title: F2-RM164 (patient derived xenograft)

value: Local recurrence


title: F2-RM27 (patient derived xenograft)

status: Public on Oct 16 2018

type: RNA

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

hyb_protocol: Hybridization was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

scan_protocol: Samples were scanned using the Gene Titan Affymetrix instrument according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

data_processing: Data were normalized by RMA using the Affy R package and batch effects were corrected using ComBat using the sva R package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Xenograft F2

label_protocol: Labeling was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.

extract_protocol: Total RNA was extracted using the Nucleospin miRNA kit (Bioke, Leiden, The Netherlands) according to the supplier’s instruction.

tag: disease state

value: CRC

tag: tissue

value: Liver metastasis

tag: gender

tag: age

tag: Stage

tag: cimp

tag: msi

tag: cms

tag: batch

tag: center

value: AMC


title: F3-RM27 (patient derived xenograft)

source_name: Xenograft F3


title: F1-RM40 (patient derived xenograft)

source_name: Xenograft F1


title: F2-CO153 (patient derived xenograft)

value: Primary tumor

value: Flevo


title: F1-CO153 (patient derived xenograft)


title: F2-CO150 (patient derived xenograft)


title: F3-CO150 (patient derived xenograft)


title: F1-RM27 (patient derived xenograft)


title: F2-RM152 (patient derived xenograft)


title: F1-RM164 (patient derived xenograft)


title: F2-RM39 (patient derived xenograft)


title: F3-RM164 (patient derived xenograft)


title: F1-CO149 (patient derived xenograft)


title: F1-CO150 (patient derived xenograft)


title: F3-RM152 (patient derived xenograft)


title: F1-CO144 (patient derived xenograft)


title: F1-RM152 (patient derived xenograft)


title: F3-CO149 (patient derived xenograft)


title: F2-CO149 (patient derived xenograft)


title: F3-CO153 (patient derived xenograft)


title: F1-CO128 (patient derived xenograft)


title: WT-2

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

country: USA

institute: PTC Therapeutics

hyb_protocol: cRNA was hybridized at 45oC for 16 h on a GeneChip Human Genome U133 plus 2.0 Array.

scan_protocol: GeneChips were analyzed using the Affymetrix scanner.

data_processing: Data analysis was performed using Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific). The MAS5 normalization method was used. ANOVA was used for statistical evaluation.

label_protocol: standard Affymetrix protocol

growth_protocol: PTC299-resistant and parent HT1080 cells were seeded in 6-well plates (5 x 105 cells/well) and incubated overnight.

extract_protocol: Total RNA was purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. cRNA was prepared according to the standard Affymetrix protocol.

tag: genotype/variation

value: wild type


title: F2-CO123 (patient derived xenograft)


title: 299R-4

value: resistant to PTC299


title: F1-CO123 (patient derived xenograft)


title: 299R-3


title: RM40 (patient tumor)

source_name: Liver metastasis

value: Male


title: F3-CO123 (patient derived xenograft)


title: F2-CO116 (patient derived xenograft)


title: RM38 (patient tumor)


title: WT-4


title: F3-CO116 (patient derived xenograft)


title: Adjacent Normal (HCC 174N)

city: Singapore

first: Kam

last: Hui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression data from Adjacent Normal tissue sample of  hepatocellular carcinoma patient

hyb_protocol: The final cRNA obtained was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data was analysed using Partek Genomics Suite version 6.6. CEL files were imported into Partek with RMA background correction, quantile normalisation and log2 transformation.Batch effects were removed based on microarray scandate factor using Partek Batch-remove algorithm.

source_name: Adjacent Normal sample from hepatocellular carcinoma patient

label_protocol: Five micrograms of total RNA were reverse-transcribed and labeled with biotin.

growth_protocol: Patients with hepatocellular carcinoma were recruited at diagnosis according to the protocol approved by the Institutional Review Board.  Informed consent was obtained from all subjects before Tissue samples were collected.

extract_protocol: Total RNA was extracted from frozen HCC biopsies using TRIZOL Reagent following the manufacturer's protocol.

treatment_protocol: The tissues were frozen immediately after collection and were stored at -80 oC.

tag: individual id

value: HCC

value: Adjacent Normal sample

value: M

tag: Sex

tag: hbv status

value: Positive


title: Adjacent Normal (HCC 175N)


title: RM30 (patient tumor)


title: 299R-1


title: Adjacent Normal (HCC 177N)


title: Adjacent Normal (HCC 178N)

value: F


title: Adjacent Normal (HCC 176N)


title: Adjacent Normal (HCC 173N)


title: Adjacent Normal (HCC 172N)


title: RM28 (patient tumor)


title: RM39 (patient tumor)


title: 299R-2


title: RM41 (patient tumor)

value: Female


title: RM37 (patient tumor)


title: RM29 (patient tumor)


title: RM152 (patient tumor)

source_name: Local recurrence


title: CO162 (patient tumor)

source_name: Primary tumor


title: RM27 (patient tumor)


title: RM164 (patient tumor)


title: Adjacent Normal (HCC 169N)


title: WT-3


title: Adjacent Normal (HCC 170N)


title: CO172 (patient tumor)


title: Adjacent Normal (HCC 171N)


title: CO170 (patient tumor)


title: CO154 (patient tumor)


title: CO150 (patient tumor)


title: Adjacent Normal (HCC 83N)


title: Adjacent Normal (HCC 167N)


title: CO153 (patient tumor)


title: Adjacent Normal (HCC 80N)


title: CO169 (patient tumor)


title: Adjacent Normal (HCC 168N)


title: Adjacent Normal (HCC 162N)


title: Adjacent Normal (HCC 84N)


title: Adjacent Normal (HCC 85N)


title: Adjacent Normal (HCC 165N)


title: Adjacent Normal (HCC 81N)


title: WT-1


title: Adjacent Normal (HCC 82N)


title: CO160 (patient tumor)


title: RM163 (patient tumor)


title: CO151 (patient tumor)


title: Adjacent Normal (HCC 166N)


title: Adjacent Normal (HCC 79N)


title: CO148 (patient tumor)


title: CO131 (patient tumor)


title: Adjacent Normal (HCC 78N)


title: CO125 (patient tumor)


title: Adjacent Normal (HCC 75N)


title: Adjacent Normal (HCC 77N)


title: CO128 (patient tumor)


title: Adjacent Normal (HCC 72N)


title: Adjacent Normal (HCC 73N)


title: CO149 (patient tumor)


title: CO144 (patient tumor)


title: CO129 (patient tumor)


title: Adjacent Normal (HCC 68N)


title: CO117 (patient tumor)


title: Adjacent Normal (HCC 67N)


title: CO115 (patient tumor)


title: CO127 (patient tumor)


title: CO123 (patient tumor)


title: KSHV EV treated HUVEC_1

city: Daejeon

first: Hyungtaek

last: Jeon

address: 77 GYERYONG-RO 771BEON-GIL, JUNG-GU

department: school of medicine, Dept. of microbiology and immunology

country: South Korea

institute: Eulji University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human umbilical vein endothelial cells treaetd with extracelluar vesicles from KSHV infected human endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in endothelial cell growth medium-2 (EGM-2; Lonza) bullet kit. The cells were maintained in a humidified atmosphere of 5 % CO2 at 37 °C

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mock-EV and KSHV-EV were treated with cultured medium for 24hr at a humidified atmosphere of 5 % CO2 at 37 °C

tag: agent

value: KSHV

tag: cell type

value: umbilical vein endothelial cells

value: female


title: Adjacent Normal (HCC 66N)


title: Adjacent Normal (HCC 65N)


title: KSHV EV treated HUVEC_2


title: Adjacent Normal (HCC 64N)


title: Adjacent Normal (HCC 56N)


title: Adjacent Normal (HCC 62N)


title: Adjacent Normal (HCC 60N)


title: F1-CO116 (patient derived xenograft)

value: CRC


title: Tumor (HCC 178T)

description: Gene expression data from HCC Tissue sample of  hepatocellular carcinoma patient

source_name: Tumor sample from hepatocellular carcinoma patient

value: Tumor sample


title: CO137 (patient tumor)

value: AMC


title: Mock EV treated HUVEC_1

source_name: Human umbilical vein endothelial cells treaetd with extracelluar vesicles from mock infected human endothelial cells

value: mock


title: Mock EV treated HUVEC_2


title: Adjacent Normal (HCC 53N)


title: Tumor (HCC 179T)


title: U937 hardware-1g ground control plus inhibitor SKF96365 rep4

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description: H/W 1g GC + SKF

hyb_protocol: Hybridization for 17.5 h to a NimbleGen expression microarray (12 × 135,000 features) employing the “Gene Expression Hybridization Kit” (Agilent Technologies)

scan_protocol: Scanning was performed using the Microarray Scanner G2505B (Agilent Technologies)

data_processing: The image files of the scanner were analyzed with the NimbleScan Software 2.6 using the robustmultiarray analysis (RMA) with the default parameters. RMA, a probe-level summarization method, identifies probes that are outliers in the overall behavior of the expression measured for a given gene. The contribution of outlier probes is reduced in the reported gene expression level, which has been demonstrated to improve the sensitivity and reproducibility of microarray results. In addition to screening outlier probes, NimbleScan software’s implementation of RMA [Irizarry et al., 2003] used quantile normalization and background correction.( R. A. Irizarry, B.Hobbs, F.Collin et al., “Exploration, normalization, and summaries of high density oligonucleotide array probe level data,” Biostatistics, vol. 4, no. 2, pp. 249–264, 2003)

source_name: U937 cells (ATCC CRL1593.2)

label_protocol: Cy3-labeling with the “Low RNA Input Linear Amplification Kit, PLUS, One-Color” (Agilent Technologies)

growth_protocol: U937 cells were cultured in RPMI 1640 medium (Biochrom/MerckMillipore, Germany), supplemented with 10% fetal bovine serum (FBS Superior; Biochrom/Merck Millipore, Germany), 2mM glutamine (Gibco/Life Technologies, Germany), and 100U/mL penicillin as well as 100 ug/mL streptomycin (Gibco/Life Technologies, Germany). Cells were seeded with a density of 0.2 × 10e6 cells/mL and the medium was exchanged every 48 hours.  number.

extract_protocol: Total RNA was extracted using the RNeasy Midi and Maxi kit (Qiagen, Germany). The RNA quality and concentration  integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Human U937 cells were exposed to altered gravity conditions during a sounding rocket flight.

value: Pleura/pleural effusion, lymphocyte, myeloid, monocyte

tag: altered gravity condition

value: hardware 1g ground control plus inhibitor SKF96365


title: U937 hardware-1g ground control plus inhibitor SKF96365 rep2

description: H/W 1g GC + SKF


title: CO116 (patient tumor)

tag: disease state

value: Primary tumor


title: Tumor (HCC 176T)

tag: tissue


title: Tumor (HCC 175T)


title: U937 hardware-1g ground control plus inhibitor SKF96365 rep1

description: H/W 1g GC + SKF


title: U937 hardware-1g ground control rep6

description: H/W 1g GC

value: hardware 1g ground control


title: Adjacent Normal (HCC 71N)

value: HCC


title: U937 hardware-1g ground control plus inhibitor SKF96365 rep3

description: H/W 1g GC + SKF


title: Tumor (HCC 172T)


title: U937 hardware-1g ground control rep5

description: H/W 1g GC


title: U937 hardware-1g ground control rep3

description: H/W 1g GC


title: Tumor (HCC 177T)


title: Tumor (HCC 173T)


title: U937 hardware-1g ground control rep2

description: H/W 1g GC


title: Tumor (HCC 171T)


title: Tumor (HCC 174T)


title: Tumor (HCC 170T)


title: U937 75s hypergravity rep5

description: BL-TX hyp-g

value: hypergravity baseline TEXUS campaign


title: Tumor (HCC 169T)


title: Tumor (HCC 168T)

value: M


title: U937 hardware-1g ground control rep4

description: H/W 1g GC


title: U937 hardware-1g ground control rep1

description: H/W 1g GC


title: U937 75s hypergravity rep1

description: BL-TX hyp-g


title: U937 75s hypergravity rep3

description: BL-TX hyp-g


title: U937 300s microgravity plus inhibitor SKF96365 rep3

description: ug + SKF

value: microgravity plus inhibitor SKF96365


title: U937 75s hypergravity rep2

description: BL-TX hyp-g


title: U937 75s hypergravity rep4

description: BL-TX hyp-g


title: Tumor (HCC 165T)

value: Positive


title: Tumor (HCC 154T)


title: U937 300s microgravity plus inhibitor SKF96365 rep2

description: ug + SKF


title: Tumor (HCC 157T)


title: Tumor (HCC 152T)


title: U937 300s microgravity plus inhibitor SKF96365 rep1

description: ug + SKF


title: Tumor (HCC 166T)


title: U937 300s microgravity plus inhibitor SKF96365 rep4

description: ug + SKF


title: U937 300s microgravity rep7

description: ug

value: microgravity


title: U937 300s microgravity rep5

description: ug


title: U937 300s microgravity rep6

description: ug


title: Tumor (HCC 133T)


title: Tumor (HCC 127T)


title: Tumor (HCC 108T)


title: Tumor (HCC 107T)


title: Tumor (HCC 126T)

value: F


title: Tumor (HCC 132T)


title: U937 300s microgravity rep1

description: ug


title: Tumor (HCC 146T)


title: Tumor (HCC 106T)


title: U937 300s microgravity rep4

description: ug


title: U937 300s microgravity rep3

description: ug


title: U937_hardware_1g_ground_control_rep6

description: H/W 1g GC

growth_protocol: U937 cells were cultured in RPMI 1640 medium (Biochrom/MerckMillipore, Germany), supplemented with 10% fetal bovine serum (FBS Superior; Biochrom/Merck Millipore, Germany), 2mM glutamine (Gibco/Life Technologies, Germany), and 100U/mL penicillin as well as 100 ug/mL streptomycin (Gibco/Life Technologies, Germany). Cells were seeded with a density of 0.2 × 10e6 cells/mL and the medium was exchanged every 48 hours.

extract_protocol: Total RNA was extracted using the RNeasy Midi and Maxi kit (Qiagen, Germany) The RNA quality and concentration  integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Human U937 cells were exposed to altered gravity conditions during a parabolic flight.


title: U937 300s microgravity rep2

description: ug


title: Tumor (HCC 104T)


title: Tumor (HCC 97T)


title: U937_hardware_1g_ground_control_rep5

description: H/W 1g GC


title: Tumor (HCC 102T)


title: Tumor (HCC 101T)


title: Tumor (HCC 167T)


title: U937_hardware_1g_ground_control_rep4

description: H/W 1g GC


title: U937_hardware_1g_ground_control_rep3

description: H/W 1g GC


title: Tumor (HCC 95T)


title: U937_hardware_1g_ground_control_rep2

description: H/W 1g GC


title: Tumor (HCC 92T)


title: Tumor (HCC 93T)


title: U937_20sec_1_8g_hypergravity_rep6

description: BL-PFC hyp-g

value: 1.8g hypergravity baseline parabolic flight campaign


title: U937_20sec_1_8g_hypergravity_rep5

description: BL-PFC hyp-g


title: Tumor (HCC 89T)


title: U937_hardware_1g_ground_control_rep1

description: H/W 1g GC


title: U937_20sec_1_8g_hypergravity_rep3

description: BL-PFC hyp-g


title: U937_20sec_1_8g_hypergravity_rep2

description: BL-PFC hyp-g


title: U937_20sec_1_8g_hypergravity_rep4

description: BL-PFC hyp-g


title: U937_20sec_1_8g_hypergravity_rep1

description: BL-PFC hyp-g


title: Tumor (HCC 88T)


title: Tumor (HCC 87T)


title: Tumor (HCC 84T)


title: U937_1g_in_flight_control_rep7

description: 1g IF

value: 1g in flight control


title: Tumor (HCC 85T)


title: Tumor (HCC 82T)


title: U937_1g_in_flight_control_rep8

description: 1g IF


title: U937_1g_in_flight_control_rep4

description: 1g IF


title: U937_1g_in_flight_control_rep6

description: 1g IF


title: U937_1g_in_flight_control_rep3

description: 1g IF


title: Tumor (HCC 80T)


title: Tumor (HCC 81T)


title: Tumor (HCC 79T)


title: Tumor (HCC 75T)


title: U937_1g_in_flight_control_rep5

description: 1g IF


title: U937_1g_in_flight_control_rep1

description: 1g IF


title: U937_20s_microgravity_rep7

description: ug


title: U937_20s_microgravity_rep6

description: ug


title: Tumor (HCC 77T)


title: U937_1g_in_flight_control_rep2

description: 1g IF


title: Tumor (HCC 72T)


title: U937_20s_microgravity_rep5

description: ug


title: U937_20s_microgravity_rep8

description: ug


title: Tumor (HCC 73T)


title: Tumor (HCC 78T)


title: Tumor (HCC 71T)


title: Tumor (HCC 67T)


title: U937_20s_microgravity_rep3

description: ug


title: U937_20s_microgravity_rep4

description: ug


title: Tumor (HCC 68T)


title: U937_20s_microgravity_rep2

description: ug


title: Tumor (HCC 65T)


title: Tumor (HCC 66T)


title: U937_20s_microgravity_rep1

description: ug


title: Tumor (HCC 64T)


title: Tumor (HCC 83T)


title: Tumor (HCC 60T)


title: Tumor (HCC 162T)


title: Tumor (HCC 54T)


title: Tumor (HCC 62T)


title: Tumor (HCC 44T)


title: Tumor (HCC 53T)


title: Tumor (HCC 55T)


title: Tumor (HCC 42T)


title: Tumor (HCC 43T)


title: Tumor (HCC 56T)


title: Tumor (HCC 37T)


title: Tumor (HCC 40T)


title: Tumor (HCC 32T)


title: Tumor (HCC 45T)


title: Col

type: SRA

city: Jinan

first: Yuebin

last: Jia

address: 88 Cultural east road

country: China

institute: Shandong University

description: col-L-RPKM

library_source: transcriptomic

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Genome_build: Tair10

organism: Arabidopsis thaliana

source_name: WT

growth_protocol: 4-day-old seedlings grown on 1/2 MS in dark were transferred to white light for 7 days, the whole seedlings were extracted for RNA sequencing.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: ecotype

value: Col

value: wild type

value: whole seedlings


title: 35SARF18OE-2

value: ARF18 overexpression line

tag: age


title: 4424_3_Huh7_XL413_GGCTACA

first: Cun

last: Wang

address: Plesmanlaan 121,

department: Division of Molecular Carcinogenesis

institute: The Netherlands Cancer Institute

description: polyA+ stranded RNA Library prep from sample

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome.  Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F  -k 5 --minins 0 --maxins 500 --fr --new-summary
Steps performed: link, count, QCstrandness, eset
Read counts are determined.Count parameters    Count library type stranded: true  Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf    mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

molecule: polyA RNA

source_name: liver cancer cell line

growth_protocol: Cells were cultured in DMEM with 10% FBS, glutamine and penicillin/streptomycin (Gibco®) at 37 °C / 5% CO2.

extract_protocol:
RNA was isolated using Rneasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hep3B and Huh7 cells pre-treated with XL413 for 10 days to induce senescence prior to sertraline treatment for 24 hours.

value: liver cancer cell line

tag: cell line

tag: treatment


title: 4424_5_Hep3B_control_GTTTCGG

value: control


title: 4424_7_Hep3B_XL413_GAGTGGA


title: 4424_8_Hep3B_XL413_sertraline_ACTGATA

value: XL413 sertraline


title: 4424_6_Hep3B_sertraline_CGTACGT

value: sertraline


title: 4424_4_Huh7_XL413_sertraline_GTGGCCT


title: 4424_2_Huh7_sertraline_TAGCTTA


title: 4424_1_Huh7_control_GATCAGA


title: 4172_2_Hep3B-XL413_ACAGTGA

extract_protocol:
Cells were treated with 10 μM XL413 for 4 days. The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: XL413 treatment


title: 4172_1_Hep3B-control_TGACCAA

treatment_protocol: Cells were treated with 10 μM XL413 for 4 days.


title: 6W5 Gast

city: Rochester

first: Joe

last: Chakkalakal

state: NY

address: 601 Elmwood Avenue, Box 711

institute: University of Rochester

data_processing:
See Bachman et al., Development 2018- Materials and methods "NGS data processing and alignment" for details
DeSeq2 normalized counts and comparisons
Genome_build: mm10
Supplementary_files_format_and_content: [DeSeq2_Processed_Data.xlsx]  This is the DeSeq2 file with normalized read counts and comparisons.
[Supplmental File 2 Seq.xlsx]  Supplemental file from Bachman et al, Development 2018 containing IPA analysis, gene ontology, and DeSeq2 changes relative to ECM, Calcium, and AMPK signalling.

organism: Mus musculus

source_name: 6W gastrocnemius

extract_protocol:
Gastrocnemius muscles were dissected and flash frozen on dry ice in Trizol. RNA was isolated using Rneasy Plus Mini Kit (Qiagen).
Library construction was performed by UR Genomics Research Center using TruSeq Tital Stranded RNA Sample Preperation Kit.

tag: strain

value: 6 weeks

value: gastrocnemius muscle


title: 8W 307_Ctl

source_name: 8W gastrocnemius

value: 8 weeks


title: 6W4 Gast


title: 8W 311_Ctl


title: 4W5 Gast

source_name: 4W gastrocnemius

value: 4 weeks


title: H1650_PTEN.deficient_cells 3

city: San Francisco

first: Nilanjana

last: Chatterjee

state: CA

address: 600 16th street

department: Department of Medicine

institute: UCSF

description: Gene expression from H1650 cells without PTEN expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Arrays (HGU133 plus 2.0).

data_processing: Raw data was processed using R/Bioconductor package with Robust Multichip Average (RMA) normalization

source_name: H1650 cells (PTEN deficient) transfected with vector expressing GFP

growth_protocol: H1650 human lung cancer cells were cultured and maintained following ATCC guidelines

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: H1650 cells were transfected with either GFP or PTEN expression vector.

value: metastatic pleural effusion bronchoalveolar carcinoma


title: Tumor (HCC 38T)

value: HCC

value: Tumor sample

value: M

value: Positive


title: H1650_PTEN.deficient_cells 2


title: H1650_PTEN.wt_cells 2

description: Gene expression from H1650 cells with PTEN expression

source_name: H1650 cells (PTEN deficient) transfected with vector expressing wild type PTEN


title: H1650_PTEN.deficient_cells 1


title: K562_UV_NAz_3min

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
K562_mutation_fractions.tsv
K562_mutation_counts.tsv

data_processing:
Library strategy: MaP-seq
adaptor removed with skewer
Reads mapped and mutations counted with ShapeMapper 2.0
RT stops mapped with STAR
Genome_build: E.coli rRNA operons B or H
Genome_build: H. sapiens rRNA
Genome_build: S. cerevisiae rRNA
Supplementary_files_format_and_content: tab-seperated text file of mutation rates (#mutations/coverage), a proxy for extent of modification, for each nucleotide in each dataset.
Supplementary_files_format_and_content: tab-seperated text file of number of RT stops at each position, a proxy for extent of modification, for each nucleotide in each dataset.

source_name: K562 cells

extract_protocol:
Modified ribosomes were isopropanol precipitated, phenol extracted, reprecipitated.
1-4μg of total RNA was fragmented by incubation at 95°C for 5 minutes with 10mM ZnCl2. Fragmentation was stopped by placing tubes on ice and immediately adding EDTA to 20mM. RNA was ethanol precipitated, resuspended in 10mM tris pH 7.0 and run on a 10% PAGE TBE-urea gel for size selection. A section corresponding to 100-120bp on a DNA ladder was cut from the gel. The gel was shredded by forcing the gel through a needle hole in a 0.5ml tube by centrifugation, and RNA was eluted into 400μl water by heating at 70°C with rapid shaking for 15 minutes. Gel pieces were filtered out with a Spin-X column (corning) and RNA was isopropanol precipitated, resuspended in PNK mix (3.5μl 10mM Tris pH 8.0, 0.5μl SUPERaseIn RNase inhibitor (Invitrogen), 0.5μl 10x PNK buffer (NEB), 0.5μl T4 PNK), and incubated at 37°C for 1 hour. Reactions were supplemented with 5μl ligation mix (3.8ul 50% PEG 8000, 0.2ul 50μM pre-adenylated linker 2 (oBZ191) (For oligos, see supplementary Table S1), 0.5μl 10X T4 RNA ligase buffer (NEB), 0.5ul T4 RNA ligase 2 truncated (NEB)) and incubated at 37°C for 3 hours, then isopropanol precipitated. For E. coli experiments, pellets were resuspended in water and split for reverse transcription with either TGIRTII (Ingex) or SSII (Invitrogen). For all other experiments, only SSII was used, and pellets were directly resuspended in annealing mixture. For TGIRTII, 10ul reactions were prepared with RNA, 2μl Invitrogen 5x FS buffer, 0.5μl 10mM dNTPs, 0.5μl SUPERaseIn, 0.5μl 100mM DTT, .5μl 25μM RT primer oBZ192, 0.5ul 10μM TGIRTII, and incubated at 60°C for 1 hour. For SSII, 6μl annealing reactions were prepared containing RNA, 0.6μl 10x MapBasic Buffer (500mM Tris pH 8.0, 750mM KCl, 100mM DTT), 25μM RT primer oBZ192. RNA was annealed to primer by incubating: 4 minutes at 65°C, 2 minutes at 55°C, 2 minutes at 45°C, 2 minutes at 42°C, hold on ice. 6ul of extension mix (2.2μl water, 0.6μl MapBasic buffer, 0.6μl 10mM dNTPs, 0.5μl SUPERaseIn, 1.44μl 50mM MnCl2, 0.6μl SSII) was added, mixed, and incubated at 42°C for 1 hour. After all RT reactions, RNA was degraded by addition of 1μl 5M NaOH, and incubation for 3 minutes at 95°C. cDNA was precipitated, resuspended in 10mM Tris pH 7, and run on a 10% TBE-UREA gel. For mutation datasets, full length RT products were isolated. For RT stop datasets, cDNA was isolated from ~20nt above the RT primer to ~20nt below the full-length product. Gel extraction was performed as above, pellets were resuspended in Circ ligase mix (15.5μl 10mM Tris pH 8.0, 2μl 10x Circ ligase buffer, 1μl 1mM ATP, 1μl 50mM MnCl2, 0.5μl Circ Ligase I (Epicentre)), and incubated at 60°C for 2 hours, then 80°C for 20 minutes. Circularized cDNA was amplified with 8-12 cycles of PCR and subjected to Illumina sequencing on a HiSeq 2500 with 50bp single-end reads.

treatment_protocol:
In vitro LASER reactions were performed in 25ul volumes in 1.5ml microcentrifuge tubes (Axygen). 25ul reactions contained 1x HEPES modification buffer (30mM K-HEPES pH 7.5, 7mM Magnesium Acetate, 100mM KCl), 2μM crude E. coli 70S ribosomes, and where indicated 4μM EF-G and 0.5mM GDPNP. Reactions were brought to the final volume of 25ul by adding 2ul of 300mM NAz in DMSO, or DMSO alone. Reducing agents (besides those present in ribosome and protein stocks) were omitted to prevent potential reactivity with NAz. Reactions were incubated for 5 minutes at 37°C, arranged uniformly around a UV lamp (20watt Zilla Desert 50 UVB Fluorescent Coil Bulb) with the tube bottoms pointed towards the bulb, and exposed to UV light for 3 minutes. Reactions were brought to 300μl with 0.3M sodium acetate pH 5.5, isopropanol precipitated, extracted twice (or until protein interface was gone) with phenol/chloroform/isoamyl alcohol, and once with chloroform, ethanol precipitated, and resuspended in 40μl water.
25ul reactions were assembled containing 1x HEPES modification buffer (30mM K-HEPES pH 7.5, 3mM Magnesium Acetate, 100mM KCl, 2mM DTT), 0.5μM each of S. cerevisiae 40S and 60S ribosomal subunits. After incubating at 25°C for 5 minutes, reactions were brought to the final volume of 25ul by adding 2.5ul of 100mM 1M7 (synthesized according to (13)) 100mM Benzoyl Cyanide (BzCN, Sigma Aldrich 115959), or 3M NAz in anhydrous DMSO, or DMSO alone, and incubated at 25°C for 6  minutes (1M7), 30 seconds (BzCN), or exposed to UV light for 3 minutes (NAz). Reactions were brought to 500μl with 0.3M sodium acetate pH 5.5, isopropanol precipitated, resuspended in 200μl 0.3M sodium acetate pH 5.5, extracted twice (or until protein interface was gone) with phenol/chloroform/isoamyl alcohol, and once with chloroform, ethanol precipitated, and resuspended in 40μl water.
K562 cells were grown in advanced RPMI 1640 media (Gibco) supplemented with 10% FBS (Gibco) and 2mM L-Glutamine (Gibco). 500,000 cells were pelleted in a 1.5ml microcentrifuge tube (Axygen), washed with 500μl 37°C PBS, pelleted again, and resuspended in 100ul PBS + 10%DMSO, or PBS + 300mM NAz. Tubes were UV exposed for 3 minutes as described for in vitro reactions. 300μl of Trizol (Invitrogen) was added to each reaction and RNA was purified with the Zymo Direct-Zol RNA miniprep kit, following the manufacturer’s directions for total RNA extraction, omitting the DNase treatment.

tag: probe

value: UV+Naz

tag: probe concentration

tag: treatment time

value: 3 minutes


title: H1650_PTEN.wt_cells 1


title: H1650_PTEN.wt_cells 3


title: 4W4 Gast


title: K562_UV_only_3min

value: UV


title: 4172_4_Huh7-XL413_CAGATCA

value: liver cancer cell line


title: 8W 308_Ctl


title: 4172_3_Huh7-control_GCCAATA

value: control


title: S3_KOstiff_1

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Transcript and gene level expression estimates were obtained with RSEM v1.2.3, by aligning preprocessed reads against the Mus musculus transcriptome.
Genome_build: Ensembl genebuild 76 (Mus musculus assembly GRCm38).
Supplementary_files_format_and_content: ENSEMBL gene IDs and TMM-normalized counts per million for each sample.

source_name: Mouse embryonic fibroblasts from Cav1KO mice

growth_protocol: All experiments were conducted with mouse embryonic fibroblasts isolated from WT and Cav1KO littermate mice.

extract_protocol:
RNA was extracted with RNAeasy micro kit (QIAGEN)
500 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies)
Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads.

treatment_protocol: Cells were grown on stiff or soft polyacrilamide matrices at low confluence. RNA extraction was preformed  24h after seeding.

value: embryonic fibroblasts

tag: genotype

value: Cells were grown on stiff poliacrylamide matrices


title: K562_UV_only_1min

value: 1 minutes


title: S4_KOstiff_2


title: S7_KOsoft_1

value: Cells were grown on soft poliacrylamide matrices


title: S6_WTsoft_2

source_name: Mouse embryonic fibroblasts from WT mice

value: WT


title: S8_KOsoft_2


title: S5_WTsoft_1


title: S2_WTstiff_2


title: 1550-1_RV [heart 8]

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.8 software was used for basecalling. All 101 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the Ensembl hg38 (release 84) .gtf, and associated bowtie2 index provided by Illumina iGenomes using tophat v2.1.1 (fr-unstranded)
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library.  However, this was merely done for later graph display.  Actual calculations of differential gene expression used htseq-count data as input to edgeR.
Genome_build: hg19 / hg38
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.

source_name: heart, right ventricle

extract_protocol:
Hearts were removed and ventricles were flash frozen in liquid nitrogen.  Total RNA was harvested from ~50 mg of tissue using a Polytron homogenizer and Trizol reagent (Invitrogen) according to the manufacturer's instructions.  Total RNA was treated with Dnase using the RNeasy Mini Kit (Qiagen) according to the manufacturer's directions.
Polyadenylated RNA enrichment was performed from 1 ug input total RNA along with RNA fragmentation and conversion to paired-end, Illumina sequencing libraries using Illumina TruSeq v2 preparation kits.

value: heart

tag: heart region

value: right ventricle

tag: heart id

value: 50 years


title: 1550-1_LV [heart 8]

source_name: heart, left ventricle

value: left ventricle

tag: Sex


title: 1550-1_septum [heart 8]

source_name: heart, interventricular septum

value: interventricular septum


title: 1548-2_septum [heart 7]

value: M

value: 47 years


title: K562_UV_NAz_1min

value: UV+Naz


title: 1548-2_RV [heart 7]


title: 1548-2_LV [heart 7]


title: S1_WTstiff_1


title: 1550-1_RA [heart 8]

source_name: heart, right atrium

value: right atrium


title: 1548-2_RA [heart 7]


title: 1547-2_LV [heart 6]

value: 35 years


title: 1547-2_RA [heart 6]


title: 1546-2_septum [heart 5]

value: 61 years


title: 1547-2_RV [heart 6]


title: 1547-2_LA [heart 6]

source_name: heart, left atrium

value: left atrium


title: 1550-1_LA [heart 8]


title: 1547-2_septum [heart 6]


title: 1546-2_LV [heart 5]


title: 1546-1_RV [heart 4]

value: 32 years


title: 1546-1_septum [heart 4]


title: 1546-2_LA [heart 5]


title: 1546-2_RA [heart 5]


title: 1546-2_RV [heart 5]


title: 1546-1_LV [heart 4]


title: 1546-1_LA [heart 4]


title: 1545-2_septum [heart 2]

value: F

value: 65 years


title: 1545-2_LA [heart 2]


title: 1545-2_RA [heart 2]


title: 1545-2_RV [heart 2]


title: 1545-2_LV [heart 2]


title: 1545-1_RV [heart 1]


title: 1545-1_septum [heart 1]


title: 1548-2_LA [heart 7]


title: Tumor (HCC 17T)

source_name: Tumor sample from hepatocellular carcinoma patient

tag: individual id

value: HCC

value: Tumor sample

tag: hbv status

value: Positive


title: 1545-1_RA [heart 1]

value: heart


title: 1545-1_LV [heart 1]


title: 1546-1_RA [heart 4]


title: 1479-2_RV [heart 3]

value: right ventricle

value: 54 years


title: 1479-2_RA [heart 3]


title: 1479-2_septum [heart 3]

value: interventricular septum


title: 1545-1_LA [heart 1]


title: GM19238_PRO-seq

city: Ithaca

first: Hojoong

last: Kwak

address: 317 Biotechnology Building

institute: Cornell University

description: Nascent RNA

data_processing:
Library strategy: PRO-seq
Trimmed out 3´ RNA adaptor sequences using cutadapt and tagged the reads with first 8mer of the sequences for unique molecular indices (UMIs).
Aligned the reads to a human ribosomal RNA reference (NR_145819.1) and filtered out the reads that are mapped to the ribosomal sequences allowing up to 2 mismatches using bowtie.
Aligned the remaining reads to the hg19 reference genome using bowtie, and used uniquely mapped reads allowing up to 2 mismatches.
Reduced duplicates with identical UMI and position to a single read using a custom script and stored in bam format.
Mapped the 5’ position of the reads and stored read counts in the bedgraph format using the bedtools suite (bedtools coverage).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedgraph format of 5' end read counts.

source_name: lymphoblastoid cells

growth_protocol: LCLs were cultured in RPMI 1640 media (Gibco) with 2 mM L-glutamine (Gibco) and 15% Fetal Bovine Serum (Gibco) supplements without antibiotics at 37°C under 5% CO2. Mid-log phase cultures were seeded at 2×10^5 cells/ml density in 15 ml suspension culture, and maintained for 24 hr before the cell harvest.

extract_protocol:
LCLs were pelleted by centrifugation at 800×g for 3 min in 4°C, washed twice by resuspension in 10 mL 4°C Phosphate Buffered Saline (PBS) and centrifugation at 800×g for 3 min, followed by resuspension in 50 µl of storage buffer (50 mM Tris-Cl pH 8.0, 25% glycerol, 5 mM magnesium acetate, 0.1 mM EDTA, 5 mM DTT). Cells were instantly frozen in liquid nitrogen, and stored at -80°C.
PRO-cap/PRO-seq

tag: cell type

value: lymphoblastoid cell line

tag: population

value: YRI

tag: individual


title: GM19222_PRO-seq

description: Nascent RNA


title: GM19239_PRO-seq

description: Nascent RNA


title: 1479-2_LV [heart 3]

tag: tissue

value: left ventricle

value: M


title: 1479-2_LA [heart 3]

tag: age


title: GM19193_PRO-seq

description: Nascent RNA


title: GM19131_PRO-seq

description: Nascent RNA


title: GM19099_PRO-seq

description: Nascent RNA


title: Primary ccRCC -2

type: genomic

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 510 20th Street South

department: Urology

institute: UAB

description:
Sample 37
7973201071_R03C01

hyb_protocol: DNA Samples were bisulfite converted with the Zymo EZ DNA Methylation kit (Zymo Research, Irvine, CA, USA).

scan_protocol: The BeadChip arrays were processed according to the manufacturer’s instructions and scanned using an Illumina iScan system (Illumina; San Diego, CA). The Illumina GenomeStudio Methylation Module software was used to analyze the BeadChip image data

data_processing: Raw data files were processed using minfi R package. Signal intensities were normalized using SWAN method. Differentially methylated probes were identified using limma R package

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human tumor

label_protocol: Standard Illumina protocol for Human Methylation450k DNA Analysis bead chip

extract_protocol: Genomic DNA was isolated from 25 mg of flash frozen tissues using the Invitrogen PureLink Genomic DNA kit (ThermoFisher Scientific; Waltham, MA).

value: Primary RCC tumor


title: Normal Renal -9

description:
Sample 35
7973201046_R04C01

source_name: Human tissue

value: Normal renal tissue


title: Primary ccRCC -8

description:
Sample 43
7973201082_R04C01


title: Primary ccRCC -7

description:
Sample 42
7973201082_R01C01


title: Primary ccRCC -9

description:
Sample 44
7973201046_R02C02


title: Primary ccRCC -4

description:
Sample 39
7973201071_R06C01


title: Primary ccRCC -5

description:
Sample 40
7973201071_R05C02


title: Normal Renal -6

description:
Sample 32
7878191022_R05C02


title: GM18522_PRO-seq

description: Nascent RNA


title: Primary ccRCC -6

description:
Sample 41
7878191022_R01C02


title: Primary ccRCC -1

description:
Sample 36
7973201071_R01C01


title: Normal Renal -7

description:
Sample 33
7973201082_R02C02


title: Primary ccRCC -3

description:
Sample 38
7973201071_R04C01


title: Normal Renal -5

description:
Sample 31
7878191022_R06C01


title: Normal Renal -8

description:
Sample 34
7973201046_R01C01


title: GM18520_PRO-seq

description: Nascent RNA


title: Breast Cancer_Young (200526210052_R04C01)

city: Valencia

first: Sara

last: OLTRA SANCHIS

state: Valencia

address: Avda Menéndez Pelayo, 4 accesorio

department: Medical Oncology

institute: INCLIVA

hyb_protocol: bisulphite converted DNA was restored, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: BeadChips were washed and scanned using the Illumina HiScan SQ scanner

data_processing: Intensities were extracted from the images using GenomeStudio (v.2011.1) and Methylation module (1.9.0) software

source_name: Breast

label_protocol: Standard Illumina Protocol

extract_protocol:
DNA FFPE samples were extracted using a commercial kit  QIAamp DNA FFPE Tissue Kit from Qiagen
QIAamp DNA FFPE Tissue Kit from Qiagen

value: Breast

tag: gender

value: Female

value: Young

tag: subgroup

value: LUMINAL B

tag: er status

tag: sample type

value: FFPE sample


title: GM19223_PRO-cap

description: Capped nascent RNA

data_processing:
Library strategy: PRO-cap
Trimmed out 3´ RNA adaptor sequences using cutadapt and tagged the reads with first 8mer of the sequences for unique molecular indices (UMIs).
Aligned the reads to a human ribosomal RNA reference (NR_145819.1) and filtered out the reads that are mapped to the ribosomal sequences allowing up to 2 mismatches using bowtie.
Aligned the remaining reads to the hg19 reference genome using bowtie, and used uniquely mapped reads allowing up to 2 mismatches.
Reduced duplicates with identical UMI and position to a single read using a custom script and stored in bam format.
Mapped the 5’ position of the reads and stored read counts in the bedgraph format using the bedtools suite (bedtools coverage).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedgraph format of 5' end read counts.


title: Breast Cancer_Young (200526210052_R08C01)

value: TRIPLE NEG


title: Normal Breast tissue_Young (200526210006_R05C01)

value: Normal Young


title: Breast Cancer_Old (200526210052_R07C01)

value: Old


title: Breast Cancer_Young (200526210006_R01C01)


title: GM18505_PRO-seq

description: Nascent RNA


title: GM19153_PRO-cap

description: Capped nascent RNA


title: Normal Renal -3

description:
Sample 29
7878191022_R03C01


title: Breast Cancer_Young (200526210006_R02C01)


title: Breast Cancer_Young (200526210006_R03C01)


title: Breast Cancer_Young (200526210052_R01C01)


title: Breast Cancer_Young (200526210135_R06C01)


title: GM19209_PRO-cap

description: Capped nascent RNA


title: Breast Cancer_Old (200526210006_R06C01)


title: GM19147_PRO-cap

description: Capped nascent RNA


title: GM19200_PRO-cap

description: Capped nascent RNA


title: Breast Cancer_Young (200526210135_R07C01)


title: Breast Cancer_Young (200526210052_R05C01)

value: LUMINAL A


title: Normal Renal -2

description:
Sample 28
7878191022_R01C01


title: Breast Cancer_Young (200526210006_R04C01)


title: Breast Cancer_Young (200526210135_R08C01)


title: GM19203_PRO-cap

description: Capped nascent RNA


title: Normal Renal -4

description:
Sample 30
7878191022_R04C01


title: GM19257_PRO-cap

description: Capped nascent RNA


title: GM18517_PRO-seq

description: Nascent RNA


title: GM19206_PRO-cap

description: Capped nascent RNA


title: Normal Renal -1

description:
Sample 27
7973201071_R01C02


title: Breast Cancer_Old (200526210135_R05C01)


title: GM19160_PRO-cap

description: Capped nascent RNA


title: GM19190_PRO-cap

description: Capped nascent RNA


title: GM19116_PRO-cap

description: Capped nascent RNA


title: Metastasis ccRCC -26

description:
Sample 26
7973201046_R06C02

value: Metastasis RCC tumor


title: GM19101_PRO-cap

description: Capped nascent RNA


title: Metastasis ccRCC -23

description:
Sample 23
7973201046_R01C02


title: GM19093_PRO-cap

description: Capped nascent RNA


title: Metastasis ccRCC -22

description:
Sample 22
7973201046_R06C01


title: Breast Cancer_Young (200526210187_R07C01)


title: Breast Cancer_Young (200526210135_R02C01)


title: GM18907_PRO-cap

description: Capped nascent RNA


title: Breast Cancer_Old (200526210187_R08C01)


title: Metastasis ccRCC -18

description:
Sample 18
7973201082_R06C02


title: Metastasis ccRCC -19

description:
Sample 19
7973201046_R02C01


title: Breast Cancer_Old (200526210135_R03C01)


title: Breast Cancer_Old (200526210187_R06C01)


title: Metastasis ccRCC -17

description:
Sample 17
7973201082_R04C02


title: Metastasis ccRCC -20

description:
Sample 20
7973201046_R03C01


title: Breast Cancer_Old (200526210187_R04C01)


title: Metastasis ccRCC -15

description:
Sample 15
7973201082_R01C02


title: Breast Cancer_Young (200526210187_R03C01)


title: Normal Breast tissue_Old (200526210135_R04C01)

value: Normal Old


title: GM19140_PRO-cap

description: Capped nascent RNA

value: lymphoblastoid cell line


title: Metastasis ccRCC -21

description:
Sample 21
7973201046_R05C01


title: Metastasis ccRCC -14

description:
Sample 14
7973201082_R06C01


title: GM19127_PRO-cap

description: Capped nascent RNA

value: YRI


title: 20.4 weeks_1

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_4_20pt4w

data_processing:
Sequencing QC: FastQC
Trimming of reads for quality: Trimmomatic
Alignment: STAR
Read binning: Htseq-count
Genome_build: GRCh38.p10 (Gencode 26)
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values, Counts, and Annotation

source_name: lung

extract_protocol:
Lung tissues were removed, flash frozen on dry ice in RNA Later, and RNA was extracted using Intron Bio Rna extraction kit.
Sequencing libraries were made using Illumina TruSeq RNA Library Prep Kit v2.

tag: Stage

value: fetal

tag: developmental stage

value: 20.4 weeks


title: GM18916_PRO-cap

description: Capped nascent RNA


title: Breast Cancer_Old (200526210139_R07C01)


title: Breast Cancer_Young (200526210139_R08C01)


title: Breast Cancer_Young (200526210187_R01C01)


title: Breast Cancer_Old (200526210139_R05C01)


title: Metastasis ccRCC -13

description:
Sample 13
7973201082_R05C01


title: Breast Cancer_Young (200526210139_R06C01)


title: Normal Breast tissue_Young (200526210139_R03C01)


title: Normal Breast tissue_Old (200526210187_R02C01)


title: Metastasis ccRCC -12

description:
Sample 12
7973201082_R03C01


title: GM19137_PRO-cap

description: Capped nascent RNA


title: GM19143_PRO-cap

description: Capped nascent RNA


title: 14.5 weeks_2

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_2_14pt5w

value: 14.5 weeks


title: GM18912_PRO-cap

description: Capped nascent RNA


title: 20.5 weeks_2

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_5_20pt5w

value: 20.5 weeks


title: 14.4 weeks_3

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_3_14pt4w

value: 14.4 weeks


title: GM18501_PRO-cap

description: Capped nascent RNA


title: Breast Cancer_Young (200526210139_R02C01)

value: Breast

value: Female


title: Orth rep7

city: Buffalo

first: Hai

address: Elm and Carlton Streets, MRC 328

department: Molecular and Cellular Biology

institute: Roswell Park Cancer Institute

data_processing:
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads derived from xenograft materials contains a mixture of human and mouse reads were separated using Xenome (version 1.0.1).
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DEseq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: GRCh38.83 and GRCm38.83
Supplementary_files_format_and_content: RSEM read counts and DESeq2 normalized gene expression matrix (VIVO_RNAseq_Normalized.RData).

source_name: xenograft breast tumor

growth_protocol: MCF-7 cells are cultured in DMEM with 10% FBS and then serve for mammary pad injection (Orthotopic tumor) or intra-illiac injection (IVBL tumor).

extract_protocol:
After homogenization, total RNA were extracted by Direct-zol RNA miniprep kit. . The first and second strand cDNA were prepared by SuperScript III First-Strand Synthesis System and NEBNext mRNA Second Strand Synthesis Module from at least 200ng total RNA for each sample. Illumina Nextera XT DNA Sample Prep Kit  was used with 1 ng of dsDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using nextera Illumina protocols

value: xenograft breast tumor

tag: derived from cell line

tag: passage

tag: reporter gene

value: Firefly Luciferase (MCF-7)


title: yeast_80S_BzCN

description:
s_cerevisiae_raw_mutation_fractions.tsv
s_cerevisiae_raw_mutation_counts.tsv

organism: Saccharomyces cerevisiae

source_name: Purified Ribosomes

tag: probe

value: BzCN

tag: probe concentration

tag: treatment time

value: 30 seconds


title: Metastasis ccRCC -10

description:
Sample 10
7878191022_R06C02


title: Orth rep6


title: Metastasis ccRCC -9

description:
Sample 9
7878191022_R04C02


title: yeast_80S_untreated_2


title: GM18504_PRO-cap

description: Capped nascent RNA

tag: cell type


title: Orth rep5


title: Breast Cancer_Young (200526210139_R04C01)

value: Young

value: LUMINAL B

value: FFPE sample


title: GM18519_PRO-cap

description: Capped nascent RNA

tag: population


title: Breast Cancer_Young (200526210010_R08C01)


title: Metastasis ccRCC -11

description:
Sample 11
7973201082_R02C01

value: Metastasis RCC tumor


title: Metastasis ccRCC -25

description:
Sample 25
7973201046_R04C02


title: yeast_80S_untreated


title: Metastasis ccRCC -8

description:
Sample 8
7878191022_R03C02


title: Metastasis ccRCC -24

description:
Sample 24
7973201046_R03C02


title: Orth rep3


title: Metastasis ccRCC -7

description:
Sample 7
7878191022_R02C02


title: Metastasis ccRCC -6

description:
Sample 6
7878191022_R05C01


title: Orth rep2


title: 20.5 weeks_3

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_6_20pt5w


title: yeast_80S_300mM_NaZ

value: UV+Naz

value: 3 minutes


title: GM18508_PRO-cap

description: Capped nascent RNA

value: lymphoblastoid cell line

value: YRI

tag: individual


title: GM18859_PRO-cap

description: Capped nascent RNA


title: Metastasis ccRCC -4

description:
Sample 4
7973201071_R04C02

tag: tissue


title: Traf6EKO skin with IMQ treatment

city: Kyoto

first: Teruki

last: Dainichi

state: Kyoto

address: 54 Kawahara-cho Shogoin Sakyo-ku

department: Dernatology

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Hybridization was performed on a Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Not provided

data_processing: Robust multiarray average algorithm was used for log transformation (log2) and normalization of the GeneChip data.

source_name: Traf6EKO skin with IMQ treatment

label_protocol: An amplified sense-strand DNA product was synthesized with the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA, USA), was fragmented and labelled by the WT Terminal Labelling and Controls Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Traf6EKO and Traf6f/f mice were treated with and without IMQ at 8 weeks age.

extract_protocol: RNA was extracted from whole mouse ears using Trizol (Invitrogen).

treatment_protocol: A daily dose of 10mg of IMQ-containing cream, was applied onto the mouse ear for 2 consecutive days.

tag: genotype

tag: imq treatment

value: yes

tag: age

value: 8 weeks

tag: Sex

value: female

value: skin


title: Breast Cancer_Old (200526210010_R07C01)

value: Breast

tag: gender

value: Female

value: Old

tag: subgroup

value: LUMINAL A

tag: er status

tag: sample type


title: Orth rep1

value: xenograft breast tumor

tag: derived from cell line

tag: passage

value: Firefly Luciferase (MCF-7)


title: Metastasis ccRCC -5

description:
Sample 5
7878191022_R02C01


title: GM18856_PRO-cap

description: Capped nascent RNA


title: MCP_post exposed_RV+NGF

city: Lucknow

first: Ruchi

last: Yadav

state: Uttar Pradesh

address: Malhour, Gomti Nagar Extension

department: Amity Institute of Biotechnology

country: India

institute: Amity University Uttar Pradesh, Lucknow Campus, Lucknow

description: Gene expression data from human umbilical cord blood mesenchymal stem cell co-exposed with MCP  and RV+NGF after cell differentiation

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' PrimeView Human Gene Expression arrays  in a GeneChip® Hybridization oven 645 (Affymetrix) according to the manufacturer’s procedures .GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix)

data_processing: The data were normalized using  RMA as implemented in the  Affy package version 1.58.0 (Bioconductor version 3.7)  including background correction and log-transformation and expression file is written as log2-scale.MeV 4.9.0 is used to analyze expression data using statistical methods (T-test,SAM ) and clustering techniques.Functional annotation and pathway mapping is done using DAVID Bioinformatics resources 6.7. A supplementary file on the series record, normalized_data_with_ERCC_controls.txt includes normalized data for all probesets including ERCC controls.

label_protocol: Total RNA was biotin labelled using GeneChip 3` IVT Express Labeling kit and  hybridised to Affymetrix PrimeView microarrays (Affymetrix) according to the manufacturer's instructions.

growth_protocol: A total of 90 blood samples (approximately 45 ml/cord) were collected from the cord vein in sterile containers having anticoagulant citrate dextrose buffer. Blood was diluted 1:1 with Dulbecco’s phosphate-buffered saline (PBS) without Ca2+and Mg2+, pH 7.5 (Stem Cell Technologies). MSCs were isolated as per manufacturer’s instructions, followed by Ficoll paque (1.077 g/cm3, Stem Cell Technologies) density-gradient centrifugation (700 X g for 30 min). Freshly isolated MSCs were cultured in plastic 25-cm2 ultra low attachment culture flask (Nunc Inc.) at a density of 1X105cells/mL in 5 mL  αMEM (Gibco, life technology, USA) supplemented with 1% glutamax-100X, 1% anti-biotic anti-mycotic  and sodium bicarbonate 1% and 20% MSC qualified FBS (Gibco, life technology, USA). Cells were adhered and maintained in Alpha MEM containing 20% MSC qualified serum, humidified atmosphere at 37°C and 5% CO2.

extract_protocol: The total RNA was isolated from both exposed cells and unexposed control sets withTrizol (Invitrogen, USA) as per the standard protocol. The RNA samples were then analyzed for quality and quantity using NanoDropTM (Thermo Fisher Scientific, MA USA) . The RNA samples showing the quality and purity above the threshold were arrayed for gene expression analysis

treatment_protocol: Proliferated Human umbilical cord blood derived mesenchymal stem cells (HUCBMSCs) were exposed to RV (10 μM), NGF (50 ng/ml) and RV+NGF (10 μM+50 ng/mL) concentrations respectively for 30 minutes .These  treatments were done before cell differentiation (pre exposed samples) and after cell differentiation (post exposed samples)

value: mesenchymal stem cell derived neuronal differentiation

tag: cell status

value: multipotent


title: Traf6EKO skin without IMQ treatment

source_name: Traf6EKO skin without IMQ treatment

value: no


title: IVBL rep8

source_name: xenograft bone lesion

value: xenograft bone lesion

tag: reporter gene


title: Breast Cancer_Old (200526210010_R03C01)

value: FFPE sample


title: Traf6f/f skin with IMQ treatment

source_name: Traf6f/f skin with IMQ treatment


title: Metastasis ccRCC -3

description:
Sample 3
7973201071_R03C02

value: Metastasis RCC tumor


title: MCP_post exposed_RV

description: Gene expression data from human umbilical cord blood mesenchymal stem cell co-exposed with MCP and  RV after cell differentiation


title: GM19204_PRO-cap

description: Capped nascent RNA

value: lymphoblastoid cell line

value: YRI


title: MCP_post exposed_NGF

description: Gene expression data from human umbilical cord blood mesenchymal stem cell co-exposed with MCP and NGF after cell differentiation


title: IVBL rep7


title: IVBL rep6


title: MITF_Dox4

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

label: Biotin

source_name: PC3 cell line

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

extract_protocol: RNA was extracted from the described tissues using NucleoSpin® RNA isolation kit from Macherey-Nagel (ref: 740955.240C)

tag: cell line

tag: treatment

value: doxycycline-treated cells


title: GM18511_PRO-cap

description: Capped nascent RNA

tag: cell type

tag: population


title: Metastasis ccRCC -16

description:
Sample 16
7973201082_R03C02

tag: tissue


title: Traf6f/f skin without IMQ treatment

source_name: Traf6f/f skin without IMQ treatment

tag: genotype

value: 8 weeks

value: female


title: GM19225_PRO-cap

description: Capped nascent RNA

tag: individual


title: MCP_pre exposed_RV+NGF

description: Gene expression data from human umbilical cord blood mesenchymal stem cell co-exposed with MCP and RV+NGF before cell differentiation


title: Normal Breast tissue_Old (200526210010_R01C01)

value: Breast

value: Normal Old


title: Metastasis ccRCC -2

description:
Sample 2
7973201071_R05C01


title: Orth rep4


title: IVBL rep5


title: GM19144_PRO-cap

description: Capped nascent RNA


title: 14.5 weeks_1

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_1_14pt5w

tag: Stage

value: fetal

tag: developmental stage

value: 14.5 weeks


title: Breast Cancer_Old (200526210010_R02C01)

tag: gender

value: Female

value: Old


title: IVBL rep4

value: Firefly Luciferase (MCF-7)


title: Metastasis ccRCC -1

description:
Sample 1
7973201071_R02C01


title: Breast Cancer_Young (200526210010_R06C01)

value: Young

tag: subgroup

value: TRIPLE NEG


title: GM19207_PRO-cap

description: Capped nascent RNA


title: GM18862_PRO-cap

description: Capped nascent RNA


title: IVBL rep3

value: xenograft bone lesion


title: IVBL rep2


title: yeast_80S_10mM_1M7_25C_3min

tag: probe

tag: probe concentration

tag: treatment time

value: 6 minutes


title: MCP_pre exposed_NGF

description: Gene expression data from human umbilical cord blood mesenchymal stem cell co-exposed with MCP and NGF before cell differentiation

value: multipotent


title: IVBL rep1

tag: derived from cell line

tag: passage


title: MITF_Dox3


title: GM19152_PRO-cap

description: Capped nascent RNA

value: lymphoblastoid cell line


title: GM19159_PRO-cap

description: Capped nascent RNA

value: YRI


title: GM19141_PRO-cap

description: Capped nascent RNA


title: MCP_pre exposed_RV

description: Gene expression data from human umbilical cord blood mesenchymal stem cell co-exposed with monocrotophos(MCP) and RV before cell differentiation

tag: cell status


title: GM19210_PRO-cap

description: Capped nascent RNA


title: MSC_RV+NGF

description: Gene expression data from human umbilical cord blood mesenchymal stem cell exposed with resveratrol and nerve growth factor(RV+NGF)


title: MITF_Dox2

tag: cell line

value: doxycycline-treated cells


title: MSC_NGF

description: Gene expression data from human umbilical cord blood mesenchymal stem cell exposed with nerve growth factor(NGF)


title: GM18853_PRO-cap

description: Capped nascent RNA


title: GM19201_PRO-cap

description: Capped nascent RNA


title: MITF_Dox1

tag: treatment


title: GM18913_PRO-cap

description: Capped nascent RNA

tag: cell type


title: MSC

description: Gene expression data from human umbilical cord blood mesenchymal stem cell as control samples


title: GM19192_PRO-cap

description: Capped nascent RNA

tag: population


title: MITF_NoDox2

value: untreated cells


title: MITF_NoDox3


title: Homo_shRNA_rep 3

city: Shenyang

first: Zi

last: Yu

state: Liaoning

address: Shenyang North New Area, Shenyang, Liaoning Province, P.R. China

institute: China Medical University

description: Gene expression data from 786O cells

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data analysis and quality control of the expression data were performed with Expression Console according to Affymetrix default analysis settings. Differential analysis was completed with GeneSpring of   Agilent Technologies Inc..

source_name: 786O, shRNA

growth_protocol: 786O cells were cultured in RPMI 1640 with 10% fetal bovine serum in a condition with air at 37℃ with 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 786O cells were transfected with lentivirus with shRNA targeting ERCC6L.

tag: genotype/variation

value: shRNA targeting ERCC6L

value: kidney renal cell carcinoma


title: MSC_RV

description: Gene expression data from human umbilical cord blood mesenchymal stem cell exposed with resveratrol(RV)


title: Homo_shRNA_rep 1

description: Gene expression data from 786O cells


title: FSGS_5

city: Nanjing

first: Hao

last: Bao

state: Jiangsu

address: 305 East Zhong Shan Road

department: National Clinical Research Center of Kidney Diseases, Jinling Hospital

institute: Nanjing university

description: expression value derived from Expression Console software

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were processed with Expression Console software (Affymetrix) for background correction and normalization.

source_name: Renal glomerular tissue

label_protocol: Total RNA was amplified, labeled and purified by Ovation® Pico WTA System V2(Cat#3302, NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Tissues were kept in RNAlater at 4°C.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Microdissection of glomeruli was performed manually under a stereomicroscope using two dissection needle holders in RNAlater at 4°C.

tag: tissue

value: glomeruli

tag: disease state

value: Focal segmental glomerulosclerosis (FSGS)


title: MITF_NoDox4


title: GM19092_PRO-cap

description: Capped nascent RNA

tag: individual


title: Homo_shNC_rep 2

description: Gene expression data from 786O cells

source_name: 786O, shNC

value: control


title: Metastasis RCC -25

description:
Sample43
7927538065_K

hyb_protocol: standard as recommended by illumina

scan_protocol: After scanning the probe array, the resulting image was analyzed using the GenomeStudio software (Illumina, Inc., San Diego, CA).

data_processing: Rawdata obtained from Illumina’s beadstudio were preprocessed using a bioconductor package “beadarray” in an open source software R v3.2.2 [https://cran.r-project.org/]. The raw signal values were quantile normalized and log2 transformed.  Then probes with no-match and bad quality were filtered out, considering 34,476 probes for further analysis. In next step differential expression analysis was performed using limma package.

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: Metastatic ccRCC tissue


title: Homo_shRNA_rep 2

description: Gene expression data from 786O cells


title: FSGS_4


title: GM19138_PRO-cap

description: Capped nascent RNA


title: Metastasis RCC -26

description:
Sample44
7927538065_L


title: FSGS_3


title: FSGS_2


title: Metastasis RCC -24

description:
Sample42
7927538065_J


title: GM19171_PRO-cap

description: Capped nascent RNA


title: Homo_shNC_rep 1

description: Gene expression data from 786O cells


title: Metastasis RCC -22

description:
Sample40
7927538065_G


title: Metastasis RCC -23

description:
Sample41
7927538065_H


title: Normal-9

description:
Sample39
7927538065_F

value: Normal renal tissue


title: Homo_shNC_rep 3

description: Gene expression data from 786O cells


title: GM19119_PRO-cap

description: Capped nascent RNA


title: 12_70S_5uM onc112_UV_NAz

description:
rRNA
e_coli_batch2_laser_raw_mutation_fractions.tsv
e_coli_batch2_laser_raw_mutation_counts.tsv

data_processing:
Library strategy: MaP-seq
adaptor removed with skewer
Reads mapped and mutations counted with ShapeMapper 2.0
RT stops mapped with STAR
Genome_build: E.coli rRNA operons B or H
Supplementary_files_format_and_content: tab-seperated text file of mutation rates (#mutations/coverage), a proxy for extent of modification, for each nucleotide in each dataset.
Supplementary_files_format_and_content: tab-seperated text file of number of RT stops at each position, a proxy for extent of modification, for each nucleotide in each dataset.

organism: Escherichia coli

value: UV+Naz

value: 3 minutes


title: 11_70S_1uM onc112_UV_NAz


title: Control_5


title: FSGS_1


title: GM19114_PRO-cap

description: Capped nascent RNA


title: 9_70S_0.05uM onc112_UV_NAz


title: GM19098_PRO-cap

description: Capped nascent RNA


title: 4_70S_UV_NAz


title: GM19130_PRO-cap

description: Capped nascent RNA


title: 3_70S_UV_NAz


title: 2_70S_UV

value: UV


title: GM18870_PRO-cap

description: Capped nascent RNA


title: 1_70S_UV


title: Control_4


title: Control_2


title: GM18855_PRO-cap

description: Capped nascent RNA


title: Breast Cancer_Old (200526210139_R01C01)

value: Breast

value: Female

value: Old

value: TRIPLE NEG

tag: er status

tag: sample type

value: FFPE sample


title: GM18858_PRO-cap

description: Capped nascent RNA

value: lymphoblastoid cell line

value: YRI


title: Control_3


title: Normal-8

description:
Sample37
7927538065_B


title: 23_70S_EFG_GDPNP_UV_NAZ_tgirt_Trunc

description:
e_coli_laser_raw_mutation_fractions.tsv
e_coli_laser_raw_mutation_counts.tsv


title: Metastasis RCC -20

description:
Sample34
7927538061_K


title: Metastasis RCC -21

description:
Sample35
7927538061_L


title: 22_70S_EFG_UV_NAZ_tgirt_Trunc


title: GM18909_PRO-cap

description: Capped nascent RNA


title: Control_1


title: Hep3B_CHRNA9_knockdown-2_rep2

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description:
CHRNA9 knockdown-2 in Hep3B cell line, replicate 2
S15_H030

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The slides scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: Raw data were normalized using the normalizeQuantiles function from 'limma' package (v. 3.30.7).

source_name: Hep3B CHRNA9 knockdown-2

label_protocol: Fluorescent aRNA targets were prepared from 1 μg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).

growth_protocol: All cancer cells (including Hep3B, A549 and MDA-MB-231) used in this study were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM)/F12 culture medium.

extract_protocol: Total RNA was extracted from the cancer cells (including Hep3B, A549 and MDA-MB-231) using TRIzol Reagent through chloroform/isopropanol purification. RNA quantity and purity was assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios are established as A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5 indicating acceptable RNA purity. RIN values are ascertained using Agilent RNA 6000 Nano assay to determine RNA integrity. Pass criteria for RIN value is established at > 6 indicating acceptable RNA integrity.

treatment_protocol: All cancer cells (including Hep3B, A549 and MDA-MB-231) were transfected with lentivirus contains CRISPR system to edit the human CHRNA9 and SLC16A7 genomic sequences. After three days of lentivirus transfection, the cells were drug selected with 2.5 mM puromycin for two days and cultured in culture medium for two days. During the experiment, the cells were PBS washed and collected for RNA isolation and purification.

tag: chrna9 knockdown

value: Yes

tag: slc16a7 knockdown

value: No


title: Hep3B_CHRNA9_knockdown-2_rep1

description:
CHRNA9 knockdown-2 in Hep3B cell line, replicate 1
S15_H029


title: Metastasis RCC -18

description:
Sample32
7927538061_I


title: Hep3B_CHRNA9_knockdown-1_rep1

description:
CHRNA9 knockdown-1 in Hep3B cell line, replicate 1
S16_H027

source_name: Hep3B CHRNA9 knockdown-1


title: GM18516_PRO-cap

description: Capped nascent RNA

source_name: lymphoblastoid cells


title: Metastasis RCC -19

description:
Sample33
7927538061_J

source_name: Human tumor


title: Primary RCC-8

description:
Sample36
7927538065_A

value: Primary ccRCC tissue


title: Hep3B_control_rep2

description:
Control (no knockdown) - Hep3B cell line, replicate 2
S13_H026

source_name: Hep3B control


title: Hep3B_CHRNA9_knockdown-1_rep2

description:
CHRNA9 knockdown-1 in Hep3B cell line, replicate 2
S16_H028


title: Metastasis RCC -17

description:
Sample31
7927538061_H


title: Metastasis RCC -16

description:
Sample30
7927538061_G


title: 21_70S_UV_NAZ_tgirt_Trunc

data_processing:
Library strategy: MaP-seq
adaptor removed with skewer
Reads mapped and mutations counted with ShapeMapper 2.0
RT stops mapped with STAR
Genome_build: E.coli rRNA operons B or H
Genome_build: H. sapiens rRNA
Genome_build: S. cerevisiae rRNA
Supplementary_files_format_and_content: tab-seperated text file of mutation rates (#mutations/coverage), a proxy for extent of modification, for each nucleotide in each dataset.
Supplementary_files_format_and_content: tab-seperated text file of number of RT stops at each position, a proxy for extent of modification, for each nucleotide in each dataset.

tag: probe

tag: probe concentration


title: GM18510_PRO-cap

description: Capped nascent RNA


title: 20_70S_UV_tgirt_Trunc

tag: treatment time


title: GM18861_PRO-cap

description: Capped nascent RNA


title: 17_70S_EFG_GDPNP_UV_NAZ_SSII_Trunc


title: GM18486_PRO-cap

description: Capped nascent RNA


title: Hep3B_control_rep1

description:
Control (no knockdown) - Hep3B cell line, replicate 1
S13_H025


title: Primary RCC-9

description:
Sample38
7927538065_E


title: 16_70S_EFG_UV_NAZ_SSII_Trunc


title: GM18507_PRO-cap

description: Capped nascent RNA


title: GM18852_PRO-cap

description: Capped nascent RNA


title: Metastasis RCC -15

description:
Sample29
7927538061_F


title: 14_70S_UV_SSII_Trunc


title: 15_70S_UV_NAZ_SSII_Trunc


title: GM18499_PRO-cap

description: Capped nascent RNA


title: GM18502_PRO-cap

description: Capped nascent RNA


title: Metastasis RCC -14

description:
Sample28
7927538061_E


title: Normal-7

description:
Sample27
7927538061_D

source_name: Human tissue


title: 19_70S_None_tgirt_Trunc


title: A549_SLC16A7_knockdown_rep2

description:
SLC16A7 knockdown in A549 cell line, replicate 2
S12_H024

source_name: A549 SLC16A7 knockdown


title: 13_70S_None_SSII_Trunc

source_name: Purified Ribosomes


title: Primary RCC-7

description:
Sample26
7927538061_C


title: 11_70S_EFG_GDPNP_UV_NAZ_tgirt_FL


title: A549_SLC16A7_knockdown_rep1

description:
SLC16A7 knockdown in A549 cell line, replicate 1
S12_H023


title: Metastasis RCC -13

description:
Sample23
7927538040_L


title: 10_70S_EFG_UV_NAZ_tgirt_FL


title: GM19238_PRO-cap

description: Capped nascent RNA


title: A549_control_rep1

description:
Control (no knockdown) - A549 cell line, replicate 1
S07_H019

source_name: A549 control


title: A549_CHRNA9_knockdown_rep2

description:
CHRNA9 knockdown in A549 cell line, replicate 2
S09_H022

source_name: A549 CHRNA9 knockdown


title: Normal-6

description:
Sample25
7927538061_B


title: Primary RCC-6

description:
Sample24
7927538061_A


title: A549_control_rep2

description:
Control (no knockdown) - A549 cell line, replicate 2
S07_H020


title: GM19131_PRO-cap

description: Capped nascent RNA


title: 9_70S_UV_NAZ_tgirt_FL


title: GM18517_PRO-cap

description: Capped nascent RNA


title: 8_70S_UV_tgirt_FL


title: A549_CHRNA9_knockdown_rep1

description:
CHRNA9 knockdown in A549 cell line, replicate 1
S09_H021


title: GM19193_PRO-cap

description: Capped nascent RNA


title: MDA-MB-231_SLC16A7_knockdown_rep1

description:
SLC16A7 knockdown in MDA-MB-231 cell line, replicate 1
S06_H017

source_name: MDA-MB-231 SLC16A7 knockdown


title: GM19222_PRO-cap

description: Capped nascent RNA


title: Metastasis RCC -11

description:
Sample21
7927538040_J


title: MDA-MB-231_SLC16A7_knockdown_rep2

description:
SLC16A7 knockdown in MDA-MB-231 cell line, replicate 2
S06_H018


title: Metastasis RCC -12

description:
Sample22
7927538040_K


title: MDA-MB-231_CHRNA9_knockdown_rep1

description:
CHRNA9 knockdown in MDA-MB-231 cell line, replicate 1
S05_H015

source_name: MDA-MB-231 CHRNA9 knockdown


title: MDA-MB-231_CHRNA9_knockdown_rep2

description:
CHRNA9 knockdown in MDA-MB-231 cell line, replicate 2
S05_H016


title: Metastasis RCC -9

description:
Sample19
7927538040_H


title: 7_70S_None_tgirt_FL

description:
e_coli_laser_raw_mutation_fractions.tsv
e_coli_laser_raw_mutation_counts.tsv


title: MDA-MB-231_control_rep1

description:
Control (no knockdown) - MDA-MB-231 cell line, replicate 1
S03_H013

source_name: MDA-MB-231 control


title: Metastasis RCC -10

description:
Sample20
7927538040_I


title: GM18522_PRO-cap

description: Capped nascent RNA


title: Metastasis RCC -8

description:
Sample18
7927538040_G


title: 5_70S_EFG_GDPNP_UV_NAZ_SSII_FL


title: 4_70S_EFG_UV_NAZ_SSII_FL


title: GM18520_PRO-cap

description: Capped nascent RNA


title: GM19099_PRO-cap

description: Capped nascent RNA


title: 3_70S_UV_NAZ_SSII_FL


title: GM18505_PRO-cap

description: Capped nascent RNA


title: GM19239_PRO-cap

description: Capped nascent RNA


title: 2_70S_UV_SSII_FL


title: 1_70S_None_SSII_FL


title: MDA-MB-231_control_rep2

description:
Control (no knockdown) - MDA-MB-231 cell line, replicate 2
S03_H014


title: Normal-4

description:
Sample14
7927538040_C


title: Metastasis RCC -7

description:
Sample13
7927538040_B


title: Primary RCC-5

description:
Sample16
7927538040_E


title: lung fibroblast_IL1B_4

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

data_processing:
Paired end reads were aligned to the human reference genome (hg38) using Hisat2 (version 2.0.4) using the following command line options: hisat2 -q --dta --rna-strandness FR –x <reference-genone.gtf> -1 <forward_strand.fa> -2 <reverse-strand file.fa> –S <output.sam>.
Output SAM files were then sorted and converted to BAM files (samtools sort -@ 8 –o output.bam output.sam) and indexed (samtools index –b output.bam) in Samtools
The profile of gene expression (using the Gencode v27 database and additional novel lncRNA ( (Roux BT et al Front Immunol 8, 1038 (2017)) in the BAM files for each samples were determined using Stringtie: stringtie <sample.BAM> -G <GenCodev26.gtf> -o <samples.gtf> -e -A <sample.txt>.
Differential expression of gene derived from Gencode v27 and our recently generated list of novel lncRNA implicated in the innate immune (Roux BT et al Front Immunol 8, 1038 (2017)) was assessed with the geometric option in Cuffdiff v2.2.1.3 using a significance threshold of q <0.05. The command line options were as follows: cuffdiff --FDR=0.05 --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled -u <reference_genome.gtf> <control_1.bam>,<control_x.bam> <activated_1.bam>,<activated_x.bam> -o <output_file_name>
Genome_build: hg38
Supplementary_files_format_and_content: TXT

source_name: lung fibroblast_IL-1β

growth_protocol: Control lung fibroblasts (5 x 10^5 cells) were seeded in 6 cell culture well plates (Corning Costar) on day 1 and left overnight

extract_protocol:
For all samples, total RNA was extracted using the RNeasy kit (Qiagen), included an on-column DNase treatment (Qiagen), according to the manufacturer’s guideline. RNA concentration was determined using the Qubit 2.0 (Life Technologies). RNA quality was measured using the Agilent Bioanalyzer and produced RIN values of >8.0.
Illumina TruSeq mRNA stranded RNA library

treatment_protocol: On day 2, the cells were serum-starved with 2 ml of fresh medium (0.1% FBS) and treated with/without 3 ng/ml IL-1β (recombinant, expressed in E. coli, Sigma-Aldrich, I9401-5UG) for 6 hrs before all supernatants were collected and cells were harvested for RNA extraction.

value: Human Lung Fibroblasts

value: 3 ng/ml of IL-1b for 6h


title: lung fibroblast_IL1B_3


title: Metastasis RCC -5

description:
Sample11
7927538015_K

value: Metastatic ccRCC tissue


title: lung fibroblast_IL1B_2


title: lung fibroblast_IL1B_1


title: Normal-5

description:
Sample17
7927538040_F

value: Normal renal tissue


title: lung fibroblast_control_4

source_name: lung fibroblast_control

value: buffer (control)


title: lung fibroblast_control_3


title: lung fibroblast_control_2


title: 10_70S_0.25uM onc112_UV_NAz

description:
rRNA
e_coli_batch2_laser_raw_mutation_fractions.tsv
e_coli_batch2_laser_raw_mutation_counts.tsv

value: UV+Naz

value: 3 minutes


title: Metastasis RCC -2

description:
Sample8
7927538015_H


title: Metastasis RCC -1

description:
Sample7
7927538015_G


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4657-5L-ILC]

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

hyb_protocol: Overnight hybridization to agilent microarray- G4862A.

scan_protocol: Microarrays were scanned on a Agilent microarray scanner and analyzed using Agilent feature extraction software.

data_processing: Gene expression was calculated as log2 Cy5/Cy3 ratios, keeping only probes with Lowess normalized intensity values greater than 10 in both Cy5 and Cy3 channels.

source_name: Mouse Ref cRNA 2ug

label_protocol: Total RNA was labeled with cyanine-5 (Cy5) dye for tumor samples and cyanine-3 (Cy3) dye for mouse reference samples 51 using the Agilent Low RNA Input Fluorescent Linear Amplification Kit. For both mouse reference RNA and tumor RNA, 2ug of labeled RNA was co-hybridized overnight to Agilent microarrays (platform G4862A).

growth_protocol: Transgenic mouse model

extract_protocol: Tumors frozen in RNAlater (Qiagen 76106) were thawed and homogenized by Qiagen TissueRupter (Qiagen 9001271). RNA was extracted using Qiagen RNeasy mini kit (Qiagen 74104). RNA quantification was determined using the Nanodrop spectrophotometer and RNA quality for microarray was determined using the Agilent Bioanalyzer.

treatment_protocol: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre mice were monitored for tumor progression.

tag: reference

value: total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups.

source_name: B4657-5L-ILC tumor cRNA 2ug.

value: Mammary tumor


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4894-5L-ILC]

source_name: B4894-5L-ILC tumor cRNA 2ug.


title: Primary RCC-3

description:
Sample6
7927538015_F


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4540-5L-ILC]

source_name: B4540-5L-ILC tumor cRNA 2ug.


title: Primary RCC-4

description:
Sample15
7927538040_D


title: Metastasis RCC -3

description:
Sample9
7927538015_I


title: Normal-2

description:
Sample4
7927538015_D


title: Normal-3

description:
Sample5
7927538015_E


title: lung fibroblast_control_1


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4538-3L-ILC]

source_name: B4538-3L-ILC tumor cRNA 2ug.


title: Metastasis RCC -6

description:
Sample12
7927538015_L

source_name: Human tumor


title: Metastasis RCC -4

description:
Sample10
7927538015_J


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4894-5R-ILC]

source_name: B4894-5R-ILC tumor cRNA 2ug.


title: 10.3 weeks_2

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_1133

source_name: lung

tag: Stage

value: fetal

tag: developmental stage

value: 10.3 weeks


title: 10.3 weeks_1

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_1118


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4713-5L-ILC]

source_name: B4713-5L-ILC tumor cRNA 2ug.


title: Primary RCC-2

description:
Sample3
7927538015_C


title: control 3

city: Shanghai

first: Wei

last: Zheng

address: 600 Yishan Road

department: department of Orthopedics

institute: Shanghai Jiao Tong University

description:
normal tendon tissues
3

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: UCSChg19
Supplementary_files_format_and_content: excel format with FPKM

source_name: tendon tissues

extract_protocol:
tendon tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Standard Total RNA Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: normal tendon tissues

value: tendon


title: biofilm state co-cultured with channel catfish mucus biological rep2

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description:
B2M
Fcol_counts_data.txt

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using the Trim Galore! software version 0.4.4. This software was used to trim low-quality ends from reads in addition to Illumina adapter removal.
The STAR RNA-seq Aligner version 2.5.3a was used for alignment of reads to the Flavobacterium columnare 94-081 genome coding sequences (CDS) after the genome was annotated by RAST. The options --quantMode and --twopassMode were employed.
Strand-specific read counts and FPKM information output from the STAR aligner were collected.
Read counts were used to calculate fold-change using the DESeq2 package version 1.18.1 in R-Bioconductor Release 3.4.2.
Genome_build: The Flavobacterium columnare transcriptome CDS sequences re-annotated by RAST from the 94-081 isolate.
Supplementary_files_format_and_content: matrix table of read counts in tab-delimited format

organism: Flavobacterium columnare

source_name: bacterial culture

extract_protocol:
Bacterial cells were harvested and stored in RNAprotect Bacteria Reagent (Qiagen) at -80°C until usage. Total RNA was extracted from each sample by enzymatic lysis and proteinase K digestion using the RNeasy Mini Kit (Qiagen) according to the supplied protocol.
DNA was removed from total RNA using Amplification-grade DNase I from Invitrogen.Total RNA was standardized to 5 µg each sample and then ribosomal RNAs (rRNA) were reduced using the Ribo-Zero Gold rRNA Removal Kit (bacteria) from Illumina. Sequencing libraries were then sent to a service provider (Novogene, Chula Vista, CA) for library preparation, where the provider created strand-specific libraries via the NEBNext Ultra Directional RNA Library Prep Kit from New England Biolabs. NEBNext Multiplex Oligos for Illumina were used as index primers.

tag: isolate

tag: time

tag: state

value: biofilm

tag: treatment

value: co-cultured with channel catfish mucus


title: 10.3 weeks_3

description:
excised piece of human fetal lung samples containing proximal and distal compartments
07Jun17_DA_filtered_annotated_RPKM.txt
processed data file header: DA_1383


title: Primary RCC-1

description:
Sample1
7927538015_A

tag: tissue


title: control 2

description:
normal tendon tissues
C2


title: biofilm state co-cultured with channel catfish mucus biological rep1

description:
B1M
Fcol_counts_data.txt


title: biofilm state co-cultured with channel catfish mucus biological rep3

description:
B3M
Fcol_counts_data.txt


title: planktonic state co-cultured with channel catfish mucus biological rep3

description:
P3M
Fcol_counts_data.txt

value: planktonic


title: control 1

description:
normal tendon tissues
C1-1


title: planktonic state co-cultured with channel catfish mucus biological rep2

description:
P2M
Fcol_counts_data.txt


title: peritendinous fibrosis 2

description:
2-3 weeks after innitial tendon injury
XJB

value: 2-3 weeks after initial tendon injury


title: peritendinous fibrosis 1

description:
2-3 weeks after innitial tendon injury
WLN


title: Normal-1

description:
Sample2
7927538015_B

source_name: Human tissue

value: Benign tissue


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4532-4R-ILC]

source_name: B4532-4R-ILC tumor cRNA 2ug.


title: planktonic state co-cultured with channel catfish mucus biological rep1

description:
P1M
Fcol_counts_data.txt


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4513-5R-ILC]

source_name: B4513-5R-ILC tumor cRNA 2ug.


title: Cdh1loxP/loxP;R26-LSL-Pik3caH1047R;Wap-Cre [B4535-1R-ILC]

source_name: B4535-1R-ILC tumor cRNA 2ug.


title: biofilm state biological rep3

description:
B3
Fcol_counts_data.txt

value: control


title: biofilm state biological rep2

description:
B2
Fcol_counts_data.txt


title: biofilm state biological rep1

description:
B1
Fcol_counts_data.txt


title: RNAseq_PnM_rep3

city: Cambridge

first: Anton

last: Goloborodko

state: Massachusetts

address: 77 Massachusetts Ave., E25-524

department: Physics

institute: MIT

data_processing:
Mapping Hi-C data: using the standard mode of seqtk trimfq v.1.2-r94, we trimmed low-quality base pairs at both ends of each side of sequenced of Hi-C molecules. This was followed by mapping the trimmed sequences using bwa mem v.0.7.15 with flags -SP.
Making Hi-C pairs: we used the pairtools parse command line tool (https://github.com/mirnylab/pairtools), to extract the coordinates of Hi-C contacts, kept read pairs that mapped uniquely to one of the two homologs, and used the standard mode of the pairtools dedup command line tool to remove PCR duplicates.
Mapping RNA-seq data: We mapped the raw RNA-seq data using STAR following the same procedure as used by the ENCODE consortium (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/tree/master/dnanexus). The uniquely mapped alignments were then aggregated into bigWig files for the plus and minus strands of the genome separately.
Genome_build: dm3
Supplementary_files_format_and_content: pairs: a tab separated file containing the coordinates of Hi-C contacts (https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md)

organism: Drosophila melanogaster

growth_protocol: Hybrid PatnMat (PnM) cells were cultured as clone8 cells with supplemented M3 media (supplemented M3 media (M3 Insect Media, 10% Fetal Bovine Serum (JRH), 2.5% Fly Extract (DGRC), 0.5 mg/ml Insulin (Sigma), 1:100 Pen-Strep (Gibco)), according to standard protocols at 25C in small culture dishes (100x 20 mm), with the following modifications: the cells were trypsinized and split at 1:5, or 1:10 every other day, and the media was replaced every day after they are washed with 1X PBS. Prior to any experiment, to ensure the cells were in log phase, the cells were split 12-18 hrs earlier.

extract_protocol:
Hi-C: This protocol was adapted from a previously published protocol (Rao et.al., Cell, 2014) with modifications. Unless otherwise specified, 75T flasks of PnM cells were cultured to 70% confluency, then washed with FBS-free Schneider's medium, and then crosslinked with 1% formaldehyde for 10 min at room temperature. Fixation was quenched with 1M glycine solution, and the cells were scraped gently off the flask, spun down at 1200 rpm, and washed once more with 1X PBS. Supernatant was removed, and cells were resuspended in 1x PBS and then counted 2.5 million cells to be used for the protocol. Nuclei were permeabilized with ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0. 2% Igepal supplemented with 5x Complete, EDTA-free Protease inhibitors (Roche). DNA was digested with 500 units of DpnII, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~700 bp with QSonica sonicator (30% power, 30 sec on, 30 off for 20 minutes, at which point ligation junctions were pulled down with Dynabeads MyOne Streptavidin beads (Invitrogen) and prepped for Illumina sequencing. Aliquots at different steps were taken to measure the concentration with Qubit dsDNA HS assay kit, and run on a 2% agarose gel with SYBR Gold nucleic acid gel stain (1:10000) to ensure quality control of the sample prepared, and to ensure efficient digest, ligation, and binding to beads.    RNA-seq: Total PnM RNA was purified from around 8 million cells per replicate using TRIzol (Life Technologies), followed by chloroform extraction, DNase treatment with RNase free DNase I recombinant (Roche), and clean up with RNeasy Mini kit (Qiagen). The quality of total RNA was determined using Agilent RNA 6000 Pico assay on a 2100 Bioanalyzer system (Agilent Technologies).
Hi-C: we used BioNEXTFLEX adaptors (Bioo Scientific) and followed manufacturer recommendations, and amplified our final library with Q5 HIFI Hot Start High Fidelity PCR and Biooscientific primer mix for 6 cycles on the beads. The final product was then diluted to 250 ul with 1 mM Tris-HCl, and separated on a magnet then transferred the supernatant to a new tube and purified with 0.7X AMPure XP bead (Beckman Coulter #A63880). Incubation times are extended to 15 minutes to maximize library recovery. To remove traces of short products, we resuspend beads in 100μl of 1X Tris buffer and add another 70μl of AMPure XP beads. Mix by pipetting 20x and incubated at room temperature for 15 min, and separated for another 15 min, and continue with the washes and drying as previously. Once the beads are dry we resuspended in 20 uL 1X Tris-HCl, incubated for 15 min, then separated for another 15 min on the magnet and transferred the final library to a fresh tube. Two replicates were prepared per sample. The library quality was assessed using the High Sensitivity DNA assay on a 2100 Bioanalyzer system (Agilent Technologies).     RNA-seq: RNA-Seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions. Poly(A)+ RNA was enriched from 1 ug of total RNA, fragmented for 10 min at 94C, and reverse transcribed in the first strand cDNA synthesis with random primers. After adaptor ligation, cDNA was size selected between 400-600 bp with Agencourt AMPure XP beads, and amplified for 12 PCR cycles. The library quality was assessed using the High Sensitivity DNA assay on a 2100 Bioanalyzer system (Agilent Technologies).

treatment_protocol: In the RNAi experiments, the synthesis of dsRNA was carried out according to standard protocols (see www.flyrnai.org for more details). Control cells were treated with blank dionized water. The dsRNA was administered to the cells using a calcium phosphate transfection kit (Invitrogen) in 60-mm well plates. PnM cells were seeded at 1e6/ml and treated with 30 ug dsRNA on the first and third day, and then harvested on the fourth. Cells from the knockdowns were counted and an aliquot was taken for RNA isolation, and once knockdown of mRNA was confirmed cells were split to be fixed for Hi-C, and for FISH.

tag: cell line

value: PnM

tag: RNAi

value: n/a (WT)

tag: replicate

tag: molecule subtype

value: rRNA-depleted RNA


title: planktonic state biological rep3

description:
P3
Fcol_counts_data.txt


title: RNAseq_PnM_rep2


title: planktonic state biological rep2

description:
P2
Fcol_counts_data.txt


title: peritendinous fibrosis 3

description:
2-3 weeks after innitial tendon injury
210


title: RNAseq_PnM_rep1


title: RNAseq_PnM_rep4


title: planktonic state biological rep1

description:
P1
Fcol_counts_data.txt


title: HiC_PnM_top2_rep2

library_source: genomic

value: Top2 RNAi


title: HiC_PnM_top2_rep1