title: alpha-amanitin treated 2-cell embryo_12

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

data_processing:
Reads were mapped to mouse reference genome mm10, depleted for sex chromosomes with STAR2.5.1b using default settings. Genes from RefSeq database that have at least ten reads in 50% of the embryos of one condition were used for further analysis. Differentially expressed genes were obtained using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: FPM.txt: Tab-delimited text file includes FPM values.

source_name: alpha-amanitin treated 2-cell embryo

growth_protocol: 48h post injection of 5 IU pregnant mare serum fully grown oocytes at the germinal vesicle stage were obtained from ovaries of 6-8 weeks old F1(C57BL/6×DBA) female mice and transferred to M2 medium without BSA, supplemented with 0.2 mM 3-isobutyl-1-methylxanthine (IBMX; Sigma-Aldrich). After 10 min of Hoechst 33342 (0.05 μg/ml) incubation SN type GVOs were injected with morpholinos designed against Tet1-3 enzymes (Gene Tools, 100 μM, see table S1) co-injected with Dextran-tetramethyl-rhodamine (Invitrogen, 3000 MW, 100 μg/ml). Morpholino injected SN GVOs were washed in IMBX free α-MEM medium supplemented with 5% FBS and 10 ng/ml EGF and incubated in a humidified atmosphere with 6% CO2, 5% O2 and 89% N2 at 37 °C for 16-18 h to complete meiotic maturation. Sperm was isolated from the cauda epididymis of adult F1(C57BL/6×DBA) male mice and capacitated by pre-incubation for 1.5 h in pre-gassed HTF medium. In vitro matured oocytes were collected 16-18 h post injection of morpholinos. Mature MII oocytes were placed into a 100 μl drop of KSOM medium with capacitated sperm and incubated at 37 °C in a humidified atmosphere of 6% CO2, 5% O2 and 89% N2. 2-cell embryos were collected 29 hours following in vitro fertilization.

extract_protocol: 2-cell embryos were collected 29 hours following in vitro fertilization and zona pellucida was removed from 2-cell embryos. Libraries were constructed using Clontech SMARTer Ultra Low Input RNA Kit, followed by NEBNext DNA Library Prep Master Mix Set

treatment_protocol: control MO injected, in vitro matured- and fertilized- zygotes at 4hpf were cultured with 0.1mg/ml α-amantin (Sigma) and derived 2-cell embryos were collected 29hpf

tag: developmental stage

value: 2-cell embryo


title: IFITM3_25

status: Public on Nov 22 2021

type: SRA

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the mouse genome using STAR 2.7.0f.
Gene-level read counts were generated using STAR 2.7.0f.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

molecule: total RNA

organism: Mus musculus

source_name: lung

growth_protocol: Mice were housed in SPF facility

extract_protocol:
lung lobes were harvested aseptically at the indicated time points and homogenized in Trizol for RNA extraction. RNA was extracted using the DirectZol kit (Zymo Research)
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: intranasal challenge with influenza virus in 50 microliter of PBS

tag: tissue

value: lung

tag: ifitm3 genotype

value: WT

tag: Sex

value: F

tag: first challenge strain

tag: second challenge strain

tag: second challenge days post infection


title: IFITM3_24


title: alpha-amanitin treated 2-cell embryo_11

molecule: polyA RNA

tag: strain


title: IFITM3_29

value: mock


title: IFITM3_30

value: KO


title: 5hmc data of TET2 knockout hippocampus replicate 2

city: Atlanta

first: Yuwen

last: Zhao

state: GA

address: 615 Michael ST NE, Suite 305

institute: Emory University

description: genome-wide 5hmC profiles

library_source: genomic

data_processing:
Library strategy: 5hmC- seq
The raw fastq files generated from the high-throughput sequencing machine were aligned to the mouse genome (mm9) using Bowtie2
The whole mouse genome (mm9) was cut into 500bp bins, and all bins with genomic features and nearby gene were annotated by Homer
The DhMRs detection was performed by comparing the bin-level read counts between cases and controls using DESeq2
After accounting for multiple testing, the bins with an adjusted p value smaller than 0.20 was deemed as DhMRs
Gene ontology and pathway enrichment analysis was performed with EnrichR
Genome_build: mm9
Supplementary_files_format_and_content: KO_WT_raw_readcounts

molecule: genomic DNA

source_name: hippocampus

extract_protocol:
5hmC enrichment was performed following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A), 20 ng of input genomic DNA or 5hmC-captured DNA were used for DNA libraries preparation (Antibody：5hmC，Active Motif，Cat# 39769, RRID:AB_10013602). Illumina Hi-seq 2000 machines were used for running sequencing libraries.
5hmC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: unstressed

tag: condition

value: unstressed

value: hippocampus

tag: genotype

value: Tet2 CKO


title: IFITM3_23


title: alpha-amanitin treated 2-cell embryo_9


title: alpha-amanitin treated 2-cell embryo_6


title: IFITM3_22


title: alpha-amanitin treated 2-cell embryo_7


title: alpha-amanitin treated 2-cell embryo_8


title: IFITM3_21

value: M


title: alpha-amanitin treated 2-cell embryo_10


title: alpha-amanitin treated 2-cell embryo_4


title: IFITM3_19


title: IFITM3_20


title: IFITM3_18


title: alpha-amanitin treated 2-cell embryo_1


title: IFITM3_15


title: IFITM3_16


title: alpha-amanitin treated 2-cell embryo_3


title: alpha-amanitin treated 2-cell embryo_2


title: IFITM3_13


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_10

source_name: 2-cell embryo


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_11


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_9


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_8


title: IFITM3_10


title: alpha-amanitin treated 2-cell embryo_5


title: IFITM3_9


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_3


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_5


title: Tet3-morpholino injected 2-cell embryo_11


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_6


title: IFITM3_11


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_7


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_4


title: IFITM3_17


title: IFITM3_3


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_1


title: IFITM3_2


title: IFITM3_6


title: IFITM3_12


title: IFITM3_4


title: Tet3-morpholino injected 2-cell embryo_10


title: IFITM3_14


title: IFITM3_7


title: Tet3-morpholino injected 2-cell embryo_7


title: Tet1-, Tet2-, Tet3-morpholino injected 2-cell embryo_2


title: Tet3-morpholino injected 2-cell embryo_6


title: Tet3-morpholino injected 2-cell embryo_8


title: Tet3-morpholino injected 2-cell embryo_9


title: female_6wks

city: Saint Louis

first: Eryn

middle: E

last: Dixon

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description:
Spatial transcriptomics
mRNA

data_processing:
SpaceRanger: FASTQ files were aligned to mm10 reference and manually aligned to respective H&E stain images using 10X Genomics Space Ranger count (spatial 3’ v1; spaceranger-1.2.1). Aligned sequencing libraries from all time point samples were integrated using agg.
Data generation: Resulting image aligned sequencing files from SpaceRanger were loaded into (1) Seurat - Version 4.0.3 - https://satijalab.org/seurat/articles/spatial_vignette.html, (2) SPOTlight - https://marcelosua.github.io/SPOTlight/#07_Visualization, and (3) Giotto - http://spatialgiotto.rc.fas.harvard.edu/giotto.dataset.example.html. All reference data was previously published by Kirita et al., 2020 and available on http://humphreyslab.com/SingleCell/.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_processed.tar.gz: Each processed spatial data file includes the outputs of SpaceRanger - cloupe, molecule_info.h5, filtered_feature_matrix.h5, metrics_summary.csv, molecule_info.h5, raw_feature_bc_matrix.h5, and all spatial images (jpg and png) with scale factors and tissue positions.

source_name: kidney

extract_protocol:
Mice were euthanized according to approved IACUC protocols and kidney tissues were collected at four time points following injury, plus from one sham control mouse. All tissues were frozen and processed according to 10X Visium instructions.
Spatial RNA libraries were generated using standard protocol from 10X Visium.
Spatial RNA libraries from individual kidney slices (n=1 per timepoint).

treatment_protocol: Kidney injury was elicited in C57BL6 female mice (8-10 weeks of age) using a bilateral ischemia reperfusion injury paradigm where renal pedicles were clamped for 34 minutes under 1.8% isoflurane.

value: Female

value: Kidney

tag: treatment

value: Bi-IRI surgery

tag: timepoint

value: 6 weeks post Bi-IRI surgery

tag: platform

value: 10X Visium


title: female_2dps

description:
Spatial transcriptomics
mRNA

value: 2 days post Bi-IRI surgery


title: Tet3-morpholino injected 2-cell embryo_5


title: IFITM3_5


title: female_4hr

description:
Spatial transcriptomics
mRNA

value: 4 hours post Bi-IRI surgery


title: Tet3-morpholino injected 2-cell embryo_4

value: 2-cell embryo


title: AG120_replicate_3

city: Cambridge

first: Kira

middle: Eileen

last: Olander

state: MA

address: 75 Ames St

department: Cancer Program

institute: Broad Institute

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v3.0.1).
Data normalization, filtering, dimensional reduction, and gene set scoring was done using Scanpy package (v1.7).
Differential expression was performed using a logistic regression model.
GSEA Pre-ranked was used to find enriched hallmark gene sets (v4.1.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples.
Supplementary_files_format_and_content: h5 files

source_name: Immune Infiltrate

growth_protocol: Mice were inoculated, orthotopically, with mIDH1 ICC tumor cells.

extract_protocol:
Tumors were harvested on day 13 post-inoculation, disassociated using the Miltenyi Mouse Tumor Dissociation Kit and gentleMACS Octo-Dissociator (Miltenyi) as per manufacturer's instructions. Tumor-infiltrating lymphocytes were enriched using Lymphocyte-M (Fisher Scientific) density gradient followed by CD45+ positive selection (Miltenyi). Cells were counted and loaded on to 10x device (10X Genomics).
Libraries were generated following standard 10X protocol (Manual CG000086 Revision K to L)  for 10X single-cell 5' RNA-seq v1.

treatment_protocol: Mice were administered AG120 treatment for six days, starting on the 7th day following challenge.

tag: cell type

value: CD45+ Immune Cells

tag: background strain

value: mIDH1 (R132C) orthotopic ICC


title: SINVNoVmB2：tick microinjection 14dpi

city: Shanghai

first: Yang

last: Li

address: 2005 Songhu Road

country: China

institute: Fudan University

description: tick infection with SINVNoVmB2 by microinjection

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Genome_build: AF174533.1,AF174534.1;KX641909.1,KX641913.1,KX641917.1;J02363.1;NC_001560.1
Supplementary_files_format_and_content: mapping results files generated by bowtie1.1.2

organism: Haemaphysalis longicornis

source_name: tick whole body

extract_protocol:
Total RNA was extracted from ticks using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

tag: infection

tag: injection way

value: microinjection


title: AG120_replicate_4


title: IFITM3_8

value: lung

value: WT

value: F


title: IFITM3_1

value: KO


title: Tet3-morpholino injected 2-cell embryo_3

tag: developmental stage


title: female_12hr

description:
Spatial transcriptomics
mRNA

tag: tissue

value: 12 hours post Bi-IRI surgery


title: female_sham

description:
Spatial transcriptomics
mRNA

value: Sham control

value: 2 days after sham surgery


title: SINVNoVB2：tick microinjection 14dpi

description: tick infection with SINVNoVB2 by microinjection


title: Tick mock

description: tick without infection

value: mock


title: control-morpholino injected 2-cell embryo_10


title: NoV△B2: tick microinjection 4dpi

description: tick infection with NoV△B2 by microinjection


title: SINV: tick microinjection 5dpi repeat

description: tick infection with SINV by microinjection

value: SINV


title: Tet3-morpholino injected 2-cell embryo_1


title: AG120_replicate_2


title: SFTSV: tick replete on BALB/c 2dpi

description: tick infection with SFTSV by blood-feeding on BALB/c

value: SFTSV

value: blood-feeding

tag: mice strains

value: BALB/c


title: control-morpholino injected 2-cell embryo_8


title: AG120_replicate_1


title: Vehicle_replicate_2

value: Vehicle


title: Vehicle_replicate_4


title: NoV: tick microinjection 4dpi

description: tick infection with NoV by microinjection

value: NoV


title: Tet3-morpholino injected 2-cell embryo_2

value: 2-cell embryo


title: Vehicle_replicate_3

value: CD45+ Immune Cells

value: mIDH1 (R132C) orthotopic ICC


title: Vehicle_replicate_1


title: control-morpholino injected 2-cell embryo_9


title: control-morpholino injected 2-cell embryo_7


title: SINV: tick replete on C57BL/6 6dpi repeat

description: tick infection with SINV by blood-feeding on C57BL/6


title: Samples #24

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep4

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

growth_protocol: mouse Embryonic Stem Cells  were cultered in DMEM High Glucose supplemented with 15% FBS and 1x of penicillin/streptomycin, 1x nonessential Amino Acids, 1x GlutaMax, 1x 2-beta-mercaptoethanol and 1000U/mL LIF

extract_protocol:
RNA was quantified and mixed at 10ng/µl. Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific).
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. Quality of libraries was assessed by using screen tape High sentisivity DNA D1000 (Agilent Technologies).

treatment_protocol: Total starvation was performed by replacing culture media with 1x Trypsin in Phosphate-buffer saline (PBS) after washing with PBS

tag: genotype/variation

value: BetaCatenin Knockout

tag: culture


title: control-morpholino injected 2-cell embryo_5


title: control-morpholino injected 2-cell embryo_6

extract_protocol:
zona pellucida was removed from 2-cell embryos
0.5uL of 1:1.25M dilution of ERCC RNA Spike-In Mix 1 (Life Technologies) were added to each sample. Libraries were constructed using Clontech SMARTer Ultra Low Input RNA Kit, followed by NEBNext DNA Library Prep Master Mix Set


title: control-morpholino injected 2-cell embryo_4


title: control-morpholino injected 2-cell embryo_1

growth_protocol: 48h post injection of 5 IU pregnant mare serum fully grown oocytes at the germinal vesicle stage were obtained from ovaries of 6-8 weeks old F1(C57BL/6×DBA) female mice and transferred to M2 medium without BSA, supplemented with 0.2 mM 3-isobutyl-1-methylxanthine (IBMX; Sigma-Aldrich). After 10 min of Hoechst 33342 (0.05 μg/ml) incubation SN type GVOs were injected with morpholinos designed against Tet1-3 enzymes (Gene Tools, 100 μM, see table S1) co-injected with Dextran-tetramethyl-rhodamine (Invitrogen, 3000 MW, 100 μg/ml). Morpholino injected SN GVOs were washed in IMBX free α-MEM medium supplemented with 5% FBS and 10 ng/ml EGF and incubated in a humidified atmosphere with 6% CO2, 5% O2 and 89% N2 at 37 °C for 16-18 h to complete meiotic maturation. Sperm was isolated from the cauda epididymis of adult F1(C57BL/6×DBA) male mice and capacitated by pre-incubation for 1.5 h in pre-gassed HTF medium. In vitro matured oocytes were collected 16-18 h post injection of morpholinos. Mature MII oocytes were placed into a 100 μl drop of KSOM medium with capacitated sperm and incubated at 37 °C in a humidified atmosphere of 6% CO2, 5% O2 and 89% N2.


title: control-morpholino injected 2-cell embryo_3


title: Samples #22

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep2


title: Samples #20

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep4


title: Samples #21

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep1


title: Samples #18

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep2


title: gADC1-PB

city: Nanjing

first: wei

last: zhao

state: Jiangsu

address: Gongqingtuan RD No.32

institute: Nanjing first hospital

data_processing:
Single cells were selected using microfluidic technology based on 10 × Genomics plat_x0002_form.
Using 10 × Genomics official analysis software Cell Ranger
Using the Seurat for further filtration, standardization, the classifi_x0002_cation of the cells, each subgroup analysis and marker gene screening differentially expressed genes
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
Single cells were selected using microfluidic technology based on 10 × Genomics plat_x0002_form.
DNA libraries were amplified by PCR, and high throughput sequencing was performed using Illumina sequencing platform’s double-terminal sequencing mode.

treatment_protocol: did not receive any other   therapy before surgery

value: PBMC

tag: Stage

value: ⅠB

tag: site

value: lesser curvature of antrum


title: gADC4-T

source_name: tumor tissue

value: tissue

value: Ⅲa

value: Antrum


title: gADC2-T

value: lesser curvature


title: gADC3-T

value: ⅢB

value: Gastric cardia


title: gADC1-P

source_name: para-carcinoma tissues


title: Samples #15

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep3


title: gADC3-P


title: gADC1-T


title: Samples #16

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep4


title: Samples #14

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep2


title: Samples #17

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep1


title: control-morpholino injected 2-cell embryo_2

tag: strain


title: Samples #13

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep1


title: Samples #23

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated with constant BetaCatenin overexpression, biological rep3


title: Samples #10

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep2


title: Samples #12

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep4


title: pNK PE_rep1

city: Hefei

first: xiuxiu

last: xu

state: Anhui

address: No.96, JinZhai Road Baohe District

institute: university of science and technology of china

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Homo sapiens GRCh38 using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with RPKM values for every gene and every sample

source_name: NK cells

extract_protocol:
NK cells were sorted. Total RNA was extracted using the TRIzol reagent and treated with DNaseI. An RNA library was prepared using 2 μg qualifited RNAs.
The KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth) was used for the construction of the RNA library.

value: peripheral blood

value: NK cells

tag: phenotype

tag: disease state

value: patient with severe pre-eclampsia

tag: age

tag: gestational age


title: pNK HP_rep3

value: healthy pregnant women (n=3)


title: Samples #11

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep3


title: pNK PE_rep2


title: pNK PE_rep3


title: pNK HP_rep2


title: pNK HP_rep1

value: healthy pregnant women (n=2)


title: Samples #9

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep1


title: Samples #19

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions but differentiated without further BetaCatenin overexpression, biological rep3


title: Control #8

description: Transcriptome profile of BetaCatenin Knockout in differentiating culture conditions, biological rep4

value: differentiating culture conditions


title: HCT116_BRWD_TKO_Clone1_PHIP_Rescue_R2

city: Chicago

first: Marc

last: Morgan

state: IL

address: 303 East Superior St, SQI 7-511

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: HCT116 cells were grown in DMEM supplemented with 15% fetal bovine serum. Mouse ESCs were grown in N2/B27 medium supplemented with 2i and leukemia inhibitory factor (LIF)

extract_protocol:
RNA was prepared usng a Qiagen Rneasy Miniprep kit. ChIP DNA was purified using phenol:chloroform
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were subjected to neuronal differentiation by culture in N2/B27 medium on lamnin coated plates.

tag: cell line

value: Colon carcinoma

tag: genotype

value: BRWD-TKO


title: Control #5

description: Transcriptome profile of BetaCatenin Knockout in differentiating culture conditions, biological rep1

value: BetaCatenin Knockout


title: Hypertrophic scar, patient 2

type: RNA

city: SHENYANG

first: KAI

last: TAO

state: State

address: Reconstructive and Plastic Surgery, The General Hospital of Northern Theater Command, No. 83, Wenhua Road, Shenhe District

description: Test

data_processing:
The normalization and data analysis were performed per the analysis tools operation guidance (https://www.genecopoeia.com/product/mirna-qpcr-arrays/).
The average of the housekeeping genes, SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, were used to mormalize gene expression.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: Hypertrophic scar samples

label_protocol: miRNA qPCR Assays were conducted with the miProfile™ Custom miRNA qPCR Arrays profile (Genecopoeia, Rockville, MD, USA) following the vendor’s instructions. 250ng RNA was reverse transcribed to cDNA with the miRNA First-Strand cDNA Synthesis Kits (Cata No. QP017, Genecopoeia) and the qPCR Mix Kits (QP001, Genecopoeia). qPCR was performed in plate format A using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR procedures were listed below. 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: Tumor tissues were collected simultaneously. All the resected samples were placed immediately into liquid nitrogen and stored at - 80°C.

extract_protocol: RNA was extracted by RNA isolation kit (Cat.No.83913, Sigma-Aldrich) per the manufacturer's protocol. 250 ng amount of RNA was reverse transcribed to cDNA by a Reverse Transcription Reaction kit (Qiagen, Hilden, Germany).

tag: condition

value: Hypertrophic scar

tag: Sex

value: male


title: Hypertrophic scar, patient 3

institute: Reconstructive and Plastic Surgery, The General Hospital of Northern Theater Command, No. 83, Wenhua Road, Shenhe District

description: Test


title: Control #7

description: Transcriptome profile of BetaCatenin Knockout in differentiating culture conditions, biological rep3


title: PP_6_3.RNA

city: New York

first: Jordan

middle: Benjamin

last: Metz

state: NY

address: 3960 Broadway Room 203A

department: Systems Biology

institute: Columbia University

description:
PP_6_3
total RNA sequencing

data_processing:
Basecalls were performed on-instrument.
Ribosome profiling: Trailing adapter sequence was removed with Cutadapt using parameters -m 25 -a CTGTAGGCACCATCAAT. Ligation-free ribosome profiling: Trailing adenines (poly-A sequence) and preceding degenerate sequence added by template-switching enzyme were removed with Cutadapt v3.5 using parameters -m 25 -u 3 -a A{10}  --discard-untrimmed.  riboPLATE-seq/PLATE-seq: Trailing poly-A sequence were removed with Cutadapt using parameters -m 25 -a A{100}.
Ribosome profiling and RNA-seq: Libraries were depleted of ribosomal RNA by alignment to 45S+5S rRNA sequences from GRCh38 with Bowtie2 v2.2.5 and discarding aligned reads, allowing alignments to contain a maximum of one mismatch.
PLATE-seq, riboPLATE-seq: PLATE-based libraries were first demultiplexed by the identity of the first read, containing the barcode sequence. This created a reference table mapping every sequenced fragment to its original well, used downstream for demultiplexing aligned reads.
PLATE-seq, riboPLATE-seq, ribosome profiling, RNA-seq: Remaining reads were retained and aligned to the GRCh38 assembly of the human genome with STAR v2.7.9a using default parameters.
PLATE-seq, riboPLATE-seq: Multiplexed aligned reads were demultiplexed using the reference built from Read 1 barcodes, generating 96 PLATE-seq and 96 riboPLATE-seq libraries per pooled library.
PLATE-seq, riboPLATE-seq, Ribosome profiling, RNA-seq: Alignments to the exons of genes in the GRCh38 RefSeq annotation were counted with featureCounts v2.0.1; Forward-stranded ribosome profiling alignments were counted with the parameters -s 1 and reverse-stranded RNA-seq alignments were counted with -s 2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count matrix for all annotated genes in all samples. The first row is unique IDs identifying each sample's drug treatment condition or ERCC spike-in status, barcode index number, and either sequence barcode for riboPLATE/PLATE-seq libraries or "ribo"/"rna" for ribosome profiling and RNA sequencing, respectively. The first column contains all gene names.

source_name: TS543 neurosphere tissue culture

growth_protocol: TS543 (riboPLATE/PLATE/riboseq/RNAseq) : TS-543 glioma neurospheres were seeded in a 96-well tissue culture plate at passage #11, to a starting density of 50K cells/mL, in 150 uL NeuroCult NS-A complete medium per well. Separately, passage #11 TS543 were seeded in a 6-well tissue culture plate (2mL medium/well), using the same media and to the same density. Cultures were allowed to expand for 36 hours. Wi38 (riboPLATE_ERCC/PLATE_ERCC) : Wi38 human fibroblasts were seeded in a 96-well plate at 3,000 cells/well in 60uL culture media, 36 hours prior to cell lysis.

extract_protocol:
PLATE-seq: Following lysis in a polysome-preserving buffer containing RNase inhibitors, cycloheximide, and magnesium, all polyadenylated RNA was isolated by pulldown on a poly(T) capture plate. riboPLATE-seq: Following lysis in polysome-preserving buffer containing RNase inhibitors, cycloheximide, and magnesium, ribosome-associated RNA was isolated by indirect IP, in which lysates were combined with streptavidin-coated magnetic beads following a pre-incubation with biotinylated y10b anti-rRNA antibody. Next, the polyadenylated subset of this ribosome-associated RNA was isolated with use of a poly(T) capture plate. Ribosome Profiling: Monosomes were isolated from RNase I-digested TS543 lysates on a sucrose gradient fractionator. RNA-Seq: Total RNA was isolated from TS543 lysates using a Qiagen RNeasy kit (cat no. 74104) and ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit from Illumina (Cat no. MRZH11124) according to the manufacturer’s instructions.
PLATE-seq/riboPLATE-seq: Polyadenylated RNA (for PLATE-seq) or ribosome-associated polyA RNA (for riboPLATE-seq) was barcoded through reverse transcription primed with barcoded, adapter-linked oligo(dT), after which single-strand cDNA were pooled. Second-strand synthesis with adapter-linked random hexamers, cDNA purification, and PCR enrichment were all performed on these 96-way multiplexed pools with the Hamilton Microlab STAR liquid handling robot according to the PLATE-seq protocol (Bush et al, 2017). Ribosome profiling : Conventional ribosome profiling libraries were prepared from size-selected ribosome footprints following the protocol given in (Ingolia et al., 2012), with minor modifications. Ligation-free ribosome profiling : Ligation-free ribosome profiling libraries were prepared from dephosphorylated foot-prints (~ 28-34 nucleotides in length) using a commercially available kit (SMARTer small RNA-Seq Library Preparation Kit, Clontech, Cat no. 635029) following manufacturer’s instructions.   RNA-Seq : rRNA depleted total RNA samples were converted to  strand-specific sequencing libraries using the NEBNext® Ultra™ Directional RNA Library Prep Kit from Illumina (Cat no.E7420S).

treatment_protocol: Drugs were dissolved in DMSO to create stock solutions, which were then diluted with NS-A basal medium lacking growth factors and heparin. Drug treatments and concentrations consisted of 50nM AZD8055, 625nM PP242, 100nM BKM120, 1uM MNK-i1, and 50uM 4EGi-1, including in pairwise combination-treated samples. Excluding 30-minute-treated DMSO and PP242 ribosome profiling and RNA sequencing samples, drug treatment proceeded for 6 hours in the tissue culture incubator prior to lysis.

tag: cell type

value: TS543 glioblastoma

tag: passages

tag: treatment

tag: spike-in

tag: library strategy

value: RNA-Seq


title: Control #6

description: Transcriptome profile of BetaCatenin Knockout in differentiating culture conditions, biological rep2

tag: genotype/variation

tag: culture


title: Samples #8

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep4

source_name: BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture, biological rep4


title: Hypertrophic scar, patient 1

description: Test


title: adjacent, patient 3

description: Control

source_name: normal skin samples

value: normal


title: HCT116_BRWD_TKO_Clone1_PHIP_Rescue_R1


title: adjacent,patient 1

description: Control


title: adjacent,patient 2

description: Control


title: HCT116_BRWD_TKO_Clone2_PHIP_Rescue_R1


title: DMSO_6_1.RNA

description:
DMSO_6_1
total RNA sequencing

value: DMSO (6 hrs)


title: DMSO_6_2.RNA

description:
DMSO_6_2
total RNA sequencing


title: DMSO_6_4.RNA

description:
DMSO_6_4
total RNA sequencing


title: HCT116_BRWD_TKO_Clone2_RNA_R2


title: Samples #6

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep2

source_name: BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture, biological rep2


title: DMSO_6_3.RNA

description:
DMSO_6_3
total RNA sequencing


title: PP_30_2.RNA

description:
PP_30_2
total RNA sequencing


title: Samples #7

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep3

source_name: BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture, biological rep3


title: PP_6_1.RNA

description:
PP_6_1
total RNA sequencing


title: PP_6_2.RNA

description:
PP_6_2
total RNA sequencing


title: Samples #4

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep4

source_name: BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture , biological rep4


title: Samples #5

description: Transcriptome profile of BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep1

source_name: BetaCatenin Knockout rescued with high amout of exogenous BetaCatenin in pluripotent culture, biological rep1


title: PP_30_3.RNA

description:
PP_30_3
total RNA sequencing


title: HCT116_BRWD_TKO_Clone1_RNA_R1


title: DMSO_30_2.RNA

description:
DMSO_30_2
total RNA sequencing

value: DMSO (30 min)


title: HCT116_BRWD_TKO_Clone2_RNA_R1


title: DMSO_30_1.RNA

description:
DMSO_30_1
total RNA sequencing


title: HCT116_BRWD_TKO_Clone1_RNA_R2


title: DMSO_30_3.RNA

description:
DMSO_30_3
total RNA sequencing


title: Samples #2

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep2

source_name: BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture , biological rep2


title: control-morpholino injected 2-cell embryo_11

source_name: 2-cell embryo

tag: developmental stage

value: 2-cell embryo


title: Control #4

description: Transcriptome profile of BetaCatenin Knockout in pluripotent culture conditions, biological rep4

source_name: BetaCatenin Knockout in pluripotent culture , biological rep4

value: pluripotent culture


title: HCT116_WT_RNA_R2

value: wild-type


title: PP_6_3.RIBO

description:
PP_6_3
ligation-free ribosome profiling

data_processing:
Library strategy: (ribosome profiling)
Basecalls were performed on-instrument.
Ribosome profiling: Trailing adapter sequence was removed with Cutadapt using parameters -m 25 -a CTGTAGGCACCATCAAT. Ligation-free ribosome profiling: Trailing adenines (poly-A sequence) and preceding degenerate sequence added by template-switching enzyme were removed with Cutadapt v3.5 using parameters -m 25 -u 3 -a A{10}  --discard-untrimmed.  riboPLATE-seq/PLATE-seq: Trailing poly-A sequence were removed with Cutadapt using parameters -m 25 -a A{100}.
Ribosome profiling and RNA-seq: Libraries were depleted of ribosomal RNA by alignment to 45S+5S rRNA sequences from GRCh38 with Bowtie2 v2.2.5 and discarding aligned reads, allowing alignments to contain a maximum of one mismatch.
PLATE-seq, riboPLATE-seq: PLATE-based libraries were first demultiplexed by the identity of the first read, containing the barcode sequence. This created a reference table mapping every sequenced fragment to its original well, used downstream for demultiplexing aligned reads.
PLATE-seq, riboPLATE-seq, ribosome profiling, RNA-seq: Remaining reads were retained and aligned to the GRCh38 assembly of the human genome with STAR v2.7.9a using default parameters.
PLATE-seq, riboPLATE-seq: Multiplexed aligned reads were demultiplexed using the reference built from Read 1 barcodes, generating 96 PLATE-seq and 96 riboPLATE-seq libraries per pooled library.
PLATE-seq, riboPLATE-seq, Ribosome profiling, RNA-seq: Alignments to the exons of genes in the GRCh38 RefSeq annotation were counted with featureCounts v2.0.1; Forward-stranded ribosome profiling alignments were counted with the parameters -s 1 and reverse-stranded RNA-seq alignments were counted with -s 2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count matrix for all annotated genes in all samples. The first row is unique IDs identifying each sample's drug treatment condition or ERCC spike-in status, barcode index number, and either sequence barcode for riboPLATE/PLATE-seq libraries or "ribo"/"rna" for ribosome profiling and RNA sequencing, respectively. The first column contains all gene names.

value: OTHER:(ribosome profiling)


title: PP_30_2.RIBO

description:
PP_30_2
ribosome profiling


title: HCT116_BRWD_TKO_Clone2_PHIP_Rescue_R2


title: DMSO_6_4.RIBO

description:
DMSO_6_4
ligation-free ribosome profiling


title: Control #3

description: Transcriptome profile of BetaCatenin Knockout in pluripotent culture conditions, biological rep3

source_name: BetaCatenin Knockout in pluripotent culture , biological rep3


title: HCT116_WT_RNA_R1


title: DMSO_30_3.RIBO

description:
DMSO_30_3
ribosome profiling


title: PP_30_1.RIBO

description:
PP_30_1
ribosome profiling


title: PP_6_1.RIBO

description:
PP_6_1
ligation-free ribosome profiling


title: RCC243 - Side Population

city: Toronto

first: Michael

last: Ohh

state: Ontario

address: 661 University Avenue

department: Department of Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

data_processing:
Sample first sequenced with the MiSeq platform using an Illumina Micro flowcell to acquire the shallow sequencing data. Using Cell Ranger and the sequencing data, an estimation was performed of the number of cells captured, as well as determining a target number of reads for the samples.
The samples were then sequenced using the Illumina NovaSeq 6000 platform using a S2 flow cell and FASTQ files were generated for data processing with Cell Ranger
Processed data files generated by aligning FASTQ files to the reference transcriptome, GRCh38-3.0.0, with Cell Ranger pipeline version 3.1.0
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Processed tsv and mtx files from the Cell Ranger pipeline that contains filtered feature-barcode matrices for analysis

source_name: Clear cell renal cell carcinoma (ccRCC) cells

growth_protocol: Cells grown in IMDM (GE Healthcare Life Sciences, SH30228.01) with 10% FBS (Wisent, 095150) on collagen (Corning, 354236) coated plates at 5% CO2, 2% O2, and at 37ᵒC (Thermo Scientific, HERAcell 150i).

extract_protocol:
RCC243 cells were trypsinized (Wisent, 325-042-CL) to acquire a single-cell suspension and then incubated with DyeCycle™  Violet (Invitrogen, V35003) for 45 minutes at 37ᵒC prior to cell sorting with the BD FACSAria Iiu, in order to acquire the side population cells. RCC243 cells were trypsinised and suspended in IMDM with 10% FBS to acquire the whole population. A cell viability of greater than 90% and cell counts more than 50,000 cells were used for single-cell RNA-sequencing sample generation.
Libraries prepared based on the Single Cell 3' Reagent Kits v3.1 user guide

value: Patient tumour derived ccRCC cells (from Lobo, N.C. et al. 2016)

value: VHLmut (from Lobo, N.C. et al. 2016)


title: RCC243 - Whole Population


title: PP_30_1.RNA

description:
PP_30_1
total RNA sequencing


title: PP_30_3.RIBO

description:
PP_30_3
ribosome profiling


title: Control #1

description: Transcriptome profile of BetaCatenin Knockout in pluripotent culture conditions, biological rep1

source_name: BetaCatenin Knockout in pluripotent culture , biological rep1


title: HeLa MYBL2 KO rep 1

first: Paul

last: Blainey

address: 415 Main Street

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
For samples that were sequenced across two runs (e.g., HS1 control rep 1), fastq files were concatenated.
Transcript counts were quantified using kallisto version 0.45.0 with default parameters.
Genome_build: hg38, Gencode release 21 annotations
Supplementary_files_format_and_content: Transcript counts and tpm estimates are stored in tab-delimited files with one row per transcript feature.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100 U/mL penicillin/streptomycin

extract_protocol:
Cells were collected using mitotic shake-off to enrich for mitotic cells, washed once in PBS, then snap frozen for later processing. RNA was extracted using 1X TCL buffer (Qiagen) supplemented with 1% beta-mercaptoethanol.
Smart-seq2 was performed as described previously (Trombetta et al., 2014).

treatment_protocol: Cas9 expression was induced with 1 ug/mL doxycycline for 3 days prior to cell collection.

value: HeLa

tag: gene target

tag: replicate


title: Samples #1

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep1

source_name: BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture , biological rep1


title: HeLa MYBL2 KO rep 2


title: DMSO_6_3.RIBO

description:
DMSO_6_3
ligation-free ribosome profiling


title: DMSO_30_2.RIBO

description:
DMSO_30_2
ribosome profiling


title: HeLa MYBL2 KO rep 3


title: riboPLATE_ERCC_pool

description:
riboPLATE_ERCC_pool
3'-end polyA RNA, ribosome IP

data_processing:
Library strategy: (riboPLATE-seq)
Basecalls were performed on-instrument.
Ribosome profiling: Trailing adapter sequence was removed with Cutadapt using parameters -m 25 -a CTGTAGGCACCATCAAT. Ligation-free ribosome profiling: Trailing adenines (poly-A sequence) and preceding degenerate sequence added by template-switching enzyme were removed with Cutadapt v3.5 using parameters -m 25 -u 3 -a A{10}  --discard-untrimmed.  riboPLATE-seq/PLATE-seq: Trailing poly-A sequence were removed with Cutadapt using parameters -m 25 -a A{100}.
Ribosome profiling and RNA-seq: Libraries were depleted of ribosomal RNA by alignment to 45S+5S rRNA sequences from GRCh38 with Bowtie2 v2.2.5 and discarding aligned reads, allowing alignments to contain a maximum of one mismatch.
PLATE-seq, riboPLATE-seq: PLATE-based libraries were first demultiplexed by the identity of the first read, containing the barcode sequence. This created a reference table mapping every sequenced fragment to its original well, used downstream for demultiplexing aligned reads.
PLATE-seq, riboPLATE-seq, ribosome profiling, RNA-seq: Remaining reads were retained and aligned to the GRCh38 assembly of the human genome with STAR v2.7.9a using default parameters.
PLATE-seq, riboPLATE-seq: Multiplexed aligned reads were demultiplexed using the reference built from Read 1 barcodes, generating 96 PLATE-seq and 96 riboPLATE-seq libraries per pooled library.
PLATE-seq, riboPLATE-seq, Ribosome profiling, RNA-seq: Alignments to the exons of genes in the GRCh38 RefSeq annotation were counted with featureCounts v2.0.1; Forward-stranded ribosome profiling alignments were counted with the parameters -s 1 and reverse-stranded RNA-seq alignments were counted with -s 2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count matrix for all annotated genes in all samples. The first row is unique IDs identifying each sample's drug treatment condition or ERCC spike-in status, barcode index number, and either sequence barcode for riboPLATE/PLATE-seq libraries or "ribo"/"rna" for ribosome profiling and RNA sequencing, respectively. The first column contains all gene names.

source_name: Wi38 fibroblast culture

value: Wi38 fibroblasts

value: ERCC+/-


title: Samples #3

description: Transcriptome profile of BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture conditions, biological rep3

source_name: BetaCatenin Knockout rescued with moderate amout of exogenous BetaCatenin in pluripotent culture , biological rep3

value: BetaCatenin Knockout


title: Control #2

description: Transcriptome profile of BetaCatenin Knockout in pluripotent culture conditions, biological rep2

source_name: BetaCatenin Knockout in pluripotent culture , biological rep2


title: PLATE_ERCC_pool

description:
PLATE_ERCC_pool
3'-end polyA RNA

data_processing:
Library strategy: (PLATE-seq)
Basecalls were performed on-instrument.
Ribosome profiling: Trailing adapter sequence was removed with Cutadapt using parameters -m 25 -a CTGTAGGCACCATCAAT. Ligation-free ribosome profiling: Trailing adenines (poly-A sequence) and preceding degenerate sequence added by template-switching enzyme were removed with Cutadapt v3.5 using parameters -m 25 -u 3 -a A{10}  --discard-untrimmed.  riboPLATE-seq/PLATE-seq: Trailing poly-A sequence were removed with Cutadapt using parameters -m 25 -a A{100}.
Ribosome profiling and RNA-seq: Libraries were depleted of ribosomal RNA by alignment to 45S+5S rRNA sequences from GRCh38 with Bowtie2 v2.2.5 and discarding aligned reads, allowing alignments to contain a maximum of one mismatch.
PLATE-seq, riboPLATE-seq: PLATE-based libraries were first demultiplexed by the identity of the first read, containing the barcode sequence. This created a reference table mapping every sequenced fragment to its original well, used downstream for demultiplexing aligned reads.
PLATE-seq, riboPLATE-seq, ribosome profiling, RNA-seq: Remaining reads were retained and aligned to the GRCh38 assembly of the human genome with STAR v2.7.9a using default parameters.
PLATE-seq, riboPLATE-seq: Multiplexed aligned reads were demultiplexed using the reference built from Read 1 barcodes, generating 96 PLATE-seq and 96 riboPLATE-seq libraries per pooled library.
PLATE-seq, riboPLATE-seq, Ribosome profiling, RNA-seq: Alignments to the exons of genes in the GRCh38 RefSeq annotation were counted with featureCounts v2.0.1; Forward-stranded ribosome profiling alignments were counted with the parameters -s 1 and reverse-stranded RNA-seq alignments were counted with -s 2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count matrix for all annotated genes in all samples. The first row is unique IDs identifying each sample's drug treatment condition or ERCC spike-in status, barcode index number, and either sequence barcode for riboPLATE/PLATE-seq libraries or "ribo"/"rna" for ribosome profiling and RNA sequencing, respectively. The first column contains all gene names.


title: riboPLATE_screen_pool

description:
riboPLATE_screen_pool
3'-end polyA RNA, ribosome IP

source_name: TS543 neurosphere tissue culture


title: DMSO_30_1.RIBO

description:
DMSO_30_1
ribosome profiling


title: HeLa HS1 control rep 3

value: negative control sgRNA


title: HeLa LIN52 KO rep 2


title: HeLa HS1 control rep 2


title: HeLa LIN52 KO rep 1


title: HeLa LIN52 KO rep 3


title: mRbm ko

city: Miaoli County

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

data_processing:
On-instrument base-calling with Illumina HiSeq 2500 BclToFastq v2.18.
Adaptor sequences were removed from raw sequences, and the quality of reads was examined by FastQC software. Low-quality regions were trimmed (Phred quality score of <20).
Using STAR to map sequenced reads to whole genome, with additional parameters: --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd  --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000
Splicing event classification was performed using rMATS v4.0.2
Gene expression level of read counts and TPM were calculated using CLC Genomics Workbench 21.
Genome_build: GRCh38/hg38, GRCm39/mm39
Supplementary_files_format_and_content: Excel xlsx files of rMATs alternative splicing results
Supplementary_files_format_and_content: tab-delimited text files include  read counts and TPM for each Sample

source_name: mESCs-CM

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, 74106). RNA quality and quantifications were inspected using an Agilent 2100 Bioanalyzer.
The mRNA sequencing libraries were prepared using a Truseq Stranded mRNA kit (Illumina), and 2x150 bp paired-read sequencing was performed using an Illumina HiSeq instrument

value: mESCs-CM


title: PLATE_screen_pool

description:
PLATE_screen_pool
3'-end polyA RNA

value: TS543 glioblastoma


title: mWT

value: wild type


title: MOplus_UPF2_KO2

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

data_processing:
The base quality of raw mRNA-seq reads for each sample was checked and analysed independently using FastQC.
The raw data files were then processed to remove low quality reads and adapters with trimmomatic
Clean mRNA-seq reads were mapped to mm10/hg38 using STAR 2.5.2a with the following options: ‘--quantMode TranscriptomeSAM --outFilterMultimapNmax 1 --outSAMstrandField intronMotif’.
The genomic alignments-‘Aligned.toUnsorted.out.bam’ were then utilized with an algorithm called IRFinder to detect IR and measure variations in the level of specific IR between samples
We used the transcript quantification tool RSEM package {Li, 2011 #109} to generate integer-based read counts from the transcript alignments-‘Aligned.toTranscriptome.out.bam’.
Genome_build: mm10
Supplementary_files_format_and_content: Intron retention text file; gene expressio FPKM text file

source_name: BM Ly6Chi_KO Upf2_Monocyte

growth_protocol: primary cells

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen). RNA quality (RNA integrity Number >7) was confirmed using RNA 6000 Nano Chips (Agilent Technologies). cDNA was generated from DNAseI-treated total RNA using SuperScript III First-Strand Synthesis System (Invitrogen)in accordance with the manufacturers’ instructions. Reactions were in 20 ul volumes containing 1x IQ SyberGreen supermix and 0.3 mM of the respective forward and reverse primers using the CFX96 Real Time PCR Machine (Bio-Rad). Cycling conditions were: 95°C for 6min followed by 95°C for 30 s, primer-specific annealing temperature for 30 s, and extension at 72°C for 30 s. Primer sequences were: Upf2 ex2-3 Forward, 5′ GGCTGCTCAGCTGAAAGAGA-3′; Upf2 ex2-3 Reverse, 5′-TTTTCCTCTGGTCGGTTGTC-3′; Hprt Forward, 5′-AGTGTTGGATACAGGCCAGAC-3′; Hprt Reverse, 5′-CGTGATTCAAATCCCTGAAGT-3′
Poly-A enriched stranded RNA library preparation was performed using the TruSeq Stranded mRNA Library Prep kit (Illumina). Sequencing was performed on a Illumina Hi-Seq 2500 platform. Both library preparation and sequencing were performed at Novogene (China). For each sample, approximately 100M paired-end 100bp strand-specific reads were acquired.

treatment_protocol: untreated

value: Monocytic cell line

value: knock out Upf2

tag: disease state

value: healthy


title: MOlow_IR

description: MO-

source_name: BM Ly6Clo_Monocyte

value: untreated


title: DicerKO2

city: Suzhou

first: Jianming

address: 199 Renai Road

institute: Soochow University

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw reads for each Sample .
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: liver

tag: age

value: post natal one month

value: Dicerloxp/loxp;Alb-cre


title: DicerKO3

tag: genotype


title: MOplus_2_IR

source_name: BM Ly6Chi_Monocyte


title: MOplus_1_IR


title: DicerKO1


title: DicerAA2

value: Dicerloxp/loxp


title: DicerAA1


title: HeLa FOXM1 KO rep 2

tag: cell line


title: cMOP_2_IR

source_name: BM cMOP


title: HeLa FOXM1 KO rep 3


title: 289-1homing

city: Beijing

first: Xian

last: Liu

address: 38 Life Science Park Street

institute: Beijing Institute of Life Omics

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2 , which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: Processed values are FPKM

source_name: CD45.2+Lin-Sca-1+ cells from recipients that received BM cells from KO mice

extract_protocol:
Total RNA was isolated using the QIAshredder and RNeasy Mini Kit (QIAGEN).
RNA libraries were constructed using TruSeq kits (Illumina). The RNA libraries were sequenced on an Illumina Hiseq 2000/2500 at the ANNOROAD GENOME Co., Ltd. (Beijing, CN) following the vendor's recommended protocol.

treatment_protocol: For BMT, 2×10^7 donor cells from bone marrow (BM) of HEMGN-/- (CD45.2+) and WT were injected intravenously via the retro-orbital route into recipients mice(CD45.1+) previously irradiated with a split dose of 9Gy. Each group contains three replicates.

value: CD45.2+Lin-Sca-1+ cells isolated from primary recipients 6h after transplantation

tag: donor cell source

value: From bone marrow (BM) of HEMGN-/- mice

value: KO


title: 289-2homing

tag: cell type


title: MOplus_UPF2_KO1


title: HeLa FOXM1 KO rep 1

value: HeLa


title: cMOP_1_IR


title: HeLa HS1 control rep 1


title: W3homing

source_name: CD45.2+Lin-Sca-1+ cells from recipients that received BM cells from WT mice

value: From bone marrow (BM) of WT mice

value: WT


title: MDP_IR

description: MDP

source_name: BM MDP


title: 289-3homing


title: W1homing


title: DicerAA3


title: BC088 IL10KO

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the hg19 by BSMAP2.7.4
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: hg19 (human WGBS)
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: T cells

growth_protocol: WT and CAR T cells were serially stimulated by culturing with tumor cells containing the cognate antigen.  Tumor cells were replaced weekly.

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration. Nuclei were exteacted for ATAC-Seq.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Novaseq 6000 following the manufacturer's protocols.

tag: time point

value: Week 4


title: IL13Ra2 CD28z Mcherry Knockout

value: KO CAR


title: W2homing


title: control C23

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

institute: Medical University of Vienna

description: control

data_processing:
Reads were trimmed using trim galore v0.4.2 and mapped to mm10 excluding all reads mapping to hg19 using bismark v0.16.3. Mapped reads were deduplicated and methylation values extracted using bismark v0.16.3.
Genome_build: mm10
Supplementary_files_format_and_content: coverage files from bismark for Read1 and Read2 for each sample

source_name: 2-cell embryo

extract_protocol:
GVOs were isolated 48h after PMS injection and injected with either control morpholino or morpholinos targeting Tet1-3. After in vitro maturation and in vitro fertilization, fertilized 2-cell embryos were collected 29hpf and subjected to BS-seq library preparation.
For library preparation a Post-Bisulfite Adapter Tagging approach (PBAT) (Lee et. al, PMID: 29224070) was used with few changes. Changes: BD buffer (Qiagen) was used for the desulphonation reaction, biotin-capture was omitted and oligos were changed to Oligo 1: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTNNNNNNNNN and oligo 2: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTNNNNNNNNN, to match the primers from the Nextera XT Index Kit, which were used for the library amplification in the last step using 12 cycles.

tag: treatment

value: control


title: Tet-TKD T32

description: Tet-TKD

value: Tet-TKD


title: Tet-TKD T33

description: Tet-TKD


title: IL13Ra2 CD28z DNMT3a Knockout


title: BC088 DNMT3aKO and  IL-10 knockout


title: control C21

description: control


title: CD19 CD28z DNMT3a Knockout


title: control C14

description: control


title: Tet-TKD T18

description: Tet-TKD


title: Her2 CD28z DNMT3a Knocout


title: control C15

description: control


title: Tet-TKD T30

description: Tet-TKD


title: Tet-TKD T31

description: Tet-TKD


title: control C13

description: control


title: 293T cells, NONO-TFE3 transduced replicate 3

city: Boston

first: Ziad

last: Bakouny

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end sequencing reads were aligned to the human genome reference build hg38 using STAR v2.7.2
Quantification was performed using RSEM v1.3.2
Expected counts and Transcripts-Per-Million (TPM) were generated using RSEM v1.3.2
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary table 3a.txt - tab-delimited text file containing expected counts for all samples and all genes
Supplementary_files_format_and_content: Supplementary table 3a.txt - tab-delimited text file containing Transcript-Per-Million (TPM) for all samplesa and all genes
Supplementary_files_format_and_content: Tab-delimited text file for each file containing expected counts, TPMs, and FPKMs for all genes

source_name: Human embryonic kidney

growth_protocol: Cell lines were grown in base media of DMEM, supplemented with 10% FBS, 100 U mL-1 penicillin, 100 μg mL-1 streptomycin, 2 mM L-glutamine, and 100 μg mL-1 Normocin (Invivogen).

extract_protocol:
Total RNA was collected using the RNeasy Plus Mini Kit (QIAGEN, #74136).
Sequencing libraries were prepared with poly(A) selection using standard Illumina protocols.

treatment_protocol: 293T cells were seeded in 6-well plates at 2 x 105 cells per well and after 24 hours were transfected with 500 ng of plasmids encoding ASPSCR1-TFE3, NONO-TFE3, PRCC-TFE3, SFPQ-TFE3, wild type (WT) TFE3, or an empty vector control (all in pLX313). All transfections were performed in three biological replicates. Cells were harvested 48 hours after transfection.

value: kidney


title: 293T cells, Mock transduction replicate 3

value: Mock


title: control C20

description: control


title: 293T cells, ASPS-TFE3 transduced replicate 3


title: 293T cells, WT TFE3 transduced replicate 3

value: WT TFE3


title: control C35

description: control


title: 293T cells, PRCC-TFE3 transduced replicate 3


title: control C22

description: control


title: Tet-TKD T17

description: Tet-TKD


title: 293T cells, Mock transduction replicate 2


title: Tet-TKD T11

description: Tet-TKD


title: control C12

description: control


title: Peritoneal wash Wild Type

value: Week 1


title: Tet-TKD T5

description: Tet-TKD


title: SJ006 DNMT3a IL-10 Knockout 2


title: Tet-TKD T4

description: Tet-TKD


title: Her2 CD28z Mcherry Knockout


title: CD19 CD28zMcherry Knockout


title: Tet-TKD T1

description: Tet-TKD


title: 293T cells, PRCC-TFE3 transduced replicate 2


title: control C7

description: control


title: 293T cells, WT TFE3 transduced replicate 2


title: SJ006 DNMT3a Knockout 2


title: 293T cells, SFPQ-TFE3 transduced replicate 2


title: HCT116_PHIP_KO_H3K4me1

value: Colon carcinoma

tag: chip antibody


title: SJ006 Mcherry Knockout 2


title: Tet-TKD T2

description: Tet-TKD


title: 293T cells, NONO-TFE3 transduced replicate 2


title: no RNA negative control_3

data_processing:
Reads were mapped to mouse reference genome mm10, depleted for sex chromosomes with STAR2.5.1b using default settings. Genes from RefSeq database that have at least ten reads in 50% of the embryos of one condition were used for further analysis. Differentially expressed genes were obtained using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: FPM.txt: Tab-delimited text file includes FPM values.

organism: synthetic construct

source_name: no RNA

extract_protocol: 2-cell embryos were collected 29 hours following in vitro fertilization and zona pellucida was removed from 2-cell embryos. Libraries were constructed using Clontech SMARTer Ultra Low Input RNA Kit, followed by NEBNext DNA Library Prep Master Mix Set

tag: control type

value: negative


title: 293T cells, ASPS-TFE3 transduced replicate 2


title: HCT116_PHIP_del_BD1_BD2_Clone1_H3K4me1


title: Peritoneal wash DNMT3a Knockout

tag: genotype/variation


title: SJ006 IL-10 Knockout 2


title: no RNA negative control_2


title: 293T cells, SFPQ-TFE3 transduced replicate 3


title: HCT116_WT_H3K4me1

value: wild-type


title: 293T cells, WT TFE3 transduced replicate 1


title: pODO1-ChIP

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

description: Petunia ODO1 ChIP-seq and RNA-seq

data_processing:
RNA-Seq reads were trimmed with cutadapt, aligned using TopHat2, counts within genes were determined using HTSeq, and differentially expressed genes were determined using DESeq2.
ChIP-Seq reads were trimmed with cutadapt, aligned using Bowtie2, and peaks were called using MACS2.
Genome_build: Petunia axillaris draft genome sequence v1.6.2

organism: Petunia x hybrida

source_name: corrola

extract_protocol: Crosslinked corolla chromatin was used for anti-GFP immunoprecipitation; immunoprecipitated DNA was recovered and used for library construction. (ChIP-Seq)

value: corolla


title: HCT116_PHIP_KO_PHIP_ChIP

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

value: PHIP


title: no RNA negative control_1


title: SJ001 Mcherry CD19 Knockout 2


title: HCT116_PHIP_del_BD1_BD2_Clone2_PHIP_ChIP


title: SJ001 IL-10 Knockout 2


title: 293T cells, Mock transduction replicate 1


title: 293T cells, PRCC-TFE3 transduced replicate 1


title: HCT116_PHIP_del_BD1_BD2_Clone2_H3K4me1


title: SJ001 DNMT3a Knockout 2


title: BC088 DNMT3a Knockout 2


title: A673/TR/shFEZF1 c6 dox

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

country: Spain

institute: INSTITUTO DE SALUD CARLOS III - IIER

data_processing:
fastq.gz files were upload on usegalaxy.org platform
Data analysis was carried out using Galaxy (usegalaxy.org), an open source, web-based platform that integrates many tools for data intensive biomedical research (doi:10.1093/nar/gky379).
Briefly, mapping and transcript quantification were performed with Salmon quant script (v0.14.1.2), using GRCh38 as transcriptome reference.
Differences in expressed features (TPM) from quantification tables were calculated with DESeq2 (v2.11.40.6).
Genome_build: GRCh38
Supplementary_files_format_and_content: DESeq values represents the differential expression among control and cells treated with doxycycline. Column headers are: GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj

source_name: Ewing sarcoma cell line

growth_protocol: Cells were cultured in DMEM plus 10% FBS plus antibiotics (Blasticidine, Puromicyn and Zeocin)

extract_protocol:
Total RNA was isolated with Trizol reagent and additionally cleaned-up with RNAeasy minielute columns.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA library prep)

treatment_protocol: Doxycycline 1 ug/mL by 72 hours

value: Ewing sarcoma cell line

tag: genetic modification

value: enginereed with a FEZF1 shRNA (doxycycline inducible)

value: doxicicline 72h (shFEZF1 expression)


title: 35S-ChIP

description: Petunia ODO1 ChIP-seq and RNA-seq


title: 293T cells, NONO-TFE3 transduced replicate 1


title: 293T cells, SFPQ-TFE3 transduced replicate 1


title: HCT116_WT_PHIP_ChIP


title: HCT116_PHIP_del_BD1_BD2_Clone1_PHIP_ChIP


title: HCT116_PHIP_del_BD1_BD2_Clone2_Input

value: Input


title: A673/TR/shFEZF1 c5 dox


title: HCT116_PHIP_KO_Input


title: BC088 Mcherry Kockout 2

value: Week 4


title: A673/TR/shFEZF1 c3 control

value: untreated


title: A673/TR/shFEZF1 c6 control


title: A673/TR/shFEZF1 bulk dox


title: UPN6 pretreatment_VDJ

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
Library strategy: TCR-seq
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor VDJ analysis: Cellranger
VDJ of Tcells were infered with cellranger vdj pipeline to get TCR contig annotations.
Genome_build: hg19

source_name: Human peripheral blood

extract_protocol: Cells from T-LGLL patients and healthy donors were loaded into the 10XChromium Controller using the Single Cell 5' Library and Gel BeadKit (10X Genomics). The Chromium Single Cell V(D)J protocol was used to profile  gene expression and T cell receptor.

value: CD3+ T cells

tag: Sex

value: M

tag: diagnosis

value: T-LGLL

tag: subject


title: 293T cells, ASPS-TFE3 transduced replicate 1

value: kidney


title: UPN15 posttreatment_VDJ

value: F


title: SJ006 DNMT3a Knockout 1

value: Week 1

value: KO CAR


title: HCT116_WT_Input

value: Colon carcinoma


title: HCT116_PHIP_ChIP

value: wild-type


title: UPN14 posttreatment_VDJ


title: A673/TR/shFEZF1 c3 dox


title: SJ001 DNMT3a Il--10 Knockout 1


title: Healthydonor7_VDJ

value: healthy


title: SJ001 IL-10 Knockout 1


title: HCT116_H4K12ac


title: SJ006 Mcherry Knockout 1


title: A673/TR/shFEZF1 bulk control


title: UPN15 pretreatment_VDJ


title: 10x Genomics single cell VDJ of patient 1

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

description:
10x Genomics single cell VDJ DNA-seq
SSHIV35_5_VDJ

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Cell Ranger (v3.0.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
Cell Ranger (v3.0.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Cell Ranger (v3.0.2) aggr method was used to aggregate the outputs from three runs of cellranger count.
Downstream analysis were perfored using R package Seurat v3.0.2 and 10x Genomics Loupe Browser.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Supplementary_files_format_and_content: 10x single cell VDJ and Transcriptome processed files were generated by cellranger vdj and cellranger count method

source_name: Blood and skin CD45+ cells

growth_protocol: Freshly isolated cells from human skin biopsy (6mm) and blood

extract_protocol:
CD45+ single cells from 6mm skin biopsy
10x scRNA-seq
10X Genomics
Human skin tissue was digested for 2h in Collagenase and DNAse passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Peripheral blood mononuclear cells were isolated from the blood using Ficoll gradients.
Illumina
SMART-seq2

value: SKIN and BLOOD

value: CD45+ cells

value: Unstimulated

tag: disease state

value: HIV+


title: SJ001 DNMT3a Knockout 1


title: 10x Genomics single cell VDJ of patient 2

description:
10x Genomics single cell VDJ DNA-seq
SSHIV35_6_VDJ


title: SJ006 DNMT3a IL-10 Knockout 1


title: UPN13 posttreatment_VDJ


title: 10x Genomics single cell VDJ of healthy control 3

description:
10x Genomics single cell VDJ DNA-seq
SSHIV35_4_VDJ

value: healthy control


title: 10x Genomics single cell VDJ of healthy control 2

description:
10x Genomics single cell VDJ DNA-seq
SSHIV35_2_VDJ


title: SJ006 IL-10 Knockout 1


title: HCT116_H3K14ac

extract_protocol:
RNA was prepared usng a Qiagen Rneasy Miniprep kit. ChIP DNA was purified using phenol:chloroform
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit


title: Healthydonor6_VDJ


title: 10x Genomics single cell VDJ of healthy control 1

description:
10x Genomics single cell VDJ DNA-seq
SSHIV35_1_VDJ


title: HCT116_PHIP_del_BD1_BD2_Clone1_Input

value: Input


title: BC088 IL-10 Knockout


title: UPN8 posttreatment_VDJ


title: HCT116_H3K4me3


title: 10x Genomics single cell transcriptome of patient 2

description:
10x Genomics single cell RNA-seq
SSHIV35_6_transcriptome


title: UPN14 pretreatment_VDJ


title: UPN13 pretreatment_VDJ


title: HCT116_H3K4me1


title: 10x Genomics single cell VDJ of patient 3

description:
10x Genomics single cell VDJ DNA-seq
SSHIV35_7_VDJ


title: HCT116_Input


title: BC088 DNMT3a IL-10 Knockout


title: BC088 DNMT3a Knockout 1


title: SJ001 Mcherry CD19 Knockout 1


title: UPN12 posttreatment_VDJ


title: Healthydonor5_VDJ


title: DNMT3a Knockout pre stimulation 4


title: 10x Genomics single cell transcriptome of patient 3

description:
10x Genomics single cell RNA-seq
SSHIV35_7_transcriptome


title: DNMT3a Knockout pre stimulation 3


title: EKO Western Diet 22 weeks rep 1

city: Milan

first: Stefano

last: Manzini

address: via Balzaretti, n. 9

department: DISFEB

institute: University of Milan

description: re-analysis of GSM4983591

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie-0.12.8, tophat-1.3.2 with parameters --no-novel-juncs, using samtools-0.1.19
Mapped reads were processed with cuffdiff (Trapnell 2012, https://doi.org/10.1038/nprot.2012.016), version 2.0.2, with options --upper-quartile-norm
Genome_build: mm10

source_name: mouse aorta

growth_protocol: Apoe knockout (EKO) or ApoE/Apoa1 knockout (DKO) mice for with either standard laboratory (chow) or high-fat (Western) diet for either 6 or 22 weeks.

extract_protocol:
Total RNA was isolated from mouse tissues using the NucleoSpin RNA extraction kit according to the manufacturer’s instructions, with on-column DNA digestion. The quality of the mRNA was tested using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) before RNA- seq; samples with RNA integrity number <7.0 were discarded.
RNA samples were processed using the RNA-Seq Sample Prep kit from Illumina (Illumina, Inc, CA). Eight to 9 tagged libraries were loaded on one lane of an Illumina flowcell, and clusters were created using the Illumina Cluster Station (Illumina, Inc, CA).

treatment_protocol: Standard laboratory diet (chow) or high-fat (Western) diet

tag: strain

value: mouse aorta

value: apolipoprotein E knockout (EKO)

value: Western diet

tag: timepoint

value: 22 weeks


title: BC088 Mcherry Knockout 1


title: SJ001 DNMT3a IL-10 Knockout 2

value: Week 4


title: UPN12 pretreatment_VDJ

value: CD3+ T cells

value: M

tag: age

value: T-LGLL


title: DNMT3a Knockout pre stimulation 2

value: Week 1

value: KO CAR


title: 10x Genomics single cell transcriptome of patient 1

description:
10x Genomics single cell RNA-seq
SSHIV35_5_transcriptome

tag: tissue


title: HCT116_H3K4me2

address: 303 East Superior St, SQI 7-511

tag: cell line

value: Colon carcinoma

tag: genotype

value: wild-type


title: EKO Western Diet 6 weeks rep 3

description: re-analysis of GSM4983590

value: 6 weeks


title: UPN1 posttreatment_VDJ

tag: cell type

value: F


title: 10x Genomics single cell transcriptome of healthy control 3

description:
10x Genomics single cell RNA-seq
SSHIV35_4_transcriptome

value: SKIN and BLOOD

value: CD45+ cells

value: Unstimulated


title: EKO Western Diet 22 weeks rep 3

description: re-analysis of GSM4983593

value: mouse aorta


title: UPN8 pretreatment_VDJ


title: DNMT3a Knockout post timulation 2

tag: time point


title: EKO Western Diet 6 weeks rep 1

description: re-analysis of GSM4983588

value: apolipoprotein E knockout (EKO)

tag: treatment


title: Mcherry post stimulation 2

value: WT


title: 10x Genomics single cell transcriptome of healthy control 2

description:
10x Genomics single cell RNA-seq
SSHIV35_2_transcriptome

value: healthy control


title: 10x Genomics single cell transcriptome of healthy control 1

description:
10x Genomics single cell RNA-seq
SSHIV35_1_transcriptome


title: Blood patient 6

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_6_PBMC

source_name: Bulk RNA PBMC

extract_protocol:
RNA/DNA microkit Qiagen
Picelli et al.
SMART-Seq
Human skin tissue was digested for 2h in Collagenase and DNAse passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Peripheral blood mononuclear cells were isolated from the blood using Ficoll gradients.
Illumina
SMART-seq2

value: BLOOD

value: PBMCs

value: HIV+ low nadir

value: 6mm snap-frozen skin biopsy


title: Blood patient 4

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_4_PBMC


title: Blood patient 5

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_5_PBMC


title: EKO Western Diet 6 weeks rep 2

description: re-analysis of GSM4983589

value: Western diet


title: EKO Western Diet 22 weeks rep 2

description: re-analysis of GSM4983592

value: 22 weeks


title: DNMT3a Knockout pre stimulation 1

value: Week 1

value: KO CAR


title: Mcherry prestimulation


title: Blood patient 3

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_3_PBMC


title: DNMT3a Knockout post stimulation 1

value: Week 4


title: UPN17 posttreatment_VDJ

value: CD3+ T cells

value: M

value: T-LGLL


title: EKO chow 22 weeks rep 3

description: re-analysis of GSM4983587

value: chow diet


title: EKO chow 22 weeks rep 2

description: re-analysis of GSM4983586

value: mouse aorta


title: UPN1 pretreatment_VDJ

value: F


title: UPN17 pretreatment_VDJ


title: Mcherry post stimulation 1

value: WT


title: Healthydonor4_VDJ

value: healthy


title: EKO chow 6 weeks rep 3

description: re-analysis of GSM4983584

value: apolipoprotein E knockout (EKO)

value: 6 weeks


title: UPN4 pretreatment_VDJ


title: Skin patient 5

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_5_SKIN

source_name: Bulk RNA SKIN

value: SKIN

value: SKIN biopsy

value: Unstimulated

value: HIV+ low nadir


title: Skin patient 6

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_6_SKIN

value: 6mm snap-frozen skin biopsy


title: EKO chow 6 weeks rep 2

description: re-analysis of GSM4983583


title: Mock_1

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Sequencing reads were aligned to the human genome using STAR 2.7.3a.
Gene-level read counts were generated using STAR 2.7.3a.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

source_name: bronchial epithelial cells

extract_protocol:
1 ml Trizol was added to 5-10 x 10^6 cells and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: bronchial epithelial cells

tag: infection

value: mock

tag: viral geographic origin

tag: viral type

tag: viral hemagglutinin

tag: viral neuraminidase


title: Mock_2


title: EKO chow 6 weeks rep 1

description: re-analysis of GSM4983582


title: Skin patient 4

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_4_SKIN


title: Vietnam_2

value: Influenza

value: Vietnam

value: A


title: UPN18 pretreatment_VDJ

value: CD3+ T cells

tag: Sex

tag: diagnosis

value: T-LGLL


title: Healthydonor3_VDJ

value: F

tag: subject


title: Vietnam_1


title: Skin patient 3

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_3_SKIN

tag: disease state


title: Blood patient 2

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_2_PBMC

value: BLOOD

value: PBMCs


title: Skin patient 2

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_2_SKIN


title: Healthydonor2_VDJ

value: healthy


title: EKO chow 22 weeks rep 1

description: re-analysis of GSM4983585

tag: strain

value: mouse aorta

value: apolipoprotein E knockout (EKO)

value: chow diet

tag: timepoint

value: 22 weeks


title: UPN4 posttreatment_VDJ

value: M

tag: age


title: DKO Western Diet 22 weeks rep 2

tag: tissue

value: double apolipoprotein E and apolipoprotein A-I knockout mice (DKO)

value: Western diet


title: Udorn_2

value: bronchial epithelial cells

value: Udorn


title: DKO Western Diet 22 weeks rep 1

tag: genotype


title: Skin patient 1

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
A_1_SKIN

value: SKIN

tag: cell type

value: SKIN biopsy

value: Unstimulated

value: HIV+ low nadir

value: 6mm snap-frozen skin biopsy


title: DKO Western Diet 6 weeks rep 3

value: 6 weeks


title: UPN19 posttreatment_VDJ

value: CD3+ T cells

value: F

value: T-LGLL


title: Skin healthy donor 5

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
HC_5_SKIN

value: healthy control


title: UPN18 posttreatment_VDJ


title: Tasmania_2

value: Influenza

value: Tasmania

value: B


title: DKO Western Diet 6 weeks rep 2

value: mouse aorta

value: double apolipoprotein E and apolipoprotein A-I knockout mice (DKO)


title: DKO Western Diet 22 weeks rep 3

value: Western diet

value: 22 weeks


title: Skin healthy donor 4

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
HC_4_SKIN

value: SKIN


title: DKO Western Diet 6 weeks rep 1


title: UPN10 posttreatment_VDJ

value: M


title: Tasmania_1

value: bronchial epithelial cells


title: UPN19 pretreatment_VDJ


title: UPN10 pretreatment_VDJ


title: Shanghai_1

value: Shanghai

value: A


title: DKO chow 22 weeks rep 3

value: chow diet


title: Shanghai_2


title: Udorn_1

value: Udorn


title: Skin healthy donor 3

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
HC_3_SKIN

value: SKIN biopsy

value: Unstimulated

value: 6mm snap-frozen skin biopsy


title: Skin healthy donor 2

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
HC_2_SKIN

value: healthy control


title: DKO chow 22 weeks rep 1


title: Peru_1

value: Influenza

value: Peru


title: UPN24 posttreatment_VDJ

value: CD3+ T cells

value: F

value: T-LGLL


title: Skin healthy donor 1

description:
Bulk RNA-seq
Gene_Raw_Count_Bulk_RNA-seq_Smart-seq2.txt
HC_1_SKIN


title: Peru_2


title: SDI_12w_naive_2

data_processing:
Sequencing reads were aligned to the mouse genome using STAR 2.6.1a.
Gene-level read counts were generated using STAR 2.6.1a.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

source_name: Bronchoalveolar lavage fluid

growth_protocol: mice were housed in SPF conditions

extract_protocol:
bronchioalveolar lavage fluid was collected (2x1ml PBS + 2mM EDTA) 4h after SDI/NanoPart administration and cells were spun down, resuspended in 100 µl Trizol. RNA was extracted using the DirectZol kit (Zymo Research)
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Mice were given 1 µg Sendai virus Defective Interfering RNA intranasally in different nanoparticle formulations, suspended in 50 µl PBS under mild sedation.

tag: immunity

value: naive

tag: agonist

value: SDI

tag: delivery

value: Control

tag: age (weeks)

value: BALB/c


title: Healthydonor7_geneexpression

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor VDJ analysis: Cellranger
VDJ of Tcells were infered with cellranger vdj pipeline to get TCR contig annotations.
Genome_build: hg19

value: M

value: healthy


title: UPN24 pretreatment_VDJ


title: DKO chow 6 weeks rep 4

value: mouse aorta

value: double apolipoprotein E and apolipoprotein A-I knockout mice (DKO)

tag: treatment

value: chow diet

value: 6 weeks


title: DKO chow 22 weeks rep 2

value: 22 weeks


title: UPN6 pretreatment_geneexpression


title: PolyIC_12w_naive_2

value: PolyIC


title: NewBrunswick_1

value: bronchial epithelial cells

tag: infection

value: Influenza

tag: viral geographic origin

value: New Brunswick

tag: viral type

value: B

tag: viral hemagglutinin


title: UPN15 posttreatment_geneexpression

value: CD3+ T cells

tag: Sex

value: F

tag: diagnosis

value: T-LGLL

tag: subject


title: NewBrunswick_2

tag: viral neuraminidase


title: DKO chow 6 weeks rep 1

tag: strain

tag: timepoint


title: DKO chow 6 weeks rep 3

tag: tissue

tag: genotype


title: A673/TR/shFEZF1 c5 control

data_processing:
fastq.gz files were upload on usegalaxy.org platform
Data analysis was carried out using Galaxy (usegalaxy.org), an open source, web-based platform that integrates many tools for data intensive biomedical research (doi:10.1093/nar/gky379).
Briefly, mapping and transcript quantification were performed with Salmon quant script (v0.14.1.2), using GRCh38 as transcriptome reference.
Differences in expressed features (TPM) from quantification tables were calculated with DESeq2 (v2.11.40.6).
Genome_builGeneIDd: GRCh38
Supplementary_files_format_and_content: DESeq values represents the differential expression among control and cells treated with doxycycline. Column headers are: GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

tag: genetic modification

value: enginereed with a FEZF1 shRNA (doxycycline inducible)

value: untreated


title: UPN15 pretreatment_geneexpression

tag: age


title: PolyIC_12w_naive_1

tag: immunity

value: naive

tag: agonist

tag: delivery

value: Control

tag: age (weeks)

value: BALB/c


title: DKO chow 6 weeks rep 2

value: mouse aorta

value: double apolipoprotein E and apolipoprotein A-I knockout mice (DKO)

tag: treatment

value: chow diet


title: Moscow_2

tag: infection

tag: viral geographic origin

value: Moscow

tag: viral type

value: A

tag: viral hemagglutinin


title: SDI_12w_naive_3

value: SDI

tag: strain


title: PSC_Pkn2KO_TGFbTreated_C

city: London

first: Angus

last: Cameron

state: Islington

address: John Vane Science Centre, Charterhouse Sq,

department: Tumour Biology

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Base calling and demultiplexing was performed using MiSeq Reporter v2.6.2.3.
Read trimming was performed by Qiagen using GeneGlobe.
Trimmed reads were aligned to the mouse genome by Qiagen using STAR RNA read mapper in GeneGlobe.
Reads were counted by Qiagen using GeneGlobe.
Count normalisation and differential expression was performed using pre-determined reference genes and DEseq2 v1.32. Reference genes:  ENSMUSG00000034601, ENSMUSG00000043323, ENSMUSG00000024383, ENSMUSG00000028651, ENSMUSG00000022771, ENSMUSG00000031706, ENSMUSG00000039759, ENSMUSG00000051390, ENSMUSG00000033961.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample for every gene in the QIAseq mouse extracellular matrix & cell adhesion molecules targeted RNA panel
Supplementary_files_format_and_content: Matrix table with reference-gene normalised gene counts for every vehicle control-treated (basal) sample for every gene in the QIAseq mouse extracellular matrix & cell adhesion molecules targeted RNA panel
Supplementary_files_format_and_content: Matrix table with reference-gene normalised gene counts for every TGF-treated sample for every gene in the QIAseq mouse extracellular matrix & cell adhesion molecules targeted RNA panel

source_name: Pancreatic stellate cells isolated from mouse pancreas using density centrifugation.

growth_protocol: PSCs were seeded at 7.5 x 104 cells in 15 cm dishes in DMEM with 10% FBS (Gibco) and Pen-strep.

extract_protocol:
After 72 h, RNA was harvested using the QIAGEN RNeasy plus kit.
100 ng RNA from each sample was processed using the QIAseq mouse extracellular matrix & cell adhesion molecules targeted RNA panel (QIAGEN) to isolate and amplify a cDNA library of 419 genes associated with the ECM and cell adhesion as per the manufacturer’s instructions. Samples were pooled to generate a 12plex cDNA library.

treatment_protocol: Plates were treated with 5 ng/ml TGF-β1 (Peprotech) or vehicle control.

value: PKN2 KO

tag: background strain

value: TGF-b

value: Pancreatic stellate cell (PSC)


title: UPN14 posttreatment_geneexpression

value: CD3+ T cells

tag: Sex

value: F

tag: diagnosis

tag: subject


title: NP3_SDI_16w_Bmal04_3

state: CA

value: Nanoparticle 3


title: PSC_Pkn2KO_TGFbTreated_B

tag: genotype

tag: cell type


title: NP3_SDI_16w_Bmal04_2


title: Moscow_1

value: bronchial epithelial cells

value: Influenza

tag: viral neuraminidase


title: UPN14 pretreatment_geneexpression

tag: age

value: T-LGLL


title: Mongolia_2

value: Mongolia


title: Mongolia_1


title: UPN13 posttreatment_geneexpression


title: PSC_Pkn2KO_TGFbTreated_A


title: UPN8 posttreatment_geneexpression

value: M


title: PSC_Pkn2WT_TGFbTreated_C

value: PKN2 WT


title: NP3_SDI_16w_Bmal04_1

tag: immunity

tag: agonist

value: BALB/c


title: NP3_SDI_12w_naive_3

value: naive

tag: delivery

tag: age (weeks)


title: SDI_12w_naive_1

value: Control


title: PSC_Pkn2WT_TGFbTreated_B

tag: treatment


title: NP3_SDI_12w_naive_2


title: Manitoba_1

tag: infection

tag: viral geographic origin

value: Manitoba

value: A


title: Delaware_2

value: Delaware

tag: viral type

tag: viral hemagglutinin


title: NP3_SDI_12w_naive_1

value: SDI

tag: strain


title: Healthydonor5_geneexpression

tag: Sex

value: healthy


title: Healthydonor6_geneexpression

value: CD3+ T cells

tag: diagnosis


title: PSC_Pkn2WT_TGFbTreated_A

tag: background strain

value: TGF-b

value: Pancreatic stellate cell (PSC)


title: Delaware_1

value: bronchial epithelial cells


title: NP3_16w_Bmal04_2

value: Nanoparticle 3


title: UPN13 pretreatment_geneexpression

value: F

value: T-LGLL

tag: subject


title: California_2

tag: cell type

value: Influenza

value: California


title: NP3_16w_Bmal04_1

value: BALB/c


title: UPN8 pretreatment_geneexpression

value: M


title: PSC_Pkn2KO_Untreated_C

tag: genotype

value: PKN2 KO

value: Control


title: California_1

value: A

tag: viral neuraminidase


title: PSC_Pkn2KO_Untreated_B


title: NP3_12w_naive_1

tag: immunity

value: naive


title: NP3_12w_naive_2

tag: agonist


title: PSC_Pkn2KO_Untreated_A


title: UPN12 posttreatment_geneexpression

tag: age


title: Healthydonor1_VDJ


title: Boston_2

value: Boston


title: Boston_1


title: NP2_SDI_12w_naive_3

value: SDI

tag: delivery

value: Nanoparticle 2

tag: age (weeks)


title: PSC_Pkn2WT_Untreated_C

value: PKN2 WT

tag: treatment


title: UPN12 pretreatment_geneexpression

value: CD3+ T cells


title: PSC_Pkn2WT_Untreated_B

value: Pancreatic stellate cell (PSC)


title: Berlin_2

value: bronchial epithelial cells

tag: infection

tag: viral geographic origin

value: Berlin


title: PSC_Pkn2WT_Untreated_A


title: Berlin_1

tag: viral type

tag: viral hemagglutinin


title: NP2_SDI_12w_naive_2

tag: strain


title: Anhui_2

value: Anhui


title: Anhui_1

value: Influenza


title: Healthydonor3_geneexpression

tag: Sex

value: F

tag: diagnosis

value: healthy


title: NP1_SDI_12w_naive_3

value: Nanoparticle 1

value: BALB/c