title: OX.7.5 roots, low sulphate, biological rep1

city: Warsaw

first: Agnieszka

last: Sirko

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

description: Gene expression data from Arabidopsis thaliana roots, 33 days old

hyb_protocol: Labelled samples were hybridized to the Arabidopsis Gene 1.1. ST array Strips (Aﬀymetrix, Santa Clara, CA).

scan_protocol: Microarrays were scanned with Aﬀymetrix GeneAtlas System and saved to CEL ﬁles.

data_processing: The CEL ﬁles were imported into the Partek Genomic Suite v 6.15 software and processed with the use of RMA (Robust Multiarray Averaging). The probe intensities were quantile normalised, log 2 transformed and median polish summarisation was applied to each of the probe sets.

source_name: Arabidopsis OX.7.5 line overexpressing NBR1, roots at low sulphate

label_protocol: 100 ng of total RNA was prepared for Aﬀymetrix whole transcriptome microarray analysis by the sequential use of the Ambion® WT Expression Kit and the Aﬀymetrix GeneChip® WT Terminal Labelling Kit according to the manufacturer's protocols.

growth_protocol: Arabidopsis seeds were stratified for 2-5 days at 4 °C in microfuge tubes with distilled H2O and then spread on watered soil-filled pots and watered every 3-4 days.

extract_protocol: Plant tissue samples were transferred to 1.5 mL Eppendorf tubes and homogenized. 900 μL of TRIZOL were then added to extract RNA using Direct-zol™ RNA MiniPrep (Epigenetics COMPANY™, ZYMO RESEARCH, #R2050). 100 ng of each RNA was cleaned with TURBO DNA-free™ kit.

treatment_protocol: 33 days old plants were collected and had the shoots divided into two halves, one of which was kept at 4 °C in 2 mL RNAlater® Solution (Ambion, #AM7020) for 24 h, then, the RNAlater® solution was removed with paper towel.

tag: plant part

value: roots


title: OX.7.5 roots, low sulphate, biological rep2

status: Public on Apr 20 2020

type: RNA

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana


title: PHPR32

type: SRA

city: Guangzhou

first: Xinping

last: Yang

state: Guangdong

address: 1838 N. Guangzhou Ave

country: China

institute: Southern Medical University

library_source: transcriptomic

data_processing:
Tophat2 (v2.1.1; run with parameters '-p 6 -r 50 -b2 -very-sensitive') + Picard MarkDuplicats (v2.2.2) + GATK (v3.5) pipeline was used to detect reliable variants from RNA-seq data. ANNOVAR (v2016-02-01) was used to annotate variants. A/G and C/T mismatches statistified (1) with allele frequency lower than 0.05 in East Asia population or without allele frequency, (2) VQSR marked as 'PASS' were retained as potential RNA editing sites.
Gene counts were calculated by STAR (v2.5.2b + HTSeq htseq-count (v0.9.0) pipeline. Raw counts of two umbilical cord blood were used to remove the influence of blood contamination on gene expressions in placenta.
Editing levels of potential RNA editing sites were defined as the ratio of reads with editing to total reads. If there is no read covering the editing site in a sample, editing ratio for this site in this sample would be assigned as zero.
Transcripts expressed in placenta were assembled from RNA-seq reads by StringTie (v1.3.4) and comapred with known transcripts from Ensembl (GRCh38.84) by Cufflinks cuffcompare (v2.2.1). Then the intron retention events were detected by comparing assembled transcripts with corresponding non-redunant canonical transcripts from GENCODE (v29).
For every intron retention (IR) event, the percent spliced in (PSI) was defined as the ratio of adjusted spliced-in reads and the sum of adjusted spliced-in and spliced-out reads. Adjusted spliced-in reads = number of reads supporting IR events / (IR event length + read length -1). Adjusted spliced-out reads = number of reads skipping corresponding introns / (read length -1).
Genome_build: hg38
Supplementary_files_format_and_content: For RNA editing sites: counts and editing ratios at potential RNA editing sites. Tab-delimited files are formatted as: chr, pos, ref, alt, func.refgene, gene.refgene, strand, non-edited.counts, edited.counts, editing.ratio
Supplementary_files_format_and_content: For gene expression: raw counts of expressed genes in placenta and umbilical cord blood; counts after removing blood contamination of expressed genes in placenta. Tab-delimited files are formatted as: ENSG id, raw counts (or normalized counts).
Supplementary_files_format_and_content: For intron retention (IR) events: counts and PSI values for IR events. Tab-delimited files are formatted as: stringtie transcript id, gene symbol, Chr, IR start, IR end, strand, reads supporting IR, reads not supporing IR, adjusted reads supporting IR, adjusted reads not supporting IR, PSI.

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using the RNeasy® Plus Universal Mini Kit (Qiagen, DEU) according to the manual manufacturer’s instruction.
RNAs with poly(A) tails were isolated, and double-stranded cDNA libraries were prepared using TruSeq RNA Kit (Illumina, USA).

tag: subject status

value: early-onset severe preeclampsia (EOSPE)

tag: tissue

value: Placenta


title: OX.7.5 roots, low sulphate, biological rep3


title: Col-0 roots, low sulphate, biological rep3

source_name: Arabidopsis ecotype Col-0 roots at low sulphate


title: PHPR30


title: Col-0 roots, low sulphate, biological rep2


title: Xenograft tumor, CBL_5

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

country: USA

institute: Tufts University

description: Table S5  rnaseq.cbl xenograft

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using Salmon v0.14.0
Quant file was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: Excel file includes Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj), log2 normalized reads of genes

molecule: polyA RNA

source_name: Xenograft tumors

growth_protocol: Burkitt Lymphoma cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: No specific treatment

value: Xenograft tumor

tag: treatment


title: Acetone G10 D

city: Beltsville

first: Wayne

middle: M

last: Jurick

state: MD

address: Building 002

department: Agricultural Research Service

institute: United States Department of Agriculture

data_processing:
FAST-QC       v. 0.11.9
Trinity de novo Alignment to reference (MD-8 genome) usegalaxy.org
Salmon transcriptome read counting usegalaxy.org
Genome_build: reference genome: GCA_000769745.1
Supplementary_files_format_and_content: gene count data from transcriptome as aligned to reference genome

organism: Penicillium crustosum

source_name: frozen mycelia

growth_protocol: biological Replicates are deliniated alphabetically with the letter after M in sample name.

extract_protocol:
trizol with bead beating in qiagen tissue lyzer
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: 5ppm difenoconazole addition to liquid shake culture for samples beginning with "D" acetone for samples beginning with "A"

value: exposed to acetone


title: Mismatched_D2T1505_Rep1

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Quality trimmed read sequences were mapped to Plasmodium chabaudi chabaudi reference genomes using TopHat2. Gene expression estimates were made as raw read counts using the Pyhton script ‘HTSeq- count’ (model type – union). Counts data were converted to counts per million (cpm) and genes were filtered if they failed to achieve a cpm value of 1 in at least 30% of libraries per conditions.
Normalization of raw read counts was done using Voom-TMM method and differential gene expression analysis was carried out using DeSeq2
Genome_build: Plasmodium chabaudi chabaudi
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each Sample

organism: Plasmodium chabaudi chabaudi

source_name: AS

growth_protocol: Hosts were 6-8 weeks old female MF1 mice housed in groups of five at 21°C with food and drinking water supplemented with 0.05 % para-aminobenzoic acid (PABA, to supplement parasite growth) provided ad libitum. All experimental infections were initiated by intravenous injection of 1 x 107 P. chabaudi (clone AS) parasitized red blood cells. Parasites at ring stage were collected at ZT0.5 (08:00 GMT) from donor mice housed in standard LD light conditions (Lights ON 07:30; Lights OFF 19:30 GMT) and immediately used to infect two groups of experimental mice. One group (termed “matched”) were entrained to the same photoperiod as the donor mice, generating infections in which parasite and host rhythms were in the same phase. The other group (termed “mismatched”) were entrained to reverse light (Lights OFF 07:30 and Lights ON 19:30 GMT) resulting in infections in which the parasite is out of phase with the host by 12 hours.

extract_protocol:
Samples were collected every three hours, over a period of 30 hours, from 09:00 GMT on day 4 to 15:00 GMT on day 5 post infection. This corresponds to a starting time of ZT1.5 for matched, and ZT13.5 for mismatched infections. At each sampling point, four mice from each group (matched/mismatched) were sacrificed and thin blood smears and RBC counts (via flow cytometry; Beckman Coulter) were taken by tail bleeds, and 50µl of blood was taken via cardiac puncture (added to 200µl of RNAlater and frozen at -80C) for RNAseq analysis. RNAlater was removed from the samples preserved with RNAlater through centrifugation and 1 ml of Trizol was added to lyse the samples. Total RNA was isolated from TRIzol treated samples according to the manufacturer’s instructions (Life Technologies).
Strand-specific mRNA libraries were prepared from total RNA using TruSeq Stranded mRNA Sample Prep Kit LS (Illumina) according to the manufacturer’s instructions. Briefly, at least 100ng of total RNA was used as starting material to prepare the libraries. PolyA+ mRNA molecules were purified from total RNA using oligo-T attached magnetic beads. First strand synthesis was performed using random primers followed by second strand synthesis where dUTP were incorporated in place of dTTP to achieve strand-specificity. Ends of the double stranded cDNA molecules were adaptor ligated and the libraries amplified by PCR for 15 cycles. Libraries were sequenced on Illumina HiSeq 4000 platform with paired-end 100/150bp read chemistry according to manufacturer’s instructions. Data from 11 timepoints were anlyzed further

tag: experimental variables

tag: strain

value: AS

tag: host

value: 6-8 weeks old female MF1 mice


title: Acetone G10 E


title: Mismatched_D2T1200_Rep2


title: PHPR26


title: Mismatched_D2T1200_Rep1


title: DIF G10 B

value: exposed to difenoconazole


title: PHPR19


title: DIF G10 A


title: Mismatched_D2T0900_Rep2


title: Mismatched_D2T1505_Rep2


title: OX.7.5 shoots, low sulphate, biological rep3

description: Gene expression data from Arabidopsis thaliana shoots, 33 days old

source_name: Arabidopsis OX.7.5 line overexpressing NBR1, shoots at low sulphate

value: shoots


title: PHPR14


title: Mismatched_D2T0900_Rep1


title: PHPR08


title: Col-0 shoots, low sulphate, biological rep3

source_name: Arabidopsis ecotype Col-0 shoots at low sulphate


title: OX.7.5 shoots, low sulphate, biological rep1


title: OX.7.5 shoots, low sulphate, biological rep2


title: Mismatched_D2T0630_Rep2


title: DIF G10 E


title: VM-CUB1_DMSO

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

data_processing:
The sequenced sample reads were trimmed and cleaned using trim_galore and then aligned to human genome (GRCh38) using TopHat v2.1.1 with default parameters.
The aligned reads were sorted using samtools and processed using HTSeq-count method from HTSeq to obatin raw read counts.
The raw read counts were normalized and differential expression analysis was performed using DESeq bioconductor package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file include normalized read counts for each sample from DESeq.

source_name: VMCUB1 cell

extract_protocol:
RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA)
Library construction was performed by Hudson Alpha Genomic Services Laboratory according to standard Illumina protocols.

tag: cell line

value: DMSO for 4 days


title: Acetone P11 A

organism: Penicillium expansum


title: Acetone P11 C


title: Col-0 roots, low sulphate, biological rep1


title: VM-CUB1_PAK4-inhibitor

value: PAK4 inhibitor (PF-3758309) at 5nM for 4 days


title: Col-0 shoots, low sulphate, biological rep2


title: VM-CUB1_ NTsiRNA

value: Non targeting siRNA transfection


title: Mismatched_D2T0630_Rep1


title: Mismatched_D2T0340_Rep2


title: Mismatched_D2T0340_Rep1


title: Acetone P11 D


title: VM-CUB1_PAK4_ siRNA

value: PAK4 siRNA transfection


title: DIF G10 C


title: Acetone P11 E


title: DIF P11 A


title: UACC_Lib2_Pro_rep2

city: Rockville

first: Tongwu

last: Zhang

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling and The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
We counted the number of reads (Only use R1 read for tag count) completely matching 10bp barcode sequences (tag counts) and the same downstream sequence context (“TCTAGAATTATTACACGGCG”) including an XbaI recognition site and the 3’ of the luc2 gene.
Supplementary_files_format_and_content: Tag abundance measurements (Count,TPM,Ratio)

source_name: UACC903 melanoma cells

growth_protocol: UACC903 cells were grown in the medium containing RPMI1640, 10% FBS, 20 mM HEPES, and penicillin/streptomycin at 37C and 5% CO2. HEK293FT cells were grown in the medium containing DMEM, 10% FBS, and penicillin/streptomycin at the same condition

extract_protocol:
Total RNA was isolated using Qiagen RNeasy kit, and mRNA was subsequently isolated using PolyA purist MAG kit. cDNA was then synthesized using Superscript III
From input DNA library (before transfections) or cDNA output, short sequences encompassing 10bp unique barcodes were amplified using Q5 high-fidelity polymerase and primers introducing Illumina TruSeq adapter sequences

treatment_protocol: Cells were transfected with each MPRA libraries using Lipofectamine 3000 (Therme Scientific) and harvested at 24 hours after transfection for RNA isolation.

tag: oligo library

tag: promoter type

value: Promoter

value: UACC903 melanoma cells


title: Col-0 shoots, low sulphate, biological rep1


title: Mismatched_D2T0040_Rep2


title: UACC_Lib2_Pro_rep1


title: OX.7.5 roots, biological rep3

source_name: Arabidopsis OX.7.5 line overexpressing NBR1, roots


title: Mismatched_D2T0040_Rep1


title: OX.7.5 roots, biological rep1


title: DIF P11 B


title: OX.7.5 roots, biological rep2


title: Mismatched_D1T2140_Rep2


title: UACC_Lib2_Enh_rep2

value: Enhancer


title: Col-0 roots, biological rep2

source_name: Arabidopsis ecotype Col-0 roots


title: Col-0 roots, biological rep3


title: DIF P11 D


title: UACC_Lib2_Enh_rep1


title: Col-0 roots, biological rep1


title: UACC_Lib1_Pro_rep2


title: Mismatched_D1T1830_Rep2


title: Mismatched_D1T1830_Rep1


title: OX.7.5 shoots, biological rep3

source_name: Arabidopsis OX.7.5 line overexpressing NBR1, shoots


title: Patient 37 -normal

hyb_protocol: Samples  were hybridized to NanoString Human Kinase Panel probes 19 hours at 65C  as per the manufacturer's instructions.

scan_protocol: Samples were scanned on the nCounter System as per the manufacturer's instructions.

data_processing: Gene Expression was quantified on the NanoString nCounter and raw counts were generated with nSolver. Raw counts were normalized against reference genes with the geNorm algorithm. nSolver text files (.csv) and NanoString.rcc files were imported into Partek Genomic Suite 6.6 (PGS, Saint Louis, MO), and differential expressions were determined by ANOVA

label: NanoString capture and reporter probe mix

source_name: Adjacent Normal

extract_protocol: RNA was harvested by employing the Qiagen RNAeasy kit and its quality was evaluated by the 260/280 ratio using NanoDrop (Thermo Fisher Scientific)

tag: individual

value: Patient 37

tag: disease state

value: muscle invasive bladder cancer (MIBC)

tag: age

tag: gender

value: male

tag: race

value: Caucasian

value: adjacent normal


title: OX.7.5 shoots, biological rep2


title: B_X9_S6

city: London

first: Adam

last: Pennycuick

address: 5 University Street

department: UCL Respiratory

country: United Kingdom

institute: University College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19.
Raw fastq files were trimmed using fastp version 0.20.1 with default options.
Fastq files were tagged with UMI information using UMItools version 1.0.1
Reads were aligned to human genome UCSC hg38 using RNA-STAR version 2.5.2b
Duplicate reads were removed using JE-suite version 1.2.1 (using the UMI-aware markdupes method)
Reads per transcript were counted using FeatureCounts version 1.6.4
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Tab delimited text file containing non-normalised count data; columns represent samples, rows represent genes.

source_name: Paediatric_FACS sorted airway basal cells

growth_protocol: Not applicable

extract_protocol:
Sorted basal cells were centrifuged at 300 x g for 5 mins at 4°C, resuspended in a 2:1 mix of Arcturus PicoPure Extraction buffer/RNAlater (Life Technologies) and stored at -80°C until use. samples were thawed, disrupted by lysis (incubation at 42°C for 30 mins followed by incubation at room temperature for 5 mins), vortexed and filtered using RNAeasy MinElute columns (Qiagen). RNA extraction was performed using the Arcturus PicoPure RNA Isolation Kit (Life Technologies Ltd; KIT0204) as per the manufacturer’s instructions. RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific).
Libraries were created by UCL Genomics Core Facility using the SMARTer Stranded Total RNAseq Kit (Clontech), cleaned using JetSeq (Bioline) and quality control analysis of RNA integrity was performed using High Sensitivity RNA ScreenTape and the TapeStation Analysis software (Agilent Technologies). RNA sequencing was performed using 0.5x NextSeq for 75 cycles (Illumina; 43PE, ~33M reads per sample; R2 contains UMI information for associated R1 file).

treatment_protocol: Bronchoscopic biopsies from the tracheal lumen were transported to the laboratory in transport medium consisting of αMEM containing penicillin/streptomycin, amphotericin B and gentamicin. Cell suspensions were generated by sequential enzymatic digestion using with dispase 16 U/mL (Corning) for 20 minutes at room temperature followed by 0.1% trypsin/EDTA (Sigma) for 30 minutes at 37°C (both in RPMI medium, Gibco). Each enzyme step was quenched with medium containing FBS, placed on ice and combined following the second digestion. Biopsies were manually homogenised using sharp dissection between digest steps and by blunt homogenization through a 100 μm cell strainer (Miltenyi Biotec). Centrifugation steps were performed at 300 x g for 5 mins at 4°C. Cells were blocked in a fluorescence-activated cell sorting (FACS) buffer composed of PBS containing 1% FBS, 25 mM HEPES buffer and 1 mM EDTA for 20 minutes in 96-well V bottomed plates (Thermo Fisher Scientific). Cells were centrifuged as above before staining for 20 minutes on ice at 4°C. The antibodies used were CD31 (BV421; Biolegend; 303124), CD45 (BV421; Biolegend; 304031), EPCAM (APC; Biolegend; 324208), PDPN (PE-Cy7; Biolegend; 337013). Cells were resuspended in FACS buffer for sorting of EPCAM+/PDPN+ live cells into epithelial cell culture medium containing Y-27632 for transport to the laboratory.

tag: group

value: Paediatric

tag: cell type

value: fresh sorted basal cells


title: UACC_Lib1_Enh_rep2


title: Patient 37 -tumor

source_name: Bladder tumor

value: tumor


title: UACC_Lib1_Enh_rep1


title: Mismatched_D1T1200_Rep2

value: AS

value: 6-8 weeks old female MF1 mice


title: Mismatched_D1T1520_Rep1


title: Patient 36 -normal

value: Patient 36


title: Mismatched_D1T1200_Rep1


title: Mismatched_D1T2140_Rep1


title: Col-0 shoots, biological rep2

source_name: Arabidopsis ecotype Col-0 shoots

tag: plant part

value: shoots


title: Patient 36 -tumor


title: Input_Lib2_Pro

library_source: genomic

molecule: other

source_name: Input DNA


title: Input_Lib2_Enh


title: Mismatched_D1T0800_Rep2


title: Patient 35 -normal

value: Patient 35


title: Col-0 shoots, biological rep3


title: Input_Lib1_Pro


title: Patient 35 -tumor


title: Mismatched_D1T1520_Rep2


title: Input_Lib1_Enh


title: Mismatched_D1T0800_Rep1


title: Patient 34 -normal

value: Patient 34


title: Col-0 shoots, biological rep1


title: Patient 34 -tumor


title: HEK_Lib2_Pro_rep2

source_name: HEK293FT cells

value: Promoter

value: HEK293FT cells


title: Matched_D2T1540_Rep1


title: HEK_Lib2_Pro_rep1


title: Patient 33 -normal

value: Patient 33


title: HEK_Lib2_Enh_rep2

value: Enhancer


title: Matched_D2T1230_Rep1


title: Patient 33 -tumor

value: muscle invasive bladder cancer (MIBC)


title: HEK_Lib2_Enh_rep1


title: Matched_D2T0940_Rep2


title: Matched_D2T0940_Rep1


title: Patient 31 -normal

value: Patient 31

value: male


title: HEK_Lib1_Pro_rep1


title: HEK_Lib1_Pro_rep2


title: Patient 31 -tumor

value: Caucasian


title: Patient 30 -normal

value: Patient 30

value: adjacent normal


title: Matched_D2T1540_Rep2


title: OX.7.5 shoots, biological rep1


title: Patient 30 -tumor

value: tumor


title: Matched_D2T0640_Rep2

value: AS


title: HEK_Lib1_Enh_rep4


title: Matched_D2T1230_Rep2

value: 6-8 weeks old female MF1 mice


title: Matched_D2T0640_Rep1


title: Patient 29 -normal

value: Patient 29


title: HEK_Lib1_Enh_rep3


title: HEK_Lib1_Enh_rep2


title: Matched_D2T0355_Rep2


title: HEK_Lib1_Enh_rep1


title: Matched_D2T0355_Rep1


title: Patient 29 -tumor


title: Matched_D2T0055_Rep1


title: Patient 26 -normal

value: Patient 26


title: Patient 26 -tumor


title: taf14∆∆ +Cr (treated)_R2

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

country: Australia

institute: Monash University

description: taf14∆∆ +Cr (treated)_R2

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using STAR (v2.6.0c https://github.com/alexdobin/STAR). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Supplementary_files_format_and_content: C albicans SC5314 assembly 21 plus AF167163 downloaded from NCBI
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.

organism: Candida albicans

source_name: Candida in Rich media (YPD)

growth_protocol: Candida albicans wild type and taf14∆∆ strains were grown to log phase in rich media, either pelleted immediately as untreated samples or after 2 hour treatment with 50 mM crotonate as treated samples.

extract_protocol:
Total RNA was extracted by the hot phenol method. One microgram of total RNA was used for library preparation by the PAT-seq method.
Library construction was by the PAT-seq approach (Harrison et al 2015)
Illumina directional RNA-seq: The libraries provided were purified using AMPure beads to remove any contaminating primers etc., and  examined using Agilent Bioanalyzer. These showed libraries with mean size of 243bp for both 18-04608  and 18-04609. Quantitation was also performed using Qubit and qPCR. From size adjusted qPCR the  libraries were 18.4nM after purification.
c-Bot Hybridization using 14pM of each library pool and on-board cluster  generation.
150bp SR sequencing using Illumina HiSeq Rapid Mode and HiSeqV2  chemistry. Illumina Protocol 15035788 Rev D, Apr 2014

treatment_protocol: 2 hour treatment with 50 mM crotonate

tag: strain backround

value: SN background

tag: strain type

tag: growth phase

value: Log phase mutant cells + Crotonate (rep 2)


title: Patient 23 -normal

value: Patient 23

value: African American

tag: tissue


title: Matched_D1T2150_Rep1

tag: experimental variables

tag: strain


title: taf14∆∆ -Cr (untreated)_R2

description: taf14∆∆ -Cr (untreated)_R2

value: Log phase mutant cells (rep 2)


title: WT +Cr (treated)_R2

description: WT +Cr (treated)_R2

value: wild type

value: Log phase wild type cells + Crotonate (rep 2)


title: Matched_D1T1850_Rep2

tag: host


title: DIF P11 E

tag: treatment

value: exposed to difenoconazole


title: Patient 17 -normal

value: Patient 17

value: muscle invasive bladder cancer (MIBC)

value: female


title: Matched_D1T1850_Rep1


title: WT -Cr (untreated)_R2

description: WT -Cr (untreated)_R2

value: Log phase wild type cells (rep 2)


title: Matched_D1T1545_Rep2


title: taf14∆∆ +Cr (treated)_R1

description: taf14∆∆ +Cr (treated)_R1

value: Log phase mutant cells + Crotonate (rep1)


title: Patient 17 -tumor

value: Caucasian

value: tumor


title: Patient 23 -tumor

value: male


title: Matched_D1T1545_Rep1

value: AS

value: 6-8 weeks old female MF1 mice


title: taf14∆∆ -Cr (untreated)_R1

description: taf14∆∆ -Cr (untreated)_R1

value: SN background

value: Log phase mutant cells (rep1)


title: Matched_D1T1230_Rep2


title: Patient 15 -tumor

value: Patient 15


title: Patient 15 -normal

value: adjacent normal


title: WT +Cr (treated)_R1

description: WT +Cr (treated)_R1

value: wild type

value: Log phase wild type cells + Crotonate (rep1)


title: UACC_Lib1_Pro_rep1

tag: oligo library

tag: promoter type

value: Promoter

tag: cell line

value: UACC903 melanoma cells


title: 2014_Harvest_Plot 24_rep c_green

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: Hybridizations were performed on a rotative Agilent Hybridization Oven, for 17h at 65°C, 10g. Afterwards, slides were washed, dried, and scanned according to the manufacturer protocol

scan_protocol: Scanning was performed at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200.

data_processing: Statistical analyses were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. Data were normalized with the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple Granny Smith fruit peel, harvested in 2014 on plot 24, at early physiological mature stage, sampled at harvest.

label_protocol: Labelling was performed with the G4140-90050_GeneExpression_TwoColor_6.9 (Agilent) protocol.

growth_protocol: Granny Smith apples were grown at the experimental station of La Moriniere (France, Saint Epain, 37216) in 2014, 2015 and 2017.

extract_protocol: Total RNA was extracted from 1 g of frozen fruit peel tissue ground in liquid nitrogen using two successive extraction procedures with a CTAB (cetyltrimethylammonium bromide) buffer (Gasic et al., 2004) and then a SSTE buffer (Chang et al., 1993) as described by Nobile et al., 2011 and Segonne et al., 2014.

tag: organ

value: Fruit

value: Peel

tag: genetic background

value: Granny Smith

tag: genotype

value: Wild-type

tag: tissus developmental stage

value: Harvested at early physiological maturity

tag: phenotype

value: Low scald

tag: plot


title: 2014_Harvest_Plot 24_rep d_red


title: Patient 14 -normal

tag: individual

value: Patient 14

tag: disease state

value: muscle invasive bladder cancer (MIBC)

tag: age

tag: gender

value: male

tag: race

value: Caucasian


title: Matched_D1T1230_Rep1

tag: experimental variables

tag: strain

value: AS

value: 6-8 weeks old female MF1 mice


title: 2014_Harvest_Plot 36_rep a_red

source_name: Apple Granny Smith fruit peel, harvested in 2014 on plot 36, at early physiological mature stage, sampled at harvest.

tag: tissue


title: 2017_Harvest_Plot 31b_rep a_red

source_name: Apple Granny Smith fruit peel, harvested in 2017 on plot 31b, at early physiological mature stage, sampled at harvest.

value: High scald


title: 2015_Harvest_Plot 31_rep a_green

source_name: Apple Granny Smith fruit peel, harvested in 2015 on plot 31, at early physiological mature stage, sampled at harvest.


title: genomic DNA from normal thyroid tissue control 2

type: genomic

city: Lund

first: Kajsa

last: Paulsson

address: Sölvegatan 19

department: Department of Clinical Genetics

country: Sweden

institute: Lund University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC  BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: thyroid

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from tumor and normal thyroid tissue samples using Qiagen DNeasy Kit according to standard instructions

value: Female

value: normal thyroid tissue


title: WT -Cr (untreated)_R1

description: WT -Cr (untreated)_R1

tag: strain backround

value: SN background

tag: strain type

value: wild type

tag: growth phase

value: Log phase wild type cells (rep 1)


title: genomic DNA from normal thyroid tissue control 1

value: Male


title: C_G10

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19.
Raw fastq files were trimmed using fastp version 0.20.1 with default options.
Reads were aligned to human genome UCSC hg38 using RNA-STAR version 2.5.2b
Reads per transcript were counted using FeatureCounts version 1.6.4
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Tab delimited text file containing non-normalised count data; columns represent samples, rows represent genes.

source_name: Paediatric_Cultured airway basal cells

growth_protocol: RNA sequencing of cultured basal cells was performed after either two or three passages in epithelial cell culture medium containing Y-27632.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. The resulting RNA was submitted for library preparation by the Wellcome-MRC Cambridge Stem Cell Institute. Initial QC was performed using Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and TapeStation Analysis software (Agilent Technologies).
600 ng RNA was used for library preparation using the NEBNext Ultra8482 II Directional RNA Library Prep Kit (Illumina) and the QIAseq FastSelect RNA Removal Kit (Qiagen). Libraries were subsequently measured using the Qubit system and visualised on a TapeStation D5000.

tag: group

value: Paediatric

tag: cell type

value: Cultured airway basal cells

tag: passage

value: two ro three passages


title: 2015_Harvest_Plot 31_rep b_red

tag: organ

value: Fruit

value: Peel

tag: genetic background

value: Granny Smith

tag: genotype

value: Wild-type

tag: tissus developmental stage

value: Harvested at early physiological maturity


title: Patient 14 -tumor

tag: individual

value: Patient 14

tag: disease state

value: muscle invasive bladder cancer (MIBC)

value: male

value: Caucasian

value: tumor


title: Matched_D1T0830_Rep1

source_name: AS

value: AS

tag: host

value: 6-8 weeks old female MF1 mice


title: 2014_Harvest_Plot 36_rep b_green

tag: phenotype

value: Low scald

tag: plot


title: Matched_D1T0830_Rep2

tag: experimental variables

tag: strain


title: Patient 13 -normal

value: Patient 13

tag: age

tag: gender

value: female

tag: race

tag: tissue

value: adjacent normal


title: C_F10

tag: group

value: Paediatric

tag: cell type

value: Cultured airway basal cells

value: two ro three passages


title: genomic DNA from normal thyroid tissue control 4

value: Female

value: normal thyroid tissue


title: MYC OFF 3_d4

city: Monrovia

first: Srividya

last: Swaminathan

state: CA

address: 1218 S. Fifth Ave

department: Systems Biology

institute: City of Hope

description: MYC OFF lymphoma spleen

data_processing:
Primary sequencing data (raw reads) were subjected to quality control (QC).
After QC, raw reads were filtered into clean reads before alignment to the reference sequences. Once alignment passed QC, we proceeded with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes).
Data was filtered reads with adaptors, reads with greater than 10% unknown bases and low quality reads. Bowtie 2 was used to map clean reads to reference gene, and HISAT was used to map reads to reference genome (mm8).
RSEM was used to compute Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm. FPKM method was used to calculate the expression levels of individual genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: spleen

extract_protocol:
Single cell suspensions were made by homogenizing spleens using a 191/2 guage needle. Following filtration using a 70mm cell strainer and RBC lysis, cells were washed with PBS and used for RNA isolation. RNA isolation was performed using the Qiagen RNeasy Mini Kit (Catalog # 74104).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: MYC OFF splenic samples were obtained by treating Em-tTA/tet-O-MYC lymphoma bearing mice with doxycycline for 4 days.

value: FVB/N

value: splenic single cell suspension

value: post natal 6-10 weeks

value: Em-tTA/tet-O-MYC (MYC OFF)


title: Patient 13 -tumor

value: muscle invasive bladder cancer (MIBC)

value: Caucasian


title: C_E10

tag: passage


title: genomic DNA from normal thyroid tissue control 3


title: genomic DNA from anaplastic thyroid cancer case 14

value: anaplastic thyroid cancer sample


title: C_D10

source_name: Adult_Cultured airway basal cells

value: Adult


title: 2014_Harvest_Plot 24_rep a_red

tag: organ

value: Fruit

value: Peel

tag: genetic background

value: Granny Smith

value: Wild-type

value: Harvested at early physiological maturity

value: Low scald


title: MYC OFF 2_d4

description: MYC OFF lymphoma spleen

tag: genotype


title: Treated_MuT_R2

description: Illumina Tru12

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using bowtie2 (v2.2.5 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: C albicans SC5314 assembly 21 plus AF167163 downloaded from NCBI
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.

growth_protocol: Candida albicans wild type and taf14∆∆ strains were grown to log phase in rich media, either pelleted immediately as untreated samples or after 2 hour treatment with 20 μg/ml of calcofluor white as treated samples.

extract_protocol:
Total RNA was extracted by the hot phenol method. One microgram of total RNA was used for library preparation by the PAT-seq method.
Library construction was by the PAT-seq approach (Harrison et al 2015)
Illumina directional RNA-seq: The libraries provided were purified using AMPure beads to remove any contaminating primers etc., and  examined using Agilent Bioanalyzer. These showed libraries with mean size of 243bp for both 18-04608  and 18-04609. Quantitation was also performed using Qubit and qPCR. From size adjusted qPCR the  libraries were 18.4nM after purification.
Cluster Generation: c-Bot Hybridization using 14pM of each library pool and on-board cluster  generation.
Sequencing chemistry: 150bp SR sequencing using Illumina HiSeq Rapid Mode and HiSeqV2  chemistry. Illumina Protocol 15035788 Rev D, Apr 2014

tag: strain backround

value: SN background

tag: strain type

tag: sample type

value: Log phase mutant cells + Calcaflour (rep 2)


title: Patient 12 -tumor

tag: individual

value: Patient 12

tag: disease state

value: female

value: tumor


title: Patient 12 -normal

value: adjacent normal


title: MYC ON 3

description: MYC ON lymphoma spleen

value: FVB/N

value: splenic single cell suspension

value: post natal 6-10 weeks

value: Em-tTA/tet-O-MYC (MYC ON)


title: C_B10

value: Adult

value: Cultured airway basal cells

value: two ro three passages


title: Patient 11 -normal

value: Patient 11

value: muscle invasive bladder cancer (MIBC)

value: male

value: Caucasian


title: Unt_Mut_R2

description: Illumina Tru11

treatment_protocol: 2 hour treatment with 20 μg/ml of calcofluor white

value: SN background

value: Log phase mutant cells (rep 2)


title: C_C10


title: 2015_Harvest_Plot 24_rep a_green

source_name: Apple Granny Smith fruit peel, harvested in 2015 on plot 24, at early physiological mature stage, sampled at harvest.

value: Fruit

value: Peel

value: Granny Smith

value: Wild-type

tag: tissus developmental stage

value: Harvested at early physiological maturity

tag: phenotype

value: High scald

tag: plot


title: 2014_Harvest_Plot 24_rep b_green

value: Low scald


title: genomic DNA from anaplastic thyroid cancer case 12

tag: gender

value: Male

value: anaplastic thyroid cancer sample


title: Treated_WT_R2

description: Illumina Tru10

value: wild type Candida

value: Log phase wild type cells + Calcaflour (rep 2)


title: 2017_Harvest_Plot 31b_rep b_green


title: Patient 11 -tumor

value: Patient 11

tag: age

tag: race

value: tumor


title: genomic DNA from anaplastic thyroid cancer case 9

value: Female

tag: tissue


title: 2015_Harvest_Plot 24_rep b_red


title: genomic DNA from anaplastic thyroid cancer case 1


title: Unt_WT_R2

description: Illumina Tru9

value: Log phase wild type cells (rep 2)


title: MYC ON 1

description: MYC ON lymphoma spleen

tag: strain

value: FVB/N

value: splenic single cell suspension

value: post natal 6-10 weeks

value: Em-tTA/tet-O-MYC (MYC ON)


title: Patient 9 -normal

source_name: Adjacent Normal

value: Patient 9

value: muscle invasive bladder cancer (MIBC)

value: male

value: Caucasian

value: adjacent normal


title: MYC OFF 1_d4

description: MYC OFF lymphoma spleen

value: Em-tTA/tet-O-MYC (MYC OFF)


title: IPS T1D Hypoxia Neurite B

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were trimmed from the 3' end of reads using cutadapt
Transcript abundances were calculated using salmon against the hg38 transcriptome
Gene abundances were calculated from transcript abundances using tximport
Genome_build: hg38
Supplementary_files_format_and_content: transcript abundances in txt format

source_name: iPS-derived motor neurons

growth_protocol: Motor neurons were differentiated from human pluripotent stem cells

extract_protocol:
RNA extraction was performed with Zymo Microprep Kits
Illumina TruSeq

treatment_protocol: Neurons were subjected to hypoxic conditions (5% O2) for 24 hours and then fractionated using transwell inserts into soma and neurite fractions

value: iPS-derived motor neurons

tag: compartment

value: neurite

tag: hypoxia

value: hypoxia


title: genomic DNA from anaplastic thyroid cancer case 13

value: Male

value: anaplastic thyroid cancer sample


title: Treated_MuT_R1

description: Illumina Tru7

value: SN background

value: Log phase mutant cells + Calcaflour (rep1)


title: genomic DNA from anaplastic thyroid cancer case 8

value: Female


title: iPS T1D Hypoxia Neurite A


title: Patient 9 -tumor

source_name: Bladder tumor

value: tumor


title: Unt_Mut_R1

description: Illumina Tru4

value: Log phase mutant cells (rep1)


title: WT 2

description: Healthy normal spleen

value: FVB/N

value: splenic single cell suspension

value: post natal 6-10 weeks

value: wildtype


title: IPS T1D Hypoxia Soma D

value: soma


title: Patient 8 -normal

value: Patient 8

value: muscle invasive bladder cancer (MIBC)

value: female

value: Caucasian

value: adjacent normal


title: WT 1

description: Healthy normal spleen


title: genomic DNA from anaplastic thyroid cancer case 7


title: genomic DNA from anaplastic thyroid cancer case 3


title: genomic DNA from anaplastic thyroid cancer case 4

value: Male


title: Sample 26: RNAseq_dTrf5_3

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

institute: University of Edinburgh - WTCCB

description: sense mRNA kit (lexogen)

data_processing:
CRAC Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped. (For the raw reads uploaded here barcodes were not clipped)
CRAC Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
CRAC Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
CRAC Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
CRAC Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign and counts over each genomic features calculated using pyReadCounters from pyCRAC package
RNAseq Demultiplexing: Reads were indexed during library preparation and demultiplexed by the sequencing platform
RNAseq Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
RNAseq Reverse Complement: Reads were reverse complemented
RNAseq Sequences filtration: Low complexity sequences were filtered out before genome alignment
RNAseq Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign, all reads mapping to non RNA polymerase II transcripts were filtered out, and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gff format

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: S.cerevisiae strains expressing C-terminal HTP or N-terminal FTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.
CRAC (as described in Delan-Forino et al, MiMB, in press) and RNA seq (Lexogen Sense mRNA kit)

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: tag

value: yeast culture

tag: barcode name

value: barcode index 7008

tag: barcode sequence

value: TGTCGA


title: Unt_WT_R1

description: Illumina Tru1

tag: strain backround

value: SN background

tag: strain type

value: wild type Candida

value: Log phase wild type cells (rep 1)


title: iPS T1D Hypoxia Soma A

value: iPS-derived motor neurons

value: hypoxia


title: genomic DNA from anaplastic thyroid cancer case 2

value: anaplastic thyroid cancer sample


title: Patient 6 -normal

tag: individual

value: Patient 6


title: Patient 8 -tumor

tag: disease state

value: tumor


title: Col-0 Rep 3 [small RNA-seq]

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

institute: Michigan State University

data_processing:
Reads were trimmed for quality using adapter trimming for small RNA sequencing tool v 0.3.2
Trimmed reads lower than 15 nucleotides were filtered, remaining reads were mapped to the Arabidopsis thaliana reference genome TAIR10 using bowtie v 1.1.2
Total aligned small RNA sequence and the number of times they were sequenced was produced
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts

growth_protocol: AIC: 3% sucrose shaking four days under 24h light

extract_protocol:
RNA's of 4 Arabidopsis lines (col-0, tt19 and two TT19 suppressors, all in  triplicate) which were under AIC (3% sucrose shaking four days under 24h light) for four days was extracted using QIAGEN RNeasy Plant Mini Kit.
Small RNA libraries were prepared by BGI company and sequenced using BGISEQ-500 as 50SE.

tag: background ecotype

tag: genotype/variation

value: Col-0 as wild type

value: seedling

tag: molecule subtype

value: Small RNAs


title: Sample 25: RNAseq_dTrf5_2

description: sense mRNA kit (lexogen)

value: barcode index 7007

value: CTAGTC


title: Patient 6 -tumor

value: muscle invasive bladder cancer (MIBC)

tag: gender

value: female

value: Caucasian


title: IPS T1D Normoxia Neurite D

value: neurite

value: normoxia


title: Treated_WT_R1

description: Illumina Tru2

value: SN background

value: wild type Candida

tag: sample type

value: Log phase wild type cells + Calcaflour (rep1)


title: Sample 24: RNAseq_dTrf5_1

description: sense mRNA kit (lexogen)

value: yeast culture

value: barcode index 7005

value: TGTGCA


title: Col-0 Rep 2 [small RNA-seq]


title: Patient 5 -normal

value: Patient 5

tag: age

tag: race

value: African American

value: adjacent normal


title: IPS T1D Hypoxia Soma B

tag: tissue

value: iPS-derived motor neurons

value: soma

value: hypoxia


title: Col-0 Rep 1 [small RNA-seq]

value: Col-0 as wild type

value: seedling

value: Small RNAs


title: IPS T1D Normoxia Neurite C

tag: compartment

value: neurite


title: Patient 5 -tumor

value: muscle invasive bladder cancer (MIBC)

value: female

value: tumor


title: Sample 23: RNAseq_WT_4

description: sense mRNA kit (lexogen)

value: barcode index 7004

value: TGCACG


title: Sample 22: RNAseq_WT_3

description: sense mRNA kit (lexogen)

value: yeast culture

value: barcode index 7003

value: ACCAGT


title: Patient 4 -normal

value: Patient 4

value: Caucasian


title: iPS T1D Normoxia Neurite A

value: iPS-derived motor neurons

tag: hypoxia

value: normoxia


title: tt19-8 Rep 2 [small RNA-seq]

value: T-DNA insertion in TT19 (AT5G17220) under Col-0 background


title: IPS T1D Normoxia Soma D

value: soma


title: Sample 21: RNAseq_WT_2

description: sense mRNA kit (lexogen)

tag: tag

value: barcode index 7002

value: GATCAC


title: Patient 4 -tumor


title: Sample 20: RNAseq_WT_1

description: sense mRNA kit (lexogen)

tag: barcode name

value: barcode index 7001

value: CAGCGT


title: IPS T1D Normoxia Soma C


title: tt19-8 Rep 1 [small RNA-seq]

value: seedling

value: Small RNAs


title: Patient 3 -normal

value: Patient 3

value: muscle invasive bladder cancer (MIBC)

value: male

value: adjacent normal


title: IPS T1D Normoxia Soma B


title: tt19-8 S7 Rep 3 [small RNA-seq]

source_name: tt19-8 S7_seedling

value: Additional point mutation in DCL4 (AT5G20320) under tt19-8 background


title: Patient 3 -tumor

value: tumor


title: IPS T1D Normoxia Neurite B

value: neurite


title: iPS T1D Normoxia Soma A

value: iPS-derived motor neurons


title: Sample 3: Trf5_1

description: RNA bound to protein of interest

data_processing:
Library strategy: CRAC
CRAC Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped. (For the raw reads uploaded here barcodes were not clipped)
CRAC Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
CRAC Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
CRAC Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
CRAC Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign and counts over each genomic features calculated using pyReadCounters from pyCRAC package
RNAseq Demultiplexing: Reads were indexed during library preparation and demultiplexed by the sequencing platform
RNAseq Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
RNAseq Reverse Complement: Reads were reverse complemented
RNAseq Sequences filtration: Low complexity sequences were filtered out before genome alignment
RNAseq Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign, all reads mapping to non RNA polymerase II transcripts were filtered out, and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gff format

value: HISx6-TEV proteas cleavage site-protA

value: yeast culture

value: Bd

tag: barcode sequence

value: NNNTCTCTAGC


title: Patient 2 -normal

value: Patient 2

value: Caucasian


title: IPS Control Hypoxia Neurite B

value: unaffected

value: hypoxia


title: Sample 4: Trf5_2

description: RNA bound to protein of interest

value: Flagx3-prescission protease site - HISx6

value: Ad

value: NNNCGCTTAGC


title: T48_rep2

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Quality trimmed read sequences were mapped to Plasmodium falciparum 3D7 reference genomes using HiSat2. Gene expression estimates were made as raw read counts using the Pyhton script ‘HTSeq- count’ (model type – union). Counts data were converted to counts per million (cpm) and genes were filtered if they failed to achieve a cpm value of 1 in at least 30% of libraries per conditions.
Normalization of raw read counts was done using voom tmm method and differential gene expression analysis was carried out using DeSeq2
Genome_build: Plasmodium falciparum 3D7
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Plasmodium falciparum

source_name: T48_P. falciparum II3

growth_protocol: Plasmodium falciparum II3 strain was maintained at 37°C, 5% O2 and 5% CO2 in AB+ human RBCs in RPMI 1640 medium containing Albumax II (Invitrogen) supplemented with 2mM L- glutamine. Culture medium was changed in every two days to avoid providing unknown 24 hour rhythmic cues that might be present in the culture medium. Cultures were routinely monitored by Giemsa’s solution-stained thin blood smears and synchronized by treating the cultures with 5% sorbitol (w/v) to kill any late stage asexual stages.  For time-series experiment mature segmented schizonts were isolated by centrifugation over cushions of 70% (v/v) isotonic Percoll (GE healthcare Life Sciences), washed twice with RPMI 1640 without Albumax and allowed to invade fresh RBCs for about two hours in a shaker maintained at 37°C . Following invasion, remaining schizonts were removed from the culture by overlaying the culture over cushions of 70% (v/v) isotonic Precool (GE healthcare Life Sciences). Pellet containing ~ two hours early ring stage infected RBCs and uninfected RBCs was then treated with 5% sorbitol (w/v) to kill the contaminating mature schizonts. Culture containing highly synchronous early ring stage parasites was then split into six-well plates. Over the course of 48 h, 1-2  mL of infected RBC culture was collected every two hours, media was removed by centrifugation for two minutes at 900g, and cells were lysed by adding 1 mL of TRIzol and immediately stored at -80°C deep freezer. The T0 time point was considered to be three hours after addition of Percoll cushion isolated segmented mature schizonts to the fresh RBCs.

extract_protocol:
Total RNA was isolated from TRIzol treated samples according to the manufacturer’s instructions (Life Technologies).
Strand-specific mRNA libraries were prepared from total RNA using TruSeq Stranded mRNA Sample Prep Kit LS (Illumina) according to the manufacturer’s instructions. Briefly, at least 100ng of total RNA was used as starting material to prepare the libraries. PolyA+ mRNA molecules were purified from total RNA using oligo-T attached magnetic beads. First strand synthesis was performed using random primers followed by second strand synthesis where dUTP were incorporated in place of dTTP to achieve strand-specificity. Ends of the double stranded cDNA molecules were adaptor ligated and the libraries amplified by PCR for 15 cycles. Libraries were sequenced on Illumina HiSeq 4000 platform with paired-end 100/150bp read chemistry according to manufacturer’s instructions. Data from 14 timepoints were anlyzed further excluding the first three time points.econd strand synthesis where dUTP were incorporated in place of dTTP to achieve strand-specificity. Ends of the double stranded cDNA molecules were adaptor ligated and the libraries amplified by PCR for 15 cycles. Libraries were sequenced on Illumina HiSeq 4000 platform with paired-end 100/150bp read chemistry according to manufacturer’s instructions. Data from 14 timepoints were anlyzed further

tag: strain

value: infected RBC culture

tag: time point


title: Patient 2 -tumor

tag: individual

value: muscle invasive bladder cancer (MIBC)

value: male


title: tt19-8 S7 Rep 1 [small RNA-seq]

value: Additional point mutation in DCL4 (AT5G20320) under tt19-8 background

value: seedling

value: Small RNAs


title: T48_rep1


title: Patient 1 -normal

value: Patient 1

tag: disease state

value: female

value: African American

value: adjacent normal


title: tt19-8 S2 Rep 3 [small RNA-seq]

source_name: tt19-8 S2_seedling

tag: background ecotype

value: Additional point mutation in RDR6 (AT3G49500) under tt19-8 background


title: iPS Control Hypoxia Neurite A

value: iPS-derived motor neurons

value: neurite


title: tt19-8 Rep 3 [small RNA-seq]

tag: genotype/variation

value: T-DNA insertion in TT19 (AT5G17220) under Col-0 background


title: tt19-8 S2 Rep 2 [small RNA-seq]

tag: molecule subtype


title: IPS Control Hypoxia Soma B

value: unaffected

value: soma

value: hypoxia


title: MYC ON 2

description: MYC ON lymphoma spleen

value: FVB/N

value: splenic single cell suspension

value: post natal 6-10 weeks

tag: genotype

value: Em-tTA/tet-O-MYC (MYC ON)


title: T46_rep2

source_name: T46_P. falciparum II3

value: infected RBC culture


title: Patient 1 -tumor

value: muscle invasive bladder cancer (MIBC)

tag: gender

value: tumor


title: T46_rep1


title: iPS Control Hypoxia Soma A


title: tt19-8 S2 Rep 1  [small RNA-seq]

value: seedling

value: Small RNAs


title: tt19-8 S7 Rep 2 [small RNA-seq]

value: Additional point mutation in DCL4 (AT5G20320) under tt19-8 background


title: T44_rep2

source_name: T44_P. falciparum II3


title: IPS Control Normoxia Neurite B

value: normoxia


title: Col-0 Rep 3

data_processing:
Quality check of raw sequenced reads was performed using fastqc v0.11.5 , then mapped to Arabidopsis genome TAIR 10 using Hisat2
Raw read counts were calculated using feature count v1.6.2 to capture all reads falling in the exon region of genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample

source_name: Seedling

extract_protocol:
Extraction protocol not provided.
Library Preparation by BGI company

treatment_protocol: anthocyanin inducing conditions (AIC): shaking in 3% sucrose for four days under 24hrs of  light

value: wildtype

value: Seedling


title: Col-0 Rep 2


title: iPS Control Normoxia Neurite A

value: iPS-derived motor neurons

value: neurite


title: T44_rep1


title: IPS Control Normoxia Soma B

value: unaffected

value: soma


title: Col-0 Rep 1


title: tt19-8 Rep 3


title: T42_rep1

source_name: T42_P. falciparum II3


title: T40_rep1

source_name: T40_P. falciparum II3


title: iPS Control Normoxia Soma A


title: T38_rep2

source_name: T38_P. falciparum II3


title: T40_rep2


title: tt19-8 Rep 2


title: tt19-8 S8 Rep 3

value: tt19; suppressor S8


title: 6-3_CD8

city: Kansas City

first: Mary

middle: A

last: Markiewicz

state: KS

address: 3901 Rainbow Blvd. MS 3029

department: Microbiology, Molecular Genetics & Immunology

institute: University of Kansas Medical Center

description:
engineered Treg RNA Seq
FOXP3_Helios-FL_CD8_cpm.txt

data_processing:
Base calling was done with bcl2fastq2 v2.20
Adaptor sequences were removed by cutadapt v1.16 with default parameter (Martin, Marcel. "Cutadapt removes adapter sequences from high-throughput sequencing reads." EMBnet. journal 17.1 (2011): 10-12.)
Sequences were aligned to hg38 using bowtie2 v2.3.4.3 with pair end option with default parameter (Langmead, Ben, and Steven L. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature methods 9.4 (2012): 357.)
Read counts for genes were calculated with RSEM v1.3.0 with default parameter. (Li, Bo, and Colin N. Dewey. "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome." BMC bioinformatics 12.1 (2011): 323.)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for all 18 samples.

source_name: Human primary T cells

growth_protocol: Human peripheral blood mononuclear cells were activated in Aim V medium (Thermo Fisher Scientific) with 2% human AB serum (Bio-Techne) (complete media). 3x10^6 PBMC at 10^6/mL were stimulated with 2 µg/mL plate-bound anti-CD3 (OKT3; Bio X Cell) and anti-CD28 (9.3; Bio X Cell). After 2 days of activation, complete medium was supplemented with 200 U/mL of recombinant human IL-2 (rhIL-2) (PeproTech). The remaining human T cells were passed every 2-3 days at 1-2x10^6 cells/ml in complete medium supplemented with rhIL-2 at 200 U/mL in tissue culture treated flasks . Cells were thenn retrovirally transduced and maintained at 1-2x10^6 cells/ml in complete medium supplemented with rhIL-2 at 200 U/mL in tissue culture treated flasks.

extract_protocol:
Cells were collected 5 days after transduction and CD4+ and CD8+ cells were isolated via flow cytometry assisted cell sorting (FACS) on a BD FACS Aria III. RNA was isolated using the RNeasy Mini Kit (Qiagen).
mRNA sequencing libraries were prepared using the NuGEN Universal Plus mRNA-seq + UDI kit (NuGEN 9144-96). Briefly, 1ug of Human Primary T cell total RNA (Agilent TapeSataion RIN values between 9.7 - 10) was enriched for mRNA by oligo-dT bead capture, fragmented, reverserse transcribed into cDNA. cDNA was end-repaired and ligated with "adapter-dimer free" Unique Dual Index (UDI) adapters, strand selected, PCR amplified with 12 cycles of amplification followed by KAPA Pure Bead (KAPA KK8002) clean-up and sizing resulting in a 290bp median sized library. 100 cycle Paired end sequencing data was generated with an Illumina NovaSeq 6000 Sequencer using NovaSeq 6000 S1 Reagent Kit - 200 cycle (Illumina 20012864).

tag: cell type

value: engineered Treg

tag: donor #

value: Donor 6

tag: cd4+ or cd8+

tag: retroviral vector expressed

value: FOXP3+ Helios-FL


title: 6-2_CD8

description:
engineered Treg RNA Seq
FOXP3_CD8_cpm.txt


title: Vehicle replicate 4, GFP+ cells from 3 mice [1-pentanethiol]

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

description: mRNA abundance data

hyb_protocol: after fragmentation cRNA was hybridized for 16 hr at 45C on Clariom S Arrays. These were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console software using default analysis settings and global scaling as normalization method.

source_name: Olfactory mucosa; Vehicle-stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 - 100 ng of total RNA.

growth_protocol: 24 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

extract_protocol: Mice were euthanized, olfactory mucosa were dissected, dissociated, and subjected to FACS.

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odor for 10 sec every 20 min.

value: FACS sample, GFP+


title: Vehicle replicate 2, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data

value: FACS sample, GFP-


title: T38_rep1

tag: tissue

value: infected RBC culture


title: T42_rep2


title: Vehicle replicate 2, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Vehicle replicate 1, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: tt19-8 S8 Rep 2


title: tt19-8 S8 Rep 1


title: 6-3_CD4

description:
engineered Treg RNA Seq
FOXP3_Helios-FL_CD4_cpm.txt


title: T36_rep2

source_name: T36_P. falciparum II3


title: 6-4_CD8

description:
engineered Treg RNA Seq
FOXP3_Helios-d3B_CD8_cpm.txt

value: FOXP3+ Helios-d3B


title: Odor replicate 4, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data

source_name: Olfactory mucosa; 1-pentanethiol stimulated


title: tt19-8 Rep 1


title: T36_rep1


title: 5-4_CD8

value: Donor 5


title: tt19-8 S7 Rep 3

value: tt19; suppressor S7


title: 6-2_CD4

description:
engineered Treg RNA Seq
FOXP3_CD4_cpm.txt


title: tt19-8 S7 Rep 2


title: Odor replicate 4, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: T32_rep2

source_name: T32_P. falciparum II3


title: T32_rep1


title: tt19-8 S5 Rep 3

value: tt19; suppressor S5


title: 5-2_CD8


title: 5-3_CD8


title: 5-4_CD4

description:
engineered Treg RNA Seq
FOXP3_Helios-d3B_CD4_cpm.txt


title: tt19-8 S7 Rep 1


title: tt19-8 S5 Rep 2


title: 6-4_CD4


title: IPS T1D Hypoxia Neurite D

source_name: iPS-derived motor neurons

tag: compartment

tag: hypoxia

value: hypoxia


title: tt19-8 S5 Rep 1

value: Seedling


title: T30_rep2

source_name: T30_P. falciparum II3


title: 5-3_CD4


title: T34_rep2

source_name: T34_P. falciparum II3


title: Odor replicate 3, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Odor replicate 2, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: T34_rep1


title: tt19-8 S4 Rep 3

value: tt19; suppressor S4


title: tt19-8 S4 Rep 2


title: 5-2_CD4


title: T28_rep2

source_name: T28_P. falciparum II3


title: Odor replicate 1, GFP+ cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: 1-3_CD8

value: Donor 1


title: tt19-8 S4 Rep 1


title: WT 3

description: Healthy normal spleen

source_name: spleen

value: FVB/N

value: splenic single cell suspension

tag: age

value: post natal 6-10 weeks

value: wildtype


title: Vehicle replicate 4, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: tt19-8 S2 Rep 3

value: tt19; suppressor S2


title: 1-2_CD8

value: engineered Treg


title: Odor replicate 1, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: Vehicle replicate 4, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Vehicle replicate 3, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data

value: FACS sample, GFP+


title: T26_rep1

source_name: T26_P. falciparum II3

tag: strain


title: Vehicle replicate 3, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data

value: FACS sample, GFP-


title: T30_rep1

value: infected RBC culture

tag: time point


title: 1-3_CD4

value: FOXP3+ Helios-FL


title: 1-4_CD4

value: FOXP3+ Helios-d3B


title: tt19-8 S2 Rep 1


title: T24_rep2

source_name: T24_P. falciparum II3


title: T24_rep1


title: 1-2_CD4


title: tt19-8 S1 Rep 3

value: tt19; suppressor S1


title: tt19-8 S1 Rep 2


title: T26_rep2


title: T22_rep2

source_name: T22_P. falciparum II3


title: T22_rep1


title: tt19-8 S1 Rep 1

source_name: Seedling


title: tt19-8 S2 Rep 2


title: Vehicle replicate 1, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: HypoxiaNeuriteC

description: polyA RNA from the neurites of hypoxia-treated human motor neurons

data_processing:
The last 75 nt of the reads for both the forward and reverse reads were removed
transcript quantification against cDNA sequences present in GencodeM17 (mm10) with salmon 0.11.1 using the flags --gcBias and --seqBias
collation of transcript abundances into gene abundances with tximport
differential expression analysis with DESeq2
Genome_build: mm10, Gencode M17
Supplementary_files_format_and_content: matrix of transcript abundances

source_name: hPSC-derived human motor neuron

extract_protocol:
Total RNA was isolated using Zymo Quick RNA Microprep kit
Kapa HyperPrep polyA kit

tag: treatment

tag: cell compartment

value: neurite


title: HypoxiaNeuriteB

value: hypoxia


title: HypoxiaSomaC

description: polyA RNA from the soma of hypoxia-treated human motor neurons

value: soma


title: HypoxiaNeuriteA


title: Vehicle replicate 2, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Vehicle replicate 2, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: HypoxiaSomaB


title: Vehicle replicate 1, GFP- cells from 3 mice [1-pentanethiol]

description: mRNA abundance data


title: T18_rep2

source_name: T18_P. falciparum II3


title: T18_rep1


title: Adult mouse kidney_rep3

city: Toronto

first: Theresa

last: Chow

state: Ontario

address: 25 Orde Street

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description: Gene expression data from native tissue

hyb_protocol: Hybridized for 16 hours at 45C

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000

data_processing: Raw CEL files were read and normalized using the R/Bioconductor packages oligo and limma. This method uses robust multi-array average (RMA) expression measure resulting in log base 2 scale. In our workflow, we mapped the CEL files directly to gene symbols, we did not use any custom probe/gene annotations.

label: Biotin allonmide triphosphate

source_name: Adult kidney

label_protocol: Samples were prepared using the Affymetrix WT PLUS kit and labelled with biotin alloamide triphosphate as per manufacturer's instructions

growth_protocol: Mouse ESC, mesoderm cells, intermediate mesoderm cells and progenitor cells were all grown in 2D culture prior to RNA extraction. Embryonic and adult kidneys were freshly dissected and immediately flash frozen for RNA extraction.

extract_protocol: Total RNA was isolated using Qiagen Rneasy Plus Kit as per manufacturer's instructions

treatment_protocol: Embryonic kidneys and adult kidneys were dissected and immediately flash frozen for RNA extraction. Mouse ESC were maintained under standing ESC conditions prior to RNA extraction. Mesoderm, intermediate mesoderm and progenitor cells were culturing under their respective differentiation media prior to RNA extraction. 8D, 14D and 21D organoids were cultured under organoid conditions prior to RNA extraction.

tag: batch

tag: cell/tissue type

value: Adult tissue


title: HypoxiaSomaA


title: Odor replicate 3, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data

source_name: Olfactory mucosa; Cigarette Smoke stimulated


title: NormoxiaNeuriteC

description: polyA RNA from the neurites of normoxia-treated human motor neurons

value: normoxia


title: T20_rep2

source_name: T20_P. falciparum II3


title: Adult mouse kidney_rep1

description: Gene expression data from native tissue


title: T16_rep2

source_name: T16_P. falciparum II3


title: Adult mouse kidney_rep2

description: Gene expression data from native tissue


title: Odor replicate 2, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: T16_rep1


title: 1-4_CD8

source_name: Human primary T cells

value: Donor 1


title: Odor replicate 3, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: NormoxiaNeuriteB


title: T14_rep1

source_name: T14_P. falciparum II3


title: T14_rep2


title: Mouse ESC_rep3

description: Gene expression data from undifferentiated ESC

source_name: Mouse embryonic stem cells

value: Undifferentiated cells


title: NormoxiaSomaC

description: polyA RNA from the soma of normoxia-treated human motor neurons


title: NormoxiaNeuriteA


title: Mouse ESC_rep2


title: T12_rep2

source_name: T12_P. falciparum II3


title: T20_rep1


title: Odor replicate 4, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Odor replicate 4, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Mouse ESC_rep1


title: Odor replicate 2, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: T12_rep1


title: E13.5 mouse kidney_rep3

description: Gene expression data from native tissue

source_name: E13.5 embryonic kidney

value: Embryonic tissue


title: NormoxiaSomaB


title: Odor replicate 1, GFP- cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Odor replicate 1, GFP+ cells from 3 mice [cigarette smoke]

description: mRNA abundance data


title: Vehicle replicate 5, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

source_name: Olfactory mucosa; Vehicle-stimulated

growth_protocol: 30 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.


title: T10_rep2

source_name: T10_P. falciparum II3


title: NormoxiaSomaA


title: T10_rep1


title: Trf5_CTD4_2

tag: protease site

value: Flagx3-prescission protease site - HISx6

tag: barcode name

value: Ca

tag: barcode sequence

value: NNNCTAGC


title: T8_rep2

source_name: T8_P. falciparum II3


title: Trf5_CTD4_1


title: Trf5_dCTD_3

value: Ad

value: NNNCGCTTAGC


title: T8_rep1

value: infected RBC culture


title: E13.5 mouse kidney_rep2

description: Gene expression data from native tissue


title: E13.5 mouse kidney_rep1

description: Gene expression data from native tissue


title: Trf5_dCTD_1

value: Bd

value: NNNTCTCTAGC


title: Vehicle replicate 4, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

tag: cell type

value: FACS sample, GFP+


title: T6_rep1

source_name: T6_P. falciparum II3


title: Vehicle replicate 4, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

value: FACS sample, GFP-


title: E12.5 mouse kidney_rep1

description: Gene expression data from native tissue

source_name: E12.5 embryonic kidney


title: Vehicle replicate 5, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: E12.5 mouse kidney_rep3

description: Gene expression data from native tissue


title: Sample 19: Hek2_2

description: RNA bound to protein of interest

source_name: yeast culture

tag: tag

value: HISx6-TEV proteas cleavage site-protA

value: yeast culture


title: E12.5 mouse kidney_rep2

description: Gene expression data from native tissue


title: 21D organoid_rep2

description: Gene expression data from kidney differentiation protocol

source_name: ESC-derived 21D organoid

value: Differentiated cells


title: Trf5_dCTD_2


title: Vehicle replicate 3, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: 21D organoid_rep3


title: Vehicle replicate 2, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: 14D oragnoid_rep3

source_name: ESC-derived 14D organoid


title: Sample 14: Mtr4 (dTrf5)_2

description: RNA bound to protein of interest

value: Bc

value: NNNCACTAGC


title: T6_rep2


title: T4_rep1

source_name: T4_P. falciparum II3


title: Sample 13: Mtr4 (dTrf5)_1

description: RNA bound to protein of interest

value: Ba

value: NNNAGAGC


title: T4_rep2


title: 21D organoid_rep1


title: Sample 12: Mtr4 (dTrf4)

description: RNA bound to protein of interest


title: T2_rep1

source_name: T2_P. falciparum II3


title: T2_rep2


title: Sample 11: Mtr4 (dAir2)_2

description: RNA bound to protein of interest

value: Bb

value: NNNGTGAGC


title: 14D oragnoid_rep2


title: Sample 10: Mtr4 (dAir2)_1

description: RNA bound to protein of interest

value: Ac

value: NNNGCGCAGC


title: Vehicle replicate 3, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: T0_rep2

source_name: T0_P. falciparum II3


title: T0_rep1


title: Odor replicate 5, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

source_name: Olfactory mucosa; ArtCigSmoke odor-stimulated


title: 14D oragnoid_rep1


title: 8D organoid_rep3

source_name: ESC-derived 8D organoid


title: Sample 11: Mtr4 (dAir1)_2

description: RNA bound to protein of interest


title: Odor replicate 5, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: hfq_C: PAO1 ∆hfq RNA-Seq

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

data_processing:
Sequencing reads from each pooled sample were demulitplexed based on their associated barcod sequence using custom scripts; allowing up to 1 mismatch in the barcode, provided this did not make assignemtn of the read to a different barcode possible. Barcode sequencese were subsequently trimmed from the first read as were terminal G's from the second read that may have been added by SMARTScirbe during template switching.
Reads were aligned to the PAO1 reference genome (NCBI RefSeq NC_002516) using BWA
Read counds were assigned to the genes and other genomic features using custom scripts
Differential expression analysis was conducted with DESeq2.
For visualization, the bam alignment files from samples 1A, 2C and 3B were sorted using samtools (version 1.10).
The sorted reads from samples 1C, 2C, and 3B were split by strand and convereted to the bedgraph file format using bedtools (version 2.92.2).
The read depth in samples 2C and 3B were normalized to the total number of mapping fragments in sample 1A using custom R scripts.
The normalized bedgraph files from Samples 1C, 2C, and 3 B were converted to the bigwig file format using the bedgraphToBigWig executable (downloaded from the USCS database) for visualization in a genome brower.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: bgwig files were generated using the bedgraphtobigwig script package from UCSC; Scores represent normalized RNASeq read density

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial cells grown to OD 0.5

growth_protocol: Bacterial cultures were started from single colonies, grown overnight, and back-diluted in LB media

extract_protocol:
Total RNA was extracted via Direct-Zol RNA Miniprep Kit (Zymo Research)
Illumina cDNA libraries were generated using a modified version of the RNAtag-Seq protocol. 500 ng - 1 µg total RNA was fragments, depleted of genomic DNA, dephosphorylated and ligated to DNA adapters carrying 5'-AN8-3' barcodes of known sequence with a 5' phosphate and a 3' blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA deplection kit (EpiCentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA usinga  primer designed to the constant region of the barcode adaptor with addition of an adapter to the 3' end of the cDNA by template switching using SMARTScribe (Clonetech); (ii) PCR amplification using primers whose 5' ends target the constant region of the 3' or 5' adaptors and whose 3' ends contain the full Illumina P5 or P7 sequences.

tag: genotype

value: PAO1 with deletion of hfq gene

value: mid-logarithmic phase culture


title: Odor replicate 4, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Sample 10: Mtr4 (dAir1)_1

description: RNA bound to protein of interest

value: Ab

value: NNNATTAGC


title: 8D organoid_rep2


title: 8D organoid_rep1


title: Odor replicate 4, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Progenitor_rep3

source_name: ESC-derived progenitor


title: hfq_B: PAO1 ∆hfq RNA-Seq


title: Progenitor_rep2


title: Sample 5: Trf4_1

description: RNA bound to protein of interest


title: Odor replicate 2, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

value: FACS sample, GFP+


title: hfq_A: PAO1 ∆hfq RNA-Seq


title: Air1_air2d_2

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.
CRAC (as described in Delan-Forino et al, MiMB, 2020) and RNA seq (Lexogen Sense mRNA kit)

value: Cc

value: NNNCTAGC


title: Air2_air1d_2

value: HISx6-TEV proteas cleavage site-protA

value: yeast culture

value: Ca


title: rsmAF_A: PAO1 ∆rsmAF RNA-Seq

value: PAO1 with deletion of rsmA and rsmF genes


title: rsmAF_C: PAO1 ∆rsmAF RNA-Seq


title: Progenitor_rep1

value: Differentiated cells


title: Intermediate mesoderm_rep3

source_name: ESC-derived intermediate mesoderm


title: Air1_air2d_1

value: Cb

value: NNNTGGAGC


title: Trf5_5xA

value: Flagx3-prescission protease site - HISx6


title: M-WT-1_B: PAO1 RNA-Seq

value: PAO1 wild-type


title: Odor replicate 2, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

value: FACS sample, GFP-


title: M-WT-1_C: PAO1 RNA-Seq


title: T28_rep1

source_name: T28_P. falciparum II3

value: infected RBC culture


title: Odor replicate 3, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Intermediate mesoderm_rep2


title: Trf5_CTD4_3

value: Ac

value: NNNGCGCAGC


title: Mesoderm_rep3

source_name: ESC-derived mesoderm


title: Odor replicate 1, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Intermediate mesoderm_rep1


title: Odor replicate 1, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Odor replicate 3, GFP- cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data


title: Air2_air1d_1

value: Ad

value: NNNCGCTTAGC


title: rsmAF_B: PAO1 ∆rsmAF RNA-Seq

value: mid-logarithmic phase culture


title: Mesoderm_rep1


title: circZbtb20 knockout

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description:
This is circZbtb20-deficient ILC3s
1x105 ILC3s were isolated from circZbtb20+/+, circZbtb20-/-, Nr4a1+/+ or Nr4a1-/- mice by FACS

hyb_protocol: hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000.

data_processing: All resulting .CEL files for each array type were processed as a single group via the Affymetrix Power Tools (APT) package using sketch normalization and the RMA algorithm to summarize probeset signal.

source_name: circZbtb20-deficient ILC3s

label_protocol: 10 mg of cRNA was carried into the second cycle, first strand cDNA synthesis reaction. 5.5 mg of single-stranded cDNA was fragmented and biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit according to The GeneChip® WT Terminal Labeling and Hybridization User Manual

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

value: circZbtb20 knockout


title: circZbtb20 wild-type

description:
This is wild-type ILC3s
1x105 ILC3s were isolated from circZbtb20+/+, circZbtb20-/-, Nr4a1+/+ or Nr4a1-/- mice by FACS

source_name: WT ILC3s

value: Wild-type


title: Nr4a1 wild-type


title: Nr4a1 knockout

description:
This is Nr4a1-deficient ILC3s
1x105 ILC3s were isolated from circZbtb20+/+, circZbtb20-/-, Nr4a1+/+ or Nr4a1-/- mice by FACS

source_name: Nr4a1-deficient ILC3s

value: Nr4a1 knockout


title: H1hESC_SMAD1_untreated_Input

status: Public on Apr 19 2020

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

description: Input DNA

data_processing:
Alignment: Sequence quality of the raw reads was evaluated using FASTQC tool. Raw reads were aligned to human genome (hg19 assembly) using BWA version 0.7.5a and default settings
Peak calling: To improve signal to noise ratio, reads from 3 biological replicates were pooled prior to peak calling. Peak calling was carried out using MACS version 1.4.2 with default settings. Normalized genome-wide coverage files were obtained by scaling each sample using total number of mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: MACS peaksets; BED files

source_name: embryonic stem cells

growth_protocol: The hESC line H1 was grown on growth factor-reduced Matrigel and maintained in mTeSR1 media

extract_protocol:
Cells were dissociated and fixed in mTeSR1 media with formaldehyde at a final concentration of 1% for 10 minutes. Fixation was quenched with glycine and cells were washed with DPBS. Cells were suspended in high salt lysis buffer and chromatin was sheared using a Bioruptor Plus to sizes of 100-400 bp. Soluble chromatin from approximately 3E+06 cells per ChIP was incubated with primary antibody (Cell Signaling Technology; CST6944) and Protein G Dynabeads at 4 degrees overnight. Dynabeads were then washed and bound chromatin was eluted. Crosslinks were reversed by incubation at 65 degrees overnight, and proteins were digested with Proteinase K. DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit.
2 ng of DNA was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer recommendations (15 cycles of PCR). Library quality and quantity were assessed on a Bioanalyser and Qubit respectively.

treatment_protocol: BMP4 was added to mTeSR1 media (50 ng/ml) for 1 hour.

tag: cell line

value: human embryonic stem cells (hESCs)

value: untreated


title: H1hESC_SMAD1_untreated_ChIP

description: ChIP DNA

tag: chip antibody

value: smad1 (Cell Signaling Technology; CST6944)


title: H1hESC_SMAD1_1hBMP4_ChIP

description: ChIP DNA


title: AGB60_1: BMP4_60_Rep1

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat2 (2.0.11) with default settings
Gene annotations were obtained from Ensembl Human genome (hg19). Gene-based read count was obtained using featureCounts function from Rsubread R Bioconductor package
Differentially expressed genes were identified using DESeq2 R Bioconductor package
Genome_build: Ensembl hg19
Supplementary_files_format_and_content: tab-delimited text file includes Gene counts for each Sample

growth_protocol: H1 human embryonic stem cells were grown on growth factor-reduced Matrigel and maintained in mTeSR1 media

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit as per manufacturer's instructions
Libraries were constructed using the Truseq stranded mRNA library kit (Illumina) as per manufacturer's instructions, starting from 500 ng of total RNA.

treatment_protocol: H1 hESC cells grown on growth factor-reduced Matrigel had human recombinant BMP4 added to mTeSR1 media (50 ng/ml).

tag: tissue

value: embryonic stem cells


title: AGB60_2: BMP4_60_Rep2


title: AGB20_2: BMP4_20_Rep2


title: AGB40_2: BMP4_40_Rep2


title: AGB40_3: BMP4_40_Rep3


title: AGB40_1: BMP4_40_Rep1


title: Mesoderm_rep2

value: Differentiated cells


title: AGB20_1: BMP4_20_Rep1


title: AGB0_1: BMP4_0_Rep1


title: AGB0_3: BMP4_0_Rep3


title: ZIKV_injection_3_8dpi

city: Washington

first: Ioannis

last: Eleftherianos

state: DC

department: Biological Sciences

institute: The George Washington University

description: strain of ZIKV: MR766

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Fastq files were aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl BDGP5.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

organism: Drosophila melanogaster

source_name: Whole fly

extract_protocol: Illumina Ribo-Zero v2

value: Whole fly

tag: time-point

value: 8 dpi

value: ZIKV


title: AGB0_2: BMP4_0_Rep2


title: ZIKV_injection_2_8dpi

description: strain of ZIKV: MR766


title: PBS_injection_3_8dpi

description: strain of ZIKV: MR766

value: PBS


title: PBS_injection_2_8dpi

description: strain of ZIKV: MR766


title: M-WT-1_A: PAO1 RNA-Seq

value: PAO1 wild-type


title: ZIKV_injection_1_8dpi

description: strain of ZIKV: MR766


title: H1hESC_SMAD1_1hBMP4_Input

description: Input DNA


title: ZIKV_injection_3_4dpi

description: strain of ZIKV: MR766

value: 4 dpi


title: PBS_injection_1_8dpi

description: strain of ZIKV: MR766


title: AGB20_3: BMP4_20_Rep3


title: PBS_injection_2_4dpi

description: strain of ZIKV: MR766


title: ZIKV_injection_2_4dpi

description: strain of ZIKV: MR766


title: PBS_injection_3_4dpi

description: strain of ZIKV: MR766


title: H1hESC_ChIP_GATA3_6h_Rep1

data_processing:
Alignment: 75bp single-end reads were trimmed for Illumina adapters using cutadapt. Reads were aligned to hg38 using bowtie (--very-sensitive). Duplicate reads were identified and removed using Picard markDuplicates. Reads mapping to multiple locations and Encode blacklisted regions were also excluded.
Peak calling: Enriched regions were identified by comparing ChIP samples to their corresponding input control using Macs2 (-q 0.05, -B, --SPMR) for 2 biological replicates.
Bigwig files were generated from bedGraph files generated by Macs2
Genome_build: hg38
Supplementary_files_format_and_content: Bed files containing peak loci called by Macs2. Bigwig files containing normalised genome coverage values converted from bedGraph files generated by Macs2

extract_protocol:
Cells were dissociated and fixed in mTeSR1 media with formaldehyde at a final concentration of 1% for 10 minutes. Fixation was quenched with glycine and cells were washed with DPBS. Cells were suspended in high salt lysis buffer and chromatin was sheared using a Bioruptor Plus to sizes of 100-400 bp. Soluble chromatin from approximately 3E+06 cells per ChIP was incubated with primary antibody (Abcam; ab199428) and Protein G Dynabeads at 4 degrees overnight. Dynabeads were then washed and bound chromatin was eluted. Crosslinks were reversed by incubation at 65 degrees overnight, and proteins were digested with Proteinase K. DNA was purified using Zymo ChIP Clean and Concentrator Kit.
Libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems).

treatment_protocol: BMP4 was added to mTeSR1 media (50 ng/ml) for 6 hours.

tag: repeat

value: GATA3 (Abcam; ab199428)


title: H1hESC_Input_GATA3_6h_Rep2


title: ZIKV_injection_1_4dpi

description: strain of ZIKV: MR766


title: PBS_injection_1_4dpi

description: strain of ZIKV: MR766


title: H1hESC_ChIP_GATA3_6h_Rep2


title: H1_TROPH_60m_3

data_processing:
Basecalls were performed using bcl2fastq v2.20
Sequence reads were trimmed for adapter and low quality bases using cutadapt-1.9.1
Reads were aligned to the human genome GRCh38 from Ensembl using STAR-2.5.2a
Gene-level quantifications were generated using RSEM-1.2.31 against human annotation release 86 from Ensembl
Genome_build: Ensembl GRCh38 release-86

growth_protocol: H1 human embryonic stem cells (hESCs) were maintained on growth factor-reduced Matrigel in mTeSR1 media.

extract_protocol:
Cells were lysed and total RNA was extracted using a QIAGEN RNeasy Kit
Libraries were constructed using a KAPA mRNA HyperPrep Kit

treatment_protocol: H1 hESCs grown on growth factor-reduced matrigel had media changed to a growth factor cocktail designed to direct differentiation towards either endoderm (TeSR-E5 + BMP4 (10 ng/ml) + FGF2 (20 ng/ml) + Activin A (100 ng/ml) + LY29004 (10 uM)), mesoderm (TeSR-E5 + BMP4 (10 ng/ml) + VEGF (10 ng/ml) + FGF2 (10 ng/ml) + Activin A (10 ng/ml)), or trophectoderm (TeSR-E5 + BMP4 (50 ng/ml)) for 20, 40, or 60 minutes

value: Trophectoderm


title: H1_TROPH_40m_1


title: H1_TROPH_40m_2


title: H1_TROPH_60m_2


title: H1_TROPH_40m_3


title: H1_TROPH_20m_2


title: H1_TROPH_20m_3


title: AGB60_3: BMP4_60_Rep3


title: H1_TROPH_20m_1


title: H1_MESO_60m_2

value: Mesoderm


title: H1_MESO_60m_1


title: H1_MESO_40m_3


title: H1_MESO_40m_2


title: H1_MESO_60m_3


title: H1_MESO_20m_3


title: H1_MESO_20m_2


title: H1_MESO_40m_1


title: H1_MESO_20m_1


title: H1_ENDO_60m_3

value: Endoderm


title: H1hESC_Input_GATA3_6h_Rep1


title: H1_TROPH_60m_1


title: H1_ENDO_40m_3


title: H1_ENDO_40m_2


title: Vehicle replicate 1, GFP+ cells from 3 mice [artificial cigarette smoke odor]

description: mRNA abundance data

source_name: Olfactory mucosa; Vehicle-stimulated

value: FACS sample, GFP+


title: H1_ENDO_40m_1


title: H1_ENDO_20m_3


title: H1_ENDO_20m_2


title: Leaf, EX43 4h

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: NCBI_GCF_000188115.3_SL2.50
Supplementary_files_format_and_content: EXCEL file includes FPKM values for each Sample

organism: Solanum lycopersicum

source_name: Micro-TOM-EX

growth_protocol: Micro-TOM and Micro-TOM-EX were sown into pots filled with soil and grown under controlled conditions (16h light，cold stress treated 0，4 or 12h) in a greenhouse at the Horticultural station of Northeast Agricultural University

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

value: Micro-TOM-EX

tag: stress

value: cold

tag: time

value: leaf


title: Leaf, EX121 12h


title: Leaf, EX122 12h


title: Leaf, EX123 12h


title: H1_ENDO_20m_1

tag: treatment


title: Leaf, EX42 4h


title: H1_ENDO_60m_2


title: H1_0m_3

value: untreated


title: H1_ENDO_60m_1

value: embryonic stem cells


title: Leaf, EX41 4h


title: Gd6-siRNA-1

city: Worcester

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

data_processing:
The FASTQ files obtained were de-multiplexed using the bcl2fastq tool as a part the Illumina basepace workflow
RSEM was used to align the reads to the human genome assembly hg19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: primary human adipocytes culture_Gd6-siRNA

extract_protocol:
Total RNA extraction was performed using TriPure Trizol reagent.  Trizol was added to the cells and incubated at room temperature for 5 minutes. Cells were collected into a GentleMACS M tube and dissociated using the GentleMACS Dissociator (Miltenyi Bio) Program RNA01.01. Tubes were centrifuged for 3 minutes at 800RPM and the mixture was transferred to a 2ml collection tube. Chloroform was added in a 1:5 ratio to the tripure/cell mix and tubes were inverted to mix, then incubated at room temperature for 3-5 minutes. Aqueous phase separation was performed, and the RNA-containing layer was mixed with an equal volume of 100% Isopropanol and incubated overnight at -20 degrees for precipitation. RNA was pelleted and washed with 80% ETOH and eluted in nuclease-free water.
cDNA library was prepared using  TruSeq® Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions. For each clone, 1 ug of total RNA was used as input to synthesize cDNA which was subsequently amplified. All samples were processed concurrently during library preparation. Illumina sequencing indexes were added to the fragmented libraries and indexed libraries were amplified.

value: primary human adipocytes

tag: genotype/variation

value: Gd6 LINC00473 siRNA knockdown

tag: replicate


title: Gd6-siRNA-3


title: Gd6-siRNA-4


title: Gd6-Scrambled-4

source_name: primary human adipocytes culture_Gd6-Scrambled

value: Gd6 Scramble


title: Gd6-siRNA-2


title: Gd6-Scrambled-3


title: Leaf, EX03 0h


title: Leaf, EX02 0h


title: Leaf, EX01 0h