeasy Micro Kit (Qiagen). For each treatment, three replicates of the RNA extractions were performed. All total RNA samples were treated with DNaseI during RNA extraction.
RNA quality was examined using a 2100 Bioanalyzer (Agilent). The RNA Integrity Number (RIN) was over 9.0 in all samples. The concentration of total RNA was measured by a Qubit (Invitrogen) instrument. For each replicate, 50ng total RNA was amplified using the Ovation RNA-seq System V2 (NuGEN). Following amplification, 3μg of cDNA was fragmented using the Covaris S-Series System. 400ng of the fragmented cDNA with an average size of 400bp was used for library preparation using the Ovation Ultralow System V2 (NuGEN).

treatment_protocol: The HYP2-GFP(5) lines were grown on MS plates for 6 days. HYP2-GFP seedlings were then transferred into liquid MS media and treated with water (mock) or 100nM RGF1 peptide in 6-well-plates for 1h. After 1h treatment with mock or RGF1, the seedlings were taken out of liquid MS media and transferred onto a 2% agarose plate.

tag: genotype/variation

value: homozygous transgenic, HYP2-GFP introduced into WT

value: root meristem

value: 6 days after germination


title: Mock rep1

tag: age

value: Mock


title: cog1-2D rep2


title: RGF1 rep3


title: RGF1 rep2


title: Mock rep3


title: Mock rep2


title: Col_GBM_1mo_noFBS_n2

city: Medford

first: David

middle: L.

last: Kaplan

state: MA

address: 4 Colby Street

institute: Tufts University

description:
18-Lau-001-18
processed data file: ProcessedRNASeqData_DS-DK.xlsx

data_processing:
Illumina Bcl2Fastq v2.17.1.14 software used for basecalling.
Sequencing read were mapped to hg38tran (iGenome) using HISAT2.
FPKM value estimated with Cufflinks.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: ProcessedRNASeqData_DS-DK.xlsx: Excel file includes FPKM values for each Sample.

source_name: Tumor

extract_protocol:
Samples were flash frozen in liquid nitrogen and stored in -80 oC in individual RNase free eppendorf tubes until RNA extraction was performed. All samples were placed on dry ice during extraction, sequentially disrupted using a liquid nitrogen chilled bio-pulverizer. Between each sample, the pulverizer was wiped with 70% ethanol to remove remnants of the previous sample, and between each sample set (different conditions), all the tools were cleaned with RNAzap. Lysis buffer was immediately added to the powdered frozen sample and placed on ice. Once all the samples were in lysis buffer on ice, a 22-gauge needle and syringe were used for sample homogenization one by one using a fresh needle and syringe every time. All the samples were spun down to remove undigested material (mainly silk scaffold) and the supernatant was transferred to clean RNase free eppendorfs. Following this, the SurePrep All Prep kit (Fischer Scientific) protocol was followed until RNA was eluted from the columns.
KAPA mRNA stranded library.

tag: diagnosis

value: GBM

value: Brain tumor

tag: tumor stage

value: Grade IV

tag: patient age

value: 55 yrs

tag: media

value: serum free

tag: time point

tag: ecm condition

value: Col


title: Col_Ependymoma_2wk_noFBS

description:
18-Lau-001-15
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: Ependymoma

value: Grade III

value: 2 yrs


title: Col_GBM_1mo_noFBS_n1

description:
18-Lau-001-17
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: AECM_Ependymoma_1.5mo_noFBS

description:
18-Lau-001-21
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: AECM


title: Col_Ependymoma_4mo_noFBS

description:
18-Lau-001-16
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: FECM_Ependymoma_1.5mo_noFBS

description:
18-Lau-001-19
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: FECM


title: AECM_GBM_1mo_noFBS_n1

description:
18-Lau-001-11
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: PKC activator

city: Québec

first: Patricia

middle: G

last: Tremblay

state: Québec

address: 2440 Hochelaga Blvd

department: Sciences animales

country: Canada

institute: Laval University

data_processing:
Using Trimmomatic, sequencing adapters were removed and base calls with a quality score below 30 were removed from the end of the reads. Reads with a minimum length of 32nt were kept for further processing. The abundances for all transcripts described in release 91 of ENSEMBL cdna gene annotation were estimated using kallisto . Differential expression of genes were then assessed using pairwise comparisons in edgeR . Lacking replicates, dispersion within edgeR was evaluated by grouping samples for similar comparisons (First for control, then for FSH, FSK, PMA and SC79 samples) and dropping the factor with the lowest impact, as suggested by the edgeR manual.
Genome_build: Ensembl (release 91)
Supplementary_files_format_and_content: tab-delimited text files include  transcript tsl, log Fold change, p-value, adjsuted p-value for each Sample ...

source_name: KGN cells

growth_protocol: KGN cells were thawed on day 1, placed in a cell culture flask (25 cm3, Sigma-Aldrich) and sub-cultured on day 3. Confluence was never over 80%. On day 6, viable cells were placed in a 6-well dish at the density of 3x10^5 per well in 3 ml of medium and grown for 72 h.

extract_protocol:
Total RNA was isolated with AllPrep DNA/RNA Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions. Total RNA integrity and concentration were evaluated on a 2100-Bioanalyzer (Agilent Technologies, Palo Alto, CA). For all samples RNA Integrity Number was 10.
The total RNA input used for sequencing was 270 ng for each treatment, a pool of 90 ng for each biological replicates. mRNA was isolated from total RNA using NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490S; NEB). PolyA-selected mRNA was fragmented to a mean size of 200 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired-end library using NEBNext Ultra RNA Library Prep kit for Illumina (E7530S; NEB) according to the manufacturer’s instructions, using Agencourt AMPure XP beads and NEBNext Mutliplex Oligos for Illumina (set1, E7335S; NEB).

treatment_protocol: For all experimental conditions, the medium was replaced with charcoal-stripped (SVFA) DMEM/F12 containing antibiotics and 100 nmol L-1 of 4-androstene-3,17-dione. The 24h treatments consisted of adding either ethanol (less than 0.05% of the culture volume) as a control or additional stimulator in ethanol to obtain either 10 mol of FSK L - 1,0.1 mol of PMA L-1, 100 ng/mL of FSH or 4 ug/mL of SC79 for final concentrations. The experiment was repeated 3 times (3 different weeks) for the RNAseq analysis and other 3 times (3 weeks) for validation by RT-qPCR.

tag: cell line

value: KGN cells

tag: cell type

value: granulosa cells

tag: treatment

value: 0.1 mmol of PMA/L


title: FSH treatment

value: 100 ng/mL of FSH


title: FECM_Ependymoma_1.5mo_FBS

description:
18-Lau-001-20
processed data file: ProcessedRNASeqData_DS-DK.xlsx

tag: tissue

value: FBS


title: AECM_Ependymoma_1.5mo_FBS

description:
18-Lau-001-22
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: PKA activator

value: 10 mmol of FSK/L


title: AECM_Ependymoma_4mo_noFBS

description:
18-Lau-001-10
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: PKB activator

value: 4 ug/mL of SC79


title: CTRL (no treatment)


title: AECM_GBM_1mo_noFBS_n2

description:
18-Lau-001-12
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: GBM

value: Brain tumor


title: AECM_Ependymoma_2wk_noFBS

description:
18-Lau-001-09
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: VL cr biological rep2

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

description: Gene expression data from monkeys consuming a calorie restricted diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Macaca mulatta

source_name: Vastus lateralis muscle, Calorie Restricted diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

tag: gender

value: male

tag: diet

value: calorie restricted


title: VL cr biological rep3


title: VL control biological rep1

description: Gene expression data from monkeys consuming a control diet

source_name: Vastus lateralis muscle, Control diet

value: control


title: VL cr biological rep4


title: VL control biological rep5


title: VL control biological rep2


title: VL cr biological rep1


title: VL control biological rep3


title: VL cr biological rep6


title: FECM_GBM_1mo_noFBS_n1

description:
18-Lau-001-05
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: Grade IV

value: 55 yrs

value: serum free


title: VL cr biological rep7


title: VL cr biological rep5


title: FECM_Ependymoma_4mo_noFBS

description:
18-Lau-001-04
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: Ependymoma

value: Grade III

value: 2 yrs


title: FECM_Ependymoma_2wk_noFBS

description:
18-Lau-001-03
processed data file: ProcessedRNASeqData_DS-DK.xlsx

value: FECM


title: mRNA_bgcn3_lane2

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

description:
mRNA sequencing of bgcn mutants Stranded polyA-selected RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
bgcn_vs_WT_DGE.xls

data_processing:
Basecalls performed using CASAVA version 1.4
For only smallRNA-Seq samples trimming of Illumina 3' adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG) was performed.
Alignment to the Drosophila genome using either bowtie, bowtie2, TopHat, or STAR depending on the original sequencing data type (see methods for details).
Scanning of genome for potential piRNA clusters.
Statistical testing for significance of differential expression of firstly genomic and TE derived mRNA. Secondly additional significance testing of changes in piRNA cluster, transposable element, and genomic mRNA 3'UTR using custom R scripts.
Tabulation of each different type of standard smallRNAs with known annotation (i.e. miRNA, tRNA, siRNA, rRNA, etc…).
Genome_build: Ensembl dm6 v90
Supplementary_files_format_and_content: Bed file containing the coordinates of the algorithmically determined large putative piRNA clusters for smallRNA samples. DGE matricies output from edgeR for mRNA samples.

source_name: Whole ovary

growth_protocol: The vasa-GFP; hs-bam bam∆86/ bam∆86 GSC line was established according to the published procedures (Niki et al. 2006)

extract_protocol:
Mutant and wildtype ovary samples were dissected in ice cold Grace Medium for RNA isolation. The GFP-positive GSCs and GFP-negative SCs were purified by sorting dissociated single cells at 20 psi with 100 um tip (BD, InFlux) immediately into TRIzol LS Reagent (Thermo Fisher Scientific, 10296028) for total RNA isolation.
Standard Illumina TruSeq Stranded mRNA-seq or smallRNA-seq.  For FACS sorted cells, prior to RNA isolation, spike-in RNA standards from ExiSEQ NGS spike-in kit (ExiSEQ, 800100) were added to the samples.

tag: stock


title: mRNA_bam86-E5-1_lane2

description:
mRNA sequencing of bam mutants Stranded polyA-selected RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
bam_vs_WT_DGE.xls


title: mRNA_WT3

description:
mRNA sequencing of WT mutants Stranded polyA-selected RNA
WT_vs_WT_DGE.xls


title: VL cr biological rep8


title: mRNA_bam86-E5-2_lane2


title: mRNA_bam86-E5-1

description:
mRNA sequencing of bam mutants Stranded polyA-selected RNA
bam_vs_WT_DGE.xls


title: mRNA_bam86-E5-3_lane2


title: mRNA_tkvM1-2_lane2

description:
mRNA sequencing of tkv mutants Stranded polyA-selected RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
tkv_vs_WT_DGE.xls


title: mRNA_tkvM1-1_lane2


title: mRNA_bam86-E5-3


title: FECM_GBM_1mo_noFBS_n2

description:
18-Lau-001-06
processed data file: ProcessedRNASeqData_DS-DK.xlsx


title: mRNA_WT2_lane2

description:
mRNA sequencing of WT mutants Stranded polyA-selected RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
WT_vs_WT_DGE.xls


title: mRNA_bgcn2

description:
mRNA sequencing of bgcn mutants Stranded polyA-selected RNA
bgcn_vs_WT_DGE.xls


title: mRNA_WT1_lane2


title: mRNA_WT3_lane2


title: VL control biological rep4


title: mRNA_tkvM1-3

description:
mRNA sequencing of tkv mutants Stranded polyA-selected RNA
tkv_vs_WT_DGE.xls


title: mRNA_bgcn1


title: mRNA_bgcn3


title: mRNA_tkvM1-2


title: mRNA_bam86-E5-2


title: mRNA_WT2


title: mRNA_SC2

description:
mRNA sequencing of SC mutants Stranded polyA-selected RNA
GSC_vs_SC_DGE.xls

source_name: cultured SCs


title: mRNA_SC1


title: smallRNA_bam86-E5-3_lane2

description:
smallRNA sequencing of bam mutants;Size fractionated (20-70 nt) RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
new_clusters.bed


title: smallRNA_tkvM1-1_lane2

description:
smallRNA sequencing of tkv mutants;Size fractionated (20-70 nt) RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
new_clusters.bed


title: smallRNA_tkvM1-2_lane2


title: smallRNA_WT1_lane2

description:
smallRNA sequencing of WT mutants;Size fractionated (20-70 nt) RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
new_clusters.bed


title: smallRNA_bgcn-1_lane2

description:
smallRNA sequencing of bgcn mutants;Size fractionated (20-70 nt) RNA; Sample sequenced across multiple lanes; Merge with sample with the same name not including "_lane2"
new_clusters.bed


title: smallRNA_bam86-E5-1_lane2


title: mRNA_GSC3

description:
mRNA sequencing of GSC mutants Stranded polyA-selected RNA
GSC_vs_SC_DGE.xls

source_name: cultured GSCs


title: mRNA_WT1


title: smallRNA_WT3_lane2


title: mRNA_GSC2


title: smallRNA_WT2_lane2


title: mRNA_GSC1


title: smallRNA_WT2

description:
smallRNA sequencing of WT mutants;Size fractionated (20-70 nt) RNA
new_clusters.bed


title: smallRNA_bgcn3_lane2


title: smallRNA_bam86-E5-2_lane2


title: mRNA_tkvM1-1


title: smallRNA_tkvM1-3_lane2


title: smallRNA_bgcn3

description:
smallRNA sequencing of bgcn mutants;Size fractionated (20-70 nt) RNA
new_clusters.bed


title: mRNA_SC3


title: smallRNA_tkvM1-1

description:
smallRNA sequencing of tkv mutants;Size fractionated (20-70 nt) RNA
new_clusters.bed


title: smallRNA_bgcn2_lane2


title: smallRNA_tkvM1-3


title: smallRNA_bam86-E5-1

description:
smallRNA sequencing of bam mutants;Size fractionated (20-70 nt) RNA
new_clusters.bed


title: smallRNA_WT3


title: smallRNA_WT1


title: smallRNA_bgcn-1


title: smallRNA_tkvM1-2


title: smallRNA_bgcn2


title: smallRNA_bam86-E5-3


title: smallRNA_SC3

description:
smallRNA sequencing of SC mutants;Size fractionated (20-70 nt) RNA
new_clusters.bed


title: smallRNA_GSC2

description:
smallRNA sequencing of GSC mutants;Size fractionated (20-70 nt) RNA
new_clusters.bed


title: smallRNA_GSC3


title: smallRNA_GSC1


title: npr8_PA14_2

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
htseq-count from HTSeq v0.10.0 was used to quantify genes and transcripts.
DESeq2 v1.22.1 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: npr-8(ok1439), 24-hrs exposure to P. aeruginosa

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain OP50.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli OP50 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with P. aeruginosa PA14 for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.  Total RNA was extracted.

tag: strain

value: 1-day old young adult

tag: infection

value: 24-hrs exposure to P. aeruginosa

value: whole animal


title: npr8_PA14_3


title: npr8_PA14_1


title: npr8_PA14_4


title: npr8_OP50_3

source_name: npr-8(ok1439), uninfected

value: uninfected


title: npr8_OP50_2


title: npr8_OP50_1


title: npr8_OP50_4


title: npr8_PA14_5


title: 17338_BDP5cntrlT26no

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

department: Molecular Biology

institute: Radboud University

data_processing:
Reads were mapped using BWA aln and BWA sampe to the P. falciparum 3D7 AnnotatedTranscriptome and Genome (PlasmoDB release 26). Libaries were filtered for mapping quality 30 (-q 30) , unmapped reads  (-F 4) were removed and uniquely mapping reads were selected for (flag XT:A:U). Reads mapping in sense were selected with flags '-f 128 -F 16' or '-f80'. Reads mapping in antisense were selected with flags  '-f 144' or '-f 64 -F 16'. Data mapped against the Genome were converted to bedgraph files scaled per million reads using the bedtools genomecov command (v2.29.0). Data mapped against the annotated transcriptome were used to extract tags per transcript and generate the counts table.
Genome_build: PlasmoDB release 26 Plasmodium falciparum 3D7 Genome; PlasmoDB release 26 Plasmodium falciparum 3D7 AnnotatedTranscriptome
Supplementary_files_format_and_content: bedgraph files were generated using bedtools genomecov; Scores represent permillion scaled coverage. Count.txt is tab-delimited text file with counts or RPKM values for each sample in sense and antisense.

organism: Plasmodium falciparum

source_name: red blood cell stage, ~26hour post red blood cell invasion

growth_protocol: Blood-stage parasites with genotypes "bdp5/taf1-2xFKBP-GF-2xFKBP (integrated) + Lyn-FRB-T2A-mCherry (DHODH plasmid)" and "bdp5/taf1-2xFKBP-GF-2xFKBP (integrated)" were maintained in a 37 °C incubator under low oxygen conditions (gas composition 3% O2, 4% CO2 and 93% N2) in human O+ red blood cells at 5% hematocrit in standard RPMI medium supplemented with 0.5% Albumax (Life Technologies) and 0.2% NaHCO3. Genomtypes were maintained by drug pressure indicted  in the 'sample' sections. Cultures were expanded and synchronized with multiple rounds of sorbitol treatments.

extract_protocol:
RNA isolation: At 2, 6 and 12 hours post induction (corresponding to 16, 20 and 26 hours post red blood cell invasion), parasite cultures were immediately placed on ice and filtered once over a Plasmodipur filter to remove remaining leukocytes. Pelleted cultures were resuspended in RLT buffer (Qiagen, #74106) supplemented with 1% β-mercaptoethanol and snap-frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, #74106; including RNA clean-up and two on-column DNase treatments), eluates were treated with Ambion TURBO DNase and again purified over RNeasy columns with on-column DNase treatment. PolyA-selection was performed on at least 2 μg of total RNA using the Oligotex mRNA Mini Kit (Qiagen, #70022) according to manufacturer’s instructions. 2000ng of PolyA-selected total RNA equivalent was fragmented by alkaline hydrolysis (40mM Tris acetate pH 8.2, 100mM potassium acetate,30mM magnesium acetate) in 150 ul aliqutoes for 1min 45sec at 85°C in a 150µl volume and precipitated as previously described in (Hoeijmakers et al., 2013). Next, PolyA-selected RNA was cleaned from remaining genomic DNA (detected by qPCR) by two additional TURBO DNase treatments (Ambion, #AM2238).
Strand-specific RNA-seq was performed as in (Kensche et al., 2015). Accordingly, first strand cDNA synthesis was performed with AT-corrected Random N9 primers (76% AT) in the presence of 0.2µg Actinomycin D (Thermo 446 Fisher Scientific). During second strand synthesis dTTPs were substituted with dUTPs to preserve strand-specific information. Next, 20 ng of each double stranded cDNA library was end repaired, extended with 3’ A-overhangs, barcoded with NextFlex adapters (Bio Scientific, #514122) and treated with USER enzyme (NEB, #M5505L) to specifically degrade the dUTP-containing second strand. Libraries were amplified by PCR (98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems, #KM2602) and NEXTflex primer mix (Bio Scientific, #514122) and subsequently gel size-selected for 300 - 400 bp using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02). After an additional ten cycles of amplification (see above), libraries were purified and adapter dimers depleted using 1x volume of Agencourt AMPure XP beads (Beckman Coulter, #A63880).

treatment_protocol: At 14 hours post red blood cell invasion invasion, cultures from each line were split and half was put on 250 nM rapalog.

tag: developmental stage

value: late trophozoite

tag: genotype

value: bdp5/taf1-2xFKBP-GF-2xFKBP (integrated)

tag: timepoint

value: 26 hours post invasion

tag: selection pressure drugs

value: 400 µg/ml Geneticin G-418 Sulpate (Geneticin Selective Antibiotic (G418 Sulpate), Gibco, Thermo Fisher Scientific, cat# 11811031)


title: 17339_BDP5cntrlT26plR

value: 250 nM rapalog


title: 17337_BDP5ksT26plR

value: bdp5/taf1-2xFKBP-GF-2xFKBP (integrated) + Lyn-FRB-T2A-mCherry (DHODH plasmid)

value: 400 µg/ml Geneticin G-418 Sulpate (Geneticin Selective Antibiotic (G418 Sulpate), Gibco, Thermo Fisher Scientific, cat# 11811031) + 0.9 μM DSM1 (MRA-590 1161, supplied by MR4/BEI Resources, NIAID, NIH)


title: 17336_BDP5ksT26no


title: smallRNA_bam86-E5-2


title: 17335_BDP5ksT20plR

source_name: red blood cell stage, ~20hour post red blood cell invasion

value: early trophozoite

value: 20 hours post invasion


title: gata2a+ runx1-

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

institute: Kanazawa University

data_processing:
Illumina RTA software was used for base-calling.
Sequence reads were mapped to the zebrafish reference genome (GRCz11) using HiSAT2 (version 2.1.0).
Reads per million (RPM) were calculated using the Subread (ver. 1.6.4).
Genome_build: GRCz11
Supplementary_files_format_and_content: Reads per million (RPM) values for each sample.

source_name: lymphoid-primed progenitors

extract_protocol:
Total RNAs were extracted from sorted cells using RNeasy Mini Kit (QIAGEN).
Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic-polycytidylic acid, and total RNA was extracted using RNeasy Mini Kit. Reverse transcription (RT) was performed using Super Script III (Thermo Fisher Scientific) and an RT primer, which contains oligo-dT, T7 promoter, and PCR target region sequences. After digestion of remaining RT primers by exonuclease I (Takara), a poly-A tail was added to the 3’ ends of the first-strand cDNAs using terminal transferase (Sigma). The second-strand DNA was then synthesized using MightyAmp DNA polymerase (Thermo Fisher Scientific) and a tagging primer, which contains oligo-dT and PCR target region sequences. PCR amplification was performed using a suppression primer, which allow to amplify small-size DNA that contains complementary sequences at both ends of the template DNA. The amplified double-strand cDNA was purified using QIAquick PCR Purification Kit (Qiagen). Library preparation was performed using Nextera XT DNA Library Preparation Kit (illumina).

value: Sorted cells from the kidney

value: gata2a+ runx1-

tag: age

value: adult

value: wild type


title: gata2a+ runx1+

source_name: HSCs

value: gata2a+ runx1+


title: npr8_OP50_5

value: 1-day old young adult


title: smallRNA_SC2


title: smallRNA_SC1


title: 17332_BDP5ksT16no

source_name: red blood cell stage, ~16hour post red blood cell invasion

value: late ring stage

value: 16 hours post invasion


title: 17333_BDP5ksT16plR


title: 17334_BDP5ksT20no


title: s13P_NS human liver cancer adjacent tissue

city: Shanghai

first: Ji-Min

last: Zhu

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital of Fudan University

description: Microarray profile of miRNA in the adjacent tissue of Hepatocellular carcinoma

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: human liver cancer adjacent tissue

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: 7 pairs of HCC and matched adjacent tumor-free tissues were collected during the surgery from HCC patients admitted to Zhongshan Hospital of Fudan University between 2008 and 2009 and All tissue samples were stored at -80℃ immediately after surgery

tag: disease state

value: hepatocellular carcinoma matched adjacent tissue

value: Male


title: s13T_NS human liver cancer tissue

source_name: human liver cancer tissue

value: hepatocellular carcinoma tissue


title: CA_shMETTL3_meRIP_rep1

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
caRNA
CA_shMETTL3_meRIP_rep1

data_processing:
For meRIP-seq (IP) and RNA-seq (input), adaptor sequences and library tails were removed by Cutadapt. Low-quality bases were trimmed using Trimmomatic48. Reads shorter than 18 nt were discarded. The remaining reads were mapped to hg19 (human) through Tophat2 with default parameters. Mapping quality less than 20 were removed by samtools. MACS2 (version 2.0.10) was used to call peaks between IP and input with the parameters --keep-dup all, --nomodel and -- extsize 100.
For miCLIP-seq data, fastx_clipper was used to remove adaptor sequences. R2 reads were transformed to reverse complementary sequences and merged with R1 reads. PolyA tails were trimmed by Cutadapt. Duplicated reads were removed by fastq2collapse. stripBarcode.pl was used to strip barcodes of remaining reads. The low-quality bases were trimmed and reads shorter than 18 nt were discarded. The remaining reads were mapped to hg19 (human) by BWA (version 0.7.10) with the parameter: -n 0.06. parseAlignment.pl (--map-qual 1 --min-len 18) and tag2collapse.pl (-EM 30 --seq-error-model alignment) were used to extract mutation information and remove PCR duplicates. The coverage (k) of mutation site and transition number (m) were calculated by CIMS.pl. The mutation sites with k ≥ 10, m ≥ 2, k/m ≥ 0.01 and k/m ≤ 0.5 were kept.
Genome_build: hg19
Supplementary_files_format_and_content: m6C sites generated by miCLIP-seq

source_name: HeLa cell

extract_protocol:
Cells were washed with cold PBS twice and scraped from the plates, then centrifuged at 1000 rpm for 5 min to pellet cells. Washed cells were lysed with 400 L of cell lysis buffer (10 mM Tris-HCl pH7.5, 150 mM NaCl, 0.15% NP-40 and proteinase inhibitor cocktail) and incubated on ice for 10 min. The suspension was carefully add at the top of sucrose buffer (10 mM Tris-HCl pH7.5, 150 mM NaCl, 24% sucrose), and centrifuged at 3200g for 10 min to collect nuclear pellets. Pellets were resuspended in 250 L of Glycerol buffer (20 mM Tris-HCl pH7.5, 75 mM NaCl, 0.5 mM EDTA pH8.0, 50% glycerol), then then immediately add 250 μl Nuclear lysis buffer (10 mM Tris-HCl pH7.5, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA pH8.0, 1% NP-40, 1M urea). Mix by vortexing for 4 s and incubate on ice for 2 min. Centrifuge the lysate at 13,000 × g for 2 min to precipitate the chromatin–RNA complex. Brieﬂy rinse the chromatin pellets with PBS-EDTA. RNA was extracted with Trizol reagent.
RNA libraries were prepared according to manual of SMARTer smRNA-Seq Kit for Illumina (Clontech, 635031).

value: HeLa cell

tag: antibody

value: anti- m6A (abcam, ab151230)


title: mRNA_shCTRL_miclip_rep1

description:
polyA RNA
mRNA_shCTRL_miclip_rep1
mRNA_shCTRL_miclip.bed


title: s11T_NS human liver cancer tissue

value: Female


title: s19P_NS human liver cancer adjacent tissue


title: s19T_NS human liver cancer tissue


title: ribo_shCTRL_miclip_rep1

description:
ribominuse RNA
ribo_shCTRL_miclip_rep1
ribo_shCTRL_miclip.bed


title: s10P_NS human liver cancer adjacent tissue


title: s6T_NS human liver cancer tissue


title: s5P_NS human liver cancer adjacent tissue


title: s6P_NS human liver cancer adjacent tissue


title: s11P_NS human liver cancer adjacent tissue


title: s5T_NS human liver cancer tissue


title: CA_shMETTL3_input_rep1

description:
caRNA
CA_shMETTL3_input_rep1


title: CA_shCTRL_miclip_rep1

description:
caRNA
CA_shCTRL_miclip_rep1
CA_shCTRL_miclip.bed


title: CA_shCTRL_miclip_rep2

description:
caRNA
CA_shCTRL_miclip_rep2