title: NN_Ox1-LN WGBS

city: Nanjing, Jiangshu Province

first: Xiaorong

last: Fan

state: Jiangshu

address: Tongwei Road 1

institute: Nanjing Agricultural University

description:
0N0N82_0NHN82_gene_intersect_dmr.dataset
0N0N82_0NHN82__dmr_zone.bed

data_processing:
After downloading raw data from sequencing machine, in order to avoid alignment error, the raw reads will be filtered and trimmed to obtain clean reads. First, remove polluted adapter reads (remove the reads with the number of contaminants in the base more than 5bp) . Second, remove the reads with base calling quality Qemo), and third, remove reads with the percentage of N >5% (For pair-end sequencing, if one end is removed, both ends will be removed). After filtering, the available data were compared with the reference genome Oryza_sativa.IRGSP-1.0.32 to obtain the alignment results using Bismark (v0.9.0) (K Felix, et al. 2011).  The uniquely mapped reads will be used to call the methylated cytosines(C) in highly enriched regions.Valid coverage of methylated cytosine, i.e. the percentage of methylated C among all C on genome, is associated with methylation level. C sites with read depths less than 5 are eliminated firstly. Then for each C site, valid coverage is calculated by for all C or C within each pattern (CpG, CGH, and CHH). Coverage is the count of C sites with more than 5 depth divided by total number of C site by its pattern. For each C site, the methylation level (%) is calculated by: 100* (reads supportted methylation)/ (total reads depth of this site). For methylated region, methylation level (%) is calculated by: 100*methylation level of all C sites in this region/Total number of C sites in this region. The conversion ratio of  Lambda DNA is around 99.5% to 99.6% in all samples.
DMR for (1) The read coverage of each C locus > 4; (2) The total number of C loci in each DMR > = 5; (3) The length of DMR > = 100bp;(4) The difference of methylation level between groups was greater than or equal to 0.3;(5) The CPG site with p-value less than 1e-10 was reserved as the final DMR.
Based on the results of DMR genome annotation, the number of genes with overlapping promoter (1KB upstream) and gene body region
Genome_build: IRGSP1
Supplementary_files_format_and_content: Processed data were stored in txt files, which included differentially methylated region in dmr_zone file, and  gene name in gene_intersect_dmr file.

organism: Oryza sativa

source_name: DNA methylation of NN_Ox1-LN

growth_protocol: For plants grow in the field, all materials were grown in plots in the Agricultural Experiment Station of Zhejiang University, Changxing, Zhejiang. Changxing is located in a subtropical monsoon climate zone. The pH of the soil is 7.2. Potassium, phosphate was fertilization at usual levels in the fields (225kg/ha and 450kg/ha). Plots size was 2 × 2.5 m and the seedlings planted in a 10 × 10 array.

extract_protocol:
For rice grow in the field, all materials were grown in plots in the Agricultural Experiment Station of Zhejiang University, Changxing, Zhejiang. Samples collected in the mature.
Samples shipped to the Anoroad Genome company(Beijing) for whole-genome bisulfite sequencing(WGBS). WGBS librarie preparation, sequencing and data analysis was described as before (??). WGBS libraries are prepared for subsequent cluster generation starting from sample DNA through adaptor ligation, library purification, and quantification. Input gDNA (5 μg) is fragmented by sonication. The fragments are blunt-ended and phosphorylated, and a single ʹAʹ nucleotide is added to the 3ʹ ends of the fragments in preparation for ligation to a methylated adapter that has a single-base ʹTʹ overhang. The ligation products are purified and size-selected by agarose gel electrophoresis. Size-selected DNA is bisulfite-treated and purified. The treated DNA is PCR-amplified to enrich the fragment that have adapters on both ends. The final purified product is then quantitated prior to cluster generation. The WGBS libraries will be sequenced using Illumina HiSeq2500 /4000 Analyzer according to the manufacturer’s instructions.

treatment_protocol: Plants were plants in the field fertilized at a rate of 300 kg N/ha as HN field, no N fertilizer as NN field and the field without N fertilizer (NN) since 2009.

value: shoot


title: blastoid 96h TROP2 pl-154303

status: Public on Sep 15 2021

type: SRA

city: Vienna

first: Giovanni

last: Sestini

address: Dr.-Bohr-Gasse 3, 1030 Wien

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

library_source: transcriptomic

data_processing:
Smart-Seq transcriptome sequencing experiments were analyzed using genome sequence and gene annotation from Ensembl GRCh38 release 103 as reference. For gene expression quantification RNA-seq reads were first trimmed using trim-galore v0.6.6 and thereafter aligned to the genome using hisat2 v2.2.1. Uniquely mapping reads in genes were quantified using htseq-count v0.13.5 with parameter -s no. TPM estimates were obtained using RSEM v1.3.3 with parameter --single-cell-prior. Further analysis was performed in R v4.0.3 with Seurat v4.0.1. Based on initial evaluation of per-cell quality control metrices and outlier identification using the median absolute deviation algorithm, cells with <= 2000 detected genes or >= 12.5% mitochondrial gene percentage were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: tsv of read counts per gene

molecule: polyA RNA

organism: Homo sapiens

source_name: blastoid

extract_protocol:
Smart-Seq2 protocol
Smart-Seq2

tag: treatment


title: C_24h_R2

city: POZUELO DE ALARCON

first: M. ESTRELLA

last: SANTAMARIA

state: MADRID

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

country: Spain

institute: CBGP (UPM-INIA)

data_processing:
Raw data obtained in FASTQ format was processed to remove adapters and poly-N sequences as well as low quality reads. DNA sequences were analysed and processed using Trimmomatic (Galaxy Version 0.38.0), dropping reads below Q15 with a sliding window of 4bp
Reads whose length was below 108bp were removed. Trimmed reads were aligned to the A. thaliana (TAIR10) genome
Kallisto was used to calculate the abundance of the transcripts as transcripts per million (TPM) by pseudo aligning the sample reads to the reference using the default k-mer length of 31 and 100 bootstrap repetitions.
Fold changes (FC) and adjusted p-values (q-value) for each gene were calculated using the Sleuth software. Each time point was compared to its corresponding control by means of a Wald test and the Lancaster aggregation method
Genome_build: A. thaliana (TAIR10) genome (https://www.arabidopsis.org)
Supplementary_files_format_and_content: abundance.tsv (results of the main quantification, i.e. the abundance estimate); run_info.json (summary of the run, including data on the number targets used for quantification, the number of bootstraps performed, the version of the program used and how it was called); abundance.h5 (contains the main quantification together with the boostraps in HDF5 format)

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: Sterilized seeds were planted in a mixture of peat moss and vermiculite (2:1 v/v) and incubated in the dark for 5 days at 4°C. Plants were then transferred to growth chambers (Sanyo MLR-350-H) under controlled conditions (23°C ± 1°C, >70% RH and a 16 h/8 h day/night photoperiod).

extract_protocol:
Frozen material was thoroughly grinded on liquid nitrogen and total RNA was extracted by means of the RNeasy plant mini kit (Qiagen), and a DNase treatment (Qiagen) following manufacturer´s instructions.
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Three-week-old plants were treated by applying 2 μL of egg extract as described above. After 3, 24 and 72 hpt, whole rosettes were sampled, introduced in liquid nitrogen and stored at –80°C until used for RNA extraction.

tag: ecotype

value: Columbia (Col-0)

tag: treatment time (h)

value: water for 24h

tag: tissue

value: Five whole rosettes pooled


title: blastoid 96h TROP2 pl-154302


title: blastoid 96h TROP2 pl-154299


title: blastoid 96h TROP2 pl-154301


title: blastoid 96h TROP2 pl-154298


title: blastoid 96h TROP2 pl-154297


title: C_24h_R1


title: Endometrium_LPR_86

type: RNA

city: Valencia

first: Patricia

last: Sebastian-Leon

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

institute: IVI-RMA Foundation

hyb_protocol: Sample preparation and hybridization of the RNA, training set and pathological samples were adapted from the Agilent technical manual (one color) (Agilent Technologies, Madrid, Spain).

scan_protocol: Hybridized microarrays were scanned in an Axon 4100A scanner (Molecular Devices, Sunnyvale, CA), and the data were extracted with the GenePix Pro 6.0 software (Molecular Devices).

data_processing: Normalized signal was obtained using limma and preprocessCore R-packages. F532 Median and B532 Meadian are the columns used for estimate probeset expression. Background was corrected using normexp method and 8 replicates for each probe were averaged.

source_name: endometrial biopsy

label_protocol: Agilent one color

extract_protocol: Endometrial samples were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was extracted using the TRIzol method according to the standard protocol (Life Technologies, Inc., Gaithersburg, MD). The RNA quality was assessed in the A2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany)

value: Endometrium

tag: gender

value: female

value: LPR


title: Endometrium_LPR_85


title: NN_Ox1-HN WGBS

country: China

library_source: genomic

molecule: genomic DNA

source_name: DNA methylation of NN_Ox1-HN

tag: genotype


title: Endometrium_LPR_83


title: Endometrium_LPR_84


title: blastoid 96h TROP2 pl-154300


title: blastoid 96h TROP2 pl-154296


title: blastoid 96h TROP2 pl-154294


title: blastoid 96h TROP2 pl-154293


title: Endometrium_LPR_82


title: normal rep30

city: Fushan

first: Jianhua

last: Xu

state: Guangdong

address: No. 12, Jinsha Avenue, Shunde District, Foshan, Guangdong, P.R. China

institute: Department of Laboratory Medicine Shunde Hospital of Guangzhou University of Chinese Medicine

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome ENSEMBL website, Tophat2 (v2.1.0) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Tophat2 (v2.1.02).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, RSEM (v1.3.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: Homo sapiens (GRCh37)
Supplementary_files_format_and_content: fpkm.csv: Comma-separated text file includes FPKM values for each Sample.

source_name: breast

extract_protocol:
Total RNA was isolated and purified using TRIzol (Life, cat.265709, CA, USA) following the manufacturer's procedure.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer (Implen, cat.N60, Munich, Germany), mRNA with poly(A) is purified from 1μg total RNA using VAHTS mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) through two rounds of purification. Subsequently, mRNA fragment was interrupted using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃ 8min and reversed transcription into cDNA which would use to synthesise U-labeled second-stranded DNAs. An A-base was added to the blunt ends of each strand to ligase the indexed adapters which contains a T-base at the tail end. After UDG enzyme treatment of the U-labeled double-strand DNA, size selection was performed with VAHTS DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). Then the ligated products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 5 min; 12-17 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, and extension at 72℃ for 30 sec; final extension at 72℃ for 5 min. The average insert size of cDNA library was 280±80 bp. After purification by VAHTS DNA Clean Beads (Vazyme, cat.N411-02, Nanjing, China), quality control of concentration and fragment size is performed by Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and Qubit assay tubes (Life, cat. 1604220, CA, USA).

value: normal breast tissue

tag: metastasis

value: yes

tag: donor


title: normal rep29

value: no


title: normal rep28


title: blastoid 96h TROP2 pl-154290


title: Endometrium_LPR_81


title: blastoid 96h TROP2 pl-154291


title: normal rep27


title: Endometrium_LPR_7


title: blastoid 96h TROP2 pl-154289


title: Endometrium_LPR_80


title: blastoid 96h TROP2 pl-154288


title: blastoid 96h TROP2 pl-154295


title: blastoid 96h TROP2 pl-154287


title: blastoid 96h TROP2 pl-154292


title: Endometrium_LPR_79


title: normal rep26


title: normal rep25


title: blastoid 96h TROP2 pl-154286


title: blastoid 96h TROP2 pl-154283


title: normal rep24


title: blastoid 96h TROP2 pl-154284


title: blastoid 96h TROP2 pl-154279


title: blastoid 96h TROP2 pl-154281


title: Endometrium_LPR_78


title: normal rep22


title: blastoid 96h TROP2 pl-154277


title: blastoid 96h TROP2 pl-154282


title: Endometrium_LPR_76


title: blastoid 96h TROP2 pl-154285


title: normal rep23


title: Endometrium_LPR_77


title: Endometrium_LPR_72


title: Endometrium_LPR_75


title: blastoid 96h TROP2 pl-154276


title: normal rep21


title: blastoid 96h TROP2 pl-154274


title: normal rep20


title: blastoid 96h TROP2 pl-154275


title: Endometrium_LPR_73


title: normal rep19


title: blastoid 96h TROP2 pl-154272


title: blastoid 96h TROP2 pl-154271


title: normal rep17


title: blastoid 96h TROP2 pl-154269


title: Endometrium_LPR_74


title: blastoid 96h TROP2 pl-154280


title: Endometrium_LPR_70


title: Endometrium_LPR_71


title: normal rep18


title: blastoid 96h TROP2 pl-154270


title: blastoid 96h TROP2 pl-154268


title: blastoid 96h TROP2 pl-154278


title: blastoid 96h TROP2 pl-154265


title: normal rep15


title: normal rep13


title: normal rep16


title: Endometrium_LPR_6


title: blastoid 96h TROP2 pl-154261


title: normal rep11


title: blastoid 96h TROP2 pl-154260


title: Endometrium_LPR_69


title: blastoid 96h TROP2 pl-154262


title: blastoid 96h TROP2 pl-154266


title: blastoid 96h TROP2 pl-154263


title: blastoid 96h TROP2 pl-154273


title: Endometrium_LPR_67


title: blastoid 96h TROP2 pl-154264


title: Endometrium_LPR_66


title: normal rep14


title: blastoid 96h TROP2 pl-154259


title: blastoid 96h TROP2 pl-154267


title: blastoid 96h TROP2 pl-154255


title: blastoid 96h TROP2 pl-154258


title: normal rep12


title: blastoid 96h TROP2 pl-154257


title: Endometrium_LPR_68


title: Endometrium_LPR_65


title: blastoid 96h TROP2 pl-154256


title: normal rep10


title: normal rep9


title: Endometrium_LPR_64


title: normal rep8


title: blastoid 96h TROP2 pl-154252


title: blastoid 96h TROP2 pl-154253


title: Endometrium_LPR_62


title: blastoid 96h TROP2 pl-154251


title: blastoid 96h TROP2 pl-154250


title: Endometrium_LPR_63


title: blastoid 96h TROP2 pl-154247


title: normal rep6


title: blastoid 96h TROP2 pl-154249


title: blastoid 96h TROP2 pl-154248


title: blastoid 96h TROP2 pl-154246


title: Endometrium_LPR_61


title: normal rep7


title: blastoid 96h TROP2 pl-154254


title: Endometrium_LPR_60


title: blastoid 96h TROP2 pl-154244


title: normal rep5


title: Endometrium_LPR_5


title: normal rep4


title: blastoid 96h TROP2 pl-154243


title: Endometrium_LPR_59


title: blastoid 96h TROP2 pl-154242


title: Endometrium_LPR_58


title: normal rep2


title: blastoid 96h TROP2 pl-154239


title: blastoid 96h TROP2 pl-154240


title: normal rep3


title: blastoid 96h TROP2 pl-154245


title: blastoid 96h TROP2 pl-154238


title: normal rep1


title: blastoid 96h TROP2 pl-154236


title: Endometrium_LPR_57


title: blastoid 96h TROP2 pl-154235


title: blastoid 96h TROP2 pl-154237


title: tumor rep30

value: breast tumor


title: blastoid 96h TROP2 pl-154232


title: blastoid 96h TROP2 pl-154233


title: blastoid 96h TROP2 pl-154234


title: tumor rep28


title: tumor rep29


title: blastoid 96h TROP2 pl-154231


title: Endometrium_LPR_55


title: Endometrium_LPR_56


title: blastoid 96h TROP2 pl-154230


title: blastoid 96h TROP2 pl-154241


title: Endometrium_LPR_53


title: Endometrium_LPR_54


title: tumor rep27


title: blastoid 96h TROP2 pl-154228


title: blastoid 96h TROP2 pl-154229


title: Endometrium_LPR_52


title: blastoid 96h TROP2 pl-154227


title: tumor rep26


title: blastoid 96h TROP2 pl-154226


title: tumor rep25


title: Endometrium_LPR_50


title: blastoid 96h TROP2 pl-154224


title: blastoid 96h TROP2 pl-154222


title: blastoid 96h TROP2 pl-154223


title: blastoid 96h TROP2 pl-154220


title: tumor rep23


title: blastoid 96h TROP2 pl-154219


title: Endometrium_LPR_49


title: blastoid 96h TROP2 pl-154218


title: tumor rep21


title: blastoid 96h TROP2 pl-154216


title: blastoid 96h TROP2 pl-154217


title: blastoid 96h TROP2 pl-154213


title: blastoid 96h TROP2 pl-154214


title: blastoid 96h TROP2 pl-154212


title: Endometrium_LPR_48


title: blastoid 96h TROP2 pl-154215


title: Endometrium_LPR_51


title: tumor rep20


title: Endometrium_LPR_46


title: Endometrium_LPR_47


title: blastoid 96h TROP2 pl-154225


title: tumor rep19


title: blastoid 96h TROP2 pl-154210


title: Endometrium_LPR_45


title: Endometrium_LPR_4


title: blastoid 96h TROP2 pl-154211


title: tumor rep22


title: blastoid 96h TROP2 pl-154208


title: tumor rep24


title: blastoid 96h TROP2 pl-154206


title: Endometrium_LPR_44


title: tumor rep16


title: blastoid 96h TROP2 pl-154207


title: Endometrium_LPR_43


title: tumor rep17


title: blastoid 60h TROP2 min-150944


title: tumor rep14


title: blastoid 60h TROP2 min-150945


title: tumor rep18


title: Endometrium_LPR_42


title: blastoid 60h TROP2 min-150943


title: Endometrium_LPR_41


title: blastoid 60h TROP2 min-150942


title: blastoid 60h TROP2 min-150946


title: tumor rep13


title: Endometrium_LPR_40


title: blastoid 96h TROP2 pl-154209


title: Endometrium_LPR_39


title: Endometrium_LPR_3


title: blastoid 60h TROP2 min-150939


title: blastoid 60h TROP2 min-150938


title: blastoid 60h TROP2 min-150941


title: tumor rep15


title: blastoid 60h TROP2 min-150935


title: tumor rep10


title: blastoid 60h TROP2 min-150937


title: tumor rep11


title: blastoid 60h TROP2 min-150934


title: Endometrium_LPR_37


title: Endometrium_LPR_38


title: blastoid 60h TROP2 min-150931


title: blastoid 60h TROP2 min-150948


title: blastoid 60h TROP2 min-150929


title: tumor rep9


title: blastoid 60h TROP2 min-150927


title: Endometrium_LPR_35


title: blastoid 60h TROP2 min-150922


title: blastoid 60h TROP2 min-150925


title: tumor rep7


title: tumor rep12


title: tumor rep8


title: Endometrium_LPR_34


title: Endometrium_LPR_36


title: blastoid 60h TROP2 min-150921


title: blastoid 60h TROP2 min-150923


title: tumor rep6


title: blastoid 60h TROP2 min-150918


title: blastoid 60h TROP2 min-150919


title: blastoid 60h TROP2 min-150915


title: tumor rep5


title: Endometrium_LPR_33


title: blastoid 60h TROP2 min-150914


title: Endometrium_LPR_32


title: tumor rep4


title: blastoid 60h TROP2 min-150912


title: Endometrium_LPR_31


title: blastoid 60h TROP2 min-150911


title: tumor rep2


title: Endometrium_LPR_2


title: tumor rep3


title: blastoid 60h TROP2 min-150907


title: blastoid 60h TROP2 min-150910


title: blastoid 60h TROP2 min-150906


title: blastoid 60h TROP2 min-150904


title: tumor rep1


title: blastoid 60h TROP2 min-150903


title: blastoid 60h TROP2 min-150902


title: blastoid 60h TROP2 min-150899


title: blastoid 60h TROP2 min-150897


title: Caco-2/15 cells infected with lentivirus shNCOR1_655 rep3

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

data_processing:
The mapping is performed with “Star 2.4.0f1”.
The basecalling is performed directly with the HiSeq instrument and run with the tool “Illumina RTA”
The “Illumina bcl2fastq v2.20” tool is used to generate the FASTQ prior to the alignment
Genome_build: 1000 genome (b37)
Supplementary_files_format_and_content: tab-delimited text file

source_name: Caco-2/15 cells

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
Libraries were generated from 250 ng of total RNA as follows: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs, Whitby, Canada). cDNA synthesis was achieved using NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England BioLabs). The remaining steps of library preparation were performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: Caco-2/15 and HT-29 cells were transduced in triplicate with either shNT or shNCOR1_655 lentiviruses and selected with 10 µg/ml of puromycin for 7 days. Total RNA from adhered cells was isolated

tag: cell type

value: Caco-2/15 colon cancer cell line

value: Lentivirus Sigma Mission shRNA shNCOR1_655 clone ID TRCN0000060655


title: Caco-2/15 cells infected with lentivirus shNCOR1_655 rep2


title: blastoid 60h TROP2 min-150896


title: Caco-2/15 cells infected with lentivirus shNCOR1_655 rep1


title: blastoid 60h TROP2 min-150895


title: blastoid 60h TROP2 min-150893


title: blastoid 60h TROP2 min-150891


title: Caco-2/15 cells infected with lentivirus shNonTarget rep3

value: Lentivirus shNonTarget Sigma clone ID SHC002


title: blastoid 60h TROP2 min-150908


title: Endometrium_LPR_27


title: Endometrium_LPR_26


title: Endometrium_LPR_29


title: Endometrium_LPR_28


title: Endometrium_LPR_25


title: Endometrium_LPR_30


title: blastoid 60h TROP2 min-150889


title: blastoid 60h TROP2 min-150890


title: blastoid 60h TROP2 min-150888


title: Endometrium_LPR_24


title: Caco-2/15 cells infected with lentivirus shNonTarget rep1


title: Caco-2/15 cells infected with lentivirus shNonTarget rep2


title: blastoid 60h TROP2 min-150886


title: blastoid 60h TROP2 min-150885


title: blastoid 60h TROP2 min-150884


title: blastoid 60h TROP2 min-150882


title: HT-29 cells infected with lentivirus shNCOR1_655 rep2

source_name: HT-29 cells

value: HT-29 colon cancer cell line


title: Endometrium_LPR_22


title: blastoid 60h TROP2 min-150881


title: Endometrium_LPR_21


title: blastoid 60h TROP2 min-150880


title: blastoid 60h TROP2 min-150878


title: HT-29 cells infected with lentivirus shNCOR1_655 rep1


title: HT-29 cells infected with lentivirus shNonTarget rep3


title: blastoid 60h TROP2 min-150877


title: blastoid 60h TROP2 min-150876


title: blastoid 60h TROP2 min-150887


title: HT-29 cells infected with lentivirus shNonTarget rep2


title: Endometrium_LPR_209


title: HT-29 cells infected with lentivirus shNCOR1_655 rep3


title: blastoid 60h TROP2 min-150873


title: Endometrium_LPR_208


title: blastoid 60h TROP2 min-150874


title: Endometrium_LPR_23


title: HT-29 cells infected with lentivirus shNonTarget rep1


title: Endometrium_LPR_207


title: LNCaP_dox-3

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

country: USA

institute: University of Texas, MD Anderson Cancer Center

description: LNCaP ishJMJD1C-1 dox replicate 3

data_processing:
Raw sequencing data (BCL format) were converted to Fastq files using Illumina Casava software (v1.8.2)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 using STAR software.
The HTSeq-count program was used to generate raw read counts for each gene
Normalized counts were generated by DESeq2 package in R
Genome_build: hg19
Supplementary_files_format_and_content: normalized counts

extract_protocol:
RNA was isolated by the RNeasy Mini Kit (Qiagen). DNA was removed by treating with DNase from the kit (Qiagen). cDNA was generated using All-In-One RT MasterMix (ABM, G490). qRT-PCR was performed with 1x SYBRTM Green PCR Master Mix (Thermo, 4309155) using primers that had been optimized for their melt curve.
Libraries were generated using Illumina’s TruSeq kit

treatment_protocol: doxycycline-inducible shRNA cassette targeting JMJD1C

value: LNCaP prostate cancer cell line

value: dox


title: Endometrium_LPR_206


title: blastoid 60h TROP2 min-150872


title: blastoid 60h TROP2 min-150870


title: blastoid 60h TROP2 min-150867


title: blastoid 60h TROP2 min-150868


title: APIPC-shJMJD1C-2-3

description: LNCaP_APIPC shJMJD1C-2 replicate 3

value: LNCaP APIPC / AR depletion prostate cancer cell line


title: Endometrium_LPR_20


title: blastoid 60h TROP2 min-150865


title: blastoid 60h TROP2 min-150866


title: Endometrium_LPR_205


title: APIPC-shJMJD1C-2-2

description: LNCaP_APIPC shJMJD1C-2 replicate 2


title: blastoid 60h TROP2 min-150864


title: Endometrium_LPR_204


title: blastoid 60h TROP2 min-150863


title: Endometrium_LPR_203


title: blastoid 60h TROP2 min-150859


title: APIPC-shJMJD1C-2-1

description: LNCaP_APIPC shJMJD1C-2 replicate 1


title: blastoid 60h TROP2 min-150861


title: blastoid 60h TROP2 min-150869


title: APIPC-shJMJD1C-1-3

description: LNCaP_APIPC shJMJD1C-1 replicate 3


title: blastoid 60h TROP2 min-150855


title: Endometrium_LPR_202


title: blastoid 60h TROP2 min-150856


title: blastoid 60h TROP2 min-150857


title: APIPC-shJMJD1C-1-2

description: LNCaP_APIPC shJMJD1C-1 replicate 2


title: blastoid 60h TROP2 min-150853


title: Endometrium_LPR_201


title: APIPC-shJMJD1C-1-1

description: LNCaP_APIPC shJMJD1C-1 replicate 1


title: blastoid 60h TROP2 min-150851


title: blastoid 60h TROP2 min-150850


title: Endometrium_LPR_1


title: 3-APIPC-NS-3

description:
LNCaP_APIPC non silencing replicate 3
Ron-YY-APIPC-R778-3-APIPC-NS-3_200930-NB501550-0598-AH7HYVBGXG-1-NoIndex
processed data file: LNCaP_APIPC.norm.counts.tsv

source_name: APIPC-NS

value: LNCaP APIPC/AR depletion prostate cancer cell line

value: Non Silencing


title: Endometrium_LPR_200


title: 2-APIPC-NS-2

description:
LNCaP_APIPC non silencing replicate 2
Ron-YY-APIPC-R778-2-APIPC-NS-2_200930-NB501550-0598-AH7HYVBGXG-1-NoIndex
processed data file: LNCaP_APIPC.norm.counts.tsv


title: blastoid 60h TROP2 min-150849


title: Endometrium_LPR_19


title: blastoid 60h TROP2 min-150847


title: 1-APIPC-NS-1

description:
LNCaP_APIPC non silencing replicate 1
Ron-YY-APIPC-R778-1-APIPC-NS-1_200930-NB501550-0598-AH7HYVBGXG-1-NoIndex
processed data file: LNCaP_APIPC.norm.counts.tsv


title: blastoid 60h TROP2 min-150846


title: Endometrium_LPR_199


title: blastoid 60h TROP2 min-150845


title: blastoid 60h TROP2 min-150844


title: Endometrium_LPR_198


title: Yohei-04_LNCaP_dox

description:
LNCaP ishJMJD1C dox replicate 1
DChakravarti-12mRNA-hg-Yohei-04_200805-NB501070-0271-AHLGHMBGXF-1-CCGTCC
processed data file: LNCaP.norm.counts.tsv


title: blastoid 60h TROP2 min-150843


title: blastoid 60h TROP2 min-150842


title: blastoid 60h TROP2 min-150852


title: blastoid 60h TROP2 min-150840


title: Yohei-03_LNCaP_no_dox

description:
LNCaP ishJMJD1C no dox replicate 3
DChakravarti-12mRNA-hg-Yohei-03_200805-NB501070-0271-AHLGHMBGXF-1-ATGTCA
processed data file: LNCaP.norm.counts.tsv

value: nodox


title: Endometrium_LPR_197

value: Endometrium


title: blastoid 60h TROP2 min-150841


title: blastoid 60h TROP2 min-150839


title: Yohei-02_LNCaP_no_dox

description:
LNCaP ishJMJD1C no dox replicate 2
DChakravarti-12mRNA-hg-Yohei-02_200805-NB501070-0271-AHLGHMBGXF-1-AGTTCC
processed data file: LNCaP.norm.counts.tsv


title: Endometrium_LPR_195

value: female


title: blastoid 60h TROP2 min-150838


title: blastoid 60h TROP2 min-150848


title: Yohei-01_LNCaP_no_dox

description:
LNCaP ishJMJD1C no dox replicate 1
DChakravarti-12mRNA-hg-Yohei-01_200805-NB501070-0271-AHLGHMBGXF-1-AGTCAA
processed data file: LNCaP.norm.counts.tsv


title: Endometrium_LPR_196

value: LPR


title: blastoid 60h TROP2 min-150836


title: blastoid 60h TROP2 min-150835


title: blastoid 60h TROP2 min-150833


title: Yohei-06_LNCaP_dox

description:
LNCaP ishJMJD1C dox replicate 2
DChakravarti-12mRNA-hg-Yohei-06_200805-NB501070-0271-AHLGHMBGXF-1-GTGAAA
processed data file: LNCaP.norm.counts.tsv


title: PC3 shJMJD1C-2-plusdox-3

description: PC3 shJMJD1C-2-dox replicate 3

value: PC3 prostate cancer cell line


title: Endometrium_LPR_193


title: blastoid 60h TROP2 min-150831


title: PC3 shJMJD1C-2-plusdox-2

description: PC3 shJMJD1C-2-dox replicate 2


title: blastoid 60h TROP2 min-150827


title: PC3 shJMJD1C-2-plusdox-1

description: PC3 shJMJD1C-2-dox replicate 1


title: Endometrium_LPR_191


title: Endometrium_LPR_192


title: blastoid 60h TROP2 min-150824


title: PC3 shJMJD1C-2-nodox-3

description: PC3 shJMJD1C-2-nodox replicate 3


title: blastoid 60h TROP2 pl-150821


title: blastoid 60h TROP2 pl-150819


title: Endometrium_LPR_190


title: PC3 shJMJD1C-2-nodox-2

description: PC3 shJMJD1C-2-nodox replicate 2


title: blastoid 60h TROP2 pl-150820


title: blastoid 60h TROP2 min-150837


title: blastoid 60h TROP2 pl-150817


title: Endometrium_LPR_18


title: PC3 shJMJD1C-2-nodox-1

description: PC3 shJMJD1C-2-nodox replicate 1


title: blastoid 60h TROP2 pl-150816


title: blastoid 60h TROP2 pl-150815


title: Endometrium_LPR_189


title: Endometrium_LPR_194


title: PC3 shJMJD1C-1-plusdox-3

description: PC3 shJMJD1C-1-dox replicate 3


title: blastoid 60h TROP2 min-150829


title: Endometrium_LPR_188


title: blastoid 60h TROP2 pl-150814


title: blastoid 60h TROP2 pl-150813


title: PC3 shJMJD1C-1-plusdox-2

description: PC3 shJMJD1C-1-dox replicate 2


title: blastoid 60h TROP2 pl-150812


title: blastoid 60h TROP2 pl-150811


title: Endometrium_LPR_187


title: PC3 shJMJD1C-1-plusdox-1

description: PC3 shJMJD1C-1-dox replicate 1


title: PC3 shJMJD1C-1-nodox-3

description: PC3 shJMJD1C-1-nodox replicate 3


title: blastoid 60h TROP2 pl-150818


title: blastoid 60h TROP2 pl-150808


title: blastoid 60h TROP2 pl-150810


title: blastoid 60h TROP2 pl-150809


title: blastoid 60h TROP2 pl-150807


title: Endometrium_LPR_184


title: blastoid 60h TROP2 pl-150805


title: blastoid 60h TROP2 pl-150804


title: PC3 shJMJD1C-1-nodox-1

description: PC3 shJMJD1C-1-nodox replicate 1


title: Endometrium_LPR_185


title: Endometrium_LPR_183


title: PC3 shJMJD1C-1-nodox-2

description: PC3 shJMJD1C-1-nodox replicate 2


title: blastoid 60h TROP2 pl-150803


title: blastoid 60h TROP2 pl-150799


title: Endometrium_LPR_182


title: Endometrium_LPR_181


title: blastoid 60h TROP2 pl-150802


title: Kuramochi H3K27ac

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Sample(s) were aligned to the hg19 revision of the human reference genome using bowtie with configuration -p 4 --best -k 2 -m 2 --sam and -l set to the read length
Reads were counted in 50bp bins using MACS 1.4 with parameters -w -S --space=50 --nomodel --shiftsize=200
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Ovarian cancer cell line

growth_protocol: Kuramochi, RPMI, 100 million cells per ChIP

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

value: Ovarian cancer cell line

tag: cell line

value: Kuramochi

tag: chip antibody

tag: antibody manu.

value: Active Motif

tag: antibody catalog


title: blastoid 60h TROP2 pl-150797


title: Endometrium_LPR_186


title: blastoid 60h TROP2 pl-150798


title: blastoid 60h TROP2 pl-150806


title: Endometrium_LPR_17


title: Endometrium_LPR_180


title: blastoid 60h TROP2 pl-150795


title: blastoid 60h TROP2 pl-150793


title: blastoid 60h TROP2 pl-150792


title: blastoid 60h TROP2 pl-150796


title: GAC_W0628_T

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt). FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
After that, clean reads were aligned to the human hg19 by tophat2 (Kim et al., 2013). Aligned reads with more than one genome location were discarded due to their ambiguous location.
Uniquely localized reads were used to calculate reads number and RPKM value (RPKM represents reads per kilobase and per million) for each gene according to reads and genes genome location. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
After getting the Expression level of all genes in all samples, differentially expressed genes were analyzed by using edgeR(Robinson et al., 2010), one of R packages. 0.01 p-value and 2 fold change were set as the threshold to define DEGs.
Alternative splicing events (ASEs) in the RNA-Seq samples and the regulated alternative splicing events (RASEs) between tumor and normal were detected and quantified by in house AS method called ABLas.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited MS Excel files including RPKM values for each Sample ...

source_name: gastric adenocarcinoma

extract_protocol:
Human tumor samples were obtained from patients following written informed consent.Samples were provided as fresh-frozen tissue specimen. Matching normal material was provided in the  form of adjacent non-tumorigenic tissue. All patient material was stored at -80 celsius.
After tissue samples treatment, total RNA was extracted from leukocyte by using TRIzol Reagent (Ambion) following the manufacturer’s instructions. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.  For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were ion fragmented at 95 ℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified. And products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing.

value: stomach

value: gastric adenocarcinoma

tag: tumor stage

value: Late

tag: phenotype

value: cancer


title: Kuramochi Input

tag: antibody lot


title: GAC_W0628_N

value: paracancer


title: blastoid 60h TROP2 pl-150791


title: Endometrium_LPR_178


title: blastoid 60h TROP2 pl-150790


title: GAC_W0627_T


title: blastoid 60h TROP2 pl-150789


title: GAC_W0620_T


title: Endometrium_LPR_176


title: Endometrium_LPR_179


title: blastoid 60h TROP2 pl-150787


title: blastoid 60h TROP2 pl-150788


title: GAC_W0505_N

value: Early


title: GAC_W0505_T


title: GAC_W0627_N


title: Endometrium_LPR_174


title: Endometrium_LPR_177


title: blastoid 60h TROP2 pl-150785


title: blastoid 60h TROP2 pl-150786


title: blastoid 60h TROP2 pl-150781


title: blastoid 60h TROP2 pl-150779


title: GAC_W0620_N


title: blastoid 60h TROP2 pl-150784


title: GAC_W0451_T


title: blastoid 60h TROP2 pl-150778


title: blastoid 60h TROP2 pl-150783


title: blastoid 60h TROP2 pl-150782


title: blastoid 60h TROP2 pl-150777


title: GAC_W0447_N


title: blastoid 60h TROP2 pl-150776


title: Endometrium_LPR_171


title: blastoid 60h TROP2 pl-150780


title: blastoid 60h TROP2 pl-150775


title: GAC_W0447_T


title: blastoid 60h TROP2 pl-150773


title: blastoid 60h TROP2 pl-150772


title: blastoid 60h TROP2 pl-150774


title: Endometrium_LPR_16


title: Endometrium_LPR_170


title: Endometrium_LPR_173


title: HCC_G0267_T

source_name: hepatocellular carcinoma

value: liver

value: hepatocellular carcinoma


title: blastoid 60h TROP2 pl-150771


title: blastoid 60h TROP2 pl-150770


title: Endometrium_LPR_172


title: blastoid 60h TROP2 pl-150769


title: Endometrium_LPR_169


title: HCC_G0228_N


title: blastoid 60h TROP2 pl-150767


title: blastoid 60h TROP2 pl-150766


title: blastoid 60h TROP2 pl-150768


title: Endometrium_LPR_168


title: HCC_G0228_T


title: blastoid 60h TROP2 pl-150765


title: blastoid 60h TROP2 pl-150764


title: HCC_G0224_N


title: blastoid 60h TROP2 pl-150763


title: Endometrium_LPR_166


title: blastoid 60h TROP2 pl-150762


title: HCC_G0224_T


title: HCC_G0267_N


title: blastoid 60h TROP2 pl-150760


title: blastoid 60h TROP2 pl-150759


title: Endometrium_LPR_175


title: Endometrium_LPR_165


title: GAC_W0451_N


title: Endometrium_LPR_164


title: blastoid 60h TROP2 pl-150758


title: HCC_G0218_T


title: blastoid 60h TROP2 pl-150757


title: blastoid 60h TROP2 pl-150756


title: Endometrium_LPR_162


title: Endometrium_LPR_163


title: Endometrium_LPR_167


title: blastoid 60h TROP2 pl-150754


title: blastoid 60h TROP2 pl-150755


title: blastoid 60h TROP2 pl-150761


title: HCC_G0213_T


title: Endometrium_LPR_161


title: blastoid 60h TROP2 pl-150753


title: blastoid 60h TROP2 pl-150752


title: blastoid 60h TROP2 pl-150751


title: Endometrium_LPR_160


title: HCC_G0164_N


title: HCC_G0218_N


title: blastoid 60h TROP2 pl-150747


title: blastoid 60h TROP2 pl-150748


title: CSCC_T0010_N

source_name: Cervical Squamous Cell

value: cervix

value: Cervical Squamous Cell


title: HCC_G0213_N


title: Endometrium_LPR_15

value: Endometrium


title: blastoid 60h TROP2 pl-150749


title: blastoid 60h TROP2 pl-150746


title: Endometrium_LPR_159

value: female


title: blastoid 60h TROP2 pl-150745


title: Endometrium_LPR_158

value: LPR


title: blastoid 60h TROP2 pl-150741


title: blastoid 60h TROP2 pl-150742


title: blastoid 60h TROP2 pl-150743


title: blastoid 60h TROP2 pl-150739


title: Endometrium_LPR_157


title: blastoid 60h TROP2 pl-150738


title: CSCC_F0297_T


title: blastoid 60h TROP2 pl-150750


title: CSCC_F0297_N


title: HCC_G0164_T


title: CSCC_F0287_N


title: Endometrium_LPR_155


title: Endometrium_LPR_156


title: blastoid 60h TROP2 pl-150736


title: blastoid 60h TROP2 pl-150744


title: blastoid 60h TROP2 pl-150735


title: blastoid 60h TROP2 pl-150733


title: blastoid 60h TROP2 pl-150731


title: CSCC_F0287_T


title: Endometrium_LPR_154


title: blastoid 60h TROP2 pl-150730


title: CSCC_T0010_T


title: SCLC_X0608_N

source_name: small cell lung

value: lung

value: small cell lung


title: Endometrium_LPR_153


title: blastoid 60h TROP2 pl-150729


title: blastoid 60h TROP2 pl-150737


title: blastoid 60h TROP2 pl-150727


title: blastoid 60h TROP2 pl-150726


title: blastoid 60h TROP2 pl-150728


title: blastoid 60h TROP2 pl-150725


title: Endometrium_LPR_152


title: SCLC_X0608_T


title: SCLC_X0272_N


title: blastoid 60h TROP2 pl-150724


title: SCLC_X0272_T


title: blastoid 60h TROP2 pl-150722


title: Endometrium_LPR_151


title: Endometrium_LPR_14


title: blastoid 60h TROP2 pl-150721


title: Endometrium_LPR_150


title: SCLC_X0242_N


title: blastoid 60h TROP2 pl-150723


title: SCLC_X0242_T


title: Endometrium_LPR_148


title: blastoid 60h TROP2 pl-150717


title: blastoid 60h TROP2 pl-150718


title: blastoid 60h TROP2 pl-150720


title: blastoid 60h TROP2 pl-150719


title: Endometrium_LPR_149


title: SCLC_X0212_T


title: blastoid 60h TROP2 pl-150715


title: blastoid 60h TROP2 pl-150714


title: blastoid 60h TROP2 pl-150716


title: Endometrium_LPR_146


title: blastoid 60h TROP2 pl-150712


title: blastoid 60h TROP2 pl-150713


title: blastoid 60h TROP2 pl-150710


title: blastoid 60h TROP2 pl-150711


title: Endometrium_LPR_144


title: LUSC_X622_T

source_name: Lung Squamous Cell

value: Lung Squamous Cell


title: LUAD_X0803_T

source_name: lung adenocarcinoma

value: lung adenocarcinoma


title: LUSC_X622_N


title: blastoid 60h TROP2 pl-150708


title: blastoid 60h TROP2 pl-150709


title: blastoid 60h TROP2 pl-150707


title: Endometrium_LPR_143


title: Endometrium_LPR_142


title: LUSC_X0753_N


title: LUSC_X0753_T


title: Endometrium_LPR_141


title: blastoid 60h TROP2 pl-150705


title: SCLC_X0212_N


title: blastoid 60h TROP2 pl-150702


title: Endometrium_LPR_13


title: Endometrium_LPR_140


title: LUAD_X0742_T


title: Endometrium_LPR_139


title: ESCC_X0724_T

source_name: esophageal squamous cell

value: esophagus

value: esophageal squamous cell


title: Endometrium_LPR_145


title: blastoid 60h TROP2 pl-150698


title: CSCC_T0024_T

value: Late


title: Endometrium_LPR_138


title: blastoid 60h TROP2 pl-150699


title: LUAD_X0742_N


title: Endometrium_LPR_137


title: blastoid 60h TROP2 pl-150700


title: ESCC_X0724_N


title: ESCC_X0704_T

value: cancer


title: blastoid 60h TROP2 pl-150697


title: blastoid 60h TROP2 pl-150696


title: Endometrium_LPR_136


title: Endometrium_LPR_147


title: blastoid 60h TROP2 pl-150703


title: blastoid 24h-150693

value: PALLY


title: blastoid 60h TROP2 pl-150704


title: blastoid 24h-150692


title: blastoid 60h TROP2 pl-150701


title: blastoid 24h-150691


title: LUSC_X0703_T


title: ESCC_X0704_N

value: paracancer


title: blastoid 24h-150690


title: blastoid 24h-150689


title: Endometrium_LPR_135


title: blastoid 24h-150686


title: blastoid 24h-150688


title: Endometrium_LPR_134


title: LUSC_X0703_N


title: blastoid 24h-150687


title: ESCC_X0702_T


title: blastoid 60h TROP2 pl-150695


title: Endometrium_LPR_132


title: Endometrium_LPR_133


title: blastoid 24h-150684


title: Endometrium_LPR_131


title: LUSC_X0689_T

value: Early


title: blastoid 24h-150680


title: blastoid 24h-150683


title: blastoid 24h-150682


title: blastoid 24h-150679


title: Endometrium_LPR_12


title: blastoid 24h-150681


title: blastoid 24h-150678


title: LUAD_X0687_T


title: Endometrium_LPR_129


title: blastoid 24h-150685


title: blastoid 24h-150677


title: Endometrium_LPR_128


title: blastoid 24h-150676


title: LUAD_X0687_N


title: ESCC_X0702_N


title: blastoid 24h-150674


title: blastoid 24h-150675


title: blastoid 24h-150672


title: LUAD_X0668_N


title: blastoid 24h-150673


title: Endometrium_LPR_127


title: LUSC_X0689_N


title: blastoid 24h-150671


title: Endometrium_LPR_130


title: blastoid 24h-150670


title: LUSC_X0627_T


title: Endometrium_LPR_126


title: blastoid 24h-150669


title: LUAD_X0668_T


title: blastoid 24h-150667


title: blastoid 24h-150668


title: Endometrium_LPR_125


title: blastoid 24h-150666


title: Endometrium_LPR_124


title: blastoid 24h-150665


title: ESCC_X0601_N


title: Endometrium_LPR_123


title: blastoid 24h-150662


title: blastoid 24h-150661


title: blastoid 24h-150659


title: ESCC_X0525_T


title: blastoid 24h-150664


title: Endometrium_LPR_121


title: LUSC_X0627_N


title: ESCC_X0525_N


title: blastoid 24h-150658


title: LUAD_X0803_N


title: blastoid 24h-150660


title: LUAD_X0147_T


title: LUAD_X0147_N


title: Endometrium_LPR_120


title: ESCC_X0601_T


title: blastoid 24h-150657


title: blastoid 24h-150655


title: blastoid 24h-150656


title: Endometrium_LPR_11


title: Endometrium_LPR_119


title: blastoid 24h-150654


title: Endometrium_LPR_118


title: blastoid 24h-150663


title: SRCC_W0207_T

source_name: Signet ring cell

value: stomach

value: Signet ring cell


title: blastoid 24h-150653


title: Endometrium_LPR_122


title: blastoid 24h-150652


title: Endometrium_LPR_117


title: SRCC_W0207_N


title: Endometrium_LPR_116


title: blastoid 24h-150648


title: blastoid 24h-150651


title: blastoid 24h-150649


title: SRCC_W0158_T


title: blastoid 24h-150647


title: blastoid 24h-150650


title: Endometrium_LPR_115


title: SRCC_W0158_N


title: blastoid 24h-150643


title: Endometrium_LPR_114


title: blastoid 24h-150646


title: blastoid 24h-150641


title: SRCC_W0064_N


title: blastoid 24h-150645


title: blastoid 24h-150639


title: blastoid 24h-150640


title: Endometrium_LPR_113


title: SRCC_W0064_T


title: CSCC_T0045_T

value: cervix

value: Cervical Squamous Cell


title: CSCC_T0045_N


title: blastoid 24h-150638


title: Endometrium_LPR_112

value: Endometrium

value: female


title: Endometrium_LPR_111

value: LPR


title: CSCC_T0024_N


title: Endometrium_LPR_110


title: PTC_J0925_T

source_name: papillary thyroid

value: thyroid

value: papillary thyroid

value: not sure


title: blastoid 24h-150633

source_name: blastoid


title: PTC_J0925_N


title: blastoid 24h-150632


title: PTC_J0924_T


title: PTC_J0924_N


title: blastoid 24h-150637


title: blastoid 24h-150627


title: blastoid 24h-150631


title: blastoid 24h-150628


title: blastoid 24h-150630


title: blastoid 24h-150629


title: Endometrium_LPR_10

source_name: endometrial biopsy


title: blastoid 24h-150626


title: blastoid 24h-150635


title: Endometrium_LPR_108


title: blastoid 24h-150623


title: blastoid 24h-150634


title: Endometrium_LPR_109


title: Endometrium_LPR_107


title: PTC_J0923_T


title: Endometrium_LPR_106


title: PTC_J0923_N


title: blastoid 24h-150621


title: blastoid 24h-150622


title: blastoid 24h-150620


title: blastoid 24h-150619


title: blastoid 60h TROP2 pl-150706


title: Endometrium_LPR_104


title: PTC_J0922_N


title: blastoid 24h-150617


title: blastoid 24h-150618


title: blastoid 24h-150616


title: blastoid 24h-150614


title: Endometrium_LPR_103


title: PTC_J0921_N


title: blastoid 24h-150625


title: PTC_J0921_T


title: blastoid 24h-150610


title: LUSC_8_T

value: lung

value: Lung Squamous Cell


title: blastoid 24h-150615


title: blastoid 24h-150613


title: Endometrium_LPR_102


title: Endometrium_LPR_101


title: LUSC_8_N

value: Late


title: blastoid 24h-150612


title: blastoid 24h-150608


title: Endometrium_LPR_105


title: blastoid 24h-150611


title: blastoid 24h-150609


title: blastoid 24h-150607


title: LUAD_3_N

value: lung adenocarcinoma


title: Endometrium_LPR_100


title: Endometrium_EPR_9

value: EPR


title: PTC_J0922_T

value: cancer


title: Endometrium_EPR_8


title: blastoid 24h-150606

value: PALLY


title: LUAD_3_T

value: Early


title: blastoid 24h-150605


title: Endometrium_EPR_7


title: blastoid 24h-150604


title: blastoid 24h-150603


title: ESCC_2_N

value: esophagus

value: esophageal squamous cell

value: paracancer


title: ESCC_2_T


title: blastoid 24h-150601


title: blastoid 24h-150602


title: blastoid 24h-150600


title: blastoid 24h-150598


title: Endometrium_EPR_6

value: Endometrium


title: Endometrium_EPR_5

value: female


title: blastoid 24h-150597


title: blastoid 24h-150596


title: blastoid 24h-150593


title: CSCC_F0209_N

value: cervix


title: CSCC_F0209_T


title: Endometrium_EPR_4


title: blastoid 24h-150594


title: SCLC_6_N


title: Endometrium_EPR_3


title: SCLC_6_T


title: blastoid 24h-150595


title: SCLC_1_N


title: blastoid 24h-150591


title: Endometrium_EPR_1


title: Endometrium_EPR_12


title: Endometrium_EPR_2


title: blastoid 24h-150590


title: SCLC_1_T


title: Endometrium_EPR_10


title: blastoid 24h-150599


title: blastoid 24h-150589


title: Endometrium_EPR_11


title: HBE-DEP [R30]

city: Beijing

first: Rui

address: No.10 Xitoutiao, You An Men

institute: Capital medical university

description: The HBE cells were available from American Type Culture Collection)

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. Full array name: Exiqon miRCURY LNA microRNA array, 6th generation [miRBase v16]

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering
Processed data file includes Normalized signal intensity with probe ID and miRNA symbol.

source_name: HBE,50 μg/ml DEP,24h

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: The HBE cells (American Type Culture Collection) were maintained in Dulbecco′s modified Eagle′s medium (DMEM). The culture medium was supplemented with 10 % (v/v) fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin at 37 °C with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Cells were exposed to 100 µg/ml Al2O3 NPs，100/500 µg/ml PM2.5, 50 µg/mlDEP.

value: HBE

value: DEP


title: blastoid 24h-150588


title: blastoid 24h-150592


title: blastoid 24h-150586


title: blastoid 24h-150585


title: blastoid 24h-150584


title: blastoid 24h-150581


title: blastoid 24h-150583


title: blastoid 24h-150582


title: blastoid 24h-150579


title: HBE-PM2.5 high [R26]


title: HBE-PM2.5 high [R27]


title: blastoid 24h-150578


title: blastoid 24h-150587


title: HBE-PM2.5 high [R25]


title: HBE-PM2.5 low [R24]


title: restricted fed 16-week old broiler breeder, biological rep 3

city: University Park

first: Francisco

middle: Javier

last: Diaz

state: PA

address: 313 Forest Resources Lab

department: Animal Science

institute: Penn State University

description: Gene expression data from prepubertal broiler breeder hens fed a restricted calorie diet.

hyb_protocol: Chip hybridization was conducted using a Thermo Fisher 3' IVT Express Kit following manufacturer's instructions.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Microarray data was processed and analyzed with R/Bioconductor using the affy, affyPLM, and limma packages. The Robust Multi-array Average (RMA) expression was used for background correction, normalization, and summarization.

label: biotin

organism: Gallus gallus

source_name: 16-week old broiler breeder ovarian cortex

label_protocol: Biotinylated aRNA was generated using a Thermo Fisher 3' IVT Express Kit following the manufacturer's instructions.

growth_protocol: Beginning at 2 weeks of age broiler breeder hens were randomly assigned to full feeding (FF) or restricted feeding (RF) diet groups and fed to 16-weeks of age.

extract_protocol: Following cervical dislocation to euthanize the hens, ovaries were extracted and small sections (<1 cm3) of cortex were isolated in RNA later. Total RNA was isolated with the Qiagen RNAeasy mini kit following the manufacturer's instructions.

value: ovarian cortex

tag: age

value: 16 week

value: restricted fed


title: restricted fed 16-week old broiler breeder, biological rep 2

tag: treatment


title: restricted fed 16-week old broiler breeder, biological rep 1


title: ad libitum fed 16-week old broiler breeder, biological rep 3

description: Gene expression data from prepubertal broiler breeder hens fed ad libitum.

value: ad libitum fed


title: HBE-DEP [R29]


title: blastoid 24h-150572


title: blastoid 24h-150576


title: blastoid 24h-150574


title: blastoid 24h-150577


title: blastoid 24h-150573


title: HBE-DEP [R28]


title: HBE-PM2.5 low [R23]


title: blastoid 24h-150570


title: blastoid 24h-150571


title: ad libitum fed 16-week old broiler breeder, biological rep 1


title: blastoid 24h-150575


title: Case25

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
cutadapt v1.8.3 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.1.1 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the canine CanFam3 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 (--library-type fr-firststrand) was used to call differentially expressed genes based on the CanFam3 reference genome+transcriptome (Ensembl).
Genome_build: CanFam3 (Ensembl)
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The 'gene_exp.diff' file contains average FPKM values for each pair of replicates as well as results for statistical testing for differential expression. The 'genes.read_group_tracking' file contains raw mapped read counts and FPKM values for individual samples.

organism: Canis lupus familiaris

source_name: healthy gingiva

growth_protocol: Tumor biopsies were collected during standard-of-care surgical procedures, and stored by the Cornell Veterinary Biobank at Cornell University’s College of Veterinary Medicine

extract_protocol:
Cryopreserved tissue was homogenized in Trizol on a bead mill using 2.8mm ceramic beads. Total RNA was isolated from the Trizol lysate, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a Nanodrop and integrity assessed on a Fragment Analyzer.
Directional RNA-seq libraries were prepared from 250ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ enrichment.

tag: breed

value: Beagle

tag: Sex

value: Male

tag: dog age

tag: sample type

value: Healthy Gingiva

tag: sample location

value: Rostral mandible


title: Case24

source_name: canine oral squamous cell carcinoma tumor

value: Mixed

value: Female

value: COSCC

value: Rostral maxilla


title: blastoid 24h-150567

value: PALLY


title: HBE-PM2.5 low [R22]


title: HBE-Al2O3 NPs [R21]

source_name: HBE,100 μg/ml Al2O3,24h

value: Al2O3 NPs


title: blastoid 24h-150569


title: ad libitum fed 16-week old broiler breeder, biological rep 2

tag: tissue


title: Case23

value: Caudal maxilla


title: blastoid 24h-150568


title: Case26

value: Staffordshire bull terrier

value: Caudal mandible


title: HBE-Al2O3 NPs [R20]

value: HBE


title: naive H9-150564

source_name: stem cells

value: PXGL


title: naive H9-150565


title: HBE-Al2O3 NPs [R19]


title: naive H9-150562


title: Case21


title: naive H9-150563


title: Case20


title: naive H9-150560


title: Case22

value: Boxer


title: HBE-PBS [R18]

source_name: HBE,100 μg/ml PBS,24h

value: PBS


title: naive H9-150561


title: Case19


title: naive H9-150559


title: HBE-PBS [R17]


title: HBE-PBS [R16]


title: Case18

value: Great Dane


title: Case16

source_name: canine acanthomatous ameloblastoma tumor

value: Labrador retriever

value: Male

value: CAA


title: naive H9-150557


title: naive H9-150558


title: naive H9-150554


title: naive H9-150556


title: Case14


title: naive H9-150555


title: Hrb87F-IR IFM 72h APF rep2

city: Martinsried-Planegg

first: Maria

middle: Lynn

last: Spletter

state: Bayern

address: Großhaderner Str. 9

department: Physiological Chemistry

country: Germany

institute: Ludwig-Maximilians-University München, Biomedical center

description: knockdown sample with Mef2-Gal4 driving knockdown of Hrb87F (hnRNPA) in all muscle, dissected IFM

data_processing:
basecalling and demultiplexing by LC Sciences using Illumina software
Sequenced reads were mapped to the Ensembl BDGP6.22 whole genome using STAR v2.7.3a
mapped reads were sorted and indexed using samtools v1.1
bam files were converted into bigwig for visualisation using ucsc-wigtobigwig v377
Counting the mapped reads on the gene and exon level using featureCounts in subread v.2.0.0
differential gene expression analysis using the R package DESeq2 v1.32.0
differential exon usage with the R package DEXSeq v1.38.0
Genome_build: BDGP6.22 from ENSEMBL
Supplementary_files_format_and_content: tab delimited text files including raw counts for both genes and exons calculated by featureCount for all libraries
Supplementary_files_format_and_content: tab delimited text files including DESeq2 and DEXSeq data for comparison of control IFM to RNAi IFM

organism: Drosophila melanogaster

source_name: indirect flight muscle

growth_protocol:
flies were grown on standard medium using standard fly husbandry protocol
grown at 27C, staged 0h white pre-pupae

extract_protocol:
total RNA isolated in Tri-Pure reagent (phenol-choloform), mRNA selection by LC Sciences
RNA libraries were prepared for sequencing by LC Sciences (Houston, TX, USA) using standard Illumina protocols

treatment_protocol: dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction (see Kao et al., JoVE, 2019 for details)

value: indirect flight muscle

tag: developmental stage

value: 72h APF

tag: muscle type

value: fibrillar

tag: genotype

value: Mef2-Gal4 / Hrb87F-RNAi (TRiP.JF01757)


title: Hrb87F-IR IFM 72h APF rep1


title: SF1-IR IFM 72h APF rep2

description: knockdown sample with Mef2-Gal4 driving knockdown of SF1 in all muscle, dissected IFM

value: Mef2-Gal4 / SF1-RNAi (GD5176)


title: naive H9-150552


title: Case13

value: Female


title: naive H9-150549


title: naive H9-150553


title: Case12


title: naive H9-150547


title: Mef2 IFM 72h APF rep2

description: control sample with only Mef2-Gal4 expressed in all muscle, dissected IFM

value: Mef2-Gal4 / +


title: Case11

value: Airedale terrier


title: SF1-IR IFM 72h APF rep1


title: Case8

value: Mixed

value: Rostral mandible


title: naive H9-150546

value: PXGL


title: naive H9-150545


title: naive H9-150544


title: Case7


title: Mef2 IFM 72h APF rep1


title: naive H9-150542


title: Mixture of GSC20 and 4T1

first: Navin

last: Varadarajan

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

data_processing:
SureCell RNA Single-Cell software was used for generating the matrix table of read counts.
Alignment, filtering, and sample tag detection were performed by SureCell RNA single-Cell software. We aligned read 2 against reference genome using STAR (STAR 2.5.2b)
Genome_build: UCSC hg19-mm10
Supplementary_files_format_and_content: rds file format; matrix table with raw gene counts for every gene and every single cell

organism:
Homo sapiens
Mus musculus

source_name: Human glioblastoma stem cell/ Mouse mammary tumor cell line

growth_protocol: 4T1, 67NR and U87 cells were cultured in RPMI 1640 supplemented with 10% FBS, 1% L-glutamine, HEPES, and penicillin-streptomycin. GSC20 cells were cultured in 50/50 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM) and Ham’s F-12 medium supplemented with 1% penicillin-streptomycin, B-27 supplement, and epidermal growth factor.

extract_protocol:
4T1, 67NR and U87 were detached using trypsin. we dissociated the GSC20 stem cells using accutase, to achieve single cells. 50/50 % mixtures of single cells from 4T1/GSC20 and 67NR/U87 cell lines were prepared.
RNA libraries were prepared for sequencing using Illumina Bio-Rad SureCell WTA 3' Library

tag: cell line

value: Mixture of GSC20 and 4T1


title: naive H9-150539


title: naive H9-150550


title: Case6

value: Unknown (adult)


title: Case5

value: Neapolitan mastiff


title: naive H9-150548


title: Case4

value: Golden retriever

value: Rostral maxilla


title: iEF-FUS-FEV_FLAG_rep2

city: Columbus

first: Megann

middle: A.

last: Boone

state: OH

address: 700 Children's Drive, WA5011

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/FEV cDNA (FFEV) was expressed via retroviral transduction. Cells were then sequenced.
iEF +  FUS/FEV (FFEV)
iEF-FUS-FEV_FLAG_rep2_S8_L006

data_processing:
FASTQC and Multiqc were used for raw sequence quality control.
Trim_galore was used to trim low-quality and overrepresented sequences.
Two-pass STAR appraoch (STAR version 2.5.2b) was used to align sequences to hg19 human reference genome.
RSeQC was used to evaluate post-mapping sequence quality.
DESeq2 was used to identify different analysis of genes.
Genome_build: hg19
Supplementary_files_format_and_content: Samples were pooled together after normalization to background and combined bigwig files were generated to depict expression of RNA-sequencing reads.

source_name: A673 cells

growth_protocol: Ewing sarcoma cells (A673) were seeded at 50-70% confluency and left to adhere overnight.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and gDNA Eliminator columns (Qiagen) were used to remove residual genomic DNA. 3 ug of total RNA was used for library prep.
TruSeq Stranded mRNA Kit

treatment_protocol: Endogenous EWS/FLI protein was knocked down in A673 cells using an shRNA targeting the 3'-UTR of the native transcript (iEF). cDNA constructs were used to rescue cells with empty vector control (Empty Vector), wild-type EWS/FLI (EF) cDNA, or one of four mutant EWS/FLI constructs (EF DBD, EF DBD+, EF DBD+ DN, or EF DBD+ DC). Antibiotic selection was used to select for cells expressing these constructs and cells were collected after 8 days.  Whole cell total RNA was extracted using a Qiagen RNeasy Extraction kit and genomic DNA was removed uisng Qiagen gDNA Eliminator columns.

tag: cell type

value: Patient-derived, female Ewing sarcoma cell line

tag: genotype/variation


title: naive H9-150538


title: naive H9-150537


title: naive H9-150536


title: Mixture of U87 and 67NR

source_name: Human primary glioblastoma/ Mouse mammary tumor cell line

value: Mixture of U87 and 67NR


title: Case2

value: Samoyed

value: Male

value: CAA


title: iEF-FUS-ETV4_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ETV4 cDNA (FETV4) was expressed via retroviral transduction. Cells were then sequenced.
iEF + FUS/ETV4 (FE4)
iEF-FUS-ETV4_FLAG_rep2_S7_L006


title: Case1

value: Great Dane


title: naive H9-150532


title: naive H9-150530


title: naive H9-150540


title: naive H9-150531


title: naive H9-150543


title: naive H9-150534


title: naive H9-150527


title: iEF-FUS-ERG_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ERG cDNA (FERG) was expressed via retroviral transduction. Cells were then sequenced.
iEF + FUS/ERG (FERG)
iEF-FUS-ERG_FLAG_rep2_S9_L006


title: Case36

value: Yorkshire terrier

value: Female

value: COSCC


title: naive H9-150528


title: iEF-562_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ERG cDNA (562) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/ERG (562)
iEF-562_FLAG_rep2_S4_L006


title: Case37

value: Podenco Canario

value: Healthy Gingiva


title: naive H9-150529

value: PXGL


title: naive H9-150526


title: iEF-563_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ETV4 cDNA (563) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/ETV4 (563)
iEF-563_FLAG_rep2_S5_L006


title: iEF-714_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (714) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/FLI (714)
iEF-714_FLAG_rep2_S3_L006


title: naive H9-150535


title: iEF-197_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and cells were sequenced.
iEF + Empty vector (197)
iEF-197_FLAG_rep2_S2_L006

value: endogenous EWS/FLI knocked-down


title: naive H9-150522


title: iEF-564_FLAG_rep2

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FEV cDNA (564) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/FEV (564)
iEF-564_FLAG_rep2_S6_L006


title: naive H9-150525


title: iEF-FUS-FEV_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/FEV cDNA (FFEV) was expressed via retroviral transduction. Cells were then sequenced.
iEF +  FUS/FEV (FFEV)
iEF-FUS-FEV_FLAG_S8_L007


title: Case28

value: Mixed

value: Unknown (adult)

value: Caudal maxilla


title: naive H9-150523


title: HCPro from potyviral chimera input tissue

city: Madrid

first: Tomas

last: Canto

state: Madrid

address: Ramiro de Maeztu 9

department: Environmental Plant Biology

institute: CSIC

data_processing:
Raw files uploaded as received from FASTERIS SA
Processed files trimmed from adaptors, cleaned from reads with erroneous characters, and analysed for sRNA abundance

organism: Nicotiana benthamiana

source_name: infected tissue

growth_protocol: Plant leaf tissue was agroinfiltrated with binary vectors expressing HCPro variants or mRFP (samples 1-8) or infected with a PVX vector expressing 6x-HCPro

extract_protocol:
Libraries were constructed by FASTERIS SA
Illumina Version NextSeq HighBase; Calling pipeline: - NextSeq Control Software 2.2.0.4 - RTA 2.4.11

treatment_protocol: At 4 days after infiltration or at 7 days after infection leaf tissues were collected and total RNAs extracted (input samples 1,3,5,7,9, 11 and 13).  HCPro variants were purified under non-denaturing conditions and the associated RNAs were then isolated (samples 2,4,6,8,10, 12 and 14)

value: plant leaf tissue

tag: type of sequence

value: sRNA reads 18-30 nt of total RNA samples

tag: viral suppressor activity

value: suppression of silencing active, untagged


title: HCPro from potyviral chimera purified protein

source_name: purified protein prep

value: purified protein prep


title: Case27

value: Pit-bull mix

value: Male

value: Rostral maxilla


title: naive H9-150518


title: naive H9-150520


title: 6x-HCPro from potyviral chimera purified protein

value: suppression of silencing active, tagged


title: naive H9-150514


title: iEF-FUS-ETV4_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ETV4 cDNA (FETV4) was expressed via retroviral transduction. Cells were then sequenced.
iEF + FUS/ETV4 (FE4)
iEF-FUS-ETV4_FLAG_S7_L007

value: Patient-derived, female Ewing sarcoma cell line


title: naive H9-150515


title: naive H9-150513


title: naive H9-150512


title: iEF-FUS-ERG_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ERG cDNA (FERG) was expressed via retroviral transduction. Cells were then sequenced.
iEF + FUS/ERG (FERG)
iEF-FUS-ERG_FLAG_S9_L007


title: 6x-HCPro from potyviral chimera input tissue


title: naive H9-150511


title: naive H9-150524


title: iEF-564_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FEV cDNA (564) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/FEV (564)
iEF-564_FLAG_S6_L007


title: naive H9-150508


title: naive H9-150510


title: naive H9-150509


title: iEF-563_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ETV4 cDNA (563) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/ETV4 (563)
iEF-563_FLAG_S5_L007


title: Treghigh_S7

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCh37 assembly using the gene, transcript, and exon features of Ensembl (release 70) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected read count values for each sample

source_name: Regulatory T-cell

extract_protocol:
RNA was purified from approximately 25,000 of FACS-isolated CD49f high and CD49f negative CD4+CD25hiCD127lo/neg Tregs using the Arcturus PicoPure Isolation Kit (Thermo Fisher Scientific, USA).
Oligo d(T) captured mRNA was processed for Next Generation Sequencing (NGS) using the NEB Next Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, UK). Quality was assessed on the Agilent 2100 Bioanalyser using the High Sensitivity DNA Kit (Agilent, USA), and quantification was based on the Qubit DNA HS Assay Kit (Molecular Probes) (Thermo Fisher Scientific, USA). Final libraries were pooled and sequenced using a High output single-end 75 cycle (version 2) sequencing kit using the Illumina Nextseq 550 platform (Illumina, USA).

value: CD4+CD25hiCD127lo/neg CD49fhi

value: PBMC

tag: disease stage

value: Healthy


title: Treglow_S8

value: CD4+CD25hiCD127lo/neg CD49f-


title: naive H9-150519

value: PXGL


title: Treglow_S6


title: iEF-562_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ERG cDNA (562) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/ERG (562)
iEF-562_FLAG_S4_L007


title: naive H9-150505


title: naive H9-150506


title: iEF-197_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and cells were sequenced.
iEF + Empty vector (197)
iEF-197_FLAG_S2_L007

value: endogenous EWS/FLI knocked-down


title: Treghigh_S5


title: Treghigh_S3


title: Treglow_S4


title: naive H9-150503


title: naive H9-150500


title: naive H9-150501


title: naive H9-150498


title: naive H9-150497


title: naive H9-150496


title: naive H9-150507


title: iEF + FUS/ERG (FERG) [20-2434_FERGR3]

description:
20-2434_FERGR3_S25
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ERG was expressed.


title: naive H9-150495


title: naive H9-150493


title: iEF-714_FLAG_rep1

description:
CUT&Tag was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (714) was expressed via retroviral transduction. Cells were then sequenced.
iEF + EWS/FLI (714)
iEF-714_FLAG_S3_L007


title: naive H9-150494


title: Treghigh_S1


title: 72h_L4D_3

city: Bethesda

first: Ludmila

last: Prokunina-Olsson

state: MD

address: 9615 Medical Center Dr

department: Division of Cancer Epidemiology and Genetics

institute: National Cancer Institute

data_processing:
The quality control analysis of RNA-seq data was carried out with FastQC pipeline.
Paired RNA-seq reads were aligned to the ENSEMBL human reference genome GRCh37.75 (hg19) with STAR v 2.5.3a using default parameters.
BAM files were generated with SAMtools v 1.5.
Genewise read counts were collected using summarizeOverlaps function form GenomicAlignments R package v 1.20.1 using the following parameters: features=ebg, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE
Genome_build: GRCh37.75 (hg19)
Supplementary_files_format_and_content: CSV files include genewise read counts values for each sample.

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4 for 72 hrs with dox

growth_protocol: Livel cancer HepG2 cells were maintained per ATCC recommendations.

extract_protocol:
Total RNA was extracted from cells using an RNeasy Mini Kit with an on-column DNase digestion (Qiagen), treated with Ribo-Zero.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Three biological replicates were performed independently. Cells were treated with doxycycline (0.5 mg/ml) for 8, 24 and 72 h, washed with PBS, and total RNA extracted from cells.

value: Hepatocellular carcinoma

value: Doxycycline


title: iEF + EWS/FEV (564) [20-2433_564R3]

description:
20-2433_564R3_S24
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FEV was expressed.


title: iEF + EWS/ETV4 (563) [20-2432_563R3]

description:
20-2432_563R3_S23
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ETV4 was expressed.


title: 72h_L4D_2


title: Treglow_S2


title: iEF +  FUS/FEV (FFEV) [20-2436_FFEVR3]

description:
20-2436_FFEVR3_S27
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/FEV was expressed.


title: naive H9-150504

first: Giovanni

address: Dr.-Bohr-Gasse 3, 1030 Wien

institute: IMBA - Institute of Molecular Biotechnology

data_processing:
Smart-Seq transcriptome sequencing experiments were analyzed using genome sequence and gene annotation from Ensembl GRCh38 release 103 as reference. For gene expression quantification RNA-seq reads were first trimmed using trim-galore v0.6.6 and thereafter aligned to the genome using hisat2 v2.2.1. Uniquely mapping reads in genes were quantified using htseq-count v0.13.5 with parameter -s no. TPM estimates were obtained using RSEM v1.3.3 with parameter --single-cell-prior. Further analysis was performed in R v4.0.3 with Seurat v4.0.1. Based on initial evaluation of per-cell quality control metrices and outlier identification using the median absolute deviation algorithm, cells with <= 2000 detected genes or >= 12.5% mitochondrial gene percentage were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: tsv of read counts per gene

extract_protocol:
Smart-Seq2 protocol
Smart-Seq2


title: naive H9-150502


title: naive H9-150492


title: naive H9-150499


title: iEF + FUS/ETV4 (FE4) [20-2435_FE4R3]

description:
20-2435_FE4R3_S26
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ETV4 was expressed.


title: naive H9-150490


title: iEF + EWS/ERG (562) [20-2431_562R3]

description:
20-2431_562R3_S22
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ERG was expressed.


title: iEF + EWS/FLI (714) [20-2430_714R3]

description:
20-2430_714R3_S21
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI (714) was expressed.


title: 72h_L3D_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ3 for 72 hrs with dox


title: 72h_L4D_1


title: naive H9-150491


title: naive H9-150487


title: naive H9-150486


title: naive H9-150485


title: 72h_L3D_2


title: 72h_L3D_1


title: naive H9-150484


title: naive H9-150483


title: iEF +  FUS/FEV (FFEV) [20-2418_FFEVR1]

description:
20-2418_FFEVR1_S9
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/FEV was expressed.


title: naive H9-150481


title: naive H9-150480


title: naive H9-150478


title: iEF + EWS/FEV (564) [20-2415_564R1]

description:
20-2415_564R1_S6
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FEV was expressed.


title: 72h_KOD_2

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4-GFP-IFNLR1KO for 72 hrs with dox


title: 72h_KOD_1


title: 72h_KOD_3


title: naive H9-150482


title: naive H9-150477


title: naive H9-150479


title: naive H9-150488


title: naive H9-150476


title: iEF + EWS/ETV4 (563) [20-2414_563R1]

description:
20-2414_563R1_S5
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ETV4 was expressed.


title: iEF + Empty vector (197) [20-2429_197R3]

description:
20-2429_197R3_S20
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down.


title: naive H9-150475


title: 72h_L4_2

source_name: 72 hrs Control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4

value: Control


title: naive H9-150473


title: naive H9-150474


title: iEF + EWS/ERG (562) [20-2413_562R1]

description:
20-2413_562R1_S4
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/ERG was expressed.


title: iEF + EWS/FLI (714) [20-2412_714R1]

description:
20-2412_714R1_S3
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI (714) was expressed.


title: naive H9-150472


title: iEF + FUS/ETV4 (FE4) [20-2417_FE4R1]

description:
20-2417_FE4R1_S8
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ETV4 was expressed.


title: naive H9-150471


title: naive H9-150470


title: iEF + Empty vector (197) [20-2411_197R1]

description:
20-2411_197R1_S2
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down.


title: 72h_L4_1


title: naive H9-150469


title: 72h_L3_3

source_name: 72 hrs control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ3


title: 72h_L3_2


title: naive H9-150465


title: naive H9-150467


title: 72h_KO_3

source_name: 72 hrs control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4-GFP-IFNLR1KO


title: naive H9-150462


title: 72h_L3_1


title: naive H9-150466


title: naive H9-150459


title: naive H9-150464


title: ncRNA-HI6-Nfatc2

city: Madison

first: Shane

middle: P

last: Simonett

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

data_processing:
Non-coding RNAseq data analysis was performed as described in Perez-Cervantes and Smith et al. 2020.
Briefly, Fastq files were aligned to UCSC genome build hg19 using STAR (v2.5.1).
Transcript assembly was performed by Stringtie (version 1.3.3) and merged with the Stringtie ‘merge’ function.
Counts were retrieved from the merged transcriptome with HTseq (v0.6)
False discovery rate (FDR) was calculated after removing the coding-gene transcripts, ncRNA that overlapped coding genes in the same strand (bedtools intersect 2.29.0), and RNAs shorter than 100 base pairs.
Differential expression was performed with R (3.4) package DEseq2 (Love et al., 2014).
Significance was considered to have been reached when FDR was <0.05 and |log2 fold-change| was >0.5.
Open chromatin peaks and TF-binding peaks were intersected with ncRNAs using Bioconductor package GenomicRanges (Lawrence et al., 2013) allowing for a 1000 bp gap upstream the 5’ end of the RNA and 50 bp into the RNA.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig files of ncRNA enriched read abundance.
Supplementary_files_format_and_content: csv file of ncRNA abundance.

source_name: Human pancreatic islets

growth_protocol: All human islets were obtained through the IIDP (Integrated Islet Distribution Program). Upon receipt, all human islets were incubated overnight in RPMI 1640 supplemented with 8.0 mM glucose, 1% antibiotic/antimycotic (Gibco), 5 mM HEPES, and 10% FBS before performing experiments.

extract_protocol:
The human islets were lysed with 350 uL of QIAzol Lysis Reagent (Qiagen) and stored at -80˚C before purifying RNA using Mini RNeasy purification kits per manufacturer’s instructions. Total RNA was treated with RiboZero purification and oligo-dT depletion in order to enrich for ncRNAs.
RNA Barcoded Libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001).

treatment_protocol: Isolated human islets were treated with an adenovirus to overexpress a constitutively active HA-tagged Nfatc2 protein. Islets were collected for ncRNA-seq 48 hours later.

value: Human pancreatic islets

value: F

tag: age

tag: expression

value: constitutively active Nfatc2


title: ncRNA-HI3-Nfatc2

value: M


title: ncRNA-HI5-Nfatc2


title: ncRNA-HI8-Nfatc2


title: ncRNA-HI8-GFP

value: Ad-GPF


title: naive H9-150463

city: Vienna

last: Sestini

source_name: stem cells

tag: treatment


title: 72h_KO_1


title: naive H9-150456


title: ncRNA-HI4-Nfatc2

tag: Sex


title: ncRNA-HI6-GFP


title: 24h_L4D_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4 for 24 hrs with dox


title: naive H9-150460


title: naive H9-150461


title: ncRNA-HI5-GFP


title: naive H9-150455


title: naive H9-150451


title: 72h_KO_2


title: 72h_L4_3


title: 24h_L4D_2


title: naive H9-150454


title: Kuramochi SOX17

source_name: Ovarian cancer cell line

value: Ovarian cancer cell line

value: Kuramochi

tag: chip antibody

tag: antibody manu.

value: R&D Systems

tag: antibody catalog

tag: antibody lot


title: naive H9-150450


title: 24h_L4D_1


title: naive H9-150449


title: 24h_L3D_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ3 for 24 hrs with dox


title: naive H9-150453


title: naive H9-150452


title: 24h_L3D_1


title: naive H9-150458


title: ncRNA-HI4-GFP

tag: tissue


title: Kuramochi PAX8

value: Cell Signaling


title: 24h_KOD_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4-GFP-IFNLR1KO for 24 hrs with dox


title: naive H9-150457


title: ncRNA-HI3-GFP


title: 24h_L3D_2


title: naive H9-150444


title: naive H9-150447


title: 24h_KOD_2


title: naive H9-150446


title: naive H9-150445


title: 24h_KOD_1


title: naive H9-150443


title: naive H9-150448


title: 7.4

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Reads quality trimmed using fastp v 0.20.1
Aligned to TAIR10 gneome using bowtie 2.3.5.1
Duplicates removed using Sambama 0.6.6
Variants called using DEEPVARIANT 1.0
gVCF files merged using GLnexus 1.2.7
Genome_build: TAIR10
Supplementary_files_format_and_content: gVCF files and VCF files

source_name: Arabidopsis leaf tissue

growth_protocol: Plants were grown at room temperature at 21°C with a 16-hour photoperiod.

extract_protocol:
DNA for Illumina NGS analysis was extracted using a DNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.
Genomic DNA library preparation was carried out using the protocol outlined in ref.30.
WGS

treatment_protocol: Parent plants were subject to eight rounds of heat stress at 37°C, followed by recovery at 21°C.

tag: strain


title: Kuramochi EVI1


title: naive H9-150440


title: naive H9-150441


title: 7.3


title: 24h_L4_3

source_name: 24 hrs Control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4


title: 7.1


title: naive H9-150439


title: okae bts5-150437


title: 7.2


title: okae bts5-150436


title: 24h_L4_2


title: naive H9-150438


title: okae bts5-150435


title: okae bts5-150434


title: 24h_L4_1


title: 14.3


title: okae bts5-150433


title: naive H9-150442


title: 24h_L3_3

source_name: 24 hrs control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ3


title: okae bts5-150432


title: 24h_L3_2


title: 14.2


title: 14.1


title: okae bts5-150431


title: 24h_L3_1


title: okae bts5-150429


title: 24h_KO_3

source_name: 24 hrs control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4-GFP-IFNLR1KO


title: okae bts5-150426


title: okae bts5-150425


title: okae bts5-150423


title: okae bts5-150427


title: okae bts5-150428


title: okae bts5-150422


title: 8h_L4D_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4 for 8 hrs with dox


title: 24h_KO_1


title: okae bts5-150430


title: 8h_L4D_2


title: okae bts5-150420


title: okae bts5-150419


title: okae bts5-150417


title: 8h_L4D_1


title: naive H9-150468


title: iEF + FUS/ERG (FERG) [20-2416_FERGR1]

description:
20-2416_FERGR1_S7
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and FUS/ERG was expressed.

source_name: A673 cells

value: Patient-derived, female Ewing sarcoma cell line


title: okae bts5-150416


title: KO

city: San Francisco

first: Lihui

last: Duan

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

description:
IL4ra_cko_GEX_counts.tar.gz
Il4ra_cko_meta_info.tar.gz

data_processing:
10x Cell Ranger Suite was used to perform sample demultiplexing and single cell UMI counting
Seurat was used to remove contained non-B cells, naive B cells and other low-quality cells.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts csv: gene x cell count matrix in csv format
Supplementary_files_format_and_content: cell annotation csv: cluster information of each cell in csv format

organism: Mus musculus

source_name: Spleen

growth_protocol: primary GC B cells

extract_protocol: 10x 5'-end single cell RNA-seq

treatment_protocol: NP-haptenated antigen in alum adjuvant immunization

value: Spleen

tag: genotype

value: Reverse chimaeras were made by reconstituting irradiated Ccl19Cre/+ Il4raf/f  with wild type bone marrows

value: B220+ CD95hi GL7hi IgD-

tag: time point

value: Day 14 after immunization with NP-haptenated antigen in alum adjuvant


title: okae bts5-150415


title: okae bts5-150424


title: 8h_L3D_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ3 for 8 hrs with dox

tag: cell type

value: Hepatocellular carcinoma

tag: cell line


title: okae bts5-150421


title: okae bts5-150413


title: Control

value: Reverse chimaeras were made by reconstituting irradiated Il4ra+/+ with wild type bone marrows


title: okae bts5-150412


title: 8h_L3D_2

value: Doxycycline


title: 8h_L3D_1


title: okae bts5-150418


title: TGF-β- T98G - T1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 24h of TGF-β treatment

hyb_protocol: End labelled RNA was hybridized to Agilent Human Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, # 5190-0404).

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing:
Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed
Log base 2

source_name: T98G GBM cells

label_protocol: Total RNA was end-labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442)

growth_protocol: T98G glioblastoma cells were cultured in in complete medium, DMEM (Invitrogen) containing 10% fetal bovine serum (FBS) supplemented with 1 mm l-glutamine and penicillin/streptomycin (Gibco).

extract_protocol: RNA was isolated using MN Nucleospin RNA plus isolation kit (Cat.No:740984.5). 10 µg of purified RNA samples were treated with recombinant DNAse1 (Invitrogen Thermo Scientific - Cat.NO: EN0521) as per manufacturer’s instructions, and the RNA samples were column purified using MN Nucleospin column purification kit.

treatment_protocol: T98G cells were treated with 10 ng/ml of TGF-β1 for 24 h

value: Brain


title: TGF-β- T98G - T3


title: TGF-β- T98G - T2


title: Control - T98G-C3


title: Control - T98G-C2


title: Control - T98G-C1


title: okae bts5-150411


title: 24h_KO_2

value: Control


title: okae bts5-150410


title: okae bts5-150409


title: 8h_KOD_3

source_name: Treated stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4-GFP-IFNLR1KO for 8 hrs with dox


title: 8h_KOD_2


title: okae bts5-150407


title: Day14_Sample2

description:
Day14_GEX_counts.tar.gz
Day14_meta_info.tar.gz

value: wild type


title: Day7_Sample2

description:
Day7_GEX_counts.tar.gz
Day14_meta_info.tar.gz

value: Day 7 after immunization with NP-haptenated antigen in alum adjuvant


title: 8h_KOD_1


title: okae bts5-150408


title: okae bts5-150405


title: 8h_L4_3

source_name: 8 hrs Control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4


title: FLD Refed Rep3

city: Los Angeles

first: Huan

last: Wang

state: California

address: 695 Charles E Young Dr RM6309

department: Human Genetics

institute: UCLA

data_processing:
RNA-seq alignment was performed with HISAT2(version 2.0.5) to the mouse genome and transcriptome (GRCm38 Ensembl release 84, using the genome_tran index)
The read counts were quantified with HTSeq (0.6.0) at the gene level and used to run DESeq2(1.20.0) for differential gene expression analysis.
Identification and statistical analysis of alternative splicing events were performed by rMATS (version 3.2.5)
Genome_build: GRCm38 Ensembl release 84, using the genome_tran index
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and exon skipping events for each comparison

source_name: mouse liver

extract_protocol:
Liver was removed, snap frozen in liquid nitrogen, and RNA was isolated using RNeasy tissue mini-kit (QIAGEN).
Libraries was prepared using Illumina standard kits (TruSeq stranded RNA v2) according to standard protocols. All samples were barcoded, and sequenced with 12 samples (n=3) per lane and 6 lanes in total, with HiSeq2000 4K using 69 bp paired-end sequencing protocol. A round robin design was implemented such that biological replicates were sequenced on different lanes, and each sample was part of more than one sequencing pool. Then samples were demultiplexed, forward and reverse read fastq files are generated for each sample. This generated ~150 million reads coverage per sample.

treatment_protocol: Mice were fasted single-housed overnight for 16 hrs (fasted), and refed for 5 hrs (refed).

value: BALB/cByJ

value: liver

value: refed


title: okae bts5-150404

source_name: stem cells


title: okae bts5-150414


title: okae bts5-150403


title: FLD Refed Rep2


title: okae bts5-150402


title: Day7_Sample1


title: Day14_Sample1


title: okae bts5-150401


title: 8h_L4_1


title: 8h_L4_2


title: WT Refed Rep3


title: okae bts5-150400


title: okae bts5-150399


title: FLD Refed Rep1


title: okae bts5-150396


title: okae bts5-150397


title: okae bts5-150398


title: WT Refed Rep2


title: okae bts5-150406


title: okae bts5-150395


title: 8h_L3_2

source_name: 8 hrs control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ3


title: okae bts5-150394


title: okae bts5-150393


title: okae bts5-150392


title: WT Refed Rep1


title: 8h_L3_1


title: FLD Fasted Rep2

value: fasted


title: FLD Fasted Rep3


title: FLD Fasted Rep1


title: 8h_KO_3

source_name: 8 hrs control stable HepG2 cell expressing doxycycline (dox)-inducible GFP-tagged IFN-λ4-GFP-IFNLR1KO


title: okae bts5-150391


title: 8h_KO_2


title: 8h_KO_1


title: okae bts5-150390


title: okae bts5-150387


title: WT Fasted Rep3


title: okae bts5-150388


title: okae bts5-150386


title: okae bts5-150383


title: InVitroCoCultureINV (C_INV)

city: New York

first: Nathaniel

middle: R

last: Campbell

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Cell ranger 3.1.0
Seurat v3
Genome_build: GRCz10, Ensembl version 81
Supplementary_files_format_and_content: csv

organism: Danio rerio

source_name: Zebrafish melanoma cell line

extract_protocol: none provided by the submitter

value: ZMEL-INV-GFP

value: Zebrafish melanoma


title: WT Fasted Rep2


title: WT Fasted Rep1


title: okae bts5-150385


title: InVitroCoCulturePRO (C_PRO)

value: ZMEL-PRO-TdTomato


title: 8h_L3_3


title: okae bts5-150384


title: InVitroINV (D_INV)


title: Liver AIN-93M diet-fed WSB strain rep3

city: Davis

first: Brian

last: Bennett

address: 430 West Health Sciences Drive

department: Obesity and Metabolism

institute: Western Human Nutrition Research Center, ARS

data_processing:
Raw read data was filtered using HTStream (version 1.1.0, https://github.com/ibest/HTStream), which included screening for contaminants (such as PhiX and rRNA), PCR deduplication readout, quality-based trimming, adapter trimming, and overlapping paired-end reads.
For deep sequenced two B6 and two CAST samples, we randomly took 50% of the reads from samples. contaminants (such as PhiX and rRNA), PCR deduplication readout, quality-based trimming, adapter trimming, and overlapping paired-end reads
STAR (version 2.7.0f) was used to align the processed data to custom reference mouse genomes constructed by incorporating genetic variants of eight founder strain into reference mouse genome GRCm38 using g2gtools (https://github.com/churchill-lab/g2gtools).
Log2 transformed count per million (CPM) were calculated. Custom R code was then used for read and alignment quality assessment as well as collating counts into a single table for downstream analysis  .
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2CPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and Total RNA was extracted from frozen liver samples with the Maxwell 16 LEV simplyRNA Tissue Kit according to the manufacturer’s protocol. The RNA-seq libraries were constructed from total RNA following the Illumina TruSeq RNA library construction protocol. The size of the adapted fragments in the libraries was determined by running an Agilent DNA 1000 Chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WSB/EiJ

value: 24 weeks

value: AIN-93M diet

value: Female


title: okae bts5-150379


title: okae bts5-150381


title: InVitroPRO (D_PRO)


title: okae bts5-150380


title: okae bts5-150389


title: Liver High fat/cholic acid diet-fed WSB strain rep3

value: High fat/cholic acid diet


title: okae bts5-150375


title: okae bts5-150377


title: okae bts5-150378


title: okae bts5-150382


title: InVivoMetINV (M_INV)


title: okae bts5-150376


title: okae bts5-150374


title: Liver AIN-93M diet-fed WSB strain rep2


title: InVivoPrimaryPRO (P_PRO)


title: Liver AIN-93M diet-fed WSB strain rep1


title: okae bts5-150373


title: Liver AIN-93M diet-fed PWK strain rep3

value: PWK/PhJ


title: Liver AIN-93M diet-fed PWK strain rep2


title: okae bts5-150372


title: okae bts5-150371


title: okae bts5-150369


title: InVivoPrimaryINV (P_INV)


title: okae bts5-150368


title: okae bts5-150370


title: Liver High fat/cholic acid diet-fed WSB strain rep2


title: Liver AIN-93M diet-fed PWK strain rep1


title: InVivoMetPRO (M_PRO)


title: okae bts5-150367


title: okae bts5-150365


title: NCM460 cells, Control

first: Wu

last: Ruiyun

address: 17 Qinghua East Road, Haidian District, Beijing

institute: China Agricultural University

data_processing:
Basecalls performed using Bcl2fastq (v2.17.1.14)
Cutadapt (v1.9.1) was used to get the "clean reads"
Mapping clean reads to hg19 whole genome using bowtie2
Fragments Per Kilobase Million (FPKM) was calculated based on the HTSeq (v0.6.1)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human colorectal cells NCM460

growth_protocol: According to previous description,the cells were cultured in the media as suggested by the ATCC (Manassas, VA, USA), supplied with 10% fetal bovine serum and 1% penicillin-streptomycin, and maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol: Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). Then libraries with different indices were multiplexed and loaded on an Illumina instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

treatment_protocol: HT-29 and NCM460 cells in response to SCS treatment SCS (100 μg/mL treatment for 24 h.

value: colorectal


title: okae bts5-150364


title: HT-29 cells, Control

source_name: Human colorectal cancer HT-29

value: Control


title: Liver AIN-93M diet-fed CAST strain rep3

value: CAST/EiJ

value: wild type


title: okae bts5-150363


title: HT-29 cells, SCS-100 μg/mL

value: SCS-100 μg/mL


title: okae bts5-150361


title: okae bts5-150362


title: Liver AIN-93M diet-fed CAST strain rep2

value: liver


title: Liver AIN-93M diet-fed CAST strain rep1


title: okae bts5-150360


title: NCM460 cells, SCS-100 μg/mL


title: okae bts5-150358


title: okae bts5-150359