title: SHR-Bh1

type: RNA

first: Xiaochen

last: Yang

address: Beixiange 5#, Xicheng District

department: Cardiology

institute: Guangan men Hospital

description: Gene expression after BSJY treatment in spontaneously hypertensive rat

hyb_protocol: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent.  Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1. 5 mL nuclease-free microfuge tube: 4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6.  Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  7. Mix well by careful pipetting.  Take care to avoid introducing bubbles.  Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base.  Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up.  Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C.  Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: Instrument: Agilent Microarray Scanner (Agilent p/n G2565BA). Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21. 6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9. 1 (Agilent) using default parameters (protocol BSJY) to obtain background subtracted and spatially detrended Processed Signal intensities.   Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: thoracic aorta

label_protocol: 1. Add 1ug of total RNA to a 1. 5-mL microcentrifuge tube.  2. Add 1. 2 μL of T7 Promoter Primer.  3. Use nuclease-free water to bring the total reaction volume to 11. 5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid.  Return the tubes to ice.  8. Add 8. 5 uL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice.  Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.  14. Add 60 μL of Transcription Master Mix to each sample tube.  Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.

growth_protocol: Forty 12-week-old male SHRs, weighing 310±10g, and ten 12-week-old male Wistar-Kyoto (WKY) rats, weighing 320±10g, were provide by Beijing Vital River Laboratory Animal Technology Co. , Ltd.  with certificate number: SCXK (Beijing) 2017-0001.  The SHRs were randomly divided into four groups (SHR-C, SHR-Bh, SHR-Bl, SHR-Ca).  Each cage contained five rats.  Details of the raising environment of experimental animals and methods can be found in our previous report.  The eight herbal granules of BSJY were provided by Sichuan New Green Pharmaceutical Science and Technology Development Co. , Ltd.  The herbal granules of BSJY were dissolved in water.  The BSJY high dose treatment (SHR-Bh) was administered 6. 75 g/ml/day.  The BSJY low dose treatment (SHR-Bl) was administered 1. 6875 g/ml/day.  Captopril tablets (SHR-Ca) were provided by Sino-American Shanghai Squibb Pharmaceuticals Co. , Ltd.  The captopril tablets were dissolved in drinking water and intragastrical administered 0. 125 g/ml/day.  The drugs were intragastrical administered once a day for 16 weeks.  An equal volume of drinking water was intragastrically administered to the control group (SHR-C) and wistar group (WKY).

extract_protocol: 1. Phase Separation.  Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes.  Add 0. 2 ml of chloroform per 1 ml of TRIzol Reagent.  Cap sample tubes securely.  Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes.  Centrifuge the samples at 12,000 × g for 15 minutes at 4°C.  Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase.  RNA remains exclusively in the aqueous phase.  The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.  2. RNA Precipitation.  Transfer the aqueous phase to a fresh tube.  Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol.  Use 0. 5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization.  Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.  3. RNA Wash.  Remove the supernatant.  Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization.  Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.  4.  Redissolving the RNA At the end of the procedure, air-dry the RNA pellet for 5-10 minutes.  Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: Thoracic aorta from SHRs and wistar rat was irradiated. a) Cryopulverization of tissue using the Biopulverizer.  Place the BioPulverizer in a shallow container and cool thoroughly with either liquid nitrogen.  Place prefrozen tissue in the well of the mortar.  Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS).  Empty the powdered contents for subsequent homogenization or extraction procedures.  b) Homogenization using the Mini-Bead-Beater-16.  Fill the 2 ml screw-cap microtube one-half full with 1. 0mm beads.  Then add TRIzol and tissue, being sure to fill the microtube almost to the top.  Exclude as much air from the microtube as possible.  Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization.  Be sure there are no beads on the threads of the microtubes when screwing down the cap.  Insert 1 to 16 microtubes into the holder.  Distribute them symmetrically as you would do with a centrifuge.  Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps.  Tighten the lid by hand so the vials are firmly held in place.  Do not overtighten.  Set the timer depending on the type of sample.  Start the machine.

value: thoracic aorta

tag: gender

value: male


title: SHR-Bh2

status: Public on Nov 01 2024

city: Beijing

country: China

molecule: total RNA

tag: tissue

tag: age


title: SHR-Bh3


title: s18775 SwDI/TWT

type: SRA

city: Minneapolis

first: Ling

last: Li

email: lil@umn.edu, linglilab@umn.edu

state: MN

address: 2001 6th Street SE Rm 4-208

department: Department of Experimental and Clinical Pharmacology

country: USA

institute: University of Minnesota

description: GEX

library_source: transcriptomic

data_processing:
10x formated output files for GEX were generated using cellranger
Further analysis was performed using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Mus musculus

source_name: Mouse frontal lobe, brain

extract_protocol:
Nuclei from six mouse brain tissues (3 for each genotype) were isolated following the 10x Genomics Demonstrated Protocol (CG000375; Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing), with the following modifications: the NP40 Lysis Buffer was used at a 20X dilution, tissue dissociation was performed on the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, Bergisch Gladbach, North Rhine-Westphalia, Germany) using a modified version of the 4C_nuclei_1 program, and no nuclei permeabilization was performed.Isolated mouse nuclei were then subjected to droplet-based 3′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 3′ Reagent Kits v3.1 per the manufacturer’s protocol (10x Genomics).
Library was generated according to Chromium Single Cell 3ʹ v3 protocol (10x Genomics).

value: Mouse frontal lobe, brain

tag: genotype

value: WT


title: SHR-Ca3

description: Gene expression after Captopril treatment in spontaneously hypertensive rat


title: SHR-Ca1


title: SHR-Ca2


title: SHR-C2

description: Gene expression in spontaneously hypertensive rat


title: SHR-C1


title: Aging_Exos_liver, replicate 2, scRNAseq

city: Chaoyang District

first: Youkun

last: Bi

state: Beijing

address: NO.15, Datun Road

department: Institute of Biophysics

institute: Chinese Academy of Sciences

library_source: transcriptomic single cell

data_processing:
Cellranger  (10X Genomics)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Skin tissues were incubated with a dissociation buffer composed of collagenase I (1 mg/mL), collagenase IV (1 mg/mL), dispase (1 mg/mL), and trypsin-EDTA (0.125%) at 37 °C for 1 h. Liver tissues were exposed to dissociation buffer containing collagenase IV (1 mg/mL) and incubated at 37 °C for 40 min. Digestion was terminated by adding cold high-glucose DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) (GIBCO). The dissociated cells were centrifuged at 1,000 rpm and 4 °C for 5 min, then resuspended in 15 mL red blood cell lysis buffer (BD Biosciences) at 37 °C for 5 min. Subsequently, these cells underwent another round of centrifugation at 1,000 rpm and 4 °C for 5 min, followed by two washes with cold PBS and resuspended in cold PBS containing 10% PBS. The cell suspension was filtered through a 40 μm strainer (BD Falcon), subjected to two PBS washes, centrifuged at 1,000 rpm and 4 °C for 5 min, and resuspended in cold PBS supplemented with 10% FBS.
The library was performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10ÍGenomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retro-transcripted to cDNA, which contains an Ilumina R1 primer sequence. Unique Molecular Identifier (UMI) and the 10ÍBarcode. The pooled barcode cDNA was then cleaned up with Silane DynaBead, 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 sequence P5 and P7 sequences and a sample index were added.

value: liver

tag: treatment

value: hESC-Exos


title: s18682 SwDI/TWT

description: GEX


title: SHR-C3


title: Dural meninges IL-33KO, PND 14, 1

city: San Francisco

first: Ari

last: Molofsky

state: CA

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (10xGenomics)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: comma-separated values files
Supplementary files format and content: Counts from aggregated full file
Supplementary files format and content: Counts from aggregated subcluster
Supplementary files format and content: Metadata from aggregated full file
Supplementary files format and content: Metadata from aggregated subcluster

source_name: Dural meninges

extract_protocol:
P14 mice were anesthetized with CO2 and perfused transcardially with cold PBS. Horizontal cuts were made to remove the skullcap and placed in ice cold FACS Wash Buffer (FWB; 0.1M PBS (pH 7.4)/NaN3/3% FBS). Under a dissecting microscope, the dural meninges were quickly removed by gentle scraping using fine forceps and pulled away in an intact sheet. Meninges were kept in ice cold cRPMI ((RPMI 1640 supplemented with 10% (vol/vol) FBS, 1% (vol/vol) Hepes, 1% (vol/vol) Sodium Pyruvate, 1% (vol/vol) penicillin-streptomycin) until all samples were isolated. To obtain a single cell suspensions, meninges were transferred to cRPMI containing 40ug/mL DNAse I and 0.2 wU/mL Liberase TM in 1 mL of RPMI and incubated at 37 degrees Celsius with shaking at 220 RPM for 30 min. After gentle trituration, meninges and solution were passed through a 70 um cell strainer; remaining tissue was firmly pressed through the filter in a circular motion using a wide tip plastic plunger from a 1 ml syringe. The strainer was flushed with additional FWB and collected into a 15 ml falcon tube. Cells were pelleted at 300 RCF for 7 min at 4°C and resuspended in FWB for downstream applications. Cell suspensions were incubated with Fc block (2.4G2) and stained with the following antibody solution in FWB (45 min at 4 degree Celsius): CD45-BUV395, CD31-AF488, CD11b-PB, PDGFRa-APC, gp38-PECy7, DAPI. Cells were washed in FWB and fluorescence activated cell sorting was performed on a BD FACS Aria Fusion. Cells were gated for viable single cells and were enriched for lymphocyte and stromal populations by sorting CD45+CD11b- (non-myeloid immune cells) and gp38+CD31- (stromal cells) separately, and adding each of those populations to 25% of total cells (1:1:2 ratio of lymphocytes: stroma: total viable populations, Fig. S1A). Genotypes of mice sequenced were IL-33 deficient (Il33mcherry/mcherry) or heterozygous controls (Il33mcherry/+). Meninges from 5-8 mice were pooled per genotype and sex to obtain sufficient number of cells for sorting.
Library was prepared according to the manufacter’s instructions (Chromium Single Cell 3’ v3 protocol, 10x Genomics).

value: Dural meninges

tag: cell type

value: Lymphocyte and stroma enrished total cells

value: 2 weeks old


title: WKY-2

description: Gene expression in Wistar-Kyoto rat


title: Dural meninges IL-33HET, PND 14, 1

description: 10x Genomics


title: Parental_MR-580C_Ct_RNA_Rep2

city: Bethesda

first: Thomas

middle: A

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

data_processing:
Basecalling RTA 3.4.4 was used for Basecalling and Bcl2fastq 2.20 was used for demultiplexing allowing 1 mismatch. Sequences were aligned to the mouse genome (mm10) using Bowtie2 2.3.4.1.  -p 8 -x ref_genome -U read1.fastq (ChIP reads). RNA reads were aligned using STAR 2.7.0f with default settings.
Cutadapt 1.18 was used for adapter trimming and quality control.
ChIP-Seq Peaks were called using HOMER program version 4.10.4 with findPeaks with following parameters; FDR<0.001, 5x fold enrichment over control, 5x fold enrichment over local background.
ChIP-Seq and eRNA heatmaps were made from normalized bigWig files using Deeptools: -of bigwig --binSize 20 --effectiveGenomeSize 2652783500 --normalizeUsing RPGC; computeMatrix reference-point --referencePoint center -S and plot heatmap -m --sortRegions no
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: bigWig (ChIP-seq) and Excel file of normed counts (RNA-seq)

source_name: Parental adenocarcinoma cells

growth_protocol: Typical growth protocols with DMEM 10% FBS. Cells were grown 24h on media with 10% charcoal stripped serum before hormone treatment.

extract_protocol:
Cells fixed in 1% Formaldehyde. Lysed, Sonicated, and ChIP'd with anti-GFP (10 μg, Abcam #AB290) or anti-GR (10ug Santa Cruz # sc-393232x. Total RNA was collected using Pure-Link RNA Mini kit (Thermo).
ChIP-Seq libraries were made by TruSeq ChIP Library Prep Kit (IP-202-1012). RNA-Seq libraries were made with TruSeq Stranded Total RNA Library Prep.
ChIP-seq was performed with Next-Seq (76bp single-end reads) and RNA-Seq was performed with NOVA-Seq (150bp stranded reads).

treatment_protocol: Aldosterone treatments were with 10 nano-molar. Corticosterone treatments were 100 nano-molar with treatment times as described in the paper.

value: 2 hour of 100nM Corticosterone treated cells


title: WKY-1

description: Gene expression in Wistar-Kyoto rat


title: Parental_MR-580C_Ct_RNA_Rep3


title: Cold_exposed_4

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

data_processing:
Reads were aligned to the Oreochromis niloticus v.1.0 genome using Hisat2
Gene expression was determined using IsoEM2
Differential gene expression was determined using IsoDE2
Genome_build: v.1.0 (NCBI)
Supplementary_files_format_and_content: tab-delimited text files with TPM values for each condition

molecule: polyA RNA

organism: Oreochromis niloticus

source_name: Midbrain

extract_protocol:
Total RNA was extracted using TRIzol reagent, per the manufacturer's instructions
mRNA was isolated from total RNA with poly(dT) oligo-attached magnetic beads and cDNA libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina)

value: cold exposed


title: Cold_exposed_2


title: Cold_exposed_3


title: Cold_exposed_1


title: Parental_MR-580C_Ct_RNA_Rep1


title: Control_2

value: normothermy


title: Parental_MR-580C_Ald_RNA_Rep3

value: 2 hour of 10nM Aldosterone treated cells


title: WKY-3

description: Gene expression in Wistar-Kyoto rat


title: Control_1


title: Gastrointestinal stromal tumors (GISTs) tissue2

city: Jinshan Distric

first: Jin

last: Wang

state: Shanghai

address: 2901 Caolang Road, Scientific Research Center, RM 319

department: Shanghai Public Health Clinical Center

institute: Fudan University

description: Gene expression data from  gastrointestinal tissue  lower than imatinib-resistant gastrointestinal stromal tumors

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Homo sapiens

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: 3 Imatinib-resistant gastrointestinal stromal tumors came from obvious lesions during operation as well as its corresponding Gastrointestinal stromal tumors (GISTs)  tissue.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The fresh samples were extremely quick intensive chilling in liquid nitrogen within 5 minutes of excision to avoid degradation. Then frozen specimens were storage at -80 °C refrigerator.


title: s18685 SwDI/TKO

description: GEX

value: KO


title: Imatinib-resistant Gastrointestinal stromal tumors tissue2

value: female


title: Parental_MR-580C_NT_RNA_Rep1

value: 2 hour of vehicle treated cells


title: Gastrointestinal stromal tumors (GISTs) tissue3


title: Gastrointestinal stromal tumors (GISTs) tissue1


title: Control_3


title: Control_4


title: Imatinib-resistant Gastrointestinal stromal tumors tissue3


title: Imatinib-resistant Gastrointestinal stromal tumors tissue1


title: Parental_MR-580C_NT_RNA_Rep3


title: GRKO_MR-580C_Ct_RNA_Rep3

source_name: GRKO adenocarcinoma cells


title: I18Ah2

city: Wuhan

first: cao

last: lu

state: Hubei

address: 7 Donghu South Road

department: Chinese Academy   of Sciences

institute: Institute of Hydrobiology

data_processing:
Raw reads were produced by an Illumina Hiseq4000 instrument with 150 bp paired end reads by the BioMarker Biotechnology Co., Ltd (Beijing).
The trimming and quality controls of raw Illumina reads were performed using Sickle (https://github.com/najoshi/sickle) and SeqPrep (https://github.com/jstjohn/SeqPrep) with the default settings.
Raw data reads in fastq format were initially processed using in-house perl scripts.
Genome_build: none
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anguilla anguilla

source_name: intestine

growth_protocol: European eels (n = 150) with a mean body mass of 50 g were obtained from Zhangpu, Fujian province of China.

extract_protocol:
Total RNA was extracted using the TRIzol? Reagent (ThermoFisher Scientific, Massachusetts, USA) according to the manufacturer's protocol.
The mRNA-seq library construction was performed with the TruseqTM RNA sample prep Kit (Illumina, California, USA ) following the manufacturer's protocol.

treatment_protocol: Prior to the experiment, fish were reared in 1000-L plastic tanks with fresh water and a normal diet (48 % protein and 5.6 % fat) for one week, and then randomly distributed into 6 aquariums (55 cm ¡Á 40 cm ¡Á 30 cm) with 25 fish in each aquarium.  Each experimental fish in 3 groups (Infection group) was intraperitoneally injected with 100 ¦ÌL of A. hydrophila suspension (1 ¡Á 108 CFU/mL in PBS), and each control fish in 3 groups (Control group) injected with the same volume of PBS. The fish were not feed during the challenge experiment, with the water temperature at 25 ¡À 1¡ãC.

value: intestine

value: infection of A. hydrophila at 18hpi


title: Parental_MR-580C_Ald_RNA_Rep2


title: GRKO_MR-580C_Ct_RNA_Rep2


title: Parental_MR-580C_Ald_RNA_Rep1


title: I18Ah1


title: L36PBS1

value: injected with PBS at 36h


title: Parental_MR-580C_NT_RNA_Rep2


title: GRKO_MR-580C_Ald_RNA_Rep3


title: L18Ah2


title: I6Ah2

value: injected with PBS at 6h


title: GRKO_MR-580C_Ald_RNA_Rep1


title: I6Ah1


title: GRKO_MR-580C_NT_RNA_Rep3


title: L18Ah1


title: L36PBS2


title: L36Ah2

value: infection of A. hydrophila at 36hpi


title: GRKO_MR-580C_Ct_RNA_Rep1


title: L36Ah1

value: liver


title: GRKO_MR-580C_NT_RNA_Rep2


title: GRKO_MR-580C_NT_RNA_Rep1


title: Sp6PBS2

source_name: spleen

value: spleen


title: GRKO_MR-580C_Ald_RNA_Rep2


title: Parental__Ald_RNA_Rep3


title: Sp6PBS1


title: I36PBS1


title: Parental__Ald_RNA_Rep2


title: Parental__Ald_RNA_Rep1


title: Parental__NT_RNA_Rep1


title: I18PBS1

value: injected with PBS at 18h


title: I18PBS2


title: Parental__NT_RNA_Rep2


title: I6PBS1


title: Parental_MR-1G12_Ct_RNA_Rep2


title: I36Ah2


title: I6PBS2


title: L18PBS2


title: Parental_MR-1G12_Ct_RNA_Rep1


title: L18PBS1


title: Parental_MR-1G12_Ald_RNA_Rep3


title: Parental_MR-1G12_Ald_RNA_Rep1


title: I36PBS2


title: L6PBS2


title: L6PBS1


title: Parental_MR-1G12_NT_RNA_Rep2


title: Parental_MR-1G12_NT_RNA_Rep1


title: L6Ah2

value: infection of A. hydrophila at 6hpi


title: Parental__NT_RNA_Rep3


title: Sp36PBS2


title: L6Ah1


title: Sp36PBS1


title: Sp36Ah1


title: I36Ah1


title: GRKO_MR-2B12_Ct_RNA_Rep3


title: GRKO_MR-2B12_Ct_RNA_Rep2


title: GRKO_MR-2B12_Ct_RNA_Rep1


title: Sp18PBS2


title: Sp36Ah2


title: GRKO_MR-2B12_Ald_RNA_Rep3


title: GRKO_MR-2B12_Ald_RNA_Rep2


title: GRKO_MR-2B12_Ald_RNA_Rep1


title: Sp18Ah1


title: Sp18Ah2


title: GRKO_MR-2B12_NT_RNA_Rep3


title: Sp18PBS1


title: Parental_MR-1G12_NT_RNA_Rep3


title: Sp6Ah2


title: GRKO_MR-2B12_NT_RNA_Rep2


title: GRKO_MR-2B12_NT_RNA_Rep1


title: Sp6Ah1


title: PAN02(POH1-Flag) MYC-CUT&Tag

city: Shanghai

first: Boshi

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

library_source: genomic

data_processing:
The raw FastQ data were qualified by FastQC (0.11.9) and then trimmed by trim_galore (0.6.6) software.
The clean reads were aligned to the mouse reference genome (GRCm38) by BWA software (0.7.17-r1188).
Peak calling was performed by macs2 2.2.7.1.
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Pancreas

extract_protocol:
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification

value: Pancreas

tag: cell line

value: pancreatic cells

value: Stably expressing POH1-Flag


title: Cuniculiplasma divulgatum early stationary phase, after 5 days

city: Bangor

first: Rafael María

last: Bargiela Bargiela

state: Gwynedd

address: Deniol Road

department: Center for Environmental Biotechnology

country: United Kingdom

institute: Bangor University

data_processing:
SeqPrep and Sickle were employed for removing low-quality and adapter contamination from raw sequencing data.
Clean data of each sample were aligned with the reference genome using Bowtie2. Then perform statistics on sequencing saturation and sequencing coverage.
Assembly: CP133772
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: Tab-delimited text file including TPM (transcripts per million) values for each sample

organism: Cuniculiplasma divulgatum

growth_protocol: For cultivation of strain Cuniculiplasma divulgatum S5T (JCM 30642T) the modified medium DSMZ 88 was used, which contained (g l-1): (NH4)2SO4 , 1.3; KH2PO4, 0.28; MgSO4 .7H2O, 0.25; CaCl2.2H2O, 0.07; FeCl3.6H2O, 0.02. Trace element solution SL-10 (DSMZ Medium 320) in proportion 1:1000, betaine 0.06% w/v) and vitamin solution Kao and Michayluk (Sigma-Aldrich, Gillingham, UK) at 1:100 (v/v) were also added. The medium was supplemented with Beef Extract and Tryptone (both Sigma-Aldrich, Gillingham, UK) at a final concentration of 1 g l-1 and with Beef Extract only at final concentration of 3 g l-1 for cultivation of M1 and S5 strains, correspondingly. The pH of the medium was adjusted to 1.0 by 10N H2SO4. The cells of both organisms were grown in triplicates, in 500 ml Erlenmeyer flasks containing 50 ml of media at 40 ºC in a shaking incubator at 100 rpm. The growth was monitored by measurement of optical density at the wavelength 600 nm in a BioPhotometer Plus (Eppendorf, Hamburg, Germany)

extract_protocol:
RNA was extracted using Pure LinkTM RNA Mini kit, and concentrations were measured by Qubit® RNA BR Assay Kit (Invitrogen, ThermoFisher Scientific, Paisley, UK
mRNA library preparation and sequencing (Illumina NovoSeq 6000 using 150 PE) were outsourced to Biomarker Technologies (BMK) GmbH (Münster, Germany) to produce a minimum of 2 Gbp reads per replicate.

treatment_protocol: Cuniculiplasma divulgatum S5 were sampled at mid-exponential (day 3 of cultivation) and early stationary (day 5) growth phases for RNA extraction


title: PAN02(Vector) MYC-CUT&Tag

value: Vector


title: PAN02(POH1-Flag) Flag-CUT&Tag


title: Cuniculiplasma divulgatum mid-log phase, after 3 days


title: pbsip2cKO_DMSO

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” which was set to 1000. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: txt, raw read count

organism: Plasmodium berghei

source_name: schizont

growth_protocol: pbsip2cKO was cultured for 16 h, and mature schizonts formed in the cultures were harvested by density gradient centrifugation using Iodixanol solution (Optiprep). The schizonts were then injected into mice and subjected to cultures again at 6 h post-injection (hpi). Parasites were then harvested for RNA extraction at 26 hpi.

extract_protocol:
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s instructions.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems),

treatment_protocol: In the second cultures, parasites were treated with 10 nM rapamycin or DMSO.

tag: strain

value: ANKA

value: schizont

value: DMSO


title: EXO2

city: yantai

first: he

last: yu

address: gaoxin

institute: he

description: RNA expression in exosomes

data_processing:
Long RNA reads were subjected to low quality read and adapter trimming using Trim Galore version 0.3.2.
Long RNA reads were mapped to the University of California Santa Cruz hg38 human genome assembly using TopHat2 version 2.0.11.
Raw read counts were generated using HTseq version 0.5.3p3 with the hg38_UCSC_alt.gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file of raw (non-normalized) read counts.
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: Tab-delimited text file of raw (non-normalized) read counts.

source_name: Human umbilical mesenchymal stem cell

extract_protocol:
Long total RNA-Seq libraries were constructed using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA).
The conditioned supernatants of MSCs were collected and centrifuged at 300 ×g for 10 min. The supernatant was centrifuged at 10000 ×g for 30 min and filtered through a sterile 0.22-μm pore filter. The filtered solution was ultracentrifuged at 120,000 ×g for 2 h. Lastly, the supernatant was discarded to obtain the exosome precipitate

value: Human umbilical mesenchymal stem cell

value: Humscs

value: primary cell


title: EXO3

description: RNA expression in exosomes


title: EXO1

description: RNA expression in exosomes


title: Whole kidney P2 DM_EXP

city: Pittsburgh

first: Dennis

last: Kostka

state: PA

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Cellranger v 2.2.0 (10X Genomics)
Cell filtering, QC and normalization (DropletUtils, scds, scater, scran)
Genome_build: mm10
Supplementary_files_format_and_content: mtx, csv, txt; genes, barcodes, metadata, counts, log-counts

source_name: maternal diabetes exposed

extract_protocol:
We harvested 1 kidney from C57BL/6J control and DM_Exp mice at P2 and generated single cell suspensions using 0.05% trypsin at 37°C for 10 minutes. Kidneys were mechanically dissociated with pipetting at 5 and 10 min. 3% fetal calf serum (FCS) in PBS was added to halt the trypsin. The cell suspension was filtered using a 40 μm filter and pelleted. The cells were resuspended in 90% FCS in DMSO and frozen.
Single-cell library preparation and sequencing was performed by GENEWIZ Inc. using the 10X Genomics Inc. Chromium 3’ Single Cell v2 library preparation kit
scRNA-seq

value: whole kidney

tag: developmental stage


title: pbsip2cKO_Rapa

value: rapamycin


title: Parental_MR-1G12_Ct_RNA_Rep3

value: 2 hour of 100nM Corticosterone treated cells


title: patient 121

type: genomic

city: fuzhou

first: Jianhui

last: Guo

address: 20 Chazhong Road

institute: First Affiliated Hospital of Fujian Medical University

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.120 BeadChip   (Illumina)

hyb_protocol: see illumina infinium LCG assay protocal on manufacturer's web site

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

source_name: CHB

label_protocol: DNA was purified in triplicate from an aliquot of blood preserved in each anticoagulant using the Gentra Puregene Blood Kit  using the Gentra Puregene Blood Kit. T

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using QIAamp DNA Mini Kit.

treatment_protocol: Patients were treated with Peg-IFNα for at least 48 weeks and subsequently observed until 72 weeks

tag: efficacy of peg-ifnα

value: suboptimal response

value: female

value: Peg-IFNα


title: patient 124

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.123 BeadChip   (Illumina)

value: male


title: patient 123

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.122 BeadChip   (Illumina)


title: patient 120

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.119 BeadChip   (Illumina)


title: CRISPR 5-3 no IFNb_1, CS028891

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NovaSeq output.
RNA-Seq reads were trimmed for adaptor sequence/low quality sequence using Cutadapt 1.18 with parameter options --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35
Trimmed sequence reads were mapped to hg38 genome using STAR 2.7.0f combined with the GENCODE (v30) annotation
Raw tag counts were obtained using featureCounts in subread 2.0.1 with parameter options:-s 2 -t exon -g gene_name
Assembly: hg38
Supplementary files format and content: comma separated text file includes raw counts for each sample

source_name: SMYD3 KO HN-6

extract_protocol:
RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA).
Libraries were constructed according to the llumina TruSeq Stranded mRNA Library Prep kit

value: SMYD3 KO HN-6

value: head and neck squamous cell carcinoma


title: Parental HN-6 no IFNb_3, CS028891


title: patient 118

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.117 BeadChip   (Illumina)


title: CRISPR 5-3 no IFNb_3, CS028891


title: Parental HN-6 no IFNb_2, CS028891


title: patient 119

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.118 BeadChip   (Illumina)


title: CRISPR 5-3 no IFNb_2, CS028891


title: cell, electrical stimulation, rep 2

city: Academic

first: Meijun

last: Jiang

state: Changchun

address: Changchun, 130021, People’s Republic of China

department: Department of Hand and Podiatric Surgery, Orthopedics Center

institute: The First Hospital of Jilin University

description: electrical stimulation

data_processing:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently. GATK (v4.1.1.0) software was used to perform SNP calling. rMATS(4.1.0) software was used to analysis the AS event.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

growth_protocol: HUVECs were maintained in an environment of 37 °C and 5% CO2 and cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin.

extract_protocol:
After corresponding treatments, each sample was added to 1ml of TRIzol. Adherent cells were detached using TRIzol and transferred to EP tubes, labeled with their respective names.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-SeqLibrary Prep Kit following manufacture`s protocols.

treatment_protocol: High-throughput cell electrical stimulator was used to perform electrical stimulation on HUVECs.We applied an electric field intensity of 150 mV/mm for 2 hours per stimulation session, changing the culture medium after each stimulation. Stimulation was conducted twice a day for two consecutive days.

value: cell line

value: HUVECs

value: vascular endothelial cells

value: WT

value: electrical stimulation


title: patient 117

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.116 BeadChip   (Illumina)


title: Parental HN-6 no IFNb_1, CS028891


title: patient 116

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.115 BeadChip   (Illumina)


title: patient 122

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.121 BeadChip   (Illumina)


title: cell, control, rep 3

description: control

value: unexposed


title: cell, electrical stimulation, rep 1

description: electrical stimulation


title: patient 115

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.114 BeadChip   (Illumina)


title: patient 114

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.113 BeadChip   (Illumina)


title: patient 113

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.112 BeadChip   (Illumina)

value: complete response


title: cell, control, rep 2

description: control


title: cell, control, rep 1

description: control


title: patient 111

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.110 BeadChip   (Illumina)


title: patient 112

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.111 BeadChip   (Illumina)


title: Caco-2 ctrl rep 11

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
cell lysate
h12.h12.ctrl.c09
dmso.3.C09

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: count files are provided as .txt files

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

tag: site

value: ctrl


title: Caco-2 ctrl rep 10

description:
cell lysate
h12.h12.ctrl.b09
dmso.3.B09


title: patient 110

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.109 BeadChip   (Illumina)


title: cell, electrical stimulation, rep 3

description: electrical stimulation


title: Caco-2 ctrl rep 9

description:
cell lysate
h12.h12.ctrl.a09
dmso.3.A09


title: patient 109

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.108 BeadChip   (Illumina)


title: patient 107

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.106 BeadChip   (Illumina)


title: JKM139, WT_b, MNase-seq

city: Beijing

first: Youyang

last: Sia

address: Haidian district

institute: Tsinghua University

data_processing:
Pair-end sequencing reads were trimmed by Trimmomatic and were mapped to sacCer3 reference genome using Bowtie2.
Reads in the range of 100-120bp and 147-167bp were selected, and those mapped to repetitive rRNA locus (chrXII: 451275–469084) were excluded.
The average density plots were generated using DANPOS3(profile) with --bin_size set to 1.
Assembly: sacCer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: 30℃, YPD, mid-log phase

extract_protocol:
Cells were harvested and converted to spheroplasts using 0.25 mg ml–1 zymolase100T (MP Biomedicals cat#320932). Spheroplasts were digested with micrococcal nuclease (NEB M0247S). Samples were treated with proteinase K (25 μg ml–1, Tiangen RT403) 30 mins at 65 °C to remove protein. Phenol:chloroform was used to extract the DNA. We incubated the sample with RNase A (100 μg ml–1, Tiangen RT405) to remove RNA.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB #E7645S)


title: JKM139, dFun30_a, MNase-seq


title: Caco-2 ctrl rep 7

description:
cell lysate
h8.h8.ctrl.c08
dmso.2.C08


title: JKM139, WT_a, MNase-seq


title: Caco-2 ctrl rep 8

description:
cell lysate
h8.h8.ctrl.d08
dmso.2.D08


title: patient 105

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.104 BeadChip   (Illumina)


title: JKM139, dFun30_b, MNase-seq


title: brain,Con,no treatment,pfc,408

city: 上海市

first: Shuai

last: Qiu

address: 上海市华东师范大学普陀校区理科大楼B327

institute: ECNU

data_processing:
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT22.
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: brain,prefrontal cortex

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: brain,prefrontal cortex

value: 3 months

value: Con,no treatment


title: patient 106

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.105 BeadChip   (Illumina)

value: suboptimal response


title: brain,Con,no treatment,pfc,401

address: 上海市华东师范大学普陀校区理科大楼B327


title: brain, VPA,75mg/kg,pfc,393

address: 上海市华东师范大学普陀校区理科大楼B327


title: Caco-2 ctrl rep 5

description:
cell lysate
h8.h8.ctrl.a08
dmso.2.A08


title: Caco-2 ctrl rep 4

description:
cell lysate
h3.h3.ctrl.d07
dmso.1.D07


title: patient 104

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.103 BeadChip   (Illumina)


title: Caco-2 ctrl rep 12

description:
cell lysate
h12.h12.ctrl.d09
dmso.3.D09


title: brain, VPA,75mg/kg,pfc,391

address: 上海市华东师范大学普陀校区理科大楼B327


title: Caco-2 ctrl rep 3

description:
cell lysate
h3.h3.ctrl.c07
dmso.1.C07


title: brain, VPA,75mg/kg,pfc,392

address: 上海市华东师范大学普陀校区理科大楼B327


title: THRBKO_ +T3_3

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
Reads were mapped to GRCh38
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38
Supplementary files format and content: Tab separated file having raw read count for each sample in singular file

source_name: BU3-10-CR2 THRBKO

growth_protocol: iPSC-derived hepatocytesl were maintained in serum free base media consisting of complete serum-free differentiation medium (cSFDM) base media supplemented with 0.05ug/ml Activin A, 0.01ug/ml BMP4, 0.01ug/ml FGF2, 0.01ug/ml VEGF, and 10 mM Y-27632. Cells were refed with the same media on day 6. From day 7 to 12 cells were kept in the same serum free base media containing BMP4 50 ng/mL, FGF2 10 ng/mL, VEGF 10 ng/mL, EGF 10 ng/mL, TGFα 20 ng/mL, HGF 100 ng/mL, and dexamethasone 0.1 μM. Then from day 13 to day 18 cells were fed with serum free base media supplemented with FGF2 10 ng/mL, VEGF 10 ng/mL, EGF 10 ng/mL, HGF 100 ng/mL, Oncostatin M 20 ng/mL, Vitamin K 6 μg/mL, dexamethasone 0.1 μM, gSI 1.5 μM, and DMSO 1%. Then from day 19 to day 25 cells were incubated with serum free base media containing HGF 100 ng/mL, Oncostatin M 20 ng/mL, Vitamin K 6 μM, and dexamethasone 0.1 μM in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep kit following manufacturer's protocols.

treatment_protocol:
Hepatocyte differentiation was induced by treatment of undiffrentiated iPSC following liver differentiation protocol published (Kaserman JE, Wilson AA. Protocol for Directed Differentiation of Human Induced Pluripotent Stem Cells (iPSCs) to a Hepatic Lineage. Methods Mol Biol 2017;1639:151-160)
100nM of T3 was added to cells for 24 hours

value: BU3-10-CR2 THRBKO

value: iPSCs-derived hepatocytes

value: THRB knockout

tag: time

value: Day 25


title: patient 103

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.102 BeadChip   (Illumina)

value: female

value: Peg-IFNα


title: THRBKO_ +T3_2


title: brain,Con,no treatment,pfc,402

address: 上海市华东师范大学普陀校区理科大楼B327


title: patient 102

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.101 BeadChip   (Illumina)

value: male


title: Caco-2 ctrl rep 2

description:
cell lysate
h3.h3.ctrl.b07
dmso.1.B07


title: THRBKO_ +T3_1


title: patient 108

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.107 BeadChip   (Illumina)


title: THRBKO_ -T3_3

value: control


title: Caco-2 ctrl rep 6

description:
cell lysate
h8.h8.ctrl.b08
dmso.2.B08


title: Caco-2 ctrl rep 1

description:
cell lysate
h3.h3.ctrl.a07
dmso.1.A07


title: THRBKO_ -T3_2


title: patient 100

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.99 BeadChip   (Illumina)


title: patient 101

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.100 BeadChip   (Illumina)


title: WT_ +T3_3

value: WT


title: Caco-2 site 74 rep 3 conc8

description:
cell lysate
h10.h10.74.h02
74.3.H02


title: WT_ +T3_1


title: patient 98

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.97 BeadChip   (Illumina)


title: WT_ -T3_1


title: WT_ -T3_2


title: patient 99

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.98 BeadChip   (Illumina)


title: WT_ +T3_2


title: Caco-2 site 74 rep 3 conc5

description:
cell lysate
h10.h10.74.e02
74.3.E02


title: Caco-2 site 74 rep 3 conc7

description:
cell lysate
h10.h10.74.g02
74.3.G02


title: WT_ -T3_3


title: patient 97

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.96 BeadChip   (Illumina)


title: Caco-2 site 74 rep 3 conc6

description:
cell lysate
h10.h10.74.f02
74.3.F02


title: NCI-H1373_EPICPool1_KRASG12Ci1

city: Basel

first: Grainne

last: Kerr

address: Fabrikstrasse 1

country: Switzerland

institute: Novartis

description: CRISPR-screen to identify mechanisms of resistance to KRASG12C and SHP2 inhibitor combinations in non-small cell lung cancer

data_processing:
Raw sequencing reads were aligned to the appropriate library using Bowtie, allowing for no mismatches, and counts were generated for each sgRNA in each sample. The drop-out value for each sgRNA was calculated using the Bioconductor R package EdgeR.
To measure the viability effect of the treatment in each sample, a negative binomial model was fitted to obtain the log fold change (logFC) of counts between the treated and DMSO arms of each sample (the parameters used are common dispersion= 0.2 and prior count= 12). This was performed for each pair to obtain a logFC per sgRNA per cell line. counts per sgRNA were normalized in pairs using the Trimmed Mean of M-values (TMM) normalization. Similarly, To measure the viability effect after 14 days of growth the plasmid (representing day 0) and sample raw counts per sgRNA were normalized in pairs using the Trimmed Mean of M-values (TMM) normalization, again a negative binomial model was fitted to obtain the log fold change (logFC) of counts between the sample and plasmid (the parameters used are common dispersion= 0.2 and prior count= 12). As a summarized gene level score, we used the median logFC of all sgRNAs targeting it.
The treated sample and DMSO sample read counts per sgRNA were normalized in pairs using the Trimmed Mean of M-values (TMM) normalization.
To measure the viability effect after 14 days of growth the plasmid (representing day 0) and sample raw counts per sgRNA were normalized in pairs using the Trimmed Mean of M-values (TMM) normalization, again a negative binomial model was fitted to obtain the log fold change (logFC) of counts between the sample and plasmid (the parameters used are common dispersion= 0.2 and prior count= 12).
As a summarized gene level score, we used the median logFC of all sgRNAs targeting it.
Assembly: hg19
Supplementary files format and content: tall and skinny, tab delimited file contains counts for sgRNA under each treatment and sgRNA counts normalized to plasmid library
Supplementary files format and content: tall and skinny, tab delimited file contains counts for gene under each treatment and gene counts normalized to plasmid library

source_name: Lung

growth_protocol: Human cancer cell lines with constitutive CAS9 expression were generated by lentiviral infection and antibiotic selection. CAS9 expression was confirmed by FACS and gene editing efficiency was tested as follows. CAS9-expressing cells were infected at a low (~0.5) multiplicity of infection (MOI) with lentivirus expressing either a control AAVS sgRNA or sgRNA targeting essential genes. HCC44 – CAS9, NCI-H23 – CAS9, NCI-H1792 – CAS9, Calu1 – CAS9 and NCI-H1373 – CAS9 cells were seeded into cell stacks (Corning # CLS3319). Twenty-four hours after plating, the culture medium was replaced with fresh medium containing 5 mg/ml polybrene and lentiviral sgRNA library at an MOI of 0.5. Twenty-four hours after infection, the culture medium was replaced with fresh 100 million (Calu1 – CAS9) cells per cell stack. The next day, cells were treated with DMSO or 0.75 µM KRASG12Ci1 or 10 µM SHP2i1 or 0.75 µM KRASG12Ci1 plus 10 µM SHP2i1, respectively. The NCI-H1373 was treated with DMSO or 0.375 µM KRASG12Ci1 or 10 µM SHP2i1 or 0.375 µM KRASG12Ci1 plus 10 µM SHP2i1. Cell culture medium containing DMSO or 0.75 µM KRASG12Ci1/0.375µM KRASG12Ci1 or 10 µM SHP2i1 or 0.75 µM KRASG12Ci1/0.375 µM KRASG12Ci1 plus 10 µM SHP2i1 was replenished every 3 days. Cells were maintained in culture and split as needed to ensure confluence did not exceed 90 %. At the end of twenty-two days, groups treated with DMSO or single agent reached five population doublings, whereas the cells treated with KRASG12Ci1+SHP2i1 combination had reached two population doublings and 100 million cells from each condition were harvested.  medium containing 2 mg/ml puromycin. Seventy-two hours after puromycin selection, cells were trypsinized and an aliquot of cells was analyzed by FACS to confirm infection and selection efficiency, and the percentage of RFP-positive cells was >90%.  PSMD1 and PSMA3 and then selected with puromycin. Cells were subsequently seeded in 6-well tissue culture plates; cell culture medium was exchanged 3 days later and the experiment was terminated at day 7. Cells were trypsinized, resuspended in cell culture medium and the live cell count was determined by trypan blue exclusion on a ViCELL instrument (Beckman Coulter).

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA Blood Maxi Kit (Qiagen #51194) as directed by manufacturer and quantified using PicoGreen (Invitrogen # P7589).
Illumina sequencing libraries were generated using PCR amplification with primers specific to the genome integrated lentiviral vector back-bone sequence. The resulting Illumina libraries were purified using 1.8x SPRI AMPure XL beads (Beckman Coulter # A63881) following the manufacturer’s instructions and qPCR quantified using primers specific to the Illumina sequences using standard methods. Illumina sequencing libraries were pooled and sequenced with a HiSeq 2500 instrument (Illumina). The number of reads was adjusted to cover each sgRNA with approximately 1000 reads.
CRISPR sequences

treatment_protocol: cells were plated into new cell stacks at 120 million (NCI-H1373 – CAS9), 80 million (NCI-H1792 – CAS9), 75 million (NCI-H23 – CAS9), 35 million (HCC44 – CAS9) and 100 million (Calu1 – CAS9) cells per cell stack. The next day, cells were treated with DMSO or 0.75 µM KRASG12Ci1 or 10 µM SHP2i1 or 0.75 µM KRASG12Ci1 plus 10 µM SHP2i1, respectively. The NCI-H1373 was treated with DMSO or 0.375 µM KRASG12Ci1 or 10 µM SHP2i1 or 0.375 µM KRASG12Ci1 plus 10 µM SHP2i1. Cell culture medium containing DMSO or 0.75 µM KRASG12Ci1/0.375µM KRASG12Ci1 or 10 µM SHP2i1 or 0.75 µM KRASG12Ci1/0.375 µM KRASG12Ci1 plus 10 µM SHP2i1 was replenished every 3 days. Cells were maintained in culture and split as needed to ensure confluence did not exceed 90 %. At the end of twenty-two days, groups treated with DMSO or single agent reached five population doublings, whereas the cells treated with KRASG12Ci1+SHP2i1 combination had reached two population doublings and 100 million cells from each condition were harvested.

value: Lung

value: Lung adenocarcinoma

value: DMSO 0mg Pool1


title: Calu-1_EPICPool2_DMSO

value: DMSO 0mg Pool3


title: Caco-2 site 74 rep 3 conc3

description:
cell lysate
h10.h10.74.c02
74.3.C02


title: Caco-2 site 74 rep 3 conc4

description:
cell lysate
h10.h10.74.d02
74.3.D02


title: NCI-H23_EPICPool3_KRASG12Ci1


title: Calu-1_EPICPool2_SHP2i1


title: Calu-1_EPICPool1_KRASG12Ci1


title: THRBKO_ -T3_1


title: patient 95

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.94 BeadChip   (Illumina)

value: complete response


title: patient 94

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.93 BeadChip   (Illumina)


title: Calu-1_EPICPool1_SHP2i1

value: KRASG12Ci1 750nM Pool1


title: NCI-H23_EPICPool2_SHP2i1

value: KRASG12Ci1 375nM Pool1


title: NCI-H1792_EPICPool2_KRASG12Ci1_SHP2i1


title: Caco-2 site 74 rep 3 conc1

description:
cell lysate
h10.h10.74.a02
74.3.A02


title: Caco-2 site 74 rep 2 conc8

description:
cell lysate
h6.h6.74.h02
74.2.H02


title: HCC-44_EPICPool3_SHP2i1

value: KRASG12Ci1 750mg Pool2


title: Calu-1_EPICPool3_DMSO


title: NCI-H23_EPICPool3_DMSO


title: patient 96

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.95 BeadChip   (Illumina)

value: suboptimal response


title: HCC-44_EPICPool3_KRASG12Ci1_SHP2i1

value: KRASG12Ci1 750mg Pool1


title: patient 92

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.91 BeadChip   (Illumina)


title: Caco-2 site 74 rep 2 conc7

description:
cell lysate
h6.h6.74.g02
74.2.G02


title: Caco-2 site 74 rep 2 conc6

description:
cell lysate
h6.h6.74.f02
74.2.F02


title: patient 91

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.90 BeadChip   (Illumina)


title: Calu-1_EPICPool1_DMSO


title: NCI-H1373_EPICPool3_KRASG12Ci1_SHP2i1

value: KRASG12Ci1 375nM Pool2


title: NCI-H1792_EPICPool2_KRASG12Ci1

value: KRASG12Ci1 750nM Pool2


title: Caco-2 site 74 rep 3 conc2

description:
cell lysate
h10.h10.74.b02
74.3.B02


title: Caco-2 site 74 rep 2 conc5

description:
cell lysate
h6.h6.74.e02
74.2.E02


title: patient 90

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.89 BeadChip   (Illumina)

value: female


title: NCI-H23_EPICPool1_SHP2i1


title: NCI-H1792_EPICPool3_KRASG12Ci1_SHP2i1


title: NCI-H1792_EPICPool1_SHP2i1

value: SHP2i1 10uM Pool3


title: NCI-H1373_EPICPool2_KRASG12Ci1_SHP2i1


title: patient 89

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.88 BeadChip   (Illumina)

value: male

value: Peg-IFNα


title: patient 93

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.92 BeadChip   (Illumina)


title: NCI-H1792_EPICPool2_SHP2i1

value: DMSO 0mg Pool2


title: patient 88

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.87 BeadChip   (Illumina)


title: HCC-44_EPICPool3_KRASG12Ci1

value: Lung


title: patient 87

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.86 BeadChip   (Illumina)


title: patient 86

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.85 BeadChip   (Illumina)


title: Caco-2 site 74 rep 2 conc3

description:
cell lysate
h6.h6.74.c02
74.2.C02


title: HCC-44_EPICPool2_KRASG12Ci1_SHP2i1

value: Lung adenocarcinoma


title: Caco-2 site 74 rep 2 conc1

description:
cell lysate
h6.h6.74.a02
74.2.A02


title: Caco-2 site 74 rep 1 conc8

description:
cell lysate
h1.h1.74.h02
74.1.H02


title: NCI-H1792_EPICPool3_KRASG12Ci1


title: patient 85

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.84 BeadChip   (Illumina)


title: Caco-2 site 74 rep 2 conc2

description:
cell lysate
h6.h6.74.b02
74.2.B02


title: NCI-H1373_EPICPool2_SHP2i1

value: KRASG12Ci1 750nM Pool3


title: Caco-2 site 74 rep 1 conc7

description:
cell lysate
h1.h1.74.g02
74.1.G02


title: patient 83

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.82 BeadChip   (Illumina)


title: NCI-H1373_EPICPool1_DMSO

value: KRASG12Ci1 750mg Pool3


title: NCI-H1373_EPICPool3_KRASG12Ci1

value: DMSO 0mg Pool1


title: Calu-1_EPICPool3_SHP2i1

value: KRASG12Ci1 | SHP2i1 750 | 10nM | uM Pool1


title: HCC-44_EPICPool2_KRASG12Ci1


title: patient 84

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.83 BeadChip   (Illumina)


title: Caco-2 site 74 rep 1 conc5

description:
cell lysate
h1.h1.74.e02
74.1.E02


title: HCC-44_EPICPool1_KRASG12Ci1_SHP2i1


title: patient 81

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.80 BeadChip   (Illumina)


title: NCI-H1373_EPICPool1_SHP2i1

value: KRASG12Ci1 | SHP2i1 750 | 10nM | uM Pool3


title: Caco-2 site 74 rep 2 conc4

description:
cell lysate
h6.h6.74.d02
74.2.D02


title: NCI-H1792_EPICPool2_DMSO

value: KRASG12Ci1 375nM Pool3


title: NCI-H1792_EPICPool1_KRASG12Ci1_SHP2i1

value: KRASG12Ci1 | SHP2i1 750 | 10nM | uM Pool2


title: patient 82

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.81 BeadChip   (Illumina)

value: complete response


title: HCC-44_EPICPool3_DMSO

description: CRISPR-screen to identify mechanisms of resistance to KRASG12C and SHP2 inhibitor combinations in non-small cell lung cancer


title: Caco-2 site 74 rep 1 conc4

description:
cell lysate
h1.h1.74.d02
74.1.D02


title: Caco-2 site 74 rep 1 conc3

description:
cell lysate
h1.h1.74.c02
74.1.C02


title: NCI-H1792_EPICPool3_DMSO


title: NCI-H23_EPICPool3_SHP2i1


title: HCC-44_EPICPool2_DMSO

value: Lung squamous cell carcinoma

value: KRASG12Ci1 | SHP2i1 750 | 10mg | mg Pool1


title: HCC-44_EPICPool1_KRASG12Ci1

value: KRASG12Ci1 | SHP2i1 750 | 10mg | mg Pool2


title: Caco-2 site 74 rep 1 conc1

description:
cell lysate
h1.h1.74.a02
74.1.A02


title: NCI-H23_EPICPool1_KRASG12Ci1_SHP2i1


title: patient 79

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.78 BeadChip   (Illumina)

value: suboptimal response


title: patient 78

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.77 BeadChip   (Illumina)

value: male


title: Calu-1_EPICPool3_KRASG12Ci1_SHP2i1

value: KRASG12Ci1 | SHP2i1 750 | 10mg | mg Pool3


title: Caco-2 site 74 rep 1 conc6

description:
cell lysate
h1.h1.74.f02
74.1.F02


title: patient 76

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.75 BeadChip   (Illumina)

value: Peg-IFNα


title: NCI-H1373_EPICPool2_KRASG12Ci1

value: Lung


title: Caco-2 site 74 rep 1 conc2

description:
cell lysate
h1.h1.74.b02
74.1.B02


title: NCI-H23_EPICPool1_KRASG12Ci1


title: Caco-2 site 49 rep 3 conc8

description:
cell lysate
h13.h13.49.h12
49.3.H12


title: HCC-44_EPICPool2_SHP2i1

value: Lung adenocarcinoma

value: SHP2i1 | KRASG12Ci1 10 | 375uM | nM Pool2


title: Calu-1_EPICPool2_KRASG12Ci1_SHP2i1

value: SHP2i1 | KRASG12Ci1 10 | 375uM | nM Pool3


title: NCI-H1373_EPICPool3_DMSO

value: SHP2i1 10uM Pool1


title: patient 75

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.74 BeadChip   (Illumina)

value: female


title: Caco-2 site 49 rep 3 conc6

description:
cell lysate
h13.h13.49.f12
49.3.F12


title: patient 74

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.73 BeadChip   (Illumina)


title: patient 73

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.72 BeadChip   (Illumina)


title: NCI-H1373_EPICPool1_KRASG12Ci1_SHP2i1


title: NCI-H23_EPICPool1_DMSO


title: Caco-2 site 49 rep 3 conc5

description:
cell lysate
h13.h13.49.e12
49.3.E12


title: patient 80

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.79 BeadChip   (Illumina)


title: HCC-44_EPICPool1_DMSO


title: Caco-2 site 49 rep 3 conc4

description:
cell lysate
h13.h13.49.d12
49.3.D12


title: NCI-H1792_EPICPool3_SHP2i1

value: DMSO 0mg Pool2


title: NCI-H1792_EPICPool1_KRASG12Ci1


title: patient 77

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.76 BeadChip   (Illumina)


title: Caco-2 site 49 rep 3 conc3

description:
cell lysate
h13.h13.49.c12
49.3.C12


title: Calu-1_EPICPool3_KRASG12Ci1

value: SHP2i1 10uM Pool2


title: patient 71

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.70 BeadChip   (Illumina)


title: NCI-H23_EPICPool2_KRASG12Ci1_SHP2i1

value: SHP2i1 | KRASG12Ci1 10 | 375uM | nM Pool1


title: NCI-H1792_EPICPool1_DMSO


title: HCC-44_EPICPool1_SHP2i1


title: patient 70

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.69 BeadChip   (Illumina)

value: complete response


title: Caco-2 site 49 rep 3 conc7

description:
cell lysate
h13.h13.49.g12
49.3.G12


title: Caco-2 site 49 rep 3 conc2

description:
cell lysate
h13.h13.49.b12
49.3.B12


title: Calu-1_EPICPool2_KRASG12Ci1

value: SHP2i1 10uM Pool3


title: Caco-2 site 49 rep 3 conc1

description:
cell lysate
h13.h13.49.a12
49.3.A12


title: NCI-H1373_EPICPool3_SHP2i1

value: Lung squamous cell carcinoma


title: patient 69

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.68 BeadChip   (Illumina)


title: Calu-1_EPICPool1_KRASG12Ci1_SHP2i1


title: NCI-H23_EPICPool3_KRASG12Ci1_SHP2i1


title: patient 68

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.67 BeadChip   (Illumina)


title: NCI-H1373_EPICPool2_DMSO


title: NCI-H23_EPICPool2_KRASG12Ci1


title: Caco-2 site 49 rep 2 conc8

description:
cell lysate
h9.h9.49.h12
49.2.H12


title: patient 67

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.66 BeadChip   (Illumina)


title: Caco-2 site 49 rep 2 conc7

description:
cell lysate
h9.h9.49.g12
49.2.G12


title: NCI-H23_EPICPool2_DMSO


title: Day15-SW620-TET2CD Colony Outside

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Human colorectal cancer cell

growth_protocol: SW480, SW620 and SW620-TET2CD were cultured for 6 days or 15 days without passage.

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

value: colorectal cancer

tag: day


title: patient 72

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.71 BeadChip   (Illumina)

value: suboptimal response


title: Day15-SW620 Colony Outside


title: Caco-2 site 49 rep 2 conc6

description:
cell lysate
h9.h9.49.f12
49.2.F12


title: Day15-SW620-TET2CD Colony Inside


title: Day15-SW620 Colony Inside


title: Day6-SW480


title: patient 64

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.63 BeadChip   (Illumina)

value: male


title: Caco-2 site 49 rep 2 conc5

description:
cell lysate
h9.h9.49.e12
49.2.E12


title: patient 65

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.64 BeadChip   (Illumina)


title: Day6-SW620 2


title: Caco-2 site 49 rep 2 conc4

description:
cell lysate
h9.h9.49.d12
49.2.D12


title: patient 63

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.62 BeadChip   (Illumina)


title: Caudal fin, 6dpa, 10X Multiome snATAC, rep1

city: St. Louis

first: Ting

state: Missouri

address: 4515 McKinley Avenue, Room 5121

department: Genetics

institute: Washington University in St. Louis School of Medicine

description: processed data file atac_fragments.tsv.gz atac_fragments.tsv.gz.tbi

library_source: genomic single cell

data_processing:
Demultiplexed snRNA-seq and snATAC-seq fastq files were inputted into the Cell Ranger ARC pipeline (version 2.0.0) with default setting. The reads were aligned to genome DanRer11, and feature counting was based on Ensembl release 104 (cellranger-arc count).
Assembly: danRer11
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz are used to build a cell-by-feature (gene/peak) expression matrix for each sample.
Supplementary files format and content: The barcodes.tsv.gz files contain barcode information organized by sample.
Supplementary files format and content: The features.tsv.gz files include gene and peak features organized by sample.
Supplementary files format and content: The matrix.mtx.gz files contain raw gene counts and raw ATAC fragment counts for each barcode, organized by sample.
Supplementary files format and content: The fragments.tsv.gz and fragments.tsv.gz.tbi files contain unique ATAC-seq fragments captured by the assay, along with related information about the fragments.

organism: Danio rerio

source_name: Caudal fin

growth_protocol: Tg(sp7:EGFP) strains are maintained under standard husbandry in the Washington University Fish Facility, with system water temperature at 28.5˚C, and a day-night cycle controlled as 14 hr-light/10 hr-dark.

extract_protocol:
For fin amputation, we anesthetized one-year old fish with 0.16g/L MS-222 in system water, and then removed the distal half of their caudal fin with sterilized razor blades. The fish were then sent back to circulating water system for recovery. We collected regenerating fin tissue from fish by doing secondary fin amputation at the primary cutting plane, with the same anesthesia and recovery procedures. For 0 dpa sample, we collected two segments of fin rays from each fish after removing the distal half of their caudal fin. Each time point has two biological replicates. Tissues were collected in 1mL 1 X PBS on ice. Fresh tissues were treated with 1mL 1X TrypLE Express enzyme (Gibco) expression in 30.5 ˚C with rotation for around 30 minutes. Isolation status was checked under microscope every 15 minutes after gentle mixing. Once the cells were well-dissociated, cells were centrifuged at 500 × g for 3 min at 4 °C to remove supernatants. 1 mL of 1X cold PBS buffer was used to wash cells, followed by centrifuging at 500 × gfor 3 min at 4 °C. For 0 dpa sample, supernatants were discarded, and the remaining fin tissue were further dissociated into a single-cell suspension with 750 µl of 0.5 mg/mL Liberase DL (Roche) in enzyme-free Cell Dissociation Buffer (Gibco) at 30.5 °C for 15 min with gentle agitation. Liberase DL contains highly purified Collagenase I and Collagenase II and facilitates cell dissociation from the intact fin tissue. After Liberase dissociation, samples were centrifuged at 500 x g for 3 min at 4 °C and supernatants were discarded, then washed with 1mL pre-cold 1X PBS and supernatants were discarded again. After enzyme dissociation, cells were filtered through 30µm or 40µm strainer followed by centrifugation at 500 × g for 3 min at 4˚C and washed in 500µl sort buffer for one time. Then, cells were resuspended in 300 µl DNase solution with pipetting mix 5 times and incubated on ice for 5 min. After adding 1mL 1X cold PBS with 0.04% BSA, samples were then centrifuged at 500 × g for 3 min at 4 °C. This wash step was repeated for two more times. Then cells were resuspended in 0.1X Lysis buffer with gentle pipetting, then incubated on ice for 3 min. 1 mL Wash buffer were added and tubes were gently inverted 3-4 times. Then, samples were centrifuged 300 × g for 3 min at 4˚C and supernatant were removed. This wash step was repeated 2 more times followed by checking nuclei status under microscope. After last round centrifugation, 10 µl supernatant were left in the tube, then 50µl of 1X Diluted nuclei buffer was added followed by centrifugation at 300xg for 3 min at 4˚C. After removing supernatants, samples were resuspended with 20 µL of 1x diluted nuclei buffer. Trypan blue was used to count nuclei. The final nuclei concentration was 2,000-2,500 nuclei/µL. The chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle from 10x Genomics was used for library preparation. Sequencing was performed using Novaseq 6000 (Illumina).
The chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle from 10x Genomics was used for library preparation. Sequencing was performed using Novaseq 6000 (Illumina).

value: Caudal fin

tag: time post_amputation_(days)


title: Caudal fin, 4dpa, 10X Multiome snATAC, rep2


title: Caco-2 site 49 rep 2 conc3

description:
cell lysate
h9.h9.49.c12
49.2.C12


title: Caudal fin, 2dpa, 10X Multiome snATAC, rep1


title: patient 62

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.61 BeadChip   (Illumina)

value: Peg-IFNα


title: Caudal fin, 2dpa, 10X Multiome snATAC, rep2


title: Caco-2 site 49 rep 2 conc2

description:
cell lysate
h9.h9.49.b12
49.2.B12


title: Caudal fin, 4dpa, 10X Multiome snATAC, rep1


title: Caco-2 site 49 rep 2 conc1

description:
cell lysate
h9.h9.49.a12
49.2.A12


title: patient 61

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.60 BeadChip   (Illumina)


title: Caudal fin, 1dpa, 10X Multiome snATAC, rep2


title: patient 60

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.59 BeadChip   (Illumina)


title: patient 66

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.65 BeadChip   (Illumina)


title: Caco-2 site 49 rep 1 conc7

description:
cell lysate
h4.h4.49.g12
49.1.G12


title: Caco-2 site 49 rep 1 conc8

description:
cell lysate
h4.h4.49.h12
49.1.H12


title: Caudal fin, 1dpa, 10X Multiome snATAC, rep1


title: patient 59

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.58 BeadChip   (Illumina)


title: Caudal fin, 6dpa, 10X Multiome snRNA, rep2

description: processed data file barcodes.tsv.gz features.tsv.gz matrix.mtx.gz

molecule: nuclear RNA


title: Caudal fin, 6dpa, 10X Multiome snATAC, rep2


title: Caudal fin, 6dpa, 10X Multiome snRNA, rep1


title: patient 58

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.57 BeadChip   (Illumina)


title: Caudal fin, 4dpa, 10X Multiome snRNA, rep1


title: Caco-2 site 49 rep 1 conc5

description:
cell lysate
h4.h4.49.e12
49.1.E12


title: Caco-2 site 49 rep 1 conc6

description:
cell lysate
h4.h4.49.f12
49.1.F12


title: Caudal fin, 4dpa, 10X Multiome snRNA, rep2


title: patient 57

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.56 BeadChip   (Illumina)


title: Caudal fin, 2dpa, 10X Multiome snRNA, rep2


title: Caudal fin, 2dpa, 10X Multiome snRNA, rep1


title: Caudal fin, 1dpa, 10X Multiome snRNA, rep1


title: Caco-2 site 49 rep 1 conc3

description:
cell lysate
h4.h4.49.c12
49.1.C12


title: Caudal fin, 1dpa, 10X Multiome snRNA, rep2


title: patient 56

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.55 BeadChip   (Illumina)


title: patient 55

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.54 BeadChip   (Illumina)


title: Caco-2 site 49 rep 1 conc2

description:
cell lysate
h4.h4.49.b12
49.1.B12


title: Caudal fin, 0dpa, 10X Multiome snRNA, rep2


title: Caudal fin, 0dpa,10X Multiome snRNA, rep1


title: CTRL OCT20 r4

city: Barcelona

first: Claudia

middle: Sanz

last: Lanzas

address: Jordi Girona 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

data_processing:
Real Time Analysis (RTA v3.4.4) software was used for basecalling and the quality scoring of the run.
Generation of FASTQ sequence files was carried out with CASAVA software.
RNA-seq reads were aligned to the GRCz11 genome reference using STAR software version 2.7.8a (Dobin et al., 2013) with ENCODE parameters. The total sequencing output was 60 million paired end reads for each sample and 100% mapped properly to the reference genome. Quality control of the mapping was performed with Samtools and Gemtools.
Differential expression analysis between CTRL and SEC treated larvae was performed with the DESeq2 (3.17) R package with the Likelihood ratio test option (Li and Dewey, 2011; Love et al., 2014).
Assembly: GRCz11
Supplementary files format and content: *.txt: Tab-delimited text files include absolute reads values (counts).
Supplementary files format and content: COUNTS_genes_WWTP.xlsx: Excel file includes absolute reads values (counts) for each sample.

source_name: whole embryo

growth_protocol: Zebrafish (Danio rerio) embryos were obtained by natural mating following standard procedures. At 2 hours post fertilization (hpf), eggs were collected, rinsed and fertilized viable eggs were transferred to embryo water (90 µg/ml of Instant Ocean -Aquarium Systems, Sarrebourg, France-, 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water) and kept under standard conditions (28.5 ºC and 12L:12D photoperiod).

extract_protocol:
ZF embryos were taken in an Eppendorf (10 larvae per replicate) and flash frozen on dry ice. Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA). Then, total RNA was assayed for quantity and quality using Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent Technologies).
Library construction and RNA-sequencing (RNA-seq) was performed by the National Center for Genomic Analysis (CNAG, Barcelona, Spain). The RNA-Seq library was prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following manufacturer recommendations using Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies). The final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp following the manufacturer’s protocol for dual indexing.

treatment_protocol: The exposure of the larvae took place from 4dpf to 5dpf and was driven through the water: SEC extracts were dissolved in fish water, to a final concentration of 20x.

value: whole embryo

value: wild type

value: 5 dpf larvae

value: CTRL


title: Caudal fin, 0dpa, 10X Multiome snATAC, rep1


title: Caudal fin, 0dpa, 10X Multiome snATAC, rep2


title: CTRL OCT20 r3


title: CTRL OCT20 r5


title: patient 54

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.53 BeadChip   (Illumina)


title: CTRL OCT20 r2


title: Caco-2 site 48 rep 3 conc8

description:
cell lysate
h10.h10.48.h03
48.3.H03


title: patient 52

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.51 BeadChip   (Illumina)


title: Caco-2 site 48 rep 3 conc7

description:
cell lysate
h10.h10.48.g03
48.3.G03


title: patient 51

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.50 BeadChip   (Illumina)


title: SEC OCT20 r4

value: exposed to "OCT20" SEC extract


title: patient 50

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.49 BeadChip   (Illumina)

value: female


title: Caco-2 site 49 rep 1 conc1

description:
cell lysate
h4.h4.49.a12
49.1.A12


title: patient 53

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.52 BeadChip   (Illumina)


title: SEC OCT20 r5


title: CTRL OCT20 r1


title: patient 49

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.48 BeadChip   (Illumina)


title: Caco-2 site 48 rep 3 conc6

description:
cell lysate
h10.h10.48.f03
48.3.F03


title: Caco-2 site 49 rep 1 conc4

description:
cell lysate
h4.h4.49.d12
49.1.D12


title: SEC OCT20 r3


title: SEC OCT20 r2


title: CTRL JUN20 r1


title: SEC JUN20 r4

value: exposed to "JUN20" SEC extract


title: patient 46

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.45 BeadChip   (Illumina)


title: Caco-2 site 48 rep 3 conc1

description:
cell lysate
h10.h10.48.a03
48.3.A03


title: SEC OCT20 r1


title: patient 48

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.47 BeadChip   (Illumina)


title: CTRL JUN20 r4


title: Caco-2 site 48 rep 3 conc4

description:
cell lysate
h10.h10.48.d03
48.3.D03


title: SEC JUN20 r2


title: CTRL JUN20 r2


title: CTRL JUN20 r3


title: patient 47

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.46 BeadChip   (Illumina)


title: CTRL JUN20 r5


title: SEC JUN20 r1


title: SEC JUN20 r5


title: patient 44

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.43 BeadChip   (Illumina)


title: DOXA12.DA [TIM8813A16]

city: Oxford

first: Kerstin

last: Timm

address: Mansfield Road

department: Pharmacology

institute: University of Oxford

data_processing:
Real time Analysis (RTA):  NovaSeq 6000 151bp platform
Base-calling: bcl2fastq v2.17.1.14
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.4 with default parameters to the Rat genome Rnor_6.0, Ensembl release 104.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 104 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Assembly: Rnor_6.0
Supplementary files format and content: tpm_gene_count_table.txt: Gene expression counts using reads aligning to annotated exon features of 32545 genes normalized to transcripts per million (TPM)

source_name: heart

extract_protocol:
RNA extraction from snap-frozen heart tissue with Qiagen fibrous tissue mini kit
Input material was normalised to equal input of 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions.
Paired-end stranded RNAseq

value: heart

value: Wistar

tag: Sex

value: DOX+AICAR


title: DOX55.S [TIM8813A17]

value: saline


title: Caco-2 site 48 rep 2 conc7

description:
cell lysate
h6.h6.48.g03
48.2.G03


title: patient 43

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.42 BeadChip   (Illumina)


title: Caco-2 site 48 rep 3 conc2

description:
cell lysate
h10.h10.48.b03
48.3.B03


title: Caco-2 site 48 rep 3 conc3

description:
cell lysate
h10.h10.48.c03
48.3.C03


title: patient 45

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.44 BeadChip   (Illumina)


title: DOX53.S [TIM8813A15]


title: Caco-2 site 48 rep 3 conc5

description:
cell lysate
h10.h10.48.e03
48.3.E03


title: SEC JUN20 r3


title: patient 42

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.41 BeadChip   (Illumina)

value: complete response


title: Caco-2 site 48 rep 2 conc6

description:
cell lysate
h6.h6.48.f03
48.2.F03


title: DOX52.S [TIM8813A14]


title: DOXA08.DA [TIM8813A18]


title: patient 41

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.40 BeadChip   (Illumina)


title: DOXA05.DS [TIM8813A13]

value: DOX+saline


title: DOX56.S [TIM8813A12]


title: DOXA03.DS [TIM8813A10]


title: DOXA02.DS [TIM8813A11]


title: DOXA11.DA [TIM8813A9]


title: Caco-2 site 48 rep 2 conc8

description:
cell lysate
h6.h6.48.h03
48.2.H03


title: Caco-2 site 48 rep 2 conc4

description:
cell lysate
h6.h6.48.d03
48.2.D03


title: DOXA10.DA [TIM8813A8]


title: patient 39

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.38 BeadChip   (Illumina)

value: suboptimal response


title: DOXA04.DS [TIM8813A7]

value: male


title: Caco-2 site 48 rep 2 conc2

description:
cell lysate
h6.h6.48.b03
48.2.B03


title: Caco-2 site 48 rep 2 conc3

description:
cell lysate
h6.h6.48.c03
48.2.C03


title: DOX54.S [TIM8813A6]


title: Caco-2 site 48 rep 2 conc1

description:
cell lysate
h6.h6.48.a03
48.2.A03


title: DOXA07.DA [TIM8813A3]


title: patient 37

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.36 BeadChip   (Illumina)


title: DOXA09.DA [TIM8813A4]


title: DOXA01.DS [TIM8813A5]


title: Caco-2 site 48 rep 2 conc5

description:
cell lysate
h6.h6.48.e03
48.2.E03


title: Caco-2 site 48 rep 1 conc8

description:
cell lysate
h1.h1.48.h03
48.1.H03


title: patient 36

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.35 BeadChip   (Illumina)


title: patient 38

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.37 BeadChip   (Illumina)


title: DOX51.S [TIM8813A2]


title: DOXA06.DS [TIM8813A1]


title: XLHZ4

city: shijiazhaung

first: yuxi

last: guo

state: china

address: Hebei Hospital of Traditional Chinese Medicine, 389 Zhongshan East Road, Chang 'an District, Shijiazhuang City, Hebei Province, China

institute: Hebei Province Traditional Chinese Medicine Hospital

data_processing:
Sequence files (fastq) were mapped to the reference genome  using Bowtie. Small RNA was classified by Unitas software.
Gene abundance was expressed as counts of exon model per million mapped reads (CPM)
Differential expression analysis for miRNA was performed using DESeq   software. Differentially expressed miRNAs with |log2(FC)| value >1 and p value <0.05,   considered as significantly modulated, were retained for further analysis. This choice is   motivated by the decision to maximize the sensitivity of this analysis, in order to perform a   massive screening and identify candidate genes to be validated with a wider sample population   with real-time PCR analysis.
Assembly: Rn6 miRBase：Release 21
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Gastric mucosal

growth_protocol: The rats were housed in the SPF-class laboratory animal center of Hebei College of Traditional Chinese Medicine, fed with common chow, and fed and watered ad libitum.

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit（50）217004 (Qiagen, Germany), after   which the RNA concentration and quality were determined by the Qubit®2.0 Fluorometer (Life   Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc.,   USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent   Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were   used for sequencing.
Paired-end libraries were synthesized by using the QIAseq miRNA Library Kit (Qaigen,   Germany) following QIAseq miRNA Library Kit Guide. The products are then purified and enriched   with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0   Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent   Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was   generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina Hiseq   Xten (Illumina, USA)

treatment_protocol: Reference [33] was used to prepare the CAG rat model by the composite moulding method. (1) N-Methyl-N'-Nitro-N-Nitrosoguanidine (MNNG) solution 180μg/ml was drunk freely from the light and changed daily; (2) 2% sodium salicylate 1ml/100g was gavaged when rats were hungry; (3) hunger and satiety disorders: rats were given 2 days of adequate food and 1 day of fasting, alternately.

value: Gastric mucosal

value: XLHZ

value: MNNG 24 weeks＋XLHZ60days


title: patient 35

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.34 BeadChip   (Illumina)

value: Peg-IFNα


title: XLHZ3


title: patient 34

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.33 BeadChip   (Illumina)


title: XLHZ2


title: Caco-2 site 48 rep 1 conc7

description:
cell lysate
h1.h1.48.g03
48.1.G03


title: Caco-2 site 48 rep 1 conc6

description:
cell lysate
h1.h1.48.f03
48.1.F03


title: Caco-2 site 48 rep 1 conc5

description:
cell lysate
h1.h1.48.e03
48.1.E03


title: XLHZ1


title: patient 33

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.32 BeadChip   (Illumina)


title: patient 40

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.39 BeadChip   (Illumina)


title: model4

value: model

value: MNNG 24 weeks


title: model3


title: model2


title: Caco-2 site 48 rep 1 conc4

description:
cell lysate
h1.h1.48.d03
48.1.D03


title: patient 32

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.31 BeadChip   (Illumina)


title: model1


title: patient 31

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.30 BeadChip   (Illumina)


title: normal4

value: normal

value: no treat


title: patient 30

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.29 BeadChip   (Illumina)


title: normal3


title: Caco-2 site 48 rep 1 conc2

description:
cell lysate
h1.h1.48.b03
48.1.B03


title: normal1


title: Caco-2 site 48 rep 1 conc1

description:
cell lysate
h1.h1.48.a03
48.1.A03


title: normal2


title: patient 28

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.27 BeadChip   (Illumina)


title: Caco-2 site 30 rep 3 conc8

description:
cell lysate
h10.h10.30.h01
30.3.H01


title: H3K23me3 ChIP, set-21(red109), rep 2

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
bigwig files were calculated using the "bamCoverage" tool with "--binSize 10 --normalizeUsing RPKM " parameters
Assembly: WS235(ce11)
Supplementary files format and content: bigwig files

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were cultured on NGM plates with OP50 at 20ºC.

extract_protocol:
Briefly, grind of approximately 5000 adult worms was corsslinked and then sonicated to 200-500bp.  Immunoprecipitation was performed using the following antibodies: anti-H3K23me3 (61500, Active Motif), anti-H3K9me3 (ab8898, Abcam).  The pulled-down complexes were reversed crosslinked by proteinase K digestion and then purified by phenol chloroform extraction.
The yielded DNA was used to construct barcoded ChIP-seq libraries using the KAPA Hyper Pre Kit (Roche) according to the manufacturer’s instruction.
standard linker ligation-based DNA library

value: whole animal

value: young adults


title: H3K23me3 ChIP, set-21(red109);set-32(red11), rep 3


title: Caco-2 site 30 rep 3 conc7

description:
cell lysate
h10.h10.30.g01
30.3.G01


title: patient 27

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.26 BeadChip   (Illumina)

value: female


title: H3K23me3 ChIP, set-21(red109), rep 3


title: H3K23me3 ChIP, set-32(red11), rep 3


title: H3K23me3 ChIP, set-21(red109);set-32(red11), rep 4


title: patient 26

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.25 BeadChip   (Illumina)


title: Caco-2 site 30 rep 3 conc6

description:
cell lysate
h10.h10.30.f01
30.3.F01


title: Caco-2 site 30 rep 3 conc5

description:
cell lysate
h10.h10.30.e01
30.3.E01


title: patient 25

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.24 BeadChip   (Illumina)


title: H3K23me3 ChIP, N2, rep 4

value: N2 (WT)


title: H3K23me2 ChIP, set-21(red109);set-32(red11), rep 4


title: H3K23me3 ChIP, N2, rep 3


title: H3K23me2 ChIP, set-21(red109);set-32(red11), rep 3


title: Caco-2 site 30 rep 3 conc4

description:
cell lysate
h10.h10.30.d01
30.3.D01


title: Caco-2 site 48 rep 1 conc3

description:
cell lysate
h1.h1.48.c03
48.1.C03


title: patient 29

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.28 BeadChip   (Illumina)


title: H3K23me2 ChIP, set-21(red109), rep 3


title: Caco-2 site 30 rep 3 conc3

description:
cell lysate
h10.h10.30.c01
30.3.C01


title: H3K23me2 ChIP, set-21(red109), rep 2


title: H3K23me2 ChIP, set-32(red11), rep 3


title: patient 23

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.22 BeadChip   (Illumina)


title: H3K23me2 ChIP, set-32(red11), rep 2


title: H3K23me2 ChIP, N2, rep 4


title: Caco-2 site 30 rep 3 conc2

description:
cell lysate
h10.h10.30.b01
30.3.B01


title: H3K23me3 ChIP, set-32(red11), rep 2


title: patient 22

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.21 BeadChip   (Illumina)


title: H3K23me2 ChIP, N2, rep 3


title: Caco-2 site 30 rep 3 conc1

description:
cell lysate
h10.h10.30.a01
30.3.A01


title: patient 21

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.20 BeadChip   (Illumina)


title: patient 20

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.19 BeadChip   (Illumina)


title: H3K23me1 ChIP, set-21(red109);set-32(red11), rep 4


title: H3K23me1 ChIP, set-21(red109), rep 3


title: H3K23me1 ChIP, set-21(red109);set-32(red11), rep 3


title: H3K23me1 ChIP, set-21(red109), rep 2


title: Caco-2 site 30 rep 2 conc6

description:
cell lysate
h6.h6.30.f01
30.2.F01


title: Caco-2 site 30 rep 2 conc8

description:
cell lysate
h6.h6.30.h01
30.2.H01


title: patient 19

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.18 BeadChip   (Illumina)


title: H3K23me1 ChIP, N2, rep 3


title: Caco-2 site 30 rep 2 conc7

description:
cell lysate
h6.h6.30.g01
30.2.G01


title: Caco-2 site 30 rep 2 conc5

description:
cell lysate
h6.h6.30.e01
30.2.E01


title: H3K23me1 ChIP, N2, rep 4


title: patient 24

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.23 BeadChip   (Illumina)


title: patient 17

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.16 BeadChip   (Illumina)


title: ChIP input, set-21(red109);set-32(red11), rep 3


title: patient 18

description: Genomic DNA extracted from CHB patients was genotyped using Infinium Asian Screening Array-24 v1.17 BeadChip   (Illumina)


title: ChIP input, set-32(red11), rep 3


title: ChIP input, set-21(red109);set-32(red11), rep 4


title: H3K23me1 ChIP, set-32(red11), rep 3


title: H3K23me1 ChIP, set-32(red11), rep 2


title: ChIP input, set-21(red109), rep 3