title: Human_SI-8-cell_BS-Seq

city: Chongqing

first: Jingyu

last: Li

address: #64, Jintang street

institute: Chongqing Reproductive and Genetics Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were trimmed to remove the adapter sequences and low quality bases.
For RNA-seq, the cleaned reads were aligned to the human hg38 reference using Tophat (v2.4.0) with default settings. And for WGBS, bisulfite-converted reads were aligned to the human refference genome (hg38) using Bismark software (v0.7.6).
For RNA-seq, RSEM (v1.3.0) with default parameters was further used to quantify transcription levels (TPM, Transcripts Per Kilobase of transcript per Million mapped reads) of annotated genes. And for WGBS, methylation level was estimated using SeqMonk (v1.39.0).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM or methylation values for each Sample

source_name: Preimplantation embryo

extract_protocol:
After removing the zona pellucida, embryos were washed with PBS and incubated in lysis buffer.
Lysis buffer and 0.5 μl proteinase K were added (final volume 12 μL) into the tubes with collected embryos, followed by incubation at 37°C for 1 h. Bisulfite conversion was performed on cell lysates using EZ DNA Methylation-Gold Kit (Zymo). λ DNA was added in this process to evaluate the conversion efficiency. Purification was performed and then DNA was eluted in 10 mM Tris-Cl. The first strand: Before incubation at 65 °C for 3 min, biotin labelled oligo 1 was added altogether with dNTPs and reaction buffer. The mix was then cooled down to 4°C for primer anneling. 50 U of Klenow exo – (NEB) was added to the samples and incubated at 4°C for 5 min, +1°C /15 s to 37°C, 37°C for 30 min. Samples were then incubated at 95°C for 1 min and transferred immediately to ice before addition of fresh oligo 1 (10 pmol), Klenow exo – (25 U), and dNTPs (1 nmol) as 2.5 μl extra volume in total. The samples were incubated at 4°C for 5 min, +1°C/15 s to 37°C, 37°C for 30 min. This random priming and extension was then repeated for four times (five rounds in total). Samples were then incubated with exonuclease I (NEB) for 1h at 37°C before DNA was purified using 0.8 × Agencourt Ampure XP beads. Samples were eluted in 10 mM Tris-Cl (pH 8.5) and incubated with washed M-280 Streptavidin Dynabeads (Life Technologies) in binding buffer for 15-20min with rotation at room temperature. The second strand: Beads were washed twice with wash buffer, once with 0.1M NaOH, twice with 10 mM Tris-Cl and them resuspended in the mix of dNTPs, oligo 2 primer and NEBuffer. Samples were incubated at 95°C for 45 s and transferred immediately to ice before addition of 100 U Klenow exo – (Enzymatics) and incubation at 4°C for 5 min, +1 °C/15 s to 37°C, 37°C for 90 min. PCR Amplification: Libraries were then amplified by PCR as follows: 95℃ 2 min, 12–13 repeats of (94 °C 80 s, 65°C 30 s, 72°C 30 s), 72 °C 3 min and 4 °C hold. Then the final libraries were purified using 0.8 × Agencourt Ampure XP beads. Library Quantification: Purified libraries were assessed for quality and quantity using Agilent Bioanalyzer and StepOnePlus Real-Time PCR System.

value: Preimplantation embryo

value: 8-cell embryo

tag: incubator

value: SI


title: CS19_12248_RNA-seq

status: Public on Jul 29 2020

type: SRA

city: Farmington

first: Tara

middle: N

last: Yankee

state: CT

address: 400 Farmington Avenue

department: Genetics and Developmental Biology

country: USA

institute: University of Connecticut Health Center

library_source: transcriptomic

data_processing:
Fastq's trimmed with trimmomatic and quality control checked with fastqc and multiqc
Aligned trimmed fastqs to genome using RailRNA 0.2.4b
Generated counts tables from RailRNA output using Recount2 pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: The combined counts table for all samples provided as a .tsv file. The bigWig and bam files are output from RailRNA. The bams were anonymized by having the sequence information removed.

molecule: total RNA

organism: Homo sapiens

source_name: Embryonic Heart Tissue

growth_protocol: Samples flash frozen immediately after collection by HDBR

extract_protocol:
miRNeasy RNA extraction kit with on-column DNAse treatment (Qiagen protocol)
TruSeq Stranded mRNA kit (Illumina)

tag: developmental stage


title: I1BIMA100_3_intestine

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

description: The group information is prefixed with I1BIMA100_3 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: All_samples.GeneExpression.FPKM.txt

organism: Mus musculus

extract_protocol:
Mouse small intestine samples were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: strain

value: ICR

tag: tissue

value: Intestine

tag: treatment


title: CS19_12135_RNA-seq


title: Human_TLM-8-cell_BS-Seq

library_source: genomic

molecule: genomic DNA

value: TLM


title: MU01-0692-Ctrl

type: RNA

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Following labeling, 21.5uL of biotin-labeled samples were hybridized for 16 hr at 48C on GeneChip miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing:
CEL files were analyzed for quality using Affymetrix Transcriptome Analysis Console 4.0 software, and the RMA-DBAG was used for summarization
algorithm-name-0 = rma-bg,pm-only,med-polish
algorithm-name-1 = pm-only,dabg.adjust-dof=1
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name = rma-bg,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: biotin

label_protocol: Biotinylated miRNA were prepared according to the standard Affymetrix FlashTag HSR protocol from 100 ng total RNA

extract_protocol: Standard urine exosome RNA isolation method by Norgen Biotek Corp.

tag: histopathology

value: Control

value: Urine


title: MU01-0651-GS6

source_name: Gleason Score 6_urine

value: Gleason Score 6


title: I1BIMA100_2_intestine

description: The group information is prefixed with I1BIMA100_2 in the column of processed data file


title: MU01-0691-GS6


title: Spike in

city: Utrecht

first: Niels

last: Geijsen

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Hubrecht institute

data_processing:
Reads were counted by first searchinge in the read file  for the CACCG sequence, located 5′ to all sgRNA inserts. The following 20nt are the gRNA, which was mapped to a reference database. Based on the 8nt barcode included in the P7 primer, the reads were assigned to a condition (e.g. a well on the 96-well PCR plate).
Analysis was conducted using “STARS”, gene-ranking method to generate FDR values developed by Doench et al. that was used to generate p-values and FDR rates
Genome_build: hg19
Supplementary_files_format_and_content: Text files detailing gRNA sequences and their abundance in the screens compared to their untreated counterparts.

molecule: other

organism: synthetic construct

source_name: Plasmid DNA Spike-in

growth_protocol: IMDM basal media with 10% Tet approved FBS, and 100μM 2-ME.

extract_protocol:
Genomic DNA (gDNA) was isolated using NucleoSpin Blood Mini (less than 5 million cells), Midi (L) (5-20 million cells) and Maxi (XL) (more than 20 million cells) kits, depending on the size of cell pellet.
A PCR of the genomic DNA and plasmid DNA was performed to attach sequencing adaptors and barcodes to samples. The PCR amplified products were purified using Agencourt AMPure XP SPRI beads according to manufacturer's instructions.
Genome wide CRIPSR/Cas9 screen

treatment_protocol: 250 ng/ml (low) or 1000ng/ml (high) doxycyline was added to growth media. DIE cells were treated with docycyline for 24 hours. Plates containing DIE cells were washed with DPBS and growth media was subsequently added. Surviving cells were harvested at two timepoints after doxycycline exposure, early (24h) and late (72h).

tag: sample type

value: plasmid DNA


title: Human_zygote_BS-Seq

value: zygote


title: CS18_13474_RNA-seq


title: MU01-0688-GS6


title: MU01-0640-GS6


title: CS18_12456_RNA-seq


title: I1WB_IMA10_3_intestine

description: The group information is prefixed with I1WB_IMA10_3 in the column of processed data file


title: I1BIMA100_1_intestine

description: The group information is prefixed with I1BIMA100_1 in the column of processed data file


title: CS17_12752_RNA-seq


title: I1WB_IMA10_1_intestine

description: The group information is prefixed with I1WB_IMA10_1 in the column of processed data file


title: I1WB_IMA10_2_intestine

description: The group information is prefixed with I1WB_IMA10_2 in the column of processed data file


title: I1WB_IMC_3_intestine

description: The group information is prefixed with I1WB_IMC_3 in the column of processed data file


title: CS19_11914_RNA-seq


title: I1WB_IMC_2_intestine

description: The group information is prefixed with I1WB_IMC_2 in the column of processed data file


title: CS16_14213_RNA-seq


title: CS17_12291_RNA-seq


title: MU01-0612-GS6


title: MU01-0600-Ctrl


title: MU01-0584-Ctrl


title: MU01-0587-Ctrl


title: CS16_14209_RNA-seq


title: I1WB_IMC_1_intestine

description: The group information is prefixed with I1WB_IMC_1 in the column of processed data file


title: CS16_12997_RNA-seq


title: I1WB_Sa_3_intestine

description: The group information is prefixed with I1WB_Sa_2 in the column of processed data file


title: CS18_12059_RNA-seq


title: MU01-0624-Ctrl


title: CS13_14401_RNA-seq


title: MU01-0622-GS7

source_name: Gleason Score 7_urine

value: Gleason Score 7


title: CS12_14131_RNA-seq


title: Trp53ΔIECAktE17K whole tumor tissue B3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.
Read alignment was performed using STAR v2.3.0.
Data were converted and sorted by samtools 1.2 and reads per gene were counted via htseq version 0.6.
Data analysis was performed using R (3.2.1) and differential gene expression was analyzed using DESeq2 (v1.8.1).
Candidate genes were filtered to a minimum of a 2-fold change and a FDR-corrected p < 0.05 (padjusted).
Genome_build: mm10

source_name: colon tumor

extract_protocol:
Rneasy Mini Kit (Qiagen)
TruSeq mRNA Sample Preparation v2 Kit (Illumina, RS-122-2002)

tag: genotype

value: Azoxymethane


title: Trp53ΔIECAktE17K whole tumor tissue B4


title: CS17_12331_RNA-seq


title: MU01-0555-Ctrl


title: MU01-0557-Ctrl


title: Trp53ΔIEC whole tumor tissue B4


title: I1WB_Sa_1_intestine

description: The group information is prefixed with I1WB_Sa_1 in the column of processed data file


title: CS13_14479_RNA-seq


title: Trp53ΔIEC whole tumor tissue B3


title: mez2mez3_input

city: Nanjing

first: tao

middle: shen

last: tong

address: Weigang street 1st

institute: Nanjing Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequences using trim_galore
Clean reads without adaptor sequences were aligned to the maize B73 v4 genome using bowtie2.3.2 with default parameters
Peaks were called using macs2.1.1 bigwig files were generated using deeptools bamCoverage with parameters --centerReads -bs 20 --smoothLength 60 --normalizeUsing RPKM and were transformed to wig files using bigWigtoWig software
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: bigwig files generated using deeptools

organism: Zea mays

source_name: leaf

growth_protocol: Seeds of maize (Zea mays “B73”) and mez mutants with B73 background were germinated at room temperature in greehouse for 10 days followed by collection

extract_protocol:
Commercial H3K27me3 (07-449, Millipore) were used to perform ChIP-seq experiments
ChIP libraries were prepared for sequencing using the standard Illumina protocols

tag: cultivar

value: leaf

tag: age

value: 10 days

tag: antibodies


title: mez3-4_input


title: Day0_Parental_3

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were aligned to Mus musculus  genome (GRCm38.81) using Bowtie2, obtaining 55% of unique mappable reads. Peak calling  was run using F-Seq 65 with the following parameters: -t14, -f1.
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / peak counts (.txt)
Supplementary_files_format_and_content: Merged peak file (.bed)
Supplementary_files_format_and_content: Peak annotation (.txt)
Supplementary_files_format_and_content: Day0 Parental peak file (.bed)
Supplementary_files_format_and_content: Day6 Parental peak file (.bed)
Supplementary_files_format_and_content: Day6 ME-Parental peak file (.bed)
Supplementary_files_format_and_content: Day9 Parental peak file (.bed)
Supplementary_files_format_and_content: Day9 ME-Parental peak file (.bed)
Supplementary_files_format_and_content: Day0 Parental wig file (.wig)
Supplementary_files_format_and_content: Day6 Parental wig file (.wig)
Supplementary_files_format_and_content: Day6 ME-Parental wig file (.wig)
Supplementary_files_format_and_content: Day9 Parental wig file (.wig)
Supplementary_files_format_and_content: Day9 ME-Parental wig file (.wig)

source_name: Hoxb8 Cell line

growth_protocol: Three pools of 50,000 ME-Parental and Parental cells each, cultured in the presence of Flt3L  and β-estradiol, were bulk sorted into 1.5ml tubes and processed as previously described in Buenrostro et al. Nature methods 2013

extract_protocol:
Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.
Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (Supplementary Table 1), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

treatment_protocol: To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations.

value: Untreated

tag: day

tag: replicate


title: mez2-1-input


title: Day0_Parental_2


title: MU01-0576-Ctrl


title: Trp53ΔIECAktE17K whole tumor tissue A1


title: MU01-0545-Ctrl


title: Trp53ΔIECAktE17K whole tumor tissue A2


title: MU01-0561-Ctrl


title: MU01-0544-GS6


title: Day0_Parental_1


title: MU01-0542-GS6


title: M-input-2

description: M-input.wig

source_name: M cell

value: M cell


title: Trp53ΔIEC whole tumor tissue B2


title: MU01-0538-Ctrl


title: MU01-0549-GS7


title: MU01-0536-GS7


title: Trp53ΔIEC whole tumor tissue B1


title: BS-input-2-2

description: BS-input.wig

source_name: BS cell

value: BS cell


title: AhrChIP_Th17_WT_R2

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

data_processing:
[CHIP-seq] CHIP-Seq reads were mapped to the mouse genome (mm9) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).  CHIP-seq peak locations were identified using Homer (Heinz et al., 2010).
Genome_build: [ChIP-seq] mm9
Supplementary_files_format_and_content: [ChIP-seq] bedgraph files for each sample

source_name: Spleen/Lymph Node CD4+ T naïve

extract_protocol:
Th17 and iTreg were differentiated from sorted naïve CD4+ T cells as described above. For ChIP of Ahr, cells were treated with FICZ (200 nM) for 4 hours before harvest. Cells were cross-linked with 1% formaldehyde for 15 min. Chromatin was sheared by sonication with Bioruptor Pico (30” on and 30” off for 25 cycles) and immunoprecipitated with anti-Ahr (Enzo Life Science)using iDeal ChIP-Seq Kit for transcription factors or True MicroChIP kit (Diagenode).
[ChIP-seq] Eluted DNA was made into indexed library according to the manual of NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter) before sequencing.

treatment_protocol: Naïve CD4+ T cells were purified from splenocytes using mouse CD4+ T cell isolation kit (Stemcell Technologies), and further sorted by FACS Aria IIu (BD Biosciences). 24-well plates were coated with 40 µg/ml anti-hamster antibody (MP Biomedical) at 37°C for 4 hours. For iTreg differentiation, naïve CD4+ T cells were cultured in T cell media IMDM (Sigma-Aldrich) supplemented with soluble 0.25 µg/ml anti-mouse CD3 (145-2C11), 1 µg/ml anti-mouse CD28 (37.51), 2 µg/ml anti-mouse IL-4 (11B11), 2 µg/ml anti-mouse IFN-γ (XMG1.2) and 5 ng/ml TGF-β, with (Th17) or without (iTreg) 20 ng/ml IL-6, for 3.5 days. For human cells, naïve T cells were enriched using the human CD4+T cell isolation kit (Stemcell) from human PBMC cells and further sorted (CD3+CD4+CD45RA+CD25−). For iTreg differentiation, the sorted naïve CD4+ T cells were seeded into 48-well plates precoated with 1 μg/mL anti-CD3 antibody (clone HIT3a), and cultured in RPMI media (Sigma-Aldrich) supplemented with IL-2 (10 ng/ml), soluble anti-CD28 (1 μg/ml; clone CD28.2) and 5 ng/ml TGF-β for 6 days.

value: Spleen and Lymph Node

tag: cell type

value: Ahr+/+

tag: antibody

value: anti-Ahr antibody (Enzo Life Science Catalog number:BML-SA210-0100)


title: AhrChIP_Th17_KO_R2

value: Ahr-/-


title: M-input-1

description: M-input.wig


title: MU01-0508-Ctrl


title: AhrChIP_Th17_KO_R1


title: MU01-0498-Ctrl


title: BS-input-1-1

description: BS-input.wig


title: mouse colon tumor organoid with control hairpin (shRen) F2

source_name: tumor organoid isolated from azoxymethane induced tumors.

tag: shRNA

value: shRen (control)

tag: isolation date

value: Doxycycline for 10 days

tag: other constructs

value: rtTA-Hygro


title: mouse colon tumor organoid with control hairpin (shRen) C2


title: M-H3K27me3-2

value: H3K27me3 (07-449, Millipore)


title: BS-H3K27me3-2


title: AhrChIP_iTreg_WT_R2

value: iTreg


title: AhrChIP_Th17_WT_R1


title: mouse colon tumor organoid with shNoch3 1339 A2

value: shNotch3 1339


title: AhrChIP_iTreg_KO_R2


title: mouse colon tumor organoid with shNoch3 1339 D2


title: d13.Riboseq.Eif3m replicate 2 [TAGCTT.ES11-10]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
The sequence GAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGAT was clipped using Cutadapt. The reads were aligned to the RefSeq transcriptome (November 2017) using Bowtie for the ribo-seq and bowtie2 for the paired RNA-seq
Differential expression analysis; The  raw count of riboseq reads aligning to the coding regions was used for genes annotated to be protein coding. For the non-protein coding genes and for the mRNAseq data the number of alignments to the entire transcript were used. The position of each read was taken to be 17 nucleotides downstream from its 5’ end. With the minimum expression level threshold of 2 reads, transcripts were sorted in ascending order and an arranged in bins of size 300. The mean and standard deviation of change in expression of the transcripts within each bin was used to determine a Z-score for each transcripts. For the remaining transcripts, of insufficient number to be binned (<300), the mean and standard deviation was obtained from the previous bin. The distribution of average Z-scores from all the replicates was compared to the average of the absolute Z-scores for genes for which all the replicates did not have the same direction (i.e. all positive or negative). The latter distribution is expected to have similar characteristics as the former in the absence of any differential expression. A FDR of 0.05 was used as a threshold of differential expression.
Genome_build: Refseq release 84
Supplementary_files_format_and_content: esmekal_counts.txt.gz is raw counts assigned to each gene in text format.

growth_protocol: FVB/N mice at 6-8 weeks of age were injected with siRNA in LNP formulations at 0.5 mg/kg via tail vein.

extract_protocol:
Epicenter ART-seq
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit

treatment_protocol: mice were injected with the control (scrambled luciferase) or eIF3m siRNA LNP formulations at 0.5 mg/kg (1 injection in 5 days) via tail vein for 9 or 13 days.

value: FVB/N

tag: sirna

value: liver

tag: library strategy

value: Ribo-Seq


title: AhrChIP_iTreg_KO_R1

tag: tissue

tag: strain


title: mouse colon tumor organoid with shNoch3 1146 A1

value: shNotch3 1146

tag: treatment


title: X605A.A4

city: Los Angeles

first: Aaron

last: Gordon

state: CA

address: Gonda Building, 695 Charles E. Young Drive South

department: Neurology

institute: UCLA

description: RNA Quant-seq

data_processing:
Reads were mapped with STAR to GRCm38 using Gencode v11. Alignment, GC bias and duplication metrics were collected using Picard tools functions CollectRnaSeqMetrics, CollectGcBiasMetrics, and MarkDuplicates and were aggregated using MultiQC.
Gene expression was quantified using Salmon.
Genome_build: GRCm38
Supplementary_files_format_and_content: *csv: Comma-separated text files

source_name: Basolateral amygdala

extract_protocol:
Fresh brain was sliced coronally at bregma and placed in a brain mold. A 1 mm slice was extracted from -1mm to -3mm of bregma. This slice was then visually inspected for the white matter tract surrounding the BLA and a 1mm punch was used to dissect out the BLA. The left and right BLA were pooled for downstream processing. RNA extraction was performed using the RNeasy Mini Kit (Qiagen).
Sample library preparation was done using Lexogen QuantSeq 3' Fwd with pre-normalized moderate to high quality RNA.

value: Basolateral amygdala

tag: genotype/variation

value: Control

tag: Sex

value: Female

tag: line


title: AhrChIP_iTreg_WT_R1

value: Spleen and Lymph Node

tag: genotype


title: d13.Riboseq.Eif3m replicate 1 [GATCAG.ES11-9]


title: X605A.A3

description: RNA Quant-seq

tag: age

value: CYFIP OE

value: Male


title: mouse colon tumor organoid with shNoch3 1146 D1


title: d13.Riboseq.cont replicate 2 [GCCAAT.ES11-3]

tag: day

value: scrambled luciferase


title: MU01-0491-GS6

tag: histopathology

value: Gleason Score 6

value: Urine


title: MU01-0493-Ctrl


title: MU01-0494-GS6


title: MU01-0495-Ctrl


title: X605A.A2

description: RNA Quant-seq


title: MU01-0480-Ctrl


title: MU01-0488-Ctrl


title: d13.Riboseq.cont replicate 1 [ACAGTG.ES11-2]


title: X605B.A4

description: RNA Quant-seq


title: MU01-0460-GS6


title: d13.RNAseq.Eif3m replicate 2 [TAGCCT.ES11-10]

extract_protocol:
RNAseq-Neoprep
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit

value: RNA-Seq


title: X605B.A7

description: RNA Quant-seq


title: MU01-0409-GS8

source_name: Gleason Score 8_urine

value: Gleason Score 8


title: X605B.A3

description: RNA Quant-seq


title: X605B.A5

description: RNA Quant-seq


title: d13.RNAseq.cont replicate 2 [TTAGGC.ES11-3]


title: MU01-0398-GS7

value: Gleason Score 7


title: d13.RNAseq.cont replicate 1 [CGATGT.ES11-2]


title: MU01-0489-Ctrl


title: X605B.A2

description: RNA Quant-seq


title: d9.Riboseq.Eif3m replicate 3 [d184006.ES34-6]


title: d9.Riboseq.Eif3m replicate 2 [d184005.ES34-5]


title: MU01-0394-GS6


title: X433A.D1

description: RNA Quant-seq


title: MU01-0386-GS7


title: d9.Riboseq.Eif3m replicate 1 [d184004.ES34-4]


title: d9.Riboseq.cont replicate 3 [d184003.ES34-3]


title: MU01-0361-GS7


title: X436B.C3

description: RNA Quant-seq


title: d9.Riboseq.cont replicate 2 [d184002.ES34-2]


title: MU01-0340-GS6


title: X433A.C4

description: RNA Quant-seq


title: MU01-0333-GS6


title: MU01-0337-GS5

source_name: Gleason Score 5_urine

value: Gleason Score 5


title: d13.RNAseq.Eif3m replicate 1 [GATCAG.ES11-9]

value: FVB/N


title: d9.Riboseq.cont replicate 1 [d184001.ES34-1]

value: liver


title: MU01-0331-GS6


title: X433A.C1

description: RNA Quant-seq


title: MU01-0329-GS8


title: X605B.A1

description: RNA Quant-seq


title: X433B.D8

description: RNA Quant-seq


title: MU01-0342-GS6


title: d1490.ES11-10.RNAseq: d13.Eif3m replicate 2

description: d13.Eif3m replicate 2

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads aligned with STAR version 2.5.3a and summarized with rsem version 1.3.0
Genome_build: mm10 with ensemble version 88 annotation
Supplementary_files_format_and_content: integer count data in txt format

source_name: liver

extract_protocol:
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit
RNAseq-Neoprep
RNA for sequencing was purified from ground mouse livers with the use of Qiagen RNeasy kit


title: d1491.ES11-11.RNAseq: d13.Eif3m replicate 3

description: d13.Eif3m replicate 3


title: d1489.ES11-9.RNAseq: d13.Eif3m replicate 1

description: d13.Eif3m replicate 1


title: MU01-0326-GS7


title: d1496.ES11-3.RNAseq: d13.cont replicate 3

description: d13.cont replicate 3

value: luciferase


title: SMC12.C4

description: RNA Quant-seq


title: SMC12.C3

description: RNA Quant-seq


title: SMC12.C7

description: RNA Quant-seq


title: d1488.ES11-2.RNAseq: d13.cont replicate 2

description: d13.cont replicate 2


title: X429.A4

description: RNA Quant-seq


title: MU01-0325-GS8


title: d1487.ES11-1.RNAseq: d13.cont replicate 1

description: d13.cont replicate 1


title: X429.A1

description: RNA Quant-seq


title: MU01-0315-GS6


title: X426.B7

description: RNA Quant-seq


title: X433A.C2

description: RNA Quant-seq


title: MU01-0322-GS6


title: X426.B6

description: RNA Quant-seq


title: X426.B5

description: RNA Quant-seq


title: MU01-0269-GS6


title: X426.B3

description: RNA Quant-seq


title: X424.C2

description: RNA Quant-seq


title: X424.C1

description: RNA Quant-seq


title: X426.B2

description: RNA Quant-seq


title: X424.C3

description: RNA Quant-seq


title: X424.C4

description: RNA Quant-seq


title: X426.B4

description: RNA Quant-seq


title: X426.B1

description: RNA Quant-seq


title: 5_KO_angII

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

description:
experiment1_deSeq2_counts.txt
experiment1_deSeq2_NormCounts.txt

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCm38 + Gencode-M22 Annotation
Supplementary_files_format_and_content: Raw and normalized counts

source_name: bone marrow differentiated macrophages

growth_protocol: Bone morrow cells were cultured in standard differentiated medium for 7 days to differentiae to macrophages per standard protocol.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations. The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.

treatment_protocol: Mice were challenged with 1 mg/kg/min,1.44 mg/kg/day) by implantation of Alzet osmotic minipumps (Model 1004, Alzet, Cupertino, CA) for 7 days before bone marrow isolation. We in vitro differentiate cells to macropages for 7 days before RNA extraction for RNA-seq analysis.

value: bone marrow differentiated macrophages


title: 2_WT_angII


title: 6_KO_angII


title: 4_WT_angII

description:
experiment2_deSeq2_counts.txt
experiment2_deSeq2_NormCounts.txt


title: 3_WT_angII


title: 1_WT_angII


title: 8_KO_angII


title: 7_KO_angII


title: MU01-0259-GS6


title: MU01-0211-GS6


title: MU01-0125-GS6


title: HEK_noAA_C

city: Vienna

first: Vitaly

last: Sedlyarov

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: Research Center for Molecular Medicine

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A6_S31181

data_processing:
basecalling: Illumina2bam, version 1.17
adapter and quality trimming: cutadapt, version 1.16
mapping: STAR, version 2.5.2b
quantification: ESAT
Genome_build: hg38
Supplementary_files_format_and_content: tsv

molecule: polyA RNA

source_name: HEK293T cell line

growth_protocol: HEK293T were obtained from ATCC and their identity and lack of contamination with mycoplasma confirmed by STR profiling and PCR, respectively. Cells were seeded in triplicate in full media (DMEM Gibco, 10% FBS Gibco, antibiotics).

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit including a DNase I digest step.
RNA-sequencing (RNA-seq) libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: Media was removed and, after a wash with PBS, substituted with DMEM starvation media lacking the indicated amino acid supplemented with 10% (v/v) dialyzed FBS (Gibco cat. 26400-044). Starvation media each lacking a single amino acid were prepared by complementing amino acid-free DMEM media (ie devoid of all 15 amino acids normally present, custom made by PAN Biotech) with the other 14 amino acids (from individual amino acid powders, SIGMA). DMEM media reconstituted with all 15 amino acids and 10% dialyzed FBS as well as full media served as controls. After 16h, media was removed, and cells were harvested in cold PBS.

tag: cell line

tag: cell type compact id

tag: depleted compound

value: noAA


title: MU01-0214-GS6


title: MU01-0037-Ctrl

value: Control


title: MU01-0275-GS6


title: MU01-0036-Ctrl


title: HEK_noAA_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A1_S31141


title: HEK_noAA_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E3_S31161


title: MU01-0039-Ctrl


title: MU01-0183-GS6


title: HEK_Vit_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F8_S31202

value: Vit


title: MU01-0116-GS7


title: MU01-0297-GS7


title: MU01-0205-GS6


title: MU01-0040-Ctrl


title: MU01-0041-Ctrl


title: MU01-0044-Ctrl


title: MU01-0103-GS6


title: HEK_Val_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H7_S31196

value: Val


title: MU01-0181-GS6


title: HEK_Val_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H2_S31156


title: HEK_Vit_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E8_S31201


title: HEK_Tyr_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G7_S31195

value: Tyr


title: MU01-0032-Ctrl


title: HEK_Val_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D5_S31176


title: MU01-0030-Ctrl


title: MU01-0143-GS7


title: HEK_Tyr_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G2_S31155


title: HEK_Tyr_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C5_S31175


title: MU01-0060-GS6


title: HEK_Trp_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F7_S31194

value: Trp


title: MU01-0031-Ctrl


title: HEK_Trp_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B5_S31174


title: HEK_Trp_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F2_S31154


title: MU01-0025-Ctrl


title: MU01-0019-Ctrl


title: MU01-0026-Ctrl


title: MU01-0029-Ctrl


title: MU01-0023-Ctrl


title: HEK_Tor1_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D8_S31200


title: MU01-0027-Ctrl


title: MU01-0012-Ctrl


title: MU01-0020-Ctrl


title: HEK_Tor1_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D3_S31160


title: MU01-0010-Ctrl


title: MU01-0021-Ctrl


title: HEK_Tor1_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H5_S31180


title: mez2mez3_rep1

data_processing:
Sequence reads were aligned to the maize B73 v4 genome using hisat2 v2.1.0 using default parameters
Expression levels were calculated using stringtie 1.13 and gene count were extracted using prepDE.py in stringtie packages
Differential expression analyses were performed using R packages DESeq2
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: table-delimited text files include raw counts for each sample

extract_protocol:
Total RNAwere extracted from leaf tissue or cells and treated with DNase I. Approximately 10 mg of total RNA was reverse-transcribed into cDNA
RNA libraries were prepared for sequencing using the manufactures Illumina protocols

tag: cultivar

tag: cell type

value: leaf

value: 10 days

tag: replicate


title: mez2mez3_rep2


title: MU01-0017-Ctrl

value: Urine


title: mez3-4_rep1


title: MU01-0024-Ctrl


title: MU01-0290-GS6

value: Gleason Score 6


title: MU01-0005-GS6


title: MU01-0003-Ctrl


title: MU01-0004-Ctrl


title: mez2-1_rep1


title: HEK_Thr_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E2_S31153

value: Thr


title: mez3-4_rep2


title: HEK_Thr_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A5_S31173


title: mez2-1_rep2


title: M-RNAseq_rep2

value: M cell


title: M-RNAseq_rep1


title: HEK_Ser_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D7_S31192

value: Ser


title: HEK_Ser_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H4_S31172


title: MU01-0002-Ctrl


title: thk1_iso17_rep1

city: Ithaca

first: Hao

last: Wu

address: 236 Tower Rd, Plant Science Building Room #236

institute: Cornell University

data_processing:
The raw reads were mapped to maize reference genome (B73 RefGen_v4, AGPv4) by HISAT2 (v2.1.0)
The output SAM files were converted to BAM files and were sorted by SAMtools (v1.9)
Mapped transcripts in sorted BAM files were assembled and normalized with StringTie (v1.3.6) using maize genome annotation file Zea_mays.B73_RefGen_v4.43.gtf downloaded from Gramene
Readcounts were calculated by HTSeq (v0.11.1)
Genome_build: B73 RefGen_v4, AGPv4
Supplementary_files_format_and_content: Tab Separated Values (TSV) files (HTSeq output file) with gene read count for each sample

source_name: Endosperm

growth_protocol: Field grown plants were self-pollinated

extract_protocol:
Dissected samples were immediately frozen in liquid N2 and ground to fine powder. The total mRNA was extracted using conventional SDS/TRIzol method
Library was prepared with a TruSeq RNA Library Prep Kit (Illumina) and 100-base paired end sequencing using an Illumina HiSeq 2500 sequencer

treatment_protocol: Endosperms were dissected at 19 DAP from WT, thk1-iso15 and thki-iso17 maize in a B73 inbred genetic background.

value: 19 DAP

value: Endosperm


title: thk1_iso17_rep2


title: HEK_Ser_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D2_S31152


title: thk1_iso15_rep3


title: thk1_iso17_rep3


title: BS-RNAseq_rep2

value: BS cell


title: BS-RNAseq_rep1


title: thk1_iso15_rep2


title: MU01-0014-GS6

source_name: Gleason Score 6_urine


title: HEK_Thr_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E7_S31193


title: HEK_Recon_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B6_S31182

value: Recon


title: HEK_Recon_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F3_S31162


title: root-H3K27me3

source_name: root

value: root

tag: antibodies

value: H3K27me3 (07-449, Millipore)


title: thk1_iso15_rep1

tag: tissue


title: HEK_Recon_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B1_S31142


title: B73_rep3

tag: strain

value: WT


title: leaf-input


title: HEK_Phe_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C7_S31191

value: Phe


title: B73_rep2


title: leaf-H3K36me3


title: HEK_Phe_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G4_S31171


title: B73_rep1


title: mez3-4_H3K27me3


title: HEK_Phe_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C2_S31151


title: mez2mez3_H3K27me3


title: HEK_Met_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B7_S31190

value: Met


title: HEK_Met_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F4_S31170


title: HEK_Met_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B2_S31150


title: M-H3K27me3-1


title: P0_3h_fresh

city: gaithersburg

first: Xiaotao

last: Qu

state: md

address: 1 medimmune way

institute: Astrazeneca

description: Mouse club cell lineages : Epcam+ Scgb1a1+ cells

data_processing:
Fastq files were generated using bcl2fastq
counts matrix was generated  using Cellranger v2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: fresh

growth_protocol: Single cell supension of freshly isolated small airways from naïve mouse

extract_protocol:
10x_scRNAseq
ChromiumTM Single Cell 3' Reagent Kit, v2 Chemistry

treatment_protocol: no treatment

tag: time

value: Day 0

value: lung

value: Epcam+ Scgb1a1+ cells


title: HEK_Lys_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A7_S31189

value: Lys


title: mez2-1_H3K27me3

value: leaf

value: 10 days


title: root-input


title: BS-H3K27me3-1


title: HEK_Leu_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H6_S31188

value: Leu


title: pgc.c1

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: Primordial germ cells

growth_protocol: Female and male rats of an outbred Hsd: Sprague Dawley SR®TM (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control or vinclozolin were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. The F1-F3 generation offspring were not themselves treated directly with vinclozolin. The control and vinclozolin lineage rats were housed in the same room with lighting, food and water.

extract_protocol:
Purified populations of primordial germ cells (PGCs) (at E13) were prepared using a mini StaPut gradient method. Briefly, fetal primordial germ cells (E13) were pooled and dissociated by incubation in 0.25% trypsin-EDTA (Sigma) with vigorous pipetting using a 1000 microliter pipette tip, and the resulting cell solution was filtered through 100 micron nylon mesh to yield a single cell suspension. This cell suspension was then loaded onto a 50 ml 2-4% bovine serum albumen (BSA) gradient prepared in KREBS buffer, and the cells were allowed to sediment at unit gravity at 4˚C for two hours as described (43, 44). The gradient was then fractionated and aliquots of the fractions were examined under phase optics to identify those enriched for PGCs on the basis of morphological characteristics. The enriched fractions were pooled to yield the final sample which was >85% pure. The pooled samples were then stored at -80°C prior to processing for DNA preparations.   Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: rat DNA pools were generated using the appropriate amount of genomic DNA from each individual for 2 pools each of control and vinclozolin lineage animals. Genomic DNA was sonicated using the Covaris M220 the following way: the pooled genomic DNA was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95˚C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution is then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚ C and then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20˚C freezer for 1 hour to overnight.  The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP pools were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. NGS was performed by the WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application.

treatment_protocol: On days 8 through 14 of gestation, the F0 females were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day) or dimethyl sulfoxide (DMSO). Vinclozolin was obtained from Chem Service Inc. (West Chester, PA) and was injected in a 20 microliter DMSO vehicle.

tag: developmental stage

value: Primordial germ cells

tag: lineage

value: control


title: HEK_Lys_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A2_S31149


title: HEK_Lys_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E4_S31169


title: pgc.c2


title: HEK_Ile_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G6_S31187

value: Ile


title: 96 hr KO rep 2

last: Griswold

address: Biotechnology Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

data_processing:
Bowtie/TopHat/Cufflinks incorporated into Ion Torrent Suite v.5.0.5.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM .xls files and raw gene counts for each sample

source_name: Testis

growth_protocol: Germ cells were isolated from fresh testis via cell sorting of PIWIL2-eGFP positive cells.

extract_protocol:
Sorted germ cells were frozen in Trizol and total RNA was recovered using Trizol manufacturer protocol.  polyA mRNA was enriched using NEBNext poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs) according to the manufacturer's instructions.
10 ng of mRNA was used to make barcoded libraries with the Ion Total RNA-seq Kit V2 (Life Technologies).  Libraries were pooled to 75 pM before loading on Ion P1 semiconductorr chips using and Ion Chef and sequenced on and Ion Proton sequencer.

treatment_protocol: Mice were treated with WIN 18,446 for 7 days then either collected or treated with retinoic acid (RA) and allowed to recover for 12, 18, 48, 72, 96, or 120 hours post-injection.

value: Derived from C57BL/6 x 129s4/SvJae

tag: genotype (stra8)

value: KO

tag: treatment

value: WIN 18,446 synchrony + RA + 96 hours


title: HEK_Leu_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D4_S31168


title: 48 hr KO rep 2

value: WIN 18,446 synchrony + RA + 48 hours


title: pgc.v2

value: vinclozolin


title: 120 hr KO rep 2

value: WIN 18,446 synchrony + RA + 120 hours


title: pgc.v1


title: HEK_Leu_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H1_S31148


title: 18 hr KO rep 2

value: WIN 18,446 synchrony + RA + 18 hours


title: 72 hr KO rep 2

value: WIN 18,446 synchrony + RA + 72 hours


title: HEK_Ile_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C4_S31167


title: HEK_Ile_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G1_S31147


title: HEK_His_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B4_S31166

value: His


title: 12 hr KO rep 2

value: WIN 18,446 synchrony + RA + 12 hours


title: HEK_Gly_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E6_S31185

value: Gly


title: 0 hr KO rep 2

value: WIN 18,446 synchrony


title: HEK_His_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F6_S31186


title: HEK_His_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F1_S31146


title: 120 hr KO rep 1


title: HEK_Gly_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E1_S31145


title: 18 hr KO rep 1


title: HEK_Gluc_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B3_S31158

value: Gluc


title: HEK_Gly_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A4_S31165


title: 96 hr KO rep 1


title: 12 hr KO rep 1


title: 48 hr KO rep 1


title: HEK_Gluc_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_F5_S31178


title: HEK_Gluc_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_B8_S31198


title: 0 hr KO rep 1


title: 120 hr WT rep 2

value: WT


title: HEK_Gln_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_E5_S31177

value: Gln


title: HEK_Gln_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A8_S31197


title: NEBNext_Ultra_II_RNA_UD_mESC_replicate_1

city: Beijing

first: Chengqi

last: Yi

address: No.5 YiHeYuan Road

institute: Peking University

data_processing:
Raw reads from sequencing were firstly subjected to Trim_galore (v0.6.4_dev) for quality control and adaptor trimming with parameters -q 20 --stringency 3 --length 20
Then trimmed reads were mapped to human (hg19) genome and transcriptome(downloaded from the table browser of UCSC database) using STAR (v2.7.1a) with parameters --runThreadN 20 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterIntronMotifs RemoveNoncanonicalUnannotated
rRNA contamination were determined through directly mapping to the dataset of human rRNA sequence downloaded from NCBI by bowtie2 (v2.2.9) with parameters -N 1 -p 20 -q
Performances related to the processing of sam/bam file were done with the help of Samtools (v1.9)
The FPKM value for annotated genes was calculated by cuffnorm (v2.2.1). Gene body coverage and nucleotide composition for each position of the first 30 bases of each sequence read per library were calculated by QoRTs (v1.1.6). Reads distribution and GC content distribution of mapped reads were calculated by RseQC (v2.6.4), and median coefficient of variation of gene coverage over the 1000 most highly expressed transcripts per library and insert size of library were calculated by Picard Tools (v2.20.6). Library complexity was calculated by Preseq (v2.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample using 293T RNA as input and Tab-delimited text files include counts for each genes in each sample using mESC RNA as input.

source_name: Mouse Embryonic Stem Cells

growth_protocol: HEK293T cells used in this study were daily maintained in DMEM medium (GIBCO) supplemented with 10% FBS (GIBCO) and 1% penicillin/streptomycin (GIBCO) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells with TRIzol (Invitrogen), according to the manufacturer’s instructions. The resulting total RNA was treated with DNase I (NEB) to avoid genomic DNA contamination. Phenol/chloroform extraction and ethanol precipitation were then performed to purify and concentrate total RNA. For mRNA isolation, two successive rounds of poly(A)+ selection were performed using oligo(dT)25 dynabeads (Invitrogen).
Reverse transcription was carried out using Superscript IV reverse transcriptase (Invitrogen) and then tagmentation reaction was performed with Tn5 transposase (Vazyme). Strand extension reaction was performed by directly adding Bst 3.0 DNA Polymerase and 1X NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB) to tagmentation products and incubating at 72°C for 15 min, followed by Bst 3.0 DNA Polymerase inactivation at 95°C for 5 min. Next, 0.2 μM indexed primers were added to perform enrichment PCR.The library was purified twice using 1X Agencourt AMPure XP beads (Beckman Coulter) and sequenced on the Illumina Hiseq X10 platform which generated 2 x 150 bp of paired-end raw reads.

value: Undifferential Mouse Embryonic Stem Cells

tag: transposase


title: NEBNext_Ultra_II_RNA_UD_mESC_replicate_2


title: NEBNext_Ultra_II_RNA_DI_mESC_replicate_3

value: Differential Mouse Embryonic Stem Cells


title: 96 hr WT rep 2

value: Derived from C57BL/6 x 129s4/SvJae


title: HEK_Gln_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_A3_S31157


title: HEK_Full_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C8_S31199

value: Full


title: 72 hr KO rep 1

value: KO


title: 48 hr WT rep 2

value: WIN 18,446 synchrony + RA + 48 hours


title: HEK_Full_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G5_S31179


title: NEBNext_Ultra_II_RNA_DI_mESC_replicate_2


title: HEK_Full_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C3_S31159


title: 18 hr WT rep 2


title: TRACE_seq_UD_mESC_replicate_3

value: TruePrep Tagment Enzyme (Vazyme, S601-01)


title: 12 hr WT rep 2


title: NEBNext_Ultra_II_RNA_DI_mESC_replicate_1


title: 0 hr WT rep 2


title: TRACE_seq_UD_mESC_replicate_2


title: HEK_Cys_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D6_S31184

value: Cys


title: 120 hr WT rep 1

value: WIN 18,446 synchrony + RA + 120 hours


title: HEK_Cys_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_D1_S31144


title: HEK_Cys_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_H3_S31164


title: TRACE_seq_UD_mESC_replicate_1


title: 96 hr WT rep 1

value: WIN 18,446 synchrony + RA + 96 hours


title: HEK_Arg_C

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C6_S31183

value: Arg


title: 72 hr WT rep 2

value: WIN 18,446 synchrony + RA + 72 hours


title: TRACE_seq_DI_mESC_replicate_3


title: HEK_Arg_B

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_G3_S31163


title: TRACE_seq_DI_mESC_replicate_2


title: 48 hr WT rep 1


title: HEK_Arg_A

description: BSF_0376_HM3T5BBXX_8_QuantSeq_R0043_C1_S31143


title: 72 hr WT rep 1


title: CD8+ T 61wt 12h

first: Chang

last: Liu

address: 301, Yanchang Road

institute: Shanghai Tenth People's Hospital

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk.
We used Hisat2（version:2.0.4） to map the cleaned reads to the mouse GRCm38 reference genome with two mismatches.
Stringtie（version:1.3.0）  was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using edgeR.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) . The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: GRCm38

source_name: Splenic CD8+ T cells

growth_protocol: Cells were cultured in RPMI 1640, supplemented with 10% (vol/vol) FBS, L-Glutamine (2mM), penicillin-streptomycin (100U/ml) and 50μM β-mercaptoethanol.

extract_protocol:
Total RNA was extracted from anti-CD3/CD28 stimulated CD8+ T cells according to the manufacturer's instructions.
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Purified libraries were quantified by Qubit® 2.0Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq X-Ten (Illumina, USA).

treatment_protocol: Splenic CD8+ T cells were stimulated with plate-bound anti-CD3 (2μg/ml) plus anti-CD28 (2μg/ml) for 12 hours.

tag: genotype

value: Splenic CD8+ T cells

value: Stimulated with anti-CD3/CD28 for 12h.


title: TRACE_seq_DI_mESC_replicate_1


title: 18 hr WT rep 1

value: WIN 18,446 synchrony + RA + 18 hours


title: 12 hr WT rep 1

value: WT

value: WIN 18,446 synchrony + RA + 12 hours


title: CD8+ T 50wt 12h


title: Input_IgG

city: Boston

first: Marco

last: Mineo

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

data_processing:
Reads were adapter trimmed (cutadapt v1.9.dev1) and reads less than 18 bp were discarded.
Mapping was performed against the full human genome (hg38) including a database of splice junctions with STAR (v 2.4.0i). Uniquely mapping reads were then run through a custom-built PCR duplicate removal script.
eCLIP data sets with multiple in-line barcodes were merged at the usable read stage, and cluster identification was performed on usable reads using CLIPper11 (available at https://github.com/YeoLab/clipper/releases/tag/1.0).
Genome_build: hg38
Supplementary_files_format_and_content: file include Chromosome, Start position, Stop position, -log10(P-value), Log2 fold enrichment in eCLIP vs. input, Strand (+ or -)

source_name: Melanoma

extract_protocol:
HNRNPH1-RNA interactions were stabilized with UV crosslinking (254 nm, 400 mJ/cm2), followed by lysis in iCLIP lysis buffer, limited digestion with RNase I (Ambion), immunoprecipitation of HNRNPH1-RNA complexes with a HNRNPH1 primary antibody (Bethyl Labs #A300-511A, at 10 μg per mL of lysate). Sample was dephosphorylated with FastAP (ThermoFisher) and T4 PNK (NEB).
A barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB). RNA was reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter was then ligated to the cDNA fragment 3′ end. Sample was PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis. Samples were sequenced on the Illumina HiSeq 4000 platform.

value: Melanoma cell line

tag: passages


title: Input_hnRNP-H1

tag: cell line


title: CD8+ T 29wt 12h


title: 0 hr WT rep 1

value: WIN 18,446 synchrony


title: IP-IgG

tag: rip antibody

value: IgG


title: IP-hnRNP-H1

value: HNRNPH1 primary antibody (Bethyl Labs #A300-511A)


title: CD8+ T 70ko 12h

value: Lrch1 KO


title: IFNg_3

data_processing:
Raw reads were examined for quality issues using FastQC.
Trimmed reads were aligned to UCSC build 38 of the human genome (hg38), augmented with transcript information from Ensembl release GRCh38 using STAR, where adapter sequences and other contaminating sequences with low PHRED quality scores were trimmed.
Count of reads aligning known genes was generated by HT-Seq. Differential expression at the gene level was calculated with DESeq.
Genome_build: hg38
Supplementary_files_format_and_content: text files include read count for each Sample

source_name: Brain

extract_protocol:
RNA was harvested from cells using RNeasy Mini Kit (Qiagen Cat#74104). Illumina RiboZero was used with 1 ug of total RNA and sequencing libraries were constructed using NEBNext Ultra II RNA library Prep Kit for Illumina (Cat#E7770)
RNA libraries were prepared for sequencing using standard NEB protocols

value: GBM patient-derived cells

value: 3 to 6

value: glioblastoma

value: interferon gamma


title: CD8+ T 69ko 12h


title: NEBNext_Ultra_II_RNA_UD_mESC_replicate_3

value: Undifferential Mouse Embryonic Stem Cells


title: d16_hns_#1

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: FOXO transcription factor daf-16 mutant fed hns mutant E. coli

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to ce10 whole genome using Tophat2 v2.0.11
Gene expression levels were calculated FPKM values using a cufflinks v.2.2.1. The FPKM values are on log2 scale.
Genome_build: ce10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

growth_protocol: Wild type N2 and daf-16 mutant C.elegans were grew up on NGM plate with E.coli BW25113 or hns KO BW25113 at 20℃

extract_protocol:
Total RNA was isolated using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
The sequencing library was prepared using the Lexogen SENSE mRNA Library Preparation Kit.

value: daf-16 mutant

value: fed hns

value: whole body


title: d16_hns_#2


title: d16_BW_#2

description: FOXO transcription factor daf-16 mutant fed BW25113 E. coli

value: fed BW


title: d16_BW_#1


title: IFNg_1


title: IFNg_2


title: Rep 3 FSH Day 4 [FSH_D4_3]

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

institute: Utrecht University

data_processing:
Sequencing data were de-multiplexed with the Illumina bcl2fastq2 software.
The raw FASTQ files were quality-checked using FastQC (v. 0.11.2), and Trimmomatic software was employed for quality trimming and adapters clipping.
The remaining reads were aligned to the bovine reference genome (Bos taurus UMD3.1) and the read counts estimated at gene level, performing these steps with the Rsubread package for the R software.
Genes with low expression counts (less than 1 count per million) were filtered out before normalization.
The between-samples normalization method applied was TMM (weighted trimmed mean of M-values).
Genome_build: bosTau8
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: bovine ovarian cortex_FSH Day 4

growth_protocol: Samples were cultured at 38.5 °C in 5% CO2 in air in a humidified chamber. Medium was completely replaced every day.

extract_protocol:
Cortical strips harvested and frozen at day 0 or after 2 and 4 days of culture were homogenized over liquid nitrogen. Total RNA was extracted using Trizol Plus RNA Purification Kit (Invitrogen, Carlsbad, CA) following manufacturer instructions. Genomic DNA was removed by a complementary on-column procedure (Life Technologies). Concentration of RNA was assessed using the Nanodrop and quality of RNA were assessed with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) or Caliper LabChip GX Analyzer.
Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer using UDI-adapter and UMI Second- Strand Synthesis modules (Lexogen). The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA). The libraries were quantified by fluorometry on a Qubit fluorometer (Life Technologies) and pooled in equimolar ratios. Libraries were sequenced in one lane of the HiSeq 4000 sequencer (Illumina, San Diego, CA) with single-end 100 bp reads.
3'-tag RNAseq

treatment_protocol: Ovarian cortex pieces were cultured with 100 ng/ml of recombinant human FSH or vehicle (water) and harvested after 2 or 4 days and snap frozen in liquid nitrogen before total RNA isolation. Day 0 control samples were obtained at the day each culture was initiated and immediately frozen to serve as uncultured controls.

value: bovine ovarian cortex

value: FSH

tag: day of culture


title: Rep 3 Vehicle Day 4 [Vehicle_D4_3]

source_name: bovine ovarian cortex_Vehicle Day 4

value: vehicle


title: Control_3

value: control


title: N2_hns_#1

description: bristol wildtype N2 fed hns mutant E. coli

value: Wild type


title: Control_2


title: Rep 3 FSH Day 2  [FSH_D2_3]

source_name: bovine ovarian cortex_FSH Day 2


title: Human_TLM-8-cell_RNA-Seq_rep3

city: Chongqing

first: Jingyu

last: Li

address: #64, Jintang street

institute: Chongqing Reproductive and Genetics Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were trimmed to remove the adapter sequences and low quality bases.
For RNA-seq, the cleaned reads were aligned to the human hg38 reference using Tophat (v2.4.0) with default settings. And for WGBS, bisulfite-converted reads were aligned to the human refference genome (hg38) using Bismark software (v0.7.6).
For RNA-seq, RSEM (v1.3.0) with default parameters was further used to quantify transcription levels (TPM, Transcripts Per Kilobase of transcript per Million mapped reads) of annotated genes. And for WGBS, methylation level was estimated using SeqMonk (v1.39.0).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM or methylation values for each Sample

source_name: Preimplantation embryo

extract_protocol:
After removing the zona pellucida, embryos were washed with PBS and incubated in lysis buffer.
The samples were collected in tubes with lysis component and ribonuclease inhibitor. Then we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2 kb. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection.

value: Preimplantation embryo

value: 8-cell embryo

tag: incubator

value: TLM


title: Control_1

tag: cell type

value: GBM patient-derived cells


title: Rep 3 Day 0 [Day0_3]

source_name: bovine ovarian cortex_Day 0


title: Rep 2 FSH Day 4 [FSH_D4_2]


title: Rep 3 Vehicle Day 2 [Vehicle_D2_3]

source_name: bovine ovarian cortex_Vehicle Day 2


title: Human_TLM-8-cell_RNA-Seq_rep2


title: Rep 2 Vehicle Day 4 [Vehicle_D4_2]


title: CD8+ T 48ko 12h

value: Lrch1 KO

value: Splenic CD8+ T cells

value: Stimulated with anti-CD3/CD28 for 12h.


title: Human_TLM-8-cell_RNA-Seq_rep1


title: Human_SI-8-cell_RNA-Seq_rep3

value: SI


title: Rep 2 FSH Day 2 [FSH_D2_2]


title: aa3 mutant_rep2

city: Busan 46241, Republic of Korea

first: Yuna

last: Oh

address: Busandaehakro63bun-gil, 2

department: Department of Integrated Biological Science

institute: Pusan national university

data_processing:
The quality of the obtained data was checked by determining the phred quality score using FastQC v0.11.5.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.32, then mapped to the whole genome of M. smegmatis using bowtie v1.1.2 with default setting.
Mapped reads per annotated gene were counted by Bam2readcount.
Counted values were nomalized in the RPKM method.
Genome_build: Mycobacterium smegmatis MC2 155 (GCF_000015005.1_ASM1500v1)
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each sample

organism: Mycolicibacterium smegmatis

source_name: in vitro aerobic culture of the aa3 mutant strain

growth_protocol: The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.

extract_protocol:
The strains were grown until an optical density at 600 nm reached 0.45 to 0.5. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users. Six ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina instrument.
The RNA sequencing libraries were created using a TruSeq RNA Sample Prep Kit v2 (Illumina) with the standard low-throughput protocol.

tag: strain background

tag: genotype/variation

tag: growth condition

value: in vitro aerobic culture


title: Rep 2 Day 0  [Day0_2]

city: Utrecht

tag: tissue


title: N2_hns_#2

tag: strain

value: fed hns


title: Rep 2 Vehicle Day 2 [Vehicle_D2_2]


title: WT_rep3

source_name: in vitro aerobic culture of the wild type strain

value: wild type


title: aa3 mutant_rep1


title: Rep 1 FSH Day 4 [FSH_D4_1]


title: WT_rep2


title: Human_SI-8-cell_RNA-Seq_rep1

tag: developmental stage


title: Human_zygote_RNA-Seq_rep3

value: zygote


title: WT_rep1


title: N2_BW_#1

description: bristol wildtype N2 fed BW25113 E. coli

value: fed BW

value: whole body


title: N2_BW_#2

description: bristol wildtype N2 fed BW25113 E. coli


title: Rep 1 Vehicle Day 4 [Vehicle_D4_1]

value: bovine ovarian cortex

value: vehicle


title: MYB134RNAi-24-3

city: Victoria

first: C. Peter

last: Constabel

state: British Columbia

address: 3800 Finnerty Rd

department: Biology

country: Canada

institute: University of Victoria

data_processing:
The alignment of sequence was performed using HISAT2 (version 2.1.0). A P. tremula genome sequence (version 1.0) was used as reference genome (Sjödin et al., 2009; http://popgenie.org/).
Cufflinks and Cuffmerge (version 2.2.1.OSX_x86_64) were used to generate a reference transcriptome and use a Populus tremula transcriptome as reference (http://popgenie.org/).
Htseq-count (version 0.6.1) was used to calculate the raw count. DESeq package in R (version 3.4.0) was used to perform the differential expression analysis.
Genome_build: P. tremula v1.0
Supplementary_files_format_and_content: Raw counts in tab-delimited text files.

organism: Populus tremula x Populus tremuloides

source_name: leaves

growth_protocol: Hybrid poplar were transferred from tissue culture to a mist chamber and grown for one month. They were then transferred to a greenhouse for two months. For sunlight treatment, plants were moved outdoors and exposed to sunlight for two weeks.

extract_protocol:
Leaves of wild type and transgenic poplars were harvested. Total RNA was extracted from frozen poplar hairy roots or ground leaf powder using the modified cetyl trimethyl ammonium bromide method for polyphenol-rich plant tissue described by Muoki et al. (2012).
MagJET enrichment kit (ThermoScientific) was used to purify mRNA from crude RNA. The mRNA was fragmented by heating the samples at 94℃ for 5 minutes. To make cDNA libraries with adaptors NEBNext ultra RNA Library Prep Kit for Illumina (NEB) was used. GeneJET NGS Cleanup Kit (ThermoScientific) was used to clean the extra adaptors. Primers for RNA-Seq were added to cDNA using NEBNext Multiplex Oligo kit (NEB). MagJET NGS Cleanup and Size Selection kit (ThermoScientific) was used to select DNA fragments around 350bp. Twelve libraries with same concentration (250ng/ul) each were pooled and sent to McGill University/GenomeQuébec.

treatment_protocol: To construct the MYB134RNAi vector, a 169 bp fragment of the MYB134 coding sequence was cloned and inserted into a pTRAIN vector is sense and antisense orientation. The sense and antisense MYB134 fragments together with a ubiquitin promoter and terminator sequence were then subcloned into the pMDC32 binary vector. The pMDC32 vector was transformed into the Agrobacterium tumefaciens strain GV3101::pMP90 by electroporation. P. tremula x P. tremuloides (clone INRA 353-38) leaves were excised and transformed.

value: MYB134 RNAi

value: leaves

value: sunlight-exposed


title: aa3 mutant_rep3


title: Rep 1 FSH Day 2 [FSH_D2_1]

value: FSH


title: Human_zygote_RNA-Seq_rep2

value: Preimplantation embryo


title: Human_zygote_RNA-Seq_rep1


title: BN207 low potassium rep3

city: Baoding

first: KE

last: XU

state: Hebei

institute: Hebei agricultural university

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Genome_build: Triticum_aestivum (Chinese Spring) IWGSC RefSeq v1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: Wheat roots

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 Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA using poly-T oligo-attached magnetic beads by two rounds of purification. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA).

tag: phenotype

value: K-deficiency sensitive

value: Wheat roots

value: low potassium


title: Rep 1 Vehicle Day 2 [Vehicle_D2_1]


title: Rep 1 Day 0  [Day0_1]


title: WT-3

value: WT


title: BN207 low potassium rep2


title: MYB134RNAi-24-2


title: 494 PDA

city: Baltimore

first: Jacquelyn

middle: W

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

description: Test

data_processing:
P-values for differential expression statistics were generated and adjusted for multiple hypothesis testing using ExpressionSuite (Thermo Fisher Scientific).
All Ct values were normalized to endogenous levels of U6 snRNA.  Fold changes were quantified utilizing the Ct method in which all PanIN groups were normalized to the normal group (normal ducts isolated from WT C57BL/6 mice).

label: FAM

source_name: pancreata

label_protocol: converted to cDNA using the TaqMan MicroRNA Reverse Transcription Kit (Thermo Fisher Scientific) with Megaplex RT Primers Rodent Pool A and B (Thermo Fisher Scientific).  cDNA was preamplified 18 cycles using the TaqMan PreAmp Master Mix (Thermo Fisher Scientific) and Megaplex PreAmp Primers Rodent Pool A and B (Thermo Fisher Scientific)

growth_protocol: Pancreata were isolated from aged KPC (4-20 weeks) or WT C57BL/6 mice and fresh-frozen in Tissue-Tek OCT (Sakura Finetek USA) or formalin-fixed and paraffin-embedded (FFPE)

extract_protocol: RNA was extracted from fresh-frozen LCM samples using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific)

treatment_protocol: Normal, low grade PanIN1, high grade PanIN2/3, and PDA tissue were microdissected using LCM (Leica LMD7000)

tag: sample type

value: PDA

tag: sample preparation

value: fresh-frozen LCM samples

value: KPC


title: Human_SI-8-cell_RNA-Seq_rep2

value: 8-cell embryo

value: SI


title: 467 PDA

description: Test


title: WT-2


title: BN207 normal potassium rep3

tag: treatment

value: normal potassium


title: BN207 normal potassium rep2


title: BN207 low potassium rep1


title: 414 P2/3

description: Test

value: High Grade P2/3


title: WT-1


title: BN207 normal potassium rep1


title: KN9204 low potassium rep3

value: K-deficiency tolerant


title: 298 PDA

description: Test


title: 307 PDA

description: Test


title: 1665 N

description: Control

value: Normal

value: WT C57BL/6


title: 1663 N

description: Control


title: 1664 N

description: Control


title: shINCA1-IFN3

data_processing:
The quality of produced data is determined by the phred quality score at each cycle. Box plot containing the average quality at each cycle is created with FastQC.
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. Trimmed reads are mapped to reference genome hg19 with HISAT2
Known genes and transcripts are assembled with StringTie based on reference genome model. After assembly, the abundance of gene/transcript is calculated in the read count and normalized value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for a sample.
Genome_build: hg19
Supplementary_files_format_and_content: text files include read count for each Sample

extract_protocol:
RNA was harvested from cells using RNeasy Mini Kit (Qiagen Cat#74104). Illumina TruSeq stranded mRNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: shRNA targeting INCA1

value: interferon gamma

value: MG Glioblastoma Cell Line


title: KN9204 normal potassium rep3


title: 1650 N

description: Control


title: KN9204 low potassium rep2


title: MYB134RNAi-24-1

value: MYB134 RNAi

value: leaves

value: sunlight-exposed


title: shINCA1-IFN2


title: KN9204 normal potassium rep1

value: Wheat roots


title: 1648 N

description: Control


title: 1560 REACTIVE

description: Test

value: Reactive


title: 428 PDA

description: Test

value: PDA

value: fresh-frozen LCM samples


title: TC5.P2

type: genomic

city: Groningen

first: Steven

last: de Jong

address: Hanzeplein 1

department: Medical Oncology

institute: University Medical Center Groningen

hyb_protocol: DNA processing, tagging and hybridization to the CHIP were performed according to the manufacturer's protocol (Illumina).

data_processing:
Genomic DNA extracted from testicular cancer PDX tumors was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina) with extra custom content.
Primary assessment and SNP call rate quality control of SNP intensity output files were performed using GenomeStudio software (Illumina).

label: Cy3 and Cy5

source_name: TC PDX tumor (TC5), mouse passage 2

extract_protocol: Simultaneous isolation of DNA and RNA from the same sample was done using the AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany).

treatment_protocol: DNA and RNA from testicular cancer PDX tumours of different generations were isolated from snap frozen tumour tissue.

tag: gender

value: male

value: Testicular cancer (TC)


title: KN9204 low potassium rep1

value: low potassium


title: shINCA1-IFN1

tag: passages


title: TC5.P1

scan_protocol: DNA processing, tagging and hybridization to the CHIP were performed according to the manufacturer's protocol (Illumina).

source_name: TC PDX tumor (TC5), mouse passage 1


title: shINCA1-C3

value: control

tag: cell line


title: 1556 P1

description: Test

value: Low Grade P1

value: KPC


title: TC5.P0

source_name: TC PDX tumor (TC5), mouse passage 0

label_protocol: DNA processing, tagging and hybridization to the CHIP were performed according to the manufacturer's protocol (Illumina).


title: 1548 P2/3

description: Test

value: High Grade P2/3


title: shINCA1-C2

value: shRNA targeting INCA1


title: shINCA1-C1


title: TC4.P2

source_name: TC PDX tumor (TC4), mouse passage 2


title: 1546 P2/3

description: Test


title: shCTRL-IFN3

value: shRNA control

value: interferon gamma


title: 1460 P1

description: Test


title: KN9204 normal potassium rep2

value: K-deficiency tolerant

value: normal potassium


title: 1457 P1

description: Test


title: TC4.P0

source_name: TC PDX tumor (TC4), mouse passage 0


title: 1446 P2/3

description: Test


title: shCTRL-IFN1

source_name: Brain

value: MG Glioblastoma Cell Line


title: 1437 P2/3

description: Test


title: TC1.P1

source_name: TC PDX tumor (TC1), mouse passage 1


title: TC1.P0

source_name: TC PDX tumor (TC1), mouse passage 0


title: shCTRL-C2


title: shCTRL-C1


title: 1407 P1

description: Test


title: TC1.Pt

source_name: Primary TC tumor (TC1)


title: caseP2-placenta2

status: Public on Jul 28 2020

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

source_name: placenta

growth_protocol: Rapid autopsy was performed for samples collection.

extract_protocol:
RNA extraction from FFPE slides was done using the FormaPure Total nucleic acid extraction kit (C16675, Beckman Coulter) according to manufacturer instructions. Three 5 um thin tissue sections from areas devoid of acute inflammation were used per sample
The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Dual-indexed pooled libraries were sequenced on the Illumina NextSeq 500 platform using a 150 cycles kit with paired end read mode.

treatment_protocol: Samples were formalin fixed for 3 days prior to embedding in paraffin and sectioning.

tag: case

tag: tissue type

value: Formalin fixed paraffin embedded tissue


title: caseP3-placenta1


title: caseP4-placenta1


title: caseP3-placenta2


title: caseP1-placenta1


title: caseP1-placenta2


title: caseJ-lung

source_name: lung

value: J

tag: pool no


title: caseP2-placenta1


title: TC4.P1

source_name: TC PDX tumor (TC4), mouse passage 1

tag: cell type


title: TC1.P2

source_name: TC PDX tumor (TC1), mouse passage 2


title: shCTRL-IFN2


title: caseD-lung

value: D


title: caseC-lung

value: C


title: shCTRL-C3


title: caseG-lung

value: G


title: case9-lung5


title: caseE-lung

value: E


title: caseB-lung

value: B


title: 1433 P1

description: Test

value: fresh-frozen LCM samples


title: case9-lung4


title: case9-lung2


title: case8-lung5


title: case9-lung3


title: case9-lung1


title: case8-lung4


title: case8-lung3


title: caseI-lung

value: I


title: case8-lung2


title: case7-lung5


title: case8-liver1

source_name: liver


title: case8-bowel1

source_name: bowel


title: case8-heart1

source_name: heart


title: caseF-lung

value: F


title: case8-lung1


title: case7-lung1


title: case7-lung2


title: case6-lung5


title: caseA-lung

value: A


title: case6-lung1


title: case6-lung2


title: case6-lung3


title: case6-lung4


title: case11-kidney1

source_name: kidney


title: case11-lung3


title: case11-bowel1


title: case11-lung1


title: case11-lung2


title: case10-lung2


title: case10-lung1


title: case7-lung4


title: case7-lung3


title: caseH-lung

value: H


title: B2d1

first: Robbelien

last: Kooistra

address: Padualaan 8

department: Cell Biology

description:
Sample 4
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts

data_processing:
sequencing on a Nextseq500
paired end
Genome_build: mapped to reference transcriptome Hg19
Supplementary_files_format_and_content: counts

source_name: hiPSC derived NPCs/neurons

growth_protocol: For neuronal differentiation of hiPSC-derived NPCs, cells were thawed and quenched with Neuronal Expansion-XF Medium, centrifuged (200 g, 5 min), resuspended in Neuronal Plating-XF medium, and plated on 12 mm (~100k per well) or 18 mm (~200k per well) pre-coated glass coverslips in respectively a 24-wells or 12-wells plate at 37°C with 5% CO2. Coating of coverslips was performed directly before plating: coverslips were first incubated with ReadySet (45 min, 37°C; ax0041+, Axol Bioscience), washed four times with sterilized water, and incubated with freshly-thawed 1x SureBond (1h, 37°C; ax0041+, Axol Bioscience) in PBS. After 24 hours (day 1), the medium was fully replaced by Neuronal Maintenance-XF Medium (ax0032, Axol Bioscience), and after another 24 hours (day 2) by Neuronal Differentiation-XF Medium (ax0034, Axol Bioscience). Three days later (day 5), half of the medium was replaced by Differentiation-XF Medium. Next day (day 6), half of the medium was replaced by Neuronal Maintenance-XF Medium, again one day later (day 7), and every three days during further maintenance.

extract_protocol:
~100,000 hiPSC-derived NPCs were plated per well for bulk RNA sequencing samples. Prior to sample preparation, all equipment and surfaces were cleaned with RNaseZap (Sigma-Aldrich). Replicates of hiPSC-derived neurons were harvested at three different timepoints of differentiation (days 1, 3, and 7) with 200 µl Trizol (Invitrogen) per sample and stored at -80 °C until sequencing.
CEL-seq2 protocol, followed by Single Cell Discoveries’s adapted protocol for bulk samples
barcoding all samples during RT with CEL-seq barcodes

tag: age

tag: seqprimer

tag: commercial cell line


title: A2d7

description:
Sample 10
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts

source_name: hiPSC derived neurons


title: B1d3

description:
Sample 7
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: A1d1

description:
Sample 1
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: A1d7

description:
Sample 9
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: A2d1

description:
Sample 2
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: B1d1

description:
Sample 3
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: B2d7

description:
Sample 12
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: B1d7

description:
Sample 11
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: A1d3

description:
Sample 5
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: H2122 LYCAT shRNA 2

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Illumina Bcl2fastq 2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA mem v0.7.15
Raw counts were calculated using featureCounts v 1.5.1, given the gene annotation of mm10
3' RNA-seq reads were aligned to reference human genome hg19 using bowtie2. UCSC genes were used for annotation, and counts per gene were generated with featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: counts table (tab-delimited text)

source_name: H2122 cells

growth_protocol: 5% CO2, 37 degree.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H2122 with transfection of control shRN or LYCAT shRNA for 48 hours, the total cell mRNA from these cells were isolated and applied to array.

tag: genotype/variation

value: LYCAT shRNA


title: A2d3

description:
Sample 6
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: H2122 LYCAT shRNA 1


title: H2122 LYCAT shRNA 3


title: T2-4

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

description: microRNA

data_processing:
A Ct threshold of 30 was used for detectable level of expression.
MiRNAs were further filtered by removing those with no expression in any samples and samples were filtered that had < 10% of miRNAs detected.
Housekeeping miRNAs were the top 10 most stable miRNAs from the NormqPCR package_x0001_, which were used to normalize raw Ct values using ∆Ct normalization
Differential expression was calculated using limma
Matrix normalized worksheet reports normalized signal (against 10 most stable housekeeping genes).

label: TaqMan

source_name: Renal Cell Carcinoma

label_protocol: Quantification of miRNA was done using the TaqMan OpenArray, which profiles 754 known miRNAs using qPCR

extract_protocol: RNA was extracted using the RecoverAllTM Total Nucleic Acid Isolation Kit according to manufacturer’s instructions

tag: metastatic

value: No

tag: tumor stage

value: M

tag: tissue

value: Renal Cell Carcinoma


title: H2122 Control shRNA 1

value: shRNA control


title: T2-22

description: microRNA

value: Yes


title: T2-8

description: microRNA


title: H2122 Control shRNA 2


title: H2122 Control shRNA 3


title: case10-lung3

value: Formalin fixed paraffin embedded tissue


title: T2-26

description: microRNA


title: T2-14

description: microRNA


title: T2-6

description: microRNA


title: T2-2

description: microRNA


title: T2-3

description: microRNA


title: B2d3

description:
Sample 8
UMC-RK-b001_HM3JFBGX9_S9_R2.ReadCounts


title: T2-23

description: microRNA


title: T1-14

description: microRNA


title: T1-15

description: microRNA


title: T1-13

description: microRNA


title: T1-11

description: microRNA


title: T1-23

description: microRNA


title: T2-21

description: microRNA


title: T2-20

description: microRNA


title: T2-19

description: microRNA


title: T1-4

description: microRNA


title: T2-17

description: microRNA


title: T1-3

description: microRNA


title: T2-13

description: microRNA


title: T2-10

description: microRNA


title: T2-1

description: microRNA


title: T1-24

description: microRNA


title: T2-11

description: microRNA


title: T1-22

description: microRNA


title: T2-12

description: microRNA


title: T1-21

description: microRNA


title: T1-20

description: microRNA


title: T1-18

description: microRNA


title: T1-19

description: microRNA


title: T2-9

description: microRNA


title: T1-17

description: microRNA


title: T1-12

description: microRNA


title: T1-10

description: microRNA


title: T1-9

description: microRNA


title: Brain: BD1

city: Riverside

first: Christi Ann

last: Scott

address: 3401 Watkins Drive

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

data_processing:
For HiSeq2000: RTA v1.7, CASAVA v1.7 used for basecalling. For NextSeq500: RTA 2.0 used for basecalling.
Reads aligned to the latest release of each of the genomes used (dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome) and quantified with kallisto (Version: kallisto 0.43.1, Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519) . Only libraries for which we obtained >75 % alignment were used for downstream analysis.
Transcript counts were summarized to gene-level using tximport package (version 1.4.0).
For any instances of detected batch effects, we removed unwanted variation using RuvR in the RuvSeq package (version_1.10.0).
Differentially expressed gene (DEG) analysis was performed with the edgeR package (version 3.18.1), using low count filtering (cpm >0.5) and TMM normalization.
Genome_build: dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome
Supplementary_files_format_and_content: tab-delimited .tsv files including counts TPM normalized read counts for each sample

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2 was used with total RNA for the construction of sequencing libraries.

tag: strain

tag: genotype

value: wild type

value: 2 months

tag: Sex

value: male

value: 1% diacetyl in PO, 5days

value: brain


title: Brain: BD2

tag: treatment


title: T1-6

description: microRNA

tag: gender


title: T1-5

description: microRNA


title: T1-7

description: microRNA


title: T1-8

description: microRNA


title: T1-2

description: microRNA


title: T1-1

description: microRNA


title: Brain: MBD_A

value: 0.1% diacetyl in PO, 5days


title: Brain: MBC_B

value: PO, 5 days (control)


title: Lung: LD1

source_name: Lung

value: lung


title: Lung: MLC_A


title: Lung: MLC_B


title: Lung: MLD_A


title: Brain: MBD_B

source_name: Brain


title: Lung: LC2


title: Brain: MBC_A


title: F. trinervia_ctrl (HighLight) 3

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Transcript de novol assemble using Trinity
Funcatonal annotation of transcripts by searching orhtolog in F. ramosissima gene reference.
mapping RNA-seq reads to assembled transcripts to quantify the abundance of transcript using RSEM
Call differentiall expressed genes between ctrl and ABA treatments using edgeR package.
Supplementary_files_format_and_content: xlsx file contains the transcript abundance of annotated genes
Supplementary_files_format_and_content: fasta file contains the de novo assembled transcripts

organism: Flaveria trinervia

source_name: newly expanded mature leaf

growth_protocol: For low high light experiment, Plants were grown in growth chamber with light intensity to be 200 μmol m-2 s-1 and temperature to be 22oC, 16h/8h light/ dark duration, 70% humidity. . Plant were watered twice a week and fertilized weekly.

extract_protocol:
Total RNA was isolated following the protocol of the PureLInkTM RNA Mini (ThermoFisher Scientific)
Next-generation RNA-seq was performed in the Illumina platform in the pair-ended mode with read length150 bp.

treatment_protocol: The light intensity of hight light condition is 1400 μmol m-2 s-1, and that of control is 500 μmol m-2 s-1.

value: leaf


title: F. trinervia_HighLight 1


title: F. trinervia_HighLight 2


title: Brain: BC2


title: Brain: BC1


title: Lung: MLD_B


title: F. trinervia_ctrl (HighLight) 2


title: F. trinervia_HighLight 3


title: Lung: LC1


title: Lung: LD2


title: RNA-seq wt rep1

city: philadelphia

first: Fange

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

data_processing:
Raw reads were mapped to reference genome (hg38) using Hisat2
Afterward, genomic alignments were counted in R using GenomicAlignments package
Gene expression levels were normalized using DEseq2

source_name: HEK 293T

growth_protocol: HEK 293T cells were cultured in Dulbecco’s Modified Eagle Medium (GIBCO, 11995065) supplemented with 10% FBS (GIBCO, 26140-079) and 1% Pen/Strep (Corning, 30-002-CI) in 37 °C, 5% CO2¬ incubator.

extract_protocol:
Total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen). mRNA was fragmented by sonication.
The library was constructed using TruSeq stranded mRNA samples preparation kit from Illumina.


title: RNA-seq E85A rep1

value: E85A variant overexpression


title: RNA-seq wt rep2