title: 2012_410_ATCACG_L007

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

data_processing:
FASTQ files were aligned to the honey bee genome using STAR 2.5.3a.
Raw counts were generated using the "featureCounts" function in Subread 1.5.2
Genome_build: Amel_HAv3.1

organism: Apis mellifera

source_name: mushroom bodies

growth_protocol: Methods were the same as in Experiment 1 except for the following. The two bee colonies (containing adult populations of ca. 8000 bees) used for this experiment were each housed in glass‐walled observation hives, which allowed us to observe whether a focal bee danced or not upon returning from the feeder. Dance provides a unique, natural and quantifiable readout of a bee's assessment of the value of collected food rewards; individuals only dance if the reward is of sufficient value, based on an assessment of the quantity, concentration and distance of the resource from the hive, and the level of colony need (Seeley 1995; von Frisch 1967). We varied the sucrose concentration in the feeder to generate either high‐ (23 or 58% w/v) or low‐ (10 or 23% w/v) value rewards. Reward value was determined empirically for each colony; most bees returned to the hive and danced for the high value reward, while most bees did not dance for the low value reward (Fig. 1).

extract_protocol:
Mushroom bodies were isolated as described in that study after treatment of flash-frozen heads with RNAlater-ice (Life Technologies, Carlsbad, CA, USA). RNA was extracted from isolated mushroom bodies or other brain regions using Picopure extraction kits (Arcturus, Grand Island, NY, USA).
After all bees were collected for each experiment, we paired bees collected from the same colony on the same day in different treatment groups. Pairs were then processed together during each step. In Experiment 1, the treatment groups were food vs. no food; Experiment 2, pollen vs. sucrose; and Experiment 3, bees that danced vs. bees that did not dance. Poly‐adenylated RNA was enriched from the total RNA pool using Oligo(dT)25 DynaBeads (Thermo Fisher Scientific Inc., Waltham, MA, U.S.A.), fragmented, and converted to complementary DNA (cDNA; NEXTflex Directional RNA‐Seq Kit dUTP Based instructions, Bioo Scientific Corporation, Austin, TX, U.S.A.). Average fragment sizes were estimated with a BioAnalyzer High sensitivity DNA assay (Agilent Technologies, Santa Clara, CA, U.S.A.); fragments were an average of 356 (Experiment 1), 348 (Experiment 2) and 351 (Experiment 3) base pairs (bp). complementary DNA libraries were labeled with NEXTflex RNA‐Seq Barcodes for multiplexing during sequencing. The final cDNA library concentration was estimated using a Qubit (Thermo Fisher Scientific Inc., Waltham, MA, U.S.A.), and then eight libraries were pooled. The total concentration of all adapter‐ligated fragments within assembled library pools was confirmed using KAPA Library Quantification kits (Kapa Biosystems, Wilmington, MA, U.S.A.). The pooled libraries were sequenced on a HiSeq 2000 (Illumina Inc., San Diego, CA, U.S.A.) at the W.M. Keck Center for Comparative and Functional Genomics within the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana‐Champaign. The average number of 100 bp, paired‐end reads was 24.7 (Experiment 1), 25.6 (Experiment 2) and 25.3 (Experiment 3) million per sample.

treatment_protocol: We used an established protocol (Lutz & Robinson 2013) to dissect a region of the brain enriched for mushroom body tissue; we obtained 63.8–702.6 (median = 412.2) ng of total RNA from each sample (N = 60).

value: mushroom bodies

tag: caste

value: worker

tag: percent dwv

tag: treatment (high-value reward ("tx") or low-value reward ("c"))

value: tx

tag: behavior (dance ("d"), no-dance ("nd"))

value: D

tag: colony


title: 2012_411_TTAGGC_L007

status: Public on Jul 02 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: c

value: ND


title: RNA-Seq Cry2KO ZT16 rep1

city: College Station

first: Christine

last: Merlin

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings. Sequencer .bcl basecall files were formatted into .fastq files using CASAVA_v1.8.2 script configureBclToFastq.pl.
Reads were mapped to the monarch genome (assembly v3; (Zhan and Reppert 2013)) using TopHat2 (Kim, Pertea et al. 2013) with parameters "--read-realign-edit-dist 2 -g 1 --b2-sensitive”.
Expression levels of transcripts were quantified using Cufflinks (Trapnell, Williams et al. 2010, Trapnell, Roberts et al. 2012).
A modified Fourier transformation was used (Wijnen, Naef et al. 2005) to identify cycling transcripts meeting the following criteria: (1) three or more reads per kilo base per million mapped reads (RPKM) in at least one time point, (2) F24 (24-hr spectral power) > 0.45, (3) p-value of the F24, as described in (Menet, Rodriguez et al. 2012) < 0.05 (i.e., experimental pF24-value is within the top 5% of the 10,000 pF24-values calculated from randomized permutation), and (3) amplitude (maximal/minimal experimental values) > 1.3.
Heat maps were produced using heatmap.2 in gplots package for R. Gene ontology and KEGG pathway enrichment analysis were performed using Metascape (metascape.org).
Genome_build: Monarch genome (assembly v3)
Supplementary_files_format_and_content: Output from cufflinks in generic FPKM Tracking Format saved as plain text files containing the estimated gene-level expression values.

organism: Danaus plexippus

source_name: 3 brains

growth_protocol: Monarch butterflies were raised in the laboratory on semi-artificial diet under 15 hours light, 9 hours dark (LD, 15:9) conditions in Percival incubators at 25ºC and 70% humidity, as previously described (Markert, Zhang et al. 2016). Adult were housed in glassine envelopes in the same lighting and temperature conditions, and were manually fed a 25% honey solution daily.

extract_protocol:
Brains free of eye photoreceptors were dissected in 0.5X RNA later (Ambion) to prevent RNA degradation, and stored at -80ºC until use. Total RNA was extracted using an RNeasy Mini kit (Qiagen).
PolyA+ RNA was isolated from 2 μg of total RNA with NEBNext Oligo d(T) magnetic beads (New England Biolabs), and multiplexed libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos (New England Biolabs) and amplified with 12 PCR cycles, following the manufacturer’s recommendations. Libraries quality and size distribution was verified on a Bioanalyzer, libraries were quantified by real-time quantitative PCR, and 16 multiplexed libraries were mixed in equimolar ratios and sequenced on a Hi-seq 2500 (Illumina) using 50bp single end reads.

treatment_protocol: Adult monarchs were entrained for a minimum of 7 days after eclosion in 15:9 LD cycles at 25ºC.

tag: time

value: Brain

tag: genotype

value: Cry2 KO

tag: Sex

value: male


title: 2012_409_GGCTAC_L006


title: Rocket_D-5_S5

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Raw, QC-ed short reads were cleaned via trimmomatic81 using set parameters (ILLUMINACLIP:all_illumina_adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:70).
The preprocessed reads were directly input into MiXCR82 for TCR profiling with default setting (https://mixcr.readthedocs.io/en/latest/rnaseq.html)
KnownTRB clonetypes in rhesus monkeys was used as reference.
The resulted TRB clonetypes were further filtered using customized threshold with a clone fraction of ≥ 0.5%.
Data from Rocket is presented in the manuscript.

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from frozen PBLs using Rneasy Plus Universal (Qiagen) and first strand cDNA was created from the poly A tailed fraction of total RNA
SMART™ Approach for Full-Length cDNA Library Construction
Enriched VDJ Enriched VDJ amplicons from each sample were uniquely dual-indexed by PCR for multiplexing compatibility during sequencing

treatment_protocol: Frozen XXX  aliqouts were thawed and rested overnight in XX  media with X% FBS prior to antibody staining and XX the next day. No XX were added

tag: time period

value: 2 days after 1st ADL infusion


title: 2012_405_CTTGTA_L001


title: 2012_408_TAGCTT_L006


title: RNA-Seq Cry2KO ZT10 rep2

value: female


title: Rocket_D-4_S6

value: 3 days after 1st ADL infusion


title: RNA-Seq Cry2KO ZT04 rep2


title: RAS1

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

data_processing:
Unaligned bam files were converted to FastQ files using Bedtools 2.17.
Original 100bp reads were trimmed down to 50bp with trimmomatic 0.33.
FastQ files were aligned against the dm6 genome using STAR 2.3.0e, using default options.
Aligned reads were imported in R using RSamtools to perform further quality control steps. Only reads with MapQ>0 (aligning to 10 sites or less) were kept for downstream procedures.
To obtain per-sample expression estimates we used the summarizeOverlaps function from the GenomicAlignments package, using the IntersectionNotEmpty mode and single end strand specific options.
Counts were used to perform a differential expression analysis using the DESeq2 package, previously removing genes without reads in any of the analyzed samples, and using the default options.
Output results were filtered to consider differentially expressed genes with |FC|>2 and Benjamini-Hochberg adjusted pvalue < 0.05.
FastQC v011 was used to perform a quality control overview of FastQ files and aligned BAM files.
Binary tracks in BigWig format were generated with the rtracklayer package, both for individual and pooled samples by group.
The log2FC information was used to rank all genes in the genome with nreads>0 and a a Gene Set Enrichment Analysis was performed with Gene Ontology, GOSLIM and KEGG collections.
Genome_build: dm6
Supplementary_files_format_and_content: DESeq2 Differentially expressed genes in RAS vs GFP including chromosomal location information (space, start, end), gene information (width, FBgn, strand, description, symbol, entrez_id, genename), sample and group counts, and DESeq2 differential expression results (log2Foldchange, stat, pvalue, BH-adj pvalue), and null hypothesis rejection column (-1: down, 0: notDE, 1: up)

organism: Drosophila melanogaster

source_name: wing imaginal disc

growth_protocol: Ap>Gal4, myrT,RasV12; TubGal80ts and Ap>Gal4, myrT,GFP-i; TubGal80ts flies where allowe to grow for 6 days at 18ºC and the shifted at 29ºC for three days prior to the dissection of the wondering L3 larvae wing imaginal dics. The followin stocks wew used Ap>Gal4 (RRID:BDSC_3041), UAS-myrT (RRID:BDSC_32222) and UAS-RasV12 (RRID:BDSC_64196)

extract_protocol:
150.000 cells were collected in Lysis Buffer (20 mM DTT, 10 mM Tris.HCl ph 7.4, 0.5% SDS, 1 μg/μl proteinase K), incubated for 15 min at 65oC and stored at -80ºC. RNA was extracted using RNA Clean XP bead suspension (Agencourt Bioscience), digested with DNAse-I, cleaned-up by a 2nd pull-down and eluted in water.
Library preparation was perfomed using the kit Quant Seq 3' mRNA-Seq Library Prerp for Illumina (Lexogen) following the manufacture's instructions
3' mRNA sequencing in a 100 nucleotides Single Read lane

treatment_protocol: Drosophila wing imaginal discs disgregated with trypsin and the FACS sorted to select the dorsal transgene expressing cells.

value: wing imaginal disc

value: RasV12 expressing

tag: replicate


title: mRNA_RectalCancer_rep9

type: RNA

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

hyb_protocol: After fragmentation, RNA was hybridized withAffymetrix Hybridization,Wash, and Stain Kit on Affymetrix PrimeView Human Gene Expression Array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA-dabg using Affymetrix Expression Console software.

label: Biotin

organism: Homo sapiens

source_name: Rectal cancer tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Micro Kit following manufacturer's instruction.

value: rectal cancer

value: M

tag: age

tag: batch

value: Batch 1


title: mRNA_RectalCancer_rep8


title: Nebula_D-5_S3


title: mRNA_RectalCancer_rep6


title: RNA-Seq Cry2KO ZT10 rep1


title: RNA-Seq Cry2KO ZT04 rep1


title: 2012_404_CAGATC_L001

value: mushroom bodies


title: Nebula_D-4_S1


title: 2012_402_GCCAAT_L001

value: worker


title: RNA-Seq WT ZT22 rep2

value: wild type


title: Nebula_D-0_S4

value: 7 days after 1st ADL infusion, intended day of transplant


title: RNA-Seq WT ZT19 rep2


title: 2012_399_ACTTGA_L005

value: tx

value: D


title: mRNA_RectalCancer_rep4


title: mRNA_RectalCancer_rep2


title: RNA-Seq WT ZT19 rep1

value: Brain


title: mRNA_RectalCancer_rep5

value: F


title: 2012_398_TTAGGC_L005

value: ND


title: RNA-Seq Cry2KO ZT16 rep2

value: Cry2 KO


title: 2012_401_ACAGTG_L001


title: SI-ILC2_rep2

city: Yokohama

first: Takaharu

last: Sasaki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Thurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

description: processed data file: rpkm.txt

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4.
Sequences were aligned to mm10 genome using STAR version 2.6.0.
Read counts were obtained using featureCounts version 1.6.0 included in Subread suite.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rpkm.txt: RPKM values in plain text.

organism: Mus musculus

source_name: Small intestine

extract_protocol:
ILC2 was sort-purified from small intestinal lamina propria and white adipose tissue using cell sorter.
Libraries were prepared according to Illumina's instructions accompanying KAPA Library Preparation Kit (#KK8230).

tag: strain/background

tag: genotype/variation

value: WT

tag: cell type

value: ILC2 cells from small intestinal lamina propria

value: 9 weeks


title: RNA-Seq WT ZT16 rep2

value: female


title: 2012_397_ATCACG_L005

value: c


title: RNA-Seq WT ZT16 rep1

value: male


title: Amazo_D-4_S8

value: 3 days after 1st ADL infusion


title: 2012_396_TGACCA_L005

value: mushroom bodies


title: RNA-Seq WT ZT22 rep1


title: WAT-ILC2_rep2

description: processed data file: rpkm.txt

source_name: Mesenteric white adipose tissue

value: ILC2 cells from mesenteric white adipose tissue


title: RNA-Seq WT ZT13 rep2

value: wild type


title: Amazo_D-plus-3_S7

value: 2 Days after 2nd ADL infusion


title: 2012_394_CTTGTA_L005

value: worker


title: 2012_395_CGATGT_L005

value: D


title: mRNA_RectalCancer_rep1

value: rectal cancer

value: M

value: Batch 1


title: Amazo_D-5_S2

value: 2 days after 1st ADL infusion


title: RNA-Seq WT ZT13 rep1

value: Brain


title: WAT-ILC2_rep1

description: processed data file: rpkm.txt

value: WT


title: 2012_393_ATCACG_L005

value: tx


title: LnCap Cells - LEP treated, biological rep1

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from LnCap cell line

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Affymterix GeneChip Human Genome U219 ArrayStrip (16 h, 45°C).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: LnCap cell line, treated with LEP 10-6M

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: LNCaP - the human prostate carcinoma cell line [LNCaP clone FGC (ATCC® CRL-1740DTM)] was purchased from ATCC (American Type Culture Collection, Manassas, Rockville, MD, USA). LNCaP cells were cultivated in the RPMI Medium 1640 (1X), supplemented with GlutaMAX, HEPES (all from Gibco, Life technologies, Carlsbad, California, USA) and antibiotics (Antibiotic/antimycotic Sigma Aldrich, Saint Louis, MO 63103, USA). Cells were grown in the 75 cm2 flask (NUNC EasyFlask with Nunclon surface, Thermo Fisher Scientific) at 37°C in a humidified atmosphere of 5% CO2. The culture medium was changed every 2 days.

extract_protocol: The total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) then purified on columns (NucleoSpin Total RNA Isolation, Qiagen GmbH, Hilden, Germany). The amount of total RNA was determined by optical density at 260 nm and its purity was estimated by 260/280 nm absorption ratio (higher than 1.8) (NanoDrop spectrophotometer, Thermo Scientific, Waltham, MA, USA). The RNA integrity and quality were checked in a Bioanalyser 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2. Each sample was diluted to the RNA concentration of 100 ng/μl, at the OD260/OD280 ratio of 1.8/2.0. From each RNA sample, 100 ng of RNA was taken for microarray experiments.

treatment_protocol: When cells reached approximately 80% confluence (about 7-8 days of cultivation), they were subcultured into 6-well plates (Nunc, Thermo Fisher Scientific, approximately 343 000 cells per one well – 9.6 cm2), to determine the effect of LEP on LNCaP transcriptome modulation. The applied experimental protocol was as follows: during the first 48 h of cultivation, the cells grew in a standard medium mentioned above. For the next 24 h, the cells were grown in starvation medium (FBS free). Afterwards, the cells were cultivated for 48 h, in a starvation medium supplemented with LEP (Recombinant Human Leptin, PeproTech, Germany) at the following concentrations: 0 (control), 1x10-6 M. After the mentioned period cell supernatants were collected and stored at - 80°C for further analyses.

value: androgen-sensitive human prostate cancer cell line


title: RNA-Seq WT ZT10 rep2

value: female


title: LnCap Cells - LEP treated, biological rep2


title: LnCap Cells - control, biological rep2

source_name: LnCap cell line, served as control


title: 2012_390_TTAGGC_L006

value: c

value: ND


title: LnCap Cells - control, biological rep1


title: 2012_388_ATCACG_L006

value: mushroom bodies


title: RNA-Seq WT ZT07 rep2


title: mRNA_RectalCancer_rep3


title: normal group

city: Shanghai

first: Yi

last: Shou

address: Haining Road 100

department: Department of Acupuncture-Moxibustion

country: China

institute: Shanghai General Hospital

description: CircRNA Expression Profiling.xls [A1]

data_processing:
Basecalls performed using cutadapt software (v1.9.3)
circRNA-seq reads were mapped to human genome by STAR software (v2.5.1b)
DCC software (v0.4.4) was used to detect and identify circRNA. The identified circRNA was annotated based on the circBase database
Genome_build: MM10
Supplementary_files_format_and_content: excel format

source_name: plasma

extract_protocol:
20μL of exosome suspension were mixed with 1mL Trizol buffer and placed on the ice for 5 minutes. Then 200μL of chloroform was added and layered on the ice for 15 minutes after fully shaking for 30 seconds, followed by centrifuged at 13500x g for 10 minutes at 4°C. After the upper layer was transferred to a new enzymatic-free tube, precooled isopropanol was added and mixed and then stay at room temperature for 10 minutes. After centrifuged at 13500x g for 10 minutes at 4°C, the supernatant was discarded and washed with 75% ethanol for twice. Then ethanol was removed and stood for 15 minutes to volatile ethanol. 24μL of RNase-free water was added into the extracted RNA and stored at -80°C.
rRNAs in total RNA was removed using Ribo-Zero rRNA Removal Kits (Illumina, USA). Then TruSeqStranded Total RNA Library Prep Kit (Illumnia, USA) was used to pre-process RNA and construct sequencing library.

tag: strain

tag: plasma

value: plasma exsome


title: RNA-Seq WT ZT07 rep1

value: wild type

value: male


title: 2012_386_CTTGTA_L006

tag: caste

value: worker

tag: percent dwv


title: MBDK-GFP-E5_RNA-seq

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University

data_processing:
paired-end sequencing on an Illumina Hiseq4000
Cutadapt  was utilized to remove reads containing undetermined bases, adaptors, and low quality bases. Then sequence quality was verified using FastQC  (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
genome build: GCA_000003055.3
Supplementary_files_format_and_content: MBDK-GFP-E5_vs_MBDK-GFP_Gene_differential_expression.xls

organism: Bos taurus

source_name: MDBK cells expressing BPV-13 E5

extract_protocol: Ambion mirVana miRNA Isolation Kit (Thermo Fisher Scientific)

value: Kidney

tag: cell line

value: MBDK

value: epithelial cells


title: 2012_385_CAGATC_L006

tag: treatment (high-value reward ("tx") or low-value reward ("c"))

tag: behavior (dance ("d"), no-dance ("nd"))

value: D

tag: colony


title: SI-ILC2_rep1

description: processed data file: rpkm.txt

value: ILC2 cells from small intestinal lamina propria

value: 9 weeks


title: model group

description: CircRNA Expression Profiling.xls [B1]

tag: genotype


title: H322_shMTHFD2_rep3

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

description: Gene expression two days after plating.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarry 8x60K Ver. 3.0 (G4851C, Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: H322, MTHFD2 knocked down cell, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% FBS RPMI1640 + penicillin/streptomycin + 2.5ug/ml puromycin

extract_protocol: Total RNA was extracted with Trizol reagent (ThermoFisher Scientific) according to the manufacturer's instructions.

tag: tissue

value: lung adenocarcinoma


title: MBDK-GFP_RNA-seq

source_name: MDBK cells expressing GFP


title: H322_shMTHFD2_rep2

description: Gene expression two days after plating.

source_name: H322, MTHFD2 knocked down cell, replicate 2


title: H322_shMTHFD2_rep1

description: Gene expression two days after plating.

source_name: H322, MTHFD2 knocked down cell, replicate 1


title: NSCLC, ALK-positive, PD-L1 positive, tumor biopsy

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description: ALK-positive, PD-L1 positive

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: Quantile normalization with GSM862609, GSM862610, GSM862611, GSM862612

source_name: Non-small-cell lung adenocarcinoma.

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

extract_protocol: Total  RNA was extracted with Magnetic Beads Total Nucleic Acid Isolation Kit for FFPE (Sileks, Russia) according to manufacturer instruction. RNA was quantified using Nanodrop.

tag: disease state

value: NSCLC

value: primary lung cancer

tag: status after 5 years

value: Alive

tag: histology

value: AD

value: 48 years

tag: Sex

tag: Stage

value: IIA

tag: smoking history

value: 10.5 pack-years


title: H322_NCT_rep3

description: Gene expression two days after plating.

source_name: H322, negative control cell, replicate 3


title: RNA-Seq WT ZT04 rep2

tag: time

value: Brain

value: wild type

value: female


title: H322_NCT_rep2

description: Gene expression two days after plating.

source_name: H322, negative control cell, replicate 2


title: 2012_346_TGACCA_L001

source_name: mushroom bodies

value: mushroom bodies

value: worker

value: tx

value: ND


title: model + EA group

description: CircRNA Expression Profiling.xls [C1]

tag: strain

value: plasma exsome


title: RNA-Seq WT ZT04 rep1

source_name: 3 brains

value: male


title: 2012_341_CGATGT_L001

value: D


title: RNA-Seq WT ZT01 rep2


title: RNA-Seq WT ZT10 rep1


title: antibiotics then faecal transplant [CRO232A20]

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
CRO232A20
processed data file: Table_TPM_values_per_gene_per_sample.txt

data_processing:
Read Trimming and adapter removal performed with Trimmomatic (version 0.36).
Read alignment and gene expression quantification were performed with RSEM (v 1.2.31) and STAR (v 2.5.2a).
Differential expression analysis was carried out with DESeq2 package (version 1.20) with R version 3.5.1.
TPM values were obtained from RSEM (genes.results files).
Genome_build: Ensembl GRCm38 release 89
Supplementary_files_format_and_content: Table_TPM_values_per_gene_per_sample.txt: Tab-delimited text file includes TPM values for each gene on each sample.

source_name: lung stromal cells CD45 negative

extract_protocol:
Preparation of CD45 negative cells was achieved by MACS magnetic separation columns according to manufacturer specifications. CD45 negative cells were collected, pelleted by centrifugation, and resuspended in the appropriate amount of RLT buffer according to manufacturer instructions (Qiagen). RNA was isolated using the Qiagen RNeasy Micro Kit.
Libraries were constructed from cDNA using the Ovation Ultralow System V2 (NuGEN Technologies).

treatment_protocol: Antibiotics-treated mice were given the following cocktail for 3-4 weeks: 100 mg ampicillin, 100 mg vancomycin, 100 mg metronidazole, and 100 mg gentamicin in 100 ml water (changed twice a week). For fecal transplants, two fecal pellets from the control group were homogenised in 1 ml PBS, and 200 μl volume were gavaged orally. Gavage occurred twice (on day 2 and day 5) post antibiotics treatment.

tag: strain/background

tag: cell type

value: Lung stromal cells CD45 negative

tag: treatment

value: Antibiotics then faecal transplant


title: antibiotics then faecal transplant [CRO232A18]

description:
CRO232A18
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: RNA-Seq WT ZT01 rep1


title: 2012_338_TAGCTT_L001

tag: caste

tag: percent dwv

value: c


title: 2012_340_GGCTAC_L001

tag: treatment (high-value reward ("tx") or low-value reward ("c"))

tag: behavior (dance ("d"), no-dance ("nd"))


title: antibiotics then faecal transplant [CRO232A15]

description:
CRO232A15
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: 2012_321_GGCTAC_L003

tag: colony


title: antibiotics [CRO232A11]

description:
CRO232A11
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: Antibiotics


title: 2012_320_TTAGGC_L002

tag: tissue


title: 2012_318_TAGCTT_L003


title: antibiotics [CRO232A10]

description:
CRO232A10
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: antibiotics [CRO232A8]

description:
CRO232A8
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: 2012_317_GATCAG_L003


title: antibiotics [CRO232A7]

description:
CRO232A7
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: Day 5 Sham Vaccine 547797A12

city: Uxbridge

first: Ronan

last: McCarthy

state: Middlesex

address: Heinz Wolff Building, Kingston Lane, Brunel University London

institute: Brunel University London

hyb_protocol: Hybridization was performed according to the NimbleGen array users guide v6 Chapter 3. See www.nimblegen.com.

scan_protocol: Scanning was performed at 2um using an Agilent array scanner.

data_processing: Microarray images were processed using DEVA v1.2.1 software to obtain a pair report containing the signal intensity values for each probe. To correct for differences in the overall intensity levels between slides robust multi-array normalisation was used (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249). Data was then processed using GeneSpring GX using manufacturer’s guidelines. For Matrix construction duplicate values (e.g RNA_SPIKE_8_EC5_U00096P00857) were removed.

organism: Sus scrofa

source_name: Day 5 Sham vaccine_tonsil cells

label_protocol: Labelling was performed using a one-color labelling kit (NimbleGen)

growth_protocol: Five days prior to challenge (day 0), the animals in group 1 (n = 9) were vaccinated with 2 ml of C-strain vaccine into the brachiocephalous muscle (as recommended by the manufacturer [Riemser Arzneimittel AG]), and group 2 (n = 9) was intranasally inoculated with 1 ml of mock virus supernatant. On day 5, groups 1 and 2 were inoculated intranasally with 105 TCID50 of CSFV Brescia strain. On day 5, 8 and 10, three animals were euthanized from groups 1 and 2, and the tonsils were collected.

extract_protocol: Rneasy Plus mini kt (Qiagen)

treatment_protocol: Tonsil cells isolated from tonsil connective tissue

tag: breed

value: Large White/Landrace crossbreed

tag: age

value: 8 to 10 weeks

tag: vaccinated with

value: mock virus supernatant; sham vaccine

tag: inoculated with

value: 10^5 TCID50 of CSFV Brescia strain

value: Tonsil cells


title: H322_NCT_rep1

description: Gene expression two days after plating.

source_name: H322, negative control cell, replicate 1

tag: cell line

value: lung adenocarcinoma


title: Day 5 Sham Vaccine 547797A10


title: Day 5 Sham Vaccine 547797A11


title: Day 5  Vaccine 547568A12

source_name: Day 5  vaccine_tonsil cells

value: C-strain vaccine


title: PCC6803_sll0729 suppressor mutant 15_rep2

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 0.6 µg of labeled RNA.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays.

data_processing:
Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and cyclicloess normalized.
Values are given as normalized log2 signal intensities.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture grown at standard growth conditions

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis sp. PCC6803 substrain PCC-M was used as WT. For physiological characterization, axenic cultures of the WT and mutants strains were grown photoautotrophically in BG11 medium at 29°C under continuous illumination of 180 µmol photons s-1 m-2 (warm light, Osram L58 W32/3). The cultures were bubbled with air enriched with 5% [v/v] CO2.

extract_protocol: Cells were lysed in 1 ml PGTX, with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine-thiocyanate, and 0.48 M guanidine hydrochloride (Pinto et al., 2009; BMC Mol Biol 10: 79). Phenol was extracted twice with chloroform:isoamyl alcohol (24:1) and RNA was precipitated with isopropanol at -20°C, followed by centrifugation at 4°C. The RNA pellet was washed with 70% ethanol and resuspended in RNase-free A. dest.

treatment_protocol: All strains were cultivated in parallel prior to sampling and RNA extraction. The cells were grown understandard growth conditions and not treated with an environmental stimulus.

value: sll0729 suppressor mutant 15


title: 2012_316_ATCACG_L002

value: mushroom bodies

value: worker


title: PCC6803_sll0729 suppressor mutant 15_rep3


title: Day 5  Vaccine 547568A10


title: Day 5  Vaccine 547568A11

source_name: Day 5 vaccine_tonsil cells


title: plain water [CRO232A6]

description:
CRO232A6
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: plain water


title: Day 3  Sham Vaccine 547797A09

source_name: Day 3  Sham vaccine_tonsil cells


title: PCC6803_sll0729 suppressor mutant 15_rep1


title: plain water [CRO232A4]

description:
CRO232A4
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: 2012_313_CTTGTA_L003

value: tx

value: ND


title: Day 3  Sham Vaccine 547797A08


title: Day 3  Sham Vaccine 547797A07


title: 2012_312_CAGATC_L002


title: plain water [CRO232A2]

description:
CRO232A2
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: Lung stromal cells CD45 negative


title: plain water [CRO232A1]

description:
CRO232A1
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: 2012_310_CTTGTA_L004


title: 2012_309_TTAGGC_L007


title: Day 3  Vaccine 547568A09

source_name: Day 3  vaccine_tonsil cells


title: 2012_308_CAGATC_L004

value: D


title: Day 3  Vaccine 547568A08


title: PCC6803_sll0729 suppressor mutant 1_rep2

value: sll0729 suppressor mutant 1


title: PCC6803_sll0729 suppressor mutant 1_rep1


title: PCC6803_WT_rep2

value: WT


title: PCC6803_sll0729 suppressor mutant 1_rep3


title: PCC6803_WT_rep3


title: PCC6803_sll0729mutant complemented with ssl1378_rep2

data_processing:
Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.
Values are given as normalized log2 signal intensities.

value: sll0729 mutant complemented with ssl1378


title: Day 0  Shaw Vaccine547797A06

source_name: Day 0  Shaw vaccine_tonsil cells

value: Large White/Landrace crossbreed

value: 8 to 10 weeks


title: PCC6803_WT_rep1


title: RAT 7 normal saline [NS3]

city: Changsha

first: Jiali

last: Shao

state: Hunan

address: 281 Tongzipo Road, Changsha, Hunan, China

department: Department of Anesthesiology

institute: The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 4 out of 8 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for eachcircRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAshaving fold changes > 2 and p-values < 0.05 are selected as the significantly differentially expressed.

organism: Rattus norvegicus

source_name: normal_spinal cord

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured by NanoDrop ND-1000.

extract_protocol: The RNA isolation was performed using TRIzol reagent(Invitrogen, Carlsbad, CA, USA) and following the manufacturer’s protocol. The purity and concentration of total RNA were determined with NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). RNA integrity was assessed by denaturing agarose gel electrophoresis.

treatment_protocol: Adult male Sprague-Dawley rats in the morphine tolerance group (MT group) received 10 μg intraperitoneal morphine (1 μg/1 μL) twice a day at 08:00–09:00 and 16:00~17:00 for 7 consecutive days.Their cohorts in the normal saline group (NS group, n = 8) received equal volumes of normal saline following the identical protocol.  On the 8 th day, one hour after the injection with morphine or saline in the morning,the rats were decapitated under deep anesthesia, and the lumbar enlargements were collected for analysis.

value: Sprague-Dawley

tag: gender

value: male

tag: developemental stage

value: adult

tag: phenotype

value: normal

value: spinal cord

tag: molecule subtype

value: circRNA


title: Day 0  Shaw Vaccine 547797A05

value: mock virus supernatant; sham vaccine

tag: cell type

value: Tonsil cells


title: RAT 8 normal saline [NS4]

tag: strain


title: 2012_307_ACTTGA_L002

value: mushroom bodies

tag: caste

value: worker

value: tx


title: 2012_306_GCCAAT_L004

tag: percent dwv

value: ND


title: 2012_305_ATCACG_L007

tag: treatment (high-value reward ("tx") or low-value reward ("c"))


title: Day 3  Vaccine 547568A07

value: C-strain vaccine

value: 10^5 TCID50 of CSFV Brescia strain


title: 2012_304_ACAGTG_L004

tag: behavior (dance ("d"), no-dance ("nd"))

value: D


title: 2012_298_ACTTGA_L007

tag: colony


title: 2012_300_GATCAG_L007

tag: tissue

value: c


title: RAT 6 normal saline [NS2]


title: Day 0  Sham Vaccine 547797A04

source_name: Day 0  Sham vaccine_tonsil cells

tag: breed

value: Large White/Landrace crossbreed

value: 8 to 10 weeks


title: RAT 3 morphine tolerance [MT3]

source_name: morphine tolerance_spinal cord

value: Sprague-Dawley

value: male

value: morphine tolerance


title: PCC6803_sll0729mutant complemented with sll0729_rep2

value: sll0729 mutant complemented with sll0729


title: PCC6803_sll0729mutant complemented with sll0729_rep1


title: RAT 4 morphine tolerance [MT4]

value: adult

value: spinal cord

value: circRNA


title: Day 0  Vaccine 547568A06

source_name: Day 0  vaccine_tonsil cells

tag: age

value: Tonsil cells


title: RAT 1 morphine tolerance [MT1]


title: PCC6803_sll0729mutant complemented with ssl1378_rep1

value: sll0729 mutant complemented with ssl1378


title: RAT 2 morphine tolerance [MT2]


title: RAT 5 normal saline [NS1]

value: normal


title: Day 0  Vaccine 547568A05

tag: vaccinated with


title: PCC6803_sll0729mutant_rep2

value: sll0729 mutant


title: Day 0  Vaccine 547568A04

value: C-strain vaccine


title: PCC6803_WT

description: WT

value: WT


title: PCC6803_sll0729mutant_rep1


title: C57BL/6J, one-week, vehicle treated, biological rep6

status: Public on Jul 01 2019

city: Baltimore

first: Susan

middle: G

last: Dorsey

state: MD

address: 655 W. Lombard Street, Room 727A

department: University of Maryland School of Nursing

institute: University Of Maryland, Baltimore

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after one-week
C57BL6_DRG_VEHICLE_1wk_6

hyb_protocol: Following fragmentation, 100 ng of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed using the R software suite. Array intensities were normalized with the robust multichip average method and probe set to gene mapping was done using the BrainArray Custom CDF version 18 (Dai, M. et al., Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33 (20), 175 (2005)). Batch effect correction was performed using nonparametric empirical Bayes methods as implemented in ComBat with naive samples serving as covariates (Johnson, W., Rabinovic, A. & Li, C., Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8 (1), 118-127 (2007)).
RMA, BrainArray Custom CDF version 18

source_name: C57BL/6J_1-week 0.9% NaCl treated_drosal root ganglia

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Adult female C57BL6/J and A/J (20–30 g; The Jackson Laboratory, Bar Harbor, ME) mice were used for the study. All mice were housed on a 12:12 h light/dark cycle with food and water available ad libitum. All experiments were approved by the institutional animal care and use committee of the University of Maryland School of Medicine, and conducted in accordance with The International Association for the Study of Pain guidelines for investigations of pain in animals. On each experimental day, the mice were weighed to detect changes in food and water consumption. Any mouse that demonstrated signs of debilitation or weight loss > 10% vs. baseline was euthanized.

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

treatment_protocol: No treatment, 4mg/kg cisplatin, or 0.9% NaCl were admissistered twice weekly over the specified time period.

value: female

value: 9 weeks

tag: treated with

value: 0.9% NaCl

tag: timepoint

value: L4-L5 dorsal root ganglia


title: C57BL/6J, one-week, vehicle treated, biological rep5

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after one-week
C57BL6_DRG_VEHICLE_1wk_5

tag: gender


title: C57BL/6J, one-week, cisplatin treated, biological rep1

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after one-week
C57BL6_DRG_CISPLATIN_1wk_1

source_name: C57BL/6J_1-week 4mg/kg cisplatin treated_drosal root ganglia

value: 4mg/kg cisplatin


title: C57BL/6J, one-week, cisplatin treated, biological rep3

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after one-week
C57BL6_DRG_CISPLATIN_1wk_3


title: C57BL/6J, one-week, cisplatin treated, biological rep4

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after one-week
C57BL6_DRG_CISPLATIN_1wk_4


title: C57BL/6J, one-week, cisplatin treated, biological rep5

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after one-week
C57BL6_DRG_CISPLATIN_1wk_5


title: C57BL/6J, one-week, vehicle treated, biological rep4

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after one-week
C57BL6_DRG_VEHICLE_1wk_4


title: C57BL/6J, one-week, vehicle treated, biological rep3

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after one-week
C57BL6_DRG_VEHICLE_1wk_3


title: C57BL/6J, one-week, cisplatin treated, biological rep2

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after one-week
C57BL6_DRG_CISPLATIN_1wk_2


title: C57BL/6J, one-week, naive, biological rep5

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after one-week
C57BL6_DRG_NAIVE_1wk_5

source_name: C57BL/6J_1-week untreated_drosal root ganglia

value: none (untreated control)


title: C57BL/6J, one-week, vehicle treated, biological rep1

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after one-week
C57BL6_DRG_VEHICLE_1wk_1


title: C57BL/6J, one-week, naive, biological rep4

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after one-week
C57BL6_DRG_NAIVE_1wk_4


title: C57BL/6J, one-week, vehicle treated, biological rep2

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after one-week
C57BL6_DRG_VEHICLE_1wk_2


title: A/J, one-week, cisplatin treated, biological rep3

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after one-week
AJ_DRG_CISPLATIN_1wk_3

source_name: A/J_1-week 4mg/kg cisplatin treated_drosal root ganglia

value: A/J


title: C57BL/6J, one-week, naive, biological rep3

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after one-week
C57BL6_DRG_NAIVE_1wk_3


title: C57BL/6J, one-week, naive, biological rep1

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after one-week
C57BL6_DRG_NAIVE_1wk_1


title: C57BL/6J, one-week, naive, biological rep2

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after one-week
C57BL6_DRG_NAIVE_1wk_2


title: A/J, one-week, vehicle treated, biological rep4

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after one-week
AJ_DRG_VEHICLE_1wk_4

source_name: A/J_1-week 0.9% NaCl treated_drosal root ganglia


title: A/J, one-week, cisplatin treated, biological rep6

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after one-week
AJ_DRG_CISPLATIN_1wk_6


title: A/J, one-week, cisplatin treated, biological rep4

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after one-week
AJ_DRG_CISPLATIN_1wk_4


title: A/J, one-week, vehicle treated, biological rep5

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after one-week
AJ_DRG_VEHICLE_1wk_5


title: C57BL/6J, four-weeks, naive, biological rep3

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after four-weeks
C57BL6_DRG_NAIVE_4wk_3

source_name: C57BL/6J_4-weeks untreated_drosal root ganglia

value: 12 weeks


title: A/J, one-week, vehicle treated, biological rep3

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after one-week
AJ_DRG_VEHICLE_1wk_3


title: C57BL/6J, four-weeks, naive, biological rep2

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after four-weeks
C57BL6_DRG_NAIVE_4wk_2


title: A/J, one-week, cisplatin treated, biological rep5

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after one-week
AJ_DRG_CISPLATIN_1wk_5


title: A/J, one-week, vehicle treated, biological rep1

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after one-week
AJ_DRG_VEHICLE_1wk_1


title: C57BL/6J, four-weeks, naive, biological rep1

description:
Gene expression data from drosal root ganglia of untreated C57BL/6J mice after four-weeks
C57BL6_DRG_NAIVE_4wk_1


title: A/J, one-week, vehicle treated, biological rep2

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after one-week
AJ_DRG_VEHICLE_1wk_2


title: A/J, one-week, cisplatin treated, biological rep1

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after one-week
AJ_DRG_CISPLATIN_1wk_1


title: C57BL/6J, four-weeks, vehicle treated, biological rep3

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after four-weeks
C57BL6_DRG_VEHICLE_4wk_3

source_name: C57BL/6J_4-weeks 0.9% NaCl treated_drosal root ganglia


title: A/J, one-week, naive, biological rep1

description:
Gene expression data from drosal root ganglia of untreated A/J mice after one-week
AJ_DRG_NAIVE_1wk_1

source_name: A/J_1-week untreated_drosal root ganglia


title: A/J, one-week, cisplatin treated, biological rep2

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after one-week
AJ_DRG_CISPLATIN_1wk_2


title: A/J, one-week, naive, biological rep3

description:
Gene expression data from drosal root ganglia of untreated A/J mice after one-week
AJ_DRG_NAIVE_1wk_3


title: C57BL/6J, four-weeks, vehicle treated, biological rep2

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after four-weeks
C57BL6_DRG_VEHICLE_4wk_2


title: A/J, one-week, naive, biological rep2

description:
Gene expression data from drosal root ganglia of untreated A/J mice after one-week
AJ_DRG_NAIVE_1wk_2


title: C57BL/6J, four-weeks, vehicle treated, biological rep1

description:
Gene expression data from drosal root ganglia of vehicle treated C57BL/6J mice after four-weeks
C57BL6_DRG_VEHICLE_4wk_1


title: C57BL/6J, four-weeks, cisplatin treated, biological rep3

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after four-weeks
C57BL6_DRG_CISPLATIN_4wk_3

source_name: C57BL/6J_4-weeks 4mg/kg cisplatin treated_drosal root ganglia


title: C57BL/6J, four-weeks, cisplatin treated, biological rep1

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after four-weeks
C57BL6_DRG_CISPLATIN_4wk_1


title: C57BL/6J, four-weeks, cisplatin treated, biological rep2

description:
Gene expression data from drosal root ganglia of cisplatin treated C57BL/6J mice after four-weeks
C57BL6_DRG_CISPLATIN_4wk_2


title: A/J, four-weeks, cisplatin treated, biological rep2

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after four-weeks
AJ_DRG_CISPLATIN_4wk_2

source_name: A/J_4-weeks 4mg/kg cisplatin treated_drosal root ganglia


title: Rag2-/- Pro-B cells + IL7 IP

type: genomic

city: Boston

first: Yuka

last: Takeuchi

state: MA

address: 185 Cambridge Street

department: Molecular biology

institute: MGH

hyb_protocol: 34 µg of test sample and 34 µg of reference sample were combined and resuspended in 12.3 µl of water. Hybridization buffer was added and hybridization permormed frollowing the CGX NimbleGen protocol.

scan_protocol: Arrays were scanned on an GenePix 4000B Microarray Scanner following manufacturer's protocol instructions.

data_processing: Arrays were procrssed using Nimblegen's standard protocol for data extraction.

molecule: genomic DNA

source_name: Input DNA from Rag2-/- mouse pro-B primary cells cultured with IL-7

label_protocol: 0.5 ug of either INP DNA or IP DNA were labeled using the NimbleGen Dual-Color DNA labeling Kit (REF 06370250001) and following manufacturer's protocol for CGX arrays.

growth_protocol: Primary CD19+ Pro-B cells from 8-9 week old RAG2-/- mice were grown for 3 days in IMDM + 20% FBS + P/S + B-Me in the presence of 10 ng/mL of the growth factor IL-7 on OP9 feeder cells and 1 day in the presence of mitomycin C-treated ST2 cells.

extract_protocol: Cells were recovered and derived from 8-week old mice by positive enrichment of CD19+ cells using MACS magnetic separation. Cells were crosslinked with formaldehyde for 10' at RT and reaction was stopped with 0.125 M of glycine for 5’ at RT. Cells were then washed twice with cold PBS and nuclei were extracted using a cold lysis buffer [10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.5% NP-40]. MNase digestion was performed at 37°C for 10' in MNase digestion buffer [10 mM NaCl, 3 mM MgCl2, 1 mM CaCl2, 4% NP-40, 10 mM TrisHCl,  pH 7.5 and PMSF] and reaction was terminated using an 30 ul of 20 mM EGTA. The nuclear suspension was sonicated, and debris was removed by centrifugation (14,000 rpm, 10 min). The chromatin solution was diluted 5-fold in ChIP dilution buffer containing 1 mM PMSF and 0.1% protease inhibitor mixture, and precleared with protein A immobilized on Sepharose 4B Fast Flow beads (Sigma) for 15' at 4°C. After centrifugation, 50 μl of the supernatant was saved to be used as input DNA and the rest of the supernatant was incubated overnight at 4°C with 30 μl of CTCF Ab (Upstate Biotechnology). Sample wes decrosslinked 5 h at 65ºC together with 1.5 ug/ul of pronase. Digests were extracted with phenol:chloroform, and DNA recovered by ethanol precipitation.

tag: genotype/variation

value: Primary CD19+ pro-B cells cultured with IL-7

tag: antibody

source_name: CTCF IP DNA from Rag2-/- mouse splenic B cells

value: Primary CD19+ splenic B cells

value: CTCF Ab (Upstate Biotechnology)


title: VIP_W4

city: Basel

first: Geoffrey

last: Fucile

address: Spitalstrasse 41

department: sciCORE

country: Switzerland

institute: University of Basel

data_processing:
Illumina software used for basecalling.
Data quality, reads repartition, and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc. Reads were mapped using STARv2.4.0 52 against the exons defined in the proprietary Mouse FAST DB v2016_1 database (PMID: 17547750), using a mismatch cutoff of 2 and discarding reads with 10 or more alignments. The minimum chimeric segment length was 15. Read counts were summarized using featureCounts in two stages. First, unique reads per exon were counted. In the second stage, multimapping reads were fractionally allocated to exons based on the distribution of unique counts of exons within a gene. Total counts were then calculated based on three constitutivity classes: class 2 includes exons present in more than 75% of annotated transcripts for a gene, class 1 includes exons present in 50-75% of transcripts, and class 0 includes alternative exons present in less than 50% of transcripts. Total counts per gene were summed from constitutivity class 2 exons if their FPKM values exceed 96% of the background FPKM based on intergenic regions. If counts from class 2 exons were insufficient to exceed the detection threshold, class 1 and eventually class 0 exon counts were included to reach the detection threshold.
Genome_build: GRCm38

source_name: Murine cortex

extract_protocol:
RNA purification was performed using RNeasy Plus Micro Kit (Qiagen)
Library preparation for all samples was performed with 50 ng of RNA using the TruSeq PolyA+ Stranded mRNA Library Prep Kit High Throughput (Illumina, RS-122-2103)

tag: genotype

value: Murine cortex

tag: molecule subtype

value: ribosome-associated RNA


title: VIP_W3


title: A/J, four-weeks, navie, biological rep3

description:
Gene expression data from drosal root ganglia of untreated A/J mice after four-weeks
AJ_DRG_NAIVE_4wk_3

source_name: A/J_4-weeks untreated_drosal root ganglia

tag: strain


title: VIP_W1


title: VIP_W2


title: SST_W5

source_name: Murine hippocampus

value: Murine hippocampus


title: A/J, four-weeks, vehicle treated, biological rep3

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after four-weeks
AJ_DRG_VEHICLE_4wk_3

source_name: A/J_4-weeks 0.9% NaCl treated_drosal root ganglia


title: SST_W3


title: Rag2-/- Pro-B cells IP

source_name: Input DNA from Rag2-/- mouse pro-B primary cells

tag: cell type

value: Primary CD19+ pro-B cells

source_name: CTCF IP DNA from Rag2-/- mouse pro-B primary cells


title: SST_W1


title: SST_4


title: SST_W2


title: SST_2


title: exo

city: Hangzhou

first: yingkuan

address: Jiefang Road 88

institute: Zhejiang Universit

description: miRNA expression

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA,Release 21.0 (8*60K,Design ID:070156) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: loveo derived Small Extracellular Vesicles

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LoVo cells were cultured in sEV-depleted (160,000xg, 16h) complete medium and the supernatant were collected after 72h. sEVs were purified and centrifuged at 100,000xg for 2.5h using a Beckman SW41Ti rotor

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

tag: source tissue

value: colorectal cancer


title: Wild-type splenic B cells INP

source_name: Input DNA from WT mouse splenic B cells

value: wild type

source_name: CTCF IP DNA from WT mouse splenic B cells


title: SST_1

value: WT


title: cell

description: miRNA expression

source_name: colorectal cancer cell lines

treatment_protocol: LoVo cells were cultured in sEV-depleted (160,000xg, 16h) complete medium and the supernatant were collected after 72h. sEVs were purified and centrifuged at 100,000xg for 2.5h using a Beckman SW41Ti rotor


title: A/J, four-weeks, navie, biological rep2

description:
Gene expression data from drosal root ganglia of untreated A/J mice after four-weeks
AJ_DRG_NAIVE_4wk_2

value: female


title: Scnn_4


title: A/J, four-weeks, navie, biological rep1

description:
Gene expression data from drosal root ganglia of untreated A/J mice after four-weeks
AJ_DRG_NAIVE_4wk_1


title: SST_3


title: A/J, four-weeks, vehicle treated, biological rep1

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after four-weeks
AJ_DRG_VEHICLE_4wk_1

value: 0.9% NaCl


title: A/J, four-weeks, cisplatin treated, biological rep1

description:
Gene expression data from drosal root ganglia of cisplatin treated A/J mice after four-weeks
AJ_DRG_CISPLATIN_4wk_1

value: L4-L5 dorsal root ganglia


title: A/J, four-weeks, vehicle treated, biological rep2

description:
Gene expression data from drosal root ganglia of vehicle treated A/J mice after four-weeks
AJ_DRG_VEHICLE_4wk_2


title: Scnn_2


title: EL2

description: mRNA expression.

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent mouse Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 13.0 (Agilent). Probes that had at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Mouse Liver Tissue Treated with Small Extracellular Vesicles

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's instructions.

treatment_protocol:
Control group was injected with PBS 10 times every other day in 21days.
Purified SW620-derived sEVs were injected to nude mice via tail vein every other day for 21 days.

tag: strain/background

value: Nude

value: Liver

tag: treatment

value: SW620-derived Small Extracellular Vesicles


title: NL2

description: mRNA expression.

source_name: Normal Mouse Liver Tissue

value: Control


title: NL1

description: mRNA expression.


title: NL3

description: mRNA expression.


title: PV_3


title: PV_4


title: EL1

description: mRNA expression.


title: Grik_W6


title: Scnn_1


title: Grik_W5


title: Grik_W4


title: PV_1


title: Grik_W3


title: CamK_4


title: CamK_W4


title: CamK_W3


title: CamK_W5


title: CamK_3


title: CamK_1


title: Scnn_3


title: CamK_W2


title: EL3

description: mRNA expression.


title: sh-ALKBH5_Ribo_seq

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

description: Ribo-seq of ALKBH5 knockdown in MEF cells

data_processing:
Library strategy: Ribo-seq
For all Ribo-seq and RNA-seq except for Rep2, adaptor was removed by Cutadapt with parameters: -a CTGTAGGCACCATCAAT -m 15
For all Ribo-seq and RNA-seq except for Rep2, the first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence). The last FOUR nucleotides were removed (3 random nucleotides)
The trimmed reads were aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead
PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428
For YTHDC2 RNA-seq and Ribo-seq rep2, the adaptor AAAAAAAAA was removed by Cutadapt with parameters: -a AAAAAAAAA -m 15. The trimmed reads were firstly aligned to rRNA, the remaining unmapped reads were then aligned to transcriptome using bowtie with parameters: -a --best -m1 --strata -S --sam-nohead
Genome_build: GRCh38 for human, mm10 for Mouse
Supplementary_files_format_and_content: Tab separated RPKM value

source_name: Mouse Embryonic Fibroblasts

growth_protocol: 293T cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation.
For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to  terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated  for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer  (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris  was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90  s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15%  PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA  fragments were dissolved by soaking overnight in 400 μl RNA elution buffer,  purified RNA fragments were re-suspended in nuclease-free water. The linker  ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the  corresponding region was excised. The cDNA was recovered by  gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer’s instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5’-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3’ (Illumina HiSeq).

treatment_protocol: YTHDC2 was knocked down in 293T cells using lentiviral shRNA (target sequence:GCCCACAGATTGGCTTATTTA).

tag: background strain

value: Mouse Embryonic Fibroblasts

tag: knockdown


title: CCL4_CD24 rep1

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: CCL4_CD24+ liver progenitor cells

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: 8-week-old mice were i.p. injected with CCL4 (2 ml/kg, Sigma-Aldrich) dissolved in olive oil at a ratio of 1:4 twice a week for 6 weeks.HACY treatment groups were intraperitoneally injected three times a week for 6 weeks.

value: 6-8 weeks

value: hepatocytes

tag: cell subtype

value: MACS-sorted CD24+ cells

value: carbon tetrachloride (CCL4)


title: PV_2

tag: tissue

value: Murine cortex

value: ribosome-associated RNA


title: CCL4_CD24 rep2

tag: age


title: HACY_CD24 rep2

source_name: HACY_CD24+ liver progenitor cells

value: a cocktail of small molecules Y-27632, A-83-01, and CHIR99021 (HACY)


title: shScram_Ribo_seq

description: Ribo-seq of scramble MEF cells

value: shScram


title: HACY_CD24 rep1


title: CamK_2

value: WT


title: 61236: ATAC-seq CpG-stimulated FO B cell

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

library_source: genomic

data_processing:
Sequence alignment: In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 nucleotides and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al., 2009). In case of ChIP-seq and ATAC-seq experiments, all sequence reads that passed the Illumina quality filtering were considered for alignment after adapter trimming. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program versions 0.12.1 and 2.1.0, respectively (Langmead et al., 2009). For ATAC-seq, additional alignment parameters were ‘-sensitive -X 5000’.
Analysis of RNA-seq data: The number of reads per gene was counted using featureCounts version 1.5.0 (Liao et al., 2014) with default settings. TPM values were calculated as described (Wagner et al., 2012).
After alignment, all four Ikaros ChIP-Seq tracks have been converted to bigWig format and normalized to reads per million using samtools 1.4 (Li et al., 2009) and UCSC kent tools (Kuhn et al., 2013). The files have been subsequently merged into one track using deeptools 3.0.1 (Ramírez et al., 2014) with the bigwigCompare commands.
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million after extension to 150 base pairs (.density_150.rpm.bw); text tab delim = TPM values in ASCII text format tab delimited

source_name: FO B cell

extract_protocol: phenol-chloroform extraction of genomic DNA

value: FO B cell

value: MD4 BCR-tg Cd23-cre Ikzf1(fl/fl)

tag: cell preparation

value: 1-day CpG stimulation, In-vitro, FACS-sorted

tag: cell sorting strategy

value: FACS-sorted

tag: chip antibody


title: 61233: ATAC-seq CpG-stimulated FO B cell

value: MD4 BCR-tg Ikzf1(fl/fl)


title: 61231: ATAC-seq naive FO B cell

source_name: naive FO B cell

value: naive FO B cell

value: Ex-vivo FACS-sorted


title: 61232: ATAC-seq naive FO B cell


title: 61230: ATAC-seq naive FO B cell


title: 61235: ATAC-seq CpG-stimulated FO B cell


title: 61229: ATAC-seq naive FO B cell


title: 49292: RNA-seq CpG-stimulated FO B cell

molecule: polyA RNA

extract_protocol: Rneasy Plus Mini Kit, Dynabeads mRNA purification kit

value: MD4 BCR-tg Cd23-cre Ikzf1(fl/-)


title: 13303: Ikaros Bio-ChIP-Seq Mature FO B cell (lymph node)

description: Series supplementary file: merged.sr.fs.rpm.bw

source_name: Mature FO B cell (lymph node)

value: Mature FO B cell (lymph node)

value: Ikzf1(ihCd2/ihCd2) Rosa26(BirA/BirA)

value: Ex-vivo MACS-sorted, CD43–

value: MACS-sorted, CD43–

value: Streptavidin


title: 61234: ATAC-seq CpG-stimulated FO B cell


title: 49293: RNA-seq CpG-stimulated FO B cell

value: MD4 BCR-tg Cd23-cre Ikzf1(fl/+)


title: 20858: Ikaros Bio-ChIP-Seq Mature FO B cell (spleen), Urea-gradient

source_name: Mature FO B cell (spleen)

value: Mature FO B cell (spleen)

value: Ex-vivo MACS-sorted, CD23+

value: MACS-sorted, CD23+


title: 49290: RNA-seq CpG-stimulated FO B cell

value: FO B cell


title: 20857: Ikaros Bio-ChIP-Seq Mature FO B cell (lymph node), Urea-gradient


title: 49289: RNA-seq CpG-stimulated FO B cell


title: 20855: Ikaros Bio-ChIP-Seq Mature FO B cell (lymph node), Urea-gradient


title: 57934: RNA-seq naive FO B cell


title: 49287: RNA-seq CpG-stimulated FO B cell


title: 57933: RNA-seq naive FO B cell

value: MD4 BCR-tg Ikzf1(fl/+)


title: 57932: RNA-seq naive FO B cell


title: 57930: RNA-seq anergic FO B cell

source_name: anergic FO B cell

value: anergic FO B cell

value: MD4 BCR-tg ML5-tg Ikzf1(fl/+)


title: 57928: RNA-seq HEL-exposed FO B cell

value: MD4 BCR-tg Cd23-cre Ikzf1(fl/fl)

value: 1day HEL i.v., Ex-vivo, FACS-sorted

value: FACS-sorted


title: 49288: RNA-seq CpG-stimulated FO B cell

value: MD4 BCR-tg Cd23-cre Ikzf1(fl/-)

value: 1-day CpG stimulation, In-vitro, FACS-sorted


title: 57931: RNA-seq anergic FO B cell

value: MD4 BCR-tg ML5-tg Cd23-Cre Ikzf1(fl/+)

value: Ex-vivo FACS-sorted


title: 57927: RNA-seq HEL-exposed FO B cell

value: MD4 BCR-tg Ikzf1(fl/fl)


title: 57929: RNA-seq anergic FO B cell

value: MD4 BCR-tg ML5-tg Ikzf1(fl/fl)


title: 57926: RNA-seq HEL-exposed FO B cell


title: 57925: RNA-seq HEL-exposed FO B cell


title: 49294: RNA-seq CpG-stimulated FO B cell

value: MD4 BCR-tg Cd23-cre Ikzf1(fl/+)


title: 57921: RNA-seq HEL-exposed FO B cell


title: 57924: RNA-seq HEL-exposed FO B cell


title: 57922: RNA-seq HEL-exposed FO B cell


title: 57920: RNA-seq HEL-exposed FO B cell


title: 57919: RNA-seq HEL-exposed FO B cell


title: 49291: RNA-seq CpG-stimulated FO B cell


title: 36428: RNA-seq naive FO B cell

value: naive FO B cell


title: STZ diabetic given the vehicle replicate 6

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. The bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Reads underwent 3’ trimming to remove bases with quality less than Phred 20 using Skewer.
Reads were mapped with to the Ensembl mouse genome (GRCm38 with version 85 gene annotations) using STAR, generating the gene-wise matrix of uniquely mapped reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression count matrix

source_name: STZ diabetic given the vehicle

growth_protocol: All animal experiments were performed in accordance with guidelines from the Alfred Medical Research and Education Precinct (AMREP) Animal Ethics Committee and the National Health and Medical Research Council of Australia. All rodents were housed in a temperature-controlled environment, with a 12-h light/dark cycle and access to chow (Specialty Feeds, Perth, WA, Australia) and water ad libitum.

extract_protocol:
Cells were disrupted with TRIzol (Qiagen, Hilde, Germany). RNA was isolated from TRIzol homogenates using the Direct-zol Kit (Zymo Research, Irvine, USA). RNA was quantified on Qubit (Thermo Fisher, Waltham, USA) and its quality was evaluated on the MultiNA bioanalyzer (Shimadzu, Kyoto, Japan).
Some 200 ng of total RNA underwent ribosomal RNA depletion using the NEBNext® rRNA Depletion Kit followed by library construction using NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (both from NEB, USA). Libraries were quantified on the MultiNA bioanalyzer (Shimadzu) and pooled to equimolar ratios for sequencing.

treatment_protocol:
Diabetes was induced in 6-week-old C57BL/6 mice by five daily intraperitoneal injections of low-dose streptozotocin (55 mg/kg; Sigma-Aldrich, St. Louis, MO) as previously described (80). Non-diabetic group was given 0.5M sodium citrate.
Diabetic and nondiabetic mice were randomized to receive either the C5aR1 peptide inhibitor PMX-53 (Ac-Phe-[Orn-Pro-dCha-Trp-Arg]) at 2mg/kg body weight provided in the drinking water or just drinking water (n=6-12) and followed for 24 weeks.

tag: disease state

value: STZ diabetes

value: control

value: Renal cortex


title: 36427: RNA-seq naive FO B cell


title: 57923: RNA-seq HEL-exposed FO B cell

value: FO B cell


title: 36425: RNA-seq naive FO B cell


title: STZ diabetic given the vehicle replicate 2


title: STZ diabetic given the vehicle replicate 4


title: STZ Diabetic treated with PMX-53 replicate 6

source_name: STZ Diabetic treated with PMX-53

value: PMX-53 administration (2mg/kg body weight via drinking water)


title: STZ Diabetic treated with PMX-53 replicate 4


title: STZ Diabetic treated with PMX-53 replicate 1


title: STZ Diabetic treated with PMX-53 replicate 2


title: STZ diabetic given the vehicle replicate 5


title: Non-diabetic given the vehicle replicate 5

source_name: Non-diabetic given the vehicle


title: Non-diabetic given the vehicle replicate 3


title: Non-diabetic given the vehicle replicate 4


title: STZ diabetic given the vehicle replicate 1


title: Non-diabetic given the vehicle replicate 2


title: STZ Diabetic treated with PMX-53 replicate 5


title: Non-diabetic given the vehicle replicate 1


title: Non-diabetic treated with PMX-53 replicate 5

source_name: Non-diabetic treated with PMX-53


title: 36426: RNA-seq naive FO B cell


title: Non-diabetic treated with PMX-53 replicate 3


title: Non-diabetic treated with PMX-53 replicate 2


title: Non-diabetic treated with PMX-53 replicate 1


title: KO kidney 602

city: Chicago

first: Jennie

last: Lin

address: 303 E Superior

institute: Northwestern University

description: KO 602

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Differential expression was determined using Cuffdiff2 and DESeq2 using standard settings per their online manuals.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice, and RNA was harvested using the miRNeasy kit by Qiagen. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney

value: 6-8 weeks old


title: KO kidney 780

description: KO 780


title: STZ Diabetic treated with PMX-53 replicate 3


title: KO kidney 591

description: KO 591


title: KO kidney 584

description: KO 584


title: KO kidney 574

description: KO 574


title: Non-diabetic given the vehicle replicate 6


title: WT kidney 777

description: WT  777

value: Wild-type


title: WT kidney 601

description: WT  601


title: WT kidney 778

description: WT  778


title: WT kidney 776

description: WT  776


title: WT kidney 590

description: WT  590


title: Non-diabetic treated with PMX-53 replicate 4


title: KO kidney 588

description: KO 588


title: Non-diabetic treated with PMX-53 replicate 6


title: mesenchymal stem cells 3

city: New York

first: Gabriel

middle: E

last: Hofman

state: New York

address: 1 Gustave L Levy Plaza

department: Department of Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
mesenchymal stem cells
MSC3_CGATGT

data_processing:
RNA-Seq reads were aligned to GRCm38/mm10with STAR v2.4.0g1 (Dobin et al., 2013). Uniquely mapping reads overlapping genes were counted with featureCounts v1.4.4 (Liao et al., 2014) using annotations from ENSEMBL GRCm38.75. All analysis used log2 counts per million (CPM) or log2 RPKM (Mortazavi et al., 2008) following TMM normalization (Robinson and Oshlack, 2010) implemented in edgeR v3.14.0 (Robinson and Oshlack, 2010). Genes with over > 1 counts per million in at least 4 samples were retained.  Differential expression analysis was performed using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene from featureCounts

source_name: Mouse mesenchymal stem cells

extract_protocol: RNA-Seq and bioinformatic analysis were performed at the Institute for Genomics and Multiscale Biology at the Icahn School of Medicine at Mount Sinai. As an initial step, Qubit QC values were evaluated and a cut-off of above 500ng total was applied. Libraries from the SPIA amplified cDNA as described above were made using the Ultralow DR library kit (NuGEN) according to manufacturer’s instructions. High-throughput RNAseq was performed using a HiSeq 2500 (Illumina) with reads between 7- 20 million among the different samples.

value: mesenchymal stem cells

tag: sample

tag: color

value: blue


title: skeletal muscle PDGFRalpha cells 1

description:
skeletal muscle PDGFRalpha cells
SM1_CGATGT

source_name: Mouse skeletal muscle PDGFRalpha cells

value: skeletal muscle PDGFRalpha cells

value: maroon


title: skeletal muscle PDGFRalpha cells 4

description:
skeletal muscle PDGFRalpha cells
SM4_CTTGTA


title: skeletal muscle PDGFRalpha cells 3

description:
skeletal muscle PDGFRalpha cells
SM3_CCGTCC


title: mesenchymal stem cells 2

description:
mesenchymal stem cells
MSC2_TGACCA


title: skeletal muscle PDGFRalpha cells 2

description:
skeletal muscle PDGFRalpha cells
SM2_ACAGTG


title: dermal fibroblasts 2

description:
dermal fibroblasts
F2_ATGTCA

source_name: Mouse dermal fibroblasts

value: dermal fibroblasts

value: orange


title: dermal fibroblasts 3

description:
dermal fibroblasts
F3_GTCCGC


title: heart PDGFRalpha 2

description:
heart PDGFRalpha
H2_CCGTCC

source_name: Mouse heart PDGFRalpha

value: heart PDGFRalpha


title: heart PDGFRalpha 1

description:
heart PDGFRalpha
H1_ACAGTG


title: embryonic stem cells  3

description:
embryonic stem cells
ESC3_CCGTCC

source_name: Mouse embryonic stem cells

value: embryonic stem cells


title: mesenchymal stem cells 1

description:
mesenchymal stem cells
MSC1_GCCAAT


title: dermal fibroblasts 4

description:
dermal fibroblasts
F4_GCCAAT


title: dermal fibroblasts 1

description:
dermal fibroblasts
F1_CAGATC


title: WT kidney 573

description: WT  573

tag: genotype


title: embryonic stem cells 1

description:
embryonic stem cells
ESC1_CGATGT


title: embryonic stem cells 4

description:
embryonic stem cells
ESC4_CTTGTA


title: heart PDGFRalpha 3

description:
heart PDGFRalpha
H3_AGTTCC


title: STZ diabetic given the vehicle replicate 3

tag: strain


title: heart PDGFRalpha 4

description:
heart PDGFRalpha
H4_CTTGTA

tag: cell type


title: embryonic stem cells 2

description:
embryonic stem cells
ESC2_ACAGTG


title: mesenchymal stem cells 4

description:
mesenchymal stem cells
MSC4_AGTCAA


title: lactic acid at 6h, biological rep3

city: Kizugawa

first: Md

middle: Zobaer

last: Hasan

state: Kyoto

address: Kunimidai 6-5-4

department: Safety Design Center

institute: Rohto Pharmaceutical CO.,Ltd

description:
LacticAcid_6H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 6 h

hyb_protocol: Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression Amplification Reagent Hybridization Controls (Cat# 900454; Lot# 4245935) and the Hybridization Module for GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720; Lot# 4275620) and mixed with amplified cDNA samples. GeneChip® Human Gene 2.0 ST Arrays (Cat# 902112; Lot# 4360273) were treated according to the manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450.

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

data_processing:
The data were analyzed after RMA normalization with Affymetrix GeneChip™ Command Console Software for QC. Statistical analyses were performed with “Moderated t” method implemented in  R package Limma 3.26.8 (Smyth, 2004).
#%affymetrix-algorithm-param-apt-engine=ProbesetSummarizeEngine
#%affymetrix-algorithm-param-apt-program-name=Expression Console
#%affymetrix-algorithm-param-apt-opt-chip-type=HuGene-2_0-st
#%affymetrix-algorithm-param-apt-opt-probe-count=2598544
#%affymetrix-algorithm-param-apt-opt-analysis-name=rma-gene-full
#%affymetrix-algorithm-param-apt-opt-set-analysis-name=rma-gene-full
#%affymetrix-algorithm-param-quantification-name=med-polish
#%affymetrix-algorithm-param-quantification-version=1.0
#%affymetrix-algorithm-param-quantification-scale=log2
#%affymetrix-algorithm-param-quantification-type=signal
#%affymetrix-algorithm-param-apt-version=1.3.1.187

source_name: Reconstructed human epidermis topically treated with lactic acid for 6 h

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

growth_protocol: Reconstruction of the human epidermis by the manufacturer (Episkin RHE/S/17) for 14 days at the air-liquid interface

extract_protocol: Qiagen RNeasy kit, protocol following the manufacturer's instructions.

treatment_protocol: Tissue samples were topically treated with lactic acid at 5% and methyl paraben at 0,2%, applied on the top of the stratum corneum of RHE/S/17

value: reconstructed human epidermis

value: lactic acid for 6 h


title: control H2O at 24h, biological rep2

description:
H2O_24H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 24 h

source_name: Reconstructed human epidermis topically treated with H2O for 24 h

value: H2O for 24 h


title: control H2O at 24h, biological rep1

description:
H2O_24H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 24 h


title: lactic acid at 24h, biological rep2

description:
LacticAcid_24H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 24 h

source_name: Reconstructed human epidermis topically treated with lactic acid for 24 h

value: lactic acid for 24 h


title: methylparaben at 24h, biological rep1

description:
MethylParaben_24H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 24 h

source_name: Reconstructed human epidermis topically treated with methylparaben for 24 h

value: methylparaben for 24 h


title: lactic acid at 6h, biological rep2

description:
LacticAcid_6H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 6 h


title: control H2O at 24h, biological rep3

description:
H2O_24H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 24 h


title: lactic acid at 24h, biological rep3

description:
LacticAcid_24H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 24 h


title: methylparaben at 6h, biological rep1

description:
MethylParaben_6H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 6 h

source_name: Reconstructed human epidermis topically treated with methylparaben for 6 h

value: methylparaben for 6 h


title: lactic acid at 1h, biological rep1

description:
LacticAcid_1H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 1 h

source_name: Reconstructed human epidermis topically treated with lactic acid for 1 h

value: lactic acid for 1 h


title: methylparaben at 24h, biological rep2

description:
MethylParaben_24H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 24 h


title: methylparaben at 1h, biological rep3

description:
MethylParaben_1H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 1 h

source_name: Reconstructed human epidermis topically treated with methylparaben for 1 h

value: methylparaben for 1 h


title: control H2O at 6h, biological rep1

description:
H2O_6H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 6 h

source_name: Reconstructed human epidermis topically treated with H2O for 6 h

value: H2O for 6 h


title: methylparaben at 24h, biological rep3

description:
MethylParaben_24H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 24 h


title: NT_2

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

description: P115_08_NT_2_log2 Signal

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalised using RMA method using the affy package from Bioconductor version 3.6

source_name: AML_untreated control

label_protocol: standard Affymetrix protocol

growth_protocol: AML cells were cultured on stroma cells in alpha-MEM, 20 % FBS + IL3, SCF,TPO and FLT3

extract_protocol: RNA was purified from one 150 000  using QIAshredder and RNEasy Mini Kit (QIAGEN).

treatment_protocol: Cell were culture with or without H4 molecule for 16 hrs

value: acute myeloid leukemia (AML) cells

value: CD45+ cells


title: lactic acid at 24h, biological rep1

description:
LacticAcid_24H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 24 h


title: control H2O at 6h, biological rep3

description:
H2O_6H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 6 h


title: control H2O at 6h, biological rep2

description:
H2O_6H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 6 h


title: lactic acid at 1h, biological rep2

description:
LacticAcid_1H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 1 h


title: methylparaben at 6h, biological rep2

description:
MethylParaben_6H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 6 h


title: NT_1

description: P115_07_NT_1_log2 Signal


title: lactic acid at 6h, biological rep1

description:
LacticAcid_6H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 6 h


title: H4_1

description: P115_01_H4_1_log2 Signal

value: H4 molecule for 16 hrs


title: methylparaben at 6h, biological rep3

description:
MethylParaben_6H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 6 h


title: control H2O at 1h, biological rep3

description:
H2O_1H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 1 h

source_name: Reconstructed human epidermis topically treated with H2O for 1 h

value: H2O for 1 h


title: lactic acid at 1h, biological rep3

description:
LacticAcid_1H-3
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with lactic acid for 1 h


title: methylparaben at 1h, biological rep2

description:
MethylParaben_1H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 1 h


title: methylparaben at 1h, biological rep1

description:
MethylParaben_1H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with methylparaben for 1 h


title: H4_2

description: P115_02_H4_2_log2 Signal


title: control H2O at 1h, biological rep2

description:
H2O_1H-2
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 1 h


title: Testis_KO_13M_sRNA

first: Chen

last: Chu

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description: 18 -40 nt

data_processing:
For transcriptome sequencing, one hundred-base pair (bp) single-ended reads were mapped to mouse genome (mm9) using the TopHat2 short read mapper version 2.1.0 and differential gene expression analysis was quantified using the ‘generalized fold change (GFOLD)’ differential expression analysis program version 1.1.4.
Small RNA sequence tags from the Solexa sequencing were subjected to data cleaning, which filtered low quality tags and contaminants. The small RNA clean reads were mapped to the mouse mm9 genome using bowtie (version 0.12.7) with settings -k 1 -v 2.Small RNA reads with 100% match to the genome were used for further analysis. Small RNA annotation was performed by alignment to GenBank (http://www.ncbi.nlm.nih.gov/genbank/), mirBase (http://mirbase.org/) , Rfam (http://rfam.sanger.ac.uk/)  and piRNABank (http://pirnabank.ibab.ac.in/) .
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are in 'txt' format and contain small RNA reads information as well as the transcriptome RPKM comparison of WT and KO.

source_name: Testis

growth_protocol: Normal growth

extract_protocol:
Pooled biological samples instead of biological replicates were used for deep sequencing experiments. Total RNA isolation was performed using Trizol reagent (Invitrogen). Total RNA concentration was measured by Nanodrop ND-2000 (Thermo Scientific), and quality was assessed using an Agilent 2100 Bioanalyzer.
For transcriptome sequencing, cDNAs were prepared from full-length mRNA transcripts using a reverse transcriptase with terminal transferase activity. A total of 2.7 μg cDNA for each sample was sonicated to 200 - 400 bp and used for library preparation with the Illumina Nextera DNA Sample Prep Kit following the standard protocol.The libraries were sequenced by Illumina Hiseq 2000. Small RNA sequencing libraries were created following the Illumina TruSeq Small RNA Sample Preparation protocol. In brief, 5’ and 3’ RNA adapters that were specifically modified to target the ends of small RNA molecules were ligated to 1 μg of high quality total RNA. Reverse transcription was performed to generate cDNA libraries and PCR was used to amplify and add unique index sequences to each library. The amplified cDNA constructs were loaded and separated by polyacrylamide gel electrophoresis (PAGE), and the fraction corresponding to 18 - 40 nt small RNAs was excised, purified and sequenced by Illumina GAIIx orHiseq 2000.

treatment_protocol: Tissue samples were prepared from seven 13-month-old WT mice and seven 13-month-old Gpx5-/- mice that were sacrificed by cervical dislocation. Epididymides were removed and freed of connective, especially fat tissues. Epididymides were then divided into caput, corpus and cauda regions. Testes and corpus epididymides were directly collected for RNA extraction. Caput and cauda epididymides were transferred to a small glass dish containing 1 ml PBS. Repeated punctures with a 26-gauge needle and a 15-min incubation at 37℃ were performed to remove spermatozoa. After sperm cell dispersion, the tissues were collected for RNA extraction.

tag: genotype/variation

value: KO

value: Testis

value: 13 month old


title: Testis_WT_13M_sRNA

description: 18 -40 nt

value: WT


title: CauEP_KO_13M_sRNA

description: 18 -40 nt

source_name: Epididymal Cauda tissue

value: Cauda


title: CauEP_WT_13M_sRNA

description: 18 -40 nt


title: CorEP_KO_13M_sRNA

description: 18 -40 nt

source_name: Epididymal Corpus tissue

value: Corpus


title: CorEP_WT_13M_sRNA

description: 18 -40 nt


title: CapEP_KO_13M_sRNA

description: 18 -40 nt

source_name: Epididymal Caput tissue

value: Caput