title: Split_4C-rep6-blastomere3

description:
Library name: 4C_Split_6_B3
Column name in counts_allsample.txt: 4C_Split_6_B3


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 009 | Full ROI

status: Public on Jun 01 2026

type: SRA

city: Boston

first: Emmanuel

last: Ogbonna

state: MA

address: 200 Longwood Ave

department: Laboratory of Systems Pharmacology

country: USA

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_B5_scan1 | 009 | Full ROI
FFPE

library_source: transcriptomic

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: tuberculosis-infected human lung tissue

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

tag: tissue

value: tuberculosis-infected human lung tissue

tag: batch

tag: histopathological region

value: TLS

tag: patient id


title: Split_4C-rep7-blastomere4

city: Xuhui, Shanghai

first: Jie

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai

country: China

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

description:
Library name: 4C_Split_7_B4
Column name in counts_allsample.txt: 4C_Split_7_B4

data_processing:
Raw reads were firstly processed through Trim Galore (v0.6.10) with the default parameters. In this step, clean reads were obtained by removing reads containing adapter and low-quality reads from raw data. Reference genome (GRCm38) and gene model annotation files (Release M25) were downloaded from GENCODE database (http://gencodegenes.org/mouse/release_M25.html). Paired-end clean reads were aligned to the reference genome using STAR (v2.7.3a). The abundance of transcripts and genes was estimated from the aligned reads using RSEM (v1.2.28). RSEM provided quantification of gene expression metrics including expected read counts, TPM (transcripts per million), and FPKM (fragments per kilobase of transcript per million mapped reads).
Assembly: GRCm10/mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

organism: Mus musculus

source_name: embryo

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent  (Invitrogen, Carlsbad, CA, USA)following the manufacturer's procedure. SMARTer cDNA synthesis starts with picogram amounts of total RNA.
To construct Smart-seq2 libraries from 2-cell or 4-cell mouse embryos/blastomeres, individual embryos (or blastomeres) are gently lysed to release mRNA, which is then reverse transcribed using an oligo-dT primer and a template-switching oligo to generate full-length cDNA.  The resulting cDNA is pre-amplified by PCR, purified using magnetic beads, and quantified.  Next, the cDNA is fragmented and tagged with sequencing adapters using a tagmentation (Nextera or Tn5) reaction. The final libraries are cleaned up, assessed for quality and concentration, and then subjected to high-throughput sequencing.

value: embryo

tag: cell type

value: 4-cell (Split)

tag: genotype

value: WT


title: Split_4C-rep6-blastomere2

description:
Library name: 4C_Split_6_B2
Column name in counts_allsample.txt: 4C_Split_6_B2


title: OSA-6

type: RNA

city: Beijing

first: shilan

last: li

address: No. 56 Nanlishi Road, Xicheng District

department: Department of Otolaryngology – Head and Neck Surgery

institute: Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health

description: glossopalatine arch mucosa

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.  scan protocol After hybridization, slides were scanned on the Agilent Microarray Scanner G5761A (Agilent technologies, Santa Clara, CA, US).

scan_protocol: the arrays were scanned using the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Raw data were extracted with Feature Extraction software (version 10.7.1.1, Agilent Technologies), and basic analysis was performed using Genespring software (version 14.8, Agilent Technologies).

label_protocol: Sample labeling, microarray hybridization, and washing were performed according to the manufacturer's protocols.

extract_protocol: In brief, total RNA was quantified with the NanoDrop ND-2000 (Thermo Scientific), and RNA integrity was evaluated using the Agilent Bioanalyzer 2100 (Agilent Technologies).

value: glossopalatine arch mucosa

tag: location

value: Beijing children hospital


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 008 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 008 | Full ROI
FFPE


title: 2DR1F9HE_S93

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DR1F9HE_S93_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq rat S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Rat S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Heart

tag: strain

value: Sprague-Dawley

tag: Sex

value: female

tag: age

value: 9 weeks

tag: treatment

tag: concentration (ppm)

tag: sample status

value: Used in Analysis

tag: qc issue


title: 2DR1F9LI_S101

description: Library name: 2DR1F9LI_S101_R1_001

source_name: Liver Left Lobe

value: Liver Left Lobe


title: young_bleo_2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Library name: S18

library_source: genomic

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore (Trim Galore) (v0.4.5) with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20 –rrbs.
Reads are aligned to mm10 with Bismark (Krueger and Andrews, 2011) (v0.22.1) using Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4) with default settings (multi-seed length of 20bp with 0 mismatches).
Alignments below a MAPQ threshold are removed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10.
MethylDackel (MethylDackel) (v0.4.0) then calls methylation rates with parameters -d 5 -D 2000 –mergeContext.
Assembly: mm10
Supplementary files format and content: bedGraph of methylation calls from MethylDackel

molecule: genomic DNA

source_name: Lung fibroblasts

extract_protocol:
Lungs were minced with a razor blade and tissue was digested with 0.2 mg/mL of Liberase DL and 100 U/mL DNase I (Roche, Indianapolis, IN, USA) for 40 min at 37 °C. Digestion was stopped with medium containing 10% FBS and cells were passed through a 40 µm cell strainer (ThermoFisherScientific, Waltham, MA). Cells were incubated with 2 mL with red cell lysis buffer for 90 seconds. Cells were centrifuged before undergoing FACS sorting using antibodies against CD45:PerCpCy5.5 (1:200, Biolegend, San Diego, CA, USA, Cat# 103132), CD31:PE (1:200, Biolegend, San Diego, CA, USA, Cat#102408), EpCAM:APC (1:200,Biolegend, San Diego, CA, USA, Cat#118214). They were also stained with DAPI (1:1000, Biolegend, San Diego, CA, USA, Cat#422801). DAPI-positive, GFP-positive cells were sorted by FACS using the BD FACS Aria II (BD Biosciences, San Jose, CA, USA).
25-75 ng of genomic DNA was digested for 16-18 hours with the MspI restriction enzyme. The digested DNA was purified by phenol-chloroform extraction, then ethanol precipitated in the presence of glycogen and sodium acetate. The precipitated DNA was resuspended in 10mM Tris-Cl pH8.5 (Buffer EB) and processed for end-repair, A-tailing, and ligation of hairpin adapters with methylated cytosines. The ligated DNA was next ran on a 1.8% Low-Range Ultra Agarose Gel in TBE buffer, and fragments of 100-200bp and 200-300bp were excised and separately purified using Qiagen Gel Extraction kit. A 2ul aliquot of each fragment was used to verify proper adapter ligation and size selection by PCR. Samples passing this QC were then subjected to bisulfite conversion with the EZ DNA Methylation Kit, but with the following changes: the samples were incubated in a thermal cycler using the following conditions: 55 cycles: 95C for 30 sec, 50C for 15 min. Hold at 4C. The bisulfite converted samples were cleaned up according to the manufacturer’s protocol and eluted in 40ul of nuclease free water. The samples were next amplified using Roche High Fidelity FastStart system with the following protocol: 94C for 5 minutes; 18 cycles of: denaturing at 94C for 20 seconds, annealing at 60C for 30 seconds, extension at 72C for 1 min. A final extension was done at 72C for 3 minutes and the reactions were kept at 4C until they were cleaned. This final library cleanup was done with Agencourt’s AMPure XP SPRI beads according to the following protocol: The beads were brought to room temperature with gentle agitation for a minimum of 30 minutes. A 1.2X volume (for short fragments) and 1.1X volume (for long fragments) of SPRI beads was added to each sample fragment, and the PCR products were purified per manufacturer’s recommendation using 500ul of 80% ethanol for washes. Each library was eluted into 33ul of elution buffer (10mM Tris-Cl pH 8.5). The libraries were quantified using Qubit’s High Sensitivity ds DNA kit, and the quality was assessed with Agilent’s High Sensitivity D1000 ScreenTape assay.

treatment_protocol: Col1a1-GFP mice on a FVB background  were obtained from Derek Radisky (Mayo Clinic, Jacksonville, Florida, USA) and were maintained in breeding colonies. Mice were allowed to mature to either 6-8 weeks (young) or > 18 months (aged) of age. Nine mice in each group (aged and young) were treated with 50 µl of either intratracheal bleomycin (1.2 U/kg, APP Pharmaceutical, Schaumburg, IL) (five mice per group) or saline (four mice per group), delivered using a MicroSprayer (Penn-Century). Mice were euthanized at day 30 post-intratracheal treatment. Fibroblasts were isolated by FACS sorting for GFP.

value: Lung fibroblasts

value: young

value: bleo


title: Split_4C-rep6-blastomere1

description:
Library name: 4C_Split_6_B1
Column name in counts_allsample.txt: 4C_Split_6_B1


title: OSA-7

description: glossopalatine arch mucosa


title: OSA-5

description: glossopalatine arch mucosa


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 007 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 007 | Full ROI
FFPE


title: 1428-NPC-TDN-Pool1-a

first: Carlos

last: Aguilar

address: 2800 Plymouth Rd.,

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

description:
Library name: 1428NPCa
Column names in processed data files: 1428aNPC

data_processing:
FASTQ samples were assessed for quality using the FASTQC toolkit.
The reads were then trimmed to 30 bases using cutadapt (v4.6).
Trimmed reads were aligned to the GRCh38 reference genome via the STAR aligner (v 2.7.5b). Transcripts were quantified via RSEM (v1.3.3).
TPM (transcripts per million) values from RSEM were filtered for input into differential expression and pathway enrichment analysis.
Downstream analysis was restricted to genes with TPM >=1 in at least one of the samples analyzed, and variance in TPM > 0.01 across the set of samples. Analysis was further restricted to ENSGID’s from Gencode (v43) that were assigned the following gene types in the Gencode GTF annotation: protein_coding, rRNA, ribozyme, sRNA, IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, Mt_rRNA, Mt_tRNA, TR_C_Genne, TR_D_gene, TR_J_gene, TR_V_gene. Limma’s voom function in R (https://bioconductor.org/packages/release/bioc/html/limma.html) was applied to transform the TPM to a log2 scale and apply quantile normalization.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Tab-delimited text file includes FPKM for each Sample.
Supplementary files format and content: Tab-delimited text file includes TPM for each Sample.
Supplementary files format and content: Tab-delimited text file includes metadata manifest information for each sample.

source_name: Neuron progenitor cells

growth_protocol: Prior to differentiation, all iPSC lines were cultured and maintained in mTeSR+ (Stem Cell Technologies) at 37 degrees C and 5% CO2 on Cultrex (R&D Systems, Bio-Techne) coated plates with 10 µM ROCK inhibitor (Y27632, Selleck Chemicals).

extract_protocol:
Total RNA was extracted from NPCs using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quality was assessed using a Bioanalyzer (Agilent Technologies).
Library preparation was performed using the KAPA Stranded mRNA-Seq Kit (Roche) following manufacturer’s instructions.

treatment_protocol: iPSC-derived NPCs were generated in Essential 6 Medium (Thermo Fisher) supplemented with small chemical inhibitors of TGF, SMAD, and Wnt pathways. iPSCs were treated with 500 nM LDN193189 (Tocris), 10 µM SB431542 (Tocris), and 2 µM XAV939 (Tocris) for the first three days and then 500 nM LDN193189 and 10µM SB431542 for the remaining nine days of differentiation. Medium was freshly made and replaced daily. NPCs were collected at Day12 for RNA-sequencing.

value: Neuron progenitor cells

tag: group

value: TDN


title: Split_4C-rep4-blastomere4

description:
Library name: 4C_Split_4_B4
Column name in counts_allsample.txt: 4C_Split_4_B4


title: OSA-4

description: glossopalatine arch mucosa


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 006 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 006 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: OSA-3

description: glossopalatine arch mucosa


title: JORRP Patient 46-2

description: Papilloma

source_name: JORRP Patient 46-2

value: Papilloma


title: OSA-2

description: glossopalatine arch mucosa


title: OSA-1

description: glossopalatine arch mucosa


title: KPC49bKO pancreatic tumor, in vivo, biological replicate 2

city: BOSTON

first: Ibrahim

middle: R

last: Eissa

state: MASSACHUSETTS

address: 55 Fruit St.,

department: Surgical Oncology

institute: Massachusetts general hospital

description:
Library name: KPC49BKO_tumor_rep2
Bulk RNA-seq of KPC49BKO tumor, in vivo. ERCC spike-ins included.

data_processing:
Raw reads were trimmed for adapters and deduplicated using fastp v.0.23.1
Trimmed reads were aligned to the Mus musculus GRCm38 + ERCC reference genome (ENSEMBL) using STAR v.2.5.2b
Unique gene hit counts were extracted using featureCounts from the Subread package v.1.5.2; only reads mapping uniquely within exon regions were counted
Differential gene expression analysis was performed using DESeq2; Wald test was used; genes with adjusted p-value < 0.05 and |log2FC| > 1 were considered significant
Gene ontology analysis was performed using GeneSCF v.1.1-p2 with the mgi GO list
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw_counts.csv: matrix of raw gene hit counts per sample (featureCounts output)
Supplementary files format and content: normalized_counts.csv and rlog_trasnformed_counts.csv: DESeq2 size-factor normalized and rlog-transformed expression values

molecule: polyA RNA

source_name: pancreatic tumor

growth_protocol: KPCWT and KPC49bKO pancreatic cancer cell lines were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2. For in vitro RNA-seq, cells were harvested at approximately 80% confluency. For in vivo experiments, 1x10^6 cells were implanted subcutaneously into the flank of syngeneic C57BL/6 mice. Once tumors reached sufficient size, they were excised and enzymatically dissociated using the Miltenyi Biotec Tumor Dissociation Kit according to the manufacturer's protocol. Dissociated tumor cells were then processed for RNA extraction and sequencing.

extract_protocol:
Total RNA was extracted from cell lines and tumor tissues. ERCC RNA spike-in controls were added prior to library preparation.
mRNA sequencing libraries were prepared using the Twist UMI mRNA sequencing library preparation system following manufacturer protocols. UMI-based deduplication was performed.

value: pancreatic tumor

tag: cell line

value: pancreatic cancer cells

value: KPC49B knockout

value: in vivo


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 005 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 005 | Full ROI
FFPE


title: KPC49bKO pancreatic tumor, in vivo, biological replicate 1

description:
Library name: KPC49BKO_tumor_rep1
Bulk RNA-seq of KPC49BKO tumor, in vivo. ERCC spike-ins included.


title: Split_4C-rep4-blastomere2

description:
Library name: 4C_Split_4_B2
Column name in counts_allsample.txt: 4C_Split_4_B2

value: embryo

value: 4-cell (Split)

value: WT


title: KPCWT pancreatic tumor, in vivo, biological replicate 2

description:
Library name: KPCWT_tumor_rep2
Bulk RNA-seq of KPCWT tumor, in vivo. ERCC spike-ins included.

value: KPCWT


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 004 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 004 | Full ROI
FFPE


title: KPCWT pancreatic tumor, in vivo, biological replicate 1

description:
Library name: KPCWT_tumor_rep1
Bulk RNA-seq of KPCWT tumor, in vivo. ERCC spike-ins included.


title: KPCWT pancreatic tumor, in vivo, biological replicate 3

description:
Library name: KPCWT_tumor_rep3
Bulk RNA-seq of KPCWT tumor, in vivo. ERCC spike-ins included.


title: 1206-NPC-ASDDM-Pool2-b

description:
Library name: 1206NPCb
Column names in processed data files: 1206bNPC

value: CHD8 mutation

value: ASDDM


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 003 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 003 | Full ROI
FFPE


title: KPC49bKO pancreatic cancer cell line, in vitro, biological replicate 2

description:
Library name: KPC49BKO_invitro_rep2
Bulk RNA-seq of KPC49BKO cell line, in vitro. ERCC spike-ins included.

value: in vitro


title: Split_4C-rep4-blastomere3

description:
Library name: 4C_Split_4_B3
Column name in counts_allsample.txt: 4C_Split_4_B3


title: Split_4C-rep4-blastomere1

description:
Library name: 4C_Split_4_B1
Column name in counts_allsample.txt: 4C_Split_4_B1


title: KPC49bKO pancreatic cancer cell line, in vitro, biological replicate 1

description:
Library name: KPC49BKO_invitro_rep1
Bulk RNA-seq of KPC49BKO cell line, in vitro. ERCC spike-ins included.


title: Split_4C-rep3-blastomere4

description:
Library name: 4C_Split_3_B4
Column name in counts_allsample.txt: 4C_Split_3_B4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 002 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 002 | Full ROI
FFPE


title: KPCWT pancreatic cancer cell line, in vitro, biological replicate 2

description:
Library name: KPCWT_invitro_rep2
Bulk RNA-seq of KPCWT cell line, in vitro. ERCC spike-ins included.


title: KPCWT pancreatic cancer cell line, in vitro, biological replicate 1

description:
Library name: KPCWT_invitro_rep1
Bulk RNA-seq of KPCWT cell line, in vitro. ERCC spike-ins included.


title: RNA-seq of splenic gamma delta T cells from day 7 post MAB infected mouse_3

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description:
Library name: spleen_day7_gdt_3
Bulk RNA-seq and γδ TCR repertoire sequencing from sorted splenic γδ T cells isolated from naïve or MAB-infected mice.

data_processing:
Raw sequencing reads were converted to FASTQ format and demultiplexed. For bulk RNA-seq, reads were quality controlled and aligned to the mouse reference genome. For TCR repertoire sequencing, TCR CDR3 sequences were extracted using MiXCR. V(D)J gene assignments were annotated according to IMGT nomenclature.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Processed files include TCR clonotype annotations, barcode-level TCR assignments, contig annotations, and clonotype frequency tables.

source_name: spleen

extract_protocol:
Sorted splenic γδ T cells were isolated from naïve and MAB-infected mice. Total RNA was extracted from purified γδ T cells using standard RNA extraction procedures. RNA quantity and integrity were assessed prior to library preparation.
For bulk RNA sequencing, indexed RNA libraries were prepared from total RNA extracted from sorted splenic γδ T cells. Libraries were assessed for concentration and insert size and sequenced on an Illumina HiSeq 4000 platform using paired-end 150 bp reads. For targeted TCR repertoire sequencing, cDNA was synthesized with incorporation of an anchor sequence. TCR γ and δ chain libraries were generated from purified amplicons using the Nextera XT Index Kit (Illumina) and sequenced on an Illumina MiSeq platform using MiSeq Reagent Kit v3 (600-cycle, paired-end).

value: spleen

value: gamma delta T cell


title: RNA-seq of splenic gamma delta T cells from day 7 post MAB infected mouse_2

description:
Library name: spleen_day7_gdt_2
Bulk RNA-seq and γδ TCR repertoire sequencing from sorted splenic γδ T cells isolated from naïve or MAB-infected mice.


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 001 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 001 | Full ROI
FFPE


title: Split_4C-rep3-blastomere3

description:
Library name: 4C_Split_3_B3
Column name in counts_allsample.txt: 4C_Split_3_B3


title: Split_4C-rep3-blastomere2

description:
Library name: 4C_Split_3_B2
Column name in counts_allsample.txt: 4C_Split_3_B2


title: RNA-seq of splenic gamma delta T cells from day 7 post MAB infected mouse_1

description:
Library name: spleen_day7_gdt_1
Bulk RNA-seq and γδ TCR repertoire sequencing from sorted splenic γδ T cells isolated from naïve or MAB-infected mice.


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 018 | Full ROI

description:
Library name: LSP16031_Scan1 | 018 | Full ROI
FFPE

value: uninvolved lung


title: RNA-seq of splenic gamma delta T cells from healthy mouse_3

description:
Library name: spleen_day0_gdt_3
Bulk RNA-seq and γδ TCR repertoire sequencing from sorted splenic γδ T cells isolated from naïve or MAB-infected mice.


title: Split_4C-rep3-blastomere1

description:
Library name: 4C_Split_3_B1
Column name in counts_allsample.txt: 4C_Split_3_B1


title: RNA-seq of splenic gamma delta T cells from healthy mouse_2

description:
Library name: spleen_day0_gdt_2
Bulk RNA-seq and γδ TCR repertoire sequencing from sorted splenic γδ T cells isolated from naïve or MAB-infected mice.


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 017 | Full ROI

description:
Library name: LSP16031_Scan1 | 017 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: RNA-seq of splenic gamma delta T cells from healthy mouse_1

description:
Library name: spleen_day0_gdt_1
Bulk RNA-seq and γδ TCR repertoire sequencing from sorted splenic γδ T cells isolated from naïve or MAB-infected mice.


title: Split_4C-rep2-blastomere4

description:
Library name: 4C_Split_2_B4
Column name in counts_allsample.txt: 4C_Split_2_B4


title: Primary microglia, WT, biol rep 7

city: New York

first: Joseph

middle: Michael

last: Castellano

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 14

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between TIMP2 KO mice relative to TIMP2 WT mice.
Assembly: Mus musculus GRCm38
Supplementary files format and content: comma separated values file includes raw counts for each sample

source_name: Primary microglia

extract_protocol:
Forebrains from neonatal mice were pooled by genotype (WT or TIMP2 KO), and then microglia were isolated and plated in 12-well poly-d-lysine-coated plates, before pelleting and storing at -80C (N = 7 samples per genotype, each sample represents a a pool of 5 pups (P6-P7), sex-matched). RNA was isolated and sequenced by Genewiz (Azenta)
Genewiz (Azenta) performed library preparaton with paired-end 150 base pair sequencing on Illumina HiSeq

value: Primary microglia

value: pooled male and female


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 016 | Full ROI

description:
Library name: LSP16031_Scan1 | 016 | Full ROI
FFPE


title: Primary microglia, KO, biol rep 7

description: Library name: 13

value: KO


title: Split_4C-rep2-blastomere3

description:
Library name: 4C_Split_2_B3
Column name in counts_allsample.txt: 4C_Split_2_B3


title: Primary microglia, WT, biol rep 6

description: Library name: 12


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 015 | Full ROI

description:
Library name: LSP16031_Scan1 | 015 | Full ROI
FFPE


title: Primary microglia, KO, biol rep 6

description: Library name: 11


title: Primary microglia, WT, biol rep 5

description: Library name: 10


title: Split_4C-rep2-blastomere2

description:
Library name: 4C_Split_2_B2
Column name in counts_allsample.txt: 4C_Split_2_B2


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 014 | Full ROI

description:
Library name: LSP16031_Scan1 | 014 | Full ROI
FFPE


title: Primary microglia, KO, biol rep 5

description: Library name: 9


title: Split_4C-rep2-blastomere1

description:
Library name: 4C_Split_2_B1
Column name in counts_allsample.txt: 4C_Split_2_B1


title: Primary microglia, WT, biol rep 4

description: Library name: 8


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 013 | Full ROI

description:
Library name: LSP16031_Scan1 | 013 | Full ROI
FFPE

value: lymph node


title: Primary microglia, KO, biol rep 4

description: Library name: 7


title: Whole_4C-rep5

description:
Library name: 4C_Whole_5
Column name in counts_allsample.txt: 4C_Whole_5

value: 4-cell (whole)


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 012 | Full ROI

description:
Library name: LSP16031_Scan1 | 012 | Full ROI
FFPE


title: Primary microglia, KO, biol rep 3

description: Library name: 5


title: Primary microglia, WT, biol rep 3

description: Library name: 6


title: Whole_4C-rep4

description:
Library name: 4C_Whole_4
Column name in counts_allsample.txt: 4C_Whole_4


title: Primary microglia, WT, biol rep 2

description: Library name: 4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 022 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 022 | Full ROI
FFPE

value: TLS


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 011 | Full ROI

description:
Library name: LSP16031_Scan1 | 011 | Full ROI
FFPE


title: SUM-44 ASH2L 276-C

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
shASH2L_vs_LacZ.txt
278Sum44_vs_271Sum44.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the Human (HG19) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: SUM-44PE breast cancer cells

growth_protocol: Cells were cultured at 37°C in 10% CO2 and passaged using Trypsin (Invitrogen Catalog # 15400-054) diluted to 1x with Hanks Buffered Salt Solution (Corning Cellgro Catalog #20-021-CV) supplemented with 1 ml/L sodium bicarbonate and 25 μg/ml gentamicin. SUM-44 cells were cultured in serum-free Ham’s F-12 medium supplemented with 1 μg/ml hydrocortisone, 1 mg/ml bovine serum albumin, 10 mM HEPES, 5 mM ethanolamine, 5 μg/ml transferrin, 10 nM triiodothyronine, 50 nM sodium selenite, 25 μg/ml gentamicin, 2.5 μg/ml fungizone, and 5 μg/ml insulin.

extract_protocol:
Total RNA was prepared using a Qiagen RNeasy Plus Mini Kit (74136, lot 151036409)
A total of 100-200 ng of total RNA was used to prepare RNA-seq libraries using the TruSeq RNA Sample Prep kit following the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: Target cells were transduced with virus in growth media supplemented with 5 μg/ml polybrene using 0.5-1.0 ml virus per 1 million cells. Cells were selected for resistance marker expression and maintained in puromycin-containing growth media beginning 24-48 hours after infection. Cells were cultured in selection media at least 5 days to allow expression of the construct. 3 μg/ml puromycin was used for selection and maintenance of shRNA-transduced SUM-44 cells.

tag: passage

tag: source

value: pleural effusion cells from metastatic ER+ breast cancer patient

tag: knockdown

value: ASH2L Sigma pLKO TRC0000019276


title: Primary microglia, KO, biol rep 2

description: Library name: 3

tag: tissue


title: Whole_4C-rep3

description:
Library name: 4C_Whole_3
Column name in counts_allsample.txt: 4C_Whole_3

value: embryo

value: WT

tag: batch


title: Primary microglia, WT, biol rep 1

description: Library name: 2


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 010 | Full ROI

description:
Library name: LSP16031_Scan1 | 010 | Full ROI
FFPE

tag: histopathological region

tag: patient id


title: Primary microglia, KO, biol rep 1

description: Library name: 1

tag: genotype


title: Whole_4C-rep1

description:
Library name: 4C_Whole_1
Column name in counts_allsample.txt: 4C_Whole_1

tag: cell type


title: 170118C_HF_del_4_4

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

description:
RNA from single cells
mRNA
processed data file: Mutant_barcodes.tsv
processed data file: Mutant_features.tsv
processed data file: Mutant_matrix.mtx

data_processing:
Transcripts from mice were mapped to the reference genome (GRCm38/mm10) using Cell Ranger Version 3.0.2.
Reference was modified to include eGFP gene sequence.
Quality control of all data sets was performed using Seurat (Version 3.0.0).
Processed files were analyzed with Seurat V3.1.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Dorsal skin epidermis

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Same as in Guerrero-Juarez, et al. Nat Commun. 2019.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Cell capture, library preparation, quality control, and sequencing were performed at Beijing CapitalBio Technology (Beijing, China).
Single Cell 3’ v3 chemistry - 10X Genomics

tag: genotype/variation

value: Dorsal skin epidermis

tag: hair growth phase

value: Anagen

value: P23/24 - tam for 3 days


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 020 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 020 | Full ROI
FFPE


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 009 | Full ROI

description:
Library name: LSP16031_Scan1 | 009 | Full ROI
FFPE


title: 170118C_HF_del_4_3

treatment_protocol: N/A. Primary cells were used in this study.

tag: treatment


title: Split_2C-rep5-blastomere2

description:
Library name: 2C_Split_5_B2
Column name in counts_allsample.txt: 2C_Split_5_B2

value: 2-cell (Split)


title: 170118C_HF_del_4_2


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 008 | Full ROI

description:
Library name: LSP16031_Scan1 | 008 | Full ROI
FFPE


title: Therapy control repeat 1 (S88)

city: Evanston

first: Anna

last: Metlushko

state: IL

address: 2236 Sherman Avenue, Unit K-2

institute: Northwestern University

description: Library name: PDL_T1_S88

data_processing:
Adapters were trimmed from reads using cutadapt version 4.2
Trimmed reads were aligned using STAR version 2.7.5
Gene counting was performed using htseq-count version 2.0.2
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw gene counts

source_name: cortical neuron

growth_protocol: Based on U.S. Provisional Patent No. 63/548,029

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Total RNA-Seq Library Prep Kit following manufacturer's protocols.

value: cortical neuron

value: wildtype

value: Peptide amphiphile


title: Split_2C-rep5-blastomere1

description:
Library name: 2C_Split_5_B1
Column name in counts_allsample.txt: 2C_Split_5_B1


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 007 | Full ROI

description:
Library name: LSP16031_Scan1 | 007 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: 170118C_HF_del_3_3


title: 170118C_HF_del_3_4


title: Split_2C-rep4-blastomere2

description:
Library name: 2C_Split_4_B2
Column name in counts_allsample.txt: 2C_Split_4_B2


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 006 | Full ROI

description:
Library name: LSP16031_Scan1 | 006 | Full ROI
FFPE


title: 170118C_HF_del_3_2


title: Split_2C-rep4-blastomere1

description:
Library name: 2C_Split_4_B1
Column name in counts_allsample.txt: 2C_Split_4_B1


title: 170118C_HF_del_3_1


title: 170118C_HF_del_2_4


title: 170118C_HF_del_2_3


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 005 | Full ROI

description:
Library name: LSP16031_Scan1 | 005 | Full ROI
FFPE


title: 170118C_HF_del_2_2


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 004 | Full ROI

description:
Library name: LSP16031_Scan1 | 004 | Full ROI
FFPE


title: 170118C_HF_del_2_1


title: Split_2C-rep3-blastomere2

description:
Library name: 2C_Split_3_B2
Column name in counts_allsample.txt: 2C_Split_3_B2


title: Split_2C-rep3-blastomere1

description:
Library name: 2C_Split_3_B1
Column name in counts_allsample.txt: 2C_Split_3_B1


title: JORRP Patient 96

description: Papilloma

source_name: JORRP Patient 96

value: Papilloma

tag: location

value: Beijing children hospital


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 003 | Full ROI

description:
Library name: LSP16031_Scan1 | 003 | Full ROI
FFPE

value: lymph node


title: 170118C_HF_del_1_4


title: 170118C_HF_del_1_2


title: 170118C_HF_del_1_3


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 002 | Full ROI

description:
Library name: LSP16031_Scan1 | 002 | Full ROI
FFPE


title: 170118C_HF_del_4_1


title: Split_2C-rep2-blastomere1

description:
Library name: 2C_Split_2_B1
Column name in counts_allsample.txt: 2C_Split_2_B1


title: 170118C_HF_del_1_1

description:
RNA from single cells
mRNA
processed data file: Mutant_barcodes.tsv
processed data file: Mutant_features.tsv
processed data file: Mutant_matrix.mtx


title: Split_2C-rep2-blastomere2

description:
Library name: 2C_Split_2_B2
Column name in counts_allsample.txt: 2C_Split_2_B2


title: 170118B_HF_ctrl_3_1

description:
RNA from single cells
mRNA
processed data file: Control_barcodes.tsv
processed data file: Control_features.tsv
processed data file: Control_matrix.mtx

value: P21/22 - tam for 3 days


title: 170118B_HF_ctrl_4_1


title: p17_e6_TB_Granulomas_GeoMx_LSP16031_Scan1 | 001 | Full ROI

description:
Library name: LSP16031_Scan1 | 001 | Full ROI
FFPE


title: Split_2C-rep1-blastomere2

description:
Library name: 2C_Split_1_B2
Column name in counts_allsample.txt: 2C_Split_1_B2


title: 170118B_HF_ctrl_2_1


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 016 | Full ROI

description:
Library name: LSP16028_Scan1 | 016 | Full ROI
FFPE

value: uninvolved lung


title: 170118B_HF_ctrl_1_1


title: Split_2C-rep1-blastomere1

description:
Library name: 2C_Split_1_B1
Column name in counts_allsample.txt: 2C_Split_1_B1


title: WT_Biological-replicate-3

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

description: Library name: WT_Biological-replicate-3

data_processing:
Libraries were prepared using a Tru-Seq Stranded mRNA Sample Prep kit (Illumina®). Sequencing was performed using a paired-end protocol to a minimum depth of 40 million reads per sample on an DNB-seq 100nt paired end (BGI Genomics, China). Raw reads were quality-trimmed and adapter sequences removed using Cutadapt (5.1). Cleaned reads were aligned to the A. thaliana reference genome using STAR (2.7.11b), with minimum and maximum intron lengths set to 50 and 5000 nt, respectively. Only uniquely mapping reads were retained for downstream analysis. Gene-level expression quantification was performed using HTSeq (2.0.5) in union mode, using the Araport11 gene annotation. Differential gene expression analysis was carried out using DESeq2, with pairwise comparisons between genotypes. Genes were considered differentially expressed if they had a false discovery rate (FDR) < 0.01.
Transcript Quantification and Differential Alternative Splicing Analysis
Transcript-level abundance estimation was performed using Kallisto with 100 bootstrap. Quantification was based on the AtRTD2 reference transcriptome (R. Zhang et al. 2017). Differential alternative splicing (DAS) analysis was conducted using SUPPA2 (Trincado et al. 2018), using transcript per million (TPM) values from Kallisto. Splicing events were considered differentially regulated if they exhibited an absolute dPSI (|dPSI|) > 0.2 and FDR < 0.01.
Assembly: Tair10
Supplementary files format and content: Normalized (DEseq2) read counts over exons per genes for Transienty assay
Supplementary files format and content: Suppa2 alternative splicing results for Transienty assay
Supplementary files format and content: Normalized (DEseq2) read counts over exons per genes for transgenic lines
Supplementary files format and content: Suppa2 alternative splicing results for Transgenic lines

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Total RNA was extracted from individual seventh leaves of 37-day-old-plants grown in an Aralab climate chamber with long day conditions (16 h light/ 8 h dark, 20°C, 60% humidity).Total RNA was extracted from pools of 10-day-old seedlings for KD- and OE-ACHLYS. TURBO™ DNase (Life Technologies) treated RNA was purified using the RNA Cleanup protocol of the RNeasy Plant Mini Kit (QIAGEN) and used for Illumina® Stranded mRNA Prep (Illumina) following the manufacturer's instructions. We performed a second library clean up to reduce primer dimer contamination. Libraries were sequenced by BGI genomics (China).

extract_protocol:
Following the manufacturer's instructions total RNA was extracted using TRI REAGENT® (Molecular Research Center, Inc.). TURBO™ DNase (Life Technologies) treated RNA was purified using the RNA Cleanup protocol of the RNeasy Plant Mini Kit (QIAGEN) and used for Illumina® Stranded mRNA Prep (Illumina) following the manufacturer's instructions. We performed a second library clean up to reduce primer dimer contamination. Libraries were sequenced by BGI genomics (China)
Libraries were construted by Illumina® Stranded mRNA Prep (Illumina) following the manufacturer's instructions. We performed a second library clean up to reduce primer dimer contamination. Libraries were sequenced by BGI genomics (China)

treatment_protocol: The transient expression in wild type (Columbia-0) or nsra A. thaliana leaves was performed according to Y. Zhang et al. 2020. Agrobacterium (GV3101 or AGL1) clones containing a vector to overexpress the lncRNA candidates, ASCO or GFP as control, were grown in liquid culture overnight (28°C). 200 µl of liquid culture was transferred to YEB-induced medium plates (0.2 mM acetosyringone) and incubated at 28°C for 36 h. Bacteria were scraped from the plate and resuspended in 2 ml washing solution (10 mM MgCl2, 100 μM acetosyringone) and diluted in infiltration solution (¼MS [pH = 6.0], 1% sucrose, 100 μM acetosyringone, 0.005%v/v Silwet L-77) to an OD600 of 0.5. The previously marked 7th leaf of 30-35-day-old plants (long day, day 20°C, night 18°C, 60% humidity) was infiltrated with agrobacteria using a 1-ml plastic syringe. The infiltrated plants were dried for 1h in the growth cabinet, incubated in the dark for 24 h and the samples were collected 88 h after infiltration.

value: Whole seedling

value: Plant


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 015 | Full ROI

description:
Library name: LSP16028_Scan1 | 015 | Full ROI
FFPE


title: Donor, 11, TRIM21_SjD59

city: Oxford

first: Lynn

middle: B

last: Dustin

state: Oxfordshire

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description: Library name: D11H

data_processing:
Raw reads were aligned on the GRCh37 reference genome (release 103) using STAR mapper (v 2.7.11). Read counts were estimated with RSEM (v 1.1.17). Count normalization and differential gene expression analysis were performed using DESeq2 (v 1.44.0).
Assembly: GRCh37
Supplementary files format and content: txt files containing either gene count or gene fkpm, as indicated, for each sample

source_name: blood

growth_protocol: IFNgamma-primed human monocyte-derived macrophages were cultured at 5000 cells/well, three wells per condition, in 96-well plates..

extract_protocol:
Cells lysed in 100 μl RLT buffer (with 2-mercaptoethanol) per well. RNA was prepared with the Qiagen Rneasy microkit. RNA from replicate wells was pooled.
Libraries were prepared and sequenced by Novogene.

treatment_protocol: Cells were treated as described (control medium only, TRIM21 only, plasma from healthy control (HC077) or Sjögren's disease (SjD) patient (SjD61 or SjD59), or a combination of TRIM21 and either HCO77 or SjD patient plasma. After 6 hours incubation, cells were lysed for RNA preparation.

value: blood

value: moncyte-derived macrophage


title: Whole_2C-rep5

description:
Library name: 2C_Whole_5
Column name in counts_allsample.txt: 2C_Whole_5

value: embryo

value: 2-cell (whole)

value: WT


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 014 | Full ROI

description:
Library name: LSP16028_Scan1 | 014 | Full ROI
FFPE


title: WT_Biological-replicate-2

description: Library name: WT_Biological-replicate-2


title: Donor, 11, SjD59_plasma_only

description: Library name: D11G


title: Whole_2C-rep4

description:
Library name: 2C_Whole_4
Column name in counts_allsample.txt: 2C_Whole_4


title: WT_Biological-replicate-1

description: Library name: WT_Biological-replicate-1


title: Whole_2C-rep3

description:
Library name: 2C_Whole_3
Column name in counts_allsample.txt: 2C_Whole_3


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 013 | Full ROI

description:
Library name: LSP16028_Scan1 | 013 | Full ROI
FFPE


title: Donor, 11, TRIM21_SjD61

description: Library name: D11F


title: Donor, 11, SjD61_plasma_only

description: Library name: D11E


description: Library name: KD-ACHLYS-AT2G15292_Biological-replicate-3


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 012 | Full ROI

description:
Library name: LSP16028_Scan1 | 012 | Full ROI
FFPE


description: Library name: KD-ACHLYS-AT2G15292_Biological-replicate-2


title: Whole_2C-rep2

description:
Library name: 2C_Whole_2
Column name in counts_allsample.txt: 2C_Whole_2


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 011 | Full ROI

description:
Library name: LSP16028_Scan1 | 011 | Full ROI
FFPE


title: Donor, 11, TRIM21_HC077

description: Library name: D11D


description: Library name: KD-ACHLYS-AT2G15292_Biological-replicate-1


title: Whole_2C-rep1

description:
Library name: 2C_Whole_1
Column name in counts_allsample.txt: 2C_Whole_1


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 010 | Full ROI

description:
Library name: LSP16028_Scan1 | 010 | Full ROI
FFPE

value: TLS


title: BV2, LPS+Pilo, biol rep3

first: Kaichun

last: Wang

address: Yishan Road No.600

institute: Shanghai Jiao Tong University

description:
Library name: Sample 9
TT3

data_processing:
fastp (0.19.5), STAR (v 2.7.1a), RSFM (v 1.3.3), DESeq2 (v 1.24.0)
Assembly: GRCm39
Supplementary files format and content: txt file includes TPM values for each sample

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). At least 1 μg total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit, following manufacturer' s protocols.

value: microglia cells

value: LPS+Pilo


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 047 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 047 | Full ROI
FFPE


title: Donor, 11, HC077_plasma_only

description: Library name: D11C


description: Library name: KD-RHAPSO-AT1G04107-A_Biological-replicate-3


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 009 | Full ROI

description:
Library name: LSP16028_Scan1 | 009 | Full ROI
FFPE


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 008 | Full ROI

description:
Library name: LSP16028_Scan1 | 008 | Full ROI
FFPE


title: Donor, 11, control

description: Library name: D11A

value: control


description: Library name: KD-RHAPSO-AT1G04107-A_Biological-replicate-1


title: BV2, LPS+Pilo, biol rep1

description:
Library name: Sample 7
TT1

value: wildtype


description: Library name: OE-ACHLYS-AT2G15292_Biological-replicate-3


title: BV2, LPS, biol rep3

description:
Library name: Sample 6
T3

value: LPS


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 006 | Full ROI

description:
Library name: LSP16028_Scan1 | 006 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: BV2, LPS, biol rep2

description:
Library name: Sample 5
T2


title: Donor, 10, TRIM21_SjD61

description: Library name: D10F


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 005 | Full ROI

description:
Library name: LSP16028_Scan1 | 005 | Full ROI
FFPE


title: BV2, LPS, biol rep1

description:
Library name: Sample 4
T1


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 004 | Full ROI

description:
Library name: LSP16028_Scan1 | 004 | Full ROI
FFPE


description: Library name: OE-ACHLYS-AT2G15292_Biological-replicate-1


title: Donor, 10, SjD61_plasma_only

description: Library name: D10E


title: BV2, Control, biol rep3

description:
Library name: Sample 3
C3


description: Library name: OE-RHAPSO-AT1G04107_Biological-replicate-3


title: Donor, 10, TRIM21_HC077

description: Library name: D10D


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 003 | Full ROI

description:
Library name: LSP16028_Scan1 | 003 | Full ROI
FFPE


title: BV2, Control, biol rep2

description:
Library name: Sample 2
C2


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 002 | Full ROI

description:
Library name: LSP16028_Scan1 | 002 | Full ROI
FFPE


title: BV2, Control, biol rep1

description:
Library name: Sample 1
C1


description: Library name: OE-RHAPSO-AT1G04107_Biological-replicate-1


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 001 | Full ROI

description:
Library name: LSP16028_Scan1 | 001 | Full ROI
FFPE


title: hippocampus, PBS, biol rep2

description: Library name: TD006476-4

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the mouse genome (mm10-2020-A) using Cell Ranger (7.1.0). To remove ambient RNA, SoupX (Young 2020, GigaScience) was performed using a manual cut off set on a sample-by-sample basis. After initial filtering, doublets were removed using DoubletFinder (McGinnis 2019, Cell Syst.). Samples were  filtered by removing genes expressed in fewer than 3 cells, cells with a UMI count under 500, and cells with only 500 genes per cell to ensure we analyzed high-quality cells. Cells with > 2% mitochondria, ribosomal large subunit (RPL) and ribosomal small subunit gene expression content were regressed out.  Integration was performed using STACAS, a semi-supervised data integration method (Andreatta & Carmona 2021, Bioinformatics). Seurat (v5.2.1) was in R programming language (version 4.4.2 or version 4.2.0) for analysis.
Assembly: mm10-2020-A
Supplementary files format and content: Hierarchical Data Format (H5 files). Each file contains per-molecule information for all nuclei with a valid barcode, a valid UMI, and library information.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Single nuceli isolation adapted from Habib et al., 2020 Nature Neuroscience. Following isolation, two biological samples from the same treatment condition were pooled to load 20,000 nuclei total (10,000 nuclei each) for a total of N = 2 samples per treatment condition.
10x Genomics Single Cell 3' v3

value: hippocampus

tag: strain

tag: age

tag: Sex

value: male

value: PBS


title: Donor, 10, TRIM21_only

description: Library name: D10B


title: Donor, 10, control

description: Library name: D10A


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 032 | Full ROI

description:
Library name: LSP16102_Scan2 | 032 | Full ROI
FFPE

source_name: tuberculosis-infected human lung tissue

value: uninvolved lung


title: hippocampus, TIMP2, biol rep2

description: Library name: TD006476-3


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 031 | Full ROI

description:
Library name: LSP16102_Scan2 | 031 | Full ROI
FFPE


title: Donor, 8, TRIM21_SjD59

description: Library name: D8H


title: GFP_Biological-replicate-3

description: Library name: GFP_Biological-replicate-3

source_name: 7th leaf

value: 7th leaf

tag: cell line

value: Plant


title: GFP_Biological-replicate-2

description: Library name: GFP_Biological-replicate-2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 030 | Full ROI

description:
Library name: LSP16102_Scan2 | 030 | Full ROI
FFPE


title: Donor, 8, SjD59_plasma_only

description: Library name: D8G

value: blood

value: moncyte-derived macrophage


title: hippocampus, TIMP2, biol rep1

description: Library name: TD006476-1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 029 | Full ROI

description:
Library name: LSP16102_Scan2 | 029 | Full ROI
FFPE


title: Donor, 8, TRIM21_SjD61

description: Library name: D8F


title: AT1G67105-ASCO_Biological-replicate-4

description: Library name: AT1G67105-ASCO_Biological-replicate-4


title: Donor, 8, SjD61_plasma_only

description: Library name: D8E


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 028 | Full ROI

description:
Library name: LSP16102_Scan2 | 028 | Full ROI
FFPE


title: NC BMMs M1-polarized (Rep2)

city: Wuhan

first: Yaoting

last: Ji

state: Hubei

address: No.237 Luoyu Road

institute: Wuhan University

description: Library name: Sample 5

data_processing:
RNA-seq
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Supplementary files format and content: (GRCm38/mm10)
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Primary cells

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306）following manufacturer's protocols.

value: Bone marrow

value: Bone marrow-derived macrophages


title: AT1G67105-ASCO_Biological-replicate-3

description: Library name: AT1G67105-ASCO_Biological-replicate-3


title: NC BMMs M1-polarized (Rep3)

description: Library name: Sample 6


title: Donor, 8, TRIM21_HC077

description: Library name: D8D


title: AT1G67105-ASCO_Biological-replicate-2

description: Library name: AT1G67105-ASCO_Biological-replicate-2


title: NC BMMs M1-polarized (Rep1)

description: Library name: Sample 4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 026 | Full ROI

description:
Library name: LSP16102_Scan2 | 026 | Full ROI
FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

value: TLS


title: Donor, 8, HC077_plasma_only

description: Library name: D8C


title: NSUN2-KO BMMs M1-polarized (Rep3)

description: Library name: Sample 3


title: AT1G67105-ASCO_Biological-replicate-1

description: Library name: AT1G67105-ASCO_Biological-replicate-1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 025 | Full ROI

description:
Library name: LSP16102_Scan2 | 025 | Full ROI
FFPE


title: Donor, 8, TRIM21_only

description: Library name: D8B


title: NSUN2-KO BMMs M1-polarized (Rep2)

description: Library name: Sample 2


description: Library name: AT2G18735-FLAIL-2-NSR_Biological-replicate-4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 024 | Full ROI

description:
Library name: LSP16102_Scan2 | 024 | Full ROI
FFPE


title: NSUN2-KO BMMs M1-polarized (Rep1)

description: Library name: Sample 1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 023 | Full ROI

description:
Library name: LSP16102_Scan2 | 023 | Full ROI
FFPE


description: Library name: AT2G18735-FLAIL-2-NSR_Biological-replicate-3


title: Bispec_combined_VehicleCtrl_treatment

city: Tarrytown

first: Qingqing

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description:
Library name: Bispec_Vh
RRBS data

data_processing:
Raw single-end reads were adaptor-trimmed and aligned to the genome using Bismark (Krueger et al, 2011) and Bowtie 2 (Langmead et al, 2012) allowing for no mismatches (-N 0) and a seed substring length of 20 (-L 20). PCR duplicates were then removed and methylation at CpG sites was extracted using Bismark.
The resulted CpG reports were processed with the methylKit R package (Akalin et al, 2012) and only CpG sites covered with at least 10 reads were retained for downstream analyses.
For differential methylation analysis, the genome was tiled into 1kb regions and significantly differentially methylated tiles were identified.
Fisher’s exact test and Chi-square test were used to identify differentially methylated sites.
Visualization of the methylation levels in selected genomic regions were performed using the Gviz R package (Hahne et al, 2016).
Assembly: hg38
Supplementary files format and content: region_differentials.txt files: a tab-delimited text file containing information on differentially methylated regions. For this file, the differential methylation test is performed on 1 kilobase regions that are tiled across the entire genome
Supplementary files format and content: bw files: containing the methylation percentage at covered CpG sites

source_name: PBMC

growth_protocol: T cells were isolated from healthy donor PBMCs (Reach Bio) using the EasySepTM Human Naive Pan T cell Isolation Kit. Following isolation, T cells were primed with 300nM DAC at 37oC for 24 hrs. Next, WSU-DLCL2 cells were incubated with DAC-primed T cells in a 1:5 cancer:T cell ratio in the presence of 300nM DAC and 100pM CD20xCD3 bispecific. Cancer cells and bispecific were replenished every two days.

extract_protocol:
Genomic DNA was extracted using the KingFisher Apex instrument per manufacturer’s instructions
100ng of gDNA was digested with TaqaI and MspI at 37⁰C. Following enzymatic digestion, samples were used for library generation using an RRBS Methyl-Seq System. In brief, digested DNA was randomly ligated and, following fragment end repair, bisulfite converted using a DNA Bisulfite conversion. After conversion and clean-up, samples were amplified using the RRBS Methyl-Seq System protocol for library amplification and purification.

treatment_protocol: T cells from healthy donors were pre-treated with DAC and the hypomethylating agent was replenished every 2 days when stimulated by CD20xCD3 for 14 days in the presence of DAC or without.

value: PBMC

value: T cells

value: CD20xCD3 bispec + vehicle control


title: Thymus from 4-week-old B6 male mouse

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

description: Library name: thymus

data_processing:
CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data, then mapped to GRCm38 whole genome using Hisat2 software.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm38
Supplementary files format and content: Excel files including fpkm values for each sample

source_name: Tissue cells

growth_protocol: mESCs were cultured in DMEM medium, added with 50 U/ml penicillin/ 50 μg/ml streptomycin, 100 uM β-mercaptoethanol, 1ng/ml human LIF, 2 mM L-glutamine, 15% FBS, and 1× MEM non-essential amino acids in petri dishes coated with 0.1% gelatin. NSCs were obtained by culturing mESCs in defined serum-free medium Ndiff® 227 at 37°C with 5% CO2 for 6 days.

extract_protocol:
Cells were collected with trypsinization and total RNA was extract with TRIzol using the protocol from the manufacturer.
Libraries were contructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® using the protocol from the manufacturer.

value: Thymus

value: Wild type


description: Library name: AT2G18735-FLAIL-2-NSR_Biological-replicate-2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 022 | Full ROI

first: Emmanuel

last: Ogbonna

address: 200 Longwood Ave

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_Scan2 | 022 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: Bispec_combined_DAC_treatment

description:
Library name: Bispec_DAC
RRBS data

value: CD20XCD3 bispec + decitabine


title: Spleen cells from 4-week-old B6 male mouse

description: Library name: spleen

value: Spleen cells


description: Library name: AT2G18735-FLAIL-2-NSR_Biological-replicate-1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 021 | Full ROI

description:
Library name: LSP16102_Scan2 | 021 | Full ROI
FFPE


description: Library name: AT2G15292-ACHLYS-1-NSR_Biological-replicate-4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 020 | Full ROI

description:
Library name: LSP16102_Scan2 | 020 | Full ROI
FFPE


title: Skeletal muscle fibers from 4-week-old B6 male mouse

description: Library name: muscle

value: Muscle fibers


description: Library name: AT2G15292-ACHLYS-1-NSR_Biological-replicate-3


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 019 | Full ROI

description:
Library name: LSP16102_Scan2 | 019 | Full ROI
FFPE


title: Donor, 8, control

description: Library name: D8A

value: control


title: iMGL-iNSpheroids, iPSC DF6-9-9T.B cell line, control 6hpt

city: Oeiras

first: Catarina

middle: Monteiro

last: Gomes

state: Lisboa

address: Av. República, Qta. do Marquês

country: Portugal

institute: iBET

description:
Library name: Ctrl-treated-6h-1
10X Genomics

data_processing:
The resultant gene expression matrix was imported into the R statistical environment for further analysis (RStudio 2024.04.2+764 "Chocolate Cosmos" Release). Ambient RNA removal was carried out using the DecontX methodology [104]. Cell filtering, data normalization, and clustering were carried out using the R package Seurat v5.0.1. Filtered feature-barcode matrices were used as input for the initial Seurat object, including only cells with at least 200 genes expressed in at least three cells. Datasets were further filtered to remove low-quality cells based on the following exclusion criteria parameters: (i) ratio of mitochondrial versus endogenous gene expression < 20% (putative dying cells); (ii) < 200 or > 5,000 total genes (putative poorly informative cells and multiplets). Data normalization, scaling, and identification of the top 3,000 most variable genes were performed using SCTransform v2.0 method, using default parameters and regressing out the percentage of genes coding for ribosomal proteins. This normalization method is claimed to outperform the classical log-normalization workflow, allowing the use of a higher principal component (PC) to capture more detailed biological variation for clustering. Principal Component Analysis (PCA) was run on each dataset and the first 30 PCs were selected for downstream analysis, based on their contribution to each PC variability (Elbow Plot). The overall significance of each PC and the corresponding p-value were calculated according to the JackStraw method. The different sample datasets were integrated into a single object using Seurat’s integration standard workflow, using the first 30 PCs, 3,000 variable features, and the SCTransform normalized data. Integration anchors were identified using reciprocal PCA and reference-based integration, with the timepoint 0 hours being used as reference. Dimensionality reduction was then performed with PCA on the batch-corrected data. Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction was performed on the calculated PCs to obtain a 2D representation for data visualization. To find the optimal clustering resolution, the Clustree package was used to compute different resolution values (0.1-1.0); the 0.1 resolution was selected for downstream analysis. Cell clusters were identified using the Louvain algorithm at resolution r = 0.1, implemented by the FindCluster function of Seurat. To characterize each cluster, a comprehensive manual annotation was performed.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Brain

extract_protocol:
Untransduced and rAAV9-mCherry transduced iMGL-iNSpheroids (derived from the iPSC(IMR90)-4 and iPS DF6-9-9T.B cell lines) were analysed by single nuclei RNA-sequencing (sn-RNAseq). Samples were collected at 0-, 6- and 24-hours post-transduction, and sedimented by centrifugation at 300 xg, for 5 min. Cells were then resuspended and cryopreserved in cell freezing medium, CryoStor CS10 (STEMCELL Technologies, cat. no. 100-1061) and stored at -80 °C until shipment. Samples were sent for nuclei isolation and sequencing at Genewiz laboratories (Leipzig, Germany).
Raw data from snRNAseq was analysed and processed into a transcript count matrix using Cell Ranger (https://www.10xgenomics.com/, v6.1.1) from the Chromium Single Cell Software Suite by 10x Genomics. Fastq files were generated using the Cell Ranger mkfastq command with default parameters. Gene counts for each cell were quantified with the Cell Ranger count command with default parameters. For all analyses, the human (GRCh38) plus the mCherry genes were used as reference.

treatment_protocol: rAAV9 encoded mCherry fluorescence protein under the CAG promoter was used at na MOI of 5 x 10^5 VG/cell. iNSpheroids-iMGL, control and treated, were collected at 0-, 6- and 24h post-transduction.

value: Brain

value: iPSC DF6-9-9T.B

value: Control


title: Primitive NSCs derived from mESCs

description: Library name: NSCs

source_name: cell line

value: NSCs

value: Primitive neural stem cells


description: Library name: AT2G15292-ACHLYS-1-NSR_Biological-replicate-2

value: 7th leaf

value: Plant


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 018 | Full ROI

city: Boston

description:
Library name: LSP16102_Scan2 | 018 | Full ROI
FFPE

value: TLS


title: NaiveTcells

description:
Library name: Naïve_Tcells
RRBS data

value: PBMC

value: T cells


title: B6 mESCs

description: Library name: mESCs

value: mESC

value: Embryonic stem cells


title: iMGL-iNSpheroids, iPSC(IMR90) clone 4 cell line, control 0h

description:
Library name: Ctrl-0h-2
10X Genomics

value: iPSC(IMR90) clone 4


description: Library name: AT2G15292-ACHLYS-1-NSR_Biological-replicate-1


title: Fat cells from 4-week-old B6 male mouse

description: Library name: adipocyte

value: Fat cells

value: Wild type


title: Donor, 11, TRIM21_only

description: Library name: D11B

value: blood

value: moncyte-derived macrophage


title: BV2, LPS+Pilo, biol rep2

description:
Library name: Sample 8
TT2

value: microglia cells

value: wildtype

value: LPS+Pilo


description: Library name: KD-RHAPSO-AT1G04107-A_Biological-replicate-2

value: Whole seedling


title: p17_e6_TB_Granulomas_GeoMx_LSP16028_Scan1 | 007 | Full ROI

description:
Library name: LSP16028_Scan1 | 007 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: Donor, 10, TRIM21_SjD59

description: Library name: D10H


title: iMGL-iNSpheroids, iPSC DF6-9-9T.B cell line, control 24hpt

description:
Library name: Ctrl-treated-24h-1
10X Genomics

value: Brain

value: iPSC DF6-9-9T.B

value: Control


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 017 | Full ROI

description:
Library name: LSP16102_Scan2 | 017 | Full ROI
FFPE

value: TLS


title: Control CT26 cells

description: Library name: CT26shCtrl

source_name: Cell line

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when knockdown cells underwent significant phenotypic change.

value: Colon cancer cell line

value: CT26 cells transfected with lentivirus carrying the empty knockdown vetor (shCtrl)


title: iMGL-iNSpheroids, iPSC DF6-9-9T.B cell line, control 0h

description:
Library name: Ctrl-0h-1
10X Genomics


title: AT5G08155-5-GRP7_Biological-replicate-4

description: Library name: AT5G08155-5-GRP7_Biological-replicate-4

value: 7th leaf

value: Plant


description: Library name: OE-ACHLYS-AT2G15292_Biological-replicate-2


title: Donor, 10, SjD59_plasma_only

description: Library name: D10G


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 016 | Full ROI

description:
Library name: LSP16102_Scan2 | 016 | Full ROI
FFPE


title: 455-HOXD13

city: Zurich

first: Masoumeh

last: Mirrahimi

state: Zurich

address: Wagistrasse 14,

department: Rheumatology

country: Switzerland

institute: University Hospital Zurich

description: Library name: 455_D13

data_processing:
R/Bioconductor package Rsubread version 1.22
Assembly: Ensembl GRCh37
Supplementary files format and content: tab-limited text files included raw counts /RPKM values for each samples

source_name: Synovium

extract_protocol:
Total RNA was isolated from SFs silenced for HOXD10, HOXD11, and HOXD13, as well as control SFs (n = 3 for each), 48hr post-transfection using the miRNeasy Mini kit (Qiagen), which includes on-column DNase I digestion
RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA protocol and the TruSeq Stranded Total RNA Sample Preparation Kit.

value: Synovium

value: Synovial Fibroblast


title: AT5G08155-5-GRP7_Biological-replicate-3

description: Library name: AT5G08155-5-GRP7_Biological-replicate-3


title: Differentiated CT26 cells induced by Setdb1 knockdown

description: Library name: CT26shSetdb1

value: Setdb1 knockdown

value: CT26 cells transfected with lentivirus for Setdb1 knockdown using shor-hairpin RNA against Setdb1 (shSetdb1)


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 015 | Full ROI

description:
Library name: LSP16102_Scan2 | 015 | Full ROI
FFPE


title: AT5G08155-5-GRP7_Biological-replicate-2

description: Library name: AT5G08155-5-GRP7_Biological-replicate-2


title: 455-HOXD11

description: Library name: 455_D11


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 014 | Full ROI

description:
Library name: LSP16102_Scan2 | 014 | Full ROI
FFPE


title: Control CT26 cells for Myod1 or Pparg expression

description: Library name: CT26Ctrl

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when cells with forced expression of Myod1 or Pparg underwent significant phenotypic change.

value: Wild type

value: CT26 cells transfected with lentivirus carrying the empty expression vector


title: 455-HOXD10

description: Library name: 455_D10


title: Differentiated CT26 cells induced by Pparg expression

description: Library name: CT26Pparg

value: Forced expression of Pparg

value: CT26 cells transfected with lentivirus for Pparg expression


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 013 | Full ROI

description:
Library name: LSP16102_Scan2 | 013 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: AT5G08155-5-GRP7_Biological-replicate-1

description: Library name: AT5G08155-5-GRP7_Biological-replicate-1


title: 455-Control

description: Library name: 455_c


description: Library name: OE-RHAPSO-AT1G04107_Biological-replicate-2

value: Whole seedling


title: AT5G07745-4-GRP7_Biological-replicate-4

description: Library name: AT5G07745-4-GRP7_Biological-replicate-4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 012 | Full ROI

description:
Library name: LSP16102_Scan2 | 012 | Full ROI
FFPE


title: Donor, 10, HC077_plasma_only

description: Library name: D10C

value: blood

value: moncyte-derived macrophage


title: 451-HOXD13

description: Library name: 451_D13


title: GFP_Biological-replicate-4

description: Library name: GFP_Biological-replicate-4


title: Differentiated CT26 cells induced by Myod1 expression

description: Library name: CT26Myod1

value: Forced expression of Myod1

value: CT26 cells transfected with lentivirus for Myod1 expression


title: Control B16F10 cells for Setdb1 knockdown

description: Library name: B16F10shCtrl

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when cells with forced expression of Myod1 or Pparg, or knockdown cells underwent significant phenotypic change.

value: Melanoma cell line

value: B16F10 cells transfected with lentivirus carrying the empty knockdown vetor (shCtrl)


title: AT5G07745-4-GRP7_Biological-replicate-3

description: Library name: AT5G07745-4-GRP7_Biological-replicate-3

value: 7th leaf

value: Plant


title: 451-HOXD11

description: Library name: 451_D11

value: Synovium

value: Synovial Fibroblast


title: Differentiated B16F10 cells induced by Setdb1 knockdown

description: Library name: B16F10shSetdb1

value: Setdb1 knockdown

value: B16F10 cells transfected with lentivirus for Setdb1 knockdown using shor-hairpin RNA against Setdb1 (shSetdb1)


title: AT5G07745-4-GRP7_Biological-replicate-2

description: Library name: AT5G07745-4-GRP7_Biological-replicate-2


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 010 | Full ROI

description:
Library name: LSP16102_Scan2 | 010 | Full ROI
FFPE

value: TLS


title: 451-HOXD10

description: Library name: 451_D10


title: Control B16F10 cells for Myod1 or Pparg expression

description: Library name: B16F10Ctrl

value: Wild type

value: B16F10 cells transfected with lentivirus carrying the empty expression vector


title: AT5G07745-4-GRP7_Biological-replicate-1

description: Library name: AT5G07745-4-GRP7_Biological-replicate-1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 009 | Full ROI

description:
Library name: LSP16102_Scan2 | 009 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue


title: Differentiated B16F10 cells induced by Pparg expression

description: Library name: B16F10Pparg

value: Forced expression of Pparg

value: B16F10 cells transfected with lentivirus for Pparg expression


title: AT3G05655-3-GRP7_Biological-replicate-4

description: Library name: AT3G05655-3-GRP7_Biological-replicate-4


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 008 | Full ROI

description:
Library name: LSP16102_Scan2 | 008 | Full ROI
FFPE


title: 456-HOXD13

description: Library name: 456_D13


title: Differentiated B16F10 cells induced by Myod1 expression

description: Library name: B16F10Myod1

value: B16F10 cells transfected with lentivirus for Myod1 expression


title: AT3G05655-3-GRP7_Biological-replicate-3

description: Library name: AT3G05655-3-GRP7_Biological-replicate-3


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 007 | Full ROI

description:
Library name: LSP16102_Scan2 | 007 | Full ROI
FFPE


title: 456-HOXD11

description: Library name: 456_D11


title: Mouse_8, mCART19

first: Monica

middle: Liliana

last: Guzman

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
Library name: Mouse_8
10 X Genomics

data_processing:
scRNA-seq data from the 6 mice were mapped to mm10 mouse genome reference using 10x Genomics Cell Ranger v7.2.0 and scanpy was used to create AnnData objects for each of the samples. After QC, samples were integrated using Harmony integration approach.
All the code used for scRNA-seq analysis is available at (https://github.com/abcwcm/alhomoud_cart_rad ).
Assembly: Mouse mm10
Supplementary files format and content: h5ad

source_name: Spleen

extract_protocol:
The spleen were collected upon euthanasia. Organs were then processed using 40uM Nylon (Corning, Arizona, United States) cell strainers to create cell suspensions. Erythrocytes were lysed using ACK lysing buffer and cells were stained and sorted for single RNA sequencing.
Single-cell RNA-seq libraries were prepared according to 10x Genomics specifications (Single Cell 3′ Reagent Kits v3.1 User Guide CG000204, 10x Genomics, Pleasanton, CA, USA). Cellular suspensions (75% viable) at a concentration between 600-1000 cells/ul, were loaded onto to the Chromium Controller to generate barcoded single-cell GEMs, targeting about 10000 single cells per sample. GEM-Reverse Transcription (53 °C for 45 min, 85 °C for 5 min; held at 4 °C) was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad, Hercules). After RT reaction, GEMs were broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified for 11 cycles (98 °C for 3 min; 98 °C for 15 s, 63°C for 20 s, 72 °C for 1).  Quality of the cDNA was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA), obtaining a product of about 1100bp. This cDNA was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads (Beckman Coulter, Indianapolis, IN) and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through 14 cycles of PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s x 14 cycles; 72 °C for 1 min; held at 4 °C). Indexed libraries were subjected a second double-sided size selection, and libraries were then quantified using Qubit fluorometric quantification (Thermo Fisher Scientific, Waltham, MA). The quality was assessed on an Agilent Bioanalyzer 2100, obtaining an average library size of 470bp.

treatment_protocol: All mice used were between 6 and 10 weeks old and kept in a pathogen-free facility. Mice were intravenously injected in the tail vein with 5 x106 A20 GFP-LUC cells. Mice were imaged at day 13 with a bioluminescent imager using an IVIS Spectrum In Vivo Imaging System (Perkin Elmer, Connecticut, US) 10 minutes after 200 uL intraperitoneal injections of reconstituted VivoGlo Luciferin (15mg/ml, Promega, Cat. P1043) to confirm engraftment. The radiation groups received 1 Gy of LD-TBI. The mouse CD19 CART groups received 1.6 million mouse anti-CD19 CART through the tail vein.

value: Spleen

value: Immune Cells


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 006 | Full ROI

description:
Library name: LSP16102_Scan2 | 006 | Full ROI
FFPE


title: AT3G05655-3-GRP7_Biological-replicate-2

description: Library name: AT3G05655-3-GRP7_Biological-replicate-2


title: Mouse_5, Cy/LD-TBI/mCART19

description:
Library name: Mouse_5
10 X Genomics


title: 456-HOXD10

description: Library name: 456_D10


title: AT3G05655-3-GRP7_Biological-replicate-1

description: Library name: AT3G05655-3-GRP7_Biological-replicate-1


title: Mouse_4, mCART19

description:
Library name: Mouse_4
10 X Genomics


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 004 | Full ROI

description:
Library name: LSP16102_Scan2 | 004 | Full ROI
FFPE


title: AT1G04107-2-GRP7_Biological-replicate-4

description: Library name: AT1G04107-2-GRP7_Biological-replicate-4


title: 456-Control

description: Library name: 456_c

value: Control


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 003 | Full ROI

description:
Library name: LSP16102_Scan2 | 003 | Full ROI
FFPE


title: Mouse_23, mCART19

description:
Library name: Mouse_23
10 X Genomics


title: CRB1 clone C4, day 35, rep 3

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

institute: UCL

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimgalore
Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters.
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using featurecounts (v2.0.3) and modelled using DESeq2 (v1.40)
Assembly: GRCh38
Supplementary files format and content: raw count per gene per sample
Supplementary files format and content: transcripts per million (TPM) values of genes per sample

source_name: iPSC derived

growth_protocol: adapted protocol based upon Eintracht et al 2022

extract_protocol:
Total RNA was isolated using Rneasy plus kit from Qiagen
RNA-seq libraries were prepared with Illumina Stranded Total RNA Prep with Ribo-Zero Plus as per manufacturers instructions

value: iPSC derived

value: Retinal organoids


title: AT1G04107-2-GRP7_Biological-replicate-3

description: Library name: AT1G04107-2-GRP7_Biological-replicate-3

value: 7th leaf

value: Plant


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 002 | Full ROI

description:
Library name: LSP16102_Scan2 | 002 | Full ROI
FFPE


title: AT1G04107-2-GRP7_Biological-replicate-2

description: Library name: AT1G04107-2-GRP7_Biological-replicate-2


title: CRB1 clone C4, day 35, rep 2


title: Mouse_13, Cy/LD-TBI/mCART19

description:
Library name: Mouse_13
10 X Genomics


title: Mouse_11, Cy/LD-TBI/mCART19

description:
Library name: Mouse_11
10 X Genomics


title: AT1G04107-2-GRP7_Biological-replicate-1

description: Library name: AT1G04107-2-GRP7_Biological-replicate-1


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 001 | Full ROI

description:
Library name: LSP16102_Scan2 | 001 | Full ROI
FFPE


title: CRB1 clone C4, day 35, rep 1


title: AT3G05955-6-GRP7_Biological-replicate-4

description: Library name: AT3G05955-6-GRP7_Biological-replicate-4


title: Running_05

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Library name: Running_05
10x Genomics

data_processing:
Sequence data were processed with CellRanger (v.6.0.2) to generate count matrices
Assembly: mm10
Supplementary files format and content: CellRanger filtered_feature_bc_matrix (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Hindpaw engrafted B16F10 melanoma

extract_protocol:
To make single cell suspension, freshly collected tumor tissues were chopped with scissors and enzymatically dissociated with tumor dissociation kit (Milteyni Biotec) and blood cells were RBC-lysed with RBC lysis buffer.
Library was constucted according to the manufacturer's instructions (10X 3' v3)

treatment_protocol: Mattress or forced wheel running

value: Hindpaw engrafted B16F10 melanoma

value: Forced wheel running


title: AT3G05955-6-GRP7_Biological-replicate-3

description: Library name: AT3G05955-6-GRP7_Biological-replicate-3


title: CRB1 clone C3, day 35, rep 3


title: Das_Alyona__BT2015050_2017_1_D1

city: Toronto

first: Alyona

last: Ivanova

state: ON

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
Library name: IDH_mut/visium_raw/2017
FF trasncriptome sequencing

data_processing:
GeoMx: All computational analysis methods were run using defaults unless otherwise specified. Raw counts were grouped into a single dataset. The expression threshold used for this study is LOQ (limit of quantitation) = 2 and frequency of 10%. With these settings all targets with LOQ of 2 or greater in at least 10% of segments were kept. Filtering by LOQ gives confidence that the target is expressed above background levels and that it is accurately quantified. Remaining genes were normalized by Q3 normalization
Visium: Preliminary data processing, including demultiplexing, alignment to the GRCh38 reference genome (version 2020-A), and UMI counting, was performed using the Space Ranger pipeline (v2.0.1) from 10x Genomics. Spatial gene expression matrices were generated using the Visium Human Transcriptome Probe Set v2.0.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: feature spatial autocorrelation analysis using Moran's I in CSV format
Supplementary files format and content: cytassist_image.tiff: input CytAssist image in original resolution that can be used to re-run the pipeline
Supplementary files format and content: aligned_tissue_image.jpg: aligned CytAssist and Microscope QC image
Supplementary files format and content: filtered_feature_bc_matrix.h5: Same information as filtered_feature_bc_matrix/ but in HDF5 format.
Supplementary files format and content: metrics_summary.csv: run summary metrics in CSV format
Supplementary files format and content: molecule_info.h5: Contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or protein barcode. This file is required for additional analysis spaceranger pipelines including aggr, targeted-compare and targeted-depth.
Supplementary files format and content: possorted_genome_bam.bam: indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, annotated with barcode information
Supplementary files format and content: possorted_genome_bam.bam.bai: Index for possorted_genome_bam.bam. In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Space Ranger v2.0+ generates a possorted_genome_bam.bam.csi index file instead.
Supplementary files format and content: probe_set.csv: Copy of the input probe set reference CSV file
Supplementary files format and content: raw_feature_bc_matrix.h5:  Same information as raw_feature_bc_matrices/ in HDF5 format.
Supplementary files format and content: raw_probe_bc_matrix.h5: Contains UMI counts of each probe for all detected barcodes in HDF5 format. Only produced when running pipelines for probe-based assays.
Supplementary files format and content: cloupe.cloupe: Loupe Browser visualization and analysis file
Supplementary files format and content: Initial Dataset_GBM.xlsx: raw GeoMx dataset.
Supplementary files format and content: NGS QC_GBM.xlsx: dataset resulting from first QC step, this is the dataset after applying technical QC parameters to primarily evaluate library prep and sequencing performance
Supplementary files format and content: Filter_Segments_defaultLOQ.xlsx: dataset resulting from filtering. In this step we established an expression threshold and a frequency at which the targets are allowed to be below that threshold. The expression threshold used for this study is LOQ (limit of quantitation) = 2 and frequency of 10%. With these setting all targets with LOQ of 2 or greater in at least 10% of segments were kept. Filtering by LOQ gives confidence that the target is expressed above background levels and that it is accurately quantified.
Supplementary files format and content: Q3_Normalize copy.xlsx: dataset resulting from Q3 normalization. Input is the filter_segments_defaultLOQ.xlsx dataset
Supplementary files format and content: OME-TIFF: OME-TIFF files,  slide images containing embedded OME-XML metadata.
Supplementary files format and content: 15-1842_18-17149_BT 201503_C folder with tiff images of each ROI
Supplementary files format and content: DCC files and PKC configuration file (GNP_config.ini): raw data files generated by the GeoMx NGS Pipeline software from sequencer output (FASTQ files). PKC files are configuration files that accompany the DCC files. They contain metadata about the probes and targets used in the experiment, allowing the analysis software to correctly interpret the raw counts in the DCC files.
Supplementary files format and content: Biological Probe QC.xlsx - dataset resulting from second QC step, this is the dataset assess probe performance (uses Grubb's outlier test). Removes any probes classified as local or global outliers.
Library strategy: Spatial Transcriptomics

source_name: astrocytoma

extract_protocol:
FFPE tissue sections for GeoMx DSP experiments were cut to a thickness of 5μm using a microtome and mounted onto Superfrost Plus slides within 1 month of spatial transcriptomics analysis.  Fresh-frozen tissue sections for Visium (10 μm thickness) were mounted onto Visium CytAssist slides, with two samples per slide. Sample preparation—including H&E staining, imaging, probe hybridization, and library construction—was carried out following the manufacturer's protocol (10X Genomics, Visium Spatial Protocols – Tissue Preparation Guide, CG000240, and Visium CytAssist Spatial Gene Expression for Fresh Frozen – Tissue Preparation Guide, CG000636, Rev A).
For GeoMx,sequencing was performed on an Illumina NovaSeq 6000 and fastq files were processed into gene count data for each sample using the GeoMx® NGS Pipeline. Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: astrocytoma


title: CRB1 clone C3, day 35, rep 2


title: Running_03

description:
Library name: Running_03
10x Genomics


title: AT3G05955-6-GRP7_Biological-replicate-2

description: Library name: AT3G05955-6-GRP7_Biological-replicate-2


title: Das_Alyona__BT2015050_2015_A1

description:
Library name: IDH_mut/visium_raw/2015
FF trasncriptome sequencing


title: CRB1 clone C3, day 35, rep 1


title: Running_02

description:
Library name: Running_02
10x Genomics


title: Running_01

description:
Library name: Running_01
10x Genomics


title: AT2G01422-2-NBS_Biological-replicate-4

description: Library name: AT2G01422-2-NBS_Biological-replicate-4


title: NT_B_LP6

city: Ghent

first: Xin

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

description: Library name: RNA017662

library_source: other

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

molecule: other

growth_protocol: HEK293T-dCas9 cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in the incubator with 5% CO₂.

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

treatment_protocol: Cells were transfected with a total of 40 ng purified sgRNA per well using Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (Invitrogen, Cat. #CMAX00003).

value: embryonic kidney cell

value: NT


title: Wildtype control 35, day 35, rep 3

value: WT


title: Wildtype control 35, day 35, rep 2


title: Mattress_04

description:
Library name: Mattress_04
10x Genomics

value: Mattress


title: NT_A_LP6

description: Library name: RNA017661


title: AT2G01422-2-NBS_Biological-replicate-3

description: Library name: AT2G01422-2-NBS_Biological-replicate-3


title: Wildtype control 35, day 35, rep 1


title: Mattress_03

description:
Library name: Mattress_03
10x Genomics


title: 451-Control

description: Library name: 451_c

value: Synovium

value: Synovial Fibroblast


title: Mock_B_LP6

description: Library name: RNA017660

value: Mock


title: Wildtype control 19, day 35, rep 3


title: AT2G01422-2-NBS_Biological-replicate-1

description: Library name: AT2G01422-2-NBS_Biological-replicate-1


title: Mock_A_LP6

description: Library name: RNA017659


title: Mattress_02

description:
Library name: Mattress_02
10x Genomics


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 005 | Full ROI

description:
Library name: LSP16102_Scan2 | 005 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: Mattress_01

description:
Library name: Mattress_01
10x Genomics


title: Wildtype control 19, day 35, rep 2


title: PoolCTL_B_LP6

description: Library name: RNA017658

value: PoolCTL


title: Stx2 + cell

first: Xinlei

last: Sun

address: 163 Xianlin Road

description: 10x Genomics

data_processing:
Post-processing and quality control were carried out using the 10×Cell Ranger package (v1.2.0; 10×Genomics).
Assembly: All reads were aligned to the GRCh38 reference assembly (v96)
Supplementary files format and content: Tab-separated value file and matrix file

source_name: Blood

extract_protocol:
Stx2-FITC was incubated with human peripheral blood immune cells for 30 min. Stx2+ cells were isolated via flow cytometry sorting (BD FACS Aria SORP). The resulting cells underwent manual counting three times with Trypan blue, ensuring that over 95% of the cells remained viable after each centrifugation. The cells were then resuspended at a concentration of ≥ 2×105/ml.
Single cells were processed using a Chromium Controller (10×Genomics) following the manufacturer's protocol. Subsequently, these single cells were run on a 10×Chromium system and underwent library preparation by LC Sciences, following the recommended protocol for the Chromium Single Cell 30 Reagent Kit (v2 Chemistry), with sequencing performed using the HiSeq4000 for Illumina.

value: Blood

value: White blood cell


title: Wildtype control 19, day 35, rep 1

value: iPSC derived

value: Retinal organoids


title: AT2G00440-1-NBS_Biological-replicate-4

description: Library name: AT2G00440-1-NBS_Biological-replicate-4

value: 7th leaf

value: Plant


title: AT2G00440-1-NBS_Biological-replicate-3

description: Library name: AT2G00440-1-NBS_Biological-replicate-3