title: CuSO4 dose level 3 bio rep 3 [Cu_P1_E4_S48]

description:
96 well plate
Cu_P1_E4_S48_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 4 bio rep 3 [Cu_P1_E5_S49]

status: Public on Jan 01 2023

type: SRA

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

country: USA

description:
96 well plate
Cu_P1_E5_S49_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.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.

molecule: total RNA

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.

tag: tissue

value: whole body

tag: developmental stage

value: larva

tag: age

value: 5 dpf/24 hr post hatch

tag: Sex

tag: treatment

tag: concentration

tag: time point

value: 24 hr


title: CuSO4 dose level 2 bio rep 3 [Cu_P1_E3_S47]

description:
96 well plate
Cu_P1_E3_S47_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: MG21hCTL2

city: Hefei

first: Kan

last: He

address: 111 Jiulong Road

department: School of life sciences

country: China

institute: Anhui University

data_processing:
PE150 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Bidirectional clustering analysis was performed for all different genes in the samples using R language Pheatmap(1.0.8) software package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes the expression values of transcripts for each Sample

organism: Mus musculus

growth_protocol: 6 to 8-week-old male C57BL/6 mice (purchased from Charles River Laboratories, Beijing, China) were housed under a 12-hour light/12-hour dark (LD) cycle. After adaptively fed for 1 week, the mice were randomly divided into two groups.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice in the treatment group (the HF group） were fed with a high-fat diet (D12492, Xietong Pharmaceutical Bio-engineering Co. Ltd., Jiangsu, China; 60 kcal% fat) for 3 months, and the age-matched mice in the control group (the CT group) were fed with a standard-fat diet (1010009, Xietong Pharmaceutical Bio-engineering Co. Ltd., Jiangsu, China; 10 kcal% fat) for 3 months.

tag: strain

value: male

value: meibomian gland

value: standard-fat diet for 3 months

tag: time


title: MG15hCTL2


title: 1241_S64

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
Data mapping using hisat2 (version 2.0.6) with paramters:--very-sensitive --score-min=C,-15,0 --seed 19
Read count extraction using htseq-count version 0.13.5
Assembly: mm10
Supplementary files format and content: csv  text files include raw counts values for each sample

source_name: hearts from female mice

growth_protocol: 16 week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks. PMID: 23312289

extract_protocol:
Qiagen miRNAeasy kit
QIAseq miRNA Library Kit

value: hearts from female mice

value: female

value: chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks


title: GL26140CD45neg_P2_H02

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)

source_name: brain

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

value: brain

tag: cell type

value: Malignant

value: Los


title: 1230_S63


title: CuSO4 dose level 1 bio rep 3 [Cu_P1_E2_S46]

description:
96 well plate
Cu_P1_E2_S46_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_E03


title: CuSO4 control bio rep 3 [Cu_P1_E1_S45]

description:
96 well plate
Cu_P1_E1_S45_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: MG9hHF6

value: high-fat diet for 3 months


title: 1228_S62


title: GL26140CD45neg_P2_G02


title: MG9hCTL3


title: CuSO4 dose level 9 bio rep 3 [Cu_P1_E10_S54]

description:
96 well plate
Cu_P1_E10_S54_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1214_S61


title: MG9hCTL2


title: 125_S2


title: CuSO4 dose level 8 bio rep 3 [Cu_P1_D9_S41]

description:
96 well plate
Cu_P1_D9_S41_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1202_S60


title: CuSO4 dose level 7 bio rep 3 [Cu_P1_D8_S40]

description:
96 well plate
Cu_P1_D8_S40_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1181_S59


title: GL26140CD45neg_P2_G05


title: GL26140CD45neg_P2_G04


title: M_USP11KO_E18_02

city: Taipei

first: Shang Yin

last: Chiang

address: 6F.-602, IBC, No.128, Sec. 2, Academia Rd., Nangang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

data_processing:
The RNA-seq reads of knockdown groups were first processed with Trimmomatic (Trimmomatic v0.33) to eliminate the adapter contamination.
The qualified reads from knockdown groups were mapped to the reference genome by Bowtie2 (version 2.3.4.3).
The qualified reads of knockdown groups were conducted with RSEM (RSEM-1.2.28). Gene expression quantification were conducted with FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
The reference genome and gene annotations were retrieved from NCBI Reference Sequence Database.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: B6 mice

growth_protocol: generate the wild type and knockout mice by corssing USP11(-/y) with USP11(+/-)

extract_protocol:
Total RNA was extracted from cortex tissue by NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
A total amount of 3 μg RNA per sample was used as in put material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out. using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H. Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: cortex

tag: genotype

value: knockout USP11


title: M_control_E18_02

value: wild type


title: GL26150CD45neg_P1_A09


title: M_USP11KO_E18_01


title: 115_S1


title: 1178_S58


title: GL26150CD45neg_P1_E07


title: M_control_E18_01


title: CuSO4 dose level 5 bio rep 3 [Cu_P1_D6_S38]

description:
96 well plate
Cu_P1_D6_S38_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: whole body


title: MG9hHF7


title: CuSO4 dose level 6 bio rep 3 [Cu_P1_D7_S39]

description:
96 well plate
Cu_P1_D7_S39_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: larva


title: GL26150CD45neg_P1_C04


title: 1139_S57


title: CuSO4 dose level 4 bio rep 3 [Cu_P1_D5_S37]

description:
96 well plate
Cu_P1_D5_S37_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: M_USP11KO_E13_02


title: 1133_S56


title: GL26150CD45neg_P1_B06


title: M_USP11KO_E13_01


title: CuSO4 dose level 3 bio rep 3 [Cu_P1_D4_S36]

description:
96 well plate
Cu_P1_D4_S36_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: 24 hr


title: CuSO4 dose level 2 bio rep 3 [Cu_P1_D3_S35]

description:
96 well plate
Cu_P1_D3_S35_L004
Cu.raw.counts.txt
na


title: 1130_S55


title: CuSO4 dose level 1 bio rep 3 [Cu_P1_D2_S34]

description:
96 well plate
Cu_P1_D2_S34_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_B12


title: M_control_E13_01


title: GL26150CD45neg_P1_H01


title: 1103_S53


title: GL26150CD45neg_P1_B05


title: GL26150CD45neg_P1_G02


title: 1115_S54


title: CuSO4 control bio rep 3 [Cu_P1_D1_S33]

description:
96 well plate
Cu_P1_D1_S33_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26150CD45neg_P1_C03


title: M_control_E13_02


title: CuSO4 dose level 9 bio rep 3 [Cu_P1_D10_S42]

description:
96 well plate
Cu_P1_D10_S42_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 8 bio rep 3 [Cu_P1_C9_S31]

description:
96 well plate
Cu_P1_C9_S31_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1099_S52


title: GL26150CD45neg_P1_H10


title: 1078_S50


title: CuSO4 dose level 7 bio rep 3 [Cu_P1_C8_S30]

description:
96 well plate
Cu_P1_C8_S30_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1088_S51


title: 1069_S49


title: CuSO4 dose level 5 bio rep 3 [Cu_P1_C6_S28]

description:
96 well plate
Cu_P1_C6_S28_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26150CD45neg_P1_G11


title: CuSO4 dose level 6 bio rep 3 [Cu_P1_C7_S29]

description:
96 well plate
Cu_P1_C7_S29_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1028_S48


title: CuSO4 dose level 4 bio rep 3 [Cu_P1_C5_S27]

description:
96 well plate
Cu_P1_C5_S27_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26150CD45neg_P1_E03

value: Oligodendrocytes


title: 1018_S47


title: GL26150CD45neg_P1_F01


title: Healthy Control_7 [N_7]

type: RNA

city: Beijing

first: chen

middle: wen

last: jia

address: Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences

institute: institute

description: Three to four RA patients cases per syndrome group respectively with Damp Heat Obstruction Syndrome (A), Phlegm Stasis Obstruction Syndrome (B), Qi-Yin Deficiency Syndrome (C), Blood Stasis Syndrome (D), Qi-Blood Deficiency Syndrome (E), Liver and Kidney Deficiency Syndrome (F), Wind-dampness Obstruction Syndrome (G) and Cold-dampness obstruction syndrome  (H) were collected as RA group, and seven healthy people were collected as normal control group (N).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the PrimeView, Human.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: whole blood_male_Healthy Control

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

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

treatment_protocol: All whole blood sample upon collection were placed in a microfuge tube, flash frozen in liquid nitrogen and stored at −80˚C.

tag: gender

value: male

tag: disease state

value: Healthy Control

tag: subtype

value: whole blood


title: RA_Cold-dampness obstruction syndrome_114 [H_114]

source_name: whole blood_male_RA_Cold-dampness obstruction syndrome

growth_protocol: Three to four RA patients cases per syndrome group respectively with Damp Heat Obstruction Syndrome (A), Phlegm Stasis Obstruction Syndrome (B), Qi-Yin Deficiency Syndrome (C), Blood Stasis Syndrome (D), Qi-Blood Deficiency Syndrome (E), Liver and Kidney Deficiency Syndrome (F), Wind-dampness Obstruction Syndrome (G) and Cold-dampness obstruction syndrome  (H) were collected as RA group, and seven healthy people were collected as normal control group (N).

value: Rheumatoid Arthritis (RA)

value: Cold-dampness obstruction syndrome


title: Healthy Control_5 [N_5]

source_name: whole blood_female_Healthy Control

value: female


title: 1010_S46

value: hearts from female mice

value: chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks


title: GL26150CD45neg_P1_F05

value: brain

value: Malignant


title: GL26150CD45neg_P1_A12


title: AC16 cells, KCl 3, 16 hours

city: Tucson

first: Hongting

last: Diao

state: AZ

address: 1316 E 7th St

department: Medical Pharmacology

institute: University of Arizona

data_processing:
Remove reads with adaptors
remove reads in which unknown bases(N) are more than 1%
remove low quality reads (we define the low quality reads as the percentage of base which quality is lesser than 15 is greater than 20% in a read). After filtering, the remianing reads are called "Clean Reads" and stored in FASTQ format
Assembly: NCBI (GCF_000001405.38_GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from control or 26 mM KCl treated AC16 cells at 16 hrs by RNeasy Kits (Qiagen) following manufacturer’s protocol
Strand-Specific mRNA Library Preparation (DNBSEQ)

value: heart

tag: cell line

value: cardiomyocytes

value: WT

value: KCl


title: RA_Cold-dampness obstruction syndrome_30 [H_30]

source_name: whole blood_female_RA_Cold-dampness obstruction syndrome


title: Healthy Control_6 [N_6]


title: GL26150CD45neg_P1_E01


title: GL26150CD45neg_P1_H12


title: Healthy Control_4 [N_4]


title: RA_Cold-dampness obstruction syndrome_82 [H_82]


title: AC16 cells, KCl 2, 16 hours


title: GL26150CD45neg_P1_A04


title: CuSO4 dose level 9 bio rep 3 [Cu_P1_C10_S32]

description:
96 well plate
Cu_P1_C10_S32_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: CuSO4 dose level 2 bio rep 3 [Cu_P1_C3_S25]

description:
96 well plate
Cu_P1_C3_S25_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: 24 hr


title: AC16 cells, control 3, 16 hours

value: untreated


title: CuSO4 control bio rep 3 [Cu_P1_C1_S23]

description:
96 well plate
Cu_P1_C1_S23_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: AC16 cells, KCl 1, 16 hours


title: CuSO4 dose level 8 bio rep 2 [Cu_P1_B9_S19]

description:
96 well plate
Cu_P1_B9_S19_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: AC16 cells, control 2, 16 hours


title: RA_Wind-dampness Obstruction Syndrome_47 [G_47]

value: Wind-dampness Obstruction Syndrome

value: whole blood


title: GL26150CD45neg_P1_H02


title: CuSO4 dose level 3 bio rep 3 [Cu_P1_C4_S26]

description:
96 well plate
Cu_P1_C4_S26_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26150CD45neg_P1_H06


title: RA_Wind-dampness Obstruction Syndrome_84 [G_84]

value: Rheumatoid Arthritis (RA)


title: CuSO4 dose level 1 bio rep 3 [Cu_P1_C2_S24]

description:
96 well plate
Cu_P1_C2_S24_L004
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 7 bio rep 2 [Cu_P1_B8_S18]

description:
96 well plate
Cu_P1_B8_S18_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: AC16 cells, control 1, 16 hours


title: GL26150CD45neg_P1_G12


title: CuSO4 dose level 6 bio rep 2 [Cu_P1_B7_S17]

description:
96 well plate
Cu_P1_B7_S17_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: RA_Wind-dampness Obstruction Syndrome_39 [G_39]

value: female


title: RA_Liver and Kidney Deficiency Syndrome_16 [F_16]

source_name: whole blood_female_RA_Liver and Kidney Deficiency Syndrome

value: Liver and Kidney Deficiency Syndrome


title: RA_Liver and Kidney Deficiency Syndrome_11 [F_11]

source_name: whole blood_male_RA_Liver and Kidney Deficiency Syndrome

value: male


title: CuSO4 dose level 5 bio rep 2 [Cu_P1_B6_S16]

description:
96 well plate
Cu_P1_B6_S16_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26150CD45neg_P1_E11

value: brain


title: BY6_BamHI_70_pct_cut_X

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: BamHI 70% cut

library_source: genomic

data_processing:
Library strategy: ORE-seq
bowtie2 (v. 2.4.4) alignment to joint S.cerevisiae/S.pombe genome Parameters  "-X 500 --no-discordant --no-mixed --no-unal"
filter multiply mapped reads using samtools view -hf 0x2
Coverage using bamCoverage (deepTools v. 3.5.1)
Genome_build: SacCer3 & EF2
Supplementary_files_format_and_content: BigWig file of genomic coverage

molecule: genomic DNA

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: S. cerevisiae/S. pombe cells

growth_protocol: Grow 7 * 109 cells of S. cerevisiae or S. pombe wild type strain in YPD or YES medium, respectively, to a density of approx. 3 * 108 cells/ml.

extract_protocol:
Genomic DNA purified with Blood & Cell Culture DNA Midi Kit (QIAGEN) using 100/G QIAGEN Genomic-tip
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

treatment_protocol: no further treatment of cells prior to harvest; genomic DNA was digested or mock digested with restriction enzymes and sheared by sonication.

tag: restriction enzyme

value: BamHI

tag: digestion degree[%]


title: GL26150CD45neg_P1_C08

tag: tissue

value: Malignant


title: BY6_BamHI_90_pct_cut_X

description: BamHI 90% cut


title: CuSO4 dose level 4 bio rep 2 [Cu_P1_B5_S15]

description:
96 well plate
Cu_P1_B5_S15_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: developmental stage


title: RA_Qi-Blood Deficiency Syndrome_18 [E_18]

source_name: whole blood_female_RA_Qi-Blood Deficiency Syndrome

value: Qi-Blood Deficiency Syndrome


title: RA_Liver and Kidney Deficiency Syndrome_7 [F_7]


title: RA_Qi-Blood Deficiency Syndrome_15 [E_15]


title: BY6_BamHI_30_pct_cut_X

description: BamHI 30% cut


title: CuSO4 dose level 3 bio rep 2 [Cu_P1_B4_S14]

description:
96 well plate
Cu_P1_B4_S14_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: age


title: CuSO4 dose level 2 bio rep 2 [Cu_P1_B3_S13]

description:
96 well plate
Cu_P1_B3_S13_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: Sex


title: GL26150CD45neg_P1_E02

tag: treatment


title: BY6_BamHI_10_pct_cut_X

description: BamHI 10% cut


title: GL26150CD45neg_P1_H09


title: RA_Qi-Blood Deficiency Syndrome_13 [E_13]


title: CuSO4 dose level 1 bio rep 2 [Cu_P1_B2_S12]

description:
96 well plate
Cu_P1_B2_S12_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: concentration


title: GL26150CD45neg_P1_C05


title: BY6_BamHI_1

description: BamHI 100% cut


title: BY6_BamHI_0_pct_cut_X

description: BamHI 0% cut


title: GL26150CD45neg_P1_C07


title: RA_Blood Stasis Syndrome_43 [D_43]

source_name: whole blood_female_RA_Blood Stasis Syndrome

value: Blood Stasis Syndrome


title: CuSO4 dose level 9 bio rep 2 [Cu_P1_B10_S20]

description:
96 well plate
Cu_P1_B10_S20_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: time point


title: 800 uM treatment of the CYP1A2+NAT2 library, 10 generations, replicate 4

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
10G IQ.xlsx

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).

value: Yeast cells (BY4743 library)

tag: strain

value: Pooled homozygous diploid deletion library

tag: expression

value: human CYP1A2 and human NAT2

value: 800 μM IQ


title: GL26150CD45neg_P1_E10

tag: cell type


title: BY6_AluI_90_pct_cut_X

description: AluI 90% cut

value: AluI


title: RA_Blood Stasis Syndrome_62 [D_62]


title: mouse skin stromal cells after injury

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

data_processing:
Processing of all raw FASTQ data was done using zUMI pipeline along with STAR to obtain expression profiles for barcoded UMI data (19,20). Mapping was done to the reference genome (mm10 / 09) concatenated with the ERCC and GFP reference. Gene annotations were obtained from Ensembl (GRCm38 / mm10 - GRCh38.84). For barcode filtering, we excluded barcodes with less than 1000 detected genes. We assessed the number of unique molecular identifiers (UMIs) for each sample using violin plots, and retained cells with a number of UMIs below 250000. Genes were only considered if they were expressed in at least 3 cells in the data set.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix (WoundHealing_SCRB_raw_counts_unfiltered.mtx) from SCRB-seq experiments with 22953 genes and 3979 cells in market matrix format and corresponding column (WoundHealing_SCRB_genes_unfiltered.txt) and row (WoundHealing_SCRB_barcodes_unfiltered.txt) labels. Cell-level metadata (WoundHealing_SCRB_unfiltered_metadata.txt).

source_name: pool of En1 sorted population and Adipoq sorted population on day 1 and day 4 after injury

extract_protocol: All samples were purified with SPRI beads (ratio 1: 0.8) after pre-amplification. Final elution was in 10 µL of nuclease-free water (Invitrogen). Later cDNA was quantified using the Quant-iT PicoGreen double stranded DNA Assay Kit (Thermo Fisher). A High Sensitivity DNA chip (Agilent Bioanalyzer), was used to verify size distributions. Samples that passed the quality and quantity control parameter, were used for constructing Nextera XT libraries from 0.8 ng of pre-amplified cDNA. Later, 3 ’end sequences were enriched with a custom made P5 primer (P5NEXTPT5, IDT), during PCR of the libraries. Following this, Libraries were pooled and selected based on their size using 2% E-Gel Agarose EX Gels (Life Technologies); a size range from 300bp to 800 bp was cut out and extracted using the MinElute kit (Qiagen). All Procedures were in accordance with the manufacturer’s recommendations. An Illumina HiSeq 1500 instrument was used to sequence libraries. Paired-end sequencing of libraries was performed on high output flow cells. To generate molecular and cellular barcodes, 16 bases were sequenced with the 1st read, 50 bps sequenced in the 2nd read into the cDNA fragment, and 8 bases were read to obtain the i7 barcode.

value: skin

tag: cell population

value: multiplexed sample (pool of En1 and Adipoq)

value: multiplexed sample (pool of day 1 and day 4)

tag: number of cells

value: multiplexed sample (pool of 1067,925,1011, 976 cells)


title: CuSO4 dose level 8 bio rep 1 [Cu_P1_A9_S9]

description:
96 well plate
Cu_P1_A9_S9_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch

value: 24 hr


title: BY6_BamHI_50_pct_cut_X

description: BamHI 50% cut

value: BamHI


title: GL26150CD45neg_P1_H04

value: brain

value: Malignant


title: GL26150CD45neg_P1_C01


title: RA_Blood Stasis Syndrome_151 [D_151]

description: Three to four RA patients cases per syndrome group respectively with Damp Heat Obstruction Syndrome (A), Phlegm Stasis Obstruction Syndrome (B), Qi-Yin Deficiency Syndrome (C), Blood Stasis Syndrome (D), Qi-Blood Deficiency Syndrome (E), Liver and Kidney Deficiency Syndrome (F), Wind-dampness Obstruction Syndrome (G) and Cold-dampness obstruction syndrome  (H) were collected as RA group, and seven healthy people were collected as normal control group (N).

tag: gender

value: female

tag: disease state

value: Rheumatoid Arthritis (RA)

value: Blood Stasis Syndrome

value: whole blood


title: BY6_AluI_70_pct_cut_X

description: AluI 70% cut


title: 800 uM treatment of the CYP1A2+NAT2 library, 10 generations, replicate 2

value: Yeast cells (BY4743 library)

value: Pooled homozygous diploid deletion library

value: human CYP1A2 and human NAT2

value: 800 μM IQ


title: GL26150CD45neg_P1_B08


title: BY6_AluI_50_pct_cut_X

description: AluI 50% cut

value: AluI


title: CuSO4 control bio rep 2 [Cu_P1_B1_S11]

description:
96 well plate
Cu_P1_B1_S11_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 5 bio rep 1 [Cu_P1_A6_S6]

description:
96 well plate
Cu_P1_A6_S6_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 6 bio rep 1 [Cu_P1_A7_S7]

description:
96 well plate
Cu_P1_A7_S7_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 800 uM treatment of the CYP1A2+NAT2 library, 10 generations, replicate 1


title: GL26150CD45neg_P1_F09


title: MeOH treatment of the CYP1A2+NAT2 library, 10 generations, replicate 4

value: 2% methanol


title: RA_Qi-Blood Deficiency Syndrome_5 [E_5]

tag: subtype

value: Qi-Blood Deficiency Syndrome


title: BY6_AluI_10_pct_cut_X

description: AluI 10% cut

tag: restriction enzyme


title: BY6_AluI_1

description: AluI 100% cut

tag: digestion degree[%]


title: CuSO4 dose level 4 bio rep 1 [Cu_P1_A5_S5]

description:
96 well plate
Cu_P1_A5_S5_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: tissue

value: whole body

value: larva


title: GL26150CD45neg_P1_C10


title: GL26150CD45neg_P1_H11


title: MeOH treatment of the CYP1A2+NAT2 library, 10 generations, replicate 3


title: MeOH treatment of the CYP1A2+NAT2 library, 10 generations, replicate 2


title: GL26150CD45neg_P1_D10


title: CuSO4 dose level 7 bio rep 1 [Cu_P1_A8_S8]

description:
96 well plate
Cu_P1_A8_S8_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: developmental stage

value: 5 dpf/24 hr post hatch

value: 24 hr


title: CuSO4 dose level 2 bio rep 1 [Cu_P1_A3_S3]

description:
96 well plate
Cu_P1_A3_S3_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: age


title: CuSO4 dose level 3 bio rep 1 [Cu_P1_A4_S4]

description:
96 well plate
Cu_P1_A4_S4_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: Sex


title: GL26150CD45neg_P1_H05

value: brain

tag: treatment


title: 800 uM treatment of the CYP1A2+NAT2 library, 10 generations, replicate 3


title: BY6_AluI_0_pct_cut_X

description: AluI 0% cut


title: CuSO4 dose level 1 bio rep 1 [Cu_P1_A2_S2]

description:
96 well plate
Cu_P1_A2_S2_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: concentration


title: GL26150CD45neg_P1_E05

value: Malignant


title: MeOH treatment of the CYP1A2+NAT2 library, 10 generations, replicate 1


title: BY6_AluI_30_pct_cut_X

description: AluI 30% cut


title: CuSO4 control bio rep 1 [Cu_P1_A1_S1]

description:
96 well plate
Cu_P1_A1_S1_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

tag: time point


title: GL26150CD45neg_P1_F06


title: 800 uM treatment of the CYP1A2+NAT2 library, 5 generations, replicate 2

description:
Cells grown for approximately 5 generations
5G IQ.xlsx

tag: strain


title: GL26150CD45neg_P1_H08


title: CuSO4 dose level 9 bio rep 1 [Cu_P1_A10_S10]

description:
96 well plate
Cu_P1_A10_S10_L003
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: Clothianidin dose level 11 bio rep 3 [Clo_M_H12_S75]

description:
96 well plate
Clo_M_H12_S75_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: Clothianidin


title: 800 uM treatment of the CYP1A2+NAT2 library, 5 generations, replicate 1

tag: expression


title: GL26150CD45neg_P1_D07

tag: cell type


title: GL26150CD45neg_P1_B10


title: MeOH treatment of the CYP1A2+NAT2 library, 5 generations, replicate 4


title: Clothianidin dose level 9 bio rep 3 [Clo_M_H10_S73]

description:
96 well plate
Clo_M_H10_S73_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26150CD45neg_P1_F07


title: Clothianidin dose level 8 bio rep 3 [Clo_M_H09_S79]

description:
96 well plate
Clo_M_H09_S79_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 800 uM treatment of the CYP1A2+NAT2 library, 5 generations, replicate 4


title: Clothianidin dose level 7 bio rep 3 [Clo_M_H08_S78]

description:
96 well plate
Clo_M_H08_S78_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: MeOH treatment of the CYP1A2+NAT2 library, 5 generations, replicate 2


title: 800 uM treatment of the CYP1A2+NAT2 library, 5 generations, replicate 3


title: GL26150CD45neg_P1_G01


title: MeOH treatment of the CYP1A2+NAT2 library, 5 generations, replicate 1


title: GL26150CD45neg_P1_D12


title: Clothianidin dose level 6 bio rep 3 [Clo_M_H07_S77]

description:
96 well plate
Clo_M_H07_S77_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26150CD45neg_P1_F04


title: Clothianidin dose level 10 bio rep 3 [Clo_M_H11_S74]

description:
96 well plate
Clo_M_H11_S74_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 5 bio rep 3 [Clo_M_H06_S76]

description:
96 well plate
Clo_M_H06_S76_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26150CD45neg_P1_B03


title: MeOH treatment of the CYP1A2+NAT2 library, 5 generations, replicate 3


title: drug-treated_time_6_Rep_3

city: Lexington

first: Robert

middle: C

last: Dickson

state: KY

address: 741 South Limestone St.

department: Molecular & Cellular Biochemistry

institute: University of Kentucky College of Medicine

data_processing:
Each library was quantitated by qPCR and sequenced on one lane for 151 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Each sample's pair of fastq files were run through trimmomatic 0.36 to first remove any remaining standard Illumina PE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove individual reads shorter than 30 bp and their paired read, regardless of length (parameters ILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:15:10 TRAILING:28 LEADING:28 MINLEN:30)
Paired reads per sample were psuedo-aligned to the R64 transcriptome and 92 ERRC spike-in control sequences using Salmon 0.8.2 with parameters -l A --numbootstraps=30 --seqBias --gcBias
Count files were processed to Transcripts Per Million (TPM- Trapnell et al., 2010) in WebMev (Wang et. al., 2017)
Assembly: R64
Supplementary files format and content: tab-delimited text file of all TPM-normalized counts for each sample, organized by Entrez ID

source_name: budding cells

growth_protocol: Culture conditions were similar to ones described previously (Hepowit et al. 2021, Aging) except for the following modifications.  Prototrophic BY4741 yeast cells were grown in 200 ml of SDC culture medium in a 1 L flask with the medium heated to 30°C before addition of EtOH (final concentration of 0.3%) (control samples). For drug-treated samples, myriocin was added after addition of EtOH to give final concentrations of 0.3% EtOH and 700ng/ml myriocin. Lastly, cells from a saturated overnight culture were diluted into the 200 ml cultures to give an initial A600nm units/ml of 0.15. Flasks were incubated at 30°C and 200 rpm on a rotary shaker.

extract_protocol:
RNA was extracted from 5 A600nm unit/ml of yeast cells, filtered at time 0 and then every hr up to 6 hrs using a membrane filter, as described previously for amino acid extraction (Hepowit et al. 2021). Filtered cells were washed once with 5 ml of ice-cold nanopure water and the filter was quickly transferred to a chilled 1.5 ml microfuge tube containing 0.5 ml cold nanopure water. Tubes were vortexed 10 sec followed by centrifugation for 15 sec. Supernatant fluid (450 μl) was transferred to a new tube and was frozen in a dry-ice EtOH bath followed by storage at -80°C. Cold acid-washed glass beads (300 μl, 0.5 mm dia.) were added to a frozen cell pellet followed by addition of 300 μl of RLT buffer (RNAeasy mini kit (Qiagen, Germantown, Maryland). Tubes were vortexed 5 min at room temperature and placed on ice for 1 min. This cycle was done 4 times followed by addition of 300 μl of ice-cold RLT buffer, mixing, and centrifugation at 13,000xg for 2 min at room temperature. Supernatant fluid (450 μl) was transferred to a new microfuge tube and then mixed with 1 ml of 70% EtOH before transfer to a RNeasy spin column and processed according to the manufacture’s instructions. Processed samples were frozen in a dry-ice EtOH bath and stored at -80°C.
Libraries were constructed with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' at the Roy J. Carver Biotechnology Center at the University of Illinois.

treatment_protocol: Control cells (containing final concentration of 0.3% EtOH) and myriocin-treated cells (final concentrations of 0.3 % EtOH and 700ng/ml myriocin) were harvested at time 0, 1, 2, 3, 4, 5 and 6 hours (all time points for each replication from the same culture flask).

value: drug-treated

tag: time

tag: replicate

tag: errc


title: drug-treated_time_6_Rep_2


title: Clothianidin dose level 3 bio rep 3 [Clo_M_H04_S82]

description:
96 well plate
Clo_M_H04_S82_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

source_name: whole body


title: Clothianidin dose level 4 bio rep 3 [Clo_M_H05_S83]

description:
96 well plate
Clo_M_H05_S83_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_G03

value: ctrl


title: drug-treated_time_5_Rep_2


title: drug-treated_time_6_Rep_1


title: GL26130CD45neg_P2_A06


title: GL26130CD45neg_P2_B11


title: Clothianidin dose level 2 bio rep 3 [Clo_M_H03_S81]

description:
96 well plate
Clo_M_H03_S81_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: drug-treated_time_4_Rep_3


title: GL26130CD45neg_P2_B07


title: drug-treated_time_4_Rep_2


title: GL26130CD45neg_P2_B02


title: Clothianidin dose level 1 bio rep 3 [Clo_M_H02_S80]

description:
96 well plate
Clo_M_H02_S80_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: drug-treated_time_5_Rep_3


title: drug-treated_time_5_Rep_1


title: GL26130CD45neg_P2_G12


title: GL26130CD45neg_P2_F12


title: Clothianidin dose level 10 bio rep 3 [Clo_M_G11_S84]

description:
96 well plate
Clo_M_G11_S84_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 11 bio rep 3 [Clo_M_G12_S87]

description:
96 well plate
Clo_M_G12_S87_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: drug-treated_time_4_Rep_1


title: Clothianidin dose level 9 bio rep 3 [Clo_M_G10_S85]

description:
96 well plate
Clo_M_G10_S85_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: drug-treated_time_3_Rep_3


title: Clothianidin dose level 7 bio rep 3 [Clo_M_G08_S91]

description:
96 well plate
Clo_M_G08_S91_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_B03


title: Clothianidin control bio rep 3 [Clo_M_H01_S86]

description:
96 well plate
Clo_M_H01_S86_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 6 bio rep 3 [Clo_M_G07_S88]

description:
96 well plate
Clo_M_G07_S88_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 8 bio rep 3 [Clo_M_G09_S90]

description:
96 well plate
Clo_M_G09_S90_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_G02


title: drug-treated_time_3_Rep_2


title: F2

city: Hohhot

first: Yuting

last: Fu

address: university west road

institute: Inner Mongolia University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: Matrix table with clean gene counts for every gene and every sample

organism: Equus asinus

source_name: diPSCS

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ear epithelial cells

value: donkey iPSCs

tag: cross

value: female donkey mated with male donkey


title: GL26130CD45neg_P2_C07

source_name: brain


title: GL26130CD45neg_P2_A12


title: Clothianidin dose level 5 bio rep 3 [Clo_M_G06_S89]

description:
96 well plate
Clo_M_G06_S89_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: F1


title: GL26130CD45neg_P2_F05


title: Clothianidin dose level 4 bio rep 3 [Clo_M_G05_S94]

description:
96 well plate
Clo_M_G05_S94_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 206238130092_R07C01

type: genomic

city: New York

first: Cristina

last: Antonescu

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: Dedifferentiated chondrosarcoma samples

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner setting

data_processing: Bioinformatic and statistical analyses were performed with R version 4.1.0 using the minfi version 1.38.0 package. Green and red channel intensities were normalized using the preprocessIllumina function with background correction.

label: Cy3, Cy5

source_name: FFPE

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FFPE tissue using the Chemagic DNA Tissue kit (PerkinElmer chemagen Technologie, GmbH, Baesweiler, Germany) after manual macrodissection to ensure at least 10% tumor content. For each sample, 250 ng of input was used for bisulfite conversion (EZ DNA Methylation Kit; Zymo Research; catalog number D5002), followed by an FFPE restoration step using the Infinium HD FFPE DNA Restore Kit (Illumina; catalog number WG-321-1002).

value: chondrosarcoma

tag: sample type

value: Dedifferentiated component

value: Altered


title: drug-treated_time_2_Rep_3


title: E2

source_name: DAFs

value: donkey adult fibroblasts


title: 205982900061_R08C01

description: Dedifferentiated chondrosarcoma samples


title: 206238130039_R05C01

description: Dedifferentiated chondrosarcoma samples


title: 206238130092_R06C01

description: Dedifferentiated chondrosarcoma samples

value: Wildtype


title: E1


title: drug-treated_time_2_Rep_2


title: 206144420055_R07C01

description: Dedifferentiated chondrosarcoma samples


title: 206238130038_R08C01

description: Dedifferentiated chondrosarcoma samples

value: Well-differentiated component


title: drug-treated_time_3_Rep_1


title: 205982900061_R07C01

description: Dedifferentiated chondrosarcoma samples


title: E3


title: Clothianidin dose level 3 bio rep 3 [Clo_M_G04_S95]

description:
96 well plate
Clo_M_G04_S95_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body

value: larva


title: GL26130CD45neg_P2_E09


title: D2987_day7_CART

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

country: Japan

institute: Keio University

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequencing adapters and low-quality bases were trimmed using Trimmomatic 0.38.
Cleaned reads were aligned to the reference genome hg38 using bowtie2. Reads with low mapping quality (< 30) or those mapped to mitochondria were filtered using samtools 1.9. PCR or optical duplicates were marked using Picard 2.18.26 and removed.
Peak calling was performed using MACS2 with the following parameters: -q 0.05 -f BAMPE --nomodel --nolambda -g hs.
Assembly: hg38
Supplementary files format and content: bigwig files

source_name: blood

growth_protocol: Human T cells were stimulated by K562 cells that express anti-CD3 mAb (clone OKT3)-derived scFV linked with the transmembrane and cytoplasmic domain of CD8a as well as CD80 (K562-OKT3/CD80) (day 0) and transduced with a CD19-targeting CAR gene (FMC63-28z) on day 2. The CAR-T cells were cultured in vitro with RPMI media supplemented with 10% FBS and 100 IU/ml human IL-2.

extract_protocol:
CAR-T cells were collected at day 7, and CD8+ CAR-T cell population was isolated by flow cytometry. The CAR-transduced T cells were detected by the expression of truncated NGFR. The purified T cells were resuspended with complete culture medium and incubated for 30 minutes at 37 degrees after supplemented with DNAse solution. The cells were washed with PBS once and cryopreserved in growth media with 10% DMSO. Sequencing analysis was performed with NovaSeq 6000 (Illumina).
Library preparation was performed using standard Illumina protocols.

value: blood

value: CD8+T cells


title: GL26130CD45neg_P2_B10

value: brain

value: Malignant


title: drug-treated_time_2_Rep_1

value: drug-treated


title: 206238130119_R07C01

description: Dedifferentiated chondrosarcoma samples


title: 206238130092_R08C01

description: Dedifferentiated chondrosarcoma samples


title: 206144420109_R08C01

description: Dedifferentiated chondrosarcoma samples


title: drug-treated_time_1_Rep_3


title: 205982900061_R06C01

description: Dedifferentiated chondrosarcoma samples


title: GL26130CD45neg_P2_G09

value: ctrl


title: ChIPseq_PROLIF_G_H3K9me3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Proliferating ASCs (gluteofemoral)

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using bowtie2 version 2.4.1
For histone ChIPs with replicates, bams files were merged.  For LMNA ChIPs, replicates were merged after peak calling.
Duplicate reads were removed using picard MarkDuplicates.  For histone ChIPs multi-mapping reads and alignments with a mapping quality below 10 were also filtered out.
For histone modification ChIPseq, peaks were called using macs2 2.2.7.1.  For H3K27me3, H3K36me3 and H3K4me1 option --broad was used.
For LMNA ChIPseq, peak calling was done using Enriched Domain Detector (EDD) version 1.1.15, run 10 times on each sample to optimize BinSize and GapPenalty settings before a final run with optimized settings.
Assembly: hg38
Supplementary files format and content: Bed EDD peak file - 4th column is EDD score.
Supplementary files format and content: bigwig (.bw) files are regular bigwig files are log2ratio of filtered ChIP/Input files, generated using bamCompare from deeptools 3.5.1 if the extension is ".grep.norm.bw".  Else if the tracks ends "_pileup.norm.bw" the track is generated from macs output files as the log 10 ratio of treat/control lamba pileup files.
Supplementary files format and content: .narrowPeak and .broadPeak files are modified bed files created by macs2 callpeaks

source_name: Adipose (gluteofemoral)

growth_protocol: Human normal ASCs purifed from adipose tissue were cultured in proliferating state in DMEM/F12 containing 10 % fetal calf serum and 20 ng/ml basic fibroblast growth factor.

extract_protocol:
For ChIP, cells were sonicated to produce chromatin fragments of 200 base-pairs, lysates were clarified by sedimentation and histone-DNA or lamin-DNA complexes were isolated from supernatants by ChIP using specific antibodies. RNA was purified from cell lysates using the RNEasy mini kit (Qiagen).
ChIP sequencing libraries were prepared according to Illumina protocols for sequencing at the Norwegian Sequencing Center.

treatment_protocol: Proliferating cells were harvested, re-seeded at confluency and cultured confluent for 48 h without fibroblast growth factor. On Day 0, ASCs were induced to differentiate with 10 µg/ml insulin, 200 µM indomethacin, 1 µM dexamethasone and 0.5 µM 3-isobutyl-1-methylxanthine.  Cells were collected at indicated timepoints for protein, RNA and chromatin preparations and analyses.

value: Human primary adipose stem cells

value: Adipose (gluteofemoral)

value: Day minus 2 (proliferating)

tag: chip antibody

value: H3K9me3 (Diagenode C15410056)


title: Clothianidin dose level 1 bio rep 3 [Clo_M_G02_S93]

description:
96 well plate
Clo_M_G02_S93_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Clothianidin

value: 24 hr


title: 206238130039_R06C01

description: Dedifferentiated chondrosarcoma samples

value: chondrosarcoma

value: Dedifferentiated component

value: Altered


title: Clothianidin dose level 2 bio rep 3 [Clo_M_G03_S92]

description:
96 well plate
Clo_M_G03_S92_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body

value: larva


title: D1_day7_CART

value: blood

value: CD8+T cells


title: F3

value: ear epithelial cells

value: donkey iPSCs

value: female donkey mated with male donkey


title: 206144420109_R07C01

description: Dedifferentiated chondrosarcoma samples

value: Well-differentiated component


title: 206144420055_R06C01

description: Dedifferentiated chondrosarcoma samples


title: 206144420055_R08C01

description: Dedifferentiated chondrosarcoma samples


title: GL26130CD45neg_P2_G07

value: brain

value: Malignant

value: ctrl


title: drug-treated_time_1_Rep_1

value: drug-treated


title: GL26130CD45neg_P2_B12


title: Clothianidin dose level 11 bio rep 3 [Clo_M_F12_S51]

description:
96 well plate
Clo_M_F12_S51_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Clothianidin


title: drug-treated_time_1_Rep_2


title: drug-treated_time_0_Rep_2


title: Clothianidin control bio rep 3 [Clo_M_G01_S96]

description:
96 well plate
Clo_M_G01_S96_L004
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 24 hr


title: drug-treated_time_0_Rep_3


title: GL26130CD45neg_P2_B05


title: ChIPseq_PROLIF_G_H3K36me3

description: Proliferating ASCs (gluteofemoral)

value: Human primary adipose stem cells

value: Adipose (gluteofemoral)

value: Day minus 2 (proliferating)

value: H3K36me3 (Diagenode C15410058)


title: Clothianidin dose level 9 bio rep 3 [Clo_M_F10_S50]

description:
96 well plate
Clo_M_F10_S50_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body

value: larva


title: 206144420109_R06C01

description: Dedifferentiated chondrosarcoma samples

value: chondrosarcoma

value: Dedifferentiated component

value: Altered


title: HuR WT, Tumor, Week 4 (P_Wk4_3)

city: Portland

first: Grace

middle: Anne

last: McCarthy

state: Oregon

address: 2730 S Moody Ave

department: Department of Surgery

institute: Oregon Health & Science University

description:
KO_Wk4vsP_Wk4_DEG.txt
P_Wk4_3

data_processing:
Base calling was done by Novogene Co., Ltd. (CASAVA)
Conversion to FASTQ was done by Novogene Co., Ltd. (bcl2fastq2)
Any low-quality data and data with adapter contamination were discarded
Sequence reads were mapped to GRCh38.p5 using STAR v2.6.1 (parameters- mismatch=2 )
HTSeq v0.6.1 was used to determine abundance of transcript (FPKM)
Read counts obtained by gene expression analysis were used to perform differential expression significant analysis of two conditions/groups by using  DESeq2v2_1.6.3, while the significant criterion is padj<0.05.
Assembly: GRCh38.p5
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: MIA PaCA-2 pancreatic tumor

growth_protocol: In vitro: Cells were cultured in standard DMEM(+++) with 10% FBS, 1% Pen-Strep, 1%L-glutamine; In vivo: 1E6 HuR WT or HuR KO cells were orthotopically injected into the tail of NRG mice pancreas and allowed tumors to form.

extract_protocol:
RNA was extracted using Qiagen RNAseEasy Kit as per manufacturer's instructions
Completed by Novogene Co., Ltd.

value: MIA PaCA-2 pancreatic tumor

value: Pancreatic ductal adenocarcinoma

tag: genotype

value: WT

tag: tumor stage

value: Orthotopic Tumor 4 Weeks Post-injection


title: HuR WT, Tumor, Week 4 (P_Wk4_4)

description:
KO_Wk4vsP_Wk4_DEG.txt
P_Wk4_4

tag: tissue


title: GL26130CD45neg_P2_H12

value: brain

value: Malignant

value: ctrl


title: Clothianidin dose level 8 bio rep 3 [Clo_M_F09_S71]

description:
96 well plate
Clo_M_F09_S71_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

tag: developmental stage

tag: age

value: 5 dpf/24 hr post hatch

value: Clothianidin

value: 24 hr


title: 206144420055_R05C01

description: Dedifferentiated chondrosarcoma samples

value: Well-differentiated component


title: ctrl_time_6_Rep_3

tag: treatment


title: HuR WT, Tumor, Week 4 (P_Wk4_2)

description:
KO_Wk4vsP_Wk4_DEG.txt
P_Wk4_2


title: GL26130CD45neg_P2_A05


title: HuR WT, Tumor, Week 3 (P_Wk3_4)

description:
KO_Wk3vsP_Wk3_DEG.txt
P_Wk3_4

value: Orthotopic Tumor 3 Weeks Post-injection


title: Clothianidin dose level 10 bio rep 3 [Clo_M_F11_S49]

description:
96 well plate
Clo_M_F11_S49_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body

tag: Sex

tag: concentration


title: HuR WT, Tumor, Week 4 (P_Wk4_1)

description:
KO_Wk4vsP_Wk4_DEG.txt
P_Wk4_1


title: 206238130119_R08C01

description: Dedifferentiated chondrosarcoma samples


title: ctrl_time_6_Rep_2


title: Clothianidin dose level 7 bio rep 3 [Clo_M_F08_S72]

description:
96 well plate
Clo_M_F08_S72_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: larva

tag: time point


title: drug-treated_time_0_Rep_1

value: drug-treated


title: GL26130CD45neg_P2_G05


title: Clothianidin dose level 6 bio rep 3 [Clo_M_F07_S69]

description:
96 well plate
Clo_M_F07_S69_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: HuR WT, Tumor, Week 3 (P_Wk3_3)

description:
KO_Wk3vsP_Wk3_DEG.txt
P_Wk3_3


title: GL26130CD45neg_P2_C02


title: GL26130CD45neg_P2_H10


title: GL26130CD45neg_P2_H01


title: HuR WT, Tumor, Week 3 (P_Wk3_2)

description:
KO_Wk3vsP_Wk3_DEG.txt
P_Wk3_2


title: Clothianidin dose level 4 bio rep 3 [Clo_M_F05_S67]

description:
96 well plate
Clo_M_F05_S67_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: HuR WT, Tumor, Week 3 (P_Wk3_1)

description:
KO_Wk3vsP_Wk3_DEG.txt
P_Wk3_1


title: ctrl_time_5_Rep_2


title: ctrl_time_5_Rep_1


title: Clothianidin dose level 3 bio rep 3 [Clo_M_F04_S68]

description:
96 well plate
Clo_M_F04_S68_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: HuR WT, Tumor, Week 2 (P_Wk2_3)

description:
KO_Wk2vsP_Wk2_DEG.txt
P_Wk2_3

value: Orthotopic Tumor 2 Weeks Post-injection


title: ctrl_time_6_Rep_1


title: GL26130CD45neg_P2_C11


title: GL26130CD45neg_P2_A02


title: Clothianidin dose level 2 bio rep 3 [Clo_M_F03_S65]

description:
96 well plate
Clo_M_F03_S65_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: ctrl_time_4_Rep_3


title: HuR WT, Tumor, Week 2 (P_Wk2_1)

description:
KO_Wk2vsP_Wk2_DEG.txt
P_Wk2_1


title: GL26130CD45neg_P2_C10


title: Clothianidin dose level 1 bio rep 3 [Clo_M_F02_S66]

description:
96 well plate
Clo_M_F02_S66_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin control bio rep 3 [Clo_M_F01_S63]

description:
96 well plate
Clo_M_F01_S63_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: ctrl_time_5_Rep_3


title: ctrl_time_4_Rep_1


title: ctrl_time_4_Rep_2


title: HuR WT, Cell Line (P_CL_3)

description:
KO_CLvsP_CL_DEG.txt
P_CL_3

source_name: MIA PaCA-2

tag: cell line

value: MIA PaCA-2

value: Cell Line


title: Clothianidin dose level 5 bio rep 3 [Clo_M_F06_S70]

description:
96 well plate
Clo_M_F06_S70_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: HuR WT, Cell Line (P_CL_4)

description:
KO_CLvsP_CL_DEG.txt
P_CL_4

tag: cell type

value: Pancreatic ductal adenocarcinoma


title: ctrl_time_3_Rep_3

tag: time


title: GL26130CD45neg_P2_C06


title: ctrl_time_3_Rep_2

tag: replicate


title: Clothianidin dose level 11 bio rep 3 [Clo_M_E12_S64]

description:
96 well plate
Clo_M_E12_S64_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: HuR WT, Cell Line (P_CL_2)

description:
KO_CLvsP_CL_DEG.txt
P_CL_2

value: WT


title: HuR WT, Cell Line (P_CL_1)

description:
KO_CLvsP_CL_DEG.txt
P_CL_1


title: GL26130CD45neg_P2_H08


title: GL26130CD45neg_P2_F07


title: Clothianidin dose level 10 bio rep 3 [Clo_M_E11_S61]

description:
96 well plate
Clo_M_E11_S61_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_D03


title: ctrl_time_3_Rep_1

tag: errc


title: ctrl_time_2_Rep_3


title: HuR KO, Tumor, Week 4 (KO_Wk4_4)

description:
KO_Wk4vsP_Wk4_DEG.txt
KO_Wk4_4

value: MIA PaCA-2 pancreatic tumor

value: HuR KO

value: Orthotopic Tumor 4 Weeks Post-injection


title: HuR KO, Tumor, Week 4 (KO_Wk4_3)

description:
KO_Wk4vsP_Wk4_DEG.txt
KO_Wk4_3


title: Clothianidin dose level 7 bio rep 3 [Clo_M_E08_S60]

description:
96 well plate
Clo_M_E08_S60_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_F11

value: brain

value: Malignant

value: ctrl


title: GL26130CD45neg_P2_E01


title: GL26130CD45neg_P2_H02


title: ctrl_time_2_Rep_2


title: Clothianidin dose level 9 bio rep 3 [Clo_M_E10_S62]

description:
96 well plate
Clo_M_E10_S62_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Clothianidin

value: 24 hr


title: ctrl_time_2_Rep_1


title: Clothianidin dose level 5 bio rep 3 [Clo_M_E06_S58]

description:
96 well plate
Clo_M_E06_S58_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body


title: Clothianidin dose level 6 bio rep 3 [Clo_M_E07_S57]

description:
96 well plate
Clo_M_E07_S57_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: larva


title: HuR KO, Tumor, Week 4 (KO_Wk4_1)

description:
KO_Wk4vsP_Wk4_DEG.txt
KO_Wk4_1


title: GL26130CD45neg_P2_A10


title: Clothianidin dose level 8 bio rep 3 [Clo_M_E09_S59]

description:
96 well plate
Clo_M_E09_S59_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: ctrl_time_1_Rep_2


title: GL26130CD45neg_P2_D06


title: GL26130CD45neg_P2_C08


title: HuR KO, Tumor, Week 3 (KO_Wk3_2)

description:
KO_Wk3vsP_Wk3_DEG.txt
KO_Wk3_2

value: Orthotopic Tumor 3 Weeks Post-injection


title: ctrl_time_1_Rep_1


title: HuR KO, Tumor, Week 3 (KO_Wk3_4)

description:
KO_Wk3vsP_Wk3_DEG.txt
KO_Wk3_4


title: ctrl_time_1_Rep_3


title: HuR KO, Tumor, Week 3 (KO_Wk3_1)

description:
KO_Wk3vsP_Wk3_DEG.txt
KO_Wk3_1


title: GL26130CD45neg_P2_E08


title: Clothianidin dose level 3 bio rep 3 [Clo_M_E04_S55]

description:
96 well plate
Clo_M_E04_S55_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: ctrl_time_0_Rep_3


title: Clothianidin dose level 2 bio rep 3 [Clo_M_E03_S54]

description:
96 well plate
Clo_M_E03_S54_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: HuR KO, Tumor, Week 4 (KO_Wk4_2)

description:
KO_Wk4vsP_Wk4_DEG.txt
KO_Wk4_2


title: HuR KO, Tumor, Week 2 (KO_Wk2_3)

description:
KO_Wk2vsP_Wk2_DEG.txt
KO_Wk2_3

value: Orthotopic Tumor 2 Weeks Post-injection


title: ctrl_time_0_Rep_2


title: GL26130CD45neg_P2_E05


title: ctrl_time_0_Rep_1


title: Clothianidin control bio rep 3 [Clo_M_E01_S52]

description:
96 well plate
Clo_M_E01_S52_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 1 bio rep 3 [Clo_M_E02_S53]

description:
96 well plate
Clo_M_E02_S53_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_G01


title: Clothianidin dose level 11 bio rep 3 [Clo_M_D12_S35]

description:
96 well plate
Clo_M_D12_S35_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_C03


title: SX3627

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: C. elegans in vivo RNA-Seq

data_processing:
Illumina NextSeq 1000/2000 Control Software 1.4.1.39716
The sequenced paired-end reads were mapped to C. elegans (ce11) genome using bowtie2 aligner v.2.2.9 (Langmead and Salzberg 2012) with default parameters. The resulting bam files were converted to bigwig tracks using deeptools bamCoverage (Ramírez et al. 2016) with parameters -bs 1 --extendReads 148 –normalizeUsing RPGC --effectiveGenomeSize 98259998. Additional paraments for bamCoverage was comprised of --MNase --minFragmentLength 100 --maxFragmentLength 200 --Offset 1 2 and --smoothLength 30.
Peak calling was performed with MACS2 (Zhang et al. 2008) with default parameters and reads were shifted by 75 bp to cover the nucleosome dyad and extended to 150 bp. Deeptools computeMatrix reference-point was used to compute the nucleosome density across a window spanning the TSS (500bp upstream to 700bp downstream). The TSS positions were extracted from Serizay et al. (Serizay et al., 2020), as the midpoint of the 300bp regions annotated as ”promoter”. Assignments of each promoter to Ubiquitous, Germline or Somatic was taken from these annotations. The resulting files were read in to R using the read.table function.
To produce metagene plots spanning the region surrounding the TSS, the signal at 10bp intervals across the region was averaged across all promoters within the categories above. The ”background” intensity was defined as the minimum value across each trace and was subtracted from each position across the window. A clear signal indicating the expected nucleosome density was only observed for Ubiquitous genes, as expected since somatic promoters do not show such well-defined nucleosome densities (Serizay et al., 2020) and L1s do not have extensive germline tissue (Sulston and Horvitz, 1977).
To compare the intensity of the +1 nucleosome across all ubiquitous promoters, the signal spanning from the TSS to 180bp downstream was extracted for each promoter and the signal for wild type subtracted from the mutant signal. To link changes in gene expression to changes in nucleosome density at promoters, the coordinates of the genes were extended by 500bp upstream and intersected with the 300bp promoter regions using bedtools slop and intersect respectively. Nine of the upregulated and 14 of the downregulated genes overlapped with ubiquitous promoters and the +1 signal was extracted and compared across strains.
RNA sequencing reads from the three experimental sets and RNA-seq data from Meeuse et al., (date) were treated in the same way. Raw reads were trimmed for adapters, low quality sequences and short reads with Trimmomatic (Bolger et al., 2014) (Version 0.39, parameters: ILLUMINACLIP: TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:20). Remaining ribosomal RNA was removed with sortmeRNA (Kopylova, Noé, & Touzet, 2012) (Version 2.1, default parameters) and then clean reads were aligned to the C. elegans WBCel235 reference genome and gene counts quantified with salmon (Patro et al., 2018 ) (Version 1.9.0, parameters: --gcBias, --sepBias, -l A).
Assembly: ce11
Supplementary files format and content: bw files for each Sample
Supplementary files format and content: raw_counts.txt contains the raw counts produced by salmon for the RNASeq experiment

organism: Caenorhabditis elegans

source_name: C. elegans L1

growth_protocol: Synchronised C. elegans L1 larvae were obtained by bleaching of gravid adults. Embryos were left to hatch in 5ml M9 rotating on a wheel at 20°C for 24 hours to obtain a synchronised population of L1s. Approx. 60,000 L1s were seeded on NGM agar plates seeded with E. coli. Subsequently, L1s were grown at 25°C for six hours. Small frozen “worm balls” were generated from L1 pellets containing little M9 buffer. This was done by dripping small amounts of animal/M9 buffer mix into a cooled ceramic bowl placed on top of dry ice and filled with liquid nitrogen using a glass Pasteur pipette. “Worm balls” were carefully collected into 1.5 ml tubes with a cooled metal spoon and stored at -70°C.

extract_protocol:
In vivo MNAse digestion was performed on purified nuclei isolated from C. elegans (WT, swsn-1-/-, swsn-1-/-; snfc-5-/-, swsn-1-/-; snfc-5-/-; ubr-5-/-) L1 frozen popcorns. Frozen popcorns containing ~60,000 L1s for each strain was individually homogenized in liquid nitrogen and purification was optimised using sigma nuclei pure prep nuclei isolation kit (NUC-201) with modifications. Purified Nuclei of 500 ng/reaction were digested with MNAse (M0247S, NEB) concentration 200U/ml or 250U/ml for 15 mins at 37 °C to generate monoucleosomal DNA. MNase digestion was terminated by adding stop solution containing 3% SDS, 20 mM EDTA. Mononuclesomes were treated with Proteinase K (Invitrogen) and incubated at 65°C for 1 hr followed by DNA purification using Zymo clean and Concentrator. Mononucleosome bands were confirmed by D5000 ScreenTape in Agilent 2200 TapeStation system. For library preparation, DNA was measured again with Qubit dsDNA HS Assay Kit and 65 ng of mononucleosomal purified DNA was used for NEBNext Ultra II DNA Library Prep Kit for Illumina with size selection.
DNA libraries were prepared for sequencing using NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: strain

value: Whole animal


title: HuR KO, Cell Line (KO_CL_3)

description:
KO_CLvsP_CL_DEG.txt
KO_CL_3

value: MIA PaCA-2

value: Cell Line


title: Clothianidin dose level 4 bio rep 3 [Clo_M_E05_S56]

city: Cincinnati

first: John

last: Martinson

address: 26 W. Martin L. King Drive

description:
96 well plate
Clo_M_E05_S56_L003
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

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.

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.


title: Clothianidin dose level 10 bio rep 3 [Clo_M_D11_S34]

description:
96 well plate
Clo_M_D11_S34_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_B08


title: HuR KO, Cell Line (KO_CL_2)

description:
KO_CLvsP_CL_DEG.txt
KO_CL_2

value: Pancreatic ductal adenocarcinoma


title: GL26130CD45neg_P2_H05


title: Clothianidin dose level 9 bio rep 3 [Clo_M_D10_S33]

description:
96 well plate
Clo_M_D10_S33_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 8 bio rep 3 [Clo_M_D09_S32]

description:
96 well plate
Clo_M_D09_S32_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: SX3714

description: C. elegans in vivo RNA-Seq


title: HuR KO, Cell Line (KO_CL_1)

description:
KO_CLvsP_CL_DEG.txt
KO_CL_1


title: GL26130CD45neg_P2_A09


title: HuR KO, Tumor, Week 2 (KO_Wk2_1)

description:
KO_Wk2vsP_Wk2_DEG.txt
KO_Wk2_1

value: MIA PaCA-2 pancreatic tumor


title: Clothianidin dose level 7 bio rep 3 [Clo_M_D08_S31]

description:
96 well plate
Clo_M_D08_S31_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26130CD45neg_P2_C12


title: N2

description: C. elegans in vivo RNA-Seq

value: N2 wild type


title: GL26130CD45neg_P2_H07


title: BA9, WS3

city: Rehovot

first: Asaf

last: Marco

address: Herzl 229

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Trimming of Illumina adapters, as well as quality trimming, was performed with Trim Galore, using the following options: --nextseq --non_directional –rrbs. Reads were mapped to the human genome (hg19) using Bismark v. 0-22-3, bowtie mode.
Methylation proportion (i.e., counting the number of methylated C’s versus number of unmethylated C’s) for each one of the identified CpG site were calculated via Bismark, methylation extractor mode, (default setting)
Differential methylation of single CpGs sites (DMSs) were extracted and calculated by edgeR generalized linear model (GLM), with the recommended cutoff of at least 8 reads per sample
DMRs were extracted and analyzed by metilene v. 0.2-8. 300 bp was detramine as the maximun distance between CpGs to be allowed in the same segment, q-value cutoff of 0.01 and minimum average difference of 0.25
Assembly: hg19
Supplementary files format and content: coverage file (genomic coordinates, methylation percentage, count methylated, count unmethylated)

source_name: BA9 in frontal cortex

extract_protocol:
Blocks of fresh-frozen control (TD) and WS human cortical brain samples from BA9 were examined. DNA was isolated using a QIAamp DNA micro-kit (#-20-56304, Qiagen) according to the manufacturer’s instructions.
Libraries were prepared using a Zymo-Seq RRBS Library Kit (Zymo) according to the manufacturer’s instructions Libraries were prepared from 100 ng of genomic DNA and quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent)

value: BA9 in frontal cortex

tag: individual

tag: condition

value: WS


title: BA9, WS2


title: HuR KO, Cell Line (KO_CL_4)

description:
KO_CLvsP_CL_DEG.txt
KO_CL_4

tag: genotype

value: HuR KO


title: BA9, TD5

value: control


title: planktonic_28_08h_r2

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

description:
planktonic_28_08h_r2
E. coli k12 BW25113

data_processing:
quality trimming step using cutadapt (v2.10) command with a quality threshold of 20
the pooled sample was demultiplexed according to the anchored barcode of the first seven nucleotides at the 5’-end from the first read
internal adaptor sequence embedding in some second reads with too short insert was also trimmed
a minimum length threshold of 20 bp for both the first and second reads was used to filter out those pair-end reads with too short insert
bowtie2 (v2.4.1) to align the second read to a reference genome (NC000913.3) (default setting)
Feature counting was carried out using R method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand-specific manner, giving rise to a read count table for each gene.
Genome_build: NC000913.3
Supplementary_files_format_and_content: gene raw count data, tab-delimited matrix table

organism: Escherichia coli BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 28.08h after subculture, replicate 2

growth_protocol: For biofilm growth, single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture.  We sub-cultured 100 uL seed into 5 mL fresh LB broth (2% volume) in 50 mL centrifuge tube and grown for two hours at 37 ℃ with shaking at 220 rpm to reach exponential stage. Next, bacteria would be loaded into microfluidic chip to grow a semicircular biofilm. When the radius of biofilm reached around 1 mm, bacteria cells would be extracted from the chip for further steps. To prepare planktonic bacterial culture, single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture. A subculture was established by cultivating the seed culture into fresh 5 mL fresh LB broth (2% volume) in 50 mL centrifuge tube and grown for two hours with shaking at 220 rpm to reach exponential stage (OD600 ~ 0.6). Such subculture was next inoculated into 300 uL M63B1 broth in 48-well plate. The 48-well plate were loaded into a microplate reader system with 220 rpm shaking and the growth curve was monitored from absorbance at 600 nm every 30 min. When reaching desired OD600, 100 uL culture was taken to extract RNA.

extract_protocol:
Bacterial RNA was obtained utilizing the RNAClean XP beads (Beckman, A63987). Lysate was prepared using lysozyme and proteinase K
miniBac-seq, a customized bacterial RNA-seq library construction method, see description of our paper for details

tag: growth mode

value: planktonic


title: Clothianidin dose level 6 bio rep 3 [Clo_M_D07_S30]

description:
96 well plate
Clo_M_D07_S30_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

tag: tissue

value: 5 dpf/24 hr post hatch

value: Clothianidin


title: GL26130CD45neg_P2_E12

city: Boston

first: Elizabeth

last: Perez

address: 30 Fruit Street

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)

value: brain

value: Malignant

value: ctrl


title: GL26130CD45neg_P2_D01


title: BA9, TD4


title: Clothianidin dose level 4 bio rep 3 [Clo_M_D05_S28]

description:
96 well plate
Clo_M_D05_S28_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body

tag: developmental stage

value: larva

value: 24 hr


title: Clothianidin dose level 5 bio rep 3 [Clo_M_D06_S29]

description:
96 well plate
Clo_M_D06_S29_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

tag: age


title: planktonic_25_28h_r2

description:
planktonic_25_28h_r2
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 25.28h after subculture, replicate 2


title: SX3715

description: C. elegans in vivo RNA-Seq

value: Whole animal

tag: treatment


title: SX3628

description: C. elegans in vivo RNA-Seq


title: planktonic_12_95h_r2

description:
planktonic_12_95h_r2
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 12.95h after subculture, replicate 2


title: BA9, TD3


title: GL26110_CD31posP2_A04_R1


title: planktonic_22_05h_r2

description:
planktonic_22_05h_r2
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 22.05h after subculture, replicate 2


title: GL26130CD45neg_P2_H11


title: Clothianidin dose level 2 bio rep 3 [Clo_M_D03_S26]

description:
96 well plate
Clo_M_D03_S26_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

tag: Sex


title: BA9, TD2


title: planktonic_11_33h_r2

description:
planktonic_11_33h_r2
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 11.33h after subculture, replicate 2


title: BA9, TD1


title: GL26110_CD31posP2_C04_R1


title: planktonic_28_08h_r1

description:
planktonic_28_08h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 28.08h after subculture, replicate 1


title: planktonic_9_8h_r2

description:
planktonic_9_8h_r2
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 9.8h after subculture, replicate 2


title: planktonic_7_62h_r2

description:
planktonic_7_62h_r2
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 7.62h after subculture, replicate 2


title: GL26110_CD31posP2_F01_R1

source_name: brain


title: GL26110_CD31posP2_H10_R1


title: Clothianidin dose level 1 bio rep 3 [Clo_M_D02_S25]

description:
96 well plate
Clo_M_D02_S25_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

source_name: whole body

tag: concentration


title: Clothianidin control bio rep 3 [Clo_M_D01_S45]

description:
96 well plate
Clo_M_D01_S45_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

tag: time point


title: BA9, WS1


title: Clothianidin dose level 11 bio rep 3 [Clo_M_C12_S46]

description:
96 well plate
Clo_M_C12_S46_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26110_CD31posP2_A03_R1


title: XAF1-ko+VSV

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

description: XAF1 knockout HT29 cells were collected for total RNA extraction with VSV infection for 6h.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differantially expressed genes.
Assembly: UCSC hg38 genome was used as reference genome.
Supplementary files format and content: Excel spreadsheet includes the FPKM value for each sample.

growth_protocol: HT29 Cells were cultured in 1640 medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Total RNA was extracted using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: HT29 Cells were infected by VSV for 0 or 6 hours

tag: cell line

value: Human epithelial cells

value: XAF1 KO

value: VSV infection


title: planktonic_25_28h_r1

description:
planktonic_25_28h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 25.28h after subculture, replicate 1


title: Vec+VSV

description: HT29 cells were collected for total RNA extraction with VSV infection for 6h.

tag: cell type

value: WT


title: GL26110_CD31posP2_E03_R1

institute: MGH


title: Clothianidin dose level 9 bio rep 3 [Clo_M_C10_S48]

description:
96 well plate
Clo_M_C10_S48_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Vec

description: HT29 cells were collected for total RNA extraction without VSV infection.

value: no treatment

tag: time


title: XAF1-ko-VSV--ip

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using Bowtie2, which produced the BAM type file directly.
Genrich were used to call peaks
IGV were used to visualize the peaks
Peaks annotation were conducted by ChIPseeker
Assembly: hg38
Supplementary files format and content: bw

source_name: HT29 cells

extract_protocol:
HT29 cells were crosslinked with 1% formaldehyde and was quenched with 0.125M glycine for 5 min. The cells were washed  and pelleted at 2500 rpm for 5 min. After lysis and sonicate on, the sonicated chromatin was spun down at 12,000 rpm.
The soluble chromatin was incubated with 2-5 mg of antibodies overnight. After incubation, pre-washed Protein G Dynabeads (10004d, Invitrogen) were added and incubated for 4 h at in a rotator. Then the magnetic Dynabeads were washed and reverse crosslink. The next day, purify DNA with QIAquick PCR purification kit (Magen, D211102) and elute with 50 mL elution buffer.

value: HT29 cells

tag: chip antibody

value: (acetyl K27) (Ab4729, Abcam)


title: Clothianidin dose level 8 bio rep 3 [Clo_M_C09_S41]

description:
96 well plate
Clo_M_C09_S41_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: planktonic_12_95h_r1

description:
planktonic_12_95h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 12.95h after subculture, replicate 1

value: planktonic


title: Clothianidin dose level 7 bio rep 3 [Clo_M_C08_S42]

description:
96 well plate
Clo_M_C08_S42_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26110_CD31posP2_H11_R1


title: planktonic_11_33h_r1

description:
planktonic_11_33h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 11.33h after subculture, replicate 1


title: GL26110_CD31posP2_G11_R1


title: planktonic_9_8h_r1

description:
planktonic_9_8h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 9.8h after subculture, replicate 1


title: GL26110_CD31posP2_B10_R1


title: Clothianidin dose level 6 bio rep 3 [Clo_M_C07_S43]

description:
96 well plate
Clo_M_C07_S43_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: Clothianidin


title: XAF1-ko

description: XAF1 knockout HT29 cells were collected for total RNA extraction without VSV infection.


title: XAF1-ko-ip

value: control


title: XAF1-ko-VSV-input

value: input


title: Clothianidin dose level 5 bio rep 3 [Clo_M_C06_S44]

description:
96 well plate
Clo_M_C06_S44_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: planktonic_7_62h_r1

description:
planktonic_7_62h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 7.62h after subculture, replicate 1


title: GL26110_CD31posP2_G02_R1

value: brain


title: Clothianidin dose level 3 bio rep 3 [Clo_M_D04_S27]

description:
96 well plate
Clo_M_D04_S27_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: whole body


title: Clothianidin dose level 10 bio rep 3 [Clo_M_C11_S47]

description:
96 well plate
Clo_M_C11_S47_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: larva


title: Vec-ko-VSV-ip


title: planktonic_22_05h_r1

description:
planktonic_22_05h_r1
E. coli k12 BW25113

source_name: Temporal transcriptome of planktonic bacteria cultured for 22.05h after subculture, replicate 1


title: GL26110_CD31posP2_H04_R1


title: XAF1-ko-input


title: b5_159um

description:
b5_159um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 159 micrometers away from biofilm edge in biofilm 5

value: biofilm


title: Vec-ko-VSV-input


title: GL26110_CD31posP2_H06_R1


title: Clothianidin dose level 4 bio rep 3 [Clo_M_C05_S37]

description:
96 well plate
Clo_M_C05_S37_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 24 hr


title: Clothianidin dose level 2 bio rep 3 [Clo_M_C03_S39]

description:
96 well plate
Clo_M_C03_S39_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26110_CD31posP2_B08_R1


title: Clothianidin dose level 1 bio rep 3 [Clo_M_C02_S40]

description:
96 well plate
Clo_M_C02_S40_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Vec-input

value: Human epithelial cells


title: b5_286um

description:
b5_286um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 286 micrometers away from biofilm edge in biofilm 5


title: b5_417um

description:
b5_417um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 417 micrometers away from biofilm edge in biofilm 5


title: Vec-ip


title: GL26110_CD31posP2_D02_R1


title: b5_29um

description:
b5_29um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 29 micrometers away from biofilm edge in biofilm 5


title: Clothianidin dose level 11 bio rep 2 [Clo_M_B12_S22]

description:
96 well plate
Clo_M_B12_S22
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 10 bio rep 2 [Clo_M_B11_S23]

description:
96 well plate
Clo_M_B11_S23
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b5_1002um

description:
b5_1002um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 1002 micrometers away from biofilm edge in biofilm 5


title: GL26110_CD31posP2_F11_R1


title: b4_54um

description:
b4_54um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 54 micrometers away from biofilm edge in biofilm 4


title: GL26110_CD31posP2_H08_R1


title: GL26110_CD31posP2_E04_R1


title: b4_198um

description:
b4_198um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 198 micrometers away from biofilm edge in biofilm 4


title: Clothianidin dose level 3 bio rep 3 [Clo_M_C04_S38]

description:
96 well plate
Clo_M_C04_S38_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 18942X27 32A_P-2

city: SLC

first: Leah

last: Owen

state: UT

address: 65 N. Mario Capecchi Dr

department: Ophthalmology

institute: John Moran Eye Center

data_processing:
Human FASTA and GTF files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Raw gene counts were filtered to remove features with zero counts and fewer than 10 reads in every sample
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Assembly: GRCh38
Supplementary files format and content: FeatureCount output files combined into a tab-delimited raw count matrix

source_name: Placenta

extract_protocol:
RNA was harvested using Qiagen ALL PREP Universal
Whole transcriptome expression analysis was performed on fetal surface placental tissues using the Illumina Stranded Total RNA Kit with Ribo-Zero Plus per the standard protocol

value: Placenta

value: placental villous tissue

value: F

tag: preeclampsia

value: N

tag: rop

value: Y


title: 18942X28 643

value: M


title: b4_356um

description:
b4_356um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 356 micrometers away from biofilm edge in biofilm 4


title: 18942X30 39A_P-1


title: GL26110_CD31posP2_F12_R1

source_name: brain


title: Clothianidin dose level 8 bio rep 2 [Clo_M_B09_S19]

description:
96 well plate
Clo_M_B09_S19
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

source_name: whole body


title: GL26110_CD31posP2_D09_R1


title: GL26110_CD31posP2_B01_R1


title: b4_504um

description:
b4_504um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 504 micrometers away from biofilm edge in biofilm 4


title: Clothianidin dose level 7 bio rep 2 [Clo_M_B08_S18]

description:
96 well plate
Clo_M_B08_S18
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b5_797um

description:
b5_797um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 797 micrometers away from biofilm edge in biofilm 5


title: Clothianidin control bio rep 3 [Clo_M_C01_S36]

description:
96 well plate
Clo_M_C01_S36_L002
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 18942X26 32A_P-1


title: GL26110_CD31posP2_G01_R1


title: 18942X29 644


title: Clothianidin dose level 6 bio rep 2 [Clo_M_B07_S21]

description:
96 well plate
Clo_M_B07_S21
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26110_CD31posP2_F09_R1


title: b4_983um

description:
b4_983um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 983 micrometers away from biofilm edge in biofilm 4


title: b4_704um

description:
b4_704um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 704 micrometers away from biofilm edge in biofilm 4


title: GL26110_CD31posP2_A01_R1


title: Clothianidin dose level 5 bio rep 2 [Clo_M_B06_S20]

description:
96 well plate
Clo_M_B06_S20
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 18942X23 41A_P-2


title: b4_1252um

description:
b4_1252um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 1252 micrometers away from biofilm edge in biofilm 4


title: Clothianidin dose level 9 bio rep 2 [Clo_M_B10_S24]

description:
96 well plate
Clo_M_B10_S24
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 4 bio rep 2 [Clo_M_B05_S15]

description:
96 well plate
Clo_M_B05_S15
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 18942X22 41A_P-1


title: 18942X21 40A_P-2


title: GL26110_CD31posP2_F04_R1


title: b3_167um

description:
b3_167um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 167 micrometers away from biofilm edge in biofilm 3


title: GL26110_CD31posP2_H02_R1


title: Clothianidin dose level 2 bio rep 2 [Clo_M_B03_S17]

description:
96 well plate
Clo_M_B03_S17
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b3_370um

description:
b3_370um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 370 micrometers away from biofilm edge in biofilm 3


title: 18942X25 25D_P-2


title: 18942X20 40A_P-1


title: Clothianidin dose level 3 bio rep 2 [Clo_M_B04_S14]

description:
96 well plate
Clo_M_B04_S14
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b3_802um

description:
b3_802um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 802 micrometers away from biofilm edge in biofilm 3


title: 18942X19 35A_P-2


title: Clothianidin dose level 1 bio rep 2 [Clo_M_B02_S16]

description:
96 well plate
Clo_M_B02_S16
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b3_1223um

description:
b3_1223um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 1223 micrometers away from biofilm edge in biofilm 3


title: Clothianidin control bio rep 2 [Clo_M_B01_S11]

description:
96 well plate
Clo_M_B01_S11
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 18942X24 25D_P-1


title: GL26110_CD31posP2_H09_R1


title: 18942X18 35A_P-1


title: Clothianidin dose level 11 bio rep 1 [Clo_M_A12_S10]

description:
96 well plate
Clo_M_A12_S10
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 10 bio rep 1 [Clo_M_A11_S13]

description:
96 well plate
Clo_M_A11_S13
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26110_CD31posP2_B06_R1

value: Malignant


title: 18942X16 641


title: GL26110_CD31posP2_E07_R1


title: b2_323um

description:
b2_323um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 323 micrometers away from biofilm edge in biofilm 2


title: GL26110_CD31posP2_C09_R1


title: b2_782um

description:
b2_782um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 782 micrometers away from biofilm edge in biofilm 2


title: Clothianidin dose level 9 bio rep 1 [Clo_M_A10_S12]

description:
96 well plate
Clo_M_A10_S12
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26110_CD31posP2_D08_R1


title: GL26110_CD31posP2_C10_R1


title: Clothianidin dose level 8 bio rep 1 [Clo_M_A09_S7]

description:
96 well plate
Clo_M_A09_S7
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

value: Clothianidin


title: 18942X14 36A_PR-1


title: 18942X13 36A_P-2


title: Clothianidin dose level 7 bio rep 1 [Clo_M_A08_S6]

description:
96 well plate
Clo_M_A08_S6
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b1_188um

description:
b1_188um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 188 micrometers away from biofilm edge in biofilm 1


title: b1_371um

description:
b1_371um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 371 micrometers away from biofilm edge in biofilm 1


title: GL26110_CD31posP2_A07_R1


title: Clothianidin dose level 6 bio rep 1 [Clo_M_A07_S9]

description:
96 well plate
Clo_M_A07_S9
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 5 bio rep 1 [Clo_M_A06_S8]

description:
96 well plate
Clo_M_A06_S8
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: GL26110_CD31posP2_C08_R1


title: 18942X11 38A_P

source_name: Placenta


title: 18942X12 36A_P-1


title: 18942X17 642


title: GL26110_CD31posP2_A09_R1


title: 18942X15 36A_PR-2