title: H1_0m_1


title: Leaf, CK123 12h

status: Public on Apr 19 2020

type: SRA

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

country: China

institute: Northeast Agricultural University

library_source: transcriptomic

data_processing:
BGI500 own software used for basecalling.
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). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: NCBI_GCF_000188115.3_SL2.50
Supplementary_files_format_and_content: EXCEL file includes FPKM values for each Sample

molecule: total RNA

organism: Solanum lycopersicum

source_name: Micro-TOM

growth_protocol: Micro-TOM and Micro-TOM-EX were sown into pots filled with soil and grown under controlled conditions (16h light，cold stress treated 0，4 or 12h) in a greenhouse at the Horticultural station of Northeast Agricultural University

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

tag: genotype

value: Micro-TOM

tag: stress

value: control

tag: time

tag: tissue

value: leaf


title: si-VEGF-C

type: RNA

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

description: Gene expression 48hr after VEGF-C being knockdowned in human gastric cancer cells

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in Agilent hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - Agilent  Technologies,Inc. Waldbronn, Germany). Following hybridization, washing was performed using the  Agilent Wash Buffer kit ( Agilent  Technologies,Inc. Waldbronn, Germany). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into Agilent software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the  Agilent software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

organism: Homo sapiens

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the Agilent Gene Expression Analysis protocol ( Agilent  Technologies,Inc. Waldbronn, Germany). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the epicentreTargetAmp 1-round aRNA amplification kit  was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol ( Agilent  Technologies,Inc. Waldbronn, Germany). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: MKN45/si-NC cells were cultrued with RPMI1640 medium and then transfected with si-NC for 48h as negative control.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: BGC823/si-VEGF-Ccells were cultrued with RPMI1640 medium and then transfected with si-VEGF-C for 48h for knockdowning VEGF-C.

tag: cell type

value: MKN-45 cells

tag: differentiation

value: poorly differentiated


title: si-NC

description: Gene expression 48hr after si-NC being transfected in human gastric cancer cells


title: Stellate-5d BDL-2

city: New Haven

first: Vikas

last: Gupta

address: 1 Gilbert Street

country: USA

institute: Yale School of Medicine

description: Stellate Cells

data_processing:
The QC was performed for each read file (fastq) using Fastqc. Gencode mouse genome version mm10 was used for alignment. STAR aligner version 2.5.2b was used to align, remove duplicates, and the read counts per gene for each dataset were calculated using FeatureCounts tool. DEseq2 was used to perform differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample.

organism: Mus musculus

source_name: Liver

extract_protocol:
The liver was sequentially perfused with liver perfusion media, pronase and collagenase. Liver was minced and further digested in vitro with pronase and collagenase. Cells  were subjected to gradient separation and sorted directly into RNA isolation buffer.
SMART-Seq2 used to prepare libraries

tag: strain

value: Mixed (C57BL/6, SWR/J)

tag: age

value: 8 Weeks

value: Gli1:CreER+/-; Ai9+/-


title: Gd6-Scrambled-2

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

data_processing:
The FASTQ files obtained were de-multiplexed using the bcl2fastq tool as a part the Illumina basepace workflow
RSEM was used to align the reads to the human genome assembly hg19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: primary human adipocytes culture_Gd6-Scrambled

extract_protocol:
Total RNA extraction was performed using TriPure Trizol reagent.  Trizol was added to the cells and incubated at room temperature for 5 minutes. Cells were collected into a GentleMACS M tube and dissociated using the GentleMACS Dissociator (Miltenyi Bio) Program RNA01.01. Tubes were centrifuged for 3 minutes at 800RPM and the mixture was transferred to a 2ml collection tube. Chloroform was added in a 1:5 ratio to the tripure/cell mix and tubes were inverted to mix, then incubated at room temperature for 3-5 minutes. Aqueous phase separation was performed, and the RNA-containing layer was mixed with an equal volume of 100% Isopropanol and incubated overnight at -20 degrees for precipitation. RNA was pelleted and washed with 80% ETOH and eluted in nuclease-free water.
cDNA library was prepared using  TruSeq® Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions. For each clone, 1 ug of total RNA was used as input to synthesize cDNA which was subsequently amplified. All samples were processed concurrently during library preparation. Illumina sequencing indexes were added to the fragmented libraries and indexed libraries were amplified.

value: primary human adipocytes

tag: genotype/variation

value: Gd6 Scramble

tag: replicate


title: Leaf, CK122 12h


title: input DNA

city: Wuhan

first: Yunping

last: Chen

state: Hubei

address: No. 299, Ba Yi Road, Wuchang

institute: Wuhan university

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the msu7 genome assembly using Bowtie.
MACS was used with a p-value cutoff of 10−5 577 for binding peaking.
The reads per million (RPM) around the peak summit (± 5 kb) was documented with a 100-nt window size to calculate the average enrichment level of the peak.
To predict binding motifs, the flanking sequences of all peak summits (± 50 bp) were filtered by RepeatMasker Web Server.
The masked sequences were subjected to Discriminative Regular Expression Motif Elicitation (DREME) to predict binding motifs.
Genome_build: msu7
Supplementary_files_format_and_content: processed files are bdg files include peak information

molecule: genomic DNA

organism: Oryza sativa Indica Group

source_name: Rice inflorescence cells

growth_protocol: 35Spro:GRF7-GFP transgenic plants were grown in Wuhan in the summer (May to October),

extract_protocol:
5 g < 0.5 cm (YP1) or < 2 cm (YP2) inflorescences were harvested and crosslinked with 1% (v/v) formaldehyde under vacuum for 30 min, then ground to powder in liquid nitrogen. The chromatin complexes were isolated, sonicated, and incubated with anti-GFP antibody (Abcam, ab290). The precipitated DNA was recovered and dissolved in 1×TE and stored at -80 °C for later in-depth analysis.
Illumina sequencing libraries were constructed with the above-prepared DNA samples by ThruPLEX DNA-seq Kit (CAT. NO. R400406) mainly according to the manufacturer’s instructions. Then, the library containing 270 bp to 330 bp fragments were purified and sequenced with Illumina Hiseq3000 system.

tag: developmental stage

value: < 2 cm

value: inflorescence

tag: beads

value: protein A+G

tag: chip antibody


title: Gd6-Scrambled-1


title: YP2_ChIPSeq

value: Anti-GFP antibody (Abcam, ab290)


title: H1_0m_2

city: London

middle: DM

last: Santos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Basecalls were performed using bcl2fastq v2.20
Sequence reads were trimmed for adapter and low quality bases using cutadapt-1.9.1
Reads were aligned to the human genome GRCh38 from Ensembl using STAR-2.5.2a
Gene-level quantifications were generated using RSEM-1.2.31 against human annotation release 86 from Ensembl
Genome_build: Ensembl GRCh38 release-86

source_name: embryonic stem cells

growth_protocol: H1 human embryonic stem cells (hESCs) were maintained on growth factor-reduced Matrigel in mTeSR1 media.

extract_protocol:
Cells were lysed and total RNA was extracted using a QIAGEN RNeasy Kit
Libraries were constructed using a KAPA mRNA HyperPrep Kit

treatment_protocol: H1 hESCs grown on growth factor-reduced matrigel had media changed to a growth factor cocktail designed to direct differentiation towards either endoderm (TeSR-E5 + BMP4 (10 ng/ml) + FGF2 (20 ng/ml) + Activin A (100 ng/ml) + LY29004 (10 uM)), mesoderm (TeSR-E5 + BMP4 (10 ng/ml) + VEGF (10 ng/ml) + FGF2 (10 ng/ml) + Activin A (10 ng/ml)), or trophectoderm (TeSR-E5 + BMP4 (50 ng/ml)) for 20, 40, or 60 minutes

value: embryonic stem cells

tag: treatment

value: untreated


title: Gd6-4

source_name: primary human adipocytes culture_Gd6

value: Gd6 LINC00473 overexpressing


title: YP1_ChIPSeq


title: GRF7OE-1

data_processing:
Illumina Alta-Cyclic software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to msu7 whole genome using bowtie.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cuffdiff software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: msu7
Supplementary_files_format_and_content: Base coverage, quanlity analysis and tab-delimited text files include RPKM values for each Sample.

source_name: Rice seedling

growth_protocol: GRF7OE transgenic plants and WT plants were grown in Wuhan in the summer (May to October),

extract_protocol:
Seedlings from the WT and GRF7OE-1 were collected to extract the total RNA. Total RNA (3 μg) was extracted with a TRIzol reagent (Invitrogen), then treated with DNaseⅠ (Fermentas) according to the user’s manual. Total RNA per sample was used as input material for the RNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rice seedling

value: tillering stage


title: Gli1-5d BDL-2

description: Gli1 PBMCs


title: Leaf, CK43 4h

value: Micro-TOM

value: control

value: leaf


title: Stellate-5d BDL-1

description: Stellate Cells

value: Mixed (C57BL/6, SWR/J)


title: Gd6-3


title: Leaf, CK42 4h


title: Gd6-2


title: Leaf, CK121 12h


title: Leaf, CK41 4h


title: Gli1-5d BDL-1

description: Gli1 PBMCs

value: 8 Weeks


title: EV-4

source_name: primary human adipocytes culture_EV

value: empty vector


title: Stellate-Uninjured-2

description: Stellate Cells

value: Gli1:CreER+/-; Ai9+/-


title: Stellate-Uninjured-1

description: Stellate Cells


title: Leaf, CK03 0h


title: WT


title: EV-3

value: primary human adipocytes


title: Gli1-Uninjured-2

description: Gli1 PBMCs


title: Leaf, CK01 0h


title: Gli1-Uninjured-1

description: Gli1 PBMCs


title: EV-1


title: AB43.22

status: Public on Apr 18 2020

city: Indianapolis

first: Andrea

last: Bonetto

state: IN

address: 980 W. Walnut Street, R3-C522

institute: Indiana University School of Medicine

description:
ILMN_443
Quadriceps mRNAseq_STAR_featurecounts

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control
Then all sequenced libraries were mapped to the mouse genome (mm10) using STAR RNA-seq aligner
The reads distribution across the genome was assessed using bamutils
Genes with read count per million (CPM) < 0.5 in more than 4 of the samples were removed.
Differential expression analysis was performed using edgeR
Genome_build: UCSC Mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

extract_protocol:
RNA extraction and purification from tissue snap frozen in liquid nitrogen was done via homogenization in Trizol and the Qiagen miRNeasy Mini Kit (skeletal muscle).
Five microliters of 2 nM pooled libraries per lane will then be denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading to HiSeq 4000 for 75b paired-end sequencing (Illumina, Inc.). Approximately 30M reads per library is generated

treatment_protocol: RNA isolation, sequencing for all quadriceps samples were done at one time.

value: Muscle

tag: Sex

value: Male

tag: tumor

value: Subcutaneous C26


title: AB43.23


title: LN2.14

value: splenic C26


title: AB43.8

value: Control


title: AB43.3


title: AB43.7


title: AB43.19


title: LN2.13


title: AB43.2


title: LN2.5

value: Sham


title: EV-2


title: LN2.11


title: Leaf, CK02 0h


title: LN2.2


title: AB43.18


title: LN2.15


title: LN2.1


title: BM_VSV2

city: Shanghai

first: zhu

last: Qingchen

address: 320 Yue Yang Rd, Xuhui District

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description: VSV 12h

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: bone marrow-derived macrophages

growth_protocol: bone marrow cells were isolated from femurs and tibias of adult WT mice and cultured for 5 days in a DMEM medium supplemented with M-CSF conditional medium

extract_protocol:
RNA was harvested using Trizol reagent followed by RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: non-treated (NT1 and NT2) or stimulated for 12 h with VSV(VSV1 and VSV2)

value: wild type

value: bone marrow


title: BM_VSV1

description: VSV 12h


title: BM_ NT2

description: NT


title: BM_ NT1

description: NT


title: 2105262: Non-smoker_1616

type: genomic

city: Hangzhou

first: Yi

last: Xu

state: Zhejiang

address: No. 17, Dazhi Road, old Zhejiang, Shangcheng District

department: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases

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

description: All samples were genotyped using the Infinium Human Exome-12 v1.1 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48 °C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

data_processing:
After genotyping, we performed the following quality control analyses on all genotyped SNPs. First, among 242 901 genotyped variants, we excluded all insertions and deletions to ensure that all base pair positions were unique and referred to the same variant. Second, any SNP with a call rate of <95% was excluded. Third, we removed those SNPs that were not in Hardy–Weinberg equilibrium at a p value of < 1.0 × 10−6. Finally, we used a 5% minor allele frequency (MAF) as a threshold to define rare and common variants, and any SNP with an MAF of <0.05 was excluded from the analysis.
Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

source_name: Blood

label_protocol: The concentration of each DNA sample was first measured using the QuantiT™ dsDNA assay kit (Life Technologies, Carlsbad, CA) and then 50 DNA samples were pooled in equimolar amounts, as suggested by the manufacturers.

extract_protocol: Genomic DNA was extracted from EDTA-treated peripheral venous blood of each subject using the Qiagen DNA purification kit. All DNA samples were treated with RNase A to remove potential contaminating RNA, and DNA quality and the concentration of each sample was determined by the A260/A280 absorbance ratio.

tag: ethnicity

value: European-American

tag: gender

value: Female

tag: cpd

tag: hsi

tag: ftnd

value: Non-smoker

value: blood


title: 2105265: Non-smoker_1618

scan_protocol: All samples were genotyped using the Infinium Human Exome-12 v1.1 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol.

tag: tissue


title: 2105261: Non-smoker_1615


title: 2105266: Non-smoker_1619


title: 2105259: Non-smoker_1613


title: 2105257: Smoker_1611

value: Smoker


title: 2105258: Non-smoker_1612


title: 2105256: Non-smoker_1610


title: Patient #9

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: pediatric bithalamic glioma tumor tissue

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.28.4) in R. The detection p-value for each sample was computed. All samples had detection p values less than 0.002. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: bithalamic glioma tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25).  Genomic DNA was extracted from these punches using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

value: male


title: Patient #7


title: 2105264: Smoker_1617


title: 2105250: Smoker_1608


title: 2105249: Smoker_1607


title: 2105245: Non-smoker_1603


title: 2105247: Non-smoker_1605


title: 2105244: Non-smoker_1602


title: 2105248: Non-smoker_1606


title: 2105243: Non-smoker_1601


title: Patient #3

value: female


title: Patient #5


title: 2105242: Smoker_1600


title: Patient #13


title: 2105238: Smoker_1597


title: 2105241: Non-smoker_1599


title: Patient #6


title: 2105235: Non-smoker_1594


title: 2105236: Non-smoker_1595


title: Patient #10


title: 2105234: Non-smoker_1593


title: 2105233: Non-smoker_1592


title: 2105237: Smoker_1596


title: 2105246: Non-smoker_1604


title: 2105239: Smoker_1598


title: Patient #4


title: 2105231: Non-smoker_1590


title: 2105232: Non-smoker_1591


title: 2105230: Non-smoker_1589


title: Patient #2


title: 2105229: Non-smoker_1588


title: 2105227: Non-smoker_1586


title: 2105228: Non-smoker_1587


title: 2105260: Non-smoker_1614


title: 2105218: Smoker_1577


title: 2105223: Smoker_1582


title: 2105221: Smoker_1580


title: 2105216: Non-smoker_1575


title: 2105220: Smoker_1579


title: 2105224: Smoker_1583


title: 2105225: Smoker_1584


title: 2105222: Smoker_1581


title: 2105226: Non-smoker_1585


title: 2105217: Non-smoker_1576


title: 2105210: Non-smoker_1571


title: 2105219: Smoker_1578


title: 2105215: Smoker_1574


title: 2105211: Non-smoker_1572


title: 2105202: Non-smoker_1565


title: 2105207: Non-smoker_1568


title: 2105208: Non-smoker_1569


title: 2105204: Smoker_1567


title: 2105209: Smoker_1570


title: 2105197: Non-smoker_1564


title: 2105203: Smoker_1566


title: 2105193: Smoker_1560


title: 2105212: Non-smoker_1573


title: 2105194: Smoker_1561


title: 2105196: Non-smoker_1563


title: Patient #1


title: 2105195: Smoker_1562


title: 2105165: Non-smoker_1554


title: 2105188: Non-smoker_1555


title: 2105192: Smoker_1559


title: 2105191: Smoker_1558


title: 2105189: Non-smoker_1556


title: 2105135: Non-smoker_1546


title: 2105190: Non-smoker_1557


title: 2105161: Smoker_1552


title: 2105138: Smoker_1548


title: 2105136: Smoker_1547


title: 2105128: Non-smoker_1543


title: 2105129: Smoker_1544


title: 2105147: Smoker_1550


title: 2105154: Smoker_1551


title: 2105164: Smoker_1553


title: 2105122: Smoker_1542


title: 2105146: Smoker_1549


title: 2105109: Smoker_1540


title: 2105131: Non-smoker_1545


title: 2105105: Smoker_1539


title: 2105114: Non-smoker_1541


title: 2105099: Non-smoker_1538


title: 2105255: Non-smoker_1609


title: 2105092: Non-smoker_1536


title: 2105091: Non-smoker_1535


title: 2105086: Non-smoker_1533


title: 2105088: Non-smoker_1534


title: 2105098: Smoker_1537


title: 2105083: Non-smoker_1532


title: 2104507: Smoker_1528


title: 2104471: Smoker_1526


title: 2104485: Smoker_1527


title: 2105073: Non-smoker_1530


title: 2104425: Smoker_1517


title: 2104433: Smoker_1519


title: 2104420: Smoker_1516


title: 2104454: Smoker_1524


title: 2104429: Non-smoker_1518


title: 2104456: Smoker_1525


title: 2104450: Non-smoker_1523


title: 2104444: Non-smoker_1521


title: 2104390: Smoker_1512


title: 2104418: Smoker_1515


title: 2104383: Smoker_1510


title: 2104515: Smoker_1529


title: 2104389: Non-smoker_1511


title: 2104436: Smoker_1520


title: 2104377: Non-smoker_1509


title: 2104415: Smoker_1514


title: 2104366: Smoker_1507


title: 2104350: Non-smoker_1506


title: 2104371: Smoker_1508


title: 2104302: Smoker_1503


title: 2104348: Smoker_1505


title: LN2.3


title: 2104331: Non-smoker_1504


title: 2105080: Non-smoker_1531


title: 2104445: Smoker_1522


title: 2104400: Smoker_1513


title: 2104299: Smoker_1502


title: 2104259: Smoker_1499


title: 2104254: Non-smoker_1497


title: 2104297: Smoker_1501


title: 2104234: Non-smoker_1495


title: 2104223: Non-smoker_1494


title: 2104258: Smoker_1498


title: 2104218: Non-smoker_1493


title: 2104235: Smoker_1496


title: 2104196: Non-smoker_1489


title: 2104190: Non-smoker_1488


title: 2104189: Smoker_1487


title: 2104180: Non-smoker_1486


title: 2104205: Non-smoker_1491


title: 2104087: Non-smoker_1478


title: 2104115: Smoker_1481


title: 2104171: Non-smoker_1484


title: 2104093: Non-smoker_1479


title: 2104102: Non-smoker_1480


title: 2104077: Smoker_1476


title: 2104082: Smoker_1477


title: 2104070: Non-smoker_1475


title: 2104034: Non-smoker_1472


title: 2104271: Smoker_1500


title: 2104042: Non-smoker_1473


title: 2104197: Non-smoker_1490


title: 2104014: Smoker_1471


title: 2104013: Smoker_1470


title: 2104007: Non-smoker_1469


title: 2103993: Smoker_1466


title: 2104172: Non-smoker_1485


title: 2104006: Smoker_1468


title: 2103963: Smoker_1464


title: 2103994: Smoker_1467


title: 2103973: Non-smoker_1465


title: 2103951: Smoker_1462


title: 2104126: Smoker_1482


title: 2103938: Smoker_1460


title: 2103939: Non-smoker_1461


title: 2104140: Non-smoker_1483


title: 2103934: Non-smoker_1458


title: 2103936: Non-smoker_1459


title: 2103923: Non-smoker_1455


title: 2103924: Non-smoker_1456


title: 2103922: Smoker_1454


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title: 2101621: Smoker_875


title: 2101610: Smoker_873


title: 2101606: Smoker_872


title: 2101605: Smoker_871


title: 2101598: Non-smoker_869


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title: 2101585: Smoker_866


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title: 2101601: Non-smoker_870


title: 2101578: Smoker_862


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title: 2101574: Smoker_861


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title: 2101583: Smoker_865


title: 2101579: Smoker_863


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title: 2101556: Smoker_858


title: 2101538: Smoker_855


title: 2101542: Non-smoker_856


title: 2101533: Non-smoker_853


title: 2101531: Non-smoker_852


title: 2101530: Non-smoker_851


title: 2101529: Non-smoker_850


title: 2101630: Non-smoker_878


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title: 2101524: Smoker_847


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title: 2101418: Smoker_817


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title: 1900262: Non-smoker_241


title: 1900248: Non-smoker_229


title: 1900247: Non-smoker_228


title: 1900246: Non-smoker_227


title: 1900250: Non-smoker_231


title: 1900245: Non-smoker_226


title: 1900243: Non-smoker_224


title: 1900241: Smoker_222


title: 1900239: Smoker_220


title: 1900236: Smoker_218


title: 1900238: Smoker_219


title: 1900242: Smoker_223


title: 1900233: Smoker_217


title: 1900232: Smoker_216


title: 1900231: Smoker_215


title: 1900230: Smoker_214


title: 1900229: Smoker_213


title: 1900227: Smoker_212


title: 1900224: Smoker_209


title: 1900225: Smoker_210


title: 1900226: Smoker_211


title: 1900221: Smoker_206


title: 1900218: Smoker_204


title: 1900216: Smoker_202


title: 1900212: Smoker_201


title: 1900222: Smoker_207


title: 1900211: Smoker_200


title: 1900217: Smoker_203


title: 1900207: Smoker_196


title: 1900223: Non-smoker_208


title: 1900219: Smoker_205


title: 1900204: Smoker_193


title: 1900240: Smoker_221


title: 1900244: Non-smoker_225


title: 1900201: Smoker_190


title: 1900209: Smoker_198


title: 1900200: Smoker_189


title: 1900249: Non-smoker_230


title: 1900205: Smoker_194


title: 1900206: Smoker_195


title: 1900199: Smoker_188


title: 1900210: Smoker_199


title: 1900190: Smoker_187


title: 1900185: Smoker_185


title: 1900176: Smoker_178


title: 1900180: Smoker_182


title: 1900208: Smoker_197


title: 1900167: Smoker_174


title: 1900166: Smoker_173


title: 1900177: Non-smoker_179


title: 1900173: Non-smoker_176


title: 1900175: Smoker_177


title: 1900178: Smoker_180


title: 1900162: Smoker_172


title: 1900182: Smoker_183


title: 1900179: Smoker_181


title: 1900203: Smoker_192


title: 1900168: Smoker_175


title: 1900202: Smoker_191


title: 1900158: Smoker_168


title: 1900160: Smoker_170


title: 1900161: Smoker_171


title: 1900155: Smoker_166


title: 1900154: Smoker_165


title: 1900153: Smoker_164


title: 1900183: Smoker_184


title: 1900186: Smoker_186


title: 1900152: Smoker_163


title: 1900151: Smoker_162


title: 1900149: Smoker_160


title: 1900146: Smoker_158


title: 1900145: Smoker_157


title: 1900157: Smoker_167


title: 1900139: Smoker_151


title: 1900142: Smoker_154


title: 1900144: Smoker_156


title: 1900137: Smoker_149


title: 1900138: Smoker_150


title: 1900141: Non-smoker_153


title: 1900132: Non-smoker_145


title: 1900134: Non-smoker_147


title: 1900133: Non-smoker_146


title: 1900135: Smoker_148


title: 1900143: Smoker_155


title: 1900126: Smoker_141


title: 1900124: Non-smoker_139


title: 1900129: Smoker_144


title: 1900127: Smoker_142


title: 1900125: Smoker_140


title: 1900150: Smoker_161


title: 1900122: Smoker_137


title: 1900121: Smoker_136


title: 1900120: Smoker_135


title: 1900147: Smoker_159


title: 1900119: Smoker_134


title: 1900113: Non-smoker_128


title: 1900116: Non-smoker_131


title: 1900110: Non-smoker_125


title: 1900102: Non-smoker_120


title: 1900117: Smoker_132


title: 1900118: Non-smoker_133


title: 1900115: Non-smoker_130


title: 1900114: Non-smoker_129


title: 1900111: Smoker_126


title: 1900112: Smoker_127


title: 1900086: Non-smoker_116


title: 1900108: Non-smoker_124


title: 1900097: Non-smoker_119


title: 1900105: Smoker_121


title: 1900123: Smoker_138


title: 1900092: Non-smoker_118


title: 1900085: Non-smoker_115


title: 1900107: Smoker_123


title: 1900083: Non-smoker_114


title: 1900081: Non-smoker_113


title: 1900078: Non-smoker_112


title: 1900077: Non-smoker_111


title: 1900072: Non-smoker_110


title: 1900140: Smoker_152


title: 1900071: Smoker_109


title: 1900159: Smoker_169


title: 1900069: Non-smoker_108


title: 1900066: Non-smoker_106


title: 1900106: Non-smoker_122


title: 1900068: Non-smoker_107


title: 1900061: Non-smoker_104


title: 1900062: Non-smoker_105


title: 1900056: Smoker_101


title: 1900047: Non-smoker_95


title: 1900053: Non-smoker_98


title: 1900057: Non-smoker_102


title: 1900055: Smoker_100


title: 1900054: Non-smoker_99


title: 1900042: Non-smoker_92


title: 1900052: Smoker_97


title: 1900045: Smoker_94


title: 1900039: Non-smoker_91


title: 1900044: Smoker_93


title: 1900038: Non-smoker_90


title: 1900034: Smoker_86


title: 1900036: Smoker_88


title: 1900037: Smoker_89


title: 1900033: Smoker_85


title: 1900028: Smoker_83


title: 1900032: Smoker_84


title: 1900058: Non-smoker_103


title: 1900024: Non-smoker_79


title: 1900027: Non-smoker_82


title: 1900051: Smoker_96


title: 1900025: Non-smoker_80


title: 1900026: Non-smoker_81


title: 1900022: Non-smoker_77


title: 1900018: Non-smoker_73


title: 1900023: Non-smoker_78


title: 1900019: Non-smoker_74


title: 1900013: Non-smoker_69


title: 1900015: Non-smoker_71


title: 1900012: Non-smoker_68


title: 1900010: Non-smoker_66


title: 1900011: Non-smoker_67


title: 1900035: Non-smoker_87


title: 1900008: Non-smoker_64


title: 1900007: Non-smoker_63


title: 1900006: Non-smoker_62


title: 1900003: Non-smoker_59


title: 1900004: Non-smoker_60


title: 215648: Smoker_55


title: 215784: Smoker_56


title: 1900016: Non-smoker_72


title: 1900020: Non-smoker_75


title: 1900001: Non-smoker_57


title: 1900014: Non-smoker_70


title: 203427: Smoker_48


title: 215091: Smoker_51


title: 215057: Smoker_50


title: 1900002: Non-smoker_58


title: 203394: Smoker_46


title: 215055: Smoker_49


title: 215570: Smoker_54


title: 203390: Smoker_43


title: 203419: Smoker_47


title: 215568: Non-smoker_52


title: 203391: Smoker_44


title: 1900005: Non-smoker_61


title: 203389: Smoker_42


title: 215569: Smoker_53


title: 203320: Smoker_40


title: 203317: Smoker_39


title: 203393: Smoker_45


title: 203313: Smoker_38


title: 203294: Smoker_37


title: 203293: Smoker_36


title: 203292: Smoker_35


title: 1900128: Smoker_143


title: 203275: Smoker_33


title: 203291: Non-smoker_34


title: 203273: Smoker_32


title: 203263: Smoker_31


title: 203261: Smoker_29


title: 203186: Smoker_26


title: 203212: Smoker_28


title: 203177: Smoker_25


title: 203170: Non-smoker_24


title: 203121: Smoker_21


title: 203151: Smoker_23


title: 203196: Smoker_27


title: 203090: Smoker_20


title: 203069: Smoker_19


title: 203323: Smoker_41


title: 202003: Smoker_17


title: 202002: Smoker_16


title: 203030: Smoker_18


title: 200537: Smoker_15


title: 1900009: Non-smoker_65


title: 203262: Smoker_30


title: 200533: Smoker_14


title: PW040-712

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences using the algorithm described by Griffiths et al, Nature Communications, 2018 before assigning read addresses for each sample.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding to beads associated with cells in our microwell system using the emptyDrops algorithm from Lun et al, Genome Biology, 2019.
We removed CBs that satisfied any of the following criteria 1) fractional alignment to the mitochondrial genome greater than 1.96 standard deviations above the mean, 2) ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons greater than 1.96 standard deviations above the mean, 3) average number of reads per molecule or average number of molecules per gene >2.5 standard deviations above the mean for a given sample, 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4..
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

molecule: polyA RNA

source_name: acute slice culture of glioma resection

growth_protocol: Tumor specimens were collected immediately after surgical removal  and kept in ice-cold artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3 for transportation. Preparation of ex vivo tissue slices was modified from methods described previously4. Briefly, the collected tumor specimens were placed in a drop of ice-cold ACSF and sliced using a tissue chopper (McIlwain) at a thickness of 500 µm under sterile conditions. The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Intact and well-shaped slices (approximately 5-10 mm diameter) were then placed on top of a porous membrane insert (0.4 µm, Millipore). Then the membrane inserts were placed into 6-well plates containing 1.5 mL maintenance medium consisting of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 µl of culture medium was added directly on top of each slice to prevent the slice surface from drying. The slices were first rested for 6 hrs with the maintenance medium in a humidified incubator at 37℃ and 5% CO2. Then, the medium was replaced with pre-warmed medium containing drugs with desired concentration (Table S1) or corresponding volume of vehicle (DMSO). Slices were then cultured with the treatment medium in a humidified incubator at 37℃ and 5% CO2 for 18 hrs before being collected for dissociation.

extract_protocol:
Collected tissue samples or tissue slices were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions.
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: acute slice culture of glioma resection

value: M

tag: location

value: right temporal

tag: diagnosis

value: Glioblastoma, WHO Grade IV

value: 0.2 uM panobinostat


title: 203122: Smoker_22

tag: age


title: 200524: Smoker_13


title: 200426: Smoker_12


title: 200410: Smoker_11


title: 200409: Ex-smoker_10

value: Male

value: Ex-smoker


title: PW040-709

value: vehicle (DMSO)


title: PW040-707


title: PW040-705


title: 200226: Non-smoker_8


title: PW040-703


title: 200225: Non-smoker_7


title: 200107: Non-smoker_6


title: 200303: Smoker_9


title: PW036-702


title: PW036-703

value: 2.5 uM etoposide


title: PW040-701


title: 200088: Smoker_4


title: 200106: Smoker_5


title: PW032-712

source_name: glioma surgical biopsy

value: glioma surgical biopsy

value: left frontal


title: PW036-701


title: 200087: Smoker_3

value: European-American

value: Female


title: PW036-705


title: PW032-711


title: 200076: Smoker_2

value: blood


title: PW032-709


title: 200005: Smoker_1

value: Smoker


title: PW040-711


title: PW032-705


title: PW032-703


title: PW032-702


title: PW032-701


title: WT_DRB.TTchemSeq_40min_release_rep2

first: Richard

middle: James

last: Mitter

state: LONDON

department: Bioinformatics & Biostatistics

description:
SC60
CUG506A60

data_processing:
library strategy: DRB/TTchem_Seq
DRB/TTchem-seq data were processed using previously a published protocol (Gregersen et al., 2020).
Reads were aligned to human GRCh38 Ensembl 86 using STAR 2.5.2a.
Sample scale factors were derived from a yeast spike-in, by aligning and counting against Saccharomyces cerevisiae R64-1-1 Ensembl 86.
Strand-specific, scaled bedgraph files were created from the aligments using BEDTools 2.27.1.  These were converted to bigWig format using the kentUtils bedGraphToBigWig function.
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig files contain sample-level, scaled read-depth coverage, split by strand.

growth_protocol: Cells were cultured in a 1:1 mixture of DMEM (Gibco) and Ham’s F10 (Invitrogen) supplemented with 10% FCS (Biowest) and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
KAPA RNA HyperPrep Kit (Roche)

treatment_protocol: 3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)

tag: cell line background

tag: cell type

value: colon cancer cell line

tag: genotype/variation

value: wild type

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)

tag: molecule subtype

value: Nascent RNA


title: WT_DRB.TTchemSeq_30min_release_rep2

description:
SC59
CUG506A59

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)


title: PW031-712

value: M

value: Glioblastoma, WHO Grade IV


title: WT_DRB.TTchemSeq_10min_release_rep2

description:
SC57
CUG506A57

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)


title: CSBKO_DRB.TTchemSeq_30min_release_rep2

description:
SC51
CUG506A51

value: CSB -/-


title: PW030-707

value: acute slice culture of glioma resection

value: right parietal

value: 1.8 nM Ispenisib


title: 1900087: Smoker_117

value: Male


title: CSBKO_DRB.TTchemSeq_40min_release_rep2

description:
SC52
CUG506A52


title: PW030-706

value: 50 uM Tazemetostat


title: PW030-708

value: 40 nM Ana-12


title: CSBKO_DRB.TTchemSeq_20min_release_rep2

description:
SC50
CUG506A50

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)


title: CSBKO_DRB.TTchemSeq_10min_release_rep2

description:
SC49
CUG506A49


title: PW030-704

value: 0.2 uM panobinostat


title: WT_DRB.TTchemSeq_40min_release_rep1

description:
SC44
CUG506A44

value: colon cancer cell line


title: PW030-703

value: 2.5 uM etoposide


title: WT_DRB.TTchemSeq_30min_release_rep1

description:
SC43
CUG506A43

value: wild type


title: WT_DRB.TTchemSeq_20min_release_rep1

description:
SC42
CUG506A42

value: Nascent RNA


title: PW030-702

value: vehicle (DMSO)


title: PW029-702

value: F

value: splenial extension into left parietal


title: WT_DRB.TTchemSeq_10min_release_rep1

description:
SC41
CUG506A41

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)


title: PW030-701

value: M

value: Glioblastoma, WHO Grade IV


title: CSBKO_DRB.TTchemSeq_30min_release_rep1

description:
SC35
CUG506A35

value: CSB -/-

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)


title: PW029-701

value: acute slice culture of glioma resection


title: CSBKO_DRB.TTchemSeq_20min_release_rep1

description:
SC34
CUG506A34


title: PW030-705

value: right parietal


title: CSBKO_DRB.TTchemSeq_10min_release_rep1

description:
SC33
CUG506A33


title: CSBKO_DRB.TTchemSeq_40min_release_rep1

description:
SC36
CUG506A36

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)


title: RESCUE ELOF1KO_DRB.TTchemSeq_40min_release_rep2

description:
SC28
CUG506A28

value: ELOF1 -/- ELOF1-FLAG-GFP


title: kd3.mrna: inhibitor 3

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

data_processing:
Bcl files were demultiplexed, adapter trimmed and converted to fastq format using 'Bcl2fastq' version 2.2.
Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, low quality 3 prime nucleotides (Phred33 < 20) were removed.
Reads were mapped to the hg38 reference genome using 'HISAT2' version 2.1.1, and reads aligning to features were counted with 'HTSeq' version 0.7.2.
non.oe.mrna.cpm.txt: tab delimited text file containing mRNA-Seq gene-level counts per million for nonsense (scrambled siRNA) and overexpression (mimic) samples
kdctrl.kd.mrna.cpm.txt: tab delimited text file containing mRNA-Seq gene-level counts per million for knockdown control (inhibitor control) and knockdown (inhibitor) samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text files containing read counts for each gene.

source_name: Neuronally differentiated SH-SY5Y

growth_protocol: SH-SY5Y cultures were neuronally differentiated using all-trans retinoic acid (ATRA, Sigma-Aldrich). One day prior to differentiation (day -1), cells were seeded into new 6 well plates at a density of 25,000 cells/cm2 in complete culture medium. The next day (day 0), standard culture medium was replaced with ATRA-supplemented medium (10µM final) and cells were wrapped in foil to protect from light exposure. ATRA-medium was subsequently replaced on day 2. On day 5, cells were washed with sterile PBS and returned to normal culture medium. Successful differentiation was confirmed by visual assessment of neurite outgrowth and quantification of neuronal marker genes (Fig 1A–C).

extract_protocol:
Cells were exposed to cycloheximide (0.1mg/mL) prior to detergent lysis and scraping as per the Illumina TruSeq Ribo Profile kit manual.
Total RNA was extracted from 300µL of clarified generated from the ribosome profiling methodology. For each sample, 1µg of high quality (RIN ≥ 8.5) total RNA was subjected to library preparation for mRNA sequencing using the TruSeq Stranded mRNA Kit (Illumina), as per the manufacturer’s instructions. Briefly, mRNA was denatured (65°C, 5 min) and ligated to oligo-dT magnetic beads (room temperature, 5 min), after which unbound RNA and non-specifically bound rRNA was discarded. mRNA was then heat fragmented (94°C, 8 min), following which reverse transcription and adapter ligation were performed as per the manufacturer’s instructions. Enrichment of cDNA fragments was subsequently conducted via 15 cycles of PCR, after which libraries were normalised, pooled and subjected to 151 cycles of sequencing using the NextSeq 500 system.

treatment_protocol: Transfections were conducted 24 hours after removal of ATRA-medium. Each culture was transfected with 5µL Lipofectamine 2000 (L2K, ThermoFisher) and 100pmol of either miR-1271-5p mimic, mimic control (scrambled siRNA), inhibitor or inhibitor control (mirVana, ThermoFisher). Briefly, L2K and RNA were mixed separately in 500µL OptiMEM (ThermoFisher) at room temperature for 5 min, after which both were combined to a final volume of 1mL and incubated for an additional 25 min. Standard culture medium was then replaced with L2K/RNA/OptiMEM and cells were incubated at 37°C for 6 hours, following which cells were returned to normal culture medium. At 72 hours post-transfection, cells were harvested as per the ribosome profiling methodology (see below), with both total RNA and ribosome protected RNA collected. In parallel to this experiment, transfection efficiency was quantified by co-transfecting additional cells with 100pmol RNA and 2µg pEZ-Lv205CT empty vector control lentiviral expression plasmid, which contains the eGFP gene under the CMV promoter. The proportion of GFP+ cells was analysed via Countess II FL automated fluorescent cell counter 72 hours post-transfection, which revealed transfection efficiencies of: 52.5% (mimic), 75% (nonsense siRNA/mimic control), 72% (inhibitor) and 79% (inhibitor scramble control).

value: Neuronally differentiated SH-SY5Y

tag: passages

value: poly(A) mRNA


title: kd3.ribo: inhibitor 3

data_processing:
Library strategy: Ribo-seq
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2.
Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, sequencing adapters were trimmed, low quality 3 prime nucleotides (Phred33 < 20) were removed and single 5 prime nucleotides were trimmed.
Reads were aligned to abundant short non-coding RNAs (rRNA, snRNA, snoRNA, miRNA) using 'Bowtie2' version 2.2.6. Unaligned reads were retained for further analysis.
Reads were mapped to the hg38 reference genome using 'Tophat2' version 2.1.1, and reads aligning to features were counted with 'HTSeq' version 0.7.2.
non.oe.ribo.cpm.txt: tab delimited text file containing Ribo-Seq gene-level counts per million for nonsense (scrambled siRNA) and overexpression (mimic) samples
kdctrl.kd.ribo.cpm.txt: tab delimited text file containing Ribo-Seq gene-level counts per million for knockdown control (inhibitor control) and knockdown (inhibitor) samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text files containing read counts for each gene.

extract_protocol:
Cells were exposed to cycloheximide (0.1mg/mL) prior to detergent lysis and scraping as per the Illumina TruSeq Ribo Profile kit manual.
Ribosome profiling was conducted using the Illumina TruSeq Ribo Profile Kit (H/M/R) according to the manufacturer’s instructions, with minor amendments. To inhibit translational activity, transfected cells were treated with culture medium supplemented with 0.1mg/mL cycloheximide (CHX) for 1 min. Cells were subsequently washed with ice-cold CHX-supplemented PBS, then harvested on ice via the addition of 1mL mammalian lysis buffer (containing 200µL 5x mammalian polysome buffer, 2µL CHX and 10 units (U) DNase I) and extensive scraping. Ribosome foot-printing was performed by adding 90U RNase I to 300µL clarified lysate and incubating samples at room temperature for 45 min, after which reactions were stopped with 15µL SUPERase inhibitor (Invitrogen). Ribosome-protected RNA fragments (RPFs) were then enriched using MicroSpin S-400 columns (GE Life Sciences), prior to ribosomal RNA depletion, RPF size selection, end repair, adapter ligation, reverse transcription and PAGE purification, conducted according to the manufacturer’s instructions. RPF cDNA libraries were subsequently produced with 12 PCR cycles, following which adapter dimers were removed via 8% native polyacrylamide gel prior to library normalization and pooling. RPF libraries were then sequenced using the Illumina NextSeq 500 system, with a total of 76 single-end cycles performed.

value: Ribosome protected mRNA


title: kd2.ribo: inhibitor 2


title: RESCUE ELOF1KO_DRB.TTchemSeq_20min_release_rep2

description:
SC26
CUG506A26

value: colon cancer cell line

tag: treatment

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)


title: kd4.mrna: inhibitor 4


title: kd2.mrna: inhibitor 2


title: ELOF1KO_DRB.TTchemSeq_40min_release_rep2

description:
SC20
CUG506A20

value: ELOF1 -/-

value: Nascent RNA


title: kdctrl4.mrna: inhibitor scramble control 4


title: RESCUE ELOF1KO_DRB.TTchemSeq_10min_release_rep2

description:
SC25
CUG506A25


title: kdctrl3.ribo: inhibitor scramble control 3


title: RESCUE ELOF1KO_DRB.TTchemSeq_30min_release_rep2

description:
SC27
CUG506A27


title: 1900021: Non-smoker_76

value: European-American

value: Female

value: Non-smoker

value: blood


title: kd1.ribo: inhibitor 1


title: ELOF1KO_DRB.TTchemSeq_30min_release_rep2

description:
SC19
CUG506A19


title: kd1.mrna: inhibitor 1


title: kdctrl3.mrna: inhibitor scramble control 3


title: ELOF1KO_DRB.TTchemSeq_10min_release_rep2

description:
SC17
CUG506A17

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)


title: RESCUE ELOF1KO_DRB.TTchemSeq_40min_release_rep1

description:
SC12
CUG506A12


title: ELOF1KO_DRB.TTchemSeq_20min_release_rep2

description:
SC18
CUG506A18


title: RESCUE ELOF1KO_DRB.TTchemSeq_30min_release_rep1

description:
SC11
CUG506A11

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)


title: kdctrl2.mrna: inhibitor scramble control 2


title: kdctrl2.ribo: inhibitor scramble control 2


title: 1900513: Smoker_407

value: Male

value: Smoker


title: kdctrl1.ribo: inhibitor scramble control 1


title: RESCUE ELOF1KO_DRB.TTchemSeq_10min_release_rep1

description:
SC9
CUG506A9


title: RESCUE ELOF1KO_DRB.TTchemSeq_20min_release_rep1

description:
SC10
CUG506A10


title: kdctrl1.mrna: inhibitor scramble control 1


title: ELOF1KO_DRB.TTchemSeq_40min_release_rep1

description:
SC4
CUG506A4

value: 100uM DRB for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)


title: oe4.mrna: mimic miR-1271-5p 4


title: ELOF1KO_DRB.TTchemSeq_30min_release_rep1

description:
SC3
CUG506A3


title: ELOF1KO_DRB.TTchemSeq_20min_release_rep1

description:
SC2
CUG506A2


title: oe3.ribo: mimic miR-1271-5p 3


title: oe3.mrna: mimic miR-1271-5p 3


title: oe2.mrna: mimic miR-1271-5p 2


title: oe1.mrna: mimic miR-1271-5p 1


title: ELOF1KO_DRB.TTchemSeq_10min_release_rep1

description:
SC1
CUG506A1


title: P1026 (10x)

city: Beijing

first: ZIyi

last: Li

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

description:
CRC.Leukocyte.10x.TPM.txt.gz
CRC.Leukocyte.10x.Metadata.txt.gz

data_processing:
The Smart-seq2 data were first processed to filter out low-quality reads when: (1) “N” bases accounting for 10% read length; or (2) bases with quality < 5 account for 50% read length; or (3) containing adapter sequences. The remaining paired-end reads were aligned to the UCSC hg38 human genome reference using kallisto (version 0.43.1) with parameters “--bootstrap-samples=100 --threads=2”. The R package tximport (version 1.9.12) was used to summarize the transcript-level estimated counts into the matrix of gene-level counts.
Low-quality cells were discarded if the cell library size or the number of expressed genes (counts larger than 0) was smaller than pre-defined thresholds, which were the medians of all cells minus 3×median absolute deviation. Cells were also removed if their proportions of mitochondrial gene expression were larger than 10% (70% for CD45- cells).
In the droplet-based 10x data, the Cell Ranger toolkit (version 2.1.0) provided by 10x Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix, using the reference genome GRCh38 and GRCm38. For each cell, we quantified the number of genes and UMIs, and kept high quality cells with the detection threshold of 600-4,000 genes and 1,600-25,000 UMIs. Cells with unusually high detection rate of mitochondrial gene expression were also excluded as described above.
Genome_build: hg38 downloaded from UCSC
Supplementary_files_format_and_content: tab-delimited text files include TPM values and metadata information for each Sample

source_name: CD45+ cells

extract_protocol: Single cells were sorted into 96-well plates (Axygen) chilled to 4°C, prepared with lysis buffer with 1 μl 10 mM dNTP mix (Invitrogen), 1 μl 10 μM Oligo dT primer, 1.9 μl 1% Triton X-100 (Sigma), and 0.1 μl 40 U/μl RNase Inhibitor (Takara). The single cell lysates were sealed and stored frozen at -80°C immediately.

tag: patient

value: CD45+ cells


title: P1025 (10x)


title: P0104 (10x)


title: P0323 (10x)


title: non4.mrna: nonsense siRNA 4

value: Neuronally differentiated SH-SY5Y


title: oe1.ribo: mimic miR-1271-5p 1


title: P0202 (10x)


title: P0613 (10x)


title: P0410 (10x)


title: non3.ribo: nonsense siRNA 3


title: non3.mrna: nonsense siRNA 3

value: poly(A) mRNA


title: non2.ribo: nonsense siRNA 2

value: Ribosome protected mRNA


title: non2.mrna: nonsense siRNA 2


title: P0123 (10x)


title: P0305 (10x)


title: P0104 (Smart-seq2)

description:
CRC.Leukocyte.Smart-seq2.TPM.txt.gz
CRC.Leukocyte.Smart-seq2.Metadata.txt.gz

source_name: CD45+ and CD45- cells

value: CD45+ and CD45- cells


title: non1.mrna: nonsense siRNA 1


title: P0408 (10x)


title: P0825 (Smart-seq2)


title: P0720 (Smart-seq2)


title: P1212 (Smart-seq2)


title: P0728 (Smart-seq2)


title: P0413 (Smart-seq2)


title: P0305 (Smart-seq2)


title: P0411 (Smart-seq2)


title: DLD-1 ZEB2 WT2 -DOX

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

description:
SG-19_S26
SG_19_DLD.1_TR21_ZEB2_WT2_mDOX

data_processing:
Samples were aligned to GRCh38 using STAR2.4.2a with default parameters.
Reads were count using STAR2.4.2a with default parameters and Ensembl v84 as reference.
Counts were normalized using the DESeq2 algorithm.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed file is counts table with in the rows the gene names (Ensembl ID) and in columns the different samples.

source_name: DLD-1 ZEB2 WT -DOX

extract_protocol:
RNA was extracted with the Nucleospin RNA Plus-kit (Machery-Nagel) according to the manufacturer’s instructions.
The mRNA libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen).

tag: cell line

tag: cell type background

value: epithelial colorectal cancer (CRC) cell line

tag: tissue source

value: colon

value: epithelial

tag: genotype/treatment

value: ZEB2 WT -DOX


title: DLD-1 ZEB2 WT37 +DOX

description:
SG-24_S32
SG_24_DLD.1_TR21_ZEB2_WT37_pDOX

source_name: DLD-1 ZEB2 WT +DOX

value: mesenchymal

value: ZEB2 WT +DOX


title: DLD-1 ZEB2 WT5 +DOX

description:
SG-22_S30
SG_22_DLD.1_TR21_ZEB2_WT5_pDOX


title: DLD-1 ZEB2 WT5 -DOX

description:
SG-21_S29
SG_21_DLD.1_TR21_ZEB2_WT5_mDOX


title: DLD-1 ZEB2 WT2 +DOX

description:
SG-20_S28
SG_20_DLD.1_TR21_ZEB2_WT2_pDOX


title: non1.ribo: nonsense siRNA 1


title: P0309 (Smart-seq2)


title: INT030-5: MDA-MB-453 scRNA

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

description: single-cell transcriptome

data_processing:
Fastqc
Trimmomatic
hisat2
featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: Expression Matrix

source_name: MDA-MB-453, spiked into blood and recovered

extract_protocol:
Manual picking
Smart-seq2

treatment_protocol: Blood spike-in; recovered by gradient-immunobeads based protocol (PLA), Aspirin (ASP), Ticagrelor (TIG), Clopidogrel (CHL), Cilostazol (CIL), Integrilin (INT), Tirofiban (TIR), and red blood lysis protocol (RBL).

value: Integrilin treated


title: INT030-6: MDA-MB-453 scRNA

description: single-cell transcriptome


title: INT030-4: MDA-MB-453 scRNA

description: single-cell transcriptome