title: CI994_326_C3_E_R1

description:
Library name: Sample 92
raw cell lysate and Illumina NextSeq 2091

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: tacedinaline

tag: index

value: GGGTTGTTA

value: CTAATGCAC

tag: group

tag: replicate


title: SPT_330_C2_E_R2

status: Public on Jul 27 2026

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Library name: Sample 75
raw cell lysate and Illumina NextSeq 2074

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: 260722_count_table_GEO.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

molecule: total RNA

organism: Homo sapiens

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRG cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRG cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 10e6 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRG Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRG Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building.
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRG cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70C followed by a temperature gradient with a ramp rate of 0.5C/min to 45C over a 50 min period, followed by a nuclease digestion at 37C for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37C, immediately followed with a 15 min enzyme denaturation at 80C to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37C for 10 min, 95C for 2 min; 6 cycles of 95C for 30 sec, 54C for 30 sec, 72C for 120 sec; 16 cycles of 95C for 30 sec; 72C for 2 min; 72C for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 5 concentrations of test chemical and refreshed with test chemical in HepaRG Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to trichostatin A ( 0.018811, 0.056433, 0.1693, 0.5079, 1.5237 µM), panobinostat (0.001468, 0.004403, 0.01321, 0.03963, 0.084 µM), valproic acid (0.100478, 0.301433, 0.9043, 2.7129, 3.038 µM), mocetinostat (0.177222, 0.531667, 1.595, 2.5, 3.9 µM), apicidin (0.041722, 0.125167, 0.3755, 0.5, 0.86 µM), tacedinaline (1.143333, 3.43, 10.29, 30.87, 44 µM), scriptaid  (4.94, 14.82, 44.46, 60, 94.5 µM), vorinostat (0.404778, 1.214333, 3.643, 10.929, 23.5 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

tag: tissue

tag: cell type

value: SPT

value: scriptaid

tag: dose

tag: well

tag: dose group

tag: plate

value: E

value: ATTCGCTCT

value: AATTCGGAA

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: GEX_G1

city: Daejeon

first: Bae-Hyeon

last: Moon

address: 193, Munji-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Library name: GEX_G1
LiverPerfusate_Blood.rds

library_source: transcriptomic single cell

data_processing:
Following tools were used for preprocessing: Cell Ranger software (v9.0.1), GRCh38 human reference genome (refdata-gex-GRCh38-2024-A), R (v4.4.2), Seurat package (v5.3.1), DoubletFinder (v.2.0.6). Donor identification was done with vireo & cellsnp-lite using SNPs from LSMC data. Uncommon genes between LSMCs and PBMCs were filtered out. We applied standard Seurat clustering and UMAP-based dimensional reduction. Batch effects were corrected using Harmony integration.
Assembly: Human reference, GRCh38 (GENCODE v44/Ensembl 110 annotations)
Supplementary files format and content: Seurat object (RDS). TCR (csv)

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
Sorted γδ T cells were subjected to library preparation using the Chromium Next GEM Single Cell 5' Kit v3, the 5' Feature Barcode Kit, and Human TCR Amplification Kit (10X Genomics). Primers for γδ TCRs were designed according to previous research by another group. (reference: Song et al., 2023, J Leukoc Biol, 114(6):630-638)
Sorted γδ T cells were subjected to library preparation using the Chromium Next GEM Single Cell 5' Kit v3, the 5' Feature Barcode Kit, and Human TCR Amplification Kit (10X Genomics). Primers for γδ TCRs were designed according to previous research by another group. (reference: Song et al., 2023, J Leukoc Biol, 114(6):630-638)

value: peripheral blood

value: Primary cell

value: gammadelta T cell


title: FB_G1

description:
Library name: FB_G1
LiverPerfusate_Blood.rds

library_source: other

data_processing:
Following tools were used for preprocessing: Cell Ranger software (v9.0.1), GRCh38 human reference genome (refdata-gex-GRCh38-2024-A), R (v4.4.2), Seurat package (v5.3.1), DoubletFinder (v.2.0.6). Donor identification was done with vireo & cellsnp-lite using SNPs from LSMC data. Uncommon genes between LSMCs and PBMCs were filtered out. We applied standard Seurat clustering and UMAP-based dimensional reduction. Batch effects were corrected using Harmony integration.
Assembly: Human reference, GRCh38 (GENCODE v44/Ensembl 110 annotations)
Supplementary files format and content: Seurat object (RDS). TCR (csv)
Library strategy: CITE-seq

molecule: protein


title: CI994_303_C2_E_R3

description:
Library name: Sample 91
raw cell lysate and Illumina NextSeq 2090

value: TAGCTCTTC

value: TGCATCTGC


title: HM9Pool_Sort4_mNeon positive

city: Bonn

first: Bianca

last: Broske

address: Venusberg-Campus 1

department: Institute of Experimental Oncology

country: Germany

institute: University Hospital Bonn

description:
Library name: HM9Pool_Sort4_Sample4
NGS-Read-Counts_HM9Pool.xlsx

library_source: genomic

data_processing:
Reads were filtered for a Q-Score > 30 and matched to AI-minibinder sequences using a self-written R script.
Assembly: Read alignment was performed against the designed sequences used for the respective oligo pool.
Supplementary files format and content: The processed data files contain all binder names and sequences present in the respective oligo pool. The target proteins used for staining are indicated in the sheet names, as well as in the header of the respective read column. Technical replicates (file names "*TechRepx") are already pooled and the different sorts indicate replicates of repeated experiments.

molecule: genomic DNA

organism: synthetic construct

source_name: Transduced HEK293T cells

extract_protocol:
Sorted cells were lysed in direct lysis buffer (1 mM CaCl2, 3 mM MgCl2, 1 mM EDTA, 1% (v/v) Triton X-100, 10 mM Tris pH 7.5) with proteinase K at 65 °C for 10 minutes and 95 °C for 15 minutes.
After lysis, genomically integrated AI-minibinder sequences were PCR amplified using 2x NEBNext High-Fidelity MasterMix (NEB). After second barcoding PCR, product purification, and NanoDrop-based quantification, AI-minibinders were sequenced on Illumina MiSeq platforms.

treatment_protocol: HEK293T cells were lentivirally transduced with plasmid libraries encoding de novo generated minibinder proteins. The HEK293T AI-minibinder libraries were harvested and incubated with respective Fc-tagged recombinant target proteins at 10 µg/mL and secondary APC-labeled anti-human IgG Fc antibody at 250 ng/mL (clone M1310G05, Biolegend). Cells were sorted immediately after staining for distinct APC-signal using the fluorescence-activated cell sorter Sony MA900.

value: Transduced HEK293T cells

tag: treatment

value: Sorted for total mNeon positive population


title: FD-6190-1-START

city: New York

first: Ezequiel

middle: Carlos

last: Dantas

state: Y

address: 550E First Street

country: USA

institute: NYU Langone

data_processing:
Read alignments were done using Galaxy (https://usegalaxy.org/), where paired-end FASTQ files were processed with Cutadapt for adapter removal.
Reads were mapped using STAR (2-pass mapping) with the GENCODE v43 basic annotation was performed on genome assembly GRCh38 (hg38).
Counts were obtained with featureCounts, and quality control was performed with FastQC and MultiQC
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Fixated Whole Blood

extract_protocol:
Total RNA was extracted from fixed whole blood using Qiagen PAXgene Blood RNA Kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA quality control was performed using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit for Illumina.Enriched RNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized and fragments were end-repaired and adenylated at 3’ends.  Universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: VLCD


title: MethylC-seq, pyramidal neurons, P13, Saline, rep1

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: S_AB_02

data_processing:
RNA-seq: Read quality was assessed using FastQC (Andrews, 2010). STAR (2.5.1b; Dobin et al., 2013) was used to map sequence reads and RSEM (version 1.2.31; Li and Dewey, 2011) was used to quantify gene expression.
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequencing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
RNA-seq: Batch correction in P0 samples was performed using ComBat-seq (Zhang et al., 2020). Mitochondrial and lowly expressed genes with fewer than 10 raw counts in all but one sample were removed before differential gene expression analysis. Differential expression analysis was conducted using DESeq2 (Love et al., 2014) with a false discovery rate 0.1. Enrichment analysis was performed by inputting differentially expressed genes into EnrichR (Kuleshov et al., 2016; Chen et al., 2013).
MethylC-seq: CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
Assembly: mm10
Supplementary files format and content: Tab-delimited file contains transcripts per million counts for each RNA-seq sample
Supplementary files format and content: Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosine Context, 5. methylated base call, 6. total mapped base call, 7. indicator of significant methylation (0: unmethylated; 1, methylated)

organism: Mus musculus

source_name: brain (frontal cortex)

extract_protocol:
Cortex dissecxtion and nuclei isolation: The frontal cortex tissue was rapidly dissected from perinatal mice on ice. The INTACT method was used to label excitatory neurons and fluoreescence-activated nuclei sorting (FANS) was used to affinity purify GFP+ nuclei. RNA-seq: RNA was extracted by using the RNeasy Mini kit with DNAse I treatment (Qiagen, 74104) for whole frontal cortex, or by using Single-Cell RNA Purification Kit (Norgen, 51800) for nuclei. Bisulfite-Seq (MethylC-seq):  Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
RNA-seq: For whole tissue RNA, strand-specific cDNA libraries were constructed by selecting poly-adenylated mRNA transcripts using Truseq Stranded mRNA High Throughput Library Prep kit (Illumina, 20015963) with TruSeq RNA CD Indexes (Illumina, 20015949). Libraries were sequenced using Illumina NextSeq500, generating 20 million reads (75 bp, paired-end sequencing, whole cortex). INTACT-purified nuclear RNA (Norgen, 51800) was converted to cDNA and amplified with the Ovation RNA-seq System V2 (Nugen, 7102-A01) and libraries prepared with Kapa LTP library preparation kit (Illumina, KK8232) with TruSeq DNA Single Indexes (Illumina, 20015960), generating 40 million reads (150 bp, paired-end sequencing using Illumina HiSeq 4000 or NovaSeq 6000).
Bisulfite-Seq (MethylC-seq):  MethylC-seq libraries were constructed using the snmC-seq2 adapted for Bulk samples (https://dx.doi.org/10.17504/protocols.io.pjvdkn6). 40ng of DNA samples  were subjected to sodium bisulfite conversion using Zymo EZ DNA Methylation-Direct Kit (D5020, D5021), 0.5% of Lambda was added to each sample, resuspended in 9ul of EB buffer, 1ul of random primer was added to each of the samples, denature for 3 min at 95°C, put in ice for 3 min, then 10ul of Random primer was added and mixed, put in thermocycler with at 4°C 5 min,  25°C 5 min, 37°C 60 min. Exonuclease/SAP mix was added next put at 37°C 30min. Samples were subjected to one round of 0.8x SPRI beads clean up. Samples were resuspended in 10ul of EB and denature once again. Adaptase mix was added next, and put at 37°C 30min and 95°C 2min. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart, 1ul of P5 index primer (30uM), and 5ul of P7 index primer (10uM), for a final vol of 50ul. The reaction products were purified using SPRI beads. MethylC-seq libraries were sequenced on Illumina HiSeq 4000 or Novaseq 6000.

treatment_protocol: Dams received IP injection of 0.9% saline or 20 mg/kg polyriboinosinic–polyribocytidylic acid potassium salt (P9582, Lot number 095M4085V, Sigma-Aldrich, St. Louis, MO) in 0.9% saline on embryonic day 12.5.

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline

tag: age

value: Postnatal day 13

tag: Sex

value: male


title: RKP Tumor

city: Houston

first: Kyung Pil

last: Ko

state: Tx

address: 1515 Holcombe Blvd

institute: The University of Texas M.D. Anderson Cancer Center

description: Library name: RKP

data_processing:
The barcoded processing, and  gene counting were performed using the Cell Ranger
Assembly: Reads were aligned to the GRCm38/mm10 genome and processed using Cell Ranger.
Supplementary files format and content: tab-seperated files and matrix files

source_name: gastric tumor

growth_protocol: Five-week-old C57BL/6 mice were housed in the Division of Laboratory Animal Resources at MD Anderson. For subcutaneous allograft experiments, 2D-cultured EKP and RKP cells (3 × 10⁶) were mixed 1:1 with Matrigel and injected into both flanks of each mouse. Tumor volume was measured every 3–4 days using calipers and calculated as (length × width²)/2.

extract_protocol:
Tumors from EKP and RKP models were harvested on the same day (day 29 and day 48, respectively). Each tumor was bisected; one half was used for single-cell RNA sequencing (scRNA-seq), and the other half was fixed and processed into formalin-fixed, paraffin-embedded (FFPE) blocks for Xenium in situ hybridization and immunohistochemistry (IHC) staining. For scRNA-seq, tumors were enzymatically dissociated into single-cell suspensions, filtered sequentially through 70 μm and 40 μm strainers, and treated with 10% FBS DMEM to inactivate trypsin. Live cells were isolated by flow cytometry, and equal numbers of viable cells were used for library construction.
Single-cell gene expression libraries were prepared using the Chromium Single Cell 3’ Gene Expression v3.1 kit (10x Genomics). Briefly, single cells were encapsulated with reverse transcription reagents and barcoded Gel Beads in oil droplets (GEMs) using the Chromium Controller. Full-length barcoded cDNA was synthesized within GEMs, followed by GEM disruption and cDNA purification with Dynabeads MyOne Silane Beads. Libraries were constructed through fragmentation, end-repair, A-tailing, adaptor ligation, and PCR amplification, and sequenced on an Illumina NovaSeq platform

tag: tissue

value: gastric tumor

tag: cell line

value: RKP

value: epithelial cell


title: GBM43 intracranial xenografts, RMC-4550 treated, sample 3

city: San Francsico

first: Sixuan

last: Pan

state: California

institute: UCSF

description:
Library name: shp2-3
PIP-seq

data_processing:
Perturb dataset: Cell Ranger (v6.1.2) was used to align reads to mm10, count UMIs, and assign sgRNAs, while deMULTIplex2 was used to demultiplex MULTI-seq sample hashes. Seurat SCTransform v2 normalization and QC filtering retained only cells with correct dual-sgRNA capture and adequate knockdown. Differential expression was performed with DElegate (DESeq2 pseudoreplicates), followed by fgsea-based pathway analysis. Perturbation signatures were visualized using LDA and UMAP, and interaction modeling between gene perturbations and drug treatment was performed using Theil-Sen regression and random forest-based feature importance.  Xeno dataset: FASTQs were processed with PIPseeker for alignment to a combined human–mouse reference, droplet calling, and UMI matrix generation. Human tumor cells were identified by >85% human read mapping. Subsequent analyses were performed in Seurat using QC filtering, SCTransform v2 normalization, and Scanorama integration. Cell states were assigned with Neftel et al. signatures, and differential gene expression and GSEA were performed to characterize drug-specific transcriptional programs.
Assembly: Perturb dataset: mm10  Xeno dataset: GRCh38
Supplementary files format and content: Feature Barcode Market Exchange Matrices

source_name: brain

extract_protocol:
Perturb datasest: SB28 glioma cells expressing dCas9-KRAB were transduced with a dual-sgRNA CRISPRi library, FACS-sorted, treated with MEK inhibitor, SHP2 inhibitor, or vehicle for five days, then collected by trypsinization. Single-cell suspensions were labeled using MULTI-seq lipid barcodes through sequential incubation with anchor, barcode, and co-anchor oligos, washed in BSA-PBS, pooled, and loaded onto the 10x Chromium Controller for droplet partitioning.  Xeno dataset: Tumors from GBM43 intracranial xenografts were surgically harvested after in vivo drug treatment, mechanically minced, and enzymatically dissociated using the Papain Dissociation System to generate a single-cell suspension. The dissociated cells were filtered through a 70-µm strainer, centrifuged, washed in PBS, and prepared on ice for downstream PIPseq single-cell RNA-sequencing.
Perturb dataset: Dual-sgRNA constructs were cloned with direct-capture tags and used to generate the CRISPRi perturbation pool. Single-cell 3′ transcriptome and sgRNA-capture libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 kit with Feature Barcoding. MULTI-seq barcode libraries were amplified separately from cDNA supernatant after the SPRI cleanup step. All libraries were sequenced on an Illumina NovaSeq X.  Xeno dataset: Single-cell suspensions were processed using the Fluent BioSciences PIPseq T20 3′ Single Cell RNA Kit (v3.0), following the manufacturer’s workflow for barcoding, reverse transcription, amplification, and library preparation. Completed libraries were sequenced on an Illumina NovaSeq X to generate paired-end FASTQ files for downstream processing.

treatment_protocol: Vehicle (DMSO), selumetinib (MEK inhibitor), or RMC-4550 (SHP2 inhibitor)

value: brain

tag: cell type

value: glioblastoma

value: RMC-4550 (SHP2 inhibitor)


title: EKP Tumor

description: Library name: EKP

value: EKP


title: HM9Pool_Sort4_Human CD276-4Ig

description:
Library name: HM9Pool_Sort4_Sample3
NGS-Read-Counts_HM9Pool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human CD276


title: SPT_326_C2_E_R1

description:
Library name: Sample 74
raw cell lysate and Illumina NextSeq 2073

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: SPT

tag: chemical longname

value: scriptaid

tag: dose

tag: well

value: E

tag: index

value: ATTCGCTCT

value: CTAATGCAC

tag: group

tag: replicate

value: test


title: FD-6190-1-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

value: Post randomization

value: VLCD


title: FD-8119-3-POS

tag: randomization

value: Sugar


title: GBM43 intracranial xenografts, RMC-4550 treated, sample 2

description:
Library name: shp2-2
PIP-seq

value: brain

value: glioblastoma

tag: treatment

value: RMC-4550 (SHP2 inhibitor)


title: MethylC-seq, pyramidal neurons, P13, Poly IC, rep6

description: Library name: P_WW_06

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

value: Postnatal day 13

value: male


title: SPT_303_C1_E_R3

description:
Library name: Sample 73
raw cell lysate and Illumina NextSeq 2072

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: SPT

value: scriptaid

tag: dose group

tag: plate

value: E

value: GAACTGTAT

value: GACGCGTTA

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: Eye-skin, MYD88-deficient ft/ft (ft/ftMyD88-/-), rep 3

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 291-XX-33

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCm38
Supplementary files format and content: count matrix

source_name: skin

growth_protocol: ft/ftMyD88 /-  mice were generated as an in-house cross between a spontaneous loss-of-function point mutation in filaggrin (ft/ft) and MyD88 deficient (MyD88-/-) mice on a BALB/c background. All mouse strains were bred and maintained under the same specific pathogen-free conditions.

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

tag: tissue

value: skin

tag: cell line

value: skin cells

tag: cell type

tag: genotype

value: MYD88-deficient ft/ft


title: HM9Pool_Sort4_HA-tag low

description:
Library name: HM9Pool_Sort4_Sample2
NGS-Read-Counts_HM9Pool.xlsx

value: Transduced HEK293T cells

value: Stained with an anti-HA-tag antibody


title: FD-6187-1-START

value: Fixated Whole Blood

value: START

value: Before randomization

tag: diet group

value: Sugar


title: MethylC-seq, pyramidal neurons, P13, Poly IC, rep5

description: Library name: P_WW_03

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

value: Postnatal day 13

tag: Sex

value: male


title: SPT_330_C1_E_R2

description:
Library name: Sample 72
raw cell lysate and Illumina NextSeq 2071

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: SPT

tag: chemical longname

value: scriptaid

tag: dose

tag: well

value: E

tag: index

value: ACTCATGTA

value: AATTCGGAA

tag: group

tag: replicate

value: test


title: HM9Pool_Sort4_HA-tag high

description:
Library name: HM9Pool_Sort4_Sample1
NGS-Read-Counts_HM9Pool.xlsx

value: Transduced HEK293T cells

tag: treatment

value: Stained with an anti-HA-tag antibody


title: FD-6187-1-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

value: Sugar


title: GBM43 intracranial xenografts, selumetinib treated, sample 3

description:
Library name: sel-3
PIP-seq

tag: tissue

value: brain

value: glioblastoma

value: selumetinib (MEK inhibitor)


title: MethylC-seq, pyramidal neurons, P13, Poly IC, rep4

description: Library name: P_WW_01

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

value: Postnatal day 13

value: male


title: SPT_326_C1_E_R1

description:
Library name: Sample 71
raw cell lysate and Illumina NextSeq 2070

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

tag: cell type

value: liver progenitor cells

value: SPT

value: scriptaid

tag: dose group

tag: plate

value: E

value: ACTCATGTA

value: CTAATGCAC

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: HM9Pool_Sort3_Murine CD276

description:
Library name: HM9Pool_Sort3_Sample5
NGS-Read-Counts_HM9Pool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant murine CD276


title: FD-5990-1-START

value: Fixated Whole Blood

value: START

value: Before randomization

tag: diet group

value: Starch


title: MethylC-seq, pyramidal neurons, P13, Poly IC, rep3

description: Library name: P_O_02

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

tag: Sex


title: PAN_303_C5_H_R3

description:
Library name: Sample 70
raw cell lysate and Illumina NextSeq 2069

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: chemical shortname

value: PAN

tag: chemical longname

value: panobinostat

tag: dose

tag: well

value: H

tag: index

value: TAGCGACAA

value: TGCCGGTAT

tag: group

tag: replicate

value: test


title: FD-5990-1-POS

tag: tissue

tag: timepoint

value: POS

tag: randomization

value: Post randomization


title: HM9Pool_Sort3_mNeon positive

description:
Library name: HM9Pool_Sort3_Sample4
NGS-Read-Counts_HM9Pool.xlsx

tag: cell line

value: Transduced HEK293T cells

tag: treatment

value: Sorted for total mNeon positive population


title: MethylC-seq, pyramidal neurons, P13, Poly IC, rep2

description: Library name: P_EE_02

tag: cell type

tag: strain

value: Postnatal day 13

value: male


title: PAN_330_C5_H_R2

description:
Library name: Sample 69
raw cell lysate and Illumina NextSeq 2068

value: liver progenitor cells

tag: dose group

tag: plate

value: TCAGCTAAT

value: AATAGGTGC

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: FD-5054-3-START

value: Fixated Whole Blood

value: START

value: Before randomization

tag: diet group

value: Starch


title: MethylC-seq, pyramidal neurons, P13, Poly IC, rep1

description: Library name: P_EE_01

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

tag: Sex


title: HM9Pool_Sort3_Human CD276-4Ig

description:
Library name: HM9Pool_Sort3_Sample3
NGS-Read-Counts_HM9Pool.xlsx

value: Stained with recombinant human CD276


title: PAN_326_C5_H_R1

description:
Library name: Sample 68
raw cell lysate and Illumina NextSeq 2067

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: chemical shortname

value: PAN

tag: chemical longname

value: panobinostat

tag: dose

tag: well

value: H

tag: index

value: ACCTGAGGC

value: ATGGTTAGA

tag: group

tag: replicate

value: test


title: HM9Pool_Sort3_HA-tag low

description:
Library name: HM9Pool_Sort3_Sample2
NGS-Read-Counts_HM9Pool.xlsx

tag: cell line

value: Transduced HEK293T cells

tag: treatment

value: Stained with an anti-HA-tag antibody


title: PAN_303_C4_H_R3

description:
Library name: Sample 67
raw cell lysate and Illumina NextSeq 2066

tag: tissue

tag: cell type

value: liver progenitor cells

tag: dose group

tag: plate

value: GCTATCGAT

value: TGCCGGTAT


title: HM9Pool_Sort3_HA-tag high

description:
Library name: HM9Pool_Sort3_Sample1
NGS-Read-Counts_HM9Pool.xlsx


title: MethylC-seq, pyramidal neurons, P0, Poly IC, rep5

description: Library name: P_ZZ_02

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

value: Postnatal day 0

value: male


title: FD-4923-9-START

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: Starch


title: PAN_330_C4_H_R2

description:
Library name: Sample 66
raw cell lysate and Illumina NextSeq 2065

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: chemical shortname

value: PAN

value: panobinostat

value: H

value: ATCGCGACT

value: AATAGGTGC

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: FD-4923-9-POS

value: POS

value: Post randomization


title: PAN_326_C4_H_R1

description:
Library name: Sample 65
raw cell lysate and Illumina NextSeq 2064

value: liver progenitor cells

tag: chemical longname

tag: dose

tag: well

tag: index

value: TAGCGACAA

value: ATGGTTAGA

value: test


title: FD-4866-3-START

value: Fixated Whole Blood

value: VLCD


title: HM9Pool_Sort2_Human CD276-4Ig

description:
Library name: HM9Pool_Sort2_Sample3
NGS-Read-Counts_HM9Pool.xlsx

tag: cell line

value: Transduced HEK293T cells

tag: treatment

value: Stained with recombinant human CD276


title: PAN_330_C3_H_R2

description:
Library name: Sample 64
raw cell lysate and Illumina NextSeq 2063

tag: tissue

value: liver tumor associated with chronic hepatitis C

tag: cell type

value: TGGAACGCT

tag: group

tag: replicate


title: MethylC-seq, pyramidal neurons, P0, Poly IC, rep3

description: Library name: P_YY_02

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

value: Postnatal day 0

tag: Sex

value: male


title: FD-4866-3-POS

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group


title: MethylC-seq, pyramidal neurons, P0, Poly IC, rep2

description: Library name: P_BB_04


title: FD-4658-1-START

value: START

value: Before randomization


title: HM9Pool_Sort2_HA-tag low

description:
Library name: HM9Pool_Sort2_Sample2
NGS-Read-Counts_HM9Pool.xlsx

value: Stained with an anti-HA-tag antibody


title: PAN_303_C2_H_R3

description:
Library name: Sample 62
raw cell lysate and Illumina NextSeq 2061

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: PAN

tag: chemical longname

value: panobinostat

tag: dose group

tag: plate

value: H

value: TCAGCTAAT

value: TGCCGGTAT

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: MethylC-seq, pyramidal neurons, P0, Poly IC, rep1

description: Library name: P_BB_02

tag: tissue

value: brain (frontal cortex)

tag: cell type

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: treatment


title: FD-4658-1-POS

value: Fixated Whole Blood

value: VLCD


title: PAN_330_C2_H_R2

description:
Library name: Sample 61
raw cell lysate and Illumina NextSeq 2060

value: liver tumor associated with chronic hepatitis C

tag: cell line

tag: dose

tag: well

tag: index

value: GATAGCGGA

value: TGTAACGGC

tag: group

tag: replicate


title: HM9Pool_Sort1_Murine CD276

description:
Library name: HM9Pool_Sort1_Sample5
NGS-Read-Counts_HM9Pool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant murine CD276


title: FD-4569-0-START

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: Sugar


title: RNA-seq, pyramidal neurons, P0, Saline, rep5

description: Library name: P0_S_AP_04

tag: strain

tag: genotype

value: Saline

tag: age

value: Postnatal day 0

tag: Sex

value: male


title: RNA-seq, pyramidal neurons, P0, Saline, rep4

description: Library name: P0_S_AR_02


title: PAN_326_C2_H_R1

description:
Library name: Sample 60
raw cell lysate and Illumina NextSeq 2059

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: PAN

tag: chemical longname

value: panobinostat

tag: dose group

tag: plate

value: H

value: ATTGGTTGC

value: ATGGTTAGA

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: RNA-seq, pyramidal neurons, P0, Saline, rep1

description: Library name: P0_S_AK_01

tag: tissue

value: brain (frontal cortex)

tag: cell type

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: treatment


title: FD-4569-0-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

value: Post randomization


title: PAN_303_C1_H_R3

description:
Library name: Sample 59
raw cell lysate and Illumina NextSeq 2058

value: liver tumor associated with chronic hepatitis C

tag: cell line

tag: dose

tag: well

tag: index

value: TGCTTATTC

value: TGCCGGTAT

tag: group

tag: replicate


title: HM9Pool_Sort1_Human CD276-4Ig

description:
Library name: HM9Pool_Sort1_Sample3
NGS-Read-Counts_HM9Pool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human CD276


title: FD-3900-0-START

value: START

tag: randomization

value: Before randomization

tag: diet group

value: VLCD


title: HM9Pool_Sort1_HA-tag low

description:
Library name: HM9Pool_Sort1_Sample2
NGS-Read-Counts_HM9Pool.xlsx

value: Stained with an anti-HA-tag antibody


title: PAN_330_C1_H_R2

description:
Library name: Sample 58
raw cell lysate and Illumina NextSeq 2057

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: PAN

tag: chemical longname

value: panobinostat

tag: dose group

value: H

value: AGCCGATTA

value: TGTAACGGC


title: FD-3900-0-POS

value: Fixated Whole Blood

value: POS

value: Post randomization


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep6

description: Library name: P0_P_AQ_05

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

value: Postnatal day 0

tag: Sex

value: male


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep5

description: Library name: P0_P_OO_05

tag: tissue

tag: cell type

tag: treatment


title: HM9Pool_Sort1_HA-tag high

description:
Library name: HM9Pool_Sort1_Sample1
NGS-Read-Counts_HM9Pool.xlsx

tag: cell line

value: Transduced HEK293T cells

value: Stained with an anti-HA-tag antibody


title: PAN_326_C1_H_R1

description:
Library name: Sample 57
raw cell lysate and Illumina NextSeq 2056

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: dose

tag: well

tag: plate

value: TGATTAAGC

value: ATGGTTAGA

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: FD-3653-1-START

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: VLCD


title: ImprovedPool_Sort6_Murine PDL1

description:
Library name: Improved Pool_Sort6_Sample3
NGS-Read-Counts_ImprovedPool.xlsx

value: Stained with recombinant murine PD-L1


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep3

description: Library name: P0_P_AQ_6

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories


title: MOC_330_C5_H_R2

description:
Library name: Sample 53
raw cell lysate and Illumina NextSeq 2052

tag: chemical shortname

value: MOC

tag: chemical longname

value: mocetinostat

tag: dose group

value: H

tag: index

value: ATTCGAATC

value: AACACAATC

tag: group

tag: replicate


title: MOC_303_C5_H_R3

description:
Library name: Sample 54
raw cell lysate and Illumina NextSeq 2053

tag: tissue

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

tag: cell type

value: liver progenitor cells

value: ACCTGAGGC

value: TAAGTTACG


title: ImprovedPool_Sort6_mNeon positive

description:
Library name: Improved Pool_Sort6_Sample2
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

tag: treatment

value: Sorted for total mNeon positive population


title: FD-3547-3-START

value: Fixated Whole Blood

value: START

value: Before randomization

value: Sugar


title: MOC_326_C5_H_R1

description:
Library name: Sample 52
raw cell lysate and Illumina NextSeq 2051

tag: dose

tag: well

tag: plate

value: GCTGCGTAT

tag: chemical type

value: test


title: ImprovedPool_Sort6_Human PDL1

description:
Library name: Improved Pool_Sort6_Sample1
NGS-Read-Counts_ImprovedPool.xlsx

value: Stained with recombinant human PD-L1


title: FD-3547-3-POS

tag: timepoint

value: POS

tag: randomization

value: Post randomization


title: MOC_303_C4_H_R3

description:
Library name: Sample 51
raw cell lysate and Illumina NextSeq 2050

value: MOC

value: mocetinostat

value: H

value: GCTATCGAT

tag: cas-nr

tag: batch nr_heparg


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep1

description: Library name: P0_P_AM_1

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

value: Postnatal day 0

tag: Sex

value: male


title: ImprovedPool_Sort5_Murine PDL1

description:
Library name: Improved Pool_Sort5_Sample3
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant murine PD-L1


title: FD-2702-3-START

value: Fixated Whole Blood

value: START

value: Before randomization

tag: diet group

value: Sugar


title: RNA-seq, pyramidal neurons, P0, Saline, rep3

description: Library name: P0_S_AK_3

tag: tissue

value: Saline


title: ImprovedPool_Sort5_mNeon positive

description:
Library name: Improved Pool_Sort5_Sample2
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Sorted for total mNeon positive population


title: MOC_330_C4_H_R2

description:
Library name: Sample 50
raw cell lysate and Illumina NextSeq 2049

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical shortname

value: MOC

tag: chemical longname

value: mocetinostat

tag: dose group

tag: index

value: ATCGCGACT

value: AACACAATC

tag: group

tag: replicate

value: test


title: FD-2702-3-POS

tag: timepoint

value: POS

tag: randomization

value: Post randomization


title: RNA-seq, pyramidal neurons, P0, Saline, rep2

description: Library name: P0_S_AK_2

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: treatment

value: Postnatal day 0

value: male


title: ImprovedPool_Sort5_Human PDL1

description:
Library name: Improved Pool_Sort5_Sample1
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human PD-L1


title: MOC_326_C4_H_R1

description:
Library name: Sample 49
raw cell lysate and Illumina NextSeq 2048

value: liver tumor associated with chronic hepatitis C

tag: dose

tag: well

tag: plate

value: H

value: TAGCGACAA

value: GCTGCGTAT

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: RNA-seq, pyramidal neurons, E15, Poly IC, rep5

description: Library name: E14_P_Q_3

tag: tissue

tag: strain

tag: genotype

value: Poly IC

tag: age

value: Embryonic day 15

tag: Sex


title: MOC_303_C3_H_R3

description:
Library name: Sample 48
raw cell lysate and Illumina NextSeq 2047

tag: cell line

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical shortname

value: MOC

tag: chemical longname

value: mocetinostat

tag: dose group

tag: index

value: TGATTAAGC

value: TAAGTTACG


title: FD-1424-6-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: Starch


title: ImprovedPool_Sort4_mNeon positive

description:
Library name: Improved Pool_Sort4_Sample5
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

tag: treatment

value: Sorted for total mNeon positive population


title: RNA-seq, pyramidal neurons, E15, Poly IC, rep4

description: Library name: E14_P_Q_1

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: male


title: MOC_330_C3_H_R2

description:
Library name: Sample 47
raw cell lysate and Illumina NextSeq 2046

value: liver tumor associated with chronic hepatitis C

tag: dose

tag: well

tag: plate

value: H

value: TGGAACGCT

value: AACACAATC

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr


title: ImprovedPool_Sort4_Human VTCN1_TechRep2

description:
Library name: Improved Pool_Sort4_Sample4
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Stained with recombinant human VTCN1


title: RNA-seq, pyramidal neurons, E15, Poly IC, rep3

description: Library name: E14_P_PP_6

tag: tissue

tag: cell type

tag: strain

tag: genotype

value: Poly IC

tag: age

value: Embryonic day 15

tag: Sex


title: ImprovedPool_Sort4_Human VTCN1_TechRep1

description:
Library name: Improved Pool_Sort4_Sample3
NGS-Read-Counts_ImprovedPool.xlsx


title: MOC_326_C3_H_R1

description:
Library name: Sample 46
raw cell lysate and Illumina NextSeq 2045

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: MOC

tag: chemical longname

value: mocetinostat

tag: dose group

tag: index

value: GCTATCGAT

value: GCTGCGTAT

tag: batch nr_heparg


title: FD-1423-2-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: VLCD


title: RNA-seq, pyramidal neurons, E15, Poly IC, rep2

description: Library name: E14_P_PP_3

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: treatment

value: male


title: MOC_303_C2_H_R3

description:
Library name: Sample 45
raw cell lysate and Illumina NextSeq 2044

value: liver tumor associated with chronic hepatitis C

tag: dose

tag: well

tag: plate

value: H

value: TCAGCTAAT

value: TAAGTTACG

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep10

description: Library name: P13_P_WW_06

tag: tissue

tag: cell type

tag: strain

tag: genotype

value: Poly IC

tag: age

value: Postnatal day 13

tag: Sex


title: ImprovedPool_Sort4_Human CD276_TechRep2

description:
Library name: Improved Pool_Sort4_Sample2
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Transduced HEK293T cells

value: Stained with recombinant human CD276


title: RNA-seq, pyramidal neurons, E15, Poly IC, rep1

description: Library name: E14_P_PP_2

value: Embryonic day 15


title: MOC_330_C2_H_R2

description:
Library name: Sample 44
raw cell lysate and Illumina NextSeq 2043

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: MOC

tag: chemical longname

value: mocetinostat

tag: dose group

tag: index

value: GATAGCGGA

value: AATAGGTGC

tag: batch nr_heparg


title: ImprovedPool_Sort4_Human CD276_TechRep1

description:
Library name: Improved Pool_Sort4_Sample1
NGS-Read-Counts_ImprovedPool.xlsx

tag: treatment


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep9

description: Library name: P13_P_WW_05

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: male


title: RNA-seq, pyramidal neurons, E15, Saline, rep4

description: Library name: E14_S_QQ_5

value: Saline


title: MOC_326_C2_H_R1

description:
Library name: Sample 43
raw cell lysate and Illumina NextSeq 2042

value: liver tumor associated with chronic hepatitis C

tag: dose

tag: well

tag: plate

value: H

value: ATTGGTTGC

value: GCTGCGTAT

tag: group

value: test


title: ImprovedPool_Sort3_Murine PDL1

description:
Library name: Improved Pool_Sort3_Sample7
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant murine PD-L1


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep8

description: Library name: P13_P_WW_04

tag: tissue

value: Poly IC

value: Postnatal day 13


title: RNA-seq, pyramidal neurons, E15, Saline, rep3

description: Library name: E14_S_QQ_3

tag: cell type

value: Embryonic day 15


title: FD-1424-6-START

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: Starch


title: MOC_303_C1_H_R3

description:
Library name: Sample 42
raw cell lysate and Illumina NextSeq 2041

value: HepaRG

value: liver progenitor cells

value: MOC

value: mocetinostat

value: TGCTTATTC

value: TAAGTTACG

tag: replicate

tag: chemical type

tag: cas-nr


title: ImprovedPool_Sort3_mNeon positive

description:
Library name: Improved Pool_Sort3_Sample6
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Sorted for total mNeon positive population


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep7

description: Library name: P13_P_WW_03

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: age

tag: Sex

value: male


title: RNA-seq, pyramidal neurons, E15, Saline, rep2

description: Library name: E14_S_QQ_2

tag: treatment

value: Saline


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep6

description: Library name: P13_P_WW_02

value: Poly IC

value: Postnatal day 13


title: ImprovedPool_Sort3_Human VTCN1_TechRep2

description:
Library name: Improved Pool_Sort3_Sample5
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human VTCN1


title: MOC_330_C1_H_R2

description:
Library name: Sample 41
raw cell lysate and Illumina NextSeq 2040

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

tag: chemical longname

tag: dose

tag: well

tag: dose group

value: H

tag: index

value: AGCCGATTA

value: AATAGGTGC

value: test

tag: batch nr_heparg


title: RNA-seq, pyramidal neurons, E15, Saline, rep1

description: Library name: E14_S_DD_5

tag: tissue

tag: cell type

value: Embryonic day 15


title: MOC_326_C1_H_R1

description:
Library name: Sample 40
raw cell lysate and Illumina NextSeq 2039

value: HepaRG

value: liver progenitor cells

value: MOC

value: mocetinostat

tag: plate

value: TGATTAAGC

value: GCTGCGTAT

tag: group

tag: replicate

tag: chemical type


title: ImprovedPool_Sort3_Human VTCN1_TechRep1

description:
Library name: Improved Pool_Sort3_Sample4
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line


title: FD-1423-2-START

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: VLCD


title: API_303_C5_H_R3

description:
Library name: Sample 15
raw cell lysate and Illumina NextSeq 2014

tag: chemical shortname

value: API

value: apicidin

value: ATTCGAATC

value: AGCTAGACC

tag: cas-nr


title: cSCC tumor, Ruxo5

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

data_processing:
Sequencing reads were pseudo aligned to genome and genes quantified using Kallisto
Assembly: GRCm38v96
Supplementary files format and content: Tab delimited table containing gene symbol and sample normalized counts

source_name: cutaneous

extract_protocol:
Total RNA was extracted using QIAGEN RNAeasy plus mini kit following manufacturer's instructions
Libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit
First stranded libraries

value: cutaneous

tag: treatment

value: RUXOLITINIB


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep5

description: Library name: P13_P_WW_01

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

value: Postnatal day 13

tag: Sex

value: male


title: ImprovedPool_Sort3_Human PDL1

description:
Library name: Improved Pool_Sort3_Sample3
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human PD-L1


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep4

description: Library name: P13_P_O_02_

tag: tissue


title: cSCC tumor, Ruxo3


title: API_330_C5_H_R2

description:
Library name: Sample 14
raw cell lysate and Illumina NextSeq 2013

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical longname

tag: dose

tag: well

tag: dose group

value: H

tag: index

value: TAGCGACAA

value: AACACAATC

value: test

tag: batch nr_heparg


title: ImprovedPool_Sort3_Human CD276_TechRep2

description:
Library name: Improved Pool_Sort3_Sample2
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Stained with recombinant human CD276


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep3

description: Library name: P13_P_O_01_


title: cSCC tumor, Ruxo2

value: cutaneous

value: RUXOLITINIB


title: API_326_C5_H_R1

description:
Library name: Sample 13
raw cell lysate and Illumina NextSeq 2012

value: API

value: apicidin

tag: plate

value: TCAGCTAAT

value: TGTAACGGC

tag: group

tag: replicate

tag: chemical type


title: ImprovedPool_Sort3_Human CD276_TechRep1

description:
Library name: Improved Pool_Sort3_Sample1
NGS-Read-Counts_ImprovedPool.xlsx

tag: treatment


title: FD-5054-3-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: Starch


title: MethylC-seq, pyramidal neurons, P0, Poly IC, rep6

description: Library name: P_ZZ_07

tag: tissue

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

tag: age

value: Postnatal day 0

tag: Sex

value: male


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep2

description: Library name: P13_P_EE_02

tag: cell type

value: Postnatal day 13


title: API_303_C4_H_R3

description:
Library name: Sample 12
raw cell lysate and Illumina NextSeq 2011

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

tag: dose

tag: well

tag: dose group

value: H

tag: index

value: ATCGCGACT

value: AGCTAGACC

value: test

tag: cas-nr


title: ImprovedPool_Sort2_Murine PDL1

description:
Library name: Improved Pool_Sort2_Sample5
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Transduced HEK293T cells

tag: treatment

value: Stained with recombinant murine PD-L1


title: RNA-seq, pyramidal neurons, P13, Poly IC, rep1

description: Library name: P13_P_EE_01


title: cSCC tumor, Ruxo1

value: cutaneous

value: RUXOLITINIB


title: MethylC-seq, pyramidal neurons, P0, Poly IC, rep4

description: Library name: P_YY_06

value: brain (frontal cortex)

value: excitatory pyramidal neurons


title: HM9Pool_Sort2_Murine CD276

description:
Library name: HM9Pool_Sort2_Sample5
NGS-Read-Counts_HM9Pool.xlsx

value: Stained with recombinant murine CD276


title: cSCC tumor, Veh5

value: VEHICLE


title: HM9Pool_Sort2_mNeon positive

description:
Library name: HM9Pool_Sort2_Sample4
NGS-Read-Counts_HM9Pool.xlsx

value: Sorted for total mNeon positive population


title: API_330_C4_H_R2

description:
Library name: Sample 11
raw cell lysate and Illumina NextSeq 2010

value: API

value: apicidin

tag: plate

value: GCTATCGAT

value: AACACAATC

tag: group

tag: replicate

tag: chemical type

tag: batch nr_heparg


title: ImprovedPool_Sort2_mNeon pos

description:
Library name: Improved Pool_Sort2_Sample4
NGS-Read-Counts_ImprovedPool.xlsx


title: RNA-seq, pyramidal neurons, P13, Saline, rep11

description: Library name: P13_S_HH_04

tag: tissue

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline

tag: age

value: Postnatal day 13

value: male


title: cSCC tumor, Veh2


title: API_326_C4_H_R1

description:
Library name: Sample 10
raw cell lysate and Illumina NextSeq 2009

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: H

value: TGCTTATTC

value: TGTAACGGC

value: test


title: ImprovedPool_Sort2_Human VTCN1_TechRep2

description:
Library name: Improved Pool_Sort2_Sample3
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human VTCN1


title: PAN_326_C3_H_R1

description:
Library name: Sample 63
raw cell lysate and Illumina NextSeq 2062

value: PAN

value: panobinostat

tag: dose

tag: well

tag: dose group

value: ATGGTTAGA


title: HM9Pool_Sort2_HA-tag high

description:
Library name: HM9Pool_Sort2_Sample1
NGS-Read-Counts_HM9Pool.xlsx

tag: cell line

value: Stained with an anti-HA-tag antibody


title: cSCC tumor, Veh1

value: cutaneous

tag: treatment

value: VEHICLE


title: ImprovedPool_Sort2_Human VTCN1_TechRep1

description:
Library name: Improved Pool_Sort2_Sample2
NGS-Read-Counts_ImprovedPool.xlsx


title: API_303_C3_H_R3

description:
Library name: Sample 9
raw cell lysate and Illumina NextSeq 2008

value: API

value: apicidin

tag: plate

tag: index

value: TGGAACGCT

value: AGCTAGACC

tag: cas-nr


title: RNA-seq, pyramidal neurons, P13, Saline, rep10

description: Library name: P13_S_HH_02

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline

value: Postnatal day 13

tag: Sex

value: male


title: RNA-seq, pyramidal neurons, P13, Saline, rep9

description: Library name: P13_S_HH_01


title: Mtb-infected Ezh2-deficient Hoxb8-derived macrophages at 3 days post-infection, biological replicate 3

city: Ithaca

first: bom nae rin

last: lee

state: NY

address: 930 Campus Road

department: Microbiology&Immunology

institute: Cornell university

description:
Library name: 7028D-BL12-EZH3TB
Column names in mouse and M. tuberculosis count matrices: EZHTB_3

data_processing:
Reads were mapped separately to the mouse GRCm39 and M. tuberculosis ASM19595v2 genome assemblies using STAR.
Gene-level raw counts were generated using STAR --quantMode GeneCounts.
DESeq2 was used to generate normalized count matrices separately for mouse and M. tuberculosis.
Assembly: GRCm39, ASM19595v2
Supplementary files format and content: ZIP archives containing raw gene-count tables and gzip-compressed tab-separated files containing DESeq2-normalized counts for mouse and M. tuberculosis.
Supplementary files format and content: The mouse raw and normalized count matrices contain all 12 libraries; the M. tuberculosis raw and normalized count matrices contain the six infected libraries.

organism:
Mycobacterium tuberculosis
Mus musculus

source_name: Cas9-expressing Hoxb8 myeloid progenitor cells

growth_protocol: Cas9-expressing, estrogen-responsive Hoxb8 myeloid progenitor cells were maintained in RPMI supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 20 ng/ml murine GM-CSF, 0.5 uM beta-estradiol, 10 mM HEPES and 1% penicillin-streptomycin. To induce macrophage differentiation, progenitor cells were washed to remove beta-estradiol and cultured in macrophage differentiation medium for 7 days at 37 degrees C with 5% CO2.

extract_protocol:
RNA was extracted using TRIzol. Total RNA from the aqueous phase was purified using the Zymo RNA Clean & Concentrator kit.
Barcoded RNA-seq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit after ribosomal RNA depletion using the QIAseq FastSelect pan-bacterial and H/M/R kits. Libraries were sequenced on an Illumina NovaSeq 6000 S4 flow cell.

treatment_protocol: EZH2-deficient cells were generated by transducing Cas9-expressing Hoxb8 progenitors with a pLentiGuide-Puro vector containing an sgRNA targeting mouse Ezh2, followed by puromycin selection. Parental Cas9-expressing Hoxb8 progenitors without an Ezh2-targeting sgRNA were used as wild-type controls. Differentiated macrophages were infected with Mycobacterium tuberculosis Erdman smyc'::mCherry at a multiplicity of infection of 2. At 3 days post-infection, mCherry-positive macrophages were isolated by flow sorting. Uninfected samples were collected in parallel.

value: Hoxb8-derived macrophages

value: Mtb infected, 3 days post-infection


title: API_330_C3_H_R2

description:
Library name: Sample 8
raw cell lysate and Illumina NextSeq 2007

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: H

value: ATTGGTTGC

value: AACACAATC

tag: group

tag: replicate

tag: chemical type

value: test

tag: batch nr_heparg


title: ImprovedPool_Sort2_Human CD276

description:
Library name: Improved Pool_Sort2_Sample1
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human CD276


title: RNA-seq, pyramidal neurons, P13, Saline, rep8

description: Library name: P13_S_GG_04

tag: tissue

value: brain (frontal cortex)

tag: strain

tag: genotype

tag: age


title: HM9Pool_Sort1_mNeon positive

description:
Library name: HM9Pool_Sort1_Sample4
NGS-Read-Counts_HM9Pool.xlsx

value: Sorted for total mNeon positive population


title: API_326_C3_H_R1

description:
Library name: Sample 7
raw cell lysate and Illumina NextSeq 2006

tag: cell type

tag: chemical shortname

value: API

tag: chemical longname

value: apicidin

tag: dose

value: TGGAACGCT

value: TGTAACGGC


title: ImprovedPool_Sort1_Murine PDL1

description:
Library name: Improved Pool_Sort1_Sample7
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

tag: treatment

value: Stained with recombinant murine PD-L1


title: Mtb-infected Ezh2-deficient Hoxb8-derived macrophages at 3 days post-infection, biological replicate 1

description:
Library name: 7028D-BL10-EZH1TB
Column names in mouse and M. tuberculosis count matrices: EZHTB_1

value: Cas9-expressing Hoxb8 myeloid progenitor cells

value: Hoxb8-derived macrophages

value: Mtb infected, 3 days post-infection


title: RNA-seq, pyramidal neurons, P13, Saline, rep7

description: Library name: P13_S_GG_02

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline

value: Postnatal day 13

value: male


title: API_303_C2_H_R3

description:
Library name: Sample 6
raw cell lysate and Illumina NextSeq 2005

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: well

tag: dose group

tag: plate

value: H

tag: index

value: GATAGCGGA

value: TAAGTTACG

value: test


title: Mtb-infected Ezh2-deficient Hoxb8-derived macrophages at 3 days post-infection, biological replicate 2

description:
Library name: 7028D-BL11-EZH2TB
Column names in mouse and M. tuberculosis count matrices: EZHTB_2


title: ImprovedPool_Sort1_mNeon positive

description:
Library name: Improved Pool_Sort1_Sample6
NGS-Read-Counts_ImprovedPool.xlsx

value: Transduced HEK293T cells

value: Sorted for total mNeon positive population


title: API_330_C2_H_R2

description:
Library name: Sample 5
raw cell lysate and Illumina NextSeq 2004

value: API

value: apicidin

value: TGATTAAGC

value: AACACAATC

tag: group

tag: replicate

tag: cas-nr


title: RNA-seq, pyramidal neurons, P13, Saline, rep6

description: Library name: P13_S_GG_01

tag: tissue

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: Sex


title: ImprovedPool_Sort1_Human VTCN1_TechRep2

description:
Library name: Improved Pool_Sort1_Sample5
NGS-Read-Counts_ImprovedPool.xlsx

value: Stained with recombinant human VTCN1


title: Mtb-infected parental Hoxb8-derived macrophages at 3 days post-infection, biological replicate 3

description:
Library name: 7028D-BL9-HOX3TB
Column names in mouse and M. tuberculosis count matrices: HOXTB_3

value: Cas9-expressing Hoxb8 myeloid progenitor cells

value: Hoxb8-derived macrophages

tag: genotype

value: Parental (WT)

value: Mtb infected, 3 days post-infection


title: RNA-seq, pyramidal neurons, P13, Saline, rep5

description: Library name: P13_S_AC_04

tag: strain

value: Saline

tag: age

value: Postnatal day 13

value: male


title: Mtb-infected parental Hoxb8-derived macrophages at 3 days post-infection, biological replicate 2

description:
Library name: 7028D-BL8-HOX2TB
Column names in mouse and M. tuberculosis count matrices: HOXTB_2

tag: cell type


title: API_326_C2_H_R1

description:
Library name: Sample 4
raw cell lysate and Illumina NextSeq 2003

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: H

value: GATAGCGGA

value: GCTGCGTAT

tag: chemical type

value: test

tag: batch nr_heparg


title: ImprovedPool_Sort1_Human VTCN1_TechRep1

description:
Library name: Improved Pool_Sort1_Sample4
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Transduced HEK293T cells

tag: treatment


title: RNA-seq, pyramidal neurons, P13, Saline, rep4

description: Library name: P13_S_AC_02

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories


title: API_303_C1_H_R3

description:
Library name: Sample 3
raw cell lysate and Illumina NextSeq 2002

value: API

value: apicidin

tag: dose

tag: well

tag: dose group

tag: plate

value: AGCCGATTA

value: TAAGTTACG


title: ImprovedPool_Sort1_Human PDL1

description:
Library name: Improved Pool_Sort1_Sample3
NGS-Read-Counts_ImprovedPool.xlsx

value: Stained with recombinant human PD-L1


title: RNA-seq, pyramidal neurons, P13, Saline, rep3

description: Library name: P13_S_AC_01

value: Saline

value: Postnatal day 13

value: male


title: Mtb-infected parental Hoxb8-derived macrophages at 3 days post-infection, biological replicate 1

description:
Library name: 7028D-BL7-HOX1TB
Column names in mouse and M. tuberculosis count matrices: HOXTB_1

value: Cas9-expressing Hoxb8 myeloid progenitor cells

value: Hoxb8-derived macrophages

value: Parental (WT)

value: Mtb infected, 3 days post-infection


title: ImprovedPool_Sort1_Human CD276_TechRep2

description:
Library name: Improved Pool_Sort1_Sample2
NGS-Read-Counts_ImprovedPool.xlsx

value: Stained with recombinant human CD276


title: Liver_Control_52

city: Los Angeles

first: Rochelle

middle: Wing-hin

last: Lai

address: 675 Charles E. Young Drive South

department: Medicine

institute: University of California Los Angeles

description: Library name: Liver_Control_52

data_processing:
Reads were trimmed and aligned to the mm10 reference genome using STAR v.2.7.10a.
Raw gene counts were generated using featureCounts (Subread v.2.1.1).
Genes with low total counts (fewer than 600 across all samples) were retained and normalized using DESeq2 (v.1.38.3) median-of-ratios in R (v.4.2.1)
Assembly: mm10
Supplementary files format and content: txt file includes normalized gene counts for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from flash-frozen tissue samples using the RNeasy Mini Kit (Qiagen, Catalog #74104).
mRNA libraries were prepared from 800 ng RNA using the KAPA RNA Hyperprep Kit (KAPA Biosystems, Catalog #KK8541). Adapters used are from KAPA single index adapters (KK8700)

value: Liver


title: API_330_C1_H_R2

description:
Library name: Sample 2
raw cell lysate and Illumina NextSeq 2001

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: H

tag: index

value: TGCTTATTC

value: AACACAATC

tag: group

tag: replicate

value: test

tag: cas-nr


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep4

description: Library name: P0_P_AM_03

tag: tissue

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC

value: Postnatal day 0

tag: Sex


title: RNA-seq, pyramidal neurons, P13, Saline, rep2

description: Library name: P13_S_AB_02

tag: cell type

value: Saline

tag: age

value: Postnatal day 13

value: male


title: Liver_Control_50

description: Library name: Liver_Control_50


title: API_326_C1_H_R1

description:
Library name: Sample 1
raw cell lysate and Illumina NextSeq 2000

tag: chemical shortname

value: API

tag: chemical longname

value: apicidin

value: AGCCGATTA

value: GCTGCGTAT

tag: chemical type

tag: batch nr_heparg


title: FD-3653-1-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: VLCD


title: RNA-seq, pyramidal neurons, P13, Saline, rep1

description: Library name: P13_S_AB_01

tag: treatment


title: ImprovedPool_Sort1_Human CD276_TechRep1

description:
Library name: Improved Pool_Sort1_Sample1
NGS-Read-Counts_ImprovedPool.xlsx

tag: cell line

value: Transduced HEK293T cells

value: Stained with recombinant human CD276


title: Liver_Control_49

description: Library name: Liver_Control_49

value: Liver


title: PilotPool_Sort3_mNeon positive_TechRep2

description:
Library name: Pilot Pool_Sort3_Sample10
NGS-Read-Counts_PilotPool.xlsx

value: Sorted for total mNeon positive population


title: Liver_Orlistat_43

description: Library name: Liver_Orlistat_43


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep15

description: Library name: P0_P_ZZ_07

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC


title: PilotPool_Sort3_mNeon positive_TechRep1

description:
Library name: Pilot Pool_Sort3_Sample9
NGS-Read-Counts_PilotPool.xlsx


title: iPSC-derived-microglia  co-maturation culture (T2)

city: Nijmegen

first: Klaas

last: Mulder

address: Geert Grooteplein 26

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description:
Library name: FLEXLib2_T2
Sample id T2, probe barcode BC002, demultiplexed from library FLEXLib2 (10x Genomics Chromium Fixed RNA/Flex assay)

data_processing:
Raw sequencing data were demultiplexed and processed using the Cell Ranger pipeline (10x Genomics, Cell Ranger v9.0.0).
Reads were aligned to the human reference genome refdata-gex-GRCh38-2024-A using the Chromium_Human_Transcriptome_Probe_Set_v1.1.0_GRCh38-2024-A probe set.
Quality control, normalization, library integration, doublet detection, clustering and differential gene expression analysis were performed in Seurat (v4.3.0) in R. Cells with fewer than 200 genes, fewer than 500 UMIs, or more than 10% mitochondrial content were removed; cells with UMI counts >2 SD above the mean, and cells with mixed expression profiles/floating cluster shape, were excluded as doublets.
Harmony (v1.2.3) was used to integrate the three batches/libraries.
Cell types were annotated based on the top differentially expressed genes per Seurat cluster; CellChat (v2.1.2) was used to infer ligand-receptor interactions (human CellChatDB, default settings, interactions with <10 cells filtered out).
Assembly: GRCh38 (refdata-gex-GRCh38-2024-A / Chromium_Human_Transcriptome_Probe_Set_v1.1.0_GRCh38-2024-A)
Supplementary files format and content: Cell Ranger multi (10x Genomics) filtered feature-barcode matrix per Sample: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Coriell, GM25256

growth_protocol: hiPSC-derived microglia progenitor cells (HPCs) and neurons were differentiated and co-matured according to the co-maturation protocol described in this manuscript; astrocytes were added to support long-term microglia survival and integration. Cultures were maintained until day in vitro (DIV) 28 prior to dissociation.

extract_protocol:
At DIV 28, cultures were dissociated using Accutase (20 min at 37°C) to obtain single-cell suspensions. Microglia monocultures received the same PLO/human laminin coating as co-cultures and were processed identically for a fair comparison, even though they required a shorter incubation than the denser neuron-glia networks.
Single-cell suspensions were fixed for 24 hours at 4°C and stored with Enhancer at -80°C. Libraries were generated using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics, PN-1000414) and the Chromium Single Cell Flex Kit (10x Genomics, protocol CG000527 Rev F). Samples were incubated for 20 hours at 42°C with an anti-human probe set. Each condition received a unique probe barcode (BC001-BC004) for multiplexing. After pooling and washing, three lanes of a 10x Chip Q were loaded, with each condition represented in every final lane/library (FLEXLib1-3).

value: Coriell, GM25256

value: Microglia + neurons + astrocytes

value: WT

tag: batch

value: FLEXLib2 (BC002)


title: iPSC-derived-microglia mono-  (M2) + co-maturation culture (T3)

description:
Library name: FLEXLib3_M2_T3
Sample id M2, probe barcode BC001, demultiplexed from library FLEXLib3 (10x Genomics Chromium Fixed RNA/Flex assay). Sample id T3, probe barcode BC002, demultiplexed from library FLEXLib3 (10x Genomics Chromium Fixed RNA/Flex assay).

value: FLEXLib3 (BC001 and BC002)


title: PilotPool_Sort3_Human PDL1_TechRep4

description:
Library name: Pilot Pool_Sort3_Sample8
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human PD-L1


title: Liver_Orlistat_42

description: Library name: Liver_Orlistat_42


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep2

description: Library name: P0_P_AO_1

value: Postnatal day 0

value: male


title: iPSC-derived-microglia mono-  (M1) + co-maturation culture (T1)

description:
Library name: FLEXLib1_M1_T1
Sample id M1, probe barcode BC001, demultiplexed from library FLEXLib1 (10x Genomics Chromium Fixed RNA/Flex assay). Sample id T1, probe barcode BC003, demultiplexed from library FLEXLib1 (10x Genomics Chromium Fixed RNA/Flex assay)

value: FLEXLib1 (BC001 and BC003)


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep13

description: Library name: P0_P_ZZ_02


title: Liver_Orlistat_41

description: Library name: Liver_Orlistat_41


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep14

description: Library name: P0_P_ZZ_04


title: rAAV2CBE, igg_ctrl, biol_rep3

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

description: Library name: rAAV2CBE sample 13

data_processing:
GitHub CUT&RUN pipeline doi: 10.5281/zenodo.5653535
genomes (human genome was excluded) using Bowtie2. Reads were sorted, and quality checked by samtools and picard before processed into coverage files (BEDtools) which were used for downstream processing. Genome coverage was computed from the aligned BAM files and scaled to sequencing depth using reads per million mapped reads (RPM).
Samples were then normalized to corresponding IgG control signal per bin across the genome. Normalized RPM signal was calculated by (Target RPM) – (IgG RPM). Negative values were set to zero and signal peaks over IgG levels were further processed. IgG normalization was performed by matching each target replicate to its corresponding IgG control replicate
Samples without a matching igg were normalized to each avalible igg for the biological condition independently then averaged between to produce a single normalized file.
Replicate normalized RPM peaks were averaged at each base pair
Assembly: Human genome (hg38)
Supplementary files format and content: bedgraph, RPM and RPM normalized to igg
Library strategy: CUT&Run

source_name: Kidney

growth_protocol: Human embryonic kidney cells (HEK293T) in Dulbecco’s modified Eagle’s medium (DMEM, high glucose; Gibco) supplemented with 5% Serum Plus and 50 µg/ml gentamicin (Gibco). All cells were cultured at 37°C and 5% CO2.

extract_protocol:
Cells were processed using the Epicypher kit (14-1048)
Libraries were prepped using the Epicypher kit (14-1001 and 14-1002)

treatment_protocol: 500,000 HEK293T cells infected for 24 hours were used per antibody reaction.

value: Kidney

value: HEK 293T

value: Human Embryonic Kidney

tag: antibody


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep12

description: Library name: P0_P_YY_06

tag: tissue


title: PilotPool_Sort3_Human PDL1_TechRep2

description:
Library name: Pilot Pool_Sort3_Sample6
NGS-Read-Counts_PilotPool.xlsx

value: Transduced HEK293T cells


title: Liver_Control_15

description: Library name: Liver_Control_15

value: Liver


title: rAAV2CBE, igg_ctrl, biol_rep2

description: Library name: rAAV2CBE sample 12


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep10

description: Library name: P0_P_RR_06

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep11

description: Library name: P0_P_YY_02

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Poly IC


title: rAAV2CBE, igg_ctrl, biol_rep1

description: Library name: rAAV2CBE sample 11


title: PilotPool_Sort3_Human CD276_TechRep4

description:
Library name: Pilot Pool_Sort3_Sample4
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human CD276


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep9

description: Library name: P0_P_RR_05

tag: Sex


title: Liver_Control_14

description: Library name: Liver_Control_14


title: PilotPool_Sort3_Human CD276_TechRep3

description:
Library name: Pilot Pool_Sort3_Sample3
NGS-Read-Counts_PilotPool.xlsx


title: rAAV2CBE, H3K9me3, biol_rep2

description: Library name: rAAV2CBE sample 9

tag: cell type


title: rAAV2CBE, H3K9me3, biol_rep3

description: Library name: rAAV2CBE sample 10


title: PilotPool_Sort3_Human PDL1_TechRep1

description:
Library name: Pilot Pool_Sort3_Sample5
NGS-Read-Counts_PilotPool.xlsx


title: Liver_Orlistat_4

description: Library name: Liver_Orlistat_4


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep8

description: Library name: P0_P_BB_04

tag: age


title: Liver_Orlistat_3

description: Library name: Liver_Orlistat_3


title: PilotPool_Sort3_Human CD276_TechRep2

description:
Library name: Pilot Pool_Sort3_Sample2
NGS-Read-Counts_PilotPool.xlsx


title: Liver_Orlistat_2

description: Library name: Liver_Orlistat_2


title: rAAV2CBE, H3K9me3, biol_rep1

description: Library name: rAAV2CBE sample 8


title: PilotPool_Sort3_Human CD276_TechRep1

description:
Library name: Pilot Pool_Sort3_Sample1
NGS-Read-Counts_PilotPool.xlsx


title: RNA-seq, pyramidal neurons, P0, Saline, rep16

description: Library name: P0_S_W_09

value: Saline


title: RNA-seq, pyramidal neurons, P0, Poly IC, rep7

description: Library name: P0_P_BB_02


title: rAAV2CBE, H3K4me3, biol_rep3

description: Library name: rAAV2CBE sample 7


title: RKP_TEAD1

description: Library name: RKP_TEAD1

data_processing:
Sequencing reads from CUT&RUN libraries were aligned to the Mus musculus M34 reference genome using Bowtie2 (v2.4.2) [PMID: 22388286] with parameters optimized for short paired-end fragments. Aligned reads were coordinate-sorted and PCR duplicates were marked using Picard (v3.0) tools (SortSam and MarkDuplicates). BAM files were generated using SAMtools (v1.21) [PMID: 33590861], and genome-wide coverage tracks were produced in BEDGRAPH format using BEDTools (v2.31.1) [PMID: 20110278] for downstream visualization and signal quantification.
Assembly: Reads were aligned to the GRCm38/mm10 genome
Supplementary files format and content: bigwig file
Library strategy: CUT&Run

source_name: RKP

extract_protocol:
2D-cultured EKP and RKP cells were harvested at 5x105 cells per sample.
CUT&RUN assays were performed using the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher) following the manufacturer’s protocol. Briefly, target cells were harvested and immobilized on Concanavalin A-coated magnetic beads. The bead-bound cells were incubated with antibodies against target proteins, followed by binding of pA-MNase. Targeted chromatin digestion was triggered by calcium activation, and DNA fragments were released and purified using a Zymo DNA Clean & Concentrator kit. For library preparation, we used the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Briefly, 6 ng of CUT&RUN DNA was used as input, and adaptor ligation was carried out with 0.6–4 pmol of adaptor, depending on dimer contamination. Post-ligation, DNA was purified using SPRIselect beads and eluted in 0.1× TE buffer. PCR amplification of adaptor-ligated DNA was performed using NEBNext Ultra II Q5 Master Mix and indexed Illumina-compatible primers for 12 cycles. The resulting libraries were further purified by bead-based size selection and quantified. Libraries were sequenced on an Illumina platform using paired-end 150 bp reads.

value: RKP

value: gastric cancer epithelial cell


title: rAAV2CBE, H3K4me3, biol_rep2

description: Library name: rAAV2CBE sample 6


title: RNA-seq, pyramidal neurons, P0, Saline, rep15

description: Library name: P0_S_W_08


title: PilotPool_Sort2_mNeon positive_TechRep4

description:
Library name: Pilot Pool_Sort2_Sample12
NGS-Read-Counts_PilotPool.xlsx

value: Sorted for total mNeon positive population


title: rAAV2CBE, H3K4me3, biol_rep1

description: Library name: rAAV2CBE sample 5


title: EKP_TEAD1

description: Library name: EKP_TEAD1

source_name: EKP

value: EKP


title: rAAV2CBE, H3K27ac, biol_rep2

description: Library name: rAAV2CBE sample 4


title: RNA-seq, pyramidal neurons, P0, Saline, rep13

description: Library name: P0_S_W_03

value: Postnatal day 0

value: male


title: RNA-seq, pyramidal neurons, P0, Saline, rep12

description: Library name: P0_S_W_02


title: rAAV2CBE, CTCF, biol_rep2

description: Library name: rAAV2CBE sample 2

value: Kidney

value: CTCF


title: PilotPool_Sort2_mNeon positive_TechRep1

description:
Library name: Pilot Pool_Sort2_Sample9
NGS-Read-Counts_PilotPool.xlsx


title: PilotPool_Sort2_Human VTCN1_TechRep2

description:
Library name: Pilot Pool_Sort2_Sample8
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human VTCN1


title: rAAV2CBE, H3K27ac, biol_rep1

description: Library name: rAAV2CBE sample 3

value: HEK 293T

value: Human Embryonic Kidney


title: RNA-seq, pyramidal neurons, P0, Saline, rep11

description: Library name: P0_S_NN_05

value: brain (frontal cortex)


title: Control-3

city: Bengbu City, Anhui Province

first: Bohan

last: Li

address: 安徽省蚌埠市东海大道2600号

department: School of Pharmacy

country: China

institute: Bengbu Medical University

description: Library name: SAMPLES 5

data_processing:
Raw reads were filtered to remove adapter sequences and low‑quality reads using  fastp (0.23.0).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 （ Hierarchical Indexing for Spliced Alignment of Transcripts ）.
Gene expression levels were used HTSeq (0.10.0) for reads count calculation. HTSeq provides three overlap resolution modes — union, intersection_strict, and intersection_nonempty — to determine whether a read is assigned to a given gene..
Differentially expressed genes (DEGs) were identified using DESeq2 (1.18.1) with edegR (3.20.9)
KEGG and GO pathway enrichment analyses were performed using clusterProfiler (4.8.2) in R.
Assembly: hg38
Supplementary files format and content: Processed data files include a gene expression matrix (FPKM values) for all samples.
Supplementary files format and content: Raw count matrix and differential expression and enrichment results are also provided.

molecule: other

source_name: Cancer

growth_protocol: Triple-negative breast cancer cells were cultured inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco) in a humidified incubator with 5% CO₂ at 37°C.

extract_protocol:
Total RNA was extracted from cells using TRIzol® reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA purity and integrity were assessed using a NanoDrop™ One/OneC spectrophotometer and anAgilent 4200 TapeStation.
RNA‑seq libraries were constructed using theAMPure XP beads following the manufacturer’s protocol

treatment_protocol: Cells were treated with MAG (40 μM) for 24 h.

value: Cancer

value: TNBC

value: Control


title: rAAV2CBE, CTCF, biol_rep1

description: Library name: rAAV2CBE sample 1


title: PilotPool_Sort2_Human VTCN1_TechRep1

description:
Library name: Pilot Pool_Sort2_Sample7
NGS-Read-Counts_PilotPool.xlsx

value: Transduced HEK293T cells


title: RNA-seq, pyramidal neurons, P0, Saline, rep10

description: Library name: P0_S_NN_04

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline


title: rAAV2, igg_ctrl, biol_rep3

description: Library name: rAAV2 sample 11


title: rAAV2, igg_ctrl, biol_rep2

description: Library name: rAAV2 sample 10


title: Control-2

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 3


title: RNA-seq, pyramidal neurons, P0, Saline, rep8

description: Library name: P0_S_LL_06


title: MAG-1

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 2

value: MAG


title: rAAV2, igg_ctrl, biol_rep1

description: Library name: rAAV2 sample 9


title: RNA-seq, pyramidal neurons, P0, Saline, rep7

description: Library name: P0_S_LL_04


title: rAAV2, H3K9me3, biol_rep2

description: Library name: rAAV2 sample 8


title: PilotPool_Sort2_Human PDL1_TechRep1

description:
Library name: Pilot Pool_Sort2_Sample3
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human PD-L1


title: RNA-seq, pyramidal neurons, P0, Saline, rep6

description: Library name: P0_S_LL_03

value: Postnatal day 0


title: rAAV2, H3K9me3, biol_rep1

description: Library name: rAAV2 sample 7


title: PilotPool_Sort2_Human CD276_TechRep2

description:
Library name: Pilot Pool_Sort2_Sample2
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human CD276


title: MZythdf2 6 hours post fertilization rep1

city: Farmington

first: Jean-Denis

last: Beaudoin

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health Center

description:
Library name: ythdf2KO_6hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv

data_processing:
Master of Pores pipeline version 2 (MOP2):The mop_preprocess module was used to basecall the raw signal with Guppy v6.0.6 (Oxford Nanopore Technologies) using the m6A-aware basecalling model rna_r9.4.1_70bps_m6A_hac.cfg (m6Abasecaller).
The DeePlexiCon algorithm was used to demultiplex multiplexed reads.
ModPhred used to encode the modification probabilities and map reads to the GRCz11 genome with minimap2 2.17-r941 using the parameters “-ax map-ont -k13”.
Per-read gene and isoform annotation using the samtools flag “-F 3488”, with Isoquant v3.3.0 using parameters “--complete_genedb --data_type nanopore” and the zebrafish Ensembl annotation version 110. Poly(A) tail length estimation was performed using the mop_tail module of MoP2 with tailfindr v1.3.
m6AB_PerRead pipeline generated replicable m6A sites and per_read tables. For isoform-level and read-level analysis, reads were required to map uniquely to a single isoform that had at least 25 reads per replicate. Reads lacking a tailfindr poly(A) tail estimate (NaN values) were removed (pa_filtered files).
Assembly: GRCz11
Supplementary files format and content: SDataset5,6,7... .csv file of per_read tables produced by the m6AB_PerRead pipeline (m6Abasecaller_per_read_analysis) that has been filtered for isoform-level and read-level analysis. This includes isoform/gene assignment, m6A modification number and location, read length, poly(A) tail length, and relevant timepoint/treatment for each read.
Supplementary files format and content: SDataset8.. .tsv file of replicable m6A sites with information on their chromosome position, coverage, and modification frequency.
Supplementary files format and content: SDataset9,10,11... .csv file of pre_read tables produced by the m6AB_PerRead pipeline that includes m6A modification number and location, chromosomal alignment information, poly(A) tail length, isoform/gene assignment information, and sample for each read.

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were maintained at 28 °C

extract_protocol:
RNA from frozen embryos was extracted using TRIzol (Invitrogen).  Poly(A)+ mRNAs were isolated with oligo d(T)25 magnetic beads (New England BioLabs) according to the manufacturer’s protocol and eluted in 30 µL of water.
RNA libraries were prepared using the direct RNA sequencing kit (SQK-RNA002), following ONT protocol version DRS_9080_v2_revI_14Aug2019 with half reactions of 250 ng of poly(A)+ RNA for each library up to the RNA Adapter (RMX) ligation step, with the following adaptations. Samples were ligated to pre-annealed custom RT adaptors (IDT) containing barcodes. For non-barcoded runs, the commercial RT adapter included in the SQK-RNA002 kit was used instead. Reverse transcription was then performed. Ligated products were purified using 1.8X Agencourt RNAClean XP beads (Fisher Scientific, NC0068576).For the final ligation, 50 ng of reverse-transcribed RNA from each reaction was pooled, and ligated with the RMX adapter. For non-barcoded runs, 200 ng of reverse-transcribed RNA was used for ligation with the RMX adapter. The ligated RNA:DNA hybrid was purified using 1X Agencourt RNAClean XP beads. Samples were run on a R9.4.1 flowcell on a MinION or PromethION device.

treatment_protocol: All injections into zebrafish embryos were performed on dechorionated one-cell stage embryos with 1 nL volumes. To inhibit RNA Polymerase II, embryos were injected with 0.2 ng of α-amanitin (Sigma-Aldrich, A2263) resuspended in nuclease-free water. To inhibit miR-430 activity, embryos were injected with 10 µM of tiny locked nucleic acid (tinyLNA), complementary to the seed region of miR-430 (5′-TAGCACTT-3′ (Exiqon)).

value: embryos

tag: sample group

value: MZythdf2 6 hours post fertilization


title: rAAV2, H3K4me3, biol_rep2

description: Library name: rAAV2 sample 6

value: Kidney


title: PilotPool_Sort2_Human CD276_TechRep1

description:
Library name: Pilot Pool_Sort2_Sample1
NGS-Read-Counts_PilotPool.xlsx


title: PAT - T2D_4

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: Library name: P19

data_processing:
Raw reads were aligned to the hg38 genome, with HISAT2 (2.2.1). FeatureCounts (2.0.6) was used to count the reads number mapped to each gene. The differentially expressed genes analyses between groups were performed using DESeq2 with the standard RNA-seq workflow, genes with counts <100 were filtered.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains fpkm data of all samples ("gene_fpkm")

source_name: Peripancreatic adipose tissue (PAT)

extract_protocol:
RNA was extracted from PAT snap frozen tissues of the 5 CTRL, 12 pancreatitis and 5 donors with T2D using the gentle MACS dissociator and the RNeasy lipid tissue kit (QIAGEN).
RNA-seq libraries were prepared and sequenced using standard Illumina protocols for a HiSeq 2500 instrument.

value: Peripancreatic adipose tissue (PAT)

tag: cell origin

value: adipose tissue

tag: condition


title: MZythdf2 2 hours post fertilization rep2

description:
Library name: ythdf2KO_2hpf_Rep2
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv

value: MZythdf2 2 hours post fertilization


title: rAAV2, H3K4me3, biol_rep1

description: Library name: rAAV2 sample 5

value: HEK 293T

value: Human Embryonic Kidney


title: PilotPool_Sort1_mNeon positive_TechRep4

description:
Library name: Pilot Pool_Sort1_Sample14
NGS-Read-Counts_PilotPool.xlsx

value: Sorted for total mNeon positive population


title: PAT - T2D_3

description: Library name: P18


title: MZythdf2 2 hours post fertilization rep1

description:
Library name: ythdf2KO_2hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv


title: rAAV2, H3K72ac, biol_rep2

description: Library name: rAAV2 sample 4


title: PilotPool_Sort1_mNeon positive_TechRep3

description:
Library name: Pilot Pool_Sort1_Sample13
NGS-Read-Counts_PilotPool.xlsx

value: Transduced HEK293T cells


title: sibling wildtype 6 hours post fertilization rep2

description:
Library name: WT-matched_6hpf_Rep2
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv

value: WT


title: rAAV2, H3K72ac, biol_rep1

description: Library name: rAAV2 sample 3


title: PilotPool_Sort3_Human PDL1_TechRep3

description:
Library name: Pilot Pool_Sort3_Sample7
NGS-Read-Counts_PilotPool.xlsx


title: PilotPool_Sort1_mNeon positive_TechRep2

description:
Library name: Pilot Pool_Sort1_Sample12
NGS-Read-Counts_PilotPool.xlsx


title: Liver_Control_16

description: Library name: Liver_Control_16

value: Liver


title: PAT - T2D_1

description: Library name: P15


title: sibling wildtype 6 hours post fertilization rep1

description:
Library name: WT-matched_6hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv


title: rAAV2, CTCF, biol_rep3

description: Library name: rAAV2 sample 2

value: CTCF


title: RNA-seq, pyramidal neurons, P0, Saline, rep14

description: Library name: P0_S_W_05

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline

value: male


title: RKP_positive control

description: Library name: RKP_H3K4Me3

value: RKP

value: gastric cancer epithelial cell


title: PilotPool_Sort2_mNeon positive_TechRep3

description:
Library name: Pilot Pool_Sort2_Sample11
NGS-Read-Counts_PilotPool.xlsx


title: PilotPool_Sort1_mNeon positive_TechRep1

description:
Library name: Pilot Pool_Sort1_Sample11
NGS-Read-Counts_PilotPool.xlsx


title: PAT - HP5

description: Library name: P27

value: Peripancreatic adipose tissue (PAT)

value: Resolved pancreatitis (HP)


title: rAAV2, CTCF, biol_rep1

description: Library name: rAAV2 sample 1

value: Kidney


title: PilotPool_Sort1_Human VTCN1_TechRep2

description:
Library name: Pilot Pool_Sort1_Sample10
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human VTCN1


title: PAT - HP4

description: Library name: P13

value: adipose tissue


title: MAG-3

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 6

value: Cancer

value: TNBC

value: MAG


title: AAV2CBE, igg_ctrl, biol_rep2

description: Library name: AAV2CBE sample 11

value: HEK 293T

value: Human Embryonic Kidney


title: sibling wildtype 2 hours post fertilization rep2

description:
Library name: WT-matched_2hpf_Rep2
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv

value: embryos

value: WT


title: PilotPool_Sort2_mNeon positive_TechRep2

description:
Library name: Pilot Pool_Sort2_Sample10
NGS-Read-Counts_PilotPool.xlsx

value: Transduced HEK293T cells

value: Sorted for total mNeon positive population


title: EKP_postive control

description: Library name: EKP_H3K4Me3

value: EKP


title: PAT - T2D_2

description: Library name: P16


title: MAG-2

address: 安徽省蚌埠市东海大道2600号

description: Library name: SAMPLES 4


title: sibling wildtype 2 hours post fertilization rep1

description:
Library name: WT-matched_2hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv


title: PilotPool_Sort2_Human PDL1_TechRep4

description:
Library name: Pilot Pool_Sort2_Sample6
NGS-Read-Counts_PilotPool.xlsx

value: Stained with recombinant human PD-L1


title: PilotPool_Sort1_Human PDL1_TechRep8

description:
Library name: Pilot Pool_Sort1_Sample8
NGS-Read-Counts_PilotPool.xlsx


title: AAV2CBE, H3K9me3, biol_rep1

description: Library name: AAV2CBE sample 9


title: PilotPool_Sort1_Human PDL1_TechRep7

description:
Library name: Pilot Pool_Sort1_Sample7
NGS-Read-Counts_PilotPool.xlsx


title: AAV2CBE, H3K4me3, biol_rep3

description: Library name: AAV2CBE sample 8


title: PilotPool_Sort1_Human VTCN1_TechRep1

description:
Library name: Pilot Pool_Sort1_Sample9
NGS-Read-Counts_PilotPool.xlsx


title: PAT - HP3

description: Library name: P12