title: mosquito Pool C

city: MILTON

first: Maria

middle: Eugenia

last: Ramos-Nino

state: VT

address: 257 LAKE RD

institute: SGU

description: Gene expression data from whole mosquito

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Culex quinquefasciatus

source_name: mosquito Pool C

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild samples

extract_protocol: RNA was extracted using TrizolTRIzol. Invitrogen™ Phasemaker™ Tubes were used for the phase separation. RNA was DNase-treated using TURBO DNA-free™ and RNA quality evaluated utilizing an Agilent 2100 Bioanalyzer

value: female

value: whole mosquito


title: Normal_Drp1 +/+_3

status: Public on Apr 29 2020

type: SRA

city: Chongqing

first: Chenyang

last: Duan

state: Chongqing

address: Changjiang Road, Yuzhong District

department: Second Department of Research Institute of Surgery, Daping Hospital

country: China

institute: Third Military Medical University

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Normal_Drp1 +/+

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

tag: age

tag: tissue

value: superior mesenteric artery


title: mosquito Pool A

type: RNA

department: Microbiology

country: USA

label: biotin

organism: Aedes aegypti

source_name: mosquito Pool A

tag: Sex


title: 5021

city: Bloomington

first: Alexandra

middle: B

last: Moussa-Tooks

state: Indiana

department: Psychological and Brain Sciences

institute: Indiana University

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC rn6
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

organism: Rattus norvegicus

source_name: Cerebellar Interpositus Nucleus

extract_protocol:
Whole brains were removed and flash frozen, then sliced into 1mm sections. 2mm round punches across 3 consecutive sections were take to extract the cerebellar interpositus nucleus. Punches were homogenized in Trizol and RNA Isolation, extraction, and purification using Qiagen RNeasy Plus Mini Kit.
KAPA mRNA Hyperprep Kit

tag: strain

value: Long-Evans

value: brain

value: postnatal day 70

value: Female

tag: treatment

value: Limited Bedding (postnatal day 2-9)


title: 6112

value: Male

value: Normal Rearing


title: TW1

city: Jerusalem

first: Hadar

last: Benyamini

address: Ein Karem

country: Israel

institute: The Hebrew University

data_processing:
Quality and adapter trimming with cutadapt 1.18, using parameters -q28,28, -O 1, --match-read-wildcards and -m 15. Remaining reads were filtered by overall quality, with fastq_quality_filter (FASTX, 0.0.14), using -q 20 and -p 90.
Alignment with TopHat 2.1.1, using parameters -G genes.gtf, -N 3, --read-gap-length 5, --read-edit-dist 8, --segment-length 23, --read-realign-edit-dist 3, --no-coverage-search.
Counting with htseq-count 0.6.0, using parameter -s no, and masking for short genes (miRNA, piRNA, etc.).
Differential expression with DESeq2 1.22.1, after discarding genes with less than 10 reads, using default parametes (except not using independentFiltering), testing either the disease state (sick vs. healthy) or the combined factor of tissue, genotype and phenotype.
Filtering significant genes, taking only genes with absolute log2FoldChange > 5/baseMean^0.5 + 0.6.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file with expression data. The first row is a header line. Columns include general gene details, raw counts, normalized counts, the baseMean, and the DESeq2 analysis results for each comparison. For each muscle type ('Ga' for Gastrocnemius; 'Q' for Quadriceps; 'T' for Tibialis), the first letter is for the numerator and the second for the denominator ('W' for wild type; 'H' for GNE M743T/M743T healthy; 'S' for GNE M743T/M743T sick). 'YN' denotes the phenotype comparison, sick as numerator and healthy as denominator. 'best' column for each comparison shows the results for the additional filtering of significant genes, 'FALSE' are non-significant, 'TRUE' are significant but below filtering threshold, 'THR' for significant genes that passed the further filtering threshold. '?' denotes missing data. Missing raw counts is due to masking genes at the counting step; missing normalized counts (but with raw counts) is due to having too few reads.

source_name: Tibialis

extract_protocol: none provided by the submitter

tag: genotype

value: Wild-type

tag: phenotype

value: healthy


title: QS4

source_name: Quadriceps

value: GNE M743T/M743T knock in

value: sick


title: Arabidopsis_RH_Polysomal_bound2

city: Riverside

first: Maureen

last: Hummel

state: California

address: 900 University Avenue

department: Botany and Plant Sciences

institute: University of California

description:
Ribosome replicate bound mRNAs rh  replicate 2
AllThanincounts.txt

data_processing:
Processing of RNA-seq data was performed using the package systemPipeR
Alignment to TAIR10 with bowtie2 2.2.5 and tophat 2.0.14
Aligned reads were counted against the Araport11 genome release 201606 using the summarizeOverlaps function in ôunionö mode
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

organism: Arabidopsis thaliana

source_name: Col-0 5 days old seedling

extract_protocol: poly(A)+ selected; library construction method based on Townsley et al., Front. Plant Sci. 6, 366 (2015)  and Kumar et al., Front. Plant Sci. 3, 202 (2012)

tag: ecotype

value: 5-days-old seedling

tag: developmental stage

value: seedling

tag: agent


title: Arabidopsis_RH_Polysomal_bound3

description:
Ribosome replicate bound mRNAs rh  replicate 3
AllThanincounts.txt


title: QS3


title: Arabidopsis_RH_Polysomal_bound1

description:
Ribosome replicate bound mRNAs rh  replicate 1
AllThanincounts.txt


title: shT28_1

city: Houston

first: Janani

last: Kumar

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: MCF7 cells stably expressing knockdown TRIM28_1

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The reads were mapped to the human genome (hg38) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release 32 (83) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genome_build: hg38
Supplementary_files_format_and_content: Number of fragments in each gene
Supplementary_files_format_and_content: raw counts

organism: Homo sapiens

growth_protocol: Stable gene expression Cells

extract_protocol:
Qiagen mRNA kit
Illumina TruSeq Stranded total RNA kit according to the manufacturer’s protocol. The libraries were sequenced using 2x76 bases paired end protocol on Illumina HiSeq 3000 instrument. Two biological replicates per condition were sequenced, generating 45-58 million pairs of reads per sample. Each pair of reads represents a cDNA fragment from the library.

tag: cell line

tag: origin

value: Breast Cancer ER +ve

tag: shRNA

value: knockdown TRIM28


title: shControl_2

description: MCF7 cells stably expressing sh scrambled Control_2

value: sh scrambled Control


title: shT28_2

description: MCF7 cells stably expressing knockdown TRIM28_2


title: 4113


title: 4111


title: 3113


title: shControl_1

description: MCF7 cells stably expressing sh scrambled Control_1


title: Arabidopsis_WT_Polysomal_bound3

description:
Ribosome replicate bound mRNAs wt  replicate 3
AllThanincounts.txt


title: QS2


title: QH4


title: 21 days old WT uterus IGF1, 2h-rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from uterus from 21 day old WT mouse that was treated for 2h with IGF1

hyb_protocol: Five and one half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

label: Biotin

label_protocol: Three hundred nanograms (300 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: pre-pubertal 21-days old female WT and ERa KO mice

extract_protocol: RNA was extracted using Trizol reagent followed by Rneasy clean up protocol

treatment_protocol: for saline vehicle: 100 ul of sailne injected intraperitoneally, tissue collected 24 hours later. For estradiol (E2) 250 ng of E2 dissolved in 100 ul of saline injected intraperitoneally, tissue collected after 2 hours or 24 hours. For IGF1 samples, 50 ug of IGF1 dissolved in PBS was injected intraperitoneally, and tissue collected after 2h, or 50 ug of IGF1 dissolved in PBS injected intraperitoneally 3 times (0, 8 and 16 hours after first injection), and tissue was collected 24h after the first injection

value: WT


title: 2K_2

description: MCF7 cells stably expressing 2K fragment_2

value: 2K fragment


title: Arabidopsis_WT_Polysomal_bound2

description:
Ribosome replicate bound mRNAs wt  replicate 2
AllThanincounts.txt


title: 2K_1

description: MCF7 cells stably expressing 2K fragment_1


title: 3112

value: Long-Evans

value: brain


title: QH3


title: 3111

value: postnatal day 70


title: control_2

description: MCF7 cells stably expressing empty vector_2

value: empty vector


title: Arabidopsis_WT_Polysomal_bound1

description:
Ribosome replicate  bound mRNAs wt replicate 1
AllThanincounts.txt


title: S. mutans FR3

city: Busan

first: Jeong Nam

last: Kim

address: Biology Building 402, Busandaehang-ro, 63beon-gil 2, Geumjeong-gu

country: South Korea

institute: Pusan National University

data_processing:
Raw data of RNA-seq results were mapped to reference genome (S. mutans UA159) using Galaxy online (https://usegalaxy.org/).
The format of FASTQ files were converted using FASTQ groomer tool and confirmed by FastQC algorithm.
Output files were aligned with reference genome for mapping using Bowtie.
Mapped reads were converted to BAM file. The transcripts were assembled and quantified by stringtie tool.
Assemblies were merged together using cuffmerge tool.
Cuffdiff tool was utilized for performing comparing expression levels of transcripts in S. mutans WT vs fluoride resistant strains, along with the quartile library normalization method and pooled dispersion estimation method.
Genome_build: S. mutans UA159
Supplementary_files_format_and_content: expression levels, fold change, p-value

organism: Streptococcus mutans

source_name: bacteria cell

growth_protocol: Cells were grown to late-exponential phase (OD600=0.6~0.7) in brain heart infusion (BHI) medium (BD Biosciences, New Jersey, USA) at 37℃ in 5% CO2 condition.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen). 1 μg of each RNA was used to construct the cDNA library.
cDNA libraries were prepared for sequencing using an Illumina Hiseq 4000 protocol

value: fluoride-resistant

tag: growth phase

value: late-exponential phase


title: 2013

value: Female

value: Normal Rearing


title: S. mutans FR2


title: control_1

description: MCF7 cells stably expressing empty vector_1


title: S. mutans WT3

value: wild-type


title: QH1

value: GNE M743T/M743T knock in

value: healthy


title: QW4

value: Wild-type


title: 2011


title: QW3


title: 1013


title: 1011


title: QW2


title: S. mutans WT2


title: PN [OV2]

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

description: processed data file: miRNA.readcount_TPM.txt

data_processing:
the NGS QC Toolkit v2.3.3 was used to filiter the reads with adapter sequences, reads with an N (unknown bases in a read＞5%) and low-quality reads (reads with a base quality ≤ 20).
Sequence alignments were performed using TopHat v2.0.12 with v2.2.3 for mapping to the reference genome (http://gigadb.org/dataset/100209, Guan et al.  2016).
The Cufflinks v2.1.1 Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from TopHat alignment results.
FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene
sRNA libraries were sequenced using the Illumina HiSeq 4000. Raw data of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze the expression and distribution on the reference.miRBase22.0 was used as reference, and modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts.The mapped sRNA tags were also mapped to Rfam, RepeatMasker, to annotate the tags and remove those originating from proteincoding genes, repeat sequences, ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). The remaining unannotated tags were used to predict novel miRNAs by exploring secondary structures, Dicer cleavage sites, and minimum free energies using the miREvo and miRDeep2 software packages.
RNA fragments with a poly (A) tail were isolated from the total RNA of mixed samples. A series of steps, including ligation of 5′RNA adaptors, digestion, ligation of double-stranded DNA adaptor, purification, and amplification were conducted and sequencing was done on an Illumina HiSeq 2500. The raw sequencing reads were processed by Illumina’s Pipeline v1.5 to obtain clean reads, which were then used to identify potentially cleaved targets.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/100209, Guan et al. 2016).
Supplementary_files_format_and_content: Text files include gene.FPKM (gene_id, PD1.FPKM, PD2.FPKM, PN1.FPKM, PN1.FPKM), miRNA.readcount_TPM (miRNA.readcount, Ov1.readcount, Ov2.readcount, Ov1.tpm, Ov2.tpm) and miRNA.targets (miRNA_id, target_id)

organism: Ginkgo biloba

source_name: pollinated ovule

growth_protocol: Ovules were obtained from 3-5 healthy G. biloba trees (~20-year-old; Fozhi cultivar) growing under natural conditions in Yangzhou University, Yangzhou, China (32°20ʹ N, 119°30ʹ E).

extract_protocol:
Samples were collected in early April 2017. Total RNAs of ovules were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: one day after pollination

value: pollinated ovule


title: PD [OV1]

source_name: mature ovule

value: secreting pollination drop

value: mature ovule


title: QW1


title: PN1

description: processed data file: genes_FPKM.txt


title: S. mutans WT1


title: 123

value: Male

value: Limited Bedding (postnatal day 2-9)


title: QH2


title: 122

value: Long-Evans

value: brain


title: PD2

description: processed data file: genes_FPKM.txt


title: PD1

description: processed data file: genes_FPKM.txt


title: 2012

value: postnatal day 70


title: GaS2

source_name: Gastrocnemius

value: sick


title: 121


title: S. mutans FR1

value: fluoride-resistant

value: late-exponential phase


title: HB_S10_2

city: Beijing

first: Shaojun

last: Liang

address: 18 Shuangqing Road

institute: Chinese academy of sciences

description: processed data file: All_samples.GeneExpression.FPKM.txt

data_processing:
Reads were filtered and mapped to the reference genome sequence (GRCh38.p11(hg38)) with HISAT v2.1.0, with a mean mapping rate of 93.63%.
Sequences were aligned to reference genes with the Bowtie2 tool, and the gene expression levels determined with the RSEM software.
The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression levels. The differentially expressed genes (DEGs) with change fold ≥ 2 and q-value ≤ 0.001 were regarded as significant.
Genome_build: GRCh38.p11(hg38)
Supplementary_files_format_and_content: All_samples.GeneExpression.FPKM.txt: Tab-delimited text file includes FPKM values for all samples.

source_name: hepatoblast

extract_protocol:
Total RNA samples were isolated with Trizol according to the manufacturer's instructions.
RNA quality was analyzed with an Agilent 2100 Bioanalyzer, and was within the standards. The cDNA library construction and sequencing were performed at Beijing Genomics Institute (BGI). Sequencing was performed with a BGISEQ-500 platform.

tag: cell type

value: hES-derived hepatoblast

tag: hes cell type

value: 10 nM TBBPS


title: GaS1

value: GNE M743T/M743T knock in


title: HB_S10_1


title: PC3+VSV-hIFNβ+RT-2

city: Miami

first: Wensi

last: Tao

state: Florida

address: 1550 nw 10 ave room 137

department: Radiation Oncology

institute: University of Miami

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Cell Culture Lysate

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: LNCaP and PC3 cells were cultured in complete medium.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: After 24 hours, the cells were treated with VSV-hIFNβ. Twenty four hours after viral treatment, both cell lines were irradiated with 5Gy. The assay was terminated 24 h after RT.  Total RNA was extracted for microarray analysis.

value: VSV-hIFNβ+RT


title: PN2

description: processed data file: genes_FPKM.txt


title: GaH3

value: healthy


title: HB_Ctrl_2


title: Col_0_WGBS

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1).
Reads with three or more consecutive methylated CHH sites were considered as “unconverted” and subsequently removed.
DNA methylation levels were calculated by #C/ (#C + #T).
Whole genome methylation was plotted with ViewBS (v0.1.8).
Genome_build: tair10
Supplementary_files_format_and_content: Wig: WGBS track file

molecule: genomic DNA

source_name: Arabidopsis flowers

growth_protocol: Plants were grown under standard long day conditions unless stated differently.

extract_protocol:
Genomic DNA was converted with bisulfite treatment with EpiTect Bisulfite Kit (Qiagen, USA).
Whole genome Bisulfite Sequencing library sequencing was done by NovoGene (Beijing, China).

value: flowers

value: 4 weeks

value: wild type


title: PC3+VSV-hIFNβ+RT-1


title: nrp1nrp2_WGBS


title: GaH2


title: GaS3


title: GaH1


title: GaW4

value: Wild-type


title: nrp1,nrp2,arp6_INPUT_R2

data_processing:
ChIP-Seq reads were aligned to the reference genome (TAIR10) with Bowtie (v1.1.2), allowing only uniquely mapping reads with 0 mismatches.
Duplicated reads were removed by Samtools.
ChIP-Seq peaks were called by MACS223 (v2.1.1.) and annotated with ChIPseeker.
Differential peaks with likelihood ratio > 1000 were called by bdgdiff function in MACS2.
Metaplots of ChIP-Seq data were plotted by deeptools (v2.5.1).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: ChIP seq track file; bed: ChIP seq peak file

extract_protocol:
ChIP seq was described in Zhong XH, et al 2012
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions


title: PC3+VSV-hIFNβ-2

value: VSV-hIFNβ


title: HB_C10_1

value: 10 nM TCBPA


title: GaW3


title: PC3-2


title: PC3+VSV-hIFNβ-1


title: PC3-1


title: HB_A10_2

value: 10 nM TBBPA


title: LNCaP+VSV-hIFNβ+RT-2

value: LNCaP


title: GaW2


title: nrp1,nrp2,arp6_H2A_R1

tag: antibody


title: GaW1


title: DE_S10_2

source_name: definitive endoderm

value: hES-derived definitive endoderm


title: nrp1,nrp2_INPUT_R1


title: LNCaP+VSV-hIFNβ+RT-1


title: HB_C10_2


title: nrp1,nrp2,arp6_INPUT_R1


title: nrp1,nrp2_H2A_R1


title: nrp1,nrp2,arp6_H2A_R2


title: HB_A10_1


title: HB_Ctrl_1


title: DE_Ctrl_2


title: nrp1,nrp2_H2A_R2


title: LNCaP+VSV-hIFNβ-2


title: LNCaP+VSV-hIFNβ-1


title: COL_INPUT_R2

value: COL


title: LNCaP-2


title: DE_Ctrl_1


title: LNCaP-1


title: nrp1,nrp2_INPUT_R2


title: DE_C10_2


title: COL_INPUT_R1


title: COL_H2A_R1


title: COL_H2A_R2


title: DE_C10_1


title: DE_S10_1


title: DE_A10_2


title: ΔarlRS rep3

city: Aurora

first: Alexander

last: Horswill

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Paired-end reads mapped using CLC Genomics Workbench version 12 (Qiagen).
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using CLC Genomics Workbench version 12 (Qiagen).
Genome_build: CP000255.1
Supplementary_files_format_and_content: csv file containing total raw counts, RPKM values, TPM values, and CPM values for each replicate.

organism: Staphylococcus aureus subsp. aureus USA300

source_name: Staphylococcus aureus USA300 LAC

growth_protocol: S. aureus cultures were grown with shaking at 37 °C to an OD600 of 1.5 in tryptic soy broth.

extract_protocol:
1 h lysis step with lysostaphin followed by RNA purification using Qiagen RNeasy Mini Kit.
rRNA depleted using Ribo-Zero rRNA Removal kit for Gram positive bacteria (Illumina) and libraries prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: 2 min treatment with RNAprotect (Qiagen).

value: delta-arlRS


title: arp6_INPUT_R2


title: ΔarlRS rep2


title: ArKO ovex uterus V rep3

description: Gene expression of uterus from ArKO mice that were ovariectomized at week 10, then rested for 10-14 days before collecting tissues

source_name: uterus

growth_protocol: mice were ovariectomized when they were 10 weeks old and rested for 10-14 days

extract_protocol: RNA was extracted using Trizol reagent and Rneasy clean-up protocol

treatment_protocol: mice were injected with 100 ul saline vehicle (V) ip and uterine tissue was collected 24 h later

value: Aromatase Knockout

value: uterus


title: DE_A10_1


title: EB treated ArKO ovex uterus V rep1

description: Gene expression of uterus from ArKO mice that were treated with EB at week 9-10, then ovariectomized at week 10, and rested for 10-14 days before collecting tissue


title: EB treated WT ovex uterus V rep1

description: Gene expression of uterus from WT mice that were treated with EB at week 9-10, then ovariectomized at week 10, and rested for 10-14 days before collecting tissue

value: WT


title: EB treated ArKO ovex uterus V rep2

value: treated with EB at week 9-10, then ovariectomized at week 10, and rested for 10-14 days before collecting tissue


title: arp6_H2A_R1


title: arp6_H2A_R2


title: ArKO ovex uterus V rep2

value: ovariectomized at week 10, then rested for 10-14 days before collecting tissues


title: EB treated WT ovex uterus V rep3


title: ΔarlRS rep1


title: arp6_INPUT_R1


title: EB treated ArKO ovex uterus V rep3


title: nrp2_RNAseq_r3

description: nrp2 RNAseq replicate3

data_processing:
ChIP-Seq reads were aligned to the reference genome (TAIR10) with Bowtie (v1.1.2), allowing only uniquely mapping reads with 0 mismatches.
Duplicated reads were removed by Samtools.
ChIP-Seq peaks were called by MACS223 (v2.1.1.) and annotated with ChIPseeker.
Differential peaks with likelihood ratio > 1000 were called by bdgdiff function in MACS2.
Metaplots of ChIP-Seq data were plotted by deeptools (v2.5.1).
clean RNA seq data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: ChIP seq track file; bed: ChIP seq peak file
Supplementary_files_format_and_content: RNA-seq: read counts

source_name: Arabidopsis whole seedling

extract_protocol:
ChIP seq was described in Zhong XH, et al 2012. For RNA seq, Total RNA was prepared from whole seedling (14DAG) using RNA Prep Pure Plant Kit (Tiangen, China).
ChIP seq libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions.  RNA seq libraries were generated using NEBNext® Ultra™ RNA Library  Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: whole seedling

tag: age

tag: cultivar


title: WT ovex uterus V rep3

description: Gene expression of uterus from WT mice that were ovariectomized at week 10, then rested for 10-14 days before collecting tissues

tag: tissue


title: WT ovex uterus V rep2


title: WT rep2

tag: strain

value: wildtype


title: EB treated WT ovex uterus V rep2

tag: treatment


title: WT rep1

tag: genotype


title: WT ovex uterus V rep1


title: nrp2_RNAseq_r2

description: nrp2 RNAseq replicate2


title: nrp1_RNAseq_r3

description: nrp1 RNAseq replicate3


title: nrp2_RNAseq_r1

description: nrp2 RNAseq replicate1


title: nrp1_RNAseq_r2

description: nrp1 RNAseq replicate2


title: 2y_2

city: Chengdu

first: Xun

state: China

address: Huimin road 211#, Wenjiang district

institute: Sichuan agricultural university

description:
microRNA
micRNAs from liver in 2-year pigeon

data_processing:
the initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences were then mapped to the pigeon reference genome (Columba livia, ColLiv2, GenBank assembly accession: GCA_001887795.1) (https://www. ncbi.nlm.nih.gov/assembly/GCA _001887795.1) with stringent criteria (0 mismatch for full length) using Bowtie software.
Next, mappable reads were extended in the reference genome as predicted miRNA precursors. Only candidate precursors that perfectly matched to known pigeon (Columba livia) mature miRNAs annotated by miRBase (Release 22.0) were identified as known pigeon miRNAs.
Subsequently, to identify the conserved miRNAs, we performed alignments between remaining candidate precursors and seed sequences of mature miRNAs from chicken (Gallus gallus), zebra finch (Taeniopygia guttata) and other mammals, allowing no mismatch.
Novel miRNAs were further predicted using the miRDeep2 core algorithm
Genome_build: Genome database:pigeon genome (assembly GCA_001887795.1); miRbase version: V22.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads

organism: Columba livia

source_name: liver tissue

extract_protocol:
Total RNA was respectively extracted from frozen liver samples with TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
The quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer with Agilent RNA 6000 nano Reagents Part 1 kit (Agilent Technologies, USA). Each development stage has three replicates that came from the three pigeons. Total RNA of each replicate was individually used for library construction. For each library, small RNA ranging from 10-45 nt in length was purified by polyacrylamide gel electrophoresis and ligated using proprietary adaptors. The modified small RNA was then reverse-transcribed to cDNA and amplified by PCR. Finally, libraries were sequenced by an Illumina Hiseq 2500 platform and generate 50 bp single-end reads.

treatment_protocol: 16 parent white king pigeons (8 male and 8 female at 2- year-old) and 48 squabs (mixed sex) were grouped into 4 stages (16 replicates for each stage): the age of 1 day (1d), 14 day (14d), 28 day (28d) and 2 years old (2y). After weighing the body weight, pigeons were anaesthetized with ether and subsequently euthanized. Next,the liver tissues from the same anatomical location were collected from pigeons. Subsequently, the samples for small RNA sequencing were stored frozen in liquid nitrogen and stored at −80◦C until RNA extraction,

tag: breed

value: white king

value: liver


title: 48h-Model

city: Guangzhou

first: Junqin

last: Zhang

state: Guangdong

address: Baishigang

institute: Institute of Animal Health, Guangdong Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to duck whole genome using Trimmomatic software (version 0.30).
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, raw data of fasta format were processed by Trimmomatic software (version 0.30) to obtain high quality clean data. The clean data were aligned and mapped to the reference genome (NCBI Genome Assembly: GCA_000355885.1) by using Hisat2 software (version 2.0.14)
Genome_build: Anas platyrhynchos (mallard) NCBI Genome Assembly: GCA_000355885.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Anas platyrhynchos

source_name: brain

extract_protocol:
The brain tissues were grinded in liquid nitrogen.Total RNA of each sample was extracted and purified using RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set (QIAGEN, Germany). RNA concentration was determined by NanoDrop ND-2000 (Thermo Fisher Scientific Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The challenge group was intramuscularly inoculated with 0.5 ml of 105.5 TCID50/ ml Tembusu virus JM strain. The control group was inoculated with an equal amount of sterile PBS.

value: sheldrake

value: brain

value: 10 day old

value: 0.5 ml of 105.5 TCID50/ ml TMUV JM strain

tag: time point


title: 2y_3

tag: developmental stage


title: ArKO ovex uterus V rep1


title: nrp1_RNAseq_r1

description: nrp1 RNAseq replicate1


title: 12h-Model


title: 24h-Model


title: double_RNAseq_r2

description: double RNAseq replicate2


title: 24h-Control

value: control PBS


title: 12h-Control


title: 28d_3

description:
microRNA
micRNAs from liver in 28-day pigeon


title: double_RNAseq_r1

description: double RNAseq replicate1


title: Col_RNAseq_r3

description: Col RNAseq replicate3


title: 28d_2


title: 48h-Control


title: 14d_3

description:
microRNA
micRNAs from liver in 14-day pigeon


title: 2y_1


title: 28d_1


title: WT rep3


title: Col_RNAseq_r1

description: Col RNAseq replicate1


title: 14d_2


title: MS D43 Live MS5

first: Haibin

last: Xi

state: CA

address: 615 Charles E Young Dr South, BSRB 257

department: MIMG

institute: UCLA

description: PAX7-GFP reporter cells derived from H9 human pluripotent stem cells were used for differentiation

data_processing:
The raw sequencing reads were processed using the Drop-seq_tools-1.13 pipeline from the McCaroll lab (https://github.com/broadinstitute/Drop-seq/releases/tag/v1.13), following the general guidelines from the Drop-seq Alignment Cookbook v1.2 (https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf) (Macosko et al., Cell, 2015). Briefly, the first 20 bp from Read1 were filtered by read quality and used to index the corresponding Read2 fragments. The first 75 bp from the indexed Read2 were trimmed off sequencing adapters and polyA sequences, followed by read quality filtration and further removal of reads fewer than 30 nucleotides of length. Processed reads from Read2 were aligned to the human reference genome (hg19) using Bowtie2 (v2.2.9 with the ‘--very-sensitive’ mode) (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Aligned reads were tagged to gene exons using Bedtools Intersect (v2.26.0) (https://github.com/arq5x/bedtools2).
After read alignment, knee plots of cell-to-read fraction were generated to estimate the number of cell barcodes representing true cells. Digital gene expression matrices (DGEs) were then generated by counting gene transcripts for the number of cell barcodes selected based on the infliction points in the knee plots. To correct for any bead synthesis errors/read errors leading to false barcodes, transcript barcodes (unique molecular identifiers; UMIs) or cell barcodes were merged when they were within 1 Hamming or 2 Levenshtein distances, respectively. Barcodes containing < 2500 reads were excluded from the DGEs.
Downstream computational analyses of scRNA-seq data were mainly performed using the R package Seurat v2.3.3 (https://github.com/satijalab/seurat/releases/tag/v2.3.3) (Butler et al., Nat Biotechnol, 2018) by largely following the standard guidelines from the Satija lab (https://satijalab.org/seurat/). Seurat objects were generated with DGEs constructed as described above. Violin plots of number of expressed genes and unique transcripts (nGene and nUMI, respectively) of each cell were generated and outliers with too high or too low nGene/nUMI were removed to exclude potential cell doublets/aggregates or low quality cells/cell debris, respectively, based on each object/sample.
After the cell filtration step, retained cell barcodes were intersected with the original DGE files for each sample to generate the processed data files for downstream single cell analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files (.tsv) containing filtered cells/barcodes as columns and unique transcript count (nUMI) for each gene in each cell/barcode as rows.

molecule: polyA RNA

source_name: myogenic culture

growth_protocol: The parental H9 human pluripotent stem cells and engineered PAX7-GFP reporter cells were maintained on Matrigel-coated tissue culture plates in mTeSR1 medium. Cells were fed with fresh medium every day and passaged with 0.5 mM of EDTA every 4-6 days. Myogenic differentiations were carried out according to published protocols: HX protocol (Xi et al., Cell Rep, 2017), JC protocol (Chal et al., Nat Biotechnol, 2015) and MS protocol (Shelton et al., Stem Cell Rep, 2014).

extract_protocol:
Prepared single cell solutions were subjected to single cell capture and droplet formation following instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper (Macosko et al., Cell, 2015). Single cells were lysed in oil droplets and polyA-tailed mRNAs were captured by beads coated with barcoded oligonucleotides containing polyT tracks.
After cells were captured and lysed in oil-bead droplets, reverse transcription and library construction were performed according to instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper (Macosko et al., Cell, 2015). In brief, after droplets breakdown, cDNAs were made using Thermo Fisher Scientific Maxima H Minus Reverse Transcriptase and amplified using Roche HiFi HotStart ReadyMix. PCR products were made into sequencing-ready libraries with Illumina Nextera XT DNA Library Preparation Kit.

value: H9 human pluripotent stem cell (hPSC)

tag: differentiation protocol

tag: differentiation length

value: 43 days

tag: sorting/enrichment strategy

value: live


title: Emb Wk7.25 AP38

source_name: whole hindlimb

tag: developmental age

value: embryonic week 7.26

tag: carnegie stage

value: whole hindlimb


title: Emb Wk5 AP37

value: embryonic week 5


title: double_RNAseq_r3

description: double RNAseq replicate3


title: 1d_2

description:
microRNA
micRNAs from liver in 2-day pigeon


title: 1d_3

description:
microRNA
micRNAs from liver in 3-day pigeon


title: saur41/40/71/72 shoot part rep 2

city: Hangzhou

first: Ting

last: Qiu

address: 866 Yuhangtang Road

department: college of life science

institute: Zhejiang University

data_processing:
The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme, NR601) following manufacturer's recommendations.
Library concentration was measured using Qubit®  RNA Assay Kit in Qubit®  3.0 to preliminary quantify. Insert size was assessed using the Agilent Bioanalyzer 2100 system, and after the insert size consistent with expectations, qualified insert size was accurate quantified using qPCR by StepOnePlus Real-Time PCR system (ABI, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System (Illumia, USA) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumia Hiseq X Ten platform and 150bp paired-end module.
Genome_build: TAIR10.1
Supplementary_files_format_and_content: tab-delimited xls files include FPKM values for each sample

organism: Arabidopsis

source_name: the shoot part

extract_protocol:
Different parts of 5-day-old Arabidopsis seedlings were frozen and ground to powder in liquid nitrogen, followed by total RNA extraction using TRizol reagent (Takara Bio Inc., Kusatsu, Shiga, Japan).
otal RNA samples were sent to Vazyme Biotech Co., Ltd (Nanjing, China) to carry out library construction, Illumina HiSeq sequencing

value: the shoot part

value: saur41 subfamily quadruple mutant


title: 1d_1

description:
microRNA
micRNAs from liver in 1-day pigeon


title: saur41/40/71/72 shoot part rep 1


title: nrp1_chip_input_r1

description: nrp1 chip input replicate1

value: flowers

value: 4 weeks


title: saur41/40/71/72 root rep 2

source_name: Root

value: root


title: nrp1_chip_input_r2

description: nrp1 chip input replicate2


title: triple_h2az_input_r2

description: triple h2az input replicate2


title: nrp1_chip_myc_r1

description: nrp1 chip myc replicate1


title: saur41/40/71/72 root rep 1


title: triple_h2az_input_r1

description: triple h2az input replicate1


title: Col_RNAseq_r2

description: Col RNAseq replicate2

value: whole seedling


title: Col0 shoot part rep 1

value: wild type


title: triple_h2az_r2

description: triple h2az replicate2


title: triple_h2az_r1

description: triple h2az replicate1


title: nrp-d_h2az_r1

description: nrp-d h2az replicate1


title: nrp-d_h2az_r2

description: nrp-d h2az replicate2


title: Col0 root rep 2


title: Col0 root rep 1


title: OE-SAUR41 shoot part rep 2

value: SAUR41 overexpression


title: nrp1_chip_myc_r2

description: nrp1 chip myc replicate2


title: nrp-d_h2az_input_r2

description: nrp-d h2az input replicate2


title: OE-SAUR41 shoot part rep 1


title: 14d_1

value: white king

value: liver


title: Col-0 shoot part rep 2


title: Col-0 shoot part rep 1


title: col_h2az_r1

description: col h2az replicate1


title: Col0 shoot part rep 2


title: 72h_PBMC_T2_2

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

institute: Seoul National University

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat v2.0.12
Gene expression level was measured with Cufflinks v2.1.1
Differential expression analysis was performed by Cuffdiff
Genome_build: UMD3.1
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

organism: Bos taurus

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Prep Kit

tag: cell type

value: in vivo driven

value: 72 h infection


title: col_h2az_input_r2

description: col h2az input replicate2


title: OE-SAUR41 root rep 2


title: 72h_PBMC_T1_2


title: Col-0 root rep 2


title: col_chip_myc_r2

description: col chip myc replicate2


title: 72h_PBMC_C3

value: 72 h control


title: 72h_PBMC_T2_1


title: col_chip_input_r2

description: col chip input replicate2


title: Pto_pad4sid2_48h_3

city: Cologne

first: Tatsuya

last: Nobori

address: Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research

country: Germany

description: count.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the P. syringae pv. tomato DC3000 genome using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Bacteria isolated from Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
For RNA extraction, the TriFast solution was mixed with 200 μl of chloroform and the aqueous phase was isolated by centrifugation (typically 400 μl). The aqueous phase was mixed with 200 μl (half volume) of ethanol and then applied to the column of RNAqueous kit (Ambion). RNA was eluted in 30 μl of RNase free water following the manufacture’s protocol and treated with 2 U of TURBO DNase (Ambion) for 30 min at 37 ºC. Plant rRNAs were removed using Ribo-Zero plant kit (Epicentre) following the manufacture’s protocol.
cDNA libraries were generated with Ovation Complete Prokaryotic RNA-Seq kit 1-8 (NuGEN)

value: Pto

tag: host genotype

value: pad4-1 sid2-2

tag: replicate


title: Col-0 root rep 1

tag: age


title: Pto_pad4_48h_3

institute: Max-Planck Institute for Plant Breeding Research

description: count.txt


title: 72h_PBMC_T1_1


title: col_chip_myc_r1

description: col chip myc replicate1

tag: cultivar


title: col_chip_input_r1

description: col chip input replicate1

tag: tissue


title: 24h_PBMC_T2_1

value: 24 h infection


title: Pto_sid2_48h_3

description: count.txt

tag: strain


title: col_h2az_r2

description: col h2az replicate2


title: Pto_col_48h_3

description: count.txt


title: arp6-1_h2az_r2

description: arp6-1 h2az replicate2


title: nrp-d_h2az_input_r1

description: nrp-d h2az input replicate1


title: arp6-1_h2az_r1

description: arp6-1 h2az replicate1


title: 72h_PBMC_C2

tag: treatment


title: 24h_PBMC_T1_2


title: Pto_pad4sid2_48h_2

description: count.txt


title: 24h_PBMC_T1_1


title: arp6-1_h2az_input_r2

description: arp6-1 h2az input replicate2


title: OE-SAUR41 root rep 1

tag: genotype


title: Pto_pad4_48h_2

description: count.txt


title: arp6-1_h2az_input_r1

description: arp6-1 h2az input replicate1


title: 24h_PBMC_C2


title: Pto_sid2_48h_2

description: count.txt


title: 24h_PBMC_T2_3


title: Ischemia 4h-2

city: Chongqing

first: Chenyang

last: Duan

institute: Third Military Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: rnor6_NCBI
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Ischemia 4h_vascular

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ischemia 4h

value: superior mesenteric artery tissues (SMAs)


title: Ischemia 4h-3


title: 24h_PBMC_C1

value: 24 h control


title: Ischemia 4h-1


title: Pto_col_48h_2

description: count.txt


title: Pto_pad4_48h_1

description: count.txt


title: Pto_sid2_48h_1

description: count.txt


title: Pto_col_48h_1

description: count.txt


title: Ischemia 1h-1

source_name: Ischemia 1h_vascular

value: Ischemia 1h


title: Ischemia 1h-3


title: 3Dmodel of the human intestine in the presence of Entamoeba histolytica [A3]

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
Cells grown in collagen matrix; E. histolytica grown in vitro in culture medium.
processed data file: AvsC.complete.xls

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome (Human genome Hh38 from Ensembl, release 94).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1)
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model including the replicate effect as pairing factor was set in order to test for the differential expression between the two conditions with and without amoeba. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Human genome hg38 from Ensembl, release 94
Supplementary_files_format_and_content: AvsC.complete.xls: DESeq2 output

organism:
Homo sapiens
Entamoeba histolytica HM-1:IMSS

source_name: Human cells and Entamoeba histolytica HM1:IMSS

growth_protocol:
We used four different cell lines. Caco-2/TL7 (ATCC, USA) cell line was added to replicate spatial distribution of epithelial colon. HT29-MTX (ATCC, USA) cells were employed to produces mucin in the epithelial layer. CCD-18Co cell line (ATCC, USA) was used to mimic the intestinal lamina propia. THP-1 cells (ATCC, USA) were differentiated to macrophages and added into lamina propia to replicate the immune response during parasites infection. As extracellular matrix (ECM), was employed Collagen type I from rat tail (Corning, USA). All the cell lines were cultured according with supplier recommended conditions (ATCC, USA). THP-1 cells differentiated to macrophages with phorbol-12-myristate-13-acetate (PMA) (SIGMA-ALDRICH, USA) at 25 ng/ml).
Entamoeba histolytica HM1:IMSS was grown under in vitro conditions using the Diamond medium (Diamond, L. S., et al. (1978). "A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba." Transactions of the Royal Society of Tropical Medicine and Hygiene 72: 431-432).

extract_protocol:
1ml of Trizol reagent (Qiagen) was added to the sample and incubated for 5 min at room temperature, then 200 µl of chloroform were added. After 2 min incubation at room temperature, the samples were spin down at 12000 x g, 15 min at 4°c. The supernatant was complete with 70% ethanol (V/V) and then transferred to a RNeasy Mini spin column (Qiagen) and the RNA was recovered according to the Qiagen' protocol.
DNase treated RNA molecules isolated from - description of conditions - were treated for library preparation using the TruSeq Stranded mRNA sample preparation kit (Illumina, San Diego, California) according to manufacturer’s instructions. An initial poly(A) RNA isolation step (included in the Illumina protocol) is performed on n ng of total RNA to keep only the polyadenylated RNA fraction and remove the ribosomal RNA. A step of fragmentation is then performed on the enriched fraction, by divalent ions at high temperature. The fragmented RNA samples were randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. No end repair step was necessary. An adenine was added to the 3'-end and specific Illumina adapters were ligated. Ligation products were submitted to PCR amplification. The obtained oriented libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen).
Sequencing was performed on the Illumina Hiseq2500 platform to generate single-end 65 bp reads bearing strand specificity.

treatment_protocol: Upon 22 days of human cells grown, E. histolytica (8x10 exp5) was added to the apical side of cell cultures and incubated at 37°C for two hours. The all sample was treated for RNA extraction.

tag: human cell line

value: Caco-2, Ht-29, ThP-1, CCD-18Co


title: Normal-3

address: Changjiang Road, Yuzhong District

value: Normal


title: Ischemia 1h-2


title: Normal-1


title: Normal-2


title: Pto_pad4sid2_48h_1

description: count.txt


title: 3Dmodel of the human intestine in the presence of Entamoeba histolytica [A2]


title: 3Dmodel of the human intestine in the presence of Entamoeba histolytica [A1]


title: Os14: Reprodutive R2

status: Public on Apr 28 2020

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

description: Plants were exposed to saline shock only at the reproductive stage (R0-R1)

data_processing:
Illumina Casava1.7 software used for basecalling.
For quality analysis of the reads was used FastQC Ver. 0.11.7 software and later the Trimmomatic Ver. 0:35 program to remove adapters and poor quality bases in each library. The reads were mapped against the O. sativa cv. Nipponbare (IRGSP build 1.0) from the MSU Rice Genome Annotation Project (RGAP 7) Database using STAR Ver. 2.7 software (Default parameters). HTSeq Ver. 0.11.1 software was used to count mapped reads.
Identification of differentially expressed genes (DEGs) was performed in the R Ver. 3.5.2 statistical environment with the edgeR Ver. 3.8 package, obtained from the Bioconductor repository. The raw reads were transformed to counts per million (CPM), keeping the genes with CPM values >1, and then normalised by the trimmed mean of M values method (TMM), considering DEGs with false discovery rates (FDRs) of <0.05 by the edgeR test.
Genome_build: MSU Ver. 7
Supplementary_files_format_and_content: tab-delimited text files include count values by gene for each sample

organism: Oryza sativa Indica Group

source_name: Reprodutive R2

growth_protocol: Rice seeds, genotype BRS Ligeirinho (Oryza sativa L. ssp. Indica), were germinated in a paper roll in a BOD type growth chamber (Model 202, EletroLab, São Paulo, Brazil), with a photoperiod of 16 h of light and 8 h of darkness and a temperature of 25±2 °C, and they were kept there for seven days. After this period, the seedlings were transferred to 8-L plastic pots, drilled at the base to ensure perfect percolation of water. As substrate, sand previously washed with water and 1% hydrochloric acid was used. The plants were kept in a greenhouse with 70% relative humidity, a temperature of 25±2 oC, and daily irrigation, alternated with water and nutrient solution of Hoagland and Arnon (1950).

extract_protocol:
Collected leaf tissues were immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen Inc., Carlsbad, CA, USA) and treated with DNase I (Invitrogen Inc., Carlsbad, CA, USA). Illumina TruSeq RNA Sample Preparation® V2 (IlluminaTM) kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: I) control (C): plants received irrigation with water and nutrient solution throughout the experiment; II) vegetative (S V ), plants were exposed to saline shock only at the vegetative stage; III) reproductive (S R ) plants were exposed to saline shock only at the reproductive stage; and IV) vegetative + productive (S V+R ), plants were exposed to saline shock at the vegetative stage (first shock event) and at the reproductive stage (recurrent event)

value: BRS Ligeirinho

value: Leaf tissue

value: Sensitive to salt stress


title: Os9: Control R1

description: Rice plants under normal condition

source_name: Control R1


title: Os16: Vegetative R2

description: Plants were exposed to saline shock only at the vegetative stage (V4)

source_name: Vegetative R2


title: Os11: Reprodutive and vegetative R1

description: Plants were exposed to saline shock at the vegetative stage (V4 - first shock event) and at the reproductive stage (R0-R1 - recurrent event)

source_name: Reprodutive and vegetative R1


title: Os10: Control R2

description: Rice plants under normal condition

source_name: Control R2


title: Os12: Reprodutive and vegetative R2

source_name: Reprodutive and vegetative R2


title: Os13: Reprodutive R1

source_name: Reprodutive R1


title: PCC6803_WT.N1

city: Freiburg

first: Vanessa

last: Krauspe

address: Schänzlestraße 1

institute: Uni Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 0.5 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normalized by the cyclicloess method.

organism: Synechocystis sp. PCC 6803

source_name: WT in the absence of nitrogen

label_protocol: DNAse treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol and as detailed by Voß and Hess (2014).

growth_protocol: Axenic cultures of glucose-tolerant Synechocystis sp. PCC 6803 strains (wild type) and a nblD knockout mutant used in this study were propagated in 50 ml liquid batch cultures in BG11 medium (Rippka et al., 1979) at 30 °C under continuous illumination and shaking, starved cultures grew 3 hours without nitrogen supply in the medium.

extract_protocol: RNA for microarray hybridization was extracted via the PGTX method adapted from Pinto et al (Pinto et al., 2009). Therefore, 30 ml cyanobacterial cultures (OD750 ~1.0) were harvested through vaccuum filtration using hydrophilic polyethersulfone filters (Pall Supor®-800, 0.8 μm). The filter were immersed in 1 ml PGTX, and snap frozen in liquid nitrogen and stored at -80°C until continuing with the extraction. Samples were then incubated for 10 min at 65°C in waterbath. After addition of 1 ml of chloroform/isoamylalcohol (24:1) and thorough agitation, samples were incubated at room temperature for 5 min. Samples were centrifuged with a swing out rotor at 4000 x g, RT for 3 min. The supernatant was transferred into sterile RNase-free 2 ml cups and mixed with an equal amount of the chloroform:isoamyl alcohol mixture (24:1) before another centrifugation step for 3 min at 4000 x g was performed and the extraction was repeated. An equal amount volume of isopropanol was added to the supernatant before incubation at -80°C overnight. Finally, the samples were centrifugated for 30 min at 12000 x g and 4°C before washing the resulting pellet with 300 µl of 70 % (v/v) cold ethanol. After removing the supernatant, the pellet was air dried. The resulting RNA was then diluted in the desired amount of RNase-free water for further use.

treatment_protocol: To induce the nitrogen depletion to wild type and mutant cultures, cells were centrifuged in sterile buckets, carefully washed with BG11 without NaNO3 and resuspended in fresh BG11 without nitrogen source. The harvesting for RNA isolation was done 3 hours after triggering the nitrogen stress.

value: WT


title: PCC6803_WT1

source_name: WT in the presence of nitrogen


title: PCC6803_KO.N1

source_name: nblD KO mutant in the absence of nitrogen

value: nblD knock out


title: PCC6803_KO2

source_name: nblD KO mutant in the presence of nitrogen


title: PCC6803_KO1


title: PCC6803_KO.N2


title: Os15: Vegetative R1

source_name: Vegetative R1


title: WT H3K27me3 rep2

city: Gif-sur-Yvette

first: Déborah

last: MANZA MIANZA

address: 630 Rue Noetzlin

institute: Institut des Sciences des Plantes - Paris Saclay

data_processing:
Trimming files where generated with Trimmomatic
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.3.3 with –very-sensitive parameter option
Peaks were called using Macs2 version 2.1.2 with the following setting: -qvalue 0.05, -extsize 200, -broad -g 1.35e8
Bigwig were generated using bamCoverage from Deeptool with the following setting:  --normalizeUsing RPGC --extsize 400, --smooth 60, --effectiveGenomeSize 120000000, exclude chromosome chloroplast and Mitocondria
Genome_build: TAIR10
Supplementary_files_format_and_content: RPGC normalized bigwig for plots generated with ComputeMatrix plotprofile of Deeptool with the following setting : -a 2000, -b 2000, -m 2000, -bs 20, -skipZeros
Supplementary_files_format_and_content: Called Peaks files were annotated with bedtools intersect with the TAIR10 genome

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis thaliana ecotype Colombia (Col-0) and gcn5 mutants (SALK_106557C and SALK_030913C) were used in this study. Plants were grown in chambers at 20°C on sterile half-strength MS medium and 0.8% agar under long-days (16h of light at 20°C, 8h of darkness at 18°C). Seeds were surface-sterilized by treatment with bayrochlore for 20 min, washed, and imbibed in sterile-water for 2–4 days at 4 °C to obtain homogeneous germination.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions using the « NEBNext Ultra II DNA library kit for Illumina »

tag: chip antibody


title: gcn5-2 H3K27me3 rep2


title: WT H3K9ac rep1


title: gcn5-2 H3K9ac rep1


title: gcn5-2 H3K9ac rep2


title: WT H3K27me3 rep1


title: gcn5-2 H3K14ac rep2


title: PCC6803_WT2


title: gcn5-2 H3K14ac rep1


title: PCC6803_WT.N2


title: WT H3K9ac rep2


title: gcn5-2 H3K27me3 rep1


title: gcn5-1 H3K14ac

value: Anti-H3K14ac (millipore 07-353)


title: WT H3K14ac rep2


title: WT H3K14ac rep1


title: GCN5-GFP rep2

value: Anti-GFP (Abcam, ab290)


title: GCN5-GFP rep1


title: gcn5-2 H3K14ac rep3


title: col_h2az_input_r1

description: col h2az input replicate1

source_name: Arabidopsis flowers

value: flowers

value: 4 weeks


title: WT27_regressive

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

description: Gene expression after preoperative chemotherapy.

hyb_protocol: The mRNA expression profile was determined using Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray according to the manufacturers recommendations.

scan_protocol: Microarrays were scanned using the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Agilent Feature Extraction Software. The limma package (PMC4402510) was then used for background correction (method="normexp", offset=16) and normalization between the arrays (method=quantile). After normalization all values were log2 transformed.

source_name: Wilms tumor, regressive

extract_protocol: Total RNA including miRNAs was isolated from tumor and control tissue using the miRNeasy Kit (Qiagen, Hilden, Germany) according to manufacturers instructions. RNA concentration and integrity were assessed using NanoDrop2000 (Thermo Fisher Scientific, Waltham, MA, USA) and bioanalyzer run using the PicoRNA Chip (Agilent Technologies, Santa Clara, CA, USA).

tag: disease state

value: Wilms tumor

tag: histological subtype

value: Regressive subtype

tag: risk group

value: intermediate risk

tag: age in month

tag: gender

value: male


title: WT23_focal_anaplasia

source_name: Wilms tumor, focal anaplasia

label_protocol: The mRNA expression profile was determined using Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray according to the manufacturers recommendations.

value: Focal anaplasia


title: WT17_blastemal-subtype

source_name: Wilms tumor, blastemal-subtype

value: Blastemal subtype

value: high risk


title: WT11_blastemal-subtype


title: WT32_triphasic-subtype

source_name: Wilms tumor, triphasic-subtype

value: Triphasic subtype

value: female


title: WT12_blastemal-subtype


title: WT21_diffuse-anaplasia

source_name: Wilms tumor, diffuse-anaplasia

value: Diffuse anaplasia


title: WT8_blastemal-subtype


title: WT19_completely-necrotic

source_name: Wilms tumor, completely-necrotic

value: Completely necrotic

value: low risk


title: WT22_epithelial-subtype

source_name: Wilms tumor, epithelial-subtype

value: Epithelial subtype


title: WT16_blastemal-subtype


title: WT24_regressive


title: WT29_stromal-subtype

source_name: Wilms tumor, stromal-subtype

value: Stromal subtype


title: WT28_regressive


title: WT30_triphasic-subtype


title: WT18_completely-necrotic


title: WT31_triphasic-subtype


title: WT15_blastemal-subtype


title: WT14_blastemal-subtype


title: WT5_blastemal-subtype


title: WT20_diffuse-anaplasia


title: WT10_blastemal-subtype


title: WT13_blastemal-subtype


title: WT7_blastemal-subtype


title: WT33_triphasic-subtype


title: WT25_regressive


title: WT26_regressive


title: WT9_blastemal-subtype


title: WT1_blastemal-subtype


title: WT4_blastemal-subtype


title: WT6_blastemal-subtype


title: MIX_par_339

city: New York

first: Kalpana

last: Gopalakrishnan

state: NY

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from Parous rat mammary tissues at postnatal day 181 following treatment with a mixture of diethyl phthalate, methyl paraben and triclosan from postnatal day 1 to postnatal day 180

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0 St arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: Quality control of .CEL files and pre-processing by robust multiarray average (RMA) method were done using expression console software (Affymetrix, CA).  Batch effects were removed using ComBat package (Leek et al. 2012) in RStudio (R 3.0.2).  Data submitted here have not been corrected for batch effects. Batch information is provided in the sample datasheet.

source_name: Parous rats treated with a mixture of diethyl phthalate, methyl paraben and triclosan from postnatal day 1 to 180

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, Affymetrix 2015).

growth_protocol: Animal studies were carried out at Cesare Maltoni Cancer Research Centre/Ramazzini Institute (CMCRC/RI) (Bentivoglio, Italy) in accordance with the rules of Italian law for Animal Welfare (Decreto Legislativo 26, 2014), following the principles of Good Laboratory Practices and Standard Operating Procedures of the CMCRC/RI facility, which include authorization by the ethical committee.  The experiment used female Sprague-Dawley (SD) rats which belong to the colony that has been used for over 40 years in the laboratory of the CMCRC/RI.  There were no siblings in each treatment group and they were randomized so as to have minimal differences in body weight among them (standard deviation <10% of the average).  Animals were housed in makrolon cages (41x25x15 cm) at 2 or 3 per cage, with a stainless steel wire top and a shallow layer of white wood shavings as bedding (Giuseppe Bordignon supplier, reviso, Italy).  All animals were kept in a single room at 23 ± 3°C and at 40-60% relative humidity.  Lighting was artificial and the light/dark cycles were tended to be 12 hours each.  All animals were given the same standard “Corticella” pellet diet (Piccioni Laboratory, Milan, Italy).  Feed and tap water were available ad libitum and were both periodically analyzed to exclude biological and chemical contamination (mycotoxins, pesticides, arsenic, lead, mercury, selenium).

extract_protocol: The fifth left and right caudal mammary glands were collected, pulverized in liquid nitrogen and total RNA was extracted using Maxwell 16 LEV simplyRNA Blood kit (Promega, WI) or by Direct-zol RNA MiniPrep kit (Zymo Research, CA).  RNA extraction information ('Promega' or 'Zymo') is provided in the sample datasheet. Total RNA concentration was determined using Nanodrop (Thermo Scientific, MA), and RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, CA). Samples with RNA Integrity Number ≥ 7 were used for microarrays.  Transcriptomes were profiled by GeneChip Rat Gene 2.0 ST arrays (Affymetrix, CA) at the Yale Center for Genome Analysis (Yale School of Medicine, CT).

treatment_protocol: There were four experimental groups: parous and age-matched nulliparous, treated with DEP or vehicle, olive oil.  There were 5 animals per experimental group.  Animals were weighed weekly to determine treatment dose.  F0 generation corresponds to breeders of the experimental animals (F1).  F1 animals were treated daily from postnatal day (PND) 1 to PND 28 through milk of their dams (F0), which were gavaged orally with DEP or vehicle.  After weaning at PND 28, F1 animals were treated with DEP or vehicle by oral gavage 3 times a week until PND 180 and sacrificed at PND 181.  Parous rats were mated (outbred) at PND 97 and treatment was continued through pregnancy, delivery of pups (F2) and lactation.  At the time of sacrifice of parous rats on PND 181, F2 pups had completed weaning.  Animals were euthanized via carbon dioxide inhalation and necropsy was immediately performed for collection of mammary tissues.  Animals were sacrificed on the same day and at random during the estrous cycle.

value: Sprague-Dawley

tag: Sex

value: Caudal mammary tissue

tag: exposure/treatment condition

value: Mixture of diethyl phthalate, methyl paraben and triclosan

tag: window of exposure

value: Birth to adulthood, Parous

tag: age at sacrifice

value: Rats sacrificed at postnatal day 181

tag: batch

value: Two

tag: rna extraction kit

value: Zymo


title: OIL_par_441

description: Gene expression data from Parous rat mammary tissues at postnatal day 181 following treatment with olive oil (control) from postnatal day 1 to postnatal day 180

source_name: Parous rats treated with olive oil (control) from postnatal day 1 to 180

tag: tissue

value: Olive oil

value: One

value: Promega


title: WT2_blastemal-subtype

value: Wilms tumor

value: Blastemal subtype

value: high risk


title: OIL_null_431

description: Gene expression data from nulliparous rat mammary tissues at postnatal day 181 following treatment with olive oil (control) from postnatal day 1 to postnatal day 180

source_name: Nulliparous rats treated with olive oil (control) from postnatal day 1 to 180

tag: strain

value: female

value: Birth to adulthood, Nulliparous


title: MIX_par_338


title: TCS_par_239

description: Gene expression data from Parous rat mammary tissues at postnatal day 181 following treatment with triclosan from postnatal day 1 to postnatal day 180

source_name: Parous rats treated with triclosan from postnatal day 1 to 180

value: Triclosan


title: OIL_par_442


title: OIL_null_428


title: TCS_par_238


title: OIL_null_429


title: WT3_blastemal-subtype


title: TCS_par_237


title: MIX_null_330

description: Gene expression data from nulliparous rat mammary tissues at postnatal day 181 following treatment with a mixture of diethyl phthalate, methyl paraben and triclosan from postnatal day 1 to postnatal day 180

source_name: Nulliparous rats treated with a mixture of diethyl phthalate, methyl paraben and triclosan from postnatal day 1 to 180


title: MIX_null_329


title: TCS_par_240


title: OIL_par_446


title: MIX_par_341


title: OIL_null_430


title: MIX_par_337


title: MIX_null_331


title: MIX_null_328


title: OIL_par_444


title: TCS_par_243


title: MIX_par_340


title: MIX_null_327


title: OIL_null_427


title: TCS_null_231

description: Gene expression data from nulliparous rat mammary tissues at postnatal day 181 following treatment with triclosan from postnatal day 1 to postnatal day 180

source_name: Nulliparous rats treated with triclosan from postnatal day 1 to 180


title: TCS_null_230


title: TCS_null_229


title: TCS_null_228


title: OIL_par_440


title: DEP_par_46

description: Gene expression data from Parous rat mammary tissues at postnatal day 181 following treatment with diethyl phthalate from postnatal day 1 to postnatal day 180

source_name: Parous rats treated with diethyl phthalate from postnatal day 1 to 180

value: Diethyl phthalate


title: MPB_par_139

description: Gene expression data from Parous rat mammary tissues at postnatal day 181 following treatment with methyl paraben from postnatal day 1 to postnatal day 180

source_name: Parous rats treated with methyl paraben from postnatal day 1 to 180

value: Sprague-Dawley

value: Methyl paraben


title: MPB_par_141

value: Caudal mammary tissue


title: MPB_par_142

value: Birth to adulthood, Parous


title: MPB_null_127

description: Gene expression data from nulliparous rat mammary tissues at postnatal day 181 following treatment with methyl paraben from postnatal day 1 to postnatal day 180

source_name: Nulliparous rats treated with methyl paraben from postnatal day 1 to 180

value: Rats sacrificed at postnatal day 181


title: DEP_par_38

value: Two


title: MPB_par_137


title: MPB_null_131

value: Zymo


title: TCS_null_227


title: MPB_null_129


title: MPB_null_130


title: DEP_par_40


title: DEP_null_30

description: Gene expression data from nulliparous rat mammary tissues at postnatal day 181 following treatment with diethyl phthalate from postnatal day 1 to postnatal day 180

source_name: Nulliparous rats treated with diethyl phthalate from postnatal day 1 to 180


title: MPB_par_143


title: MPB_null_128


title: DEP_par_37


title: DEP_par_41


title: DEP_null_29


title: VP29

city: Houston

first: Nicholas

last: Mitsiades

state: Texas

address: One Baylor Plaza

department: Medicine-Hematology & Oncology

institute: Baylor College of Medicine

description: SAMPLE 11

hyb_protocol: The aRNA was prepared for direct hybridization by diluting to the appropriate concentration following the Whole-Genome Gene Expression Direct Hybridization (Illumina, Inc.; San Diego, CA) assay guide. The biotin-labeled samples were loaded onto Beadchip arrays which contain complementary gene-specific sequences and incubated at 58°C for approximately 18 hrs. The arrays were removed from overnight incubation and washed as per the manufacturer’s recommendation.

scan_protocol: Cy3-Streptavidin was added to introduce fluorescent and differential detection of the signal to the analytical probes that have been hybridized to the array by the use of the Illumina iScan (Illumina, Inc.; San Diego, CA). An internal laser was utilized to excite the fluorophore product on the array allowing light emissions to be recorded in high-resolution imagery. The GenomeStudio (V2011.1) Gene Expression Analysis Module (v1.9.0) was applied to the scanned microarray images where preliminary quality control data was assessed.

data_processing:
Raw data were imported to the R environment and processed using the Illumina-specific package lumi. Background Correction (bgAdjust), Variance-stabilizing transformation (VST), and quantile normalization were applied.
Gene expression differences were derived utilizing the t-test and imposing a fold change exceeding 4/3x (p<0.05), using the R statistical system. Enriched pathways were inferred using the Gene Set Enrichment Analysis (GSEA) method1, and the Molecular Signature Database (MSigDB) pathway collection2. Gene sets with a nominal P value <0.05 and FDR < 0.25 were defined as significantly enriched.

label_protocol: RNA samples were put through the Illumina TotalPrep RNA Amplification Kit (Ambion by Life Technologies; Carlsbad, CA) to generate biotinylated, amplified RNA (aRNA) for downstream processing. In summary, a reverse transcriptase with an oligo(dT) primer was utilized in first strand synthesis to produce cDNA containing a T7 promoter sequence.  Second strand synthesis followed, whereby the product became the template for in vitro transcription with T7 RNA polymerase along with biotin-UTP.  After purification of the aRNA, the samples were subjected to quantitation utilizing the spectrometric Quant-iT RiboGreen assay (Invitrogen, Ltd.; Eugene, OR).

growth_protocol: The Mel202 cell line (carrying both a GNAQ Q209L and a GNAQ R210K mutations) was established from a previously irradiated, locally recurrent primary uveal melanoma by Dr. B.R. Ksander (Schepens Eye Research Institute, Boston, USA) and was generously provided by Dr. Demetrios Vavvas, Massachusetts Eye and Ear Infirmary and Schepens Eye Research Institute, Harvard Medical School, Boston, MA. Cells were confirmed to be BRAF-wt. Cells were grown in DMEM/F12 (Invitrogen, Carlsbad, CA) with 100 units/ml penicillin, 100 μg/ml streptomycin, and 10% FBS (in a 37C incubator in a humid environment with 5% CO2) and were passaged for <6 months.

extract_protocol: Following treatment, cells were harvested in RNAlater (Qiagen; Germantown, MD) and RNA was isolated using the RNeasy Micro Kit (Qiagen). Briefly, an equal number of cells were centrifuged at high speeds to remove RNAlater. Buffer RLT with 1% beta-mercaptoethanol was utilized for cell lysis followed by homogenization using a QIAshredder spin column.  RNA was precipitated with 70% EtOH and transferred to the RNeasy MinElute spin column.  Samples were treated with DNase, washed, and eluted as per the manufacturer’s instructions. The RNA integrity for each sample was assessed with a RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent; Santa Clara, CA). RNA integrity score (RIN) for all samples was at least 9.9.

treatment_protocol: ICG-001 was purchased from Selleckchem (Houston, TX). GNAQ-mutant Mel202 uveal melanoma cells were treated, in their regular medium, with ICG-001 (3 μM, dissolved in DMSO) or DMSO control for 24h or 48h in 6-well plates.

tag: cell line

tag: cell type

value: uveal melanoma (UM) cell line

tag: treatment


title: VP31a

description: SAMPLE 13


title: VP28

description: SAMPLE 10

source_name: Mel202_48 hr DMSO Control

value: 48 Hr. DMSO Control


title: VP31b

description: SAMPLE 14


title: DEP_null_31


title: CRTX_10mAD135

city: Jerusalem

first: Naomi

last: Habib

address: Safra Campus

department: Center for brain sciences

institute: Hebrew University of Jerusalem

description: Admouse_Crtx_7-10m_Astrocytes_UMIcounts.csv

data_processing:
De-multiplexing, alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using the Cellranger toolkit (version 2.1.1, chemistry V2, or version 3.0.2, chemistry V3) provided by 10X Genomics for chemistry Single Cell 3’, and run using cloud computing on the Terra platform (https://Terra.bio).
Filtering of cells with less than 400 detected genes,  filtering of genes that were detected in fewer than 10 nuclei, in R
Selecting astrocyte cells and merging datasets with Seurat software version 3.0
Genome_build: mm10
Supplementary_files_format_and_content: Unique mulecule identifiers (UMIs, or transcripts) counts per gene (rows) across cell (columns)

source_name: Brain

extract_protocol:
Brain tissue was frozen after dissociation until nuclei isolation. Tissue was transferred into a dounce homogenizer with 2mL of EZ Lysis Buffer or NP40 Lysis Buffer. Tissue was carefully dounced while on ice, then transferred to a 15mL conical tube. with 3mL of additional lysis buffer. When using EZ, the lysis homogenate was incubated on ice for 5 mins, for NP40 buffer no incubation was done. The samples were centrifuged with a swinging bucket rotor at 500g for 5 mins at 4C. Supernatant was removed and the pellet was resuspended in PBS (for EZ lysis) or Tris buffer (for NP40 lysis). Resuspended nuclei were gently filtered through 40um FlowMi cell strainers into 1.5mL Eppendorf tubes.
10,000 nuclei were used as input to 10X Genomics single-cell 3’ Gene Expression v2 assay (22 samples) or v3 assay (10 samples). Libraries were prepared following the manufacturer’s protocol.

tag: age

tag: region

value: Cortex


title: HIP_WT_74

description: Admouse_Hippocampus_7m_AllNuclei_UMIcounts.txt

value: Hippocampus


title: VP11

description: SAMPLE 6


title: VP27b

description: SAMPLE 9


title: DEP_null_27


title: VP09b

description: SAMPLE 5


title: VP12

description: SAMPLE 7


title: VP07

description: SAMPLE 1

source_name: Mel202_24 hr DMSO Control

value: 24 Hr. DMSO Control


title: CRTX_10mWT124


title: HipR-AD-G3-2w


title: CRTX_7mAD343


title: HipR-AD-G1-4w


title: HIP_WT_39


title: HIP_10mAD135

description: Admouse_Hippocampus_3TimeCourses_Astrocytes_WT_AD_Aging.csv


title: HIP_AD-untreat_52


title: VP08b

description: SAMPLE 3


title: CRTX_7mWT341


title: HIP_10mWT124


title: Untreated-Hip-R-N37


title: HIP_7mAD343


title: HIP_4mAD186


title: HIP_6wWT330


title: Wt-Hip-R-N74


title: HIP_6wAD331


title: HIP_7mWT341


title: HipR-WT-G1-4w


title: HipR-WT-G3-2w


title: zebrafish_990s_P3

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the zebrafish reference genome (danRer11) using TapHat2, Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the three sample-plates (plate_123, plate_989, plate_990) were combined into one expression matrix file
counts data was processed and analyzed using velocyto, SingleCellExperiment and pagoda2 packages in R-software
Genome_build: GRCz11 (danRer11)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

organism: Danio rerio

source_name: zebrafish

extract_protocol:
FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin-EDTA and 10U Dnase I for 30min at 30°C
RNA libraries were prepared using standard SmartSeq2 protocol

value: embryo trunk

tag: starin

value: vegfc:Gal4FF;UASGFP; kdrl:mCherry

value: 48 hpf


title: zebrafish_990s_P8


title: zebrafish_990s_P7


title: zebrafish_990s_P9


title: zebrafish_990s_P6


title: zebrafish_990s_P5


title: zebrafish_990s_P21


title: zebrafish_990s_P19


title: zebrafish_990s_P22


title: zebrafish_990s_P17


title: HIP_4mWT185

organism: Mus musculus


title: zebrafish_990s_P18


title: zebrafish_990s_P20


title: zebrafish_990s_P16


title: zebrafish_990s_P15


title: zebrafish_990s_P14


title: zebrafish_990s_P13


title: zebrafish_990s_P12


title: VP08a

description: SAMPLE 2


title: zebrafish_990s_O7


title: zebrafish_990s_O9


title: zebrafish_990s_P10


title: zebrafish_990s_O5


title: zebrafish_990s_O24


title: zebrafish_990s_O3


title: zebrafish_990s_P2


title: zebrafish_990s_O4


title: zebrafish_990s_O23


title: zebrafish_990s_O21


title: zebrafish_990s_O20


title: zebrafish_990s_O2


title: zebrafish_990s_O19


title: zebrafish_990s_O18


title: zebrafish_990s_O17


title: zebrafish_990s_P11


title: zebrafish_990s_O16


title: zebrafish_990s_O8


title: zebrafish_990s_P1


title: zebrafish_990s_O15


title: zebrafish_990s_O14


title: zebrafish_990s_O6


title: zebrafish_990s_O12


title: zebrafish_990s_O13


title: zebrafish_990s_O10


title: zebrafish_990s_N9


title: zebrafish_990s_O11


title: zebrafish_990s_O22


title: zebrafish_990s_N8


title: zebrafish_990s_O1


title: zebrafish_990s_N6


title: zebrafish_990s_N4


title: zebrafish_990s_N3


title: zebrafish_990s_N24


title: zebrafish_990s_N22


title: zebrafish_990s_N21


title: zebrafish_990s_N20


title: zebrafish_990s_N19


title: zebrafish_990s_N11


title: zebrafish_990s_N16


title: zebrafish_990s_N12


title: zebrafish_990s_N13


title: zebrafish_990s_N18


title: zebrafish_990s_N17


title: zebrafish_990s_N5


title: zebrafish_990s_N10


title: zebrafish_990s_M7


title: zebrafish_990s_M9


title: zebrafish_990s_M6


title: zebrafish_990s_M4


title: zebrafish_990s_M5


title: zebrafish_990s_M3


title: zebrafish_990s_M23


title: zebrafish_990s_M22


title: zebrafish_990s_M8


title: zebrafish_990s_M21


title: zebrafish_990s_N23


title: zebrafish_990s_N2


title: zebrafish_990s_M2


title: zebrafish_990s_M18


title: zebrafish_990s_N1


title: zebrafish_990s_M13


title: zebrafish_990s_M15


title: zebrafish_990s_M16


title: zebrafish_990s_M17


title: zebrafish_990s_M12


title: zebrafish_990s_M19


title: zebrafish_990s_M14


title: zebrafish_990s_M24


title: zebrafish_990s_M10


title: zebrafish_990s_M11


title: zebrafish_990s_L5


title: zebrafish_990s_L8


title: zebrafish_990s_L6


title: zebrafish_990s_L9


title: zebrafish_990s_L4


title: zebrafish_990s_L7


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title: zebrafish_990s_L3


title: zebrafish_990s_M20


title: zebrafish_990s_L22


title: zebrafish_990s_L21


title: zebrafish_990s_L24


title: zebrafish_990s_L20


title: DEP_null_28

value: female

value: Birth to adulthood, Nulliparous


title: VP27a

description: SAMPLE 8


title: zebrafish_990s_L2


title: zebrafish_990s_L19


title: VP09a

description: SAMPLE 4


title: VP30

description: SAMPLE 12


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title: zebrafish_990s_C24


title: zebrafish_990s_B3


title: zebrafish_990s_B24


title: vtRNA1.3KO_starvation_rep3

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

data_processing:
sequencings were performed in tecnical replicates, which is why per count table 4 fastq files exist
Mapping performed using Kallisto software v0.44.0 (-b 100 --rf-stranded)
counting was performed using Kallisto
DESeq analysis was performed using the Sleuth software v 0.20.0
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: counts table

source_name: HeLa cells

growth_protocol: Cells were grown to 80% confluency and starved for 24h (where indicated).

extract_protocol:
Cells were washed in PBS, all liquid was removed and cells were lysed in TRI reagent. RNA was double purified using PCI.
[mRNA enrichment]  poly-A-Enrichment via oligo-dT-beads
polyA enriched mRNAs were transformed into a cDNA library using the Illumina TrueSeq stranded mRNA Kit. Library size was determined using Qbit.
mSeq of poly-A enriched RNA

value: HeLa

tag: vtrna expression

value: KO cells, no vtRNA1.3 expression

value: starvation


title: vtRNA1.3KO_starvation_rep1


title: vtRNA1.3KO_control_condition_rep3


title: zebrafish_990s_B22


title: vtRNA1.3KO_control_condition_rep1


title: zebrafish_990s_B21


title: zebrafish_990s_B20


title: vtRNA1.3KO_control_condition_rep2


title: zebrafish_990s_C10


title: zebrafish_990s_C11


title: zebrafish_990s_B19


title: zebrafish_990s_B2


title: zebrafish_990s_B9


title: vtRNA1.1KO_starvation_rep1

value: KO cells, no vtRNA1.1 expression


title: vtRNA1.1KO_starvation_rep2


title: vtRNA1.1KO_control_condition_rep3


title: zebrafish_990s_B18


title: vtRNA1.1KO_control_condition_rep2


title: zebrafish_990s_B17


title: zebrafish_990s_B16


title: vtRNA1.3KO_starvation_rep2


title: zebrafish_990s_B15


title: zebrafish_990s_I3


title: zebrafish_990s_B14


title: vtRNA1.1KO_control_condition_rep1


title: vtRNA1.1KO_compensation_starvation_rep3

value: KO cells, lentiviral transduction


title: zebrafish_990s_B23


title: vtRNA1.1KO_compensation_starvation_rep2


title: zebrafish_990s_B13


title: vtRNA1.1KO_compensation_starvation_rep1


title: zebrafish_990s_B12


title: vtRNA1.1KO_starvation_rep3


title: vtRNA1.1KO_compensation_control_condition_rep3


title: zebrafish_990s_B11


title: vtRNA1.1KO_compensation_control_condition_rep2


title: WT_total mRNA_starvation_rep3

value: WT cells - endogenous expression


title: zebrafish_990s_A8


title: WT_total mRNA_starvation_rep1


title: zebrafish_990s_A9


title: zebrafish_990s_A7


title: WT_total mRNA_starvation_rep2


title: WT_total mRNA_control_condition_rep3


title: zebrafish_990s_A6


title: zebrafish_990s_A5


title: zebrafish_990s_A4


title: WT_total mRNA_control_condition_rep1


title: WT_total mRNA_control_condition_rep2


title: zebrafish_990s_A3


title: zebrafish_990s_A24


title: zebrafish_990s_A23


title: zebrafish_990s_A22


title: zebrafish_990s_B10


title: zebrafish_990s_B1


title: vtRNA1.1KO_compensation_control_condition_rep1


title: zebrafish_990s_A20


title: zebrafish_990s_A2


title: zebrafish_990s_A19


title: zebrafish_990s_A18


title: T-5488

city: Hefei

first: Bin

last: Li

address: NO. 96 Jinzhai Road

institute: University of Science and Technology of China

description: ftATAC-seq data of mouse thymoctyes

data_processing:
We used BOWTIE2 to map the trimmed sequencing data to the corresponding genome index and used PICARD for the sorting, duplicate removal, and fragment length counting of the aligned data.
We calls peaks from the merged single-cell profiles of all cells using MACS2 to ensure that the entire analysis is unsupervised. We then ranked and filtered out the low quality peaks based on the false discovery rate (Q-value).
Genomic locations of the peaks were annotated by HOMER, and motifs searched by FIMO.
We calculates the number of fragments and the percent of reads mapped to the TSS region (±2000 BP) for each cell, and filters out high quality cells for downstream analysis.
We integrate all processing steps as a pre-process script of APEC.
Genome_build: mm9
Supplementary_files_format_and_content: The cell.csv file is a CSV format file containing the information of filtered cells; the features.bed file is a BED format file containing the information of filtered peaks; the matrix.mtx file is the fragment count matrix stored in MTX format.

source_name: mouse thymoctyes

extract_protocol:
Thymus tissues isolated from 6- to 8-week-old male mice were gently ground in 1 mL of RPMI-1640. Thymocytes in a single-cell suspension were counted after passing through a 40 μm nylon mesh. A total of 1 × 106 thymocytes were stained with PerCP-Cy5.5-anti-CD45, PE-anti-CD8a and APC-Cy7-anti-CD4 antibodies (Biolegend) and then fixed in 1× PBS containing 1% methanal at room temperature for 5 min. After washing twice with 1× PBS, the cells were counted again. A total of 1 × 105 fixed cells were resuspended in 40 μL of 1× TD buffer (5 mM Tris-HCl, pH 8.0, 5 mM MgCl2 , and 10% DMF) containing 0.1% NP-40. Then, 10 μL of fluorescent transposomes were added and mixed gently. Fluorescent tagmentation was conducted at 55 °C for 30 min and stopped by adding 200 µL of 100 mM EDTA directly to the reaction mixture. The cells were loaded on a Sony SH800S sorter, and single cells of the CD45+/AF488-Tn5hi population were index-sorted into each well of 384-well plates. The 384-well plates used to acquire sorted cells were loaded with 2 µL of release buffer (50 mM EDTA, 0.02% SDS) before use. After sorting, the cells in the wells were incubated for 1 min. Plates that were not processed immediately were preserved at -80 °C.
To prepare a single-cell ATAC-seq library, plates containing fluorescently tagmented cells were incubated at 55 °C for 30 min. Then, 4.2 μL of PCR round 1 buffer (1 μL of 100 μM MgCl2, 3 μL of 2× I-5 PCR mix [MCLAB], and 0.1 μL each of 10 μM R1 and R2 primers) were added to each well, followed by PCR: 72 °C for 10 min; 98 °C for 3 min; 10 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Thereafter, each well received 4 µL of PCR round 2 buffer (2 μL of I-5 PCR Mix, 0.5 μL each of Ad1 and barcoded Ad2 primers, and 1 μL of ddH2O), and final PCR amplification was carried out: 98 °C for 3 min; 12 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Wells containing different Ad2 barcodes were collected together and purified with a QIAquick PCR purification kit (Qiagen).

value: thymocytes

value: 6-8 weeks


title: T-5489

description: ftATAC-seq data of mouse thymoctyes


title: T-5487

description: ftATAC-seq data of mouse thymoctyes


title: T-5492

description: ftATAC-seq data of mouse thymoctyes


title: T-5495

description: ftATAC-seq data of mouse thymoctyes


title: T-5496

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_990s_A17


title: T-5486

description: ftATAC-seq data of mouse thymoctyes


title: T-5493

description: ftATAC-seq data of mouse thymoctyes


title: T-5490

description: ftATAC-seq data of mouse thymoctyes


title: T-5485

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_990s_A15


title: zebrafish_990s_A14


title: T-5494

description: ftATAC-seq data of mouse thymoctyes


title: T-5484

description: ftATAC-seq data of mouse thymoctyes


title: T-5483

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_990s_A21


title: zebrafish_990s_A12


title: T-5482

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_990s_A13


title: T-5491

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_990s_A11


title: zebrafish_990s_A10


title: T-5479

description: ftATAC-seq data of mouse thymoctyes


title: T-5480

description: ftATAC-seq data of mouse thymoctyes


title: T-5481

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_990s_A1


title: zebrafish_990s_A16


title: zebrafish_989s_P6


title: T-5475

description: ftATAC-seq data of mouse thymoctyes


title: T-5478

description: ftATAC-seq data of mouse thymoctyes


title: T-5474

description: ftATAC-seq data of mouse thymoctyes


title: T-5476

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P8


title: zebrafish_989s_P3


title: T-5477

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P9


title: zebrafish_989s_P22


title: zebrafish_989s_P4