title: Gulf War Illness #10


title: 990707_IL33_2

status: Public on Dec 10 2025

type: SRA

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

country: USA

institute: Regeneron Pharmaceuticals

description:
Library name: 990707
experiment2_IL33_spleen_mouse2

library_source: transcriptomic

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM for  each Sample/gene

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Tissues/Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen) on the Kingfisher Flex machine (Thermofisher).
Experiment 1-2: The strand-specific RNA-seq libraries were prepared from 500 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2500 (Illumina) by multiplexed single-read run with 33 cycles.  Experiment 3: mRNA was enriched from 4 ug total RNA using two rounds of Dynabeads® Oligo (dT)25 mRNA purification (Invitrogen). Half of the resulting mRNA was converted to mRNA-seq libraries using the ScriptSeq™ mRNA-Seq Library Preparation Kit (EPICENTRE Biotechnologies). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2500 (Illumina) by multiplexed single-read run with 33 cycles.

tag: tissue

value: spleen

tag: treatment

tag: batch


title: 990705_IL13_5

description:
Library name: 990705
experiment2_IL13_spleen_mouse5


title: PT6_10uM_OTA_1

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Library name: PT6_O1

data_processing:
Read quality was assessed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then reads were aligned to the Ensembl GRCh38 patch release 27 genome using the HISAT2 aligner .
Reads were imported into R, summarized as reads/gene using the Bioconductor Rsubread package , and then analyzed using the limma-voom  pipeline. An additional fold change criterion was included in the analysis to restrict to those genes with likely biologically meaningful changes in expression .
Assembly: GRCh38 patch release 27 genome
Supplementary files format and content: All counts are provided in a single file called Counts.txt, with samples in columns and genes in rows. The first column provides the Ensembl Gene ID for that row.

organism: Homo sapiens

source_name: kidney

growth_protocol: Human primary tubule epithelial cells were cultured in DMEM (Gibco, 1130-032) with 1x ITS-A (Gibco, 51300044), 50 nM hydrocortisone (Sigma, H6909) and 1x Antimicrobic-Antimycotic (Gibco, 2520056) until confluence. Cells were passaged using 0.05% trypsin-EDTA (Gibco, 25200056) and neutralized with defined trypsin inhibitor (Gibco, R007100), centrifuged at 400g for 5 minutes, and re-plated with supplemented DMEM solution. Cells are incubated at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891).
Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 or NovaSeq X instrument (Illumina, San Diego, CA).

treatment_protocol: PTECs, in triplicate, were plated in two 24-well plates (Costar, 3548) in supplemented DMEM medium and grown to confluence. Treatment group samples were pre-treated for 48 hours with DMEM medium and either sulforaphane (Sigma, S4441), or tBHQ (Sigma, 112941) and controls were treated with supplemented DMEM medium. Then, plates were treated for 72 hours with ochratoxin-A (Sigma, O1877) in either supplemented DMEM, supplemented DMEM + sulforaphane, or supplemented DMEM + tBHQ. Following 72-hour incubation, cells were lysed with Buffer RLT (Qiagen, 74004).

value: kidney

tag: cell type

value: primary proximal tubule epithelial cells


title: DRG, RA, timepoint 12d, scRNAseq 8

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Pooled libraries were sequenced on Illumina sequencing platform NovaSeq 6000 system on SP-100 flowcells with 91 bp sequenced into the 3’ end (5’ to 3’) of the mRNAs in National Genomics Infrastructure (SciLifeLab). Raw sequencing data were de-multiplexed, converted into fastq format, and aligned to mouse reference mm10 using the STAR aligner to generate the gene-cell matrices.
Samples were aligned with Cellranger 5.1.0 to the mm10 10X reference.
Data was analized using Seurat 4, for cell filtering, dimension reduction and clustering. RDS object also includes final cell type annotations.
Assembly: mm10
Supplementary files format and content: h5 files from Cellranger 5.0.1 output genome assembly mm10 of the filtered feature and barcode matrixes.
Supplementary files format and content: RDS file containing a Seurat object of the final dataset used for analysis, su_seurat.rds

source_name: Dorsal root ganglion

extract_protocol:
C57BL/6N mice (8-10 wk, Charles River, Sweden) were sacrificed with overdosage of isoflurane. Spines were removed and fresh cervical and lumbar dorsal root ganglia (DRGs) were dissected in a 6 cm Petri-dish with DPBS (Sigma) on ice. And 2 male mice were included for each suspension experiment. The following DRG single cell suspension was performed according to our previous protocol with modifications (5). Briefly, dissected DRGs were chopped with microscissors 1-2 times in 2mL Papain (25 unit/mL, Worthington Biochemical) and then incubated at 37 °C, with a mixture of digestion enzymes of Papain/Collagenase/Dispase (Papain, 25 unit/mL, 4 mL; DNase I, 55 unit/mL, 0.5 mL, Worthington Biochemical; and Collagenase and Dispase 20 mg/mL, 800 uL, Worthington Biochemical). The DRGs were triturated up and down 10 times of every 10 min using glass Pasteur pipettes with decreasing diameter (pre-coated with 0.5% BSA). Cell suspension was filtered through a 30 µm cell strainer (CellTrics, Sysmex) and washed with additional 1.5 mL artificial cerebrospinal fluid (ACSF,  87 mM NaCl, 2.5 mM KCl, NaH2PO4 1.25 mM, NaHCO3 26 mM, Sucrose 75 mM, Glucose 20 mM, CaCl2 0.5 mM, MgSO4 4 mM) and 0.5 mL DPBS. Cells were pelleted by centrifugation (300 g 6 min, 4 °C) and resuspended with 1.5 mL cold ACSF with 0.5 mL DPBS. The cell suspension was carefully loaded on top of the same volume of OptiPrep density gradient medium (Sigma) and centrifuged with 700 g ×10 min at 4 °C. The cell pellet was resuspended with 3 mL cold ACSF. SYTOX Blue (Invitrogen, ThermoFisher Scientific) was added to stain dead cells. Thereafter, alive SYTOX Blue-negative cells were sorted with fluorescence activated cell sorting (FACS, BD FACSAria Fusion / BD FACSAria III) at 4 °C. Cells were concentrated by centrifugation (300 g × 5 min, 4 °C) and resuspended with proper volume (~1 000 cells/ µL) of ACSF solution.
Sorted cells were loaded onto the 10× Chromium chip G to yield single cell droplet with v3.1 kit (10× genomics). Targeted cell recovery for each well was settled to 5 000 cells (10% neurons). Reverse transcription, cDNA amplification and library construction were performed according to the user guide provided by 10× genomics.

value: DRG cells

value: Dorsal root ganglion

tag: strain

tag: age

value: 8-10 weeks old

tag: timepoint


title: DRG, RA, timepoint 12d, scRNAseq 7

description: 10x Genomics


title: 990378_ev_10

description:
Library name: 990378
experiment2_empty-vector_spleen_mouse10

value: empty-vector


title: PT6_Control_3

description: Library name: PT6_C3

value: Control


title: 990377_ev_9

description:
Library name: 990377
experiment2_empty-vector_spleen_mouse9


title: PT6_Control_2

description: Library name: PT6_C2


title: Gulf War Illness #7

type: RNA

city: Southport

first: Natalie

last: Eaton-Fitch

state: Queensland

address: Parklands Dr

country: Australia

institute: Griffith University

hyb_protocol: Processed according to nCounter manufacturers instructions

data_processing:
Raw gene expression data was normalised against positive and negative controls to account for background noise and platform-associated variation. Normalisation and analysis were performed using Rosalind Bio (San Diego, CA, USA) using geometric means of housekeeping genes (ABCF1, ALAS1, EEF1G, G6PD, GAPDH, GUSB, HPRT1, OAZ1, POLR1B, POLR2A, PPIA, RPL19, SDHA, TBP, TUBB) (Supplementary Material 1). Differential expression is reported between ME/CFS and long COVID with HC.
Ingenuity Pathway Analysis (IPA) (Qiagen Digital Insights, California, USA) was used for the interpretation of RNA in biological pathways and networks. The following filters were applied to all analyses, a fold change (FC) >1.5 or <-1.5 and a P-value <0.05.   Normality of participant data was determined using the Shapiro-Wilk test. Normally distributed continuous data was compared using one-way analysis of variance (ANOVA) corrected using Bonferroni, and non-normally distributed continuous data was compared using the Kruskal-Wallis test with Dunn’s corrections. Continuous data are presented as mean ± standard deviation (SD) unless otherwise stated. Categorical variables were compared using the Chi-Square test and the Fisher’s exact test. Participant demographic data was analysed using SPSS (version 27). Cell profile abundance scores were compared using one-way ANOVA corrected using Bonferroni or the Kruskal-Wallis test with Dunn’s corrections using GraphPad Prism (version 10). Significance is set at p<0.05. Adjusted (Adj.) p-values are provided unless otherwise stated.

source_name: Primary Whole Blood, PBMCs

growth_protocol:
[culture protocol]  Human primary cells
10^7 PBMCs were resuspended in fetal bovine serum (FBS) (Invitrogen Life Technologies, Carlsbad, CA, USA) containing 10% dimethyl sulfoxide (DMSO) for storage at -80oC until ribonucleic acid (RNA) extraction. Frozen PBMCs were thawed and immediately pelleted by centrifugation.

extract_protocol: Total RNA was isolated from PBMC pellets (5-10x106 cells) using either Trizol or an RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer instructions. The concentration and quality of the RNA were checked using Nanodrop.

value: blood

value: PBMCs

tag: age (years)

tag: Sex

value: Male

tag: disease

value: Gulf War Illness


title: PT6_Control_1

description: Library name: PT6_C1


title: 990376_ev_8

description:
Library name: 990376
experiment2_empty-vector_spleen_mouse8


title: DRG, RA, timepoint 0.25d, scRNAseq 2

description: 10x Genomics


title: Gulf War Illness #6

scan_protocol: Processed according to nCounter manufacturers instructions


title: Gulf War Illness #9


title: 990374_IL25_2

description:
Library name: 990374
experiment2_IL25_spleen_mouse2


title: Gulf War Illness #5


title: DRG, control,  timepoint 0, scRNAseq 10

description: 10x Genomics


title: 990373_IL25_5

description:
Library name: 990373
experiment2_IL25_spleen_mouse5


title: Gulf War Illness #2


title: Gulf War Illness #8


title: Gulf War Illness #3


title: SF13

city: Boston

first: William

last: Crisler

state: Massachusetts

address: 221 Longwood Ave

department: Dermatology

institute: Brigham & Women's Hospital

description: Samples were run using the Nanostring Human nCounter PanCancer Immune Panel [NS_Immunology_v2_C2328]

hyb_protocol: 100 ng of total RNA was hybridized to the reporter and capture probes in 30 μL reaction volume for 20 hours at 65°C.

scan_protocol: The captured targets were immobilized on the nCounter cartridge on the NanoString PrepStation. The cartridge was scanned at 555 fields of view (FOV) on the nCounter Digital Analyzer. Images were processed into a digital format (RCC files). All samples were analyzed using a single lot of reagents.

data_processing: Raw data appraisal, quality control, processing, and normalization were all performed using nSolver analysis software V4.0. Background subtraction was performed using the module's negative controls. Samples were then normalized using internal positive controls and housekeeping genes included in the module. Raw counts were normalized according to nSolver guidelines. nSolver V4.0 was further used to analyze differentially expressed genes (DEGs). In addition to the combined 28-sample normalization matrix deposited here, subgroup analyses were also performed in nSolver v4.0: (i) FA severe rejection (grades 3 and 2–3) versus FA grade 0, and (ii) SF severe rejection (grades 3 and 2–3) versus SF grade 0, with rejection status as predictor and patient identity included as a confounder.

label: Nanostring reporter probes

source_name: Sentinel flap skin

label_protocol: We used the NanoString nCounter PanCancer Immune Panel with probes representing 730 genes. Samples were processed on the NanoString nCounter Analysis System according to the manufacturer’s protocol (NanoString Technologies).

extract_protocol: RNA was extracted from six consecutive 10um sections from FFPE skin biopsies (14 facial allograft, 14 sentinel flap). Deparaffinization with xylene and RNA extraction were carried out using the RNeasy FFPE Kit (Qiagen). RNA concentration and purity were measured with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed using the 260/280 nm absorbance ratio.

value: male

tag: banff grade

value: grade 2-3

tag: race

value: white


title: DRG, RA, timepoint 0.5d, scRNAseq 3

description: 10x Genomics


title: SF12


title: 990370_IL25_4

description:
Library name: 990370
experiment2_IL25_spleen_mouse4


title: DRG, RA, timepoint 0.5d, scRNAseq 4

description: 10x Genomics


title: DRG, control,  timepoint 0, scRNAseq 9

description: 10x Genomics


title: 990369_IL25_3

description:
Library name: 990369
experiment2_IL25_spleen_mouse3


title: 990375_ev_7

description:
Library name: 990375
experiment2_empty-vector_spleen_mouse7


title: DRG, RA, timepoint 0.5d, scRNAseq 8

description: 10x Genomics


title: DRG, RA, timepoint 0.25d, scRNAseq 1

description: 10x Genomics


title: DRG, RA, timepoint 0.5d, scRNAseq 7

description: 10x Genomics


title: SF11

value: grade 2


title: SF14

value: grade 0


title: 990365_IL33_5

description:
Library name: 990365
experiment2_IL33_spleen_mouse5

value: spleen


title: SF10

value: grade 1


title: DRG, RA, timepoint 2d, scRNAseq 6

description: 10x Genomics


title: Gulf War Illness #4


title: SF9


title: Mouse_lung_B16F10_1

city: Denver

first: Sonia

middle: M

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

description: Fresh tissue; imaging-based spatial transcriptomics; 100-gene panel

hyb_protocol: After fixation, lung tissues were processed for paraffin embedding, and formalin-fixed paraffin-embedded (FFPE) blocks were prepared. Sections were then cut at 5um thickness onto Xenium slides in the Pathology Shared Resource at Dartmouth (RRID: SCR_023479) according to 10x Genomics protocol CG000580).  Slides were then transferred to the Genomics and Molecular Biology Shared Resource (RRID:SCR_021293) and processed following the manufacturer’s instructions for FFPE tissue sections (Protocol: CG000581) followed by probe hybridization, ligation and amplification (Protocol: CG000582).

scan_protocol: Slides were run on a Xenium Analyzer instrument running Xenium instrument software version 2.0.1.0 and On-Board Analysis software version 2.0.0.10 to produce the output data bundle used for downstream analysis. Following the Xenium run, slides were H&E stained on a Sakura Tissue-Tek Prism stainer and whole slide imaging conducted at 40x magnification using an Aperio GT450 instrument (Leica).

data_processing: Xenium spatial transcriptomics analysis was then processed and performed using Xenium Explorer 3 (10x Genomics). Data upload includes files for use in Xenium Explorer.

molecule: polyA RNA

source_name: Mouse, lung, B16F10, rep1

extract_protocol: Lung tissues from two mice with B16F10 tumors (melanoma model) and two mice with KPAR1.3 tumors (adenocarcinoma model) were perfused with 10% Neutral Buffered Formalin (NBF) to remove circulating blood. The lungs were then inflated with NBF to preserve tissue architecture and fixed by submersion in 10% NBF for 12 hours at room temperature.

value: lung

tag: replicate

value: replicate 1

value: melanoma


title: DRG, RA, timepoint 2d, scRNAseq 5

description: 10x Genomics

value: DRG cells

value: Dorsal root ganglion

value: 8-10 weeks old


title: DRG, RA, timepoint 1d, scRNAseq 4

description: 10x Genomics


title: 990363_IL33_4

description:
Library name: 990363
experiment2_IL33_spleen_mouse4


title: SF8


title: 990361_ev_11

description:
Library name: 990361
experiment2_empty-vector_spleen_mouse11

value: empty-vector


title: DRG, RA, timepoint 1d, scRNAseq 3

description: 10x Genomics


title: SF7

value: female


title: 1408482_ev_spleen_11

description:
Library name: 1408482
experiment1_empty-vector_spleen_mouse11


title: Retina_slide 5 and 6

city: Aurora

first: Samuel

middle: Alexander

last: Budoff

state: co

address: RC1 North Tower, P18-7101 Mail Stop

department: Physiology & Biophysics

institute: Colorado University Anschutz Medica

hyb_protocol: 10X - Xenium

scan_protocol: 10X - Xenium

data_processing:
github.com/sbudoff/MappingAllMurineRGCs
Puncta counts per cell

label: 10X Xenium Probe Panel

source_name: En face Retina

label_protocol: 10X - Xenium

growth_protocol: Wild type mouse, grown without manipulation and ad libidum food and water

extract_protocol: Retinas were extracted and en face cryosectioned at 20 um as per DOI: 10.3791/68171-v

value: retina


title: SF6


title: Mouse_lung_KPAR_2

source_name: Mouse, lung, KPAR, rep2

value: replicate 2

value: adenocarcinoma


title: Mouse_lung_KPAR_1

source_name: Mouse, lung, KPAR, rep1


title: 990367_IL25_1

description:
Library name: 990367
experiment2_IL25_spleen_mouse1


title: Mouse_lung_B16F10_2

source_name: Mouse, lung, B16F10, rep2


title: Retina_slide 3 and 4


title: DRG, control,  timepoint 0, scRNAseq 2

description: 10x Genomics


title: SF5

value: male

value: grade 3


title: 1408483_ev_spleen_10

description:
Library name: 1408483
experiment1_empty-vector_spleen_mouse10


title: Retina_slide 1 and 2


title: RGC_CrossSection_slide 1 and 2

source_name: Cross Sectioned Retina

extract_protocol: Retinas were extracted, crude dissected based on temporal pole brand and superior rectus, and crossectionallly cryosectioned at 20 um similar to DOI: 10.3791/68171-v


title: DRG, control,  timepoint 0, scRNAseq 1

description: 10x Genomics


title: SF4

value: grade 2-3

value: white


title: 1408485_ev_spleen_8

description:
Library name: 1408485
experiment1_empty-vector_spleen_mouse8

value: spleen


title: SF3

value: grade 2


title: Sandfly salivary gland extract-treated fibroblasts, replicate 6

city: York

first: Yonca

last: Keskek Turk

address: Heslington Road

department: Skin Research Centre

country: United Kingdom

institute: University of York

description: Library name: YT-SGE6

data_processing:
Reads were trimmed with trimgalore, mapped with STAR against the Mus musculus GRCm39 genome (GenCode M36), and and then quantified from the resulting BAM file using Salmon
Assembly: Mus musculus GRCm39 (GenCode M36)
Supplementary files format and content: Raw gene-level read counts from STAR/Salmon in a single, merged CSV file

source_name: Skin

extract_protocol:
Fibroblasts were isolated using the Magnetic Activated Cell Separation (MACS) technique using the Tumor-Associated Fibroblast Isolation Kit (mouse) from Miltenyi Biotec, Germany as per the manufacturer's instructions. RNA was extracted using the Zymo Research Quick-RNA Microprep Kit, as per the manufacturer's instructions.
Quality of extracted RNA was assessed using the Agilent Bioanalyzer  RNA pico chips, and high quality RNA (RIN > 8.5) was taken forward into RNA-Seq library preparation. Firstly, oligo(dT)-primed, full-length cDNA was synthesised and amplified from total RNA input using the SMART-Seq mRNA kits (Takara Bio), as per the manufacturer's guidelines. cDNA was quantified using the Agilent Bioanalyzer HS DNA chips, and ~5 ng cDNA was taken into library preparation using the NEBNext Ultra II FS library preparation kits for Illumina (New England Biolabs).

value: Skin

value: Fibroblast

value: Sandfly salivary gland extract


title: glomeruli, WT3

city: Guangzhou

first: DEWEI

last: YE

state: Guangdong

address: 280 Waihuan East Road, Guangzhou Higher Education Mega

country: China

institute: Guangdong Pharmaceutical University

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence of GRCm38.p6.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: renal glomeruli

extract_protocol:
Total RNA was etracted using Trizol reagents (Thermo Fisher Scientific) and purified by Oligo(dT)-attached magnetic beads.
Samples of RNA-seq libraries were sequenced on the DNBSEQ platform.

value: renal glomeruli

tag: genotype

value: WT

tag: disease state

value: diabetic kidney disease


title: glomeruli, WT2


title: Retina_slide 7 and 8


title: 1408486_ev_spleen_7

description:
Library name: 1408486
experiment1_empty-vector_spleen_mouse7

value: empty-vector


title: SF2


title: Gulf War Illness #1

value: blood

value: PBMCs

value: Male

value: Gulf War Illness


title: 1408476_mIL33_spleen_5

description:
Library name: 1408476
experiment1_mIL33_spleen_mouse5


title: glomeruli, WT1


title: Sandfly salivary gland extract-treated fibroblasts, replicate 5

description: Library name: YT-SGE5


title: SF1

value: male


title: glomeruli, PR3 KO3

value: PR3 knockout


title: FA14

source_name: Facial allograft skin

value: grade 1


title: 1408475_mIL33_spleen_4

description:
Library name: 1408475
experiment1_mIL33_spleen_mouse4


title: 1408474_mIL33_spleen_3

description:
Library name: 1408474
experiment1_mIL33_spleen_mouse3


title: Sandfly salivary gland extract-treated fibroblasts, replicate 2

description: Library name: YT-SGE2


title: 1408484_ev_spleen_9

description:
Library name: 1408484
experiment1_empty-vector_spleen_mouse9


title: 1408473_mIL33_spleen_2

description:
Library name: 1408473
experiment1_mIL33_spleen_mouse2


title: Sandfly salivary gland extract-treated fibroblasts, replicate 3

description: Library name: YT-SGE3


title: Sandfly salivary gland extract-treated fibroblasts, replicate 1

description: Library name: YT-SGE1


title: FA12

description: Samples were run using the Nanostring Human nCounter PanCancer Immune Panel [NS_Immunology_v2_C2328]

value: grade 3

value: white


title: FA11


title: FA13


title: 7dpci_3

city: Potsdam

first: Juliane

last: Münch

state: Brandenburg

address: Karl-Liebknecht-Strasse 24-25

department: Biochemistry and Biology

country: Germany

institute: University of Potsdam

description: Library name: 7d post cryioinjury_3

data_processing:
Reads were aligned to the Danio rerio reference genome (GRCz10, Ensemble_90) and mapped for quality control.
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were normalized with median of the geometric mean (Anders und Huber 2010).
For analysis Tuxedo suite was used, including the Cufinks, Cuffmerge and Cuffdiff steps
Assembly: GRCz10
Supplementary files format and content: Normalized FPKM (abundance) for each coding sequence (CDS) for each sample in txt. format
Supplementary files format and content: Normalized fragment count estimation for each gene for each sample in txt. format

organism: Danio rerio

source_name: heart

extract_protocol:
RNA was extracted using sonication in a waterbath (BIORUPTOR Plus, Diagenode)and Quick-RNA Microprep Kit (Zymo Research).
RNA libraries of 4 samples per timepoint were prepared with Illumina TruSeq Stranded Total RNA Library Prep Kit

value: heart

tag: Stage

value: 7 dpci


title: Resting fibroblasts, replicate 6

description: Library name: YT-R6

value: Skin

value: Fibroblast

value: Resting


title: 1408472_mIL33_spleen_1

description:
Library name: 1408472
experiment1_mIL33_spleen_mouse1

value: spleen


title: 7dpci_2

description: Library name: 7d post cryioinjury_2

value: WT


title: 7dpci_1

description: Library name: 7d post cryioinjury_1


title: Sandfly salivary gland extract-treated fibroblasts, replicate 4

description: Library name: YT-SGE4

value: Sandfly salivary gland extract


title: mNF1_ASPA_Vh_2

city: Santander

first: Fernando

last: Calvo

state: Cantabria

address: C. Albert Einstein, 22

country: Spain

institute: IBBTEC

description:
Library name: AS4986
Column name in counts matrix: AS4986

data_processing:
nf-core/rnaseq
METHOD: Aligner: STAR, Quantification: Salmon (default)
Assembly: GRCm38
Supplementary files format and content: salmon.merged.gene_counts.tsv: Tab-delimited file with raw-counts of each sample, column name is sample name
Supplementary files format and content: salmon.merged.gene_tpm.tsv: Tab-delimited file with tpm-counts of each sample, column name is sample name

source_name: mammary gland

growth_protocol: Murine fibroblasts from FVB/n normal mammary glands (NF1) and MMTV-PyMT mammary carcinoma (CAF1) were maintained in high glucose DMEM supplemented with 10% Fetal Bovine Serum (FBS), 1% GlutaMax and Pen/Strep antibiotics in a standard humidified 5% CO2 incubator at 37C.

extract_protocol:
After 48 h of transfection, RNA was extracted with the NZY Total Isolation Kit (NZYTech), according to manufacturer’s instructions. RNA was checked by RNA ScreenTape analysis in an Agilent TapeStation system (Agilent Technologies)
Samples were then sent to the Centro Nacional de Análisis Genómico (CNAG) for RNA sequencing analysis. Samples were first quality checked and transformed into a library of stranded mRNA molecules using the TrueSeq® Stranded mRNA library preparation kit (Illumina), following manufacter´s intructions.

treatment_protocol:
Fibroblasts were seeded at 60% confluence and transfected using DharmaFECT 1 (Dharmacon) with siRNA (100 nM final concentration) following manufacturer’s instructions. Cells received either control, Hsp90aa1 or Hsp90ab1 (smartpool) RNAi.
Where indicated, TGFβ1 was added to a final concentration of 5 ng/mL into the cell culture media 5 h after transfection, and the stimuli was maintained throughout the whole experiment.

value: mammary gland

tag: cell line

value: normal fibroblasts

value: ASPA

value: Doxycyclin-Vehicle

value: Rep 2


title: mNF1_ASPA_TGFB1_2

description:
Library name: AS4987
Column name in counts matrix: AS4987

tag: tissue


title: Resting fibroblasts, replicate 4

description: Library name: YT-R4

tag: treatment


title: Resting fibroblasts, replicate 5

description: Library name: YT-R5


title: FA9

value: male

value: grade 0


title: Resting fibroblasts, replicate 3

description: Library name: YT-R3


title: FA8

value: grade 2-3


title: glomeruli, PR3 KO2

value: renal glomeruli

value: PR3 knockout

value: diabetic kidney disease


title: mNF1_CONTROL_Vh_2

description:
Library name: AS4984
Column name in counts matrix: AS4984

value: CONTROL

value: Vehicle-Vehicle

tag: batch


title: 3dpci_3

description: Library name: 3d post cryoinjury_3

value: heart

value: 3 dpci


title: Resting fibroblasts, replicate 2

description: Library name: YT-R2

value: Skin

tag: cell type

value: Fibroblast

value: Resting


title: FA7

value: female

value: grade 1

value: white


title: mNF1_ASPA_TGFB1_1

description:
Library name: AS4983
Column name in counts matrix: AS4983

value: mammary gland

value: normal fibroblasts

value: ASPA

value: Rep 1


title: 3dpci_1

description: Library name: 3d post cryoinjury_1

value: WT


title: mNF1_ASPA_Vh_1

description:
Library name: AS4982
Column name in counts matrix: AS4982

value: Doxycyclin-Vehicle


title: FA5

value: male

value: grade 3


title: ∆S701-5,DSS day3

city: Wuhan

first: Jingjing

last: Tong

state: Hubei

address: NO.152 Luoyu Road

institute: Central China Normal University

data_processing:
HISAT2 (version 2.1.0)
RNA-seq reads containing adapter, reads containing ploy-N and low-quality reads were removed from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. These clean reads were then mapped on the mouse reference (GRCm38_release95) by HISAT2 (version 2.1.0) with the default options. The number of reads mapped to each of genes was counted by using HTSeq (version 0.11.2) with the option-m intersection-nonempty.
Assembly: GRCm38_release95
Supplementary files format and content: a matrix table includes raw counts for each sample
Supplementary files format and content: a matrix table includes FPKM for each sample

source_name: colon

extract_protocol:
RNA was extracted with Trizol reagent (#DP424, TianGen). 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries forRNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: mice were treated with 3% DSS in their drinking water ad libitum for 3 days

value: colon

value: DSS


title: FA10

value: grade 0


title: 3dpci_4

description: Library name: 3d post cryoinjury_4

value: heart

value: 3 dpci


title: FA4

value: grade 2-3


title: ∆S701-4,DSS day3


title: 1.5dpci_4

description: Library name: 1.5d post cryoinjury_4

value: 1.5 dpci


title: mNF1_CONTROL_TGFB1_1

description:
Library name: AS4981
Column name in counts matrix: AS4981

value: CONTROL


title: 1.5dpci_3

description: Library name: 1.5d post cryoinjury_3


title: mNF1_CONTROL_TGFB1_2

description:
Library name: AS4985
Column name in counts matrix: AS4985

value: Rep 2


title: mNF1_CONTROL_Vh_1

description:
Library name: AS4980
Column name in counts matrix: AS4980

value: mammary gland

value: Vehicle-Vehicle


title: ∆S701-3,DSS day3


title: ∆S701-2,DSS day3


title: 3dpci_2

description: Library name: 3d post cryoinjury_2


title: ∆S701-1,DSS day3


title: 1.5dpci_1

description: Library name: 1.5d post cryoinjury_1


title: mNF1_sh3-ASPA_3

description:
Library name: AS4978
Column name in counts matrix: AS4978

value: normal fibroblasts

value: doxycyclin 5 days

value: Rep 3


title: Patient 30_WT-TFND_3

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

institute: IDIBELL

description: Total RNA for all formalin-fixed paraffin-embedded (FFPE) tissues were extracted using the miRNeasy FFPE kit (QIAGEN).

hyb_protocol: Samples were denatured at 85°C for 5 min and then hybridized at 65°C for 16 h.

scan_protocol: Fluorescent reporter tags were scanned by an automated multi-channel epifluorescence scanner, generating the raw counts, using the MAX/FLEX Analysis System and software. Barcodes for each target molecule were counted across a maximum resolution of 555 fields of view (FOV).

data_processing:
miRNAs that did not match between codeset versions v3a and v3b were removed and only the endogenous miRNAs were kept.  Then, the miRNA data expression was adjusted using the trimmed mean of M values (TMM) method and the effective library size was calculated. miRNAs were considered detectable if they had expression levels of 10 counts per million (CPM) in more than 70 % of the samples in the discovery cohort, resulting in 540 detectable miRNAs. Subsequently, differential expression analysis was performed using the quasi-likelihood negative binomial generalized log-linear model (GLM) functions provided by the EdgeR package (4.10.16). The linear model was fitted using the batches of interest (experiment run#, version of the chip and sample source).
Normalized counts using the trimmed mean of M values (TMM) method

source_name: Benign thyroid lesion, control

label_protocol: not applicable

extract_protocol: Total RNA for all fresh frozen tissue (FFT) were extracted using the mirVana miRNA isolation kit (ThermoFisher) and all formalin-fixed paraffin-embedded (FFPE) tissues were extracted using the miRNeasy FFPE kit (QIAGEN).

value: Thyroid

tag: histology

value: Thyroid follicular nodular disease (TFND)

tag: benign/malignant

value: Benign

tag: sample source

value: FFPE

tag: version of the chip

tag: experiment run #

tag: other sample title


title: FA3

tag: Sex

value: male

tag: banff grade

value: grade 2

value: white


title: mNF1_sh4-ASPA_3

description:
Library name: AS4979
Column name in counts matrix: AS4979


title: FA2

tag: race


title: noci_4

description: Library name: no cryoinjury_4

value: heart

value: no cryoinjury

tag: genotype

value: WT


title: WT-5,DSS day3

value: colon

value: DSS


title: glomeruli, PR3 KO1

tag: strain

value: renal glomeruli

value: PR3 knockout

tag: disease state

value: diabetic kidney disease


title: FA6

value: grade 0


title: 1.5dpci_2

description: Library name: 1.5d post cryoinjury_2

tag: Stage

value: 1.5 dpci


title: Patient 29_WT-TFND_2

tag: tissue

value: Thyroid


title: FA1


title: mNF1_shC_3

description:
Library name: AS4977
Column name in counts matrix: AS4977

value: mammary gland

tag: cell line

value: normal fibroblasts

value: shControl

tag: treatment

value: doxycyclin 5 days

value: Rep 3


title: WT-4,DSS day3


title: noci_3

description: Library name: no cryoinjury_3


title: mNF1_sh4-ASPA_2

description:
Library name: AS4976
Column name in counts matrix: AS4976

tag: cell type

tag: batch

value: Rep 2


title: Patient 28_WT-TFND_1

tag: histology

value: Thyroid follicular nodular disease (TFND)

tag: benign/malignant

value: Benign

value: FFPE


title: Patient 22_WT-FVPTC_2

description: Total RNA for all fresh frozen tissue (FFT) were extracted using the mirVana miRNA isolation kit (ThermoFisher)

source_name: Malignant thyroid lesion, control

value: Follicular variant of papillary thyroid cancer (FVPTC)

value: Malignant

tag: sample source

value: FFT

tag: version of the chip


title: noci_2

description: Library name: no cryoinjury_2

value: heart

value: no cryoinjury

value: WT


title: mNF1_sh3-ASPA_2

description:
Library name: AS4975
Column name in counts matrix: AS4975


title: noci_1

description: Library name: no cryoinjury_1


title: Patient 21_WT-FVPTC_1

tag: experiment run #

tag: other sample title


title: WT-3,DSS day3

value: colon

value: DSS


title: WT-1,DSS day3


title: WT-2,DSS day3


title: Patient 8_DGCR8-TFND_5

source_name: Benign thyroid lesion, DGCR8-mutated

value: Thyroid

value: Sample 591


title: 14dpci_4

description: Library name: 14d post cryoinjury_4

value: 14 dpci


title: mNF1_sh3-ASPA_1

description:
Library name: AS4972
Column name in counts matrix: AS4972

value: mammary gland

value: normal fibroblasts

value: doxycyclin 5 days

value: Rep 1


title: mNF1_sh4-ASPA_1

description:
Library name: AS4973
Column name in counts matrix: AS4973


title: 14dpci_3

description: Library name: 14d post cryoinjury_3


title: Patient 7_DGCR8-TFND_4

value: Thyroid follicular nodular disease (TFND)

value: Benign

value: Sample 592


title: F3

city: Changchun

first: Yusong

last: Cao

address: Renmin Street 5625

institute: Changchun Institute of Applied Chemistry

description: Library name: Sample 18

data_processing:
The image data of sequencing fragments measured by high-throughput sequencers are converted into sequence data (reads) through CASAVA base recognition. The files are in fastq format and mainly contain the sequence information of the sequencing fragments and their corresponding sequencing quality information. The raw data obtained from sequencing contains a small number of reads with sequencing headers or of low sequencing quality. To ensure the quality and reliability of data analysis, it is necessary to filter the original data. This should include removing reads with adapters, reads containing N(where N indicates that the base information cannot be determined), and low-quality reads(where the number of bases with Qphred <=5 accounts for more than 50% of the entire read length)
Assembly: GRCm39
Supplementary files format and content: gene.read_count.xlsx

organism: Mus

extract_protocol:
1. Add chloroform accounting for 1/5 of the total volume. Tightly close the lid of the centrifuge tube, shake vigorously for 15 seconds, and let it stand at room temperature for 2 to 3 minutes. Centrifuge at 12,000 rpm and 4°C for 10 to 15 minutes. Note: 1) After centrifugation, the mixture can be divided into three layers: the upper layer is a colorless water sample layer, the middle layer, and the lower layer is a red organic phenol chloroform layer. RNA is invariably present in the aqueous layer. 2) The capacity of this part is approximately 50-60% of the Total amount of Total RNA Extraction Reagent added. Such as using 1 ml of Total RNA Extraction Reagent is extracted, and the upper layer of water is approximately 500-600 μl. It is recommended to draw 400-500 μl. Do not draw it too completely. To prevent inhaling the middle layer and causing genomic contamination. 3) The organic phase and intermediate layer are proteins and DNA. If necessary, please retain them and conduct relevant purification experiments. 3. Carefully draw the upper aqueous phase into a new centrifuge tube and add an equal volume of isopropyl alcohol. Invert and mix well, then let it stand at room temperature 10 minutes. RNA precipitates are usually invisible before centrifugation and form gel-like precipitates on the side and bottom of the tube after centrifugation. Centrifuge at 12,000rpm and 4°C for 10 minutes. 5. Carefully discard the supernatant and add 1 ml of 75% ethanol prepared with DEPC water. Thoroughly wash the pipe cap and pipe wall, and gently tap the pipe At the bottom, let the sediment suspend. For every 1ml of Total RNA Extraction Reagent, precipitate with 1ml of 75% ethanol Wash. Centrifuge at 12,000 rpm at 4°C for 3 minutes, discard the supernatant, and be careful not to lose the RNA precipitate. Note: The remaining small amount of liquid can be briefly centrifuged and then aspirated with a pipette tip. Be careful not to discard the precipitate. 7. Let it stand at room temperature for 2 to 3 minutes to dry. Add an appropriate amount of RNase free water (DEPC water). After it is completely dissolved, take a small amount Test and store the rest at -80°C.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: treated by PPLG-4V-SA after stimulated by LPS


title: Patient 6_DGCR8-TFND_3

value: FFPE


title: F2

description: Library name: Sample 17


title: 14dpci_2

description: Library name: 14d post cryoinjury_2

value: heart


title: F1

description: Library name: Sample 16


title: 14dpci_1

description: Library name: 14d post cryoinjury_1


title: Patient 5_DGCR8-TFND_2

value: Sample 593


title: E3

description: Library name: Sample 15

value: treated by PPLG-2V-SA after stimulated by LPS


title: 7dpci_4

description: Library name: 7d post cryioinjury_4

value: 7 dpci

value: WT


title: E2

description: Library name: Sample 14


title: set-24 Mutant, 20 degrees, Generation 0 3 srna

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

institute: University of Cambridge

description: Library name: mj617_3_20P0_srna

library_source: other

data_processing:
RNASeq- Quality and Adaptor Trimming - Trimmomatc
RNASeq- Read alignment and counting - Salmon
RNASeq- Differential expression analysis - DESEq2
ChIP-Seq- Quality and Adaptor Trimming - Cutadapt
ChIP-Seq- Read aligment- BWA
ChIP-Seq- Peak calling and bdg generations- MACS3
ChIP-Seq- Differential enrichment analysis- DiffBind
Assembly: Ensembl - WBCel235
Supplementary files format and content: raw_counts.txt - This file contains the raw counts obtained from Salmon alignment  for each sample in matrix fromat
Supplementary files format and content: regularized_log_normalised_counts.txt - This file contain rlog normalsed counts for each sample n matrix format
Supplementary files format and content: All bdgs - These files contain the log2 normalized enrichments in bedgraph format.

molecule: other

organism: Caenorhabditis elegans

source_name: Whole Organism

extract_protocol:
RNAs were extracted using Trizol, chloroform, and isopropanol and treated with DNase I. DNA Chromatin was crosslinbked with formalaldehyde and fragmented by sonnication. Specific fragments were inmunoprecipitated with it's coresponding antibody.
mRNAs were purified from total RNA using PolyT oligo-attached beads and converted to cDNAs for library preparation. cDNA libraries were sequenced using a paired-end 150 bp sequencing strategy. ChIP-Seq libraries were prepared from the inmunoprecipitated fragments using a standard paired end 150bp DNA sequencing strategy.

value: Whole Organism


title: female mice, PAXIP1-AS1 reference C allele (Ref), rep2

first: Cunyou

last: Zhao

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

description: Library name: femal_REF-2

data_processing:
The raw sequencing data obtained from the Illumina platform, referred to as Raw Reads, undergoes data processing to generate high-quality sequences, known as Clean Reads. This processing involves the removal of low-quality sequences and the elimination of adapter contamination. The Clean Reads are then aligned to the hg19 reference genome using the STAR aligner with default parameters. Quantification is performed using FeatureCounts, resulting in the generation of Counts and FPKM values.
Assembly: hg19
Supplementary files format and content: FPKM, TPM, Count values

source_name: prefrontal cortex

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Using magnetic beads coated with Oligo(dT), mRNA with polyA tails is enriched and purified from RNA samples. Fragmentation Buffer is then added to the purified mRNA to fragment it. The resulting RNA fragments serve as templates for the reverse transcription process, utilizing random primers to synthesize the first strand of cDNA. Subsequently, a 2nd Strand Marking Buffer and a 2nd Strand/End Repair Enzyme Mix are introduced to synthesize the second strand of cDNA. Following this, end repair is performed, an adenine base is added, and sequencing adapters are ligated. The target fragments are then recovered through magnetic bead selection and subjected to PCR amplification, thereby completing the entire library preparation process.

value: prefrontal cortex


title: female mice, PAXIP1-AS1 alternative G allele (Alt), rep1

description: Library name: femal_ALT-1


title: E1

description: Library name: Sample 13


title: female mice, PAXIP1-AS1 reference C allele (Ref), rep1

description: Library name: femal_REF-1


title: female mice, PAXIP1-AS1 alternative G allele (Alt), rep2

description: Library name: femal_ALT-2


title: Patient 2_DGCR8-FVPTC_1

source_name: Malignant thyroid lesion, DGCR8-mutated

value: Thyroid

value: Follicular variant of papillary thyroid cancer (FVPTC)

value: Malignant

value: FFT


title: set-24 Mutant, 20 degrees, Generation 0 1 srna

description: Library name: mj617_1_20P0_srna


title: mNF1_shC_1

description:
Library name: AS4971
Column name in counts matrix: AS4971

value: mammary gland

value: normal fibroblasts

value: shControl

value: doxycyclin 5 days

value: Rep 1


title: D3

description: Library name: Sample 12

value: treated by PPLG-SA after stimulated by LPS


title: D2

description: Library name: Sample 11


title: female mice, Ctrl, rep3

description: Library name: femal_ctrl-3


title: Patient 3_DGCR8-FVPTC_2


title: D1

description: Library name: Sample 10


title: N2, 20 degrees, Generation 0 2 srna

description: Library name: n2_2_20P0_srna

value: Wild-type N2


title: N2, 20 degrees, Generation 0 3 srna

description: Library name: n2_3_20P0_srna


title: Cd-3 50mg/L Treatment

city: Chengdu

first: xiumei

last: luo

address: Shuangliu

department: Institute of Urban Agriculture

institute: Chinese Academy of Agricultural Sciences

description:
Library name: Cd50_3
Coelastrella tenuitheca S93-3 exposed to 50 mg/L CdCl₂ for 7 days for bioremediation study

data_processing:
StringTie v2.2.1 was used to assemble transcripts and estimate expression levels in transcripts per million (TPM) for each sample.
Differential gene expression between treatment groups was identified using DESeq2 v1.34.0 with a false discovery rate (FDR) cutoff of 0.05 and fold-change threshold of 2.
Cleaned reads were aligned to the Coelastrella tenuitheca reference genome using STAR v2.7.10a with default parameters for RNA-seq alignment.
Differentially expressed genes were annotated using BLASTP against the NCBI non-redundant protein database and assigned GO terms using InterProScan.
Assembly: C. tenuitheca lacks a reference genome, we first conducted chromosome-level genome sequencing of S93-3. Through Hi-C genome sequencing and genome assembly, 17 chromosomes with a total length of 80,587,029 bp were built, which account for about 99.96% of the whole genome assembly (80,587,429 bp), individually ranging from 1.78 Mb (Chr17) to 9.68 Mb (Chr1) in length and the assemble genome with GCA_051903525.1, with accession number of SRR35180137.
Supplementary files format and content: The processed data files are in tab-delimited text format and contain the results of differential expression analysis for three comparisons: Cd20 vs Control, Cd50 vs Control, and Cd50 vs Cd20. Each file includes the following columns: GeneID, log2FoldChange, pvalue, adjusted p-value (padj), and gene annotation. These files are being submitted to the Gene Expression Omnibus (GEO) and are not included in this SRA submission

organism: Coelastrella tenuitheca

source_name: whole cell

growth_protocol: Coelastrella tenuitheca strain S93-3 was pre-cultured in modified BG-11 liquid media supplemented with 20 g/L glucose for 5 days at 28°C with constant shaking at 150 rpm under continuous light (50 μmol photons/m²/s).

extract_protocol:
Total RNA was extracted from 50 mg of algal biomass using TRIzol reagent following the manufacturer's protocol, with DNase I treatment to remove genomic DNA contamination. RNA quality was assessed using an Agilent Bioanalyzer, and only samples with RIN > 8.0 were used for library construction.
RNA-seq libraries were prepared from 1 μg of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit. Poly(A) mRNA was selected using oligo-dT magnetic beads, followed by fragmentation and first-strand cDNA synthesis. Second-strand cDNA was synthesized with dUTP for strand specificity. After end repair, A-tailing, and adapter ligation, libraries were size-selected (300-500 bp) and PCR-amplified for 12 cycles. Final libraries were quantified by Qubit and quality-checked by Bioanalyzer.

treatment_protocol: For cadmium exposure, cultures with an initial OD₆₈₀ of 0.5 were inoculated into fresh modified BG-11 media containing either 0 mg/L (control), 20 mg/L, or 50 mg/L cadmium chloride (CdCl₂). Treated cultures were incubated under the same conditions for 7 days, with daily monitoring of growth and biomass.

value: whole cell

value: photosynthetic microalgal cell

value: wild type

value: 50 mg/L CdCl₂ exposure


title: Cd-2 50mg/L Treatment

description:
Library name: Cd50_2
Coelastrella tenuitheca S93-3 exposed to 50 mg/L CdCl₂ for 7 days for bioremediation study


title: female mice, Ctrl, rep1

description: Library name: femal_ctrl-1


title: Cd-1 50mg/L Treatment

description:
Library name: Cd50_1
Coelastrella tenuitheca S93-3 exposed to 50 mg/L CdCl₂ for 7 days for bioremediation study


title: C3

description: Library name: Sample 9

value: treated by POx-SA after stimulated by LPS


title: N2, 20 degrees, Generation 0 1 srna

description: Library name: n2_1_20P0_srna

value: Whole Organism


title: Cd-3 20mg/L Treatment

description:
Library name: Cd20_3
Coelastrella tenuitheca S93-3 exposed to 20 mg/L CdCl₂ for 7 days for bioremediation study

value: 20 mg/L CdCl₂ exposure


title: C2

description: Library name: Sample 8


title: Ile WT rep 4

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

description:
Library name: Sample 27
fpkm WT_Ileum_3

data_processing:
Reads were trimmed and filtered using Trimmomatic (v 0.39), then aligned to UCSC mouse genome mm10 using Bowtie2 and Tophat (2.1.1). Assembly of transcriptomes and quantification was performed with Cufflinks (2.1.1). Expression levels are expressed as fragments per kilobase of exon per million fragments mapped (FPKM). Data was further analyzed and visualized using CummeRbund run under the R package (4.1.3). Statistical significance in differential gene expression between groups was assessed with Cuffdiff (2.1.1)
Hierarchical clustering of genes was generated using Complete Linkage as the clustering method, Euclidian distance as the similarity measure, and Z-Score as normalization with TIBCO Spotfire Software (Palo Alto, CA). Pathway analysis was performed using Gene Set Enrichment Analysis (GSEA) (Broad Institute, software.broadinstitute.org/gsea), a computational method that determines statistical significance of a priori defined set of genes between two groups and ClueGo within Cytoscape software v3.10.3 using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, WikiPathways (WP), Reactome pathways and Reactome reaction pathways, as well as GO biological process (GO BP).
Assembly: UCSC mm10
Supplementary files format and content: xlsx files contain FPKM values for each sample

source_name: Ileum

growth_protocol: RNA was extracted from 6-8 weeks old male mice, non-littermate wildtype (WT) and the previously established Cystic Fibrosis (CF) (G542X/G542X) mice on the C57Bl6/J background. Mice had unrestricted access to D12451i diet (research Diets, 45 kcal % fat) with acidifeid water

extract_protocol:
The small intestine was extracted in its entirety from stomach to cecum and flushed with cold phosphate buffered saline (PBS). Three-inch long intestinal segments were collected from the beginning, middle and end of the small intestine to correspond with duodenum, jejunum, and ileum respectively and frozen immediately in liquid nitrogen. The jejunum section was divided in half lengthwise prior to freezing, using one section for whole tissue RNA and the other for crypt isolation and subsequent RNA extraction. RNA was isolated using Rneasy mini kit (Qiagen), concentration and quality checked with the Nanodrop (ThermoScientific).
RNA-seq libraries were generated using TruSeq stranded Total RNA Ribo-Zero mouse gold kit (Illumina, San Diego, CA) and the quality of resulting libraries was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). Ileum (WT n=4, CF n=5) sequencing was carried out using an Illumina HiSeq 2500 Rapid Run flow cell – 2x100bp run. Duodenum (WT n=9, CF n=9), jejunum (WT n=8, CF n=9) and jejunum crypts (WT n=8, CF n=9) sequencing was carried out using an Illumina NextSeq 550 HO flowcell – 2x75bp run

value: Ileum

value: Wild type


title: Ile WT rep 3

description:
Library name: Sample 26
fpkm WT_Ileum_2


title: set-24 Mutant, 20 degrees, Generation 0 4 rna

description: Library name: SX3735_4_20P0_rna


title: Cd-2 20mg/L Treatment

description:
Library name: Cd20_2
Coelastrella tenuitheca S93-3 exposed to 20 mg/L CdCl₂ for 7 days for bioremediation study


title: Patient 4_DGCR8-TFND_1

value: Thyroid

value: Thyroid follicular nodular disease (TFND)

value: Benign

value: FFPE

value: Sample 590


title: C1

description: Library name: Sample 7


title: Cd-1 20mg/L Treatment

description:
Library name: Cd20_1
Coelastrella tenuitheca S93-3 exposed to 20 mg/L CdCl₂ for 7 days for bioremediation study


title: Ile WT rep 2

description:
Library name: Sample 25
fpkm WT_Ileum_1


title: set-24 Mutant, 20 degrees, Generation 0 3 rna

description: Library name: SX3735_3_20P0_rna


title: female mice, Ctrl, rep2

description: Library name: femal_ctrl-2

value: prefrontal cortex


title: B3

description: Library name: Sample 6

value: without any treatment


title: set-24 Mutant, 20 degrees, Generation 0 2 rna

description: Library name: SX3735_2_20P0_rna


title: Ile WT rep 1

description:
Library name: Sample 24
fpkm WT_Ileum_0


title: Control-3 Treatment

description:
Library name: CK_3
Control sample of Coelastrella tenuitheca S93-3 grown in modified BG-11 media

value: control (0 mg/L CdCl₂)


title: set-24 Mutant, 20 degrees, Generation 0 1 rna

description: Library name: SX3735_1_20P0_rna


title: Ile CF rep 5

description:
Library name: Sample 23
fpkm CF_Ileum_4


title: B2

description: Library name: Sample 5


title: B1

description: Library name: Sample 4


title: Control-2 Treatment

description:
Library name: CK_2
Control sample of Coelastrella tenuitheca S93-3 grown in modified BG-11 media

value: whole cell


title: Ile CF rep 4

description:
Library name: Sample 22
fpkm CF_Ileum_3


title: Control-1 Treatment

description:
Library name: CK_1
Control sample of Coelastrella tenuitheca S93-3 grown in modified BG-11 media

value: photosynthetic microalgal cell


title: N2, 20 degrees, Generation 0 3 rna

description: Library name: n2_3_20P0_rna

value: Wild-type N2


title: Ile CF rep 3

description:
Library name: Sample 21
fpkm CF_Ileum_2


title: A3

description: Library name: Sample 3

value: stimulated by LPS


title: strain in oligotrophic medium

city: Fuzhou

first: Lingjun

last: Yu

address: No. 18 Wulongjiang Middle Avenue, Shangjie Town, Minhou County

institute: Fujian Normal University

description:
Sample 2
oligotrophic medium

data_processing:
Quality assessment of raw sequencing data using FastQC v 0.11.2.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v 0.36.
Trimmed sequence reads were mapped to reference genome using Bowtie2 v 2.3.2.
Homogeneity distribution inspection and genome structure distribution were conducted using Qualimap v 2.2.1.
Statistical analysis of gene coverage and analysis of sequencing sequence distribution on the genome were performed using BEDTools v 2.26.0
Assembly: Rockhopper v 2.0.3
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 FPKM values for each Sample

organism: Streptomyces seoulensis

source_name: bacterial cell

growth_protocol: The wild-type of marine Streptomyces sp. FJNU027 strain was grown in modified Gauze's medium and oligotrophic medium at 28°C for 8 d.

extract_protocol:
RNA was harvested using Total RNA Extractor kit (Sangon), 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTSTM Stranded mRNA-seq V2 Library Prep kit following manufacturer's protocols.

value: bacterial cell

value: WT


title: N2, 20 degrees, Generation 0 2 rna

description: Library name: n2_2_20P0_rna

value: Whole Organism


title: Ile CF rep 2

description:
Library name: Sample 20
fpkm CF_Ileum_1

value: Ileum


title: strain in modified Gauze's medium

description:
Sample 1
modified Gauze's medium


title: A2

description: Library name: Sample 2


title: N2, 20 degrees, Generation 0 1 rna

description: Library name: n2_1_20P0_rna


title: Ile CF rep 1

description:
Library name: Sample 19
fpkm CF_Ileum_0


title: S31 cells, IGF-1 Treated, IGF 3

status: Public on Dec 09 2025

city: Oklahoma City

first: Shannon

middle: M.

last: Conley

state: Oklahoma

address: 940 Stanton L Young Blvd BMSB 100/105

department: Cell Biology

institute: University of Oklahoma Health Campus

description:
Library name: Sample 9
Column name in normalized_counts_fpkm_all.csv: PDGF-NS-3

data_processing:
Raw sequence reads were mapped to the reference genome using GSNAP.
Expression (fragments per kilobase per million mapped fragments, FPKM) values were derived by Cufflinks.
Differential expression was analyzed with ANOVA in R.
Canonical pathway analysis was performed using Ingenuity Pathway Analysis (IPA) (QIAGEN Inc., https://digitalinsights.qiagen.com/IPA) to identify significantly changed pathways based on differentially expressed genes (DEGs).
Gene Ontology (AmiGO) was used to identify genes annotated with GO terms of interest.
Assembly: Rattus norvegicus genome (Rnor_5)
Supplementary files format and content: normalized_counts_fpkm_all.csv contains normalized counts (FPKM values)

organism: Rattus norvegicus

growth_protocol: Experiments were performed using primary S31 VSMCs originally isolated from cardiac microvessels of male Wistar Kyoto rats. S31 VSMCs were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Invitrogen/ThermoFisher, Carlsbad, CA) supplemented with 10% heat-inactivated fetal bovine serum (Gemini Benchmark Fetal Bovine Serum, Gemini Bio, West Sacramento, CA) plus antibiotic/anti-mycotic (Invitrogen/ThermoFisher) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cultured cells using Trizol Reagent (Invitrogen/ ThermoFisher) per the manufacturer’s protocol. 1 μg of RNA was used per library.
RNA libraries for RNAseq were prepared using Lexogen’s SENSE mRNA Library Prep kit v2 using the manufacturers protocols.

treatment_protocol: Cells were first synchronized by by 48 hours of serum starvation in fresh serum-free medium (DMEM supplemented with 0.02% lactalbumin hydrolysate and 1X antibiotic-antimycotic; Invitrogen/ThermoFisher) prior to growth factor treatment. Growth factor treatments were performed by diluting growth factors in serum-free medium, and replenishing growth factors every 24 hours (when necessary).  Growth factors and doses were as follows: recombinant rat PDGF-BB (25 ng/ml; R&D Systems, Minneapolis, MN), recombinant human IGF-1 (25 ng/ml). Control cells received fresh serum-free medium lacking any added growth factors. Total RNA was extracted at 24 hours post treatment for (control & IGF-1) and 48 hours post treatment (PDGF-BB).

value: primary vascular smooth muscle cells

value: recombinant human IGF-1 (25 ng/ml)


title: S31 cells, IGF-1 Treated, IGF 1

description:
Library name: Sample 7
Column name in normalized_counts_fpkm_all.csv: PDGF-NS-1


title: S31 cells, IGF-1 Treated, IGF 2

description:
Library name: Sample 8
Column name in normalized_counts_fpkm_all.csv: PDGF-NS-2


title: S31 cells, PDGF-BB Treated, PDGF 3

description:
Library name: Sample 6
Column name in normalized_counts_fpkm_all.csv: IGF-NS-3

value: recombinant rat PDGF-BB (25 ng/ml)


title: S31 cells, PDGF-BB Treated, PDGF 2

description:
Library name: Sample 5
Column name in normalized_counts_fpkm_all.csv: IGF-NS-2


title: S31 cells, PDGF-BB Treated, PDGF 1

description:
Library name: Sample 4
Column name in normalized_counts_fpkm_all.csv: IGF-NS-1


title: mNF1_shC_2

description:
Library name: AS4974
Column name in counts matrix: AS4974

value: mammary gland

value: normal fibroblasts

value: shControl

value: doxycyclin 5 days

value: Rep 2


title: S31 cells, Control, LH 2

description:
Library name: Sample 2
Column name in normalized_counts_fpkm_all.csv: LH-NS-2

value: Control


title: MCF7 cells-ZN-c5 treated_24 hours Rep2

city: SAN DIEGO

first: Jianhui

last: Ma

state: CA

address: 10275 Science center Dr, Suite 200

institute: Zentalis Pharmarceuticals

description: Library name: KP868-JM2

data_processing:
Cutadapt and perl scripts in LC Science were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC
HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/. The mapped reads of each sample were assembled using StringTie.
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
StringTiewa s used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR
Assembly: GRch38
Supplementary files format and content: xlsx files include FPKM values for each sample
Supplementary files format and content: text file include raw counts

source_name: Cell line

growth_protocol: MCF-7 cells were maintained in DMEM/F12 (Gibco 11330-032), supplemented with Non-Essential Amino Acids (NEAA) (Gibco 11140-050), Na-pyruvate (Gibco 11360-070) and Fetal bovine serum (FBS) (Hyclone SH30084)

extract_protocol:
RNA was extracted from cells treated with DMSO or indicated compounds using the RNeasy Kit (Qiagen) per the manufacturer’s instruction, quantified by NanoDrop 8000 (Thermo Fisher Scientific) and reverse-transcribed with cDNA Archive Kit (Applied Biosystems).
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

treatment_protocol: MCF-7 cells were seeded in phenol red free medium supplemented with 10% charcoal stripped FBS. 48 hours later, the cells were treated with ZN-c5 or 4-OH tamoxifen at 1 µM for 24 hours.

value: Cell line

value: ER-positive Breast cancer cell


title: MCF7 cells-ZN-c5 treated_24 hours Rep1

description: Library name: KP868-JM1


title: MCF7 cells-DMSO treated_24 hours Rep1

description: Library name: Ctrl-JM1

value: DMSO


title: MCF7 cells-ZN-c5 treated_24 hours Rep3

description: Library name: KP868-JM3


title: MCF7 cells-DMSO treated_24 hours Rep3

description: Library name: Ctrl-JM3


title: MCF7 cells4-OH Tamaxifen treated_24 hours Rep3

description: Library name: Tamo-JM3

value: Tamoxifen


title: N2, 20 degrees, Generation 0 4 rna

description: Library name: n2_4_20P0_rna

value: Wild-type N2


title: MCF7 cells4-OH Tamaxifen treated_24 hours Rep2

description: Library name: Tamo-JM2

value: WT


title: S31 cells, Control, LH 3

description:
Library name: Sample 3
Column name in normalized_counts_fpkm_all.csv: LH-NS-3


title: MCF7 cells4-OH Tamaxifen treated_24 hours Rep1

description: Library name: Tamo-JM1


title: MCF7 cells-DMSO treated_24 hours Rep2

description: Library name: Ctrl-JM2


title: A1

description: Library name: Sample 1

value: stimulated by LPS


title: GI2_Rep2_UT

city: Palo Alto

first: Ben

last: Herken

address: 3181 porter dr.

institute: Arc Institute

description: Library name: DMSO_R2

library_source: genomic

data_processing:
Align to library reference file with hamming distance = 1, see github: https://github.com/bherken/herken2024_originalcode & Differential expression analysis from raw counts with DeSeq2, See STAR Methods
Assembly: dualsgrna_alignedlibrary.txt & GRCh38
Supplementary files format and content: .txt,  counts table
Library strategy: CRISPR Screen

molecule: genomic DNA

extract_protocol:
Genomics DNA using MN Blood XL Kit, see STAR Method & Total RNA from Zymo Direct-Zol kit
PCR from genomic DNA, see STAR Method & Lexogen Quantseq FWD kit with UMI add-on


title: GI2_Rep1_ETOP

description: Library name: ETOP_R1

value: Etoposide


title: GI2_Rep1_KETO

description: Library name: KETO_R1

value: Glucose Starve


title: GI2_Rep2_KETO

description: Library name: KETO_R2


title: GI2_Rep1_UT

description: Library name: DMSO_R1


title: GI1_Rep2_UT

description: Library name: R2_UT


title: GI2_Rep2_T0

description: Library name: T0_R2


title: GI1_Rep1_ATR

description: Library name: R1_DRUG

value: ATRi


title: GI1_Rep2_ATR

description: Library name: R2_DRUG


title: GI1_Rep1_UT

description: Library name: R1_UT


title: S31 cells, Control, LH 1

description:
Library name: Sample 1
Column name in normalized_counts_fpkm_all.csv: LH-NS-1

value: primary vascular smooth muscle cells


title: GI1_Rep1_T0

description: Library name: R1_T0


title: GI1_Rep2_T0

description: Library name: R2_T0


title: MP3

city: 北京市

first: ZHIYU

last: FAN

state: 北京

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

institute: University of Chinese Academy of Sciences

description: Library name: SAMPLE12

data_processing:
Raw data processing and downstream analyses were conducted on BGI's Dr. TOM platform
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPkM walues for each sample

source_name: umbilical vein

extract_protocol:
Total RNA was extracted from the shear stress treated endothelial cells using RNAsimple Total RNA Kit (DP419,TIANGEN BIOTECH) according to the manufacturer's protocol. RNA quantification and purity were determined using Nanodrop One (Thermo Fisher Scientific).
Qualified RNA samples were sent to BGI-Shenzhen (Shenzhen, China) for strand-specific library construction using the NEBNext Ultra II RNA Library Prep Kit (NEB #E7770),

value: umbilical vein

value: Human Umbilical Vein Endothelial Cells

value: medium presure


title: GI2_Rep2_ETOP

description: Library name: ETOP_R2


title: MP2

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE11


title: MP1

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE10


title: HP1

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE7

value: high pressure


title: MSS2

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE5

value: medium shear stress


title: HP3

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE9


title: LSS3

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE3

value: low shear stress


title: MSS1

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE4


title: MSS3

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE6


title: HP2

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE8


title: LSS2

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE2


title: ATAC_WT_1

city: Hangzhou

first: Yan

last: Wang

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province, China

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Basecalls were performed using bcl2fastq v2.19
Low-quality data including adaptors, reads containing more than 10% of unknown nucleotides, or reads containing more than 50% of low quality, q-value<=20 bases were filtered  using fastp v0.23.0
Clean reads were aligned to the rice reference genome by Bowtie2 v2.4.4 with the parameters “–X 2000”
Peak calling was performed using MACS v2.1.2 with parameters “--nomodel --shift -100 --extsize 200 -B -q 0.05".
Peak annotations were confirmed using ChIPseeker v1.16.1
Assembly: MSU v7.0
Supplementary files format and content: bigWig and comma-separated values files include all peaks information

organism: Oryza sativa

source_name: WT plants, HP conditions, rep1

growth_protocol: Plants were grown in a greenhouse under a 12-h light (30°C) /12h dark (22°C) photoperiod, ~200 μmol m-2 s-1 photon densities, and ~60% humidity.

extract_protocol:
Leaf blades were harvested to extract nuclear protein, then Tn5 transposase (Illumina) were added into nuclei suspensions and incubated in a Transposition Mix at 37°C for 30 min to obtain fragmented DNA, then the resulting products were purified using a QIAGEN MinElute Kit.
ATAC-seq libraries were prepared using TruePrep DNA Library Prep Kit (Vazyme, TD501), following the manufacturer’s instructions.

treatment_protocol: Seedlings grown under HP conditions for 28 d.

value: Leaf blades

value: HP 28d


title: ATAC_WT_2

source_name: WT plants, HP conditions, rep2


title: ATAC_hmg_1

source_name: Oshmgb1 mutants, HP conditions, rep1


title: ATAC_hmg_2

source_name: Oshmgb1 mutants, HP conditions, rep2


title: GI2_Rep1_T0

description: Library name: T0_R1

value: DMSO


title: LSS1

address: 雁栖湖校区：北京市怀柔区怀北镇怀北庄380号

description: Library name: SAMPLE1


title: RNA_WT_2

data_processing:
Basecalls were performed using bcl2fastq v2.19
Data was filtered and mapped to rice reference genome by HISAT v2.0.5
StringTie v1.3.6 was used to perform expression level for mRNAs by calculating FPKM.
Assembly: MSU v7.0
Supplementary files format and content: Comma-separated values files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from related plant tissues using a plant RNA Extraction kit (Macherey-Nagel) according to the manufacturer's instructions.
1 ug of total RNA were used to construct libraries using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.


title: RNA_WT_3

source_name: WT plants, HP conditions, rep3


title: RNA_WT_1


title: HCT116 mAID2-RAD21 + auxin replicate 2 Hi-C

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: HCT116_mAID2-RAD21_sorbitol_auxin_rep2
Hi-C of HCT116 cells at 1h

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Hi-C contact matrices in .hic format (hg38 reference genome) are provided for all samples, including both individual biological replicates and merged replicate datasets (“megaMaps”) for each condition. Datasets include HCT116 wild-type cells (control and 1 h sorbitol treatment), HCT116 mAID2-CTCF and mAID2-RAD21 degron cell lines treated with 1 μM 5-Ph-IAA to rapidly and reversibly degrade CTCF or RAD21 (1 h sorbitol and 6 h auxin treatment), HEK293 wild-type cells from the Phanstiel lab (control and sorbitol treatment), HEK293 eGFP-YAP cells from the Cai lab (control and sorbitol treatment), a HEK293 wild-type sorbitol time course (10 min, 30 min, 1 h, 3 h, 6 h, 12 h, 24 h), and HEK293 eGFP-YAPdTAD cells from the Cai lab (control and sorbitol treatment). MegaMap files represent merged biological replicates for increased sequencing depth. Spike-in normalized 5 kb loop calls are provided for eGFP-YAP conditions, and differential loop analysis (diffLoops_eGFP-YAP_noDroso_10kb.rds) comparing control vs sorbitol treatment is included for eGFP-YAP samples.

growth_protocol: HEK293T and HCT116 cells were cultured at 37 °C in a humidified incubator with 5% CO₂. HEK293T cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin. HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and penicillin/streptomycin. Cells were routinely monitored for mycoplasma contamination and maintained at ~70–80% confluence to ensure log-phase growth. Cells were harvested for experiments only when healthy and within 5–15 passages from thaw.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
In situ Hi-C libraries were prepared using MboI restriction digestion, fill-in with biotinylated nucleotides, proximity ligation, reverse crosslinking, and DNA purification. Libraries were size-selected and PCR-amplified prior to sequencing.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

value: 0.2M sorbitol for 1h; 1uM 5PhIAA for 6h


title: HCT116 mAID2-CTCF + auxin replicate 1 Hi-C

description:
Library name: HCT116_mAID2-CTCF_sorbitol_auxin_rep1
Hi-C of HCT116 cells at 1h


title: HCT116 mAID2-CTCF + auxin replicate 2 Hi-C

description:
Library name: HCT116_mAID2-CTCF_sorbitol_auxin_rep2
Hi-C of HCT116 cells at 1h


title: HCT116 mAID2-CTCF control replicate 2 Hi-C

description:
Library name: HCT116_mAID2-CTCF_sorbitol_control_rep2
Hi-C of HCT116 cells at 1h

value: 0.2M sorbitol for 1h


title: RNA_hmg_3

source_name: Oshmgb1 mutants, HP conditions, rep3


title: HCT116 mAID2-RAD21 + auxin replicate 1 Hi-C

description:
Library name: HCT116_mAID2-RAD21_sorbitol_auxin_rep1
Hi-C of HCT116 cells at 1h


title: RNA_hmg_2


title: HCT116 mAID2-RAD21 control replicate 2 Hi-C

description:
Library name: HCT116_mAID2-RAD21_sorbitol_control_rep2
Hi-C of HCT116 cells at 1h


title: RNA_hmg_1


title: HCT116 mAID2-RAD21 control replicate 1 Hi-C

description:
Library name: HCT116_mAID2-RAD21_sorbitol_control_rep1
Hi-C of HCT116 cells at 1h


title: Oshmgb1 mutants, LP conditions, rep3

data_processing:
Basecalls were performed using Illumina Casava v2.17
Data was filtered and mapped to rice reference genome by HISAT v2.0.5.
StringTie v1.3.6 was used to perform expression level for mRNAs by calculating FPKM
Assembly: MSU v7.0
Supplementary files format and content: Comma-separated values files include FPKM values for each Sample

source_name: Leaf blades

treatment_protocol: Seedlings grown under HPconditions for 14 d and were transfered to HP or LP conditions for another 7 d.

value: HP 14d, LP 7d


title: WT plants, LP conditions, rep2

value: WT


title: Human growth plate, cultured vehicle, rep3 (file2)

city: Gothenburg

first: Andrei

middle: S

last: Chagin

state: Västra Götaland

address: Guldhedsgatan 10a

department: Institute of Medicine

institute: University of Gothenburg

description: Library name: P25452_005

data_processing:
Cellranger (v7.1.0 human and v7.0.1 mouse) was used for alignment
Assembly: GRCh38-2020-A / mm10-2020-A
Supplementary files format and content: Cell Ranger filtered feature matrix

source_name: growth plate

extract_protocol:
The obtained slices were dissected from bone under a stereo microscope, ground into small fragments, transferred to fresh, ice-cold HBSS, and thoroughly pipetted to remove residual blood. Then HBSS was replaced with a digestion solution comprising Collagenase P (3 U/mL, Roche) and TrypLE™ Select Enzyme (1X, Thermo Fisher Scientific, Catalog No: A1217701) in HBSS. The tubes were incubated for 30–40 minutes at 37°C with shaking at 120 rpm. During digestion, the tissue fragments were disrupted every 10 minutes using a 1-mL pipette. The digestion was terminated by the addition of 10 mL of 2% FBS in cold HBSS. The mixture was centrifuged at 300 rpm for 10 minutes at 4°C. The supernatant was carefully removed, and the pellet was resuspended in 100 µL of 2% FBS in 1X PBS. Ice-cold methanol (400 µL) was added dropwise to the suspension, and the sample was placed on ice for 10 minutes. The cells were stored at -80°C for a maximum of six months prior to library preparation.
10X protocol

treatment_protocol: To investigate the mechanisms underlying GH action, human growth plate slices were cultured for 24 hours with or without 40 ng/ml of GH (Norditropin, Novo Nordisk). Following the culture period, the slices were washed with ice-cold PBS, dissected from bone under a stereo microscope, and subjected to single-cell preparation. The explants were incubated at 37°C with 5% carbon dioxide in a culture medium consisting of DMEM/F12 (without phenol red), gentamycin (20 µg/ml), 0.2% bovine serum albumin (BSA), β-glycerophosphate (1 mM), ascorbic acid (5 µg/ml), and 2% fetal bovine serum (FBS)

value: growth plate

value: cartilage

value: wt

value: vehicle


title: Human growth plate, cultured gh, rep3 (file1)

description: Library name: P25452_007

value: growth hormone


title: Human growth plate, cultured gh, rep3 (file2)

description: Library name: P25452_008


title: WT plants, LP conditions, rep3


title: WT plants, LP conditions, rep1


title: Human growth plate, rep4

description: Library name: P22202_1015

value: primary tissue


title: Human growth plate, cultured vehicle, rep3 (file1)

description: Library name: P25452_004


title: Human growth plate, rep3

description: Library name: P25452_001


title: HCT116 mAID2-CTCF control replicate 1 Hi-C

description:
Library name: HCT116_mAID2-CTCF_sorbitol_control_rep1
Hi-C of HCT116 cells at 1h


title: Oshmgb1 mutants, LP conditions, rep2


title: WT plants, HP conditions, rep3

value: HP 21d


title: Human growth plate, cultured gh, rep2

description: Library name: P31011_1003


title: Oshmgb1 mutants, LP conditions, rep1


title: Human growth plate, cultured vehicle, rep2

description: Library name: P31011_1002


title: WT plants, HP conditions, rep2


title: Oshmgb1 mutants, HP conditions, rep3


title: Human growth plate, rep2

description: Library name: P31011_1001


title: Human growth plate, cultured vehicle, rep1

description: Library name: P30453_1002


title: Oshmgb1 mutants, HP conditions, rep2


title: Oshmgb1 mutants, HP conditions, rep1


title: Human growth plate, rep1

description: Library name: P30453_1001


title: Rv::pN-smpB, replicate 6

city: Delhi

first: Vinay

middle: K.

last: Nadnicoori

state: DELHI

address: National Institute of Immunology, Near JNU EAST GATE, ARUNA ASAF ALI MARG, NEW DELHI-110067

country: India

institute: National Institute of Immunology

data_processing:
FastQC for quality check
The trimmed counts were aligned using Bowtie2 to Mycobacterium tuberculosis H37Rv (Rv) genome
Read count extraction and normalization was performed using HT-Seq
DESEq2 (Version: 1.124.0) was used for differential expression
Assembly: Ensembl ASM19595v2
Supplementary files format and content: tab-delimited tet files contain raw counts of each sample as calculated with HT-Seq

organism: Mycobacterium tuberculosis H37Rv

growth_protocol: we cloned ssB and smpB genes into pNit-3F vector under an isovaleronitrile (IVN) inducible promoter and electroporated the clones into H37Rv (Rv) along with an empty pNit-3F as a control. 3 replicate cultures were taken of each strain.The cultures were grown in 7H9 media supplemented with 10% ADC(albumin, dextrose, NaCl and catalase) and when A600 reached 0.8 A600 the culture was subcultured into 300 ml Difco 7H9 media(10%ADC) at 0.1 A600, with 5uM IVN and grown for 2 days till A600 reached 0.8

extract_protocol:
Cells were resuspended in TRIzol (Ambion), mixed with 0.1 mm zirconium beads and lysed using a bead beater. The cell debris were pelleted doen and the supenatant collcetd in a fresh tube, RNA extracted using chloroform, followed by precipitation with isopropanol and further washing with 70% ethanol. The RNA was treated with DNaseI to eliminate contaminating genomic DNA. The RNA was further passed through RNAeasy mini plus kit columns (Qiagen) following the manufacturer's protocol.
RNA-seq ibraries were prepared using Agilent RNA 6000 Nano Kit following manufacturer's protocol

treatment_protocol: The cells were induced with 5uM isovaleronitrile (IVN)(Sigma) on inoculation at 0.1A600 in 300 ml culture

value: whole cell

value: Bacterial cell(H37Rv)

value: 5uM IVN


title: Rv::pN-smpB, replicate 5


title: J-H3K9ac-shBDH1-IP-2

first: Jin

last: Xu

address: 115 East Lake Road, Wuhan, Hubei, 430071, P. R. China

institute: Wuhan university

description: Library name: Sample14

data_processing:
ChIP-seq raw reads were aligned to the human genome (hg38) with STAR (version 2.7.6a) with default settings. Read coverage was analyzed using deepTools and visualized in the UCSC genome browser. Peaks were called using the bdgdiff command from MACS3 (version 3.0.3), and heatmaps were generated using the computeMatrix command from deepTools. Motif analysis was conducted using the MEME suite.
Assembly: hg38
Supplementary files format and content: BED, Peak, bedGraph.

source_name: human T-ALL cells

extract_protocol:
Jurkat cells were transfected with lentivirus expressing control or BDH1 shRNA, and puromycin selection (2 μg/mL) for 48 h.
Jurkat cells were initially crosslinked with 1% paraformaldehyde for 10 min and then were quenched with glycine for 5 min. After cell lysis, fixed chromatin underwent fragmentation to achieve DNA sizes ranging from 200 to 600 bp utilizing a DiagenodeBruptor Plus DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads (Smart-Lifesciences). 1-10 ng of immunoprecipitated DNA was employed for DNA library preparation.

value: human T-ALL cells

value: Jurkat

value: T-ALL cell lines


title: Rv::pN-ssb, replicate 5


title: J-H3K9ac-BDH1-input

description: Library name: Sample10


title: Rv::pN-smpB, replicate 2


title: J-H3K9ac-control-IP-1

description: Library name: Sample11


title: Rv::pN-ssb, replicate 3


title: Rv::pN-ssb, replicate 2


title: J-H3K9ac-control-input

description: Library name: Sample9


title: Human growth plate, cultured gh, rep1

description: Library name: P30453_1003


title: WT plants, HP conditions, rep1

value: Leaf blades


title: Rv::pN, replicate 5


title: J-H3K9bhb-shBDH1-IP-2

description: Library name: Sample8


title: J-H3K9bhb-shBDH1-IP-1

description: Library name: Sample7


title: J-H3K9bhb-control-IP-1

description: Library name: Sample5


title: Rv::pN, replicate 2


title: J-H3K9bhb-shBDH1-input-2

description: Library name: Sample4


title: J-H3K9bhb-shBDH1-input-1

description: Library name: Sample3


title: J-H3K9bhb-control-input-2

description: Library name: Sample2


title: MHCC97H_siSETD1B_ZEB1

city: Shanghai

first: Wenying

last: Qiu

address: Dongan road 270

institute: Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences

description: Library name: Sample 8

data_processing:
For CUT&Tag analysis, 150-bp paired-end sequencing reads were aligned to the human reference genome (GRCh38) using Bowtie2 with default alignment parameters.
Assembly: hg38
Supplementary files format and content: We provide FASTQ files for our CUT&Tag data.
Library strategy: CUT&Tag

source_name: Liver

growth_protocol: All the cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Basalmedia, Shanghai, China) supplemented with 10% fetal bovine serum (FBS; Gibco, NY, USA) under standard culture conditions (37 °C, 5% CO₂).

extract_protocol:
All experimental procedures were performed following the manufacturer's protocol for a NovoNGS® CUT&Tag® 4.0 High-Sensitivity Kit (Novoprotein, Suzhou, China).
All experimental procedures were performed following the manufacturer's protocol for a NovoNGS® CUT&Tag® 4.0 High-Sensitivity Kit (Novoprotein, Suzhou, China).

value: Liver

value: Liver cancer cell


title: J-H3K9ac-shBDH1-IP-1

description: Library name: Sample13


title: MHCC97H_siNC_H3K4me3

description: Library name: Sample 9


title: MHCC97H_siSETD1B_H3K4me3

description: Library name: Sample 10


title: HepG2_H3K27me3

description: Library name: Sample 6


title: MHCC97H_siNC_ZEB1

description: Library name: Sample 7


title: J-H3K9ac-control-IP-2

description: Library name: Sample12


title: set-24 Mutant, 20 degrees, Generation 0 2 srna

description: Library name: mj617_2_20P0_srna

data_processing:
RNASeq- Quality and Adaptor Trimming - Trimmomatc
RNASeq- Read alignment and counting - Salmon
RNASeq- Differential expression analysis - DESEq2
ChIP-Seq- Quality and Adaptor Trimming - Cutadapt
ChIP-Seq- Read aligment- BWA
ChIP-Seq- Peak calling and bdg generations- MACS3
ChIP-Seq- Differential enrichment analysis- DiffBind
Assembly: Ensembl - WBCel235
Supplementary files format and content: raw_counts.txt - This file contains the raw counts obtained from Salmon alignment  for each sample in matrix fromat
Supplementary files format and content: regularized_log_normalised_counts.txt - This file contain rlog normalsed counts for each sample n matrix format
Supplementary files format and content: All bdgs - These files contain the log2 normalized enrichments in bedgraph format.

source_name: Whole Organism

value: Whole Organism


title: mutant, Pmel treatment, rep3

city: Aurora

first: Sarah

middle: E

last: Clark

state: CO

address: 12700 E 19th Ave, Mail Stop 8333

institute: University of Colorado School of Medicine

description: Library name: ZplusM_6_S22

data_processing:
Adapter contamination removal with BBDuk
Tx Quantification with Salmon
Gene-level summaries with Tximport
Assembly: GRCh38 (Gencode H37)
Supplementary files format and content: CSV, rownames are genes, columns are samples, values are Salmon calculated counts

extract_protocol:
RNA extraction by Rneasy kit (Qiagen)
Nugen Universal Plus mRNA kit

value: CF

value: P. melaninogenica strain ATCCÒ 25845, heat-killed


title: Rv::pN, replicate 6


title: mutant, Pmel treatment, rep1

description: Library name: ZplusM_4_S20


title: J-H3K9bhb-control-IP-2

city: Wuhan

description: Library name: Sample6


title: MHCC97H_H3K9ac

description: Library name: Sample 3


title: HepG2_H3K9ac

description: Library name: Sample 4


title: mutant, untreated, rep2

description: Library name: Z_2_S18


title: mutant, untreated, rep3

description: Library name: Z_3_S19


title: MHCC97H_ZEB1

description: Library name: Sample 1


title: mutant, untreated, rep1

description: Library name: Z_1_S17


title: MHCC97H_SETD1B

description: Library name: Sample 2


title: MDA-MB-231 cells, si-ATP6V0D2-2

city: Shijiazhuang

first: Zhenchun

last: Song

state: Hebei Province

address: 169 Tianshan Street, Yuhua District, Shijiazhuang City

department: breast center

institute: The Fourth Affiliated Hospital of Hebei Medical University

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: 231-Si2

data_processing:
1, Data quality control The image data of the sequenced fragments measured by high-throughput sequencers are converted into sequence data (reads) by CASAVA base recognition, and the files are in fastq format, which mainly contain the sequence information of the sequenced fragments as well as their corresponding sequencing quality information. In order to ensure the quality and reliability of data analysis, we need to filter the raw data. To ensure the quality and reliability of the data analysis, we need to filter the raw data, including removing reads with adapters, removing reads containing N (N means that the information of bases cannot be determined), and removing low-quality reads (Qphred <= 20 bases accounted for more than 50% of the total length of the reads). At the same time, Q30 and GC content calculations were performed on clean data. All subsequent analyses were high-quality analyses based on clean data.
2, Sequence alignment to a reference genome Download the reference genome and gene model annotation files directly from the genome website. The index of the reference genome was constructed using HISAT2 v2.0.5, and paired-end clean reads were compared to the reference genome using HISAT2 v2.0.5. We chose HISAT2 as the comparison tool because HISAT2 can generate a spliced linked database based on the gene model annotation files, and therefore has better comparison results than other non-spliced comparison tools.
3, Quantification of gene expression levels The FPKM of each gene is calculated based on the length of the gene and the number of reads mapped to that gene is calculated.FPKM refers to the expected number of fragments per kilobase per million base pairs of sequenced transcript sequence fragments. The effects of sequencing depth and gene length on read counts are also taken into account and are currently the most commonly used method for estimating gene expression levels
4, Differential expression analysis For samples with biological duplicates, differential expression analyses between the two comparison combinations were performed using the DESeq2 software.DESeq2 provides statistical procedures for identifying differential expression in numerical gene expression data using models based on negative binomial distributions. The method of Benjamini and Hochberg was used to adjust the resulting p-values to control for false discovery rates. Genes with adjusted P-values <= 0.05 were found to be assigned as differentially expressed by DESeq2. For those without biological replicates were analysed using DESeq software
Assembly: The index of the reference genome was constructed using HISAT2 v2.0.5, and paired-end clean reads were compared to the reference genome using HISAT2 v2.0.5.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: cell line

growth_protocol: Human breast cancer cell lines MDA-MB-231 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. All cells were incubated at 37°C in a 5% CO₂ humidified atmosphere.

extract_protocol:
Total RNA was isolated from three sets of control MDA-MB-231 cells and those treated with siRNA against ATP6V0D2  by TRIzol reagent (Takara, Japan). 1.3ug of total RNA was used for the construction of sequencing libraries.
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

value: cell line

value: Human breast cancer cell

value: ATP6V0D2 knockdown


title: MDA-MB-231 cells, si-ATP6V0D2-3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: 231-Si3


title: MDA-MB-231 cells, si-ATP6V0D2-1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: 231-Si1


title: wildtype, Pmel treatment, rep2

description: Library name: QplusM_11_S27

value: wildtype


title: MDA-MB-231 cells, si-NC-3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: 231-NC3

value: negative control


title: wildtype, Pmel treatment, rep1

description: Library name: QplusM_10_S26


title: MDA-MB-231 cells, si-NC-1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: 231-NC1


title: wildtype, untreated, rep1

description: Library name: Q_7_S23

value: vehicle


title: wildtype, untreated, rep3

description: Library name: Q_9_S25


title: J-H3K9bhb-control-input-1

description: Library name: Sample1


title: MHCC97H_H3K27me3

description: Library name: Sample 5


title: wildtype, untreated, rep2

description: Library name: Q_8_S24


title: A549 cells, aPC, Experiment 3

city: Kalyani

first: Kaushik

last: Das

state: West Bengal

address: N.S.S. Kalyani Nadia

institute: National Institute of Biomedical Genomics

description: Library name: Sample 6

data_processing:
Raw sequencing reads were subjected to quality control using FastQC
Adapter trimming and quality filtering were performed using Trim Galore! (v0.6.6)
High-quality reads were aligned to the human reference genome (Ensembl release 112) and miRBase miRBase (release 22.1) and  using STAR aligner (v2.7.9a)
read counts were quantified using HTSeq (v0.13.5)
Assembly: hg38
Supplementary files format and content: excel, gene count

source_name: Lung cancer

growth_protocol: The human lung epithelial adenocarcinoma cell line, A549 was maintained in F-12K, supplemented with 10% fetal bovine serum and 1X penicillin-streptomycin solution. The cells were grown at 37°C with 5% CO2 in a humidified atmosphere.

extract_protocol:
MicroRNA was isolated from equal number of control- or aPC-treated EVs by using mirPremier microRNA Isolation Kit (Sigma) and subjected to miR expression analysis by deep-sequencing.
Illumina NovaSeq 6000 platform, generating 50 bp single-end reads

treatment_protocol: A549 cells were serum starved for 1 h followed by the treatment with a control vehicle or aPC (Sigma). After 16 h, the supernatant was subjected to EV isolation by differential centrifugation. After counting the EVs by NTA Nano-Sight, the EVs were subjected to miR isolation.

value: Lung cancer

value: A549 cells

value: Non-small cell lung cancer cells

value: activated protein C


title: MDA-MB-231 cells, si-NC-2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: 231-NC2


title: HC_17_60, bulk RNA

first: Tianyi

last: Zhu

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine

description:
Library name: HC_17_60
HC_17_60

data_processing:
For PBMCs sequencing, raw fastq data were subjected to quality control using fastp-0.12.4. Alignment was performed using hisat2-2.2.0, referencing the GRCh38 human genome, which included ERCC spike sequences. Sorted SAM files were processed using GATK4-4.2.6.0, and transcript assembly and abundance estimation were carried out using stringtie-2.2.1. Batch effects were corrected using ERCC spike-in as references, employing the R package RUVSeq-1.30.0 for normalization.
Assembly: hg38
Supplementary files format and content: For PBMCs sequencing, tab-delimited text file includes ERCC counts for each Sample

source_name: PBMC

extract_protocol:
Peripheral blood samples were collected and stored at 4℃ in EDTA anticoagulant tubes and processed promptly. PBMC isolation was performed using a Ficoll density gradient centrifugation with the following steps: whole blood samples were diluted 1:1 with phosphate buffered saline (PBS), and the diluted blood samples were gently layered over Ficoll solution in a centrifuge tube. The mixture was centrifuged at 400g for 30 minutes at room temperature, with the acceleration and brake settings of the centrifuge set to 1. After centrifugation, the intermediate cloudy layer containing the PBMCs was carefully collected. This layer was mixed with three volumes of PBS and centrifuged again at 500g for 10 minutes at room temperature. The resulting PBMC pellet was washed further with PBS and centrifuged to enrich the cells. Samples with significant red blood cell contamination were treated with ACK Lysing Buffer (A10492-01, Gibco) for red blood cell lysis.
For PBMCs sequencing, the total RNA was mixed with ERCC RNA Spike-in Mix (4456740, Invitrogen) in proportion for transcriptome library construction. The sequencing library was prepared using the RNA-seq Library Prep Kit for MGI (NRM605, Vazyme) and sequenced in batches on the DNBSEQ-T7 platform.

value: PBMC


title: HC_17_61, bulk RNA

description:
Library name: HC_17_61
HC_17_61


title: A549 cells, aPC, Experiment 2

description: Library name: Sample 5


title: A549 cells, aPC, Experiment 1

description: Library name: Sample 4


title: wildtype, Pmel treatment, rep3

description: Library name: QplusM_12_S28


title: A549 cells, Control, Experiment 3

description: Library name: Sample 3

value: control


title: HC_17_55, bulk RNA

description:
Library name: HC_17_55
HC_17_55


title: HC_17_56, bulk RNA

description:
Library name: HC_17_56
HC_17_56


title: A549 cells, Control, Experiment 1

description: Library name: Sample 1


title: HC_16_54, bulk RNA

description:
Library name: HC_16_54
HC_16_54