title: Samples 25 to 32 from cmo feature table associated to CR02_H_GEX_L003

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
Library name: CR02_H_GEX_L003
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308

data_processing:
Raw 10x reads were demultiplexed into fastq files for individual libraries using Cellranger (version 7.0.0), which was also used to demultiplex samples based on CMOs, align unique reads to map the reads to the reference genome, assign reads to individual cells based on 10X Genomics barcodes, remove duplicate reads and filter for valid cells.
The conversion from fastq to sparse count matrices was performed using Cellranger multi (version 7.0.0)
Assembly: Human (GRCh38) and mouse (GRCm39) reference - 2024-A
Supplementary files format and content: sparse matrices 10xGenomic format

source_name: homo sapiens lung cancer cell line in humanise  mice

growth_protocol: IRAK1-silenced, LAPhigh and wild-type (WT) NCI-H2228 cells were injected in Hu-CD34+ mice, which are characterized by a reconstituted human immune system.

extract_protocol:
For each sample, live cells were transferred to 2 mL DNA LoBind tube  in mL PBS/0.04% w/v BSA and centrifuged at room temperature at 300×g for 5 min. The pellets were resuspended in 100 μL of a distinct Cell Multiplexing Oligo (CMO; 3' CellPlex Kit Set A, PN-1000261, 10X Genomics; Pleasanton, CA). After 5 min of incubation at room temperature, cells washed 3 times with 2 mL ice-cold PBS/1% w/v BSA by centrifuging at 300×g for 5 min at 4 °C, then incubated with 10% v/v 7-aminoactinomycin D (7-AAD) in 200 µL PBS/2% w/v BSA for 10 min. 5×105 7-AAD+(live) single cells per sample were sorted with Sony SH800S Cell Sorter (Sony Biotechnology, San Jose, CA) in sterile tubes kept at 4°C, containing 100 µL RPMI + 0.2 U/mL RNAse inhibitor (ThermoFisher Scientific, Waltham, MA). Samples were subsequently pooled in a 2 mL DNA LoBind tube, pelleted at 300×g for 5 min at 4°C, and diluted to a final concentration of 1.5×106 cells/mL. 49,500 cells were loaded in a single channel of a Chromium Next GEM Chip G to prepare scRNA-Seq libraries using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and the Chromium X controller (all from 10X Genomics, Pleasanton, CA), following the manufacturer’s instructions to prepare gene expression (GEX) and CMO libraries (protocol CG000388 Rev B).
GEMs were broken and cDNAs were purified, pre-amplified by 11 cycles of PCR, and quality controlled using an Agilent D5000 ScreenTape and an Agilent 2150 Tapestation (Agilent, Santa Clara, CA). 25% of each cDNA was fragmented, end-repaired, A-tailed, ligated to Illumina adapters, and amplified by 12 cycles of PCR using an individual primer pair from the Dual Index Kit TT, Set A (10X Genomics) to generate GEX libraries. CMO libraries were generated using the Dual Index Kit NN, Set A (10X Genomics), quality controlled using an Agilent D1000 ScreenTape and an Agilent 2150 Tapestation, quantified using the Qubit dsDNA HS Assay (Invitrogen), and pooled at 6:1 molar ratio for GEX:CMO. The library pool was sequenced using an Illumina NovaSeq 6000 (Illumina, San Diego, CA) flow cell, performing 28 cycles for read 1, 90 cycles for read 20, and 10 cycles for each index.

treatment_protocol: Mice harboring IRAK1-silenced, LAPhigh and wild-type (WT) NCI-H2228 tumors were treated with cisplatin and etomoxir.

value: adenocarcinoma

value: TP53 (Q331*) and EML4-ALK gene fusion

value: untreated, cisplatin and etomoxir as described in cmo_feature_table


title: Wild type control rep 1

status: Public on Apr 13 2026

type: SRA

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

country: Canada

institute: University Of British Columbia

description: Library name: WT-1_CK

library_source: genomic

data_processing:
Adapter sequences were removed from paired end FASTQ files using cutadapt (version 4.9), before aligning to the sacCer3 genome using BWA (version 0.7.17-r1188).
Samtools view (version 1.21) was used to retain uniquely mapping and properly paired reads with a Mapping Quality (MAPQ) score of 10 or higher.  Note the due to sequence similarity between DDI2 and DDI3, approximately 55% of reads mapping to these loci were discarded.
BAM files were converted to BED files using awk (version 20200816), and coverage tracks, representing reads per genome coverage (RPGC), were calculated using the Java Genomics Toolkit (https://github.com/timpalpant/java-genomics-toolkit) scripts, ngs.BaseAlignCounts and wigmath.Scale.
Assembly: sacCer3.fa
Supplementary files format and content: wig files normalized to genomic mean

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: BY4741 wild-type and its isogenic fzf1∆::KanMX4 mutant were grown to log phase and treated with 20 mM cyanamide for 2 hours.

extract_protocol:
Cells were resuspended in spheroplast buffer, and 10% cross-linked Schizosaccharomyces pombe cells were added to each sample as a spike-in. Cells were treated with 2 mg of zymolyase for 15 mins at 25°C with rotation, then digested with 60 units of micrococcal nuclease (MNase) and 30 units of ExoIII for 11 minutes at 37°C. Residual proteins and RNAs were removed, and DNA was purified with a QIAGEN MinElute PCR Purification Kit.
Libraries were prepared with NEB DNA Ultra II kit, and sequenced on an Illumina NextSeq.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 15 minutes and quenched by glycine addition to a final concentration of 300 mM for 5 minutes. Pellets were washed three times with cold 10 mM Tris-Cl pH 7.5, 100 mM NaCl and then flash frozen.

tag: cell line

tag: genotype

value: MATa his3D1 leu2D0 met15D0 ura3D0


title: Samples 25 to 32 from cmo feature table associated to CR02_H_GEX_L004

description:
Library name: CR02_H_GEX_L004
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

value: homo sapiens lung cancer cell line in humanise  mice

tag: cell type

tag: treatment

tag: batch


title: 102325_abe_2cell_7

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

country: USA

institute: UPenn Perelman SOM and CHOP

description: Library name: 102325_abe_2cell_7

library_source: transcriptomic

data_processing:
RNA-sequencing Analysis. To exclude low-complexity libraries, single embryos were required to exhibit detectable expression in a minimum number of genes. Thresholds were selected separately for each developmental stage and dataset based on inspection of the distribution of detected genes per sample, using the inflection point preceding the major drop-off in library complexity. Stage-specific cutoffs ranged from 6000-8000 detected genes. Samples failing these criteria were excluded from downstream analyses. Raw gene-level counts were analyzed in R (v4.5.1) using DESeq2 (v1.48.2). Genes were retained if they achieved at least 2.5 counts per million (CPM) in at least 80% of samples within at least one treatment group. Genes failing these criteria were removed from downstream analysis. Differential expression was modeled using a negative binomial generalized linear model with batch (embryo collection date) as a variable and Wald tests were performed to assess differential expression between each treatment level and designated control group. Normalized counts and full differential expression statistics were exported for downstream analysis. Given the limited statistical power of single-embryo sequencing due to the nature of the experimental design, nominal p-values were used for candidate identification, while enrichment and pathway-level analyses incorporated multiple-testing correction.  Computational Analysis for REMORA-AGO. Raw FASTQ files were processed using an adaptation of the MARINE pipeline developed by the Yeo Lab. Adapter trimming and low-quality base removal were performed using Cutadapt, followed by per-sample quality assessment with FastQC. Trimmed reads were aligned to the Mus musculus reference genome (mm10) using STAR, retaining uniquely mapped reads for downstream analysis. Gene-level read quantification was performed using featureCounts. To detect RNA editing events, MARINE applied its internal A-to-I (A→G) editing identification module downstream of STAR alignment and filtered using the dbSNP database mm10 to remove any SNPs.  RNA editing quantification and normalization. Editing counts were aggregated by summing site-levels counts within each gene and genomic region (CDS, 3’UTR, or intron) for each sample. Region definitions and gene/region lengths were derived from the GENCODE mouse GTF (gencode.vM10). Transcript-level intervals were collapsed to gene-level unions by gene symbol. Intronic intervals were defined per gene as the gene body minus the union of annotated exons. For each sample, the number of RNA-seq alignments overlapping CDS, inferred 3’UTRs, or introns were quantified from genome-aligned BAM files using featureCounts in SAF mode, producing region-specific mapped-read denominators. Editing activity was normalized to region length and region-specific library depth by computing editing events per kilobase per million mapped reads (EPKM); EPKM=edit_counts×10^9/(〖mapped_reads〗_region×region_bp). The resulting gene-by-sample EPKM matrices for CDS, 3’UTR, and introns were used for downstream comparisons across experimental conditions.  Statistical identification of miRNA-directed RNA editing targets. To account for small differences in global editing activity across conditions given the nature of embryo microinjections, EPKM values were further normalized within each replicate by scaling to a total of one million, generating edits per million (EPM) values that represent the fraction of total editing attributable to each transcript. Per-gene RNA editing levels were quantified for each single embryo as editing events per million mapped reads (EPM). To stabilize variance and accommodate zero-inflated distributions, EPM values were transformed at the embryo level as log₂(EPM + 1). For each gene, the mean log₂(EPM + 1) was calculated separately across rABE_Ago embryos and rABE_Ago + miR-200c-3p embryos. The change in editing was defined as the difference in these means. Editing abundance was defined as the average of the two group means. These values were visualized in an MA-style plot to separate editing abundance from miR-200c-3p–induced editing shifts. Statistical significance was assessed per gene using an unpaired one-sided Wilcoxon rank-sum test comparing log₂(EPM+1) values between conditions. Genes were required to have data from at least three embryos per group to be tested. Given the limited power and inherent variability of single-embryo RNA-sequencing, nominal p-values were interpreted alongside effect size and reproducibility across embryos.
Assembly: MM10
Supplementary files format and content: xlsx spreadsheet with one tab per /comparison

organism: Mus musculus

source_name: 2-cell parthenote

growth_protocol: Male (8-12 weeks old) and female (5-7 weeks old) FVB/NJ mice were derived from breeders obtained from Jackson Laboratory (Strain #001800) and maintained in-house.  Mouse parthenogenesis and embryogenesis were performed as previously described9. Briefly, oocytes were isolated from superovulated females and activated to generate parthenotes using KSOM with 10 mM SrCl2, 4 mM EGTA, and 0.05 μg/mL cytochalasin B for 1 hour. In Vitro Fertilization was performed in HTF with 1 mM glutathione with capacitated sperm for 3 hours. Embryos were cultured in KSOM under standard conditions 37°C, 5% CO2, and 5% O2 until microinjection and to the indicated developmental stages. Detailed step-by-step procedures are available in Lee et al., STAR Protocols

extract_protocol:
For sperm RNA and embryo isolations for single embryo RNA-seq see Trigg and Conine et al. 2024
Small RNA sequencing from sperm was performed largely as previously described10. Briefly, total sperm RNA was isolated and size-selected for small RNAs. In contrast to the original protocol (18-40 nucleotides), libraries in this study were size-selected for 18-24 nucleotide fragments to enrich specifically for mature miRNAs. Libraries were prepared using a modified Illumina Tru-Seq small RNA library prep protocol and sequenced on an Illumina NextSeq 1000/2000 platform. Libraries were mapped and normalized to reads per million as described previously (Trigg and Conine 2024).  Single-embryo RNA-sequencing. Following microinjection, individual embryos were collected 28 hours (late 2-cell), 46 hours (4-cell), or 70 hours (compacted morula) post activation or fertilization in 5 μL of TCL buffer (Qiagen, Cat. No. 1070498) with 1% 2-mercaptoethanol. Samples were immediately placed in -80°C until all replicates were collected. Libraries were generated using the SMART-Seq protocol11. Briefly, lysed embryos were isolated using RNAClean-XP beads and polyadenylated RNA was reverse transcribed using Superscript II. cDNA was amplified and indexed using the Nextera XT kit and sequenced on an Illumina NextSeq 1000/2000 platform (paired-end 50 bp, ~5 million reads per sample). Reads were mapped against the Mus musculus (mm10) genome using RSEM.

treatment_protocol: Embryo Microinjection. Cytoplasmic microinjections were performed on parthenotes or embryos as described previously9, delivering ~53 fL of injection solution per embryo. For each experimental replicate, embryos were collected from ~5 females derived from one or two litters, pooled, and randomly assigned to all injection conditions to minimize litter-specific effects. Within each experimental day, all treatments groups were represented in parallel. Embryos were distributed to ensure approximately matched numbers per condition (typically ~8 embryos per group and embryonic stage per replicate), preventing confounding by collection date or maternal origin. At least 24 embryos per condition were collected across three independent biological replicates. In one experiment with high embryo yield and injection efficiency, sufficient embryos were obtained across two replicates to meet this threshold.

value: 2-cell parthenote


title: 102325_abe_2cell_9

description: Library name: 102325_abe_2cell_9


title: 102325_abe_2cell_3

description: Library name: 102325_abe_2cell_3


title: Wild type control rep2

description: Library name: WT-2_CK


title: Samples 25 to 32 from cmo feature table associated to CR02_H_GEX_L002

description:
Library name: CR02_H_GEX_L002
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: 102325_abe_2cell_2

description: Library name: 102325_abe_2cell_2


title: 102325_ago_mir465_2cell_26

description: Library name: 102325_ago_mir465_2cell_26


title: 102325_abe_2cell_17

description: Library name: 102325_abe_2cell_17


title: Samples 25 to 32 from cmo feature table associated to CR02_G_GEX_L004

description:
Library name: CR02_G_GEX_L004
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: 102325_ago_mir200_2cell_11

description: Library name: 102325_ago_mir200_2cell_11


title: 102325_ago_mir465_2cell_27

description: Library name: 102325_ago_mir465_2cell_27


title: Samples 25 to 32 from cmo feature table associated to CR02_H_GEX_L001

description:
Library name: CR02_H_GEX_L001
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: Samples 25 to 32 from cmo feature table associated to CR02_F_GEX_L002

description:
Library name: CR02_F_GEX_L002
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: Samples 25 to 32 from cmo feature table associated to CR02_F_GEX_L003

description:
Library name: CR02_F_GEX_L003
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: 102325_abe_2cell_1

description: Library name: 102325_abe_2cell_1


title: Samples 17 to 24 from cmo feature table associated to CR02_E_GEX_L003

description:
Library name: CR02_E_GEX_L003
experiment:cmo 17_H2228_WT_NZ_25072022:303; 18_H2228_WT_NZ_Pt_25072022:304; 19_H2228_shTFEB_CTRL_25072022:307; 20_H2228_shTFEB_Pt_25072022:308; 21_H2228_shTFEB_NZ_25072022:309; 22_H2228_shTEB_NZ_Pt_25072022:310; 23_H2228_shIRAK1_CTRL_25072022:311; 24_H2228_shIRAK1_Pt_25072022:312


title: Samples 25 to 32 from cmo feature table associated to CR02_G_GEX_L002

description:
Library name: CR02_G_GEX_L002
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: Samples 25 to 32 from cmo feature table associated to CR02_F_GEX_L004

description:
Library name: CR02_F_GEX_L004
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: parth465_morula_low_miR465_5

description: Library name: parth465_morula_low_miR465_5

source_name: Morula parthenote

value: Morula parthenote


title: 102325_abe_2cell_11

description: Library name: 102325_abe_2cell_11


title: 102325_abe_2cell_13

description: Library name: 102325_abe_2cell_13


title: Samples 25 to 32 from cmo feature table associated to CR02_G_GEX_L003

description:
Library name: CR02_G_GEX_L003
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: 102325_abe_2cell_10

description: Library name: 102325_abe_2cell_10


title: Samples 25 to 32 from cmo feature table associated to CR02_F_GEX_L001

description:
Library name: CR02_F_GEX_L001
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: Samples 17 to 24 from cmo feature table associated to CR02_E_GEX_L002

description:
Library name: CR02_E_GEX_L002
experiment:cmo 17_H2228_WT_NZ_25072022:303; 18_H2228_WT_NZ_Pt_25072022:304; 19_H2228_shTFEB_CTRL_25072022:307; 20_H2228_shTFEB_Pt_25072022:308; 21_H2228_shTFEB_NZ_25072022:309; 22_H2228_shTEB_NZ_Pt_25072022:310; 23_H2228_shIRAK1_CTRL_25072022:311; 24_H2228_shIRAK1_Pt_25072022:312


title: 102325_abe_2cell_16

description: Library name: 102325_abe_2cell_16


title: 102325_abe_2cell_14

description: Library name: 102325_abe_2cell_14


title: parth465_morula_low_miR465_6

description: Library name: parth465_morula_low_miR465_6


title: parth465_morula_low_miR465_9

description: Library name: parth465_morula_low_miR465_9


title: parth465_morula_low_miR465_8

description: Library name: parth465_morula_low_miR465_8


title: fzf1 control rep 1

description: Library name: fzf1-1_CK

value: MATa his3D1 leu2D0 met15D0 ura3D0 fzf1D::KanMX4


title: Samples 17 to 24 from cmo feature table associated to CR02_E_GEX_L004

description:
Library name: CR02_E_GEX_L004
experiment:cmo 17_H2228_WT_NZ_25072022:303; 18_H2228_WT_NZ_Pt_25072022:304; 19_H2228_shTFEB_CTRL_25072022:307; 20_H2228_shTFEB_Pt_25072022:308; 21_H2228_shTFEB_NZ_25072022:309; 22_H2228_shTEB_NZ_Pt_25072022:310; 23_H2228_shIRAK1_CTRL_25072022:311; 24_H2228_shIRAK1_Pt_25072022:312


title: Samples 25 to 32 from cmo feature table associated to CR02_G_GEX_L001

description:
Library name: CR02_G_GEX_L001
experiment:cmo 25_H2228_WT_NZ_26072022:301; 26_H2228_WT_NZ_Pt_26072022:302; 27_H2228_shTFEB_CTRL_26072022:303; 28_H2228_shTFEB_Pt_26072022:304; 29_H2228_shTFEB_NZ_26072022:305; 30_H2228_shTEB_NZ_Pt_26072022:306; 31_H2228_shIRAK1_CTRL_26072022:307; 32_H2228_shIRAK1_Pt_26072022:308


title: 102325_ago_mir200_2cell_20

description: Library name: 102325_ago_mir200_2cell_20


title: Samples 17 to 24 from cmo feature table associated to CR02_E_GEX_L001

description:
Library name: CR02_E_GEX_L001
experiment:cmo 17_H2228_WT_NZ_25072022:303; 18_H2228_WT_NZ_Pt_25072022:304; 19_H2228_shTFEB_CTRL_25072022:307; 20_H2228_shTFEB_Pt_25072022:308; 21_H2228_shTFEB_NZ_25072022:309; 22_H2228_shTEB_NZ_Pt_25072022:310; 23_H2228_shIRAK1_CTRL_25072022:311; 24_H2228_shIRAK1_Pt_25072022:312


title: parth465_morula_low_miR465_3

description: Library name: parth465_morula_low_miR465_3


title: Samples 9 to 16 from cmo feature table associated to CR02_D_GEX_L004

description:
Library name: CR02_D_GEX_L004
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312


title: parth465_morula_low_miR465_35

description: Library name: parth465_morula_low_miR465_35


title: parth465_morula_low_miR465_34

description: Library name: parth465_morula_low_miR465_34


title: Samples 9 to 16 from cmo feature table associated to CR02_D_GEX_L003

description:
Library name: CR02_D_GEX_L003
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312


title: parth465_morula_low_miR465_2

description: Library name: parth465_morula_low_miR465_2


title: Samples 9 to 16 from cmo feature table associated to CR02_C_GEX_L004

description:
Library name: CR02_C_GEX_L004
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312;


title: Samples 1 to 8 from cmo feature table associated to CR02_B_GEX_L003

description:
Library name: CR02_B_GEX_L003
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312;


title: parth465_morula_low_miR465_31

description: Library name: parth465_morula_low_miR465_31


title: parth465_morula_low_miR465_30

description: Library name: parth465_morula_low_miR465_30


title: Samples 9 to 16 from cmo feature table associated to CR02_C_GEX_L003

description:
Library name: CR02_C_GEX_L003
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312;


title: parth465_morula_low_miR465_29

description: Library name: parth465_morula_low_miR465_29


title: Samples 1 to 8 from cmo feature table associated to CR02_B_GEX_L002

description:
Library name: CR02_B_GEX_L002
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312;


title: parth465_morula_low_miR465_28

description: Library name: parth465_morula_low_miR465_28


title: Samples 9 to 16 from cmo feature table associated to CR02_D_GEX_L001

description:
Library name: CR02_D_GEX_L001
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312


title: Samples 1 to 8 from cmo feature table associated to CR02_B_GEX_L001

description:
Library name: CR02_B_GEX_L001
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312;


title: parth465_morula_low_miR465_27

description: Library name: parth465_morula_low_miR465_27


title: ivf200_morula_miR200_9

description: Library name: ivf200_morula_miR200_9

source_name: Morula embryo

value: Morula embryo


title: ivf200_morula_miR200_8

description: Library name: ivf200_morula_miR200_8


title: Samples 1 to 8 from cmo feature table associated to CR02_B_GEX_L004

description:
Library name: CR02_B_GEX_L004
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312;


title: Samples 9 to 16 from cmo feature table associated to CR02_C_GEX_L001

description:
Library name: CR02_C_GEX_L001
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312;


title: Samples 9 to 16 from cmo feature table associated to CR02_C_GEX_L002

description:
Library name: CR02_C_GEX_L002
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312;


title: parth465_morula_low_miR465_33

description: Library name: parth465_morula_low_miR465_33


title: parth465_morula_low_miR465_32

description: Library name: parth465_morula_low_miR465_32


title: Samples 1 to 8 from cmo feature table associated to CR02_A_GEX_L004

description:
Library name: CR02_A_GEX_L004
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312


title: 102325_abe_2cell_12

description: Library name: 102325_abe_2cell_12


title: ivf200_morula_miR200_7

description: Library name: ivf200_morula_miR200_7


title: Samples 1 to 8 from cmo feature table associated to CR02_A_GEX_L003

description:
Library name: CR02_A_GEX_L003
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312


title: ivf200_morula_miR200_6

description: Library name: ivf200_morula_miR200_6


title: ivf200_morula_miR200_5

description: Library name: ivf200_morula_miR200_5


title: Samples 1 to 8 from cmo feature table associated to CR02_A_GEX_L002

description:
Library name: CR02_A_GEX_L002
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312


title: Samples 1 to 8 from cmo feature table associated to CR02_A_GEX_L001

description:
Library name: CR02_A_GEX_L001
experiment:cmo 1_H2228_WT_CTRL_19072022:305; 2_H2228_WT_Pt_19072022:306; 3_H2228_WT_Eto_19072022:307; 4_H2228_WT_Eto_19072022:308; 5_H2228_LAP_CTRL_19072022:309; 6_H2228_LAP_Pt_19072022:310; 7_H2228_LAP_Eto_19072022:311; 8_H2228_LAP_Eto_Pt_19072022:312


title: ivf200_morula_miR200_3

description: Library name: ivf200_morula_miR200_3


title: ivf200_morula_miR200_4

description: Library name: ivf200_morula_miR200_4


title: ivf200_morula_miR200_23

description: Library name: ivf200_morula_miR200_23


title: 102325_ago_mir200_2cell_17

description: Library name: 102325_ago_mir200_2cell_17


title: ivf200_morula_miR200_2

description: Library name: ivf200_morula_miR200_2


title: ivf200_morula_miR200_21

description: Library name: ivf200_morula_miR200_21


title: ivf200_morula_miR200_22

description: Library name: ivf200_morula_miR200_22


title: ivf200_morula_miR200_1

description: Library name: ivf200_morula_miR200_1


title: ivf200_morula_miR200_18

description: Library name: ivf200_morula_miR200_18


title: ivf200_morula_miR200_19

description: Library name: ivf200_morula_miR200_19


title: Neonatal saliva exposed male sample 1

type: RNA

city: Boston

first: Tomoko

last: Kaneko-Tarui

state: Massachusetts

address: 800 Washington St., Box #394

department: Women, Mother + Baby Research Institute

institute: Tufts Medical Center

description: Saliva collected within 48 hours after birth

hyb_protocol: mRNA expression profiling was performed using the NanoString nCounter Analysis System with a custom CodeSet targeting 72 genes of interest, including housekeeping genes. Samples were prepared using the NanoString Low RNA Input Kit according to the manufacturer's instructions. Eight pre-amplification cycles were used. Pre-amplified RNA was hybridized with the Reporter CodeSet and Capture ProbeSet at 65C for 22 hours.

scan_protocol: Hybridized samples were processed and scanned on the NanoString nCounter platform according to the manufacturer's instructions, generating RCC files for each assay instance.

data_processing: Raw RCC files were analyzed in ROSALIND using the NanoString nCounter Advanced Analysis workflow for quality control, normalization, and downstream analyses. A total of 36 assay instances were generated. Most assay instances corresponded to independent neonatal saliva samples from different patients, while two biological samples were assayed more than once using newly extracted RNA. Eighteen unique neonatal saliva samples passed QC and were retained for downstream analysis. Assay instances that failed QC are provided as raw supplementary files only and are not represented in the processed expression matrix. Normalization was performed using the housekeeping genes GAPDH, HPRT1, and YWHAZ. Normalized values were log2-transformed. No missing-value imputation was performed. Normalized values were log2-transformed. No missing-value imputation was performed.

molecule: total RNA

source_name: neonatal saliva

extract_protocol: Saliva samples were collected from neonates within 48 hours of birth using a 1-mL insulin syringe attached to low-pressure wall suction for 15-30 seconds. To minimize breast milk and associated maternal RNA contamination, saliva was collected before feeding or at least 30 minutes after feeding. Saliva was immediately placed in 250 uL RNAprotect Saliva Reagent (Qiagen). Total RNA was isolated using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment using RNase-free DNase I. Extracted RNA was stored at -80C until analysis.

value: saliva

tag: Sex

value: male

tag: prenatal opioid exposure

value: exposed

tag: final analysis inclusion

value: yes

tag: qc status

value: passed


title: Neonatal saliva exposed male sample 3


title: Neonatal saliva exposed female sample 3

value: female


title: Neonatal saliva exposed male sample 4


title: Neonatal saliva exposed female sample 2


title: ivf200_morula_miR200_20

description: Library name: ivf200_morula_miR200_20


title: ivf200_morula_miR200_17

description: Library name: ivf200_morula_miR200_17


title: ivf200_morula_miR200_16

description: Library name: ivf200_morula_miR200_16


title: Neonatal saliva exposed male sample 5


title: Neonatal saliva exposed male sample 2


title: Neonatal saliva exposed male sample 6


title: ivf200_morula_miR200_15

description: Library name: ivf200_morula_miR200_15


title: ivf200_morula_miR200_14

description: Library name: ivf200_morula_miR200_14


title: Neonatal saliva non-exposed male sample 1

value: non-exposed


title: Neonatal saliva non-exposed male sample 2


title: parth465_morula_low_miR465_4

description: Library name: parth465_morula_low_miR465_4


title: Neonatal saliva exposed female sample 1


title: ivf200_morula_miR200_13

description: Library name: ivf200_morula_miR200_13


title: ivf200_morula_miR200_12

description: Library name: ivf200_morula_miR200_12


title: Neonatal saliva non-exposed female sample 4


title: Neonatal saliva non-exposed female sample 5


title: ivf200_morula_miR200_11

description: Library name: ivf200_morula_miR200_11


title: ivf200_morula_control_9

description: Library name: ivf200_morula_control_9


title: Neonatal saliva non-exposed female sample 6


title: Neonatal saliva non-exposed female sample 7


title: Neonatal saliva non-exposed female sample 3


title: Neonatal saliva non-exposed female sample 1


title: Neonatal saliva non-exposed female sample 2


title: ivf200_morula_miR200_10

description: Library name: ivf200_morula_miR200_10


title: ivf200_morula_control_8

description: Library name: ivf200_morula_control_8


title: CTC_mixed

city: Basel

first: Yongzhan

last: Zhang

address: Otto-Stern-Weg 7 HPL H17.2

country: Switzerland

institute: ETH Zurich

description: Library name: Sample 3

data_processing:
Guide RNA sequences were extracted from raw sequencing reads using Cutadapt (v4.9), allowing an adapter mismatch error rate of 0.1 to ensure accurate trimming of flanking sequences. Sequences with a length of 20 nt, corresponding to the gRNA spacer sequences length, were kept and final reads were aligned to the custmized sgRNA library using bowtie2 (v2.5.1), allowing for one mismatch. Normalized sgRNA abundances were calculated using MAGeCK (v0.5.9.4). A detection threshold of ≥10 reads per sgRNA was applied. Differential sgRNA representation between conditions was assessed using MAGeCK’s robust ranking aggregation (RRA) algorithm.
Assembly: customized sgRNA library (provided in processed data file)
Supplementary files format and content: comma seperated values for each sample
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA from sorted cells was extracted using the Puregene Cell Kit and quantified with a NanoDrop ND-1000 spectrophotometer. sgRNA inserts were amplified via targeted and nested PCR using primers with Illumina adaptors. Libraries were sequenced on the Illumina MiSeq platform with 50 bp single-end reads.
Illumina MiSeq

value: Breast cancer cells


title: ivf200_morula_control_6

description: Library name: ivf200_morula_control_6


title: Tumor_mixed

description: Library name: Sample 4


title: Injection_control_2

description: Library name: Sample 2


title: ivf200_morula_control_5

description: Library name: ivf200_morula_control_5


title: ivf200_morula_control_4

description: Library name: ivf200_morula_control_4


title: mRNA_tif3-del_b

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: 49 Convent Dr Building 49 RM 2C08

department: NICHD

institute: NIH

description:
Library name: mRNA_tif3-del_b
RNA-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software, 3' adapter trimming with FastX-toolkit.
rRNA alignment with bowtie2 and unmapped reads were applied for downstream analysis.
rRNA removed reads were mapped to yeast genome using TopHat.
Wiggle files were produced from the alignment files using "wiggle-track" function in RiboSeq (https://github.com/ingolia-lab/RiboSeq), generating two wiggle files, each for genes on the Watson or Crick strand. Wiggle files were normalized by multiplying the size factor "q" (Normalized by total reads) in the wiggle-track function (-q).
Differential expression analysis of changes in mRNA, foot-print and translation efficincy(TE) was performed using DESeq2 (Love et al., 2014).
Assembly: R64-1-1 S288C Sac cer3 Genome Assembly
Supplementary files format and content: Wiggle files

growth_protocol: Yeast cells were grown to an OD600 of ~ 0.7 in synthetic complete medium at 30°C.

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen in liquid nitrogen. Whole cell extracts were prepared by breaking cells in freezer mill in cell lysis buffer.
Total mRNA isolated from whole cell extract using miRNeasy minikt (Qiagen). Total RNA fragmentation, Size selection, linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to to remove ribosome contamination after linker ligation step.

treatment_protocol: No additional treatment for the cell.

value: Yeast strain

value: MATa his3_del_1 leu2_deL_0 lys2_deL-0 met15_del_0 ura3_del_0 tif3_del::hisG


title: mRNA_tif3-del_a

description:
Library name: mRNA_tif3-del_a
RNA-Seq


title: mRNA_WT_for_tif3_a

description:
Library name: mRNA_WT_for_tif3_a
RNA-Seq

value: MATa his3_del_1 leu2_del_0 lys2_del_0 met15_del_0 ura3_del_0 TIF3


title: Injection_control_1

description: Library name: Sample 1


title: ivf200_morula_control_3

description: Library name: ivf200_morula_control_3


title: ivf200_morula_control_2

description: Library name: ivf200_morula_control_2


title: peritoneal macrophage, ID8 chemotherapy model, high fat  diet, RNAseq [HFD3]

city: Guangzhou

first: Chaoyun

last: Pan

address: 74 Zhongshan Er Rd.

country: China

institute: Sun Yat-sen University

description: Library name: HFD3

data_processing:
Raw sequencing reads were quality‑assessed and adapter‑trimmed using Fastp (v0.19.7). Transcript abundance was quantified with Salmon (v1.10.2) against the reference transcriptome. The resulting counts were imported into R using the tximport package (v1.32.0) and differential gene expression analysis was conducted with DESeq2 (v1.44.0). GSEA software and clusterProfiler were used for downstream functional pathway annotation analysis.
Assembly: mm10
Supplementary files format and content: CSV file (Comma-Separated Values)

source_name: peritoneal macrophage

extract_protocol:
Peritoneal lavage was performed by injecting 5 mL of ice-cold phosphate-buffered saline (PBS) into the peritoneal cavity of euthanized mice. The lavage fluid was collected and centrifuged at 300 × g for 5 minutes at 4°C. The resulting cell pellet was resuspended in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were then incubated at 37°C in a 5% CO₂ atmosphere for 2 hours to allow for adherence. Non-adherent cells were removed by gentle washing with warm PBS. The adherent cells (peritoneal macrophages) were harvested using a cell scraper for subsequent analysis. For flow cytometry verification, cells were stained with antibodies against CD45 and F4/80 to identify the macrophage population. Data acquisition was performed on a flow cytometer, and analysis was conducted using appropriate gating strategies to exclude debris and doublets.
Total RNA was isolated from peritoneal macrophages harvested from the ID8 syngeneic ovarian cancer model at specified time points using the RNeasy Mini Kit (Qiagen). To ensure high‑quality RNA, cell suspensions were treated with a debris removal solution (Miltenyi Biotec, Cat# 130‑109‑398) prior to extraction for efficient clearance of cellular debris. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: peritoneal macrophage

value: macrophage

value: high fat diet


title: mRNA_WT_for_tif3_b

description:
Library name: mRNA_WT_for_tif3_b
RNA-Seq

value: MATa his3_deL1 leu2_del_0 lys2_del_0 met15_del_0 ura3_del_0 TIF3


title: ivf200_morula_control_23

description: Library name: ivf200_morula_control_23


title: ivf200_morula_control_20

description: Library name: ivf200_morula_control_20


title: ivf200_morula_control_24

description: Library name: ivf200_morula_control_24


title: peritoneal macrophage, ID8 chemotherapy model, control diet, RNAseq [CTR3]

description: Library name: CTR3

value: control diet


title: ivf200_morula_control_21

description: Library name: ivf200_morula_control_21

value: Morula embryo


title: ivf200_morula_control_22

description: Library name: ivf200_morula_control_22


title: peritoneal macrophage, ID8 chemotherapy model, high fat  diet, RNAseq [HFD1]

description: Library name: HFD1


title: peritoneal macrophage, ID8 chemotherapy model, control diet, RNAseq [CTR1]

description: Library name: CTR1


title: peritoneal macrophage, ID8 chemotherapy model, control diet, RNAseq [CTR2]

description: Library name: CTR2


title: ivf200_morula_control_19

description: Library name: ivf200_morula_control_19


title: peritoneal macrophage, ID8 chemotherapy model, high fat  diet, RNAseq [HFD2]

description: Library name: HFD2


title: Bronchoscopy Brush6, rep1

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health

description:
Library name: VA-BB6-1
Healthy, non-smoking donor, fresh cells obtained from bronchoscopic brushings of large airways

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the bbduk tool from the BBMap Suite (v. 38.73) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20 ftr=36’
Trimmed reads were mapped to the human genome (hg38; downloaded from the UCSC genome browser on September 16, 2019, with corresponding hisat2 index files) using hisat2 (v. 2.1.0)
Resulting SAM files were converted to BAM format using samtools view (v. 1.9) with arguments ‘-S -b’, duplicates were removed using picard tools MarkDuplicates (v. 2.26.6) and then resulting BAM files were sorted and indexed using samtools sort and index, respectively.
Assembly: hg38
Supplementary files format and content: BAM files are sorted binary read files aligned to the hg38 genome with duplicates removed

source_name: Airway epithelial brush

growth_protocol: Cell lines were cultured in submerged conditions. Primary cells were cultured in submerged or air-liquid interface culture settings as indicated. Culture procedures are described in the manuscript. Primary cells obtained from brushings are designated under "tissue." These cells were processed directly after brushings were performed on healthy non-smoking donors who consented to de-identified tissue collection through existing protocols.

extract_protocol:
Cells were washed once with 1X PBS and dissociated from cytology brushes prior to counting. Approximately 50K cells were pelleted and processed in duplicate or quadruplicate as described in the Omni-ATAC-seq protocol published by Corces et al (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NextSeq instrument using 150 bp paired-end reads.

treatment_protocol: Cells in culture were treated with either WSP (1 mg/ml), UPM (300 ug/ml), or TCDD (10 nM) as described in the manuscript. Briefly, for submerged conditions, the treatment was added to the culture media. For air-liquid interface cultures, the treatment was added to both the apical surface and basal media.

value: Airway epithelial brush


title: ivf200_morula_control_17

description: Library name: ivf200_morula_control_17


title: Bronchoscopy Brush6, rep2

description:
Library name: VA-BB6-2
Healthy, non-smoking donor, fresh cells obtained from bronchoscopic brushings of large airways


title: ivf200_morula_control_15

description: Library name: ivf200_morula_control_15


title: ivf200_morula_control_16

description: Library name: ivf200_morula_control_16


title: Bronchoscopy Brush5, rep4

description:
Library name: VA-BB5-R2
Healthy, non-smoking donor, fresh cells obtained from bronchoscopic brushings of large airways


title: ivf200_morula_control_14

description: Library name: ivf200_morula_control_14


title: Bronchoscopy Brush5, rep3

description:
Library name: VA-BB5-R1
Healthy, non-smoking donor, fresh cells obtained from bronchoscopic brushings of large airways


title: ivf200_morula_control_13

description: Library name: ivf200_morula_control_13


title: ivf200_morula_control_12

description: Library name: ivf200_morula_control_12


title: Bronchoscopy Brush5, rep1

description:
Library name: VA-BB5-L1
Healthy, non-smoking donor, fresh cells obtained from bronchoscopic brushings of large airways


title: Sm36, ALId7, TCDD30, rep2

description:
Library name: Sm36ALId7-TCDD30-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated

source_name: Small Airway epithelial - Air-liquid Interface

value: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) 30 min


title: ivf200_morula_control_11

description: Library name: ivf200_morula_control_11


title: ivf200_morula_control_10

description: Library name: ivf200_morula_control_10


title: parth465_morula_low_miR465_25

description: Library name: parth465_morula_low_miR465_25

value: Morula parthenote


title: Bronchoscopy Brush5, rep2

description:
Library name: VA-BB5-L2
Healthy, non-smoking donor, fresh cells obtained from bronchoscopic brushings of large airways


title: parth465_morula_low_miR465_23

description: Library name: parth465_morula_low_miR465_23


title: Sm36, ALId7, veh, rep1

description:
Library name: Sm36ALId7-veh-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated

value: Small Airway epithelial - Air-liquid Interface

value: Vehicle control (DMSO) 120 min


title: parth465_morula_low_miR465_24

description: Library name: parth465_morula_low_miR465_24


title: parth465_morula_low_miR465_22

description: Library name: parth465_morula_low_miR465_22


title: Sm36, ALId7, TCDD30, rep1

description:
Library name: Sm36ALId7-TCDD30-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, ALId21, veh, rep1

description:
Library name: Sm36ALId21-veh-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, ALId7, TCDD120, rep1

description:
Library name: Sm36ALId7-TCDD120-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated

value: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) 120 min


title: parth465_morula_low_miR465_21

description: Library name: parth465_morula_low_miR465_21


title: Sm36, ALId7, TCDD120, rep2

description:
Library name: Sm36ALId7-TCDD120-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, ALId21, veh, rep2

description:
Library name: Sm36ALId21-veh-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, ALId21, TCDD30, rep2

description:
Library name: Sm36ALId21-TCDD30-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_low_miR465_19

description: Library name: parth465_morula_low_miR465_19


title: Sm36, ALId7, veh, rep2

description:
Library name: Sm36ALId7-veh-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: ivf200_morula_control_7

description: Library name: ivf200_morula_control_7


title: parth465_morula_low_miR465_20

description: Library name: parth465_morula_low_miR465_20


title: Sm36, ALId21, TCDD120, rep1

description:
Library name: Sm36ALId21-TCDD120-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, ALId21, TCDD120, rep2

description:
Library name: Sm36ALId21-TCDD120-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_low_miR465_18

description: Library name: parth465_morula_low_miR465_18


title: Sm36, ALId21, TCDD30, rep1

description:
Library name: Sm36ALId21-TCDD30-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_low_miR465_14

description: Library name: parth465_morula_low_miR465_14


title: parth465_morula_low_miR465_16

description: Library name: parth465_morula_low_miR465_16


title: parth465_morula_low_miR465_12

description: Library name: parth465_morula_low_miR465_12


title: Sm36, ALId0, veh, rep1

description:
Library name: Sm36ALId0-veh-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, ALId0, TCDD30, rep2

description:
Library name: Sm36ALId0-TCDD30-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_low_miR465_13

description: Library name: parth465_morula_low_miR465_13


title: Sm36, ALId0, TCDD30, rep1

description:
Library name: Sm36ALId0-TCDD30-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_low_miR465_11

description: Library name: parth465_morula_low_miR465_11


title: Sm36, submerged, WSP30, rep1

description:
Library name: Sm36-WSP30-1
Healthy, non-smoking donor

source_name: Small Airway epithelial

value: Small Airway epithelial

value: Wood Smoke Particles (WSP) 30 min


title: Sm36, ALId0, TCDD120, rep1

description:
Library name: Sm36ALId0-TCDD120-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm36, submerged, WSP30, rep2

description:
Library name: Sm36-WSP30-2
Healthy, non-smoking donor


title: Samples 9 to 16 from cmo feature table associated to CR02_D_GEX_L002

description:
Library name: CR02_D_GEX_L002
experiment:cmo 9_H2228_WT_CTRL_20072022:301; 10_H2228_WT_Pt_20072022:302; 11_H2228_Wt_Eto_Pt_20072022:307; 12_H2228_Wt_Eto_Pt_20072022:308; 13_H2228_LAP_CTRL_20072022:309; 14_H2228_LAP_Pt_20072022:310; 15_H2228_LAP_Eto_20072022:311; 16_H2228_LAP_Eto_Pt_20072022:312

value: homo sapiens lung cancer cell line in humanise  mice

value: adenocarcinoma

value: TP53 (Q331*) and EML4-ALK gene fusion

value: untreated, cisplatin and etomoxir as described in cmo_feature_table


title: parth465_morula_high_miR465_9

description: Library name: parth465_morula_high_miR465_9


title: parth465_morula_high_miR465_5

description: Library name: parth465_morula_high_miR465_5


title: parth465_morula_high_miR465_8

description: Library name: parth465_morula_high_miR465_8


title: Sm36, submerged, WSP120, rep2

description:
Library name: Sm36-WSP120-2
Healthy, non-smoking donor

value: Wood Smoke Particles (WSP) 120 min


title: parth465_morula_high_miR465_4

description: Library name: parth465_morula_high_miR465_4


title: Sm36, ALId0, TCDD120, rep2

description:
Library name: Sm36ALId0-TCDD120-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_3

description: Library name: parth465_morula_high_miR465_3


title: parth465_morula_high_miR465_7

description: Library name: parth465_morula_high_miR465_7


title: Sm36, submerged, WSP120, rep1

description:
Library name: Sm36-WSP120-1
Healthy, non-smoking donor


title: parth465_morula_high_miR465_30

description: Library name: parth465_morula_high_miR465_30


title: Sm25, submerged, WSP30, rep2

description:
Library name: Sm25-WSP30-2
Healthy, non-smoking donor


title: parth465_morula_high_miR465_6

description: Library name: parth465_morula_high_miR465_6


title: parth465_morula_high_miR465_2

description: Library name: parth465_morula_high_miR465_2


title: Sm36, ALId0, veh, rep2

description:
Library name: Sm36ALId0-veh-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Sm25, submerged, WSP120, rep2

description:
Library name: Sm25-WSP120-2
Healthy, non-smoking donor


title: parth465_morula_high_miR465_29

description: Library name: parth465_morula_high_miR465_29


title: parth465_morula_high_miR465_28

description: Library name: parth465_morula_high_miR465_28


title: parth465_morula_high_miR465_27

description: Library name: parth465_morula_high_miR465_27


title: NEC32, ALId7, VEH, rep1

description:
Library name: NEC32-d7-V1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated

source_name: Nasal Airway epithelial - Air-liquid Interface

value: Vehicle control (1X Phosphate Buffered Saline, VEH) 30 min


title: parth465_morula_high_miR465_26

description: Library name: parth465_morula_high_miR465_26


title: Sm25, submerged, WSP30, rep1

description:
Library name: Sm25-WSP30-1
Healthy, non-smoking donor


title: parth465_morula_high_miR465_24

description: Library name: parth465_morula_high_miR465_24


title: Sm25, submerged, WSP120, rep1

description:
Library name: Sm25-WSP120-1
Healthy, non-smoking donor


title: NEC32, ALId27, VEH, rep2

description:
Library name: NEC32-d27-V2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated

value: Nasal Airway epithelial - Air-liquid Interface


title: parth465_morula_high_miR465_23

description: Library name: parth465_morula_high_miR465_23


title: ivf200_morula_control_1

description: Library name: ivf200_morula_control_1


title: NEC32, ALId7, VEH, rep2

description:
Library name: NEC32-d7-V2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_22

description: Library name: parth465_morula_high_miR465_22


title: parth465_morula_high_miR465_1

description: Library name: parth465_morula_high_miR465_1


title: parth465_morula_high_miR465_19

description: Library name: parth465_morula_high_miR465_19


title: NEC32, ALId7, UPM, rep2

description:
Library name: NEC32-d7-UPM-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated

value: Urban Particulate Matter (UPM) 30 min


title: NEC32, ALId0, VEH, rep1

description:
Library name: NEC32-d0-V1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_25

description: Library name: parth465_morula_high_miR465_25


title: parth465_morula_high_miR465_21

description: Library name: parth465_morula_high_miR465_21


title: NEC32, ALId0, UPM, rep2

description:
Library name: NEC32-d0-UPM-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_16

description: Library name: parth465_morula_high_miR465_16


title: parth465_morula_high_miR465_18

description: Library name: parth465_morula_high_miR465_18


title: NEC32, ALId27, VEH, rep1

description:
Library name: NEC32-d27-V1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_15

description: Library name: parth465_morula_high_miR465_15


title: NEC32, ALId27, UPM, rep2

description:
Library name: NEC32-d27-UPM2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC14, ALId7, VEH, rep2

description:
Library name: NEC14-d7-V2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC32, ALId7, UPM, rep1

description:
Library name: NEC32-d7-UPM-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC32, ALId0, UPM, rep1

description:
Library name: NEC32-d0-UPM-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_17

description: Library name: parth465_morula_high_miR465_17


title: NEC32, ALId0, VEH, rep2

description:
Library name: NEC32-d0-V2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC14, ALId7, UPM, rep2

description:
Library name: NEC14-d7-UPM-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_12

description: Library name: parth465_morula_high_miR465_12


title: parth465_morula_high_miR465_14

description: Library name: parth465_morula_high_miR465_14


title: NEC14, ALId7, VEH, rep1

description:
Library name: NEC14-d7-V1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC14, ALId21, VEH, rep2

description:
Library name: NEC14-d21-V3
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_11

description: Library name: parth465_morula_high_miR465_11


title: NEC14, ALId7, UPM, rep1

description:
Library name: NEC14-d7-UPM-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC14, ALId21, VEH, rep1

description:
Library name: NEC14-d21-V2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_high_miR465_10

description: Library name: parth465_morula_high_miR465_10


title: parth465_morula_control_9

description: Library name: parth465_morula_control_9


title: parth465_morula_control_8

description: Library name: parth465_morula_control_8


title: NEC14, ALId21, UPM, rep1

description:
Library name: NEC14-d21-UPM-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_control_7

description: Library name: parth465_morula_control_7


title: NEC14, ALId0, VEH, rep2

description:
Library name: NEC14-d0-V2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC14, ALId21, UPM, rep2

description:
Library name: NEC14-d21-UPM-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_control_6

description: Library name: parth465_morula_control_6


title: NEC14, ALId0, UPM, rep2

description:
Library name: NEC14-d0-UPM-2
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: NEC14, ALId0, UPM, rep1

description:
Library name: NEC14-d0-UPM-1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: Nasal Brush, rep2

description:
Library name: NB2
Healthy, non-smoking donor, fresh cells obtained from nasal brushings

source_name: Nasal Airway brush

value: Nasal Airway brush


title: Nasal Brush, rep1

description:
Library name: NB1
Healthy, non-smoking donor, fresh cells obtained from nasal brushings


title: parth465_morula_control_24

description: Library name: parth465_morula_control_24


title: NEC14, ALId0, VEH, rep1

description:
Library name: NEC14-d0-V1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: B2B, TCDD30, rep2

description: Library name: B2B-TCDD30-2


title: parth465_morula_control_5

description: Library name: parth465_morula_control_5


title: parth465_morula_control_2

description: Library name: parth465_morula_control_2


title: B2B, TCDD30, rep1

description: Library name: B2B-TCDD30-1


title: B2B, TCDD120, rep1

description: Library name: B2B-TCDD120-1


title: B2B, TCDD120, rep2

description: Library name: B2B-TCDD120-2


title: parth465_morula_control_21

description: Library name: parth465_morula_control_21


title: parth465_morula_control_23

description: Library name: parth465_morula_control_23


title: NEC32, ALId27, UPM, rep1

description:
Library name: NEC32-d27-UPM1
Healthy, non-smoking donor, primary cells cultured at air-liquid interface for days (d) stated


title: parth465_morula_control_22

description: Library name: parth465_morula_control_22


title: parth465_morula_control_20

description: Library name: parth465_morula_control_20


title: parth465_morula_control_1

description: Library name: parth465_morula_control_1


title: hESC derived mesenchymal cells

city: Cambridge

first: Nicholas

middle: T

last: Hutchins

state: MA

address: 455 Main St.

institute: Massachusetts Institute of Technology

description:
Library name: mesenchyme_screen
10X Genomics

data_processing:
Sequencing reads were aligned using CellRanger v4.0.0
Assembly: GRCh28
Supplementary files format and content: Processed data are in .mtx, .tsv formats.

source_name: H1A derived mesenchymal tissue

growth_protocol: hESCs were grown in mTesR-Plus media and passaged every three days to ensure they were in an undifferentiated state.

extract_protocol:
Cells were sorted using DAPI staining and RNA was extracted according to the protocol of the 10X Chromium kit.
Libraries were constructed according to Manufacturer's protocol (Sigma LMO001) and the 10X Chromium kit.

value: H1A derived mesenchymal tissue

value: Wildtype


title: LM2_Mki67-/-_KO2_2

description: Library name: Sample 8

data_processing:
Sequencing reads were trimmed from the 3’ end until the final base had a quality score >30, utilizing Trimmomatic (v0.33). Quality assessment of RNA-seq data was performed using FastQC (v0.11.4). Trimmed reads were aligned to the appropriate reference genomes using STAR (v2.7.3a): the human genome (GRCh38) for LM2 samples and the mouse genome (GRCm39) for MVT1 samples. Gene-level expression counts were quantified with HTSeq (v2.0.5), using GENCODE gene annotations (release 44 for human, release M33 for mouse).
Aligned reads were counted using HTSeq.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
Illumina Truseq mRNA

value: Breast cancer cells


title: LM2_Mki67-/-_KO2_1

description: Library name: Sample 7


title: LM2_MKI67-/-_KO1_3

description: Library name: Sample 6


title: parth465_morula_control_17

description: Library name: parth465_morula_control_17

value: Morula parthenote


title: parth465_morula_control_14

description: Library name: parth465_morula_control_14


title: parth465_morula_control_3

description: Library name: parth465_morula_control_3


title: parth465_morula_control_13

description: Library name: parth465_morula_control_13


title: LM2_WT_3

description: Library name: Sample 3


title: parth465_morula_control_26

description: Library name: parth465_morula_control_26


title: parth465_morula_control_18

description: Library name: parth465_morula_control_18


title: parth465_morula_control_12

description: Library name: parth465_morula_control_12


title: LM2_WT_2

description: Library name: Sample 2


title: LM2_MKI67-/-_KO1_2

description: Library name: Sample 5


title: parth465_morula_control_11

description: Library name: parth465_morula_control_11


title: LM2_WT_1

description: Library name: Sample 1


title: parth465_4cell_low_miR465_8

description: Library name: parth465_4cell_low_miR465_8

source_name: 4-cell parthenote

value: 4-cell parthenote


title: parth465_4cell_low_miR465_9

description: Library name: parth465_4cell_low_miR465_9


title: parth465_morula_control_15

description: Library name: parth465_morula_control_15


title: parth465_4cell_low_miR465_5

description: Library name: parth465_4cell_low_miR465_5


title: parth465_morula_control_10

description: Library name: parth465_morula_control_10


title: LM2_MKI67-/-_KO1_1

description: Library name: Sample 4


title: PBMC TCR, BCG, TBT04301114-Mbovis-D7

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

description: Library name: 1114-Mbovis-PBMC-AIM-TCR

data_processing:
scRNA-seq Barcode assignment, Unique Molecular Identifier (UMI) tagging, and sequence alignment for the BAL samples were conducted using the Cell Ranger count pipeline (v6.0.1), employing the human reference genome GRCh38 (GENCODE version 32/Ensembl 98) provided by 10x Genomics 48. TCR clonotypes in the BAL samples were determined using the Cell Ranger V(D)J pipeline (v6.0.1), with the GRCh38 Human V(D)J Reference (v7.1.0) from 10x Genomics. For PBMC samples, the Cell Ranger multi pipeline (v6.0.1) was utilized, processing data from the 5’ gene expression, V(D)J, and cell surface protein libraries, using the same human reference genome and V(D)J reference as for the BAL samples. Bulk TCR-seq Alignment of FASTQ files from the bulk TCR-seq data and assembly of TCR sequences were performed using the Cogent NGS Immune Profiler (v1.6, Takara Bio) with the default settings.
Assembly: Human reference genome GRCh38 (GENCODE version 32/Ensembl 98) provided by 10x Genomics, and the  GRCh38 Human V(D)J Reference (v7.1.0) from 10x Genomics.
Supplementary files format and content: scRNA-seq h5 file: gene expression matrix csv file: TCR clone information for each cell Bulk TCR-seq csv file: TCR clone information

source_name: Blood

extract_protocol:
scRNA-seq of BAL samples BAL cells from all three saline controls and three selected volunteers receiving BCG from each group were processed for scRNA-seq. The three volunteers receiving BCG were selected to allow for batched processing with saline controls where possible, followed by consideration of cell availability for single-cell processing. BAL volume was recorded, and tubes from the same volunteer were pooled before being centrifuged (400×g, 10min, maximum brake) to separate the BAL cells from the supernatant BAL fluid (BALF). BAL cells were incubated in 5 ml of red blood cell (RBC) lysis solution (Qiagen #158103) for 5 minutes, followed by washing and resuspension for counting using a Countess II FL (Thermo Fisher #AMQAX1000). Cells were spun at 300×g for 10 minutes at 4°C and resuspended in the R10 medium (no streptomycin), aiming to recover 5000 cells per well. Resuspended cells were transferred on ice to the Oxford Genomics Centre (OGC) for further processing. Group 1 samples initially underwent attempts at Magnetic Cell Separation (MACSTM) bead (Miltenyi Biotec #130-097-043) sorting as part of the original plan to enrich the T cell population, particularly for TCR sequencing. MACSTM CD3 MicroBeads and Magnetic Separation (MS) column (Miltenyi Biotec #130-042-201) were used to positively select CD3+ cells as per the manufacturer’s instructions. Due to technical issues with cell counting equipment at the time, all cells were recombined and sent for sequencing in their original proportions after these attempts at separation, allowing for comparisons across different groups. The BAL samples collected from volunteers in the groups 2 and onwards did not undergo any cell sorting attempts. scRNA-seq of PBMC samples Frozen PBMCs (1 ml) were thawed at 37 °C and gradually diluted into 9 ml of warm R10 medium, followed by centrifugation at 400×g for 7 minutes at room temperature. The pellet was resuspended in 2 ml R10, and cell count and viability were assessed using (Solution 13 Chemometec #910-3013) on the NC-slide A8TM (Chemometec #942-0003). Cells were then spun at 300×g for 5 minutes, resuspended in cell staining buffer at 1×107 cells/ml, and blocked with Human TruStain FcXTM (BioLegend #422301) for 10 minutes at 4 °C. TotalSeq-C cell hashing antibody (2 μl, BioLegend #394661, #394663, #394665) was added and incubated for 30 minutes at 4 °C. Cells were washed three times with staining buffer and resuspended in 100 μl of 0.04% PBS (Sigma #D8537)/BSA (bovine serum albumin, Miltenyi Biotec #130-091-376). Count and viability were reassessed before pooling. Bulk TCR-seq of PBMC samples Frozen PBMC samples were thawed, and around 2 million cells were disrupted in 350 μl of the RLT Plus buffer (Qiagen #1053393) with β-mercaptoethanol (BME, Sigma #M3148) (10 μl/ml). RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen #80224) following the manufacturer’s instructions. RNA was eluted into 35 μl of RNase-free water (Thermo Fisher #AM9937) with the concentration quantified by the Nanodrop. RNA was then concentrated using the RNeasy MinElute Cleanup Kit (Qiagen #74204) following the manufacturer’s instructions and eluted into 20 μl of RNase-free water. RNA concentration was quantified using the Nanodrop, and RNA integrity was assessed using the Agilent 4150 TapeStation System. Bulk TCR-seq of AIM+ cells Cells were thawed as they were in the processing of scRNA-seq, except that the cells were resuspended in 2 ml of the R10 medium with 2×benzonase (4 μl/ml, Sigma #E1014). Cells were incubated in 5% CO2 at 37°C for 10 minutes and then counted using Countess II FL. Cells were washed, resuspended, and seeded at a density of 1×106 cells per 100 μl per well in a 96-well U-bottom plate. Cells were incubated with a purified anti-CD40 monoclonal antibody (100 μg/ml; 5 μl per million cells, Miltenyi Biotec #130-094-133) for 15 minutes at room temperature to block CD40-mediated signalling pathways. No washing step was performed between the blocking and stimulation stages. Cells were stimulated with PPD (20 μg/ml), BCG (2×105 CFU/ml, AJ Vaccines) or M.bovis lysate (10 μg/ml, BEI Resources) in a total volume of 200 μl for 24 hours at 37 °C with 5% CO2. Post-incubation, cells were centrifuged at 440×g for 5 minutes. The cell pellet was washed with cold PBS, transferred to a V-bottom plate, and centrifuged again under the same conditions. After discarding the supernatant, cells were stained with a Live/Dead Aqua stain (diluted 1:100 in PBS, Thermo Fisher #L34957) in a total volume of 5 μl for 10 minutes at 4°C. This was followed by staining with a cell surface antibody cocktail for 30 minutes at 4°C. Cells were then washed with 2% BSA/PBS, resuspended in 100 μl of 2% BSA/PBS. AIM+ CD4⁺ or CD8⁺ T cells, identified by co-expression of CD134 and CD137, CD154 and CD134, CD154 and CD137, CD69 and CD134, CD69 and CD137, or CD69 and CD154 , were then sorted using the FACSAria Fusion flow cytometer (BD Biosciences) to 350 μl RLT buffer. RNA was extracted using the Qiagen RNeasy Micro kit (Qiagen #74004) following the manufacturer’s instructions.
scRNA-seq of BAL samples Samples from each volunteer were separated into two Gel beads-in-emulsion (GEM) wells, aiming for 5000 cells per well. 5’ gene expression libraries and V(D)J libraries were generated as per the manufacturer’s instructions. Samples from the Groups 1 and 2 (Batch 1) were processed using the Chromium Next GEM Single Cell V(D)J Reagent kits v1.1 (10x Genomics) and sequenced using a single index configuration. Due to changes in reagents availability, the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10x Genomics) were used for library construction for Groups 3-5 (Batch 2) samples. Libraries were sequenced using the Illumina NovaSeq 6000 platform to achieve a minimum sequencing depth of 30,000 mean reads per cell with 50% sequencing saturation. scRNA-seq of PBMC samples PBMCs from three donors (1.4×104 cells each) were pooled and processed using the Chromium Next GEM Single Cell 5’ HT Reagent Kit (v2) to generate gene expression, surface protein, and V(D)J libraries, following the manufacturer’s protocols. Libraries were sequenced on the Illumina NovaSeq-X platform (paired-end 150 bp), targeting ≥45,000 reads/cell for gene expression and ≥7,500 reads/cell for V(D)J and surface protein libraries. Bulk TCR-seq of PBMC samples 500-1,000 ng RNA was used as input for TCR library construction using the SMART-Seq Human TCR (with UMIs) kit (Takara Bio #634779). TCR libraries were quantified using the Qubit (Thermo Fisher #Q32851) and TapeStation and sequenced on the Illumina NovaSeq 6000 SP flow cell to achieve a target sequencing depth of 1.5×107 reads per PBMC sample. Bulk TCR-seq of AIM+ cells RNA was then processed and sequenced as mentioned in the Bulk TCR sequencing part, except the target sequencing depth was 1×105 reads per 1,000 sorted cells.

value: Blood


title: parth465_4cell_low_miR465_4

description: Library name: parth465_4cell_low_miR465_4


title: PBMC TCR, BCG, TBT04301086-Mbovis-D7

description: Library name: 1086-Mbovis-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_3

description: Library name: parth465_4cell_low_miR465_3


title: PBMC TCR, BCG, TBT04301114-PPD-D7

description: Library name: 1114-PPD-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_7

description: Library name: parth465_4cell_low_miR465_7


title: PBMC TCR, BCG, TBT04301114-BCG-D7

description: Library name: 1114-BCG-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_2

description: Library name: parth465_4cell_low_miR465_2


title: PBMC TCR, BCG, TBT04301083-Mbovis-D7

description: Library name: 1083-Mbovis-PBMC-AIM-TCR


title: PBMC TCR, BCG, TBT04301086-PPD-D7

description: Library name: 1086-PPD-PBMC-AIM-TCR


title: PBMC TCR, BCG, TBT04301083-BCG-D7

description: Library name: 1083-BCG-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_27

description: Library name: parth465_4cell_low_miR465_27


title: parth465_4cell_low_miR465_24

description: Library name: parth465_4cell_low_miR465_24


title: parth465_4cell_low_miR465_26

description: Library name: parth465_4cell_low_miR465_26


title: parth465_4cell_low_miR465_25

description: Library name: parth465_4cell_low_miR465_25


title: PBMC TCR, BCG, TBT04301124-Mbovis-D7

description: Library name: 1124-Mbovis-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_23

description: Library name: parth465_4cell_low_miR465_23


title: PBMC TCR, BCG, TBT04301124-PPD-D7

description: Library name: 1124-PPD-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_22

description: Library name: parth465_4cell_low_miR465_22


title: PBMC TCR, BCG, TBT04301083-PPD-D7

description: Library name: 1083-PPD-PBMC-AIM-TCR


title: PBMC TCR, BCG, TBT04301062-Mbovis-D7

description: Library name: 1062-Mbovis-PBMC-AIM-TCR


title: PBMC TCR, BCG, TBT04301058-PPD-D7

description: Library name: 1058-PPD-PBMC-AIM-TCR


title: PBMC TCR, BCG, TBT04301062-PPD-D7

description: Library name: 1062-PPD-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_20

description: Library name: parth465_4cell_low_miR465_20


title: PBMC TCR, BCG, TBT04301029-PPD-D7

description: Library name: 1029-PPD-PBMC-AIM-TCR


title: PBMC TCR, BCG, TBT04301058-Mbovis-D7

description: Library name: 1058-Mbovis-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_14

description: Library name: parth465_4cell_low_miR465_14


title: parth465_4cell_low_miR465_16

description: Library name: parth465_4cell_low_miR465_16


title: PBMC TCR, BCG, TBT04301026-Mbovis-D7

description: Library name: 1026-Mbovis-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_13

description: Library name: parth465_4cell_low_miR465_13


title: parth465_4cell_low_miR465_18

description: Library name: parth465_4cell_low_miR465_18


title: PBMC TCR, BCG, TBT04301029-BCG-D7

description: Library name: 1029-BCG-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_15

description: Library name: parth465_4cell_low_miR465_15


title: PBMC TCR, BCG, TBT04301026-PPD-D7

description: Library name: 1026-PPD-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_10

description: Library name: parth465_4cell_low_miR465_10


title: PBMC TCR, BCG, TBT04301086-D28

description: Library name: 1086-D28-PBMC-TCR


title: parth465_4cell_low_miR465_12

description: Library name: parth465_4cell_low_miR465_12


title: parth465_4cell_low_miR465_17

description: Library name: parth465_4cell_low_miR465_17


title: parth465_4cell_high_miR465_7

description: Library name: parth465_4cell_high_miR465_7


title: parth465_4cell_high_miR465_8

description: Library name: parth465_4cell_high_miR465_8


title: parth465_4cell_high_miR465_9

description: Library name: parth465_4cell_high_miR465_9


title: PBMC TCR, BCG, TBT04301026-BCG-D7

description: Library name: 1026-BCG-PBMC-AIM-TCR


title: PBMC TCR, Saline, TBT04301011-D7

description: Library name: 1011-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301029-Mbovis-D7

description: Library name: 1029-Mbovis-PBMC-AIM-TCR


title: parth465_4cell_low_miR465_19

description: Library name: parth465_4cell_low_miR465_19


title: PBMC TCR, BCG, TBT04301086-D14

description: Library name: 1086-D14-PBMC-TCR


title: PBMC TCR, BCG, TBT04301083-D28

description: Library name: 1083-D28-PBMC-TCR


title: parth465_4cell_low_miR465_21

description: Library name: parth465_4cell_low_miR465_21


title: PBMC TCR, BCG, TBT04301114-D14

description: Library name: 1114-D14-PBMC-TCR


title: PBMC TCR, BCG, TBT04301083-D14

description: Library name: 1083-D14-PBMC-TCR


title: PBMC TCR, Saline, TBT04301011-D0

description: Library name: 1011-D0-PBMC-TCR


title: PBMC TCR, Saline, TBT04301005-D7

description: Library name: 1005-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301114-D28

description: Library name: 1114-D28-PBMC-TCR


title: parth465_4cell_high_miR465_6

description: Library name: parth465_4cell_high_miR465_6


title: PBMC TCR, Saline, TBT04301005-D0

description: Library name: 1005-D0-PBMC-TCR


title: parth465_4cell_high_miR465_3

description: Library name: parth465_4cell_high_miR465_3


title: parth465_4cell_high_miR465_4

description: Library name: parth465_4cell_high_miR465_4


title: parth465_4cell_high_miR465_23

description: Library name: parth465_4cell_high_miR465_23


title: PBMC TCR, BCG, TBT04301097-D84

description: Library name: 1097-D84-PBMC-TCR


title: PBMC TCR, BCG, TBT04301097-D28

description: Library name: 1097-D28-PBMC-TCR


title: parth465_4cell_high_miR465_2

description: Library name: parth465_4cell_high_miR465_2


title: parth465_4cell_high_miR465_22

description: Library name: parth465_4cell_high_miR465_22


title: PBMC TCR, BCG, TBT04301097-D14

description: Library name: 1097-D14-PBMC-TCR


title: PBMC TCR, BCG, TBT04301097-D7

description: Library name: 1097-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301072-D56

description: Library name: 1072-D56-PBMC-TCR


title: parth465_4cell_high_miR465_16

description: Library name: parth465_4cell_high_miR465_16


title: parth465_4cell_high_miR465_20

description: Library name: parth465_4cell_high_miR465_20


title: PBMC TCR, BCG, TBT04301072-D14

description: Library name: 1072-D14-PBMC-TCR


title: parth465_4cell_high_miR465_5

description: Library name: parth465_4cell_high_miR465_5


title: PBMC TCR, BCG, TBT04301097-D2

description: Library name: 1097-D2-PBMC-TCR


title: PBMC TCR, BCG, TBT04301072-D7

description: Library name: 1072-D7-PBMC-TCR


title: parth465_4cell_high_miR465_1

description: Library name: parth465_4cell_high_miR465_1


title: parth465_4cell_high_miR465_18

description: Library name: parth465_4cell_high_miR465_18


title: parth465_4cell_high_miR465_19

description: Library name: parth465_4cell_high_miR465_19


title: PBMC TCR, BCG, TBT04301072-D28

description: Library name: 1072-D28-PBMC-TCR


title: parth465_4cell_high_miR465_10

description: Library name: parth465_4cell_high_miR465_10


title: parth465_4cell_control_9

description: Library name: parth465_4cell_control_9


title: PBMC TCR, BCG, TBT04301072-D2

description: Library name: 1072-D2-PBMC-TCR


title: parth465_4cell_control_8

description: Library name: parth465_4cell_control_8


title: PBMC TCR, BCG, TBT04301072-D0

description: Library name: 1072-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301097-D0

description: Library name: 1097-D0-PBMC-TCR


title: parth465_4cell_control_7

description: Library name: parth465_4cell_control_7


title: parth465_4cell_control_6

description: Library name: parth465_4cell_control_6


title: PBMC TCR, BCG, TBT04301062-D28

description: Library name: 1062-D28-PBMC-TCR


title: PBMC TCR, BCG, TBT04301062-D14

description: Library name: 1062-D14-PBMC-TCR


title: parth465_4cell_control_4

description: Library name: parth465_4cell_control_4


title: PBMC TCR, BCG, TBT04301062-D84

description: Library name: 1062-D84-PBMC-TCR


title: PBMC TCR, BCG, TBT04301062-D0

description: Library name: 1062-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301059-D56

description: Library name: 1059-D56-PBMC-TCR


title: parth465_4cell_control_5

description: Library name: parth465_4cell_control_5


title: parth465_4cell_control_23

description: Library name: parth465_4cell_control_23


title: parth465_4cell_control_20

description: Library name: parth465_4cell_control_20


title: PBMC TCR, BCG, TBT04301062-D7

description: Library name: 1062-D7-PBMC-TCR


title: parth465_4cell_control_22

description: Library name: parth465_4cell_control_22


title: PBMC TCR, BCG, TBT04301059-D7

description: Library name: 1059-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301059-D14

description: Library name: 1059-D14-PBMC-TCR


title: parth465_4cell_control_1

description: Library name: parth465_4cell_control_1


title: PBMC TCR, BCG, TBT04301059-D2

description: Library name: 1059-D2-PBMC-TCR


title: parth465_4cell_control_19

description: Library name: parth465_4cell_control_19


title: parth465_4cell_control_3

description: Library name: parth465_4cell_control_3


title: parth465_4cell_control_16

description: Library name: parth465_4cell_control_16


title: PBMC TCR, BCG, TBT04301058-D56

description: Library name: 1058-D56-PBMC-TCR


title: parth465_4cell_control_18

description: Library name: parth465_4cell_control_18


title: parth465_4cell_control_24

description: Library name: parth465_4cell_control_24


title: PBMC TCR, BCG, TBT04301058-D28

description: Library name: 1058-D28-PBMC-TCR


title: PBMC TCR, BCG, TBT04301062-D2

description: Library name: 1062-D2-PBMC-TCR


title: parth465_4cell_control_17

description: Library name: parth465_4cell_control_17


title: PBMC TCR, BCG, TBT04301059-D0

description: Library name: 1059-D0-PBMC-TCR


title: parth465_4cell_control_15

description: Library name: parth465_4cell_control_15


title: parth465_4cell_control_27

description: Library name: parth465_4cell_control_27


title: PBMC TCR, BCG, TBT04301058-D14

description: Library name: 1058-D14-PBMC-TCR


title: parth465_4cell_control_14

description: Library name: parth465_4cell_control_14


title: PBMC TCR, BCG, TBT04301059-D28

description: Library name: 1059-D28-PBMC-TCR


title: PBMC TCR, BCG, TBT04301058-D2

description: Library name: 1058-D2-PBMC-TCR


title: PBMC TCR, BCG, TBT04301058-D7

description: Library name: 1058-D7-PBMC-TCR


title: parth465_4cell_control_13

description: Library name: parth465_4cell_control_13


title: parth465_4cell_control_12

description: Library name: parth465_4cell_control_12


title: PBMC TCR, BCG, TBT04301058-D0

description: Library name: 1058-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301051-D28

description: Library name: 1051-D28-PBMC-TCR


title: PBMC TCR, BCG, TBT04301051-D56

description: Library name: 1051-D56-PBMC-TCR


title: parth465_4cell_control_11

description: Library name: parth465_4cell_control_11


title: parth465_4cell_control_10

description: Library name: parth465_4cell_control_10


title: PBMC TCR, BCG, TBT04301051-D7

description: Library name: 1051-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301051-D2

description: Library name: 1051-D2-PBMC-TCR


title: PBMC TCR, BCG, TBT04301051-D0

description: Library name: 1051-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301125-D14

description: Library name: 1125-D14-PBMC-TCR


title: PBMC TCR, BCG, TBT04301051-D14

description: Library name: 1051-D14-PBMC-TCR


title: parth465_2cell_miR465_8

description: Library name: parth465_2cell_miR465_8

value: 2-cell parthenote


title: parth465_2cell_miR465_6

description: Library name: parth465_2cell_miR465_6


title: PBMC TCR, BCG, TBT04301125-D0

description: Library name: 1125-D0-PBMC-TCR


title: parth465_2cell_miR465_4

description: Library name: parth465_2cell_miR465_4


title: parth465_2cell_miR465_2

description: Library name: parth465_2cell_miR465_2


title: PBMC TCR, BCG, TBT04301114-D7

description: Library name: 1114-D7-PBMC-TCR


title: parth465_2cell_miR465_5

description: Library name: parth465_2cell_miR465_5


title: parth465_2cell_miR465_7

description: Library name: parth465_2cell_miR465_7


title: parth465_2cell_miR465_9

description: Library name: parth465_2cell_miR465_9


title: PBMC TCR, BCG, TBT04301114-D0

description: Library name: 1114-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301124-D7

description: Library name: 1124-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301124-D0

description: Library name: 1124-D0-PBMC-TCR


title: parth465_2cell_miR465_3

description: Library name: parth465_2cell_miR465_3


title: parth465_2cell_miR465_24

description: Library name: parth465_2cell_miR465_24


title: PBMC TCR, BCG, TBT04301086-D7

description: Library name: 1086-D7-PBMC-TCR


title: parth465_2cell_miR465_23

description: Library name: parth465_2cell_miR465_23


title: parth465_2cell_miR465_22

description: Library name: parth465_2cell_miR465_22


title: parth465_2cell_miR465_20

description: Library name: parth465_2cell_miR465_20


title: PBMC TCR, BCG, TBT04301086-D0

description: Library name: 1086-D0-PBMC-TCR


title: parth465_2cell_miR465_1

description: Library name: parth465_2cell_miR465_1


title: PBMC TCR, BCG, TBT04301083-D0

description: Library name: 1083-D0-PBMC-TCR


title: parth465_2cell_miR465_21

description: Library name: parth465_2cell_miR465_21


title: PBMC TCR, BCG, TBT04301083-D7

description: Library name: 1083-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301030-D7

description: Library name: 1030-D7-PBMC-TCR


title: parth465_2cell_miR465_19

description: Library name: parth465_2cell_miR465_19


title: PBMC TCR, BCG, TBT04301030-D0

description: Library name: 1030-D0-PBMC-TCR


title: parth465_2cell_miR465_18

description: Library name: parth465_2cell_miR465_18


title: PBMC TCR, BCG, TBT04301029-D7

description: Library name: 1029-D7-PBMC-TCR


title: parth465_2cell_miR465_17

description: Library name: parth465_2cell_miR465_17


title: PBMC TCR, BCG, TBT04301026-D0

description: Library name: 1026-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301026-D7

description: Library name: 1026-D7-PBMC-TCR


title: parth465_2cell_miR465_16

description: Library name: parth465_2cell_miR465_16


title: parth465_2cell_miR465_10

description: Library name: parth465_2cell_miR465_10


title: parth465_2cell_miR465_13

description: Library name: parth465_2cell_miR465_13


title: parth465_2cell_control_9

description: Library name: parth465_2cell_control_9


title: PBMC TCR, BCG, TBT04301021-D0

description: Library name: 1021-D0-PBMC-TCR


title: PBMC TCR, BCG, TBT04301020-D0

description: Library name: 1020-D0-PBMC-TCR


title: parth465_2cell_miR465_15

description: Library name: parth465_2cell_miR465_15


title: parth465_2cell_control_8

description: Library name: parth465_2cell_control_8


title: parth465_2cell_control_7

description: Library name: parth465_2cell_control_7


title: PBMC TCR, BCG, TBT04301021-D7

description: Library name: 1021-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301020-D7

description: Library name: 1020-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301007-D7

description: Library name: 1007-D7-PBMC-TCR


title: PBMC TCR, BCG, TBT04301029-D0

description: Library name: 1029-D0-PBMC-TCR


title: parth465_2cell_control_6

description: Library name: parth465_2cell_control_6


title: PBMC TCR, BCG, TBT04301007-D0

description: Library name: 1007-D0-PBMC-TCR


title: parth465_2cell_control_5

description: Library name: parth465_2cell_control_5


title: parth465_2cell_control_3

description: Library name: parth465_2cell_control_3


title: BAL TCR, BCG D7, rep 3

description: Library name: TBT04301030-BAL-TCR

source_name: BAL

value: BAL


title: BAL TCR, BCG D7, rep 1

description: Library name: TBT04301026-BAL-TCR


title: parth465_2cell_control_4

description: Library name: parth465_2cell_control_4


title: BAL TCR, BCG D7, rep 2

description: Library name: TBT04301029-BAL-TCR


title: BAL TCR, Saline D7, rep 3

description: Library name: TBT04301038-BAL-TCR


title: parth465_2cell_control_2

description: Library name: parth465_2cell_control_2


title: BAL TCR, Saline D7, rep 2

description: Library name: TBT04301034-BAL-TCR


title: parth465_2cell_control_23

description: Library name: parth465_2cell_control_23


title: BAL TCR, Saline D7, rep 1

description: Library name: TBT04301025-BAL-TCR


title: parth465_2cell_control_24

description: Library name: parth465_2cell_control_24


title: parth465_2cell_control_21

description: Library name: parth465_2cell_control_21


title: BAL TCR, BCG D2, rep 3

description: Library name: TBT04301021-BAL-TCR


title: BAL TCR, BCG D2, rep 2

description: Library name: TBT04301020-BAL-TCR


title: hESC derived endodermal cells

description:
Library name: endoderm_screen
10X Genomics

source_name: H1A derived endodermal tissue

value: H1A derived endodermal tissue


title: parth465_2cell_control_20

description: Library name: parth465_2cell_control_20


title: parth465_2cell_control_1

description: Library name: parth465_2cell_control_1


title: BAL TCR, BCG D2, rep 1

description: Library name: TBT04301007-BAL-TCR


title: BAL TCR, Saline D2, rep 3

description: Library name: TBT04301011-BAL-TCR


title: parth465_2cell_control_19

description: Library name: parth465_2cell_control_19


title: parth465_2cell_control_18

description: Library name: parth465_2cell_control_18


title: BAL TCR, BCG D56, rep 3

description: Library name: TBT04301125-BAL-TCR


title: BAL TCR, Saline D2, rep 1

description: Library name: TBT04301005-BAL-TCR


title: BAL TCR, BCG D56, rep 2

description: Library name: TBT04301124-BAL-TCR


title: parth465_2cell_control_16

description: Library name: parth465_2cell_control_16


title: parth465_2cell_control_22

description: Library name: parth465_2cell_control_22


title: parth465_2cell_control_13

description: Library name: parth465_2cell_control_13


title: parth465_2cell_control_11

description: Library name: parth465_2cell_control_11


title: parth465_2cell_control_17

description: Library name: parth465_2cell_control_17


title: parth465_2cell_control_10

description: Library name: parth465_2cell_control_10


title: BAL TCR, Saline D56, rep 3

description: Library name: TBT04301082-BAL-TCR


title: parth465_2cell_control_15

description: Library name: parth465_2cell_control_15


title: BAL TCR, BCG D56, rep 1

description: Library name: TBT04301122-BAL-TCR


title: BAL TCR, Saline D56, rep 2

description: Library name: TBT04301075-BAL-TCR


title: BAL TCR, Saline D56, rep 1

description: Library name: TBT04301064-BAL-TCR


title: BAL TCR, Saline D2, rep 2

description: Library name: TBT04301006-BAL-TCR


title: ivf200_4cell_miR200_8

description: Library name: ivf200_4cell_miR200_8

source_name: 4-cell embryo

value: 4-cell embryo


title: BAL TCR, BCG D28, rep 2

description: Library name: TBT04301086-BAL-TCR


title: BAL TCR, BCG D28, rep 3

description: Library name: TBT04301114-BAL-TCR


title: BAL TCR, Saline D28, rep 3

description: Library name: TBT04301116-BAL-TCR


title: ivf200_4cell_miR200_4

description: Library name: ivf200_4cell_miR200_4


title: BAL TCR, Saline D28, rep 2

description: Library name: TBT04301113-BAL-TCR


title: BAL TCR, BCG D28, rep 1

description: Library name: TBT04301083-BAL-TCR


title: ivf200_4cell_miR200_9

description: Library name: ivf200_4cell_miR200_9


title: ivf200_4cell_miR200_6

description: Library name: ivf200_4cell_miR200_6


title: ivf200_4cell_miR200_3

description: Library name: ivf200_4cell_miR200_3


title: BAL TCR, BCG D14, rep 3

description: Library name: TBT04301097-BAL-TCR


title: ivf200_4cell_miR200_7

description: Library name: ivf200_4cell_miR200_7


title: BAL TCR, BCG D14, rep 1

description: Library name: TBT04301058-BAL-TCR


title: ivf200_4cell_miR200_22

description: Library name: ivf200_4cell_miR200_22


title: ivf200_4cell_miR200_2

description: Library name: ivf200_4cell_miR200_2


title: BAL TCR, Saline D14, rep 3

description: Library name: TBT04301096-BAL-TCR


title: ivf200_4cell_miR200_23

description: Library name: ivf200_4cell_miR200_23


title: ivf200_4cell_miR200_5

description: Library name: ivf200_4cell_miR200_5


title: BAL TCR, Saline D28, rep 1

description: Library name: TBT04301089-BAL-TCR


title: BAL GEX, BCG D56, rep 1

description: Library name: TBT04301122-BAL-GEX


title: ivf200_4cell_miR200_24

description: Library name: ivf200_4cell_miR200_24


title: BAL GEX, BCG D56, rep 2

description: Library name: TBT04301124-BAL-GEX


title: ivf200_4cell_miR200_19

description: Library name: ivf200_4cell_miR200_19


title: ivf200_4cell_miR200_21

description: Library name: ivf200_4cell_miR200_21


title: BAL GEX, Saline D56, rep 3

description: Library name: TBT04301082-BAL-GEX


title: ivf200_4cell_miR200_20

description: Library name: ivf200_4cell_miR200_20


title: BAL TCR, BCG D14, rep 2

description: Library name: TBT04301062-BAL-TCR


title: BAL GEX, BCG D56, rep 3

description: Library name: TBT04301125-BAL-GEX


title: ivf200_4cell_miR200_16

description: Library name: ivf200_4cell_miR200_16


title: ivf200_4cell_miR200_15

description: Library name: ivf200_4cell_miR200_15


title: BAL TCR, Saline D14, rep 2

description: Library name: TBT04301087-BAL-TCR


title: BAL GEX, Saline D56, rep 2

description: Library name: TBT04301075-BAL-GEX


title: BAL GEX, BCG D28, rep 3

description: Library name: TBT04301114-BAL-GEX


title: ivf200_4cell_miR200_12

description: Library name: ivf200_4cell_miR200_12


title: BAL GEX, BCG D28, rep 2

description: Library name: TBT04301086-BAL-GEX


title: ivf200_4cell_miR200_13

description: Library name: ivf200_4cell_miR200_13


title: BAL GEX, BCG D28, rep 1

description: Library name: TBT04301083-BAL-GEX


title: ivf200_4cell_miR200_11

description: Library name: ivf200_4cell_miR200_11


title: ivf200_4cell_miR200_17

description: Library name: ivf200_4cell_miR200_17


title: ivf200_4cell_control_9

description: Library name: ivf200_4cell_control_9


title: ivf200_4cell_control_8

description: Library name: ivf200_4cell_control_8


title: BAL GEX, Saline D56, rep 1

description: Library name: TBT04301064-BAL-GEX


title: ivf200_4cell_control_7

description: Library name: ivf200_4cell_control_7


title: BAL GEX, BCG D14, rep 3

description: Library name: TBT04301097-BAL-GEX


title: BAL GEX, Saline D28, rep 1

description: Library name: TBT04301089-BAL-GEX


title: BAL GEX, BCG D14, rep 2

description: Library name: TBT04301062-BAL-GEX


title: ivf200_4cell_control_5

description: Library name: ivf200_4cell_control_5


title: ivf200_4cell_control_6

description: Library name: ivf200_4cell_control_6


title: ivf200_4cell_miR200_10

description: Library name: ivf200_4cell_miR200_10


title: ivf200_4cell_control_2

description: Library name: ivf200_4cell_control_2


title: ivf200_4cell_control_3

description: Library name: ivf200_4cell_control_3


title: BAL GEX, Saline D14, rep 2

description: Library name: TBT04301087-BAL-GEX


title: BAL GEX, Saline D28, rep 2

description: Library name: TBT04301113-BAL-GEX


title: BAL GEX, BCG D14, rep 1

description: Library name: TBT04301058-BAL-GEX


title: ivf200_4cell_control_24

description: Library name: ivf200_4cell_control_24


title: BAL GEX, Saline D14, rep 3

description: Library name: TBT04301096-BAL-GEX


title: ivf200_4cell_control_23

description: Library name: ivf200_4cell_control_23


title: BAL GEX, Saline D14, rep 1

description: Library name: TBT04301056-BAL-GEX


title: BAL GEX, Saline D28, rep 3

description: Library name: TBT04301116-BAL-GEX


title: 40

city: Kobe

first: Yusei

last: Hosokawa

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: 1Division of Diabetes and Endocrinology, Department of Internal Medicine

country: Japan

institute: Kobe University graduate school of medicine

description: Library name: Patient40

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read Count, FPKM, TPM values for each Sample

source_name: visceral white adipose tissue

extract_protocol:
Total RNA was extracted from tissues with RNeasy minikit (QIAGEN).
RNA libraries for RNA-Seq were Prepared using TruSeq stranded mRNA Library Prep. Kit Following manufacturers Protocols

value: visceral white adipose tissue


title: ivf200_4cell_control_20

description: Library name: ivf200_4cell_control_20


title: 41

description: Library name: Patient41


title: 43

description: Library name: Patient43


title: ivf200_4cell_control_21

description: Library name: ivf200_4cell_control_21


title: 39

description: Library name: Patient39


title: ivf200_4cell_control_19

description: Library name: ivf200_4cell_control_19


title: ivf200_4cell_control_1

description: Library name: ivf200_4cell_control_1


title: 37

description: Library name: Patient37


title: ivf200_4cell_control_16

description: Library name: ivf200_4cell_control_16