title: macrophage, uninfected with ZLM at 24h, Rep3

value: uninfected macrophages with ZLM (control) at 24h


title: macrophage, uninfected with ZLM at 24h, Rep2

status: Public on Jan 17 2025

type: SRA

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 1800 East-West Rd

country: USA

institute: University of Hawaii

library_source: transcriptomic

data_processing:
The RNA-seq paired-end reads in FASTQ format were explored using FastQC and cleaned using Trimmomatic. The cleaning procedure included trimming low quality reads from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, and filtering out reads having mean quality score less than 30 and length below 20 nucleotides. The house mouse (Mus musculus) reference genome (GRCm38) was indexed and aligned against by HiSAT. The resulting SAM (Sequence Alignment and Mapped) files were sorted and converted to BAM files using SAMtools, and then used to generate count reads using HTSeq.
Assembly: GRCm38
Supplementary files format and content: non-normalized count data are provided. Ensembl gene accession numbers are provided.

molecule: total RNA

organism: Mus musculus

growth_protocol: M. tuberculosis mc2 6206 bacteria (Mtb) were cultured in Sauton's medium supplemented with 6μM zinc sulfate (zinc-replete medium - ZRM) or Sauton's medium without zinc sumplementation (zinc-limited medium - ZLM).  The auxotroph also needs 50 μg/mL L-Leucine and 48 μg/mL D-pantothenate supplemetation. Bacteria were grown for 8 days, harvested and enriched for single cells before the infection. RAW 264.7 cell line was cultured in DMEM with 10% fetal bovine serum.

extract_protocol:
TRIzol reagent was added to the macrophages at 4 hpi and 24 hpi, the TRIzol extractions were collected, and centrifuged to remove debris and pellet Mtb. RNA was isolated and purified using the PureLink RNA mini kit (ThermoFisher).
Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® HiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080).

treatment_protocol: After 8 days of growth in ZRM and ZLM Sautons media, Mtb aggregates were removed by centrifuging the cultures at 800 xg for 10 minutes followed by passing them through 10 μm strainers once. Mtb grown in ZRM (Mtb-ZLM) and Mtb grown in ZLM (Mtb-ZLM) were resuspended in ZRM and ZLM, respectively. Macrophages were infected with Mtb-ZRM and Mtb-ZLM, and ZRM and ZLM were added to macrophages as controls. Macrophage RNA was harvested from all conditions at 4 hours post-infection (hpi) and 24 hpi.

tag: cell line

tag: cell type

value: macrophage-like

tag: treatment


title: Cervix_16 [sample110]

type: genomic

city: Innsbruck

first: Martin

last: Widschwendter

address: Innrain 52

country: Austria

institute: University of Innsbruck

description: Cervix biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Minfi v1.46
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Cervix, Mouse DNA, Tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from cells and different organs using AllPrep DNA/RNA Mini Kits (cat #80204, Qiagen Ltd), following the manufacturer’s protocol.

tag: Sex

value: Female

tag: tissue

value: Cervix

tag: diet

value: Normal diet

value: MPA/DMBA+ MIF-

value: Discovery set

value: No

value: No tumor


title: macrophage, uninfected with ZLM at 24h, Rep1


title: macrophage, uninfected with ZRM at 24h, Rep3

value: uninfected macrophages with ZRM (control) at 24h


title: Kidney_16 [sample116]

description: Kidney biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Kidney, Mouse DNA, Tissue

value: Kidney


title: Cervix_14 [sample109]


title: macrophage, uninfected with ZRM at 24h, Rep2


title: Cervix_13 [sample108]


title: macrophage, uninfected with ZRM at 24h, Rep1


title: implantation A-1

city: Guangzhou

first: Zhenxing

last: Wang

state: Guangdong

address: Guangzhou, P. R. China.

department: School of Materials Science and Engineering

country: China

institute: South China University of Technology

description:
Library name: implantation A-1
implantation A-1

data_processing:
fastp
hisat2
htseq
DESeq2
clusterProfiler
Assembly: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: the raw count file and normalization TPM expression file with tsv format

molecule: polyA RNA

organism: Sus scrofa

source_name: penile corpus cavernosum

extract_protocol:
not collection
TruSeq RNA Library Prep Kit v2

value: penile corpus cavernosum


title: Cervix_12 [sample107]


title: macrophage, infected with Mtb-ZRM for 4h, Rep3

value: macrophages infected with Mtb-ZRM at 4hpi


title: macrophage, infected with Mtb-ZLM for 4h, Rep2

value: macrophages infected with Mtb-ZLM at 4hpi


title: macrophage, infected with Mtb-ZLM for 4h, Rep1


title: Cervix_10 [sample105]


title: Breast_tumor_16 [sample104]

description: Breast tumor biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Breast tumor, Mouse DNA, Tissue

value: Breast tumor


title: macrophage, infected with Mtb-ZRM for 4h, Rep1


title: macrophage, uninfected with ZLM at 4h, Rep2

value: uninfected macrophages with ZLM (control) at 4h


title: macrophage, infected with Mtb-ZRM for 4h, Rep2


title: Cervix_11 [sample106]


title: Kidney_10 [sample111]


title: macrophage, uninfected with ZLM at 4h, Rep3


title: Breast_tumor_14 [sample103]


title: macrophage, uninfected with ZLM at 4h, Rep1


title: macrophage, uninfected with ZRM at 4h, Rep3

value: uninfected macrophages with ZRM (control) at 4h


title: Breast_tumor_11 [sample101]


title: macrophage, uninfected with ZRM at 4h, Rep2


title: Breast_tumor_13 [sample102]


title: macrophage, uninfected with ZRM at 4h, Rep1


title: Lung_15 [sample127]

description: Lung biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Lung, Mouse DNA, Tissue

value: Lung


title: Breast_16 [sample098]

description: Breast biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Breast, Mouse DNA, Tissue

value: Breast


title: Breast_13 [sample096]

value: Female


title: Breast_tumor_17 [sample099]


title: Adipose_tissue_15 [sample093]

description: Adipose tissue biology in a mouse treated with medroxyprogesterone (MPA, P) and 7,12-dimethylbenzanthracene (DMBA, D) and on a normal diet

source_name: Adipose tissue, Mouse DNA, Tissue

value: Adipose tissue


title: Breast_14 [sample097]

value: Normal diet


title: macrophage, infected with Mtb-ZLM for 4h, Rep3

value: macrophage-like


title: Adipose_tissue_14 [sample092]

value: MPA/DMBA+ MIF-

value: Discovery set


title: Breast_11 [sample095]

value: No

value: No tumor


title: Breast_10 [sample094]


title: Adipose_tissue_13 [sample091]


title: Adipose_tissue_12 [sample090]


title: Adipose_tissue_10 [sample088]


title: Spleen_09 [sample087]

description: Spleen biology in a mouse on a normal diet

source_name: Spleen, Mouse DNA, Tissue

value: Spleen

value: MPA/DMBA- MIF-


title: Spleen_03 [sample083]


title: Spleen_08 [sample086]


title: Spleen_02 [sample082]


title: PBMCs_05 [sample080]

description: PBMC biology in a mouse on a normal diet

source_name: PBMCs, Mouse DNA

value: PBMC


title: Breast_tumor_10 [sample100]


title: PBMCs_03 [sample078]


title: Adipose_tissue_11 [sample089]


title: Spleen_01 [sample081]


title: PBMCs_02 [sample077]


title: Spleen_04 [sample084]


title: PBMCs_08 [sample075]


title: PBMCs_04 [sample079]


title: PBMCs_01 [sample072]


title: PBMCs_09 [sample076]


title: Oviduct_09 [sample071]

description: Oviduct biology in a mouse on a normal diet

source_name: Oviduct, Mouse DNA, Tissue

value: Oviduct


title: PBMCs_06 [sample073]


title: Oviduct_07 [sample070]


title: PBMCs_07 [sample074]


title: Oviduct_05 [sample068]


title: Oviduct_01 [sample064]


title: Lymph_nodes_09 [sample063]

description: Lymph nodes biology in a mouse on a normal diet

source_name: Lymph nodes, Mouse DNA, Tissue

value: Lymph nodes


title: Oviduct_04 [sample067]


title: Lymph_nodes_07 [sample061]


title: Oviduct_02 [sample065]


title: Oviduct_03 [sample066]


title: Oviduct_06 [sample069]


title: Spleen_07 [sample085]


title: Lymph_nodes_04 [sample058]


title: Lymph_nodes_05 [sample059]


title: Lymph_nodes_06 [sample060]


title: Lymph_nodes_01 [sample055]


title: Lung_06 [sample054]

description: Lung biology in a mouse on a normal diet


title: Lung_04 [sample052]


title: Lung_02 [sample050]


title: Lung_03 [sample051]


title: Lung_01 [sample049]


title: Lung_09 [sample048]


title: Lung_07 [sample046]


title: Liver_09 [sample045]

description: Liver biology in a mouse on a normal diet

source_name: Liver, Mouse DNA, Tissue

value: Liver


title: Lung_08 [sample047]


title: Lung_05 [sample053]


title: Liver_08 [sample044]


title: Liver_06 [sample042]


title: Liver_05 [sample041]


title: BMAC scRNA OA - 77

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

library_source: transcriptomic single cell

data_processing:
R, Cellranger, Linux server commndline
Assembly: grch38
Supplementary files format and content: tab delimited barcode, feature and count matrices

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
3' mRNA was barcoded using 10x Genomics Chromium instrument
10x Genomics 3' GEX kitwas used as per manufacturer's manual

value: Bone Marrow

value: knee - OA

value: BMAC


title: Liver_04 [sample040]

value: Female


title: Lymph_nodes_08 [sample062]


title: Lymph_nodes_03 [sample057]


title: SCRNEO4

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
First strand 150bp paired-end reads were  analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human genome (GRCh38) with TopHat2 using Bowtie1 and Samtools, allowing 4 mismatches and 20 multihits. The GENCODE v36.GRCh38.Ensembl_102 gene annotation was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, keeping only those genes with more than 2 normalized counts in at least 30% of the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis to evaluate the potential implication of certain biological processes. Gene signatures were obtained from the Molecular Signatures Database (KEGG pathways (C2), cancer hallmarks (H), oncogenic signatures (C6), ontology gene sets (C5), immunological (C7) and chromosome location (C1). Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCh38
Supplementary files format and content: Tabulated text file with DESeq2 normalized counts

source_name: Bladder, urothelial carcinoma

extract_protocol:
Total RNA was obtained from either 0.75 mm-wide punches or two 10  µm sections from the tumor or non-tumoral areas previously identified by the pathologist in  the collected tissue samples from the cystectomy and the TURBT. Nucleic acids were  extracted using either the truXTRAC FFPE DNA microtube Kit (Covaris, cat no 520161) or  the truXTRAC FFPE RNA microTUBE kit (Covaris, cat no 520136). RNA concentration was determined by  Nanodrop 1000 (Thermo Fisher Scientific) and integrity was assessed using Agilent  Bioanalyzer 2100 (Agilent Technologies).  The percentage of RNA fragments larger than  200nt (DV 200 ) was determined to identify those RNAs with an extreme poor integrity  (DV 200 <30%).
RNA-seq libraries were constructed and sequenced on an Illumina HiSeq PE150 platform with 150-bp paired-end reads (Novogene, China). After the QC procedures, mRNA from eukaryotic organisms were enriched using oligo(dT) beads and rRNA was removed using the Ribo-Zero. Once random mRNA fragmentation and cDNA synthesis by using mRNA template and random hexamers primer were performed, a customized second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second strand synthesis. Following several steps which included terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment and several quality control processes (Qubit 2.0, Agilent 2100 bioanalyzer and Q-PCR). The qualified libraries were fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

value: Bladder, urothelial carcinoma

tag: tissue preparation

value: FFPE human sample

value: Diagnostic sample (trans-urethral resection of bladder tumour) collected previously to the initiation of neoadyuvant treatment


title: BMAC scRNA OA - 75


title: Liver_03 [sample039]

value: Normal diet


title: SCRNEO8


title: BMAC scRNA OA - 76


title: Liver_02 [sample038]

value: Discovery set


title: SCRNEO3


title: Lymph_nodes_02 [sample056]

value: No


title: BMAC scRNA OA - 74


title: Liver_01 [sample037]

value: No tumor


title: SCRNEO24


title: SCRNEO22


title: SCRNEO26


title: Liver_07 [sample043]


title: SCRNEO2


title: Kidney_08 [sample035]

description: Kidney biology in a mouse on a normal diet

value: Kidney


title: BMAC scRNA OA - 73


title: BMAC scRNA OA - 72


title: p65 KO HEK293A cells, p65 2CS_9

city: Charlestown

first: Xu

last: Wu

state: MA

institute: Massachusetts General Hospital

description:
Library name: p652CS_9
Column name in gene_count.xls: p652CS_9

data_processing:
Data quanlity control
Readsmapping to the reference genome
Quantification of gene expression level
Differential expression analysis
Enrichment analysis of differentially expressed genes
Assembly: Hisat2 v2.0.5
Supplementary files format and content: text files include raw counts of each sample

source_name: kidney

growth_protocol: p65 KO HEK293A cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (74104, QIAGEN) and analyzed using Bioanalyzer (Agilent Technologies).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, andpurification

treatment_protocol: p65 KO HEK293A cells were transfected with vecotr or p65 WT or p65 2CS plasmids. After 24h, cells were treated with 20ng/mL TNFα for 2h.

value: kidney

value: HEK293A cells

value: human embryonic kidney cells

tag: genotype

value: p65 2CS expressing

value: 20ng/mL TNFα


title: Kidney_09 [sample036]

value: MPA/DMBA- MIF-


title: BMAC scRNA OA - 71

value: Bone Marrow

value: knee - OA


title: p65 KO HEK293A cells, p65 2CS_8

description:
Library name: p652CS_8
Column name in gene_count.xls: p652CS_8


title: SCRNEO21


title: p65 KO HEK293A cells, p65 2CS_7

description:
Library name: p652CS_7
Column name in gene_count.xls: p652CS_7


title: SCRNEO5


title: Kidney_07 [sample034]

value: Female


title: BMAC scRNA OA - 70

value: BMAC


title: SCRNEO18

value: Bladder, urothelial carcinoma

value: FFPE human sample


title: Kidney_06 [sample033]

value: Normal diet


title: p65 KO HEK293A cells, p65 WT_6

description:
Library name: p65wt_6
Column name in gene_count.xls: p65wt_6

value: p65 WT expressing


title: Kidney_05 [sample032]

value: Discovery set

value: No


title: SCRNEO16

value: Diagnostic sample (trans-urethral resection of bladder tumour) collected previously to the initiation of neoadyuvant treatment


title: BMAC scRNA OA - 69


title: p65 KO HEK293A cells, p65 WT_5

description:
Library name: p65wt_5
Column name in gene_count.xls: p65wt_5

value: kidney


title: p65 KO HEK293A cells, p65 WT_4

description:
Library name: p65wt_4
Column name in gene_count.xls: p65wt_4

value: HEK293A cells


title: Kidney_04 [sample031]

value: Kidney

value: No tumor


title: BMAC scRNA OA - 68


title: SCRNEO14


title: BMAC scRNA OA - 67


title: SCRNEO15

source_name: Bladder, squamous cell carcinoma

value: Bladder, squamous cell carcinoma


title: p65 KO HEK293A cells, vector_2

description:
Library name: vector_2
Column name in gene_count.xls: vector_2

value: human embryonic kidney cells

value: p65 knockout

value: 20ng/mL TNFα


title: BMAC scRNA OA - 66

value: Bone Marrow

value: knee - OA


title: p65 KO HEK293A cells, vector_1

description:
Library name: vector_1
Column name in gene_count.xls: vector_1


title: BMAC scRNA OA - 65

value: BMAC


title: p65 KO HEK293A cells, vector_3

description:
Library name: vector_3
Column name in gene_count.xls: vector_3


title: Kidney_02 [sample029]

value: Female

value: MPA/DMBA- MIF-


title: SCRNEO11

value: Bladder, urothelial carcinoma

value: FFPE human sample


title: Kidney_01 [sample028]

value: Normal diet

value: Discovery set

value: No


title: Cervix_09 [sample027]

description: Cervix biology in a mouse on a normal diet

value: Cervix


title: SCRNEO10

value: Diagnostic sample (trans-urethral resection of bladder tumour) collected previously to the initiation of neoadyuvant treatment


title: QNEO5

value: Surgical sample (Cystectomy) collected after completion of neoadjuvant treatment


title: BMAC scRNA OA - 63


title: BMAC scRNA OA - 64


title: Cervix_06 [sample024]

value: No tumor


title: QNEO17


title: QNEO2


title: Cervix_07 [sample025]


title: Mtb-ZLM-24h-Rep3

type: RNA

hyb_protocol: hybridize for approximately 18 hours at 65C

scan_protocol: The samples were then loaded onto the nCounter Prep Station for purification and cartridge loading, then moved to the nCounter Digital Analyzer for Probe imaging and decoding.

data_processing: The .RCC files and panel file (.rlf) were analyzed using the nSolver v4.0 software (NanoString). The default settings were used to determine and calculate the raw counts and normalized counts, respectively. Default settings in the nSolver v4.0 software (NanoString)

label_protocol: 100ng of purified total RNA was combined with the nCounter Mouse Host Response Panel probes

growth_protocol: Mycobacterium tuberculosis (Mtb) were cultured in Sauton's medium with zinc (Mtb-ZRM) and without zinc (Mtb-ZLM) for 8 days. Single cells of Mtb-ZRM and Mtb-ZLM were isolated, and RAW 264.7 macrophages were infected at MOI 20 for 4 hours (4h) and 24 hours (24h).

extract_protocol: TRIzol reagent (ThermoFisher Scientific) was added to macrophages after 4h and 24h of infection, and macrophage RNA was isolated using the Direct-Zol RNA miniprep kit (Zymo)

treatment_protocol: After 8 dyas of growth in Sauton's medium, single cells of Mtb-ZRM and Mtb-ZLM were isolated, and RAW 264.7 macrophages were infected at MOI 20 for 4 hours (4h) and 24 hours (24h).

value: macrophages that were infected with zinc-limited Mtb for 24 hours


title: SCRNEO1

value: Bladder, squamous cell carcinoma


title: Kidney_03 [sample030]

value: Kidney


title: Mtb-ZRM-24h-Rep1

value: macrophages that were infected with zinc-replete Mtb for 24 hours


title: Cervix_05 [sample023]


title: QNEO16


title: BMAC scRNA OA - 60

value: Bone Marrow

value: knee - OA


title: BMAC scRNA OA - 62

value: BMAC


title: Mtb-ZLM-24h-Rep1


title: QNEO13


title: BMAC scRNA OA - 58


title: BMAC scRNA OA - 59


title: Mtb-ZLM-24h-Rep2


title: BMAC scRNA OA - 61


title: Cervix_08 [sample026]

value: Female

value: MPA/DMBA- MIF-


title: Cervix_03 [sample021]


title: Cervix_04 [sample022]


title: QNEO18

value: Bladder, urothelial carcinoma

value: FFPE human sample


title: Cervix_02 [sample020]

value: Normal diet

value: Discovery set


title: BMAC scRNA OA - 57


title: Mtb-ZRM-24h-Rep2


title: Mtb-ZRM-24h-Rep3


title: QNEO12


title: Cervix_01 [sample019]

value: Cervix

value: No


title: Uninfected-24h-Rep2

value: uninfected macrophages after 24 hours


title: BMAC scRNA OA - 55


title: Uninfected-24h-Rep1


title: BMAC scRNA OA - 56


title: Breast_09 [sample018]

description: Breast biology in a mouse on a normal diet

value: Breast

value: No tumor


title: QNEO1

value: Bladder, squamous cell carcinoma

value: Surgical sample (Cystectomy) collected after completion of neoadjuvant treatment


title: QNEO10


title: QNEO15


title: Mtb-ZRM-4h-Rep3

value: macrophages that were infected with zinc-replete Mtb for 4 hours


title: BMAC scRNA OA - 54

value: Bone Marrow


title: NSCLC_KRAS_13_lpwgs

city: New York

first: Somnath

last: Tagore

state: NY

address: 650W, 168th Street

institute: Columbia University

description: low pass whole genome sequencing

library_source: genomic

data_processing:
library strategy: low pass whole genome sequencing
fastq to sam conversion using bowtie2 v2.4.5
sam to bam conversion using samtools v1.16.1
bam to wig conversion using readCounter (hmmcopy_utils)
wig to seg file conversion using ichorCNA v0.2.0
Assembly: hg38
Supplementary files format and content: segementation file for CNA
Supplementary files format and content: ichorcna tumor cna prediction segmentation file
Supplementary files format and content: cna prediction segmentation file

source_name: NSCLC primary tumor

extract_protocol:
Nuclei from snRNA-seq sample preparations were collected by centrifugation (500g, 5 min), snap frozen after removing excess ST buffer, and stored at -20C until further processing. If insufficient nuclei (<100,000) were present, additional tissue curls were cut and processed in the same manner as for single-nuclei extraction. Genomic DNA was extracted from nuclei using DNeasy Blood and Tissue kit (Qiagen, catalog no.69504) according to manufacturer's instructions. DNA was quantified using a Nanodrop.
20-50 ng of genomic DNA was utilized for input for library prepation with Lotus DNA Library Prep Kit (Integrated DNA Technologies- IDT, Corlville, IA) using xGEN Stubby Adapter and UDI Primer pairs according to manufacturer's instructions with the folllowing specifications. During the enzymatic preparation program, sampless were held at 32C for 9 minutees. Adapters were not diluted, and the optional PCR (5 cycles) and cleanup were performed. After library cleanup with AMPure beads (Beckman Coulter, Brea, CA), libraries were quantified with Tapestation D5000 HS tapes (Agilent) and stored at -20C until sequencing

tag: metastatic site

value: PT

tag: patient id

tag: stk11 mutation

value: WT

tag: kras mutation status

value: KRAS G12V

tag: sequencing technique

value: lp-WGS

tag: tcr-seq

value: yes


title: NSCLC_KRAS_12_lpwgs

description: low pass whole genome sequencing

value: KRAS Q61H


title: Uninfected-24h-Rep3


title: BMAC scRNA OA - 52

value: knee - OA

value: BMAC


title: NSCLC_KRAS_11_lpwgs

description: low pass whole genome sequencing

value: KRAS G12D


title: Breast_07 [sample016]

value: Female

value: Normal diet

value: MPA/DMBA- MIF-

value: Discovery set

value: No


title: Breast_06 [sample015]

value: Breast

value: No tumor


title: Mtb-ZRM-4h-Rep2

value: macrophages that were infected with zinc-replete Mtb for 4 hours


title: BMAC scRNA OA - 53

value: Bone Marrow


title: BMAC scRNA OA - 51


title: Mtb-ZRM-4h-Rep1


title: BMAC scRNA OA - 50


title: NSCLC_KRAS_10_lpwgs

description: low pass whole genome sequencing

value: PT

value: WT

value: KRAS G12C


title: Mtb-ZLM-4h-Rep3

value: macrophages that were infected with zinc-limited Mtb for 4 hours


title: NSCLC_KRAS_17_lpwgs

description: low pass whole genome sequencing

source_name: NSCLC brain metastasis

value: BM

value: lp-WGS

value: yes


title: Mtb-ZLM-4h-Rep1


title: Breast_04 [sample013]


title: Mtb-ZLM-4h-Rep2


title: Wang_HiC_BWX5864_repB

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.   For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.

value: Bacillus subtilis PY79

value: Bacterial

tag: strain genetic_information

value: parS∆9 no a.b., wt parS in spo0J no a.b., yhdG::Pxyl hns phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: Breast_08 [sample017]

value: Female

value: Normal diet

value: MPA/DMBA- MIF-

value: Discovery set


title: Breast_02 [sample011]

value: Breast

value: No

value: No tumor


title: Wang_HiC_BWX5864_repA


title: BMAC scRNA OA - 49

value: Bone Marrow

value: knee - OA

value: BMAC


title: BMAC scRNA OA - 48


title: Wang_HiC_BWX5490_repD

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hns-mCherry phleo


title: NSCLC_KRAS_6_lpwgs

description: low pass whole genome sequencing

value: BM

value: WT

value: KRAS G12C

value: lp-WGS


title: NSCLC_KRAS_7_lpwgs

description: low pass whole genome sequencing

value: yes


title: NSCLC_KRAS_8_lpwgs

description: low pass whole genome sequencing


title: BMAC scRNA OA - 46


title: Wang_HiC_BWX5490_repC

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: NSCLC_STK_22dot2_lpwgs

description: low pass whole genome sequencing

value: PT

value: KRAS WT


title: BMAC scRNA OA - 47


title: Breast_01 [sample010]

value: Female

value: Breast

value: Normal diet

value: MPA/DMBA- MIF-

value: Discovery set


title: Breast_05 [sample014]

value: No

value: No tumor


title: Adipose_tissue_09 [sample009]

description: Adipose tissue biology in a mouse on a normal diet

value: Adipose tissue


title: Adipose_tissue_08 [sample008]


title: BMAC scRNA OA - 45

value: Bone Marrow

value: knee - OA

value: BMAC


title: Wang_WGS_BWX001

value: wild type

value: Cells were growing in CH medium at 37˚C to exponential phase


title: NSCLC_STK_20_lpwgs

description: low pass whole genome sequencing

value: lp-WGS

value: yes


title: Adipose_tissue_06 [sample006]


title: BMAC scRNA OA - 43


title: NSCLC_STK_15_lpwgs

description: low pass whole genome sequencing

value: PT

value: STK11 p.P221Lfs

value: KRAS G12D


title: NSCLC_STK_21_lpwgs

description: low pass whole genome sequencing

value: STK11 c.169delG p.E57fs*

value: KRAS WT


title: Breast_03 [sample012]

value: Female

value: Breast

value: Normal diet

value: MPA/DMBA- MIF-


title: Wang_ChIP_antiHNS_BWX5864

value: Bacillus subtilis PY79

value: Bacterial

value: parS∆9 no a.b., wt parS in spo0J no a.b., yhdG::Pxyl hns phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.

tag: antibody

value: ChIP using anti-HNS antibodies


title: Adipose_tissue_07 [sample007]

value: Adipose tissue

value: Discovery set

value: No

value: No tumor


title: BMAC scRNA OA - 42

value: Bone Marrow

value: knee - OA

value: BMAC


title: Adipose_tissue_04 [sample004]


title: NSCLC_STK_18_lpwgs

description: low pass whole genome sequencing

value: BM

value: STK11 Q305X

value: KRAS Q61H

value: lp-WGS

value: yes


title: Wang_WGS_BWX5864

value: Bacillus subtilis PY79


title: BMAC scRNA OA - 41


title: Wang_ChIP_antiHNS_BWX001

value: Bacterial

value: wild type

value: Cells were growing in CH medium at 37˚C to exponential phase


title: Wang_ChIP_antiRok_BWX001

value: ChIP using anti-Rok antibodies


title: NSCLC_STK_14_lpwgs

description: low pass whole genome sequencing

value: KRAS G12C


title: Wang_HiC_BWX5663_IPTG25min

value: parS∆9 no a.b., ∆spo0J spec (no loxP), wt parS in spo0J, yvbJ::Pspank (optRBS) spo0J ∆parS cat, yhdG::Pxyl hns-mCherry phleo

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 25 mins.


title: NSCLC_STK_5dot2_lpwgs

description: low pass whole genome sequencing

value: STK11 c.836delG, p.G279fs


title: NSCLC_STK_5dot1_lpwgs

description: low pass whole genome sequencing


title: Adipose_tissue_03 [sample003]

value: Female

value: Adipose tissue

value: Normal diet

value: MPA/DMBA- MIF-

value: Discovery set

value: No

value: No tumor


title: BMAC scRNA OA - 40

value: Bone Marrow

value: knee - OA

value: BMAC


title: BMAC scRNA OA - 44


title: Adipose_tissue_02 [sample002]


title: BMAC scRNA OA - 38


title: Wang_HiC_BWX5663_IPTG15min

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 15 mins.


title: BMAC scRNA OA - 37


title: Wang_HiC_BWX5663_IPTG35min

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 35 mins.


title: Adipose_tissue_01 [sample001]


title: NSCLC_STK_1_lpwgs

description: low pass whole genome sequencing

value: BM

value: STK11 deletion exons 2-5

value: KRAS G13C

value: lp-WGS

value: yes


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, BD98, Replicate3

first: Andres

last: Mansisidor

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

description:
Library name: Sample 113
MNase-seq

data_processing:
UMI demultiplexing (custom script)
adapter trimming (custom script)
alignment to HBV genome (Bowtie2 v2.3.4.3)
nucleosome coverage mapping (nucleoATAC)
Bedgraphs from both RNA- and MNase-seq were plotted using Sushi package v1.30.0 in R v4.1.0
Assembly: NC_003977.2 (offset by 500 bp)
Supplementary files format and content: bedgraph files that include coverage of fragment centers (50 bp windows)
adapter trimming (TrimGalore v0.4.5, cutadapt v1.15, FastQC v0.11.5)
alignment to hg38 and HBV genome (bowtie2 v2.3.4.1
deduplication (Picard Tools v2.16.0)
For read counts related to the in vitro chromatin assembly of the HBV genome, the percentage of mapped reads was determined based on the total number of unique reads in the de-duplicated bam files
Assembly: hg38 (human alignment), NC_003977.2 (offset by 500 bp, HBV alignment)

extract_protocol:
In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin.
For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37°C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37°C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293, HepG2.2.15, and HepAD38 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 125–2000 units of enzyme that was incubated for 5 minutes at 37 °C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 °C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture’s protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads.
Following assembly, HBV minichromosomes were submitted at MSKCC’s Epigenetics Research Innovation Lab for processing. ATAC-seq was carried out as previously described with minor modifications using in house prepared transposase (Tn5) enzyme. Upon Mg precipitation, two replicates were used and analyzed for each condition. Briefly, a total of 130 ng chromatinized material was reconstituted in 50 μL transposition buffer containing 25 μL TD buffer (2 0mM Tris HCl pH 7.5, 10 mM MgCl2, 20 % Dimethyl Formamide), 2.5 μL Tn5 transposase, 0.1 % Tween20, 0.01 % Digitonin, 16.5 µl 1X PBS and 5.4 μL ddH2O. Samples were then incubated at 37 °C for 25 min. DNA was isolated using a ZYMO Kit (D4014).
ATAC-seq libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541), a uniquely barcoded primer per sample, and a universal primer. Samples were first subjected to 5 cycles of initial amplification in order to identify the number or cycles needed for each partially amplified library. Upon completion of final amplification, samples were subject to a dual size selection (0.55x–1.5x) using SPRIselect beads (Beckman Coulter, B23317). Fragment distribution of libraries was assessed with an Agilent Bioanalyzer and the sequencing libraries were sent to the MSKCC Integrated Genomics Operation core facility for sequencing on a NovaSeq 6000 flow cell in a 50 bp paired-end (50PE) mode.

value: Human hepatoma cell line

value: WT

value: HBV cccDNA transfected

value: 1 µM BD98


title: NSCLC_STK_3_lpwgs

description: low pass whole genome sequencing

value: STK11 splice site 863-1G>T


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, CBL137, Replicate3

description:
Library name: Sample 112
MNase-seq


title: BMAC scRNA OA - 36

value: Bone Marrow


title: BMAC scRNA OA - 35

value: knee - OA


title: Adipose_tissue_05 [sample005]

value: Female

value: Adipose tissue

value: Normal diet

value: MPA/DMBA- MIF-

value: Discovery set

value: No

value: No tumor


title: Wang_HiC_BWX5603_IPTG25min

value: Bacillus subtilis PY79

value: Bacterial

value: parS∆9 no a.b., ∆spo0J spec (no loxP), wt parS in spo0J, yvbJ::Pspank (optRBS) spo0J ∆parS cat, yhdG::Pxyl hmfA-mCherry phleo, yuxG::xylR-Pxyl-hmfB erm

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 25 mins.


title: Wang_HiC_BWX5603_IPTG15min

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 15 mins.


title: NSCLC_PA125_lpwgs

description: low pass whole genome sequencing

value: BM

value: lp-WGS

value: yes


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, DMSO, Replicate3

description:
Library name: Sample 110
MNase-seq

value: Human hepatoma cell line

value: WT

value: HBV cccDNA transfected

value: DMSO


title: BMAC scRNA OA - 39

value: Bone Marrow

value: knee - OA

value: BMAC


title: NSCLC_PA141_lpwgs

description: low pass whole genome sequencing


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, PHA-767491, Replicate3

description:
Library name: Sample 111
MNase-seq


title: BMAC scRNA OA - 33


title: BMAC scRNA OA - 34


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, BD98, Replicate2

description:
Library name: Sample 109
MNase-seq

value: 1 µM BD98


title: Wang_HiC_BWX5663_IPTG0min

value: parS∆9 no a.b., ∆spo0J spec (no loxP), wt parS in spo0J, yvbJ::Pspank (optRBS) spo0J ∆parS cat, yhdG::Pxyl hns-mCherry phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: Wang_HiC_BWX5602_IPTG35min

value: Bacillus subtilis PY79

value: Bacterial

value: parS∆9 no a.b., ∆spo0J spec (no loxP), wt parS in spo0J, yvbJ::Pspank (optRBS) spo0J ∆parS cat, yhdG::Pxyl hupA-mCherry phleo, yuxG::xylR-Pxyl-hupB erm

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 35 mins.


title: Wang_HiC_BWX5603_IPTG0min

value: parS∆9 no a.b., ∆spo0J spec (no loxP), wt parS in spo0J, yvbJ::Pspank (optRBS) spo0J ∆parS cat, yhdG::Pxyl hmfA-mCherry phleo, yuxG::xylR-Pxyl-hmfB erm


title: BMAC scRNA OA - 32


title: BMAC scRNA OA - 31


title: NSCLC_N586_lpwgs

description: low pass whole genome sequencing

value: PT

value: lp-WGS


title: NSCLC_PA072_lpwgs

description: low pass whole genome sequencing

value: BM

value: yes


title: BMAC scRNA OA - 30


title: Wang_HiC_BWX5602_IPTG25min

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 25 mins.


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, PHA-767491, Replicate2

description:
Library name: Sample 107
MNase-seq

value: Human hepatoma cell line

value: WT

value: HBV cccDNA transfected


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, CBL137, Replicate2

description:
Library name: Sample 108
MNase-seq


title: NSCLC_PA104_lpwgs

description: low pass whole genome sequencing


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, DMSO, Replicate2

description:
Library name: Sample 106
MNase-seq

value: DMSO


title: Wang_HiC_BWX5602_IPTG15min

value: Cells were growing in CH medium with 0.5% xylose for 90 mins at 37˚C and then treated with 0.5mM IPTG for 15 mins.


title: Wang_HiC_BWX5603_IPTG35min


title: Wang_HiC_BWX5602_IPTG0min


title: NSCLC_PA070_lpwgs

description: low pass whole genome sequencing


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, BD98, Replicate1

description:
Library name: Sample 105
MNase-seq

value: 1 µM BD98


title: BMAC scRNA OA - 29

value: Bone Marrow

value: knee - OA

value: BMAC


title: NSCLC_PA068_lpwgs

description: low pass whole genome sequencing


title: BMAC scRNA OA - 28


title: Wang_HiC_BWX4070_IPTG35min

value: Bacillus subtilis PY79

value: Bacterial

value: parS∆9 no a.b., ∆spo0J spec (no loxP), wt parS in spo0J, yvbJ::Pspank (optRBS) spo0J ∆parS cat


title: NSCLC_PA067_lpwgs

description: low pass whole genome sequencing


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, CBL137, Replicate1

description:
Library name: Sample 104
MNase-seq


title: NSCLC_PA080_lpwgs

description: low pass whole genome sequencing


title: Wang_HiC_BWX4070_IPTG25min


title: BMAC scRNA OA - 27


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, PHA-767491, Replicate1

description:
Library name: Sample 103
MNase-seq


title: NSCLC_PA060_lpwgs

description: low pass whole genome sequencing


title: BMAC scRNA OA - 26


title: Wang_HiC_BWX4070_IPTG15min


title: NSCLC_PA054_lpwgs

description: low pass whole genome sequencing


title: NSCLC_PA056_lpwgs

description: low pass whole genome sequencing


title: BMAC scRNA OA - 25


title: Mnase-seq, HepG2 cells, HBV cccDNA transfection, DMSO, Replicate1

description:
Library name: Sample 102
MNase-seq


title: Wang_HiC_BWX5558_repB

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hmfA-mCherry, yuxG::xylR-Pxyl-hmfB erm

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: BMAC scRNA OA - 24


title: Wang_HiC_BWX4070_IPTG0min


title: BMAC scRNA OA - 23


title: BMAC scRNA OA - 22


title: NSCLC_PA043_lpwgs

description: low pass whole genome sequencing

value: BM

value: lp-WGS


title: NSCLC_PA048_lpwgs

description: low pass whole genome sequencing

value: yes


title: Wang_HiC_BWX5498_repA

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hmfB- mCherry phleo


title: Wang_HiC_BWX5558_repA


title: NSCLC_PA034_lpwgs

description: low pass whole genome sequencing


title: BMAC scRNA OA - 21


title: NSCLC_PA042_lpwgs

description: low pass whole genome sequencing


title: Wang_HiC_BWX5496_repA

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hmfA- mCherry phleo


title: BMAC scRNA OA - 20


title: NSCLC_PA005_lpwgs

description: low pass whole genome sequencing


title: Wang_HiC_BWX5490_repA

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hns-mCherry phleo


title: NSCLC_PA025_lpwgs

description: low pass whole genome sequencing


title: C3

city: Chengdu

first: xiaojing

last: zhang

address: Sichuan University, No. 24 South Section 1, Yanshan Road, Chengdu, Sichuan Province, China

institute: Sichuan University

description:
Library name: sample9
C3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2[2] software. The mapped reads of each sample were assembled byStringTie[3] in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq . DEGs with |log2FC| ≧ 1 and FDR≤ 0.05(DESeq2 ) or FDR ≤0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Assembly: GRCm39
Supplementary files format and content: processed data.xlsx

source_name: murine alveolar macrophage cells (MH-S)

extract_protocol:
Total RNA was extracted from the cells using TRIzol® Reagent according the manufacturer,s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/23≥2.0, RIN≥ 6.5, 28S:18S≥1.0, > 1μg) was used toconstruct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The XX RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequencedwith the NovaSeqXplus sequencer (Illumina, San Diego, CA, USA).

value: murine alveolar macrophage cells (MH-S)

value: 20 μg/ml CuO NPs + 10 μM TTM


title: BMAC scRNA OA - 19


title: BMAC scRNA OA - 18


title: Wang_HiC_BWX5556_repB

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hupA-mCherry phleo, yuxG::xylR-Pxyl-hupB erm


title: C2

description:
Library name: sample8
C2


title: BMAC scRNA OA - 17

value: Bone Marrow


title: Wang_HiC_BWX5556_repA


title: NSCLC_PA004_lpwgs

description: low pass whole genome sequencing


title: NSCLC_PA001_lpwgs

description: low pass whole genome sequencing


title: C1

description:
Library name: sample7
C1


title: BMAC scRNA OA - 16

value: knee - OA


title: B3

description:
Library name: sample6
B3

value: 20 μg/ml CuO NPs


title: NSCLC_KRAS_12_slideseq

description: Single-nuclei RNA sequencing, SlideSeqV2

data_processing:
library strategy: single-nuclei RNAseq; SlideSeqV2
We used the Slide-seq tools pipeline (Stickels et al., 2021) to process our Slide-seq data, and loaded the data into Seurat.
Assembly: GRCh38
Supplementary files format and content: Counts data (*.counts.csv.gz) and Spatial coordinates data (*.coords.csv.gz)

extract_protocol:
RNA from 10 uM frozen tumor sections was extracted and spatially indexed as described in Stickels et al. (Nature Biotechnology, 2021). Briefly, sections were cut and then mounted on a "puck". RNA was hybridized for 15 min in 6x SCC and then reveres transcribed using Maxima RT.  Tissue was then digested and cleared using clearing buffer and proteinase K and unbound capture oligos were removed using EXO-I treatment. 2nd strand synthesis was then performed using sn-SMRT oligos and Klenow Enzyme and the libraries were amplified using PCR with Truseq and SMART PCR primers.
Libraries after PCR amplification were tagmented and indexed using Nextera XT kit and Nextera N70x oligos. After SPRI cleanup libraries were quantified using D5000 tapestation and prepared for sequencing.

value: Primary Tumor

tag: stk11 mutation status

value: WT

value: KRAS Q61H

value: snRNA-seq, SlideSeqV2

value: no


title: NSCLC_KRAS_11_slideseq

value: KRAS G12D


title: Wang_HiC_BWX5494_repA

tag: cell line

value: Bacillus subtilis PY79

value: Bacterial

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hupB-mCherry phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: B2

description:
Library name: sample5
B2


title: Wang_HiC_BWX5490_repB

tag: cell type

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hns-mCherry phleo


title: Wang_HiC_BWX3370_repB

value: parS∆9 no a.b., wt parS in spo0J no a.b.

tag: treatment


title: Wang_HiC_BWX5492_repA

value: parS∆9 no a.b., -1˚ parS no a.b., yhdG::Pxyl hupA-mCherry phleo


title: NSCLC_KRAS_10_slideseq

value: KRAS G12C

value: yes


title: B1

description:
Library name: sample4
B1

value: murine alveolar macrophage cells (MH-S)


title: Wang_HiC_BWX3370_repA


title: BMAC scRNA OA - 13

value: Bone Marrow

value: knee - OA

value: BMAC


title: A3

description:
Library name: sample3
A3

value: control


title: Wang_WGS_BWX5600


title: BMAC scRNA OA - 12


title: NSCLC_STK_20_slideseq

value: Primary Tumor

value: KRAS WT

value: snRNA-seq, SlideSeqV2


title: A2

description:
Library name: sample2
A2


title: BMAC scRNA OA - 11


title: A1

description:
Library name: sample1
A1


title: NSCLC_STK_15_slideseq

value: STK11 p.P221Lfs

value: KRAS G12D

value: no


title: Wang_WGS_BWX5427

value: Bacillus subtilis PY79

value: Bacterial

value: yhdG::Pxyl hmfA-mCherry phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: BMAC scRNA OA - 10


title: Macrophage, Mastitis group (Cytokine)

city: Pecs

first: Hairui

last: Ou

address: Rokus

country: Hungary

institute: University of Pecs

description:
Mastitis
SAMPLE 3

data_processing:
The qPCR data analysis was conducted using ExpressionSuite v1.3 (Thermo Fisher Scientific, Waltham, USA). The relative quantification (RQ) was calculated via the 2−△△Ct method, ensuring a 95% confidence level for the data derived.
For the normalization it uses the average of 2 housekeeping genes: HPRT1-Hs99999909_m1  18S-Hs99999901_s1.
Target gene signals normalized to housekeeping genes; 2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol], where ΔCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control ratios.

label: Taqman probe(FAM)

source_name: Monocyte-derived human primary macrophages treated with mastitis milk-derived EVs

label_protocol: Gene expression was determined using TaqMan Array Human Cytokine Network 96-well Plate (REF. 4418901, Applied Biosystems, USA).

growth_protocol: Peripheral blood was acquired from the Pécs Regional Blood Transfusion Center (Pécs, Hungary) and processed using Lymphocyte Separation Medium 1077 (Promocell, Heidelberg, Germany) in accordance with the manufacturer's instructions. Subsequently, the viable mononuclear cells were isolated, counted, and seeded into 6-well plates at a density of 1,000,000 cells per well.   The culture medium was specifically formulated using RPMI-1640 medium (Biowest, Nuaillé, France), enriched with 1% L-glutamine (Lonza, Basel, Switzerland), 2% penicillin/streptomycin (Lonza, Basel, Switzerland), and 10% exosome-depleted FBS (Thermo Fisher Scientific, Waltham, USA) to minimize EV interference from bovine serum, further supplemented with 100 ng/mL Peprotech M-CSF 300-25 (Gibco, Waltham, USA). The cells were cultured for 5 days in a 5% CO2 incubator at 37 °C, resulting in the differentiation of all monocytes into macrophages (M0) (Cao et al., 2019).

extract_protocol: RNA was isolated from cultured cells using Monarch Total RNA Miniprep Kit (New England Biolabs, Ipswich, USA), according to the manufacturer’s specifications. Subsequent determination of RNA concentrations was performed utilizing a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, USA). The isolated RNA was reverse transcribed to cDNA employing the 2720 Thermal Cycler (Applied Biosystems, Foster City, USA) using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, USA) adhering to the manufacturer's protocol. The cDNA synthesis protocol involved incubating samples for 10 minutes at 25 °C and 120 minutes at 37 °C, followed by a final extension for 5 minutes at 85 °C.

treatment_protocol: Differentiated macrophages were treated with MEV (Milk-derived extracellular vesicles) from healthy and mastitis groups separately to achieve the final concentration of 2×10^11 particles/mL. Additionally, untreated cell cultures with the same volume of PBS were maintained as negative controls. After 48 hours, macrophage supernatants were collected and stored at -80 °C (for a maximum of 3 months) for future experiments.

value: human primary macrophages

tag: activation reagent

value: with mastitis milk-derived Evs

tag: time

value: 2 days


title: BMAC scRNA OA - 15

tag: tissue

value: Bone Marrow


title: Wang_WGS_BWX5598

value: yhdG::Pxyl hupA-mCherry phleo, yuxG::xylR-Pxyl-hupB erm


title: BMAC scRNA OA - 9

value: knee - OA

value: BMAC


title: BMAC scRNA OA - 14


title: NSCLC_STK_14_slideseq

value: Brain Metastasis

value: KRAS G12C

value: yes


title: NSCLC_N586_slideseq

value: Primary Tumor

value: snRNA-seq, SlideSeqV2


title: BMAC scRNA OA - 8


title: BMAC scRNA OA - 7


title: Macrophage, Healthy group (Cytokine)

description:
Healthy
SAMPLE 2

source_name: Monocyte-derived human primary macrophages treated with healthy milk-derived EVs

value: with healthy milk-derived Evs


title: Macrophage, Negative control (Cytokine)

description:
Control
SAMPLE 1

source_name: Monocyte-derived human primary macrophages without any EV treatment

value: without any EV treatment


title: NSCLC_STK22dot2_slideseq

value: KRAS WT

value: no


title: Wang_WGS_BWX5271

value: Bacillus subtilis PY79

value: Bacterial

value: yhdG::Pxyl hupB-mCherry phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: NSCLC_N254_slideseq


title: Wang_WGS_BWX5269

value: yhdG::Pxyl hupA-mCherry phleo


title: Caco-2, Mastitis group (Cytokine)

description:
Mastitis
SAMPLE 3

data_processing:
The qPCR data analysis was conducted using ExpressionSuite v1.3 (Thermo Fisher Scientific, Waltham, USA). The relative quantification (RQ) was calculated via the 2−△△Ct method, ensuring a 95% confidence level for the data derived.
For the normalization it uses the average of 2 housekeeping genes: GAPDH-Hs99999905_m1  HPRT1-Hs99999909_m1.
Target gene signals normalized to housekeeping genes; 2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol], where ΔCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control ratios.

source_name: colorectal adenocarcinoma patient

growth_protocol: Human colorectal adenocarcinoma Caco-2 cells were purchased from the American Type Culture Collection and were used from passages 52 to 58 following the supplier’s recommendations. Caco-2 cells were cultured in DMEM medium (Biosera, Cholet, France) with 10% exosome-depleted FBS (Thermo Fisher Scientific, Waltham, USA). Cells (30,000 per well) were seeded in 24 well plates one day before treatment.

extract_protocol: After 48 hours of treatment, RNA was isolated from cultured cells using Monarch Total RNA Miniprep Kit (New England Biolabs, Ipswich, USA), according to the manufacturer’s specifications. Subsequent determination of RNA concentrations was performed utilizing a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, USA). The isolated RNA was reverse transcribed to cDNA employing the 2720 Thermal Cycler (Applied Biosystems, Foster City, USA) using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, USA) adhering to the manufacturer's protocol. The cDNA synthesis protocol involved incubating samples for 10 minutes at 25 °C and 120 minutes at 37 °C, followed by a final extension for 5 minutes at 85 °C.

treatment_protocol: The supernatant from macrophages accounted for 1/3 of the total volume of the Caco-2 culture medium. The experimental groups were divided into negative control, healthy group and mastitis group.

value: with mastitis ev treated macrophages supernatant

value: 2 days


title: Wang_WGS_BWX5429

value: yhdG::Pxyl hmfB-mCherry phleo


title: NSCLC_PA056_slideseq

value: Brain Metastasis


title: BMAC scRNA OA - 6

value: Bone Marrow

value: knee - OA

value: BMAC


title: Wang_WGS_BWX523

value: sacA::hbsu-mCherry Kan


title: BMAC scRNA OA - 5


title: NSCLC_PA054_slideseq

value: snRNA-seq, SlideSeqV2

value: yes


title: Caco-2, Negative control (Cytokine)

description:
Control
SAMPLE 1

value: without macrophages supernatant


title: Caco-2, Healthy group (Cytokine)

description:
Healthy
SAMPLE 2

value: with healthy ev treated macrophages supernatant


title: BMAC scRNA OA - 4


title: Wang_ChIP_antimCherry_BWX5600

value: Bacillus subtilis PY79

value: ChIP using anti-mCherry antibodies


title: NSCLC_STK_18_slideseq

value: STK11 Q305X

value: KRAS Q61H

value: no


title: NSCLC_PA025_slideseq


title: 2d-96h

city: Beijing

first: Bing

last: Peng

state: Beijing

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

description: 10x Genomics

data_processing:
For single-cell RNA seq, cellranger was used for the pre-processing and Seurat was used for the downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Samples were dissociated into single cells and resuspended in 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).


title: 2d-48h

description: 10x Genomics


title: Wang_ChIP_antimCherry_BWX5429

value: Bacterial

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: BMAC scRNA OA - 3


title: NSCLC_PA019_slideseq


title: 2d-4h

description: 10x Genomics


title: Wang_WGS_BWX5256

value: yhdG::Pxyl hns-mCherry phleo


title: NSCLC_KRAS_13_tcr

description: Single-nuclei RNA sequencing

data_processing:
library strategy: single-cell RNAseq (TCR-seq)
Fastq files were analyzed using vdj in Cell Ranger (v6.1.1, 10x Genomics). Transcripts were aligned to the human GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger vdj output files (csv)

extract_protocol:
Single-nuclei suspension from frozen NSCLC metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST)  followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics  5' v1.1 or 5' V2.0  reagents and a Chromium controller.
Chromium Single Cell V(D)J Enrichment Kit for human T cells Reagent Kit, v 1.1 or Single Cell Human TCR Amplification Kit were utilized for snTCR library generation (10X genomics) depending on whether 5' V1 or 5' V2 kits were utilized for cDNA library generation, respectively. Final sequencing libraries were prepared using Single Index Kit T Set A or Library construction kit (catalog no. 1000190) and Dual Index Kit TT set A (catalog no. 1000215).

value: PT

value: WT

value: KRAS G12V

value: snRNA-seq


title: NSCLC_KRAS_12_tcr

description: Single-nuclei RNA sequencing


title: Wang_ChIP_antimCherry_BWX5427

value: yhdG::Pxyl hmfA-mCherry phleo


title: P121_LUT

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program and subsequently trimmed using fastp 0.21.0 to remove Illumina adapter sequences. STAR 2.7.9a was used to index the human reference genome (hg38/GRCh38) and align the resultant fastq files. Mapped reads were then counted in annotated exons using featureCounts v1.5.1. The gene annotations (Homo_sapiens.GRCh38.101.gtf) and reference genome were obtained from Ensembl.
Assembly: hg38/GRCh38
Supplementary files format and content: Comma seperated file with raw gene counts for all luteal samples
Supplementary files format and content: Comma seperated file with normalized values of relevant luteal sample

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and placed in RLT Plus Lysis buffer (QIAGEN, Hilden, Germany), and homogenized using a TissueLyzer II machine (QIAGEN). An AllPrep DNA/RNA Mini Kit (QIAGEN) was used for RNA isolation and purification, and RNA quality was assessed by determining the RNA integrity number (RIN). A TruSeq mRNA SEq Library Prep kit (Illumina, San Diego, USA) was used to convert mRNA to cDNA libraries. Libraries (barcoded) were pooled and sequenced using Novaseq 6000 PE 150-bp (Illumina).
To construct libraries suitable for sequencing the Illumina stranded mRNA prep ligation protocol was used with starting concentration of 200 ng total RNA. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation. The indexed cDNA libraries were normalized and combined and the pools were sequenced on the Illumina NovaSeq S6000 on one lane of an S4-300 flowcell (PE 2X150).

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

value: Female

tag: time point

value: Luteal


title: BMAC scRNA OA - 2

value: Bone Marrow

value: knee - OA

value: BMAC


title: Wang_ChIP_antimCherry_BWX5598

value: Bacillus subtilis PY79

value: yhdG::Pxyl hupA-mCherry phleo, yuxG::xylR-Pxyl-hupB erm

value: ChIP using anti-mCherry antibodies


title: NSCLC_KRAS_11_tcr

description: Single-nuclei RNA sequencing

tag: metastatic site

tag: patient id

value: KRAS G12D

value: yes


title: Wang_ChIP_antimCherry_BWX5269

value: Bacterial

value: yhdG::Pxyl hupA-mCherry phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.


title: Wang_ChIP_antimCherry_BWX5271

value: yhdG::Pxyl hupB-mCherry phleo


title: P120_LUT


title: blastomere-2-5nM-P4

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters.
The expression count matrix was obtained by FeatureCounts.
Data were normalized by total mapped reads of each library (CPM: count per million).
Assembly: mm10

source_name: ICR

extract_protocol:
DNA and RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme)

value: ICR

value: embryo

tag: genotype

value: WT

value: cultured in 2iLP medium


title: 2d-24h

description: 10x Genomics


title: placenta_ys

description: 10x Genomics

source_name: placenta+yolk sac

value: placenta+yolk sac


title: NSCLC_KRAS_10_tcr

description: Single-nuclei RNA sequencing

value: PT

tag: kras mutation status

value: KRAS G12C

tag: sequencing technique

value: snRNA-seq


title: BMAC scRNA OA - 1

value: Bone Marrow

value: knee - OA

value: BMAC


title: P119_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Female

value: Luteal


title: P118_LUT


title: NSCLC_KRAS_17_tcr

description: Single-nuclei RNA sequencing

value: BM

tag: tcr-seq

value: yes


title: blastomere-2-5nM-P5

value: ICR


title: blastomere-4nM-P4

value: embryo


title: Wang_ChIP_antimCherry_BWX523

value: Bacillus subtilis PY79

value: Bacterial

tag: strain genetic_information

value: sacA::hbsu-mCherry Kan

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.

tag: antibody

value: ChIP using anti-mCherry antibodies


title: NSCLC_KRAS_8_tcr

description: Single-nuclei RNA sequencing

tag: stk11 mutation status

value: WT

value: KRAS G12C

value: snRNA-seq


title: P117_LUT


title: blastomere-4nM-P5

tag: cell line

tag: cell type

value: cultured in 2iLP medium


title: P116_LUT

value: Ectocervix


title: Wang_ChIP_antiHBsu_BWX523

value: wild type

tag: treatment

value: Cells were growing in CH medium at 37˚C to exponential phase

value: ChIP using anti-HBsu antibodies


title: P115_LUT

value: Kenyan female sex workers

value: Female

value: Luteal


title: P114_LUT


title: ZHBTc4-2MYC-P3

value: mESC

value: cultured in 2MYC medium supplemented with dox

tag: time


title: CaMKiiα Cre +/-; Mef2c fl/fl Treated 3

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
FastQC for raw read quality
Trimmomatic for trimming reads and adapters
STAR for read alignment to MM10 genome
DESeq2 analysis for DEGs
GO analysis using ToppFunn and SynGO
Assembly: MM10
Supplementary files format and content: Xlsx, CPM values

source_name: Brain

extract_protocol:
RNA extraction
150 bp paired end reads

tag: tissue

value: Brain

value: CaMKiialpha Cre +/-; Mef2c fl/fl

value: 100 uM Picrotoxin and 100 uM 4 Aminopyridine


title: NSCLC_KRAS_7_tcr

description: Single-nuclei RNA sequencing

value: BM

value: yes


title: ZHBTc4-2MYCP-P12-DOX

value: WT

value: cultured in 2MYCP medium supplemented with dox


title: NSCLC_STK_22dot2_tcr

description: Single-nuclei RNA sequencing

value: PT

value: KRAS WT

value: snRNA-seq


title: NSCLC_KRAS_6_tcr

description: Single-nuclei RNA sequencing

value: KRAS G12C


title: P113_LUT

value: Ectocervix

tag: subject group


title: CaMKiiα Cre +/-; Mef2c fl/fl Treated 1


title: CaMKiiα Cre +/-; Mef2c fl/fl Treated 2


title: ZHBTc4-2MYCP-P12

value: cultured in 2MYCP medium


title: ZHBTc4-2MYC-P2


title: CaMKiiα Cre +/-; Mef2c fl/fl Vehicle 3

value: 1% DMSO + 1% Water


title: P112_LUT

value: Kenyan female sex workers

tag: Sex

value: Female

value: Luteal


title: Wang_ChIP_antimCherry_BWX5256

value: Bacillus subtilis PY79

value: Bacterial

value: yhdG::Pxyl hns-mCherry phleo

value: Cells were growing in CH medium at 37˚C to exponential phase and treated with 0.5% xylose for 90 mins.

value: ChIP using anti-mCherry antibodies


title: EB-TSC

value: mESC

value: WT

value: cultured in TSC medium


title: CaMKiiα Cre +/-; Mef2c fl/fl Vehicle 2

value: Brain

value: CaMKiialpha Cre +/-; Mef2c fl/fl


title: P111_LUT

tag: time point


title: NSCLC_STK_15_tcr

description: Single-nuclei RNA sequencing

tag: metastatic site

value: PT

value: STK11 p.P221Lfs

value: KRAS G12D

value: snRNA-seq

value: yes


title: CaMKiiα Cre +/-; Mef2c fl/fl Vehicle 1

value: 1% DMSO + 1% Water


title: P8-withoutC

value: cultured in 2MYP medium


title: P110_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Female

value: Luteal


title: NSCLC_STK_2_tcr

description: Single-nuclei RNA sequencing

tag: patient id

value: KRAS G12A


title: P7-withoutC

value: mESC

tag: genotype


title: P109_LUT


title: NSCLC_STK_18_tcr

description: Single-nuclei RNA sequencing

value: BM

value: STK11 Q305X

tag: kras mutation status

value: KRAS Q61H


title: Mef2c fl/fl Treated 3 (FLX_CAMK17_2_M_TREATED_S20)

value: Brain

value: Mef2c fl/fl

value: 100 uM Picrotoxin and 100 uM 4 Aminopyridine


title: NTF96h

value: WT

value: cultured in NTF medium


title: NSCLC_STK_21_tcr

description: Single-nuclei RNA sequencing

value: PT

value: STK11 c.169delG p.E57fs*

value: KRAS WT

tag: sequencing technique

value: snRNA-seq

value: yes


title: Mef2c fl/fl Treated 2


title: P108_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Female


title: P106_LUT

value: Luteal


title: NSCLC_STK_5dot2_tcr

description: Single-nuclei RNA sequencing

value: BM

value: STK11 c.836delG, p.G279fs

value: KRAS G12C

tag: tcr-seq


title: NTF72h

value: mESC


title: Mef2c fl/fl Vehicle 3

value: Brain

value: Mef2c fl/fl

value: 1% DMSO + 1% Water


title: NTF48h

value: WT

value: cultured in NTF medium


title: P107_LUT


title: NSCLC_STK_14_tcr

description: Single-nuclei RNA sequencing


title: NTF24h


title: NSCLC_STK_5dot1_tcr

description: Single-nuclei RNA sequencing


title: NSCLC_STK_20_tcr

description: Single-nuclei RNA sequencing

value: PT


title: Mef2c fl/fl Vehicle 2


title: P105_LUT


title: P104_LUT


title: Mef2c fl/fl Vehicle 1


title: NTF10h


title: NSCLC_STK_1_tcr

description: Single-nuclei RNA sequencing

value: STK11 deletion exons 2-5

value: KRAS G13C


title: NTF4h


title: NSCLC_N586_tcr

description: Single-nuclei RNA sequencing

value: snRNA-seq

value: yes


title: OrgRNA_,HTO

first: John

last: Blair

address: 101 6th Avenue

institute: New York Genome center

description:
Library name: OrgRNA_ADT
OrgRNA_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode and UMI is in R1;  R3 contains UMI and HTO index

library_source: other

data_processing:
Sequencing runs were demultiplexed with bcl2fastq v2.20.0.422
Demultiplexed FASTQs were processed using Cellranger count (for scRNA-seq), Cellranger-atac Count (for scATAC-seq) and Cellranger-arc count (for scRNA-seq and scATAC-seq). ADTs and HTOs were processed using  alevin-fry v0.4.3 (https://combine-lab.github.io/alevin-fry-tutorials/2021/af-feature-bc/)
Single-cell data was read into Seurat v4 and filtered for cell doublets and unassigned HTO-cells using the HTOdemux function (https://satijalab.org/seurat/) and/or (for brain organoids) Vireo (v0.5.8) derived genotype assigned on a per-cell basis (https://github.com/single-cell-genetics/vireo)
Assembly: hg38
Supplementary files format and content: Counts Matrix files for ATAC,RNA,HTO and ADT library types: ATAC.csv, ADT.csv, HTO.csv, RNA.csv
Supplementary files format and content: fragments files for ATAC library types

molecule: protein

source_name: iPS-derived Brain Organoids

growth_protocol: K562 cells were maintained in IMDM + 10% FBS Growth media. HEK cells were maintained in DMEM + 10% FBS growth media. iPS cells were maintained in mTESR media. All cell lines were maintained in a 37C incubator at 5% CO2 and split according to confluence. Retinal Organoids were derived from iPS cells and differentiated using the AMASS protocol (Cowan, et al .2020). Brain organoids were derived from iPS cells and differentiated according to Giandomenico et al, 2020.

extract_protocol:
K562 cells were centrifuged in growth media at 300 x g for 5 mins. Adherent cells (HEK and iPS) were dissociated with accutase, resuspended in PBS and centrifuged at 300 x g for 5 mins. Organoids (Brain and Retinal) were dissociated with a papain-based solution, cryopreserved, thawed and centrifuged at 300 x g. Single cells were encapsulated in GEMs using the 10X chromium controller with the associated kit (scATAC v1.1 for Phospho-seq, scATAC+RNA for Phospho-seq-multi, and scRNA v3.1 for Organoid RNA-seq
scATAC-seq, scRNA-seq libraries were constructed according to the associated kits methods from 10X genomics. ADT and HTO libraries were constructed according to the ASAP-seq methods (Mimitou et al, 2021) and Phospho-seq methods (https://phospho-seq.com/post/)

treatment_protocol: For Pilot experiment, K562 cells were stimulated with 50 ng/ml EGF for 15 mins or inhibited with 500 nm PX-866 for 4 hrs.

value: iPS-derived Brain Organoids

tag: library type

value: HTO

tag: protocol

value: Prepared with the 10X genomics scRNA protocol + Hashing


title: OrgRNA, RNA

description:
Library name: OrgRNA_RNA
scRNA-seq Library
Cell Barcode and UMI is in R1;  R3 contains mRNA sequences

value: RNA

value: Prepared with the 10X genomics scRNA protocol


title: NTF0h


title: Mef2c fl/fl Treated 1

value: 100 uM Picrotoxin and 100 uM 4 Aminopyridine


title: P102_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Female

value: Luteal


title: NSCLC_N254_tcr

description: Single-nuclei RNA sequencing

tag: stk11 mutation status


title: mTBLC-ATAC

data_processing:
Trimmomatic software was used to trim the adapters.
Bowtie2 was used for the alignment to the mm10 reference genome
MACS3 was used to call peaks. EdgeR R package was used to normalize the count matrix and calculate the differential peaks
Assembly: mm10

extract_protocol:
50,000 living cells were collected in a tube, centrifuged at 500 g at 4°C.
ATAC-seq was performed as the previously described method (Corces et al., 2017) with some  modification.

tag: cell line

value: mESC


title: NSCLC_PA141_tcr

description: Single-nuclei RNA sequencing

value: BM


title: mES-ATAC

tag: cell type


title: NSCLC_STK_3_tcr

description: Single-nuclei RNA sequencing

value: STK11 splice site 863-1G>T


title: P100_LUT


title: NSCLC_PA125_tcr

description: Single-nuclei RNA sequencing


title: Phospho-seq BrainOrg, ADT

description:
Library name: BrainOrg_ADT
BrainOrg_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3

value: ADT

value: Prepared with the Phospho-seq Protocol


title: mTBLC-H3K27AC

data_processing:
library strategy: Cut&tag
CUT&Tag-seq reads were trimmed by TrimGalore software
CUT&Tag-seq reads were aligned to the mouse genome (mm10) with Bowtie2. Samtools was used to filter and keep the mapped read pairs.
Peaks were called uing SEACR
Assembly: mm10
Supplementary files format and content: bigWig, mapped reads

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated.
Cut&tag libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme).

tag: chip antibody

tag: chip antibody_info.

value: Thermo Fisher Scientific (Cat#39133)


title: Bridge-Multi, ATAC

description:
Library name: Bridge-Multi_ATAC
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences

library_source: genomic single cell

value: ATAC

value: Prepared with the 10X genomics scATAC+scRNA protocol


title: NSCLC_PA104_tcr

description: Single-nuclei RNA sequencing

value: snRNA-seq

value: yes


title: P099_LUT

tag: tissue


title: NSCLC_PA080_tcr

description: Single-nuclei RNA sequencing


title: P098_LUT

tag: subject group


title: mES-H3K27AC


title: mTBLC-H3K9ME3

value: Abcam (Cat#ab8898)


title: NSCLC_PA076_tcr

description: Single-nuclei RNA sequencing


title: P103_LUT

tag: Sex


title: Phospho-seq BrainOrg, ATAC

description:
Library name: BrainOrg_ATAC
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences

value: iPS-derived Brain Organoids


title: mES-H3K9ME3


title: Phospho-Multi, ADT

description:
Library name: Phospho-Multi_ADT
RetOrgMulti_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3

source_name: iPS-derived Retinal Organoids

value: iPS-derived Retinal Organoids


title: NSCLC_PA072_tcr

description: Single-nuclei RNA sequencing


title: NSCLC_PA070_tcr

description: Single-nuclei RNA sequencing


title: P096_LUT

value: Ectocervix

tag: time point


title: P095_LUT

value: Kenyan female sex workers


title: mTBLC-Pol2


title: Bridge-Multi, RNA

description:
Library name: Bridge-Multi_RNA
scRNA-seq Library
Cell Barcode and UMI is in R1;  R3 contains mRNA sequences

value: RNA


title: P101_LUT

value: Female

value: Luteal


title: Phospho-Multi, ATAC

description:
Library name: Phospho-Multi_ATAC
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences


title: mES-Pol2

value: mESC


title: NSCLC_PA067_tcr

description: Single-nuclei RNA sequencing

tag: metastatic site

value: BM


title: NSCLC_PA068_tcr

description: Single-nuclei RNA sequencing

tag: patient id


title: mTBLC-H3K27me3

value: Diagenode (Cat#pAb-069-050)


title: P094_LUT


title: Phospho-seq BrainOrg, HTO

description:
Library name: BrainOrg_HTO
BrainOrg_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode is R2; UMI is in R1; HTO index is in R3

value: HTO

value: Prepared with the Phospho-seq Protocol


title: Phospho-seq RetOrg, HTO

description:
Library name: RetOrg_HTO
RetOrg_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode is R2; UMI is in R1; HTO index is in R3


title: Phospho-seq RetOrg, ADT

description:
Library name: RetOrg_ADT
RetOrg_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3

value: ADT


title: P097_LUT


title: NSCLC_PA060_tcr

description: Single-nuclei RNA sequencing


title: mES-H3K27me3


title: P092_LUT


title: NSCLC_PA056_tcr

description: Single-nuclei RNA sequencing


title: mTBLC-H3K4me3

value: Millipore (Cat#04-475)


title: P091_LUT


title: Phospho-seq RetOrg, ATAC

description:
Library name: RetOrg_ATAC
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences

value: ATAC


title: mES-H3K4me3


title: ASAP-seq Benchmark_2, ADT

description:
Library name: ASAP_Benchmark_2_ADT
Phos_Bench_2_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3

tag: treatment

value: Stimulated/Inhibited K562

value: Prepared with the ASAP-seq Protocol


title: P090_LUT


title: Phospho-Multi, RNA

description:
Library name: Phospho-Multi_RNA
scRNA-seq Library
Cell Barcode and UMI is in R1;  R3 contains mRNA sequences


title: P089_LUT


title: NSCLC_PA048_tcr

description: Single-nuclei RNA sequencing

tag: kras mutation status

value: snRNA-seq

value: yes


title: SC-mTBLC

description: 10x Genomics

data_processing:
For single-cell RNA seq, cellranger was used for the pre-processing and Seurat was used for the downstream analysis.
Assembly: mm10

source_name: mTBLC

value: mTBLC


title: ASAP-seq Benchmark_2, ATAC

description:
Library name: ASAP_Benchmark_2_ATAC
Phos_Bench_2_features.csv
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences


title: NSCLC_PA043_tcr

description: Single-nuclei RNA sequencing

tag: sequencing technique


title: P093_LUT

value: Ectocervix

value: Kenyan female sex workers


title: SC-blastoid

description: 10x Genomics

source_name: blastoid

value: blastoid


title: P088_LUT

value: Female

value: Luteal


title: Phospho-seq Benchmark_2, ADT

description:
Library name: Benchmark_2_ADT
Phos_Bench_2_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3


title: P086_LUT


title: P085_LUT


title: SC-teratoma-mTBLC

description: 10x Genomics

source_name: teratoma-mTBLC

value: teratoma-mTBLC


title: PSC-2

value: mESC

tag: genotype

value: WT

value: cultured inS/L medium


title: NSCLC_PA034_tcr

description: Single-nuclei RNA sequencing

value: BM

tag: tcr-seq


title: NSCLC_PA042_tcr

description: Single-nuclei RNA sequencing


title: Phospho-seq Benchmark_2, HTO

description:
Library name: Benchmark_2_HTO
Phos_Bench_2_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode is R2; UMI is in R1; HTO index is in R3

tag: library type

value: HTO

tag: protocol

value: Prepared with the Phospho-seq Protocol


title: Phospho-seq Benchmark_2, ATAC

description:
Library name: Benchmark_2_ATAC
Phos_Bench_2_features.csv
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences

tag: cell line

value: Stimulated/Inhibited K562

value: ATAC


title: 2mycp-TBLC-P0

tag: cell type


title: P083_LUT


title: NSCLC_PA025_tcr

description: Single-nuclei RNA sequencing

tag: stk11 mutation status

value: snRNA-seq


title: NSCLC_PA019_tcr

description: Single-nuclei RNA sequencing

value: yes


title: TBLC-EB-DAY12

value: cultured in serum medium

tag: time


title: P082_LUT

tag: tissue

value: Ectocervix


title: Phospho-seq Benchmark, ADT

description:
Library name: Benchmark_ADT
Phos_Bench_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3

value: ADT


title: NSCLC_PA054_tcr

description: Single-nuclei RNA sequencing


title: ASAP-seq Benchmark_2, HTO

description:
Library name: ASAP_Benchmark_2_HTO
Phos_Bench_2_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode is R2; UMI is in R1; HTO index is in R3

value: Prepared with the ASAP-seq Protocol


title: TBLC-EB-DAY10


title: NSCLC_PA005_tcr

description: Single-nuclei RNA sequencing


title: P081_LUT

tag: subject group

value: Kenyan female sex workers

value: Female


title: Phospho-seq Benchmark, ATAC

description:
Library name: Benchmark_ATAC
Phos_Bench_features.csv
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences


title: TBLC-EB-DAY8


title: P080_LUT

tag: Sex

value: Luteal


title: NSCLC_PA004_tcr

description: Single-nuclei RNA sequencing


title: Phospho-seq Pilot, ADT

description:
Library name: Pilot_ADT
PhosPilot_features.csv
Antibody Derived Tag (ADT)
Cell Barcode is R2; UMI and ADT index are in R3

value: Mixed Sample (Stimulated/Inhibited K562, untreated iPS)


title: TBLC-EB-DAY3

value: mESC

value: WT


title: P079_LUT

tag: time point


title: NSCLC_PA001_tcr

description: Single-nuclei RNA sequencing

tag: metastatic site

value: BM


title: Phospho-seq Pilot, HTO

description:
Library name: Pilot_HTO
PhosPilot_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode is R2; UMI is in R1; HTO index is in R3

value: HTO


title: Tc1-EB-DAY10


title: NSCLC_PT11

description:
Single-nuclei RNA sequencing
KRAS_13

data_processing:
library strategy: single nuclei RNAseq
Raw snRNA-seq data were analyzed using Cell Ranger (v5.0.1). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.2.0). Gene expression matrices were processed individually in R (v4.1.2) using Seurat (v4.0.5).
Filters were applied to keep cells with 500–10,000 genes, 1,000–60,000 UMIs, and <10% of mitochondrial reads in each individual sample.
Scrublet v0.2.1 (Wolock et al., 2019) was applied to identify and remove doublets with an expected doublet rate ranging from 2.8–6.4% based on the loading rate.
Assembly: GRCh38
Supplementary files format and content: mtx file (MatrixMarket format) of combined gene expression count matrix
Supplementary files format and content: csv file of gene names corresponding to the combined gene expression count matrix
Supplementary files format and content: csv file of integrated gene expression matrix

source_name: NSCLC primary tumor

extract_protocol:
Single-nuclei suspension from frozen NSCLC metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST)  followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics  5' v1.1 or 5' v2.0 reagents and a Chromium controller.
Single-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 5' (V1.1 and V2) reagents according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.

value: PT

tag: patient id

tag: stk11 mutation

value: KRAS G12V


title: NSCLC_PT10

description:
Single-nuclei RNA sequencing
KRAS_12

tag: kras mutation status

value: KRAS Q61H


title: P075_LUT


title: Phospho-seq Pilot, ATAC

description:
Library name: Pilot_ATAC
scATAC-seq Library
Cell Barcode is R2; R1 and R3 contain ATAC sequences

tag: treatment

value: ATAC

value: Prepared with the Phospho-seq Protocol


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_Z_RNA

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

description: Library name: NaiveCD4_PATIENT_Z_RNA

data_processing:
Raw Fastq files were pseudoaligned using Kallisto software (version > 0.44.0). Abundance output from Kallisto were read into R using tximport and gene-level count information are provided here.
Assembly: hg38
Supplementary files format and content: Raw_Counts_RNA_Fig3.txt contains the kallisto pseudoaligned counts from the first cohort of lupus patients and healthy controls and includes multiple CD4 T cell subsets.
Supplementary files format and content: Raw_Counts_RNA_Fig5.txt contains the kallisto pseudoaligned counts from the first and second cohorts of lupus patients and healthy controls and includes only Naïve CD4 T cells.
Supplementary files format and content: Raw_Counts_RNA_Fig6.txt contains the kallisto pseudoaligned counts from the first , second, and third  cohorts of lupus patients and healthy controls and includes only Naïve CD4 T cells.

source_name: Blood

extract_protocol:
Cryopreserved PBMCs were thawed and enriched using negative selection (Stem Cell technologies human CD4 Isolation kit #100-0696) ) for CD4 T cells. They were then stained with flourescent antibodies and cells were sorted using flourescent activated cell sorter (Aria C). CD45RA+CD27+ naive TH, CXCR5+PD1+ICOS+CD38+ AcTfh, CXCR5+PD1+ICOSCD38- cTfh, and CXCR5-PD1-CXCR3+ Th1 cells were sorted. In most cases, 5000 cells were sorted. Immediately following sorting, cells were processed for RNA-seq following manufacturer protocols (Takara SMART-Seq® v4 Ultra Low Input RNA Kit). Cells were processed directly to cDNA without separate RNA isolation per the protocol.
Libaries were prepared following standard protocols and utilizing Illumina indexes. Fractionation and size selection were performed. Size selection was done using bead-based enrichment.

value: Blood

tag: timpoint

value: A

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

value: No

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race

value: White


title: P074_LUT

tag: tissue

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

value: Female

tag: time point

value: Luteal


title: Phospho-seq Benchmark, HTO

description:
Library name: Benchmark_HTO
Phos_Bench_features.csv
Hashtag-derived Oligonucleotide (HTO)
Cell Barcode is R2; UMI is in R1; HTO index is in R3

tag: cell line

tag: library type

tag: protocol


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_Y_RNA

description: Library name: NaiveCD4_PATIENT_Y_RNA

tag: cell type

tag: timpoint

tag: disease

value: Yes

value: Losartan

value: yes

value: Black/AfricanAmerican


title: Tc1-EB-DAY3

value: mESC

tag: genotype

value: WT

tag: treatment

value: cultured in serum medium

tag: time


title: P073_LUT


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_X_RNA

description: Library name: NaiveCD4_PATIENT_X_RNA

value: Blood

value: Healthy

tag: batch

tag: treatment arb_active

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

value: UKN


title: NSCLC_PT08

description:
Single-nuclei RNA sequencing
KRAS_10

tag: metastatic site

value: PT

tag: patient id

tag: stk11 mutation

tag: kras mutation status

value: KRAS G12C

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: NSCLC_BM32

description:
Single-nuclei RNA sequencing
KRAS_17

source_name: NSCLC brain metastasis

value: BM


title: P072_LUT

tag: tissue

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

tag: time point


title: E3.5-blastcyst

description: E3.5_blastcyst_bulk Rnaseq-origin.xlsx

source_name: ICR-embryo

tag: cell line

value: ICR-embryo

tag: genotype


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_V_RNA

description: Library name: NaiveCD4_PATIENT_V_RNA

value: Female

tag: cell type

tag: timpoint

value: A

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

value: Yes

value: Valasartan

value: No

tag: disease _severity_sledai

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race


title: P071_LUT

value: Luteal


title: NSCLC_BM31

description:
Single-nuclei RNA sequencing
KRAS_8

tag: metastatic site

tag: patient id

tag: stk11 mutation

value: WT

tag: kras mutation status

value: yes


title: Blatoid-1

description: Blastoid_bulk RNAseq-origin.xlsx

value: mESC

tag: treatment

value: cultured in TNKM medium


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_U_RNA

description: Library name: NaiveCD4_PATIENT_U_RNA

tag: tissue

value: Blood

tag: Sex

tag: treatment arb_type

value: Losartan

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

value: Asian


title: NSCLC_BM30

description:
Single-nuclei RNA sequencing
KRAS_7

value: BM

value: KRAS G12C

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: P070_LUT

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

value: Female

tag: time point


title: P077_LUT


title: Tc1-EB-DAY12

tag: cell line

tag: cell type

tag: genotype

value: cultured in serum medium

tag: time


title: PreLC-p2

value: cultured in SFH medium


title: Tc1-EB-DAY8


title: P069_LUT


title: NSCLC_BM29

description:
Single-nuclei RNA sequencing
KRAS_6

tag: metastatic site

tag: patient id

tag: stk11 mutation


title: NSCLC_PT07

description:
Single-nuclei RNA sequencing
STK_22dot2

value: PT

tag: kras mutation status

value: KRAS WT


title: P068_LUT

tag: tissue

tag: Sex

value: Luteal


title: NSCLC_PT09

description:
Single-nuclei RNA sequencing
KRAS_11

value: WT

value: KRAS G12D

value: yes


title: PreLC-p1

value: mESC

tag: treatment


title: P067_LUT


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_S_RNA

description: Library name: NaiveCD4_PATIENT_S_RNA

value: Blood

tag: timpoint

value: A

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

value: Yes

tag: treatment arb_type

value: Losartan

tag: treatment rituximab_ever

value: No

tag: treatment rituximab_active

tag: disease _severity_sledai

tag: ethnicity

value: Not Hispanic or Latino/a

tag: race

value: White


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_R_RNA

description: Library name: NaiveCD4_PATIENT_R_RNA

value: Female

tag: cell type

value: Healthy

tag: treatment acei_active

value: UKN


title: TELC-p2

tag: cell line

tag: genotype

value: cultured in SFH medium

tag: time


title: NSCLC_PT06

description:
Single-nuclei RNA sequencing
STK_21

tag: metastatic site

value: PT

tag: patient id

tag: stk11 mutation

value: STK11 c.169delG p.E57fs*

tag: kras mutation status

value: KRAS WT

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: P066_LUT

tag: tissue

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

tag: time point

value: Luteal


title: PreLC-p0

value: mESC

value: WT

tag: treatment


title: NSCLC_PT05

description:
Single-nuclei RNA sequencing
STK_20

value: yes


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AC_RNA

description: Library name: NaiveCD4_PATIENT_AC_RNA

value: Blood

tag: timpoint

value: A

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

value: No

tag: treatment arb_type

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: disease _severity_sledai

tag: ethnicity

tag: race


title: TELC-p1

tag: cell line

tag: cell type

tag: genotype

tag: time


title: NSCLC_PT04

description:
Single-nuclei RNA sequencing
STK_15

tag: metastatic site

tag: patient id

tag: stk11 mutation

value: STK11 p.P221Lfs

tag: kras mutation status

value: KRAS G12D

tag: sequencing technique

tag: tcr-seq


title: Blatoid-2

description: Blastoid_bulk RNAseq-origin.xlsx

tag: treatment

value: cultured in TNKM medium


title: P065_LUT

tag: tissue

tag: subject group

tag: Sex

value: Female

tag: time point


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AB_RNA

description: Library name: NaiveCD4_PATIENT_AB_RNA

tag: timpoint

tag: disease

tag: batch

tag: treatment arb_active

value: Yes

tag: treatment arb_type

value: Losartan

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

value: Not Hispanic or Latino/a

value: Black/AfricanAmerican


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_T_RNA

description: Library name: NaiveCD4_PATIENT_T_RNA

tag: cell type

tag: race


title: NSCLC_PT03

description:
Single-nuclei RNA sequencing
STK_2

tag: metastatic site

value: PT

tag: patient id

tag: stk11 mutation

tag: kras mutation status

value: KRAS G12A

tag: sequencing technique

value: snRNA-seq

tag: tcr-seq


title: P064_LUT

tag: tissue

value: Ectocervix

tag: subject group

value: Kenyan female sex workers

tag: Sex

tag: time point

value: Luteal


title: TELC-p0

tag: cell line

value: mESC

tag: genotype

value: WT

tag: treatment

value: cultured in SFH medium

tag: time


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_AA_RNA

description: Library name: NaiveCD4_PATIENT_AA_RNA

value: Blood

tag: timpoint

value: A

tag: disease

value: Lupus

tag: batch

tag: treatment arb_active

value: No

tag: treatment arb_type

tag: treatment rituximab_ever

value: yes

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

tag: ethnicity

value: White


title: NSCLC_BM27

description:
Single-nuclei RNA sequencing
STK_18

tag: metastatic site

value: BM

tag: patient id

tag: stk11 mutation

value: STK11 Q305X

tag: kras mutation status

value: KRAS Q61H

tag: sequencing technique

tag: tcr-seq


title: SFH-d96

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: time


title: P063_LUT

tag: tissue

tag: subject group

tag: Sex

value: Female

tag: time point


title: P062_LUT


title: SFH-d92


title: NSCLC_BM26

description:
Single-nuclei RNA sequencing
STK_14

value: KRAS G12C

value: snRNA-seq


title: SFH-d88


title: Human PBMC-derived CD4 T cells NaiveCD4_PATIENT_Q_2_RNA

description: Library name: NaiveCD4_PATIENT_Q_2_RNA

tag: timpoint

value: B

tag: disease

tag: batch

tag: treatment arb_active

value: Yes

tag: treatment arb_type

value: Losartan

tag: treatment rituximab_ever

tag: treatment rituximab_active

tag: treatment acei_active

tag: disease _severity_sledai

value: Not Hispanic or Latino/a

tag: race


title: P061_LUT

value: Ectocervix

value: Kenyan female sex workers

value: Luteal


title: NSCLC_BM25

description:
Single-nuclei RNA sequencing
STK_5dot2

tag: metastatic site

tag: patient id

tag: stk11 mutation

value: STK11 c.836delG, p.G279fs

tag: kras mutation status

tag: sequencing technique

tag: tcr-seq