title: mES_scATAC

data_processing:
The raw sequencing data from the Illumina sequencer was de-multiplexed and processed using Cell Ranger ATAC v2.1 (10X Genomics) pipeline.
FASTQ files were generated with the command ‘cellranger-atac mkfastq’. The mapping of raw reads to mm10 mouse genome and generating count matrices of cell and unique molecular identifier (UMI) barcodes was performed with ‘cellranger-atac count’.
The resulting filtered feature-barcode matrices were further processed using Signac R package v1.11.0(ref) under R v4.3.1
Assembly: mm10
Supplementary files format and content: filtered feature-barcode matrices stored in Hierarchical Data Format (HDF5 or H5)

extract_protocol:
Cell cultures at the growths of log phase were collected and checked for cell number and viability using TC20 automated counter (Bio-Rad). Samples with >90 % viability were processed to prepare single cell suspensions and diluted into target numbers plus multiplet rate (1000 cells plus 0.8 % per library).
Single cell ATAC sequencing libraries were generated using the Chromium Next GEM Single Cell ATAC kit v2 (10x Genomics), following the manufacturer’s manual. Briefly, nuclei suspensions were prepared from single cells diluted in nuclei buffer. The transposition reaction of the nuclei was performed in the mixture of ATAC buffer and enzyme using 30-minute incubation time. The transposed nuclei and barcoding reagents are loaded on the chromium controller to capture single nucleus gel beads and then to perform in-droplet barcoding PCR. Sequencing libraries were constructed by the index PCR of the barcoded free DNA fragments. The resulting ATAC libraries were purified with solid-phase reversible immobilization SPIRI beads (Beckman) and checked on a BioAnalyzer High sensitivity chip (Agilent) and a Qubit fluorometer (InVitrogen) for DNA concentrations and size distributions, respectively.


title: V6.5-meGFP-BRD4 WGS

status: Public on Feb 15 2026

type: SRA

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: V6.5-meGFP-BRD4 WGS

library_source: genomic

data_processing:
Raw FASTQ reads were aligned to the mm10 revision of the mouse reference genome using bowtie v1.2.2 in single-end mode with parameters -k 1 -m 1 -n 2 and -l set to the read length. Coverage in 50bp bins was computed with MACS v1.4.1 with parameters -w -S –shiftsize=200 –space=50 –nomodel and converted to bigWig format using wigToBigWig v4.
Assembly: mm10
Supplementary files format and content: bigWig files with genome-wide read coverage in 50bp bins

molecule: genomic DNA

organism: Mus musculus

growth_protocol: mESC V6.5 cells are male cells derived from a C57BL/6(F) x 129/sv(M) cross. All cell lines were cultured in 2i + LIF medium.

extract_protocol:
Genomic DNA was isolated from three mouse ES cell lines, which are V6.5, V6.5-meGFP-Brd4-meGFP and V6.5-meGFP-Med1, using the QIAGEN AllPrep DNA/RNA Mini kit (QIAGEN, Cat# 80204) and quantified using a Qubit fluorometer with the dsDNA BR kit (Thermo Fisher Scientific, Cat# Q32853). High-molecular-weight DNA was used for library preparation.
Whole-genome sequencing libraries were prepared using the KAPA HyperPrep Library Preparation kit (Roche, Ref# KR0961) according to the manufacturer’s instructions. Briefly, 500 ng of genomic DNA of each cell line was sheared to an average insert size of approximately 350 bp using a Covaris LE220, followed by end repair, A-tailing, and ligation of adapters from ITD for Illumina TrueSeq DNA UDI v2 (Illumina, Ref# 20042113). Adapter-ligated DNA was purified using AmPure XP beads (Beckman Coulter, Ref# A63881) and amplified by 3 cycles of PCR. Amplified libraries were assessed for size distribution and concentration using HS D1000 Screen Tape (Agilent, part# 5067) on a TapeStation system (Agilent, part# 4200) prior to sequencing. Further QC of Libraries was performed using Illumina MiSeq Nano kits. Libraries were pooled at equimolar concentrations and loaded according to Illumina’s recommended loading concentrations. The final sequencing was performed on an Illumina NextSeq 2000 platform using a P1 flow cell with a 300-cycle kit, generating paired-end 150 bp, and 25M PF reads for each sample. Base calling and demultiplexing were carried out using Illumina’s onboard software.

tag: cell line

tag: cell type

value: emborynic stem cells


title: V6.5-meGFP-MED1 WGS

description: Library name: V6.5-meGFP-MED1 WGS


title: BIHi264-A, paclitaxel 3

city: Berlin

first: Christian

last: Schinke

address: Charitéplatz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

description:
Library name: p264_3_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

library_source: transcriptomic

data_processing:
Computational Methods. RNA Seq reads were mapped to human genome (GRCh38.p7) with STAR-version 2.7.3a [95] using the default parameters. Reads were assigned to genes with featureCounts version 2.0.0 [96] with the following parameters: -t exon -g gene_id -s 0 -p, gene annotation - Gencode GRCh38/v25. The differential expression analysis was carried out with DESeq2-version 1.32.0 [97] using the default parameters. We kept genes that have at least 5 reads in at least 3 samples. Gene set enrichment analysis was carried out with R/tmod package version 0.50.07 using MSigDB gene sets [98].
Assembly: GRCh38/v25
Supplementary files format and content: export_raw_counts.00_202501_All_lines_contrasts_full.PTX_vs_DMSO_ID0.all.csv: contains all raw counts of the iPSC-DSN cell lines BIHi005-A, BIHi263-A, BIHi264-A, BIHi272-A, BIHi273-A that were treated with DMSO or paclitaxel.//export_raw_counts.all_Timecourse.csv: contains all raw counts for the different time points of iPSC-DSN BIHi264-A treated with paclitaxel or DMSO.//00_202501_All_lines_contrasts_full.PTX_vs_DMSO_ID0.xlsx: contains differential expression analyses of paclitaxel vs. DMSO treated iPSC-DSN with pooled data of the 5 iPSC-DSN cell lines mentioned above.//01_contrasts_full.2h_PTX_vs_DMSO_ID1.xlsx, 02_contrasts_full.6h_PTX_vs_DMSO_ID2.xlsx, 03_contrast.12h_PTX_vs_DMSO_ID3.andTPMs, 04_contrast.24h_PTX_vs_DMSO_ID4.andTPMs.xls, 05_contrasts_full.48h_PTX_vs_DMSO_ID5.xlsx, 06_contrasts_full.72h_PTX_vs_DMSO_ID0.xlsx and 07_contrasts_full.5d_PTX_vs_DMSO_ID6.xlsx are the differential expression analyses tables of iPSC-DSN BIHi264-A treated with paclitaxel or DMSO for the respective time points mentioned in the tables.
Supplementary files format and content: see above

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC-DSN

growth_protocol: iPSC lines Experiments from this study were conducted in sensory neurons derived from five different iPSC lines, s.c. BIHi263-A, BIHi264-A, BIHi272-A, BIHi273-A (all female, ClinicalTrials identifier NCT02753036; ethics approval at Charité [EA4/069/14], referenced in [32]) and the established reference stem cell line BIHi005-A (male donor, https://hpscreg.eu/cell-line/BIHi005-A). Written informed consent was obtained from all individuals prior to sample acquisition. iPSC were reprogrammed from peripheral mononuclear blood cells (PBMC) or dermal fibroblasts (only BIHi005-A) using Sendai viral vectors, according to established protocols [90-92]. iPSC were tested for the absence of the reprogramming vector with immunofluorescence staining for pluripotency markers, in-vitro directed differentiation into the three germ layers, karyotyping using SNP arrays and g banding and absence of mycoplasma contamination [90, 91]. iPSC were maintained on growth factor reduced Geltrex (Gibco) in E8 media, which was exchanged daily. Cells were enzymatically clump-passaged every 2-4 days when >70% confluency was reached using EDTA (UltraPure™ 0.5 M EDTA, Thermo Fisher). Sensory neuron differentiation and maintenance Differentiation was performed as described previously [30] according to the protocol of Chambers et al. [26] with modification in media formulations according to the s.c. P2 protocol by Schwartzentruber et al. [93]. In brief, >70% confluent clump-passaged iPSCs were single-cell seeded at a density between 200.000-400.000/well into 6-well plates (Falcon) coated with growth factor reduced Geltrex (Gibco) and cultivated in E8 media until 70-80% confluency was achieved, which usually required 48 to 72h. On day 0, neural induction was commenced by replacing E8 media with Knockout Serum Replacement Media (500ml DMEM-KO [Gibco]) supplemented with 130ml CTS KnockOut SR XenoFree Medium (Gibco), 1x MEM-Non-essential Amino Acid Solution (Sigma), 1x Glutamax (Gibco) and 0.01mM β-Mercapto-ethanol (Gibco) containing the two small molecule inhibitors ‘2i’: 100 nM LDN-193189 (Sigma) and 10 µM SB-431542 (Peprotech) to drive neuroectoderm differentiation. On day 2, ‘3i’ consisting of 3 µM CHIR99021 (Sigma), 10µM DAPT (Sigma) and 10 µM SU5402 (Sigma) were added to promote neural crest specification. On day 4, N2B27 media (500ml Neurobasal-Medium [Gibco], 5ml of N-2 (100x) supplement [Gibco], 10ml of B27-supplement (50x) without Vitamin A [Gibco], 1x Glutamax and 0.01mM β-Mercapto-ethanol [Sigma]) was progressively phased in. From day 6 onwards, ‘2i’ addition was ceased but ‘3i’ continued to be added until Day 11. On day 11, iPSC-DSN were reseeded using TrypLe select (Gibco) for dissociation and resuspended in N2B27 maintenance media containing 10 μM ROCK inhibitor, at densities of 48.000/well into geltrex-coated 96-well plates for cell viability/cytotoxicity assays and MTT live assays, 1mio/well into 6-well plates for transcriptomic, proteomic and lipidomic experiments, 30.000cells/well in 48-well MEA plates for electrophysiological assessment, 100.000/well in 8-chamber-slides (ibidi) for calcium imaging or staining and in a droplet at 50.000-100.000cells/well onto coverslips for patch-clamp experiments. ROCK inhibitor containing N2B27 media was removed 24h after reseeding and replaced with N2B27 supplemented with BDNF, GDNF, βNGF and NT3 (all at 25 ng/ml, Peprotech). On day 14, cells were treated with 1 µg/ml Mitomycin C (Sigma) for 2h to eliminate few dividing non-neuronal cells. From day 14 onwards, 1x Pen/Strep (Gibco) was also supplemented. iPSC-DSN were maturated for at least 4 more weeks for viability assays (>d40), at least 40 more days for stainings, calcium imaging and patch-clamp experiments (>d50) and 50 more days for multi-electrode-arrays, transcriptome and proteome analyses (>d60) for relative functional maturity [27]. Half media change was performed every 3-4 days with N2B27 supplemented with BDNF, GDNF, βNGF and NT3 (all at 25ng/ml, Peprotech; summary of differentiation timeline in Suppl. Fig. 7). For references, please refer to our CDDis manuscript.

extract_protocol:
RNA was harvested with the Aurum™ Total RNA Mini Kit according to manufacturers’ instructions.
RNA sequencing was performed by Brooks Life Sciences Genewiz® with PolyA selection for RNA removal, 2x150 bp sequencing configuration and 20-30 million reads per sample. RNA Library Preparation and NovaSeq Sequencing by AzentaLifeSciences Genewiz: RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies) and RNA integrity was checked with an RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB, Ipswich). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies), and quantified by using Qubit 4.0 Fluorometer (Invitrogen). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and basecalling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was tolerated for index sequence identification.

treatment_protocol: Compound preparation Paclitaxel (Adipogen) was dissolved in the appropriate amount of DMSO to reach a 6mM stock solution, which was further diluted in N2B27 media to reach the final concentrations 100pM, 1nM, 10nM, 100nM, 1µM and 10µM. Concentrations of the vehicles were adapted to the amount of DMSO in which the highest paclitaxel dosage was dissolved, e.g., 1/600 DMSO for cell viability experiments (as paclitaxel concentrations reached a maximum of 10µM for viability curve calculation), or 1/60.000 for RNA sequencing, proteomic and lipidomic experiments (paclitaxel concentration of 100nM). All solutions were prepared on the day of experimentation. Cell viability and cytotoxicity assays For the calculation of cell viability, RealTime-Glo™ MT Cell Viability Assays (Promega) were performed in white wall, clear bottom 96-well imaging plates (Greiner), according to the manufacturers’ instructions. Luminescence intensities were measured every 12 hours up to 108 h using the Berthold TriStar LB 941 luminescence reader, with Mikrowin Software, and all values were background subtracted and normalized to the individual well baseline and vehicle control [94].

tag: tissue

value: iPSC-DSN

value: Maturation more than 55d

tag: genotype

value: Wildtype

tag: treatment

value: Paclitaxel 100 nM, 48h

tag: batch

value: Batch 1


title: Plate3: LowAuto_STARV_R2(A1 to A12),HighAuto_STARV_R2(E9 to F8),Unsort_STARV_R1(F9 to G10),Unsort_STARV_R2 (G11 to H12)

city: Manhattan

first: Mohamad

last: Assi

state: NY

address: 550 1st Ave

department: Radiation Oncology

institute: NYU Medical Center

data_processing:
Analysis of screening data was performed using the Apron tool from the Broad institute
Log-normalized read counts were calculated and guides below three standard deviations were removed
Unsorted samples were used as reference and Log-fold change was calculated by subtracting the reference from the sample of interest
Z-scores were calculated per gene using Stouffer’s method and P-value was determined and adjusted at the sample level using the Benjamini-Hochberg procedure
To determine 3D-specific targets, read counts from 3D screens were subtracted from 2D starvation screens.
Assembly: hg38
Supplementary files format and content: Data are submitted in Excel format with Z-scores for each sample

source_name: Cell line

growth_protocol: DMEM 10% FBS, 1% Pen/Strep with 3% Matrigel for 3 days in ultralow attachment plates. Or 2D monolyer under nutrient starvation (no FBS, no amino acids, no sodium pyruvate) for 24h.

extract_protocol:
DNA was extracted from frozen pellets (51194, Qiagen)
PCR performed on genomic DNA to attach sequencing adaptors

value: Cell line

value: Pancreatic cancer cells


title: V6.5 WGS

description: Library name: V6.5 WGS


title: BIHi264-A, paclitaxel 2

description:
Library name: p264_2_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi264-A, paclitaxel 1

description:
Library name: p264_1_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi264-A, DMSO 2

description:
Library name: p264_2_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: Plate2: LowAuto_3D_R2 (A1 to A12), HighAuto_3D_R2 (E12 to F9), Unsort_3D_R1 (F10 to G11), Unsort_3D_R2 (G12 to H12)


title: BIHi263-A, paclitaxel 3

description:
Library name: p263_6_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi263-A, DMSO 3

description:
Library name: p263_6_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: WT_1

city: Montreal

first: Philippe

last: Roux

state: Quebec

address: 2950 Polytechnic Rd

country: Canada

institute: Université de Montréal

description: Library name: WT_1

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode 32
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 32 transcript annotations
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

molecule: total RNA

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: mammary epithelial

value: Serum-growing

value: Same


title: SP16_3

description: Library name: SP16_3


title: BIHi264-A, DMSO 3

description:
Library name: p264_3_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi264-A, DMSO 1

description:
Library name: p264_1_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: WT_3

description: Library name: WT_3


title: WT_2

description: Library name: WT_2


title: SP16_2

description: Library name: SP16_2


title: BIHi263-A, paclitaxel 1

description:
Library name: p263_4_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi005-A, paclitaxel 3

description:
Library name: p005_15_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

value: Maturation more than 60d


title: BIHi263-A, DMSO 2

description:
Library name: p263_5_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: SP16_1

description: Library name: SP16_1


title: BIHi005-A, DMSO 3

description:
Library name: p005_15_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi263-A, paclitaxel 2

description:
Library name: p263_5_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: BIHi005-A, paclitaxel 2

description:
Library name: p005_14_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: MOCK_3

description: Library name: MOCK_3

value: Empty vector


title: BIHi263-A, DMSO 1

description:
Library name: p263_4_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: MOCK_2

description: Library name: MOCK_2


title: Sample39_Pt_RNAseq_withoutIL6_24h

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRDA

country: Japan

institute: Kumamoto University

description: Library name: Sample39

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore.
Trimmed sequence reads were mapped to hg19 using STAR 2.7.8a.
Read count extraction and normalization were performed using RSEM v1.3.3.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM for each sample.

source_name: multiple myeloma cells

growth_protocol: Multiple myeloma cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 mM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Multiple myeloma cells were treated with or without IL-6. For knockdown experiments, multiple myeloma cells expressing Cas9 were transduced with sgRNA by lentivirus. The infected cells were selected with puromycin for 2 days.

value: multiple myeloma cells

value: without IL-6 for 24 h

tag: matrix column_name


title: BIHi005-A, DMSO 1

description:
Library name: p005_13_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: Sample40_Pt_RNAseq_withIL6_24h

description: Library name: Sample40

value: with IL-6 for 24 h


title: BIHi005-A, DMSO 2

description:
Library name: p005_14_Control
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO


title: Sample38_INA6_RNAseq_sgELL2_withIL6_rep2

description: Library name: Sample38

value: multiple myeloma cell line

value: sgELL2, with IL-6


title: Sample35_INA6_RNAseq_sgPOU2AF1_withIL6_rep1

description: Library name: Sample35

value: sgPOU2AF1, with IL-6


title: HEK293T-input-IV-rep1

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

description: Library name: Library-53

data_processing:
Only R2 reads were used except for the sictrl and siDKC1 samples as described below.
Trim adapter: Adapter sequence of “AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT” was first trimmed from the 3’ end of poly-A RNA R2
Deduplicate using bbmap clumpify.sh
Trim UMI: Reads R2 from samples generated with superscript III were trimmed 6 nt on the 5’ end and 5 nt on the 3’ end, whereas reads from samples generated with superscript IV was trimmed 7nt on the 5’ end and 5nt on the 3’ end as superscript IV tends to elongate for one more nucleotide.
For the sictrl and siDKC1 samples, paired end sequencing were used. However, reads R1 and R2 were first merged, then decomplexed based on the internal barcodes. The resulting files are therefore uploaded as one file for each sample and labeled as "single-end" even though they were merged paired-end reads. The internal barcodes and UMI (8 nt in total on the 5' end and 5 nt in total on the 3' end) need to be trimmed after reads de-duplication.
Reads after adapter trimming, deduplication and UMI trimming were mapped to hg38 using hisat2 with options of “--known-splicesite-infile --rna-strandness F --no-softclip”.
Assembly: hg38
Supplementary files format and content: The .xlsx files contain information of candidate modification sites identified in different cell lines and under different conditions and the change of enrichment levels under the control and DKC1 knockdown conditions.

source_name: HEK 293T

growth_protocol: HEK 293T, HeLa and LN229 cell lines were grown and maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C with 5% CO2. The day before transfection, 2 × 10⁶ HEK293T cells were seeded onto each 15 cm cell culture plate.

extract_protocol:
RNAs were extracted from cells using Trizol reagent and polyA RNA were extracted using Dynabeads® mRNA DIRECT™ Kit for two rounds. Messenger RNAs were extracted with an additional ribosome RNA removal step using the RiboMinus™ Eukaryote Kit v2.
Libraries were constructed using a customized protocol. For the experiments of DKC1 knockdown, internally barcoded RNA adapters, wo that the four input samples (2 sictrl reps and 2 siDKC1 reps) and the four pull-down samples can be pooled together right after the RNA ligation. For IVT RNA, the RNA was mixed with rice mRNA in 1:1 ratio and then proceeded with library construction using ELAP-seq.

treatment_protocol: For interferon stimulation, interferon-α was added to LN229 cell lines at 500 U/mL when cells were at least 80% confluency and incubated for 24 h before collecting cells for RNA isolation. For siRNA knockdown experiments, transfection was performed using RNAiMax transfection reagent following manufacturer's instructions. For one 15 cm plate, 20 μL of 20 μM siDKC1 (Qiagen, Hs_DKC1_6 FlexiTube siRNA) or siCtrl (Sigma Aldrich, catalog # sic001) was used. Cells were harvested 72–96 hours post-transfection.

value: HEK 293T

value: cancer cells

value: WT


title: Plate1: LowAuto_3D_R1 (A1 to A6), HighAuto_3D_R1 (C8 to C12), LowAuto_STARV_R1 (D1 to D6), HighAuto_STARV_R1 (H1 to H7)


title: BIHi005-A, paclitaxel 1

description:
Library name: p005_13_Treatment
RNA Seq data of 5different iPSC-DSN cell lines, paclitaxel vs. DMSO

value: iPSC-DSN

value: Wildtype

value: Paclitaxel 100 nM, 48h

value: Batch 1


title: Sample34_INA6_RNAseq_sgEGFP_withIL6_rep2

description: Library name: Sample34

value: sgEGFP, with IL-6


title: Sample33_INA6_RNAseq_sgEGFP_withIL6_rep1

description: Library name: Sample33


title: Sample37_INA6_RNAseq_sgELL2_withIL6_rep1

description: Library name: Sample37


title: HEK293T-input-IV-rep2

description: Library name: Library-54


title: Sample36_INA6_RNAseq_sgPOU2AF1_withIL6_rep2

description: Library name: Sample36


title: Sample32_MM1S_RNAseq_sgELL2_withIL6_rep2

description: Library name: Sample32

value: sgELL2, with IL-6 for 24 h


title: RNA-seq, mRNA, im, 1h, patient 3 after 6 months of imatinib

city: New Haven

first: Paulina

last: Podszywalow-Bartnicka

state: CT

address: 333 Cedar Street

department: Department of Molecular Biophysics and Biochemistry

institute: Yale University

description: Library name: CML_IM1h4

data_processing:
Fastp was used to filter raw reads for quality and trim; STAR was used to align reads to the reference genome; FeatureCounts was used to determine number of reads per gene in each sample in the STAR output bam file.
Assembly: GRCh38.p14
Supplementary files format and content: The ‘CML_featurecounts.txt’ is a file containing featureCounts output numbers of reads assigned to genes (Geneid) for each STAR output bam file.

source_name: CML CD34

growth_protocol: Primary CD34+ cells were enriched from CML patient samples using magnetic beads with anti-CD34 antibodies and separated on columns, following the manufacturer’s protocol (Miltenyi).

extract_protocol:
Trizol (TRI Reagent) is used to isolate total RNA from whole cells.
mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Samples are then fragmented using heat and magnesium. 1st strand synthesis is performed using random priming.  2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA.  Adapters are then ligated and the library is amplified.  Strands marked with dUTPs are not amplified allowing for strand-specific sequencing.  Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using KAPA Biosystems kit (# KK4854) and insert size distribution determined with Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: Imatinib was pre-diluted in growth media and added to the cell culture at 1uM.

value: CML CD34

value: patient 3_6months_IM

value: im for 1h


title: RNA-seq, mRNA, untreated, patient 3 after 6 months of imatinib

description: Library name: CML_untr4

value: untreated


title: RNA-seq, mRNA, im, 1h, patient 2

description: Library name: CML_IM1h2

value: patient 2


title: RNA-seq, mRNA, untreated, patient 3

description: Library name: CML_untr3

value: patient 3_diagnosis


title: MOCK_1

description: Library name: MOCK_1

value: mammary epithelial

value: Empty vector

value: Serum-growing

value: Same


title: Sample30_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_withIL6_rep2

description: Library name: Sample30

value: multiple myeloma cell line

value: sgEGFP, with IL-6 for 24 h


title: RNA-seq, mRNA, im, 1h, patient 1

description: Library name: CML_IM1h1

value: patient 1


title: Sample29_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_withIL6_rep1

description: Library name: Sample29


title: Sample28_MM1S_RNAseq_sgPOU2AF1_withIL6_rep2

description: Library name: Sample28

value: sgPOU2AF1, with IL-6 for 24 h


title: RNA-seq, mRNA, untreated, patient 2

description: Library name: CML_untr2


title: Sample26_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_withIL6_rep2

description: Library name: Sample26


title: Sample25_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_withIL6_rep1

description: Library name: Sample25


title: Sample24_INA6_RNAseq_withIL6_24h_rep2

description: Library name: Sample24

value: with IL-6 for 24 h


title: Sample39_MM1S_RNAseq_sgSRSF1_withIL6_rep3

description: Library name: Sample39

data_processing:
Sequence reads in FASTQ were processed for alignment with STAR(2.7.10b) with basic two-pass mode.
Sequence reads with primary alignment were selected with samtools (1.19.2).
Sequence reads were analyzed for PSI using PSI-Sigma (2.3) with supporting read threshold >= 10 and GRCh38 Ensembl version 108 as reference.
Assembly: GRCh38, Ensembl version 108
Supplementary files format and content: output values from PSI-sigma

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Strand-specific mRNA library construction were performed at BGI Genomics (Shenzhen, China) or Novogene (Bejing, China).

value: sgSRSF1, with IL-6 for 24 h


title: Sample41_MM1S_RNAseq_sgHNRNPL_withIL6_rep2

description: Library name: Sample41

value: sgHNRNPL, with IL-6 for 24 h


title: Sample21_INA6_RNAseq_withoutIL6_24h_rep1

description: Library name: Sample21

value: without IL-6 for 24 h


title: Sample22_INA6_RNAseq_withoutIL6_24h_rep2

description: Library name: Sample22


title: Sample37_MM1S_RNAseq_sgSRSF1_withIL6_rep1

description: Library name: Sample37


title: Sample20_MM1S_RNAseq_withIL6_24h_rep2

description: Library name: Sample20


title: Sample38_MM1S_RNAseq_sgSRSF1_withIL6_rep2

description: Library name: Sample38


title: Sample19_MM1S_RNAseq_withIL6_24h_rep1

description: Library name: Sample19


title: Sample42_MM1S_RNAseq_sgHNRNPL_withIL6_rep3

description: Library name: Sample42


title: Sample36_MM1S_RNAseq_sgEGFP_ctrl_for_sgSRSF1sgHNRNPL_withIL6_rep3

description: Library name: Sample36


title: Sample35_MM1S_RNAseq_sgEGFP_ctrl_for_sgSRSF1sgHNRNPL_withIL6_rep2

description: Library name: Sample35


title: Sample17_MM1S_RNAseq_withoutIL6_24h_rep1

description: Library name: Sample17


title: Sample16_MM1S_RNAseq_sgELL2_rep2

description: Library name: Sample16


title: HEK-siDKC1-IP-IV-rep2

description: Library name: Library-72

extract_protocol:
RNAs were extracted from cells using Trizol reagent and polyA RNA were extracted using Dynabeads® mRNA DIRECT™ Kit for two rounds. Messenger RNAs were extracted with an additional ribosome RNA removal step using the RiboMinus™ Eukaryote Kit v2.
Libraries were constructed using a customized protocol. For the experiments of DKC1 knockdown, internally barcoded RNA adapters, wo that the four input samples (2 sictrl reps and 2 siDKC1 reps) and the four pull-down samples can be pooled together right after the RNA ligation.  For IVT RNA, the RNA was mixed with rice mRNA in 1:1 ratio and then proceeded with library construction using ELAP-seq.

value: HEK 293T

value: cancer cells

value: DKC1 KD


title: HEK-siDKC1-IP-IV-rep1

description: Library name: Library-68


title: Sample15_MM1S_RNAseq_sgELL2_rep1

description: Library name: Sample15


title: Sample14_MM1S_RNAseq_sgEGFP_ctrl_for_sgELL2_rep2

description: Library name: Sample14

value: sgEGFP


title: HEK-sictrl-IP-IV-rep2

description: Library name: Library-64

value: WT


title: Sample12_MM1S_RNAseq_sgPOU2AF1_rep2

description: Library name: Sample12


title: HEK-IP-IV-rep3

description: Library name: Library-48


title: HEK-IP-III-rep3

description: Library name: Library-47


title: Sample11_MM1S_RNAseq_sgPOU2AF1_rep1

description: Library name: Sample11


title: Sample10_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_rep2

description: Library name: Sample10


title: HEK-input-IV-rep3

description: Library name: Library-46


title: Sample8_INA6_RNAseq_withIL6_4h_rep2

description: Library name: Sample8

value: with IL-6 for 4 h


title: HEK-input-III-rep3

description: Library name: Library-45


title: HeLa-IP-IV-rep3

description: Library name: Library-44

source_name: HeLa

value: HeLa


title: Sample7_INA6_RNAseq_withIL6_4h_rep1

description: Library name: Sample7


title: HeLa-IP-III-rep3

description: Library name: Library-43


title: Sample6_INA6_RNAseq_withoutIL6_4h_rep2

description: Library name: Sample6

value: without IL-6 for 4 h


title: HeLa-input-IV-rep3

description: Library name: Library-42


title: Sample5_INA6_RNAseq_withoutIL6_4h_rep1

description: Library name: Sample5


title: Sample4_MM1S_RNAseq_withIL6_4h_rep2

description: Library name: Sample4


title: HeLa-input-III-rep3

description: Library name: Library-41


title: Sample9_MM1S_RNAseq_sgEGFP_ctrl_for_sgPOU2AF1_rep1

description: Library name: Sample9


title: RNA-seq, nuclear RNA, jte, 1h, biol rep 3

description: Library name: nuclear_jte1h3

library_source: other

data_processing:
Fastp was used to filter raw reads for quality and trim; STAR was used to align reads to the reference genome; FeatureCounts was used to determine number of reads per gene in each sample in the STAR output bam file.
Assembly: GRCh38.p14
Supplementary files format and content: The ‘_featurecounts.txt’ is a file containing featureCounts output numbers of reads assigned to genes (Geneid) for each STAR output bam file for mRNA or nuclear RNA analysis respectively.

molecule: other

growth_protocol: Cells were cultured in suspension, in 175cm2 flasks, RPMI1640 media supplemented with 10% FBS heat inactivated, Pen/Strep; in the atmosphere of 5% CO2 at 37oC.

extract_protocol:
Cell fractionation, nascent RNA isolation, polyA-RNA and rRNA depletion, and library preparation steps were performed following the protocol described by Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). Briefly, nascent RNA was isolated from the chromatin fraction after washing in PBS. The chromatin pellet was lyzed in Trizol, followed by chloroform extraction and RNA isolation from the aqueous phase using RNAeasy Mini Kit (including on-column treatment with RNAse-free DNAse). Then poly(A)+ RNA was depleted using DynaBeads mRNA Direct Micro Purification kit, followed by rRNA depletion using RiboMinus Eukaryote Kit v2.
Nuclear RNA:  Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351), rRNA is depleted starting from 25-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA.   mRNA: mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Samples are then fragmented using heat and magnesium. 1st strand synthesis is performed using random priming.  2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA.  Adapters are then ligated and the library is amplified.  Strands marked with dUTPs are not amplified allowing for strand-specific sequencing.  Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using KAPA Biosystems kit (# KK4854) and insert size distribution determined with Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: Cells were seeded a day before the addition of treatment. To induce hyperosmotic shock 110mM KCl was added to the media. Imatinib was pre-diluted in growth media and added to the cell culture at 1uM, and JTE-607 at 5uM. Nascent RNA was isolated from cells treated for 45min with KCl, 1h or 18h with IM, or 1h with JTE.

value: jte for 1h


title: Sample3_MM1S_RNAseq_withIL6_4h_rep1

description: Library name: Sample3

value: multiple myeloma cell line


title: RNA-seq, nuclear RNA, jte, 1h, biol rep 2

description: Library name: nuclear_jte1h2


title: Sample2_MM1S_RNAseq_withoutIL6_4h_rep2

description: Library name: Sample2


title: RNA-seq, nuclear RNA, jte, 1h, biol rep 1

description: Library name: nuclear_jte1h1


title: RNA-seq, nuclear RNA, im, 18h, biol rep 3

description: Library name: nuclear_im18h3

value: im for 18h


title: MM1S_ELL2_ChIP_withIL6_24h

description: Library name: Sample14

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore.
Trimmed sequence reads were mapped to hg19 using bowtie2. For spike-in ChIP-seq, reads were also mapped to dm6, and normalized to million-mapped Drosophila reads (reference normalize reads per million).
PCR duplicates were removed from mapped reads using Picard Tools.
Peaks were called using MACS2 version 2.2.7 with a default setting.
BAM files were converted to bigWig files using bamCoverage tool in deepTools.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 mM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
MM.1S cells were crosslinked with 1% formaldehyde (and 2 mM disuccinimidyl glutarate for ChIP with anti-POU2AF1 and anti-ELL2 antibodies). After quenching, the samples were lysed and sonicated using Bioruptor Pico (Diagenode). For ChIP with reference exogenous genome, spike-in chromatin (Active Motif, 53083) was then added. The protein-bound DNA fragments were then immunoprecipitated with specific antibodies. After reverse-crosslinking, DNA was purified using QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

treatment_protocol: MM.1S cells were treated with or without IL-6 for 4 or 24 h.

tag: chip antibody

value: ELL2 (Bethyl Laboratoties, A302-505A), Spike-in antibody (Active Motif, 61686)

tag: spike-in chromatin


title: RNA-seq, nuclear RNA, im, 18h, biol rep 2

description: Library name: nuclear_im18h2


title: MM1S_ELL2_ChIP_withoutIL6_24h

description: Library name: Sample13


title: Sample1_MM1S_RNAseq_withoutIL6_4h_rep1

description: Library name: Sample1


title: RNA-seq, nuclear RNA, im, 18h, biol rep 1

description: Library name: nuclear_im18h1


title: MM1S_POU2AF1_ChIP_withoutIL6_24h

description: Library name: Sample11

value: POU2AF1 (Thermo Fisher, 703325), Spike-in antibody (Active Motif, 61686)


title: MM1S_POU2AF1_ChIP_withIL6_24h

description: Library name: Sample12

value: with IL-6 for 24 h


title: RNA-seq, nuclear RNA, im, 1h, biol rep 2

description: Library name: nuclear_im1h2

value: im for 1h


title: RNA-seq, nuclear RNA, im, 1h, biol rep 3

description: Library name: nuclear_im1h3


title: MM1S_ELL2_ChIP

description: Library name: Sample10

value: ELL2 (Bethyl Laboratoties, A302-505A)


title: MM1S_POU2AF1_ChIP

description: Library name: Sample9

value: POU2AF1 (Thermo Fisher, 703325)


title: RNA-seq, nuclear RNA, im, 1h, biol rep 1

description: Library name: nuclear_im1h1


title: HEK293T-input-III-rep2

description: Library name: Library-52

value: HEK 293T


title: RNA-seq, nuclear RNA, kcl, 1h, biol rep 3

description: Library name: nuclear_kcl1h3

value: kcl for 1h


title: MM1S_pSTAT3_ChIP_withIL6_4h

description: Library name: Sample8

value: p-STAT3 (CST, 9145), Spike-in antibody (Active Motif, 61686)


title: S412_1

status: Public on Feb 16 2026

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

description: Library name: A1

data_processing:
Completed by Novogene
R studio (2023.12.0+369) and R packages ggplot2 (3.4.4),
pheatmap (1.0.12),
biomaRT (2.58.2),
clusterProfiler (4.10.0), org.Hs.eg.db (3.18.0), and AnnotationDbi (1.64.1)
Assembly: hg38
Supplementary files format and content: The processed .tsv file is a tab-delimited text file containing structured data.

source_name: Ovarian

growth_protocol: Cells were grown in 10% RPMI media

extract_protocol:
Trizol
Completed by Novogene

treatment_protocol: 3 uM vorinostat for 48 hours

value: Ovarian

value: Ovarian Cancer

value: DMSO


title: HEK293T-input-III-rep1

description: Library name: Library-51

value: cancer cells

value: WT


title: RNA-seq, nuclear RNA, kcl, 1h, biol rep 2

description: Library name: nuclear_kcl1h2


title: MM1S_H3K27me3_ChIP_withIL6_4h

description: Library name: Sample6

value: H3K27me3 (Merck Millipore, 07-449), Spike-in antibody (Active Motif, 61686)

value: with IL-6 for 4 h


title: MM1S_pSTAT3_ChIP_withoutIL6_4h

description: Library name: Sample7

value: multiple myeloma cell line

value: without IL-6 for 4 h


title: RNA-seq, nuclear RNA, untreated, biol rep 3

description: Library name: nuclear_ctrl3

value: untreated


title: MM1S_H3K27me3_ChIP_withoutIL6_4h

description: Library name: Sample5


title: RNA-seq, nuclear RNA, kcl, 1h, biol rep 1

description: Library name: nuclear_kcl1h1


title: Sample31_MM1S_RNAseq_sgELL2_withIL6_rep1

description: Library name: Sample31

value: sgELL2, with IL-6 for 24 h


title: RNA-seq, nuclear RNA, untreated, biol rep 2

description: Library name: nuclear_ctrl2


title: Sample27_MM1S_RNAseq_sgPOU2AF1_withIL6_rep1

description: Library name: Sample27

value: sgPOU2AF1, with IL-6 for 24 h


title: RNA-seq, mRNA, im, 1h, patient 3

description: Library name: CML_IM1h3

value: CML CD34

value: patient 3_diagnosis

value: im for 1h


title: RNA-seq, nuclear RNA, untreated, biol rep 1

description: Library name: nuclear_ctrl1


title: MM1S_H3K27ac_ChIP_withIL6_4h

description: Library name: Sample4

value: H3K27ac (Abcam, ab4729), Spike-in antibody (Active Motif, 61686)


title: MM1S_H3K27ac_ChIP_withoutIL6_4h

description: Library name: Sample3


title: RNA-seq, mRNA, jte, 18h, biol rep 3

description: Library name: mRNA_jte18h3

value: jte for 18h


title: long-read, nascent RNA, untreated, biol rep 2

description: Library name: LRS_CTRL_2

data_processing:
The data analysis pipeline encompassed pre-processing using modules Cutadapt to trim the adapters, Minimap2 for read alignment, and UMICollapse for deduplication. Custom-made scripts were used to filter poly(A)+ reads, filter and separate categories of reads according to the alignment region, calculating gene readthrough transcription index, and other downstream analyses. Pre-processing steps and custom scripts to filter poly(A)+ reads were consolidated in Snakemake. The code used for data analysis is available at https://github.com/NeugebauerLab/Cancer-stress.
Assembly: GRCh38.p14
Supplementary files format and content: For each sample, the LRS_readthroughCounts.txt contains the number of reads per gene that aligned to the last exon and the downstream of gene region (readthrough). This is an output of a custom-made notebook (splicingANDreadthrough) that calculates the readthrough transcription index of poly(A)-filtered reads (*_polyA_filtered_polyAfiltered_sorted_unique_no_splicing_int.bed), a result of the Snakemake pipeline.

extract_protocol:
Cell fractionation, nascent RNA isolation, polyA-RNA and rRNA depletion, and library preparation steps were performed following the protocol described by Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). Following cell fractionation, RNA was isolated from the chromatin after Trizol/chloroform extraction using RNAeasy Mini Kit (including on-column treatment with RNAse-free DNAse). Then poly(A)+ RNA was depleted using DynaBeads mRNA Direct Micro Purification kit, followed by rRNA depletion using RiboMinus Eukaryote Kit v2. and ligation of a 3’end adapter to each nascent RNA.
Libraries for PacBio sequencing were prepared following the protocol described by Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). After poly(A)+ RNA and rRNA depletion steps, a 3’end DNA adapter with UMI was ligated to each nascent RNA. The PacBio HiFi library for SMARTER/Advantage2 PCR amplified cDNA size selected for fragments longer than 500nt was prepared using SMRTbell Express Template Prep Kit 2.0 from PacBio following the manufacturer’s instructions.


title: L-2

city: Nantong

first: Chen

last: Chen

state: Jiangsu Province

address: Qixiu Road,Nantong,226001,Jiangsu,China

country: China

institute: Nantong university

description:
Library name: Sample8
L-2_tpm

data_processing:
1. Raw data processing:    - Sequencing was performed on the Illumina NovaSeq 6000 platform, generating paired - end reads in FASTQ format.    - Raw reads were first subjected to quality control using FastQC v0.11.9 to assess the quality metrics such as base quality, GC content, and adapter contamination. Reads with low - quality bases (Phred score < 20) and adapter sequences were trimmed using Trimmomatic v0.39 with the following parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36. 2. Read alignment:    - The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome using HISAT2 v2.2.1 with the gene annotation file from GENCODE v38.    - The alignment was performed with the default parameters of HISAT2, except for --rna - strandness RF to account for the stranded library preparation. 3. Gene expression quantification:    - Gene expression levels were quantified as fragments per kilobase of exon per million mapped reads (FPKM) using StringTie v2.1.4. StringTie was run with the --rf option to be consistent with the stranded library. 4. Differential expression analysis:    - Differential expression analysis was performed using DESeq2 v1.32.0. Genes with an adjusted p - value < 0.05 and a fold - change > 2 were considered as differentially expressed genes. 5. Batch effect correction:    - Batch effects were corrected using the ComBat function in the sva R package to remove potential batch - related variations.
Assembly: Mus musculus, GRCm39
Supplementary files format and content: The processed data files are in TSV format. The main file named 'gene_expression_matrix.tsv' contains a gene expression matrix. The first column lists the Ensembl gene IDs, followed by columns representing different samples (Sample1, Sample2, ..., SampleN). The values in each cell are the FPKM (fragments per kilobase of exon per million mapped reads) values, which represent the normalized gene expression levels. Another file named 'diff_expression_results.tsv' shows the results of differential expression analysis. It has columns for gene ID, log2 fold change, p - value, adjusted p - value, and base mean as described above.

source_name: primary cell

extract_protocol:
1. Sample source: Mouse spinal meninges tissue 2. Sample status: Freshly collected primary cell samples without special treatment 3. Extraction reagents and materials     - Lysis buffer: TRIzol reagent (Invitrogen, Cat. No. 15596026)     - Chloroform (Sigma - Aldrich, Cat. No. C2432)     - Isopropanol (Sigma - Aldrich, Cat. No. I9516)     - 75% ethanol (self - made, prepared with RNase - free water and absolute ethanol)     - RNase - free water (Qiagen, Cat. No. 129114) 4. Extraction steps     - Sample lysis: Take approximately 300 ul of cell, add 1 ml of TRIzol reagent, homogenize on ice for 2 - 3 minutes using a homogenizer, and then let it stand at room temperature for 5 minutes.     - Phase separation: Add 0.2 ml of chloroform, vortex vigorously for 15 seconds, let it stand at room temperature for 2 - 3 minutes, and then centrifuge at 12,000 rpm for 15 minutes at 4°C.     - RNA precipitation: Transfer the upper aqueous phase to a new tube, add 0.5 ml of isopropanol, let it stand at room temperature for 10 minutes, and then centrifuge at 12,000 rpm for 10 minutes at 4°C.     - RNA washing: Discard the supernatant, add 1 ml of 75% ethanol, gently invert the tube to mix well, centrifuge at 7,500 rpm for 5 minutes at 4°C, discard the supernatant, and repeat the washing step once.     - RNA dissolution: Air - dry the RNA pellet at room temperature for 5 - 10 minutes, add 50 μl of RNase - free water, and incubate at 55 - 60°C for 10 minutes. 5. Quality control     - RNA concentration measurement: Measured using Nanodrop 2000, and the RNA concentration was 500 ng/μl.     - RNA integrity detection: Detected by Agilent Bioanalyzer, and the RIN value of RNA was 8.5.
1. Starting materials:     - RNA input amount: 1 μg of total RNA     - RNA quality: RIN value of 8.0 2. Library construction kit:     - Kit name: Illumina TruSeq Stranded Total RNA Library Prep Kit     - Manufacturer: Illumina     - Product number: RS - 122 - 2201 3. Main experimental steps:     - RNA fragmentation:         - Fragmentation method: Chemical fragmentation using magnesium ions at high temperature         - Fragmentation conditions: Fragmentation at 94°C for 8 minutes     - Reverse transcription:         - Reverse transcriptase: SuperScript III Reverse Transcriptase (Invitrogen)         - Primer type: Random primers         - Reaction conditions: Reverse transcription at 50°C for 60 minutes     - Adapter ligation:         - Adapter type: Illumina TruSeq adapters         - Ligase: T4 DNA Ligase (NEB)         - Ligation conditions: Ligation at 20°C for 15 minutes     - PCR amplification:         - PCR primers: Universal primers provided by Illumina         - PCR enzyme: Phusion High - Fidelity DNA Polymerase (NEB)         - Number of amplification cycles: 12 cycles         - Amplification conditions: Denaturation at 98°C for 10 seconds, annealing at 65°C for 30 seconds, extension at 72°C for 30 seconds 4. Quality control:     - Library concentration measurement: Measured by Qubit fluorescence quantification, the library concentration was 20 nM     - Library size distribution detection: Detected by Agilent Bioanalyzer, the average library size was 350 bp

value: spinal cord

value: fibroblast


title: RNA-seq, mRNA, jte, 18h, biol rep 2

description: Library name: mRNA_jte18h2


title: Sample40_MM1S_RNAseq_sgHNRNPL_withIL6_rep1

description: Library name: Sample40

value: sgHNRNPL, with IL-6 for 24 h


title: Sample23_INA6_RNAseq_withIL6_24h_rep1

description: Library name: Sample23

value: with IL-6 for 24 h


title: RNA-seq, mRNA, jte, 18h, biol rep 1

description: Library name: mRNA_jte18h1


title: MM1S_H3K4me3_ChIP_withIL6_4h

description: Library name: Sample2

value: H3K4me3 (Merck Millipore, 07-473), Spike-in antibody (Active Motif, 61686)


title: MM1S_H3K4me3_ChIP_withoutIL6_4h

description: Library name: Sample1


title: IVT-RNA-IP-IV-rep2

description: Library name: Library-56

value: HEK 293T

value: cancer cells


title: IVT-RNA-IP-III-rep2

description: Library name: Library-55


title: RNA-seq, mRNA, jte, 6h, biol rep 2

description: Library name: mRNA_jte6h2

value: jte for 6h


title: RNA-seq, mRNA, jte, 6h, biol rep 3

description: Library name: mRNA_jte6h3


title: IVT-RNA-input-IV-rep2

description: Library name: Library-54


title: C-2

description:
Library name: Sample2
C-2_tpm


title: RNA-seq, mRNA, jte, 6h, biol rep 1

description: Library name: mRNA_jte6h1


title: RNA-seq, mRNA, jte, 1h, biol rep 3

description: Library name: mRNA_jte1h3

value: jte for 1h


title: RNA-seq, mRNA, jte, 1h, biol rep 2

description: Library name: mRNA_jte1h2


title: IVT-RNA-input-III-rep2

description: Library name: Library-53


title: IVT-RNA-IP-IV-rep1

description: Library name: Library-52


title: IVT-RNA-IP-III-rep1

description: Library name: Library-51


title: RNA-seq, mRNA, jte, 1h, biol rep 1

description: Library name: mRNA_jte1h1


title: RNA-seq, mRNA, im, 18h, biol rep 3

description: Library name: mRNA_im18h3

value: im for 18h


title: IVT-RNA-input-IV-rep1

description: Library name: Library-50


title: RNA-seq, mRNA, im, 18h, biol rep 2

description: Library name: mRNA_im18h2


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ INPUT, replicate 1

city: Houston

first: Christoforos

last: Thomas

state: Texas

address: 6670 Bertner Avenue

department: Department of Medicine

institute: Houston Methodist Research Institute

description:
Series supplementary file: KOERb1_vs_KOERbIN.peaks.narrowPeak
Series supplementary file: KOERb2_vs_KOERbIN.peaks.narrowPeak
Series supplementary file: KOERb3_vs_KOERbIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt

data_processing:
Quality control check using FASTQC
Sequences reads trimmed with Trim-Galore and had their adapters identified and removed using Minion
Genomic alignment (GRCh38 assembly) was performed with bowtie2 at default settings
Alignment files were processed with samtools and bedtools to retain uniquely mapped reads and filter out problematic “ENCODE blacklist” (i.e. hg38-blacklist.v2.bed) regions
Peaks were called using MACS2 (FDR < 0.05) for individual pairs of samples and replicate MACS2 results were combined with MSPC. Briefly, Fisher’s meta-analysis was applied in overlapping peaks between replicates to obtain combined (FDR-corrected) significance levels for each peak and rescue weak peaks that occur in more than one replicate. For the significant peaks, counts of uniquely aligned reads were obtained with bedtools.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, tab-separated significant peak counts (MACS2)

extract_protocol:
KPL4 cells with different ERβ levels (Control, ERβKO and ERβΚΟ+ERβ) were developed and characterized as previously described in Al Absi et al. (2018). Control and ERβ-expressing SUM149 cells were generated by infection with lentivirus containing the pLenti6/V5-FLAG-ERβ1 (full length ERβ) construct. Cells were maintained in HAM’s-F12 media (Corning) supplemented with 7% fetal bovine serum (FBS) (Sigma), 10 mM HEPES (Thermo Fisher), 5 μg/mL insulin (Sigma), 1μg/mL hydrocortisone (Sigma) at 37°C in 5% CO 2. For ligand treatments, cells were cultured in phenol red-free media supplemented with 1% dextran-coated charcoal-treated FBS (Thermo Fisher) for 72 hours prior to treatment with the ERβ agonist LY500307 (ApexBio) or DMSO (Sigma) for 2 hours in the same media. All the cell lines were tested negative for mycoplasma, authenticated by short tandem repeat (STR) profiling and used within three passages after thawing.
ChIP libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645). Quality control of the final libraries was performed on Agilent 2100 Bioanalyzer (Agilent Technologies)

value: breast adenocarcinoma cells

value: ER{beta} knockout + exogenous ER{beta} INPUT


title: ChIP-Seq - KPL4 cells, ERβ-KO, INPUT, replicate 1

description:
Series supplementary file: KO1_vs_KOIN.peaks.narrowPeak
Series supplementary file: KO2_vs_KOIN.peaks.narrowPeak
Series supplementary file: KO3_vs_KOIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt

value: ER{beta} knockout INPUT


title: IVT-RNA-input-III-rep1

description: Library name: Library-49


title: RNA-seq, mRNA, im, 18h, biol rep 1

description: Library name: mRNA_im18h1


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ, replicate 3

description:
Series supplementary file: KOERb3_vs_KOERbIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt

value: ER{beta} knockout + exogenous ER{beta}


title: RNA-seq, mRNA, im, 6h, biol rep 3

description: Library name: mRNA_im6h3

value: im for 6h


title: Sample34_MM1S_RNAseq_sgEGFP_ctrl_for_sgSRSF1sgHNRNPL_withIL6_rep1

description: Library name: Sample34

value: multiple myeloma cell line

value: sgEGFP, with IL-6 for 24 h


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ, replicate 1

description:
Series supplementary file: KOERb1_vs_KOERbIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt


title: RNA-seq, mRNA, im, 6h, biol rep 2

description: Library name: mRNA_im6h2


title: RNA-seq, mRNA, im, 1h, biol rep 3

description: Library name: mRNA_im1h3

value: im for 1h


title: ChIP-Seq - KPL4 cells, ERβ-KO, replicate 3

description:
Series supplementary file: KO3_vs_KOIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt

value: ER{beta} knockout


title: RNA-seq, mRNA, im, 1h, biol rep 2

description: Library name: mRNA_im1h2


title: RNA-seq, mRNA, im, 6h, biol rep 1

description: Library name: mRNA_im6h1


title: ChIP-Seq - KPL4 cells, ERβ-KO, replicate 2

description:
Series supplementary file: KO2_vs_KOIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ, replicate 2

description:
Series supplementary file: KOERb2_vs_KOERbIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt


title: RNA-seq, mRNA, im, 1h, biol rep 1

description: Library name: mRNA_im1h1


title: ChIP-Seq - KPL4 cells, ERβ-KO, replicate 1

description:
Series supplementary file: KO1_vs_KOIN.peaks.narrowPeak
Series supplementary file: ERb-pos_KO_macs2_signif_counts.txt


title: RNA-seq, mRNA, kcl, 3h, biol rep 3

description: Library name: mRNA_kcl3h3

value: kcl for 3h


title: ChIP-Seq - SUM149 cells, Control + exogenous ERβ, replicate 3

description:
Series supplementary file: 8_SUM149ERb3_5_SUM149ERbINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt

value: Control + exogenous ER{beta}


title: ChIP-Seq - SUM149 cells, Control + exogenous ERβ, replicate 2

description:
Series supplementary file: 7_SUM149ERb2_5_SUM149ERbINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt


title: RNA-seq, mRNA, kcl, 3h, biol rep 1

description: Library name: mRNA_kcl3h1


title: ChIP-Seq - SUM149 cells, Control + exogenous ERβ, replicate 1

description:
Series supplementary file: 6_SUM149ERb_5_SUM149ERbINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt


title: RNA-seq, mRNA, kcl, 1h, biol rep 2

description: Library name: mRNA_kcl1h2

value: kcl for 1h


title: ChIP-Seq - SUM149 cells, Control (endogenous ERβ), replicate 3

description:
Series supplementary file: 4_SUM149Lenti3_1_SUM149LentiINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt

value: Control


title: RNA-seq, mRNA, kcl, 1h, biol rep 3

description: Library name: mRNA_kcl1h3


title: ChIP-Seq - SUM149 cells, Control + exogenous ERβ INPUT, replicate 1

description:
Series supplementary file: 6_SUM149ERb_5_SUM149ERbINPUT_peaks.narrowPeak
Series supplementary file: 7_SUM149ERb2_5_SUM149ERbINPUT_peaks.narrowPeak
Series supplementary file: 8_SUM149ERb3_5_SUM149ERbINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt

value: Control + exogenous ER{beta} INPUT


title: RNA-seq, mRNA, kcl, 1h, biol rep 1

description: Library name: mRNA_kcl1h1


title: RNA-seq, mRNA, untreated, biol rep 3

description: Library name: mRNA_ctrl3

value: untreated


title: ChIP-Seq - SUM149 cells, Control (endogenous ERβ), replicate 1

description:
Series supplementary file: 2_SUM149Lenti_1_SUM149LentiINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt


title: ChIP-Seq - SUM149 cells, Control (endogenous ERβ), replicate 2

description:
Series supplementary file: 3_SUM149Lenti2_1_SUM149LentiINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt


title: RNA-seq, mRNA, untreated, biol rep 2

description: Library name: mRNA_ctrl2


title: ChIP-Seq - SUM149 cells, Control (endogenous ERβ),  INPUT, replicate 1

description:
Series supplementary file: 2_SUM149Lenti_1_SUM149LentiINPUT_peaks.narrowPeak
Series supplementary file: 3_SUM149Lenti2_1_SUM149LentiINPUT_peaks.narrowPeak
Series supplementary file: 4_SUM149Lenti3_1_SUM149LentiINPUT_peaks.narrowPeak
Series supplementary file: ERb_KO_SUM_macs2_signif_counts.txt

value: Control INPUT


title: RNA-seq, mRNA, untreated, biol rep 1

description: Library name: mRNA_ctrl1


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + ligand INPUT, replicate 1

description: Series supplementary file: LY5_VH_macs2_signif_counts.txt

value: ER{beta} knockout + exogenous ER{beta} + ligand INPUT


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + vehicle INPUT, replicate 1

value: breast adenocarcinoma cells

value: ER{beta} knockout + exogenous ER{beta} + vehicle INPUT


title: Tumor, CRC 86, ab TCR

first: Erin

last: Adams

state: IL

description: 10x Genomics

data_processing:
Sequences were deconvoluted using Cellranger software v.3.0 and imported into R. Initial QC and gene expression and clustering analysis was conducted using the standard Seurat v5 pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Colon tissue was collected into MACS Tissue Storage Solution (Miltenyi 130-100-008) at 4°C. Tissue was then cut into 1-5mm fragments, before transferring up to 4 x 5 mg slices into vials containing 1 mL freezing media (50:40:10 FBS:RPMI:DMSO). To thaw, vials were warmed for minimum necessary time in 37°C bath, then immediately transferred to 50 mL conical tube filled with RPMI, and centrifuged at 400 xg for 5 minutes. Tissue was dissociated as described (REF: doi: 10.1016/j.cell.2020.06.001), briefly each pellet was resuspended in 5 mL of collagenase-containing enzymatic digestion solution prepared according to manufacturer’s instructions (Miltenyi Human Tumor Dissociation Kit #30-095-929), prewarmed to 37°C. Tissue was incubated at 37°C for 20 min with gentle vortexing at 2–3-minute intervals. Dissociated cells were transferred to 70 μm nylon mesh filter, and filtered cells were centrifuged and resuspended in 3 mL ACK red blood cell lysis buffer (Gibco #A1049201) for 1 minute at RT, then immediately diluted with 10 mL of PBS with 1% FBS. Cells were centrifuged and subsequently resuspended in Live/dead Fixable Near-IR Dead Cell Stain Kit (Thermo # L34975) viability dye solution (1:1000 in PBS), followed by 15 min incubation at RT in the dark. Following viability dye staining, cells were washed and stained for sorting and single-cell RNA sequencing.
Samples were processed for sequencing using the 10X Genomics 5’ Single Cell Immune Profiling workflow. γδ TCR libraries were generated using the 10X universal forward primers and nested custom reverse primers (TRG outer Reverse: AGTCTTCATGGTGTTCCCCTCC, TRG inner Reverse: AAAATAGTGGGCTTGGGGGA, TRD outer Reverse GTCGTGTTGAACTGAACATGTCAC, TRD inner Reverse CAGACAAGCGACATTTGTTCCA). Libraries for all samples were pooled and sequenced on a NovaSeq6000 or NovaX (Illumina) and resultant FASTQs were demultiplexed by the University of Chicago Genomics Facility.
scRNA-seq, CITE-seq, and VDJ libraries

tag: disease state

value: CRC

value: Colon

tag: tissue type

value: Tumor

value: T cells

tag: library type

value: VDJ - ab TCR


title: Normal, CRC 86, ab TCR

description: 10x Genomics

value: adjacent normal


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + ligand, replicate 3

description:
Series supplementary file: 6-Erb-LY5-3_S6_3-ERbVH-3_S3_peaks.narrowPeak
Series supplementary file: LY5_VH_macs2_signif_counts.txt

value: ER{beta} knockout + exogenous ER{beta} + ligand


title: Tumor, CRC 85, ab TCR

description: 10x Genomics


title: Normal, CRC 85, ab TCR

description: 10x Genomics


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + ligand, replicate 1

description:
Series supplementary file: 4-Erb-LY5-1_S4_1-ERbVH-1_S1_peaks.narrowPeak
Series supplementary file: LY5_VH_macs2_signif_counts.txt


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + ligand, replicate 2

description:
Series supplementary file: 5-Erb-LY5-2_S5_2-ERbVH-2_S2_peaks.narrowPeak
Series supplementary file: LY5_VH_macs2_signif_counts.txt


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERb + vehicle, replicate 3

value: ER{beta} knockout + exogenous ER{beta} + vehicle


title: Tumor, CRC 91, ab TCR

description: 10x Genomics


title: Normal, CRC 91, ab TCR

description: 10x Genomics


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + vehicle, replicate 2


title: Tumor, CRC 86, gd TCR

description: 10x Genomics

value: VDJ - gd TCR


title: ChIP-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + vehicle, replicate 1


title: Normal, CRC 86, gd TCR

description: 10x Genomics


title: RNA-Seq - KPL4 cells Control (endogenous ERβ), replicate 3

data_processing:
Quality control check using FASTQC
Sequences reads trimmed with Trim-Galore and had their adapters identified and removed using Minion
Trimmed reads were aligned to GRCh38 human genome with Ensembl v104 annotation using GMAP aligner parameterized for splce-aware execution
Quantification of relative abundance estimates was performed using RSEM
Assembly: GRCh38
Supplementary files format and content: including raw gene counts for each Sample
Supplementary files format and content: including raw transcript counts for each Sample

growth_protocol: Cells were maintained in HAM’s-F12 media (Corning) supplemented with 7% fetal bovine serum (FBS) (Sigma), 10 mM HEPES (Thermo Fisher), 5 μg/mL insulin (Sigma), 1μg/mL hydrocortisone (Sigma) at 37°C in 5% CO 2 . For ligand treatments, cells were cultured in phenol red-free media supplemented with 1% dextran-coated charcoal-treated FBS (Thermo Fisher) for 72 hours prior to treatment with the ERβ agonist LY500307 (ApexBio) or DMSO (Sigma) for 2 (ChIP-Seq) οr 24 (RNA-Seq) hours in the same media.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit (Qiagen) and quantitated in NanoDrop 1000 spectrophotometer (Thermo Fisher). The quality of RNA was evaluated by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries for total RNA were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina)

treatment_protocol: Cells were cultured in phenol red-free media supplemented with 1% dextran-coated charcoal-treated FBS (Thermo Fisher) for 72 hours prior to treatment with 200 nM of the ERβ agonist LY500307 (ApexBio) or DMSO (Sigma) for 24 hours in the same media.

value: endogenous ER{beta}


title: Tumor, CRC 85, gd TCR

description: 10x Genomics


title: Normal, CRC 85, gd TCR

description: 10x Genomics


title: RNA-Seq - KPL4 cells Control (endogenous ERβ), replicate 2


title: RNA-Seq - KPL4 cells, ERβ-KO + exoganous ERβ + ligand, replicate 2

value: ER{beta} knockout + exogneous ER{beta} + ligand


title: Tumor, CRC 91, gd TCR

description: 10x Genomics


title: Normal, CRC 91, gd TCR

description: 10x Genomics


title: RNA-Seq - KPL4 cells Control (endogenous ERβ), replicate 1


title: Tumor, CRC 86, Surface

description:
10x Genomics
T86_barcodes.tsv.gz
T86_features.tsv.gz
T86_matrix.mtx.gz

data_processing:
Sequences were deconvoluted using Cellranger software v.3.0 and imported into R. Initial QC and gene expression and clustering analysis was conducted using the standard Seurat v5 pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

value: Surface

tag: adt

value: TotalSeq C0090 Mouse IgG1k, TotalSeq C0045 anti-human CD4, TotalSeq C0046 anti-human CD8, TotalSeq C0063 anti-human CD45RA, TotalSeq C0148 anti-human CCR7, TotalSeq C0251 anti-human Hashtag 1, TotalSeq C0139 anti-human TCR γ/δ, CD1d-unl tetramer, CD1d-PBS57 tetramer, MR1-5OPRU tetramers


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + ligand, replicate 1


title: RNA-Seq - KPL4 cells, ERβ-KO + exoganous ERβ + ligand, replicate 3


title: Tumor, CRC 85, Surface

description:
10x Genomics
T85_barcodes.tsv.gz
T85_features.tsv.gz
T85_matrix.mtx.gz


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + vehicle, replicate 3


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + vehicle, replicate 2


title: Normal, CRC 86, Surface

description:
10x Genomics
N86_barcodes.tsv.gz
N86_features.tsv.gz
N86_matrix.mtx.gz


title: RNA-seq, mRNA, kcl, 3h, biol rep 2

description: Library name: mRNA_kcl3h2

value: kcl for 3h


title: Normal, CRC 85, Surface

description:
10x Genomics
N85_barcodes.tsv
N85_features.tsv
N85_matrix.mtx


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ + vehicle, replicate 1


title: Tumor, CRC 91, Surface

description:
10x Genomics
T91_barcodes.tsv
T91_features.tsv
T91_matrix.mtx


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ, replicate 3

value: ER{beta} knockout + exogenous ER{beta}


title: Normal, CRC 91, Surface

description:
10x Genomics
N91_barcodes.tsv
N91_features.tsv
N91_matrix.mtx


title: Tumor, CRC 86, Gex


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ, replicate 2

value: breast adenocarcinoma cells


title: Normal, CRC 86, Gex


title: RNA-Seq - KPL4 cells, ERβ-KO + exogenous ERβ, replicate 1


title: Tumor, CRC 85, Gex


title: RNA-Seq - KPL4 cells, ERβ-KO, replicate 2

value: ER{beta} knockout


title: RNA-Seq - KPL4 cells, ERβ-KO, replicate 3


title: RNA-Seq - KPL4 cells, ERβ-KO, replicate 1


title: Tumor, CRC 91, Gex

value: CRC


title: KPL4 cells, ERβ-KO, replicate 2

data_processing:
sRNA-Seq libraries were subjected to automatic quality control, preprocessed and quantified for miRNAs using DIANA-mAP workflow that utilizes FASTQC, Trim-Galore, Minion and DNApi for adapter-contaminant inference and removal and quality trimming and performs quantification using miRDeep2 using precursor/mature miRNA sequences from miRBase v22.1.
Assembly: GRCh38
Supplementary files format and content: Including miRNA counts for each Sample

growth_protocol: Cells were maintained in HAM’s-F12 media (Corning) supplemented with 7% fetal bovine serum (FBS) (Sigma), 10 mM HEPES (Thermo Fisher), 5 μg/mL insulin (Sigma), 1μg/mL hydrocortisone (Sigma) at 37°C in 5% CO 2 .

extract_protocol:
miRNA was reverse transcribed from 20 ng total RNA using the TaqMan™ MicroRNA Reverse Transcription Kit (Thermo Fisher) and miRNA-specific RT-primers
Libraries for miRNA were prepared using the QIAseq miRNA Library Prep Kit for Illumina (QIAGEN). The quality control of the final libraries was performed on an Agilent 2100 Bioanalyzer


title: Normal, CRC 91, Gex

value: Colon


title: Normal, CRC 85, Gex


title: Tumor, CRC 79, ab TCR

description: 10x Genomics

value: Tumor


title: KPL4 cells, ERβ-KO, replicate 3


title: KPL4 cells, ERβ-KO, replicate 1


title: Normal, CRC 79, ab TCR

description: 10x Genomics

value: T cells


title: KPL4 cells, ERβ-KO + exogenous ERβ, replicate 3


title: Tumor, CRC 77, ab TCR

description: 10x Genomics

value: VDJ - ab TCR


title: KPL4 cells, ERβ-KO + exogenous ERβ, replicate 2


title: Normal, CRC 77, ab TCR

description: 10x Genomics

value: adjacent normal


title: Tumor, CRC 79, gd TCR

description: 10x Genomics


title: Normal, CRC 79, gd TCR

description: 10x Genomics


title: long-read, nascent RNA, IM, 18h, biol rep 3

description: Library name: LRS_IM18h_3

value: IM for 18h


title: KPL4 cells, ERβ-KO + exogenous ERβ, replicate 1


title: long-read, nascent RNA, IM, 18h, biol rep 2

description: Library name: LRS_IM18h_2


title: Tumor, CRC 77, gd TCR

description: 10x Genomics


title: Normal, CRC 77, gd TCR

description: 10x Genomics


title: long-read, nascent RNA, IM, 18h, biol rep 1

description: Library name: LRS_IM18h_1


title: long-read, nascent RNA, IM, 1h, biol rep 3

description: Library name: LRS_IM1h_3

value: IM for 1h


title: Tumor, CRC 79, Surface

description:
10x Genomics
T79_barcodes.tsv.gz
T79_features.tsv.gz
T79_matrix.mtx.gz

value: TotalSeq C0090 Mouse IgG1k, TotalSeq C0045 anti-human CD4, TotalSeq C0046 anti-human CD8, TotalSeq C0063 anti-human CD45RA, TotalSeq C0148 anti-human CCR7, CD1d-unl tetramer, CD1d-PBS57 tetramer, MR1-Msmeg,MR1-Msmeg


title: long-read, nascent RNA, IM, 1h, biol rep 2

description: Library name: LRS_IM1h_2


title: long-read, nascent RNA, IM, 1h, biol rep 1

description: Library name: LRS_IM1h_1


title: Tumor, CRC 77, Surface

description:
10x Genomics
T77_barcodes.tsv
T77_features.tsv
T77_matrix.mtx


title: Normal, CRC 77, Surface

description:
10x Genomics
N77_barcodes.tsv
N77_features.tsv
N77_matrix.mtx


title: long-read, nascent RNA, untreated IM control, biol rep 3

description: Library name: LRS_CTRLim_3

value: untreated


title: long-read, nascent RNA, untreated IM control, biol rep 2

description: Library name: LRS_CTRLim_2


title: Tumor, CRC 79, Gex


title: Normal, CRC 79, Gex

description:
10x Genomics
N79_barcodes.tsv
N79_features.tsv
N79_matrix.mtx


title: Normal, CRC 79, Surface


title: Tumor, CRC 77, Gex


title: Normal, CRC 77, Gex


title: THP-1, cinnamaldehyde, rep4

city: Hefei

first: Wenqian

last: Li

address: Longzihu Road

institute: Anhui University of Chinese Medicine

description:
Library name: Sample16
CIN_4

data_processing:
The raw paired-end reads were trimmed and quality controlled by fastp with default parameters. Then, clean reads were separately aligned to the reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method, and RSEM was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: table-delimited text file includes read counts for each sample
Supplementary files format and content: table-delimited text file includes tpm for each sample

source_name: cell line

growth_protocol: Plate THP-1 cells at 8 × 10⁵ cells/mL in a 6-well plate and induce differentiation with 100 ng/mL PMA for 24 h.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

treatment_protocol: Plate THP-1 cells at a density of 8 × 10⁵ cells/mL in a 6-well plate. Induce differentiation with 100 ng/mL PMA for 24 h. After cells adhere, add Candida albicans (final concentration: 2.4 × 10⁶ CFU/mL) and cinnamaldehyde (final concentration: 62.5 μg/mL), then incubate for 2 h. Following incubation, aspirate the medium. Wash cells by slowly adding 1 mL of ice-cold PBS down the side of each well, gently rocking the plate for a few seconds, and aspirating the PBS. Add 500 μL of TRIzol reagent to each well, pipette to homogenize, and transfer the lysate to pre-chilled RNase-free cryovials.

value: cell line

value: Macrophages

value: wild type

value: Macrophages were Infected with Candida albicans in the presence of cinnamaldehyde


title: THP-1, cinnamaldehyde, rep5

description:
Library name: Sample17
CIN_5


title: Tumor, CRC 81, ab TCR

description: 10x Genomics


title: long-read, nascent RNA, untreated IM control, biol rep 1

description: Library name: LRS_CTRLim_1


title: THP-1, cinnamaldehyde, rep6

description:
Library name: Sample18
CIN_6


title: Normal, CRC 81, ab TCR

description: 10x Genomics


title: THP-1, cinnamaldehyde, rep3

description:
Library name: Sample15
CIN_3


title: THP-1, cinnamaldehyde, rep2

description:
Library name: Sample14
CIN_2


title: Tumor, CRC 78, ab TCR

description: 10x Genomics


title: THP-1, cinnamaldehyde, rep1

description:
Library name: Sample13
CIN_1


title: THP-1, Model, rep6

description:
Library name: Sample12
Model_6

value: Macrophages were Infected with Candida albicans in the absence of cinnamaldehyde


title: THP-1, Model, rep5

description:
Library name: Sample11
Model_5


title: Normal, CRC 81, gd TCR

description: 10x Genomics

value: VDJ - gd TCR


title: THP-1, Model, rep4

description:
Library name: Sample10
Model_4


title: Tumor, CRC 78, gd TCR

description: 10x Genomics


title: THP-1, Model, rep2

description:
Library name: Sample8
Model_2


title: Normal, CRC 78, ab TCR

description: 10x Genomics


title: Tumor, CRC 81, Surface

description:
10x Genomics
T81_barcodes.tsv.gz
T81_features.tsv.gz
T81_matrix.mtx.gz

value: Surface


title: Normal, CRC 81, Surface

description:
10x Genomics
N81_barcodes.tsv.gz
N81_features.tsv.gz
N81_matrix.mtx.gz

value: CRC


title: THP-1, Control, rep6

description:
Library name: Sample6
Control_6

value: Incubate at 37 ℃ without the infection of Candida albicans


title: THP-1, Control, rep5

description:
Library name: Sample5
Control_5


title: THP-1, Model, rep3

description:
Library name: Sample9
Model_3


title: Tumor, CRC 78, Surface

description:
10x Genomics
T78_barcodes.tsv.gz
T78_features.tsv.gz
T78_matrix.mtx.gz

value: Colon

value: Tumor


title: Normal, CRC 78, Surface

description:
10x Genomics
N78_barcodes.tsv.gz
N78_features.tsv.gz
N78_matrix.mtx.gz

value: T cells


title: Normal, CRC 78, gd TCR

description: 10x Genomics

value: adjacent normal


title: Tumor, CRC 81, Gex


title: THP-1, Control, rep3

description:
Library name: Sample3
Control_3


title: Normal, CRC 81, Gex


title: THP-1, Model, rep1

description:
Library name: Sample7
Model_1


title: THP-1, Control, rep4

description:
Library name: Sample4
Control_4


title: THP-1, Control, rep2

description:
Library name: Sample2
Control_2


title: Tumor, CRC 78, Gex


title: THP-1, Control, rep1

description:
Library name: Sample1
Control_1


title: Normal, CRC 78, Gex


title: C. scindens defined media at 24 hours - rep C

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

description:
Library name: C24
JNorth009_C24_386_260123_S43_L001

data_processing:
Raw sequencing reads were processed using Trimmomatic v0.38. Adapter sequences and low-quality bases were removed using the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:50. Reads were trimmed based on when the average quality of the bases dropped below a Phred score of 15 and reads lower than 50 bases after trimming were discarded.
Trimmed reads were aligned with the Clostridium scindens reference genome using Bowtie2 v2.4.1. Alignment output files were written into SAM format.
Alignments were sorted based on chromosomal coordinates using samtools v1.17.
Duplicate reads were identified and marked using the MarkDuplicates function in picard v3.0.0, with the alignment sort order set to “coordinate,” then retained for downstream analysis.
Gene-level read counts were aligned to an annotated reference genome using the featureCounts tool from the subread v2.0.8 package. Reads were aligned to genomic features type gene using gene identification as meta-features. A count table was exported as a text file for downstream analysis. Differential gene expression analysis was conducted using the R package DESeq2 v1.46.0
Assembly: NCBI RefSeq Assembly: GCF_004295125.1
Supplementary files format and content: .txt file. Includes summarized read counts generated by featurecounts using subread

organism: [Clostridium] scindens

source_name: Strain

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit following the manufacturer’s protocol
Ribosomal RNA was depleted from the extracted RNA using the Hybridized Probe, rRNA Depletion, and Probe Removal reaction mixtures from the Illumina Stranded Total RNA Prep (Illumina Inc., San Diego, CA, USA). rRNA-depleted samples were purified using a 2.0x sbeadex SAB bead cleanup (Biosearch Technologies, Hoddesdon, UK) with a single 80% ethanol wash. Following cDNA library construction and indexing, the cDNA libraries were quantified using the Qubit™ 1X dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Thermo Fisher, Carlsbad, CA, USA) and the fragment sizes were assessed using a 4150 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).

value: Strain

value: Bacteria


title: 31-AF-RA_D01_AF_RA

type: genomic

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

hyb_protocol: Array hibridisation was carried out at the QMUL Genome Centre following manufacturer specifications with Infinium MethylationEPIC v2.0 Kit.

scan_protocol: Array scanning was carried out at the QMUL Genome Centre following manufacturer specifications for Infinium MethylationEPIC v2.0 (GPL33022)

data_processing:
Methylation array data was processed to quantify methylation levels for a total of 930,698 CpG sites using the R Bioconductor package meffil (v1.3.6) (Min et al., 2018). Briefly, functional normalisation was applied to array intensity data (“.idat” files) to correct for between-array technical variation. As a quality control, sex of the individuals was properly assigned based on X and Y chromosome probes measurements and multidimensional scaling visualisation displayed clear grouping of anatomical side pairs per individual, confirming the expected inter-individual variability in DNAm signals. Low-quality and sex chromosome probes were removed.
*processed value definition: Methylation status was reported for all measured CpG sites as β-values ranging from 0 to 1 representing the fraction of DNAm signal compared to the total locus signal intensity.

label: biotin (ddCTP and ddGTP) and DNP (ddATP and ddUTP)

source_name: heart right atrium

label_protocol: Bisulfite treatment and subsequent amplification and hybridisation to methylation profiling microarray was performed by the QMUL Genome Centre. The Infinium MethylationEPIC v2.0 kit was used, providing coverage of approximately 930K CpGs, including RefSeq annotated genes, CpG islands and enhancer regions. Even and random distribution of biological groups across two chips of 8 samples each was assigned using the OSAT R Bioconductor package (Yan et al., 2012).

extract_protocol: Genomic DNA was isolated from 16 heart atrial biopsies (AF-LA, n=6; AF-RA, n=5; SR-LA, n=4; SR-RA, n=4) using the DNeasy Blood & Tissue Kit (Qiagen). DNA quality was determined with a NanoDrop Spectrophotometer.

value: heart right atrium

value: atrial fibrillation


title: PATU8902 spheroids, Input_n2

data_processing:
Data quality control was performed using FastQC
Mapping onto human genome and peak calling were performed using BWA and MACS, respectively
functional analysis of peak-associated genes and pathway analysis were performed with GOSeq/topGO, Bioconductor and KOBAS
Assembly: hg38
Supplementary files format and content: Data are submitted as bigwig files for each sample

growth_protocol: DMEM 10% FBS, 1% Pen/Strep with 3% Matrigel for 3 days in ultralow attachment plates

extract_protocol:
SimpleChIP® Enzymatic Chromatin IP Kit (9003S, Cell signaling Tech)
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Cell line

value: Pancreatic cancer cells


title: C. scindens defined media at 24 hours - rep A

description:
Library name: C22
JNorth009_C22_386_260123_S41_L001


title: PATU8902 spheroids, YAP1-pulldown_n2


title: C. scindens supplemented with riboflavin at 24 hours - rep B

description:
Library name: C20
JNorth009_C20_386_260123_S39_L001


title: PATU8902 spheroids, YAP1-pulldown_n1


title: C. scindens supplemented with riboflavin at 24 hours - rep A

description:
Library name: C19
JNorth009_C19_386_260123_S38_L001


title: C. scindens defined media at 24 hours - rep B

description:
Library name: C23
JNorth009_C23_386_260123_S42_L001


title: PATU8902 spheroids, IgG-pulldown_n2 (control)


title: C. scindens supplemented with riboflavin at 24 hours - rep C

description:
Library name: C21
JNorth009_C21_386_260123_S40_L001


title: D_3

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

description:
Library name: Sample 6
4T1 cells were collected from Control group for 24 h

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 6000 platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Assembly: reference sequence used for mice
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: breast

growth_protocol: 4T1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. 4T1 cells transcriptomics were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequencing. The mRNA libraries were constructed and sequenced. In brief, mRNA was purified with poly-T oligo beads and fragmented. First-strand cDNA was synthesized by random hexamer primers, and followed by second-strand synthesis. cDNA products were end-repaired and A-tailed before size selection and adapter ligation. The AMPure XP system was preferentially selected cDNA fragments between 150 and 200 bp in length. Individual sequence libraries were amplified by PCR. Libraries were pooled, and 150 basepair paired-end reads were sequenced.
the mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4T1 cells (5 × 105) were seeded in a six-well plate and incubated for 24 h, and then CS-HA-DAP( 1.17mg·mL-1) were added to the wells and then incubated in an incubator overnight.

value: breast

value: cancer cell

value: WT


title: C. scindens defined media at 14 hours - rep B

description:
Library name: C17
JNorth009_C17_386_260123_S36_L001


title: C. scindens defined media at 14 hours - rep C

description:
Library name: C18
JNorth009_C18_386_260123_S37_L001


title: D_2

description:
Library name: Sample 5
4T1 cells were collected from Control group for 24 h


title: C. scindens defined media at 14 hours - rep A

description:
Library name: C16
JNorth009_C16_386_260123_S35_L001


title: PATU8902 spheroids, 10% of cells with highest autophagy_n3

data_processing:
Raw data of FASTQ format were firstly processed through fastp to generate clean data.
Paired-ends were there mapped to the reference genome using TopHat v2.0.9 software
Cuffdiff (v2.1.1) was used to calculate FPKM of coding genes in each sample
ClusterProfiler software was used for enrichment analysis
Assembly: hg38
Supplementary files format and content: Text file contains FPKM values for each sample

extract_protocol:
RNAqueous Kit (AM1912, Ambion)
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA)

value: 3D-cultured in Matrigel and flow-sorting

tag: group

value: high (High-Auto) autophagy levels


title: Tumor, CRC 81, gd TCR

description: 10x Genomics

value: CRC

value: VDJ - gd TCR


title: C. scindens supplemented with riboflavin at 14 hours - rep C

description:
Library name: C15
JNorth009_C15_386_260123_S34_L001


title: C. scindens supplemented with riboflavin at 14 hours - rep B

description:
Library name: C14
JNorth009_C14_386_260123_S33_L001


title: C. scindens supplemented with riboflavin at 14 hours - rep A

description:
Library name: C13
JNorth009_C13_386_260123_S32_L001


title: PATU8902 spheroids, 10% of cells with highest autophagy_n2


title: CS_HA_DAP_3

description:
Library name: Sample 3
4T1 cells were collected from CS_HA_DAP group for 24 h


title: CS_HA_DAP_2

description:
Library name: Sample 2
4T1 cells were collected from CS_HA_DAP group for 24 h


title: PATU8902 spheroids, 10% of cells with lowest autophagy_n3

value: low (Low-Auto) autophagy levels


title: PATU8902 spheroids, 10% of cells with highest autophagy_n1


title: C. scindens defined media at 12 hours - rep C

description:
Library name: C12
JNorth009_C12_386_260123_S31_L001


title: C. scindens defined media at 12 hours - rep B

description:
Library name: C11
JNorth009_C11_386_260123_S30_L001


title: C. scindens defined media at 12 hours - rep A

description:
Library name: C10
JNorth009_C10_386_260123_S29_L001


title: C. scindens supplemented with riboflavin at 12 hours - rep B

description:
Library name: C08
JNorth009_C08_386_260123_S27_L001


title: CS_HA_DAP_1

description:
Library name: Sample 1
4T1 cells were collected from CS_HA_DAP group for 24 h


title: PATU8902 spheroids, 10% of cells with lowest autophagy_n2


title: C. scindens supplemented with riboflavin at 12 hours - rep A

description:
Library name: C07
JNorth009_C07_386_260123_S26_L001


title: C. scindens supplemented with riboflavin at 11 hours - rep B

description:
Library name: C05
JNorth009_C05_386_260123_S24_L001


title: bsn-37_3

city: xinxing

first: xiaojing

last: xia

address: hualandadao

institute: HENAN INSTITUTE OF SCIENCE AND TECHNOLOGY

description:
Library name: b3
b3_FPKM
b3_SRPBM

data_processing:
The transcrptome was assembled using the String Tle based on the reads mapped to the reference genome .The assembled transcripts were annotated using the gffcompare program . The unknowntranscripts were used to screen for putative IncRNAs. Four computational approaches include CPC2/CNCIPfam/CPAT were combined to sort non-protein codingRNA candidates from putative protetn-coding RNAs In the unknown transcripts Putative proleln- coding RNAs were fitered out using aminimum length and exon number threshold . Transcripts with lengths more than 200 nt and have more than two exons were selected as IncRNA candidates and further screened using CPC2ICNCIPfam/CPAT that have the power to distinguish the protein-coding genes trom the non- coding genes. As well as the different types of IncRNAs Include lIncRNA IntronidncRNA, antl-sense IncRNA, sense IncRNA were selected using cuffcompare
Assembly: GRCm38_release79
Supplementary files format and content: .xls Gene Expression Matrix

source_name: Peritoneal cavity

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitcred on 1.5% agarose gels.RNA concentration and purity was mesured using the advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing
A total amount of 1.5 ug RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, IMadison, WI, USA) Sequencing libraries were generated using NEBNext Uitra TlM Directional RNA Library Prep Kit for Iluminaß (NEB, USA) following manufacturer's recommendations and index codes were added to attrbute sequences to each sample. Briely, Fragmenlation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Butfer (5X) , First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonucleaseipolymerase activitles. Atter adenylalion of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragmenls were punified with AlAPure XP Beads (Beckman Coulter, Beverty, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-igated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelty DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purtied (Al, (Pure XP system) and library quality was assessed on the Agilent Bloanalyzer 2100 and qPCR

value: Peritoneal cavity

value: Marcrophages


title: PATU8902 spheroids, 10% of cells with lowest autophagy_n1


title: bsn-37_2

description:
Library name: b2
b2_FPKM
b2_SRPBM


title: one pooled sample of dissected salivary glands from 3 Tabanus nipponicus female adult

city: Obihiro

first: Noboru

last: Inoue

state: Hokkaido

address: 11 Nishi 2-sen, Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

description:
Library name: Sample 1
Assembled unigene file：TnSG_unigenes.fasta

data_processing:
CLC Genomics Workbench 26.
Sequence reads were trimmed for adapter sequences and low-quality bases using CLC Genomics Workbench with a quality threshold of 0.05.
Read count extraction and normalization were performed using CLC Genomic Workbench.
Assembly: De novo transcriptome assembly was performed using CLC Genomics Workbench.
Supplementary files format and content: FASTA file containing de novo assembled unigenes from the salivary gland transcriptome of Tabanus nipponicus.
Supplementary files format and content: Excel file containing the gene expression results (FPKM/TPM values) of de novo assembled unigenes from the salivary gland transcriptome of Tabanus nipponicus.

organism: Tabanus nipponicus

source_name: salivary gland

growth_protocol: Not applicable.

extract_protocol:
RNA was harvested using TRIZOL reagent (Invitrogen). 1.2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kits (Roche) following manufacturer’s protocols.

treatment_protocol: Under sterile conditions, quickly dissect 3 adult female horse flies, collect the salivary glands, and pool them into a single sample.

value: salivary gland

value: Wild-caught horse flies of 3 individuals after morphological identification were dissected for harvesting salivary gland pooled sample


title: PANC2.03 cells, siITGA3_n3

growth_protocol: DMEM 10% FBS, 1% Pen/Strep.

value: ITGA3 knockdown

value: siRNA-transfected


title: bsn-37_1

description:
Library name: b1
b1_FPKM
b1_SRPBM


title: palbo +rsl3 7

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: Library name: 38084 P+R7

data_processing:
Sequencing reads were mapped separately to Human (GRCh38) and Mouse (GRCm37) genomes using STAR aligner (version 2.7.11a)
R-package XenofilteR was then used to separate mouse reads from human sequence reads. Gene based counting was performed on the human reads using the featureCount function from Rsubread package
Gene count data was used assess inter-sample relationships using hierarchal clustering and PCA.Differential expression analysis was performed using DESeq2 v1.48.2 (Love, Huber, and Anders 2014). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by Rsubread package.

source_name: Xenographt tumor

growth_protocol: 2.5*10^6 cells were injected subcoutaneusly in the mice. When tumor reach 100 mm^3, mice were randomized in 4 experimental group: vehicle, rsl3, palbociclib and Palbociclib+rsl3.

extract_protocol:
RNA was extracted performing the lysis of the tissue with the use of Trizol and Chloroform. Then we extracted the RNA using the Qiagen Rneasy Mini Kit
NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module

value: Xenographt tumor

value: prostate cancer

tag: sample group

value: palbo +rsl3


title: palbo +rsl3 6

description: Library name: 38085 P+R6


title: PANC2.03 cells, siITGA3_n2

value: Cell line

value: Pancreatic cancer cells


title: palbo +rsl3 5

description: Library name: 38096 P+R5


title: PANC2.03 cells, siITGA3_n1


title: Control2

description:
Library name: C2
c2_FPKM
c2_SRPBM


title: palbo +rsl3 4

description: Library name: 38212 P+R4


title: palbo +rsl3 3

description: Library name: 38304 P+R3


title: Control1

description:
Library name: C1
c1_FPKM
c1_SRPBM


title: palbo +rsl3 2

description: Library name: 38300 P+R2


title: PANC2.03 cells, Scr_n3 (control)

value: WT


title: palbo +rsl3 1

description: Library name: 38094 P+R1


title: palbo 6

description: Library name: 38098 P6

value: palbo


title: PANC2.03 cells, Scr_n2 (control)