title: H358_PD-L1_Unsorted_LibraryA_Replicate2

description:
Unsorted Library A Replicate 2
genomic DNA PCR product

data_processing:
Raw reads were trimmed using inhouse scripts to extract the exact sgRNA
Trimmed reads were mapping to library using bowtie 1.0.1, require perfect, unique match
Summarize bowtie results to sgRNA count using inhouse script
Normalize each sample to total reads, and combine library A and library B
Call significant gene using RIGER
Genome_build: hg19
Supplementary_files_format_and_content: excel sheet containing total normalized sgRNA counts in each sample.

source_name: human lung cancer H358 cells

growth_protocol: Cell lines used in this study were obtained from ATCC and cultured under standard conditions.

extract_protocol:
DNA was extracted from the unsorted cells using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions. Extractions were performed on 4x10^7 cells using 5x10^6 cells per column to ensure enough gDNA for 300X coverage of the library. DNA was eluted by adding 125 µL of water to each column. The same eluate was added back to the column for a second elution. The DNA concentration in the final eluate was assessed using the Qubit dsDNA BR assay kit (Thermo Fisher). To facilitate maximum recovery of gDNA from the sorted cells, a previously described method (Largaespada, et al., 2008) was used with the following modifications: Sorted cell pellets were resuspended in 500 µL of tissue lysis buffer, consisting of 460 µL of STE buffer [1 mM EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), 100 mM NaCl] supplemented with 10 µL of 0.5 M EDTA, 10 µL of proteinase K [10 mg/mL in TE buffer containing 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA], and 20 µL of 10% SDS. Pellets were digested overnight at 55°C while shaking at 1000 rpm on a Thermomixer (Eppendorf). The following day, 5 µL of 2 mg/mL RNase A was added to each tube and incubated at 37°C for 1 hr while shaking at 1000 rpm. Extractions were performed with an equal volume of pH 7.9-buffer saturated phenol, followed by phenol:chloroform:isoamyl alcohol (25:24:1), followed by chloroform. 20 µg of glycogen (Roche) and 1.5 mL of 100% ethanol was added to each tube and DNA was precipitated at -80°C for 1 hr followed by centrifugation at 18,000 g for 10 min at 4°C. Pellets were washed with 1 mL of 75% ethanol, dried, and resuspended in 21 µL of water by incubating at 37°C for a minimum of 4 hrs. DNA concentration was determined with the Qubit dsDNA BR assay kit.  Methods to prepare PCR amplicon libraries for deep sequencing were adapted from a previously published protocol (Shalem, et al., 2014). All primer sequences are provided in Supplementary Table 8. For unsorted cells, an initial round of PCR (PCR I) was performed using 6.6 µg of gDNA per 100 µL PCR reaction. To maintain 300X coverage, 20 reactions were assembled for each sample. For sorted cells, all extracted gDNA for a given sample was distributed into two 100 µL reactions. In both cases, 18 cycles of amplification were performed using Herculase II Fusion polymerase (Agilent). All reactions for a given sample from PCR I were then pooled together and a second round of PCR (PCR II) was performed to add the necessary adapters for Illumina sequencing. Due to variable PCR efficiency between samples, the cycle number for PCR II was adjusted so that each library was amplified in a 50 µL reaction to a common endpoint with respect to DNA quantity (approximately 50 ng of DNA library in a 50 µL PCR sample). DNA was purified for sequencing using AMPure XP beads (Agencourt) according to the manufacturer’s instructions with the following modifications: Each 50 uL PCR II reaction was mixed with 25 uL of beads and incubated for 5 minutes. Magnetic separation was used to collect the supernatant. The supernatant was mixed with 90 µL of beads and incubated for 5 minutes. The supernatant was collected and discarded. Beads were washed twice with 200 µL of 70% ethanol and then dried for approximately 12 minutes. Bound DNA was eluted from the beads using 40 µL of water.
Constructed as per Shalem et al, Science 2014 and Golden et al, Nature 2017
Genome-scale CRISPR-Cas9 Screen (GeCKO)

treatment_protocol: Two days prior to sorting, ten 15 cm dishes with 1.2x10^7 cells per dish were seeded for each sample. On day of sorting, cells were stained with an APC-PD-L1 antibody as per Biolegend instruction manual.


title: H358_PD-L1_Unsorted_LibraryA_Replicate1

status: Public on Feb 01 2020

type: SRA

city: Dallas

first: Shruthy

last: Suresh

state: Texas

address: 6000 Harry Hines Blvd NA6.300

department: Molecular Biology

country: USA

institute: UT Southwestern Medical Center

description:
Unsorted Library A Replicate 1
genomic DNA PCR product

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line


title: metastatic neuroendocrine tumor

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

description: metastatic lesion

library_source: transcriptomic

data_processing:
single-cell RNA-sequencing data was pre-processed using Cell Ranger 3.0.1 using default settings from 10X Genomics.
Downstream bioinformatic analysis was performed using Seurat 3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: gzipped file format containing "filtered_feature_bc_matrix" folder contents from cellranger outputs

molecule: total RNA

source_name: liver

extract_protocol:
Both primary neuroendocrine tumor and metastatic liver lesion were processed simulatneously, to avoid batch effects. Single cell suspensions were prepared via both mechanical and enzymatic digestion protocols (collagenase I, DNAseI and TrpLE) .Viable cell count was determined using trypan blue exclusion and a total of 10,000 cells per sample were loaded onto the 10X microfluidic chip.  mRNA from individual cells were captured and tagged with barcodes using 10X-Genomics microfluidic platform. cDNA was then prepared in the encapsulated gel bead emulsion and the emsulion was broken for further library preparation.
Barcoded cDNA libraries were prepared according to manufacturer's instructions, 10X Genomics.

tag: disease diagnosis

value: metastatic neuroendocrine tumor

tag: differentiation status

value: well-differentiated

tag: tissue

value: liver


title: BS-seq replicate2 of CR stage 1

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

data_processing:
For RNA-seq analysis, HISAT (v0.1.6) was used to map clean reads to rice reference genome (RGAP version 7.0). Cufflinks (v2.2.1) and Cuffdiff (v2.2.1) were used to splice transcripts and find differential expressed genes. A strict criteria (fold change>4, q value<0.01) was used to filter differentially expressed genes. For BS-seq analysis, clean reads were mapped to rice reference genome (RGAP version 7.0) by BS-seeker2 (v2.1.8). MethylKit (v3.6) was used to identify differentially methylated regions (DMRs) with win.size equal to 1000 and step.size equal to 100. To avoid bins with few cytosines, we selected bins with at least four cytosines and covered by at least ten reads. Q value less than 0.01 as well as absolute methylation difference of 0.7, 0.5, and 0.1 for CG, CHG, and CHH, respectively, were selected as Tan et al. (2016) suggested. Adjacent bins with overlapping were merged into one DMR.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: bed files are tab-delimited text files containing gene expression profile information
Supplementary_files_format_and_content: diff.txt files are blank-delimited text files containing differentially methylated region information

organism: Oryza sativa Japonica Group

source_name: rice crown root initials

growth_protocol: Rice (Oryza sativa spp japonica) material used in this study is from ‘Hwayoung’ (HY) background. For germination culture, seeds were surface-sterilized and germinated in medium containing 0.8% agar supplemented with 3% (w/v) sucrose at 28°C (in light) and 24°C (in dark) with a 14-h-light/10-h-dark cycle. For growth in field, germinated rice seedling was transferred to greenhouse at 25–30 °C under 14-h-light followed by 10-h-dark.

extract_protocol:
Twelve µm sections of crown, lateral, and embryonic root initials tissues were put onto RNase-free PEN membrane glass slide (Carl Zeiss, 415190-9041-000). Lasser catpture microdissection (LCM) was performed using the ZEISS PALM MicroBeam system.The RNA of dissected tissues was isolated with RNeasy Plus Micro Kit (Qiagen, 74034). The DNA of dissected tissues was isolated with DNA Micro Kit (Qiagen, 56304).
For RNA-seq library construction, Smart-seq v4 Ultra Low Input RNA Kit (Takara, 091817) was used for amplifying purified mRNA. The amplified DNA was sheared to 200-500 bp range by sonication and purified with AMPure XP beads. 1 μg DNA was used for following library construction. Purified DNA was end repaired, added with adenylate in the 3’ ends, ligated with adapters, and amplified with PCR for 7-8 cycles with the reagents from TruSeq® ChIP Sample Preparation Kit (Illumina). For BS-seq library construction, Bisulfite conversion was performed by utilizing Zymo EZ Methylation Direct Kit (Zymo, D5020). Converted DNA was purified with PureLink PCR Purification Column Kit (Invitrogen, K210012) with minor modification (add M-Desulphonation Buffer to the column and hold for 15 mins before washing) as Clark et al. (2017) suggested. The converted ssDNA was then used for following BS-seq libraries construction with TruSeq® DNA Methylation Kit (Illumina).

value: stage 1 of crown root initials

tag: genotype/variation

value: Hwayoung cultivar


title: H358_PD-L1_Low_LibraryB_Replicate2

description:
PD-L1 Low GeCKO Library B Replicate 2
genomic DNA PCR product


title: db/db_IF_10A

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

institute: BGI

data_processing:
Filtering and trimming the reads using Trimmomatic v0.38 with parameters “HEADCROP:15 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:20”.
Clean reads were mapped to the Mus musculus genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6 ) using Hisat2 v2-2.1.0 with default parameters.
The reads of each sample were then assembled into transcripts and compared with reference gene models using StringTie v1.3.4d.
Merging the 31 transcripts to obtain a consensus transcript using StringTie-Merge program.
The gene expression FPKM values were calculated using StringTie based on the consensus transcript.
DEG analysis was performed using Ballgown v2.12.0.
Unsupervised co-expression network analysis of all genes was performed using R package WGCNA v1.64 with ‘‘signed’’ and “bicor” parameter. Using a best soft threshold power of 6 obtained from WGCNA function ‘pickSoftThreshold’.
Supplementary_files_format_and_content: FPKM

organism: Mus musculus

source_name: hippocampus

extract_protocol:
A phenol-chloroform extraction
RNA libraries were prepared for sequencing using standard BGI-500 protocols

tag: strain

tag: age

value: hippocampus

tag: genotype

value: db/db


title: BS-seq replicate1 of CR stage 1


title: H358_PD-L1_Low_LibraryB_Replicate1

description:
PD-L1 Low GeCKO Library B Replicate 1
genomic DNA PCR product


title: db/db_IF_9A


title: BS-seq replicate2 of LR stage 0

source_name: rice lateral root initials

value: cell layer from where lateral root initiates  (stage0)


title: primary neuroendocrine tumor

description: primary tumor

source_name: small intestine

value: primary neuroendocrine tumor

value: small intestine


title: BS-seq replicate2 of CR stage 0

value: cell layer from where crown root initiates (stage0)


title: H358_PD-L1_Unsorted_LibraryB_Replicate2

description:
Unsorted Library B Replicate 2
genomic DNA PCR product


title: H358_PD-L1_Low_LibraryA_Replicate2

description:
PD-L1 Low GeCKO Library A Replicate 2
genomic DNA PCR product


title: BS-seq replicate1 of CR stage 0


title: db/db_IF_8A


title: db/db_IF_7A


title: H358_PD-L1_Low_LibraryA_Replicate1

description:
PD-L1 Low GeCKO Library A Replicate 1
genomic DNA PCR product


title: H358_PD-L1_Unsorted_LibraryB_Replicate1

description:
Unsorted Library B Replicate 1
genomic DNA PCR product


title: RNA-seq replicate2 of ER stage 3

description: all-genes-spatiotemporal-expression-matrix.txt

source_name: rice embryonic root initials

value: stage 3 of embryonic root initials


title: H358_PD-L1_High_LibraryB_Replicate2

description:
PD-L1 High GeCKO Library B Replicate 2
genomic DNA PCR product


title: RNA-seq replicate1 of ER stage 3


title: H358_PD-L1_High_LibraryB_Replicate1

description:
PD-L1 High GeCKO Library B Replicate 1
genomic DNA PCR product


title: db/db_IF_5A


title: db/db_IF_11A


title: H358_PD-L1_High_LibraryA_Replicate2

description:
PD-L1 High GeCKO Library A Replicate 2
genomic DNA PCR product


title: db/db_IF_4A


title: RNA-seq replicate2 of ER stage 2

value: stage 2 of embryonic root initials


title: RNA-seq replicate1 of ER stage 2


title: H358_PD-L1_High_LibraryA_Replicate1

description:
PD-L1 High GeCKO Library A Replicate 1
genomic DNA PCR product


title: db/db_IF_2A


title: RNA-seq replicate2 of ER stage 1

value: stage 1 of embryonic root initials


title: db/db_IF_1A


title: db/db_10A


title: L2G a2si III

city: Chicago

first: Huiping

last: Liu

state: IL

address: 303 E Superior

institute: Northwestern University

data_processing:
Read trimming: cutadapt
Genome alignment: STAR
Read counting: Htseq
Differential expression analysis: DESeq2
Genome_build: hg38

source_name: breast cancer cell line

growth_protocol: Cells were routinely cultured in DMEM high glucose medium supplemented with 10% FBS and 1% PS.

extract_protocol:
Trizol protocol was followed for RNA extraction and RNA was resuspended in RNAse free water.
TruSeq Total RNA-Seq Library Prep

treatment_protocol: Cells were transfected with dharmafect and siRNA oligos (control and ITGA2).

value: breast cancer cell line

value: ITGA2 knockdown


title: db/db_9A


title: ChIPseq_Par_H3K4me3_REP2

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

description:
MDAMB231_Par_H3K4me3_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.32
Trimmed reads were aligned using Bowtie2 v2.3.4.3 to hg19 using standard parameters and a maximum fragment length of 2000
Duplicate reads were determined using Picard tools v2.18.21
Bam files were filtered using samtools -F 1804
For consensus peak calling filtered bam files were merged. Peak calling was performed using MACS2 v2.1.2 with the option --broad.
Motif finding was performed using HOMER v4.10.
Reads that fell within consensus peaks were determined using featureCounts
DESeq2 was used to determine differential histone signal
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (merge of replicates for each IP and input), bed (consensus peak for each IP), txt (DESeq2 results and raw counts)

source_name: MDA-MB-231 breast cancer cell line

growth_protocol: Cells were grown in monolayer in DMEM + 10% FBS + Penicillin-streptomycin at 37ºC, 5% CO2 for 3 days

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min. Chromatin was prepared and immunoprecipitated as previously described (Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park IH, Kim TH: Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Rep 2015, 13(7):1444-1455.).
DNA libraries were prepared using ThruPLEX DNA-seq Kit (Takara)

tag: cell type

value: mammary gland/breast epithelial cell

tag: target molecule


title: ChIPseq_Par_H3K4me3_REP1


title: ChIPseq_Par_input

value: input


title: RNA-seq replicate2 of ER stage 0

value: globular embryo  (stage0)


title: L2G control si III

value: knockdown control


title: RNA-seq replicate1 of ER stage 1


title: db/db_8A


title: RNA-seq replicate1 of ER stage 0


title: ChIPseq_Par_H3K27ac_REP2

description:
MDAMB231_Par_H3K27ac_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K27ac_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K27ac_merge_peaks.broadPeak.counts.txt


title: 231 a2si II


title: db/db_IF_6A


title: RNA-seq replicate2 of LR stage 3

value: stage 3 of lateral root initials


title: 231 control si II


title: ChIPseq_Par_H3K27ac_REP1


title: db/db_7A


title: RNA-seq replicate1 of LR stage 3

value: Hwayoung cultivar


title: ChIPseq_LM_input

source_name: MDA-MB-231 breast cancer cell line lung metastatic variant

value: MDA-MB-231 LM2


title: 231 a2si I


title: db/db_6A

value: hippocampus

value: db/db


title: RNA-seq replicate2 of LR stage 2

value: stage 2 of lateral root initials


title: db/db_5A


title: HTE_1

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BosTau6 whole genome using bwa-0.7.7 with default parameters.
enrich information of peaks was analysised using MACS2
Genome_build: Angus cattle(BosTau8,A two-week-old female calf was referred to the Clinic for Ruminants at the Vetsuisse Faculty, University of Bern, Switzerland,Genome infomation can be downloaded from ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/bigZips/chromFa.tar.gz)
Supplementary_files_format_and_content: tab-delimited text files include peaks information of Angus cattle.

organism: Bos taurus

source_name: Angus cattle

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA purification kit (Promega, Madison, WI). DNA concentrations were measured by the Qubit dsDNA Broad-Range Assay (Invitrogen, Carlsbad, CA). The MBD-seq method was used to identify methylated DNA regions and elution of the captured methylated DNA was done using three salt gradients, namely low, medium and high concentrations as our previous report [48]. MethylCap kit (Diagenode，Denville, NJ) was used to obtain DNA containing methylated CpGs. Briefly, DNA was extracted and dissolved to reach 0.1μg/μl for a final volume of 40 μl in a 1.5 ml tube. The DNA was sheared into 300-500 bp fragments using the Bioruptor® Sonicator (Diagenode) and visualized on an agarose gel to verify the size of the resultant segments. A 141.8 μl capture reaction mix containing 12 μl of sheared DNA and lacking the MethylCap protein was prepared. From this preparation, 119 μl of capture reaction mix was incubated with 1 μl of diluted MethylCap protein at 40 rpm on a rotating wheel for 2 hours and at 4°C to allow the interaction.  The remaining solution (22.8 μl) was used as an input sample. Magnetic beads captured methylated DNA. Unbound DNA was washed off and the eluted DNA collected. For the elution, 150 μl of low, medium, and high concentration elution buffer was used serially per capture. These three elutions are corresponding to high, medium, and low methylation parts of the whole genome, respectively [37]. All fractions and input were purified using the MiniElute PCR Purification Kit (QIAGEN, Valencia, CA). Quantitative PCR (qPCR) (iCycler iQ PCR system, Bio-Rad, Hercules, CA) was performed in duplicate for each sample to test the enrichment efficiency. Method 2-∆∆Ct was applied to determine relative fold enrichments and compared enrichment values of a positive TGFB3 to a negative primer pair MON2, between experimental (methyl DNA) and reference (input DNA) samples.
The sequencing libraries  were constructed as follows: NEBNext® End Repair Module (NEB, Ipswich, MA) was used for the end repair of the fragmented methylated DNA, a 3’ A was added using DNA Polymerase I, Large (Klenow) Fragment (NEB), then a pair of Solexa adaptors (Illumina, San Diego, CA) was ligated to the repaired ends by T4 ligase (Promega). Filtration in a 2% agarose gel was used to select fragments (DNA plus adaptors) from 200 to 500bp. PCR enriched purified DNA templates were amplified by Phusion® Hot Start High-Fidelity DNA Polymerase (NEB). After purification, DNA quality was examined. The DNA library was diluted and the concentration double-checked using the Qubit assay (Life Technology). A total of 12 libraries were constructed for three gradient-eluted DNA from two replicates of two groups. Sequencing analysis was performed in the Solexa 1G Genome Analyzer (Illumina) according to manufacturer protocols.Finally, the libraries identified by the 6-bp index were sequenced at 50 bp squence read using an IlluminaHiSeq 2000 sequencer.

value: longissimus dorsi

tag: library construction elute

value: high gradient

tag: beef toughness

value: tender


title: 231 control si I


title: RNA-seq replicate1 of LR stage 2


title: ChIPseq_LM_H3K4me3_REP1

description:
MDAMB231_LM_H3K4me3_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.counts.txt


title: ChIPseq_LM_H3K27ac_REP2

description:
MDAMB231_LM_H3K27ac_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K27ac_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K27ac_merge_peaks.broadPeak.counts.txt


title: RNA-seq replicate2 of LR stage 1

value: stage 1 of lateral root initials


title: ATACseq_Par_REP2

description:
MDAMB231_Par_atac.merge.nomt.bs5.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_atac.splitbysummit.narrowPeak.unique.bed
BRCA_raw_counts.peaks_mda_par_rep2_sort_dedup.counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.32
Trimmed reads were aligned using Bowtie2 v2.3.4.3 to hg19 using standard parameters and a maximum fragment length of 2000
Duplicate reads were determined using Picard tools v2.18.21
Bam files were filtered using samtools -F 1804
Reads were then processed where only the most 5' base pair for each read was kept and forward strand reads were shifted +4bp, and reverse strand reads were shifted -5bp.
For a consensus peak set, all bam files were merged using samtools and used for peak calling
Peak calling was performed using MACS2 v2.1.2 with parameters --nomodel --keep-dup all -s 1 --shift -75 --extsize 150 --call-summits. Peaks were then split evenly using summits.
featureCounts was used to count reads from replicates that fall within the consensus peak set using default parameters
DEseq2 was used to determine differential accessibility using counts.
For analysis of Corces et al. dataset, raw reads were processed using PEPATAC v0.8.6 and reads falling under BRCA TCGA ATAC-seq peaks were counted.
Genome_build: hg19
!Sample_data_processing = Supplementary_files_format_and_content: bigwig (Merged rep1, rep2), bed (all ATAC peaks), txt (raw counts)

extract_protocol:
50,000 cells were treated with Transposase. Protocol as previously described in Corces et al (Nat.Methods 2017).
DNA libraries were prepared as previously described in Corces et al (Nat.Methods 2017).

value: genomic DNA


title: db/db_4A


title: db/db_3A


title: ATACseq_Par_REP1

description:
MDAMB231_Par_atac.merge.nomt.bs5.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_atac.splitbysummit.narrowPeak.unique.bed
BRCA_raw_counts.peaks_mda_par_rep1_sort_dedup.counts.txt


title: db/db_2A


title: ChIPseq_LM_H3K27ac_REP1


title: db/db_1A


title: ATACseq_LM_REP2

description:
MDAMB231_LM_atac.merge.nomt.bs5.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_atac.splitbysummit.narrowPeak.unique.bed
BRCA_raw_counts.peaks_mda_lm_rep2_sort_dedup.counts.txt


title: RNA-seq replicate2 of LR stage 0

value: cell layer from where lateral root initiates  (stage0)


title: RNA-seq replicate1 of LR stage 0


title: ATACseq_LM_REP1

description:
MDAMB231_LM_atac.merge.nomt.bs5.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_atac.splitbysummit.narrowPeak.unique.bed
BRCA_raw_counts.peaks_mda_lm_rep1_sort_dedup.counts.txt


title: ChIPseq_BrM_H3K4me3_REP2

description:
MDAMB231_BrM_H3K4me3_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.counts.txt

source_name: MDA-MB-231 breast cancer cell line brain metastatic variant

value: MDA-MB-231 BrM2


title: ChIPseq_BrM_input

value: mammary gland/breast epithelial cell


title: db/m_11A

value: db/m


title: ChIPseq_LM_H3K4me3_REP2


title: ATACseq_BrM_REP1

description:
MDAMB231_BrM_atac.merge.nomt.bs5.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_atac.splitbysummit.narrowPeak.unique.bed
BRCA_raw_counts.peaks_mda_brm_rep1_sort_dedup.counts.txt


title: db/m_9A


title: ChIPseq_BrM_H3K27ac_REP2

description:
MDAMB231_BrM_H3K27ac_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K27ac_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K27ac_merge_peaks.broadPeak.counts.txt


title: db/m_10A


title: ChIPseq_BrM_H3K4me3_REP1


title: ATACseq_BrM_REP2

description:
MDAMB231_BrM_atac.merge.nomt.bs5.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_atac.splitbysummit.narrowPeak.unique.bed
BRCA_raw_counts.peaks_mda_brm_rep2_sort_dedup.counts.txt


title: RNA-seq replicate1 of CR stage 3

description: all-genes-spatiotemporal-expression-matrix.txt

value: stage 3 of crown root initials


title: RNA-seq replicate2 of CR stage 2

value: stage 2 of crown root initials


title: D5

city: Hangzhou

first: Qingfeng

last: Yu

state: Zhejiang

address: No.88 Jiefang Road

department: Department of Hematology and Cancer Institute

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0 with default parameters.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group.
Differential expression analysis of two conditions was performed using the DEGseq R package (1.28.0). Pvalue <0.05 and |FoldChange|>1.5 were set as the threshold for significantly differential expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

source_name: MOLM-13_POLR2A knockout

growth_protocol: seed out at ca. 1.0 x 10^6 cells/ml; split saturated culture 1:2 to 1:3 every 2-3 days; maintain at ca 0.4-2.0 x 10^6 cells/m.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Molm-13/Tet-on Cas9 cells were generated by transducing Molm-13 cells with pCW-Cas9 lentivirus. Subsequently, Molm-13/Tet-on Cas9 cells were transduced with POLR2A sgRNA lentivirus or the control lentuvirus.

value: acute myeloid leukemia (AML) cell line

tag: cytogenetics

value: human hyperdiploid karyotype with 4% polyploidy - 51(48-52)<2n>XY, +8, +8, +8, +13, del(8)(p1?p2?), ins(11;9)(q23;p22p23) - resembles published karyotype - sideline with idem, +19 - carries occult insertion effecting KMT2A-MLLT3 (MLL-MLLT3; MLL-A12) fusion


title: RNA-seq replicate1 of LR stage 1

value: Hwayoung cultivar


title: ChIPseq_BrM_H3K27ac_REP1


title: RNA-seq replicate1 of CR stage 2


title: db/m_7A

value: hippocampus


title: D3

value: human hyperdiploid karyotype with 4% polyploidy - 51(48-52)<2n>XY, +8, +8, +8, +13, del(8)(p1?p2?), ins(11;9)(q23;p22p23) - resembles published karyotype - sideline with idem, +19 - carries occult insertion effecting KMT2A-MLLT3 (MLL-MLLT3; MLL-A11) fusion


title: db/m_8A


title: MSI1 shRNA replicate 3

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

data_processing:
Reads were mapped to GRCh38 using STAR (v2.4.2a) and Gencode v25 gene annotations
STAR --genomeDir /STARgenomes/hg38_Gencode25 --outFileNamePrefix $sampleName"_" --readFilesIn /path/to/read1 /path/to/read2 --readFilesCommand zcat --runThreadN 8 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --sjdbGTFfile /path/to/gencode.v25.annotation.gtf
Read counts from STAR were merged along with gene annotations using bespoke R script
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited file containing read counts per gene

source_name: SU_MB002 shMsi1

growth_protocol: SU_MB002 were expanded using BTIC enrichment media composed of NeuroCult complete media (StemCell Technologies, 10 ng/mL bFGF, 20 ng/mL EGF, 2 μg/mL heparin).

extract_protocol:
Total RNA was extracted from 1 primary human medulloblastoma cell line using the Norgen Total RNA isolation kit (Norgen, 17250). mRNA was quantified using the nanodrop spectrophotmeter ND-1000 and the quality of the total RNA was checked using the Agilent BioAnalyzer RNA Nano Kit. mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used according to the protocol for the library prep. The library fragment size distribution was verified using the Agilent High Sensitivity DNA Kit. The  libraries were quantified by qPCR and pooled in equimolar amounts, then the library pool was subject to qPCR and BioAnalyzer verification once again. The the libraries were sequenced on a HiSeq Rapid v2 flow cell using a 2x76 bp configuration with onboard cluster generation.
RNA libraries were prepared for sequencing using standard Illumina® protocols using the NEBNEXT® Ultra™ II Directional RNA Library Kit for Illumina® following the polyA-containing mRNA workflow.

treatment_protocol: SU_MB002 were transduced with scrambled control or shMsi1 lentivirus and puromycin selected 48 hours post-transduction.

tag: cell line source

value: 3 year old male

value: Group 3 medulloblastoma

value: MSI1 shRNA


title: RNA-seq replicate2 of CR stage 1

value: stage 1 of crown root initials


title: db/m_6A


title: Control

value: wild type

value: human hyperdiploid karyotype with 4% polyploidy - 51(48-52)<2n>XY, +8, +8, +8, +13, del(8)(p1?p2?), ins(11;9)(q23;p22p23) - resembles published karyotype - sideline with idem, +19 - carries occult insertion effecting KMT2A-MLLT3 (MLL-MLLT3; MLL-AF9) fusion


title: RNA-seq replicate2 of CR stage 3


title: db/m_5A


title: MSI1 shRNA replicate 1


title: Su(var)2-10_RNAi_RNAseq1

city: Ithaca

first: Yicheng

last: Luo

address: 215 Tower Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
RNA-seq reads aligning to rRNA were removed by mapping to Drosophila rRNA sequences using bowtie allowing 3 mismatches
Reads were mapped to the Drosophila genome allowing 2 mismatches and 1 mapping position or 0 mismatches and 10000 mapping positions for TE analysis
UCSC genome browser tracks were were generated from aligned reads (-v 2 -m 1) using BedTools and BigWig tools.
Genome_build: dm3
Supplementary_files_format_and_content: UCSC genome browser tracks (bigWig format)

organism: Drosophila melanogaster

source_name: S2 cell line Total RNA

growth_protocol: Cell lines were maintained at 25C with Schneider's Drosophila Medium plus 10% heatshocked FBS

extract_protocol:
Total RNA from S2 cell line was isolated with Ribozol reagent, and rRNA was depleted with Ribo-Zero™ rRNA Removal Kit supplemented with Drosophila rRNA oligonucleotides according to the manufacturer's instruction.
RNA-seq libraries were made by using NEBNext® Ultra™ Directional RNA Library Prep Kit. Libraries were sequenced on the Illumina HiSeq 2000 platform.

treatment_protocol: S2 cell line was treated with dsRNA for 5 days before extracting total RNA

tag: knockdown


title: RNA-seq replicate2 of CR stage 0

value: cell layer from where crown root initiates (stage0)


title: Control replicate 3

source_name: SU_MB002 shControl

value: shControl


title: db/m_4A


title: RNA-seq replicate1 of CR stage 1


title: db/m_3A


title: GFP_RNAi_RNAseq2

value: GFP


title: Control replicate 1


title: Smt3_RNAi_RNAseq1


title: db/m_2A

value: db/m


title: Control replicate 2


title: RNA-seq replicate1 of CR stage 0


title: D2

value: human hyperdiploid karyotype with 4% polyploidy - 51(48-52)<2n>XY, +8, +8, +8, +13, del(8)(p1?p2?), ins(11;9)(q23;p22p23) - resembles published karyotype - sideline with idem, +19 - carries occult insertion effecting KMT2A-MLLT3 (MLL-MLLT3; MLL-A10) fusion


title: Adult-Isoseq

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

description: This library was not used in expression table, rather it was used to confirm data.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using the aligner torrent mapper version 3.4.1. The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites.
Genome_build: Xenopus tropicalis v9.1
Supplementary_files_format_and_content: .txt files reporting the poly(A) sites and  transcriptional start sites

organism: Xenopus tropicalis

source_name: Whole body

extract_protocol:
Iso-seq libraries were constructed by the Genomics Core Laboratory, Washington State University. The Iso-seq method includes several major steps: poly(A)+ RNA enrichment, full length cDNA synthesis, duplex-specific nuclease normalization, PCR amplification, size selection. Three fractions of cDNA, 1-2kb, 2-3kb, 3+kb were collected and sequenced.
Total RNA was harvested using Trizol reagent.

value: Whole body

tag: developmental stage

value: Adult


title: Ag ion 2

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3, NC_002947.4,L27758.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism:
Escherichia coli K-12
Pseudomonas putida KT2440

source_name: E. coli bacteria + P. putida bacteria + IncPα plasmid

growth_protocol: liquid LB culture at 37 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid were cultured in triplicate in 10 mL PBS containing 0 and 1 μg/L AgNPs or Ag ion for 2h, at 25 °C, without shaking

tag: e coli substr

tag: treatment

value: Ag ion

tag: transmission

value: IncPα RP4 plasmid


title: Embryo-Isoseq

source_name: Embryo

extract_protocol:
Iso-seq libraries were constructed by the Genomics Core Laboratory, Washington State University. The Iso-seq method includes several major steps: poly(A)+ RNA enrichment, full length cDNA synthesis,  PCR amplification, size selection. Two fractions of cDNA, 1-2kb, 2-3kb were collected and sequenced.
Total RNA was harvested using Trizol reagent.

value: Embryos

value: Five stages


title: db/m_1A

value: hippocampus


title: GFP_RNAi_RNAseq1

tag: cell line


title: MSI1 shRNA replicate 2

value: 3 year old male

value: Group 3 medulloblastoma


title: Ag ion 1


title: eij1_P3

city: Guangzhou

first: Hailun

address: No.723, Xingke Road, Tianhe District

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
GO analysis was performed by the GO Annotation of TAIR.
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: Tab-delimited excel files include counts, FPKM values and FDR-adjusted P-values for each differentially expressed genes

organism: Arabidopsis

source_name: eij1-1_Pst DC3000_leaves

growth_protocol: Arabidopsis plants were grown at 22°C under short day conditions (12 h light/12 h dark).

extract_protocol:
Total RNA was extracted from the treated seeds by Plant RNA Kit (Promega, LS1040)
The libraries constructed using Ultra RNA sample preparation kit (Illumina) reached high quality before RNA-sequencing. RNA sequencing was performed by the Biomarker Technologies Corporation (Beijing, China) using an Illumina NovaSeq platform

treatment_protocol: Three-week-old of eij1-1 and Col plants were dip inoculated with Pst DC3000 (OD600 = 0.1). The treated leaves were collected at 24 hpi.

tag: ecotype background

value: Three-week-old

value: Dip inoculated with Pst DC3000 (OD600 = 0.1)

tag: time point

value: 24 hpi

tag: tissue

value: leaves


title: Aedes.Be.d0.2

city: Philadelphia

first: Michael

last: Povelones

state: PA

address: 3800 Spruce St.

department: Pathobiology

institute: University of Pennsylvania School of Veterinary Medicine

data_processing:
Fastq files were mapped to the Aedes aegypti Liverpool strain transcriptome (version AGWG AaegL5.1) using Kallisto or Dirofilaria immitis transcriptome (PRJEB1797 version nDi.2.2) using Kallisto, version 0.44.0
abundance data were read into the R/bioconductor environment using the TxImport package, version 1.0.2
For analysis of Aedes transcripts, transcripts with low/no read counts in three of the cultured samples or any of the mosquito samples were eliminated
data was normalized using the calcNormFactors function from Limma (3.34.4), using the TMM method
precision weights were applied to expression data using the Limma/VOOM function
Genome_build: differentially expressed genes (0.05 adjusted Pval and 2 fold change) for Ae. aegypti transcripts were identified using linear modeling and Bayesian statistics using the Limma package

organism: Aedes aegypti

source_name: Malpighian tubules of Aedes aegypti

growth_protocol: Blood containing Dirofilaria immitis microfilariae was obtained from an experimentally infected dog. Blood used to infect Ae. aegypti(S) to generate L3i to establish the dog was obtained from a shelter in Charleston, NC. The average microfilaremia during these experiments was approximately 50,000 mf/mL. All animal studies were performed under Institutional Animal Care and Use Committee approved protocols and in accordance with the guidelines of the Institutional Animal Care and Use Committee of the University of Pennsylvania (IACUC, protocol 805059). Blood was diluted with the appropriate volume of heparinized sheep blood (Hemostat) to a concentration of 3000-4000 mf/mL. Blood containing microfilariae was heated to 37 ºC placed in an artificial membrane feeder consisting of the indentation in the bottom of a 300 mL plastic baby bottle (Advent, Phillips) filled with 37 ºC water. The blood was then covered with thinly-stretched Parafilm. The bottle was inverted, placed on top of netted mosquito cups, and removed after 20 minutes. The indentation holds approximately 3.5 mL of blood resulting in an average uptake of 14 mf/mosquito (range 5-24 mf/mosquito) for D. immitis  at the concentration used. Immediately following the feed, blood fed mosquitoes were separated using CO2 anesthesia.

extract_protocol:
Malpighian tubules were dissected into PBS by pulling at the last abdominal segment with forceps until the hindgut emerges. Next, the abdomen is opened where it joins the thorax and the midgut was separated from the thorax. The hindgut, midgut, and Malpighian tubules are removed from the posterior abdomen by pulling again on the previously separated posterior segment with forceps. The hindgut and midgut were separated, leaving a set of tubules. Tubules from five mosquitoes were transferred together to a tube containing Trizol (Life Technologies) and stored at -80 ºC until processing according to the manufacturer’s instructions. Purified total RNA was resuspended in water and treated with Turbo DNA-free (Invitrogen) to remove potentially contaminating genomic DNA. The RNA concentration and quality were assayed using a NanoDrop (ThermoFisher), 4200 TapeStation (Agilent) and Qubit 3 Fluorometer (ThermoFisher). Overall, 23 libraries were generated from the 24 conditions, as one replicate of Ae. aegyptiS control did not yield a sufficient quantity of RNA for library production
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the 9 manufacturer’s instructions. Samples were run on Illumina NextSeq 500 using a two High Output v2 kit flow cells to generate 75-base pair, single-end reads.

treatment_protocol: Malpighian tubules from susceptible "Blackeye" strain of Ae. aegypti (S) and the "Liverpool" refractory strain of Ae. aegypti (R) mosquitoes were isolated at day 1, day 2, and day 3 following infection by D. immitis and from sugar fed controls. Ae. aegypti (S),  Blackeye Liverpool (NR-48921 BEI Resources) is a D. immitis and B. malayi susceptible strain. Ae. aegypti (R) Liverpool Strain (LVP-IB12; MRA-735, contributed by David W. Severson to BEI Resouces) is a D. immitis and B. malayi refractory strain.

value: Malpighian tubules

tag: strain

value: Blackeye

tag: infection

value: No

tag: timepoint (day)

tag: biological replicate


title: eij1_P2

tag: age

tag: genotype/variation


title: AgNPs 2

value: 1 μg/L AgNPs


title: Aedes.Lvp.d0.3

value: Liverpool


title: Ag ion 3


title: eij1_P1


title: Control 3

value: control


title: Adult-male6-WTTSseq

extract_protocol:
WTTS-seq libraries were constructed based on our protocols. The WTTS-seq method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, size selection and PCR amplification
Total RNA was harvested using Trizol reagent.

value: Whole body

value: Adult


title: Aedes.Lvp.d0.2


title: CDR1AS expressing cells

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Colon cancer cell lines expressing CDR1AS RNA

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: DMEM supplemented with 10%FBS

extract_protocol: Standard Trizol Reagent for the RNA extraction.

treatment_protocol: Normal culture

tag: cell type

value: Colon carcinoma

tag: genotype

value: CDR1AS expressing cells


title: Adult-femalepool-CAGEseq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using the aligner torrent mapper version 3.4.1. The starts of mapped reads within 20bp of each other on the same strand were clustered for transcriptional start sites detection.
Genome_build: Xenopus tropicalis v9.1
Supplementary_files_format_and_content: .txt files reporting the poly(A) sites and  transcriptional start sites

extract_protocol:
CAGE-seq was constructed by CAGE Library Preparation kit (DNAFORM, Yokohama, Japan)
Total RNA was harvested using Trizol reagent.


title: Col_P2

source_name: WT_Pst DC3000_leaves

value: wild type


title: Col_P3


title: AgNPs 3

value: IncPα RP4 plasmid


title: Control 1


title: Col_P1


title: Aedes.Lvp.d0.1


title: A549_DPP1

status: Public on Jan 31 2020

city: Huai'an

first: Jie

last: Zhang

state: Jiangsu

address: Huaihai South Road

department: Department of Respiratory Diseases

institute: the Affiliated Huai’an Hospital of Xuzhou Medical University

data_processing:
Illumina Hiseq™ raw image data files were transformed into original Sequenced Reads by CASAVA Base Calling analysis.
HISAT2 was used to compare the effective data of the sample to the reference genome, and the Mapping information was collected
Bwtools was used to evaluate the sequence conservation of lncrnas based on phastcon score of UCSC database; MiRPara was used to predict mirnas and their precursors, while Blast+ and miRBase precursor databases were used to obtain known precursor sequences.
StringTie and gene model were used to evaluate gene expression and WGCNA was used for gene co-expression analysis
DESeq2 was used to analyze the expression difference of transcripts, and the expression difference analysis results were visualized
Supplementary_files_format_and_content: The processed data (xls) files include RPKM values for each Sample

source_name: Human lung tissue

growth_protocol: The cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal  220 calf serum, streptomycin (100 mg/mL), and penicillin (100 µg/mL) at 5% CO2 and 37 ℃. The medium  221 used for culturing A549/DDP cells was supplemented with 1 µg/mL DDP to maintain the drug-resistant  222 phenotype. The cells in logarithmic phase were used for all experimental analyses.

extract_protocol:
The lncRNA libraries were constructed using the rRNA-depleted RNA sample and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA). The divalent cations were used for fragmentation. The synthesis of the first-strand cDNA was performed using M-MuLV reverse transcriptase and a random hexamer primer. The second-strand cDNA synthesis was performed using RNase H and DNA polymerase I. The 3'-end of the DNA fragments was adenylated and ligated with the NEBNext adaptor containing a hairpin-loop structure. AMPure XP system was used to select the cDNA fragments with a size range of 150–200 bp. The cDNA libraries were sequenced on an Illumina HiSeq 4000 platform.
Small RNA library was prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina®. Briefly, the NEB 3' SR adaptor was ligated to the 3'-end of miRNAs. The single-stranded DNA adaptor was converted into a double-stranded DNA molecule. The 5'-end adaptor was ligated to the 5'-end of miRNAs. The DNA fragments of size 140–160 bp were dissolved in 8 μL of an elution buffer. The libraries were sequenced on an Illumina HiSeq 2500 platform.

value: Human lung

value: cisplatin-resistant cell line

tag: passages


title: MHCC97hCell-shScr-rep1

first: Cai

last: Xiujun

state: State...

address: #204b  Conant Road 204B

department: general surgery

institute: university of Zhejiang

description:
s97H.PLKO
Circular RNA expression after knocking down scramble sequence

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 4 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes >2 and p-values >0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: Human HCC cell line MHCC-97h, knocking down scramble sequence, replication 1

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: All the cells were maintained in DMEM (Invitrogen, Grand Island, NY) with 10% fetal bovine serum (FBS), 1% Glutamine; and 1% Penicillin/Streptomycin.

extract_protocol: Total RNAs were isolated using Trizol reagent (Invitrogen). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

treatment_protocol: The stable transfected cells was established by using lenti-virus system.


title: A549_DPP3


title: LO2Cell-oeAR-rep1

description:
LO2.AR
Circular RNA expression after overexpressing AR

source_name: Human liver cell line LO2, overexpress AR, replication 1

value: AR overexpressed


title: AgNPs 1


title: LO2Cell-vector-rep1

description:
LO2.PWPI
Circular RNA expression after overexpressing vector

source_name: Human liver cell line LO2, overexpress vector, replication 1


title: A549_1

value: cisplatin-sensitive cell line


title: A549_2


title: Aedes.Be.d0.1


title: control cells

description: Colon cancer cell lines containing control lentiviruses


title: A549_DPP2


title: 502818

city: Vicksburg

first: Emily

middle: Alice

last: Woolard

state: Mississippi

address: 3909 Halls Ferry Rd

institute: U.S. Army Engineer and Research Development Center

data_processing:
The size and purity of the libraries were determined on the D1000 ScreenTape on the Agilent TapeStation 2200. The quantity of the individual libraries was assessed using the KAPA Library Quantification Kit for Illumina Libraries  and confirmed using the dsDNA HS Kit on the Qubit 3.0 Fluorometer.
The concentrations of the libraries were then normalized, the libraries were pooled together with eight libraries per pool, and the pools were quantified using the dsDNA HS Kit on the Qubit 3.0 Fluorometer, followed by further dilution to 5nM
The pools were then sequenced on a HiSeq 4000 system  at 1x150 cycles single-read using the HiSeq 3000/4000 SBS kit following the manufacturer’s instructions
Genome_build: A custom reference transcriptome was built using FHM liver samples from another study, and was blasted against the fathead minnow and zebrafish mRNA sequences in Genbank for annotation purpose
Supplementary_files_format_and_content: salmon .sf output files

organism: Pimephales promelas

source_name: Liver

extract_protocol:
Livers were removed from fish, frozen at -80C until processing, homogenized, and had RNA harvested with Nucleospin RNA XS kit. 125ng of total RNA was used per sample to prepare libraries with the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA, USA) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: field site

value: MIM

value: liver

tag: Sex

value: male


title: 502822


title: 502834


title: 502831


title: 502830


title: 502829


title: 502832


title: 502821


title: 502817


title: 502820


title: 502833


title: A549_3


title: 502809

value: MIP


title: 502819


title: 502806


title: 502798


title: 502805


title: 502797


title: MHCC97hCell-shAR-rep1

description:
s97H.shAR
Circular RNA expression after knocking down AR

source_name: Human HCC cell line MHCC-97h, knocking down AR, replication 1

value: AR knocked down


title: 502808


title: 502807


title: 502796


title: 502793


title: 502784

value: Field control


title: 502785


title: Control 2

tag: e coli substr

tag: treatment

value: control


title: 502783


title: 502782


title: 502781


title: 502758

value: MEF


title: 502773


title: 502772


title: 502759


title: 502771


title: 502760


title: 502769


title: 502770


title: 502749

value: MIE


title: 502748


title: 502757


title: 502786


title: 6d_1_O2_rep1

city: Cambridge

first: Sarah

middle: E

last: Calvo

state: Massachusetts

address: 415 Main St

institute: Broad Institute

data_processing:
Cufflinks suite (tophat, cuffquant, cuffnorm) as previously described (Trapnell et al., 2012)
Supplementary_files_format_and_content: tab-delimited text file contains FPKM values for each gene (row) for each sample (column)

extract_protocol:
Qiagen RNAeasy kit.
Picelli et al, 2014 (Smart-seq2 including PolyA selection)

tag: cell line

tag: oxygen level


title: 24h_1_O2_rep3

tag: time point


title: 502774

tag: tissue


title: 502794


title: 3d_1_O2_rep2


title: 3d_1_O2_rep3


title: 502762


title: 3d_1_O2_rep1


title: 6d_1_O2_rep2


title: 6d_1_O2_rep3


title: 24h_1_O2_rep2


title: 502746


title: 502745


title: 502795


title: 24h_1_O2_rep1


title: 6h_1_O2_rep3


title: 502747


title: 502737


title: 6h_1_O2_rep1


title: 6d_5_O2_rep3


title: 502735


title: 502738


title: 6d_5_O2_rep2


title: 6h_1_O2_rep2


title: 3d_5_O2_rep2


title: 502733


title: 6d_5_O2_rep1


title: 502726


title: 24h_5_O2_rep1


title: 502734


title: 502721


title: 24h_5_O2_rep3


title: 3d_5_O2_rep3


title: 502724


title: 502722


title: 502723


title: 3d_5_O2_rep1


title: 502725


title: 502714

value: UCJ


title: 6h_5_O2_rep3


title: 24h_5_O2_rep2


title: 502713


title: 6h_5_O2_rep2


title: 502736


title: 6h_5_O2_rep1


title: 502712


title: 6d_21_O2_rep3


title: 502711


title: 502710


title: 6d_21_O2_rep2


title: 502709


title: 3d_21_O2_rep3


title: 6d_21_O2_rep1


title: 502702


title: 3d_21_O2_rep1


title: 502700


title: 502701


title: 24h_21_O2_rep3


title: 24h_21_O2_rep1


title: 24h_21_O2_rep2


title: 502699


title: 502698


title: 6h_21_O2_rep2


title: 6h_21_O2_rep3


title: 502687

value: MEC


title: 502688


title: GPR8_DD_3 [GPR8DD_3]

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

description: 48112_GTGAAA_CAJ0NANXX_8_20170113B_20170113

data_processing:
The mapping of reads was performed using bowtie2 with standard parameter setting
The resulting files were further processed using samtools
The comparison to the annotation was performed using bedtools
Values were calculated for each annotated transcript based on the results of the mapping (RSEM)
Genome_build: https://genome.jgi.doe.gov/Trire2/Trire2.home.html
Supplementary_files_format_and_content: The Excel file contains FPKM values of normalized samples (values for all samples in this file).

organism: Trichoderma reesei

source_name: ∆gpr8_DD_fungal mycelium

growth_protocol: Precultures for cultivation on cellulose were performed on plates with malt extract agar (3 % w/v) in constant darkness for 14 days in order to avoid interference of light pulses or circadian rhythms with transcriptome analysis. An inoculum of 10^9 conidia/L was applied to 100 ml of Mandels Andreotti minimal medium with 1 % (w/v) microcrystalline cellulose (Alfa Aesar, Karlsruhe, Germany) and 0.1 % (w/v) peptone to induce germination.

extract_protocol:
Mycelia were harvested by filtration and frozen in liquid nitrogen. Total RNA was isolated essentially as described previously (Tisch et al., 2011 PMID  21220037) using the QIAGEN plant RNA kit (QIAGEN, Hilden, Germany) according to manufacturers instructions. Quality control of total RNA was performed using Bioanalyzer 2100 (Agilent) and only high quality RNA was used for further analysis.
Next generation sequencing was performed at the core facility VetCORE (Vienna, Austria) on a HiSeq2000/SR50 machine.

treatment_protocol: Strains were grown in constant light (1600 lux) or constant darkness at 28°C for 72 hours at 200 rpm. Harvesting of dark cultures was done under red safety light (darkroom lamp, Philips PF712E, red, 15 W)

tag: strain

value: recombinant strain

tag: light condition

tag: carbon source

value: 1 % w/v microcrystalline cellulose

value: mycelium


title: 502685


title: 502686


title: 6h_21_O2_rep1


title: 502697


title: 502678


title: GPR8_DD_2 [GPR8DD_2]

description: 48111_CTTGTA_CAJ0NANXX_8_20170113B_20170113

value: constant darkness at 28°C for 72 hours at 200 rpm


title: 502677


title: 502675


title: QM6a_DD_3 [QM DD_3]

description: 48109_GCCAAT_CAJ0NANXX_8_20170113B_20170113

source_name: QM6a_DD_fungal mycelium

value: wild type


title: GPR8_DD_1 [GPR8DD_1]

description: 48110_CAGATC_CAJ0NANXX_8_20170113B_20170113


title: 502674


title: QM6a_DD_2 [QM DD_2]

description: 48108_ACAGTG_CAJ0NANXX_8_20170113B_20170113


title: 3d_21_O2_rep2


title: 502676


title: 502673


title: 502666


title: 502689


title: GPR8_LL_3 [GPR8LL_3]

description: 41737_TAGCTT_C9N4GANXX_2_20160819B_20160819

source_name: ∆gpr8_LL_fungal mycelium

value: constant light (1600 lux) for 72 hours at 200 rpm


title: 502665


title: 502664


title: GPR8_LL_1 [GPR8LL_1]

description: 41736_GTTTCG_C9N4GANXX_2_20160819B_20160819


title: 502663


title: 502662


title: QM6a_LL_3 [QMLL_3]

description: 41735_AGTCAA_C9N4GANXX_2_20160819B_20160819

source_name: QM6a_LL_fungal mycelium


title: QM6a_LL_2 [QMLL_2]

description: 41734_GTCCGC_C9N4GANXX_3_20160819B_20160819


title: QM6a_LL_1 [QMLL_1]

description: 41734_GTCCGC_C9N4GANXX_2_20160819B_20160819


title: QM6a_LL_4 [QMLL_4]

description: 41735_AGTCAA_C9N4GANXX_3_20160819B_20160819


title: QM6a_DD_1 [QM DD_1]

description: 48107_CGATGT_CAJ0NANXX_8_20170113B_20170113


title: GPR8_LL_4 [GPR8LL_4]

description: 41737_TAGCTT_C9N4GANXX_3_20160819B_20160819


title: GPR8_LL_2 [GPR8LL_2]

description: 41736_GTTTCG_C9N4GANXX_3_20160819B_20160819


title: 502638

value: MED


title: 502652

value: liver


title: 502626

value: MET

value: male


title: 502640


title: 502642


title: 502649


title: 502661


title: 502639


title: 502654


title: 502641


title: 502604


title: 502605


title: 502613


title: 502630


title: 502617


title: 502618


title: 502616


title: 502627


title: 502615


title: 502606


title: 502637


title: 502628


title: 502629


title: 502625


title: 502603


title: 502602


title: 502614


title: 502651


title: 502653


title: 502650


title: 502601


title: QDG5-smallRNAseq

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

data_processing:
The sequencing quality of raw data of fastq format was assessed with FastQC and then low quality data were filtered using NGSQC. The clean reads with high quality were then aligned to the reference genome using Tophat2 with default parameters. The rat genome version of RGSC6.0/RN6 (UCSC) was used as the reference.
miRNA reads were normalized with TPM（Transcripts Reads Number Per Million）
Differential expression analyses were performed using the limma package.
Genome_build: RGSC6.0/RN6 (UCSC)
Supplementary_files_format_and_content: tab_delimited text files include TPM values for each Sample

organism: Rattus norvegicus

source_name: heart tissue

extract_protocol:
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEB Next®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: heart

tag: group

value: QDG Treatment


title: QDG4-smallRNAseq


title: QDG6-smallRNAseq


title: SHR4-smallRNAseq

value: Hypertension


title: SHR6-smallRNAseq


title: QDG2-smallRNAseq


title: QDG1-smallRNAseq


title: SHR2-mRNAseq

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: RGSC6.0/RN6 (UCSC)
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

extract_protocol:
The hearts were dissected and cardiac tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.


title: SHR6-mRNAseq


title: QDG6-mRNAseq


title: WKY1-smallRNAseq

value: Normal


title: WKY2-smallRNAseq


title: WKY6-smallRNAseq


title: SHR4-mRNAseq


title: SHR2-smallRNAseq


title: WKY4-smallRNAseq


title: QDG5-mRNAseq


title: SHR3-mRNAseq


title: SHR5-mRNAseq


title: WKY5-smallRNAseq


title: SHR3-smallRNAseq


title: QDG1-mRNAseq


title: WKY3-smallRNAseq


title: SHR1-smallRNAseq


title: QDG4-mRNAseq


title: QDG3-mRNAseq


title: SHR5-smallRNAseq


title: QDG2-mRNAseq


title: QDG3-smallRNAseq


title: SHR1-mRNAseq


title: WKY5-mRNAseq


title: WKY4-mRNAseq


title: W72_607_2

city: xinxiang

first: changwei

last: shen

state: henan

address: East Section of Hualan Avenue

institute: Henan Institute of Science and Technology

description: After 72 hours of germination under waterlogging treatment

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the Triticum aestivum L. reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: IWGSC_RefSeqv1.0
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Triticum aestivum

source_name: seed

growth_protocol: All seeds were grown in a growth chamber at 25 ℃and a 75% relative humidity (16 h light / 8 h dark cycle).

extract_protocol:
A total of 18 wheat seeds samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experimental treatment: the 50 plump seeds were placed in a beaker with a water depth of 10 cm for waterlogging treatment. After 72 h of waterlogging, the seeds were taken out and germinated in a plate petri dish (to ensure that the seeds were in contact with water but not submerged by water). Control treatment: germination was conducted on the seeds that were suctioned for 24 h. The experimental and control treatments were given 5 repetitions respectively.

tag: variety

value: seed

tag: developmental stage

value: germination stage


title: WKY6-mRNAseq


title: W72_607_3


title: W72_607_1


title: W72_207_3


title: W72_207_1


title: WKY2-mRNAseq


title: W72_22_2


title: C72_607_3

description: After 72 hours of germination under control treatment


title: W72_22_3


title: C72_22_3


title: WKY1-mRNAseq


title: C72_207_3


title: C72_22_2


title: C72_207_1


title: WKY3-mRNAseq


title: W72_207_2


title: C72_607_1


title: C72_607_2


title: C72_22_1


title: W72_22_1


title: NPC3_Chr11_DMSO_ExpB

status: Public on Jan 30 2020

city: La Jolla

first: Meiyan

last: Wang

state: CA

address: 10010 N. Torrey Pines Road

institute: The Salk Institute for biological studies

description: HTGTS

data_processing:
Library strategy: LAM-HTGTS
HTGTS Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
HTGTS reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
Mapped reads were processed using HTGTS (http://robinmeyers.github.io/transloc_pipeline/)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files (translocation junctions) contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); cigar for bait sequence (B_Cigar); cigar for prey sequence (Cigar); the entire stitched paired end read sequence (Seq); 10 bp sequence around the junction, 5bp from bait and 5bp from prey (J_seq); barcode used for demultiplex (Barcode); number of unaligned sequences (unaligned); pass (0) or fail (1) the “Bait only” filter (baitonly); pass (0) or fail (1) the “Uncut” filter (uncut); number of nucleotides not aligned to the bait (misprimed); pass (0) or fail (1) the “Frequent cutter” filter (freqcut); number of nucleotides between bait and prey sequences (largegap); pass (0) or fail (1) the “Map quality” filter (mapqual); pass (0) or fail (1) the “Breaksite” filter (breaksite); pass (0) or fail (1) the “Sequential” filter (sequential); pass (0) or fail (1) the “Repeat sequence” filter (repeatseq); number of duplicates in this library (duplicate); and the experiment associated with the read if applicable (note).

source_name: hESC-derived neural progenitor cells

growth_protocol: Human ESC- and iPSC-derived NPCs were cultured as described before (Yu et al., 2014; Marchetto et al., 2017).  Human ESC-derived GPCs were cultured and expanded as described before (Santos et al., 2017). Primary dermal fibroblasts were expanded as described before (Mertens et al., 2015).

extract_protocol:
Genomic DNA was extracted overnight at 55 degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH 8.0, 0.2 mg/mL proteinase K, prior to DNA fragmentation
LAM-PCR-mediated HTGTS (Frock et al., 2015, Hu et al., 2016, Wei et al, 2016; see manuscript for details)

treatment_protocol: Cells were treated by vehicle control (DMSO) or the addition of 0.5 μM aphidicolin (APH, Sigma) for 3 days and then 0.25 μM APH for 1 day.

tag: cell type

value: Neural progenitor cells

tag: passage

value: DMSO


title: NPC3_Chr11_APH_ExpC

description: HTGTS

value: APH


title: NPC3_Chr11_APH_ExpB

description: HTGTS


title: NPC3_Chr11_DMSO_ExpA

description: HTGTS


title: NPC2_Chr11_DMSO_ExpC

description: HTGTS

source_name: hiPSC-derived neural progenitor cells


title: NPC3_Chr11_DMSO_ExpC

description: HTGTS


title: NPC2_Chr11_DMSO_ExpA

description: HTGTS


title: NPC2_Chr11_DMSO_ExpB

description: HTGTS


title: C72_207_2


title: NPC1_Chr11_DMSO_ExpC

description: HTGTS


title: NPC2_Chr11_APH_ExpB

description: HTGTS


title: NPC1_Chr11_APH_ExpC

description: HTGTS


title: NPC2_Chr11_APH_ExpA

description: HTGTS


title: NPC1_Chr11_DMSO_ExpA

description: HTGTS


title: NPC1_Chr11_DMSO_ExpB

description: HTGTS


title: NPC1_Chr11_APH_ExpB

description: HTGTS


title: NPC1_Chr11_APH_ExpA

description: HTGTS


title: CTRL3_Chr1_DMSO_ExpC

description: HTGTS


title: CTRL3_Chr1_DMSO_ExpA

description: HTGTS


title: CTRL3_Chr1_DMSO_ExpB

description: HTGTS


title: CTRL1_Chr1_DMSO_ExpC

description: HTGTS


title: CTRL2_Chr1_DMSO_ExpD

description: HTGTS


title: CTRL2_Chr1_DMSO_ExpB

description: HTGTS


title: CTRL2_Chr1_DMSO_ExpC

description: HTGTS


title: NPC3_Chr11_APH_ExpA

description: HTGTS


title: CTRL2_Chr1_DMSO_ExpA

description: HTGTS


title: CTRL1_Chr1_DMSO_ExpA

description: HTGTS


title: CTRL1_Chr1_DMSO_ExpB

description: HTGTS


title: ASD3_Chr1_DMSO_ExpB

description: HTGTS


title: NPC2_Chr11_APH_ExpC

description: HTGTS


title: ASD3_Chr1_DMSO_ExpC

description: HTGTS


title: ASD3_Chr1_DMSO_ExpA

description: HTGTS


title: ASD2_Chr1_DMSO_ExpB

description: HTGTS


title: ASD2_Chr1_DMSO_ExpC

description: HTGTS


title: ASD2_Chr1_DMSO_ExpA

description: HTGTS


title: ASD1_Chr1_DMSO_ExpC

description: HTGTS


title: ASD1_Chr1_DMSO_ExpD

description: HTGTS


title: ASD1_Chr1_DMSO_ExpB

description: HTGTS


title: ASD1_Chr1_DMSO_ExpA

description: HTGTS


title: NPC3_Chr1_DMSO_ExpC

description: HTGTS


title: NPC3_Chr1_DMSO_ExpB

description: HTGTS


title: NPC3_Chr1_DMSO_ExpA

description: HTGTS


title: NPC3_Chr1_APH_ExpB

description: HTGTS


title: NPC3_Chr1_APH_ExpD

description: HTGTS


title: NPC3_Chr1_APH_ExpA

description: HTGTS


title: ASD3_Chr1_DMSO_ExpD

description: HTGTS


title: NPC2_Chr1_DMSO_ExpD

description: HTGTS


title: NPC2_Chr1_DMSO_ExpB

description: HTGTS


title: NPC2_Chr1_DMSO_ExpC

description: HTGTS


title: NPC2_Chr1_DMSO_ExpA

description: HTGTS


title: NPC2_Chr1_APH_ExpE

description: HTGTS


title: NPC2_Chr1_APH_ExpA

description: HTGTS


title: NPC2_Chr1_APH_ExpC

description: HTGTS


title: NPC2_Chr1_APH_ExpF

description: HTGTS


title: NPC2_Chr1_APH_ExpB

description: HTGTS


title: NPC2_Chr1_APH_ExpD

description: HTGTS


title: NPC1_Chr1_DMSO_ExpD

description: HTGTS


title: NPC1_Chr1_DMSO_ExpA

description: HTGTS


title: NPC1_Chr1_DMSO_ExpC

description: HTGTS


title: NPC1_Chr1_DMSO_ExpB

description: HTGTS


title: NPC1_Chr1_APH_ExpC

description: HTGTS


title: NPC1_Chr1_APH_ExpD

description: HTGTS


title: NPC3_Chr1_DMSO_ExpD

description: HTGTS


title: NPC1_Chr1_APH_ExpB

description: HTGTS


title: NPC3_Chr1_APH_ExpC

description: HTGTS


title: Input DNA_for_RNAPII

city: Los Angeles

first: Kim

last: Ngo

address: 611 Charles E Young Dr. East

department: MIMG

institute: University of California, Los Angeles

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed using cutadapt v1.9.1
Raw reads were aligned to the mouse mm10 genome with bowtie2/2.3 with parameters --non-deterministic --mm --phred33 -p 2 --very-sensitive -x mm10 -U
Mapped reads were filtered using samtools view with parameters -F 2820 -q 30
Duplicate mapped reads were removed using MarkDuplicates (Picard v1.13)
Uniquely mapped BAM files were used to generate bigwig files containing tracks using bamCoverage with parameters —binSize 1 —extendReads 250. For each ChIP-seq sample, input was used as control.
Genome_build: mm10
Supplementary_files_format_and_content: The bw files contain ChIP-seq tracks for each ChIP-seq sample

source_name: primary mouse embryonic fibroblasts (MEFs)

growth_protocol: MEF cells were grown in DMEM medium containing 10% BCS, supplemented with penicillin (100 units/ml), streptomycin (100 ug/ml). All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence for passaging

extract_protocol:
After stimulating MEFs with TNF, MEF cells were washed with PBS and double cross-linked with 100mM disuccinimidyl glutarate/PBS solution (DSG, ThermoFisher Scientific) for 30-min followed by 1% methanol-free Formaldehye/PBS solution (ThermoFisher Scientific) for 15-min. Cross-linked cell pellets were quenched with 125mM Glycine for 5-min. Cell lysates were washed with PBS, incubated in lysis buffer, and sonicated to obtain DNA fragments of 250 to 1000 bp. Cells were sonicated with Diagenode Bioruptor 300 sonication system. DNA fragments were incubated with 5 ug anti-Pol II antibody (Santa Cruz Biotechnology, sc-899) overnight and immunoprecipitated DNA fragments were subjected to reverse cross-linking and cleaned up by AMPure XP magnetic beads.
5ng of input or ChIP DNA were subjected for library synthesis without size selection using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer's instruction. ChIP DNA libraries were quantified using Qubit 2.0 Fluorometer.

treatment_protocol: 8 million MEF cells were serum-starved by overnight incubation in Dulbecco’s Modified Eagle’s Medium supplemented with 0.5% bovine calf serum (BCS), 1% penicillin-streptomycin and 1% L-Glutamine prior to stimulation. Following day, cells were treated with TNF (10 ng/ml) for up to 3 hours prior to ChIP assays.

value: embryo

tag: genotype

value: wild-type

tag: chip-antibody

value: none (input)


title: RNAPII_ChIPseq_WT TNF 3H

value: primary mouse embryonic fibroblasts (MEFs)

tag: agent

value: TNF

value: Pol II antibody Santa Cruz Biotech sc-899


title: RNAPII_ChIPseq_WT TNF 0H


title: RNAPII_ChIPseq_WT TNF 0.5H


title: NPC1_Chr1_APH_ExpA

description: HTGTS


title: RelA-DB Input DNA, rep 2

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed using cutadapt v1.9.1
Raw reads were aligned to the mouse mm10 genome with bowtie2/2.3 with parameters --non-deterministic --mm --phred33 -p 2 --very-sensitive -x mm10 -U
Mapped reads were filtered using samtools view with parameters -F 2820 -q 30
Duplicate mapped reads were removed using MarkDuplicates (Picard v1.13)
Uniquely mapped BAM files were used to generate bigwig files containing tracks using bamCoverage with parameters —binSize 1 —extendReads 250. For each ChIP-seq sample, input was used as control.
For RelA ChIP-seq, bed files for peak calls were generated using macs2 with parameters —nomodel, —extsize 250, and FDR 0.01 threshold. Peak bed file was created from bam files of ChIP-seq sample normalized to input sample.
Genome_build: mm10
Supplementary_files_format_and_content: The bw files contain ChIP-seq tracks for each ChIP-seq sample

growth_protocol: p53-/-crel-/-rela-/- MEF cells were grown in DMEM medium containing 10% BCS, supplemented with penicillin (100 units/ml), streptomycin (100 ug/ml). All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence for passaging. p53-/-crel-/-rela-/- MEF cells were retrovirally transduced with pBABE-puro RelA-WT or RelA-DB vector and clones were selected with puromycin for 72 hours. Clone cell lines were passaged twice prior to plating for ChIP experiments.

extract_protocol:
After stimulating MEFs with TNF, MEF cells were washed with PBS and double cross-linked with 100mM disuccinimidyl glutarate/PBS solution (DSG, ThermoFisher Scientific) for 30-min followed by 1% methanol-free Formaldehye/PBS solution (ThermoFisher Scientific) for 15-min. Cross-linked cell pellets were quenched with 125mM Glycine for 5-min. Cell lysates were washed with PBS, incubated in lysis buffer, and sonicated to obtain DNA fragments of 250 to 1000 bp. Cells were sonicated with Diagenode Bioruptor 300 sonication system. DNA fragments were incubated with 5 ug anti-RelA antibody (Santa Cruz Biotechnology, sc-372) overnight and immunoprecipitated DNA fragments were subjected to reverse cross-linking and cleaned up by AMPure XP magnetic beads.
5ng of input or ChIP DNA were subjected for library synthesis without size selection using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer's instruction. ChIP DNA libraries were quantified using Qubit 2.0 Fluorometer.

tag: background genotype

value: p65 antibody Santa Cruz Biotech sc-372


title: RelA-DB Input DNA, rep 1


title: RelA_ChIPseq_RelA-WT TNF 0.5H, rep 2


title: RelA_ChIPseq_RelA-DB TNF 0.5H, rep 1


title: RelA-WT Input DNA, rep 1


title: RelA_ChIPseq_RelA-DB TNF 0H, rep 2


title: RelA_ChIPseq_RelA-WT TNF 0H, rep 1


title: RelA_ChIPseq_RelA-WT TNF 0H, rep 2


title: RelA_ChIPseq_RelA-WT TNF 0.5H, rep 1


title: RelA-WT Input DNA, rep 2


title: Sfrp1 KO 3 CSC

city: Navi Mumbai

first: SANJEEV

middle: K

last: WAGHMARE

state: MAHARASHTRA

address: Sector 22, Kharghar

department: STEM CELL BIOLOGY GROUP

country: India

institute: ACTREC, TATA MEMORIAL CENTRE

description: Gene expression data from Sfrp1 KO 3 CSCs

hyb_protocol: The fragmented and labelled cDNA product was hybridized by loading onto GeneChip® MTA 1.0 array (Affymetrix, USA)

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000. Streptavidin-Phycoerythrin (Molecular Probes) was used as the fluorescent conjugate to detect hybridized target sequences. Raw intensity data from the GeneChip array were analyzed by GeneChip Operating Software (Affymetrix).

data_processing: The raw signal intensity data (.CEL files) obtained from the Affymetrix GeneChip® Command Console (AGCC) software were normalized and summarized using the RMA sketch algorithm implemented in Expression Console to generate normalized intensity data (.CHP files).

label: Biotin

source_name: Cancer Stem Cells

label_protocol: 1 μg total RNA was reverse transcribed to cDNA with T7 Oligo d (T) primer (Affymetrix). The purified, sense-strand cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues that break the DNA strand. The fragmented cDNA was labelled by terminal deoxynucleotidyl transferase (TdT) by using the Affymetrix proprietary DNA Labelling Reagent that is covalently linked to biotin.

growth_protocol: The WT and Sfrp1-/- mice were maintained with proper food and water  at 22°C with 12 hrs of light and dark cycles.

extract_protocol: RNA was extracted from the FACS sorted CSCs by using the absolutely RNA miniprep kit  (Agilent technologies). The RNA quality was assessed by Agilent RNA 6000 pico kit on the Agilent 2100 bioanalyzer.

treatment_protocol: The mice were treated with DMBA for 3days at PD-23,25 and 27 followed by TPA  treatment twice every week up to 30-40 weeks to generate squamous cell carcinomas.

tag: genotype/variation

tag: tumor stage

value: Skin squamous cell carcinoma


title: WT_TNF-3H-R2: RelA_ChIPseq_WT TNF 3H, rep 2

data_processing:
Illumina HiSeq 2000 reads were demultiplexed and trimmed using cutadapt v1.9.1
Raw reads were aligned to the mouse mm10 genome with bowtie2/2.3 with parameters --non-deterministic --mm --phred33 -p 2 --very-sensitive -x mm10 -U
Mapped reads were filtered using samtools view with parameters -F 2820 -q 30
Duplicate mapped reads were removed using MarkDuplicates (Picard v1.13)
Uniquely mapped BAM files were used to generate bigwig files containing tracks using bamCoverage with parameters —binSize 1 —extendReads 250. For each ChIP-seq sample, input was used as control.
For RelA ChIP-seq, bed files for peak calls were generated using macs2 with parameters —nomodel, —extsize 250, and FDR 0.01 threshold. Peak bed file was created from bam files of ChIP-seq sample normalized to input sample.
Genome_build: mm10
Supplementary_files_format_and_content: The bw files contain ChIP-seq tracks for each ChIP-seq sample
Supplementary_files_format_and_content: The bed file contains all RelA called peaks in MEFs with TNF stimulation using MACS2 peak calling


title: WT_TNF-3H-R1: RelA_ChIPseq_WT TNF 3H, rep 1


title: WT1 CSC

description: Gene expression data from WT-1 CSCs

value: WT


title: WT3 CSC

description: Gene expression data from WT-3 CSCs


title: Sfrp1 KO 1 CSC

description: Gene expression data from Sfrp1 KO 1 CSCs


title: Sfrp1 KO 2 CSC

description: Gene expression data from Sfrp1 KO 2 CSCs


title: WT_TNF-0.5H-R1: RelA_ChIPseq_WT TNF 0.5H, rep 1


title: WT_TNF-0H-R1: RelA_ChIPseq_WT TNF 0H, rep 1


title: Input-R2: Input DNA, rep 2


title: WT_TNF-0H-R2: RelA_ChIPseq_WT TNF 0H, rep 2


title: WT_TNF-0.5H-R2: RelA_ChIPseq_WT TNF 0.5H, rep 2


title: WT2 CSC

description: Gene expression data from WT-2 CSCs


title: RelA_ChIPseq_RelA-DB TNF 0H, rep 1


title: RelA_ChIPseq_RelA-DB TNF 0.5H, rep 2


title: Input-R1: Input DNA, rep 1


title: RNA-seq rep 3,4,5

city: seattle

first: wei

last: zhou

state: wa

address: 4747 30th ave NE

department: genome sciences

institute: University of Washington

description:
RNA-seq experiment
RT_barcode_sampleID_exp2.txt
gene_anno.txt
gene_count.txt

data_processing:
For RNA-seq processing, base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2). RT barcode (10bp) and UMI (8bp) sequence in Read1 is attached to the read name of Read2. Reads not matching to the expected RT barcodes were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.  Trimmed reads were mapped to the yeast reference genome (R64), using STAR/v 2.5.2b (38) with default settings and gene annotations (R64-1-1.87). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, and read 2 end-coordinate. Mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs mapping to the exonic and intronic regions of each gene, for each cell; generally, fewer than 3% of total UMIs strand-specifically mapped to multiple genes. For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded.
For calling-card processing, base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2). In read1, the first segment is the universal primer sequence: CGTCAATTTTACGCAGACTATCTTTCTAGGG followed by the flanking genome sequence of 39 bp. The first 8 bp of read2 is the UMI sequence used to identify unique insertion events. UMI (8bp) sequence in Read2 is attached to the read name of Read1. Reads not matching to the expected universal primer sequence were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.  Trimmed reads were mapped to the yeast reference genome (R64), using STAR/v 2.5.2b (38) with default settings . Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), and read end-coordinate. Then we quantified independent PiggyBac insertions based on the UMIs detected in each sample. Finally, we called significant PiggyBac insertion peaks by MACS2, a peak-calling algorithm (Zhang et al. 2008).
Genome_build: R64
Supplementary_files_format_and_content: Processed data files are in txt format including a variant annotation file, gene (for RNA-seq) or peak (for Calling card-seq) annotation file, and a gene count sparse matrix (for RNA-seq) or peak count sparse matrix (for Calling card-seq).

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Plasmids were transformed into yeast (BY4705 MATα) with a deleted endogenous copy of STE12 by high-efficiency lithium acetate transformation (Gietz et al. 2002). Cells were grown into exponential phase (5 replicates). RNA was extracted using acid phenol extraction, as previously described (Cuperus et al. 2015).

extract_protocol:
yeast RNA were extracted using Hot Acid Phenol Extraction method (Martine A. Collart and Salvatore Oliviero, 1993)
Total cDNA was generated using anchored oligo-dT primer (5′-ACGACGCTCTTCCGATCTNNNNNNNN[10bp index]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3′, where “N” is any base and “V” is either “A”, “C” or “G”; IDT) and SuperScript IV (Life Technologies) with the standard protocol. Second strand synthesis was carried out at 16°C for 180 min with NEBnext Second Strand Synthesis module (NEB) following the commercial protocol. cDNA was tagmented with Nextera tagmentation kit (Illumina) at 55°C for 5 min following commerical protocol. The reaction was stopped by adding 1x DNA binding buffer (Zymo) 6 and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter) following the commerical protocol and eluted in 16 μL of buffer EB (Qiagen). Each sample was then mixed with 2μL of 10 μM indexed P5 primers (5′- AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3′; ID) and P7 primers (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT) and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 10 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min. The library was purified with 0.8x AMPure XP beads (Beckman Coulter) and prepared for sequencing using Illumina Nextseq.

treatment_protocol: six different Ste12 variant were transformed into yeast strain seperatedly

tag: yeast strain

value: BY4705 strain

tag: expression method

value: plasmid overexpression

tag: group setting

value: RNA-seq with all groups

tag: replicate

value: replicate 3,4,5


title: MAX_affinity

city: St. Louis

first: Jiayue

last: Liu

state: MO

address: 4515 McKinley Research Building

department: Genetics

institute: Washington University in St. Louis

data_processing:
Library strategy: Calling Cards Reporter Arrays
We use our python analysis source code for data processing. The code is available on Gitlab
Genome_build: not applicable
Supplementary_files_format_and_content: The processed data files is in CSV format each row as a synthetic promoter sequence. Columns contain transposition insertion information and read count information.

source_name: Synthetic library designed based on yeast promoters

extract_protocol:
After TF directed transposition induction and selection, plasmid DNA is extracted using Qiagen mini prep kit
We amplify all TF directed transpositions from library plasmids DNA by PCR

tag: strain

tag: tissue


title: RNA-seq rep 1 and 2

description:
RNA-seq experiment
RT_barcode_sampleID_exp1.txt
gene_anno.txt
gene_count.txt

value: replicate 1 and replicate 2


title: BB160865: Non-Diabetic

city: Austin

first: Aaron

last: Baker

address: 1 University Station

institute: University Of Texas At Austin

data_processing:
Illumina bcl2fastq2 was used for base calling.
Sequenced reads were assessed for quality issues using fastqc. Sequence quality was high and adapter contamination was low, but there was a sequence bias in the first 10 bases of the reads, so those were trimmed.
Kallisto 0.43.0 was used for pseudo mapping and quantification using the GRh38 human transcriptome.
Counts provided by Kallisto were read into DESeq2 and summarized at the gene level. They were variance stabilized and normalized using DESeq2 normalization.
Genome_build: GRh38
Supplementary_files_format_and_content: tab-delimited text files include map1, map2, ENGG, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, fold change, and SE

source_name: Non-Diabetic

extract_protocol:
Skin samples were harvested, formalin fixed, and embedded in paraffin for sectioning. RNA was isolated using RNeasy FFPE kit (Qiagen). The mRNA was sequenced using an Illumina HiSeq 4000 at the Genomic Sequencing and Analysis Facility at UT Austin
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: age

tag: disease state

value: Non-Diabetic


title: BB150611: Non-Diabetic


title: BB150710: Non-Diabetic


title: GCU042D: Non-Diabetic


title: GCU148prox: Type 2 diabetic

source_name: Type 2 diabetic

value: Type 2 diabetic


title: GCU033EG8: Non-Diabetic


title: GCU148distal: Type 2 diabetic


title: BB160509: Type 2 diabetic


title: BB160234: Non-Diabetic


title: GCU033EG3: Non-Diabetic


title: GCU152: Type 2 diabetic


title: BB151692: Non-Diabetic


title: GCU150: Type 2 diabetic


title: GCU035edistal: Type 2 diabetic


title: GCU082foot: Type 2 diabetic


title: GCU155: Type 2 diabetic


title: GCU083prox: Type 2 diabetic


title: GCU111prox: Type 2 diabetic


title: GCU041: Type 2 diabetic


title: GCU030: Type 2 diabetic


title: GCU029: Type 2 diabetic


title: GCU084distal: Non-Diabetic


title: GCU042C: Non-Diabetic


title: BB161146: Non-Diabetic


title: GCU028: Type 2 diabetic


title: GCU032: Non-Diabetic


title: Feno_rep3_81

first: Yachen

last: Shen

address: 3400 Civic Center Blvd, Philadelphia, PA 19104

institute: University of Pennsylvania

description:
LFD + Feno
Feno_rep3_81

data_processing:
Raw sequenced reads were filtered to retain only high-quality reads. In addition, ribosomal reads and repeats were eliminated by NGSC. Remaining reads were processed with RNA-Seq Unified Mapper (RUM)
RUM aligns reads to the set of known transcripts included in RefSeq, UCSC known genes, and ENSEMBL transcripts, and the genome, and outputs feature-level quantitation (transcript, exon, and  intron).
To analyze global gene expression profiles, the number of uniquely aligning read counts to mRNA transcripts in RefSeq were extracted from the RUM output and processed using a custom script to carry out differential expression analysis using Bioconductor software’s package edgeR to compute a p-value and fold-change for each transcript.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: brown adipose tissue

growth_protocol: Mice were housed at room tempature and received normal chow diet for the first 8 weeks of life.

extract_protocol:
Brown adipose tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Paired-end sequencing libraries using the NEBNext Ultra RNA library preparation kit according to the manufacturer’s instructions

treatment_protocol: Male F1 intercross progeny of C57BL/6J and 129S1SvImJ mice (Jackson Labs stock number: JAX 101043) mice received for two weeks a control low fat diet (Research Diets D12450B, n=5), or the same diet wtih 0.005% rosiglitazone (n=5), or with 0.2% fenofibrate (n=5).

tag: tag

value: brown adipose tissue

value: 8 weeks


title: Feno_rep5_82

description:
LFD + Feno
Feno_rep5_82


title: Feno_rep1_78

description:
LFD + Feno
Feno_rep1_78


title: Feno_rep4_80

description:
LFD + Feno
Feno_rep4_80


title: Rosi_rep5_69

description:
LFD + Rosi
Rosi_rep5_69


title: Feno_rep2_79

description:
LFD + Feno
Feno_rep2_79


title: Rosi_rep4_67

description:
LFD + Rosi
Rosi_rep4_67


title: Rosi_rep3_70

description:
LFD + Rosi
Rosi_rep3_70


title: Rosi_rep2_68

description:
LFD + Rosi
Rosi_rep2_68


title: GCU031: Type 2 diabetic


title: Control_rep5_26

description:
LFD
Control_rep5_26


title: Control_rep3_29

description:
LFD
Control_rep3_29


title: Control_rep2_28

description:
LFD
Control_rep2_28


title: Control_rep4_25

description:
LFD
Control_rep4_25


title: Control_rep1_27

description:
LFD
Control_rep1_27


title: 6681

city: Madison

first: Feyza

last: Engin

state: Wisconsin

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison

description:
ClusterWT_KO_alpha_DEG_mean.txt
ClusterWT_KO_beta_DEG_mean.txt
ClusterWT_KO_delta_DEG_mean.txt

data_processing:
Cell Ranger mkfastq v3.0.0
Cell Ranger count v3.0.0
cellranger-aggr v3.0.0
Genome_build: mm10
Supplementary_files_format_and_content: txt files of differential gene expression analysis of either beta, alpha, or delta cells

source_name: Pancreatic islets

growth_protocol: Housed under a 12:12-hr light/dark cycle, with unrestricted access to food and drinking water in an animal housing facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol:
Islets were isolated using the standard collagenase/protease digestion method. The pancreatic duct was cannulated and distended with 4°C collagenase/protease solution. Islets were separated from the exocrine tissue using Histopaque-1077. Hand-picked islets were cultured overnight at 37°C in RPMI-1640 media containing 10% FBS and 1% Penicillin/Streptomycin. Cells were dissociated using accutase digestion.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: To induce Cre recombinase activity, tamoxifen was dissolved in sterilized corn oil  by shaking overnight at 37°C. The solution was protected from light, and 10 mg/ml tamoxifen was administrated via intraperitoneal injection twice every 24 hours in five consecutive days.

value: NOD/ShiLtJ

value: Pancreatic islets

value: 5 weeks old


title: 6680