title: 98

description:
20180327_K10_101_05
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

value: keratinizing

tag: tumor_cell_budding (2 tier)

value: small

value: low

value: big

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PR

value: Oral cavity


title: 96

status: Public on Jun 01 2023

type: RNA

city: Berlin

first: Raik

last: Otto

state: Berlin

address: Rudower Chaussee 25

department: Computer Sciences

country: Germany

institute: Humboldt-Universität zu Berlin

description:
20180327_K09_96_12
Nanostring nCounter HSNCC Custom Panel

hyb_protocol: For mRNA expression analyses 400 ng (concentration 100 ng/µl) isolated RNA per sample were hybridized on a nCounter Analysis System using a customized NanoString panel consisting of 231 genes according to manufacturer’s instructions (NanoString Technologies, Seattle, WA).

scan_protocol: Slides were scanned on a slide scanner (Aperio AT2, Leica Biosystems GmbH, Nussloch, Germany) and evaluated on a standard monitor (Fujitsu B24T-7, Fujitsu Limited, Tokyo, Japan, resolution 1920 x 1080) utilizing Aperio ImageScope x64 (version 12.4.0.7018; Leica Biosystems GmbH, Nussloch, Germany). One digitized high-power field (HPF) comprised 97464 µm2 which corresponded to a field diameter of 0.35 mm in light microscopy.

data_processing: Dataset normalization was conducted with the ‘NanoStringNorm’ R-package, version 1.2.1 (36). The ‘stringR’ and ‘ggplot2’ packages in conjunction with the ‘pheatmap’ R-package (RRID:SCR_016418) were utilized for visualization and string manipulation (37,38). For differential expression analyses, the ‘LIMMA’ R-package was utilized (39,40). For computational analysis R (version 4.1.3) (41) and SPSS v25 (International Business Machines Corporation (IBM), Armonk, NY)  were used.

label: NanoString

molecule: total RNA

organism: Homo sapiens

source_name: Tumor tissue

label_protocol: Labels are artificial numbers without semantical meaning

growth_protocol: Direct in-vivo biopsy

extract_protocol: RNA extraction and NanoString analyses were conducted as previously described (35). In short, H&E stained slides of HNSCC cases were examined to identify tumor regions and to estimate tumor cell content. FFPE material with a minimal tumor cell content of 20 % (median 65 %)  was used for subsequent microdissection of RNA from 3 µm thick sections. RNA was then extracted according to manufacturer’s instructions on a Maxwell extraction system (Promega, Madison, WI) and quantified by Qubit (Thermo Fisher Scientific, Waltham, MA).

tag: histotyp

tag: keratinization

value: high

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: Sex

tag: dcr

value: PD

value: Oropharynx


title: 97

description:
20180327_K10_100_04
Nanostring nCounter HSNCC Custom Panel

value: MS

value: Unknown

value: Hypopharynx


title: Muscle mononuclear cells, mdx_Spencer

type: SRA

city: Irvine

first: S.

middle: Armando

last: Villalta

state: California

address: 843 Health Sciences Rd

country: USA

institute: University of California Irvine

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: rms files

organism: Mus musculus

source_name: Muscle

extract_protocol:
WT C57BL/6, WT C57BL/10, mdx, B6A/J mice were humanely euthanized, perfused to clear circulating immune cells, and hind limb lymph nodes removed. Single-cell suspensions were prepared from healthy and dystrophic muscle by mechanical dissociation and enzymatic digestion with collagenase and DNase. Cell suspensions were washed and filtered sequentially through 70- and 40-micron cell strainers. Live muscle macrophages were FACS-sorted based on their expression of F4/80 and CD11b, and single-cell libraries constructed with the 10X Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: Muscle

tag: cell type

value: All mononuclear cells

tag: genotype

value: B10 mdx


title: Sample 38: HepG2_Total_RNA_siControl_Input_rep3

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

library_source: transcriptomic

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (https://sourceforge.net/projects/bbmap/), 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt tool. Remaining reads were aligned to hg38 genome using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) allowing at most three mismatches. The generated .bam files were split into positive and negative strands and sorted using Samtools (http://samtools.sourceforge.net/). Sequence variants were identified by measuring the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. A to T or C to T or G to T mutation ratio at each Nm candidate site were calculated by data output from bam-readcount pipeline and confirmed by direct visualization through IGV software (https://software.broadinstitute.org/software/igv/).  The input of Nm-Mut-seq is equivalent to regular RNA-seq, therefore we quantified the gene-level read counts of input samples that aligned to hg38 for differential gene expression analysis. Cufflinks and Cuffdiff were used to make inferential tests where differentially expressed genes were identified at FDR < 0.05 cut-off. Gene ontology analysis was performed using the online analysis software DAVID v6.8 (https://david.ncifcrf.gov) and REViGO tool (http://revigo.irb.hr).
Genome_build: hg38
Supplementary_files_format_and_content: xlsx (excel)

source_name: cell culture

growth_protocol: HepG2 were used for Nm analysis in this study were purchased from the American Type Culture Collection (ATCC). HepG2 was maintained in a low glucose DMEM medium (1g/L glucose) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Cellular total RNA was isolated with TRIzol reagent (Invitrogen) following manufacturer’s protocol by isopropanol precipitation. When extracting polyA+ RNA for sequencing Nm in RNA, Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment.
For purified total RNA, after DNase I treatment for cellular DNA removal, we removed small RNA species by MEGAclear Transcription Cleanup Kit (Invitrogen). We next performed two-rounds of polyA+ RNA enrichment with 50 μg total RNA harvested from the last step, using Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen™). The yield of polyA+ RNA in this step is roughly 0.5~1 μg. Then the eluted polyA+ RNA or total RNA  was fragmented into 50-80 nt length using Na2CO3/NaHCO3 buffer (pH 9.2) and heated at 95 °C for 8 min, followed by purification with RNA Clean & Concentrator (Zymo Research). 50-100 ng of RNA was used for 3’-/5’-adaptor ligation. Starting with the 3’-adaptor ligation, the RNA oligos were incubated with 0.5 μL (12 μM) customized adaptors 5’App-NNNNN ATCACGAGATCGGAAGAGCACACGTCT-3SpC3 (containing five randomized nucleotides sequence (NNNNN) together with a 6-mer in-line barcode) at 70 °C for 2 mins and immediately placed on ice. 10 µL 3´ Ligation Reaction Buffer (2X) (NEB) and 3 µL 3´ Ligation Enzyme Mix (NEB) were added to the RNA-adapter mixture. The reaction was incubated at 25 °C for 2 hrs. Then 1.0 µL SR RT Primer for Illumina (NEB) was added to the mixture, followed by 5 minutes at 75°C, 15 minutes at 37°C, 15 minutes at 25°C, and then on ice. The denatured 0.5 µL 5’-Adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUCNNNNN-3’) was added into the mixture, together with 1.0 µL 5´ Ligation Reaction Buffer (10X) (NEB) and 2.5 µL 5´ Ligation Enzyme Mix (NEB). The reaction was incubated at 25 °C for 2 hrs followed by 16 °C for 4 hrs, followed by RNA Clean & Concentrator purification.  The purified RNA was eluted with 20 μL RNase-free water and subjected to reverse transcription. Two independent RT reactions (10 μL RNA for each reaction) were conducted with evolved RT 41B4 under two dNTP conditions: one RT reaction (as “input”) incubated with 1.0 mM dNTP without generating mutations on Nm sites; the other RT reaction (as “Nm-Mut-seq”) with 2 μM dNTP + 1 mM dATP would reveal mutations on Am, Cm and Gm sites. The RT reactions were performed at 37°C for 1 hour, followed by 80°C inactivation for 10 min. The libraries were amplified using the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina).
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: HepG2 cells were transfected using siRNAs purchased from Qiagen, targeting FBL (ATCGAGGATGCTCGACACCCA) or FTSJ3(AAGTTCGGTGTTGGAGCGATA) or non-targeting sequence (AllStars Neg. Control, SI03650318, Qiagen). To prepare siRNA/lipofectamine (Lipofectamine RNAiMAX Reagent, Invitrogen) mixture for one 15-cm plate, 400 pmol of siRNAs were diluted in 1.75 mL of Opti-MEM I Reduced Serum Media (Gibco) and 40 μL of lipofectamine was diluted in 1.75 mL of the same media in a separate tube. The siRNA and lipofectamine were mixed together and incubated at room temperature for 15 min. The combined 3.5 mL transfection solution was added into HepG2 cells which have already grown for 12 hours. Cellular total RNA was extracted for further analysis at 48 hrs or 72 hrs after the transfection.

value: HepG2 cells


title: Sample 47: HepG2_polyA_RNA_siControl_Treated_rep3

molecule: polyA RNA


title: 231

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 37
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 37 transcript annotations
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: Primary breast cancer

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

tag: disease state

value: breast cancer

value: Invasive ductal carcinoma

value: Neoplastic mammary epithelial tisssue

tag: breast cancer type

value: Hormone-receptor positive


title: Sample 39: HepG2_Total_RNA_siControl_Treated_rep1


title: 2049

value: Triple negative


title: 94

description:
20180327_K09_94_10
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

value: small

value: low

tag: inflammatory_infiltrate (2 tier)

value: SD


title: 95

description:
20180327_K09_95_11
Nanostring nCounter HSNCC Custom Panel

tag: histotyp

value: keratinizing

tag: keratinization

value: high

value: big

tag: lymphangiosis

value: PR

value: Tongue


title: 99

description:
20180327_K10_102_06
Nanostring nCounter HSNCC Custom Panel

value: MS

value: Unknown


title: Macrophage, B6AJ1

description: Integrated_B6_B10_MDX_B6AJ_SFigure10.rds

value: Muscle

value: Macrophage


title: Sample 37: HepG2_Total_RNA_siControl_Input_rep2

value: HepG2 cells


title: 1029

value: breast cancer

value: Invasive ductal carcinoma

value: Neoplastic mammary epithelial tisssue

value: Hormone-receptor positive


title: Macrophge, B6_WT1

value: B6 WT


title: Sample 36: HepG2_Total_RNA_siControl_Input_rep1


title: Sample 41: HepG2_Total_RNA_siControl_Treated_rep3


title: Sample 15: HepG2_polyA_RNA_Treated_rep3

growth_protocol: Hela and HepG2 were used for Nm analysis in this study were purchased from the American Type Culture Collection (ATCC). Hela cells were maintained in DMEM medium (4.5g/L glucose) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). . HepG2 was maintained in a low glucose DMEM medium (1g/L glucose) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

treatment_protocol: Wild-type cells were used for library construction.


title: 344-17T_Breast

value: Invasive carcinoma


title: 346


title: 93

description:
20180327_K09_93_09
Nanostring nCounter HSNCC Custom Panel

value: non-keratinizing

value: low

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: small


title: 92

description:
20180327_K09_92_08
Nanostring nCounter HSNCC Custom Panel

value: BA

value: high

value: big

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

value: SD

value: Oral cavity


title: Pdca1+ BM_01

city: Austin

first: Alessandra

middle: Machado

last: Araujo

state: TX

address: 2500 Speedway, MBB 3.312B

department: Chemical Engineering

institute: University of Texas at Austin

description:
10x Genomics
JA20116_cellranger_mm10

data_processing:
. Cellranger (v3.0.2) was used to demultiplex samples, to map data to the mouse transcriptome (mm10) and quantify genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Pdca1+ C57/BL6 bone marrow cells were magnetically sorted using MACS columns into culture medium, washed once with PBS + 0.04% BSA, and re-suspended in 32 μl PBS + 0.04% BSA. Single cell suspensions were processed in the University of Texas Genomic Sequencing and Analysis Facility. Cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics).
processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics). The resulting libraries were examined for size and quality using the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche). Samples were sequenced on the NovaSeq 6000 instrument (paired end, read 1: 28 cycles, read 2: 90 cycles) with a targeted depth of >30000 reads/cell.

value: Pdca1+ Bm cells

tag: tissue

value: Bone Marrow

tag: strain

tag: age

value: 6-8 weeks old


title: 91

description:
20180327_K09_91_07
Nanostring nCounter HSNCC Custom Panel

tag: Sex

tag: dcr

value: Oropharynx


title: Sample 14: HepG2_polyA_RNA_Treated_rep2

value: HepG2 cells


title: Sample 13: HepG2_polyA_RNA_Treated_rep1


title: 1160-16T_Breast

tag: disease state

value: breast cancer

tag: cell type

value: Neoplastic mammary epithelial tisssue

tag: breast cancer type


title: G1208_06, D2, M, CORT+DFP

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

library_source: genomic

data_processing:
Mus musculus (mouse) reference genome (GRCm38) and gene model annotation files were downloaded from the Ensembl genome browser (https://useast.ensembl.org/). Indices of the reference genome were built using STAR v2.5.0a (Dobin et al., 2013) and paired-end clean reads aligned to the reference genome. STAR using the method of Maximal Mappable Prefix to generate a precise mapping result for junction reads.
For quantification of DNA methylation, the bam files were loaded to the MEDIPS R package (version 1.44.0) using the MEDIPS.createSet function with the following parameters: uniq = 1, extend = 150, ws = 150, shift = 0. This divided the mm10 mouse genome into 150 bp non-overlapping windows, and reads were counted for each bin. The MEDIPS.couplingVector function was used to compute the local CpG density (coupling factor or CF), and the read counts were normalized to the CF using the function MEDIPS.meth. To retain only 150 bp bins that had sufficient coverage for reliable quantification and statistical analyses, we implemented the following filters: (1) bins with no CpGs (CF = 0) and mean read counts ≤ 1 were excluded, resulting in 5,724,879 bins; (2) these were loaded to the EdgeR R package (version 3.34.1) and further filtered on the basis of counts per million (CPM) to retain only reads with more than 1 CPM in 2 or more libraries. This resulted in 210,191 CpG regions that were then normalized by the library size using the calcNormFactors function. RPKM values were then extracted using the parameters gene.length = 150, log = TRUE, and the CpG regions were annotated using the HOMER software.
Assembly: GRCm38
Supplementary files format and content: Log RPKM

molecule: genomic DNA

source_name: Prefrontal cortex (PFC)

extract_protocol:
Genomic DNA with DNeasy Blood & Tissue Kit from Qiagen
Affinity-based CpG enrichment was done using the Invitrogen MethylMiner Methylated DNA Enrichment Kit (ThermoFisher Scientific, Waltham, MA, USA), which relies on the MBD2 protein.1,2 First, 1 µg of DNA in 110 μl low TE buffer was sheared to ~150 bp fragments using a Covaris S2 ultrasonicator (Covaris, Woburn, MA, USA). Sonication settings were the same as described in Sandoval-Sierra3 with cycle/burst of 1 for 10 cycles of 60 s, duty cycle of 10%, and intensity of 5.0. DNA fragment size and quality were assessed using the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). MBD-capture reaction was done according to the standard manufacturer’s protocol, followed by a single step elution with 2 M NaCl solution. The enriched DNA were then re-concentrated by ethanol precipitation, and the final concentration of methylated-CpG enriched DNA ranged from 0.17 to 2.1 ηg per μl (0.87 ± 0.39). This was followed by standard library prep for sequencing
Sequencing was done to 40 million reads per sample (150 paired-end) on the Illumina NovaSeq 6000

treatment_protocol: Treatment consisted of corticosterone in the drinking water (20 mg% w/v) for 7 days followed by i.p. injection of 4.0 mg kg-1 diisopropyl fluorophosphate (DFP, a sarin surrogate). CORT+DFP versus control

value: Prefrontal cortex (PFC)

tag: treatment

value: CORT+DFP

value: M

tag: age (days)

tag: body weight


title: Sample 12: HepG2_polyA_RNA_Input_rep3


title: G1208_04, D2, F, Control

value: Control

value: F


title: Sample 11: HepG2_polyA_RNA_Input_rep2


title: W308R ABCA3 mutant iAEC2s containing the ABCA3:GFP fusion reporter, rep3

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description:
W308R-AG-3
human iPSC line: Contains a CRISPR/Cas9-mutagenized biallelic W308R mutant ABCA3:GFP fusion product upon expression, clone # 168.

data_processing:
Reads were aligned to the ENSEMBL human reference genome GRCh38.91 using STAR
We used the Bioconductor package edgeR to import, filter and normalize the count matrix, followed by the limma package and voom, for linear model fitting and differential expression testing, using empirical Bayes moderation for estimating gene-wise variability prior to significance testing based on the moderated t-statistic.
Assembly: GRCh38.91
Supplementary files format and content: Raw read counts

growth_protocol: Directed differentiation of iAEC2s were performed as detailed in our previously published protocol (Jacob et al., 2017,  2019). In brief, day 0 PSCs were differentiated into definitive endoderm followed by anterior foregut endoderm, then further specified into NKX2-1+ lung epithelial progenitors. On day 15, NKX2-1 expressing lung epithelial progenitors were sorted by CD47hi/CD26lo sorting  to enrich for NKX2-1+ cells (as described in Hawkins et al., 2016). Sorted cells were plated in 3D Matrigel cultures and fed with distalizing media as detailed in Jacob et al. (2017).    Additionally, to increase the frequencies of SFTPCtdTomato expressing iAEC2s, CHIR “withdrawal and addback” to distal lung progenitor cells was conducted as previously published in Jacob et al. (2019)  and refed with distal media until day of sort

extract_protocol:
FACS sorting for single, live, ABCA3:GFP+ cells
RNA extraction was done using QIAzol (Qiagen) RNeasy Kit
Sequencing libraries were prepared from total RNA extracted from each indicated sample using Illumina TruSeq RNA Sample Preparation Kit v2. mRNA was isolated using magnetic bead-based poly(A) selection, fragmented, and randomly fragmented for reverse transcription, followed by synthesis of cDNA fragments. cDNA fragments were then end-paired, and ligated to Illumina Paired-End sequencing adapters. The products were end-paired and PCR-amplified to create the final cDNA library.

tag: cell line

value: iPSC-derived iAEC2s

tag: genotype

value: W308R mutant ABCA3

tag: developmental stage

value: day 43 of human distal lung directed differentiation


title: 89

description:
20180327_K09_89_05
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: MS

tag: histotyp

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

value: low

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: SD

value: Larynx


title: W308R ABCA3 mutant iAEC2s containing the ABCA3:GFP fusion reporter, rep2

description:
W308R-AG-2
human iPSC line: Contains a CRISPR/Cas9-mutagenized biallelic W308R mutant ABCA3:GFP fusion product upon expression, clone # 168.

tag: cell type


title: 88

description:
20180327_K09_88_04
Nanostring nCounter HSNCC Custom Panel

tag: necrosis

tag: necrosis (2 tier)

tag: Sex

tag: dcr

value: PR


title: G1208_05, D2, M, Control

tag: tissue

tag: strain

tag: treatment

tag: age (days)

tag: body weight


title: W308R ABCA3 mutant iAEC2s containing the ABCA3:GFP fusion reporter, rep1

description:
W308R-AG-1
human iPSC line: Contains a CRISPR/Cas9-mutagenized biallelic W308R mutant ABCA3:GFP fusion product upon expression, clone # 168.

tag: cell line

tag: genotype

tag: developmental stage


title: E690K ABCA3 mutant iAEC2s containing the ABCA3:GFP fusion reporter, rep3

description:
E690K-AG-3
human iPSC line: BU3_AG23_CR6_E690K_13  Contains a CRISPR/Cas9-mutagenized biallelic E690K mutant ABCA3:GFP fusion product upon expression, clone #13.

value: E690K mutant ABCA3


title: 86

description:
20180327_K09_86_02
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

tag: histotyp

value: keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: big

value: PD

value: Oral cavity


title: E690K ABCA3 mutant iAEC2s containing the ABCA3:GFP fusion reporter, rep2

description:
E690K-AG-2
human iPSC line: BU3_AG23_CR6_E690K_13  Contains a CRISPR/Cas9-mutagenized biallelic E690K mutant ABCA3:GFP fusion product upon expression, clone #13.

tag: cell type

value: iPSC-derived iAEC2s


title: G1208_07, D2, M, CORT+DFP

value: Prefrontal cortex (PFC)

value: CORT+DFP

tag: Sex

value: M


title: 85

description:
20180327_K09_85_01
Nanostring nCounter HSNCC Custom Panel

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: dcr


title: G1208_02, D2, F, Control

tag: tissue

tag: strain

tag: treatment

value: Control

value: F

tag: age (days)

tag: body weight


title: Sample 9: HeLa_polyA_RNA_Treated_rep3

value: HeLa cells


title: E690K ABCA3 mutant iAEC2s containing the ABCA3:GFP fusion reporter, rep1

description:
E690K-AG-1
human iPSC line: BU3_AG23_CR6_E690K_13  Contains a CRISPR/Cas9-mutagenized biallelic E690K mutant ABCA3:GFP fusion product upon expression, clone #13.

tag: cell line

tag: genotype

tag: developmental stage

value: day 43 of human distal lung directed differentiation


title: G1208_01, D2, F, CORT+DFP


title: 87

description:
20180327_K09_87_03
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

value: Unknown

value: Hypopharynx


title: Sample 8: HeLa_polyA_RNA_Treated_rep2


title: 77

description:
20180322_K08_77_05
Nanostring nCounter HSNCC Custom Panel

tag: histotyp

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

value: low

tag: nuclear_size (2 tier)

value: Larynx


title: 72

description:
20180322_K07_72_12
Nanostring nCounter HSNCC Custom Panel

value: keratinizing

value: big

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: Sex

value: SD


title: G1208_03, D2, F, CORT+DFP

tag: tissue

value: Prefrontal cortex (PFC)

tag: strain

tag: treatment

value: CORT+DFP

tag: age (days)

tag: body weight


title: Wildtype ABCA3 iAEC2s containing the ABCA3:GFP fusion reporter, rep3

description:
WT-AG-3
human iPSC line: BU3_AG23_CR6  BU3 genetic background, biallelically targeted with GFP at the C-terminus of endogenous ABCA3 locus resulting in ABCA3:GFP fusion product upon expression. Cre-excised puromycin selection cassette clone #6

tag: cell line

value: WT-AG

tag: cell type

value: iPSC-derived iAEC2s

tag: genotype

value: Wildtype ABCA3

tag: developmental stage


title: G1118_08, B6, M, CORT+DFP

value: M


title: Sample 7: HeLa_polyA_RNA_Treated_rep1

value: HeLa cells


title: G1118_07, B6, M, Control

value: Control


title: Wildtype ABCA3 iAEC2s containing the ABCA3:GFP fusion reporter, rep2

description:
WT-AG-2
human iPSC line: BU3_AG23_CR6  BU3 genetic background, biallelically targeted with GFP at the C-terminus of endogenous ABCA3 locus resulting in ABCA3:GFP fusion product upon expression. Cre-excised puromycin selection cassette clone #6

value: day 43 of human distal lung directed differentiation


title: Sample 10: HepG2_polyA_RNA_Input_rep1

value: HepG2 cells


title: 71

description:
20180322_K07_71_11
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: MS

tag: histotyp

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: dcr

value: Oropharynx


title: Sample 6: HeLa_polyA_RNA_Input_rep3


title: G1118_06, B6, M, Control

tag: Sex


title: Wildtype ABCA3 iAEC2s containing the ABCA3:GFP fusion reporter, rep1

description:
WT-AG-1
human iPSC line: BU3_AG23_CR6  BU3 genetic background, biallelically targeted with GFP at the C-terminus of endogenous ABCA3 locus resulting in ABCA3:GFP fusion product upon expression. Cre-excised puromycin selection cassette clone #6


title: G1118_05, B6, M, Control

tag: tissue


title: Sample 5: HeLa_polyA_RNA_Input_rep2


title: W308 gene-corrrected  iAEC2s, rep3

description:
cW308-R3
human iPSC line: W308R_ST13_CR17_Corr18  “W308 corrected patient iPSC line”  Patient iPSC line containing homozygous W308R mutation. The line contains tdTomato reporter  mono-allelically targeted to the start codon of the endogenous SFTPC gene locus clone #13.  Subsequently underwent cre-exision of puromycin selection cassette clone # 17. Underwent  subsequent CRISPR/Cas9 single nucleotide editing to correct W308R mutation to the wildtype  W308 codon, clone #18.

source_name: W308 gene-corrrected  iAEC2s

extract_protocol:
FACS sorting for single, live, tdTomato+ cells
RNA extraction was done using QIAzol (Qiagen) RNeasy Kit
Sequencing libraries were prepared from total RNA extracted from each indicated sample using Illumina TruSeq RNA Sample Preparation Kit v2. mRNA was isolated using magnetic bead-based poly(A) selection, fragmented, and randomly fragmented for reverse transcription, followed by synthesis of cDNA fragments. cDNA fragments were then end-paired, and ligated to Illumina Paired-End sequencing adapters. The products were end-paired and PCR-amplified to create the final cDNA library.

value: patient iPSC-derived iAEC2s

value: W308 gene-corrrected


title: Sample 4: HeLa_polyA_RNA_Input_rep1


title: W308 gene-corrrected  iAEC2s, rep2

description:
cW308-R2
human iPSC line: W308R_ST13_CR17_Corr18  “W308 corrected patient iPSC line”  Patient iPSC line containing homozygous W308R mutation. The line contains tdTomato reporter  mono-allelically targeted to the start codon of the endogenous SFTPC gene locus clone #13.  Subsequently underwent cre-exision of puromycin selection cassette clone # 17. Underwent  subsequent CRISPR/Cas9 single nucleotide editing to correct W308R mutation to the wildtype  W308 codon, clone #18.


title: 68

description:
20180322_K07_68_08
Nanostring nCounter HSNCC Custom Panel

value: Unknown

tag: lymphangiosis

value: SD


title: Sample 3: HeLa_Total_RNA_Treated_rep2


title: 69

description:
20180322_K07_69_09
Nanostring nCounter HSNCC Custom Panel

value: NE

value: Hypopharynx


title: 70

description:
20180322_K07_70_10
Nanostring nCounter HSNCC Custom Panel

value: PR

value: Larynx


title: G1118_04, B6, F, Control

value: Prefrontal cortex (PFC)

tag: strain

tag: treatment

value: F


title: E690 gene-corrrected  iAEC2s, rep3

description:
cE690-R3
human iPSC line: E690K_ST12_CR1_SS21_Corr32  “E690 corrected patient iPSC line”  Patient iPSC line containing homozygous E690K mutation secondary to paternal disomy. The  line contains tdTomato reporter mono-allelically targeted to the start codon of the endogenous  SFTPC gene locus clone #12. Subsequently underwent cre-excision of puromycin selection  cassette clone # 1. Followed by single cell sorted and cultured from one-cell outgrowth clone  #21. Underwent subsequent CRISPR/Cas9 single nucleotide editing to correct E690K mutation  to the wildtype E690 codon, clone #32.

source_name: E690 gene-corrrected  iAEC2s

value: E690 gene-corrrected

value: day 44 of human distal lung directed differentiation


title: W308 gene-corrrected  iAEC2s, rep1

description:
cW308-R1
human iPSC line: W308R_ST13_CR17_Corr18  “W308 corrected patient iPSC line”  Patient iPSC line containing homozygous W308R mutation. The line contains tdTomato reporter  mono-allelically targeted to the start codon of the endogenous SFTPC gene locus clone #13.  Subsequently underwent cre-exision of puromycin selection cassette clone # 17. Underwent  subsequent CRISPR/Cas9 single nucleotide editing to correct W308R mutation to the wildtype  W308 codon, clone #18.

value: day 43 of human distal lung directed differentiation


title: G1118_02, B6, F, CORT+DFP

value: CORT+DFP

tag: age (days)

tag: body weight


title: G1118_03, B6, F, Control

value: Control


title: Sample 2: HeLa_Total_RNA_Treated_rep1

value: HeLa cells


title: 66

description:
20180322_K07_66_06
Nanostring nCounter HSNCC Custom Panel

value: BA

value: keratinizing

value: high

value: small

value: low

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)


title: Sample 1: HeLa_Total_RNA_Input


title: G1118_01, B6, F, CORT+DFP


title: 65

description:
20180322_K07_65_05
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

tag: histotyp

tag: keratinization

value: big

value: SD

value: Oropharynx


title: E690 gene-corrrected  iAEC2s, rep2

description:
cE690-R2
human iPSC line: E690K_ST12_CR1_SS21_Corr32  “E690 corrected patient iPSC line”  Patient iPSC line containing homozygous E690K mutation secondary to paternal disomy. The  line contains tdTomato reporter mono-allelically targeted to the start codon of the endogenous  SFTPC gene locus clone #12. Subsequently underwent cre-excision of puromycin selection  cassette clone # 1. Followed by single cell sorted and cultured from one-cell outgrowth clone  #21. Underwent subsequent CRISPR/Cas9 single nucleotide editing to correct E690K mutation  to the wildtype E690 codon, clone #32.

tag: cell line

tag: cell type

value: patient iPSC-derived iAEC2s

tag: genotype

tag: developmental stage


title: G1014_09, B6, M, CORT+DFP

tag: tissue

value: Prefrontal cortex (PFC)

tag: Sex

value: M


title: ZEBARFISH WT AB9  Sample 23

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

institute: Max Planck Institute for heart and lung research

description: FISH.counts.matrix

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10, dm6, sacCer1, GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: ZEBARFISH

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: G1014_08, B6, M, CORT+DFP

tag: strain

tag: treatment


title: 63

description:
20180322_K07_63_03
Nanostring nCounter HSNCC Custom Panel

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: lymphangiosis

tag: dcr

value: PR

value: Larynx


title: W308R ABCA3 mutant iAEC2s, rep3

description:
W308R-R3
human iPSC line: W308R_ST13_CR17 (Parent, unedited line, core nomenclature: ABCA3-5) Patient iPSC line containing homozygous W308R mutation. The line contains tdTomato reporter  mono-allelically targeted to the start codon of the endogenous SFTPC gene locus clone #13.  Subsequently underwent cre-exision of puromycin selection cassette clone # 17.

source_name: W308R ABCA3 mutant iAEC2s

value: W308R ABCA3 mutant

value: day 43 of human distal lung directed differentiation


title: E690 gene-corrrected  iAEC2s, rep1

description:
cE690-R1
human iPSC line: E690K_ST12_CR1_SS21_Corr32  “E690 corrected patient iPSC line”  Patient iPSC line containing homozygous E690K mutation secondary to paternal disomy. The  line contains tdTomato reporter mono-allelically targeted to the start codon of the endogenous  SFTPC gene locus clone #12. Subsequently underwent cre-excision of puromycin selection  cassette clone # 1. Followed by single cell sorted and cultured from one-cell outgrowth clone  #21. Underwent subsequent CRISPR/Cas9 single nucleotide editing to correct E690K mutation  to the wildtype E690 codon, clone #32.

value: E690 gene-corrrected

value: day 44 of human distal lung directed differentiation


title: 64

description:
20180322_K07_64_04
Nanostring nCounter HSNCC Custom Panel

value: BA

value: keratinizing

value: high

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

value: Tongue


title: ZEBARFISH WT AB9  Sample 21

description: FISH.counts.matrix

tag: cell line


title: W308R ABCA3 mutant iAEC2s, rep2

description:
W308R-R2
human iPSC line: W308R_ST13_CR17 (Parent, unedited line, core nomenclature: ABCA3-5) Patient iPSC line containing homozygous W308R mutation. The line contains tdTomato reporter  mono-allelically targeted to the start codon of the endogenous SFTPC gene locus clone #13.  Subsequently underwent cre-exision of puromycin selection cassette clone # 17.

tag: cell type

tag: genotype


title: 62

description:
20180322_K07_62_02
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

tag: keratinization

value: low

value: big

value: small

value: Tonsil


title: G1014_06, B6, F, CORT+DFP

tag: tissue

value: Prefrontal cortex (PFC)

tag: strain

tag: treatment

value: CORT+DFP

tag: Sex

value: F

tag: age (days)

tag: body weight


title: G1014_05, D2, M, Control

value: Control

value: M


title: ZEBARFISH KO AB9  Sample 20

description: FISH.counts.matrix

value: KO


title: 59

description:
20180320_K05_59_11
Nanostring nCounter HSNCC Custom Panel

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: lymphangiosis

tag: dcr

value: SD


title: E690K ABCA3 mutant iAEC2s, rep3

description:
E690K-R3
human iPSC line: E690K_ST12_CR1_SS21"E690K mutant patient iPSC line" (CReM iPSC Core parent line nomenclature ABCA3-1).        Patient iPSC line containing homozygous E690K mutation secondary to paternal disomy. The  line contains tdTomato reporter mono-allelically targeted to the start codon of the endogenous  SFTPC gene locus clone #12. Subsequently underwent cre-exision of puromycin selection  cassette clone # 1. Followed by single cell sorted and cultured from one-cell outgrowth clone  #21.

source_name: E690K ABCA3 mutant iAEC2s

tag: cell line

tag: cell type

value: patient iPSC-derived iAEC2s

value: E690K ABCA3 mutant

tag: developmental stage


title: ZEBARFISH KO AB9  Sample 22

description: FISH.counts.matrix

tag: genotype


title: W308R ABCA3 mutant iAEC2s, rep1

description:
W308R-R1
human iPSC line: W308R_ST13_CR17 (Parent, unedited line, core nomenclature: ABCA3-5) Patient iPSC line containing homozygous W308R mutation. The line contains tdTomato reporter  mono-allelically targeted to the start codon of the endogenous SFTPC gene locus clone #13.  Subsequently underwent cre-exision of puromycin selection cassette clone # 17.

value: W308R ABCA3 mutant

value: day 43 of human distal lung directed differentiation


title: G1014_04, D2, M, Control


title: E690K ABCA3 mutant iAEC2s, rep2

description:
E690K-R2
human iPSC line: E690K_ST12_CR1_SS21"E690K mutant patient iPSC line" (CReM iPSC Core parent line nomenclature ABCA3-1).        Patient iPSC line containing homozygous E690K mutation secondary to paternal disomy. The  line contains tdTomato reporter mono-allelically targeted to the start codon of the endogenous  SFTPC gene locus clone #12. Subsequently underwent cre-exision of puromycin selection  cassette clone # 1. Followed by single cell sorted and cultured from one-cell outgrowth clone  #21.

value: day 44 of human distal lung directed differentiation


title: G1014_03, D2, F, Control


title: 56

description:
20180320_K05_56_08
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: keratinizing

tag: keratinization

value: high

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

value: Oral cavity


title: 57

description:
20180320_K05_57_09
Nanostring nCounter HSNCC Custom Panel

value: MS

tag: tumor_cell_budding (2 tier)

value: small

value: low

tag: Sex

value: PR

value: Larynx


title: G1014_02, D2, M, CORT+DFP

tag: tissue

value: Prefrontal cortex (PFC)

tag: strain

tag: treatment

value: CORT+DFP

value: M

tag: age (days)

tag: body weight


title: Point mutant Matα2, No selection

city: San Francisco

first: Kyle

last: Fowler

address: 600 16th Street

institute: University of California San Francisco

description: Point-mutant library

data_processing:
R v4.0.3; Shortread package v1.48; Biostrings package v2.58
Sequence reads were first trimmed based on their Phred quality scores to remove bases distal to the point a read’s quality drops below 20 (corresponding to 1% error).
Trimmed sequences were then aligned to the MATα2 reference sequence and reads were eliminated if they did not fully span the mutated region, had indels, or other unexpected mutation.
Sequences passing these quality filters were tabulated to determine the abundance of all unique sequences in each sample and these counts were also normalized to the sequencing depth (i.e., reads per million).
Assembly: N/A
Supplementary files format and content: CSV file of all unique variants and their abundances. Each file contains the following data columns: DNA sequence of the mutant region, its amino acid translation, the mutant's sequence read count, and the normalized sequence read count (reads per million).
Library strategy: amplicon sequencing for deep mutation scan

organism: Saccharomyces cerevisiae

growth_protocol: Cells containing the library of Matα2 mutants were grown overnight in YEPD to expand the library, and was subsequently used to innoculate 500 mL SD (synthetic defined) media lacking arginine. "Pre" samples were collected following growth in YEPD.

extract_protocol:
In each case, cells were pelleted by centrifugation, washed in PBS, and the pellets frozen at -80°C. Subsequent extraction of plasmid DNA was accomplished by thawing and boiling the cells for 5 minutes followed by bead-beating in the presence of phenol and chloroform. DNA was ethanol precipitated and purified using a QIAGEN QIAprep miniprep kit.
Sequencing libraries were prepared using PCR to amplify the variable region of MATα2 from the plasmid pool using primers containing Illumina adapter sequences and sample specific barcodes. For each sample/library, ten 50 µL PCR reactions were pooled after nine PCR cycles. The 500 µL PCR pool was cleaned and concentrated using a QIAGEN MinElute PCR Purification Kit and quantified using either an Agilent Bioanalyzer or TapeStation (High sensititivity DNA kit).

treatment_protocol: SD cultures supplemented with canavanine (25 or 250 ug/mL to select for functional Matα2-Mcm1 interactions) were grown for 24 hours shaking at 30°C. Control SD cultures were grown in parallel without canavanine.

value: growth in SD


title: Point mutant Matα2, Low selection

description: Point-mutant library

value: growth in SD + 25 ug/mL canavanine


title: E690K ABCA3 mutant iAEC2s, rep1

description:
E690K-R1
human iPSC line: E690K_ST12_CR1_SS21"E690K mutant patient iPSC line" (CReM iPSC Core parent line nomenclature ABCA3-1).        Patient iPSC line containing homozygous E690K mutation secondary to paternal disomy. The  line contains tdTomato reporter mono-allelically targeted to the start codon of the endogenous  SFTPC gene locus clone #12. Subsequently underwent cre-exision of puromycin selection  cassette clone # 1. Followed by single cell sorted and cultured from one-cell outgrowth clone  #21.

tag: cell line

tag: cell type

value: patient iPSC-derived iAEC2s

value: E690K ABCA3 mutant


title: 60

description:
20180320_K05_60_12
Nanostring nCounter HSNCC Custom Panel

value: Unknown

tag: lymphangiosis

tag: dcr

value: SD


title: Point mutant Matα2, Pre-selection

description: Point-mutant library


title: Point mutant Matα2, High selection

description: Point-mutant library

value: growth in SD + 250 ug/mL canavanine


title: Randomized Matα2, High selection, rep2

description: Randomized library


title: 55

description:
20180320_K05_55_07
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: keratinizing

value: high

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: big

value: NE

value: Oropharynx


title: G1014_01, D2, F, CORT+DFP

value: F


title: Low uptake rep3

city: Riverside

first: Min

last: Xue

state: CA

address: 501 Big Spring Rd

department: Chemistry

institute: University of California, Riverside

data_processing:
Raw fastp data underwent trim and QC using fastp standard protocols
The trimmed data was then proccessed using STAR to align to the human genome
The expression levels were quantified using featureCounts
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Count   FPKM    TPM values for each Sample

growth_protocol: U87 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the RNeasy Micro Kit following manufacture's protocols
Library was constructed using the NEBNext ultra II directional library prep kit following manufacture's protocols

treatment_protocol: Cells were treated with 500 nM Rhodamine-EPP6 at 37C for 1 hour, detached, and then processed using FACS.

value: glioblastoma cell line

tag: genotype

value: WT

value: Rhodamine-EPP6 uptake


title: Randomized Matα2, Low selection, rep2

description: Randomized library


title: D4_siZfp352

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

country: China

institute: Zhejiang University School of Medicine

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v2.9
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR,Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (parameters- --outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1).
Quantification was calculated by FeatureCounts v2.0.0(parameters- -p -B -P -C)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by R package EdgeR v3.30.3
Assembly: GRCm38(mm10)
Supplementary files format and content: bigwig

source_name: mouse embryo

growth_protocol: ICR female mice (8-12 weeks old) were super ovulated by i.p. injection of 10 IU pregnant mare’s serum gonadotropin (PMSG, CEN’S, Hangzhou, China) and 48 h later, 10 IU human chorionic gonadotropin (hCG, CEN’S, Hangzhou, China). For in vivo produced embryos, females were then mated with ICR male mice (10-18 weeks old). The zygotes were collected from dissected oviducts at 0.5 dpc. and put into KSOM medium (ARK Resource Co., Ltd.).

extract_protocol:
Injected embryos were cultured in KSOM medium under mineral oil in 35 mm petri dishes (Corning Life Sciences, 430165) in the humidified multi-gas incubator (5% O2, 6% CO2 and 89% N2) at 37°C.Embryos were obtained and placed into a 0.2-ml thin-walled PCR tube containing 2 µl of cell lysis buffer (with 5% RNase inhibitor and 95% Triton X-100), 1 µl of 10 µM oligo-dT primer and 1 µl of dNTP mix (10 mM each; Fermentas, R0192). The mix was quickly vortexed and then span down at 700g for 10 s at room temperature) and immediately transferred on ice. The samples were incubated at 72°C for 3 min and immediately put back on ice. 5.7 µl of the RT mix containing SuperScript II reverse transcriptase (Invitrogen, cat. no. 18064-014), RNAse inhibitor (10U), 5X Superscript II first-strand buffer, 100mM DTT (Invitrogen, 18064-014), 5M Betaine (BioUltra ≥99.0%; Sigma-Aldrich, 61962), 1M MgCl2, 100 µM TSO were mixed by gently pipetting up and down. The sample was incubated at 42°C for reverse transcription, and then amplified with First-strand reaction KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2601).
The cDNA was used for library construction using Vazyme TruePrep DNA Library Prep Kit V2 for Illumina kit (TD503-01)

treatment_protocol: For siRNA injections, the in vivo collected zygotes were randomly allocated into three groups: siZfp352,siNC.60 μM of siRNA and were injected into the cytoplasm of zygotes using microinjection glass capillary

value: mouse embryo

value: ICR mouse

tag: time


title: 50

description:
20180320_K05_50_02
Nanostring nCounter HSNCC Custom Panel

value: CL

value: basaloid

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: small

tag: stroma_content (2 tier)

value: low

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: Sex

value: Oral cavity


title: 58

description:
20180320_K05_58_10
Nanostring nCounter HSNCC Custom Panel

value: MS

value: non-keratinizing

value: CR

value: Hypopharynx


title: 54

description:
20180320_K05_54_06
Nanostring nCounter HSNCC Custom Panel

value: high

value: PR


title: Randomized Matα2, No selection, rep2

description: Randomized library

tag: strain

tag: treatment

value: growth in SD


title: D4_siNC

tag: tissue

value: siNC


title: Low uptake rep2

tag: cell line

tag: cell type

value: glioblastoma cell line

value: WT


title: High uptake rep4

value: Rhodamine-EPP6 uptake


title: D3_siZfp352_rep2

value: mouse embryo

value: ICR mouse


title: Randomized Matα2, Pre-selection, rep2

description: Randomized library


title: 49

description:
20180320_K05_49_01
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

tag: histotyp

value: keratinizing

tag: cell_nest_size (2 tier)

value: big

tag: lymphangiosis

tag: dcr

value: SD


title: 48

description:
20180320_K04_48_12
Nanostring nCounter HSNCC Custom Panel

value: MS

value: basaloid

tag: keratinization

value: small

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: low

value: Oropharynx


title: Low uptake rep4

tag: genotype


title: High uptake rep3


title: Randomized Matα2, High selection, rep1

description: Randomized library

value: growth in SD + 250 ug/mL canavanine


title: High uptake rep2


title: D3_siNC_rep2

tag: time


title: D3_siZfp352_rep1


title: D3_siNC_rep1


title: Randomized Matα2, No selection, rep1

description: Randomized library

value: growth in SD


title: 47

description:
20180320_K04_47_11
Nanostring nCounter HSNCC Custom Panel

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

value: high

value: Larynx


title: 45

description:
20180320_K04_45_09
Nanostring nCounter HSNCC Custom Panel

tag: Sex

value: PR


title: SM-KIPJ7

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Bulk RNA data were processed using St. Jude Cloud workflow for the analysis of RNA-Seq differential expression (WARDEN) (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Blood

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

tag: tissue

value: Blood

tag: cell type

tag: group

value: Healthy


title: SM-KIPJ8


title: Randomized Matα2, Pre-selection, rep1

description: Randomized library

tag: strain

tag: treatment


title: D2_siNC

value: mouse embryo

value: ICR mouse

value: siNC


title: D2_siZfp352


title: SM-KIPJC


title: SM-KIPJD


title: 44

description:
20180320_K04_44_08
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

tag: histotyp

value: keratinizing

tag: cell_nest_size (2 tier)

value: big

tag: lymphangiosis

tag: dcr


title: SM-KIPJ6


title: 42

description:
20180320_K04_42_06
Nanostring nCounter HSNCC Custom Panel

tag: keratinization

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: small

value: Tongue


title: 43

description:
20180320_K04_43_07
Nanostring nCounter HSNCC Custom Panel

value: BA

value: Unknown

value: CR


title: 41

description:
20180320_K04_41_05
Nanostring nCounter HSNCC Custom Panel

value: MS

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

tag: stroma_content (2 tier)

value: low

tag: necrosis

value: SD


title: JGY2000 Sorbitol +DMS Rep A

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description:
Sorbitol sample treated with DMS, rep A
2000A_Sorbitol_DMS_TruePolyAPairs_5'endfreqs_Normed_1.145xTo20M.txt
2000AandB_Sorbitol_DMS_TruePolyAPairs_5'endfreqs_Normed_1.045xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt

data_processing:
Remove 4 random nt from each read, count and remove initial Ts from R1 reads, truncate remainder of each read to 17nt max (starting at nt 2 for the R2 side), discard reads containijng Ns or with with fewer than 9nt remaining after T removal (python)
Genomic mapping using bowtie with one mismatch and m1, X1000 (Bowtie)
Exclude reads with a number of initial Ts that could have been genomically encoded, as opposed to representing post-transcriptionally added As; normalize processed read counts per sample (python)
Readjust mapped first position of R2 back by 2 nt: one to compensate for having started mapping from nt 2, and one more because the potential DMS-modified nt is 1 nt upstream of the last reverse-transcribed position (python)
Consolidate instances of possible DMS-modified positions (mapped R2 read start position minus 2) for every 3' isoform (python)
For every isoform, compare A and C positions of DMS-treated and control samples, subtracting read count of control from DMS sample to obtain net reads for the position (python/Microsoft Excel)
Assembly: S. cerevisiae Sac cer 3; S. pombe EF2
Supplementary files format and content: Tab-delimited text files containing consolidated normalized reads for each 3' isoform
Supplementary files format and content: Consolidated A+B replicates, DMS minus untreated control values for normalized 5' positions corresponding to each 3' isoform
Library strategy: 3' READS

growth_protocol: Yeast strain JGY2000 (MATa, his3Δ0, leu2Δ0, met15Δ0, ura3Δ0, rpb1::RPB1–FRB, rpl13::RPL13–FK512) contains an anchor-away allele of Rpb1, the largest subunit of Pol II that permits rapid depletion of Pol II upon treatment with rapamycin.  Duplicate cultures were grown to early- to mid-log phase in the following conditions: YPD broth; YP medium containing 2% galactose (YPGal), osmotic stress medium consisting of YPD + 1M sorbitol (Sorbitol); and nutrient-poor minimal medium containing 2% dextrose and yeast nitrogen base without amino acids but supplemented with uracil and essential amino acids (Minimal).  Cultures were spiked with 4x106 of S. pombe cells that served as an internal control to normalize RNA levels among samples.

extract_protocol:
Total RNA was isolated and purified from 15-20 ml of cells using the hot acid phenol method followed by purification using QIAGEN RNeasy with DNase I treatment per the manufacturer's instructions.
For measuring levels of 3’ mRNA isoforms, 3’ READS was performed with 25 mg of purified total RNA with 18 cycles of amplification as described (Jin et al., 2015).  For DREADS (Moqtaderi et al, 2018), poly(A) RNA was isolated from 25 µg of total RNA via purification with magnetic oligo dT(25) beads (New England Biolabs) and was then bound to beads pre-coated with a U45T5 biotinylated mRNA capture oligonucleotide.  Bead-immobilized mRNA tails were trimmed with RNase H (New England Biolabs) to generate shortened poly(A) sequences averaging ~5 A’s as described.  After ligation of 5’ pre-adenylated adapter A to the trimmed mRNA 3’ ends, mRNAs were reverse transcribed with Superscript III (Life Technologies) using primer B.  cDNAs were ligated with T4 DNA Ligase (NEB) to splint adapter C, and the single-stranded DNA products (110 – 500 nt) were purified on 8% polyacrylamide-urea gels. DNA fragments were amplified by 18 cycles of PCR with barcoded oligonucleotides. Amplified libraries were purified with SizeSelector-I beads (Aline Biosciences), quantified via Bioanalyzer 2100 (Agilent Technologies), pooled, and further purified by electrophoresis on 8% polyacrylamide gels.
3' READS: Jin, Y., et al., Mapping 3' mRNA isoforms on a genomic scale. Curr. Protoc. Mol. Biol., 2015. 110: p. 4.23.1-4.23.17
DREADS: Moqtaderi, Z., J.V. Geisberg, and K. Struhl, Extensive structural differences of cloesly related 3’ mRNA isoforms: links to Pab1 binding and mRNA stability. Mol. Cell, 2018. 72: p. 849-861

treatment_protocol: For half-life determination, cells were treated with rapamycin to induce Pol II depletion, and time points were taken at 0, 20, 40, 60, 90 and 120 minutes after rapamycin addition.  For examining isoform structure, cell cultures grown as above were mock treated (-DMS) or incubated with 500 µl DMS (+DMS) for 2 min at room temperature, quenched twice with 30 ml stop solution (30% beta-mercaptoethanol, 25% isoamyl alcohol), washed with 1 ml of H2O, and frozen at -70˚C.

tag: agent

value: DMS-treated sample

tag: method

value: DREADS

tag: genotype

value: (MATa, his3delta0, leu2delta0, met15delta0, ura3delta0, rpb1::RPB1-FRB, rpl13::RPL13-FK512)

tag: culture medium

value: YPD + 1M sorbitol


title: JGY2000 Sorbitol noDMS Rep B

description:
Sorbitol sample without DMS, rep B
2000B_Sorbitol_noDMS_TruePolyAPairs_5'endfreqs_Normed_1.325xTo20M.txt
2000AandB_Sorbitol_DMS_TruePolyAPairs_5'endfreqs_Normed_1.045xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt

value: mock-treated sample without DMS

tag: strain


title: JGY2000 Sorbitol +DMS Rep B

description:
Sorbitol sample treated with DMS, rep B
2000B_Sorbitol_DMS_TruePolyAPairs_5'endfreqs_Normed_0.961xTo20M.txt
2000AandB_Sorbitol_DMS_TruePolyAPairs_5'endfreqs_Normed_1.045xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt


title: SM-KIPJ5

tag: tissue

value: Blood

tag: cell type

tag: group

value: Healthy


title: Pancreatic islets T cells, ADT-derived cDNA, biol rep4

city: Salt Lake City

first: Maria

last: Bettini

address: University of Utah

institute: University of Utah

description: Antibody-derived oligonucleotide (ADT)

data_processing:
scRNAseq and CITE-seq data were analyzed with Seurat.
Cells with greater than 5% mitochondrial DNA were excluded from the analysis. Cells with between 300 and 3000 expressed genes were used in downstream analysis to exclude doublets and ensure high quality reads.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files

source_name: Pancreatic islets

extract_protocol:
Islets were harvested from NOD female mice and labelled with anti-TCRvb (BioLegend, APC, clone H57-597, 1:300), anti-CD4 (BioLegend, TotalSeq-C0001, clone RM4-5, barcode- AACAAGACCCTTGAG, 1:1000), anti-CD8b-biotin (BioLegend, clone YTS156.7.7, 1:8000), anti-CD62L (BioLegend, TotalSeq-C0112, clone MEL-14, barcode- TGGGCCTAAGTCATC, 1:1000), and anti-CD11a (BioLegend, TotalSeq-C0595, clone M17/4, barcode AGAGTCTCCCTTTAG, 1:1000) primary antibodies followed by secondary labelling with PE SA (BioLegend, TotalSeq-C0951, barcode- AACCTTTGCCACTGC, 1:8000). DAPI was used to exclude dead cells while sorting. Live TCR+ cells were sorted from the islets on an Aria sorter and resuspended at 1000 cells/ul in PBS with 0.04% bovine serum albumin
Libraries were generated using Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein and Immune Receptor Mapping. All amplification steps used a ThermoFisher Proflex System thermocycler. The resulting GEM’s were transferred to new tubes for GEM-RT. After the GEM-RT incubation the samples were cleaned-up and readied for cDNA amplification using 11 cycles of amplification. Amplified cDNA was size-selected using SPRIselect Beads (BECKMAN COULTER). The quality and concentration of the isolated cDNA was determined using a Fragment Analyzer (Agilent).
The resulting cDNA was used to generated the various library types; V(D)J TCR,  5 ‘ Gene Expression (GEX) and Cell Surface Receptor.

value: Pancreatic islets

value: NOD

value: T cells

tag: library type

value: ADT

tag: Sex

value: Female

tag: disease state

value: Pre-diabetic

tag: antibody

value: anti-CD4 (TotalSeq-C0001), anti-CD8b-biotin+PE-SA(TotalSeq-C0951), anti-CD62L (TotalSeq-C0112), and anti-CD11a (TotalSeq-C0595)

tag: age

value: 12 week old


title: Randomized Matα2, Low selection, rep1

description: Randomized library

tag: treatment

value: growth in SD + 25 ug/mL canavanine


title: Pancreatic islets T cells, ADT-derived cDNA, biol rep2

description: Antibody-derived oligonucleotide (ADT)


title: Pancreatic islets T cells, ADT-derived cDNA, biol rep3

description: Antibody-derived oligonucleotide (ADT)


title: JGY2000 Sorbitol noDMS Rep A

description:
Sorbitol sample without DMS, rep A
2000A_Sorbitol_noDMS_TruePolyAPairs_5'endfreqs_Normed_1.221xTo20M.txt
2000AandB_Sorbitol_DMS_TruePolyAPairs_5'endfreqs_Normed_1.045xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt


title: 46

description:
20180320_K04_46_10
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: low

tag: cell_nest_size (2 tier)

value: big

tag: mitotic_count (2 tier)

value: high

tag: nuclear_size (2 tier)

value: small

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: dcr

value: PR

value: Oral cavity


title: 40

description:
20180320_K04_40_04
Nanostring nCounter HSNCC Custom Panel

value: CL

value: Unknown


title: Pancreatic islets T cells, ADT-derived cDNA, biol rep1

description: Antibody-derived oligonucleotide (ADT)

tag: tissue

value: Pancreatic islets

tag: strain

value: NOD

tag: cell type

value: T cells

tag: library type


title: SM-KIPJ2

value: Blood

tag: group

value: Healthy


title: 39

description:
20180320_K04_39_03
Nanostring nCounter HSNCC Custom Panel

value: MS

tag: stroma_content (2 tier)

tag: necrosis

tag: Sex

value: PD

value: Tonsil


title: JGY2000 Minimal +DMS Rep B

description:
Minimal medium sample treated with DMS, rep B
2000B_MM_DMS_TruePolyAPairs_5'endfreqs_Normed_1.2xTo20M.txt
2000AandB_MM_DMS_TruePolyAPairs_5'endfreqs_Normed_0.903xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt

tag: agent

value: DMS-treated sample

tag: method

value: DREADS

tag: genotype

value: (MATa, his3delta0, leu2delta0, met15delta0, ura3delta0, rpb1::RPB1-FRB, rpl13::RPL13-FK512)

tag: culture medium

value: Minimal


title: SM-KIPJB


title: 38

description:
20180320_K04_38_02
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: big

value: low

value: Hypopharynx


title: Pancreatic islets T cells, TCR-derived cDNA, biol rep1

description: 5' mRNA

tag: tissue

value: Pancreatic islets

tag: strain

value: NOD

tag: cell type

value: T cells

value: TCR

value: Female

tag: disease state

value: Pre-diabetic

tag: age

value: 12 week old


title: Pancreatic islets T cells, TCR-derived cDNA, biol rep2

description: 5' mRNA

tag: library type

tag: Sex


title: Pancreatic islets T cells, TCR-derived cDNA, biol rep4

description: 5' mRNA


title: Pancreatic islets T cells, TCR-derived cDNA, biol rep3

description: 5' mRNA


title: JGY2000 Minimal +DMS Rep A

description:
Minimal medium sample treated with DMS, rep A
2000A_MM_DMS_TruePolyAPairs_5'endfreqs_Normed_0.724xTo20M.txt
2000AandB_MM_DMS_TruePolyAPairs_5'endfreqs_Normed_0.903xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt

tag: agent

value: DMS-treated sample

tag: method

value: DREADS


title: JGY2000 Minimal noDMS Rep B

description:
Minimal medium sample without DMS, rep B
2000B_MM_noDMS_TruePolyAPairs_5'endfreqs_Normed_0.991xTo20M.txt
2000AandB_MM_DMS_TruePolyAPairs_5'endfreqs_Normed_0.903xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt

value: mock-treated sample without DMS

tag: genotype

value: (MATa, his3delta0, leu2delta0, met15delta0, ura3delta0, rpb1::RPB1-FRB, rpl13::RPL13-FK512)

tag: culture medium

value: Minimal


title: JGY2000 Minimal noDMS Rep A

description:
Minimal medium sample without DMS, rep A
2000A_MM_noDMS_TruePolyAPairs_5'endfreqs_Normed_2.256xTo20M.txt
2000AandB_MM_DMS_TruePolyAPairs_5'endfreqs_Normed_0.903xTo40M_DMS_minusNon_ifTotalDMSin317over1.txt


title: JGY2000 YPGal +DMS Rep B

description:
YPGal sample treated with DMS, rep B
2000B_YPGal_DMS_5'endfreqs_Normed_1.2xTo20MtruePolyA.txt
2000AandB_YPGal_DMS_5'endfreqs_Normed_1.13xTo40MtruePolyA_DMS_minusNon_ifTotalDMSin317over1.txt

value: YP + 2percent galactose


title: SM-KIPJA

value: Blood

tag: group

value: Healthy


title: SM-KIPJ4


title: Pancreatic islets T cells, mRNA-derived cDNA, biol rep4

description: 5' mRNA

value: mRNA


title: 36

description:
20180307_K03_47_12
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: histotyp

value: keratinizing

tag: keratinization

value: high

value: small

value: low

value: big

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: dcr

value: PR

value: Tongue


title: 37

description:
20180320_K04_37_01
Nanostring nCounter HSNCC Custom Panel

value: CL

value: basaloid

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: NE

value: Oropharynx


title: 34

description:
20180307_K03_45_10
Nanostring nCounter HSNCC Custom Panel

value: MS

tag: Sex

value: Tonsil


title: SM-KIPJ3

tag: tissue

value: Blood

tag: cell type


title: JGY2000 YPGal +DMS Rep A

description:
YPGal sample treated with DMS, rep A
2000A_YPGal_DMS_5'endfreqs_Normed_1.07xTo20MtruePolyA.txt
2000AandB_YPGal_DMS_5'endfreqs_Normed_1.13xTo40MtruePolyA_DMS_minusNon_ifTotalDMSin317over1.txt

tag: agent

value: DMS-treated sample

tag: method

value: DREADS

tag: strain

tag: genotype

value: (MATa, his3delta0, leu2delta0, met15delta0, ura3delta0, rpb1::RPB1-FRB, rpl13::RPL13-FK512)

tag: culture medium

value: YP + 2percent galactose


title: SM-KIPIZ

tag: group

value: Healthy


title: JGY2000 YPGal noDMS Rep B

description:
YPGal sample without DMS, rep B
2000B_YPGal_noDMS_5'endfreqs_Normed_1.37xTo20MtruePolyA.txt
2000AandB_YPGal_DMS_5'endfreqs_Normed_1.13xTo40MtruePolyA_DMS_minusNon_ifTotalDMSin317over1.txt

value: mock-treated sample without DMS


title: JGY2000 YPGal noDMS Rep A

description:
YPGal sample without DMS, rep A
2000A_YPGal_noDMS_5'endfreqs_Normed_2.0xTo20MtruePolyA.txt
2000AandB_YPGal_DMS_5'endfreqs_Normed_1.13xTo40MtruePolyA_DMS_minusNon_ifTotalDMSin317over1.txt


title: SM-KIPJ9


title: SM-KIPJ1


title: Pancreatic islets T cells, mRNA-derived cDNA, biol rep1

description: 5' mRNA

value: Pancreatic islets

value: NOD

value: T cells

tag: library type

value: mRNA

value: Female

tag: disease state

value: Pre-diabetic

tag: age

value: 12 week old


title: Pancreatic islets T cells, mRNA-derived cDNA, biol rep3

description: 5' mRNA


title: Pancreatic islets T cells, mRNA-derived cDNA, biol rep2

description: 5' mRNA


title: 33

description:
20180307_K03_44_09
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: keratinizing

tag: keratinization

value: high

value: small

value: big

tag: stroma_content (2 tier)

value: low

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: dcr

value: PR


title: SM-KIPIV

tag: tissue

value: Blood

tag: cell type


title: SM-KIPIT


title: Pancreatic islets T cells, TCR-derived cDNA, 16wk

description: 5' mRNA

data_processing:
scRNAseq data were analyzed with Seurat.
Cells with greater than 5% mitochondrial DNA were excluded from the analysis. Cells with between 300 and 3000 expressed genes were used in downstream analysis to exclude doublets and ensure high quality reads.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files

extract_protocol:
Islets were harvested from NOD female mice and labelled with anti-TCRvb (BioLegend, APC, clone H57-597, 1:300). DAPI was used to exclude dead cells while sorting. Live TCR+ cells were sorted from the islets on an Aria sorter and resuspended at 1000 cells/ul in PBS with 0.04% bovine serum albumin
Libraries were generated using Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein and Immune Receptor Mapping. All amplification steps used a ThermoFisher Proflex System thermocycler. The resulting GEM’s were transferred to new tubes for GEM-RT. After the GEM-RT incubation the samples were cleaned-up and readied for cDNA amplification using 11 cycles of amplification. Amplified cDNA was size-selected using SPRIselect Beads (BECKMAN COULTER). The quality and concentration of the isolated cDNA was determined using a Fragment Analyzer (Agilent).
The resulting cDNA was used to generated the various library types; V(D)J TCR,  5 ‘ Gene Expression (GEX)

tag: strain

tag: Sex


title: 35

description:
20180307_K03_46_11
Nanostring nCounter HSNCC Custom Panel

value: MS

value: basaloid

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: Tonsil


title: Pancreatic islets T cells, TCR-derived cDNA, 8wk

description: 5' mRNA

value: Pancreatic islets

tag: library type

tag: disease state

tag: age


title: 32

description:
20180307_K03_43_08
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

tag: histotyp

tag: keratinization

tag: stroma_content (2 tier)


title: 29

description:
20180307_K03_40_05
Nanostring nCounter HSNCC Custom Panel

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: CR

value: Hypopharynx


title: SM-KIPIR

tag: tissue

tag: cell type

tag: group

value: Healthy


title: 30

description:
20180307_K03_41_06
Nanostring nCounter HSNCC Custom Panel

value: BA

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: Sex

tag: dcr

value: Tongue


title: 31

description:
20180307_K03_42_07
Nanostring nCounter HSNCC Custom Panel

value: keratinizing

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: high


title: Budding yeast, CD, replicate 2, MNase-seq

city: Houston

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description:
Call_Nucleosomes_on_merged_K.interval
Gaussian_smooth_on_merged_K.wig

data_processing:
Paired end sequence reads were mapped to sacCer3 reference genome using Bowtie for Illumina version 2.4.1. Reads that are mapped to the repetitive rRNA locus (chrXII: 451275 -469084) were filtered out. Dyad density maps were obtained for the mapped reads by considering the center of the paired sequence reads after normalizing to the mean genome wide coverage. Stereotypic nucleosome positions are identified using a greedy algorithm in a similar fashion as described for Gene Track. These nucleosome calls include standard deviation (fuzziness) and nucleosome occupancy values. The data was processed using web based genomic data analysis software “Galaxy” and additional resources used can be found at http://palpant.us/java-genomics-toolkit/. Further processing of data was performed in Matlab Ver. 7.12.0.635 (R2011a). Called nucleosomes that showed two or more-fold reduction or increase in nucleosome occupancy between WT Snf2 and ΔAT hook, or ΔSnAC or catalytic dead were aligned back to the transcription start and end sites (TSS/TES). A total of 6,289 genes with well-defined transcription start and end sites were used. Genes were aligned to each other based on the position of the +1 nucleosomes and a plot generated to display the extent of change in nucleosome occupancy at each position.
Assembly: SacCer3
Supplementary files format and content: wig, tabular, interval

growth_protocol: Cells were grown in final 425mL YPD at 30oC to an OD600 of 0.8.

extract_protocol:
Final 1% formaldehyde was treated for crosslinking at 30oC for 15mins and the reaction was terminated by final 125mM of glycine. Cells were harvested by 3,000rpm centrifugation for 5mins and washed twice by 10mL of 1M Sorbitol. The washed cell pellets were resuspended in 4.785mL of YLE buffer (1M Sortibol and 5mM beta-mercaptoethanol). Check the OD600 of 10uL of cells with 90uL of 1% SDS. Cells were lysed by 225uL of 2mg/mL Zymolase-100T at 30oC with rotating on nutator. Wash the lysed cells twice by 5mL of 1M Sorbitol when the OD600 of 10uL of lysed cells with 90uL 1% SDS was decreased up to 10~20% of initial OD600. The washed cells were resuspended in 1.2mL of SDB buffer (1M Sorbitol, 50mM NaCl, 10mM Tris-HCl pH7.5, 5mM MgCl2, 1mM CaCl2, 1mM beta-mercaptoechanol, 0.5mM Spermidine and 0.075% of NP-40). 1,130U of MNase was treated for 300uL of cells at 37oC and aliquot 100uL of the MNase-treated cells to stop the reaction by adding final 10mM of EDTA and 20mM EGTA. Final 0.12% of SDS and 2.1ug of proteinase K were treated at 65oC for overnight. The DNA was purified by Phenol:Chloroform extraction and 30ug of RNase A at 37oC for 1hr. The sample was purified by Phenol:Chloroform:Isoamyl Alcohol and precipitated by final 0.3M Sodium Acetate and Isopropanol for 5mins at RT. The DNA was collected by 13,500rpm for 30mins at 40oC and washed twice by 500uL of ice cold 80% Ethanol. The DNA were dissolved in 18uL of TE at 37oC with tapping for ~20mins. The purified DNA was ran in 1.5% of 1xTBE gel to take mononucleosomal DNA bands through Qiagen gel extraction kit if the mononucleosomal DNA is 70~80% of the sample.
100ng of mononucleosomal DNA was used for library preparation by Illumina TruSeq DNA PCR-Free kit.

tag: strain

tag: genotype

value: Catalytic Dead (K798A)


title: Budding yeast, CD, replicate 3, MNase-seq


title: SM-KIPIS


title: Pancreatic islets T cells, mRNA-derived cDNA, 16wk

description: 5' mRNA

value: NOD

value: T cells

tag: library type

value: mRNA

value: Female

tag: disease state

value: Pre-diabetic

tag: age


title: Budding yeast, dSnf2, replicate 1, MNase-seq

description:
Call_Nucleosomes_on_merged_dSnf2.interval
Gaussian_smooth_on_merged_dSnf2.wig


title: SM-KIPIU

value: Blood


title: 28

description:
20180307_K03_39_04
Nanostring nCounter HSNCC Custom Panel

extract_protocol: RNA extraction and NanoString analyses were conducted as previously described (35). In short, H&E stained slides of HNSCC cases were examined to identify tumor regions and to estimate tumor cell content. FFPE material with a minimal tumor cell content of 20 % (median 65 %)  was used for subsequent microdissection of RNA from 3 µm thick sections. RNA was then extracted according to manufacturer’s instructions on a Maxwell extraction system (Promega, Madison, WI) and quantified by Qubit (Thermo Fisher Scientific, Waltham, MA).

tag: subtype

tag: histotyp

tag: keratinization

value: low

value: big

value: small

tag: stroma_content (2 tier)

tag: necrosis

tag: necrosis (2 tier)


title: Zfp352OE,ATAC

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
Tn5 adapter (AGATGTGTATAAGAGACAG) was trimmed by cutadapt v2.9
STAR v2.7.0e 54 was used for alignment onto human reference genome GRCm38.99. Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (--outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1).
By creating STAR index without general feature format file and not allowing intron length (--alignIntronMax 1), the splice junction was neglected. PCR duplicates were removed by Samtools v1.2 70 rmdup function.
ATAC-seq peaks were defined using MACS2 v2.2.7.1 71 callpeaks function with default parameters. Bigwig tracks were generated using deeptools v3.4.3 65 by normalizing to RPKM using binsize of 10bp. ATAC-seq signals over genomic regions were plotted by deeptools v3.2.1
Assembly: GRCm38(mm10)
Supplementary files format and content: bigWig

source_name: E14 WT

growth_protocol: E14 cells were cultured in DMEM high glucose with 15% FBS,100X NEAA,100X L-Glutamine,1000X β–Mercaptoethanol,homemade LIF on gelatin pre-coated plate.

extract_protocol:
mESC pellet was treated transposase at 37°C for 30min
ATAC-seq was performed as previously described 69 using MagicSeq Tn5 DNA Library Prep Kit for Illumina (Magic-Bio, M3141). mESC pellet was treated transposase at 37°C for 30min, purified using MinElute PCR Purification Kit (QIAGEN, 28006), and amplified using 1xNEBnext PCR master mix (NEB, M0541S) using custom Nextera PCR primers 1 and 2. Upon purification with MinElute PCR Purification Kit (QIAGEN, 28006). Libraries were subjected to Nova pair-end 150bp sequencing.

treatment_protocol: Zfp352 and control empty plasmid were over-expressed in cell for 12h

tag: cell line

value: E14 WT

tag: cell type

value: embryonic stem cell

tag: condition

value: Zfp352 overexpression


title: Budding yeast, dSnf2, replicate 2, MNase-seq


title: 27

description:
20180307_K03_38_03
Nanostring nCounter HSNCC Custom Panel

data_processing: Dataset normalization was conducted with the ‘NanoStringNorm’ R-package, version 1.2.1 (36). The ‘stringR’ and ‘ggplot2’ packages in conjunction with the ‘pheatmap’ R-package (RRID:SCR_016418) were utilized for visualization and string manipulation (37,38). For differential expression analyses, the ‘LIMMA’ R-package was utilized (39,40). For computational analysis R (version 4.1.3) (41) and SPSS v25 (International Business Machines Corporation (IBM), Armonk, NY)  were used.

value: BA

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

tag: Sex

tag: dcr

value: PR

value: Larynx


title: Budding yeast, dSnAC, replicate 3, MNase-seq

description:
Call_Nucleosomes_on_merged_dSnAC_rep1rep3.interval
Gaussian_smooth_on_merged_dSnAC_rep1rep3.wig

tag: strain

tag: genotype

value: dSnAC


title: SM-KIPIQ

tag: tissue

tag: group

value: PostCA


title: Budding yeast, CD, replicate 1, MNase-seq

value: Catalytic Dead (K798A)


title: SM-KIPIY

value: Healthy


title: Budding yeast, dSnAC, replicate 1, MNase-seq


title: SM-KIPIP


title: Zfp352+DuxOE,input

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v2.9
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR,Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (parameters- --outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1).
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per kilobase per Million mapped reads, rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: GRCm38(mm10)
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the illumina DNA sequencing Library Prep Kit

treatment_protocol: Zfp352 and Dux was over-expressed in cell for 12h

value: Zfp352+Dux over expression

tag: chip antibody

value: none (input)


title: emptyOE,ATAC

value: empty vector


title: Budding yeast, dSnAC, replicate 2, MNase-seq


title: SM-KIPIX

value: Blood


title: 26

description:
20180307_K03_37_02
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: keratinizing

tag: keratinization

value: high

tag: mitotic_count (2 tier)

value: low

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)


title: Zfp352+DuxOE,ZFP352

tag: cell line

value: E14 WT

tag: cell type

value: embryonic stem cell

tag: condition

value: anti-HA


title: 24

description:
20180306_K02_35_12
Nanostring nCounter HSNCC Custom Panel

value: BA

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

value: small

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PR


title: SM-KIPIO

tag: tissue

tag: group

value: PostCA


title: Zfp352OE,input

value: Zfp352 over expression

tag: chip antibody


title: SM-KIPIN


title: 22

description:
20180306_K02_33_10
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: non-keratinizing

tag: Sex

value: NE

value: Hypopharynx


title: Zfp352OE,ZFP352


title: Budding yeast, dAT, replicate 3, MNase-seq

description:
Call_Nucleosomes_on_merged_ATboth_rep2rep3.interval
Gaussian_smooth_on_merged_ATboth_rep2rep3.wig

tag: strain

tag: genotype

value: dAT


title: 20

description:
20180306_K02_31_08
Nanostring nCounter HSNCC Custom Panel

value: CL

tag: keratinization

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: dcr

value: PD

value: Larynx


title: Pancreatic islets T cells, mRNA-derived cDNA, 8wk

description: 5' mRNA

value: Pancreatic islets

value: NOD

tag: cell type

value: T cells

tag: library type

value: mRNA

value: Female

tag: disease state

value: Pre-diabetic

tag: age


title: SM-KIPIW

tag: tissue

value: Blood

value: Healthy


title: Microglia, APP/PS1, p38KO, animal 4

city: Lexington

first: Linda

middle: J

last: Van Eldik

state: KY

address: 789 S. Limestone St.

department: Sanders-Brown Center on Aging

institute: University of Kentucky

data_processing:
Raw data uploaded to Partek Flow v10.0.22.0828
Data were trimmed for low quality bases using Partek Flow "trimmed bases" algorithm based on quality score (parameters: end min quality level [Phred] = 30; trim from = 3-prime; min read length = 25; quality encoding = auto detect)
Trimmed sequence reads were aligned to mm10 using the Partek Flow STAR alignment algorithm
Read count extraction and normalization were performed using Partek Flow "quantify to annotation model (Partek E/M)" algorithms (parameters: strict paired-end compatibility = true; require junction reads to match introns = true; strand specificity = no; minimum read overlap with feature = 100%; min reads = 10; report unexplained regions = false)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with normalized gene counts and transcript counts in matrix format (samples in separate columns)

source_name: whole brain

extract_protocol:
PFA-fixed left brain hemispheres were dounce homogenized. Microglial-containing fractions were separated by 30% Percoll gradient (GE #17-5445-01) in RPMI 1640 (Gibco #11835030). Cells were incubated with 1:100 Zombie NIR dye solution (Biolegend #423106), and 1:50 CD11b-VioB (Miltenyi Biotec Cat# 130-113-810, RRID:AB_2726327) and P2ry12-PE (BioLegend cat. No. 848004; RRID: AB_2721645) antibodies. Approximately 10,000 live cells co-expressing CD11b and P2ry12 were sorted per mouse using a Sony Cell Sorter and immediately lysed in RLT Plus buffer and RNA extracted by RNeasy Plus Micro Kit (Qiagen #74034) according to manufacturer’s instructions. Samples with high RIN values (M = 8.3, minimum = 6.7, maximum = 9.1) were sent to Novogene for transcriptome sequencing.
cDNA library was generated with NEBNext Ultra II RNA kit and run on Illumina Platform PE150

value: whole brain

value: microglia

tag: background

value: M


title: Budding yeast, WT, replicate 3, MNase-seq

description:
Call_Nucleosomes_on_merged_WT.interval
Gaussian_smooth_on_merged_WT.wig

value: WT


title: 23

description:
20180306_K02_34_11
Nanostring nCounter HSNCC Custom Panel

value: BA

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

value: low

tag: necrosis

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PR


title: SM-KIPIJ

tag: group

value: PostCA


title: Budding yeast, dAT, replicate 2, MNase-seq

tag: strain

tag: genotype

value: dAT


title: 21

description:
20180306_K02_32_09
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: keratinizing

tag: keratinization

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)

tag: Sex

value: Tongue


title: Microglia, APP/PS1, p38KO, animal 3

tag: tissue

tag: cell type

tag: background


title: Microglia, APP/PS1, p38KO, animal 1

value: F


title: SM-KIPIH

value: Blood


title: Budding yeast, WT, replicate 2, MNase-seq


title: Microglia, APP/PS1, p38+/+, animal 4

value: whole brain


title: Liver, sugar glider, rep 1

first: Alexander

last: Tyshkovskiy

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

organism: Petaurus breviceps

source_name: Liver

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: Liver

value: male

tag: age

value: adult

value: wild type


title: SM-KIPII


title: Liver, beaver, rep 2

organism: Castor canadensis


title: Budding yeast, dAT, replicate 1, MNase-seq


title: 18

first: Raik

last: Otto

address: Rudower Chaussee 25

institute: Humboldt-Universität zu Berlin

description:
20180306_K02_29_06
Nanostring nCounter HSNCC Custom Panel

source_name: Tumor tissue

value: BA

value: non-keratinizing

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)

tag: necrosis

tag: necrosis (2 tier)

tag: dcr

value: Larynx


title: SM-KIPIG

tag: group


title: 17

description:
20180306_K02_28_05
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

value: high

value: small

value: low

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PD

value: Hypopharynx


title: SM-KIPIF

value: PostCA


title: Brain, beaver, rep 2

source_name: Brain

value: Brain

tag: genotype


title: Microglia, APP/PS1, p38KO, animal 2

value: microglia

tag: strain

value: M


title: 8

description:
20180221_K01_008_08
Nanostring nCounter HSNCC Custom Panel

value: MS

tag: histotyp

tag: keratinization

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)


title: 9

description:
20180221_K01_009_09
Nanostring nCounter HSNCC Custom Panel

value: big

tag: Sex

value: SD

value: Oropharynx


title: SM-KIPID

tag: tissue

value: Blood

tag: cell type


title: Liver, beaver, rep 1

value: Liver

value: male

tag: age

value: adult

value: wild type


title: SM-KIPIC


title: Microglia, APP/PS1, p38+/+, animal 3

value: whole brain

tag: background


title: Brain, beaver, rep 1


title: 19

description:
20180306_K02_30_07
Nanostring nCounter HSNCC Custom Panel

value: BA

value: keratinizing

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

value: low

tag: necrosis

tag: necrosis (2 tier)

tag: dcr

value: PR

value: Larynx


title: SM-KIPIM

tag: group

value: PostCA


title: SM-KIPIE


title: Microglia, wild-type, p38KO, animal 3

value: microglia

tag: strain

tag: genotype

value: M


title: 10

description:
20180221_K01_010_10
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: MS

value: Unknown

tag: lymphangiosis

value: CR


title: Microglia, APP/PS1, p38+/+, animal 1

value: F


title: Microglia, APP/PS1, p38+/+, animal 2


title: Budding yeast, WT, replicate 1, MNase-seq

value: WT


title: NACE2i treatment, lung alveoli_H023 6

city: Brisbane

first: Quan

last: Nguyen

state: Queensland

address: 22 Burns Street, Indooroopilly

country: Australia

institute: Institute for Molecular Bioscience

data_processing:
save-interim-files=false
quality-trim-score=20
2color-trimming=True
adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length=10
adapter-trim-max-mismatch=3
barcode-max-mismatch=1
stitching-max-mismatch=2
dedup-hd=1
threads=4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx Seq

organism: Mesocricetus auratus

source_name: lung

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: lung

tag: tissue region

value: alveoli

value: multiple cell types

tag: disease

value: SARS-CoV-2 infection

tag: treatment

tag: slide id

tag: roi number

tag: area


title: Liver, sugar glider, rep 2

tag: tissue

value: Liver

tag: Sex

value: male

tag: age

value: adult

value: wild type


title: 7

description:
20180221_K01_007_07
Nanostring nCounter HSNCC Custom Panel

value: BA

tag: histotyp

value: keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

value: low

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)

tag: necrosis

tag: inflammatory_infiltrate (2 tier)

value: PD

value: Hypopharynx


title: 5

description:
20180221_K01_005_05
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: MS

value: non-keratinizing

tag: necrosis (2 tier)

tag: lymphangiosis

tag: dcr

value: SD


title: SM-KIPIL

value: Blood

tag: cell type

tag: group

value: PostCA


title: Microglia, wild-type, p38KO, animal 4

tag: tissue

value: whole brain

value: microglia

tag: strain

tag: background

tag: genotype

tag: Sex

value: M


title: SM-KIPIK


title: 11

description:
20180221_K01_011_11
Nanostring nCounter HSNCC Custom Panel

value: CL

tag: histotyp

tag: keratinization

tag: tumor_cell_budding (2 tier)

tag: cell_nest_size (2 tier)


title: 6

description:
20180221_K01_006_06
Nanostring nCounter HSNCC Custom Panel

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

tag: stroma_content (2 tier)

tag: necrosis


title: 4

description:
20180221_K01_004_04
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: BA

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis


title: Microglia, wild-type, p38KO, animal 2

tag: tissue

tag: cell type

value: F


title: Microglia, wild-type, p38KO, animal 1

tag: strain

tag: background


title: NACE2i treatment, lung alveoli_H023 4

value: lung

tag: tissue region

value: alveoli

value: multiple cell types

tag: disease

value: SARS-CoV-2 infection

tag: treatment

tag: slide id

tag: roi number

tag: area


title: Microglia, wild-type, p38+/+, animal 4

tag: genotype

tag: Sex


title: NACE2i treatment, lung alveoli_H023 5


title: SM-KIPI7

tag: group


title: NACE2i treatment, lung alveoli_H023 3


title: 3

description:
20180221_K01_003_03
Nanostring nCounter HSNCC Custom Panel

tag: subtype

tag: histotyp

value: keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: high

tag: cell_nest_size (2 tier)

value: small

tag: mitotic_count (2 tier)

tag: nuclear_size (2 tier)

value: big

tag: stroma_content (2 tier)

value: low

tag: necrosis

tag: dcr

value: CR

value: Oropharynx


title: Microglia, wild-type, p38+/+, animal 3

tag: tissue

value: whole brain

tag: cell type

tag: strain

tag: background


title: SM-KIPI6

value: Blood

value: PostCA


title: 2

description:
20180221_K01_002_02
Nanostring nCounter HSNCC Custom Panel

tag: necrosis (2 tier)

tag: inflammatory_infiltrate (2 tier)

tag: lymphangiosis

value: PR

value: Hypopharynx


title: SM-KIPI5

tag: group


title: Microglia, wild-type, p38+/+, animal 1

value: microglia

tag: genotype

tag: Sex

value: F


title: Microglia, wild-type, p38+/+, animal 2

value: M


title: SM-KIPI4


title: 1

description:
20180221_K01_001_01
Nanostring nCounter HSNCC Custom Panel

tag: subtype

value: CL

tag: histotyp

value: non-keratinizing

tag: keratinization

tag: tumor_cell_budding (2 tier)

value: PD


title: Hem_KO

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

country: France

institute: Inserm

description: 10x Genomics

data_processing:
Raw sequencing reads were processed to counts matrix with Cell Ranger version 3.1.0 using default parameters and the mm10 mouse genome reference to which the sequenced of YFP and tdTomato were added.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryonic brain

extract_protocol:
For each dataset, a region spanning the dorsal pallial midline was dissected on both hemispheres and dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) on the gentleMACS Octo Dissociator following the manufacturer’s instructions. Remaining clumps of cells and debris were removed via two rounds of centrifugation for 3 min at 200 g followed by filtration through 30 µm cell strainers (Miltenyi Biotec). To ensure all remaining cells aggregates were dissociated, we finally pipetted the suspension through Gel Saver tips (QSP) and proceeded to a last filtration through a 10 µm cell strainer (pluriSelect). Cell viability and concentration were assessed using a MACSQuant flow cytometer (Miltenyi Biotec). Approximatively 20000 cells were used as input on the 10X Genomics Chromium Controller for a targeted cell recovery of 10000 cells per library. The entire procedure, from the sacrifice of the pregnant female until loading the controller, was achieved in 2h.
Single Cell 3′ Library and Gel Bead Kit v3

value: embryonic brain

tag: developmental stage

value: Gmnc-/-


title: NACE2i treatment, lung bronchiole_H023 6

value: lung

tag: tissue region

value: bronchiole

value: multiple cell types

tag: disease

value: SARS-CoV-2 infection

tag: treatment

tag: slide id

tag: roi number

tag: area


title: NACE2i treatment, lung alveoli_H023 1

tag: tissue

value: alveoli

tag: cell type


title: NACE2i treatment, lung alveoli_H023 2


title: SM-KIPI3

value: Blood