title: PARP1_PAR-CLiP

data_processing:
PAR-CLiP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) sequencing for PARP-1 binding in the human genome was performed in two runs by the Genomic Sequencing Facility at the University of California-Berkeley on 10/22/2015 and 11/23/2015 using an Illumina HiSeq 2500 v2 rapid mode.  The first dataset was a pilot study in order to test out the sample construction for PAR-CLiP data.  As a result, a number of primer-dimers and adapter dimers were thought to occur.  The second dataset fixed these technical issues.  The replicates in each study are technical replicates, with variation on the technical steps taken to prepare samples.   All samples were combined into a single pooled sample set.
Base-calling was performed using CASAVA bcl2fastq_v2.17.
GSL was used to demultiplex data.
Adapters and primers were trimmed using Trimmomatic v0.33
Quality control was performed using FastQC v0.11.4
Trimmed reads were then concatenated as single-end reads and aligned to the human hg38.  Reads were aligned to the genome first without a reference transcriptome using bowtie v1.1.1 and then with a reference transcriptome using tophat v2.0.13 and the Ensembl v82 gtf
PAR-CLiP peaks were detected using PARalyzer v1.5.
Results from PARalyzer were then parsed into evidence and sequence files for input into the motif detection program cERMIT v1.0.1 .
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated file of PARalyzer-detected peaks

source_name: HeLa cell lines

growth_protocol: HeLa cells were used for PAR-CLiP experiments – a human cell line, derived from cervical cancer cells. Cells were grown at 37°C in a humidified environment containing 5% CO2 and 95% air in Dulbecco’s modified Eagle’s medium (Sigma) containing 1 mM sodium pyruvate, 0.1 mM nonessential amino acids and supplemented with 10 % fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin. For each experiment, approximately 6 × 108 cells (~ 60 X 15 cm cell culture plates) were used.

extract_protocol:
PAR-CLIP was performed as previously described (Spitzer et al, 2014) with some modifications. Briefly, 10 ml of packed cell pellet - UV-treated cells, were lysed with 3 volumes of 1× NP40 lysis buffer on ice for 5 mins. Cells were pelleted by centrifugation at 18,000g for 15 min using an Eppendorf 5810R centrifuge 5810R with an A-4-81swing bucket rotor.  The supernatant was filtered using a 5 µm syringe filter (Nalgene) to remove cellular debris. The filtrate was then partially treated with RNase T1 (Roche) to a final concentration of 1 U/µl for 15 min. The supernatant was then incubated with 600 μl of protein A dynabeads (Invitrogen) bound to 15 μg of anti-PARP1 antibody (Active Motif) or control IgG antibody for 2 h. The beads were washed 3 times and the immunoprecipitated RNA was digested again with RNase T1 to a final concentration of 63 U/µl for 15 min.  After dephosphorylation, the RNA segments crosslinked to PARP1 were 5’-radiolabeled using γ-32P-ATP and T4 polynucleotide kinase (Promega) in one original bead volume. After several washes, each CLIP sample (on the beads) was then treated with 5U of DNase1 (NEB) for every 100 μl of bead volume for 15 min at 37°C. DNase1 was inactivated by adding 5 mM EDTA and heated at 65°C for 10min. Samples were then resuspended in SDS-PAGE loading buffer, incubated at 95°C for 5 min to denature and release the PARP1-RNA cross-links. The samples were then separated on 4 –12 % NuPAGE gels (Invitrogen) and transferred onto nitrocellulose membranes (1/10th of the sample was used for immunoblotting and the rest of the sample was used for autoradiography). The gel containing 1/10th of the sample and the membrane containing 9/10th of the sample were exposed to a phosphorimager screen overnight and visualized by scanning on a Typhoon FLA 9500. PARP1–RNA complexes were cut from the membrane, treated with proteinase K (Roche) followed by Phenol/Chloroform/IAA extractions and ethanol precipitation. The recovered RNA further was used for cDNA library preparation.
For this purpose we used NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1). Library preparation including 3’ and 5’ SR Adaptor ligations, reverse transcription and PCR amplification, were performed per manufacturer’s protocol. To remove adaptor-only ligation products, after every step of the protocol (3’adapter ligation and 5’adapter ligation) samples were purified using 15% acrylamide-8M Urea gels. Lastly after limited PCR amplification PCR products were size-selected on a 3.5% NuSieve (Lonza) low-melting point agarose gel. Expectant PCR products were eluted using the ‘crush and soak’ method, followed by purification using a Qiagen min-elute PCR column. Samples were then first cloned into the Topo TA vector for pilot analysis and then sequenced using Illumina sequencing.

value: HeLa

value: anti-PARP1 antibody (Active Motif 39559)


title: B4

status: Public on Feb 14 2018

type: SRA

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

country: USA

institute: Purdue University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was observed using FastQC v. 0.11.2
quality trimming was performed using FastX-Toolkit version 0.0.14 with a trimscore of 30 and a trim length of 50
Topha2t version 2.1.0 was used to align trimmed reads to the human genome with default parameters other than that 1 mismatch was allowed
The htseq-count script was used in HTSeq v 0.6.1 to count the number of reads mapping to each gene.  HTSeq used Biopython v.2.7.3.
BPSC in R, version 0.99.1 was used to determine normalize genes based on library size and to identify differentially expressed genes. A Benjamini-Hochmerg FDR of 0.05 was used as the cutoff.
IPA version
Genome_build: ENSEMBL version GrCh38.p7
Supplementary_files_format_and_content: counts generated from HTSeq are provided, along with 5 rows at the end of the matrix which include information about where reads aligned in the genome, how many alignments there were for each, etc.

molecule: total RNA

organism: Homo sapiens

source_name: low passage patient-derived PDAC cells

growth_protocol: All cells were maintained at 37 degrees Celsius in 5% Carbon dioxide and grown in DMEM.

extract_protocol:
The C1 fluidigm instrument was used to capture single cells, extract RNA, reverse transcribe cDNA using the SMARTer system.
The Nextera kit was used to prepare the library.

treatment_protocol: To transfect cells 1x10^5 cells were plated per well of a 6-well plate and allowed to attach overnight.  The next dat Lipofectamine RNAiMax reagent was used to transfect according to the manufacturer's protocol.

tag: transfection

value: APE1 siRNA


title: NSC11 cells treated with 2Gy, collected at 1h, Polysome-bound RNA RNA, biological replicate 6

city: Bethesda

first: Philip

middle: J

last: Tofilon

state: Maryland

address: 10 Center Drive-MSC 1002

department: Radiation Oncology

institute: NCI

description: Polysome-bound RNA

data_processing:
The HiSeq Real Time Analysis software (RTA 1.18) was used for processing image files, the Illumina CASAVA_v1.8.4 was used for demultiplex and converting binary base calls and qualities to fastq format.
The sequencing reads were trimmed of adapters and low quality bases using Trimmomatic (version 0.3), the trimmed reads were aligned to human hg19 reference genome (GRCh37/UCSC hg19) and Ensembl annotation version 70 using TopHat_v2.0.8 software.
Given the aligned sequencing reads and a list of genomic features, counts of mapped reads for each gene were calculated using HTSeq
A table of RNA-Seq read counts covering the entire length of transcripts was assembled in R.
Pairwise differential expression analyses between untreated control and irradiated groups for polysome-bound RNA or total RNA samples was conducted with the DESeq2 package, which provides read counts per gene and fold changes between treatments
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: GSC cells

growth_protocol: GSC enerated from a glioblastoma surgical specimen. Neurospheres were maintained in stem cell medium consisting of DMEM/F12 (Invitrogen), B27 supplement (Invitrogen), and human recombinant bFGF and EGF (50 ng/ml each, R&D Systems) at 37°C, 5%CO2/5%O2

extract_protocol:
For polysome-bound RNA, cells incubated in 100 μg of cycloheximide/mL for 15 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1 mL of polysome buffer [15 mmol/L Tris-HCl (pH 7.5), 300 mmol/L NaCl, 15 mmol/L MgCl2, 1% Triton X100, 100 μg/mL cycloheximide, 1 mg/mL heparin, and 500 units/mL RNasin (Promega)]. After 15 minutes on ice, lysates were centrifuged (12,000 × g for 15 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 × g for 3 hours at 4°C and polysome-bound fractions were collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIzol LS (Invitrogen).  Trizol extraction of total RNA was performed according to the manufacturer's instructions.
between 100ng to 1µg of total RNA was used as the input for mRNA capture with oligo-dT coated magnetic beads.  The mRNA was fragmented followed by random-primed cDNA synthesis. The resulting double-strand cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification to generate a sequencing ready library.  The final library was then quantitated by qPCR before cluster generation and sequencing on the Illumina HiSeq2500 sequencer.

treatment_protocol: Cells were grown to ∼80% confluence in 150-mm2 tissue culture dishes and mock irradiated or irradiated with 2Gy and collected  1h after.  Radiation was delivered using a 320 kV X-ray machine (Precision XRay Inc.) at a dose rate of 2.3 Gy/min.

tag: strain

tag: tissue

value: Glioblastoma stem-like cells


title: NSC11 cells mock irradiated, collected at 1h, Polysome-bound RNA, biological replicate 5

description: Polysome-bound RNA


title: B3


title: NSC11 cells treated with 2Gy, collected at 1h, Polysome-bound RNA RNA, biological replicate 5

description: Polysome-bound RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Polysome-bound RNA RNA, biological replicate 1

description: Polysome-bound RNA


title: NSC11 cells mock irradiated, collected at 1h, Polysome-bound RNA, biological replicate 6

description: Polysome-bound RNA


title: E6


title: NSC11 cells treated with 2Gy, collected at 1h, Polysome-bound RNA RNA, biological replicate 2

description: Polysome-bound RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Polysome-bound RNA RNA, biological replicate 4

description: Polysome-bound RNA


title: A7

value: scrambled siRNA


title: NSC11 cells treated with 2Gy, collected at 1h, Polysome-bound RNA RNA, biological replicate 3

description: Polysome-bound RNA


title: B2


title: A6


title: WT.H3N2.D1C

city: New York

first: Christian

last: Forst

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The sequencing reads were aligned to the human hg19 genome using star aligner (version 2.5.0b).
featureCounts was used to quantify gene expression at the gene and exon levels based on Ensembl gene model GRCh37.70. Genes with at least 1 count per million (CPM) reads in at least 1 sample were considered expressed, otherwise absent and hence discarded.
The gene level read counts data was normalized using edgeR, multi-dimensional scaling and cluster analysis were performed to check for potential sample outliers.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited tex file using log2-tranformed CPM values for each sample

source_name: A549 cells

growth_protocol: A549-wt and A549-DOCK5-ko cells were seeded into T-75 tissue culture flasks to approximately 80% confluency (~ 2.5 x 10^6 cells/flask) at the time of infection.

extract_protocol:
Total RNA was extracted from each sample using Qiagen RNeasy Mini Kit, with genomic DNA removed by on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549-WT and A549-DOCK5-c28 cells were each infected at MOI of  0.5 TCID50/cell of the PR8 (H1N1) virus, the A/New York/238/2015 (H3N2) virus, or Mock infected. The infected cells were incubated at 37C incubator with 5% CO2 for 1 or 2 days.

tag: genotype

value: wild type

tag: treatment

tag: dpi


title: NSC11 cells mock irradiated, collected at 1h, Polysome-bound RNA, biological replicate 3

description: Polysome-bound RNA


title: NSC11 cells mock irradiated, collected at 1h, Polysome-bound RNA, biological replicate 1

description: Polysome-bound RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Total RNA, biological replicate 6

description: Total cellular RNA


title: NSC11 cells mock irradiated, collected at 1h, Polysome-bound RNA, biological replicate 4

description: Polysome-bound RNA


title: NSC11 cells mock irradiated, collected at 1h, Polysome-bound RNA, biological replicate 2

description: Polysome-bound RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Total RNA, biological replicate 5

description: Total cellular RNA


title: NSC11 cells mock irradiated, collected at 1h, Total RNA, biological replicate 5

description: Total cellular RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Total RNA, biological replicate 4

description: Total cellular RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Total RNA, biological replicate 2

description: Total cellular RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Total RNA, biological replicate 3

description: Total cellular RNA


title: NSC11 cells mock irradiated, collected at 1h, Total RNA, biological replicate 6

description: Total cellular RNA


title: NSC11 cells treated with 2Gy, collected at 1h, Total RNA, biological replicate 1

description: Total cellular RNA


title: NSC11 cells mock irradiated, collected at 1h, Total RNA, biological replicate 4

description: Total cellular RNA


title: NSC11 cells mock irradiated, collected at 1h, Total RNA, biological replicate 1

description: Total cellular RNA


title: NSC11 cells mock irradiated, collected at 1h, Total RNA, biological replicate 3

description: Total cellular RNA


title: B23

city: Bronx

first: Deepa

last: Rastogi

address: 1300 Morris Park Ave

department: Pediatrics

institute: Albert Einstein College of Medicine

data_processing:
Picard-tools v 1.119 was used to demultipex and generate FastQ files
Trim Galore! v. 0.3.7 was used to trim poor quality bases and adaptor sequences
STAR v. 2.5.1b and gene annotations from Ensembl release 83 were used to align the trimmed reads to the UCSC hg38 human genome assembly
The gene counts were normalized and between-group comparison was performed using DESeq on R statistical software, version 3.2.2
Principal component analysis and multivariate linear regression analysis were performed on R version 3.2.2.
Genome_build: UCSC hg38 human genome assembly

source_name: obese child with asthma_CD4+ T cells

extract_protocol:
Ficoll hypaque method for PBMC separation followed by negative T cell isolation using magnetic beads
Briefly, after removal of ribosomal RNA with the Ribo Zero-rRNA removal kit (Illumina Inc., San Diego, CA), reverse transcription was done using SuperSriptIII First-Strand Synthesis system followed by second strand cDNA synthesis using dUTP. The double stranded cDNA was fragmented with Covaris (200-300bp target length), end-repaired, dA tailed and adaptors added for the Illumina sequencer to allow multiplexing of 8 samples per lane. To maintain directional information, i.e. transcribing strand-specific information (PMID:24733242), a combination of dUTP incorporation and uracil-DNA glycosylase were used. All libraries underwent bioanalyzer testing for quality control and were sequenced on Illumina HiSeq 2500 as 100bp single-end reads.

tag: subject status

value: obese child with asthma

tag: age

tag: gender

value: Female

tag: ethnicity

value: Hispanic

tag: insulin (iu/ml)

tag: cell type

value: CD4+ T cells

tag: sequencing batch

tag: total number of reads

tag: protein coding reads

tag: percent duplicate


title: NSC11 cells mock irradiated, collected at 1h, Total RNA, biological replicate 2

description: Total cellular RNA


title: B13


title: B14


title: B12

value: African American


title: B22

value: Male


title: B21


title: B16


title: B24


title: B03


title: B09


title: B08


title: B11


title: B04


title: B06


title: B18


title: A24

source_name: normal-weight child with asthma_CD4+ T cells

value: normal-weight child with asthma


title: B02


title: B05


title: A21


title: B07


title: B17


title: A25


title: A17


title: A23


title: A15


title: A20


title: A14


title: B15


title: A16


title: A19


title: B01


title: A10


title: A07


title: A13


title: A12


title: A09


title: A05


title: A11


title: A03


title: A04


title: A06


title: ETB11-2

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
Bowtie2 (v 2-2.1.0) and Tophat2 (v 2.0.9) were used for alignment
Cufflinks(v2.2.0) was used to determine fpkms and cuffmerge and cuffdiff were used to identify differentially expressed genes
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab-delimited txt file includes FPKM values for all samples

molecule: polyA RNA

source_name: A375 melanoma cell line

growth_protocol: A375 cells grown in 10cm tissue culture plates passaged on reaching 70-90% confluency

extract_protocol:
RNA was harvested from cells using Trizol reagent. Illumina TruSeq Stranded RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA protocol

treatment_protocol: Stable overexpression of GDF6 or SMAD1DVD or empty vector control and/or stable knockdown of GDF6 or EGFP control

value: A375 melanoma cells

tag: expression

value: empty vector + GDF6 knockdown


title: GDF6-1

value: GDF6 overexpression


title: ETB11-3


title: DVDB11-3

value: SMAD1 overexpression + GDF6 knockdown


title: ETGFP-3

value: empty vector + EGFP knockdown


title: ETGFP-1


title: ETGFP-2


title: ETB11-1


title: DVDB11-1


title: GDF6-3


title: ET-3

value: empty vector


title: GDF6-2


title: ET-1


title: DVDB11-2


title: ET-2


title: A02


title: NAC9myc-a-myc

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

library_source: genomic

data_processing:
Illumina Hiseq 2500 with 101 bp single end read
checked the read quality through the average quality score from FASTQ files and nucleotide distribution at each position using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) to identify potential sequencing errors and biases.
Reads was mapped using the alignment software BOWTIE (http://bowite-bio.sourceforge.net/index.shtml)
and analyzed using HOMER (Hypergeometric Optimization of Motif EnRichment, http://liulab.dfci.harvard.edu/MACS/)
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text  files include RPKM values and fold ratio for each Sample. After removing background peaks (each immunoprecipitaed sample's peak *minus *NT-a-myc's peak (negative peak)), and calculated RPKM, and fold ratio, log2 (each NACmyc/NTtotal input).

molecule: genomic DNA

organism: Oryza sativa

source_name: OsNAC9myc (overexpression)

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

extract_protocol:
roots of NT and RCc3::6xmyc-OsNACs plants were cross-linked with a buffer (0.4 M sucrose, 10 mM Tris-HCl [pH 8], 5 mM β –mercaptoethanol, and 1 % formaldehyde) by vacuum infiltration for 15 min. The chromatin was isolated using sucrose cushion and sonicated to shear DNA to size range of 100-300 bp.
The ChIP-Seq library was constructed according to Illumina’s instructions with some modifications. The library was purified using an Agencourt AMPure XP system. Purified DNA were used to prepare libraries with Illumina TruSeq ChIP sample preparation protocol

value: roots

value: 20 days

tag: cultivar

value: Illmi

tag: chip antibody

value: α-myc (sc-789, Santa Cruz)


title: NAC10myc-a-myc

source_name: OsNAC10myc (overexpression)

tag: tissue


title: NAC6myc-a-myc

source_name: OsNAC6myc (overexpression)


title: NT-a-myc

description: NT-a-myc

source_name: NT (nontransgenic)


title: RCc3:OsNAC10-myc_2

data_processing:
Single-end seq were generated and raw seq reads were trimmed to removed adaptor seq, and those with a quality lower than Q20 were removed using the clc quality trim software (CLCBIO).
Duplicate paired short reads were removed using FastUniq.
All reads were assembled with the clc_ref_assmble 6 (version 4.06) program, using annotated gene and noncoding RNA seq from the rapdb (http://rapdb.dna.affrc.go.jp).
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: abundance measurements

source_name: RCc3:OsNAC10-myc (root specific promoter transgenic plants)

extract_protocol:
Total RNA was extracted from the roots of 2-week-old OsNAC6 overexpressors, knockout mutant, and NT rice seedlings grown under normal growth conditions using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
A modified TruSeq method was used to construct a strand-specific RNA-seq library with different index primers and libraries were sequenced in the Illumina HiSeq 2000 system in the MACROGEN. Cutoff criteria to eliminate genes that showed no significant difference were more than 2 fold up- and down-regulation in RCc3:myc-OsNAC5, OsANC6-myc, myc-OsNAC9, or OsANC10-myc compared to NT (Illmi).


title: NT-total-input

description: NT-total-input


title: RCc3:myc-OsNAC9_2

source_name: RCc3:myc-OsNAC9 (root specific promoter transgenic plants)


title: RCc3:OsNAC10-myc_1


title: nontransgenic control_2

source_name: NT (nontransgenic rice plant)


title: RCc3:myc-OsNAC9_1


title: RCc3:myc-OsNAC5_1

source_name: RCc3:myc-OsNAC5 (root specific promoter transgenic plants)


title: RCc3:OsNAC6-myc_1

source_name: RCc3:OsNAC6-myc (root specific promoter transgenic plants)


title: nontransgenic control_1


title: ox- 1:100,000 AthHEN1_S2-S+mES (replica 3)

city: Vienna

first: Chiara

last: Alberti

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
18-30 nt size selection for miRNA seq
57687

data_processing:
Basecalling RTA 1.18.64.0
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1).
The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The processed reads were filtered in respect of their size selection (18-30nt).
All reads were aligned first to M.musculus (mm10) genome with tailor (v1.1). The minimum length of exact match was 18.
Remaining unaligned reads were aligned to D.melanogaster (dm3) genome with tailor (v1.1). The minimum length of exact match was 18.
Reads were assigned to miRNA arms with htseq-count (v0.6.1p1). The parameters were stranded=yes, “intersection-nonempty” and a SAM file was the output. GTFs containing pre-miRNAs annotations (mirBase) of mouse and fly was used. The annotation was split in two halves assigned to 5' an and 3' of each miRNA region, respectively. Assigned reads (SAM file) were summed up for each miRNA half. Multimapping reads were counted only as fraction (1/number of mapped locations).
Genome_build: mm10 & dm3
Supplementary_files_format_and_content: count data of mouse and fly miRNAs in one tab separated text file

organism:
Drosophila melanogaster
Mus musculus

source_name: Drosophila S2 cells + mouse embryonic stem cells

growth_protocol: Mouse embryonic stem (mES) cells (clone AN3-12) were cultured in 15 % FBS (Gibco), 1x Penicillin-Streptomycin solution (100 U/ml Penicillin, 0.1 mg/ml Streptomycin, Sigma), 2 mM L-Glutamine (Sigma), 1x MEM Non-essential amino acid solution (Sigma), 1 mM sodium pyruvate (Sigma), 50 µM 2-Mercaptoethanol (Gibco) and 20 ng/ml LIF (in-house produced). Cells were maintained at 37°C with 5% CO2 and passaged every second day. Drosophila S2 cells were grown in Schneider’s medium (Invitrogen) supplemented with 10% (v/v) FBS (Sigma) at 28°C.

extract_protocol:
Total RNA was extracted from cell pellets in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from 50 µg of total RNA (sum of Mmu RNA + Dme RNA; the samples were then split into two: 25µg RNA/library ox- and 25 µg RNA/library ox+)
Small RNA libraries were constructed and sequenced as described in Ameres et al. (2010) with some modifications. 18-30 nt long RNAs for were size selected. Subsequent 2SrRNA depletion was performed with Dynabeads MyOne streptavidin C1 beads (Invitrogen) as described in Seitz et al. (2008). Small RNAs were ligated to 3’ and 5’ barcode adapters containing 4 random nucleotides at their ends to minimize ligation bias (Jayaprakash et al., 2011). Subsequent reverse transcription was performed with SuperScript III Reverse Transcriptase (Invitrogen) and cDNA samples were PCR amplified with the KAPA Real-Time Library Amplification Kit (Peqlab). Amplified cDNA was agarose gel purified and sequenced in an Illumina HiSeq2000 instrument.

treatment_protocol: 50µg of total RNA (sum of Dme and Mmu total RNA) was used for the input and each dilution . Total RNA from mouse ES cells was mixed with decreasing amounts of total RNA from Drosophila S2 Hen1KO cells expressing AthHEN1, in the following ratios [Dme:Mmu]= 1:1; 1:10; 1:100; 1:1,000; 1:10,000; 1:100,000 (10 fold dilution of S2 total RNA). Each sample was split into two: one was subjected to treatment with sodium periodate (oxidised, +ox), the other was left untreated (unoxidised, -ox).

value: Untreated sample

tag: genotype

value: DmHen1-KO; FLAG-MYC-AthHEN1

value: Cultured Cells


title: WT2 RNAseq

city: Nanjing

first: Wukui

last: Zhao

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

country: China

institute: Nanjing University

data_processing:
Mapping reads with the reference genome use TopHat 2.0.12
Assemble reads use Cufflinks 2.2.1
Gene expression level analysis HTSeq 0.6.0
Alternative splicing prediction use Cuffcompare 2.2.1
Differential expression gene analysis use DEGSeq 1.18.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: ES cells were cultured with mouse embryonic fibroblasts (MEFs) inactivated with mitomycin-C in DMEM supplemented with15% fetal calf serum , leukemia inhibitory factor , L-glutamine , non-essential amino acids , 0.1 mM betamercaptoethanol , and penicillin/streptomycin. All ES cell lines were maintained at 37°C in 5% CO2.

extract_protocol:
RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、A-tailing and adapter added were implemented. The aimed products were retrieved by agarose gel electrophoresis and PCR was performed, then the library was completed.

treatment_protocol: Pcgf3, Pcgf5 and double KO ES cells were generated by Cas9 technology.

tag: strain

value: wild type

value: mouse embryonic stem cells


title: NAC5myc-a-myc

source_name: OsNAC5myc (overexpression)


title: Pcgf5KO2 RNAseq


title: ox+ 1:100,000 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57688

tag: treatment

value: Periodate-mediated oxidation


title: WT1 RNAseq


title: Pcgf3KO2 RNAseq


title: Pcgf3KO1 RNAseq


title: ox+ 1:10,000 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57686


title: Pcgf5KO1 RNAseq


title: RCc3:OsNAC6-myc_2


title: Pcgf3;5KO1 RNAseq

value: Pcgf3/5 DKO


title: Pcgf3;5KO2 RNAseq


title: ox+ 1:1,000 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57684


title: RCc3:myc-OsNAC5_2


title: ox- 1:100 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57681


title: ox+ 1:100 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57682


title: ox- 1:1 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57678


title: ox- 1:10 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57679


title: ox+ 1:10 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57680


title: A12

source_name: low passage patient-derived PDAC cells

tag: transfection

value: scrambled siRNA


title: ox+ 1:100,000 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57674


title: ox+ 1:1 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57677


title: ox- 1:100,000 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57673


title: ox+ 1:10,000 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57672


title: ox- 1:10,000 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57685


title: ox+ 1:1,000 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57670


title: ox- 1:10,000 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57671


title: ox- 1:1,000 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57669


title: ox+ 1:100 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57668


title: ox- 1:100 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57667


title: ox+ 1:1 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57663


title: ox+ 1:10 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57666


title: ox- 1:1,000 AthHEN1_S2-S+mES (replica 3)

description:
18-30 nt size selection for miRNA seq
57683


title: ox- 1:100,000 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq

extract_protocol:
Total RNA was extracted from cell pellets in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from an input of at least 25ug total RNA.
Small RNA libraries were constructed and sequenced as described in Ameres et al. (2010) with some modifications. 18-30 nt long RNAs for were size selected. Subsequent 2SrRNA depletion was performed with Dynabeads MyOne streptavidin C1 beads (Invitrogen) as described in Seitz et al. (2008). Small RNAs were ligated to 3’ and 5’ barcode adapters containing 4 random nucleotides at their ends to minimize ligation bias (Jayaprakash et al., 2011). Subsequent reverse transcription was performed with SuperScript III Reverse Transcriptase (Invitrogen) and cDNA samples were PCR amplified with the KAPA Real-Time Library Amplification Kit (Peqlab). Amplified cDNA was agarose gel purified and sequenced in an Illumina HiSeq2500 instrument.

treatment_protocol: 25µg of total RNA from mouse ES cells was mixed with decreasing amounts of total RNA from Drosophila S2 Hen1KO cells expressing AthHEN1, in the following ratios [Dme:Mmu]= 1:1; 1:10; 1:100; 1:1,000; 1:10,000; 1:100,000 (10 fold dilution of S2 total RNA). After size selection and 2SrRNA depletion, each sample was split into two: one was subjected to treatment with sodium periodate (oxidised, +ox), the other was left untreated (unoxidised, -ox). Each sample was then subjected to small RNA library preparation as described below.


title: ox- 1:10 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57665


title: ox+ 1:100,000 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: ox+ 1:1,000 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: ox- 1:10,000 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: Ribosome_profiling_muscle_Leu5

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description:
mRNA
Processed data file: RNA_RPF_RawCts.xlsx
Processed data file: EdgeR_RiboSeq.xlsx

data_processing:
Library strategy: Ribo-Seq
Sequence reads were trimmed of adapter sequences using Hannon lab Fastx toolkit.
rRNA sequences were removed using bowtie alignments to mouse 43SrRNA.
RefSeq FASTA sequences were obtained from the UCSC genome browser (mm9). These FASTA files were reduced to a single entry for each mRNA corresponding to the longest isoform. Uniquely aligning sequences, allowing for 2 mismatches, were identified using the Bowtie sequence aligner. Differential expression was analyzed using Bioconductor and EdgeR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA_RPF_RawCts.xlsx: Excel file includes raw counts mapping to each gene for each sample; RNA-Seq Cts (RNA), Ribosome profiling Cts (RPF).
Supplementary_files_format_and_content: EdgeR_RiboSeq.xlsx: Excel file includes EdgeR differential expression.
Supplementary_files_format_and_content: EdgeR_RNASeq.xlsx: Excel file includes EdgeR differential expression.

source_name: Quadriceps muscle, leucine

extract_protocol:
Total RNA was isolated by bead mill "beating" of frozen tissue.
RNA-Seq: Muscle total RNA was isolated by QIAzol extraction. rRNA was removed using Ribo-Zero (Illumina), fragmented, and libraries constructed using the NEB Next small RNA kit (New England Biolabs). Sequencing was done using the Illumina HiSeq2000 instrument.
Ribosome Profiling: 100mg of muscle tissue was homogenized, and crude polysomes digested with RNase1, monosomes were isolated by centrifugation through sucrose, rRNA was removed using Ribo-zero (Illumina), and ribosome footprints isolated by QIAzol extraction. Libraries were constructed using NEBnext Small RNA Sample Preparation kit. Sequencing was done using the Illumina HiSeq2000 instrument.

treatment_protocol: Mice were fasted overnight and received an oral gavage 30 minutes prior to euthanasia and muscle harvesting.

tag: strain/background

value: Quadriceps muscle

tag: diet

value: Oral gavage leucine


title: ox+ 1:1 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: ox- 1:1 AthHEN1_S2-S+mES (replica 2)

description:
18-30 nt size selection for miRNA seq
57664


title: ox+ 1:100 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: ox- 1:100 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: Ribosome_profiling_muscle_Leu3


title: ox- 1:1,000 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: ox+ 1:10 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: ox- 1:10 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: Ribosome_profiling_muscle_Leu2


title: Ribosome_profiling_muscle_Leu6


title: ox- 1:1 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: Ribosome_profiling_muscle_control5

source_name: Quadriceps muscle, vehicle

value: Oral gavage vehicle


title: Ribosome_profiling_muscle_Leu1


title: Ribosome_profiling_muscle_control3


title: RNASeq_muscle_Leu6

description:
mRNA
Processed data file: RNA_RPF_RawCts.xlsx
Processed data file: EdgeR_RNASeq.xlsx

data_processing:
Sequence reads were trimmed of adapter sequences using Hannon lab Fastx toolkit.
rRNA sequences were removed using bowtie alignments to mouse 43SrRNA.
RefSeq FASTA sequences were obtained from the UCSC genome browser (mm9). These FASTA files were reduced to a single entry for each mRNA corresponding to the longest isoform. Uniquely aligning sequences, allowing for 2 mismatches, were identified using the Bowtie sequence aligner. Differential expression was analyzed using Bioconductor and EdgeR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA_RPF_RawCts.xlsx: Excel file includes raw counts mapping to each gene for each sample; RNA-Seq Cts (RNA), Ribosome profiling Cts (RPF).
Supplementary_files_format_and_content: EdgeR_RiboSeq.xlsx: Excel file includes EdgeR differential expression.
Supplementary_files_format_and_content: EdgeR_RNASeq.xlsx: Excel file includes EdgeR differential expression.


title: Ribosome_profiling_muscle_control2


title: Ribosome_profiling_muscle_control4


title: ox+ 1:10,000 AthHEN1_S2-S+mES

description: 18-30 nt size selection for miRNA seq


title: RNASeq_muscle_Leu3


title: RNASeq_muscle_Leu2


title: RNASeq_muscle_Leu4


title: Ribosome_profiling_muscle_Leu4


title: RNASeq_muscle_control5


title: RNASeq_muscle_control2


title: Ribosome_profiling_muscle_control1


title: RNASeq_muscle_Leu1


title: control eutopic endometrium lncRNA, patient 25

city: Beijing

first: Luyang

address: 28 Fuxing Road, HaiDian District

department: Department of Gynecology and Obstetrics

institute: People’s Liberation Army (PLA) Medical School, Chinese PLA General Hospital

data_processing:
Data Filtering:Remove the adaptor-polluted reads (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out).Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads;Remove reads with number of N bases accounting for more than 5 %; Remove reads mapped in rRNA database.
Alignment:Primary sequencing data, or raw reads, produced on the Illumina system were filtered into clean reads that were aligned to the reference genome using TopHat.The parameter was defaulted and the version was v2.0.12 in this project using TopHat.
Calculate the count value:We got reads count of mRNA and known lncRNA by using HTSeq (version 0.6.0,--stranded reverse).
Genome_build: Homo_sapiens.GRCh38.83

source_name: eutopic endometrium

extract_protocol:
Total RNA was extracted using a single-step acid guanidinium thiocyanate-phenol-chloroform method. The quality and purity of RNA were examined by a Nanodrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). RNA integrity was analyzed using the RNA 6000 Nano Kit and Small RNA Kit with the and a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The samples with the absorbance wavelength ratio (A260/A280) ≥1.9 and a the RNA integrity number ≥ 8 were included. For small RNA sequencing, 3 μg of total RNA was used for library preparation.  3 μg of RNA per sample was prepared for library preparation.
The Ribo-Zero Gold Kit (Epicentre, USA) and NEB Next Ultra RNA Library Prep Kit (NEB, Ispawich, USA) were used for rRNA removal and library construction following the manufacturer's protocols. For high-throughput sequencing, paired-end 150-bp sequencing of the cDNAs was performed on an Illumina HiSeq 4000 system (Illumina, USA) conducted by Annoroad Genome (Beijing, China).

tag: disease state

value: control

tag: patient

tag: rafs stage

value: IV


title: RNASeq_muscle_control1


title: RNASeq_muscle_control3


title: RNASeq_muscle_control4


title: control eutopic endometrium lncRNA, patient 21


title: control eutopic endometrium lncRNA, patient 18

value: III


title: control eutopic endometrium lncRNA, patient 11


title: control eutopic endometrium lncRNA, patient 5


title: control eutopic endometrium lncRNA, patient 1


title: control eutopic endometrium lncRNA, patient 7


title: ectopic endometrium lncRNA, patient 25

source_name: ectopic endometrium

value: case


title: ectopic endometrium lncRNA, patient 18


title: control eutopic endometrium lncRNA, patient 6


title: ectopic endometrium lncRNA, patient 21


title: 7 PMP22-SCs

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

description: stable cell line

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include FPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 50 bp single-end libraries were sequenced using Illumina HiSeq 2000.

tag: cell type

value: hiPSC derived-SCs from PMP22 group

tag: passage/days

value: day 28


title: ectopic endometrium lncRNA, patient 6


title: 6 CMT1A-SCs

description: stable cell line

value: hiPSC derived-SCs from CMT1A group


title: ectopic endometrium lncRNA, patient 7


title: ectopic endometrium lncRNA, patient 5


title: ectopic endometrium lncRNA, patient 1


title: 3 Control-NCSCs

description: stable cell line

source_name: Control-NCSCs

value: hiPSC derived-NCSCs from control group


title: 2 CMT1A-hiPSCs

description: stable cell line

value: hiPSCs derived from CMT1A sample


title: 1 Control-hiPSCs

description: stable cell line

source_name: Control-hiPSCs

value: hiPSCs derived from normal sample


title: 5 Control-SCs

description: stable cell line

source_name: Control-SCs

value: hiPSC derived-SCs from Control group


title: 4 CMT1A-NCSCs

description: stable cell line

value: hiPSC derived-NCSCs from CMT1A group


title: HTLV1_TAX_PBM_RNA_seq_Rep3

city: Lyon

first: Emiliano

middle: P

last: Ricci

address: 46 allée d'Italie

department: Centre International de Recherche en Infectiologie

country: France

institute: INSERM

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were first split with respect to their dual barcode sequences. After this, 3′-adaptor sequences were removed from reads when present. Reads were then aligned to a custom set of sequences corresponding to ribosomal RNA and tRNA sequences using Bowtie2 v1.1.1 with parameters -fast -fr in order to remove contaminants. Remaining reads were aligned to the human genome and transcriptome (hg19 assembly) using TopHat2 v2.0.13 with parameters --library-type fr-secondstrand --no-coverage-search --b2-sensitive -i 30 -m 0 -g 10 --max-coverage-intron 1000000
Read counts per gene were obtained using HTSeq v0.6.1p1 with parameters -s yes -m intersection-strict --type=exon –idattr=gene_id (using the UCSC hg19 annotation file).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include exon gene counts values for each Sample. Bedgraphs files for each biological replicate.

source_name: HTLV infected T cells

growth_protocol: T lymphocytes isolated from the spleen of WT or ∆PBM infected hu-mice were cultured in complete RPMI medium containing IL2.

extract_protocol:
Total RNA was extracted from cytoplasmic extracts using Trizol
Libraries were constructed following the SmartSeq2 protocol (Picelli S 2013 Nature Methods)

treatment_protocol: Cells (5x10^6) were then washed with ice-cold PBS, centrifuged at 500g for 5 min at 4°C and lysed in 1 mL of lysis buffer (10mM Tris-HCl pH7.5, 5mM MgCl2, 100mM KCl, 2mM DTT, protease inhibitor EDTA-free Roche, 1% Triton X-100). Lysates were gently homogenized and incubated at 4 °C for 10 min, centrifuged at 1,300g for 10 min at 4 °C and the supernatant (corresponding to the cytoplasmic fraction) was recovered.

tag: host organism

value: hu-mice

value: T cell

tag: infected with

value: Human T-lymphotropic virus type 1 (HTLV-1)

tag: virus genotype

value: Tax delta_PBM


title: HTLV1_TAX_PBM_RNA_seq_Rep2


title: HTLV1_TAX_PBM_RNA_seq_Rep1


title: HTLV1_WT_RNA_seq_Rep3

value: WT


title: HTLV1_WT_RNA_seq_Rep1


title: HTLV1_WT_RNA_seq_Rep2


title: RNASeq_muscle_Leu5

value: Quadriceps muscle

value: Oral gavage leucine


title: shGDF6 input DNA

data_processing:
ChIP-seq reads were aligned to the human GRCh37 genome assembly using Bowtie version 1.0.0
PCR duplicates were filtered out from the aligned reads
Peaks were called using MACS2 (v 2.1.1.20160226)  with default q-value.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab-delimited files were generated using MACS2. Information include: chromosome name; start position of peak; end position of peak; length of peak region; absolute peak summit position pileup height at peak summit, -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10); fold enrichment for this peak summit against random Poisson distribution with local lambda, -log10(qvalue) at peak summit

source_name: A375 melanoma cell line

extract_protocol:
ChIP was performed using the Simple ChIP Plus Enzymatic Chromatin IP kit as per manufacturer’s instructions (Cell Signaling#9001) with the phospho-SMAD1/5/8 antibody (Cell Signaling#11971; 1:100).
ChIP-ed DNA fragments were added with 'A' base to the 3' end and adapters were ligated. This was followed by PCR amplfication and size selection (100-300bp). After QC, these were used for cluster preparation and HiSeq sequencing.

treatment_protocol: Stable knockdown of GDF6 or EGFP control

value: A375 melanoma cells

tag: antibody

tag: stable knockdown


title: shGDF61


title: shGFP input DNA

value: EGFP control


title: ectopic endometrium lncRNA, patient 11

value: case

value: III


title: shGFP2


title: Esrp1 & 2 DKO 5dpf zebrafish embryos replicate 2 run 1

city: Barcelona

first: Demian

last: Burguera

address: Diagonal 643

department: Genetics, Faculty of Biology

country: Spain

institute: University of Barcelona

description:
Embr_5dpf_ESRP_DKO_b
cRPKM-Dre4.tab

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences were downloaded from Ensembl for zebrafish and from Echinobase from sea urchin. For each gene, the canonical transcript was selected for gene expression analysis based on ORF lenght.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: zebrafish: danRer10. sea urchin: Spur_v3.1
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above) for each gene's canonical transcript in each condition

organism: Danio rerio

source_name: Zebrafish whole embryos 5dpf

extract_protocol:
mRNA was purified using QIAGEN RNA purification kit for zebrafish and AMBION kit for sea urchin
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: genotype/variation

value: Esrp1 & Esrp2 KO


title: Control 5dpf zebrafish embryos replicate 2 run 1

description:
Embr_5dpf_ESRP_WT_b
cRPKM-Dre4.tab

value: Wild type


title: shGFP1


title: da-plus-CN

city: Fukuoka

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

country: Japan

institute: Kyushu University

data_processing:
Read quality was checked for each sample using FASTQC (version 0.11.5).
We aligned more than 40 M reads onto the reference D. melanogaster genome sequence (UCSC dm6) using the TopHat program version 2.0.13, with default parameters.
Cufflinks (version 2.2.1) was employed with default parameters for transcript assembly. The expression level of each gene was quantified as FPKMs (fragments per kilobase of exon per million mapped fragments).
Genome_build: UCSC dm6
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample

organism: Drosophila melanogaster

source_name: adult male whole body

extract_protocol:
Total RNA was extracted from 15-day-old adults using the Trizol reagent (Invitrogen). The isolated RNAs were used for the construction of single-end mRNA-seq libraries, using a NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MS) according to the manufacturer's recommendations. mRNA-seq was performed on an Illumina Hiseq 1000 instrument (Illumina, San Diego, CA) using 51-bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: developmental stage

value: adult

tag: age

tag: tissue

value: whole body


title: da-miR-305

tag: strain


title: ZF melanoma rep4

data_processing:
Star v2.3 was used to align the reads
htseq-count was used to count mappped reads
DESeq2 was used to perform differential gene expression analysis
Genome_build: Zebrafish Zv9
Supplementary_files_format_and_content: tab-delimited txt file includes FPKM values for all samples

source_name: melanoma

growth_protocol: Unpigmented EGFP-positive melanocytes and melanoma cells were isolated by FACS

extract_protocol:
RNA was harvested from cells using Trizol reagent.
Illumina TruSeq

value: melanoma


title: henn-1(0) (MLC405) Treatment

description: 18-30 nt size selection for miRNA seq

data_processing:
Basecalling RTA 1.18.64.0
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.0).
The random 4mers on 5' and 3' were removed with a custom perl script. The processed reads were filtered in respect of their size selection (18-30nt).
All reads were aligned to the C.elegans genome with tailor (v1.1). The minimum length of exact match was 18.
Reads were assigned to miRNA arms with htseq-count (v0.6.1p1). The parameters were stranded=yes, “intersection-nonempty” and a SAM file was the output. A GTF containing pre-miRNAs annotations (mirBase) was used. The annotation was split in two halves assigned to 5' an and 3' of each miRNA region, respectively. Assigned reads (SAM file) were summed up for each miRNA half. Multimapping reads were counted only as fraction (1/number of mapped locations).
Nextflow pipeline of above steps can be found at https://gitlab.com/tburk/smallRNA-meth (v1.0.2).
Genome_build: WBcel235
Supplementary_files_format_and_content: count data as tab separated text

organism: Caenorhabditis elegans

source_name: whole L1-staged worms

extract_protocol:
Total RNA was extracted from L1 staged-worms collected in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from an input of at least 20ug total RNA.
RNA libraries were constructed as described in Newman et al. (2011)

tag: treatment

value: Periodate-mediated oxidation

tag: genotype

value: Larval 1 (L1)


title: henn-1(0) (MLC405) No Treatment

description: 18-30 nt size selection for miRNA seq

value: Untreated sample


title: ZF melanoma rep1


title: ZF melanoma rep2


title: ZF melanoma rep3


title: ZF melanocytes rep4

source_name: scale melanocytes

value: scale melanocytes


title: ASE:HEN1 repl 9 (MLC750) Treatment 42750

description: 18-30 nt size selection for miRNA seq

data_processing:
Basecalling RTA 1.18.64.0
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1).
The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The processed reads were filtered in respect of their size selection (18-30nt).
All reads were aligned to the C.elegans genome with tailor (v1.1). The minimum length of exact match was 18.
Reads were assigned to miRNA arms with htseq-count (v0.6.1p1). The parameters were stranded=yes, “intersection-nonempty” and a SAM file was the output. A GTF containing pre-miRNAs annotations (mirBase) was used. The annotation was split in two halves assigned to 5' an and 3' of each miRNA region, respectively. Assigned reads (SAM file) were summed up for each miRNA half. Multimapping reads were counted only as fraction (1/number of mapped locations).
Genome_build: WBcel235
Supplementary_files_format_and_content: count data as tab separated text

value: ASE:Ath-HEN1, henn-1(0)


title: ASE:HEN1 repl 9 (MLC750) No Treatment 42749

description: 18-30 nt size selection for miRNA seq


title: ZF melanocytes rep3


title: shGDF62


title: ASE:HEN1 repl 5 (MLC749) No Treatment 42747

description: 18-30 nt size selection for miRNA seq


title: ZF melanocytes rep2


title: ASE:HEN1 repl 9 (MLC703) No Treatment 40636

description: 18-30 nt size selection for miRNA seq

value: ASE:Ath-HEN1, wild type


title: ZF melanocytes rep1


title: ASE:HEN1 repl 9 (MLC703) Treatment 40637

description: 18-30 nt size selection for miRNA seq


title: ASE:HEN1 repl 5 (MLC749) Treatment 42748

description: 18-30 nt size selection for miRNA seq


title: myo-3:HEN1 repl 2.2 (MLC900) Treatment  49406

description: 18-30 nt size selection for miRNA seq

value: myo-3:Ath-HEN1, henn-1(0)


title: ASE:HEN1 repl 5 (MLC702) No Treatment 40634

description: 18-30 nt size selection for miRNA seq


title: ASE:HEN1 repl 5 (MLC702) Treatment 40635

description: 18-30 nt size selection for miRNA seq


title: myo-3:HEN1 repl 11.16 (MLC901) No Treatment  49407

description: 18-30 nt size selection for miRNA seq


title: myo-3:HEN1 repl 2.2 (MLC900) No Treatment  49405

description: 18-30 nt size selection for miRNA seq


title: myo-3:HEN1 repl 11 (MLC890) Treatment  49404

description: 18-30 nt size selection for miRNA seq

value: myo-3:Ath-HEN1, wild type


title: myo-3:HEN1 repl 11.16 (MLC901) Treatment  49408

description: 18-30 nt size selection for miRNA seq


title: Control 5dpf zebrafish embryos replicate 1 run 1

description:
Embr_5dpf_ESRP_WT_a
cRPKM-Dre4.tab


title: myo-3:HEN1 repl 2 (MLC889) Treatment  49402

description: 18-30 nt size selection for miRNA seq


title: Esrp1 & 2 DKO 5dpf zebrafish embryos replicate 1 run 1

description:
Embr_5dpf_ESRP_DKO_a
cRPKM-Dre4.tab


title: myo-3:HEN1 repl 11 (MLC890) No Treatment  49403

description: 18-30 nt size selection for miRNA seq


title: myo-2:HEN1 repl 30 (MLC529) No Treatment 42755

description: 18-30 nt size selection for miRNA seq

value: myo-2:Ath-HEN1, henn-1(0)


title: myo-2:HEN1 repl 7 (MLC528) No Treatment 42753

description: 18-30 nt size selection for miRNA seq


title: myo-2:HEN1 repl 7 (MLC528) Treatment 42754

description: 18-30 nt size selection for miRNA seq


title: elt-2:HEN1 repl 8.1 (MLC631) Treatment 37021

description: 18-30 nt size selection for miRNA seq

value: elt-2:Ath-HEN1, henn-1(0)


title: elt-2:HEN1 repl 8.1 (MLC631) No Treatment 37020

description: 18-30 nt size selection for miRNA seq


title: elt-2:HEN1 repl 3A (MLC559) Treatment 36213

description: 18-30 nt size selection for miRNA seq


title: BMH25-DL

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the GRCh38 human genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.86.gtf
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: MSCs_1MT (1mM)

growth_protocol: Mesenchymal stromal cells (MSC) were isolated from the marrow of five healthy human donors, passaged in α-MEM supplemented with penicillin, streptomycin and 10% human platelet lysate. Cells were trypsinized and 50,00 were plated per well in a 12-welled plate, in duplicate. Cells were plated in RPMI 1640 +Pen/Strep, +L-glut, +1-% fetal calf serum.

extract_protocol:
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Cells treated with vehicle (RPMI 1640 +Pen/Strep, +L-glut, +1-% fetal calf serum), with TCDD (10nM) or 1MT (1mM) for 24h, then trypsinized, washed with PBS and stored at -80˚C until RNA analysis.

tag: subject id

value: healthy human donor #25

value: Mesenchymal stromal cells (MSC)

tag: treated with

value: 1MT (1mM) for 24h


title: BMH25-TCDD

source_name: MSCs_TCDD (10nM)

tag: cell type

value: TCDD (10nM) for 24h


title: rgef-1:HEN1 repl  14C (MLC665) No Treatment 37024

description: 18-30 nt size selection for miRNA seq

value: rgef-1:Ath-HEN1, henn-1(0)


title: rgef-1:HEN1 repl  14C (MLC665) Treatment 37025

description: 18-30 nt size selection for miRNA seq


title: BMH25-NoRx

source_name: MSCs_vehicle (NoRx)

value: vehicle (NoRx)


title: BMH17-DL

value: healthy human donor #17


title: BMH17-TCDD


title: rgef-1:HEN1 repl  3A (MLC664) Treatment 37023

description: 18-30 nt size selection for miRNA seq

value: Periodate-mediated oxidation


title: unc-31:HEN1 repl 5 (MLC531) Treatment 32954

description: 18-30 nt size selection for miRNA seq

value: unc-31:Ath-HEN1, henn-1(0)

value: Larval 1 (L1)


title: rgef-1:HEN1 repl  3A (MLC664) No Treatment 37022

description: 18-30 nt size selection for miRNA seq

value: Untreated sample


title: unc-31:HEN1 repl 1 (MLC530) Treatment 32953

description: 18-30 nt size selection for miRNA seq


title: BMH14-DL

value: healthy human donor #14


title: BMH14-NoRx


title: BMH17-NoRx


title: BMH14-TCDD


title: rab-3:HEN1 repl 14 (MLC450) Treatment 32797

description: 18-30 nt size selection for miRNA seq

value: rab-3:Ath-HEN1, henn-1(0)


title: BMH6-DL

value: healthy human donor #6


title: BMH6-TCDD


title: unc-31:HEN1 repl 1 (MLC530) No Treatment 32950

description: 18-30 nt size selection for miRNA seq


title: myo-3:HEN1 repl 2 (MLC889) No Treatment  49401

description: 18-30 nt size selection for miRNA seq

value: myo-3:Ath-HEN1, wild type


title: myo-2:HEN1 repl 30 (MLC529) Treatment 42756

description: 18-30 nt size selection for miRNA seq

value: myo-2:Ath-HEN1, henn-1(0)


title: rab-3:HEN1 repl 18.4 (MLC451) Treatment 32798

description: 18-30 nt size selection for miRNA seq


title: elt-2:HEN1 repl 3A (MLC559) No Treatment 36212

description: 18-30 nt size selection for miRNA seq

value: elt-2:Ath-HEN1, henn-1(0)


title: rab-3:HEN1 repl 18.4 (MLC451) No Treatment 32796

description: 18-30 nt size selection for miRNA seq


title: BMH6-NoRx


title: rps-5:HEN1 repl 16.1 (MLC558) Treatment 42752

description: 18-30 nt size selection for miRNA seq

value: rps-5:Ath-HEN1, henn-1(0)


title: rab-3:HEN1 repl 14 (MLC450) No Treatment 32795

description: 18-30 nt size selection for miRNA seq


title: BMH4-DL

value: healthy human donor #4

value: Mesenchymal stromal cells (MSC)


title: BMH4-TCDD

value: TCDD (10nM) for 24h


title: rps-5:HEN1 repl 16.1 (MLC558) No Treatment 42751

description: 18-30 nt size selection for miRNA seq


title: BMH4-NoRx


title: rps-5:HEN1 repl 22.3 (MLC557) Treatment 42746

description: 18-30 nt size selection for miRNA seq


title: rps-5:HEN1 repl 22.3 (MLC557) No Treatment 42745

description: 18-30 nt size selection for miRNA seq


title: WT Treatment (N2) 34093

description: 18-30 nt size selection for miRNA seq

value: wild type


title: WT No Treatment (N2) 32793

description: 18-30 nt size selection for miRNA seq


title: WT No Treatment (N2) 34092

description: 18-30 nt size selection for miRNA seq


title: S2 hen1 ko AthHEN1 #2 CM -ox

description: 18-30 nt size selection for miRNA seq

data_processing:
Basecalling RTA 1.18.64.0
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1).
The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The processed reads were filtered in respect of their size selection (18-30nt).
Putative contamination was filtered out by aligning to sequences of S2 viruses (derived from Genbank) with tailor (v1.1).
Reads were aligned to D.melanogaster (dm3) genome with tailor (v1.1). The minimum length of exact match was 18.
Reads were assigned to miRNA arms with htseq-count (v0.6.1p1). The parameters were stranded=yes, “intersection-nonempty” and a SAM file was the output. GTFs containing pre-miRNAs annotations (FlyBase r5.57) was used. The annotation was split in two halves assigned to 5' an and 3' of each miRNA region, respectively. Assigned reads (SAM file) were summed up for each miRNA half. Multimapping reads were counted only as fraction (1/number of mapped locations).
Genome_build: dm3 (FlyBase r5.57)
Supplementary_files_format_and_content: count data as tab separated text file

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells were grown in Schneider’s medium (Invitrogen) supplemented with 10% (v/v) FBS (Sigma) at 28°C.

extract_protocol:
Total RNA was extracted from cell pellets in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from an input of at least 20ug total RNA.
Small RNA libraries were constructed and sequenced as described in Ameres et al. (2010) with some modifications. For miRNA deep sequencing datasets, 18-30 nt long RNAs for were size selected. Subsequent 2SrRNA depletion was performed with Dynabeads MyOne streptavidin C1 beads (Invitrogen) as described in Seitz et al. (2008). Small RNAs were ligated to 3’ and 5’ barcode adapters containing 4 random nucleotides at their ends to minimize ligation bias (Jayaprakash et al., 2011). Subsequent reverse transcription was performed with SuperScript III Reverse Transcriptase (Invitrogen) and cDNA samples were PCR amplified with the KAPA Real-Time Library Amplification Kit (Peqlab). Amplified cDNA was agarose gel purified and sequenced in an Illumina HiSeq2500 instrument.

treatment_protocol: Total RNA (min starting amount was 20 µg) was size selected (18-30 nt) and 2S rRNA was depleted using 2S rRNA-specific-biotin oligo (40.1) coupled to MyOne-Streptavidin beads. Each sample was split into two: one was subjected to treatment with sodium periodate (oxidised, +ox), the other was left untreated (unoxidised, -ox).

value: DmHen1-KO; FLAG-MYC-AthHEN1

value: Cultured Cells


title: WT Treatment (N2) 32794

description: 18-30 nt size selection for miRNA seq

value: Periodate-mediated oxidation


title: Act88F female +ox

description: 18-30 nt size selection for miRNA seq

source_name: Drosophila Melanogaster

growth_protocol: the flies were grown on standard food and kept at 25 deg C. The respective Gal4 fly lines were crossed with the transgenic UAS::AthHEN1 fly lines and the F1 female flies were collected and aged for 2-5 days.

extract_protocol:
Total RNA was extracted from 2-5 days old adult female flies collected in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from an input of at least 80ug total RNA.
Small RNA libraries were constructed and sequenced as described in Ameres et al. (2010) with some modifications. For miRNA deep sequencing datasets, 18-30 nt long RNAs were size selected. Subsequent 2S rRNA depletion was performed with Dynabeads MyOne streptavidin C1 beads (Invitrogen) as described in Seitz et al. (2008). Small RNAs were ligated to 3’ and 5’ barcode adapters containing 4 random nucleotides at their ends to minimize ligation bias (Jayaprakash et al., 2011). Subsequent reverse transcription was performed with SuperScript III Reverse Transcriptase (Invitrogen) and cDNA samples were PCR amplified with the KAPA Real-Time Library Amplification Kit (Peqlab). Amplified cDNA was agarose gel purified and sequenced in an Illumina HiSeq2500 instrument.

treatment_protocol: Total RNA (min starting amount was 80 µg) was size selected (18-30 nt) and 2S rRNA was depleted using 2S rRNA-specific-biotin oligo (40.1) coupled to MyOne-Streptavidin beads. Each sample was split into two: one was subjected to treatment with sodium periodate (oxidized, +ox), the other was left untreated (unoxidized, -ox).

value: Act88F-Gal4/+; +/+; UAST::AthHEN1/+

value: adult female flies


title: Act88F female -ox

description: 18-30 nt size selection for miRNA seq

value: Untreated sample


title: S2 hen1 ko AthHEN1 #2 WT -ox

description: 18-30 nt size selection for miRNA seq


title: MHC female -ox

description: 18-30 nt size selection for miRNA seq

value: MHC-Gal4/+; +/+; UAST::AthHEN1/+


title: MHC female +ox

description: 18-30 nt size selection for miRNA seq


title: wt female +ox

description: 18-30 nt size selection for miRNA seq


title: ASP_31_22

city: Ames

first: Nicole

last: Valenzuela

state: IA

address: 251 Bessey Hal

institute: Iowa State University

description:
NV020
RawCounts.ASP

data_processing:
Read trimming: Trimmomatic, version 0.27
Transcriptome assembly: Trinity (r2013-02-25)
Read mapping: gsnap (2012-12-31)
Read quantification: HTSeq
Genome_build: Chrysemys picta v 3.0.1 [https://www.ncbi.nlm.nih.gov/assembly/GCF_000241765.2]

organism: Apalone spinifera

source_name: gonad

extract_protocol:
Total RNA was extracted from trunks (stage-9), adrenal-kidney-gonadal (AKG) complex (stages 12, 15) and gonads alone (stages 19, 22). RNeasy Kits(Valenzuela,2008a). RNA was quanti-fied with a NanoDropVRND-1000 Spectrophotometer,and its quality assessed by the presence of ribosomal bands in agarose gels
Paired end Illumina libraries

value: developmental stage 22


title: ASP_31_19

description:
NV019
RawCounts.ASP

value: developmental stage 19


title: ASP_31_15

description:
NV018
RawCounts.ASP

source_name: AKG

value: developmental stage 15


title: ASP_31_12

description:
NV017
RawCounts.ASP

value: developmental stage 12


title: ASP_26_22

description:
NV015
RawCounts.ASP


title: unc-31:HEN1 repl 5 (MLC531) No Treatment 32951

description: 18-30 nt size selection for miRNA seq

value: unc-31:Ath-HEN1, henn-1(0)

value: Larval 1 (L1)


title: rps-5:HEN1 repl 16.1 (MLC558) Treatment 36209

description: 18-30 nt size selection for miRNA seq

value: rps-5:Ath-HEN1, henn-1(0)


title: c25-B-K79me2

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

data_processing:
BWA alignment
MACS2 Peak-calling
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; ChIP-seq signal

source_name: Cancer cell line

extract_protocol:
Chromatin-IP
Following NEB ChIP-seq library preparation kit (E6200S)

tag: tumor type

value: Melanoma

tag: chip antibody

value: H3K79me2, Abcam, ab3594

value: DOT1L loss-of-function mutant


title: ASP_26_12

description:
NV012
RawCounts.ASP


title: rps-5:HEN1 repl 16.1 (MLC558) No Treatment 36208

description: 18-30 nt size selection for miRNA seq


title: ASP_26_15

description:
NV013
RawCounts.ASP


title: c21-shDOT1L-B-K79me2

value: DOT1L shRNA knockdown


title: c21-shDOT1L-A-K79me2


title: c25-A-K79me2


title: c21-B-K79me2

value: DOT1L wild type


title: CPI_31_12

description:
NV007
RawCounts.CPI

organism: Chrysemys picta


title: S2 hen1 ko AthHEN1 #2 WT +ox

description: 18-30 nt size selection for miRNA seq

value: Periodate-mediated oxidation

value: DmHen1-KO; FLAG-MYC-AthHEN1

value: Cultured Cells


title: ASP_26_19

description:
NV014
RawCounts.ASP


title: wt female -ox

description: 18-30 nt size selection for miRNA seq

value: Untreated sample

value: wild type

value: adult female flies


title: CPI_31_15

description:
NV008
RawCounts.CPI


title: CPI_31_9

description:
NV006
RawCounts.CPI

source_name: trunk

value: developmental stage 9


title: CPI_26_22

description:
NV005
RawCounts.CPI

value: developmental stage 22


title: ASP_31_9

description:
NV016
RawCounts.ASP


title: CPI_26_19

description:
NV004
RawCounts.CPI

value: developmental stage 19


title: CPI_26_9

description:
NV001
RawCounts.CPI


title: CPI_26_15

description:
NV003
RawCounts.CPI

value: developmental stage 15


title: IU9602 Rep3

city: Bloomington

first: Ram

last: Podicheti

institute: Indiana University

data_processing:
Bases were called using bcl2fasta v2.16.0.10
Using Trimmomatic ver. 0.33 (Bolger et al., 2014), reads were adaptor trimmed and quality filtered setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 15 bases post-trimming were excluded.
Cleaned reads were mapped to the complete genome of Streptococcus pneumoniae D39 (NC_008533.1) using bowtie2 ver. 2.1.0.
For each library, tables are generated which contain count of uniquely mapped reads overlapping with each of 100nt fixed width non-overlapping bins of the reference genome.
These counts are generated using htseq-counts ver. 0.5.4p1.
Genome_build: NC_008533.1
Supplementary_files_format_and_content: The counts files contain tables of counts of uniqulely mapped reads overlapping with each of 100nt fixed with non-overlapping bins. Each table has four columns - Reference, Start position for bin, End position for bin, Count of uniquely mapped reads overlapping with that bin.

organism: Streptococcus pneumoniae

source_name: Exponentially grown cells

growth_protocol: Cultures of strains IU1945 (WT), IU9602 (khpA-L-FLAG3), and IU10664 (khpA-L-FLAG3) grown exponentially in BHI media at 37ºC to OD620 ≈0.25 to 0.4. Starter cultures were used to inoculate 400 mL cultures of BHI broth in 500 mL bottles.

extract_protocol:
Cells were collected by centrifugation (8,000 X g for 10 min at 4ºC). Cell pellets were washed once with 30 mL of cold 1XPBS (4ºC) and resuspended in 2 mL of cold lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X100 (v/v) containing protease inhibitor (ThermoFisher; cat#78429)). Suspensions (2 mL) were transferred into 2 lysing matrix B tubes (1 mL each) (MB Biomedicals, Inc.). Tubes were shaken in a FastPrep homogenizer at 4ºC for ten 40s cycles (4X shaking; 5 min on ice; 3X shaking; 5 min on ice; 3X shaking) at a setting of 6.0 M/s. Cell debris was removed by centrifuging at 16,000 X g for 5 min at 4ºC. Protein concentration was determined by DCTM protein assay (Bio-Rad). About 1 mL of lysate with similar protein amount was added to tubes with 50 μL of anti-FLAG magnetic beads (Sigma) and rotated for 2 h at 4ºC. The beads were washed 3 times with 1 mL of lysis buffer for 10 min with rotation at 4ºC. FLAG3-tagged protein bound to RNA was eluted by incubation with 100 μL of FLAG elution solution (150 ng of 3X FLAG peptide per μL) (Sigma) for 30 min at 4ºC. RNA was extracted by phenol-chloroform extraction. 100 μL of phenol/chloroform/isoamyl alcohol (125:24:1, pH 4.3, ThermoFisher) was added to the eluted solution and vortexed for 10 sec before incubation at room temperature for 5 min. The mixture was centrifuged at 16,000 X g for 5 min. The upper phase was transferred to a new 1.5 mL tube. 2 volume of isopropanol and 1/10 volume of 3 M sodium acetate (pH 5.2) was added, followed by incubation for 10 min at -80ºC to precipitate RNA. Precipitated material was collected by centrifugation (16,000 X g for 30 min, 4ºC) and washed with 500 μL of 80% ethanol. Pellets were dried at room temperature for 10 min and resuspended in 30 μL of nuclease-free water.
cDNA libraries were prepared from total RNA by the Center for Genomics and Bioinformatics at Indiana University in Bloomington, Indiana. Bacterial RNA was depleted of ribosomal sequences using the rRNA-removal reagents from the Illumina Scriptseq Complete (Bacterial) kit. rRNA-depleted samples were then made into sequencing libraries using the Illumina Stranded mRNA library kit
Single-end, 80bp sequencing was performed using an Illumina NextSeq 500 sequencer. Images were analyzed using the standard Illumina pipeline, version 1.8.2.

tag: peptide tag

value: FLAG tag

tag: rip antibody

value: anti-FLAG magnetic beads (Sigma, catalog# M8823-1ML, lot# SLBS1873V)


title: IU10664 Rep2


title: ASP_26_9

description:
NV011
RawCounts.ASP


title: IU10664 Rep1


title: IU9602 Rep2


title: IU10664 Rep3


title: IU9602 Rep1


title: IU1945 Rep3


title: IU1945 Rep2


title: c21-A-K79me2

value: Melanoma


title: CPI_31_22

description:
NV010
RawCounts.CPI


title: MeCP2 KO rep2

city: Kansas

first: Aritra

last: Bhattacherjee

state: Kansas

address: 3901 Rainbow Blvd

department: Molecular and Integrative Physiology

institute: University of Kansas Medical Center

data_processing:
bcl2fastq Conversion Software v1.8.4 from illumina was used to generate fastq files
reads were  mapped to the Rat Rnor_5.0 genome with STAR_2.3.1z --genomeDir   Rnor_5.0 --readFilesIn R1.fastq R2.fastq --runThreadN 16  --readFilesCommand zcat      --outSAMstrandField intronMotif   --outFilterIntronMotifs RemoveNoncanonicalUnannotated
differential gene expression was deterimined using cufflinks -p 16 -b genome.fa -u -G annotation.gtf cuffdiff --max-bundle-frags 100000000 --max-mle-iterations 15000 -v --emit-count-tables -u -b genome.fa -p 16
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id

organism: Rattus norvegicus

source_name: dorsal root ganglia

extract_protocol:
Dorsal root ganglia were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 250g of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SD

value: dorsal root ganglia

value: post natal day 30


title: MeCP2 KO rep3


title: IU1945 Rep1


title: MeCP2 KO rep1


title: WT rep4


title: CPI_31_19

description:
NV009
RawCounts.CPI


title: WT rep1


title: WT rep3


title: CPI_26_12

description:
NV002
RawCounts.CPI

value: developmental stage 12


title: Short-DF-group [JF56]

city: Wuhan

first: Adeyinka

middle: Abiola

last: Adetula

state: Hubei

address: No. 1 Shizishan Road, Hongshan District

department: Animal genetics, Breeding, and Reproduction

institute: Huazhong Agricultural University

data_processing:
Mapping was done using Tophat, followed by transcript assembly using String tie. Gffcompare was used to compare assembly with known transcript.
Protein-coding transcripts were identified and removed with the software programme Coding-Non-Coding Index (CNCI > 0) and Coding Potential Calculator (CPC > 0). Similarly, Pfam (http://pfam.xfam.org) was used to remove transcripts with significant protein domain.
DE-lncRNAs were called using edgeR with the following setting: The threshold value of log2 (Fold change) ≥ 2 with q-values ≤ 0.01 and P-value ≤ 0.05.
Genome_build: GG4
Supplementary_files_format_and_content: gtf file was generated using String Tie (version: 1.3.0), which represent genomic information for the identified lncRNAs.

organism: Gallus gallus

source_name: Low fertility egg-type chicken

extract_protocol:
Total RNA was isolated from the UVJ using the RNeasy mini kit (Qiagen, Germany). The quality and concentration of RNA were analyzed by NanoDrop ND2000 (Thermo Fisher Scientific, Waltham, MA, USA) spectrophotometer and gel electrophoresis.
Briefly, the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA polymerase I and RNase H. Fourteen cDNA libraries were constructed using Illumina HiSeq 2500.

value: utero-vaginal junction (UVJ)


title: WT rep2


title: Short-DF-group [JF21]


title: Short-DF-group [JH130]


title: Short-DF-group [JH68]


title: Short-DF-group [JF40]


title: Short-DF-group [JH109]


title: MeCP2 KO rep4


title: Owacja_D10_3

city: Poznań

first: Marcin

middle: Andrzej

last: Pieczynski

address: Wieniawskiego 1

country: Poland

institute: Adam Mickiewicz University

description:
Processed data file: res_ow0_ow10_deseq_full.tsv
Processed data file: res_ow6_ow10_deseq_full.tsv
Processed data file: res_ow10_tj10_deseq_full.tsv

data_processing:
Clean reads were first tested for quality with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then, as the quality was not questionable, mapped to the reference potato genome (Solanaceae Genomics Resource, S. tuberosum Group Phureja DM1-3 Assembly Version 3 DM, PGSC Version 4.03 Pseudomolecule Sequence) using TopHat2 [PMID: 23618408] software. Number of mapped reads was obtained using FluxCapacitor v. 1.6.1 [PMID: 20220756] and a Python script - fluxgtf2counts.py, which retrieves and concatenates transcripts counts from flux capacitor GTF files (available at https://github.com/lpryszcz/bin/blob/master/fluxgtf2counts.py). FluxCapacitor is a program that predicts abundances for transcript molecules and alternative splicing events from RNA-seq experiments. The input for the FluxCapacitor is the annotation of a reference transcriptome (Solanaceae Genomics Resource, PGSC_DM_V403_genes.gtf - Gene annotation for the v4.03 Pseudomolecules in GFF3 format) and reads from RNA-seq technologies aligned to the genome. The tables prepared in such a way are then ready to be used for statistical analysis. Statistical analysis was performed to identify gene expression differences between samples studied (package R [R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/ ]). FluxCapacitor was run for each fastq file for every biological replicate from every condition. Afterwards, all the results were gathered in tables using mentioned scripts - one table per one comparison (e.g., a table with 3 biological replicates from one variety stressed with drought for 6 days and 3 replicates for the same variety in control conditions). These tables were then fed in DESeq - R package suitable for analysis of differential gene expression based on the negative binomial distribution [PMID: 20979621].
Genome_build: S. tuberosum Group Phureja DM1-3 Assembly Version 3 DM, PGSC Version 4.03 Pseudomolecule Sequence
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include data before (mean value for each sample) and after statistical analysis.

organism: Solanum tuberosum

source_name: Owacja, leaves, drought day 10

growth_protocol: Plants were grown in 14 liter pot filled with thin layer of gravel at the bottom and 12 liter of universal vegetable soil substrate with the addition of chalk, pH range 5.5-6.5 (Hollas company). The gum pipe was installed inside of each pot for better soil aeration. Pest and diseases control was carried out according to the needs. Plants were watered everyday with optimal water amount according to volumetric water content (VWC) in soil measured using 5TM Decagon sensors. For control conditions, VWC was 0.361 m3/m3.

extract_protocol:
During the drought experiment, leaves-samples were taken everyday from three different plants for each variety at given time point, and immediately frozen in liquid nitrogen for storage and further use. Third, fourth and fifth whirl from the top of the plant complex leaves were taken from each plant.
Total RNA was extracted from plant tissue using TRIzol and chloroform reagents followed by ethanol precipitation. Quality of RNA samples was tested with the use of Agilent RNA 6000 Nano Kit Guide (Agilent Technologies), only samples with: 28S:18S > 1.0, RIN≥ 6.5, OD 260/280 ≥1.8 and OD 260/230 ≥ 1.8 were used.
Strand-specific library constructions and RNA-seq (PE100) using Illumina HiSeq 2500 were conducted by BGI Tech Solutions Co. Ltd. (Hong Kong).

treatment_protocol: Three weeks after the initiation of the tuberisation process, half of the plant population was subjected to soil drought stress by withdrawal of irrigation, while control plants were still watered. Results of VWC measurements in subsequent days of drought were as follows: 0.121, -0.040, -0.066 and -0.106 at 3rd, 6th, 9th and 13th day of drought, respectively. After rewatering the plants, VWC was increased to control level. All experiments were performed in three biological replicates.

tag: cultivar

value: Owacja

tag: condition

value: soil drought

tag: day of drought

value: leaf


title: Owacja_D10_1


title: Owacja_D10_2


title: Long-DF-group [JF61]

source_name: High fertility egg-type chicken


title: Long-DF-group [JH104]


title: Long-DF-group [JH95]


title: Owacja_D6_2

description:
Processed data file: res_ow0_ow6_deseq_full.tsv
Processed data file: res_ow6_ow10_deseq_full.tsv
Processed data file: res_ow6_tj6_deseq_full.tsv

source_name: Owacja, leaves, drought day 6


title: Long-DF-group [JH25]


title: Long-DF-group [JH14]

source_name: Egg-laying chickens


title: Owacja_D6_1


title: Owacja_D0_1

description:
Processed data file: res_ow0_ow6_deseq_full.tsv
Processed data file: res_ow0_ow10_deseq_full.tsv
Processed data file: res_ow0_tj0_deseq_full.tsv

source_name: Owacja, leaves, day 0 control

value: control


title: Owacja_D0_2


title: untagged-antiMyc ChIPseq

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

data_processing:
Reads were aligned to the Sacccer2 version (SGD June 2008) of the S. cerevisiae S288C genome, using Bowtie, allowing for 2 mismatches. Reads that matched more than once in the genome or matching to mitochondrial or ribosomal DNA were eliminated from further analysis.
Single end reads were extended to a size of 150bp, the estimated size of our sonicated chromatin preparations
Scaling: Aligned and extended reads were then normalized using a custom script as follows: for normalization, for the untagged control, the top and bottom outliers of the distribution (Q3+1.5IQR and Q1-1.5IQR, respectively) were removed. The average read number per position (coverage) of the remaining reads of the untagged control was then normalized to 1 (scaled untagged control). Similarly, top and bottom outliers of the distribution were removed from the average read number in the tagged samples. Average coverage for the remaining reads was then calculated for the tagged and untagged control at the same positions. This was used to compute the IP/untagged control ratio. Then all reads of the tagged sample were scaled using this ratio (scaled tagged control).
Both scaled tagged and untagged samples were converted to big wig format, and the scaled untagged sample was substracted from the scaled tagged sample.
Genome_build: Saccer2
Supplementary_files_format_and_content: bigwile format files

organism: Saccharomyces cerevisiae

source_name: SK1 meiotic cells t=4 h

growth_protocol: For synchronous meiosis, cells were grown in SPS presporulation medium and transferred to 1% potassium acetate with vigorous shaking at 30˚C

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 apparatus.

treatment_protocol: 1. 109 cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and then chromatin immunoprecipitation was performed as described (Borde et al, 2009)

value: c-Myc monoclonal antibody (9E10, Santa Cruz)


title: Owacja_D6_3


title: Spo16-Myc ChIPseq#2


title: Tajfun_D10_3

description:
Processed data file: res_ow10_tj10_deseq_full.tsv
Processed data file: res_tj6_tj10_deseq_full.tsv
Processed data file: res_tj0_tj10_deseq_full.tsv

source_name: Tajfun, leaves, drought day 10

value: Tajfun


title: Tajfun_D10_2


title: Owacja_D0_3


title: untagged-antiFlag ChIPseq

value: FLAG monoclonal antibody M2 (Sigma)


title: Tajfun_D10_1


title: Short-DF-group [JH49]


title: Tajfun_D6_3

description:
Processed data file: res_ow6_tj6_deseq_full.tsv
Processed data file: res_tj0_tj6_deseq_full.tsv
Processed data file: res_tj6_tj10_deseq_full.tsv

source_name: Tajfun, leaves, drought day 6


title: Spo16-Myc ChIPseq#1


title: Long-DF-group [JF64]


title: Zip4-Flag ChIPseq#2


title: Long-DF-group [JF25]


title: Tajfun_D6_1


title: Zip3-Flag ChIPseq#2


title: Tajfun_D0_3

description:
Processed data file: res_ow0_tj0_deseq_full.tsv
Processed data file: res_tj0_tj6_deseq_full.tsv
Processed data file: res_tj0_tj10_deseq_full.tsv

source_name: Tajfun, leaves, day 0 control


title: Zip2-Flag ChIPseq#2


title: Zip3-Flag ChIPseq#1


title: Tajfun_D0_2


title: Zip2-Flag ChIPseq#1


title: Oberon_D10_3

description:
Processed data file: res_gd10_ob10_deseq_full.tsv
Processed data file: res_ob0_ob10_deseq_full.tsv
Processed data file: res_ob6_ob10_deseq_full.tsv

source_name: Oberon, leaves, drought day 10

value: Oberon


title: Tajfun_D0_1


title: Mix3T3-293T

city: hangzhou

first: guoji

last: guo

state: zhejiang

address: yuhangtang road 388

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description: mouse3T3 is from Stuart Orkin Lab ,human293T is from Stuart Orkin Lab

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism:
Homo sapiens
Mus musculus

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: cell line

value: 3T3 and 293T


title: ciaR_complementary_Rep3

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

description: replicate 3

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using Rockhopper v. 2.03
Analyses were run on default parameter settings with verbose output adjusted for reads to the reverse complement in order to obtain expression data. Significance was represented by a q-value ≤ 0.01 adjusted for a false discovery rate of 1%.
Genome_build: Streptococcus sanguinis reference genome
Supplementary_files_format_and_content: tab-delimited text file includes transcription and translation start/stop site, strand direction, gene name and ID, gene product, raw and normalized counts for each replicate, Reads Per Kilobase of exon per Megabase of library size (RPKM), expression, p-value and Rockhopper's adjusted q-value for the mutant expression vs. the wild-type SK36 expression

organism: Streptococcus sanguinis SK36

source_name: ciaR complementary strain

growth_protocol: Cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. The ciaR mutant and complementary strain were supplemented with kanamycin (500 µg/ml) for selection of the antibiotic resistance cassette.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2, 11, 12, 13, 15, 16, 18, 20, 21, 22). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: growth phase

value: late-log


title: Oberon_D10_2


title: ciaR_mutant_Rep3

description: replicate 3

source_name: ciaR deletion mutant


title: ciaR_complementary_Rep1

description: replicate 1


title: ciaR_complementary_Rep2

description: replicate 2


title: Oberon_D6_2

description:
Processed data file: res_gd6_ob6_deseq_full.tsv
Processed data file: res_ob0_ob6_deseq_full.tsv
Processed data file: res_ob6_ob10_deseq_full.tsv

source_name: Oberon, leaves, drought day 6


title: Oberon_D10_1


title: Pool of samples from strain R: 9 & 10 (R-15-20 & R-15-10)

city: Swansea

first: Rebecca

middle: Jane

last: Pawluk

address: Swansea Univeristy

department: Biosciences

country: United Kingdom

institute: Swansea Univeristy

data_processing:
Raw sequences were processed using Trimmomatic, version 0.33
De novo transcriptome assembly was conducted with reads from all combined samples using Trinity version r2013-02-25
With in silico normalisation with an optimised K value of 40
Annotation: BlastX (ensembl:Zebrafish, Human, Mouse, Medaka, Stickleback) and Blastn, see optimized join all file and http://www.ensembl.org/index.html
Three sequences pools made to ensure equal pool numbers. Alignment using Bowtie2 and read count generation with samtools
Supplementary_files_format_and_content: Expression (cacluated with EdgeR) data set 1: Combined strain treatment groups. 2. Strain R data 3. Strain DAN data

organism: Kryptolebias marmoratus

source_name: Whole fish tissue RNA

extract_protocol:
Bioline Isolate II RNA mini kit (Bioline, London, United Kingdom) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Twenty fish of each line were individually infected with one single Argulus foliaceus raised in brackish water, whereas the other twenty from each line were unexposed to serve as controls. Fish were exposed to the parasite for 48 hours

tag: sample type

value: T2 strain infected

tag: line

value: R


title: ciaR_mutant_Rep2

description: replicate 2

tag: strain


title: Oberon_D6_3

tag: tissue


title: Pool of samples from strain R: 6,7,8 (R-15-01, R-15-07, R-15-11)

value: T3 strain infected


title: Oberon_D6_1


title: Oberon_D0_3

description:
Processed data file: res_gd0_ob0_deseq_full.tsv
Processed data file: res_ob0_ob6_deseq_full.tsv
Processed data file: res_ob0_ob10_deseq_full.tsv

source_name: Oberon, leaves, day 0 control


title: Zip4-Flag ChIPseq#1


title: Tajfun_D6_2


title: Pool of samples from strain DAN: 2 & 3 (DAN-15-16 & DAN-15-18)

value: T1 strain infected

value: DAN


title: Oberon_D0_2


title: Pool of samples from strain DAN: 1,4,5 (DAN-15-14, DAN-15-02, DAN-15-03)

value: T4 strain infected


title: Oberon_D0_1


title: Gwiazda_D10_2

description:
Processed data file: res_gd0_gd10_deseq_full.tsv
Processed data file: res_gd6_gd10_deseq_full.tsv
Processed data file: res_gd10_ob10_deseq_full.tsv

source_name: Gwiazda, leaves, drought day 10

value: Gwiazda


title: Pool of samples from strain DAN: 12, 13, 15 (DAN-15-22, DAN-15-23, DAN-15-25)

value: C3 strain control


title: Pool of samples from strain R: 17 & 18 (R-15-22 & R-15-23)

value: C2 strain control


title: Gwiazda_D10_3

value: soil drought

value: leaf


title: Wild-type_SK36_Rep1

description: replicate 1

source_name: Wild-type SK36

tag: genotype


title: Gwiazda_D10_1


title: Wild-type_SK36_Rep2

description: replicate 2


title: Gwiazda_D6_3

description:
Processed data file: res_gd0_gd6_deseq_full.tsv
Processed data file: res_gd6_gd10_deseq_full.tsv
Processed data file: res_gd6_ob6_deseq_full.tsv

source_name: Gwiazda, leaves, drought day 6


title: Pool of samples from strain DAN: 11 & 14 ( DAN-15-21 & DAN-15-24)

value: C1 strain control


title: Gwiazda_D6_1


title: ciaR_mutant_Rep1

description: replicate 1


title: Gwiazda_D6_2


title: Gwiazda_D0_1

description:
Processed data file: res_gd0_gd6_deseq_full.tsv
Processed data file: res_gd0_gd10_deseq_full.tsv
Processed data file: res_gd0_ob0_deseq_full.tsv

source_name: Gwiazda, leaves, day 0 control

value: control


title: Panax-notoginseng-root-sample-r19

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

description: small RNA

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences whose lengths are greater than or equal to 18 bp (the 3' adapter sequences of reads had been removed by the sequencing facility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to a self-assembled transcriptome with SOAP2
Supplementary_files_format_and_content: sequences and count values

organism: Panax notoginseng

source_name: grow in Wenshan, Yunnan, China

growth_protocol: The Panax notoginseng were grown in field in Wenshan, Yunnan ,China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: no treatment

value: root tuber


title: Panax-notoginseng-root-sample-r52

description: small RNA


title: Panax-notoginseng-root-sample-r60

description: small RNA


title: Panax-notoginseng-root-sample-r3

description: small RNA


title: Panax-notoginseng-whole-plant-sample-M2-1

description: small RNA

value: whole plant