title: MmGtsf1-Strep eCLIP - crosslinked_ip2

data_processing:
Library strategy: eCLIP
Basecalling was performed with bcl2fastq2 v2.19 (Illumina).
Forward and reverse reads were joined using FLASH version 1.2.11; flash -m 25 -M 175 -O
Adapter dimers, adapter trimming, and PCR duplicate removal was performed using custom scripts, after which the reverse complement was taken to generate the original sense of the input material
Reads were mapped using STAR version 2.5.2b allowing for 50 multi-mapping sites; STAR_2.5.2b --genomeDir mm10 --runThreadN 12  --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts TranscriptomeSAM --outSAMattributes NH HI nM AS NM MD --outFilterMultimapNmax 50 --outFilterMismatchNoverReadLmax 0.05 --outFilterMismatchNmax 999
Alignment files were converted to .bed format using bedtools v2.29.0; bamtobed
Reads were annotated using custom gene annotations, filtering by class based on order of presumed biological abundance (custom scripts). rRNA > snoRNA > scaRNA > snRNA > ribozyme > lncRNA > tRNA > pseudogene_tRNA > mttRNA > miRNA > pri-miRNA > exon > TE_DNA > TE_SINE > TE_LINE > TE_Satellite > TE_LTR > TE_RNA > TE_RC > TE_Other > TE_Unknown > intron > pre-mRNA > piRNA_cluster > sncRNA > miscRNA > pseudogene > asRNA > no_annotation
Reads counts were then adjusted to include 1/n-normalization for multimapping reads within a class (custom scripts).
Read counts were then normalized to reads per million, and pileups were calculated for each annotation (custom scripts).
Final analysis compared the various datasets to subtract background and calculate fold-enrichment scores for each annotation after thresholding for low read counts custom scripts).
Genome_build: mm10
Supplementary_files_format_and_content: *_annotation_pileup_normalized.txt; Tab-delimited text files; Column 1 = annotation_class:annotation; Column 2 = 1/n-normalized read count pileup; Column 3 = 1/n-normalized read count pileup in rpm
Supplementary_files_format_and_content: Supplementary file: *_enrichment.txt; Tab-delimited text file; Column 1 = annotation; Column 2 = annotation class; Column 3 = average fold-enrichment calculated after background subtraction and normalization

source_name: P19 embryonal carcinoma cells

growth_protocol: P19 (mouse embryonal carcinoma; ATCC CRL-1825) cells were maintained in minimum essential medium with ribonucleosides and deoxribonucleosides (Gibco), supplemented with bovine calf serum and fetal bovine serum (7.5% and 2.5% final concentration, respectively) (Seradigm). Cells were cultured at 37°C in a 5% CO2 atmosphere. Cultures were monitored for Mycoplasma contamination using the MycoAlert Mycoplasma Detection Kit (Lonza). Mycoplasma contamination was not detected. The identity of the cultured cells was confirmed by short tandem repeat (STR) profiling, serviced by ATCC.

extract_protocol:
Cells were grown to 75% confluency in 150 mm culture dishes. Four hours prior to transfection, the medium was refreshed. To transfect, 30 μg of DNA (MmGtst1-TEV-Strep in pEF) was premixed with 60 μL of X-tremeGENE HP DNA transfection reagent (Roche) in serum-free medium for 15 minutes. After a 15-minute incubation, this mixture was added to the cultures. Forty-eight hours post-transfection, the cells were rinsed with ice-cold phosphate-buffered saline (PBS) and taken for crosslinking.
UV cross-linking was performed at 254 nm for ~45 seconds (400 mJ) in an HL-2000 Hybrilinker. Crosslinked cells were harvested then stored frozen at -80°C until ready to proceed.
Cell pellets were thawed in 1 mL of lysis buffer (50 mM Tris, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% deoxycholate, and protease inhibitors), resuspended by pipetting, then incubated on ice for 15 minutes. The cell suspension was further lysed using a Bioruptor ('low' setting at 4°C for 5 minutes [30 seconds on, 30 seconds off]).
Two microliters of Turbo DNase (2 U/μL) (LifeTech) were added to each sample as well as 10 μL of RNase I (4 U/μL) (LifeTech) and mixed by pipetting. The samples were then incubated at 37°C for exactly 5 minutes with mixing (1200 rpm in a ThermoMixer). After the five-minute incubation, the samples were placed on ice and murine RNase inhibitor (40 U/μL) (NEB) was added immediately. Cell debris was removed by centrifugation at 15,000g for 15 minutes at 4°C and the clarified supernatants were transferred to fresh tubes.
MagStrep type 3 XT beads (IBA) were equilibrated in 50 mM Tris, pH 8.0, 100 mM NaCl, 1% NP-40, 0.1% SDS, and 0.5% sodium deoxycholate with protease inhibitors. Fifty microliters of bead resuspension were used per sample. Beads were added to each sample and incubated with gentle agitation at 4°C for 2.5 hours. Input samples were reserved for both sequencing and Western blotting; these samples were stored at 4°C until needed. Affinity-precipitated material was isolated by magnetic separation, followed by several wash steps.
Libraries were generated essentially as described in Van Nostrand et al. (2016). Briefly, RNA ends were prepared by first treating with FastAP to remove terminal phosphates, then 5' phosphorylating using PNK. Barcoded adapters were then appended using 3' linker ligation with T4 ligase. Samples were then subjected to SDS-PAGE followed by blotting. Regions of the blot corresponding to the crosslinked protein of interest were cut out, and the RNA released from the membrane by Proteinase K treatment followed by nucleic acid extraction. Samples were reverse transcribed, RNA removed, and an additional barcoded adapter appended by 3' linker ligation. Samples were cleaned up using MyOne silane beads, then taken for final PCR amplification of the library.
Libraries were pooled in equimolar ratios according to their quantification by Bioanalyzer. Paired-end reads with two, 8-basepair, barcodes were generated on an Illumina NextSeq resulting in approximately 100 million paired-end reads (~15-20 million reads per library).

tag: pull-down

value: MagStrep XT beads

tag: crosslinking

value: crosslinked with UV 254


title: MmGtsf1-Strep eCLIP - non-crosslinked_ip

status: Public on Feb 20 2021

type: SRA

city: Cold Spring Harbor

first: Jonathan

middle: James

last: Ipsaro

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line


title: ins-Str10_r3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

data_processing:
The raw FASTQ files were inspected using FastQC, the adapter sequences were trimmed using Cutadapt and additional quality control steps taken by fastq_quality_filter program as part of FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The mapping process was performed using align function in Rsubread package by aligning the clean fastq files against the cow reference genome retrieved from Ensembl release 96 (Bos taurus) and only uniquely-mapped alignments were recorded. The resulting BAM files were sorted and indexed by SAMtools. The reads were summarized at the gene level by means of featureCounts. DESeq2 in a paired sample design was used to identify differentially expressed protein-coding genes based on the cut-offs of a p value < 0.05 and a log2 Fold Change > 0.1 or < -0.1.
Genome_build: Bos taurus - Ensembl release 96

organism: Bos taurus

source_name: endometrium stroma

extract_protocol:
Total RNA was extracted from epithelial and stromal cells using the Mini RNeasy kit (Qiagen, Crawley, UK) following the manufacturer's recommendations. Cell samples were homogenized in 700 µL of Qiazol via vortexing for 1 min at RT. On-column DNase digestion was performed (15 min at room temperature (RT)) and RNA was eluted in 14 µL of RNase/DNase free water from the spin column membrane following centrifugation for 2 min at full speed and this step was performed twice.
Stranded RNA sequencing libraries were constructed using the Encore Complete RNA-Seq library system of NuGEN
All libraries were sequenced on Illumina NextSeq generating 75 bp single-end reads

tag: treatment

value: insulin 10 ng/mL treatment


title: ins-Str1_r1

value: insulin 1 ng/mL treatment


title: Sar09L_CD45po_TCR

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Sar09L_CD45po
TCR
Sar09L_TCR_all_contig_annotations.csv

data_processing:
The Cell Ranger software pipeline (v3.1.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the human reference genome (refdata-cellranger-GRCh38-3.0.0) (command cellranger count). The CITE-seq antibody and barcode information was included in a feature reference csv file and passed to the cellranger count command. As the output, we obtained the feature-barcode matrix that contains gene expression counts alongside CITE-seq counts for each cell barcode.
TCR-seq data for each sample were assembled by the Cell Ranger software (v3.1.0, 10x Genomics) with the command cellranger vdj using the reference genome (refdata-cellranger-vdjGRCh38-alts-ensembl-3.1.0). For each sample, Cell Ranger generated an output file, filtered_contig_annotations.csv, containing TCR α-chain and β-chain CDR3 nucleotide sequences for single cells that were identified by barcodes.
Genome_build: GRCh38-3.0.0

organism: Homo sapiens

source_name: BALF

extract_protocol:
FACS-sorted BAL fluid cells
10X Genomics

tag: cell type

value: CD45 positive

tag: disease

tag: patient id


title: Sar09L_EpCAM_ADT

description:
Sar09L_EpCAM
surface protein
Sar09L_EpCAM__barcodes.tsv.gz
Sar09L_EpCAM__features.tsv.gz
Sar09L_EpCAM__matrix.mtx.gz


title: Sar09L_EpCAM_GEX

description:
Sar09L_EpCAM
RNA
Sar09L_EpCAM__barcodes.tsv.gz
Sar09L_EpCAM__features.tsv.gz
Sar09L_EpCAM__matrix.mtx.gz


title: MmGtsf1-Strep eCLIP - crosslinked_ip1


title: Sar09L_CD45po_GEX

description:
Sar09L_CD45po
RNA
Sar09L_CD45po_barcodes.tsv.gz
Sar09L_CD45po_features.tsv.gz
Sar09L_CD45po_matrix.mtx.gz


title: Sar09L_CD45po_ADT

description:
Sar09L_CD45po
surface protein
Sar09L_CD45po_barcodes.tsv.gz
Sar09L_CD45po_features.tsv.gz
Sar09L_CD45po_matrix.mtx.gz


title: ins-Str10_r2


title: ins-Str10_r1


title: ins-EpiV_r3

source_name: endometrium epithelium

value: insulin Vehicle


title: Sar09L_CD45ne_GEX

description:
Sar09L_CD45ne
RNA
Sar09L_CD45ne_barcodes.tsv.gz
Sar09L_CD45ne_features.tsv.gz
Sar09L_CD45ne_matrix.mtx.gz

value: CD45 negative


title: E17endo_2

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: CROWN.GRCm38_76.rsem_counts.txt file contains ENSEMBL gene Ids and RSEM-estimated raw counts for each gene and sample.

molecule: polyA RNA

source_name: Endocardial cells from murine embryonic hearts

extract_protocol:
RNA from freshly FACS sorted cell populations, from dissociated fetal hearts,  was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). Library preparation (New England Biolabs Nest Ultra RNA library prep Kit) and single read Next-generation sequencing (Illumina HiSeq 2500) were performed at the Genomics Unit at Centro Nacional de Investigaciones Cardiovasculares (CNIC).
200 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated, followed by uracile excision from the adaptor and PCR amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific)

tag: batch

tag: developmental stage


title: MmGtsf1-Strep eCLIP - crosslinked_input2

value: input


title: MmGtsf1-Strep eCLIP - non-crosslinked_input


title: Sar09L_CD45ne_ADT

description:
Sar09L_CD45ne
surface protein
Sar09L_CD45ne_barcodes.tsv.gz
Sar09L_CD45ne_features.tsv.gz
Sar09L_CD45ne_matrix.mtx.gz


title: Sar08L_CD3pos_GEX

description:
Sar08L_CD3pos
RNA
Sar08L_CD3pos_barcodes.tsv.gz
Sar08L_CD3pos_features.tsv.gz
Sar08L_CD3pos_matrix.mtx.gz

value: CD3 positive


title: ins-EpiV_r2


title: Sar08L_CD3pos_ADT

description:
Sar08L_CD3pos
surface protein
Sar08L_CD3pos_barcodes.tsv.gz
Sar08L_CD3pos_features.tsv.gz
Sar08L_CD3pos_matrix.mtx.gz


title: Sar08B_CD3pos_TCR

description:
Sar08B_CD3pos
TCR
Sar08B_TCR_all_contig_annotations.csv

source_name: blood


title: Sar08L_CD3neg_ADT

description:
Sar08L_CD3neg
surface protein
Sar08L_CD3neg_barcodes.tsv.gz
Sar08L_CD3neg_features.tsv.gz
Sar08L_CD3neg_matrix.mtx.gz

value: CD3 negative


title: MmGtsf1-Strep eCLIP - crosslinked_input1


title: Sar08B_CD3pos_GEX

description:
Sar08B_CD3pos
RNA
Sar08B_CD3pos_barcodes.tsv.gz
Sar08B_CD3pos_features.tsv.gz
Sar08B_CD3pos_matrix.mtx.gz


title: bulk_Donor18OC_olig

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

data_processing:
Single nucleus: Cell ranger v3.0.0 with pre-mRNA reference. Bulk: Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform (1.10.18).
Genome_build: GRCh38

source_name: brain

extract_protocol:
Nuclei isolation by lysing cryosections of frozen brain tissue in a sucrose buffer with Triton. Then purifying the nuclei by dense sucrose gradient ultracentrifugation. Nuclei are FACS sorted on DAPI positive expression, NeuN and Olig2.
10x Genomics Single Cell v3 kit or 3' Quantseq FWD (Lexogen)

tag: tissue

value: brain

tag: library type

value: bulk RNA sequencing

tag: nuclei population

tag: region

value: occipital cortex

tag: age

tag: gender

value: M

tag: clinical diagnosis

value: AD

tag: sample group

tag: rin

tag: braak/abc score


title: Sar08B_CD3pos_ADT

description:
Sar08B_CD3pos
surface protein
Sar08B_CD3pos_barcodes.tsv.gz
Sar08B_CD3pos_features.tsv.gz
Sar08B_CD3pos_matrix.mtx.gz


title: ins-Epi1_r3


title: Sar08L_CD3pos_TCR

description:
Sar08L_CD3pos
TCR
Sar08L_TCR_all_contig_annotations.csv


title: ins-Epi1_r2


title: bulk_Donor17OC_olig

value: F


title: Sar07L_CD3pos_TCR

description:
Sar07L_CD3pos
TCR
Sar07L_TCR_all_contig_annotations.csv


title: Sar07L_CD3pos_ADT

description:
Sar07L_CD3pos
surface protein
Sar07L_CD3pos_barcodes.tsv.gz
Sar07L_CD3pos_features.tsv.gz
Sar07L_CD3pos_matrix.mtx.gz


title: Sar07L_CD3pos_GEX

description:
Sar07L_CD3pos
RNA
Sar07L_CD3pos_barcodes.tsv.gz
Sar07L_CD3pos_features.tsv.gz
Sar07L_CD3pos_matrix.mtx.gz


title: ins-Epi1_r1


title: Sar07L_CD3neg_ADT

description:
Sar07L_CD3neg
surface protein
Sar07L_CD3neg_barcodes.tsv.gz
Sar07L_CD3neg_features.tsv.gz
Sar07L_CD3neg_matrix.mtx.gz


title: bulk_Donor16OTC_olig

value: occipitotemporal cortex


title: ins-Epi10_r3


title: Sar07B_CD3pos_GEX

description:
Sar07B_CD3pos
RNA
Sar07B_CD3pos_barcodes.tsv.gz
Sar07B_CD3pos_features.tsv.gz
Sar07B_CD3pos_matrix.mtx.gz


title: ins-Epi10_r2


title: Sar07L_CD3neg_GEX

description:
Sar07L_CD3neg
RNA
Sar07L_CD3neg_barcodes.tsv.gz
Sar07L_CD3neg_features.tsv.gz
Sar07L_CD3neg_matrix.mtx.gz


title: bulk_Donor16OC_olig


title: Sar07B_CD3pos_ADT

description:
Sar07B_CD3pos
surface protein
Sar07B_CD3pos_barcodes.tsv.gz
Sar07B_CD3pos_features.tsv.gz
Sar07B_CD3pos_matrix.mtx.gz


title: bulk_Donor18OTC_olig


title: ins-EpiV_r1


title: Sar08L_CD3neg_GEX

description:
Sar08L_CD3neg
RNA
Sar08L_CD3neg_barcodes.tsv.gz
Sar08L_CD3neg_features.tsv.gz
Sar08L_CD3neg_matrix.mtx.gz


title: bulk_Donor15OTC_olig


title: Sar05L_CD3pos_TCR

description:
Sar05L_CD3pos
TCR
Sar05L_TCR_all_contig_annotations.csv


title: Sar05L_CD3pos_GEX

description:
Sar05L_CD3pos
RNA
Sar05L_CD3pos_barcodes.tsv.gz
Sar05L_CD3pos_features.tsv.gz
Sar05L_CD3pos_matrix.mtx.gz


title: ins-Epi10_r1


title: bulk_Donor17OTC_olig


title: bulk_Donor15OC_olig


title: gluc-Str50_r3

value: glucose 50 mM treatment


title: Sar05L_CD3neg_GEX

description:
Sar05L_CD3neg
RNA
Sar05L_CD3neg_barcodes.tsv.gz
Sar05L_CD3neg_features.tsv.gz
Sar05L_CD3neg_matrix.mtx.gz


title: Sar05L_CD3pos_ADT

description:
Sar05L_CD3pos
surface protein
Sar05L_CD3pos_barcodes.tsv.gz
Sar05L_CD3pos_features.tsv.gz
Sar05L_CD3pos_matrix.mtx.gz


title: Sar05L_CD3neg_ADT

description:
Sar05L_CD3neg
surface protein
Sar05L_CD3neg_barcodes.tsv.gz
Sar05L_CD3neg_features.tsv.gz
Sar05L_CD3neg_matrix.mtx.gz


title: Sar05B_CD3pos_TCR

description:
Sar05B_CD3pos
TCR
Sar05B_TCR_all_contig_annotations.csv


title: gluc-Str50_r2


title: Sar05B_CD3pos_GEX

description:
Sar05B_CD3pos
RNA
Sar05B_CD3pos_barcodes.tsv.gz
Sar05B_CD3pos_features.tsv.gz
Sar05B_CD3pos_matrix.mtx.gz


title: Sar07B_CD3pos_TCR

description:
Sar07B_CD3pos
TCR
Sar07B_TCR_all_contig_annotations.csv


title: Sar05B_CD3pos_ADT

description:
Sar05B_CD3pos
surface protein
Sar05B_CD3pos_barcodes.tsv.gz
Sar05B_CD3pos_features.tsv.gz
Sar05B_CD3pos_matrix.mtx.gz


title: gluc-Str5_r3

value: glucose 5 mM treatment


title: Sar04L_CD3pos_TCR

description:
Sar04L_CD3pos
TCR
Sar04L_TCR_all_contig_annotations.csv


title: bulk_Donor14OC_olig


title: Sar04L_CD3pos_GEX

description:
Sar04L_CD3pos
RNA
Sar04L_CD3pos_barcodes.tsv.gz
Sar04L_CD3pos_features.tsv.gz
Sar04L_CD3pos_matrix.mtx.gz


title: bulk_Donor13OTC_olig

value: IV


title: gluc-Str50_r1


title: gluc-Str5_r2


title: Sar04L_CD3neg_GEX

description:
Sar04L_CD3neg
RNA
Sar04L_CD3neg_barcodes.tsv.gz
Sar04L_CD3neg_features.tsv.gz
Sar04L_CD3neg_matrix.mtx.gz


title: Sar04L_CD3pos_ADT

description:
Sar04L_CD3pos
surface protein
Sar04L_CD3pos_barcodes.tsv.gz
Sar04L_CD3pos_features.tsv.gz
Sar04L_CD3pos_matrix.mtx.gz


title: MycER-BclXL-Fzd9 wt mouse 2

type: RNA

city: Barcelona

first: Mariano

middle: F

last: Zacarias-Fluck

address: Natzaret, 115-117

department: Preclinical and Translational Research Program

institute: Vall d'Hebron Institute of Oncology (VHIO)

hyb_protocol: Total RNA was linearly amplified using WT Plus (Affymetrix). The resulting ssDNA was used to hybridize Affimetrix microarrays. Hybridization data was acquired using the Affimetrix GeneChip/GeneTitan platforms. Transcriptomes were determined on a genome wide Mouse Gene 2.1 Array (Affimetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Partek Genomic Suite followed by GSEA 3.0 software from Broad Institute.

label: Biotin

source_name: Insulinoma from MycER-BclXL-Fzd9 wt mouse

label_protocol: Labeling of samples was carried out according to the manufacturer’s standard protocol

growth_protocol: MycER;BclXl Fzd9 wt and Fzd9-/- C57Bl/6 mice

extract_protocol: 50-100 mg of tumor tissue was homogenized with a pestle in TRIzol. Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were treated with Tamoxifen i.p. for three days

tag: genotype

value: Fzd9 wt

tag: tumor type

value: Insulinoma


title: bulk_Donor12OTC_olig

value: II


title: gluc-Str5_r1

tag: treatment


title: Sar04L_CD3neg_ADT

description:
Sar04L_CD3neg
surface protein
Sar04L_CD3neg_barcodes.tsv.gz
Sar04L_CD3neg_features.tsv.gz
Sar04L_CD3neg_matrix.mtx.gz

tag: cell type

tag: disease


title: bulk_Donor12OC_olig


title: Sar04B_CD3pos_TCR

description:
Sar04B_CD3pos
TCR
Sar04B_TCR_all_contig_annotations.csv

tag: patient id


title: gluc-Epi_5_r3


title: bulk_Donor11OTC_olig

value: II-III


title: bulk_Donor14OTC_olig


title: Sar04B_CD3pos_ADT

description:
Sar04B_CD3pos
surface protein
Sar04B_CD3pos_barcodes.tsv.gz
Sar04B_CD3pos_features.tsv.gz
Sar04B_CD3pos_matrix.mtx.gz


title: Sar03L_CD3pos_GEX

description:
Sar03L_CD3pos
RNA
Sar03L_CD3pos_barcodes.tsv.gz
Sar03L_CD3pos_features.tsv.gz
Sar03L_CD3pos_matrix.mtx.gz


title: gluc-Epi50_r3


title: bulk_Donor11OC_olig


title: Sar03L_CD3neg_GEX

description:
Sar03L_CD3neg
RNA
Sar03L_CD3neg_barcodes.tsv.gz
Sar03L_CD3neg_features.tsv.gz
Sar03L_CD3neg_matrix.mtx.gz


title: gluc-Epi_5_r2


title: Sar03L_CD3pos_ADT

description:
Sar03L_CD3pos
surface protein
Sar03L_CD3pos_barcodes.tsv.gz
Sar03L_CD3pos_features.tsv.gz
Sar03L_CD3pos_matrix.mtx.gz


title: bulk_Donor13OC_olig


title: Sar03B_CD3pos_TCR

description:
Sar03B_CD3pos
TCR
Sar03B_TCR_all_contig_annotations.csv


title: Sar03L_CD3neg_ADT

description:
Sar03L_CD3neg
surface protein
Sar03L_CD3neg_barcodes.tsv.gz
Sar03L_CD3neg_features.tsv.gz
Sar03L_CD3neg_matrix.mtx.gz


title: bulk_Donor5OTC_olig

value: CTR


title: gluc-Epi50_r2


title: bulk_Donor5OC_olig


title: bulk_Donor4OTC_olig


title: Sar03B_CD3pos_ADT

description:
Sar03B_CD3pos
surface protein
Sar03B_CD3pos_barcodes.tsv.gz
Sar03B_CD3pos_features.tsv.gz
Sar03B_CD3pos_matrix.mtx.gz

value: CD3 positive


title: Sar02L_CD3pos_TCR

description:
Sar02L_CD3pos
TCR
Sar02L_TCR_all_contig_annotations.csv


title: Sar02L_CD3pos_GEX

description:
Sar02L_CD3pos
RNA
Sar02L_CD3pos_barcodes.tsv.gz
Sar02L_CD3pos_features.tsv.gz
Sar02L_CD3pos_matrix.mtx.gz


title: Sar02L_CD3pos_ADT

description:
Sar02L_CD3pos
surface protein
Sar02L_CD3pos_barcodes.tsv.gz
Sar02L_CD3pos_features.tsv.gz
Sar02L_CD3pos_matrix.mtx.gz


title: NTSW204

city: Charlotte

first: Adam

last: Reitzel

state: NC

address: 9201 University City Blvd

department: Biological Sciences

institute: University of North Carolina Charlotte

description:
S122
NTSW204
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

data_processing:
Sequenced reads were concatenated and renamed based on sample ID.
Each Illumina read was trimmed of the adapter and PCR duplicates were removed.
Quality filtering was performed using fastx_toolkit.
Transcriptome mapping was performed using Bowtie2.
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: allcountsFINAL.txt: Tab-delimited table of counts per gene for each sample.

organism: Nematostella vectensis

source_name: whole-organism

growth_protocol: Animals were maintained as described in Hand et al. (1994).

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011).

treatment_protocol: Animals were exposed to all conditions for 7 days. For antibiotic removed condition, the antibiotics were removed 3 days prior to extraction.

value: Whole body

value: Adult

value: No antibiotic + CFS Pseudoalteromonas spiralis


title: bulk_Donor4OC_olig

value: brain

value: bulk RNA sequencing

value: occipital cortex


title: gluc-Epi50_r1


title: Sar04B_CD3pos_GEX

description:
Sar04B_CD3pos
RNA
Sar04B_CD3pos_barcodes.tsv.gz
Sar04B_CD3pos_features.tsv.gz
Sar04B_CD3pos_matrix.mtx.gz


title: Sar03L_CD3pos_TCR

description:
Sar03L_CD3pos
TCR
Sar03L_TCR_all_contig_annotations.csv


title: bulk_Donor7OTC_olig

value: F

value: CTR+


title: NTSW203

description:
S121
NTSW203
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor7OC_olig


title: NTSW202

description:
S120
NTSW202
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Sar02L_CD3neg_ADT

description:
Sar02L_CD3neg
surface protein
Sar02L_CD3neg_barcodes.tsv.gz
Sar02L_CD3neg_features.tsv.gz
Sar02L_CD3neg_matrix.mtx.gz

value: CD3 negative


title: Sar02B_CD3pos_TCR

description:
Sar02B_CD3pos
TCR
Sar02B_TCR_all_contig_annotations.csv


title: Sar02B_CD3pos_ADT

description:
Sar02B_CD3pos
surface protein
Sar02B_CD3pos_barcodes.tsv.gz
Sar02B_CD3pos_features.tsv.gz
Sar02B_CD3pos_matrix.mtx.gz


title: Sar03B_CD3pos_GEX

description:
Sar03B_CD3pos
RNA
Sar03B_CD3pos_barcodes.tsv.gz
Sar03B_CD3pos_features.tsv.gz
Sar03B_CD3pos_matrix.mtx.gz


title: Sar01L_CD3pos_TCR

description:
Sar01L_CD3pos
TCR
Sar01L_TCR_all_contig_annotations.csv


title: Sar01L_CD3pos_GEX

description:
Sar01L_CD3pos
RNA
Sar01L_CD3pos_barcodes.tsv.gz
Sar01L_CD3pos_features.tsv.gz
Sar01L_CD3pos_matrix.mtx.gz


title: NTSA64

description:
S90
NTSA64
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + CFS Vibrio alginolyticus


title: NTSW201

description:
S119
NTSW201
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor3OC_olig


title: bulk_Donor6OTC_olig

value: occipitotemporal cortex

value: M

value: I


title: gluc-Epi_5_r1

value: glucose 5 mM treatment


title: NTSA63

description:
S89
NTSA63
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor6OC_olig


title: Sar01B_CD3pos_TCR

description:
Sar01B_CD3pos
TCR
Sar01B_TCR_all_contig_annotations.csv


title: Sar01B_CD3pos_GEX

description:
Sar01B_CD3pos
RNA
Sar01B_CD3pos_barcodes.tsv.gz
Sar01B_CD3pos_features.tsv.gz
Sar01B_CD3pos_matrix.mtx.gz


title: Sar01B_CD3pos_ADT

description:
Sar01B_CD3pos
surface protein
Sar01B_CD3pos_barcodes.tsv.gz
Sar01B_CD3pos_features.tsv.gz
Sar01B_CD3pos_matrix.mtx.gz


title: Sar02L_CD3neg_GEX

description:
Sar02L_CD3neg
RNA
Sar02L_CD3neg_barcodes.tsv.gz
Sar02L_CD3neg_features.tsv.gz
Sar02L_CD3neg_matrix.mtx.gz


title: NTSA61

description:
S87
NTSA61
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: NTSA62

description:
S88
NTSA62
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Bac20L_CD3pos_GEX

description:
Bac20L_CD3pos
RNA
Bac20L_CD3pos_barcodes.tsv.gz
Bac20L_CD3pos_features.tsv.gz
Bac20L_CD3pos_matrix.mtx.gz

value: Bacterial pneumonia


title: Sar02B_CD3pos_GEX

description:
Sar02B_CD3pos
RNA
Sar02B_CD3pos_barcodes.tsv.gz
Sar02B_CD3pos_features.tsv.gz
Sar02B_CD3pos_matrix.mtx.gz


title: Bac20L_CD3pos_TCR

description:
Bac20L_CD3pos
TCR
Bac20L_TCR_all_contig_annotations.csv


title: bulk_Donor18OC_neun

value: NEUNpos

value: AD


title: Sar01L_CD3neg_ADT

description:
Sar01L_CD3neg
surface protein
Sar01L_CD3neg_barcodes.tsv.gz
Sar01L_CD3neg_features.tsv.gz
Sar01L_CD3neg_matrix.mtx.gz


title: Bac20L_CD3pos_ADT

description:
Bac20L_CD3pos
surface protein
Bac20L_CD3pos_barcodes.tsv.gz
Bac20L_CD3pos_features.tsv.gz
Bac20L_CD3pos_matrix.mtx.gz

value: CD3 positive


title: Bac20L_CD3neg_GEX

description:
Bac20L_CD3neg
RNA
Bac20L_CD3neg_barcodes.tsv.gz
Bac20L_CD3neg_features.tsv.gz
Bac20L_CD3neg_matrix.mtx.gz


title: bulk_Donor3OTC_olig

value: CTR


title: Bac20L_CD3neg_ADT

description:
Bac20L_CD3neg
surface protein
Bac20L_CD3neg_barcodes.tsv.gz
Bac20L_CD3neg_features.tsv.gz
Bac20L_CD3neg_matrix.mtx.gz


title: Sar01L_CD3neg_GEX

description:
Sar01L_CD3neg
RNA
Sar01L_CD3neg_barcodes.tsv.gz
Sar01L_CD3neg_features.tsv.gz
Sar01L_CD3neg_matrix.mtx.gz


title: bulk_Donor17OTC_neun


title: NTSA213

description:
S105
NTSA213
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body

value: Adult

value: No antibiotic + CFS Bacillus velezensis


title: Sar01L_CD3pos_ADT

description:
Sar01L_CD3pos
surface protein
Sar01L_CD3pos_barcodes.tsv.gz
Sar01L_CD3pos_features.tsv.gz
Sar01L_CD3pos_matrix.mtx.gz


title: Bac20B_CD3pos_TCR

description:
Bac20B_CD3pos
TCR
Bac20B_TCR_all_contig_annotations.csv


title: bulk_Donor17OC_neun

value: brain

value: bulk RNA sequencing

value: occipital cortex


title: Bac20B_CD3pos_GEX

description:
Bac20B_CD3pos
RNA
Bac20B_CD3pos_barcodes.tsv.gz
Bac20B_CD3pos_features.tsv.gz
Bac20B_CD3pos_matrix.mtx.gz


title: Bac20B_CD3pos_ADT

description:
Bac20B_CD3pos
surface protein
Bac20B_CD3pos_barcodes.tsv.gz
Bac20B_CD3pos_features.tsv.gz
Bac20B_CD3pos_matrix.mtx.gz


title: Bac19L_CD3pos_TCR

description:
Bac19L_CD3pos
TCR
Bac19L_TCR_all_contig_annotations.csv


title: bulk_Donor16OTC_neun

value: F


title: bulk_Donor18OTC_neun


title: NTSA212

description:
S104
NTSA212
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: NTSA211

description:
S103
NTSA211
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Bac19L_CD3pos_ADT

description:
Bac19L_CD3pos
surface protein
Bac19L_CD3pos_barcodes.tsv.gz
Bac19L_CD3pos_features.tsv.gz
Bac19L_CD3pos_matrix.mtx.gz


title: Bac19L_CD3pos_GEX

description:
Bac19L_CD3pos
RNA
Bac19L_CD3pos_barcodes.tsv.gz
Bac19L_CD3pos_features.tsv.gz
Bac19L_CD3pos_matrix.mtx.gz


title: Bac19B_CD3pos_TCR

description:
Bac19B_CD3pos
TCR
Bac19B_TCR_all_contig_annotations.csv


title: bulk_Donor15OTC_neun


title: NTLW204

description:
S114
NTLW204
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + Pseudoalteromonas spiralis


title: Bac19B_CD3pos_GEX

description:
Bac19B_CD3pos
RNA
Bac19B_CD3pos_barcodes.tsv.gz
Bac19B_CD3pos_features.tsv.gz
Bac19B_CD3pos_matrix.mtx.gz


title: bulk_Donor15OC_neun


title: Bac19B_CD3pos_ADT

description:
Bac19B_CD3pos
surface protein
Bac19B_CD3pos_barcodes.tsv.gz
Bac19B_CD3pos_features.tsv.gz
Bac19B_CD3pos_matrix.mtx.gz


title: NTLW202

description:
S112
NTLW202
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: NTSA214

description:
S106
NTSA214
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Bac18L_CD3pos_GEX

description:
Bac18L_CD3pos
RNA
Bac18L_CD3pos_barcodes.tsv.gz
Bac18L_CD3pos_features.tsv.gz
Bac18L_CD3pos_matrix.mtx.gz


title: bulk_Donor14OTC_neun

value: occipitotemporal cortex


title: Bac18L_CD3pos_ADT

description:
Bac18L_CD3pos
surface protein
Bac18L_CD3pos_barcodes.tsv.gz
Bac18L_CD3pos_features.tsv.gz
Bac18L_CD3pos_matrix.mtx.gz


title: NTLW201

description:
S111
NTLW201
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Bac18L_CD3neg_ADT

description:
Bac18L_CD3neg
surface protein
Bac18L_CD3neg_barcodes.tsv.gz
Bac18L_CD3neg_features.tsv.gz
Bac18L_CD3neg_matrix.mtx.gz

value: CD3 negative


title: Bac18B_CD3pos_TCR

description:
Bac18B_CD3pos
TCR
Bac18B_TCR_all_contig_annotations.csv


title: bulk_Donor13OTC_neun

value: IV


title: NTLA64

description:
S82
NTLA64
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + Vibrio alginolyticus


title: Bac18L_CD3neg_GEX

description:
Bac18L_CD3neg
RNA
Bac18L_CD3neg_barcodes.tsv.gz
Bac18L_CD3neg_features.tsv.gz
Bac18L_CD3neg_matrix.mtx.gz

value: Bacterial pneumonia


title: Bac18B_CD3pos_GEX

description:
Bac18B_CD3pos
RNA
Bac18B_CD3pos_barcodes.tsv.gz
Bac18B_CD3pos_features.tsv.gz
Bac18B_CD3pos_matrix.mtx.gz


title: bulk_Donor14OC_neun

value: NEUNpos


title: NTLA63

description:
S81
NTLA63
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor16OC_neun

value: AD


title: Bac17L_CD3pos_TCR

description:
Bac17L_CD3pos
TCR
Bac17L_TCR_all_contig_annotations.csv

value: CD3 positive


title: bulk_Donor13OC_neun


title: Bac17L_CD3pos_GEX

description:
Bac17L_CD3pos
RNA
Bac17L_CD3pos_barcodes.tsv.gz
Bac17L_CD3pos_features.tsv.gz
Bac17L_CD3pos_matrix.mtx.gz


title: NTLA62

description:
S80
NTLA62
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Bac18B_CD3pos_ADT

description:
Bac18B_CD3pos
surface protein
Bac18B_CD3pos_barcodes.tsv.gz
Bac18B_CD3pos_features.tsv.gz
Bac18B_CD3pos_matrix.mtx.gz


title: bulk_Donor12OTC_neun

value: II


title: Bac17L_CD3pos_ADT

description:
Bac17L_CD3pos
surface protein
Bac17L_CD3pos_barcodes.tsv.gz
Bac17L_CD3pos_features.tsv.gz
Bac17L_CD3pos_matrix.mtx.gz


title: NTLA61

description:
S79
NTLA61
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: NTLW203

description:
S113
NTLW203
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult


title: Bac18L_CD3pos_TCR

description:
Bac18L_CD3pos
TCR
Bac18L_TCR_all_contig_annotations.csv


title: bulk_Donor12OC_neun


title: Bac17L_CD3neg_GEX

description:
Bac17L_CD3neg
RNA
Bac17L_CD3neg_barcodes.tsv.gz
Bac17L_CD3neg_features.tsv.gz
Bac17L_CD3neg_matrix.mtx.gz


title: Bac17L_CD3neg_ADT

description:
Bac17L_CD3neg
surface protein
Bac17L_CD3neg_barcodes.tsv.gz
Bac17L_CD3neg_features.tsv.gz
Bac17L_CD3neg_matrix.mtx.gz


title: Bac17B_CD3pos_TCR

description:
Bac17B_CD3pos
TCR
Bac17B_TCR_all_contig_annotations.csv


title: NTLA214

description:
S98
NTLA214
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + Bacillus velezensis


title: Bac17B_CD3pos_GEX

description:
Bac17B_CD3pos
RNA
Bac17B_CD3pos_barcodes.tsv.gz
Bac17B_CD3pos_features.tsv.gz
Bac17B_CD3pos_matrix.mtx.gz


title: NTLA213

description:
S97
NTLA213
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor11OC_neun

value: brain

value: M

value: II-III


title: NTLA212

description:
S96
NTLA212
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Nalm6 cells, THZ1_3

city: Shanghai

first: xia

last: jing

address: 1678 Dongfang Road

country: China

institute: Shanghai Children’s Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Cutadapt
Sequenced reads were mapped to GRCh37 whole genome using STAR with parameters --outFileNamePrefix starout  --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesCommand gunzip -c
The raw gene counts was calculated using htseq with parameters -f sam -r name -s reverse -t exon -i gene_id -m union
The gene expression level (FPKM) was calculated according to the RSEM
Genome_build: GRCh37
Supplementary_files_format_and_content: gene_expression.txt (tab-delimited text file includes FPKM values for each Sample)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt (Matrix table with raw gene counts for every gene and every sample)

extract_protocol:
Total cellular RNA was isolated using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nalm6 cells were seeded at a density of 1× 10e6 cells/ml and treated with 500nm THZ1or DMSO for 24h.

tag: cell line


title: bulk_Donor10OTC_neun

tag: tissue

value: bulk RNA sequencing

value: F


title: Nalm6 cells, THZ1_2


title: Nalm6 cells, DMSO_3

value: DMSO


title: Nalm6 cells, DMSO_2


title: NTLA211

description:
S95
NTLA211
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor10OC_neun

tag: library type

value: occipital cortex


title: Nalm6 cells, THZ1_1


title: NTL5ug4

description:
S130
NTL5ug4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + 5ug/mL LPS


title: NTL5ug3

description:
S129
NTL5ug3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor9OC_neun

tag: nuclei population

value: III


title: MM1.S treated with CCF642-34 rep2

city: Cleveland

first: Babal

middle: K

last: Jha

state: Ohio

address: 9500 Euclid Ave, NE6-253

department: Translational Hematology and Oncology

institute: Cleveland Clinic

data_processing:
Raw reads were mapped to human genome, hg19, using RNA STAR. Computational analysis was performed using Galaxy server (https.usegalaxy.org).
Differential expression and gene set enrichment analysis was assessed using edgeR 3.24.3 and limma 3.38.3 with R 3.5.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: MM1.S Cell line

growth_protocol: MM1S cell lines were cultured in RPMI-1640 with 10% FBS and 100 U/ml pen-strep.

extract_protocol:
RNA was purified by using NucleoSpin RNA kit ((Takara Bio USA, Inc Cat #740955) according to the manufacturer’s instruction. RNA quality was validated by RNA integrity number (RIN >9) calculated by Agilent 2100 Bioanalyzer. mRNA was enriched using oligo(dT) beads.
RNA was fragmented randomly by adding fragmentation buffer. The cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina, dNTPs, RNase H and DNA polymerase I) was added to initiate the second-strand synthesis. After a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Cells at density of 0.3 M/ml were treated with 3 µM CCF642, CCF642-34, or DMSO for 6 hours

value: 3µM of CCF642-34


title: MM1.S treated with CCF642-34 rep1


title: bulk_Donor9OTC_neun

value: NEUNpos

tag: region

value: occipitotemporal cortex


title: Nalm6 cells, DMSO_1


title: MM1.S treated with CCF-642 rep2

value: 3µM of CCF642


title: bulk_Donor11OTC_neun

tag: age

value: AD


title: NTL5ug2

description:
S128
NTL5ug2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: MM1.S treated with DMSO rep2


title: NTL5ug1

description:
S127
NTL5ug1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult


title: MM1.S treated with CCF-642 rep1


title: bulk_Donor8OC_neun

tag: gender

value: CTR

value: CTR+


title: CT27_hTSC_p52

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

institute: Cerevance ltd

description: placenta derived trophoblast stem cell culture

data_processing:
STAR alignement
HTseq-count
Genome_build: hg38
Supplementary_files_format_and_content: raw reads count text format

source_name: trophoblast stem cell culture

extract_protocol:
Cell lysate and RNA are prepared using Trizol/Chloroform
Sequencing libraries are prepared using TruSeq RNA Sample Prep Kit( Illumina), following ribosomal RNA depletion using Ribozero(Illumina)


title: NTL5ng4

description:
S138
NTL5ng4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + 5ng/mL LPS


title: Bac17B_CD3pos_ADT

description:
Bac17B_CD3pos
surface protein
Bac17B_CD3pos_barcodes.tsv.gz
Bac17B_CD3pos_features.tsv.gz
Bac17B_CD3pos_matrix.mtx.gz

value: CD3 positive

value: Bacterial pneumonia


title: bulk_Donor8OTC_neun

value: brain

value: bulk RNA sequencing

value: M

tag: clinical diagnosis


title: CT27_hTSC_p51

value: placenta derived trophoblast stem cell culture


title: MM1.S treated with DMSO rep1

value: DMSO


title: bulk_Donor5OTC_neun

value: F

tag: sample group


title: niPSC4_PD_MEF_hTS_P5

value: pluripotent stem cell derived trophoblast stem cell cultures


title: niPSC4_PD_MEF_hTS_P2

description: stem cell derived trophoblast stem cell cultures


title: NTL5ng3

description:
S137
NTL5ng3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: 35Spro:RIF #1 red receptacles rep3

city: Málaga

first: David

last: Posé

address: Avenida Louis Pasteur, 49

institute: Instituto de Hortofruticultura Subtropical y Mediterránea

description:
35SRIF_#1_S3
TPC2020-RA-00833R1_SuppDS1_35SRIF.txt

data_processing:
CLC Genomics Workbench 9 software for trimming, mapping and expression analyses
Raw sequences were trimmed and mapped against using the assembly and annotation version v4.0.a1 of the F. vesca reference genome (https://www.rosacea.org/species/fragaria_vesca/genome_v4.0.a1; Edger et al., 2018; doi: 10.1093/gigascience/gix124)
Supplementary_files_format_and_content: txt files including the RPKM values, statistical analysis, and gene annotations

organism: Fragaria x ananassa

source_name: red strawberry receptacles

growth_protocol: 35Spro:RIF-RNAi transgenic lines and their respective control line were grown in a shading house, and EXP2pro:RIF-RNAi and 35S:RIF transgenic lines and their respective control line in a greenhouse. In both cases, they were grown under natural sunlight and ambient temperature. Each biological replicate comprise a minimum of 20 receptacles at either white or red stages of ripening.

extract_protocol:
Total RNA was isolated as previously described (Gambino et al., 2008; doi: 10.1002/pca.1078) from three biological replicates of receptacles after the removal of achenes for the control and transgenic lines.
Illumina mRNA libraries were generated using the strand specific mRNA library as described (Zhong et al., 2011; doi:10.1101/pdb-prot5652) for 35Spro:RIF-RNAi and control experiment. For EXP2pro:RIF-RNAi, 35S:RIF and control experiment, the libraries were generated using TruSeq stranded mRNA according to the manufacturer’s instructions (Illumina Inc., San Diego, CA, USA)

tag: cultivar

value: Camarosa

value: Strawberry receptacles

tag: ripening stage

value: red


title: bulk_Donor4OTC_neun

value: NEUNpos

value: occipitotemporal cortex

tag: rin

tag: braak/abc score


title: niPSC4_PD/A8301_MEF_hTS_P5


title: 35Spro:RIF #1 red receptacles rep2

description:
35SRIF_#1_S2
TPC2020-RA-00833R1_SuppDS1_35SRIF.txt


title: NTL5ng1

description:
S135
NTL5ng1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body

value: Adult

tag: treatment


title: bulk_Donor4OC_neun

value: occipital cortex

value: CTR


title: NTC4

description:
S74
NTC4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No treatment control


title: EXP2pro:RIF-RNAi #7 red receptacles rep3

description:
EXP2RIF-RNAi_#7_S3
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt


title: bulk_Donor7OTC_neun

value: brain

value: CTR+


title: niPSC2_PD_MEF_hTS_P5

tag: cell type


title: bulk_Donor7OC_neun

value: bulk RNA sequencing


title: niPSC2_PD_MEF_hTS_P2


title: NTC2

description:
S72
NTC2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: EXP2pro:RIF-RNAi #7 red receptacles rep2

description:
EXP2RIF-RNAi_#7_S2
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt


title: NTC3

description:
S73
NTC3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor3OTC_neun


title: niPSC2_PD/A8301_MEF_hTS_p6


title: EXP2pro:RIF-RNAi #7 red receptacles rep1

description:
EXP2RIF-RNAi_#7_S1
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt


title: bulk_Donor3OC_neun


title: EXP2pro:RIF-RNAi #1 red receptacles rep3

description:
EXP2RIF-RNAi_#1_S3
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt


title: niPSC2_PD/A8301_MEF_hTS_p2


title: NTC1

description:
S71
NTC1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor5OC_neun


title: ABSW204

description:
S126
ABSW204
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + CFS Pseudoalteromonas spiralis


title: hNES1_PD_MEF_hTS_P6


title: EXP2pro:RIF-RNAi #1 red receptacles rep2

description:
EXP2RIF-RNAi_#1_S2
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt


title: NTL5ng2

description:
S136
NTL5ng2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt

value: No antibiotic + 5ng/mL LPS


title: bulk_Donor6OTC_neun

value: M

value: I


title: ABSW203

description:
S125
ABSW203
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: niPSC4_PD/A8301_MEF_hTS_P2

value: pluripotent stem cell derived trophoblast stem cell cultures


title: bulk_Donor6OC_neun


title: hNES1_PD_MEF_hTS_p2

description: stem cell derived trophoblast stem cell cultures


title: 35Spro:RIF #1 red receptacles rep1

description:
35SRIF_#1_S1
TPC2020-RA-00833R1_SuppDS1_35SRIF.txt

value: Camarosa

value: Strawberry receptacles


title: hNES1_PD/A8301_MEF_hTS_p6


title: EXP2pro:RIF-RNAi #1 red receptacles rep1

description:
EXP2RIF-RNAi_#1_S1
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt

value: red


title: ABSW202

description:
S124
ABSW202
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: bulk_Donor1OC_neun

value: NEUNpos


title: Control red receptacles rep3 (control for EXPpro:RIF-RNAi and 35S:RIF samples)

description:
Control_for_EXP2RIF-RNAi_and_35S-RIF_S3
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt
TPC2020-RA-00833R1_SuppDS1_35SRIF.txt


title: ABSW201

description:
S123
ABSW201
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: SN_Donor18OTC

value: single-nucleus RNA sequencing

value: occipitotemporal cortex

value: AD


title: ABSA64

description:
S94
ABSA64
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult

value: Antibiotics + CFS Vibrio alginolyticus


title: LB_AMD_HPbCD_3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: Amiodarone-and HPbCD-treated LB cells

data_processing:
Sequenced reads from fasq files were mapped to GRCh38.95 whole genome using STAR 2.7.3a aligner following ENCODE standard option in STAR manual.
Transcripts Per Kilobase Million (TPM) value of each gene was calculated using RSEM 1.3.1.
Genome_build: GRCh38.95
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample .

source_name: A549 cells

growth_protocol: A549 cells and LB cells were maintained under 5% CO2 at 37°C in RPMI supplemented with 10% FBS, HEPES, sodium pyruvate and 100 U/ml penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Quiagen) according to manufacturer's protocol.
Library preparation was performed with the TrueSeq stranded mRNA sample preparation kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: A549 cells and LB cells were seeded with or without 10 mg/ml HPbCD. After incubation for 24 h, the cells were treated with 10 μM amiodarone or 0.1% DMSO as a vehicle control for 24h.

value: LB cells

value: Amiodarone+HPbCD


title: Control red receptacles rep2 (control for EXPpro:RIF-RNAi and 35S:RIF samples)

description:
Control_for_EXP2RIF-RNAi_and_35S-RIF_S2
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt
TPC2020-RA-00833R1_SuppDS1_35SRIF.txt


title: ABSA63

description:
S93
ABSA63
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: LB_AMD_HPbCD_2

description: Amiodarone-and HPbCD-treated LB cells


title: Control red receptacles rep1 (control for EXPpro:RIF-RNAi and 35S:RIF samples)

description:
Control_for_EXP2RIF-RNAi_and_35S-RIF_S1
TPC2020-RA-00833R1_SuppDS1_EXP2RIF-RNAi.txt
TPC2020-RA-00833R1_SuppDS1_35SRIF.txt


title: SN_Donor18OC

value: brain

value: occipital cortex


title: FTO MO m6A-IP

city: Daejeon

first: Young-suk

last: Lee

address: 1113 CMS(E16), 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

country: South Korea

institute: KAIST

description: m6A-seq from FTO MO

data_processing:
Library strategy: m6A-seq
Illumina Miseq reads from both the input and IP were mapped to the Xenopus laevis v9.2 genome from Xenbase (Karimi, 2018) using Bowtie2 v2.2.6 with the “--local” option (Langmead, 2012).
Aligned m6A-seq reads was first processed using samtools v1.8 (Li, 2009). The read coverage of the aligned m6A-IP reads and RNA input reads were computed for the genes of interest (i.e. known ciliary genes and transcriptional factors) in a strand-specific manner using bedtools v2.26 with command “coverage” and parameters -s and -d (Quinlan, 2010).
Genome_build: Xenopus laevis v9.2
Supplementary_files_format_and_content: .depth files are in BED format and the last column represents the number of m6A-seq reads mapped at the single nucleotide location.

organism: Xenopus laevis

source_name: Animal cap explants from FTO MO

growth_protocol: Xenopus laevis were obtained from the Korean Xenopus Resource Center for Research and from Nasco (Wisconsin, USA).

extract_protocol:
PolyA+ RNAs were fragmented using fragmentation buffer (Ambion #AM8740) to yield ~200 nt lengths RNA fragments. Polyclonal anti-m6A antibody (Synaptic Systems) was incubated with fragmented RNAs in RIP buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% NP40) supplemented with RNase inhibitors, RNasin (promega) and Superase-in (Ambion), for 4 hours at 4 °C. Along with this, Dynabeads protein A (Invitrogen #10002D) was washed and pre-blocked with 0.5 mg/ml BSA for 2 hours at 4 °C. Beads were then added to antibody-RNA complex and incubated for an additional 1 hour at 4 °C. Bound RNA was eluted after extensive washing with RIP buffer by competitive elution with buffer containing 7 mM m6A (Abcam #ab145715) twice each for 1 hour at 4 °C. Eluted RNAs were then precipitated with ethanol and used for m6A-sequencing library preparation.
Sequencing libraries were prepared using SMARTer Stranded RNA-seq kit (Clontech) according to the manufacturer’s protocol. Purified m6A-seq libraries were sequenced on an Illumina MiSeq platform with 10-20% PhiX control library (Illumina).

treatment_protocol: Briefly, 600 units of Human chorionic gonadotropin (Daesung Microbiological Labs) were injected into a female Xenopus laevis 12 hours before collecting eggs. Eggs were obtained in 1X MMR (Marc’s Modified Ringer) solution containing 100 mM NaCl, 2 mM KCl, 2 mM CaCl2, 1 mM MgCl2 and 5 mM HEPES, pH 7.4. Eggs were in vitro fertilized using excised testis. In vitro synthesized mRNAs and/or morpholino oligonucleotides were introduced into the embryos by microinjection using an IM 300 Microinjector (Narishige International USA, Inc).

tag: fraction

value: Co-immunoprecipitated RNAs

tag: antibody

value: Animal cap

tag: condition

value: FTO morpholino


title: LB_AMD_HPbCD_1

description: Amiodarone-and HPbCD-treated LB cells

tag: cell line


title: SN_Donor17OC

tag: tissue

tag: library type

value: F


title: SN_Donor17OTC

tag: nuclei population

tag: region


title: ABSA62

description:
S92
ABSA62
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt

tag: age


title: FTO MO input

description: Input control for m6A-seq from FTO MO

value: Input RNAs

value: none (input)


title: Con MO m6A-IP

description: m6A-seq from Con MO

source_name: Animal cap explants from Con MO

value: Control morpholino


title: Con MO input

description: Input control for m6A-seq from Con MO


title: ABSA61

description:
S91
ABSA61
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: SN_Donor16OTC

value: single-nucleus RNA sequencing

tag: gender

tag: clinical diagnosis


title: SN_Donor16OC

tag: sample group


title: LB_AMD_1

description: Amiodarone-treated LB cells

value: Amiodarone


title: LB_AMD_3

description: Amiodarone-treated LB cells


title: ABSA214

description:
S110
ABSA214
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + CFS Bacillus velezensis


title: ABSA213

description:
S109
ABSA213
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult


title: LB_DMSO_3

description: DMSO-treated LB cells

value: DMSO


title: LB_AMD_2

description: Amiodarone-treated LB cells

value: LB cells


title: hNES1_PD/A8301_MEF_hTS_p2

value: pluripotent stem cell derived trophoblast stem cell cultures


title: SN_Donor15OTC

value: brain

value: occipitotemporal cortex

value: AD


title: ABLW204

description:
S118
ABLW204
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + Pseudoalteromonas spiralis


title: LB_DMSO_1

description: DMSO-treated LB cells


title: Post 3

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
Basecalling was performed with Casava (v1.8).
Quality score trimming and filtering were performed with Trimmomatic (v0.32).
Trimmed reads were aligned to Drosophila melanogaster rRNA gene sequences using Bowtie2 (v2.1.0) to filter out reads originating from rRNA
rRNA filtered reads were aligned to the annotated Dm genome (build BDGP5, Ensembl release 70) using TopHat (v2.0.10)
Per gene read counts were calculated from the TopHat output using htseq-count (v0.5.4p5)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated using Cufflinks (2.2.1)
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Genome_build: BDGP dm6
Supplementary_files_format_and_content: tab-delimited text files include FBGN number and RPKM values for each sample.

organism: Drosophila melanogaster

source_name: lymph gland

extract_protocol:
RNA were extracted with Arcturus PicoPure RNA kit and samples were converted to cDNA using Nugen’s Ovation RNA-Seq System.
Library preparation was performed using Kapa Biosystems library preparation kit. Samples were multiplexed using the following barcodes: Ant1 (CAGATC), Ant2 ( ACTTGA), Ant3 (GATCAG),  Post1 (TAGCTT),  Post2 (GGCTAC), Post3 (CTTGTA).

treatment_protocol: Third instar larval lymph glands were dissected in ice cold PBS.

tag: genotype

value: Blood

value: third instar larvae

tag: position

value: posterior


title: ABSA212

description:
S108
ABSA212
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: SN_Donor14OC

value: occipital cortex

value: F

tag: rin

tag: braak/abc score


title: Post 1


title: SN_Donor15OC


title: ABLW203

description:
S117
ABLW203
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body

tag: treatment


title: Post 2


title: SN_Donor13OTC

value: single-nucleus RNA sequencing

value: IV


title: ABSA211

description:
S107
ABSA211
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + CFS Bacillus velezensis


title: SN_Donor14OTC


title: LB_DMSO_2

description: DMSO-treated LB cells


title: A549_2

description: DMSO-treated A549 cells

value: A549 cells


title: Ant 1

value: anterior


title: SN_Donor13OC


title: A549_3

description: DMSO-treated A549 cells

value: DMSO


title: Ant 3


title: Ant 2


title: ABLW201

description:
S115
ABLW201
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult


title: ABLW202

description:
S116
ABLW202
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Left CAd +CART 4

city: Houston

first: Masataka

last: Suzuki

state: Texas

address: 1102 Bates Ave

institute: Baylor College of Medicine

description: Subcutaneous PDAC tumor

data_processing: Data quality control, normalization, and Advanced Analysis were performed using nSolver 4.0 analysis software following NanoString analysis guidelines

source_name: Left PDAC tumor

growth_protocol: Whole PDAC tumor was isolated from humanized mice at 31 days post-treatment, and  total RNA from tumor was extracted using RNAeasy Plus Mini kit (QIAGEN)

extract_protocol: More than 400 ng RNA/sample was subjected to Nanostring

tag: sample type

value: Left PDAC tumor

value: CAd +CART


title: A549_1

description: DMSO-treated A549 cells


title: Asterix-FLAG eCLIP - crosslinked_ip2

data_processing:
Library strategy: eCLIP
Basecalling was performed with bcl2fastq2 v2.19 (Illumina).
Forward and reverse reads were joined using FLASH version 1.2.11; flash -m 25 -M 175 -O
Adapter dimers, adapter trimming, and PCR duplicate removal was performed using custom scripts, after which the reverse complement was taken to generate the original sense of the input material
Reads were mapped using STAR version 2.5.2b allowing for 50 multi-mapping sites; STAR_2.5.2b --genomeDir mm10 --runThreadN 12  --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts TranscriptomeSAM --outSAMattributes NH HI nM AS NM MD --outFilterMultimapNmax 50 --outFilterMismatchNoverReadLmax 0.05 --outFilterMismatchNmax 999
Alignment files were converted to .bed format using bedtools v2.29.0; bamtobed
Reads were annotated using custom gene annotations, filtering by class based on order of presumed biological abundance (custom scripts). rRNA > intron_28SrRNA-Psi > pseudogene_5SrRNA-Psi > pseudogene_5.8SrRNA-Psi > pseudogene_28SrRNA-Psi > pseudogene_2SrRNA-Psi > pseudogene_18SrRNA-Psi > snoRNA > snRNA > structRNA_7SLRNA > structRNA_RNaseP > structRNA_RNaseMRP > structRNA_sbRNA > structRNA_scaRNA > intron_lncRNA > lncRNA > intron_tRNA > tRNA > pseudogene_tRNA > mttRNA > intron_hpRNA > miRNA > hairpin > pri-miRNA > exon > TE_DNA > TE_LINE > TE_Satellite > TE_LTR > TE_RNA > TE_Other > TE_Unknown > TE_RC > TE_ARTEFACT > intron_SteXh > intron_Ste12DOR-RB > intron_Ste > intron_sisRNA > intron > mRNA > piRNA_cluster > intron_snmRNA > snmRNA > intron_His-Psi > pseudogene_His-Psi > pseudogene > intron_asRNA > asRNA > no_annotation
Reads counts were then adjusted to include 1/n-normalization for multimapping reads within a class (custom scripts).
Read counts were then normalized to reads per million, and pileups were calculated for each annotation (custom scripts).
Final analysis compared the various datasets to subtract background and calculate fold-enrichment scores for each annotation after thresholding for low read counts custom scripts).
Genome_build: dm6
Supplementary_files_format_and_content: *annotation_pileup_normalized.txt; Tab-delimited text files; Column 1 = annotation_class:annotation; Column 2 = 1/n-normalized read count pileup; Column 3 = 1/n-normalized read count pileup in rpm
Supplementary_files_format_and_content: Supplementary file: *_enrichment.txt; Tab-delimited text file; Column 1 = annotation; Column 2 = annotation class; Column 3 = average fold-enrichment calculated after background subtraction and normalization

source_name: OSS cells

growth_protocol: Drosophila OSS (ovarian somatic sheath) cells were maintained in OSS medium (Shields and Sang M3 Insect Medium [Sigma] supplemented with approximately 5 mM potassium glutamate, 5 mM potassium bicarbonate, 10% heat-inactivated fetal calf serum [Invitrogen], 10% fly extract [Drosophila Genomics Resource Center], 2 mM reduced glutathione [Sigma], 1x GlutaMAX [Gibco], 0.01 mg/mL human insulin [Sigma], and an antibiotic-antimycotic [Gibco] consisting of penicillin, streptomycin, and Amphotericin B). Cells were cultured at ~23°C. Cultures were monitored for Mycoplasma contamination using the MycoAlert Mycoplasma Detection Kit (Lonza). Mycoplasma contamination was not detected.

extract_protocol:
Cells were grown to 80% confluency in 150 mm culture dishes. Before crosslinking, the cells were rinsed with ice-cold phosphate-buffered saline (PBS).
UV cross-linking was performed at 254 nm for ~45 seconds (400 mJ) in an HL-2000 Hybrilinker. Crosslinked cells were harvested then stored frozen at -80°C until ready to proceed.
Cell pellets were thawed in 1 mL of lysis buffer (50 mM Tris, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% deoxycholate, and protease inhibitors), resuspended by pipetting, then incubated on ice for 15 minutes. The cell suspension was further lysed using a Bioruptor ('low' setting at 4°C for 5 minutes [30 seconds on, 30 seconds off]).
Two microliters of Turbo DNase (2 U/μL) (LifeTech) were added to each sample as well as 10 μL of RNase I (4 U/μL) (LifeTech) and mixed by pipetting. The samples were then incubated at 37°C for exactly 5 minutes with mixing (1200 rpm in a ThermoMixer). After the five-minute incubation, the samples were placed on ice and murine RNase inhibitor (40 U/μL) (NEB) was added immediately. Cell debris was removed by centrifugation at 15,000g for 15 minutes at 4°C and the clarified supernatants were transferred to fresh tubes.
Anti-FLAG M2 magnetic beads were equilibrated in 50 mM Tris, pH 8.0, 100 mM NaCl, 1% NP-40, 0.1% SDS, and 0.5% sodium deoxycholate with protease inhibitors. Fifty microliters of bead resuspension were used per sample. Beads were added to each sample and incubated with gentle agitation at 4°C for 2.5 hours. Input samples were reserved for both sequencing and Western blotting; these samples were stored at 4°C until needed. Immuno-precipitated material was isolated by magnetic separation, followed by several wash steps.
Libraries were generated essentially as described in Van Nostrand et al. (2016). Briefly, RNA ends were prepared by first treating with FastAP to remove terminal phosphates, then 5' phosphorylating using PNK. Barcoded adapters were then appended using 3' linker ligation with T4 ligase. Samples were then subjected to SDS-PAGE followed by blotting. Regions of the blot corresponding to the crosslinked protein of interest were cut out, and the RNA released from the membrane by Proteinase K treatment followed by nucleic acid extraction. Samples were reverse transcribed, RNA removed, and an additional barcoded adapter appended by 3' linker ligation. Samples were cleaned up using MyOne silane beads, then taken for final PCR amplification of the library.
Libraries were pooled in equimolar ratios according to their quantification by Bioanalyzer. Paired-end reads with two, 8-basepair, barcodes were generated on an Illumina NextSeq resulting in approximately 100 million paired-end reads (~15-20 million reads per library).

value: OSS

tag: pull-down

value: Anti-FLAG M2 magnetic beads

tag: crosslinking

value: crosslinked with UV 254


title: ABLA64

description:
S86
ABLA64
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + Vibrio alginolyticus


title: SN_Donor12OTC

value: brain

value: occipitotemporal cortex

value: AD

value: II


title: ABLA63

description:
S85
ABLA63
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: Asterix-FLAG eCLIP - crosslinked_ip1

tag: cell line


title: Asterix-FLAG eCLIP - non-crosslinked_ip


title: SN_Donor11OTC

tag: tissue

value: single-nucleus RNA sequencing

value: M

value: II-III


title: Left CAd +CART 3

description: Subcutaneous PDAC tumor


title: Asterix-FLAG eCLIP - crosslinked_input2

value: input


title: Left CAd +CART 2

description: Subcutaneous PDAC tumor


title: ABLA214

description:
S102
ABLA214
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + Bacillus velezensis


title: ABLA61

description:
S83
ABLA61
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult


title: SN_Donor10OC

tag: library type

value: occipital cortex

value: F


title: ABLA62

description:
S84
ABLA62
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Asterix-FLAG eCLIP - crosslinked_input1

value: OSS


title: Asterix-FLAG eCLIP - non-crosslinked_input


title: SN_Donor10OTC

tag: nuclei population


title: Left CAd +CART 1

description: Subcutaneous PDAC tumor

value: Left PDAC tumor

value: CAd +CART


title: ABLA213

description:
S101
ABLA213
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Left CAdTrio 3

description: Subcutaneous PDAC tumor

value: CAdTrio


title: SN_Donor11OC

value: brain

tag: region


title: SN_Donor12OC

tag: age


title: ABLA212

description:
S100
ABLA212
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Left CAdTrio 2

description: Subcutaneous PDAC tumor


title: SN_Donor9OTC

value: occipitotemporal cortex

tag: gender

value: III


title: Asterix-Strep eCLIP - crosslinked_ip2

extract_protocol:
Cells were grown to 75% confluency in 150 mm culture dishes. Four hours prior to transfection, the medium was refreshed. To transfect, 50 μg of DNA (Asterix-TEV-Strep in pAWG) was premixed with 15 μL of Xfect Polymer transfection reagent (Takara) in 500 μL Xfect buffer. OSS medium was removed from the cells and replaced with Shields and Sang M3 Insect Medium supplemented only with potassium bicarbonate and potassium glutamate. After a 10-minute incubation of the DNA with the transfection reagent, the transfection mixture was added to the cultures. Two hours post-transfection, the M3 medium was removed and replaced with fully-supplemented OSS medium. Seventy-two hours post-transfection, the cells were rinsed with ice-cold phosphate-buffered saline (PBS) and taken for crosslinking.
UV cross-linking was performed at 254 nm for ~45 seconds (400 mJ) in an HL-2000 Hybrilinker. Crosslinked cells were harvested then stored frozen at -80°C until ready to proceed.
Cell pellets were thawed in 1 mL of lysis buffer (50 mM Tris, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% deoxycholate, and protease inhibitors), resuspended by pipetting, then incubated on ice for 15 minutes. The cell suspension was further lysed using a Bioruptor ('low' setting at 4°C for 5 minutes [30 seconds on, 30 seconds off]).
Two microliters of Turbo DNase (2 U/μL) (LifeTech) were added to each sample as well as 10 μL of RNase I (4 U/μL) (LifeTech) and mixed by pipetting. The samples were then incubated at 37°C for exactly 5 minutes with mixing (1200 rpm in a ThermoMixer). After the five-minute incubation, the samples were placed on ice and murine RNase inhibitor (40 U/μL) (NEB) was added immediately. Cell debris was removed by centrifugation at 15,000g for 15 minutes at 4°C and the clarified supernatants were transferred to fresh tubes.
MagStrep type 3 XT beads (IBA) were equilibrated in 50 mM Tris, pH 8.0, 100 mM NaCl, 1% NP-40, 0.1% SDS, and 0.5% sodium deoxycholate with protease inhibitors. Fifty microliters of bead resuspension were used per sample. Beads were added to each sample and incubated with gentle agitation at 4°C for 2.5 hours. Input samples were reserved for both sequencing and Western blotting; these samples were stored at 4°C until needed. Affinity-precipitated material was isolated by magnetic separation, followed by several wash steps.
Libraries were generated essentially as described in Van Nostrand et al. (2016). Briefly, RNA ends were prepared by first treating with FastAP to remove terminal phosphates, then 5' phosphorylating using PNK. Barcoded adapters were then appended using 3' linker ligation with T4 ligase. Samples were then subjected to SDS-PAGE followed by blotting. Regions of the blot corresponding to the crosslinked protein of interest were cut out, and the RNA released from the membrane by Proteinase K treatment followed by nucleic acid extraction. Samples were reverse transcribed, RNA removed, and an additional barcoded adapter appended by 3' linker ligation. Samples were cleaned up using MyOne silane beads, then taken for final PCR amplification of the library.
Libraries were pooled in equimolar ratios according to their quantification by Bioanalyzer. Paired-end reads with two, 8-basepair, barcodes were generated on an Illumina NextSeq resulting in approximately 100 million paired-end reads (~15-20 million reads per library).

value: MagStrep XT beads

value: crosslinked with UV 254


title: SN_Donor9OC

value: single-nucleus RNA sequencing

tag: clinical diagnosis

value: AD


title: Asterix-Strep eCLIP - crosslinked_ip1


title: ABLA211

description:
S99
ABLA211
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: ABL5ug4

description:
S134
ABL5ug4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + 5ug/mL LPS


title: SN_Donor8OTC

value: M

value: CTR

tag: sample group

value: CTR+


title: Left CAdTrio 1

description: Subcutaneous PDAC tumor


title: SN_Donor8OC

value: occipital cortex


title: Asterix-Strep eCLIP - crosslinked_input2

value: OSS

value: input


title: ABL5ug3

description:
S133
ABL5ug3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult


title: Left CART 3

description: Subcutaneous PDAC tumor

value: Left PDAC tumor

value: CART


title: SN_Donor5OTC

value: brain

value: occipitotemporal cortex

value: F


title: ABL5ug2

description:
S132
ABL5ug2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Asterix-Strep eCLIP - crosslinked_input1

value: crosslinked with UV 254


title: Left CART 2

description: Subcutaneous PDAC tumor


title: ABL5ug1

description:
S131
ABL5ug1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: SN_Donor5OC

value: single-nucleus RNA sequencing


title: SN_Donor4OTC


title: ABL5ng4

description:
S142
ABL5ng4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Antibiotics + 5ng/mL LPS


title: Left CART 1

description: Subcutaneous PDAC tumor


title: SN_Donor4OC


title: Left Control 2

description: Subcutaneous PDAC tumor

value: control


title: ABL5ng3

description:
S141
ABL5ng3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: PA0833_2

city: Chongqing

first: Jintao

last: Zou

state: China

address: Gaotanyanstreet

institute: Army Medical University

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 reference genome using HISAT2
Transcript abundance was calculated using STRINGTIE
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample

growth_protocol: RAW264.7 were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA was extracted from cell samples using Trizol reagent combined with Qiagen miRNeasy Mini Kit.
Performed by Genminix Informatics Co., Ltd. (Shanghai, China) in accordance with standard Illumina protocols.

treatment_protocol: RAW264.7 were treated with His,PA0833,Hla-PA0833(HPF)


title: Asterix-Strep eCLIP - non-crosslinked_ip

value: MagStrep XT beads


title: ABL5ng2

description:
S140
ABL5ng2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Hla-PA0833(HPF)_1

value: Hla-PA0833 (HPF)


title: Hla-PA0833(HPF)_2


title: Left Control 1

description: Subcutaneous PDAC tumor


title: Left CART 4

description: Subcutaneous PDAC tumor


title: SN_Donor7OC

value: CTR

value: CTR+


title: ABL5ng1

description:
S139
ABL5ng1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Right CAdTrio 3

description: Subcutaneous PDAC tumor

source_name: Right PDAC tumor

value: Right PDAC tumor

value: CAdTrio


title: Asterix-Strep eCLIP - non-crosslinked_input

value: OSS

value: input


title: ABC4

description:
S70
ABC4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult

value: Antibiotics constant control; maintained


title: Right CAdTrio 2

description: Subcutaneous PDAC tumor


title: His_2

value: His


title: SN_Donor3OTC

value: brain

value: occipitotemporal cortex

value: F


title: Left Control 3

description: Subcutaneous PDAC tumor

value: Left PDAC tumor


title: His_1


title: Right CAdTrio 1

description: Subcutaneous PDAC tumor


title: ABC2

description:
S68
ABC2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: SN_Donor3OC

value: single-nucleus RNA sequencing

value: occipital cortex


title: SN_Donor6OTC

value: M

value: I


title: SN_Donor7OTC

value: CTR


title: ABC3

description:
S69
ABC3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body


title: SN_Donor6OC

value: CTR+


title: Ink4a/Arf-/-/PDGFRa/PDGF-A [R17023449LR01_S11_L007]

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

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 Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. 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. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Astrocytes

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
From purified polyA RNA

tag: disease

value: tumor

tag: cell type

value: glioma cells

tag: agent

value: 10 microM SHP099


title: Right CART 3

description: Subcutaneous PDAC tumor

value: Right PDAC tumor

value: CART


title: Right CART 4

description: Subcutaneous PDAC tumor


title: Ink4a/Arf-/-/PDGFRa/PDGF-A  [R17023449LR01_S11_L006]


title: PA0833_1


title: Ink4a/Arf-/-/PDGFRa/PDGF-A [R17023449LR01_S10_L007]

value: 5 microM SHP099


title: AB4

description:
S78
AB4
Replicate 4
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Adult

value: Antibiotics control; removed


title: SN_Donor2OTC

value: brain

value: occipitotemporal cortex

tag: rin

tag: braak/abc score


title: AB3

description:
S77
AB3
Replicate 3
genome Putnam et al. (2007)
allcountsFINAL.txt

tag: treatment


title: SN_Donor1OTC

value: single-nucleus RNA sequencing


title: Right CART 1

description: Subcutaneous PDAC tumor

tag: sample type


title: Ink4a/Arf-/-/PDGFRa/PDGF-A [R17023449LR01_S9_L007]

value: 0 microM SHP099


title: SN_Donor1OC

value: occipital cortex

value: M


title: AB2

description:
S76
AB2
Replicate 2
genome Putnam et al. (2007)
allcountsFINAL.txt


title: AB1

description:
S75
AB1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt


title: Ink4a/Arf-/-/PDGFRa/PDGF-A  [R17023449LR01_S9_L006]


title: SN_Donor2OC

value: CTR


title: Ink4a/Arf-/-/PDGFRa/PDGF-A  [R17023449LR01_S10_L006]


title: Right Control 3

description: Subcutaneous PDAC tumor

value: control


title: Right Control 1

description: Subcutaneous PDAC tumor


title: ABC1

description:
S67
ABC1
Replicate 1
genome Putnam et al. (2007)
allcountsFINAL.txt

value: Whole body

value: Antibiotics constant control; maintained


title: A549 infection Delta-HA rep3 - 12h total RNA

status: Public on Feb 19 2021

city: Minneapolis

first: Wei-Shou

last: Hu

state: MN

address: 421 Washington Ave. SE

institute: University of Minnesota

description:
Delta_HAPB1_FPKM.xlsx
30-HA-12

data_processing:
All the raw RNA-Seq reads were first trimmed off adapters and removed low-quality bases by Trimmomatic and checked for quality using FASTQC
All the trimmed reads with a minimum read length of 38bp and average quality per base higher than 30 were mapped into the combined genome of host+IAV by STAR v2.5.3a
The expression level of all the genes, including host and viral genes, were quantified by Cufflinks
Genome_build: CanFam3.1 for MDCK cells, GRCh38.p13 for A549 cells, and NCBI Taxon ID 211044 for IAV PR/8/34
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism:
Homo sapiens
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

growth_protocol: Madin-Darby canine kidney (MDCK) and Human lung adenocarcinoma epithelial A549 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS. Recombinant A/Puerto Rico/8/34 (H1N1) was rescued by plasmid-based transfection, plaque purified and propagated in embryonic chicken eggs.  The single-cycle virus (Delta-HA and Delta-PB1) were created by replacing the coding sequence of HA and PB1 by mCherry and amplified in MDCK cells engineered to express HA and PB1, respectively. Viral titers were determined by plaque assay in MDCK cells.

extract_protocol:
MDCK total RNA were extracted using RNeasy Mini Kit (QIAGEN). A549 total RNA were extracted using TRIzol.
MDCK cDNA libraries were prepared using the Clontech Pico SMARTer Stranded Total RNA-Seq kit v2. For the third MDCK infection, the RNA was also prepped by Illumina TruSeq Stranded mRNA Rrep kit to isolate mRNA only. A549 cDNA libraries were prepared using the Stranded Total RNA v2 PicoMammalian kit (Takara).

treatment_protocol: MDCK cells were infected with IAV PR8 (MOI =0.5) and incubated at 4ºC for 30 minutes to allow for the virus to adsorb to the cell surface but not to enter the cytosol. Synchronized IAV infection was initiated by shifting the temperature to 37ºC. Infections with single-cycle viruses (Delta-HA and Delta-PB1) were performed in A549 cells in infection media at an MOI of 1. Infections were also synchronized at 4ºC for 30 minutes then incubated at 37ºC.

value: adenocarcinomic alveolar basal epithelial cells

value: single-cycle infection of IAV delta_HA, 12h


title: A549 infection Delta-PB1 rep1 - 12h total RNA

description:
Delta_HAPB1_FPKM.xlsx
31-PB1-12

value: single-cycle infection of IAV delta_PB1, 12h


title: A549 infection Delta-PB1 rep3 - 12h total RNA

description:
Delta_HAPB1_FPKM.xlsx
33-PB1-12


title: A549 infection Delta-PB1 rep2 - 12h total RNA

description:
Delta_HAPB1_FPKM.xlsx
32-PB1-12


title: A549 infection Delta-PB1 rep3 - 9h total RNA

description:
Delta_HAPB1_FPKM.xlsx
27-PB1-9

value: single-cycle infection of IAV delta_PB1, 9h


title: A549 infection Delta-HA rep2 - 12h total RNA

description:
Delta_HAPB1_FPKM.xlsx
29-HA-12


title: A549 infection Delta-HA rep1 - 12h total RNA

description:
Delta_HAPB1_FPKM.xlsx
28-HA-12


title: A549 infection Delta-PB1 rep2 - 9h total RNA

description:
Delta_HAPB1_FPKM.xlsx
26-PB1-9


title: A549 infection Delta-HA rep2 - 9h total RNA

description:
Delta_HAPB1_FPKM.xlsx
23-HA-9

value: single-cycle infection of IAV delta_HA, 9h


title: A549 infection Delta-HA rep3 - 9h total RNA

description:
Delta_HAPB1_FPKM.xlsx
24-HA-9


title: Right CART 2

description: Subcutaneous PDAC tumor

value: Right PDAC tumor

value: CART


title: A549 infection Delta-HA rep1 - 9h total RNA

description:
Delta_HAPB1_FPKM.xlsx
22-HA-9


title: A549 infection Delta-PB1 rep3 - 6h total RNA

description:
Delta_HAPB1_FPKM.xlsx
21-PB1-6

value: single-cycle infection of IAV delta_PB1, 6h


title: A549 infection Delta-PB1 rep1 - 6h total RNA

description:
Delta_HAPB1_FPKM.xlsx
19-PB1-6


title: A549 infection Delta-PB1 rep2 - 6h total RNA

description:
Delta_HAPB1_FPKM.xlsx
20-PB1-6


title: A549 infection Delta-PB1 rep3 - 3h total RNA

description:
Delta_HAPB1_FPKM.xlsx
15-PB1-3

value: single-cycle infection of IAV delta_PB1, 3h


title: Right Control 2

description: Subcutaneous PDAC tumor


title: A549 infection Delta-HA rep2 - 6h total RNA

description:
Delta_HAPB1_FPKM.xlsx
17-HA-6

value: single-cycle infection of IAV delta_HA, 6h


title: A549 infection Delta-HA rep3 - 6h total RNA

description:
Delta_HAPB1_FPKM.xlsx
18-HA-6


title: A549 infection Delta-HA rep3 - 3h total RNA

description:
Delta_HAPB1_FPKM.xlsx
12-HA-3

value: single-cycle infection of IAV delta_HA, 3h


title: A549 infection Delta-PB1 rep2 - 3h total RNA

description:
Delta_HAPB1_FPKM.xlsx
14-PB1-3


title: A549 infection Delta-HA rep2 - 3h total RNA

description:
Delta_HAPB1_FPKM.xlsx
11-HA-3


title: A549 infection Delta-PB1 rep1 - 3h total RNA

description:
Delta_HAPB1_FPKM.xlsx
13-PB1-3


title: A549 infection Delta-HA rep1 - 3h total RNA

description:
Delta_HAPB1_FPKM.xlsx
10-HA-3


title: A549 infection Delta-PB1 rep2 - 0h total RNA

description:
Delta_HAPB1_FPKM.xlsx
8-PB1-0

value: single-cycle infection of IAV delta_PB1, 0h


title: A549 infection Delta-PB1 rep1 - 9h total RNA

description:
Delta_HAPB1_FPKM.xlsx
25-PB1-9


title: A549 infection Delta-PB1 rep3 - 0h total RNA

description:
Delta_HAPB1_FPKM.xlsx
9-PB1-0


title: A549 infection Delta-HA rep3 - 0h total RNA

description:
Delta_HAPB1_FPKM.xlsx
6-HA-0

value: single-cycle infection of IAV delta_HA, 0h


title: A549 infection Delta-PB1 rep1 - 0h total RNA

description:
Delta_HAPB1_FPKM.xlsx
7-PB1-0


title: A549 infection Delta-HA rep2 - 0h total RNA

description:
Delta_HAPB1_FPKM.xlsx
5-HA-0


title: A549 infection Delta-HA rep1 - 0h total RNA

description:
Delta_HAPB1_FPKM.xlsx
4-HA-0


title: MDCK infection rep3 - 4h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t3_4

organism:
Canis lupus familiaris
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: MDCK cells

value: immortalized kidney epithelial cells

value: MDCK

value: single-cycle infection of IAV PR/8/34, 4h


title: MDCK infection rep3 - 6h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t3_6

value: single-cycle infection of IAV PR/8/34, 6h


title: MDCK infection rep3 - 8h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t3_8

value: single-cycle infection of IAV PR/8/34, 8h


title: MDCK infection rep3 - 6h mRNA

description:
PR8_infection_FPKM.xlsx
PR8_m3_6


title: MDCK infection rep3 - 0h mRNA

description:
PR8_infection_FPKM.xlsx
PR8_m3_0

value: single-cycle infection of IAV PR/8/34, 0h


title: MDCK infection rep3 - 0h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t3_0


title: A549 infection Delta-HA rep1 - 6h total RNA

description:
Delta_HAPB1_FPKM.xlsx
16-HA-6

value: adenocarcinomic alveolar basal epithelial cells


title: MDCK infection rep3 - 8h mRNA

description:
PR8_infection_FPKM.xlsx
PR8_m3_8


title: MDCK infection rep3 - 2h mRNA

description:
PR8_infection_FPKM.xlsx
PR8_m3_2

value: single-cycle infection of IAV PR/8/34, 2h


title: MDCK infection rep3 - 2h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t3_2


title: MDCK infection rep2 - 12h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t2_12

value: single-cycle infection of IAV PR/8/34, 12h


title: MDCK infection rep2 - 8h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t2_8


title: MDCK infection rep2 - 2h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t2_2


title: MDCK infection rep2 - 4h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t2_4


title: MDCK infection rep3 - 12h mRNA

description:
PR8_infection_FPKM.xlsx
PR8_m3_12


title: A549 infection Delta-HA rep1 - uninfected total RNA

description:
Delta_HAPB1_FPKM.xlsx
1-naive-0

value: uninfected


title: MDCK infection rep3 - 12h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t3_12


title: MDCK infection rep3 - 4h mRNA

description:
PR8_infection_FPKM.xlsx
PR8_m3_4


title: SolaVAX+CpG1018-3

city: Fort Collins

first: Raymond

last: Goodrich

state: Colorado

address: 3185 Rampart Road

department: Microbiology, Immunology, anad Pathology

institute: Colorado State University

description: single cells

data_processing:
Cell ranger mkfastq software for demultiplexing
Cell ranger count pipeline to perform alignment, filtering, barcode counting, and UMI counting
Genome_build: Mesocricetus auratus (accession GCA_000349665)
Supplementary_files_format_and_content: Filtered feature barcode matrices

organism: Mesocricetus auratus

source_name: Vaccinated including Th1-promoting adjuvant

extract_protocol:
a portion of the left cranial lung lobe from each hamster were aseptically transferred from PBS into DMEM then teased apart. Lungs were treated with a solution of DNase IV (500 units/mL) and Liberase (0.5 mg/mL) for 30 minutes at 37°C to dissociate and digest collagen. Cells were homogenized using a syringe plunger and passed through a 70 µm filter to prepare single cell suspension
Library construction was performed as per 10x genomics single cell v3’ chemistry instructions
scRNA-seq

value: Lung

tag: treatment type

value: vaccinated with SolaVAX and CpG1018 adjuvant

tag: disease state

value: SARS-CoV-2 infected


title: SolaVAX+ODN1668-1

description: single cells

tag: tissue

value: vaccinated with SolaVAX and ODN1668 adjuvant


title: SolaVAX+ODN1668-3

description: single cells


title: SolaVAX+CpG1018-2

description: single cells


title: SolaVAX+ODN1668-2

description: single cells


title: SolaVax-1

description: single cells

source_name: Vaccinated (no adjuvant) subject

value: vaccinated with SolaVAX


title: Control-1

description: single cells

source_name: Unvaccinated control subject

value: no vaccination


title: Control-3

description: single cells


title: Control-2

description: single cells


title: SolaVax-2

description: single cells


title: SolaVax-3

description: single cells


title: MDCK infection rep2 - 0h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t2_0

tag: cell line


title: Patient 1 Pretreatment

city: Durham

first: Nicholas

last: DeVito

address: 2301 Erwin Road

institute: Duke University

hyb_protocol: Agilent 2100 Bioanalyzer (Agilent) and NanoDrop (ThermoFisher) were used to determine the purity and concentration of the RNA. A DV300 Agilent Bioanalyzer smear analysis was used to determine the percentage of fragments greater than 300 nucleotides to determine the starting amount of RNA.   Gene expression codesets (designed and produced by NanoString Technologies, Seattle, WA), hybridization buffer and total RNA were hybridized in a thermocycler for 16 hours at 67 °C prior to being processed in the nCounter Max Prep Station following the NanoString manual, MAN-10056-02 for gene expression assays.  Data collection using the nCounter Digital Analyzer was performed by following the NanoString manual, MAN-C0035-07 using the maximum field of view setting.

data_processing: Samples were analyzed on a NanoString nCounter Max system using the nCounter Vantage 3D Human Wnt Pathways Panel (N2_WNT_Pth_v1.0), which is comprised of Wnt ligands, receptors, regulators, gene targets, and other pathway components with the addition of a custom gene panel composed of cytolytic T cell markers and IDO1.  Analysis was performed using the nSolver software.

source_name: Tumor

extract_protocol:
Sample acquisition: Pre and post ETC-159 (PORCN inhibitor) samples were taken from Patient 1 (colorectal cancer with RSPO fusion) and Patient 2 (presumed cholangiocarcinoma)
Two-to-three 10 mM FFPE scrolls were collected from FFPE sectioning of biopsies taken prior to treatment, and RNA extraction was performed with using RSC FFPE RNA extraction kit (Promega) according to manufacturer`s instruction.
de-identified patient samples were labeled according to response and time of sample acquisition

tag: subject age

tag: subject gender

value: F

tag: subject status

value: colorectal cancer with RSPO fusion

tag: time point

value: Pretreatment


title: Patient 1 Posttreatment

value: Posttreatment


title: Skin&Cells，Psoriasis，rep2

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

institute: the Third Xiangya Hospital, Central South University

data_processing:
Illumina NextSeq 500. Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing  run on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-404-  2005, Illumina), according to the manufacturer’s instructions.
Raw data files in FASTQ format were generated from the Illumina sequencer. To examine the sequencing quality, the quality score plot of each sample was plotted. Quality score Q is logarithmically related to the base calling error probability (P)
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Excel file with differentially expressed genes

source_name: Lesions on extensor aspect of extremities

extract_protocol:
Total RNA was isolated from skin or cells using TRIzol® reagent (Invitrogen; Thermo Fisher Scientific, Inc.) according to manufacturer’s guidelines.
Sequencing Library Preparation：Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer

tag: gender

value: Male

value: Psoriasis

value: skin


title: Skin&Cells，Normal，rep3

value: Female

value: Normal


title: Skin&Cells，Normal，rep2


title: Patient 2 Pretreatment

value: M

value: Cholangiocarcinoma


title: Skin&Cells，Normal，rep1


title: Skin&Cells，Psoriasis，rep3


title: Skin&Cells，Psoriasis，rep1


title: RNA-HCMV

city: Los Angeles

last: Strugatsky

state: CA

address: 615 CHARLES E YOUNG DR S

department: MIMG

institute: UCLA

data_processing:
Sequencing quality was examined by FastQC
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to cytoplasmic mature-tRNA sequences from GtRNAdb and mitochondrial tRNA sequences from mitotRNAdb using BWA. The  maximum allowed mismatch stringecy was 2.
The tRNAs expression profiling was calculated based on multiply mapped mrcount (deposited as Expression_Count.xlsx) and uniquely mapped ucounts.
tRNA differential expression was analyzed using R package edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tRNA isodecoder expression levels in as mrcounts (multiply mapped counts).

source_name: human cytomegalovirus virions

growth_protocol: Human fibroblast MRC-5 cells were seeded on 18x175 cm2 flasks in Eagle’s Minimum Essential Medium supplemented with 10% fetal bovine serum and 100U/ml of Penicillin-Streptomycin and cultured until they reached ~80-90% confluency, about a week. The cells were then infected with HCMV (AD169 strain). The growth media were replaced with fresh ones 4 days after infection. The media containing secreted HCMV virions were collected at 8 days post infection.

extract_protocol:
The growth media from infected MRC-5 cells were spun on SW28 rotor (Beckman) at 80,000 x g for 1 hour at 4°C. The supernatant was discarded and the pellet in each tube was resuspended in 50 µl of cold phosphate buffered saline (PBS). About 0.7 ml of combined pellet suspension from all ultracentrifuge tubes was loaded on 15%-50% linear gradient of sucrose made in PBS and spun in SW41 (Beckman) rotor at 80,000 x g for 1 hour at 4°C. About 1 ml of visible virus-containing band was collected into a new tube and mixed with 10 ml of sterile PBS solution in order to dilute sucrose. The virions were concentrated at 80,000 x g for 1 hour at 4°C and resuspended in 0.1 ml of PBS and used for total RNA isolation. 3 µg of total RNA isolated from RNase pre-treated virions was separated on urea-polyacrylamide gel, and tRNA was further isolated from a size window of 60-100 nt.
tRNAs were purified from total RNA samples. m1A and m3C modifications were demethylated. The tRNAs were then partially hydrolyzed and 5' re-phosphorylated using Hydro-tRNAseq method [PMID:28793268]. Small RNA sequencing libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (New England Biolabs). Size selected PCR amplified fragments (140-155 bp, corresponding to 19-35 nt tRNA fragments size range) sequenced for 50 cycles on Illumina NextSeq 500 system using NextSeq 500/550 High-Output v2 kit (75 cycles).

value: Human fibroblast MRC-5


title: Patient 2 Posttreatment


title: MDCK infection rep2 - 6h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t2_6

value: immortalized kidney epithelial cells

value: MDCK

value: single-cycle infection of IAV PR/8/34, 6h


title: Neutrophils from HC blood of ICH patient number HC067973 on day 1 of study - replicate 3

city: New Haven

first: Lauren

last: Sansing

state: CT

address: 300 George Street, suite 353

institute: Yale School of Medicine

description:
ICHseqBatch4g_D06
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

data_processing:
Following sequencing, BAM files were converted to merged, demultiplexed FASTQs. Paired-end reads were mapped to the UCSC hg19 genome using STAR and RSEM.
Aligned expression matrices generated by STAR were first filtered based on read depth and captured gene depth to remove low quality samples. A minimum of 4 x 106 FASTQ fragments and a minimum of 9,000 (for monocytes/MDMs) or 8,500 (for neutrophils) captured genes were used as inclusion criteria.
filtered counts from technical replicates were collapsed together using the “edgeR” pipeline prior to generation of a log-FPKM gene expression matrix
Samples lacking patient metadata or occurring later than 171h post-ICH were excluded, removing two additional samples for each cell type. Genes with fewer than 1 count per million (CPM) in greater than 80% of the samples of a given cell type were considered unexpressed and filtered out prior to downstream analysis.
Trimmed mean of M values library size normalization of was used to account for differences in sequenced reads between samples; normalized library sizes were used for frequency estimation in generation of log-FPKM matrices.
edgeR was used to convert counts matrices to FPKM expression matrices;  gene lengths used for this are in the "gene_lengths.txt" file. Log-fpkm+1 matrices were generated from these using base R.
To generate "monos_log_fpkm_techreps_collapsed.csv" and "grans_log_fpkm_techreps_collapsed.csv", filtered counts from technical replicates were collapsed together using the “edgeR” pipeline prior to generation of a log-FPKM gene expression matrix.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: [monos_counts.csv]  comma separated text file of raw counts of CD14+ monos/macs gene expression
[monos_log_fpkm_all_samples.csv]  comma separated text file of log Fragments Per Kilobase of transcript per Million mapped reads (log FPKM) from all monos/macs samples, including technical replicates
[monos_log_fpkm_techreps_collapsed.csv]  comma separated text file of log Fragments Per Kilobase of transcript per Million mapped reads (log FPKM) from monos/macs samples. Technical replicates were collapsed together by adding together their counts prior to generation of log-FPKM.
[neuts_counts.csv]  comma separated text file of raw counts of neutrophils gene expression
[neuts_log_fpkm_all_samples.csv]  comma separated text file of log Fragments Per Kilobase of transcript per Million mapped reads (log FPKM) from all neutrophils samples, including technical replicates
[neuts_log_fpkm_techreps_collapsed.csv]  comma separated text file of log Fragments Per Kilobase of transcript per Million mapped reads (log FPKM) from neutrophils samples. Technical replicates were collapsed together by adding together their counts prior to generation of log-FPKM.
[gene_lengths.txt]  tab-delimited text file containing gene names, lengths, and "effective lengths" accounting for differences in how likely that gene is to generate a mappable fragment.

source_name: HC blood

extract_protocol:
CD14 monos/macs and neutrophils were sorted from purified leukocytes preparations directly into RA1 cell lysis buffer and RNA was isolated using NucleoSpin RNA XS kit (Macherey-Nagel, #740902).
Smart-Seq2 cDNA synthesis was performed with the following modifications: 1) input RNA was normalized prior to cDNA generation by diluting to ~1,000 cells per reaction, 2) reverse transcription was performed with Superscript III (ThermoFisher, #18080-085) in place of Superscript II according to the manufacturer instructions. Paired-end sequencing libraries were prepared using the Nextera XT DNA sample Prep Kit (Illumina, #FC-131) according to the manufacturer’s instructions.

value: neuts

tag: batch

value: J

tag: patientid

tag: day of trial

tag: hrs after symptom onset

tag: techrep

tag: senot determined

value: XXXX

tag: race

value: White

tag: age

tag: nih stroke score

tag: glasgow coma score

tag: initial ich volume

tag: adjusted disease severity index

tag: modified rankin score at 1 year post-ich

tag: 1 yr gcs <4


title: Neutrophils from HC blood of ICH patient number HC067973 on day 1 of study - replicate 2

description:
ICHseqBatch4g_D09
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: cell type


title: Neutrophils from HC blood of ICH patient number HC067371 on day 1 of study - replicate 3

description:
ICHseqBatch4g_B08
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv


title: Neutrophils from HC blood of ICH patient number HC067591 on day 1 of study - replicate 2

description:
ICHseqBatch4g_B06
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv


title: Neutrophils from HC blood of ICH patient number HC067412 on day 1 of study - replicate 2

description:
ICHSeq7gandtPA_D08
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

value: F


title: Neutrophils from HC blood of ICH patient number HC067591 on day 1 of study - replicate 3

description:
ICHseqBatch4g_B05
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv


title: Neutrophils from HC blood of ICH patient number HC067973 on day 1 of study - replicate 1

description:
ICHseqBatch4g_B04
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv


title: SolaVAX+CpG1018-1

description: single cells

tag: tissue

value: Lung

tag: treatment type

value: vaccinated with SolaVAX and CpG1018 adjuvant

tag: disease state

value: SARS-CoV-2 infected


title: Neutrophils from HC blood of ICH patient number HC067371 on day 1 of study - replicate 1

description:
ICHseqBatch4g_B02
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: batch

tag: patientid


title: Neutrophils from HC blood of ICH patient number HC067076 on day 1 of study - replicate 2

description:
ICHSeq7gandtPA_D10
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: day of trial

tag: hrs after symptom onset


title: Neutrophils from blood of ICH patient number 2287 on day 5 of study - replicate 1

description:
ICHSeq7gandtPA_C10
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

source_name: blood

tag: techrep

tag: senot determined

value: Male

value: TRUE


title: Neutrophils from blood of ICH patient number 2287 on day 4 of study - replicate 1

description:
ICHSeq7gandtPA_C09
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: race

tag: age


title: Neutrophils from blood of ICH patient number 2287 on day 3 of study - replicate 1

description:
ICHSeq7gandtPA_C08
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: nih stroke score

tag: glasgow coma score


title: Neutrophils from blood of ICH patient number 2287 on day 2 of study - replicate 1

description:
ICHSeq7gandtPA_C07
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: initial ich volume

tag: adjusted disease severity index


title: Neutrophils from hematoma of ICH patient number 2287 on day 3 of study - replicate 1

description:
ICHSeq7gandtPA_D03
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

source_name: hematoma

tag: modified rankin score at 1 year post-ich

tag: 1 yr gcs <4


title: Neutrophils from hematoma of ICH patient number 2287 on day 1 of study - replicate 2

description:
ICHSeq7gandtPA_D04
neuts_counts.csv
neuts_log_fpkm_all_samples.csv
neuts_log_fpkm_techreps_collapsed.csv

tag: cell type