title: H2O2+ad-CTSV 4


title: ad-CTSV 2

status: Public on Mar 01 2026

type: SRA

city: changsha

first: Chan

last: Li

state: Hunan

address: No 87 Xiangya road, Changsha, Hunan, China.

country: China

institute: Xiangya Hospital, Central South University

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by
(1) Removing reads containing sequencing adapter
(2) Removing reads whose low-quality base ratio (base   quality less than or equal to 5) is more than 20%
(3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored   in FASTQ format.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Umbilical Vein

growth_protocol: Primary human vein endothelial cells (HUVECs) were obtained from sciencecell research laboratory and cultured with endothelial cell medium (ECM) containing 5% fetal bovine serum (FBS) and 1% endothelial cell growth supplement (ECGS) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according   to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2   mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The   mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a   new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for   15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper   aqueous phase where RNA remained was transferred into a new tube with equal volume of   supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After   deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix   was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the   pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated   water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using   a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Recombinant CatV adenovirus (ad-CatV, Shanghai Genechem Co., Ltd, China) or negative control adenovirus (ad-NC, Shanghai Genechem Co., Ltd, China) was added to 60% confluent cultured HUVECs and removed after 8 hours. Subsequently, HUVECs were cultured in complete growth medium for 40 hours and simulated with 400μM H2O2 for another 24 hours before RNA extraction.

tag: tissue

value: Umbilical Vein

tag: cell line

value: HUVEC

tag: cell type

value: endothelial cell

tag: genotype

value: WT

tag: treatment

value: ad-CTSV


title: sample 1 of liver constituent cells from a normal liver

city: Suita

first: Seiya

last: Kato

state: Osaka

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

country: Japan

institute: Osaka University

description:
Library name: normal 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The resulting raw data were processed with Cell Ranger 7.1.0 (10x Genomics). Briefly, trimmed FASTQ files were generated using the CellRanger mkfastq command. Primary data analysis for alignment, filtering, and unique molecular identifier counting were performed to determine the gene transcript counts per cell using CellRanger software. GRCh38 (hg19) was used for genome assembly/annotation references.
Assembly: GRCh38
Supplementary files format and content: HDF files containing cell barcodes and Gene Expression Counts

source_name: liver

extract_protocol:
Frozen surgical liver tissue was cut into pieces approximately 1 mm3, fixed with formalin using a Chromium Next GEM Single-Cell Fixed RNA Sample Preparation Kit (10x Genomics, Pleasanton, CA), and then dispersed into single cells using gentleMACS (Miltenyi Biotec) according to the manufacturer’s instructions.
For the construction of the scRNA-seq library, a Chromium Fixed RNA Kit, Human Transcriptome, 1BC (10x Genomics) was used according to the manufacturer’s instructions. Libraries were sequenced on a DNBSEQ-G400RS (MGI Tech) at a read length of 28 × 90.

value: liver

value: liver constituent cells

tag: batch


title: sample 2 of liver constituent cells from a FALD liver

description:
Library name: FALD 2
10x Genomics


title: H2O2 1


title: H2O2 2


title: Control 3

value: ad-NC


title: Control 2


title: Control 1


title: 9_T48_V3-KI

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

description: Library name: Sample_9

data_processing:
Quality of the raw sequenced reads was accessed with FastQC (v0.11.9). Adapter sequences were removed with Trimmomatic (v0.39).
Clean reads were aligned to the reference genome assembly of Pv11 cell line (Pv11_5.2.0) with Hisat2 (v2.2.1).
Aligned reads counted on the transcript level with HTSeq-count (v2.0.9).
Assembly: Pv11_5.2.0
Supplementary files format and content: Gene expression matrix with raw counts per sample

molecule: polyA RNA

organism: Polypedilum vanderplanki

growth_protocol: Cells grown in IPL-41 medium (Thermo Fisher Scientific) supplemented with 2.6 g/L tryptone phosphate broth (Becton, Dickinson and Company), 10% (v/v) fetal bovine serum (MP Biomedicals), and 0.05% (v/v) of an antibiotic and antimycotic mixture (penicillin, amphotericin B, and streptomycin; Merck).

extract_protocol:
Total RNA was extracted with an RNA Plus kit (Takara Bio) and genomic DNA was digested with TURBO DNase (Thermo Fisher Scientific).
NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol:
Pv11 cells and the clonal cell lines were incubated in trehalose mixture (600 mMtrehalose containing 10% (v/v) IPL-41 medium) at a density of 2 × 107 cells per mL for 48 h at 25℃.
After trehalose treatment for 48h, the cells were centrifuged and resuspended in fresh trehalose mixture at density of 1 × 108 cells per mL. Twenty microliters of the cell suspension containing 2 × 106 cells were aliquoted onto a 48-well plate, and the plated was covered with a breathable sealing film (BMF-BS-25, BMBio). The 48-well plates were immediately transferred into a desiccator containing 1 kg of silica gel to reach a relative humidity < 10% at 25℃, and cells were desiccated for 11 days. Cells were rehydrated with 500 μL IPL-41 medium.

tag: genetic modification

value: HSF1 KO

tag: overexpression

value: HSF1 isoform V3

value: trehalose


title: 70_HS6h_WT

description: Library name: Sample_70

value: wild type

value: heat shock


title: 72_HS6h_WT

description: Library name: Sample_72


title: 6_T48_V2-KI

description: Library name: Sample_6

value: HSF1 isoform V2


title: 8_T48_V3-KI

description: Library name: Sample_8


title: 68_HS6h_HSF1-KO

description: Library name: Sample_68


title: 69_HS6h_HSF1-KO

description: Library name: Sample_69


title: 64_HS6h_Dmb-KI

description: Library name: Sample_64

value: Drosophila HSF1b


title: 7_T48_V3-KI

description: Library name: Sample_7


title: 66_HS6h_Dmb-KI

description: Library name: Sample_66


title: 67_HS6h_HSF1-KO

description: Library name: Sample_67


title: 63_HS6h_Dma-KI

description: Library name: Sample_63

value: Drosophila HSF1a


title: 62_HS6h_Dma-KI

description: Library name: Sample_62


title: 61_HS6h_Dma-KI

description: Library name: Sample_61


title: Control 4


title: 5_T48_V2-KI

description: Library name: Sample_5


title: 57_HS6h_V4

description: Library name: Sample_57

value: HSF1 isoform V4


title: 58_HS6h_V5-6

description: Library name: Sample_58

value: HSF1 isoform V5-6


title: 54_HS6h_V3

description: Library name: Sample_54


title: 55_HS6h_V4

description: Library name: Sample_55


title: 71_HS6h_WT

description: Library name: Sample_71


title: 53_HS6h_V3

description: Library name: Sample_53


title: 50_HS6h_V2

description: Library name: Sample_50


title: 52_HS6h_V3

description: Library name: Sample_52


title: 65_HS6h-Dmb-KI

description: Library name: Sample_65


title: 51_HS6h_V2

description: Library name: Sample_51


title: 60_HS6h_V5-6

description: Library name: Sample_60


title: 59_HS6h_V5-6

description: Library name: Sample_59


title: 45_R24_WT

description: Library name: Sample_45

value: rehydration


title: 49_HS6h_V2

description: Library name: Sample_49


title: Mettl3-ASO_rep5

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

institute: Kyoto University

description: Library name: Sample10

data_processing:
The sequencing reads were mapped to the mouse genome (mm10) using STAR aligner software (v2.7.10.a). Gene expression levels were calculated using RSEM (ver. 1.3.3).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by RSEM (v1.3.3).

organism: Mus musculus

source_name: Morula stage embryo

growth_protocol: Superovulated mouse oocytes were in vitro fertilized and resulting embryos were cultured in KSOM up to the morula stage (72 hpi).

extract_protocol:
RNA-seq library was generated from ten morula stage embryos (ASO-Control and Mettl3-ASO groups), by using SMART-Seq v4 PLUS Kit (Takara Bio USA) according to the manufacturer’s manual.
SMART-Seq v4 PLUS Kit (Takara Bio USA) was used according to the manufacturer’s manual.

treatment_protocol: One-cell stage embryos at 3–6 hpi were microinjected with non-targeting or Mettl3-targeting ASOs and further cultured up to morula stage (72 hpi).

value: Morula stage embryo

value: in vitro produced, Mettl3-ASO treated from the one-cell stage


title: 56_HS6h_V4

description: Library name: Sample_56


title: 4_T48_V2-KI

description: Library name: Sample_4


title: 44_R24_WT

description: Library name: Sample_44


title: 46_HS6h_V1

description: Library name: Sample_46

value: HSF1 isoform V1


title: ASO-Control_rep3

description: Library name: Sample3

value: in vitro produced, ASO-Control treated from the one-cell stage


title: Mettl3-ASO_rep4

description: Library name: Sample9


title: ASO-Control_rep4

description: Library name: Sample4


title: Mettl3-ASO_rep3

description: Library name: Sample8


title: 43_R24_WT

description: Library name: Sample_43


title: Mettl3-ASO_rep2

description: Library name: Sample4

source_name: Embryo

value: Embryo

tag: strain

value: ICR

tag: developmental stage

value: morula stage embryo


title: 48_HS6h_V1

description: Library name: Sample_48

value: HSF1 KO


title: Mettl3-ASO_rep1

description: Library name: Sample3


title: 42_R24_V5-6-KI

description: Library name: Sample_42


title: 41_R24_V5-6-KI

description: Library name: Sample_41


title: ASO-Control_rep5

description: Library name: Sample5


title: 40_R24_V5-6-KI

description: Library name: Sample_40


title: ASO-Control_rep2

description: Library name: Sample2


title: ASO-Control_rep1

description: Library name: Sample1


title: 3_T48_V1-KI

description: Library name: Sample_3

value: trehalose


title: 47_HS6h_V1

description: Library name: Sample_47


title: 39_R24_V4-KI

description: Library name: Sample_39


title: 38_R24_V4-KI

description: Library name: Sample_38


title: ΔRv3060c Replicate 2

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

data_processing:
Data was subjected to quality control check by FastQC
Adaptor sequences were removed by Trim Galore
Reference genomes were indexed using Bowtie2
Reads were mapped to H37Rv genome by TopHat
Mapped files in SAM format were converted to Bam using SAMtools
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Assembly: ASM19595v2 (H37Rv)
Supplementary files format and content: tab-delimited text files include FPKM values for FadR KO study.

organism: Mycobacterium tuberculosis H37Rv

source_name: Bacterial cell

growth_protocol: All strains were grow in 7H9 medium supplemented with 1X ADS (Albumin Dextrose and Saline)

extract_protocol:
RNA was isolated by bead beating the strains in Trizol,  extracted by phenol-chloroform, precipitated with isopropanol and eluted using Qiagen RNA isolation kit
TruSeq stranded mRNA sample preparation protocol

treatment_protocol: Cultures were grown till mid-log phase

value: Bacterial cell


title: ΔRv0165c Replicate 2


title: ΔRv0165c Replicate 1


title: 36_R24_V3-KI

description: Library name: Sample_36

value: HSF1 isoform V3


title: ΔRv3060c Replicate 1


title: 37_R24_V4-KI

description: Library name: Sample_37


title: ΔRv0043c Replicate 1


title: 34_R24_V3-KI

description: Library name: Sample_34


title: H37Rv Control Replicate 2

description: Rv0043c-deletion.txt,  Rv0165c-deletion.txt,  Rv3060c-deletion.txt

value: H37Rv (Control)


title: 2_T48_V1-KI

description: Library name: Sample_2


title: 29_R24_V1-KI

description: Library name: Sample_29


title: 32_R24_V2-KI

description: Library name: Sample_32

value: HSF1 isoform V2


title: ΔRv0043c Replicate 2


title: 33_R24_V2-KI

description: Library name: Sample_33


title: 31_R24_V2-KI

description: Library name: Sample_31


title: 35_R24_V3-KI

description: Library name: Sample_35


title: H37Rv Control Replicate 1


title: 30_R24_V1-KI

description: Library name: Sample_30


title: 27_T48_Dmb-KI

description: Library name: Sample_27

value: Drosophila HSF1b


title: EPN24-Rep1

city: Qingdao

first: yuhua

last: jiao

address: No. 72 Binhai Road, Jimo District

institute: shandong university

description: Library name: Sample3

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences. Processed reads were then aligned to the human genome (hg38) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04. The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1) with parameters: -g gene_id -t exon --primary -Q 30.  Raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and Cas13d binding targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in EPN24-Cas13d versus EPN24  samples by DESeq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM

source_name: HEK293T cell line

growth_protocol: HEK293T cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml).

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC,1:1000) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 20 μl nuclease-free water.
5 μl supernatant RNA was used for library construction with modified VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically,  5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification 17 cycles according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on  DNBSEQ-T7 platform (GenePlus, China).

value: HEK293T cell line

value: Human Embryonic Kidney


title: WT_TSB_DIP_3

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

country: USA

institute: Ohio University

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped
Assembly: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary files format and content: Expression values for each sample are calculated as RPKM values.

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking (200 rpm)

extract_protocol:
Cell pellets were thawed and washed twice with 0.5mL of lysis buffer (20mM RNase-free Sodium acetate, 1mM EDTA, 0.5% SDS). The cells were lysed by the addition of 4μg lysostaphin and incubated for 40min at 37°C until confluent lysis was observed. RNA was isolated using TRIzol reagent according to the manufacturer's instructions
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were washed with PBS, resuspended in 500 µL with RNA protect (QIAGEN), pelleted by centrifugation, and stored at −80°C

value: Bacterial cells, pelleted

value: Wild-type

tag: growth medium

value: TSB + 120 mM 2,2-dipyridy

value: LAC (JMB1100)

value: 120 mM 2,2-dipyridy


title: EPN24-Rep2

description: Library name: Sample4


title: EPN24-Cas13d-Rep2

description: Library name: Sample2


title: EPN24-Cas13d-Rep1

description: Library name: Sample1


title: 28_R24_V1-KI

description: Library name: Sample_28

value: HSF1 isoform V1

value: rehydration


title: WT_TSB_DIP_1


title: WT_TSB_DIP_2


title: fur_TSB_2

value: fur mutant

value: TSB


title: 24_T48_Dma-KI

description: Library name: Sample_24

value: HSF1 KO

value: Drosophila HSF1a

value: trehalose


title: 26_T48_Dmb-KI

description: Library name: Sample_26


title: 21_T48_WT

description: Library name: Sample_21

value: wild type


title: fur_TSB_3


title: fur_TSB_DIP_1


title: 25_T48_Dmb-KI

description: Library name: Sample_25


title: fur_TSB_1


title: fur_TSB_DIP_3


title: 23_T48_Dma-KI

description: Library name: Sample_23


title: WT_TSB_3


title: 20_T48_WT

description: Library name: Sample_20


title: Cadict-1

city: Guangzhou

first: Shaoqing

last: Huang

address: No. 58, Zhongshan 2nd Road, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Library name: sample7

data_processing:
Base-calling was performed with the BGISEQ-500 software.
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were alignment to the reference genome, GRCh38.p13 using HISAT2 (v2.1.0).
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: xls file include FPKM, TPM and read_count values for each sample and each gene

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (#RC112-01, Vazyme), according to manufacturer’s instructions.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads, then fragmented. Then cDNA were sythesized, added A and adaptor ligation, and put into PCR system. Finally, PCR products were circularized and single-stranded circle DNA molecules were replicated via rolling cycle amplificationa to generate a DNA nanoball (DNB), which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Cadict


title: Cadict-2

description: Library name: sample8


title: WT_TSB_2


title: 1_T48_V1-KI

description: Library name: Sample_1


title: Cu-Cys-3

description: Library name: sample6

value: Cu-Cys


title: Cadict-3

description: Library name: sample9


title: 18_T48_HSF1-KO

description: Library name: Sample_18


title: WT_TSB_1


title: 19_T48_WT

description: Library name: Sample_19


title: Cu-Cys-2

description: Library name: sample5


title: 15_T48_V5-6-KI

description: Library name: Sample_15

value: HSF1 isoform V5-6


title: 13_T48_V5-6-KI

description: Library name: Sample_13


title: Cu-Cys-1

description: Library name: sample4


title: 11_T48_V4-KI

description: Library name: Sample_11

value: HSF1 isoform V4


title: fur_TSB_DIP_2

value: Bacterial cells, pelleted


title: 22_T48_Dma-KI

description: Library name: Sample_22


title: CTL-2

description: Library name: sample2

value: DMSO


title: 12_T48_V4-KI

description: Library name: Sample_12


title: 10_T48_V4-KI

description: Library name: Sample_10


title: 17_T48_HSF1-KO

description: Library name: Sample_17


title: Corynebacterium striatum, mono culture3

city: 广州

first: Zhou

last: Jiewen

address: 广东省广州市越秀区中山大学北校区

institute: 中山大学附属第一医院

description: Library name: CS3

data_processing:
The RNA-sequencing data were processed through a series of quality control steps using FastQC (version 0.11.9).
Fastp (version 0.39) was employed to filter out low-quality reads and adapter sequences.
The clean reads were then aligned to the human reference genome (hg38) using the HISAT2 alignment tool (version 2.2.1).
Assembly: StringTie assembler (version 2.1.4)
Supplementary files format and content: tab-delimited text file includes raw counts

organism: Corynebacterium striatum

source_name: Corynebacterium striatum, mono culture

extract_protocol:
RNA extraction from samples was accomplished using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s prescribed protocol.
RNA-sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA), following the recommended kit procedures.

value: bacteria

value: WT


title: CTL-1

description: Library name: sample1


title: 14_T48_V5-6-KI

description: Library name: Sample_14


title: CTL-3

description: Library name: sample3


title: Corynebacterium striatum, mono culture1

address: 广东省广州市越秀区中山大学北校区

description: Library name: CS1


title: Liver, Upstream, Johnny Darter, biol rep 4

city: Waterloo

first: Louis

middle: Joseph

last: Pfeifer

state: ON

address: 200 University Ave W

department: Biology

country: Canada

institute: University of Waterloo

description:
Library name: JK4_S52
Column name in J_Trinity_trans_gene_counts_matrix.txt: JK4_S52

data_processing:
Raw paired-end reads were processed using Trimmomatic (v0.36) (Sliding Window: 5:20; leading/trailing threshold: 20) to remove sequences with low-quality bases (Q<20), trim adapters and low quality leading/trailing ends, and filter sequences shorter than 45 bp
Trimmed reads were assembled de novo with Trinity (v2.13.2) under default parameters
Reads were mapped to their respective assemblies using Bowtie2 (v2.2.7) and abundance estimation using RSEM (v1.3.1)
Assembly: Trimmed reads were assembled de novo with Trinity (v2.13.2) under default parameters
Supplementary files format and content: Tab-delimited text file including raw counts for each sample
Supplementary files format and content: Tab-delimited text file including TPM values for each sample

organism: Etheostoma nigrum

source_name: Liver

extract_protocol:
RNA was extracted using QIAzol and chloroform (Qiagen), precipitated with isopropanol, eluted with 50μl of nuclease free water. 2 ug of totla RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols

value: Liver

value: Upstream


title: aHIEs2_229E_1_48h_37C

city: Wrocław

first: Heng-Chang

last: Chen

address: Stablowicka 147

country: Poland

institute: Łukasiewicz Research Network – PORT Polish Center for Technology Development

description:
Library name: Sample 47
instrument model: Salus Pro

data_processing:
Sequencing reads from total RNA were mapped to GENCODE protein-coding transcript sequence Human GRCh38.p14, released 45 (ENCODE Project Consortium, 2012) with kallisto (Bray et al., 2016) with options ‘quant’ (the quantification algorithm)  ‘–single’ (single-end mode), ‘–s 20’ (fragment length 20 nucleotides) and ‘–l 200’ (s.d. 200 nucleotides). The counts of the different isoforms were summed, thus generating a total count per gene copy in transcripts per million.
Assembly: GENCODE protein-coding transcript sequence Human GRCh38.p14, released 45 (ENCODE Project Consortium, 2012)
Supplementary files format and content: *abundance.tsv files include tpm

source_name: human intestinal enteroids

growth_protocol: ~1×10^5 cells (enteroids) were seeded in 100 µl of the medium onto each insert, and 300 µl of proliferation medium was added to the basolateral site. The proliferation medium was refreshed every 3-4 days until monolayer was confluent. Once the monolayer was confluent, proliferation medium was replaced with a differentiation medium consisting of a 1:1 (v/v) mix of OGMh human basal medium component and AdDMEM+++, to stimulate cell differentiation. The differentiation medium was refreshed every 3 – 4 days, and monolayers were maintained for 7 days.

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Plus (Zymo Research).
RNA libraries for RNAseq were prepared using the QIAseq Stranded RNA Library Kit (Qiagen, Germany) following the manufacturer’s protocol, with integrated globin transcript depletion using the QIAseq FastSelect – Globin Kit (Qiagen, Germany)

treatment_protocol: 6 different human intestinal enteroids (2 fetal donors, 2 pediatric donors, and 2 adult donors) were generated, differentiated, and subsequently infected for 48h with clinical strain of  human coronavirus 229E at either 32C or 37C. Controls included mock-infected enteroids.

value: human intestinal enteroids

tag: developmental age

value: adult

tag: temperature [c]

value: Virus


title: Liver, Upstream, Johnny Darter, biol rep 6

description:
Library name: JK6_S54
Column name in J_Trinity_trans_gene_counts_matrix.txt: JK6_S54


title: aHIEs2_229E_2_48h_32C

description:
Library name: Sample 44
instrument model: Salus Pro


title: aHIEs2_Mock_2_48h_37C

description:
Library name: Sample 46
instrument model: Salus Pro

value: Mock


title: aHIEs2_229E_1_48h_32C

description:
Library name: Sample 43
instrument model: Salus Pro


title: 16_T48_HSF1-KO

description: Library name: Sample_16

value: HSF1 KO


title: Liver, Upstream, Johnny Darter, biol rep 2

description:
Library name: JK2_S50
Column name in J_Trinity_trans_gene_counts_matrix.txt: JK2_S50


title: Liver, Downstream, Johnny Darter, biol rep 6

description:
Library name: JE6_S48
Column name in J_Trinity_trans_gene_counts_matrix.txt: JE6_S48

value: Downstream


title: Liver, Downstream, Johnny Darter, biol rep 5

description:
Library name: JE5_S47
Column name in J_Trinity_trans_gene_counts_matrix.txt: JE5_S47


title: Liver, Upstream, Johnny Darter, biol rep 5

description:
Library name: JK5_S53
Column name in J_Trinity_trans_gene_counts_matrix.txt: JK5_S53


title: Liver, Downstream, Johnny Darter, biol rep 4

description:
Library name: JE4_S46
Column name in J_Trinity_trans_gene_counts_matrix.txt: JE4_S46


title: aHIEs2_Mock_1_48h_37C

description:
Library name: Sample 45
instrument model: Salus Pro


title: aHIEs2_229E_2_48h_37C

description:
Library name: Sample 48
instrument model: Salus Pro


title: Liver, Upstream, Johnny Darter, biol rep 3

description:
Library name: JK3_S51
Column name in J_Trinity_trans_gene_counts_matrix.txt: JK3_S51


title: aHIEs1_Mock_1_48h_37C

description:
Library name: Sample 37
instrument model: Salus Pro


title: Liver, Downstream, Johnny Darter, biol rep 2

description:
Library name: JE2_S44
Column name in J_Trinity_trans_gene_counts_matrix.txt: JE2_S44


title: Liver, Downstream, Johnny Darter, biol rep 1

description:
Library name: JE1_S43
Column name in J_Trinity_trans_gene_counts_matrix.txt: JE1_S43


title: aHIEs1_Mock_2_48h_32C

description:
Library name: Sample 34
instrument model: Salus Pro


title: aHIEs1_229E_1_48h_32C

description:
Library name: Sample 35
instrument model: Salus Pro


title: aHIEs2_Mock_1_48h_32C

description:
Library name: Sample 41
instrument model: Salus Pro


title: Liver, Upstream, Johnny Darter, biol rep 1

description:
Library name: JK1_S49
Column name in J_Trinity_trans_gene_counts_matrix.txt: JK1_S49


title: aHIEs1_229E_1_48h_37C

description:
Library name: Sample 39
instrument model: Salus Pro


title: aHIEs1_Mock_2_48h_37C

description:
Library name: Sample 38
instrument model: Salus Pro


title: aHIEs1_229E_2_48h_37C

description:
Library name: Sample 40
instrument model: Salus Pro


title: Corynebacterium striatum, mono culture2

address: 广东省广州市越秀区中山大学北校区

description: Library name: CS2


title: Liver, Downstream, Johnny Darter, biol rep 3

description:
Library name: JE3_S45
Column name in J_Trinity_trans_gene_counts_matrix.txt: JE3_S45


title: Retired 57

city: Dublin 2

first: Jeffrey

last: O'Callaghan

state: Dublin

address: Smurfit Institute

country: Ireland

institute: Trinity College, Dublin

description: Library name: DBB1601

data_processing:
100 bp paired-end reads were sequenced on a NovaSeq 6000 (Illumina). Raw FASTQ files were trimmed with Cutadapt (part of Trim Galore) and aligned to the Gencode GRCh38 Release 43 reference using STAR. The resulting BAM files were sorted with STAR and indexed with Samtools. Gene quantification was performed using the RSEM’s rsem-calculate-expression tool. Count matrices produced by RSEM were processed with tximport and differential expression analysis was performed using DESeq2 v.1.38.3 in R. Alignment metrics were generated using the Genome Analysis Toolkit (GATK)’s CollectAlignmentSummaryMetrics. The distribution of the bases within the transcripts was determined using GATK’s CollectRnaSeqMetrics. Quality control reports were generated with FastQC (part of Trim Galore) and amalgamated into a single report with MultiQC.
Assembly: GRCh38
Supplementary files format and content: counts.csv contains gene-level expression estimates from RNA-seq for all samples used in the study. Each row corresponds to a single gene (identified by Ensembl gene ID and annotation), and each column corresponds to a sample.

source_name: Blood

growth_protocol: Blood samples from non-fasted participants were collected between 8 am and 10 am into serum separator tubes and EDTA-coated tubes for serum and PBMC isolation respectively. Samples arrived in the lab ~30 minutes later. After clotting for a total of 1 hour, serum was separated by centrifugation at 300 g for 10 min at room temperature and aliquoted and frozen at -80oC. PBMCs were separated via layering of blood samples diluted twofold in PBS (Thermo Fisher Scientific, cat. no. 14190) over Lymphoprep density gradient medium (STEMCELL Technologies, cat. no. 07851) followed by centrifugation at 400 g for 15 min at room temperature. Plasma was collected and stored at -80oC and PBMC layer was collected into a new 50 ml falcon tube, resuspended to 50 ml with PBS and centrifuged at 300 g for 5 min at room temperature. PBMCs were resuspended in 50 ml PBS and centrifuged at 200 g for 10 min at room temperature. PBMCs were resuspended to 2 x 106 cells/ml in RPMI 1640 media with L-glutamine (Lonza, cat. no. LZBE12-702F) supplemented with 50 % fetal bovine serum (Merck, cat. no. F7524) and 10 % DMSO (Merck, cat. no. D5879) and frozen at -800C overnight before being moved to liquid nitrogen for long term storage. Typically, PBMCs were frozen approximately 2 hours after sample collection.

extract_protocol:
PBMCs were thawed in a bead bath at 37 °C, topped up with PBS to 10 ml and centrifuged at 300 g for 5 min at room temperature. RNA was isolated from 2 × 106 PBMCs with the E.Z.N.A. Total RNA Kit I (Omega Bio-tek, cat. no. R6834-02) according to the manufacturer’s recommendations. RNA samples were analysed on a TapeStation 2200 (Agilent Technologies) and samples with an RNA integrity number value greater than 7 and ribosomal RNA ratio greater than 1 were used for library preparation and RNA-sequencing
Libraries were prepared from 100 ng RNA with the Watchmaker RNA Library Preparation Kit (Watchmaker Genomics).

value: Blood

value: Peripheral blood mononuclear cells


title: aHIEs1_229E_2_48h_32C

description:
Library name: Sample 36
instrument model: Salus Pro


title: Control 7

description: Library name: C029


title: pHIEs2_Mock_2_48h_37C

description:
Library name: Sample 30
instrument model: Salus Pro

value: pediatric


title: Control 5

description: Library name: C021


title: Control 4

description: Library name: C009


title: aHIEs2_Mock_2_48h_32C

description:
Library name: Sample 42
instrument model: Salus Pro


title: Retired 56

description: Library name: DB2016


title: pHIEs2_229E_2_48h_37C

description:
Library name: Sample 32
instrument model: Salus Pro


title: Control 8

description: Library name: C032


title: aHIEs1_Mock_1_48h_32C

description:
Library name: Sample 33
instrument model: Salus Pro


title: Control 6

description: Library name: C028


title: pHIEs2_229E_1_48h_37C

description:
Library name: Sample 31
instrument model: Salus Pro


title: pHIEs2_Mock_1_48h_37C

description:
Library name: Sample 29
instrument model: Salus Pro


title: pHIEs2_229E_2_48h_32C

description:
Library name: Sample 28
instrument model: Salus Pro


title: pHIEs1_229E_1_48h_37C

description:
Library name: Sample 23
instrument model: Salus Pro


title: pHIEs2_229E_1_48h_32C

description:
Library name: Sample 27
instrument model: Salus Pro


title: pHIEs2_Mock_2_48h_32C

description:
Library name: Sample 26
instrument model: Salus Pro


title: Control 3

description: Library name: C006


title: pHIEs1_Mock_1_48h_37C

description:
Library name: Sample 21
instrument model: Salus Pro


title: Retired 49

description: Library name: 16628912


title: pHIEs2_Mock_1_48h_32C

description:
Library name: Sample 25
instrument model: Salus Pro


title: Retired 53

description: Library name: 17259462


title: Retired 55

description: Library name: 17457952


title: Retired 48

description: Library name: 16444082


title: pHIEs1_229E_2_48h_37C

description:
Library name: Sample 24
instrument model: Salus Pro


title: Retired 54

description: Library name: 17290442


title: pHIEs1_229E_1_48h_32C

description:
Library name: Sample 19
instrument model: Salus Pro


title: Retired 52

description: Library name: 17137812


title: Retired 50

description: Library name: 16943262


title: Retired 51

description: Library name: 17079412


title: fHIEs2_229E_2_48h_37C

description:
Library name: Sample 16
instrument model: Salus Pro

value: fetal


title: pHIEs1_229E_2_48h_32C

description:
Library name: Sample 20
instrument model: Salus Pro


title: pHIEs1_Mock_2_48h_32C

description:
Library name: Sample 18
instrument model: Salus Pro


title: Retired 45

description: Library name: 16321792


title: fHIEs2_229E_1_48h_37C

description:
Library name: Sample 15
instrument model: Salus Pro


title: Retired 43

description: Library name: 16309932


title: Retired 47

description: Library name: 16353742


title: pHIEs1_Mock_2_48h_37C

description:
Library name: Sample 22
instrument model: Salus Pro


title: pHIEs1_Mock_1_48h_32C

description:
Library name: Sample 17
instrument model: Salus Pro


title: Retired 46

description: Library name: 16349222


title: fHIEs2_Mock_1_48h_37C

description:
Library name: Sample 13
instrument model: Salus Pro


title: fHIEs2_Mock_2_48h_37C

description:
Library name: Sample 14
instrument model: Salus Pro


title: Retired 42

description: Library name: 16309772


title: Retired 40

description: Library name: 16116512


title: Retired 41

description: Library name: 16171012


title: fHIEs2_229E_2_48h_32C

description:
Library name: Sample 12
instrument model: Salus Pro


title: fHIEs1_229E_2_48h_37C

description:
Library name: Sample 8
instrument model: Salus Pro


title: Retired 39

description: Library name: 1847551


title: fHIEs2_229E_1_48h_32C

description:
Library name: Sample 11
instrument model: Salus Pro


title: Retired 44

description: Library name: 16321772


title: fHIEs1_229E_1_48h_37C

description:
Library name: Sample 7
instrument model: Salus Pro


title: fHIEs2_Mock_2_48h_32C

description:
Library name: Sample 10
instrument model: Salus Pro


title: Control 2

description: Library name: 1835797


title: Retired 38

description: Library name: 1842172


title: fHIEs2_Mock_1_48h_32C

description:
Library name: Sample 9
instrument model: Salus Pro


title: Retired 37

description: Library name: 1841089


title: fHIEs1_Mock_2_48h_37C

description:
Library name: Sample 6
instrument model: Salus Pro


title: fHIEs1_Mock_1_48h_37C

description:
Library name: Sample 5
instrument model: Salus Pro


title: Retired 36

description: Library name: 1822910


title: fHIEs1_Mock_1_48h_32C

description:
Library name: Sample 1
instrument model: Salus Pro


title: Retired 31

description: Library name: 1730603


title: Small RNAseq MAs sample #4

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Sample from INS-1 832/13 cells used for small RNAseq, batch K, MAs-treated
smRNA_INS1_MAs_DESeq_normalized_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq), aligned and quantified using STAR/Salmon (RNAseq), or aligned and quantified using the ChROseq pipeline (ChROseq).
All sequencing types were processed with DESeq2.
Assembly: rn6
Supplementary files format and content: Normalized counts

organism: Rattus norvegicus

source_name: beta-cell line

growth_protocol: The INS-1 832/13 rat insulinoma beta-cell line was maintained at 5% CO2, 37oC in RPMI 1640 media supplemented with 2 mM L-glutamine media, 10% FBS, 10 mM HEPES media, 1 mM sodium pyruvate media, 100 U/mL penicillin media, 100 μg/mL streptomycin media, and 0.05 mM β-mercaptoethanol.

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (small RNAseq), NEBNext Ultra II RNA kit (RNAseq), or according to the ChROseq protocol.

treatment_protocol: INS-1 832/13 cells were either untreated, treated with sodium arsenite (iAs), or with methylarsine oxide (Mas)

value: beta-cell line

value: MAs-treated


title: Retired 34

description: Library name: 1796300


title: Small RNAseq MAs sample #3


title: Retired 29

description: Library name: 1725946


title: Small RNAseq MAs sample #1


title: Retired 35

description: Library name: 1811555


title: Retired 26

description: Library name: 1694326


title: Retired 24

description: Library name: 1684346


title: fHIEs1_229E_2_48h_32C

description:
Library name: Sample 4
instrument model: Salus Pro


title: fHIEs1_229E_1_48h_32C

description:
Library name: Sample 3
instrument model: Salus Pro


title: fHIEs1_Mock_2_48h_32C

description:
Library name: Sample 2
instrument model: Salus Pro


title: Small RNAseq iAs sample #1

description:
Sample from INS-1 832/13 cells used for small RNAseq, batch R, iAs-treated
smRNA_INS1_iAs_DESeq_normalized_counts.csv

value: iAs-treated


title: Retired 33

description: Library name: 1745795


title: Retired 22

description: Library name: 1649469


title: Retired 32

description: Library name: 1740376


title: Small RNAseq iAs sample #4

description:
Sample from INS-1 832/13 cells used for small RNAseq, batch K, iAs-treated
smRNA_INS1_iAs_DESeq_normalized_counts.csv


title: Small RNAseq control sample #5

description:
Sample from INS-1 832/13 cells used for small RNAseq, batch K, control
smRNA_INS1_iAs_DESeq_normalized_counts.csv
smRNA_INS1_MAs_DESeq_normalized_counts.csv

value: control


title: Retired 28

description: Library name: 1713781


title: Small RNAseq iAs sample #5


title: Small RNAseq iAs sample #2


title: Retired 27

description: Library name: 1707941


title: Small RNAseq iAs sample #3


title: Retired 25

description: Library name: 1692124


title: Small RNAseq control sample #2

description:
Sample from INS-1 832/13 cells used for small RNAseq, batch R, control
smRNA_INS1_iAs_DESeq_normalized_counts.csv


title: Retired 18

description: Library name: 1644408


title: Small RNAseq control sample #1


title: Retired 30

description: Library name: 1729044


title: Retired 23

description: Library name: 1662891


title: Liver, Upstream, Fantail Darter, biol rep 6

description:
Library name: FK7_S42
Column name in F_Trinity_trans_gene_counts_matrix.txt: FK7.RSEM

organism: Etheostoma flabellare


title: Small RNAseq control sample #3


title: Small RNAseq control sample #4


title: Retired 21

description: Library name: 1648656


title: Liver, Upstream, Fantail Darter, biol rep 5

description:
Library name: FK6_S41
Column name in F_Trinity_trans_gene_counts_matrix.txt: FK6.RSEM


title: Control 1

description: Library name: 1674262


title: Retired 20

description: Library name: 1647993


title: Liver, Upstream, Fantail Darter, biol rep 4

description:
Library name: FK5_S40
Column name in F_Trinity_trans_gene_counts_matrix.txt: FK5.RSEM


title: Retired 19

description: Library name: 1646665


title: Retired 14

description: Library name: 1640888


title: Retired 15

description: Library name: 1642299


title: Retired 16

description: Library name: 1643035


title: Retired 17

description: Library name: 1643036


title: Retired 13

description: Library name: 1635374


title: Retired 12

description: Library name: 1634922


title: Liver, Upstream, Fantail Darter, biol rep 1

description:
Library name: FK1_S37
Column name in F_Trinity_trans_gene_counts_matrix.txt: FK1.RSEM


title: Liver, Downstream, Fantail Darter, biol rep 5

description:
Library name: FE6_S34
Column name in F_Trinity_trans_gene_counts_matrix.txt: FE6.RSEM


title: Liver, Downstream, Fantail Darter, biol rep 4

description:
Library name: FE5_S33
Column name in F_Trinity_trans_gene_counts_matrix.txt: FE5.RSEM


title: Retired 11

description: Library name: 1633435


title: Liver, Downstream, Fantail Darter, biol rep 6

description:
Library name: FE7_S35
Column name in F_Trinity_trans_gene_counts_matrix.txt: FE7.RSEM


title: Liver, Downstream, Fantail Darter, biol rep 3

description:
Library name: FE2_S32
Column name in F_Trinity_trans_gene_counts_matrix.txt: FE2.RSEM


title: Retired 9

description: Library name: 1632179


title: Retired 10

description: Library name: 1632181


title: Retired 8

description: Library name: 1632177


title: Liver, Upstream, Fantail Darter, biol rep 2

description:
Library name: FK3_S38
Column name in F_Trinity_trans_gene_counts_matrix.txt: FK3.RSEM


title: Retired 7

description: Library name: 1630993


title: Liver, Upstream, Fantail Darter, biol rep 3

description:
Library name: FK4_S39
Column name in F_Trinity_trans_gene_counts_matrix.txt: FK4.RSEM


title: Retired 5

description: Library name: 1629890


title: Liver, Downstream, Fantail Darter, biol rep 2

description:
Library name: FE10_S36
Column name in F_Trinity_trans_gene_counts_matrix.txt: FE10.RSEM


title: Liver, Downstream, Fantail Darter, biol rep 1

description:
Library name: FE1_S31
Column name in F_Trinity_trans_gene_counts_matrix.txt: FE1.RSEM


title: Retired 6

description: Library name: 1630977


title: Liver, S-Venlafaxine, Rainbow Darter, biol rep 5

description:
Library name: S14C3_S34
Column name in Trinity_trans.gene.counts.matrix.txt S14C3_S34.RSEM

data_processing:
Raw paired-end reads sequenced from separate lanes were concatenated for each sample
Raw paired-end reads were processed using Trimmomatic (v0.36) (Sliding Window: 5:20; leading/trailing threshold: 20) to remove sequences with low-quality bases (Q<20), trim adapters and low quality leading/trailing ends, and filter sequences shorter than 45 bp
Trimmed reads were assembled de novo with Trinity (v2.13.2) under default parameters
Reads were mapped to their respective assemblies using Bowtie2 (v2.2.7) and abundance estimation using RSEM (v1.3.1)
Assembly: trinity_out_dir_VEN.Trinity.fasta
Supplementary files format and content: Tab-delimited text file including raw counts for each sample
Supplementary files format and content: Tab-delimited text file including TPM values for each sample
Supplementary files format and content: FASTA file with the Trinity assembled sequences

organism: Etheostoma caeruleum

growth_protocol: Wild Etheostoma caeruleum (Rainbow Darter) were collected from the Grand River, Ontario, Canada (56°32.6"N, 80°19'32.8"W), and transported alive to the Waterloo Aquatic Threats in Environmental Research (WATER) facility, University of Waterloo, Ontario. Fish were housed in individual 10 L acrylic tanks (Aquatic Habitats unit) at 18 °C, matching ambient river temperature. Water was replaced at a rate of 10% per day. A 12 h light/dark cycle was maintained, and fish were fed San Francisco Bay Brand frozen bloodworms to satiation twice daily. PVC structures provided habitat enrichment.

extract_protocol:
RNA was extracted from liver tissue using QIAzol and chloroform (Qiagen), precipitated with isopropanol, eluted with 50μl of nuclease free water. 2 ug of totla RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols

treatment_protocol: Fish underwent a 14-day acclimation period for contaminant depuration. Following acclimation, fish were transferred to 12 L glass aquaria placed within a temperature-controlled water trough. Each experimental tank housed n ≥6 fish, with non-transparent dividers used to minimize inter-tank interaction. Tanks were randomly assigned to one of three treatment groups: Control, R-Venlafaxine (R-VEN), or S-Venlafaxine (S-VEN). Exposure concentrations were 1 µg/L for each enantiomer, maintained via daily 10% water replacement 1 hour after feeding. Control tanks received no venlafaxine. Water samples were collected 1 hour post-replacement to confirm exposure concentrations. Fish were fed once daily during the exposure period.

value: S-Venlafaxine, 14 days


title: Retired 4

description: Library name: 1611651


title: Retired 3

description: Library name: 1611444


title: Liver, S-Venlafaxine, Rainbow Darter, biol rep 3

description:
Library name: S14B2_S32
Column name in Trinity_trans.gene.counts.matrix.txt S14B2_S32.RSEM

value: Liver


title: Retired 2

description: Library name: 1295867


title: Retired 1

description: Library name: 1646667


title: placenta, villus, HV8

city: São Paulo

first: Maria

middle: Notomi

last: Sato

state: São Paulo

address: Av. Dr. Eneas de Carvalho Aguia, 470

department: Dermatology

country: Brazil

institute: University of São Paulo

description:
Library name: HV8
RNA-seq of human placenta villus tissue from HIV patient (HV8)

data_processing:
Quality control; Gene-level quantificantion and differential expression analysis
Raw sequencing reads underwent quality assessment with FASTQC
Adapter trimming, base correction, and filtering
Clean reads were aligned to the human reference genome GRCh38.p13 (Ensembl release 104)
Gene-level quantification was performed using FeatureCounts
FPKM-normalized values were obtained using the DESeq2 workflow
Differential expression calculation
Assembly: Processed data files include: (1) a raw gene count matrix in CSV format, containing genes in rows and samples in columns; and (2) an FPKM-normalized expression matrix in TSV format. Gene identifiers are provided as Ensembl IDs and gene symbols. Normalized values were generated using DESeq2.
Supplementary files format and content: A raw gene count matrix provided as a comma-separated values (CSV) file. Rows correspond to gene gene symbols, and columns correspond to individual samples. Values represent raw, unnormalized read counts generated after alignment to the human reference genome GRCh38.p13 (Ensembl release 104) and quantification
Supplementary files format and content: An FPKM-normalized expression matrix provided as a tab-separated values (TSV) file. Rows contain gene identifiers, and columns represent samples. Values correspond to FPKM-normalized gene expression levels generated using standard normalization procedures with DESeq2.

source_name: placenta

growth_protocol: Placental tissue: Two to three cotyledons were separated from the placenta shortly after delivery and transported to the laboratory in transport solution. The samples were washed with saline and separated into maternal (decidua) and fetal (villus) sides. Approximately 30 µg of each side was stored in a microtube (Eppendorf) with RNALater solution (Sigma Chemical Co, St. Louis, MO, USA) at -80°C. For immunohistochemistry and immunofluorescence analyses, a 1 cm by 1 cm section was made from the cotyledon, including the decidua and villus. This fragment was stored in a histological cassette and placed in a vial immersed in 10% formalin.

extract_protocol:
Libraries for sequencing were constructed with purified RNAs and TruSeq Stranded mRNA Library Prep kits (Illumina, San Diego, CA, USA), following the manufacturer's instructions.
These libraries were sequenced on the Illumina NovaSeq 6000 using the V2.5 Mid Output kit, 2 x 75 cycles.

treatment_protocol: To obtain mRNA, placenta samples stored in RNALater were thawed and fragmented using the Tissue Ruptor apparatus (Qiagen, Hilden, Germany) and the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's recommendations.

value: placenta

value: villous trophoblasts

value: villus

value: HIV

value: villus - HIV


title: Liver, R-Venlafaxine, Rainbow Darter, biol rep 5

description:
Library name: R14C5_S28
Column name in Trinity_trans.gene.counts.matrix.txt R14C5_S28.RSEM

value: R-Venlafaxine, 14 days


title: Liver, S-Venlafaxine, Rainbow Darter, biol rep 6

description:
Library name: S14C4_S35
Column name in Trinity_trans.gene.counts.matrix.txt S14C4_S35.RSEM


title: Liver, S-Venlafaxine, Rainbow Darter, biol rep 2

description:
Library name: S14A6_S31
Column name in Trinity_trans.gene.counts.matrix.txt S14A6_S31.RSEM


title: Small RNAseq MAs sample #2

description:
Sample from INS-1 832/13 cells used for small RNAseq, batch K, MAs-treated
smRNA_INS1_MAs_DESeq_normalized_counts.csv


title: placenta, villus, HV6

description:
Library name: HV6
RNA-seq of human placenta villus tissue from HIV patient (HV6)


title: Liver, R-Venlafaxine, Rainbow Darter, biol rep 6

description:
Library name: R14C6_S29
Column name in Trinity_trans.gene.counts.matrix.txt R14C6_S29.RSEM


title: placenta, villus, HV7

description:
Library name: HV7
RNA-seq of human placenta villus tissue from HIV patient (HV7)


title: Liver, S-Venlafaxine, Rainbow Darter, biol rep 4

description:
Library name: S14B4_S33
Column name in Trinity_trans.gene.counts.matrix.txt S14B4_S33.RSEM


title: Liver, R-Venlafaxine, Rainbow Darter, biol rep 4

description:
Library name: R14B6_S27
Column name in Trinity_trans.gene.counts.matrix.txt R14B6_S27.RSEM


title: Liver, S-Venlafaxine, Rainbow Darter, biol rep 1

description:
Library name: S14A4_S30
Column name in Trinity_trans.gene.counts.matrix.txt S14A4_S30.RSEM


title: Liver, Control, Rainbow Darter, biol rep 4

description:
Library name: C14B5_S21
Column name in Trinity_trans.gene.counts.matrix.txt C14B5_S21.RSEM

value: Control, 14 days


title: Liver, Control, Rainbow Darter, biol rep 6

description:
Library name: C14C2_S23
Column name in Trinity_trans.gene.counts.matrix.txt C14C2_S23.RSEM


title: Liver, Control, Rainbow Darter, biol rep 3

description:
Library name: C14B2_S20
Column name in Trinity_trans.gene.counts.matrix.txt C14B2_S20.RSEM


title: Liver, R-Venlafaxine, Rainbow Darter, biol rep 2

description:
Library name: R14A5_S25
Column name in Trinity_trans.gene.counts.matrix.txt R14A5_S25.RSEM


title: Liver, R-Venlafaxine, Rainbow Darter, biol rep 1

description:
Library name: R14A2_S24
Column name in Trinity_trans.gene.counts.matrix.txt R14A2_S24.RSEM


title: placenta, decidua, HD7

description:
Library name: HD7
RNA-seq of human placenta decidua tissue from HIV patient (HD7)

value: decidual immune cells

value: decidua

value: decidua - HIV


title: placenta, decidua, HD5

description:
Library name: HD5
RNA-seq of human placenta decidua tissue from HIV patient (HD5)


title: placenta, villus, HV2

description:
Library name: HV2
RNA-seq of human placenta villus tissue from HIV patient (HV2)


title: placenta, villus, HV3

description:
Library name: HV3
RNA-seq of human placenta villus tissue from HIV patient (HV3)


title: placenta, villus, HV1

description:
Library name: HV1
RNA-seq of human placenta villus tissue from HIV patient (HV1)


title: placenta, decidua, HD6

description:
Library name: HD6
RNA-seq of human placenta decidua tissue from HIV patient (HD6)


title: Liver, Control, Rainbow Darter, biol rep 5

description:
Library name: C14C1_S22
Column name in Trinity_trans.gene.counts.matrix.txt C14C1_S22.RSEM


title: Liver, Downstream, Rainbow Darter, biol rep 4

description:
Library name: RE6_S10
Column name in R_Trinity_trans_gene_counts_matrix.txt: RE6.RSEM

value: Downstream


title: placenta, villus, HV4

description:
Library name: HV4
RNA-seq of human placenta villus tissue from HIV patient (HV4)


title: placenta, decidua, HD8

description:
Library name: HD8
RNA-seq of human placenta decidua tissue from HIV patient (HD8)


title: Liver, Control, Rainbow Darter, biol rep 2

description:
Library name: C14A6_S19
Column name in Trinity_trans.gene.counts.matrix.txt C14A6_S19.RSEM


title: Liver, Control, Rainbow Darter, biol rep 1

description:
Library name: C14A5_S18
Column name in Trinity_trans.gene.counts.matrix.txt C14A5_S18.RSEM


title: Liver, Downstream, Rainbow Darter, biol rep 3

description:
Library name: RE5_S9
Column name in R_Trinity_trans_gene_counts_matrix.txt: RE5.RSEM


title: placenta, decidua, HD4

description:
Library name: HD4
RNA-seq of human placenta decidua tissue from HIV patient (HD4)


title: Liver, R-Venlafaxine, Rainbow Darter, biol rep 3

description:
Library name: R14B3_S26
Column name in Trinity_trans.gene.counts.matrix.txt R14B3_S26.RSEM


title: Liver, Downstream, Rainbow Darter, biol rep 6

description:
Library name: RE12_S12
Column name in R_Trinity_trans_gene_counts_matrix.txt: RE12.RSEM


title: placenta, villus, HV5

description:
Library name: HV5
RNA-seq of human placenta villus tissue from HIV patient (HV5)


title: placenta, decidua, HD3

description:
Library name: HD3
RNA-seq of human placenta decidua tissue from HIV patient (HD3)


title: placenta, decidua, HD2

description:
Library name: HD2
RNA-seq of human placenta decidua tissue from HIV patient (HD2)


title: Liver, Downstream, Rainbow Darter, biol rep 5

description:
Library name: RE11_S11
Column name in R_Trinity_trans_gene_counts_matrix.txt: RE11.RSEM


title: Liver, Downstream, Rainbow Darter, biol rep 2

description:
Library name: RE2_S8
Column name in R_Trinity_trans_gene_counts_matrix.txt: RE2.RSEM


title: placenta, villus, CV7

description:
Library name: CV7
RNA-seq of human placenta villus tissue from control (CV7)

value: Control

value: villus - control


title: placenta, decidua, HD1

description:
Library name: HD1
RNA-seq of human placenta decidua tissue from HIV patient (HD1)


title: placenta, villus, CV5

description:
Library name: CV5
RNA-seq of human placenta villus tissue from control (CV5)


title: Liver, Upstream, Rainbow Darter, biol rep 5

description:
Library name: RK11_S17
Column name in R_Trinity_trans_gene_counts_matrix.txt: RK11.RSEM

value: Upstream


title: placenta, villus, CV3

description:
Library name: CV3
RNA-seq of human placenta villus tissue from control (CV3)


title: Liver, Upstream, Rainbow Darter, biol rep 4

description:
Library name: RK10_S16
Column name in R_Trinity_trans_gene_counts_matrix.txt: RK10.RSEM


title: placenta, villus, CV6

description:
Library name: CV6
RNA-seq of human placenta villus tissue from control (CV6)


title: Liver, Upstream, Rainbow Darter, biol rep 2

description:
Library name: RK4_S14
Column name in R_Trinity_trans_gene_counts_matrix.txt: RK4.RSEM


title: Liver, Upstream, Rainbow Darter, biol rep 6

description:
Library name: RK12_S18
Column name in R_Trinity_trans_gene_counts_matrix.txt: RK12.RSEM


title: placenta, villus, CV8

description:
Library name: CV8
RNA-seq of human placenta villus tissue from control (CV8)


title: placenta, villus, CV4

description:
Library name: CV4
RNA-seq of human placenta villus tissue from control (CV4)


title: Liver, Downstream, Rainbow Darter, biol rep 1

description:
Library name: RE1_S7
Column name in R_Trinity_trans_gene_counts_matrix.txt: RE1.RSEM


title: placenta, villus, CV2

description:
Library name: CV2
RNA-seq of human placenta villus tissue from control (CV2)


title: Liver, Upstream, Rainbow Darter, biol rep 3

description:
Library name: RK5_S15
Column name in R_Trinity_trans_gene_counts_matrix.txt: RK5.RSEM


title: D20_2

city: Shanghai

first: Rui

last: Cheng

state: Shanghai

address: No. 1630 East Road, Pudong New Area

institute: Shanghai Jiao Tong University

description: Library name: sample13

data_processing:
The raw sequencing data (FASTQ files) were processed using DynamicEX software (https://github.com/DynamicBiosystems/DynamicEX) to extract unique molecular identifiers (UMIs; 13-20 bp) and cell barcodes (1-12 bp) from Read 1, while the cDNA sequences of Read 2 were aligned to the mouse reference genome (mm10, Gencode release vM13) using STAR (v2.7.11a.42). The BAM files generated by DynamicEX were rigorously filtered to remove unmapped reads, secondary alignments, and uniquely mapped reads with alignment scores ≤10. The retained reads were grouped by UMI, cell barcode, and gene annotation, and consensus base calling was performed at each genomic position by selecting the most frequently observed base within each UMI group to minimize sequencing errors. Based on the consensus sequences and alignment information, the frequencies of base conversion events were systematically quantified, and UMIs/transcripts with at least one T-to-C substitution were designated as nascent RNA-labeled molecules. Finally, the counts of labeled and unlabeled mRNA for each gene were integrated to construct a digital expression matrix with genes as rows and cells as columns.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt files include the transcript counts for each gene in each sample

source_name: Kindey

extract_protocol:
In this study, 6-8-week-old female mice bearing orthotopic renal carcinoma models received tail vein injection of 4-thiouridine (4sU) for 1.5-hour metabolic labeling before kidney tissue collection. Tissue dissociation was performed using the Multi Tissue Dissociation Kit 2 with gentleMACS Octo Dissociator, followed by filtration through 100 μm and 40 μm strainers to obtain single-cell suspensions. The Well-paired-seq microfluidic chip was employed to pair cells with barcoded beads in dual-chamber structures, with cell lysis achieved using 5% sodium lauroyl sarcosinate to facilitate mRNA capture on beads, establishing the foundation for subsequent transcriptomic analysis of 4sU-labeled newly synthesized RNA versus total RNA.
Following cell lysis and mRNA capture, barcoded beads underwent 4sU-to-C chemical conversion using iodoacetamide treatment. Reverse transcription with template switching was performed, followed by Exonuclease I digestion to remove excess primers. Second-strand synthesis utilized Klenow exo- enzyme and cDNA was amplified via PCR. The resulting products were purified twice with DNA Clean Beads, and sequencing libraries were prepared using a Vazyme Kit with 5 ng input. Final libraries underwent additional bead purification and were sequenced on a HiSeq X Ten platform with 150 bp paired-end reads.

value: Kindey


title: D11_2

description: Library name: sample11


title: D9_2

description: Library name: sample9


title: D9_1

description: Library name: sample8


title: placenta, decidua, CD8

description:
Library name: CD8
RNA-seq of human placenta decidua tissue from control (CD8)

value: decidua - control


title: D20_1

description: Library name: sample12


title: placenta, decidua, CD5

description:
Library name: CD5
RNA-seq of human placenta decidua tissue from control (CD5)


title: placenta, villus, CV1

description:
Library name: CV1
RNA-seq of human placenta villus tissue from control (CV1)


title: placenta, decidua, CD4

description:
Library name: CD4
RNA-seq of human placenta decidua tissue from control (CD4)


title: Liver, Upstream, Rainbow Darter, biol rep 1

description:
Library name: RK3_S13
Column name in R_Trinity_trans_gene_counts_matrix.txt: RK3.RSEM

value: Liver


title: placenta, decidua, CD1

description:
Library name: CD1
RNA-seq of human placenta decidua tissue from control (CD1)

value: placenta


title: placenta, decidua, CD3

description:
Library name: CD3
RNA-seq of human placenta decidua tissue from control (CD3)


title: D7_1

description: Library name: sample6


title: placenta, decidua, CD2

description:
Library name: CD2
RNA-seq of human placenta decidua tissue from control (CD2)


title: D11_1

description: Library name: sample10


title: D7_2

description: Library name: sample7


title: D3

description: Library name: sample3


title: placenta, decidua, CD6

description:
Library name: CD6
RNA-seq of human placenta decidua tissue from control (CD6)


title: placenta, decidua, CD7

description:
Library name: CD7
RNA-seq of human placenta decidua tissue from control (CD7)


title: D5_2

description: Library name: sample5


title: D5_1

description: Library name: sample4


title: iGLUTs_D21_3182_gRNA_R3

city: Las Vegas

first: Huanyao

last: Gao

state: Nevada

address: 11845 Ampucia Ct

department: Department of Psychiatry

institute: Yale University

description: Library name: MG30_GDO

library_source: other

data_processing:
cDNA was mapped to GRCh38 reference file using CellRanger. gRNA was mapped to gRNA library sequence using kallisto-kite pipeline (see attached feature_sequence file.)
Assembly: GRCh38
Supplementary files format and content: sparse matrix output from CellRanger (cDNA) and kallisto (gRNA)
Library strategy: CRISPR Screen

molecule: other

source_name: iPSC derived cell

growth_protocol: Transient transcription factor overexpression from stable clonal hiPSCs was used to induce control hiPSCs to iNPCs (here SNaPs), GLUTs, and iGABAs. iNPCs are rapidly generated by 48-hour induction with NGN2. iGLUTs are induced via transient overexpression of NGN2, and iGABA neurons are induced via transient overexpression of ASCL1 and DLX2.

extract_protocol:
iNPCs and DIV7 iGLUTs were dissociated in accutase, and DIV21 iGLUTs and DIV36 iGABAs were dissociated with papain, washed with and resuspeded in DMEM/10%FBS, and submitted for single cell RNAseq (10X single cell 5' v2 HT with CRISPR barcode kit) in four lanes per cell type, targeting 20,000 cells per lane for a total of ~80,000 targeted cells per cell type.
Single-cell libraries were prepared (polyA enriched) using the Chromium Next GEM Single Cell 5' Reagent Kits 10xV2 according to the manufacturer’s instructions.gRNA guides were reverse transcribed and amplified using Lentiviral Cas9v2-HygroR specific primers

treatment_protocol: Lentiviral Cas9v2-HygroR and pooled LentiArray-gRNA-PuroR CRISPR-KO library including 29 genes (ARID1B, ASH1L, CHD2, MED13L, NRXN1, PHF21A, SETD5, SIN3A, SMARCC2, BCL11A, CHD8, KDM5B, KDM6B, KMT2C, MBD5, PHF12, SKI, WAC, CREBBP, ASXL3, ANK3, POGZ, SCN2A, SHANK3, SLC6A1, PPP2R5D, FOXP2, DPYSL2) as well as scrambled gRNA were packaged as high-titer lentiviruses were transduced via spinfection three days prior to harvest (e.g., d4 for D7 iGLUTs, d18 for D21 iGLUTs, d33 for d36 iGABA) (MOI 0.3-0.5).

value: iPSC derived cell

value: mature glutamatergic neuron


title: iGLUTs_D21_3182_gRNA_R1

description: Library name: MG28_GDO


title: iGABAs_D36_553_gRNA_R3

description: Library name: MG11_GDO

value: gabaergic neuron


title: iGLUTs_D21_3182_gRNA_R4

description: Library name: MG31_GDO


title: iGLUTs_D21_3182_gRNA_R2

description: Library name: MG29_GDO


title: NC_2

description: Library name: sample2


title: iGABAs_D36_553_gRNA_R4

description: Library name: MG12_GDO


title: iGABAs_D36_553_gRNA_R1

description: Library name: MG9_GDO


title: NPC__3182_gRNA_R4

description: Library name: MG4_GDO

value: Neural progenitor cells


title: iGLUTs_D7_3182_gRNA_R2

description: Library name: MG6_GDO

value: Immature glutamatergic neuron


title: NC_1

description: Library name: sample1


title: iGLUTs_D7_3182_gRNA_R1

description: Library name: MG5_GDO


title: iGLUTs_D7_3182_gRNA_R4

description: Library name: MG8_GDO


title: Cabozantinib_7

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Xenograft model

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Lenvatinib-resistant Hep3B cell line

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Female athymic mice (BALB/c-nu/nu; 8 weeks old; 20–25 g) were provided from Japan SLC Inc. (Shizuoka, Japan). The animals were maintained under Specific pathogen-free conditions were prepared for animals using a laminar air flow rack. Mice freely accessed to food (CLEA Japan, Tokyo, Japan) sterilized by gamma irradiation, and autoclaved water. All procedures were approved by the Institutional Committee on Experimental Animals of Kagawa University, Kagawa, Japan, and were conducted according to the ARRIVE guidelines 2.0. Hep3B-LR cells (2×106 cells per animal) were injected subcutaneously in nude mice. Mice were randomly assigned to a control or treated group, when the shortest diameter of the xenografts grew to an average of 6 mm.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: treated mice (n = 9) were orally fed with 1,200 µg of cabozantinib dissolved in 150 µL of dimethyl sulfoxide (DMSO) five times a week. A week consisted of three days of injection followed by a day off, then two days of injection and a subsequent day off. The control group (n=9) was administered only DMSO.

value: Lenvatinib-resistant Hep3B

value: Treated by Cabozantinib


title: Cabozantinib_8

description: Xenograft model


title: iGABAs_D36_553_gRNA_R2

description: Library name: MG10_GDO


title: iGLUTs_D7_3182_gRNA_R3

description: Library name: MG7_GDO


title: Cabozantinib_4

description: Xenograft model


title: Cabozantinib_2

description: Xenograft model


title: Cabozantinib_6

description: Xenograft model


title: Cabozantinib_3

description: Xenograft model


title: Cabozantinib_9

description: Xenograft model


title: NPC__3182_gRNA_R3

description: Library name: MG3_GDO


title: NPC__3182_gRNA_R1

description: Library name: MG1_GDO


title: Cabozantinib_5

description: Xenograft model


title: Cabozantinib_1

description: Xenograft model


title: NPC__3182_gRNA_R2

description: Library name: MG2_GDO


title: Mock_9

description: Xenograft model


title: iGLUTs_D21_3182_mRNA_R4

description: Library name: MG31_GEX

data_processing:
cDNA was mapped to GRCh38 reference file using CellRanger. gRNA was mapped to gRNA library sequence using kallisto-kite pipeline (see attached feature_sequence file.)
Assembly: GRCh38
Supplementary files format and content: sparse matrix output from CellRanger (cDNA) and kallisto (gRNA)


title: iGLUTs_D21_3182_mRNA_R2

description: Library name: MG29_GEX


title: Mock_8

description: Xenograft model


title: iGLUTs_D21_3182_mRNA_R3

description: Library name: MG30_GEX


title: iGLUTs_D21_3182_mRNA_R1

description: Library name: MG28_GEX


title: Mock_7

description: Xenograft model


title: Mock_6

description: Xenograft model


title: Mock_5

description: Xenograft model


title: non-cancer healthy  donor [Donor O_SH13439_Cell1]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.

hyb_protocol: Hybridized for 17 h at 42 C. Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

treatment_protocol: The whole blood specimens were collected and processed at each institution using red/gray topped gel barrier tubes (Becton Dickinson Vacutainer® SST™ Tubes 367988, Franklin Lakes, NJ). The blood specimens were allowed to clot for 30 - 35 minutes at room temperature. The tubes were then centrifuged at either 4°C or room-temperature at 1,100 – 1,300 g for 10 minutes. After centrifugation, aliquots of 0.5 mL of serum were stored at or below -80 °C within 90 minutes of collection.

tag: Sex

value: female

tag: age

tag: category

value: NonCancer Healthy


title: iGLUTs_D7_3182_mRNA_R2

description: Library name: MG6_GEX


title: iGLUTs_D7_3182_mRNA_R3

description: Library name: MG7_GEX


title: iGABAs_D36_553_mRNA_R4

description: Library name: MG12_GEX


title: iGABAs_D36_553_mRNA_R3

description: Library name: MG11_GEX


title: NPC__3182_mRNA_R4

description: Library name: MG4_GEX


title: non-cancer healthy  donor [Donor O_SH13434_Cell2]


title: Mock_4

description: Xenograft model


title: iGLUTs_D7_3182_mRNA_R4

description: Library name: MG8_GEX


title: Mock_3

description: Xenograft model


title: non-cancer healthy  donor [Donor O_SH13437_Cell3]


title: non-cancer healthy  donor [Donor O_SH13436_Cell4]


title: iGLUTs_D7_3182_mRNA_R1

description: Library name: MG5_GEX


title: Mock_2

description: Xenograft model


title: iGABAs_D36_553_mRNA_R2

description: Library name: MG10_GEX


title: NPC__3182_mRNA_R1

description: Library name: MG1_GEX


title: non-cancer healthy  donor [Donor O_SH13433_Cell3]


title: non-cancer healthy  donor [Donor O_SH13439_Cell4]


title: NC1

city: Wenzhou

first: Xiulan

last: Lou

address: Chashan

institute: Wenzhou Medical University

description:
Library name: NC1
NC1:fpkm

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing
Assembly: GRCh38
Supplementary files format and content: csv files include Reads count for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: CELL LINE

extract_protocol:
Total RNA was extracted HEL cell line using the FastPureComplex Tissue/Cell Total RNA Isolation Kit (Vazyme, Nanjing, China).According to the manufacturer’s instructions. The concentration and purity of the isolated RNA were assessed using a NanoDrop spectrophotometer
RNA-seq libraries were prepared using the poly(A) mRNA enrichment method.

value: CELL LINE

value: HEL

value: AML CELL


title: NC4

description:
Library name: NC4
NC4:fpkm


title: NPC__3182_mRNA_R3

description: Library name: MG3_GEX


title: NC3

description:
Library name: NC3
NC3:fpkm


title: Mock_1

description: Xenograft model

value: Control


title: NPC__3182_mRNA_R2

description: Library name: MG2_GEX


title: non-cancer healthy  donor [Donor N_SH13437_Cell1]


title: F12_4

description:
Library name: F12_4
F12_4:fpkm


title: non-cancer healthy  donor [Donor M_SH13432_Cell3]


title: non-cancer healthy  donor [Donor N_SH13431_Cell4]


title: non-cancer healthy  donor [Donor N_SH13435_Cell1]


title: NC2

description:
Library name: NC2
NC2:fpkm


title: non-cancer healthy  donor [Donor M_SH13437_Cell2]


title: non-cancer healthy  donor [Donor N_SH13438_Cell3]


title: F12_2

description:
Library name: F12_2
F12_2:fpkm


title: non-cancer healthy  donor [Donor N_SH13434_Cell3]


title: F12_1

description:
Library name: F12_1
F12_1:fpkm


title: non-cancer healthy  donor [Donor N_SH13439_Cell3]


title: RNA-seq of XNM_ctrl6

description:
Library name: XNM_ctrl6
XNM_ctrl6:fpkm

source_name: BM

value: BM

value: Primary cells

value: Mononuclear cells


title: non-cancer healthy  donor [Donor M_SH13433_Cell2]


title: non-cancer healthy  donor [Donor L_SH13438_Cell4]


title: RNA-seq of CML_ctrl9

description:
Library name: CML_ctrl9
CML_ctrl9:fpkm


title: non-cancer healthy  donor [Donor M_SH13432_Cell2]


title: RNA-seq of JZL_ctrl4

description:
Library name: JZL_ctrl4
JZL_ctrl4:fpkm


title: F12_3

description:
Library name: F12_3
F12_3:fpkm


title: non-cancer healthy  donor [Donor L_SH13431_Cell3]


title: RNA-seq of AML3_XBZ

description:
Library name: AML3_XBZ
AML3_XBZ:fpkm


title: non-cancer healthy  donor [Donor M_SH13432_Cell1]


title: iGABAs_D36_553_mRNA_R1

description: Library name: MG9_GEX


title: non-cancer healthy  donor [Donor K_SH13439_Cell2]


title: non-cancer healthy  donor [Donor M_SH13438_Cell2]


title: RNA-seq of CJH_ctrl1

description:
Library name: CJH_ctrl1
CJH_ctrl1:fpkm


title: RNA-seq of AML12_CRD

description:
Library name: AML12_CRD
AML12_CRD:fpkm


title: Patient 27-05_ADT timepoint T04 replicate 1 scRNAseq

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

description:
Library name: 27-05_ADT rep1
antibody-derived oligonucleotide

data_processing:
CellRanger version 3.1.0 (10x Genomics) was used to align the raw sequencing data and to generate count matrices (gene expression and ADT barcode counts). The ADT library sequences were aligned to a customized reference genome provided by BD containing the oligonucleotide sequences corresponding to each antibody.
Pre-processing of aligned sequencing data and identification of single nucleotide polymorphisms was performed using the Genome Analysis Toolkit (McKenna et al., 2010). We used demuxlet (Kang et al., 2018) (https://github.com/statgen/demuxlet) for sample deconvolution of multiplexed PBMC samples.
Further processing was done with Scanpy v1.4.6 (concatenation of samples, filtering for high quality cells, normalization, batch correction, clustering, annotation, and differential gene expression analysis). The .h5ad files are demultiplexed, concatenated, filtered, and annotated, but otherwise represent raw data prior to all processing steps.
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: Cell Ranger output filtered matrix files for both scRNA-seq libraries and CITE-seq (feature barcoding) libraries: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.
Library strategy: CITE-seq

molecule: protein

source_name: Biliary tract cancer (BTC)

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were obtained from patients with biliary tract cancer as part of a Phase II trial of pembrolizumab and GM-CSF. Blood samples were processed using ficoll; after centrifugation, the PBMC layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered human serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. Samples were then incubated for DNAse I before washing and counting. 1 x10>6 cells from 16 unique samples were combined and stained with one pooled cocktail containing 99 AbSeq antibody-oligonucleotide conjugates (BD Biosciences) per standard protocols (Olvera JG et al., 2018), following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution). Samples from different individuals and timepoints were randomly mixed across experiments to minimize batch and confounding effects.
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3, according to manufacturer instructions. For preparation of ADT libraries, we followed the standard protocol available from Olvera JG et al., 2018 following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution, Biolegend). Briefly, cell suspensions were combined with master mix and loaded into the chip with gel beads to generate the gel bead-in-emulsion (GEM), which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Reverse transcription was performed on the poly-A RNA within each GEM. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. To prepare libraries from cDNA, SPRIselect beads were used to isolate the correct size fragments. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added during library construction.

value: Biliary tract cancer (BTC)

value: peripheral blood mononuclear cells (PBMCs)

value: GM-CSF and pembrolizumab

tag: library type

value: ADT

tag: time


title: Patient 27-01_ADT timepoint T01 scRNAseq

description:
Library name: 27-01_ADT
antibody-derived oligonucleotide

tag: tissue


title: non-cancer healthy  donor [Donor L_SH13436_Cell1]


title: Patient 27-05_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 27-05_ADT rep2
antibody-derived oligonucleotide

tag: cell type


title: non-cancer healthy  donor [Donor L_SH13438_Cell1]


title: non-cancer healthy  donor [Donor L_SH13431_Cell2]


title: Patient 26-04_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 26-04_ADT rep2
antibody-derived oligonucleotide


title: non-cancer healthy  donor [Donor K_SH13431_Cell1]


title: Patient 26-04_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 26-04_ADT rep1
antibody-derived oligonucleotide


title: x4 replicate_3 [Be_SH11M52_Cell3]

source_name: serum

value: mixture

value: BreastBenign


title: non-cancer healthy  donor [Donor L_SH13433_Cell4]


title: Patient 26-03_ADT timepoint T03 scRNAseq

description:
Library name: 26-03_ADT
antibody-derived oligonucleotide


title: non-cancer healthy  donor [Donor K_SH13436_Cell2]


title: x1 replicate_3 [Be_SH11M52_Cell1]


title: Patient 25-06_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 25-06_ADT rep1
antibody-derived oligonucleotide


title: RNA-seq of AML6_CHF

description:
Library name: AML6_CHF
AML6_CHF:fpkm

tag: cell line


title: RNA-seq of ZBY_ctrl8

description:
Library name: ZBY_ctrl8
ZBY_ctrl8:fpkm


title: Patient 27-02_ADT timepoint T02 scRNAseq

description:
Library name: 27-02_ADT
antibody-derived oligonucleotide

tag: treatment


title: Patient 27-03_ADT timepoint T03 scRNAseq

description:
Library name: 27-03_ADT
antibody-derived oligonucleotide


title: Patient 25-04_ADT timepoint T02 scRNAseq

description:
Library name: 25-04_ADT
antibody-derived oligonucleotide


title: x8 replicate_1 [Be_SH11M50_Cell4]


title: Patient 26-02_ADT timepoint T02 scRNAseq

description:
Library name: 26-02_ADT
antibody-derived oligonucleotide


title: x8 replicate_3 [Be_SH11M52_Cell4]


title: Patient 24-05_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 24-05_ADT rep1
antibody-derived oligonucleotide


title: Patient 26-01_ADT timepoint T01 scRNAseq

description:
Library name: 26-01_ADT
antibody-derived oligonucleotide


title: x2 replicate_1 [Be_SH11M50_Cell2]


title: non-cancer healthy  donor [Donor K_SH13434_Cell1]


title: x2 replicate_2 [Be_SH11M51_Cell2]


title: x4 replicate_1 [Be_SH11M50_Cell3]


title: x2 replicate_3 [Be_SH11M52_Cell2]


title: non-cancer healthy  donor [Donor K_SH13432_Cell4]


title: Patient 25-06_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 25-06_ADT rep2
antibody-derived oligonucleotide


title: non-cancer healthy  donor [Donor K_SH13435_Cell3]


title: Patient 24-03_ADT timepoint T02 scRNAseq

description:
Library name: 24-03_ADT
antibody-derived oligonucleotide


title: x8 replicate_3 [BC_SH11M48_Cell4]

value: BreastCancer


title: x8 replicate_2 [Be_SH11M51_Cell4]


title: x4 replicate_2 [Be_SH11M51_Cell3]


title: Patient 23-05_ADT timepoint T04 scRNAseq

description:
Library name: 23-05_ADT
antibody-derived oligonucleotide


title: x2 replicate_3 [BC_SH11M48_Cell2]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: Patient 25-06_ADT timepoint T03 scRNAseq

description:
Library name: 25-05_ADT
antibody-derived oligonucleotide


title: Patient 25-03_ADT timepoint T01 scRNAseq

description:
Library name: 25-03_ADT
antibody-derived oligonucleotide


title: Patient 24-05_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 24-05_ADT rep2
antibody-derived oligonucleotide


title: x1 replicate_2 [BC_SH11M45_Cell1]


title: Patient 22-05_ADT timepoint T04 scRNAseq

description:
Library name: 22-05_ADT
antibody-derived oligonucleotide


title: Patient 22-04_ADT timepoint T03 scRNAseq

description:
Library name: 22-04_ADT
antibody-derived oligonucleotide


title: x1 replicate_2 [Be_SH11M51_Cell1]


title: Patient 24-02_ADT timepoint T01 scRNAseq

description:
Library name: 24-02_ADT
antibody-derived oligonucleotide


title: x2 replicate_2 [BC_SH11M45_Cell2]


title: x2 replicate_1 [BC_SH11M44_Cell2]


title: x8 replicate_2 [BC_SH11M45_Cell4]


title: Patient 22-02_ADT timepoint T01 replicate 1 scRNAseq

description:
Library name: 22-02_ADT rep1
antibody-derived oligonucleotide


title: x1 replicate_1 [BC_SH11M44_Cell1]


title: Patient 23-04_ADT timepoint T03 scRNAseq

description:
Library name: 23-04_ADT
antibody-derived oligonucleotide


title: x1 replicate_3 [BC_SH11M48_Cell1]


title: x1 replicate_1 [Be_SH11M50_Cell1]


title: Patient 23-03_ADT timepoint T02 scRNAseq

description:
Library name: 23-03_ADT
antibody-derived oligonucleotide


title: Patient 21-04_ADT timepoint T03 scRNAseq

description:
Library name: 21-04_ADT
antibody-derived oligonucleotide


title: x4 replicate_3 [BC_SH11M48_Cell3]


title: Patient 23-02_ADT timepoint T01 replicate 2 scRNAseq

description:
Library name: 23-02_ADT rep2
antibody-derived oligonucleotide


title: Patient 22-03_ADT timepoint T02 scRNAseq

description:
Library name: 22-03_ADT
antibody-derived oligonucleotide


title: Patient 24-04_ADT timepoint T03 scRNAseq

description:
Library name: 24-04_ADT
antibody-derived oligonucleotide


title: x4 replicate_2 [BC_SH11M45_Cell3]


title: Patient 23-02_ADT timepoint T01 replicate 1 scRNAseq

description:
Library name: 23-02_ADT rep1
antibody-derived oligonucleotide


title: Patient 22-02_ADT timepoint T01 replicate 2 scRNAseq

description:
Library name: 22-02_ADT rep2
antibody-derived oligonucleotide


title: Patient 20-05_ADT timepoint T04 scRNAseq

description:
Library name: 20-05_ADT
antibody-derived oligonucleotide


title: x4 replicate_1 [BC_SH11M44_Cell3]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: x8 replicate_1 [BC_SH11M44_Cell4]


title: Patient 20-03_ADT timepoint T02 scRNAseq

description:
Library name: 20-03_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 262_SH11R08_Cell3]

value: Test


title: Patient 21-02_ADT timepoint T01 scRNAseq

description:
Library name: 21-02_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 265_SH0ZE21_Cell2]

value: female


title: Breast Cancer [Patient 263_SH0ZH01_Cell2]


title: Patient 20-02_ADT timepoint T01 replicate 2 scRNAseq

description:
Library name: 20-02_ADT rep2
antibody-derived oligonucleotide


title: Patient 20-02_ADT timepoint T01 replicate 1 scRNAseq

description:
Library name: 20-02_ADT rep1
antibody-derived oligonucleotide


title: Breast Cancer [Patient 261_SH06Y49_Cell4]


title: Patient 19-05_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 19-05_ADT rep2
antibody-derived oligonucleotide


title: Breast Cancer [Patient 258_SH08L25_Cell1]


title: Patient 19-04_ADT timepoint T03 scRNAseq

description:
Library name: 19-04_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 264_SH0ZE33_Cell1]


title: Breast Cancer [Patient 256_SH0ZE30_Cell1]


title: Breast Cancer [Patient 260_SH0ZE30_Cell4]


title: Patient 18-03_ADT timepoint T03 scRNAseq

description:
Library name: 18-03_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 253_SH06Y51_Cell3]


title: Breast Cancer [Patient 254_SH08L16_Cell3]


title: Breast Cancer [Patient 251_SH06Y53_Cell4]


title: Patient 17-04_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 17-04_ADT rep2
antibody-derived oligonucleotide


title: Breast Cancer [Patient 257_SH06Y39_Cell4]


title: Breast Cancer [Patient 249_SH09X56_Cell1]


title: Patient 19-02_ADT timepoint T01 scRNAseq

description:
Library name: 19-02_ADT
antibody-derived oligonucleotide


title: Patient 17-02_ADT timepoint T02 scRNAseq

description:
Library name: 17-02_ADT
antibody-derived oligonucleotide


title: Patient 19-03_ADT timepoint T02 replicate 1 scRNAseq

description:
Library name: 19-03_ADT rep1
antibody-derived oligonucleotide


title: Patient 17-03_ADT timepoint T03 scRNAseq

description:
Library name: 17-03_ADT
antibody-derived oligonucleotide


title: Patient 19-03_ADT timepoint T02 replicate 2 scRNAseq

description:
Library name: 19-03_ADT rep2
antibody-derived oligonucleotide


title: Patient 18-01_ADT timepoint T01 scRNAseq

description:
Library name: 18-01_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 259_SH0ZE32_Cell4]


title: Breast Cancer [Patient 252_SH08L44_Cell3]


title: Patient 19-05_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 19-05_ADT rep1
antibody-derived oligonucleotide


title: Patient 18-02_ADT timepoint T02 scRNAseq

description:
Library name: 18-02_ADT
antibody-derived oligonucleotide


title: Patient 16-04_ADT timepoint T03 replicate 2 scRNAseq

description:
Library name: 16-04_ADT rep2
antibody-derived oligonucleotide


title: Patient 17-01_ADT timepoint T01 scRNAseq

description:
Library name: 17-01_ADT
antibody-derived oligonucleotide


title: Patient 17-04_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 17-04_ADT rep1
antibody-derived oligonucleotide


title: Patient 16-05_ADT timepoint T04 scRNAseq

description:
Library name: 16-05_ADT
antibody-derived oligonucleotide


title: Patient 16-04_ADT timepoint T03 replicate 1 scRNAseq

description:
Library name: 16-04_ADT rep1
antibody-derived oligonucleotide


title: Patient 16-03_ADT timepoint T02 scRNAseq

description:
Library name: 16-03_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 250_SH09X48_Cell4]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: Breast Cancer [Patient 242_SH0ZE29_Cell2]


title: Breast Cancer [Patient 243_SH08L37_Cell4]


title: Breast Cancer [Patient 245_SH0ZH01_Cell4]


title: Breast Cancer [Patient 255_SH11R01_Cell4]


title: Patient 15-05_ADT timepoint T04 scRNAseq

description:
Library name: 15-05_ADT
antibody-derived oligonucleotide


title: Breast Cancer [Patient 248_SH06Y35_Cell1]


title: Breast Cancer [Patient 247_SH0ZE12_Cell2]


title: Breast Benign Disease [Patient 239_SH08L18_Cell4]


title: Patient 15-04_ADT timepoint T03 replicate 1 scRNAseq

description:
Library name: 15-04_ADT rep1
antibody-derived oligonucleotide


title: Patient 15-03_ADT timepoint T02 scRNAseq

description:
Library name: 15-03_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 238_SH0ZE12_Cell1]


title: Breast Benign Disease [Patient 237_SH0ZE29_Cell4]


title: Patient 16-02_ADT timepoint T01 scRNAseq

description:
Library name: 16-02_ADT
antibody-derived oligonucleotide


title: Patient 14-04_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 14-04_ADT rep1
antibody-derived oligonucleotide


title: Patient 14-04_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 14-04_ADT rep2
antibody-derived oligonucleotide


title: Breast Cancer [Patient 246_SH06854_Cell2]


title: Patient 15-02_ADT timepoint T01 scRNAseq

description:
Library name: 15-02_ADT
antibody-derived oligonucleotide


title: Patient 14-01_ADT timepoint T01 scRNAseq

description:
Library name: 14-01_ADT
antibody-derived oligonucleotide


title: Patient 15-04_ADT timepoint T03 replicate 2 scRNAseq

description:
Library name: 15-04_ADT rep2
antibody-derived oligonucleotide


title: Breast Cancer [Patient 244_SH06Y52_Cell1]


title: Breast Benign Disease [Patient 241_SH0ZE10_Cell1]


title: Breast Benign Disease [Patient 232_SH06Y38_Cell1]


title: Patient 13-04_ADT timepoint T03 scRNAseq

description:
Library name: 13-04_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 235_SH06Y34_Cell3]


title: Breast Benign Disease [Patient 229_SH08L23_Cell4]


title: Breast Benign Disease [Patient 230_SH06Y51_Cell4]


title: Patient 13-02_ADT timepoint T01 scRNAseq

description:
Library name: 13-02_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 231_SH08L28_Cell3]


title: Breast Benign Disease [Patient 234_SH08L39_Cell1]


title: Patient 13-05_ADT timepoint T04 scRNAseq

description:
Library name: 13-05_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 236_SH08L24_Cell3]


title: Breast Benign Disease [Patient 228_SH08L24_Cell4]


title: Breast Benign Disease [Patient 240_SH11R06_Cell3]


title: Patient 11-06_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 11-06_ADT rep2
antibody-derived oligonucleotide


title: Patient 14-03_ADT timepoint T03 scRNAseq

description:
Library name: 14-03_ADT
antibody-derived oligonucleotide


title: Patient 14-02_ADT timepoint T02 scRNAseq

description:
Library name: 14-02_ADT
antibody-derived oligonucleotide


title: Patient 11-03_ADT timepoint T02 scRNAseq

description:
Library name: 11-03_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 233_SH08L27_Cell4]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: Breast Benign Disease [Patient 221_SH0ZE14_Cell4]


title: Breast Benign Disease [Patient 224_SH05T42_Cell3]


title: Breast Benign Disease [Patient 225_SH06Y29_Cell3]


title: Breast Benign Disease [Patient 219_SH08L41_Cell2]


title: Patient 12-05_ADT timepoint T04 scRNAseq

description:
Library name: 12-05_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 227_SH0ZE16_Cell2]


title: Patient 12-02_ADT timepoint T02 scRNAseq

description:
Library name: 12-02_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 226_SH06902_Cell2]


title: Breast Benign Disease [Patient 222_SH08L27_Cell3]


title: Patient 12-01_ADT timepoint T01 scRNAseq

description:
Library name: 12-01_ADT
antibody-derived oligonucleotide


title: Patient 13-03_ADT timepoint T02 scRNAseq

description:
Library name: 13-03_ADT
antibody-derived oligonucleotide


title: Patient 10-06_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 10-06_ADT rep1
antibody-derived oligonucleotide


title: Patient 10-06_ADT timepoint T04 replicate 2 scRNAseq

description:
Library name: 10-06_ADT rep2
antibody-derived oligonucleotide


title: Patient 11-06_ADT timepoint T04 replicate 1 scRNAseq

description:
Library name: 11-06_ADT rep1
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 218_SH06F24_Cell2]


title: Patient 11-05_ADT timepoint T03 scRNAseq

description:
Library name: 11-05_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 220_SH08L34_Cell3]


title: Patient 11-02_ADT timepoint T01 scRNAseq

description:
Library name: 11-02_ADT
antibody-derived oligonucleotide


title: Patient 12-04_ADT timepoint T03 scRNAseq

description:
Library name: 12-04_ADT
antibody-derived oligonucleotide


title: Patient 27-05_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 27-05_GEX rep2
polyA RNA

value: mRNA


title: Breast Benign Disease [Patient 213_SH06910_Cell3]


title: Breast Benign Disease [Patient 223_SH08L49_Cell2]


title: Breast Benign Disease [Patient 212_SH06Y56_Cell4]


title: Breast Benign Disease [Patient 211_SH08L13_Cell1]


title: Breast Benign Disease [Patient 215_SH06Y54_Cell1]


title: Patient 27-02_GEX timepoint T02 scRNAseq

description:
Library name: 27-02_GEX
polyA RNA


title: Patient 10-05_ADT timepoint T03 scRNAseq

description:
Library name: 10-05_ADT
antibody-derived oligonucleotide


title: Patient 27-01_GEX timepoint T01 scRNAseq

description:
Library name: 27-01_GEX
polyA RNA


title: Breast Benign Disease [Patient 209_SH08L39_Cell3]


title: Breast Benign Disease [Patient 210_SH08L44_Cell1]


title: Breast Benign Disease [Patient 208_SH08L25_Cell4]


title: Patient 10-03_ADT timepoint T02 replicate 2 scRNAseq

description:
Library name: 10-03_ADT rep2
antibody-derived oligonucleotide


title: Patient 27-05_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 27-05_GEX rep1
polyA RNA


title: Breast Benign Disease [Patient 205_SH05T50_Cell3]


title: Patient 27-03_GEX timepoint T03 scRNAseq

description:
Library name: 27-03_GEX
polyA RNA


title: Patient 10-02_ADT timepoint T01 scRNAseq

description:
Library name: 10-02_ADT
antibody-derived oligonucleotide


title: Breast Benign Disease [Patient 216_SH09X60_Cell3]


title: Patient 10-03_ADT timepoint T02 replicate 1 scRNAseq

description:
Library name: 10-03_ADT rep1
antibody-derived oligonucleotide


title: Patient 26-04_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 26-04_GEX rep2
polyA RNA


title: Breast Benign Disease [Patient 214_SH0ZE27_Cell2]


title: Patient 26-04_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 26-04_GEX rep1
polyA RNA


title: Patient 26-02_GEX timepoint T02 scRNAseq

description:
Library name: 26-02_GEX
polyA RNA


title: Breast Benign Disease [Patient 217_SH09X59_Cell1]


title: Patient 26-01_GEX timepoint T01 scRNAseq

description:
Library name: 26-01_GEX
polyA RNA


title: Breast Benign Disease [Patient 206_SH09X59_Cell3]


title: Patient 25-06_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 25-06_GEX rep1
polyA RNA


title: Breast Benign Disease [Patient 202_SH06849_Cell3]


title: Breast Benign Disease [Patient 207_SH0ZE28_Cell2]


title: Patient 26-03_GEX timepoint T03 scRNAseq

description:
Library name: 26-03_GEX
polyA RNA


title: Breast Benign Disease [Patient 204_SH0ZE10_Cell3]


title: Breast Benign Disease [Patient 195_SH05T42_Cell2]


title: Breast Benign Disease [Patient 201_SH0ZE18_Cell4]


title: Patient 25-06_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 25-06_GEX rep2
polyA RNA


title: Patient 25-04_GEX timepoint T02 scRNAseq

description:
Library name: 25-04_GEX
polyA RNA


title: Patient 25-06_GEX timepoint T03 scRNAseq

description:
Library name: 25-05_GEX
polyA RNA


title: Patient 24-05_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 24-05_GEX rep1
polyA RNA


title: Breast Benign Disease [Patient 192_SH08L45_Cell4]


title: Breast Benign Disease [Patient 193_SH08L24_Cell1]


title: Patient 25-03_GEX timepoint T01 scRNAseq

description:
Library name: 25-03_GEX
polyA RNA


title: Breast Benign Disease [Patient 191_SH11R18_Cell3]


title: Patient 24-03_GEX timepoint T02 scRNAseq

description:
Library name: 24-03_GEX
polyA RNA


title: Breast Benign Disease [Patient 200_SH09X53_Cell4]


title: Patient 24-05_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 24-05_GEX rep2
polyA RNA


title: Breast Benign Disease [Patient 196_SH06Y49_Cell3]


title: Patient 24-04_GEX timepoint T03 scRNAseq

description:
Library name: 24-04_GEX
polyA RNA


title: Patient 24-02_GEX timepoint T01 scRNAseq

description:
Library name: 24-02_GEX
polyA RNA


title: Patient 23-05_GEX timepoint T04 scRNAseq

description:
Library name: 23-05_GEX
polyA RNA