title: MIA PaCa-2 normoxia Exp 1 B

city: Ajman

first: Raefa

last: Abou Khouzam

address: AL JURF - 1 Rashid Al-Khadar St - Al Jerf 1

department: Thumbay Research Institute for Precision Medicine

country: United Arab Emirates

institute: Gulf Medical University

description: SST-RMA expression value derived from Transcriptome Analysis Console; Gene+Exon analysis

hyb_protocol: Samples were hybridized with Human Clariom™ D Arrays (Affymetrix); washed and stained using the the GeneChip™ WT PLUS Reagent Kit (Applied Biosystems™) and the GeneChip Fluidics Station 450 (Affymetrix/Thermo Scientific inc); and scanned with the GeneChip™ Scanner 3000 7G (Affymetrix/Thermo Scientific inc).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Transcriptome Analysis Console (TAC) 4.2 software (Applied Biosystem). Gene+Exon summarization using the Signal Space Transformation-Robust Multi-Array Average (SST-RMA) algorithm was first applied to summarize, background-subtract, and normalize the CEL files. CHP files were imported back to TAC to carry out differential gene expression analysis using ANOVA method for statistical testing with ebayes (Empirical Bayes Statistics for Differential Expression) correction for small sample size. The hypoxia samples in each cell line were compared to their respective normoxia samples. Significant results were considered for transcript clusters that showed a fold change of ≤ -2 or ≥ 2 with FDR p-value ≤ 0.05.

label: biotin

source_name: MIA PaCa-2

label_protocol: 100 ng of total RNA was used to prepare fragmented and labeled single stranded cDNA with the GeneChip™ WT PLUS Reagent Kit (Applied Biosystems™) based on manufacturer’s instructions

growth_protocol: The three most sensitive cell lines, H226, MCF-7 and HT-29, as well as the three least senstive cell lines, Capan-1, SKOV-3, MIA PaCa-2, were maintained in a 5% CO2, 21% O2 humidified incubator (ESCO Cell Culture incubator, USA) in appropriate cell culture media.

extract_protocol: For samples in hypoxia, RNA from the twenieth passage was isolated within the Hypoxiachamber, otherwise the isolation was done in normal oxygen conditions. For each sample 1 mL of EasyBlue (iNtRON Biotechnology, Korea) was used to collect cell lysate after washing with PBS1X. Isolation and purification was done as per the manufacturer's protocol and quantification and purity check was done using the Nanodrop while integrity was determined by agarose gel electrophoresis.

treatment_protocol: Two independent experiments were conducted and at each seeding time, cells were allowed to adhere for 24 hours before incubating in hypoxia (1% O2, 5% CO2) or placing in normoxia. Hypoxic conditions maintained using the humidified Whitley H35 HypoxyStation (Don Whitley123 Scientific Limited, UK). Cells were passaged twenty times in the two conditions.

value: MIA PaCa-2

value: Pancreatic cancer cell


title: MIA PaCa-2 hypoxia Exp 2 B

status: Public on Mar 29 2023

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: serum_shortRNA_PH046_w0h0

type: SRA

city: Birmingham

first: Kaleen

middle: M

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

country: USA

institute: University of Alabama at Birmingham

description:
small RNA from serum extracellular vesicles
serumEV_small_counts.txt

library_source: transcriptomic

data_processing:
Long reads were aligned using STAR to GRCh38 and LNCpedia; separately, long reads were used to identify circular RNA using CIRI2; small reads were aligned using exceRpt
Long RNA count data were generated using featureCounts
Assembly: GRCh38
Supplementary files format and content: txt file containing read counts for genes and samples

source_name: serum EV

extract_protocol:
Skeletal muscle RNA was extracted using Qiagen miRNeasy kit (Cat. No. 217004); serum EV RNA was extracted using Qiagen exoRNeasy kits (Cat. No. 77144).
Long RNA libraries for both skeletal muscle and serum EVs were constructed using Takara Bio SMARTer Stranded Total RNA-Seq kit v2 Pico Input Mammalian (Cat. No. 634418) and SMARTer RNA Unique Dual Index Kit (Cat. No. 634452). Small RNA libraries for both skeletal muscle and serum EVs were prepared using NEXTflex Small RNA Library Prep Kit v3 (Ca. No. # NOVA-5132-23, Perkin Elmer

tag: tissue

value: serum EV

tag: timepoint

tag: cohort

value: TRAD

tag: Sex

value: F


title: PT 29 II li LL

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Sequencing reads in fastq format were adapter-trimmed using BBDuk (38.80)
Sequence quality was checked using FastQC (0.11.9)
Reads were mapped to the human reference genome (GRCh38/hg38) with STAR aligner  (2.7.1a).
Read counts for NCBI Gene/Refseq annotation were calculated using featureCounts (2.0.0).
Differentially expressed genes were calculated and read count normalization were performed using the R package DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited matrix text file include raw counts for each sample and each gene
Supplementary files format and content: tab-delimited matrix text file include normalized counts for each sample and each gene

source_name: liver

extract_protocol:
Tissue homogenization using Tissue Ruptor (Qiagen), sample lysis and RNA isolation using miRNeasy Mini Kit (Qiagen)
Lexogen QuantSeq 3' FWD kit (polyA mRNA-seq)

value: liver

tag: sample type

value: POST


title: MIA PaCa-2 hypoxia Exp 2 A


title: MIA PaCa-2 hypoxia Exp 1 B


title: serum_shortRNA_PH029_w0h24


title: serum_shortRNA_PH029_w0h3


title: LP-CN_C4

type: genomic

city: Yayoi, Bunkyo-ku

first: Chika

last: Ando

state: Tokyo

country: Japan

institute: University of Tokyo

hyb_protocol: 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation. Microarrays were hybridize d at 42°C during 16 to 20h with Cy 3 5 labelled DNA in Nimble Gen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit ( NimbleGen Systems, Inc., Madison, WI, USA). For array hybridization, ArrayStar Rat RefSeq Promoter Array was used, which is a single array designs that includes 23 ,148 gene promoter regions (from about 1300bp to +500bp of the TSSs) totally covered by ~180,000 probes with approxim ately 210 bp spacing, dependent on the sequence composition of the region

scan_protocol: Scanning was performed by using Agilent Scanner G2505C

data_processing:
Raw data was extracted as txt files by Agilent Feature Extraction softwar e (version 11.0.1.1) 11.0.1.1). We perform Median centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2 ratio data (*_ratio.gff file) was created for each sample. From the nor malized log2 ratio data, a sliding window peak finding algorithm provided by NimbleScan v2.5 (Roche NimbleGen) was applied to find the enriched peaks with specified parameter s (sliding window width: 1 5 0 0bp; mini probes per peak: 2; P value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500bp). After getting the *_peaks.gff files, the identified peaks were mapped
NimbleScan detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged. PeakMvalue is the median log2-ratio from probes within the peak.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Kidney of rat

label_protocol: For DNA labelling, the NimbleGen Dual Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP chip protocol NimbleGen Syst ems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5 9mer primer (IP sample) or Cy3 9mer primer (Input sample) sample). Then, 100 pmol of deoxynucleoside

extract_protocol: DNA from the kidney was extracted using DNAiso Reagent (Takara Bio, Tokyo, Japan).  The samples were checked for quality via electrophoresis (100 V, 20 min) using a 1.2% agarose gel and the DNA concentrations were measured using a NanoDrop instrument (ND-1000, NanoDrop Technologies)and a Qubit instrument (Thermo Fisher Scientific, Waltham, MA, USA).

value: Kidney

tag: maternal diet

value: LP

tag: offspring diet

value: CN

tag: age


title: CN-CN_C2


title: serum_shortRNA_PH024_w0pre

value: HITT

value: M


title: MIA PaCa-2 hypoxia Exp 1 A


title: CN-CN_C3


title: CN-CN_C1


title: PT 29 I re LL

value: PRE


title: serum_shortRNA_PH029_w0h0


title: MIA PaCa-2 normoxia Exp 1 A


title: serum_shortRNA_PH024_w0h0


title: serum_shortRNA_PH024_w0h3


title: MIA PaCa-2 normoxia Exp 2 A


title: serum_shortRNA_PH024_w0h24


title: PT 24 II re LL


title: PT 22 II li LL


title: SKOV-3 hypoxia Exp 2 B

value: Ovarian cancer cell


title: SKOV-3 normoxia Exp 1 B


title: PT 24 I li LL


title: serum_shortRNA_PH018_w0h24


title: PT 17 II li LL


title: serum_shortRNA_PH018_w0h0


title: SKOV-3 hypoxia Exp 1 B


title: serum_shortRNA_PH018_w0h3


title: serum_shortRNA_PH011_w0pre


title: serum_shortRNA_PH011_w0h3


title: SKOV-3 hypoxia Exp 2 A


title: PT 17 I re LL


title: serum_shortRNA_PH011_w0h0


title: serum_shortRNA_PH011_w0h24


title: PT 22 I reLL


title: serum_shortRNA_PH018_w0pre


title: SKOV-3 hypoxia Exp 1 A


title: serum_shortRNA_PH010_w0h3


title: PT 15 II li LL


title: serum_shortRNA_PH010_w0h24


title: SKOV-3 normoxia Exp 2 A


title: PT 13 II li LL


title: muscle_shortRNA_PH183_w0pre

description:
small RNA from skeletal muscle
muscle_longRNA_small_counts.txt

source_name: skeletal muscle

value: skeletal muscle


title: serum_shortRNA_PH010_w0h0


title: PT 15 I re LL


title: muscle_shortRNA_PH181_w0pre


title: muscle_shortRNA_PH183_w0h24


title: SKOV-3 normoxia Exp 1 A


title: Capan-1 hypoxia Exp 2 B


title: muscle_shortRNA_PH181_w0h24


title: PT 10 II re LL


title: Capan-1 hypoxia Exp 1 B


title: PT 10 I li LL


title: muscle_shortRNA_PH181_w0h3


title: Capan-1 normoxia Exp 1 B


title: muscle_shortRNA_PH180_w0h3


title: muscle_shortRNA_PH180_w0h24


title: muscle_shortRNA_PH177_w0pre


title: muscle_shortRNA_PH180_w0pre


title: muscle_shortRNA_PH177_w0h3


title: PT 8 II li LL


title: Capan-1 hypoxia Exp 2 A


title: serum_shortRNA_PH010_w0pre


title: PT 8 I re LL


title: Capan-1 hypoxia Exp 1 A


title: muscle_shortRNA_PH177_w0h24


title: muscle_shortRNA_PH183_w0h3


title: PT 13 I re LL


title: PT 5 II re LL


title: muscle_shortRNA_PH175_w0pre


title: PT 5 I


title: muscle_shortRNA_PH174_w0pre


title: Capan-1 normoxia Exp 2 A


title: muscle_shortRNA_PH175_w0h24


title: muscle_shortRNA_PH174_w0h3


title: HT-29 normoxia Exp 2 B

value: colon cancer cell


title: Capan-1 normoxia Exp 1 A


title: UOK_SHTFEIII_3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of UOK_SHTFE3, biological rep3

data_processing:
For the analysis, the sequence reads were trimmed BBDuk (sourceforge.net/projects/bbmap/) to remove adapter sequences and low-quality end bases (Q < 20). Alignment was performed with STAR 2.6.0a on the Hg38 reference provided by UCSC Genome Browser. the reads were trimmed toremove adapter sequences and low-quality ends and reads mapping to contaminating  sequences (e.g., ribosomal RNA, phIX control) were filtered-out.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: renal tumor cell line

growth_protocol: cells were cultured in in DMEM high glucose supplemented with 10% inactivated FBS, 2 mM glutamine, penicillin (100 IU/ml) and streptomycin (100 μg/ml)and maintained at 37 °C and 5% CO2.

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq 6000(Illumina) with a read length of 100 bp

treatment_protocol: We infected UOK257 cells with lentiviral vectors encoding short hairpin RNAs that target TFEB (sh-TFEB) or TFE3(sh-TFE3), or with control vector (sh-Luciferase)

tag: treatment

value: silenced for TFE3

tag: gender

value: male


title: UOK_SHTFEIII_2

description: Transcriptome profile of UOK_SHTFE3, biological rep2


title: muscle_shortRNA_PH170_w0h3


title: muscle_shortRNA_PH170_w0h24


title: muscle_shortRNA_PH174_w0h24


title: HT-29 hypoxia Exp 1 B


title: UOK_SHTFEIII_4

description: Transcriptome profile of UOK_SHTFE3, biological rep4


title: HT-29 hypoxia Exp 2 B


title: muscle_shortRNA_PH170_w0pre


title: muscle_shortRNA_PH166_w0h3


title: UOK_SHTFEIII_1

description: Transcriptome profile of UOK_SHTFE3, biological rep1


title: muscle_shortRNA_PH165_w0pre


title: UOK_SHTFEB_3

description: Transcriptome profile of UOK_SHTFEB, biological rep3

value: silenced for TFEB


title: HT-29 hypoxia Exp 1 A


title: muscle_shortRNA_PH165_w0h24


title: muscle_shortRNA_PH175_w0h3


title: UOK_SHTFEB_2

description: Transcriptome profile of UOK_SHTFEB, biological rep2


title: muscle_shortRNA_PH150_w0pre


title: UOK_SHTFEB_1

description: Transcriptome profile of UOK_SHTFEB, biological rep1


title: HT-29 normoxia Exp 2 A


title: muscle_shortRNA_PH150_w0h3


title: HT-29 normoxia Exp 1 A


title: muscle_shortRNA_PH166_w0pre


title: muscle_shortRNA_PH149_w0pre


title: UOK_SHLUC_3

description: Transcriptome profile of UOK_SHLUC, biological rep3

value: silenced for luciferase


title: HT-29 hypoxia Exp 2 A


title: muscle_shortRNA_PH149_w0h24


title: muscle_shortRNA_PH149_w0h3


title: muscle_shortRNA_PH135_w0h24

value: TRAD


title: MCF-7 normoxia Exp 1 B

value: breast cancer cell


title: UOK_SHLUC_4

description: Transcriptome profile of UOK_SHLUC, biological rep4


title: muscle_shortRNA_PH166_w0h24


title: UOK_SHLUC_2

description: Transcriptome profile of UOK_SHLUC, biological rep2


title: MCF-7 hypoxia Exp 1 B


title: UOK_SHLUC_1

description: Transcriptome profile of UOK_SHLUC, biological rep1


title: MCF-7 hypoxia Exp 2 B


title: muscle_shortRNA_PH165_w0h3

value: F


title: MCF-7 normoxia Exp 2 A


title: muscle_shortRNA_PH134_w0h3


title: muscle_shortRNA_PH134_w0h24


title: muscle_shortRNA_PH135_w0pre


title: muscle_shortRNA_PH128_w0pre


title: muscle_shortRNA_PH150_w0h24


title: MCF-7 normoxia Exp 1 A


title: muscle_shortRNA_PH128_w0h24


title: MCF-7 hypoxia Exp 2 A


title: muscle_shortRNA_PH128_w0h3


title: MCF-7 hypoxia Exp 1 A


title: muscle_shortRNA_PH126_w0h3


title: muscle_shortRNA_PH135_w0h3


title: muscle_shortRNA_PH126_w0h24


title: muscle_shortRNA_PH134_w0pre


title: muscle_shortRNA_PH125_w0pre


title: H226 normoxia Exp 1 B

value: lung cancer cell


title: H226 hypoxia Exp 2 B


title: muscle_shortRNA_PH125_w0h3


title: muscle_shortRNA_PH125_w0h24


title: H226 hypoxia Exp 1 B


title: H226 hypoxia Exp 2 A


title: muscle_shortRNA_PH124_w0h24


title: muscle_shortRNA_PH120_w0pre


title: muscle_shortRNA_PH120_w0h3


title: muscle_shortRNA_PH120_w0h24


title: H226 hypoxia Exp 1 A


title: muscle_shortRNA_PH116_w0pre


title: iBeta-like rep5

city: Barcelona

first: Rosa

last: Gasa

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

data_processing:
We generated a custom transcriptome by adding the Gencode M10 mouse transcripts from the transgenes Pdx1, Pax4, Neurog3 and Mafa to the human GENCODE release 39 human transcripts.
We assigned reads to this custom transcriptome using Salmon v.1.3.0 with parameters “-l A --validateMappings”.
Assembly: Custom hg38 with some transcripts from mm10
Supplementary files format and content: Tab-delimited quant.sf files outputed by Salmon

source_name: Foreskin

growth_protocol: Parental fibroblasts and reprogrammed cells were maintained in RPMI-1640 with 6% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using NucleoSpin RNA XS (Mackerey Nagel).
Total RNA  (200ng) was used to construct mRNA strand-specific RNA libraries using the Illumina® Stranded mRNA Prep Ligation kit (Ref.20040532) and IDT for Illumina RNA UD Indexes (Ref.20040553).

treatment_protocol: When fibroblasts reached 80% confluence, they were infected with a polycystronic adenovirus expressing Ngn3+Pdx1+Mafa (day 1). At days 4 and 7, cells were treated with adenoviruses encoding Pax4 and Nkx2-2 respectively.

value: Foreskin

value: fibroblast

value: Overexpression Ngn3, Pdx1,Mafa,Pax4, Nkx2-2


title: H226 normoxia Exp 2 A


title: iBeta-like rep6


title: muscle_shortRNA_PH116_w0h3

value: HITT


title: H226 normoxia Exp 1 A


title: muscle_shortRNA_PH126_w0pre

value: M


title: Control fibroblasts rep3


title: male marine snail, consecutive sexual maturation [OK-M3_1/2]

city: Higashi-Hiroshima

first: Fumihiro

last: Morishita

state: Hiroshima

department: Graduate School of Integrated Sciences for Life

institute: Hiroshima University

data_processing:
Adaptor and imcomplete sequences were removed by Trim Garore (ver. 0.6.6)
Model transcripts were organized by assembling short-read sequences with Trinity (ver 2.12.0)
Short-read sequences were mapped on the model transcripts by Salmon (ver 1.5.2)
Duplicates were removed and re-mapped with seqkit (ver 0.15.0)
Gene models were made by clustring transcript modesl with corset (ver 1.09)
Supplementary files format and content: multifasta, file name : clusters.fasta.txt

organism: Reishia clavigera

source_name: ganglion

extract_protocol:
RNA was extracted with Sepazol Super G RNA (Nakarai Tesque), followed by Dnase digestion with NucleoSpin RNA XS column kit. 0.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: ganglion

tag: genotype

value: consecutive sexual maturation


title: iBeta-like rep4


title: muscle_shortRNA_PH109_w0pre

value: skeletal muscle


title: Control fibroblasts rep2


title: male marine snail, consecutive sexual maturation [OK-M2_1/2]


title: muscle_shortRNA_PH124_w0pre


title: muscle_shortRNA_PH124_w0h3


title: muscle_shortRNA_PH109_w0h3


title: Control fibroblasts rep1


title: muscle_shortRNA_PH109_w0h24


title: 1317_GA_Neg

city: La Jolla

first: Cecilia

middle: Sofie

last: Lindestam

state: CA

address: 9420 Athena Circle

department: Sette

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: blood - PBMC

growth_protocol: PBMC were thawed and added at a density of 1 million cells per well to a round-bottom 96-well plate.

extract_protocol:
After 24 hrs, cells were resuspended in PBS with 10% (v/v) FBS and incubated at 4C for 10 min. Cells were then stained with fixable viability dye eFluor506 (eBioscience) and an antibody mixture containing anti-human CD3-AF700 (UCHT1; ThermoFisher), CD4-APCeFluor780 (RPA-T4; eBioscience), CD8-BV650 (RPA-T8; BioLegend), CCR7-PerCPCy5.5 (G043H7, Biolegend) CD14-V500 (M5E2; BD Bioscience), CD19-V500 (HIB19; BD Bioscience), CD25-FITC (M-A251; BD Bioscience), CD45RA-eFluor450 (HI100, eBiosciences), CD137-APC (4B4-1; BioLegend), OX40-PECy7 (Ber-ACT35; BioLegend), and PD-L1-PE (29E.2A3; BioLegend) for 20 min at room temperature. Cells were washed and resuspended in PBS before being transferred into a 5 ml polypropylene FACS tube (BD Bioscience). PBMCs were sorted, based on forward and side scatter excluding debris and doublets, on a FACSAria into TRIzol LS (Thermo Fisher). Acquisition files were analyzed using FlowJo. Total RNA was extracted from ~100,000 cells in TRIzol LS using the miRNeasy Micro Kit (Qiagen) on a QIAcube (Qiagen). Total RNA was amplified according to Smart Seq protocol (2). cDNA was purified using AMPure XP beads. cDNA was used to prepare a standard barcoded sequencing library (Illumina). Samples were sequenced using an Illumina HiSeq2500 to obtain 50-bp single end reads. Samples that failed to be sequenced due to limited sample availability or failed the quality control were eliminated from further sequencing and analysis. The full protocol can be found at protocols.io (http://dx.doi.org/10.17504/protocols.io.bxr6pm9e).
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: PBMCs were stimulated for 24hrs at 37 degree C with MTB300, Mtb whole cell lysate, as well as left unstimulated as a negative control. After 24hrs cells were stained for sorting

tag: with susceptibiliy allele

value: yes

tag: stimulation

value: Unstim

value: PBMC


title: female marine snail, consecutive sexual maturation [OK-F3_1/2]


title: muscle_shortRNA_PH107_w0pre


title: 1157_GA_Neg


title: female marine snail, consecutive sexual maturation [OK-F2_1/2]


title: muscle_shortRNA_PH107_w0h3


title: female marine snail, consecutive sexual maturation [OK-F1_1/2]


title: HEKNIH, dry ice

city: Paris

first: Stuart

last: EDELSTEIN

state: Île-de-France

address: 29 rue du Faubourg Saint Jacques, Pépinière Paris Santé Cochin

country: France

institute: Scipio bioscience

description: Scipio bioscience. All provided R1 and R2 FASTQ files are already demultiplexed by sample index.

library_source: transcriptomic single cell

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
For each sample subfraction (3 subfractions per sample were sequenced), one couple of R1 and R2 FASTQ files was generated;
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files of each sample subfraction to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample subfraction by applying the distance-based knee method of UMI-tools based on 12,5 millions input raw reads randomly sampled from the concatenated R1 FASTQ file of the sample subfraction.
Raw read downsampling was perfomed for each sample subfraction by randomly subsampling raw reads from the FASTQ files such that the mean number of raw reads belonging to cell-associated barcodes was 50,000.
The provided processed data is composed of one count matrix per sample subfraction (thus 3 count matrices per sample), computed after raw read downsampling, such that for each sample the same sequencing depth is simulated at 50,000 mean number of raw reads per cell.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38) and mouse species (GRCm38).  Unique Genome Name in Cytonaut v6.7.0: Human_Mouse_Scipio_2022_A;  Species: Homo_sapiens & Mus_musculus;  Genome Source: ensembl & ensembl;  Genome Version: GRCh38 & GRCm38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/ & ftp.ensembl.org//pub/release-99/fasta/mus_musculus/dna/;  Annotation Source: ensembl & ensembl;  Annotation Version: 99 & 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/ & ftp.ensembl.org//pub/release-99/gtf/mus_musculus/.
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: NIH; HEK

extract_protocol:
For each sample, scRNA was extracted from a mix of NIH and HEK cells (50%-50%; 10,000 cell input), according to the RevGel-Seq protocol instructions. Briefly, Barcode beads and cells are attached via a bifunctional chemical linker. These tandems are dispersed in an hydrogel in the liquid state and immobilized upon gelation. For the sample HEKNIH freezer and HEKNIH dry ice, the hydrogel with cell-bead tandems is frozen right after immersion to lysis buffer. This freezeing was done in -80°C freezer for the sample HEKNIH freezer, on dry ice for the sample HEKNIH dry ice. The day after, the frozen sample was thawed at 25°C for 15 min to resume cel lyeis step.  Following cell lysis, polyA+ RNA molecules are captured on the barcoded beads via polyA-polyT interactions. Barcoded beads (and associated RNA molecules) are recovered following degelation, and reverse transcription and subsequent second strand synthesis with random primer are performed. Each sample is then split in 8 subfractions and PCR-amplified to obtain cell barocded cDNA.
For each of the 3 samples, cDNA from 3 subfractions of PCR were individually purified with SPRIselect to remove short fragments. Sequencing libraries were prepared with illumina's Nextera XT kit for each of the 3 purified barcoded cDNA according to manufacturer's instructions with the following adaptations: 600pg of the cDNA was subjected to tagmentation reaction. The tagmented DNA was amplified by 12 cycles PCR. During this PCR, DNA fragments with cell barcode sequence at one end are selectively amplified by using a primer pair of custom P5-read1 primer to the original barcode end and Nextera N7xx P7 index primer to the tagmented end. Paired end sequencing was done.

value: NIH; HEK

tag: strain


title: HEKNIH, freezer


title: male marine snail, normal [HS-M3_1/2]

value: WT


title: muscle_shortRNA_PH107_w0h24


title: HEKNIH, control


title: muscle_shortRNA_PH116_w0h24


title: 14 day mock surgery stroma enriched submandibular salivary gland

city: Albany

first: Melinda

last: Larsen

state: NY

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting  were made using the Cell Ranger software v6.0.1 at the University at Albany Center for Functional Genomics.
The raw sequencing files from Cell Ranger were loaded into R Studio, where we removed doublets and dead cells using the Seurat package with the feature cutoffs >200 and <9000 and mt genes <5%.
Ligated and mock datasets were merged using 14 dimensions with a resolution of 0.3 for downstream analysis. The merged dataset was scaled and normalized using the Seurat package.
A subset of the dataset expressing stromal genes (Pdgfra > 0.5, Pdgfrb > 0.5, or Gli1 > 0 ) was selected and 14 dimensions with 0.025 resolution was used for downstream analysis. This subset was scaled and normalized using the Seurat package.
All exported files were generated using the AverageExpression function within the Seurat package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Supplementary files are in comma separated values (CSV) format files containing the average expression of selected genes per cell cluster.

organism: Mus musculus

source_name: Submandibular Salivary Gland

extract_protocol:
Two ligated or mock surgery submandibular and sublingual glands were harvested, and excess fat and interstitial tissue was removed. The glands were then transferred to a dish containing 1X PBS, liberase TL Research Grade low Thermolysin (Roche), DNase I, and dispase and microdissected for 7 minutes. The sample was then incubated in a 37°C incubator for 15 minutes and triturated. After trituration, the sample was incubated for an additional 5 minutes in a 37°C incubator and triturated once more. A 15 mL conical tube was placed on ice and the entire sample was transferred to the conical tube and incubated for 10 minutes. The supernatant was isolated and transferred to a fresh conical tube and was centrifuged for 5? minutes at 450xg. The supernatant was removed and discarded, and the cell pellet was resuspended in isolation buffer composed of sterile-filtered Ca2+- and Mg2+-free 1X PBS, 0.1% bovine serum albumin, and 2mM ethylenediaminetetraacetic acid. 5 mg of EpCAM-A647 (catalog: 118212, BioLegend) and Ter119 (catalog: 50-133-27, eBioscience/ThermoFisher) was added to the cell suspension and incubated at 4°C for 10 minutes for depletion of epithelial and red blood cells, respectively. The cell suspension was washed using isolation buffer and centrifuged at 450xg for 5 minutes. The supernatant was discarded, and the cell pellet was resuspended in 1 mL of isolation buffer and 25 uL of sheep anti-rat Dynabeads, which bind to the EpCAM and Ter119 labeled cells, (catalog: 11035, Invitrogen) before incubating on ice for 20 minutes on a rocker. The sample was placed on a microcentrifuge magnet for 2 minutes, and the supernatant was transferred to a fresh microcentrifuge tube to remove labeled epithelial and red blood cells. An additional epithelial and red blood cell depletion was performed. The sample was then depleted of dead cells using a dead cell removal kit (catalog: 130-090-101, Miltenyi Biotec) following manufacturer’s instructions. Cells were counted and resuspended to a concentration of 1000 cells/mL. Following the manufacturer’s protocol for the Chromium Next GEM Single Cell 3’ Reagent kits v3.1, scRNAseq libraries were generated.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Mice underwent either a 14 day ligation surgery, where a metal clip was applied to the main ducts of the submandibular and sublingual glands and remained in place for 14 days prior to harvest or a 14 day mock surgery, where the main ducts of the submandibular and sublingual glands were located, but not clipped and the mouse was allowed to heal for 14 days.

value: Female

value: 14 weeks

value: Submandibular Salivary Gland

value: Stromal Enriched

value: 14 day mock surgery


title: male marine snail, normal [HS-M2_1/2]


title: muscle_shortRNA_PH101_w0pre


title: mix NIH-HEK, Scipio, replicate 3, scRNAseq

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
For each sample, the R1 (resp. R2) FASTQ files of the 8 sample subfractions were concatenated into one R1 (resp. R2) FASTQ file.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools based on 100 millions input raw reads randomly sampled from the concatenated R1 FASTQ file of the sample.
Raw read downsampling was perfomed for each sample by randomly subsampling raw reads from the concatenated FASTQ files such that the mean number of raw reads belonging to cell-associated barcodes was 50,000.
The provided processed data is composed of one count matrix per sample, computed after raw read downsampling, such that for each sample the same sequencing depth is simulated at 50,000 mean number of raw reads per cell.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38) and mouse species (GRCm38).  Unique Genome Name in Cytonaut v6.7.0: Human_Mouse_Scipio_2022_A;  Species: Homo_sapiens & Mus_musculus;  Genome Source: ensembl & ensembl;  Genome Version: GRCh38 & GRCm38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/ & ftp.ensembl.org//pub/release-99/fasta/mus_musculus/dna/;  Annotation Source: ensembl & ensembl;  Annotation Version: 99 & 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/ & ftp.ensembl.org//pub/release-99/gtf/mus_musculus/.
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: mixture: NIH; HEK

extract_protocol:
scRNA was extracted from a mix of NIH and HEK cells (50%-50%; 10,000 cell input), according to the RevGel-Seq protocol instructions. Briefly, Barcode beads and cells are attached via a bifunctional chemical linker. These tandems are dispersed in an hydrogel in the liquid state and immobilized upon gelation. Following cell lysis, polyA+ RNA molecules are captured on the barcoded beads via polyA-polyT interactions. Barcoded beads (and associated RNA molecules) are recovered following degelation, and reverse transcription and subsequent second strand synthesis with random primer are performed. Each sample is then split in 8 subfractions and PCR-amplified to obtain cell barocded cDNA.
Each of the 8 fractions of barcoded cDNA was purified with SPRIselect to remove short fragments. Sequencing libraries were prepared with illumina's Nextera XT kit for each of the 8 purified barcoded cDNA  according to manufacturer's instructions with the following adaptations: 600pg of the cDNA was subjected to tagmentation reaction.The tagmented DNA was amplified by 12 cycles PCR. During this PCR, DNA fragments with cell barcode sequence at one end are selectively amplified by using a primer pair of custom P5-read1 primer to the original barcode end and Nextera N7xx P7 index primer to the tagmented end.Paired end sequencing was done.

value: mixture:NIH; HEK


title: mix NIH-HEK, Scipio, replicate 2, scRNAseq


title: male marine snail, consecutive sexual maturation [OK-M1_1/2]


title: male marine snail, normal [HS-M1_1/2]


title: muscle_shortRNA_PH101_w0h24


title: muscle_shortRNA_PH100_w0pre

value: F


title: female marine snail, normal [HS-F4_1/2]


title: mix NIH-HEK, Scipio, replicate 1, scRNAseq


title: female marine snail, normal [HS-F3_1/2]


title: female marine snail, normal [HS-F2_1/2]


title: 1154_GA_Neg


title: muscle_shortRNA_PH100_w0h3

value: HITT


title: muscle_shortRNA_PH100_w0h24


title: muscle_shortRNA_PH098_w0pre

value: TRAD

value: M


title: female marine snail, normal [HS-F1_1/2]

value: ganglion


title: muscle_shortRNA_PH098_w0h3

value: skeletal muscle


title: muscle_shortRNA_PH098_w0h24


title: muscle_shortRNA_PH101_w0h3


title: muscle_shortRNA_PH090_w0h3


title: muscle_shortRNA_PH090_w0h24


title: muscle_shortRNA_PH086_w0pre


title: muscle_shortRNA_PH086_w0h3


title: Cd69WT term diff 2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

data_processing:
Basecalls for RNA-seq were performed using bcl2fastq v2.20 for Nextseq output.
RNA-seq reads were aligned to the UCSCmm10 genome using Bowtie version 2.3.4. and TopHat 1.3.2.
Fragments per kilobase of exon per million mapped reads for each gene for RNA-seq were calculated using the Cufflinks 2.2.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+ T cells

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.The generated RNA-seq libraries were sequenced using a 76 cycle (single-end reads) with a NextSeq500 (Illumina).
For cDNA library construction, we used a SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) in accordance with the manufacturer’s protocol.

value: CD8+ T cells

value: BALB/c

value: wild type

tag: cell subset

value: term diff


title: Cd69KO term diff 2


title: Cd69KO term diff 1


title: Cd69KO stem-like 2

value: stem-like


title: muscle_shortRNA_PH090_w0pre


title: Pck1-CKO-1

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

institute: Tokushima University Graduate School of Biomedical Sciences

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent DNA Microarray Scanner (G2505C) Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Kidneys

label_protocol: Agilent Low Input Quick Amp Labeling Kit, one-color labeling protocol

growth_protocol: Renal proximal tubule-specific Pck1 knockout (Pck1-/-) mice (CKO mice) were created by crossing Pck1 flox/flox mice on a C57BL/6J background with γGT-Cre mice (Jackson Laboratory). The following three types of control mice were created using this breeding process: Pck1 flox/flox, Pck1 flox/+, and Pck1 flox/+/γGT-Cre tg/+. In the subsequent studies, Pck1 flox/+/γGT-Cre tg/+ mice were crossed with Pck1 flox/flox mice to create Pck1 flox/flox/γGT-Cre tg/+ (PT-specific Pck1-/-) mice (Pck1 CKO mice).  Age- and sex-matched littermates were used as WT control mice.

extract_protocol: RNA was prepared using the QIAzol Lysis Reagent and Rneasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.

treatment_protocol: Mice in the Pck1-CKO and WT groups were killed at 32weeks of age. Kidneys weere immediately used for total RNA isolation and subjected to analysis on microarray chips.

value: Kidneys


title: Cd69KO stem-like 1


title: muscle_shortRNA_PH085_w0pre


title: Cd69WT term diff 1


title: Pck1-CKO-3


title: 1314_GA_Neg

value: no

value: Unstim

value: PBMC


title: Pck1-CKO-2


title: WT-2

value: wild-type


title: WT-1


title: Cd69WT stem-like 2


title: muscle_shortRNA_PH085_w0h3


title: muscle_shortRNA_PH086_w0h24


title: Day 7_rep3

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression in blood, day 7 after irradiation

hyb_protocol: Agilent recommended protocols were used for hybridizations

scan_protocol: Slides were  scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Macaca mulatta

source_name: Day 7_rep3

label_protocol: We processed 4-7 samples from each of the following groups: pre-irradiation, day 3, day 5 and day 7 RNA for microarray hybridization. Previous studies have shown the usefulness of human microarray platforms for the detection of non-human primate gene expression.  We used Agilent Whole Rhesus Genome 4X44K v2 microarrays for measurement of levels of Rhesus transcripts, following the Agilent recommended protocol.

growth_protocol: We obtained whole blood samples pre-irradiation and post-irradiation (days 3, 5 and 7) from 8 NHP exposed to 4 Gy X-rays total body irradiation

extract_protocol: We isolated RNA from the blood using the PAXgene Blood RNA method (PreAnalytix GmBH, catalog#762165), and then depleted Globin transcripts using the Ambion GLOBINclear-Human kit (Life Technologies, Grand Island, NY, catalog#AM1980). We evaluated the samples for RNA integrity using the Agilent 2100 bioanalyzer and samples with RINs >8.0 were used for further analysis.

treatment_protocol: The intent of irradiation was to deliver 4 Gy to the total body

value: whole blood

value: Male

tag: dose (gy)

tag: day


title: WT-3

tag: tissue


title: Day 7_rep7

source_name: Day 7_rep7

value: Female


title: Day 7_rep6

source_name: Day 7_rep6


title: Day 7_rep4

source_name: Day 7_rep4


title: Cd69WT stem-like 1

tag: cell type


title: Day 7_rep2

source_name: Day 7_rep2


title: Day 7_rep1

source_name: Day 7_rep1


title: Day 7_rep5

source_name: Day 7_rep5


title: muscle_shortRNA_PH085_w0h24

source_name: skeletal muscle

tag: timepoint

tag: cohort

value: TRAD

value: F


title: 14 day ligated stroma enriched submandibular salivary gland

description: 10X Genomics

tag: Sex

value: 14 weeks

value: Submandibular Salivary Gland

value: Stromal Enriched

value: 14 day ligation surgery


title: Day 5_rep3

description: Gene expression in blood, day 5 after irradiation

source_name: Day 5_rep3


title: PS+ day10 biol repl5

city: Planegg-Martinsried

first: Jan

last: Kranich

address: Großhaderner Straße 9

department: Biomedical Center, Institute for Immunology

country: Germany

institute: Ludwig-Maximilians-Universität Munich

data_processing:
Sequencing reads were aligned to the mouse reference genome (version GRCm38.99) with STAR (version 2.6.1d). Expression values (TPM) were calculated with RSEM (version 1.3.0).
Post-processing was performed in R/Bioconductor (version 4.0.0) using default parameters if not indicated otherwise. Differential gene expression analysis was performed with 'DEseq2' (version 1.26.0). An adjusted p value (FDR) of less than 0.1 was used to classify significantly changed expression. Gene set enrichment analyses were conducted with 'clusterProfiler' (version 3.18.1) on the statistic reported by DEseq2.
Assembly: mm10 (GRCm38)
Supplementary files format and content: result summary EV+ vs EV- effector CD8.xlsx: Excel table containing expression values of each gene and sample.

source_name: spleen

extract_protocol:
Cells were lysed in Trizol. RNA purification was done using Monarch Cleanup Kits (New England Biolabs).
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, first strand cDNA was synthesized using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. After fragmentation, the first-strand cDNA was purified and the Illumina TruSeq sequencing adapter was ligated in a strand specific manner to the 5' ends of the cDNA fragments. The cDNA was PCR amplified to about 10-20 ng/μl using a high fidelity DNA polymerase (cycle numbers are indicated in Table 2). The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool in the size range of 300 – 400 bp was eluted from a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA pools were sequenced in four runs on an Illumina NextSeq 500 system using 1x75 bp read length.

value: spleen

value: PS+ CD44+ CD62L- CD8 T cells

value: LCMV Armstrong infection

tag: time point


title: 1310_GA_Neg


title: PS+ day10 biol repl4


title: Day 5_rep6

source_name: Day 5_rep6


title: muscle_shortRNA_PH082_w0h24

value: skeletal muscle

value: HITT


title: PS+ day10 biol repl3


title: Day 5_rep4

source_name: Day 5_rep4


title: muscle_shortRNA_PH077_w0pre

value: M


title: PS+ day10 biol repl2


title: muscle_shortRNA_PH077_w0h3


title: muscle_shortRNA_PH077_w0h24


title: PS+ day10 biol repl1


title: muscle_shortRNA_PH076_w0pre


title: muscle_shortRNA_PH082_w0pre


title: Day 5_rep1

source_name: Day 5_rep1


title: PS- day10 biol repl5

value: PS- CD44+ CD62L- CD8 T cells


title: Day 3_rep4

description: Gene expression in blood, day 3 after irradiation

source_name: Day 3_rep4


title: Day 3_rep7

source_name: Day 3_rep7


title: Day 5_rep2

source_name: Day 5_rep2


title: muscle_shortRNA_PH082_w0h3


title: PS- day10 biol repl4


title: muscle_shortRNA_PH076_w0h3


title: PS- day10 biol repl3


title: muscle_shortRNA_PH076_w0h24


title: muscle_shortRNA_PH071_w0pre


title: PS- day10 biol repl2


title: PS- day10 biol repl1


title: muscle_shortRNA_PH071_w0h3


title: Day 3_rep2

source_name: Day 3_rep2


title: Pre-irradiation_rep7

description: Gene expression in blood, pre-irradiation control


title: 1144_GA_Neg

source_name: blood - PBMC

value: no

value: Unstim

value: PBMC


title: PS+ day5 biol repl5


title: Day 3_rep1

source_name: Day 3_rep1

value: whole blood

value: Male


title: muscle_shortRNA_PH071_w0h24

description:
small RNA from skeletal muscle
muscle_longRNA_small_counts.txt

value: TRAD


title: Pre-irradiation_rep6

value: Female


title: muscle_shortRNA_PH070_w0pre

value: F


title: 1043_GA_Neg


title: Pre-irradiation_rep5


title: PS+ day5 biol repl4


title: muscle_shortRNA_PH070_w0h3


title: PS+ day5 biol repl3


title: muscle_shortRNA_PH070_w0h24


title: PS+ day5 biol repl2


title: Pre-irradiation_rep2


title: muscle_shortRNA_PH061_w0pre


title: Pre-irradiation_rep3


title: PS+ day5 biol repl1


title: PS- day5 biol repl5


title: Dppa5a_KD_R1

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

country: China

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 2.19
Reads were mapped to mm10 genome using tophat2 (version 2.0.8) with default parameters.
For RNA-seq, fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using cufflinks version 2.1.1; Differentialy expressed genes were determined using cuffdiff (version 2.1.1).
For RIP-seq, raw counts of genes were counted using htseq software (version 0.6.1) with mouse RefSeq annotation and used for differentially expressed genes analysis using DEGseq (version 1.38.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq Sample
Supplementary files format and content: tab-delimited text files include counts for each RIP-seq Sample

source_name: home made

growth_protocol: Mouse embryonic fibroblasts were cultured in DMEM supplemented with 10% FBS. Mouse embryonic stem cells (mESCs) were routinely maintained on inactivated mouse embryonic fibroblasts in the culture medium: Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) medium supplemented with 20% Knockout serum replacement,1 mM sodium pyruvate, 2 mM L-glutamine, 1% non-essential amino acids, 0.1mM β-mercaptoethanol, penicillin (100 U/mL)/streptomycin (100 μg/mL) and 1000 units/mL mouse leukemia inhibitory factor (LIF). To harvest mESCs, cells were passaged twice on gelatin coated dishes.

extract_protocol:
Total RNA or immunoprecipitated RNAs were extracted using standard Trizol procedure.
RNA libraries were constructed by Novogene Corporation (Beijing, China). RNA-seq libraries were constructed using Illumina NEBNext® UltraTM RNA Library Prep Kit.

tag: cell line

value: home made

value: Mouse embyonic stem cells

value: Dppa5a knockdown

value: untreated

tag: rip antibody


title: KD_control_R2

value: wild type

tag: treatment


title: KD_control_R1


title: Dppa5a_KD_R2


title: muscle_shortRNA_PH061_w0h3

value: skeletal muscle


title: TU0075_MTB300

value: yes


title: Pre-irradiation_rep1

tag: gender


title: TDLN_Cd69KO 2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scRNA-seq were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor-draining lymph nodes

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s protocol (10X Genomics).

value: CD8+ T cells

value: BALB/c

tag: genotype

value: tumor-draining lymph nodes


title: muscle_shortRNA_PH061_w0h24

value: M


title: TDLN_Cd69KO 1


title: Day 5_rep7

source_name: Day 5_rep7


title: PS- day5 biol repl3

value: spleen

value: PS- CD44+ CD62L- CD8 T cells

value: LCMV Armstrong infection


title: TDLN_wild-type 2

value: wild-type


title: PS- day5 biol repl2


title: muscle_shortRNA_PH059_w0h3

value: HITT


title: Pre-irradiation_rep4

value: whole blood

value: Male


title: TME_anti-CD69+anti-PD-1 2

source_name: tumor microenvironment

value: tumor microenvironment


title: PS- day5 biol repl1


title: TDLN_wild-type 1


title: muscle_shortRNA_PH046_w0pre

value: TRAD

value: F


title: muscle_shortRNA_PH059_w0h24


title: PS- day5 biol repl4


title: TME_anti-CD69+anti-PD-1 1


title: TME_anti-PD-1 2


title: 2055_GA_MTB300

tag: with susceptibiliy allele

value: PBMC


title: muscle_shortRNA_PH046_w0h3

value: skeletal muscle


title: RNA-seq comparing SPPL3 knockout 221 cells, repeat-3

city: Bethesda

first: Xiaoxuan

last: Zhuang

state: MD

address: 10 Center Dr, RM 6N105

institute: NIH

description:
SPPL3-KO-3
SPPL3-KO_RNA-Seq_edgeR_normalized_cpm.csv
SPPL3-KO_edgeR_trt_KO_vs_WT_all.csv

data_processing:
Mapping the the library file using MAGeCK pipeline.
sgRNA count and defferential analysis by MAGeCK
Supplementary files format and content: sgRNA counts and differental analysis, normalized CPMs

extract_protocol:
For genomic DNA extraction, the kit QIAmp DNA Blood Max kit (Qiagen) for large scale and PureLink DNA mini kit (Invitrogent) for small scale was used. RNA extraction was done by Allprep DNA/RNA mini kit (Qiagen)
Follow the protocol from this paper: Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening PMID 28333914

value: B cell lymphoblast

value: Expressing Cas9 and sgSPPL3

value: No


title: muscle_shortRNA_PH046_w0h24

data_processing:
Long reads were aligned using STAR to GRCh38 and LNCpedia; separately, long reads were used to identify circular RNA using CIRI2; small reads were aligned using exceRpt
Long RNA count data were generated using featureCounts
Assembly: GRCh38
Supplementary files format and content: txt file containing read counts for genes and samples

extract_protocol:
Skeletal muscle RNA was extracted using Qiagen miRNeasy kit (Cat. No. 217004); serum EV RNA was extracted using Qiagen exoRNeasy kits (Cat. No. 77144).
Long RNA libraries for both skeletal muscle and serum EVs were constructed using Takara Bio SMARTer Stranded Total RNA-Seq kit v2 Pico Input Mammalian (Cat. No. 634418) and SMARTer RNA Unique Dual Index Kit (Cat. No. 634452). Small RNA libraries for both skeletal muscle and serum EVs were prepared using NEXTflex Small RNA Library Prep Kit v3 (Ca. No. # NOVA-5132-23, Perkin Elmer


title: RNA-seq comparing SPPL3 knockout 221 cells, repeat-1

description:
SPPL3-KO-1
SPPL3-KO_RNA-Seq_edgeR_normalized_cpm.csv
SPPL3-KO_edgeR_trt_KO_vs_WT_all.csv


title: RNA-seq comparing SPPL3 knockout 221 cells, repeat-2

description:
SPPL3-KO-2
SPPL3-KO_RNA-Seq_edgeR_normalized_cpm.csv
SPPL3-KO_edgeR_trt_KO_vs_WT_all.csv


title: RNA-seq comparing sgNT 221 cells, repeat-3

description:
ctrl-3
SPPL3-KO_RNA-Seq_edgeR_normalized_cpm.csv
SPPL3-KO_edgeR_trt_KO_vs_WT_all.csv

value: Expressing Cas9 and sgNT


title: muscle_shortRNA_PH029_w0pre


title: TME_anti-PD-1 1

value: CD8+ T cells

value: BALB/c


title: RNA-seq comparing sgNT 221 cells, repeat-2

description:
ctrl-2
SPPL3-KO_RNA-Seq_edgeR_normalized_cpm.csv
SPPL3-KO_edgeR_trt_KO_vs_WT_all.csv


title: muscle_shortRNA_PH059_w0pre

value: M


title: TME_anti-CD69 1


title: RNA-seq comparing sgNT 221 cells, repeat-1

description:
ctrl-1
SPPL3-KO_RNA-Seq_edgeR_normalized_cpm.csv
SPPL3-KO_edgeR_trt_KO_vs_WT_all.csv


title: Glycosylation secondary screen in sgSPPL3 221 cells,surviving, repeat-2

description:
sgSPPL3_surv_2
SPPL3_KO_screen.count_normalized.txt
sgSPPL3_glycoScreen_2.gene_summary.txt

library_source: genomic

value: Expressing Cas9, sgSPPL3 and the GlycoGen CRISPR library

value: Co-culture with NK cells


title: TME_control IgG 2

value: wild-type


title: 1304_GA_MTB300

value: yes

tag: stimulation


title: TME_control IgG 1

tag: strain


title: muscle_shortRNA_PH024_w0h3

value: HITT


title: Glycosylation secondary screen in sgSPPL3 221 cells,surviving, repeat-1

description:
sgSPPL3_surv_1
SPPL3_KO_screen.count_normalized.txt
sgSPPL3_glycoScreen_1.gene_summary.txt


title: muscle_shortRNA_PH024_w0h24


title: Glycosylation secondary screen in sgSPPL3 221 cells,control, repeat-2

description:
sgSPPL3_ctrl_2
SPPL3_KO_screen.count_normalized.txt
sgSPPL3_glycoScreen_2.gene_summary.txt


title: Glycosylation secondary screen in sgSPPL3 221 cells,control, repeat-1

description:
sgSPPL3_ctrl_1
SPPL3_KO_screen.count_normalized.txt
sgSPPL3_glycoScreen_1.gene_summary.txt


title: TME_Cd69KO 2

value: tumor microenvironment


title: TME_Cd69KO 1


title: TME_wild-type 2


title: muscle_shortRNA_PH011_w0pre


title: TME_anti-CD69 2


title: Glycosylation secondary screen in sgNT 221 cells,surviving, repeat-2

description:
sgNT_surv_2
SPPL3_KO_screen.count_normalized.txt
sgNT_glycoScreen_2.gene_summary.txt

value: Expressing Cas9, sgNT and the GlycoGen CRISPR library


title: muscle_shortRNA_PH018_w0h24


title: muscle_shortRNA_PH018_w0h3


title: 1046_GA_MTB300


title: Glycosylation secondary screen in sgNT 221 cells,control, repeat-2

description:
sgNT_ctrl_2
SPPL3_KO_screen.count_normalized.txt
sgNT_glycoScreen_2.gene_summary.txt


title: Glycosylation secondary screen in sgNT 221 cells,control, repeat-1

description:
sgNT_ctrl_1
SPPL3_KO_screen.count_normalized.txt
sgNT_glycoScreen_1.gene_summary.txt


title: muscle_shortRNA_PH024_w0pre


title: CRISPR ATRX KO clone KO-B_MSCV IDH1-R132H_rep 3

city: Durham

first: David

last: Ashley

state: NC

address: 203 Research Dr, MSRB1

department: Neurosurgery

institute: Duke University

data_processing:
Conventional base calls using Illumina 1.9
Reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b with soft clipping clip3pNbases = 10. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.6.3. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: Single matrix table with raw gene counts for every gene and every sample

growth_protocol: CT2A cells were a kind gift of Peter Fecci (Duke University Medical Center, Durham NC). Cells were maintained in DMEM (high glucose) containing 10% FBS.

extract_protocol:
RNA was extracted from monolayer cell cultures using miRNeasy Mini kit (Qiagen, Germantown, MD). 300ng of RNA was used for cDNA prep and construction of sequencing libraries using KAPA Stranded mRNA-Seq kit for Illumina platforms - KR0960 - v6.17.
Library construction was performed as per manufacturer's instructions on Sciclone G3 Liquid Handler, 10 PCR cycles.

treatment_protocol: No treatment

value: Glioma

value: ATRX KO IDH1-R132H


title: CRISPR ATRX KO clone KO-B_MSCV IDH1-R132H_rep 2


title: TME_wild-type 1


title: CRISPR ATRX KO clone KO-B_MSCV EV control_rep 3

value: ATRX KO - IDH1 WT


title: muscle_shortRNA_PH011_w0h24

value: skeletal muscle

value: F


title: muscle_shortRNA_PH011_w0h3


title: 221 NK killing CRISPR screen surviving, repeat-1

description:
trt_1
new_counts.count_normalized.txt
221_mle_as_duplicates_useCTRLgRNAs_more_than5gRNAs.gene_summary.csv

value: B cell lymphoblast

value: Transduced with Cas9 and GeCKO V2 CRISPR library


title: muscle_shortRNA_PH029_w0h24

value: TRAD


title: TU0081_MTB300

value: no

value: PBMC


title: muscle_shortRNA_PH010_w0pre


title: CRISPR ATRX KO clone KO-B_MSCV EV control_rep 2


title: 221 NK killing CRISPR screen control, repeat-1

description:
ctrl_1
new_counts.count_normalized.txt
221_mle_as_duplicates_useCTRLgRNAs_more_than5gRNAs.gene_summary.csv

value: No


title: muscle_shortRNA_PH010_w0h3


title: muscle_shortRNA_PH018_w0pre

value: M


title: muscle_shortRNA_PH010_w0h24


title: muscle_shortRNA_PH029_w0h3


title: CRISPR ATRX KO clone KO-A_MSCV IDH1-R132H_rep 3


title: CRISPR ATRX KO clone KO-A_MSCV IDH1-R132H_rep 2


title: 222 NK killing CRISPR screen surviving, repeat-2

description:
trt_2
new_counts.count_normalized.txt
221_mle_as_duplicates_useCTRLgRNAs_more_than5gRNAs.gene_summary.csv

value: Co-culture with NK cells


title: LX2 cells, PTH4

city: Shanghai

first: Ting

last: Hong

state: Shanghai

address: 180 Fenglin Road, Xuhui District

department: Department of Endocrinology and Metabolism

institute: Zhongshan Hospital, Fudan University, Shanghai, China

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: liver

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: stellate cell

value: PTH


title: LX2 cells, PTH3


title: TU0025_MTB300


title: CRISPR ATRX KO clone KO-A_MSCV IDH1-R132H_rep 1


title: Hepatocytes miR-206, 2

city: Minneapolis

first: Guisheng

last: Song

state: MN

address: MMC36 (PWB1-143), 516 DELAWARE ST SE

institute: University of Minnesota

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
Qiagen RNeasy Micro Kit was used to isolate total RNA
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

value: male

tag: age

value: Eight-week

value: Hepatocytes

value: miR-206 overexpression


title: LX2 cells, PTH2


title: Hepatocytes miR-206, 1


title: Hepatocytes miR-206, 3


title: Hepatocytes control, 3

value: Wild-type

value: Empty vector


title: LX2 cells, PTH1


title: CRISPR ATRX KO clone KO-A_MSCV EV control_rep 2

value: Glioma

value: ATRX KO - IDH1 WT


title: CRISPR ATRX KO clone KO-A_MSCV EV control_rep 3


title: Hepatocytes control, 2


title: LX2 cells, con3

value: PBS


title: CRISPR ATRX KO clone KO-A_MSCV EV control_rep 1


title: Hepatocytes control, 1


title: LX2 cells, con2


title: LX2 cells, con1


title: CRISPR control_MSCV IDH1-R132H_rep 2

value: ATRX WT - IDH1-R132H


title: CRISPR control_MSCV IDH1-R132H_rep 3


title: CRISPR control_MSCV IDH1-R132H_rep 1


title: LAN5_SiHAND2_3_Rep3

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR 2.5.1.
Counts per million (CPM) were quantified using the Partek E/M model.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA-seq_LAN5_SiMYCN_plus_SiHAND2_CPM.txt: Tab-delimited text file includes CPM values for each Sample.

growth_protocol: LAN5 cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: siRNAs were transiently transfected into LAN5 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 72 hr before RNA extraction.

value: Neuroblastoma

tag: sirna


title: tMCAO_MG_DE_1 [C142]

city: Guangzhou

first: Xiaoyan

last: Huang

state: Guangdong

address: 137 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
After genome mapping, Cufflinks v2.1.1  was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using Cuffdiff.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
The fold-changes were also estimated according to the FPKM in each sample.
The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts and FPKM values for each Sample

source_name: brain

growth_protocol: CX3CR1creER/+:R26iDTR/+ mice were administered two doses of tamoxifen (T5648, Sigma, Darmstadt) every other day by oral gavage when they were 7-8 weeks. After 30 days, these animals were administered diphtheria toxin (DT, 50 ng/g BW, List Biological Lab, California) for 3 continuous days to deplete microglia(Parkhurst et al., 2013)

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany)
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

treatment_protocol: Six- to eight-week-old male mice were anesthetized and maintained with 2% isoflurane in 60% oxygen. After making a 2 cm curved skin incision on the midline of the neck, the temporal muscle was retracted laterally. Then, the right common carotid artery (CCA), the external carotid artery (ECA), and the internal carotid artery (ICA) were isolated. The tMCAO was achieved by carrying forward a 0.22-0.23 mm monofilament nylon suture with a rounded tip to the right ICA via ECA until slight resistance was felt. 60 min after the onset of MCAO, the nylon suture was removed for reperfusion. During the process, a warming blanket was applied to maintain the temperature of the mice.

value: brain

value: CX3CR1creER/+ :Rosa36iDTR/+

value: tamoxifen and diphtheria toxin; tMCAO surgery


title: tMCAO_MG_DE_2 [C148]

value: CX3CR1creER/+ :Rosa37iDTR/+


title: tMCAO_MG_CON_4 [C98]

value: CX3CR1creER/+ :Rosa35iDTR/+

value: tamoxifen and normal saline; sham surgery


title: LAN5_SiHAND2_3_Rep2


title: tMCAO_MG_CON_3 [C169]

value: CX3CR1creER/+ :Rosa34iDTR/+

value: tamoxifen and normal saline; tMCAO surgery


title: CRISPR control_MSCV EV control_rep 2

value: ATRX WT - IDH1 WT


title: LAN5_SiMYCN_2_Rep3


title: LAN5_SiHAND2_3_Rep1


title: tMCAO_MG_CON_2 [C165]

value: CX3CR1creER/+ :Rosa33iDTR/+


title: 1313_GA_MTB300

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

extract_protocol:
After 24 hrs, cells were resuspended in PBS with 10% (v/v) FBS and incubated at 4C for 10 min. Cells were then stained with fixable viability dye eFluor506 (eBioscience) and an antibody mixture containing anti-human CD3-AF700 (UCHT1; ThermoFisher), CD4-APCeFluor780 (RPA-T4; eBioscience), CD8-BV650 (RPA-T8; BioLegend), CCR7-PerCPCy5.5 (G043H7, Biolegend) CD14-V500 (M5E2; BD Bioscience), CD19-V500 (HIB19; BD Bioscience), CD25-FITC (M-A251; BD Bioscience), CD45RA-eFluor450 (HI100, eBiosciences), CD137-APC (4B4-1; BioLegend), OX40-PECy7 (Ber-ACT35; BioLegend), and PD-L1-PE (29E.2A3; BioLegend) for 20 min at room temperature. Cells were washed and resuspended in PBS before being transferred into a 5 ml polypropylene FACS tube (BD Bioscience). PBMCs were sorted, based on forward and side scatter excluding debris and doublets, on a FACSAria into TRIzol LS (Thermo Fisher). Acquisition files were analyzed using FlowJo. Total RNA was extracted from ~100,000 cells in TRIzol LS using the miRNeasy Micro Kit (Qiagen) on a QIAcube (Qiagen). Total RNA was amplified according to Smart Seq protocol (2). cDNA was purified using AMPure XP beads. cDNA was used to prepare a standard barcoded sequencing library (Illumina). Samples were sequenced using an Illumina HiSeq2500 to obtain 50-bp single end reads. Samples that failed to be sequenced due to limited sample availability or failed the quality control were eliminated from further sequencing and analysis. The full protocol can be found at protocols.io (http://dx.doi.org/10.17504/protocols.io.bxr6pm9e).
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

value: no

value: PBMC


title: CRISPR control_MSCV EV control_rep 1

value: Glioma


title: tMCAO_MG_CON_1 [C155]

value: CX3CR1creER/+ :Rosa32iDTR/+


title: LAN5_SiMYCN_2_Rep2


title: LAN5_SiMYCN_2_Rep1


title: sham_MG_DE_3 [C162]

value: CX3CR1creER/+ :Rosa30iDTR/+

value: tamoxifen and diphtheria toxin; sham surgery


title: sham_MG_DE_2 [C146]

value: CX3CR1creER/+ :Rosa29iDTR/+


title: LAN5_SiCTR_Rep2

value: Neuroblastoma

value: siCTR


title: POA-US

city: st louis

first: Hong

last: Chen

state: MO

address: 4511 Forest Park Ave

institute: Washington University in st louis

description: 10x Genomics

data_processing:
The raw sequencing data were processed using the 10X Genomics CellRanger pipeline (version 6.1.1) based on the reference mouse genome (mm10-2020-A) with the default parameters. The data were normalized to the lowest saturated sample, leading to 83,113 reads (mean), 3,207 genes (median), and 7,353 unique molecular identifier (UMI) counts (median) per cell in the control group (n = 4 mice). The UIH group (n = 4 mice) contained 77,898 reads, 2,998 genes, and 6,498 UMI counts per cell.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hypothalamic preoptic area of the brain

extract_protocol:
Approximately 1 h after ultrasound stimulation, mice were transcardially perfused with ice-cold phosphate-buffered saline (1X PBS). The POA was extracted from each brain and homogenized in a Dounce Homogenizer (Kimble) containing 0.4 mL of freshly prepared nuclear extraction buffer [250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH8.0), 0.1% Triton X-100,  0.2U/μl recombinant ribonuclease inhibitor  (Invitrogen™ RNaseOUT™)] applying 4 strokes with the A pestle followed by 8 strokes with the B pestle. The homogenate of four mice from the control group and four mice from the US group was pooled for nucleus isolation. Samples were filtered through a 30 µm cell strainer tube (Corning™ Falcon™) and centrifuged at 500xg for 5 min at 4°C to precipitate nuclei. The dissociated nuclei were washed once with and gently resuspended with nuclear storage buffer (PBS with 1% BSA, 0.2U/μl recombinant ribonuclease inhibitor). To purify neuron nuclei for single-nucleus RNA-seq, the nuclei suspension was incubated with Alexa Fluor®488 conjugated mouse anti-NeuN antibody (Millipore sigma, MAB377X, 1:200) for 30mins on ice. After incubation, the nuclei were washed once with and resuspended with nuclear storage buffer with 1ug/ml DAPI. Samples were filtered through a 30 µm cell strainer tube and shortly sorted using FACS (MoFlo, Beckman Coulter) using FlowJo (v10.8) software. The neuron nuclei were sorted on DAPI+/NeuN+ nuclei and collected into 1.5 ml Eppendorf tubes. Approximately 25,000 neuron nuclei were collected from each of the control and US groups and sent to GTAC@MGI for single-cell RNA-seq (10X Genomics).
Using a Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics), neuron nuclei were immediately loaded onto a Chromium Single Cell Processor (10X Genomics) for RNA barcoding from single nuclei. Sequencing libraries were constructed according to the manufacturer's instructions, and resulting cDNA samples were run on an Agilent Bioanalyzer using the High Sensitivity DNA Chip to determine cDNA concentrations. The samples were combined and run on an Illumina Nova Seq 6000.

value: Hypothalamic preoptic area of the brain

value: 6-9 weeks old

value: Neuron

value: WT

value: Ultrasound stimulation


title: POA-CON

description: 10x Genomics

value: Sham treatment (control)


title: LAN5_SiCTR_Rep1


title: sham_MG_DE_1 [C145]

value: brain

value: CX3CR1creER/+ :Rosa28iDTR/+


title: Glycosylation secondary screen in sgNT 221 cells,surviving, repeat-1

description:
sgNT_surv_1
SPPL3_KO_screen.count_normalized.txt
sgNT_glycoScreen_1.gene_summary.txt

value: B cell lymphoblast

value: Expressing Cas9, sgNT and the GlycoGen CRISPR library

value: Co-culture with NK cells


title: IMR32_SiM2+SiH2_3_Rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR 2.5.1.
Counts per million (CPM) were quantified using the Partek E/M model.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA-seq_IMR32_SiMYCN+SiHAND2_CPM.txt: Tab-delimited text file includes CPM values for each Sample.

source_name: IMR32 Cells

growth_protocol: IMR32 cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

treatment_protocol: siRNAs were transiently transfected into IMR32 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 72 hr before RNA extraction.


title: sham_MG_CON_2 [C150]

value: CX3CR1creER/+ :Rosa26iDTR/+

value: tamoxifen and normal saline; sham surgery


title: IMR32_SiM2+SiH2_3_Rep2


title: CRISPR control_MSCV EV control_rep 3

value: Glioma

value: ATRX WT - IDH1 WT


title: sham_MG_CON_3 [C166]

value: CX3CR1creER/+ :Rosa27iDTR/+


title: sham_MG_CON_1 [C141]


title: MQ_NS4, day10

city: Xi'an

first: Meng

last: Xing

address: No. 2 Xihuamen, Lianhu District

institute: Shanxi Hospital of Traditional Chinese Medicine

data_processing:
llumina Novaseq 6000 platform
Raw reads of fastq format were firstly processed using fastp
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files inckude RPKM valuse for each sample

source_name: skin

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: BALB/c

value: skin

value: IMQ-induced psoriasis mice model


title: MQ_NS3, day10


title: sham_MG_DE_4 [C168]

value: CX3CR1creER/+ :Rosa31iDTR/+

value: tamoxifen and diphtheria toxin; sham surgery


title: IMR32_SiHAND2_3_Rep3

value: Neuroblastoma


title: MQ_NS2, day10

value: WT


title: C_ko

city: Klosterneuburg

first: Lisa

middle: Sophie

last: Knaus

address: Am Campus 1

institute: IST Austria

data_processing:
Demultiplexed raw sequencing reads were trimmed before alignment according to the guidelines provided by Lexogen, i.e. random primer sequence, adapter contamination and low quality tails were filtered using BBDuk from the BBMap package
Reads were aligned using STAR version 2.5.4 (genome: GrCm38/mm10, gene annotation: Gencode release M8). Reads that didn’t align uniquely were discarded. Parameters: --outSAMtype BAM SortedByCoordinate --alignIntronMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 1 --quantMode GeneCounts
Read counts per gene were also calculated using STAR (option - quantMode GeneCounts).
Differential expression analysis was performed in Galaxy.org
Assembly: GRCm38/mm10
Supplementary files format and content: Read count table STAR format (column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA (used for quantSeq libraries), column 4: counts for the 2nd read trand aligned with RNA

source_name: cortex

extract_protocol:
Total RNA of one cortical hemisphere was extracted using TRIzol™ Reagent (Invitrogen™) and chloroform (Sigma Aldrich), followed by centrifugation at 12000 g for 15 min at 4°C. The upper phase was transferred to a fresh tube and 1.5 volumes of 100% EtOH were added. Total RNA was purified by using the RNA Clean&Concentrator-5 prep Kit (Zymo Research). The samples were further treated with RQ1 RNase-Free DNase (Promega) as described in the kit instructions manual. RNA concentration and quality was assessed by using the NanoDrop spectrophotometer (Thermo Fisher Scientific) and the Bioanalyzer 2100 with the RNA 6000 Nano kit (Agilent).
cDNA libraries were generated with the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) using 1.5 µg total RNA. The quality of the generated libraries was monitored by using the High Sensitivity DNA Analysis Kit (Agilent) and the Bioanalyzer 2100. Libraries were sequenced on an Illumina HiSeq 2500 instrument.

treatment_protocol: Pups were decapitated and the brains rapidly dissected on ice. Cortices were dissected and rapidly snap frozen. Samples were stored at -80 until processed.

value: cortex

value: Slc7a5fl/fl; Emx1Cre+


title: 1151_GA_MTB300

city: La Jolla

first: Cecilia

last: Lindestam

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

value: no

value: PBMC


title: C_wt

value: Slc7a5fl/fl; Emx1Cre-


title: IMR32_SiM2+SiH2_3_Rep1


title: MQ_NS1, day10


title: IMR32_SiHAND2_3_Rep1


title: B_ko


title: IMQ_BZLF4, day10

value: applying BZLF to the skin lesions in an IMQ-induced psoriasis mice model


title: IMR32_SiMYCN_2_Rep3


title: B_wt


title: IMQ_BZLF3, day10


title: LAN5_SiCTR_Rep3

value: siCTR


title: IMR32_SiMYCN_2_Rep2


title: A_ko


title: IMQ_BZLF2, day10


title: IMR32_SiMYCN_2_Rep1


title: IMR32_SiCTR_Rep3


title: A_wt


title: Abl1-KO/IL3-, Exp2

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
STAR with Encode parramenter for mapping
cuffdiff with -u flag for differental gene expression
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts and FPKMs values for each sample

source_name: murine bone marrow cells

growth_protocol: 32DAbl1KO cells

extract_protocol:
RNA was extracted from 5 × 106 cells using a Qiagen RNeasy Plus Mini Kit according to the manufacturer’s protocol. Total RNA was depleted of the ribosomal RNA component using RiboZero (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: a murine pre-B-cell

value: Abl1 KO

value: without IL-3


title: Control4, day10

value: BALB/c

value: white space handling


title: IMR32_SiHAND2_3_Rep2


title: Control3, day10

value: skin


title: Abl1-KO/IL3-, Exp1


title: IMR32_SiCTR_Rep1


title: Abl1-KO/IL3+, Control1

value: with IL-3


title: Control1, day10


title: Control2, day10


title: Abl1-KO/IL3+, Control2


title: Eed urothelium-specific KO mouse bladder mucosa CPP and urinary tract infection day 1

city: Los Angeles

first: Xue

last: Li

address: 8700 Beverly Blvd, Davis 3089

institute: Samuel Oschin Comprehensive Cancer Institute

data_processing:
1, Total RNA qualification; 2, mRNA enrichment; 3, Double-stranded cDNA synthesis; 4, End repair, poly-A and adaptor addition; 5, fragments selection and PCR; and 6, Library qualifty assessement.
for Base Calling: (1) HWI-ST1276:71 HWI-ST1276,Instrument – unique identifier of the sequencer; 71,run number – Run number on instrument; (2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX(Flowcell ID)flowcell,line 1, 1101 tile is(x=1208,y=2458); (3) 1:N:0:CGATGT the first number is 1 or 2, 1 means single reads or the first read of paired ends, 2 means the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence.
For data filtering: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Novogene used STAR software to align and map the sequence read
Differential expression analysis was performed by using the EdgeR R package
Supplementary files format and content: Excel files that list all genes after differential expression analysis

source_name: Female bladder mucosa

extract_protocol: RNeasy RNA isolation kit (Qiagen) was used to isolate total RNA from micro-dissected bladder urothelium.

value: Female bladder mucosa

value: Eed urothelium-specific KO

value: Severe/super infection


title: wild type mouse bladder mucosa CPP and urinary tract infection day 1

value: wild type


title: TPO4/AKPS organoids, replicate 4

city: Gelderland

first: Jelmer

last: Dijkstra

state: Nederland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Science (RIMLS)/Radboud University

data_processing:
Sequenced reads were aligned to the human hg38 genome with HISAT2 (PMID 31375807). Duplicate reads were removed with PICARD (http://broadinstitute.github.io/picard) and count tables for downstream analyses were generated with HTSeq (PMID 25260700).
Assembly: hg38
Supplementary files format and content: txt file containing the results from HTSEQ-count for all listed files.

source_name: colon

growth_protocol: Human colon APK (APCKO, P53KO, KRASG12D) and APKS (APCKO, P53KO, KRASG12D, SMAD4KO) organoids were embedded in in a mix of 90% ice-cold RGF BME Type 2 PathClear (Cultrex, R&D Systems) and 10% Dulbecco’s modified Eagles Medium/F12 (DMEM/F12) (Gibco) and left to polymerize for 15’ at 37oC. Afterwards, organoids were maintained in DMEM/F12 (Gibco), supplemented with 1x Penicillin-Streptomycin (Gibco), 10 mM HEPES (Gibco), 1x Glutamax (Gibco), 1x B27 (Gibco) 1.25 mM N-acetylcysteine (Sigma Aldrich) , 50 ng/ml mEGF (Gibco), 10% final volume Noggin conditioned medium, 10 mM nicotinamide (Sigma Aldrich), 500 nM A83-01 (Cayman Chemical), and 10 mM SB202190 (Cayman Chemical) at 37oC, 5% CO2.

extract_protocol:
RNA was extracted from snap-frozen organoid pellets using the RNeasy RNA extraction kit (Qiagen) with DNaseI treatment.
A total of 1 µg RNA per replicate was used as input to generate RNA-seq libraries with the KAPA Stranded RNA-Seq Kit with RiboErase (HMR), following the manufacturer’s instructions with the following adjustments. Fragmentation of RNA was performed for 6.5 minutes at 94°C for a desired library insert size of 200-300 bp, and at the end of the library preparation, libraries were subjected to a 0.8 X cleanup, followed by a 1 X clean-up.

value: colon

value: colorectal cancer organoid


title: TPO4/AKPS organoids, replicate 3


title: wild type mouse bladder mucosa urinary tract infection day 1

data_processing:
Illumina CASAVA v1.8 was used for base calling
(1) Discard reads with adaptor contamination; (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%); (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
TopHat2 was used for aligment, TMR (total mapped reads) larger than 70%  and MMR (Multiple mapped reads) less than 10% are used
HTSeq software was used to analyze the gene expression levels, using the union mode. FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expression or not.
Supplementary files format and content: excel files that list all genes after differential expression analysis

extract_protocol:
RNeasy RNA isolation kit (Qiagen) was used to isolate total RNA from micro-dissected bladder urothelium.
1, Total RNA qualification; 2, mRNA enrichment; 3, Double-stranded cDNA synthesis; 4, End repair, poly-A and adaptor addition; 5, fragments selection and PCR; and 6, Library qualifty assessement.

value: Acute urinary tract infection


title: TPO4/AKPS organoids, replicate 2


title: lung, La-Cer, rep3

city: shanghai

first: JIE

last: ZHENG

state: shanghai

address: 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai jiaotong university

description:
emollient(La-Cer)
Y3-Lu

data_processing:
Bcl2fastq (v2.17.1.14) were used for base calling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v 1.9.1)
Trimmed sequence reads were mapped to GRCm38 usingHisat2(v2.0.1)
Assembly: GRCm38.100
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: lung

extract_protocol:
RNA was harvested using Eastep Super Total RNA Extraction Kit (Promega, Shanghai). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: mice were treated with 4nmol calcipotriol and 50μg Ovalbumin alone or with a linoleic acid-ceramide-containing emollient for 28 days before execution.

value: lung

value: female

tag: time

value: 28 days

value: WT

tag: disease state

value: AD


title: wild type mouse bladder mucosa PBS day 1

tag: tissue

value: PBS


title: IMQ_BZLF1, day10

value: BALB/c

tag: cell type

value: applying BZLF to the skin lesions in an IMQ-induced psoriasis mice model


title: C57bl/6 mice, C+P4

value: liver

value: PTH


title: TPO4/AKPS organoids, replicate 1


title: skin, La-Cer, rep3

description:
emollient(La-Cer)
Y3s

value: skin


title: C57bl/6 mice, C+P3


title: skin, La-Cer, rep2

description:
emollient(La-Cer)
Y2s


title: IMR32_SiCTR_Rep2

value: Neuroblastoma

value: siCTR


title: C57bl/6 mice, C+P2


title: TPO3/AKP organoids, replicate 3


title: skin, La-Cer, rep1

description:
emollient(La-Cer)
Y1s


title: TPO3/AKP organoids, replicate 1


title: TPO3/AKP organoids, replicate 2


title: C57bl/6 mice, C+P1


title: lung, AD, rep3

description:
AD
M4-LU


title: C57bl/6 mice, C3


title: lung, La-Cer, rep2

description:
emollient(La-Cer)
Y2-Lu


title: lung, La-Cer, rep1

description:
emollient(La-Cer)
Y1-Lu


title: H3R17me2a

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
CHIP-seq data was aligned using bowtie against hg19 version of the mouse genome and HOMER was used to create normalized bigwig files
Assembly: hg19
Supplementary files format and content: Prosessed files contains the CHIP-seq signal in bigwig format

source_name: A1847 cell line

extract_protocol:
A Zymo ChIP DNA Clean and Concentrator Kit (Zymo Research, catalog no. D5205) was used to purify the DNA for ChIP-seq.
For ChIP-seq, purified DNA was used for library construction using the NEBNext Ultra DNA Library Prep Kit (NEB, E7645) following the manufacturer’s instructions

value: A1847 cell line

tag: ChIP

tag: replicate


title: C57bl/6 mice, C1


title: C57bl/6 mice, C2


title: CARM1


title: lung, control, rep3

description:
control
c3lu

tag: Sex

value: control


title: lung, AD, rep1

description:
AD
M1-LU


title: KOC3-H1299-KO-control3

city: Buffalo

first: Jia

last: Fang

state: New York

address: Elm & Carlton Streets

department: Department of Pharmacology & Therapeutics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Quality control for the raw reads was performed with fastqc
Spliced alignment of the reads to the reference genome was done with TopHat2
Quality control was done using RSeQC
Mapped reads are quantified at the gene level in a raw counts matrix using HTSeq
Non-empty overlap option was used (maximal stringency)
Assembly: human genome build GRCh38.p7 and the corresponding GENCODE annotation version 25
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: H1299 cells

growth_protocol: Control and SETDB1 knockout H1299 cell lines were cultured in RPMI-1640 with FBS, penicillin/streptomycin, and puromycin.

extract_protocol:
Cells were collected, flash frozen with liquid nitrogen. Total RNA was purified with commercial kits (Illumina, Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Non-small cell lung cancer

tag: sgrna

value: Control sg2

tag: cell line


title: 1303_GA_Lysate

source_name: blood - PBMC

value: yes

value: Lysate

value: PBMC


title: TPO3/AKP organoids, replicate 4

value: colon

value: colorectal cancer organoid


title: lung, control rep2

description:
control
c2lu

value: lung

value: female

value: 28 days

value: WT

tag: treatment


title: lung, control, rep1

description:
control
c1lu


title: KOC1-H1299-KO-control1


title: KOC2-H1299-KO-control2


title: KO3-H1299-SETDB1-KO3

value: hSETDB1 sg1


title: skin, AD, rep2

description:
AD
om3s

value: skin

value: AD


title: skin, AD, rep3

description:
AD
om4s


title: KO2-H1299-SETDB1-KO2


title: lung, AD, rep2

description:
AD
M2-LU


title: 1142_GA_Lysate


title: IMR32_pTetOne_H2_T_r1

data_processing:
Basecalls performed using CASAVA version 1.4
Data was analyzed by Encode ATAC-seq pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

source_name: IMR32 cells

growth_protocol: The HAND2 stably transfected IMR32 cells (IMR32tetHAND2) cells are cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Chromatin extraction and ATAC-seq was performed as previously described by William J Greenleaf and Howard Y Chang's group (Nature Methods. 960 | VOL.14 NO.10 | OCTOBER 2017, PMID 28846090).
Libraries were prepared according to the protocol from William J Greenleaf and Howard Y Chang's group using Illumina's Nextera DNA library prep kit.

treatment_protocol: ATACseq experiment was performed after IMR32tetHAND2 cells being treated with or without Dox for 36 hr.

value: Neuroblastoma


title: skin, AD, rep1

description:
AD
om2s


title: KO1-H1299-SETDB1-KO1


title: skin, control, rep2

description:
control
c3s


title: skin, control, rep3

description:
control
c4s


title: skin, control, rep1

description:
control
c2s


title: TU0137_Lysate

value: no


title: IMR32_pTetOne_H2_C_r2


title: IMR32_pTetOne_H2_C_r1


title: IMR32_siPHOX2B_r2

treatment_protocol: siRNAs were transiently transfected into IMR32 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 24hr or 72 hr, then ATAC-seq experiment was performed.

tag: transfection


title: cutaneous wound,10µMCAP, Day6 rep2

city: Taipei

first: SU-YI

last: SU

address: No. 280, Sec. 4, Renai Rd.,

department: Department of Medical Research

country: Taiwan

institute: Cathay General Hospital

data_processing:
BaseCall Conversion: Illumina's official basecalling program, the bcl2fastq conversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Adaptor Clipping: Adaptors are short nucleotide sequences which have to be ligated to every single DNA molecule during library preparation, and allow DNA fragments to bind to a flow cell for next generation sequencing. Removal of adapter sequences, a process called 'adaptor trimming', or clipping, is one of the first steps in analyzing NGS data.
Sequence Quality Trimming: Quality trimming was proformed to remove low quality reads/bases. Lower quality bases from the the 3' end were removed using a sliding-window approach as the per base quality gradually drops toward the 3' end of reads.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: cutaneous wound

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technology, USA).
RNA libraries for RNA-seq were prepared using SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) following manufacturer's protocols.

treatment_protocol:
The experimental mice (10 µM capsaicin) were received 200 µL of capsaicin (10 µM, Sigma-Aldrich Corp., St. Louis, MO, USA) once daily, through Pluronic F127 gel (25% in saline; Merck, Darmstadt, Germany) topically.
Aliquots of 200 µL of Pluronic F127 were applied on the wounds once daily in the sham group (Pluronic-F127) for the same duration.

value: cutaneous wound

value: male

value: 10 uM capsaicin in Pluronic F127

value: Day 6


title: IMR32_siPHOX2B_r1


title: cutaneous wound,10µMCAP, Day6 rep3


title: cutaneous wound, P-F127, Day6 rep2

value: Pluronic F127


title: IMR32_siGATA3_r2


title: cutaneous wound, P-F127, Day6 rep3


title: IMR32_siGATA3_r1


title: IMR32_siCtrl_r2

value: siCtrl


title: cutaneous wound,10µMCAP, Day3 rep3

value: Day 3


title: cutaneous wound,10µMCAP, Day3 rep2


title: IMR32_8_siH_M_r2


title: IMR32_pTetOne_H2_T_r2


title: TU0005_Lysate

value: Lysate

value: PBMC


title: IMR32_siCtrl_r1


title: TU0055_Lysate


title: IMR32_7_siMYCN_r2

value: siMYCN


title: cutaneous wound,10µMCAP, Day3 rep1


title: IMR32_5_siCtrl_r2


title: IMR32_6_siHAND2_r2


title: CRISPR ATRX KO clone KO-B_MSCV EV control_rep 1

data_processing:
Conventional base calls using Illumina 1.9
Reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b with soft clipping clip3pNbases = 10. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.6.3. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: Single matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted from monolayer cell cultures using miRNeasy Mini kit (Qiagen, Germantown, MD). 300ng of RNA was used for cDNA prep and construction of sequencing libraries using KAPA Stranded mRNA-Seq kit for Illumina platforms - KR0960 - v6.17.
Library construction was performed as per manufacturer's instructions on Sciclone G3 Liquid Handler, 10 PCR cycles.

value: Glioma

tag: genotype

value: ATRX KO - IDH1 WT


title: IMR32_4_siH_M_r1


title: 222 NK killing CRISPR screen control, repeat-2

city: Bethesda

first: Xiaoxuan

last: Zhuang

address: 10 Center Dr, RM 6N105

institute: NIH

description:
ctrl_2
new_counts.count_normalized.txt
221_mle_as_duplicates_useCTRLgRNAs_more_than5gRNAs.gene_summary.csv

data_processing:
Mapping the the library file using MAGeCK pipeline.
sgRNA count and defferential analysis by MAGeCK
Supplementary files format and content: sgRNA counts and differental analysis, normalized CPMs

extract_protocol:
For genomic DNA extraction, the kit QIAmp DNA Blood Max kit (Qiagen) for large scale and PureLink DNA mini kit (Invitrogent) for small scale was used. RNA extraction was done by Allprep DNA/RNA mini kit (Qiagen)
Follow the protocol from this paper: Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening PMID 28333914

value: B cell lymphoblast

value: Transduced with Cas9 and GeCKO V2 CRISPR library

value: No


title: cutaneous wound, P-F127, Day3 rep1


title: cutaneous wound,10µMCAP, Day6 rep1


title: Pancreas islet, control, rep 2

city: Paris

first: Stuart

last: EDELSTEIN

address: 29 rue du Faubourg Saint Jacques, Pépinière Paris Santé Cochin

institute: Scipio bioscience

description: Scipio bioscience. All provided R1 and R2 FASTQ files are already demultiplexed by sample index.

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
For each sample, the R1 (resp. R2) FASTQ files of the 3 sequenced sample subfractions were concatenated into one R1 (resp. R2) FASTQ file.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools based on 87,5 millions input raw reads randomly sampled from the concatenated R1 FASTQ file of the sample.
The provided processed data is composed of one count matrix per sample at full sequencing depth (i.e. no raw read downsampling was applied as sequencing depths were similar between the 2 replicate samples).
Data post-processing (filtering, normalization, HVG, PCA, 2D embedding, clustering, DGE) was performed using Seurat and automated cell annotation was performed using SingleR algorithm and the reference dataset BaronPancreasData.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for mouse species (GRCm38).  Unique Genome Name in Cytonaut v6.7.0: Mouse_Scipio_2022_A;  Species: Mus_musculus;  Genome Source: ensembl;  Genome Version: GRCm38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/mus_musculus/dna/;  Annotation Source: ensembl;  Annotation Version: 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/mus_musculus/.
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: pancreas

extract_protocol:
For each replicate, scRNA was extracted from a 10,000 pancreas islet cells according to the RevGel-Seq protocol instructions. Pancreas islets were at fisrt isolated from whole pancreas by collagenase injection followed by handpicking under microscope. The islets were then dissociated with trypin-EDTA and the cell suspension was re-suspended in DPBS with 2% FBS and 0.5mM EDTA prior to following RevGel seq protocol. Barcode beads and cells are attached via a bifunctional chemical linker. These tandems are dispersed in an hydrogel in the liquid state and immobilized upon gelation. Following cell lysis, polyA+ RNA molecules are captured on the barcoded beads via polyA-polyT interactions. Barcoded beads (and associated RNA molecules) are recovered following degelation, and reverse transcription and subsequent second strand synthesis are performed. Each sample is then split in 8 subfractions and PCR-amplified to obtain cell barocded cDNA. The amplified cDNA was pooled into three groups, 2 groups from 3  PCR tubes and 1 group of 2 PCR tubes, for purification with 0.6X SPRI select for subsequent sequencing library preparation.
Sequencing libraries were prepared with illumina's Nextera XT kit for each of 3 purified barcoded cDNA according to manufacturer's instructions with the following adaptations: 600pg of the cDNA was subjected to tagmentation reaction. The tagmented DNA was amplified by 12 cycles PCR. During this PCR, DNA fragments with cell barcode sequence at one end are selectively amplified by using a primer pair of custom P5-read1 primer to the original barcode end and Nextera N7xx P7 index primer to the tagmented end. Paired end sequencing was done.

value: pancreas islet cell

value: pancreas

value: 8 weeks


title: cutaneous wound, P-F127, Day6 rep1

value: cutaneous wound

value: male


title: Pancreas islet, control, rep 1


title: IMR32_2_siHAND2_r1

value: Neuroblastoma


title: CRISPR ATRX KO clone KO-B_MSCV IDH1-R132H_rep 1

city: Durham

first: David

last: Ashley

address: 203 Research Dr, MSRB1

institute: Duke University

value: ATRX KO IDH1-R132H


title: IMR32_1_siCtrl_r1

value: siCtrl