title: MCF7_siUSP1_1

source_name: breast cancer cell line MCF7, transfected with USP1 specific siRNA-1

value: USP1 siRNA-1


title: MCF7_siCTR

status: Public on Mar 14 2021

type: SRA

city: shanghai

first: aihui

last: ma

address: 800, Dongchuan Road

country: China

institute: shanghai cancer institute

library_source: transcriptomic

data_processing:
Illumina HiSeq 2500 reads were trimmed for adaptor sequences, ribosome RNA reads and low-quality sequences by Seqtk (https://github.com/lh3/seqtk).
Clean reads were mapped to human genome (hg19) with TopHat (version:2.0.9).
The gene fragments were counted by HTSeq (Bioinformatics, 2015. 31(2):p.166-9). Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were normalized by TMM (trimmed mean of M values) method (Genome Biol, 2010. 11(3):p.R25).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM/count values for each gene in each sample.

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer cell line MCF7, transfected with control siRNA

growth_protocol: MCF7 cells were grown in Dulbecco’s Modified Eagle Medium plus 10% fetal bovine serum, 100 units/ml penicillin and 100  μg/mL streptomycin.

extract_protocol:
Total RNA was extracted by TRIZOL Reagent (Life Technologies, Inc) and quantified by Agilent Bioanalyzer 2100 (Agilent technologies).
The cDNA fragments were subjected to an end repair process, added a single ‘A’ base, and ligated with the adapters. The products were then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Cells were maintained at 37 °C with 5% CO2, grown to 80% confluence, and then transfected with control siRNA or USP1-specific siRNA using Lipofectamine 2000 Transfection Reagent (Thermo Fisher Scientific).

tag: cell line

tag: transfection

value: control siRNA

tag: tissue

value: breast cancer cell line


title: med8_P2

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description: med8 stressed replicate 2

data_processing:
Demultiplexing and FASTQ data generation was carried out on BaseSpace (Illumina’s cloud-base resource).
Adapter sequences and low-quality base pairs (length below 20bp) were trimmed with Trim Galore v0.3.3 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) retaining high-quality reads of at least 50 bp in length.
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 v2.1.0 (Kim et al., 2013).
The number of reads per gene was quantified with the feature Counts function as implemented in the Subread package v1.4.6 (Liao et al., 2014).
Genome_build: Araport11

organism: Arabidopsis thaliana

source_name: Two-week-old seedling

growth_protocol: For the in vitro stress assays, seeds were first sterilized using gas sterilization and stratified for 3 days. Seeds were then sown on growth medium containing half-strength MS salts, 1% (w/v) sucrose, 100 mg L−1 myo-inositol, 500 mg L−1 MES, 0.5 mg L−1 nicotinic acid, 0.5 mg L−1 pyridoxine, 1 mg L−1 thiamine and 7% plant tissue culture agar (Duchefa) at 21°C and long-day conditions (16 h light [80 μmol m−2 s−1]/8 h dark). For methyl viologen 25 nM was added to the growth media,

extract_protocol:
Total RNA was isolated in triplicates from Arabidopsis seedlings using TRIzol reagent (Thermo Fisher Scientific), purified using RNeasy mini spin column (Qiagen) and treated with DNase.
The Illumina NextSeq 500 High sequencer was used to generate 75 bp single end reads at the VIB nucleomics core facility (http://nucleomics.be/). Sequencing libraries were constructed with the TruSeq Stranded LT mRNA Library Preparation Kit (Illumina).

treatment_protocol: Plants seedlings were harvested from control and treatment after 2 weeks on growth

tag: genotype

value: med8 mutant

tag: treatment

value: methyl viologen


title: med8_P1

description: med8 stressed replicate 1


title: female-wt-3

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mouse genome (mm10) using the STAR RNA-seq aligner software (version STAR_2.5.0a )
The STAR genome database was built with the gencode annotation file (version M12)
Raw read counts for 49585 Gencode-annotated gene-level features were determined using HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts

organism: Mus musculus

source_name: liver

growth_protocol: Mice were grouped housed in IVC cages (up to 5 animals/cage) in a specific pathogen free environment and fed standard chow diet (Altromin 1324; total pathogen free, irradiated with 25kGy) and water ad libitum.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: liver

tag: Sex

value: Female

value: wild type

tag: age

value: 5-7 months


title: Sample_5_AML1566_AraC_repl2_RNAseq

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

country: USA

institute: Weill Cornell Medical College

description: human patient-derived AML cells

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
TPM were obtained using Rsubread using RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: AML ex vivo

extract_protocol: RNA-seq libraries were prepared using the TruSeq RNA Kit according to the manufacturer

treatment_protocol: Included as additional column of SAMPLES section

tag: agent

value: AraC  (1000nM)

tag: time point


title: med8_C3

description: med8 control replicate 3

value: Control


title: female-tg-3


title: med8_C2

description: med8 control replicate 2


title: female-wt-2


title: med8_C1

description: med8 control replicate 1


title: Col-0_P3

description: Col-0 stressed replicate 3

value: wid-type


title: Col-0_P2

description: Col-0 stressed replicate 2


title: Col-0_P1

description: Col-0 stressed replicate 1


title: med8_P3

description: med8 stressed replicate 3


title: male-tg-7

value: Male


title: female-wt-4


title: Col-0_C1

description: Col-0 control replicate 1


title: SH4_3

city: West Haven

first: Wenxue

last: Li

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

institute: Yale University

data_processing:
Reads are trimmed to remove low quality basse-calls upto 45 reads
HISAT2 was used for alignment of trimmed reads.
StringTie was used to generate gene counts
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each gene and each sample

molecule: polyA RNA

source_name: Melanoma cancer cells

growth_protocol: The cell culture was conducted according to the ATCC described prrotocol.

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

tag: type

value: Metastatic


title: Col-0_C3

description: Col-0 control replicate 3


title: SH4_1


title: male-tg-4


title: male-tg-5


title: female-wt-1


title: SH4_2


title: HTB-69_2


title: HTB-69_1


title: HTB-69_3


title: male-tg-3


title: Cancerous Renal Tissue 052

type: RNA

city: Vilnius

first: Raimonda

last: Kubiliūtė

state: Saulėtekis

address: Sauletekio al., 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description: Gene expression profile in primary renal tumor from patient R052

hyb_protocol: All amount of labeled cRNA was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human Gene Expression 8×60K microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies).

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7.3.1 (Agilent Technologies) using default parameters. Background subtracted and spatially detrended signals were obtained.

source_name: Cancerous renal tissue, donor R052

label_protocol: Cyanine-3 labeled cRNA was prepared from 200 ng of purified RNA using Low Input Quick Amp Labeling Kit, One Color and RNA Spike-In Kit, One Color acording to manufacturer's protocol (Agilent Technologies), followed by purification with RNeasy Mini Kit (Qiagen). Dye incorporation and cRNA yield was measured with NanoDrop 2000.

extract_protocol: Total RNA was extracted from 10-30 ng of mechanically homogenized tissue with mirVana miRNA Isolation Kit according to manufacturer’s protocol (Life Technologies). Extracted RNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Tissue samples were obtained from partial or radical nephrectomy material of patients diagnosed with clear cell renal cell carcinoma. None of the patients had preoperatively received radiotherapy, chemotherapy, or hormone therapy.

tag: gender

value: renal cancer

tag: histological subtype

value: clear cell Renal Cell Carcinoma (ccRCC)

tag: pathological tumor stage

tag: tumor size

value: 95 mm


title: Non-cancerous Renal Tissue 034

description: Gene expression profile in non-cancerous renal tissue adjacent primary renal tumor from patient R034

source_name: Non-cancerous renal tissue, donor R034

value: non-cancerous renal tissue

value: Not applicable


title: Non-cancerous Renal Tissue 052

description: Gene expression profile in non-cancerous renal tissue adjacent primary renal tumor from patient R052

source_name: Non-cancerous renal tissue, donor R052


title: Cancerous Renal Tissue 050

description: Gene expression profile in primary renal tumor from patient R050

source_name: Cancerous renal tissue, donor R050

value: 85 mm


title: Col-0_C2

description: Col-0 control replicate 2


title: AML1566_Ctrl_scRNAseq

data_processing:
Single-cell expression was analyzed using the Cell Ranger Single Cell Software Suite (v3.0.2) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 3’ gene counting.
Sequencing reads were aligned to the refdata-cellranger-hg19-3.0.0 transcriptome using the Cell Ranger suite with default parameters. Samples were merged using Cellranger aggregate function with default parameters.
Libraries were pooled and normalized to 2nM and clustered on a HiSeq4000 high output mode on a pair end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs), followed by 8 cycles of I7 Index (sample Index), and 98 bases on R2 (transcript). Primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA).
Genome_build: hg19
Supplementary_files_format_and_content: matrix and tab-delimited

growth_protocol: patient-derived AML cells were cultured on stroma cells in presence of cytokines

extract_protocol: Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v3 Reagent Kit (10× Genomics) following the directions of the manufacturer. Briefly, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10× cell barcodes, unique molecular identifiers (UMI), and poly(dT) sequences. GEM-Reverse Transcription (53 °C for 45 min, 85 °C for 5 min; held at 4 °C) was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad, Hercules). After RT reaction, GEMs were broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified for 12 cycles (98 °C for 3 min; 98 °C for 15 s, 63°C for 20 s, 72 °C for 1).  Quality of the cDNA was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA), obtaining a product of about 1400bp. This cDNA was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads (Beckman Coulter, Indianapolis, IN) and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through 12 cycles of PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s x 14 cycles; 72 °C for 1 min; held at 4 °C).

value: AML ex vivo

value: AML cells were treated with vehicle control


title: Non-cancerous Renal Tissue 050

description: Gene expression profile in non-cancerous renal tissue adjacent primary renal tumor from patient R050

source_name: Non-cancerous renal tissue, donor R050


title: male-tg-2

value: liver


title: HTB-67_2

value: Primary


title: male-tg-6


title: HTB-67_3


title: HTB-67_1


title: Cancerous Renal Tissue 034

description: Gene expression profile in primary renal tumor from patient R034

source_name: Cancerous renal tissue, donor R034

value: 45 mm


title: Non-cancerous Renal Tissue 019

description: Gene expression profile in non-cancerous renal tissue adjacent primary renal tumor from patient R019

source_name: Non-cancerous renal tissue, donor R019


title: Sample_1_AML1566_Vehicle_repl1_RNAseq

description: human patient-derived AML cells

value: DMSO vehicle control


title: HTB-66_3


title: male-wt-7

value: wild type

value: 5-7 months


title: male-tg-1


title: Cancerous Renal Tissue 019

description: Gene expression profile in primary renal tumor from patient R019

source_name: Cancerous renal tissue, donor R019

value: 93 mm


title: HTB-66_1


title: AML1566_AraC_scRNAseq

value: AML cells were treated with AraC (1000 nM) for 3days


title: male-wt-6

value: Male


title: R406_CUT and Tag

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the mouse mm10 reference genome assembly using Bowtie2 (v2.2.5) (Langmead et al., 2012) with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
For peak calling, parameters used were macs2 (v2.1.2) (Zhang et al., 2008) callpeak -p 1e-5 -f BAMPE -g hs -n sample-name -B --keep-dup all. The peaks visualization in genome was showed by IGV software (Robinson et al., 2011).
The peaks annotations and heatmaps were performed with R package ChIPseeker (Yu et al., 2015) from the bioconductor project. Motif enrichment was done using HOMER with options: -fdr 0.25 -len 8,10,12.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamcoverage
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were infected with rtTA and TetO-Flag-Nfatc1 lentivirus and passaged at 1×10^4 per plate. MEFs were cultured with Stage 1+Dox medium and treated with DMSO or R406 for 4 days.

extract_protocol:
NovoNGS® ConA Beads were pipetted into a new tube, 10 μl per sample, and washed by ConA Binding Buffer. 1×10^5 cells on d4 were harvested and washed by Wash buffer. The cells were mixed with ConA Beads and incubated with Monoclonal ANTI-FLAG® M2 antibody (Sigma) (1:50) or without primary antibody (Blank) overnight at 4°C. Goat anti-mouse IgG antibody (Kitgen) was diluted at 1:500 and added into the sample, then the sample was incubated for 1 hr at RT. After washing away the unbounded secondary antibody, NovoNGS® ChiTag™ 2.0 Transposome was added and incubated with cells for 1 hr at RT. The sample was washed by ChiTag Buffer, and followed with tagmentation by Tagmentation Buffer. Next, DNA was isolated by NovoNGS® DNA Clean Beads, and dissolved in TE-RA-Buffer.
DNA was amplified with N5 and N7 primers and purified with NovoNGS® DNA Clean Beads for high-throughput sequencing.
CUT and Tag

treatment_protocol: Cells were infected with TetO-Flag-Nfatc1 lentivirus and treated with DMSO and R406 for 4 days at the early stage of reprogramming

value: CBA-Tg(Pou5f1-EGFP)2Mnn/J (OG2)

tag: cell type

value: d4 cells in pluripotent reprogramming

tag: developmental stage

value: embryonic day 13.5


title: G361_3

tag: cell line


title: G361_1


title: male-wt-4


title: male-wt-5


title: G361_2


title: DMSO_CUT and Tag


title: Blank_CUT and Tag


title: male-wt-3


title: HTB-66_2

value: Metastatic


title: A375_3


title: R406_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the mouse mm10 reference genome assembly using HISAT2(v2.1.0)(Kim et al., 2015) with the default parameter settings.
Gene expression based on GENCODE vM17 annotations (Mudge et al., 2015) was determined using stringtie(v2.0)(Pertea et al., 2015) with the default parameter settings. Transcripts per million reads (TPM) were calculated for represented the expression of each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene TPM for every gene and every sample

growth_protocol: 4×10^5 MEFs (at passage 3) were seeded onto one plate and cultured in MEF medium. One day later (d0), medium was changed to Stage 1 medium. Stage 1 medium contains DMEM, 10% KSR, 10% FBS, 1% NEAA, 1% P/S, 0.055 mM β-ME and 20 ng/ml bFGF, 0.5 mM VPA, 20 μM CHIR99021, 10 μM 616452, 5 μM Parnate, 50 μM Forskolin, 0.5 μM AM580, 5 μM EPZ004777 and 250 μM vitamin C (Vc). Stage 1 medium was changed every 4 days for 12 days.

extract_protocol:
Cells were havested and total RNA was isolated using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: 2 samples were treated with DMSO and other 2 samples were treated with R406.

value: intermediates of pluripotent reprogramming


title: Sample_1_AML53_day29

hyb_protocol: Labeled cRNA products were randomly fragmented and hybridized onto Affymetrix GeneChips.

scan_protocol: Protocol not available

data_processing: CEL files were annotated to refSeq using custom CDF annotation via BrainArray V23.  Expression was normalized using rma() function from affy R package.

label: biotin

source_name: Primary AML 53

label_protocol: Total RNAs were reverse transcribed into cDNA, then transcribed and labeled into biotinylated cRNA.

growth_protocol: Patient-derived AML cells engrafted in NSG mice.

extract_protocol: Human AML cells from NSG mice were collected from bones and spleen and purified using an anti-human CD45 antibody after before therapy at day 0 and after therapy at day 8 and day 29.

treatment_protocol: PDX models were treated with AraC (Cytarabine) for 5 consecutive days with 60 mg/kg (i.p.).

tag: disease state

value: Primary AML

value: patient-derived xenograft in NSG mice

value: cytarabine (AraC)

tag: time

value: AML cells


title: Sample_1_AML53_day8

tag: tissue


title: male-wt-2

value: liver

tag: genotype


title: DMSO_2

tag: strain

value: DMSO


title: R406_1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the mouse mm10 reference genome assembly using HISAT2(v2.1.0)(Kim et al., 2015) with the default parameter settings.
Gene expression based on GENCODE vM17 annotations (Mudge et al., 2015) was determined using stringtie(v2.0)(Pertea et al. 2015) with the default parameter settings. Transcripts per million reads (TPM) were calculated for represented the expression of each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene TPM for every gene and every sample


title: male-wt-1

tag: Sex


title: A375_1

value: Primary


title: DMSO_1


title: Sample_1_AML53_day0

value: control


title: Sample_1_AML325_day8

source_name: Primary AML 325


title: Sample_10_AML2741_AraC_repl2_RNAseq

description: human patient-derived AML cells

value: AraC  (100nM)


title: LOAD case - P9

status: Public on Mar 13 2021

city: Thuwal

first: Antonio

last: Adamo

state: Makkah

address: Thuwal 23955-6900 KAUST

department: iological, Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
RNA AmpliSeq
Matrix_counts.txt

data_processing:
Ampliseq sequencing data were analyzed and adjusted by quality using the tool SAMStat v 1.5.
Data were mapped over the reference annotation UCSC Hg19 (TDB, 2014), using the Ion Torrent Mapping Alignment Program (TMAP), which is optimized for aligning the raw sequencing reads against reference sequences targeted by the AmpliSeq kit primers.
Estimation of abundances with BEDTools v 2.26 were performed.
Differentially expressed genes (DEGs) were determined using the R package DeSeq2 v.1.12.4, available from Bioconductor. For the final estimation of DEGs, adjusted significance values (padj) were calculated and the Benjamini - Hochberg correction was applied to estimate the false discovery rate (FDR).
DEG thresholds of the significance value padj ≤ 0.05, FDR ≤ 0.1 and -0.5 ≥ log2FC ≥ 0.5.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: Matrix_counts.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Blood

extract_protocol:
Initial RNA extraction was performed using the Tempus™ Spin RNA Isolation Kit (Ref. 4380204, ThermoFisher Scientific, USA) following the manufacturer's recommendations. The total RNA obtained was quantified and evaluated using the Agilent RNA 6000 Pico microfluidics chip (reference 5067-1513) in the Bioanalyzer 2100 equipment (Agilent Technologies, Palo Alto, Calif.) following the manufacturer's instructions.
Library was prepared on 40 ng of total RNA using the AmpliSeq Transcriptome Kit v2 (reference 4475936, Thermo Fisher Scientific, USA) in combination with barcodes Ion Xpress™ 01-16 Kit (4471250AB, Thermo Fisher Scientific, EE.) following the manufacturer's specifications.

value: Blood

value: Late-onset Alzheimer disease (LOAD)

value: Female


title: LOAD case - P6

description:
RNA AmpliSeq
Matrix_counts.txt


title: LOAD case - P5

description:
RNA AmpliSeq
Matrix_counts.txt


title: Healthy control - F9

description:
RNA AmpliSeq
Matrix_counts.txt

value: Healthy


title: LOAD case - P10

description:
RNA AmpliSeq
Matrix_counts.txt


title: LOAD case - P8

description:
RNA AmpliSeq
Matrix_counts.txt


title: Healthy control - F8

description:
RNA AmpliSeq
Matrix_counts.txt


title: Healthy control - F5

description:
RNA AmpliSeq
Matrix_counts.txt


title: Healthy control - F6

description:
RNA AmpliSeq
Matrix_counts.txt


title: A375_2


title: Healthy control - F10

description:
RNA AmpliSeq
Matrix_counts.txt


title: Sample_1_AML325_day0


title: Healthy control - C4

description:
RNA AmpliSeq
Matrix_counts.txt


title: Sample_1_AML262_day8

source_name: Primary AML 262


title: Sample_1_AML262_day29


title: Healthy control - C6

description:
RNA AmpliSeq
Matrix_counts.txt


title: Sample_1_AML262_day0


title: Healthy control - C3

description:
RNA AmpliSeq
Matrix_counts.txt


title: Healthy control - C1

description:
RNA AmpliSeq
Matrix_counts.txt


title: Sample_1_AML325_day29


title: WMH_E_L38_1

city: Beijing

first: Lu

last: Haocheng

address: No. 17 Tsinghua East Road, Beijing, 100083, China.

institute: China Agricultural University

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference grapevine genome V2 using Bowtie. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using FPKM method.
Genome_build: De novo assembled reference transcriptome generated from the mixture of all samples
Supplementary_files_format_and_content: Results include length, excepted_count and FPKM and the description of gene for each sample were shown in xls table files.

organism: Vitis vinifera

source_name: Muscat Hamburg_E-L 38_Winter_grape berry

growth_protocol: The experiment was conducted in 2014 on seven-year-old grapevines grafted onto SO4 rootstock in southern China. The grape viticulture regime in this subtropical region was dominated by double cropping systems per year. The vines were planted in east-west rows under a rain-shelter treatment with an inter- and intra-row vine spacing of 3.5 m × 1.5 m and were managed in a closing Y-shaped training system with 2 × 4/5 shoots per meter and 1.0 m cordon above ground.

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

treatment_protocol: The vines are pruned twice and the grapes are harvested twice per year. To produce the first crop, the vines were pruned and enforced with 2.5%-3.0% hydrogen cyanamide in mid-February when the temperature was maintained above 10 °C. The terminal bud was not sprayed to avoid apical dominance. Then, the grapevines were in full bloom around mid-April, while the veraison stage ranged from mid-June to early July, followed by the harvest stage (summer grape). This whole period was termed the summer cropping cycle. Then, the vines were pruned and forced again in August, leading to the second crop (winter grape) in early January of the following year. In detail, the grapevines were pruned on approximately 20th August, were manually defoliated and an average of 5-10 buds were left for each cane. Hydrogen cyanamide was smeared only at the terminal bud and in the vicinity of the pruning-wound surface. Then, the bud burst 5-8 days later and initiated the winter cropping cycle.

tag: cultivar

value: Muscat Hamburg

tag: Stage

tag: crop

value: Winter

value: grape berry


title: WMH_E_L38_2


title: WMH_E_L38_3


title: WMH_E_L35_2

source_name: Muscat Hamburg_E-L 35_Winter_grape berry


title: WMH_E_L36_1

source_name: Muscat Hamburg_E-L 36_Winter_grape berry


title: SMH_E_L38_3

source_name: Muscat Hamburg_E-L 38_Summer_grape berry

value: Summer


title: SMH_E_L36_3

source_name: Muscat Hamburg_E-L 36_Summer_grape berry


title: WMH_E_L36_2


title: SMH_E_L38_1


title: WMH_E_L35_1


title: SMH_E_L38_2


title: Healthy control - C5

description:
RNA AmpliSeq
Matrix_counts.txt


title: Male_control_3 [21725_3]

city: Glasgow

first: Katarzyna

middle: Kinga

last: Modrzynska

state: Glasgow (City of)

address: B627 Sir Graeme Davies Building, 120 University Place

country: United Kingdom

institute: Wellcome Trust Centre for Molecular Parasitology

data_processing:
base calling, quality checking, index sorting and generation of initial *cram files performed using the automatic pipelines of the sequencing service of the Wellcome Trust Sanger Institute. All details of the processing are included in the *cram file header.
concatenation of the *cram files from the two lanes of HiSeq2500 run using samtools (v.1.3.1)
generation of *fastq file from *cram files using Picard-tools SamToFastq (v.2.3)
re-alignment of the reads with from *fastq files against the reference genome in a splice-aware manner using hisat2-2.0.0-beta software and generation of *sam files
sorting and indexing of the resulting *sam files using samtools (v.1.3.1)
counting of the reads aligned to each of the Plasmodium genes using htseq-count command from  HTSeq Python library (v. 0.6.1) with  option '-s reverse'  and gff file matching the reference genome, http://plasmodb.org/common/downloads/release-30/PbergheiANKA/gff/data/
Genome_build: http://plasmodb.org/common/downloads/release-30/PbergheiANKA/fasta/data/
Supplementary_files_format_and_content: *.htseq_count.txt files containing the raw read counts for all the genes in Plasmodium berghei genome

organism: Plasmodium berghei

source_name: inducible AP2-G overexpression line_Male_control

growth_protocol: Female, outbred Theiler’s Original (TO) mice, 8-12 weeks old were injected with PBGAMi parasites synchronized to late schizont stage. The gametocyte conversion was induced in half of the animals by intraperitoneal injection of 4 mg/kg of rapamycin. Blood containing the developing parasites was harvested at different time point post induction  (0h, 6h, 12h, 18h, 24h and 30h) via cardiac puncture. Leucocyte depletion was achieved by filtration of the blood through two sequential Plasmodipur ® filters (Europroxima) according to the manufacturer’s instructions. Remaining red blood cells were resuspended in 10 volumes of pre-chilled erythrocyte lysis buffer (150mM NH4Cl; 10mM KHCO3; 1mM EDTA) and incubated on ice for 15min. After lysis parasites were pelleted by centrifugation for 8 minutes at 450g and washed with 1x phosphate buffered saline until complete removal of the coloration of the supernatant. Parasite pallet was resuspended in 1ml of Trizol reagent (Ambion) lysed for 10 min at room temperature and stored at -80°C for later RNA extraction. For each time point at least two independent biological replicates of treated parasites and matched untreated controls were generated.

extract_protocol:
Complete RNA was isolated from the samples using Trizol/chloroform extraction followed by isopropanol precipitation and its concentration and integrity was verified using Agilent Bioanalyzer (RNA 6000 Nano kit) and NanoDrop 1000 spectrophotometer.
1-2μg of total RNA from each sample (all complete sample if the yield was lower) was used for mRNA isolation (Magnetic mRNA Isolation Kit, NEB). First strand cDNA synthesis was performed using the SuperScript III First-Strand Synthesis System and a 1:1 mix of Oligo(dT) and random primers (Invitrogen). The DNA/RNA hybrids were purified using Agencourt RNACleanXP beads (Beckman Coulter) and the second cDNA strand was synthesized using a 10 mM dUTP nucleotide mix, DNA Polymerase I (Invitrogen) and RNAseH (NEB) for 2.5 h at 16°C. The long cDNA fragments were purified and fragmented using a Covaris S220 system (duty cycles= 20, intensity = 5,cycles/burst =200,time= 30s). The ~200 bp long fragments were end-repaired, dA-tailed and ligated to “PCR-free” adapters (Kozarewa et al., 2009) with index tags using NEBNext kits according to the manufacturer’s instructions. Excess adapters were removed by two rounds of clean-up with 1xvolume of Agencourt AMPure XP beads. Final libraries were eluted in 30μl water, quality-controlled using Agilent Bioanalyzer (High Sensitivity DNA chip) digested with USER enzyme (NEB) and quantified by qPCR. For some libraries, additional 5 cycles of PCR amplification were performed, using KAPA HiFi HotStart PCR mix and tag-specific primers to obtain enough material for sequencing. Pools of indexed libraries were sequenced using an Illumina HiSeq2500 system (100 bp paired-end reads) according to manufacturer’s manual.

tag: genotype/variation

value: inducible AP2-G overexpression line

tag: rapamycin treated?

value: NO

tag: time (hours post induction)

value: mixed


title: Male_control_2 [21725_2]


title: Male_control_1 [21725_1]


title: WMH_E_L36_3


title: Female_control_3 [21725_6]

source_name: inducible AP2-G overexpression line_Female_control


title: Female_control_2 [21725_5]


title: SMH_E_L35_3

source_name: Muscat Hamburg_E-L 35_Summer_grape berry


title: SMH_E_L36_2


title: SMH_E_L35_2


title: Female_control_1 [21725_4]


title: WV_E_L38_3

source_name: Victoria_E-L 38_Winter_grape berry

value: Victoria


title: SMH_E_L35_1


title: WV_E_L38_2


title: 4h_R+_1 [13674_3]

source_name: inducible AP2-G overexpression line_4h_R+

value: YES


title: 4h_R+_3 [17446_15]


title: 4h_R+_2 [15786_16]


title: 4h_R-_2 [15786_15]

source_name: inducible AP2-G overexpression line_4h_R-


title: WV_E_L36_2

source_name: Victoria_E-L 36_Winter_grape berry


title: WV_E_L36_3


title: WV_E_L38_1


title: 4h_R-_3 [17446_7]


title: WV_E_L36_1


title: WV_E_L35_2

source_name: Victoria_E-L 35_Winter_grape berry


title: 3h_R+_1 [15786_14]

source_name: inducible AP2-G overexpression line_3h_R+


title: 4h_R-_1 [13674_9]


title: 2h_R+_4 [21384_14]

source_name: inducible AP2-G overexpression line_2h_R+


title: SV_E_L38_3

source_name: Victoria_E-L 38_Summer_grape berry


title: 3h_R-_1 [15786_13]

source_name: inducible AP2-G overexpression line_3h_R-


title: WMH_E_L35_3


title: 2h_R+_3 [21384_13]


title: WV_E_L35_1


title: 2h_R+_1 [15786_12]


title: SV_E_L38_2


title: 2h_R-_4 [21384_4]

source_name: inducible AP2-G overexpression line_2h_R-


title: 2h_R+_2 [17446_14]


title: SV_E_L38_1


title: 2h_R-_3 [21384_3]


title: 2h_R-_2 [17446_6]


title: 2h_R-_1 [15786_11]


title: SMH_E_L36_1


title: 1h_R+_3 [21384_25]

source_name: inducible AP2-G overexpression line_1h_R+


title: SV_E_L36_1

source_name: Victoria_E-L 36_Summer_grape berry


title: SV_E_L35_3

source_name: Victoria_E-L 35_Summer_grape berry


title: SV_E_L36_2


title: SV_E_L35_2


title: 1h_R+_2 [15786_9]


title: WV_E_L35_3


title: SV_E_L36_3


title: 1h_R+_1 [13674_2]


title: 1h_R-_1 [13674_8]

source_name: inducible AP2-G overexpression line_1h_R-


title: 2.5E8 mRBC-OVA-4-1BBL-IL-12 treated tumor - Mouse 4 RUB170_2_5E8_4_4_tumor

city: Cambridge

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

data_processing:
Raw data were processed using the standard immunoSEQ Analyzer from Adaptive Biotechnologies Corporation.
*** Raw fastq files not provided by third party provider ***
*** Third party provider only releases processed data which consist of nucleotide sequences generated through V(D)J recombination as well as associated information including amino acid translation and V, D and J gene and allele identifications.***
Genome_build: Third party provider description: "Sequences were not aligned against a reference genome; instead they were aligned and annotated based on our custom pipeline using primers designed to IMGT reference V and J genes. The CDR3 regions were defined as per IMGT beginning with the second conserved cysteine encoded by 3’ portion of V gene segment.  IMGT reference: Yousfi Monod, M., Giudicelli, V., Chaume, D. & Lefranc, M. P. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, (Suppl 1): i379–i385 (2004).
Supplementary_files_format_and_content: TCRbeta rearrangement text files

source_name: Tumor

growth_protocol: Murine lymphoma cell lines EL4 (TIB-39™) and EG7.OVA (CRL-2113™) were obtained from American Type Culture Collection (ATCC®) and cultured as recommended by ATCC.

extract_protocol:
Blood was collected by submandibular bleed or cardiac puncture in BD Microtainer® blood collection tubes with K2EDTA (BD Biosciences) and the tubes were kept on ice until analysis. Genomic DNA (gDNA) was extracted from 50‒60 μL of anticoagulated blood using DNeasy® Blood and Tissue Kit (Qiagen® Inc.) according to the manufacturer’s instructions. Tumors were digested in gentleMACS™ C‑tubes (Miltenyi Biotec, Inc.) using the murine Tumor Dissociation Kit. Cell suspensions were generated using a gentleMACS Octo Dissociator with Heaters instrument (Miltenyi Biotec, Inc.) according to the manufacturer’s instructions. Digested tissue was then filtered through a 70 µm cell strainer and washed.  gDNA was extracted from one quarter of the tumor single cell suspensions using the DNeasy Blood and Tissue Kit (Qiagen Inc.) according to the manufacturer’s instructions.
Immunosequencing of the CDR3 regions of mouse TCRβ chains was performed using the ImmunoSEQÒ platform (Adaptive Biotechnologies Corporation). In brief, extracted DNA was amplified in a bias-controlled multiplex polymerase chain reaction (PCR), followed by high‑throughput sequencing. Sequences were then collapsed and filtered in order to identify and quantitate the absolute abundance of each unique TCRβ CDR3 region for further analysis as previously described.

treatment_protocol: For paired blood and tumor analyses (RUB170), Pep Boy (CD45.1 B6) mice were injected subcutaneously in the flank with 2×106 EG7.OVA at a 1:1 ratio in Roswell Park Memorial Institute (RPMI) 1640 media and Matrigel® matrix (Corning, PA, USA). Tumor-bearing mice were randomized when the average tumor volume reached ~175 mm3 and 1×106 naive OT-1 cells were administered to all groups no later than one day after randomization by tail vein injection. Several hours after T cell injection, mice were treated intravenously 1×109 mRBC-CTRL or a dose titration of mRBC-OVA-4-1BBL-IL-12 (1×109, 2.5×108) in 200 μL PBS on days 0 and 3. For blood analyses before and after tumor re-challenge (RUB157), CD45.1 Pep Boy mice were randomized when EG7.OVA tumors (2×106 injected) reached ~230 mm3, treated with 1×106 naïve OT-1 cells, and dosed with 2.5×108 mRBC-OVA-4-1BBL-IL-12. Mice cured of original EG7.OVA tumors (n=7) were rechallenged on day 66 with EG7.OVA. Age-matched naïve CD45.1 Pep Boy mice (n=5) were treated on day 65 with 5×105 naïve OT-1 cells one day before challenge with EG7.OVA cells, as controls. All previously cured mice rejected EG7.OVA rechallenge. At 61 days post-second EG7.OVA challenge on day 127, cured mice (n=7) along with age-matched naïve control mice (n=5) were challenged with EL4.

value: B6.SJL-Ptprc<a> Pepc<b>/BoyJ

tag: treatment

value: 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatments on Days 0 and 3, sample collected on Day 7


title: 2.5E8 mRBC-OVA-4-1BBL-IL-12 treated tumor - Mouse 2 RUB170_2_5E8_4_2_tumor


title: 2.5E8 mRBC-OVA-4-1BBL-IL-12 treated tumor - Mouse 5 RUB170_2_5E8_4_5_tumor


title: 1h_R-_3 [21384_22]


title: 1h_R-_2 [15786_10]


title: 1E9 mRBC-OVA-4-1BBL-IL-12 reated tumor - Mouse 5 RUB170_1E9_3_5_tumor

value: 1E9 mRBC-OVA-4-1BBL-IL-12 treatments on Days 0 and 3, sample collected on Day 7


title: 1E9 mRBC-OVA-4-1BBL-IL-12 reated tumor - Mouse 3 RUB170_1E9_3_3_tumor


title: 2.5E8 mRBC-OVA-4-1BBL-IL-12 treated tumor - Mouse 1 RUB170_2_5E8_4_1_tumor


title: 1E9 mRBC-OVA-4-1BBL-IL-12 reated tumor - Mouse 4 RUB170_1E9_3_4_tumor


title: 1E9 mRBC-OVA-4-1BBL-IL-12 reated tumor - Mouse 2 RUB170_1E9_3_2_tumor


title: mRBC-CTRL treated tumor - Mouse 4 RUB170_Control_2_4_tumor

description: mRBC-CTRL treated tumor - Mouse 4

value: mRBC-CTRL treatments on Days 0 and 3, sample collected on Day 7


title: 1E9 mRBC-OVA-4-1BBL-IL-12 reated tumor - Mouse 1 RUB170_1E9_3_1_tumor


title: SV_E_L35_1


title: 2.5E8 mRBC-OVA-4-1BBL-IL-12 treated tumor - Mouse 3 RUB170_2_5E8_4_3_tumor


title: mRBC-CTRL treated tumor - Mouse 5 RUB170_Control_2_5_tumor

description: mRBC-CTRL treated tumor - Mouse 5


title: mRBC-CTRL treated tumor - Mouse 1 RUB170_Control_2_1_tumor

description: mRBC-CTRL treated tumor - Mouse 1


title: post 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 2 RUB170_2_5E8_4_2_postblood

source_name: Blood


title: carotid plaque, asymptomatic, biological rep4

city: Pittsburgh

first: ROBERT

middle: MAX

last: FRIEDLANDER

state: PA

address: Suite B-400, 200 Lothrop Street

department: Neurological Surgery

institute: University of Pittsburgh Medical Center

hyb_protocol: The cDNA (3.5 µg) was incubated with fragmentation buffer (NuGEN, 37°C x 30 min, 95°C x 2 min), mixed in a hybridization cocktail with water (220 μl) and hybridized on arrays (Affymetrix GeneChip HG U133 2.0, ThermoFisher Scientific, 45°C x 18 hours). The arrays were then washed and stained with streptavidin-phycoerythrin in a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChip Scanner 3000 (Affymetrix)

data_processing: RMA algorithm using the Expression Console software (version 1.2.0.20; Affymetrix).

source_name: Post-bifurcation internal carotid plaque from asymptomatic patient

label_protocol: Encore Biotin Module (NuGen)

extract_protocol: Carotid plaques were collected from patients undergoing carotid endarterectomy, dissected into pre-bifurcation, bifurcation and post-bifurcation segments, and immediately flash frozen.  The frozen plaque fragments were transferred to RNALater-ICE (-20°C x 16 h) (ThermoFisher Scientific, Waltham, MA) prior to storage at -80°C. Individual samples were subsequently homogenized in TRIzol Reagent and the total RNA was isolated per the manufacturer’s protocol (ThermoFisher Scientific). Extracted total RNA was of high purity (OD 260/280: 1.8 to 2.0, Nanodrop1000 Spectrophotometer, ThermoFisher Scientific, Waltham, MA) with RIN <8.0 (Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA) requiring an mRNA replication and amplification strategy validated to capture transcriptomes with partial fragmentation. We performed 1st strand cDNA synthesis using DNA/RNA chimeric primers (NuGEN Ovation FFPE WTA; protocol #3403, NuGEN, San Carlos, CA) which hybridize to 5’ poly A sequence and randomly across all transcripts. The reverse transcriptase extends the 3’ DNA end of each primer generating a cDNA/RNA hybrid with a unique RNA sequence at the 5’ end of the cDNA strand (100 ng RNA; 2 min x 65⁰C, 2 min x 4⁰C, 30 min x 25⁰C, 15 min x 42⁰C, 15 min x 70⁰C). This hybrid complex forms the DNA polymerase priming site for 2nd strand synthesis generating dsDNA ending with the unique DNA/RNA heteroduplex (1 min x 4⁰C, 10 min x 25⁰C, 30 min x 50⁰C, 20 min x 80⁰C). The cDNA product was purified using magnetic beads (Agencourt Beads, Beckmann Coulter Genomics, Indianapolis, IN) and air dried after 70% ethanol wash (3X) leaving the dsDNA appended to the beads for initiation of isothermal strand displacement amplification (SPIA™ Amplification). The SPIA master mix eluted the DNA from the beads and removed the 5’ RNA portion of the duplex exposing the DNA polymerase primer site for SPIA primer binding and initiation of strand replication displacing the existing strand (1 min x 4⁰C, 60 min x 47⁰C, 5 min x 95⁰C). After amplification, the DNA underwent column purification (Qiagen #28004 minElute PCR kit, Qiagen, Hilden, Germany). Overall cDNA diversity was evaluated using the Bioanalyzer and concentration was assessed using strand specific fluorometry (Qubit, ThermoFisher, Waltham, MA). The SPIA sample yield (≥3.5 µg) and size diversity (average size 3-4 kb) was not significantly different than results obtained from a laboratory human FFPE RNA standard (normal human kidney RNA) and a Universal Human Reference RNA (Stratagene, La Jolla, CA) that underwent identical processing.

tag: individual

value: asymptomatic patient

tag: sample type

value: carotid plaque


title: post 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 5 RUB170_2_5E8_4_5_postblood


title: post 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 1 RUB170_2_5E8_4_1_postblood


title: mRBC-CTRL treated tumor - Mouse 2 RUB170_Control_2_2_tumor

description: mRBC-CTRL treated tumor - Mouse 2


title: post 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 5 RUB170_1E9_3_5_postblood


title: carotid plaque, asymptomatic, biological rep6


title: SR1-1

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

description:
14222_252800417429_1_1
SAMPLE 1

hyb_protocol: According to manufature's protocol

scan_protocol: According to manufature's protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Spheres of Cp70_SR-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The parental Cp70 were cultured in RPMI-1640  supplemented with NEAA, sodium pyruvate and either 10% FBS, and plated in standard cell culture dishes. To enrich spheroid cells carrying stemness properties, Cp70 were harvested and cultured in ultra-low attachment plates with DMEM/F12 medium, a high glucose concentration and 5% FBS.  The cells were cultured in suspension, and starting from 14 days, the cultures were examined every day for sphere formation. Spheres were then dissociated and passaged at least eight times in 2 months to generate spheres.

extract_protocol: The total RNA was harvested by using a Qiagen RNeasy kit. An additional DNase I digestion procedure was included in the isolation of RNA to remove contaminating DNA according to the manufacturer's protocol.  The mRNA quality has achieved the ratio of  28S/18S >1 and RNA quality indicator (RQI) > 7 by using Agilent 2100 Bioanalyzer to send to the core service unit (WELGENE Biotech Co.,Ltd, Taiwan) for whole genome expression analysis.

tag: gender

value: female

tag: cell line source

tag: source cell type

value: ovarian cancer cells

tag: cell type

value: ovarian cancer stem cells (CSCs)

tag: morphology

value: smooth surface of spheres


title: carotid plaque, asymptomatic, biological rep7


title: carotid plaque, asymptomatic, biological rep9


title: carotid plaque, asymptomatic, biological rep8


title: SR1-2

description:
14224_252800417429_1_2
SAMPLE 2


title: post 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 3 RUB170_2_5E8_4_3_postblood


title: post 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 3 RUB170_1E9_3_3_postblood


title: mRBC-CTRL treated tumor - Mouse 3 RUB170_Control_2_3_tumor

description: mRBC-CTRL treated tumor - Mouse 3


title: carotid plaque, asymptomatic, biological rep5


title: carotid plaque, asymptomatic, biological rep1


title: carotid plaque, symptomatic, biological rep6

source_name: Post-bifurcation internal carotid plaque from symptomatic patient

value: symptomatic patient


title: post 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 4 RUB170_1E9_3_4_postblood


title: carotid plaque, symptomatic, biological rep9


title: post 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 4 RUB170_2_5E8_4_4_postblood


title: post 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 2 RUB170_1E9_3_2_postblood


title: SR2

description:
14226_252800417429_1_3
SAMPLE 3

source_name: Spheres of Cp70_SR-2

value: morula-like surface of spheres


title: carotid plaque, asymptomatic, biological rep3


title: post mRBC-CTRL treatment blood - Mouse 5 RUB170_Control_2_5_postblood


title: post 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 1 RUB170_1E9_3_1_postblood


title: carotid plaque, symptomatic, biological rep3


title: post mRBC-CTRL treatment blood - Mouse 4 RUB170_Control_2_4_postblood


title: carotid plaque, symptomatic, biological rep7


title: post mRBC-CTRL treatment blood - Mouse 2 RUB170_Control_2_2_postblood


title: pre 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 5 RUB170_2_5E8_4_5_preblood

value: 5min post OT-1 transfer, prior to 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment


title: pre 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 4 RUB170_2_5E8_4_4_preblood


title: carotid plaque, symptomatic, biological rep8


title: pre 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 2 RUB170_2_5E8_4_2_preblood


title: post mRBC-CTRL treatment blood - Mouse 3 RUB170_Control_2_3_postblood


title: carotid plaque, symptomatic, biological rep4


title: pre 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 3 RUB170_2_5E8_4_3_preblood


title: carotid plaque, asymptomatic, biological rep2


title: pre 2.5E8 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 1 RUB170_2_5E8_4_1_preblood


title: carotid plaque, symptomatic, biological rep1


title: pre 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 4 RUB170_1E9_3_4_preblood

value: 5min post OT-1 transfer, prior to 1E9 mRBC-OVA-4-1BBL-IL-12 treatment


title: seedlings_3h_RLs_exp4

city: Compiègne

first: Sonia

last: Rippa

address: Rue du Dr Schweitzer

department: Génie Biologique

country: France

institute: Université de Technologie de Compiègne

description:
EXP4_3h_RL
Gene expression after 3 hours treated with mono-RLs.

hyb_protocol: 1.65µg of Cy3-labelled cRNAs were fragmented at 60°C for exactly 30 min in a reaction volume of 55µL, containing 10x Gene expression blocking agent (11µL), 25x fragmentation buffer (2.2µL) and nuclease-free water following manufacturer's instructions. In completion, 2x HI-RPM Hybridization buffer (55µL) were added in the fragmentation mix and hybridized in the Agilent oven rotator at 10 rpm and 65°C for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G1662-90043) using the AgilentG3_GX_1color protocol.

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol AgilentG3_6X_1color and Grid: 021169_D_F_20160208).
Background correction and signal intensity normalisation were realised using Bioconductor and limma, function backgroundCorrect with normexp method and function normalizeBetweenArrays with quantile method as described in limma user guide Linear Models for Microarray and RNA-Seq Data (see 17.4 Single-Channel Case Studie with Agilent Arrays https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf ).

source_name: 10-day-old seedlings_3h_RL

label_protocol: Labelling was performed with 100ng RNAs using the Agilent One-Color Low Input Quick Amp Labelling protocol. Labelled cRNAs were purified by the Qiagen RNeasy Mini Kit.

growth_protocol: Arabidopsis Col-0 seeds were sown in solid MS medium for a 4 days germination at 4°C (day -4). Seeds were transferred into a phytotron at 21°C, 60% of relative humidity and 12 hours of photoperiod (at 150µEm^-2.s^-1)(day 0). After 4 days, seeds were transferred in a liquid medium (day 4). This medium was replaced by fresh medium after 5 days (day 9). Seedlings were treated by mono-rhamnolipids or water and harvested the next day (day 10).

extract_protocol: Total RNA were extracted using the Qiagen RNeasy Plant Mini Kit following the manufacturer's protocol. RNAs were quantified using Nanodrop2000.

treatment_protocol: Seedlings were treated after a ten-day growth by root absorption with 100µM of purified mono-Rhamnolipids (in 0.5% EtOH), or water (0.5% EtOH).

tag: ecotype

tag: tissue

value: Seedling

tag: age

value: 10 days

value: mono-rhamnolipids

tag: time after treatment

value: 3 hours


title: pre 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 3 RUB170_1E9_3_3_preblood

tag: strain

value: B6.SJL-Ptprc<a> Pepc<b>/BoyJ


title: pre 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 5 RUB170_1E9_3_5_preblood


title: carotid plaque, symptomatic, biological rep5


title: seedlings_3h_RLs_exp1

description:
EXP1_3h_RL
Gene expression after 3 hours treated with mono-RLs.


title: seedlings_3h_RLs_exp2

description:
EXP2_3h_RL
Gene expression after 3 hours treated with mono-RLs.


title: pre 1E9 mRBC-OVA-4-1BBL-IL-12 treatment blood - Mouse 2 RUB170_1E9_3_2_preblood


title: pre mRBC-CTRL treatment blood - Mouse 5 RUB170_Control_2_5_preblood

description: pre mRBC-CTRL treatment blood - Mouse 5

value: 5min post OT-1 transfer, prior to mRBC-CTRL treatment


title: seedlings_3h_RLs_exp3

description:
EXP3_3h_RL
Gene expression after 3 hours treated with mono-RLs.


title: seedlings_3h_water_exp5

description:
EXP5_3h_Control
Gene expression after 3 hours treated with water + EtOH.

source_name: 10-day-old seedlings_3h_water

value: water + EtOH


title: pre mRBC-CTRL treatment blood - Mouse 4 RUB170_Control_2_4_preblood

description: pre mRBC-CTRL treatment blood - Mouse 4


title: pre mRBC-CTRL treatment blood - Mouse 2 RUB170_Control_2_2_preblood

description: pre mRBC-CTRL treatment blood - Mouse 2


title: pre mRBC-CTRL treatment blood - Mouse 3 RUB170_Control_2_3_preblood

description: pre mRBC-CTRL treatment blood - Mouse 3


title: Cured post EL4 tumor challenge blood - Mouse 7 RUB157_5_7_Cured_post_EL4_blood

value: mRBC-OVA-4-1BBL-IL12 & EG7.OVA rechallenged cured mouse, 9 day post EL4 challenge


title: Cured post EL4 tumor challenge blood - Mouse 6 RUB157_5_6_Cured_post_EL4_blood


title: Cured post EL4 tumor challenge blood - Mouse 5 RUB157_5_5_Cured_post_EL4_blood


title: pre mRBC-CTRL treatment blood - Mouse 1 RUB170_Control_2_1_preblood

description: pre mRBC-CTRL treatment blood - Mouse 1


title: carotid plaque, symptomatic, biological rep2

value: carotid plaque


title: seedlings_3h_water_exp2

description:
EXP2_3h_Control
Gene expression after 3 hours treated with water + EtOH.


title: seedlings_3h_water_exp3

description:
EXP3_3h_Control
Gene expression after 3 hours treated with water + EtOH.


title: seedlings_1h_RLs_exp4

description:
EXP4_1h_RL
Gene expression after 1 hour treated with mono-RLs.

source_name: 10-day-old seedlings_1h_RL

value: 1 hour


title: seedlings_1h_RLs_exp2

description:
EXP2_1h_RL
Gene expression after 1 hour treated with mono-RLs.


title: seedlings_1h_RLs_exp5

description:
EXP5_1h_RL
Gene expression after 1 hour treated with mono-RLs.


title: seedlings_1h_water_exp3

description:
EXP3_1h_Control
Gene expression after 1 hour treated with water + EtOH.

source_name: 10-day-old seedlings_1h_water


title: Cured post EL4 tumor challenge blood - Mouse 3 RUB157_5_3_Cured_post_EL4_blood


title: Cured post EL4 tumor challenge blood - Mouse 4 RUB157_5_4_Cured_post_EL4_blood


title: seedlings_1h_RLs_exp3

description:
EXP3_1h_RL
Gene expression after 1 hour treated with mono-RLs.


title: seedlings_1h_water_exp4

description:
EXP4_1h_Control
Gene expression after 1 hour treated with water + EtOH.


title: seedlings_3h_water_exp1

description:
EXP1_3h_Control
Gene expression after 3 hours treated with water + EtOH.


title: seedlings_1h_water_exp1

description:
EXP1_1h_Control
Gene expression after 1 hour treated with water + EtOH.


title: Cured post EL4 tumor challenge blood - Mouse 1 RUB157_5_1_Cured_post_EL4_blood


title: seedlings_1h_RLs_exp1

description:
EXP1_1h_RL
Gene expression after 1 hour treated with mono-RLs.


title: Cured post EL4 tumor challenge blood - Mouse 2 RUB157_5_2_Cured_post_EL4_blood


title: seedlings_1h_water_exp2

description:
EXP2_1h_Control
Gene expression after 1 hour treated with water + EtOH.


title: seedlings_1h_water_exp5

description:
EXP5_1h_Control
Gene expression after 1 hour treated with water + EtOH.


title: seedlings_0h_exp2

description:
EXP2_0h
Initial gene expression.

source_name: 10-day-old seedlings_no treatment

value: No treatment

value: 0 hour


title: PBS-2

first: Kelvin

last: Zhang

state: Massachusetts

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

data_processing:
RNA-seq FASTQ files were processed using the customized bulk RNA-seq data analysis pipeline in OmicSoft ArraySuite, version 9.
Specifically, raw reads were first filtered based on quality control (QC) and then aligned to the reference genome (mouse genome mm10) using OSA.
After alignment, gene expression levels (raw read counts) were quantified by the RSEM algorithm with the mouse gene model Ensembl.R88.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample ...

growth_protocol: To establish syngeneic tumor models, B16F10 (1×106 cells to C57BL/6) were injected subcutaneously to the right flank of mice.

extract_protocol:
Tumors were lysed Trizol solution with mechanical disruption. RNAs were isolated by using RNeasy Lipid Tissue Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS, unloaded EVs, CDN2 (20 µg), and exoCDN2 (0.1 µg) were injected intratumorally into B16F10 tumors and tumors were collected 24 h after dose. Additional tumors were injected again 3 days after first dose and collected 24 h after second dose.

value: B16F10 tumors

tag: agent

value: PBS


title: seedlings_0h_exp5

description:
EXP5_0h
Initial gene expression.


title: seedlings_0h_exp3

description:
EXP3_0h
Initial gene expression.


title: seedlings_3h_RLs_exp5

description:
EXP5_3h_RL
Gene expression after 3 hours treated with mono-RLs.


title: PBS-1


title: seedlings_0h_exp1

description:
EXP1_0h
Initial gene expression.


title: exoCL656-2


title: Cured pre EL4 tumor challenge blood - Mouse 6 RUB157_5_6_Cured_pre_EL4_blood

value: mRBC-OVA-4-1BBL-IL12 & EG7.OVA rechallenged cured mouse, 1 day before EL4 challenge


title: CL656-20ug-2d-2


title: Cured pre EL4 tumor challenge blood - Mouse 7 RUB157_5_7_Cured_pre_EL4_blood


title: Cured pre EL4 tumor challenge blood - Mouse 3 RUB157_5_3_Cured_pre_EL4_blood


title: Cured pre EL4 tumor challenge blood - Mouse 5 RUB157_5_5_Cured_pre_EL4_blood


title: CL656-20ug-2d-1


title: exoCL656-1


title: Cured pre EL4 tumor challenge blood - Mouse 4 RUB157_5_4_Cured_pre_EL4_blood


title: Cured pre EL4 tumor challenge blood - Mouse 1 RUB157_5_1_Cured_pre_EL4_blood


title: Cured post-EG7.OVA tumor challenge blood - Mouse 7 RUB157_5_7_Cured_postblood

value: mRBC-OVA-4-1BBL-IL12 with prior OT-1 T cell transfer cured mouse, 7 days post EG7.OVA rechallenge


title: seedlings_3h_water_exp4

description:
EXP4_3h_Control
Gene expression after 3 hours treated with water + EtOH.


title: Cured pre EL4 tumor challenge blood - Mouse 2 RUB157_5_2_Cured_pre_EL4_blood


title: Cured post EG7.OVA tumor challenge blood - Mouse 6 RUB157_5_6_Cured_postblood


title: CYP2C9_activity_library_plasmid

city: Seattle

first: Clara

last: Amorosi

state: Washington

address: 3720 15th Ave. NE

department: Genome Sciences

institute: University of Washington

description: Targeted barcode amplification from plasmid DNA.

data_processing:
Libraries were sequenced on NextSeq 550 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
Sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq.
Barcode and UMI sequencing reads for all CYP2C9 activity replicates were trimmed and filtered for minimum base quality Q20 using FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and collapsed according to UMI sequences using a custom script. Barcode paired sequencing reads for all CYP2C9 abundance replicates were joined using PEAR software (https://cme.h-its.org/exelixis/web/software/pear/). FASTQ files from technical replicate amplification were concatenated for analysis with Enrich2.
The abundance and activity scores for CYP2C9 were calculated as follows: The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average was calculated for each variant. Finally, for each experiment, an abundance or activity score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of synonymous variants, which was given a score of 1, and the median weighted average value for nonsense variants, which was given a score of 0. The final activity or abundance score for each variant was calculated by taking the mean of the min-max normalized scores across the replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed.
Genome_build: None
Supplementary_files_format_and_content: The CYP2C9_activity_barcode_variant_map.tsv and CYP2C9_abundance_barcode_variant_map.tsv processed data files are tab-separated text file format, containing the variant-barcode map determined by PacBio sequencing for the activity and abundance libraries, respectively. The CYP2C9_activity_abundance_scores.csv processed data file is a comma-separated text file format, containing the CYP2C9 variant activity and abundance scores calculated as described above.

organism: Escherichia coli

source_name: Synthetic sequence

growth_protocol: Yeast cells were grown in YPD media supplemented with 200 μg/mL G418 until saturated, then diluted into YP media containing 2% (w/v) raffinose supplemented with 200 μg/mL G418 and grown for at least two cell doublings, then cells were inoculated to OD 0.0125 into fresh YP media containing 2% (w/v) galactose and 200 μg/mL G418 and collected after 7 doublings. HEK 293T TetBxb1BFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2.5 μg/mL doxycycline.

extract_protocol:
Cells were collected, pelleted by centrifugation and stored at −20 °C. For the activity library, plasmid DNA was prepared using a Zymoprep Yeast Plasmid Miniprep I kit (Zymo). For the abundance library, genomic DNA was prepared using a DNeasy kit, according to the manufacturer’s instructions (Qiagen), with the addition of a 30 min incubation at 37 °C with RNase in the re-suspension step.
For the activity library: for each bin, the purified DNA was split over two 25 uL PCR reactions containing Kapa Robust master mix, and CJA120/CJA124 primers to tag the barcodes with a unique molecular index (UMI). UMI-tagging PCR was performed using the following conditions: initial denaturation 95˚C 3 minutes, followed by two cycles of (95 ˚C 20 seconds, 60 ˚C 15 seconds, 72 ˚C 30 seconds), then purified using 1X AMPure XP beads (Beckman Coulter). Purified UMI-tagged amplicons were then amplified with various forward and reverse indexing primers to index each sample and add the p5 and p7 Illumina cluster-generating sequences. This PCR was performed with Kapa Robust and SYBR green on a Bio-Rad MiniOpticon qPCR machine with the following PCR conditions: 95°C for 3 minutes, up to 30 cycles of (95°C for 20 seconds, 65°C for 15 seconds, 72°C for 30 seconds), reactions were monitored and removed before saturation of the SYBR green signal, at around 20 cycles. The amplicons were pooled and gel purified. For the abundance library: for each bin, the purified DNA was split over eight 50 μL PCR reactions containing Q5 High-Fidelity Master Mix and KAM499/VKORampR 1.1 primers. The reaction conditions were 98 °C for 30 seconds, five cycles of (98°C for 10 seconds, 65°C for 20 seconds, 72°C for 1 minute), 72°C for 2 minutes. The eight PCR reactions were pooled and purified using 1x Ampure XP (Beckman Coulter). Next, to add indices and Illumina cluster-generating sequences, the cleaned product was mixed with Q5 High-Fidelity Master Mix; VKOR_indexF_1.1 and one of the indexed reverse primers, PTEN_seq_R1a through PTEN_seq_R2a. These reactions were run with SYBR Green on a Bio-Rad MiniOpticon; reactions conditions were 3 minutes at 95°C, 20 cycles of (95°C for 15 seconds, 60°C for 15 seconds, 72°C for 30 seconds), and 72°C for 3 min. The amplicons were pooled and gel purified.


title: CL656-1


title: Cured post EG7.OVA tumor challenge blood - Mouse 4 RUB157_5_4_Cured_postblood


title: PBS-2_1dose


title: Cured post EG7.OVA tumor challenge blood - Mouse 5 RUB157_5_5_Cured_postblood


title: NAC_2_1

city: Guangzhou

first: Zhen

last: Cheng

state: China

address: 58 Zhongshan Er Road, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-Sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Supplementary_files_format_and_content: core_table_gene.xls

source_name: KHM-5M thyroid cancer cell

growth_protocol: KHM-5M cells were cultured in RPMI-1640 (Gibco) with 10% fetal bovine serum (FBS, Gibco).

extract_protocol:
Total RNA was extracted using Trizol reagent.
Total RNA was purified by Oligo(dT)-attached magnetic beads. Purified RNA was fragmented into small pieces, and the first-strand cDNA was generated using random priming, followed with second-strand cDNA synthesis. After end repairing, the cDNA was amplified by PCR and the products were validated on the Agilent Technologies. The final library was generated after heated denature and circularization of the PCR products. Then the single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Thyroid cancer cells(KHM-5M) were treated with sodium selenite or PBS (negative control). Cells were harvested and Total RNA was extracted.

tag: cell line

tag: tumor

value: anaplastic thyroid cancer

tag: treatment group

value: treated with NAC and sodium selenite


title: seedlings_0h_exp4

description:
EXP4_0h
Initial gene expression.

value: Seedling

value: 10 days

tag: treatment


title: Cured post EG7.OVA tumor challenge blood - Mouse 3 RUB157_5_3_Cured_postblood


title: NAC_1_1


title: Cured post EG7.OVA tumor challenge blood - Mouse 1 RUB157_5_2_Cured_postblood


title: Cured pre EG7.OVA tumor challenge blood - Mouse 7 RUB157_5_7_Cured_preblood

value: mRBC-OVA-4-1BBL-IL12 with prior OT-1 T cell transfer cured mouse, 1 day before EG7.OVA rechallenge


title: exoCL656-2_1dose


title: Cured post EG7.OVA tumor challenge blood - Mouse 1 RUB157_5_1_Cured_postblood

value: B6.SJL-Ptprc<a> Pepc<b>/BoyJ


title: Cured pre EG7.OVA tumor challenge blood - Mouse 6 RUB157_5_6_Cured_preblood


title: SS5_1_1

value: Treated with sodium selenite


title: Cured pre EG7.OVA tumor challenge blood - Mouse 5 RUB157_5_5_Cured_preblood


title: exoCL656-1_1dose


title: SS0_1_1

value: control group


title: Cured pre EG7.OVA tumor challenge blood - Mouse 4 RUB157_5_4_Cured_preblood


title: CL656-2


title: Cured pre EG7.OVA tumor challenge blood - Mouse 2 RUB157_5_2_Cured_preblood


title: Exo-2_1dose

value: Exosomes


title: Cured pre EG7.OVA tumor challenge blood - Mouse 3 RUB157_5_3_Cured_preblood


title: Cured pre EG7.OVA tumor challenge blood - Mouse 1 RUB157_5_1_Cured_preblood


title: SS5_2_1


title: Exo-1_1dose


title: Naive post EG7.OVA tumor challenge blood - Mouse 5 RUB157_1_5_Naive_postblood

value: treatment naïve mouse, with OT-1 T cell transfer, 7 days post EG7.OVA rechallenge


title: KN99 - fra10ac1 day 3, replicate 1

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry

institute: UCSF

data_processing:
remove adapter with cutadapt 2.4 with Python 3.5.2   cutadapt -a AGATCGGAAGA -A AGATCGGAAGA --trim-n -m 25 -q 10
concatenate files for first direction and second direction from multiple lanes run on same day.
Run STAR_2.5.3 genome generate: STAR --runThreadN 15 --runMode genomeGenerate --genomeDir /data/jade/Data/RNA-seq_Data/STAR/STARindex --genomeFastaFiles /data/jade/H99/150908_H99chr.fasta --sjdbGTFfile /home/jordan/GENOMES/CNA3_all_transcripts.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 99
Align read to genome with 2-pass STAR: STAR first pass with --alignIntronMin 20 --alignIntronMax 2000 --outSJfilterReads Unique, run STAR second pass with --alignIntronMin 20 --alignIntronMax 2000 --outSJfilterReads Unique  --outSAMstrandField intronMotif --outFilterMultimapNmax 1 -sjdbFileChrStartEnd [all .tab files from first pass]
count transcripts with DEseq2: htseq-count -f bam -s reverse -t gene -i ID
Identify splice isoforms with JUM_2.0.2: Step A: --JuncThreshold 5 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 5 --Readlength 100 --Thread 20 Step B: --Test pvalue --Cutoff 1 --TotalFileNum 4 Step C: --Test pvalue --Cutoff 1 --TotalCondition1FileNum 2 --TotalCondition2FileNum 2 --REF CN_refGene_correct.txt
Supplementary_files_format_and_content: txt files from JUM contain information as described https://github.com/qqwang-berkeley/JUM/wiki/2.2-Output-files-(v2.0-and-up)

organism: Cryptococcus neoformans

source_name: KN99 cells

growth_protocol: Two-liter liquid cultures of all strains were grown in YPAD medium (Difco) by inoculation at low density (0.002-0.004 OD 600 nm) followed by overnight growth with shaking 30C. For RNA-seq experiments, cells were harvested at OD600 of ~ 1

extract_protocol:
Cells were lyophilized and then treated with Trizol and agitated with silica beads in an Omni bead mill homogenizer. RNA was extracted from whole cell extract by phase separation with 1 volume chloroform to produce a phenol:chloroform ratio of 1:1, and then washed with 1 volume chloroform. RNA was precipitated in 50% isopropanol, then recovered by centrifugation for 30 min at 18400xg at 4 C and washed with 70% ethanol. RNA from whole cell extract was polyA selected with Streptavidin MagneSphere® Paramagnetic Particles (Promega) and DNase treated with RNA Clean & Concentrator Kit 5 (Zymo).
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina and mixed before being run over multiple lanes

tag: genotype


title: CL656-20ug-2


title: Naive post EG7.OVA tumor challenge blood - Mouse 2 RUB157_1_2_Naive_postblood


title: Naive post EG7.OVA tumor challenge blood - Mouse 3 RUB157_1_3_Naive_postblood


title: Naive post EG7.OVA tumor challenge blood - Mouse 4 RUB157_1_4_Naive_postblood


title: KN99 - fra10ac1 day 3, replicate 2


title: KN99 - rrp6 day 3, replicate 1


title: Naive post EG7.OVA tumor challenge blood - Mouse 1 RUB157_1_1_Naive_postblood


title: Naive pre EG7.OVA tumor challenge blood - Mouse 5 RUB157_1_5_Naive_preblood

value: treatment naïve mouse, with OT-1 T cell transfer, 1 day before EG7.OVA rechallenge


title: SS0_2_1


title: Naive pre EG7.OVA tumor challenge blood - Mouse 4 RUB157_1_4_Naive_preblood


title: CL656-100ug-2


title: KN99 - ctnnbl1 day 3, replicate 2


title: Naive pre EG7.OVA tumor challenge blood - Mouse 3 RUB157_1_3_Naive_preblood


title: Naive pre EG7.OVA tumor challenge blood - Mouse 2 RUB157_1_2_Naive_preblood


title: CL656-100ug-1


title: Naive pre EG7.OVA tumor challenge blood - Mouse 1 RUB157_1_1_Naive_preblood


title: KN99 - ctnnbl1 day 3, replicate 1


title: PBS-1_1dose


title: 16_HC_Night_Rep B

first: Jacob

last: Valenzuela

address: 401 Terry Ave. N

institute: Institute for Systems Biology

data_processing:
Read files were cleaned with Trimmomatic
pseudoalignment to a T. pseudonana reference genome with Kallisto v.46.2
read quantification using Kallisto v.46.2
Differential gene expression analysis was performed using DESeq2 package v1.28.1
Supplementary_files_format_and_content: tab-delimited text files include normalized counts  for each Sample ...

organism: Thalassiosira pseudonana

source_name: Thalassiosira pseudonana

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA Kit
RNA libraries were prepared using the Illumina Truseq Stranded mRNA HT Library Prep Kit

value: CCMP 1335

tag: carbon

value: HC (High Carbon pH 7.6)

tag: diel

value: Dark

tag: replicate

value: Rep B

tag: timepoint

value: Timepoint 4


title: KN99 - cxorf56 day 3, replicate 2


title: CL656-20ug-1

value: B16F10 tumors


title: 14_HC_Night_Rep B

value: Timepoint 2


title: KN99 - cxorf56 day 3, replicate 1


title: 13_HC_Day_Rep B

value: Light

value: Timepoint 1


title: 12_HC_Night_Rep A

value: Rep A


title: KN99 - rrp6 day 3, replicate 2


title: KN99 - WT day 3, replicate 1

value: CM025 - WT


title: KN99 - nosip day 2, replicate 2


title: KN99 - WT day 3, replicate 2


title: 11_HC_Day_Rep A

value: Timepoint 3


title: 15_HC_Day_Rep B


title: 10_HC_Night_Rep A


title: KN99 - nosip day 2, replicate 1


title: 09_HC_Day_Rep A


title: KN99 - znf830 day 2, replicate 1


title: carotid plaque, asymptomatic, biological rep4

hyb_protocol: Samples were hybridized to microarrays (Affymetrix GeneChip miRNA 4.0 arrays, ThermoFisher Scientific) in a hybridization cocktail (132 μl, 48°C x 18 hours) to interrogate all mature miRNA sequences in miRBase Release 20. The arrays were then washed and stained with streptavidin-phycoerythrin in the Fluidics Station 450.

data_processing: RMA + DABG- algorithm to obtain human-only outputs. Expression Console software (version 1.2.0.20; Affymetrix).

label_protocol: Affymetrix FlashTag™ Biotin HSR RNA Labeling Kit (ThermoFisher Scientific) following the manufacturer’s specifications. Briefly, total RNA (500 ng) was subjected to a tailing reaction (Poly A polymerase in ATP master mix, 37°C x15 minutes) followed by ligation to a Biotin labelled DNA dendrimer (25°C x 30 min) stopped by addition of HSR Stop Solution.

extract_protocol: Carotid plaques were collected from patients undergoing carotid endarterectomy, dissected into pre-bifurcation, bifurcation and post-bifurcation segments, and immediately flash frozen, and transferred to RNALater-ICE (-20°C x 16 h) (ThermoFisher Scientific, Waltham, MA) prior to storage at -80°C. Individual samples were subsequently homogenized in TRIzol Reagent and the total RNA was isolated per the manufacturer’s protocol (ThermoFisher Scientific).

tag: phenotype

value: Asymptomatic

tag: description

value: Post-bifurcation internal carotid plaque from asymptomatic patient

tag: disease state

value: patient undergoing carotid endarterectomy (CEA)


title: carotid plaque, symptomatic, biological rep9

value: Symptomatic

value: Post-bifurcation internal carotid plaque from symptomatic patient


title: carotid plaque, asymptomatic, biological rep7


title: carotid plaque, asymptomatic, biological rep5


title: carotid plaque, asymptomatic, biological rep8


title: carotid plaque, asymptomatic, biological rep6


title: carotid plaque, asymptomatic, biological rep1


title: carotid plaque, asymptomatic, biological rep3


title: carotid plaque, asymptomatic, biological rep9


title: carotid plaque, symptomatic, biological rep7


title: KN99 - ik day 2, replicate 2


title: carotid plaque, symptomatic, biological rep6


title: carotid plaque, asymptomatic, biological rep2


title: carotid plaque, symptomatic, biological rep8


title: KN99 - ik day 2, replicate 1


title: carotid plaque, symptomatic, biological rep5


title: 06_LC_Night_Rep B

value: CCMP 1335

value: LC (Low Carbon pH 7.9)


title: KN99 - fam32a day 2, replicate 2


title: carotid plaque, symptomatic, biological rep3


title: KN99 - fam32a day 2, replicate 1


title: KN99 - znf830 day 2, replicate 2


title: 04_LC_Night_Rep A

value: Dark


title: carotid plaque, symptomatic, biological rep2


title: 08_LC_Night_Rep B

value: Rep B


title: 07_LC_Day_Rep B


title: KN99 - fam50a day 2, replicate 2


title: 03_LC_Day_Rep A


title: KN99 - fam50a day 2, replicate 1


title: 01_LC_Day_Rep A


title: KN99 - WT day 2, replicate 2


title: KN99 - WT day 2, replicate 1


title: KN99 - sap18 day 1, replicate 2


title: ALS_F2_C

city: ULM

first: Alberto

last: Catanese

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp
Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM gene count

source_name: hiPSC-derived motor neurons

growth_protocol: Motor neurons were chemically differentiated from hiPSC as described in Catanese et al., 2019 (doi: 10.1080/15548627.2019.1589257)

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit from Qiagen (Cat No./ID: 74104), following the protocol provided with the kit.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Day in Vitro 35

value: ALS patient (FUS mutation, II)

value: replicate 3


title: ALS_F2_B

value: replicate 2


title: 05_LC_Day_Rep B

value: Light

value: Timepoint 1


title: ALS_F2_A

value: replicate 1


title: ALS_F1_C

value: ALS patient (FUS mutation, I)


title: KN99 - gpatch1 day 1, replicate 2


title: KN99 - sap18 day 1, replicate 1


title: ALS_F1_B


title: KN99 - gpatch1 day 1, replicate 1


title: 02_LC_Night_Rep A

value: Rep A

value: Timepoint 2


title: KN99 - dhx35 day 1, replicate 2


title: Treated HV RAJI, biological rep2

city: México City

first: Daniel

middle: Ortega

last: Bernal

state: México City

address: Calzada del Hueso 1100

department: Atención a la Salud

country: Mexico

institute: Universidad Autónoma Metropolitana, Unidad Xochimilco

description: Gene expression data from RAJI cells treated with hydralazine and valproate, biological replicate 2

hyb_protocol: cDNA was hybridized to HuGene-2_0-st] affymetrix microarrays according protocol.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 30007G. GeneChip Operating Software (GCOS, Affymetrix) was used to data collect.

data_processing: Raw data probes were normalized using Signal Space Transformation-Robust Multichip Analysis for background correction and to obtain the quantile algorithm. To define the different conditions' differential expression profiles, two-way ANOVA was performed in the Affymetrix Transcriptome Analysis Console software (version 4.0).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured at 37˚C in a humidified atmosphere containing 5% CO2 in complete medium, comprising RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution.

extract_protocol: Total RNA was isolated using TRIzol extraction performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with hydralazine and valproate; the medium containing drugs was replaced daily.

tag: tissue

value: Burkitt lymphoma

value: RAJI

value: hydralazine and valproate


title: ALS_F1_A

tag: age


title: Treated HV RAJI, biological rep3

description: Gene expression data from RAJI cells treated with hydralazine and valproate, biological replicate 3


title: Control RAJI, biological rep2

description: Gene expression data from RAJI cells no treatment, biological replicate 2

source_name: RAJI cells no treatment

value: control


title: carotid plaque, symptomatic, biological rep1

value: Symptomatic

value: Post-bifurcation internal carotid plaque from symptomatic patient

value: patient undergoing carotid endarterectomy (CEA)


title: Treated HV HUT, biological rep3

description: Gene expression data from HuT78 cells treated with hydralazine and valproate, biological replicate 3

value: cutaneous T-Cell lymphoma


title: KN99 - dhx35 day 1, replicate 1


title: Control RAJI, biological rep3

description: Gene expression data from RAJI cells no treatment, biological replicate 3


title: Treated HV RAJI, biological rep1

description: Gene expression data from RAJI cells treated with hydralazine and valproate, biological replicate 1


title: ALS_C2_A

value: Day in Vitro 35

value: ALS patient (C9orf72 mutation, II)


title: ALS_C2_B

value: replicate 2


title: CYP2C9_activity_PacBio_SMRT_cell_2

description: Library and barcode cassette sequencing from plasmid DNA.


title: KN99 - rbm17 day 1, replicate 1


title: KN99 - rbm17 day 1, replicate 2


title: Treated HV HUT, biological rep1

description: Gene expression data from HuT78 cells treated with hydralazine and valproate, biological replicate 1


title: Control RAJI, biological rep1

description: Gene expression data from RAJI cells no treatment, biological replicate 1


title: Treated HV HUT, biological rep2

description: Gene expression data from HuT78 cells treated with hydralazine and valproate, biological replicate 2


title: Control HUT, biological rep2

description: Gene expression data from HuT78 cells no treatment, biological replicate 2

source_name: HuT78 cells no treatment


title: KN99 - ccdc12 day 1, replicate 2


title: Control HUT, biological rep3

description: Gene expression data from HuT78 cells no treatment, biological replicate 3


title: ALS_C1_C

value: ALS patient (C9orf72 mutation, I)

value: replicate 3


title: CYP2C9_activity_PacBio_SMRT_cell_1


title: NC_3: SKM-1_U2AF1-WT_rep3

city: Shanghai

first: Yuqian

last: Zhu

address: 600 Yi Shan Road

department: Department of Hematology

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Bone marrow

extract_protocol:
Cells were administered the vehicle control and S34F mutants in triplicate for 96 h, and total RNA was extracted with TRIzol reagent following the vendor's process.
RNA sequencing was performed using standard Illumina protocols

value: wild type


title: ALS_C1_B


title: KN99 - ccdc12 day 1, replicate 1


title: KN99 - rbm5 day 1, replicate 2


title: NC_1: SKM-1_U2AF1-WT_rep1


title: Control HUT, biological rep1

description: Gene expression data from HuT78 cells no treatment, biological replicate 1


title: WT_2_C

value: Isogenic Control (corrected ALS patient C9orf72 I)


title: MT_3: SKM-1_U2AF1-S34F_rep3

value: S34F mutant U2AF1


title: NC_2: SKM-1_U2AF1-WT_rep2


title: ALS_C1_A

value: replicate 1


title: ALS_C2_C


title: KN99 - rbm5 day 1, replicate 1


title: MT_2: SKM-1_U2AF1-S34F_rep2


title: KN99 - WT day 1, replicate 1

value: CM025 - WT


title: WT_2_A


title: WT_1_C

value: Healthy Control


title: MT_1: SKM-1_U2AF1-S34F_rep1


title: CYP2C9_activity_Exp5

organism: Saccharomyces cerevisiae

source_name: Laboratory yeast strain


title: carotid plaque, symptomatic, biological rep4


title: CYP2C9_abundance_PacBio_SMRT_cell_2


title: WT_1_B


title: CYP2C9_activity_Exp4


title: CYP2C9_abundance_Exp3

description: Targeted barcode amplification from genomic DNA.

source_name: Human-derived cultured cell line

value: HEK 293T TetBxb1BFP


title: WT_2_B


title: CYP2C9_abundance_PacBio_SMRT_cell_1


title: CYP2C9_activity_Exp2


title: CYP2C9_abundance_Exp2


title: CYP2C9_activity_Exp1


title: WT_1_A


title: KN99 - WT day 1, replicate 2


title: Flp-1215-3

status: Public on Mar 12 2021

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.  Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and converted into read1 and read2 fastq files from each sample.
RNA-seq reads were aligned to a combined human + mouse transcriptome reference (Ensembl Mus_musculus GRCm38 and Homo_sapiens. GRCh38 transcriptomes v94) using the stranded library option of Kallisto v0.46.0 (Bray et al., 2016) using a concatenated mouse-human index. Based on comparisons with pure mouse and human RNA samples, the Kallisto pseudo-alignment algorithm was able to accurately distinguish and assign transcripts to the proper species reference.
From each Kallisto-processed mouse-human RNAseq sample, an expression matrix was constructed to generate human-specific TPMs (transcripts per million) as follows. Human transcript counts and TPM values were extracted and adjusted based on (1) per million human reads per mouse-human sample; (2) transcript-level TPM values were summed per gene; (3) gene TPM values were converted to log2(TPM+1) values, (4) 19,701 genes were selected with log2(TPM+1) ≥ 1 in at least one of the thirty samples, and (5) the resulting gene-level values were per-sample quantile-polished to reduce sample-sample variability (Zyprych-Walczak et al., 2015).  Genes for subsequent analyses were selected from 17,004 gene IDs with log2(TPM+1) ≥ 2 in at least one of the thirty samples. Below we refer to log2(TPM+1) values as “logTPM” values.
DEG analyses used “moderated” t-tests as implemented in limma v3.42.2 (Law et al., 2014) with the limma-trend procedure (fit = eBayes(fit, trend = TRUE)) that uses an Empirical Bayes Model to effect “shrinkage of the estimated sample variances towards a pooled estimate” (Smyth 2004) which can increase power in the face of culture-culture variability. The use of this approach on logTPM data is conservative, which we consider appropriate with a small cohort. R scripts for DEG analyses are included as supplementary material.
Genome_build: Ensembl Mus_musculus GRCm38 and Homo_sapiens. GRCh38 transcriptomes v94.
Supplementary_files_format_and_content: Kallisto output file

organism:
Homo sapiens
Mus musculus

source_name: iN (induced neuron) derived from engineered iPSC

growth_protocol: Neurons were generated from feeder-dependent iPS cells: (Day -1) iPS cells were plated and infected on Matrigel coated 24-well plate. Per 6-well of iPS cells grown on feeders, cells were washed 1x with PBS. 0.5 ml of CTK (0.25% Trypsin no phenol red, 0.1 mg/ml collagenase IV, 0.5 ml 1 mM CaCl2, 20% KnockOut Serum Replacement in sterile water) was added to remove the feeders at 37°C until feeder cells lift off. CTK was removed and washed 2x with PBS. iPS cells were treated with 0.5 ml Accutase briefly, resuspended in 1 ml hES media and spun down at 150 g x 5 min. Cell pellets were resuspended in 50% hES media/50% mTeSR plus Y-27632, and lentiviruses. Typically 200,000 - 300,000 cells were plated per well of a 24-well plate with 1 uL of viruses (rtTA and Ngn2-puro) in 1 ml of mixed media. (Day 0) Half of the virus-containing media was removed and fresh Neural induction medium (NIM; DMEM F12 medium supplemented with 1% N2, 1% non-essential amino acids, 10 μg/l human BDNF, 10 μg/l human NT-3, and 0.2 mg/l mouse laminin) was added supplemented with Doxycycline (2 mg/l) and Y-27632 to induce Ngn2-puro expression. (Day 1-2) 24 hours later, Puromycin (1 mg/l) was added to NIM for 24-48 hours and media was changed daily. (Day 3) neurons were washed 1-2x with PBS. Freshly isolated or previously cryopreserved mouse glial cells (~75,000 cells per well of a 24-well plate) were added in Neural differentiation medium plus Dox (NDM; Neurobasal A medium supplemented with 2% B27, 1% glutamax, 2 μM AraC, 10 μg/l human BDNF, 10 μg/l human NT-3, and 0.2 mg/l mouse laminin). (Day 5) Half of the media was changed using NDM plus Dox. Media change occurred every 2-3 days until Day 10. (Day 10) Half of media was replaced with Maturation medium (MM; MEM supplemented with 0.5% glucose, 0.02% NaHCO3, 0.1 mg/ml transferrin, 5% FBS, 0.5 mM L-glutamine, 2% B27, and 2 μM AraC). Dox was withdrawn from this time point forward. (Day 13) Additional MM (0.5 mL per well of a 24-well plate) was added and neurons were incubated for 7 days without media change. (Day 20) Half of media was replaced with fresh MM. Media change occurred weekly until RNA extraction.

extract_protocol:
Total RNA was prepared from the entire plate and thus contained both mouse and human total RNA
RNA-seq libraries were prepared from total RNA using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Neurons from engineered iPS cells were treated with the same protocol except additional treatment of lentivirus expressing Ubiquitin-Flp-GFP and Ubiquitin-Cre-GFP at Day -1.

value: WT

tag: sample group

value: engineered

tag: culture batch pair-group

tag: nrxn1 transcript mutation effect


title: Cre-1215-2

description: alpha/beta

value: HET

value: alpha/beta


title: Cre-1215-3

description: alpha/beta


title: C8905a-2

source_name: iN (induced neuron) derived from iPSC

value: clinical sample iPSC derived


title: C8905a-1


title: Flp-1215-1


title: C8905a-3


title: C2463c-3


title: C2463c-1


title: Flp-1215-2


title: C3141a-3


title: C3141a-2


title: C3141a-1


title: C2463c-2


title: CYP2C9_abundance_Exp6

tag: cell line


title: N1884a-3

description: alpha

value: alpha


title: N1884a-1

description: alpha


title: N9540c-2

description: alpha/beta


title: N3320a-3

description: alpha


title: N3320a-2

description: alpha


title: N9540c-1

description: alpha/beta


title: Cre-1215-1

description: alpha/beta


title: N9540c-3

description: alpha/beta


title: prp2-1_MG_28

city: Ithaca

first: Jeffrey

last: Pleiss

address: 453 Biotech

institute: Cornell University

description:
prp2-1_combined_total_counts_raw.txt
prp2-1_combined_concordant_unspliced_counts_raw.txt
prp2-1_combined_branch_to3ss_counts_raw.txt
prp2-1_combined_lariat_int_counts_raw.txt
prp2-1_combined_pre1st_step_adjusted.txt
prp2-1_combined_lariat_int_adjusted.txt
prp2-1_combined_concordant_unspliced_counts_norm.txt
prp2-1_combined_pre1st_step_counts_norm.txt
prp2-1_combined_lariat_int_counts_norm.txt
prp2-1_combined_SI.txt

data_processing:
Trimming was performed via Fastp version 0.20.0 with parameters: --disable_trim_poly_g --adapter_sequence CTGTCTCTTATACACATCT --adapter_sequence_r2 CTGTCTCTTATACACATCT
Alignment was performed via STAR (version 2.7.2b) with the following parameters --clip5pNbases 7 0 --peOverlapNbasesMin 5 --peOverlapMMp 0.1 --outFilterMultimapNmax 1 --alignIntronMin 10 --alignIntronMax 1100 --outSAMattributes All --runThreadN 8 --outSAMunmapped Within KeepPairs --alignSJoverhangMin 3 --alignSplicedMateMapLmin 3 --alignMatesGapMax 3000 --alignEndsType EndToEnd6
Target intron isoform counting was performed using custom scripts.
Genome_build: SGD S. cerevisiae reference genome assembly R64-1-124
Supplementary_files_format_and_content: tab deliminated files of feature counts for introns  (rows) by sample (columns)
Supplementary_files_format_and_content: *SI.txt files: tab deliminated splice index values (unspliced reads/spliced reads). Samples are columns and introns are rows

source_name: Filter collected cells from culture medium

growth_protocol: Yeast strains were grown in standard synthetic medium (CSM)

extract_protocol:
Total RNA was extracted using standard hot phenol chloroform extraction. A fixed quantity of total RNA plus a fixed quantity of in vitro transcribed 4-thiouracil labeled s. pombe derived spike-in RNAs were combined for each sample. 4-thiouracil labeled RNA was purified via biotinylation and pull-down with streptavidin beads.
Libraries were constructed via multiplexed primer extension sequencing (MPE-seq)

treatment_protocol: Actively growing cells were treated with 4-thiouracil. Samples were collected in regular intervals in a time course. Sample collection involved filter collection followed by rapid freezing in dry ice.

tag: labeling time (sec)

tag: strain

tag: rna population

value: Nascent RNA


title: prp2-1_MG_27


title: prp2-1_MG_29


title: prp2-1_MG_26


title: prp2-1_MG_22


title: prp2-1_MG_25


title: prp2-1_MG_23


title: prp2-1_MG_24


title: prp2-1_MG_21


title: N3320a-1

description: alpha


title: prp2-1_MG_20


title: prp2-1_MG_18


title: prp2-1_MG_17


title: N1884a-2

description: alpha


title: prp2-1_MG_19


title: prp2-1_MG_16


title: prp2-1_MG_13


title: prp2-1_MG_10


title: prp2-1_MG_9


title: prp2-1_MG_14


title: prp2-1_MG_15


title: prp2-1_MG_8


title: prp2-1_MG_7


title: prp2-1_MG_6


title: prp2-1_MG_3


title: prp2-1_MG_1


title: prp2-1_MG_4


title: prp2-1_MG_2


title: WT_MG_30

description:
WT_combined_total_counts_raw.txt
WT_combined_concordant_unspliced_counts_raw.txt
WT_combined_branch_to3ss_counts_raw.txt
WT_combined_lariat_int_counts_raw.txt
WT_combined_pre1st_step_adjusted.txt
WT_combined_lariat_int_adjusted.txt
WT_combined_concordant_unspliced_counts_norm.txt
WT_combined_pre1st_step_counts_norm.txt
WT_combined_lariat_int_counts_norm.txt
WT_combined_SI.txt


title: WT_MG_28


title: WT_MG_27


title: WT_MG_22


title: WT_MG_21


title: prp2-1_MG_11


title: WT_MG_25


title: WT_MG_26


title: WT_MG_23


title: WT_MG_20


title: WT_MG_24


title: WT_MG_11


title: prp2-1_MG_5


title: WT_MG_16


title: WT_MG_10


title: WT_MG_17


title: WT_MG_12


title: WT_MG_19


title: WT_MG_15


title: WT_MG_8


title: WT_MG_14


title: WT_MG_29


title: WT_MG_7


title: WT_MG_4


title: WT_MG_5


title: prp2-1_MG_12


title: WT_MG_6


title: WT_MG_3


title: WT_MG_2


title: U87 h3k9me3 sg646-2

first: David

last: Wu

state: California

address: 35 Medical Center Way

description: WT U87 cells with control sgLOC646329 replicate 2

data_processing:
Quality assessment using fastqc, adapter and quality trimming using cutadapt
Alignment to reference genome (hisat2) and quantification (featureCounts)
Genome_build: hg19
Supplementary_files_format_and_content: featureCounts quantitation at gene promoters

growth_protocol: DMEM 10% FBS 1% Antibiotics

extract_protocol:
Lysates were extracted from sonicated nuclei and histone-DNA complexes were isolated with  antibody.
ChIP-Seq libraries were prepared using the Illumina DNA Prep Kit

treatment_protocol: sgRNA lentiviral transduction

tag: cell line background

tag: genotype/variation


title: WT_MG_18


title: U87 h3k9me3 sg646-1

description: WT U87 cells with control sgLOC646329 replicate 1


title: 1789018_A17_4_LRF_CHIP

city: Memphis

first: Yong

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

description: ABEmax, TCACCGGGAGGAAAGAGAAA, edited Hudep2

data_processing:
FASTQ files were mapped to hg19 by using BWA mem (v0.7.16a).
Bigwiggle files were generated using DeepTools (v3.2.0)
ChIP-seq peaks were called by using MACS2 (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

growth_protocol: Approximately 2.5 × 1E+7 cells were used for each immunoprecipitation. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with rotation, and the reaction was quenched with glycine at a final concentration of 125 mM. Cross-linked cells were then lysed and resuspended in 2 mL of RIPA buffer and sonicated for 12 cycles with a Branson 250 sonifier (10 s on/90 s off for a total of 2 min of pulses with 20% output from the micro-tip) to obtain fragments of chromatin approximately 200–300 bp in size. Supernatants were precleared by incubation with 200 µL of protein A/G agarose bead slurry (Thermo Fisher Scientific, cat. #15918014) overnight at 4°C with rotation. Meanwhile, 12.5 µg of IP antibody was incubated with 50 µL of protein A/G agarose bead slurry in 1 mL of PBS overnight at 4°C with rotation. Saved precleared chromatin (20 µL) was used as the input sample. Precleared chromatin was incubated with the antibody–bead complex for 7 h at 4°C with rotation. Cross-linking of DNA was reversed by incubation with RNase A (1 µg/µL), proteinase K (0.2 mg/mL), and 0.25 M NaCl overnight at 65°C.

extract_protocol: Immunoprecipitated DNA was purified using the Qiagen PCR Extraction Kit and eluted with 20 µL of EB elution buffer. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, cat. #E7645) with homemade TruSeq adaptors. Libraries were sequenced using an Illumina HiSeq 4000 system. NA

tag: antibody


title: 1819031_A17_4_LRF_CHIP


title: 1819032_Input_HUDEP2

description: input

value: input