title: H4B

city: Nijmegen

first: Ivo

last: Rieu

state: Gelderland

address: Heyendaalseweg 135

department: Plant Systems & Physiology

country: Netherlands

institute: Radboud University

description: pol LTMH_4

data_processing:
Illumina Casava1.8 software was used for basecalling.
Raw reads were filtered to remove reads with adaptor contamination, when uncertain nucleotides constitute more than 10 percents of either read, or when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
Mapping to reference genome was performed using Tophat v2.0.12, mismatch = 2, and default setting for other parameters
HTseq v0.6.1 software was used to analyze the gene expression levels, using the union mode.
Genome_build: ITAG3.2
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized abundance measurements (FPKM values) for each sample

organism: Solanum lycopersicum

source_name: anther

growth_protocol: Solanum lycopersicum (cv. Micro-Tom) plants were grown on potting soil (No.4, Horticoop, Lentse Potgrond, Slingerland Potgrond) with 4 g/L Osmocote® Exact Standard 3–4 M (Everris), in climate-controlled cabinets (MC1600, Snijders Labs), using a 12/12-hour photoperiod (Philips Green Power LED DR/B/FR 120, ~250 µmol m-2s-1 at plant height), at 25°C during day-time, and 19°C during the night and 50% relative humidity (RH) ("CT conditions").

extract_protocol:
RNA was isolated via TRI-reagent extraction with clean-up on Qiagen Plant RNeasy (catalog no. 74104) columns. All RNAs were treated with DNaseI using the Plant RNeasy Kit. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and MMuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.

treatment_protocol: Plants were moved into LTMH conditions upon flowering, with 34°C during day-time, and 28°C during the night and 68% RH, or left in CT conditions for control samples. Anther samples were isolated approximately 5 hours into the light period after four days for tetrad stage anthers, after six days for free microspore stage anthers, and after eight days for and polarized microspore stage anthers. Six anthers were pooled per replicate.

value: anther

value: polarized microspore

tag: temperature

value: LTMH


title: H3B

status: Public on Jan 01 2023

type: SRA

description: pol LTMH_3

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: developmental stage


title: 18942X10 640

city: SLC

first: Leah

last: Owen

state: UT

address: 65 N. Mario Capecchi Dr

department: Ophthalmology

country: USA

institute: John Moran Eye Center

data_processing:
Human FASTA and GTF files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Raw gene counts were filtered to remove features with zero counts and fewer than 10 reads in every sample
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Assembly: GRCh38
Supplementary files format and content: FeatureCount output files combined into a tab-delimited raw count matrix

organism: Homo sapiens

source_name: Placenta

extract_protocol:
RNA was harvested using Qiagen ALL PREP Universal
Whole transcriptome expression analysis was performed on fetal surface placental tissues using the Illumina Stranded Total RNA Kit with Ribo-Zero Plus per the standard protocol

value: Placenta

tag: cell type

value: placental villous tissue

tag: Sex

value: M

tag: preeclampsia

value: Y

tag: rop


title: GL26110_CD31posP2_D03_R1

city: Boston

first: Elizabeth

last: Perez

state: MA

address: 30 Fruit Street

institute: MGH

library_source: transcriptomic single cell

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

organism: Mus musculus

source_name: brain

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

value: brain

tag: treatment


title: Clothianidin dose level 4 bio rep 1 [Clo_M_A05_S3]

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

description:
96 well plate
Clo_M_A05_S3
Clo.raw.counts.txt
Clo.filtered.normFinal.txt

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads from each sample's RNA-Seq fastq(.gz) file were mapped with STAR (Dobin, et. al) v2.7.1a to indexed FHM genome with 26,150 gene models loaded within the genome (WIOS00000000; BioSample SAMN12875914). STAR "--quantMode GeneCounts" was used to produce raw counts from the mapping; reverse strand count column was used as dictated by sequencing protocol. Genomic gene and transcript coordinates and associated annotations are contained in files WIOS01.1.gbff.gz, WIOS01.2.gbff.gz and WIOS01.3.gbff.gz available at https://www.ncbi.nlm.nih.gov/Traces/wgs/WIOS01?display=contigs. Uniprot accessions associated with gene models are available from the authors.
Samples with <2 million raw counts and/or less than 50% unique mapping rate were removed, and within-chemical features (genes) with mean raw counts <5 across all samples were filtered from respective raw counts matrices.
For each chemical, the raw counts for the remaining features were normalized to counts per million reads (CPM), and after adding a pseudo-count of 1 to prevent taking log of zero counts, log2 transformed.
For each chemical, an MDS plot of the normalized data was generated. Individual samples separated from all remaining samples on either principle component #1 (PC1) or principle component #2 (PC2) by >2x the span of all other samples on the corresponding PC were removed from further analysis. Qualitative assessment was applied and samples with a relatively large Euclidean distance from all other remaining samples on MDS plots were also excluded, along with samples especially distant from corresponding replicates within dose.
Assembly: EPA_FHM_2.0.b
Supplementary files format and content: For each chemical, tab delimited text matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: For each sample, tab delimited text matrix table with normalized expression values for every gene and every sample that passed all filtering.

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Larvae remained in their 1 mL deep wells, exposure solution was removed and replaced with lysis buffer, a bead was added to each well, and subjects were homogenized in their wells.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

treatment_protocol: For ten different chemicals, 24h post-hatch individual fathead minnow larvae were statically exposed in 96 deep well plates to controls and a half-log dilution series of treatment concentrations. Exposures were for 24 hours. Subjects from all doses that did not exhibit excessive levels of mortality were further processed.

value: whole body

value: larva

tag: age

value: 5 dpf/24 hr post hatch

value: Clothianidin

tag: concentration

tag: time point

value: 24 hr


title: Clothianidin dose level 3 bio rep 1 [Clo_M_A04_S4]

description:
96 well plate
Clo_M_A04_S4
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b2_1262um

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

description:
b2_1262um
E. coli k12 BW25113

data_processing:
quality trimming step using cutadapt (v2.10) command with a quality threshold of 20
the pooled sample was demultiplexed according to the anchored barcode of the first seven nucleotides at the 5’-end from the first read
internal adaptor sequence embedding in some second reads with too short insert was also trimmed
a minimum length threshold of 20 bp for both the first and second reads was used to filter out those pair-end reads with too short insert
bowtie2 (v2.4.1) to align the second read to a reference genome (NC000913.3) (default setting)
Feature counting was carried out using R method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand-specific manner, giving rise to a read count table for each gene.
Genome_build: NC000913.3
Supplementary_files_format_and_content: gene raw count data, tab-delimited matrix table

organism: Escherichia coli BW25113

source_name: Spatial transcriptome of the layer 1262 micrometers away from biofilm edge in biofilm 2

growth_protocol: For biofilm growth, single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture.  We sub-cultured 100 uL seed into 5 mL fresh LB broth (2% volume) in 50 mL centrifuge tube and grown for two hours at 37 ℃ with shaking at 220 rpm to reach exponential stage. Next, bacteria would be loaded into microfluidic chip to grow a semicircular biofilm. When the radius of biofilm reached around 1 mm, bacteria cells would be extracted from the chip for further steps. To prepare planktonic bacterial culture, single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture. A subculture was established by cultivating the seed culture into fresh 5 mL fresh LB broth (2% volume) in 50 mL centrifuge tube and grown for two hours with shaking at 220 rpm to reach exponential stage (OD600 ~ 0.6). Such subculture was next inoculated into 300 uL M63B1 broth in 48-well plate. The 48-well plate were loaded into a microplate reader system with 220 rpm shaking and the growth curve was monitored from absorbance at 600 nm every 30 min. When reaching desired OD600, 100 uL culture was taken to extract RNA.

extract_protocol:
Bacterial RNA was obtained utilizing the RNAClean XP beads (Beckman, A63987). Lysate was prepared using lysozyme and proteinase K
miniBac-seq, a customized bacterial RNA-seq library construction method, see description of our paper for details

tag: growth mode

value: biofilm


title: 18942X9 639


title: GL26110_CD31posP2_D10_R1


title: H2B

description: pol LTMH_2


title: b2_139um

description:
b2_139um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 139 micrometers away from biofilm edge in biofilm 2


title: 18942X8 42C_P-2

value: N


title: H1B

description: pol LTMH_1


title: GL26110_CD31posP2_G09_R1


title: GL26110_CD31posP2_G10_R1


title: Clothianidin dose level 2 bio rep 1 [Clo_M_A03_S1]

description:
96 well plate
Clo_M_A03_S1
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: Clothianidin dose level 1 bio rep 1 [Clo_M_A02_S2]

description:
96 well plate
Clo_M_A02_S2
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: 18942X7 42C_P-1


title: GL26110_CD31posP2_B03_R1


title: Clothianidin control bio rep 1 [Clo_M_A01_S5]

description:
96 well plate
Clo_M_A01_S5
Clo.raw.counts.txt
Clo.filtered.normFinal.txt


title: b1_998um

description:
b1_998um
E. coli k12 BW25113

source_name: Spatial transcriptome of the layer 998 micrometers away from biofilm edge in biofilm 1


title: 18942X6 42B_P-2

value: F


title: GL26110_CD31posP2_F07_R1


title: H3A

description: mic LTMH_3

value: free microspore


title: 18942X5 42B_P-1


title: GL26110_CD31posP2_H05_R1


title: H2A

description: mic LTMH_2

value: anther


title: 18942X3 26A_P-1


title: 18942X4 26A_P-2


title: H1A

description: mic LTMH_1


title: H4D

description: tet LTMH_4

value: tetrad


title: GL26110_CD31posP2_E11_R1


title: H4A

description: mic LTMH_4

value: LTMH


title: 18942X2 15A_P-2

value: Placenta


title: H3D

description: tet LTMH_3


title: GL26110_CD31posP2_B07_R1


title: GL26110_CD31posP2_C02_R1


title: GL26110_CD31posP2_D12_R1


title: H2D

description: tet LTMH_2


title: 18942X1 15A_P-1

value: placental villous tissue


title: GL26110_CD31posP2_B12_R1


title: H1D

description: tet LTMH_1


title: DU145_si-TSPAN18#2

city: Guangzhou

first: Qianghua

last: Zhou

address: Urology

institute: Sun yat-sen memorial hospital

data_processing:
Base-calling: bcl2fastq2 v2.19.1
Data filtering : in house
Read alignment: hisat2 v2.1.0
transcript assemble: htseq-count v0.6.1
Assembly: hg19
Supplementary files format and content: excel files include normalize values for each Sample

source_name: prostate cancer cell line DU145

growth_protocol: DU145 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

tag: sirna

value: siTSPAN18#2 targeting TSPAN18 were transfected in the cell

tag: cell line


title: GL26110_CD31posP2_A02_R1


title: DU145_si-TSPAN18#1

value: siTSPAN18#1 targeting TSPAN18 were transfected in the cell


title: C4B

description: pol CT_4

value: polarized microspore

value: CT


title: GL26110_CD31posP2_F03_R1

value: brain


title: C3B

description: pol CT_3


title: PCI-35, U0126, Day1

city: Sendai

first: Tomohiko

last: Ishikawa

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Otolaryngology - Head and Neck Surgery

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
HISAT2
StringTie
Supplementary files format and content: A spreadsheet file (xlsx) include FPKM values and Read count for each Sample

growth_protocol: MIAPaCa-2 was maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C. AsPC-1 and PCI-35 were maintained in RPMI1640, and the other conditions were the same as MIAPaCa-2.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit Gold (Illumina) following manufacturer's protocols.

treatment_protocol:
The pancreatic cancer cells were seeded in 100-mm culture dishes at 5 × 105 cells per dish with an appropriate culture medium containing 10% FBS, and cultured under 37℃ in 5% CO2 with the appropriate humidity.
After 24 hours, the medium was replaced with a medium containing U0126 dissolved in dimethyl sulfoxide (DMSO) at a final concentration of 10μmol/L, or replaced with a medium containing the same volume of DMSO without U0126 as a control. After 24 hours, RNA isolation was carried out.

value: cancer cell line

tag: genotype

value: WT

tag: time

value: Day 1


title: DU145_Control

value: Negetive control


title: GL26110_CD31posP2_G08_R1


title: PCI-35, control, Day1


title: Raw264.7, AdipoAI, 3

type: RNA

city: GuangZhou

first: Yu

middle: Hong

last: Wen

state: GuangDong

address: No. 1023-1063, South Shatai Road, Baiyun District, Guangzhou City

institute: Southern Medical University

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Raw264.7, AdipoAI for 24h

label_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: Total RNA of cells was   extracted, and 5-μg total RNA from each cell sample was sent to  Arraystar Inc. (Rockville, MD, USA) for microarray analysis.

treatment_protocol: Raw264.7 cells were stimulated with AdipoAI for 24 h followed by  incubation with 100 ng/ml of LPS (E. coli 0111: B4, Sigma-Aldrich,   St. Louis, MO, USA) for an additional 6 h.

value: macrophages cells

value: AdipoAI


title: C2B

description: pol CT_2


title: Raw264.7, AdipoAI, 2


title: GL26110_CD31posP2_E10_R1


title: Raw264.7, LPS, 3

source_name: Raw264.7, LPS for 6h

value: LPS


title: Raw264.7, AdipoAI+LPS, 1

source_name: Raw264.7, AdipoAI for 24h then LPS for 6h

value: AdipoAI+LPS


title: Raw264.7, AdipoAI+LPS, 3


title: Raw264.7, AdipoAI+LPS, 2


title: Raw264.7, AdipoAI, 1


title: Raw264.7, LPS, 2


title: C1B

description: pol CT_1

value: anther


title: GL26110_CD31posP2_F06_R1


title: AsPC-1, U0126, Day1


title: AsPC-1, control, Day1


title: MIAPaCa-2, U0126, Day1


title: C4A

description: mic CT_4

value: free microspore


title: C3A

description: mic CT_3


title: GL26110_CD31posP2_A08_R1


title: MIAPaCa-2, control, Day1


title: GL26110_CD31posP2_A05_R1


title: C2A

description: mic CT_2


title: GL26110_CD31posP2_G03_R1

value: Malignant


title: Raw264.7, LPS, 1


title: Raw264.7, DMSO, 3

source_name: Raw264.7, DMSO for 24h

value: DMSO


title: Raw264.7, DMSO, 2


title: Raw264.7, DMSO, 1


title: GL26110_CD31posP2_E12_R1


title: AsPC-1, si LINC00941 #1, Day1

data_processing:
HISAT2
StringTie
Supplementary files format and content: A spreadsheet file (xlsx) include TPM values, FPKM values, and Read count for each Sample

growth_protocol: AsPC-1 was maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

treatment_protocol:
The pancreatic cancer cells were seeded in 100-mm culture dishes at 5 × 105 cells per dish with an appropriate culture medium containing 10% FBS, and cultured under 37℃ in 5% CO2 with the appropriate humidity.
After 24 hours, the cells were transfected with siRNA at 200nmol/L using Oligofectamine Transfection Reagent (Invitrogen) according to the manufactureer's instructions. After 24 hours, RNA isolation was carried out.

value: siLINC00941 #1 (Thermo Fisher Scientific)


title: GRK-beta1AR_LV_Veh_rep2

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

description: Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). Each labeled cRNA was then fragmented, and the mixture was heated at 60°C for 30min. Lastly, labeled cRNAs were loaded into gasket slides and assembled to microarray slides. The slides were then incubated for 17h at 65°C in the SureHyb Hybridization Chamber (Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: LV_Veh_1 week

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit).

extract_protocol: Total RNAs from LVs were prepared using Qiagen RNeasy Plus kit. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: group

tag: gender

value: male

tag: strain

value: LV

value: 9 week age


title: C4D

description: tet CT_4

tag: tissue

tag: developmental stage

value: tetrad

tag: temperature

value: CT


title: C3D

description: tet CT_3


title: AsPC-1, si LINC00941 #2, Day1

tag: cell type

value: cancer cell line

value: WT

value: siLINC00941 #2 (Thermo Fisher Scientific)


title: AsPC-1, si Control, Day1

value: si control (Thermo Fisher Scientific)

value: Day 1


title: GL26110_CD31posP2_G06_R1

value: brain


title: GL26110_CD31posP2_B09_R1


title: C1A

description: mic CT_1


title: C1D

description: tet CT_1


title: GL26110_CD31posP2_F10_R1


title: UMUC3 cells, si-circPTK2-2

city: Wuhan

first: Li

last: weiquan

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Urology

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

data_processing:
libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina NovaSeq sequencer (Illumina)
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).

value: bladder cancer cell

value: circPTK2 knockdown


title: GL26110_CD31posP2_A11_R1


title: Uninjured Mouse Liver Nuclei sample 2

city: Edinburgh

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description: Single nuclei 3' gene expression v3

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using CellRanger 3.1.0.
Assembly: Modified GRCh38 Ensembl89 with introns included
Supplementary files format and content: mtx: raw count matrix in sparse matrix format
Supplementary files format and content: barcodes: raw barcode ids per sample
Supplementary files format and content: features: raw feature ids per sample

source_name: Liver

extract_protocol:
Tris-salt based nuclei extraction
10x Genomics single nuclei 3' gene expression v3

value: Liver


title: UMUC3 cells, si-circPTK2-CON

value: control


title: UMUC3 cells, si-circPTK2-1


title: GL26110_CD31posP2_B05_R1


title: Uninjured Mouse Liver Nuclei sample 1

description: Single nuclei 3' gene expression v3


title: C2D

description: tet CT_2

value: anther


title: T24 cells, si-circPTK2-CON


title: GRK-beta1AR_LV_Veh_rep3

value: 12 week age


title: GRK-beta1AR_LV_Veh_rep1

value: female


title: GRK-beta1AR_LV_ISO_rep2

source_name: LV_ISO_1 week

value: male

value: LV

value: 10 week age


title: GRK-beta1AR_LV_ISO_rep3


title: GRK-beta1AR_LV_ISO_rep1

value: 9 week age


title: GRK-beta1AR/miR150_LV_Veh_rep3


title: GRK-beta1AR/miR150_LV_Veh_rep2


title: T24 cells, si-circPTK2-1


title: MI-3

first: Jianyong

last: Sun

address: 115 Jinzun Road, Pudong New District

department: Laboratory of Oral Microbiota and Systemic Diseases

institute: Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casavasoftware used for basecalling.
(1)Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )(2)Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).(3)Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
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 HISAT v2.1.0, and FPKM (Fragments Per KilobaseMillonMapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_Foldchange|≥1 are identified as differentially expressed genes.
The GO (Gene Ontology, http://geneontology.org/)enrichment of DEGs was implemented by the hypergeometric test. GO terms with q<0.05 were considered to be significantly enriched.  The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: liver

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

value: liver

value: post natal week 12

value: wild type


title: GL26110_CD31posP2_E05_R1

value: Oligodendrocytes


title: GL26110_CD31posP2_G12_R1


title: MI-2


title: T24 cells, si-circPTK2-2


title: GL26110_CD31posP2_C03_R1


title: MI-1


title: Sham3


title: GL26110_CD31posP2_D11_R1


title: GRK-beta1AR/miR150_LV_Veh_rep1


title: Sham2


title: GL26110_CD31posP2_C07_R1


title: Engineered Heart Tissue, treated with vehicle, replicate 7

city: San Francisco

first: Anthony

middle: J.

last: Baker

state: CA

address: 4150 Clement St

department: VA Medical Center and Department of Medicine

institute: University of California San Francisco

data_processing:
Transcript abundance was quantified individually for each sample from the raw sequencing data by the pseudo-mapping approach, using the program kallisto; in average, 73% of the read pairs were mapped to transcripts.
Gene-level quantification of expression levels were performed using the package sleuth within the statistical computing environment R. "Gene mode" was used to combine the transcript-level expression measurements into gene expression measurements. The measurements are in Scaled Reads per Base.
Assembly: Homo_sapiens.GRCh38.96
Supplementary files format and content: GeneExpressionBySample.csv: File in CSV format. Each column is a sample. Each row is a gene, labeled with the Hugo gene symbol. The expression levels are in units of Scaled Reads per Base.

source_name: Engineered Heart Tissue

growth_protocol: Engineered heart tissues (EHTs) were formed with 1 million human iPSC-CM (PGP1 cell line; Coriell Institute, male) and 50,000 human cardiac fibroblasts per tissue, using decellularized porcine myocardial scaffolds (dimensions 150 micrometers thick, 2.75 mm wide, 6.34 mm long) that were incorporated into a polymer cassette (MyoPod™). EHTs were cultured at 37 degrees C for 3-5 wk. in DMEM with B27 supplement. After 3 wk. culture, EHTs were mounted at culture length (0% stretch) in the Myolab™ mechanical testing system. EHTs were superfused at 0.3 mL/minute with DMEM media at 37 degrees C. EHTs were electrically stimulated with square wave stimuli of 5 ms duration, 9-12 V amplitude, and 1-1.4 Hz frequency. EHTs were preconditioned with three slow stretch cycles from -5% to +5% of culture length. EHTs were returned to culture length and electrically paced until baseline peak twitch force reached equilibrium.

extract_protocol:
EHTs were preserved individually with RNA stabilization solution (RNAlaterTM, ThermoFisher), stored at -80C for approx. 2 wk, and shipped on dry ice to UC Davis for RNA-seq analysis. For RNA extraction, individual EHTs were transferred to a 1.5 mL Eppendorf tube on dry ice and homogenized using a cold pestle followed by addition of 0.25 mL of Trizol (Life Technologies, 15596026), vortexed for 1 min and incubated at room temperature (RT) for 10 mins. Samples were transferred to a QIAshredder tube (Qiagen LLC, 79654), centrifuged at 4°C, 14,000g for 2 mins. Eluate was returned to the original 1.5 mL Eppendorf tube, an additional 0.75 mL of Trizol was added, vortexed for 1 min and incubated at RT for 10 mins. Chloroform (0.2 mL) was added, briefly vortexed and centrifuged at 4°C, 14,500g for 15 mins. The clear aqueous phase was transferred to a new 1.5 mL Eppendorf tube, avoiding the phenol-chloroform phase. RNA was precipitated from aqueous phase by adding 0.6 mL of isopropyl alcohol, incubating for 5 min at RT, and centrifuging at 4°C, 14,500g for 15 mins. The supernatant was carefully discarded without disturbing the pellet. Three ethanol washes were performed using 0.75 mL of 70% ETOH preceding RNA clean up. After the last wash, the tubes were left to air dry for 30 mins at RT. RNA was dissolved in 50 µL of nuclease-free water and incubated at 55°C for 5 mins. Purification of RNA was followed immediately after extraction using an RNA Clean & Concentrator kit (Zymo Research, R1017). Briefly, two volumes of RNA Binding Buffer were added to the eluate and mixed, followed by an equal amount of 100% of ETOH, mixed, and transferred to a Zymo-spin column. Sample was centrifuged at 13,000g for 30 seconds and supernatant discarded. DNase treatment was performed in column by adding 75 µL of DNA digestion buffer and 5 µL of DNase I (Zymo Research, E1010) and incubating for 15 mins at RT. Following incubation, 0.4 mL Prep Buffer was added, centrifuged at RT, 13,000g for 30 sec and supernatant discarded; 0.7 mL of RNA wash buffer was then added, centrifuged at RT, 13,000g for 30 sec and supernatant discarded. A second round of 0.4 mL of RNA wash buffer was added, centrifuged at RT, 13,000g for 30 sec and supernatant discarded. RNA was eluted by adding 30 µL of RNase-free water, incubating for 1 min, and centrifuging at RT, 13,000g for 30 seconds. Samples required an RNA integrity number (RIN) >7.0 and an A260/280 ratio of absorbance > 1.7 to proceed.
Strand-specific and barcode indexed RNA-seq libraries were generated from 100-200 ng total RNA from each EHT and after poly-A enrichment using the Kapa mRNA-seq Hyper kit (Kapa Biosystems, Cape Town, South Africa) following the manufacturer instructions. The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA). The libraries were quantified by fluorometry on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA) and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems) and sequenced on an Illumina NovaSeq 6000 system (Illumina, San Diego, CA) run with paired-end 150 bp reads.

treatment_protocol: The EHT were mechanically tested in the Myolab™ after 3 wk. of culture, then EHT were returned to culture for a further 2 wk. and chronically treated with either: 10 nM A61603; or vehicle control (vitamin C and HCl), with media changed every other day. After 2 wk., plus a 24-hr. washout of drug, EHT mechanical testing was repeated.

value: Engineered Heart Tissue

value: PGP1 cell line, Coriell Institute, male

value: iPSC derived cardiomyocytes and fibroblasts

value: Vehicle (Vitamin C and HCl)


title: Engineered Heart Tissue, treated with vehicle, replicate 6


title: Engineered Heart Tissue, treated with A61603, replicate 6

value: a1A-AR agonist A61603


title: Sham1


title: GL26110_CD31posP2_F05_R1

value: brain


title: Engineered Heart Tissue, treated with A61603, replicate 5


title: GL26110_CD31posP2_E02_R1


title: GL26110_CD31posP2_E08_R1


title: GL26110_CD31posP2_G05_R1


title: GL26110_CD31posP2_D04_R1


title: KO1


title: Engineered Heart Tissue, treated with A61603, replicate 4


title: GL26110_CD31posP2_H01_R1


title: Engineered Heart Tissue, treated with vehicle, replicate 4


title: KO2


title: GL26110_CD31posP2_E06_R1


title: Engineered Heart Tissue, treated with vehicle, replicate 3


title: KO1 sham


title: Engineered Heart Tissue, treated with vehicle, replicate 5


title: Engineered Heart Tissue, treated with A61603, replicate 3


title: KO3


title: Sham rep6 [Sham25]

city: Hang Zhou

first: Qiao

last: Jin

address: Sandun Town, Xihu District

department: College of Animal Sciences

institute: Zhe Jiang university

data_processing:
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads
Trimmed sequence reads were mapped to rn6 using Hisat2 (Default parameters)
Read count extraction and normalization were performed using featureCounts
Assembly: rn6
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

source_name: Left ventricle

extract_protocol:
The fresh heart MI regions were harvested from rat 7 d post-MI and patch implantation.Total RNA was extracted from heart tissues by Trizol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codeswere added to attribute sequences to each sample.

value: Sprague Dawley

value: left ventricle

value: Sham


title: GRK-beta1AR/miR150_LV_ISO_rep2

value: male

value: 11 week age


title: attached SAS 72h, rep4

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA was hybridized to the Agilent expression microarray according to the manufacturer's instruction.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Data processig was performed using Agilent Feature Extraction v11.0.1.1.

label_protocol: Labeled cRNA was prepared from total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: Attched SAS cells were cultured at standard plate in Dulbecco's modified Eagle's medium containing 10% fetal calf serum for 72h. Detached SAS cells were cultured at low attachment plate in Dulbecco's modified Eagle's medium containing 10% fetal calf serum for 72h.

extract_protocol: Total RNA was isolated using TRIzol reagent according to the manufacturer's instruction.

value: SAS

value: tongue cancer cell

tag: culture method

value: SAS cells cultured at standard plate


title: GRK-beta1AR/miR150_LV_ISO_rep3

value: female

value: LV

value: 12 week age


title: attached SAS 72h, rep2


title: Engineered Heart Tissue, treated with vehicle, replicate 2

value: Engineered Heart Tissue

tag: treatment


title: detached SAS 72h, rep2

value: SAS cells cultured at low attachment plate


title: detached SAS 72h, rep3


title: GRK-beta1AR/miR150_LV_ISO_rep1

tag: age

value: 10 week age


title: detached SAS 72h, rep4


title: KO3 sham

value: liver

value: post natal week 12


title: attached SAS 72h, rep3


title: detached SAS 72h, rep1


title: KO2 sham


title: W3

value: wild type


title: GL26110_CD31posP2_E01_R1

value: brain


title: attached SAS 72h, rep1


title: W2


title: Sham rep4 [Sham23]

value: Sprague Dawley

value: left ventricle


title: Sham rep5 [Sham24]

value: Sham


title: Engineered Heart Tissue, treated with A61603, replicate 1

value: PGP1 cell line, Coriell Institute, male

value: iPSC derived cardiomyocytes and fibroblasts

value: a1A-AR agonist A61603


title: GL26110_CD31posP2_C01_R1


title: W1


title: W3 sham


title: GL26110_CD31posP2_H12_R1


title: Sham rep2 [Sham21]


title: Engineered Heart Tissue, treated with A61603, replicate 2


title: GL26110_CD31posP2_B04_R1


title: Sham rep1 [Sham20]


title: GL26110_CD31posP2_G04_R1


title: W2 sham


title: Microneedle patch rep6 [P18]

value: Microneedle patch


title: GL26110_CD31posP2_C05_R1


title: W1 sham


title: GL26110_CD31posP2_D07_R1


title: Engineered Heart Tissue, treated with vehicle, replicate 1

value: Vehicle (Vitamin C and HCl)


title: GL26110_CD31posP2_A12_R1


title: Microneedle patch rep4 [P16]


title: Sham rep3 [Sham22]


title: Microneedle patch rep5 [P17]


title: GL26110_CD31posP2_D01_R1


title: GL26110_CD31posP2_C06_R1


title: Microneedle patch rep3 [P15]


title: GL26110_CD31posP2_D05_R1


title: A549 cells, tRF-5003b

city: Patras

first: Constantinos

last: Stathopoulos

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

description:
RNA extracted after using tRF-5003b in A549 lung cancer cell line
tRF_5003.xlsx

data_processing:
miRNAs, tRFs and tRNAs were analyzed using an in-house build script.
human tRFs from the tRFdatabase (http://genome.bioch.virginia.edu/trfdb/) were counted directly in the fastq files.
tRNAs were mapped to an artificial tRNA genome consisting of unique sequences of hg38 tRNAs (http://gtrnadb.ucsc.edu/) using bowtie and further counted using bedtools coverage
miRNAs were mapped to an artificial miRNA genome consisting of human miRNAs from the miRdatabase (http://www.mirbase.org/)  using bowtie and further counted using bedtools coverage
Genome_build: hg38
Supplementary_files_format_and_content: abundance measurements

source_name: Lung cancer cell line (A549)

growth_protocol: Tumor specimens were obtained by surgical procedures

extract_protocol:
Frozen tissues were immediately lysed, and small and large RNA fractions were extracted and isolated using PureLink RNA mini Kit and mirVana miRNA Isolation Kit (Ambion)
Ion Total RNA-Seq Kit v2 protocol for small RNA sequencing

value: A549 lung cancer cell line


title: KD_random rep1

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to mm10 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Normalized count were calculated using a protocol from Davide Risso et al., Nature biotechnology, 2014.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include Normalized count values for each Sample.

source_name: Embryonic stem cell

growth_protocol: Mouse E14 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma). .

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: The shRNA of MuERVL was cloned into pSuper puro vector .WT mESCs were transfected  with 1000ng  pSuper puro vector . After transfection for 24h,the cells were treated with 1ug/ml puromycine for 4days and the medium were changed  every 24h.


title: KD_MERVL rep2

value: MERVL knocked down


title: KD_random rep2


title: KD_MERVL rep1


title: Microneedle patch rep1 [P13]


title: GL26110_CD31posP2_B11_R1

source_name: brain


title: Sutured patch rep6 [P12]

value: Sutured patch


title: A549 cells, tRF-3021a

description:
RNA extracted after using tRF-3021a in A549 lung cancer cell line
tRF_3021.xlsx


title: Microneedle patch rep2 [P14]


title: shRNA1-2

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Clean datas were mapped to the human genome (UCSC hg38) using Hisat2 (v2.2.1).
Transcripts were assembled using StringTie (v2.2.1). Gene expression levels were quantified as gene counts using PrepDE.py script.
DEseq2 was used to perform differential expression analysis.
Assembly: hg38
Supplementary files format and content: Gene counts for every gene in different samples were calculated by StringTie (v2.2.1) and PrepDE.p.

source_name: human hepatocellular carcinoma cell

growth_protocol: HepG2 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37 ℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The lentiviruses expressing control or shCARM1 shRNA were employed to infect HepG2 cells to obtain stable expression cells. These cells were treated with 10 µM Sorafenib for 24 hours.

value: CARM1 shRNA1


title: shRNA2-2

value: CARM1 shRNA2


title: Sutured patch rep5 [P11]


title: A549 cells, Si Luc

description:
RNA extracted after using Si RNA for Luciferase in A549 lung cancer cell line
tRF_3021.xlsx
tRF_5003.xlsx

value: Si RNA for Luciferase


title: GL26110_CD31posP2_H03_R1

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)


title: Pilot 2 2.0mm 3s

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

institute: Stanford University

description: UMI Matrix

data_processing:
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)

molecule: polyA RNA

organism: Zea mays

source_name: anther

growth_protocol: individuals were grown under greenhouse conditions in Stanford, CA, USA with 14-h day/10-h night lighting, approximating half of peak summer solar radiation including UV-A. Daily irrigation and fertilization maintained robust growth

extract_protocol:
Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.

value: anther

value: anther single cell


title: control-2

value: liver

value: control


title: GL26110_CD31posP2_C11_R1

last: Perez

address: 30 Fruit Street

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

value: brain


title: shRNA1-1


title: Pilot 2 2.0mm 6s

description: UMI Matrix


title: Sutured patch rep3 [P9]

value: Sprague Dawley

value: left ventricle


title: control-1


title: shRNA2-1


title: Pilot 1 2.0mm 61s

description: UMI Matrix


title: GL26110_CD31posP2_A06_R1

value: Malignant


title: Sutured patch rep2 [P8]


title: GL26110_CD31posP2_A10_R1


title: GL26150_CD31posP2_E05_R1


title: GL26110_CD31posP2_F08_R1


title: MI rep6 [Mi6]

value: MI


title: HUVEC, IgG (ab6702)

city: shanghai

first: Erzhen

last: Chen

address: ruijin hospital

institute: ruijin hospital

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag 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
Clean reads were aligned to the UCSC hg38 genome using BWA. Only uniquely mapping reads with at most two mismatches were retained.
To create CUT&Tag coverage plots, the locations of the mapped CUT&Tag reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS2. The arguments used were: macs2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B –SPMR。
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: HUVEC

extract_protocol:
Chromatin was digested with Tn5 and extracted with Trizol according to manufactor's protocol.
Libraries were prepared according to NEB's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were purified using MinElute PCR Purification Kit (Qiangen). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

value: HUVEC

value: umbilical vein endothelial cells

tag: antibody


title: GL26150_CD31posP2_E04_R1

city: Boston

first: Elizabeth

institute: MGH


title: HUVEC,H3K14la(PTM1414) rep1


title: GL26150_CD31posP2_B12_R1


title: Pilot 1 2.0mm 40s

description: UMI Matrix


title: Sutured patch rep1 [P7]


title: B3

city: Jingan district

first: Hanjie

last: Yu

state: Shanghai

institute: Shanghai Tenth People’s Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: blood

extract_protocol:
2 ml PBMCs from gout patients were obtained in EDTA-anticoagulated and the whole blood was diluted with 1×PBS. Equal volume Ficoll lymphocyte separation solution (solarbio, P4350) was added into the 50ml centrifuge tube, and the diluted blood was slowly spread onto the lymphocyte separation solution. Centrifugation was conducted at 20 ℃ with the horizontal rotor at 2000rpm for 20min, and break was set to 0. Carefully drain the intermediate white membrane (PBMC) cells into the new 15ml centrifuge tube. White membrane layer cells were washed with 10ml 1×PBS. 300g, centrifuged for 10min. The supernatant was discarded, then the cells were suspended with 5ml 1×PBS, centrifuged at 300g for 10min and washed twice, then the supernatant was discarded, and the cells were suspended with 1ml RPMI 1640 medium (Conring, Art. 10-040-CVR) supplemented with 0.04%BSA. Luna cell counter or Trypan blue staining was used to count single cell suspension concentration and cell viability
Single-cell RNA-seq libraries were generated by using Chromium Single cell 3’ Reagent v2 Kits according to the manufacturer’s protocol. PBMC suspensions were loaded on the Chromium Single Cell Controller Instrument (10×Genomics) to with partitioning oil, reverse transcription (RT) reagents, and a collection of gel beads that contained 3,500,000 unique 10× barcodes. generate single cell gel beads in emulsions (GEMs). Following GEMs generation, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and barcoded-cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). Whereafter, cDNAs were amplified with appropriate cycles (98°C for 3 min; cycled 12 times: 98°C for 15 sec, 63°C for 20 sec, and 72°C for 1 min; 72°C for 1 min; end at 4°C) and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter, USA). Subsequently, the amplified cDNA was fragmented, end-repaired, polyA-tailed, index adaptor ligated. PCR amplified with sample indexing primers (98°C for 45 sec; 14-16 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min; end at 4°C), and double-sided size selected with SPRIselect beads. Then these libraries were sequenced on the Illumina sequencing platform (Illumina novaseq 6000) and 150 bp paired-end reads were generated.

value: blood

value: PBMCs

tag: disease state

value: Remission


title: Pilot 2 2.0mm 74s

description: UMI Matrix


title: B2

description: 10x Genomics


title: Pilot 1 2.0mm 13s

description: UMI Matrix


title: MI rep4 [Mi4]


title: Sutured patch rep4 [P10]

value: Sutured patch


title: B1

description: 10x Genomics


title: GL26150_CD31posP2_A01_R1


title: Pilot 2 2.0mm 96s

description: UMI Matrix


title: A3

description: 10x Genomics

value: Acute flare


title: MI rep3 [Mi3]


title: GL26150_CD31posP2_B02_R1


title: MI rep2 [Mi2]


title: Pilot 2 2.0mm 85s

description: UMI Matrix


title: A2

description: 10x Genomics


title: Pilot 1 2.0mm 94s

description: UMI Matrix


title: MI rep5 [Mi5]


title: Pilot 2 2.0mm 27s

description: UMI Matrix


title: GL26150_CD31posP2_F10_R1


title: GL26150_CD31posP2_A09_R1


title: GL26150_CD31posP2_D04_R1


title: A1

description: 10x Genomics


title: GL26150_CD31posP2_A07_R1


title: SA 10uM PSMalpha3 6h

city: La Jolla

first: Michael

middle: R

last: Williams

address: 9500 Gilman Drive

department: Dermatology

institute: UC San Diego

data_processing:
Fastqc-->STAR-->featurecounts-->Rstudio (EdgeR)
Assembly: Gencode GrCh38.p13
Supplementary files format and content: excel workbork files

source_name: nHEK

growth_protocol: nHEK cells were maintained in Epilife medium (60uM CaCl2) supplemented with human keratnocyte growth supplement (HKGS)  and antibiotic/antimycotic in humidified atmosphere with 5% CO2 at 37C. Used between passages 3-5.

extract_protocol:
mRNA was harvested using Purelinke RNA Mini kit.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following manufacturer's protocols.

treatment_protocol:
10uM of synthetic S. epidermidis or S. aureus PSMS were applied to 70% confluent (48h 2mM CaCl2 differentiated) nHEKs for 6h.
PSM peptide dissolved in DMSO and treated at final concentraiton of 0.1% on nHEK cells.

value: nHEK

value: primary neonatal human epidermal keratinocyte

value: WT

value: 10uM SA PSMalpha3


title: Pilot 1 2.0mm 1s

description: UMI Matrix

value: anther

value: anther single cell


title: SE 10uM delta-toxin 6h

value: 10uM SE delta-toxin


title: SE 10uM PSMepsilon 6h

value: 10uM SE PSMepsilon


title: Pilot 1 2.0mm 62s

description: UMI Matrix


title: Pilot 1 2.0mm 79s

description: UMI Matrix


title: GL26150_CD31posP2_C06_R1

value: brain


title: GL26150_CD31posP2_F02_R1

value: Malignant


title: SE 10uM PSMdelta 6h

value: 10uM SE PSMdelta


title: Pilot 2 2.0mm 21s

description: UMI Matrix


title: Pilot 1 2.0mm 41s

description: UMI Matrix


title: GL26150_CD31posP2_C01_R1


title: Pilot 1 2.0mm 80s

description: UMI Matrix


title: MI rep1 [Mi1]

value: Sprague Dawley

value: left ventricle

value: MI


title: SE 10uM PSMalpha 6h

value: 10uM SE PSMalpha


title: DMSO (-) Control 6h

value: DMSO only


title: Pilot 1 2.0mm 14s

description: UMI Matrix


title: GL26150_CD31posP2_G06_R1


title: SH-SY5Y, 6OHDA, 18hr, rep4

city: Gebze

first: Tunahan

last: Cakir

state: Kocaeli

address: Gebze, Kocaeli, Turkey

department: Department of Bioengineering

country: Turkey

institute: Gebze Technical University

description: Gene expression at 18th hour from 6OHDA treated cell lines

hyb_protocol: The labeled cDNA was hybridized to Human Gene Expression Array 8 × 60 K (The SurePrint G3 Human Gene Exp v3, Agilent) by using Gene Expression Hybridization Kit (#5188-5242).

scan_protocol: After hybridization, slides were scanned using NimbleScan 2.5 software to get the raw expression data.

data_processing: The raw data was normalized by using the limma package in R (Ritchie et al, 2015). Specifically, background correction was performed by using the normexp method with an offset value of 10, followed by quantile normalization.

source_name: SH-SY5Y, 6-OHDA treated, 18th hour

label_protocol: RNA samples were converted to cDNA by using RNA Spike-In One-color kit (#5188-5282) and labeled with Agilent Low Input Quick Amp Labeling Kit (#5190-2305).

extract_protocol: RNA samples were isolated using Absolutely RNA isolation kit (#400805, Agilent), Agilent RNA 6000 Nano Kit Agilent and Bioanalyzer System were used for quality check.

value: in vitro Parkinson’s Disease (PD) model


title: SH-SY5Y, 6OHDA, 18hr, rep3


title: Static HUVECs -BMSC-CM 3

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

data_processing:
Paired end sequencing was performed on an Illumina NovaSeq 6000 using 100 cycles for each mate.
Fastq files were constructed using bcl2fastq (v2.20.0.422).
SMARTer + polyT adapters were removed using fqtrim (v0.9.7)
Pseudo counts were measured on the trimmed Fastq files using salmon (v1.3.0) using flags gcBias seqBias.
Database used for the analysis ensembl GRCh38.rel98
Data was analysed with DESeq2 package retrieved from bioconductor
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs, single donnor) were obtained from Lonza

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions. RNA concentration and size distribution profile were analyzed on an Agilent Bioanalyzer RNA 6000 Pico chip (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMSCs were seeded into T75 cm2 flasks at a density of 10 4 cells/cm 2 and grown until 70-80% confluence. After washes, cells were refreshed with α-MEM containing 0.1% BSA and incubated under 3% O2 for 48h as described. Supernatant (conditioned medium) was collected. HUVECs were treated with 300uM CoCl2 in the presence or abscence of BMSC-CM for 24h in static condition or dynamic condition

value: Umbillical cord

value: Human umbilical vein endothelial cells

value: 24h treated with 50%EBM+50%BMSC-CM and CoCl2


title: Static HUVECs -BMSC-CM 2


title: GL26150_CD31posP2_H08_R1


title: SH-SY5Y, 6OHDA, 18hr, rep2


title: Pilot 2 2.0mm 90s

description: UMI Matrix


title: SH-SY5Y, 6OHDA, 12hr, rep3

description: Gene expression at 12th hour from 6OHDA treated cell lines

source_name: SH-SY5Y, 6-OHDA treated, 12th hour


title: Pilot 2 2.0mm 83s

description: UMI Matrix


title: SH-SY5Y, 6OHDA, 18hr, rep1


title: GL26150_CD31posP2_D05_R1


title: GL26150_CD31posP2_E03_R1


title: Pilot 2 2.0mm 88s

description: UMI Matrix


title: Static HUVECs -Control 3

value: 24h treated with 50% Endothelial Cell Growth Basal Medium+50%BSA and CoCl2


title: SH-SY5Y, 6OHDA, 12hr, rep2


title: Static HUVECs -BMSC-CM 1


title: Static HUVECs -Control 1


title: Pilot 2 2.0mm 8s

description: UMI Matrix

value: anther


title: Static HUVECs -Control 2


title: Pilot 2 2.0mm 30s

description: UMI Matrix

value: anther single cell


title: GL26150_CD31posP2_H07_R1


title: SH-SY5Y, 6OHDA, 12hr, rep4


title: GL26150_CD31posP2_B05_R1


title: GL26150_CD31posP2_E06_R1


title: Pilot 1 2.0mm 83s

description: UMI Matrix


title: SH-SY5Y, Control, 18hr, rep4

description: Gene expression at 18th hour from control cell lines

source_name: SH-SY5Y, untreated, 18th hour

value: control


title: GL26150_CD31posP2_B04_R1


title: GL26150_CD31posP2_H01_R1


title: Pilot 2 2.0mm 92s

description: UMI Matrix


title: SH-SY5Y, Control, 18hr, rep3


title: SH-SY5Y, Control, 12hr, rep4

description: Gene expression at 12th hour from control cell lines

source_name: SH-SY5Y, untreated, 12th hour


title: SH-SY5Y, Control, 18hr, rep2


title: SH-SY5Y, Control, 18hr, rep1


title: GL26150_CD31posP2_B08_R1


title: SH-SY5Y, 6OHDA, 12hr, rep1


title: Dynamic HUVECs -Control 3


title: Pilot 1 2.0mm 59s

description: UMI Matrix


title: GL26150_CD31posP2_E08_R1


title: GL26150_CD31posP2_D08_R1


title: Dynamic HUVECs -BMSC-CM 3


title: Dynamic HUVECs -Control 2


title: GL26150_CD31posP2_E11_R1


title: Pilot 1 2.0mm 57s

description: UMI Matrix


title: Human baby foreskin APCs from colonized tissue, loaded cells with Staphylococcus epidermidis antigens; mRNA

first: Antonin

last: Weckel

address: 513 Parnassus

institute: UCSF

description: 3' library, aligned to the genome GRCh38 with Cell Ranger

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Foreskin

extract_protocol:
Skin was digested with collagenase and cells sorted to isolate live CD45+ HLA-DR+ antigen presenting cells, loaded with S.epidermidis antigens (zsgreen-pos) or not  (zsgreen neg)
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics)

treatment_protocol: 4 Human baby Foreskins were split in two and set up in an explant system. Staphylococcus epidermidis Tu3298 expressing the zsgreen fluorochrome was added topically to the explants for 4h.

value: Foreskin

value: antigen presenting cells

tag: bacterial antigen_loading_status

value: loaded


title: GL26150_CD31posP2_G10_R1

value: brain

value: Malignant


title: Dynamic HUVECs -BMSC-CM 2


title: Dynamic HUVECs -Control 1


title: Pilot 1 2.0mm 90s

description: UMI Matrix


title: Human baby foreskin APCs from colonized tissue, non-loaded cells; mRNA

value: non-loaded


title: Pilot 1 2.0mm 3s

description: UMI Matrix


title: GL26150_CD31posP2_B07_R1


title: Pilot 2 2.0mm 7s

description: UMI Matrix


title: Pilot 2 2.0mm 28s

description: UMI Matrix


title: GL26150_CD31posP2_F05_R1


title: Ovarian follicular aspirate, normal, rep4

city: LEXINGTON

first: Yohan

last: Choi

state: KY

address: 800 Rose St, UKMC MS341

institute: University of Kentucky

description: 10X Genomics

data_processing:
The single-cell RNA sequencing output was gone through mkfastq and count pipelines in the Cell Ranger Single Cell Software Suite (v3.1.0) using default parameters.
Supplementary files format and content: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Ovarian ovulatory follicle

extract_protocol:
Immediately after retrieval of cumulus-oocyte complexes, the cells in the aspirates were subjected to red blood cell lysis in an ACK RBC lysis buffer to remove erythrocytes. The remaining cells were thoroughly resuspended and filtered through a 40-µm cell strainer to dissociate cell clumps into single-cells.
Only samples showing acceptable viability (above 85%) were subjected to the following processes. 0.5 x 10^6 cells were used to generate single-cell cDNA libraries using the Chromium Single Cell 3’ v3 Reagent kit at the Art & Science Imaging Center of the University of Kentucky. Briefly, individual cells were separated into droplets and barcoded in gel beads, including 10x cell barcodes, unique molecular identifier (UMI), and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA.

value: Ovarian ovulatory follicle

value: Various cell types (cumulus-oocyte complexes)


title: Ovarian follicular aspirate, normal, rep3

description: 10X Genomics


title: Pilot 2 2.0mm 16s

description: UMI Matrix


title: GL26150_CD31posP2_C08_R1


title: Pilot 1 2.0mm 88s

description: UMI Matrix


title: PDL1.IPF_rep2

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 8.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Primary isolated cells, Lung Epithelial cells

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2  µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

extract_protocol: Qiagene plus micro kit

tag: source

value: IPF

tag: htll-280 status

value: low

tag: pd-l1 status

value: high


title: GL26150_CD31posP2_C03_R1


title: PDL1.IPF_rep1


title: Ovarian follicular aspirate, normal, rep2

description: 10X Genomics


title: Ovarian follicular aspirate, normal, rep1

description: 10X Genomics


title: Pilot 1 2.0mm 86s

description: UMI Matrix

tag: genotype


title: Pilot 2 2.0mm 59s

description: UMI Matrix


title: ATP2.IPF_rep2


title: sgCdkn1a rep5

city: SHANGHAI

first: Peng

state: SHANGHAI

address: No.197 RUIJIN ER RD

institute: SHANGH RUIJIN HOSPITAL

data_processing:
Trim-Galore was utilized to remove the adapter sequences
Sequenced clean reads were mapped to GRCz11 zebrafish genome using STAR (v2.7.8)
HT-Seq (v0.13.5) was used to obtain the raw count
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Zebrafish

extract_protocol:
Total RNA was extracted and purified with TRIzol (Invitrogen, United States) as described by the manufacturer. RNA quantity and purity was determined with the NanoDrop ND-1000 (NanoDrop, Wilmington, United States) and Bioanalyzer 2100 (Agilent, USA). Only RNAs with a high RNA integrity number (RIN > 7) were selected and used for the subsequent sequencing.
RNA libraries were prepared for sequencing using Illumina Novaseq™ 6000


title: SH-SY5Y, Control, 12hr, rep1

tag: cell line

tag: time


title: Human, ACTA2 R179H variant, ascending aortic aneurysm

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

description:
ACTA2_human
Acta2 R179H aortopathy
Single Lane (3 total raw files).

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite’. Raw, indexed base-call files from NovaSeq 6000 runs were demultiplexed to generate FASTQ files (included here as raw data files) using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) or human (hg19) genome as appropriate. Cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline.
Output files from the Cellranger pipeline (individual cell barcode, feature, and matrix files for each sample) are included in this repository as processed data files.
Assembly: mm10, hg19
Supplementary files format and content: 'barcodes.tsv.gz' is a column of unique barcodes corresponding to individual cells in the dataset.
Supplementary files format and content: 'features.tsv.gz' is a column of gene name identifiers from the specified genome build to which the samples were aligned.
Supplementary files format and content: 'matrix.mtx.gz' is a matrix of gene counts per cell with cell identifier barcodes arranged in columns and gene names (features) arranged in rows.

source_name: Ascending aorta

extract_protocol:
Aortic tissues were cleaned and rinsed with saline to remove residual blood. Tissues were finely minced and digested enzymatically in collagenase/elastase cocktail. Single cell suspensions were then pelleted, washed, and sorted for live cells using fluorescence-activated cell sorting.
Individual sample libraries were generated from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Ascending aorta

value: ACTA2 R179H variant

value: Aortic aneurysm

value: pediatric


title: Pilot 2 2.0mm 80s

description: UMI Matrix

value: anther

value: anther single cell


title: sgCdkn1a rep4


title: GL26150_CD31posP2_A08_R1


title: Human, pediatric healthy donor, ascending aorta

description:
Donor_human
Donor control
Sequenced on two lanes (6 total raw files).

value: Control

value: Healthy control


title: sgCdkn1a rep3


title: ATP2.IPF_rep1


title: ATP2.Donor_rep2

value: Donor


title: GL26150_CD31posP2_C10_R1

value: brain


title: PDL1.Donor_rep1


title: SK_RNA_ASA_REP3

city: Chicago

first: Sonia

middle: S

last: Kupfer

state: IL

department: Human Genetics

institute: University of Chicago

data_processing:
ATAC-seq fastq reads aligned with bwa mem (v 0.7.17)
ATAC-seq read filtering performed with samtools (v 1.10)
ATAC-seq peak calling performed with MACS2 (v 2.1.0)
ATAC-seq differential peak calling performed with R packages DiffBind and edgeR
ATAC-seq motif enrichment and peak annotation performed with HOMER (v 4.11.1). Differential transcription activity assessed with diffTF (v 1.8).
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2
Assembly: RNA-seq reads were aligned to the transcriptome reference, which was generated from the 1000genomes Phase2 Reference Genome Sequence (hs37d5) and transcript annotations from the Gencode comprehensive gene annotation GTF (Release 29). ATAC-seq reads were aligned to the Homo_sapiens_assembly38.fasta assembly (downloaded from the UCSC Genome Browser website)
Supplementary files format and content: peak files are MACS2 outputted narrowPeak files for treated and untreated ATAC-seq samples

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: The organoids were harvested using cold Advanced DMEM, pipetted up and down 10 times, moved to centrifuge tube, and then spun at 400 g for 5 min at 4°C. Upper media and Biomedical engineering (BME) were carefully aspirated and discarded. mRNA was then isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. ATAC-seq: Cells were  treated using the Omni-ATAC protocol17 with some modifications. Briefly, the cells were treated with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then suspended in the transposition reaction mix (50% TD Tagment DNA Buffer, 5% TDE1 Tagment DNA Enzyme, 33% PBS) for 30 min
RNA-seq: RNA-seq libraries were prepared using Illumina mRNA TruSeq Kits as protocolled by Illumina. ATAC-seq: Libraries were prepared using the Nextera DNA CD Idx (Illumina 20018708).

treatment_protocol: After 24 hours of culturing in the basal media (which did not contain ASA), organoids were treated with either 3 mM ASA or vehicle control (0.1% DMSO) for 24 hours. The treatments were performed in triplicate.

tag: sample type

value: organoid

value: rectosigmoid mucosa

value: ASA 24 hrs


title: Pilot 1 2.0mm 27s

description: UMI Matrix

tag: tissue


title: SK_RNA_ASA_REP2


title: GL26150_CD31posP2_F08_R1

source_name: brain


title: Pilot 1 2.0mm 87s

description: UMI Matrix


title: GL26150_CD31posP2_A06_R1

value: Malignant


title: sgCdkn1a rep2

last: Jin


title: ATP2.Donor_rep1


title: Pilot 2 2.0mm 4s

description: UMI Matrix


title: sgCdkn1a rep1


title: SK_RNA_ASA_REP1


title: PDL1.Donor_rep2


title: Control rep5


title: GL26150_CD31posP2_A04_R1


title: Pilot 1 2.0mm 63s

description: UMI Matrix


title: SK_RNA_DMSO_REP6

value: DMSO 24 hrs


title: GL26150_CD31posP2_E12_R1


title: GL26150_CD31posP2_D02_R1


title: Pilot 1 2.0mm 69s

description: UMI Matrix


title: SH-SY5Y, Control, 12hr, rep3

value: control


title: SK_RNA_DMSO_REP5


title: SH-SY5Y, Control, 12hr, rep2


title: Pilot 2 2.0mm 55s

description: UMI Matrix


title: Control rep3


title: Pilot 1 2.0mm 16s

description: UMI Matrix


title: GL26150_CD31posP2_B10_R1


title: Control rep4


title: SK_RNA_DMSO_REP4


title: Pilot 2 2.0mm 81s

description: UMI Matrix


title: Control rep2


title: GL26150_CD31posP2_A10_R1


title: Pilot 2 2.0mm 34s

description: UMI Matrix


title: Control rep1


title: GL26150_CD31posP2_C07_R1


title: GL26150_CD31posP2_F06_R1


title: GLYR1-negative sample 1

city: Shanghai

first: Yan

last: Gu

address: 800 Xiangyin Road

department: Immunology

institute: Second Miilitary Medical University

data_processing:
Raw data (raw reads) were processed using Seqtk. Clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads.
Clean reads were mapped to reference sequences and/or reference gene set using Hisat2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample
The gene expression level is calculated by using FPKM method (Fragments Per Kilobase of exon model per Million mapped reads),
We use "q-value ≤0.05 and the absolute value of log2Ratio ≥1" as the threshold to judge the significance of gene expression difference.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values for each Sample

source_name: human pancreatic ductal adenocarcinoma

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Ribosomal RNA was removed from total RNA using Ribo-Zero rRNA removal beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

treatment_protocol: Fresh human pancreatic ductal adenocarcinoma were prepared by laser capture microdissection (LCM). In brief, surgically removed tissues were sectioned for H&E staining and LCM (Life technologies) was performed. Tumor tissues (stroma were excluded) were used for RNA extraction, and sequencing. Immunohistochemistry was used to identify GLYR1-positive samples. And GLYR1-negative samples were taken as controls.

value: pancreas


title: Pilot 1 2.0mm 36s

description: UMI Matrix

source_name: anther


title: GLYR1-negative sample 3


title: GLYR1-negative sample 2


title: Model Day7 rep3

value: post DEX day 7


title: Pilot 2 2.0mm 63s

description: UMI Matrix


title: Model Day7 rep2


title: Pilot 1 2.0mm 91s

description: UMI Matrix


title: Model Day7 rep1


title: GLYR1-positive sample 3


title: GLYR1-positive sample 2


title: GL26150_CD31posP2_B11_R1


title: GL26150_CD31posP2_B01_R1


title: GL26150_CD31posP2_A03_R1


title: Pilot 1 2.0mm 29s

description: UMI Matrix


title: Pilot 2 2.0mm 89s

description: UMI Matrix


title: GL26150_CD31posP2_H02_R1


title: Model Day6 rep3

value: post DEX day 6


title: GL26150_CD31posP2_C05_R1


title: CG14: iAEC2s (+MRC5s/insert)

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to hg19 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: hg19 with TdTomato reporter
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: SPC2-ST-B2 (SFTPCtdT/WT)  human iPSC line

extract_protocol:
cells were lysed in Trizol
single cells were captured for sequencing library prepration using a 10X Chromium
3' RNA-seq single cells

tag: developmental stage

value: day 114 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: FACS purification for live EPCAM+ cells


title: Model Day6 rep1


title: GLYR1-positive sample 1

tag: cell type


title: Model Day6 rep2

tag: treatment


title: Pilot 2 2.0mm 38s

description: UMI Matrix

value: anther

value: anther single cell


title: GL26150_CD31posP2_H10_R1


title: CG13: iAEC2s (3D/insert)

value: FACS purification for live cells


title: Model Day5 rep3

value: post DEX day 5


title: Pilot 2 2.0mm 91s

description: UMI Matrix


title: CG12: iAEC2s (3D)


title: Model Day5 rep2


title: CG8: 1˚ AEC2s (pre-culture; PL1)

source_name: EPCAM+/HTII-280+ FACS purified 1˚ AEC2s

value: adult

value: FACS purification for live EPCAM+/HTII-280+ cells


title: GL26150_CD31posP2_H05_R1

value: brain


title: Pilot 1 2.0mm 82s

description: UMI Matrix


title: Pilot 2 2.0mm 15s

description: UMI Matrix


title: Model Day5 rep1


title: CG7: 1˚ AEC2s (pre-culture; PL2)


title: Pilot 2 2.0mm 1s

description: UMI Matrix


title: Model Day4 rep3

value: post DEX day 4


title: GL26150_CD31posP2_F04_R1

value: Malignant


title: Model Day4 rep2


title: CG5: 1˚ AEC2s (cultured; P0 PL2)

source_name: EPCAM+/HTII-280+ FACS purified 1˚ AEC2s cultured with MRC5 fibroblasts


title: Pilot 1 2.0mm 20s

description: UMI Matrix


title: GL26150_CD31posP2_G08_R1


title: Pilot 2 2.0mm 29s

description: UMI Matrix


title: CG6: 1˚ AEC2s (cultured; P0 PL1)


title: Model Day4 rep1


title: Model Day3 rep3

value: post DEX day 3


title: GL26150_CD31posP2_D03_R1


title: Pilot 1 2.0mm 32s

description: UMI Matrix


title: AsPC-1_shARG2 #2_ATAC_rep2

first: Nada

middle: Y

last: Kalaany

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

data_processing:
RNA-seq: Data was aligned to the GRCh38 genome using STAR aligner (version 2.7.8a). Read counts were obtained using HTseq (version 0.13.5) and analyzed using DESeq2.
ATAC-seq: Data was aligned to the GRCh38 genome using Bowtie2 (version 2.4.2). Enriched regions were identified using MACS2. Bedtool (version 2.30) and DESeq2 were used to calculate the number of reads and determine differentially marked regions.
Genome_build: RNA-seq and ATAC-seq: GRCh38
Supplementary_files_format_and_content: RNA-seq: raw gene counts file; ATAC-seq: MACS2 called peaks

source_name: AsPC-1 cells

growth_protocol:
Grown in RPMI medium with 10% fetal bovine serum
please see above for each sample subset.

extract_protocol:
RNA-seq: Total RNA was isolated and purified using miRNeasy Mini Kit (Qiagen, 217004).
ATAC-seq: Cells were resuspended in 50 μl ice-cold ATAC lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) and centrifuged at 500 g at 4°C to isolate nuclear pellets that were then treated in 50 μl reactions with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 30 min at 37°C.
RNA-seq: mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
ATAC-seq: Transposed DNA was purified using a PCR purification kit (Zymo research, D4034) and then amplified immediately in 50 μl reactions with high-fidelity 2X PCR Master Mix (New England Biolabs) using a common forward primer and different reverse primers with unique barcodes for each sample. From the reaction mix, 45 μl was kept on ice after 5 cycles of PCR, while 5 μl was amplified by qPCR for 20 additional cycles; the remaining 45 μl was then amplified for the 5-7 cycles required to achieve 1/3 of the maximum qPCR fluorescence intensity. Amplified DNA was purified over columns and primer dimers (<100 bp) were removed using AMPure beads (Beckman Coulter).

treatment_protocol:
RNA-seq: Cells were seeded overnight at 250,000 cells per 10 cm plate. The cells were then washed once with PBS and incubated in RPMI medium with 0.1% fetal bovine serum and 100 ng ml−1 IGF-1 for 24 h.
ATAC-seq: Cells were seeded overnight at 100,000 cells per well in 6-well plates. The cells were then washed once with PBS and incubated in RPMI medium with 0.1% fetal bovine serum and 100 ng ml−1 IGF-1 for 24 h.

tag: shRNA

value: shARG2 #2


title: GL26150_CD31posP2_G03_R1


title: GL26150_CD31posP2_D01_R1


title: GL26150_CD31posP2_G04_R1


title: Model Day3 rep2


title: Pilot 1 2.0mm 84s

description: UMI Matrix


title: Model Day3 rep1


title: GL26150_CD31posP2_G01_R1


title: Pilot 2 2.0mm 41s

description: UMI Matrix


title: GL26150_CD31posP2_D11_R1


title: AsPC-1_shARG2 #1_ATAC_rep2

value: shARG2 #1


title: Pilot 1 2.0mm 93s

description: UMI Matrix


title: Mock4

first: Christina

last: Sigurdson

address: 9500 Gilman Dr

description:
tpm_filtered.csv
deseq2_results.csv

data_processing:
Adapters trimmed with cutadapt (v1.4.0)
Reads mapping to repetitive elements (RepBase v18.04) with STAR were removed
Remaining reads were mapped to mouse genome mm9 with STAR (v2.4.0i)
FeatureCounts was used to assign reads to genes (v1.5.0)
Assembly: mm9
Supplementary files format and content: tpm_filtered.csv, comma separated file with transcripts per million calculated for all expressed genes.
Supplementary files format and content: deseq2_results.csv, comma separated file with results from differential expression analysis (prion vs mock) calculated with DESeq2

source_name: Hippocampus

extract_protocol:
Hippocampus were homogenized TRIzol (1 mL per 100 mg of tissue) and incubated for 24 hours. Samples were then incubated in chloroform for 5 min, then centrifuged at 12,000 g for 15 min at 4 ̊C. The aqueous upper phase containing RNA was transferred to a tube containing an equal volume of 70% ethanol and vortexed. RNA was treated with DNases and isolated using the PureLink RNA isolation kit (ThermoFisher Scientific Cat# 12183025)
To generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions, modifying RNA shear time to five min. Resulting libraries were multiplexed and sequenced with 75 basepair (bp) single reads (SR75) to a depth of approximately 25 million reads per sample on an Illumina HiSeq4000

treatment_protocol: C57/BL6J mice were maintained under specific pathogen-free conditions on a 12:12 light/dark cycle. Mice had access to standard laboratory chow and water ad libitum. Mice (6-8 weeks old) were anesthetized with ketamine and xylazine and inoculated into the left parietal cortex with 30 µl of 1% 22L prion-infected brain homogenate prepared from terminally ill mice.

value: Hippocampus

tag: strain

tag: Sex

value: Male

value: Wild type

value: mock intracraneal inoculation


title: AsPC-1_shOAT #2_ATAC_rep2

value: shOAT #2


title: AsPC-1_shARG2 #1_ATAC_rep1


title: AsPC-1_shOAT #2_ATAC_rep1


title: AsPC-1_shOAT #1_ATAC_rep2

value: shOAT #1


title: Mock2

description:
tpm_filtered.csv
deseq2_results.csv


title: Pilot 2 2.0mm 35s

first: D.

last: Marchant

description: UMI Matrix

extract_protocol:
Anthers dissected, fixed, digested, isolated using a Hana Cell Sorter (NamoCell) following FX-Cell protocol (Marchant et al. 2022)
CEL-Seq2 (Hashimshony et al., 2016) with modifications per Nelms and Walbot 2019.

value: anther

value: anther single cell


title: GL26150_CD31posP2_F07_R1

last: Perez

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)


title: AsPC-1_shARG2 #2_ATAC_rep1


title: Pilot 1 2.0mm 25s

description: UMI Matrix

data_processing:
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Assembly: AgpV4
Supplementary files format and content: CSV containing the UMI counts for each cell (column) and gene (row)


title: Pilot 1 2.0mm 5s

description: UMI Matrix


title: AsPC-1_shOAT #1_ATAC_rep1


title: Mock3

description:
tpm_filtered.csv
deseq2_results.csv


title: Prion2

description:
tpm_filtered.csv
deseq2_results.csv

value: prion (22L stain) intracraneal inoculation


title: GL26150_CD31posP2_G02_R1


title: GL26150_CD31posP2_F11_R1


title: AsPC-1_shODC1 #2_ATAC_rep2

value: shODC1 #2


title: Pilot 2 2.0mm 17s

description: UMI Matrix


title: AsPC-1_shODC1 #2_ATAC_rep1


title: Prion1

description:
tpm_filtered.csv
deseq2_results.csv


title: GL26150_CD31posP2_E01_R1


title: Pilot 1 2.0mm 74s

description: UMI Matrix


title: AsPC-1_shODC1 #1_ATAC_rep2

value: shODC1 #1


title: GL26150_CD31posP2_F01_R1

value: brain


title: GL26150_CD31posP2_H11_R1


title: GL26150_CD31posP2_D09_R1


title: Pilot 2 2.0mm 26s

description: UMI Matrix


title: microglia in PLX-treated old mice (bio rep 4)

city: Baltimore

first: Rodney

middle: Matthew

last: Ritzel

state: MD

address: 655 W. Baltimore Street

department: Anesthesiology

institute: University of Maryland School of Medicine

data_processing:
Data quality were analyzed using FastQC v0.11.8
Transcript-level abundance was quantified using the quasi-mapping-based mode in Salmon v1.0.0, mapping to GRCm38 (mm10) mouse reference genome.
Transcript-level abundance were aggregated to gene-level abundance using tximport.
Genes with abundance of 0 in any samples were filtered out from further analysis.
DESeq2 (55) was used for differential expression analyses.
Assembly: mm10
Supplementary files format and content: normalized gene abundance aggregated by tximport, filtered genes with abundance of 0

source_name: Brain

extract_protocol:
FACS sorted microglia cells were flash frozen in dry ice into 300 μL RNAprotect cell reagent (Qiagen).  Total RNA was extracted using RNeasy mini kit (Qiagen).
Amplification of cDNA from the total RNA samples were performed using Ovation RNA-seq system kit (Tecan), following by low input RNA-seq library preparation.

value: Brain

tag: age

value: microglia


title: microglia in PLX-treated old mice (bio rep 3)


title: GL26150_CD31posP2_H03_R1

first: Elizabeth

value: Malignant


title: Pilot 1 2.0mm 56s

description: UMI Matrix


title: microglia in PLX-treated old mice (bio rep 2)


title: Prion3

description:
tpm_filtered.csv
deseq2_results.csv


title: Pilot 1 2.0mm 68s

description: UMI Matrix


title: AsPC-1_shScr_ATAC_rep2

value: shScr


title: Pilot 2 2.0mm 31s

description: UMI Matrix


title: GL26150_CD31posP2_B03_R1


title: microglia in PLX-treated old mice (bio rep 1)


title: AsPC-1_shScr_ATAC_rep1


title: GL26150_CD31posP2_F03_R1


title: GL26150_CD31posP2_C04_R1


title: AsPC-1_shARG2 #2_RNA_rep3

value: shARG2 #2


title: microglia in young mice (bio rep 3)


title: GL26140_CD31posP2_G01_R1

value: Los


title: microglia in young mice (bio rep 2)


title: Pilot 2 2.0mm 78s

description: UMI Matrix


title: Pilot 2 2.0mm 57s

description: UMI Matrix


title: microglia in young mice (bio rep 1)


title: AsPC-1_shARG2 #2_RNA_rep2


title: AsPC-1_shODC1 #1_ATAC_rep1


title: Pilot 2 2.0mm 94s

description: UMI Matrix


title: AsPC-1_shARG2 #2_RNA_rep1


title: AsPC-1_shARG2 #1_RNA_rep3

value: shARG2 #1


title: GL26140_CD31posP2_H09_R1


title: low autofluorescent microglia in old mice (bio rep 3)

tag: autofluorescence

value: low autofluorescent


title: Pilot 2 2.0mm 32s

description: UMI Matrix


title: GL26140_CD31posP2_C04_R1


title: AsPC-1_shARG2 #1_RNA_rep2


title: low autofluorescent microglia in old mice (bio rep 1)


title: GL26140_CD31posP2_A07_R1


title: low autofluorescent microglia in old mice (bio rep 2)


title: Pilot 1 2.0mm 55s

description: UMI Matrix


title: AsPC-1_shARG2 #1_RNA_rep1


title: Pilot 2 2.0mm 76s

description: UMI Matrix


title: Pilot 2 2.0mm 64s

description: UMI Matrix


title: high autofluorescent microglia in old mice (bio rep 5)

value: high autofluorescent


title: GL26140_CD31posP2_B12_R1


title: AsPC-1_shOAT #2_RNA_rep3

value: shOAT #2


title: Pilot 1 2.0mm 46s

description: UMI Matrix


title: GL26140_CD31posP2_E02_R1


title: high autofluorescent microglia in old mice (bio rep 3)


title: high autofluorescent microglia in old mice (bio rep 4)


title: Pilot 2 2.0mm 77s

description: UMI Matrix


title: AsPC-1_shOAT #2_RNA_rep2


title: AsPC-1_shOAT #2_RNA_rep1


title: Pilot 2 2.0mm 9s

description: UMI Matrix


title: high autofluorescent microglia in old mice (bio rep 2)


title: AsPC-1_shOAT #1_RNA_rep3

value: shOAT #1


title: GL26140_CD31posP2_G09_R1


title: Pilot 2 2.0mm 86s

description: UMI Matrix

value: anther


title: GL26140_CD31posP2_C05_R1


title: GL26140_CD31posP2_D10_R1


title: high autofluorescent microglia in old mice (bio rep 1)


title: Pilot 1 2.0mm 28s

description: UMI Matrix

value: anther single cell


title: AsPC-1_shOAT #1_RNA_rep2


title: AsPC-1_shOAT #1_RNA_rep1


title: female cisplatin IM rep 5

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

description:
72 after single i.p, injection
FC5

data_processing:
GeneWiz provided fastq files to the lab.
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star2.7.3a.  Counts were generated with the subread v2.0.1 and the featureCounts -p -t expm -g gene_id a -o
Count matrixes were then analyzed using DESeq2 v1.28.1 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Genome_build: mm10
Supplementary_files_format_and_content: excel files with Deseq2 log2FC and statistics, and normalize counts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Inner medullae were quickly dissected and snap frozen in liquid nitrogen.  RNA was extracted using the Zymo Direct-Zol RNA miniprep kit.  RNA quality, quantity was assessed by GeneWiz, followed by cDNA library prepration and sequencing by Genewiz.
RNA libraries were prepared for sequencing using standard Illumina protocols, and poly A selection by GeneWiz

treatment_protocol: each mouse at 9-10 weeks of age was given a single, i.p. injection of saline or 15 mg/kg cisplatin (dissolved in saline) in 100 ul.  72 hours later mice were euthanized and samples collected

value: inner medulla

value: female

value: cisplatin


title: female cisplatin IM rep 4

description:
72 after single i.p, injection
FC4


title: AsPC-1_shODC1 #2_RNA_rep3

state: MA

value: shODC1 #2


title: GL26140_CD31posP2_G06_R1

value: brain


title: Pilot 2 2.0mm 10s

address: Gilbert Biological Sciences Building, 371 Serra Mall

institute: Stanford University

description: UMI Matrix


title: GL26140_CD31posP2_F04_R1

address: 30 Fruit Street


title: GL26140_CD31posP2_C10_R1


title: Pilot 1 2.0mm 43s

description: UMI Matrix


title: female cisplatin IM rep 3

description:
72 after single i.p, injection
FC3


title: GL26140_CD31posP2_E05_R1


title: Pilot 2 2.0mm 37s

description: UMI Matrix


title: AsPC-1_shODC1 #2_RNA_rep1


title: AsPC-1_shODC1 #2_RNA_rep2


title: female saline IM rep 7

description:
72 after single i.p, injection
FS7

value: saline control


title: Pilot 2 2.0mm 23s

description: UMI Matrix


title: GL26140_CD31posP2_G12_R1


title: AsPC-1_shODC1 #1_RNA_rep3

value: shODC1 #1


title: AsPC-1_shODC1 #1_RNA_rep2


title: GL26140_CD31posP2_B07_R1


title: GL26140_CD31posP2_D08_R1

value: Malignant


title: female saline IM rep 6

description:
72 after single i.p, injection
FS6


title: Pilot 2 2.0mm 46s

description: UMI Matrix


title: Pilot 2 2.0mm 19s

description: UMI Matrix


title: Pilot 2 2.0mm 87s

description: UMI Matrix


title: GL26140_CD31posP2_F08_R1


title: AsPC-1_shScr_RNA_rep3

value: shScr


title: GL26140_CD31posP2_F09_R1

value: Los


title: Pilot 2 2.0mm 25s

description: UMI Matrix


title: female saline IM rep 5

description:
72 after single i.p, injection
FS5


title: AsPC-1_shScr_RNA_rep2


title: female saline IM rep 4

description:
72 after single i.p, injection
FS4


title: AsPC-1_shODC1 #1_RNA_rep1


title: female cisplatin IM rep 2

description:
72 after single i.p, injection
FC2


title: GL26140_CD31posP2_B10_R1


title: female saline IM rep 3

description:
72 after single i.p, injection
FS3


title: GL26140_CD31posP2_E10_R1


title: Pilot 1 2.0mm 2s

description: UMI Matrix


title: AsPC-1_shScr_RNA_rep1


title: GL26140_CD31posP2_C01_R1


title: Pilot 2 2.0mm 18s

description: UMI Matrix


title: female cisplatin IM rep 1

description:
72 after single i.p, injection
FC1


title: RNF6 shRNA2

first: Yile

last: SUN

address: HuaiHai west road

institute: Shanghai chest hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated.
All the downstream analyses were based on clean data with high quality.
Genome_build: GRch38
Supplementary_files_format_and_content: count, fpkm

source_name: H3255 cells

growth_protocol: H3255 lung adenocarcinoma cells cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FCS)

extract_protocol:
Total RNA was isolated using TRIzol reagent (Takara, Shiga, Japan) based on instructions provided by the manufacturer
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations

treatment_protocol: H3255 lung adenocarcinoma cells transfected with shRNF6 vs. scramble

value: H3255 lung adenocarcinoma cells

value: RNF6 shRNA2


title: GL26140_CD31posP2_H03_R1

institute: MGH


title: GL26140_CD31posP2_G02_R1


title: Pilot 2 2.0mm 65s

description: UMI Matrix