title: EX63_6h

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

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

source_name: Micro-TOM-EX_drought stress for 6hrs

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

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

value: Micro-TOM-EX

tag: growth condition

value: drought stress for 6hrs

value: leaf


title: dcl4_MS_smRNA_rep1

status: Public on Apr 13 2020

type: SRA

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

library_source: transcriptomic

data_processing:
Sequence reads were filtered and then mapped to TAIR10 genome using Bowtie-1.2.2 with following parameters: -v  0  -a  -M  3  --best  --strata
22-nt small RNA read were selected using samtools v1.9
Tags Per Million (TPM) were calculated and differential 21- and 22-nt siRNA production genes were called out using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons

molecule: total RNA

organism: Arabidopsis thaliana

source_name: dcl4-2  seedlings on MS medium

growth_protocol: plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old were collected for small RNA extraction.

extract_protocol:
miRNeasy mini kit(Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina

treatment_protocol: No treatment

tag: genotype

tag: tissue

value: whole seedling

tag: age

value: 14-day-old plant

tag: growth

value: grown on MS medium


title: EX62_6h

organism: Solanum lycopersicum

tag: cultivar


title: WS_2h_2

city: Wuhan

first: Zengdong

last: Tan

state: Hubei

address: shizishan street

institute: HZAU

data_processing:
The fastqc program is used to evaluate the quality of all original reads, and the trimmetric software filters them with default parameters to obtain clean data.
The clean reading of all samples was consistent with the reference genome of maize B73 (ref_gen4), which was downloaded from maizegdb (www.maizegdb. ORG) using hisat2 (v2.0.5) and default parameters.
The featurecount software in the rsubread package is used for quantification and standardization to obtain the read count and TPM (one million transcripts per thousand bases) value of each expressed gene, where TPMS represents the expression level of each transcripts.
Genome_build: Zea_mays.AGPv4.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Zea mays

source_name: Root

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen, Gaithersburg, MD, USA) and purified with an RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. RNA integrity was detected by gel electrophoresis. High-quality RNA was used for library construction using the Illumina TruSeq Stranded RNA Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: waterlogging time

value: root


title: Sal_7d2

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

country: USA

institute: USDA -ARS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and those with N (based underterminded) > 10% or low quality bases (Qscore <=5) >50% were removed.
The filtered reads were mapped to lettuce (v8) whole genome using STAR v2.5.2  with default parameters; the resulting BAM files were used to count reads at the gene-level using featureCounts.
Counts per million (CPM) mapped reads for each of biological samples were calculated using edgeR based on raw counts of STAR.
Genome_build: version8; id 37106
Supplementary_files_format_and_content: A comma-delimited text file includes CPM values for each of all samples

organism: Lactuca sativa

source_name: aerial tissue

growth_protocol: Plants were grown on soil in pots in a growth chamber at 20°C under a 16-h photoperiod with a light intensity of 350-400 μmol m−2 sec−1.

extract_protocol:
Total RNA was isolated for each experimental replicate using Plant RNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the 18-day-old plants were exposed to low temperature (4°C) for 4 h, 24 h, or 7 days at about 100 μmol m−2 sec−1 under a 16-h photoperiod.

value: Salinas

value: 18 days

value: aerial tissue

tag: treatment

value: 4°C for 7 days


title: Sal_7d1


title: Col-0_MS_smRNA_rep2

source_name: Col-0 seedlings on MS medium


title: Sal_24h3

value: 4°C for 24h


title: EX61_6h


title: Col-0_MS_smRNA_rep1


title: EX33_3h

source_name: Micro-TOM-EX_drought stress for 3hrs

value: drought stress for 3hrs


title: WS_0h_3


title: WS_0h_2


title: EX32_3h


title: Sal_24h2


title: Sal_24h1


title: EX31_3h


title: WS_0h_1


title: CSC_rep2

city: Iowa City

first: Songhai

last: Chen

state: IOWA

address: 51 Newton Road, 2-250 BSB

department: Pharmacology

institute: University of Iowa

data_processing:
FastQC and MultiQC was applied to assess reads quality. Trim galore was used to remove low quality reads and adapter sequences
Alignment-free salmon was used for transcripts quantification. Tximport was used to convert transcript level to gene level expression and add annotation.
Deseq2 was used to determine differential expressed genes.
Genome_build: Homo_sapiens-GRCh38-dbSNP150.genometemplate
Supplementary_files_format_and_content: tab-delimited text files include TPM count values for each sample calcuated by Salmon

organism: Homo sapiens

source_name: PC3 cancer stem cells (SORE6+)

growth_protocol: PC3 cells expressing the SORE6-dsGFP reporter were gerenated by lentiviral infection and stable cells were selected by puromycin (5 ug/ml) for at least 1 week. Cells were cultured in DMEM containing 10% FCS and routinely passaged at less than 80% confluency

extract_protocol:
Total RNA was prepared using Rneasy mcrio kit (Qiagen).
RNA libraries were prepared for sequencing using the protocols for the BGISEQ-500 platform

tag: cell line

value: prostate cancer cell line PC3

tag: cell type

value: PC3 cancer stem cells (SORE6+)

tag: passsages


title: Sal_4h2

value: 4°C for 4h


title: Sal_4h3


title: EX03_0h

value: control


title: EX02_0h

value: Micro-TOM-EX


title: WS_2h_1


title: Sal_4h1


title: EX01_0h


title: CT_rep1

source_name: PC3 non cancer stem cells (SORE6-)

value: PC3 non cancer stem cells (SORE6-)


title: Sal_0h3

value: warm-grown


title: CT_rep2


title: CK62_6h

source_name: Micro-TOM_drought stress for 6hrs

value: Micro-TOM

value: drought stress for 6hrs

value: leaf


title: Sal_0h1


title: Rif1^1/Rif1^2_OvarianFollicleCell_2C_Replicate1

city: Nashville

first: Jared

last: Nordman

state: Tennessee

address: 465 21st Ave South MRB III 4268

institute: Vanderbilt University

data_processing:
Reads from G1 and S samples were aligned to the dm6 reference genome (Release 6.04) using Bowtie 2 (v2.3.2) default parameters (Langmead et al. 2009).
Reads with a MAPQ score greater than 10 were retained using SAMtools (v1.9) (Li et al. 2009).
txtTools coverage (v2.26.0) was used to quantify the number of reads mapping to each 100kb window, with results normalized to read depth (Quinlan and Hall 2010).
Replication timing (RT) values were obtained by averaging the S/G1 ratio of reads per million (RPM) value from each S phase replicate for a particular window size. Profiles were generated by plotting the RT value at each window versus genomic location.
Quantile normalization was performed for comparisons between samples through the preprocess Core R package to equalize the dynamic range of RT values (Bolstad 2016).
The limma statistical package was used to identify 100kb windows with significantly altered RT values (lmFit, p value adjusted for multiple testing (p<0.01); absolute log2 fold change > 0.1) (Newville et al. 2014).
BEDTools intersect (v2.26.0) was used to determine overlap of 100kb windows with -f 0.5 and -u parameters (Quinlan and Hall 2010).
TopHat default parameters (v2.1.1) (Trapnell et al. 2012) were used to align single-end reads to the dm6 version of the Drosophila genome.
Transcriptomes were generated using Cufflinks (v2.2.1, see supplementary materials for parameters). We combined the Cufflinks generated transcriptome with transposons annotated by RepeatMasker (Smit et al. 2013-2015).
Differentially expressed transcripts were determined via edgeR statistical analysis (p value <0.01) (Robinson et al. 2010; McCarthy et al. 2012).
We assigned the RT log2 fold-change and associated limma-generated adjusted p-value determined at 10kb windows to individual transcripts; if a transcript overlapped multiple 10kb windows, we assigned the average RT log2 fold change and average adjusted p-value of all from all overlapping windows to that transcript.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: all_raw_avgRT_values.txt, bigWig files

organism: Drosophila melanogaster

source_name: Adult ovarian follicle cell

extract_protocol:
Follicle cells were isolated by trypsinizing ovaries from OregonR or Rif1^1/Rif1^2 adult females as described in (Cayirliogu et al., MCB 2003). Follicle cells were FACS sorted into TRIzol LS (Invitrogen) based on their ploidy and RNA was extracted according to the manufacturer’s recommendation. 250,000 – 500,000 follicle cells were used per replicate.
rRNA was depleted using the RiboMinus™ Eukaryote Kit for RNA-Seq (Invitrogen) and libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit.

tag: genotype/variation

value: Ovarian follicle cell

tag: Sex

value: Female

tag: developmental stage

value: Adult


title: CK63_6h


title: SK-OV-3_shCTL_3

type: RNA

city: Barcelona

first: Alfonso

last: Parrilla

address: Paseo Vall Hebron (VHIR)

country: Spain

institute: Vall Hebron Research Institute (VHIR)

description: SK-OV-3 cells transduced with shCTL lentiviral particle 48h. Replicate 3

hyb_protocol: Performed at UAT (VHIR)

scan_protocol: Performed at UAT (VHIR)

data_processing: Data was processed with Expression Console and Transcription Analysis Console (TAC)

label: biotin

label_protocol: Biotinylated

growth_protocol: SK-OV-3 cells were transduced for 48h with shCTL and shBora viruses

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (miRNeasy; Qiagen).

value: Human Ovarian Cancer Cell Line


title: SK-OV-3_shCTL_2

description: SK-OV-3 cells transduced with shCTL lentiviral particle 48h. Replicate 2


title: Sal_0h2

value: Salinas

value: 18 days

value: aerial tissue


title: Rif1^1/Rif1^2_OvarianFollicleCell_2C_Replicate2


title: SK-OV-3_shCTL_1

description: SK-OV-3 cells transduced with shCTL lentiviral particle 48h. Replicate 1


title: CK33_3h

source_name: Micro-TOM_drought stress for 3hrs

value: drought stress for 3hrs


title: SK-OV-3_shBora_2

description: SK-OV-3 cells transduced with shBora lentiviral particle 48h. Replicate 2


title: CSC_rep1

value: prostate cancer cell line PC3

value: PC3 cancer stem cells (SORE6+)


title: CK61_6h


title: ORR_OvarianFollicleCell_4C_Replicate1

value: ORR


title: ORR_OvarianFollicleCell_2C_Replicate2


title: CK32_3h


title: SK-OV-3_shBora_3

description: SK-OV-3 cells transduced with shBora lentiviral particle 48h. Replicate 3


title: SK-OV-3_shBora_1

description: SK-OV-3 cells transduced with shBora lentiviral particle 48h. Replicate 1


title: Mouse PAX8 2

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

institute: CABIMER

description: Gene expression data from murine pancreatic islets

hyb_protocol: Following fragmentation, 3.8 µg of single-stranded cDNA were hybridized for 16 hr at 45ºC on Clariom™ S Assay, Mouse chips. Chips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Command Console® 2.0 Technical Manual (Affymetrix).

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix AGCC software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis (ANOVA unpaired one-way) were performed using the TAC software (Transcriptome Analysis Console) developed by Affymetrix.

organism: Mus musculus

source_name: Mouse Pax8 +/- pancreatic islets

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 50ng total RNA Labeling Protocol (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression ArraysWT Pico Reagent Kit, ©2015 Affymetrix Inc.)

extract_protocol:
Islet preparations were washed, handpicked and processed for RNA exptraction.
Total RNA was extracted using the RNAeasy plus micro kit (Qiagen) following the instructions of the manufacturer.

value: Murine pancreatic islets


title: CK03_0h

value: control


title: CK31_3h


title: Mouse PAX8 3


title: WPMY-1-ASPN D14 variant overexpressing, biological rep3

city: Baltimore

first: Robert

middle: M

last: Hughes

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

description: Gene expression data from WPMY-1-ASPN D14 overexpressing cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip scanner 3000 with G7 upgrade (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

data_processing: All bioinformatics analyses were performed in R.  Dataset was normalized at a transcript level for core transcripts with the R/Bioconductor package oligo and annotated with the NetAffx Biological Annotations.  Artifacts from technical batches were removed with ComBat [64] implemented in the R/Bioconductor package SVA.  Differential expression analyses were performed on ComBat adjusted data using the R/Bioconductor package LIMMA.  Genes with FDR adjusted p-values below 0.05 and absolute log fold change greater than or equal to two were called statistically significant.  Exploratory pathway analysis was performed on WikiPathways using the Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) with an overrepresentation test based on genes that were called statistically significant from the LIMMA analysis.

source_name: WPMY-1 human benign prostate fibroblast cell line (ATCC) stably transfected as per Hurley et al. (PMID: 26446945)

label_protocol: biotin

growth_protocol: WPMY-1-ASPN variant overexpressing cells or WPMY-1-Neo control cells (stably transfected as per Hurley et al. PMID: 26446945) were cultured under normal growth conditions to 50-70% confluency prior to RNA isolation.  Three independent samples were assessed per experimental group

extract_protocol: RNA was isolated using the Qiagen RNeasy kit.

value: benign prostate fibroblast cells


title: ORR_OvarianFollicleCell_2C_Replicate1


title: Mouse PAX8 1


title: Yellow-white_WingDisc_RNA_resequence_Replicate3

source_name: female 3rd instar larval wing disc

extract_protocol:
Total RNA was isolated from 40 3rd instar wing imaginal discs. Wing imaginal discs were homogenized in Trizol (Invitrogen) and flash frozen in liquid nitrogen. RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research).
rRNA was depleted using the RiboMinus™ Eukaryote Kit for RNA-Seq (Invitrogen) and libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit.

value: Yellow-white

value: Wing disc

value: 3rd instar larvae


title: WPMY-1-ASPN D14 variant overexpressing, biological rep2


title: Mouse Control3

source_name: Mouse Control pancreatic islets

value: Control


title: WPMY-1-ASPN D13 variant overexpressing, biological rep1

description: Gene expression data from WPMY-1-ASPN D13 overexpressing cells


title: WPMY-1-ASPN D13 variant overexpressing, biological rep3


title: CK02_0h

value: Micro-TOM

value: leaf


title: Mouse Control2


title: WPMY-1-ASPN D14 variant overexpressing, biological rep1


title: ORR_OvarianFollicleCell_4C_Replicate2

value: Ovarian follicle cell

value: Female

value: Adult


title: WPMY-1-ASPN D13 variant overexpressing, biological rep2


title: Yellow-white_WingDisc_RNA_resequence_Replicate1


title: PP1_OvarianFollicle Cell_MS_Replicate1

description:
S phase DNA
processed data file: all_raw_avgRT_values.txt

library_source: genomic

molecule: genomic DNA

extract_protocol:
Adult female flies were fattened for 2 days on wet yeast and ~200 pairs of ovaries were dissected out by hand dissection. Tissue was disrupted by douncing and filtered over a 30 mM filter to collect follicle cell nuclei. DAPI-stained nuclei were sorted by 5-Laser FACS Aria III and G1 and S-phase populations were collected. Genomic DNA was fragmented by sonication and extracted by using a standard Phenol-Chloroform extraction protocol and precipitated with sodium acetate, glycogen, and isopropanol.
Libraries were prepared according to the protocol accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).

tag: phase

value: S phase


title: PP1_OvarianFollicle Cell_MS_Replicate2


title: WPMY-1-Neo control, biological rep3

description: Gene expression data from WPMY-1-Neo control cells


title: JMJ6-OE rep3

city: Guangzhou

first: Li

last: Zhiwei

address: No.723,Xingke Road

institute: South China Botanical Garden, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the tomato reference genome (version SL3.0) using HISAT2.2.4 with "-rna-strandness RF" and other parameters set as a default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

source_name: Ailsa Craig

growth_protocol: Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.

extract_protocol:
Pericarp tissues were collected, immediately frozen in liquid nitrogen, and total RNA was extracted using Trizol reagent kit. mRNA Seq Kit (Illumina) 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: At 37 days after anthesis (dpa)

value: Pericarp

value: transgenic line (JMJ6-OE)


title: Rif1nullCyo_OvarianFollicleCell_MS_Replicate1


title: Rif1nullCyo_OvarianFollicleCell_MS_Replicate2


title: M0-4_c-Maf_Ab

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Quality control using fastQC
Data filtering using BGI programs. Removed if: 1) The ratio of N in whole read was over 10% 2) unknown bases are more than 10% 3) The ratio of base whose quality was less than 20 was over 10%
Allignment to the mm10 reference genome was performed using SOAPaligner/SOAP2 (Version: 2.21t)
Peak calling was performed using MACS (Model-based Analysis for  ChIP -Seq, version: MACS-1.4.2) with the command line options -B -p 0.01.
Differential peaks were determined using the MACS2 bdgdiff command with command line options --d1 21370300 --d2 21370300 -c 2 -g 60 -l 120.
Genome_build: mm10
Supplementary_files_format_and_content: counts normalized bigWig files

source_name: In vitro polarized M2 BMM

extract_protocol:
Freshly prepared In vitro polarized M2 BMM were used for ChIP studies as described previously (Wang et al. 2011, Lung Cancer). In brief, cells were subjected to sonication using a sonicator (AFA Focused ultrasonicator S220) to obtain chromatin fragments of 100-500 bp. Fragmented chromatin was incubated with c-Maf Ab (LifeSpan BioSciences, Inc) or control normal rabbit IgG (Cell Signaling Technology) and incubated for crosslinking with the beads (Dynabeads Protein G, Invitrogen). After crosslinking, crosslinks were reversed (65C for 12-16 h), and precipitated DNA was treated with Proteinase K and then purified (QIAquick PCR purification kit, Qiagen).
(1) DNA-protein cross-linking by formaldehyde (2) Add Lysis Buffer to get whole cell lysate (3)  Lysate sonication (100-500bp) (4) Immunoprecipitation: Add primary antibody and beads to samples (5) Elution and reverse cross-links (6) Qpcr for Quality Crontrol (7)  DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor (8) PCR amplification and size selection (100-300bp including adaptor sequence)

value: In vitro polarized M2 BMM

tag: strain background


title: M0-4_Input


title: ORR_OvarianFollicleCell_ES_Replicate2

value: Oregon-R


title: WT rep3

value: wild type (WT)


title: ORR_OvarianFollicleCell_ES_Replicate1


title: Rif1null_OvarianFollicleCell_ES_Replicate2


title: M0-4_Iso


title: JMJ6-OE rep1


title: CK01_0h

value: control


title: Rif1null_OvarianFollicleCell_MS_Replicate2


title: Mouse Control1

value: Murine pancreatic islets


title: WT rep2


title: M0-3_Iso


title: M0-3_c-Maf_Ab


title: Rif1null_OvarianFollicleCell_MS_Replicate1


title: WT rep1


title: WPMY-1-Neo control, biological rep2

value: benign prostate fibroblast cells


title: WPMY-1-Neo control, biological rep1


title: Cerebrum_WT_02

status: Public on Apr 12 2020

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

data_processing:
Transcript abundances were calculated using Salmon 0.14.1
Differential gene expression analysis was performed using EdgeR 3.9
Genome_build: GRCm38 transcriptome build (Tol transcript sequence was added)
Supplementary_files_format_and_content: tsv files contain transcript abundances per gene (rows) for each sample from an organ. These were the input files for EdgeR.

molecule: polyA RNA

source_name: Cerebrum

extract_protocol:
RNA was extracted from the indicated frozen tissues using the RNeasy Mini Kit (Qiagen).
Whole transcriptome sequencing samples were prepared with the TruSeq Stranded mRNA Kit (Illumina)

tag: strain

value: WT

value: Cerebrum


title: Thymus_WT_04

source_name: Thymus

value: Thymus


title: Thymus_WT_03


title: Cerebellum_WT_02

source_name: Cerebellum

value: Cerebellum


title: Cerebellum_Tol_02

value: Tol


title: Thymus_WT_01


title: Cerebellum_WT_03


title: Cerebellum_WT_01


title: Cerebrum_WT_01


title: Cerebrum_WT_04


title: Cerebrum_Tol_04


title: Cerebrum_WT_03


title: Rif1null_OvarianFollicleCell_ES_Replicate1

value: Ovarian follicle cell

value: Female


title: Cerebrum_Tol_01


title: Thymus_WT_02


title: Thymus_Tol_04


title: Cerebellum_WT_04


title: Cerebrum_Tol_03


title: Thymus_Tol_02


title: Thymus_Tol_03


title: Thymus_Tol_01


title: Cerebellum_Tol_01


title: 14pre

city: Aarhus N

first: Jesper

last: Just

address: Palle Juul-Jensens boulevard 99

department: Clinical Medicine

country: Denmark

institute: Aarhus University

data_processing:
Trim galore was used to trim low-quality ends from raw reads in addition to adaptor removal (Babraham Bioinformatics). A Phred33 cut-off score of 20 was applied before adaptor trimming, and all sequences below 16 bp were subsequently removed
The clean reads were then analysed by the nc-PRO-seq pipeline using the standard settings (37). Shortly, the reads were aligned to the HG19 genome with Bowtie and overlaps between read alignments and genomic annotations (Rfam, RepeatMasker and miRbase) were investigated using BEDTools. Due to miRNA-end heterogeneity, miRNA annotations were extended 2 bases in both upstream and downstream regions
The raw miRNA counts were then normalised and tested for differential expression (DE) using the R Bioconductor package DESeq2, implementing a model design testing for differences between pre and post BFRE while correcting for inter-person variability (38). DE miRNAs were considered significant with an FDR adjusted p-value < 0.05, a log2 fold change > ±0.5 and a base mean count > 100.
Genome_build: hg19
Supplementary_files_format_and_content: csv file with the output from differential expression analysis in DESeq2

source_name: Pre BFRE_EV from plasma

growth_protocol: Blood samples were collected in EDTA vacuum tubes immediately before the BFRE bout and after 1 hour of post-exercise recovery. Plasma was isolated by centrifugation (1900g for 10 min, 5°C), aliquoted, and stored at −80°C. Before EV isolation, plasma was thawed at 4°C and centrifuged at 15,000g for 15 min at 4°C. EVs were purified by the miRCURY Exosome Isolation Kit – Serum and Plasma (Exiqon, Denmark) according to manufacturer’s instructions.

extract_protocol:
Total RNA from purified EVs was isolated using miRCURY RNA isolation kit - plasma and serum (Exiqon) and eluted in 100 µl RNase free water. To concentrate RNA, 10 µl 3M, pH 5.5 Sodium Acetate, 250 µl pre-chilled 99% ethanol and 1 µl Glycoblue (Ambion, MA, USA) were added and incubated at -20°C overnight. RNA was pelleted by centrifugation at 16,000g for 10 min at 4°C and re-suspended in 6 µl RNase free water
The small RNA library of EVs was constructed using Illumina TruSeq Small RNA Sample Prep Kit (Illumina, CA, USA) by adding 5 µl of total RNA as input. Due to lower RNA input compared to the standard protocol, the amount of adaptors was reduced to 1/10, the other reagents were reduced by half, and PCR cycles were increased from 12 to 15. The library was purified in the size range 140bp-160bp by Pippin Prep (Sage Science, MA, USA). The size and purity of the cDNA libraries were validated on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent, CA, USA) and the concentration was quantified using KAPA Library Quantification Kit (KAPA biosystems, Switzerland)
The libraries were pooled as required and sequenced on the Illumina Nextseq 500 instrument by Exiqon

treatment_protocol: The BFRE bout consisted of five sets of knee extensions to volitional failure with 30% of 1-RM under partial blood flow restriction, which was achieved by placing a 135 mm wide curved pneumatic cuff (VBM Medizintechnik, Germany) around the proximal part of the thigh and inflating it to a pressure of 100 mmHg (Digital Tourniquet 9000, VBM Medizintechnik)

tag: subject status

value: healthy volunteer

tag: condition

value: Pre Blood flow-restricted resistance exercise (BFRE)

tag: tissue/cell type

value: Extracellular Vesicles (EV) from plasma

tag: molecule subtype

value: small non-coding RNA


title: 15post

source_name: Post BFRE_EV from plasma

value: Post Blood flow-restricted resistance exercise (BFRE)


title: Cerebrum_Tol_02

tag: genotype

tag: tissue


title: 19post


title: 15pre


title: 14post


title: 12post


title: 6pre


title: 19pre


title: 12pre


title: 5post


title: 5pre


title: A549 cells, sci-fate

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: sci-fate library

data_processing:
For sc-RNA-seq processing, read alignment and gene count matrix generation for single cell RNA-seq was the same with sci-RNA-seq ("J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017).") with minor modifications: Reads were mapped to a chimeric reference genome of human (hg19) and mouse (mm10) for RNA-seq from A594, HEK293T and NIH/3T3 cells, and mouse (mm10) only for RNA-seq from mouse kidney experiment with STAR/v 2.5.2b, with gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse). The transcriptome barcode information for each cell or treatment conditions are listed in the cell annotation file of processed data. For mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated. Cells with over 80% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells or “collisions”.
The single cell sam files were first converted into alignment tsv file using sam2tsv function in jvarkit. Next, for each single cell alignment file, mutations matching the background SNPs were filtered out. For background SNP reference of A549 cells, we downloaded the paired-end bulk RNA-seq data for A549 cells from ENCODE (sampled name: ENCFF542FVG, ENCFF538ZTA, ENCFF214JEZ, ENCFF629LOL, ENCFF149CJD, ENCFF006WNO, ENCFF828WTU, ENCFF380VGD).  Each paired-end fastq files were first adaptor-clipped using trim_galore/0.4.1 with default settings, aligned to human hg19 genome build with STAR/v2.5.2b. Unmapped and multiple mapped reads were removed by  samtools/v1.3. Duplicated reads were filtered out by MarkDuplicates function in picard/1.105. De-duplicated reads from all samples were combined and sorted with samtools/v1.3. Background SNPs were called by mpileup function in samtools/v1.3 and mpileup2snp function in VarScan/2.3.9. For HEK293T and NIH/3T3 test experiment, background SNP reference was generated in a similar pipeline above, with the aggregated single cell sam data from control condition (no S4U labeling and no IAA treatment condition).   For each single cell alignment file, all mutations with quality score <= 13 were removed. Mutations at the both ends of each reads were mostly due to sequencing errors, and thus also were filtered out. For each read, we checked if there are T > C mutations for sense strand or A > G mutations for antisense strand, and labeled these mutated reads as newly synthesized.  Each cell was characterized by two digital gene expression matrixes from the full sequencing data and newly synthesized RNA data as described above.
Genome_build: human reference genome (hg19), mouse reference genome (mm10)
Supplementary_files_format_and_content: Processed data files are in txt format including a cell annotation file, gene annotation file, and a gene count sparse matrix for boh full sequencing data and newly synthesized RNA data
HEK293T_3T3_cell_annotate.txt: Cell annotation file for full transcriptome data: sample is cell id of each single cell with the reverse transcription barcode attached; exon_reads are number of UMIs mapping to exon region, intron_reads are number of UMIs mapping to intron region, all_reads are number of total UMIs, human_reads are number of UMIs mapping to human genome, mouse_reads are number of UMIs mapping to mouse genome, source are the human/mouse source of cells based on the ratio of human UMIs
HEK293T_3T3_gene_annotate.txt: Gene annotation file for full transcriptome data including gene id, gene typeand gene short name.
HEK293T_3T3_gene_count.txt: A sparse matrix file for full transcriptome data: each row corresponds to gene id (with gene information in the HEK293T_3T3_gene_annotate.txt; each column corresponds to each cell (with cell source information in the HEK293T_3T3_cell_annotate.txt); each value in the matrix corresponds to UMI count.
HEK293T_3T3_cell_annotate_newly_synthesised.txt: Cell annotation file for newly synthesized transcriptome data: sample is cell id of each single cell with the reverse transcription barcode attached; exon_reads are number of UMIs mapping to exon region, intron_reads are number of UMIs mapping to intron region, all_reads are number of total UMIs.
HEK293T_3T3_gene_annotate_newly_synthesised.txt: Gene annotation file for newly synthesized transcriptome data including gene id, gene typeand gene short name.
HEK293T_3T3_gene_count_newly_synthesised.txt: A sparse matrix file for newly synthesized transcriptome data: each row corresponds to gene id (with gene information in the HEK293T_3T3_gene_annotate_newly_synthesised.txt; each column corresponds to each cell (with cell source information in the HEK293T_3T3_cell_annotate_newly_synthesised.txt); each value in the matrix corresponds to UMI count.
A549_cell_annotate.txt: Cell annotation file for full transcriptome data: sample is cell id of each single cell with the reverse transcription barcode attached; all_exon are number of UMIs mapping to exon region, all_intron are number of UMIs mapping to intron region, all_reads are number of total UMIs, treatment_time is the DEX treatment time, and doublet_score is the doublet score calculated per cell from the doublet analysis.
A549_gene_annotate.txt: Gene annotation file for full transcriptome data including gene id, gene typeand gene short name.
A549_gene_count.txt: A sparse matrix file for full transcriptome data: each row corresponds to gene id (with gene information in the A549_gene_annotate.txt; each column corresponds to each cell (with cell source information in the A549_cell_annotate.txt); each value in the matrix corresponds to UMI count.
A549_cell_annotate_newly_synthesised.txt: Cell annotation file for newly synthesized transcriptome data: sample is cell id of each single cell with the reverse transcription barcode attached; all_exon are number of UMIs mapping to exon region, all_intron are number of UMIs mapping to intron region, all_reads are number of total UMIs, treatment_time is the DEX treatment time, and doublet_score is the doublet score calculated per cell from the doublet analysis.
A549_gene_annotate_newly_synthesised.txt: Gene annotation file for newly synthesized transcriptome data including gene id, gene typeand gene short name.
A549_gene_count_newly_synthesised.txt: A sparse matrix file for newly synthesized transcriptome data: each row corresponds to gene id (with gene information in the A549_gene_annotate_newly_synthesised.txt; each column corresponds to each cell (with cell source information in the A549_cell_annotate_newly_synthesised.txt); each value in the matrix corresponds to UMI count.

source_name: cell line

growth_protocol: All mammalian cells were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) for HEK293T and NIH/3T3 cells or DMEM/F12 medium for A549 cells, both supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin). Cells were trypsinized with 0.25% typsin-EDTA (Gibco cat. no. 25200-056) and split 1:10 three times a week.

extract_protocol:
All cell lines (A549, HEK293T and NIH/3T3 cells) were trypsinized, spun down at 300xg for 5 min (4°C) and washed once in 1X ice-cold PBS. All cells were fixed with 4ml ice cold 4% paraformaldehyde (EMS) for 15 min on ice. After fixation, cells were pelleted at 500xg for 3 min (4°C) and washed once with 1ml PBSR (1 x PBS, pH 7.4, 1% BSA, 1% SuperRnaseIn, 1% 10mM DTT). After wash, cells were resuspended in PBSR at 10 million cells per ml, and flash frozen and stored in liquid nitrogen.
Paraformaldehyde fixed cells were thawed on 37°C water bath, spun down at 500xg for 5 min, and incubated with 500ul PBSR including 0.2% Triton X-100 for 3min on ice. Cells were pelleted and resuspended in 500ul nuclease free water including 1% SuperRnaseIn. 3ml 0.1N HCl were added into the cells for 5min incubation on ice. 3.5ml Tris-HCl (pH = 8.0) and 35ul 10% Triton X-100 were added into cells to neutralize HCl. Cells were pelleted and washed with 1ml PBSR. Cells were resuspended in 100ul PBSR. 100ul PBSR with fixed cells were incubated with mixture including 40ul Iodoacetamide (IAA, 100mM), 40ul sodium phosphate buffer (500mM, pH = 8.0), 200ul DMSO and 20ul H2O, at 50°C for 15min. The reaction was quenched by 8ul DTT (1M) and 8.5ml PBS. Cells were pelleted and resuspended in 100ul PBSI (1 x PBS, pH 7.4, 1% BSA, 1% SuperRnaseIn). For all later washes, nuclei were pelleted by centrifugation at 500xg for 5 min (4°C).   The following steps are similar with sci-RNA-seq protocol with paraformaldehyde fixed nuclei. Briefly, cells were distributed into four 96-well plates. For each well, 5,000 nuclei (2 µL) were mixed with 1 µl of 25 µM anchored oligo-dT primer (5′-ACGACGCTCTTCCGATCTNNNNNNNN[10bp index]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3′, where “N” is any base and “V” is either “A”, “C” or “G”; IDT) and 0.25 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 1.75 µL of first-strand reaction mix, containing 1 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 0.25 µl 100 mM DTT (Invitrogen), 0.25 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 0.25 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well. Reverse transcription was carried out by incubating plates at the following temperature gradient: 4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes. All cells (or nuclei) were then pooled, stained with 4',6-diamidino-2-phenylindole (DAPI, Invitrogen) at a final concentration of 3 μM, and sorted at 25 nuclei per well into 5 μL EB buffer. Cells were gated based on DAPI stain such that singlets were discriminated from doublets and sorted into each well. 0.66 μl mRNA Second Strand Synthesis buffer (NEB) and 0.34 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min. Each well was then mixed with 5 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enzyme (25 nM, Illumina, diluted in Nextera TD buffer), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was stopped by adding 12 μL DNA binding buffer (Zymo) and incubating at room temperature for 5 min. Each well was then purified using 36 uL AMPure XP beads (Beckman Coulter), eluted in 16 μL of buffer EB (Qiagen), then transferred to a fresh multi-well plate.  For PCR reactions, each well was mixed with 2μL of 10 μM P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′; IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 18-22 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min. After PCR, samples were pooled and purified using 0.8 volumes of AMPure XP beads. Library concentrations were determined by Qubit (Invitrogen) and the libraries were visualized by electrophoresis on a 6% TBE-PAGE gel. Libraries were sequenced on the NextSeq 500 platform (Illumina) using a V2 150 cycle kit (Read 1: 18 cycles, Read 2: 130 cycles, Index 1: 10 cycles, Index 2: 10 cycles).

treatment_protocol: A549 cells were treated with 100 nM DEX for 0h, 2h, 4h, 6h, 8h and 10h before harvest. Control cells were treated with same volume of EtOH. Cells in all treatment conditions were incubated with 200uM S4U for the last two hours before cell harvest. For HEK293T and NIH/3T3 cells, cells were incubated with 200uM S4U for 6 hours before cell harvest.

value: 101 nM DEX for 0h, 2h, 4h, 6h, 8h and 10h before harvest


title: Morphine-HTO

city: Boston

first: Christine

last: Cheng

state: Massachusetts

address: 24 Cummington Mall

institute: Boston University

description:
10x Genomics single cell 3' v2
Read 1 contains the cell barcodes while Read 2 contains the antibody/sample barcode.

data_processing:
Each sequencing library was demultiplexed based on the sample index read and HTO barcode to generate FASTQ files for the RNA and HTO pair-end reads using Cell Ranger version 2.1.
Gene-cell barcode matrices for RNA count data were generated using 10X genomics Cell Ranger 2.1
HTO count data were generated using Cite-seq-Count with reference HTO list
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file for 10X RNA-UMI count data; comma-delimited file for HTO count data

source_name: Peripheral blood mononuclear cells

extract_protocol:
15 mL of fresh whole blood from healthy donors (Research Blood Components, Boston MA) was diluted 1:1 with warm PBS +2% FBS, mixed, and gently layered atop 30mL Ficoll-Paque density gradient medium (GE Healthcare, Ficoll Paque PLUS, Cat# 17-1440) in 50mL conical tubes. This process was repeated 7 times in processing 100mL of blood. Tubes were centrifuged for 20 min at 1200xg to separate leukocytes from red blood cells and plasma. The leukocyte-containing buffy coat was carefully transferred into new tubes, washed with warm PBS +2% FBS, counted, resuspended in DMSO and aliquoted. Isolated cells were then stored in liquid nitrogen until later experimental use.
scRNA-seq libraries were prepared following Chromium Single Cell 3’ scRNA-seq method. Additional primers were included in the cDNA amplification step to account for the TotalSeq oligonucleotide tags. During the post-amplification cleanup, supernatant containing amplified TotalSeq tags was collected and processed parallel to the standard 10X library fraction.
10x Genomics single cell 3' v2

treatment_protocol: 400K cells per condition were revived, plated into non-tissue-culture-treated 96 well plates, and either mock treated or treated with morphine sulfate (100uM) alone for 24 hours. At the end of the incubation period cells were again treated either with medium or LPS for 3 hours, after which they were collected, washed, and each sample was “hashed” using unique oligonucleotide-barcoded antibodies to track the cells’ well/condition of origin. Samples were then normalized to 1000 cells/uL, mixed in equal measure (20uL each), and used to perform the Chromium Single Cell 3’ scRNA-seq method as described previously. Additional primers were included in the cDNA amplification step to account for the TotalSeq oligonucleotide tags. During the post-amplification cleanup, supernatant containing amplified TotalSeq tags was collected and processed parallel to the standard 10X library fraction.

value: Peripheral blood mononuclear cells

tag: antibodies/tags

value: Mock, +Morphine,Mock+LPS, +Mor+LPS


title: 6post


title: Morphine-RNA-UMI

description:
10x Genomics single cell 3' v2
Read 1 includes the cell barcode while Read 2 contains the cDNA fragment.


title: CLP3

first: Sheng

address: 660 W Redwood Street, Howard Hall 564

department: Anesthesiology

institute: University of Maryland Baltimore

description:
24 hours post-surgery
SV18278_0009_S9_R1_001.fastq

data_processing:
exceRpt small RNA-seq Pipeline (v4.6.2) was used for small RNA-seq data analysis
Genome_build: miRBase version 21 and mm10
Supplementary_files_format_and_content: TXT file includes miRNA read counts for each sample

source_name: plasma

extract_protocol:
Platelet-free plasma was prepared from whole blood by centrifugation (1000xg at 4°C from 10 min, followed by 10000xg at 4°C from 10 min). Total RNA was extracted from 100 ul plasma using the Trizol LS reagent (Life Technologies).
cDNA libraries were prepared from 100ng plasma RNA using Small RNA library prep kit by Norgen Biotek Corp (Thorold, Canada), following manufacturer instructions, including 3' and 5' adapter ligation, followed by reverse transcription and then the indexing PCR. The target band is then excised from PAGE gel and purified.Library QC is performed on the purified sample bands to estimate library size and concentration using Bioanalyzer/qPCR. Samples are then pooled in equimolar ratios before starting the NGS run.

tag: gender

value: male

tag: surgery

value: cecal ligation and puncture (CLP)

value: wild type


title: CLP7

description:
24 hours post-surgery
SV18278_0013_S13_R1_001.fastq


title: Sham5

description:
24 hours post-surgery
SV18278_0005_S5_R1_001.fastq

value: Sham


title: Sham6

description:
24 hours post-surgery
SV18278_0006_S6_R1_001.fastq


title: CLP9

description:
24 hours post-surgery
SV18278_0015_S15_R1_001.fastq


title: CLP8

description:
24 hours post-surgery
SV18278_0014_S14_R1_001.fastq


title: CLP6

description:
24 hours post-surgery
SV18278_0012_S12_R1_001.fastq


title: CLP4

description:
24 hours post-surgery
SV18278_0010_S10_R1_001.fastq


title: Sham4

description:
24 hours post-surgery
SV18278_0004_S4_R1_001.fastq


title: CLP2

description:
24 hours post-surgery
SV18278_0008_S8_R1_001.fastq


title: CLP1

description:
24 hours post-surgery
SV18278_0007_S7_R1_001.fastq


title: CLP5

description:
24 hours post-surgery
SV18278_0011_S11_R1_001.fastq


title: Sham3

description:
24 hours post-surgery
SV18278_0003_S3_R1_001.fastq


title: Sham2

description:
24 hours post-surgery
SV18278_0002_S2_R1_001.fastq


title: Sham1

description:
24 hours post-surgery
SV18278_0001_S1_R1_001.fastq


title: N+Fe_T24_id_60969

city: Santa Cruz

first: Jonathan

middle: David

last: Magasin

state: CA

address: 1156 High Street

department: Ocean Sciences

institute: UC Santa Cruz

description:
N shorthand for nitrate
environmental sample

hyb_protocol: Provisional:  Cy3-labeled cDNA was hybridized at the Roy J. Carver Center for Genomics (The University of Iowa, USA) using a Gene Expression Hybridization Kit (Cat# 5188‐5242) and following a protocol based on One-Color Microarray-Based Gene Expression Analysis: Low Input Quick Amp Labeling [Version 6.7, September 2014].  From each Cy3-labeled sample, a volume equivalent to 3.0 ug of target DNA was taken and added to water to a total volume of 44.00 ul.  To each sample was added 66.0 ul of hybridization master mix (10x GE blocking agent [11.0 ul], 2x Hi-RPM Hyb Buffer [55.0 ul]) for a total volume of 110 ul.  The sample was mixed, then incubated at 95 degrees Celsius for 3 min, then placed on ice, and then briefly centrifuged. From each sample 100 ul was taken and loaded onto a MicroTOOLs microarray (4 arrays per slide).  Arrays were hybridized at 65 degrees Celsius and for ~18 hours. After hybridization, arrays were washed using the Gene Expression Wash Buffer (Cat# 5188‐5327).

scan_protocol: Microarrays were scanned at the Roy J. Carver Center for Genomics at the University of Iowa using an Agilent SureScan Microarray Scanner G2600D (Serial #: SG13134301) and using the Agilent scanning protocol GE1_1200_Jun14 (Feature Extractor software version 11.5.1.1).

data_processing: All microarray analyses were done using the MicroTOOLs R package (ver. 1.1; available at https://www.jzehrlab.com). The transcription values for each gene were obtained by robust multi-array averaging of hybridization values for all probes and quantile normalization across all samples.  Additional data processing steps were performed for gene detection and determination of differentially expressed genes and gene sets (described in our publication), but those steps do not affect the values in the sample matrices.

organism: uncultured marine microorganism

source_name: CCS Stn. 38 surface water (25 m)

label_protocol: Provisional:  cDNA was labeled at the Roy J. Carver Center for Genomics (The University of Iowa, USA) using the Agilent SureTag DNA Labeling Kit (Cat# 5190-3400) and by following a protocol based on Agilent Oligonucleotide Array‐Based CGH for Genomic DNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues [Version 7.3 March 2014].  For each sample the following steps were performed.  0.5 ug of cDNA was diluted to 19.2 ng/ul [26.0 ul total].  The diluted cDNA was then denatured and annealed with random primers: cDNA was combined with 5.0 ul of random primers and the resulting 31.0 ul sample was incubated at 95 degrees Celsius for 5 min, then immediately placed on ice for 5 min, and then centrifuged at 6kxg for 1 min.  19.0 ug of labeled master mix was prepared (5x reaction [10.0 ul], 10x dNTP [5.0 ul]; cyanine [3.0 ul]; Exo-Klenow [1.0 ul]) and then pipetted into the sample.  The sample was briefly centrifuged, then incubated at 37 degrees Celsius for 2 hrs and at 65 degrees Celsius for 10 minutes, and then transferred on ice (and possibly stored overnight at -20 Celsius).  Labeled cDNA was then cleaned using the Agilent SureTag DNA Labeling Kit, which included purification columns.  A Nanodrop spectrophotometer was used to check that the yield and specific activity of Cy3 were within expected ranges.

growth_protocol: Environmental samples were collected during the Nitrogen Effects on Marine microOrganisms (NEMO) Cruise NH1417 in  2014. Seawater collected from 25 m depth at Stn. 38 on 24 August was used in on-deck perturbation experiments with different nitrogen substrates (nitrate, ammonium, urea, iron, nitrate with iron, and also with filtered deep water collected from 600 m depth).  Experimental bottles were incubated on deck for 48 h, with RNA collected at 24 h for all treatments and also at the start of the incubation for controls (no substrate added). Experimental setup and physiological responses to added nutrients observed at 48 h are described in detail in Shilova et al. 2017.

extract_protocol: Total RNA was extracted from environmental samples using DirectZol (Zymo Research). DNA was removed in a solution using RNase-Free DNase Kit (Qiagen), and RNA was purified again with RNA Clean & Concentrator™-25 (Zymo Research)  according to the manufacturer’s protocol.  The RNA quality and quantity were evaluated using the Agilent BioAnalyzer RNA Nano Kit and Qiagen Qubit. All samples with an RNA Integrity Number greater than 9 were processed for microarray analyses as described in Shilova et al., 2014.

treatment_protocol: After 24 h incubation with N and Fe substrates, 2 L of seawater from each incubation were collected before sunrise and filtered onto 0.2 µm Supor membrane filters (Pall Corp., Ann Arbor, Michigan, U.S.A.) using peristaltic pumps. Filters were flash frozen in liquid nitrogen immediately after filtering and stored at -80°C until processing in the lab.

tag: category

value: treated sample

tag: treatment

value: N+Fe


title: Liver_batch2_obesity+fucoidan_HBx,src,p53-_replicate 1

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: #35 Keyan Road

country: Taiwan

institute: National Health Research Institutes

description:
Gene expression data from adult HBx,src,p53-/+  zebrafish, diet-induced obesity oral gavage with OF, sample 1
HBx,src,p53-_DIO+OF-2

hyb_protocol: An automated Hyb-Wash-Scan workflow with ZebGene1.1ST Array Plate was performed with the GeneTitan™ Multi-Channel (MC) Instrument (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 702933 Rev. 2).

scan_protocol: Hybridized arrays were washed and the signal intensity of the chip was scanned using a "High Throughput Array Scanner" .

data_processing: Data analysis was performed by Transcriptome Analysis Console (TAC) Software 4.0 (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703150 Rev. 6).

organism: Danio rerio

label_protocol: Target cRNA and ss-cDNA samples were prepared stepwise from 100 ng of total RNA diluted into 3 ul of volume using GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, US) according to the manufacturer manual (P/N 703147 Rev. 3). The resulting purified ss-cDNA samples were fragmented and labelled with terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin (Thermo Fisher Scientific, US).

growth_protocol: The HBx,Src and HBx,Src,p53–/+ transgenic zebrafish (Danio rerio) were used and growth for 6 months.

extract_protocol: Total RNA was isolated by NucleoSpin® RNA kit (MACHEREY-NAGEL, US) following the manufacturer manual, and RNA samples was eluted in 40 μl RNase-free water. RNA quantity and purity were assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7.

treatment_protocol: Three-month-old female HBx,Src and HBx,Src,p53–/+ transgenic zebrafish were allocated to 2 different diets: normal diet (NOR) and diet-induced obesity (DIO). The amount of Artemia fed to the NOR and DIO groups was approximately 6.9 mg and 83 mg cysts/fish/day respectively. OF (300 mg/kg) was administrated by oral gavage for one month starting at 4 months of age, totally 2 months dietary induction.The fish were sacrificed and the hepatic tissue was immediately frozen in liquid nitrogen and stored at −80 °C for later RNA extraction and hybridization on Affymetrix microarrays.

value: Liver

tag: feeding

value: diet-induced obesity (DIO)

value: oral gavage with OF (300 mg/kg) thrice a week for one month

tag: age

value: 6 months


title: Liver_batch2_obesity_HBx,src,p53-_replicate 3

description:
Gene expression data from adult HBx,src,p53-/+  zebrafish diet-induced obesity, sample 3
HBx,src,p53-_DIO-3

value: no treatment (mock)


title: NO3_T24_id_60956

description: environmental sample


title: Liver_batch2_obesity+fucoidan_HBx,src,p53-_replicate 2

description:
Gene expression data from adult HBx,src,p53-/+  zebrafish, diet-induced obesity oral gavage with OF, sample 2
HBx,src,p53-_DIO+OF-3


title: Liver_batch1_obesity_HBx,src_replicate 1

description:
Gene expression data from adult HBx,src zebrafish diet-induced obesity, sample 1
HBx,src_DIO-1

value: HBx,src


title: Liver_batch1_obesity+fucoidan_HBx,src_replicate 1

description:
Gene expression data from adult HBx,src zebrafish, diet-induced obesity oral gavage with OF, sample 1
HBx,src_DIO+OF-1


title: N+Fe_T24_id_60968


title: Liver_batch2_obesity+fucoidan_HBx,src,p53-_replicate 3

description:
Gene expression data from adult HBx,src,p53-/+  zebrafish, diet-induced obesity oral gavage with OF, sample 3
HBx,src,p53-_DIO+OF-6


title: FDW_T24_id_60962

description:
FDW = 600 m filtered sea water
environmental sample

value: FDW


title: Liver_batch2_control_HBx,src,p53-_replicate 2

description:
Gene expression data from adult HBx,src,p53-/+ zebrafish normal diet, sample 2
HBx,src,p53-_NOR-2

value: normal diet (NOR)


title: NH4_T24_id_60954

description: environmental sample


title: JMJ6-OE rep2

tag: developmental stage

value: At 37 days after anthesis (dpa)

value: Pericarp

value: transgenic line (JMJ6-OE)


title: Liver_batch1_obesity_HBx,src_replicate 2

description:
Gene expression data from adult HBx,src zebrafish diet-induced obesity, sample 2
HBx,src_DIO-2


title: Liver_batch1_obesity+fucoidan_HBx,src_replicate 2

description:
Gene expression data from adult HBx,src zebrafish, diet-induced obesity oral gavage with OF, sample 2
HBx,src_DIO+OF-7


title: Liver_batch2_control_HBx,src,p53-_replicate 1

description:
Gene expression data from adult HBx,src,p53-/+ zebrafish normal diet, sample 1
HBx,src,p53-_NOR-1


title: Liver_batch1_obesity_HBx,src_replicate 3

description:
Gene expression data from adult HBx,src zebrafish diet-induced obesity, sample 3
HBx,src_DIO-4


title: HEK293T, NIH/3T3, sci-fate

description: sci-fate library

organism:
Homo sapiens
Mus musculus

tag: cell line

value: HEK293T, NIH/3T3

value: 100 nM DEX for 0h, 2h, 4h, 6h, 8h and 10h before harvest


title: Post_noPhage_rep3

city: Los Angeles

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Sequencing genomic DNA barcodes. Library of Phaeobacter inhibens transposon insertion mutants were incubated with and without Phaeobacter phage MD18.
P.i_fitness_scores.txt.gz

data_processing:
Library strategy: Bar-Seq
Counts for each barcoded transposon insertion mutant were determined in Unix as follows:  20 bp barcode sequences were extracted from each sample and these extracted barcode reads were sorted before counting the number of counts of each barcode. Counts were normalized as a proportion of total reads per sample and all samples were aggregated together in R. Finally, P. inhibens fitness scores were calculated in R by assigning barcodes to the gene they were inserted into and, for each gene, determining the relative abundance of each barcode before and after challenge by bacteriophage compared to the relative abundance without bacteriophage. Results stored in file: P.i_fitness_scores.txt.gz.
Genome_build: P. inhibens DSM 17395 genome (Genbank no. CP002976.1)
Supplementary_files_format_and_content: P.i_fitness_scores.txt:  "gene" (Gene in P. inhibens); "start" (Initial genome coordinate of gene); "end"(Initial genome coordinate of gene); "num_knockouts"  (Number of transposon insertion mutants overlapping gene; "pre_ave"(Sum of all barcode counts before treatment); "post_0_ave"(Sum of all barcode counts after NO PHAGE treatment); "post_2_ave"(Sum of all barcode counts after PHAGE treatment); "post_0_fitness" (Change in barcode frequencies after growth with no phage); "post_2_fitness" (Change in barcode frequencies after growth with phage);  "overall_fitness" (log2 ratio of post_2_fitness to post_0_fitness); "desc(empty column to fill with gene description).
*_BarcodeCounts.txt:  "counts" (normalized barcode read counts in sample); "Barcode" (Barcode Sequence).

organism: Phaeobacter inhibens

source_name: Phaeobacter inhibens

extract_protocol:
Genomic DNA from all samples was harvested using a Promega Maxwell RSC PureFood GMO and Authentication Kit
Sequencing libraries were constructed using a two-step PCR. The first PCR amplifies barcoded transposon sequences from the genomic insertion sites and the second PCR adds Illumina sequencing primer sites and flow cell adapter sequences.

tag: growth medium

value: Marine Broth

value: incubated without Phaeobacter phage MD18

tag: Stage


title: Post_Phage_rep3

tag: strain

value: incubated with Phaeobacter phage MD18


title: Liver_batch1_control_HBx,src_replicate 3

description:
Gene expression data from adult HBx,src zebrafish normal diet, sample 3
HBx,src_NOR-4


title: Liver_batch1_control_HBx,src_replicate 2

description:
Gene expression data from adult HBx,src zebrafish normal diet, sample 2
HBx,src_NOR-3


title: Pre_growth_rep3


title: FDW_T24_id_60963

value: treated sample


title: Post_noPhage_rep1


title: N+Fe_T24_id_60967

value: N+Fe


title: Fe_T24_id_60966

description:
Fe shorthand for Fe3+
environmental sample

value: Fe


title: Liver_batch1_control_HBx,src_replicate 1

description:
Gene expression data from adult HBx,src zebrafish normal diet, sample 1
HBx,src_NOR-2

value: Liver


title: NH4_T24_id_60952

description: environmental sample


title: Urea_T24_id_60959

description: environmental sample

value: Urea


title: FDW_T24_id_60961


title: NO3_T24_id_60957

description: environmental sample


title: Fe_T24_id_60965


title: NO3_T24_id_60955

description: environmental sample


title: Urea_T24_id_60958

description: environmental sample


title: Urea_T24_id_60960

description: environmental sample


title: NT siRNA CB2 Nov

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: NT siRNA 2

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: NT siRNA CD34+ cells

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments.  Briefly, biotinylated cRNA were prepared according to the standard GeneChip® 3' IVT PLUS Reagent Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza) as previously reported (Norfo R. Blood 2014). Briefly, starting from the day after CD34+ cell purification, each sample was electroporated three times, once every 24 hours, with a small interfering RNA (siRNA) targeting human CALR mRNAs (Life Technologies, siRNA ID s115). For each electroporation, 4×105 CD34+ cells were resuspended in 100 μL of P3 Primary Cell Solution (Lonza), containing 3 μg of siRNA, and pulsed with the program DS112. To exclude non-specific effects caused by interfering RNA (RNAi) nucleofection, a sample transfected with a nontargeting siRNA (NTsiRNA; Life Technologies) was included.

value: Cord Blood

tag: cell type

value: CD34+ cells

tag: treated with

value: non-targeting (NT) siRNA


title: Post_Phage_rep1


title: NR8383_4h_2 µg/mL_of_NPZnO_rep3

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

description: Gene expression in NR8383 cells after 4 h in presence of NP-ZnO exposure (2 µg/mL)

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA were fragmented at 60°C for 30 min in a reaction volume of 25 µL following the manufacturer’s instructions. 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Rat GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent).

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 074036_D_F_20150914 ) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

organism: Rattus norvegicus

source_name: NR8383, 4 h, 2 µg/mL of NP-ZnO, replicate 3

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: NR8383 cell line provides a homogenous source of alveolar macarophages, they were established from normal rat by lung lavage and was obtained from American Type Culture Collection (ATCC® CRL-2192™, Manassas, VA, USA). Cells, with a 50% adherent and 50% floating cell phenotype, were grown in DMEM medium supplemented with 15 % of heat-inactivated fetal bovine serum, 2mM L-glutamine, as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma Aldrich). Cells were incubated at 37°C in an atmosphere composed of 95 % air, 5 % CO2 and medium are changed every 2-3 days.

extract_protocol: The quality of the RNA extracted by RNA-Solv Reagent (Omega Bio-tek, USA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 7.5, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: Cell were seeded in Petri dishes at a density of 3 x 10^5 cells / mL. Cells were then incubated without (control) or with zinc oxide nanoparticles (2 µg/mL) for 4 h in absence of fetal bovine serum.

value: lung

value: macrophages


title: Liver_batch2_obesity_HBx,src,p53-_replicate 2

description:
Gene expression data from adult HBx,src,p53-/+  zebrafish diet-induced obesity, sample 2
HBx,src,p53-_DIO-2

value: diet-induced obesity (DIO)

value: no treatment (mock)

value: 6 months


title: Liver_batch2_obesity_HBx,src,p53-_replicate 1

description:
Gene expression data from adult HBx,src,p53-/+  zebrafish diet-induced obesity, sample 1
HBx,src,p53-_DIO-1


title: Fe_T24_id_60964


title: Pre_growth_rep1


title: NTsiRNA CB1 Nov

description: NT siRNA 1


title: Post_Phage_rep2


title: CALR siRNA CB2 Nov

description: siRNA CALR 2

source_name: CALR siRNA CD34+ cells

value: CALR siRNA


title: Total_H3_ChIP-seq_DIPG7_with_WT_H3_3_overexpression_untreated

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The quality of fastq files was accessed using FastQC
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads
The ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (v. 2.3.2).
Samtools (v. 1.5) was used to convert the sam files into bam files, to filter out unmapped reads and to sort the bam files.
When the total number of reads per sample was inferior to 40M, the libraries were re-sequenced and the additional bam files generated from the second sequencing were merged with the bam files from the first sequencing.
The total number of reads used for peak calling was normalized using samtools view -hs (random extraction of a specified percentage of reads). The same number of reads was used for the RNA polymerase II ChIP-seq and for the inputs.
Samtools sort was used to sort the bam files after read extraction.
Bam files were indexed using samtools index.
Bedtools genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files from the bedgraph files.
Peaks were called using macs2 (v. 2.1.1.20160309) with default parameters using python (v. 2.7.14).
Peak locations were further annotated using the ChIPseeker R package.
For pausing indices, the promoter region was defined as -200 bp upstream to +400 bp downstream and the body region was the remainder of the entire gene body.
The average coverage of each promoter and each gene body was calculated with the valr R package using the bed_coverage function.
ECDF plots were made in R version 3.5.0 using the ecdf function.
Genome_build: hg38
Supplementary_files_format_and_content: The tdf files were generated with igvtools toTDF.

source_name: diffuse intrinsic pontine glioma

growth_protocol: DIPG7 cells were cultured in tumor stem media (TSM) consisting of Neurobasal(-A) (Invitrogen), B27(-A) (Invitrogen), human-basic FGF (20 ng/mL; Shenandoah Biotech), human-EGF (20 ng/mL; Shenandoah Biotech), human PDGF-AB (20 ng/mL; Shenandoah Biotech), heparin (10 ng/mL) and with 10% fetal bovine serum (FBS)(Atlanta Biologicals).

extract_protocol:
The growth medium was aspirated from cells (70% confluence) and replaced with a 1% formaldehyde in 1X DPBS for 9 min at room temperature. The cross-linking was terminated by addition of glycine to a final concentration of 0.125 M and incubation for 5 min. The cells were washed twice with cold PBS and scraped in ChIP lysis buffer (1% SDS, 10 mM EDTA and 50 mM Tris-HCl pH 8.1) containing COmplete EDTA free protease inhibitors (Sigma). The cell lysates were sonicated with a Bioruptor Plus (Diagenode) for 25 cycles (30 seconds ON and 30 seconds OFF). The size of the sonicated DNA fragments was checked on an 1X TAE1 % agarose gel electrophoresis and ranged between 250 to 500 bp. After removing the debris via centrifugation, chromatin extracts were collected and protein concentration was determined by BCA protein assay reagents (Pierce).  For immunoprecipitation, chromatin extracts with 1 mg of total protein for each sample were incubated with primary antibodies (dilution 1:50) overnight at 4ºC. Primary antibodies used are included in table under “Western blotting” below. After incubation with the primary antibody, 20 uL of pre-washed magnetic beads (Magna ChIP Protein A+G Magnetic Beads, Millipore Sigma) were added to each sample for 2 hours at 4ºC. Using a magnetic rack, the immunoprecipitates were washed successively with 1 ml of low salt buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), high salt buffer (20 mM Tris-HCl [pH 8.0], 500 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), LiCl washing buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, , 1.0% NP40, 1.0% deoxycholate, 1 mM EDTA) and twice with TE buffer. The DNA-protein complexes were eluted with 300 μl of IP elution buffer (1% SDS, 0.1 M NaHCO3). The eluents were pooled together and the cross-links were reversed by adding NaCl (a final concentration 0.2 M) into the eluents and incubating them at 65 ºC overnight. The DNAs were recovered by proteinase K and RNase A digestion, followed by phenol/chloroform extraction and ethanol precipitation. Pellets were resuspended in 50 μl of 10 mM Tris-HCl [pH 8.0]. ChIP-DNA was quantified using the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific).
Libraries were prepared according to Nugen's instructions accompanying their Ovation Ultralow System V2 kit.

treatment_protocol: The small molecule inhibitor atuveciclib (BAY-1143572) was obtained from MedChemExpress. It was dissolved in DMSO per vendor instructions to make stock concentrations for use in in vitro experiments.

value: DIPG7 cells

value: with WT H3.3 overexpression

value: untreated

tag: passages

tag: chip antibody

value: Histone H3 antibody rabbit pAb - Abcam (ab1791)


title: Post_noPhage_rep2

value: Marine Broth

value: incubated without Phaeobacter phage MD18


title: Control_T24_id_60951

description: environmental sample

value: control sample


title: Control_T24_id_60950

description: environmental sample


title: Control_T24_id_60949

description: environmental sample


title: NR8383_4h_0 µg/mL_of_NPZnO_rep3

description: Gene expression in NR8383 cells after 4 h in absence of NP-ZnO exposure (0 µg/mL)

source_name: NR8383, 4 h, 0 µg/mL of NP-ZnO, replicate 3

tag: tissue


title: NR8383_4h_0 µg/mL_of_NPZnO_rep2

source_name: NR8383, 4 h, 0 µg/mL of NP-ZnO, replicate 2


title: NR8383_4h_0 µg/mL_of_NPZnO_rep4

source_name: NR8383, 4 h, 0 µg/mL of NP-ZnO, replicate 4


title: NR8383_4h_2 µg/mL_of_NPZnO_rep2

source_name: NR8383, 4 h, 2 µg/mL of NP-ZnO, replicate 2


title: LXIDN 8.5.14

description: LXIDN  exp 3

source_name: LXIDN CD34+ cells

treatment_protocol: Transduction of CB CD34+ cells was performed  24h after isolation. Retroviral transduction was performed by four cycles of infection (one every 12h) with viral supernatant with the addition of polybrene (8 μg/ml), 20% HS and human cytokines (SCF, Flt3-l, TPO, IL-6 and IL-3 as described above) in retronectin-coated plates. Untreated 24-wells plates were coated with retronectin (10μg/cm2) (Takara Bio Inc, Japan) following the manufacturer’s protocol. To achieve optimal expansion and infection of primary CD34+ cells, the retronectin-coated plates were pre-incubated with retroviral supernatant for 4h, then CD34+ cells were seeded in 24-wells plate at 3x10^5 cells/ml (1ml/well) in fresh viral supernatant. After transduction, CB CD34+ cells were maintained in the above described liquid culture conditions for additional 36h. Transduced CD34+ cells were subsequently purified by means of immunomagnetic selection (EasySep “Do-It-Yourself” Selection Kit; StemCell Technologies) using the anti-human p75-NGFR mouse monoclonal antibody (BD Biosciences). Purity of the NGFR+ cell fraction was assessed by flow cytometry after labeling with PE-conjugated anti-NGFR monoclonal antibody (Miltenyi) 48h post-purification and was always >90%.

tag: transduced with

value: empty vector control LXIDN

tag: cell fraction

value: NGFR+ cell


title: siRNA CALR CB Agosto

description: siRNA CALR 3

value: Cord Blood

value: CD34+ cells


title: NR8383_4h_2 µg/mL_of_NPZnO_rep1

source_name: NR8383, 4 h, 2 µg/mL of NP-ZnO, replicate 1

value: lung


title: Control_T0_id_64222

description: environmental sample


title: Pre_growth_rep2


title: Control_T0_id_64220

description: environmental sample

source_name: California Current System (CCS) Stn. 38 surface water (25 m)


title: Control_T0_id_64221

description: environmental sample


title: Total_H3_ChIP-seq_DIPG7_without_WT_H3_3_overexpression_untreated

tag: genotype

value: without WT H3.3 overexpression


title: H3K27me_ChIP-seq_DIPG7_with_WT_H3_3_overexpression_untreated

value: Tri-Methyl-Histone H3 (Lys27) rabbit mAb - Cell Signaling (C36B11) #9733


title: H3K27me3_ChIP-seq_DIPG7_without_WT_H3_3_overexpression_untreated


title: NT siRNA CB Agosto

description: NT siRNA 3

value: non-targeting (NT) siRNA


title: CALR WT 2.4.14

description: LCALRIDN exp 2

source_name: LCALRIDN CD34+ cells

value: retroviral vector LCALRIDN


title: LXIDN 2.4.14

description: LXIDN  exp 2


title: CALR WT 8.5.14

description: LCALRIDN exp 3


title: siRNA CALR CB1 Nov

description: siRNA CALR 1

value: CALR siRNA


title: SKOV3 cells with PLAGL2 siRNA rep1

first: Anna

last: Santamaria

address: Pg/Vall Hebron 119-129

institute: Vall Hebron Institut de REcerca

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with siRNA against PLAGL2 gene
Plagl2(1)

hyb_protocol: Hybridization were prepared according to the standard Affymetrix protocol (GeneChip® WT PLUS Reagent Kit, Manual Target Preparation for GeneChip®, Whole Transcript (WT) Expression Arrays)

scan_protocol: Scan was performed according to the standard Affymetrix protocol (GeneChip® WT PLUS Reagent Kit, Manual Target Preparation for GeneChip®, Whole Transcript (WT) Expression Arrays)

data_processing: Raw data was obtained from the High Technology Unit (VHIR) and was processed by Expression Console and TAC software, both publicly available. Briefly, normalization of the raw data (CEL files) and generation of principal component analysis were done with Affymetrix Expression Console software. To perform differential expression analysis between control and siCDCP1 or siPLAGL2 data, Affymetrix TAC software was used, which automatically analyze the fold change and statistical p-values based on one-way ANOVA t-test.

source_name: SKOV3 cells after treatment with siRNA against PLAGL2 during 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT PLUS Reagent Kit, Manual Target Preparation for GeneChip®, Whole Transcript (WT) Expression Arrays)

growth_protocol: 48 hours after transfecting the SKOV3 cell line with the corresponding siRNAs, cells were collected and harvested for total RNA extraction.

extract_protocol: Total RNA was extracted using miRNAeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with lipofectamine and 50 nM siRNA concentration for 48 h

value: siRNA against PLAGL2 during 48h

value: Ovarian cancer


title: H3K27ac_ChIP-seq_DIPG7_without_WT_H3_3_overexpression_untreated

value: DIPG7 cells

value: untreated

value: Histone H3 (acetyl K27) rabbit pAb - Abcam (ab4729)


title: RNA_polymerase_II_ChIP-seq_atuveciclib_DIPG7

value: atuveciclib

value: RNA polymerase II CTD mouse mAb - Abcam [8WG16] (ab817)


title: CALR WT 24.3.14

description: LCALRIDN exp 1


title: Liver_batch1_obesity+fucoidan_HBx,src_replicate 3

description:
Gene expression data from adult HBx,src zebrafish, diet-induced obesity oral gavage with OF, sample 3
HBx,src_DIO+OF-8

value: Liver

value: HBx,src

value: diet-induced obesity (DIO)

value: oral gavage with OF (300 mg/kg) thrice a week for one month

value: 6 months


title: H3K27ac_ChIP-seq_DIPG7_with_WT_H3_3_overexpression_untreated

value: with WT H3.3 overexpression


title: LXIDN 24.3.14

description: LXIDN  exp 1

value: Cord Blood

value: CD34+ cells

value: empty vector control LXIDN

value: NGFR+ cell


title: SKOV3 cells with CDCP1 siRNA rep3

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with siRNA against CDCP1 gene
CDCP1(3)

source_name: SKOV3 cells after treatment with siRNA against CDCP1 during 48h

value: siRNA against CDCP1 during 48h


title: NA2

first: zou

middle: mei

last: sheng

address: 1838 N Guangzhou Ave

institute: Nanfang Hospital, Southern Medical 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. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction.Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 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 each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed.

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/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total tissue RNA was extracted from human TAD and NA tissues using TRIzol reagent according to the manufacturer’s instructions.

tag: gender

value: male

value: thoracic aortas

value: control


title: NA1

tag: treatment


title: NA3


title: NR8383_4h_0 µg/mL_of_NPZnO_rep1

source_name: NR8383, 4 h, 0 µg/mL of NP-ZnO, replicate 1

value: lung

value: macrophages


title: RNA_polymerase_II_ChIP-seq_DMSO_DIPG7

value: DIPG7 cells

value: DMSO

value: RNA polymerase II CTD mouse mAb - Abcam [8WG16] (ab817)


title: Input_atuveciclib_DIPG7

value: atuveciclib


title: SKOV3 cells with PLAGL2 siRNA rep3

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with siRNA against PLAGL2 gene
Plagl2(3)

value: siRNA against PLAGL2 during 48h

value: Ovarian cancer


title: TAD2

source_name: TAD

value: thoracic aortic dissection


title: Input_DMSO_DIPG7


title: SKOV3 cells with PLAGL2 siRNA rep2

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with siRNA against PLAGL2 gene
Plagl2(2)


title: SKOV3 cells with control siRNA (LaminA) rep3

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with control siRNA
C3

source_name: SKOV3 cells after treatment with control siRNA during 48h

value: control siRNA during 48h


title: TAD3


title: SKOV3 cells with CDCP1 siRNA rep1

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with siRNA against CDCP1 gene
CDCP1(1)


title: SKOV3 cells with control siRNA (LaminA) rep2

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with control siRNA
C2


title: SKOV3 cells with CDCP1 siRNA rep2

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with siRNA against CDCP1 gene
CDCP1(2)


title: TAD1


title: CT48 WT Biological Replicate 3

status: Public on Apr 11 2020

city: New York

first: Rosemary

middle: V

last: Sampogna

state: NY

department: Medicine

institute: Columbia University

description:
AR127
CT48-s127

data_processing:
Bases were called with RTA (Illumina), and bcl2fastq.gz2 (version 2.17) was used for converting BCL to fastq.gz format, with adaptor trimming.
Reads were mapped to UCSC/mm10 using STAR (2.5.2b), and summarized to gene-level counts with featureCounts (v1.5.0-p3). One sample at embryonic day 18 and 12hr (E18.5) was removed from the dataset due to poor quality.
Genes that were not represented by more than five counts in at least two replicates were filtered out of downstream analysis. To  correct for differences in sequencing depth, the data then underwent upper-quartile normalization by the betweenLaneNormalization function from the EDASeq package. Removal of unwanted variation (RUV) normalization was performed by the RUVg function from the RUVSeq package, which uses factor analysis and a list of in silico empirical negative control genes to reduce variation from unknown technical effects.
Empirical controls, which can be considered non-rhythmic transcripts, were obtained by first-pass meta2d analysis using MetaCycle on the upper-quartile-normalized dataset (settings: cycMethod = c("JTK", "LS"), minper = 20, maxper = 28).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for each sample and rhythmic analysis of transcripts using MetaCycle (v.1.2.0). Results ranked by decreasing integrated q-value (FDR-adusted p-value).

source_name: Fetal Kidney

extract_protocol:
Fetal kidneys were extracted, stored in RNAlater, and RNA was isolated using the QIASymphony kit. Poly-A pull-down was used for mRNA enrichment. Libraries were prepared using Illumina TruSeq RNA Prep Kit, and sequenced on Illumina HiSeq2500/HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney


title: CT44 WT Biological Replicate 3

description:
AR126
CT44-s126


title: CT48 WT Biological Replicate 2

description:
AR117
CT48-s117


title: CT44 WT Biological Replicate 4

description:
AR136
CT44-s136


title: CT44 WT Biological Replicate 2

description:
AR116
CT44-s116


title: CT48 WT Biological Replicate 1

description:
AR107
CT48-s107


title: CT44 WT Biological Replicate 1

description:
AR106
CT44-s106


title: SKOV3 cells with control siRNA (LaminA) rep1

description:
Gene expression data from ovarian cancer SKOV3 cell line upon depletion with control siRNA
C1


title: CT40 WT Biological Replicate 3

description:
AR125
CT40-s125


title: CT36 WT Biological Replicate 1

description:
AR104
CT36-s104


title: CT40 WT Biological Replicate 1

description:
AR105
CT40-s105


title: CT40 WT Biological Replicate 2

description:
AR115
CT40-s115


title: CT36 WT Biological Replicate 3

description:
AL999
CT36-s999


title: CT40 WT Biological Replicate 4

description:
AR135
CT40-s135


title: CT32 WT Biological Replicate 4

description:
AR133
CT32-s133

value: E19 + 8 HRS


title: CT36 WT Biological Replicate 2

description:
AR114
CT36-s114


title: CT36 WT Biological Replicate 4

description:
AR134
CT36-s134


title: CT32 WT Biological Replicate 3

description:
AR123
CT32-s123


title: CT48 WT Biological Replicate 4

description:
AR137
CT48-s137


title: CT32 WT Biological Replicate 2

description:
AR113
CT32-s113


title: CT32 WT Biological Replicate 1

description:
AR103
CT32-s103


title: CT28 WT Biological Replicate 3

description:
AR122
CT28-s122

value: E19 + 4 HRS


title: CT28 WT Biological Replicate 2

description:
AR112
CT28-s112


title: CT28 WT Biological Replicate 4

description:
AR132
CT28-s132


title: CT28 WT Biological Replicate 1

description:
AR102
CT28-s102


title: 12_Ps2Ex3M1_WT_6month_F3_95_Fem

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

data_processing:
Illumina BaseSpace was used for basecalling
Reads were trimmed using cutadapt v1.14 with settings -m35 --trim-n --max-n 1 --nextseq-trim=30
Trimmed reads were aligned to GRCz11 (Ensembl Release 98) using STAR 2.7.0d with default settings
Reads were summarised at the gene level using featureCounts (Subread 1.5.2) using the file Danio_rerio.GRCz11.98.chr.gtf from Ensembl, with the settings -Q 10 -s 2 -p --fracOverlap 1
Genome_build: GRCz11
Supplementary_files_format_and_content: A counts matrix as output by featureCounts contains gene-levels counts from each sample

source_name: Brain

growth_protocol: All fish were raised together in the same tank until 6 months of age

extract_protocol:
Total RNA was extracted from pooled larvae using the mirVanaTM miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA).
rRNA was depleted from total RNA samples using the rRNAseH rRNA depletion method [Adiconis et al, Nat Methods 2013 Jul (10) 7 623-629] and a combination of human/rat/mouse sequences. 500ng of RNA was used for rNRA depletion, followed by the KAPA Hyper Library Prep kit, fragmentation at 85 degrees (C) for 6 mins and 11 PCR cycles. Sequencing was performed by the Australian Cancer Research Foundation Cancer Genomics Facility in Adelaide, South Australia

value: Whole brain

value: 6 months


title: CT24 WT Biological Replicate 4

description:
AR037
CT24-s037


title: 9_Ps2Ex3M1_WT_6month_F3_79_Fem


title: 8_Ps2Ex3M1_Hom_6month_F3_85_Fem


title: 10_Ps2Ex3M1_WT_6month_F3_86_Fem


title: CT20 WT Biological Replicate 3

description:
AR036
CT20-s036


title: CT24 WT Biological Replicate 2

description:
AR017
CT24-s017


title: CT24 WT Biological Replicate 1

description:
AR007
CT24-s007


title: 6_Ps2Ex3M1_Hom_6month_F3_82_Fem


title: BL21(DE3)_heatshock_2h

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

hyb_protocol: The fragmented and labeled RNA was hybridized with the tiling array for 17 hours at 65°C.

scan_protocol: After the hybridization and wash steps described in the array manufacturer’s instructions, arrays were scanned using an Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: Signal intensity and local background were determined using Feature Extraction software (Agilent Technologies).

organism: Escherichia coli BL21(DE3)

source_name: 42°C, time=2h

label_protocol: The resulting RNA was directly labeled with Cy3 using a Label IT µArray Labeling Kit (Mirus, Madison, WI, USA), per the manufacturer’s instruction.

growth_protocol: Chemostat cultures were grown in glucose-limited defined medium with the dilution rate of 0.1 h-1. The temperature was shifted from 37°C to 42°C within 3.5 min.

extract_protocol: Total RNA was prepared using a mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA), per the manufacturer’s instruction. Any contaminating DNA was digested with Turbo DNase (Applied Biosystems, Austin, TX, USA) for 30 minutes at 37C and then removed using the filter cartridges supplied with the mirVana miRNA Isolation Kit.

treatment_protocol: Culture broth (4.0 × 10e8 cells) was immediately mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen, Düsseldorf, Germany).

tag: culture medium

value: Modified R (minimal medium)

tag: cell density in od600

tag: temperature

tag: time


title: CT20 WT Biological Replicate 2

description:
AR026
CT20-s026

tag: developmental stage


title: 5_Ps2Ex3M1_Hom_6month_F3_78_Fem

tag: age


title: CT20 WT Biological Replicate 1

description:
AR006
CT20-s006

tag: strain


title: CT16 WT Biological Replicate 4

description:
AR035
CT16-s035


title: 3_Ps2Ex3M1_Heter_6month_F3_84_Fem


title: CT16 WT Biological Replicate 3

description:
AR025
CT16-s025


title: TC71 scRNA-Seq

city: San Antonio

first: Henry

last: Miller

state: TX

address: 8403 Floyd Curl Drive

department: Cell Systems and Anatomy

institute: UT Health San Antonio

data_processing:
Fastq files were processed with cellranger v3.1.0 using the 'count' function. For CHLA9 and CHLA10, fastq files from NovaSeq and HiSeq were entered as a comma-separated list as recommended by 10X genomics.
Genome_build: hg38
Supplementary_files_format_and_content: cellranger count output (filtered feature bc matrices)

source_name: Ewing sarcoma cell line

growth_protocol: Ewing Sarcoma cell lines CHLA-9 and CHLA-10 were maintained in in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco) supplemented with 20% heat-inactivated Fetal Bovine Serum (FBS, ATLANTA biologicals), 1% Insulin-transferrin-sodium selenite (ITS, Corning) and 1X Antibiotic Antimycotic Solution (Corning). Ewing Sarcoma TC-71 cell line was maintained in RPMI-1640 Medium (Gibco) supplemented with 10% FBS (ATLANTA biologicals) and 1X Antibiotic Antimycotic Solution (Corning). All cell lines were culture at 37 °C in a humidified incubator containing 95% room air plus 5% CO2 atmosphere.

extract_protocol:
When the cells were around 70-80% confluent, the cells were washed twice with HBSS (Corning), recollected using 0.25% Trypsin, 2.21mM EDTA, 1X sodium bicarbonate solution (Corning) and centrifuged for 5 minutes at 300 rcf at 4 °C. Cell pellets were then resuspended in cold DPBS (containing no calcium and no magnesium) (Corning) supplemented with 0.04% Bovine Serum Albumin (BSA) to minimize cell sticking. Viable cells were consequently counted using an automated cell counter (Nexcelom), centrifuged as above described and resuspended at the desired final concentration in cold DPBS (containing no calcium and no magnesium) - 0.04% BSA. Finally, single cell suspensions were strain through a 70 um cell sieve and processed for sequencing. Immediatly prior to processing on the 10X single cell controller, cell density and viability were checked one last time by BioRad TC20 Automated Cell Counter by mixing 10ul cells and 10ul 0.4% trypan blue stian and also reviewed under microscope
10X Genomics Chromium Single Cell 3' V3.1 kit

tag: cell line


title: 24 weeks old [E12]

city: Toronto

first: Bibaswan

last: Ghoshal

address: 600 University Avenue

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description: individual organoids

data_processing:
Cellrangar 2.0 is run on the FASTQ files to generate matrix
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on lirary size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimesion reduction, cluster identification, PCA and tSNE are performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix in .mtx format generated by cellranger filtered_bc_matrices. The csv files contain normalized expression data from combined whole epithelium, crypts and 170 FACS sorted cells with indepth sequencing.

source_name: cerebral organoids

extract_protocol:
Cerebral organoids were cut and dissociated to isolate single cells and then subjected to 10X Genomics single cell RNA sequencing following manufacturer’s recommendations. Illumina HiSeq 3000 was used for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: 24 weeks old


title: 4_Ps2Ex3M1_Heter_6month_F3_89_Fem


title: BL21(DE3)_heatshock_4h

source_name: 42°C, time=4h


title: 11_Ps2Ex3M1_WT_6month_F3_88_Fem


title: 2_Ps2Ex3M1_Heter_6month_F3_81_Fem


title: 24 weeks old [F06]

description: individual organoids


title: 1_Ps2Ex3M1_Heter_6month_F3_80_Fem


title: BL21(DE3)_heatshock_40h

source_name: 42°C, time=40h


title: CT16 WT Biological Replicate 2

description:
AR015
CT16-s015


title: BL21(DE3)_heatshock_minus30min

source_name: 37°C, time=-30min


title: CT16 WT Biological Replicate 1

description:
AR005
CT16-s005


title: 24 weeks old [F03]

description: individual organoids


title: 24 weeks old [F04]

description: individual organoids


title: CT12 WT Biological Replicate 3

description:
AR034
CT12-s034


title: BL21(DE3)_heatshock_1h

source_name: 42°C, time=1h


title: BL21(DE3)_heatshock_10min

source_name: 42°C, time=10min


title: CT12 WT Biological Replicate 4

description:
AL998
CT12-s998


title: BL21(DE3)_heatshock_30min

source_name: 42°C, time=30min


title: 24 weeks old [F02]

description: individual organoids


title: CHLA10 scRNA-Seq


title: Hela_Drosha_WT

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

description:
WTR1, WTR2
Stranded RNA-seq for control HeLa cells.
polyA RNA
processed data file: Hela_Drosha_KD_genes_FPKM_res.txt

data_processing:
RNA-seq: Adapter sequences, low-quality bases and Ns were first trimmed using cutadapt.
RNA-seq: RNA-seq data were mapped to the human reference genome (hg19) using tophat2 (TopHat v2.1.0).
RNA-seq: Gene expression levels were calculated by cufflinks (cufflinks v2.2.1).
Small RNA-seq: Adapter sequences, low-quality bases and Ns were first trimmed using cutadapt.
Small RNA-seq: Clean reads were next mapped to the human reference genome (hg19) with STAR (Version 2.5.2b).
Small RNA-seq: Read numbers were counted by featureCounts (Version 2.0.0) and the CPM values were calculated using a custom perl script.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Gene FPKM values produced by cufflinks.
Supplementary_files_format_and_content: miRNA counts produced by featureCounts.

source_name: HeLa cell line

extract_protocol:
Total RNA was extracted with TRIzol and Direct-zol RNA Kits (Zymo Research).
mRNA was selected using Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). Libraries were sequenced on Hiseq X10 (Illumina) to produce paired-end 150 bp reads.

value: HeLa

tag: genotype/variation

value: Drosha WT


title: CT12 WT Biological Replicate 2

description:
AR024
CT12-s024