title: Paroxetine dose level 8 bio rep 7 [Par_P3_G09_S13]

description:
96 well plate
Par_P3_G09_S13_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650049_R07C01]

status: Public on Jan 01 2023

type: genomic

city: Alhambra

first: Yi-Tsung

last: Lu

state: CA

address: 516 SAN PASQUAL DR

country: USA

institute: University of Southern California

description: pre-treatment

hyb_protocol: cfDNA was prepared using Infinium HD FFPE Assay, and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
data was processed using Sesame package in R
processed data matrix: beta value was calculated based on default parameters of Sesame package

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: cfDNA methylation

label_protocol: Standard Illumina Protocol

extract_protocol: cfDNA extracted by QIAamp Circulating Nucleic Acid kit

tag: response

value: STA/INC

tag: disease

value: muscle invasive bladder cancer


title: GL26150_CD3posP1_A08_R1

type: SRA

city: Boston

first: Elizabeth

last: Perez

state: MA

address: 30 Fruit Street

institute: MGH

library_source: transcriptomic single cell

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

tag: tissue

value: brain

tag: cell type

value: Tcell

tag: treatment


title: Paroxetine dose level 7 bio rep 7 [Par_P3_G08_S12]

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

description:
96 well plate
Par_P3_G08_S12_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

library_source: transcriptomic

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads from each sample's RNA-Seq fastq(.gz) file were mapped with STAR (Dobin, et. al) v2.7.1a to indexed FHM genome with 26,150 gene models loaded within the genome (WIOS00000000; BioSample SAMN12875914). STAR "--quantMode GeneCounts" was used to produce raw counts from the mapping; reverse strand count column was used as dictated by sequencing protocol. Genomic gene and transcript coordinates and associated annotations are contained in files WIOS01.1.gbff.gz, WIOS01.2.gbff.gz and WIOS01.3.gbff.gz available at https://www.ncbi.nlm.nih.gov/Traces/wgs/WIOS01?display=contigs. Uniprot accessions associated with gene models are available from the authors.
Samples with <2 million raw counts and/or less than 50% unique mapping rate were removed, and within-chemical features (genes) with mean raw counts <5 across all samples were filtered from respective raw counts matrices.
For each chemical, the raw counts for the remaining features were normalized to counts per million reads (CPM), and after adding a pseudo-count of 1 to prevent taking log of zero counts, log2 transformed.
For each chemical, an MDS plot of the normalized data was generated. Individual samples separated from all remaining samples on either principle component #1 (PC1) or principle component #2 (PC2) by >2x the span of all other samples on the corresponding PC were removed from further analysis. Qualitative assessment was applied and samples with a relatively large Euclidean distance from all other remaining samples on MDS plots were also excluded, along with samples especially distant from corresponding replicates within dose.
Assembly: EPA_FHM_2.0.b
Supplementary files format and content: For each chemical, tab delimited text matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: For each sample, tab delimited text matrix table with normalized expression values for every gene and every sample that passed all filtering.

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Larvae remained in their 1 mL deep wells, exposure solution was removed and replaced with lysis buffer, a bead was added to each well, and subjects were homogenized in their wells.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

treatment_protocol: For ten different chemicals, 24h post-hatch individual fathead minnow larvae were statically exposed in 96 deep well plates to controls and a half-log dilution series of treatment concentrations. Exposures were for 24 hours. Subjects from all doses that did not exhibit excessive levels of mortality were further processed.

value: whole body

tag: developmental stage

value: larva

tag: age

value: 5 dpf/24 hr post hatch

tag: Sex

value: Paroxetine

tag: concentration

tag: time point

value: 24 hr


title: cfDNA from pre-treatment patients [203490650049_R06C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650045_R06C01]

description: pre-treatment


title: Paroxetine dose level 6 bio rep 7 [Par_P3_G07_S11]

description:
96 well plate
Par_P3_G07_S11_L006
Par.raw.counts.txt
na


title: GL26150_CD3posP1_F07_R1


title: GL26150_CD3posP1_F12_R1


title: cfDNA from pre-treatment patients [203490650014_R04C01]

description: pre-treatment


title: Paroxetine control bio rep 8 [Par_P3_H01_S16]

description:
96 well plate
Par_P3_H01_S16_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650042_R04C01]

description: pre-treatment


title: Paroxetine dose level 5 bio rep 7 [Par_P3_G06_S10]

description:
96 well plate
Par_P3_G06_S10_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650016_R04C01]

description: pre-treatment

value: DWNSTG


title: Paroxetine dose level 4 bio rep 7 [Par_P3_G05_S9]

description:
96 well plate
Par_P3_G05_S9_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_G09_R1


title: GL26150_CD3posP1_A04_R1


title: cfDNA from pre-treatment patients [203490650016_R03C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650045_R04C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650044_R04C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650023_R05C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650045_R03C01]

description: pre-treatment


title: GL26150_CD3posP1_F01_R1


title: Paroxetine dose level 3 bio rep 7 [Par_P3_G04_S8]

description:
96 well plate
Par_P3_G04_S8_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_H12_R1


title: Paroxetine dose level 2 bio rep 7 [Par_P3_G03_S7]

description:
96 well plate
Par_P3_G03_S7_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650016_R02C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650014_R03C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650042_R03C01]

description: pre-treatment


title: GL26150_CD3posP1_F08_R1


title: cfDNA from pre-treatment patients [203490650028_R07C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650045_R05C01]

description: pre-treatment


title: Paroxetine dose level 1 bio rep 7 [Par_P3_G02_S6]

description:
96 well plate
Par_P3_G02_S6_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_H11_R1


title: cfDNA from pre-treatment patients [203490650020_R05C01]

description: pre-treatment


title: GL26150_CD3posP1_E10_R1


title: cfDNA from pre-treatment patients [203490650028_R06C01]

description: pre-treatment


title: Paroxetine dose level 10 bio rep 6 [Par_P3_F11_S76]

description:
96 well plate
Par_P3_F11_S76_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650020_R06C01]

description: pre-treatment


title: GL26150_CD3posP1_G01_R1


title: cfDNA from pre-treatment patients [203490650028_R05C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650063_R05C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650028_R04C01]

description: pre-treatment


title: Paroxetine dose level 8 bio rep 6 [Par_P3_F09_S78]

description:
96 well plate
Par_P3_F09_S78_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650049_R05C01]

description: pre-treatment


title: Paroxetine dose level 9 bio rep 6 [Par_P3_F10_S77]

description:
96 well plate
Par_P3_F10_S77_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650045_R02C01]

description: pre-treatment


title: GL26150_CD3posP1_D01_R1


title: GL26150_CD3posP1_E04_R1


title: cfDNA from pre-treatment patients [203490650020_R04C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650028_R03C01]

description: pre-treatment


title: GL26150_CD3posP1_E05_R1


title: cfDNA from pre-treatment patients [203490650044_R03C01]

description: pre-treatment


title: Paroxetine dose level 5 bio rep 6 [Par_P3_F06_S74]

description:
96 well plate
Par_P3_F06_S74_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650020_R03C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650042_R02C01]

description: pre-treatment


title: Paroxetine dose level 4 bio rep 6 [Par_P3_F05_S75]

description:
96 well plate
Par_P3_F05_S75_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650023_R04C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650028_R02C01]

description: pre-treatment


title: GL26150_CD3posP1_H08_R1


title: Paroxetine control bio rep 7 [Par_P3_G01_S22]

description:
96 well plate
Par_P3_G01_S22_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_F05_R1


title: cfDNA from pre-treatment patients [203490650028_R01C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650014_R02C01]

description: pre-treatment


title: Paroxetine dose level 2 bio rep 6 [Par_P3_F03_S70]

description:
96 well plate
Par_P3_F03_S70_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_G06_R1


title: Paroxetine dose level 3 bio rep 6 [Par_P3_F04_S69]

description:
96 well plate
Par_P3_F04_S69_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 1 bio rep 6 [Par_P3_F02_S71]

description:
96 well plate
Par_P3_F02_S71_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 7 bio rep 6 [Par_P3_F08_S73]

description:
96 well plate
Par_P3_F08_S73_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_A03_R1


title: cfDNA from pre-treatment patients [203490650020_R02C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650014_R01C01]

description: pre-treatment


title: GL26150_CD3posP1_A10_R1


title: GL26150_CD3posP1_D03_R1


title: cfDNA from pre-treatment patients [203490650016_R01C01]

description: pre-treatment


title: Paroxetine control bio rep 6 [Par_P3_F01_S72]

description:
96 well plate
Par_P3_F01_S72_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650044_R02C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650023_R02C01]

description: pre-treatment


title: Paroxetine dose level 10 bio rep 5 [Par_P3_E11_S65]

description:
96 well plate
Par_P3_E11_S65_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650023_R01C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650020_R01C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650049_R03C01]

description: pre-treatment


title: GL26150_CD3posP1_E02_R1


title: cfDNA from pre-treatment patients [203490650023_R03C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650042_R01C01]

description: pre-treatment


title: GL26150_CD3posP1_D08_R1


title: Paroxetine dose level 8 bio rep 5 [Par_P3_E09_S67]

description:
96 well plate
Par_P3_E09_S67_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650049_R02C01]

description: pre-treatment


title: GL26150_CD3posP1_H02_R1


title: cfDNA from pre-treatment patients [203490650049_R01C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650044_R01C01]

description: pre-treatment


title: Paroxetine dose level 7 bio rep 5 [Par_P3_E08_S68]

description:
96 well plate
Par_P3_E08_S68_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650045_R01C01]

description: pre-treatment


title: Paroxetine dose level 6 bio rep 5 [Par_P3_E07_S83]

description:
96 well plate
Par_P3_E07_S83_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from healthy donor 2, 50ng [203220070049_R08C01]

description: HD

value: healthy


title: cfDNA from healthy donor 2, 20ng [203220070049_R07C01]

description: HD


title: GL26150_CD3posP1_C01_R1


title: Paroxetine dose level 5 bio rep 5 [Par_P3_E06_S82]

description:
96 well plate
Par_P3_E06_S82_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from healthy donor 2, 10ng [203220070049_R06C01]

description: HD


title: cfDNA from healthy donor 2, 10ng [203220070049_R05C01]

description: HD


title: Paroxetine dose level 4 bio rep 5 [Par_P3_E05_S85]

description:
96 well plate
Par_P3_E05_S85_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_F10_R1


title: GL26150_CD3posP1_C10_R1


title: cfDNA from healthy donor 1, 50ng [203220070049_R04C01]

description: HD


title: GL26150_CD3posP1_F03_R1


title: cfDNA from healthy donor 1, 20ng [203220070049_R03C01]

description: HD


title: Paroxetine dose level 9 bio rep 5 [Par_P3_E10_S66]

description:
96 well plate
Par_P3_E10_S66_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 3 bio rep 5 [Par_P3_E04_S84]

description:
96 well plate
Par_P3_E04_S84_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_B02_R1


title: Paroxetine dose level 2 bio rep 5 [Par_P3_E03_S80]

description:
96 well plate
Par_P3_E03_S80_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from healthy donor 1, 10ng [203220070049_R01C01]

description: HD


title: GL26150_CD3posP1_F04_R1


title: Paroxetine dose level 1 bio rep 5 [Par_P3_E02_S79]

description:
96 well plate
Par_P3_E02_S79_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from healthy donor 1, 10ng [203220070049_R02C01]

description: HD


title: GL26150_CD3posP1_G11_R1


title: Inactivated vaccine bio rep3

city: Tianjin

first: Zexing

last: Li

address: No.92 Weijin road

department: School of Life Sciences

country: China

institute: Tianjin University

data_processing:
The raw fastq files were analyzed using FastQC (v0.11.9)
Sequencing adaptors and low quality (base quality score<20) reads were trimmed by trim galore (v0.6.6). Reads shorter than 20nt were discarded.
The trimmed reads were aligned to the Gallus gallus (chicken) (GCF_016699485.2) by Hisat2 (v2.2.1)
The aligned data was further proceeded by Samtools (v1.3.1).
The transcript was quantified by String Tie (v2.1.7).
Assembly: bGalGal1.mat.broiler.GRCg7b(GCF_016699485.2)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample, csv format file inludes gene count matrix for each Sample

organism: Gallus gallus

source_name: bursa of Fabricius

extract_protocol:
RNA was harvested using TRIzol Reagent (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 2 week old chickens were immunized for the indicated vaccination program and  three chickens were randomly selected in each group. The total RNA of bursa of Fabricius  were isolated and sent to RNA-seq

value: bursa of Fabricius

tag: genotype

value: Inactivated vaccine


title: Inactivated vaccine bio rep1


title: H1520-165-200C-miRNA [CXA]

city: Reykjavík

first: Quentin

last: Horta-Lacueva

address: Sturlugötu 7

country: Iceland

institute: University of Iceland

description: H1520-165-200C-miRNA [CXA]

data_processing:
reads quality assesment with FASTQC
adapter sequence removal with Cutadapt (only for miRNA files)
miRNA: transcripts quantification with MiRDeep2
miRNA: pre-processing and genome mapping with the MiRDeep2 Mapping module
miRNA: read couting with miRDeep2 Quantifier module, using the MiRBase reference database for all species
miRNA: removed sequences exhibiting at least 95% similarity across species using Cd-hit
mRNA: reads alignment with STAR, options --outSAMstrandField intronMotif  --twopassMode Basic
mRNA: read counts with FeatureCounts, gene level
Genome_build: ASM291031v2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Salvelinus alpinus

source_name: whole embryo

growth_protocol: embryos were reared in a common hatching tray

extract_protocol:
Total RNA was isolated from the samples and enriched for small RNAs using the mirVana kit (Ambion).
The samples were divided into 3 batches, each containing 3 embryos per family, to produce the sequencing libraries.

tag: cross type

value: PLxSB

tag: family

tag: individual

value: C

tag: developmental timepoint

tag: sequencing batch


title: H1520-165-200B-miRNA [BYA]

description: H1520-165-200B-miRNA [BYA]

value: B


title: Paroxetine dose level 10 bio rep 4 [Par_P3_D11_S51]

description:
96 well plate
Par_P3_D11_S51_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine control bio rep 5 [Par_P3_E01_S81]

description:
96 well plate
Par_P3_E01_S81_L007
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: ST1814G/H5HA bio rep2


title: GL26150_CD3posP1_C09_R1


title: ST1814G/H5HA bio rep3


title: Inactivated vaccine bio rep2


title: Paroxetine dose level 9 bio rep 4 [Par_P3_D10_S48]

description:
96 well plate
Par_P3_D10_S48_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: ST1814G/H5HA bio rep1


title: H1520-165-200A-miRNA [AYA]

description: H1520-165-200A-miRNA [AYA]

value: A


title: GL26150_CD3posP1_E01_R1


title: H1520-165-150C-miRNA [CWA]

description: H1520-165-150C-miRNA [CWA]


title: ST1814G bio rep3


title: Paroxetine dose level 8 bio rep 4 [Par_P3_D09_S47]

description:
96 well plate
Par_P3_D09_S47_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: H1520-165-150B-miRNA [BXA]

description: H1520-165-150B-miRNA [BXA]


title: GL26150_CD3posP1_D10_R1


title: ST1814G bio rep2


title: H1520-165-150A-miRNA [AXA]

description: H1520-165-150A-miRNA [AXA]


title: Paroxetine dose level 6 bio rep 4 [Par_P3_D07_S49]

description:
96 well plate
Par_P3_D07_S49_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_E03_R1


title: GL26150_CD3posP1_A05_R1


title: ST1814G bio rep1


title: H1516-161-200C-miRNA [CVA]

description: H1516-161-200C-miRNA [CVA]

value: PLxPL


title: Paroxetine dose level 5 bio rep 4 [Par_P3_D06_S44]

description:
96 well plate
Par_P3_D06_S44_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_H01_R1


title: GL26150_CD3posP1_C07_R1


title: Paroxetine dose level 4 bio rep 4 [Par_P3_D05_S43]

description:
96 well plate
Par_P3_D05_S43_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: sham Cer_18

city: Bronx

first: Rita

last: De Gasperi

state: NY

address: 130 West Kingsbridge Road

institute: JJ Peters VA Medical Center

data_processing:
Original data file form high throughput sequencing transformed into raw data by CASAVA
Data filtering: remove reads containing adaptors, reads with uncertain bases when uncertain nucleotides are >10%, remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 20.
HSAT2 to map filtered sequence to reference genome
Assembly: rattus norvegisu relase 80
Supplementary files format and content: tab delimited text files

organism: Rattus norvegicus

source_name: brain-cerebellum

extract_protocol:
RNA extracted with Qiazol reagent and purified by RNAeasy mini kit (Qiagen)
Libraries were constructed from 1 mg of total RNA using the NEBNextUltraRNA Library Prep kit from Illumina (NEB, Ipswich, MA)

value: brain-cerebellum

value: 6wk post exposure

value: sham-exposed


title: sham Cer_16


title: GL26150_CD3posP1_B03_R1

value: brain

value: Tcell


title: H1516-161-200A-miRNA [AWA]

description: H1516-161-200A-miRNA [AWA]


title: sham Cer_10


title: H1516-161-150C-miRNA [CTA]

description: H1516-161-150C-miRNA [CTA]


title: sham Cer_13


title: GL26150_CD3posP1_A11_R1


title: H1516-161-150B-miRNA [BVA]

description: H1516-161-150B-miRNA [BVA]


title: Paroxetine dose level 7 bio rep 4 [Par_P3_D08_S50]

description:
96 well plate
Par_P3_D08_S50_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: Paroxetine dose level 1 bio rep 4 [Par_P3_D02_S59]

description:
96 well plate
Par_P3_D02_S59_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

value: Paroxetine

value: 24 hr


title: Paroxetine dose level 2 bio rep 4 [Par_P3_D03_S45]

description:
96 well plate
Par_P3_D03_S45_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast Cer_9

value: blast-exposed


title: Paroxetine control bio rep 4 [Par_P3_D01_S60]

description:
96 well plate
Par_P3_D01_S60_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_A09_R1


title: H1516-161-150A-miRNA [AVA]

description: H1516-161-150A-miRNA [AVA]


title: Paroxetine dose level 10 bio rep 3 [Par_P3_C11_S57]

description:
96 well plate
Par_P3_C11_S57_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_F09_R1


title: H1514-159-200C-miRNA [CSA]

description: H1514-159-200C-miRNA [CSA]


title: GL26150_CD3posP1_C11_R1


title: H1514-159-200B-miRNA [BTA]

description: H1514-159-200B-miRNA [BTA]


title: Paroxetine dose level 9 bio rep 3 [Par_P3_C10_S58]

description:
96 well plate
Par_P3_C10_S58_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast Cer_5


title: GL26150_CD3posP1_D06_R1


title: blast Cer_6


title: H1516-161-200B-miRNA [BWA]

description: H1516-161-200B-miRNA [BWA]


title: H1514-159-200A-miRNA [ATA]

description: H1514-159-200A-miRNA [ATA]


title: blast Cer_2


title: blast Cer_1


title: Paroxetine dose level 8 bio rep 3 [Par_P3_C09_S63]

description:
96 well plate
Par_P3_C09_S63_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 3 bio rep 4 [Par_P3_D04_S46]

description:
96 well plate
Par_P3_D04_S46_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_C06_R1


title: GL26150_CD3posP1_C12_R1


title: H1514-159-150C-miRNA [CRA]

description: H1514-159-150C-miRNA [CRA]


title: GL26150_CD3posP1_D07_R1


title: Paroxetine dose level 7 bio rep 3 [Par_P3_C08_S64]

description:
96 well plate
Par_P3_C08_S64_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: H1514-159-150B-miRNA [BSA]

description: H1514-159-150B-miRNA [BSA]


title: sham AC-16

source_name: brain-anterior cortex

value: brain-anterior cortex


title: Paroxetine dose level 5 bio rep 3 [Par_P3_C06_S62]

description:
96 well plate
Par_P3_C06_S62_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_E11_R1


title: H1514-159-150A-miRNA [ASA]

description: H1514-159-150A-miRNA [ASA]

value: PLxSB


title: sham AC_13


title: H1513-158-200C-miRNA [CUA]

description: H1513-158-200C-miRNA [CUA]

value: C


title: sham AC_12


title: GL26150_CD3posP1_A07_R1


title: Paroxetine dose level 4 bio rep 3 [Par_P3_C05_S54]

description:
96 well plate
Par_P3_C05_S54_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: sham AC_10


title: GL26150_CD3posP1_C05_R1


title: Paroxetine dose level 3 bio rep 3 [Par_P3_C04_S55]

description:
96 well plate
Par_P3_C04_S55_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 2 bio rep 3 [Par_P3_C03_S52]

description:
96 well plate
Par_P3_C03_S52_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_H07_R1


title: H1513-158-200A-miRNA [ARA]

description: H1513-158-200A-miRNA [ARA]


title: Paroxetine dose level 1 bio rep 3 [Par_P3_C02_S53]

description:
96 well plate
Par_P3_C02_S53_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast AC_6


title: sham AC_18


title: H1513-158-150C-miRNA [CQA]

description: H1513-158-150C-miRNA [CQA]


title: blast AC_1


title: blast AC_5


title: GL26150_CD3posP1_B04_R1


title: Paroxetine dose level 10 bio rep 2 [Par_P3_B11_S24]

description:
96 well plate
Par_P3_B11_S24_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine control bio rep 3 [Par_P3_C01_S56]

description:
96 well plate
Par_P3_C01_S56_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_H04_R1


title: H1513-158-150B-miRNA [BQ7]

description: H1513-158-150B-miRNA [BQ7]

value: B


title: GL26150_CD3posP1_B12_R1


title: Paroxetine dose level 6 bio rep 3 [Par_P3_C07_S61]

description:
96 well plate
Par_P3_C07_S61_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: sham Amy-16

source_name: brain-amygdala

value: brain-amygdala


title: sham Amy_18


title: GL26150_CD3posP1_E07_R1


title: GL26150_CD3posP1_E06_R1


title: H1512-157-200B-miRNA [BPA]

description: H1512-157-200B-miRNA [BPA]


title: H1512-157-200C-miRNA [CPA]

description: H1512-157-200C-miRNA [CPA]


title: Paroxetine dose level 9 bio rep 2 [Par_P3_B10_S22]

description:
96 well plate
Par_P3_B10_S22_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: sham Amy_13


title: H1513-158-200B-miRNA [BRA]

description: H1513-158-200B-miRNA [BRA]

value: PLxPL


title: H1512-157-150C-miRNA [COA]

description: H1512-157-150C-miRNA [COA]


title: Paroxetine dose level 7 bio rep 2 [Par_P3_B08_S35]

description:
96 well plate
Par_P3_B08_S35_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_H06_R1


title: sham Amy_12


title: H1512-157-200A-miRNA [APA]

description: H1512-157-200A-miRNA [APA]

value: A


title: H1513-158-150A-miRNA [AQA]

description: H1513-158-150A-miRNA [AQA]


title: H1512-157-150B-miRNA [BOA]

description: H1512-157-150B-miRNA [BOA]


title: GL26150_CD3posP1_A06_R1


title: GL26150_CD3posP1_B11_R1


title: Paroxetine dose level 5 bio rep 2 [Par_P3_B06_S33]

description:
96 well plate
Par_P3_B06_S33_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast Amy_9

value: 6wk post exposure


title: Paroxetine dose level 6 bio rep 2 [Par_P3_B07_S34]

description:
96 well plate
Par_P3_B07_S34_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 4 bio rep 2 [Par_P3_B05_S32]

description:
96 well plate
Par_P3_B05_S32_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast Amy_5


title: blast Amy_2


title: GL26150_CD3posP1_G03_R1


title: Paroxetine dose level 8 bio rep 2 [Par_P3_B09_S23]

description:
96 well plate
Par_P3_B09_S23_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast Amy_6


title: Paroxetine dose level 2 bio rep 2 [Par_P3_B03_S38]

description:
96 well plate
Par_P3_B03_S38_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_F06_R1


title: H1512-157-150A-miRNA [AOA]

description: H1512-157-150A-miRNA [AOA]


title: H1509-154-200B-miRNA [BNA]

description: H1509-154-200B-miRNA [BNA]


title: H1509-154-200A-miRNA [ANA]

description: H1509-154-200A-miRNA [ANA]


title: H1509-154-200C-miRNA [CNA]

description: H1509-154-200C-miRNA [CNA]


title: Paroxetine dose level 3 bio rep 2 [Par_P3_B04_S39]

description:
96 well plate
Par_P3_B04_S39_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_B01_R1


title: H1509-154-150C-miRNA [CMA]

description: H1509-154-150C-miRNA [CMA]


title: blast Amy_1


title: H1509-154-150B-miRNA [BMA]

description: H1509-154-150B-miRNA [BMA]


title: Paroxetine dose level 10 bio rep 1 [Par_P3_A11_S28]

description:
96 well plate
Par_P3_A11_S28_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 1 bio rep 2 [Par_P3_B02_S37]

description:
96 well plate
Par_P3_B02_S37_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_A12_R1


title: sham Hip_18

source_name: brain-hippocampus

value: brain-hippocampus

value: sham-exposed


title: GL26150_CD3posP1_B06_R1

value: brain

value: Tcell


title: sham Hip_16


title: H1509-154-150A-miRNA [AMA]

description: H1509-154-150A-miRNA [AMA]


title: Paroxetine control bio rep 2 [Par_P3_B01_S36]

description:
96 well plate
Par_P3_B01_S36_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

value: whole body

value: larva


title: GL26150_CD3posP1_B07_R1


title: sham Hip_12


title: Paroxetine dose level 9 bio rep 1 [Par_P3_A10_S27]

description:
96 well plate
Par_P3_A10_S27_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Paroxetine


title: GL26140_CD3posP1_G08_R1

value: Los


title: H1507-152-200C-miRNA [CLA]

description: H1507-152-200C-miRNA [CLA]

value: SBxPL


title: sham Hip_10


title: H1507-152-200B-miRNA [BLA]

description: H1507-152-200B-miRNA [BLA]


title: sham Hip_13


title: GL26140_CD3posP1_B12_R1


title: GL26140_CD3posP1_H08_R1


title: Paroxetine dose level 7 bio rep 1 [Par_P3_A08_S25]

description:
96 well plate
Par_P3_A08_S25_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

value: 24 hr


title: blast Hip_9

value: blast-exposed


title: GL26140_CD3posP1_G11_R1


title: Paroxetine dose level 5 bio rep 1 [Par_P3_A06_S31]

description:
96 well plate
Par_P3_A06_S31_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: H1507-152-150C-miRNA [CKA]

description: H1507-152-150C-miRNA [CKA]

value: C


title: blast Hip_6_re


title: blast Hip_5


title: Paroxetine dose level 4 bio rep 1 [Par_P3_A05_S30]

description:
96 well plate
Par_P3_A05_S30_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: H1507-152-200A-miRNA [ALA]

description: H1507-152-200A-miRNA [ALA]


title: GL26140_CD3posP1_A05_R1


title: GL26140_CD3posP1_A07_R1


title: H1507-152-150B-miRNA [BKA]

description: H1507-152-150B-miRNA [BKA]

value: B


title: blast Hip_2


title: GL26140_CD3posP1_C09_R1


title: H1507-152-150A-miRNA [AKA]

description: H1507-152-150A-miRNA [AKA]


title: Paroxetine dose level 2 bio rep 1 [Par_P3_A03_S40]

description:
96 well plate
Par_P3_A03_S40_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 8 bio rep 1 [Par_P3_A09_S26]

description:
96 well plate
Par_P3_A09_S26_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: blast Hip_1


title: Paroxetine dose level 1 bio rep 1 [Par_P3_A02_S41]

description:
96 well plate
Par_P3_A02_S41_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Cer33

data_processing:
Original data file form hihj throughput sequencing transformed into raw data by CASAVA
Data filtering: remove reads containing adaptors, reads with uncertain bases when uncertain nucleotides are >10%, ,ermove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 20.
HSAT2 to map filtered sequence to reference genome
Assembly: rattus norvegicus release 80
Supplementary files format and content: tab delimited text files

extract_protocol:
RNA exgtracted with Qiazol reagent and purified by RNAeasy mini kit (Qiagen)
Libraries were constructed from 1 mg of total RNA using the NEBNextUltraRNA Library Prep kit from Illumina (NEB, Ipswich, MA)

value: brain-cerebellum


title: GL26140_CD3posP1_G12_R1


title: H1506-151-200C-miRNA [CJA]

description: H1506-151-200C-miRNA [CJA]


title: Paroxetine control bio rep 1 [Par_P3_A01_S42]

description:
96 well plate
Par_P3_A01_S42_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Cer15


title: GL26140_CD3posP1_F09_R1


title: H1506-151-200A-miRNA [AJA]

description: H1506-151-200A-miRNA [AJA]

value: A


title: Thiacloprid dose level 10 bio rep 8 [Thi_R_H11_S6]

description:
96 well plate
Thi_R_H11_S6_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: Thiacloprid


title: Cer14


title: Cer13


title: GL26140_CD3posP1_E09_R1


title: H1506-151-150C-miRNA [CIA]

description: H1506-151-150C-miRNA [CIA]


title: H1506-151-150B-miRNA [BIA]

description: H1506-151-150B-miRNA [BIA]


title: Paroxetine dose level 3 bio rep 1 [Par_P3_A04_S29]

description:
96 well plate
Par_P3_A04_S29_L005
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Thiacloprid dose level 8 bio rep 8 [Thi_R_H09_S5]

description:
96 well plate
Thi_R_H09_S5_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 7 bio rep 8 [Thi_R_H08_S22]

description:
96 well plate
Thi_R_H08_S22_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1506-151-150A-miRNA [AIA]

description: H1506-151-150A-miRNA [AIA]


title: GL26140_CD3posP1_A01_R1

value: Microglia


title: H1505-150-200C-miRNA [CHA]

description: H1505-150-200C-miRNA [CHA]


title: Thiacloprid dose level 6 bio rep 8 [Thi_R_H07_S21]

description:
96 well plate
Thi_R_H07_S21_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Cer88


title: H1506-151-200B-miRNA [BJA]

description: H1506-151-200B-miRNA [BJA]


title: GL26140_CD3posP1_C05_R1


title: H1505-150-200B-miRNA [BHA]

description: H1505-150-200B-miRNA [BHA]


title: Thiacloprid dose level 4 bio rep 8 [Thi_R_H05_S19]

description:
96 well plate
Thi_R_H05_S19_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 5 bio rep 8 [Thi_R_H06_S20]

description:
96 well plate
Thi_R_H06_S20_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Cer22


title: Thiacloprid dose level 9 bio rep 8 [Thi_R_H10_S4]

description:
96 well plate
Thi_R_H10_S4_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_C08_R1


title: H1505-150-200A-miRNA [AHA]

description: H1505-150-200A-miRNA [AHA]


title: H1505-150-150C-miRNA [CGA]

description: H1505-150-150C-miRNA [CGA]


title: Thiacloprid dose level 3 bio rep 8 [Thi_R_H04_S18]

description:
96 well plate
Thi_R_H04_S18_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_H10_R1


title: Cer4


title: Cer8


title: Cer11

value: sham-exposed


title: AC_33

value: brain-anterior cortex


title: H1505-150-150B-miRNA [BGA]

description: H1505-150-150B-miRNA [BGA]


title: Cer666


title: Thiacloprid dose level 1 bio rep 8 [Thi_R_H02_S16]

description:
96 well plate
Thi_R_H02_S16_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1505-150-150A-miRNA [AGA]

description: H1505-150-150A-miRNA [AGA]


title: GL26140_CD3posP1_B04_R1

value: brain

value: Tcell


title: AC-15


title: GL26140_CD3posP1_D03_R1


title: H1504-149-200C-miRNA [CFA]

description: H1504-149-200C-miRNA [CFA]

value: SBxSB


title: Thiacloprid control bio rep 8 [Thi_R_H01_S15]

description:
96 well plate
Thi_R_H01_S15_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: AC_14


title: GL26140_CD3posP1_H01_R1

value: Los


title: GL26140_CD3posP1_F01_R1


title: H1504-149-200B-miRNA [BFA]

description: H1504-149-200B-miRNA [BFA]


title: AC_13


title: Thiacloprid dose level 10 bio rep 7 [Thi_R_G11_S14]

description:
96 well plate
Thi_R_G11_S14_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 24 hr


title: Thiacloprid dose level 9 bio rep 7 [Thi_R_G10_S13]

description:
96 well plate
Thi_R_G10_S13_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_E11_R1


title: H1504-149-200A-miRNA [AFA]

description: H1504-149-200A-miRNA [AFA]


title: Thiacloprid dose level 2 bio rep 8 [Thi_R_H03_S17]

description:
96 well plate
Thi_R_H03_S17_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: AC_11


title: GL26140_CD3posP1_H06_R1


title: AC_666

value: blast-exposed


title: GL26140_CD3posP1_B02_R1


title: H1504-149-150C-miRNA [CEA]

description: H1504-149-150C-miRNA [CEA]

value: C


title: Thiacloprid dose level 8 bio rep 7 [Thi_R_G09_S12]

description:
96 well plate
Thi_R_G09_S12_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_A08_R1


title: Thiacloprid dose level 7 bio rep 7 [Thi_R_G08_S11]

description:
96 well plate
Thi_R_G08_S11_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_H05_R1


title: H1504-149-150B-miRNA [BEA]

description: H1504-149-150B-miRNA [BEA]

value: B


title: GL26140_CD3posP1_F02_R1


title: H1503-148-200C-miRNA [CDA]

description: H1503-148-200C-miRNA [CDA]


title: AC_88


title: AC_8


title: GL26140_CD3posP1_A11_R1


title: AC_4


title: Thiacloprid dose level 4 bio rep 7 [Thi_R_G05_S8]

description:
96 well plate
Thi_R_G05_S8_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1504-149-150A-miRNA [AEA]

description: H1504-149-150A-miRNA [AEA]


title: GL26140_CD3posP1_G04_R1


title: GL26140_CD3posP1_C07_R1


title: GL26140_CD3posP1_D10_R1


title: Thiacloprid dose level 3 bio rep 7 [Thi_R_G04_S7]

description:
96 well plate
Thi_R_G04_S7_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1503-148-200B-miRNA [BDA]

description: H1503-148-200B-miRNA [BDA]


title: Amy_33

value: brain-amygdala


title: Thiacloprid dose level 5 bio rep 7 [Thi_R_G06_S9]

description:
96 well plate
Thi_R_G06_S9_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Amy-15


title: Thiacloprid dose level 2 bio rep 7 [Thi_R_G03_S1]

description:
96 well plate
Thi_R_G03_S1_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_G09_R1


title: Amy_14


title: Amy_12


title: Thiacloprid dose level 1 bio rep 7 [Thi_R_G02_S2]

description:
96 well plate
Thi_R_G02_S2_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 10 bio rep 6 [Thi_R_F11_S31]

description:
96 well plate
Thi_R_F11_S31_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1503-148-150B-miRNA [BCA]

description: H1503-148-150B-miRNA [BCA]


title: H1503-148-150A-miRNA [ACA]

description: H1503-148-150A-miRNA [ACA]

value: A


title: GL26140_CD3posP1_D09_R1


title: AC_22


title: Amy_666


title: GL26140_CD3posP1_C02_R1


title: H1502-147-200A-miRNA [ABA]

description: H1502-147-200A-miRNA [ABA]


title: H1502-147-200C-miRNA [CBA]

description: H1502-147-200C-miRNA [CBA]


title: GL26140_CD3posP1_A12_R1


title: Thiacloprid dose level 6 bio rep 7 [Thi_R_G07_S10]

description:
96 well plate
Thi_R_G07_S10_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: Thiacloprid


title: Amy_11


title: Thiacloprid dose level 7 bio rep 6 [Thi_R_F08_S34]

description:
96 well plate
Thi_R_F08_S34_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1503-148-200A-miRNA [ADA]

description: H1503-148-200A-miRNA [ADA]


title: Thiacloprid control bio rep 7 [Thi_R_G01_S3]

description:
96 well plate
Thi_R_G01_S3_L002
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 9 bio rep 6 [Thi_R_F10_S32]

description:
96 well plate
Thi_R_F10_S32_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_C10_R1


title: GL26140_CD3posP1_D12_R1


title: GL26140_CD3posP1_A06_R1


title: Thiacloprid dose level 8 bio rep 6 [Thi_R_F09_S33]

description:
96 well plate
Thi_R_F09_S33_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1502-147-200B-miRNA [BBA]

description: H1502-147-200B-miRNA [BBA]


title: H1502-147-150C-miRNA [CAA]

description: H1502-147-150C-miRNA [CAA]


title: GL26140_CD3posP1_C06_R1

value: Microglia


title: Amy_22


title: Amy_88


title: H1502-147-150B-miRNA [BAA]

description: H1502-147-150B-miRNA [BAA]


title: Thiacloprid dose level 6 bio rep 6 [Thi_R_F07_S35]

description:
96 well plate
Thi_R_F07_S35_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 4 bio rep 6 [Thi_R_F05_S24]

description:
96 well plate
Thi_R_F05_S24_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_A10_R1


title: Amy_8


title: Thiacloprid dose level 3 bio rep 6 [Thi_R_F04_S25]

description:
96 well plate
Thi_R_F04_S25_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1502-147-150A-miRNA [AAA]

description: H1502-147-150A-miRNA [AAA]


title: Thiacloprid dose level 5 bio rep 6 [Thi_R_F06_S23]

description:
96 well plate
Thi_R_F06_S23_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Amy_4


title: H1503-148-150C-miRNA [CCA]

description: H1503-148-150C-miRNA [CCA]


title: GL26140_CD3posP1_F04_R1


title: GL26140_CD3posP1_E08_R1


title: Thiacloprid dose level 2 bio rep 6 [Thi_R_F03_S26]

description:
96 well plate
Thi_R_F03_S26_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Hip_33

value: brain-hippocampus

value: sham-exposed


title: Hip_14


title: H1520-165-200B-mRNA

description: RNA-seq data

value: PLxSB


title: GL26140_CD3posP1_E12_R1

value: brain

value: Tcell


title: H1520-165-200C-mRNA

description: RNA-seq data


title: Thiacloprid dose level 1 bio rep 6 [Thi_R_F02_S27]

description:
96 well plate
Thi_R_F02_S27_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: whole body


title: H1520-165-150C-mRNA

description: RNA-seq data


title: GL26140_CD3posP1_D06_R1


title: Hip_15


title: Hip_13


title: GL26140_CD3posP1_E06_R1


title: H1520-165-150B-mRNA

description: RNA-seq data


title: Thiacloprid control bio rep 6 [Thi_R_F01_S28]

description:
96 well plate
Thi_R_F01_S28_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: larva


title: Hip_11


title: GL26140_CD3posP1_A03_R1


title: H1520-165-150A-mRNA

description: RNA-seq data


title: Thiacloprid dose level 10 bio rep 5 [Thi_R_E11_S29]

description:
96 well plate
Thi_R_E11_S29_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: Hip_666


title: GL26140_CD3posP1_F08_R1

value: Los


title: H1516-161-200C-mRNA

description: RNA-seq data

value: PLxPL


title: H1520-165-200A-mRNA

description: RNA-seq data


title: Thiacloprid dose level 9 bio rep 5 [Thi_R_E10_S30]

description:
96 well plate
Thi_R_E10_S30_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 24 hr


title: Hip_88

value: blast-exposed


title: Thiacloprid dose level 8 bio rep 5 [Thi_R_E09_S38]

description:
96 well plate
Thi_R_E09_S38_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Hip_22


title: H1516-161-200A-mRNA

description: RNA-seq data


title: GL26140_CD3posP1_A09_R1


title: Thiacloprid dose level 7 bio rep 5 [Thi_R_E08_S37]

description:
96 well plate
Thi_R_E08_S37_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_G01_R1


title: GL26140_CD3posP1_G03_R1


title: Thiacloprid dose level 5 bio rep 5 [Thi_R_E06_S39]

description:
96 well plate
Thi_R_E06_S39_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 6 bio rep 5 [Thi_R_E07_S40]

description:
96 well plate
Thi_R_E07_S40_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_H12_R1


title: H1516-161-150B-mRNA

description: RNA-seq data

value: B


title: H1516-161-150A-mRNA

description: RNA-seq data


title: Hip_4


title: Thiacloprid dose level 4 bio rep 5 [Thi_R_E05_S42]

description:
96 well plate
Thi_R_E05_S42_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_D05_R1


title: Prefrontal cortex acu 5

city: Guangzhou

first: Xin

last: Jiang

state: Guangdong

address: No.232 Waihuandong Road, Panyu District, Guangzhou

institute: Guangzhou University of Chinese Medicine

data_processing:
HTSeq v0.6.0  software used for basecalling
Raw data were first processed through in-house perl scripts. Reads containing adapter, ploy-N, and low-quality reads were removed from raw data to obtain clean reads.
HTSeq v0.6.0 was used to count the reads mapped to each gene. Then, the FPKM of each gene was calculated to estimate gene expression levels.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Prefrontal cortex

extract_protocol:
Prefrontal cortex were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA)  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: acupuncture

tag: strain

value: SD

value: prefrontal cortex

value: post natal day 28


title: Prefrontal cortex acu 55


title: H1516-161-200B-mRNA

description: RNA-seq data


title: Thiacloprid dose level 3 bio rep 5 [Thi_R_E04_S41]

description:
96 well plate
Thi_R_E04_S41_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: Thiacloprid


title: H1516-161-150C-mRNA

description: RNA-seq data

value: C


title: GL26140_CD3posP1_F03_R1


title: GL26140_CD3posP1_B06_R1


title: H1514-159-200C-mRNA

description: RNA-seq data

value: PLxSB


title: H1514-159-200B-mRNA

description: RNA-seq data


title: GL26140_CD3posP1_E03_R1

value: brain


title: Prefrontal cortex mod 8

value: Hypoxic-ischemic brain damage (HIBD) model


title: Thiacloprid dose level 1 bio rep 5 [Thi_R_E02_S43]

description:
96 well plate
Thi_R_E02_S43_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: whole body


title: GL26140_CD3posP1_F10_R1

value: Tcell


title: Prefrontal cortex acu 22


title: Thiacloprid control bio rep 5 [Thi_R_E01_S36]

description:
96 well plate
Thi_R_E01_S36_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: H1514-159-150C-mRNA

description: RNA-seq data


title: Prefrontal cortex mod 18


title: H1514-159-150B-mRNA

description: RNA-seq data


title: Thiacloprid dose level 10 bio rep 4 [Thi_R_D11_S1]

description:
96 well plate
Thi_R_D11_S1_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_G06_R1

value: Los


title: H1514-159-150A-mRNA

description: RNA-seq data

value: A


title: Thiacloprid dose level 9 bio rep 4 [Thi_R_D10_S3]

description:
96 well plate
Thi_R_D10_S3_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 24 hr


title: Prefrontal cortex mod 2


title: Hip_8

value: brain-hippocampus

value: blast-exposed


title: Thiacloprid dose level 2 bio rep 5 [Thi_R_E03_S44]

description:
96 well plate
Thi_R_E03_S44_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 7 bio rep 4 [Thi_R_D08_S5]

description:
96 well plate
Thi_R_D08_S5_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1513-158-200A-mRNA

description: RNA-seq data

value: PLxPL


title: Prefrontal cortex mod 16

value: SD

value: prefrontal cortex


title: Prefrontal cortex acu 35

value: acupuncture

value: post natal day 28


title: GL26140_CD3posP1_D02_R1


title: GL26140_CD3posP1_B07_R1


title: Prefrontal cortex nor 8

value: normal


title: H1513-158-200B-mRNA

description: RNA-seq data

value: B


title: GL26140_CD3posP1_E07_R1

value: brain


title: Thiacloprid dose level 4 bio rep 4 [Thi_R_D05_S6]

description:
96 well plate
Thi_R_D05_S6_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: whole body

value: Thiacloprid


title: GL26140_CD3posP1_G05_R1

value: Tcell


title: GL26140_CD3posP1_E04_R1


title: Thiacloprid dose level 8 bio rep 4 [Thi_R_D09_S2]

description:
96 well plate
Thi_R_D09_S2_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: Thiacloprid dose level 3 bio rep 4 [Thi_R_D04_S17]

description:
96 well plate
Thi_R_D04_S17_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_H02_R1

value: Los


title: H1514-159-200A-mRNA

description: RNA-seq data

value: PLxSB

value: A


title: Prefrontal cortex nor 13


title: GL26140_CD3posP1_C11_R1


title: Prefrontal cortex nor 11


title: Thiacloprid dose level 6 bio rep 4 [Thi_R_D07_S4]

description:
96 well plate
Thi_R_D07_S4_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 24 hr


title: H1513-158-150C-mRNA

description: RNA-seq data

value: PLxPL

value: C


title: GL26140_CD3posP1_G02_R1


title: GL26140_CD3posP1_F05_R1


title: Thiacloprid dose level 5 bio rep 4 [Thi_R_D06_S7]

description:
96 well plate
Thi_R_D06_S7_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 1 bio rep 4 [Thi_R_D02_S15]

description:
96 well plate
Thi_R_D02_S15_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1512-157-200B-mRNA

description: RNA-seq data


title: Thiacloprid control bio rep 4 [Thi_R_D01_S16]

description:
96 well plate
Thi_R_D01_S16_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_B01_R1


title: C. albicans in RPMI+AAT replicate 2

type: RNA

city: Jena

first: Mark

middle: S.

last: Gresnigt

address: Beutenebergstraße 11a

department: Adaptive Pathogenicity Mechanisms

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute

description: AAT treatment 2

hyb_protocol: Genome-wide gene expression of C. albicans was analyzed with C. albicans-specific microarrays (ClinEuroDiag). The red channel represents hybridization with Cy5-labeled C. albicans RNA from experimental conditions while the green channel shows hybridization with Cy3-labeled RNA from C. albicans the common control. Two micrograms of the Cy3- and Cy5-labeled cRNA were hybridized to the C. albicans arrays overnight at 42°C in DIG Easy Hyb solution (Roche). The slides were washed at RT using gene expression wash buffer 1 and 2 (Agilent), acetonitrile and stabilization and drying solution (Agilent) according to the manufacturers protocol.

scan_protocol: Hybridized slides were scanned with an Axon 4000B scanner at a 10 mm resolution.

data_processing: Data were extracted by GenePix 4.1 software (Axon). Data processing was performed in R using packages provided by Bioconductor 2.26 (86). The microarray data were pre-processed using the limma package (87). “Printtiplowess” normalization was used on each array separately to correct for spatial effects or cross-hybridization. Array spots corresponding to the same gene were summarized using the duplicated correlation function of limma. Normalization of the arrays was performed using between-array quantile normalization. Log2 fold-changes (log2-FC) were calculated between in vitro samples and the common reference using limma.

organism: Candida albicans

source_name: C. albicans+AAT(test)

label_protocol: Cy3- and Cy5- labeled cRNA were prepared from 5 mg of mRNA by use of the Agilent fluorescent linear amplification kit and protocol (Agilent technologies).

growth_protocol: C. albicans SC5314 was grown overnight in YPD broth. For the experiment cells were washed enumirated.

extract_protocol: The supernatant was removed and replaced with RNeasy Lysis (RLT) buffer (Qiagen), containing 1% β-mercaptoethanol (Roth). Cells were detached using cell scraper and snap-frozen in liquid nitrogen. As a common control C. albicans growing logarithmically in standard YPD medium at 37 °C with shaking was used, and snap-frozen in RNeasy Lysis (RLT) buffer (Qiagen), containing 1% β-mercaptoethanol (Roth). Samples were stored at -80°C until RNA-isolation. Samples were thawed on ice and centrifuged for 10 min (20,000g, 4°C). The supernatant was discarded and fungal RNA was isolated from the pellet, using a freezing-thawing method (Wachtler et al 2011 PLoS One) Fungal RNA concentrations were quantified using a NanoDrop 1000 Spectrophotometer (ThermoFisher Scientific) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: C. albicans was grown for 3 h at 37°C and 5 % CO2 in 6-well plates at 1×10^6 CFU/well in RPMI 1640 medium or RPMI 1640 medium containing 100 mg/mL AAT.

tag: time

value: cultivation in RPMI1640+alpha1antitrypsin 100ug/ml

source_name: C. albicans (reference)

value: YPD


title: Prefrontal cortex nor 10

value: SD

tag: tissue

value: prefrontal cortex

value: post natal day 28


title: Thiacloprid dose level 10 bio rep 3 [Thi_R_C11_S21]

description:
96 well plate
Thi_R_C11_S21_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: C. albicans in RPMI+AAT replicate 1

description: AAT treatment 1


title: H1513-158-200C-mRNA

description: RNA-seq data


title: H1512-157-150B-mRNA

description: RNA-seq data

value: B


title: H1513-158-150A-mRNA

description: RNA-seq data


title: Thiacloprid dose level 8 bio rep 3 [Thi_R_C09_S19]

description:
96 well plate
Thi_R_C09_S19_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: whole body


title: H1512-157-150A-mRNA

description: RNA-seq data


title: C. albicans in RPMI replicate 3

description: Medium control 3

source_name: C. albicans (test)

value: cultivation in RPMI1640


title: H1512-157-200C-mRNA

description: RNA-seq data


title: C. albicans in RPMI+AAT replicate 4

description: AAT treatment 4


title: GL26140_CD3posP1_B11_R1

value: brain

tag: cell type

value: Tcell


title: C. albicans in RPMI+AAT replicate 3

description: AAT treatment 3

tag: treatment


title: H1512-157-200A-mRNA

description: RNA-seq data


title: H1512-157-150C-mRNA

description: RNA-seq data


title: H1513-158-150B-mRNA

description: RNA-seq data


title: GL26140_CD3posP1_H11_R1


title: C. albicans in RPMI replicate 2

description: Medium control 2


title: Thiacloprid dose level 2 bio rep 4 [Thi_R_D03_S18]

description:
96 well plate
Thi_R_D03_S18_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

tag: developmental stage

value: larva

value: 5 dpf/24 hr post hatch

value: Thiacloprid


title: C. albicans in RPMI replicate 4

description: Medium control 4


title: H1509-154-200A-mRNA

description: RNA-seq data

value: A


title: Thiacloprid dose level 5 bio rep 3 [Thi_R_C06_S11]

description:
96 well plate
Thi_R_C06_S11_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

tag: age

value: 24 hr


title: Thiacloprid dose level 9 bio rep 3 [Thi_R_C10_S22]

description:
96 well plate
Thi_R_C10_S22_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

tag: Sex


title: GL26140_CD3posP1_F07_R1

value: Los


title: MiSeq 1 2.0mm 39s

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

institute: Stanford University

description: UMI Matrix

data_processing:
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)

molecule: polyA RNA

organism: Zea mays

source_name: anther

growth_protocol: individuals were grown under greenhouse conditions in Stanford, CA, USA with 14-h day/10-h night lighting, approximating half of peak summer solar radiation including UV-A. Daily irrigation and fertilization maintained robust growth

extract_protocol:
Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.

value: anther

value: anther single cell


title: H1509-154-200C-mRNA

description: RNA-seq data

value: PLxPL

value: C


title: GL26140_CD3posP1_D11_R1


title: Thiacloprid dose level 7 bio rep 3 [Thi_R_C08_S20]

description:
96 well plate
Thi_R_C08_S20_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

tag: concentration


title: GL26140_CD3posP1_A04_R1


title: MiSeq 1 2.0mm 1s

description: UMI Matrix


title: MiSeq 2 2.0mm 8s

description: UMI Matrix


title: GL26140_CD3posP1_D07_R1


title: Thiacloprid dose level 4 bio rep 3 [Thi_R_C05_S8]

description:
96 well plate
Thi_R_C05_S8_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

tag: time point


title: H1509-154-200B-mRNA

description: RNA-seq data


title: C. albicans in RPMI replicate 1

description: Medium control 1

value: YPD


title: H1509-154-150A-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 10s

description: UMI Matrix

tag: genotype


title: MiSeq 2 2.0mm 89s

description: UMI Matrix


title: GL26140_CD3posP1_H09_R1


title: Thiacloprid dose level 3 bio rep 3 [Thi_R_C04_S9]

description:
96 well plate
Thi_R_C04_S9_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 2 2.0mm 40s

description: UMI Matrix


title: Thiacloprid dose level 6 bio rep 3 [Thi_R_C07_S10]

description:
96 well plate
Thi_R_C07_S10_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid dose level 1 bio rep 3 [Thi_R_C02_S14]

description:
96 well plate
Thi_R_C02_S14_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 2 2.0mm 34s

description: UMI Matrix


title: GL26140_CD3posP1_C04_R1


title: H1509-154-150C-mRNA

description: RNA-seq data

tag: cross type


title: GL26140_CD3posP1_B08_R1


title: MiSeq 2 2.0mm 36s

description: UMI Matrix


title: Thiacloprid dose level 2 bio rep 3 [Thi_R_C03_S13]

description:
96 well plate
Thi_R_C03_S13_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_D04_R1


title: GL26140_CD3posP1_E01_R1


title: MiSeq 2 2.0mm 15s

description: UMI Matrix


title: H1509-154-150B-mRNA

description: RNA-seq data

tag: family


title: GL26140_CD3posP1_F11_R1


title: H1507-152-150C-mRNA

description: RNA-seq data

value: SBxPL

tag: individual


title: Thiacloprid dose level 10 bio rep 2 [Thi_R_B11_S6]

description:
96 well plate
Thi_R_B11_S6_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: Thiacloprid control bio rep 3 [Thi_R_C01_S12]

description:
96 well plate
Thi_R_C01_S12_L007
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 2 2.0mm 32s

description: UMI Matrix


title: Thiacloprid dose level 9 bio rep 2 [Thi_R_B10_S18]

description:
96 well plate
Thi_R_B10_S18_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1507-152-200A-mRNA

description: RNA-seq data

tag: developmental timepoint


title: MiSeq 2 2.0mm 27s

description: UMI Matrix


title: GL26140_CD3posP1_G07_R1


title: GL26140_CD3posP1_F12_R1


title: Thiacloprid dose level 8 bio rep 2 [Thi_R_B09_S17]

description:
96 well plate
Thi_R_B09_S17_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 1 2.0mm 17s

description: UMI Matrix


title: H1507-152-200C-mRNA

description: RNA-seq data

tag: sequencing batch


title: H1507-152-150B-mRNA

description: RNA-seq data

value: B


title: H1507-152-150A-mRNA

description: RNA-seq data


title: Thiacloprid dose level 7 bio rep 2 [Thi_R_B08_S16]

description:
96 well plate
Thi_R_B08_S16_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: whole body


title: MiSeq 1 2.0mm 15s

description: UMI Matrix


title: H1507-152-200B-mRNA

description: RNA-seq data


title: Thiacloprid dose level 5 bio rep 2 [Thi_R_B06_S22]

description:
96 well plate
Thi_R_B06_S22_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_E10_R1


title: Thiacloprid dose level 6 bio rep 2 [Thi_R_B07_S15]

description:
96 well plate
Thi_R_B07_S15_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1506-151-200C-mRNA

description: RNA-seq data


title: H1506-151-200A-mRNA

description: RNA-seq data


title: Thiacloprid dose level 4 bio rep 2 [Thi_R_B05_S21]

description:
96 well plate
Thi_R_B05_S21_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_C03_R1


title: GL26140_CD3posP1_C12_R1


title: H1506-151-150C-mRNA

description: RNA-seq data


title: H1506-151-200B-mRNA

description: RNA-seq data


title: GL26140_CD3posP1_E02_R1


title: MiSeq 1 2.0mm 82s

description: UMI Matrix


title: MiSeq 2 2.0mm 16s

description: UMI Matrix


title: H1506-151-150B-mRNA

description: RNA-seq data


title: Thiacloprid dose level 3 bio rep 2 [Thi_R_B04_S20]

description:
96 well plate
Thi_R_B04_S20_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26130_CD3posP1_A05_R1

value: ctrl


title: MiSeq 1 2.0mm 13s

description: UMI Matrix


title: Thiacloprid dose level 2 bio rep 2 [Thi_R_B03_S19]

description:
96 well plate
Thi_R_B03_S19_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26140_CD3posP1_E05_R1

value: brain


title: GL26130_CD3posP1_F09_R1

value: Tcell


title: MiSeq 2 2.0mm 11s

description: UMI Matrix


title: Thiacloprid dose level 1 bio rep 2 [Thi_R_B02_S10]

description:
96 well plate
Thi_R_B02_S10_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: larva


title: GL26130_CD3posP1_G11_R1


title: H1506-151-150A-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 94s

description: UMI Matrix


title: H1505-150-200B-mRNA

description: RNA-seq data


title: Thiacloprid control bio rep 2 [Thi_R_B01_S9]

description:
96 well plate
Thi_R_B01_S9_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26130_CD3posP1_B01_R1


title: H1505-150-200C-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 21s

description: UMI Matrix


title: H1505-150-200A-mRNA

description: RNA-seq data


title: H1505-150-150C-mRNA

description: RNA-seq data


title: GL26130_CD3posP1_E05_R1


title: MiSeq 2 2.0mm 24s

description: UMI Matrix


title: Thiacloprid dose level 9 bio rep 1 [Thi_R_A10_S7]

description:
96 well plate
Thi_R_A10_S7_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: Thiacloprid


title: Thiacloprid dose level 8 bio rep 1 [Thi_R_A09_S14]

description:
96 well plate
Thi_R_A09_S14_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 2 2.0mm 31s

description: UMI Matrix


title: Thiacloprid dose level 7 bio rep 1 [Thi_R_A08_S13]

description:
96 well plate
Thi_R_A08_S13_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26130_CD3posP1_G03_R1


title: MiSeq 2 2.0mm 22s

description: UMI Matrix


title: MiSeq 2 2.0mm 33s

description: UMI Matrix


title: GL26130_CD3posP1_H08_R1


title: H1505-150-150B-mRNA

description: RNA-seq data


title: Thiacloprid dose level 6 bio rep 1 [Thi_R_A07_S12]

description:
96 well plate
Thi_R_A07_S12_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: GL26130_CD3posP1_D02_R1


title: Thiacloprid dose level 5 bio rep 1 [Thi_R_A06_S11]

description:
96 well plate
Thi_R_A06_S11_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1504-149-200C-mRNA

description: RNA-seq data

value: SBxSB


title: MiSeq 1 2.0mm 35s

description: UMI Matrix


title: MiSeq 1 2.0mm 14s

description: UMI Matrix


title: Thiacloprid dose level 4 bio rep 1 [Thi_R_A05_S3]

description:
96 well plate
Thi_R_A05_S3_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt

value: 24 hr


title: H1504-149-200B-mRNA

description: RNA-seq data


title: GL26130_CD3posP1_A07_R1


title: GL26130_CD3posP1_A02_R1


title: H1504-149-200A-mRNA

description: RNA-seq data

value: A


title: GL26130_CD3posP1_G05_R1


title: Thiacloprid dose level 10 bio rep 1 [Thi_R_A11_S8]

description:
96 well plate
Thi_R_A11_S8_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 2 2.0mm 29s

description: UMI Matrix

value: anther


title: MiSeq 2 2.0mm 64s

description: UMI Matrix

value: anther single cell


title: H1504-149-150C-mRNA

description: RNA-seq data


title: GL26130_CD3posP1_H09_R1


title: GL26130_CD3posP1_A03_R1


title: Thiacloprid dose level 2 bio rep 1 [Thi_R_A03_S5]

description:
96 well plate
Thi_R_A03_S5_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1504-149-150B-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 9s

description: UMI Matrix


title: H1505-150-150A-mRNA

description: RNA-seq data


title: H1504-149-150A-mRNA

description: RNA-seq data


title: Thiacloprid control bio rep 1 [Thi_R_A01_S1]

description:
96 well plate
Thi_R_A01_S1_L008
Thi.raw.counts.txt
na


title: MiSeq 2 2.0mm 6s

description: UMI Matrix


title: GL26130_CD3posP1_F10_R1


title: MiSeq 2 2.0mm 74s

description: UMI Matrix


title: MiSeq 2 2.0mm 30s

description: UMI Matrix


title: NiSO4 dose level 9 bio rep 8 [Ni_P1_H10_S70]

description:
96 well plate
Ni_P1_H10_S70_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: H1503-148-200C-mRNA

description: RNA-seq data


title: H1503-148-200B-mRNA

description: RNA-seq data


title: GL26130_CD3posP1_B06_R1

value: Microglia


title: NiSO4 dose level 8 bio rep 8 [Ni_P1_H09_S72]

description:
96 well plate
Ni_P1_H09_S72_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: NiSO4 dose level 7 bio rep 8 [Ni_P1_H08_S71]

description:
96 well plate
Ni_P1_H08_S71_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: H1503-148-200A-mRNA

description: RNA-seq data


title: NiSO4 dose level 6 bio rep 8 [Ni_P1_H07_S78]

description:
96 well plate
Ni_P1_H07_S78_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_D09_R1


title: Thiacloprid dose level 3 bio rep 1 [Thi_R_A04_S2]

description:
96 well plate
Thi_R_A04_S2_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: MiSeq 1 2.0mm 16s

description: UMI Matrix


title: MiSeq 2 2.0mm 13s

description: UMI Matrix


title: Thiacloprid dose level 1 bio rep 1 [Thi_R_A02_S4]

description:
96 well plate
Thi_R_A02_S4_L008
Thi.raw.counts.txt
Thi.sansA01.filtered.normFinal.txt


title: H1503-148-150C-mRNA

description: RNA-seq data

value: C


title: GL26130_CD3posP1_B12_R1


title: H1503-148-150B-mRNA

description: RNA-seq data


title: GL26130_CD3posP1_B02_R1


title: MiSeq 2 2.0mm 7s

description: UMI Matrix


title: NiSO4 dose level 4 bio rep 8 [Ni_P1_H05_S80]

description:
96 well plate
Ni_P1_H05_S80_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: H1502-147-200C-mRNA

description: RNA-seq data


title: GL26130_CD3posP1_E10_R1


title: NiSO4 dose level 2 bio rep 8 [Ni_P1_H03_S74]

description:
96 well plate
Ni_P1_H03_S74_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 28s

description: UMI Matrix


title: GL26130_CD3posP1_B07_R1


title: H1503-148-150A-mRNA

description: RNA-seq data


title: NiSO4 dose level 3 bio rep 8 [Ni_P1_H04_S79]

description:
96 well plate
Ni_P1_H04_S79_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 26s

description: UMI Matrix


title: H1502-147-200A-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 95s

description: UMI Matrix


title: H1502-147-200B-mRNA

description: RNA-seq data


title: NiSO4 dose level 1 bio rep 8 [Ni_P1_H02_S73]

description:
96 well plate
Ni_P1_H02_S73_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_C11_R1


title: GL26130_CD3posP1_C05_R1


title: NiSO4 control bio rep 8 [Ni_P1_H01_S76]

description:
96 well plate
Ni_P1_H01_S76_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_F11_R1


title: MiSeq 2 2.0mm 66s

description: UMI Matrix


title: NiSO4 dose level 5 bio rep 8 [Ni_P1_H06_S77]

description:
96 well plate
Ni_P1_H06_S77_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: H1502-147-150B-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 38s

description: UMI Matrix


title: GL26130_CD3posP1_E09_R1


title: H1502-147-150A-mRNA

description: RNA-seq data


title: NiSO4 dose level 9 bio rep 7 [Ni_P1_G10_S75]

description:
96 well plate
Ni_P1_G10_S75_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 12s

description: UMI Matrix


title: MiSeq 2 2.0mm 3s

description: UMI Matrix


title: GL26130_CD3posP1_C09_R1


title: GL26130_CD3posP1_D05_R1


title: NiSO4 dose level 8 bio rep 7 [Ni_P1_G09_S67]

description:
96 well plate
Ni_P1_G09_S67_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 91s

description: UMI Matrix


title: H1502-147-150C-mRNA

description: RNA-seq data


title: MiSeq 2 2.0mm 81s

description: UMI Matrix


title: H_7d_2

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The  WT and ΔAopex14/17 mutant strains  were cultured in PDA medium at 28°C for  5 d.

extract_protocol:
The WT and ΔAopex14/17 mutant strains were cultured in PD shaking at 28 °C, 180 rpm for 5 and 7 days.
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae


title: NiSO4 dose level 7 bio rep 7 [Ni_P1_G08_S68]

description:
96 well plate
Ni_P1_G08_S68_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_H12_R1


title: MiSeq 2 2.0mm 20s

description: UMI Matrix


title: NiSO4 dose level 5 bio rep 7 [Ni_P1_G06_S66]

description:
96 well plate
Ni_P1_G06_S66_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: NiSO4 dose level 6 bio rep 7 [Ni_P1_G07_S65]

description:
96 well plate
Ni_P1_G07_S65_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: H_7d_1


title: MiSeq 2 2.0mm 56s

description: UMI Matrix


title: MiSeq 2 2.0mm 4s

description: UMI Matrix


title: GL26130_CD3posP1_H11_R1


title: GL26130_CD3posP1_D08_R1


title: NiSO4 dose level 4 bio rep 7 [Ni_P1_G05_S63]

description:
96 well plate
Ni_P1_G05_S63_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: H_5d_3


title: MiSeq 1 2.0mm 41s

description: UMI Matrix


title: NiSO4 dose level 3 bio rep 7 [Ni_P1_G04_S64]

description:
96 well plate
Ni_P1_G04_S64_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_E11_R1


title: H_5d_2


title: H_5d_1


title: NiSO4 dose level 2 bio rep 7 [Ni_P1_G03_S61]

description:
96 well plate
Ni_P1_G03_S61_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_C04_R1


title: MiSeq 2 2.0mm 41s

description: UMI Matrix


title: H_7d_3


title: GL26130_CD3posP1_G07_R1


title: NiSO4 dose level 1 bio rep 7 [Ni_P1_G02_S62]

description:
96 well plate
Ni_P1_G02_S62_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 1 2.0mm 29s

description: UMI Matrix


title: GL26130_CD3posP1_B11_R1


title: NiSO4 control bio rep 7 [Ni_P1_G01_S69]

description:
96 well plate
Ni_P1_G01_S69_L007
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 17s

description: UMI Matrix


title: A_7d_1

value: WT


title: GL26130_CD3posP1_D10_R1


title: A_5d_3


title: MiSeq 2 2.0mm 55s

description: UMI Matrix


title: MiSeq 2 2.0mm 35s

description: UMI Matrix


title: GL26130_CD3posP1_E04_R1


title: A_5d_2


title: GL26130_CD3posP1_H10_R1


title: A_5d_1


title: GL26130_CD3posP1_H04_R1


title: NiSO4 dose level 7 bio rep 6 [Ni_P1_F08_S46]

description:
96 well plate
Ni_P1_F08_S46_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: NiSO4 dose level 8 bio rep 6 [Ni_P1_F09_S45]

description:
96 well plate
Ni_P1_F09_S45_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 18s

description: UMI Matrix


title: NiSO4 dose level 6 bio rep 6 [Ni_P1_F07_S43]

description:
96 well plate
Ni_P1_F07_S43_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 1 2.0mm 28s

description: UMI Matrix


title: GL26130_CD3posP1_B03_R1


title: A_7d_2


title: MiSeq 1 2.0mm 18s

description: UMI Matrix


title: GL26130_CD3posP1_G09_R1


title: NiSO4 dose level 4 bio rep 6 [Ni_P1_F05_S41]

description:
96 well plate
Ni_P1_F05_S41_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MiSeq 2 2.0mm 39s

description: UMI Matrix


title: A_7d_3


title: NiSO4 dose level 9 bio rep 6 [Ni_P1_F10_S47]

description:
96 well plate
Ni_P1_F10_S47_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_F01_R1


title: NiSO4 dose level 5 bio rep 6 [Ni_P1_F06_S44]

description:
96 well plate
Ni_P1_F06_S44_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: NiSO4 dose level 3 bio rep 6 [Ni_P1_F04_S42]

description:
96 well plate
Ni_P1_F04_S42_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_G04_R1


title: GRK-beta1AR_LV_Veh_rep3

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

description: Each transcript is represented by a circular junction-specific probe which can identify individual transcript accurately.

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2, and incubated for 17h at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned by the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.
Normalized signal intensity after quantile normalization of the raw data.

source_name: LV_Veh_1 week

label_protocol: Total RNAs from each sample were treated with Rnase R to enrich circular RNA. The enriched circular RNAs were then amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar Super RNA labeling protocol.

extract_protocol: Total RNAs from LVs were prepared using Qiagen RNeasy Plus kit.

tag: gender

value: male

value: LV

tag: age upon harvesting

value: 12 week age


title: GRK-beta1AR_LV_Veh_rep2

tag: strain

value: 9 week age


title: GRK-beta1AR_LV_Veh_rep1

value: female

tag: tissue


title: GRK-beta1AR_LV_ISO_rep2

source_name: LV_ISO_1 week

value: 10 week age


title: NiSO4 dose level 2 bio rep 6 [Ni_P1_F03_S55]

description:
96 well plate
Ni_P1_F03_S55_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: Untreated untransformed library, replicate 3

city: Albany

first: Michael

middle: Thomas

last: Fasullo

state: New York

address: 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description:
Cells grown for approximately 10 generations
NoP450_Significant_ORFs_Negative_M-Values.xlsx, NoP450_Significant_ORFs_Positive_M-Values.xlsx

library_source: genomic

data_processing:
Quality assessment to generate fastq file. This ensures reads pass quality filter and determines where the barcodes are in the reads. Software: fastx_quality_stats from fastx toolkit.
Demultiplex. This splits original fastq file into fastq files for each experimental condition (samples provided here are already demultiplexed). Software: fastx_barcode_splitter.pl. Parameters: No mismatches allowed.
Trim Reads . Description: Trim reads in demultiplexed fastq files to remove sequences flanking barcodes to reduce processing time. Software: fastx_trimmer from fastx toolbox. Parameters: Reads trimmed based on quality assessment, reads trimmed to 20 bp barcode sequences (where each base is represented approximately equally at each position), while trimming off flanking sequences that have nearly 100% sequence similarity.
Count barcodes. Description: Count number of reads matching each barcode from each experiment, assign counts to corresponding ORFs. Software: BarSeqAnalyzer (In-house program). Parameters: 1 mismatch allowed. Barcode list charactarized by Smith, et al (2009). Quantitative phenotyping via deep barcode sequencing. Genome Research, 19: 1836-1842
Analyze barcode count data. Description: Determine differential abundances of strains between treatment and control across all replicates. Further, determine which strains are differentially abundant at both concentrations of IQ when compared to control. Software: R version 4.2.1, bioconductors TCC package 1.36.0 (Sun et al. (2013). TCC: an R package for comparing tag count data with robust normailzation strategies. BMC Bioinformatics, 14:219). Parameters: Normalization method: tmm, test method: edger, FDR: 0.1, floorPDEG: 0.05, iteration: 3
Supplementary files format and content: Processed data files are excel spreadsheets including the results of the differential abundance analysis (Significant strains only) and the subsequent filtering of lists: unique strains (Identified by the knocked-out ORF) identified across both treatments, overlapping strains between lists of different treatment concentrations and refining of the overlap lists to remove dubious ORFs and ORFs without a known function.

organism: Saccharomyces cerevisiae

source_name: Yeast cells (BY4743 library)

growth_protocol: Frozen pooled libraries were thawed on ice. 100 μL of pooled sample was innoculated into 2 mL of YPD (Original library) or SC-Ura (Library expressing CYP1A2 and NAT2) for 2 hours to recover.

extract_protocol:
Cells washed 3x in sterile water, then DNA extracted with the "smash and grab" protocol of Hoffman and Winston.
Polymerase chain reaction was used to amplify and extract DNA barcodes from chromosomal DNA. Oligos used included 6-nucleotide multiplex indices specific for each experiment. Oligos contained regions homologous to barcode-flanking regions and also included adapter sequences to bind to the flow cell of the Illumina HiSeq 2000/2500
Equal amounts of PCR amplified barcodes were pooled for DNA sequencing (single-end read) using the Illumina HiSeq 2500 platform (Bauer Core Facility, Harvard Univsersity)

treatment_protocol: Recovered pools were innoculated at 1:50 (5 generations) or 1:200 (10 generations) into 2 mL of medium (YPD for samples of the original library, SC-Ura for samples of the library expressing CYP1A2 and NAT2). Treatments included: nothing, 2% methanol (+0.1% acetic acid), 400 μM IQ, or 800 μM IQ. Treatments performed in quadruplicate in all cases. Treated samples were grown for either 5 generations (10 hours for samples expressing CYP1A2 and NAT2; samples labeled "5G") or 10 generations (15 hours for samples not expressing exogenous proteins, or 20 hours for samples expressing CYP1A2 and NAT2; samples labeled "10G" and samples without any generation number specified).

tag: cell type

value: Yeast cells (BY4743 library)

value: Pooled homozygous diploid deletion library

tag: expression

value: No exogenous expression

value: No treatment


title: Untreated untransformed library, replicate 2

tag: treatment


title: NiSO4 control bio rep 6 [Ni_P1_F01_S53]

description:
96 well plate
Ni_P1_F01_S53_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

tag: developmental stage

tag: age

value: 24 hr


title: Untreated untransformed library, replicate 1


title: GL26130_CD3posP1_G12_R1

source_name: brain

value: brain

value: Tcell

value: ctrl


title: GL26130_CD3posP1_D03_R1


title: GL26130_CD3posP1_C03_R1


title: NiSO4 dose level 1 bio rep 6 [Ni_P1_F02_S54]

description:
96 well plate
Ni_P1_F02_S54_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

source_name: whole body

tag: Sex

tag: concentration


title: GL26130_CD3posP1_D01_R1


title: GRK-beta1AR_LV_ISO_rep1


title: MeOH treatment of the untransformed library, replicate 4

value: 2% methanol


title: GRK-beta1AR/miR150_LV_Veh_rep3

value: male

value: LV


title: NiSO4 dose level 9 bio rep 5 [Ni_P1_E10_S52]

description:
96 well plate
Ni_P1_E10_S52_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

tag: time point


title: GRK-beta1AR/miR150_LV_Veh_rep2


title: NiSO4 dose level 8 bio rep 5 [Ni_P1_E09_S51]

description:
96 well plate
Ni_P1_E09_S51_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_F03_R1


title: GRK-beta1AR_LV_ISO_rep3


title: GRK-beta1AR/miR150_LV_Veh_rep1


title: GL26130_CD3posP1_F05_R1


title: NiSO4 dose level 7 bio rep 5 [Ni_P1_E08_S50]

description:
96 well plate
Ni_P1_E08_S50_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Untreated untransformed library, replicate 4


title: MeOH treatment of the untransformed library, replicate 2


title: GRK-beta1AR/miR150_LV_ISO_rep3

value: 12 week age


title: GL26130_CD3posP1_B05_R1


title: NiSO4 dose level 6 bio rep 5 [Ni_P1_E07_S49]

description:
96 well plate
Ni_P1_E07_S49_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_F06_R1


title: GRK-beta1AR/miR150_LV_ISO_rep2

value: 11 week age


title: MeOH treatment of the untransformed library, replicate 1


title: 800 μM IQ treatment of the untransformed library, replicate 4

value: 800 μM IQ


title: GL26130_CD3posP1_D12_R1


title: NiSO4 dose level 4 bio rep 5 [Ni_P1_E05_S60]

description:
96 well plate
Ni_P1_E05_S60_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body


title: MeOH treatment of the untransformed library, replicate 3


title: 800 μM IQ treatment of the untransformed library, replicate 2


title: NiSO4 dose level 3 bio rep 5 [Ni_P1_E04_S59]

description:
96 well plate
Ni_P1_E04_S59_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: larva


title: KO+CLP 6

city: Minami-ku

first: Kazuya

last: Kikutani

state: Hiroshima

address: 1-2-3 Kasumi

department: Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima Univeristy

data_processing: Analysis of genes expressed differentially between groups was performed using a web-based analysis platform for RNA data (Dr. Tom, BGI Genomics, Shenzhen, China) and ShinyGO

source_name: Hippocampus

extract_protocol:
The tissue was homogenized by Bead crushers with 3.0 mm stainless beads and total ribonucleic acid (RNA) was extracted from tissues using a NucleoSpin RNA kit (Takara Bio, Japan) according to the manufacturer’s instructions.
The cDNA library generated by PCR amplification was examined using a Bioanalyzer 2100 system (Agilent Technologies, Inc., Santa Clara, USA) for quality control and sequenced with BGIseq-500.

value: Hippocampus

tag: genotype

value: TSPOKO

value: CLP


title: GL26130_CD3posP1_H06_R1


title: KO+CLP 5


title: NiSO4 dose level 2 bio rep 5 [Ni_P1_E03_S58]

description:
96 well plate
Ni_P1_E03_S58_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26130_CD3posP1_G06_R1


title: KO+CLP 4


title: NiSO4 dose level 1 bio rep 5 [Ni_P1_E02_S57]

description:
96 well plate
Ni_P1_E02_S57_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: 800 μM IQ treatment of the untransformed library, replicate 1

value: Yeast cells (BY4743 library)

value: Pooled homozygous diploid deletion library

value: No exogenous expression


title: 400 μM IQ treatment of the untransformed library, replicate 4

value: 400 μM IQ


title: GL26130_CD3posP1_C12_R1

value: brain

value: Tcell

value: ctrl


title: KO+CLP 3


title: GL26130_CD3posP1_C02_R1


title: 400 μM IQ treatment of the untransformed library, replicate 3


title: NiSO4 dose level 9 bio rep 4 [Ni_P1_D10_S40]

description:
96 well plate
Ni_P1_D10_S40_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 24 hr


title: 400 μM IQ treatment of the untransformed library, replicate 2


title: GL26130_CD3posP1_A08_R1


title: NiSO4 control bio rep 5 [Ni_P1_E01_S56]

description:
96 well plate
Ni_P1_E01_S56_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: KO+CLP 2


title: GRK-beta1AR/miR150_LV_ISO_rep1

value: male

value: LV

value: 10 week age


title: NiSO4 dose level 5 bio rep 5 [Ni_P1_E06_S48]

description:
96 well plate
Ni_P1_E06_S48_L006
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body


title: NiSO4 dose level 8 bio rep 4 [Ni_P1_D09_S39]

description:
96 well plate
Ni_P1_D09_S39_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: larva


title: KO+CLP 1

value: Hippocampus


title: GL26130_CD3posP1_A10_R1


title: 400 μM IQ treatment of the untransformed library, replicate 1


title: GL26130_CD3posP1_D07_R1


title: 800 μM IQ treatment of the untransformed library, replicate 3

value: 800 μM IQ


title: Untreated CYP1A2+NAT2 library, replicate 4

description:
Cells grown for approximately 10 generations
CYP1A2+NAT2_Significant_ORFs_Negative_M-Values.xlsx, CYP1A2+NAT2_Significant_ORFs_Positive_M-Values.xlsx

value: human CYP1A2 and human NAT2

value: No treatment


title: WT+CLP 6

value: WT

value: CLP


title: NiSO4 dose level 6 bio rep 4 [Ni_P1_D07_S30]

description:
96 well plate
Ni_P1_D07_S30_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26130_CD3posP1_H01_R1

value: Microglia


title: WT+CLP 5


title: Untreated CYP1A2+NAT2 library, replicate 3

value: Yeast cells (BY4743 library)

value: Pooled homozygous diploid deletion library


title: GL26130_CD3posP1_A09_R1

value: brain

value: Tcell

value: ctrl


title: Untreated CYP1A2+NAT2 library, replicate 2


title: NiSO4 dose level 4 bio rep 4 [Ni_P1_D05_S32]

description:
96 well plate
Ni_P1_D05_S32_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 24 hr


title: GL26130_CD3posP1_C06_R1


title: NiSO4 dose level 5 bio rep 4 [Ni_P1_D06_S29]

description:
96 well plate
Ni_P1_D06_S29_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_D11_R1


title: MeOH treatment of the CYP1A2+NAT2 library, replicate 4

value: 2% methanol


title: WT+CLP 4


title: GL26130_CD3posP1_G01_R1


title: WT+CLP 2


title: WT+CLP 3


title: NiSO4 dose level 3 bio rep 4 [Ni_P1_D04_S31]

description:
96 well plate
Ni_P1_D04_S31_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body


title: WT+CLP 1


title: NiSO4 dose level 2 bio rep 4 [Ni_P1_D03_S34]

description:
96 well plate
Ni_P1_D03_S34_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: larva


title: MeOH treatment of the CYP1A2+NAT2 library, replicate 3


title: GL26130_CD3posP1_H03_R1


title: MeOH treatment of the CYP1A2+NAT2 library, replicate 2


title: WT+Sham 5

value: Hippocampus

value: Sham


title: NiSO4 dose level 1 bio rep 4 [Ni_P1_D02_S33]

description:
96 well plate
Ni_P1_D02_S33_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: WT+Sham 6


title: GL26130_CD3posP1_D06_R1


title: GL26130_CD3posP1_E12_R1


title: NiSO4 control bio rep 4 [Ni_P1_D01_S36]

description:
96 well plate
Ni_P1_D01_S36_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: 800 μM IQ treatment of the CYP1A2+NAT2 library, replicate 4

value: human CYP1A2 and human NAT2

value: 800 μM IQ


title: NiSO4 dose level 7 bio rep 4 [Ni_P1_D08_S38]

description:
96 well plate
Ni_P1_D08_S38_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: MeOH treatment of the CYP1A2+NAT2 library, replicate 1


title: GL26130_CD3posP1_E08_R1


title: NiSO4 dose level 8 bio rep 3 [Ni_P1_C09_S22]

description:
96 well plate
Ni_P1_C09_S22_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: 800 μM IQ treatment of the CYP1A2+NAT2 library, replicate 3


title: WT+Sham 4

value: WT


title: WT+Sham 3


title: GL26130_CD3posP1_H05_R1


title: WT+Sham 2


title: GL26130_CD3posP1_B09_R1


title: 400 μM IQ treatment of the CYP1A2+NAT2 library, replicate 4

value: 400 μM IQ


title: WT+Sham 1


title: 800 μM IQ treatment of the CYP1A2+NAT2 library, replicate 2


title: 800 μM IQ treatment of the CYP1A2+NAT2 library, replicate 1


title: NiSO4 dose level 7 bio rep 3 [Ni_P1_C08_S21]

description:
96 well plate
Ni_P1_C08_S21_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: Tumor2,Day80

first: HUI

last: CHEN

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ovary

growth_protocol: MBA-MD-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen) .25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on MGIseq500 platform (BGI-Shenzhen, China)

tag: strain background

value: balb/c-nude

value: ovary

tag: cell line

value: cancer cell

value: Tumor

value: subcutaneous injected MBA-MD-232


title: NiSO4 dose level 4 bio rep 3 [Ni_P1_C05_S26]

description:
96 well plate
Ni_P1_C05_S26_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Untreated CYP1A2+NAT2 library, replicate 1

value: Yeast cells (BY4743 library)

value: Pooled homozygous diploid deletion library

value: No treatment


title: GL26130_CD3posP1_B04_R1

value: brain

value: Tcell

value: ctrl


title: NiSO4 dose level 6 bio rep 3 [Ni_P1_C07_S24]

description:
96 well plate
Ni_P1_C07_S24_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body

value: larva

value: 24 hr


title: NiSO4 dose level 9 bio rep 3 [Ni_P1_C10_S35]

description:
96 well plate
Ni_P1_C10_S35_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Tumor3,Day80

value: subcutaneous injected MBA-MD-233


title: Tumor1,Day80

value: subcutaneous injected MBA-MD-231


title: NiSO4 dose level 3 bio rep 3 [Ni_P1_C04_S25]

description:
96 well plate
Ni_P1_C04_S25_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: NiSO4 dose level 5 bio rep 3 [Ni_P1_C06_S23]

description:
96 well plate
Ni_P1_C06_S23_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: 400 μM IQ treatment of the CYP1A2+NAT2 library, replicate 2

value: human CYP1A2 and human NAT2

value: 400 μM IQ


title: GL26130_CD3posP1_G08_R1


title: GL26130_CD3posP1_C08_R1


title: Control2,Day80

value: balb/c-nude

value: ovary

value: Control


title: NiSO4 dose level 1 bio rep 3 [Ni_P1_C02_S27]

description:
96 well plate
Ni_P1_C02_S27_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: 400 μM IQ treatment of the CYP1A2+NAT2 library, replicate 1

description:
Cells grown for approximately 10 generations
CYP1A2+NAT2_Significant_ORFs_Negative_M-Values.xlsx, CYP1A2+NAT2_Significant_ORFs_Positive_M-Values.xlsx

value: Yeast cells (BY4743 library)


title: GL26130_CD3posP1_B08_R1


title: control1,Day80


title: GL26130_CD3posP1_C10_R1


title: Ykl-8

first: Sung-Hee

middle: Seanna

last: Yoon

address: 50 Blossom St

institute: Massachusetts General Hospital

description: Bulk-RNA Seq

data_processing:
Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR v.2.7.2b.
Transcript abundances were calculated using RSEM v.1.3.0
Differential gene expression analysis was performed using DESeq2
Supplementary files format and content: Excel table with FPKM values for all genes in all samples

source_name: whole kidney

extract_protocol:
Whole mouse kidneys were subjected to Trizol/Chloroform based RNA extraction
mRNAs were isolated by PAGE, followed by adaptor ligation and RT with PCR amplification. PCR products were again purified by PAGE and dissolved in EB solution. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final sequencing library. The library was amplified with phi29 to general DNA nanoballs (DNBs) which were loaded into the patterned nanoarray. Libraries were sequenced on the BGISEQ500 platform.

value: whole kidney

value: male


title: 400 μM IQ treatment of the CYP1A2+NAT2 library, replicate 3

value: Pooled homozygous diploid deletion library


title: NiSO4 dose level 9 bio rep 2 [Ni_P1_B10_S14]

description:
96 well plate
Ni_P1_B10_S14_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26130_CD3posP1_F12_R1

value: brain

value: Tcell


title: Tumor5_tRNA

city: Patras

first: Constantinos

last: Stathopoulos

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

description:
RNA from lung cancer biopsies followed by size selection
tRNAs.xlsx

data_processing:
miRNAs, tRFs and tRNAs were analyzed using an in-house build script.
human tRFs from the tRFdatabase (http://genome.bioch.virginia.edu/trfdb/) were counted directly in the fastq files.
tRNAs were mapped to an artificial tRNA genome consisting of unique sequences of hg38 tRNAs (http://gtrnadb.ucsc.edu/) using bowtie and further counted using bedtools coverage
miRNAs were mapped to an artificial miRNA genome consisting of human miRNAs from the miRdatabase (http://www.mirbase.org/)  using bowtie and further counted using bedtools coverage
Genome_build: hg38
Supplementary_files_format_and_content: abundance measurements

source_name: lung cancer biopsy tissue

growth_protocol: Tumor specimens were obtained by surgical procedures

extract_protocol:
Frozen tissues were immediately lysed, and small and large RNA fractions were extracted and isolated using PureLink RNA mini Kit and mirVana miRNA Isolation Kit (Ambion)
Ion Total RNA-Seq Kit v2 protocol for small RNA sequencing

value: lung cancer biopsies


title: Ykl-7

description: Bulk-RNA Seq


title: GL26130_CD3posP1_H02_R1

value: ctrl


title: GL26130_CD3posP1_E06_R1


title: Thin Subcutaneous replicate 1

city: Tabriz

first: Sana

last: Farhadi

address: Golgasht street

country: Iran

institute: Tabriz University

data_processing:
Fastqc-Trimmomatics-Tophat-Cufflink-Cuffmerge-cuffdiff-rstudio-Enrichment analysis-Network analysis
Sequenced reads were trimmed for adaptor and low-quality sequence
Clean reads mapped to Ovis-aries whole genome using Tophat software
Assembled reads
individual transcripts were merged to form a single transcript assembly
merged transcript was used for quantification of the transcripts
Genome_build: Ovis-aries
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Ovis aries

source_name: Fat Subcutaneous

growth_protocol: All lambs were weaned at 90 days of age and then fostered under similar conditions at the research station of the Faculty of Agriculture, University of Tabriz, Tabriz, Iran (Khalatpoushan). The lambs were housed in individual pens and provided the same diet ad libitum for 120 days. Animals were slaughtered after 7 months.ll of the chicks were mintained under normal condition until 21 days of age and then cold temperature was employed to induce ascites in almost all of the ascites susceptible chickens

extract_protocol:
Total RNA was extracted using TRIzol reagent using manufacturer instractions
PolyA enriched RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Iranian native Sheep breed


title: Ykl-6

description: Bulk-RNA Seq


title: NiSO4 dose level 8 bio rep 2 [Ni_P1_B09_S15]

description:
96 well plate
Ni_P1_B09_S15_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body

value: larva

value: 24 hr


title: Tumor4_tRNA


title: Ykl-5

description: Bulk-RNA Seq


title: NiSO4 dose level 7 bio rep 2 [Ni_P1_B08_S16]

description:
96 well plate
Ni_P1_B08_S16_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26130_CD3posP1_G02_R1

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)


title: Tumor3_tRNA


title: GL26130_CD3posP1_G10_R1


title: Tumor2_tRNA