title: T24_NC_biological rep3

city: Lanzhou

first: YANJUN

last: GAO

state: Gansu

address: 222 Tianshui South Road

department: Urology

institute: the 2nd Hospital of Lanzhou University

description: Gene expression data from T24 cells tranduced with lentiviruses expressing control vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Genechip® Primeview Human Gene expression Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring Software GX 13.0 using  default analysis settings and global scaling as normalization method.

source_name: T24 cells tranduced with control lentiviruses

label_protocol: Biotinylated cRNA were prepared using GeneChip 3’IVT Express Kit according to the standard Affymetrix protocol

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C supplied with 5% CO2 atmosphere

extract_protocol: Total RNA was isolated with RNAiso Plus according to the manufacturer's manual.

treatment_protocol: The lentiviruses were mixed with 8μg/ml polybrene before addition to T24  cells according to the manufacturer's manual.

value: urinary bladder

tag: cell line

tag: genotype/variation

value: control


title: UACC-812-flag

status: Public on Jan 10 2019

type: SRA

city: Harbin

first: Xu

last: Shouping

address: No.157 Baojian Road

country: China

institute: Harbin Medical University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Adaptors were removed using cutadapt 1.19
Data were filtered using fastX toolkit 0.0.14
ChIP-seq reads were aligned to the GRCh38 genome using bowtie2 2.3.0
Peaks were called using macs2 2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor cell

extract_protocol:
A total of 1 × 106 cells were fixed in 1% formaldehyde at room temperature for 10 min, and the nuclei were isolated with nuclear lysis buffer supplemented with a protease inhibitor.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

value: UACC-812 flag cell line

tag: tissue

value: breast

tag: chip antibody

value: CMYC


title: UACC-812-flag-input

value: RNA-pol-II


title: control group2

city: Guangzhou

first: Jing

last: Li

address: Zhongshan Road

institute: Zhongshan university

library_source: transcriptomic

data_processing:
Sequenced reads were for filtered to remove those low-complexity or low-quality sequences to get clean sequences.
After quality control using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA), we utilized a HiSeq2500 (Illumina, CA, USA) to analyze and sequence DNA fragments.
we used FastQC software to output.
we used BWA software to iditify the sequences to the genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Excel. The processed data files enntitled 7.xls  included the comparison of circRNAs expressioin indentified in control and induction groups of dental follicle cells during osteogenic differentiation.

molecule: total RNA

organism: Rattus norvegicus

source_name: Sprague-Dawley rats

extract_protocol:
Total RNA was extracted separately from rDFCs of the induction and control groups. DNA and linear RNA were removed from the samples for circRNAs assays. The A260/A280 ratios of RNA samples were between 1.9 and 2.1, and the RNA integrity number was greater than 8.0; thus, the samples were acceptable for the following assays.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: 3 healthy Sprague-Dawley rats (postnatal 5-7 days) were provided by the Laboratory Animal Center of Sun Yat-sen University (This study has received permission from the institutional Animal Care and Use Committee). rDFCs were isolated from the tooth germs of the first and second mandibular molars of each rat and were cultured separately in alpha-modified Eagle medium (GIBCO-BRL Life Technologies, Guangzhou Genewindows Biotech, Ltd., Guangzhou, China) containing 10% fetal bovine serum (FBS) (GIBCO-BRL Life Technologies, Guangzhou Genewindows Biotech, Ltd., Guangzhou, China). rDFCs were incubated at 37°C with 5% CO2 (Xiao et al. 2000).  During osteogenic differentiation, rDFCs at passage 3-4 were cultured for 28 days in osteogenic induction medium, which consisted of 5% FBS, 1% osteogenic induction liquid (0.010 mmol/L dexamethasone, 0.028 mmol/L ascorbic acid, and 1.000 mol/L β-glycerophosphate) and alpha-modified Eagle medium, whereas control cells were cultured in control medium containing 5% FBS and alpha-modified Eagle medium. The medium was exchanged every 3 days.

tag: cell type

value: dental follicle cells

tag: age

value: 5-7 days old


title: ctrl Dam3

city: Regensburg

first: Mathias

last: Rass

address: Universitätsstraße 31

department: Developmental Biology

country: Germany

institute: University of Regensburg

description: Processed data file: ctrl.gatc.average.bedgraph

data_processing:
Library strategy: DamID
.bam files are converted to .fastq files and were gunzipped
log2(DamPolII/Dam) in bedgraph format have been generated by DamIDseq_pipeline provided by Marshall and Brand (2015)
single datasets have been combined and averaged to one single log2(DamPolII/Dam) per genotype with the average_tracks script provided by Marshall and Brand (2015)
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files generated

organism: Drosophila melanogaster

source_name: ctrl Dam

growth_protocol: development at 18°C. 1-3 day old flies were shifted to 29°C for 24h.

extract_protocol:
Flies were snapfrozen in liquid nitrogen and heads were removed by vortexing and sieving. Further procedures where executed as described in Southall et al. (2016)
libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: Fuss expressing neurons

tag: genotype

value: tubgal80ts/Dam; fussdelds-Gal4/+

value: 1-3 day old adult flies

tag: gender

value: pooled male and female

tag: sample composition

value: 50 males, 50 females


title: induction group1


title: ctrl Dam2


title: UACC-812-cmyc-input

value: UACC-812 C-MYC overexpression cell line


title: control group1


title: ctrl Dam1


title: ATAC-seq_dopaminergic neuron sample 3

status: Public on Jan 09 2019

city: Paris

first: Philippe

last: Ravassard

address: 47, boulevard de l'Hôpital

country: France

institute: Brain & Spine Institute

description: ATAC-seq

data_processing:
Steps for quality control were identical to those used for RNA-seq data treatment (Trimmomatic, FastQC). Paired-end reads were mapped to the mouse genome (build mm9) with Bowtie2. Duplicate reads were discarded with the Picard tools. Peaks were called using the MACS2 program with the option callpeak. Individual peaks separated by less than 100 bp were merged with BEDOPS and features annotations were obtained from the HOMER mm9 database. Data from ATAC-seq and RNA-seq results were intersected based on overlaps between a given ATAC peak and the first/last nucleotide of a TSS/TTS, respectively.
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: excel files containing FPKM for each 5HT and DA sample
Supplementary_files_format_and_content: ATAC-seq BED file (6+3 BED file see http://genome.ucsc.edu/FAQ/FAQformat.html#format13) with peak

organism: Mus musculus

source_name: dopaminergic neurons from 14.5 day embryo

growth_protocol: All procedures were conducted in compliance with the European and French legislations (EU directive 2010/63/UE), and were approved by a committee for ethical experiments (A751319).   To purify dopaminergic (DA) neurons by fluorescence-activated cell sorting (FACS) prior to RNA-seq and ATAC-seq, we used TH-GFP mice, in which GFP is expressed under the control of the Th promoter40. This transgenic line, maintained on C57BL/6J background, was generously given by H. Okano. To isolate serotonergic (5-HT) neurons by FACS, we were generously given by C. Parras Mash1-CRE x ROSA YFP mice, in which YFP is expressed in 5-HT neurons43. Mice had ad libitum access to food and water, and were housed in cages containing up to 5 animals under temperature-controlled conditions and maintained on a 12:12 hours light/dark cycle. To obtain E14.5 embryos, males from these transgenic lines were mated with Swiss wild-type females overnight, and pregnancies confirmed the next morning by inspection of the vaginal plug, defining embryonic day 0.5.

extract_protocol:
Total RNA was extracted from DA or 5-HT neurons using an RNeasy Microkit (Qiagen) following manufacturer´s instructions. RNA was treated with DNAse I (Qiagen) for 20 minutes at room temperature to prevent genomic DNA contamination. For RT-qPCR, RNA concentrations were determined by spectrophotometry (Nanodrop 2000c, THERMO Scientific). For RNA-seq, a High Sensitivity RNA ScreenTAPE analyzer (Agilent Technologies) was used to assess RNA concentrations as well as the RNA integrity number (RIN) to verify RNA quality for all tested samples. RNA was stored at−80 °C until reverse transcription or RNA-Seq.
Stranded library was prepared using TotalScript RNA sequencing kit (Epicentre) following manufacturer’s recommendation. For purified samples of 5HT neurons, non-stranded library were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) following manufacturer’s recommendation. 3 DA and 3 5-HT libraries were sequenced using NextSeq500 HighOutputKit v2 (300cycles) cartridge (FC-404-2004 Illumina). Sorted cells by FACS were collected in Neurobasal medium with B27 supplement (Life Technologies), 2% FBS and kept at 4°C until ATAC-Seq. Cells were centrifuged at 500 g, at 4°C during 20 min. Cells were resuspended in 25 μl of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) during 10 min at 4°C. Then supernatant was taken out after a centrifugation at 500 g, at 4°C during 30 min. For transposase reaction, the pellet was resuspended in 25 μl of 12.5 μl 2x TN buffer; 2 μl of Tn5; 10.5 μl d’H2O and incubated at 37°C for 1 h. Then 5 μl of clean-up buffer (900 mM NaCl, 300 mM EDTA, 5% SDS) were added with 2 μl of 5% SDS and 2 μl of Proteinase K, and cells were incubated for 30 min at 40°C. Samples were then cleaned with two SPRI clean up (Agencourt © AMPure ©XP), with 68 μl of SPRI beads, eluted in 13 μl of buffer EB (Qiagen Cat No./ID: 19086). Extracted DNA concentration was measured by ScreenTAPE analyzer (Agilent Technologies). To generate libraries, PCR reactions were performed using the kapa PCR mix (Kapa biosystem) with 12.5 μl Kapa, 1 μl primers and 11.5 μl of sample, with the NextEra primers (1 μl /primer). PCR conditions were performed as described: 98°C during 2 min and then 9 cycles of 98°C during 20 s, 63°C during 30 s, 72°C during 1 min. Then, a new SPRI clean-up was made to do a size cut off of amplified PCR products and after that, DNA concentration was measured by ScreenTAPE analyzer (Agilent Technologies). Finally, a second PCR was performed with the same conditions as the first one and a last SPRI clean-up was made and library of tagged open chromatin was ready to be sequenced.

value: TH-GFP

value: dopaminergic neuron

tag: developmental stage

value: embryo

tag: age (day)


title: ATAC-seq_serotoninergic neurons sample 1

description: ATAC-seq

source_name: serotoninergic neurons from 14.5 day embryo

value: Mash1-CRE x ROSA YFP

value: serotoninergic neuron


title: 293_HA_SNIP1

city: Shanghai

first: Fei

last: Lan

address: No131 Dongan Road, Xuhui District.

institute: Institute of Biochemical Science

data_processing:
Basecalls were performed by CASAVA (v 1.7).
ChIP-seq reads were trimmed by Trim_Galore (v 0.4.4).
Trimmed reads (only R1) were aligned to the hg19 genome assembly using bowtie (version 1) with the following setting: -M 1 --best --strata.
Peaks were called using macs2 (v 2.1.1) with the following setting: callpeak -q 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using macs2 (v 2.1.1).

growth_protocol: HEK293T cells were routinely cultured in DMEM plus 5% FBS

extract_protocol:
Lysates were clarified from crosslinked and sonicated nuclei, then protein-DNA complex were isolated with HA beads.
Libraries were prepared by KAPA Hyper Prep Kit (KAPABIOSYSTEMS, KK8505)

treatment_protocol: Overexpressing FLAG-TET2 and HA-SNIP1 after SNIP1 knockdown

value: HA beads(FF AGM90054)


title: 293T_Input


title: ATAC-seq_serotoninergic neurons sample 2

description: ATAC-seq


title: UACC-812-cmyc

value: breast


title: RNA-seq_dopaminergic neuron sample 2

description:
lncRNA
sample name: ARN13avril15_2
DA-2
DA_FPKM_allTranscripts.xlsx


title: RNA-seq_dopaminergic neuron sample 1

description:
lncRNA
sample name: ARN13avril15_1
DA-1
DA_FPKM_allTranscripts.xlsx


title: RNA-seq_serotoninergic neurons sample 3

description:
lncRNA
sample name: TPH2_3
5HT-3
5HT_FPKM_allTranscripts.xlsx


title: RNA-seq_dopaminergic neuron sample 3

description:
lncRNA
sample name: ARN13mars15
DA-3
DA_FPKM_allTranscripts.xlsx


title: ATAC-seq_dopaminergic neuron sample 2

description: ATAC-seq


title: T24_NC_biological rep2

type: RNA

label: biotin

value: urinary bladder

value: control


title: T24_NC_biological rep1


title: 24hpi_replicate_C

city: Gainesville

first: Zsolt

last: Toth

state: FL

country: USA

institute: University of Florida

data_processing:
Sequenced raw reads were aligned to the hg38 human genome with STAR aligner using default parameters in Partek FLOW software analysis package (Partek Inc., St. Louis, MO).
Aligned reads in BAM files were imported into the Partek Genomics Suite software analysis package (Partek Inc., St. Louis, MO), and RPKM counts per genes (RefSeq Transcripts 83 - 2017-11-01) were generated using their standard RNA-seq analysis pipeline with default settings.
Genome_build: hg38 (human genome)
Supplementary_files_format_and_content: Tab-limited text file include gene-level RPKM values for all 12 samples.

source_name: TRExBCBL1-3xFLAG-RTA (recombinant KSHV+ PEL cell line)

growth_protocol: PEL cells were cultured in RPMI medium containing 10% Tet system approved FBS (Takara), P/S, and 20ug/ml Hygromycin. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cells were resuspended in TRIzol (Invitrogen), and RNA prepared on RNeasy kit (Qiagen) columns.
Strand-specific RNA-seq cDNA libraries were constructed by the facility with their default Illumina protocol.

treatment_protocol: The expression of the N-terminally 3xFLAG-tagged RTA was induced by adding 1 μg/ml doxycycline (Dox) to the medium for 0, 6,12 or 24 hours as indicated, resulting in KSHV lytic reactivation.

tag: treatment

value: doxycycline treated cells


title: 6hpi_replicate_C


title: 0hpi_replicate_B

value: untreated cells


title: 12hpi_FLAG-RTA_ChIP-seq

data_processing:
Raw reads aligned to the hg38 human genome using Bowtie2 with the standard Partek FLOW software analysis package settings (Partek Inc., St. Louis, MO).
Aligned reads were imported to and further processed in Partek Genomics Suite software package (Partek Inc., St. Louis, MO) to identify RTA peaks genome-wide using the built-in MACS2 algorithm.
Genome_build: hg38 (human genome)
Supplementary_files_format_and_content: Tab-limited text file include the final processed data with coordinates and further specifications of the identified RTA peaks at 12hpi, as identified by the MACS2 peak calling algorithm.

source_name: TRExBCBL1-3xFLAG-RTA (recombinant KSHV+ PEL cell line) at 12hpi

extract_protocol:
Genomic DNA from Input and from the FLAG (RTA) ChIP DNA was extracted using standard phenol:chloroform:isoamylalcohol protocol prior to downstream library construction.
Libraries were constructed using a standard NuGEN library construction method.

treatment_protocol: The expression of the N-terminally 3xFLAG-tagged RTA was induced by adding 1 μg/ml doxycycline (Dox) to the medium for 12 hours, resulting in KSHV lytic reactivation.


title: 6hpi_replicate_B


title: 24hpi_replicate_A


title: 12hpi_replicate_A


title: 0hpi_replicate_C


title: 24hpi_replicate_B


title: 12hpi_replicate_B


title: 12hpi_replicate_C


title: T24_KD_biological rep1

description: Gene expression data from T24 cells tranduced with lentiviruses expressing shTRIP13

source_name: T24 cells tranduced with shTRIP13 lentiviruses


title: T24_KD_biological rep2


title: T24_KD_biological rep3


title: 0hpi_replicate_A


title: 12hpi_Input


title: ctrl DamPol3

source_name: ctrl DamPol

value: Fuss expressing neurons

value: tubgal80ts/DamPol; fussdelds-Gal4/+


title: ATAC-seq_dopaminergic neuron sample 1

description: ATAC-seq


title: RNA-seq_serotoninergic neurons sample 1

description:
lncRNA
sample name: TPH2_1
5HT-1
5HT_FPKM_allTranscripts.xlsx


title: RNA-seq_serotoninergic neurons sample 2

description:
lncRNA
sample name: TPH2_2
5HT-2
5HT_FPKM_allTranscripts.xlsx


title: VC_rep2

city: Qingdao

first: Mei

last: Wang

state: Shandong

address: Binhai road 72

institute: Shandong University

description: Gene expression data from Arabidopsis transgenic line carrying an empty vector

hyb_protocol: Samples were prepared for hybridization to the ATH1 GeneChips™ using the Affymetrix GeneChip Hybridization, Wash and Stain Kit. Samples were hybridized overnight in an Affymetrix GeneChip Hybridization Oven 640. Samples were then processed on the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using the MessageAmp™ Premier RNA Amplification Kit (Ambion)).

growth_protocol: The transgenic plants were grown at the growth chamber with a 16 h photoperiod (120 μmol m–2 s–1 light) and ~70% relative humidity at 22 ± 1°C/16 ± 4°C.

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

treatment_protocol: 12-day-old seedlings under normal growth conditions

value: 12-day-old seedlings


title: sh-M_Pam3_2

city: La jolla

first: Qiong

last: Zhang

state: California

address: 9500 Gilman Dr.

department: Pediatrics

institute: UCSD

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
GRCh38.gencode.v26
Genome_build: count matrix with rows as genes and columns as samples

source_name: THP1-derived macrophages

extract_protocol:
TRIZOL extraction of RNA, then digested with DNAase
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell treatment

value: Pam3CSK4 stimulated for 8 hours


title: NC_Pam3_1


title: NC_Pam3_2


title: sh-M_Pam3_1


title: LncM_Pam3_1


title: FSL_1_8hrs_1

data_processing:
RNA-seq data from the HiSeq2000 were processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on the index sequences.
Reads were mapped to the hg19 genome with Gencode 19 annotations using STAR 2.3.1z with the following parameters:--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1--outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif.
Genome_build: hg19

source_name: Macrophages

growth_protocol: THP1 cells were cultured in RPMI (Mediatech) supplemented with 10% fetal bovine serum (FBS) and 50 μM β-mercaptoethanol (Sigma). Cells were treated with 5 ng/ml phorbol-12-myristate-13-acetate (PMA) overnight to induce differentiation into macrophages

extract_protocol:
RNA was isolated from the cells using Trizol reagent following standard protocols.
Ribo-depleted RNA was prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s recommendation with 15 cycles of PCR. The final libraries were size selected on 2% agarose gels to obtain products with library sizes between 280 and 380 bases in length. The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end 100 base pair reads with 7 base index reads

treatment_protocol: To treat the THP1 cells with ligands, aliquots of 1 × 106 cells were seeded in 6-well plate, and then incubated with medium containing the Pam3CSK4 (100 ng/ml), LPS (100 ng/ml), and FSL-1 (100 ng/ml) for 8 h.

value: THP1 derived macrophages

tag: passages

tag: tlr ligands

value: human TLR1–9 Agonist kit from Invivogen (# tlrl-kit1hw)

tag: sample type

value: FSL THP1


title: Untreated Control_8hrs_2

value: control THP1


title: Untreated Control_8hrs_1


title: PAM_8hrs_1

value: PAM THP1


title: LPS_8hrs_2

value: LPS THP1


title: U2OS_siCtr_Pol2_S2P_input

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

data_processing:
Reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore
Processed reads were aligned to  the hg38 genome using Bowtie directly executed from the R package QuasR with standard alignment parameters allowing up to 2 missmatches and excluding multi-mappers
Coordinates of unique reads that map only once to the human genome were converted to GenomicRanges format for further analysis and to the WIG format for visualisation.
Genome_build: hg38
Supplementary_files_format_and_content: wig track format: read coverage per consecutive 100bp windows

growth_protocol: Human U-2 OS cells were grown under standard cell culture conditions (humidified atmosphere, 5% CO2) in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (GIBCO) and penicillin-streptomycin antibiotics.

extract_protocol:
Chromain Immunoprecipitation using anti phosphoserine-2 RNA Polymerase antibodies.
Sequencing libraries were prepared using the NEB-next ChIP-seq library Kit following the manual instruction and using indexed primers.
The individual libraries were generated in paralel for all ChIPs and input samples. Libraries were pooled and sequenced on an Illumina HiSeq 4000 machine.

treatment_protocol: Transfections with siRNA were performed for 72h using Ambion Silencer Select siRNAs at a final concentration of 25nM and Lipofectamine RNAiMAX (Thermo Fisher Scientific). WDR33 was depleted using siRNA ID s30772, Neg2 from Ambion was used as non-targeting control.

value: U-2 OS

tag: sirna

value: siControl


title: Mock_Pam3_1

tag: cell line


title: Mock_Pam3_2


title: FSL_1_8hrs_2


title: LPS_8hrs_1


title: PAM_8hrs_2


title: 3 day HIF induced hearts

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

description: Each channel has 2 pooled samples per condition.

hyb_protocol: Performed by LC Sciences. Samples hybridized to a μParaflo microfluidic chip.

scan_protocol: Scanned using an Axon GenePix 4000B Microarray Scanner. Images were quantified using ArrayPro.

data_processing: Global normalization used and background subtracted from processed Cy5/Cy3 signal ratios using ArrayPro software.

source_name: heart tissue

label_protocol: Performed by LC Sciences. On dox pooled samples were labeled with Cy3 and 3 day HIF induced samples were labeled with Cy5.

growth_protocol: Mice were kept on doxycycline from pregnancy until 6-8 weeks of age before inducing HIF-PPN expression in cardiomyocytes by removal of doxycycline.

extract_protocol: Enriched miRNA fractions were isolated using Qiagen miRNeasy mini kit according to manufacturer’s instructions.

treatment_protocol: HIF-PPN expression was induced by removal of doxycycline for 3 days and  compared to control hearts that remained on doxycycline (uninduced).

value: on doxycycline (control)

value: enriched miRNA

value: 3 days off dox (HIF induced)


title: AR-ChIP-seq_WT-Cap_rep2

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
ChIP-seq sample
processed data file: AR-ChIP-seq_WT-Cap.bed

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against mouse genome mm10 with Bowtie software (version 0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best mm10.
Peak calling was done in HOMER (version 4.10.3) using findPeaks command and appropriate input as a control.
Overlapping peaks from two replicates were analyzed using bedTools (intersectBed) and used for further analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *-Cap.bed: Genomic intervals of AR binding sites that are common to two replicates are given in bed format.

source_name: Caput epididymis (containing initial segment)

extract_protocol:
For one sample, caput epididymides (containing initial segments) were pooled from three animals. Tissues were dissected, crosslinked with 1% formaldehyde and homogenized in Hexylene glycol buffer. After centrifugation, samples were resuspended in RIPA buffer and sonicated using Misonix 3000. ChIP was done using rabbit polyclonal anti-AR antibody K183 (Karvonen et al., 1997 J Biol Chem) bound to protein G Dynabeads (Invitrogen). Fragmented, de-crosslinked chromatin was used for input samples.
Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina Hiseq2500 at EMBL GeneCore (Heidelberg, Germany).

tag: strain/background

value: C57Bl/6N; 129 hybrid

tag: genotype/variation

value: WT

value: 3 months

value: Anti-AR antibody K183


title: Mucor R7B virulent strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate b

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

country: Spain

institute: Universidad de Murcia

description:
R7BMb
TableS1.xlsx
TableS2.xlsx

data_processing:
Data filtering by FASTQC and Trim Galore!
Read alignment by STAR
Differential expression analyses by CuffDiff
Genome_build: Mucor circinelloides f. lusitanicus CBS277.49 v2.0 (JGI)
Genome_build: mm10
Supplementary_files_format_and_content: Gene differential expression analysis table from CuffDiff

molecule: polyA RNA

source_name: Fungal spore-macrophage coculture

extract_protocol:
Cultures were frozen with liquid nitrogen and grinded into dust. Total RNA was extracted using RNeasy® Plant Mini Kit (Qiagen, Hilden, Germany) following the supplier’s recommendations
mRNA enrichment by poly (A) purification capture and cDNA libraries were prepared at BaseClear (Leiden, The Netherlands) using TruSeq RNA Library preparation kits

tag: culture duration

value: 5 hours

tag: culture type

value: coculture

tag: culture media

value: L15 cell culture medium

tag: fungal parental strain


title: AR-ChIP-seq_ArKI-Cap_rep2

description:
ChIP-seq sample
processed data file: AR-ChIP-seq_ArKI-Cap.bed

value: ArKI

tag: tissue

value: Caput epididymis (containing initial segment)

tag: age

tag: chip antibody


title: AR-ChIP-seq_WT-Cap_rep1


title: Mucor R7B virulent cocultured w/ macrophages (cell line J774A.1) for 5 hrs used as a control for both atf mutants, rep b

description:
Mucor R7B virulent strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, used as a control for both atf mutants, replicate b
wtR7BMb
TableS5.xlsx

value: Mucor circinelloides f. lusitanicus CBS277.49


title: Mucor R7B virulent cocultured w/ macrophages (cell line J774A.1) for 5 hrs used as a control for both atf mutants, rep a

description:
Mucor R7B virulent strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, used as a control for both atf mutants, replicate a
wtR7BMa
TableS5.xlsx


title: Mouse macrophages (cell line J774A.1) singlecultured in cell media for 5 hours, replicate c

description:
Mc
TableS2.xlsx

source_name: Cell culture

value: single


title: Input_ArKI-Cap

description:
Control (fragmented chromatin of ArKI caput).
processed data file: AR-ChIP-seq_ArKI-Cap.bed


title: Mucor NRRL3631 avirulent strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate a

description:
NRRLMa
TableS1.xlsx
TableS2.xlsx


title: Mucor NRRL3631 avirulent strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate b

description:
NRRLMb
TableS1.xlsx
TableS2.xlsx


title: Mouse macrophages (cell line J774A.1) singlecultured in cell media for 5 hours, replicate b

description:
Mb
TableS2.xlsx


title: Mouse macrophages (cell line J774A.1) singlecultured in cell media for 5 hours, replicate a

description:
Ma
TableS2.xlsx


title: Mouse macrophages (cell line J774A.1) singlecultured in cell media for 5 hours, replicate d

description:
Md
TableS2.xlsx


title: Human breast cancer cell line MCF-7 was transfected with LincK siRNA-2 to cells for 48 hours rep3

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

description: Gene expression data in MCF-7 which kncok down with LincK siRNAs

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 2.1 ST Arrays, and then washed and stained slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Arrays were scanned using standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: These arrays were pre-processed with RMA, which includes normalization, summarization of probes to probesets, and background correction.Analysis Method: rma-gene-full.Data Transformation: log2

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: MCF-7 were cultured in H-DMEM supplemented with 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin.

treatment_protocol: siRNAs used to knockdown target lncRNAs or mRNAs were designed by online tool (BLOCK-iT™ RNAi Designer) and synthesized by the GenePharma company (Suzhou,China).Lentivirus shRNA expression vector targeting the same sequences as siRNAs were constructed and packaged by Genepharma. For transfection of siRNAs, miRNA or plasmids, Lipofectamine 2000 (Life Technology) was used according to the manufacturer’s recommendations.


title: Input_WT-Cap

description:
Control (fragmented chromatin of WT caput).
processed data file: AR-ChIP-seq_WT-Cap.bed


title: HO1-N-1

city: Bunkyo-ku

first: Akane

last: Wada

state: Tokyo

address: 1-5-45 Yushima

department: Oral Pathology

country: Japan

institute: Tokyo Medical and Dental University

description: SAMPLE 2

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized with rotation at 60 rpm for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Array (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HO1-N-1, oral scuamos cell carcinoma

label_protocol: Biotinylated cRNA were prepared using GeneChip WT PLUS Reagent Kit, according to the standard Affymetrix protocol from 250ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2017, Affymetrix).

extract_protocol: NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany) was performed according to the manufacturer's instructions.

tag: cell type

value: human oral squamous cell carcinoma cells


title: Human breast cancer cell line MCF-7 was transfected with LincK siRNA-1 to cells for 48 hours rep3


title: Human breast cancer cell line MCF-7 was transfected with LincK siRNA-2 to cells for 48 hours rep1


title: Human breast cancer cell line MCF-7 was transfected with LincK siRNA-1 to cells for 48 hours rep1


title: Mucor atf2 mutants cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate b

description:
Atf2Mb
TableS5.xlsx


title: Human breast cancer cell line MCF-7 was transfected with LincK siRNA-2 to cells for 48 hours rep2


title: AR-ChIP-seq_ArKI-Cap_rep1


title: Human breast cancer cell line MCF-7 was transfected with a control non-targeting siRNA to cells for 48 hours rep3

description: Gene expression data in MCF-7 which kncok down with control siRNAs


title: Human breast cancer cell line MCF-7 was transfected with LincK siRNA-1 to cells for 48 hours rep2


title: Mucor R7B virulent strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate a

description:
R7BMa
TableS1.xlsx
TableS2.xlsx


title: 3A

description: SAMPLE 1

source_name: 3A, oral scuamos cell carcinoma


title: Human breast cancer cell line MCF-7 was transfected with a control non-targeting siRNA to cells for 48 hours rep1


title: Human breast cancer cell line MCF-7 was transfected with a control non-targeting siRNA to cells for 48 hours rep2


title: Mucor atf1 mutants cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate b

description:
Atf1Mb
TableS5.xlsx


title: Mucor atf2 mutants cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate a

description:
Atf2Ma
TableS5.xlsx


title: Mucor atf1 mutants cocultured with mouse macrophages (cell line J774A.1) for 5 hours, replicate a

description:
Atf1Ma
TableS5.xlsx


title: HFF_iMARGI

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Drive MC 0412

department: Bioengineering

description: in situ ligation of nuclear RNA and genomic DNA

data_processing:
Library strategy: iMARGI
Illumina Casava1.8 software used for basecalling
Paired-end read pairs were aligned to the hg38 genome assembly using bwa mem (0.7.17) with parameter '-SP5M'
pairtools (v0.2.0) and in-house scripts were used to parse, deduplicate and filter the mapped read pairs.
Genome_build: hg38
Supplementary_files_format_and_content: The processed BEDPE file shows the valid RNA-DNA interaction read pairs. BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format), the 1,2,3 and 9 colums show the genomic coordinate of RNA end (Read 1), and the 4, 5, 6, and 10 columns show that of DNA end (Read 2).

source_name: Clonal line 6 derived from hTert immortalized HFF parental line

extract_protocol:
Approximately 5 million cells were used for construction of an iMARGI sequencing library. Cells were crosslinked in 1% formaldehyde at room temperature (RT) for 10 minutes with rotation. Crosslinking reaction was quenched with glycine at 0.2 M concentration and incubated at RT for 10 minutes. Cells were pelleted, washed using 1 × PBS and aliquoted into ~ 5 million in each tube. To prepare nuclei, crosslinked cells was incubated in 1 mL of cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% Nonidet P-40, 1× protease inhibitor) on ice for 15 minutes and homogenized with dounce homogenizer pestle A for 20 strokes on ice. Nuclei were pelleted and weighed to estimate the pellet volume (10 mg of nuclei pellet was estimated to be about 10 µL). Nuclei pellet were incubated with SDS buffer (0.5× Cutsmart buffer, 0.5% SDS) with 1:3 volume ratio at 62 °C for 10 minutes with mixing and immediately quenched with a final of 1% Triton X-100. To digest chromatin, washed nuclei pellet was re-suspended in AluI chromatin digestion mix (2.3 U/µL AluI (NEB), 0.3 U/µL RNasinPlus, 1× Cutsmart buffer) and incubated at 37 °C overnight with mixing. After chromatin digestion, 1 µL of RNase I (1:10 diluted in 1× PBS) was directly added to the reaction mixture and incubated at 37 °C for 3 minutes to fragment RNA. Nuclei were pelleted and washed twice using PNK wash buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2). To prepare the RNA and DNA ends for linker ligation, nuclei were incubated in 200 µL RNA 3´ end dephosphorylation reaction mix (0.5 U/µL T4 PNK (NEB), 0.4 U/µL RNasinPlus, 1× PNK phosphatase buffer pH 6.5) at 37°C for 30 minutes with mixing. Nuclei were washed twice with PNK buffer, resuspended in 200 µL DNA A-tailing mix (0.3 U/µL Klenow fragment 3´-5´ exo- (NEB), 0.1 mM dATP, 0.1% Triton X-100, 1× NEB buffer 2) and incubated at 37°C for 30 minutes with mixing. The same linker sequence as described in the previous MARGI paper was used. For in situ RNA-linker ligation, nuclei were resuspended in 200 µL ligation mix (38 µL adenylated and annealed linker, 10 U/ µL T4 RNA ligase 2-truncated KQ (NEB), 1× T4 RNA ligase reaction buffer, 20% PEG 8000, 0.1% Triton X-100, 0.4 U/µL RNasinPlus) and incubated at 22°C for 6 hour and then 16°C overnight with mixing. After ligation, the nuclei were washed five times with PNK buffer to remove excess free linker. For in situ RNA-DNA proximity ligation, nuclei were resuspended in 2 mL of proximity ligation mixture (4 U/µL T4 DNA ligase (NEB), 1× DNA ligase reaction buffer, 0.1% Triton X-100, 1 mg/mL BSA (NEB), 0.5 U/µL RNasinPlus) and incubated at 16 °C overnight.
To reverse crosslinking, nuclei were washed twice with 1× PBS, resuspended in 250 µL of extraction buffer (1 mg/mL Proteinase K [NEB], 50 mM Tris-HCl pH 7.5, 1% SDS, 1 mM EDTA, 100 mM NaCl) and incubated at 65 °C for 3 hours. DNA and RNA were extracted by adding an equal volume of Phenol:Chloroform:Isoamyl Alcohol (pH 7.9, Ambion) followed by ethanol precipitation. The subsequent steps including removal of biotin from non-proximity ligated linkers, pulldown of RNA-DNA chimera, reverse transcription of RNA, DNA denaturation, circularization, oligo annealing and BamHI (NEB) digestion and sequencing library generation were performed as previously described. iMARGI libraries were subsequently subject to pair-end 100-cycle sequencing on Illumina HiSeq 4000. The circularization and library construction strategy can phase RNA and DNA ends into Read 1 and Read 2 as shown Fig. 1A, which is the same with MARGI library configuration. Since AluI restriction enzyme recognizes "AGCT" sequence and leaves "CT" at the 5´ end of the cut, we expect the first two bases of DNA end (Read 2) to be enriched with "CT".

tag: assay

value: iMARGI


title: D18-3375 : ND ST3 (AGCGATAGCCTATCCT)

first: Christopher

middle: Joseph

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

data_processing:
The quality of the RNA-Seq sequence data was first evaluated using FastQC prior to further downstream analysis. Low quality sequences were trimmed and poor quality reads were removed using Trimmomatic.
Differential gene (DE) expression analysis was conducted using The Star Aligner to map high quality single end reads to the genome, X. laevis v9.2 and the gene annotation was downloaded from Xenbase. Gene expression was obtained using RSEM
The expected read counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM), were extracted for further analysis. The estimated read counts were used as input for edgeR to perform DE analysis
A generalize linear regression model was developed to identify DE genes and the thresholds were set at FDR 0.05 and fold change of greater than 2 or less than 0.5. Three comparisons were performed (comparing Control, Sham, and Prog-Device amongst each other).
Genome_build: X. laevis v9.2
Supplementary_files_format_and_content: Excel sheet with normalized counts for each sample, log2 fold change, p-value, gene identifier.

organism: Xenopus laevis

source_name: Stump

extract_protocol:
Total RNA for each sample was isolated by using TRIzolTM Reagent (Ambion, Invitrogen #15596018) –chloroform, following standard manufacturer’s protocol.
NGS analyses were performed by The MIT BioMicro Center (Boston, MA). Samples were quality controlled on a Fragment Analyzer (Advanced Analytical) to determine DV200 scores. The mRNA from 1 μg of total RNA was isolated using Illumina human/mouse/rat RiboZero Gold and prepared into Illumina libraries using the Kapa RNA HyperPrep kit and 10 cycles of amplification. Final libraries were pooled and quality controlled using qPCR (Roche LC480II) as well as the Fragment Analyzer and sequenced on HiSeq2000 for 40 nucleotides.  Following sequencing, data processing was performed using the standard Illumina pipeline. Fastq files were generated for data processing and assembly.

value: Stump

tag: treatment

value: no device


title: MCF-7 cells co-cultured with hAD-MSCs for 10 days

description: Gene expression of total RNAs in MCF-7 which  co-cultured with hAD-MSCs for 8 and 10 days

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7. Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7.

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images. The signal ratio of Cy5 intensity and Cy3 intensity on the same array was subjected to quantile normalization followed by log2-scale transformation. After obtaining the normalized expression value of the probes, we first re-annotated the probes by mapping the probe sequences to gene sequences from the Gencode database (GencodeV19) using the Blat software with the parameter –minIdentity = 100. Only probes mapping to the unique gene sequence without mismatch were retained. If more than one probe was mapped to a gene, the median expression values of these probes would be used to represent the expression value of this gene. The eBayes moderated t statistic was used to obtain the differentially expressed genes (DEGs) using a Limma package in R. p value ≤ 0.05 and 2-fold change in its expression level were chosen as the cut-off criteria.

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

growth_protocol: MCF-7  were cultured in H-DMEM supplemented with 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000.


title: D18-3368 : ND BL2 (TCTCGCGCGGCTCTGA)

source_name: Blastema

value: Blastema


title: D18-3370 : ND BR1 (TCTCGCGCTAATCTTA)

source_name: Brain

value: Brain


title: D18-3374 : ND ST2 (AGCGATAGATAGAGGC)


title: D18-3369 : ND BL3 (TCTCGCGCAGGCGAAG)


title: D18-3373 : ND ST1 (AGCGATAGTATAGCCT)


title: D18-3367 : ND BL1 (TCTCGCGCCCTATCCT)


title: D18-3366 : Pro ST3 (TCTCGCGCATAGAGGC)

value: Progesterone treatment


title: D18-3365 : Pro ST2 (TCTCGCGCTATAGCCT)


title: D18-3363 : Pro BR3 (TCCGCGAACAGGACGT)


title: D18-3362 : Pro BR2 (TCCGCGAATAATCTTA)


title: HEK_iMARGI

source_name: Embryonic kidney that expresses SV40 large T antigen


title: D18-3371 : NDBR2 (TCTCGCGCCAGGACGT)


title: D18-3360 : Pro BL3 (TCCGCGAAGGCTCTGA)

value: progesterone treatment


title: D18-3356 : Silk ST2 (CGGCTATGGTACTGAC)

value: Silk treatment


title: D18-3357 : Silk ST3 (TCCGCGAATATAGCCT)


title: D18-3372 : NDBR3 (TCTCGCGCGTACTGAC)


title: MCF-7 cells co-cultured with hAD-MSCs for 2 days

description: Gene expression of total RNAs in MCF-7 which  co-cultured with hAD-MSCs for 0 and 2 days


title: MCF-7 cells co-cultured with hAD-MSCs for 4 days

description: Gene expression of total RNAs in MCF-7 which  co-cultured with hAD-MSCs for 2 and 4 days


title: MCF-7 cells cultured alone (0 day)

source_name: MCF-7 cells cultured alone (0 day)


title: MCF-7 cells co-cultured with hAD-MSCs for 6 days


title: D18-3364 : Pro ST1 (TCCGCGAAGTACTGAC)


title: D18-3361 : Pro BR1 (TCCGCGAAAGGCGAAG)


title: D18-3359 : Pro BL2 (TCCGCGAACCTATCCT)


title: MCF-7 cells co-cultured with hAD-MSCs for 8 days


title: D18-3355 : Silk ST1 (CGGCTATGCAGGACGT)


title: D18-3353 : Silk BR2 (CGGCTATGAGGCGAAG)


title: D18-3351 : Silk BL3 (CGGCTATGCCTATCCT)


title: D18-3354 : Silk BR3 (CGGCTATGTAATCTTA)


title: D18-3352 : Silk BR1 (CGGCTATGGGCTCTGA)


title: D18-3349 : Silk BL1 (CGGCTATGTATAGCCT)


title: D18-3358 : Pro BL1 (TCCGCGAAATAGAGGC)


title: TW24-3

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

description:
after 24 hours control (0.5% Tween-20) treated coleoptiles
gene_expression-2.txt

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk and FASTX-Toolkit.
mRNA-seq reads were aligned to the Triticum aestivum Chinesespring genome sequence (TGACv1) using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.4
Expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method. The normalized expression levels of different samples were converted to FPKM (fragments per kilobase transcriptome per million fragments)
Differential expression were analysed  using edgeR.
Genome_build: Triticum aestivum Chinesespring genome sequence (TGACv1) from ftp://ftp.ensemblgenomes.org/pub/plants/release-39/fasta/triticum_aestivum/
Supplementary_files_format_and_content: Tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Triticum aestivum

source_name: wheat coleoptiles

growth_protocol: Grow the wheat seedling in the growth chamber for 3 day under controlled environment conditions at 25 °C with a 12 h light/12 h dark photoperiod

extract_protocol:
Total RNA was isolated using EasyPure Plant RNA kit (Transgen biotech) according to the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrated number (RIN) value of 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Fusarium graminearum inoculation: Mock, wild-type PH-1 and ∆fg3_54 inoculate wheat seedling. For compound treatment: add 2μl fusaoctaxin A (0.5mM) or 0.5% tween-20 onto wound site of wheat coleoptiles.

tag: cultivars

value: Zhongyuan 98-68

tag: days post inoculation


title: FA24-3

description:
after 24 hours fusaoctaxin A-treated coleoptiles
gene_expression-2.txt


title: TW24-1


title: FA24-1


title: KI_testis_3

description:
sequencing batch 1
countdata.txt

data_processing:
The base calling was done using bcl2fastq (v1.8.4)
Read alignment was done using star (2.5.0) to mm10 mouse genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: mm10
Supplementary_files_format_and_content: countdata.txt is a tab delimited text file containing raw counts.

source_name: KI testis

extract_protocol:
Tissues were dissected, flash frozen on liq. nitrogen, and RNA was isolated using Trisure reagent.
Library preparation was done according to Illumina TruSeq® RNA Sample Preparation v2 Guide

tag: strain

value: C57Bl/6N; 129 hybrid

value: testis

value: 3 months

tag: genotype


title: FA24-2


title: TW3-3

description:
after 3 hours control (0.5% Tween-20) treated coleoptiles
gene_expression-2.txt


title: KI_testis_1

description:
sequencing batch 1
countdata.txt

value: ArKI


title: KI_testis_2

description:
sequencing batch 1
countdata.txt


title: EZH2-/- miRNA-seq replicate 2

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
miRNA
KO2
processed data file: Normalized_counts_miR.txt
processed data file: DESeq2_KO_WT_miR_padj005_norm_counts.csv

data_processing:
Reads were aligned to the human genome (UCSC version hg38) using BWA.
Mapped reads were counted with bedtools and differentially expressed miRNAs were identified using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: *txt: Normalized miRNA and gene counts provided in tab-delimited txt files.
Supplementary_files_format_and_content: DESeq2_KO_WT_miR_padj005_norm_counts.csv: Differentially expressed miRNAs in EZH2-/- compared to WT in csv format.

growth_protocol: T98G cells (ATCC-CRL-1690 and ATCC-HTB14) were grown in EMEM with 10% FBS (Gibco). All cell lines were maintained at 37oC and 5% CO2.

extract_protocol: Libraries were prepared using NEBNext multiplex small RNA library preparation kit (E7300S). Following PCR, miRNA fraction was gel extracted and ethanol precipitated before sequencing.

treatment_protocol: Doxycycline treatment for VP55 overexpression.

tag: cell line


title: WT miRNA-seq replicate 1

description:
miRNA
WT1
processed data file: Normalized_counts_miR.txt
processed data file: DESeq2_KO_WT_miR_padj005_norm_counts.csv

value: WT


title: EZH2-/- miRNA-seq replicate 1

description:
miRNA
KO1
processed data file: Normalized_counts_miR.txt
processed data file: DESeq2_KO_WT_miR_padj005_norm_counts.csv


title: WT miRNA-seq replicate 2

description:
miRNA
WT2
processed data file: Normalized_counts_miR.txt
processed data file: DESeq2_KO_WT_miR_padj005_norm_counts.csv


title: Control_testis_3

description:
sequencing batch 1
countdata.txt

source_name: Control testis


title: TW24-2


title: m21

city: Cleveland

first: Ludovica

last: Buttó

state: OH

address: 2109 ADELBERT ROAD

institute: CWRU

description: laser captured ISC niche

data_processing:
Raw FASTQ files were preprocessed using the RNA-Seq pipeline
Trimmomatic was then used to trim adapters and perform QC (Bolger et al., 2014). BAM files were then generated using the STAR aligner in combination with the GRCm38.91 mouse genome assembly (Dobin et al., 2013).
Read count matrices were computed using HTSeq software from BAM files (Anders et al., 2015).
Normalization and differential expression analysis was performed using count matrices using the DESeq2 R package (Love et al., 2014).
Differential expression across all conditions was computed using the Likelihood Ratio test, while pairwise comparisons were computed using the Wald Test.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: Excel file with FPKM

source_name: small ISC niche

growth_protocol: Intestinal crypts were cultured as previously described (Sato et al., 2009).

extract_protocol:
Intestinal stem cell niche was collected by laser microdissection. Total RNA was isolated using Micro QIAGEN kit according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AKR

value: small intestine

value: wild type


title: m27

description: laser captured ISC niche

value: SAMP/YitFc


title: m22

description: laser captured ISC niche


title: m41

description: laser captured ISC niche


title: m30

description: laser captured ISC niche


title: m25

description: laser captured ISC niche


title: m24

description: laser captured ISC niche


title: m23

description: laser captured ISC niche


title: m31

description: laser captured ISC niche


title: WT +Dox (VP55 overexpression) miRNA-seq replicate 2

description:
miRNA
WT_VP_C12
processed data file: Normalized_counts_VP55_miR.txt

value: WT +Dox (VP55 overexpression)


title: TW3-2


title: AGO2_iCLIP_BR1

description: processed data file: AGO2_common_peaks_noreps.bed

data_processing:
Library strategy: iCLIP
iCLIP reads were first processed to remove duplicate reads using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and then aligned to the human genome (UCSC version 19) using bowtie2. Reads mapping to repeat regions were filtered out using Repeat Masker. Peaks were then called using CLIPper using default parameters and filtered based on reproducibility across replicates (Lovci et al. 2013).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: AGO2_common_peaks_noreps.bed: bed file with iCLIP peak coordinates.

extract_protocol: AGO2 iCLIP experiments were performed as previously described (König et al., 2010).


title: AGO2_iCLIP_BR2


title: Control_testis_2

description:
sequencing batch 1
countdata.txt


title: EZH2-/- +Dox (VP55 overexpression) miRNA-seq replicate 2

description:
miRNA
KO_VP_C3
processed data file: Normalized_counts_VP55_miR.txt

value: EZH2-/- +Dox (VP55 overexpression)


title: Cap_KI_5

description:
sequencing batch 2
countdata1.txt

source_name: Cap KI

value: Caput epididymidis


title: Control_testis_1

description:
sequencing batch 1
countdata.txt


title: Cap_KI_4

description:
sequencing batch 2
countdata1.txt


title: WT -Dox (VP55 overexpression) miRNA-seq replicate 2

description:
miRNA
WT_NO_C12
processed data file: Normalized_counts_VP55_miR.txt

value: WT -Dox (VP55 overexpression)


title: EZH2-/- -Dox (VP55 overexpression) miRNA-seq replicate 2

description:
miRNA
KO_NO_C3
processed data file: Normalized_counts_VP55_miR.txt

value: EZH2-/- -Dox (VP55 overexpression)


title: Cap_KI_3

description:
sequencing batch 2
countdata1.txt


title: FA3-3

description:
after 3 hours fusaoctaxin A-treated coleoptiles
gene_expression-2.txt


title: FA3-2


title: Cap_KI_1

description:
sequencing batch 2
countdata1.txt


title: WT +Dox (VP55 overexpression) miRNA-seq replicate 1

description:
miRNA
WT_VP_C11
processed data file: Normalized_counts_VP55_miR.txt


title: Cap_WT_3

description:
sequencing batch 2
countdata1.txt

source_name: Cap WT


title: FA3-1


title: EZH2-/- +Dox (VP55 overexpression) miRNA-seq replicate 1

description:
miRNA
KO_VP_C1
processed data file: Normalized_counts_VP55_miR.txt


title: Cap_WT_2

description:
sequencing batch 2
countdata1.txt


title: WT -Dox (VP55 overexpression) miRNA-seq replicate 1

description:
miRNA
WT_NO_C11
processed data file: Normalized_counts_VP55_miR.txt


title: Cap_WT_1

description:
sequencing batch 2
countdata1.txt


title: IS_WT_5

description:
sequencing batch 2
countdata1.txt

source_name: IS WT

value: initial segment epididymidis


title: IS_WT_4

description:
sequencing batch 2
countdata1.txt


title: EZH2-/- -Dox (VP55 overexpression) miRNA-seq replicate 1

description:
miRNA
KO_NO_C1
processed data file: Normalized_counts_VP55_miR.txt


title: IS_WT_3

description:
sequencing batch 2
countdata1.txt


title: BT-1

description:
before compound treatment
gene_expression-2.txt


title: Cap_WT_4

description:
sequencing batch 2
countdata1.txt


title: Cap_WT_5

description:
sequencing batch 2
countdata1.txt


title: BT-3


title: TW3-1


title: BT-2


title: Cap_KI_2

description:
sequencing batch 2
countdata1.txt


title: IS_WT_2

description:
sequencing batch 2
countdata1.txt


title: WT Replicate 1

description: PolyA RNA

data_processing:
Reads were aligned to the human genome (UCSC version hg38) using Hisat (Kim et al. 2015). FeatureCounts was then used to count reads mapping to genes and differential gene expression analysis was performed using DESeq2 with default parameters (Liao et al. 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Differentially expressed genes with normalized counts in csv.

extract_protocol:
RNA-seq experiments were performed on poly-A selected mRNA (Bioo 512980).
Libraries were prepared using NEBNext multiplex small RNA library preparation kit (E7300S).


title: WT Replicate 2

description: PolyA RNA


title: 6hpi_replicate_A

data_processing:
Sequenced raw reads were aligned to the hg38 human genome with STAR aligner using default parameters in Partek FLOW software analysis package (Partek Inc., St. Louis, MO).
Aligned reads in BAM files were imported into the Partek Genomics Suite software analysis package (Partek Inc., St. Louis, MO), and RPKM counts per genes (RefSeq Transcripts 83 - 2017-11-01) were generated using their standard RNA-seq analysis pipeline with default settings.
Genome_build: hg38 (human genome)
Supplementary_files_format_and_content: Tab-limited text file include gene-level RPKM values for all 12 samples.

source_name: TRExBCBL1-3xFLAG-RTA (recombinant KSHV+ PEL cell line)

extract_protocol:
Cells were resuspended in TRIzol (Invitrogen), and RNA prepared on RNeasy kit (Qiagen) columns.
Strand-specific RNA-seq cDNA libraries were constructed by the facility with their default Illumina protocol.

value: doxycycline treated cells


title: IS_WT_1

description:
sequencing batch 2
countdata1.txt


title: LncM_Pam3_2

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
GRCh38.gencode.v26
Genome_build: count matrix with rows as genes and columns as samples

source_name: THP1-derived macrophages

extract_protocol:
TRIZOL extraction of RNA, then digested with DNAase
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell treatment

value: Pam3CSK4 stimulated for 8 hours


title: EZH2-/- Replicate 2

description: PolyA RNA

tag: genotype/variation


title: IS_KI_5

description:
sequencing batch 2
countdata1.txt

source_name: IS KI

value: C57Bl/6N; 129 hybrid


title: EZH2-/- Replicate 1

description: PolyA RNA


title: EZH2-/- + Dox (VP55 overexpression) replicate 2

description: PolyA RNA


title: IS_KI_4

description:
sequencing batch 2
countdata1.txt


title: IS_KI_2

description:
sequencing batch 2
countdata1.txt


title: IS_KI_3

description:
sequencing batch 2
countdata1.txt


title: WT + Dox (VP55 overexpression) replicate 2

description: PolyA RNA


title: m_L3 (miRNA-Seq)

city: Riverside

first: Genbo

last: Xu

address: 900 University Ave

institute: University of California, Riverside

description:
m_L_DESeq2_results.txt
m_L.txt

data_processing:
Raw reads were trimmed off using the FASTX toolkit (Cambridge, UK), to obtain a mean Phred score ≥30.
The processed reads were mapped to the Fugu rubripes genome, and both known and novel miRNAs were identified using miRDeep2
Read counts generated from miRDeep2 were used for differential expression analysis using DESeq2.
Supplementary_files_format_and_content: miRNA raw read counts; differential expression

organism: Sciaenops ocellatus

source_name: whole embryo

growth_protocol: Red drum embryos were collect from brood stock tanks at the Texas Parks and Wildlife – CCA Marine Development Center in Corpus Christi, Tx. Embryos were transported to The University of Texas Marine Science Institute under constant aeration whereby they were treated with formalin for 1 h. Embryos were rinsed with sterilized seawater and spawn quality was assessed by checking buoyancy and coloration using a Nikon SMZ2800N. Spawns with poor fertilization rates and quality were not used.

extract_protocol:
miRNAs of pooled samples were isolated using the miRNeasy mini kit from Qiagen (Valencia, CA).  The quality and concentration of miRNA were determined using the Agilent 2100 small RNA chip (Santa Clara, CA).
miRNA libraries were made using the New England Biolabs NEBNext Multiplex Small RNA Sample Prep kit (Ipswich, MA) following the manufacturer’s protocol. The size distribution and concentration of the libraries were determined using the Agilent High Sensitivity DNA Assay Chip (Santa Clara, CA).

treatment_protocol: Two different types of oil were used in this study. The first was a naturally weathered oil collected from the surface of the Gulf of Mexico on June 29, 2010 from hold barge CT02404 referred to as OFS. The second is a source oil collected from a Massachusetts pipeline, denoted as MASS, that has previously been designated as a surrogate for Deepwater Horizon source oil. Oil exposures were generated following previously used described protocols for high-energy water accommodated fractions (HEWAFs). Oil was loaded with seawater (35 ppt) at a rate of 1 g with 1 l seawater. Exposures were generated using percent by volume mixed with fresh sterilized seawater (35 ppt).

value: whole larva

tag: developmental stage

value: source oil

tag: concentration


title: m_H3 (miRNA-Seq)

description:
m_H_DESeq2_results.txt
m_H.txt


title: EZH2-/- - Dox (VP55 overexpression) replicate 2

description: PolyA RNA


title: WT + Dox (VP55 overexpression) replicate 1

description: PolyA RNA


title: m_M2 (miRNA-Seq)

description:
m_M_DESeq2_results.txt
m_M.txt


title: WT - Dox (VP55 overexpression) replicate 2

description: PolyA RNA


title: m_L2 (miRNA-Seq)

description:
m_L_DESeq2_results.txt
m_L.txt


title: m_M3 (miRNA-Seq)

description:
m_M_DESeq2_results.txt
m_M.txt


title: C7539-2

description:
∆fg3_54 inoculated coleoptiles
gene_expression-1.txt

value: Zhongyuan 98-68


title: m_H2 (miRNA-Seq)

description:
m_H_DESeq2_results.txt
m_H.txt


title: C7539-3


title: m_L1 (miRNA-Seq)

description:
m_L_DESeq2_results.txt
m_L.txt


title: C7539-1


title: EZH2-/- + Dox (VP55 overexpression) replicate 1

description: PolyA RNA


title: WT - Dox (VP55 overexpression) replicate 1

description: PolyA RNA


title: PH-1-3

description:
wild-type PH-1 inoculated coleoptiles
gene_expression-1.txt


title: m_C3 (miRNA-Seq)

description:
m_L_DESeq2_results.txt
m_L.txt
m_M.txt
m_H.txt

value: control


title: EZH2-/- - Dox (VP55 overexpression) replicate 1

description: PolyA RNA


title: m_H1 (miRNA-Seq)

description:
m_H_DESeq2_results.txt
m_H.txt


title: IS_KI_1

description:
sequencing batch 2
countdata1.txt

value: 3 months

value: ArKI


title: m_C1 (miRNA-Seq)


title: Input Replicate 2

data_processing:
Reads were aligned to the human genome (hg38) using BWA and peaks were called using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: *.filtered.narrowPeak.gz: narrowPeak files generated by MACS2.

extract_protocol:
Antibodies used were – EZH2 (Abcam 186006), and H3K27me3 (Millipore 07-449).
Libraries were prepared according to the New England Biolabs NEBNext library prep kit (E6240L). Ampure XP beads (A63881) were used for size-selection and clean-up steps.


title: Input Replicate 1


title: PH-1-1


title: PH-1-2


title: s_M3 (miRNA-Seq)

description:
s_M_DESeq2_results.txt
s_M.txt

value: slick oil


title: s_H2 (miRNA-Seq)

description:
s_H_DESeq2_results.txt
s_H.txt


title: H3K27me3 ChIP-seq Replicate 2

description: processed data file: T98_H3k27me3_HsCmb.filtered.narrowPeak


title: MOCK-2

description:
mock-inoculated coleoptiles
gene_expression-1.txt


title: s_H3 (miRNA-Seq)

description:
s_H_DESeq2_results.txt
s_H.txt


title: s_H1 (miRNA-Seq)

description:
s_H_DESeq2_results.txt
s_H.txt


title: MOCK-3


title: m_C2 (miRNA-Seq)


title: HighGFP_4

city: Dresden

first: Jaydeep

last: Sidhaye

state: Sachsen

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

data_processing:
bcl2fastq version 2.17.1.14
Alignment of the fragments to zebrafish reference genome (release GRCz10) was done with GSNAP (v2017-03-17) (Wu and Nacu, 2010) and Ensembl annotation 81 (release July 2015) was used to detect fragments spanning splice sites
Uniquely aligned fragments were counted with featureCounts (v.1.5.2) and Ensembl annotation 81
Genome_build: GRCz10
Supplementary_files_format_and_content: tab separated file with gene information (e.g. name, start, end, strand, length), followed by the counts for the 8 listed samples
Supplementary_files_format_and_content: normalised count data
Supplementary_files_format_and_content: raw count data

organism: Danio rerio

extract_protocol:
10 Optic vesicles each were dissected manually from about 18 ss wild-type (control) embryos and Tg(vsx2::GFP) embryos. The dissected optic vesicles were kept in 100 μl PBS at room temperature. The cells were dissociated manually by pipetting several times and the volume was adjusted to 300 μl. This procedure was performed within half an hour and samples were used for FACS.
For the RNA-seq experiment, the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit - HV from Takara Bio USA (formerly known as Clontech Laboratories) was used to reverse transcribe the RNA and amplify full-length cDNA according to the user manual. After amplification of cDNA, the cDNA was sheared to a fragment length of 200 bp in the ultrasonicator Covaris LE220, followed by a library prep using NEBNext® Ultra DNA Library Prep Kit for Illumina (NEB). The resulting libraries were pooled and sequenced on an Illumina® HiSeq 2500, resulting in ca. 25 – 60 million single-end reads.

value: retinal neuroepithelial cells in 18-20ss developing optic cup

value: High expression vsx2::GFP


title: LowGFP_4

value: rim cells in 18-20ss developing optic cup

value: Low expression vsx2::GFP


title: HighGFP_2


title: HighGFP_3


title: H3K27me3 ChIP-seq Replicate 1


title: LowGFP_2


title: LowGFP_3


title: EZH2 ChIP-seq

description: processed data file: T98_EZH2_HsAbcam1.filtered.narrowPeak


title: LowGFP_1


title: s_M2 (miRNA-Seq)

description:
s_M_DESeq2_results.txt
s_M.txt


title: B. natans light 3

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

data_processing:
Sequencing adaptors removed using Cutadapt.
G. theta mapping (nuclear, nucleomorph, plastid and mitochondrial genomes): “filter tool” and PatMaN in the UEA sRNA workbench v3.2. Filtration: low complexity, <16 nt in length, mapping to G. theta rRNA/tRNA.
B. natans mapping (nuclear, nucleomorph, plastid and mitochondrial genomes): Bowtie2 v2.3.1.
Annotation of nucleomorph sRNA-expressing loci was done by visual inspection of sRNA-seq peaks mapped to nucleomorph genomes.
Transcript abundance was estimated using RSEM v1.2.3 and converted to TMM matrices, which were used with the Bioconductor package EdgerR for differential expression analyses.
Genome_build: Guillardia theta nucleomorph chromosomes: NCBI reference sequences NC_002752, NC_002753, NC_002751. Bigelowiella natans nucleomorph chromosomes: reference sequences NC_010004, NC_010005, NC_010006.
Supplementary_files_format_and_content: The processed data file Processed_data_NM-AA.xlsx is a Microsoft Excel file containing, for each sRNA, (1) counts in Transcripts Per Million TPM (2) normalized abundance measurements (output from EdgeR).

organism: Bigelowiella natans

source_name: Total algal cell

growth_protocol: Guillardia theta was cultured in H2 medium and B. natans was grown in f/2-Si medium. All algal cultures were maintained at 22°C under a 12:12 h light:dark regimen.

extract_protocol:
Cultures were harvested by centrifugation and flash-frozen in liquid nitrogen. Low molecular weight RNA was extracted using the mirVana miRNA isolation kit, using the protocol for enrichment of <200 nt RNAs provided by the manufacturer (Thermo Fisher Scientific). For G. theta sRNA, an aliquot of one of the replicates was treated with Terminator Exonuclease, using the standard protocol (Epicentre).
The SMARTer smRNA-seq kit (TaKaRa) was used to prepare barcoded sRNA-seq libraries (TruSeq HT indexes) in preparation for Illumina sequencing. Inserts were enriched for amplicons <150 bp using Agencourt AMPure XP beads (Beckman Coulter). The G. theta and B. natans libraries were sequenced separately on a MiSeq instrument.

treatment_protocol: The cultures were temporally synchronized and harvested at a density of 0.5-0.8e6 cells/ml, 6 h after the onset of the light or dark phase.

tag: cell collection condition

value: Light

tag: replicate

tag: terminator exonuclease treatment

value: No


title: HighGFP_1


title: s_M1 (miRNA-Seq)

description:
s_M_DESeq2_results.txt
s_M.txt

tag: tissue


title: B. natans dark 3

value: Darkness


title: MOCK-1

tag: age


title: s_L3 (miRNA-Seq)

description:
s_L_DESeq2_results.txt
s_L.txt


title: MAM_female_3

city: Beijing

first: Chunyue

last: Huo

address: You an men wai Xi tou tiao Road 10

institute: Capital Medical University

data_processing:
Illumina X-10
Tophat/Hisat
cufflink
cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Prefrontal cortex

extract_protocol:
After behavioral evaluations, mice were killed by decapitation. Their brains were rapidly removed from the skull and were frozen on dry ice.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prefrontal cortex

value: MAM

tag: gender

value: female


title: lsm8_NaCl_B

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

data_processing:
read trimming
alignment (TopHat2)
Feature extraction: binGenome() (ASpli 1.6.0)
Read counting: readCounts() (ASpli 1.6.0)
Alternative splicing discovery using junctions: AsDiscover() (ASpli 1.6.0)
Differential expression and Differential Usage estimation: DUreport() (ASpli 1.6.0)
Genome_build: TAIR10 (SAMN03081427)
Supplementary_files_format_and_content: .tab; information summary reported in tables about both genomic and junction metadata

source_name: lsm8-1 mutant seedlings under salt conditions

extract_protocol:
QIAGEN rneasy plant mini kit
Truseq stranded mRNA kit (Illumina)

tag: organ

value: whole seedlings

tag: ecotype

tag: growth conditions

value: in vitro, 14 days at 150 mM NaCl


title: lsm8_NaCl_C


title: lsm8_NaCl_A


title: MAM_female_2

tag: treatment


title: lsm8_20_C

source_name: lsm8-1 mutant seedlings under standard conditions

value: soil, 14 days at standard conditions (20ºC)


title: B. natans dark 2

tag: strain


title: B. natans light 2


title: MAM_female_1


title: m_M1 (miRNA-Seq)

description:
m_M_DESeq2_results.txt
m_M.txt

value: whole larva

value: source oil


title: lsm8_20_B


title: s_L2 (miRNA-Seq)

description:
s_L_DESeq2_results.txt
s_L.txt


title: B. natans light 1


title: B. natans dark 1


title: MAM_male_2

value: male


title: MAM_male_3


title: lsm8_20_A


title: s_C2 (miRNA-Seq)

description:
s_L_DESeq2_results.txt
s_L.txt
s_M.txt
s_H.txt

value: control


title: Leaves Heat treatment H3

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the Populus tomentosa genome database downloaded from (ftp://ftp.ensemblgenomes.org/pub/release-40/plants/fasta/populus_trichocarpa/) using TopHat v2.0.12 software with default parameters.
The read counts for each gene was calculated by HTSeq v0.6.1.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-40/plants/fasta/populus_trichocarpa/
Supplementary_files_format_and_content: The tab-delimited text file includes genes read count for each sample (.txt)

organism: Populus tomentosa

source_name: Heat

growth_protocol: 25°C/20°C (day/night); photoperiod: 16h/8h (day/night) with photosynthetically active radiation (PAR) in the day photoperiod at about 350 μmol m-2 s-1 provided by fluorescent tubes (Philips Electronics Trading & Services Co Ltd, Shanghai, China)

extract_protocol:
The leaves of control and heat treatments were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control: The day/night temperatures were set at 25/20°C as the “control temperature (CK); Heat: After growth 75 days, the heat treatment (H) groups were subjected to elevated temperatures in growth chambers from the beginning of day photoperiod: 25°C→37°C, 0.5 h; non-lethal temperature (37°C, 2 h); 37 °C→45 °C, 0.5 h; and then at 45 °C 5 h for samplings.

value: 45°C for 5 hours

value: leaves


title: s_L1 (miRNA-Seq)

description:
s_L_DESeq2_results.txt
s_L.txt

value: slick oil


title: s_C1 (miRNA-Seq)


title: MAM_male_1


title: D18-3350 : Silk BL2 (CGGCTATGATAGAGGC)

city: Gainesville

data_processing:
The quality of the RNA-Seq sequence data was first evaluated using FastQC prior to further downstream analysis. Low quality sequences were trimmed and poor quality reads were removed using Trimmomatic.
Differential gene (DE) expression analysis was conducted using The Star Aligner to map high quality single end reads to the genome, X. laevis v9.2 and the gene annotation was downloaded from Xenbase. Gene expression was obtained using RSEM
The expected read counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM), were extracted for further analysis. The estimated read counts were used as input for edgeR to perform DE analysis
A generalize linear regression model was developed to identify DE genes and the thresholds were set at FDR 0.05 and fold change of greater than 2 or less than 0.5. Three comparisons were performed (comparing Control, Sham, and Prog-Device amongst each other).
Genome_build: X. laevis v9.2
Supplementary_files_format_and_content: Excel sheet with normalized counts for each sample, log2 fold change, p-value, gene identifier.

source_name: Blastema

extract_protocol:
Total RNA for each sample was isolated by using TRIzolTM Reagent (Ambion, Invitrogen #15596018) –chloroform, following standard manufacturer’s protocol.
NGS analyses were performed by The MIT BioMicro Center (Boston, MA). Samples were quality controlled on a Fragment Analyzer (Advanced Analytical) to determine DV200 scores. The mRNA from 1 μg of total RNA was isolated using Illumina human/mouse/rat RiboZero Gold and prepared into Illumina libraries using the Kapa RNA HyperPrep kit and 10 cycles of amplification. Final libraries were pooled and quality controlled using qPCR (Roche LC480II) as well as the Fragment Analyzer and sequenced on HiSeq2000 for 40 nucleotides.  Following sequencing, data processing was performed using the standard Illumina pipeline. Fastq files were generated for data processing and assembly.

value: Blastema

value: Silk treatment


title: s_C3 (miRNA-Seq)


title: Leaves Heat treatment H2


title: WT_female_3

value: untreated


title: lsm8_4_B

source_name: lsm8-1 mutant seedlings under cold conditions

value: soil, 13 days at standard conditions (20ºC) + 1 day at cold (4ºC)


title: Leaves Heat treatment H1


title: WT_female_2

value: prefrontal cortex


title: Leaves Control CK3

source_name: Control

value: 25°C/20°C (day/night)


title: pfd246_20_C

source_name: pfd2,4,6 triple mutant seedlings under standard conditions


title: lsm8_4_C


title: WT_female_1

value: female


title: Leaves Control CK2


title: WT_male_3


title: pfd246_20_B

value: whole seedlings


title: m_M3

description: treated

data_processing:
Raw sequences were trimmed off Illumina adapter sequences and filtered out sequences that did not meet the quality thresholds using Trimmomatic (version 0.33)
All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25.
Reads were mapped to the Trinity assembled de novo transcriptome to estimate the transcript/Unigene abundance using RSEM (RNA-Seq by Expectation-Maximization) (version 1.2.21) with the default aligner Bowtie (version 1.1.1)
Differential expression analysis using DESeq in Trinity (version 2.2.0)

growth_protocol: Embryonic red drum were collected from brood stock tanks at the Texas Parks and Wildlife – CCA Marine Development Center in Corpus Christi, Texas and transported under constant aeration to the University of Texas Marine Science Institute. Embryos were subsequently treated with formalin during aeration. Embryos were then rinsed with sterilized seawater and checked for buoyancy and coloration using a Nikon SMZ2800N microscope. Spawns with low fertilization rates or poor egg quality were not used.

extract_protocol:
Pooled larvae were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio).Total RNA was isolated and purified with RNeasy Mini Kit (Qiagen, Valencia, California) and quantified by NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
200 ng of total RNA was used to prepare RNA-Seq libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following the protocol described by the manufacturer (Ipswich, MA).

treatment_protocol: Bulk dilutions were prepared by adding the appropriate volume of slick or source oil HEWAF to 1 µm filtered, UV-sterilized seawater in 5 L glass bottles,  vigorously spinning for several minutes with a stir bar followed by decanting into each of the replicate 1 L glass beakers.   Freshly fertilized embryos were then gently added to each replicate using a glass transfer pipette and each beaker covered with a glass petri dish.  The test was performed in an environmental control chamber set at 25 °C and 30 ppt salinity with a 14:10 h light: dark photoperiod. Survival was assessed daily.  A minimum of a 70% hatching success was required followed by a 80% survival for all tests.


title: Leaves Control CK1


title: m_H3

description: treated


title: WT_male_2


title: pfd246_20_A


title: m_H1

description: treated


title: m_M2

description: treated


title: pfd4_NaCl_A

source_name: pfd4 mutant seedlings under salt conditions

value: in vitro, 14 days at 150 mM NaCl


title: WT_male_1


title: VL648_R24

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

description: VL648: Transgenic strain expressing Pnhr-86::nhr-86::GFP

data_processing:
 The raw sequencing data were first clipped for adaptor sequences and then mapped to the C. elegans genome (ce10, UC Santa Cruz) by the Burrows-Wheeler Aligner algorithm (BWA MEM, BWA version 0.7.15). The output SAM files were processed and sorted with the Picard tools. The output mapping files (BAM files) were filtered with SAMtools to remove any read that had a mapping quality less than 10 (SAMtools view –b –q 10 input.bam > output.bam). Peaks were determined using MACS version 2.1 with the no-model parameter. The final set of peaks were called if the difference in intensity values of samples had a significance level of p-value < 0.01.
Genome_build: ce10
Supplementary_files_format_and_content: peaks files

organism: Caenorhabditis elegans

source_name: VL648_R24, whole animal

extract_protocol:
Exposed animals were collected and washed with 4℃ M9 and phosphate-buffered saline to remove bacteria. Cross-linking of protein and DNA was performed in 2% formaldehyde for 30 minutes at room temperature. Cross-linking was quenched with 100 mM glycine, animals were washed in M9, resuspended in lysis buffer (50 mM Hepes–KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate, 0.5% (v/v) N-Lauroylsarcosine, and protease inhibitors) and lysed with a Teflon homogenizer. Lysates were then sonicated using a Bioruptor UCD-200 for 10 cycles (30 s on, 30 s off) to obtain 500-1000 bp DNA fragments. Sonicated lysates (2 mg) were pre-cleared with protein G Dynabeads (Invitrogen) and incubated with 5 μg anti-GFP antibody (Roche Cat#11814460001, Lot#19958500) overnight. Immune complexes were collected with protein G Dynabeads, washed, and eluted from beads. Cross-links were reversed at 65℃ overnight and DNA fragments were purified with PCR purification columns (Qiagen).
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence). Qualified library for sequencing.

treatment_protocol: Synchronized L1 staged C. elegans wild-type and nhr-86 loss of function animals were grown to L4 to young adult stage, transferred to 70 μM R24 or solvent control (DMSO, 1% final concentration) assay plates and incubated at 20°C overnight.

tag: genotype

value: Whole animal

tag: chip antibody


title: VL648_DMSO

source_name: VL648_DMSO, whole animal

value: DMSO

value: anti-GFP antibody (Roche Cat#11814460001, Lot#19958500)


title: pfd4_20_C

source_name: pfd4 mutant seedlings under standard conditions

value: soil, 14 days at standard conditions (20ºC)


title: m_M1

description: treated

value: whole larva


title: m_L3

description: treated


title: nhr-86(ums12) R24 rep3

data_processing:
mRNA-seq data analysis was performed by BGI Americas Corp.
Supplementary_files_format_and_content: FPKM values for each sample

source_name: nhr-86(ums12) R24, whole animal

extract_protocol:
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Synchronized L1 staged C. elegans wild-type and nhr-86 loss of function animals were grown to L4 to young adult stage, transferred to 70 μM R24 or solvent control (DMSO, 1% final concentration) assay and incubated at 20°C overnight.


title: lsm8_4_A


title: m_H2

description: treated


title: m_L2

description: treated


title: pfd4_20_B


title: m_L1

description: treated


title: pfd4_NaCl_C


title: nhr-86(ums12) R24 rep1


title: nhr-86(ums12) R24 rep2


title: pfd4_4_C

source_name: pfd4 mutant seedlings under cold conditions


title: m_C3

description: control


title: pfd4_4_A


title: nhr-86(ums12) DMSO rep2

source_name: nhr-86(ums12) DMSO, whole animal


title: nhr-86(ums12) DMSO rep3


title: Mucor R7B virulent strain singlecultured in MMC medium during 24 hrs, used as a control for both atf mutants, rep a

description:
Mucor R7B virulent strain singlecultured in MMC medium during 24 hours, used as a control for both atf mutants, replicate a
wtR7Bmmc26a
TableS5.xlsx

data_processing:
Data filtering by FASTQC and Trim Galore!
Read alignment by STAR
Differential expression analyses by CuffDiff
Genome_build: Mucor circinelloides f. lusitanicus CBS277.49 v2.0 (JGI)
Genome_build: mm10
Supplementary_files_format_and_content: Gene differential expression analysis table from CuffDiff

organism: Mucor lusitanicus

source_name: Mycelium

extract_protocol:
Cultures were frozen with liquid nitrogen and grinded into dust. Total RNA was extracted using RNeasy® Plant Mini Kit (Qiagen, Hilden, Germany) following the supplier’s recommendations
mRNA enrichment by poly (A) purification capture and cDNA libraries were prepared at BaseClear (Leiden, The Netherlands) using TruSeq RNA Library preparation kits

tag: culture duration

value: 24 hours

tag: culture type

value: single

tag: culture media

value: MMC

tag: fungal parental strain


title: Mucor R7B virulent strain singlecultured in cell media for 5 hours, replicate b

description:
R7BCb
TableS1.xlsx

source_name: Fungal spores

value: 5 hours

value: L15 cell culture medium

value: Mucor circinelloides f. lusitanicus CBS277.49


title: Mucor R7B virulent strain singlecultured in MMC medium during 24 hrs, used as a control for both atf mutants, rep b

description:
Mucor R7B virulent strain singlecultured in MMC medium during 24 hours, used as a control for both atf mutants, replicate b
wtR7Bmmc26b
TableS5.xlsx


title: m_C1

description: control

source_name: whole embryo

tag: developmental stage

tag: concentration


title: m_C2

description: control


title: Mucor R7B virulent strain singlecultured in cell media for 5 hours, replicate a

description:
R7BCa
TableS1.xlsx


title: nhr-86(tm2590) R24 rep3

source_name: nhr-86(tm2590) R24, whole animal


title: Col_NaCl_B

source_name: WT Col-0 seedlings under salt conditions


title: s_H3

description: treated


title: nhr-86(ums12) DMSO rep1


title: Mucor NRRL3631 avirulent strain singlecultured in cell media for 5 hours, replicate b

description:
NRRLCb
TableS1.xlsx


title: s_H2

description: treated


title: Col_NaCl_C


title: Col_NaCl_A


title: nhr-86(tm2590) R24 rep2


title: GFP_low-cells

city: Münster

first: Susanne

last: Höing

state: Select if applicable

address: Röntgenstraße 20

institute: Max Planck Institute for Molecular Biomedicine

description: SAMPLE 2

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in Illumina GenomeStudio. Signal intensities below 10 were arbitrarily trimmed to the value of 10.

source_name: Cell culture

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA in put: 400ng, IVT: 12h

growth_protocol: Hb9-GFP mouse ESCs were grown on feeder cells in 20% serum. MNs were differentiated using embryoid bodies treated with retinoic acid and purmorphamine.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion

tag: cell type

value: HB9-GFP mouse embryonic stem cells

tag: gfp level

value: GFP low


title: Mucor NRRL3631 avirulent strain singlecultured in cell media for 5 hours, replicate a

description:
NRRLCa
TableS1.xlsx


title: pfd4_4_B

value: soil, 13 days at standard conditions (20ºC) + 1 day at cold (4ºC)


title: Col_20_C

source_name: WT Col-0 seedlings under standard conditions


title: GFP_negative-cells

description: SAMPLE 3

value: GFP negative


title: Col_20_B

value: whole seedlings


title: Mucor atf2 mutants singlecultured in MMC medium during 24 hours, replicate b

description:
Atf2mmc26b
TableS5.xlsx


title: s_H1

description: treated

tag: tissue


title: nhr-86(tm2590) R24 rep1


title: GFP_high-cells (motor-neurons)

description: SAMPLE 1

value: GFP high


title: nhr-86(tm2590) DMSO rep3

source_name: nhr-86(tm2590) DMSO, whole animal

value: Whole animal


title: Mucor atf2 mutants singlecultured in MMC medium during 24 hours, replicate a

description:
Atf2mmc26a
TableS5.xlsx


title: Col_20_A


title: s_M2

description: treated


title: Mucor atf1 mutants singlecultured in MMC medium during 24 hours, replicate b

description:
Atf1mmc26b
TableS5.xlsx


title: nhr-86(tm2590) DMSO rep2

value: DMSO


title: s_M1

description: treated


title: nhr-86(tm2590) DMSO rep1


title: Mucor atf1 mutants singlecultured in MMC medium during 24 hours, replicate a

description:
Atf1mmc26a
TableS5.xlsx


title: WT_R24 rep3

source_name: WT_R24, whole animal

value: wild-type


title: G. theta light 1 +TE

description: The TE-treatment was included for qualitative, not quantitative, analysis. They were used only for visual inspection of sRNA read alignment.

organism: Guillardia theta

source_name: Total algal cell

tag: cell collection condition

value: Light

tag: replicate

tag: terminator exonuclease treatment

value: Yes


title: s_L3

description: treated

value: whole larva


title: Col_4_A

source_name: WT Col-0 seedlings under cold conditions

tag: organ

tag: ecotype

tag: growth conditions


title: WT_R24 rep2

tag: strain

tag: treatment

tag: genotype


title: G. theta light 2

value: No


title: s_M3

description: treated


title: Col_4_C


title: WT_R24 rep1


title: s_L2

description: treated


title: s_C3

description: control


title: s_C2

description: control


title: G. theta light 1


title: WT_DMSO rep3

source_name: WT_DMSO, whole animal


title: G. theta dark 2

value: Darkness


title: WT_DMSO rep2


title: s_L1

description: treated


title: G. theta dark 1 +TE


title: s_C1

description: control


title: WT_DMSO rep1


title: H3K4me2_GFI-KD

status: Public on Jan 08 2019

city: Frankfurt am Main

first: Michael

last: Rieger

address: Theodor-Stern-Kai 7

institute: Universitätsklinikum Frankfurt/DKFZ

data_processing:
Base calling was performed by RTA 1.18.64
De-multiplexing was performed using Illumina CASAVA 1.8.2
Illumina fastq files were aligned to mouse mm10 genome version using the UNIPRO UGENE-1.20.0 Software and the BWA_MEM algorithm and the universal workflow for RAW ChIP-Seq analysis. The workflow takes FASTQ files as input and processes the data as follows:
Filtration of the input sequencing reads by the CASAVA header, cutting of adapter sequences, trimming of the sequencing reads by quality. The default settings were used. Quality threshold: 20. Min length 10. Trim both ends: false
Mapping of the reads to the mm10 reference sequence using BWA-MEM. Removal of PCR duplicates. Conversion to BAM format. Parameters used: Min seed length: 19; Band width: 100; Dropoff: 100; Internal seed length: 1,5000; Skip seed threshold: 10000; Drop chain threshold: 0,500; Rounds of mate rescues: 100; Skip mate rescue: 0; Skip pairing: False; Mismatch penalty: 1; Mismatch penalty: 4; Gap open penalty: 6; Gap extension penalty: 1; Penalty for clipping: 5; Penalty unpaired: 17; Score threshold: 30
Genome_build: mm10, GRCm38
Supplementary_files_format_and_content: processed data is in BED6 format generated from BAM files using bedtools V 2.27.0

source_name: Lineage negative BM cells

growth_protocol: cells were isolated directly from the BM of mice followed by isolation of Lineage negative cells via magnetic columns

extract_protocol:
Lysates from 4 x 10^6  were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext® UltraTM DNA Library Prep Kit for Illumina®(New England Biolabs, Cat# E7370S, Lot# 0071505) combined with NEBNext® Multiplex Oligos for Illumina®, Index Primer Set 1 (New England Biolabs, Cat# E7335S, Lot# 0061412)

treatment_protocol: no treatment

value: bone marrow

tag: chip antibody


title: H3K4me2_GFI1-WT


title: HP_2

city: Dallas

first: Wanpen

last: Vongpatanasin

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015).
Aligned reads were quantified using featurecount (v1.4.6) (Liao et al., 2014) per gene ID against Gencode version 10 (Mudge and Harrow, 2015).
Differential gene expression analysis was done using the R package DEseq2 (v 1.6.3).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and FPKM values for all samples.

extract_protocol:
Total RNA was extracted from gastrocnemius muscle 12wks after treatment, using TRIzol (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All experiments were performed using 20-24 week-old C57BL6 male mice obtained from UT Southwestern breeding core. Mice in the high Pi (HP) group were fed with diet containing 2.0% inorganic Pi (2.3% total Pi), TD08020, Envigo Teklad Diets, Madison, WI) for 12 weeks. Mice in the control group (NP) were fed with diet containing 0.6% inorganic Pi (0.9% total Pi, TD160114) for 12 weeks. Other mineral contents of the 2 diets are the same (0.3% magnesium, 1.9% calcium, 1.8% potassium, and 0.9% sodium).

value: gastrocnemius

tag: background strain

tag: diet

value: high phosphate

tag: diet time

value: 12 weeks


title: HP_1


title: NP_3

value: normal phosphate


title: G. theta dark 1


title: HP_3


title: NP_1


title: Col_4_B

value: soil, 13 days at standard conditions (20ºC) + 1 day at cold (4ºC)


title: Lens_E16.5_rep1

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

description: lens

data_processing:
RNA seq datafiles were trimmed using the Trimmomatic tool
Reads were aligned against Mus musculus reference genome (mm10) using Tophat v2.0.9  and gene-, cds-, and transcripts-level expression were computed through Cufflinks
The transcript expression counts generated using “classic-FPKM” normalization method Cuffnorm
Genome_build: Mus musculus reference genome (mm10)
Supplementary_files_format_and_content: matrix table with counts-per-million from all samples in a tab-delimited text file

source_name: Lens

extract_protocol:
Mouse C57BL/6NTac strain (Taconic Biosciences) lenses were micro-dissected at stages E10.5, E12.5, E14.5 and E16.5.  Total RNA was purified using Qiagen RNAeasy kit from three biological replicates for each stage; each biological replicate contained multiple lenses (E10.5, n=50 lenses/replicate; E12.5, n=29 lenses/replicate; E14.5, n=18 lenses/replicate; E16.5, n=17 lenses/replicate).  Mouse whole embryos at E10.5, E11.5 and E12.5 were dissected and total RNA was isolated from each stage in three biological replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina HiSeq 2500

value: C57BL/6NTac strain

value: wild type

tag: age

value: embryonic day E16.5


title: Lens_E14.5_rep3

description: lens

value: embryonic day E14.5


title: WholeBody_rep1

description: Whole embryo

source_name: Whole embryo

value: embryonic day E10.5-12.5


title: Lens_E16.5_rep3

description: lens


title: WholeBody_rep3

description: Whole embryo


title: Lens_E16.5_rep2

description: lens


title: Lens_E14.5_rep2

description: lens


title: Lens_E12.5_rep3

description: lens

value: embryonic day E12.5


title: WholeBody_rep2

description: Whole embryo


title: Lens_E12.5_rep1

description: lens


title: Lens_E14.5_rep1

description: lens


title: Lens_E12.5_rep2

description: lens


title: Lens_E10.5_rep3

description: lens

value: embryonic day E10.5


title: Lens_E10.5_rep2

description: lens


title: Lens_E10.5_rep1

description: lens


title: NP_2


title: I3_R1_001

city: Birmingham

first: Beatriz

last: Leon Ruiz

state: Alabama

address: 1825 University Blvd

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
All RNA-seq analyses were performed using the Penn State Galaxy publicly available server using the tuxedo suite analysis tools. Fastq files were aligned to the mm10 reference genome using TopHat (Galaxy Tool Version 0.9; Tool Version TopHat v2.0.14 for all studies except for the glutamine studies, Galaxy Tool Version 2.1.0 and Tool Version TopHat v2.1.0) were used with default parameters.
Cufflinks, Cuffmerge, Cuffquant, and Cuffnorm were performed to define RPKM values for genes. Cufflinks (Galaxy Tool Version 2.2.2.0; Tool Version Cufflinks v2.2.1.0) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffmerge (Galaxy Tool Version 2.2.1.0) was performed using default parameters. Cuffquant (Galaxy Tool Version 2.2.1.0; Tool Version Cuffquant v2.2.1) was performed using default parameters for all settings except bias and multi-read correction was performed.
Cuffdiff (Galaxy Tool Version 2.2.1.3; Tool Version Cuffdiff v2.2.1) was performed using default parameters (using Cuffquant output files). Cuffnorm (Galaxy Tool Version 2.2.1.1; Tool Version Cuffnorm v2.2.1) was performed using default parameters with a Cuffdiff format output.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel Open XML Format Spreadsheet files showing RPKM values for each individual sample

source_name: mLN

extract_protocol:
RNA was isolated using the RNA Isolation Kit: Rneasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols. All samples (Genewiz)

tag: cell type

value: CD11b+ mDCs

value: 24H post i.n. sensitization with HDM+LPS