title: DES-MMSC RNAseq

data_processing:
Reads were mapped to the UCSC rat reference genome rn6 using HISAT2.
featureCounts was used to evaluate gene expression level as read counts
edgeR was used to determine significantly changed genes, with significance achieved for fdr<0.05
Genome_build: rn6
Supplementary_files_format_and_content: Gene expression expressed as read counts, in a comma-separated variable format

growth_protocol: Eker rat MMSCs were growth in cell culture plates coated with attachment factor protein. Cells were grown in regular SMBM medium. The cells were maintained at 370C in an incubator in a humidified atmosphere at 2% hypoxia.

extract_protocol: The RNeasy RNA isolation kit (Qiagen, Valencia, CA) was used to isolated RNA for RNA-seq analysis

treatment_protocol: DES-MMSC and VEH-MMSC were prepared  in 5 month adult Eker rats myometrium PND 10-12  exposed to DES or VEH respectively. FACS was used to isolate MMSC using Stro-1/CD44 antibodies


title: IonXpress_020-D-26_2hr_con

status: Public on Aug 07 2023

type: SRA

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

country: USA

institute: Ohio State University

library_source: transcriptomic

data_processing:
Torrent Suite Software v 5.2 was used for basecalling, alignment, and mapping validated reads to HG19 transcriptome and AmpliSeq specific bed files.
TMAP: The Torrent Mapping Alignment Program for Ion Torrent Data provides a fast and accurate aligner through the integration of a novel alignment algorithm and three popular algorithms:BWA-short(Li and Durbin, 2009),BWA-long(Li and Durbin, 2010), SSAHA(Ning et al, 2001)
BaseCaller steps include: Remove low-quality reads. From the signal values, create the sequence of bases. Estimate the base quality value for each base. Assign each read to a barcode. Trim the barcode sequence away. Trim extra bases at the 5' end. Filter out reads that are too short.  Filter out reads that do not have the correct library key. Trim the P1 adapter (at the 3' end). Perform quality trimming.
The Torrent Suite software generates counts per transcript as well as normalized reads per million (RPM)
Additional processing using EdgeR and Qiagen Integrated Pathway Analysis (IPA)
Genome_build: Hg19
Supplementary_files_format_and_content: Super-maximal Exact Matching (Li 2012)

molecule: total RNA

organism: Homo sapiens

source_name: Human alveolar macrophages

growth_protocol: Alveolar macropahges (AMs) were adhered in either a 24-well plate (1.5x105 cells/well) or 96-well plate (5x104 cells/well) in RPMI containing 10% human AB serum and Penicillin G (10,000 U/ml) for 2h. Then, medium was replaced and incubations continued until 24 and 72h to collect culture supernatants and TRIzol-lysed cells to repeat protein and RNA analysis, respectively

extract_protocol:
Cells were lysed in Trizol. Ethanol was added to the Trizol lysate and the mix was applied to Directzol columns (Zymo Research). Colums were washed and RNA eluted per manufacturer instructions.
The AmpliSeq human transcriptome gene expression kit was used to prepare libraries covering 20,803 human transcripts, including coding and non-coding RNA. cDNA was synthesized from 10 ng of total RNA. Targeted amplification, digestion, adapter ligation and cleanup was per protocol. Libraries were quantified withqPCR.

treatment_protocol: Adhered AMs after 2h were infected with luminescence-producing M.tb strain (M.tb-Lux) and the cellular uptake, adaptation, and intracellular growth of M.tb were assessed as relative luminescence units (RLUs) at 2, 24, 48, and 72h using a multiwell plate reader Glomax. For technical reasons, AM uptake and growth assays from donors 1-16 were incubated in 24 well plates, while AMs from donors 17-28 were incubated in 96 well plates.

tag: time point

tag: sample group

value: Control

tag: cell type

value: Human alveolar macrophages


title: VEH-MMSC RNAseq

city: Chicago

first: Qiwei

last: Yang

address: 909 S. Wolcott Ave

department: Surgery

institute: University of Illinois at Chicago

organism: Rattus norvegicus

source_name: myometrial stem cells from myometrium of  5 month Eker Rats exposed to VEH

value: Myometrial stem cells

tag: treatment

value: VEH


title: S2_D1_2AM

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were trimmed out from the raw sequencing data by tool Trimmomatic.
Surviving reads were then aligned to human reference genome hg38 by STAR aligner. Gene counts were quantified by STAR --quantMode GeneCounts function.
Assembly: hg38
Supplementary files format and content: Tab file for gene counts

molecule: polyA RNA

source_name: Blood

extract_protocol:
Blood samples were then collected every two hours for 48 hours (total 24 samples). Blood was then immediately processed in the Center for Human Integrative Physiology. Blood was centrifuged (1900 RCF x 10 min) and the buffy coats were collected and immediately snap frozen in liquid nitrogen for storage at -80C.
Illumina prep kit

tag: tissue

value: Blood

tag: gender

value: Male

tag: subject

value: 18 hr


title: IonXpress_002-D-23_2hr_con


title: CM_Pep_3D-1

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Calculated manually based on the method in the following paper. (Lee, J., Jang, H., Kang, W. H., & Yeom, S. I. (2023). Transcriptome analysis of pepper-phytophthora infestans interaction based on a pipeline of a simplified and effective RNA-seq analysis (PoRAS).)
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of FPKM/RPKM for each sample

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves

tag: genotype

value: WT

value: PepMoV

tag: timepoint


title: IonXpress_019-D-26_2hr_Mtb

value: Mtb-infected cells


title: DES-MMSC H3K4me4

library_source: genomic

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the rat genome build UCSC rn6 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Genome_build: rn6
Supplementary_files_format_and_content: ChIP-Seq tracks represented signal normalized to reads per million mapped in TDF format

molecule: genomic DNA

source_name: myometrial stem cells from myometrium of  5 month Eker Rats exposed to DES

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

tag: chip antibody

value: DES


title: VEH-MMSC H3K4me3


title: IonXpress_018-D-25_72hr_con


title: S2_D1_12AM

value: 16 hr


title: CM_Pep_2D-3


title: VEH-MMSC input


title: IonXpress_017-D-25_72hr_Mtb


title: CM_Pep_2D-2


title: DES-MMSC input


title: S1_D2_6PM

value: 34 hr


title: IonXpress_016-D-25_24hr_con


title: CM_Pep_2D-1


title: CM-PC-TDW-12h-2


title: CM_Pep_1D-3


title: se-1_mRNA_rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

data_processing:
PCR duplicates were removed using fastuniq (52). Adapters were trimmed and the 9-nt random sequences were clipped from the 5’ ends using trim galore (0.6.7)
Clean RNA reads were mapped to the Arabidopsis genome (TAIR10 version) using STAR (2.7.2b)
The expression level of each gene was normalized to fragments per kilobase of transcript per million mapped reads using Cuffnorm. P value was calculated using Cuffdiff
All scripts used for data analysis were uploaded to https://github.com/Chipeyown/cyp71_analysis.
Assembly: Arabidopsis TAIR10
Supplementary files format and content: txt text format. Column1 is the gene id; column2 is the FPKM value of the gene.

organism: Arabidopsis thaliana

source_name: 2-week-old seedling

growth_protocol: All plants were grown under long photoperiod conditions (16 h light, 22 °C/8 h dark, 18 °C). Two-week-old seedlings were collected for mRNA isolation.

extract_protocol:
Total RNA was purified from 2-week-old seedlings using TRIzol. mRNAs were enriched using VAHTS mRNA Capture Beads (Vazyme, N401)
Enriched RNAs were fragmented to 200-300 bp by incubating with 1 × Frag/Prime Buffer for 5 min at 94°C. Fragmented RNAs were used for first strand synthesis, followed by second strand synthesis. Double stranded cDNAs were end-repaired and ligated to adapters. Ligated products were purified and sorted with VAHTS DNA Clean Beads (Vazyme, N411). Purified products were amplified for 12-15 cycles and the PCR products were cleaned by Agencourt AMPure XP beads (Beckman Coulter, A63881). Samples were barcoded and subjected to Illumina sequencing by Annoroad Biotech (Beijing).

value: 2-week-old seedling


title: se-1_mRNA_rep2


title: IonXpress_015-D-25_24hr_Mtb


title: CM_Pep_1D-2


title: S2_D1_4AM

value: 20 hr


title: CM_Pep_3D-2


title: CM_Pep_1D-1


title: IonXpress_014-D-25_2hr_con


title: S1_D2_2PM

value: 30 hr


title: S1_D2_12PM

value: 28 hr


title: se-1_mRNA_rep1


title: IonXpress_013-D-25_2hr_Mtb

value: Human alveolar macrophages


title: cyp71-3_mRNA_rep3


title: S1_D2_10PM

value: 38 hr


title: S1_D2_8PM

value: 36 hr


title: cyp71-3_mRNA_rep2


title: IonXpress_012-D-24_72hr_con

value: Control


title: CM_Pep_4h-3


title: CM_Pep_4h-2


title: IonXpress_010-D-24_24hr_con


title: S1_D2_8AM

value: Blood

value: Male

value: 24 hr


title: CM_Pep_4h-1

value: Leaves

value: WT


title: Col-0_mRNA_rep3


title: cyp71-3_mRNA_rep1


title: S1_D2_4PM

value: 32 hr


title: Col-0_mRNA_rep2


title: S1_D2_4AM

value: 44 hr


title: IonXpress_009-D-20-24hr_inf

value: Mtb-infected cells


title: IonXpress_001-D-23_2hr_Mtb


title: CM_Pep_30m-2

value: PepMoV


title: S1_D2_2AM

value: 42 hr


title: CM_Pep_30m-3


title: Col-0_mRNA_rep1

value: 2-week-old seedling


title: IonXpress_011-D-24_72hr_Mtb


title: IonXpress_008-D-20-2hr_con


title: CM_Pep_30m-1


title: S1_D2_10AM

value: 26 hr


title: S1_D2_12AM

value: 40 hr


title: Zebrafish_PrP_BMD5/50 [PrP_BMD5_50_3]

city: Seoul

first: Cong

middle: Minh

last: Tran

address: 232 Goneung-ro, Nowon-gu

country: South Africa

institute: Seoul National University of Science and Technology

data_processing:
Filtered reads, quality (>20) and length (>50), were aligned to the Ensembl reference genome on Danio_rerio (GCA_000002035.4).
Assembly: GCA_000002035.4
Supplementary files format and content: RPKM, TPM values

organism: Danio rerio

source_name: Whole body

extract_protocol:
The RNA extraction was conducted with RNAzol® reagent (Molecular Research Center Inc., Cincinnati, OH, USA), and appropriate amounts (>200 ng) of RNA were obtained.
A KAPA Library Quantification Kit was used to quantify the sequencing library

tag: strain

value: AB (wild type)

value: Whole body

tag: developmental stage

value: 120 hpf


title: S1_D1_10PM

value: 14 hr


title: CM-P0-3D-3


title: S1_D2_6AM

value: Blood

value: 46 hr


title: Zebrafish_PrP_BMD5/50 [PrP_BMD5_50_1]


title: CM-P0-3D-1


title: Zebrafish_PrP_BMD5/50 [PrP_BMD5_50_2]


title: IonXpress_005-D-19-72hr_inf

value: Human alveolar macrophages


title: IonXpress_006-D-19-72hr_con

value: Control


title: S1_D1_8PM

value: Male

value: 12 hr


title: CM-P0-2D-3

value: Leaves

value: WT


title: IonXpress_004-D-19-24hr_con


title: S1_D1_6PM

value: 10 hr


title: Zebrafish_PrP_BMD5/10 [PrP_BMD5_10_3]


title: Zebrafish_PrP_BMD5/10 [PrP_BMD5_10_2]


title: S1_D1_4PM

value: 8 hr


title: S1_D1_2PM

value: 6 hr


title: CM-P0-2D-2


title: Zebrafish_PrP_BMD5/10 [PrP_BMD5_10_1]


title: IonXpress_007-D-20-2hr_inf

value: Mtb-infected cells


title: CM-P0-2D-1


title: S1_D1_12PM

value: 4 hr


title: Zebrafish_PrP_BMD5 [PrP_BMD5_3]

value: AB (wild type)


title: CM-P0-3D-2


title: CM-P0-1D-3


title: S1_D1_10AM

value: 2 hr


title: Zebrafish_PrP_BMD5 [PrP_BMD5_2]

value: Whole body

value: 120 hpf


title: CM-P0-1D-2


title: IonXpress_023-D-22-72hr_inf


title: S1_D1_8AM

value: Blood

value: 0 hr


title: CM-P0-4h-3


title: Zebrafish_EtP_BMD5/50 [EtP_BMD5_50_3]


title: Zebrafish_PrP_BMD5 [PrP_BMD5_1]


title: CM-P0-1D-1


title: S1_D1_4AM

value: 20 hr


title: IonXpress_021-D-22-24hr_inf

value: Human alveolar macrophages


title: S1_D1_6AM

value: Male

value: 22 hr


title: IonXpress_002-D-19-2hr_con

value: Control


title: Zebrafish_EtP_BMD5/50 [EtP_BMD5_50_2]


title: CM-P0-4h-2

value: Leaves

value: WT


title: IonXpress_019-D-22-2hr_inf


title: IonXpress_003-D-19-24hr_inf


title: Zebrafish_EtP_BMD5/50 [EtP_BMD5_50_1]


title: CM-P0-4h-1


title: IonXpress_024-D-22-72hr_con


title: S1_D1_2AM

value: 18 hr


title: Zebrafish_EtP_BMD5/10 [EtP_BMD5_10_3]


title: IonXpress_022-D-22-24hr_con


title: CM-P0-30m-3


title: S1_D1_12AM

value: 16 hr


title: IonXpress_018-D-21-72hr_con


title: TAMR Control Late 1 [RNA-seq]

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

data_processing:
Sequence adaptors were trimmed using Trim Galore (v.0.11.2), reads were processed with Xenome v.10.1. (Conway et al., 2012) to remove mouse sequences and remaining reads were mapped with STAR (v.2.7.7a) (Dobin et al., 2013) to the hg38/GRCh38 human genome build with GENCODE v33 used as a reference transcriptome (parameter settings: –quantMode TranscriptomeSAM–outFilterMatchNmin 101 –outFilterMultimapNmax 20).
TPM counts for each sample were obtained from DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: normalized transcript abundance measurment

source_name: TAMR cell line

growth_protocol: Tamoxifen-resistant MCF7 cells (TAMR) were previously generated by the long-term culture of MCF7 cells in phenol red-free RPMI medium containing 10% charcoal-stripped FBS (Gibco) and 4-OH-tamoxifen (1 × 10−7 M; TAM).

extract_protocol:
RNA was extracted from harvested cells using the Trizol.
RNA was prepared for sequencing using the TruSeq Stranded mRNA Library Prep kit (Illumina) and libraries were sequenced on Illumina NovaSeq S4 in paired-end mode.

treatment_protocol: Cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control Early”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35. Matched control cells were cultured for 35 days in normal media and harvested at day 35 for “Control Late”.

value: Tamoxifen-resistant (TAMR) MCF7 cells

value: Control Late

tag: replicate


title: TAMR Control Late 2 [RNA-seq]


title: Zebrafish_EtP_BMD5/10 [EtP_BMD5_10_2]

value: AB (wild type)


title: CM-P0-30m-2


title: Zebrafish_EtP_BMD5/10 [EtP_BMD5_10_1]


title: IonXpress_020-D-22-2hr_con


title: CM-P0-30m-1


title: TAMR Decitabine Recovery 2 [RNA-seq]

value: Decitabine Recovery


title: IonXpress_016-D-21-24hr_con


title: Zebrafish_EtP_BMD5 [EtP_BMD5_3]

value: Whole body


title: IonXpress_015-D-21-24hr_inf

value: Mtb-infected cells


title: TAMR Decitabine Recovery 1 [RNA-seq]


title: Zebrafish_EtP_BMD5 [EtP_BMD5_2]

value: 120 hpf


title: CM-Mock-V-3D-2


title: IonXpress_014-D-21-2hr_con


title: Zebrafish_EtP_BMD5 [EtP_BMD5_1]


title: TAMR Decitabine Day 7 2 [RNA-seq]

value: Decitabine Day 7


title: CM-Mock-V-3D-1


title: Zebrafish_MtP_BMD5/50 [MtP_BMD5_50_3]


title: Zebrafish_MtP_BMD5/50 [MtP_BMD5_50_2]


title: IonXpress_012-D-20-72hr_con


title: IonXpress_013-D-21-2hr_inf


title: CM-Mock-V-2D-3


title: IonXpress_017-D-21-72hr_inf


title: TAMR Decitabine Day 7 1 [RNA-seq]


title: CM-Mock-V-2D-2


title: IonXpress_011-D-20-72hr_inf


title: TAMR Control Early 1 [RNA-seq]

value: Control Early


title: Zebrafish_MtP_BMD5/50 [MtP_BMD5_50_1]


title: IonXpress_010-D-20-24hr_con

value: Human alveolar macrophages


title: CM-Mock-V-2D-1


title: TAMR Control Late 2 [PCHi-C]

data_processing:
PCHi-C sequenced reads were mapped and filtered using HiCUP (v.0.7.4) (Wingett et al., 2015) with hg38/GRCh38 genome digested with –arima flag and minimum di-tag length set to 20.
Unique, valid mapped reads from HiCUP were converted into .chinput files using bam2chicago.sh utility and obtained chinput files were further filtered and processed with CHiCAGO (v.1.14.0)
Assembly: GRCh38/hg38
Supplementary files format and content: chinput files containing unique, valid mapped reads.

extract_protocol:
Hi-C experiments were performed on fresh-frozen tumour samples using the Arima Hi-C+ kit (Arima Genomics, Inc.) with minor modifications. Hi-C libraries were then used for Promoter Capture enrichment.
PCHi-C libraries were prepared using the SureSelect target enrichment system (SureSelect XT HS2 DNA kit, Agilent Technologies) using custom-design RNA bait library.


title: CM-Mock-V-3D-3


title: Zebrafish_MtP_BMD5/10 [MtP_BMD5_10_3]


title: TAMR Control Early 2 [RNA-seq]


title: CM-Mock-V-1D-3


title: IonXpress_001-D-19-2hr_inf


title: TAMR Control Late 1 [PCHi-C]


title: IonXpress_096-D-18_72hr_con


title: CM-Mock-V-1D-2


title: Zebrafish_MtP_BMD5/10 [MtP_BMD5_10_2]


title: TAMR Decitabine Recovery 2 [PCHi-C]


title: CM-Mock-V-1D-1


title: IonXpress_095-D-18_72hr_Mtb


title: TAMR Decitabine Recovery 1 [PCHi-C]


title: Zebrafish_MtP_BMD5 [MtP_BMD5_3]


title: CM-Mock-V-4h-3


title: CM-Mock-V-4h-2


title: IonXpress_094-D-18_24hr_con


title: IonXpress_093-D-18_24hr_Mtb


title: TAMR Decitabine Day 7 1 [PCHi-C]


title: Zebrafish_MtP_BMD5 [MtP_BMD5_2]


title: IonXpress_091-D-18_2hr_Mtb


title: TAMR Control Early 2 [PCHi-C]


title: Zebrafish_Control [C_3]


title: Zebrafish_MtP_BMD5 [MtP_BMD5_1]


title: IonXpress_089-D-17_72hr_Mtb


title: TAMR Control Early 1 [PCHi-C]


title: Zebrafish_Control [C_2]


title: CM-Mock-V-30m-2


title: CM-Mock-V-30m-3


title: CM-Mock-V-30m-1


title: IonXpress_087-D-17_24hr_Mtb


title: Zebrafish_MtP_BMD5/10 [MtP_BMD5_10_1]


title: IonXpress_088-D-17_24hr_con


title: CM-Mock-V-0-3


title: TAMR Decitabine Day 7 2 [PCHi-C]


title: IonXpress_084-D-16_72hr_con


title: HEC265_Paclitaxel/SM08502_1

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

description:
HEC265_Paclitaxel_vs_HEC265_Paclitaxel+SM08502_rMATS.tar.gz
HEC265_SM08502_vs_HEC265_Paclitaxel+SM08502_rMATS.tar.gz
HEC265_VehicleControl_vs_HEC265_Paclitaxel+SM08502_rMATS.tar.gz

data_processing:
Raw sequence data was demultiplexed and FASTQ files were generated using the Illumina bcl2fastq converter (version v2.20.0.422).
Gene expression analysis: Raw FASTQ files were uploaded to https://maayanlab.cloud/biojupies/upload and aligned by kallisto pseudoaligner to the human genome. Differential genes were identified by comparing Log normalized counts per million (CPM). A False Discovery Rate (FDR) < 0.05 was deemed significant.
Splicing analysis:  BBDuk (version 38.90, https://sourceforge.net/projects/bbmap/) was used to remove Illumina TruSeq adapters and remove sequence reads with a remaining length of less than 50 nt.
Reads were aligned to the GRCh38 assembly of the human genome with the STAR mapper (version 2.7.9a, https://github.com/alexdobin/STAR) in end-to-end alignment mode, using splice junction information from Ensembl realease 104 (https://may2021.archive.ensembl.org/Homo_sapiens/).
Alternative splicing events were detected and compared between treatments within each cell line using rMATS (version 4.1.2, https://github.com/Xinglab/rmats-turbo) with transcript annotations from Ensembl release 104.
Assembly: GRCh38
Supplementary files format and content: logCPM.txt.gz: Gzipped tab-separated table of all samples and genes with normalized expression as base-10 logarithm(fragment counts per million aligned fragments + 1), log10(CPM + 1)
Supplementary files format and content: *_rMATS.tar.gz: Gzipped tar ball of rMATS results for the comparison denoted in the file name

growth_protocol: Endometrial cancer cells (1.5 x 10^6) were plated in duplicate and allowed to attach for 16 hrs. Cells were treated with vehicle control (0.1% DMSO), Paclitaxel (IC50) and/or SM08502 (IC50) for 24 hrs. Cells were all grown in media with 5 to 20% fetal bovine serum and penicillin/streptomycin. Cells were collected for RNA extraction.

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Columns
Ribosomal RNA depletion was performed using QIAseq FastSelect -rRNA kit (Qiagen, Cat. #335376). 350 ng input RNA was used for ISH cells; 500 ng input RNA was used for SNGM, HEC265, and S33Y cells. Step 1 of fragmentation was performed for 7 minutes at 94°C, followed by FastSelect hybridization. First-strand synthesis, second-strand synthesis, A-tailing, adapter ligation, and library amplification were performed using the KAPA mRNA HyperPrep kit (Roche, Cat. #08105952001). We used 3.33 μL of 1.5 μM KAPA single index adapters for Illumina (Roche, Cat #0800577001) for adapter ligation. We performed 11 amplification cycles. KAPA Pure magnetic beads (Roche, Cat. #08105901001) were used for all cleanup steps. Library quality was confirmed by TapeStation by the University of Colorado Cancer Center Pathology Shared Resource. Sequencing was performed on a NovaSeq6000 instrument by the University of Colorado Genomics and Microarray Core.

treatment_protocol: Endometrial cancer cell lines were treated with the cell viability 50% inhibitory concentration (IC50) of Paclitaxel and SM08502 for 24 hrs. Ishikawa (Paclitaxel 11 nM; SM08502 80 nM); Ishikawa-S33Y (Paclitaxel 6 nM; SM08502 85 nM); SNGM (Paclitaxel 11.7 nM; SM08502 350.7 nM); HEC265 (Paclitaxel 5.6 nM; SM08502 149 nM)

tag: cell line

value: Endometrial Cancer


title: HEC265_SM08502_2

description:
HEC265_SM08502_vs_HEC265_Paclitaxel+SM08502_rMATS.tar.gz
HEC265_VehicleControl_vs_HEC265_SM08502_rMATS.tar.gz


title: SW1353

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1).
CanFam3.1
Supplementary files format and content: tab-delimited text fike included normalised read count for each sample

source_name: Bone

growth_protocol: SW1353 sensitive and resistance cell lines was cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37oC

extract_protocol:
RNA was haversted using TRIzol reagent
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: SW1353-R was culture in the medium containing 1uM cisplatin (Sigma)

value: Bone

value: fibroblast


title: SW1353-R

value: cisplatin resistance

value: cisplatin


title: CM-Mock-V-0-2

value: Leaves

value: WT


title: CM-Mock-V-4h-1


title: HEC265_SM08502_1


title: CM-Mock-V-0-1


title: IonXpress_082-D-16_24hr_con

value: Control


title: HEC265_Paclitaxel/SM08502_2


title: IonXpress_083-D-16_72hr_Mtb


title: Zebrafish_Control [C_1]


title: IonXpress_081-D-16_24hr_Mtb


title: H9 cerebral organoids, Control +ROS Inhibitor, resub-Ru18

city: Raleigh

first: Thomas

last: Rudibaugh

state: North Carolina

address: 840 Main Campus Dr, Partners II Room 3700

institute: North Carolina State University

description:
resub-Ru18_R1_001
Supplemental Excel File 3.xlsx

data_processing:
Raw FASTQ formatted sequence reads were imported into CLC Genomics Workbench (v.21.0.5 Qiagen, https://digitalinsights.qiagen.com/). Adaptor sequences and bases with low quality were trimmed and reads were mapped to the reference genome (GRCh38.102) using the RNA-seq analysis tool with the default parameters recommended for RNA-seq analysis. Principal component analysis and differential expression analysis were performed using ‘PCA for RNA-seq’ and ‘Differential Gene Expression for RNA-seq’ toolsets. Differential gene expression was performed by comparing organoids either acutely or chronically dosed with dopamine or cocaine against the ascorbic acid dosed controls. Genes were considered differentially expressed if they had a log2FC>|1| and a false discovery rate (FDR)<0.05.
Assembly: hg38
Supplementary files format and content: Supplemental Excel File 3.xlsx; Differentially expressed genes following chronic dopamine exposure with or without an ROS inhibito relative to ascorbic acid dosed vehicle controls with or without an ROS inhibitor.
Supplementary files format and content: Supplemental Excel File 4.xlsx; Differentially expressed genes following chronic cocaine exposure with or without an ROS inhibito relative to ascorbic acid dosed vehicle controls with or without an ROS inhibitor.
Supplementary files format and content: Rudibaugh2023_counts_TPMs.xlsx

source_name: H9 hESC cell line (NIH 0062)

growth_protocol:
The Xiang ventral forebrain protocol organoids were generated as previously described with small modifications32. Stem cells were grown to 75% confluency before dissociation into a single cell suspension using EDTA and Accutase (Fisher). 9,000 cells were plated into a low attachment U-bottomed 96 well plate(VWR) in Induction media supplemented with 50µM Y-27632(LC Labs) and 5% v/v heat-inactivated fetal bovine serum (Corning). Induction media contained DMEM-F12(Gibco), 15%v/v knockout serum replacement (Thermo Fisher), 1% v/v MEM-NEAA(VWR), 1% v/v Glutamax(Gibco), 7µL/L β-mercaptoethanol(Amresco), 100nM LDN193189 (Sigma), 10μM SB431452 (Abcam), and 2μM XAV939 (Sigma). After 48 hours, half of the media was replaced with Induction media containing Y-27632 and without heat-inactivated FBS. After another 48 hours, half the media was again removed and replaced with Induction media without Y-27632. From days 6-10 organoids were cultured in a 37̊C tissue culture incubator with 5% CO2 and received regular half media changes every 48 hours.
After day 10, organoids were transferred to a deep bottom tissue culture treated 10cm plate (Thermo Fisher) containing differentiation media supplemented with 100ng/mL SHH (VWR) and 1µM purmorphamine (VWR). Differentiation media contained DMEM-F12, 0.15% w/v Dextrose (Sigma), 7µL/L β-mercaptoethanol, 1% v/v N2 Supplement (Thermo Fisher), 1% v/v Glutamax, 0.5% v/v MEM-NEAA, 0.025% insulin solution (VWR), and 2% v/v B27 supplement without vitamin A (Thermo Fisher). Cell culture plates were placed on a shaker in the tissue culture incubator and rotated at 70rpm/min. On day 14 media was removed and replaced with fresh differentiation supplemented with SHH and purmorphamine. On day 18 differentiation media was removed and replaced with maturation media containing vitamin A. Maturation media consisted of a 1:1 mixture of DMEM-F12 and Neurobasal media (VWR), along with 0.5% v/v N2 supplement, 1% v/v B27 supplement with vitamin A (Thermo Fisher), 1% v/v Glutamax, 0.5% v/v MEM-NEAA, 0.025% v/v human insulin solution, 3.5µL/L β-mercaptoethanol, and 1% v/v Penicillin/Streptomycin (VWR). In addition, 20ng/mL of BDNF (Peprotech) and 20ng/mL GDNF (Peprotech) were added to the media. From day 18, organoids were cultured on the orbital shaker with weekly media changes in maturation media.

extract_protocol:
Total RNA was extracted on site by Azenta Sciences
Library preparation was carried out by Azenta Sciences according to their protocol

treatment_protocol: D83 organoids were treated with either a dose of dopamine diluted in 100µM of ascorbic acid, cocaine (NIDA Drug supply program) diluted in 100µM of ascorbic acid, or 100µM ascorbic acid as a control for 1 hour before media was removed and replaced with fresh maturation media. Final concentrations of dopamine and cocaine were 1µM while the concentration of ascorbic acid was kept constant. For chronic samples, organoids were dosed daily for 1 week before a final 1-hour dose was administered. For all organoids treated with the ROS inhibitor, 100µM of acetylcysteine was added to the media prior to dosing with dopamine or cocaine. For the final dose following the 1-hour incubation, organoids were either immediately washed once with cold PBS and fixed for sectioning and immunostaining or washed twice with cold PBS before the samples were flash frozen in liquid nitrogen and shipped on dry ice for RNA extraction and sequencing.

value: H9 hESC cell line (NIH 0062)

value: Neural Cultures

value: Control +ROS Inhibitor


title: 9-3-RAW264dot7plusF133VplusDMSO

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

data_processing:
RNA-Seq libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility
The raw reads were aligned to the Mouse reference genome build GRCm38, using STAR RNASeq alignment software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
The raw counts are normalized and expression analysis is performed using the DEseq2 package.
Assembly: GRCm38
Supplementary files format and content: Gene-Level Read Count files

organism: Mus musculus

source_name: [SPOP mutant (F133V)- and vector control (empty vector, EV)-transduced RM-1-BM mouse prostate cancer cells and RAW264.7 mouse macrophage cells

extract_protocol:
Fresh SPOP mutant (F133V) and vector control RM-1-BM mouse prostate cancer cells and RAW264.7 mouse macrophage cells treated with vehicle or olaparib were used for total RNA isolation with Trizol (Invitrogen), and subjected to RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: mouse macrophage cells

value: DMSO


title: IonXpress_080-D-16_2hr_con


title: HEC265_Paclitaxel_1

description:
HEC265_Paclitaxel_vs_HEC265_Paclitaxel+SM08502_rMATS.tar.gz
HEC265_VehicleControl_vs_HEC265_Paclitaxel_rMATS.tar.gz

value: Paclitaxel


title: HEC265_Paclitaxel_2


title: H9 cerebral organoids, Control +ROS Inhibitor, resub-Ru16

description:
resub-Ru16_R1_001
Supplemental Excel File 3.xlsx


title: H9 cerebral organoids, Control, resub-Ru15

description:
resub-Ru15_R1_001
Supplemental Excel File 3.xlsx


title: H9 cerebral organoids, Control +ROS Inhibitor, resub-Ru17

description:
resub-Ru17_R1_001
Supplemental Excel File 3.xlsx


title: IonXpress_079-D-16_2hr_Mtb

value: Mtb-infected cells


title: 9-2-RAW264dot7plusF133VplusDMSO


title: IonXpress_078-D-15_72hr_con


title: H9 cerebral organoids, Control, resub-Ru14

description:
resub-Ru14_R1_001
Supplemental Excel File 3.xlsx


title: HEC265_Vehicle Control_1

description:
HEC265_VehicleControl_vs_HEC265_Paclitaxel+SM08502_rMATS.tar.gz
HEC265_VehicleControl_vs_HEC265_Paclitaxel_rMATS.tar.gz
HEC265_VehicleControl_vs_HEC265_SM08502_rMATS.tar.gz

value: Vehicle Control


title: H9 cerebral organoids, Control, resub-Ru13

description:
resub-Ru13_R1_001
Supplemental Excel File 3.xlsx


title: 9-1-RAW264dot7plusF133VplusDMSO


title: SNGM_Paclitaxel/SM08502_2

description:
SNGM_Paclitaxel_vs_SNGM_Paclitaxel+SM08502_rMATS.tar.gz
SNGM_SM08502_vs_SNGM_Paclitaxel+SM08502_rMATS.tar.gz
SNGM_VehicleControl_vs_SNGM_Paclitaxel+SM08502_rMATS.tar.gz

source_name: SNGM

value: SNGM


title: 4-3-RAW264dot7plusOla

value: Olaparib

value: wild type


title: 4-2-RAW264dot7plusOla


title: IonXpress_077-D-15_72hr_Mtb

value: Human alveolar macrophages


title: 4-1-RAW264dot7plusOla


title: HEC265_Vehicle Control_2

value: Endometrial Cancer


title: SNGM_SM08502_2

description:
SNGM_SM08502_vs_SNGM_Paclitaxel+SM08502_rMATS.tar.gz
SNGM_VehicleControl_vs_SNGM_SM08502_rMATS.tar.gz


title: SNGM_Paclitaxel/SM08502_1


title: IonXpress_076-D-15_24hr_con


title: IonXpress_075-D-15_24hr_Mtb


title: H9 cerebral organoids, Dopamine +ROS Inhibitor, resub-Ru12

description:
resub-Ru12_R1_001
Supplemental Excel File 3.xlsx

value: Dopamine +ROS Inhibitor


title: H9 cerebral organoids, Dopamine +ROS Inhibitor, resub-Ru11

description:
resub-Ru11_R1_001
Supplemental Excel File 3.xlsx


title: SNGM_SM08502_1


title: IonXpress_074-D-15_2hr_con


title: 3-1-RAW264dot7plusEVplusDMSO


title: IonXpress_073-D-15_2hr_Mtb


title: H9 cerebral organoids, Dopamine +ROS Inhibitor, resub-Ru10

description:
resub-Ru10_R1_001
Supplemental Excel File 3.xlsx


title: H9 cerebral organoids, Dopamine, resub-Ru9

description:
resub-Ru9_R1_001
Supplemental Excel File 3.xlsx

value: Dopamine


title: SNGM_Paclitaxel_2

description:
SNGM_Paclitaxel_vs_SNGM_Paclitaxel+SM08502_rMATS.tar.gz
SNGM_VehicleControl_vs_SNGM_Paclitaxel_rMATS.tar.gz


title: H9 cerebral organoids, Dopamine, resub-Ru8

description:
resub-Ru8_R1_001
Supplemental Excel File 3.xlsx


title: SNGM_Paclitaxel_1


title: 26-3-F133VplusRAW264dot7plusOla

value: mouse prostate cancer cells


title: IonXpress_096-D-14_72hr_con

value: Control


title: H9 cerebral organoids, Dopamine, resub-Ru7

description:
resub-Ru7_R1_001
Supplemental Excel File 3.xlsx

value: H9 hESC cell line (NIH 0062)


title: 26-2-F133VplusRAW264dot7plusOla


title: SNGM_Vehicle Control_2

description:
SNGM_VehicleControl_vs_SNGM_Paclitaxel+SM08502_rMATS.tar.gz
SNGM_VehicleControl_vs_SNGM_Paclitaxel_rMATS.tar.gz
SNGM_VehicleControl_vs_SNGM_SM08502_rMATS.tar.gz


title: SNGM_Vehicle Control_1


title: 26-1-F133VplusRAW264dot7plusOla


title: IonXpress_095-D-14_72hr_Mtb


title: IonXpress_094-D-14_24hr_con


title: H9 cerebral organoids, Cocaine +ROS Inhibitor, resub-Ru6

description:
resub-Ru6_R1_001
Supplemental Excel File 4.xlsx

value: Neural Cultures

value: Cocaine +ROS Inhibitor


title: 3-3-RAW264dot7plusEVplusDMSO

value: mouse macrophage cells


title: 3-2-RAW264dot7plusEVplusDMSO

value: DMSO


title: CM_Pep_3D-3

value: Leaves

value: WT

value: PepMoV


title: IonXpress_093-D-14_24hr_Mtb

value: Mtb-infected cells


title: H9 cerebral organoids, Cocaine +ROS Inhibitor, resub-Ru5

description:
resub-Ru5_R1_001
Supplemental Excel File 4.xlsx


title: 25-3-F133VplusRAW264dot7plusDMSO


title: Ishikawa-S33Y_Paclitaxel/SM08502_2

description:
Ishikawa-S33Y_Paclitaxel_vs_Ishikawa-S33Y_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa-S33Y_SM08502_vs_Ishikawa-S33Y_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa-S33Y_VehicleControl_vs_Ishikawa-S33Y_Paclitaxel+SM08502_rMATS.tar.gz


title: H9 cerebral organoids, Cocaine +ROS Inhibitor, resub-Ru4

description:
resub-Ru4_R1_001
Supplemental Excel File 4.xlsx


title: Ishikawa-S33Y_Paclitaxel/SM08502_1


title: 25-2-F133VplusRAW264dot7plusDMSO


title: H9 cerebral organoids, Cocaine, resub-Ru3

description:
resub-Ru3_R1_001
Supplemental Excel File 4.xlsx

value: Cocaine


title: Ishikawa-S33Y_SM08502_1

description:
Ishikawa-S33Y_SM08502_vs_Ishikawa-S33Y_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa-S33Y_VehicleControl_vs_Ishikawa-S33Y_SM08502_rMATS.tar.gz


title: Ishikawa-S33Y_SM08502_2


title: 25-1-F133VplusRAW264dot7plusDMSO


title: IonXpress_092-D-14_2hr_con


title: H9 cerebral organoids, Cocaine, resub-Ru2

description:
resub-Ru2_R1_001
Supplemental Excel File 4.xlsx


title: IonXpress_091-D-14_2hr_Mtb


title: H9 cerebral organoids, Cocaine, resub-Ru1

description:
resub-Ru1_R1_001
Supplemental Excel File 4.xlsx


title: 20-2-EVplusRAW264dot7plusOla

value: Olaparib

value: wild type


title: 20-3-EVplusRAW264dot7plusOla


title: IonXpress_090-D-13_72hr_con

value: Human alveolar macrophages


title: Ishikawa-S33Y_Paclitaxel_2

description:
Ishikawa-S33Y_Paclitaxel_vs_Ishikawa-S33Y_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa-S33Y_VehicleControl_vs_Ishikawa-S33Y_Paclitaxel_rMATS.tar.gz

value: Endometrial Cancer

value: Paclitaxel


title: IonXpress_089-D-13_72hr_Mtb


title: Ishikawa-S33Y_Paclitaxel_1


title: IonXpress_088-D-13_24hr_con


title: Ishikawa-S33Y_Vehicle Control_2

description:
Ishikawa-S33Y_VehicleControl_vs_Ishikawa-S33Y_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa-S33Y_VehicleControl_vs_Ishikawa-S33Y_Paclitaxel_rMATS.tar.gz
Ishikawa-S33Y_VehicleControl_vs_Ishikawa-S33Y_SM08502_rMATS.tar.gz

value: Vehicle Control


title: 19-3-EVplusRAW264dot7plusDMSO

value: mouse prostate cancer cells


title: IonXpress_087-D-13_24hr_Mtb


title: Ishikawa-S33Y_Vehicle Control_1


title: 19-2-EVplusRAW264dot7plusDMSO


title: IonXpress_086-D-13_2hr_con

value: Control


title: IonXpress_085-D-13_2hr_Mtb


title: H9 cerebral organoids, Control, Ru16

data_processing:
Raw FASTQ formatted sequence reads were imported into CLC Genomics Workbench (v.21.0.5 Qiagen, https://digitalinsights.qiagen.com/). Adaptor sequences and bases with low quality were trimmed and reads were mapped to the reference genome (GRCh38.102) using the RNA-seq analysis tool with the default parameters recommended for RNA-seq analysis. Principal component analysis and differential expression analysis were performed using ‘PCA for RNA-seq’ and ‘Differential Gene Expression for RNA-seq’ toolsets. Differential gene expression was performed by comparing organoids either acutely or chronically dosed with dopamine or cocaine against the ascorbic acid dosed controls. Genes were considered differentially expressed if they had a log2FC>|1| and a false discovery rate (FDR)<0.05.
Assembly: hg38
Supplementary files format and content: Supplemental Excel File 1.xlsx; Differentially expressed genes following acute and chronic dopamine exposure relative to ascorbic acid dosed vehicle controls
Supplementary files format and content: Rudibaugh2022_counts_TPMs.xlsx

extract_protocol:
Total RNA was extracted on site by LC Sciences using the Qiagen, RNAeasy Mini Kit (#74104)
Library preparation was carried out by LC Sciences according to their protocol. Briefly, Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp.

treatment_protocol: D83 organoids were treated with either a dose of dopamine diluted in 100µM of ascorbic acid or 100µM ascorbic acid as a control for 1 hour before media was removed and replaced with fresh maturation media. Final concentrations of dopamine and cocaine were 1µM while the concentration of ascorbic acid was kept constant. For chronic samples, organoids were dosed daily for 1 week before a final 1-hour dose was administered. Acute samples and controls were dosed with ascorbic acid during the week prior before an acute dose of either dopamine or ascorbic acid was added. For the final dose following the 1-hour incubation, organoids were either immediately washed once with cold PBS and fixed for sectioning and immunostaining or washed twice with cold PBS before the samples were flash frozen in liquid nitrogen and shipped on dry ice for RNA extraction and sequencing.

value: H9 hESC cell line (NIH 0062)

value: Neural Cultures


title: H9 cerebral organoids, Acute, Ru15

value: Acute dopamine


title: 19-1-EVplusRAW264dot7plusDMSO

value: DMSO


title: IonXpress_083-D-12_72hr_Mtb


title: H9 cerebral organoids, Acute, Ru14


title: 18-3-F133VplusOla


title: H9 cerebral organoids, Acute, Ru13


title: IonXpress_082-D-12_24hr_con


title: 18-2-F133VplusOla


title: 20-1-EVplusRAW264dot7plusOla


title: IonXpress_081-D-12_24hr_Mtb


title: H9 cerebral organoids, Chronic, Ru12

value: Chronic dopamine


title: H9 cerebral organoids, Control, Ru17


title: H9 cerebral organoids, Control, Ru18


title: 17-3-F133VplusDMSO


title: 18-1-F133VplusOla


title: Ishikawa_Paclitaxel/SM08502_1

description:
Ishikawa_Paclitaxel_vs_Ishikawa_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa_SM08502_vs_Ishikawa_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa_VehicleControl_vs_Ishikawa_Paclitaxel+SM08502_rMATS.tar.gz

source_name: Ishikawa

value: Ishikawa


title: Ishikawa_Paclitaxel_2

description:
Ishikawa_Paclitaxel_vs_Ishikawa_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa_VehicleControl_vs_Ishikawa_Paclitaxel_rMATS.tar.gz


title: Ishikawa_Paclitaxel/SM08502_2


title: Ishikawa_Paclitaxel_1


title: Ishikawa_SM08502_2

description:
Ishikawa_SM08502_vs_Ishikawa_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa_VehicleControl_vs_Ishikawa_SM08502_rMATS.tar.gz


title: IonXpress_080-D-12_2hr_con


title: Ishikawa_SM08502_1


title: 17-2-F133VplusDMSO


title: IonXpress_079-D-12_2hr_Mtb


title: H9 cerebral organoids, Chronic, Ru10


title: H9 cerebral organoids, Chronic, Ru11


title: 17-1-F133VplusDMSO


title: Ishikawa_Vehicle Control_2

description:
Ishikawa_VehicleControl_vs_Ishikawa_Paclitaxel+SM08502_rMATS.tar.gz
Ishikawa_VehicleControl_vs_Ishikawa_Paclitaxel_rMATS.tar.gz
Ishikawa_VehicleControl_vs_Ishikawa_SM08502_rMATS.tar.gz


title: IonXpress_078-D-11_72hr_con


title: Ishikawa_Vehicle Control_1


title: H1 cerebral organoids, Control, Ru9

source_name: H1 hESC cell line (NIH 0043)

value: H1 hESC cell line (NIH 0043)


title: IonXpress_077-D-11_72hr_Mtb

value: Mtb-infected cells


title: H1 cerebral organoids, Control, Ru8


title: 12-3-EVplusOla

value: EV+Ola


title: IonXpress_076-D-11_24hr_con


title: H1 cerebral organoids, Control, Ru7


title: SARS-CoV-2 Infected L-001

city: Accra

first: JOHN

middle: DEMBY

last: SANDI

address: Legon Boundary

department: Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana

description: SARS-CoV-2 Infected

data_processing:
Illumina Novaseq 6000 output  read files were adapter trimmed and demultiplexed using bcl2fastq v2.20.0.422 (Illumina) to generate unique fastq files per sample. This allows for  for zero mismatches.
Kallisto v0.48.0 was used to psuedo-align fastq files  to an index genome generated from the human cDNA fasta sequence (GRCh38). This output both transcript abundance file (.TSV)  and transcript abundance.h5 file (transcript per million (TPM)), used for differential analysis
Transcript counts were normalized and log2 transformed
Sleuth v0.27.3 was used for differential  gene expression analysis between groups while accounting for differences in gender and age  using the Likelihood ratio test (lrt) and Wald test (wt)
NA
Assembly: GRCh38
Supplementary files format and content: comma-separated values file (csv) format, containing sample metadata
Supplementary files format and content: Tab-separated values (TSV) and Hierarchical Data Format (h5) files containing transcript abundances in transcript per million (TPM)

source_name: Upper airway epithelial tissue

extract_protocol:
Total RNA was extracted from 300ul of VTM containing nasophryngeal swab using the Quick-RNA Miniprep Plus kit (Zymo Research) following the manufacturer's instructions. Briefly, samples were lysed for 30mins, and nucleic acid was precipitated using absolute ethanol. Sample enrichment for RNA was archived by DNase treatment followed by column purification. RNA was eluted in nuclease-free water, and only RNA samples with A260/A280 ratio > 1.8 and concentrations above 1ng/ml were considered for library preparation.
The NEBNext® Ultra II Directional RNA Library Prep Kit (#7760L) for Illumina (New England Biolab) protocol was used for sequencing libraries construction according to manufacturers' instructions.

value: Upper airway epithelial tissue

value: Severe


title: 12-2-EVplusOla

value: Olaparib

value: wild type


title: SARS-CoV-2 Infected L-003

description: SARS-CoV-2 Infected

value: Mild


title: SARS-CoV-2 Uninfected  L-008

description: SARS-CoV-2 Uninfected

value: Uninfected Control


title: H1 cerebral organoids, Acute, Ru6


title: IonXpress_075-D-11_24hr_Mtb

value: Human alveolar macrophages


title: IonXpress_073-D-11_2hr_Mtb


title: 11-2-EVplusDMSO

value: EV+DMSO

value: mouse prostate cancer cells


title: 11-3-EVplusDMSO


title: IonXpress_074-D-11_2hr_con

value: Control


title: SARS-CoV-2 Infected L-010

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Infected L-012

description: SARS-CoV-2 Infected


title: H1 cerebral organoids, Chronic, Ru3

value: Neural Cultures


title: 11-1-EVplusDMSO

value: DMSO


title: IonXpress_024-D_4_72hr_con_CA


title: SARS-CoV-2 Infected L-014

description: SARS-CoV-2 Infected


title: H1 cerebral organoids, Acute, Ru4

value: Acute dopamine


title: H1 cerebral organoids, Chronic, Ru2

value: Chronic dopamine


title: IonXpress_021-D_4_24hr_mtb_CA


title: SARS-CoV-2 Infected L-015

description: SARS-CoV-2 Infected


title: 10-2-RAW264dot7plusF133VplusOla

value: mouse macrophage cells


title: IonXpress_019-D_4_2hr_mtb_CA

value: Mtb-infected cells


title: H1 cerebral organoids, Chronic, Ru1

value: H1 hESC cell line (NIH 0043)


title: 12-1-EVplusOla

value: EV+Ola


title: IonXpress_018-D_3_72hr_con_CA


title: IonXpress_017-D_3_72hr_mtb_CA


title: P0627_P

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

library_source: transcriptomic single cell

data_processing:
Data was demultiplexed and counted using Cell Ranger version 6.0.0
Cell Ranger output was analyzed using Seurat version 4.1.1
Supplementary files format and content: Cell Ranger output

extract_protocol:
Biopsies were briefly washed with DMEM/15%FBS, minced, digested with dispase (5000 caseinolytic Units) followed by trypsin (0.25%). Single cell suspensions were washed in PBS/2% BSA and checked for viability > 85%
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Esophageal mucosal biopsy

tag: esophagus region

value: Proximal

tag: disease state

value: Eosinophilic Esophagitis

tag: subject id


title: SARS-CoV-2 Infected L-013

description: SARS-CoV-2 Infected

value: Upper airway epithelial tissue

value: Mild


title: SARS-CoV-2 Infected L-019

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Infected L-017

description: SARS-CoV-2 Infected


title: P0633_D

value: Distal


title: H1 cerebral organoids, Acute, Ru5


title: IonXpress_015-D_3_24hr_mtb_CA

tag: time point

tag: sample group

value: Human alveolar macrophages


title: SARS-CoV-2 Infected L-021

description: SARS-CoV-2 Infected


title: P0597_D


title: SARS-CoV-2 Infected L-020

description: SARS-CoV-2 Infected


title: pancreatic acinar KO2 D4

city: Brussel

first: Zhaolong

last: Pan

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
Low quality ends (<Q20) were trimmed using FastX 0.0.14. Reads shorter than 35bp after trimming were removed. Using FastX 0.0.14 and ShortRead 1.44.3, polyA reads (more than 90% of bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases <Q25), and artifacts reads (all but three bases in the read equal one base type) were removed.
Within- and between-sample normalization was corrected for using full quantile normalization with the EDASeq package from Bioconductor. The number of reads was counted in the alignment that overlapped with gene features using featureCounts 1.5.3.
FPKM values were determined by dividing for each sample the normalized counts by the total number of counts (in millions). Then for each gene, the scaled counts were divided by the gene length (in kbp). As such we got the number of Fragments Per Kilobase of gene sequence and per Million fragments of library size.
Assembly: reference genome of Mus musculus Ensembl.GRCm38.82 (GRCm3882)
Supplementary files format and content: raw counts of each sample
Supplementary files format and content: FPKM values after preprocessing of each sample

source_name: pancreatic acinar cells

growth_protocol: Fresh isolated pancreatic acinar cells of WT or xCT KO mouse were maintained in Advanced RPMI medium.

extract_protocol:
Total RNA was isolated from cells using NucleoSpin RNA isolation kit (Macherey-Nagel).
TruSeq Library Prep Kit

treatment_protocol: Mouse acinar cells were cultured in suspension to allow dedifferentiation.

tag: cell type

value: pancreatic acinar cells

value: xCT KO


title: 10-3-RAW264dot7plusF133VplusOla

tag: tissue

tag: treatment

value: Olaparib

value: wild type


title: pancreatic acinar KO1 D4


title: pancreatic acinar KO3 D4


title: P0597_P


title: pancreatic acinar WT3 D4

value: WT


title: IonXpress_013-D_3_2hr_mtb


title: IonXpress_014-D_3_2hr_con_CA

value: Control


title: P0550_D


title: P0633_P


title: pancreatic acinar WT2 D4


title: SARS-CoV-2 Infected L-023

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Infected L-024

description: SARS-CoV-2 Infected


title: IonXpress_012-D-2_72hr con


title: P0485_D


title: pancreatic acinar KO3 D1


title: P0550_P


title: SARS-CoV-2 Infected L-025

description: SARS-CoV-2 Infected


title: IonXpress_011-D-2_72hr inf


title: 10-1-RAW264dot7plusF133VplusOla

value: mouse macrophage cells


title: SARS-CoV-2 Uninfected  L-022

description: SARS-CoV-2 Uninfected

value: Uninfected Control


title: IonXpress_016-D_3_24hr_con_CA


title: pancreatic acinar KO2 D1


title: P0485_P


title: IonXpress_010-D-2_24hr con


title: SARS-CoV-2 Infected L-028

description: SARS-CoV-2 Infected


title: pancreatic acinar KO1 D1


title: P0435_D


title: IonXpress_008-D-2_2hr con


title: P0435_P


title: SARS-CoV-2 Infected L-033

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Infected L-034

description: SARS-CoV-2 Infected


title: pancreatic acinar WT3 D1


title: HCE051_D

value: Healthy


title: pancreatic acinar WT1 D4


title: pancreatic acinar WT2 D1


title: pancreatic acinar WT1 D1


title: HCE051_P


title: SARS-CoV-2 Infected L-036

description: SARS-CoV-2 Infected


title: IonXpress_007-D-2_2hr inf

value: Mtb-infected cells


title: IonXpress_006-D-1_72hr con


title: SARS-CoV-2 Infected L-037

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Infected L-038

description: SARS-CoV-2 Infected


title: pancreatic acinar KO2 D0


title: pancreatic acinar KO3 D0


title: HCE049_P

value: Esophageal mucosal biopsy


title: IonXpress_005-D-1_72hr inf


title: HCE049_D


title: IonXpress_004-D-1_24hr con


title: HCE048_D


title: SARS-CoV-2 Infected L-039

description: SARS-CoV-2 Infected


title: IonXpress_003-D-1_24hr inf


title: IonXpress_009-D-2_24hr inf


title: pancreatic acinar WT3 D0


title: SARS-CoV-2 Infected L-040

description: SARS-CoV-2 Infected


title: IonXpress_002-D-1_2hr con


title: IonXpress_001-D-1_2hr inf


title: pancreatic acinar WT2 D0


title: HCE047_D


title: SARS-CoV-2 Infected L-035

description: SARS-CoV-2 Infected

value: Severe


title: HCE047_P

value: Proximal


title: pancreatic acinar WT1 D0


title: HCE043_D


title: pancreatic acinar KO1 D0


title: neutrophil, engaged, exp 4

city: New York

first: Mariano

last: Aufiero

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: EXP 4-Engaged

data_processing:
FASTQ files were mapped to the target genome using the rnaStar aligner that maps reads on a genomic basis and resolves reads across splice junctions.
The 2pass mapping method [103] was used, in which the first mapping pass uses a list of known annotated junctions from Ensembl.
Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was performed in which the Remove Noncanoncial flag was used.
After mapping, the output SAM files were post processed using the PICARD tool AddOrReplaceReadGroups to add read groups, sort the files, and covert them to the compressed BAM format.
The expression count matrix was then computed from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases. The raw count matrix generated by HTSeq was then processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which was used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: bystander lung neutrophil

extract_protocol:
Cells were lysed in TRIzol Reagent and phase separation was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide, washed with 75% ethanol and resuspended in nuclease-free water.
10 ng total RNA with RNA integrity numbers ranging from 8.8 to 9.5 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit from Clonetech following the manufacture's protocol. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems).

value: bystander lung neutrophil

value: lung neutrophil

value: Aspergillus challenge

tag: time

value: 24 hours


title: neutrophil, engaged, exp 3

description: EXP 4-Bystander


title: SARS-CoV-2 Infected L-043

description: SARS-CoV-2 Infected

value: Upper airway epithelial tissue

tag: genotype

value: Mild


title: SARS-CoV-2 Infected L-044

description: SARS-CoV-2 Infected


title: Cdo1-LKO 2

city: Shanghai

first: Min

last: Chen

address: YangPu

institute: Shanghai University of sports

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm8
Supplementary files format and content: tab-delimited tex files include ROW counts each sample
Supplementary files format and content: tab-delimited tex files include RPKM values each sample

source_name: Liver

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard IIIumina protocols

value: Liver

value: Cdo1 liver KO

value: HFD feeding 12 weeks


title: neutrophil, engaged, exp 2

description: EXP 3-Engaged


title: Cdo1-LKO 3


title: HCE040_D

value: Distal


title: neutrophil, engaged, exp 1

description: EXP 3-Bystander


title: Cdo1-LKO 1


title: HCE048_P


title: SARS-CoV-2 Infected L-046

description: SARS-CoV-2 Infected


title: HCE040_P


title: SARS-CoV-2 Infected L-048

description: SARS-CoV-2 Infected


title: Neutrophil, bystander, exp 4

description: EXP 2-Engaged


title: SARS-CoV-2 Infected L-041

description: SARS-CoV-2 Infected


title: Tetrathiomolybdate treated, biological rep 2

first: Matthew

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

institute: University of Chicago

data_processing:
The fastqc (0.11.9) and trim-galore (0.6.7) packages were used for (i) quality control and (ii) to remove low-qualified bases and adapter-containing reads from raw KAS-seq data, respectively. Trimmed reads shorter than length 30 bp were discarded.
Paired end reads were mapped to reference STAR genomes generated from the hg39 genome build
Assembly: hg38
Supplementary files format and content: .tab, tables of read counts

extract_protocol:
Total RNA were extracted from cells by using Trizol reagent (Thermo, 15596026). RiboMinus Eukaryote Kit was used to remove rRNA.
RNA were used for library construction by using SMARTer Stranded RNA-seq kit (Takara, 634839).

value: breast adenocarcinoma

value: WT

value: Tetrathiomolybdate


title: WT 2


title: WT 3


title: SARS-CoV-2 Infected L-049

description: SARS-CoV-2 Infected


title: Neutrophil, bystander, exp 2

description: EXP 1-Engaged


title: SARS-CoV-2 Infected L-042

description: SARS-CoV-2 Infected


title: Tetrathiomolybdate treated, biological rep 1


title: DCAC50 treated, biological rep 2


title: SARS-CoV-2 Infected L-053

description: SARS-CoV-2 Infected


title: WT 1


title: HCE043_P

value: Healthy


title: mESC-WT_polyA-RNA_Input_rep3

first: Li-Sheng

last: Zhang

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
The code for sequencing processing and mutation calling has been packaged into one App (docker image), and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: mm10
Assembly: synthetic
Supplementary files format and content: xlsx (excel)

source_name: cell line

growth_protocol: mESC cells were purchased from the American Type Culture Collection (ATCC). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Total RNA isolation: cellular total RNA was isolated according to TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation. PolyA+ RNA isolation: Dynabeads™ mRNA Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment, from the purified total RNA.
Wild-type mESC cells (three replicates for each sample, one 3.5-cm plate per replicate)  were prepared. After extracting the polyA+ RNA from mESC cells or mouse tissues, around 10 ng RNA was fragmented using RNA Fragmentation Reagents (catalog no. AM8740, Invitrogen) and heated at 70 °C for 14 min, followed by purification with RNA Clean and Concentrator (Zymo Research). 3′-End repair and 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). RNA was mixed with 3 µL 10× T4 PNK reaction buffer (catalog no. B0201S, NEB) and 3 µl T4 PNK, diluted to a final volume of 30 µl, and incubated at 37 °C for 45 min; then 1.5 µl T4 PNK and 1.5 µl 10 mM ATP were added for another incubation at 37 °C for 45 min, followed by RNA Clean and Concentrator (Zymo Research) purification eluting with 10 µl RNase-free water. To perform 3′-adapter ligation, 10 µl 3′-repaired and 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNN AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.  The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.  A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.

treatment_protocol: Wild-type cells are used for these RNA-seq libraries.

value: cell line

value: mESC

value: embryonic stem cell


title: Neutrophil, bystander, exp 1

description: EXP 1-Bystander

value: bystander lung neutrophil


title: SARS-CoV-2 Uninfected  L-055

description: SARS-CoV-2 Uninfected

value: Uninfected Control


title: DCAC50 treated, biological rep 1


title: SARS-CoV-2 Uninfected  L-056

description: SARS-CoV-2 Uninfected


title: DMSO treated, biological rep 1

value: DMSO


title: SARS-CoV-2 Uninfected  L-057

description: SARS-CoV-2 Uninfected


title: mESC-WT_polyA-RNA_Treated_rep3


title: mESC-WT_polyA-RNA_Input_rep1


title: SARS-CoV-2 Uninfected  L-059

description: SARS-CoV-2 Uninfected


title: mESC-WT_polyA-RNA_Input_rep2


title: DMSO treated, biological rep 2

value: 24 hours


title: SARS-CoV-2 Uninfected  L-060

description: SARS-CoV-2 Uninfected

value: Upper airway epithelial tissue


title: Neutrophil, bystander, exp 3

description: EXP 2-Bystander

value: lung neutrophil

value: Aspergillus challenge


title: MDA-MB-231_shT_2 rep3

city: Changchun

first: HUAN

last: HE

state: Jilin Province

address: No.1163 Xinmin Street

department: School of Public Health

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MDA-MB-231 cells

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Triple negative breast cancer

tag: genotype/variation

value: TAB182 knockdown


title: mESC-WT_polyA-RNA_Treated_rep2


title: MDA-MB-231_shT_2 rep2


title: SARS-CoV-2 Uninfected  L-061

description: SARS-CoV-2 Uninfected


title: SARS-CoV-2 Uninfected  L-062

description: SARS-CoV-2 Uninfected


title: MDA-MB-231_shT_2 rep1


title: MDA-MB-231_shNC rep3

value: Control


title: BVSC Gastruloid, 142h, STELLA+, rep1

city: London

first: Naomi

last: Moris

address: 1 Midland Way

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Base calling by bcl2fastq 2.20.0
Quantification using Cell Ranger 6.1.2 against refdata-gex-mm10-2020-A
Downstream analysis using Seurat 4.0.3 in R 4.1.1
Assembly: mm10
Supplementary files format and content: Tarball archive of Cell Ranger raw and filtered feature matrices
Supplementary files format and content: Plain text file of cell barcodes used in the analysis

source_name: Mouse gastruloid

growth_protocol: Mouse ESC lines were routinely cultured in 2iLif in N2B27 (NDiff227 Takara Bio, Y40002, supplemented with 3µM CHIR99021 (Chi), 1µM PD0325901 (PD03) and 11ng/ml mLIF) on gelatinised (0.1% gelatin) tissue culture flasks or 6-well plates kept in humidified incubators at 37°C, 5% CO2. Cells were passaged into new flasks or plates every two days with media exchanged daily.

extract_protocol:
Gastruloids were collected and washed twice in PBS before incubating at room temperature for 8 mins in Trypsin-EDTA before quenching with 10% FBS in PBS. Cells were pelleted at 230xg for 5mins before resuspending in filtered 1% FBS in PBS. Cell solution was passed through tube filter (35µm) then counted and divided into tubes before antibody addition. Incubated at 4°C on rotator for 1 hour then centrifuged at 800 rpm for 5 mins at 4°C. Supernatants were aspirated and sample washed with filtered 1% FBS in PBS before repeating wash and transferring to chilled flow tubes. Cells were loaded onto a BD FACSAria™ Fusion III (BD Biosciences) for sorting. Sorting was based on the reporters Stella::CFP, Blimp1::mVenus or PECAM1-PE and SSEA1-A647 antibodies. Sorted cells were transferred to DNA low-bind tubes and centrifuged at 300 rcf for 5 mins at 4°C. The supernatant was aspirated and, using cut tips, 1ml of chilled PBS pipetted up and down 10 times. This was repeated twice more, and after the final centrifugation step the cells were resuspended in 200µl chilled PBS then 800µl of chilled 100% methanol added dropwise and with stirring. Fixed cells were stored at -80°C until ready for 10x preparation for scRNAseq.
The sorted, fixed and frozen cells were thawed on ice for 5 minutes before centrifugation at 1,000 xg for 5 minutes (at 4°C). Supernatant was carefully aspirated without disturbing the pellet before resuspending the pellet in the appropriate volume of Wash-Resuspension buffer; 3x SSC Buffer (Invitrogen, 15557-044) supplemented with 0.04% Bovine Serum Albumin (BSA) (Invitrogen, AM2616), 1mM DL-Dithiothreitol solution (DTT) (Sigma-Aldrich, 646563) and 0.2U/µl Protector RNase inhibitor (Roche, 3335399001) to give 1000 cells/µl in 50µl or minimum volume of 50µl if not possible to obtain that concentration. Quality control on the cells and counts were performed on a Luna FX7 cell counter (Logos biosystems) prior to applying to 10x Chromium library preparation performed according to manufacturer’s instructions. Single cell libraries of 100 bp paired-end reads were pooled and sequenced on HiSeq 4000 to perform single cell RNA sequencing (scRNAseq).

treatment_protocol: Gastruloids were prepared following published protocols. Briefly, mESCs were trypsinized and pelleted, with the cell pellet washed in PBS before repeating the process then resuspending in N2B27. The cells were counted and diluted to provide 300 cells per well, before pipetting into cell-repellent, ultra-low attachment 96-well plates (Greiner). Aggregates were incubated at 37°C, 5% CO2 in a humidified incubator. After 48 hours, N2B27 supplemented with 3µM Chi was added, and every subsequent 24 hours the media was aspirated and replaced with fresh N2B27.

value: Mouse gastruloid

tag: timepoint

value: 142h after aggregation

tag: sorted population

value: STELLA+


title: BVSC Gastruloid, 96h, STELLA+, rep1

value: 96h after aggregation


title: SARS-CoV-2 Uninfected  L-063

description: SARS-CoV-2 Uninfected


title: SARS-CoV-2 Uninfected  L-066

description: SARS-CoV-2 Uninfected


title: MDA-MB-231_shNC rep1

tag: strain


title: BVSC Gastruloid, 120h, STELLA+, rep2

value: 120h after aggregation


title: SARS-CoV-2 Uninfected  L-068

description: SARS-CoV-2 Uninfected


title: BVSC Gastruloid, 142h, PECAM+, rep1

value: PECAM+


title: SARS-CoV-2 Uninfected  L-069

description: SARS-CoV-2 Uninfected


title: K562 DAC3L3

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

data_processing:
Library strategy: scDyad-sq
Illumina bcl2fastq2 v 2.20 software used for basecalling
A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify site specific 5mC as well as the status of CpG dyads as fully or hemi-methylated.
For genomic site specific 5mC detection (for absolute 5mC (or 5hmC) level calling), exact duplicates were removed using Clumpify from BBTools. A custom Perl script was use to extract the single cell barcode and UMI from each read. Then read 1 and 2 were trimmed using TrimGalore in paired end mode. The 5’ end of read 1 was clipped by 20 bases and the 3’ end of read 2 was hard clipped 34 bases after detection of the PCR amplification sequence CCACATCACCCAAACC to remove potential bias from enzymatic digestion and to avoid recounting CpG dyad detections utilized in the maintenance measurement. The 5’ end of read 2 was clipped by 9 bases to remove potential bias from the linear amplification 9-mer. The 3’ end of read 1 was also hard clipped 9 bases after detection of the Illumina adapter was performed. Each read was mapped individually using Bismark v0.21.0 in conjunction with Bowtie2 v2.3.5 to MM10 or hg19 for mouse or human samples, respectively. Using Bismark, both resulting sam files were deduplicated further using UMI, cell barcode and mapping location. The bismark_methylation_extractor tool was then used to extract detected cytosines. After which custom Perl code was used to connect detected cytosines to their respective cell. CpG detection files from the same DNA strand for read 1 and read 2 were then combined and any duplicate detections where the same cytosine was read in both read 1 and read 2 were removed using the UMI. Custom codes for analyzing Dyad-seq data and the accompanying documentation is provided with this work.
For genomic CpG Dyad specific calling (for 5mCpG (or 5hmC) maintenance calling), Read 1 was trimmed to 86 bases. Then exact duplicates were removed using Clumpify from BBTools. A custom Perl script was use to extract the single cell barcode and UMI from each read. Then read 1 was trimmed using the default settings of TrimGalore. Read 1 was mapped using Bismark v0.21.0 in conjunction with Bowtie2 v2.3.5 to MM10 or hg19 for mouse or human samples, respectively. Using Bismark, both resulting sam files were deduplicated further using UMI, cell barcode and mapping location. For library preparation using MspJI, a custom Perl script was used to identify 5mC positions in the genome as detected by MspJI and interrogate the methylation status of the opposing cytosine in a CpG or CpHpG dyad context from the nucleobase conversion. For library preparation using AbaSI, a custom Perl script was used to identify 5hmC positions in the genome as detected by AbaSI and interrogate the methylation status of the opposing cytosine in a CpG dyad context from the nucleobase conversion.
For bulk RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq MM10 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 12. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis.
For single cell RNA based reads, Read 2 was trimmed using the default settings of TrimGalore. After trimming, STARsolo (STAR aligner version 2.7.8a) was used to map the reads to MM10 using the gene annotation file from Ensembl . The reads were again mapped to MM10 using the transposable elements annotation file described in TEtranscripts. Transcripts with the same UMI were deduplicated, transcripts detected from genes or transposable elements were analyzed together and any that were not detected in at least one cell were removed from any downstream analysis.
Required code to go from raw FASTQ files to processed data can be found on github at https://github.com/alexchialastri/scDyad-T-seq
Genome_build: MM10 and hg19
Supplementary_files_format_and_content: 5mCpG Dyad maintenance detection files [noted in the naming of the file as *_CGMaintained.txt (for loci detected as maintained {e.g. fully methylated dyads for M-M-Dyad-seq}) and *_CGNonMaintained.txt (for loci detected as not maintained  {e.g. hemi-methylated dyads for M-M-Dyad-seq})] list detected methylated or unmethylated CpG maintenance sites. Column 1 is the cell number (in bulk this is the sample replicate indicator), column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, column 4 is the UMI detected and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Absolute 5mCpG detection files [noted in the naming of the file as *_BS-CpG_All.txt or *BS-CpG_All_BothStrands_Unique.txt] list detected methylated or unmethylated CpG sites. Column 1 is the cell number (in bulk this is the sample replicate indicator), column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, column 4 is the the strand of the detected mark, column 5 is the UMI detected and column 6 indicates if the cytosine was methylated (Z) or unmethylated (z) .
Supplementary_files_format_and_content: For Bulk samples RNA-seq gene count files (noted in the naming of the file as *-READ_COUNTS_c.txt.gz) is a matrix with the columns indicating  sample (replicate) number, and each row indicating the number of counts detected for a given gene.
Supplementary_files_format_and_content: Single cell transcript counts contain 6 files. 3 refer to the detection of unique transcripts related to genes (*_Genes_matrix.mtx.gz, *_Genes_features.tsv.gz, and *_Genes_barcodes.tsv.gz) and 3 refer to the detection of unique transcripts related to transposable elements (*_TE_matrix.mtx.gz, *_TE_features.tsv.gz, and *_TE_barcodes.tsv.gz). These set of 3 files are in the standard 10x sparse data matrix format (Market Exchange Format). The *_barcodes.tsv.gz file gives the list of cell barcodes used in the experiment. Note: these are in alphabetical order and not ordered by cell number, see supplementary file ('SingleCell_barcodesOrdered.csv') on main page for which barcodes refer to what cell number. The *_features.tsv.gz file gives the list of gene or transposable elements names. The *_matrix.mtx.gz gives the location and value of non zero elements in gene or transposable elements detection matrix, with column 1 refering to the feature, column 2 to the cell number, and column 3 to the number of transcripts detected.

growth_protocol: All cells were maintained in incubators at 37°C and 5% CO2. Mouse embryonic stem cell line ES-E14TG2a (E14) were grown on gelatin (Millipore Sigma, ES-006-B) coated tissue culture plates with media containing high glucose DMEM (Gibco, 10569044), 1% non-essential amino acid (Gibco, 11140050), 1% Glutamax (Gibco, 35050061), 1x Penicillin-Streptomycin (Gibco, 15140122), and 15% stem cell qualified serum (Millipore Sigma, ES-009-B). The media was frozen in aliquots and used thereafter for a maximum of 2 weeks after thawing while storing it at 4°C. Once thawed, 1 µL of beta-mercaptoethanol (Gibco, 21985023), and 1 µL of LIF (Gibco, A35933) were added for every 1 mL of thawed media. Cells were washed with 1x DPBS (Gibco, 14190250) and the media was exchanged daily. Cells were routinely passaged 1:6 once they reached 75% confluency using 0.25% trypsin-EDTA (Gibco, 25200056). E14 cells grown under these conditions also describe the SL experimental group. For FACS sorting, a single-cell suspension was made using 0.25% trypsin-EDTA. The trypsin was then inactivated using serum containing medium. Afterwards, the cells were washed with 1x DPBS before being passed through a cell strainer and sorted for single cells into 384-well plates.  K562 cells were grown in RPMI (Gibco, 61870036) with 10% serum (Gibco, 10437028) and 1x Penicillin-Streptomycin. When the culture reached a density of approximately 1 million cells per mL, they were split and resuspended at a density of 200,000 cells per mL. Cells were washed and FACS sorted as described for E14 cells.

extract_protocol:
Bulk genomic DNA was extracted using the DNeasy kit (Qiagen, 69504) according to the manufacturer’s recommendations. Bulk total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s recommendations. For single cell experiments, whole cell lysate was used by soring cells via FACs directly into lysis buffer.
scDyad-seq is performed similar to scDyad&T-seq, except the initial reverse transcription and second strand synthesis steps are replaced with the equivalent volume of 1x NEBuffer 4. In addition, as the transcriptome is not captured, IVT is not performed and steps involving RNA enrichment and processing are omitted.

treatment_protocol:
Decitabine treatment: E14 mouse embryonic stem cells were cultured as described above. Upon passage of the E14 cells, SL media was supplemented with 0.05 µM of Decitabine. After 24 hours, cells were harvested using 0.25% trypsin-EDTA. The trypsin was then inactivated using serum containing medium. The cells were washed with 1x DPBS and then resuspended in 200 µL of DPBS. Genomic DNA was extracted using the DNeasy kit (Qiagen, 69504) according to the manufacturer’s recommendations.
K562 cells were cultured as described above. Upon passage, the media was supplemented with 0.6 µM of Decitabine or DMSO vehicle control. After 24 hours the cells were washed and single-cell FACS sorting was performed as described above.
Transition from serum to 2i and other media conditions: E14 mouse embryonic stem cells were cultured in SL conditions as described above. Upon passage, cells were resuspended in the following media depending on the condition studied. Commercial 2i media containing LIF (Millipore, SF016-200) was used for BL, G, 2i, and M experiments. For 2i, all components were used according to the manufacturer's recommendations. For G and M conditions, only the GSK3B inhibitor or MEK1/2 inhibitor was added, respectively. For the BL condition, no inhibitors were added. For the No condition, commercial 2i media without LIF (Millipore, SF002-100) was used with no inhibitors added. After 24 hours, the cells were washed with 1x DPBS and the media was exchanged. 48 hours after the initial media switch, the cells were collected using 0.25% trypsin-EDTA, quenched using serum containing media, washed in 1x DPBS and finally resuspended in 1x DPBS. The sample was then split in half for genomic DNA and total RNA extraction.
In single-cell serum to 2i experiments, the same process was followed with cells being isolated into a reaction well of a 384 well plate using FACS after 3, 6, or 10 days in 2i. Cells grown in 2i were split 1:6 every other day.

tag: conditions

value: Cells 1-48:DMSO vehicle control 24hr; Cells 49:96:0.6 µM DAC 24hr

tag: strategy

value: scDyad-sq


title: BVSC Gastruloid, 120h, PECAM+, rep2

tag: cell line


title: K562 DAC3L2


title: SARS-CoV-2 Uninfected  L-070

description: SARS-CoV-2 Uninfected

value: Uninfected Control


title: K562 DAC3L1


title: BVSC Gastruloid, 142h, Blimp1-Venus+SSEA1+, rep1


title: BVSC Gastruloid, 144h, Blimp1-Venus+SSEA1+, rep1

value: 144h after aggregation


title: SARS-CoV-2 Uninfected  L-072

description: SARS-CoV-2 Uninfected


title: mESC-WT_polyA-RNA_Treated_rep1

city: Chicago

value: cell line

value: mESC

value: embryonic stem cell


title: SARS-CoV-2 Uninfected  L-071

description: SARS-CoV-2 Uninfected

value: Upper airway epithelial tissue


title: HA-MITF-K206R_Input_control

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

description: Input control for K206R mutant

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Three technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} against hg38 build
Mapped SAM-files were used for peak calling using the Homer package {Heinz, 2010}
Homer was used to generated bedgraphs with bp resolution with counts normalised to 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph of normalised counts for uniqely aligned reads

source_name: Input control for K206R mutant

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
30x-15cm dishes of 501mel cells were fixed in 0.4% PFA then cheared with a Covaris S220 for 15 minutes (160 W peak incident power, 5% duty cycle and 200 cycles per burst). The sonicated chromatin were precleared and ChIP was performed using 120ug of the indicated antibodies. Purification of the ChIP-DNA was done using QIAGEN PCR clean-up column
Libraries were prepared using recommended Illumina protocols

treatment_protocol: Cells were grown overnight with or without 20ng/ml Doxycycline, prior to fixation in 0.4% PFA in PBS (as described in Louphrasitthiphol et al., 2019)

value: melanoma

tag: chip antibody

value: none (input)


title: HA-MITF-K206R_100ng_Dox_Replicate2

description: HA-MITF-K206R ChIP with 100ng/ml Dox relicate 2


title: SARS-CoV-2 Uninfected  L-074

description: SARS-CoV-2 Uninfected


title: SARS-CoV-2 Uninfected  L-073

description: SARS-CoV-2 Uninfected


title: HA-MITF-K206R_20ng_Dox_Replicate2

description: HA-MITF-K206R ChIP with 20ng/ml Dox relicate 2


title: SARS-CoV-2 Infected L-075

description: SARS-CoV-2 Infected

value: Mild


title: HA-MITF-K206R_100ng_Dox_Replicate1

description: HA-MITF-K206R ChIP with 100ng/ml Dox relicate 1


title: SARS-CoV-2 Infected L-080

description: SARS-CoV-2 Infected


title: HA-MITF-K206R_20ng_Dox_Replicate1

description: HA-MITF-K206R ChIP with 20ng/ml Dox relicate 1


title: BVSC Gastruloid, 120h, Blimp1-Venus+SSEA1+, rep2

value: Mouse gastruloid


title: SARS-CoV-2 Infected L-082

description: SARS-CoV-2 Infected


title: 7: iBMDM cells, DSF, LPS-1

first: Yang

last: Bai

address: Yueyang Road No.320

institute: Chinese Academy of Sciences

data_processing:
Libaries were sequenced on an Illumina Novaseq 6000 platform (Illumina).
Image analysis and base calling were conducted using the Illumina RTA software.
Sequencing reads were aligned to the Mus musculus reference genome (GRCm39) obtained from GENCODE.
R package DESeq2 was used to analyze differential expression and fold change.
Assembly: GRCm39
Supplementary files format and content: Excel file includes raw counts and for each sample

source_name: iBMDM

growth_protocol: Cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine (Gibco), 50 U/ml penicillin and 50 mg/ ml streptomycin (Gibco), and 50 μM 2-ME at 37°C in humidified air with 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Thermo Fisher Scientific, 15596026) according the manufacturer’s instructions as described. 20 to 30 μg of total RNA each group was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the VAHTS mRNA-seq V3 library prep kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: iBMDMs were pretreated with 5 μM DSF or DMSO for 0.5 hr and then challenged with 1 μg/ml LPS or equal volume of vehicle (ddwater) for 4 hr.

value: iBMDM

value: immortalized macrophage

value: WT

value: DSF pretreated, LPS stimulated


title: MDA-MB-231_shNC rep2

value: Triple negative breast cancer

value: Control


title: 8: iBMDM cells, DSF, LPS-2


title: HA-MITF-K206R_0ng_Dox_Replicate2

description: HA-MITF-K206R ChIP with no Dox relicate 2


title: 6: iBMDM cells, LPS-2

value: LPS stimulated


title: 5: iBMDM cells, LPS-1


title: SARS-CoV-2 Infected L-086

description: SARS-CoV-2 Infected


title: 3: iBMDM cells, DSF-1

value: DSF pretreated


title: BVSC Gastruloid, 96h, Blimp1-Venus+SSEA1+, rep1

value: 96h after aggregation


title: 4: iBMDM cells, DSF-2


title: HA-MITF-K206R_0ng_Dox_Replicate1

description: HA-MITF-K206R ChIP with no Dox relicate 1


title: HA-MITF-K206Q_100ng_Dox_Replicate2

description: HA-MITF-K206Q ChIP with 100ng/ml Dox relicate 2


title: SARS-CoV-2 Infected L-091

description: SARS-CoV-2 Infected

value: Severe


title: HA-MITF-K206Q_100ng_Dox_Replicate1

description: HA-MITF-K206Q ChIP with 100ng/ml Dox relicate 1


title: 1: iBMDM cells, control-1


title: 2: iBMDM cells, control-2


title: SARS-CoV-2 Infected L-093

description: SARS-CoV-2 Infected


title: HA-MITF-K206Q_20ng_Dox_Replicate2

description: HA-MITF-K206Q ChIP with 20ng/ml Dox relicate 2


title: SARS-CoV-2 Uninfected  L-094

description: SARS-CoV-2 Uninfected

value: Uninfected Control


title: HA-MITF-K206Q_20ng_Dox_Replicate1

description: HA-MITF-K206Q ChIP with 20ng/ml Dox relicate 1


title: SARS-CoV-2 Infected L-095

description: SARS-CoV-2 Infected


title: HA-MITF-K206Q_0ng_Dox_Replicate1

description: HA-MITF-K206Q ChIP with no Dox relicate 1


title: SARS-CoV-2 Uninfected  L-096

description: SARS-CoV-2 Uninfected


title: HA-MITF-K206Q_0ng_Dox_Replicate2

description: HA-MITF-K206Q ChIP with no Dox relicate 2


title: knockout PDH memory T-cell sample 4

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr

institute: NHGRI

data_processing:
Raw ATAC-seq data were trimmed to remove residual adapter sequences using Trimmomatic. Adapter seqeunces were supplied by the developed of Trimmomatic in NexteraPE-PE.fa file.
Trimmed reads were mapped to mouse genome reference seqeunce GRCm38 using BWA MEM (v. 0.7.17)
Reads mapping low mappability regions (supplied in ENCFF547MET.bed) were filtered using samtools.
ATAC-seq peaks were identfied using MACS2 software (v. 2.2.7.1)
Assembly: GRCm38
Supplementary files format and content: narrowPeak, bedgraph files

source_name: TPdh-/- T-memory

extract_protocol: Tagmented DNA samples were amplified to add single indexed adapters using the Kapa HiFi PCR MasterMix (Roche). The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt).

value: TPdh-/- T-memory

value: memory T-cell

value: TPdh-/-


title: knockout PDH memory T-cell sample 1


title: knockout PDH memory T-cell sample 2


title: SARS-CoV-2 Uninfected  L-097

description: SARS-CoV-2 Uninfected

value: Upper airway epithelial tissue


title: HA-MITF-K206Q_Input_control

description: Input control for K206Q mutant

source_name: Input control for K206Q mutant

value: melanoma

value: none (input)


title: SARS-CoV-2 Infected L-118

description: SARS-CoV-2 Infected

value: Mild


title: wildtype PDH memory T-cell sample 4

source_name: wildtype T-memory

value: wildtype T-memory

value: TPdh+/+


title: wildtype PDH memory T-cell sample 3


title: SARS-CoV-2 Infected L-089

description: SARS-CoV-2 Infected


title: HA-MITF-WT_Input_control

description: Input control for WT

source_name: Input control for WT


title: wildtype PDH memory T-cell sample 2


title: HA-MITF-WT_100ng_Dox_Replicate2

source_name: HA-MITF-WT ChIP with 100ng/ml Dox relicate 2


title: HA-MITF-WT_20ng_Dox_Replicate2

description: HA-MITF-WT ChIP with 20ng/ml Dox relicate 2


title: HA-MITF-WT_100ng_Dox_Replicate1

description: HA-MITF-WT ChIP with 100ng/ml Dox relicate 1


title: SARS-CoV-2 Infected L-119

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Infected L-088

description: SARS-CoV-2 Infected


title: SARS-CoV-2 Uninfected  L-201

description: SARS-CoV-2 Uninfected


title: wildtype PDH memory T-cell sample 1


title: knockout PDH memory T-cell sample 3


title: HA-MITF-WT_0ng_Dox_Replicate2

description: HA-MITF-WT ChIP with no Dox relicate 2

source_name: HA-MITF-WT ChIP with no Dox relicate 2


title: knockout PDH effector T-cell sample 4

source_name: TPdh-/- T-effector

value: TPdh-/- T-effector

value: effector T-cell


title: IMR32_SMARCC2

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to reference genome of homo sapiens using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for reads distribution analysis. The MACS2 software (Version 2.1.1) was used for peak calling. The bedtools (Version 2.25.0) was used for peaks annotation and peak distribution analysis.
Assembly: hg38
Supplementary files format and content: Read densities were visualized by preparing normalized BigWig files using HOMER.

source_name: IMR-32 cells

growth_protocol: Human neuroblastoma cell line IMR-32 was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Cells were fixed in 1% formaldehyde for 10 min at room temperature, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction.

value: neuroblastoma

tag: passages

tag: antibody

value: SMARCC2 antibody


title: IMR32_CNBP

value: CNBP antibody


title: HA-MITF-WT_20ng_Dox_Replicate1

description: HA-MITF-WT ChIP with 20ng/ml Dox relicate 1


title: HA-MITF-WT_0ng_Dox_Replicate1

description: HA-MITF-WT ChIP with no Dox relicate 1

source_name: HA-MITF-WT ChIP with no Dox relicate 1


title: knockout PDH effector T-cell sample 2


title: IMR32_Input

value: Input genomic DNA


title: wildtype PDH effector T-cell sample 3

source_name: wildtype T-effector

value: wildtype T-effector


title: Wild-type pollen RNA, CMC-treated, replicate 2

city: Dunedin

first: Rowan

middle: Paul

last: Herridge

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Adapter trimming (Fastx clipper, v0.0.14)
De-multiplexing (Fastx collapser v0.0.14)
Mapping (Bowtie2 v2.3.4.1)
feature counts (bedtools v2.29.0)
Assembly: TAIR10
Supplementary files format and content: Gene/TE name, sequence length, and RPM
Supplementary files format and content: Sequence, readcount (for pus7 and pus10 samples)

source_name: pollen

extract_protocol:
tissue ground in liquid nitrogen, Trizol total RNA extraction, 15% urea PAGE fractionation, 17-40nt cut and eluted ON
NEBNext small RNA sequencing kit (CMC samples); Perkin Elmer Nextflex v3 (IP samples)

treatment_protocol: N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)

value: pollen

value: CMC


title: Yeast_total_RNA_ModSeq_Mg

city: New Haven

first: Rafael

middle: de Cesaris

last: Araujo Tavares

state: Connecticut

address: 260 Whitney Ave

institute: Yale University

data_processing:
ShapeMapper2 (Busan et al.2018)
Mg libraries = untreated samples; Mn libraries = modified samples; use ‘--output-counted-mutations’ flag to output counted mutations
Assembly: human 18S rRNA (NCBI ID: 100008588), human 28S rRNA (NCBI ID: 100008589), human 5.8S rRNA (NCBI ID: 100008587), E. coli 16S rRNA (GeneBank ID: J01859.1), E coli 23S rRNA (GeneBank ID: V00331.1), S cerevisiae 18S rRNA (RNAcentral ID: URS00005F2C2D_4932), S cerevisiae 25S rRNA (RNAcentral ID: URS000061F377_4932)
Supplementary files format and content: profile.txt files = csv containing calculated mutation rates for each nucleotide position in the reference sequence; mutation_counts.txt files = csv containing mutation rate compositions for each nucleotide position in the reference sequence

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Human cell lines were grown in DMEM supplemented with 10% fetal bovine serum and 1X antimycotic-antibiotic at 37 deg C; E coli cells were grown in Luria Broth media at 37 deg C; Saccaramyces cerevisiae were grown in YPD at 30 deg C

extract_protocol:
Trizol
cDNA was prepared from total RNA from each source using random nonamer primers and MarathonRT enzyme in the presence of either Mg or Mn as enzymatic cofactors; second-strand synthesis was carried out from each cDNA sample using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module; library preparation was carried out from the resulting dsDNA sample using the Nextera XT DNA kit
Illumina Nextera XT DNA

value: WT strain


title: knockout PDH effector T-cell sample 1

value: TPdh-/-