title: CART+N6-BTP2 rep1

city: Hangzhou

first: XIN

last: GUO

state: Zhejiang

address: yuhangtang road

institute: Zhejiang University

data_processing:
Cutadapt software (v 1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100)
Sequenced reads were aligned to the human reference genome (GRCh38) using the HISAT2  software (version 2.0.4).
The mapped reads of each sample were assembled using StringTie(v1.3.4) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(v0.9.8). StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Principal component analysis and differential expression analysis were performed using edgeR package  (v 3.26.8) in R (v 3.6.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix tables with raw gene counts or FPKM values for every gene and every sample

source_name: human T cells

growth_protocol: Positive transduced T cells were sorted 5 days post initial activation and expanded in culture for 3-7 days. Fresh IL-2-containing medium was changed every 2 days.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peripheral blood was obtained from healthy volunteers. All blood samples were handled following the required ethical and safety procedures. Peripheral blood mononuclear cells were isolated by density gradient centrifugation. T cells were purified and stimulated with anti-CD3/CD28 beads (Life Technologies) at a 3:1 bead:cell ratio in T cell medium for 24 hours prior to lentiviral transduction. Condensed viral supernatant was used for transduction in accordance with a multiplicity of infection (MOI) of 2. Positive transduced T cells were sorted 5 days post initial activation and expanded in culture for 3-7 days. Then, CAR T cells were exposed to Nalm-6 stimulation, and the remaining CAR-T cells were collected and treated with calcium inhibitors for 72 hours. CAR T cells and CAR T cells exposed to Nalm6 stimulation  followed by treatment with DMSO, BAPTA and BTP-2 were used to extract RNA.

value: T cells

value: N6 and BTP2


title: SAMPLE 20: 000025-TN-1

status: Public on Nov 19 2021

type: RNA

city: Beijing

first: Yuntao

last: Bing

address: No.49 Huayuan North Road

department: Department of General Surgery

country: China

institute: Peking University Third Hospital

description: HCC

data_processing:
The above 40 pairs of samples were tested in 3 times due to different collection times of the samples,in cluding 10 pairs of samples once time, 17 pairs of samples once time and 13 pairs of samples once time.
Experiments from different batches were calibrated using experimental data of samples from the previous batch.
Standard curve method was used to analyze the final result.  β-actin as the house keeping gene. Three replicates for each sample.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: liver

label_protocol: The cDNAs for circRNA, mRNA, or miRNA measurement were synthesized using random, oligo(dT)18, or stem-loop primers, respectively, using a RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, USA). qRT-PCR was performed in triplicate using Maxima SYBR Green qPCR Master Mix (Thermo Fisher Scientific) on the CFX connect real-time system (Bio-Rad, Hercules, CA, USA).

extract_protocol: Total RNA was extracted by Trizol.

treatment_protocol: Paired tissue specimens (tumor and adjacent normal tissues) were collected from the patients, immediately frozen in liquid nitrogen, and stored at -80°C until use.

tag: tissue

value: HCC tissue

tag: paired sample


title: CART+N6-BTP2 rep3

type: SRA

library_source: transcriptomic

value: blood

tag: cell type

tag: treatment


title: CART+N6-BTP2 rep2


title: PancreaticTumour_Pkn2KO_F

city: London

first: Angus

last: Cameron

state: Islington

address: John Vane Science Centre, Charterhouse Sq,

department: Tumour Biology

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Base calling was conducted by the NovaSeq Control Software. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq v2.19 software. One mis-match was allowed for index sequence identification.
Raw FASTQ reads were adapter and quality trimmed using trimmomatic.
Trimmed reads were aligned to the mouse genome in strand-specific mode using HISAT2 (v2.1.0).
Uniquely aligned reads (q > 10) to the exonic region of each gene were counted using HTSeq (v0.11.2).
Count matrix normalisation was performed using DESeq2 v(1.32) or edgeR v(3.32.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample and for every gene.
Supplementary_files_format_and_content: Matrix table with DESeq2-Normalised gene counts for every sample and for every gene.

organism: Mus musculus

source_name: Orthotopic Pancreatic Tumour

growth_protocol: Orthotopic injections of 1000 WTPKN2 TB32048 cells in a 1:1 solution of DMEM and Matrigel into the pancreas.

extract_protocol:
Tumours were extracted and stored in RNAlater (ThermoFisher Scientific, AM7020) at -20oC. To extract RNA, samples were macerated using the TissueLyzer II (QIAGEN) with 5 mm TissueLyzer beads (QIAGEN, 69989) in RLT buffer. RNA was prepared using the RNeasy mini kit (QIAGEN) as per manufacturer’s instructions. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA)
The library was prepared using NEB Next Ultra II Directional RNA Library Prep Kit for Illumina using manufacturer’s recommendations (NEB).

tag: genotype

value: PKN2 KO

tag: strain

value: Orthotopic Pancreatic Tumour

value: 1000 WTPKN2 TB32048 cells into the pancreas.


title: PancreaticTumour_Pkn2Wt_C

value: PKN2 WT


title: SAMPLE 18: 000011-TN-1

description: HCC


title: PancreaticTumour_Pkn2Wt_D


title: CART+N6-BAPTA rep2

value: N6 and BAPTA


title: CART+N6-BAPTA rep3


title: PancreaticTumour_Pkn2KO_E


title: SAMPLE 17: 000004-TN-1

description: HCC


title: PancreaticTumour_Pkn2KO_D


title: DC2_blood_2

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline,
Adapters and base quality trimming were performed using Trim Galore script with parameters -length 50, then to improve the quality of the mapping, reads were further trimmed at the 3’ to a length of 72bp using fastx_trimmer from the FASTX-toolkit
reads were mapped onto the Ensembl human transcriptome (version 84) and quantified at the transcript level using Salmon (--validateMappings flag)
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2 package
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analyzed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Genome_build: Ensembl human transcriptome (version 84)
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

value: Freshly isolated cells


title: DC2_blood_3


title: PancreaticTumour_Pkn2Wt_E


title: CART+N6-BAPTA rep1


title: SAMPLE 16: 000002-TN-1

description: HCC


title: CART+N6-DMSO rep3

value: N6 and DMSO


title: PancreaticTumour_Pkn2KO_C


title: PancreaticTumour_Pkn2KO_B


title: CART+N6-DMSO rep2


title: SAMPLE 15: 000024-TN-1

description: HCC


title: CART+N6-DMSO rep1


title: DC2_blood_1


title: CL_mono_5

value: "classical" (CL) CD14++CD16- monocytes


title: PancreaticTumour_Pkn2Wt_B


title: SAMPLE 13: 000018-TN-1

description: HCC


title: CAR T rep3

value: untreated


title: CAR T rep2


title: SAMPLE 12: 000014-TN-1

description: HCC


title: CL_mono_4


title: CAR T rep1


title: PancreaticTumour_Pkn2Wt_A


title: SPC+_BLM_3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: BLM-treated iPS-AT2 cells

data_processing:
Sequencing reads of SPC-GFP+ cells were aligned to GRCh37 using STAR 2.6.0c.
TPM values were calculated using Genedata Profiler Genome (Genedata, 13.0.11)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample .

source_name: SPC+ cells isolated from alveolar organoids, P3 day17

growth_protocol: Human iPSC-derived SPC-GFP+ cells were isolated by FACS using  EpCAM-APC antibody. Sorted SPC-GFP+ cells were mixed with human fetal lung fibroblasts in 200 μL of 50% Growth Factor Reduced Matrigel diluted with DCIK medium (Ham's F12 containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA, 15 mM HEPES, 0.8 mM CaCl2, 0.1% ITS premix and 50 U/mL penicillin–streptomycin) supplemented with 10 μM Y-27632. 200 μL of the mixed cells were placed on a 12-well cell culture insert and 1 mL of DCIK medium containing 10 μM Y-27632 was added to the lower chamber. Culture medium in the lower chamber was replaced with DCIK medium every 2-3 days.

extract_protocol:
Total RNA of SPC-GFP+ cells isolated by FACS was extracted using RNeasy micro (Qiagen).
10 ng of total RNA was reverse-transcribed and amplified with 8 cycles using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). The amplified cDNAs were used to prepare sequence libraries using Nextera XT DNA Library Preparation Kit (illumina)

treatment_protocol: Three time passaged alveolar organoids were treated with DMSO or 3 μg/mL BLM from day 11 to day14, then each reagent was washed out, and the organoids were incubated for another 3 days in dexamethasone-free DCIK medium.

value: iPSC derived SPC+

value: BLM


title: DropSeq_CUS_rep4

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

country: USA

institute: New York Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Multiplexed libraries were submitted for sequencing on the Illumina HiSeq 2500 platform at the University of Pennsylvania Next Generation Sequencing Core facility. FASTQ files for each RNA sequencing library were mapped to the mouse mm10 genome by STAR using the parameters of ‘--outFilterMultimapNmax 1 --outFilterMismatchNmax 3’. The read number of each gene was counted by in-house Perl programs as previously described (Zhao et al. 2018). The edgeR (Robinson et al. 2010) was used to normalize raw counts and to compare between control and CUS samples.
Read mapping, Clustering and Marker gene identification. Paired-end sequencing reads of sNucDrop-seq were processed as previous described in Hu et al., 2017. Briefly, after mapping the reads to the mouse genome (mm10, Gencode release vM13), both exonic and intronic reads mapped to the predicted strands of annotated genes were retrieved for the cell type classification. Uniquely mapped reads were grouped by cell barcode. To digitally count gene transcripts, a list of UMIs in each gene, within each nucleus, was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given nuclei. Raw digital expression matrices were generated for the 4 Nextseq 500 sequencing runs.   The raw digital expression matrices of libraries from control and CUS mice were combined and loaded into the R package Seurat2 (version 3.1.1.9002). For normalization, UMI counts for all cells were scaled by library size (total UMI counts), multiplied by 10,000 and transformed to log space. Only genes found to be expressing in >10 cells were retained. Cell with a high percentage of UMIs mapping to mitochondrial genes (>=0.05), fewer than 600 detected genes, or more than 5,000 detected genes were discarded. In addition, doublet analysis tool, Scrublet3 (version 0.2), was used to remove cells with doublet score > 0.2 for each sample. As a result, 31,806 nuclei from 8 samples (4 control and 4 CUS) were kept for downstream analysis. The top 2,000 highly variable genes (HVGs) were identified using the function FindVariableFeatures with "vst" method. The expression levels of HVGs in the nuclei were scaled and centered along each gene and was subjected to PCA analysis. Assessing a number of different PCs for clustering revealed that the variation of PC number selection was relatively insensitive to the clustering results. The top 50 PCs were selected and used for 2-dimension reduction by Uniform Manifold Approximation and Projection (UMAP). Clusters were identified using the function FindCluster in Seurat with the resolution parameter set to 1.  Cells were classified into 21-45 clusters with the resolution parameter from 0.3 to 2. Clustering resolution parameters were varied quantitatively based on the number of cells being clustered. After the clustering results with different resolutions were compared and evaluated, we chose a resolution value of 1. Using this approach we were able to assign 31,806 cells to 28 clusters. Marker genes were then identified using the function FindAllMarkers in Seurat. Cell type was annotated based on top ranked marker genes. Two cell clusters, which co-expressed multiple cell type specific markers, were empirically considered as doublets. In all, 546 nuclei (1.7% of input data) were removed from the downstream analysis and 31,260 cells were finally assigned into 26 cell clusters (Fig 3a and 3b).
Identification of cell-type-specific differentially expressed genes between Control and CUS nuclei. In this study, we randomly selected 4 mice (2 control and 2 CUS) from each batch, in total 8 animals from 2 batches. After quick assessment of transcriptional signature of control and CUS mice by MDS plot, we found batch effect is profound in differential expression gene test. To account for the batch effect in gene expression, edgeR4 genralized linear model (GLM) was used to analyze the gene expression difference under different group (Control or CUS) and different batch. Twenty-three cell clusters with more than 200 nuclei were subjected to differential expression test. For each cell type, raw gene counts were aggregated by gene and animal identity. To filter out low expressed genes and compensate for different nuclei size of clusters, we kept the genes whose aggregated UMI was more than 10% of nuclei number in a cluster. By doing this, we obtained comparable number of genes that were subjected into the differential expression test across clusters, varied from 11,336 genes to 14,856 genes. Then model.matrix function in edgeR was used to construct the design matrix with two factors, group and batch. Likelihood ratio test by functions glmFit and glmLRT was performed to test the differential expression of genes between Control and CUS mice. Genes with FDR < 0.2 were considered significantly expressed between Control and CUS nuclei (Fig 3c).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Cortex

extract_protocol:
Mouse neocortical tissues were rapidly resected on ice 24h after the final CUS stressor, flash-frozen in liquid nitrogen, and stored at -80°C before nuclear isolation. Cortical nuclei were isolated as described in Johnson et al., 2017 and Hu et al., 2017.  Briefly, tissues were dounce homogenized on ice in 12 mL of sucrose homogenization buffer containing 0.32M sucrose (Sigma-Aldrich, RNase & DNase free, ultra pure grade), 5 mM CaCl2 (Sigma-Aldrich), 3mM MgAc2 (Sigma-Aldrich), 10 mM Tris-HCl pH 8.0 (Invitrogen), 0.1% Triton X-100 (Sigma-Aldrich), 0.1 mM EDTA (Invitrogen), and protease inhibitor cocktail (Roche), gently layered on top of 14 mL of sucrose cushion buffer (1.8 M sucrose, 10 mM Tris-HCl pH 8.0, 3 mM MgAc2, protease inhibitor cocktail) in a 1”x3.5” sterile centrifuge tube (Beckman), and isolated by ultracentrifugation at 25,000 rpm at 4°C for 2h using a Beckman Coulter SW28 swinging bucket rotor. For bulk nuclear RNA-seq experiments, nuclei were resuspended in 1 mL of ice-cold PBS containing EDTA-free protease inhibitor cocktail tablet (Roche), and RNasin ribonuclease inhibitor (Promega) and transferred to a 1.5 mL tube. For sNuc Drop-seq nuclei were resuspended in 1 mL of ice-cold PBS containing 0.01% BSA (Sigma-Aldrich), EDTA-free protease inhibitor cocktail tablet (Roche), and RNasin ribonuclease inhibitor (Promega) and transferred to a 1.5 mL tube.
RNAseq: Nuclei were pelleted at 5,000 rpm for 10 min at 4°C. The supernatant was subsequently removed, and total nuclear RNA was isolated by Trizol (Thermo Fisher) and chloroform (Fisher) extraction. Samples were prepared for RNA-sequencing using the TruSeq Stranded Total RNA library prep kit with RiboZero depletion (Illumina).
Drop-seq: Single-nucleus Drop-seq and data analysis. sNuc Drop-seq of cortical nuclei was performed as described in Hu et al., 2017. Briefly, nuclei suspensions were run through an Aquapel-coated PDMS microfluidic device (uFluidix) with barcoded beads (ChemGenes) to co-encapsulate individual nuclei with a single bead. Barcoded beads were resuspended in lysis buffer (200 mM Tris-HCl pH8.0, 20 mM EDTA, 6% Ficoll PM-400 (GE Healthcare/Fisher Scientific), 0.2% Sarkosyl (Sigma-Aldrich), and 50 mM DTT (Fermentas) at a concentration of 120 beads/uL. Droplet breakage with Perfluoro-1-octanol (Sigma-Aldrich), reverse transcription using Maxima H Minus Reverse Transcriptase (ThermoFisher) and exonuclease I treatment were subsequently performed. cDNA was amplified by PCR (KAPA HiFi hotstart Readymix, KAPA biosystems) using a pre-determined, optimized number of cycles and purified twice with 0.6X SPRISelect beads (Beckman Coulter). cDNA was then tagmented cDNA using the Nextera XT DNA sample preparation kit (Illumina, cat# FC-131-1096) and further amplified using 12 enrichment PCR cycles. Libraries were sequenced on an Illumina NextSeq 500 using the 75-cycle High Output v2 Kit (Illumina), each loaded at a concentration of 2.0 pM. In total, 8 individual mouse cortex samples (4 controls, 4 CUS) were analyzed by sNucDrop-seq with 2 independent batches (2 controls, 2 CUS samples per batch) sequenced twice.

treatment_protocol: CUS was performed in 9-10 week-old mice as described in Supplemental Table 1 and Yohn and Blendy, 2017. Three different stressors were performed each day for variable lengths of time over a 12-day period in dedicated procedure rooms. The first CUS stressor began at 8 a.m., the second at 1 p.m., and the last stress began at 6 p.m. and continued until 7 a.m. the following morning. Mice were group housed (4-5 mice per cage) and controls were housed in a separate room from CUS animals and gently handled daily during the duration of CUS.

tag: age

value: post natal day 80

value: CUS


title: SPC+_BLM_2

description: BLM-treated iPS-AT2 cells


title: SAMPLE 9: 000020-PN-1

description: Ctrl

value: Paracancerous tissue


title: SAMPLE 14: 000021-TN-2

description: HCC


title: PancreaticTumour_Pkn2KO_A


title: SAMPLE 8: 000006-PN-1

description: Ctrl


title: DropSeq_CUS_rep3


title: DropSeq_CUS_rep2


title: SPC+_BLM_1

description: BLM-treated iPS-AT2 cells


title: METTL5 KO 1 RPF

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

description: Sepich-Poore_2021_METTL5_mouse_TE_rpkm_with_foldchange.txt

data_processing:
Library strategy: Ribo-Seq
Base calling was performed with Illumina bcl2fastq software.
Quality of sequenced reads was assessed with FastQC v0.11.5
Adapters were trimmed and quality filtering was performed with BBDuk (https://sourceforge.net/projects/bbmap/) from BBTools version 38.84 using a reference fasta file of the NEBNext adapter sequences and settings ktrim = 4, qtrim = rl, trimq = 20, k = 31, mink = 11, hdist = 1, entropy = 0.5, entropywindow = 30, entropyk = 5, minlen = 25 and maxlen = 34 (for RPFs), and minlen = 15 (for inputs) (BBtools: sourceforge.net/projects/bbmap/). For input files, trimming was done for both pairs together.
For input files, both reads were used for analysis in paired-end mode. Alignment to human genome hg38 was performed using STAR 2.7.3a  in quantMode TranscriptomeSAM. Bam files were sorted and uniquely mapped reads extracted with samtools, followed by featureCounts v1.6.0  to create a counts table from mapped reads with options -s 1, -g gene_id, and -t exon --countReadPairs
For RPFs, only R1 was used for analysis. rRNA reads were removed from RPF Fasta files using BBDuk with a reference fasta file of mouse rRNA sequences. Analysis was then performed on the RiboToolkit server (http://rnabioinfor.tch.harvard.edu/RiboToolkit/). First, RPF files were uploaded for single-case submission in collapsed fasta format with the following options: species = mus musculus (mm10), RPF interval = 25-34, allowed mismatch = 2, max multiple-mapping = 1, no duplicate removal, offsets to infer P-sites - calculate by RiboToolkit, min coverage for pause sites = 10, fold change for pause sites = 20, ORF p-value = 0.05. Input counts table and single case Job IDs were then used as inputs for group case analysis with F value = 2 and P-value = 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: (For inputs): tab-delimited text file includes information about gene location and transcript counts in each sample. (For RPFs): tab-delimited text file includes information about geneID, gene name, transcript counts and RPF counts for each sample, log2FoldChange, and p-values.

source_name: KO mouse 1 (littermate of WT mouse 1)

growth_protocol: A Mettl5 conditional knockout line was made in which exon 2 was floxed, such that presence of Cre would induce exon 2 deletion by creating a frame shift mutation. The construct was electroporated with gRNA/Cas9 protein into ES cells that are F1 hybrid of C57bl/6 x 129S6. F1 mice were transferred from Janelia Research Campus to the University of Chicago where the second generation was backcrossed to the B6 strain. To generate a whole body knockout, the conditional knockout strain described above was then crossed with the B6.C-Tg(CMV-cre)1Cgn/J line (The Jackson Laboratory, 006054) (63). All mice were housed in a specific pathogen-free facility.

extract_protocol:
Each sample was resuspended by gently pipetting 10 times before transferring it to a clean microcentrifuge tube, and leaving on ice for 3-5 more minutes to ensure complete lysis. Samples were spun at 2000g for 5 minutes at 4ºC to pellet the nuclei and tissue debris. The supernatant was transferred to a fresh tube and spun at 12,000g for 5 minutes at 4ºC to pellet the remaining cellular debris. Again the supernatant was transferred to a fresh tube to start DNase treatment.
To the clarified lysate, Turbo DNase (Thermo Fisher) was added and samples were incubated at room temperature 15 minutes then centrifuged again to clear the lysate. About 20% of the sample was saved as input with 3 volumes of Trizol added, while the other 80% was treated with MNase (NEB) in 1x MNase buffer for 15 minutes at room temperature to digest RNA not covered by ribosomes. Additional SUPERaseIN (Invitrogen) was added to a final concentration of 0.5mM to quench the reaction. Then, samples were loaded on 5-50% w/v sucrose gradients, ultracentrifuged at 28,000 rpm for 3 hours,  and fractionated by Gradient Station (BioComp) equipped with an ECONO UV monitor (BioRad) and fraction collector (Gilson).
Fractions containing the digested monosomes were collected and pooled, and three volumes of Trizol (Invitrogen) were added to each sample. RNA purification was performed for both input and ribosome-protected fragment (RPF) samples by chloroform extraction followed by isopropanol precipitation, and one round of rRNA depletion was performed. Input RNA was fragmented by combining 20μL RNA with 7.5 μL PNK buffer A (Thermo Fisher) and incubating at 94ºC for 25 minutes, then end repaired by diluting in 37.5μL nuclease-free water, adding 10μL T4 PNK (Thermo Fisher) and incubating at 37ºC for 30 minutes. Then, 12μL 10mM ATP (EMD Millipore), 2μL 10x PNK buffer A, and 6μL T4 PNK were added to incubate at 37ºC for 30 minutes. These samples were purified using the RNA clean and concentrator-5 kit (Zymo Research).
Purified RPF RNA was run in 1x Novex TBU sample buffer (Thermo Fisher) on a 10% TBE-urea gel (Thermo Fisher) in 1x RNase-free TBE buffer (Thermo Fisher) with an IDT 10/60 loading control (IDT) for 1 hour at 180V. The gel was stained 15 minutes in 1x SYBR gold in TBE with gentle shaking and visualized using a Biorad Gel Doc EZ Imager. Fragments between 26-34 nucleotides were excised and purified by Small-RNA PAGE recovery kit (Zymo Research) per manufacturer’s instructions. RPFs were end repaired similarly to inputs with T4 PNK. Input and RPF RNA samples were used to prepare libraries for sequencing using the NEBNext Small RNA Library Prep Kit (NEB) per manufacturer’s instructions, and were sequenced by Illumina NovaSeq6000 with 50bp paired-end reads.

treatment_protocol:
Mice were sacrificed and livers were removed and snap-frozen very quickly following standard procedures, then stored at -80ºC . Each tissue sample was ground to powder under liquid nitrogen by mortar and pestle, and the powder was transferred to a sterile 10 cm cell culture plate on dry ice.
An appropriate volume (~1 mL per ~200mg tissue) of lysis buffer containing cycloheximide (10mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.5% w/v sodium deoxycholate, 1% v/v NP-40 alternative, 10 mM DTT, 150 μg/mL cycloheximide, 1 U/μL SUPERase In RNase inhibitor, and 1x EDTA-free Roche protease inhibitor cocktail in RNase-free water) was added to the powder sample immediately upon removal from dry ice to resuspend it, and the plate was placed on ice for 1-2 minutes.

value: cycloheximide (CHX)

tag: condition

value: ribosome-protected-fragments (RPFs)

tag: genotype/variation

value: METTL5 KO


title: SPC+_DMDO_3

description: DMSO-treated iPS-AT2 cells

value: DMSO


title: DropSeq_CUS_rep1


title: SAMPLE 7: 000005-PN-1

description: Ctrl


title: SPC+_DMSO_2

description: DMSO-treated iPS-AT2 cells


title: DropSeq_control_rep4

value: Control


title: Wildtype2 RPF

source_name: WT mouse 2 (littermate of KO mouse 2)

value: wild type


title: SAMPLE 5: 000026-PN-1

description: Ctrl


title: SAMPLE 10: 000024-PN-1

description: Ctrl


title: SAMPLE 11: 000012-TN-1

description: HCC

value: HCC tissue


title: METTL5 KO 3 RPF

source_name: KO mouse 3 (littermate of WT mouse 3)


title: SPC+_DMSO_1

description: DMSO-treated iPS-AT2 cells


title: METTL5 KO 2 RPF

source_name: KO mouse 2 (littermate of WT mouse 2)


title: Wildtype3 RPF

source_name: WT mouse 3 (littermate of KO mouse 3)


title: SAMPLE 4: 000020-PN-1

description: Ctrl


title: HFLF_BLM_3

description: BLM-treated HFLF

data_processing:
Sequenced reads of the fibroblasts were trimmed using fastp, and the trimmed reads were aligned to the GRCh38 using STAR 2.7.3a.
Transcripts per million (TPM) values were calculated using RSEM.

source_name: HFLF 3D all cell, day17

growth_protocol: Human iPSC-derived SPC-GFP+ cells were isolated by FACS using EpCAM-APC antibody. Sorted SPC-GFP+ cells were mixed with human fetal lung fibroblasts in 200 μL of 50% Growth Factor Reduced Matrigel diluted with DCIK medium (Ham's F12 containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA, 15 mM HEPES, 0.8 mM CaCl2, 0.1% ITS premix and 50 U/mL penicillin–streptomycin) supplemented with 10 μM Y-27632. 200 μL of the mixed cells were placed on a 12-well cell culture insert and 1 mL of DCIK medium containing 10 μM Y-27632 was added to the lower chamber. Culture medium in the lower chamber was replaced with DCIK medium every 2-3 days.

extract_protocol:
Co-cultured fibroblasts were isolated by negative selection of EpCAM+ cells from alveolar organoids. In fibroblast-only culture, all cells were collected. Total RNA of fibroblasts on each condition was extracted using RNeasy micro (Qiagen).
Sequence libraries of the fibroblasts RNA were prepared using the NEBNext Ultra RNA LP Kit (New England Biolabs).

treatment_protocol: Three time passaged alveolar organoids or fibroblast-only culture were treated with DMSO or 3 μg/mL BLM from day 11 to day14, then washed out of BLM, and incubated for another 3 days in dexamethason free DCIK medium.

value: HFLF


title: HFLF_BLM_2

description: BLM-treated HFLF


title: METTL5 KO 1 input

description: Sepich-Poore_METTL5_mouse_riboseq_input_merged_featurecount.txt

data_processing:
Base calling was performed with Illumina bcl2fastq software.
Quality of sequenced reads was assessed with FastQC v0.11.5
Adapters were trimmed and quality filtering was performed with BBDuk (https://sourceforge.net/projects/bbmap/) from BBTools version 38.84 using a reference fasta file of the NEBNext adapter sequences and settings ktrim = 4, qtrim = rl, trimq = 20, k = 31, mink = 11, hdist = 1, entropy = 0.5, entropywindow = 30, entropyk = 5, minlen = 25 and maxlen = 34 (for RPFs), and minlen = 15 (for inputs) (BBtools: sourceforge.net/projects/bbmap/). For input files, trimming was done for both pairs together.
For input files, both reads were used for analysis in paired-end mode. Alignment to human genome hg38 was performed using STAR 2.7.3a  in quantMode TranscriptomeSAM. Bam files were sorted and uniquely mapped reads extracted with samtools, followed by featureCounts v1.6.0  to create a counts table from mapped reads with options -s 1, -g gene_id, and -t exon --countReadPairs
For RPFs, only R1 was used for analysis. rRNA reads were removed from RPF Fasta files using BBDuk with a reference fasta file of mouse rRNA sequences. Analysis was then performed on the RiboToolkit server (http://rnabioinfor.tch.harvard.edu/RiboToolkit/). First, RPF files were uploaded for single-case submission in collapsed fasta format with the following options: species = mus musculus (mm10), RPF interval = 25-34, allowed mismatch = 2, max multiple-mapping = 1, no duplicate removal, offsets to infer P-sites - calculate by RiboToolkit, min coverage for pause sites = 10, fold change for pause sites = 20, ORF p-value = 0.05. Input counts table and single case Job IDs were then used as inputs for group case analysis with F value = 2 and P-value = 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: (For inputs): tab-delimited text file includes information about gene location and transcript counts in each sample. (For RPFs): tab-delimited text file includes information about geneID, gene name, transcript counts and RPF counts for each sample, log2FoldChange, and p-values.

value: input


title: DropSeq_control_rep3


title: SAMPLE 3: 000017-PN-1

description: Ctrl


title: METTL5 KO 3 input


title: Wildtype1 RPF

source_name: WT mouse 1 (littermate of KO mouse 1)


title: METTL5 KO 2 input


title: HFLF_BLM_1

description: BLM-treated HFLF


title: SAMPLE 6: 000001-PN-1

description: Ctrl


title: SAMPLE 2: 000013-PN-2

description: Ctrl


title: DropSeq_control_rep2


title: DropSeq_control_rep1


title: HFLF_DMSO_3

description: DMSO-treated HFLF


title: SAMPLE 1: 000011-PN-1

description: Ctrl


title: Wildtype3 input


title: HFLF_DMSO_2

description: DMSO-treated HFLF


title: DC2_tonsil_3

source_name: Tonsil

value: Freshly isolated cells

value: tonsil


title: EpCAM-_formFDAO_BLM_3

description: BLM-treated EpCAM- cells isolated from alveolar organoids

source_name: EpCAM- cells from alveolar organoids, P3 day17

value: EpCAM- cells from alveolar organoids


title: Wildtype1 input


title: HFLF_DMSO_1

description: DMSO-treated HFLF


title: EpCAM-_formFDAO_BLM_2


title: EpCAM-_formFDAO_BLM_1


title: Wildtype2 input


title: EpCAM-_formFDAO_DMSO_3

description: DMSO-treated EpCAM- cells isolated from alveolar organoids


title: EpCAM-_formFDAO_DMSO_1


title: KO_3

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

data_processing:
STAR v2.5: Read Alignment
htseq-count: fpkm
DESeq2: Differential expression analysis
Genome_build: mm10

source_name: spleen Ter119+ cells

extract_protocol: Total RNA was extracted from mouse spleen Ter119+ erythroid cell using the PureLink™ RNA Mini Kit (Thermo Fisher) and subjected to library preparation using Illumina TrueSeq RNA kit V2 manufacturer’s protocol with 1 ug of total RNA for the construction of sequencing libraries.

value: mixed B6;129P2 background

value: 2-3 month

value: knockout


title: WT_2


title: WT_1


title: KO_1


title: KO_2


title: 18_TWposIL_17_3_18

city: La Jolla

first: Rinkesh

last: Gupta

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
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 featureCounts v1.6.5 (-s 2 -p -t exon -g gene_id -Q 10) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Skin Keratinocyte_TWEAK +IL-17A stimulated

growth_protocol: Human epidermal keratinocytes from neonates (nHEK) were grown in Dermal Cell Basal Medium.

extract_protocol:
Cells were harvested in Trizol and processed for RNA-seq analysis.
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: Cells were cultured (Seeding density; 3x105 cells/well) in triplicates using a 6-well format plate and stimulated with predetermined optimal concentrations of either human rTWEAK (100 ng/ml), human rIL-17A (100 ng/ml), or human rTNF (10 ng/ml), or a combination of rTWEAK with rIL-17A or rTNF for 48 h.

tag: cell line

value: nHEK

value: TWEAK (100 ng/ml) +IL-17A (100 ng/ml) stimulated


title: 17_TWposIL_17_2_17

value: Human epidermal keratinocytes from neonates (nHEK)


title: EpCAM-_formFDAO_DMSO_2


title: 16_TWposIL_17_1_16


title: WT_3


title: 15_TWposTNF_3_15

source_name: Skin Keratinocyte_TWEAK +TNF stimulated

value: TWEAK (100 ng/ml) +TNF (10 ng/ml) stimulated


title: 14_TWposTNF_2_14


title: LT-HSC -IL-10 mouse 3

city: Boston

first: David

middle: Allan

last: Williams

state: MA

address: 300 Longwood Ave.

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
RNAseq analysis was performed by first aligning sequenced reads to the University of California Santa Cruz (UCSC) mm10 reference genome assembly and gene counts were quantified using STAR (v2.5.1b) (Dobin et al., Bioinformatics, 2013).
Differential gene expression testing was performed by DESeq2 (v1.10.1) (Love et al., Genome Biol., 2014) and normalized read counts in terms of fragments per kilobase of exon per million mapped fragments (FPKM) were calculated using Cufflinks (v2.2.1) (Trapnell et al., Nat. Biotechnol., 2010).

source_name: bone marrow

extract_protocol:
RNA was extracted with the RNeasy Micro Kit Cat no 74004 (Qiagen, Germantown, MD), and Ambion RNase inhibitor Cat no AM2682 (Thermo Fisher Scientific, Waltham, MA) was added for a final concentration of 1 U/uL
The cDNA was synthesized with SmartSeq v4 (Takara, Mountain View, CA) reagents from 3 ng of RNA. Full length cDNA was fragmented to a mean size of 200 bp with an M220 ultrasonicator (Covaris, Woburn, MA) and Illumina (San Diego, CA) sequencing libraries were prepared from 2 ng of sheared cDNA using Swift 2S Acel reagents on a Biomek i7 (Beckman Coulter, Brea, CA) according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with IL-10 (20 ng/mL) for 48 hours in SCGM Cellgenix (Cat no 20802-0500) media containing 100 ng/mL SCF, 100 ng/mL Flt3-L, 100 ng/mL TPO, and 20 ng/mL IL-3

value: LT-HSC

value: untreated (PBS)


title: 12_IL_17_3_12

source_name: Skin Keratinocyte_IL-17A stimulated

value: IL-17A (100 ng/ml) stimulated


title: LT-HSC +IL-10 mouse 2

value: treated with IL-10 (20 ng/mL) 48 hours


title: LT-HSC -IL-10 mouse 1


title: LT-HSC +IL-10 mouse 1


title: Calu3-2-12h-infected

city: Heidelberg

first: Florian

last: Heigwer

address: Im Neuenheimer Feld 580

department: Signaling and Functional genomics

country: Germany

institute: Deutsches Krebsforschungszentrum (DKFZ)

description: replicate 2

hyb_protocol: Hybridization was done according to manufacturer’s protocol for Thermo Fisher Scientific (Affymetrix) Gene Chip WT PLUS Reagent Kit. 5.5 μg of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Thermo Fisher Scientific (Affymetrix) human Clariom S Arrays.

scan_protocol: Chip scanning Gene Expression Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to GeneChip Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: First, data was collected for all samples after Robust Multi-Array Average (RMA) quantile normalization with R using the function ‘normalize.quantiles’ from Bioconductor package preprocessCore for probe set equalization. Second, data was then log transformed and PCA including all samples was performed using R/prcomp (R version 4.0.0). The rotation for each sample is shown. After PCA quality control and check for equal distribution of log- transformed probe intensities, data was gathered, and time-points were pooled as ‘early’ (4h and 8 h time-point) or ‘late’ (12 h and 24 h). R/limma’s lmFit, eBayes and topTable functions were then used with a model “matrix of expression ~ treatment + time” (limma version 3.40.6,79), to estimate base mean expression and differential expression for the contrast infected vs mock treatment. This analysis was performed individually for each cell line as differences between the lines would have obscured a model by driving the variance, as apparent in the PCA analysis. R/limma’s topTable function employs Benjamini Hochberg correction for multiple testing on all p-values. Genes were called significant if their adjusted p-value was smaller than 0.1 (False Discovery Rate, FDR < 10%).

label: biotin

source_name: Calu3 submucosal gland cell line

label_protocol: For microarray chip analysis total RNA was extracted from cells and hybridized on an Affymetrix Clariom S human array performed by the Microarray Unit of the Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ). Labeling was done using the Thermo Fisher Scientific (Affymetrix) Gene Chip WT PLUS Reagent to generate labeled ss-cDNA from input amounts of 50 ng total RNA.

growth_protocol: Calu-3 adn A549 cells were infected  with SARS-CoV-2 and the host transcriptional profiles were determined over the time course  of infection.

extract_protocol: According to Qiagen RNAeasy

treatment_protocol: SARS-CoV-2 predominantly targets airway and lung tissue in infected individuals. In order to  determine the effects of SARS-CoV-2 on human lung epithelial cells, Calu-3 cells were infected  with SARS-CoV-2 and the host transcriptional profiles were determined over the time course  of infection. Following infection, we observed an increase in intracellular viral RNA starting at  4 h post infection, which continued to increase up to 24 h post infection. Increased extracellular viral RNA was observed starting at 6 h post infection, which was  paralleled by the release of infectious virus.  To determine the effects of SARS-CoV-2 infection on the host transcriptional profile,  total RNA was isolated from infected cells and analyzed by microarray . For these studies, we took into account that the SARS-CoV-2  replication cycle in cell culture is 6-16 h, followed by death of infected cells 28. Therefore, to  the direct effects of virus infection and avoid the analysis of secondary infection events  or cell death effects, we did not extend our analysis beyond 24 h post infection.

tag: developmental stage

value: adult

value: wild type genotype

tag: disease

value: severe acute respiratory syndrome

tag: time

value: 12 hour


title: LT-HSC -IL-10 mouse 2


title: LT-HSC +IL-10 mouse 3


title: Calu3-2-24h-mock

description: replicate 2

value: Mock

value: 24 hour


title: Calu3-2-8h-mock

description: replicate 2

value: 8 hour


title: Calu3-2-4h-infected

description: replicate 2

value: 4 hour


title: MPP2 +IL-10 mouse 2


title: Calu3-1-24h-infected

description: replicate 1


title: 11_IL_17_2_11


title: Calu3-1-24h-mock

description: replicate 1


title: MPP2 +IL-10 mouse 1


title: Calu3-2-8h-infected

description: replicate 2


title: 13_TWposTNF_1_13


title: Calu3-2-4h-mock

description: replicate 2


title: Calu3-2-24h-infected

description: replicate 2


title: Calu3-1-12h-mock

description: replicate 1


title: Calu3-1-8h-infected

description: replicate 1


title: 10_IL_17_1_10


title: 8_TNF_2_8

source_name: Skin Keratinocyte_TNF stimulated

value: TNF (10 ng/ml) stimulated


title: MPP2 +IL-10 mouse 3


title: MPP2 -IL-10 mouse 2


title: 6_TW3_6

source_name: Skin Keratinocyte_TWEAK stimulated

value: nHEK

value: TWEAK (100ng/ml) stimulated


title: MPP2 -IL-10 mouse 3


title: MPP2 -IL-10 mouse 1


title: Calu3-1-4h-infected

description: replicate 1


title: 7_TNF_1_7

value: Human epidermal keratinocytes from neonates (nHEK)


title: cdKO ope3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

description:
S001_03_S99
dKO-ope-FAP-NO3

data_processing:
Adapters were trimmed using TrimGalore (version: 0.6.6).
The reads were mapped by the aligning software HISAT2 (version 2.2.1) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 2.0.1).
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.26.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix of RNA-seq

source_name: FAPs in overloaded plantaris muscle from cdKO mice

extract_protocol:
The cells were sorted to each 1000 cells into tube contained lysis buffer using Cell sorter.  Libraries were constructed following the protocol as shown previously (Hashimshony et al., 2016).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cdKO (Pdgfra-CreERT2::Yap1 flox/flox ::Taz flox/flox)

value: overloaded plantaris muscle

tag: tag

value: Pdgfra+


title: cdKO ope2

description:
S001_02_S98
dKO-ope-FAP-NO2


title: Calu3-2-12h-mock

description: replicate 2


title: 5_TW2_5


title: cdKO ope1

description:
S001_01_S97
dKO-ope-FAP-NO1


title: Calu3-1-12h-infected

description: replicate 1


title: Calu3-1-8h-mock

description: replicate 1


title: A549-2-24h-infected

description: replicate 2

source_name: A549 adenocarcinomic human alveolar basal epithelial cells


title: A549-2-12h-infected

description: replicate 2


title: 4_TW1_4


title: A549-2-8h-infected

description: replicate 2


title: RNAseq_CUS_rep5

source_name: Cortex

value: post natal day 90

value: CUS


title: cdKO sham2

description:
S001_05_S101
dKO-sham-FAP-NO2

source_name: FAPs in sham plantaris muscle from cdKO mice

value: sham plantaris muscle


title: Calu3-1-4h-mock

description: replicate 1

value: adult

value: wild type genotype


title: 9_TNF_3_9


title: 3_C3_3

source_name: Skin Keratinocyte_PBS Stimulated

value: PBS Stimulated


title: 2_C2_2


title: A549-2-8h-mock

description: replicate 2

value: Mock


title: 1_C1_1


title: Cont ope2

description:
S001_08_S104
Control-ope-FAP-NO2

source_name: FAPs in overloaded plantaris muscle from control mice

value: Control (Pdgfra-CreERT2)


title: RNAseq_CUS_rep3


title: A549-2-24h-mock

description: replicate 2

value: 24 hour


title: cdKO sham3

description:
S001_06_S102
dKO-sham-FAP-NO3


title: A549-2-4h-infected

description: replicate 2

value: severe acute respiratory syndrome

value: 4 hour


title: LCuA rep3

city: Montreal

first: Liangliang

last: Kong

state: Quebec

address: 1205 Docteur Penfield

department: Biology

country: Canada

institute: McGill

data_processing:
RNA-seq produced 42.2 to 51.6 million raw reads per sample (6.33 to 7.74 Gb raw bases per sample). Raw reads were processed by Trimmomatic v0.36 (Bolger et al., 2014) with default parameters to remove Illumina adapters and low-quality reads: only high-quality reads with a Phred quality score >30 and a minimum length of 75 bp after trimming were retained for subsequent analysis. The clean reads from all 6 samples (37.2 Gb accounting for 86.9% of total raw bases) were used for de novo transcriptome assembly using Trinity with default parameters (Haas et al., 2013). To quantify gene transcription levels, clean reads from each sample were mapped to the assembled transcriptome. Read mapping rates are 88.8% to 90.0% among samples. Transcript abundance was calculated by RSEM (RNA-Seq by Expectation Maximization; Li and Dewey, 2011) and expressed as RPKM (Reads Per Kilobase of exon per Million reads mapped) values.
Genome_build: de novo assembled transcriptome
Supplementary_files_format_and_content: matrix table of raw counts of each gene
Supplementary_files_format_and_content: matrix table of RPKM values of each gene

organism: Thalassiosira oceanica CCMP1005

source_name: single cell

growth_protocol: LCuA and CCuA cells were acclimated in Cu-deficient (1 nM Cu) Aquil medium at 20°C under continuous illumination of 200 μmol photons · m-2 · s-1 supplied by Phillips cool white fluorescent bulbs

extract_protocol:
Total RNA was isolated from the filtered cells (~70 million cells) using a TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific) with an on-column DNase (TURBO DNase, Thermo Fisher Scientific) digestion step to remove genomic DNA, as per the manufacturer’s recommendation.
Messenger RNA was isolated from 1 μg high-quality (RIN≥6.5) total RNA using oligo-dT attached magnetic beads and cDNA sequencing libraries were constructed with fragmented mRNA by a TruSeqTM RNA Sample Preparation Kit (Illumina, CA, USA), as per the manufacturer’s recommendation.

value: Cells acclimated in Cu-deficient medium for 2250 generations

tag: group

value: Treatment


title: Cont ope1

description:
S001_07_S103
Control-ope-FAP-NO1


title: A549-2-4h-mock

description: replicate 2


title: LCuA rep2


title: A549-2-12h-mock

description: replicate 2

value: 12 hour


title: RNAseq_CUS_rep2


title: RNAseq_CUS_rep4


title: RNAseq_CUS_rep1


title: Cont sham3

description:
S001_12_S108
Control-sham-FAP-NO3

source_name: FAPs in sham plantaris muscle from control mice


title: A549-1-24h-infected

description: replicate 1


title: A549-1-24h-mock

description: replicate 1


title: Cont sham2

description:
S001_11_S107
Control-sham-FAP-NO2


title: Cont ope3

description:
S001_09_S105
Control-ope-FAP-NO3


title: A549-1-12h-infected

description: replicate 1


title: CCuA rep2

value: Cells acclimated in Cu-sufficient medium for 3600 generations

value: Control


title: RNAseq_control_rep3


title: RNAseq_control_rep4


title: Cont sham1

description:
S001_10_S106
Control-sham-FAP-NO1

value: Pdgfra+


title: CCuA rep3


title: A549-1-12h-mock

description: replicate 1


title: RNAseq_control_rep1

value: post natal day 90


title: LCuA rep1


title: p33

status: Public on Nov 18 2021

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

description: 7h PMI

data_processing:
Cell Raner (v3.0.2) were used for reads alignment, filtering, UMI and barcode counting
Seurat (v3) was used for quality control, batch correction, dimension reduction and cell clustering
Please refer STAR methods for more details
Genome_build: Mmul10; susScr11
Supplementary_files_format_and_content: tab-delimited text files including meta annotation for each cell; tab-delimited text files including UMI counts; tab-delimited text files for gene symbols

organism: Sus scrofa

source_name: Pig hippocampus

extract_protocol:
The brain cell nuclei were isolated according to our previous protocol (Li et al., 2018; Zhu et al., 2018) with some modifications. Hippocampal regions (DG, CA1, CA2-4, Sub) and adjacent entorhinal cortex were dissected from three frozen adult human brains (Table S1). In order to avoid experimental bias and evenly dissociate the tissue for cell nuclei isolation, whole tissue was finely pulverized to powder in liquid nitrogen with mortar and pestle (Coorstek #60316, #60317). All buffers were ice cold and all reagents used for consequent nuclear isolation were molecular biology grade unless stated otherwise. 5 - 10 mg of pulverized tissue was added into 5 ml of ice-cold lysis buffer consisting of 320 mM sucrose (Sigma #S0389), 5 mM CaCl2 (Sigma #21115), 3 mM Mg(Ace)2 (Sigma #63052), 10mM Tris-HCl (pH 8) (AmericanBio #AB14043), protease inhibitors w/o EDTA (Roche #11836170001), 0.1 mM EDTA (AmericanBio #AB00502), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186), and  0.1% TX-100 (v/v) (Sigma#T8787). DTT, RNAse Protector, protease inhibitors, and TX-100 were added immediately before use. The suspension was transferred to Dounce tissue grinder (15ml volume, Wheaton #357544; autoclaved, RNAse free, ice-cold) and homogenized with loose and tight pestles, 30 cycles each, with constant pressure and without introduction of air. The homogenate was strained through 40 um tube top cell strainer (Corning #352340) which was pre-wetted with 1ml wash buffer: (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)). Additional 4 ml of wash buffer was added to wash the strainer. Final 10 ml of solution was mixed with 10 ml of 50% Optiprep (Axis-Shield# 1114542) solution (50% iodixanol (v/v), 250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)) by inverting the tube 10x and carefully pipetted into 2 centrifuge tubes (Corning #430791). The tubes were centrifuged at 1000g, for 30 min at 4 ˚C on centrifuge (Eppendorf #5804R) and rotor (Eppendorf #S-4-72). Upon end of centrifugation, the supernatant was carefully and completely removed and total of 5 ml of resuspension buffer (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)) was added carefully on the pellets in tubes and centrifuged at 1000g, for 10 min at 4 ˚C on the same centrifuge and rotor. Supernatants were then carefully and completely removed, pellets were gently dissolved by adding 100 ul of resuspension buffer (see above) and pipetting 30x with 1ml pipette tip, pooled and filtered through 35 um tube top cell strainer (Corning #352340). Finally, nuclei were counted on hemocytometer and diluted to 1 million/ml with sample-run buffer: 0.1% BSA (Gemini Bio-Products #700-106P), RNAse inhibitor (80U/ml) (Roche#03335402001), 1mM DTT (Sigma #43186) in DPBS (Gibco #14190).
10X Chromium Single Cell 3ʹ v3

value: Hippocampus

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA


title: p26

description: 7h PMI

tag: tissue


title: p32

description: 7h PMI


title: p40

description: 1h PMI


title: p38

description: 1h PMI


title: p39

description: 1h PMI


title: p43

description: 30min PMI


title: p42

description: 30min PMI


title: CCuA rep1


title: A549-1-4h-infected

description: replicate 1

value: adult


title: Testing SBCLN_Sample 197

city: Wuhan

first: Wei

last: Zhang

state: Hubei

address: Jiefang Avenue

department: Hematology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Not applicable

hyb_protocol: Briefly, 154 genes and 13 housekeeping gene probes were hybridized to 200 ng of the total RNA for 16 h at 65°C, and applied to the nCounter Preparation Station for automated removal of excess probe and immobilization of probe transcript complexes on a streptavidin-coated cartridge

scan_protocol: Digital gene expression of samples was performed on the NanoString platform, using the “high sensitivity” setting on the nCounter™ PrepStation and 550 field of view (FOV) on the nCounter™ Analyzer

data_processing: Gene expression values were normalized through housekeeping genes. Normalized count data were log2 transformed and agglomerative hierarchical clustering of gene expression were performed

label: Not applicable

label_protocol: Not applicable

growth_protocol: Not applicable

extract_protocol: The concentration of genomic RNA was quantitatively determined on a Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA)

treatment_protocol: Not applicable

value: female

value: Fresh tissue


title: Testing SBCLN_Sample 196

description: Not applicable

source_name: Other small B-cell lymphoid neoplasm

value: male


title: Testing SBCLN_Sample 191

description: Not applicable


title: Testing SBCLN_Sample 193

description: Not applicable

source_name: Chronic lymphocytic leukemia/Small lymphocytic lymphoma


title: Testing SBCLN_Sample 189

description: Not applicable


title: Testing SBCLN_Sample 190

description: Not applicable


title: A549-1-4h-mock

description: replicate 1

value: Mock


title: A549-1-8h-infected

description: replicate 1

value: severe acute respiratory syndrome

value: 8 hour


title: Testing SBCLN_Sample 188

description: Not applicable


title: Testing SBCLN_Sample 187

description: Not applicable


title: Testing SBCLN_Sample 186

description: Not applicable


title: Testing SBCLN_Sample 185

description: Not applicable


title: Testing SBCLN_Sample 184

description: Not applicable


title: A549-1-8h-mock

description: replicate 1


title: Testing SBCLN_Sample 180

description: Not applicable


title: Testing SBCLN_Sample 181

description: Not applicable


title: Testing SBCLN_Sample 183

description: Not applicable


title: Testing SBCLN_Sample 182

description: Not applicable


title: Testing SBCLN_Sample 194

description: Not applicable

source_name: Follicular lymphoma


title: Testing SBCLN_Sample 195

description: Not applicable


title: Testing SBCLN_Sample 192

description: Not applicable

source_name: Marginal zone lymphoma


title: Testing SBCLN_Sample 178

description: Not applicable


title: Testing SBCLN_Sample 176

description: Not applicable


title: Testing SBCLN_Sample 177

description: Not applicable


title: Testing SBCLN_Sample 179

description: Not applicable


title: Testing SBCLN_Sample 173

description: Not applicable


title: Testing SBCLN_Sample 175

description: Not applicable


title: Testing SBCLN_Sample 170

description: Not applicable


title: Testing SBCLN_Sample 171

description: Not applicable


title: Testing SBCLN_Sample 174

description: Not applicable


title: Testing SBCLN_Sample 169

description: Not applicable


title: Testing SBCLN_Sample 168

description: Not applicable


title: Testing SBCLN_Sample 167

description: Not applicable


title: Testing SBCLN_Sample 172

description: Not applicable


title: Testing SBCLN_Sample 166

description: Not applicable


title: RNAseq_control_rep2


title: Testing SBCLN_Sample 165

description: Not applicable


title: Testing SBCLN_Sample 164

description: Not applicable


title: Testing SBCLN_Sample 163

description: Not applicable


title: Testing SBCLN_Sample 162

description: Not applicable


title: Testing SBCLN_Sample 161

description: Not applicable


title: Testing SBCLN_Sample 159

description: Not applicable


title: Testing SBCLN_Sample 157

description: Not applicable


title: Testing SBCLN_Sample 155

description: Not applicable


title: Testing SBCLN_Sample 158

description: Not applicable


title: Testing SBCLN_Sample 156

description: Not applicable


title: Testing SBCLN_Sample 153

description: Not applicable


title: Testing SBCLN_Sample 160

description: Not applicable


title: Testing SBCLN_Sample 151

description: Not applicable


title: Testing SBCLN_Sample 150

description: Not applicable


title: Testing SBCLN_Sample 154

description: Not applicable


title: Testing SBCLN_Sample 149

description: Not applicable


title: Testing SBCLN_Sample 152

description: Not applicable


title: Testing SBCLN_Sample 145

description: Not applicable

source_name: Conventional mantle cell lymphoma


title: Testing SBCLN_Sample 146

description: Not applicable


title: Testing SBCLN_Sample 148

description: Not applicable


title: Testing SBCLN_Sample 147

description: Not applicable


title: Testing SBCLN_Sample 142

description: Not applicable


title: Testing SBCLN_Sample 141

description: Not applicable


title: Testing SBCLN_Sample 143

description: Not applicable


title: Testing SBCLN_Sample 139

description: Not applicable


title: Testing SBCLN_Sample 140

description: Not applicable


title: Testing SBCLN_Sample 144

description: Not applicable


title: Testing SBCLN_Sample 138

description: Not applicable

source_name: Leukemic non-nodal mantle cell lymphoma


title: Testing SBCLN_Sample 135

description: Not applicable


title: Testing SBCLN_Sample 136

description: Not applicable


title: Testing SBCLN_Sample 137

description: Not applicable


title: Testing SBCLN_Sample 133

description: Not applicable


title: Testing SBCLN_Sample 132

description: Not applicable


title: Testing SBCLN_Sample 130

description: Not applicable


title: Testing SBCLN_Sample 131

description: Not applicable


title: Testing SBCLN_Sample 129

description: Not applicable


title: Testing SBCLN_Sample 124

description: Not applicable


title: Testing SBCLN_Sample 125

description: Not applicable


title: Testing SBCLN_Sample 126

description: Not applicable


title: Testing SBCLN_Sample 123

description: Not applicable


title: Testing SBCLN_Sample 122

description: Not applicable


title: Testing SBCLN_Sample 121

description: Not applicable


title: Testing SBCLN_Sample 134

description: Not applicable


title: Testing SBCLN_Sample 127

description: Not applicable


title: Testing SBCLN_Sample 119

description: Not applicable


title: Testing SBCLN_Sample 116

description: Not applicable


title: Testing SBCLN_Sample 113

description: Not applicable


title: Testing SBCLN_Sample 110

description: Not applicable


title: Testing SBCLN_Sample 115

description: Not applicable


title: Testing SBCLN_Sample 114

description: Not applicable


title: Testing SBCLN_Sample 111

description: Not applicable


title: Testing SBCLN_Sample 112

description: Not applicable


title: Testing SBCLN_Sample 128

description: Not applicable


title: Testing SBCLN_Sample 109

description: Not applicable


title: Testing SBCLN_Sample 108

description: Not applicable


title: Testing SBCLN_Sample 106

description: Not applicable


title: Testing SBCLN_Sample 105

description: Not applicable


title: Testing SBCLN_Sample 107

description: Not applicable


title: Testing SBCLN_Sample 104

description: Not applicable


title: Testing SBCLN_Sample 103

description: Not applicable


title: Testing SBCLN_Sample 102

description: Not applicable


title: Testing SBCLN_Sample 120

description: Not applicable


title: Testing SBCLN_Sample 118

description: Not applicable


title: Testing SBCLN_Sample 101

description: Not applicable


title: Testing SBCLN_Sample 117

description: Not applicable


title: Testing SBCLN_Sample 99

description: Not applicable


title: Testing SBCLN_Sample 98

description: Not applicable


title: Testing SBCLN_Sample 100

description: Not applicable


title: Testing SBCLN_Sample 94

description: Not applicable


title: Testing SBCLN_Sample 96

description: Not applicable


title: Testing SBCLN_Sample 97

description: Not applicable


title: cdKO sham1

description:
S001_04_S100
dKO-sham-FAP-NO1

value: cdKO (Pdgfra-CreERT2::Yap1 flox/flox ::Taz flox/flox)

value: sham plantaris muscle


title: Testing SBCLN_Sample 89

description: Not applicable


title: Testing SBCLN_Sample 91

description: Not applicable


title: Testing SBCLN_Sample 95

description: Not applicable


title: Testing SBCLN_Sample 92

description: Not applicable


title: Testing SBCLN_Sample 93

description: Not applicable


title: Testing SBCLN_Sample 88

description: Not applicable


title: Testing SBCLN_Sample 86

description: Not applicable


title: Testing SBCLN_Sample 90

description: Not applicable


title: Testing SBCLN_Sample 87

description: Not applicable


title: Testing SBCLN_Sample 85

description: Not applicable


title: Testing SBCLN_Sample 83

description: Not applicable


title: Testing SBCLN_Sample 82

description: Not applicable


title: Testing SBCLN_Sample 79

description: Not applicable


title: Testing SBCLN_Sample 81

description: Not applicable


title: Testing SBCLN_Sample 80

description: Not applicable


title: Testing SBCLN_Sample 78

description: Not applicable


title: Testing SBCLN_Sample 76

description: Not applicable


title: Testing SBCLN_Sample 75

description: Not applicable


title: Testing SBCLN_Sample 74

description: Not applicable


title: Testing SBCLN_Sample 84

description: Not applicable


title: Testing SBCLN_Sample 73

description: Not applicable


title: Testing SBCLN_Sample 72

description: Not applicable


title: Testing SBCLN_Sample 71

description: Not applicable


title: Testing SBCLN_Sample 70

description: Not applicable


title: Testing SBCLN_Sample 68

description: Not applicable


title: Testing SBCLN_Sample 63

description: Not applicable


title: Testing SBCLN_Sample 67

description: Not applicable


title: Testing SBCLN_Sample 69

description: Not applicable


title: Testing SBCLN_Sample 65

description: Not applicable


title: Testing SBCLN_Sample 64

description: Not applicable


title: Testing SBCLN_Sample 61

description: Not applicable


title: Testing SBCLN_Sample 59

description: Not applicable


title: Testing SBCLN_Sample 60

description: Not applicable

tag: pediatric


title: Testing SBCLN_Sample 57

description: Not applicable


title: Testing SBCLN_Sample 77

description: Not applicable


title: Testing SBCLN_Sample 58

description: Not applicable


title: Testing SBCLN_Sample 56

description: Not applicable


title: Testing SBCLN_Sample 53

description: Not applicable


title: Testing SBCLN_Sample 52

description: Not applicable


title: Testing SBCLN_Sample 55

description: Not applicable


title: Testing SBCLN_Sample 50

description: Not applicable


title: p41

description: 30min PMI


title: Testing SBCLN_Sample 54

description: Not applicable


title: Testing SBCLN_Sample 66

description: Not applicable


title: Testing SBCLN_Sample 43

description: Not applicable


title: Testing SBCLN_Sample 45

description: Not applicable


title: Testing SBCLN_Sample 49

description: Not applicable


title: Testing SBCLN_Sample 48

description: Not applicable


title: Testing SBCLN_Sample 42

description: Not applicable


title: Testing SBCLN_Sample 46

description: Not applicable


title: Testing SBCLN_Sample 62

description: Not applicable


title: Testing SBCLN_Sample 41

description: Not applicable


title: Testing SBCLN_Sample 36

description: Not applicable


title: Testing SBCLN_Sample 39

description: Not applicable


title: Testing SBCLN_Sample 38

description: Not applicable


title: Testing SBCLN_Sample 40

description: Not applicable


title: Testing SBCLN_Sample 37

description: Not applicable


title: Testing SBCLN_Sample 35

description: Not applicable


title: Testing SBCLN_Sample 47

description: Not applicable


title: Testing SBCLN_Sample 33

description: Not applicable


title: Testing SBCLN_Sample 30

description: Not applicable


title: Testing SBCLN_Sample 31

description: Not applicable


title: Testing SBCLN_Sample 25

description: Not applicable


title: Testing SBCLN_Sample 24

description: Not applicable


title: Testing SBCLN_Sample 23

description: Not applicable


title: Testing SBCLN_Sample 19

description: Not applicable


title: Testing SBCLN_Sample 22

description: Not applicable


title: Testing SBCLN_Sample 34

description: Not applicable


title: Testing SBCLN_Sample 18

description: Not applicable


title: Testing SBCLN_Sample 16

description: Not applicable


title: Testing SBCLN_Sample 17

description: Not applicable


title: Testing SBCLN_Sample 21

description: Not applicable


title: Testing SBCLN_Sample 20

description: Not applicable


title: Testing SBCLN_Sample 44

description: Not applicable


title: Testing SBCLN_Sample 14

description: Not applicable


title: Testing SBCLN_Sample 32

description: Not applicable


title: Testing SBCLN_Sample 29

description: Not applicable


title: Testing SBCLN_Sample 15

description: Not applicable


title: Testing SBCLN_Sample 27

description: Not applicable


title: Testing SBCLN_Sample 13

description: Not applicable


title: Testing SBCLN_Sample 11

description: Not applicable


title: Testing SBCLN_Sample 10

description: Not applicable


title: Testing SBCLN_Sample 12

description: Not applicable


title: Testing SBCLN_Sample 8

description: Not applicable


title: Testing SBCLN_Sample 7

description: Not applicable


title: Testing SBCLN_Sample 51

description: Not applicable


title: Testing SBCLN_Sample 5

description: Not applicable


title: Testing SBCLN_Sample 2

description: Not applicable


title: Testing SBCLN_Sample 3

description: Not applicable


title: Testing SBCLN_Sample 4

description: Not applicable


title: Testing SBCLN_Sample 1

description: Not applicable


title: Testing SBCLN_Sample 28

description: Not applicable


title: Testing SBCLN_Sample 6

description: Not applicable


title: Training Control_Sample 99

description: Not applicable

source_name: Peripheral blood/bone marrow


title: Training Control_Sample 100

description: Not applicable


title: Training Control_Sample 101

description: Not applicable


title: Training Control_Sample 98

description: Not applicable


title: Training Control_Sample 94

description: Not applicable


title: Training Control_Sample 95

description: Not applicable


title: Testing SBCLN_Sample 9

description: Not applicable


title: Training Control_Sample 97

description: Not applicable


title: Training Control_Sample 96

description: Not applicable


title: Testing SBCLN_Sample 26

description: Not applicable


title: Training Control_Sample 90

description: Not applicable


title: Training Control_Sample 88

description: Not applicable


title: Training Control_Sample 102

description: Not applicable


title: Training Control_Sample 89

description: Not applicable


title: Training Control_Sample 87

description: Not applicable


title: Training Control_Sample 91

description: Not applicable


title: Training Control_Sample 84

description: Not applicable


title: Training Control_Sample 83

description: Not applicable


title: Training Control_Sample 85

description: Not applicable


title: Training Control_Sample 82

description: Not applicable


title: Training Control_Sample 81

description: Not applicable


title: Training Control_Sample 80

description: Not applicable


title: Training Control_Sample 92

description: Not applicable


title: Training Control_Sample 77

description: Not applicable


title: Training Control_Sample 78

description: Not applicable


title: Training Control_Sample 76

description: Not applicable


title: Training Control_Sample 74

description: Not applicable


title: Training Control_Sample 86

description: Not applicable


title: Training Control_Sample 93

description: Not applicable


title: Training Control_Sample 75

description: Not applicable


title: Training Control_Sample 68

description: Not applicable

source_name: Extranodal tissue


title: Training Control_Sample 69

description: Not applicable


title: Training Control_Sample 70

description: Not applicable

source_name: Lymph node/Waldeyer's ring


title: Training Control_Sample 71

description: Not applicable


title: Training Control_Sample 73

description: Not applicable


title: Training Control_Sample 72

description: Not applicable


title: Training Control_Sample 79

description: Not applicable


title: Training Control_Sample 65

description: Not applicable


title: Training Control_Sample 67

description: Not applicable


title: Training Control_Sample 66

description: Not applicable


title: Training Control_Sample 60

description: Not applicable


title: Training Control_Sample 63

description: Not applicable


title: Training Control_Sample 64

description: Not applicable


title: Training Control_Sample 62

description: Not applicable


title: Training Control_Sample 61

description: Not applicable


title: Training Control_Sample 58

description: Not applicable


title: Training Control_Sample 57

description: Not applicable


title: Training Control_Sample 59

description: Not applicable


title: Training Control_Sample 54

description: Not applicable


title: Training Control_Sample 53

description: Not applicable


title: Training Control_Sample 56

description: Not applicable


title: Training Control_Sample 55

description: Not applicable


title: Training Control_Sample 50

description: Not applicable


title: Training Control_Sample 49

description: Not applicable


title: Training Control_Sample 51

description: Not applicable


title: Training Control_Sample 45

description: Not applicable


title: Training Control_Sample 48

description: Not applicable


title: Training Control_Sample 44

description: Not applicable


title: Training Control_Sample 42

description: Not applicable


title: Training Control_Sample 52

description: Not applicable


title: Training Control_Sample 47

description: Not applicable


title: Training Control_Sample 39

description: Not applicable


title: Training Control_Sample 34

description: Not applicable


title: Training Control_Sample 35

description: Not applicable


title: Training Control_Sample 43

description: Not applicable


title: Training Control_Sample 38

description: Not applicable


title: Training Control_Sample 32

description: Not applicable


title: Training Control_Sample 30

description: Not applicable


title: Training Control_Sample 40

description: Not applicable


title: Training Control_Sample 33

description: Not applicable


title: Training Control_Sample 31

description: Not applicable


title: Training Control_Sample 37

description: Not applicable


title: Training Control_Sample 27

description: Not applicable


title: Training Control_Sample 28

description: Not applicable


title: Training Control_Sample 46

description: Not applicable


title: Training Control_Sample 23

description: Not applicable


title: Training Control_Sample 41

description: Not applicable


title: Training Control_Sample 21

description: Not applicable


title: Training Control_Sample 22

description: Not applicable


title: Training Control_Sample 36

description: Not applicable


title: Training Control_Sample 19

description: Not applicable


title: Training Control_Sample 18

description: Not applicable


title: Training Control_Sample 16

description: Not applicable


title: Training Control_Sample 26

description: Not applicable


title: Training Control_Sample 29

description: Not applicable


title: Training Control_Sample 13

description: Not applicable


title: Training Control_Sample 25

description: Not applicable


title: Training Control_Sample 10

description: Not applicable


title: Training Control_Sample 15

description: Not applicable


title: Training Control_Sample 6

description: Not applicable


title: Training Control_Sample 7

description: Not applicable


title: Training Control_Sample 24

description: Not applicable


title: Training Control_Sample 12

description: Not applicable


title: Training Control_Sample 14

description: Not applicable


title: Training Control_Sample 8

description: Not applicable


title: Training Control_Sample 20

description: Not applicable


title: Training Control_Sample 11

description: Not applicable


title: Training Control_Sample 9

description: Not applicable


title: Training Control_Sample 1

description: Not applicable


title: Training SBCLN_Sample 57

description: Not applicable


title: Training Control_Sample 3

description: Not applicable


title: Training Control_Sample 2

description: Not applicable


title: Training Control_Sample 4

description: Not applicable


title: Training SBCLN_Sample 54

description: Not applicable


title: Training Control_Sample 17

description: Not applicable


title: Training SBCLN_Sample 53

description: Not applicable


title: Training SBCLN_Sample 52

description: Not applicable


title: Training SBCLN_Sample 55

description: Not applicable


title: Training Control_Sample 5

description: Not applicable


title: Training SBCLN_Sample 56

description: Not applicable


title: Training SBCLN_Sample 48

description: Not applicable


title: Training SBCLN_Sample 50

description: Not applicable


title: Training SBCLN_Sample 51

description: Not applicable


title: Training SBCLN_Sample 45

description: Not applicable


title: Training SBCLN_Sample 44

description: Not applicable


title: Training SBCLN_Sample 47

description: Not applicable


title: Training SBCLN_Sample 42

description: Not applicable


title: Training SBCLN_Sample 43

description: Not applicable


title: Training SBCLN_Sample 46

description: Not applicable


title: Training SBCLN_Sample 40

description: Not applicable


title: Training SBCLN_Sample 41

description: Not applicable


title: Training SBCLN_Sample 37

description: Not applicable


title: Training SBCLN_Sample 36

description: Not applicable


title: Training SBCLN_Sample 34

description: Not applicable


title: Training SBCLN_Sample 38

description: Not applicable


title: Training SBCLN_Sample 33

description: Not applicable


title: Training SBCLN_Sample 32

description: Not applicable


title: Training SBCLN_Sample 31

description: Not applicable


title: Training SBCLN_Sample 30

description: Not applicable


title: Training SBCLN_Sample 29

description: Not applicable


title: Training SBCLN_Sample 26

description: Not applicable


title: Training SBCLN_Sample 49

description: Not applicable


title: Training SBCLN_Sample 24

description: Not applicable


title: Training SBCLN_Sample 25

description: Not applicable


title: Training SBCLN_Sample 23

description: Not applicable


title: Training SBCLN_Sample 22

description: Not applicable


title: Training SBCLN_Sample 39

description: Not applicable


title: Training SBCLN_Sample 27

description: Not applicable


title: Training SBCLN_Sample 21

description: Not applicable


title: Training SBCLN_Sample 19

description: Not applicable


title: Training SBCLN_Sample 17

description: Not applicable


title: Training SBCLN_Sample 20

description: Not applicable


title: Training SBCLN_Sample 35

description: Not applicable


title: Training SBCLN_Sample 18

description: Not applicable


title: Training SBCLN_Sample 15

description: Not applicable


title: Training SBCLN_Sample 16

description: Not applicable


title: Training SBCLN_Sample 13

description: Not applicable


title: Training SBCLN_Sample 12

description: Not applicable


title: Training SBCLN_Sample 14

description: Not applicable


title: Training SBCLN_Sample 9

description: Not applicable


title: Training SBCLN_Sample 11

description: Not applicable


title: Training SBCLN_Sample 8

description: Not applicable


title: Training SBCLN_Sample 10

description: Not applicable


title: Training SBCLN_Sample 28

description: Not applicable


title: Training SBCLN_Sample 7

description: Not applicable


title: Training SBCLN_Sample 6

description: Not applicable


title: Training SBCLN_Sample 5

description: Not applicable


title: KO_2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

description: Hsd3b6−/− meibomian gland acinar cells

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: meibomian gland acinar cells

extract_protocol:
For preparation of RNA-seq samples, Itgav(+);CD45(−) meibomian gland cells from WT and Hsd3b6−/− mice were obtained by FACS. We used four mice per replicate, with two replicates for both genotypes. Tarsal plates from four mice were pooled into HBSS containing 0.25% Trypsin and 50 µg/mL DNaseI, incubated for 15 min at 37℃, and minced. Then, digested tissues were dissociated in PBS containing 20% FBS and 0.5 mM EDTA and filtered through 70-µm strainer. Cell were resuspended into ice-cold PBS containing 2% FBS, 0.5 mM EDTA, and 50 µg/mL BSA) and further incubated with anti‐CD45-APC/Cyanine7 (Biolegend) and anti‐Itgav-PE (Biolegend). Cell sorting was performed using a FACSAria II Flow cytometer with FACSDiva software (BD Biosciences). Itgav(+);CD45(−) meibomian gland cells (approximately 10,000 cells per replicate) were sorted into DMEM/Ham's F12 medium containing 10% FBS. FACS-purified meibomian cells were pelleted and directly lysed into RLT buffer (Qiagen) containing 1% 2-mercaptoethanol. Total RNA was extracted using an Rneasy micro kit (Qiagen).
Total RNA was amplified using a SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). Then RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturers’ protocols.

tag: cell

value: meibomian gland acinar cells


title: WT_2

description: wild-type meibomian gland acinar cells

value: wild-type


title: KO_1

description: Hsd3b6−/− meibomian gland acinar cells


title: Training SBCLN_Sample 3

description: Not applicable


title: Training SBCLN_Sample 2

description: Not applicable


title: Training SBCLN_Sample 1

description: Not applicable


title: Training SBCLN_Sample 4

description: Not applicable


title: WT_1

description: wild-type meibomian gland acinar cells


title: OR15

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: Mouse: GRCm38
Supplementary_files_format_and_content: estimated counts for each transcript
Supplementary_files_format_and_content: transcripts per million (tpm) values for each transcript

source_name: total RNA extracted from mice lung

growth_protocol: Female CD-1 mice weighing 27-32 g were obtained from Charles River Laboratories Ltd. U.K. Prior to exposure, animals were habituated for 5 days. All mice were housed in filter-top cages in an enviromentally controled room and maintained at 21°C and 55% humidity. Lighting was set to mimic a 12/12 h dawn to dusk cycle. Animals had acess to food and water ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice were anesthetized by an interperitoneal injection of ketamine (1.9 mg/mouse) and xylazine (0.19 mg/mouse), and were intranasally (50 µl/nostril) intoxicated with crude ricin  (1.7 µg/kg  or 10 µg/kg  ) or intranasally infected with SARS-CoV-2 ( 5 x 106 PFU).

tag: treatment

value: 48 hr post 10 µg/kg ricin

value: lung


title: OR14


title: OR022

value: 96 hr post  5x10^6 PFU per mouse SARS-Cov-2


title: OR16


title: OR023


title: OR021


title: OR13


title: OR12

value: 96 hr post 1.7 µg/kg ricin + 5x10^6 PFU per mouse SARS-Cov-2


title: OR11


title: OR10


title: OR07

value: 96 hr post 1.7 µg/kg ricin


title: OR05


title: OR06


title: OR09


title: OR20 control

value: NO TREATMENT


title: OR08


title: OR18 control


title: OR17 control


title: OR19 control


title: 0_Per_2_F31

city: San Diego

first: Oscar

middle: E

last: Echeagaray

state: CA

address: 5500 Campanile Drive

institute: San Diego State University

data_processing:
The raw data was processed on the SpaceRanger pipeline (10X Genomics; version 1.2.2). Sequencing reads were aligned to the 10x mouse genome mm10-2020-A.
Preparations derived from slide preparation yielded 4933 barcoded spots for analysis, from which 1315 corresponded to Control (842 male, 473 female), and 3618 corresponded to 0% vape group (1565 male, 2053 female). Final removal of unwanted sources of variation and batch effect corrections was performed using Seurat R Package (v4.0.3).
Sequencing reads were aligned to the 10x mouse genome mm10-2020-A. Spots maintained comparable UMI and gene count detection throughout the tissue section
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

molecule: polyA RNA

source_name: Vaped Female

extract_protocol:
Freshly obtained cryosections were placed in Visium gene expression slides (10X Genomics, Cat# 2000233) for processing. Tissue staining with hematoxylin and eosin and image collections were done as suggested by  10X Genomics Visium protocol.
Spatial transcriptomic libraries were prepared using Visium Spatial Gene Expression Slide & Reagent Kit following manufacturer’s protocol (10X Genomics, PN-1000184). Lung permabilization time was optimized Visium Spatial Tissue Optimization Slide & Reagent Kit (10X Genomics, PN-1000193). Samples were processed together to avoid introduction of technical batch effects. Sequencing libraries were submitted to the UCSD IGM Genomics Core for sequencing (NovaSeq 6000), aiming for > 50K reads per spot.

tag: sample group

value: Vaped (V)

value: upper pulmonary brances


title: CTL_2_F62

source_name: Non-Vaped Female

value: Non-Vaped (NV)

value: female


title: splenic Tregs, KO5

city: Zürich

first: Claudia

last: Haftmann

address: Winterthurerstr. 190

department: Experimental Immunology

country: Switzerland

institute: University of Zurich

data_processing:
Raw reads were aligned to mouse genome build GRCm38 using STAR aligner. Read counts per gene were calculated using the featureCounts (part of the Subread package) based on GENCODE gene annotation version M16. Principal Component Analysis (PCA) was performed using the DESeq2 package on the trimmed and normalized raw counts after variance stabilizing transformation in RStudio. Genes that were differentially-expressed (DEGs) between cell types were identified using edgeR packages (72)  and volcano plot and heatmap presentation have been obtained on logarithmically transformed expression values.
Genome_build: GRCm38
Supplementary_files_format_and_content: Count_QC-raw-count-2.txt

source_name: spleen

extract_protocol:
Total RNA was isolated from Treg cells of spleen sorted directly into RNA lysis buffer (RNeasy, Qiagen). RNA quality was controlled by Bioanalyzer (Agilent Technologies) RNA 6000 Pico kit (Agilent Technologies) regarding RIN > 9.
cDNA from each sample were subjected to tagmention and amplification using Illumina Nextera XT kit. The resulting libraries were pooled, double-sided size selected (0.5x followed by 0.8x ratio using Beckman Ampure XP beads) and quantified using an Agilent 4200 TapeStation System. The pool of libraries was sequenced in an Illumina NovaSeq 6000 sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
amplicon

treatment_protocol: qiagenRNeasy micro

value: spleen

tag: cell type

value: splenic Tregs

tag: mouse id

tag: genotype

value: Foxn1Cre x NIKfl/fl

tag: strain


title: cKit_N_DDR2_P

data_processing:
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 3.0.1). Reads were aligned to the 10x mouse genome mm10.
Preparations derived from cell surface sorting strategy yielded 12286 barcoded cells for analysis, from which 3603 corresponded to cKit+DDR2-, 2755 corresponded to cKit-DDR2+, 4546 corresponded to cKit+DDR2+, and 1382 corresponded to cKit+DDR2+CD45-. Final removal of unwanted sources of variation and batch effect corrections was performed using Seurat R Package (v4.0.4)
Sequenced reads were aligned to the human reference genome mm-10
Genome_build: mm-10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

extract_protocol:
Briefly, heart samples were mechanically minced into 1-mm3 pieces and digested in collagenase II (150 U mg/mL, Worthington, LS004174) followed by brief low-speed (850 rpm for 2 minutes) centrifugation to remove cardiomyocytes and tissue debris. After removing cardiomyocytes by cell strainers, cKit +/-DDR2 +/- cardiac interstitial cells were obtained by FACS sorting with cKit antibody and DDR2 antibody and surface depletion of CD45 in the double positive population.
The Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (PN- 1000268), Chromium Single Cell 3' Chip G kit v2 (PN-1000120) and Dual Index Kit TT Set A, (PN-1000215) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V3.1 User Guide.

value: cardiac interstitial cells

tag: cell subtype


title: cKit_P_DDR2_P_CD45_N


title: cKit_P_DDR2_N


title: cKit_P_DDR2_N_1


title: 0_Per_1_M24

source_name: Vaped Male

value: male


title: CND_cKit_P_DDR2_P


title: splenic Tregs, WT3

value: Foxn1Cre x NIKfl/wt


title: splenic Tregs, WT5


title: splenic Tregs, KO2


title: splenic Tregs, KO1


title: splenic Tregs, WT2


title: splenic Tregs, WT1


title: splenic Tregs, WT4


title: IgG_rep1,rep2,rep3,rep4,rep5

city: New York

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: 10x scRNA

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 3.1.0).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 3.1.0) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each sample with five mouse using antibody barcode patterns from TotalSeq.
Mouse specific barcodes were demultiplexed by HTO using Seurat (version 3.2.3).
Genome_build: Ensembl mm10
Supplementary_files_format_and_content: Hirschhorn_Gene_counts.csv Raw gene count matrix
Supplementary_files_format_and_content: Hirschhorn_annotations.txt Annotation data, cell barcode to mouse by HTO, barcoded VDJ sequences
Supplementary_files_format_and_content: contig_annotations.csv

extract_protocol:
N/A (10X Genomics)
Chromium Single Cell 5' Reagent Kit
Chromium Single Cell V(D)J Enrichment Kit Mouse T Cell
Chromium Single Cell 5' Feature Barcode Library Kit

treatment_protocol: Cohorts of 5 mice were injected with B16. On day 8, CTX was injected. The next day,  mice were injected with anti-GITR antibody or IgG. Additional cohorts of mice were  injected with B16 on day 8, on day 15 mice were injected with DTA or IgG. After 1 week,  all cohorts of mice were sacrificed, and single cell suspensions were prepared.  Asynchronous B16 challenge was needed for the CTX groups a week apart given the  lack of immune infiltrates caused by chemotherapy treatment. Single cell suspensions  were simultaneously stained with anti-CD5-PE (BD Bioscience) and TotalSeq™- antimouse  hashtag antibodies (C0301, C0302, C0303, C0304, C0305; Biolegend). The cells  were FACS sorted based on CD5+ and next next-generation TCR coupled with 10X  sequencing was performed.

value: Tumor infiltrating T cells

value: IgG


title: CTX_rep1,rep2,rep3,rep4,rep5

description: 10x scRNA

value: CTX


title: DTA_rep1,rep2,rep3,rep4,rep5

description: 10x scRNA

value: anti-GITR


title: CTXDTA_rep1,rep2,rep3,rep4,rep5

description: 10x scRNA

value: CTX + anti-GITR


title: splenic Tregs, KO3


title: splenic Tregs, KO4


title: Sample 498_Cdh1803_P18_R9

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description: BSSE_QGF_141060_HLLWMDRXX_2_Cdh1803_P18_GGCGCCATTG_ACCGCGCAAT_S188_L002

data_processing:
Paired-end reads were aligned to the mouse genome (UCSC version mm10 analysis set) with STAR with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
The output was sorted and indexed with samtools. Read and alignment quality was evaluated using the qQCReport function of the Bioconductor package QuasR.
The featureCounts function from Bioconductor package subread was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (with used gene model provided by ensembl v96).
Processing of the read count matrix for genes was done according to the steps illustrated in Bioconductor Single Cell Analysis workflow (Amezquita et al., 2020).
Genome_build: mm10
Supplementary_files_format_and_content: TXT file (with tab separated values) with raw counts for Ensembl Genes, 1.column is Ensembl Gene ID, 2. and remaining columns contain raw counts

source_name: Murine mammary tumor cell lines derived from tumors of lineage-traced MMTV-PyMT transgenic mice

growth_protocol: Cells were directly sorted from tumors of mice

extract_protocol:
FACS-sorted cells were collected as 5-cell pools in 2.5µl of 0.2% TX-100 and 2U/μl RNase inhibitor (TakaraBio, 2313B) in PBS into 96-well plates (Thermo Fisher Scientific, 4346906) and kept in -80°C prior to use. RNAseq libraries were prepared according to the Smart-seq2 method (Picelli, 2014).
5-cell RNA-seq: RNA/cDNA preamplification and Nextera XT library preparation reactions were set up with a Mosquito HV system (SPT Labtech). After reverse transcription and amplification, the concentration of cDNA generated from each sample was measured using PicoGreen (Thermo Fisher Scientific). cDNA was normalized to 0.1-0.15ng/µl and 0.75 µl were used for library preparation with the Nextera XT DNA library preparation kit (Illumina). Multiplexed library pools were then pooled and PE 2x51 sequenced with an Illumina NovaSeq 6000 system, v1 reagents.

treatment_protocol: Each mouse was treated with 2mg of Tamoxifen twice per week starting at 9 weeks of age and continuing until sacrifice (around 13 to 14 weeks of age)

tag: system

value: Cdh

tag: mouse

tag: population

tag: egfp

value: neg

tag: mcherry

value: high

tag: epcam

tag: passedqc

value: FALSE


title: Sample 493_Cdh1739_P18_R8

description: BSSE_QGF_141055_HLLWMDRXX_2_Cdh1739_P18_ATGTCCAGCA_CAGCGGACAA_S183_L002

value: TRUE


title: Sample 495_Cdh1803_P18_R8

description: BSSE_QGF_141057_HLLWMDRXX_2_Cdh1803_P18_GTTGTGACTA_ACATAACGGA_S185_L002


title: Sample 501_Cdh1739_P18_R11

description: BSSE_QGF_141063_HLLWMDRXX_2_Cdh1739_P18_CCAATGATAC_GAGTGTGCCG_S191_L002


title: Sample 496_Cdh1739_P18_R9

description: BSSE_QGF_141058_HLLWMDRXX_2_Cdh1739_P18_GTAACAATCT_CTCTGTATAC_S186_L002


title: Sample 499_Cdh1739_P18_R10

description: BSSE_QGF_141061_HLLWMDRXX_2_Cdh1739_P18_TACCGCCTCG_CCTCGCAACC_S189_L002


title: Sample 502_Cdh1803_P18_R11

description: BSSE_QGF_141064_HLLWMDRXX_2_Cdh1803_P18_CTTCCTAGGA_CCTAGAGTAT_S192_L002


title: Sample 497_Cdh1739_P15_R9

description: BSSE_QGF_141059_HLLWMDRXX_2_Cdh1739_P15_CAGCGGTAGA_GCAACAGGTG_S187_L002


title: Sample 491_Cdh1725_P15_R5

description: BSSE_QGF_141053_HLLWMDRXX_2_Cdh1725_P15_TTCATGGTTC_GACATTGTCA_S181_L002


title: Sample 504_Cdh1803_P18_R12

description: BSSE_QGF_141066_HLLWMDRXX_2_Cdh1803_P18_AGCTGGAATG_ACGGAATGCG_S194_L002


title: Sample 490_Cdh1739_P15_R7

description: BSSE_QGF_141052_HLLWMDRXX_2_Cdh1739_P15_CCTGCAACCT_GTAGAGTCAG_S180_L002


title: Sample 488_Cdh1803_P18_R6

description: BSSE_QGF_141050_HLLWMDRXX_2_Cdh1803_P18_ATAGTTAGCA_CTCTAAGTAG_S178_L002


title: Sample 489_Cdh1739_P18_R7

description: BSSE_QGF_141051_HLLWMDRXX_2_Cdh1739_P18_TGAACGCGGA_CTTCGAAGGA_S179_L002


title: Sample 486_Cdh1739_P15_R6

description: BSSE_QGF_141048_HLLWMDRXX_2_Cdh1739_P15_CTGTGGTGAC_GACAGACAGG_S176_L002


title: Sample 485_Cdh1739_P18_R6

description: BSSE_QGF_141047_HLLWMDRXX_2_Cdh1739_P18_TACAAGACTT_CAGGTGTTCA_S175_L002


title: Sample 483_Cdh1725_P18_R17

description: BSSE_QGF_141045_HLLWMDRXX_2_Cdh1725_P18_GCTTCATATT_CGTTCAGCCT_S173_L002


title: Sample 500_Cdh1803_P18_R10

description: BSSE_QGF_141062_HLLWMDRXX_2_Cdh1803_P18_AAGAGAGTCT_TACGAATCTT_S190_L002


title: Sample 484_Cdh1803_P18_R5

description: BSSE_QGF_141046_HLLWMDRXX_2_Cdh1803_P18_ACTAGCGCTA_TTACTTCCTC_S174_L002


title: Sample 480_Cdh1803_P18_R4

description: BSSE_QGF_141042_HLLWMDRXX_2_Cdh1803_P18_CTAAGTACGC_AACATACCTA_S170_L002


title: Sample 479_Cdh1725_P18_R16

description: BSSE_QGF_141041_HLLWMDRXX_2_Cdh1725_P18_TTACAGTTAG_ACATGCATAT_S169_L002


title: Sample 487_Cdh1725_P15_R4

description: BSSE_QGF_141049_HLLWMDRXX_2_Cdh1725_P15_CTCCACTAAT_TGTACTTGTT_S177_L002


title: Sample 481_Cdh1739_P18_R5

description: BSSE_QGF_141043_HLLWMDRXX_2_Cdh1739_P18_TAGTGGAAGC_AGTACCTATA_S171_L002


title: Sample 503_Cdh1739_P18_R12

description: BSSE_QGF_141065_HLLWMDRXX_2_Cdh1739_P18_TATCACTCTG_AACGTTACAT_S193_L002


title: Sample 494_Cdh1739_P15_R8

description: BSSE_QGF_141056_HLLWMDRXX_2_Cdh1739_P15_CAACGTTCGG_GGATCCGCAT_S184_L002


title: Sample 492_Cdh1803_P18_R7

description: BSSE_QGF_141054_HLLWMDRXX_2_Cdh1803_P18_ATCCTCTCAA_TCCGCAAGGC_S182_L002


title: Sample 477_Cdh1739_P18_R4

description: BSSE_QGF_141039_HLLWMDRXX_2_Cdh1739_P18_CACTATCAAC_TCAGTTAATG_S167_L002


title: Sample 473_Cdh1739_P18_R3

description: BSSE_QGF_141035_HLLWMDRXX_2_Cdh1739_P18_GCTAGACTAT_AATACGACAT_S163_L002


title: Sample 478_Cdh1739_P15_R4

description: BSSE_QGF_141040_HLLWMDRXX_2_Cdh1739_P15_TTGCTCTATT_GTGACCTTGA_S168_L002


title: Sample 469_Cdh1739_P18_R2

description: BSSE_QGF_141031_HLLWMDRXX_2_Cdh1739_P18_AACCGAGTTC_GATCTCTGGA_S159_L002


title: Sample 470_Cdh1739_P15_R2

description: BSSE_QGF_141032_HLLWMDRXX_2_Cdh1739_P15_TGTGATAACT_CAGGCGCCAT_S160_L002


title: Sample 467_CTRL_R16

description: BSSE_QGF_141029_HLLWMDRXX_2_negative_no_template_control__CGCACGACTG_GGACCAACAG_S157_L002

source_name: Empty well

value: CTRL


title: Sample 471_Cdh1725_P18_R14

description: BSSE_QGF_141033_HLLWMDRXX_2_Cdh1725_P18_AGTATGCTAC_TTAATAGACC_S161_L002


title: Sample 472_Cdh1803_P18_R2

description: BSSE_QGF_141034_HLLWMDRXX_2_Cdh1803_P18_GTAACTGAAG_GGAGTCGCGA_S162_L002


title: Sample 468_CTRL_R17

description: BSSE_QGF_141030_HLLWMDRXX_2_negative_no_template_control__GAGGTTAGAC_AATGTATTGC_S158_L002


title: Sample 474_Cdh1739_P15_R3

description: BSSE_QGF_141036_HLLWMDRXX_2_Cdh1739_P15_AGCTACTATA_GTTATATGGC_S164_L002


title: Sample 476_Cdh1803_P18_R3

description: BSSE_QGF_141038_HLLWMDRXX_2_Cdh1803_P18_CTTACCGCAC_TAAGACCTAT_S166_L002


title: Sample 465_Cdh1803_P15_R1

description: BSSE_QGF_141027_HLLWMDRXX_2_Cdh1803_P15_TCCTGGTTGT_CTGACCGGCA_S155_L002


title: Sample 462_Cdh1739_P15_R1

description: BSSE_QGF_141024_HLLWMDRXX_2_Cdh1739_P15_CGAGGCCAAG_GTGTTACCGG_S152_L002


title: Sample 463_Cdh1725_P18_R13

description: BSSE_QGF_141025_HLLWMDRXX_2_Cdh1725_P18_TTCACGAGAC_AGATTGTTAC_S153_L002


title: Sample 464_Cdh1803_P18_R1

description: BSSE_QGF_141026_HLLWMDRXX_2_Cdh1803_P18_GCGTGGATGG_TTGACCAATG_S154_L002


title: Sample 466_CTRL_R15

description: BSSE_QGF_141028_HLLWMDRXX_2_negative_no_template_control__TAATTCTGCT_TCTCATCAAT_S156_L002


title: Sample 458_Cdh1624_P18_R12

description: BSSE_QGF_141020_HLLWMDRXX_2_Cdh1624_P18_AGCGCCACAC_CTAATGTCTT_S148_L002


title: Sample 457_Cdh1654_P18_R12

description: BSSE_QGF_141019_HLLWMDRXX_2_Cdh1654_P18_GTAACTTGGT_CGCCATACCT_S147_L002


title: Sample 461_Cdh1739_P18_R1

description: BSSE_QGF_141023_HLLWMDRXX_2_Cdh1739_P18_TCTCATGATA_AACACGTGGA_S151_L002


title: Sample 460_Cdh1725_P05_R12

description: BSSE_QGF_141022_HLLWMDRXX_2_Cdh1725_P5_CACCTTAATC_TTAGGATAGA_S150_L002


title: Sample 459_Cdh1725_P18_R12

description: BSSE_QGF_141021_HLLWMDRXX_2_Cdh1725_P18_TGCTACTGCC_CAACCGGAGG_S149_L002


title: Sample 456_Cdh1624_P15_R7

description: BSSE_QGF_141018_HLLWMDRXX_2_Cdh1624_P15_ACGGTCCAAC_TCTTACATCA_S146_L002


title: Sample 454_Cdh1725_P18_R11

description: BSSE_QGF_141016_HLLWMDRXX_2_Cdh1725_P18_CGCTGTCTCA_ATTACTCACC_S144_L002


title: Sample 452_Cdh1654_P18_R11

description: BSSE_QGF_141014_HLLWMDRXX_2_Cdh1654_P18_GATCGTCGCG_CTGGATATGT_S142_L002


title: Sample 455_Cdh1725_P05_R11

description: BSSE_QGF_141017_HLLWMDRXX_2_Cdh1725_P5_AATTCTTGGA_TTGTCAACTT_S145_L002


title: Sample 453_Cdh1624_P18_R11

description: BSSE_QGF_141015_HLLWMDRXX_2_Cdh1624_P18_TATCCGAGGC_GGCCAATAAG_S143_L002