title: CS2_3 Octant stage Seed coat RNA-seq replicate 3

source_name: Octant stage Seed coat

value: Octant stage


title: RS7_2 Mature stage Seed coat replicate 2

status: Public on Aug 22 2021

type: SRA

city: Saskatoon

first: Daoquan

last: Xiang

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

country: Canada

institute: National Research Council of Canada

description:
replicate 2
Sample_TPM.xlsx

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Salmon was used for fast and accurate alignment of cleaned reads to released brassica transcriptome databases (http://brassicadb.org/brad/datasets/pub/Genomes/), respectively.
Salmon was used to obtain transcripts per million reads (TPM) of each sample.
To summarize expression levels from the transcript level to the gene level, we used R tximport package to process the TPM values obtained from Salmon.
Genome_build: Brassica transcriptome databases (http://brassicadb.org/brad/datasets/pub/Genomes/)
Supplementary_files_format_and_content: Matrix table files include TPM for each Sample

molecule: total RNA

organism: Brassica rapa

source_name: Mature stage Seed coat

growth_protocol: Plants were grown under 16h of light, 22°C and 8h of dark, 20°C photoperiod 120-150 μE m−2 s−1 light intensity.

extract_protocol:
Embryo isolations were performed using a dissecting microscope, fine forceps and needles in a 4.8% Sucrose solution that contained 0.1% RNALater solution.For seed coat isolation, the embryos were manually removed, and the remaining seed coat was kept. Total RNA was extracted from each stage embryo sample following the protocol of RNAqueous-micro kit.
RNA-seq libraries were prepared using the NEBNext Single Cell/Low Input RNA library Prep Kit for Illumina.

treatment_protocol: Brassica flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.

tag: tissue

value: Seed coat

tag: Stage

value: Mature

tag: ecotype

value: Parkland


title: RUO_2 Unfertilized stage ovule replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Unfertilized stage ovule

value: ovule

value: Unfertilized


title: CUO_3 Unfertilized stage ovule RNA-seq replicate 3

organism: Brassica carinata

tag: satge

value: Unfertilized stage


title: NE2_1 Octant stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

organism: Brassica nigra

source_name: Octant stage Embryo

value: Embryo

value: Octant


title: CS1_3 Zygote stage Seed coat RNA-seq replicate 3

source_name: Zygote stage Seed coat

value: Zygote stage


title: NE1_3 Zygote stage Embryo RNA-seq replicate 3

description: Zygote stage Embryo RNA-seq replicate 3

source_name: Zygote stage Embryo


title: CE7_3 Mature_stage Embryo RNA-seq replicate 3

description: Mature_stage Embryo RNA-seq replicate 3

source_name: Mature_stage Embryo


title: NE1_2 Zygote stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Zygote


title: RUO_1 Unfertilized stage ovule replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RS6_2 Bent stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Bent stage Seed coat

value: Bent


title: RS1_2 Zygote stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CE3_3 Globular stage Embryo RNA-seq replicate 3

source_name: Globular stage Embryo

value: Globular stage


title: NE2_2 Octant stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CS6_3 Bent stage Seed coat RNA-seq replicate 3

value: Bent stage


title: NE1_1 Zygote stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CS4_3 Heart stage Seed coat RNA-seq replicate 3

source_name: Heart stage Seed coat

value: Heart stage


title: CS3_3 Globular stage Seed coat RNA-seq replicate 3

source_name: Globular stage Seed coat


title: CE2_3 Octant stage Embryo RNA-seq replicate 3

description: Octant stage Embryo RNA-seq replicate 3


title: RS5_2 Torpedo stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Torpedo stage Seed coat

value: Torpedo


title: RS6_1 Bent stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RS7_1 Mature stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NE4_2 Heart stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Heart stage Embryo

value: Heart


title: CE4_3 Heart stage Embryo RNA-seq replicate 3

description: Heart stage Embryo RNA-seq replicate 3


title: CE6_3 Bent stage Embryo RNA-seq replicate 3

description: Bent stage Embryo RNA-seq replicate 3

source_name: Bent stage Embryo


title: NE4_1 Heart stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CE2_2 Octant stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CE5_3 Torpedo stage Embryo RNA-seq replicate 3

source_name: Torpedo stage Embryo

value: Torpedo stage


title: CE2_1 Octant stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CE1_2 Zygote stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CE1_3 Zygote stage Embryo RNA-seq replicate 3

description: Zygote stage Embryo RNA-seq replicate 3


title: NE3_2 Globular stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Globular


title: RS4_2 Heart stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Seed coat


title: NS1_2 Zygote stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CE1_1 Zygote stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NS1_1 Zygote stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CE3_2 Globular stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CE4_1 Heart stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RS3_2 Globular stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Parkland


title: CE3_1 Globular stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RS5_1 Torpedo stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NUO_2 Unfertilized stage ovule replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: ovule


title: CS7_2 Mature stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Mature


title: CUO_1 Unfertilized stage ovule replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Unfertilized


title: CUO_2 Unfertilized stage ovule replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CS6_2 Bent stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: NE3_1 Globular stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Embryo


title: CE4_2 Heart stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: RS4_1 Heart stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CS6_1 Bent stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CS5_2 Torpedo stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: NS6_1 Bent stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NS6_2 Bent stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: RS2_2 Octant stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Octant


title: RE7_1 Mature stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

source_name: Mature stage Embryo


title: RS2_1 Octant stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NS7_1 Mature stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CS7_1 Mature stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NUO_1 Unfertilized stage ovule replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: RE7_2 Mature stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: NS7_2 Mature stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: RE6_2 Bent stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: R72h3

city: Nanjing

first: Peijie

last: Gong

address: Weigang Nr.1

country: China

institute: Nanjing Agricultural University

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads mapping to the reference genome.
Quantification of gene expression level featureCounts   v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Genome_build: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome
Supplementary_files_format_and_content: tab-delimited excel (xls.) files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Vitis vinifera

source_name: fresh leaf discs

growth_protocol: V. vinifera cv. ‘Zitian Seedless’ and Vitis rootstocks ‘Kober 5BB’ were cultivated in the Grape Repository of Nanjing Agricultural University, Nanjing, Jiangsu, China under the natural environment with normal management.

extract_protocol:
The total RNA was extracted separately by using the Trizol (Invitrogen) method following the steps as described in instructions. The genomic DNA was digested using DNase (TAKARA, Dalian, China).RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA,
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample
RNA-Seq The clustering of the index-coded samples was performed on a cBot Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to  the manufacturer’s instructions. After cluster generation, the library preparations were  sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were  generated

treatment_protocol: The leaves (from 4th to the 7th of shoot) related to each grape genotype were detached and thoroughly rinsed at both sides with distilled water. The freshly excised leaves were used for next infection experiment. Single-sporangia strains of P. viticola were used to assure the high reproducibility of results.

tag: cultivars

value: Vitis rootstocks‘Kober 5BB’

tag: infected timepoint

value: 72 hour

tag: pathogen strain

value: Plasmopara viticola BS-4-MW


title: NS5_2 Torpedo stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: R72h2


title: CS4_2 Heart stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: RS3_1 Globular stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: S72h2

value: V. vinifera cv.‘Zitian Seedless’


title: RE6_1 Bent stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Bent


title: CS5_1 Torpedo stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: S72h3


title: RE5_2 Torpedo stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CS4_1 Heart stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: R72h1


title: NS4_2 Heart stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: S72h1


title: NS5_1 Torpedo stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: CS3_2 Globular stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: R24h3

value: 24 hour


title: R24h2


title: RE5_1 Torpedo stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Torpedo


title: NS3_2 Globular stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CS2_2 Octant stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

source_name: Octant stage Seed coat


title: ATAC-seq Luminal terminal endbuds replicate 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
Libraries were sequenced on an Illumina NextSeq 500 to generate 75bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Bowtie2 version 2.3.4.3.
Peaks were called using MACS2 peaks on the pooled libraries for each of the four tissue/cell population groups. The four peak sets were then merged by merging overlapping peaks. Read counts were summarized by peak in each sample using the Read Count Quantification function in SeqMonk version 1.46.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are tab-delimited text files giving read counts for each peak. The first three columns are the same as the BED file (Chromosome, Start position, End position) and the fourth column gives read counts. The supplementary file PeakCountMatrix.txt contains the matrix of read counts combining all the processed files. Peaks.bed is a BED file specifying the genomic locations of the peaks.

molecule: genomic DNA

organism: Mus musculus

source_name: Mammary gland

extract_protocol:
Transposed genomic DNA was extracted to generate libraries for accessible chromatin analysis.
As described by Buenrostro et al (2015).

tag: mouse strain

value: terminal end buds

tag: cell population

value: luminal epithelium


title: CS1_2 Zygote stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Zygote


title: NS3_1 Globular stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Seed coat

value: Globular


title: CS1_1 Zygote stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: R0h3

value: 0 hour


title: R0h1


title: NS2_2 Octant stage Seed coat replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: R24h1


title: ATAC-seq Luminal ducts replicate 2

value: ducts


title: NE7_1 Mature stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Mature


title: CE7_1 Mature stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Embryo


title: ATAC-seq Luminal terminal endbuds replicate 1


title: S24h2


title: ATAC-seq Basal terminal endbuds replicate 3

value: basal epithelium


title: ATAC-seq Luminal terminal endbuds replicate 2


title: CE7_2 Mature stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: NE7_2 Mature stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: S24h3


title: CS2_1 Octant stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Octant


title: CS3_1 Globular stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: NS2_1 Octant stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: ATAC-seq Basal terminal endbuds replicate 2


title: R0h2

value: Vitis rootstocks‘Kober 5BB’


title: NS4_1 Heart stage Seed coat replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Heart


title: NE6_2 Bent stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: S0h3

value: V. vinifera cv.‘Zitian Seedless’

value: Plasmopara viticola BS-4-MW


title: ATAC-seq Luminal ducts replicate 3


title: NE6_1 Bent stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx

value: Bent


title: NE5_2 Torpedo stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx

value: Torpedo


title: ATAC-seq Basal terminal endbuds replicate 1

value: terminal end buds


title: ATAC-seq Luminal ducts replicate 1

value: luminal epithelium


title: ATAC-seq Basal ducts replicate 3


title: CE6_2 Bent stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: NE5_1 Torpedo stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: ATAC-seq Basal ducts replicate 1


title: S0h2


title: S0h1


title: CE5_2 Torpedo stage Embryo replicate 2

description:
replicate 2
Sample_TPM.xlsx


title: CE5_1 Torpedo stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: S24h1

value: 24 hour


title: CE6_1 Bent stage Embryo replicate 1

description:
replicate 1
Sample_TPM.xlsx


title: L_24h

status: Public on Aug 21 2021

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

institute: CNRRI

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: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: excel files include FPKM values for all Samples.

organism: Oryza sativa

source_name: mesocotyl

extract_protocol:
Total RNA was extracted from mesocotyl tissue using the TRIzol reagent (Invitrogen, Waltham, MA, USA), following the supplier’s protocol. The resulting RNA preparations were quantified and their purity tested using, respectively, a Bioanalyzer 2100 device and an RNA 6000 Nano Lab Chip kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 μg of total RNA was treated with magnetic beads coated with poly-T (Invitrogen) to capture the poly (A) mRNA.
The RNA fragments were reverse-transcribed to create a cDNA library, following the protocol supplied with an Illumina mRNA-Seq sample preparation kit; the average insert size was 300±50bp. Paired-end sequencing was performed by LC-Bio (Hangzhou, China) using an Illumina Hiseq 2500 device

treatment_protocol: The mesocotyls of indica rice cultivar P25 (cv. P25) were sampled from one to five days old seedlings grown in the dark (respectively, D_1d, D_3d, D_5d) and then from five day old dark-grown seedlings exposed to light for 30 min, 60 min or 24 h (L_0.5h, L_1h, L_24h).

tag: growth/treatment

value: 24h after light exposure of seedlings in the dark for 5 days

value: mesocotyl

tag: cultivar


title: L_1h

value: 1h after light exposure of seedlings in the dark for 5 days


title: L_0.5h

value: 0.5h after light exposure of seedlings in the dark for 5 days


title: D_3d

value: 3 day after sowing in the dark


title: D_1d

value: 1 day after sowing in the dark


title: D_5d

value: 5 day after sowing in the dark


title: L_1h_miRNA_3

description: repeat 3

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: excel,expression profiles

growth_protocol: The rice grains were raised at 30°C in the dark for five days on a Murashige and Skoog medium, then exposed to light for 1 h

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA).And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: The mesocotyls of indica rice cultivar P25 (cv. P25) were sampled for five days old seedlings grown in the dark (D_5d) and then from five day old dark-grown seedlings exposed to light for 60 min (L_1h).Three individual repeates for each treatment

tag: treatment

value: light exposure for 1 h


title: H2087_H3K4me3

city: Daegu

first: Hyo-Gyoung

last: Kang

address: Hoguk-ro, Buk-gu

department: Cell and Matrix Research Institute, School of Medicine

country: South Korea

institute: Kyungpook National University

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
The cleaned reads were aligned to the human genome (UCSC hg19) using Bowtie (version 1.1.1 parameter set -n 2 -m 1 -X 500) (Langmead et al., 2009) allowing up to 2 nucleotide mismatches to the reference genome per seed and returning only uniquely mapped reads. Mapped data (SAM file format) were performed sorting and indexing using SAMtools (version 1.2) (Li et al., 2009). Then, duplicate reads were excluded using a MarkDuplicates module in Picard (version 1.118).
Peaks were called in the aligned sequence data using a model-based analysis of ChIP-seq (MACS version 2.1.0) (Zhang et al., 2008). The following parameters were used: macs2 callpeak -t ChIP.bam -c Control.bam -g hs -q 0.01 --call-summits --keep-dup 1.
ChIPseeker (version 1.6.6) (Yu et al., 2015), a bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq data, was used to identify nearby genes and transcripts from the peaks obtained from MACS.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: bed, bigwig

organism: Homo sapiens

source_name: H2087 cells

growth_protocol: H2087 cells were cultured at 37˚C in a humidified atmosphere with 5% CO2 in Corning® RPMI medium (Corning Inc., Corning, NY, USA) supplemented with 10% Corning® Fetal Bovine Serum (Corning Inc., Corning, NY, USA), and 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIPSeq library preparation was performed with TruSeq® ChIP Library Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed on an Illumina HiSeq4000.

treatment_protocol: Untreated

tag: cell line

tag: cell type

value: Lung adenocarcinoma

value: Untreated

tag: chip antibody

value: H3K4me3 (abcam, ab8580)


title: H2087

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh37 whole genome by using HISAT2 version 2.0.5 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

growth_protocol: H2087 and H596 cells were cultured at 37˚C in a humidified atmosphere with 5% CO2 in Corning® RPMI medium (Corning Inc., Corning, NY, USA) supplemented with 10% Corning® Fetal Bovine Serum (Corning Inc., Corning, NY, USA), and 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Total RNAs from cells were isolated using TRIzol® (Invitrogen, Carlsbad, CA, USA). TruSeq Stranded mRNA LT Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide(Part #15031047 Rev. E) protocols.


title: D_5d_degradome

data_processing:
Library strategy: Degradome-Seq
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2，3，or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: excel,expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the  manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer  2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0.
The libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: The mesocotyls of indica rice cultivar P25 (cv. P25) were sampled for five days old seedlings grown in the dark (D_5d) and then from five day old dark-grown seedlings exposed to light for 60 min (L_1h).


title: L_1h_miRNA_1

description: repeat 1


title: H596

source_name: H596 cells


title: D_5d_miRNA_2

description: repeat 2


title: D_5d_miRNA_3

description: repeat 3


title: L_1h_degradome


title: H2087_H3K27ac

value: H3K27ac (abcam, ab4729)


title: H2087_Input


title: ME8347_ACAGTG_L6

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

country: USA

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count and Differentially expressed gene list

source_name: ileum

growth_protocol: Human intestinal organoids were cultured in CMGF medium supplemented with 50 ng/ml epidermal growth factor (EGF) (Invitrogen), 10 nM gastrin I, 500 nM A-83-01, 1× B27 supplement, 1× N2 supplement, and 1 mM N-acetylcysteine.

extract_protocol:
Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer’s protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina’s Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity.
Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample.

treatment_protocol: 5 days treatment with media

tag: donor

value: Donor 2

value: mock

tag: timepoint


title: ME8347_ACAGTG_L7


title: ME8347_ACAGTG_L8


title: ME8345_TTAGGC_L8

value: Donor 1


title: ME8347_ACAGTG_L5


title: Untreated

type: RNA

city: Izumo

first: Yoshio

last: Honma

address: 89-1 Enya

department: Biochemistry

country: Japan

institute: Shimane University

description: Gene expression data from untreated Panc1 cells.

hyb_protocol: cRNA was hybridized for 16 hours at 45oC on GeneChip Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization.

label: biotin

source_name: Pancreatic cancer

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit from 100 ng total RNA.

growth_protocol: Panc1 cells were cultured in RPMI1640 medium with 10% fetal bovine serum at 37oC.

extract_protocol: Total RNA was extracted using TRI reagent.

treatment_protocol: Panc1 cells were treated with romidepsin and/or tamoxifen for 24 hours.

value: Pancreatic cancer cells


title: Tam

description: Gene expression data from Panc1 cells treated with tamoxifen.

value: Tamoxifen


title: ME8345_TTAGGC_L7


title: ME8345_TTAGGC_L6


title: D_5d_miRNA_1

description: repeat 1

tag: tissue


title: Rom

description: Gene expression data from Panc1 cells treated with romidepsin.

value: Romidepsin


title: ME8341_CGTACG_L5


title: ME8345_TTAGGC_L5


title: ME8341_CGTACG_L8


title: Combo

description: Gene expression data from Panc1 cells treated with romidepsin plus tamoxifen.

value: Romidepsin plus tamoxifen


title: ME8337_GTCCGC_L4


title: L_1h_miRNA_2

description: repeat 2

value: mesocotyl


title: ME8337_GTCCGC_L3


title: ME8341_CGTACG_L7


title: ME8341_CGTACG_L6


title: ME8337_GTCCGC_L2


title: ME8337_GTCCGC_L1


title: 0.5hr_rep3

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Tophat (2.1.0) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: mm10

source_name: mouse back skin

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: UV irradiation

tag: genotype

value: wild type


title: 12hr_rep1


title: 0.5hr_rep2


title: 2hr_rep2


title: 24hr_rep1


title: 2hr_rep3


title: 6hr_rep3


title: 24hr_rep2


title: 6hr_rep1


title: 12hr_rep2


title: 2hr_rep1


title: T0_rep1

value: no treatment


title: Single cell WGA product (B3) from the embryo E31 in the pedigree Cross17 [E31_B3_Cross17]

type: genomic

city: Leuven

first: Joris

middle: R.

last: Vermeesch

address: Herestraat 49 box 606

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description: Single cell WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

hyb_protocol: According to the manufacturer's protocol of Infinium HD Assay for BovineHD BeadChip arrays.

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA) according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA)

data_processing:
Samples were genotyped using the BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA. The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75. We subsequently analysed these data with haplarithmisis adapted for bovine (Zamani Esteki et al. 2015, AJHG).
[value definition] Genotypes: AA,AB,BB or NC (No Call); BAF: B-allele frequency; logR: log2ratio

organism: Bos taurus

source_name: single cell

label_protocol: 200 ng of gDNA and 600 ng of whole-genome amplified DNA was used as input for processing the samples according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA).

growth_protocol: Embryos were in vitro produced according to previously described methods (Catteeuw et al., 2017). Cleavage-kinetics of the first division were monitored from 21 h post fertilization onwards by cultivation of embryos in a time-lapse monitoring system.

extract_protocol: Extraction of gDNA from sperm, blood and ovarian tissue was performed using the Qiagen DNeasy Blood and Tissue kit according to the manufacturer's protocol (sperm: user-developed protocol for purification of total DNA from animal sperm using the DNeasy® Blood & Tissue Kit; protocol 2). Single blastomere and whole-embryo DNA was whole-genome amplified using the REPLI-g SC kit (Qiagen) according to the manufacturer's instructions with full or half reaction volumes and a 3 h incubation reaction.

treatment_protocol: Single blastomeres or cells derived from bovine embryos identified to have undergone a multipolar zygotic division by time-lapse imaging were dissociated immediately following  the first division (E01_Cross01 to E25_Cross12) or at the blastocyst stage (E26_Cross13 to E30_Cross17) and whole-genome amplified. Briefly, the zona pellucida was removed by pronase treatment and single blastomeres were dissociated mehcanically and picked individually. For dissociation at the blastocyst stage, pronase treatment and a subsequent combination of trypisinsation and mechanical dissociation was used to pick single cells.

value: Embryonic

tag: molecule subtype

value: Whole-genome amplified DNA


title: Single cell WGA product (B4) from the embryo E31 in the pedigree Cross17 [E31_B4_Cross17]


title: Single cell WGA product (B1) from the embryo E31 in the pedigree Cross17 [E31_B1_Cross17]


title: Single cell WGA product (B7) from the embryo E31 in the pedigree Cross17 [E31_B7_Cross17]


title: Single cell WGA product (B5) from the embryo E31 in the pedigree Cross17 [E31_B5_Cross17]


title: Single cell WGA product (B2) from the embryo E31 in the pedigree Cross17 [E31_B2_Cross17]


title: Sibling embryo WGA product in the pedigree Cross17 [Sibling_Cross17]

description: WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: embryo


title: Single cell WGA product (B9) from the embryo E31 in the pedigree Cross17 [E31_B9_Cross17]


title: Cow gDNA for pedigrees of Cross16 [Cow_Cross16]

description: Genomic DNA extracted from cow ovarian tissue was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: cow ovarian tissue

value: Ovarian


title: Single cell WGA product (B11) from the embryo E31 in the pedigree Cross17 [E31_B11_Cross17]


title: Single cell WGA product (B10) from the embryo E31 in the pedigree Cross17 [E31_B10_Cross17]


title: Cow gDNA for pedigrees of Cross17 [Cow_Cross17]


title: Sibling embryo WGA product in the pedigree Cross16 [Sibling_Cross16]


title: T0_rep2


title: Single cell WGA product (B8) from the embryo E31 in the pedigree Cross17 [E31_B8_Cross17]


title: Single cell WGA product (B6) from the embryo E31 in the pedigree Cross17 [E31_B6_Cross17]


title: Single cell WGA product (B8) from the embryo E30 in the pedigree Cross16 [E30_B8_Cross16]


title: Single cell WGA product (B6) from the embryo E30 in the pedigree Cross16 [E30_B6_Cross16]


title: Single cell WGA product (B3) from the embryo E30 in the pedigree Cross16 [E30_B3_Cross16]


title: Single cell WGA product (B8) from the embryo E29 in the pedigree Cross15 [E29_B8_Cross15]


title: Single cell WGA product (B7) from the embryo E30 in the pedigree Cross16 [E30_B7_Cross16]


title: Single cell WGA product (B7) from the embryo E29 in the pedigree Cross15 [E29_B7_Cross15]


title: Cow gDNA for pedigrees of Cross15 [Cow_Cross15]


title: Single cell WGA product (B5) from the embryo E30 in the pedigree Cross16 [E30_B5_Cross16]


title: Single cell WGA product (B11) from the embryo E29 in the pedigree Cross15 [E29_B11_Cross15]


title: Single cell WGA product (B9) from the embryo E28 in the pedigree Cross15 [E28_B9_Cross15]


title: Single cell WGA product (B1) from the embryo E29 in the pedigree Cross15 [E29_B1_Cross15]


title: Single cell WGA product (B3) from the embryo E29 in the pedigree Cross15 [E29_B3_Cross15]


title: Single cell WGA product (B4) from the embryo E30 in the pedigree Cross16 [E30_B4_Cross16]


title: Sibling embryo WGA product in the pedigree Cross15 [Sibling_Cross15]


title: Single cell WGA product (B5) from the embryo E28 in the pedigree Cross15 [E28_B5_Cross15]


title: Single cell WGA product (B9) from the embryo E29 in the pedigree Cross15 [E29_B9_Cross15]


title: Single cell WGA product (B7) from the embryo E28 in the pedigree Cross15 [E28_B7_Cross15]


title: Single cell WGA product (B10) from the embryo E29 in the pedigree Cross15 [E29_B10_Cross15]


title: Single cell WGA product (B6) from the embryo E29 in the pedigree Cross15 [E29_B6_Cross15]


title: Single cell WGA product (B6) from the embryo E28 in the pedigree Cross15 [E28_B6_Cross15]


title: Single cell WGA product (B1) from the embryo E30 in the pedigree Cross16 [E30_B1_Cross16]


title: 6hr_rep2


title: Single cell WGA product (B4) from the embryo E28 in the pedigree Cross15 [E28_B4_Cross15]


title: Single cell WGA product (B2) from the embryo E29 in the pedigree Cross15 [E29_B2_Cross15]


title: Single cell WGA product (B8) from the embryo E28 in the pedigree Cross15 [E28_B8_Cross15]


title: Single cell WGA product (B2) from the embryo E28 in the pedigree Cross15 [E28_B2_Cross15]


title: Single cell WGA product (B3) from the embryo E28 in the pedigree Cross15 [E28_B3_Cross15]


title: Single cell WGA product (B2) from the embryo E30 in the pedigree Cross16 [E30_B2_Cross16]


title: Single cell WGA product (B4) from the embryo E29 in the pedigree Cross15 [E29_B4_Cross15]


title: Cow gDNA for pedigrees of Cross14 [Cow_Cross14]


title: Single cell WGA product (B11) from the embryo E27 in the pedigree Cross14 [E27_B11_Cross14]


title: Single cell WGA product (B5) from the embryo E27 in the pedigree Cross14 [E27_B5_Cross14]


title: Single cell WGA product (B9) from the embryo E27 in the pedigree Cross14 [E27_B9_Cross14]


title: Single cell WGA product (B10) from the embryo E27 in the pedigree Cross14 [E27_B10_Cross14]


title: Single cell WGA product (B7) from the embryo E27 in the pedigree Cross14 [E27_B7_Cross14]


title: Single cell WGA product (B12) from the embryo E27 in the pedigree Cross14 [E27_B12_Cross14]


title: Sibling embryo WGA product in the pedigree Cross14 [Sibling_Cross14]


title: Single cell WGA product (B8) from the embryo E27 in the pedigree Cross14 [E27_B8_Cross14]


title: Single cell WGA product (B10) from the embryo E26 in the pedigree Cross13 [E26_B10_Cross13]


title: Single cell WGA product (B5) from the embryo E29 in the pedigree Cross15 [E29_B5_Cross15]


title: Single cell WGA product (B1) from the embryo E27 in the pedigree Cross14 [E27_B1_Cross14]


title: Single cell WGA product (B5) from the embryo E26 in the pedigree Cross13 [E26_B5_Cross13]


title: Single cell WGA product (B1) from the embryo E28 in the pedigree Cross15 [E28_B1_Cross15]


title: Single cell WGA product (B4) from the embryo E27 in the pedigree Cross14 [E27_B4_Cross14]


title: Single cell WGA product (B4) from the embryo E26 in the pedigree Cross13 [E26_B4_Cross13]


title: Single cell WGA product (B9) from the embryo E26 in the pedigree Cross13 [E26_B9_Cross13]


title: Single cell WGA product (B11) from the embryo E26 in the pedigree Cross13 [E26_B11_Cross13]


title: Sibling embryo WGA product in the pedigree Cross13 [Sibling_Cross13]


title: Single cell WGA product (B7) from the embryo E26 in the pedigree Cross13 [E26_B7_Cross13]


title: Single cell WGA product (B6) from the embryo E26 in the pedigree Cross13 [E26_B6_Cross13]


title: Cow gDNA for pedigrees of  Cross13 [Cow_Cross13]


title: Single cell WGA product (B6) from the embryo E27 in the pedigree Cross14 [E27_B6_Cross14]


title: Single cell WGA product (B2) from the embryo E27 in the pedigree Cross14 [E27_B2_Cross14]


title: Single cell WGA product (B3) from the embryo E26 in the pedigree Cross13 [E26_B3_Cross13]


title: Single cell WGA product (B2) from the embryo E26 in the pedigree Cross13 [E26_B2_Cross13]


title: Cow gDNA for pedigrees of  Cross12 [Cow_Cross12]


title: Single blastomere WGA product (B4) from the embryo E25 in the pedigree Cross12 [E25_B4_Cross12]

description: Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: blastomere


title: Single cell WGA product (B1) from the embryo E26 in the pedigree Cross13 [E26_B1_Cross13]


title: Single cell WGA product (B3) from the embryo E27 in the pedigree Cross14 [E27_B3_Cross14]


title: Single blastomere WGA product (B3) from the embryo E25 in the pedigree Cross12 [E25_B3_Cross12]


title: Single cell WGA product (B8) from the embryo E26 in the pedigree Cross13 [E26_B8_Cross13]


title: Single blastomere WGA product (B1) from the embryo E24 in the pedigree Cross12 [E24_B1_Cross12]


title: Cow gDNA for pedigrees of  Cross11 [Cow_Cross11]


title: Single blastomere WGA product (B1) from the embryo E25 in the pedigree Cross12 [E25_B1_Cross12]


title: Sibling embryo WGA product in the pedigree Cross09 [Sibling_Cross09]


title: Single blastomere WGA product (B2) from the embryo E23 in the pedigree Cross11 [E23_B2_Cross11]


title: Sibling embryo WGA product in the pedigree Cross11 [Sibling_Cross11]


title: Cow gDNA for pedigrees of  Cross09 [Cow_Cross09]


title: Sibling embryo WGA product in the pedigree Cross10 [Sibling_Cross10]


title: Single blastomere WGA product (B3) from the embryo E23 in the pedigree Cross11 [E23_B3_Cross11]


title: Single blastomere WGA product (B1) from the embryo E22 in the pedigree Cross10 [E22_B1_Cross10]


title: Single blastomere WGA product (B2) from the embryo E20 in the pedigree Cross08 [E20_B2_Cross08]


title: Single blastomere WGA product (B2) from the embryo E21 in the pedigree Cross09 [E21_B2_Cross09]


title: Single blastomere WGA product (B1) from the embryo E21 in the pedigree Cross09 [E21_B1_Cross09]


title: Single blastomere WGA product (B3) from the embryo E22 in the pedigree Cross10 [E22_B3_Cross10]


title: Cow gDNA for pedigrees of  Cross10 [Cow_Cross10]


title: Single blastomere WGA product (B3) from the embryo E24 in the pedigree Cross12 [E24_B3_Cross12]


title: Single blastomere WGA product (B4) from the embryo E21 in the pedigree Cross09 [E21_B4_Cross09]


title: Single blastomere WGA product (B2) from the embryo E22 in the pedigree Cross10 [E22_B2_Cross10]


title: Single blastomere WGA product (B3) from the embryo E21 in the pedigree Cross09 [E21_B3_Cross09]


title: Single blastomere WGA product (B3) from the embryo E20 in the pedigree Cross08 [E20_B3_Cross08]


title: Sibling embryo WGA product in the pedigree Cross08 [Sibling_Cross08]


title: Single blastomere WGA product (B1) from the embryo E23 in the pedigree Cross11 [E23_B1_Cross11]


title: Single blastomere WGA product (B2) from the embryo E19 in the pedigree Cross08 [E19_B2_Cross08]


title: Single blastomere WGA product (B2) from the embryo E25 in the pedigree Cross12 [E25_B2_Cross12]


title: Single blastomere WGA product (B3) from the embryo E18 in the pedigree Cross08 [E18_B3_Cross08]


title: Single blastomere WGA product (B2) from the embryo E24 in the pedigree Cross12 [E24_B2_Cross12]


title: Single blastomere WGA product (B3) from the embryo E19 in the pedigree Cross08 [E19_B3_Cross08]


title: Single blastomere WGA product (B1) from the embryo E19 in the pedigree Cross08 [E19_B1_Cross08]


title: Single blastomere WGA product (B2) from the embryo E18 in the pedigree Cross08 [E18_B2_Cross08]


title: Single blastomere WGA product (B1) from the embryo E18 in the pedigree Cross08 [E18_B1_Cross08]


title: Single blastomere WGA product (B2) from the embryo E20 in the pedigree Cross08 [E20_B1_Cross08]


title: Cow gDNA for pedigrees of  Cross08 [Cow_Cross08]


title: Cow gDNA for pedigrees of  Cross07 [Cow_Cross07]


title: Single fragment WGA product (F1) from the embryo E17 in the pedigree Cross07 [E17_F1_Cross07]

description: Single fragment WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: fragment


title: Single blastomere WGA product (B2) from the embryo E17 in the pedigree Cross07 [E17_B2_Cross07]


title: Single blastomere WGA product (B3) from the embryo E17 in the pedigree Cross07 [E17_B3_Cross07]


title: Single blastomere WGA product (B3) from the embryo E16 in the pedigree Cross07 [E16_B3_Cross07]


title: Single blastomere WGA product (B4) from the embryo E16 in the pedigree Cross07 [E16_B4_Cross07]


title: Single blastomere WGA product (B1) from the embryo E17 in the pedigree Cross07 [E17_B1_Cross07]


title: Single blastomere WGA product (B2) from the embryo E16 in the pedigree Cross07 [E16_B2_Cross07]


title: Sibling embryo WGA product in the pedigree Cross07 [Sibling_Cross07]


title: Treg_Spleen_rep3 (SN_WT_SP5-8)

city: Brisbane

first: Dylan

middle: Patrick

last: Carter-Cusack

state: Queensland

address: 300 Herston Rd

department: Department of Immunology

institute: QIMR Berghofer Medical Research Institute

description:
Batch3
SP_vs_BM.genes.ExpectedCounts.csv
SP_vs_BM.genes.FPKM.csv
SP_vs_BM.isoforms.ExpectedCounts.csv
SP_vs_BM.isoforms.FPKM.csv

data_processing:
base calling performed with Illumina basecaller
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.9) and aligned using STAR (version 2.5.2a) to the Mus musculus GRCm38 assembly with the gene, transcript, and exon features of Ensembl (release 70) gene model. Quality control metrics were computed using RNA-SeQC (version 1.1.8)
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited tsv files include raw counts for each sample

source_name: Spleen

extract_protocol:
RNA was extracted with Qiagen’s RNeasy micro kit from >100,000 FACS isolated cells as per instructions. For generation of sequencing libraries, 15ng of RNA (RIN value >7) were submitted to SPIA amplification (NuGen).
Nugen Ovation RNA-Seq system V2 (for SPIA amplifications and cDNA generation) using Nugen protocol M01206v5, 2013; followed by Ovation Ultralow System V2 (for rest of library preparation) using Nugen protocol M01379v1, 2014.

value: Spleen

tag: gender

value: male


title: Treg_BM_rep2 (WT BM8)

description:
Batch1
SP_vs_BM.genes.ExpectedCounts.csv
SP_vs_BM.genes.FPKM.csv
SP_vs_BM.isoforms.ExpectedCounts.csv
SP_vs_BM.isoforms.FPKM.csv

source_name: Bone marrow

value: Bone marrow

value: female


title: Treg_BM_rep4 (SN_WT_BM12)


title: Treg_BM_rep3 (WT BM9)


title: Single blastomere WGA product (B1) from the embryo E15 in the pedigree Cross07 [E15_B3_Cross07]


title: Treg_Spleen_rep4 (SN_WT_SP6-9)


title: Treg_Spleen_rep2 (SN_WT_SP3-6)


title: Single blastomere WGA product (B1) from the embryo E16 in the pedigree Cross07 [E16_B1_Cross07]


title: Treg_BM_rep1 (WT BM5)


title: Single blastomere WGA product (B4) from the embryo E14 in the pedigree Cross07 [E14_B4_Cross07]


title: Single blastomere WGA product (B1) from the embryo E15 in the pedigree Cross07 [E15_B1_Cross07]


title: Single blastomere WGA product (B3) from the embryo E14 in the pedigree Cross07 [E14_B3_Cross07]


title: Treg_Spleen_rep1 (SN_WT_SP1-4)


title: Single blastomere WGA product (B2) from the embryo E14 in the pedigree Cross07 [E14_B2_Cross07]


title: Single blastomere WGA product (B1) from the embryo E14 in the pedigree Cross07 [E14_B1_Cross07]


title: Single blastomere WGA product (B1) from the embryo E15 in the pedigree Cross07 [E15_B2_Cross07]


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-4_Tim01

city: MILL VALLEY

first: Brian

middle: A

last: Hodge

state: CA

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

hyb_protocol: Samples were hybridized to the 12-plex Gene Expression array platform according to the manufacturers' protocol. NimbleGen's Sample Tracking Controls (05223512001), Hybridization Kit reagents (05583683001) and Wash Buffers (05584507001) were used. Each 12-plex array was sealed with a H12 mixer, provided with the Gene Expression array. 4µg of each Cy3 labeled sample was loaded onto an array on the 12-plex chip, using a Gilson M100 pipette. Hybridization was completed overnight on a NimbleGen Hybridization System 4 unit, at 42℃ for 16hrs.

scan_protocol: After the 12-plex chip was washed and dried, the chip was scanned on a GenePix 4200A scanner at 300PMT, 100POW. Arrays were then quantitated using NimbleGen's NimbleScan2 software.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003); The *Cycle data provides the processed data that has been analyzed with the JTK_CYCLE algorithm.

organism: Drosophila melanogaster

source_name: 35 female Tim01 mutant flies reared on DR-diet for seven days

label_protocol: For each experimental sample, approximately 150ng of total RNA was amplified with Sigma's TransPlex Complete Whole Transcriptome Amplification Kit (WTA2). Qiagen's QIAquick PCR Purification Kit (28104) was used to purify the amplified samples. Following purification, the samples were further processed on the QIAcube according to the manufacturers' protocol: QIAquick PCR Purification-Standard. For each biological sample the NimbleGen (Roche) One-Color DNA Labeling kit (05223555011) was used to label dscDNA with Cy3 according to the manufacturers' protocol.

extract_protocol: Total RNA was extracted from whole fly lystates of approximately 35 flies (4 biological replicates per diet and time-point) with Qiagen's Rneasy Lipid Tissue Mini Kit (74804). Samples were then lysed in Qiagen's Qiazol lysis buffer with Qiagen's TissueLyser (pulverized for approximately nine minutes). Qiagen's QIAcube robot was used to futher proccess the samples utilizing a modified version of Qiagen's QIAcube protocol: RNeasy Lipid Tissue Mini-Animal Tissues-Aqueous Phase.

treatment_protocol: Four-day old mated female flies (Canton-S and Tim01) were sorted on either Ad libitum (5.0% yeast-extract) or Dietary Restriction (0.5% yeast-extract) and reared in a 12:12hr light-dark cycle for seven days. On the seventh day flies were collected every four hours for 20 hours (6 timepoints) starting at ZT 0 (lights on).

tag: strain

tag: time of collection

tag: diet

value: Dietary restriction (0.5% yeast-extract)


title: Single blastomere WGA product (B1) from the embryo E13 in the pedigree Cross06 [E13_B1_Cross06]


title: Single blastomere WGA product (B2) from the embryo E13 in the pedigree Cross06 [E13_B2_Cross06]


title: Single blastomere WGA product (B3) from the embryo E13 in the pedigree Cross06 [E13_B3_Cross06]


title: Sibling embryo WGA product in the pedigree Cross05 [Sibling_Cross05]


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-3_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: Cow gDNA for pedigrees of  Cross06 [Cow_Cross06]


title: Cow gDNA for pedigrees of  Cross05 [Cow_Cross05]


title: Single blastomere WGA product (B3) from the embryo E12 in the pedigree Cross05 [E12_B3_Cross05]


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-2_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Single blastomere WGA product (B2) from the embryo E12 in the pedigree Cross05 [E12_B2_Cross05]


title: mst12_gfp_rep2_input

city: Norwich

first: Jitender

last: Cheema

address: Colney lane

country: United Kingdom

institute: JIC

data_processing:
Reads were mapped cleaned and aligned to M. oryzae genome v.8 using BWA aligner v. 0.5.7.
Peaks were identified by MACS2 version 2.1.1 66 with the following parameters: -g 41027733 -q 0.1 --bdg ---nomodel --extsize 180 --broad --broad-cutoff 0.1.
Sequences under the peaks were predicted ± 2kb flanks and analysed using Python
Genome_build: M. oryzae genome MG8 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002495.2)
Supplementary_files_format_and_content: peak files

organism: Pyricularia oryzae

source_name: liquid mycelium

growth_protocol: ChIP seq carried out from mycelium cultures grown in CM for 48h. Mycelium cultures of Dhox7:hox73Xflag and Dmst12:Mst12-GFP. ChIP samples are after Chromatin Immunoprecipitation experiments. Input samples are Chromatin samples before IP.

extract_protocol:
Cross-linked mycelium samples were gound into fine powder and resuspended in Honda buffer
Libraries were prepared according to Illumina's instructions by BGI (Hong Kong)

treatment_protocol: Two grams of mycelia were cross-linked with 1% formaldehyde for 15 min and followed by 5 mins of incubation with 125 mM glycine.

value: mycelium

tag: background strain


title: mst12_gfp_rep2_IP

value: GFP-Trap® Agarose;monoclonal anti-Green Fluorescent Protein (GFP) single domain antibody (sdAb); Cat#gta-100; Chromotek


title: mst12_gfp_rep1_IP


title: Single blastomere WGA product (B1) from the embryo E12 in the pedigree Cross05 [E12_B1_Cross05]


title: Sibling embryo WGA product in the pedigree Cross06 [Sibling_Cross06]


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-1_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-1_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-2_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-3_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: Raw RA data for A15619 strain

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: cDNA labelling for A15619 strain

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a GE Typhoon FLA7000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted were normalized by the median of the euploid strains. The normalized value for each gene was corrected by percentage of guanines (RA data) or uracils (SR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: A15619 haploid strain disomic for chromosomes I, VI & XIII

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC for at least 15 hours to reach early exponential phase at 0.4-0.5 OD600. Then cells were spun-down and were collected and frozen in liquid nitrogen

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: W303 genetic background


title: Raw RA data for A12691 strain

description: cDNA labelling for A12691 strain

source_name: A12691 haploid strain disomic for chromosomes XI & XV


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-3_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.

value: ZT 12 (8:00pm, lights off)


title: Raw RA data for A13979 strain

description: cDNA labelling for A13979 strain

source_name: A13979 haploid strain disomic for chromosome XIV


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-4_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-4_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-2_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Raw RA data for A12687 strain

description: cDNA labelling for A12687 strain

source_name: A12687 haploid strain disomic for chromosome IV


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-1_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-4_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: Single blastomere WGA product (B4) from the embryo E11 in the pedigree Cross05 [E11_B4_Cross05]

description: Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).


title: Single blastomere WGA product (B3) from the embryo E11 in the pedigree Cross05 [E11_B3_Cross05]


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-3_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: Hox7_flag_rep3_IP

value: Anti-Flag® M2 Affinity Gel; M2, monoclonal; Cat#:A2220-1ML; Sigma


title: Single blastomere WGA product (B1) from the embryo E11 in the pedigree Cross05 [E11_B1_Cross05]

description: Single fragment WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).


title: Hox7_flag_rep3_input


title: Single blastomere WGA product (B4) from the embryo E10 in the pedigree Cross05 [E10_B4_Cross05]


title: mst12_gfp_rep1_input


title: Hox7_flag_rep2_input


title: Single blastomere WGA product (B3) from the embryo E10 in the pedigree Cross05 [E10_B3_Cross05]


title: Single blastomere WGA product (B2) from the embryo E11 in the pedigree Cross05 [E11_B2_Cross05]


title: Raw RA data for A2587 strain

description: cDNA labelling for A2587 strain

source_name: A2587 haploid strain


title: Raw RA data for A702 strain

description: cDNA labelling for A702 strain

source_name: A702 diploid strain


title: Hox7_flag_rep1_IP


title: Single blastomere WGA product (B2) from the embryo E10 in the pedigree Cross05 [E10_B2_Cross05]


title: Raw RA data for A18349 strain

description: cDNA labelling for A18349 strain

source_name: A18349 diploid strain trisomic for chromosome XIV


title: Raw RA data for A18345 strain

description: cDNA labelling for A18345 strain

source_name: A18345 diploid strain trisomic for chromosome I


title: Hox7_flag_rep1_input


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-2_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-1_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-2_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-4_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-3_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: Raw RA data for A18347 strain

description: cDNA labelling for A18346 strain

source_name: A18347 diploid strain trisomic for chromosome VIII


title: Raw RA data for A18346 strain

description: cDNA labelling for A18347 strain

source_name: A18346 diploid strain trisomic for chromosome V


title: Raw RA data for A13628 strain

description: cDNA labelling for A13628 strain

source_name: A13628 haploid strain disomic for chromosome VIII


title: Cow gDNA for pedigrees of  Cross04 [Cow_Cross04]

description: Genomic DNA extracted from cow ovarian tissue was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: cow ovarian tissue


title: Sibling embryo WGA product in the pedigree Cross04 [Sibling_Cross04]

description: WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: embryo


title: RNAseq  Brg1flox/flox rep2

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
Mars-seq: Reads were trimmed using Cutadapt
Mars-seq: Reads were aligned to the genome using STAR
Mars-seq: Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
ATAC-seq: Reads were aligned to the genome using Bowtie2
ATAC-seq: Normalized read coverage files were computed by deepTools
ATAC-seq: Peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with Deseq2 output, bigWig read coverage

molecule: polyA RNA

source_name: Spleen

growth_protocol: Splenic B cells were isolated using magnetic separation (CD43/Ly-48 Microbeads, Miltenyi Biotec) and cultivated in a density of 1 million/mL in RPMI-1640 medium including 25mM HEPES, supplemented with 10% fetal calf serum, L-glutamine, pyruvate, non-essential amino acids, β-mercapto-ethanol

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

treatment_protocol: B cells taken into culture were immediately treated with with 10 µg/mL LPS and 20 ng/mL IL-4 for 72 hours, up until lysates were generated for RNA extraction and library preparation

value: B cells

tag: mouse strain

value: Brg1fl/fl CD23Cre +/-


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-4_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

value: ZT 0 (8:00am, lights on)


title: RNAseq  Brg1flox/flox rep3


title: Raw SR data for A12691 strain

description: GRO labelling for A12691 strain


title: Hox7_flag_rep2_IP


title: Raw RA data for A6863 strain

description: cDNA labelling for A6863 strain

source_name: A6863 haploid strain disomic for chromosome I


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-1_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.

source_name: 35 female Tim01 mutant flies reared on DR-diet for seven days


title: RNAseq  Brg1flox/flox rep1


title: Single blastomere WGA product (B1) from the embryo E10 in the pedigree Cross05 [E10_B1_Cross05]

source_name: blastomere


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-3_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: RNAseq  Brg1 flox/plus rep2

value: Brg1fl/+ CD23Cre +/-


title: RNAseq  Brg1 flox/plus rep1


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-2_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Raw SR data for A12687 strain

description: GRO labelling for A12687 strain


title: Single blastomere WGA product (B1) from the embryo E09 in the pedigree Cross04 [E09_B1_Cross04]

value: Embryonic


title: Single blastomere WGA product (B2) from the embryo E09 in the pedigree Cross04 [E09_B2_Cross04]

value: Whole-genome amplified DNA


title: RNAseq  Littermate rep3

value: Brg1fl/+ CD23-WT


title: Raw SR data for A15619 strain

description: GRO labelling for A15619 strain

source_name: A15619 haploid strain disomic for chromosomes I, VI & XIII


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-4_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

source_name: 35 female Tim01 mutant flies reared on AL-diet for seven days

value: Ad libitum (5% yeast-extract)


title: Raw SR data for A13979 strain

description: GRO labelling for A13979 strain

source_name: A13979 haploid strain disomic for chromosome XIV


title: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-1_Tim01

description:
processed data file: Tim01_DR_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: Single blastomere WGA product (B3) from the embryo E09 in the pedigree Cross04 [E09_B3_Cross04]


title: Raw SR data for A2587 strain

description: GRO labelling for A2587 strain


title: Single blastomere WGA product (B1) from the embryo E08 in the pedigree Cross04 [E08_B1_Cross04]


title: Single blastomere WGA product (B3) from the embryo E07 in the pedigree Cross04 [E07_B3_Cross04]


title: Hom_KO

city: South Bend

first: Qingfei

last: Wang

state: IN

address: 1234 N Notre Dame Ave, Harper Hall A121

department: Harper Cancer Research Institute

institute: University of Notre Dame

data_processing:
Library strategy: Drop-seq
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene…

source_name: brain metastasis-associated myeloid cells

extract_protocol:
Mice were perfused with PBS and brains extracted. Brains digested with papain-based neural tissue dissocation kit (Miltenyi). Mononuclear cells enriched by 70%/37%/30% percoll gradient centrifugation. Mononuclear cells enriched by MACS-based Cd11b enrichment (Miltenyi).
RNA libraries were prepared for sequencing using standard Illumina protocols for Nextera XT DNA sample prep kit

tag: sequencer

value: NextSeq 500

tag: 1 brain or pooled

value: 2 brains pooled

tag: genotype/variation

value: metastases


title: Raw SR data for A702 strain

description: GRO labelling for A702 strain


title: RNAseq  Littermate rep2


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-3_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-1_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: Single blastomere WGA product (B2) from the embryo E07 in the pedigree Cross04 [E07_B2_Cross04]

description: Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-2_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Met Rep 2

value: 1 brain


title: RNAseq Littermate rep1


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-4_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: WT Rep 2

source_name: naïve brain myeloid cells

value: wild type


title: Het


title: Single blastomere WGA product (B4) from the embryo E06 in the pedigree Cross04 [E06_B3_Cross04]


title: Single blastomere WGA product (B3) from the embryo E08 in the pedigree Cross04 [E08_B3_Cross04]


title: Raw SR data for A18349 strain

description: GRO labelling for A18349 strain


title: Raw SR data for A18347 strain

description: GRO labelling for A18346 strain


title: Single blastomere WGA product (B2) from the embryo E08 in the pedigree Cross04 [E08_B2_Cross04]


title: Raw SR data for A18345 strain

description: GRO labelling for A18345 strain


title: Raw SR data for A6863 strain

description: GRO labelling for A6863 strain


title: Single blastomere WGA product (B1) from the embryo E07 in the pedigree Cross04 [E07_B1_Cross04]


title: Raw SR data for A13628 strain

description: GRO labelling for A13628 strain


title: Raw SR data for A18346 strain

description: GRO labelling for A18347 strain


title: Pm64_2

city: ChangChun

first: JiaQi

last: Zhang

address: XinCheng Street

institute: Jilin Agricultural University

data_processing:
Illumina Casava 1.8 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
Reads Per Kilobase of exon per Megabase of library size calculated using a protocol from Chepelev et al.,virulence Research,2020.In short,exons from all isoforms.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: nasal cavity

extract_protocol:
Nasal mucus were removed ,flash frozen on dry ice, and RNA was harvested using Trizol. Illumina TruSeq RNA Sample Prep kit(Cat#FC-122-1001) was used with 1 ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: Pasteurella multocida

value: nasal cavity


title: Pm64_3


title: Single blastomere WGA product (B2) from the embryo E06 in the pedigree Cross04 [E06_B1_Cross04]


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-2_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Single blastomere WGA product (B3) from the embryo E06 in the pedigree Cross04 [E06_B2_Cross04]


title: Pm64_1


title: RPE-J MLA control 1 hour

city: Kalamazoo

first: Cindy

last: Linn

state: MI

address: 1903 W. Michigan Avenue

department: Biological Sciences

institute: Western Michigan University

data_processing:
Illumina HiSeq, 2x150bp configuration, single index, per lane with ~350M raw paired-end reads per lane
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of geneexpression between control treated vs PNU treated groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: text (tab delimited) files of log2 fold changes in RPE-J cells between control (DMSO, MLA, or nicotine) and PNU-282987 treated groups.

organism: Rattus norvegicus

source_name: Retinal pigment epithelial cells

growth_protocol: Retinal pigment epithelial cells derived from rats (RPE-J; 4-6 passages) were grown in Dulbecco’s modified Eagle’s medium containing 8% fetal bovine serum, 1% L-Glutamine, and 1% penicillin-streptomycin, using standard cell culture techniques and incubated at 33°C with 5% CO2.

extract_protocol:
Treated RPE-J cells were removed from T75 flasks with trypsin and collected. Cells were processed using Trizol reagent and Total RNA was collected using Direct-zol RNA mini-prep kit (Zymo).
RNA library preperation with polyA selection from GeneWiz

treatment_protocol: RPE-J cells were treated with 100 nM PNU-282987, 1 µM nicotine, 100 nM MLA, or DMSO in regular culture media. Cells were left in the incubator for either 30 minutes, 1 hour, 3 hours, 8 hours, or 12 hours before cells were collected for RNA extraction.

tag: cell line

value: RPE-J epithelial SV40 transformed cell line

value: Long-Evans

tag: treatment

value: MLA treated for 1 hour


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-1_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: RPE-J PNU 12 hours

value: PNU-282987 treated for 12 hours


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-3_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-4_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

value: ZT 12 (8:00pm, lights off)


title: Single fragment WGA product (F1) from the embryo E06 in the pedigree Cross04 [E06_F1_Cross04]


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-3_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: RPE-J PNU 8 hours

value: PNU-282987 treated for 8 hours


title: RPE-J DMSO Control 12 hours

value: DMSO treated for 12 hours


title: Sibling embryo WGA product in the pedigree Cross03 [Sibling_Cross03]

description: WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

value: Embryonic

value: Whole-genome amplified DNA


title: RPE-J PNU 3 hours

value: PNU-282987 treated for 3 hours


title: Cow gDNA for pedigrees of  Cross03 [Cow_Cross03]

description: Genomic DNA extracted from cow ovarian tissue was genotyped using BovineHD BeadChip arrays (Illumina).

value: Ovarian


title: RPE-J PNU 1 hour

value: PNU-282987 treated for 1 hour


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-4_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

value: Ad libitum (5% yeast-extract)


title: Single blastomere WGA product (B3) from the embryo E05 in the pedigree Cross03 [E05_B3_Cross03]


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-2_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Pm3_1


title: Single blastomere WGA product (B1) from the embryo E05 in the pedigree Cross03 [E05_B1_Cross03]


title: Single blastomere WGA product (B2) from the embryo E05 in the pedigree Cross03 [E05_B2_Cross03]


title: RPE-J Nicotine control 12 hours

value: Nicotine treated for 12 hours


title: RPE-J PNU 30 minutes

value: PNU-282987 treated for 30 min


title: RPE-J MLA control 12 hours

value: MLA treated for 12 hours


title: Pm3_2

value: Pasteurella multocida

value: nasal cavity


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-3_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-4_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: Single blastomere WGA product (B3) from the embryo E04 in the pedigree Cross03 [E04_B3_Cross02]


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-1_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-1_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: RPE-J Nicotine control 1 hour

value: RPE-J epithelial SV40 transformed cell line

value: Long-Evans

value: Nicotine treated for 1 hour


title: Single blastomere WGA product (B2) from the embryo E04 in the pedigree Cross02 [E04_B2_Cross02]


title: Hut78 CSH71 (NCI) rep2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: CSH71_treated sample

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 2.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: Hut78 CSH71 (NCI) rep2

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

growth_protocol: Hut78 cells cultured as previously described in our published paper (2018), in 10% serum IMDM medium 37oC incubation.

extract_protocol: Using Qiagene mini RNA Isolation kit, we extracted RNAs from cell pellets (30mg, each) of cultured Hut78 cells -  CSH71 (250nM, 30h) treated and untreated Hut78 cells, respectively (each sample in duplicates). We then provided to the core facility of COH for microarray analysis.

treatment_protocol: CSH71 (250nM, for 30h) treated and untreated Hut78 cells (each sample in duplicates).

value: Hut78 CTCL Cancer cell line

value: CSH71_treated sample


title: Cow gDNA for pedigrees of  Cross02 [Cow_Cross02]


title: Hut78 Ctr rep2

description: untreated sample

source_name: Hut78 Ctr rep2

value: untreated sample


title: C1qbp-KO-DNAme rep1

city: Xiamen

first: liu

last: kai

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

data_processing:
Image analysis and base calling were performed with Illumina CASAVA pipeline
Adapter trimming was performed using trimmomatic version 0.36
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools version 3.2.1
Supplementary_files_format_and_content: peak text files in .gz

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA mini kit (Qiagen).
A total amount of 1.5 μg genomic DNA spiked with moderate lambda DNA were handled by MspI, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to DNA as per manufacturer’s instructions. Then these DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research).

treatment_protocol: On day 5 post-infection with LCMV Armstrong, transferred P14 cells were sorted from the spleen of donor mice.

value: spleen

value: C1qpb KO

tag: Sex

value: male

value: day 5 post-infection

tag: age

value: 12 weeks


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-2_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.

value: Ad libitum (5% yeast-extract)


title: C1qbp-KO-DNAme rep2

tag: tissue


title: Sibling embryo WGA product in the pedigree Cross02 [Sibling_Cross02]

value: Embryonic

value: Whole-genome amplified DNA


title: PDAC tissue 4

city: Kunming

first: Hongjin

state: China / Yunnan

address: Xichang Road#295

institute: The NHC Key Laboratory of Drug Addiction Medicine

data_processing:
RNA-seq data were aligned to the human reference genome (GrCH37, Ensembl build 74) using Tophat version 2.0.12.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Gene expression levels, which are represented as fragments per kilo-base per million mapped reads (FPKM), were obtained for 63,783 genes/transcripts annotated using Ensemble GrCH37 database release 74.
Genome_build: human reference genome (GrCH37, Ensembl build 74)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: human pancreas

extract_protocol:
Following resection, the tumor tissues were examined by a pathologist and then placed in cryotubes with RNAlater reagent and frozen in liquid nitrogen. Samples were transported on dry ice, and stored at -80 ºC. Total RNA was isolated using RNeasy mini (Qiagen) according to the manufacturer's protocol. The quantity and quality of the samples were assessed using NanoDrop 2000 spectrophotometer and Agilent 2100 Bioanalyzer, respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic adjacent tissues

tag: pathologic types

value: Cancer


title: PDAC tissue 5


title: Hut78 CSH71 (NCI) rep1

description: CSH71_treated sample

source_name: Hut78 CSH71 (NCI) rep1


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-3_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: Single blastomere WGA product (B1) from the embryo E04 in the pedigree Cross02 [E04_B1_Cross02]

description: Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

tag: molecule subtype


title: Cow gDNA for pedigrees of  Cross01 [Cow_Cross01]

source_name: cow ovarian tissue

value: Ovarian


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-2_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: Sibling embryo WGA product in the pedigree Cross01 [Sibling_Cross01]

source_name: embryo


title: Normal pancreas tissue 5

value: Pancreatic cancer tissues

value: Adjacent


title: Normal pancreas tissue 4


title: Hut78 Ctr rep1

description: untreated sample

source_name: Hut78 Ctr rep1


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-1_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: Pm3_3

value: Pasteurella multocida

value: nasal cavity


title: PDAC tissue 6


title: Normal pancreas tissue 6


title: Single blastomere WGA product (B3) from the embryo E03 in the pedigree Cross01 [E03_B3_Cross01]


title: Single blastomere WGA product (B2) from the embryo E03 in the pedigree Cross01 [E03_B2_Cross01]


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-4_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

value: ZT 0 (8:00am, lights on)


title: WT-DNAme rep1

source_name: Spleen

tag: genotype

value: wild type


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-2_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.

tag: strain