title: Input2

city: Edinburgh

first: Marcel

last: Lafos

state: Scotland

address: Max Born Crescent

department: Institute of Cell Biology

institute: University of Edinburgh

data_processing:
Quality filtering was performed using trimmomatic v0.36. Read mapping was performed using bwa v0.7.17 to S. pombe genome GCF_000002945.1. Bigwigs were generated using bamCompare v3.1.3 from deeptools. Peak calling was performed using macs2 v2.1.2. Overlap of the peak files were called using bamtools v2.5.1.
Genome_build: GCF_000002945.1
Supplementary_files_format_and_content: Bigwigs were generated using bamCompare v3.1.3 from deeptools.

organism: Schizosaccharomyces pombe

source_name: cell

growth_protocol: Schizosaccharomyces pombe cell were gwon in rich medium (1X YES).

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
ChIP-seq libraries were prepared essentially as described in Shukla et al., 2017.

tag: strain

value: Hap2-GFP Arp5-3HA

tag: chip antibody


title: Input1

status: Public on Dec 31 2019

type: SRA

country: United Kingdom

library_source: genomic

molecule: genomic DNA


title: 4-III-16-2-150 [MS_038]

city: Fort Pierce

first: Joshua

last: Voss

state: FL

address: 5600 N US Highway 1

country: USA

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

library_source: transcriptomic

data_processing:
Data processing was completed using the analysis pipeline available on GitHub:
https://github.com/mstudiva/tagseq-modified-scripts
Genome_build: concatenated M. cavernosa (https://github.com/mstudiva/Mcav-Annotated-Transcriptome.git) and Symbiodinium Clade C (ftp://marchanon:anon@rc-ns-ftp.its.unc.edu/CladeC_Symbiodinium_transcriptome.zip) transcriptomes
Supplementary_files_format_and_content: tab-delimited text file containing gene counts per sample and isogroup annotations

molecule: total RNA

organism: Montastraea cavernosa

tag: site

value: CBC

tag: depth

value: shallow


title: C-R-2

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: Gene expression data from pUC9 inoculated roots

data_processing:
Base calling and adapter trimming was performed automatically by Torrent Suite software.
Residual rRNA and ERCC reads were identified and filtered out using bbsplit and filterbyname scripts from BBTools suite (Brian Bushnell).
Reads were aligned to genome using TMAP 5.0.13. with soft clipping from both ends and returning all the mappings with the best score. Other settings were set according to Torrent Suite defaults. Unaligned reads were aligned with BBMap (Brian Bushnell).
Quantitation to ITAG3.2 transcripts and differential expression analysis was performed in Partek Flow (Partek Inc.) using Partek GSA algorithm.
Genome_build: ITAG3
Supplementary_files_format_and_content: gene read counts - Table with raw read counts derived from Partek E/M Quantification Algorithm. Genes are in rows, samlples - in columns
Supplementary_files_format_and_content: differential expression table - table containing results of GSA differential gene expression analysis. For each comparison (Contrast), values of p-value, q-value,FDR, ratio and fold change are presented in column for each gene (in rows)

organism: Solanum lycopersicum

source_name: Solanum lycopersicum roots inoculated with pUC9

growth_protocol: Inoculated tomato plants were maintained in a greenhouse at 28-30ºC for 16 h and at 25ºC for 8 h in the dark.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit according to manufacturer’s instruction (Qiagen). Contaminating DNA was removed from the extracted RNA using TURBO DNase-free TM Kit (Ambion).
ERCC RNA Spike-In Mix 1 (Thermo Fisher) was added as internal control to each sample. Ribosomal RNA was removed using Ribo-Zero Plant rRNA Removal Kit (Illumina).  Libraries were prepared with Ion Total RNA-Seq Kit v2 and Ion Xpress RNA-Seq Barcode 1-16 Kit according to user guide. Sequencing template was generated with Ion PI™ Template OT2 200 Kit v3 on Ion OneTouch™ 2 System. Sequencing was performed on Ion PI™ chip v2 and Ion Proton™ sequencer using Ion PI™ Sequencing 200 Kit v2

treatment_protocol: Two μg of purified plasmids containing monomeric full-length cDNAs of PSTVd-M (GenBank nr X76844) or PSTVd-S23 (GenBank nr X76846) and empty pUC9 plasmid as a control were mechanically inoculated into  tomato leaves. Whole roots were collected at 17 days post inoculation.

tag: organ

value: roots

tag: infecious variants


title: C-R-3


title: C-R-1


title: 6-III-16-1-89 [MS_055]


title: 8-III-16-3-2 [MS_033]

value: mesophotic


title: S23-R-3

description: Gene expression data from PSTVd-S23 inoculated roots

source_name: Solanum lycopersicum roots inoculated with PSTVd-S23


title: 6-III-16-1-87 [MS_032]


title: 6-III-16-2-1 [MS_029]


title: S23-R-1


title: 8-III-16-2-2 [MS_031]


title: M-R-3

description: Gene expression data from PSTVd-M inoculated roots

source_name: Solanum lycopersicum roots inoculated with PSTVd-M

value: PSTVd-M


title: 6-III-16-2-93 [MS_030]


title: M-R-2


title: 5-III-16-1-147 [MS_027]


title: 6-III-16-3-94 [MS_028]


title: 5-III-16-2-144 [MS_025]


title: M-R-1


title: 6-III-16-2-85 [MS_024]


title: 4-III-16-2-70 [MS_021]


title: 4-III-16-2-149 [MS_022]


title: 6-III-16-3-96 [MS_020]


title: DOM_M21_P4

city: Riverside

first: Polly

last: Campbell

state: CA

address: 3401 Watkins Drive

department: Evolution, Ecology, and Organismal Biology

institute: University of California Riverside

data_processing:
QC of raw sequencing reads and trimming were performed in Trim Galore! 0.4.5 (Brabraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), using a phred score cutoff of 30 and minimum sequence length of 100 after trimming.
A pseudo-hybrid (Mus domesticus X Mus spretus) genome using was generated based on the mouse genome (GRCm38.89) using  the genome preparation tool of the program SNPsplit (Brabraham Bioinformatics). All placenta samples were mapped to the pseudo-hybrid genome.
Mapping was done using HISAT2 2.1
After mapping we filtered the resulting alignment files using SAMtools 0.1.19, retaining only high quality (HISAT2 MAPQ score 40), uniquely mapped, paired reads for analysis.
All alignments were randomly downsampled to ~40 million reads using SAMtools 0.1.19 to account for a possible mapping bias and to improve comparability.
Transcript quantification and annotation was done using StringTie 1.3.3. Gene annotation information was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org) for Mus spretus (SPRET/EiJ_v1.86) and Mus domesticus (WSB/EiJ_v1.86). Mouse genome annotation was used for samples mapped to the pseudo-hybrid genome (GRCm38.89). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential gene expression.
Differential expression was tested with DESeq2 1.16.1. Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt). Low counts were removed by the independent filtering process implemented in DESeq2.
Genome_build: MPA samples were mapped to WSB/EiJ_v1 for Mus domesticus and SPRET/EiJ_v1 for Mus spretus; All placenta samples were mapped to the pseudo-hybrid genome.
Supplementary_files_format_and_content: comma-separated text files include raw counts, tab-delimited supplementary text files include DEseq2 normalized counts and DESeq2 differential expression analysis outputs for each comparison

organism: Mus musculus domesticus

source_name: Mus domesticus e17.5 placenta

extract_protocol:
Pregnant females (n=5/type of pregnancy) were euthanized by cervical dislocation between 10:00 and 11:00 AM on embryonic day 17-18 (e17.5) and the maternal brain was extracted. Embryos were separated from placentas and placentas were weighed, and the maternally-derived decidual layer was removed as previously described (Qu et al. 2014) and discarded.  Only fetally-derived placental tissue was used in this study. All tissues were transferred immediately to RNAlater (Thermo Fisher, USA), kept at 4°C overnight to allow RNAlater perfusion, and stored at -20°C until microdissection and RNA extraction. The maternal MPoA was localized using the Mouse Brain atlas (Figs. 26-33, (Paxinos and Franklin 2013)), and microdissected by sectioning the RNAlater perfused brain at 100μm on a Leica CM 1950 cryostat, followed by dissection under a dissecting microscope in chilled PBS droplets for improved visibility of brain microstructure.
Library preparation was performed by the sequencing facility (Novogene, Sacramento, CA), using the NEB Next Ultra RNA library prep kit for Illumina.
RNAseq was performed on the Illumina HiSeq 4000 platform, producing >30 million, 150bp paired-end reads per sample.

tag: tissue

value: placenta

tag: pregnancy type code

value: DOM

tag: placenta weight (g)

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

value: f

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter


title: DOM_M21_P2

value: m


title: 7-III-16-2-99 [MS_016]


title: 6-III-16-1-88 [MS_018]


title: DOM_M8_P3


title: 6-III-16-1-3 [MS_017]


title: DOM_M18_P4


title: S23-R-2


title: DOM_M18_P3


title: 6-III-16-3-95 [MS_026]


title: DOM_M16_P2


title: DOM_M8_P1


title: 6-III-16-3-5 [MS_019]


title: 7-III-16-3-1 [MS_023]


title: 7-III-16-2-133 [MS_012]


title: DOM_M15_P1


title: 8-III-16-1-1 [MS_009]


title: DOM_M15_P2


title: 6-III-16-3-84 [MS_010]


title: DOMhI_M9_B_MPA

source_name: Mus domesticus maternal MPA during e17.5 Mus domesticus X Mus spretus pregnancy

value: maternal hypothalamus medial preoptic area

value: DOMhl


title: 7-III-16-2-127 [MS_013]


title: 6-III-16-2-97 [MS_014]


title: 8-III-16-3-136 [MS_007]


title: DOM_M21_B_MPA

source_name: Mus domesticus maternal MPA during e17.5 Mus domesticus pregnancy


title: DOMhI_M11_B_MPA


title: 8-III-16-1-3 [MS_008]


title: DOMhI_M20_B_MPA


title: DOMhI_M19_B_MPA


title: DOMhI_M10_B_MPA


title: DOM_M18_B_MPA


title: DOM_M16_P1


title: 8-III-16-1-138 [MS_011]


title: 5-III-16-1-2 [MS_003]


title: circKcnt2_KO

type: RNA

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

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

country: China

institute: Institute of Biophysics, CAS

description:
This is circKcnt2-deficient ILC3s
1x105 ILC3s were isolated from WT or circKcnt2-deleted mice by FACS

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

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

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

label: biotin

organism: Mus musculus

source_name: circKcnt2-deficient ILC3s

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

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

tag: genotype

value: circKcnt2 knockout


title: circKcnt2_WT

description:
This is wild-type ILC3s
1x105 ILC3s were isolated from WT or circKcnt2-deleted mice by FACS

source_name: WT ILC3s

value: Wild-type


title: DOM_M16_B_MPA


title: 6-III-16-3-6 [MS_006]


title: 8-III-16-1-5 [MS_004]


title: DOM_M8_B_MPA


title: 7-III-16-2-130 [MS_005]


title: 4-III-16-2-148 [MS_002]


title: 6-III-16-1-2 [MS_015]


title: 8-III-16-3-134 [MS_001]


title: DOM_M15_B_MPA


title: PBCAB Replicate 3

city: Worcester

first: William

last: Stanney

state: MA

address: 364 Plantation Street, LRB-870D

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description:
RSEM_GFP_NFYADN_PBCAB_12hpf_zebrafish_genes_expression_tpm.tsv
PBCAB_v_GFP_alldetected_genes.tsv

data_processing:
Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2.
Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM_v1.2.28 with parameters -p4 --bowtie-e 70 --bowtie-chunkmbs 100.
PBCAB replicate 2 was excluded as an outlier.
Differentially expressed genes were determined using DESeq2.
Genome_build: GRCz10/danrer10
Supplementary_files_format_and_content: TSV files contain transcripts per million (TPM) values for each sample.

organism: Danio rerio

source_name: Whole Embryo

growth_protocol: Injected embryos were raised to 12 hours in egg water (60μg/uL Instant Ocean, 0.0002% methylene blue) at 29°C.

extract_protocol:
Embryos were collected in Trizol (ThermoFisher Scientific) and frozen at -80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit (Qiagen) and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer (Agilent), with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0.
Library preparation and sequencing were carried out by BGI, Inc. Polyadenylated RNAs were selected using oligo dT beads, fragmented, and reverse-transcribed into double-stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ-500 platform.

treatment_protocol: Zebrafish embryos at the 1-cell stage were injected with a mixture of mRNA, 0.1% phenol red, and water. The mRNAs encoded either a dominant negative Pbx (PBCAB), dominant negative NF-YA (NF-YA DN), or GFP (control).

tag: Stage

value: 12 hpf

tag: treatment

value: PBCAB


title: 15AN3

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

data_processing:
TopHat (v2.0.13) was used to aligned the obtained reads to the genome of Panax notoginseng.
Cufflinks (v2.2.1) was used to obtain the genes and transcripts and genes with the Panax notoginseng annotation.
Cuffmerge (v1.0.0) was used to merge the assembled genes and transcripts from individual libraries.
CuffCompare (v2.2.1) was used to compare the merged genes and transcripts to the annotated genes and transcripts in the Panax notoginseng database.
Cuffquant (v2.2.1) was used to quantify the expression levels (FPKM) values of genes and transcripts.
Cuffnorm (v2.2.1) was used to normalize the FPKM values of genes and transcripts.
Genome_build: Panax notoginseng. Chen et al. 2017 Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng. PubMed ID: 28315474. Genome sequence and gene annotation downloaded from: http://www.herbal-genome.cn
Supplementary_files_format_and_content: FPKM values of genes. A FASTA file is available on the series record with the transcript sequences.

organism: Panax notoginseng

source_name: roots

growth_protocol: Plants were grown in hydroponic culture. For all experiments, 3-day-old seedlings were used.

extract_protocol:
Total RNA were extracted with Trizol (Amion).
RNA libraries were prepared for sequencing using standard Illumina protocols with only ribosomal RNA removal.

treatment_protocol: no treatment

tag: developmental stage

value: Ammonia and nitrate


title: 3h

city: Zhenjiang

first: Kaili

last: Wang

state: Jiangsu

address: Xuefu Road 301

department: School of food and biological engineering

institute: Jiangsu University

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism:
Penicillium expansum
Malus pumila

source_name: Fungus and apple

growth_protocol: Penicillium expansum spores inoculate on  Malus pumila Mill for 0, 1, 3, 6h and cultured at 95% relative humidity, 25℃

extract_protocol:
Apple tissues after inoculated Penicillium expansum spores  were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: The sample of 0h is the control which did not contact before extract RNA, sample 1h was inoculated on apple tissues at 1 hour post inoculation,sample 3h was inoculated on apple tissues at 3 hour post inoculation,  sample 6h was inoculated on apple tissues at 6 hour post inoculation.

tag: time

tag: growth

value: 95 % relative humidity, 25 C


title: PBCAB Replicate 2


title: 15AN1


title: SPRET_M7_P3

organism: Mus spretus

source_name: Mus spretus e17.5 placenta

value: SPRET


title: PBCAB Replicate 1


title: SPRET_M7_P1


title: 1h

value: Penicillium expansum spores inoculate on  Malus pumila Mill


title: 15N3

value: Nitrate

value: roots


title: NF-YA DN Replicate 3

description:
RSEM_GFP_NFYADN_PBCAB_12hpf_zebrafish_genes_expression_tpm.tsv
NFYA_DN_v_GFP_alldetected_genes.tsv

value: NF-YA DN


title: NF-YA DN Replicate 2


title: SPRET_M6_P3

value: placenta


title: 15N1


title: 15AN2


title: SPRET_M14_P4


title: 0h


title: NF-YA DN Replicate 1


title: SPRET_M6_P2


title: GFP Replicate 3

description: RSEM_GFP_NFYADN_PBCAB_12hpf_zebrafish_genes_expression_tpm.tsv

value: GFP


title: 15N2


title: 15A3

value: Ammonia


title: T2_1

city: Shouguang

first: Liang

last: Guoting

state: Shandong

address: No.1299, Jinguang street

institute: Weifang University of Science and Technology

data_processing:
Adaptor sequences, poly-N reads and low quality reads were removed  using FastQC (V 0.11.5) and Trimmomatic (V 0.36) software to obtain clean reads from raw data (containing more than 50% bases with Q ≤ 30)
Trinity software was used to perform de novo assembly with a k-mer length of 25 and other default parameters. The transcripts were clustered with a TGI clustering tool, and the longest transcripts were defined as unigenes.
We used InterProScan(v 2.0) program to search functional annotation in the multiple protein databases.
FEELnc(V 0.1.1), PLncPRO(V 1.1), RNAplonc(V 1.0) were used to predict LncRNA and the union obtained by the three software predictions as the total LncRNA
RSEM was used to calculate FPKM in each sample. Then, the DESeq R software package was used for comparing differential expression. In multiple tests and analysis, we used FDR to identify the P-value threshold

source_name: leaf

growth_protocol: Tomato seeds were planted in plug plate (Wei Nong company, Taizhou, China).

extract_protocol:
All samples were frozen in liquid nitrogen and stored at –80°C. Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s instructions. DNase I (TaKaRa, Dalian, China) was used to treat RNA samples to avoid genomic DNA contamination. The quantity and purity of the total RNA was measured with a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) (RIN number >7.0). Equal parts of RNA samples for the same treatment were mixed for transcriptome sequencing and sRNA sequencing. Subsequently, the total mixed RNA sample for leaves was prepared for degradome sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: one month later, we treat the S. lycopersicum plants with  different concentration of p-Hydroxybenzoic acid (0mmol/L, 15mmol/L and 30mmol/L) for 2 day.

value: para-hydroxybenzoic acid concentration of 30 mM/L

tag: cultivar

value: Diana

value: leaf

tag: age

value: one month after planted


title: 6h


title: SPRET_M14_P3

tag: tissue

tag: pregnancy type code

value: m


title: GFP Replicate 2

value: 12 hpf


title: T2_2


title: 15A2


title: T2_3


title: SPRET_M13_P4

tag: placenta weight (g)

tag: embryo weight (g)

value: f


title: GFP Replicate 1


title: T1_3

value: para-hydroxybenzoic acid concentration of 15 mM/L


title: SPRET_M13_P1

tag: placenta (percent embryo weight)

tag: embryo sex


title: petal_1

description:
grown in greenhouse, Kunming university of science and technology, Kunming, Yunnan, China
rose-cDNA-fpkm.xls

data_processing:
Trinity (v2.0.6) was used to the options of "--seqType fq --max_memory 400G --min_contig_length 150 --CPU 30 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr"
Align_and_estimate_abundance.pl in the Trinity package was used to estimate the abundances of trinity sequences in the 8 genomics RNA sequencing profiles.
Supplementary_files_format_and_content: FPKM values of genes

organism: Rosa rugosa

source_name: petal

growth_protocol: The rose were grown in greenhouse, Kunming university of science and technology, Kunming, Yunnan, China

value: petal


title: 15A1


title: SPRET_M12_P2

value: SPRET

tag: # males in litter

tag: # females in litter


title: T1_2


title: SPRET_M12_P1

tag: litter size

tag: proportion males in litter


title: CK_3

value: untreated


title: SPRET_M7_B_MPA

source_name: Mus spretus maternal MPA during e17.5 Mus spretus pregnancy

value: maternal hypothalamus medial preoptic area


title: leaf_1


title: T1_1


title: CK2

value: control

value: roots


title: CK_1


title: leaf_2


title: SPRET_M6_B_MPA


title: panax-ck

first: Peiran

last: Liao

address: No.727 South Jingming Rd., Chenggong District, Kunming 650500, China

institute: Kunming University of Science and Technology

data_processing:
TopHat (v2.0.13) was used to aligned the obtained reads to the genome of  Panax notoginseng.
Cufflinks (v2.2.1) was used to obtain the genes and transcripts.
Cuffmerge (v1.0.0) was used to merge the assembled genes and transcripts from individual libraries.
CuffCompare (v2.2.1) was used to compare the merged genes and transcripts.
Cuffquant (v2.2.1) was used to quantify the expression levels (FPKM) values of genes and transcripts.
Cuffnorm (v2.2.1) was used to normalize the FPKM values of genes and transcripts.
Genome_build: the reference genome of Panax notoginseng is NCBI Sequence ReadArchive under Project ID SRP091819
Supplementary_files_format_and_content: FPKM values of genes

source_name: root

growth_protocol: The Panax notoginseng were grown in field in Kunming, Yunnan ,China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
RNA libraries were prepared by following the Illumina's protocol.

treatment_protocol: no treatment VS 5 uM of cadmium treatment

value: root

tag: location

value: grow in Kunming, Yunnan, China


title: SPRET_M13_B_MPA


title: panax-cd-5

tag: treatment

value: 5 uM of cadmium


title: SPRET_M14_B_MPA


title: SPRET_M12_B_MPA


title: HYBRID_M9_P3

organism: Mus musculus domesticus x Mus spretus

source_name: Mus domesticus X Mus spretus e17.5 placenta

value: placenta

value: HYBRID


title: petal_2


title: HYBRID_M9_P1


title: CK1

tag: developmental stage


title: CK_2

value: Diana

value: leaf


title: HYBRID_M20_P1

value: m


title: D42_T3 miRNA-seq

city: Qingdao

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

description: sRNA.readcount

data_processing:
After calculating the Q20, Q30, and GC-content, raw reads were filtered by removing the following reads: N% > 10%, low quality, 5_adapter_contamine, 3_adapter_null or insert_null, and reads with ployA/T/G/C. Then, the remaining clean reads were mapped to genome sequences of the Japanese flounder via Bowtie.
Furthermore, the obtained reads were mapped to the RFam database (http://rfam.janelia.org), the Japanese flounder mRNA database, and the Repbase (http://www.girinst.org/repbase) to filter for non-coding RNA families except for miRNA, mRNA, and repetitive sequences. Subsequently, known miRNAs were obtained via mapping with miRBase 21.0 and novel miRNA were predicted via miREvo and mirdeep2.
Genome_build: Paralichtys olivaceus genome
Supplementary_files_format_and_content: readcount and TPM of miRNAs.xls

organism: Paralichthys olivaceus

source_name: 42 DAH larvae of T3 treated Paralichtys olivaceus

extract_protocol:
Larvae of D42 in T3 treatment group and the control group were collected and the total RNAs were extracted using Trizol reagent. Approximately 3 μg RNA of an RNA integrity number (RIN) >7.0 from each group was used for the subsequent cDNA library construction following the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the beginning of the experiment, 1000 individual larvae of the Japanese flounder at 16 DAH were separately treated with 0.01 mg/L thyroid hormone T3 (3,3′,5-triiodo-L-thyronine, sigma), 0.05 mg/L thyroid hormone T4 (levothyroxine sodium hydrate, sigma), or 20 mg/L TU (thiourea, sigma) for 10 continuous days. 1000 untreated individuals were used as control group. At 17, 20, 23, 28, 42, 47, and 57 DAH, four groups of fishes were sampled and body color were measured. The period with the maximal difference in body color was submitted for high-throughput miRNA sequencing analysis.

value: the whole body

value: 42 DAH (days after hatchery)

value: T3 treatment


title: D42_Con miRNA-seq

source_name: 42 DAH larvae of control Paralichtys olivaceus

value: No treatment


title: MM_2

data_processing:
After the adapters were removed from raw reads, those reads with low quality including reads with more than 10% unknown nucleotides and more than 50% low quality bases (Q-value < 20) were removed from the data set. The data were subsequently assembled with Trinity. Taken these assembled transcripts as the reference sequence, clean reads were mapping by RSEM software.
And the longest transcript in each gene-Unigene, was used for the representative of each gene. The Unigene was annotated by ways of seven database including Nr, Nt, Pfam, KOG/COG, Swiss-prot, KEGG and GO. The CDS was further predicted by Nr, Swissprot database or Estscan (3.0.3) software.
Supplementary_files_format_and_content: the sequences of the unigene

organism: Platichthys stellatus

source_name: the muscle of male Platichthys stellatus

extract_protocol:
Three samples for each tissue were used for the following experiment. A total of 24 samples named MB1-3, ML1-3, MG1-3, MM1-3, FB1-3, FL1-3, FG1-3, and FM1-3 were acquired and their total RNAs were extracted via Trizol reagent (Invitrogen, USA) and measured with the Agilent 2100 RNA 6000 Nano kit (Agilent, USA) for quality control. Twenty-four cDNA libraries were constructed using 3 μg RNA (RIN > 7.0) from each sample via the conventional protocol, and the subsequent sequencing was conducted with an Illumina HiseqTM 4000 by Novogene Co. Ltd (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle

value: three-year-old

tag: gender

value: male


title: HYBRID_M11_P2


title: HYBRID_M19_P1


title: HYBRID_M10_P2

value: f


title: E_6_vs_E_48_replC

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: Biological replicate:C; Lame: 3; TF-1 cells treated with EPO for 6 hrs vs TF-1 cells treated with EPO for 48 hrs.

hyb_protocol: 750ng of each cRNA were fragmented in the fragmentation buffer, in presence of blocking agent. Subsequently, samples were hybridized with hybridization buffer on microarrays slides in a Surhyb gasket for 17h at 65°C

scan_protocol: Slides were scanned by an Agilent G2565CA Microarray Scanner Images were quantified using Agilent Feature Extraction Software software version 2.5

data_processing: Data were processed in the R statistical environement using the Limma package. Normalization was performed using Loess. Between-array normalization was performed using Aquantile method.

organism: Homo sapiens

label_protocol: Labeling was perfomed according to the manufacturer’s protocol, using 200ng of total RNA for the preparation of cDNA probes and Cy5- and Cy3-labeled cRNA probes (Low RNA Input Linear Amplification Kit, PLUS, Two-Color).

growth_protocol: TF-1 cells were cultured in RPMI 1640 medium containing 10% (v/v) of fetal calf serum, 1% (v/v) of antibiotic-antimycotic and 2mM of L-glutamine at 37°C, 5% CO2 in the presence of 5 ng/mL human recombinant GM-CSF or 10 U/mL human recombinant EPO

extract_protocol: Total RNA was extracted from a batch of 1 to 2 milion cells by TRIzol and cleanup was performed with the RNeasy Mini Kit (Qiagen). Quantification of RNA was assessed by using Nanodrop.  RNA integrity value was verified using an Agilent Bioanalyzer 2100.

treatment_protocol: Treatments with TNFα (20ng/mL);  were started in the exponential growth phase, 24 h after seeding with 3x106 cells. The stop of cell treatment were performed after 0, 6, 24 and 48 h.

tag: cell line

value: EPO

tag: time


title: MM_1

tag: age


title: GT_6_vs_G_6_replC

description: Biological replicate:C; Lame: 3; TF-1 cells treated with GM-CSF + TNF for 6 hrs vs TF-1 cells treated with GM-CSF for 6 hrs.

value: GM-CSF + TNF

value: GM-CSF


title: E_0_vs_G_6_replC

description: Biological replicate:C; Lame: 3; TF-1 cells treated with EPO for 0 hrs vs TF-1 cells treated with GM-CSF for 6 hrs.


title: ET_48_vs_E_48_replC

description: Biological replicate:C; Lame: 3; TF-1 cells treated with EPO + TNF for 48 hrs vs TF-1 cells treated with EPO for 48 hrs.

value: EPO + TNF


title: HYBRID_M10_P1

tag: tissue

value: placenta


title: ET_6_vs_E_6_replC

description: Biological replicate:C; Lame: 3; TF-1 cells treated with EPO + TNF for 6 hrs vs TF-1 cells treated with EPO for 6 hrs.


title: MG_2

source_name: the gonad of male Platichthys stellatus

value: gonad


title: WT3

city: Shanghai

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to rn6 or Macaca5 reference genome using hisat2 v2.1.0 with default parameters.
Gene expression for each sample was quantified using featureCounts(v 1.6.1) and  DEseq2(v 1.2.0).
Genome_build: rn6;Macaca_fascicularis_5.0
Supplementary_files_format_and_content: rat_all_normat.csv: abundance measurements(DESeq2, log2-transformed)
Supplementary_files_format_and_content: geneCounts_featureCounts_macaca.tab: abundance measurements(raw counts)

organism: Macaca fascicularis

source_name: liver

extract_protocol:
Total RNA was extracted from snap-frozen liver samples using TRIzol (Life Technologies) according to the manufacturer’s instructions. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies).
the libraries were sequenced on an Illumina Hiseq X platform and 150 bp paired-end reads were generated sequencing libraries were generated using the rRNA- depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA)

value: liver


title: ET_6_vs_ET_24_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO + TNF for 6 hrs vs TF-1 cells treated with EPO + TNF for 24 hrs.


title: ET_0_vs_E_0_replC

description: Biological replicate:C; Lame: 3; TF-1 cells treated with EPO + TNF for 0 hrs vs TF-1 cells treated with EPO for 0 hrs.


title: ET_0_vs_GT_6_replB

description: Biological replicate:B; Lame: 3; TF-1 cells treated with EPO + TNF for 0 hrs vs TF-1 cells treated with GM-CSF + TNF for 6 hrs.


title: WT2


title: MG_1


title: ML_2

source_name: the liver of male Platichthys stellatus


title: HYBRID_M19_P2

tag: pregnancy type code

value: HYBRID


title: ET_0_vs_ET_6_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO + TNF for 0 hrs vs TF-1 cells treated with EPO + TNF for 6 hrs.


title: HYBRID_M11_P1

tag: placenta weight (g)


title: WT1


title: ET_24_vs_E_24_replC

description: Biological replicate:C; Lame: 3; TF-1 cells treated with EPO + TNF for 24 hrs vs TF-1 cells treated with EPO for 24 hrs.


title: ML_1


title: CM3


title: CM2


title: ET_24_vs_ET_48_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO + TNF for 24 hrs vs TF-1 cells treated with EPO + TNF for 48 hrs.


title: CM1


title: MB_1

source_name: the brain of male Platichthys stellatus

value: brain


title: MB_2


title: FM_2

source_name: the muscle of female Platichthys stellatus

value: female


title: G_6_vs_E_0_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with GM-CSF for 6 hrs vs TF-1 cells treated with EPO for 0 hrs.


title: ET_48_vs_ET_0_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO + TNF for 48 hrs vs TF-1 cells treated with EPO + TNF for 0 hrs.


title: FM_1


title: CK3

value: control

value: roots


title: E_0_vs_E_48_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO for 0 hrs vs TF-1 cells treated with EPO for 48 hrs.


title: SP4_ATAC_rep2

city: Wuhan

first: jin

last: jing

state: Hubei

address: Wuhan, Hubei Province, P.R.China

department: College of Life Sciences

institute: Wuhan University

data_processing:
Raw reads of ATAC-seq, ChIP-seq and RNA-seq were separately aligned to the O.sativa Nipponbare release 7 of the MSU Rice Genome Annotation Project reference using Bowtie2, SOAP2 aligner and HISAT2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks of ATAC-seq and ChIP-seq were identified using the MACS and SICER
Genome_build: MSU7
Supplementary_files_format_and_content: bed file were generated by MACS, scores represent -10*log10(pvalue); wig files were generated using SICER, Scores represent probability；tab-delimited text files include RPKM values for each sample.

organism: Oryza sativa

source_name: Sterility male of WXS at uninucleate period

growth_protocol: The rice PTGMS line WXS (O. sativa ssp. indica) were grown in the paddy field of Wuhan University (30.35°N, 114.33°E), Wuhan, China, in summer. From 20 July to 30 August 2016, the average temperatures were? , with a 14h light/10 h dark photoperiod, which caused WXS male sterility (WXS(S)). When panicle length reached ~ 1 cm (before the stages of early premeiosis), half of the plants were transferred to growth chamber at an average temperature of 22°C with a 14h light/10h dark photoperiod and 77% relative humidity, ensuring the illumination, humidity values and other environment factors in the growth chamber close to the natural condition as far as possible, which could make WXS convert into male fertility (WXS(F))

extract_protocol:
Tn5 Transposase treatment (Using the Illumina Nextera kit) was performed on the intact nuclei isolated by Plant Nuclei Isolation/Extraction Kit (CELLYTPN1, sigma) from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit. Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers. Total RNA of WXS was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Chromatin from panicle of WXS was immunoprecipitated with antibodies against H3K4me2 and H3K9ac. The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
The genomic fragments of Tn5, RNA libraries and ChIP-ed DNA were separately prepared for sequencing using standard Illumina protocols

treatment_protocol: Young panicles were collected and were immediately frozen in liquid nitrogen. All collected samples were ground into fine powder for ChIP-seq, ATAC-seq and RNA-seq experiments.

tag: line

value: Wuxiang S (WXS)

tag: genotype

value: photo-thermosensitive genic male sterile (PTGMS) rice line

value: panicle

tag: period

value: uninucleate


title: SP4_ATAC_rep1


title: E_48_vs_E_24_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO for 48 hrs vs TF-1 cells treated with EPO for 24 hrs.


title: E_6_vs_E_0_replB

description: Biological replicate:B; Lame: 1; TF-1 cells treated with EPO for 6 hrs vs TF-1 cells treated with EPO for 0 hrs.


title: FP4_ATAC_rep1

source_name: Fertility male of WXS at uninucleate period


title: FL_1

source_name: the liver of female Platichthys stellatus

value: three-year-old


title: SP3_ATAC_rep2

source_name: Sterility male of WXS at meiosis period

value: meiosis


title: SP3_ATAC_rep1


title: FB_2

source_name: the brain of female Platichthys stellatus


title: PS_Drought

city: Tlaxcala

first: Josefat

last: Gregorio Jorge

state: Tlaxcala

address: Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla Km 1.5, Tlaxcala

department: Biotecnología Genómica

country: Mexico

institute: Instituto Politécnico Nacional

data_processing:
Illumina CASAVA-1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptors and then data were quality-assessed using the FastQC tool. Low-quality reads were discarded, and the generated clean data were aligned to the reference genome of P. vulgaris (G19833) (Schmutz et al. 2014) using TopHat (Trapnell et al. 2009).
Cuffdiff was used to compare the expression level of transcripts, and to test the statistical significance between two conditions (Trapnell et al. 2012). To identify differentially expressed genes (DEGs), genes were ranked according to normalized fragments per kilobase per million mapped reads (FPKM). FPKM values were assigned to each gene by comparing the FPKM value under the drought treatment to that in the control condition. Genes that were induced or reduced at least 2-fold change (log2) and P value ≤ 0.05 were identified as DEGs by Cuffdiff (Ghosh and Chan 2016).
Genome_build: P. vulgaris (G19833)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample …

organism: Phaseolus vulgaris

source_name: Aerial tissues

growth_protocol: Seeds were washed five times with sterile distilled water before planting in sterile aluminum trays containing a layer of wet sheets of paper. Trays were covered with aluminum foil and incubated at 30°C for a week. Then, seedlings were transferred into plant pots and incubated in greenhouse conditions using sterile vermiculite as substrate. All plants were watered with Hoagland´s basal salt solution in increasing concentrations every week (from 0.1X to 1X).

extract_protocol:
Pooled plant samples were powdered by grinding the frozen tissue. Each pool included 6-9 plants of each cultivar under control conditions or drought treatment. Thus, 12 RNA samples were extracted in two replicates under either drought or control conditions. Total RNA was extracted using 200 mL of the powdered sample and adding 700 mL of the Z6-extraction buffer (8 M guanidinium-HCl, 20 mM MES, 20 mM EDTA, 50 mM β-mercaptoethanol, pH 7.5). Then, an equal volume of phenol was added to carry out the extraction of RNA, followed by purification using the ssDNA/RNA Clean & Concentrator™ kit (Zymo Research Corp, Orange, CA, USA), according to the manufacturer's instructions. Equal amount of RNA from control and drought conditions were pooled together for further analysis, resulting in two RNA populations. The integrity of RNA was checked by agarose gel electrophoresis and the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). The concentration of total RNA was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE).
Two libraries were constructed for each treatment using the TruSeq RNA Sample Preparation Kit (Illumina, Inc., San Diego, US-CA), following the manufacturer’s recommendations. In brief, poly(A)-tailed mRNA was enriched and fragmented, followed by first cDNA synthesis. Subsequent second strand cDNA synthesis and the final reactions were cleaned up prior to perform the end repair step, and the addition of a single adenylate into the 3´ends. Adapters were ligated to both ends of the short fragments, which were enriched by 36 PCR cycles prior to be cleaned up and validated. cDNA fragments pools were loaded to Illumina MiSeq (Illumina, Inc., San Diego, US-CA) platform for single-ended sequencing.

treatment_protocol: Forty-five-day-old seedlings showing three trifoliate leaves were assigned into three groups for the experiment, namely plants without any treatment (Control), drought-treated plants (Drought) and post-drought recovery plants (Recovery). Whereas plants of the control group (C) grew under continuous irrigation, drought-treated plants (D) were submitted to a period of progressive water deﬁcit for two weeks by suppression of irrigation. Some plants subjected to the drought treatment were re-watered with Hoagland´s solution to allow plant recovery and classified as post-drought recovery plants (R).

value: wild type

tag: cultivar

value: Pinto Saltillo

tag: condition

value: Drought

tag: description

value: Forty-five-day-old seedlings


title: FP3_ATAC_rep2

source_name: Fertility male of WXS at meiosis period


title: E_24_vs_E_6_replB

description: Biological replicate:B; Lame: 2; TF-1 cells treated with EPO for 24 hrs vs TF-1 cells treated with EPO for 6 hrs.

value: EPO


title: FG_2

source_name: the gonad of female Platichthys stellatus

value: gonad


title: FB_1


title: GT_6_vs_ET_0_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with GM-CSF + TNF for 6 hrs vs TF-1 cells treated with EPO + TNF for 0 hrs.

value: GM-CSF + TNF

value: EPO + TNF


title: FL_2

value: liver

value: female


title: PS_Control

value: Control


title: FP3_ATAC_rep1

value: Wuxiang S (WXS)


title: female GRloxP/loxPαMHCCre/+ mice (designated cardioGRKO) 1

status: Public on Dec 30 2019

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Heart_GRKO_htseq_count_DESeq_exp_log2_normalized.xlsx

data_processing:
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
RNA-SEQ reads (~45M per sample) were aligned to the UCSC mm9 reference genome using TopHat2.
The quantification results from htseq-count were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm9
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: Heart

extract_protocol:
Heart were collected after treatment and RNA extracted with Trizol and purified with with Qiagen Rneasy Kit
Libraries were constructed with the use of the Illumina TruSeq library construction kit V2 (Cat #RS-122-2001) according to manufacturer's protocol. Libaries were pooled and sequenced on the Illumina NextSeq500 sequencer

tag: background

value: Female

value: heart

tag: timepoint

value: 2 months of age

value: No treatment

value: wild-type


title: female GRloxP/loxPαMHCCre/+ mice (designated cardioGRKO) 2

tag: treatment


title: female Homozygous GR floxed (GRloxP,loxP)  3


title: female Homozygous GR floxed (GRloxP,loxP)  2


title: female Homozygous GR floxed (GRloxP,loxP)  1


title: female GRloxP/loxPαMHCCre/+ mice (designated cardioGRKO) 3


title: male GRloxP/loxPαMHCCre/+ mice (designated cardioGRKO) 3

value: Male


title: male GRloxP/loxPαMHCCre/+ mice (designated cardioGRKO) 2


title: male GRloxP/loxPαMHCCre/+ mice (designated cardioGRKO) 1


title: E_48_vs_E_6_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with EPO for 48 hrs vs TF-1 cells treated with EPO for 6 hrs.


title: male Homozygous GR floxed (GRloxP,loxP)  3


title: male Homozygous GR floxed (GRloxP,loxP)  2


title: E_6_vs_ET_6_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with EPO for 6 hrs vs TF-1 cells treated with EPO + TNF for 6 hrs.


title: male Homozygous GR floxed (GRloxP,loxP)  1


title: G_6_vs_GT_6_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with GM-CSF for 6 hrs vs TF-1 cells treated with GM-CSF + TNF for 6 hrs.

value: GM-CSF


title: MCP-1-treated CRL 1932, bio rep-1

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: CRL-1932 cell line treated with MCP-1(5ng/mL) for 16h

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Affymetrix Expression Console Software (version 1.4) which normalizes array signals using  Signal Space Transformation (SST) and  robust multiarray averaging (RMA) algorithm.
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.mps
Normalized expression in SST-RMA signal intensity (log2 based values) from Affymetrix Expression Console Software (version 1.4)

source_name: Kidney cell line CRL-1932,  MCP-1(5ng/mL), 16h

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% FBS, penicillin (100 U/mL) and streptomycin (100 μg/mL). Cells were maintained at 37°C in a humidified 5% CO2 incubator

extract_protocol: Total RNA were extracted from cultured cells using RNeasy Mini-kit (Qiagen, MD, USA) followed the manufacturer’s protocol as described previously.

treatment_protocol: Cells were treated with MCP-1(5ng/mL). Untreated cells of the same passage were used as controls.

value: kidney

tag: tumor type

value: clear cell renal cell carcinoma


title: E_48_vs_ET_48_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with EPO for 48 hrs vs TF-1 cells treated with EPO + TNF for 48 hrs.

value: EPO


title: E_24_vs_ET_24_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with EPO for 24 hrs vs TF-1 cells treated with EPO + TNF for 24 hrs.


title: MCP-1-treated CRL 1932, bio rep-2


title: CRL1932-untreated-rep-2

description: untreated CRL-1932

source_name: Kidney cell line CRL-1932, untreated

value: untreated


title: E_0_vs_ET_0_replA

description: Biological replicate:A; Lame: 1; TF-1 cells treated with EPO for 0 hrs vs TF-1 cells treated with EPO + TNF for 0 hrs.


title: shortMedLong_HepG2_DNA_rep4

city: South San Francisco

first: Vikram

last: Agarwal

address: 1130 Veterans Blvd

institute: Calico Life Sciences

description:
Targeted barcode amplification from DNA
ShortMedLong.ActivityRatios.tsv
ShortMedLong.ActivityRatios.IndividualReps.tsv

data_processing:
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software. Multiplexed paired end (PE) Illumina sequencing data was split based on sample index allowing up to zero substitutions in the barcode sequence. In some cases, technical replicates were concatenated to achieve sufficient read counts.
The MPRAflow pipeline (Gordon et al, 2019), freely available on Github, was used to process the MPRA data. A brief overview of this pipeline is described here:
For oligo validation, consensus sequences were aligned to all designed oligo sequences using BWA MEM (Li and Durbin 2009) with parameters penalizing soft-clipping of alignment ends (-L 80). For RNA/DNA counts, sequences were matched against the designed barcode sequences.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
To determine the RNA/DNA ratios per insert, we summed up the counts of all barcodes contributing and determined the ratio of the average normalized counts.
Genome_build: GRCh37
Supplementary_files_format_and_content: *elements.fa (FASTA) and *sequences_coordinates.tsv (tab-separated value) files contain all designed oligo sequences for barcode association mapping, along with chromosomal coordinates of each element, and element type (positive control, negative control, or other). *assignments.tsv.gz files contain the mappings between barcodes and their associated element, along with barcode counts supporting the association. *ActivityRatios*.tsv files contain RNA/DNA ratios for individual replicates or with replicates averaged.

source_name: hepatocellular carcinoma cell line

growth_protocol: HepG2 cells (ATCC) were maintained in DMEM supplemented with 10% FCS, glutamine (2 mM), penicillin (100 U/ml) and streptomycin (50 μg/ml)

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen). Messenger RNA (mRNA) was purified from the total RNA using Oligotex mRNA mini kit (Qiagen) and treated with Turbo DNase to remove contaminating DNA.
For each RNA replicate, 3x500ng was reverse transcribed with Superscript IV (Invitrogen) using a primer downstream of the barcode, which contained a UMI. The resulting cDNA was pooled and split into 8 reactions, amplified with Kapa Robust polymerase for 3 cycles using an indexed P5 primer and P7. PCR products are then cleaned up with AMPure XP beads (Beckman Coulter) to remove the primers and concentrate the products. These products underwent a second round of amplification in 6 reactions per replicate and followed in real time with Sybr Green. All reactions were pooled at this point, cleaned up with AMPure CP beads, run on an agarose gel, and submitted for sequencing.

treatment_protocol: 2.4million cells were seeded in 10cm dishes. For plasmid-based MPRAs, the cells were transfected with 10 ug of plasmid libraries (HSS, ORI, and pGL4) using X-tremeGENE HP (Roche) with an Xtreme-GENE:DNA ratio of 2:1. For the lentiMPRAs, cels were infected with lentiviral libraries (5’/5’ WT/MT, 5’/3’ WT/MT, and 3’/3’ WT/MT) along with 8ug/ml polybrene, with the estimated MOI of 50 for wild-type and 100 for mutant libraries. Cells were incubated for 3 days. All experiments for nine libraries were carried out simultaneously to minimize batch effect. Three independent replicate cultures were transfected on different days.

tag: cell type

value: hepatocellular carcinoma cell line


title: forwardReverse_HepG2_RNA_rep1

description:
Targeted barcode amplification from RNA
ForwardReverse.ActivityRatios.tsv
ForwardReverse.ActivityRatios.IndividualReps.tsv

molecule: polyA RNA

tag: cell line


title: shortMedLong_HepG2_RNA_rep4

description:
Targeted barcode amplification from RNA
ShortMedLong.ActivityRatios.tsv
ShortMedLong.ActivityRatios.IndividualReps.tsv


title: forwardReverse_HepG2_DNA_rep1

description:
Targeted barcode amplification from DNA
ForwardReverse.ActivityRatios.tsv
ForwardReverse.ActivityRatios.IndividualReps.tsv


title: forwardReverse_HepG2_DNA_rep2


title: Cloned_array_oligo_library_reverse

description:
Amplication from cloned library
ForwardReverse_sequences_coordinates.tsv

molecule: other

source_name: oligo array synthesis

growth_protocol: Array-synthesized 230bp oligos (Agilent Technologies) were synthesized either containing the complete construct to be cloned or as overlapping fragments for Multiplex Pairwise Assembly or Hierarchical Multiplex Pairwise Assembly.

value: cloned oligonucleotide library

value: 10-beta electrocompetent E. coli (C3020)


title: Cloned_array_oligo_library_shortMedLong

description: Amplication from cloned library


title: forwardReverse_HepG2_RNA_rep2


title: shortMedLong_HepG2_DNA_rep1


title: shortMedLong_HepG2_DNA_rep3


title: shortMedLong_HepG2_RNA_rep1


title: forwardReverse_HepG2_DNA_rep4


title: forwardReverse_HepG2_RNA_rep4


title: pGL4_HepG2_RNA_rep3

description:
Targeted barcode amplification from RNA
9MPRA.ActivityRatios.tsv
9MPRA.ActivityRatios.IndividualReps.tsv


title: forwardReverse_HepG2_RNA_rep3


title: Cloned_array_oligo_library_9_MPRA_libraries

description: Amplication from cloned library


title: shortMedLong_HepG2_RNA_rep2


title: pGL4_HepG2_DNA_rep3

description:
Targeted barcode amplification from DNA
9MPRA.ActivityRatios.tsv
9MPRA.ActivityRatios.IndividualReps.tsv


title: forwardReverse_HepG2_DNA_rep3


title: pGL4_HepG2_RNA_rep2


title: shortMedLong_HepG2_RNA_rep3


title: shortMedLong_HepG2_DNA_rep2


title: HSS_b2_HepG2_DNA_rep3


title: HSS_b2_HepG2_RNA_rep1


title: HSS_b2_HepG2_DNA_rep2


title: pGL4_HepG2_DNA_rep1


title: HSS_b2_HepG2_RNA_rep3


title: ORI_b2_HepG2_RNA_rep3


title: ORI_b2_HepG2_RNA_rep2


title: ORI_b2_HepG2_DNA_rep3


title: pGL4_HepG2_DNA_rep2


title: pGL4_HepG2_RNA_rep1


title: ORI_b2_HepG2_DNA_rep2


title: HSS_b2_HepG2_RNA_rep2


title: ORI_full_HepG2_DNA_rep2


title: HSS_full_HepG2_RNA_rep3


title: HSS_full_HepG2_DNA_rep2


title: HSS_full_HepG2_DNA_rep1


title: HSS_full_HepG2_DNA_rep3


title: ORI_b2_HepG2_DNA_rep1


title: HSS_full_HepG2_RNA_rep2


title: ORI_full_HepG2_RNA_rep1


title: HSS_full_HepG2_RNA_rep1


title: ORI_full_HepG2_DNA_rep1


title: ORI_full_HepG2_RNA_rep2


title: ORI_full_HepG2_DNA_rep3


title: ORI_b2_HepG2_RNA_rep1


title: HSS_b2_HepG2_DNA_rep1


title: HSS_HepG2_RNA_rep3


title: ORI_full_HepG2_RNA_rep3


title: HSS_HepG2_DNA_rep3


title: HSS_HepG2_DNA_rep1


title: ORI_HepG2_RNA_rep3


title: ORI_HepG2_RNA_rep2


title: ORI_HepG2_RNA_rep1


title: HSS_HepG2_DNA_rep2


title: ORI_HepG2_DNA_rep3


title: 33_Wild-type_integrase_HepG2_RNA_rep2


title: HSS_HepG2_RNA_rep1


title: HSS_HepG2_RNA_rep2


title: 33_Wild-type_integrase_HepG2_DNA_rep3


title: 33_Mutant_integrase_HepG2_RNA_rep2


title: ORI_HepG2_DNA_rep1


title: 33_Wild-type_integrase_HepG2_RNA_rep3


title: 33_Wild-type_integrase_HepG2_DNA_rep2


title: 33_Mutant_integrase_HepG2_DNA_rep2


title: 33_Mutant_integrase_HepG2_RNA_rep1


title: ORI_HepG2_DNA_rep2


title: 33_Mutant_integrase_HepG2_DNA_rep3


title: 53_Wild-type_integrase_HepG2_DNA_rep3


title: 53_Wild-type_integrase_HepG2_DNA_rep2


title: 33_Mutant_integrase_HepG2_DNA_rep1


title: 53_Wild-type_integrase_HepG2_RNA_rep2


title: 53_Wild-type_integrase_HepG2_RNA_rep1


title: 33_Mutant_integrase_HepG2_RNA_rep3


title: 53_Wild-type_integrase_HepG2_RNA_rep3


title: 33_Wild-type_integrase_HepG2_RNA_rep1


title: 33_Wild-type_integrase_HepG2_DNA_rep1


title: 53_Mutant_integrase_HepG2_RNA_rep3


title: 53_Wild-type_integrase_HepG2_DNA_rep1


title: 53_Mutant_integrase_HepG2_DNA_rep2


title: 55_Wild-type_integrase_HepG2_RNA_rep3


title: 53_Mutant_integrase_HepG2_RNA_rep2


title: 53_Mutant_integrase_HepG2_RNA_rep1


title: 55_Wild-type_integrase_HepG2_DNA_rep2


title: 53_Mutant_integrase_HepG2_DNA_rep1


title: 55_Wild-type_integrase_HepG2_RNA_rep1


title: 55_Mutant_integrase_HepG2_RNA_rep2


title: 55_Mutant_integrase_HepG2_DNA_rep3


title: 55_Wild-type_integrase_HepG2_DNA_rep1


title: 55_Mutant_integrase_HepG2_DNA_rep2


title: 55_Mutant_integrase_HepG2_RNA_rep1


title: 55_Mutant_integrase_HepG2_RNA_rep3


title: RTA_21nt_6w_repD

city: Seattle

first: Paul

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

department: Medicine

institute: University of Washington

description: small RNA

data_processing:
small RNA sequencing reads were sorted by barcode, barcode removed (4nt), linker-1 clipped and aligned to mouse hairpins from mirBase release 15 using bowtie (version 0.12.7) with 2 mismatches and command -- best
Genome_build: mm9, mirBase release 15
Supplementary_files_format_and_content: File of reads per million (RPM) mapped microRNA hits for mouse small RNA sequencing samples in tab delimited text format

source_name: Tibialis anterior

extract_protocol:
Liver samples were snap frozen in liquid nitrogen and ground into powder.  Samples were homogenized and RNA was extracted by Trizol
3ug of RNA for liver samples and 1ug of alll other samples were ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (based on an 18-36nt small RNA fraction) on 15% PAGE. The 5’ ends RNA were ligated to 4nt barcoded adapters. Dual-ligated RNA was reverse transcribed, PCR amplified and size selected on 4% NuSieve (Lonza) agarose.  Small RNA sequencing was performed on the Illumina miSeq platform.

value: Tibialis anterior

tag: strain

tag: time after aav6-shrna

tag: stem


title: 55_Mutant_integrase_HepG2_DNA_rep1


title: RTA_21nt_6w_repC

description: small RNA

tag: tissue


title: RTA_21nt_6w_repB

description: small RNA


title: CRL1932-untreated-rep-1

description: untreated CRL-1932


title: 53_Mutant_integrase_HepG2_DNA_rep3


title: 55_Wild-type_integrase_HepG2_DNA_rep3


title: 55_Wild-type_integrase_HepG2_RNA_rep2


title: RTA_21nt_2w_repA

description: small RNA


title: RTA_21nt_2w_repC

description: small RNA


title: RTA_21nt_2w_repB

description: small RNA


title: RTA_21nt_6w_repA

description: small RNA


title: RTA_19nt_6w_repC

description: small RNA


title: RTA_19nt_6w_repA

description: small RNA


title: FP4_ATAC_rep2

value: photo-thermosensitive genic male sterile (PTGMS) rice line

value: panicle

value: uninucleate


title: RTA_19nt_2w_repB

description: small RNA


title: RTA_19nt_2w_repC

description: small RNA


title: LTA_21nt_6w_repE

description: small RNA


title: RQ_21nt_6w_repC

description: small RNA

source_name: Quadriceps

value: Quadriceps


title: RQ_19nt_6w_repB

description: small RNA


title: RQ_19nt_6w_repA

description: small RNA


title: RQ_19nt_2w_repB

description: small RNA


title: RQ_21nt_2w_repC

description: small RNA


title: RQ_19nt_6w_repC

description: small RNA


title: RQ_19nt_2w_repA

description: small RNA


title: RQ_21nt_6w_repB

description: small RNA


title: RQ_21nt_6w_repA

description: small RNA


title: RQ_21nt_2w_repB

description: small RNA


title: RQ_19nt_2w_repC

description: small RNA


title: RG_21nt_6w_repB

description: small RNA

source_name: Gastrocnemius

value: Gastrocnemius


title: LG_21nt_6w_repC

description: small RNA


title: RG_21nt_6w_repA

description: small RNA


title: RG_21nt_2w_repC

description: small RNA


title: RTA_19nt_6w_repB

description: small RNA


title: RG_21nt_2w_repA

description: small RNA


title: RG_21nt_2w_repB

description: small RNA


title: RTA_19nt_2w_repA

description: small RNA


title: RG_19nt_6w_repA

description: small RNA


title: RG_19nt_2w_repB

description: small RNA


title: RG_19nt_6w_repB

description: small RNA


title: RG_19nt_6w_repC

description: small RNA


title: RG_19nt_2w_repC

description: small RNA


title: RQ_21nt_2w_repA

description: small RNA


title: LIV_21nt_6w_repB

description: small RNA

source_name: Liver

value: Liver


title: LIV_21nt_6w_repA

description: small RNA


title: LIV_21nt_6w_repC

description: small RNA


title: LIV_21nt_2w_repB

description: small RNA


title: LIV_21nt_2w_repC

description: small RNA


title: LIV_19nt_2w_repC

description: small RNA


title: LIV_21nt_2w_repA

description: small RNA


title: LIV_19nt_6w_repC

description: small RNA


title: LIV_19nt_6w_repA

description: small RNA


title: HRT_uninjected_repC

description: small RNA

value: Heart

value: uninjected


title: LIV_19nt_2w_repA

description: small RNA


title: HRT_uninjected_repD

description: small RNA


title: LIV_19nt_2w_repB

description: small RNA


title: LIV_19nt_6w_repB

description: small RNA


title: HRT_uninjected_repA

description: small RNA


title: HRT_uninjected_repB

description: small RNA


title: HRT_RSV_AP_repB

description: small RNA

value: AP


title: HRT_RSV_AP_repA

description: small RNA


title: HRT_21nt_6w_repC

description: small RNA


title: RG_19nt_2w_repA

description: small RNA


title: HRT_21nt_6w_repB

description: small RNA


title: HRT_21nt_2w_repA

description: small RNA


title: HRT_19nt_6w_repC

description: small RNA


title: HRT_21nt_12w_repA

description: small RNA


title: HRT_21nt_6w_repA

description: small RNA


title: HRT_19nt_6w_repB

description: small RNA


title: HRT_21nt_2w_repB

description: small RNA


title: HRT_21nt_12w_repB

description: small RNA


title: HRT_21nt_2w_repC

description: small RNA


title: HRT_19nt_2w_repB

description: small RNA


title: HRT_19nt_6w_repA

description: small RNA


title: HRT_19nt_2w_repC

description: small RNA


title: HRT_19nt_2w_repA

description: small RNA


title: HRT_19nt_12w_repC

description: small RNA


title: HRT_RSV_AP_repC

description: small RNA


title: DIA_21nt_2w_repB

description: small RNA

source_name: Diaphragm

value: Diaphragm


title: DIA_21nt_6w_repA

description: small RNA


title: Dia_21nt_6w_repB

description: small RNA


title: DIA_21nt_2w_repA

description: small RNA


title: HRT_19nt_12w_repA

description: small RNA


title: HRT_19nt_12w_repB

description: small RNA


title: DIA_19nt_2w_repB

description: small RNA


title: DIA_19nt_2w_repC

description: small RNA


title: DIA_19nt_6w_repA

description: small RNA


title: DIA_21nt_2w_repC

description: small RNA


title: DIA_19nt_6w_repC

description: small RNA


title: DIA_19nt_6w_repB

description: small RNA


title: GF rep2

city: Gainesville

first: Christian

last: Jobin

state: Florida

institute: University of Florida

data_processing:
CAP-miRSeq analysis: sequences were filtered and trimmed using cutadapt. Quantification of miRNA was done using miRDeep2 and differentially expressed miRNAs were detected using edgeR
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of EdgeR normalized expression

source_name: stool

extract_protocol:
mirVana miRNA isolation kit
NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (E7300, NEB)

treatment_protocol: biofilm-negative , biofilm-positive, no treatment

value: no treatment


title: GF rep3


title: GF rep4


title: BX rep5

value: biofilm-negative


title: BX rep7


title: BX rep4


title: BX rep6


title: BX rep2


title: BX rep3


title: BT rep10

value: biofilm-positive


title: BT rep8


title: BX rep1


title: BT rep9


title: DIA_21nt_6w_repC

description: small RNA


title: GF rep1


title: BT rep7


title: BT rep4


title: BT rep3


title: BT rep5


title: BT rep1


title: BT rep6


title: Neurod2 shRNA-1 replicate 1

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

description: Experimental

data_processing:
Fastq Groomer (Galaxy tool version 1.0.4)
Filter by Quality (Galaxy tool version 1.0.0)
Tophat (Galaxy tool version 2.0.14)
Cufflinks (Galaxy tool version 2.2.1.0)
Cuffdiff (Galaxy tool version 2.2.1.3)
Genome_build: mm10
Supplementary_files_format_and_content: Format: txt; Content: GeneID, Chr, Start, End, Sample, Values, Log2(FC), p-value, q-value

source_name: primary cortical cultures

growth_protocol: Cerebral cortex was dissected from E14.5 embryos from timed pregnant mice. Briefly, tissue was digested with papain, followed by trypsin inhibitor treatment. Cell suspension was electroporated (Lonza nucelofector) with respective shRNA plasmids (cloned in pSuperneoGFP backbone) and immediately plated in Basal Media Eagle supplemented with N-2, B-27, Glutamax, and 10% serum. At 4 DIV total RNA was collected and library preparation was carried out for single-end RNA-Seq.

extract_protocol:
Absolutely RNA Microprep Kit (Agilent Technologies) was used.
Library was prepared for 1 x 50bp single-end read Illumina HiSeq 2500 platform by Genewiz, Inc.

treatment_protocol: nucleofection with different shRNAs

value: Balb/c

tag: transfection method

value: nucleofection


title: non-silencing replicate 1

description: Control


title: Neurod2 shRNA-1 replicate 2

description: Experimental


title: WT iTreg input replicate 1

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

institute: UCL Cancer Institute

data_processing:
Basecalls performed using CASAVA
Reads were filtered to remove adapters using fastq-mcf and for quality using seqkt
Reads were then aligned to the mouse genome (mm9) with Bowtie2 (default settings)
Regions of significant enrichment (10^-7) were identified using MACS version 1.4 (Zhang et al., 2008) using input as background, with the setting –keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks derived from analyses

source_name: iTreg

growth_protocol: CD4+ T cells from spleens and lymph nodes of 4- to 10-wk-old mice were purified by CD4 positive selection (Miltenyi Biotec) followed by sorting of naive CD4+CD25-CD62LhighCD44low cells using a FACSAria II (BD Biosciences). Cells were activated by plate-bound anti-CD3 and anti-CD28 (both 10 ug/ml; clones 145-2C11 and 37.51, respectively; Bio X Cell)

extract_protocol:
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent.  Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 10 µl of purified anti-T-bet serum (9856; Jenner et al., PNAS 2009). Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNAseA, proteinase K and phenol:chloroform extraction followed by ethanol precipitation
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 35 or 50 bp single-end read sequencing with an Illumina GAIIx or HiSeq 2000 sequencer

treatment_protocol: iTreg cells were generated by culturing in recombinant human TGF-β1 (33 ng/ml) and IL-2 (20 ng/ml; R & D Systems) for 7 days

value: iTreg

tag: chip antibody

value: Custom rabbit anti-T-bet serum (9856)


title: non-silencing replicate 2

description: Control


title: Neurod2 shRNA-2 replicate 1

description: Experimental


title: WT iTreg T-bet ChIP replicate 1


title: BT rep2

tag: genotype


title: Neurod2 shRNA-2 replicate 2

description: Experimental


title: Healthy Donor # 30a  (miRNA)

city: Setia Alam

first: Ezalia

last: Esa

address: NIH

department: Haematology unit

country: Malaysia

institute: Institute for Medical Research

description: 30a ctrl

hyb_protocol: Standard Nanostring protocol

scan_protocol: After hybridization of probe, the miRNA counts were measured using Nanostring digital analyser.

data_processing: Data generated by the digital analyser is interpreted by Nanostring in-house software, the nSolver. Raw data was normalised by in-house housekeeping genes provided by Nanostring.

label: Biotin

source_name: donor

label_protocol: Quantification of miRNA profiles was done using the nCounter Human v3 miRNA expression assay kit (Nanostring Technologies, Seattle, WA, USA), following the manufacturer’s protocols. The product utilizes the direct ligation of oligonucleotide tags onto total RNA, thus allowing miRNA and mRNA to be directly measured with great specificity and sensitivity while eliminating the use of reverse transcriptase or amplification.

extract_protocol: Buffy coat was separated from the peripheral blood using Ficoll-Paque density gradient media. Buffy coat is lysed using Qiazol lysis reagent (Qiagen, Hilden, Germany) followed by total RNA extraction using miRNeasy kit (Qiagen, Hilden, Germany).

tag: individual

value: Donor # 30a

tag: disease state

value: Healthy

value: Blood

tag: age

tag: gender

value: Female

tag: ethnicity

value: Malay


title: Healthy Donor # 53b  (miRNA)

description: 53b ctrl

value: Donor # 53b

value: Male


title: Healthy Donor # 14b  (miRNA)

description: 14b ctrl

value: Donor # 14b


title: Healthy Donor # 46b  (miRNA)

description: 46b ctrl

value: Donor # 46b

value: Chinese


title: Healthy Donor # 41b  (miRNA)

description: 41b ctrl

value: Donor # 41b


title: Healthy Donor # 12b  (miRNA)

description: 12b ctrl

value: Donor # 12b


title: Healthy Donor # 28b  (miRNA)

description: 28b ctrl

value: Donor # 28b


title: Healthy Donor # 15b  (miRNA)

description: 15b ctrl

value: Donor # 15b


title: Healthy Donor # 56b  (miRNA)

description: 56b ctrl

value: Donor # 56b


title: Healthy Donor # 8b  (miRNA)

description: 9b ctrl

value: Donor # 8b


title: Healthy Donor # 3b  (miRNA)

description: 3b ctrl

value: Donor # 3b


title: Healthy Donor # 25a  (miRNA)

description: 25a ctrl

value: Donor # 25a


title: Healthy Donor # 9b  (miRNA)

description: 8b ctrl

value: Donor # 9b

value: Healthy


title: Healthy Donor # 25  (miRNA)

description: 25 ctrl

value: Donor # 25

value: Blood

value: Female


title: Healthy Donor # 1b  (miRNA)

description: 1b ctrl

value: Donor # 1b


title: Healthy Donor # 28  (miRNA)

description: 28 ctrl

value: Donor # 28

value: Malay


title: Healthy Donor # 16  (miRNA)

description: 16 ctrl

value: Donor # 16

value: Male

value: Indian


title: Healthy Donor # 15  (miRNA)

description: 15 ctrl

value: Donor # 15


title: Healthy Donor # 7 (miRNA)

description: 7 ctrl

value: Donor # 7

value: Chinese


title: Healthy Donor # 11  (miRNA)

description: 11 ctrl

value: Donor # 11


title: Healthy Donor # 8  (miRNA)

description: 8 ctrl

value: Donor # 8


title: Healthy Donor # 9 (miRNA)

description: 9 ctrl

value: Donor # 9


title: Newly diagnosed CN-AML Patient # 103  (miRNA)

description: 103 case

source_name: primary leukemia

value: Patient # 103

value: Newly diagnosed with CN-AML


title: Newly diagnosed CN-AML Patient # 106  (miRNA)

description: 106 case

value: Patient # 106


title: Newly diagnosed CN-AML Patient # 105  (miRNA)

description: 105 case

value: Patient # 105

value: Blood


title: Healthy Donor # 6b  (miRNA)

description: 6b ctrl

value: Donor # 6b

value: Healthy

value: Female


title: Newly diagnosed CN-AML Patient # 95  (miRNA)

description: 95 case

value: Patient # 95


title: Newly diagnosed CN-AML Patient # 91 (miRNA)

description: 91 case

value: Patient # 91

value: Malay


title: Healthy Donor # 30  (miRNA)

description: 30 ctrl

value: Donor # 30


title: Newly diagnosed CN-AML Patient # 88  (miRNA)

description: 88 case

value: Patient # 88

value: Male


title: Newly diagnosed CN-AML Patient # 86  (miRNA)

description: 86 case

value: Patient # 86


title: Newly diagnosed CN-AML Patient # 97  (miRNA)

description: 97 case

value: Patient # 97

value: Chinese


title: Newly diagnosed CN-AML Patient # 66 (miRNA)

description: 66 case

value: Patient # 66


title: Newly diagnosed CN-AML Patient # 67 (miRNA)

description: 67 case

value: Patient # 67

value: Newly diagnosed with CN-AML


title: Newly diagnosed CN-AML Patient # 78 (miRNA)

description: 78 case

value: Patient # 78


title: Newly diagnosed CN-AML Patient # 76 (miRNA)

description: 76 case

value: Patient # 76

value: Blood


title: Newly diagnosed CN-AML Patient # 80 (miRNA)

description: 80 case

value: Patient # 80


title: Newly diagnosed CN-AML Patient # 29 (miRNA)

description: 29 case

value: Patient # 29


title: Newly diagnosed CN-AML Patient # 85  (miRNA)

description: 85 case

value: Patient # 85

value: Female


title: Newly diagnosed CN-AML Patient # 82  (miRNA)

description: 82 case

value: Patient # 82


title: 11_52 RNA-seq

city: Chengdu

first: keying

last: Lu

state: Sichuan

address: Wuhou

department: State Key Laboratory of Biotherapy

institute: Sichuan university

data_processing:
RNA-seq: The fastq files generated by the Illumina workflow underwent read-level quality control before mapping, using FastQC (v0.11.4). For sample with poor read quality, quality trimming was performed using Trim Galore (v0.4.4, Quality Phred score cut-off: 30).The HISAT2 (v2.0.5, default parameters) was utilized for mapping the reads with the Mmul 8.0.1 reference genome and the Mmul 8.0.1.91 transcriptomic annotation GTF. Read counts of genes were generated using HTSeq (v0.6.1).
ATAC-seq: paired-end reads were aligned to the rhesus macaque genome (Mmul 8.0.1, downloaded from ENSEMBL), using bwa mem (v0.7.12) with -M parameter. First, PCR duplicates were removed using Picard (v1.119). Reads mapped to mitochondrial DNA were then excluded. Only uniquely mapped and properly paired reads with insert size less than 2kb and mapping quality over 30 were kept for downstream analysis. UCSC bedGraphToBigWig was used to generate bigWig files. Peak calling was performed with MACS2 (v2.1.0.20151222) using parameters ?--nomodel --nolambda --shift 100 --extsize 200 -B --SPMR?.
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample; bigwig

organism: Macaca mulatta

source_name: pituitarium

extract_protocol:
RNA-seq:RNA degradation and contamination was detected by 1% agarose gels; Then, RNA purity was checked using the kaiao K5500® Spectrophotometer (Kaiao, Beijing, China). The RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). ATAC-seq:A total amount of 10,000 cells at 500g for 5 min, cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix for 30 min at 37 °C, sample was purified using a Qiagen MinElute kit.
RNA-seq:A total amount of 3 ?g RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Epicentre Ribo-Zero? Gold Kits(Human/Mouse/Rat) (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra? Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) . ATAC-seq: The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 ?L. Libraries were amplified for a total of 10?15 cycles. Libraries were sequenced on Illumina NextSeq 500 (Next500 kit v2 High Output 150 cycles).

tag: macaque id

value: Rhesus 11

value: brain

value: female

value: 9.8 years


title: 11_51 RNA-seq

source_name: globus pallidus


title: Newly diagnosed CN-AML Patient # 43 (miRNA)

description: 43 case

value: Patient # 43

value: Male


title: Newly diagnosed CN-AML Patient # 34 (miRNA)

description: 34 case

value: Patient # 34

value: Indian


title: 11_50 RNA-seq

source_name: putamen


title: Newly diagnosed CN-AML Patient # 27 (miRNA)

description: 27 case

value: Patient # 27

value: Newly diagnosed with CN-AML

value: Chinese


title: Newly diagnosed CN-AML Patient # 28 (miRNA)

description: 28 case

value: Patient # 28

value: Blood


title: Newly diagnosed CN-AML Patient # 46 (miRNA)

description: 46 case

value: Patient # 46

value: Malay


title: 11_49 RNA-seq

source_name: caudate nucleus


title: Newly diagnosed CN-AML Patient # 45 (miRNA)

description: 45 case

value: Patient # 45

value: Female


title: 11_45 RNA-seq

source_name: dentate gyrus

value: Rhesus 11


title: Newly diagnosed CN-AML Patient # 63 (miRNA)

description: 63 case

value: Patient # 63


title: 11_46 RNA-seq

value: brain

value: female


title: 11_47 RNA-seq

value: 9.8 years


title: 11_43 RNA-seq

description: Sample was excluded from downstream expression analysis and therefore not included in Rhesus_RNA_gene_count.txt

source_name: midbrain


title: Newly diagnosed CN-AML Patient # 35 (miRNA)

description: 35 case

value: Patient # 35


title: 11_42 RNA-seq

source_name: Substantia Nigra


title: 11_44 RNA-seq

source_name: amygdala


title: 11_40 RNA-seq

source_name: cerebellum vermis


title: 11_39 RNA-seq

source_name: cerebellar cortex


title: 11_41 RNA-seq

source_name: Ventral tegmental area


title: 11_38 RNA-seq

source_name: pons


title: 11_37 RNA-seq

source_name: medulla oblongata


title: 11_48 RNA-seq

source_name: accumbens nucleus


title: 11_34 RNA-seq

source_name: corpus callosum


title: 11_35 RNA-seq

source_name: thalamus


title: 11_31 RNA-seq

source_name: lingual gyrus


title: 11_32 RNA-seq

source_name: posterior cingular gyrus


title: 11_29 RNA-seq

source_name: fusiform gyrus


title: 11_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 11_24 RNA-seq

source_name: occipito-temporal gyrus


title: 11_21 RNA-seq

source_name: anterior superior occipital gyrus


title: 11_23 RNA-seq

source_name: inferior occipital gyrus


title: 11_19 RNA-seq

source_name: annectant gyri, in macaque


title: 11_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 11_18 RNA-seq

source_name: AG, angular gyrus


title: 11_26 RNA-seq

source_name: superior temporal gyrus


title: 11_16 RNA-seq

source_name: Intraparietal sulcus


title: 11_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 11_20 RNA-seq

source_name: cuneus gyrus


title: 11_12 RNA-seq

source_name: superior postcentral gyrus


title: 11_10 RNA-seq

source_name: superior precentral gyrus


title: 11_11 RNA-seq

source_name: inferior precentral gyrus


title: 11_27 RNA-seq

source_name: temporal polar gyrus


title: 11_33 RNA-seq

source_name: anterior cingular gyrus


title: 11_8 RNA-seq

source_name: medial orbital gyrus


title: 11_14 RNA-seq

source_name: superior parietal lobule


title: 11_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 11_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 11_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: 11_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 11_25 RNA-seq

source_name: inferior temporal gyrus


title: 11_4 RNA-seq

source_name: posterior superior frontal gyrus


title: 11_2 RNA-seq

source_name: middle frontal gyrus


title: 11_3 RNA-seq

source_name: inferior frontal gyrus


title: 11_1 RNA-seq

source_name: Olfactory bulb


title: 10_52 RNA-seq

source_name: pituitarium

value: Rhesus 10

value: 5 years


title: 10_49 RNA-seq

source_name: caudate nucleus


title: 10_51 RNA-seq

source_name: globus pallidus


title: 10_50 RNA-seq

source_name: putamen


title: 11_13 RNA-seq

source_name: inferior postcentral gyrus


title: 10_43 RNA-seq

source_name: midbrain


title: 10_44 RNA-seq

source_name: amygdala


title: 10_42 RNA-seq

source_name: Substantia Nigra


title: 10_41 RNA-seq

source_name: Ventral tegmental area


title: 10_40 RNA-seq

source_name: cerebellum vermis


title: 10_39 RNA-seq

source_name: cerebellar cortex


title: 11_28 RNA-seq

source_name: entorhinal cortex & perirhinal cortex


title: 10_38 RNA-seq

source_name: pons


title: 10_37 RNA-seq

source_name: medulla oblongata


title: 10_34 RNA-seq

source_name: corpus callosum


title: 10_36 RNA-seq

source_name: hypothalamus


title: 10_33 RNA-seq

source_name: anterior cingular gyrus


title: 10_32 RNA-seq

source_name: posterior cingular gyrus


title: 10_31 RNA-seq

source_name: lingual gyrus


title: 10_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 10_28 RNA-seq


title: 10_29 RNA-seq

source_name: fusiform gyrus


title: 10_27 RNA-seq

source_name: temporal polar gyrus


title: 10_47 RNA-seq


title: 10_46 RNA-seq


title: 10_26 RNA-seq

source_name: superior temporal gyrus


title: 10_45 RNA-seq

source_name: dentate gyrus


title: 10_24 RNA-seq

source_name: occipito-temporal gyrus


title: 10_48 RNA-seq

source_name: accumbens nucleus


title: 10_25 RNA-seq

source_name: inferior temporal gyrus


title: 10_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 10_20 RNA-seq

source_name: cuneus gyrus


title: 10_21 RNA-seq

source_name: anterior superior occipital gyrus


title: 10_23 RNA-seq

source_name: inferior occipital gyrus


title: 10_35 RNA-seq

source_name: thalamus


title: 10_18 RNA-seq

source_name: AG, angular gyrus


title: 10_19 RNA-seq

source_name: annectant gyri, in macaque


title: 10_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 10_16 RNA-seq

source_name: Intraparietal sulcus


title: 10_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 10_13 RNA-seq

source_name: inferior postcentral gyrus


title: 10_11 RNA-seq

source_name: inferior precentral gyrus


title: 10_12 RNA-seq

source_name: superior postcentral gyrus


title: 10_14 RNA-seq

source_name: superior parietal lobule


title: 10_9 RNA-seq

source_name: insula


title: 10_8 RNA-seq

source_name: medial orbital gyrus


title: 10_10 RNA-seq

source_name: superior precentral gyrus


title: 10_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 10_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: 10_4 RNA-seq

source_name: posterior superior frontal gyrus


title: 10_1 RNA-seq

source_name: Olfactory bulb


title: 10_2 RNA-seq

source_name: middle frontal gyrus


title: 10_3 RNA-seq

source_name: inferior frontal gyrus


title: 8_51 RNA-seq

source_name: globus pallidus

value: Rhesus 8

value: male

value: 3.8 years


title: 8_50 RNA-seq

source_name: putamen


title: 8_49 RNA-seq

source_name: caudate nucleus


title: 8_52 RNA-seq

source_name: pituitarium


title: 8_47 RNA-seq


title: 8_48 RNA-seq

source_name: accumbens nucleus


title: 8_46 RNA-seq


title: 8_45 RNA-seq

source_name: dentate gyrus


title: 8_44 RNA-seq

source_name: amygdala


title: 8_42 RNA-seq

source_name: Substantia Nigra


title: 8_41 RNA-seq

source_name: Ventral tegmental area


title: 8_40 RNA-seq

source_name: cerebellum vermis


title: 8_39 RNA-seq

source_name: cerebellar cortex


title: 8_36 RNA-seq

source_name: hypothalamus


title: 8_37 RNA-seq

source_name: medulla oblongata


title: 8_35 RNA-seq

source_name: thalamus


title: 10_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 8_33 RNA-seq

source_name: anterior cingular gyrus


title: 8_43 RNA-seq

source_name: midbrain


title: 8_32 RNA-seq

source_name: posterior cingular gyrus


title: 8_31 RNA-seq

source_name: lingual gyrus


title: 8_28 RNA-seq

source_name: entorhinal cortex & perirhinal cortex


title: 8_24 RNA-seq

source_name: occipito-temporal gyrus


title: 8_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 8_26 RNA-seq

source_name: superior temporal gyrus


title: 8_25 RNA-seq

source_name: inferior temporal gyrus


title: 8_23 RNA-seq

source_name: inferior occipital gyrus


title: 8_21 RNA-seq

source_name: anterior superior occipital gyrus


title: 8_20 RNA-seq

source_name: cuneus gyrus


title: 8_19 RNA-seq

source_name: annectant gyri, in macaque


title: 8_18 RNA-seq

source_name: AG, angular gyrus


title: 8_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 8_38 RNA-seq

source_name: pons


title: 8_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 8_13 RNA-seq

source_name: inferior postcentral gyrus


title: 8_12 RNA-seq

source_name: superior postcentral gyrus


title: 8_27 RNA-seq

source_name: temporal polar gyrus


title: 8_11 RNA-seq

source_name: inferior precentral gyrus


title: 8_10 RNA-seq

source_name: superior precentral gyrus


title: 8_9 RNA-seq

source_name: insula


title: 8_34 RNA-seq

source_name: corpus callosum


title: 8_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 8_29 RNA-seq

source_name: fusiform gyrus


title: 8_8 RNA-seq

source_name: medial orbital gyrus


title: 8_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: 8_4 RNA-seq

source_name: posterior superior frontal gyrus


title: 8_16 RNA-seq

source_name: Intraparietal sulcus


title: 8_2 RNA-seq

source_name: middle frontal gyrus


title: 8_1 RNA-seq

source_name: Olfactory bulb


title: 8_3 RNA-seq

source_name: inferior frontal gyrus


title: 7_52 RNA-seq

source_name: pituitarium

value: Rhesus 7

value: 4 years


title: 7_51 RNA-seq

source_name: globus pallidus


title: 7_49 RNA-seq

source_name: caudate nucleus


title: 7_50 RNA-seq

source_name: putamen


title: 7_48 RNA-seq

source_name: accumbens nucleus


title: 7_45 RNA-seq

source_name: dentate gyrus


title: 7_46 RNA-seq


title: 7_47 RNA-seq


title: 8_14 RNA-seq

source_name: superior parietal lobule


title: 7_44 RNA-seq

source_name: amygdala


title: 7_42 RNA-seq

source_name: Substantia Nigra


title: 8_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 7_43 RNA-seq

source_name: midbrain


title: 7_39 RNA-seq

source_name: cerebellar cortex


title: 7_40 RNA-seq

source_name: cerebellum vermis


title: 7_41 RNA-seq

source_name: Ventral tegmental area


title: 7_35 RNA-seq

source_name: thalamus


title: 7_37 RNA-seq

source_name: medulla oblongata


title: 7_38 RNA-seq

source_name: pons


title: 8_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 7_34 RNA-seq

source_name: corpus callosum


title: 7_36 RNA-seq

source_name: hypothalamus


title: 7_31 RNA-seq

source_name: lingual gyrus


title: 7_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 7_29 RNA-seq

source_name: fusiform gyrus


title: 7_24 RNA-seq

source_name: occipito-temporal gyrus


title: 7_26 RNA-seq

source_name: superior temporal gyrus


title: 7_28 RNA-seq

source_name: entorhinal cortex & perirhinal cortex


title: 7_32 RNA-seq

source_name: posterior cingular gyrus


title: 7_25 RNA-seq

source_name: inferior temporal gyrus


title: 7_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 7_23 RNA-seq

source_name: inferior occipital gyrus


title: 7_21 RNA-seq

source_name: anterior superior occipital gyrus


title: 7_19 RNA-seq

source_name: annectant gyri, in macaque


title: 7_18 RNA-seq

source_name: AG, angular gyrus


title: 7_20 RNA-seq

source_name: cuneus gyrus


title: 7_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 7_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 7_16 RNA-seq

source_name: Intraparietal sulcus


title: 7_33 RNA-seq

source_name: anterior cingular gyrus


title: 7_13 RNA-seq

source_name: inferior postcentral gyrus


title: 7_12 RNA-seq

source_name: superior postcentral gyrus


title: 7_10 RNA-seq

source_name: superior precentral gyrus


title: 7_14 RNA-seq

source_name: superior parietal lobule


title: 7_9 RNA-seq

source_name: insula


title: 7_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 11_9 RNA-seq


title: 7_11 RNA-seq

source_name: inferior precentral gyrus


title: 7_8 RNA-seq

source_name: medial orbital gyrus


title: 7_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: 7_4 RNA-seq

source_name: posterior superior frontal gyrus


title: 7_3 RNA-seq

source_name: inferior frontal gyrus


title: 7_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 7_1 RNA-seq

source_name: Olfactory bulb


title: 7_2 RNA-seq

source_name: middle frontal gyrus


title: 6_52 RNA-seq

source_name: pituitarium

value: Rhesus 6

value: 10 years


title: 6_50 RNA-seq

source_name: putamen


title: 6_48 RNA-seq

source_name: accumbens nucleus


title: 6_49 RNA-seq

source_name: caudate nucleus


title: 6_47 RNA-seq


title: 6_44 RNA-seq

source_name: amygdala


title: 6_45 RNA-seq

source_name: dentate gyrus


title: 6_46 RNA-seq


title: 11_36 RNA-seq

source_name: hypothalamus


title: 6_41 RNA-seq

source_name: Ventral tegmental area


title: 6_38 RNA-seq

source_name: pons


title: 6_42 RNA-seq

source_name: Substantia Nigra


title: 6_39 RNA-seq

source_name: cerebellar cortex


title: 6_40 RNA-seq

source_name: cerebellum vermis


title: 6_33 RNA-seq

source_name: anterior cingular gyrus


title: 6_37 RNA-seq

source_name: medulla oblongata


title: 6_31 RNA-seq

source_name: lingual gyrus


title: 6_34 RNA-seq

source_name: corpus callosum


title: 6_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 6_36 RNA-seq


title: 6_35 RNA-seq

source_name: thalamus


title: 6_32 RNA-seq

source_name: posterior cingular gyrus


title: 6_29 RNA-seq

source_name: fusiform gyrus


title: 6_51 RNA-seq

source_name: globus pallidus


title: 6_27 RNA-seq

source_name: temporal polar gyrus


title: 6_24 RNA-seq

source_name: occipito-temporal gyrus


title: 6_28 RNA-seq

source_name: entorhinal cortex & perirhinal cortex


title: 6_26 RNA-seq

source_name: superior temporal gyrus


title: 6_23 RNA-seq

source_name: inferior occipital gyrus


title: 6_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 6_43 RNA-seq

source_name: midbrain


title: 6_25 RNA-seq

source_name: inferior temporal gyrus


title: 6_20 RNA-seq

source_name: cuneus gyrus


title: 6_21 RNA-seq

source_name: anterior superior occipital gyrus


title: 6_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 6_14 RNA-seq

source_name: superior parietal lobule


title: 6_12 RNA-seq

source_name: superior postcentral gyrus


title: 6_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 6_13 RNA-seq

source_name: inferior postcentral gyrus


title: 6_16 RNA-seq

source_name: Intraparietal sulcus


title: 6_18 RNA-seq

source_name: AG, angular gyrus


title: 6_8 RNA-seq

source_name: medial orbital gyrus


title: 6_10 RNA-seq

source_name: superior precentral gyrus


title: 6_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: 6_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 6_9 RNA-seq

source_name: insula


title: 6_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 4_52 RNA-seq

source_name: pituitarium

value: Rhesus 4

value: 3.2 years


title: 6_3 RNA-seq

source_name: inferior frontal gyrus


title: 6_1 RNA-seq

source_name: Olfactory bulb


title: 6_4 RNA-seq

source_name: posterior superior frontal gyrus


title: 4_51 RNA-seq

source_name: globus pallidus


title: 6_11 RNA-seq

source_name: inferior precentral gyrus


title: 4_49 RNA-seq

source_name: caudate nucleus


title: 6_19 RNA-seq

source_name: annectant gyri, in macaque


title: 4_50 RNA-seq

source_name: putamen


title: 4_46 RNA-seq


title: 4_45 RNA-seq

source_name: dentate gyrus


title: 4_44 RNA-seq

source_name: amygdala


title: 4_41 RNA-seq

source_name: Ventral tegmental area


title: 4_39 RNA-seq

source_name: cerebellar cortex


title: 4_48 RNA-seq

source_name: accumbens nucleus


title: 4_43 RNA-seq

source_name: midbrain


title: 4_42 RNA-seq

source_name: Substantia Nigra


title: 4_34 RNA-seq

source_name: corpus callosum


title: 4_37 RNA-seq

source_name: medulla oblongata


title: 4_35 RNA-seq

source_name: thalamus


title: 4_33 RNA-seq

source_name: anterior cingular gyrus


title: 4_28 RNA-seq

source_name: entorhinal cortex & perirhinal cortex


title: 4_29 RNA-seq

source_name: fusiform gyrus


title: 4_32 RNA-seq

source_name: posterior cingular gyrus


title: 4_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: 4_27 RNA-seq

source_name: temporal polar gyrus


title: 4_31 RNA-seq

source_name: lingual gyrus


title: 4_47 RNA-seq


title: 4_25 RNA-seq

source_name: inferior temporal gyrus


title: 4_26 RNA-seq

source_name: superior temporal gyrus


title: 4_24 RNA-seq

source_name: occipito-temporal gyrus


title: 4_21 RNA-seq

source_name: anterior superior occipital gyrus


title: 4_36 RNA-seq

source_name: hypothalamus


title: 4_40 RNA-seq

source_name: cerebellum vermis


title: 4_18 RNA-seq

source_name: AG, angular gyrus


title: 4_20 RNA-seq

source_name: cuneus gyrus


title: 4_17 RNA-seq

source_name: anterior/posterior marginal gyrus


title: 4_16 RNA-seq

source_name: Intraparietal sulcus


title: 4_11 RNA-seq

source_name: inferior precentral gyrus


title: 4_15 RNA-seq

source_name: posterior superior parietal gyrus


title: 4_13 RNA-seq

source_name: inferior postcentral gyrus


title: 4_10 RNA-seq

source_name: superior precentral gyrus


title: 4_14 RNA-seq

source_name: superior parietal lobule


title: 4_12 RNA-seq

source_name: superior postcentral gyrus


title: 4_9 RNA-seq

source_name: insula


title: 4_22 RNA-seq

source_name: posterior superior occipital gyrus


title: 4_23 RNA-seq

source_name: inferior occipital gyrus


title: 4_4 RNA-seq

source_name: posterior superior frontal gyrus


title: 4_5 RNA-seq

source_name: anterior superior frontal gyrus


title: 4_6 RNA-seq

source_name: anterior arcuate sulcus gyrus


title: 4_8 RNA-seq

source_name: medial orbital gyrus


title: 4_3 RNA-seq

source_name: inferior frontal gyrus


title: 4_7 RNA-seq

source_name: ventromedial prefrontal cortex


title: 4_19 RNA-seq

source_name: annectant gyri, in macaque


title: 4_1 RNA-seq

source_name: Olfactory bulb


title: 3_51 RNA-seq

source_name: globus pallidus

value: Rhesus 3


title: 3_52 RNA-seq

source_name: pituitarium


title: 3_50 RNA-seq

source_name: putamen


title: 4_2 RNA-seq

source_name: middle frontal gyrus


title: 3_49 RNA-seq

source_name: caudate nucleus


title: 3_48 RNA-seq

source_name: accumbens nucleus


title: 3_45 RNA-seq

source_name: dentate gyrus


title: 7_27 RNA-seq

source_name: temporal polar gyrus


title: 3_46 RNA-seq


title: 3_47 RNA-seq


title: 3_43 RNA-seq

source_name: midbrain


title: 3_44 RNA-seq

source_name: amygdala


title: 3_40 RNA-seq

source_name: cerebellum vermis


title: 3_42 RNA-seq

source_name: Substantia Nigra


title: 3_41 RNA-seq

source_name: Ventral tegmental area


title: 3_39 RNA-seq

source_name: cerebellar cortex


title: 3_37 RNA-seq

source_name: medulla oblongata


title: 6_2 RNA-seq


title: 3_36 RNA-seq

source_name: hypothalamus


title: 3_35 RNA-seq

source_name: thalamus


title: 3_34 RNA-seq

source_name: corpus callosum


title: 3_31 RNA-seq

source_name: lingual gyrus


title: 3_30 RNA-seq

source_name: hippocampal gyrus or Parahippocampal gyrus


title: S1_RNAseq

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

data_processing:
Quality control was done with an in-house R script
Adapter trimmng was done with reaper (EMBL-EBI)
Clean reads were mapped to Arabidopsis TAIR10 genome using bismark. To increase the coverage, mates from the paired-end were mapped as independent single end reads: R1 as directional and R2 and non-directional
Mapping sam files were deduplicated using samtools rmdup
bismark_methylation_extractor was used to do the methylation calling of cytosines covered by 3 or more reads
Methylation status of a cytosines was calculated as #C/(#C+#NC) where #C is the absolute number of reads in which C was converted to T by bisulfite treatment and NC is the absolute number of reads in which C was unafected by bisulphite treatment
For transcriptomic analysis, the raw RNA-seq libraries were mapped to the TAIR10 genome using STAR. In the analysis of differentially expressed genes, raw RNA-seq reads were mapped using bowtie2. Expression counts were generated using summarizeOverlaps using the AtRTD2 transcriptome or the TAIR10 TE annotation as references. Differential expression was detected using DESeq2 with absolute log2FoldChange >= 1 and FDR <= 0.05 as expression thresholds.
Subsequent analysis were performed in R. The gene and transposable element models used were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph of converted and non converted cytosines per methylation context, filtered by coverage < 3 after merging the biological replicates. Those files were used as input for the detection of DMRs
Supplementary_files_format_and_content: Text files of the matrix of normalized counts per gene transcript and TEs

organism: Arabidopsis thaliana

source_name: Mature leaf

growth_protocol: The Arabidopsis thaliana (L.) Heynh wild-type accession Columbia (Col) was used in all experiments. Seeds were sown on 0.5× basal salts Murashige and Skoog (MS) medium (Duchefa, Haarlem, The Netherlands), stratified at 4°C for one day and then transferred to growth chambers for germination at 20°C under short day (SD, 8 h light) photoperiods for ten days before being transferred to soil. Plants were grown for 42 days under short day (SD, 8 h light) photoperiods.

extract_protocol:
For the RNA-seq, RNA extraction and reverse transcription were performed as described previously (Alexandre et al., 2009) with minor modifications. DNA-free RNA was reverse-transcribed using a RevertAid First Strand cDNA Synthesis Kit (Fermentas, Helsingborg, Sweden).
The Ultraovation kit from NUGEN was used to perform the bisulphite conversion. RNA-seq libraries were constructed using the TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: On the 42nd day, leaves number 5-6th from the rosette were individually covered with a black cloth mitten. Tissue was collected on the 48th day at 10:00. Non-senescent tissue corresponds to a mix of the uncovered leaves from the same plants.

tag: ecotype

value: Columbia

value: WT

value: leaves no. 5-6th darkened for 5 days

value: 48 days old

tag: biological replicate


title: NS2_RNAseq

value: uncovered leaves


title: S2_RNAseq


title: 3_27 RNA-seq

value: brain