title: resistant clone 8A treated with  3.9 μM of compound 14

first: Genomics-core-facility

last: WCM

address: 1300 York Ave.

institute: Weill Cornell Medicine

description:
6
In vitro grown culture

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters -t 20 -l 45; then mapped to the NCBI Mycobacterium tuberculosis H37Rv complete genome using bwa v0.6.1 with default parameters.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package, following a protocol from "Trapnell C. et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocol, 2012 Mar 1;7(3):562-78.". Reads that aligned to rRNAs were masked by "--mask-file" option.
Genome_build: H37Rv
Supplementary_files_format_and_content: excel file including gene name, ENTREZ_GENE_ID, locus, RPKM values of both conditions, for each gene

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacterium tuberculosis was cultured in complete 7H9 medium (7H9 supplemented with 10% OADC, 0.2% glycerol and 0.02% tyloxapol) at 37°C with 5% CO2 and 20% O2 until the cultures reached am OD580 of 0.6-0.8.

extract_protocol:
Equal volume of 4M guaidinium thicyanate was added to the bacterial suspension and the pellet collected by centrifugation. The pellet was suspended in 1mL of Trizol and transferred to scewcap tubes containing ~0.5 mL of zirconia beads. The cells were lysed by bead-beating (3 cycles) and the lysate collected by centrifugation. Chloroform extraction was performed on the lysate and the aqueous fraction transferred to RNAeasy columns (Qiagen) for purification of RNA. The RNA sample was subjected to DNase (Ambion) digestion for 1h and then treated with the MicrobExpress bacterial mRNA purification kit (Ambion) to remove contaminating rRNA and tRNA. The enriched samples were then used for library construction.
TruSeq RNA sample preparation kit v2 from Illumina was used to generate the libraries by following the Low Sample (LS) protocol. The following adaptors were used: 1) Sample 1: AR005 2) Sample 2: AR004 3) Sample 3: AR012 4) Sample 4: AR019 5) Sample 5: AR002 6) Sample 6: AR004.

treatment_protocol: The log phase culture was diluted to an OD of 0.5 in 7H9 complete medium and split in to two equal parts, 1 arm received the vehicle (DMSO) and the other arm received compound 14 at a final concentration of 3.9 μM. The exposure lasted 4 hours, at which point the bacterial pellet was collected and processed for RNA extraction.

tag: strain

value: resistant clone 8A


title: resistant clone 1A treated with vehicle control (DMSO)

status: Public on Jul 01 2016

type: SRA

city: New York

state: NY

country: USA

description:
3
In vitro grown culture

library_source: transcriptomic

molecule: total RNA

value: resistant clone 1A


title: NuclearRNA

city: Granville

first: Phil

middle: Chi Khang

last: Au

state: New South Wales

address: 10/23 Elizabeth Street

country: Australia

institute: CSIRO

data_processing:
RNA-IP or RNA-seq reads were trimmed for adaptor sequences and low quality bases on ends and reads less than 30 nt were removed
Trimmed and filtered reads were mapped using the CLC genomics workbench (version 4.9) RNA-seq application allowing a maximum of three mismatches and a match of at least 70% similarity in order to account for SNP differences between the experimental ecotype (Landsberg erecta, Ler) against the sequenced Arabidopsis reference genome (Col-0, TAIR10 version)
Mapping up to 20 locations was allowed to avoid removing reads that map to repeat sequences.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cufflinks file containing FPKM values of AGO4-bound transcripts

organism: Arabidopsis thaliana

source_name: 3-week-old seedling arial tissues

growth_protocol: All plants were grown in controlled conditions under 16 h light at 22 °C on MSN medium/agar.

extract_protocol:
Nuclei were isolated  using Honda buffer and nuclear lysates were using for immuniprecipitation or RNA extraction of total nuclear RNA.
cDNA libraries were prepared using the template-switch method derived from Zhao et al (2010, Mol Cell)

treatment_protocol: Arial tissues of 3-week old seedlings were collected for formaldehyde cross-linking and frozen.

tag: ecotype

value: Landsberg erecta

tag: genotype

value: ago4-1/FLAGAGO4 complemented

tag: tissue

value: seedling


title: resistant clone 1A treated with  3.9 μM of compound 14

description:
4
In vitro grown culture


title: HCT116_IDO1ovx_DMF

city: Seoul

first: Ji-Hee

last: Shin

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: AmpliSeq Transcriptome sequencing of DMF treated hIDO1 overexpressing HCT116 cell line

data_processing:
Data were analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Bed file for target region is hg19_AmpliSeq_Transcriptome_21K_v1.bed, which was downloaded from https://ioncommunity.thermofisher.com
human genome hg19 fasta, index_version tmap-f3, was downloaded from https://ioncommunity.thermofisher.com
Genome_build: hg19
Supplementary_files_format_and_content: Four tab-delimited matrix table excel files, each includes raw counts of sequencing reads of 4 Samples for each repeat

organism: Homo sapiens

source_name: human colon cancer cell line (HCT116)

extract_protocol:
RNA was isolated from cells using RNAqueous-4PCR kit (Ambion, Austin, TX, USA) following the manufacturer's instruction.
cDNA libraries were constructed using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher). Samples were barcoded using the Ion Xpress Barcode Adapter kits (Thermo Fisher)

tag: cell line

value: hIDO1 overexpressing


title: resistant clone 8A treated with vehicle control (DMSO)

description:
5
In vitro grown culture


title: AGO4RNA-IP


title: wild type strain, H37Rv, treated with vehicle control (DMSO)

description:
1
In vitro grown culture


title: NegativeRNA-IP

value: ago4-1/AGO4 complemented


title: HCT116_IDO1ovx_Indole

description: AmpliSeq Transcriptome sequencing of Indole treated hIDO1 overexpressing HCT116 cell line


title: HCT116_DMF

description: AmpliSeq Transcriptome sequencing of DMF treated HCT116 cell line

value: wild type


title: WT-2

city: San Michele all'Adige

first: Carmen

last: Leida

address: E. Mach, 1

country: Italy

institute: Fondazione E. Mach

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,  with qtrim v0.94 .
The resulting pre-processed reads were aligned to the reference transcriptome of Vitis vinifera (V1 grapevine annotation - http://genomes.cribi.unipd.it/grape/) using the bowtie2 aligner v2.2.3
Genome_build: Vitis vinifera (V1 grapevine annotation - http://genomes.cribi.unipd.it/grape/)
Supplementary_files_format_and_content: tab-delimited text files include summarized raw read counts values for each Sample

organism: Vitis vinifera

source_name: WT

growth_protocol: in vitro cultivated grapevine plant were micropropagated on jars in WPM and grown under cool white lights (70 µM/m2s) with a 16 h photoperiod.

extract_protocol:
Leaves were sampled from a pool of five different biological replicates, frozen on liquid N2 powdered and RNA was exctracted using SpectrumTM Plant Total RNA kit (Sigma-Aldrich, St Louis, MO) and adding 1% PVP40 in the extraction buffer solution. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with at least 10 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth protocol

value: in vitro cultivated grapevine plant

tag: genotype/variation

value: WT

value: leaf


title: WT-1


title: L15-2

value: VvERF045 OE


title: L15-1


title: Clone 34 day5 Replicate2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Expression profile of hF x mESC fuction, Day 5

data_processing:
Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 and Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene were counted using  HTSeq
FPKM values were computed using R script
Mumber of SNP-overlapping reads for mjor and minor allele was obtained using SAMtools mpileup version 0.1.18
Genome_build: hg19 & mm9
Supplementary_files_format_and_content: hg19 FPKM values
Supplementary_files_format_and_content: Number of reads overlapping with major and minor alleles at selected SNPs on chrX

organism: Homo sapiens x Mus musculus hybrid cell line

source_name: hF x mESC fusion

growth_protocol: Human fibrobalst (hF) clones were maintainedat 3% O2  in DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine and antibiotics (10 µg/ml penicillin and streptomycin). After hF x mESC fusion, cells were cultured in mouse ESC medium (KO-DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine, 50μM β-mercaptoethanol, antibiotics (10 µg/ml penicillin and streptomycin) and LIF) and selected 12hrs after by adding puromycin (1.5 μg/ml) and HAT (20μM hypoxantine, 0.08 mM aminopterin, and 3.2 mM thymidine; Sigma).

extract_protocol:
Total RNA was exacted by RNABee (Amsbio), treated with RNAse-free DNAseI (Ambion) and cleaned-up with RNAeasy Mini-elute columns.
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). For the ligation step, 2 μl of adaptors were used. Libraries were amplified 14 cycles before deep-sequencing.

treatment_protocol: hF clones were fused with mESC by PEG (Roche)

tag: cell type

value: fibroblast clone (derived from TERT-immortalised NHDF17914) fused with mouse ESC (E14Tg2a:puroR)


title: L15-3


title: KO_1

city: Manchester

first: Georges

last: Lacaud

address: Wilmslow Road

department: Cancer Research UK Manchester Institute

institute: University of Manchester

data_processing:
Basecall files generated from the NextSeq 500 sequencing run were converted to FASTQ format with Illumina’s bcl2fast v2.14. Lane-wise alignment was performed by bowtie2 v2.21 to GRCm38 reference genome with default parameters. Generated SAM files from bowtie2 alignment were converted to BAM files by samtools v0.1.19. Parameters for samtools SAM to BAM conversion: -q 10 -f 2 -F 268. Resulting lane-wise BAM files from the same sequence library were merged into one BAM file used for downstream analysis. Read counts from BAM files were extracted under the R environment (R v3.1.0) with the package Rsubread v1.16.1. Only genes with at least 1 count per million in at least three samples were retained for differential expression analysis. Count table was loaded to edgeR v3.8.5 and differentially expressed genes between groups were identified by exact test function.
Genome_build: GRCm38
Supplementary_files_format_and_content: PreMegE_Counts.txt: Tab-delimited text file includes raw counts for each Sample.

organism: Mus musculus

source_name: Bone marrow Pre-Megakaryocyte/Erythroid progenitor, KO

extract_protocol:
Mouse bone marrow (from 3 mice per sample) was flushed into DMEM supplemented with 10% Foetal Bovine Serum and stained with fluorescently conjugated antibodies. Pre-Megakaryocytic/Erythroid (PreMegE) progenitor cells were isolated by Fluorescence Activated Cell Sorting and RNA was harvested using the QIAGEN RNeasy Plus Micro Kit.
Indexed PolyA libraries were prepared using 50ng of total RNA and 16 cycles of amplification in the Agilent Sure Select Strand Specific RNA Library Prep kit for Illumina Sequencing (Agilent).

tag: strain/background

value: adult bone marrow

tag: age

value: 12-16 weeks

value: PreMegE

value: RUNX1C knockout


title: KO_3


title: rep 3_48 hpi

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
libraries were sequenced on an Illumina MiSeq, running Control Software version 2.5.0.5 using default parameters
Reads were trimmed by CLC genomics workbench 7.0.4.  Sequences were trimmed based on quality (limit 0.05) and ambiguity (max of 2 ambiguous bases).  MiSeq adaptors were removed from both strands.
RNAseq analysis was performed by CLC genomics workbench 7.0.4.  Parameters were:  mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8, max of 10 hits for a read
Gene expression was estimated by extracting read counts as integers from the CLC Genomics alignments. The count data were normalized to generate effective library sizes using the scaling method Trimmed Means of M-values (TMM). Statistical analysis was performed with these data using a generalized linear model linked to the negative binomial distribution performed using the EdgeR package (Robinson and Oshlack, 2010). Pair-wise analyses were performed to assess differential gene expression using the control library as a common reference standard.
Genes were considered differentially expressed where the probability after adjustment for multiple hypothesis testing [false discovery rate (FDR)] was less than 0.05. The extent of the observed differential expression was considered meaningful if the fold change exceeded a factor of two.
All significantly up-regulated genes at different sampling times were assigned a functional classification using the BLAST2GO plugin (v1.4.4) in the CLC Genomics Workbench 8.0.1 for functional annotation using Interpro and the NCBI refseq protein database. Then gene ontology (GO) terms to each gene were extracted. The results were filtered to remove top-level annotations and apply the GO-slim categorization from Aspergillus in order to summarize the results. Blast2GO ran ANNEX (Myhre et al., 2006) to add implicit GO terms for a more complete annotation. Finally, Blast2GO was used to calculate the abundance of GO classifications for the significantly up-regulated genes for each time point.
Genome_build: Sclerotinia sclerotiorum 2 transcripts (Broad Institute)
Supplementary_files_format_and_content: MS Excel file containing the counts per million (counts normalized for library size)

molecule: polyA RNA

organism:
Brassica napus
Sclerotinia sclerotiorum

source_name: hyphae and area of leaf under hyphae

growth_protocol: The sclerotinia was grown on minimal salts-glucose (MS–Glu: 2 g/L NH4NO3, 1 g/L KH2PO4, 0.1 g/L MgSO4:7H2O, 0.5 g/L yeast extract, 3 g/L DL-malic acid, 1 g/L NaOH, supplemented with 1% glucose) medium at room temperature, shaken continuously at 40 rpm for 72 hours.

extract_protocol:
The samples were ground to a fine powder with an RNAse-free mortar and pestle precooled with liquid nitrogen. Total RNA was extracted using an Illustra RNAspin mini RNA isolation kit (Illumina, San Diego, USA). RNA quantity and quality was assessed using a Qubit fluorometry assay (Invitrogen Corp., Carlsbad, CA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), respectively.
Libraries were prepared using a Truseq stranded mRNA kit (Illumina, San Diego, USA) following the manufacturer’s instructions.

treatment_protocol: One gram of mycelia (wet weight) was spread over a 5-cm diameter circle on a detached B. napus leaf and incubated in a sealed, humidified tray at room temperature.  After the appropriate infection time, mycelia and the leaf material under the mycelia were collected and flash frozen in liquid nitrogen.

value: hyphae and area of leaf under hyphae

tag: sclerotinia sclerotiorum strain

value: Sclerotinia sclerotiorum 1980

tag: brassica napus strain

value: Brassica napus DH12075

tag: time

value: 48 hous post-innoculation


title: rep 3_12 hpi

value: 12 hours post innoculation


title: rep 3_6 hpi

value: 6 hours post innoculation


title: rep 3_3 hpi

value: 3 hours post innocultion


title: rep 3_1 hpi

value: 1 hour post innoculation


title: pEAE rep1

first: Ioanna

last: Sevastou

address: 149 Tottenham Court Road

department: Translational Research Office

institute: UCL

data_processing:
Illumina software was used for basecalling.
TopHat2 software (Illumina) was used to align the FASTQ data to the UCSC Mus musculus mm10 refererence genome.
Downstream analysis  was performed using Cufflinks software (Illumina).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: Spinal cord

extract_protocol:
Frozen tissue was disrupted in TRIzol® Reagent on ice, using a rotor-stator homogeniser.  Following 5 min incubation at room temperature, chloroform was added to the samples, which were shaken, left to rest and then centrifuged at 12000 g for 15 minutes. The resulting upper aqueous phase was washed with 70% ethanol, mixed well and loaded on an RNeasy column. Thereafter the Qiagen RNeasy® Mini Kit protocol was followed to extract and purify mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse model

value: Biozzi ABH

value: Spinal cord

tag: developmental stage

value: adult

value: pEAE


title: rep 2_48 hpi


title: pEAE rep2


title: WT-3

value: in vitro cultivated grapevine plant

value: WT

value: leaf


title: rep 2_12 hpi


title: WT rep3

value: wild type


title: rep 2_24 hpi

value: 24 hours post-innoculation


title: L_japonica_Yellow_flower

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

description:
All nine tissues for L. japonica, namely, shoot apex, stem, leaf-1 (youngest leaf near shoot apex), leaf-2 (second leaf), leaf-3 (mature leaf), green floral bud, white floral bud, white flower, and yellow flower were harvested in June 2014. L. japonica plants were cultivated in the natural environment of Chiba University pharmaceutical garden, Chiba (located at 35˚36’17.7’’N; 140˚08’06.9’’E).
Lonicera_japonica_de_novo_transcriptome_assembly.fasta
Lonicera_japonica_FPKM_annotation_description.xlsx

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
De novo transcriptome assembly for L. japonica was obtained by merging three popular assemblers, namely, SOAPdenovo-Trans, Trinity v 2.0.6, and CLC Genomics workbench v8.0.3 (https://www.qiagenbioinformatics.com/) (Qiagen, USA). For  SOAPdenovo-Trans, we performed six independent de novo transcriptome assemblies using kmer-sizes as 31, 41, 51, 63, 71, and 91, and resultant assemblies were analysed using perl script from assemblathon_2 to obtain N50-values and other assembly related stats . De novo transcriptome assembly using Trinity, and CLC Genomics workbench were performed using default kmer size and default parameters. Resultant transcriptome assemblies from SOAPdenovo-Trans using kmer size as 31 emerged as the best assembly on the basis of different assembly parameters, which was then pooled together with assemblies from Trinity , and CLC Genomics workbench into one merged assembly, and were processed by CD-HIT-EST v 4.6 (built on Mar 5, 2015) with parameters used as “-c 0.95 –n 8” to remove sequence redundancy. Sequences with a length less than 200 bps were dropped, and resulted de novo transcriptome assembly were used for further characterization.
For transcriptome expression analysis, clean pair reads for each tissue were used for alignment over L. japonica transcriptome assembly using Bowtie 2.0 program , and RSEM program was used for abundance estimation. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method. Unsupervised principal component analysis for all nine tissues was performed by DESeq 2 program using count data for unigenes obtained from RSEM program.
Supplementary_files_format_and_content: .fasta file as De novo transcriptome assembly obtained using transcripts from nine tissues of L. japonica.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were alligned on Lonicera japonicus de novo transcriptome assembly, and abundace were measured using RSEM  program. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM, and IsoPct for each tissues. FPKM values for each tissues were used for furthur analysis.
Supplementary_files_format_and_content: .xlsx files include Transcript_id, Gene_id, Given_Unigene_id_for_manuscript,  FPKM values for transcripts from all nine tissues of L. japonica, and blastx based annotation and top hits associated with each transcript. This  processed dataset combines top-hit blastx annotaion of transcripts and their abundance across different tissues of L. japonica.

organism: Lonicera japonica

source_name: Yellow flower

growth_protocol: All nine tissues for L. japonica, namely, shoot apex, stem, leaf-1 (youngest leaf near shoot apex), leaf-2 (second leaf), leaf-3 (mature leaf), green floral bud, white floral bud, white flower, and yellow flower were harvested in June 2014. L. japonica plants were cultivated in the natural environment of Chiba University pharmaceutical garden, Chiba (located at 35˚36’17.7’’N; 140˚08’06.9’’E). All tissues from L. japonica were harvested on the ice, cut into small pieces, and were snap freezed by liquid N2 before storing at -80˚C prior to RNA extraction.

extract_protocol:
The frozen tissues from L. japonica were powdered using a Multi beads shocker (Yasui Kikai, Japan), and were used for subsequent extraction of total RNA using RNeasy Plant Mini Kit (Qiagen, USA) according to manufacturer’s instructions. RNA quality was assessed using Agilent Bioanalyzer 2100 (Agilent Technology, USA), and RNA samples with RNA integrity number (RIN) above 8 were used for cDNA library preparation.
mRNA for each samples were isolated from the total RNA by using beads with oligo (dT), and were added with fragmentation buffer to shear mRNA into short fragments, which were then used as template for the synthesis of first strand of cDNA using random hexamer primers. cDNA library for Illumina sequencing was prepared using SureSelect Strand specific RNA library kit (Agilent Technology, USA) according to manufacturer’s instructions.

treatment_protocol: Not applicable

tag: tissues

value: Yellow flower


title: WT rep1


title: L_japonica_Green_floral_bud

source_name: Green floral bud

value: Green floral bud


title: L_japonica_White_flower

source_name: White flower

value: White flower


title: L_japonica_White_floral_bud

source_name: White floral bud

value: White floral bud


title: rep 2_3 hpi

value: hyphae and area of leaf under hyphae

value: Sclerotinia sclerotiorum 1980

value: Brassica napus DH12075


title: KO_2

value: adult bone marrow

value: 12-16 weeks

value: PreMegE

value: RUNX1C knockout


title: rep 2_6 hpi

value: 6 hours post innoculation


title: rep 2_1 hpi

value: 1 hour post innoculation


title: pEAE rep3

value: Biozzi ABH

value: Spinal cord

value: adult

value: pEAE


title: rep 3_24 hpi

value: 24 hours post-innoculation


title: rep 1_24 hpi


title: L_japonica_Stem

source_name: Stem

value: Stem


title: rep 1_48 hpi

value: 48 hous post-innoculation


title: L_japonica_Shoot_apex

source_name: Shoot apex

value: Shoot apex


title: WT rep2

value: wild type


title: Swertia_japonica_roots

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
De novo transcriptome assemblies were constructed using three popular transcriptome assemblers, namely, SOAPdenovo-Trans, Trinity v2.1 , and CLC Genome Workbench v8.0.3, and resulting assemblies were merged together to give rise to the final S. japonica transcriptome assembly. Using SOAPdenovo-Trans, we obtained de novo transcriptome assemblies using kmer-sizes as 31, 41, 51, 63, 71, and 91, resulting in the six different transcriptome assemblies. Resulting assemblies were analysed using assemblathon_2.pl scripts, and corresponding N50-values and other assembly characteristics were obtained. On the basis of transcriptome assembly characteristics such as N50-value, number of incorporated nucleotides, mean length, and median length, de novo transcriptome assembly by SOAPdenovo-Trans program, using kmer-size as 31, emerged as the best among all of the six assemblies. For the Trinity and CLC genomic workbench, default kmer-size and other parameters were used, and resultant assemblies were analysed using assemblathon_2.pl scripts to obtain assembly characteristics. Transcriptome assemblies thus obtained using Trinity, CLC genomic workbench, and SOAPdenovo-Trans (kmer-size 31) were pooled together into one merged assembly, and were processed using CD-HIT-EST v4.6 program (built on Mar 5, 2015) with the parameters used as, “-c 0.95 –n 8” , for the removal of sequence redundancy. Sequences with a length less than 200 bps were dropped, and de novo transcriptome assembly for S. japonica thus obtained was used for the subsequent annotation and characterization, and for the expression analysis.
For the transcripts expression analysis, clean paired end reads for each tissues were aligned to the S. japonica transcriptome assembly using Bowtie2.0 program, and transcripts abundance was estimated using RSEM program. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: .results files were generated using RSEM program. Clean reads for each tissues were aligned on Swertia Japonica de novo transcriptome assembly that were generated using Trinity, and abundace were measured using RSEM. Content of each file contains transcript_id (which is contig), gene_id (which is unigene), length, effective_length, expected_count, TPM, FPKM, and IsoPct for each tissues. FPKM values for each tissues were used for furthur analysis.
Supplementary_files_format_and_content: .xlsx file includes unigene_id, and FPKM values for the aerial-tissues and the roots of S. japonica. FPKM values were calculated using RSEM program. results files for all tissues were used to extract FPKM values for each tissues, and were combind/aligned against transcript_id and gene_id

organism: Swertia japonica

growth_protocol: Plants of S. japonica were grown in the natural environment conditions at the Chiba University medicinal garden, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan (located at 35°36’17.7’’ N; 140°08’06.9’’ E). Six months old plants were harvested on the ice (Fig 1A), roots and aerial-tissues were dissected, and snap freezed by liquid N2 before storing samples at -80°C prior to the RNA extraction.

extract_protocol:
The frozen samples of S. japonica were powdered using a multi beads shaker (Yasui Kikai, Japan), and were used for the subsequent RNA extraction. Total RNA for each tissue types were isolated using RNeasy Plant Mini Kit (Qiagen, USA) according to the manufacturer’s instruction. The extracted RNA samples were treated with RNase free DNase (Takara, Japan), purified by column binding, and further purified through ethanol precipitation. RNA quality for each sample was assessed by the Agilent Bioanalyzer 2100 (Agilent Technology, USA), and samples with RNA integrity number (RIN) value above 8 were selected for the cDNA library preparation.
For the cDNA library construction, firstly, mRNA for each samples were isolated from the total RNA using beads with oligo (dT). mRNA thus obtained were added with the fragmentation buffer to shear it in the small fragments, which were used as templates for the synthesis of the first strand of cDNA using random hexamer primers. cDNA library was then prepared using SureSelect Strand Specific RNA library kit (Agilent Technology, USA) according to the manufacturer’s instruction.

value: Root

value: 6 month-old


title: L_japonica_Leaf-2

source_name: Leaf

value: second leaf


title: Swertia_japonica_aerial-tissues

value: Aerial-tissues


title: rep 1_6 hpi

value: hyphae and area of leaf under hyphae

value: Sclerotinia sclerotiorum 1980

value: Brassica napus DH12075


title: rep 1_3 hpi

value: 3 hours post innocultion


title: L_japonica_Leaf-1

value: youngest leaf


title: L_japonica_Leaf-3

value: mature leaf


title: rep 1_0 hpi

organism: Sclerotinia sclerotiorum

source_name: hyphae

value: hyphae

value: pre-innoculation


title: H2-26

city: Saarbrücken

first: Bogdan

last: Tokovenko

address: Campus C2.3

country: Germany

institute: Helmholtz Institute for Pharmaceutical Research Saarland

data_processing:
Basecalling: Illumina CASAVA1.8
Preprocessing: prinseq-lite.pl -min_len 20 -trim_tail_left 4 -trim_tail_right 4 -trim_ns_left 1 -trim_ns_right 1 -trim_qual_left 20 -trim_qual_right 20 -trim_qual_type mean -trim_qual_window 3
Mapping: novoalign 3.00.04, -r Random -H
Computational rRNA depletion: reads mapping within any of the 7 rRNA clusters were discarded.
Genome_build: NC_020990.1, with appended 200 bps of Ns, followed by the H2-26-act cosmid
Supplementary_files_format_and_content: Tab-delimited files with raw read counts and a matrix (CSV) file with DESeq normalized values and processing results.

organism: Streptomyces albus

source_name: mycelium

growth_protocol: S. albus H2-26-act and S. albus H2-26 were inoculated in TSB medium and cultivated at 28 °C and 180 rpm for 24 hours. Obtained precultures were reinoculated into SG production medium. The strains were cultivated for 3 days at 28 °C and 180 rpm until the onset of secondary metabolite production.

extract_protocol:
Mycelium was harvested by centrifugation.
Briefly, ribosomal RNA depletion of isolated total RNA was performed with a Ribo-Zero Bacteria kit from Epicentre (Madison, WI, USA). The rRNA-depleted RNA was fragmented with RNase III, and 5′PPP structures were removed using RNA 5′ polyphosphatase (Epicentre). Next, RNA fragments were poly(A)-tailed using poly(A) polymerase. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was amplified and purified, and fragments in the length range of 250 – 500 bp were sequenced on an Illumina HiSeq 2000 machine (San Diego, CA, USA) with 100 bp read length.

tag: cosmid


title: H2-26-act

tag: strain

value: Lanact


title: TXY deltaRepA mESCs -dox_ATAC-seq

status: Public on Jun 30 2016

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

description: processed data file: RepA_minusdox_merge.bed_peaks.narrowPeak

library_source: genomic

data_processing:
library strategy: ATAC-seq
ATAC adapters and barcodes were trimmed using CutAdapt Software
Sequences were aligned to the mm9 genome using Bowtie2 software
Non-concordant reads and reads mapping to the mm9 blacklist were filtered out
Peaks were called using Macs2 software with a no-shifting model - peaks were called separately for the X chromosome and the autosomes and then merged
Peaks were filtered using IDR software with a  cutoff of 0.05.
Number of allelic reads (SNP-containing reads) per peak was quantified and added to the peak file
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files with normalized allelic signal for each sample.
Supplementary_files_format_and_content: Bed files for each replicate are MACS2 output of peak lists.  Bed files for each cell type contain list of merged peaks with p<0.05 (IDR).  Columns:  chromosome, peak start, peak end, confidence of peak, length of peak, total number of reads, # 129 reads, # Cast reads
Supplementary_files_format_and_content: signals in corrected.bw bigWigs were corrected for Xist+ cells

molecule: genomic DNA

source_name: mouse embryonic stem cells

extract_protocol:
Nuclei were isolated using NP-40-containing buffer and subsequently transposed with adapter-loaded hyperactive Tn5 transposase (Illumina).
Following clean-up transposed fragments were directly amplified and barcoded using Nextera indexes
Libraries were then sequenced using Illumina NextSeq 500 with 2x75 bp reads

tag: gender

value: male

value: TXY deltaRepA

tag: cross

value: male cells with inducible Xist on X with RepA deletion

tag: treated with

value: none (untreated control)

tag: cell number

value: 50K per replicate


title: rep 3_0 hpi

tag: tissue


title: TXY deltaRepA mESCs +dox_ATAC-seq

tag: cell line

tag: genotype/variation

value: with 2ug/mL doxycycline for 48hrs


title: wild type strain, H37Rv, treated with 3.9 μM of compound 14

description:
2
In vitro grown culture


title: deltaFT NPCs

data_processing:
ATAC adapters and barcodes were trimmed using CutAdapt Software
Sequences were aligned to the mm9 genome using Bowtie2 software
Non-concordant reads and reads mapping to the mm9 blacklist were filtered out
Peaks were called using Macs2 software with a no-shifting model - peaks were called separately for the X chromosome and the autosomes and then merged
Peaks were filtered using IDR software with a  cutoff of 0.05.
Number of allelic reads (SNP-containing reads) per peak was quantified and added to the peak file
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files with normalized allelic signal for each sample.
Supplementary_files_format_and_content: Bed files for each replicate are MACS2 output of peak lists.  Bed files for each cell type contain list of merged peaks with p<0.05 (IDR).  Columns:  chromosome, peak start, peak end, confidence of peak, length of peak, total number of reads, # 129 reads, # Cast reads

source_name: neural progenitor cells

tag: cell line name

value: 129S1 x Cast:EiJ F1

tag: growth protocol

value: NPCs were grown in N2/B27 media supplemented with 10 ng/mL FGF and EGF on 0.2% gelatin-coated plates

value: female


title: WT NPCs

value: NPCs were grown in N2/B27 media supplemented with 10 ng/mL FGF and EGF on 0.2% gelatin coated plates


title: WT mESCs

value: mESCs were grown in medium supplemented with fetal bovine serum (FBS) and mLIF on 0.2% gelatin-coated plates.


title: Arabidopsis_cer6axr3-1_W4

city: La Jolla

first: Carl

last: Procko

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2)
Reads were aligned to Arabidopsis TAIR10 or B. rapa FPsc v1.3 using TopHat version 2.0.9 and Bowtie 2.1.0 (strand-specific).
Cufflinks, Cuffmerge and Cuffdiff versions 2.1.1 were used for transcriptome assembly and differential expression analysis using default parameters.
In addition, Brassica samples were analyzed using multi-mapped read correction parameter in Cufflinks and Cuffdiff.
Genome_build: TAIR10 (Arabidopsis) or FPsc v1.3 (Brassica)
Supplementary_files_format_and_content: Excel spreadsheets showing differential gene expression for relevant pairwise comparisons as given from the Cuffdiff gene expression output; showing fpkm, log2 fold change, and fold-change significance.

source_name: whole-seedlings

growth_protocol: Seedlings are grown in continuous W light on 1/2 LS 0.7% agar plates.

extract_protocol:
RNA was extracted using Qiagen RNeasy micro kit and digested with DNase I. Agilent Tape Station was used to determine RNA integrity (RIN) numbers prior to library preparation.
Stranded mRNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Libraries were then quantified, pooled and sequenced at single-end 50 base-pair reads using the Illumina HiSeq 2500 platform. Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2).

treatment_protocol: Seedlings are treated with W light or shade (low red:far red light).

tag: genotype

tag: treatment

value: W light


title: Arabidopsis_cer6axr3-1_Sh2

value: Shade


title: TXY WT mESCs -dox_ATAC-seq

description: processed data file: Wt_minusdox_merge.bed_peaks.narrowPeak

value: TXY WT

value: male cells with inducible Xist on X


title: Arabidopsis_cer6axr3-1_Sh1


title: Arabidopsis_cer6axr3-1_W2


title: Arabidopsis_cer6axr3-1_W1


title: rep 1_1 hpi

value: hyphae and area of leaf under hyphae

tag: sclerotinia sclerotiorum strain

value: Sclerotinia sclerotiorum 1980

tag: brassica napus strain

value: Brassica napus DH12075

tag: time

value: 1 hour post innoculation


title: Arabidopsis_cer6axr3-1_Sh4


title: Arabidopsis_control_Sh3

value: control


title: Arabidopsis_control_Sh4


title: Arabidopsis_control_Sh2


title: Arabidopsis_control_W4


title: Arabidopsis_control_W2


title: Arabidopsis_control_W3


title: Arabidopsis_control_W1


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 70

city: Irvine

first: Weihua

last: Zeng

address: 2300E Bio Sci III

department: Dev & Cell Biology

institute: UCIrvine

data_processing:
reads were aligned using STAR v.2.4.2a with parameters ‘--outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.07 --outFilterMultimapNmax 10’
gene expression was measured using RSEM v.1.2.12
Genes with TPM >= 1.0 in at least 5 nuclei (for lncRNA analysis) or 10 nuclei (for other analyses) were included in the final matrices.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM or count values for each Sample ...

source_name: immortalized myoblast KD3

growth_protocol: KD3 cells were grown on dishes coated with collagen in high glucose DMEM(Gibco) supplemented with 20% FBS (Omega Scientific,inc), 1% Pen-Strep(Gibco), and  2% Ultrasor G (Crescent Chemical Co.)

extract_protocol:
The cell membrane was ruptured with cold cell lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.005% IGEPAL CA-630) for 4-5 mins to release nucleus and the lysis efficiency was checked by Trypan blue (Lonza) staining.
Single cells and nuclei were isolated using the Fluidigm C1 System. We used the largest integrated fluidic circuits (IFCs) of 17-25mm for KD3 cells. Single nuclei C1 runs were completed using the smallest IFC (5-10mm).  After capturing, the IFC was loaded with Clontech SMARTer kit lysis, RT, and PCR amplification reagents. Lysis, RT, and PCR amplification was completed overnight and harvested the following day. After harvesting, libraries were constructed using Illumina’s Nextera XT library prep kit per Fluidigm’s protocol. Constructed libraries were multiplexed and purified using AMPure beads.

treatment_protocol: Upon reaching 80% confluence, we induced differentiation using high glucose DMEM medium supplemented with 2% FBS and ITS supplement (insulin 0.1%, 0.000067% sodium selenite, 0.055% transferrin; Invitrogen). Fresh differentiation medium was changed every 24hrs.   Myotubes and MNCs were harvested at 72 hrs after induction of differentiation.

tag: stages

value: mononucleated cell nucleus


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 68


title: Arabidopsis_cer6axr3-1_Sh3


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 65


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 67


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 64


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 66


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 63


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 61


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 56


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 57


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 55


title: rep 1_12 hpi

value: 12 hours post innoculation


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 59


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 58


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 52


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 53


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 51


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 50


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 48


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 60


title: TATCre+hSS1 tumor 3

city: Salt Lake City

first: Kevin

middle: B

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

institute: University of Utah

data_processing:
Reads were aligned to mm10 chromosome sequence + splice junction sequences using Novoalign (v2.08.03), allowing up to 50 alignments for each read. Splice junctions were created by running USeq (v8.8.8) MakeTranscriptome application using Ensembl transcript annotations.
The resulting alignment file was processed with the USeq (v8.8.8) application SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities.  SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq's DefinedRegionDifferentialSeq application was used to calculate FPKMs
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing FPKMs

source_name: TATCre+hSS1 tumor

growth_protocol: Mice with Cre-lox inducible alleles of either SS18-SSX1 or SS18-SSX2 were injected in the pre-tibial soft-tissues with TATCre protein to induce tumors, which were harvested approximately 1 year later from each.

extract_protocol:
Tumors were harvested and snap frozen. Total RNA was extracted using Rneasy kits from Qiagen.
Ribo-Zero method of coding sequence selection was used for library generation

treatment_protocol: No treatments

value: containing Cre-lox inducible allele of SS18-SSX1

tag: injected with

value: TATCre protein

tag: time point

value: 1 year after the injection

value: tumor from leg


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 45


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 42


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 44


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 43


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 41


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 39


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 46


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 38


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 40


title: HCT116_Indole

description: AmpliSeq Transcriptome sequencing of Indole treated HCT116 cell line

source_name: human colon cancer cell line (HCT116)

value: wild type


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 37


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 34


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 49


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 33


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 36


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 47


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 30


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 32


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 29


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 28


title: TXY WT mESCs +dox_ATAC-seq

tag: gender

value: male

value: with 2ug/mL doxycycline for 48hrs

value: 50K per replicate


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 25


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 24


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 26


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 23


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 27


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 22


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 21


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 18


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 69


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 35


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 62


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 19


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 31


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 14


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 15


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 17


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 13


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 11


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 9


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 16


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 8


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 6


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 7


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 3


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 5


title: rep 2_0 hpi

value: hyphae

value: pre-innoculation


title: differentiated KD3 myotube single-nucleus RNA-seq 49

value: myotube nucleus


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 54


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 2


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 1


title: differentiated KD3 myotube single-nucleus RNA-seq 50


title: differentiated KD3 myotube single-nucleus RNA-seq 46


title: differentiated KD3 myotube single-nucleus RNA-seq 47


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 12


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 10


title: differentiated KD3 myotube single-nucleus RNA-seq 45


title: differentiated KD3 myotube single-nucleus RNA-seq 44


title: differentiated KD3 myotube single-nucleus RNA-seq 43


title: differentiated KD3 myotube single-nucleus RNA-seq 48


title: Arabidopsis_cer6axr3-1_W3

value: W light


title: differentiated KD3 myotube single-nucleus RNA-seq 36


title: differentiated KD3 myotube single-nucleus RNA-seq 37


title: differentiated KD3 myotube single-nucleus RNA-seq 38


title: differentiated KD3 myotube single-nucleus RNA-seq 42


title: differentiated KD3 myotube single-nucleus RNA-seq 39


title: differentiated KD3 myotube single-nucleus RNA-seq 40


title: differentiated KD3 myotube single-nucleus RNA-seq 41


title: differentiated KD3 myotube single-nucleus RNA-seq 34


title: differentiated KD3 myotube single-nucleus RNA-seq 29


title: differentiated KD3 myotube single-nucleus RNA-seq 28


title: differentiated KD3 myotube single-nucleus RNA-seq 32


title: differentiated KD3 myotube single-nucleus RNA-seq 27


title: differentiated KD3 myotube single-nucleus RNA-seq 31


title: differentiated KD3 myotube single-nucleus RNA-seq 33


title: differentiated KD3 myotube single-nucleus RNA-seq 24


title: differentiated KD3 myotube single-nucleus RNA-seq 30


title: differentiated KD3 myotube single-nucleus RNA-seq 25


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 4


title: differentiated KD3 myotube single-nucleus RNA-seq 26


title: differentiated KD3 myotube single-nucleus RNA-seq 22


title: differentiated KD3 myotube single-nucleus RNA-seq 21


title: differentiated KD3 myotube single-nucleus RNA-seq 19


title: differentiated KD3 myotube single-nucleus RNA-seq 20


title: differentiated KD3 mononucleated cell (MNC) single-nucleus RNA-seq 20


title: differentiated KD3 myotube single-nucleus RNA-seq 17


title: differentiated KD3 myotube single-nucleus RNA-seq 18


title: differentiated KD3 myotube single-nucleus RNA-seq 16


title: differentiated KD3 myotube single-nucleus RNA-seq 13


title: differentiated KD3 myotube single-nucleus RNA-seq 14


title: differentiated KD3 myotube single-nucleus RNA-seq 12


title: differentiated KD3 myotube single-nucleus RNA-seq 10


title: differentiated KD3 myotube single-nucleus RNA-seq 5


title: differentiated KD3 myotube single-nucleus RNA-seq 23


title: differentiated KD3 myotube single-nucleus RNA-seq 7


title: differentiated KD3 myotube single-nucleus RNA-seq 6


title: differentiated KD3 myotube single-nucleus RNA-seq 4


title: differentiated KD3 myotube single-nucleus RNA-seq 2


title: differentiated KD3 myotube single-nucleus RNA-seq 1


title: differentiated KD3 myotube single-nucleus RNA-seq 35


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 57

value: myoblast nucleus


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 58


title: differentiated KD3 myotube single-nucleus RNA-seq 8


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 55


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 54


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 56


title: differentiated KD3 myotube single-nucleus RNA-seq 3


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 51


title: Arabidopsis_control_Sh1

value: Shade


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 49


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 53


title: differentiated KD3 myotube single-nucleus RNA-seq 15


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 48


title: differentiated KD3 myotube single-nucleus RNA-seq 11


title: differentiated KD3 myotube single-nucleus RNA-seq 9


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 50


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 45


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 59


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 47


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 44


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 52


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 41


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 38


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 42


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 46


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 37


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 43


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 35


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 33


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 39


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 34


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 30


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 31


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 27


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 32


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 25


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 28


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 24


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 23


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 26


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 21


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 36


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 22


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 18


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 19


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 16


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 17


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 40


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 15


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 13


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 14


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 12


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 29


title: Williams83_SMV-LRB_degradome-seq

first: Hui

last: Chen

state: Ontario

address: 1391 Sandford St.

description:
Poly (A)+ RNA
Williams82_degradome-seq_Alignment_Report.txt

data_processing:
For RNA-seq analysis, the raw sequences were aligned to the soybean reference transcriptome (Glyma1, Ensembl genes and transcripts) using the Strand NGS software (Strand Life Sciences, version 2.1) following RNA alignment and RNA-seq analysis pipeline with standard parameters.
For sRNA-seq analysis, after the low quality reads and the adapter sequences were trimmed, the sequences were mapped to the Glycine max reference genome (Glyma1, Ensembl) and aligned to the known miRNA gene of Glycine max (miRBase 21) using the Strand NGS software (Strand Life Sciences, version 2.1) following small RNA alignment and small RNA analysis pipeline with standard parameters.
For degradome-seq analysis, the adaptor sequences, tRNA/rRNA sequences and low complexity sequences were removed from raw reads, then the length of degradome sequences and small RNA sequences were trimmed to 20-21 nt and 19-24 nt, respectively. Any sequences without a match to the soybean genome (Glyma1, Ensembl) were also removed from further analysis. The potential targets of small RNAs were identified and validated using the UEA small RNA workbench following the PAREsnip pipeline under a high stringency setting with the Glycine max reference genome (Glyma1, Ensembl) and the known miRNAs of Glycine max (miRBase 21).
Genome_build: Soybean reference transcriptome (Glyma1, Ensembl) and soybean known miRNA (miRBase 21)
Supplementary_files_format_and_content: The txt files of alignment reports were geneated using the Strand NGS software (Strand Life Sciences, version 2.1) following various alignment and analysis pipeline with standard parameters.

organism: Glycine max

source_name: leaves tissues

growth_protocol: Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.

extract_protocol:
Total RNA and small RNA fractions (≤ 200 nt) were extracted from the leaves inoculated by SMV-L,SMV-LRB,SMV-G7 and Mock using a mirVana miRNA isolation kit (Ambion) and the Poly (A)+ RNA was isolated using the NucleoTrap@ mRNA purification kits (Machery-Nagel) according to the instructions of the supplier.
RNA-seq and sRNA-seq libraries were prepared following the manufacturer's instructions using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2501) and TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012),respectively. Degradome-seq libraries were constructed as previously described using Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0024)(German, M. A. et al., Nature Biotechology, 2008; German et al., Nature Protocols, 2009; Zhai et al., 2014).

treatment_protocol: Leaves were mechanically inoculated  by SMV-L, SMV-LRB,SMV-G7 and Mock (buffer) after germination at 10 days.

tag: cultivar

value: Susceptible

tag: agent

value: SMV-LRB

tag: age

value: 14 days post-inoculation


title: Williams82_SMV-G7_degradome-seq


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 9


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 11


title: Williams82_SMV-L_degradome-seq

value: SMV-L


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 10


title: Williams82_SMV-G7_sRNA-seq

description:
Small RNA fractions (≤ 200 nt)
Williams82_sRNA-seq_Alignment_Report.txt


title: Williams83_SMV-LRB_sRNA-seq


title: Williams82_SMV-L_sRNA-seq


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 6


title: Williams82_Mock_sRNA-seq

value: Mock


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 5


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 20


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 4


title: Williams82_SMV-G7_RNA-seq


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 2


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 3


title: Williams83_SMV-LRB_RNA-seq

value: 15 days post-inoculation


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 1


title: Williams82_SMV-L_RNA-seq


title: undifferentiated KD3 myoblast single-cell RNA-seq 74

value: myoblast


title: undifferentiated KD3 myoblast single-cell RNA-seq 73


title: Williams82_Mock_RNA-seq


title: undifferentiated KD3 myoblast single-cell RNA-seq 72


title: undifferentiated KD3 myoblast single-cell RNA-seq 70


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 8


title: undifferentiated KD3 myoblast single-cell RNA-seq 75


title: undifferentiated KD3 myoblast single-cell RNA-seq 68


title: Williams82_Mock_degradome-seq


title: undifferentiated KD3 myoblast single-cell RNA-seq 67


title: undifferentiated KD3 myoblast single-cell RNA-seq 71


title: undifferentiated KD3 myoblast single-cell RNA-seq 65


title: undifferentiated KD3 myoblast single-nucleus RNA-seq 7


title: undifferentiated KD3 myoblast single-cell RNA-seq 66


title: undifferentiated KD3 myoblast single-cell RNA-seq 64


title: undifferentiated KD3 myoblast single-cell RNA-seq 63


title: undifferentiated KD3 myoblast single-cell RNA-seq 62


title: undifferentiated KD3 myoblast single-cell RNA-seq 61


title: undifferentiated KD3 myoblast single-cell RNA-seq 60


title: undifferentiated KD3 myoblast single-cell RNA-seq 59


title: undifferentiated KD3 myoblast single-cell RNA-seq 58


title: undifferentiated KD3 myoblast single-cell RNA-seq 57


title: undifferentiated KD3 myoblast single-cell RNA-seq 55


title: undifferentiated KD3 myoblast single-cell RNA-seq 53


title: undifferentiated KD3 myoblast single-cell RNA-seq 56


title: undifferentiated KD3 myoblast single-cell RNA-seq 52


title: undifferentiated KD3 myoblast single-cell RNA-seq 54


title: undifferentiated KD3 myoblast single-cell RNA-seq 50


title: undifferentiated KD3 myoblast single-cell RNA-seq 49


title: undifferentiated KD3 myoblast single-cell RNA-seq 69


title: undifferentiated KD3 myoblast single-cell RNA-seq 48


title: undifferentiated KD3 myoblast single-cell RNA-seq 47


title: undifferentiated KD3 myoblast single-cell RNA-seq 44


title: undifferentiated KD3 myoblast single-cell RNA-seq 39


title: undifferentiated KD3 myoblast single-cell RNA-seq 43


title: undifferentiated KD3 myoblast single-cell RNA-seq 41


title: undifferentiated KD3 myoblast single-cell RNA-seq 38


title: undifferentiated KD3 myoblast single-cell RNA-seq 36


title: undifferentiated KD3 myoblast single-cell RNA-seq 35


title: undifferentiated KD3 myoblast single-cell RNA-seq 34


title: undifferentiated KD3 myoblast single-cell RNA-seq 33


title: undifferentiated KD3 myoblast single-cell RNA-seq 32


title: undifferentiated KD3 myoblast single-cell RNA-seq 30


title: undifferentiated KD3 myoblast single-cell RNA-seq 29


title: undifferentiated KD3 myoblast single-cell RNA-seq 28


title: undifferentiated KD3 myoblast single-cell RNA-seq 31


title: undifferentiated KD3 myoblast single-cell RNA-seq 46


title: undifferentiated KD3 myoblast single-cell RNA-seq 27


title: undifferentiated KD3 myoblast single-cell RNA-seq 51


title: undifferentiated KD3 myoblast single-cell RNA-seq 37


title: undifferentiated KD3 myoblast single-cell RNA-seq 42


title: undifferentiated KD3 myoblast single-cell RNA-seq 45


title: undifferentiated KD3 myoblast single-cell RNA-seq 23


title: undifferentiated KD3 myoblast single-cell RNA-seq 26


title: undifferentiated KD3 myoblast single-cell RNA-seq 25


title: undifferentiated KD3 myoblast single-cell RNA-seq 22


title: undifferentiated KD3 myoblast single-cell RNA-seq 21


title: undifferentiated KD3 myoblast single-cell RNA-seq 24


title: undifferentiated KD3 myoblast single-cell RNA-seq 20


title: undifferentiated KD3 myoblast single-cell RNA-seq 19


title: undifferentiated KD3 myoblast single-cell RNA-seq 40


title: undifferentiated KD3 myoblast single-cell RNA-seq 18


title: undifferentiated KD3 myoblast single-cell RNA-seq 16


title: undifferentiated KD3 myoblast single-cell RNA-seq 13


title: undifferentiated KD3 myoblast single-cell RNA-seq 15


title: undifferentiated KD3 myoblast single-cell RNA-seq 17


title: undifferentiated KD3 myoblast single-cell RNA-seq 14


title: undifferentiated KD3 myoblast single-cell RNA-seq 12


title: undifferentiated KD3 myoblast single-cell RNA-seq 11


title: undifferentiated KD3 myoblast single-cell RNA-seq 9


title: undifferentiated KD3 myoblast single-cell RNA-seq 8


title: undifferentiated KD3 myoblast single-cell RNA-seq 7


title: undifferentiated KD3 myoblast single-cell RNA-seq 10


title: undifferentiated KD3 myoblast single-cell RNA-seq 5


title: undifferentiated KD3 myoblast single-cell RNA-seq 6


title: undifferentiated KD3 myoblast single-cell RNA-seq 2


title: undifferentiated KD3 myoblast single-cell RNA-seq 3


title: undifferentiated KD3 myoblast single-cell RNA-seq 1


title: Beta cell 204

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using CLC bio Genomics Workbench Version 7.0 (CLC Bio) allowing one mismatch.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Pancreatic islets

extract_protocol:
Single islet cells were captured with C1 Integrated Fluidic Circuit. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (Protocol #100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).

tag: tissue

value: Pancreatic islets

tag: group

value: Old

value: 26 months

tag: Sex


title: Beta cell 207

value: male


title: Beta cell 205


title: Beta cell 200


title: Beta cell 201


title: Beta cell 203


title: Beta cell 198


title: Beta cell 206


title: Beta cell 197


title: Beta cell 196


title: Beta cell 199


title: Beta cell 193


title: E14 DRIP-seq

city: Davis

first: Yoong Wearn

last: Lim

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

description:
RNA/DNA hybrids
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

data_processing:
Library strategy: DRIP-Seq
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCm38 (mm9)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.

source_name: embryonic stem cell line

extract_protocol: Standard Illumina protocols.

tag: cell line


title: Beta cell 192


title: Beta cell 202


title: Beta cell 195


title: Beta cell 191


title: 3T3 DRIP-seq

source_name: embryonic fibroblast cell line


title: Beta cell 189


title: undifferentiated KD3 myoblast single-cell RNA-seq 4


title: Beta cell 190


title: Beta cell 188


title: Beta cell 194


title: Beta cell 187


title: Beta cell 186


title: Beta cell 185


title: Beta cell 184


title: Beta cell 182


title: Beta cell 179


title: Beta cell 183


title: Beta cell 180


title: Beta cell 178


title: Beta cell 173


title: Beta cell 176


title: Beta cell 181


title: Beta cell 167


title: Beta cell 175


title: Beta cell 177


title: Beta cell 171


title: Beta cell 172


title: Beta cell 164


title: Beta cell 163


title: Beta cell 169


title: Beta cell 166


title: Beta cell 168


title: Beta cell 162


title: Beta cell 158


title: Beta cell 174


title: Beta cell 160


title: Beta cell 161


title: Beta cell 154


title: Beta cell 155


title: Beta cell 157


title: Beta cell 156


title: Beta cell 159


title: Beta cell 153


title: Beta cell 170


title: Beta cell 152


title: Beta cell 150


title: Beta cell 151


title: Beta cell 149


title: Beta cell 165


title: Beta cell 147


title: Beta cell 148


title: Beta cell 146


title: Beta cell 142


title: Beta cell 145


title: Beta cell 139


title: Beta cell 138

value: Young

value: 3 months


title: Beta cell 136


title: Beta cell 137


title: Beta cell 143


title: Beta cell 135


title: Beta cell 131


title: Beta cell 134


title: Beta cell 127


title: Beta cell 132


title: Beta cell 129


title: Beta cell 133


title: Beta cell 130


title: Beta cell 125


title: Beta cell 123


title: Beta cell 124


title: Beta cell 144


title: Beta cell 120


title: Beta cell 119


title: Beta cell 121


title: Beta cell 140


title: Beta cell 115


title: Beta cell 117


title: Beta cell 118


title: Beta cell 116


title: Beta cell 114


title: Beta cell 112


title: Beta cell 113


title: Beta cell 141


title: Beta cell 109


title: Beta cell 126


title: Beta cell 111


title: Beta cell 102


title: Beta cell 107


title: Beta cell 110


title: Beta cell 101


title: Beta cell 106


title: Beta cell 128


title: Beta cell 122


title: Beta cell 103


title: Beta cell 104


title: Beta cell 99


title: Beta cell 100


title: Beta cell 97


title: Beta cell 95


title: Beta cell 94


title: Beta cell 93


title: Beta cell 92


title: Beta cell 98


title: Beta cell 91


title: Beta cell 89


title: Beta cell 90


title: Beta cell 88


title: Beta cell 96


title: Beta cell 108


title: Beta cell 87


title: Beta cell 86


title: Beta cell 85


title: Beta cell 105


title: Beta cell 83


title: Beta cell 84


title: Beta cell 82


title: Beta cell 80


title: Beta cell 81


title: Beta cell 79


title: Beta cell 78


title: Beta cell 75


title: Beta cell 74


title: Beta cell 77


title: Beta cell 76


title: Beta cell 72


title: Beta cell 70


title: Beta cell 71


title: Beta cell 69


title: Beta cell 67


title: Beta cell 65


title: Beta cell 68


title: Beta cell 64


title: Beta cell 62


title: Beta cell 60


title: Beta cell 59


title: Beta cell 63


title: Beta cell 58


title: Beta cell 57


title: Beta cell 61


title: Beta cell 54


title: Beta cell 56


title: Beta cell 55


title: Beta cell 52


title: Beta cell 53


title: Beta cell 51


title: Beta cell 73


title: Beta cell 46


title: Beta cell 44


title: Beta cell 50


title: Beta cell 49


title: Beta cell 47


title: Beta cell 43


title: Beta cell 66


title: Beta cell 45


title: Beta cell 42


title: Beta cell 40


title: Beta cell 41


title: Beta cell 39


title: Beta cell 38


title: Beta cell 33


title: Beta cell 32


title: Beta cell 31


title: Beta cell 30


title: Beta cell 29


title: Beta cell 27


title: Beta cell 28


title: Beta cell 26


title: Beta cell 48


title: Beta cell 25


title: Beta cell 24


title: Beta cell 22


title: Beta cell 20


title: Beta cell 21


title: Beta cell 17


title: Beta cell 15


title: Beta cell 37


title: Beta cell 18


title: Beta cell 16


title: Beta cell 13


title: EVOO

city: Madrid

first: Lidia

middle: Ángeles

last: Daimiel-Ruiz

state: Madrid

address: Ctra. Cantoblanco, Km 8

department: Nutritional Genomics of Cardiovascular Disease and Obesity

country: Spain

institute: Institute IMDEA Food

data_processing:
Standard Ion PGM basecalling procedure
Sequenced reads were trimmed for adaptor sequences
Then samples aligning with the MS2 carrier were removed
Quality control included a Phred QC 20 filtering
Samples with a QC value higher than 20 were aligned against Viridiplanate clade using Bowtie 2
Supplementary_files_format_and_content: tab-delimited text files

organism: Olea europaea

source_name: 30 mL starting material

extract_protocol: Trizol

value: extra virgin olive oil


title: Beta cell 23


title: Beta cell 14


title: Beta cell 11


title: Beta cell 12


title: Beta cell 9


title: Beta cell 35


title: Beta cell 8


title: Beta cell 10


title: Beta cell 36


title: Beta cell 7


title: Beta cell 6


title: Beta cell 4


title: Beta cell 1


title: Beta cell 5


title: Beta cell 3


title: Beta cell 2


title: 3T3 DRIPc-seq

data_processing:
Library strategy: DRIPc-Seq
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCm38 (mm9)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.


title: Beta cell 19


title: Beta cell 34


title: KI_H3K36me3_ChIPSeq input

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v1.2.3
ChIP-Seq reads were filtered to keep only uniquely mapped reads
Two biological replicates for each sample were merged into one dataset
ChIP-Seq peaks were called using ZINBA v2.0.2.03
Genome_build: mm9

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. After high-speed spin soluble chromatin was removed and used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: spermatocytes

value: 15 days post-partum

tag: strain

tag: chip antibody

value: input


title: B6_H3K36me3_ChIPSeq input


title: Gill_RNASeq [G1-L]

city: Xiamen

first: Huang

last: zekun

state: Fujian

address: Xiang'an South Road

country: China

institute: Xiamen University

data_processing:
Cleanning raw reads use perl script to produce clean reads
Mapping clean reads onto reference use tophat
Calculatint gene RPKM use cufflinks
GO and KEGG annotation and enrichment use perl script
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample.
Supplementary_files_format_and_content: Please note that the identifiers in the 'all.gene.rpkm.020415.txt' (e.g. OYG_10012474_10035047 etc.) are used internally in the Crassostrea gigas Genome Database but not are searchable in a public database. Therefore, the NR Blast results (e.g. gi|405967949|gb|EKC33063.1|/0/Elongation factor 1-alpha [Crassostrea gigas] etc.) are included in the file instead.

organism: Magallana angulata

source_name: Gill

growth_protocol: Fujian oyster, Crassostrea angulata, of a very similar body weight and size were collected from the oyster culture zone (Yunxiao, Fujian province, China).

extract_protocol:
Total RNA was extracted from these tissues using Trizol reagent (Gibco BRL) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Fujian oysters with different body Cu concentration were picked up for RNA-Seq.

tag: develomental stage

value: adult

tag: cu body conc.

value: low

value: Gill


title: Gill_RNASeq [G2-L]


title: Mantle_RNASeq [M1-L]

source_name: Mantle

value: Mantle


title: Gill_RNASeq [G1-H]

value: high


title: Gill_RNASeq [G2-H]


title: W1118_3

city: Birmingham

first: Maria

last: De Luca

state: Alabama

address: Webb 451 - 1720 Second Ave. South

institute: UAB

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped to UCSC dm3 using TopHat v2.0.10 guided by dm3 GTF from UCSC with default parameters.
Underlying Bowtie2 v2.1.0 was used within the TopHat tool.
Transcript abundances were calculated using Cufflinks v2.1.1 (Cufflinks -> Cuffmerge -> Cuffdiff) with default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text output file from Cuffdiff which includes FPKM values for both Samples.

organism: Drosophila melanogaster

source_name: Abdomen fly extracts enriched in fat body content

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit
The polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers. The resulting first strand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques.  The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment.  The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

value: Four-six day old flies

tag: genotype

value: Control


title: MIR30_MIMIC_2

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Bcl2fastq/1.8.4 was used for base analysis and demultiplexing using default parameters by the UNC Highthroughput Sequencing Facility.
Sequencing quality was assessed using fastqc/0.11.3
Reads were aligned using Mapsplice/2.1.4 to the UCSC mm10 reference genome and BOWTIE index. The --fusion parameter was used to search for both canonical and semi-canonical splice junctions.
Alignments were sorted using samtools/0.1.19, and bedtools/2.17.0 multicov was used to generate isoform counts tables for differential gene expression analyisis using the UCSC mm10 knownGene reference table which was accessed 06/09/2015 and converted to bed format.
Isoform counts were read into R version 3.1.2 (2014-10-31). A table of Gene based counts was generated by taking the maximum count of all isoforms for a given gene. edgeR/3.8.6 was used to normalize counts (TMM) and conduct differential gene expression analysis. Genes were filtered for low expression using the criteria CPM > 1 in 3+ samples. A table of normalized CPM values for each gene included in differential gene expression analysis is included as processed data.
Genome_build: mm10
Supplementary_files_format_and_content: Table of TMM normalized CPM for each sample and gene.

source_name: Liver

extract_protocol:
RNA was extracted from flash-frozen mouse liver using the MP Biomedicals 1.4 mm ceramic bead lysing matrix and Norgen Animal Tissue RNA Extraction kit as per the manufacturers instructions. Samples were treated with the optional on-column DNaseI treatment. Following RNA isolation, samples were nanodropped and tested for quality using Agilent RNA 6000 Nano kit on the Bioanalyzer 2100. All samples had RINs above 8.
Libraries were prepared using Tru-seq Stranded mRNA as per the manufacturer's instructions by the UNC High Throughput Sequencing Core Facility. The samples were sequenced on an Illumina HiSeq 2500, paired-end, 48bp reads.

treatment_protocol: At an age of 8 weeks, we started the mice on Western diet for one month and then injected them with either PBS or increasing dose of Scramble or miR-30c mimic (2.5, 5.0, and 7.5 mg/kg) for 6 weeks.

tag: treatment

value: miR-30c mimic

value: Male

value: liver

tag: rin


title: MIR30_MIMIC_1


title: Mantle_RNASeq [M1-H]


title: Way_3

city: San Francisco

first: Philip

middle: L

last: Ballard

address: 513 Parnassus St

department: Neonatology

institute: UCSF

data_processing:
RNAseq reads were aligned using Tophat software to Ensembl Human GRCh38.78
Alignments were aggregated on a per gene basis using Htseq-count
Raw data was converted to counts per million (cpm)
Genome_build: GRCh38.78
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each sample

source_name: cultured 4 days as explants without budesonide

growth_protocol: Mid-gestation (23 week) human fetal lungs were collected with IRB approval from elective pregnancy terminations in healthy consenting women.  Explants were prepared by chopping the lung into 1mm cubes using a semi-automated tissue chopping device.  After chopping, an aliquot of tissue was snap frozen to represent the Pre-Culture (PC) condition. The explants were cultured in Waymouth's media without serum.

extract_protocol:
Total RNA was extracted from three different lungs before culture (preculture) and after 96 h culture (control and budesonide 30 nM) using RNeasy kits (Qiagen) and quantified and quality-checked using the Bioanalyzer 2100
Illumina TruSeq Stranded mRNA Library Prep Kit. All samples multi-plexed together in two lanes on an Illumina Hiseq 2500

treatment_protocol: Explants were treated with serum-free control (Waymouth) medium or medium containing 30 nM budesonide for 4 days.

value: fetal lung


title: MIR30_MIMIC_4


title: Mantle_RNASeq [M2-L]


title: MIR30_MIMIC_3


title: Way_1


title: Way_2


title: PC_3

source_name: preculture


title: SCRAMBLE_1

value: Scramble oligomer


title: PC_1


title: PBS_3

value: PBS


title: PC_2


title: SCRAMBLE_3


title: KI_H3K36me3_ChIPSeq

value: 14 days post-partum


title: Mantle_RNASeq [M2-H]


title: PBS_2


title: Bud_3

source_name: cultured 4 days as explants with budesonide


title: PBS_1


title: Scdi6

value: fat body-specific Sdc RNAi knockdown


title: Bud_2


title: Bud_1


title: SCRAMBLE_2


title: FLOX 485

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

description: Sample 6

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm9 using TopHat with default parameters
RNAseq: FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

source_name: perigonadal white adipose tissue from female flox

extract_protocol:
RNA extraction was performed using Lipid Tissue Mini Kit (Qiagen 74804) according to the manufacturer’s instructions.
Illumina TruSeq PE 51x2 (RNA-seq)

value: perigonadal white adipose tissue

tag: genotype/variation

value: Wild type


title: FLOX 369

description: Sample 4


title: AR10KO 466

description: Sample 5

source_name: adipose Rab10 ko mice ~28weeks old


title: AR10KO 341

description: Sample 3


title: AR10KO 302

description: Sample 2


title: PBS_4


title: FLOX 282

description: Sample 1


title: siGLI1_DMSO_4hr rep3

city: East Melbourne

first: Katrina

middle: Joy

last: Falkenberg

state: Victoria

address: St Andrews Place

department: Research Division

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were quality checked by FastQC and trimmed if necessary for low base quality or adaptor, and then mapped to the human reference genome (GRCh37) using Tophat2 v.2.0.8b with maximum number of multiple hits set to 1 and using the option to map first to the reference transcriptome (Ensembl v69).
Counts per gene were obtained using HTSeq and normalised using the limma-voom method.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample

source_name: colorectal carcinoma cell line

growth_protocol: Cells were cultured in RPMI 1640 (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% sodium pyruvate, 2.5g/L glucose.

extract_protocol:
RNA was extracted from cells using the Rneasy RNA extraction kit (QIAGEN) as per the manufacturer's protocol.  RNA was quantitated using spectrophotometry (Nanodrop).
2ug RNA was prepared for sequencing using the TruSeq RNA Sample Preparation v2 Guide with all kit reagents purchased from Illumina.

treatment_protocol: Cells were reverse transfected in 12 well plates with the appropriate siRNA (final concentration 40nM, Dharmacon siGENOME SMARTpools, Thermo Fisher) or lipid only as a control (mock transfection). Each well contained 3.5 x 10^5 cells and 1.0ul of Dharmafect 2 (Thermo Fisher).  Media was refreshed after 24hrs and after 48hrs, cells were treated with 2.5uM vorinostat or DMSO (solvent) as a control.  Cells were harvested by trypsinisation after 4hrs, 8hrs or 12hrs of drug treatment.

value: vorinostat-resistant HCT116

value: siGLI1 DMSO

tag: timepoint


title: mock_vorinostat_8hr rep3

value: mock vorinostat


title: siPSMD13_DMSO_8hr rep3

value: siPSMD13 DMSO


title: siPSMD13_vorinostat_8hr rep3

value: siPSMD13 vorinostat


title: siGLI1_vorinostat_8hr rep3

value: siGLI1 vorinostat


title: siPSMD13_vorinostat_12hr rep3


title: mock_vorinostat_12hr rep3


title: siPSDM13_DMSO_12hr rep3

value: siPSDM13 DMSO


title: siGLI1_vorinostat_4hr rep3


title: mock_DMSO_4hr rep3

value: mock DMSO


title: mock_DMSO_12hr rep3


title: mock_DMSO_8hr rep3


title: siPSMD13_vorinostat_12hr rep2


title: siPSMD13_vorinostat_8hr rep2


title: siGLI1_vorinostat_8hr rep2


title: siPSDM13_DMSO_12hr rep2


title: siPSMD13_DMSO_8hr rep2


title: siGLI1_vorinostat_4hr rep2


title: siGLI1_DMSO_8hr rep2


title: siGLI1_DMSO_8hr rep3


title: mock_vorinostat_8hr rep2


title: mock_DMSO_12hr rep2


title: mock_DMSO_4hr rep2


title: mock_vorinostat_4hr rep3


title: mock_vorinostat_4hr rep2


title: siPSMD13_vorinostat_12hr rep1


title: siPSMD13_vorinostat_8hr rep1


title: siGLI1_DMSO_4hr rep2


title: mock_vorinostat_12hr rep2


title: siPSDM13_DMSO_12hr rep1


title: mock_vorinostat_8hr rep1


title: siGLI1_DMSO_4hr rep1


title: siGLI1_DMSO_8hr rep1


title: siGLI1_vorinostat_4hr rep1


title: siPSMD13_DMSO_8hr rep1


title: mock_DMSO_8hr rep1


title: E 4h_mRNA-seq (hs)

city: Anyang

first: Du

last: Xiongming

state: Henan

address: 38# Huanghe Avenue

institute: Institute of cotton research of CAAS

data_processing: After filtering of low-quality and dirty raw reads, transcriptome de novo assembly was carried out using the paired-end assembly method as implemented in Trinity (http://trinityrnaseq.sourceforge.net/; trinityrnaseq_r2012-10-05) [123]. After removal of repeats from the spliced sequences, transcripts were obtained of the expected length and size.

organism: Gossypium hirsutum

source_name: United States

growth_protocol: Pre-germinated seeds of each genotype were sown in 20 pots (1-L volume) (6 seeds per pot) containing a sterile mixture of sand and gardening soil in a KR-III phytotron (Henan Ke-rui, Zhengzhou, China) under the following conditions: 28/22 °C day/night temperatures, 60–80% relative humidity, and a 14-h/10-h light/dark cycle under 450 µmol× m−2× s−1 light intensity.

extract_protocol:
Samples were harvested directly into liquid nitrogen and stored at −80°C until used for RNA extraction.Total RNA was isolated from cotton leaf samples treated with either high temperature or 28°C (as a control) for 4 or 8 h using a modified CTAB method and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany to use with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After about 20 days, when the seedlings had produced three leaves, they were randomly divided into three groups. In the middle of the day (about 6 h after the onset of light), two group was transferred into a plant growth chamber and subjected to a constant elevated temperature of 45 °C for 4 and 8 h, and the remaining one was the control (28 °C).

value: Earlistaple 7

tag: phenotype

value: heat sensitive

value: leaf

tag: culture condition

value: 1/2´ Hoagland’s solution


title: mock_vorinostat_12hr rep1


title: mock_vorinostat_4hr rep1


title: mock_DMSO_12hr rep1


title: E 8h_mRNA-seq (hs)


title: N 8h_mRNA-seq (ht)

source_name: China

value: Nan Dan Ba Di Da Hua

value: heat tolerant


title: N 4h_mRNA-seq (ht)


title: UHRF1 KI

city: Shanghai

first: Hao

last: Cheng

address: 320,Yueyang Road

institute: PICB,SIBS,CAS

data_processing:
RRBS reads were mapped to mouse genome (mm9) by using bismark (v0.12.20). Only CpGs with at least 5 reads coverage were used to do the next step analysis.
Genome_build: mm9

source_name: liver

extract_protocol: Genomic  DNA was  prepared  from the liver  tissues  of  3 month old  WT  and  KI  male mice.  To  minimize  the  potential  individual  differences,  genomic  DNAs  from  three mice were pooled together for RRBS analysis.

value: liver

value: knock out


title: mock_DMSO_4hr rep1


title: E ck_mRNA-seq (hs)


title: N ck_mRNA-seq (ht)


title: mock_DMSO_8hr rep2


title: UHRF1 WT

value: wild type


title: 489215_SF/SCL ampulla

city: Pirassununga

first: Angela

middle: Maria

last: Gonella

state: SP

address: Rua Duque de Caxias Norte, 255

department: Departamento de Reprodução Animal

country: Brazil

institute: Universidade de São Paulo

data_processing:
CASAVA v1.8.2.
seqyClean v1.3.12. (https://bitbucket.org/izhbannikov/seqyclean/get/stable.zip) using 26 Phred quality parameter for maximum average error, and vector and adaptor sequences from the Univec database (https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/) were use as guide to remove possible contaminants. Only high quality paired-end sequences were kept for further analyses
The reads were mapped with Tophat v.2.0.8 and Bowtie2 v2.1.0 on the masked bovine genome assembly (Bos taurus UMD 3.1, NCBI).
The mapping file was sorted using SAMTools v 0.1.18 and read counts were obtained using the script from HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). The differential expression analysis was performed with package DESEq v1.12.1, from R/Bioconductor.
Using the function estimateSizeFactors, the normalized counts were obtained (baseMean values, which are the number of reads divided by the size factor or normalization constant). The standard deviation along the baseMean values was also calculated for each transcript. In order to avoid artifacts caused by low expression profiles and high expression variance, only transcripts that had an average of baseMean > 5 and the mean greater than the standard variation were analyzed.
The method to test for differential expression was the negative binonial distribution, through the nbinomTest function on DESeq. The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR- Benjamini-Hochberg.
Genome_build:  Bos taurus (assembly Bos_taurus_UMD_3.1.1)

organism: Bos indicus

source_name: Ampulla

extract_protocol:
Total RNA was extracted from frozen ampulla and isthmus samples using the AlLrep® DNA/RNA/Protein Mini kit (No. 80004, Qiagen), as recommended by manufacturer’s instructions. cDNA was generated by a routine RNA library preparation TruSeq protocol developed by Illumina Technologies (San Diego, CA) using 1 μg of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were pre-synchronized by intramuscular injection of Prostaglandin F2α analog (PGF; 0.5 mg of sodium cloprostenol; Sincrocio, Ouro Fino, Cravinhos, Brazil) and, 7 days later an injection of GnRH agonist (1 µg of buserelin acetate; Sincroforte, Ouro Fino, Cravinhos, Brazil). At this day (D-20) animals received an Estrotect device and estrus detection was performed twice daily from D-20 to D-10. All animals received a new intravaginal P4-releasing device (1g; Sincrogest) on D-10 along with an intramuscular injection of 2 mg estradiol benzoate (Sincrodiol, Ouro Fino). Simultaneously, cows in the LF-LCL received an intramuscular injection of PGF. Additionally, P4 device removal was performed earlier in animals of the LF-LCL group. Specifically, devices were removed 42h and 30 h before the GnRH injection in the LF-LCL and the SF-SCL groups, respectively. All animals received a PGF injection at P4 device removal and a second PGF injection 6h later. Ovulation was induced by an injection of GnRH agonist on D0. On day 4, cows were stunned using captive bolt and euthanized by jugular exsanguination at the University slaughterhouse.

tag: developmental stage

value: multiparous cows

tag: health status

value: Healthy

tag: breed

value: Nelore

value: ampulla


title: siGLI1_vorinostat_8hr rep1

value: vorinostat-resistant HCT116


title: 856_SF/SCL ampulla

tag: tissue


title: 97_SF/SCL ampulla


title: 617_LF/LCL ampulla


title: 79_LF/LCL ampulla


title: neuron_cultures_ehmt1_wt_rna_seq_rep1

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
alignment was done with GSNAP-gmap-2015-06-23
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
GO enrichment was performed in GENE DAVID
Genome_build: rn6
Supplementary_files_format_and_content: Excel tables including the normalized read counts for all the samples, as well as the DEseq2 pvalues for each of the comparisons. The normalized counts are found in the columns. The values in these columns represent the deseq-normalized counts multiplied by 42 (bp coverage of tag) divided by the gene length. There are 5 pair-wise comparisons of expression and each has its table. Wt_ttx and shrna_ttx for the study of ttx effect in wt samples or transduced sampes. Startpoint_wt_shrna_VS_wt for the effect of shrna alone on wt neurons. Endpoint_ttx_shrna_VS_ttx for the effect of shrna on the TTX treated samples. Rattus_shrna_total_6vs_6_effect for the effect of shrna regardless to the TTX treatment. Gene David GO enrichments for the TT down-regulated genes (Down-reg), their shrna blocked subset (Blocked_shrna) and shrna independent subset (Common).

organism: Rattus norvegicus

source_name: cortical neurons

extract_protocol:
Total RNA was Trizol extracted from 3 wild-type, 3 wildtype ttx samples, 3 ehmt1 kd and 3 emht1 kd ttx samples. RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.

value: Wistar

tag: culture

value: primary cortical neuronal cultures

value: brain

value: cortical neuron

tag: age


title: neuron_cultures_ehmt1_wt_rna_seq_rep2

tag: strain

tag: cell type


title: neuron_cultures_ehmt1_wt_rna_seq_rep3


title: neuron_cultures_ehmt1_wt_ttx_rna_seq_rep2


title: T. brucei H3VKO2

city: Athens

first: David

last: Reynolds

state: Georgia

address: 120 E Green St

department: Biochemistry and Molecular Biology

institute: University of Georgia

data_processing:
Smalll RNA reads were quality and adapter trimmed using Cutadapt [81] and reads shorter than 18 nucleotides were discarded. Reads were mapped to the T. brucei reference genome using Bowtie2 version 2.2.3 with the following parameters “-a -D 10 -R 5 -N 1 -L 15 -i S,1,0.50“ [78] and further processed using Samtools 1.2 [79], BEDTools [82], and custom scripts.
Genome_build: Trypanosoma brucei Lister 427 (v6.0 from TriTrypDB.org) [http://tritrypdb.org/common/downloads/release-6.0/TbruceiLister427/fasta/data/TriTrypDB-6.0_TbruceiLister427_Genome.fasta]
Supplementary_files_format_and_content: .wig and .bedgraph report small RNAseq data (not ChIP-seq data)

organism: Trypanosoma brucei

source_name: H3VKO parasite

growth_protocol: Bloodstream form T. brucei cells were grown as described in Hirumi et al. (1980). Parasitology 80, 371–382.

extract_protocol:
For small RNA sequencing by the Georgia Genomics Facility (GGF), total RNA was isolated from log phase T. brucei using Trizol according to the manufacturer's instructions. 5x10^7 cells were used for each prep. For all other small RNA sequencing libraries, small RNAs were isolated using a Qiagen miRNEASY kit according to the manufacturer's instructions. 5x10^7 cells were used for each prep.
For small RNA sequencing by GGF, the small RNA-seq libraries were prepared using approximately 250ng total RNA using the Illumina-compatible NEBNext small RNA library preparation kit following the manufacturer protocol (New England Biolabs). For remaining small RNA-seq samples, libraries were prepared using approximately 250ng small RNA by Vertis Biotechnology AG. The small RNA sample was poly(A)-tailed using poly(A) polymerase. Then, the 5'PPP and CAP structures were removed using tobacco acid pyrophosphatase (TAP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μL using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: DMOG treatment of cells was performed by supplementing media with 1mM DMOG for 5 days in T. brucei

value: 221a of strain 427

tag: lifestage

value: bloodstream form

tag: sample

value: small RNA


title: neuron_cultures_ehmt1_wt_ttx_rna_seq_rep3


title: neuron_cultures_ehmt1_shrna_ttx_rna_seq_rep1


title: neuron_cultures_ehmt1_shrna_ttx_rna_seq_rep2


title: neuron_cultures_ehmt1_shrna_rna_seq_rep1


title: T. brucei WT DMOG2

source_name: WT parasite

value: WT

value: DMOG (an inhibitor of J synthesis)