title: c-JunΔLysM 1

city: Erlangen

first: Aline

last: Bozec

address: Ulmenweg 18

institute: Universitätsklinikum Erlangen, Department of Internal Medicine 3 – Rheumatology and Immunology

hyb_protocol: following fragmentation, 600ng of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 8x60K Agilent Mouse Gene Expression_v2 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.6.6)

scan_protocol: Microarrays were scanned using Agilent G2565C Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.7.1 (Agilent Technologies Germany). Data extraction using protocol GE1_1105_Oct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR). Entities differentially expressed mean an at least 2-fold change in expression level in all c-JunΔMx compared to wild-type macrophages were further analysed.

source_name: peritoneal macrophages from c-JunΔMx mice 1

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 50ng total RNA (One-Color Microarray-based gene expression analysis v.6.65)

growth_protocol: The mice were bred and maintained on a 129/C57Bl6 background. Littermate mice were used as wild-type controls. All experiments were performed with male or female mice at the age of 8 weeks. Animals were housed in standardized conditions following the guidelines of the German Animal Welfare Act. Animals were kept in a standard diet and water ad libitum and kept with a 12 hour day/night cycle. All experiments with animals are authorized by the local ethics committee.

extract_protocol: RNeasy Mini Kit, Cat no 74104, Qiagen

tag: genotype

value: cJunfl/fl LysMCre-/+

value: peritoneal macrophages


title: MSA103_F21_methylbenzethonium chloride 8.6_uM 6_hours 2476-D1-2

status: Public on Oct 31 2018

type: RNA

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

country: USA

institute: ASU-Banner Neurodegenerative Disease Research Center

description: 24 hiPSC-derived NPCs and 8 CCLs were used (total: 32 cell lines). Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: a) phase 1 had 6/79 drugs from pilot, and 73/79 phase 1 test compounds, b) phase 2 had 6 pilot drugs re-tested, 6/73 phase 1 drugs re-tested, and 67/79 phase 2 compounds. 135 unique compounds were tested.

hyb_protocol: PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.

scan_protocol: Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead

data_processing: Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.

extract_protocol: Cells were lysed with cell lysis buffer (110 µL per well), and stored at -80⁰C

tag: perturbagen

value: methylbenzethonium chloride

tag: cell id

tag: dosage

tag: batch

tag: duration

tag: perturbation type

value: test

tag: well id

tag: plate id


title: MSA103_F20_anisomycin 10_uM 6_hours 690-2-1

value: anisomycin


title: MSA103_F18_DMSO NA 6_hours 690-2-1

value: DMSO

value: vehicle


title: WT Round

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

country: Japan

institute: Kyoto University

hyb_protocol: The labeled cRNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner 3000 7G.

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. Normakisation and data analyses were performed by using Affymetrix GeneChip Command Console Software 6.

organism: Mus musculus

source_name: Round chondrocytes, WT mice cartilage

label_protocol: cRNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cRNA.

tag: cell type

value: Round chondrocytes

tag: strain

tag: tissue

value: cartilage

tag: developmental stage

value: E17.5 embryo


title: whole_larva_esfenvalerate_0ug/L_rep4 [229_2_1]

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of esfenvalerate

hyb_protocol: Individual samples were hybridized onto separate Agilent microarrays, where eight arrays were printed onto a single glass slide. Placement of each treatment within and between slides was balanced as much as possible, given the number of arrays per slide and number of replicates per condition. Samples were fragmented and mixed with a blocking agent per recommended protocols, then quickly added onto the microarrays. Microarrays were hybridized at 65° C for 17 hours with constant rotation, disassembled in Wash Buffer 1, washed in Wash Buffer 1 for one minute, then transferred to Wash Buffer 2 at 65° C for 1 minute, 100% acetonitrile for 10 s, followed by drying and stabilization solution for 30 s.

scan_protocol: Slides were covered with an ozone-barrier slide and scanned in an Agilent C scanner with the following settings: Dye channel: G; scan resolution: 3 µm; TIFF file dynamic range: 20 bit; green PMI gain: 100%. TIFF images were uploaded to the Agilent Feature Extraction program and extracted data were used in downstream analysis.

data_processing: Probe intensities (median foreground spot intensity without background subtraction) from each hybridization were quantile normalized, and probeset intensities for individual hybridizations were calculated as the median (within an array) intensity of the replicated probes constituting that probeset. Probeset intensities were then log-base2 transformed.

organism: Pimephales promelas

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 4

label_protocol: Samples were processed according to the Agilent One-color Microarray-Based Gene Expression Analysis protocols (Agilent Technologies, Santa Clara, CA). Isolated total RNA was diluted to 100 ng/µL for labeling. , combined with RNA Spike-in controls and converted to cDNA using Affinity Script Reverse Transcriptase.  cDNA was then converted to cRNA with the inclusion of Cyanine-3 (Cy-3) labeled-CTP.  Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and cRNA was eluted twice in a total of 70 µL warm water. Yield and specific activity of purified labeled cRNA were evaluated using the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop, Wilmington, DE) using the microarray measurement package. Samples with yields <0.825 µg or specific activity <6 pmol Cy3 per µg cRNA were excluded from further analysis. In these cases, an alternative sample was selected for analysis; however, when none were available, failed samples were re-labeled.

growth_protocol: Fathead minnow were raised indoors in labline water. Labline water was produced by passing tempered tap water through a set of activated carbon filters, for the removal of chlorine and organics, and then adding liquid calcium chloride to supplement the hardness. Fish were maintained at 20-25 degC, pH 7.0 to 8.0. dissolved oxygen between 6 and 9 mg/L, and conductivity of 510-660 uS. Fish were fed a mixture of high-protein fin-fish starter food (0.6-0.85 um crumb size) and brine shrimp nauplii. At the start of exposures, fathead larvae were about 48 hours post-hatch.

extract_protocol: Following  48-hour exposure, RNA was isolated separately from 10 pairs of whole larval fish exposed to each of (nominally) two pyrethroid concentrations (Table 1), and DMSO carrier added to water. RNA was isolated using the RiboPure kit (Ambion, Austin, TX) according to the manufacturer’s protocol. RNA was eluted in 60 µL. Following RNA isolation, DNA contamination was removed using Turbo DNA-free (Ambion) according to the manufacturer’s protocol. RNA was concentrated through ethanol precipitation, and integrity was assessed using denaturing gel electrophoresis.

treatment_protocol: 48-hour flow-through exposures were conducted in 10 L tanks, each renewed with exposure media (from continuous mixing of lab water and concentrated pyrethroid stock solution) at a rate of 40 mL/min. The system was pre-equilibrated under flow-through conditions with their respective chemicals nominally at their target concentrations for 24 hours prior to introducing test organisms. Five adult (ranging from six to ten months old) male fathead minnows (FHM; Pimephales promelas) were placed in each tank, as were an exposure vessel containing 10 larval (48 hours post hatch) FHM. The exposure vessels consisted of a three-inch section of 1.5 inch diameter PVC pipe covered on both ends with 400 µm Nitrex mesh. Four exposure experiments were conducted at least one week apart. Each experiment included eight nominal concentrations of a single pyrethroid, and a carrier solvent control (0.002% DMSO; used for the carrier control and as a carrier for pyrethroids, which have very low water solubility). Successive nominal concentrations, targeted to be half the next highest concentration, were achieved by serial dilution. Three replicate tanks were used for each concentration, and chemical concentrations of each tank were measured daily. Tank location in the diluter apparatus was balanced with respect to concentration to minimize location effects. Test organisms were randomly assigned to tanks. Between experiments, water supply lines were replaced, tanks were rinsed with 0.01% DMSO solution overnight, followed by 100% methanol and 24-hour water rinses. Tanks were subsequently scrubbed and rinsed with DMSO and tap water.

value: whole larva

tag: age

value: 48 hours post-hatch

tag: chemical

value: esfenvalerate

value: larva


title: wild-type 14

country: Germany

source_name: peritoneal macrophages from wild-type mice 4

value: wild-type


title: MSA103_F17_DMSO NA 6_hours 2476-D1-2


title: whole_larva_esfenvalerate_0ug/L_rep2 [224_1_3]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 2


title: whole_larva_esfenvalerate_0ug/L_rep1 [222_1_3]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 1


title: wild-type 5

source_name: peritoneal macrophages from wild-type mice 1


title: MSA103_F16_tyloxapol 4_uM 6_hours 690-2-1

value: tyloxapol


title: MSA103_F15_tyloxapol 4_uM 6_hours 2476-D1-2


title: MSA103_G06_melatonin 1_uM 6_hours 1835-1-5

value: melatonin


title: c-JunΔLysM 9

source_name: peritoneal macrophages from c-JunΔMx mice 2

value: cJunfl/fl LysMCre-/+


title: whole_larva_esfenvalerate_0ug/L_rep3 [223_2_2]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 3


title: MSA103_F12_DMSO NA 6_hours 690-2-1


title: MSA103_F13_diphemanil metilsulfate 10_uM 6_hours 2476-D1-2

value: diphemanil metilsulfate


title: MSA103_F14_diphemanil metilsulfate 10_uM 6_hours 690-2-1


title: MSA103_F10_nordihydroguaiaretic acid 1_uM 6_hours 690-2-1

value: nordihydroguaiaretic acid


title: whole_larva_cypermethrin_1ug/L_rep9 [220_2_2]

description: Whole body gene expression after exposure of fathead larvae to 1 ug/L of cypermethrin

source_name: whole larva, cypermethrin, 1 ug/L, replicate 9

value: cypermethrin


title: NeptuneCTOTProgressUrineB37A7

type: SRA

city: Ann Arbor

first: Markus

last: Bitzer

state: MI

address: 1500 E Medical Center Dr SPC 5361

institute: University of Michigan

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with 3' adapter sequences corresponding to the "3' adapter sequence" characteristic. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Urine

extract_protocol:
rna isolation kit: 450 ul biofluid sample were mixed with 105 ul buffer P, digested with 28 ul Proteinase K working solution at 65C for 8 minutes, extracted with 517 ul ED2 working solution, cooled to 10C, phase separation was induced after adding 110 ul chloroform, approx. 600 ul aqueous supernatants were mixed with 1200 ul buffer VB2G, loaded on Zymo-I 96-well silica matrix plate, washed twice with 970 ul EWL, once with 970 ul 100% ethanol, twice with 500 ul 80% ethanol and eluted into 20 ul TrisHCl pH 7.5. Protocol was executed on epMotion 5075 liquid handling system.
Low speed centrifugation (1200 g x 10 minutes) was used. A self-developed method and self-developed solutions were used for nucleic-acid extraction, nucleic-acid partitioning, and column purification (RNA isolation). 450 ul biofluid sample were mixed with 105 ul buffer P, digested with 28 ul Proteinase K working solution at 65C for 8 minutes, extracted with 517 ul ED2 working solution, cooled to 10C, phase separation was induced after adding 110 ul chloroform, approx. 600 ul aqueous supernatants were mixed with 1200 ul buffer VB2G, loaded on Zymo-I 96-well silica matrix plate, washed twice with 970 ul EWL, once with 970 ul 100% ethanol, twice with 500 ul 80% ethanol and eluted into 20 ul TrisHCl pH 7.5. Protocol was executed on epMotion 5075 liquid handling system. Use of two sets of spike-in calibrators added 1) prior to RNA isolation (set1), 2) at prior to cDNA library preparation (set2), to determine RNA quality and yield of miRNAs and other RNA molecules with 5P/3OH ends. Each set consists of 0.2 attomoles of ten individual 22-nt calibrators that do not map to the human genome. Calibrator sequences (labeled by set) are: >Set1_cali_01_rc TCCACGACGTCTCATGTATTTC, >Set1_cali_04_rc GGGTACCATACCGGTTGTCTTA, >Set1_cali_17_rc TCATGAGTCCGTACCTTGATTG, >Set1_cali_18_rc ATCATTTACGATTCGGAGCTGT, >Set1_cali_20_rc GATAGTTCGGGATCGCTGTAAC, >Set1_cali_24_rc TGCTACTCCGATCTTTAGCCTC, >Set1_cali_25_rc AGGGCCCTTTAGGCACTAATAG, >Set1_cali_27_rc GTAGCTGTCAGTACGTTCGTGC, >Set1_cali_43_rc TCTAGTTGCGTGATGGAGAGAA, >Set1_cali_44_rc AGCCGCATTTCGTAGTGATATT, >Set2_cali_07_rc GTCCCACTCCGTAGATCTGTTC, >Set2_cali_11_rc GATGTAACGAGTTGGAATGCAA, >Set2_cali_12_rc TAGCATATCGAGCCTGAGAACA, >Set2_cali_14_rc CATCGGTCGAACTTATGTGAAA, >Set2_cali_15_rc GAAGCACATTCGCACATCATAT, >Set2_cali_16_rc TCTTAACCCGGACCAGAAACTA, >Set2_cali_26_rc AGGTTCCGGATAAGTAAGAGCC, >Set2_cali_28_rc TAACTCCTTAAGCGAATCTCGC, >Set2_cali_31_rc AAAGTAGCATCCGAAATACGGA, >Set2_cali_35_rc TGATACGGATGTTATACGCAGC
No Kit was used. Multiplexed Small RNA library preparation protocol developed by Tuschl lab. Adenylated DNA adapters each containing a unique 5-nt barcode sequence were ligated to the 3end of the RNA overnight at 4C.The barcoded adapters allow 24 individual RNA samples to be pooled into one lane.The pooled samples were purified on a 15% polyacrylamide gel and size-selection was guided by radiolabeled RNA markers corresponding to a sRNA size of 19-30 nt. Next, a 26-nt RNA adapter compatible with Illumina sequencing was ligated to the 5end of the RNA at 37C for 1 hour and samples were purified on a 12% polyacrylamide gel.  The cDNA libraries were then generated by reverse transcription and amplified using up to 20 PCR cycles, and the final libraries ranging from 90-101 nt were purified on a 2.5% agarose gel and sequenced in a single Illumina HiSeq lane.

tag: condition

value: Nephrotic Syndrome

tag: anatomical location

value: Urinary system structure

tag: rna source

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: NeptuneCTOTProgressUrineB37A11

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: MSA103_F09_nordihydroguaiaretic acid 1_uM 6_hours 2476-D1-2

tag: perturbagen

tag: cell id

value: test


title: NeptuneCTOTProgressUrineB37A8

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: NeptuneCTOTProgressUrineB37A9

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_1ug/L_rep7 [222_1_4]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 7

value: whole larva

value: 48 hours post-hatch


title: MSA103_F07_bumetanide 10_uM 6_hours 2476-D1-2

value: bumetanide

tag: dosage

tag: batch


title: NeptuneCTOTProgressUrineB37A10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: wild-type 11

source_name: peritoneal macrophages from wild-type mice 2

tag: genotype

value: wild-type

value: peritoneal macrophages


title: whole_larva_cypermethrin_1ug/L_rep8 [221_1_2]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 8

value: larva


title: MSA103_F04_nefopam 1.38_uM 6_hours 690-2-1

value: nefopam

tag: duration

tag: perturbation type

tag: well id


title: whole_larva_cypermethrin_1ug/L_rep5 [234_1_1]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 5

value: cypermethrin


title: MSA103_F03_nefopam 1.38_uM 6_hours 2476-D1-2

tag: plate id


title: MSA103_F06_furosemide 10_uM 6_hours 690-2-1

value: furosemide


title: whole_larva_cypermethrin_1ug/L_rep4 [233_2_2]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 4

tag: tissue


title: NeptuneCTOTProgressUrineB37A6

value: Nephrotic Syndrome

value: Urinary system structure

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: MSA103_F08_bumetanide 10_uM 6_hours 690-2-1


title: NeptuneCTOTProgressUrineB37A4

value: total cell-free biofluid RNA

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: MSA103_F01_phenazone 1_uM 6_hours 2476-D1-2

value: phenazone

value: test


title: whole_larva_cypermethrin_1ug/L_rep6 [222_2_3]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 6

value: whole larva


title: NeptuneCTOTProgressUrineB37A3

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: MSA103_F02_phenazone 1_uM 6_hours 690-2-1


title: NeptuneCTOTProgressUrineB37A5

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_1ug/L_rep3 [232_1_2]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 3

value: 48 hours post-hatch


title: whole_larva_cypermethrin_1ug/L_rep2 [229_2_3]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 2


title: MSA103_E18_DMSO NA 6_hours 1835-1-5

value: DMSO

value: vehicle


title: MSA103_E19_anisomycin 10_uM 6_hours 3651-A-A

value: anisomycin


title: MSA103_E24_LY379268 0.1_uM 6_hours 1835-1-5


title: whole_larva_cypermethrin_1ug/L_rep1 [231_2_1]

source_name: whole larva, cypermethrin, 1 ug/L, replicate 1

value: larva


title: MSA103_E20_anisomycin 10_uM 6_hours 1835-1-5


title: MSA103_F05_furosemide 10_uM 6_hours 2476-D1-2


title: NeptuneCTOTProgressUrineB37A1

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: NeptuneCTOTProgressUrineB37A2

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: MSA103_E22_methylbenzethonium chloride 8.6_uM 6_hours 1835-1-5

value: methylbenzethonium chloride


title: whole_larva_cypermethrin_0.5ug/L_rep10 [227_1_1]

description: Whole body gene expression after exposure of fathead larvae to 0.5 ug/L of cypermethrin

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 10

value: cypermethrin


title: whole_larva_cypermethrin_0.5ug/L_rep9 [225_1_2]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 9


title: MSA103_E23_LY379268 0.1_uM 6_hours 3651-A-A


title: NeptuneUrineB36A24

value: Nephrotic Syndrome

value: Urinary system structure

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0.5ug/L_rep8 [226_2_1]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 8


title: NeptuneUrineB36A23

value: total cell-free biofluid RNA

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB36A22

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: MSA103_E21_methylbenzethonium chloride 8.6_uM 6_hours 3651-A-A

value: test


title: MSA103_E15_tyloxapol 4_uM 6_hours 3651-A-A

value: tyloxapol


title: MSA103_E14_diphemanil metilsulfate 10_uM 6_hours 1835-1-5

value: diphemanil metilsulfate


title: NeptuneUrineB36A21

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: MSA103_E13_diphemanil metilsulfate 10_uM 6_hours 3651-A-A


title: MSA103_E11_DMSO NA 6_hours 3651-A-A

value: DMSO

value: vehicle


title: whole_larva_cypermethrin_0.5ug/L_rep7 [221_2_3]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 7

value: whole larva

value: 48 hours post-hatch

value: larva


title: MSA103_E12_DMSO NA 6_hours 1835-1-5


title: NeptuneUrineB36A20

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: MSA103_E16_tyloxapol 4_uM 6_hours 1835-1-5


title: MSA103_E10_nordihydroguaiaretic acid 1_uM 6_hours 1835-1-5

value: nordihydroguaiaretic acid


title: whole_larva_cypermethrin_0.5ug/L_rep6 [224_2_1]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 6

value: cypermethrin


title: NeptuneUrineB36A19

value: Nephrotic Syndrome

value: Urinary system structure

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0.5ug/L_rep5 [223_1_1]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 5


title: whole_larva_cypermethrin_0.5ug/L_rep4 [222_2_1]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 4


title: MSA103_E09_nordihydroguaiaretic acid 1_uM 6_hours 3651-A-A


title: NeptuneUrineB36A18

source_name: Urine

value: total cell-free biofluid RNA

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: MSA103_E06_furosemide 10_uM 6_hours 1835-1-5

value: furosemide

value: test


title: MSA103_E05_furosemide 10_uM 6_hours 3651-A-A


title: NeptuneUrineB36A17

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0.5ug/L_rep2 [220_1_4]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 2


title: MSA103_E04_nefopam 1.38_uM 6_hours 1835-1-5

value: nefopam


title: NeptuneUrineB36A16

value: TTACATCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0.5ug/L_rep3 [233_1_3]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 3


title: NeptuneUrineB36A15

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0ug/L_rep9 [231_1_2]

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of cypermethrin

source_name: whole larva, cypermethrin, 0 ug/L, replicate 9

value: whole larva


title: MSA103_E02_phenazone 1_uM 6_hours 1835-1-5

value: phenazone


title: MSA103_E03_nefopam 1.38_uM 6_hours 3651-A-A


title: MSA103_E07_bumetanide 10_uM 6_hours 3651-A-A

value: bumetanide


title: MSA103_E01_phenazone 1_uM 6_hours 3651-A-A


title: MSA103_E08_bumetanide 10_uM 6_hours 1835-1-5


title: MSA103_D22_hydroquinine 1_uM 6_hours 690-2-1

value: hydroquinine


title: MSA103_D23_quinpirole 0.1_uM 6_hours 2476-D1-2

value: quinpirole


title: whole_larva_cypermethrin_0.5ug/L_rep1 [234_2_1]

source_name: whole larva, cypermethrin, 0.5 ug/L, replicate 1

value: 48 hours post-hatch

value: cypermethrin

value: larva


title: MSA103_D24_quinpirole 0.1_uM 6_hours 690-2-1


title: whole_larva_cypermethrin_0ug/L_rep8 [232_2_3]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 8


title: MSA103_D20_haloperidol 0.1_uM 6_hours 690-2-1

value: haloperidol


title: NeptuneUrineB36A12

value: Nephrotic Syndrome

value: Urinary system structure

value: total cell-free biofluid RNA

value: TAATATCGTATGCCGTCTTCTGCTTG


title: MSA103_D18_ethionamide 10_uM 6_hours 690-2-1

value: ethionamide

value: test


title: MSA103_D21_hydroquinine 1_uM 6_hours 2476-D1-2


title: MSA103_D19_haloperidol 0.1_uM 6_hours 2476-D1-2


title: NeptuneUrineB36A14

value: TATCATCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0ug/L_rep6 [229_1_2]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 6


title: MSA103_D17_ethionamide 10_uM 6_hours 2476-D1-2


title: whole_larva_cypermethrin_0ug/L_rep7 [227_2_1]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 7


title: whole_larva_cypermethrin_0ug/L_rep5 [226_1_4]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 5


title: NeptuneUrineB36A10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB36A9

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB36A11

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB36A8

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: MSA103_D12_BAS-012416453 10_uM 6_hours 690-2-1


title: MSA103_D14_tanespimycin NA 6_hours 690-2-1

value: tanespimycin

value: poscon


title: MSA103_D11_BAS-012416453 10_uM 6_hours 2476-D1-2


title: MSA103_D16_zardaverine 10_uM 6_hours 690-2-1

value: zardaverine


title: MSA103_D15_zardaverine 10_uM 6_hours 2476-D1-2


title: NeptuneUrineB36A7

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB36A6

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0ug/L_rep4 [230_2_3]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 4

value: whole larva

value: 48 hours post-hatch

value: cypermethrin

value: larva


title: MSA103_D09_DMSO NA 6_hours 2476-D1-2

value: DMSO

value: vehicle


title: MSA103_F11_DMSO NA 6_hours 2476-D1-2


title: NeptuneUrineB36A5

value: Nephrotic Syndrome

value: Urinary system structure

value: total cell-free biofluid RNA

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB36A4

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: MSA103_D08_Vorinostat 1_uM 6_hours 690-2-1

value: Vorinostat

value: test


title: MSA103_E17_DMSO NA 6_hours 3651-A-A


title: MSA103_D13_tanespimycin NA 6_hours 2476-D1-2

value: tanespimycin

value: poscon


title: NeptuneUrineB36A3

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: whole_larva_cypermethrin_0ug/L_rep3 [225_2_3]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 3


title: MSA103_D07_Vorinostat 1_uM 6_hours 2476-D1-2


title: MSA103_D05_DMSO NA 6_hours 2476-D1-2


title: MSA103_D04_alpha-ergocryptine 7_uM 6_hours 690-2-1

value: alpha-ergocryptine


title: MSA103_D06_DMSO NA 6_hours 690-2-1


title: whole_larva_cypermethrin_0ug/L_rep1 [223_2_1]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 1

value: whole larva


title: whole_larva_cypermethrin_0ug/L_rep2 [224_1_2]

source_name: whole larva, cypermethrin, 0 ug/L, replicate 2

value: 48 hours post-hatch


title: NeptuneUrineB36A2

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: whole_larva_bifenthrin_0.297ug/L_rep11 [220_1_3]

description: Whole body gene expression after exposure of fathead larvae to 0.297 ug/L of bifenthrin

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 11

value: bifenthrin

value: larva


title: NeptuneUrineB36A1

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: MSA103_D01_moxonidine 1_uM 6_hours 2476-D1-2

value: moxonidine


title: MSA103_D02_moxonidine 1_uM 6_hours 690-2-1


title: MSA103_D03_alpha-ergocryptine 7_uM 6_hours 2476-D1-2


title: MSA103_C22_hydroquinine 1_uM 6_hours 1835-1-5

value: hydroquinine


title: MSA103_C24_quinpirole 0.1_uM 6_hours 1835-1-5

value: quinpirole


title: MSA103_C23_quinpirole 0.1_uM 6_hours 3651-A-A


title: MSA103_C21_hydroquinine 1_uM 6_hours 3651-A-A


title: NeptuneUrineB35A24

value: Nephrotic Syndrome

value: Urinary system structure

value: total cell-free biofluid RNA

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: MSA103_D10_DMSO NA 6_hours 690-2-1

value: DMSO

value: vehicle


title: whole_larva_bifenthrin_0.297ug/L_rep10 [221_2_4]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 10


title: whole_larva_bifenthrin_0.297ug/L_rep9 [222_1_1]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 9


title: MSA103_C20_haloperidol 0.1_uM 6_hours 1835-1-5

value: haloperidol

value: test


title: MSA103_C18_ethionamide 10_uM 6_hours 1835-1-5

value: ethionamide


title: MSA103_C19_haloperidol 0.1_uM 6_hours 3651-A-A


title: MSA103_C17_ethionamide 10_uM 6_hours 3651-A-A


title: NeptuneUrineB35A23

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: whole_larva_bifenthrin_0.297ug/L_rep6 [234_2_3]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 6

value: whole larva

value: 48 hours post-hatch


title: whole_larva_bifenthrin_0.297ug/L_rep8 [232_2_2]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 8

value: bifenthrin

value: larva


title: NeptuneUrineB35A22

source_name: Urine

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: whole_larva_bifenthrin_0.297ug/L_rep5 [230_2_2]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 5


title: whole_larva_bifenthrin_0.297ug/L_rep7 [231_1_1]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 7


title: NeptuneUrineB35A21

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A20

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A19

value: Nephrotic Syndrome

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: MSA103_C15_zardaverine 10_uM 6_hours 3651-A-A

value: zardaverine


title: MSA103_C14_tanespimycin NA 6_hours 1835-1-5

value: tanespimycin

value: poscon


title: MSA103_C12_BAS-012416453 10_uM 6_hours 1835-1-5


title: NeptuneUrineB35A18

value: Urinary system structure

value: total cell-free biofluid RNA

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: MSA103_C10_DMSO NA 6_hours 1835-1-5

value: DMSO

value: vehicle


title: NeptuneUrineB35A17

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: MSA103_C09_DMSO NA 6_hours 3651-A-A


title: MSA103_C13_tanespimycin NA 6_hours 3651-A-A


title: MSA103_C11_BAS-012416453 10_uM 6_hours 3651-A-A

value: test


title: MSA103_C16_zardaverine 10_uM 6_hours 1835-1-5


title: whole_larva_bifenthrin_0.297ug/L_rep4 [227_2_3]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 4

value: whole larva

value: 48 hours post-hatch

value: bifenthrin


title: MSA103_C08_Vorinostat 1_uM 6_hours 1835-1-5

value: Vorinostat


title: whole_larva_bifenthrin_0.297ug/L_rep2 [229_1_3]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 2

value: larva


title: MSA103_C06_DMSO NA 6_hours 1835-1-5


title: whole_larva_bifenthrin_0.148ug/L_rep11 [225_2_4]

description: Whole body gene expression after exposure of fathead larvae to 0.148 ug/L of bifenthrin

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 11


title: MSA103_C04_alpha-ergocryptine 7_uM 6_hours 1835-1-5

value: alpha-ergocryptine


title: MSA103_C05_DMSO NA 6_hours 3651-A-A


title: whole_larva_bifenthrin_0.297ug/L_rep1 [226_1_3]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 1


title: NeptuneUrineB35A16

value: Nephrotic Syndrome

value: TTACATCGTATGCCGTCTTCTGCTTG


title: MSA103_C03_alpha-ergocryptine 7_uM 6_hours 3651-A-A


title: MSA103_C07_Vorinostat 1_uM 6_hours 3651-A-A


title: whole_larva_bifenthrin_0.148ug/L_rep10 [223_2_3]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 10


title: NeptuneUrineB35A12

value: TAATATCGTATGCCGTCTTCTGCTTG


title: whole_larva_bifenthrin_0.148ug/L_rep8 [224_1_4]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 8


title: NeptuneUrineB35A15

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: MSA103_C02_moxonidine 1_uM 6_hours 1835-1-5

value: moxonidine


title: whole_larva_bifenthrin_0.148ug/L_rep7 [221_2_1]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 7


title: MSA103_B24_trimethadione 10_uM 6_hours 690-2-1

value: trimethadione


title: NeptuneUrineB35A11

value: Urinary system structure

value: total cell-free biofluid RNA

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: whole_larva_bifenthrin_0.148ug/L_rep9 [222_1_2]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 9


title: MSA103_C01_moxonidine 1_uM 6_hours 3651-A-A


title: whole_larva_bifenthrin_0.297ug/L_rep3 [225_2_2]

source_name: whole larva, bifenthrin, 0.297 ug/L, replicate 3


title: whole_larva_bifenthrin_0.148ug/L_rep6 [233_2_1]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 6


title: NeptuneUrineB35A10

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A13

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: MSA103_B23_trimethadione 10_uM 6_hours 2476-D1-2

value: test


title: MSA103_B18_naringenin 10_uM 6_hours 690-2-1

value: naringenin


title: MSA103_B21_DMSO NA 6_hours 2476-D1-2

value: DMSO

value: vehicle


title: whole_larva_bifenthrin_0.148ug/L_rep4 [233_1_1]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 4

value: whole larva

value: 48 hours post-hatch

value: bifenthrin

value: larva


title: MSA103_B19_phenelzine 10_uM 6_hours 2476-D1-2

value: phenelzine


title: MSA103_B20_phenelzine 10_uM 6_hours 690-2-1


title: whole_larva_bifenthrin_0.148ug/L_rep5 [220_1_2]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 5


title: MSA103_B16_Aripiprazole 1_uM 6_hours 690-2-1

value: Aripiprazole


title: MSA103_B22_DMSO NA 6_hours 690-2-1


title: MSA103_B14_chenodeoxycholic acid 10_uM 6_hours 690-2-1

value: chenodeoxycholic acid


title: MSA103_B17_naringenin 10_uM 6_hours 2476-D1-2


title: MSA103_B13_chenodeoxycholic acid 10_uM 6_hours 2476-D1-2


title: MSA103_B15_Aripiprazole 1_uM 6_hours 2476-D1-2


title: MSA103_B12_fendiline 10_uM 6_hours 690-2-1

value: fendiline


title: NeptuneUrineB35A9

value: Nephrotic Syndrome

value: Urinary system structure

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: whole_larva_bifenthrin_0.148ug/L_rep3 [234_1_2]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 3


title: MSA103_B09_diclofenamide 10_uM 6_hours 2476-D1-2

value: diclofenamide


title: whole_larva_bifenthrin_0.148ug/L_rep2 [232_1_4]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 2


title: MSA103_B10_diclofenamide 10_uM 6_hours 690-2-1


title: MSA103_B08_arachidonyltrifluoromethane 10_uM 6_hours 690-2-1

value: arachidonyltrifluoromethane


title: NeptuneUrineB35A7

source_name: Urine

value: total cell-free biofluid RNA

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A5

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A4

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A6

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: MSA103_B07_arachidonyltrifluoromethane 10_uM 6_hours 2476-D1-2

value: test


title: whole_larva_bifenthrin_0ug/L_rep8 [227_2_2]

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of bifenthrin

source_name: whole larva, bifenthrin, 0 ug/L, replicate 8

value: whole larva

value: 48 hours post-hatch

value: bifenthrin


title: MSA103_B11_fendiline 10_uM 6_hours 2476-D1-2


title: MSA103_B06_Chlorpromazine 0.1_uM 6_hours 690-2-1

value: Chlorpromazine


title: whole_larva_bifenthrin_0ug/L_rep6 [226_1_2]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 6

value: larva


title: NeptuneUrineB35A3

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: MSA103_B05_Chlorpromazine 0.1_uM 6_hours 2476-D1-2


title: whole_larva_bifenthrin_0ug/L_rep7 [230_2_1]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 7


title: whole_larva_bifenthrin_0ug/L_rep5 [229_1_1]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 5


title: MSA103_B04_dihydroergocristine 1_uM 6_hours 690-2-1

value: dihydroergocristine


title: NeptuneUrineB35A2

value: Nephrotic Syndrome

value: Urinary system structure

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB35A1

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A24

value: total cell-free biofluid RNA

value: TGCCATCGTATGCCGTCTTCTGCTTG


title: RNAseq_CAID_3_p14

city: Montréal

first: Gregor

middle: Ulrich

last: Andelfinger

state: QC

address: 3175, Chemin de la Côte-Sainte-Catherine

department: Cardiology

country: Canada

institute: CHU Sainte-Justine

description: raw_counts_RNAseq_CAID_syndrome_p8_p14.txt

data_processing:
Trimmomatic (v.0.32) was used to remove Illumina adapters from the raw reads. Reads with a quality score <30 and smaller than 32 bp were eliminated.
The remaining reads were mapped to the hg19 human reference using Bowtie2 (v.2.1.0) and TopHat (v.2.1.0)
FeatureCounts (v.1.5.0) was used to count mapped reads.
Limma was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts values for all the samples.

source_name: Human dermal fibroblasts

growth_protocol: Cells where cultured in DMEM, 10% FBS, 1% pen/strep

extract_protocol:
RNA was extracted unsing miRNAeasy mini kit (217004, Qiagen) on automated QIAcube according to the manufacturer’s instructions
The cDNA libraries were generated on 500 ng of RNA with RNA integrity number (RIN) >9 using the Illumina TruSeq Stranded Total RNA Sample preparation kit (20020596, Illumina)

tag: cell type

value: Dermal fibroblasts

tag: passage


title: RNAseq_CAID_2_p14


title: NeptuneUrineB33A23

value: TGTTATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A22

value: TTGTATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A21

value: TTGACTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A20

value: TTCATTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A19

value: TTATTTCGTATGCCGTCTTCTGCTTG


title: MSA103_A23_trimethadione 10_uM 6_hours 3651-A-A

value: trimethadione

value: test


title: MSA103_B03_dihydroergocristine 1_uM 6_hours 2476-D1-2


title: RNAseq_CAID_1_p14


title: RNAseq_control_2_p14

value: wild type


title: RNAseq_control_1_p14


title: RNAseq_control_3_p14


title: NeptuneUrineB35A8

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: RNAseq_CAID_3_p8


title: NeptuneUrineB33A18

value: TAGCCTCGTATGCCGTCTTCTGCTTG


title: MSA103_A24_trimethadione 10_uM 6_hours 1835-1-5


title: NeptuneUrineB33A17

value: Nephrotic Syndrome

value: TACTCTCGTATGCCGTCTTCTGCTTG


title: MSA103_A22_DMSO NA 6_hours 1835-1-5

value: DMSO

value: vehicle


title: MSA103_A15_Aripiprazole 1_uM 6_hours 3651-A-A

value: Aripiprazole


title: RNAseq_CAID_2_p8


title: MSA103_A20_phenelzine 10_uM 6_hours 1835-1-5

value: phenelzine


title: whole_larva_bifenthrin_0ug/L_rep3 [221_2_2]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 3

value: whole larva

tag: age

value: 48 hours post-hatch

tag: chemical

value: bifenthrin

value: larva


title: MSA103_A16_Aripiprazole 1_uM 6_hours 1835-1-5


title: MSA103_A18_naringenin 10_uM 6_hours 1835-1-5

value: naringenin


title: whole_larva_bifenthrin_0ug/L_rep1 [220_1_1]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 1


title: MSA103_A13_chenodeoxycholic acid 10_uM 6_hours 3651-A-A

value: chenodeoxycholic acid


title: MSA103_A10_diclofenamide 10_uM 6_hours 1835-1-5

value: diclofenamide


title: MSA103_A21_DMSO NA 6_hours 3651-A-A


title: MSA103_A05_Chlorpromazine 0.1_uM 6_hours 3651-A-A

value: Chlorpromazine

value: test


title: MSA103_A08_arachidonyltrifluoromethane 10_uM 6_hours 1835-1-5

value: arachidonyltrifluoromethane


title: MSA103_A09_diclofenamide 10_uM 6_hours 3651-A-A


title: whole_larva_bifenthrin_0.148ug/L_rep1 [231_2_3]

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 1


title: MSA103_A06_Chlorpromazine 0.1_uM 6_hours 1835-1-5


title: MSA103_A07_arachidonyltrifluoromethane 10_uM 6_hours 3651-A-A


title: MSA103_A17_naringenin 10_uM 6_hours 3651-A-A


title: MSA103_A14_chenodeoxycholic acid 10_uM 6_hours 1835-1-5


title: RNAseq_control_3_p8

value: Dermal fibroblasts

value: wild type


title: MSA103_A12_fendiline 10_uM 6_hours 1835-1-5

value: fendiline


title: NeptuneUrineB33A15

tag: condition

value: Nephrotic Syndrome

tag: anatomical location

value: Urinary system structure

value: total cell-free biofluid RNA

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: RNAseq_control_2_p8


title: whole_larva_bifenthrin_0ug/L_rep4 [224_1_1]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 4

value: whole larva


title: NeptuneUrineB33A13

tag: rna source

tag: 3' adapter sequence

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: RNAseq_control_1_p8


title: NeptuneUrineB33A14

value: TATCATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A12

value: TAATATCGTATGCCGTCTTCTGCTTG


title: MSA103_A03_dihydroergocristine 1_uM 6_hours 3651-A-A

tag: perturbagen

value: dihydroergocristine

tag: cell id


title: MSA102_P23_Nimodipine 1_uM 6_hours MCF7

source_name: cancerCells

value: Nimodipine

tag: dosage

tag: batch


title: MSA103_A11_fendiline 10_uM 6_hours 3651-A-A

tag: duration


title: MSA103_A19_phenelzine 10_uM 6_hours 3651-A-A

value: phenelzine

tag: perturbation type


title: whole_larva_bifenthrin_0ug/L_rep2 [225_2_1]

source_name: whole larva, bifenthrin, 0 ug/L, replicate 2

value: 48 hours post-hatch

value: bifenthrin

value: larva


title: RNAseq_CAID_1_p8

value: Dermal fibroblasts

tag: genotype


title: MSA103_A04_dihydroergocristine 1_uM 6_hours 1835-1-5

value: test

tag: well id

tag: plate id


title: MSA102_P21_sotalol 10_uM 6_hours MCF7

value: sotalol


title: MSA102_P22_sotalol 10_uM 6_hours SH-SY5Y


title: MSA102_P24_Nimodipine 1_uM 6_hours SH-SY5Y


title: MSA102_P19_sulconazole 8.6_uM 6_hours MCF7

value: sulconazole


title: NeptuneUrineB33A10

value: Nephrotic Syndrome

value: Urinary system structure

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: MSA102_P17_lansoprazole 10_uM 6_hours MCF7

value: lansoprazole


title: NeptuneUrineB33A11

value: total cell-free biofluid RNA

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A7

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A9

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: MSA102_P13_DMSO NA 6_hours MCF7

value: DMSO

value: vehicle


title: MSA102_P15_levothyroxine sodium 1_uM 6_hours MCF7

value: levothyroxine sodium


title: MSA102_P16_levothyroxine sodium 1_uM 6_hours SH-SY5Y


title: MSA102_P20_sulconazole 8.6_uM 6_hours SH-SY5Y


title: 13627551

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA

description:
Sf9p40(2) vs DL80(2)
Date:2009/02/24

hyb_protocol: Corning Pronto : 1600.0 ng at 42 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : loess, Background norm. : none, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Spodoptera frugiperda

label_protocol: Promega Chipshot labeling

extract_protocol: Illustra RNAspin

tag: sample

tag: cell passage

tag: cell line

tag: treatment group

value: lethal dose 80 (LD) of Cry1C toxin


title: MSA102_P18_lansoprazole 10_uM 6_hours SH-SY5Y


title: NeptuneUrineB33A8

tag: condition

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: MSA102_P14_DMSO NA 6_hours SH-SY5Y


title: MSA102_P12_BUCLADESINE SODIUM 10_uM 6_hours SH-SY5Y

value: BUCLADESINE SODIUM


title: NeptuneUrineB33A4

tag: anatomical location

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: 13627550

description:
DL80(2) vs Sf9p40(2)
Date:2009/02/24


title: MSA102_P06_carbimazole 10_uM 6_hours SH-SY5Y

value: carbimazole

value: test


title: MSA102_P07_flecainide 8.4_uM 6_hours MCF7

value: flecainide


title: MSA102_P09_niflumic acid 10_uM 6_hours MCF7

value: niflumic acid


title: MSA102_P11_BUCLADESINE SODIUM 10_uM 6_hours MCF7


title: MSA102_P10_niflumic acid 10_uM 6_hours SH-SY5Y


title: 13627548

description:
Sf9p40(1) vs DL80(1)
Date:2009/02/06


title: MSA102_P08_flecainide 8.4_uM 6_hours SH-SY5Y


title: MSA102_P04_DMSO NA 6_hours SH-SY5Y


title: NeptuneUrineB33A5

value: Nephrotic Syndrome

value: Urinary system structure

tag: rna source

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: NeptuneUrineB33A2

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: 13627544

description:
Sf9p40(3) vs DL50(3)
Date:2009/01/23

value: lethal dose 50 (LD) of Cry1C toxin


title: 13627547

description:
DL50(3) vs Sf9p40(3)
Date:2009/01/23


title: NeptuneUrineB33A3

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: MSA102_O24_Nimodipine 1_uM 6_hours 2011-3-12

tag: perturbagen

value: Nimodipine


title: MSA102_P01_salsolidin 1_uM 6_hours MCF7

value: salsolidin

tag: cell id


title: MSA102_P02_salsolidin 1_uM 6_hours SH-SY5Y

tag: dosage


title: MSA102_O21_sotalol 10_uM 6_hours 3121-2-1

value: sotalol

tag: batch


title: MSA102_O22_sotalol 10_uM 6_hours 2011-3-12

tag: duration


title: 13627542

description:
Sf9p40(2) vs DL50(2)
Date:2009/01/23


title: 13627549

description:
DL80(1) vs Sf9p40(1)
Date:2009/02/06

value: lethal dose 80 (LD) of Cry1C toxin


title: MSA102_O23_Nimodipine 1_uM 6_hours 3121-2-1

tag: perturbation type


title: 13627536

description:
Sf9p40(1) vs Sf9p8(1)
Date:2009/01/09


title: 13627545

description:
DL50(2) vs Sf9p40(2)
Date:2009/01/23


title: MSA102_P03_DMSO NA 6_hours MCF7

value: DMSO

value: vehicle


title: NeptuneUrineB33A1

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: 13627539

description:
Sf9p8(3) vs Sf9p40(3)
Date:2009/01/14


title: MSA102_O15_levothyroxine sodium 1_uM 6_hours 3121-2-1

value: levothyroxine sodium

value: test


title: MSA102_O14_DMSO NA 6_hours 2011-3-12


title: 13627537

description:
Sf9p8(1) vs Sf9p40(1)
Date:2009/01/09


title: DKs8.cell.nt.1

city: Nashville

first: James

middle: G

last: Patton

state: Tennessee

address: Biological Sciences, Vanderbilt University

department: Department of Biological Sciences

institute: Vanderbilt University

data_processing:
All reads are mapped to hg19 using tophat2 with gene annotation from GENCODE v19. Read counts are then obtained using HTSeq's htseq-count (v0.6.1p1).
Genome_build: hg19
Supplementary_files_format_and_content: Each processed data file is a table of  read counts.

source_name: Colorectal cancer cell line

extract_protocol:
Total RNA was isolated using TrIzol followed by miRNeasy Kit purification. Cell removal method was low speed centrifugation (1000rpm, 10 minutes, room temperature). Extracellular vesicles were isolated via multi-step centrifugation followed by filtration and ultracentrifugation. First, centrifugation (2000xg, 0.42 hours, 4C) was performed to remove cell debris and large vesicles. Next,centrifugation (10000xg, 0.5 hours, 4C) was performed to remove microvesicles. Third, filtration was performed (0.22-um polyether-sulfone (100,000 mw cut off) (Nalgene, Rochester, NY) to reduce microparticle contamination, 3400g, duration of 35 min). Finally, ultracentrifugation (100000xg, 17 hours, 4C) was performed.
NEBNext kit was used for library construction. Type of starting material was total RNA.

tag: cell type

value: Colorectal cancer

value: Colon

value: whole cell

tag: rna isolation kit

value: Trizol + miRNeasy (Qiagen)

tag: genotype

value: WT/-


title: DKs8.cell.nt.2


title: DLD1.cell.nt.3

value: WT/MUT


title: MSA102_O09_niflumic acid 10_uM 6_hours 3121-2-1

value: niflumic acid

tag: well id

tag: plate id


title: 13624752

description:
Sf9p8(2) vs Sf9p40(2)
Date:2009/01/14

tag: sample

tag: cell passage

tag: cell line


title: MSA102_O20_sulconazole 8.6_uM 6_hours 2011-3-12

value: sulconazole


title: MSA102_O17_lansoprazole 10_uM 6_hours 3121-2-1

value: lansoprazole


title: MSA102_O18_lansoprazole 10_uM 6_hours 2011-3-12


title: MSA102_O19_sulconazole 8.6_uM 6_hours 3121-2-1


title: DKs8.cell.nt.3

tag: anatomical location


title: DLD1.cell.nt.1

tag: rna source


title: MSA102_O12_BUCLADESINE SODIUM 10_uM 6_hours 2011-3-12

value: BUCLADESINE SODIUM


title: MSA102_O16_levothyroxine sodium 1_uM 6_hours 2011-3-12


title: DLD1.cell.nt.2


title: MSA102_O13_DMSO NA 6_hours 3121-2-1


title: MSA102_O11_BUCLADESINE SODIUM 10_uM 6_hours 3121-2-1


title: NeptuneUrineB33A6

tag: condition

value: Nephrotic Syndrome

value: Urinary system structure

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: 13627541

description:
Sf9p40(2) vs Sf9p8(2)
Date:2009/01/14


title: 13627538

description:
Sf9p40(3) vs Sf9p8(3)
Date:2009/01/14


title: 13627540

description:
DL50(1) vs Sf9p40(1)
Date:2009/02/06

tag: treatment group

value: lethal dose 50 (LD) of Cry1C toxin


title: 13627543

description:
Sf9p40(1) vs DL50(1)
Date:2009/02/06


title: MSA102_O10_niflumic acid 10_uM 6_hours 2011-3-12

tag: perturbagen

tag: cell id

tag: dosage


title: MSA102_O06_carbimazole 10_uM 6_hours 2011-3-12

value: carbimazole

tag: batch

tag: duration

tag: perturbation type


title: MSA102_O08_flecainide 8.4_uM 6_hours 2011-3-12

value: flecainide

value: test


title: DKO1.cell.nt.1

tag: cell type

value: Colorectal cancer

value: Colon

tag: rna isolation kit

tag: genotype

value: -/MUT


title: MSA102_O07_flecainide 8.4_uM 6_hours 3121-2-1

tag: well id

tag: plate id


title: DKO1.cell.nt.3

value: whole cell

value: Trizol + miRNeasy (Qiagen)

tag: cell line


title: DKs8.cell.ionomycin.2

tag: anatomical location

value: WT/-


title: MSA102_O05_carbimazole 10_uM 6_hours 3121-2-1


title: MSA102_O03_DMSO NA 6_hours 3121-2-1

value: DMSO

value: vehicle


title: 13627552

description:
DL80(3) vs Sf9p40(3)
Date:2009/02/24

tag: sample

tag: cell passage

value: lethal dose 80 (LD) of Cry1C toxin


title: DKs8.cell.ionomycin.1

tag: rna source


title: MSA102_O04_DMSO NA 6_hours 2011-3-12


title: MSA102_O01_salsolidin 1_uM 6_hours 3121-2-1

value: salsolidin


title: DKs8.cell.ionomycin.3


title: DKO1.cell.nt.2


title: DLD1.cell.ionomycin.3

value: WT/MUT


title: MSA102_O02_salsolidin 1_uM 6_hours 2011-3-12


title: DLD1.cell.ionomycin.2


title: MSA102_N23_BAY K8644 1_uM 6_hours MCF7

value: BAY K8644


title: MSA102_N22_phenyl biguanide 10_uM 6_hours SH-SY5Y

value: phenyl biguanide


title: MSA102_N16_trazodone 1_uM 6_hours SH-SY5Y

value: trazodone


title: MSA102_N15_trazodone 1_uM 6_hours MCF7


title: MSA102_N20_cephaeline 6_uM 6_hours SH-SY5Y

value: cephaeline


title: ESCC_GE060T_SNP5

type: genomic

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: Hybridized to Affymetrix SNP array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip®Operating Software (GCOS version1.4). Genotype calls were generated by using GTYPE4.1. The raw date[.CELfile] were loaded using R/biocunductor and aroma. Affymetrix.For more details, go to htpp://www.aroma-project.org/. We used the CRMA function implemented in the Aroma to preprocess and applied CBS method for segmentation. We combined the segmentation results from two platforms, and imported to Nexus Copy Number 6.1 followed the manual ( www. Biodiscovery.com). We used Q-Bound cut off at 0.5 and G-Score cut off at 1.0. to identify the focal regions of amplification and deletion with FDR q-value 0.25 for copy number using GISTIC 2.0 as recommended.

label: Biotin

molecule: genomic DNA

source_name: tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: tumor DNA was isolated from frozen tummor tissue using the Allprep Kit (Qiagen) per the manufacturer's instruction. Germline DNA was isolated from the same patient's venous blood. DNA quality and quantity were determined using NanoDrop 2000 (Thermo Scientific).

tag: disease state

value: ESCC

tag: case id

tag: tissue

value: esophageal squamous cell carcinoma tissue


title: 13627553

description:
Sf9p40(3) vs DL80(3)
Date:2009/02/24

tag: treatment group


title: MSA102_N24_BAY K8644 1_uM 6_hours SH-SY5Y

tag: perturbagen

tag: cell id

tag: dosage

tag: batch

value: test


title: MSA102_N21_phenyl biguanide 10_uM 6_hours MCF7

tag: duration

tag: perturbation type


title: MSA102_P05_carbimazole 10_uM 6_hours MCF7

value: carbimazole

tag: well id


title: MSA102_N13_pizotifen 1_uM 6_hours MCF7

value: pizotifen

tag: plate id


title: MSA102_N18_trichostatin NA 6_hours SH-SY5Y

value: trichostatin

value: poscon


title: DKO1.cell.ionomycin.3

tag: cell type

value: Colorectal cancer

value: Colon

value: whole cell

tag: rna isolation kit

value: Trizol + miRNeasy (Qiagen)

tag: cell line

tag: genotype

value: -/MUT


title: ESCC_GE058T_SNP5

description: Hybridized to Affymetrix SNP array


title: DKO1.cell.ionomycin.2

tag: anatomical location

tag: rna source


title: MSA102_N19_cephaeline 6_uM 6_hours MCF7


title: DLD1.EV.2

value: extracellular vesicle

value: WT/MUT


title: MSA102_N17_trichostatin NA 6_hours MCF7


title: MSA102_N10_liothyronine 3.2_uM 6_hours SH-SY5Y

value: liothyronine


title: MSA102_N14_pizotifen 1_uM 6_hours SH-SY5Y


title: DKO1.cell.ionomycin.1


title: MSA102_N04_niclosamide 10_uM 6_hours SH-SY5Y

value: niclosamide


title: MSA102_N07_DMSO NA 6_hours MCF7

value: DMSO

value: vehicle


title: MSA102_N09_liothyronine 3.2_uM 6_hours MCF7


title: ESCC_GE059T_SNP5

description: Hybridized to Affymetrix SNP array

tag: disease state

value: ESCC

tag: case id

value: esophageal squamous cell carcinoma tissue


title: MSA102_N12_nadolol 10_uM 6_hours SH-SY5Y

value: nadolol

value: test


title: ESCC_GE060B_SNP5

description: Hybridized to Affymetrix SNP array

source_name: whole blood

tag: tissue

value: blood from esophageal squamous cell carcinoma patient


title: MSA102_N11_nadolol 10_uM 6_hours MCF7

tag: perturbagen


title: MSA102_N06_Quetiapine 10_uM 6_hours SH-SY5Y

value: Quetiapine

tag: cell id


title: MSA102_N08_DMSO NA 6_hours SH-SY5Y


title: MSA102_N01_repaglinide 8.8_uM 6_hours MCF7

value: repaglinide

tag: dosage


title: ESCC_GE059B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_N05_Quetiapine 10_uM 6_hours MCF7

tag: batch


title: ESCC_GE055T_SNP5

description: Hybridized to Affymetrix SNP array


title: DLD1.EV.3

value: Colorectal cancer

value: Colon


title: ESCC_GE056B_SNP5

description: Hybridized to Affymetrix SNP array


title: DKO1.EV.3

value: Trizol + miRNeasy (Qiagen)


title: ESCC_GE057T_SNP5

description: Hybridized to Affymetrix SNP array


title: DLD1.EV.1


title: ESCC_GE058B_SNP5

description: Hybridized to Affymetrix SNP array


title: DLD1.cell.ionomycin.1

value: whole cell


title: ESCC_GE056T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_M22_phenyl biguanide 10_uM 6_hours 2011-3-12

value: phenyl biguanide

tag: duration


title: MSA102_M21_phenyl biguanide 10_uM 6_hours 3121-2-1

tag: perturbation type


title: MSA102_N02_repaglinide 8.8_uM 6_hours SH-SY5Y

tag: well id


title: MSA102_M23_BAY K8644 1_uM 6_hours 3121-2-1

value: BAY K8644

tag: plate id


title: DKO1.EV.2

tag: cell type

value: extracellular vesicle

value: -/MUT


title: MSA102_M19_cephaeline 6_uM 6_hours 3121-2-1

value: cephaeline


title: MSA102_N03_niclosamide 10_uM 6_hours MCF7

value: niclosamide


title: MSA102_M20_cephaeline 6_uM 6_hours 2011-3-12


title: DKO1.EV.1

tag: rna isolation kit


title: ESCC_GE055B_SNP5

description: Hybridized to Affymetrix SNP array

value: ESCC


title: ESCC_GE057B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_M24_BAY K8644 1_uM 6_hours 2011-3-12


title: DKs8.EV.1

tag: cell line

value: WT/-


title: DKs8.EV.3

tag: genotype


title: MSA102_M18_trichostatin NA 6_hours 2011-3-12

value: trichostatin

value: poscon


title: ESCC_GE053T_SNP5

description: Hybridized to Affymetrix SNP array

value: esophageal squamous cell carcinoma tissue


title: DKs8.EV.2

tag: anatomical location


title: ESCC_GE054B_SNP5

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: ESCC_GE052T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE053B_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE054T_SNP5

description: Hybridized to Affymetrix SNP array


title: HPV-16 E6, Rep 3

city: Morgantown

first: Ivan

last: Martinez

state: WV

address: 1838 MBRCC PO Box 9300

department: Microbiology / Cancer Center

institute: West Virginia University

data_processing:
FASTQ files were imported into Strand NGS suites for analysis.
Reads were aligned to the human hg19 reference genomes using the Bowtie algorithm.
These were then quantified against Ensemble transcript and including small and lncRNA annotations. Any lncRNA that were detected in human subjects were used for further analysis.
Raw lncRNA counts were then normalized to the total number of lncRNA reads per sample and expression values calculated against the control samples.
Further Mapping rate visualization done using Strand NGS software.
Genome_build: human hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and fold changes for each sample.

source_name: Primary foreskin keratinocytes

growth_protocol: HEKa cells (C-005-5C) were cultured according to Invitrogen manufacturer's protocol (Epilife Media and HKGS supplement)

extract_protocol:
Stably expressing HEKa cells were harvested on ice and RNA was extracted using TRIzol reagent and Dnase treated with TURBO Dnase (Thermo Fisher)
RNA libraries were prepared using TruSeq RNA Library Prep X9
RNA-seq was run using HiSeq 2X150bp PE Rapid Run mode 1 flow cell (2 lanes).

treatment_protocol: Early passage HEKa cells were cultured with recombinant retrovirus for 8 hours to express HPV-16 E6 or GFP proteins, cultured 48 hours to recover, selected with puromycin (2.5ug/mL), and allowed to recover for at least 72 hours prior to pelleting to perform RNA extraction, RT-PCR analysis to confirm HPV-16 E6 expression, and RNA-seq analysis.

tag: cell lineage

value: foreskin

value: HPV-16 E6 positive


title: HPV-16 E6, Rep 2


title: HPV-16 E6, Rep 1


title: GFP control, Rep 3

value: HPV-16 E6 negative


title: MSA102_M17_trichostatin NA 6_hours 3121-2-1


title: MSA102_M13_pizotifen 1_uM 6_hours 3121-2-1

value: pizotifen

value: test


title: MSA102_M11_nadolol 10_uM 6_hours 3121-2-1

value: nadolol


title: MSA102_M09_liothyronine 3.2_uM 6_hours 3121-2-1

value: liothyronine


title: MSA102_M10_liothyronine 3.2_uM 6_hours 2011-3-12


title: MSA102_M12_nadolol 10_uM 6_hours 2011-3-12


title: MSA102_M15_trazodone 1_uM 6_hours 3121-2-1

value: trazodone


title: GFP control, Rep 1


title: GFP control, Rep 2


title: hSRSF6_iCLIP_hg19_Rep3

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt

description:
iCLIP
hSRSF6_all_hg19_iCLIP_tags.bed

data_processing:
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: hg19
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tags combined replicates (3-4 replicates). .bed files containing the genomic coordinates for significant CLIP tag clusters from combined replicates.

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was separated into 3 size fractions by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonukelotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
iCLIP

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: antibody

value: anti-EGFP

tag: barcode sequence

value: TGGC


title: ESCC_GE051T_SNP5

description: Hybridized to Affymetrix SNP array

tag: disease state

tag: case id

tag: tissue


title: ESCC_GE050T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE052B_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE050B_SNP5

description: Hybridized to Affymetrix SNP array


title: hSRSF6_iCLIP_hg19_Rep2

description:
iCLIP
hSRSF6_all_hg19_iCLIP_tags.bed

value: CCGG


title: hSRSF6_iCLIP_hg19_Rep1

description:
iCLIP
hSRSF6_all_hg19_iCLIP_tags.bed

value: TTGT


title: ESCC_GE049T_SNP5

description: Hybridized to Affymetrix SNP array

value: ESCC


title: MSA102_L21_bergenin 1_uM 6_hours MCF7

tag: perturbagen

value: bergenin

tag: cell id

tag: dosage


title: MSA102_L19_DMSO NA 6_hours MCF7

value: DMSO

tag: batch

tag: duration

tag: perturbation type

value: vehicle


title: MSA102_M07_DMSO NA 6_hours 3121-2-1

tag: well id

tag: plate id


title: MSA102_M02_repaglinide 8.8_uM 6_hours 2011-3-12

value: repaglinide


title: hSRSF5_iCLIP_hg19_Rep4

description:
iCLIP
hSRSF5_all_hg19_iCLIP_tags.bed

tag: cell line

value: CAAT


title: MSA102_M06_Quetiapine 10_uM 6_hours 2011-3-12

value: Quetiapine


title: MSA102_M14_pizotifen 1_uM 6_hours 2011-3-12


title: MSA102_L23_MDL100907 0.5_uM 6_hours MCF7


title: MSA102_M05_Quetiapine 10_uM 6_hours 3121-2-1


title: ESCC_GE051B_SNP5

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: MSA102_M01_repaglinide 8.8_uM 6_hours 3121-2-1


title: MSA102_M08_DMSO NA 6_hours 2011-3-12


title: MSA102_L24_MDL100907 0.5_uM 6_hours SH-SY5Y


title: hSRSF5_iCLIP_hg19_Rep3

description:
iCLIP
hSRSF5_all_hg19_iCLIP_tags.bed


title: MSA102_M16_trazodone 1_uM 6_hours 2011-3-12


title: MSA102_L18_celastrol 2.5_uM 6_hours SH-SY5Y

value: celastrol


title: MSA102_L17_celastrol 2.5_uM 6_hours MCF7

value: test


title: hSRSF5_iCLIP_hg19_Rep2

description:
iCLIP
hSRSF5_all_hg19_iCLIP_tags.bed

value: GGCG


title: MSA102_M03_niclosamide 10_uM 6_hours 3121-2-1

value: niclosamide


title: MSA102_L22_bergenin 1_uM 6_hours SH-SY5Y


title: hSRSF5_iCLIP_hg19_Rep1

description:
iCLIP
hSRSF5_all_hg19_iCLIP_tags.bed


title: hSRSF2_iCLIP_hg19_Rep3

description:
iCLIP
hSRSF2_all_hg19_iCLIP_tags.bed


title: MSA102_L20_DMSO NA 6_hours SH-SY5Y


title: MSA102_L16_PK11195 1_uM 6_hours SH-SY5Y


title: MSA102_M04_niclosamide 10_uM 6_hours 2011-3-12


title: MSA102_L15_PK11195 1_uM 6_hours MCF7


title: MSA102_L14_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours SH-SY5Y

value: Myeloperoxidase Inhibitor-I


title: MSA102_L10_Amoxapine 0.1_uM 6_hours SH-SY5Y

value: Amoxapine


title: MSA102_L13_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours MCF7


title: ESCC_GE049B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_L09_Amoxapine 0.1_uM 6_hours MCF7


title: MSA102_L11_arcaine 10_uM 6_hours MCF7

value: arcaine


title: MSA102_L12_arcaine 10_uM 6_hours SH-SY5Y


title: hSRSF2_iCLIP_hg19_Rep2

description:
iCLIP
hSRSF2_all_hg19_iCLIP_tags.bed

value: anti-EGFP


title: MSA102_L08_isoniazid 10_uM 6_hours SH-SY5Y

value: isoniazid


title: Ribominus total RNAseq whole cell 2

description: WT Replicate B

data_processing:
Adaptor sequences were trimmed from reads using Flexbar
RNA-seq reads were aligned to hg19 using Tophat v2.0.0 coupled with Bowtie v1.1.1
Reads were counted into features using samtools with (-c) option. Bedcoverage tool was used to count reads into transcripts.
RPKM values were calculated using the formula: counts * 10^9 / length of feature * total mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: Bed file containing RPKM values of lincRNAs and protein-coding transcripts.

extract_protocol:
Cells were harvested and RNA was extracted using the TRIZol. Genomic DNA was digested with DNaseI. rRNA was removed with the RiboMinus Kit.
Library was prepared using NEBNext mRNA Sample Prep Master Mix Set kit (NEB).
TRU-seq

tag: sample type

value: Ribominus total RNAseq whole cell


title: hSRSF2_iCLIP_hg19_Rep1

description:
iCLIP
hSRSF2_all_hg19_iCLIP_tags.bed

value: GGTT


title: MSA102_L04_tanespimycin NA 6_hours SH-SY5Y

value: tanespimycin

value: poscon


title: MSA102_L06_ronidazole 1_uM 6_hours SH-SY5Y

value: ronidazole


title: MSA102_L05_ronidazole 1_uM 6_hours MCF7


title: MSA102_L07_isoniazid 10_uM 6_hours MCF7


title: ESCC_GE045B_SNP5

description: Hybridized to Affymetrix SNP array

value: ESCC


title: ESCC_GE045T_SNP5

description: Hybridized to Affymetrix SNP array

value: esophageal squamous cell carcinoma tissue


title: MSA102_L03_tanespimycin NA 6_hours MCF7


title: Ribominus total RNAseq whole cell 1

description: WT Replicate A


title: MSA102_L02_budesonide 9.2_uM 6_hours SH-SY5Y

value: budesonide


title: ESCC_GE022T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE048B_SNP5

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: ESCC_GE048T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_L01_budesonide 9.2_uM 6_hours MCF7

value: test


title: ESCC_GE047T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE022B_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE047B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_K24_MDL100907 0.5_uM 6_hours 2011-3-12


title: MSA102_K22_bergenin 1_uM 6_hours 2011-3-12

value: bergenin


title: MSA102_K21_bergenin 1_uM 6_hours 3121-2-1


title: autologous nerve grafting 14d post surgery

type: protein

city: Nantong

first: Sheng

last: Yi

state: Jiangsu, China

address: 19 Qixiu Road

country: China

institute: Nantong University

description:
autologous-14d
Bridge nerve gap with autologous nerve, collect nerve stump at 14 days post surgery.

hyb_protocol: In a tube, add 6 ml of Coupling Solution and one tube of biotinylated sample (25 ug). Vortex briefly to mix. Label it as “Protein Coupling Mix.” Place the slide in any clean well of the Coupling Chamber. Slowly pour all 6 ml of Protein Coupling Mix over the slide. Make sure the slide is completely submerged. Cover the Coupling Chamber. Incubate on an orbital shaker rotating at 35 rpm for 2 hours at room temperature. Transfer the slide to a 100x15 mm Petri dish containing 30 ml of 1X Wash Solution. Incubate on an orbital shaker rotating at 55 rpm for 10 minutes at room temperature. Discard the wash solution. Repeat the wash step 3 times. Rinse the slide extensively with Milli-Q Place the slide in a 50-ml conical tube. Fill the tube with 45 ml of water. Close the cap. Shake for 10 seconds. Discard the water. Repeat ten times. Shake off excessive water on the slide surface. Add 60 ul of Cy3-Streptavidin (0.5 mg/ml) to 60 ml of Detection Buffer. Pour 30 ml of Cy3-Streptavidin Solution into a 100x15 mm Petri dish. Submerge the slide in the Cy3-Streptavidin solution. Incubate on an orbital shaker rotating at 55 rpm for 20 minutes at room temperature in the dark or covered with aluminum foil. Transfer the slide to a new 100x15 mm Petri dish containing 30 ml of 1X Wash Solution. Incubate on an orbital shaker set at 55 rpm for 10 minutes at room temperature. Discard the wash solution. Repeat the wash step twice. Rinse the slide extensively with Milli-Q grade water as follows: Place the slide in a 50-ml conical tube. Fill the tube with 45 ml of water. Close the cap. Shake for 10 seconds. Discard the water. Repeat ten times. Dry the slide with compressed nitrogen (or air) or by centrifugation. The slide is now ready for scanning.

scan_protocol: The slides were scanned (GenePix 4000B, Axon Instruments, USA).

data_processing: The fluorescence signal of each antibody was obtained from the fluorescence intensity of this antibody spot after subtraction of the blank signal (spot in the absence of antibody). Two technical replicates were performed for each sample. Median signal intensity for each spot was extracted from array images and the average intensity for each antibody reaction with the protein was determined for replicate spots. Data were normalized utilizing the median intensity values for the 1318 antibodies on each array (Normalized data = Average Signal Intensity of Replicate Spots / Median Signal).

label: Biotin/DMF

molecule: protein

organism: Rattus norvegicus

source_name: sciatic nerve stump, autologous nerve graft, 14d post surgery

label_protocol: Briefly centrifuge Biotin Reagent before use. Add 100 ul of DMF (N,N-Dimethylformamide) to 1 mg of Biotin Reagent to give a concentration of 10 ug/ul. Label this solution as Biotin/DMF. Aliquot 10 – 25 ul of lysate. Add Labeling Buffer to the sample to bring the volume to 67 ul. Add 3 ul of the Biotin/DMF solution to the sample. Incubate the mixture at room temperature for 2 hours with mixing. Add 30 ul of Stop Reagent. Incubate for 30 minutes at room temperature with mixing. Proceed immediately to the next step, or store the biotinylated sample at -80°C for future use.

growth_protocol: Rat sciatic nerve was exposed and lifted to transect a 0.6-cm-long nerve segment at the site just proximal to the division of tibial and common peroneal nerves. Nerve gap was bridged with inverted autologous nerve (autologous group) or tissue engineered nerve with chitosan conduit and silk fibroin fillers (catheter group). At 4, 7, and 14 days after nerve transection, rats were killed by decapitation and their sciatic nerve segments were collected for execution and validation of antibody array assay.

extract_protocol: Wash tissues with cold 1X PBS (4°C) with vortexing. Remove and discard PBS. Repeat 3 – 5 times. Add one tube of lysis beads to 10 – 40 mg of tissues, add 500 ul of Extraction Buffer. Mix rigorously by vortexing for 30 seconds. Incubate the mixture on ice for 30 seconds. Repeat vortexing 3 times. Centrifuge the mixture at 10,000 x g (14000 rpm) for 15 minutes at 4°C. Transfer the clear supernatant to a clean tube. Discard the beads.

treatment_protocol: Inverted autologous nerve (autologous group) or tissue engineered nerve with chitosan conduit and silk fibroin fillers (catheter group).

value: sciatic nerve

tag: treatment

value: autologous nerve graft

tag: time point

value: 14d post surgery


title: ESCC_GE023T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE021T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_K20_DMSO NA 6_hours 2011-3-12

value: DMSO

value: vehicle


title: autologous nerve grafting 4d post surgery

description:
autologous-4d
Bridge nerve gap with autologous nerve, collect nerve stump at 4 days post surgery.

source_name: sciatic nerve stump, autologous nerve graft, 4d post surgery

value: 4d post surgery


title: tissue engineering 14d post surgery

description:
catheter-14d
Bridge nerve gap with chitosan+silk fibroin, collect nerve stump at 14 days post surgery.

source_name: sciatic nerve stump, tissue engineered nerve graft, 14d post surgery

value: tissue engineered nerve graft


title: MSA102_K19_DMSO NA 6_hours 3121-2-1


title: ESCC_GE023B_SNP5

description: Hybridized to Affymetrix SNP array


title: tissue engineering 7d post surgery

description:
catheter-7d
Bridge nerve gap with chitosan+silk fibroin, collect nerve stump at 7 days post surgery.

source_name: sciatic nerve stump, tissue engineered nerve graft, 7d post surgery

value: 7d post surgery


title: ESCC_GE020T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE021B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_K13_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 3121-2-1

value: Myeloperoxidase Inhibitor-I


title: MSA102_K17_celastrol 2.5_uM 6_hours 3121-2-1

value: celastrol


title: MSA102_K16_PK11195 1_uM 6_hours 2011-3-12


title: MSA102_K15_PK11195 1_uM 6_hours 3121-2-1


title: MSA102_K14_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 2011-3-12


title: ESCC_GE020B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_K18_celastrol 2.5_uM 6_hours 2011-3-12


title: MSA102_K12_arcaine 10_uM 6_hours 2011-3-12

value: arcaine


title: tissue engineering 4d post surgery

description:
catheter-4d
Bridge nerve gap with chitosan+silk fibroin, collect nerve stump at 4 days post surgery.

source_name: sciatic nerve stump, tissue engineered nerve graft, 4d post surgery


title: ESCC_GE019B_SNP5

description: Hybridized to Affymetrix SNP array

value: ESCC


title: ESCC_GE019T_SNP5

description: Hybridized to Affymetrix SNP array

value: esophageal squamous cell carcinoma tissue


title: sham surgery 14d post surgery

description:
Sham-14d
Sham surgery, collect nerve stump at 14 days post surgery.

source_name: sciatic nerve stump, sham surgery, 14d post surgery

value: sham surgery


title: ESCC_GE018T_SNP5

description: Hybridized to Affymetrix SNP array


title: sham surgery 7d post surgery

description:
Sham-7d
Sham surgery, collect nerve stump at 7 days post surgery.

source_name: sciatic nerve stump, sham surgery, 7d post surgery


title: MSA102_K23_MDL100907 0.5_uM 6_hours 3121-2-1


title: ESCC_GE018B_SNP5

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: MSA102_K10_Amoxapine 0.1_uM 6_hours 2011-3-12

value: Amoxapine

value: test


title: Column_20_Estrogen

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

data_processing:
Fastq files for each column of the IFC were further demultiplexed using Fluidigm's API for demultiplexing, resulting in a single fastq file for each cell capture site (40 sites per column).
Pseudoalignment and transcript quantification of each fastq file was performed with Kallisto (0.44.0)
Capture sites with zero or >1 cell, those with apoptotic cells, and those that led to poor-quality data (low number of sequencing reads, high mitochondrial proportion) were all filtered
Expression counts were normalized using scaling factors calculated using scran. Normalized values were imputed using MAGIC.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files containing raw counts, imputed logged expression, and metadata for each cell

source_name: Ovarian surface epithelial cells

growth_protocol: mOSE cells were cultured in media consisting of a-Minimum Essential Medium (Corning) supplemented with 5% FBS, 0.01mg/mL ITSS (Roche), 2ug/mL EGF (R&D Systems).

extract_protocol:
Single cell suspensions of control and E2-treated mOSE were processed using the Fluidigm HT 3' scRNA-seq protocol. The left cell inlet of the integrated fluidics circuit (IFC; leading to columns 1-10 of the plate) were loaded with control cells, while E2-treated cells were loaded into the right inlet (columns 11-20 of the IFC plate)
Library were constructed using the standard protocol described for the Fluidigm HT 3' scRNA-seq. Libraries were sequenced on a NextSeq500 high-out 26x75bp run

treatment_protocol: Cells were seeded and allowed to normalize to hormone-free media consisting of 5% charcoal-stripped FBS in phenol red-free DMEM-F12 media (Sigma) for 48 hours before treating with 100nM E2 (Sigma). An equivalent volume of 100% EtOH (vehicle) was added to control dishes for a final concentration of 0.0002% EtOH. Media was refreshed every 3-4 days and cells were collected for scRNA-seq after 15 days in culture.

tag: cell type

value: Ovarian surface epithelial cells


title: ESCC_GE017B_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_19_Estrogen


title: MSA102_K11_arcaine 10_uM 6_hours 3121-2-1


title: MSA102_K09_Amoxapine 0.1_uM 6_hours 3121-2-1


title: MSA102_K04_tanespimycin NA 6_hours 2011-3-12

value: tanespimycin

value: poscon


title: sham surgery 4d post surgery

description:
Sham-4d
Sham surgery, collect nerve stump at 4 days post surgery.

source_name: sciatic nerve stump, sham surgery, 4d post surgery

value: sciatic nerve


title: MSA102_K05_ronidazole 1_uM 6_hours 3121-2-1

description: 24 hiPSC-derived NPCs and 8 CCLs were used (total: 32 cell lines). Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: a) phase 1 had 6/79 drugs from pilot, and 73/79 phase 1 test compounds, b) phase 2 had 6 pilot drugs re-tested, 6/73 phase 1 drugs re-tested, and 67/79 phase 2 compounds. 135 unique compounds were tested.

value: ronidazole


title: MSA102_K06_ronidazole 1_uM 6_hours 2011-3-12


title: Column_18_Estrogen


title: ESCC_GE017T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE016T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_K07_isoniazid 10_uM 6_hours 3121-2-1

value: isoniazid


title: Column_17_Estrogen


title: MSA102_K08_isoniazid 10_uM 6_hours 2011-3-12


title: autologous nerve grafting 7d post surgery

description:
autologous-7d
Bridge nerve gap with autologous nerve, collect nerve stump at 7 days post surgery.

source_name: sciatic nerve stump, autologous nerve graft, 7d post surgery

value: autologous nerve graft


title: MSA102_K03_tanespimycin NA 6_hours 3121-2-1


title: MSA102_K02_budesonide 9.2_uM 6_hours 2011-3-12

value: budesonide


title: MSA102_J24_TCB-2 0.1_uM 6_hours SH-SY5Y

source_name: cancerCells


title: MSA102_J21_lycorine 10_uM 6_hours MCF7

value: lycorine


title: MSA102_J23_TCB-2 0.1_uM 6_hours MCF7


title: Column_16_Estrogen


title: MSA102_K01_budesonide 9.2_uM 6_hours 3121-2-1


title: MSA102_J20_diltiazem 3_uM 6_hours SH-SY5Y

value: diltiazem


title: Column_14_Estrogen


title: ESCC_GE016B_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_13_Estrogen


title: MSA102_J22_lycorine 10_uM 6_hours SH-SY5Y


title: ESCC_GE015B_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_15_Estrogen


title: ESCC_GE015T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_J19_diltiazem 3_uM 6_hours MCF7


title: ESCC_GE014T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE014B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_J17_Ziprasidone 0.1_uM 6_hours MCF7

value: Ziprasidone


title: MSA102_J15_DMSO NA 6_hours MCF7

value: DMSO

value: vehicle


title: MSA102_J14_suloctidil 10_uM 6_hours SH-SY5Y

value: suloctidil


title: MSA102_J16_DMSO NA 6_hours SH-SY5Y


title: Column_12_Estrogen


title: MSA102_J18_Ziprasidone 0.1_uM 6_hours SH-SY5Y


title: MSA102_J13_suloctidil 10_uM 6_hours MCF7


title: Column_10_Control

value: EtOH (vehicle control)


title: ESCC_GE013T_SNP5

description: Hybridized to Affymetrix SNP array

value: ESCC

value: esophageal squamous cell carcinoma tissue


title: Column_11_Estrogen

value: Ovarian surface epithelial cells


title: MSA102_J11_vigabatrin 10_uM 6_hours MCF7

value: vigabatrin

value: test


title: Column_9_Control


title: MSA102_J09_spiradoline 0.1_uM 6_hours MCF7

value: spiradoline


title: Column_8_Control


title: ESCC_GE013B_SNP5

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: MSA102_J06_trimethobenzamide 1_uM 6_hours SH-SY5Y

value: trimethobenzamide


title: Column_6_Control


title: MSA102_J07_chlorcyclizine 1_uM 6_hours MCF7

value: chlorcyclizine


title: ESCC_GE012T_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE012B_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_7_Control


title: MSA102_J12_vigabatrin 10_uM 6_hours SH-SY5Y


title: MSA102_J08_chlorcyclizine 1_uM 6_hours SH-SY5Y


title: MSA102_J04_mebendazole 10_uM 6_hours SH-SY5Y

value: mebendazole


title: ESCC_GE011T_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_5_Control


title: MSA102_J05_trimethobenzamide 1_uM 6_hours MCF7


title: MSA102_I23_TCB-2 0.1_uM 6_hours 3121-2-1


title: Column_4_Control


title: MSA102_J03_mebendazole 10_uM 6_hours MCF7


title: MSA102_I22_lycorine 10_uM 6_hours 2011-3-12

value: lycorine


title: MSA102_J01_DMSO NA 6_hours MCF7


title: MSA102_J02_DMSO NA 6_hours SH-SY5Y


title: MSA102_I21_lycorine 10_uM 6_hours 3121-2-1


title: ESCC_GE011B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_I24_TCB-2 0.1_uM 6_hours 2011-3-12


title: Column_2_Control


title: ESCC_GE008B_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_3_Control


title: ESCC_GE008T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_I20_diltiazem 3_uM 6_hours 2011-3-12

value: diltiazem


title: MSA102_I19_diltiazem 3_uM 6_hours 3121-2-1


title: ESCC_GE007T_SNP5

description: Hybridized to Affymetrix SNP array


title: Column_1 _Control


title: MSA102_I17_Ziprasidone 0.1_uM 6_hours 3121-2-1

value: Ziprasidone


title: MSA102_I18_Ziprasidone 0.1_uM 6_hours 2011-3-12


title: ESCC_GE006T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_I16_DMSO NA 6_hours 2011-3-12

value: DMSO


title: ESCC_GE006B_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE007B_SNP5

description: Hybridized to Affymetrix SNP array


title: refed-240min_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Basecalls with RTA v2 (Illumina)
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Mapping: alignment versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a  with the parameter “--outFilterMismatchNoverLmax 0.1"
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: library size and batch effect normalized count tables

source_name: Liver

extract_protocol:
mRNA was isolated following the manufacture’s instructions (Qiagen RNeasy Mini Kit)
Library has been generated using the lluminas TruSeq mRNA stranded protocol, following the manufacture’s instructions

tag: strain

tag: genotype

value: WT

value: 16h fasting + 240min caged food


title: caged-240min_3


title: caged-240min_1

value: 16h fasting + 240min refed


title: MSA102_I13_suloctidil 10_uM 6_hours 3121-2-1

value: suloctidil


title: caged-240min_2


title: ESCC_GE005T_SNP5

description: Hybridized to Affymetrix SNP array

tag: disease state

value: ESCC

tag: case id

value: esophageal squamous cell carcinoma tissue


title: MSA102_I12_vigabatrin 10_uM 6_hours 2011-3-12

tag: perturbagen

value: vigabatrin


title: MSA102_J10_spiradoline 0.1_uM 6_hours SH-SY5Y

tag: cell id

value: test


title: MSA102_I06_trimethobenzamide 1_uM 6_hours 2011-3-12

tag: dosage


title: MSA102_I11_vigabatrin 10_uM 6_hours 3121-2-1

tag: batch


title: MSA102_I09_spiradoline 0.1_uM 6_hours 3121-2-1

value: spiradoline

tag: duration


title: MSA102_I14_suloctidil 10_uM 6_hours 2011-3-12

tag: perturbation type


title: MSA102_I07_chlorcyclizine 1_uM 6_hours 3121-2-1

tag: well id


title: ESCC_GE004B_SNP5

description: Hybridized to Affymetrix SNP array

tag: tissue

value: blood from esophageal squamous cell carcinoma patient


title: MSA102_I05_trimethobenzamide 1_uM 6_hours 3121-2-1

value: trimethobenzamide

tag: plate id


title: MSA102_I10_spiradoline 0.1_uM 6_hours 2011-3-12


title: refed-240min_1


title: MSA102_I15_DMSO NA 6_hours 3121-2-1

value: vehicle


title: caged-120min_3

value: 16h fasting + 120min caged food


title: ESCC_GE005B_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_I08_chlorcyclizine 1_uM 6_hours 2011-3-12

value: chlorcyclizine


title: MSA102_I04_mebendazole 10_uM 6_hours 2011-3-12

value: mebendazole


title: ESCC_GE003B_SNP5

description: Hybridized to Affymetrix SNP array


title: ESCC_GE004T_SNP5

description: Hybridized to Affymetrix SNP array


title: MSA102_I02_DMSO NA 6_hours 2011-3-12


title: MSA102_I01_DMSO NA 6_hours 3121-2-1


title: B5_18

city: New York

first: Gregory

last: David

state: NY

address: 550 1st Avenue, 411

department: Biochemistry and Molecular Pharmacology

institute: New York University School of Medicine

data_processing:
Reads were evaluated using FastQC
Raw reads were trimmed using Trimmomatic with a window size of 4 and quality threshold of 10
Reads were alligned to the genome using Tophat with default settings
Read counts were generated using HTSeq-count
To determine differntial expression the edgeR statistical package was used and the generalized linear model likelihood ratio test was applied using the function glmLRT()
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files including logCPM and logFC

growth_protocol: T98G cells were maintained in 10%FBS in 1X DMEM with 1%P/S.

extract_protocol:
Cells were scraped into RLT Buffer and RNA was harvested using Qiagen's Rneasy Mini Kit.
RNA quality was evaluated using an Agilent 2100 Bioanalyzer instrument. 500ng of RNA was used to prepare libraries using the TruSeq Stranded Total RNA kit from Illumina on an automated platform.

treatment_protocol: To induce quiescence, cells were serum starved for 72 hours. After subculturing cells, they were washed 3X with 1XPBS and once with 1X DMEM + 1%P/S. Then cells were kept in fresh 1X DMEM +1%P/S. After 72 hours, plates were released into 10% FBS in 1XDMEM and harvested at indicated time points.

tag: cell line

value: Human glioblastoma multiforme

tag: group

value: CRISPR KO Clone

tag: treatment/time point

value: 18 hours after serum addition

tag: genotype/variation

value: Sin3B KO


title: caged-120min_1

tag: strain

value: WT

tag: treatment


title: ESCC_GE001T_SNP5

description: Hybridized to Affymetrix SNP array

tag: disease state


title: B5_T10

tag: cell type

value: 10 hours after serum addition


title: G6_T18


title: ESCC_GE003T_SNP5

description: Hybridized to Affymetrix SNP array

value: ESCC

tag: case id


title: ESCC_GE002B_SNP5

description: Hybridized to Affymetrix SNP array


title: refed-120min_3

tag: genotype

value: 16h fasting + 120min refed


title: caged-120min_2


title: MSA102_H20_DL-thiorphan 1_uM 6_hours SH-SY5Y

tag: perturbagen

value: DL-thiorphan

tag: cell id

tag: dosage


title: G6_T0

value: Serum starved


title: ESCC_GE002T_SNP5

description: Hybridized to Affymetrix SNP array

value: esophageal squamous cell carcinoma tissue


title: B5_T0


title: MSA102_H19_DL-thiorphan 1_uM 6_hours MCF7

tag: batch

tag: duration

tag: perturbation type

value: test


title: MSA102_I03_mebendazole 10_uM 6_hours 3121-2-1

tag: well id

tag: plate id


title: G6_T10

tag: cell line

tag: group


title: refed-120min_1


title: refed-120min_2


title: fasted_3

value: 16h fasting


title: D11_T0

value: CRISPR WT Clone

tag: treatment/time point

tag: genotype/variation

value: wild type


title: refed-240min_2

tag: strain

tag: treatment

value: 16h fasting + 240min refed


title: WT_T18

tag: cell type

value: Parental cell line

value: parental


title: ESCC_GE001B_SNP5

description: Hybridized to Affymetrix SNP array

tag: disease state

tag: case id

tag: tissue

value: blood from esophageal squamous cell carcinoma patient


title: D11_T10

value: Human glioblastoma multiforme


title: D11_T18

value: 18 hours after serum addition


title: WT_T10


title: WT_T0


title: fasted_2

tag: genotype

value: WT


title: caged-60min_3

value: 16h fasting + 60min caged food


title: fasted_1


title: D456_CHD7_32_B

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

data_processing:
adapter trimming using trimgalore v0.4.1
fastqc v0.10.1 for quality score assessment
star version v2,5,2b for alignment
ht-seq-gene v 0.5.3 to consoldiate reads to features
Genome_build: hg37
Supplementary_files_format_and_content: raw count table at the gene level for all 12 samples

molecule: polyA RNA

source_name: D456 GBM xenograft cells

growth_protocol: Cells were grown in DMEM/F12, 1% pen/strep, 1% sodium pyruvate and 10ug recombinant EGF and FGF. Maintained at 37C with 5% CO2.

extract_protocol:
RNA was extracted with TRIzol.
NEBNext Ultra RNA Library Prep Kit for Illumina with polyA selection

treatment_protocol: Cells were infected with lentivirus containing shRNA targeting CHD7 and grown for 72 hours with puromycin to select for the plasmid.

value: CHD7 shRNA#32

tag: replicate #


title: caged-60min_1


title: caged-60min_2


title: D456_CHD7_29_B

value: CHD7 shRNA#29


title: D456_NT_B

value: non-targeting shRNA


title: MSA102_H21_3-acetamidocoumarin 10_uM 6_hours MCF7

tag: perturbagen

tag: cell id

tag: dosage

tag: batch


title: MSA102_H22_3-acetamidocoumarin 10_uM 6_hours SH-SY5Y

tag: duration

tag: perturbation type

tag: well id

tag: plate id


title: refed-60min_3

value: 16h fasting + 60min refed


title: refed-60min_2


title: NPC_CHD7_32_B

source_name: Neural progenitor cells


title: MSA102_H15_prenylamine 9.6_uM 6_hours MCF7

value: prenylamine


title: MSA102_H10_trichostatin NA 6_hours SH-SY5Y

value: trichostatin

value: poscon


title: MSA102_H17_Prestwick-675 10_uM 6_hours MCF7

value: test


title: MSA102_H18_Prestwick-675 10_uM 6_hours SH-SY5Y


title: MSA102_H23_DMSO NA 6_hours MCF7

value: DMSO

value: vehicle


title: refed-60min_1


title: NPC_CHD7_29_B


title: MSA102_H24_DMSO NA 6_hours SH-SY5Y


title: MSA102_H12_4-hydroxyphenazone 10_uM 6_hours SH-SY5Y


title: NPC_NT_B


title: caged-30min_3

value: 16h fasting + 30min caged food


title: MSA102_H09_trichostatin NA 6_hours MCF7


title: MSA102_H07_emetine 7.2_uM 6_hours MCF7

value: emetine


title: MSA102_H03_Loxapine 1_uM 6_hours MCF7

value: Loxapine


title: MSA102_H06_melatonin 1_uM 6_hours SH-SY5Y

value: melatonin


title: MSA102_H14_Primidone 10_uM 6_hours SH-SY5Y

value: Primidone


title: MSA102_G23_DMSO NA 6_hours 3121-2-1


title: MSA102_H11_4-hydroxyphenazone 10_uM 6_hours MCF7


title: MSA102_G21_3-acetamidocoumarin 10_uM 6_hours 3121-2-1


title: MSA102_G24_DMSO NA 6_hours 2011-3-12


title: MSA102_H08_emetine 7.2_uM 6_hours SH-SY5Y


title: MSA102_H05_melatonin 1_uM 6_hours MCF7


title: MSA102_H13_Primidone 10_uM 6_hours MCF7


title: MSA102_H04_Loxapine 1_uM 6_hours SH-SY5Y


title: MSA102_H16_prenylamine 9.6_uM 6_hours SH-SY5Y


title: caged-30min_1

value: WT


title: D456_CHD7_32_A


title: MSA102_G22_3-acetamidocoumarin 10_uM 6_hours 2011-3-12


title: MSA102_H01_diflorasone 8_uM 6_hours MCF7

value: diflorasone


title: MSA102_G18_Prestwick-675 10_uM 6_hours 2011-3-12


title: MSA102_G20_DL-thiorphan 1_uM 6_hours 2011-3-12

value: DL-thiorphan


title: MSA102_G19_DL-thiorphan 1_uM 6_hours 3121-2-1


title: D456_CHD7_29_A

value: CHD7 shRNA#29


title: refed-30min_2

value: 16h fasting + 30min refed


title: refed-30min_3


title: D456_NT_A

value: non-targeting shRNA


title: NPC_CHD7_29_A


title: NPC_CHD7_32_A

value: CHD7 shRNA#32


title: MSA102_G17_Prestwick-675 10_uM 6_hours 3121-2-1


title: refed-30min_1


title: MSA102_H02_diflorasone 8_uM 6_hours SH-SY5Y


title: caged-30min_2


title: NPC_NT_A


title: Sample_LI-48

data_processing:
Single-end reads were aligned using STAR (Version 2.5.1b)
Mapped reads were counted using subread featurecounts function
Genes with at least 1 count per million mapped reads in at least 5 libraries were retained for further analysis
Gene counts were normalized using the TMM method, and transformed using the voom function
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include a matrix of genes x samples. Values for "Readhead_2018_RNAseq_gene_counts.txt" are gene counts, and values for "Readhead_2018_RNAseq_gene_normalized.txt" are log2 normalized gene abundance.

source_name: SZ_hiPSC NPCs_MPB

growth_protocol: hiPSC forebrain NPCs were derived as described previously (Brennand et al., 2011 Nature; Hoffman et al, 2017 Nat Communications). For hiPSC NPCs, growth media used was DMEM/F12 + GlutaMAX™ -I (ThermoFisher Scientific, Cat. No. 10565, Lot No. 1715888) containing 1x N2 (ThermoFisher Scientific, Cat. No. 17502-048, Lot No. 1672893), 1x B27-RA (ThermoFisher Scientific, Cat. No. 12587-010, Lot No. 1731195) and 20 ng·ml−1 FGF2 (R&D Systems, Cat. No. 233-FB, Lot No. HKW12815061). Accutase for cell dissociation was from Innovative Cell Technologies (Cat. No. AT-104, Lot No. 5S2415A). Cyto One (USA Scientific) and Corning (Fisher Scientific) culture plasticware was used for expansion and plating of cells. hiPSC NPCs were grown on Matrigel (BD Biosciences, Cat. No. 354230, Lot No. 3018665) coated plates in NPC media. NPC experiments were conducted on myocoplasma-free passage-matched populations, generally between passages five and seven.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols (Ribo-Zero)

treatment_protocol: NPCs were treated for 6 hours with equivalent volumes of DMSO, methylparaben (10uM) or loxapine (1uM) for 6 hours.

tag: diagnosis

value: SZ

value: hiPSC Neural Progenitor Cells

value: MPB


title: MSA102_G15_prenylamine 9.6_uM 6_hours 3121-2-1

data_processing: Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.

extract_protocol: Cells were lysed with cell lysis buffer (110 µL per well), and stored at -80⁰C

value: prenylamine

value: test


title: MSA102_G12_4-hydroxyphenazone 10_uM 6_hours 2011-3-12


title: MSA102_G14_Primidone 10_uM 6_hours 2011-3-12


title: Sample_LI-47

source_name: SZ_hiPSC NPCs_DMSO

value: DMSO


title: MSA102_G08_emetine 7.2_uM 6_hours 2011-3-12

value: emetine


title: MSA102_G10_trichostatin NA 6_hours 2011-3-12

value: trichostatin

value: poscon


title: MSA102_G16_prenylamine 9.6_uM 6_hours 2011-3-12