title: Stage 19 gonad, male, rep2

city: Dos Hermanas

first: Iván

last: Barberá Aura

address: Avenida Rectora Rosario Valpuesta 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo (CABD)

description:
Library name: male_19_rep2
10x genomics

data_processing:
The demultiplexing, barcoded processing, alignment to genome and transcriptome, gene counting and aggregation was performed using the Cell Ranger software (v7.0.2)
Assembly: UM_NZW_1.0 (GCA_009806435.2)
Supplementary files format and content: Barcode, feature tsv files and matrix files from filtered CellRanger output.

organism: Oryctolagus cuniculus

source_name: Embryonic gonad

growth_protocol: Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). For 24 and 28 dpc, fetal ovaries were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France).

extract_protocol:
Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). Dissected gonads were dissociated into single-cells by incubating them with 0.05% Trypsin-EDTA (Gibco cat#25300-054) in addition to 1/10 portion of 5% BSA (Sigma-Aldrich cat#A7030-50G) /DPBS for 7-10 minutes at 37ºC. Dissociation was facilitated by pipetting gently every 2-3 minutes. Residual connective tissue, which appeared as whitish clumps at the end of the dissociation process, was discarded. Trypsin activity was halted by adding 2 portions of 5% BSA/DPBS. Cell suspension was passed through a 40 µm FlowMi cell strainer (Fisher Scientific cat#15342931) to remove cell clumps and debris. Filtrated cells were collected by centrifugation at 250-300g for 5 minutes at 4°C. The cell pellet was resuspended in DPBS for counting and viability check using 50% v/v trypan blue staining (Sigma Aldrich cat#T8154-20ML) under a light microscope. Only samples with ≥ 80% were used for downstream single-cell library preparation. Finally cells were fixed with 98% methanol added drop by drop and stored in -80°C freezer. For ovaries collected at 24 and 28 dpc, gonads were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France). The two gonads from the same fetus were pooled per stage in 500 µl of Trypsin-EDTA 0.05% at 37°C for 30 min. Dissociation was facilitated by gently pipetting every 5 minutes. Tryspin activity was stopped by adding SVF for a final 2% concentration. The cell suspension was passed through a 70 µm filter, then a 40 µm FlowMi Cell Strainer (Sigma-Aldrich cat #BAH136800040) to remove cell clumps and debris. The filtrated cells were collected by centrifugation at 300g for 10 minutes. The cell pellet was resuspended in 500 µL (24 dpc) or 1 mL (28 dpc) of DMEM/F12-SVF 2%. To determine whether the obtained cells were suitable for downstream analysis (cell viability > 80%), cell viability was evaluated using trypan blue staining with a haemocytometer r (TC20, Bio-Rad cat#1450102). The cell concentration was then adjusted to around 1000 cells/μl before loading onto the single-cell chip.
For the data from gonads at the stages 13-21 dpc, fixed cells were equilibrated to 4ºC on ice for at least 5 minutes. Subsequently, the cells were pelleted at 1,000g for 5 minutes at 4℃. The cells were rehydrated and gently washed with rehydration buffer (0.04% BSA, 1mM DTT (Life Technologies cat#707265ML), 0.4U/µl RNaseIn (Life Technologies cat#AM2682), 0.2U/µl SuperaseIn (Life Technologies cat#AM2696), in DPBS), using wide-bore tips (Corning Axygen Cat#T- 205-WB-C-R-S). Cell number and quality after rehydration were assessed using 50% v/v trypan blue staining. Cell suspensions were adjusted to a final concentration of 700-1,200 cells/µl. Single-cell libraries were generated using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics), according to manufacturer’s instructions, targeting 10,000 cells per reaction. Two libraries were prepared for each developmental stage and sex, except for female gonads at stage 15, for which only one library was prepared. Libraries were sequenced to a minimum depth of 200 million reads per library using the paired-end sequencing format: Read 1, 28 cycles; I7 index, 10 cycles; I5 index, 10 cycles; Read 2, 90 cycles.  For the data from ovaries at 24 and 28 dpc, Gel-Bead in Emulsions (GEMs) were generated using a Chromium 10X Single Cell System (10X Genomics) and cDNA libraries were prepared using the Chromium Next GEM Single Cell 5' Reagent v2 (10X Genomics). Two libraries were prepared for each developmental stage. The I2BC High-throughput Sequencing Platform (https://www.i2bc.paris-saclay.fr/sequencing/ng-sequencing/; Université Paris-Saclay, Gif-sur-Yvette, France) provided the facilities and expertise for library preparation and sequencing (Paired-end 28-64 bp, Illumina NextSeq500).

value: Embryonic gonad

value: male

value: Stage 19


title: CD68+, Scar4, MGC WO-002

status: Public on Jun 30 2026

type: SRA

city: Rozzano

first: Anna Rita

last: Putignano

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
Library name: DSP-1001660036826-A-G05
CD68+ AOI from skin lesion, secondary intention healing patient Scar4, slide: CD68_Slide6, ROI: Scar4-MGC_WO-002, area: 12637.93 um2, nuclei: 77

library_source: transcriptomic

data_processing:
For each AOI, digital count conversion (.dcc) files were generated from fastqs using the GeoMx NGS Pipeline (version 3.1.1).
From each tissue under investigation DCC files were read into a NanoStringGeoMxSet object using the readNanoStringGeoMxSet function from GeomxTools R package (version 3.5, R version 4.3.3), and segments were assessed for sequence quality.
After generating gene-level counts, segments with high fraction of genes detected below the limit of quantification (LOQ) were removed. Count matrix, sample annotations, and feature annotations were read into a SpatialExperiment object and analyzed with standR package (version 1.6) workflow.
Genes with low expression levels were removed. Counts were normalized using the upper-quartile method from the edgeR package (version 4.0.16).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files containing raw expression values for each AOI/sample
Supplementary files format and content: DCC files containing raw probe read counts for each AOI/sample; RTS_IDs are interpretable using the accompanying PKC file

molecule: total RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
After deparaffinization and target retrieval, slides were incubated with 0.1 μg/mL proteinase K for 15 minutes at 37°C and then post fixed for 5 minutes in 10% neutral buffered formalin followed by two washes in NBF stop buffer (24.5 g Tris base and 15 g Glycine in 2 L DEPC water). Slides were incubated with the Whole Transcriptome Atlas (WTA) RNA Probe set (121401102, NanoString), according to the manufacturer’s protocol.
Following probe incubation, slides were washed and incubated with the morphology marker solution: AlexaFluor™ 647 anti-human CD68 (BL13756, 375606 BioLegend, 1:400, RRID:AB_3097193) plus SYTO 13 (provided in GeoMx Nuclear Stain Morphology Kit, 121300303, NanoString) for 1 hour at RT and processed through the GeoMx® Digital Spatial Profiler instrument. Regions of interest (ROIs) with a circular shape and a diameter of 600 μm were selected, with an average of 3 ROIs without MGCs and 5 ROIs with MGCs per patient. For each ROI, the CD68+ area of interest (AOI) was selected to collect barcodes in a 96-well plate. Barcoded oligonucleotides were prepared for Illumina-based sequencing to generate target probe-specific count files, which were then saved in a digital count conversion format.

tag: tissue

value: skin

tag: cell type

value: macrophages


title: Long-Bridge RT Probe Test BC002

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

description:
Library name: FIX08824-002
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the Fixed RNA Profiling capability (version 9.0.1), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

growth_protocol: VST culture and fixation: Culture was performed using GREX-10, 6 well plates (Wilson Wolf), largely following a previously published rapid expansion protocol (Lazarski 2021). Briefly, PBMC were thawed, pelleted at 400 xg and resuspended in 2% BSA/PBS for counting. Cells were pelleted once again and resuspended at 1.5x107 cells per mL in CTL culture media including 300ng/mL each of CMV derived pp65 and IE-1 peptide pools (Peptivator, Milltenyi) or vehicle control (water). CTL culture media contained 44% RPMI, 44% Clicks, 10% FBS, 1% PenStrep, 1x Glutamax. Cells were incubated/pulsed for 1h at 37C. Following peptide pulse, cells were distributed into GREX-10 6 well plates containing 30mL total volume CTL media. Media was supplemented with IL4 (400U/mL), IL7, and/or IL15 (10ng/mL) as indicated. On day 7 of culture, the upper 15mL of media was carefully removed from each well without disturbing cells and replaced with 15mL fresh CTL media including 2x cytokine addition. If applicable, treatment with metabolic inhibitors UK5099 (Sigma), TWS-119 (Selleck Chem.) or vehicle/DMSO, was initiated on day 1 of culture. Further addition of inhibitors was done at 1x concentration and occurred only during day 7 media exchange. Individual wells were harvested at indicated timepoints during VST culture. Upon harvest, cells were washed 1x with cold 0.4% BSA/PBS followed by 1x with cold PBS alone prior to pelleting and resuspension in cold 10x fixation buffer per the standard FLEX protocol. Cells were counted and fixed at a maximum of 1x107 per mL fixation buffer. Fixation occurred for 20-26 hours at 4C. After fixation, cells were pelleted at 850 xg and resuspended in 1mL ice cold quenching buffer per 10x FLEX guideline. 10x Enhancer and 50% glycerol were added, prior to storage at -80°C, per 10x FLEX guidelines.

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell FLEX GEM Library and Gel Bead kit.
REFLEX (Library prep, pre-amp): Following GEM incubation, 125 μL of Recovery Agent was added to break the GEM emulsion. Mixtures were inverted 10x and incubated for 2 minutes at room temperature. 125 μL of recovery agent was then carefully removed from the bottom of each well. The remaining approximately 65 μL of recovered GEM sample was combined with a master mix containing 27 μL of Amp Mix (10X PN-2000047), 10 μL of Pre-Amp Primers B (10XPN-20000529), 1.5 μL of TruSeq1 [1 μM], and 3 μL of a pre-mixed TCR Variable Primer Pool (See Supplemental Note [REF]) [0.66 μM] for a total volume of 106.5 μL of master mix plus recovered GEM. Samples were inverted 10x to mix and placed in a thermal cycler with the following cycling conditions: 98C for 3 minutes; 8 cycles of 98C/20 seconds, 60C for 30 seconds, 72C for 2 minutes; 72C for 5 minutes, 4C infinite hold. Upon completion of the PCR, tubes were pulsed briefly on a minifuge to collect liquid. 90 μL was then transferred into a new 1.5 mL Eppendorf tube. A 1.8X SPRI bead cleanup was performed and sample was eluted into 100 μL of elution solution in accordance with 10X User Guide CG000673 Rev B.
REFLEX (library prep, re-amplification): Pre-amplified library eluates were split into two or three pools for preparation of gene expression libraries,TCR libraries, and ADT libraries (when applicable). Gene expression and ADT libraries were prepared using 20uL pre-amp product and following 10x guidelines for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev B). Linear PCR master mix for TCR libraries consisted of 20 μL 1X KAPA HiFi HotStart (Roche, KK260), 10 uL molecular biology grade water (Fisher, BP2819100), and 0.5 μL TruSeq2 primer at 123.4 nM per reaction. TCR libraries utilized 40 μL of pre-amp product total, divided into 4, 10 μL aliquots. Each 10 μL aliquot was combined with 30.5 μL master mix in a PCR strip tube and incubated with the following PCR program: 95C/3min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeat x4 for 5 total cycles, 72C/5min final extension, hold 4C. After the 5 cycle linear PCR was completed, 0.5 μL TruSeq1, at 123.4 nM per reaction, was spiked into each reaction and an exponential PCR was performed with the following conditions: 95C/3 min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeated x7 for 8 total cycles, 72C/5min final extension, hold 4C. Following exponential PCR, each of the four 41 μL reactions per library condition were repooled for a total volume of 164 μL. Samples were SPRI cleaned at 0.8X ratio, eluted in 50 μL aforementioned “elution solution ”.
REFLEX (Indexing TCR Libraries): PCR indexing master mix was prepared with 50 μL 1X Kapa HiFi HotStart and 10 μL molecular biology grade water per reaction. Indexing reactions combined 20 μL cleaned re-amplified product, 60 μL master mix, and 20 μL Dual Index TT Set A (10X Genomics, PN-1000215). Each library used a unique TT index well enabling later identification via sequencing. Samples were inverted to mix and briefly spun down. Thermocycler conditions used were as follows: 98C/45s activation [98C/20s denaturation, 54C/30s annealing, 72C/90s] repeated x12-15 for 13-16 total cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. A final SPRIselect bead clean up was performed at a 0.7X ratio with cleaned product eluted into 40 μL Buffer EB (Qiagen, Cat No. 19086).
REFLEX (Indexing GEX libraries): GEX library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 4.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TS Set A primers (PN-3000511). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
REFLEX (Indexing ADT libraries): ADT library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 5.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TN Set A primers for the ADT libraries (10X, PN 1000250). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
Sequencing: Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300 or NextSeq2000 P4 300 cycle flow cell, Read1:80 Read2:200. A read depth of 5000 reads per cell for TCR libraries or 10,000 reads per cell for GEX libraries was targeted. ADT or CITEseq libraries were targeted at 5000 reads per cell.

treatment_protocol: Cell Lines: Parental Jurkat T cells were originally purchased from ATCC and were transduced with pMW39 lentivirus (CXCR4 sgRNA) + pMW5 lentivirus (dCas9 ) by our group for use in other studies. No modifications were made to the native Jurkat TCR. The Raji CCL-86 cell line was purchased from ATCC.

value: Blood

value: PBMC

tag: treatment

tag: subject id

tag: age at_blood_drawn

tag: Sex

value: Female

tag: ethnicity/race

value: Caucasian/Non-Hispanic

tag: cmv stats

value: Unknown

tag: treatment time

tag: batch id

tag: pool id

value: PA

tag: batch pool

tag: probe barcode_id


title: Yeast, Metformin, MTX, replicate B

city: Montreal

first: Adrian

middle: W R

last: Serohijos

state: QC

address: 5155 Chem. de la Rampe

department: Department of Biochemistry

country: Canada

institute: University of Montreal

library_source: genomic

data_processing:
*library strategy: DNA barcode sequencing
Demultiplexing: Using AdapterRemoval (version 2.3.2), we allowed at most 2 mismatches within the inner-adapters (--barcode-mm-r1 = 2 and --barcode-mm-r2 = 2) to account for mutations that could arise from PCR and/or NGS.
Barcode extracting: Extracting the strains barcodes from the reads using the command bartender_extractor_com of Bartender (version 1.1)
Barcode mapping: we mapped extracted barcodes to the 361 unique strains using in-house Python scripts (https://github.com/ladyson1806/SerohijosLab-piQTL).
Assembly: not applicable
Supplementary files format and content: comma-separated files contain the read numbers of the barcoded strains under the specified conditions.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: in house yeast library

growth_protocol: 40 μL of frozen cells (~4 x 10^5 cells) were inoculated into 760 μL SD media (minimal synthetic defined bases, 2% glucose, 120 mg/L Leucine) in 96 deep-well plates. The cells were grown at 30°C for 96 hours and passaged every 24 hours at a ratio of 1:8 (100 μL of cultured cells were added into 700 μL of fresh media).

extract_protocol:
To extract the gDNA, the cell pellets were resuspended in 300 μL of 50 mM EDTA containing 1 unit of Zymolyase (US Biological Life Sciences). We centrifuged the mixtures at 1,900 x g for 10 minutes after incubating them for 30 to 60 minutes at 37°C. By aspirating the supernatant, we removed the excess liquid. Next, we added 200 μL of lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10% Tris-HCl, 1 mM EDTA, pH 8), 2 μL of RNaseA, and 2 μL of protease K, and incubated for 10 minutes at 55 °C. The samples were vortexed, centrifuged at 1,900 x g for 10 minutes, and 200 μL of the supernatant was then transferred to fresh deep-well plates with 600 μL of 100% ethanol in each well. The samples were kept at room temperature for 15 minutes, then centrifuged at 1,900 x g for 10 minutes at 4°C, discarding the supernatant. We next obtained the isolated genome pellets, washed them using 150 liters of 70% ethanol, and centrifuged them at 1,900 x g for 10 minutes at 4°C. We removed the supernatant and let the pellet air dry at 60 °C for 5-10 minutes. The pellets were rehydrated for an hour at 65°C after being dissolved in 40 μL of TE.
Strain barcodes were amplified from the extracted genomic DNA in a two-step PCR. The first PCR was performed using PrimeSTAR GXL polymerase and 1:2000 SYBR Green I (20 μL/reaction) with 2 μL of extracted genomic DNA per reaction as a template. Because the concentrations of extracted genomic DNA varied, the number of PCR cycles was first determined by qPCR; the number of PCR cycles was chosen such that the amplification curve reached the mid to late log-linear phase (typically ~24 cycles). The PCR amplification conditions were one cycle of 98°C for 3 min (initiation), followed by amplification cycles of 98°C for 10 sec, 55°C for 15 sec, and 68°C for 30 sec, repeated until the amplification curve reached the mid to late log-linear phase. The PCR products were pooled per growth media condition and purified with DNA Clean & Concentrator (Zymo Research). The second PCR was performed using PrimeSTAR GXL polymerase with 5 ng of purified product from the previous PCR was used as a template (50 μL/reaction). Primers were unique pairs of index primers (i5 and i7) from the Nextera XT DNA library preparation kit (Illumina). The PCR amplification conditions were one cycle of 98°C for 45 sec, then 12 cycles each of 98°C for 10 s, 55°C for 15 s, and 68°C for 30 s. The second PCR products were purified using Agencourt AMPure XP PCR purification kit (Beckman Coulter). We performed pair-end sequencing on Illumina NextSeq platforms with 30% balanced DNA (phiX).

treatment_protocol: For drug treatments, the following concentrations of drugs were added to the growth medium: 10 μg/mL methotrexate (MTX), 0.2 μM 5-FC, 100 μM fluconazole, 50 mM metformin, and 17.5 μM trifluoperazine.

tag: cell line

value: in house yeast library

value: Metformin, MTX

tag: time


title: CD68+, Scar4, MGC WO-001

description:
Library name: DSP-1001660036826-A-G04
CD68+ AOI from skin lesion, secondary intention healing patient Scar4, slide: CD68_Slide6, ROI: Scar4-MGC_WO-001, area: 12345.83 um2, nuclei: 65


title: Stage 19 gonad, male, rep1

description:
Library name: male_19_rep1
10x genomics

tag: genotype

value: WT


title: Long-Bridge RT Probe Test BC001

description:
Library name: FIX08824-001
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Yeast, Fluconazole, MTX, replicate B

value: Fluconazole, MTX


title: CD68+, Scar3, MGC W-005

description:
Library name: DSP-1001660036826-A-G03
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_W-005, area: 47149.58 um2, nuclei: 132


title: Stage 19 gonad, female, rep2

description:
Library name: female_19_rep2
10x genomics

value: female


title: Single nuclei CT29

city: Edmonton

first: Meghan

last: Riddell

state: AB

institute: University of Alberta

description: Library name: sn_seq_sample_2

data_processing:
Bulk seq libraries were quality processed and trimmed utilizing the FASTQC pipeline. Trimmed sequenced were mapped to GRCh38/hg38 utilizing STAR v2.7.11
Data was extracted in Ubuntu utilizing FeatureCounts. Data was analyzed utilizing the DESeq2 package in R.
Demultiplexing, barcode processing, gene counting and aggregatiosn were made utilizing CellRanger 9.0.1 in Ubuntu.
Assembly: hg38
Supplementary files format and content: tab delimited text including raw counts for each sample
Supplementary files format and content: tab delimited values and matrix files

molecule: nuclear RNA

growth_protocol: Both the CT27 and CT 29 lines were maintained on 5 µg/mL collagen IV coated plates and using human TSC culture medium in a humidified incubator at 37 degrees and 5% CO2. Organoids were generated using a rotatory cell culture system.

extract_protocol:
Placental organoids were pelleted and resuspended in trizol before being mechanically dissociated utilizing a tissue lyser. RNA was extracted by utilizing Invitrogen PureLink RNA Mini Kit.
CT27 and CT29 cell lines were flash-frozen and the nuclei for both cell lines were collected using the 10X Chromium Nuclei Isolation Kit with RNAse inhibitor following the manufacturer's intructions.
Bulk seq libraries were contructed using the Illumina Stranded mRNA Prep Kit.
Single nuclei libraries were prepared using the 10X GEM-X Universal 3' Gene expression v4 4-plex according to manufacturer's instructions.

treatment_protocol: CT29 knockdowns were achieved utilizing PRKCZ-targetting siRNA that was transfected into the cell line using Opti-MEM I Reduced Serum Medium and Lipofectamine LTX Reagent with PLUS reagent.

value: Trophoblast stem cells


title: Yeast, 5-FC, MTX, replicate B

value: 5-FC, MTX


title: CD68+, Scar3, MGC W-004

description:
Library name: DSP-1001660036826-A-G02
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_W-004, area: 55531.92 um2, nuclei: 97


title: Single nuclei CT27

description: Library name: sn_seq_sample_1


title: CD68+, Scar3, MGC W-003

description:
Library name: DSP-1001660036826-A-G01
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_W-003, area: 71129.79 um2, nuclei: 252


title: FIX04861-042-6811BW PBMC culture_no_stim

description:
Library name: FIX04861-042
10x Genomics Flex

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Cells mapping to dendritic cell populations were removed. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

growth_protocol: Frozen Ficoll purified PBMC from healthy subjects were acquired from Bloodworks Northwest (#4570). T cells, B cells, NK cells or CD14 monocytes in each donor from freshly thawed frozen PBMC were enriched by magnetic negative selection kits (STEMCELL technologies) for human T cells (#19051), human pan B  cells (#19554), human NK cells (#19055) or human CD14 monocytes (#19059), respectively. To ensure high purity in enriched B, NK, and CD14 monocytes, contaminated T cells were further depleted by using CD3 kit (STEMCELL technologies #17851). Three to eight hundred thousand of enriched cells from each immune cell subset or total PBMC were seeded in 200 uL of 10 % human AB serum (Millipore Sigma #H3667-20ML) containing RPMI-1640 media (ThermoScientific #11875093) per well.

extract_protocol:
After 21 hour stimulation with various IFNs, cells were washed, counted, and fixed in 4% Paraformaldehyde for 1 hour (25°C). Fixed samples were quenched and subsequently washed with an additional 200 uL of PBS + 0.02% BSA (Costar). Samples were barcoded for multiplexing using 10X Genomics Fixed RNA Feature Barcode Multiplexing Kit (#PN-1000628). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A). Up to 2 million fixed cells were hybridized per sample. After 16-24 hours of probe hybridization incubation (42°C), samples were diluted in Post-Hyb Wash buffer and 11 µL was removed for counting. The counting fraction was stained 1:5 with 44 uL of PI solution and counted on a Nexcelom Cellaca MX cell counter.
Samples were then pooled at equivalent cell concentrations at a minimum of 50,000 cells/sample, incubated for 3 rounds of 10 minutes at 42°C, washed in Post-Hyb wash buffer, and strained using 30 uM strainers (Miltenyi). The single cell suspension pool was loaded onto Chip Q for GEM generation at an overloaded concentration of 400,000 cells. Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300, Novaseq S2 PE200, or a NovaSeq S4 PE100 flow cell, targeting a minimum read depth of 10,000 reads per cell.

treatment_protocol: Each enriced immune cells were stimulated with IFN-a2A (1000 units/mL, PBL Assay Science #11101-2) or IFN-b (100 units/mL, R&D #8499-IF-010/CF) or IFN-g (25 ng/mL, Biolegend #570206) or IFN-L1 (100 ng/mL, R&D #1598-IL-025/CF) or no stimulation for 21 hours in 37°C.

value: male

tag: ethnics/race

value: Caucasian/Non-hisp

value: Positive

value: 21 hours

value: PD


title: Yeast, no drug, no MTX, replicate A

value: no stimulation


title: Stage 17 gonad, male, rep1

description:
Library name: male_17_rep1
10x genomics

tag: tissue

value: Embryonic gonad

value: Stage 17


title: CD68+, Scar3, MGC W-002

description:
Library name: DSP-1001660036826-A-F12
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_W-002, area: 51001.82 um2, nuclei: 143

value: skin

tag: cell type

value: macrophages


title: Stage 17 gonad, female, rep2

description:
Library name: female_17_rep2
10x genomics

tag: treatment


title: CD68+, Scar3, MGC W-001

description:
Library name: DSP-1001660036826-A-F11
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_W-001, area: 36828.61 um2, nuclei: 86


title: Yeast, Metformin, no MTX, replicate A

value: in house yeast library

value: Metformin


title: FIX00234-3955BW PBMC culture_no_stim

description:
Library name: FIX00234
10x Genomics Flex

value: Blood

value: PBMC

tag: subject id

value: Negative


title: Yeast, Fluconazole, no MTX, replicate A

value: Fluconazole


title: FIX00224-3955BW PBMC culture_no_stim

description:
Library name: FIX00224
10x Genomics Flex

tag: age at_blood_drawn

value: female

value: PC


title: CD68+, Scar3, MGC WO-005

description:
Library name: DSP-1001660036826-A-F10
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_WO-005, area: 48512.11 um2, nuclei: 200


title: Yeast, 5-FC, no MTX, replicate A


title: WT

city: Wuhan

first: Bingyi

last: Liu

address: 1037 Luoyu Road, Hongshan District

country: China

institute: Huazhong University of science and technology

description: Library name: Sample2

data_processing:
Library construction and the quality inspection was carried out using Illumina HiSeqTM 2000 for sequencing
The counts and FPKM values of each transcript were calculated by RSEM software
The R language package DESeq2 was used for differential analysis; The differential gene screening conditions were reater than 1.5 times and p<0.05 absolute value of differential folds
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Mus musculus

source_name: bone marrow derived macrophages

growth_protocol: The prepared DMEM medium (MCSF 20ng/ml) was added and then cultured for 5 days

extract_protocol:
Bone marrow derived macrophages (BMDM)were obtained from SPP1fl/fl and SPP1fl/fl-Lyz2-icre mice according to the experimental protocol,  cells were culture with MCSF for 5 days and the total RNA was extracted with Trizol.
Total RNAs from cells were extracted according to the manual of TRIzol®reagent (Invitrogen, Shanghai, China)

value: bone marrow derived macrophages


title: CD68+, Scar3, MGC WO-004

description:
Library name: DSP-1001660036826-A-F09
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_WO-004, area: 31045.81 um2, nuclei: 125


title: FIX00235-3491BW PBMC culture_no_stim

description:
Library name: FIX00235
10x Genomics Flex

tag: Sex

value: male

value: Caucasian/Non-hisp

value: Positive


title: Yeast, Trifluoperazine, MTX, replicate A

value: Trifluoperazine, MTX


title: KO

description: Library name: Sample1


title: CD68+, Scar3, MGC WO-003

description:
Library name: DSP-1001660036826-A-F08
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_WO-003, area: 33527.12 um2, nuclei: 65


title: FIX00226-3491BW PBMC culture_no_stim

description:
Library name: FIX00226
10x Genomics Flex

value: 21 hours


title: Yeast, no drug, MTX, replicate A

value: MTX


title: testis, 3 mg/L vitamin C, biol rep3

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description: Library name: VP3

data_processing:
The reads were first preprocessed with fastp (v0.23.2), an ultra-fast all-in-one FASTQ preprocessor, which does quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data
The fastp-processed reads were then mapped on medaka genome (Oryzias_latipes.ASM223467v1) using STAR (2.7.7a)
Finally, DESeq2 (v1.34.0) was used to generate normalized count data for all samples.
Assembly: Oryzias_latipes.ASM223467v1
Supplementary files format and content: perchlorate_testis_rnaseq_normExpr.tsv: Normalized expression values obtained from DESeq2 for all samples in tab-delimited text-file

organism: Oryzias latipes

source_name: testis

extract_protocol:
Total RNA was extracted using the ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructional manual
RNA sequencing library was prepared with NEBNext® UltraTM II RNA Library Prep Kit for Illumina following the manufacturer's instructional manual.

value: testis

value: 3 mg/L vitamin C


title: CD68+, Scar3, MGC WO-002

description:
Library name: DSP-1001660036826-A-F07
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_WO-002, area: 29982.35 um2, nuclei: 108

value: skin

value: macrophages


title: FIX04862-040-3283BW PBMC culture_no_stim

description:
Library name: FIX04862-040
10x Genomics Flex

value: Blood

value: Asian/Non-hisp

value: PD


title: Yeast, Metformin, MTX, replicate A

value: in house yeast library

value: Metformin, MTX


title: testis, 3 mg/L vitamin C, biol rep2

description: Library name: VP2


title: CD68+, Scar3, MGC WO-001

description:
Library name: DSP-1001660036826-A-F06
CD68+ AOI from skin lesion, secondary intention healing patient Scar3, slide: CD68_Slide6, ROI: Scar3-MGC_WO-001, area: 33006.48 um2, nuclei: 66


title: FIX04862-038-3283BW PBMC culture_no_stim

description:
Library name: FIX04862-038
10x Genomics Flex

value: PBMC

value: female

value: PC


title: Yeast, Fluconazole, MTX, replicate A

value: Fluconazole, MTX


title: testis, 3 mg/L vitamin C, biol rep1

description: Library name: VP1


title: CD68+, Scar1, MGC W-006

description:
Library name: DSP-1001660036826-A-F05
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_W-006, area: 12190.35 um2, nuclei: 121


title: FIX00225-2616BW PBMC culture_no_stim

description:
Library name: FIX00225
10x Genomics Flex

value: male

value: Caucasian/Non-hisp

value: Negative


title: Yeast, 5-FC, MTX, replicate A

value: 5-FC, MTX


title: testis, 10 mg/L KClO4 + 3 mg/L vitamin C, biol rep3

description: Library name: V10KP3

value: testis

value: 10 mg/L KClO4 + 3 mg/L vitamin C


title: CD68+, Scar1, MGC W-005

description:
Library name: DSP-1001660036826-A-F04
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_W-005, area: 11703.32 um2, nuclei: 129

value: skin


title: FIX04861-043-6811BW PBMC culture_IFNa

description:
Library name: FIX04861-043
10x Genomics Flex

value: Positive

value: 21 hours


title: C57Bl/6J, mH2A1.2 KD, CFC+60, Rep 4

city: Mississauga

first: Iva

last: Zovkic

state: ON

address: 3359 Missisauga Road, DV1015 (Zovkic Lab)

department: Psychological and Brain Sciences

institute: University of Toronto Mississauga

description: Library name: Sample 33

data_processing:
Adaptors were trimmed with trimmomatic (v0.39).
Trimmed reads were mapped to GrCM38/mm10 using Bowtie 2 (v2.5.1). Aligned reads were filtered and deduplicated with samtools (v1.12) to keep only uniquely paired reads with a quality score over 20.
Peaks were called by comparing the ChIP samples against the merged input using MACS3 (v3.0.1) with a q-value cutoff of 0.1.
bigWig files were generated using deepTools (v3.5.6).
Assembly: mm10
Supplementary files format and content: bigWig
Adaptors trimmed using soft-clipping in Rsubread
Reads aligned using Rsubread in R (version 2.12.3, R version 4.2.3)
Aligned reads counted using featureCounts in Rsubread library (version 2.12.3) (genes with count sum <20 across all samples removed prior to analysis)
Differential expression analysis performed in DESeq2 in R using padj<0.05
Assembly: mm39
Supplementary files format and content: bigWig

molecule: polyA RNA

source_name: Dorsal CA1 hippocampus

extract_protocol:
Whole bilateral hippocampi from 10-12 week old male C57BL/6 mice were homogenized in 1xPBS containing 1x Protease Inhibitor Cocktail (1xPIC; Cell Signaling #5871) and crosslinked in 1% formaldehyde for 5min at RT, then quenched with 125mM glycine for 5min at RT and spun at 2000g for 3min at 4ºC. Pellets were washed 3x with 200uL ice-cold PBS containing PIC, then resuspended in 1mL ice-cold LB1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) containing PIC and rotated for 10min at 4ºC. Nuclei were collected by centrifugation at 2000g for 5mins at 4ºC, washed by rotating for 5 min at 4ºC in 200uL TM2 (10mM Tris-HCl pH 8.0, 2mM MgCl2) containing PIC, then resuspended in 200uL TM2 and warmed for 5mins at 37ºC before adding 1mM CaCl2.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocol. Input samples were merged before library preparation.
Total RNA was extracted from AAV-shRNA infected dorsal hippocampal tissue using Qiagen RNeasy kit. Eluate was sent to CD Genomics (Shirley, NY) for polyA selection and library prep
Library preparation performed at CD Genomics (Shirley, NY)

value: Dorsal CA1 hippocampus

value: mH2A1.2 KD

value: mH2A1.2 shRNA AAV injection in dorsal CA1 hippocampus


title: CD68+, Scar1, MGC W-004

description:
Library name: DSP-1001660036826-A-F03
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_W-004, area: 9165.11 um2, nuclei: 82

value: macrophages


title: FIX04861-040-6811BW PBMC culture_IFNa

description:
Library name: FIX04861-040
10x Genomics Flex

value: Blood

value: PBMC


title: C57Bl/6J, mH2A1.2 KD, CFC+60, Rep 3

description: Library name: Sample 32


title: testis, 10 mg/L KClO4 + 3 mg/L vitamin C, biol rep1

description: Library name: V10KP1


title: CD68+, Scar1, MGC W-003

description:
Library name: DSP-1001660036826-A-F02
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_W-003, area: 10043.46 um2, nuclei: 135


title: FIX00236-3955BW PBMC culture_IFNa

description:
Library name: FIX00236
10x Genomics Flex

value: female

value: PD


title: CD68+, PDAC1, MGC WO-002

description:
Library name: DSP-1001660035205-B-A03
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_WO-002, area: 33620.95 um2, nuclei: 129

source_name: pancreas

value: pancreas


title: Long-Bridge RT Probe Test BC007

description:
Library name: FIX08824-007
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

tag: ethnicity/race

value: Caucasian/Non-Hispanic

value: Unknown

value: PA


title: C57Bl/6J, mH2A1.2 KD, CFC+60, Rep 2

description: Library name: Sample 31


title: testis, 10 mg/L KClO4, biol rep3

description: Library name: 10KP3

value: testis

value: 10 mg/L KClO4


title: CD68+, Scar1, MGC W-002

description:
Library name: DSP-1001660036826-A-F01
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_W-002, area: 24813.23 um2, nuclei: 146

value: skin


title: FIX00227-3955BW PBMC culture_IFNa

description:
Library name: FIX00227
10x Genomics Flex

value: Caucasian/Non-hisp

tag: cmv stats

value: Negative

value: 21 hours

value: PC


title: C57Bl/6J, mH2A1.2 KD, CFC+60, Rep 1

description: Library name: Sample 30

value: Dorsal CA1 hippocampus

value: mH2A1.2 KD

value: mH2A1.2 shRNA AAV injection in dorsal CA1 hippocampus


title: testis, 10 mg/L KClO4, biol rep2

description: Library name: 10KP2


title: Long-Bridge RT Probe Test BC004

description:
Library name: FIX08824-004
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC

tag: treatment time


title: con-2

city: 咸阳市

first: YouJie

last: Cui

state: 陕西省

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院

data_processing:
The original sequencing data contains adapter sequences, low-quality bases, and undetermined bases (denoted as N), which can significantly interfere with subsequent data analysis. To remove these interfering elements and obtain reliable data, a thorough filtering process is performed, resulting in clean data or clean reads. The format of the clean data file is identical to that of the raw data.  The filtering process is conducted using SOAPnuke software (v2.1.0) [1]. The main parameters used are: --lowQual=20, --nRate=0.005, --qualRate=0.5, with other parameters set to default values. The steps involved in data processing are as follows:  Filtering out paired reads that contain adapter sequences. Removing paired reads with an N content (representing undetermined bases) exceeding 0.5%. Discarding low-quality paired reads, where the number of bases with a Qphred score less than or equal to 20 constitutes more than 50% of the total read length.
Assembly: Genome assembly Sscrofa11.1
Supplementary files format and content: Gene expression information for each sample

organism: Sus scrofa

source_name: Pigtesticles

extract_protocol:
Aspirate the culture medium from the culture dish and wash once with 1 mL of PBS. Aspirate the PBS (removing as much as possible) and add 1 mL of TRIzol. Incubate for 5 minutes, gently pipette against the bottom of the dish, then aspirate the TRIzol and transfer it to a 1.5 mL centrifuge tube. Allow it to stand at room temperature for 5 minutes. Add 250 µL of chloroform, vortex for 30 seconds. Allow it to stand at room temperature for 5 minutes. Centrifuge at 12,000 rpm for 5 minutes; carefully transfer the aqueous phase to another 1.5 mL centrifuge tube using a pipette. Add 500 µL of isopropanol to the aqueous phase, mix gently, and incubate at 4°C overnight. Centrifuge at maximum speed (12,000 rpm) for 20 minutes. Discard the isopropanol, wash the pellet with 1 mL of 75% ethanol. Centrifuge at 12,000 rpm for 5 minutes. Discard the ethanol and air-dry the pellet. Dissolve the RNA pellet in approximately 30 µL of DEPC-treated water and store at -80°C.
1Two biological RNA samples from two independent experiments were sent to Frasergen (Wuhan, China) for mRNA sequencing library construction.Briefly, these libraries were sequenced using the MGI high-throughput sequencing platform. Raw reads were filtered using SOAPnuke (v2.1.0) software to obtain clean reads, which were then aligned to the pig genome (Sscrofa 11.1) using HISAT2 (v2.2.1). The quality-controlled second-generation sequences were subsequently mapped to the reference transcriptome sequences using bowtie2 (v2.3.5) software. RSEM (v1.3.3) was used to count the number of reads mapped to each transcript in each sample and convert them to FPKM (Fragments Per Kilobase of transcript per Million mapped reads), thereby obtaining the expression levels of genes and transcripts. Finally, the DESeq2 algorithm was employed with a moderate cutoff value (Pvalue < 0.05) to filter differentially expressed genes (DEGs).

value: Pigtesticles

value: Immature spermatogonia from the porcine

value: WT


title: CD68+, Scar1, MGC W-001

description:
Library name: DSP-1001660036826-A-E12
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_W-001, area: 19037.88 um2, nuclei: 128

value: macrophages


title: FIX00237-3491BW PBMC culture_IFNa

description:
Library name: FIX00237
10x Genomics Flex

value: male

value: Positive

tag: batch id

value: PD


title: C57Bl/6J, mH2A1.2 KD, HC, Rep 3

description: Library name: Sample 29


title: testis, 10 mg/L KClO4, biol rep1

description: Library name: 10KP1

value: testis

value: 10 mg/L KClO4


title: CD68+, Scar1, MGC WO-005

description:
Library name: DSP-1001660036826-A-E11
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_WO-005, area: 11909.04 um2, nuclei: 118

value: skin


title: FIX00230-3491BW PBMC culture_IFNa

description:
Library name: FIX00230
10x Genomics Flex

value: Caucasian/Non-hisp

value: 21 hours

tag: pool id


title: C57Bl/6J, mH2A1.2 KD, HC, Rep 2

description: Library name: Sample 28

value: Dorsal CA1 hippocampus


title: testis, 0.01 mg/L KClO4, biol rep3

description: Library name: 10P3

value: 0.01 mg/L KClO4


title: CD68+, Scar1, MGC WO-004

description:
Library name: DSP-1001660036826-A-E10
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_WO-004, area: 16722.19 um2, nuclei: 165


title: FIX04862-041-3283BW PBMC culture_IFNa

description:
Library name: FIX04862-041
10x Genomics Flex

value: female

value: Asian/Non-hisp

tag: batch pool


title: testis, 10 mg/L KClO4 + 3 mg/L vitamin C, biol rep2

description: Library name: V10KP2

value: 10 mg/L KClO4 + 3 mg/L vitamin C


title: C57Bl/6J, mH2A1.2 KD, HC, Rep 1

description: Library name: Sample 27

value: mH2A1.2 KD

value: mH2A1.2 shRNA AAV injection in dorsal CA1 hippocampus


title: testis, 0.01 mg/L KClO4, biol rep2

description: Library name: 10P2


title: BW2164-Day 7-IL15/7-Pep-

description:
Library name: FIX10435-011
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC

value: Female

value: Other/ Non-Hispanic Origin

value: CMV+

value: PC

tag: probe barcode_id


title: CD68+, Scar1, MGC WO-003

description:
Library name: DSP-1001660036826-A-E09
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_WO-003, area: 24290.05 um2, nuclei: 260

value: macrophages


title: FIX04862-039-3283BW PBMC culture_IFNa

description:
Library name: FIX04862-039
10x Genomics Flex

value: Positive


title: C57Bl/6J, mH2A1.1 KD, CFC+60, Rep 4

description: Library name: Sample 26

value: mH2A1.1 KD

value: mH2A1.1 shRNA AAV injection in dorsal CA1 hippocampus


title: Stage 19 gonad, female, rep1

description:
Library name: female_19_rep1
10x genomics

value: Embryonic gonad

value: WT

value: Stage 19


title: CD68+, Scar1, MGC WO-002

description:
Library name: DSP-1001660036826-A-E08
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_WO-002, area: 18091.54 um2, nuclei: 146

value: skin


title: testis, 0.01 mg/L KClO4, biol rep1

description: Library name: 10P1

value: testis

value: 0.01 mg/L KClO4


title: Yeast, Trifluoperazine, no MTX, replicate A

tag: cell line

value: in house yeast library

value: Trifluoperazine


title: FIX00228-2616BW PBMC culture_IFNa

description:
Library name: FIX00228
10x Genomics Flex

value: Blood

value: PBMC

value: male

value: Caucasian/Non-hisp

value: Negative

value: 21 hours


title: C57Bl/6J, mH2A1.1 KD, CFC+60, Rep 3

description: Library name: Sample 25

value: Dorsal CA1 hippocampus


title: Stage 17 gonad, male, rep2

description:
Library name: male_17_rep2
10x genomics

value: Stage 17


title: testis, control, biol rep3

description: Library name: CP3

value: control


title: CD68+, Scar1, MGC WO-001

description:
Library name: DSP-1001660036826-A-E07
CD68+ AOI from skin lesion, secondary intention healing patient Scar1, slide: CD68_Slide5, ROI: Scar1-MGC_WO-001, area: 10746.84 um2, nuclei: 105

value: macrophages


title: FIX04861-041-6811BW PBMC Fresh

description:
Library name: FIX04861-041
10x Genomics Flex

value: Fresh

value: Positive

value: PD


title: C57Bl/6J, mH2A1.1 KD, CFC+60, Rep 2

description: Library name: Sample 24

value: mH2A1.1 KD

value: mH2A1.1 shRNA AAV injection in dorsal CA1 hippocampus


title: testis, control, biol rep2

description: Library name: CP2

value: testis


title: CD68+, Scar2, MGC W-002

description:
Library name: DSP-1001660036826-A-E06
CD68+ AOI from skin lesion, secondary intention healing patient Scar2, slide: CD68_Slide5, ROI: Scar2-MGC_W-002, area: 42680.5 um2, nuclei: 171

value: skin


title: FIX04861-038-6811BW PBMC Fresh

description:
Library name: FIX04861-038
10x Genomics Flex

value: Blood

value: PC


title: FIX04861-039-6811BW PBMC culture_no_stim

description:
Library name: FIX04861-039
10x Genomics Flex

value: PBMC

value: male


title: testis, control, biol rep1

description: Library name: CP1


title: CD68+, Scar2, MGC W-001

description:
Library name: DSP-1001660036826-A-E05
CD68+ AOI from skin lesion, secondary intention healing patient Scar2, slide: CD68_Slide5, ROI: Scar2-MGC_W-001, area: 69444.42 um2, nuclei: 333


title: C57Bl/6J, mH2A1.1 KD, CFC+60, Rep 1

description: Library name: Sample 23


title: FIX00231-3955BW PBMC Fresh

description:
Library name: FIX00231
10x Genomics Flex

value: female

value: Caucasian/Non-hisp

value: Negative


title: C57Bl/6J, mH2A1.1 KD, HC, Rep 4

description: Library name: Sample 22

value: Dorsal CA1 hippocampus


title: CD68+, Scar2, MGC WO-001

description:
Library name: DSP-1001660036826-A-E04
CD68+ AOI from skin lesion, secondary intention healing patient Scar2, slide: CD68_Slide5, ROI: Scar2-MGC_WO-001, area: 18642.61 um2, nuclei: 78


title: E15 rat small intestine-derived enteric neural cells, DIV21

city: Seoul

first: Soryung

last: Jung

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

description:
Library name: E15_rat_ENS_DIV21
10X Genomics

data_processing:
RNA libraries were sequenced on the Illumina NovaSeq X platform with paired-end 151 bp reads. Sequencing reads were processed with cellranger count (Cell Ranger v9.0.1).
Assembly: GRCr8 (Rattus norvegicus, Ensembl release 114)
Supplementary files format and content: Tab-separated values (TSV) files and a matrix file. The TSV files list cell barcodes and gene features, and the matrix file contains the corresponding UMI counts.

organism: Rattus norvegicus

source_name: small intestine

growth_protocol: Small intestines were dissected from embryonic day 15 rat embryos and cut into 8–10 fragments. Tissue fragments were seeded onto poly-L-lysine-coated culture plates and maintained in CRL-2690-conditioned medium. After 5 days, intestinal fragments were removed, and migrated cells were detached, collected, and re-seeded onto fresh poly-L-lysine-coated plates. Cultures were maintained with half-medium changes every two days until day 21.

extract_protocol:
Cells were dissociated using Accutase for 3 min and collected into Neurobasal medium. Following centrifugation at 1300 rpm for 3 min, the cell pellet was processed for single-cell RNA sequencing using the 10x Genomics platform according to the manufacturer's protocol.
Single-cell RNA-seq libraries were constructed from single-cell suspensions using the Chromium GEM-X Single Cell 5' Kit v3 (10x Genomics), following the manufacturer's protocol.

treatment_protocol: 5 µM cytosine β-D-arabinofuranoside (AraC; Tocris, 4520) was added to the cultures on DIV −1 to reduce the number of highly proliferative cells.

value: small intestine

value: enteric neural cells

tag: developmental stage

tag: time

value: day 21 in vitro


title: E19.5 colon, maternal obesity group, sample2

city: Beijing

first: Huanling

last: Yu

address: No.10, Xi Tou Tiao, You An Men Wai, Fengtai District, Beijing 100069, P. R. China.

institute: Capital Medical University

description:
Library name: HFD2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Rattus norvegicus
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
The tissues were washed three times with Hank's balanced salt solution (HBSS) including 1 mM EDTA, 1 mM DTT, 100 IU/mL penicillin and 100 mg/mL streptomycin, 10mM HEPES. Then the tissues were sliced into small fragments roughly and digested with 0.5 mg/mL type IV collagenase (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China), 0.005% pancreatic enzymes, 0.002% EDTA and 500μg/mL DNaseI (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China) at 37℃ for 45-55 min. A 1:1 ratio of DMEM, 10% fetal bovine serum was added to stop the digestion. The cell suspension was passed through a 40-μm filter and isolated via centrifugation (300 g, 4℃, 5 min). Cells was resuspended in 3 mL of red blood cell lysate until no red and then was stopped by 3 mL 0.1%BSA. The cells were isolated via centrifugation (300 g, 4℃, 5 min) and washed with 0.1%BSA. After re-centrifugation, the single-cell suspension was obtained. The cell viability was more than 80% and the caking rate was less than 5% in the present study. Dissociated cells with cell concentration in the range of 700-1200 cells/μL were stored in 0.1%BSA on ice until loading on a Chromium Controller (10x Genomics).
During library preparation, Gel Beads carrying Poly-T primers tagged with Cell Barcodes and Unique Molecular Identifiers (UMIs), along with cells, are co-encapsulated within "oil droplets" to form Gel Beads-in-Emulsion (GEMs). Within this reaction system, cells are lysed and reverse transcription is performed to generate full-length cDNA sequences. Subsequently, the cDNA is purified via emulsion breaking and amplified by PCR to increase yield. Following quality control, the cDNA is chemically fragmented into ~200–300 bp segments, which then undergo end repair, A-tailing, and size selection. P7 Adapter linkers are ligated, and sample indices are introduced via PCR, ultimately yielding the sequencing library after a final round of size selection.

value: colon

tag: genotype

value: WT

tag: sample group

value: maternal obesity


title: FIX00233-3491BW PBMC Fresh

description:
Library name: FIX00233
10x Genomics Flex

tag: tissue

tag: cell type

value: Fresh

tag: ethnics/race

value: Positive

value: 21 hours

value: PD


title: E19.5 colon, control group, sample1

description:
Library name: CON1
10x Genomics

value: control


title: CD68+, PDAC4, MGC W-004

description:
Library name: DSP-1001660036826-A-H11
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_W-004, area: 40614.92 um2, nuclei: 32

value: pancreas

value: macrophages


title: FIX00223-3491BW PBMC Fresh

description:
Library name: FIX00223
10x Genomics Flex

value: Blood

value: PBMC

tag: treatment

tag: subject id

tag: age at_blood_drawn

value: male

value: PC


title: C57Bl/6J, mH2A1.1 KD, HC, Rep 1

description: Library name: Sample 19

value: Dorsal CA1 hippocampus

value: mH2A1.1 KD

value: mH2A1.1 shRNA AAV injection in dorsal CA1 hippocampus


title: TrichlorfonGuanitoxinMalathion0.5+0.5+0.5 3

city: Dübendorf

first: Colette

last: vom Berg

address: Überlandstrasse 133

department: Environmental Toxicology

country: Switzerland

institute: EAWAG

description:
Library name: Sample_29
Column name in raw_counts.txt: TGM_Exp3

data_processing:
Raw sequencing data were obtained from Illumina NovaSeq X platform with a 300-cycle 10B flow cell, generating an average of 20 million single-end reads per sample. Library quality was verified using Illumina iSeq platform prior to high-throughput sequencing.
Transcript quantification was performed using pseudo-alignment with Kallisto (v0.50.1), based on the Ensembl reference transcriptome for Danio rerio (GRCz11/GCA_000002035.4).
Data analysis was performed using DESeq2 (v1.48.1) in R (v4.5.0). Low-count genes (<10) were filtered and counts were normalized using DESeq2 size factor estimation. Transcriptomic variability between samples was assessed using principal component analysis (PCA) on variance-stabilized transformed (VST) counts.Differential expression analysis (DEA) was computed using Wald tests between exposure conditions and respective control conditions with DESeq2 results() function. Genes were considered significantly differentially expressed with absolute log fold change >1 and Benjamini-Hochberg adjusted p-value ≤ 0.05.
Assembly: Danio rerio (Zebrafish) GRCz11/GCA_000002035.4 (Ensembl reference transcriptome)
Supplementary files format and content: Count_Matrix.txt

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA was extracted from batches of 20 zebrafish larvae using the Qiagen RNeasy Mini Kit (Qiagen GmbH, Germany). Frozen tissue was homogenized in lysis buffer (RLT buffer with β-mercaptoethanol) by repeated vortexing for 30 seconds and incubation for 5 minutes. Following the procedure for purification of RNA from animal and human tissues, RNA was extracted using RNeasy MinElute spin columns. An on-column DNase I digestion was performed to reduce genomic DNA contamination. RNA concentration and purity were assessed using NanoDrop fluorometer (ThermoFisher Scientific Inc., USA). RNA integrity was verified using the 2200 TapeStation system (Agilent Technologies, USA).
The Lexogen QuantSeq 3' mRNA-Seq V2 (FWD) kit with 12-nucleotide Unique Dual Indices (UDIs) was employed for preparation of Illumina-compatible libraries from polyadenylated RNA. First-strand cDNA synthesis was performed through reverse transcription using an oligo(dT) primer containing a 5' adapter sequence. RNA template was enzymatically degraded to facilitate efficient second cDNA strand synthesis. Second-strand synthesis was primed by a random primer harboring a 5' sequence, resulting in double-stranded DNA (dsDNA). Libraries were purified using magnetic beads and amplified via PCR for 12 to 26 cycles to incorporate full-length adapter sequences and 12-nt UDIs. For each sample, 10 µl of appropriate UDI primer pair was added with one unique index pair per sample. Final libraries were purified and prepared for quality control assessment, pooling, and cluster generation for high-throughput sequencing.

treatment_protocol: The following treatments were applied to zebrafish larvae from 0-5 days postfertilization: Individual exposures: Guanitoxin C5 (125 mg/L), Trichlorfon C4 (15 mg/L), Malathion C4 (1mg/L); Binary mixtures: (C7, i.e. 0.5+0.5 EC50s) GM 5.14 mg/L+ 0.34 mg/L, MT 0.34 mg/L + 4.48 mg/L, TG 4.48 mg/L + 5.14 mg/L; Tertiary mixture: (C6, i.e. 0.5+0.5+0.5 EC50s) TGM 4.48 mg/L + 5.14 mg/L + 0.34 mg/L. For each treatment, 20 larvae were pooled, RNA extracted from the pool and sequenced

value: larvae


title: FIX00232-2616BW PBMC Fresh

description:
Library name: FIX00232
10x Genomics Flex

tag: Sex

value: Caucasian/Non-hisp

tag: cmv stats

value: Negative


title: C57BL/6J, Scr, CFC+60, Rep 4

description: Library name: Sample 18

value: WT

value: scrambled shRNA AAV injection in dorsal CA1 hippocampus


title: CD68+, PDAC4, MGC W-003

description:
Library name: DSP-1001660036826-A-H10
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_W-003, area: 62329.36 um2, nuclei: 103


title: TrichlorfonGuanitoxinMalathion0.5+0.5+0.5 2

description:
Library name: Sample_28
Column name in raw_counts.txt: TGM_Exp2


title: FIX00239-3491BW Bcell IFNg

description:
Library name: FIX00239
10x Genomics Flex

value: Bcell

value: IFNg

value: Positive

tag: treatment time

value: 21 hours

tag: batch id


title: C57BL/6J, Scr, CFC+60, Rep 3

description: Library name: Sample 17


title: CD68+, PDAC4, MGC W-002

description:
Library name: DSP-1001660036826-A-H09
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_W-002, area: 63253.04 um2, nuclei: 122

value: pancreas

value: macrophages


title: CD68+, PDAC4, MGC W-001

description:
Library name: DSP-1001660036826-A-H08
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_W-001, area: 50429.36 um2, nuclei: 56


title: FIX00222-2616BW PBMC Fresh

description:
Library name: FIX00222
10x Genomics Flex

value: Blood

value: PBMC

value: Fresh

tag: pool id

tag: batch pool


title: TrichlorfonGuanitoxinMalathion0.5+0.5+0.5 1

description:
Library name: Sample_27
Column name in raw_counts.txt: TGM_Exp1


title: ControlTrichlorfonGuanitoxinMalathionControl 2

description:
Library name: Sample_26
Column name in raw_counts.txt: TGM_Ctl8


title: CD68+, PDAC4, MGC WO-003

description:
Library name: DSP-1001660036826-A-H07
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_WO-003, area: 26658.04 um2, nuclei: 81


title: C57BL/6J, Scr, CFC+60, Rep 1

description: Library name: Sample 15

value: Dorsal CA1 hippocampus


title: Human derived non-small cell lung cancer cells, mRNA, drug resistance experiment group, biol repl3

city: Lanzhou

first: Miao

last: He

state: Gansu

address: No.82, Cuiyingmen street, Chengguan District

institute: Lanzhou University Second Clinical Medical School: Lanzhou University Second Hospital

description:
Library name: OR3_mRNA
Column name in gene_count_lncRNA.csv: OR3

data_processing:
Firstly, all clean mapped tags were aligned with miRNAs in the miRBase22.0 database (http://www.mirb ase.org/) to got known miRNA. Then the rest of tags were aligned with Rfam database and Repbase database to remove ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. Next, the unannotated tags were predicted to be and identified as novel miRNAs using miRdeep2 software, according to the tag positions in the genome and their hairpin structures.
Transcripts were reconstructed using StringTie with default parameters using the mapped clean reads. Then the known lncRNAs were identified by comparing merged transcripts with reference transcripts, which annotated lncRNA in GFF/GTF and lncRNA database. Furthermore, novel potential lncRNA transcripts were identified according to the transcript length ( > 200 bp) and exon number (>2). Then, CNCI (score < 0), CPC (score <0.5) ,CPAT (score <0.5) and Pfam (e-value < 1e-3 no pass) were used to predict the protein-coding potential of the transcripts. Finally, the intersection of both non-protein-coding potential results were chosen as novel lncRNAs.
After the clean reads were aligned to the reference genome, junctions of the unmapped reads were identified using a back-splice algorithm. CIRI2 and Findcirc was used to predict circRNAs. The expression levels of circRNAs were reflected by the number of mapped back-splicing junction reads per million mapped reads (RPM).
Assembly: hg38
Supplementary files format and content: CSV reads count values of genes for each sample

source_name: non-small cell lung cancer

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample was used to construct sequencing library. smallRNA libraries were generated using QIAseq miRNA Library Kit (Qiagen) following manufacturer’s recommendations, and mRNA+lncNRA+circRNA libraries were generated by Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus.

value: non-small cell lung cancer


title: MalathionTrichlorfon0.5+0.5 3

description:
Library name: Sample_25
Column name in raw_counts.txt: MT_Exp3


title: CD68+, PDAC4, MGC WO-002

description:
Library name: DSP-1001660036826-A-H06
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_WO-002, area: 23708.71 um2, nuclei: 95


title: Human derived non-small cell lung cancer cells, mRNA, drug resistance experiment group, biol repl2

description:
Library name: OR2_mRNA
Column name in gene_count_lncRNA.csv: OR2


title: C57BL/6J, Scr, HC, Rep 5

description: Library name: Sample 14


title: MalathionTrichlorfon0.5+0.5 2

description:
Library name: Sample_24
Column name in raw_counts.txt: MT_Exp2


title: CD68+, PDAC4, MGC WO-001

description:
Library name: DSP-1001660036826-A-H05
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_WO-001, area: 34997.74 um2, nuclei: 138


title: Human derived non-small cell lung cancer cells, mRNA, drug resistance experiment group, biol repl1

description:
Library name: OR1_mRNA
Column name in gene_count_lncRNA.csv: OR1


title: C57BL/6J, Scr, HC, Rep 4

description: Library name: Sample 13


title: CD68+, TB1, MGC W-005

description:
Library name: DSP-1001660036826-A-D05
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_W-005, area: 40506.67 um2, nuclei: 182

source_name: lung

value: lung


title: MalathionTrichlorfon0.5+0.5 1

description:
Library name: Sample_23
Column name in raw_counts.txt: MT_Exp1

value: larvae


title: Human derived non-small cell lung cancer cells, mRNA, control group, biol repl3

description:
Library name: CON3_mRNA
Column name in gene_count_lncRNA.csv: CON3


title: C57BL/6J, Scr, HC, Rep 3

description: Library name: Sample 12


title: GuanitoxinMalathion0.5+0.5 3

description:
Library name: Sample_22
Column name in raw_counts.txt: GM_Exp3


title: CD68+, TB1, MGC W-004

description:
Library name: DSP-1001660036826-A-D04
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_W-004, area: 35046.87 um2, nuclei: 74


title: Human derived non-small cell lung cancer cells, mRNA, control group, biol repl2

description:
Library name: CON2_mRNA
Column name in gene_count_lncRNA.csv: CON2


title: C57BL/6J, Scr, HC, Rep 2

description: Library name: Sample 11


title: CD68+, TB1, MGC W-003

description:
Library name: DSP-1001660036826-A-D03
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_W-003, area: 41086.1 um2, nuclei: 124


title: GuanitoxinMalathion0.5+0.5 2

description:
Library name: Sample_21
Column name in raw_counts.txt: GM_Exp2


title: Human derived non-small cell lung cancer cells, mRNA, control group, biol repl1

description:
Library name: CON1_mRNA
Column name in gene_count_lncRNA.csv: CON1


title: C57BL/6J, Scr, HC, Rep 1

description: Library name: Sample 10


title: C57Bl/6J, mH2A1.1 KD, HC, Rep 3

description: Library name: Sample 21

value: mH2A1.1 KD

value: mH2A1.1 shRNA AAV injection in dorsal CA1 hippocampus


title: FIX00221-3955BW PBMC Fresh

description:
Library name: FIX00221
10x Genomics Flex

value: female

value: Caucasian/Non-hisp

value: Negative

value: PC

tag: probe barcode_id


title: GuanitoxinMalathion0.5+0.5 1

description:
Library name: Sample_20
Column name in raw_counts.txt: GM_Exp1

value: WT


title: CD68+, PDAC4, MGC W-005

description:
Library name: DSP-1001660036826-A-H12
CD68+ AOI from PDAC patient PDAC4, slide: CD68_Slide7_Rev, ROI: PDAC4-MGC_W-005, area: 48216.37 um2, nuclei: 80


title: CD68+, TB1, MGC W-002

description:
Library name: DSP-1001660036826-A-D02
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_W-002, area: 30457.18 um2, nuclei: 76


title: C57Bl/6J, mH2A1.1 KD, HC, Rep 2

description: Library name: Sample 20


title: Human derived non-small cell lung cancer cells, miRNA, drug resistance experiment group, biol repl3

description:
Library name: OR3_miRNA
Column name in gene_count_miRNA.csv: OR3


title: KO mouse with control diet, replicate 6

city: Baltimore

first: Hyun Jun

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 (M22) using salmon (0.14.10).
Assembly: Gencode vM21 (GRCm38.p6; primary assembly)
Supplementary files format and content: tab-delimited text files include TPM values for each sample
Supplementary files format and content: tab-delimited text files include raw gene counts for each gene

source_name: Pax8-rtTA, TRE-LC-1, MRflox/flox

growth_protocol: For induction of Nr3c2 knockout, mice were freely accessed to 2mg/ml doxycycline in 5% Sucrose water for 2 weeks and then washout with rescue diet for 2 weeks. Control mice (non-induction) were supplied with 5% Sucrose water not containing doxycycline.

extract_protocol:
The microdissected tubules were washed in PBS three times and lyzed in Trizon solution. Total RNA was extracted using Direct-zol RNA Microprep kit (ZYMO RESEARCH).
For library preparation, cDNA was synthesized using SMART-Seq HT Kit (Clontech) and Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: After doxycycline treatment, four groups were prepared to distinguish between K+ diet and MR knockout effects for 4 days: 1) control mice on normal K+ diet (CT-NK) or 2) high K+ diet (CT-HK) and 3) MR knockout mice on normal K+ diet (KO-NK) or 4) low K+ diet (KO-LK).

value: Kidney

value: Connecting tubule and collecting duct cell

value: Nr3c2 knockout

value: Control diet


title: TrichlorfonGuanitoxin0.5+0.5 3

description:
Library name: Sample_19
Column name in raw_counts.txt: TG_Exp3


title: Human derived non-small cell lung cancer cells, miRNA, drug resistance experiment group, biol repl2

description:
Library name: OR2_miRNA
Column name in gene_count_miRNA.csv: OR2


title: CD68+, TB1, MGC W-001

description:
Library name: DSP-1001660036826-A-D01
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_W-001, area: 14947.12 um2, nuclei: 36

value: macrophages


title: KO mouse with control diet, replicate 5


title: CD68+, TB1, MGC WO-005

description:
Library name: DSP-1001660036826-A-C12
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_WO-005, area: 19269.75 um2, nuclei: 86


title: TrichlorfonGuanitoxin0.5+0.5 2

description:
Library name: Sample_18
Column name in raw_counts.txt: TG_Exp2


title: Human derived non-small cell lung cancer cells, miRNA, drug resistance experiment group, biol repl1

description:
Library name: OR1_miRNA
Column name in gene_count_miRNA.csv: OR1


title: Sample 20_#89 MCFD2 SKO - #2

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

country: Germany

institute: University Clinic Bonn

data_processing:
Fastqc was used for quality analysis of the sequences. Cutadapt was used to remove the illumina universal adapter sequence in the reads. miARma-seq pipeline as used for further analysis, tophat2 with bowtie algorithm was used as a mapper whereas gtf file of genome build HG38 from ensemble was used as annotation file. Read counts were generated from miARma-seq and Qlucore omics explorer 3.6 was used to convert read counts into expression value. Trimmed mean of M-values (TMM) normalization was performed using Qlucore Omics explorer 3.5, same gtf file was used to annotate genes. Gene with less than 5 read counts in a sample were removed, also if gene is not expressed in both replicates of a sample were also removed.
Assembly: hg38
Supplementary files format and content: tab delimited text file included TMM normalized values for each sample and have ensembl gene Ids and gene symbols

source_name: Embryonic Kidney

growth_protocol: Different cell line with specific knockouts where cultured until about 70% confluency in six well plates

extract_protocol:
RNA was purified using the PureLink™ RNA mini kit according to manufacturer’s instructions (Invitrogen 12183018A) from the collected cell pellets
The concentration of the RNA was determined by measuring absorbance at 260 nm using NanoDrop One (ThermoFisher Scientific). The RNA and subjected to the Illumina sequencing protocol
3' RNA-seq (Illumina HiSeq 2500 V4 platform)

treatment_protocol: No treatment

value: Embryonic Kidney

tag: cell line

value: human embryonic kidney 293 cells

value: CRISPR-KO


title: CD68+, TB1, MGC WO-004

description:
Library name: DSP-1001660036826-A-C11
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_WO-004, area: 31970.12 um2, nuclei: 109

value: lung


title: TrichlorfonGuanitoxin0.5+0.5 1

description:
Library name: Sample_17
Column name in raw_counts.txt: TG_Exp1

value: larvae


title: Human derived non-small cell lung cancer cells, miRNA, control group, biol repl3

description:
Library name: CON3_miRNA
Column name in gene_count_miRNA.csv: CON3

value: non-small cell lung cancer


title: KO mouse with control diet, replicate 3


title: Malathion C4.3

description:
Library name: Sample_16
Column name in raw_counts.txt: Malathion_Exp3


title: CD68+, TB1, MGC WO-003

description:
Library name: DSP-1001660036826-A-C10
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_WO-003, area: 30147.5 um2, nuclei: 96


title: Human derived non-small cell lung cancer cells, miRNA, control group, biol repl2

description:
Library name: CON2_miRNA
Column name in gene_count_miRNA.csv: CON2


title: KO mouse with control diet, replicate 2


title: Malathion C4.2

description:
Library name: Sample_15
Column name in raw_counts.txt: Malathion_Exp2


title: CD68+, TB1, MGC WO-002

description:
Library name: DSP-1001660036826-A-C09
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_WO-002, area: 77488.69 um2, nuclei: 187


title: C57BL/6J, Scr, CFC+60, Rep 2

description: Library name: Sample 16

value: Dorsal CA1 hippocampus

value: scrambled shRNA AAV injection in dorsal CA1 hippocampus


title: KO mouse with control diet, replicate 1


title: Human derived non-small cell lung cancer cells, miRNA, control group, biol repl1

description:
Library name: CON1_miRNA
Column name in gene_count_miRNA.csv: CON1


title: Malathion C4.1

description:
Library name: Sample_14
Column name in raw_counts.txt: Malathion_Exp1


title: CD68+, TB1, MGC WO-001

description:
Library name: DSP-1001660036826-A-C08
CD68+ AOI from tuberculosis patient TB1, slide: CD68_Slide2, ROI: TB1-MGC_WO-001, area: 47863.74 um2, nuclei: 142


title: Human derived non-small cell lung cancer cells, circRNA, drug resistance experiment group, biol repl3

description:
Library name: OR3_circRNA
Column name in gene_count_circle.csv: OR3


title: KO mouse with low potassium diet, replicate 6

value: Low potassium diet


title: ControlMalathion Control 2

description:
Library name: Sample_13
Column name in raw_counts.txt: TGM_Ctl7


title: CD68+, TB2, MGC W-005

description:
Library name: DSP-1001660036826-A-C07
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_W-005, area: 32706.94 um2, nuclei: 72


title: KO mouse with control diet, replicate 4


title: Human derived non-small cell lung cancer cells, circRNA, drug resistance experiment group, biol repl2

description:
Library name: OR2_circRNA
Column name in gene_count_circle.csv: OR2


title: KO mouse with low potassium diet, replicate 5


title: ChIP-seq of H3K9me3 in condition CEC4, rep2

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

description:
rep2
H3K9me3_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

data_processing:
ChIP-seq reads were aligned to the C. elegans WBcel235 reference genome using BWA with default parameters.
Fragment length and quality assessments were performed using PyMASC.
MACS2 was employed for peak calling using -q 0.5 to lower the threshold of reported peaks. Peak calling results from different replicates within a given IP and condition were then filtered using ChIP-R to assess the irreproducible discovery rate (IDR).
ChIP-seq samples were normalized using their respective input controls with bamCompare (deepTools), applying specific parameters including --minMappingQuality 20, --binSize 10, --smoothLength 30, --extendReads, --scaleFactorsMethod readCount, --operation log2, and --pseudocount 1.
Assembly: WBcel235/ce11
Supplementary files format and content: macs2 peak calling filtered by chipr
Supplementary files format and content: Input normalised bigwig
Supplementary files format and content: Differential zscore bigwig

organism: Caenorhabditis elegans

source_name: embryos

growth_protocol: C. elegans were cultured on nematode growth medium (NGM) plates seeded with E. coli OP50-1 according to Lewis and Fleming (1995). NGM plates supplemented with ten times excess peptone were employed for growing worms destined for Hi-C and ChIP-seq experiments. The wild-type strain used was N2. The C. elegans strains utilized, along with their genotypes, are as follows: lin-61(tm2649) (Koester-Eiserfunke and Fischle, 2011), hpl-2(tm1489) (Schott et al., 2006), set-32(red11); met-2(n4256) set-25(n5021) (Kalinava et al., 2017), and cec-4(ok3124) (Gonzalez-Sandoval et al., 2015). The hpl-2(I158A) allele was created using a CRISPR/Cas9 approach; further details can be provided upon request. The genotypes of all C. elegans strains were routinely confirmed by single-worm PCR.

extract_protocol:
ChIP was conducted with slight adjustments following the method described by Ercan et al. (2007). Post-crosslinking, C. elegans embryos underwent a wash with 100 mM Tris-HCl, pH 7.5, followed by two washes with FA buffer (50 mM HEPES-KOH, pH 7.5; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 150 mM NaCl; 1x protease inhibitor (cOmplete™, Sigma, Germany)). Nuclei were sheared as for Hi-C and then centrifuged at 13,000 xg for 15 minutes at 4°C to gather extracts. Immunoprecipitations were arranged using extracts equivalent to 3 mg along with 3–5 μg of antibodies in a total volume of 500 μL FA buffer. Prior to antibody addition, 10% of the reactions were kept aside as input. After 16 hours of incubation at 65°C with agitation, complexes were recovered by adding 20 μL of Protein A/G beads (Pierce™ Protein A/G Magnetic Beads, USA) and washed twice with FA buffer supplemented to 1 M NaCl, followed by two washes with FA buffer supplemented to 500 mM NaCl. Beads were treated with 1% (w/v) SDS in TE containing 250 mM NaCl at 65°C for 30 minutes to elute the complexes. Samples and inputs were treated with 2 μL of 10 mg/mL Proteinase K for 1 hour at 55°C. Decrosslinking was carried out at 65°C overnight in a thermomixer. DNA purification was executed with a PCR clean-up kit (Macherey-Nagel™, Germany) and quantified using Qubit Fluorometric Quantification. Library preparation followed the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, USA) protocol. Libraries were sequenced on Novaseq 6000 PE150 S4 flow cells. Various antibodies were employed for ChIP experiments: anti-HPL-2 (Novus Biologicals 38630002), anti-LIN-61 (Novus Biologicals 29590002), anti-LEM-2 (Novus Biologicals 48540002), anti-H3K9me2 (Abcam ab1220), anti-H3K9me3 (VWR 309M3-B), anti-H3K4me1 (Abcam ab8895), anti-H3K4me3 (Active Motif 39159), anti-H3K27me3 (Abcam ab6002), and anti-H3K27ac (Active Motif Ab39133). All ChIP-seq experiments were conducted as biological independent triplicates.
Immunoprecipitation of C. elegans nuclear extracts utilized anti-LIN-61 (Novus Biologicals 29590002), anti-HPL-2 (Novus Biologicals 38630002), and anti-T7 (Abcam ab9138) antibodies. The antibodies were crosslinked to dynabeads M-280 sheep anti-rabbit IgG (Pierce, USA) overnight at 4°C on a nutator, following the manufacturer’s instructions. Unbound antibodies were removed by washing the beads with 1xPBS three times. Beads were then resuspended in 1 mL 0.2 M triethanolamine, pH 8.2, 20 mM DMP at room temperature for 60 minutes. Cross-linking was halted by adding 1 mL 50 mM Tris-HCL, pH 7.5, at room temperature for 60 minutes. After three washes with 1xPBS, 5 mg of total protein C. elegans extracts in 500 μL were added to the beads and incubated for 30 minutes at room temperature. Subsequently, beads underwent six washes with buffer D (each wash involving incubation with 1 mL buffer D for 5 minutes followed by centrifugation at 2000 xg for 1 minute at room temperature). Bound proteins were released from the beads in SDS-PAGE sample buffer by incubating at 95°C for 10 minutes. The proteins were resolved on SDS-PAGE and subjected to analysis by western blotting following standard procedures.

treatment_protocol: Crosslinking of C. elegans embryos and nuclei preparation followed the protocol outlined by Crane et al. (2015). Gravid adult worms were harvested and bleached to yield a late-stage embryo pellet of at least 1 or 4 mL for ChIP-seq or Hi-C experiments, respectively. The embryos underwent two washes in 1xPBS, were flash-frozen in liquid nitrogen, and stored at -80 °C. Thawed on ice, the embryos were then crosslinked in 50 mL of 2% (v/v) formaldehyde in PBS for 30 minutes at room temperature on a nutator. Subsequent to crosslinking, they were sequentially washed in 100 mM Tris-HCl, pH 7.5, twice in 1xPBS, and once in lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 0.2% (v/v) Igepal CA-630 (Sigma, Germany); 5 mM DTT; 0.5 mM EGTA; 1x protease inhibitor (cOmplete™, Sigma, Germany)). The embryos were then dounced 25 times with pestle A and 25 times with pestle B (PYREX® 7 mL Dounce Tissue Grinder, Corning, USA) while kept on ice. The resulting extract was centrifuged at 100 xg at 4 °C, and the supernatant containing nuclei was collected. This extraction process was repeated up to six times, with each supernatant checked for the presence of DAPI-stained nuclei under a fluorescence microscope. Supernatants containing pure nuclei were combined and centrifuged for 5 minutes at 2000 xg at 4 °C to collect material for further experimentation.

value: embryos


title: ControlMalathion Control 1

description:
Library name: Sample_12
Column name in raw_counts.txt: TGM_Ctl6


title: CD68+, TB2, MGC W-004

description:
Library name: DSP-1001660036826-A-C06
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_W-004, area: 43460.43 um2, nuclei: 91


title: Human derived non-small cell lung cancer cells, circRNA, drug resistance experiment group, biol repl1

description:
Library name: OR1_circRNA
Column name in gene_count_circle.csv: OR1


title: Guanitoxin C5.3

description:
Library name: Sample_11
Column name in raw_counts.txt: Guanitoxin_Exp3


title: KO mouse with low potassium diet, replicate 4


title: CD68+, TB2, MGC W-003

description:
Library name: DSP-1001660036826-A-C05
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_W-003, area: 34081.99 um2, nuclei: 142


title: Human derived non-small cell lung cancer cells, circRNA, control group, biol repl3

description:
Library name: CON3_circRNA
Column name in gene_count_circle.csv: CON3


title: KO mouse with low potassium diet, replicate 3


title: CD68+, PDAC3, MGC W-004

description:
Library name: DSP-1001660035205-B-B04
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_W-004, area: 17668.06 um2, nuclei: 62

value: pancreas


title: Guanitoxin C5.2

description:
Library name: Sample_10
Column name in raw_counts.txt: Guanitoxin_Exp2

value: WT


title: CD68+, TB2, MGC W-002

description:
Library name: DSP-1001660036826-A-C04
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_W-002, area: 27093.89 um2, nuclei: 62


title: Human derived non-small cell lung cancer cells, circRNA, control group, biol repl2

description:
Library name: CON2_circRNA
Column name in gene_count_circle.csv: CON2


title: Sample 10_#36 GABA L1 SKO -#1


title: KO mouse with low potassium diet, replicate 2

value: Kidney


title: CD68+, TB2, MGC W-001

description:
Library name: DSP-1001660036826-A-C03
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_W-001, area: 26006.97 um2, nuclei: 62


title: Human derived non-small cell lung cancer cells, circRNA, control group, biol repl1

description:
Library name: CON1_circRNA
Column name in gene_count_circle.csv: CON1


title: Guanitoxin C5.1

description:
Library name: Sample_9
Column name in raw_counts.txt: Guanitoxin_Exp1


title: KO mouse with low potassium diet, replicate 1

value: Connecting tubule and collecting duct cell


title: ControlGuanitoxin Control 2

description:
Library name: Sample_8
Column name in raw_counts.txt: TGM_Ctl5


title: CD68+, TB2, MGC WO-005

description:
Library name: DSP-1001660036826-A-C02
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_WO-005, area: 15026.68 um2, nuclei: 43


title: Control mouse with control diet, replicate 5

value: control


title: CD68+, TB2, MGC WO-004

description:
Library name: DSP-1001660036826-A-C01
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_WO-004, area: 29039.18 um2, nuclei: 70


title: ControlGuanitoxin Control 1

description:
Library name: Sample_7
Column name in raw_counts.txt: TGM_Ctl4


title: Tumor_P7_Post_infusion_VDJ

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description: Library name: Tumor_P7_Post_infusion_VDJ

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
genome build/assembly: GRCh38
processed data files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
processed data files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
processed data files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples

source_name: CAR T cells

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: CAR T cells

value: Primary cells

value: EGFR Potential copy number gain

value: 2.5e7 bivalent CAR T cells (EGFR, IL13RA2)

tag: batch


title: Trichlorfon C4.3

description:
Library name: Sample_6
Column name in raw_counts.txt: Trichlorfon_Exp3

tag: genotype


title: Control mouse with control diet, replicate 4

value: Control diet


title: Tumor_P4_Post_infusion_VDJ

description: Library name: Tumor_P4_Post_infusion_VDJ

value: EGFR Copy number gain


title: CD68+, TB2, MGC WO-003

description:
Library name: DSP-1001660036826-A-B12
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_WO-003, area: 26480.53 um2, nuclei: 76

data_processing:
For each AOI, digital count conversion (.dcc) files were generated from fastqs using the GeoMx NGS Pipeline (version 3.1.1).
From each tissue under investigation DCC files were read into a NanoStringGeoMxSet object using the readNanoStringGeoMxSet function from GeomxTools R package (version 3.5, R version 4.3.3), and segments were assessed for sequence quality.
After generating gene-level counts, segments with high fraction of genes detected below the limit of quantification (LOQ) were removed. Count matrix, sample annotations, and feature annotations were read into a SpatialExperiment object and analyzed with standR package (version 1.6) workflow.
Genes with low expression levels were removed. Counts were normalized using the upper-quartile method from the edgeR package (version 4.0.16).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files containing raw expression values for each AOI/sample
Supplementary files format and content: DCC files containing raw probe read counts for each AOI/sample; RTS_IDs are interpretable using the accompanying PKC file

extract_protocol:
After deparaffinization and target retrieval, slides were incubated with 0.1 μg/mL proteinase K for 15 minutes at 37°C and then post fixed for 5 minutes in 10% neutral buffered formalin followed by two washes in NBF stop buffer (24.5 g Tris base and 15 g Glycine in 2 L DEPC water). Slides were incubated with the Whole Transcriptome Atlas (WTA) RNA Probe set (121401102, NanoString), according to the manufacturer’s protocol.
Following probe incubation, slides were washed and incubated with the morphology marker solution: AlexaFluor™ 647 anti-human CD68 (BL13756, 375606 BioLegend, 1:400, RRID:AB_3097193) plus SYTO 13 (provided in GeoMx Nuclear Stain Morphology Kit, 121300303, NanoString) for 1 hour at RT and processed through the GeoMx® Digital Spatial Profiler instrument. Regions of interest (ROIs) with a circular shape and a diameter of 600 μm were selected, with an average of 3 ROIs without MGCs and 5 ROIs with MGCs per patient. For each ROI, the CD68+ area of interest (AOI) was selected to collect barcodes in a 96-well plate. Barcoded oligonucleotides were prepared for Illumina-based sequencing to generate target probe-specific count files, which were then saved in a digital count conversion format.

value: lung

value: macrophages


title: Control mouse with control diet, replicate 3


title: Trichlorfon C4.2

description:
Library name: Sample_5
Column name in raw_counts.txt: Trichlorfon_Exp2

value: larvae


title: CD68+, TB2, MGC WO-002

description:
Library name: DSP-1001660036826-A-B11
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_WO-002, area: 24099.39 um2, nuclei: 43


title: Control mouse with control diet, replicate 2


title: CD68+, TB2, MGC WO-001

description:
Library name: DSP-1001660036826-A-B10
CD68+ AOI from tuberculosis patient TB2, slide: CD68_Slide2, ROI: TB2-MGC_WO-001, area: 43502.27 um2, nuclei: 107


title: Trichlorfon C4.1

description:
Library name: Sample_4
Column name in raw_counts.txt: Trichlorfon_Exp1


title: Tumor_P1_Post_infusion_VDJ

description: Library name: Tumor_P1_Post_infusion_VDJ

value: Copy number gain, p.R108K

value: 1e7 bivalent CAR T cells (EGFR, IL13RA2)


title: Control mouse with control diet, replicate 1


title: CD68+, TB3, MGC W-005

description:
Library name: DSP-1001660036826-A-B09
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_W-005, area: 30622.81 um2, nuclei: 124


title: ControlTrichlorfonGuanitoxinMalathionControl 1

description:
Library name: Sample_3
Column name in raw_counts.txt: TGM_Ctl3


title: Control mouse with high potassium diet, replicate 6

value: High potassium diet


title: ControlTrichlorfon Control 2

description:
Library name: Sample_2
Column name in raw_counts.txt: TGM_Ctl2


title: CD68+, TB3, MGC W-004

description:
Library name: DSP-1001660036826-A-B08
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_W-004, area: 52458.97 um2, nuclei: 209


title: Control mouse with high potassium diet, replicate 5


title: ControlTrichlorfon Control 1

description:
Library name: Sample_1
Column name in raw_counts.txt: TGM_Ctl1


title: CD68+, TB3, MGC W-003

description:
Library name: DSP-1001660036826-A-B07
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_W-003, area: 42158.92 um2, nuclei: 165


title: Tumor_P7_Post_infusion_GEX

description: Library name: Tumor_P7_Post_infusion_GEX


title: 207448290038_R09C01

type: genomic

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

description: Sample name: 11017

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
The raw IDAT file produced from the array were processed using the openSesame function in the Sesame R package. We processed the arrays with the Sesame preprocessing code “0CDB” that applies a non-linear dye bias correction and background subtraction using the noob method (Norm-Exp out of band signal), which deconvolves out-of-band fluorescent signal from true signal. The beta values are calculated by the ratio of the methylated signal to unmethylated signal for each probe. These processing steps produced a beta measurement for each probe and patient, along with a corresponding Sesame signal detection p-value that is used as a quality score. Signal detection p-values were assigned using the pOOBAH method (P-value with out-of-band (OOB) array hybridization.) Probes that did not map to a CpG site in the Imprintome were discarded, and any remaining probes were also discarded if their signal detection p-value exceeded 0.2 for more than 10% of samples measured. For cases where multiple probes targeted the same CpG site, we averaged the beta values to produce beta measurements for each CpG site and participant. Finally, we averaged the beta values across CpG sites that correspond to the same ICR, which produced beta measurements for each ICR site and participant.   A series of student t-tests were performed to compare cases and controls (null hypothesis of µ = 0, two-tailed, α = 0.05, unpaired, unequal variance assumed) between methylation fractions, beta values. Beta values represent a number between 0 and 1 and are calculated by comparing the intensity of methylated beads to the total intensity of the locus. CpG sites were selected based on the statistical significance of differential methylation between cases and controls examined in this analysis. P-values from the t-test were corrected based on false discovery rate for the number of ICR sites tested. CpG sites were reported as significant based on an adjusted p-value < 0.05.
matrix processed value definition: Raw beta values (see supplementary linked to the Series record)

label: Cy3, Cy5

source_name: leukocytes from whole blood

label_protocol: Illumina protocol

extract_protocol: For the preparation of samples, 200 ng of DNA were bisulfite converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

value: leukocytes

tag: disease state

value: HCC case


title: Control mouse with high potassium diet, replicate 4

tag: tissue

value: Kidney


title: CD68+, TB3, MGC W-002

city: Rozzano

first: Anna Rita

description:
Library name: DSP-1001660036826-A-B06
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_W-002, area: 66799.39 um2, nuclei: 311

tag: cell type


title: Tumor_P4_Post_infusion_GEX

description: Library name: Tumor_P4_Post_infusion_GEX


title: 207448290038_R07C01

description: Sample name: 11016


title: CD68+, TB3, MGC W-001

description:
Library name: DSP-1001660036826-A-B05
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_W-001, area: 67290.55 um2, nuclei: 254


title: Tumor_P4_Pre_infusion_GEX

description: Library name: Tumor_P4_Pre_infusion_GEX

value: Pre-treatment


title: 207448290038_R05C01

description: Sample name: 11011


title: CD68+, TB3, MGC WO-005

description:
Library name: DSP-1001660036826-A-B04
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_WO-005, area: 27512.14 um2, nuclei: 112


title: Control mouse with high potassium diet, replicate 2

value: Connecting tubule and collecting duct cell

value: control


title: 207448290038_R03C01

description: Sample name: 11010


title: CD68+, TB3, MGC WO-004

description:
Library name: DSP-1001660036826-A-B03
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_WO-004, area: 30532.15 um2, nuclei: 178


title: Control mouse with high potassium diet, replicate 1


title: Tumor_P1_Pre_Infusion_GEX

description: Library name: Tumor_P1_Pre_Infusion_GEX

value: CAR T cells

value: Primary cells


title: 207448290038_R01C01

description: Sample name: 11004


title: IP_P6_VDJ

description: Library name: IP_P6_VDJ

value: Normal