title: AB20913

description: Library name: Sample 182

value: aPD-1 CAR


title: AB15655

status: Public on Jul 21 2026

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample1681
MARS_v2

library_source: transcriptomic

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

molecule: polyA RNA

organism: Homo sapiens

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

tag: tissue

value: BM

tag: gate

tag: batch


title: Whole Blood, ID14, M5, Booster, 2hour

city: Hamilton

first: Vincent

last: Munster

state: Montana

department: NIAID

country: USA

institute: NIH

description: Library name: VA0002000012

data_processing:
Bulk RNA-seq FASTQ files were processed using the OpenOmics/RNA-seek (https://doi.org/10.5281/zenodo.13312679) v1.9.5 pipeline to run QC and quantify gene transcript counts.
Assembly: GRCh38
Supplementary files format and content: RSEM counts

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes for 221 study samples using the QIAsymphony PAXgene Blood RNA Kit and the QIAsymphony SP instrument (both Qiagen) according to the manufacturer instructions including DNase I digestion and Proteinase K treatment.  RNA concentration was determined by Quant-iT RiboGreen assay (ThermoFisher) using a Biotek Synergy H1 plate reader (Agilent Technologies) and RINs assessed using Agilent 4200 TapeStation (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA using Universal Plus mRNA-seq Kit with NuQuant Human Globin AnyDeplete kit (Tecan Genomics) on a Biomek Fx robot (Beckman). First, messenger RNA transcripts were captured, fragmented, and converted to complementary DNA. Following second-strand synthesis and end repair, DNA fragments were ligated with dual-indexed adapters compatible with the Illumina platform. Libraries were subjected to strand selection and removal of globin transcripts, followed by 14 cycles of amplification. Purified libraries were analyzed with the Biotek Synergy H1 plate reader and Agilent 4200 TapeStation (Agilent Technologies) to assess concentration and size distribution, respectively, then normalized and pooled for sequencing. Final molarity of the pool was determined by quantitative polymerase chain reaction using the KAPA library quantification kit (Roche). Paired-end sequencing was performed on the NextSeq 2000 (Illumina) using P3 300 cycles kits in 2 × 150-base pair (bp) format.

value: Whole Blood

tag: individual

tag: Sex

value: female

tag: age

tag: treatment

value: Booster

tag: time

value: Month 5

tag: timepoint

value: 2 hour

tag: reaction type

value: ISRR

tag: reaction type_severity

value: VeryMild


title: Foz_Regression_2

city: La Jolla

first: Souradipta

last: Ganguly

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description:
Library name: R8w_8268_231010
Column name in All_HTSeq_Counts.txt: R8w_8268_231010

data_processing:
The paired-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were then aligned to the GRCm38.p4 reference genome and Gencode M9 annotations using STAR (v 2.6.1).
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via the SAMtools to generate SAM files.
Read counts to each genomic feature were obtained with featureCounts (v 1.6.5).
Assembly: GRCm38
Supplementary files format and content: Tab seperated values of rxaw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
Total RNA was extracted using RNeasy Mini columns (Qiagen, Valencia, CA). mRNA selection was completed using 500ng of total RNA input using NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were prepped using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Heart

tag: liver phenotype

tag: heart phenotype

tag: genotype

value: Foz

value: Regression


title: AB15195

description:
Library name: Sample1680
MARS_v2


title: AB20912

description: Library name: Sample 181

library_source: transcriptomic single cell

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the mouse reference genome (GRCm38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: tab delimited cell metadata

source_name: brain

extract_protocol:
Mice were transcardially perfused with sterile PBS, and brain, spinal cord, spleen, lung and CSF were extracted 10 days post CAR T administration.
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

treatment_protocol: For each mouse, 4 days after EAE induction, 3x10^⁶ cells in 100ul were injected retro-orbitally under isoflurane anesthesia, or 100ul of PBS for the control EAE untreated group. Tissues were harvested for scRNA-seq on day 14.

value: brain

tag: mouse

tag: score

tag: eae model

value: peptide MOG


title: Whole Blood, ID14, M5, Booster, 35min

description: Library name: VA0001990012

tag: tissue

value: 35 min


title: Foz_Regression_1

description:
Library name: R8w_8275_231010
Column name in All_HTSeq_Counts.txt: R8w_8275_231010


title: AB20911

description: Library name: Sample 180

tag: gate

value: CD45.1+ mCherry+


title: WT_WD_24w_3

description:
Library name: WWD24w_8152_231010
Column name in All_HTSeq_Counts.txt: WWD24w_8152_231010

value: WT


title: Whole Blood, ID14, M5, Booster, Baseline

description: Library name: VA0001980016

value: Baseline

tag: batch


title: AB20910

description: Library name: Sample 179

value: aPD-1 CAR


title: AB15117

description:
Library name: Sample1678
MARS_v2

value: BM

value: PC


title: Whole Blood, ID14, D2, Vaccine, 24hour

description: Library name: VA0001080007

value: Whole Blood

tag: individual

value: female

value: Vaccine

value: Day 2

value: 24 hour

value: Severe


title: AB15119

description:
Library name: Sample1679
MARS_v2


title: WT_WD_24w_2

description:
Library name: WWD24w_8151_231010
Column name in All_HTSeq_Counts.txt: WWD24w_8151_231010

value: Heart


title: AB15116

description:
Library name: Sample1677
MARS_v2


title: AB20909

description: Library name: Sample 178


title: Whole Blood, ID14, D2, Vaccine, 6hour

description: Library name: VA0001070005

tag: Sex

value: 6 hour

value: ISRR


title: WT_WD_24w_1

description:
Library name: WWD24w_8191_231010
Column name in All_HTSeq_Counts.txt: WWD24w_8191_231010


title: AB20908

description: Library name: Sample 177

value: brain

value: peptide MOG


title: AB15115

description:
Library name: Sample1676
MARS_v2


title: Foz_WD_24w_3

description:
Library name: FW24w_8217_231010
Column name in All_HTSeq_Counts.txt: FW24w_8217_231010

value: Foz


title: Whole Blood, ID14, D2, Vaccine, 2hour

description: Library name: VA0001060030

tag: age

value: 2 hour


title: Whole Blood, ID14, D2, Vaccine, 35min

description: Library name: VA0001050012

tag: treatment

value: 35 min


title: AB15113

description:
Library name: Sample1675
MARS_v2


title: AB19803

description: Library name: Sample 176

source_name: spinal cord

value: spinal cord

value: Untreated (PBS)


title: Foz_WD_24w_2

description:
Library name: FW24w_8237_231010
Column name in All_HTSeq_Counts.txt: FW24w_8237_231010


title: AB19802

description: Library name: Sample 175


title: AB15112

description:
Library name: Sample1674
MARS_v2

value: BM

value: PC


title: Whole Blood, ID14, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0001040030

value: Whole Blood

value: female

value: Placebo/Vaccine

tag: time

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/ISRR

value: None/Severe


title: Foz_WD_24w_1

description:
Library name: FW24w_8218_231010
Column name in All_HTSeq_Counts.txt: FW24w_8218_231010

value: Heart


title: AB19801

description: Library name: Sample 174

value: aPD-1 CAR + IL-10


title: AB15111

description:
Library name: Sample1673
MARS_v2


title: Whole Blood, ID14, D1, Placebo, 6hour

description: Library name: VA0001030005

value: Placebo

value: Day 1

tag: timepoint

value: 6 hour


title: scRNA_Treated_GEX_lib_3mice

city: Faridabad

first: Avinash

last: Bajaj

state: Haryana

address: Faridabad-Gurgaon Expressway

country: India

institute: Regional Centre for Biotechnology

description:
Library name: BUP_GEX_lib
10X Genomics 5' v2; gene expression (GEX)

data_processing:
Demultiplexed raw FASTQ files corresponding to 5ʹ single-cell gene expression libraries from each lane of 10X Genomics run were mapped to the mouse reference genome GRCm39-2024-A using 10X Genomics’ cellranger (v8.0.1) multi pipeline.
Individual 10X Genomics run was processed independently using the R-based Seurat package (v5.0.1)  were merged if the experiments were performed concomitantly.
Assembly: GRCm39-2024-A
Supplementary files format and content: Default ouput files as part of cellranger multi pipeline. "barcodes.tsv.gz" contains barcodes for all captured cells. "features.tsv" contains annotated transcripts. "matrix.mtx.gz" contains the count matrix for all cells for all corresponding annotated transcripts.

source_name: Subcutaneous CT26 Tumours

extract_protocol:
Tumours were excised from untreated group and BUP-Gel treated mice and harvested in cold 1X PBS. Tumours were finely chopped, homogenized, and subjected to enzymatic digestion using collagenase IV and DNase I for 45 minutes at 37 C on constant shaking. Tumor suspension was further strained using cell strainers and single cells were obtained.These cells were stained for immune cells using anti-CD45 antibody followed by live dead staining. Sorting of live CD45+ and CD45- cells were done using FACS.
CD45+ and CD45- cells were pooled in 4:1 ratio and run on seperate lanes for untreated and treated conditions seperately.

value: Subcutaneous CT26 Tumours

value: BUP-Gel


title: AB19800

description: Library name: Sample 173

value: brain

value: peptide MOG


title: AB15110

description:
Library name: Sample1672
MARS_v2

value: BM

value: PC


title: Whole Blood, ID14, D1, Placebo, 2hour

description: Library name: VA0001020030

value: Whole Blood

value: female

value: 2 hour

tag: reaction type


title: scRNA_Untreated_GEX_lib_3mice

description:
Library name: UT_GEX_lib
10X Genomics 5' v2; gene expression (GEX)


title: AB15109

description:
Library name: Sample1671
MARS_v2


title: AB19799

description: Library name: Sample 172

value: spinal cord

value: Untreated (PBS)


title: Whole Blood, ID14, D1, Placebo, 35min

description: Library name: VA0001010012

value: 35 min

tag: reaction type_severity


title: Pool 2C, CMO

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
Library name: Pool_2C_CMO
Pool 2C, primary microglia from 12 animals, cell multiplexing oligo library

data_processing:
Raw reads were aligned to the mouse genome via the GRCm39-2024-A index provided by10X Genomics, which is based on Gencode v33, and gene-level counts (including from reads that align to introns) were obtained with cellranger multi (10X Genomics, version 9.0) using default parameters. Filtered cell counts across libraries were aggregated into a single matrix with the cellranger aggr --normalize="none" command (10X Genomics, version 9.0).
Assembly: GRCm39
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file is an HDF5 file generated with the following comman: cellranger aggr --normalize="none" --csv=aggregation.csv. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). The aggregation.csv file used by the cellranger aggr command specifies the mapping between sample (animal) and the cell barcode suffix, e.g. cells with the _1 suffix are from the sample listed in the first row of the aggregation.csv file, those with suffix _2 are from the sample in the second row, etc.
Supplementary files format and content: The aggregation.csv file used by the cellranger aggr command specifies the mapping between sample (animal) and the cell barcode suffix, e.g. cells with the _1 suffix are from the sample listed in the first row of the aggregation.csv file, those with suffix _2 are from the sample in the second row, etc.
Supplementary files format and content: The feature_reference.csv file used by the cellranger multi command to assign gene identifiers and CMO sequences to the features reported in the filtered_feature_bc_matrix.h5 file
Supplementary files format and content: The sample_annotations.csv file contains annotations for each sample (=animal) that contributed to each of the pools.

extract_protocol:
For each animal, three-quarters of the brain, excluding the olfactory bulb and cerebellum, was dissociated into a single-cell suspension following the Miltenyi Adult Mouse Brain Dissociation protocol (Miltenyi, 130-107-677) with modifications. Anisomycin (2 µM final concentration), Actinomycin D (5 µM final concentration), and Hyaluronidase Type I-S (5,600 U/mL final concentration) were added to the Miltenyi Enzyme Mix 1 to facilitate extracellular matrix breakdown and inhibit transcriptional and translational activity. Single-cell suspensions were co-labeled with FC block, CD45, CD11b, CD44, and Ly6G (1:100 dilution) for 30 minutes on ice. Following a washing step, equal numbers of cells from each animal were also labeled with individual Cell Multiplexing Oligos (CMO, 10X Genomics, 1000261) per the manufacturer’s protocol, substituting the PBS wash buffer with NbActiv-1 + 1% BSA. The same number of labelled cells from each animal was pooled and CD11b+CD45−Ly6G− primary microglia were isolated from the pool using FACS. This microglia pool was then loaded them onto a Chromium microfluidic chip G, following the Chromium NextGEMS Single Cell 3' v3.1 Cell Multiplexing RevB User Guide (10X Genomics, CG000388), targeting an estimated capture of 3,000 microglia per animal.
After reverse transcription, GEM purification, and cDNA amplification, the amplified material was split into two fractions: 3' Gene Expression (GEX) DNA and Cell Multiplexing (CMO) DNA, using a dual-side size selection bead purification. Five microliters of the CMO DNA was PCR-amplified to introduce Illumina sequencing indices, while one-quarter of the GEX DNA was used for library preparation following the user guide. For each cohort, GEX libraries were pooled in equimolar amounts and subjected to a QC sequencing run on an Illumina MiSeq to determine the number of captured cells. Based on the MiSeq results, the libraries were re-pooled along with the CMO libraries, and sequenced on an Illumina NovaSeq 6000 instrument (28 × 10 × 10 × 90 cycles) at SeqMatic (Fremont, CA, USA), targeting a read depth of 50,000 reads per cell for mRNA transcripts and 5,000 reads per cell for demultiplexing CellPlex oligos.

tag: library type

value: CMO

tag: region

value: forebrain

tag: cell type

value: primary microglia

value: 8 months

tag: pool

value: male

tag: strain


title: AB19798

description: Library name: Sample 171

tag: mouse

tag: score

tag: eae model


title: Whole Blood, ID14, D1, Placebo, Baseline

description: Library name: VA0001000034

tag: tissue

value: Placebo

value: Day 1

value: Baseline

tag: batch


title: AB15108

description:
Library name: Sample1670
MARS_v2

tag: gate


title: AB19797

description: Library name: Sample 170

value: peptide MOG


title: Pool 2B, CMO

description:
Library name: Pool_2B_CMO
Pool 2B, primary microglia from 12 animals, cell multiplexing oligo library

value: brain

tag: age

tag: Sex


title: AB15107

description:
Library name: Sample1669
MARS_v2

value: BM


title: Whole Blood, ID10, M5, Booster, 2hour

description: Library name: VA0001790030

value: Whole Blood

tag: individual

tag: treatment

value: Booster

tag: time

value: Month 5


title: Pool 1C, CMO

description:
Library name: Pool_1C_CMO
Pool 1C, primary microglia from 12 animals, cell multiplexing oligo library


title: AB19796

description: Library name: Sample 169


title: AB15106

description:
Library name: Sample1668
MARS_v2

value: PC


title: Whole Blood, ID10, M5, Booster, 35min

description: Library name: VA0001780012

tag: timepoint

tag: reaction type

tag: reaction type_severity


title: Pool 1B, CMO

description:
Library name: Pool_1B_CMO
Pool 1B, primary microglia from 12 animals, cell multiplexing oligo library

tag: library type

tag: region

tag: cell type


title: Whole Blood, ID10, M5, Booster, Baseline

description: Library name: VA0001770034


title: AB15105

description:
Library name: Sample1667
MARS_v2


title: AB19794

description: Library name: Sample 167

tag: mouse

value: aPD-1 CAR


title: AB19795

description: Library name: Sample 168

value: spinal cord

tag: score


title: Pool 1A, CMO

description:
Library name: Pool_1A_CMO
Pool 1A, primary microglia from 12 animals, cell multiplexing oligo library

value: CMO

tag: pool

tag: strain


title: Whole Blood, ID10, D2, Vaccine, 24hour

description: Library name: VA0000940027

tag: tissue

value: Vaccine

value: Day 2

value: 24 hour

value: ISRR

value: Mild

tag: batch


title: AB15104

description:
Library name: Sample1666
MARS_v2

tag: gate


title: Pool 2C, GEX

description:
Library name: Pool_2C_GEX
Pool 2C, primary microglia from 12 animals, gene expression library

value: mRNA

value: forebrain

value: primary microglia

tag: age

value: 8 months

tag: Sex

value: male


title: AB19793

description: Library name: Sample 166

tag: treatment

value: aPD-1 CAR + IL-10

tag: eae model

value: peptide MOG


title: AB15102

description:
Library name: Sample1665
MARS_v2

value: BM


title: Whole Blood, ID10, D2, Vaccine, 6hour

description: Library name: VA0000930027

value: Whole Blood

tag: individual

tag: time

tag: timepoint

value: 6 hour


title: Pool 2B, GEX

description:
Library name: Pool_2B_GEX
Pool 2B, primary microglia from 12 animals, gene expression library

tag: library type

value: brain


title: AB19792

description: Library name: Sample 165


title: AB15101

description:
Library name: Sample1664
MARS_v2

value: PC


title: Whole Blood, ID10, D2, Vaccine, 2hour

description: Library name: VA0000920052

value: Vaccine

value: 2 hour

tag: reaction type

tag: reaction type_severity


title: Pool 1C, GEX

description:
Library name: Pool_1C_GEX
Pool 1C, primary microglia from 12 animals, gene expression library

tag: region

tag: cell type


title: AB14996

description:
Library name: Sample1663
MARS_v2


title: AB19791

description: Library name: Sample 164

value: spinal cord

tag: mouse

tag: score


title: Whole Blood, ID10, D2, Vaccine, 35min

description: Library name: VA0000910036

tag: tissue

value: Day 2

value: 35 min

value: ISRR


title: Pool 1B, GEX

description:
Library name: Pool_1B_GEX
Pool 1B, primary microglia from 12 animals, gene expression library

value: mRNA

value: forebrain

tag: pool

tag: batch

tag: strain


title: Whole Blood, ID10, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0000900052

tag: Sex

tag: age

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Mild/Mild


title: Pool 1A, GEX

description:
Library name: Pool_1A_GEX
Pool 1A, primary microglia from 12 animals, gene expression library

value: primary microglia

value: 8 months

value: male


title: AB19789

description: Library name: Sample 162

tag: gate

tag: treatment

value: aPD-1 CAR

tag: eae model

value: peptide MOG


title: AB14992

description:
Library name: Sample1661
MARS_v2

value: BM

value: PC


title: AB19790

description: Library name: Sample 163

value: brain


title: AB14995

description:
Library name: Sample1662
MARS_v2


title: Whole Blood, ID10, D1, Placebo, 6hour

description: Library name: VA0000890027

value: Whole Blood

tag: individual

value: Placebo

tag: time

value: Day 1

tag: timepoint

value: 6 hour

value: Mild


title: Pool 7, CMO

description:
Library name: Pool_7_CMO
Pool 7, primary microglia from 8 animals, cell multiplexing oligo library

data_processing:
Raw reads were aligned to the mouse genome via the GRCm39-2024-A index provided by10X Genomics, which is based on Gencode v33, and gene-level counts (including from reads that align to introns) were obtained with cellranger multi (10X Genomics, version 9.0) using default parameters. Filtered cell counts across libraries were aggregated into a single matrix with the cellranger aggr --normalize="none" command (10X Genomics, version 9.0).
Assembly: GRCm39
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file is an HDF5 file generated with the following comman: cellranger aggr --normalize="none" --csv=aggregation.csv. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). The aggregation.csv file used by the cellranger aggr command specifies the mapping between sample (animal) and the cell barcode suffix, e.g. cells with the _1 suffix are from the sample listed in the first row of the aggregation.csv file, those with suffix _2 are from the sample in the second row, etc.
Supplementary files format and content: The aggregation.csv file used by the cellranger aggr command specifies the mapping between sample (animal) and the cell barcode suffix, e.g. cells with the _1 suffix are from the sample listed in the first row of the aggregation.csv file, those with suffix _2 are from the sample in the second row, etc.
Supplementary files format and content: The feature_reference.csv file used by the cellranger multi command to assign gene identifiers and CMO sequences to the features reported in the filtered_feature_bc_matrix.h5 file

extract_protocol:
For each animal, three-quarters of the brain, excluding the olfactory bulb and cerebellum, was dissociated into a single-cell suspension following the Miltenyi Adult Mouse Brain Dissociation protocol (Miltenyi, 130-107-677) with modifications. Anisomycin (2 µM final concentration), Actinomycin D (5 µM final concentration), and Hyaluronidase Type I-S (5,600 U/mL final concentration) were added to the Miltenyi Enzyme Mix 1 to facilitate extracellular matrix breakdown and inhibit transcriptional and translational activity. [Due to an operator error, cells from two animals (17931, 17932) were pooled before labeling; as these animals were from the same experimental group, they were treated as a single animal / replicate in the downstream analysis.] Single-cell suspensions were co-labeled with FC block, CD45, CD11b, CD44, and Ly6G (1:100 dilution) for 30 minutes on ice. Following a washing step, equal numbers of cells from each animal were also labeled with individual Cell Multiplexing Oligos (CMO, 10X Genomics, 1000261) per the manufacturer’s protocol, substituting the PBS wash buffer with NbActiv-1 + 1% BSA. The same number of labelled cells from each animal was pooled and CD11b+CD45−Ly6G− primary microglia were isolated from the pool using FACS. This microglia pool was then loaded them onto a Chromium microfluidic chip G, following the Chromium NextGEMS Single Cell 3' v3.1 Cell Multiplexing RevB User Guide (10X Genomics, CG000388), targeting an estimated capture of 3,000 microglia per animal.
After reverse transcription, GEM purification, and cDNA amplification, the amplified material was split into two fractions: 3' Gene Expression (GEX) DNA and Cell Multiplexing (CMO) DNA, using a dual-side size selection bead purification. Five microliters of the CMO DNA was PCR-amplified to introduce Illumina sequencing indices, while one-quarter of the GEX DNA was used for library preparation following the user guide. For each cohort, GEX libraries were pooled in equimolar amounts and subjected to a QC sequencing run on an Illumina MiSeq to determine the number of captured cells. Based on the MiSeq results, the libraries were re-pooled along with the CMO libraries, and sequenced on an Illumina NovaSeq S2 instrument (28 × 10 × 10 × 90 cycles) at SeqMatic (Fremont, CA, USA), targeting a read depth of 50,000 reads per cell for mRNA transcripts and 5,000 reads per cell for demultiplexing CellPlex oligos.

tag: library type

value: CMO

value: forebrain

tag: genotype

value: WT

value: 4 months


title: AB14991

description:
Library name: Sample1660
MARS_v2


title: AB19788

description: Library name: Sample 161

source_name: lung

value: lung

value: Untreated (PBS)


title: Whole Blood, ID10, D1, Placebo, 2hour

description: Library name: VA0000880052

value: male

value: 2 hour

tag: reaction type

value: ISRR

tag: reaction type_severity


title: AB19787

description: Library name: Sample 160

value: spinal cord

tag: mouse

tag: score

value: peptide MOG


title: Pool 5, CMO

description:
Library name: Pool_5_CMO
Pool 5, primary microglia from 8 animals, cell multiplexing oligo library

tag: tissue

value: brain

tag: region

tag: cell type

value: primary microglia

tag: pool


title: AB14989

description:
Library name: Sample1659
MARS_v2

value: BM

value: PC

tag: batch


title: Whole Blood, ID10, D1, Placebo, 35min

description: Library name: VA0000870034

value: Whole Blood

tag: Sex

tag: age

value: Placebo

value: Day 1

value: 35 min


title: AB19786

description: Library name: Sample 159

tag: gate

tag: treatment

tag: eae model


title: Whole Blood, ID10, D1, Placebo, Baseline

description: Library name: VA0000860056

tag: individual

tag: time

tag: timepoint

value: Baseline

value: Mild


title: Pool 3, CMO

description:
Library name: Pool_3_CMO
Pool 3, primary microglia from 8 animals, cell multiplexing oligo library

tag: library type

value: CMO

value: forebrain

tag: genotype

value: WT

value: 4 months

tag: strain


title: AB14988

description:
Library name: Sample1658
MARS_v2


title: AB19785

description: Library name: Sample 158

value: lung

tag: mouse

tag: score

value: aPD-1 CAR + IL-10


title: AB14987

description:
Library name: Sample1657
MARS_v2

tag: tissue


title: Whole Blood, ID9, M5, Booster, 2hour

description: Library name: VA0001660012

value: female

value: Booster

value: Month 5

value: 2 hour

tag: reaction type

tag: reaction type_severity


title: Pool 5, GEX

description:
Library name: Pool_5_GEX
Pool 5, primary microglia from 8 animals, gene expression library

value: mRNA

value: brain

tag: region

tag: cell type

value: primary microglia

tag: pool

value: male


title: Pool 7, GEX

description:
Library name: Pool_7_GEX
Pool 7, primary microglia from 8 animals, gene expression library

tag: age

tag: Sex


title: AB19784

description: Library name: Sample 157

source_name: spleen

value: spleen

tag: gate

tag: treatment

tag: eae model

value: peptide MOG

tag: batch


title: AB14986

description:
Library name: Sample1656
MARS_v2

value: BM


title: Whole Blood, ID9, M5, Booster, 35min

description: Library name: VA0001650012

value: Whole Blood

tag: individual

tag: time

tag: timepoint

value: 35 min


title: Pool 3, GEX

description:
Library name: Pool_3_GEX
Pool 3, primary microglia from 8 animals, gene expression library

tag: library type

value: forebrain

tag: genotype

value: WT

tag: strain


title: Whole Blood, ID9, M5, Booster, Baseline

description: Library name: VA0001640016

tag: tissue

value: Baseline

tag: reaction type


title: AB14984

description:
Library name: Sample1655
MARS_v2

value: PC


title: AB19782

description: Library name: Sample 155

value: spinal cord

tag: mouse

tag: score

value: aPD-1 CAR + IL-10


title: AB14982

description:
Library name: Sample1654
MARS_v2


title: AB19783

description: Library name: Sample 156

value: CD45.1+ mCherry+


title: Whole Blood, ID9, D2, Vaccine, 24hour

description: Library name: VA0000850027

value: female

value: Vaccine

value: Day 2

value: 24 hour

tag: reaction type_severity


title: Whole Blood, ID18, M5, Booster, 2hour

type: protein

hyb_protocol: Hybridization protocol done in accordance with SomaLogic standard operating procedures and best practices.

scan_protocol: The SomaScan Assay was performed on a Tecan Fluent 780 high throughput automation system according to manufacturer’s instructions. Assay data were normalized using SomaLogic’s standard procedure utilizing adaptive normalization by maximum likelihood (Candia, JPR, 2024 (PMID: 39473295)).

data_processing: Protein abundancy was quantified expressed as Relative Fluorescence Units (RFU) and log2 transformed for comparison analysis. Comparison of each timepoint to the baseline for each reaction separately, or comparisons of the groups with reactions to the vaccine to the no-reaction group at each timepoint were completed in R v4.4.2 using R packages lmerTest v3.1-3 and emmeans v1.10.7 to create a linear mixed effects model using the Satterthwaite approximation. Models were set up as an interaction of response and timepoint while blocking on individual group.  Adjusted p-values calculated using Bonferroni correction did not indicate changes with p<0.05 due to the small sample size and thus p-value was used instead of the adjusted p-value.

label: SOMAmer reagents

molecule: protein

source_name: peripheral blood serum

label_protocol: Label protocol done in accordance with SomaLogic standard operating procedures and best practices.

extract_protocol: Blood samples were collected before (baseline or time 0) the second vaccine dose or placebo injections, and 35 min, 2 h, 6 h and 24 h following injections.  For the vaccine booster, samples were obtained before, 35 min and 2 h after the dose. Blood samples were collected using serum separator tubes (BD Biosciences) for high throughput proteomic analysis using the SomaScan platform (SomaLogic).

tag: age

value: Booster

tag: day

value: Month 5

value: 2 hour

value: ISRR

tag: reaction type severity

value: Severe


title: LN_CD4+

city: Wuhan

first: Hao

last: Panax

address: 1277# Jie-Fang Avenue

country: China

institute: Huazhong University of Science and Technology

description: Library name: SAMPLE1

data_processing:
Raw data quality control was performed to eliminate low-quality cells with less than 200–300 expressed genes, high mitochondrial gene content, and doublets with comparatively large library sizes.
The results of several runs were combined to analyze more than one sample. The gene-barcode matrix was reconstituted and the sequencing depth was normalized.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: mediastinal lymph nodes

growth_protocol: 15000 CD4+ T cells with 95% viability were sorted using FACS.

extract_protocol:
total RNA
To build libraries and add index codes, NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was utilized. The library fragments were purified using AMPure XP technology (Beckman Coulter, Beverly, MA, USA) to select 250–300 bp cDNA fragments.

treatment_protocol: Subsequently, 700 cells/μL of CD4+ T cells were encapsulated into the droplets.

value: mediastinal lymph nodes

tag: cell type

value: CD4+ T cells


title: AB19781

description: Library name: Sample 154

value: brain

tag: gate

tag: treatment

tag: eae model

value: peptide MOG


title: AB14981

description:
Library name: Sample1653
MARS_v2

value: BM

value: PC

tag: batch


title: Whole Blood, ID9, D2, Vaccine, 6hour

description: Library name: VA0000840027

value: Whole Blood

tag: individual

tag: Sex

tag: time

tag: timepoint

value: 6 hour


title: AB19780

description: Library name: Sample 153

tag: tissue

value: aPD-1 CAR + IL-10


title: Whole Blood, ID18, M5, Booster, 35min

value: female

value: 35 min

tag: reaction type


title: Whole Blood, ID9, D2, Vaccine, 2hour

description: Library name: VA0000830052

value: Vaccine

value: Day 2


title: AB14980

description:
Library name: Sample1652
MARS_v2


title: AB19779

description: Library name: Sample 152

value: lung

tag: mouse


title: AB14978

description:
Library name: Sample1651
MARS_v2


title: Whole Blood, ID18, M5, Booster, Baseline

value: Booster

value: Month 5

value: Baseline


title: AB19778

description: Library name: Sample 151

value: spleen

tag: score


title: Whole Blood, ID9, D2, Vaccine, 35min

description: Library name: VA0000820034

tag: reaction type_severity


title: Whole Blood, ID18, D2, Vaccine, 24hour

tag: age

value: 24 hour

value: ISRR

value: Mild


title: AB14975

description:
Library name: Sample1650
MARS_v2

value: BM


title: AB19777

description: Library name: Sample 150

value: spinal cord

value: peptide MOG


title: AB14974

description:
Library name: Sample1649
MARS_v2


title: Whole Blood, ID9, D1, Placebo, 6hour

description: Library name: VA0000800027

value: Whole Blood

value: Placebo

value: Day 1

value: 6 hour


title: Whole Blood, ID9, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0000810052

value: female

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/None


title: AB14973

description:
Library name: Sample1648
MARS_v2

value: PC


title: Whole Blood, ID18, D2, Vaccine, 6hour

value: Vaccine

tag: day

value: Day 2


title: AB14970

description:
Library name: Sample1647
MARS_v2


title: Whole Blood, ID18, D2, Vaccine, 2hour

value: 2 hour

value: ISRR

tag: reaction type severity


title: AB19775

description: Library name: Sample 148

value: brain


title: Whole Blood, ID18, D2, Vaccine, 35min

value: 35 min

value: Mild


title: AB19774

description: Library name: Sample 147

value: peptide MOG


title: AB14968

description:
Library name: Sample1646
MARS_v2

value: BM


title: Whole Blood, ID9, D1, Placebo, 35min

description: Library name: VA0000780034

value: Whole Blood

value: Placebo

value: Day 1


title: Whole Blood, ID18, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: female

value: Placebo/Vaccine

value: ISRR/ISRR

value: Severe/Mild


title: AB19773

description: Library name: Sample 146

value: CD45.1+ mCherry+

value: aPD-1 CAR


title: Whole Blood, ID9, D1, Placebo, Baseline

description: Library name: VA0000770056

value: Baseline


title: Whole Blood, ID18, D1, Placebo, 6hour

value: 6 hour

value: Severe


title: AB14967

description:
Library name: Sample1645
MARS_v2


title: Whole Blood, ID8, M5, Booster, 2hour

description: Library name: VA0001610012

value: Booster

value: Month 5

value: 2 hour

value: ISRR


title: Whole Blood, ID18, D1, Placebo, 2hour


title: AB19772

description: Library name: Sample 145

value: brain

value: peptide MOG


title: AB14966

description:
Library name: Sample1644
MARS_v2

value: BM


title: Whole Blood, ID8, M5, Booster, 35min

description: Library name: VA0001600012

value: Whole Blood

value: 35 min

value: Mild


title: Whole Blood, ID18, D1, Placebo, 35min

value: female

value: Placebo

value: Day 1


title: AB14964

description:
Library name: Sample1643
MARS_v2

value: PC


title: AB19771

description: Library name: Sample 144

value: spleen


title: Whole Blood, ID8, M5, Booster, Baseline

description: Library name: VA0001590016

value: Baseline


title: AB19770

description: Library name: Sample 143

value: Untreated (PBS)


title: AB14962

description:
Library name: Sample1642
MARS_v2


title: Whole Blood, ID8, D2, Placebo, 24hour

description: Library name: VA0000750001

value: Day 2

value: 24 hour

value: VeryMild


title: Whole Blood, ID18, D1, Placebo, Baseline

value: ISRR

value: Severe


title: AB19769

description: Library name: Sample 142

value: lung

value: aPD-1 CAR

value: peptide MOG


title: Whole Blood, ID17, M5, Booster, 2hour

value: Booster

value: Month 5

value: 2 hour

value: Allergic


title: AB14959

description:
Library name: Sample1641
MARS_v2

value: BM


title: Whole Blood, ID8, D2, Placebo, 6hour

description: Library name: VA0000740001

value: Whole Blood

value: female

value: Placebo

value: 6 hour


title: DRG culture, siJun, t=42h, rep4

city: San Francisco

first: Trent

middle: A.

last: Watkins

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

description: Library name: siJun_4

data_processing:
Kallisto paired-end quantification
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: A comma-separated values (.csv) file contains kallisto estimated counts for siRNA samples.
Supplementary files format and content: A comma-separated values (.csv) file contains kallisto estimated counts for mRNA samples.

source_name: primary adult dorsal root ganglia cell culture

growth_protocol: Dissociated cells cultured in Neurobasal-A medium with B27 supplement.

extract_protocol:
RNA was extracted using the Qiagen RNeasy micro kit (#74004).
Illumina Stranded mRNA Prep

treatment_protocol: Dharnafect 2-mediated transfection of Dharnacon ON-TARGETplus siRNA pools or custom mRNA generated by GenScript.

tag: cell type

tag: genotype

value: wildtype

value: siJun


title: AB19768

description: Library name: Sample 141

value: spinal cord

tag: gate

value: CD45.1+ mCherry+

tag: treatment


title: Whole Blood, ID17, M5, Booster, 35min

value: 35 min

tag: batch


title: Whole Blood, ID8, D2, Placebo, 2hour

description: Library name: VA0000730001

tag: individual

value: Day 2

value: ISRR

value: VeryMild


title: AB14957

description:
Library name: Sample1640
MARS_v2

value: PC


title: AB19767

description: Library name: Sample 140

value: aPD-1 CAR

tag: eae model

value: peptide MOG


title: AB12106

description: Library name: Sample 100

value: Untreated (PBS)


title: AB14955

description:
Library name: Sample1639
MARS_v2

value: BM


title: Whole Blood, ID17, M5, Booster, Baseline

tag: Sex

value: Booster

value: Month 5

value: Baseline

value: Allergic


title: Whole Blood, ID8, D2, Placebo, 35min

description: Library name: VA0000720001

value: Whole Blood

value: female

value: Placebo

tag: time

tag: timepoint


title: AB19766

description: Library name: Sample 139

tag: tissue

value: brain


title: Whole Blood, ID9, D1, Placebo, 2hour

description: Library name: VA0000790052

value: Day 1

value: 2 hour

tag: reaction type


title: Whole Blood, ID17, D2, Placebo, 24hour

value: Day 2

value: 24 hour

value: ISRR

value: Severe


title: AB14954

description:
Library name: Sample1638
MARS_v2

value: PC


title: AB19765

description: Library name: Sample 138

value: CD45.1+ mCherry+

tag: mouse

tag: score

value: aPD-1 CAR

value: peptide MOG


title: Whole Blood, ID17, D2, Placebo, 6hour

tag: age

value: 6 hour


title: Whole Blood, ID8, D1, Vaccine, 6hour

description: Library name: VA0000700001

value: Vaccine

tag: reaction type_severity

value: Mild


title: Whole Blood, ID17, D2, Placebo, 2hour

tag: day

tag: reaction type severity


title: AB14953

description:
Library name: Sample1637
MARS_v2

value: BM


title: Whole Blood, ID8, D1, Vaccine, 2hour

description: Library name: VA0000690001

value: Whole Blood

value: female


title: Lean Control rep 6

description: Library name: DEX-27061

data_processing:
Data was processed using nf-core/rnaseq (v3.14.0) of the nf-core collection of workflows, using STAR (v2.7.9a) and salmon (v1.10.1) for alignment of reads to the GRCm39 mouse reference genome and quantification of Gencode (M31) gene models, respectively.
UMIs were extracted from each aligned reads using the following regular expression: ^(?P.{6})(?P.{4}).* . The following extra arguments were provided to STAR to account for the 3’ tag nature of the library: --alignIntronMax 1000000 --alignIntronMin 20 -- alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 -- outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA. Salmon quantification was performed without length correction by specifying the –noLengthCorrection argument.
Downstream analysis was performed with the edgeR (v4.6.2) Bioconductor package using R v4.5.1. Normalized log2 transformed counts per million (CPMs) were obtained by subsetting the raw count matrix to protein-coding genes, calculating library size factors with edgeR's normLibSizes function using the TMM method, and exporting CPMs with edgeR's cpm function.
Assembly: GRCm39
Supplementary files format and content: excel file with four worksheets containing 1) sample annotations, 2) gene annotations, 3) raw gene-level counts and 4) TMM normalized counts (log2 counts per million)

source_name: hypothalamus

growth_protocol: Adult male wild-type C57BL/6JGpt mice were maintained on a high-fat diet from 6 weeks of age for at least 16 weeks to induce obesity prior to study initiation. Non-dosed background-, sex, and age-matched chow-fed mice were included as non-obese (lean) controls.

extract_protocol:
To isolate RNA, each hypothalamus tissue sample was placed in a 1.5 mL centrifuge tube containing a 3 mm steel bead (Fisher, 50-206-7603). Subsequently, 350 µL of RLT Plus buffer (Qiagen) supplemented with β-mercaptoethanol was added to the tube. Homogenization was performed using a Tissuelyser II (Qiagen) for two cycles at 25 Hz for 3 minutes each. Following homogenization, samples were centrifuged at 16,000 × g for 3 minutes, and the clarified lysates were collected. RNA isolation was then carried out according to the manufacturer’s protocol using the RNeasy Plus Micro Kit (Qiagen, Cat. No. 74034). Purified RNA was transferred to 1.5 mL DNA LoBind tubes (Eppendorf), snap-frozen on dry ice, and stored at −80 °C until further processing for RNA sequencing.
For each of the 18 independent biological samples, a sequencing library was prepared with the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173). The UMI second strand synthesis module was used to introduce unique molecular identifiers (UMIs), following the protocol defined by the manufacturer.  Briefly, oligo dT primers were hybridized to total RNA for reverse transcription, followed by RNA removal after first strand synthesis. UMIs were introduced during second strand synthesis and cDNA was purified using magnetic beads, followed by 18 cycles of PCR with dual indexes and PCR purification. Library quantity and quality were assessed with Qubit™ 1X dsDNA HS Assay Kits (Invitrogen Q33231) and Bioanalyzer High Sense DNA chip (Agilent 5067-4626). Libraries were pooled in equimolar ratios, and the sequencing pool was purified with magnetic beads to remove residual adaptor dimers.

treatment_protocol: To minimize handling stress-induced weight changes, the mice were acclimated by twice daily oral gavage of the vehicle solution for 14 consecutive days prior to study start. One day before dosing initiation, DIO animals underwent body composition assessment using MRI before being randomized into treatment groups to ensure balanced baseline body weight and body composition. NLRP3 inhibitor TN-783 (50 mg/kg) or its vehicle was administered by oral gavage twice daily for 29 days. Body weight was measured daily throughout the study. The lean controls did not receive drug treatment.

value: hypothalamus

tag: organ

value: brain

value: male

tag: strain

value: Untreated

tag: diet

value: Control

tag: replicate

tag: rin


title: Whole Blood, ID17, D2, Placebo, 35min

tag: individual

tag: treatment

value: Placebo

value: Day 2

value: 35 min

value: ISRR

tag: batch


title: Whole cell, grown to mid log phase, RNA replicate 2 [SC6]

city: Glasgow

first: Paul

last: Hoskisson

state: Glasgow

address: Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street

department: SIPBS

country: United Kingdom

institute: University of Strathclyde

data_processing:
Salmon was used to generate quantification files.
DEseq2 was used for differential comparison.
R scripts used are available at https://github.com/PaulHoskisson/industrial-lineage-of-S.clavuligerus
For SC3-SC5, SC2 was used for reference and indicated below
Assembly: SC2_19-01-22_snippy.fa
Supplementary files format and content: Salmon qunatification files

organism: Streptomyces clavuligerus

growth_protocol: S. clavuligerus SC2-SC6 were grown in 250 ml Erlenmeyer flasks in 50 ml Tryptone soy broth (TSB; Oxoid) from ~1x 108 spore stocks, in triplicate, at 26 oC with shaking at 250 rpm.  After 48 hrs, cells were centrifuged at 4000 x g, and resuspended at an OD600nm of 0.4 and 2 ml inoculated into fresh medium.  Samples were grown to late exponential phase (~48 hrs).  Samples (1 ml of culture) were centrifuged at max speed (16,160 x g) in 2 ml screw capped tubes and resuspended in 1 ml of RNA-later (~5 volumes to 100-200 µL of biomass) and stored at -20oC until extraction (a minimum of 30 minutes).

extract_protocol:
Samples were centrifuged, supernatant removed and resuspended in 300 µL TE buffer (Tris-HCl 50 mM, EDTA 20 mM) with 100 mg\mL lysozyme and incubated at 30oC for 30 minutes.  To each sample, 50 µL 10% SDS was added and mixed, then 85 µL of 5M NaCl and mixed.  Trizol was added (1 mL) to each, vortexed for 15 seconds and centrifuged for 10 minutes.  The top, clear, colourless aqueous phase was removed and combined with 300 µL chloroform, vortexed and centrifuged.  The upper aqueous phase was removed and passaged through Qiagen RNeasy kit following the manufacturers instructions.  On column DNase treatment (using Qiagen RNase free DNase) following manufacturers instructions (in brief: following first was with RW1, 10 µL DNase was added to 70 µL RDD buffer and incubated on column at RT for 20 minutes). Samples were resuspended in 90 µL RNase free water and an off column DNase Treatment carried out (following manufacturers instructions: to each sample, add 7.5 (in brief: following first was with RW1, 10 µL DNase was added to 70 µL RDD buffer and incubated on column at RT for 20 minutes) RDD buffer and 2.5 µL DNase, incubate at room temperature for 20 minutes, add 100 µL RLT buffer and 100 µL 90% EtOH and apply to fresh column).  Samples were passed through a second round of RNeasy kit extraction minus DNase steps.  Samples were then submitted to Novogene for sequencing and the following broad steps taken.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was then end repaired, poly A-tailed, adapters ligated, size selected, amplified, and purified and sequenced.

treatment_protocol: Samples treated same, genotype is what is being investigated


title: Whole cell, grown to mid log phase, RNA replicate 3 [SC6_3]


title: Lean Control rep 5

description: Library name: DEX-27060

tag: Sex


title: Whole Blood, ID8, D1, Vaccine, 35min

description: Library name: VA0000680001

tag: tissue

tag: time

value: Day 1

tag: timepoint


title: Whole cell, grown to mid log phase, RNA replicate 1 [SC6_1]


title: Lean Control rep 4

description: Library name: DEX-27059


title: Whole Blood, ID8, D1, Vaccine, Baseline

description: Library name: VA0000670001

value: Baseline

tag: reaction type


title: Whole Blood, ID17, D1/D2, Vaccine/Placebo, 24hour/Baseline

tag: age

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: Allergic/ISRR

value: None/Severe


title: AB19776

description: Library name: Sample 149

value: spinal cord

tag: gate

tag: mouse

tag: score

tag: eae model

value: peptide MOG


title: Whole Blood, ID17, D1, Vaccine, 6hour

value: female

value: Vaccine

tag: day

value: 6 hour

value: Allergic

tag: reaction type severity


title: Whole Blood, ID7, M5, Booster, 2hour

description: Library name: VA0001580012

value: Whole Blood

value: Booster

value: Month 5

value: 2 hour

tag: reaction type_severity

value: Moderate


title: Whole cell, grown to mid log phase, RNA replicate 3 [SC5_3]

tag: strain


title: Lean Control rep 3

description: Library name: DEX-27058

value: hypothalamus

tag: organ

value: brain

value: male

value: Untreated

tag: diet

value: Control

tag: replicate

tag: rin


title: Lean Control rep 2

description: Library name: DEX-27057

tag: tissue

tag: Sex

tag: treatment


title: Whole Blood, ID7, M5, Booster, 35min

description: Library name: VA0001570012

tag: individual

tag: time

tag: timepoint

value: 35 min

tag: reaction type

value: ISRR

tag: batch


title: Whole cell, grown to mid log phase, RNA replicate 2 [SC5]


title: Whole Blood, ID17, D1, Vaccine, 2hour

tag: age

value: Day 1


title: Whole cell, grown to mid log phase, RNA replicate 1 [SC5_1]


title: Lean Control rep 1

description: Library name: DEX-27056


title: Whole Blood, ID7, M5, Booster, Baseline

description: Library name: VA0001560016

value: female

value: Baseline


title: Whole Blood, ID17, D1, Vaccine, Baseline

value: Vaccine

tag: day


title: Whole cell, grown to mid log phase, RNA replicate 3 [SC4_3]


title: DIO+ TN-783 rep 6

description: Library name: DEX-27055

value: DIO


title: Whole Blood, ID7, D2, Vaccine, 24hour

description: Library name: VA0000650032

value: Whole Blood

value: Day 2

value: 24 hour

value: VeryMild


title: Whole Blood, ID16, M5, Booster, 2hour

value: Booster

value: Month 5

value: 2 hour

tag: reaction type severity

value: Mild


title: Whole Blood, ID16, M5, Booster, 35min


title: DIO+ TN-783 rep 5

description: Library name: DEX-27054

value: hypothalamus

value: brain

value: male


title: Whole cell, grown to mid log phase, RNA replicate 2 [SC4]


title: Whole Blood, ID7, D2, Vaccine, 6hour

description: Library name: VA0000640028

value: 6 hour

value: ISRR

tag: reaction type_severity


title: Whole Blood, ID16, D2, Placebo, 24hour

value: female

value: Placebo

value: Severe


title: DIO+ Vehicle rep 6

description: Library name: DEX-27053

tag: strain

value: Vehicle

value: DIO


title: Whole cell, grown to mid log phase, RNA replicate 1 [SC4_1]


title: DIO+ Vehicle rep 5

description: Library name: DEX-27052

tag: organ


title: Whole Blood, ID7, D2, Vaccine, 2hour

description: Library name: VA0000630053

value: Whole Blood

value: Vaccine

value: Day 2


title: Whole Blood, ID7, D2, Vaccine, 35min

description: Library name: VA0000620035

value: 35 min

value: VeryMild


title: DIO+ TN-783 rep 4

description: Library name: DEX-27051

tag: diet


title: Whole Blood, ID16, D2, Placebo, 2hour

value: 2 hour


title: Whole cell, grown to mid log phase, RNA replicate 2 [SC3]


title: Whole Blood, ID7, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0000610057

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Severe/VeryMild


title: Whole cell, grown to mid log phase, RNA replicate 3 [SC3_3]


title: DIO+ TN-783 rep 3

description: Library name: DEX-27050

value: hypothalamus

value: brain

value: male

tag: replicate


title: Whole Blood, ID16, D2, Placebo, 35min

value: female

value: Placebo

value: ISRR

value: Severe


title: Whole cell, grown to mid log phase, RNA replicate 1 [SC3_1]


title: Whole Blood, ID7, D1, Placebo, 6hour

description: Library name: VA0000600028

value: Whole Blood

value: Day 1

value: 6 hour


title: Whole Blood, ID8, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0000710001

value: Vaccine/Placebo

value: Mild/VeryMild


title: DIO+ Vehicle rep 4

description: Library name: DEX-27049

value: Vehicle

value: DIO

tag: rin


title: Whole Blood, ID16, D1/D2, Vaccine/Placebo, 24hour/Baseline

value: Day 1/Day 2

value: 24 hour/Baseline

value: Moderate/Severe


title: Whole cell, grown to mid log phase, RNA replicate 3 [SC2_3]


title: DIO+ Vehicle rep 3

description: Library name: DEX-27048

tag: tissue

value: hypothalamus


title: Whole cell, grown to mid log phase, RNA replicate 2 [SC2]


title: Whole Blood, ID7, D1, Placebo, 35min

description: Library name: VA0000580035

tag: Sex

value: 35 min


title: Whole Blood, ID16, D1, Vaccine, 6hour

tag: treatment

value: Vaccine

value: Moderate


title: Whole Blood, ID7, D1, Placebo, 2hour

description: Library name: VA0000590053

tag: individual

value: female

value: Placebo

value: 2 hour


title: DIO+ TN-783 rep 2

description: Library name: DEX-27047

value: brain

value: male


title: Whole cell, grown to mid log phase, RNA replicate 1 [SC2_1]


title: Whole Blood, ID7, D1, Placebo, Baseline

description: Library name: VA0000570057

value: Whole Blood

tag: time

value: Day 1

value: Baseline

value: ISRR

value: Severe


title: Whole Blood, ID16, D1, Vaccine, 2hour

tag: timepoint


title: Whole Blood, ID16, D1, Vaccine, 35min

tag: reaction type


title: DIO+ TN-783 rep 1

description: Library name: DEX-27046

value: DIO


title: SC5314, 24 hr, 1.5% AA, rep 2

city: Merced

first: Clarissa

last: Nobile

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

description: Library name: MG6RPMI_AA2

data_processing:
Single-end reads were trimmed using bbduk (v39.10), and quality was assessed using FastQC (v0.11.5)
Gene annotations were supplemented with 3’-UTR annotations and trimmed reads were mapped using STAR (v2.7.11b)
Differential expression analysis was performed using DESeq2 (v1.44.0).
Assembly: A21
Supplementary files format and content: tab-delimited txt file contains transcript abundance counts for all samples.

organism: Candida albicans

source_name: Biofilm

growth_protocol: C. albicans overnight cultures washed in 1x PBS. Cells were counted using a hemocytometer and suspensions were adjusted to 1x10^6 cells/mL in RPMI-1640 or RPMI-1640 with amino acids, and 100 µL of each suspension was inoculated per well. Plates were incubated at 37 °C for 90 minutes to allow for adherence. Biofilm culture wells were washed 1x with phosphate buffered saline (PBS) to remove loosely adhered cells, and plates were incubated for 24 hours at 37 °C.

extract_protocol:
Total RNA was extracted using the Invitrogen RiboPure RNA Purification Kit according to the manufacturer’s instructions. Two biological replicates of 1.5% AA in RPMI-1640 treated samples and corresponding RPMI-1640 alone controls were used for downstream analysis.
RNA-seq libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and sequenced (single-end, 101 bp) on an Illumina HiSeq3000 platform.

treatment_protocol: Cells were grown in RPMI-1640 (control) or RPMI-1640 with amino acids (treatment)

tag: cell type

value: Biofilm


title: Whole Blood, ID13, M5, Booster, 2hour

description: Library name: VA0001960056

tag: age

value: Booster

value: Month 5

value: Mild

tag: batch


title: DIO+ Vehicle rep 2

description: Library name: DEX-27045

value: hypothalamus

value: Vehicle


title: SC5314, 24 hr, 1.5% AA, rep 1

description: Library name: MG5RPMI_AA1


title: Whole Blood, ID16, D1, Vaccine, Baseline

value: female

value: Vaccine

tag: day

tag: reaction type severity

value: Moderate


title: Whole Blood, ID13, M5, Booster, 35min

description: Library name: VA0001950056

value: 35 min

tag: reaction type_severity


title: DIO+ Vehicle rep 1

description: Library name: DEX-27044

tag: organ

value: brain

value: male

tag: strain


title: SC5314, 24 hr, control, rep 2

description: Library name: MG2RPMI2

value: Control


title: Whole Blood, ID13, M5, Booster, Baseline

description: Library name: VA0001940056

value: Whole Blood

value: Baseline


title: Whole Blood, ID11, M5, Booster, 2hour

value: 2 hour

value: ISRR


title: Pool 2B, CMO

extract_protocol:
For each animal, three-quarters of the brain, excluding the olfactory bulb and cerebellum, was dissociated into a single-cell suspension following the Miltenyi Adult Mouse Brain Dissociation protocol (Miltenyi, 130-107-677) with modifications. Anisomycin (2 µM final concentration), Actinomycin D (5 µM final concentration), and Hyaluronidase Type I-S (5,600 U/mL final concentration) were added to the Miltenyi Enzyme Mix 1 to facilitate extracellular matrix breakdown and inhibit transcriptional and translational activity. Single-cell suspensions were co-labeled with FC block, CD45, CD11b, CD44, and Ly6G (1:100 dilution) for 30 minutes on ice. Following a washing step, equal numbers of cells from each animal were also labeled with individual Cell Multiplexing Oligos (CMO, 10X Genomics, 1000261) per the manufacturer’s protocol, substituting the PBS wash buffer with NbActiv-1 + 1% BSA. The same number of labelled cells from each animal was pooled and CD11b+CD45−Ly6G− primary microglia were isolated from the pool using FACS. Each microglia pool was loaded onto two Chromium microfluidic chips G, following the Chromium NextGEMS Single Cell 3' v3.1 Cell Multiplexing RevB User Guide (10X Genomics, CG000388), targeting an estimated capture of 3,000 microglia per animal.
After reverse transcription, GEM purification, and cDNA amplification, the amplified material was split into two fractions: 3' Gene Expression (GEX) DNA and Cell Multiplexing (CMO) DNA, using a dual-side size selection bead purification. Five microliters of the CMO DNA was PCR-amplified to introduce Illumina sequencing indices, while one-quarter of the GEX DNA was used for library preparation following the user guide. For each cohort, GEX libraries were pooled in equimolar amounts and subjected to a QC sequencing run on an Illumina MiSeq to determine the number of captured cells. Based on the MiSeq results, the libraries were re-pooled along with the CMO libraries, and sequenced on an Illumina NovaSeq 6000 instrument (28 × 10 × 10 × 90 cycles) at SeqMatic (Fremont, CA, USA), targeting a read depth of 50,000 reads per cell for mRNA transcripts and 5,000 reads per cell for demultiplexing CellPlex oligos.

tag: region

value: forebrain

value: primary microglia

tag: genotype

value: WT

value: 17 months

tag: pool

tag: library type

value: CMO


title: SC5314, 24 hr, control, rep 1

description: Library name: MG1RPMI1

value: Biofilm

tag: treatment


title: Whole Blood, ID11, M5, Booster, 35min

tag: individual

tag: Sex

value: female

value: Booster

value: Month 5

value: Mild


title: Whole Blood, ID13, D2, Placebo, 24hour

description: Library name: VA0000990005

tag: tissue

value: Placebo

tag: time

value: Day 2

tag: timepoint

value: 24 hour


title: DPN6

city: Richardson

first: Diana

last: Tavares-Ferreira

address: 800 W Campbell Rd

department: Department of Neuroscience

institute: University of Texas at Dallas

description:
Library name: DPN6
DPN sural nerve samples were obtained from patients undergoing lower limb amputation for nonreconstructable tissue, osteomyelitis, or critical limb ischemia. Tissue was placed in a sterile specimen cup, flash frozen in liquid nitrogen, and stored at −80 °C. miRNA was extracted and sequenced in NovaSeqX at Psomagen.

library_source: other

data_processing:
Raw data were processed with miRNA-Analysis pipeline: https://github.com/utdal/miRNA-Analysis
Assembly: GRCh38.p13
Supplementary files format and content: raw and normalized miRNA counts

molecule: other

source_name: sural nerve

extract_protocol:
Human sural nerves were collected from patients undergoing lower limb amputation or cross-facial nerve grafting procedures.
Purification of miRNA was done following the protocol for Qiagen miRNAeasy MicroKit for all 12 samples. Library preparation was completed using Nextflex Small RNA Library v4 per protocol and sequencing was done on NovaSeq X (Psomagen).

value: sural nerve


title: Pool 2A, CMO

description:
Library name: Pool_2A_CMO
Pool 2A, primary microglia from 12 animals, cell multiplexing oligo library

value: brain

tag: cell type

tag: age

value: male


title: Whole Blood, ID13, D2, Placebo, 6hour

description: Library name: VA0000550005

value: Whole Blood

value: 6 hour

tag: reaction type

value: ISRR

tag: batch


title: Pool 1B, CMO

value: forebrain

value: primary microglia

value: WT


title: Whole Blood, ID11, M5, Booster, Baseline

tag: day

value: Baseline

tag: reaction type severity


title: Whole Blood, ID13, D2, Placebo, 2hour

description: Library name: VA0000540030

value: female

value: 2 hour

tag: reaction type_severity


title: Whole Blood, ID11, D2, Placebo, 24hour


title: DPN5

description:
Library name: DPN5
DPN sural nerve samples were obtained from patients undergoing lower limb amputation for nonreconstructable tissue, osteomyelitis, or critical limb ischemia. Tissue was placed in a sterile specimen cup, flash frozen in liquid nitrogen, and stored at −80 °C. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID11, D2, Placebo, 6hour


title: Pool 1A, CMO

tag: region

value: 17 months

tag: strain

value: CMO


title: DPN4

description:
Library name: DPN4
DPN sural nerve samples were obtained from patients undergoing lower limb amputation for nonreconstructable tissue, osteomyelitis, or critical limb ischemia. Tissue was placed in a sterile specimen cup, flash frozen in liquid nitrogen, and stored at −80 °C. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID13, D2, Placebo, 35min

description: Library name: VA0000530012

value: Placebo

value: 35 min

value: Mild


title: Pool 2B, GEX

tag: genotype

tag: pool

value: mRNA


title: DPN3

description:
Library name: DPN3
DPN sural nerve samples were obtained from patients undergoing lower limb amputation for nonreconstructable tissue, osteomyelitis, or critical limb ischemia. Tissue was placed in a sterile specimen cup, flash frozen in liquid nitrogen, and stored at −80 °C. miRNA was extracted and sequenced in NovaSeqX at Psomagen.

value: sural nerve


title: Whole Blood, ID13, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0000520030

tag: treatment

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/ISRR

value: None/Mild


title: Pool 2A, GEX

description:
Library name: Pool_2A_GEX
Pool 2A, primary microglia from 12 animals, gene expression library

value: brain

value: forebrain

value: primary microglia

value: male

tag: library type


title: DPN2

description:
Library name: DPN2
DPN sural nerve samples were obtained from patients undergoing lower limb amputation for nonreconstructable tissue, osteomyelitis, or critical limb ischemia. Tissue was placed in a sterile specimen cup, flash frozen in liquid nitrogen, and stored at −80 °C. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID11, D2, Placebo, 35min

tag: individual

tag: Sex

value: female

value: Day 2

value: ISRR


title: Whole Blood, ID13, D1, Vaccine, 6hour

description: Library name: VA0000510005

tag: tissue

value: Whole Blood

value: Vaccine

tag: time

value: Day 1

value: 6 hour


title: Whole Blood, ID11, D2, Placebo, 2hour

value: Placebo

tag: timepoint

value: 2 hour

value: Mild


title: Whole Blood, ID11, D1/D2, Vaccine/Baseline, 24hour/Baseline

tag: age

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/ISRR

value: Moderate/Mild


title: Pool 1B, GEX

value: brain

value: forebrain

tag: cell type

value: primary microglia

value: WT

value: 17 months

value: mRNA


title: DPN1

description:
Library name: DPN1
DPN sural nerve samples were obtained from patients undergoing lower limb amputation for nonreconstructable tissue, osteomyelitis, or critical limb ischemia. Tissue was placed in a sterile specimen cup, flash frozen in liquid nitrogen, and stored at −80 °C. miRNA was extracted and sequenced in NovaSeqX at Psomagen.

value: sural nerve

tag: batch


title: Whole Blood, ID13, D1, Vaccine, 2hour

description: Library name: VA0000500030

value: Whole Blood

value: female

value: Vaccine

value: Day 1

tag: reaction type


title: Pool 1A, GEX

value: male


title: Whole Blood, ID11, D1, Vaccine, 6hour

tag: day

value: 6 hour

value: ISRR

tag: reaction type severity

value: Moderate


title: Control6

description:
Library name: Control6
Control sural nerve samples were obtained from patients undergoing cross facial nerve grafting for facial paralysis. The nerve was harvested through a 3 cm incision between the lateral malleolus and Achilles tendon and excised by cutting the proximal and distal ends. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID13, D1, Vaccine, 35min

description: Library name: VA0000490012

value: 35 min

tag: reaction type_severity


title: AB14178

description:
Library name: Sample1605
MARS_v2

value: BM

tag: gate

value: PC


title: Whole Blood, ID11, D1, Vaccine, 2hour

value: 2 hour


title: Deep water biological replicate 2

city: zabol

first: yasoub

last: shiri

department: agricultur

country: Iran

institute: Rizabol

description: Library name: T2

data_processing:
Raw sequencing reads were quality assessed and adapter sequences were removed using CLC Genomics Workbench version 23.0.
The first 15 nucleotides, ambiguous nucleotides, low-quality bases and duplicate reads were removed during quality trimming.
High-quality reads were mapped to the Dunaliella salina Dunsal1 v2 reference genome (GenBank assembly accession GCA_002284615.2) using CLC Genomics Workbench.
Gene-level raw read counts were generated from the mapped reads using the Create Expression Values tool in CLC Genomics Workbench.
Differential gene expression analysis was performed in R (version 4.5.1) using the DESeq2 package with Benjamini-Hochberg correction for multiple testing.
Genes with an adjusted P value < 0.05 and an absolute log2 fold change ≥ 1 were considered differentially expressed.
Assembly: Dunaliella salina Dunsal1 v2 reference genome (GenBank assembly accession GCA_002284615.2)
Supplementary files format and content: The processed data file contains the raw gene count matrix used for differential expression analysis. Rows represent genes (GeneID) and columns represent the four RNA-seq samples (two control and two deep water-treated biological replicates). Count data were analyzed using DESeq2.

organism: Dunaliella salina

source_name: whole culture

growth_protocol: Dunaliella salina cultures were maintained under controlled laboratory conditions in standard culture medium containing 30 g/L NaCl. Cultures were grown under a 16 h light/8 h dark photoperiod at 25 ± 2°C with continuous aeration until reaching the exponential growth phase.

extract_protocol:
Total RNA was extracted from Dunaliella salina cultures using the RNX-Plus reagent according to the manufacturer's instructions. RNA quantity and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared following the Illumina standard library preparation protocol.

treatment_protocol: Exponentially growing cultures were divided into control and treatment groups. Control cultures were maintained in the standard culture medium (30 g/L NaCl), whereas treatment cultures were cultivated in Sistan deep water under identical environmental conditions. Cells were harvested at the designated sampling time for total RNA extraction and RNA sequencing.

value: whole culture

value: vegetative cells

tag: genotype

value: wild type

value: Deep water


title: Whole Blood, ID13, D1, Vaccine, Baseline

description: Library name: VA0000480034

value: Baseline


title: Control5

description:
Library name: Control5
Control sural nerve samples were obtained from patients undergoing cross facial nerve grafting for facial paralysis. The nerve was harvested through a 3 cm incision between the lateral malleolus and Achilles tendon and excised by cutting the proximal and distal ends. miRNA was extracted and sequenced in NovaSeqX at Psomagen.

value: sural nerve


title: Whole Blood, ID11, D1, Vaccine, 35min

value: female


title: Control4

description:
Library name: Control4
Control sural nerve samples were obtained from patients undergoing cross facial nerve grafting for facial paralysis. The nerve was harvested through a 3 cm incision between the lateral malleolus and Achilles tendon and excised by cutting the proximal and distal ends. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID5, M5, Booster, 2hour

description: Library name: VA0001390012

value: Whole Blood

value: Booster

value: Month 5

value: VeryMild


title: Control biological replicate 2

description: Library name: C2

value: Control


title: Control3

description:
Library name: Control3
Control sural nerve samples were obtained from patients undergoing cross facial nerve grafting for facial paralysis. The nerve was harvested through a 3 cm incision between the lateral malleolus and Achilles tendon and excised by cutting the proximal and distal ends. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID11, D1, Vaccine, Baseline

value: Vaccine

value: Day 1

value: ISRR

value: Moderate


title: Control2

description:
Library name: Control2
Control sural nerve samples were obtained from patients undergoing cross facial nerve grafting for facial paralysis. The nerve was harvested through a 3 cm incision between the lateral malleolus and Achilles tendon and excised by cutting the proximal and distal ends. miRNA was extracted and sequenced in NovaSeqX at Psomagen.


title: Whole Blood, ID5, M5, Booster, 35min

description: Library name: VA0001380012

value: 35 min


title: Deep water biological replicate 1

description: Library name: T1

value: whole culture


title: Control biological replicate 1

description: Library name: C1

value: vegetative cells


title: Whole Blood, ID5, M5, Booster, Baseline

description: Library name: VA0001370016


title: Whole Blood, ID15, M5, Booster, 2hour

value: 2 hour


title: Whole Blood, ID15, M5, Booster, 35min


title: HiC GN, top1_2b_KD, FANS, IVE+day8, rep3

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description: Library name: Hi-C_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

library_source: genomic

data_processing:
Hi-C reads were aligned to the mm10 reference genome with Bowtie2 and HiC-Pro. Uniquely mapped paired-end reads were assigned to MboI restriction fragments and valid pairs with a minimum genomic distance of 1Kb were filtered for PCR duplicates. Interaction matrices were normalized using Knight-Ruiz (KR) matrix balancing and observed divided by expected (o/e) transformation and visualized using hic files in Juicebox
Assembly: mm10
Supplementary files format and content: hic files

molecule: genomic DNA

source_name: cerebellum

extract_protocol:
The cerebellum from postnatal day 6 or 22 mice or cerebellar vermis from mice at day 1 to 28 after electroporation were removed and microdissected. For electroporated samples, electroporation efficiency was assessed under a stereomicroscope and mCherry+/NeuN+ nuclei were enriched using fluorescence activated nuclei sorting with a SH800S cell sorter (Sony). The genomic DNA was digested with MboI and re-ligated after the biotin fill-in reaction, followed by sonication. The fragmented DNA was then subjected to biotin-IP.
Hi-C libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit (#E7645).

treatment_protocol: For in vivo electroporation (IVE), the cerebellum of P6 mouse pups was electroporated with the pCAG-mCherry-NLS plasmid together with a vector encoding U6-sgRNA targeting the indicated genes or control sequences and dissected at day 1 to 28 after electroporation.

value: cerebellum

value: granule neurons

value: top1/2b sgRNAs in dCas9-KRAB


title: Whole Blood, ID5, D2, Placebo, 24hour

description: Library name: VA0000450027

value: female

value: Placebo

value: Day 2

value: 24 hour


title: Control1

description:
Library name: Control1
Control sural nerve samples were obtained from patients undergoing cross facial nerve grafting for facial paralysis. The nerve was harvested through a 3 cm incision between the lateral malleolus and Achilles tendon and excised by cutting the proximal and distal ends. miRNA was extracted and sequenced in NovaSeqX at Psomagen.

value: sural nerve


title: HiC GN, top1_2b_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: HEK293T_U2AF2_CnR_Rep4_(241016_WW_HsEc_WW1254)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: HEK293T_U2AF2_CnR_Rep4
CUT&RUN targeting U2AF2 in HEK293T

data_processing:
1. We used cutadapt 4.4 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.5.7 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.17 "view" to extract properly paired reads from the alignments.
4. We used bedtools 2.30 "genomecov" to make a normalized count track which is the fraction of counts at each base pair scaled by the size of the reference sequence so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag-direct for whole cells with CUTAC  V.4 dx.doi.org/10.17504/protocols.io.x54v9mkmzg3e/v4
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: Abcam, ab37530


title: Whole Blood, ID5, D2, Placebo, 6hour

description: Library name: VA0000440027

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes for 221 study samples using the QIAsymphony PAXgene Blood RNA Kit and the QIAsymphony SP instrument (both Qiagen) according to the manufacturer instructions including DNase I digestion and Proteinase K treatment.  RNA concentration was determined by Quant-iT RiboGreen assay (ThermoFisher) using a Biotek Synergy H1 plate reader (Agilent Technologies) and RINs assessed using Agilent 4200 TapeStation (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA using Universal Plus mRNA-seq Kit with NuQuant Human Globin AnyDeplete kit (Tecan Genomics) on a Biomek Fx robot (Beckman). First, messenger RNA transcripts were captured, fragmented, and converted to complementary DNA. Following second-strand synthesis and end repair, DNA fragments were ligated with dual-indexed adapters compatible with the Illumina platform. Libraries were subjected to strand selection and removal of globin transcripts, followed by 14 cycles of amplification. Purified libraries were analyzed with the Biotek Synergy H1 plate reader and Agilent 4200 TapeStation (Agilent Technologies) to assess concentration and size distribution, respectively, then normalized and pooled for sequencing. Final molarity of the pool was determined by quantitative polymerase chain reaction using the KAPA library quantification kit (Roche). Paired-end sequencing was performed on the NextSeq 2000 (Illumina) using P3 300 cycles kits in 2 × 150-base pair (bp) format.

value: Whole Blood

tag: treatment

value: 6 hour


title: HiC GN, top1_2b_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_top1_2b_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: Whole Blood, ID15, M5, Booster, Baseline

value: Booster

value: Month 5

value: Baseline

value: ISRR

value: VeryMild


title: Whole Blood, ID15, D2, Vaccine, 24hour

value: Vaccine


title: HEK293T_U2AF2_CnR_Rep3_(241016_WW_HsEc_WW1253)

description:
Library name: HEK293T_U2AF2_CnR_Rep3
CUT&RUN targeting U2AF2 in HEK293T


title: Whole Blood, ID5, D2, Placebo, 2hour

description: Library name: VA0000430052

value: 2 hour


title: HiC GN, p300_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_p300_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: cerebellum

value: granule neurons

value: p300 sgRNAs in dCas9-KRAB


title: Whole Blood, ID5, D2, Placebo, 35min

description: Library name: VA0000420034

value: female

value: Placebo

value: 35 min


title: HEK293T_U2AF2_CnR_Rep2_(241016_WW_HsEc_WW1252)

description:
Library name: HEK293T_U2AF2_CnR_Rep2
CUT&RUN targeting U2AF2 in HEK293T


title: Whole Blood, ID15, D2, Vaccine, 2hour

value: Day 2


title: HiC GN, p300_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_p300_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: Whole Blood, ID15, D2, Vaccine, 6hour


title: HEK293T_U2AF2_CnR_Rep1_(241016_WW_HsEc_WW1251)

description:
Library name: HEK293T_U2AF2_CnR_Rep1
CUT&RUN targeting U2AF2 in HEK293T

value: Abcam, ab37530


title: Whole Blood, ID5, D1/D2, Vaccine/Placebo, 24hour/Baseline

description: Library name: VA0000410056

value: Whole Blood

value: Vaccine/Placebo

value: Day 1/Day 2

value: 24 hour/Baseline

value: ISRR/None

value: VeryMild/None


title: AB14025

description:
Library name: Sample1601
MARS_v2

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: BM

value: PC


title: HiC GN, p300_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_p300_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: Whole Blood, ID15, D2, Vaccine, 35min

value: Vaccine


title: HEK293T_H3K36me3_CnT_Rep4_(231128_WW_HsDm_WW868)

description:
Library name: HEK293T_H3K36me3_CnT_Rep4
CUT&Tag targeting H3K36me3 in K562

value: Epicypher, SKU:13-0058


title: Whole Blood, ID5, D1, Vaccine, 6hour

description: Library name: VA0000400027

data_processing:
Bulk RNA-seq FASTQ files were processed using the OpenOmics/RNA-seek (https://doi.org/10.5281/zenodo.13312679) v1.9.5 pipeline to run QC and quantify gene transcript counts.
Assembly: GRCh38
Supplementary files format and content: RSEM counts

value: Day 1

value: 6 hour

value: ISRR

value: VeryMild


title: Whole Blood, ID5, D1, Vaccine, 2hour

description: Library name: VA0000390038

value: female

value: 2 hour


title: Whole Blood, ID15, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: Placebo/Vaccine

value: None/None


title: HEK293T_H3K36me3_CnT_Rep3_(231128_WW_HsDm_WW847)

description:
Library name: HEK293T_H3K36me3_CnT_Rep3
CUT&Tag targeting H3K36me3 in K562


title: HEK293T_H3K36me3_CnT_Rep2_(231019_WW_HsDm_WW757)

description:
Library name: HEK293T_H3K36me3_CnT_Rep2
CUT&Tag targeting H3K36me3 in K562


title: AB14019

description:
Library name: Sample1597
MARS_v2


title: HiC GN, nup153_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_nup153_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: cerebellum

value: granule neurons

value: nup153 sgRNAs in dCas9-KRAB


title: HiC GN, nup153_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_nup153_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: Whole Blood, ID5, D1, Vaccine, 35min

description: Library name: VA0000380038

value: Whole Blood

value: 35 min


title: Whole Blood, ID15, D1, Placebo, 6hour

value: Placebo


title: HiC GN, nup153_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_nup153_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: Whole Blood, ID15, D1, Placebo, 2hour


title: Whole Blood, ID5, D1, Vaccine, Baseline

description: Library name: VA0000370056

value: Baseline


title: HEK293T_H3K36me3_CnT_Rep1_(231019_WW_HsDm_WW716)

description:
Library name: HEK293T_H3K36me3_CnT_Rep1
CUT&Tag targeting H3K36me3 in K562


title: 118 Baseline Bond 2JJ4_1 | 003 | Full ROI

city: Chapel hill

first: Brent

last: Hanks

state: North Carolina

address: 450 West Dr

department: Medicine

institute: UNC at Chapel Hill

description:
Library name: GE_118BaselineBond2JJ4.1.003
Formalin-fixed paraffin-embedded spatial transcriptome sequencing

data_processing:
A pan-cytokeratin IF marker was used to identify epithelial tumor tissue while CD8 and elastase IF markers were used to assess tumor-infiltrating CD8+ T cell and PMN/neutrophil cell populations
Human Whole Transcriptome Atlas probe was hybridized overnight, slides were washed twice in fresh 2X saline-sodium citrate (SSC, Sigma-Aldrich, S6639-1L) and loaded onto the GeoMx DSP.
UV light was used to cleave oligos that were then collected in a 96-well plate for library preparation and were sequenced on an Illumina NextSeq2000 by the UNC High-Throughput Sequencing Facility (HTSF)
All transcriptional data was analyzed using GeoMx DSP Data Analysis software
dimensionality reduction (PCA) and normalization techniques (Q3 normalization) were used to identify potential outliers
Assembly: GRCh38
Supplementary files format and content: Quantitative counts of genes or proteins  ( .dcc files)
Supplementary files format and content: GE_counts.csv
Supplementary files format and content: Hs_R_NGS_CTA_v1.0.pkc
Library strategy: Spatial Transcriptomics

source_name: Gastric tumor tissue

extract_protocol:
library preparation and were sequenced on an Illumina NextSeq2000
FFPE tissue samples were prepared

value: Gastric tumor tissue

tag: cd8+ count

value: Low

tag: neutrophil count

value: High

tag: clinical response

value: PD

value: baseline


title: K562_PolIISer2p_KASCnT_IP_Flavopiridol_Rep2_(241230_WW_HsDm_WW1465)

description:
Library name: K562_PolIISer2p_KASCnT_IP_Flavopiridol_Rep2
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells treated with Flavopiridol

value: Cell Signaling Technology, 13499S


title: HiC GN, med1_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_med1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

tag: tissue

value: med1 sgRNAs in dCas9-KRAB


title: Whole Blood, ID15, D1, Placebo, 35min

tag: individual

tag: Sex

value: female

value: Day 1


title: Whole Blood, ID4, M5, Booster, 2hour

description: Library name: VA0001440012

tag: age

value: Booster

tag: time

value: Month 5

tag: timepoint

value: 2 hour

value: Allergic


title: HiC GN, med1_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_med1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: cerebellum

tag: cell type

value: granule neurons


title: Whole Blood, ID15, D1, Placebo, Baseline

value: Placebo

tag: day

tag: reaction type

tag: batch


title: Whole Blood, ID4, M5, Booster, 35min

description: Library name: VA0001430012

value: Whole Blood

value: 35 min

tag: reaction type_severity


title: K562_PolIISer2p_KASCnT_IP_Flavopiridol_Rep1_(241230_WW_HsDm_WW1464)

description:
Library name: K562_PolIISer2p_KASCnT_IP_Flavopiridol_Rep1
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells treated with Flavopiridol


title: HiC GN, med1_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_med1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1

tag: genotype


title: K562_PolIISer2p_KASCnT_Input_Flavopiridol_Rep2_(241230_WW_HsDm_WW1481)

description:
Library name: K562_PolIISer2p_KASCnT_Input_Flavopiridol_Rep2
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells treated with Flavopiridol

tag: antibody


title: 118 Baseline Bond 2JJ4_1 | 002 | Full ROI

description:
Library name: GE_118BaselineBond2JJ4.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing

value: Gastric tumor tissue

value: Low

tag: treatment


title: Whole Blood, ID14, M5, Booster, 2hour

value: ISRR

tag: reaction type severity

value: VeryMild


title: HiC GN, lmna_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_lmna_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3

value: lmna sgRNAs in dCas9-KRAB


title: K562_PolIISer2p_KASCnT_Input_Flavopiridol_Rep1_(241230_WW_HsDm_WW1480)

description:
Library name: K562_PolIISer2p_KASCnT_Input_Flavopiridol_Rep1
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells treated with Flavopiridol

value: Cell Signaling Technology, 13499S


title: Whole Blood, ID14, M5, Booster, Baseline

value: female

value: Baseline


title: Whole Blood, ID4, M5, Booster, Baseline

description: Library name: VA0001420016

value: Booster


title: Whole Blood, ID4, D2, Placebo, 24hour

description: Library name: VA0000350027

value: Day 2

value: 24 hour

value: Moderate


title: K562_PolIISer2p_KASCnT_IP_C1_minus_biotin_Rep2_(241125_WW_Hs_WW1290)

description:
Library name: K562_PolIISer2p_KASCnT_IP_C1_minus_biotin_Rep2
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (-biotin+C1 streptavidin beads )


title: Whole Blood, ID4, D2, Placebo, 6hour

description: Library name: VA0000340034

value: 6 hour


title: Whole Blood, ID14, D2, Vaccine, 24hour

value: Vaccine

value: Severe


title: K562_PolIISer2p_KASCnT_IP_C1_minus_biotin_Rep1_(241125_WW_Hs_WW1280)

description:
Library name: K562_PolIISer2p_KASCnT_IP_C1_minus_biotin_Rep1
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (-biotin+C1 streptavidin beads )


title: Whole Blood, ID4, D2, Placebo, 35min

description: Library name: VA0000320034

value: Whole Blood

value: Placebo


title: HiC GN, etv1_KD, FANS, IVE+day8, rep4

description: Library name: Hi-C_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_4

value: cerebellum

value: granule neurons

value: etv1 sgRNAs in dCas9-KRAB


title: K562_PolIISer2p_KASCnT_IP_C1_plus_biotin_Rep2_(241125_WW_Hs_WW1289)

description:
Library name: K562_PolIISer2p_KASCnT_IP_C1_plus_biotin_Rep2
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (+biotin+C1 streptavidin beads )


title: K562_PolIISer2p_KASCnT_Input_C1_minus_biotin_Rep1_(241125_WW_Hs_WW1285)

description:
Library name: K562_PolIISer2p_KASCnT_Input_C1_minus_biotin_Rep1
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (-biotin+C1 streptavidin beads )


title: Whole Blood, ID4, D1, Vaccine, 6hour

description: Library name: VA0000300034

value: Day 1

value: Allergic


title: Whole Blood, ID4, D1, Vaccine, 2hour

description: Library name: VA0000290034

value: 2 hour


title: HiC GN, etv1_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3


title: Whole Blood, ID14, D1, Placebo, 6hour

value: female


title: HiC GN, etv1_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: K562_PolIISer2p_KASCnT_Input_C1_plus_biotin_Rep2_(241125_WW_Hs_WW1291)

description:
Library name: K562_PolIISer2p_KASCnT_Input_C1_plus_biotin_Rep2
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (+biotin+C1 streptavidin beads )

value: Cell Signaling Technology, 13499S


title: Whole Blood, ID4, D1, Vaccine, 35min

description: Library name: VA0000280034

value: 35 min


title: Whole Blood, ID14, D1, Placebo, 2hour


title: Whole Blood, ID4, D1, Vaccine, Baseline

description: Library name: VA0000270056

value: Baseline


title: K562_PolIISer2p_KASCnT_Input_C1_plus_biotin_Rep1_(241125_WW_Hs_WW1281)

description:
Library name: K562_PolIISer2p_KASCnT_Input_C1_plus_biotin_Rep1
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (+biotin+C1 streptavidin beads )


title: HiC GN, brd4_KD, FANS, IVE+day8, rep4

description: Library name: Hi-C_brd4_KD-FANS_IVEd8-dCas9_KRAB-pnd14_4

value: brd4 sgRNAs in dCas9-KRAB


title: K562_PolIISer2p_KASCnT_IP_T1_minus_biotin_Rep2_(241125_WW_Hs_WW1276)

description:
Library name: K562_PolIISer2p_KASCnT_IP_T1_minus_biotin_Rep2
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (-biotin+T1 streptavidin beads )


title: Whole Blood, ID14, D1, Placebo, 35min


title: Whole Blood, ID3, M5, Booster, 2hour

description: Library name: VA0001250012

value: Booster

value: Month 5

value: ISRR

value: VeryMild


title: HiC GN, brd4_KD, FANS, IVE+day8, rep3

description: Library name: Hi-C_brd4_KD-FANS_IVEd8-dCas9_KRAB-pnd14_3


title: K562_PolIISer2p_KASCnT_IP_T1_minus_biotin_Rep1_(241125_WW_Hs_WW1266)

description:
Library name: K562_PolIISer2p_KASCnT_IP_T1_minus_biotin_Rep1
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (-biotin+T1 streptavidin beads )


title: Whole Blood, ID3, M5, Booster, 35min

description: Library name: VA0001240012

value: Whole Blood


title: K562_PolIISer2p_KASCnT_Input_T1_minus_biotin_Rep2_(241125_WW_Hs_WW1278)

description:
Library name: K562_PolIISer2p_KASCnT_Input_T1_minus_biotin_Rep2
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (-biotin+T1 streptavidin beads )


title: Whole Blood, ID3, M5, Booster, Baseline

description: Library name: VA0001230016


title: Whole Blood, ID10, M5, Booster, 2hour

value: male


title: Whole Blood, ID10, M5, Booster, 35min


title: K562_PolIISer2p_KASCnT_Input_T1_minus_biotin_Rep1_(241125_WW_Hs_WW1271)

description:
Library name: K562_PolIISer2p_KASCnT_Input_T1_minus_biotin_Rep1
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (-biotin+T1 streptavidin beads )


title: Whole Blood, ID3, D2, Vaccine, 24hour

description: Library name: VA0000260034

value: Vaccine

value: Day 2

value: 24 hour

value: Moderate


title: K562_PolIISer2p_KASCnT_IP_T1_plus_biotin_Rep2_(241125_WW_Hs_WW1275)

description:
Library name: K562_PolIISer2p_KASCnT_IP_T1_plus_biotin_Rep2
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (+biotin+T1 streptavidin beads )


title: HiC GN, ctrl, FANS, IVE+day14, rep7

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_7

value: cerebellum

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB


title: Whole Blood, ID10, M5, Booster, Baseline


title: Whole Blood, ID3, D2, Vaccine, 6hour

description: Library name: VA0000250034

value: female

value: 6 hour


title: HiC GN, lmna_KD, FANS, IVE+day8, rep2

description: Library name: Hi-C_lmna_KD-FANS_IVEd8-dCas9_KRAB-pnd14_2

value: lmna sgRNAs in dCas9-KRAB


title: Whole Blood, ID10, D2, Vaccine, 24hour

value: Mild


title: Whole Blood, ID14, M5, Booster, 35min

value: Booster

value: 35 min


title: HiC GN, lmna_KD, FANS, IVE+day8, rep1

description: Library name: Hi-C_lmna_KD-FANS_IVEd8-dCas9_KRAB-pnd14_1


title: K562_PolIISer2p_KASCnT_IP_T1_plus_biotin_Rep1_(241125_WW_Hs_WW1265)

description:
Library name: K562_PolIISer2p_KASCnT_IP_T1_plus_biotin_Rep1
KAS-CUT&Tag IP targeting Pol II-Ser2P in K562 cells (+biotin+T1 streptavidin beads )

value: Cell Signaling Technology, 13499S


title: HiC GN, etv1_KD, FANS, IVE+day8, rep6

description: Library name: Hi-C_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_6

value: etv1 sgRNAs in dCas9-KRAB


title: Whole Blood, ID3, D2, Vaccine, 2hour

description: Library name: VA0000240034

value: Whole Blood

value: 2 hour

value: ISRR


title: HiC GN, etv1_KD, FANS, IVE+day8, rep5

description: Library name: Hi-C_etv1_KD-FANS_IVEd8-dCas9_KRAB-pnd14_5


title: K562_PolIISer2p_KASCnT_Input_C1_minus_biotin_Rep2_(241125_WW_Hs_WW1292)

description:
Library name: K562_PolIISer2p_KASCnT_Input_C1_minus_biotin_Rep2
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (-biotin+C1 streptavidin beads )


title: HiC GN, ctrl, FANS, IVE+day14, rep5

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_5


title: Whole Blood, ID14, D2, Vaccine, 2hour

value: Vaccine

value: Day 2

value: Severe


title: Whole Blood, ID14, D1/D2, Placebo/Vaccine, 24hour/Baseline

value: Placebo/Vaccine

value: Day 1/Day 2

value: 24 hour/Baseline

value: None/ISRR

value: None/Severe


title: Whole Blood, ID14, D2, Vaccine, 35min

value: female


title: Whole Blood, ID3, D2, Vaccine, 35min

description: Library name: VA0000230034

value: Moderate


title: Whole Blood, ID10, D2, Vaccine, 2hour

value: male

value: Mild


title: K562_PolIISer2p_KASCnT_Input_T1_plus_biotin_Rep1_(241125_WW_Hs_WW1267)

description:
Library name: K562_PolIISer2p_KASCnT_Input_T1_plus_biotin_Rep1
KAS-CUT&Tag input targeting Pol II-Ser2P in K562 cells (+biotin+T1 streptavidin beads )

value: Cell Signaling Technology, 13499S


title: HiC GN, ctrl, FANS, IVE+day14, rep4

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_4

value: cerebellum

value: granule neurons

value: ctrl sgRNAs in dCas9-KRAB


title: Whole Blood, ID3, D1/D2, Placebo/Vaccine, 24hour/Baseline

description: Library name: VA0000220034

value: Whole Blood

value: ISRR/ISRR

value: Mild/Moderate


title: K562_NPAT_KASCnT_IP_G2_Rep2_(250411_WW_Hs_WW1568)

description:
Library name: K562_NPAT_KASCnT_IP_G2_Rep2
KAS-CUT&Tag IP targeting NPAT in K562 G2 cells

value: Invitrogen, PA565419


title: HiC GN, ctrl, FANS, IVE+day14, rep3

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_3


title: Whole Blood, ID10, D2, Vaccine, 35min

value: Vaccine

value: Day 2

value: 35 min

value: ISRR


title: Whole Blood, ID3, D1, Placebo, 6hour

description: Library name: VA0000210034

value: Placebo

value: Day 1

value: 6 hour


title: HiC GN, ctrl, FANS, IVE+day14, rep2

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_2


title: K562_NPAT_KASCnT_IP_G2_Rep1_(250411_WW_Hs_WW1567)

description:
Library name: K562_NPAT_KASCnT_IP_G2_Rep1
KAS-CUT&Tag IP targeting NPAT in K562 G2 cells


title: Whole Blood, ID10, D1, Placebo, 6hour

value: male


title: HiC GN, ctrl, FANS, IVE+day14, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd14-dCas9_KRAB-pnd20_1


title: Whole Blood, ID3, D1, Placebo, Baseline

description: Library name: VA0000190056

value: female

value: Baseline

value: Mild


title: K562_NPAT_KASCnT_Input_G2_Rep2_(250411_WW_Hs_WW1592)

description:
Library name: K562_NPAT_KASCnT_Input_G2_Rep2
KAS-CUT&Tag input targeting NPAT in K562 G2 cells


title: HiC GN, ctrl, FANS, IVE+day9, rep1

description: Library name: Hi-C_ctrl-FANS_IVEd9-dCas9_KRAB-pnd15_1

value: cerebellum

value: granule neurons


title: K562_NPAT_KASCnT_Input_G2_Rep1_(250411_WW_Hs_WW1591)

description:
Library name: K562_NPAT_KASCnT_Input_G2_Rep1
KAS-CUT&Tag input targeting NPAT in K562 G2 cells


title: Whole Blood, ID10, D1, Placebo, 2hour

value: 2 hour


title: Whole Blood, ID2, M5, Booster, 2hour

description: Library name: VA0001210030

value: Whole Blood

value: Booster

value: Month 5


title: HiC GN, ctrl, FANS, IVE+day8, rep5

description: Library name: Hi-C_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_5

value: ctrl sgRNAs in dCas9-KRAB


title: K562_NPAT_KASCnT_IP_S_Rep2_(250411_WW_Hs_WW1562)

description:
Library name: K562_NPAT_KASCnT_IP_S_Rep2
KAS-CUT&Tag IP targeting NPAT in K562 S cells

value: Invitrogen, PA565419


title: Whole Blood, ID2, M5, Booster, 35min

description: Library name: VA0001200012

value: 35 min


title: Whole Blood, ID10, D1, Placebo, Baseline

value: ISRR


title: K562_NPAT_KASCnT_IP_S_Rep1_(250411_WW_Hs_WW1561)

description:
Library name: K562_NPAT_KASCnT_IP_S_Rep1
KAS-CUT&Tag IP targeting NPAT in K562 S cells


title: Whole Blood, ID2, M5, Booster, Baseline

description: Library name: VA0001190034


title: K562_NPAT_KASCnT_Input_S_Rep2_(250411_WW_Hs_WW1586)

description:
Library name: K562_NPAT_KASCnT_Input_S_Rep2
KAS-CUT&Tag input targeting NPAT in K562 S cells


title: Whole Blood, ID2, D2, Vaccine, 24hour

description: Library name: VA0000180029

value: Vaccine

value: Day 2

value: 24 hour


title: Whole Blood, ID9, M5, Booster, 35min


title: HiC GN, ctrl, FANS, IVE+day8, rep2

description: Library name: Hi-C_ctrl-FANS_IVEd8-dCas9_KRAB-pnd14_2


title: K562_NPAT_KASCnT_Input_S_Rep1_(250411_WW_Hs_WW1585)

description:
Library name: K562_NPAT_KASCnT_Input_S_Rep1
KAS-CUT&Tag input targeting NPAT in K562 S cells


title: Whole Blood, ID2, D2, Vaccine, 6hour

description: Library name: VA0000170029

value: 6 hour