title: AML28

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v16

value: depleted


title: AML27

status: Public on Aug 27 2024

type: RNA

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v15

hyb_protocol: As per Nanostring's recommendations

scan_protocol: nCounter MAX/FLEX

data_processing: Normalized using ROSALIND® according to Nanostring's recommendations

molecule: total RNA

organism: Homo sapiens

source_name: diagnostic bone biopsy (trephine) taken from the crista

extract_protocol: RNeasy FFPE KIT (Qiagen) according to manufacturers recommendations

tag: disease

value: childhood AML

tag: tissue

value: bone biopsy

tag: immune infiltration status


title: SH386_TR_GU01CTC

type: SRA

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: counts.csv is a comma-separated-values file with rows corresponding to a gene, columns corresponding to a sample, and values giving the number of reads aligned to the gene.

molecule: polyA RNA

source_name: CTC

extract_protocol:
Single cells were picked or sorted into lysate buffer and RNA was released.
single cell cDNA was amplified using SMART-seq2 protocol

value: CTC

tag: donor

tag: cell type

value: EpCAM+ and/or PSMA+


title: BCaT_90

city: TLALPAN

first: Cristian

last: Arriaga

state: Federal District

address: AV. SAN FERNANDO, COL. SECCIÓN XVI

country: Mexico

institute: Mexican National Cancer Institute

data_processing:
The quality of the sequencing files was determined with the reports generated with the FastQC 0.12.0
Reads were mapped to the human reference with STAR aligner v.2.7.1a
Gene expression quantification was done with featureCounts from the rsubread package on the STAR bam files
Gene expression quantification was also done by aligning to the transcriptome withSalmon v.1.10.3. Data were normalized to TPM and is included as matrix (processed file bcat_counts.csv)
Differential expression analysis was performed with DEseq2 v.1.44.0
Assembly: Reads were mapped to the human reference genome assembly version hg38 (gencode v40)
Supplementary files format and content: Count matrix from Salmon counts is included. Each row correspond to Ensembl gene ID, and each column correspond to the ID of BCaT samples.

source_name: Biopsy from primary mammary adenocarcinoma (thick needle)

extract_protocol:
RNA was isolated using the AllPrep kit (QIAGEN, No. 80204); RNA concentration and quality analysis (RIN value) were performed by Tape Station 2200 bioanalyzer (Agilent Technologies)
1 ug of RNA with RIN associated greater than 8.0 were used to generate sequencing libraries using the TruSeq Stranded mRNA library prep kit from illumina according to the manufacturer’s instruction

value: Breast cancer

tag: molecular subtype

value: Luminal B

tag: group

value: Non-responder (RD)

tag: treatment

value: Neoadjuvant Chemotherapy


title: Pt6

city: Palo Alto

first: Nazish

last: Sayed

state: California

address: 240 Pasteur Drive, 3500 BMI

institute: Stanford University

data_processing:
RNAseq reads are trimmed using trimmomatic and HISAT2 tool is used for alignment
RPKM values are calculated using excel and read counts using featureCounts
differential analysis is perfomed using deseq2
Assembly: hg38
Supplementary files format and content: raw counts

source_name: artery

extract_protocol:
Total RNA was extracted from COs using RNeasy plus mini-Kit (Qiagen) as per manufacturer’s instructions
Dyna Oligo(dT) beads (Life technologies) were used to purify mRNA and then fragmentated to 200-300 bp fragments to prepare index-tagged paired-end cDNA libraries as previously descibed7. Illumina sequencing adapters were ligated to cDNA fragments through PCR and sequencing was performed on Novaseq 6000. Obtained fastq (paired end) sequencing reads were mapped to human reference genome (hg38) using STAR (2.5.4b), and quantified raw counts and RPKM values were annotated using Homer (analyzeRepeats.pl). Heatmaps were generated through normalized DESEQ2 counts. Gene ontology analysis was conducted using R package.

value: artery

tag: disease state

value: Long Covid


title: BCaT_67

value: Biopsy from primary mammary adenocarcinoma (thick needle)


title: Pt5


title: BCaT_56


title: SH385_TR_GU01CTC


title: Liver, LeuD, GCN2 KO, 15 bio rep1

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley rd

department: Nutritional Sciences

institute: Rutgers University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes.
Assembly: GRCm39
Supplementary files format and content: Processed data contains the Deseq output of comparisons between our experimental groups.

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Plus Kit (Zymo Research) following instructions provided by the manufacturer.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’-ends and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated with the TapeStation System (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific). Further validation of the libraries was carried out by quantitative PCR (KAPA Biosystems) of selected genes.

treatment_protocol: WT and GCN2 KO mice were individually housed and given ad libitum access to food and water and placed on their normal 12-h light-dark cycle. Following a 2-day adjustment period to a control diet, the mice either remained on the control diet (Control) or were switched to a leucine-devoid diet (LeuD) at the start of the dark cycle. 24-hours following this switch, the lights were turned off and stayed off for the remaining 8-day period. Following the 8-day darkness period, the mice were killed under red light at either circadian time (CT) 03 or 15, and their livers were collected and immediately snap frozen in liquid nitrogen.

value: Liver

tag: time

tag: genotype

value: GCN2 KO

tag: diet

value: LeuD


title: SH384_TR_GU01CTC


title: HC7 2

value: WT


title: HC7 1


title: SH383_TR_GU01CTC


title: BCaT_50


title: AML25

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v13


title: HC6 2


title: BCaT_46


title: AML24

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v12


title: SH699_TR_GU02CTC


title: SH378_TR_GU01CTC


title: AML23

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v11


title: HC6 1


title: SH376_TR_GU01CTC


title: BCaT_44


title: BCaT_43


title: AML22

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v10


title: AML26

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v14


title: AML21

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v9


title: Pt9

value: PAD


title: CM_EC_minus_Day6_r2

state: CA

address: 240 Pasteur Dr

data_processing:
RNAseq reads are trimmed using trimglore 0.5.0 version and mapped to  human reference genome(hg38) using STAR (2.5.4b). FPKM values are calculated using cufflinks and read counts using htseq-count. Differential  analysis is performed using deseq2.
Assembly: hg38
Supplementary files format and content: text, FPKM

source_name: patient-specific iPSCs

extract_protocol:
Total RNA was extracted from COs using RNeasy plus mini-Kit (Qiagen) as per manufacturer’s instructions
Dyna Oligo(dT) beads (Life technologies) were used to purify mRNA and then fragmentated to 200-300 bp fragments to prepare index-tagged paired-end cDNA libraries as previously descibed7. Illumina sequencing adapters were ligated to cDNA fragments through PCR and sequencing was performed on Illumina HiSeq platform. Obtained fastq (paired end) sequencing reads were mapped to human reference genome (hg38) using STAR (2.5.4b), and quantified raw counts and RPKM values were annotated using Homer (analyzeRepeats.pl). Heatmaps were generated from RPKM values of the differential gene list and Gene ontology analysis was conducted using R package.

treatment_protocol: SARS-CoV-2 pseudovirus was obtained commercially (Montana Molecular) where these pseudoviruses (as BSL-1 baculoviruses) were pseudotyped with Spike (S) proteins. As per manufacturer’s instructions, these pseudovirus does not replicate inside the cells, but exhibit high affinity for the host receptor ACE2 in ECs. iPSC-ECs or COs were infected with SARS-CoV-2 pseudovirus at the titer of 2x10^10 VG/ml in EGM2 media (for iPSC-ECs) or a mixture of RPMI-B27 + EGM2 (for COs) for respective time periods. For washout experiments the medium containing the SARS-CoV-2 pseudovirus was replaced with fresh media every 3 days until day 15.

value: patient-specific iPSCs

value: vehicle


title: BCaT_35


title: CM_EC_plus_Day6_r2

value: exposure to pseudo SARS-CoV2 virus


title: BCaT_37

value: Responder (pCR)


title: Sirloin muscle treated rep 4

city: Pyeongchang-gun

first: Borhan

last: Shokrollahi

state: Gangwon-do

address: 국립축산과학원 한우연구소 강원도 평창군 대관령면 경강로 4937, 25340

country: South Korea

institute: National Institute of animal science

data_processing:
Sequencing reads were first quality checked using FastQC. Trimmomatic was used for adapter trimming, and reads were then aligned to the Bos_taurus_ARS-UCD1.2 reference genome using STAR. FeatureCounts was used to quantify gene expression. Differential expression analysis was performed using DESeq2.
Assembly: Bos_taurus_ARS-UCD1.2
Supplementary files format and content: The processed data files include raw read counts (TXT format), normalized expression values (TXT format), and differential expression results (TXT format). Each file contains gene IDs, read counts, and expression levels for each sample.

organism: Bos taurus

source_name: Sirloin muscle

growth_protocol: Eight Hanwoo cows were managed under standard farm conditions. The control group received 100% of their nutritional requirements, while the treated group received 150% of their nutritional requirements during mid to late pregnancy.

extract_protocol:
Muscle tissue samples from the round and sirloin muscles were collected immediately postpartum. Total RNA was extracted using TRIzol reagent following the manufacturer's instructions, with subsequent purification using a Qiagen RNeasy Mini Kit.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Library Prep Kit according to the manufacturer's protocol, including poly(A) selection and reverse transcription to generate cDNA libraries. Libraries were indexed and amplified.

treatment_protocol: The control group was fed a standard diet (100% nutritional requirements) and the treated group was overfed (150% nutritional requirements) during mid to late pregnancy. Postpartum, calves were monitored without additional interventions.

value: Sirloin muscle

value: Treated


title: Sirloin muscle treated rep 2


title: SH374_TR_GU01CTC

value: CTC

value: EpCAM+ and/or PSMA+


title: Pt8


title: BCaT_28

value: Breast cancer

value: Luminal B

value: Neoadjuvant Chemotherapy


title: CM_EC_minus_Day15_r2


title: BCaT_30

value: Biopsy from primary mammary adenocarcinoma (thick needle)


title: BCaT_27

value: Non-responder (RD)


title: CM_EC_plus_Day15_r2


title: AML16

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v8

value: childhood AML

value: bone biopsy

value: depleted


title: Sirloin muscle treated rep 3


title: AML13

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v7


title: AML6

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v5

value: infiltrated


title: Sirloin muscle control rep 4

value: Control


title: Sirloin muscle treated rep 1


title: CM_EC_minus_Day6_r1

value: patient-specific iPSCs

value: vehicle


title: Sirloin muscle control rep 3


title: BCaT_25


title: AML4

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v4


title: AML12

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v6


title: CM_EC_plus_Day6_r1

value: exposure to pseudo SARS-CoV2 virus


title: AML2

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v2


title: Sirloin muscle control rep 2

value: Sirloin muscle


title: AML3

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v3


title: Sirloin muscle control rep 1


title: Round muscle Treated rep 4

source_name: Round muscle

value: Round muscle

value: Treated


title: jmj4_4_2

city: Hangzhou

first: Chenxu

last: Liu

state: Zhejiang

address: Xihu District, No.866 Yuhangtang Road

department: Horticulture

country: China

institute: Zhejiang university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-endcleanreads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: Tab-delimited text file inlcludes raw counts for each sample.

organism: Solanum lycopersicum

source_name: Leaves

extract_protocol:
Total RNA extraction was conducted as manufacturer’s instruction (Accurate Biology AG21019, Changsha, China).
The RNA sequencing library was constructed by RNA library Prep Kit for Illumina (NEB E7770, Ipswich MA, USA).

value: Leaves

value: jmj4 mutant

value: Cold


title: CM_EC_plus_Day15_r1


title: jmj4_4_3


title: AML1

description: For full sample details, please see the manuscript: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v1


title: jmj4_4_1


title: BCaT_16

value: Breast cancer

value: Luminal B

value: Neoadjuvant Chemotherapy


title: BCaT_14

value: Biopsy from primary mammary adenocarcinoma (thick needle)

value: Non-responder (RD)


title: Suc-24h

first: Meidan

last: Ying

address: No.866 Yuhangtang Road

department: College of Pharmaceutical Sciences

institute: Zhejiang University

data_processing:
First, the raw image files were obtained, then base calling and error filtering were performed to finally obtain the raw sequencing reads that can be used for analysis.
The raw reads obtained from sequencing were filtered to get clean reads for data analysis. Seqtk was used for filtering.
Hisat2 (version: 2.0.4) 's spliced mapping algorithm was applied for genome mapping of the preprocessed reads, using default parameters. The mapping generated alignment results in BAM format.
Analyze the curve of the number of detected genes increasing with the increase of sequencing amount.
We first used Stringtie (version: 1.3.0) to count the number of fragments for each gene after Hisat2 alignment, then performed normalization using the TMM (trimmed mean of M values) method, and finally calculated the FPKM value for each gene using a perl script.
Assembly: hg38
Supplementary files format and content: gene_expression.txt include FPKM values and counts of each group.

source_name: Haematopoietic and Lymphoid

extract_protocol:
Total RNA was extracted using RNAiso Plus Total RNA extraction reagent (Cat#9109, TAKARA)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).
According to the experimental protocol, purified Total RNA was used for mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, 3' end A addition, adapter ligation, and enrichment to construct the sequencing library.

value: Haematopoietic and Lymphoid

tag: cell line

value: Adult Acute Myeloid Leukemia cell

value: WT

value: Succinate 24h


title: BCaT_24

value: Responder (pCR)


title: Non-COVID_PAD

first: Yu

address: 1215 Welch Road

department: CVI

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: hg38
Supplementary files format and content: COVID-PAD_matrix.mtx.gz
Supplementary files format and content: COVID-PAD_features.tsv.gz
Supplementary files format and content: COVID-PAD_barcodes.tsv.gz
Supplementary files format and content: NCPAD_matrix.mtx.gz
Supplementary files format and content: NCPAD_features.tsv.gz
Supplementary files format and content: NCPAD_barcodes.tsv.gz

molecule: nuclear RNA

source_name: Anterior tibial arteries

extract_protocol:
Anterior tibial arteries from long COVID patients were carefully dissected to remove the existing plaques and were cut into small pieces (1-3 mm3). All pieces were then incubated at 37°C with freshly prepared Liberase solution (5 mg/ml) (R&D) for 30 min. Following the incubation, the samples were vortexed, and the dissected tissues were incubated again with fresh Liberase solution for another 30 mins. The stop the incubation, endothelium media and 5% FBS was added to the digested tissues.
Following digestion of human anterior tibial arteries (described above), prepared cells were resuspended in MAC sorting buffer containing 0.5% BSA as 1000 cells per μl. Following this, an estimated 10,000 cells per sample were captured as per instructions from the ChromiumTM single-cell 3’ (10x Genomics) reagent kit user guide. Single cells were partitioned into microfluidic chambers using a 10x Genomics Chromium controller and then encapsulated in a gel bead containing sequencing adapters and primers, molecular barcodes, a unique molecular identifier (UMI), and oligo-dT to prime polyadenylated RNA transcripts to generate single-cell barcoded droplets (GEMs). After formation of GEMs, mRNA was reverse transcribed to barcoded cDNA libraries and resulting libraries were sequenced on an Illumina NovaSeq 6000 (Illumina).

value: Anterior tibial arteries


title: WT_4_3

value: Wild type


title: BCaT_22


title: Round muscle Treated rep 1

value: Round muscle


title: Round muscle Treated rep 2

value: Treated


title: WT_4_2

value: Leaves


title: WT_4_1


title: BCaT_23


title: Round muscle control rep 4

value: Control


title: Suc-0h

value: saline


title: CM_EC_minus_Day15_r1

value: patient-specific iPSCs

value: vehicle


title: G77 blastocysts RNA-seq_r2

city: Shanghai

first: Xinyu

last: Wang

address: Siping Road 1239

institute: Tongji University

description: G77 E4.5 blastocysts RNA-seq replicate2

data_processing:
For raw paired-end transcriptome sequencing data, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. STAR v2.6.1c was used to align the clean sequence data to the mouse reference genome (mm10), and RSEM v1.3.1 was used to quantify gene expression from the aligned sequences for each gene. The gene annotation file was obtained from the mouse GENCODE release (GRCm38.99). The R package DESeq2 v1.42.1 was used to identify differentially expressed genes between distinct Isca2 groups in mice. GSEA analysis was performed using the R package clusterProfiler v4.10.1, providing normalized enrichment scores and nominal p-values. KEGG functional annotation was conducted using the KOBAS online tool (http://bioinfo.org/kobas).
Assembly: mm10
Supplementary files format and content: aligned sequence file(bam) and gene expression quantification file(genes.results)

source_name: E4.5 blastocysts

growth_protocol: Animal welfare and the experimental procedures adhered to the ethical provisions on the Care and Use of Experimental Animals of Wenzhou Medical University and were approved and authorized by the Animal Experimental Committee of the University (No. xmsq2021-0068). Animals were maintained under a 12 h light/dark cycle and provided with food and water ad libitum in individually ventilated units.

extract_protocol:
To collected pre-implantation embryos, Isca2+/- female mouse intraperitoneal with 6.5 international unit of pregnant mares’ serum gonadotropin and, 45 to 47 h later, with 5 IU of human chorionic gonadotropin and crossed to Isca2+/- males. Embryos were isolated in M2 medium (Sigma: M7167) and cultured in potassium-supplemented optimised medium (Merck: MR-121-D) at 37℃ in 5% CO2.
The RNA-seq procedure was performed as previously described【】. Briefly, E4.5 blastocysts were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the single cell full length mRNA-amplification kit (N712, Vazyme). Library preparation was performed using the TruePrep DNA Library Prep Kit (TD501, Vazyme) according to the manufacturer’s instructions. All libraries were sequenced using the NovaSeq X Plus (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: E4.5 blastocysts

value: Isca2 G77S/G77S


title: G77 blastocysts RNA-seq_r3

description: G77 E4.5 blastocysts RNA-seq replicate3


title: Round muscle control rep 3


title: Round muscle control rep 2


title: CM_EC_plus_COVID_r4

data_processing:
RNAseq reads are trimmed using trim glore 0.5.0 version and star tool is used for alignment
FPKM values are calculated using cufflinks and read counts using htseq-count
differential analysis is perfomed using deseq2
Assembly: hg38
Supplementary files format and content: raw count

source_name: Cardiac Organoids

growth_protocol: COs were fabricated with iPSC-CMs alone or iPSC-CM and iPSC-ECs. For co-culture organoids, iPSC-CMs and iPSC-ECs were dissociated using TrypLE Express (Sigma) and mixed in at 4:1 (CM:EC) ratio. To generate COs, the cells were dispensed at a final cell density of 1 × 10^6 cells/ml into an agarose mold replica (Microtissues® Inc) featuring a 9 x 9 microwell array. Cell sedimentation into the microwells and self-assembly of the COs occurred over 48 hours. After 48 hours, spontaneously beating COs were then maintained in RPMI-B27 with insulin at 37°C and 5% CO2 until further experiments with SARS-CoV2.

extract_protocol:
Total RNA was extracted from COs using RNeasy plus mini-Kit (Qiagen) as per manufacturer’s instructions.
Dyna Oligo(dT) beads (Life technologies) were used to purify mRNA and then fragmentated to 200-300 bp fragments to prepare index-tagged paired-end cDNA libraries.

treatment_protocol: SARS-CoV-2 pseudovirus was obtained commercially (Montana Molecular). iPSC-ECs or COs were infected with SARS-CoV-2 pseudovirus at the titer of 2x1010 VG/ml in EGM2 media (for iPSC-ECs) or a mixture of RPMI-B27 + EGM2 (for COs) for respective time periods. For washout experiments the medium containing the SARS-CoV-2 pseudovirus was replaced with fresh media every 3 days until day 15.

value: Cardiac Organoids

value: iPSC-ECs and iPSC-CMs

tag: infection

value: Infected with SARS CoV-2 pseudovirus


title: CM_EC_plus_COVID_r3


title: Round muscle control rep 1


title: KO blastocysts RNA-seq_r2

description: KO E4.5 blastocysts RNA-seq replicate2

value: Isca2 -/-


title: Round muscle Treated rep 3


title: COVID_PAD

description: 10X Genomics


title: jmj4_25_1

value: jmj4 mutant


title: jmj4_25_2


title: WT_25_3


title: BCaT_17

value: Biopsy from primary mammary adenocarcinoma (thick needle)

value: Breast cancer

value: Luminal B

value: Non-responder (RD)

value: Neoadjuvant Chemotherapy


title: KO blastocysts RNA-seq_r1

description: KO E4.5 blastocysts RNA-seq replicate1


title: Suc-3h

value: Haematopoietic and Lymphoid

value: Adult Acute Myeloid Leukemia cell

value: WT

value: Succinate 3h


title: WT_25_1

value: Leaves

value: Wild type

value: Control


title: WT blastocysts RNA-seq_r2

description: WT E4.5 blastocysts RNA-seq replicate2

value: E4.5 blastocysts

value: wild type


title: CM_EC_minus_noCOVID_r4

value: Cardiac Organoids

value: iPSC-ECs and iPSC-CMs

value: noCOVID


title: WT blastocysts RNA-seq_r1

description: WT E4.5 blastocysts  RNA-seq replicate1


title: CM_EC_minus_noCOVID_r3


title: jmj4_H3K27me3_4_2

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11)software.
Assembly: Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to thereference genome using BWA mem (v 0.7.12).
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
ChIP assay was performed by EpiQuik Plant ChIP Kit (EPIGENTEK P-2014, Farmingdale NY, USA).
The library was constructed by NovogeneCorporation (Beijing, China).

value: jmj4 mutant

value: Cold


title: CM_EC_minus_noCOVID_r2


title: jmj4_H3K27me3_4_1


title: NK cells, tumor injection

city: Seoul

first: Jinju

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu

institute: University of Ulsan

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: splenocyte

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: splenocyte


title: jmj4_25_3


title: HT29 shZBTB7B 3

city: Zhuzhou

first: Huan

last: Chen

state: Hunan

address: No.116, Changjiang South Road, Tianyuan District, Zhuzhou, China

institute: Zhuzhou Central Hospital

data_processing:
MGIseq-2000
Assembly: Genome build:3G
Supplementary files format and content: tab-delimited text includes raw counts for each sample

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modifed probe, the probe was captured by a streptavidin magnetic b


title: HT29 shZBTB7B 1


title: NK cells, ctrl injection


title: jmj4_Input_4


title: CM_EC_plus_COVID_r2

value: Infected with SARS CoV-2 pseudovirus


title: CM_EC_plus_COVID_r1


title: CM_plus_COVID_r2

value: iPSC-CMs


title: CM_plus_COVID_r1


title: WT_25_2


title: HT29 CTRL 3(shZBTB7B)


title: WT blastocysts RNA-seq_r3

description: WT E4.5 blastocysts RNA-seq replicate3


title: HT29 CTRL 2(shZBTB7B)


title: CM_minus_noCOVID_r2


title: ST2p2

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

data_processing:
none provided
Supplementary files format and content: counts

source_name: Spleen

extract_protocol: none provided

value: Spleen

value: Tregs

value: WT-ST2 High


title: WT_H3K27me3_4_2


title: ST2p1


title: WT_H3K27me3_4_1


title: HT29 CTRL 1(shZBTB7B)


title: HT29 shZBTB7B 2


title: CM_minus_noCOVID_r1


title: ST2m3

value: WT-ST2 Low


title: jmj4_H3K27me3_25_2

value: Leaves


title: HT29 CTRL 3(CM10)


title: jmj4_H3K27me3_25_1


title: ST2m2


title: CM_EC_minus_noCOVID_r1


title: ST2p3


title: HT29 CTRL 1(CM10)


title: ST2m1


title: WT_Input_4

value: Wild type


title: HT29 CM10 3


title: WT_H3K27me3_25_2

value: Control


title: ST2KO3


title: ST2KO2


title: HT29 CM10 1


title: HT29 CM10 2


title: ST2KO1


title: WT_Input_25


title: HT29 CTRL 2(CM10)


title: jmj4_Input_25


title: WT_H3K27me3_25_1


title: RealDRG LOT#SN866658 Week 1 Maturation

status: Public on Aug 26 2024

city: Minneapolis

first: Vincent

last: Truong

state: MINNESOTA

address: 2112 Broadway ST NE, STE 135

institute: Anatomic Incorporated

data_processing:
Reads were aligned with STAR (v2.7.10a) and quantified using RSEM (v.1.3.1). In total, over 42 billion reads passed QC, or the equivalent of over 100 NextSeq lanes. For each sample, reads passing quality filters were used to generate transcript annotations using StringTie (v2.2.1). The Gencode annotation gtf was used to guide transcript assembly. Next, all novel transcript assemblies were merged and compared to the Gencode annotation using gffcompare (v0.12.6). The transcript map (.tmap) file was processed in R and class ‘s’ transcript annotations were discarded. RSEM quantifications of both gene and transcript level counts were loaded using the tximeta (v1.16.1) package with R 4.2.2. Transcripts with minimal expression (< 5 counts across all samples) were discarded. The function DESeqDataSetFromTximport was used to import quantifications and create a DESeq2 (v1.38.3) object for differential transcript and gene expression analysis.
Assembly: Release 109 of the Human GRCh38 primary assembly was retrieved from ftp.ensembl.org. Release 43 of Gencode annotations for the Human primary assembly were retrieved from gencodegenes.org
Supplementary files format and content: BAM file

source_name: hiPSC sensory neurons

extract_protocol:
Total RNA was collected at weekly timepoints for each line through four weeks. Pellets were formed by swirling cultures to release the cultures as a sheet before collection and centrifugation at 300g for 5 minutes. Cells were lysed and RNA extracted according to the RNA isolation kit instructions (Qiagen, #74104).
Sequencing libraries were generated using Illumina TruSeq Stranded mRNA Library Prep Kit. Equimolar quantities from each library were sequenced on a NextSeq 550 High Output Kit v2.5 (75 cycles) at approximately 30 million single-end reads per sample.

value: hiPSC sensory neurons

value: derived from ANAT001

value: WT Female

value: Week 1 Maturation


title: Sublibrary 7

data_processing:
Demultiplexing of sequencing libraries was performed using the Parse Biosciences Pipeline (v1.0.5p) to generate count matrices for individual samples. All downstream analysis including quality control, dimensional reduction, leiden clustering, and differential gene expression was performed within the Scanpy package (v1.9.2).
Assembly: GRCh38
Supplementary files format and content: h5ad

extract_protocol:
Adhered sensory neurons were washed from cell culture plates with PBS and centrifuged at 500g for 5 minutes at 4°C to form a pellet. Following pellet aggregation, cells were lyzed and nuclei were isolated according to manufacture protocol for the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma-Aldrich). Nuclei were then passed through a 40 µm strainer to remove cellular debris and fixed according to manufacturer protocol within the Parse Biosciences fixation kit. Fixed nuclei from each collection point were stored at -80°C in a Mr. Frosty Freezing Container (Thermo Scientific).
Sequencing libraries were generated using the Evercode Whole Transcriptome 100k v1 Kit (Parse Biosciences). Each sample used 12 of the available 48 wells of the library preparation kit, and individual nuclei were distributed evenly among wells.


title: RealDRG LOT#SN866658 Week 4 Maturation

value: Week 4 Maturation


title: Sublibrary 8


title: RealDRG LOT#SN866658 Week 2 Maturation

value: Week 2 Maturation


title: RealDRG LOT#SN423118 Week 3 Maturation

value: Week 3 Maturation


title: Sublibrary 3


title: RealDRG LOT#SN423118 Week 4 Maturation


title: RealDRG LOT#SN866658 Week 3 Maturation


title: Sublibrary 1


title: Sublibrary 2


title: Sublibrary 6


title: Sublibrary 4


title: Sublibrary 5


title: RealDRG LOT#SN007819 Week 4 Maturation


title: RealDRG LOT#SN423118 Week 1 Maturation


title: RealDRG LOT#SN007819 Week 2 Maturation


title: RealDRG LOT#SN007819 Week 3 Maturation


title: RealDRG LOT#SN007819 Week 1 Maturation


title: HAdV_lung

city: New Orleans

first: Jay

middle: K

last: Kolls

state: LA

address: 333 S Liberty St

department: Medicine

institute: Tulane University

data_processing:
Barcode processing, gene counting, and aggregation were performed using Cell Ranger version 7.1 (10x Genomics). Data were data integrated with a publicly available naïve spleen dataset (10X Genomics, https://www.10xgenomics.com/resources/datasets/integrated-gex-and-vdj-analysis-of-connect-generated-library-from-mouse-splenocytes-2-standard-6-0-1).
Assembly: mm39
Supplementary files format and content: Comma-separated values and matrix files

source_name: lung

extract_protocol:
At the time of euthanasia, mice were anesthetized with isoflurane, then injected with 2μg of anti-mouse CD45.2 PE (Biolegend, cat. #109807). 2 minutes later, mice were euthanized by CO2 asphyxiation. Subsequently, one or both lungs were removed, minced with dissection scissors, and digested in IMDM (Gibco) with 2 mg/mL collagenase (Sigma) and 20 U/mL DNAse-1 (Sigma) at 37C for 60-90 minutes with gentle rotation. Digested tissue solution was filtered through a 70-micron cell strainer (Fisherbrand), and red blood cells were removed by ACK lysis (Gibco). Intravascular CD45-PE labeled single-cell lung suspension was subjected to depletion using anti-PE microbeads (Miltenyi, cat. #130-408-801), then positive selection using a mouse CD3ε microbead kit (Miltenyi, cat. #130-094-973) according to the manufacturer’s instructions. Cell numbers and viability were validated by Nexcelom Cellometer Auto 2000 (Nexcelom Bioscience) and AO/PI viability dye (Nexcelom Bioscience, cat. #CS2-0106) prior to preparation of single cell RNAseq library.
To perform the 10x single cell V(D)J seq assay, 5000 live cells per sample were used to create GEMs by combining barcoded Single Cell 5’ Gel Beads (10X Genomics, cat. #1000265). After GEM-RT, RT cleanup, full-length cDNA amplification and QC, T-cell receptor enriched libraries and 5’ gene expression libraries were generated with Illumina P5 and P7 adapters. The libraries were quality controlled using Agilent High Sensitive DNA kit (Agilent, cat. #5067-4626) with Agilent 2100 Bioanalyzer (Agilient, cat. # G2939BA) and quantified by Qubit 2.0 fluorometer (Thermo, cat. #Q32886). Finally, the pooled libraries were sequenced with paired end single index configuration by  Illumina NextSeq 2000 (Illumina) at a final concentration of 750 pM.

value: lung

value: Received 1e9 PFU of HAdV-GFP 4 weeks prior to euthanasia


title: MUT5_EAX

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against the GRCm38.99 transcriptome using RSEM.
Estimated counts calculated by RSEM were normalized with the EdgeR package from Bioconductor, using the TMM method.
Assembly: GRCm38.99
Supplementary files format and content: Ensembl gene ID, gene name, and normalized counts for 14,732 genes, in each sample, for the collection of genes with more than 1 CPM in at least three samples.

source_name: OFT

extract_protocol:
RNA was harvested using Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific)
Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated, followed by second strand removal, uracil excision from the adaptor, and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher)

value: OFT


title: MUT3_EAX


title: MUT4_EAX


title: nat10_GV_2

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

institute: Guangxi university

description: lace-seq

data_processing:
The adapter sequences and low-quality bases of raw reads were removed using trim-galore (v.0.6.7)
Clean reads were first aligned to mouse pre-rRNA using Bowtie software (v.2.3.5.1)
The remaining unmapped reads were then aligned to the mouse (mm10) reference genome by hisat2 (v.2.2.1)
Then the PCR duplicates were removed by sambamba (v.0.7.1)
The correlation between LACE-seq replicates was calculated as following: the LACE-seq correlation was calculated by deepTools (v.3.5.1)
Assembly: mm10
Supplementary files format and content: bigWig files for each Sample
Library strategy: ac4C LACE-seq

source_name: Ovary

extract_protocol:
LACE-seq experiments were carried out according to the published protocol. In short, 50 oocytes were collected in 1.5 mL Eppendorf LoBind microcentrifuge tubes and quickly spun down to the bottom with a mini centrifuge. Samples were lysed on ice using 50 μl wash buffer for 10 min. Next, 1 μl SUPERase·In RNase inhibitor (Ambion, AM2696) and 4 μl RQ1 DNase (Promega, M6101) were applied to the lysate and incubated at 37 °C for 3 min. After snap-chilling the tube on ice for 3 min, 2 μg ac4c antibody and rotated at 4 °C for 1 h. Next, the samples were irradiated twice with UV-C light on the ice at 400 mJ, then 10 μl protein A/G beads were added to the sample and rotated for 2 h at 4 °C. After extensive wash steps, the immunoprecipitated RNAs were fragmented, and experienced 3′-dephosphorylation and linker ligation, followed by reverse transcription on-beads. Then, first-strand cDNAs were derived from protein A/G beads and further captured by streptavidin C1 beads for pre-PCR and added 3’-cDNA linker to produce dsDNA as the template for in vitro transcription (IVT). IVT products were purified by the removals of the DNA template using Turbo DNase and further purified by Agencourt RNA Clean beads based on the instructions of the manufacturer.
Then, linear amplified RNA was transformed into cDNA and amplified by PCR with P7 and barcoded P5 index primers. Final PCR products with a size of 250–500 bp were excised from a 2% agarose gel and purified by a gel purification kit (Qiagen, Catalog # 28604) as per the manufacturer's instructions.

value: Ovary

value: Oocyte

value: WT

value: no


title: WT3_EAX


title: IgG_GV

description: lace-seq


title: ac4c_GV_1

description: lace-seq


title: nat10_GV_1

description: lace-seq


title: WT5_EAX


title: ac4c_GV_2

description: lace-seq


title: WT4_EAX


title: MUT1_EAX


title: RealDRG LOT#SN423118 Week 2 Maturation


title: ac4c_KO_GV_1

description: lace-seq


title: F420 Osteosarcoma lung met Visium

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description: This is 10x Visium data from a C57BL/6 mouse that was tailvein injected with F420 cells. Lung metastases were collected and processed for 10x Visium using the cytassist instrument using the probe-based library preparation method

data_processing:
Raw fastq files were aligned to the mm10 genome using 10x Space Ranger software (v2.1.1)
Assembly: mm10
Supplementary files format and content: The processed file is a tar.gz file which contains the contents of the "spatial" and "filtered_feature_bc_matrix" folder from the Space Ranger output
Library strategy: Spatial Transcriptomics

source_name: lung tumor

extract_protocol:
Fixed, paraffin embedded tissue was histologically sectioned and stained with H&E. We then imaged the sections and used the 10x Cytassist instrument to prepare Visium libraries using the 10x Probe-based chemistry. Following further library processing, the libraries were sequenced on an Illumina NextSeq 2000
Visium Cytassist Probe-based chemistry

value: lung tumor


title: HEK293T_Mettl3_KO_rep3_sup

city: Barcelona

first: Gregor

last: Diensthuber

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Genome Biology

institute: Center for Genomic Regulation (CRG)

data_processing:
Processing of raw fast5 files was peformed using the MasterOfPores nextflow pipeline. Reads were basecalled using guppy (v6.0.6) with each of the three tested basecalling models (default, ivt and sup).
Alignments to both reference genome ( -uf -ax splice -k14)  and transcriptome (-ax map-ont -k14) were performed using minimap2 (v2.17). Highly modified synthetic constructs and the corresponding unmodified control were mapped using graphmap (v0.5.2) with sensitive settings (--rebuild-index -v 1 --double-index --mapq -1 -x sensitive -z 1 -K fastq --min-read-len 0 -A 7 -k 5)
To extract error signature on a per-nucleotide basis, EpinanoRMS (v1.1) was run. For in vivo m6A analyisis, pairwise-comparisons between wildtype and knockout samples were performed using eligos2(v2.1.0). Cross-species comparison of read accuacies was performed on reads uniquely mapped to the reference transcriptome (-F 3840) with a mapping quality > 15 (-q 15). To balance reads for strongly varying expression profiles at most the 10 longest reads for each transcript were extracted (bam2select.py). Read identis were extracted using identity_density.py
Assembly: Reference files include curlcake_constructs_EcoRV_BamHI_digestion.fasta, riboswitches.fa and 2021-8_eGFP_mRNA.v2.fa for curlcakes, riboswitches and the syntehtic eGFP vaccine, respectively. We used the following genomic reference for H. sapiens : Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa. And transcriptomic references Homo_sapiens.GRCh38.cdna.all.fa, Mus_musculus.GRCm39.cdna.all.fa, xlaevisMRNA.fasta, Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa and Arabidopsis_thaliana.TAIR10.cdna.all.fa for H. sapiens, M. musculus, X. laevis, S. cervisiae and A. thaliana, respecitvely.
Supplementary files format and content: Files ending in <model>_per_position.csv, contain EpinanoRMS results on a per position basis. Files ending in <model>_per_5mer.tsv contain EpinanoRMS results on a 5-mer basis generated by converting per position results using epinano_to_kmer.R.
Supplementary files format and content: Files ending in _eligos2.txt contain results generated by eligos2 for pairwise comparisons which were already filtered to remove  non-A-positions and homopolymer sequences.
Supplementary files format and content: Files starting with <species>.tsv contain read accuracies per aligned read (rows) for all three models (column 1).

source_name: human embryonic kidney

extract_protocol:
In vitro constructs were artifically poly-A-tailed using PAP (NEB, M0276S), and cleaned up using the RNEasy MinElute kit (Quiagen,  74204) for curlcake constructs and Zymo Clean and Concentrator kit (Zymo Resarch, R1013). Concentrations were determined using a Qubit 2.0 Fluorometer. For libraries that were not generated as part of this work please refer to the respective publications
Direct RNA-seqeuncing libraries were generated using the SQK-RNA002 according to the manufacturer's protocol (version : DRS_9080_v2_revR_14Aug2019-minion). For curlcakes a final library of 800ng war generated (200ng per curlcake construct) while 750ng for the UNM-S libraries was used (250ng per riboswitch). The reverse transcription step was peformed using SuperScript III R(Thermo Fisher Scientific, 18080044) in the case of ac4C, m5U-containing curlcake constructs and UNM-S, and Superscript IV (Thermo Fisher Scientific, 18090010) in the case of m1Ψ. For libraries that were not generated as part of this work please refer to the respective publications.

value: human embryonic kidney

value: Mettl3 KO


title: HEK293T_Mettl3_KO_rep3_ivt


title: HEK293T_Mettl3_KO_rep2_sup


title: HEK293T_Mettl3_KO_rep2_ivt


title: HEK293T_Mettl3_KO_rep1_default


title: HEK293T_Mettl3_KO_rep1_sup


title: G77 blastocysts RNA-seq_r1

description: G77 E4.5 blastocysts RNA-seq replicate1

value: E4.5 blastocysts

value: Isca2 G77S/G77S


title: HEK293T_WT_rep3_sup


title: HEK293T_WT_rep3_ivt


title: HEK293T_WT_rep3_default


title: HEK293T_Mettl3_KO_rep2_default


title: HEK293T_WT_rep2_ivt


title: HEK293T_WT_rep2_sup


title: WT_Wound1

city: Nanjing

first: Dongqing

last: Li

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing, China

institute: Hospital for Skin Diseases, Institute of  Dermatology, Chinese Academy of Medical Sciences &  Peking Union Medical College

description: Gene expression data of the epidermis of WT mice wound

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:  Array Type: Clariom_S_Human  Analysis Type: Expression (Gene)  Analysis Version: version 2  Summarization Method: Gene Level - SST-RMA  Pos vs Neg AUC Threshold: 0,7  Genome Version: hg38 (Homo sapiens)  Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv  Condition (Comparison): circRNA kd; ctr
Expression Analysis Settings:  • Gene-Level Fold Change < -2 or > 2  • Gene-Level P-Value < 0,05  • Anova Method: ebayes  • A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.  • DABG < 0,05

label: biotin

source_name: Wound epidermis

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: All the mice were breed in specific pathogen-free conditions in Comparative Medicine Biomedicum (KMB) animal facility in Karolinska Institutet.

extract_protocol: The total RNA was extracted by miRNeasy mini Kits (Qiagen) following the manufacture instruction.

treatment_protocol: Briefly, all the mice were caged individually prior wound making. The back skin of 8-weeks old Snhg26 knockout mice and littermate control in in the telogen (resting) phase of the hair cycle were shaved with clippers followed by a depilatory cream. Two 4-mm full-thickness wounds extending through the panniculus carnosus were made on the dorsum on each side of midline by using biopsy punch. The mice were caged individually after surgical procedure to minimize the clawing from other mice. During the first 2 days, the animals received s.c. buprenorphine (0.03 mg/kg) twice a day for relief the pain and distress caused by the procedure. The wound edge tissues were collected by using biopunch.

value: epidermis

tag: condition

value: wound edge


title: HEK293T_Mettl3_KO_rep1_ivt


title: KO_Wound3

description: Gene expression data of the epidermis of Snhg28 KO mice wound

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

value: Snhg26 KO


title: WT_Wound2


title: WT_Wound3


title: KO_Wound2

description: Gene expression data of the epidermis of Snhg27 KO mice wound


title: KO_Skin3

description: Gene expression data of the epidermis of Snhg26 KO mice skin

source_name: Skin epidermis

value: unwounded skin


title: HEK293T_WT_rep1_sup


title: HEK293T_WT_rep2_default


title: HEK293T_WT_rep1_ivt


title: HEK293T_WT_rep1_default


title: KO_Skin1


title: MBMP.3_0.5uM

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_285

library_source: other

data_processing:
Reads were demutliplexed from BCL files and processed into FASTQ files on Illumina Basespace using DRAGEN v1.3.0
Fastq files were aligned to the Human Whole Transcriptome v2.1 probes references sequences (provided by BioSpyder) using STAR aligner 2.7.8b
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Assembly: Biospyder human whole transcriptome gene set
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

molecule: other

growth_protocol: MCF-7 cells were routinely cultured in Dulbecco's modified Eagle's medium (EMEM; 30-2003, ATCC, Manassas, VA) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific), at 37°C in a humidified atmosphere with 5% CO2. Cells were maintained in routine culture for 7 days post-thaw prior to treatment, as this was determined to be the length of time required for cells to express the human PGR marker.

extract_protocol:
Following the exposure, cells were washed with phosphate-buffered saline (PBS) and lysed for Templated Oligo-Sequencing (TempO-Seq®) using 2xTempO-Seq lysis buffer diluted with PBS. Cell lysates were used directly for TempO-Seq library building.
Gene expression changes were measured using the TempO-Seq Human Whole Transcriptome Panel v2.1 Assay, Index E, F, G (BioSpyder Technologies Inc, Carlsbad, California) following manufacturer’s instructions. Briefly, 1X TempO-Seq Enhanced Lysis Buffer was added to exposed MCF-7 cells to achieve cell lysis. Cell lysates were frozen and stored at -80°C for less than six months prior to library building. At the onset of library building, thawed cell lysates and technical controls (1) Human Universal Reference RNA—uhrRNA Agilent Cat No. 740000, Santa Clara, California, and 2) Human Brain Total RNA brRNA—ThermoFisher AM7962, Waltham, Massachusetts) were added to assay plates. Freshly prepared annealing mix, containing the whole human genome Detector Oligo (DO) Pool to be annealed to the sample RNA, was added to the assay plates. The mixture was incubated at 70°C for 10 minutes, then ramped to 45°C over 50 minutes, then held at 45°C for 16 hours, and finally cooled to 25°C to hybridize the DO pool. Assay plates were frozen overnight at -20°C. Freshly prepared Nuclease Mix was added to each well of the thawed assay plates and then the assay plates were incubated for 90 minutes at 37°C to ensure removal of unbound DOs. Freshly prepared Ligation Mix was added to each well of the assay plate and then plates were incubated for 1 hour at 37°C, then immediately at 80°C for 15 minutes to ligate adjacent DOs together. For DO amplification, PCR Pre-Mix and PCR primers were mixed with the ligated assay products and then amplified on a thermocycler using the following protocol: 1) 37°C 10 minutes; 2) 95°C 1 minute; 3) 25 cycles of 95°C 10 sec, 65°C 30 sec, 68°C 30 sec; 4) 68°C 2 minutes; 5) hold at 25°C. After amplification, assay plates were stored at -20°C prior to purification. When all three assay plates in the study completed amplification, the plates were thawed and amplicons were purified using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit. Libraries were pooled in equimolar amounts prior to sequencing.
Human TempO-Seq Whole Transcriptome - Index Sets E, F, and G were used to index libraries

treatment_protocol: At the start of the experiment, cells were seeded into 96-well plates at a density of 3.0 × 104 cells per well in EMEM supplemented with 10% FBS to promote cell attachment to the plate. On Day 0, the medium was removed and replaced with 100 µL/well of fresh phenol red-free DMEM (DMEM; 31053-028, Gibco, Thermo Fisher Scientific) containing the treatment and supplemented with 10% charcoal-dextran stripped FBS to eliminate estrogenic components of the medium. Cells were exposed in triplicates for 48 hours to: (1) BPA and 11 alternative chemicals sharing structural similarity (Table 1;Figure 1) at six different concentrations (0.1, 0.5, 1, 5, 10, 25 µM); (2) the positive control 17β-estradiol (E2; 0.001, 0.01, 0.1, 1, 10 nM); (3) the non-ER-acting controls dexamethasone (Dex; 0.0001, 0.001, 0.01, 0.1, 1 µM) and Bis(4-chlorophenyl) sulfone (BCPS; 0.1, 0.5, 1, 5, 10, 25 µM); (4) the vehicle control (final (v/v) 1% DMSO, or 1% MeOH). The top concentration of 25 µM was chosen as higher concentrations of BPA alternatives (i.e., 50-100 µM) have been shown to cause cell stress, reduced cell count, or precipitation.

tag: batch

tag: index

value: G

tag: chemical

tag: dose


title: RA.4_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_288

value: Rosalic Acid


title: MBMP.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_283


title: MBMP.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_284


title: HEK293T_Mettl3_KO_rep3_default

tag: tissue


title: DMSO.3e

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_286

value: Dimethyl sulfoxide Treatment Control


title: BPP.4_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_287

value: Bisphenol P


title: MBMP.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_282


title: WT_Skin2

description: Gene expression data of the epidermis of WT mice skin


title: MBMP.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_281


title: WT_Skin3


title: ac4c_KO_GV_2

description: lace-seq

value: Ovary


title: RA.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_280


title: 1X Lysis Buffer_3

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_278

value: No cells; 1X Lysis buffer


title: WT_Skin1

value: WT


title: RA.3_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_277


title: BPP.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_279


title: RA.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_275


title: RA.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_276


title: RA.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_273


title: RA.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_272


title: BPG.3_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_269

value: Bisphenol G


title: Media.2_CTR2

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_270

value: Media Negative


title: ARC3

type: genomic

city: Mudanjiang City

first: Xiaoya

state: Heilongjiang Province

address: No.4 Tongxiang Street, Aimin District, Mudanjiang City, Heilongjiang Province

institute: 牡丹江医学院

description: SAMPLE 6

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was   fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x  Agilent fragmentation buffer and 2x Agilent blocking agent following the   manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of  2x Agilent hybridization buffer was added to the fragmentation mixture and   hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a   rotating Agilent hybridization oven. After hybridization, microarrays were washed 1   minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C  GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray  Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area  61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set   to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1  (Agilent) using default parameters to obtain background subtracted and spatially   detrended Processed Signal intensities as the raw data. Raw data were normalized   in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2   samples flagged as Detected were maintained.

source_name: Capsula anterior lentis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color  Low RNA Input Linear Amplification PLUS kit (Agilent) according to the   manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,  Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop  ND-1000 Spectrophotometer.

growth_protocol: Materials were taken during the operation

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n  AM1556 ) following the manufacturer's instructions

treatment_protocol: Frozen in liquid nitrogen after sampling

value: Capsula anterior lentis

tag: gender

value: Male

value: Capsula anterior lentis in cataract patients


title: BPG.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_266


title: BPG.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_268


title: RA.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_264


title: BPG.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_265


title: DMSO.3c

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_262


title: BPG.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_267


title: KO_Skin2

description: Gene expression data of the epidermis of Snhg26 KO mice skin


title: RA.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_274


title: KO_Wound1

description: Gene expression data of the epidermis of Snhg26 KO mice wound


title: TMolBPA.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_261

value: Tetramethylol Bisphenol A


title: TMolBPA.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_259


title: TMolBPA.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_260


title: RA.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_256


title: RS.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_253

value: Resorcinol sulfide


title: ARC2

description: SAMPLE 5

value: Female


title: NOR3

description: SAMPLE 3

value: Normal anterior capsular membrane of lens


title: TMolBPA.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_258


title: BPP.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_255


title: RS.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_252


title: RS.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_251


title: TMolBPA.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_257


title: DMSO.3d

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_248


title: NOR1

description: SAMPLE 1


title: BPP.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_271


title: DMSO.3b

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_246


title: RS.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_250


title: TMBPS.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_243

value: Tetra Methyl Bisphenol S


title: TMBPS.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_245

value: G


title: TMBPS.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_244


title: NOR2

description: SAMPLE 2


title: 2,4BPA.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_237

value: 2,4'-Bisphenol A


title: E2.3_10nM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_239


title: TMBPS.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_241


title: 2,4BPA.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_236


title: Media.3

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_240


title: 2,4BPA.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_235


title: DEX.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_238

value: Dexamethasone


title: BPP.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_263

value: Bisphenol P


title: 2,4BPA.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_233


title: RS.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_249


title: 2,4BPA.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_234


title: Isonox129.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_228


title: BPP.3_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_230


title: MeOH.3b

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_247

value: Methanol Treatment Control


title: ARC1

description: SAMPLE 4


title: Isonox129.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_229


title: Isonox129.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_227


title: TMBPS.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_242


title: BPG.4_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_232


title: MBMP.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_231


title: Isonox129.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_226


title: Isonox129.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_225


title: BPP.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_222


title: MBMP.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_223


title: BPG.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_224


title: THPE.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_221


title: THPE.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_220


title: THPE.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_219


title: BPG.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_216


title: THPE.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_217


title: BPP.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_214


title: THPE.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_218


title: BPA.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_212

value: Bisphenol A


title: BPA.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_211


title: MBMP.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_207


title: MBMP.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_215


title: MeOH.3a

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_203


title: BPA.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_210


title: BPG.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_208


title: Brain.3

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_204

value: No cells; Brain positive control


title: BPA.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_209


title: BCPS.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_201

value: BCPS-CTL

value: 4,4′-Dichlorodiphenyl sulfone


title: BPG.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_200

value: Bisphenol G


title: DMSO.3a

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_202

value: Dimethyl sulfoxide Treatment Control


title: BPP.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_198


title: MBMP.4_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_199


title: BPP.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_206


title: Universal.3

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_205

value: No cells; Universal human positive control


title: BPBP.3_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_196

value: Bisphenol BP


title: BPBP.3_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_195


title: BPA.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_213


title: BPBP.3_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_197


title: RS.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_192

value: F

value: Resorcinol sulfide


title: BPBP.3_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_193


title: BPBP.3_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_194


title: BPP.2_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_189


title: BPP.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_187


title: BPP.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_188


title: TMolBPA.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_183

value: Tetramethylol Bisphenol A


title: BPP.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_185


title: RS.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_184


title: MBMP.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_181


title: Isonox129.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_182


title: MBMP.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_179


title: MBMP.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_180


title: MBMP.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_178


title: RS.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_176


title: Isonox129.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_190


title: TMolBPA.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_191


title: RA.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_172

value: Rosalic Acid


title: Isonox129.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_174


title: TMolBPA.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_175


title: MBMP.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_177


title: RA.2_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_173


title: BPP.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_186


title: RA.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_169


title: Isonox129.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_166


title: RA.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_170


title: RS.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_168


title: RA.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_171


title: TMBPS.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_161

value: Tetra Methyl Bisphenol S


title: RS.4_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_160


title: TMBPS.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_162


title: TMolBPA.4_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_159


title: TMolBPA.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_157


title: Isonox129.4_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_158


title: TMolBPA.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_156


title: TMolBPA.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_167


title: TMolBPA.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_154


title: TMolBPA.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_155


title: MeOH.1d

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_152


title: TMolBPA.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_153


title: TMBPS.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_165


title: TMBPS.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_164


title: RS.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_149


title: RS.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_147


title: TMBPS.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_163


title: MeOH.2b

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_150


title: DEX.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_144


title: E2.2_10nM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_142


title: THPE.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_140


title: THPE.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_139


title: THPE.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_138


title: RS.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_145


title: RS.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_148


title: RS.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_146


title: Media.2

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_143

value: Media Negative


title: THPE.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_137


title: THPE.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_141


title: BPG.2_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_134


title: DMSO.2e

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_135


title: 2,4BPA.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_133

value: 2,4'-Bisphenol A


title: 2,4BPA.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_132


title: 2,4BPA.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_131


title: 2,4BPA.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_129


title: 2,4BPA.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_130


title: DMSO.2d

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_127


title: TMBPS.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_128


title: DMSO.2b

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_151


title: TMBPS.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_136


title: TMBPS.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_120


title: Isonox129.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_124


title: Isonox129.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_125


title: BPG.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_118


title: Isonox129.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_122


title: BPBP.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_117


title: 1X Lysis Buffer_2

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_119

value: No cells; 1X Lysis buffer


title: BPBP.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_115


title: Isonox129.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_121


title: BPBP.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_114


title: BPG.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_110


title: BPA.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_107


title: BPBP.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_113


title: TMBPS.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_112


title: DMSO.2c

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_111


title: BPA.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_109


title: BPA.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_106


title: BPG.2_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_102


title: BPG.2_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_126


title: BPA.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_105


title: Universal.2

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_101


title: BPBP.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_116


title: Isonox129.2_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_123


title: Brain.2

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_100


title: DMSO.2a

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_98


title: BCPS.2_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_97


title: BPA.2_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_108


title: 1X Lysis Buffer_1

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_95

value: E


title: BPG.1_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_93


title: BPA.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_94

value: Bisphenol A


title: BPG.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_91


title: BPG.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_90


title: BPG.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_92


title: MeOH.2a

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_99

value: Methanol Treatment Control


title: THPE.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_88


title: BPP.1_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_85

value: Bisphenol P


title: Media.1_CTR2

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_87


title: BPP.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_84


title: BPA.4_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_86


title: DMSO.1e

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_79


title: BPG.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_89


title: THPE.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_96


title: MBMP.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_77


title: BPP.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_82


title: BPP.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_83


title: MBMP.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_75


title: MBMP.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_74


title: THPE.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_72


title: THPE.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_80


title: MBMP.1_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_73


title: RS.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_69


title: RS.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_67


title: RS.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_68


title: RS.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_66


title: RS.1_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_65


title: MeOH.1c

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_71


title: BPP.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_81


title: DMSO.1d

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_63


title: BPA.4_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_70


title: THPE.4_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_64


title: BPA.4_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_78


title: BPA.4_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_62


title: TMBPS.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_60


title: MBMP.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_76


title: TMBPS.1_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_57


title: TMBPS.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_59


title: TMolBPA.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_53


title: E2.1_10nM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_55


title: TMBPS.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_58


title: TMolBPA.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_52


title: DMSO.1c

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_56


title: MeOH.1b

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_48


title: DMSO.1b

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_54


title: TMolBPA.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_51


title: TMolBPA.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_50


title: MTB-TAN tumor5

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

data_processing:
adapters removed, reads containing N>10% removed, Qscore<=5 removed by Novogene
data was provided by Novogene as .fq.gz files
data was analyzed using Genialis software and the standard RNA-seq pipeling
Assembly: GRCm39_ens109
Supplementary files format and content: xlsx file containing featurecounts data

source_name: mammary tumor

growth_protocol: mice were weaned at 21 days of age and placed on solid food

extract_protocol:
Total RNA was extracted using the miRVana miRNA extraction kit from Thermo Fisher Scientific
libraries were created by Novogene using Illumina kits

treatment_protocol: beginning at 21 days of age, mice were provide rodent chow with 2g of doxycycline/kg chow

value: mammary tumor

value: tissue

tag: cell type

value: Neu transgenic

value: 2g doxycycline/kg chow for >58days


title: DEX.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_47

value: Dexamethasone


title: Media.1

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_46


title: Isonox129.1_1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_44


title: Isonox129.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_43


title: TMolBPA.1_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_49


title: TMBPS.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_61


title: MTB-TAN tumor1


title: MTB-TAN tumor4


title: MTB-TANba429 55D mg5

source_name: mammary gland

value: mammary gland

value: Neu and miR-200b/200a/429 transgenic

value: 2g doxycycline/kg chow for 34days


title: MTB-TAN tumor2


title: Isonox129.1_10uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_42


title: MTB-TAN tumor3


title: Isonox129.1_25uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_41


title: MTB-TANba429 55D mg3


title: RA.1_0.1uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_38

value: Rosalic Acid


title: Isonox129.1_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_45


title: 2,4BPA.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_40


title: MTB-TAN 55D mg2


title: MTB-TANba429 55D mg4


title: BPBP.4_0.5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_39

value: Bisphenol BP


title: MTB-TAN 55D mg4


title: MTB-TANba429 55D mg2


title: THPE.1_5uM

description:
Templated oligo sequencing with the Human Whole Transcriptome 2.1 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
22P_35


title: MTB-TANba429 55D mg1