title: H187 Lurbi 1

description: Library name: Sample 4

value: H187 Lurbi 1


title: U87 CTR mycLARP6-INPUT_smallRNAseq

status: Public on Jan 22 2026

type: SRA

city: Oxford

first: Faraz

middle: K.

last: Mardakheh

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: INPUT_CTR1_SE50

library_source: transcriptomic

data_processing:
iCLIP data analysis was performed as detailed in (https://doi.org/10.1101/2024.09.20.614075). Briefly, demultiplexed reads were uploaded on the webserver iMAPS (imaps.goodwright.com) for primary iCLIP data analysis. The human genome GRCh38.p13 GENCODE V42 was used with the primary assembly comprehensive annotation. Reads were first trimmed with TrimGalore! (software developed by Felix Krueger), to remove remaining adapters and low-quality reads, then pre-mapped to rRNA and tRNA sequences with Bowtie 2 and discarded. This step ensured that reads mapping to repetitive regions were not misaligned to mRNA. The remaining unmapped reads were then mapped to the genome with STAR. PCR duplicates were removed with UMI-tools based on the presence of identical UMIs in reads mapping to the same position. The exact crosslink position was then identified as the first nucleotide after the experimental barcode, and this data was downloaded from the webserver and processed further offline. The crosslink information was used to call the peaks, which represent the binding sites of LARP6, for each individual replicate. The peak caller Clippy (version 1.5.0) was used with the following settings: rolling mean 15; minimum counts per gene 3; minimum counts per peak 3; prominence 1 (default); peak threshold 0.4 (default). The peaks called for the individual replicates were then combined into one file per mutant by merging the peaks and summing their peak scores using bedtools (version 2.30.0), with the peak scores indicative of the binding strength. Background normalisation was performed by subtracting the peaks that were called in the parental negative control from each combined peak file, using bedtools.
Total RNA-Seq data analysis was performed as detailed in (https://doi.org/10.1101/2024.09.20.614075). Briefly, demultiplexed reads were trimmed with TrimGalore! (version 0.6.10) to remove the remaining adapter sequences and low-quality reads. Reads were then mapped to the human genome GRCh38.p13 GENCODE V42 with STAR (version 2.7.10b). Default parameters were used, and gene counts were generated directly from the mapping step by enabling the –quantMode GenerateCounts option. The gene counts from the RNAseq were used for iCLIP data normalisation. The iCLIP peak scores were normalised for transcript abundance according to the following formula: normalised peak score=((peak score)/(gene count)*1000).
Assembly: GRCh38.p13 GENCODE V42
Supplementary files format and content: peaks.bed (iCLIP peak scores)
Supplementary files format and content: .out (INPUT RNA-seq read counts)

molecule: total RNA

organism: Homo sapiens

source_name: Brain

growth_protocol: U-87 MG (PURCHASED FROM ATCC) cells were grown in DMEM media (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. U-87 MG myc-LARP6 inducible cell lines were grown as above, and myc-LARP6 expression was induced with 60 ng/mL Doxycycline. All cells were maintained in a humidified incubator at 37°C, 5% CO2. Cells were passaged consistently before reaching confluence with Trypsin-EDTA (Gibco), and tested regularly for mycoplasma, using the MycoAlert Mycoplasma Detection Kit (Lonza Bioscience).

extract_protocol:
For iCLIP, cells were UV-C crosslinked, lysed, and subjected to iCLIP as indicated in (https://doi.org/10.1101/2024.09.20.614075). Briefly, 20 million cells per condition were grown in 15 cm dishes and myc-LARP6 mutants were induced with 60 ng/mL doxycycline for 24 hours. Cells were crosslinked on ice at 150 mJ/cm2 at 254 nm in a Hoefer Scientific UV crosslinker to form covalent bonds between RBPs and RNAs that were in direct contact, then scraped in PBS and pelleted. Cell pellets were lysed in iCLIP lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate, cOmplete protease inhibitor cocktail (Roche), 1 mM PMSF), cleared, and diluted to 1 mg/mL in 1 mL volume. Samples were then treated with 0.2 units/mL lysate RNase I (Thermo Scientific, catalogue number EN0602) and 2 μL Turbo DNase (Ambion) for 3 minutes at 37°C to partially digest the RNA. 50 μL Dynabeads Protein G (Invitrogen) per sample were first conjugated with 4 μg (10 μL) mouse anti-myc-tag antibody (Cell Signaling, 9B11) for one hour at RT in a rotating wheel, then added to the samples to perform the immunoprecipitation (IP) for one hour at 4°C in a rotating wheel. After the IP, samples were stringently washed twice with high-salt wash buffer (50 mM Tris-HCl, pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate), then once with PNK wash buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 0.2% Tween-20).
For Input RNA-seq, cells grown under the same conditions as the ones used in the iCLIP experiment was subjected to RNA extraction with TRIzol. The purified RNAs were quantified with the Qubit RNA High-sensitivity assay, and the quality was validated with the Agilent High Sensitivity RNA ScreenTape assay, with all samples having a RIN ≥ 9.3. The whole transcriptome RNAseq library preparation and sequencing was outsourced to Novogene.
For iCLIP, The RNA fragments were dephosphorylated on the beads at the 3’ end, followed by 3’ end ligation of different barcoded adapters, to allow for downstream multiplexing of each replicate into one sample. The samples were then eluted from the beads, run on an SDS-PAGE gel, followed by isolation of the RNA fragments and subsequent library preparation as described previously. The amplified libraries were quantified and validated with the Qubit dsDNA High-sensitivity and Agilent D1000 high sensitivity ScreenTape assays, pooled in an equimolar ratio, and deep sequenced on an Illumina NextSeq 500 instrument, using a single-end 100 nt workflow. Sequencing was performed at the Barts and The London Genome Centre.
For Input RNA-seq, rRNA depletion whole transcriptome sequencing using two protocols (short and long RNAs) was performed by Novogene (https://www.novogene.com/eu-en/services/research-services/transcriptome-sequencing/whole-transcriptome-sequencing/)

treatment_protocol: 60 ng/mL Doxycycline for 24hrs.

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: Glioblastoma

tag: genotype

value: LARP6 deltaCTR

tag: antibody

value: myc-tag

tag: replicate


title: BAT, Control2

city: Ribeirão Preto

first: Carlos

middle: H

last: Sponton

state: São Paulo

address: Av. Bandeirantes, 3900

department: Department of Physiology, Ribeirão Preto Medical School, Universidade de São Paulo (FMRP-USP)

country: Brazil

institute: USP

description: Library name: Sample2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality using Trimmomatic tool
All workflow was using the tool Irna
Assembly: mm10
Supplementary files format and content: normalized counts

organism: Mus musculus

source_name: Brown adipose tissue

extract_protocol:
RNA was harvested using Pure Link RNA Mini kit (Invitrogen)
RNA libraries were prepared by Novogene

value: Brown adipose tissue

value: Control

tag: treatment

value: HFD 10 weeks


title: macrophage, mfap4:mCherry positive, UNCUT, 29hpA, rep 2

city: Montpellier

first: Mai-Eva

last: Nguyen-chi

address: Pl. Eugène Bataillon

country: France

institute: CNRS

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing were performed using Illumina's conversion software (bcl2fastq v2.20). The quality of the raw data was assessed using FastQC (v0.11.9) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). Contaminant screening was done using FastQ Screen (v0.15.1).
Adapters sequences were trimmed before alignment. Reads were aligned to the genome using TopHat (v2.1.1) and gene counts were obtained using featureCounts (v2.0.0 for 5hpA/29hpA samples, v2.0.3 for 2hpA samples).
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include geneID|gene symbol for 2hpA samples, gene symbols for 5hpA and 29hpA samples, and raw counts values for each sample

organism: Danio rerio

growth_protocol: Tg(mfap4:mCherry-F) embryos were maintained in embryo water at 28°C during 3 days.

extract_protocol:
Macrophages were sorted by FACS and RNA was harvested using Rneasy mini plus kit (Qiagen). Between 5ng-10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit from Takara Bio and DNA Prep Kit from Illumina following manufacturer's protocols.
RNA-seq single read (100nt)

treatment_protocol:
At 3 days post-fertilization, the fin folds of Tg(mfap4:mCherry-F) embryos were amputated or kept intact.
Cell dissociation was done at 2 hours post-amputation (4 replicates), 5 hours post-amputation (4 replicates) and 29 hours post-amputation (4 replicates).

value: macrophage

value: mCherryF+

tag: time


title: H187 DMSO 2

city: Indianapolis

first: Misty

last: Shields

state: IN

address: 980 W. Walnut St

country: USA

institute: Indiana University

description: Library name: Sample 2

data_processing:
The sequence data were mapped to the human reference genome hg38 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bamutils (from ngsutils v.0.4.17).
Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -Q 10”. The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR (v.4.2.0).
False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung cancer cells

growth_protocol: All cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Qiagen RNeasy Plus MiniKit
100 nanograms of total RNA was used for library preparation with the llumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit

value: Lung cancer cells

value: H187 DMSO 2


title: No.10-Alveoli_04

city: Houston

first: Akira

last: Yamamoto

state: Texas

address: One Baylor Plaza

country: Japan

institute: Baylor College of Medicine

description:
Library name: DSP-1001660021516-H-H03
Control_No.10-Alveoli_04_1.Normal_distal

data_processing:
Raw sequencing data (FASTQ files) were processed using the NanoString GeoMx DSP analysis pipeline to generate DCC files.
Quality control was performed to remove low-quality segments and outlier probes based on sequencing and probe-level QC metrics.
Gene-level counts were generated by collapsing probe counts to target genes.
Counts were normalized using Q3 (75th percentile) normalization and background correction based on negative control probes.
Assembly: GRCh38
Supplementary files format and content: Processed data include NanoString GeoMx DSP DCC files containing gene-level counts for each ROI, and a tab-delimited matrix file containing normalized gene expression values (genes × ROIs).
Library strategy: Spatial transcriptomics

source_name: lung

growth_protocol: Human lung tissue specimens were obtained from explanted lungs at the time of lung transplantation or from pneumonectomy specimens for lung cancer.

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) lung tissue sections using the NanoString GeoMx DSP RNA Whole Transcriptome Atlas protocol according to the manufacturer’s instructions.
Sequencing libraries were prepared using the NanoString GeoMx DSP RNA Whole Transcriptome Atlas (Human) following the manufacturer’s protocol.

treatment_protocol: No experimental treatment was applied to the tissue prior to RNA extraction.

value: lung

value: Alveoli

value: wild type

tag: batch


title: No.10-Interstitium_02

description:
Library name: DSP-1001660021516-H-H08
Control_No.10-Interstitium_02_1.Normal_proximal

value: Interstitium


title: macrophage, mfap4:mCherry positive, UNCUT, 29hpA, rep 4


title: CD45+ Immune Cells in the Mouse Brain – Control of H2030 Brain Metastasis (BrM)

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description:
Library name: Cd45+_immune_cells_in_CTR_BrM
10x Genomics

library_source: transcriptomic single cell

data_processing:
Seven 10x barcoded sequencing libraries were generated using the 10x Single Cell 3' v3 kits (10x Genomics, Inc.). These libraries were sequenced in multiple rounds until each sample achieved a mean depth of 25,000 reads per cell. The mean number of reads per cell was calculated by processing the accumulated raw FASTQ files from each sequencing round with CellRanger Count (10X Genomics Cell Ranger v7.1.0) using default parameters. The sequencing data were aligned to the prebuilt 10x mouse GRCh38 (GENCODE v32/Ensembl 98) scRNA-seq reference genome (mm10-2020-A). This analysis yielded a median of 264 million sequenced reads per sample, with individual sample reads as follows: CTR_BrM: 264,577,836; BrM_VEH: 236,382,953; BrM_IBU: 295,303,588; CTR_MS: 96,922,258; MS: 222,018,909; CTR_AD: 335,324,101; AD: 275,467,604.
Initial assessments of the cancer model samples revealed the presence of metastatic cells of human origin, raising concerns regarding potential contamination with human environmental RNA. To facilitate simultaneous analysis of all samples while addressing human cell and RNA contamination, the raw FASTQ data from the gene expression libraries of all samples were aligned to the human GRCh38 (GENCODE v32/Ensembl 98) and mouse GRCh38 (GENCODE v32/Ensembl 98) 10x prebuilt scRNA-seq reference genome (GRCh38_and_mm10-2020-A). This alignment was processed using CellRanger Count (10X Genomics Cell Ranger v7.1.0) with default parameters.
In total, 12,219 cells were retrieved from CTR_BrM, 9,445 from BrM_VEH, 11,850 from BrM_IBU, 29,818 from CTR_AD, 11,388 from AD, 13,189 from CTR_MS, and 18,849 from MS. Background ambient RNA and barcode-swapped reads were subsequently removed from the count matrix using the Cellbender v0.3.0 Python package (Fleming et al., 2023) (Python v3.7.12 (Van Rossum and Drake, 2009)) with default parameters. This processing yielded a refined count matrix, identifying barcodes corresponding to genuine cells.
After applying Cellbender, the cell counts were adjusted to 10,237 in CTR_BrM, 9,452 in BrM_VEH, 11,383 in BrM_IBU, 12,143 in CTR_AD, 10,262 in AD, 3,665 in CTR_MS, and 8,530 in MS. The removal of doublet artifacts was performed using the Scrublet v0.2.3 Python package (Wolock et al., 2019) (Python v3.7.10 (Van Rossum and Drake, 2009)) with default parameters. Following doublet removal, the final cell counts were 10,159 in CTR_BrM, 9,379 in BrM_VEH, 11,370 in BrM_IBU, 12,143 in CTR_AD, 9,283 in AD, 3,659 in CTR_MS, and 8,528 in MS.
All subsequent single-cell transcriptomic analyses were conducted using R Statistical Software (v4.2.0) with the Seurat v5 (v4.9.9.9059) package (Hao et al., 2021; R: The R Project for Statistical Computing). For quality control, human genes and those expressed in fewer than three cells were excluded. After filtering out human genes, cells with more than 5% mitochondrial content or fewer than 1,500 detected mouse genes were also excluded. This filtering resulted in a total of 43,245 high-quality cells, distributed as follows: 7,360 in CTR_BrM, 5,202 in BrM_VEH, 5,870 in BrM_IBU, 9,108 in CTR_AD, 6,363 in AD, 2,885 in CTR_MS, and 6,457 in MS.
For each sample, UMI count data were normalized using a regularized negative binomial regression approach via SCTransform (sctransform v0.3.5). SCTransform was executed with the parameter vst.flavor set to "v2" to enhance regularization, and the method was set to "glmGamPoi" to fit a generalized linear Gamma-Poisson model, thereby improving the speed of the learning procedure and enhancing computational efficiency. In the subsequent step, mitochondrial content was regressed out in a second non-regularized linear regression.
To ensure that SCTransform residuals were computed for the top variable genes across all samples, the SelectIntegrationFeatures function was utilized to identify the top 3,000 highly variable genes (HVGs). These features were then employed in the PrepSCTIntegration function to recompute residuals for any missing values across the selected HVGs, utilizing stored model parameters. Upon obtaining the residuals for the common HVGs, Principal Component Analysis (PCA) was conducted on the SCT-normalized data of each sample, focusing on the top 3,000 HVGs.
Integration anchors were identified using the FindIntegrationAnchors function, specifying SCT as the normalization method, the top 3,000 HVGs as anchor features, and employing reciprocal PCA (RPCA) for reduction over the top 30 PCA components, with k set to 20 for anchor selection.
The seven datasets were integrated into a single dataset using the IntegrateData function, applying the previously identified anchors, SCT normalization, and the top 30 dimensions for the anchor weighting procedure. To facilitate dimensionality reduction, a new PCA was performed on the integrated dataset, followed by a nonlinear dimensionality reduction using Uniform Manifold Approximation and Projection (UMAP) applied to the 30 most significant PCA dimensions.
A Shared Nearest-Neighbor (SNN) graph was constructed utilizing the FindNeighbors function, based on the 30 most significant principal components (PCs). Cell clusters were subsequently identified through the implementation of the FindClusters function with default parameters.
For differential expression analysis within the integrated object comprising multiple SCT models, the dataset was prepared using the PrepSCTFindMarkers function. Differentially expressed genes between identified clusters were determined via a Wilcoxon rank-sum test, implemented through the Seurat package’s FindAllMarkers function, with default parameters. This analytical approach culminated in the identification of 16 distinct immune subpopulations. Gene expression plots were generated using the FeaturePlot function.
Enrichment scores for the identified gene signatures were computed using the AddModuleScore function with default settings, facilitating a systematic assessment of gene expression patterns across clusters and conditions. The visualizations were enhanced with the "RdBu" gradient color scheme from the RColorBrewer package. To enhance the interpretability of the expression data, the maximum and minimum cutoff values for visualization were adjusted, emphasizing biologically relevant expression ranges.
Assembly: Human GRCh38 (GENCODE v32/Ensembl 98) and mouse GRCh38 (GENCODE v32/Ensembl 98) 10x prebuilt scRNA-seq reference genome (GRCh38_and_mm10-2020-A)
Supplementary files format and content: Single cell Seurat object: Seurat_integrated_immune_populations_in_BrM_AD_MS.rds
Supplementary files format and content: CTR_BrM - Cell barcode: CTR_BrM_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: CTR_BrM - Gene name: CTR_BrM_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: CTR_BrM - Expression matrix: CTR_BrM_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: BrM_VEH - Cell barcode: BrM_VEH_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: BrM_VEH - Gene name: BrM_VEH_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: BrM_VEH - Expression matrix: BrM_VEH_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: BrM_IBU - Cell barcode: BrM_IBU_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: BrM_IBU - Gene name: BrM_IBU_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: BrM_IBU - Expression matrix: BrM_IBU_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: CTR_AD - Cell barcode: CTR_AD_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: CTR_AD - Gene name: CTR_AD_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: CTR_AD - Expression matrix: CTR_AD_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: AD - Cell barcode: AD_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: AD - Gene name: AD_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: AD - Expression matrix: AD_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: CTR_MS - Cell barcode: CTR_MS_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: CTR_MS - Gene name: CTR_MS_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: CTR_MS - Expression matrix: CTR_MS_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: MS - Cell barcode: MS_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: MS - Gene name: MS_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: MS - Expression matrix: MS_post_cellbender_filtered_matrix.mtx.gz

molecule: polyA RNA

extract_protocol:
CD45+ cells were isolated by FACS
FACS-purified CD45⁺ cells were processed for library preparation using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121), following the manufacturer’s instructions. The protocol included GEM generation, barcoding, GEM-RT clean-up, cDNA amplification, and library construction. The sequencing was conducted on an Illumina NextSeq 550 instrument equipped with v2.5 reagent kits, employing a PairEnd run type of 28 bp R1 and 56 bp R2. Primary data processing, including image analysis, per-cycle basecalling, and quality score assignment, was carried out using Real Time Analysis software (RTA v2, Illumina). Additionally, the conversion of BCL files to FASTQ format was executed with bcl2fastq2 within the Local Run Manager RNAfusion Analysis Module v2 (Illumina).

tag: library name

value: Immune cells

value: WT

value: No treatment


title: U87 LaMod mycLARP6-INPUT_smallRNAseq

description: Library name: INPUT_LaMod_SE50

value: Brain

value: Glioblastoma

value: LARP6 deltaLa-module


title: macrophage, mfap4:mCherry positive, CUT, 29hpA, rep 4


title: U87 NTD mycLARP6-INPUT_longRNAseq

description: Library name: INPUT_NTD_PE150

value: LARP6 deltaNTD

value: myc-tag


title: No.10-Ep_02

description:
Library name: DSP-1001660021516-H-H05
Control_No.10-Ep_02_1.Normal_proximal

value: Ep


title: macrophage, mfap4:mCherry positive, UNCUT, 29hpA, rep 1

value: macrophage


title: BAT, Control4

description: Library name: Sample4

value: Brown adipose tissue

value: Control

value: HFD 10 weeks


title: BAT, Control3

description: Library name: Sample3


title: No.10-Alveoli_03

description:
Library name: DSP-1001660021516-H-H02
Control_No.10-Alveoli_03_1.Normal_distal

value: lung


title: No.10-Interstitium_01

description:
Library name: DSP-1001660021516-H-H07
Control_No.10-Interstitium_01_1.Normal_proximal


title: U87 LaMod mycLARP6-INPUT_longRNAseq

description: Library name: INPUT_LaMod_PE150


title: U87 CTR mycLARP6-INPUT_longRNAseq

description: Library name: INPUT_CTR1_PE150

value: LARP6 deltaCTR


title: No.10-Alveoli_02

description:
Library name: DSP-1001660021516-H-H01
Control_No.10-Alveoli_02_1.Normal_distal

value: Alveoli

value: wild type


title: macrophage, mfap4:mCherry positive, CUT, 29hpA, rep 1

value: mCherryF+


title: mouse NK cells, antiNK1.1 + IL-12 stimulated with AP1inhibitor, STAT4, rep2

city: New York

first: Hyunu

last: Kim

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: mNK_400k_STAT4_aNK11IL12AP1i_2

library_source: other

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie 2 (v2.4.1).
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as a control using narrow peak parameters with cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
The peak atlas was generated by merging via union of peaks called by each sample after filtering out bottom 25% of peaks by MACS2 calculated qValue. Resulting peak atlas was further filtered to only retain peaks that were called by two or more replicates within each sample group, as well as peaks that do not overlap the Encode’s DAC Exclusion List Regions (ENCFF547MET).
Assembly: mm10
Supplementary files format and content: NK_peakatlas_normCounts.tsv
Library strategy: CUT&Run

molecule: other

source_name: NK

extract_protocol:
Following CUT&RUN preparation, DNA was extracted using the Qiagen MinElute Kit.
For library preparation, we used the KAPA Hyper Prep Kit and followed the kit's instructions. Amplification cycle number was determined by running qPCR after 4 cycles of amplification and assessing required additional cycles.

treatment_protocol: NK cells were treated with 50uM pan-AP1 inhibitor (SR 11302, Tocris, cat. 2476) for 1h, then stimulated with aNK1.1 for 3h (or unstimulated as control), sorted, and stimulated for 1h with IL-12 .

value: NK

tag: cell count

tag: stimulation

tag: batch id


title: U87 NTD mycLARP6-INPUT_smallRNAseq

description: Library name: INPUT_NTD_SE50


title: No.10-Ep_01

description:
Library name: DSP-1001660021516-H-H04
Control_No.10-Ep_01_1.Normal_proximal


title: macrophage, mfap4:mCherry positive, CUT, 29hpA, rep 2


title: H157_Vehicle

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

country: China

institute: Sun Yat-Sen university

description: Library name: H157_Vehicle

data_processing:
Sequencing was performed on the BGISEQ platform at BGI Tech (Wuhan, China). The FASTQ-formatted sequence data were analyzed by using a standard BWA–Bowtie–Cufflinks workflow. Sequence reads were mapped to GRCh38/hg38 assembly with BWA and Biotie software. The Cufflinks package was used for transcript assembly, quantification of normalized gene and isoform expression, and analysis of different expression.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H157 cells were cultured in RPMI1640 supplemented with 10% FBS. Cells were grown at 37 °C in 5% CO2 incubators.

extract_protocol:
The extraction steps of total RNA were according to the manufacturer's protocol of the Vazyme Super FastPure Cell RNA Isolation Kit (Vazyme Biotech, Nanjing, China)
Transcriptomic sequencing of RNA-seq libraries were validated through MGISEQ2000 machine (BGI Tech, China).

treatment_protocol: H157 cells were treated with vehicle (DMSO) or W6134 (2.5 μM) for 48 hours.

value: non-small cell lung adenocarcinoma cells

value: WT

value: Vehicle


title: DKO_Foxo1

city: Los Angeles

first: Mingyi

last: Zhang

state: CA

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description:
Library name: DKO_Foxo1
Epicypher

library_source: genomic

data_processing:
fastq files were trimmed for adapters and low-quality sequences using Galore and subsequently mapped to the mouse mm10 reference genome using Bowtie2 with default parameters.
PCR duplicates were marked using Picard.
Coverage tracks were generated using the bamCoverage tool from deepTools with the RPKM normalization method, and peak calling was conducted using MACS2.
Peak annotation was performed with ChIPseeker (RStudio) to annotate peaks.
Assembly: mm10
Supplementary files format and content: Bigwig files
Library strategy: CUT&Run

molecule: genomic DNA

source_name: incisor mesenchyme

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Freshly collected proximal mouse incisor from DKO mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes . The prepared cells were tested for viability before process the extraction. Cells viability  higher than 80% were used for nucleis extranction for the scATACseq.
Library was performed according to the manufacter's introduction (Epicypher).

treatment_protocol: 20ml/ml concentrated tamxifen was administered to mice via intraperitoneal injection at a dosage of 1.5mg/10g body weight

value: incisor mesenchyme


title: U87 NTR mycLARP6-INPUT_smallRNAseq

description: Library name: INPUT_NTR_SE50

value: Brain

value: Glioblastoma

value: LARP6 deltaNTR


title: macrophage, mfap4:mCherry positive, CUT, 29hpA, rep 3

value: macrophage


title: No.09-Interstitium_02

description:
Library name: DSP-1001660021516-H-G11
Control_No.09-Interstitium_02_1.Normal_proximal

value: Interstitium


description: Library name: Sample_ATAC_TotalNK_Unstim_6hr_2_IGO_12002_B_12

data_processing:
For RNA-seq dataset generated in this study, transcript quantification was based on the mm10 University of California, Santa Cruz (UCSC) Known Gene models and performed using the quasi-mapping-based mode of Salmon (v0.13.1) correcting for potential GC bias. Transcript was summarized to gene level using tximport (v1.10.1).
For ATAC-seq data, reproducible peaks showing an IDR value of 0.05 or less in each condition were retained, aggregated across the experiment and merged via union generate the final atlas, and annotated with the UCSC Known Gene model. Reads were mapped to the final atlas and counted with the summarizeOverlaps function from the GenomicAlignment package (v1.34.1).
Assembly: mm10
Supplementary files format and content: Project_12001_rawCounts.txt
Supplementary files format and content: Project_12002_B_peakAtlas.txt
Supplementary files format and content: Project_12002_B_rawCounts.txt

source_name: Spleen

extract_protocol:
For RNA-seq: RNA was isolated from sorted cells and/or stimulated cells as described using PicoPure RNA Isolation Kit (ThermoFisher Scientific, cat. KIT0214). After RiboGreen quantification and quality control by Agilent BioAnalyzer. For ATAC-seq: ATAC-seq was performed as described previously. Briefly, sorted, stimulated cells were washed in cold PBS and lysed. The transposition reaction was incubated at 37 °C for 30 min. DNA was cleaned with the MinElute PCR Purification kit (QIAGEN, cat. 28004).
For RNA-seq: RNA amplified using SMART-Seq v.4 Ultra Low Input RNA kit (Clontech, cat. 63488). Subsequently, amplified complementary DNA was used to prepare libraries with KAPA HyperPrep Kit (Kapa Biosystems, cat. KK8504). Samples were barcoded and ran on NovaSeq6000 in a 100bp/100bp paired-end run. For ATAC-seq: DNA materials were amplified and the final product was cleaned by AMPure XP beads (Beckman Coulter catalog no. A63882) at a 1× ratio, and size selection was performed at a 0.5× ratio. Libraries were sequenced on a NovaSeq6000 in a 100 bp/100 bp paired-end run, using the NovaSeq6000 S2 or S4 Reagent kit (Illumina).

treatment_protocol: For in vitro stimulation: High-binding 96-well flat-bottom plates were coated with 100 μl per well of PBS + 20 μg/ml anti-NK1.1 (Clone PK136, BioLegend, cat. 108759), 20 μg/ml anti-Ly49H or none (unstimulated control) at 4 °C overnight. NK cells were cultured in IMDM (10% FBS, 1× L-glutamine, 1× sodium pyruvate, 1× BME, 1× MEM-NAA and 25 mM HEPES). To prevent antigen-receptor signaling in negative controls, we used negative enrichment. NK cells were stimulated for 6h in 96 wells coated with anti-NK1.1, anti-Ly49H or in uncoated wells.

value: Spleen

value: Total NK cells

value: wild-type


title: No.09-Ep_01

description:
Library name: DSP-1001660021516-H-G08
Control_No.09-Ep_01_1.Normal_proximal

value: lung

value: Ep


title: No.10-Alveoli_01

description:
Library name: DSP-1001660021516-H-G12
Control_No.10-Alveoli_01_1.Normal_distal

value: Alveoli

value: wild type


description: Library name: Sample_ATAC_TotalNK_Unstim_6hr_1_IGO_12002_B_11


title: BAT, Control1

description: Library name: Sample1

value: Brown adipose tissue

value: Control

value: HFD 10 weeks


title: U87 Control-INPUT_smallRNAseq

description: Library name: INPUT_U87_SE50

value: WT


title: mouse NK cells, antiNK1.1 + IL-12 stimulated with AP1inhibitor, STAT4, rep3

description: Library name: mNK_400k_STAT4_aNK11IL12AP1i_3

value: NK


title: U87 NTR mycLARP6-INPUT_longRNAseq

description: Library name: INPUT_NTR_PE150

value: Brain

value: myc-tag


title: U87 Control-INPUT_longRNAseq

description: Library name: INPUT_U87_PE150

value: Glioblastoma


title: macrophage, mfap4:mCherry positive, UNCUT, 5hpA, rep 2

value: macrophage

value: mCherryF+


title: macrophage, mfap4:mCherry positive,UNCUT, 5hpA, rep 3


title: macrophage, mfap4:mCherry positive, CUT, 5hpA, rep 3


title: ATAC_TotalNK_NK11_6hr_2_IGO_12002_B_20

description: Library name: Sample_ATAC_TotalNK_NK11_6hr_2_IGO_12002_B_20

value: Spleen


title: ATAC_TotalNK_NK11_6hr_1_IGO_12002_B_19

description: Library name: Sample_ATAC_TotalNK_NK11_6hr_1_IGO_12002_B_19

value: Total NK cells


title: U87 Full-length mycLARP6-INPUT_longRNAseq

description: Library name: INPUT_FL_PE150

value: LARP6 FL


title: ATAC_TotalNK_NK11_6hr_3_IGO_12002_B_21

description: Library name: Sample_ATAC_TotalNK_NK11_6hr_3_IGO_12002_B_21

value: wild-type


title: mouse NK cells, antiNK1.1 + IL-12 stimulated with AP1inhibitor, STAT4, rep1

description: Library name: mNK_400k_STAT4_aNK11IL12AP1i_1


title: U87 Full-length mycLARP6-INPUT_smallRNAseq

description: Library name: INPUT_FL_SE50


title: macrophage, mfap4:mCherry positive, UNCUT, 5hpA, rep 4


title: macrophage, mfap4:mCherry positive, UNCUT, 5hpA, rep 1


title: No.09-Ep_02

description:
Library name: DSP-1001660021516-H-G09
Control_No.09-Ep_02_1.Normal_proximal

value: lung

value: Ep


title: macrophage, mfap4:mCherry positive, CUT, 5hpA, rep 2


title: macrophage, mfap4:mCherry positive, CUT, 5hpA, rep 1


title: macrophage, mfap4:mCherry positive, CUT, 5hpA, rep 4


title: No.09-Alveoli_01

description:
Library name: DSP-1001660021516-H-G06
Control_No.09-Alveoli_01_1.Normal_distal

value: Alveoli

value: wild type


title: Lung_tumor_HDM_rep3

type: genomic

city: La Jolla

first: Shams

last: Al-Azzam

address: 9500 Gilman Dr

institute: University of California San Diego

description:
Infinium Mouse Methylation BeadChip v1.0
R05C02

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium Mouse Methylation BeadChip v1.0 according to the manufacturer’s protocol.

scan_protocol: BeadChips were scanned using the Illumina iScan System following the manufacturer’s recommended settings.

data_processing:
Genome-wide DNA methylation data were analyzed from Illumina Infinium raw IDAT files. Tumor and Normal tissue cohorts were analyzed separately, each comprising three biological replicates per condition (HDM, n = 3; VEH, n = 3). IDAT files were processed in R using RnBeads (v3.9) with default settings unless otherwise specified. Probes on sex chromosomes were removed, and sample identities were mapped using the Sample_ID annotation field. Data were normalized using the wm.dasen method with methylumi background correction (noob). Analyses were performed against the mm10 genome assembly using the RnBeads.mm10 annotation package. Differential methylation analyses were defined by the Treatment annotation column (HDM vs VEH), and site-level differential reports were generated. Results were exported as CSV files for tiling regions, gene bodies, promoters, and CpG islands.
Processed values represent DNA methylation beta values (ratio of methylated signal to total signal) for individual CpG probes derived from normalized Illumina Infinium array intensities. Differentially methylated sites were identified using a significance threshold of absolute beta value change ≥ 0.20 and p < 0.05. Differential methylation was summarized as counts of hyper- and hypomethylated loci across tissues and genomic feature classes, including genes, promoters, CpG islands, and tiling regions.

label: biotin

source_name: Lung

label_protocol: Genomic DNA (1 µg) was bisulfite converted and processed for DNA methylation analysis using the Infinium Mouse Methylation BeadChip Kit v1.0 (Illumina, Cat. No. 20041558) according to the manufacturer’s instructions.

growth_protocol: Not applicable. Samples were collected prior to DNA extraction; no in vitro growth was performed for this assay.

extract_protocol: Genomic DNA and total RNA were co-extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Cat. No. 80204). Tissue was homogenized with PowerTube beads (Cat. No. 13117-50) using the Omni Bead Ruptor 12 (Cat. No. 19-050A). DNA concentration was quantified using the Qubit™ 1X dsDNA HS Assay Kit (Cat. No. Q33231) on the Qubit 4 Fluorometer (Cat. No. Q33226). All DNA and RNA samples had a DNA Integrity Number (DIN) and RNA Integrity Number (RIN), respectively, greater than 6.

treatment_protocol: No additional treatment was applied prior to DNA methylation profiling.

value: Lung

tag: tissue type

value: tumor

value: HDM


title: No.09-Alveoli_02

description:
Library name: DSP-1001660021516-H-G07
Control_No.09-Alveoli_02_1.Normal_proximal


title: No.08-Ep_01

description:
Library name: DSP-1001660021516-H-G04
BO_No.08-Ep_01_1.Normal_proximal


title: ATAC_TotalNK_Ly49H_6hr_4_IGO_12002_B_18

description: Library name: Sample_ATAC_TotalNK_Ly49H_6hr_4_IGO_12002_B_18


title: No.09-Interstitium_01

description:
Library name: DSP-1001660021516-H-G10
Control_No.09-Interstitium_01_1.Normal_proximal

value: Interstitium


title: No.08-Alveoli_02

description:
Library name: DSP-1001660021516-H-G03
BO_No.08-Alveoli_02_1.Normal_distal


title: ATAC_TotalNK_Ly49H_6hr_2_IGO_12002_B_16

description: Library name: Sample_ATAC_TotalNK_Ly49H_6hr_2_IGO_12002_B_16


title: No.08-Interstitium_01

description:
Library name: DSP-1001660021516-H-G05
BO_No.08-Interstitium_01_1.Normal_proximal


title: RNA_TotalNK_Unstim_6hr_2_IGO_12001_14

description: Library name: Sample_RNA_TotalNK_Unstim_6hr_2_IGO_12001_14


title: macrophage, mfap4:mCherry positive, UNCUT, 2hpA, rep 4


title: No.08-Alveoli_01

description:
Library name: DSP-1001660021516-H-G02
BO_No.08-Alveoli_01_1.Normal_distal


title: macrophage, mfap4:mCherry positive, UNCUT, 2hpA,  rep 1


title: No.07-Alveoli_04

description:
Library name: DSP-1001660021516-H-G01
BO_No.07-Alveoli_04_1.Normal_distal


title: ATAC_TotalNK_Ly49H_6hr_1_IGO_12002_B_15

description: Library name: Sample_ATAC_TotalNK_Ly49H_6hr_1_IGO_12002_B_15


title: RNA_TotalNK_NK11_6hr_2_IGO_12001_18

description: Library name: Sample_RNA_TotalNK_NK11_6hr_2_IGO_12001_18


title: Lung_normal_HDM_rep1

description:
Infinium Mouse Methylation BeadChip v1.0
R02C02

value: normal

value: WT


title: RNA_TotalNK_NK11_6hr_3_IGO_12001_19

description: Library name: Sample_RNA_TotalNK_NK11_6hr_3_IGO_12001_19


title: No.07-Alveoli_03

description:
Library name: DSP-1001660021516-H-F12
BO_No.07-Alveoli_03_1.Normal_distal


title: Lung_normal_HDM_rep2

description:
Infinium Mouse Methylation BeadChip v1.0
R04C02


title: macrophage, mfap4:mCherry positive, UNCUT, 2hpA, rep 2


title: macrophage, mfap4:mCherry positive, UNCUT, 2hpA, rep 3


title: RNA_TotalNK_Unstim_6hr_1_IGO_12001_13

description: Library name: Sample_RNA_TotalNK_Unstim_6hr_1_IGO_12001_13


title: Lung_normal_HDM_rep3

description:
Infinium Mouse Methylation BeadChip v1.0
R06C02


title: macrophage, mfap4:mCherry positive, CUT, 2hpA,  rep 3


title: macrophage, mfap4:mCherry positive, CUT, 2hpA,  rep 4


title: No.07-Alveoli_01

description:
Library name: DSP-1001660021516-H-F10
BO_No.07-Alveoli_01_1.Normal_distal


title: No.06-Vessels_01

description:
Library name: DSP-1001660021516-H-F09
BO_No.06-Vessels_01_3.Middle_distal

value: Vessels


title: No.07-Alveoli_02

description:
Library name: DSP-1001660021516-H-F11
BO_No.07-Alveoli_02_1.Normal_distal


title: Lung_tumor_HDM_rep2

description:
Infinium Mouse Methylation BeadChip v1.0
R03C02


title: macrophage, mfap4:mCherry positive, CUT, 2hpA, rep 2

value: macrophage


title: RNA_TotalNK_NK11_6hr_1_IGO_12001_17

description: Library name: Sample_RNA_TotalNK_NK11_6hr_1_IGO_12001_17


title: RNA_TotalNK_Ly49H_6hr_2_IGO_12001_22

description: Library name: Sample_RNA_TotalNK_Ly49H_6hr_2_IGO_12001_22


title: Thal 3month KO Mouse 99_3

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: Library name: samp99_3_Thal_C7_S62

data_processing:
Raw fastq files were processed with our pipeline at https://github.com/seanken/BulkIsoform/tree/main/Pipeline. Most notably the data was processed with Salmon to get expression information. This expression information was loaded into R with tximport and processed with DESeq2 for downstream processing.
Assembly: mm10
Supplementary files format and content: The processed files are tab seperated files, as produced from Salmon, with each row corresponding to a transcript, columns with information about expression. See the Salmon documentatiomn for more details

growth_protocol: brains from 18d and 3mo old male GPR34 KO or Wt C57BL6J mice were microdisected by brain region

extract_protocol:
Each brain region from each animal was then separately prepared for bulk RNA sequencing. RNA was isolated from tissues using the Qiagen RNeasy Mini Kit per manufacturer’s instructions.
. Bulk sequencing libraries were prepared using Illumina TruSeq Stranded mRNA Kit (Catalog #20020595) per manufacturer’s instructions. 300 ng of total RNA from each sample was used and the concentration of resulting cDNA library was measured with High Sensitivity DNA chips (Agilent) using a 2100 Bioanalyzer Instrument (Agilent). A 5 nM normalized library was pooled, and sequencing was performed on a NovaSeq X 25B (Illumina) with 50 bases each for reads 1 and 2 and 8 bases each for index reads 1 and 2. The depth of sequencing for each individual library ranged from 30.5 million to 645 million before downsampling, with a median of 49 million reads.

treatment_protocol: No additional treaments were administered

value: Brain

value: KO

tag: brain region

value: Thal

tag: age

tag: mouse

value: Single Batch


title: No.06-FoamCells_03

description:
Library name: DSP-1001660021516-H-F08
BO_No.06-FoamCells_03_3.Middle_inside

tag: tissue


title: hTECs treated with Ad-RORγ replicate 2

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

description:
Library name: Sample 5
HKR2

data_processing:
The raw sequencing data were processed using the SMRT Analysis software suite (IsoSeq v4.0). The core analysis steps were as follows: (1) Full-length read identification: Circular Consensus Sequencing (CCS) reads were generated, and the lima tool was used to identify full-length reads based on primer sequences. (2) Refinement: Full-length non-concatemer (FLNC) reads were obtained by removing polyA tails and concatemer sequences using the refine step. (3) Clustering and polishing: Redundant FLNC reads were iteratively clustered using the isoseq cluster algorithm, and high-quality consensus sequences were generated. (4) Quantification: The obtained consensus transcripts were quantified to generate an expression count matrix for all samples.
Assembly: The analysis for this human transcriptome study was conducted using the GRCh38 (hg38) reference genome assembly from the National Center for Biotechnology Information (NCBI). All identified transcript isoforms can be mapped and traced to this assembly. If a specific patch version (e.g., GRCh38.p13) was used, it is indicated in the relevant analysis files.
Supplementary files format and content: The processed data for this Iso-Seq study is provided as a tab-delimited text matrix file. This file contains the quantitative expression data used for downstream analyses. Each row represents a feature—specifically, a high-quality consensus transcript isoform identified by the IsoSeq pipeline. Each column represents a sequenced biological sample, with column headers corresponding to the sample/library names. The cell values contain the raw read counts (or, if applicable, normalized values such as TPM) quantifying the abundance of each transcript in each sample. This matrix provides the complete expression profile for all detected transcript isoforms across all samples, as required for repository submission.

source_name: Kidney

extract_protocol:
Sample QC of input Total RNA samples assessed by measuring the RNA Integrity Number (RIN) and concentration using a Agilent 2100 instrument. RNA purity and contamination can be assessed through UV-spectrophotometry using a Nanodrop spectrophotometer.
A total amount of 2 μg RNA was used as input material for the RNA sample preparation. Use the NEBNext®Single Cell/Low Input cDNA Synthesis & Amplification Module and PacBio Iso-Seq Express Oligo Kit to perform first-strand cDNA synthesis (reverse transcription and template switching) and PCR amplification. SMRTbellTM Template Prep Kit was used to generate SMRTbellTM libraries by following to the processes of DNA Damage repair, end-repair, A-tailing and adaptor ligation. library quality was assessed on the Agilent Bioanalyzer 2100 system. At last，Binding the primers and enzyme to the SMRT template to form a complete SMRT bell library.

value: Kidney

tag: cell line

value: Human renal tubular epithelial cells

value: transfected with Ad-RORγ


title: mouse OT-1 CD8+ T cells, SIIQFEHL stimulated, cJUN, rep2

description: Library name: CD8_400k_cJun_Q4H7_2

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie 2 (v2.4.1).
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as a control using narrow peak parameters with cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
The peak atlas was generated by merging via union of peaks called by each sample after filtering out bottom 25% of peaks by MACS2 calculated qValue. Resulting peak atlas was further filtered to only retain peaks that were called by two or more replicates within each sample group, as well as peaks that do not overlap the Encode’s DAC Exclusion List Regions (ENCFF547MET).
Assembly: mm10
Supplementary files format and content: bigwig files are unscaled pileups of reads aligned to the reference genome
Supplementary files format and content: tsv file is tab delimited table of peak atlas
Library strategy: CUT&Run

extract_protocol:
Following CUT&RUN preparation, DNA was extracted using the Qiagen MinElute Kit.
For library preparation, we used the KAPA Hyper Prep Kit and followed the kit's instructions. Amplification cycle number was determined by running qPCR after 5 cycles of pre-amplification and assessing required additional cycles using qPCR.

treatment_protocol: NK cells were stimulated with aNK1.1 for 3h (or unstimulated as control), sorted, and stimulated for 1h with IL-12. OT-1 CD8+ T cells were stimulated with the respective peptide ((presented by splenocytes) for 3h.

tag: cell type

value: cJun


title: Lung_normal_VEH_rep2

description:
Infinium Mouse Methylation BeadChip v1.0
R04C01

tag: genotype

value: VEH


title: No.06-FoamCells_01

description:
Library name: DSP-1001660021516-H-F06
BO_No.06-FoamCells_01_3.Middle_inside

value: lung

value: wild type


title: RNA_TotalNK_Ly49H_6hr_1_IGO_12001_21

description: Library name: Sample_RNA_TotalNK_Ly49H_6hr_1_IGO_12001_21

value: Spleen

value: Total NK cells

value: wild-type


title: No.06-FoamCells_02

description:
Library name: DSP-1001660021516-H-F07
BO_No.06-FoamCells_02_3.Middle_inside


title: Hind 3month KO Mouse 99_3

description: Library name: samp99_3_Hind_E10_S61

value: Hind


title: macrophage, mfap4:mCherry positive, CUT, 2hpA, rep 1

value: mCherryF+


title: Lung_tumor_VEH_rep1

description:
Infinium Mouse Methylation BeadChip v1.0
R01C01

value: Lung

value: tumor

value: WT


title: hTECs treated with Ad-RORγ replicate 3

description:
Library name: Sample 6
HKR3


title: RNA_TotalNK_Ly49H_6hr_3_IGO_12001_23

description: Library name: Sample_RNA_TotalNK_Ly49H_6hr_3_IGO_12001_23


title: Lung_tumor_HDM_rep1

description:
Infinium Mouse Methylation BeadChip v1.0
R01C02

value: HDM


title: No.05-FoamCells_02 (F05)

description:
Library name: DSP-1001660021516-H-F05
BO_No.05-FoamCells_02_4.Late_inside


title: Lung_tumor_VEH_rep2

description:
Infinium Mouse Methylation BeadChip v1.0
R03C01


title: Thal 3month KO Mouse 99_2

description: Library name: samp99_2_Thal_C6_S60

value: Brain

value: KO

value: Thal

value: Single Batch


title: mouse OT-1 CD8+ T cells, SIIQFEHL stimulated, cJUN, rep1

description: Library name: CD8_400k_cJun_Q4H7_1

tag: antibody

value: cJun


title: Lung_tumor_VEH_rep3

description:
Infinium Mouse Methylation BeadChip v1.0
R05C01

value: VEH


title: hTECs treated with Ad-RORγ replicate 1

description:
Library name: Sample 4
HKR1

value: Kidney

value: Human renal tubular epithelial cells

value: transfected with Ad-RORγ


title: hTECs treated with Ad-null replicate 3

description:
Library name: Sample 3
HK3

value: transfected with Ad-null


title: Hind 3month KO Mouse 99_2

description: Library name: samp99_2_Hind_E9_S59


title: Hind 3month KO Mouse 99_1

description: Library name: samp99_1_Hind_E8_S57


title: No.05-FoamCells_01 (F04)

description:
Library name: DSP-1001660021516-H-F04
BO_No.05-FoamCells_01_4.Late_inside

value: lung

value: wild type


title: Thal 3month KO Mouse 99_1

description: Library name: samp99_1_Thal_C5_S58


title: mouse NK cells, cJun, unstimulated, rep3

description: Library name: NK_300k_Jun69A8_unstim_3

value: NK

value: unstim

tag: replicate


title: Lung_normal_VEH_rep1

description:
Infinium Mouse Methylation BeadChip v1.0
R02C01

value: Lung

value: normal

tag: treatment


title: mouse OT-1 CD8+ T cells, SIINFEKL stimulated, cJUN, rep1

description: Library name: CD8_400k_cJun_N4_1


title: U251 LOXL3-KD cell biol rep 4

city: São Paulo

first: Talita

middle: Sousa

last: Laurentino

address: Av Dr Arnaldo, 455. Room 4110

department: Neurologia

institute: Faculdade de Medicina da Universidade de S&#x00E3

description:
Library name: 8D
Column name in raw_counts_U251_Samples.txt: LOXL3KD

data_processing:
TapeStation 4200 (Agilent Technologies) with a D1000 ScreenTape was utilized to determine the size distribution of individual libraries
Pooled DNA libraries underwent sequencing on a NextSeq 500 (Illumina)
STAR software was used to align raw reads to hg38.
Gene expression data quantification was performed using featureCounts software. The trimmed mean method in edgeR software was applied for data normalization.
Expression levels were calculated as counts per million (CPM).The limma framework was applied for differential expression analysis among groups and log2-CPM data transformation
Assembly: HG38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample Groups (U87MG and U251)

source_name: brain

growth_protocol: Glioblastoma cells were maintened in DMEM supplemented with 10% fetal bovine serum (FBS), and antibiotics in humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA-seq libraries were prepared using QuantSeq 3’mRNA-Seq Library Prep Kit-FWD for Illumina (Lexogen). Libraries were constructed in quadruplicate using 500 ng of total RNA from each sample, parental, control empty vetor and LOXL3-KD cells.

treatment_protocol: The knockdown was performed by CRISPR-Cas9

value: brain

value: glioblastoma

value: LOXL3 KNOCKDOWN


title: mouse OT-1 CD8+ T cells, SIINFEKL stimulated, cJUN, rep2

description: Library name: CD8_400k_cJun_N4_2


title: No.05,06-Ep_03

description:
Library name: DSP-1001660021516-H-F03
BO_No.05,06-Ep_03_1.Normal_proximal

value: Ep


title: Hipp 18day KO Mouse 89_6

description: Library name: samp89_6_Hipp_H1_S55

value: Brain

value: KO

value: Hipp

value: Single Batch


title: mouse NK cells, cJun, unstimulated, rep2

description: Library name: NK_250k_cJun_unstim_2

value: cJun


title: No.05,06-Ep_01

description:
Library name: DSP-1001660021516-H-F01
BO_No.05,06-Ep_01_1.Normal_proximal


title: No.05,06-Alveoli_04

description:
Library name: DSP-1001660021516-H-E12
BO_No.05,06-Alveoli_04_1.Normal_distal

value: Alveoli


title: Thal 18day KO Mouse 89_6

description: Library name: samp89_6_Thal_B12_S56

value: Thal


title: hTECs treated with Ad-null replicate 2

description:
Library name: Sample 2
HK2

value: Kidney

value: Human renal tubular epithelial cells

value: transfected with Ad-null


title: No.05,06-Ep_02

description:
Library name: DSP-1001660021516-H-F02
BO_No.05,06-Ep_02_1.Normal_proximal

value: lung

value: wild type


title: mouse NK cells, cJun, antiNK1.1 stimulated, rep3

description: Library name: NK_300k_Jun69A8_aNK11_3

value: NK


title: U251 LOXL3-KD cell biol rep 3

description:
Library name: 8C
Column name in raw_counts_U251_Samples.txt: LOXL3KD

value: brain


title: Hind 18day KO Mouse 89_6

description: Library name: samp89_6_Hind_E5_S54

value: Hind


title: hTECs treated with Ad-null replicate 1

description:
Library name: Sample 1
HK1


title: mouse NK cells, cJun, antiNK1.1 stimulated, rep2

description: Library name: NK_250k_cJun_aNK11_2


title: Lung_normal_VEH_rep3

description:
Infinium Mouse Methylation BeadChip v1.0
R06C01

value: Lung

value: normal

value: WT

value: VEH


title: U251 empty vector cell biol rep 4

description:
Library name: 6D
Column name in raw_counts_U251_Samples.txt: Empty vector

value: glioblastoma

value: CRISPR-Cas9 empty vector


title: U251 LOXL3-KD cell biol rep 2

description:
Library name: 8B
Column name in raw_counts_U251_Samples.txt: LOXL3KD

value: LOXL3 KNOCKDOWN


title: Hipp 18day KO Mouse 89_12

description: Library name: samp89_12_Hipp_H3_S52

value: Brain

value: KO

value: Hipp

value: Single Batch


title: No.05,06-Alveoli_02

description:
Library name: DSP-1001660021516-H-E10
BO_No.05,06-Alveoli_02_1.Normal_distal

value: Alveoli


title: U251 LOXL3-KD cell biol rep 1

description:
Library name: 8A
Column name in raw_counts_U251_Samples.txt: LOXL3KD


title: U251 empty vector cell biol rep 3

description:
Library name: 6C
Column name in raw_counts_U251_Samples.txt: Empty vector


title: Hind 18day KO Mouse 89_12

description: Library name: samp89_12_Hind_E7_S51


title: mouse NK cells, cJun, unstimulated, rep1

description: Library name: NK_250k_cJun_unstim_1

value: cJun

value: unstim


title: Thal 18day KO Mouse 89_12

description: Library name: samp89_12_Thal_C2_S53

value: Thal


title: mouse NK cells, STAT5, unstimulated, rep1

description: Library name: NK_250k_STAT5_unstim_1

value: NK


title: U251 empty vector cell biol rep 1

description:
Library name: 6A
Column name in raw_counts_U251_Samples.txt: Empty vector

value: brain


title: mouse NK cells, STAT5, antiNK1.1 stimulated, rep1

description: Library name: NK_250k_STAT5_aNK11_1


title: mouse NK cells, cJun, antiNK1.1 stimulated, rep1

description: Library name: NK_250k_cJun_aNK11_1


title: U251 parental cell  biol rep 4

description:
Library name: 5D
Column name in raw_counts_U251_Samples.txt: PARENTAL

value: PARENTAL


title: No.05,06-Alveoli_01

description:
Library name: DSP-1001660021516-H-E09
BO_No.05,06-Alveoli_01_1.Normal_distal

value: lung

value: wild type


title: U251 empty vector cell biol rep 2

description:
Library name: 6B
Column name in raw_counts_U251_Samples.txt: Empty vector

value: WT


title: mouse NK cells, STAT5, antiNK1.1 stimulated, rep2

description: Library name: NK_250k_STAT5_aNK11_2


title: Thal 18day KO Mouse 89_11

description: Library name: samp89_11_Thal_C1_S50


title: mouse NK cells, STAT1, unstimulated, rep2

description: Library name: NK_250k_STAT1_unstim_2


title: mouse NK cells, STAT5, unstimulated, rep2

description: Library name: NK_250k_STAT5_unstim_2


title: No.05-FoamCells_02 (E08)

description:
Library name: DSP-1001660021516-H-E08
BO_No.05-FoamCells_02_3.Middle_inside


title: Hipp 18day KO Mouse 89_11

description: Library name: samp89_11_Hipp_H2_S49


title: No.05-FoamCells_01 (E07)

description:
Library name: DSP-1001660021516-H-E07
BO_No.05-FoamCells_01_3.Middle_inside


title: Thal 18day WT Mouse 88_9

description: Library name: samp88_9_Thal_B9_S47


title: No.05-FormCells-02

description:
Library name: DSP-1001660021516-H-E05
BO_No.05-FormCells-02_4.Late_outside


title: No.05-FormCells-03

description:
Library name: DSP-1001660021516-H-E06
BO_No.05-FormCells-03_4.Late_outside


title: mouse NK cells, STAT1, unstimulated, rep1

description: Library name: NK_250k_STAT1_unstim_1


title: Hipp 18day WT Mouse 88_9

description: Library name: samp88_9_Hipp_G10_S46


title: U251 parental cell  biol rep 3

description:
Library name: 5C
Column name in raw_counts_U251_Samples.txt: PARENTAL

value: glioblastoma


title: Hind 18day KO Mouse 89_11

description: Library name: samp89_11_Hind_E6_S48

value: Hind


title: U251 parental cell  biol rep 2

description:
Library name: 5B
Column name in raw_counts_U251_Samples.txt: PARENTAL


title: No.05-FoamCells_02 (E03)

description:
Library name: DSP-1001660021516-H-E03
BO_No.05-FoamCells_02_3.Middle_outside


title: mouse NK cells, STAT1, antiNK1.1 stimulated, rep1

description: Library name: NK_250k_STAT1_aNK11_1


title: Hind 18day WT Mouse 88_9

description: Library name: samp88_9_Hind_E1_S45


title: U251 parental cell  biol rep 1

description:
Library name: 5A
Column name in raw_counts_U251_Samples.txt: PARENTAL


title: mouse NK cells, STAT1, antiNK1.1 stimulated, rep2

description: Library name: NK_250k_STAT1_aNK11_2


title: No.05-FormCells-01

description:
Library name: DSP-1001660021516-H-E04
BO_No.05-FormCells-01_4.Late_outside


title: No.05-FoamCells_01 (E02)

description:
Library name: DSP-1001660021516-H-E02
BO_No.05-FoamCells_01_3.Middle_inside


title: No.04-Vessels_02

description:
Library name: DSP-1001660021516-H-E01
BO_No.04-Vessels_02_2.Early_distal

value: Vessels


title: U87MG LOXL3-KD cell biol rep 3

description:
Library name: 3C
Column name in raw_counts_U87MG_Samples.txt: LOXL3KD

value: LOXL3 KNOCKDOWN


title: U87MG LOXL3-KD cell biol rep 4

description:
Library name: 3D
Column name in raw_counts_U87MG_Samples.txt: LOXL3KD


title: mouse NK cells, unstimulated, rep4

description: Library name: NK_25k_unstim_4

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie 2 (v2.4.1) corrected for Tn5.
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as a control using narrow peak parameters with cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
Reproducible peaks showing an IDR value of 0.05 or less in each condition were retained, aggregated across the experiment and merged via union generate the final atlas, and annotated with the UCSC Known Gene model. Reads were mapped to the final atlas and counted with the summarizeOverlaps function from the GenomicAlignment package (v1.34.1).
Assembly: mm10
Supplementary files format and content: bigwig files are unscaled pileups of reads aligned to the reference genome
Supplementary files format and content: tsv file is tab delimited table of peak atlas

extract_protocol:
ATAC-seq was performed as described previously. Briefly, sorted, stimulated cells were washed in cold PBS and lysed. The transposition reaction was incubated at 37 °C for 30 min. DNA was cleaned with the MinElute PCR Purification kit (QIAGEN, cat. 28004).
DNA materials were amplified and the final product was cleaned by AMPure XP beads (Beckman Coulter catalog no. A63882) at a 1× ratio, and size selection was performed at a 0.5× ratio. Libraries were sequenced on a NovaSeq6000 in a 100 bp/100 bp paired-end run, using the NovaSeq6000 S2 or S4 Reagent kit (Illumina).

treatment_protocol: NK cells were stimulated with AP1i for 1h and aNK1.1 for 3h (or unstimulated as control), sorted and subjected to transposase reaction and library amplification as described in the manuscript.


title: mouse NK cells, unstimulated, rep2

description: Library name: NK_25k_unstim_2


title: Thal 18day WT Mouse 88_8

description: Library name: samp88_8_Thal_B8_S44

value: Brain


title: Thal 18day KO Mouse 88_7

description: Library name: samp88_7_Thal_B7_S41

value: KO


title: Hind 18day WT Mouse 88_8

description: Library name: samp88_8_Hind_D12_S42

value: Single Batch


title: U87MG empty vector cell biol rep 4

description:
Library name: 2D
Column name in raw_counts_U87MG_Samples.txt: Empty vector

value: CRISPR-Cas9 empty vector


title: Hind 18day KO Mouse 88_7

description: Library name: samp88_7_Hind_D11_S39


title: No.04-Interstitium_02

description:
Library name: DSP-1001660021516-H-D11
BO_No.04-Interstitium_02_2.Early_proximal

value: Interstitium


title: mouse NK cells, unstimulated, rep3

description: Library name: NK_25k_unstim_3

value: unstim


title: U87MG LOXL3-KD cell biol rep 2

description:
Library name: 3B
Column name in raw_counts_U87MG_Samples.txt: LOXL3KD


title: No.04-FoamCells_11

description:
Library name: DSP-1001660021516-H-D09
BO_No.04-FoamCells_11_3.Middle_outside


title: U87MG LOXL3-KD cell biol rep 1

description:
Library name: 3A
Column name in raw_counts_U87MG_Samples.txt: LOXL3KD


title: No.04-Interstitium_01

description:
Library name: DSP-1001660021516-H-D10
BO_No.04-Interstitium_01_2.Early_proximal


title: Hipp 18day WT Mouse 88_8

description: Library name: samp88_8_Hipp_G9_S43

value: Hipp


title: No.04-FoamCells_10

description:
Library name: DSP-1001660021516-H-D08
BO_No.04-FoamCells_10_3.Middle_outside


title: mouse NK cells, unstimulated, rep1

description: Library name: NK_25k_unstim_1

value: NK


title: mouse NK cells, AP1i stimulated, rep4

description: Library name: NK_25k_AP1i_4


title: U87MG empty vector cell biol rep 2

description:
Library name: 2B
Column name in raw_counts_U87MG_Samples.txt: Empty vector

value: brain


title: No.05,06-Alveoli_03

description:
Library name: DSP-1001660021516-H-E11
BO_No.05,06-Alveoli_03_1.Normal_distal

value: Alveoli


title: No.04-Vessels_01

description:
Library name: DSP-1001660021516-H-D12
BO_No.04-Vessels_01_2.Early_proximal

value: lung


title: mouse NK cells, AP1i stimulated, rep3

description: Library name: NK_25k_AP1i_3


title: mouse NK cells, AP1i stimulated, rep1

description: Library name: NK_25k_AP1i_1


title: Hind 18day WT Mouse 88_6

description: Library name: samp88_6_Hind_D10_S36


title: No.04-FoamCells_07

description:
Library name: DSP-1001660021516-H-D05
BO_No.04-FoamCells_07_3.Middle_outside

value: wild type


title: mouse NK cells, antiNK1.1 + AP1i stimulated, rep4

description: Library name: NK_25k_aNK11AP1i_4


title: U87MG empty vector cell biol rep 3

description:
Library name: 2C
Column name in raw_counts_U87MG_Samples.txt: Empty vector

value: WT


title: U87MG empty vector cell biol rep 1

description:
Library name: 2A
Column name in raw_counts_U87MG_Samples.txt: Empty vector

value: glioblastoma


title: U87MG parental cell  biol rep 3

description:
Library name: 1C
Column name in raw_counts_U87MG_Samples.txt: PARENTAL

value: PARENTAL


title: Thal 18day WT Mouse 88_6

description: Library name: samp88_6_Thal_B6_S38

value: Thal


title: No.04-FoamCells_09

description:
Library name: DSP-1001660021516-H-D07
BO_No.04-FoamCells_09_3.Middle_outside


title: mouse NK cells, AP1i stimulated, rep2

description: Library name: NK_25k_AP1i_2


title: No.04-FoamCells_06

description:
Library name: DSP-1001660021516-H-D04
BO_No.04-FoamCells_06_3.Middle_outside


title: Hipp 18day KO Mouse 88_7

description: Library name: samp88_7_Hipp_G8_S40


title: Hipp 18day WT Mouse 88_6

description: Library name: samp88_6_Hipp_G7_S37


title: Hipp 18day KO Mouse 88_5

description: Library name: samp88_5_Hipp_G6_S34


title: U87MG parental cell  biol rep 4

description:
Library name: 1D
Column name in raw_counts_U87MG_Samples.txt: PARENTAL


title: mouse NK cells, antiNK1.1 + AP1i stimulated, rep1

description: Library name: NK_25k_aNK11AP1i_1


title: Hind 18day KO Mouse 88_5

description: Library name: samp88_5_Hind_D9_S33

value: Hind


title: No.04-FoamCells_08

description:
Library name: DSP-1001660021516-H-D06
BO_No.04-FoamCells_08_2.Early_inside


title: mouse NK cells, antiNK1.1 + AP1i stimulated, rep2

description: Library name: NK_25k_aNK11AP1i_2


title: No.04-FoamCells_05

description:
Library name: DSP-1001660021516-H-D03
BO_No.04-FoamCells_05_3.Middle_outside


title: U87MG parental cell  biol rep 2

description:
Library name: 1B
Column name in raw_counts_U87MG_Samples.txt: PARENTAL


title: No.04-FoamCells_03

description:
Library name: DSP-1001660021516-H-D01
BO_No.04-FoamCells_03_2.Early_inside


title: Thal 18day KO Mouse 88_5

description: Library name: samp88_5_Thal_B5_S35

value: Brain


title: mouse NK cells, antiNK1.1 + AP1i stimulated, rep3

description: Library name: NK_25k_aNK11AP1i_3


title: No.04-FoamCells_02

description:
Library name: DSP-1001660021516-H-C12
BO_No.04-FoamCells_02_2.Early_inside


title: U87MG parental cell  biol rep 1

description:
Library name: 1A
Column name in raw_counts_U87MG_Samples.txt: PARENTAL


title: mouse NK cells, antiNK1.1 stimulated, rep4

description: Library name: NK_25k_aNK11_4


title: Rep3_DeltaNTR_scr_protrusion

description:
Library name: Quantseq_Sample_35
column names in the processed file are the same as sample titles

data_processing:
The demultiplexed fastq reads were uploaded on the Lexogen Data Analysis Solution, which allowed the automated pre-processing of the data. Adapters were trimmed and low-quality reads removed using Cutadapt (V1.18) (software developed by Marcel Martin). Trimmed reads were aligned to the human genome (GRCh38, Ensembl release 107) with STAR (V2.6.1a)25. Gene counting was performed with FeatureCounts (V1.6.4)26 and only uniquely mapped reads were considered.
Assembly: human genome (GRCh38, Ensembl release 107)
Supplementary files format and content: txt

extract_protocol:
RNA was extracted from each sample using TRIzol LS, according to the manufacturer’s instructions. The total RNA concentration was measured with the Qubit RNA High-sensitivity assay (Invitrogen) on a Qubit 4 Fluorometer (Invitrogen). The quality of the RNA was validated with the Agilent High Sensitivity RNA ScreenTape assay at an Agilent TapeStation 4000 instrument, with all samples having a quality score RIN ≥ 9.1. Library preparation was performed with the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices according to the manufacturer’s instructions. Each replicate was processed individually to avoid batch effect. 330 ng total RNA in 5 μL volume was used as input. The amplified libraries were quantified and validated with the Qubit dsDNA High-sensitivity and Agilent D1000 high sensitivity ScreenTape assays, pooled in an equimolar ratio, and deep sequenced on an Illumina NextSeq 2000 instrument, using a single-end 100 nt reverse complement workflow. Sequencing was performed at the Barts and The London Genome Centre.
Library preparation was performed with the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices according to the manufacturer’s instructions. Each replicate was processed individually. 330 ng total RNA in 5 μL volume was used as input. The amplified libraries were quantified and validated with the Qubit dsDNA High-sensitivity and Agilent D1000 high sensitivity ScreenTape assays, pooled in an equimolar ratio, and deep sequenced on an Illumina NextSeq 2000 instrument, using a single-end 100 nt reverse complement workflow. Sequencing was performed at the Barts and The London Genome Centre, Queen Mary University of London.

treatment_protocol: To induce FL or deltaNTR myc-LARP6, cells were treated with 60ng/mL of doxycycline. Cells were subsequently seeded in tissue culture plates 24 hours before transfection. An siRNA selectively targeting the 3’UTR of endogenous LARP6, but not the myc-LARP6 mutants (si3UTR), and a non-targeting scrambled siRNA control (scr) were then transfected into the cells with lipofectamine RNAiMAX (Thermo Fisher), following the manufacturer’s protocol, using a final siRNA concentration of 40 nM. Cells were split or harvested 72 hours post-transfection for transwell protrusion analyses. Briefly, each treated cell-line was seeded onto10 cm polycarbonate membrane transwell filters with 3 μm pores (Costar, catalogue number 3420) pre-coated on both the top and bottom side with collagen I (PureCol, 3 mg/mL, diluted in water 1:30; Coating was performed ON at 4°C, followed by complete transwell drying). Media was then added to the bottom chamber and cells were incubated in the 37°C humidified incubator for 90 minutes to form protrusions through the pores. The protrusions that formed on the bottom side of the filters were then separated from the cell bodies at the top of the filters by shaving using a glass cover slip, and the two fractions were collected in 4% SDS buffer (100 mM Tris-HCl pH 7.5, 4% SDS, RNase-free).

value: U-87 MG

value: Glioblastoma

value: deltaNTR myc-LARP6

value: scrambled siRNA

value: protrusions


title: Hipp 18day KO Mouse 88_2

description: Library name: samp88_2_Hipp_G5_S31

value: KO

value: Hipp

value: Single Batch


title: Hind 18day KO Mouse 88_2

description: Library name: samp88_2_Hind_D8_S30


title: mouse NK cells, antiNK1.1 stimulated, rep3

description: Library name: NK_25k_aNK11_3

value: NK


title: Thal 18day KO Mouse 88_2

description: Library name: samp88_2_Thal_B4_S32


title: mouse NK cells, antiNK1.1 stimulated, rep2

description: Library name: NK_25k_aNK11_2


title: Rep3_DeltaNTR_si3_protrusion

description:
Library name: Quantseq_Sample_36
column names in the processed file are the same as sample titles

value: LARP6 3'UTR siRNA


title: No.04-FoamCells_01

description:
Library name: DSP-1001660021516-H-C11
BO_No.04-FoamCells_01_3.Middle_inside

value: lung

value: wild type


title: Rep3_DeltaNTR_si3_body

description:
Library name: Quantseq_Sample_34
column names in the processed file are the same as sample titles

value: cell-body


title: No.04-FoamCells_04

description:
Library name: DSP-1001660021516-H-D02
BO_No.04-FoamCells_04_2.Early_inside


title: mouse NK cells, antiNK1.1 stimulated, rep1

description: Library name: NK_25k_aNK11_1


title: No.04-Ep_02

description:
Library name: DSP-1001660021516-H-C10
BO_No.04-Ep_02_2.Early_proximal

value: Ep


title: Rep3_FL_si3_protrusion

description:
Library name: Quantseq_Sample_32
column names in the processed file are the same as sample titles

value: FL myc-LARP6


title: Thal 18day WT Mouse 88_1

description: Library name: samp88_1_Thal_B3_S29

value: WT

value: Thal


title: Rep3_DeltaNTR_scr_body

description:
Library name: Quantseq_Sample_33
column names in the processed file are the same as sample titles

value: Brain

value: U-87 MG


title: No.04-Ep_01

description:
Library name: DSP-1001660021516-H-C09
BO_No.04-Ep_01_3.Middle_proximal


title: Rep3_FL_scr_protrusion

description:
Library name: Quantseq_Sample_31
column names in the processed file are the same as sample titles

value: Glioblastoma


title: SGLT2i_UTI_15

city: Bonn

first: Georg

last: Sendtner

address: Venusberg Campus 1a

department: Medical Clinic 1, Nephrology Section

country: Germany

institute: University Hospital Bonn

description: Library name: DE78NGSUKBR131950_1

data_processing:
Adapter trimming was performed using Cutadapt, and reads were aligned to the mouse reference genome (GRCm38) with STAR. Gene-level read counts were obtained with featureCounts using Ensembl annotations.
Assembly: GRCh38
Supplementary files format and content: csv file contains raw_counts for each sample

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 3'mRNA Library Prep Kit

treatment_protocol: Female C57BL/6J mice were treated with 20 mg/L empagliflozin or control for three days prior to urethral infection with uropathogenic E. coli strain 536.

value: Kidney

value: 20 mg/L empagliflozin

tag: strain

tag: Sex

value: Female


title: Thal 18day WT Mouse 88_11

description: Library name: samp88_11_Thal_B11_S26

tag: batch


title: No.03-Vessels_01

description:
Library name: DSP-1001660021516-H-C07
BO_No.03-Vessels_01_3.Middle_distal

value: Vessels


title: Hind 18day WT Mouse 88_1

description: Library name: samp88_1_Hind_D7_S27

value: Hind

value: Single Batch


title: SGLT2i_UTI_13

description: Library name: DE35NGSUKBR131948_1


title: SGLT2_UTI_14

description: Library name: DE08NGSUKBR131949_1


title: Rep3_FL_scr_body

description:
Library name: Quantseq_Sample_29
column names in the processed file are the same as sample titles

value: scrambled siRNA


title: No.03-Vessels_02

description:
Library name: DSP-1001660021516-H-C08
BO_No.03-Vessels_02_3.Middle_proximal

value: lung


title: Hipp 18day WT Mouse 88_11

description: Library name: samp88_11_Hipp_G12_S25

value: Hipp


title: Hind 18day WT Mouse 88_11

description: Library name: samp88_11_Hind_E4_S24


title: SGLT2i_UTI_12

description: Library name: DE62NGSUKBR131947_1


title: Rep3_U87_si3_protrusion

description:
Library name: Quantseq_Sample_28
column names in the processed file are the same as sample titles

value: Wild-type

value: LARP6 3'UTR siRNA

value: protrusions


title: Hipp 18day WT Mouse 88_1

description: Library name: samp88_1_Hipp_G4_S28

value: WT


title: SGLT2i_UTI_11

description: Library name: DE89NGSUKBR131946_1


title: No.03-Interstitium_01

description:
Library name: DSP-1001660021516-H-C05
BO_No.03-Interstitium(CD68-)_01_3.Middle_proximal

value: Interstitium

value: wild type


title: Rep3_U87_si3_body

description:
Library name: Quantseq_Sample_26
column names in the processed file are the same as sample titles

value: Brain

value: U-87 MG

value: cell-body


title: No.03-FoamCells_04

description:
Library name: DSP-1001660021516-H-C04
BO_No.03-FoamCells_04_3.Middle_outside


title: Rep3_FL_si3_body

description:
Library name: Quantseq_Sample_30
column names in the processed file are the same as sample titles

value: Glioblastoma

value: FL myc-LARP6


title: Hipp 18day KO Mouse 88_10

description: Library name: samp88_10_Hipp_G11_S22

value: KO


title: No.03-FoamCells_03

description:
Library name: DSP-1001660021516-H-C03
BO_No.03-FoamCells_03_3.Middle_inside


title: SGLT2i_UTI_10

description: Library name: DE19NGSUKBR131945_1

value: Kidney

value: 20 mg/L empagliflozin

value: Female


title: No.03-FoamCells_01

description:
Library name: DSP-1001660021516-H-C01
BO_No.03-FoamCells_01_3.Middle_outside

value: lung


title: Ctr_UTI_9

description: Library name: DE46NGSUKBR131944_1

value: control


title: Thal 18day KO Mouse 88_10

description: Library name: samp88_10_Thal_B10_S23

value: Thal

value: Single Batch


title: Hind 18day KO Mouse 88_10

description: Library name: samp88_10_Hind_E3_S21

value: Hind


title: Ctr_UTI_8

description: Library name: DE73NGSUKBR131943_1


title: No.03-FoamCells_02

description:
Library name: DSP-1001660021516-H-C02
BO_No.03-FoamCells_02_3.Middle_outside


title: Rep2_DeltaNTR_si3_protrusion

description:
Library name: Quantseq_Sample_24
column names in the processed file are the same as sample titles

value: deltaNTR myc-LARP6

value: LARP6 3'UTR siRNA

value: protrusions


title: Rep3_U87_scr_protrusion

description:
Library name: Quantseq_Sample_27
column names in the processed file are the same as sample titles

value: Brain

value: Wild-type

value: scrambled siRNA


title: Rep3_U87_scr_body

description:
Library name: Quantseq_Sample_25
column names in the processed file are the same as sample titles

value: U-87 MG

value: Glioblastoma

value: cell-body


title: No.03-Interstitium_02

description:
Library name: DSP-1001660021516-H-C06
BO_No.03-Interstitium(CD68-)_02_3.Middle_proximal

value: Interstitium

value: wild type


title: Ctr_UTI_7

description: Library name: DE03NGSUKBR131942_1

value: Kidney

value: Female


title: Hind 3month WT Mouse 81_2

description: Library name: samp81_2_Hind_D6_S19

value: WT


title: No.03-Ep_01

description:
Library name: DSP-1001660021516-H-B12
BO_No.03-Ep_01_3.Middle_proximal

value: lung

value: Ep


title: Rep2_DeltaNTR_si3_body

description:
Library name: Quantseq_Sample_22
column names in the processed file are the same as sample titles


title: Ctr_UTI_6

description: Library name: DE30NGSUKBR131941_1

value: control


title: Hind 3month WT Mouse 81_1

description: Library name: samp81_1_Hind_D5_S17

value: Hind

value: Single Batch


title: Thal 3month WT Mouse 81_2

description: Library name: samp81_2_Thal_B2_S20

value: Thal


title: Rep2_DeltaNTR_scr_protrusion

description:
Library name: Quantseq_Sample_23
column names in the processed file are the same as sample titles

value: Brain

value: deltaNTR myc-LARP6

value: protrusions


title: No.03-Alveoli_02

description:
Library name: DSP-1001660021516-H-B10
BO_No.03-Alveoli_02_3.Middle_distal

value: Alveoli


title: Ctr_UTI_2

description: Library name: DE41NGSUKBR131937_1


title: Thal 3month WT Mouse 7_4

description: Library name: samp07_4_Thal_A12_S16


title: No.03-Alveoli_01

description:
Library name: DSP-1001660021516-H-B09
BO_No.03-Alveoli_01_3.Middle_distal


title: Rep2_DeltaNTR_scr_body

description:
Library name: Quantseq_Sample_21
column names in the processed file are the same as sample titles

value: U-87 MG

value: Glioblastoma

value: scrambled siRNA


title: No.02-Vessel_01

description:
Library name: DSP-1001660021516-H-B07
BO_No.02-Vessel_01_3.Middle_distal

value: Vessels

value: wild type


title: No.03-Alveoli_03

description:
Library name: DSP-1001660021516-H-B11
BO_No.03-Alveoli_03_3.Middle_distal


title: No.02-Vessel_02

description:
Library name: DSP-1001660021516-H-B08
BO_No.02-Vessel_02_3.Middle_distal


title: Ctr_UTI_1

description: Library name: DE68NGSUKBR131936_1

value: Kidney

value: Female


title: Rep2_FL_scr_body

description:
Library name: Quantseq_Sample_17
column names in the processed file are the same as sample titles

value: FL myc-LARP6

value: cell-body


title: No.02-Interstitium_02

description:
Library name: DSP-1001660021516-H-B05
BO_No.02-Interstitium_02_3.Middle_distal

value: lung

value: Interstitium


title: No.02-Interstitium_01

description:
Library name: DSP-1001660021516-H-B06
BO_No.02-Interstitium_01_3.Middle_distal


title: Thal 3month WT Mouse 81_1

description: Library name: samp81_1_Thal_B1_S18

value: WT

value: Single Batch


title: Hind 3month KO Mouse 7_3

description: Library name: samp07_3_Hind_D2_S13

value: Brain

value: KO

value: Hind


title: Ctr_UTI_5

description: Library name: DE57NGSUKBR131940_1

value: control


title: Rep2_FL_scr_protrusion

description:
Library name: Quantseq_Sample_19
column names in the processed file are the same as sample titles

value: U-87 MG

value: protrusions


title: Ctr_UTI_4

description: Library name: DE84NGSUKBR131939_1


title: KO96H

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Library name: Sample 24

data_processing:
Adapter sequences and low quality reads were filtered by Trimmoatic
Surviving reads were aligned to reference genome using STAR aligner
Assembly: mm10
Supplementary files format and content: TAB file for gene count

source_name: liver

extract_protocol:
Total RNA was extracted from snap-frozen liver tissue using TRIzol reagent (Life Technologies, Carlsbad, CA). For baseline (0 hour) samples, RNA was isolated from individual mice (n = 4 per genotype). For the 12 to 96 hour time points, RNA from three biological replicates per genotype per time point was pooled prior to sequencing (n = 3 mice pooled per group).
Following Illumina library prep and RNA-seq protocols.

value: liver


title: Rep2_U87_si3_protrusion

description:
Library name: Quantseq_Sample_16
column names in the processed file are the same as sample titles

value: Glioblastoma

value: Wild-type

value: LARP6 3'UTR siRNA


title: Thal 3month KO Mouse 7_3

description: Library name: samp07_3_Thal_A11_S14

value: Thal


title: No.02-FoamCells_04

description:
Library name: DSP-1001660021516-H-B04
BO_No.02-FoamCells_04_3.Middle_inside

value: wild type


title: Hind 3month WT Mouse 7_4

description: Library name: samp07_4_Hind_D4_S15


title: KO72H

description: Library name: Sample 23


title: Hind 3month KO Mouse 7_2

description: Library name: samp07_2_Hind_D1_S11


title: Rep2_U87_scr_protrusion

description:
Library name: Quantseq_Sample_15
column names in the processed file are the same as sample titles

value: scrambled siRNA


title: Rep2_FL_si3_body

description:
Library name: Quantseq_Sample_18
column names in the processed file are the same as sample titles

value: FL myc-LARP6

value: cell-body


title: KO24H

description: Library name: Sample 21


title: Rep2_U87_si3_body

description:
Library name: Quantseq_Sample_14
column names in the processed file are the same as sample titles


title: KO48H

description: Library name: Sample 22


title: No.02-FoamCells_03

description:
Library name: DSP-1001660021516-H-B03
BO_No.02-FoamCells_03_3.Middle_inside

value: lung


title: Thal 3month KO Mouse 7_2

description: Library name: samp07_2_Thal_A10_S12

value: Single Batch


title: Thal 3month WT Mouse 7_1

description: Library name: samp07_1_Thal_A9_S10

value: Brain

value: WT


title: Rep1_DeltaNTR_si3_protrusion

description:
Library name: Quantseq_Sample_12
column names in the processed file are the same as sample titles

value: deltaNTR myc-LARP6


title: No.02-Ep_02

description:
Library name: DSP-1001660021516-H-A12
BO_No.02-Ep_02_3.Middle_proximal

value: Ep


title: Thal 3month WT Mouse 5_4

description: Library name: samp05_4_Thal_A8_S8


title: KO12H

description: Library name: Sample 20

value: KO


title: KO0Hx4

description: Library name: Sample 19


title: KO0Hx3

description: Library name: Sample 18


title: Rep2_FL_si3_protrusion

description:
Library name: Quantseq_Sample_20
column names in the processed file are the same as sample titles

value: U-87 MG

value: protrusions


title: Hind 3month WT Mouse 5_4

description: Library name: samp05_4_Hind_C11_S7

value: Hind


title: No.02-Alveoli_02

description:
Library name: DSP-1001660021516-H-A10
BO_No.02-Alveoli_02_3.Middle_proximal

value: Alveoli


title: No.02-Ep_01

description:
Library name: DSP-1001660021516-H-A11
BO_No.02-Ep_01_3.Middle_proximal


title: KO0Hx2

description: Library name: Sample 17

value: liver


title: Hind 3month WT Mouse 7_1

description: Library name: samp07_1_Hind_C12_S9


title: KO0Hx1

description: Library name: Sample 16


title: Thal 3month KO Mouse 5_3

description: Library name: samp05_3_Thal_A7_S6

value: Thal


title: Rep2_U87_scr_body

description:
Library name: Quantseq_Sample_13
column names in the processed file are the same as sample titles

value: Glioblastoma

value: Wild-type


title: Rep1_FL_si3_protrusion

description:
Library name: Quantseq_Sample_8
column names in the processed file are the same as sample titles

value: FL myc-LARP6

value: LARP6 3'UTR siRNA


title: Hind 3month KO Mouse 5_3

description: Library name: samp05_3_Hind_C10_S5


title: WT72H

description: Library name: Sample 14


title: No.02-Alveoli_01

description:
Library name: DSP-1001660021516-H-A09
BO_No.02-Alveoli_01_3.Middle_proximal

value: lung

value: wild type


title: Rep1_DeltaNTR_scr_body

description:
Library name: Quantseq_Sample_9
column names in the processed file are the same as sample titles

value: Brain

value: scrambled siRNA

value: cell-body


title: WT96H

description: Library name: Sample 15

value: WT


title: Rep1_FL_scr_protrusion

description:
Library name: Quantseq_Sample_7
column names in the processed file are the same as sample titles


title: No.02-FoamCells_01

description:
Library name: DSP-1001660021516-H-B01
BO_No.02-FoamCells_01_3.Middle_inside


title: No.01-Interstitium_02

description:
Library name: DSP-1001660021516-H-A08
BO_No.01-Interstitium_02_3.Middle_proximal

value: Interstitium


title: Rep1_DeltaNTR_scr_protrusion

description:
Library name: Quantseq_Sample_11
column names in the processed file are the same as sample titles

value: U-87 MG

value: deltaNTR myc-LARP6


title: Rep1_DeltaNTR_si3_body

description:
Library name: Quantseq_Sample_10
column names in the processed file are the same as sample titles


title: Hind 3month KO Mouse 5_2

description: Library name: samp05_2_Hind_C9_S3

value: KO

value: Hind

value: Single Batch


title: No.01-FoamCells_03

description:
Library name: DSP-1001660021516-H-A06
BO_No.01-FoamCells_03_2.Early_inside


title: No.01-Interstitium_01

description:
Library name: DSP-1001660021516-H-A07
BO_No.01-Interstitium_01_3.Middle_proximal


title: Thal 3month KO Mouse samp05_1

description: Library name: samp05_1_Thal_A5_S2

value: Thal


title: Rep1_FL_scr_body

description:
Library name: Quantseq_Sample_5
column names in the processed file are the same as sample titles

value: Glioblastoma


title: Rep1_FL_si3_body

description:
Library name: Quantseq_Sample_6
column names in the processed file are the same as sample titles


title: WT24H

description: Library name: Sample 12

value: liver


title: Thal 3month KO Mouse 5_2

description: Library name: samp05_2_Thal_A6_S4


title: No.01-FoamCells_01

description:
Library name: DSP-1001660021516-H-A04
BO_No.01-FoamCells_01_2.Early_inside


title: Hind 3month KO Mouse samp05_1

description: Library name: samp05_1_Hind_C8_S1


title: Rep1_U87_si3_protrusion

description:
Library name: Quantseq_Sample_4
column names in the processed file are the same as sample titles

value: Wild-type

value: protrusions


title: SSC 3month KO Mouse 99_3

description: Library name: samp99_3_SSC_G3_S63

value: SSC


title: Hipp 3month KO Mouse 99_3

description: Library name: samp99_3_Hipp_H6_S61

value: Hipp


title: WT0Hx2

description: Library name: Sample 8


title: WT0Hx3

description: Library name: Sample 9


title: WT0Hx4

description: Library name: Sample 10


title: SSC 3month KO Mouse 99_2

description: Library name: samp99_2_SSC_G2_S60

value: Brain


title: MC 3month KO Mouse 99_3

description: Library name: samp99_3_MC_E2_S62

value: MC


title: Rep1_U87_scr_protrusion

description:
Library name: Quantseq_Sample_3
column names in the processed file are the same as sample titles

value: scrambled siRNA


title: WT12H

description: Library name: Sample 11

value: WT


title: HPF cell, TGFB, 72 hrs, LIGHT, 24 hrs, rep2

first: Michael

last: Croft

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Library name: 230428_NG_Sample_29

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2
Filtered reads were mapped against the human GRCh38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: tsv counts matrix with rows as genes and columns as samples

growth_protocol: Human pulmonary fibroblasts were cultured in fibroblast media, serum starved prior  cytokine treatment

extract_protocol:
Zymo Direct-zol
NEB mRNA Directional

treatment_protocol: Human pulmonary fibroblasts (HPF) stimulated with 50 ng/ml LIGHT, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or Il17A with LIGHT. HPF were also pretreated with 5 ng/ml of TGFb followed by 50 ng/ml LIGHT treatment.

value: Lung

value: HPF

value: Fibroblasts

value: TGFB 72 hrs followed by LIGHT 24 hrs

value: batch 1


title: No.01-FoamCells_02

description:
Library name: DSP-1001660021516-H-A05
BO_No.01-FoamCells_02_2.Early_inside

value: lung

value: wild type


title: Rep1_U87_scr_body

description:
Library name: Quantseq_Sample_1
column names in the processed file are the same as sample titles

value: U-87 MG

value: Glioblastoma

value: cell-body


title: No.01-Alveoli_01

description:
Library name: DSP-1001660021516-H-A02
BO_No.01-Alveoli_01_3.Middle_proximal

value: Alveoli


title: No.01-Alveoli_02

description:
Library name: DSP-1001660021516-H-A03
BO_No.01-Alveoli_02_3.Middle_proximal


title: HPF cell, TGFB, 72 hrs, LIGHT, 24 hrs, rep3

description: Library name: 230428_NG_Sample_30


title: MC 3month KO Mouse 99_2

description: Library name: samp99_2_MC_E1_S59

value: KO

value: Single Batch


title: Ribo-seq, 19-28z-1A T cells, RPF 3

first: Yuzhe

last: Shi

address: 1250 First Avenue

department: Immunolgy

description: Library name: RPF6_1A_6

data_processing:
samples were processed with Eclipsebio's proprietary analysis pipeline (v1). Unique molecular identifiers (UMIs) were pruned from read sequences using UMI-tools (v1.1.1). Next 3' adapters were trimmed from reads using Cutadapt (v3.2). Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a), and during the alignment, multimapping reads were not retained. The exclusion of multimapping reads reduces false positive differential and pausing calls (Halpin, Jangi, and Street). The removal of multimapping reads may lead to underestimates of counts for genes with high rates of pseudogenization or duplication events. PCR duplicates were removed using UMI-tools (v1.1.1). Gene coverage was calculated using Subread featureCounts (v2.0.1) and ribosome occupancy was calculated by dividing coverage in the ribosome protected footprint (RPF) library by the RNA-Seq library. Differentially expressed and occupied genes were identified using DESeq2. For transcriptome analyses, reads were also aligned to the transcriptome with STAR (v2.7.7a). Transcriptome aligned reads were processed with riboWaltz and custom analysis programs developed by Eclipsebio to determine codon usage, stall sites, 5' UTR loading, and 3' read through. ORF detection was performed on genome alignments using ribotricer (v1.3.3).
Assembly: hg38
Supplementary files format and content: counts, TPM, FPKM
Library strategy: Ribo-Seq

source_name: Primary T cell

extract_protocol:
Cells were lysed and 1 µg of total RNA was isolated for RNA-Seq while 9 µg of total RNA was digested with RNase I to isolate ribosome protected RNA footprints (RPFs). Both sample types were taken through rRNA depletion and RNA-seq samples were heat fragmented.
Sample types then underwent adapter ligation. Ligated RNA was reverse transcribed, libraries were generated via PCR.

value: Primary T cell

tag: disease state

value: Healthy Donor

value: 19-28z-1A T cells


title: Hipp 3month KO Mouse 99_2

description: Library name: samp99_2_Hipp_H5_S58

value: Brain

value: Hipp


title: WT0Hx1

description: Library name: Sample 7

value: liver

value: WT


title: Rep1_U87_si3_body

first: Faraz

last: Mardakheh

address: South Parks Road

description:
Library name: Quantseq_Sample_2
column names in the processed file are the same as sample titles

value: Wild-type

value: LARP6 3'UTR siRNA


title: CRE0Hx3

description: Library name: Sample 6

value: CRE


title: SSC 3month KO Mouse 99_1

description: Library name: samp99_1_SSC_G1_S57

value: SSC


title: Hipp 3month KO Mouse 99_1

description: Library name: samp99_1_Hipp_H4_S55


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_18

value: Lung

value: HPF

value: Fibroblasts

value: IL17A 72 hrs followed by LIGHT 24 hrs


title: HPF cell, TGFB, 72 hrs, rep3

description: Library name: 230428_NG_Sample_27

value: TGFB 72 hrs

value: batch 1


title: HPF cell, TGFB, 72 hrs, rep1

description: Library name: 230428_NG_Sample_25


title: CRE0Hx1

description: Library name: Sample 4


title: NULL0Hx2

description: Library name: Sample 2


title: Ribo-seq, 19-28z-1A T cells, RPF 2

description: Library name: RPF5_1A_5

value: Primary T cell


title: MC 3month KO Mouse 99_1

description: Library name: samp99_1_MC_D12_S56

value: KO

value: MC

value: Single Batch


title: CRE0Hx2

description: Library name: Sample 5


title: NULL0Hx1

description: Library name: Sample 1


title: SSC 18day KO Mouse 89_12

description: Library name: samp89_12_SSC_F12_S52

value: Brain


title: MC 18day KO Mouse 89_6

description: Library name: samp89_6_MC_D9_S53


title: HPF cell, TGFB, 72 hrs, rep2

description: Library name: 230428_NG_Sample_26


title: Ribo-seq, 19-28z T cells, RPF 1

description: Library name: RPF1_28z_4

value: Healthy Donor

value: 19-28z T cells


title: NULL0Hx3

description: Library name: Sample 3

value: liver


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_16


title: Ribo-seq, 19-28z T cells, RPF 3

description: Library name: RPF3_28z_6


title: Ribo-seq, 19-28z T cells, RPF 2

description: Library name: RPF2_28z_5


title: Input_1

description:
Library name: Control_Input_1
Epicypher

extract_protocol:
Freshly collected proximal mouse incisor fromcontrol mice and digested mesenchymal cells from the proximal mouse incisor tissue with enzymes . The prepared cells were tested for viability before process the extraction. Cells viability  higher than 80% were used for nucleis extranction for the scATACseq.
Library was performed according to the manufacter's introduction (Epicypher).

value: incisor mesenchyme

value: wild type

value: Input


title: SSC 18day KO Mouse 89_6

description: Library name: samp89_6_SSC_F10_S54

value: SSC


title: Input_2

description:
Library name: Control_Input_2
Epicypher


title: HPF cell, IL17A, 72 hrs, rep3

description: Library name: 231107_NG_Sample_15

value: Lung

value: HPF

value: IL17A 72 hrs


title: IgG

description:
Library name: Control_IgG
Epicypher

value: IgG


title: Ribo-seq, 19-28z-1A T cells, RPF 1

description: Library name: RPF4_1A_4

value: 19-28z-1A T cells


title: Ribo-seq, 19-28z-1A T cells, RNA 3

description: Library name: RNA_Seq6_1A_6

value: Primary T cell


title: WT48H

description: Library name: Sample 13

value: WT


title: MC 18day KO Mouse 89_11

description: Library name: samp89_11_MC_D10_S49

value: KO

value: MC


title: HPF cell, IL17A, 72 hrs, rep2

description: Library name: 231107_NG_Sample_14

value: Fibroblasts


title: Foxo1_2

description:
Library name: Control_Foxo1_2
Epicypher


title: HPF cell, TGFB, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 230428_NG_Sample_28

value: TGFB 72 hrs followed by LIGHT 24 hrs

value: batch 1


title: HPF cell, IL17A, 72 hrs, rep1

description: Library name: 231107_NG_Sample_13


title: Ribo-seq, 19-28z-1A T cells, RNA 2

description: Library name: RNA_Seq5_1A_5

value: Healthy Donor


title: HPF cell, IL17A, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_17

value: IL17A 72 hrs followed by LIGHT 24 hrs


title: MC 18day WT Mouse 88_9

description: Library name: samp88_9_MC_D6_S47

value: Brain

value: Single Batch


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_10

value: IL13 72hrs followed by LIGHT 24hrs


title: SSC 18day KO Mouse 89_11

description: Library name: samp89_11_SSC_F11_S50

value: SSC


title: YBX1 eCLIP, 19-28z-1A T cells, IP1

description: Library name: IP3_1A_1

data_processing:
Samples were processed with Eclipsebio's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). Peaks were identified within eCLIP samples using the peak caller CLIPper (v2.0.1). For each peak, IP versus input fold enrichments and pvalues were calculated. Peaks were annotated using transcript information from GENCODE v41 with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
Assembly: hg38
Supplementary files format and content: gene_counts.txt

extract_protocol:
Cell pellets were lysed using 1mL of eCLIP lysis mix with a modified composition of 6µL of Proteinase Inhibitor Cocktail and 20µL of Murine RNase Inhibitor. Samples were then subjected to one round of sonication for 5 minutes with 30 second ON/OFF at 75% amplitude. Pre-validated antibodies against YBX1 (Abcam cat. Ab76149) were then pre-coupled to Anti-Rabbit IgG Dynabeads (ThermoFisher), added to lysate, and incubated overnight at 4°C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers.
IP and input samples were cut from the membrane at the relative band size to 75kDa above. RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed.


title: MC 18day KO Mouse 89_12

description: Library name: samp89_12_MC_D11_S51


title: Ribo-seq, 19-28z-1A T cells, RNA 1

description: Library name: RNA_Seq4_1A_4


title: Ribo-seq, 19-28z T cells, RNA 2

description: Library name: RNA_Seq2_28z_5

value: 19-28z T cells


title: Arid1b_2

description:
Library name: Control_Arid1b_2
Epicypher

value: incisor mesenchyme

value: wild type


title: Dlx2_2

description:
Library name: Control_Dxl2_2
Epicypher


title: MC 18day WT Mouse 88_8

description: Library name: samp88_8_MC_D5_S45


title: HPF cell, IL13, 72 hrs, rep3

description: Library name: 231107_NG_Sample_9

value: Lung

value: HPF

value: IL13 72 hrs


title: Ribo-seq, 19-28z T cells, RNA 1

description: Library name: RNA_Seq1_28z_4

value: Primary T cell


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep2

description: Library name: 231107_NG_Sample_11


title: HPF cell, IL13, 72 hrs, rep1

description: Library name: 231107_NG_Sample_7