title: H508-TRAMET-0-01-LAST-3

value: trametinib, 0.01 uM


title: H508-TRAMET-0-01-LAST-4

status: Public on Mar 09 2023

type: SRA

city: New York

first: Andrea

last: Califano

state: NY

address: 1130 St. Nicholas Avenue

department: Department of Systems Biology

country: USA

institute: Califano Laboratory of Systems Biology

library_source: transcriptomic

data_processing:
Alignment of NGS with sgRNA guides was conducted using the “Biostrings” R-package (2.64.1). Essential genes for the DMSO vs T0 comparison were obtained from a generalized resource (MAGeCKFlute ), as well as a CRC-specific subset of DepMap, filtered to the 10% quantile of the gene effect. Differential expression analysis was conducted separately for each guide with the “DESeq2” R-package (1.36.0). P-values were integrated using Stouffer’s Method and corrected for multiple-testing by the Benjamini-Hochberg FDR approach.
Supplementary files format and content: Differential gene expression results of DEseq2 are provided in CSV format.
Library strategy: sgRNA-seq

molecule: total RNA

organism: Homo sapiens

growth_protocol: sgRNA containing lentiviruses were transduced into Cas9 expressing CRC cell lines (in 15cm plate-format) in quadruplicates (in presence of 8μg/ml polybrene), at an estimated MOI = 0.2   0.3. After 24h, the lentivirus containing media was removed, cells were washed with PBS, and puromycin-containing media (3μg/ml) was added to the cells for 48-96h until all control cells (not virus-infected) were dead. After this the cells were cultured for extra couple of days so that the plates reached approx. 80% confluency.

extract_protocol:
After the screen, the genomic DNA from the first and the last timepoints (DMSO & Drug perturbed) were extracted by using Blood and Cell culture DNA Maxi kits (Qiagen).
NGS library preparations were done the following way: Briefly, 40 μg of gDNA, theoretically corresponding to 6 million diploid cells, was used as PCR template in 4 parallel PCR1 reactions (10 μg template DNA each) using ExTaq DNA polymerase (Takara bio). After 18 cycles, the reactions were pooled. 2 μl of pooled PCR1 product was used as template for PCR2 which was run with qPCR with index primers and stopped before the amplification started to saturate. The resulting products of approx. 360 bp were gel purified (GeneJet), pooled together and Next generation sequenced.

treatment_protocol: At this point the cells were divided into 3 parts; 1/3 going into -80 °C as time point 1 to assess sgRNA representation baseline, 1/3 to continue to culture with DMSO and 1/3 to continue to culture with either with Linsitinib or Trametinib. Cells were always maintained at >1,500 cells per guide throughout the screens and finally harvested after 10 population doublings (the exact time (in days) for this varied for DMSO / Linsitinib / Trametinib with different cell lines) to assess gene essentiality.

tag: time

tag: cell line

tag: cell type

value: colorectal adenocarcinoma

tag: crispr-ko

value: kinases, phosphatases, E3 ligases

tag: treatment


title: HCT-15-DMSO-LAST-1

value: DMSO (Control)


title: HCT-15-TRAMET-0-7-LAST-3

value: trametinib, 0.7 uM


title: H508-TRAMET-0-01-LAST-2


title: H508-TRAMET-0-01-LAST-1


title: H508-TRAMET-0-005-LAST-4

value: trametinib, 0.005 uM


title: H508-TP1-3


title: H508-TRAMET-0-005-LAST-2


title: H508-TRAMET-0-005-LAST-3


title: H508-TP1-4


title: H508-TP1-2


title: H508-TP1-1


title: H508-DMSO-LAST-4


title: H508-DMSO-LAST-3


title: mLAP3

city: Beijing

first: Gexuan

last: Feng

address: FengtaiNo.10, Youanmen Waixi 1st Alley

country: China

institute: Capital Medical University

data_processing:
A total of 18 samples were tested using the DNBSEQ platform, with an average yield of 1.19G data per sample. The average alignment ratio of the sample comparison genome was 94.90%, which was comparative The average alignment of the gene set was 80.35%; a total of 18782 genes were detected.
Reference Genome Version：GCF_000001405.39_GRCh38.p13
The raw data for sequencing contains reads of low quality, adaptor contamination, and excessively high levels of unknown base N. These reads need to be removed before data analysis to ensure the reliability of the results. For the quality index of filtered reads, see the filtered reads quality statistics table and the raw data filtering component statistics chart. For the base content distribution and quality distribution, see the base content distribution chart of clean reads and the base quality distribution chart of clean reads.
After getting clean reads, we used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

extract_protocol: RNA extracted from 1×10^7 cells in 1 mL TRIZOL reagen

value: lung


title: H508-DMSO-LAST-2


title: mLC3


title: LC5


title: H508-DMSO-LAST-1


title: LAP4


title: LAP2


title: LC4


title: LC2


title: H508-TRAMET-0-005-LAST-1


title: 24 months, male, rep 5

city: Providence

first: Gregorio

last: Valdez

state: RI

address: 70 Ship St

institute: Brown University

description: Ribosome-associated RNA

data_processing:
Data were trimmed for both adaptor and quality using a combination of eautils and Btrim
Sequencing reads were aligned to the genome using HiSat2 and counted via HTSeq.
QC summary statistics were examined to identify any problematic samples (e.g. total read counts, quality and base composition profiles (+/- trimming)
mRNA differential expression was determined using contrasts of and tested for significance using the Benjamini-Hochberg corrected Wald Test in the R-package DESeq2
Failed samples were identified by visual inspection of pairs plots and removed from further analysis
Assembly: Illumina ultra-low input
Supplementary files format and content: tab-delimited text files include normalized read counts for each sample

organism: Mus musculus

source_name: spinal cord

extract_protocol:
Ribosomal-associated mRNAs were co-immunoprecipitated with Hemagglutinin-tagged ribosomal protein L22. mRNA isolated from precipitates using the Qiagen Rneasy Plus Micro Kit. Protocol based on: Sanz E et al. Cell-type-specific isolation of ribosome-associated mRNA from complex tissues.. Proc. Natl. Acad. Sci. U. S. A. 2009;106(33):13939–44
GRCm38.93

tag: tissue

value: spinal cord

value: cholinergic neurons

tag: genotype

value: Chat Cre; Ribotag

tag: Sex

value: Male

tag: age

value: 24 months


title: 24 months, male, rep 4

description: Ribosome-associated RNA


title: 24 months, female, rep 1

description: Ribosome-associated RNA

value: Female


title: 24 months, male, rep 1

description: Ribosome-associated RNA


title: 24 months, male, rep 3

description: Ribosome-associated RNA


title: 18 months, female, rep 4

description: Ribosome-associated RNA

value: 18 months


title: 18 months, male, rep 4

description: Ribosome-associated RNA


title: 18 months, female, rep 5

description: Ribosome-associated RNA


title: 18 months, female, rep 3

description: Ribosome-associated RNA


title: 18 months, male, rep 3

description: Ribosome-associated RNA


title: 18 months, male, rep 2

description: Ribosome-associated RNA


title: 18 months, female, rep 2

description: Ribosome-associated RNA


title: LC3


title: LAP5


title: LAP3


title: 24 months, male, rep 2

description: Ribosome-associated RNA


title: 3 months, female, rep 4

description: Ribosome-associated RNA

value: 3 months


title: 12 months, male, rep 1

description: Ribosome-associated RNA

value: 12 months


title: 12 months, female, rep 4

description: Ribosome-associated RNA


title: 18 months, female, rep 1

description: Ribosome-associated RNA


title: 12 months, male, rep 3

description: Ribosome-associated RNA


title: 12 months, female, rep 2

description: Ribosome-associated RNA


title: 12 months, female, rep 1

description: Ribosome-associated RNA


title: 12 months, female, rep 3

description: Ribosome-associated RNA


title: 12 months, male, rep 2

description: Ribosome-associated RNA


title: 18 months, male, rep 1

description: Ribosome-associated RNA


title: 18 months, male, rep 5

description: Ribosome-associated RNA


title: 3 months, female, rep 3

description: Ribosome-associated RNA


title: 3 months, female, rep 2

description: Ribosome-associated RNA


title: 3 months, female, rep 1

description: Ribosome-associated RNA


title: 3 months, male, rep 2

description: Ribosome-associated RNA


title: 3 months, male, rep 3

description: Ribosome-associated RNA


title: 3 months, male, rep 1

description: Ribosome-associated RNA


title: 12 months, female, rep 5

description: Ribosome-associated RNA


title: 12 months, male, rep 4

description: Ribosome-associated RNA


title: Day 0, pre-injury, scRNAseq

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell expression data were processed using the Cell Ranger Single Cell Software Suite (v2.1.1) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 30 gene counting. Sequencing reads were aligned to the mouse reference genome GRCh38 using the Cell Ranger suite with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Carotid artery

extract_protocol:
In brief, carotids were cut in small pieces and digested for 1h at 37°C with an enzyme mix containing collagenase type XI (125 U/ml), collagenase type I (450 U/ml), hyaluronidase (60 U/ml) and deoxyribonuclease I (60 U/ml). Digestion was stopped with stopping solution (PBS; 2% FCS; 1mM EDTA) and cell suspension was strained. Dead cells were removed by MACS Dead cell removal kit (Miltenyi, Germany). Cells were washed and resuspended in PBS and used for droplet scRNA-seq. Cellular suspensions were loaded on a 10x Chromium Controller (10x Genomics) according to manufacturer’s protocol.
All scRNA-seq libraries were prepared using Chromium Single Cell 30 v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. In brief, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10x cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Germany). Bulk cDNA was amplified using a Biometra Thermocycler TProfessional Basic Gradient with 96-Well Sample Block (98°C for 3min; cycled 14x: 98°C for 15 s, 67°C for 20 s, and 72°C for 1min; 72°C for 1min; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter, USA). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 30 v2 Reagent Kit, as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment were performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics, USA).

value: Carotid artery

tag: strain

value: 11 weeks old (pre-injury)

value: Day 0, pre-injury


title: Day 7, post-injury, scRNAseq

description: 10x Genomics

value: Day 7, post-injury


title: PBS-5-3

first: David

middle: C

last: Lyden

address: 413 East 69th Street, Room BB1228

department: Cell and Developmental Biology

institute: Weill Cornell Medicine

description: This PBS group was used as control for the 4T1-Tb group

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (Version2.0.11)
Transcriptome reconstruction was performed by Cufflinks (Version 2.1.1), and the abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Gene expression profiles were constructed for differential expression, cluster, and principal component analyses with the DESeq2 package
For differential expression analysis, pairwise comparisons between two or more groups using parametric tests where read-counts follow a negative binomial distribution with a gene-specific dispersion parameter. Corrected p-values were calculated based on the Benjamini-Hochberg method to adjusted for multiple testing.
Assembly: mm9
Supplementary files format and content: Excel file with Log2FC, p-value and q-value for each gene expressed in the livers from tumor-bearing or EVP-educated mice, compared to their respective controls.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen. Total RNA was extracted using TRIzol reagent, and RNA was further purified using RNeasy Mini kit including a DNase digest following the manufacturer’s instructions
RNA libraries were prepared using TruSeq Stranded mRNA Library Preparation (Illumina) following the manufacturer’s instructions

value: Liver

value: BALB/c

value: Four weeks post mammary fat pad injection of 50 ul of PBS


title: PBS-5-2


title: 4T1-Tb-2

value: Four weeks post mammary fat pad injection of 1×105 of  4T1 cells in 50 ul of PBS


title: 4T1-Tb-1


title: PBS-5-1


title: 4T1-Tb-3


title: Mouse, carotid artery, scRNA-seq

description: 10x Genomics

extract_protocol:
Eight carotid arteries were cut into small pieces in an enzyme mixture containing 125 U/mL collagenase type XI, 450 U/mL collagenase type I, 60 U/mL hyaluronidase type I-s and 60 U/mL DNase 1 in PBS containing Ca2+ and 20 mM Hepes (pH. 7.4) and subsequently incubated at 37 ◦C for 30 minutes in a total volume of 5 mL. Every 10 minutes the solution was resuspended by pipetting. Digestion was stopped with stopping solution (PBS; 2% FCS; 1 mM EDTA) and cell suspension was strained.
All scRNA-seq libraries were prepared using Chromium Single Cell 30 v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. In brief, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10x cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Germany). Bulk cDNA was amplified using a Biometra Thermocycler TProfessional Basic Gradient with 96-Well Sample Block (98°C for 3min; cycled 14x: 98°C for 15 s, 67°C for 20 s, and 72°C for 1min; 72°C for 1min; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter, USA). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 30 v2 Reagent Kit, as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment were performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics, USA).

value: 11 weeks old


title: 67NR-Tb-3

value: Four weeks post mammary fat pad injection of 1×105 of  67NR cells in 50 ul of PBS


title: 67NR-Tb-1


title: PBS-3-2

description: This PBS group was used as control for the 67NR-Tb group


title: PBS-3-3


title: 67NR-Tb-2


title: PBS-1-1

description: This PBS group was used as control for the B16F10-Tb group

value: Three weeks post  subcutaneous injection of 100 ul of PBS


title: PBS-1-3


title: PBS-1-2


title: B16F10-Tb-2

value: Three weeks post  subcutaneous injection of 5×105 of  B16F10 cells in 100 ul of PBS


title: B16F10-Tb-1


title: Day 14, post-injury, scRNAseq

description: 10x Genomics

value: Day 14, post-injury


title: BRAFYAP_2

first: Mahesh

last: Saqcena

address: 1275 York Ave, Box 296

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: 1 tumor

data_processing:
Illumina Bcl2fastq v2.2 software was used for basecalling.
Sequence reads were aligned to mm10 genome assembly using STAR aligner v2.6.1d, and aligned reads were quantified using Partek E/M annotation model and mm10 ensembl release 95.
Transcripts Per Million (TPM) was used for normalization and 0.0001 was added to obtain non-zero noramlized gene expression counts matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: thyroid cancer cells

extract_protocol:
Thyroid tumors were dissected and placed in ice-cold digestion media (HBSS, 5%FBS, 10mM HEPES, 1.5mg/ml Collagenase A, 4mg/mL DNase I) and minced. The desegregated tissue was collected in digestion media and incubated at 37C for 1hour, briefly vortexing every 15 minutes. The cells were passed through 70 µM filter to remove tissue debris and obtain single cell suspension and washed with PBS. The cells were resuspended in FACS buffer (HBSS, 5%FBS, 10mM HEPES) and sorted by +Kate using a BD FACS Aria flow cytometer and ~20,000 Kate positive cells were collected into TRIzol LS (Invitrogen, #10296010) for RNA-sequencing.
The total RNA was amplified using SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. The amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR, barcoded, and run on a HiSeq 4000 in a PE50 run using the HiSeq 3000/4000 SBS Kit (Illumina).

treatment_protocol: At four weeks of age mice were placed on doxycycline (dox)-impregnated chow (TD01306, Envigo) to induce mutant YAP expression in thyroid follicular cells.

tag: species

tag: sample origin

value: Kate-positive sorted cells

value: doxycycline-induced thyroid-specific YAPS127A expression in combination with endogenous expression of BrafV600E


title: Day 3, post-injury, scRNAseq

description: 10x Genomics

value: Day 3, post-injury


title: YAP_1

description: 3 pooled tumors

value: doxycycline-induced thyroid-specific YAPS127A expression


title: BRAFYAP_1

description: 1 tumor


title: YAP_2

description: 3 pooled tumors


title: M_AE12

city: Birmingham

first: Thomas

middle: W

last: Buford

state: Alabama

address: 1313 13th Street South

institute: University of Alabama at Birmingham

data_processing:
Paired- end fastq files generated from sequencing were checked for quality using FastQC adapters and low-quality reads (PHRED < 20) using Trim Galore and CutAdapt
Alignment to the rat genome (Rnor_5.0) and gene counts were then generated using Spliced Transcripts Alignment to a Reference (STAR)
Supplementary files format and content: Excel file includes read_counts

organism: Rattus norvegicus

source_name: Skeletal Muscle

extract_protocol:
mRNA was purified from total RNA using polyT, oligo-attached magnetic beads, followed by fragmentation using divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNase H). Second strand cDNA synthesis was then performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of 250~300 bp, the library fragments were purified with AMPure XP system (Beckman Coulter). Then, 3 μl USER Enzyme (New England BioLabs) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min, which was followed by another incubation of 5 min at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Lastly, 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

treatment_protocol: The treatment groups were orally gavaged with 2x1011 CFU/kg body weight of probiotics or an equal volume of buffer 3 times per week. Groups randomized to the exercise intervention (CONEx; LPEx;LPAEx) performed a treadmill intervention, 5 days per week for 12 weeks.

value: Skeletal Muscle

value: Male

value: Ang (1-7) Probiotic

tag: activity

value: Exercise


title: M_AE9


title: PBS-3-1

value: Liver


title: M_AE4


title: M_AS11

value: No Exercise


title: M_AE7


title: M_AS9


title: M_AS7


title: M_AS6


title: B16F10-Tb-3


title: M_PE11

value: Probiotic


title: M_PE8


title: M_AS4


title: M_AS5


title: BRAFYAP_6

description: 1 tumor


title: M_PE4


title: M_PE6


title: M_PS13


title: M_PE3


title: M_PS8


title: M_PS10


title: M_PS7


title: YAP_3

description: 3 pooled tumors


title: M_AE11


title: M_CE11

value: Control


title: M_CE12


title: M_PS5


title: M_AE6


title: M_CE10


title: M_CE7


title: M_CE9


title: M_CE5


title: M_CS10


title: M_PE10


title: M_CS7


title: M_CS8


title: M_CS4


title: M_CS6


title: C_AE9

source_name: Colon

value: Colon


title: C_AE11


title: M_CS3


title: C_AS11


title: C_AE6


title: C_AE7


title: C_AE4


title: C_AE12


title: M_PS4


title: C_AS9


title: C_AS6


title: C_AS5


title: C_PE11


title: C_PE10


title: C_PE8


title: C_PE6


title: C_PE4


title: C_PE3


title: C_PS13


title: C_PS8


title: C_PS10


title: C_PS7


title: C_CE12


title: C_CE11


title: C_PS4


title: C_CE9


title: C_CE5


title: C_CE7


title: C_AS7


title: C_CS6


title: C_CS7


title: C_CS10


title: C_CS3


title: L_AS9


title: C_CS8


title: L_AE6


title: L_AS5


title: L_AE12


title: L_AE9


title: C_PS5


title: L_AE11


title: C_AS4


title: C_CE10


title: L_AS7


title: L_AS11


title: L_PE11


title: L_AE4


title: L_AS4


title: L_AE7


title: L_PE10


title: L_AS6


title: L_PE6


title: L_PE8


title: L_PE4


title: C_CS4


title: L_PS13


title: L_PS10


title: L_PS5


title: L_PS8


title: L_PS7


title: L_PS4


title: L_CE7


title: L_CS8


title: L_CE12


title: L_CE11


title: L_CS10


title: L_CS7


title: L_CE5


title: L_CS4


title: L_CS6


title: L_CE10


title: HippoAE6

source_name: Hippocampus

value: Hippocampus


title: HippoAE9


title: HippoAE7


title: L_CS3


title: HippoAE12


title: HippoAS11


title: HippoAS5


title: HippoAS6


title: HippoAS4


title: HippoPE11


title: L_CE9


title: HippoPE10


title: HippoPE8


title: HippoPE4


title: HippoPE3


title: HippoAE11


title: HippoPS13


title: HippoPS10


title: HippoCE9


title: HippoPS8


title: HippoPS4


title: HippoCE11


title: HippoCE10


title: HippoPS5


title: HippoAS7


title: HippoCE12


title: HippoCE7


title: PFC_AE11

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: HippoCS7


title: HippoCS6


title: HippoAS9


title: HippoCS4


title: HippoCS3


title: HippoCE5


title: PFC_AE12


title: HippoCS8


title: PFC_AE9


title: HippoCS10


title: HippoPE6


title: PFC_AE4


title: PFC_AS11


title: HippoPS7


title: PFC_AS9


title: PFC_AE6


title: PFC_AS7


title: PFC_AS5


title: PFC_AS4


title: PFC_AS6


title: PFC_CE9


title: PFC_CE5


title: PFC_PS4


title: PFC_PS5


title: PFC_CE11


title: PFC_CS8


title: PFC_CE12


title: PFC_CS10


title: PFC_CE7


title: PFC_CE10


title: PFC_CS7


title: PFC_CS4


title: single cell RNAseq (10x Genomics) of small mesenteric artery in Rattus norvegicus, SM07

city: Albuquerque

first: Jay

middle: S

last: Naik

state: NM

address: 915 Camino De Salud

department: Cell Biology and Physiology

institute: University of New Mexico SOM

description: 10x Genomics

data_processing:
Illumina NovaSEQ 6000 at University of Colorado Anschutz Medical Campus Genomics Shared Resource Cancer Center, demultiplexed with bcl2fastq v2.20.0.422 with “--barcode-mismatches” set to 1
Aligned and counted with CellRanger v3.1.1
Assembly: Rnor_6.0
Supplementary files format and content: CellRanger (v3.2.2) output files, Tab-separated values files and matrix files

source_name: mesenteric artery - small (< 150 um)

extract_protocol:
Artery segments were transferred to tubes containing warm dissociation buffer: HEPES (mmol/l: 1.4 CaCl2, 0.03 EDTA, 10.10 glucose, 10 HEPES, 6 KCl, 2.13 MgSO4 and 134 NaCl), 0.1% bovine serum albumin, 13 U/mL papain, 427 U/mL collagenase II, 1 mg/mL dithiothreitol, and 150 U/mL deoxyribonuclease I. Arteries were incubated in a dissociation buffer for 40 min @ 37°C. Artery segments were then gently triturated with a small-bore glass pipette to release cells. Isolated cells were then passed through a 70 µM cell strainer and rinsed with 5 mL cold wash buffer (1X PBS containing 1% bovine serum albumin). Cells were pelleted by centrifugation at 1050 rpm for 10 min at 4°C. The supernatant was aspirated, and cell pellets were resuspended in cold wash buffer prior to cell counting and 10X library prep.
Cell concentrations and viability were determined using the Cell Countess II FL (ThermoFisher) prior to calculating cell counts and loading the suspension into the Next GEM Chip G and Chromium Controller (10x Genomics) per the manufacturer’s protocol for GEM formation. The 10x Chromium Next GEM 3’ protocol was used to create 3’ libraries; briefly, cells were lysed and barcoded within each GEM prior to first strand cDNA synthesis, also within each GEM. After GEM’s are broken, cells are pooled prior to library completion as described in the manufacture’s protocol. Library quality was assess after cDNA synthesis and after completion on the BioAnalyzer using a DNA High Sensitivity Chip (Agilent). Prior to sequencing, Agilent Tape Station 4200 and Invitrogen Qubit 4.0 reagents were used determine final library concentrations prior to dilution, normalization and pooling at 4nM. qPCR was used to determine cluster efficiency.

tag: gender

value: male

value: Sprague-Dawley

value: mesenteric artery - small (< 150 um)


title: single cell RNAseq (10x Genomics) of large mesenteric artery in Rattus norvegicus, LG08

description: 10x Genomics

source_name: mesenteric artery - large (> 300 um)

value: mesenteric artery - large (> 300 um)


title: single cell RNAseq (10x Genomics) of small mesenteric artery in Rattus norvegicus, SM06

description: 10x Genomics


title: single cell RNAseq (10x Genomics) of small mesenteric artery in Rattus norvegicus, SM08

description: 10x Genomics

source_name: mesenteric artery - small (<150 um)

value: mesenteric artery - small (<150 um)


title: PFC_AE7


title: HippoAE4


title: PFC_CS6


title: PFC_CS3


title: single cell RNAseq (10x Genomics) of large mesenteric artery in Rattus norvegicus, LG06

description: 10x Genomics

source_name: mesenteric artery - large (>300 um)

value: mesenteric artery - large (>300 um)


title: single cell RNAseq (10x Genomics) of large mesenteric artery in Rattus norvegicus, LG07

description: 10x Genomics


title: PFC_PS10


title: PFC_PS13


title: PFC_PS8


title: PFC_PE10


title: PFC_PE8


title: PFC_PE6


title: PFC_PS7


title: PFC_PE4


title: PFC_PE3


title: PFC_PE11


title: Monocytes_healthy_rep2

type: RNA

city: Torino

first: Federico Alessandro

last: Ruffinatti

state: Torino

address: via Accademia Albertina 13

department: Department of Life Sciences and Systems Biology

country: Italy

institute: University of Turin

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C11

hyb_protocol: Hybridization and washing were performed following the manufacturers protocols (Agilent Technologies). 600 ng of labeled specimens were hybridized on Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K arrays. After 17 hours slides were washed and scanned.

scan_protocol: After hybridization, slides were scanned with an Agilent dual-laser microarray scanner Version C (G2505C, Agilent Technologies).

data_processing: Images obtained from the scanner were analyzed using the Feature Extraction software Agilent (version 10.7). Background correction was performed with the normexp method with an offset of 50, and quantile-quntile normalization procedure was used for between-array normalization.

source_name: Human monocyte primary culture, healthy, replicate 2

label_protocol: Labeling was performed following the manufacturers protocols (Agilent Technologies). mRNA from 100 ng of total RNA was amplified, labeled with Cy3, and purified with columns.

extract_protocol: For each sample, total RNA was isolated using TriReagent (Life Technologies, Monza, Italy) from 5x10^6 freshly isolated monocytes. RNA quality was assessed using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Isolated monocytes


title: Monocytes_healthy_rep10

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C9

source_name: Human monocyte primary culture, healthy, replicate 10


title: Monocytes_healthy_rep4

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C14

source_name: Human monocyte primary culture, healthy, replicate 4

value: female


title: Monocytes_healthy_rep6

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C2

source_name: Human monocyte primary culture, healthy, replicate 6


title: Monocytes_healthy_rep8

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C6

source_name: Human monocyte primary culture, healthy, replicate 8


title: Monocytes_anti-TNFalpha_rep4

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
E5

source_name: Human monocyte primary culture, anti-TNFalpha, replicate 4

tag: comorbidity


title: Monocytes_healthy_rep9

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C7

source_name: Human monocyte primary culture, healthy, replicate 9


title: Monocytes_anti-TNFalpha_rep1

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
E1

source_name: Human monocyte primary culture, anti-TNFalpha, replicate 1


title: Monocytes_anti-TNFalpha_rep3

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
E4

source_name: Human monocyte primary culture, anti-TNFalpha, replicate 3

value: osteoporosis


title: Monocytes_healthy_rep5

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C15

source_name: Human monocyte primary culture, healthy, replicate 5


title: Monocytes_abatacept_rep5

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
A6

source_name: Human monocyte primary culture, abatacept, replicate 5


title: Monocytes_abatacept_rep3

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
A4

source_name: Human monocyte primary culture, abatacept, replicate 3


title: Monocytes_healthy_rep3

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C13

source_name: Human monocyte primary culture, healthy, replicate 3


title: Monocytes_abatacept_rep4

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
A5

source_name: Human monocyte primary culture, abatacept, replicate 4


title: Monocytes_anti-TNFalpha_rep5

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
E6

source_name: Human monocyte primary culture, anti-TNFalpha, replicate 5


title: Monocytes_MTX_rep2

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
N5

source_name: Human monocyte primary culture, MTX, replicate 2


title: Monocytes_MTX_rep1

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
N4

source_name: Human monocyte primary culture, MTX, replicate 1


title: Monocytes_healthy_rep1

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C10

source_name: Human monocyte primary culture, healthy, replicate 1


title: Monocytes_healthy_rep7

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
C3

source_name: Human monocyte primary culture, healthy, replicate 7


title: Monocytes_MTX_rep5

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
N8

source_name: Human monocyte primary culture, MTX, replicate 5


title: Monocytes_tocilizumab_rep1

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
T1

source_name: Human monocyte primary culture, tocilizumab, replicate 1


title: Monocytes_anti-TNFalpha_rep2

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
E2

source_name: Human monocyte primary culture, anti-TNFalpha, replicate 2


title: Monocytes_MTX_rep3

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
N6

source_name: Human monocyte primary culture, MTX, replicate 3

value: schizoaffective disorder


title: Monocytes_tocilizumab_rep3

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
T3

source_name: Human monocyte primary culture, tocilizumab, replicate 3


title: Monocytes_tocilizumab_rep4

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
T4

source_name: Human monocyte primary culture, tocilizumab, replicate 4


title: Monocytes_MTX_rep4

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
N7

source_name: Human monocyte primary culture, MTX, replicate 4

value: arthrosis


title: Monocytes_tocilizumab_rep5

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
T8

source_name: Human monocyte primary culture, tocilizumab, replicate 5


title: Monocytes_tocilizumab_rep2

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
T2

source_name: Human monocyte primary culture, tocilizumab, replicate 2


title: Monocytes_MTX_rep6

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
N9

source_name: Human monocyte primary culture, MTX, replicate 6


title: Monocytes_abatacept_rep2

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
A3

source_name: Human monocyte primary culture, abatacept, replicate 2


title: Unaffected parts of Tumor Nephrectomy  [CprobeT_13-527]

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene Expression data from the Tubular compartment of human Kidney Disease

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing:
The data were analyzed using a modified Affy package using the RMA method and Human Entrez Gene custom CDF annotation version 19.
Each of the hybridizations was normalized seperately and the last sheet contains the batch corrected data using Combat

label: biotin

source_name: Kidney Biopsy from Human kidney disease

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol

tag: sample group

value: Unaffected parts of Tumor Nephrectomy

value: Tubuli from kidney biopsy


title: MCD [CprobeT_geo10061]

value: MCD


title: LN-WHO V [CprobeT_geo10035]

value: LN-WHO V


title: MN [CprobeT_geo10048]

value: MN


title: Unaffected parts of Tumor Nephrectomy  [CprobeT_13-808]


title: Unaffected parts of Tumor Nephrectomy  [CprobeT_13-793]


title: Unaffected parts of Tumor Nephrectomy  [CprobeT_13-509]


title: MN [CprobeT_geo10034]


title: Thin-BMD [CprobeT_geo10041]

value: Thin-BMD


title: Unaffected parts of Tumor Nephrectomy  [CprobeT_12-293]


title: CKD with mod-severe Interstitial fibrosis [CprobeT_geo10042]


title: Unaffected parts of Tumor Nephrectomy  [CprobeT_13-379]


title: Monocytes_abatacept_rep1

description:
Inclusion criteria for patients were: age ≥18 years, established RA (disease duration ≥3 years) diagnosed according to current ACR/EULAR classification, no smoking habit, no other chronic diseases.
A1

source_name: Human monocyte primary culture, abatacept, replicate 1

value: hypothyroidism


title: Thin-BMD [CprobeT_geo10053]


title: LN-WHO-I/II [CprobeT_geo10037]

value: LN-WHO-I/II


title: Hypertensive Nephrosclerosis [CprobeT_geo10045]

value: Hypertensive Nephrosclerosis


title: LN-WHO V [CprobeT_geo10049]


title: LN-WHO III [CprobeT_geo10054]

value: LN-WHO III


title: LN-WHO IV+V [CprobeT_geo10022]

value: LN-WHO IV+V


title: LN-WHO IV  [CprobeT_geo10043]

value: LN-WHO IV


title: LN-WHO III+V [CprobeT_geo10031]

value: LN-WHO III+V


title: LN-WHO III+V [CprobeT_geo10027]


title: LN-WHO III [CprobeT_geo10028]


title: LN-WHO III [CprobeT_geo10052]


title: LN-WHO III [CprobeT_geo10024]


title: Carotid artery, Day 28 (post-injury), Replicate 1

data_processing:
The MACE-reads were demultiplexed according to the sample IDs, PCR duplicates were removed with the help of the “TrueQuant” UMI barcodes.
Salmon (v1.9.0) transcript quantification against mm39 transcriptome
DESeq2 (v1.36.0) differential gene expression analysis
Assembly: mm39
Supplementary files format and content: DESeq2 results for each time point versus control (Day 0, pre-injury)
Library strategy: MACE-seq

source_name: carotid artery

extract_protocol:
Frozen tissue sections were mounted on special LCM membrane slides and stained immunohistochemically with Hematoxylin and Eosin to detect carotids and elastic laminas. Carotid sections containing outer elastic lamina and neointima were then cut and catapulted into the lid of a collection tube by the laser. After collection of up to 70 sections, total RNA was extracted using an RNeasy Micro Kit (Qiagen, Hilden, Germany). nanoMACEseq was performed for further analysis.
The library preparation was conducted by GenXPro. 3’mRNA libraries were prepared using GenXPros “Rapid MACE-Seq Kit” for low-input mRNA according to the manual of the manufacturers. Briefly, RNA was fragmented to an average size of 350 bps, followed by poly-A specific cDNA synthesis, pooling and amplification by PCR using the minimum number of cycles as described in the manual. The PCR product was purified by SPRI purification. The final product of 200-400 bps was quality controlled on a Perkin Elmer LabChip GXII, the concentration was measured on Qbit.

value: carotid artery

value: WT

tag: mouse strain

value: injury

value: Day 28


title: Carotid artery, Day 28 (post-injury), Replicate 2

tag: time


title: Carotid artery, Day 21 (post-injury), Replicate 4

value: Day 21


title: Carotid artery, Day 21 (post-injury), Replicate 3


title: Carotid artery, Day 21 (post-injury), Replicate 1


title: LN-WHO III [CprobeT_geo10029]

value: Tubuli from kidney biopsy


title: Hypertensive Nephrosclerosis [CprobeT_geo10039]


title: Carotid artery, Day 28 (post-injury), Replicate 3


title: LN-WHO III [CprobeT_geo10057]


title: Interstitial nephritis  [CprobeT_geo10032]

value: Interstitial nephritis


title: IgAN  [CprobeT_geo10055]

value: IgAN


title: IgAN  [CprobeT_geo10047]


title: IgAN [CprobeT_geo10050]


title: IgAN  [CprobeT_geo10062]


title: Hydronephrosis [CprobeT_geo10065]

value: Hydronephrosis


title: Interstitial nephritis   [CprobeT_geo10063]


title: LN-WHO III+V [CprobeT_geo10051]


title: Carotid artery, Day 14 (post-injury), Replicate 3

value: Day 14


title: Carotid artery, Day 21 (post-injury), Replicate 2


title: Carotid artery, Day 14 (post-injury), Replicate 1


title: Carotid artery, Day 7 (post-injury), Replicate 4

value: Day 7


title: Carotid artery, Day 14 (post-injury), Replicate 2


title: Carotid artery, Day 7 (post-injury), Replicate 2


title: Carotid artery, Day 7 (post-injury), Replicate 3


title: Carotid artery, Day 0 (pre-injury), Replicate 4

value: pre-injury

value: Day 0


title: Carotid artery, Day 7 (post-injury), Replicate 1


title: Carotid artery, Day 0 (pre-injury), Replicate 3


title: Carotid artery, Day 0 (pre-injury), Replicate 2


title: FGGS [CprobeT_geo10044]

value: FGGS


title: FGGS [CprobeT_geo10038]


title: FSGS [CprobeT_geo10066]

value: FSGS


title: FGGS [CprobeT_geo10033]


title: Nuclei from P26-P28 animals (Sample 8)

city: Boston

first: Lisa

middle: V

last: Goodrich

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: OCN Sample 8

data_processing:
Raw reads were converted to fastq files, demultiplexed, and aligned to the mm10 reference transcriptome using cellranger v. 3.0.2.
Quality filtering: genes were removed if they were not expressed in at least 3 cells; cells were excluded if more than 1% of detected transcripts were mitochondrial genes or if the number of unique molecular identifiers (UMI) or genes detected was more than two standard deviations away from the mean. For samples 1A-4, cells were also discarded if fewer than 1,000 unique UMI or 750 genes were detected. For samples 5-8, cells were additionally discarded if fewer than 750 UMI or 500 genes were detected.
Clustering: Data was normalized in Seurat v. 3 using the scTransform package, batch-corrected using CCA-based integration, and clustered using the FindNeighbors and FindClusters algorithms in Seurat.
Normalization: Counts were normalized by dividing the counts for each gene by the total number of counts for each cell. These values were then multiplied by 10,000 and natural-log transformed.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include log-normalized data and associated cell-type identities, established as described in the data processing steps above. Column names include the cell-type cluster ID followed by a cellular barcode, separated by an underscore.

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Portions of the ventral brainstem were dissected and tissue was manually dissociated with a dounce homogenizer and nuclei were isolated using differential centrifugation. Enrichment for cholinergic nuclei was achieved by collecting GFP+ nuclei via FACS. Individual nuclei were captured through the 10x Genomics Platform.
Libraries were generated following manufacturer's directions (Single Cell 3' v3 for Samples 1A-4, Single Cell 3' v2 for Samples 5-8).

value: Brain

value: OCNs

value: ChAT-Cre; Rosa26-Sun1-GFP


title: Nuclei from P26-P28 animals (Sample 7)

description: OCN Sample 7


title: Nuclei from P26-P28 animals (Sample 6)

description: OCN Sample 6


title: Nuclei from P5 animals (Sample 3)

description: OCN Sample 3


title: Nuclei from P1 animals (Sample 4)

description: OCN Sample 4


title: Light-Chain Deposit Disease (IgG lambda) [CprobeT_geo10059]


title: FGGS [CprobeT_geo10046]


title: FSGS [CprobeT_geo10030]


title: Nuclei from P1 animals (Sample 2B)

description:
OCN Sample 2B
Samples 2A and 2B were derived from the same animals but collected independently on the 10x Controller.


title: Nuclei from P1 animals (Sample 2A)

description:
OCN Sample 2A
Samples 2A and 2B were derived from the same animals but collected independently on the 10x Controller.


title: DN [CprobeT_geo10058]

value: DN


title: DN [CprobeT_geo10036]


title: Carotid artery, Day 0 (pre-injury), Replicate 1

value: carotid artery

value: WT


title: FSGS [CprobeT_geo10023]


title: Nuclei from P5 animals (Sample 1B)

description:
OCN Sample 1B
Samples 1A and 1B were derived from the same animals but collected independently on the 10x Controller.


title: DN [CprobeT_geo10025]


title: Living donor [CProbeT_LD_30_147]

description: Gene Expression data from the Tubular compartment of human healthy living donor

source_name: Kidney Biopsy from Human Living donor

value: Living donor


title: chronic Glomerulonephritis (GN) with infiltration by CLL [CprobeT_geo10040]

value: Tubuli from kidney biopsy


title: DN [CprobeT_geo10026]


title: Nuclei from P26-P28 animals (Sample 5)

description: OCN Sample 5


title: FGGS [CprobeT_geo10060]


title: Living donor [CProbeT_LD_30_150]


title: 2' FSGS [CprobeT_geo10064]

value: 2' FSGS


title: Living donor [CProbeT_LD_30_25]


title: Living donor [CProbeT_LD_30_142]


title: J130_S92

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, and leading and trailing basepairs below a quality score of 3
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 14 --dta -x GCF_002263795.1_ARS-UCD1.2
Read assembly and quantification was performed with StringTie v2.1.7 with parameters -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.32.1.
Assembly: GCF_002263795.1
Supplementary files format and content: comma-delimited text file of gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit per product instruction.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: disease

value: Y

tag: saletype

value: Direct

tag: vaccinated

tag: pen number

tag: animal id

tag: arrival weight (lbs)


title: J123_S90

value: Auction

value: N


title: J122_S89


title: Living donor [CProbeT_LD_30_109]

tag: tissue


title: J113_S87


title: Living donor [CProbeT_LD_30_146]


title: Living donor [CProbeT_LD_30_131]


title: Living donor [CProbeT_LD_30_138]


title: J121_S88


title: Living donor [CProbeT_LD_30_103]


title: J111_S85


title: Unaffected parts of Tumor Nephrectomy  [CProbeG_TN_13-793]

description: Gene Expression data from the glomerular compartment of human Glomerular Disease

source_name: Kidney Biopsy from Human Glomerular Disease

value: Unaffected parts of Tumor Nephrectomy

value: Glomeruli from kidney biopsy


title: Unaffected parts of Tumor Nephrectomy  [CProbeG_TN_13-527]


title: Nuclei from P5 animals (Sample 1A)

description:
OCN Sample 1A
Samples 1A and 1B were derived from the same animals but collected independently on the 10x Controller.

tag: cell type

tag: genotype

tag: age


title: J124_S91


title: J112_S86


title: J092_S80


title: J103_S82


title: Unaffected parts of Tumor Nephrectomy  [CProbeG_TN_13-509]


title: J097_S81


title: Interstitial nephritis  [CprobeG_geo10032]

value: Interstitial nephritis


title: Hypertensive Nephrosclerosis [CprobeG_geo10039]

value: Hypertensive Nephrosclerosis


title: Unaffected parts of Tumor Nephrectomy  [CProbeG_TN_13-379]


title: J091_S79


title: LN-WHO III+V [CprobeG_geo10031]

value: LN-WHO III+V


title: J086_S78


title: FSGS [CprobeG_geo10030]

value: FSGS


title: J078_S77


title: J109_S84


title: J108_S83


title: Unaffected parts of Tumor Nephrectomy  [CProbeG_TN_13-808]


title: J076_S76


title: J062_S74


title: J059_S73


title: CKD with mod-severe Interstitial fibrosis [CprobeG_geo10042]


title: J055_S72


title: J071_S75


title: J052_S70


title: Unaffected parts of Tumor Nephrectomy  [CProbeG_TN_12-293]


title: J053_S71


title: J050_S69


title: J047_S68


title: J043_S67


title: J041_S66


title: chronic Glomerulonephritis (GN) with infiltration by CLL [CprobeG_geo10040]


title: LN-WHO-I/II [CprobeG_geo10037]

value: LN-WHO-I/II


title: Thin-BMD [CprobeG_geo10041]

value: Thin-BMD


title: J040_S65


title: FGGS [CprobeG_geo10038]

value: FGGS


title: Fibrillary GN [CprobeG_geo10021]

value: Fibrillary GN


title: J038_S64


title: DN [CprobeG_geo10036]

value: DN


title: FGGS [CprobeG_geo10033]


title: LN-WHO V [CprobeG_geo10035]

value: LN-WHO V


title: LN-WHO III [CprobeG_geo10029]

value: LN-WHO III


title: DN [CprobeG_geo10026]


title: LN-WHO III+V [CprobeG_geo10027]


title: FGGS [CprobeG_geo10044]


title: LN-WHO III [CprobeG_geo10028]


title: J032_S62


title: J031_S61

value: Y


title: MN [CprobeG_geo10034]

value: MN


title: J026_S59

value: Direct


title: J033_S63

value: Auction

value: N


title: LN-WHO-V [CprobeG_geo10020]

value: LN-WHO-V

value: Glomeruli from kidney biopsy


title: LN-WHO IV+V [CprobeG_geo10022]

value: LN-WHO IV+V


title: LN-WHO IV  [CprobeG_geo10043]

value: LN-WHO IV


title: J027_S60


title: J024_S58


title: J023_S57


title: J019_S55


title: J017_S54


title: J022_S56


title: J015_S53


title: J014_S52


title: 2'FSGS [CprobeG_geo10017]


title: Thin-BMD [CprobeG_geo10018]


title: Immuncomplex GN [CprobeG_geo10013]

value: Immuncomplex GN


title: J013_S51


title: Donor_5_Stress_Granules

city: Toulouse

first: Don-Marc

last: Franchini

address: 2 Av. Hubert Curien

country: France

institute: CRCT

data_processing:
bcl2 files conversion to FASTQ format using bcl2fastq algorithm
align to the GRCh38 reference transcriptome using bowtie2
Expression calculation using rsem-calculate-expression
Preprocessing, normalization of FPKM, and QC, and downstream analysis were performed using the R
The processed (sample x gene) matrix of FPKM are provided.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw FPKM for every gene and every sample

source_name: T lymphocytes isolated from PBMCs of healthy donor

growth_protocol: CD3+ T lymphocytes were maintained in RMPI medium supplemented with 10% FCS for the duration of stimulation.

extract_protocol:
RNA was extracted with the Direct-zol RNA kit (ZymoResearch)
RNA libraries were prepared with the Illumina TruSeq Stranded Total RNA (Illumina)

value: Total CD3+

tag: experimental isolation

value: cell lysis + immunoprecipitation of G3BP1


title: Donor_5_Cytosol

value: cell lysis


title: J011_S50


title: IgAN [CprobeG_geo10014]

value: IgAN


title: FGGS [CprobeG_geo10012]

value: FGGS


title: 2'FSGS [CprobeG_geo10009]


title: LN-WHO III [CprobeG_geo10005]


title: LN-WHO III [CprobeG_geo10010]


title: Donor_5_Processing_Bodies

value: cell lysis + immunoprecipitation of DCP1A


title: Donor_4_Processing_Bodies


title: infection-associated GN [CprobeG_geo10016]

value: infection-associated GN


title: FGGS [CprobeG_geo10008]


title: LN-WHO V [CprobeG_geo10006]

value: LN-WHO V


title: MN [CprobeG_geo10067]

value: MN


title: Membrano-Proliferative GN   [CprobeG_geo10056]

value: Membrano-Proliferative GN


title: LN-WHO IV [CprobeG_geo10007]


title: AKI [CprobeG_geo10068]

value: AKI


title: Donor_4_Cytosol


title: DN [CprobeG_geo10004]

value: DN


title: Donor_3_Processing_Bodies


title: OxCt2

city: LUND

first: Daniel

middle: P

last: Brink

address: Naturvetarvagen 14

department: Applied Microbiology

country: Sweden

institute: Lund University

data_processing:
Base-calling: The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
Filtering: TrimGalore (v0.6.1) running cutadapt (v2.3)
Read alignment: Hisat2 (v2.2.1)
Mapping statistics: were assessed with RSeQC
Differential gene expression: DEseq2 (R-package)
Genome_build: JAJJYS000000000
Supplementary_files_format_and_content: tsv file with the results of the DEseq2 analysis for each of the genes predicted in the genome annotation. Includes raw counts and DEseq2-normalized counts from each of the 12 samples, and calculated differential expression data for four compared conditions (g2_vs_g1, x2_vs_x1, x1_vs_g1, x2_vs_g2)

organism: Pseudozyma hubeiensis

source_name: nitrogen-starvation (time point 2), xylose, biological replicate C

growth_protocol: YNB (without ammonium sulfate) supplemented with glucose and ammonium sulfate to a carbon-to-nitrogen (C/N) ratio of 80 g/g

extract_protocol:
RNeasy Mini Kit (Qiagen, Germany; Purification of Total RNA from Yeast protocol); Precellys evolution bead mill (Bertin Instruments, Montigny-le-Bretonneux, France) for 4 cycles à 45 s at 6000 rpm
Illumina TruSeq Stranded mRNA library kit with Poly-A selection

treatment_protocol: Quenching by liquid nitrogen

tag: strain

value: BOT-O

tag: growth condition

value: nitrogen-starvation

tag: sugar

value: xylose


title: Donor_3_Cytosol


title: OxAt2

source_name: nitrogen-starvation (time point 2), xylose, biological replicate A


title: Donor_2_Processing_Bodies


title: OgBt2

source_name: nitrogen-starvation (time point 2), glucose, biological replicate B

value: glucose


title: amyloidosis [CprobeG_geo10003]

tag: sample group

value: amyloidosis

value: Glomeruli from kidney biopsy


title: OgAt2

source_name: nitrogen-starvation (time point 2), glucose, biological replicate A


title: DN [CprobeG_geo10025]


title: Donor_4_Stress_Granules

value: Total CD3+

value: cell lysis + immunoprecipitation of G3BP1


title: Donor_2_Cytosol

value: cell lysis


title: Donor_2_Stress_Granules


title: OxCt1

source_name: exponential growth (time point 1), xylose, biological replicate C

value: exponential growth


title: OxBt2

source_name: nitrogen-starvation (time point 2), xylose, biological replicate B


title: Donor_1_Stress_Granules


title: FSGS [CprobeG_geo10001]

value: FSGS


title: OgCt2

source_name: nitrogen-starvation (time point 2), glucose, biological replicate C


title: LN-WHO IV [CprobeG_geo10002]

value: LN-WHO IV


title: OgCt1

source_name: exponential growth (time point 1), glucose, biological replicate C


title: Donor_3_Stress_Granules


title: OxBt1

source_name: exponential growth (time point 1), xylose, biological replicate B


title: OxAt1

source_name: exponential growth (time point 1), xylose, biological replicate A


title: infection-associated GN [CprobeG_geo10019]

value: infection-associated GN


title: FSGS [CprobeG_geo10023]


title: Living donor [CProbeG_LD_30_151]

value: Living donor


title: OgBt1

source_name: exponential growth (time point 1), glucose, biological replicate B


title: Donor_1_Cytosol


title: Donor_1_Processing_Bodies

value: cell lysis + immunoprecipitation of DCP1A


title: LN-WHO III [CprobeG_geo10024]

value: LN-WHO III


title: HMC-1.3, clone 2, rep 3

city: Bethesda

first: Ana

last: Olivera

state: MD

address: 10 Center Dr, Bldg 10

institute: NIAID (National Institutes of Health)

data_processing:
Raw reads were trimmed for adapters and low-quality bases using Cutadapt v2.10
Reads were aligned to the human reference genome (hg38) and the Gencode Release 39 annotation using STAR v2.5.3 in two-pass mode
PCR duplicates were marked using Picard MarkDuplicates v2.27.3
Gene-level quantification was performed using RSEM v1.3.0
Pairwise differential expression was performed using DESeq2
Assembly: hg38, Gencode Release 39 annotation
Supplementary files format and content: RawCountFile_RSEM_genes.txt is a tsv file with expected counts output from RSEM
Supplementary files format and content: fpkm.txt is a tsv file with FPKM normalized counts

molecule: polyA RNA

extract_protocol:
total RNA from 2 × 10^6 cells was extracted using the RNeasy plus mini kit (Qiagen, Valencia, CA) and treated with DNase (Bio-Rad, Hercules, CA) to eliminate gDNA contamination
lllumina Stranded mRNA Prep Ligation Library Prep

tag: cell line

value: HMC-1.3 (subclone 2)

value: Human mast cell


title: OgAt1

source_name: exponential growth (time point 1), glucose, biological replicate A

value: BOT-O


title: HMC-1.3, clone 1, rep 3

value: HMC-1.3 (subclone 1)


title: HMC-1.3, clone 1, rep 2


title: Control [C9_S27]

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

data_processing:
Illumina adapters and low-quality reads were removed from raw sequencing reads using cutadapt. Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the Mycobacterium tuberculosis H37RV, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, using hisat2 with default parameters. Uniquely aligned reads were counted using featureCounts of Subread package. There were 4008 genes in the gtf file, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, for which we had count information. Genes with total read count 10 across all the samples were removed resulting in 3987 genes for SigA knockdown experiment and 3999 genes for SigB knockout experiment, which were used for further analysis. Differential gene expression analysis was performed using DESeq2. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 0.5 were considered differentially expressed. For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Genome_build: Mycobacterium tuberculosis H37RV GCF_000195955.2_ASM19595v2
Supplementary_files_format_and_content: Featurecount count file

organism: Mycobacterium tuberculosis

source_name: Control

growth_protocol: SigA conditional mutant strains was grown in 7H9 + ADC media till 0.8 OD (In presence or absence of Atc).  Mycobacterial strains (SigB gene replacement strain) was cultured in Middlebrook 7H9 medium (BD Biosciences) supplemented with 10% albumin, dextrose, NaCl, catalase (ADC) along with 0.2% glycerol (Sigma) and 0.05% Tween-80 (Sigma).

extract_protocol: RNA was isolated from exponentially growing cultures equivalent to 10 O.D.600 units. The collected cells were resuspended in TRIzol reagent (Invitrogen), lysed using a bead beater (MP FastPrep system, MP Biomedicals) as per manufacturer's instructions, and the TRIzol-lysed cell mix was extracted with chloroform, followed by precipitation of RNA using isopropanol. The RNA pellet was dissolved in RNase-free water (30 µl with 2 µl of RiboLock (Thermo Scientific). DNA contamination was removed by DNase I (Invitrogen) treatment, and the RNA was further purified using RNeasy mini columns (Qiagen).

treatment_protocol: SigA samples were treated with 1mM/ml anhydrotetracycline for 3 days

tag: genotype/variation

value: Control


title: Control [C8_S26]


title: HMC-1.3, clone 2, rep 1


title: HMC-1.3, clone 1, rep 1


title: RvΔsigA + Atc [3rd-Day-ATC5_S10]

source_name: RvΔsigA + Atc

value: SigA conditional knockdown

tag: treatment

value: 1mM/ml anhydrotetracycline for 3 days


title: control-3

city: Nanjing

first: Yu

last: Zhang

state: Jiangsu

address: No.215,Guangzhou Road

department: Respiratory Medcine

institute: Nanjing Chest Hospital

description: N, adjacent normal tissue  matched to lung adenocarcinoma tissue

hyb_protocol: 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 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA 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 using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: adjacent normal tissue

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). 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.

extract_protocol: fresh frozen tissue on dry ice, and RNA was harvested using Trizol reagent. The RNA quantity and quality were measured by NanoDrop ND-1000 (NanoDrop products, Wilmington, DE, USA). The RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

tag: gender

value: male


title: control-5

value: Female


title: Liver from patient with benign pancreatic lesion, #55

first: Linda

last: Bojmar

address: 413 E 69th St, Belfer Research Bldg

department: Department of Pediatrics

description:
55_Liver_IGO_06756_I_4
F

data_processing:
The output data (FASTQ files) are mapped to the target genome using the STAR aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used).
After mapping we post process the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: Normalized count matrix

source_name: liver

extract_protocol:
total RNA from 5 mg of fresh-frozen liver tissue was extracted using the RNeasy Mini Kit (QIAGEN catalog # 74104)
Samples underwent ribosomal RNA depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202

treatment_protocol: fresh liver tissue was snap frozen in liquid nitrogen and stored in -80C until RNA extraction

value: liver

tag: disease state

value: benign pancreatic lesion


title: RvΔsigA + Atc [3rd-Day-ATC4_S9]


title: infection-associated GN [CprobeG_geo10015]

source_name: Kidney Biopsy from Human Glomerular Disease

value: Glomeruli from kidney biopsy


title: Living donor [CProbeG_LD_30_131]

source_name: Kidney Biopsy from Human Living donor


title: Living donor [CProbeG_LD_30_109]


title: HMC-1.2, rep 2


title: cancer-5

description: C,treatment-naive lung adenocarcinoma tissue

source_name: lung adenocarcinoma tissue


title: control-4


title: FGGS [CprobeG_geo10011]

value: FGGS


title: cancer-4


title: control-2


title: Living donor [CProbeG_LD_30_147]


title: Living donor [CProbeG_LD_30_146]


title: Living donor [CProbeG_LD_30_138]


title: Normal liver from patient with hepatocellular adenoma, #FCL6

description:
FCL6_Liver_IGO_06756_I_17
E

source_name: normal liver adjacent

value: normal liver adjacent

value: hepatocellular adenoma


title: RvΔsigA - Atc [Day3-ATC5_S7]

source_name: RvΔsigA - Atc


title: RvΔsigA - Atc [Day3-ATC4_S6]


title: cancer-3


title: RvΔsigB [S6_S32]

source_name: RvΔsigB

value: SigB knockout


title: Living donor [CProbeG_LD_30_142]

value: Living donor


title: Normal liver from patient with hepatocellular adenoma, #FCL2

description:
FCL2_Liver_IGO_06756_I_13
C


title: RvΔsigB [S5_S31]


title: HMC-1.1, rep 2


title: HMC-1.3, clone 2, rep 2

value: HMC-1.3 (subclone 2)


title: control-1

description: N, adjacent normal tissue  matched to s766c


title: Liver from patient with benign pancreatic lesion, #45

description:
45ID_Liver_IGO_06756_G_24
I


title: HMC-1.2, rep 3

value: Human mast cell


title: cancer-2


title: Living donor [CProbeG_LD_30_103]


title: HMC-1.2, rep 1


title: cancer-1


title: RvΔsigA + Atc [3rd-Day-ATC3_S8]


title: mCherryRNAi_1

first: Mary

last: Baylies

state: New York

description: PE50 run

data_processing:
QC and trimming was performed with the Rfastp (version 1.0.0) package.
Reads were aligned to the Drosophila genome Rsubread (version 2.4.3) package.
Reads were counted using Rsamtools (version 2.6.0), GenomicRanges (version 1.42.0) and GenomicAlignments (1.26.0) packages.
Read count normalization and differential gene expression between groups was performed using DESeq2 (version 1.30.1) package.
Assembly: dm6
Supplementary files format and content: comma-separated .csv table including normalized counts for each sample

organism: Drosophila melanogaster

source_name: Adult body wall musculature

growth_protocol: Larvae grown for ~90h (late third instars)

extract_protocol:
Trizol extraction
RNA libraries were prepared using SMARTerAmpSeq

treatment_protocol: Tissue-specific knockdown under Mef2 promotor and knock-down imrpoved by dicer2

value: Adult body wall musculature

value: Muscle enriched

value: Control knockdown


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB13_liver]

city: Szeged

first: Lajos

last: Mates

address: Temesvari krt. 62.

department: Institute of Genetics

country: Hungary

institute: Biological Research Centre

library_source: genomic

data_processing:
Paired-end reads from Illumina FASTQ files were assembled using PEAR and filtered for the presence of PB and SB ITR sequences using Smith – Watermann algorithm.  Following the trimming of Illumina adapters and ITR sequences using Cutadapt reads extending at least 15 bp were considered for further analysis.
Burrows-Wheeler algorithm (BWA) was used to map trimmed reads to the Mus musculus genome version GRCm39.
To assure the quality of mapping we utilized a custom method to identify genomic regions where mismapped reads accumulate due to the imperfections of reference genome assemblies. We mapped reads from two different whole genome sequencing experiments (SRR7278720 and SRR7278736) using BWA applying the mem -a parameter. Genomic regions with 100x the average read coverage were identified. Mapped reads from our experiments residing in these identified high read coverage regions were excluded from further analysis.
The integration sites were determined as those genomic coordinates where at least 3 reads had their start point and integration site sequences were identified as the first 2 and 4 nucleotides for SB and PB transposons, respectively.
Assembly: Mus musculus genome version GRCm39.
Supplementary files format and content: PB1-17 and SB1-13 ...bed files contain the unique filtered vector integration sites identified in individual animals
Supplementary files format and content: The PB- and SBmerged_1_12 ...bed files contain the unique filtered vector integration sites merged from 1-12 animals. The number of repetitions for each recurrent integration site across the 12 experimental animals is indicated.
Library strategy: Tn-Seq

molecule: genomic DNA

extract_protocol:
For SBE-seq whole livers of gene therapeutically treated animals were lysed in 150 ml lysis buffer (100 mM TRIS-HCl pH8, 5 mM EDTA pH8, 200 mM NaCl, 0.2% SDS) and incubated overnight at 50 °C in the presence of 300 µg/ml ProteinaseK (VWR Chemicals). 1 ml of the lysate was used for standard phenol/chloroform extraction. DNA precipitation was done with 3 volumes of absolute ethanol in the presence of 1/10 volume sodium acetate (3M). Pelleted DNA was washed with 70% ethanol, air-dryed and dissolved in nuclease-free water (SigmaAldrich).
5 μg genomic DNA from mouse liver was enzymatically fragmented, end-repaired and dA-tailed using the QIAseq FX DNA Library Kit (Qiagen). DNA was cleaned with AmpPure XP beads following each steps. Next, a linker with a special structure, disfavouring the formation of linker-linker PCR products was ligated to the genomic DNA fragments. Then the 400-1500 bp range of ligated fragments were selected using a Pippin Prep instrument (Sage Science). Next, on this selected fragment pool two nested PCRs were carried out, where one member of the PCR primer pairs was transposon-specific and the other was linker-specific. The 1st PCR was performed for 16 cycles using a biotinylated transposon-specific primer. Then the biotinylated PCR products were purified with streptavidin-coated paramagnetic beads. The 2nd PCR was performed on the purified PCR products for another 16 cycles using transposon- and linker-specific primers carrying the Illumina indexing-specific paired-end adapters to create the final NGS library. The libraries were cleaned with AmpPure XP beads. Each step of creating the NGS libraries was verified by analysing sample aliquots on a TapeStation4200 instrument (Agilent) using D1000 screen tapes. The final concentration of each library was determined by a Qubit fluorometer, and libraries were spiked with 10% PhiX control library before proceeding with Illumina run. On the Illumina instruments custom-made Read2 and Index Read primers were used instead of the standard Illumina primers. The sequencing of SBE-seq libraries was performed using an Illumina MiSeq instrument.

tag: group

value: SB


title: Living donor [CProbeG_LD_30_25]


title: fly_ovary_Pcif1M6stop_3

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Reads were sorted into individual libraries based on the barcodes and mapped to the fly transcriptome (Ensembl release 95) using salmon v1.3.0 (salmon quant with options -l A  --validateMappings --gcBias) (Patro et al., 2017). Further analysis was performed using R version 3.6.3 and Bioconductor (Huber et al., 2015). The DESeq function of DESeq2_1.25.10 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression between control and mutant samples and the adjusted p-values.
Assembly: BDGP6 (Ensembl release 95)
Supplementary files format and content: The csv file contains gene expression data.

source_name: ovary

growth_protocol: To investigate the physiological role of Drosophila Pcif1, we used the CRISPR-Cas9 genome engineering tool to generate a genomic deletion in the region encoding for the NLS in the w1118 background. Two mutated alleles were identified: Pcif1M6stop and Pcif1F9ΔNLS. The deletion in the Pcif1M6stop allele corresponds to a frameshift ending in a premature stop codon. On the other hand, the Pcif1F9ΔNLS allele has an in-frame deletion of the NLS, generating a protein of 829 amino acids.  To clean up any potential off-target mutations, the selected alleles were backcrossed for up to ten generations with a fly line carrying a P-element inserted in the first intron of Pcif1 (P{GT1}CG11399BG02557), also referred to as the Pcif1BG02557 line.

extract_protocol:
Three pairs of ovaries were collected per line for RNA extraction with Trizol reagent.
Ribozero-depleted deep sequencing libraries were prepared and sequenced as previously described (Pandey et al., 2020). Specifically, the  NEB Next ultra kit (NEB: E7760L kit) was used to prepare the pair-end libraries which were sequenced in high-mode on Next-seq 500 at GeneCore, EMBL.

value: ovary


title: Normal liver from patient with hepatocellular adenoma, #FCL4

city: New York

description:
FCL4_Liver_IGO_06756_I_15
D


title: RvΔsigA - Atc [Day3-ATC1_S5]

value: SigA conditional knockdown


title: HMC-1.1, rep 3


title: fly_ovary_Pcif1M6stop_2


title: tmodRNAi_1

description: PE50 run

value: tmod knockdown


title: tmodRNAi_2

description: PE50 run


title: fly_ovary_Pcif1M6stop_1


title: mCherryRNAi_3

description: PE50 run


title: Liver from patient with localized pancreatic cancer, #46

description:
46FM_Liver_IGO_06756_G_25
N

value: liver

value: localized pancreatic cancer


title: tmodRNAi_3

description: PE50 run


title: fly_ovary_Pcif1BG02557_2


title: mCherryRNAi_2

description: PE50 run


title: Liver from patient with benign pancreatic lesion, #31

description:
31VK_Liver_IGO_06756_G_14
H

value: benign pancreatic lesion


title: HMC-1.1, rep 1


title: Liver from patient with benign pancreatic lesion, #17

description:
17LD_Liver_IGO_06756_G_12
G


title: Sample#5 (Tg Epith paired with esophagus)

city: Anderlecht

first: Alizee

last: Vercauteren Drubbel

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: Epithelial cells from the circumvallate and the foliate papillae of the tongue have been sorted based on EpCam expression

data_processing:
Data were demuliplexed using cellranger demux with Illumina bcl2fastq to generate FASTQs for R1 and R2 paired-end as well as the sample index.
Cell Ranger version 3.1.0 pipeline with the RNA-seq aligner STAR were used to generate output files aligned on mm10 reference genome
Assembly: mm10
Supplementary files format and content: H5 binary format. Feature Barcode Matrix of single cell sequencing in hierarchical data format

source_name: Tongue

extract_protocol:
Tissues were digested and sorted in 1ml PBS 0.04% BSA. Samples were loaded on a chromium chip and processed using the Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) following manufacturer’s recommendations.
Multiplexed libraries were obtained following manufacturer’s recommendations of Chromium Single Cell 3’ Reagent kits v3 (10x Genomics) and loaded on a Novaseq 6000 (Illumina). Briefly, samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tongue

value: Krt8-YFP mice


title: fly_ovary_Pcif1F9ΔNLS_2


title: fly_ovary_Pcif1F9ΔNLS_3


title: Liver from patient with benign pancreatic lesion, #5

description:
5VS_IGO_06756_D_1
J


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB8_liver]


title: fly_ovary_Pcif1F9ΔNLS_1


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB9_liver]


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB12_liver]


title: Sample#4 (Up Epith esophagus paired with tongue)

description: Epithelial cells from cevical segment of the esophagus have been sorted based on EpCam expression

source_name: Cervical Esophagus

value: Cervical Esophagus


title: Liver from patient with localized pancreatic cancer, #48

description:
48MS_Liver_IGO_06756_G_26
O


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB11_liver]


title: fly_ovary_Pcif1BG02557_1


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB10_liver]


title: Sample#2 (Up Tot esophagus)

description: All living cells from cervical segment of the esophagus have been sorted

value: wild type CD1 mice


title: fly_ovary_Pcif1BG02557_3


title: Liver from patient with localized pancreatic cancer, #37

description:
37IL_Liver_IGO_06756_G_17
M


title: Liver from patient with localized pancreatic cancer, #10

description:
10FC_Liver_IGO_06756_G_6
L


title: Sample#3 (Up Epith esophagus)


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB7_liver]


title: TG Old DN3a - replicate 2

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 1.29.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's built-in NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: DN3a thymocytes

extract_protocol:
RNA was extracted using RNeasy Plus Micro (Qiagen)
Libraries were constructed using the Illumina TrueSeq library construction kit
Single-end 100 bp RNA-sequencing short reads were generated using an Illumina HiSeq 2000, yielding between 7 and 12 million reads for each sample

tag: age (weeks)

tag: age category

value: Old

tag: mouse

value: Female


title: TG Old DN3a - replicate 3


title: SKBR3_CTTN_rep3

city: Seoul

first: Gu

last: Kong

address: 222, Wangsimni-ro, Seongdong-gu

department: College of Medicine

country: South Korea

institute: Hanyang University

data_processing:
bcl2fastq2-v2.20.0 software used for basecalling.
TRIMMOMATIC software used for base trimming with TruSeq3-PE.fa
STAR used for alignment
Cufflinks used for assembly, merging, quantification and normalization
Assembly: GRCh38

source_name: breast cancer cell line

extract_protocol:
Total RNA was extracted from control and CTTN overexpressed SKBR3 stable cell lines tumors using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA). RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: mammary gland/breast

tag: cell type

value: epithelial

value: adenocarcinoma

tag: transfection

value: pLVX-CTTN


title: Sample#1 (Tho Tot esophagus)

description: All living cells from thoracic segment of the esophagus have been sorted

source_name: Thoracic sophagus

value: Thoracic sophagus

tag: genotype

value: wild type CD1 mouse


title: SKBR3_CTTN_rep2


title: Tg K8YFPneg rep1

description:
processed sample name: Tg YFPneg 1
Epithelial Krt8 negative cells from foliate and circumvallate papillae of the tongue have been sorted based on EpCam and negative YFP expression

data_processing:
Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software (version 2.5.3a)
Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq
Total raw counts were uploaded on degust 4.1.1 and analyzed using EdgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample and genome annotations

extract_protocol:
Tissues were digested, sorted in TRK lysis buffer and extracted using E.Z.N.A Total RNA Kit. RNA quality was checked before library preparation using a Bioanalyzer 2100.
Libraries were obtained using the Ovation Solo RNA-seq System (NuGen) following manufacturer's recommendations and loaded on a Novaseq 6000 (Illumina)


title: SKBR3_CTTN_rep1


title: Tg K8YFPneg rep2

description:
processed sample name: Tg YFPneg 2
Epithelial Krt8 negative cells from foliate and circumvallate papillae of the tongue have been sorted based on EpCam and negative YFP expression


title: TG Old DN3a - replicate 1

tag: strain


title: Tg K8YFP+ rep2

description:
processed sample name: Tg YFP+ 2
Epithelial Krt8+ cells from the foliate and circumvallate papillae of the tongue have been sorted based on EpCam and YFP co-expression


title: WT Old DN3a - replicate 3

value: Wild-type


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB4_liver]

value: SB


title: SKBR3_Con_rep3

value: pLVX vector


title: Tg K8YFP+ rep1

description:
processed sample name: Tg YFP+ 1
Epithelial Krt8+ cells from the foliate and circumvallate papillae of the tongue have been sorted based on EpCam and YFP co-expression


title: SKBR3_Con_rep2


title: WT Old DN3a - replicate 2


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB3_liver]

value: liver


title: Eso Up K8YFPneg rep2

description:
processed sample name: up YFPneg 2
Epithelial Krt8 negative cells from cevical segment of the esophagus have been sorted based on EpCam and negative YFP expression


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB6_liver]


title: Liver from patient with localized pancreatic cancer, #2

institute: Weill Cornell Medicine

description:
2NS_re_Liver_IGO_06756_G_2
K

value: localized pancreatic cancer


title: TG Young DN3a - replicate 3

value: Young


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB1_liver]


title: Eso Up K8YFPneg rep1

description:
processed sample name: up YFPneg 1
Epithelial Krt8 negative cells from cevical segment of the esophagus have been sorted based on EpCam and negative YFP expression


title: WT Old DN3a - replicate 1


title: SKBR3_Con_rep1


title: Eso Up K8YFP+ rep1

description:
processed sample name: up YFP+ 1
Epithelial Krt8+ cells from cevical segment of the esophagus have been sorted based on EpCam and YFP co-expression


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB2_liver]


title: TG Young DN3a - replicate 1

value: Male


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB17_liver]

value: PB


title: SALMATD_2

city: peking

first: kong

last: lu

address: capital medical university

institute: ccmu

data_processing:
A total of 18 samples were tested using the DNBSEQ platform, with an average yield of 1.19G data per sample. The average alignment ratio of the sample comparison genome was 94.90%, which was comparative The average alignment of the gene set was 80.35%; a total of 18782 genes were detected.
Reference Genome Version：GCF_000001405.39_GRCh38.p13
The raw data for sequencing contains reads of low quality, adaptor contamination, and excessively high levels of unknown base N. These reads need to be removed before data analysis to ensure the reliability of the results. For the quality index of filtered reads, see the filtered reads quality statistics table and the raw data filtering component statistics chart. For the base content distribution and quality distribution, see the base content distribution chart of clean reads and the base quality distribution chart of clean reads.
After getting clean reads, we used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.Align clean reads to the reference genes by using Bowtie2 to get the alignment result.

source_name: salivary adenoid cystic carcinoma

extract_protocol: RNA extracted from 1×10^7 cells in 1 mL TRIZOL reagen

value: salivary adenoid cystic carcinoma

value: 1 uM ATRA+10 uM DDP


title: TG Young DN3a - replicate 2

value: Female


title: WT Young DN3a - replicate 2


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ SB5_liver]


title: SALMATD_1


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB16_liver]


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB15_liver]


title: Eso Down K8YFPneg rep1

description:
processed sample name: down YFPneg 1
Epithelial Krt8 negative cells from thoracic segment of the esophagus have been sorted based on EpCam and negative YFP expression


title: WT Young DN3a - replicate 3


title: SALMAT_3

value: 1 uM ATRA


title: WT Young DN3a - replicate 1


title: Eso Down K8YFPneg rep2

description:
processed sample name: down YFPneg 2
Epithelial Krt8 negative cells from thoracic segment of the esophagus have been sorted based on EpCam and negative YFP expression


title: SALMATD_3


title: SALMAT_2


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB13_liver]


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB14_liver]


title: SALMAT_1


title: Hepatocytes, TNFα, 24h-3

first: David

last: Lyden

address: 413 East 69th Street, Room BB1228

description: TNFa vs PBS treated primary hepatocytes.xls

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (Version2.0.11)
Transcriptome reconstruction was performed by Cufflinks (Version 2.1.1), and the abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Gene expression profiles were constructed for differential expression, cluster, and principal component analyses with the DESeq2 package
For differential expression analysis, pairwise comparisons between two or more groups using parametric tests where read-counts follow a negative binomial distribution with a gene-specific dispersion parameter. Corrected p-values were calculated based on the Benjamini-Hochberg method to adjusted for multiple testing.
Assembly: mm9
Supplementary files format and content: Excel file with Log2FC, p-value and q-value for each gene expressed in the TNFα treated primary hepatocytes, compared to control PBS treated primary hepatocytes.

source_name: Primary hepatocyes

extract_protocol:
Total RNA was extracted using TRIzol reagent, and RNA was further purified using RNeasy Mini kit including a DNase digest following the manufacturer’s instructions
RNA libraries were prepared using TruSeq Stranded mRNA Library Preparation (Illumina) following the manufacturer’s instructions

value: Primary hepatocyes

value: WT

value: TNFα treated for 24 h


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB12_liver]


title: SALM_3

value: DMSO


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB11_liver]


title: Hepatocytes, TNFα, 24h-2


title: TG Young DN2 - replicate 3

source_name: DN2 thymocytes


title: SALM_2


title: WT Young DN2 - replicate 2


title: Hepatocytes, TNFα, 24h-1


title: TG Young DN2 - replicate 1


title: Eso Up K8YFP+ rep2

description:
processed sample name: up YFP+ 2
Epithelial Krt8+ cells from cevical segment of the esophagus have been sorted based on EpCam and YFP co-expression

value: Cervical Esophagus


title: WT Young DN2 - replicate 1

value: Wild-type


title: SA83AT_3


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB9_liver]

source_name: liver


title: Hepatocytes, Control, 24h-2

value: PBS treated for 24 h


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB7_liver]


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB8_liver]


title: TG Young DN2 - replicate 2


title: SA83AT_1


title: Hepatocytes, Control, 24h-1


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB6_liver]


title: SA83AT_2


title: Replicate 3 L1 F4+3 starved

city: New YorK

first: Columbia

middle: Carlotta

last: University

state: NEW YORK

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: HHMI/Columbia University

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S12_N2_L1_SS

data_processing:
Alignment to WS220 using subread package and featurecounts
differential gene expression analysis was done using DESeq2
Assembly: WS220
Supplementary files format and content: Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups contains all transripts with normalized counts for each sample from the D1 adults. Statistics for all comparisons are included
Supplementary files format and content: Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups contains all transripts with normalized counts for each sample from the L1 animals. Statistics for all comparisons are included

organism: Caenorhabditis elegans

source_name: whole worm (n~10000)

extract_protocol:
Animals were collected at the respective stage as described above. At the time of collection, animals were washed off the plate with M9, washed 3x with M9, mechanically homogenized in TRIzolusing disposable tissue grinder  ).  Total RNA was isolated using RNeasy Minelute kit according to manufacturer (Qiagen).
RNA-seq libraries were prepped using the Ovation Universal RNA-seq kit (Nugen) according to manufacters instructions

value: strain N2

tag: developmental stage

tag: current nutritional status

value: starved

tag: own or ancestral l1 experience

value: starved (ancestral)


title: Replicate 3 L1 F4+3 fed

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S11_N2_L1_SF

value: fed


title: SA83_3


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB5_liver]

value: liver


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB10_liver]

value: PB


title: RNA_seq_BCAS_4

city: Shanghai

first: Zengyu

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

data_processing:
Raw data were first evaluated by FastQC for quality control to determine whether the sequencing data were suitable for subsequent analyses.
Adapter sequences, low-quality reads, and too short reads were removed from raw data with Trim-galore to obtain clean data.
Sequencing reads were aligned to annotated RefSeq genes in the mouse reference genome (UCSC mm10) with HISAT2. And Samtools v1.9 was used to sort and build the alignment file index.
A gene count matrix that contained raw transcript counts for each annotated gene were generated using the featureCounts v1.6.3.
To determine the most appropriate threshold for removing genes with low counts, we relied on the automatic and independent filtering performed by DESeq2 R package (1.16.1). And raw transcript counts were normalized, log2 transformed, and analyzed using the default procedures in DESeq2 to identify genes that were differentially regulated following CCH.
Assembly: mm10
Supplementary files format and content: raw gene counts text files

source_name: brain

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water

extract_protocol:
RNA was harvested using the TRIzol Reagent (Life technologies, California, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol:
The control group was exposed to sham operation
The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

tag: cell line

value: brain

value: right cerebral cortex

tag: time

value: 3 weeks


title: Replicate 3 L1 Control fed

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S9_N2_L1_FF

value: fed (ancestral)


title: RNA_seq_BCAS_3

tag: treatment

value: bilateral carotid artery stenosis (BCAS) operation


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB4_liver]


title: SALM_1

value: salivary adenoid cystic carcinoma


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB3_liver]


title: SA83_1


title: SA83_2


title: RNA_seq_BCAS_2

value: WT


title: Replicate 3 L1 Control starved

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S10_N2_L1_FS


title: RNA_seq_BCAS_1


title: Replicate 2 L1 F4+3 starved

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S8_N2_L1_SS


title: Hepatocytes, Control, 24h-3

value: Primary hepatocyes


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB2_liver]


title: ACCLM_WT_3A


title: ACCLM_WT_2A


title: Sequencing of therapeutic transposon insertions from TT1 mouse liver [ PB1_liver]


title: ACCLM_WT_1A


title: Replicate 2 L1 Control starved

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S6_N2_L1_FS


title: Replicate 2 L1 Control fed

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S5_N2_L1_FF


title: RNA_seq_Sham_4

value: Sham operation


title: Replicate 2 L1 F4+3 fed

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S7_N2_L1_SF


title: Replicate 1 L1 F4+3 starved

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S4_N2_L1_SS


title: RNA_seq_Sham_3


title: ACCLM_NICDKD_2A

value: NICD knockdown


title: RNA_seq_Sham_1