title: TT150630 DMSO rep2

city: Beijing

first: Yu

last: Sun

state: China

address: No.6,tiantan xili,Dongcheng District

institute: Beijing Tiantan Hospital, Capital Medical University

data_processing:
Basecalls performed using CASAVA version 1.8.
Total RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic. Then, RNA-seq was mapped to the human reference genome (hg38) with HISAT2.
Fragments per kilobase per million reads sequenced (FPKM) were calculated using Cufflinks. Differential testing and log2 fold change calculation were performed using Cuffdiff with two biological replicates.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited text files include FPKM values for each Sample.

source_name: DIPG cell

growth_protocol: DIPG cells were cultured in Matrigel (356243, BD, 1%, 4 –12 h at 37°C) coated plates with serum-free medium containing DMEM (C11995500BT, Invitrogen), B27 (1:50), N2 (1:100), insulin (20ug/ml), bFGF (20ng/ml), EGF (20ng/ml), PDGF-AB (20 ng/ml) (Peprotec).

extract_protocol:
Total RNA was extracted by using Total RNA Purification Kit (GeneMark, Taiwan).
RNA was prepared for sequencing by (Novogen, China) using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: One day after passaging, DIPG cells TT150630 were treated with palbociclib 100nM or 0.1% DMSO. After 48h-treatment, the cells were washed with PBS twice and harvested using RNA lysis buffer (GeneMark, Taiwan).

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: DMSO

tag: dose

tag: treatment time


title: TT150630 palbociclib rep2

status: Public on Jun 20 2019

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

value: Palbociclib


title: skin from fish given sham treatment biological rep4

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

country: USA

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using the TrimGalore! software version 0.5.0. This software was used to trim low-quality ends from reads and for Illumina adapter removal.
Bowtie2 version 2.3.4.2 was used for alignment of reads to the channel catfish transcriptome using the alignment parameters as recommended by the eXpress software.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters, but including the strand information, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package in R-Bioconductor Release 3.5.1.
Genome_build: RefSeq transcripts from the channel catfish genome (assembly IpCoco_1.2)
Supplementary_files_format_and_content: tab-delimited text files of effective read counts, rounded to the nearest whole number

organism: Ictalurus punctatus

source_name: skin explant

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).

value: control

tag: time

tag: tissue

value: skin


title: 53-J14

city: Paris

first: James

last: Di Santo

address: 28 Rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
Bioinformatic  analyses were performed using Sequana RNA-Seq pipeline. Cokelaer et al.  'Sequana' a set of snakemake NGS pipelines. J Open Source Soft 2, 10.21105/joss.00352 (2017)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g ID -O -s 2)
Differential analysis was performed using DESeq2 R package using default parameters
Functional analysis was performed using the Camera method from the limma package using default parameters
Genome_build: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/bigZips
Supplementary_files_format_and_content: table is in cvs format, with rows corresponding to each gene and coloumns corresponding to each sample as described above. The numbers correspond to the read counts per gene per sample

organism: Macaca fascicularis

source_name: PBMC samples collected after immunization

extract_protocol:
total RNA was extracted from PBMCs using the RNeasy extraction kit (Qiagen)
The library was prepared using the NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific)

value: peripheral blood mononuclear cells

tag: day after immunization


title: 31-J4


title: skin from fish given DnaK taken 1 week post treatment biological rep2

value: rDNAK immunized

value: 1 week


title: skin from fish given sham treatment biological rep3


title: TT150630 palbociclib rep1


title: Ola-1

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

data_processing:
Illunima Casava 1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads  containing adapter, reads containing poly-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.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using STAR and paired-end  clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the  method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Tab-delimited xls files include FPKM values for all Samples

molecule: polyA RNA

source_name: A2780 cell lines

extract_protocol:
RNAs were isolated from A2780 cells using the TRIzol (Invitrogen) reagent by following the company manual. RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0  Flurometer (Life Technologies, CA, USA).  RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: A2780 cells were treated with DMSO, Olaparib, Palbociclib, and their combination (Ola/PD) for 24 hours.

value: ovarian carcinoma

tag: morphology

value: Epithelial

value: Olaparib - treated


title: hypoxia 24h, biological rep1

type: RNA

city: Chongqing

first: Xin

last: Zhou

state: Chongqing

address: Xinqiao Road, Sha Ping Ba District

department: Department of Plastic and Cosmetic Surgery, Xinqiao Hospital

institute: Army Medical University

description: Gene expression data from hacat cells from hypoxia treament for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom D Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: epidermal cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After the HaCaT cells were inoculated into the culture dish, the normoxic group was placed in a conventional incubator, and the hypoxic group was placed in a hypoxic incubator.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment was performed in the normoxic group, and the hypoxic group was treated in a hypoxic incubator for 0.5, 1, 3, and 24 hours, respectively.

value: HaCaT

value: hypoxia treament for 24h


title: Ola-2


title: 41-J14


title: skin from fish given sham treatment biological rep2


title: hypoxia 3h, biological rep2

description: Gene expression data from hacat cells from hypoxia treament for 3h

value: hypoxia treament for 3h


title: TT150630 DMSO rep1


title: 31-J14


title: skin from fish given sham treatment biological rep1


title: hypoxia 24h, biological rep2


title: 09-J0


title: Validation_Exp5

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: genomic

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts implemented in the bap-barcode modeule.
Paired-end reads were aligned to hg19 reference genome using BWA
A custom python script was used to extract random oligonucleotide tags from the sequencing libraries.
Duplicate reads and all downstream processing, including inference of a bead merging statistic was performed using the bead-based scATAC-seq processing (bap) tool. Two versions of the summary statistics are presented for bap 1 (v0.5.0) and bap2 (v0.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: Summary statistics regarding bead merging computed by bap or bap2 and corresponding shared oligo tag abundances per barcode pair

molecule: genomic DNA

source_name: peripheral blood mononuclear cells

growth_protocol: Cryopreserved human peripheral blood mononuclear cells were purchased from Allcells. Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (IMDM medium supplemented with 10% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I (Thermo Fisher Scientific) in 10 mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once and then twice with ice cold 1x PBS + 0.1% BSA. Cells were then filtered with a 35 μm cell strainer (Corning) and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter (Bio-Rad). Cell viability was greater than 80% for all samples.

extract_protocol:
Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1X PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (parts of the SureCell ATAC-Seq Library Prep Kit - 17004620, Bio-Rad). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator (12004336, Bio-Rad). Single-cell ATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing was performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module (1851197, Bio-Rad): 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads (A63880, Beckman Coulter). Barcoded ATAC amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were loaded at 1.5 pM on a NextSeq 550 (SY-415-1002, Illumina) using the NextSeq High Output Kit (150 cycles; 20024907, Illumina) and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit). A library of high-diversity oligonucleotides were spiked into the droplet mixture before cell loading to provide an orthogonal validation for bead loading.
SureCell scATAC-seq

tag: bead concentration


title: hypoxia 1h, biological rep3

description: Gene expression data from hacat cells from hypoxia treament for 1h

value: hypoxia treament for 1h


title: hypoxia 3h, biological rep1


title: Validation_Exp4


title: hypoxia 1h, biological rep2


title: hypoxia 1h, biological rep1


title: 41-J0


title: hypoxia 3h, biological rep3


title: Validation_Exp3


title: Validation_Exp2


title: 31-J0


title: 53-J0


title: WT_FP_rep2

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
Low quality reads was filtered using internal software SOAPnuke
Clean reads were mapped to reference using Bowtie2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Mus musculus

source_name: Mouse kidney

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from whole kidney were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

value: kidney

tag: strain


title: Validation_Exp1


title: hypoxia 0.5h, biological rep3

description: Gene expression data from hacat cells from hypoxia treament for 0.5h

value: hypoxia treament for 0.5h


title: C. albicans WT_ exponential phase_rep2.

city: Hsinchu

first: Hsueh-Fen

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

country: Taiwan

institute: National Tsing Hua University

description: gene expression of exponential phase cells in SC medium

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Custom Microarray 8x15K (ID:071303) (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Candida albicans

source_name: C. albicans WT_ exponential phase_replicate 2

label_protocol: 0.2 μg of total RNA was amplified by a Agilent Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Cells were grown overnight in YPD medium at 30°C, subcultured into fresh SC medium and incubated until log phase (OD600 = 1).

extract_protocol: RNA was prepared using the Trizol reagent following the manufacturer's recommendations.

tag: culture medium

value: SC medium


title: C. albicans WT_ exponential phase_rep1.

source_name: C. albicans WT_ exponential phase_replicate 1


title: C. albicans sfp1∆_ exponential phase_rep1.

source_name: C. albicans sfp1∆_ exponential phase_replicate 1


title: hypoxia 0.5h, biological rep2


title: C. albicans sfp1∆_ exponential phase_rep2.

source_name: C. albicans sfp1∆_ exponential phase_replicate 2


title: Ileum_WheatGlutenMeal_susscrofa_7

status: Public on Jun 19 2019

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

hyb_protocol: The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays were scanned using the DNA microarray scanner with Surescan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for one colour gene expression.

data_processing: The data were analysed by using R by executing different packages, including LIMMA and arrayQualityMetrics. The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA [1] from Bioconductor [2]. Quantile normalisation of the data was performed between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes was removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1 and 3) the gene/probe must be expressed in each of the samples in an experimental condition (e.g. in ileum d 14 control).

organism: Sus scrofa

source_name: Ileum, WheatGlutenMeal

label_protocol: Labelling of RNA was performed as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA and 600 ng of labelled cRNA was used on the eight pack array.  Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies).

growth_protocol: A total of 40 growing pigs (boars) (Topigs 20 × Tempo from Van Beek, Lelystad, the Netherlands) aged 10 weeks with an average initial body weight of 34.9 ± 3.4 kg on the day (d) of arrival (d 0) were used. Pigs were blocked on litter and pigs within a block were randomly allocated to one of the five experimental diets, with eight pigs per experimental diet. Pigs were housed individually in metabolic cages (1.3 x 1.3 m or  2.0 x 1.0 m) with a tender foot floor.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer's protocol. RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: During d 1 to 6, pigs were fed a commercial diet and gradually adapted to the experimental diets. From d 7 and onwards, pigs were fed only the experimental diets. The experimental diets were provided in a mash form and mixed with water at a ratio of 1 : 2. Water supply was restricted and only 0.3 l of extra water was provided per animal after each feeding. The feeding level was 2.5 times the maintenance requirement for energy (293 kJ NE/kg  BW0.75). During d 7 to 26, the daily feed allowance was divided into two equal amounts, fed at 8.00 h and 16.00 h. During d 27 to dissection days i.e. (d 28-29), the feed allowance was divided into six equal portions, fed starting at 5.30 h at intervals of 3 hours. Pigs were anesthetised by injecting pentobarbitone in the ear vein and sacrificed to collect samples. The small intestine was separated from the stomach and the large intestine. Each of jejunum and ileum were divided into three equal segments; proximal, middle, and distal. From the middle segment in each tissue, two sub-segment were sampled for collection of the intestinal mucosa. For collection of the intestinal mucosa, one of the sub-segment was cut open longitudinally along the lumen, washed with sterile normal saline solution. With sterile glass slide mucosal layer was collected, snap frozen in liquid nitrogen and stored at -80ºC for further analysis of genome-wide gene expression profiling.

value: Ileum

value: WheatGlutenMeal

tag: age

value: 10 weeks

tag: Sex

value: male


title: normoxia 0h, biological rep3

description: Gene expression data from hacat cells from normoxia condition

value: normoxia


title: hypoxia 0.5h, biological rep1


title: normoxia 0h, biological rep2


title: Ileum_WheatGlutenMeal_susscrofa_5


title: Ileum_WheatGlutenMeal_susscrofa_46


title: Ileum_WheatGlutenMeal_susscrofa_16


title: Ileum_WheatGlutenMeal_susscrofa_26


title: normoxia 0h, biological rep1


title: Ileum_WheatGlutenMeal_susscrofa_23


title: Ileum_SoyBeanMeal_susscrofa_29

source_name: Ileum, SoyBeanMeal

value: SoyBeanMeal


title: Ileum_RapeSeedMeal_susscrofa_24

source_name: Ileum, RapeSeedMeal

value: RapeSeedMeal


title: Ileum_SoyBeanMeal_susscrofa_39


title: Ileum_WheatGlutenMeal_susscrofa_37


title: Ileum_SoyBeanMeal_susscrofa_42


title: Ileum_SoyBeanMeal_susscrofa_15


title: Ileum_SoyBeanMeal_susscrofa_19


title: Ileum_RapeSeedMeal_susscrofa_18


title: Ileum_RapeSeedMeal_susscrofa_34


title: Ileum_SoyBeanMeal_susscrofa_8


title: Ileum_RapeSeedMeal_susscrofa_41


title: Ileum_SoyBeanMeal_susscrofa_21


title: Ileum_SprayDriedPlasmaProtein_susscrofa_36

source_name: Ileum, SprayDriedPlasmaProtein

value: SprayDriedPlasmaProtein


title: Ileum_WheatGlutenMeal_susscrofa_14


title: Ileum_RapeSeedMeal_susscrofa_10


title: Ileum_SoyBeanMeal_susscrofa_2


title: Ileum_RapeSeedMeal_susscrofa_12


title: Ileum_RapeSeedMeal_susscrofa_32


title: Ileum_SprayDriedPlasmaProtein_susscrofa_6


title: Ileum_SprayDriedPlasmaProtein_susscrofa_17


title: Ileum_SprayDriedPlasmaProtein_susscrofa_31


title: Ileum_SprayDriedPlasmaProtein_susscrofa_25


title: Ileum_RapeSeedMeal_susscrofa_1


title: Ileum_SprayDriedPlasmaProtein_susscrofa_4


title: Ileum_BlackSoldierFly_susscrofa_9

source_name: Ileum, BlackSoldierFly

value: BlackSoldierFly


title: Ileum_BlackSoldierFly_susscrofa_3


title: Ileum_BlackSoldierFly_susscrofa_28


title: Ileum_BlackSoldierFly_susscrofa_22


title: Ileum_BlackSoldierFly_susscrofa_11


title: Ileum_BlackSoldierFly_susscrofa_44


title: Jejunum_WheatGlutenMeal_susscrofa_7

source_name: Jejunum, WheatGlutenMeal

value: Jejunum


title: Ileum_SprayDriedPlasmaProtein_susscrofa_43


title: Jejunum_WheatGlutenMeal_susscrofa_5


title: Jejunum_WheatGlutenMeal_susscrofa_26


title: Jejunum_WheatGlutenMeal_susscrofa_14


title: Jejunum_WheatGlutenMeal_susscrofa_16


title: Ileum_BlackSoldierFly_susscrofa_20


title: Jejunum_WheatGlutenMeal_susscrofa_23


title: Jejunum_SoyBeanMeal_susscrofa_42

source_name: Jejunum, SoyBeanMeal


title: Jejunum_SoyBeanMeal_susscrofa_19


title: Jejunum_SoyBeanMeal_susscrofa_29


title: Jejunum_SoyBeanMeal_susscrofa_21


title: Jejunum_SoyBeanMeal_susscrofa_15


title: Jejunum_SoyBeanMeal_susscrofa_2


title: Jejunum_RapeSeedMeal_susscrofa_24

source_name: Jejunum, RapeSeedMeal


title: Jejunum_RapeSeedMeal_susscrofa_32


title: Jejunum_WheatGlutenMeal_susscrofa_37


title: Jejunum_RapeSeedMeal_susscrofa_34


title: Jejunum_WheatGlutenMeal_susscrofa_46


title: Jejunum_SoyBeanMeal_susscrofa_39


title: Jejunum_RapeSeedMeal_susscrofa_18


title: Ileum_BlackSoldierFly_susscrofa_33


title: Jejunum_SprayDriedPlasmaProtein_susscrofa_6

source_name: Jejunum, SprayDriedPlasmaProtein


title: XM001-PP1_Rep2_Lane7

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

data_processing:
RNA-seq data was quantified from FASTQ files using salmon (0.11.3) quant with options --validateMappings --rangeFactorizationBins 4 --numBootstraps 100 --seqBias --gcBias.
Supplementary_files_format_and_content: SF file containg quantifications

source_name: Control iPS derived pancreatic precursor cells

growth_protocol: hiPSCs were cultured on 1:100 diluted Matrigel (BD Biosciences, CA, Cat #354277) in mTeSR™1 medium (STEMCELL technologies, Catalog # 85850). At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen, Cat#14190) followed by incubation with TrypLE Select Enzyme (1x) (Life Technologies, Cat#12563011) for 3–5 min at 37 °C. Single cells were rinsed with mTeSR™1 medium, and spun at 1,000 rpm for 3 min. The resulting cell pellet was resuspended in mTeSR™1 medium supplemented with Y-27632 (10 μM; Sigma-Aldrich; MO, Cat#Y0503), and the single cell suspension was seeded at ~0.75 × 105 cells/cm2 on Matrigel-coated surfaces. Cultures were fed every day with mTeSR™1 medium and differentiation was initiated 72 h following seeding with ~90% starting confluency. All the cell lines were confirmed mycoplasma-free by using the Lonza MycoAlert Mycoplasma Detection Kit (Lonza, Cat# LT07-418).

extract_protocol:
Total RNA from PDX1+/-, PDX1P33T/P33T, PDX1C18R/C18R and XM001 lines was extracted using miRNeasy Mini kit (Qiagen, #217004) and RNA integrity was checked using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Pico Kit).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina).
Stranded RNA-Seq

treatment_protocol: S1: definitive endoderm (3 d)   Cells were first rinsed with 1× DPBS without Mg2+ and Ca2+ and then exposed to MCDB 131 medium (Life Technologies, Cat# 10372-019) further supplemented with 1.5 g/l sodium bicarbonate (Sigma, MO, Cat# S6297), 1× Glutamax (Life Technologies, Cat# 35050-079), 10 mM final glucose (Sigma, Cat# G8769) concentration, 0.5% bovine serum albumin fraction V, fatty acid free (Sigma, Cat# 10775835001), 100 ng/ml Activin-A (R&D Systems Inc, Cat# 338-AC-050/CF), and 3 μM or 5 μM of CHIR-99021 (GSK3β inhibitor, SelleckChem, Cat# S2924) for day 1. For day 2, cells were cultured in MCDB with 0.5% BSA, 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM glucose, 100 ng/ml Activin-A and 0.3 μM CHIR-99021. On day 3, cells were cultured in MCDB 131 with 0.5% BSA, 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM glucose and 100 ng/ml Activin-A.   S2: primitive gut tube (2 d)  Cells were rinsed with 1× DPBS without Mg2+ and Ca2+ and then exposed to MCDB 131 medium further supplemented with 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM final glucose concentration, 0.5% BSA, 0.25 mM ascorbic acid (Sigma, Cat# A4544), 50 ng/ml FGF7 (R & D Systems, Cat# 251-KG-010/CF) or/and 1.25 μM IWP-2 (Tocris Bioscience, Cat# 3533) for 2 d.  S3: posterior foregut (2 d)  Cells were then added for 2 d in MCDB 131 medium supplemented with 2.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM glucose concentration, 2% BSA, 0.25 mM ascorbic acid, 50 ng/ml FGF7, 0.25 μM SANT-1 (Sigma, Cat# S4572), 1 μM retinoic acid (RA; Sigma, Cat#R2625), 100 nM LDN193189 (LDN; BMP receptor inhibitor, Stemgent, CA, Cat#04-0019), 1:200 ITS-X (Life Technologies, Cat#51500056), and 200 nM TPB (PKC activator, custom synthesis, ChemPartner).

tag: genotype

value: WT

tag: lane

tag: replicate

value: Replicate 2


title: XM001-PP1_Rep3_Lane5

value: Replicate 3


title: Jejunum_RapeSeedMeal_susscrofa_10


title: XM001-PP1_Rep3_Lane7


title: XM001-PP1_Rep2_Lane6


title: XM001-PP1_Rep2_Lane5


title: Jejunum_SprayDriedPlasmaProtein_susscrofa_36


title: XM001-PP1_Rep1_Lane6

value: Replicate 1


title: Jejunum_SprayDriedPlasmaProtein_susscrofa_43


title: XM001-PP1_Rep1_Lane7


title: XM001-PP1_Rep3_Lane6


title: Jejunum_RapeSeedMeal_susscrofa_12


title: Jejunum_BlackSoldierFly_susscrofa_22

source_name: Jejunum, BlackSoldierFly


title: Jejunum_BlackSoldierFly_susscrofa_33


title: Jejunum_SprayDriedPlasmaProtein_susscrofa_25


title: Jejunum_BlackSoldierFly_susscrofa_3


title: Jejunum_RapeSeedMeal_susscrofa_41


title: XM001-iPSC_Rep4_Lane7

source_name: Control iPS cells

value: Replicate 4


title: Jejunum_BlackSoldierFly_susscrofa_11


title: XM001-iPSC_Rep4_Lane6


title: Jejunum_BlackSoldierFly_susscrofa_44


title: Jejunum_RapeSeedMeal_susscrofa_1


title: XM001-PP1_Rep1_Lane5


title: Jejunum_BlackSoldierFly_susscrofa_28


title: Jejunum_BlackSoldierFly_susscrofa_9


title: XM001-iPSC_Rep4_Lane5


title: XM001-iPSC_Rep3_Lane7


title: XM001-iPSC_Rep3_Lane6


title: XM001-iPSC_Rep1_Lane6


title: XM001-iPSC_Rep2_Lane7


title: XM001-iPSC_Rep1_Lane5


title: PDX1-P33T-Hom-PP1_Rep4_Lane7

source_name: PDX1P33T/P33T iPS derived pancreatic precursor cells


title: XM001-iPSC_Rep1_Lane7


title: XM001-iPSC_Rep2_Lane6


title: XM001-iPSC_Rep3_Lane5


title: XM001-iPSC_Rep2_Lane5


title: PDX1-P33T-Hom-PP1_Rep4_Lane5


title: PDX1-P33T-Hom-PP1_Rep3_Lane7


title: PDX1-P33T-Hom-PP1_Rep3_Lane5


title: Jejunum_SprayDriedPlasmaProtein_susscrofa_31


title: PDX1-P33T-Hom-PP1_Rep3_Lane6


title: PDX1-P33T-Hom-PP1_Rep2_Lane6


title: PDX1-P33T-Hom-PP1_Rep2_Lane7


title: PDX1-P33T-Hom-PP1_Rep1_Lane6


title: PDX1-P33T-Hom-PP1_Rep1_Lane5


title: Jejunum_SoyBeanMeal_susscrofa_8


title: PDX1-KO-Het-PP1_Rep4_Lane7

source_name: PDX1-/+ iPS derived pancreatic precursor cells


title: Jejunum_BlackSoldierFly_susscrofa_20


title: PDX1-KO-Het-PP1_Rep4_Lane6


title: PDX1-KO-Het-PP1_Rep4_Lane5


title: PDX1-KO-Het-PP1_Rep3_Lane7


title: PDX1-KO-Het-PP1_Rep3_Lane6


title: PDX1-P33T-Hom-PP1_Rep4_Lane6


title: PDX1-P33T-Hom-PP1_Rep2_Lane5


title: PDX1-P33T-Hom-PP1_Rep1_Lane7


title: PDX1-KO-Het-PP1_Rep3_Lane5


title: PDX1-KO-Het-PP1_Rep2_Lane6


title: PDX1-KO-Het-PP1_Rep2_Lane5


title: PDX1-KO-Het-PP1_Rep1_Lane5


title: PDX1-KO-Het-PP1_Rep1_Lane6


title: PDX1-C18R-Hom-PP1_Rep4_Lane6

source_name: PDX1C18R/C18R iPS derived pancreatic precursor cells


title: PDX1-C18R-Hom-PP1_Rep4_Lane5


title: PDX1-C18R-Hom-PP1_Rep4_Lane7


title: PDX1-KO-Het-PP1_Rep1_Lane7


title: PDX1-C18R-Hom-PP1_Rep3_Lane7


title: PDX1-C18R-Hom-PP1_Rep3_Lane6


title: PDX1-C18R-Hom-PP1_Rep2_Lane5


title: PDX1-C18R-Hom-PP1_Rep2_Lane7


title: PDX1-C18R-Hom-PP1_Rep2_Lane6


title: PDX1-C18R-Hom-PP1_Rep1_Lane6


title: PDX1-C18R-Hom-PP1_Rep1_Lane5


title: HFQ_RNA

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: Total RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first discarded if containing more than 2-N bases, then reads were processed by clipping adaptor and removing low quality bases, too short reads (less than 13nt) were also dropped. FASTX-Toolkit (Version 0.0.13) was used to get the clean reads.
clean reads were aligned to the reference genome by bowtie2 v2.1.0 with 2 mismatches. Aligned reads with more than one genome location were discarded due to their ambiguous location. Uniquely localized reads were used to do the following analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using in house perl scripts. Other statistical results, such as gene coverage and depth, reads distribution around start codon and stop codon, were also obtained.
For CLIP-Seq aligment, peak calling was performed by 4-fold threshold between HFQ_Flag CLIP-Seq and HFQ_Flag RNA-Seq to define the Hfq-bound or -unbound RNA peaks.
Genome_build: Yersinia pestis biovar Microtus 91001
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Yersinia pestis

source_name: Yersinia pestis hfq mutant

growth_protocol: Bacteria were grown in brain heart infusion (BHI) broth (Difco) supplemented with appropriate antibiotics overnight at 26 °C with shaking at 200 rpm until exponential growth phase (OD620 = 0.8).

extract_protocol:
For RNA-seq, total RNAs were extracted from Y. pestis Hfq-Flag and WT-Flag strains mentioned above by using Trizol Reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacterial growth was stopped by centrifugation for 6 min at 5,000 rpm at 4°C. The pellets were frozen into liquid nitrogen and stored at -80°C until cells were lysed.

value: Yersinia pestis hfq mutant

tag: growth condition

value: grown to exponential phase in BHI

tag: growth temperature

value: 26 °C


title: Jejunum_SprayDriedPlasmaProtein_susscrofa_4


title: WT_Flag_RNA

description: Total RNA

source_name: Yersinia pestis wild-type strain 201 carrying pACYC184-Flag


title: HFQ_Flag_CLIP

description: RNA moiety by crosslinked immunoprecipitation by Hfq using Flag antibody

source_name: Yersinia pestis hfq mutant carrying pACYC184-Hfq-Flag

extract_protocol:
For CLIP-seq, the cultures grown under the same conditions were collected and resuspended in 10 mM Tris-HCl (pH8.0), respectively. The pellets were dispersed on a petri dish and irritated uncovered with 400 mJ/cm2 of UV 254 nm to form the crosslinked RNA-protein complex. Bacterial cells were collected and lysed in RIP Lysis buffer and subjected to co-immunoprecipitation (Co-IP).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WT_Flag_CLIP

value: Yersinia pestis wild-type strain 201 carrying pACYC184-Flag


title: PDX1-KO-Het-PP1_Rep2_Lane7


title: Root_Salt__rep2

city: Nanjing

first: Zheng

middle: dong

last: yang

address: weigang NO.1

department: college of agronomy

institute: NJAU

data_processing:
reads  with low-quality sequence were removed , then mapped to   rice genome (TIGR release 7)  whole genome using  Tophat v2.0.13 with parameters -G   -p 10  -o ./
Cufflinks (v2.2.1)  with parameters   -p 10 -G -o   were used to assembles transcripts, estimates their abundances(FPKM), and tests for differential expression and regulation in RNA-Seq samples
Cuffdiff, a part of the Cufflinks package,with default parameters takes the aligned reads from two conditions and reports genes and transcripts that are differentially expressed using a rigorous statistical analysis
Genome_build: rice7（TIGR release 7）
Supplementary_files_format_and_content: tab-delimited text files include gene expression file
Supplementary_files_format_and_content: abundance measurements output from cufflinks

organism: Oryza sativa

source_name: shoot

growth_protocol: Germinated rice cultivar "Nipponbare" seeds were transferred into 96-well PCR plates with cut bottom. The plants grew in the liquid culture medium in the green house for two weeks.

extract_protocol:
total RNAs were extracted from the leaf and root tissues with 24 h post-salt treatment and the corresponding CK using RNeasy plant Mini kit (Qiagen, Cat#: 74904). Each tissue was biologically replicated for preparation of RNA-seq libraries and subsequent sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two-week-hydro-cultured seedlings were split into two halves, one part continued to grow in the normal condition (CK),one part are used to 150mmol NaCL treatment ,after 24h material were collected

value: shoot

value: two weeks

tag: cultivar

value: Nipponbare

value: salt


title: Root_CK_rep1

value: control


title: Root_CK_rep2


title: Leaf_CK_rep2

source_name: seedling

value: seedling


title: Leaf_Salt_rep1


title: PDX1-C18R-Hom-PP1_Rep3_Lane5


title: Leaf_CK_rep1


title: Leaf_Salt_rep2


title: Root_Salt__rep1


title: PDX1-C18R-Hom-PP1_Rep1_Lane7


title: HFQ_Flag_RNA

description: Total RNA

value: Yersinia pestis hfq mutant carrying pACYC184-Hfq-Flag


title: 18606C

city: Bar Harbor

first: Kate

last: Foley

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description:
processed data file:
GeneCount_C.txt

data_processing:
RNA quality was measured via the Bioanalyzer 2100 (Agilent Technologies) and poly(A) RNA-seq sequencing libraries were compiled by TruSeq RNA Sample preparation kit v2 (Illumina).
Quantification was performed using qPCR (Kapa Biosystems).
RNA-seq was performed on the HiSeq 4,000 platform (Illumina) for 2x100bp reads for a total of 45 million reads according to the manufacturer’s instructions.
Quality control for each sample was completed using NGSQCToolkit v2.3 which removed adaptors and trimmed low quality bases (Phred<30)
To quantify gene expression of the trimmed reads, we used RSEM v1.2.12 which uses Bowtie2 v2.2.0 for alignment of these reads
Differential gene expression (DGE) analysis was completed on the hippocampus and cortex separately, using EdgeR 3.20.9
Normalization of trimmed mean of M values (TMM) was performed and quasi-likelihood F-test was used to attain DGE
Genome_build: mm10
Supplementary_files_format_and_content: GeneCount_H.txt: all gene counts for hippocampal samples
Supplementary_files_format_and_content: GeneCount_C.txt: all gene counts for cortical samples
Supplementary_files_format_and_content: OneYearRun2017_H_hilow_RunHi_vs_Sed.txt: FDR and P values for all hippocampal high running vs high running samples
Supplementary_files_format_and_content: OneYearRun2017_H_hilow_RunLow_vs_Sed.txt: FDR and P values for all hippocampal sedentary vs low running samples
Supplementary_files_format_and_content: OneYearRun2017_C_hilow_RunHi_vs_Sed.txt: FDR and P values for all cortical sedentary vs high running samples
Supplementary_files_format_and_content: OneYearRun2017_C_hilow_RunLow_vs_Sed.txt: FDR and P values for all hippocampal sedentary vs low running samples
Supplementary_files_format_and_content: Early_Diet_hippo_8wkrun_wo18606_CD.8weeks.Run.H_vs_CD.8weeks.Sed.H.txt: FDR and P values for all young running vs sedentary samples
Supplementary_files_format_and_content: Early_Diet_cortex_8wkrun_CD.8weeks.Run.C_vs_CD.8weeks.Sed.C.txt: FDR and P values for all cortical running vs sedentary samples

source_name: Cortex

extract_protocol:
MagMAX mirVana Total RNA
HiSeq4000, 2x100, 45 million reads

tag: brain region

value: Cortex

value: Young

tag: activity

value: Sed


title: 18605H

description:
processed data file:
GeneCount_H.txt

source_name: Hippocampus

value: Hippocampus


title: 18528C

description:
processed data file:
GeneCount_C.txt

value: Run


title: 18626H

description:
processed data file:
GeneCount_H.txt


title: 18627H

description:
processed data file:
GeneCount_H.txt


title: 18289H

description:
processed data file:
GeneCount_H.txt


title: 18681C

description:
processed data file:
GeneCount_C.txt


title: 18606H

description:
processed data file:
GeneCount_H.txt


title: 18626C

description:
processed data file:
GeneCount_C.txt


title: 18627C

description:
processed data file:
GeneCount_C.txt


title: 18527H

description:
processed data file:
GeneCount_H.txt


title: 18605C

description:
processed data file:
GeneCount_C.txt


title: 18526H

description:
processed data file:
GeneCount_H.txt


title: 18527C

description:
processed data file:
GeneCount_C.txt


title: 18290H

description:
processed data file:
GeneCount_H.txt


title: 18681H

description:
processed data file:
GeneCount_H.txt


title: 18290C

description:
processed data file:
GeneCount_C.txt


title: 18289C

description:
processed data file:
GeneCount_C.txt


title: 6967H

description:
processed data file:
GeneCount_H.txt

value: One Year


title: 18528H

description:
processed data file:
GeneCount_H.txt


title: 0533H

description:
processed data file:
GeneCount_H.txt

value: RunLow


title: 5915H

description:
processed data file:
GeneCount_H.txt


title: 5943H

description:
processed data file:
GeneCount_H.txt


title: 18526C

description:
processed data file:
GeneCount_C.txt


title: 9926H

description:
processed data file:
GeneCount_H.txt

value: RunHi


title: 4857H

description:
processed data file:
GeneCount_H.txt


title: 5581H

description:
processed data file:
GeneCount_H.txt


title: 4468H

description:
processed data file:
GeneCount_H.txt


title: 7785H

description:
processed data file:
GeneCount_H.txt


title: 2747H

description:
processed data file:
GeneCount_H.txt


title: 23886H

description:
processed data file:
GeneCount_H.txt


title: 3597H

description:
processed data file:
GeneCount_H.txt


title: 5915C

description:
processed data file:
GeneCount_C.txt


title: 6859H

description:
processed data file:
GeneCount_H.txt


title: 9555H

description:
processed data file:
GeneCount_H.txt


title: 0304H

description:
processed data file:
GeneCount_H.txt


title: 5581C

description:
processed data file:
GeneCount_C.txt


title: 1388H

description:
processed data file:
GeneCount_H.txt


title: 3545H

description:
processed data file:
GeneCount_H.txt


title: 6859C

description:
processed data file:
GeneCount_C.txt


title: 1003H

description:
processed data file:
GeneCount_H.txt


title: 7383H

description:
processed data file:
GeneCount_H.txt


title: 1388C

description:
processed data file:
GeneCount_C.txt


title: 9926C

description:
processed data file:
GeneCount_C.txt


title: 3545C

description:
processed data file:
GeneCount_C.txt


title: 7182C

description:
processed data file:
GeneCount_C.txt


title: 2084H

description:
processed data file:
GeneCount_H.txt


title: 7182H

description:
processed data file:
GeneCount_H.txt


title: 9555C

description:
processed data file:
GeneCount_C.txt


title: 6967C

description:
processed data file:
GeneCount_C.txt


title: 2084C

description:
processed data file:
GeneCount_C.txt


title: 0304C

description:
processed data file:
GeneCount_C.txt


title: 1990C

description:
processed data file:
GeneCount_C.txt


title: 2747C

description:
processed data file:
GeneCount_C.txt


title: 6332H

description:
processed data file:
GeneCount_H.txt


title: 6332C

description:
processed data file:
GeneCount_C.txt


title: 7383C

description:
processed data file:
GeneCount_C.txt


title: 1990H

description:
processed data file:
GeneCount_H.txt


title: 7785C

description:
processed data file:
GeneCount_C.txt


title: 5943C

description:
processed data file:
GeneCount_C.txt


title: 3597C

description:
processed data file:
GeneCount_C.txt


title: 3494C

description:
processed data file:
GeneCount_C.txt


title: 23886C

description:
processed data file:
GeneCount_C.txt


title: 0533C

description:
processed data file:
GeneCount_C.txt


title: 1003C

description:
processed data file:
GeneCount_C.txt


title: KPC2_FibroblastEnriched

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

state: NY

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

description: Mouse ID DT25872

data_processing:
*R1_001.fastq.gz files contain the cell barcode (first 16 nt) and UMI barcode (next 10 nt)
*R2_001.fastq.gz files contain the 98 bp RNA sequence
scRNA-seq reads were processed into FASTQ files and aligned to the mm10 reference genome (GRCm38.84) using the 10X Genomics Cell Ranger Pipeline v1.2.0 with default parameters.
From the alignment, a digital gene-cell counts matrix was generated for each sample by Cell Ranger.
Samples were combined for two further analyses as follows. First, the DAPI-negative, flow-sorted samples (i.e. samples KPC1_Viable, KPC2_Viable, KPC3_Viable, and KPC4_Viable) were combined into a single "All_Viable_expression" analysis. Second, the DAPI-negative, CD45-negative, CD31-negative, and EpCAM-negative, flow-sorted samples (i.e. samples KPC1_FibroblastEnriched, KPC2_FibroblastEnriched, KPC3_FibroblastEnriched, and KPC4_FibroblastEnriched) were combined into a second "Fibroblast-enriched_expression" analysis. For each analysis, the following steps were performed: samples were combined using the Cell Ranger aggregate function which subsamples digital counts matrices such that the number of confidently mapped transcriptomic reads are equal among all samples and creates a unified digital counts matrix.
Each unified counts matrix was filtered to remove cells with fewer than 500 UMI counts and genes with fewer than 2 counts in 2 cells.
Each filtered counts matrix was then normalized such that the number of UMIs in each cell is equal to the median UMI count across the dataset and natural log transformed.
The two final matrices were made into csv files (All_Viable_expression.csv, Fibroblast-enriched_expression.csv). These files show normalized expression of each gene, in each cell in the analysis. The first column includes the gene ENSEMBL IDs. The column headings in the first row are individual 16 base-pair cell barcodes, followed by a hyphen, followed by the mouse from which the sample was derived (KPC1, KPC2, KPC3, or KPC4).
Genome_build: GRCm38.84

source_name: Flow-sorted mouse pancreas tumor tissue

growth_protocol: KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre (KPC) mice were bred, and allowed to grow until they developed palpable tumors 1-2 cm in diameter.

extract_protocol:
Single-cell barcoding and library preparation were performed using the 10X ChromiumTM version 2 chemistry, according to the manufacturer’s protocol.
cDNA and libraries were prepared using the 10X ChromiumTM version 2 chemistry, according to the manufacturer’s protocol.

treatment_protocol: Tumor specimens from KPC mice were minced and enzymatically digested in 10% FBS/DMEM supplemented with 2.5 mg/mL Collagenase D , 0.5 mg/mL Liberase DL, and 0.2 mg/mL DNase I for 45 minutes at 37°C with agitation. Cell digests were strained through a 100 μm cell strainer and quenched with 2% FBS/PBS. The solution was spun down, and cells were resuspended in ACK lysis buffer to eliminate red blood cells. After a 3 minute incubation on ice, the ACK was quenched with 2% FBS/PBS. Cells were spun down, resuspended in PBS supplemented with 0.5% BSA and 2 mM EDTA and blocked with anti-mouse CD16/CD32 Fc Block for 15 minutes at 4°C. Staining of mouse tissue for flow sorting was performed with the following antibodies: CD45-AF647, CD31-AF647, and EpCAM-AF647, for 30 minutes at 4°C. Prior to sorting, DAPI was added to the cell suspension. Cells were sorted using a BD FACSAria Fusion instrument. Following exclusion of debris, 50,000-100,000  DAPI-negative cells were collected from each sample (for ‘all viable cell’ fraction). Then sorting for DAPI-, CD45-, CD31- and EpCAM-negative cells was performed (for ‘fibroblast-enriched’ fraction). Both fractions were collected in 20% FBS/PBS. Sorted cells were washed and resuspended in PBS containing 0.04% BSA. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips for single cell capture.

tag: mouse background

tag: mouse genotype

tag: tissue origin

value: Pancreatic ductal adenocarcinoma

tag: sorting strategy


title: ATAC_DCA_rep3

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

description:
ATAC_DCA3
ATAC_DCA3_GTAGAGGA

data_processing:
DNA fragments were aligned to the mm10 reference genome and processed using the Kundaje lab's AQUAS ChIPseq and ATACseq pipelines (https://github.com/kundajelab/chipseq_pipeline and https://github.com/kundajelab/atac_dnase_pipelines).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file plotting the p-value of enrichment over input (ChIPseq) or background (ATACseq) for each condition (replicates pooled together)
Supplementary_files_format_and_content: Peak file showing the peaks identified in multiple replicates of each condition using the 'naïve overlapping' approach from the Kundaje lab's AQUAS ChIPseq and ATACseq pipelines. Encode mm10 blacklist regions have been filtered out.

extract_protocol:
ChIPseq: Chromatin IP was performed according to a previously published protocol (Schmidt et al., 2009) with a few adjustments. Briefly, sciatic L4-L6 DRGs (10 mice/sample) were extracted 24 hours after surgery and crushed using an automatic pestle and chemically cross-linked with a 1% formaldehyde solution containing 50mM Hepes-KOH pH7.5, 100mM NaCl, 1mM EDTA and 0.5mM EDTA, for 15 minutes at room temperature. Nuclear extracts were then sonicated for 30 min using a Bioruptor (Diagenode) and successful chromatin shearing (200-800 bp) was confirmed by agarose gel analysis. Immunoprecipitation was performed overnight with Protein G Dynabeads (Invitrogen) bound to 10 μg of of H3K27ac (Ab4729, Abcam), or H3K9ac (Ab10812, Abcam), or H3K27me3 (C15410195, Diagenode) antibodies. After washing, elution and reverse crosslinking, DNA was treated with RNAse A and Proteinase K and purified using Qiagen PCR purification columns. The concentration of the recovered DNA was quantified with Picogreen assay and the enrichment of the immunoprecipitate calculated with respect to the input and IgG.
ChIPseq: Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit from Illumina (NEW ENGLAND BioLabs) following the manufacturer’s protocol. Briefly, 2 ng of Input and IP DNA were end repaired and adaptor ligated, using a dilution of 1:20 of adaptors. Samples were cleaned to remove unligated adaptors and size selection was performed to select and enrich fragments of 200bp in size. Libraries were amplified by PCR using multiplex oligo following manufacturer’s protocol. Prior to sequencing, libraries were run on an Agilent Bioanalyser for size and quality control checking. Sequencing was performed in an Illumina HiSeq2000, generating 50bp single ended reads.
ATACseq: ATAC-seq was performed according to a previously published protocol (Buenrostro, 2015; Buenrostro, 2013). Briefly, sciatic L4-L6 DRGs (1 mouse/sample) were extracted 24 hours after surgery and crushed using an automatic pestle in Lysis buffer containing 0.1% Igepal (Sigma). 50000 nuclei were used for the transposition reaction with Nextera Tn5 Transposase (Illumina, FC-121-1030). The product was purified using the minElute PCR purification kit (Qiagen).
ATACseq: Transposase-accessible purified DNA was amplified by 11 cycle PCR using barcoded primers. Libraries were run on an Agilent Bioanalyser for size and quality control checking, quantified using Qbit (ThermoFisher), and multiplexed. Sequencing was performed in an Illumina HiSeq4000, generating 75bp pair-ended reads.

treatment_protocol: Mice (6-8 weeks old) underwent the following procedures: a) spinal cord dorsal column axotomy (DCA), b) laminectomy (Lam), c) sciatic nerve axotomy (SNA), and  d) sham sciatic nerve surgery (Sham).

value: 6-8 weeks old

tag: tissue

value: Dorsal Root Ganglia (DRG)

tag: chip antibody

tag: index sequence

value: GTAGAGGA


title: ATAC_Lam_rep3

description:
ATAC_Lam3
ATAC_Lam3_GCTACGCT

tag: strain

tag: age

value: GCTACGCT


title: ATAC_DCA_rep2

description:
ATAC_DCA2
ATAC_DCA2_AAGAGGCA

value: AAGAGGCA


title: KPC1_FibroblastEnriched

description: Mouse ID DT24825


title: KPC2_Viable

description: Mouse ID DT25872

value: DAPI-


title: KPC4_FibroblastEnriched

description: Mouse ID A510


title: KPC3_Viable

description: Mouse ID DT26463


title: KPC3_FibroblastEnriched

description: Mouse ID DT26463


title: KPC1_Viable

description: Mouse ID DT24825


title: ATAC_DCA_rep1

description:
ATAC_DCA1
ATAC_DCA1_CGAGGCTG

value: CGAGGCTG


title: ATAC_Lam_rep1

description:
ATAC_Lam1
ATAC_Lam1_CTCTCTAC

value: CTCTCTAC


title: KPC4_Viable

description: Mouse ID A510


title: ATAC_DCA_Vehicle_2

description: index sequence: GGACTCCT

data_processing:
ATACseq: DNA fragments were aligned to the mm10 reference genome and processed using the Kundaje lab's AQUAS ATACseq pipelines (https://github.com/kundajelab/chipseq_pipeline and https://github.com/kundajelab/atac_dnase_pipelines).
Supplementary_files_format_and_content: ATACseq: Peak file showing the peaks identified in multiple replicates of each condition using the 'naïve overlapping' approach from the Kundaje lab's ATACseq pipelines. Encode mm10 blacklist regions have been filtered out.
RNAseq: Sequence reads were aligned to the mm10 mouse reference genome sequence using STAR 2.7.0
RNAseq: Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to STAR during the alignment step
RNAseq: The aligned reads were sorted and read counts per gene were obtained from mapped reads using STAR 2.7.0
RNAseq: EdgeR version 3.24.3 (using limma-3.38.3) in R-3.5.0 was used to identify differentially expressed genes.
RNAseq: Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Genome_build: mm10

source_name: DRG

extract_protocol:
RNAseq: RNA was extracted using RNeasy kit (Qiagen), according to manufacturer’s guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 8.0 was used for library preparation.
RNA-Seq: Libraries were generated using the NEBNext poly(A) mRNA magnetic isolation module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the recommended manufacturer protocol.  Ligation and library integrity was verified using a Tapestation and Glowmax station. The NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) adapter sequences were ligated to each sample in each group to allow for sequencing multiplexing. Sample libraries ligated with unique adapter sequences, were multiplexed, and sequencing was performed in an Illumina HiSeq4000, generating 75bp pair-ended reads.
ATACseq: ATAC-seq was performed according to a previously published protocol (Buenrostro, 2015; Buenrostro, 2013). Briefly, sciatic L4-L6 DRGs (1 mouse/sample) were extracted 24 hours after surgery and crushed using an automatic pestle in Lysis buffer containing 0.1% Igepal (Sigma). 50000 nuclei were used for the transposition reaction with Nextera Tn5 Transposase (Illumina, FC-121-1030). The product was purified using the minElute PCR purification kit (Qiagen).
ATACseq: Transposase-accessible purified DNA was amplified by 11 cycle PCR using barcoded primers. Libraries were run on an Agilent Bioanalyser for size and quality control checking, quantified using Qbit (ThermoFisher), and multiplexed. Sequencing was performed in an Illumina HiSeq4000, generating 75bp pair-ended reads.

treatment_protocol: Mice (6-8 weeks old) underwent the following procedures: a) spinal cord dorsal column axotomy (DCA) plus 12 mg/kg MS275 intraperitoneal injection b) spinal cord dorsal column axotomy (DCA) plus vehicle (3.2% Tween80, 20% PEG300, 4% DMSO) intraperitoneal injection. MS275 or vehicle were injected intraperitoneally at the time of the injury and 2 h before sacrifice.

tag: treatment

value: spinal cord dorsal column axotomy (DCA) + vehicle

value: L4-L6 Dorsal Root Ganglia


title: ATAC_DCA_Vehicle_1

description: index sequence: TCCTGAGC


title: ATAC_DCA_MS275_2

description: index sequence: CGTACTAG

value: spinal cord dorsal column axotomy (DCA) + MS275


title: RNA_DCA_MS275_3

description: index sequence: GAATTCGT


title: RNA_DCA_Vehicle_2

description: index sequence: TCCGGAGA


title: ATAC_DCA_Vehicle_3

description: index sequence: TAGGCATG


title: RNA_DCA_MS275_2

description: index sequence: ATTCAGAA


title: ATAC_DCA_MS275_3

description: index sequence: AGGCAGAA


title: ATAC_DCA_MS275_1

description: index sequence: TAAGGCGA


title: RNA_DCA_MS275_1

description: index sequence: GAGATTCC


title: RNA_DCA_Vehicle_3

description: index sequence: CGCTCATT


title: ATAC_SNA_rep3

description:
ATAC_SNA3
ATAC_SNA3_TAGGCATG

value: TAGGCATG


title: RNA_DCA_Vehicle_1

description: index sequence: ATTACTCG


title: ATAC_Lam_rep2

description:
ATAC_Lam2
ATAC_Lam2_CAGAGAGG

value: CAGAGAGG


title: ATAC_SNA_rep1

description:
ATAC_SNA1
ATAC_SNA1_TCCTGAGC

value: TCCTGAGC


title: ATAC_Sham_rep3

description:
ATAC_Sham3
ATAC_Sham3_AGGCAGAA

value: AGGCAGAA


title: ATAC_Sham_rep2

description:
ATAC_Sham2
ATAC_Sham2_CGTACTAG

value: CGTACTAG


title: fip1-2 replica 1

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

data_processing:
Basecalls performed using CASAVA version 1.4
Clean (FastQC software (Babraham-Bioinformatics, 2014).  Reads are mapped to a reference sequences using HISAT2 with 8 mismatches allowed.
Reads count to a reference  genome  (TAIR 42.gff3) using the htseq-count tool.
Differential expression analysis was calculated with edgeR with the following parameters: FDR<0.05, fold change >2 fold  or   < -2 fold
Genome_build: Atabidopsis thaliannTAIR 10
Supplementary_files_format_and_content: tab-delimited text files including normalized counts.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis SKP2B::GUS (control; Manzano et al., 2012) and fip1-2 mutant were grown for 8 in Murashige and Skoog medium.

extract_protocol:
Total  RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized  using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short  fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent  2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using  Illumina HiSeqTM 2000 or other sequencer when necessary

tag: ecotype

value: Columbia

value: whole seedling

tag: genotype


title: control replica 2

value: control


title: control replica 1


title: TNFR1kd_g4_TNFa_Rep1

city: Salt Lake City

first: Robert

middle: Sean

last: Bowles

state: UT

department: Biomedical Engineering

institute: University of Utah

description:
TNFR1_g4_tnfa_10ngml_r1
PolyA RNA
10ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv

data_processing:
Reads were aligned to the hg19 build of the human genome using hisat2 V 2.0.4 with the following commands: hisat2 --dta -t -q
Counts were quantified with Subread FeatureCounts V. 1.5.1.
Differential expression was determined using DESeq2 V 1.14.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *tsv: Tab-separated values. These files contain raw and normalized counts for genes from the hg19 genome.

source_name: intervertebral disc - nucleus pulposus

growth_protocol: Nucleus pulposus tissue-derived cells were cultured in base culture media (DMEM high glucose with 10% FBS, 50 µg/mL gentamicin, 25 mM HEPES) supplemented fresh with 2 ng/mL fibroblast growth factor 2 (FGF-2) (Peptrotech).

extract_protocol:
RNA was harvested using Purelink RNA micro kit (Invitrogen).
Poly(A)-selected RNA-seq libraries were constructed with KAPA Stranded mRNA-seq kit (Kapa Biosystems) using 500 ng total RNA.

treatment_protocol: Patient nucleus pulposus cells (NTC and TNFR1 edited, 26 yr male) were plated in base culture media. The following day, cells were treated with 0 or 10 ng/mL of TNF-α for 24 hours.

tag: cell type

value: Pathological intervertebral disc cells from the nucleus pulposus

tag: Sex

value: Male

value: 26 yr

tag: genotype/variation

value: TNFR1 downregulated

value: 10ng/ml TNF-alpha


title: NT_TNFa_Rep1

description:
NT_tnfa_10ngml_r1
PolyA RNA
10ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv

value: Nontargeting control


title: fip1-2 replica 2


title: ATAC_Sham_rep1

description:
ATAC_Sham1
ATAC_Sham1_TAAGGCGA

value: 6-8 weeks old

value: Dorsal Root Ganglia (DRG)

value: TAAGGCGA


title: NT_Rep2

description:
NT_r2
PolyA RNA
0ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv

value: 0ng/ml TNF-alpha


title: TNFR1kd_g4_Rep2

description:
TNFR1_g4_r2
PolyA RNA
0ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv


title: TNFR1kd_g4_Rep1

description:
TNFR1_g4_r1
PolyA RNA
0ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv


title: siNRG1_P3

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

description:
thyroid primary cells on Day 5
TAD10_30_2_NRG1

data_processing:
RNA-Seq reads were first mapped to the human genome hg19 using TopHat2 (Kim et al., 2013).
Raw read counts for each gene were quantified by using featureCounts software (Liao et al., 2014) that uses GENCODE v.22 Gene Transfer Format (GTF) file as a transcript reference (GENCODE annotation).
Genes with counts below 5 for at least 2 samples out of 3 within each group were filtered out. Then the counts were normalized toward the common library size. The count data were assumed to follow a negative binomial distribution.
To improve the estimate of over-dispersion and to identify genes differentially expressed between samples, R package DESeq2 (Love et al., 2014) was used to estimate the smoothed over-dispersion parameters and to calculate p-values with Wald test for group comparison under a generalized linear model. The p-value cut-offs were determined by controlling the mean number of false positives (Gordon et al., 2007).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized abundance measurements

source_name: thyroid primary cells

growth_protocol: Human primary thyroid cells were cultured in 6H medium after digested from the fresh thyroid tissue. 6H medium was made from modified F-12M medium (Coon’s modification of Ham’s F-12 medium) by adding 5% Heat Inactivated FBS, 2 mM Glutamine, 2.6 g/l NaHCO3, 5 ug/ml gentamicin, 1% NEAA and six nutrition factors: 10mU/ml TSH, 10 mU/ml Insulin, 1 nM Hydrocortisone, 2 ng/ml Glycyl-Histidyl-L-Lysine Acetate, 5µg/ml Transferrin and 10ng/ml Somatostatin.

extract_protocol:
The total RNA samples for RNA-seq were extracted by TRIzol reagent (Invitrogen) and then treated byDNase-1 (Ambion) in order to eliminate the DNA contamination. Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (catalog #RS-122-2201) was used to transform RNA into cDNA after removing rRNA and mitochondrial RNA. The RNA-seq libraries were prepared according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary cells were electroporated by Nucleofector®II device (Amaxa) with 75pmol Human NRG1 siRNA (ON-TARGET plus SMART pool)  in 100μl of Basic Nucleofector Medium for Primary Mammalian Epithelial Cells (Lonza, VPI-1005) for each well of 6-well plates. Cells were then resuspended in 6H medium, incubated for 24 hours and used for further analysis.

value: nontumorous fresh thyroid tissue

value: thyroid primary cell cultures

value: NRG1 knockdown

tag: time

value: Day 5


title: ATAC_SNA_rep2

description:
ATAC_SNA2
ATAC_SNA2_GGACTCCT

value: GGACTCCT


title: siControl_P1

description:
thyroid primary cells on Day 5
TAD10_6_control

treatment_protocol: Primary cells were electroporated by Nucleofector®II device (Amaxa) with 75pmol Human negative control siRNA (ON-TARGET plus control pool)  in 100μl of Basic Nucleofector Medium for Primary Mammalian Epithelial Cells (Lonza, VPI-1005) for each well of 6-well plates. Cells were then resuspended in 6H medium, incubated for 24 hours and used for further analysis.


title: siControl_P2

description:
thyroid primary cells on Day 5
TAD10_30_1_control


title: NT_TNFa_Rep2

description:
NT_tnfa_10ngml_r2
PolyA RNA
10ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv


title: siNRG1_P1

description:
thyroid primary cells on Day 5
TAD10_6_1_NRG1


title: MEL270.SF3B1_K700E

city: Seattle

first: Guo-Liang

last: Chew

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

description:
processed data file:RNA_seq_TPMs.txt
MEL270.SF3B1_K700E_rnaseq

data_processing:
Merge gene annotations from UCSC knownGene, Ensembl 71, MISO v2.0
RNA-seq: RSEM v1.2.4 used to call Bowtie with option '-v 2' to align to merged annotation, remaining reads mapped to genome with TopHat v2.1.1, Isoform ratios were quantified with MISO V2
ChIP-Seq: Bowtie v1.0.045 with the arguments '-v 2 -k 1 -m 1 --best --strata' to align to merged annotation. Peaks were called using MACS2 v2.1.1.2016030949 against input control libraries with p < 10-5 and subsequently filtered to remove peaks contained within ENCODE blacklisted regions50 and the mitochondrial genome.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression estimates (TPM); .narrowPeak: output from MACS2 peak calling against input; ChIP-seq bigwig coverage

growth_protocol: K562 and MEL270 cell lines were cultured in RPMI/10% FCS, with penicillin (100 U/ml) and streptomycin (100 μg/ml).

extract_protocol:
RNA for RNA-seq was extracted with TRIzol (Thermo Fisher) according to manufacturer's protocols
RNA-seq libraries were prepared from TRIzol-isolated (Thermo Fisher catalog no. 15596026) RNA using the Illumina TruSeq RNA Library Prep Kit v2 (Illumina catalog no. RS-122-2001/2).

treatment_protocol: Dox, DMSO, 6 days

tag: cell line

tag: lentiviral vector


title: siControl_P3

description:
thyroid primary cells on Day 5
TAD10_30_2_control


title: K562.SF3B1_K700E_rep2

description:
processed data file:RNA_seq_TPMs.txt
K562.SF3B1_K700E_rep2_rnaseq


title: K562.SF3B1_K700E_rep1

description:
processed data file:RNA_seq_TPMs.txt
K562.SF3B1_K700E_rep1_rnaseq


title: MEL270.DMSO

description:
processed data file:RNA_seq_TPMs.txt
MEL270.DMSO_rnaseq

value: pINDUCER eGFP empty


title: K562.WT

description:
processed data file:RNA_seq_TPMs.txt
K562.WT_rnaseq

value: WT


title: MEL270.dBRD9

description:
processed data file:RNA_seq_TPMs.txt
MEL270.dBRD9_rnaseq

treatment_protocol: Dox, 500nM dBRD9, 6 days


title: siNRG1_P2

description:
thyroid primary cells on Day 5
TAD10_30_1_NRG1


title: MEL270.SF3B1_WT

description:
processed data file:RNA_seq_TPMs.txt
MEL270.SF3B1_WT_rnaseq


title: NT_Rep1

description:
NT_r1
PolyA RNA
0ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv

value: Pathological intervertebral disc cells from the nucleus pulposus


title: TNFR1kd_g4_TNFa_Rep2

description:
TNFR1_g4_tnfa_10ngml_r2
PolyA RNA
10ng/ml TNF-α
processed data file: normalizedCounts_farhang_humanGeneTherapy_2019.tsv
processed data file: rawCounts_farhang_humanGeneTherapy_2019.tsv

value: Male


title: ADSCD7P3L

city: Beijing

first: Zhou

address: Beilishi Street 167, Xi Cheng District

institute: Fuwai Hospital, the Chinese Academy of Medical Sciences

description:
Affected thigh of lymphedema patient.
PolyA RNA
mRNA-seq

data_processing:
The expression of the transcripts was quantified with kallisto v0.43.1 under default settings.
Genome_build: GRCh37
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include TPM values for each sample.

source_name: adipose-derived mesenchymal stem cells

extract_protocol:
Total cellular RNA was extracted using a miRNeasy Mini Kit (217004, Qiagen) according to the manufacturer’s instructions.
Library construction was performed by using a NEBNext Ultra RNA library Prep Kit for Illumina (#E7530L, NEB).

tag: disease diagnosis

value: Lymphedema

value: Adipose-derived mesenchymal stem cells

tag: sampling position

value: Affected thigh

tag: patient


title: ADSCD7P3

description:
Normal upper abdomen of lymphedema patient.
PolyA RNA
mRNA-seq

value: Normal upper abdomen


title: ADSCD8P3


title: ADSCD8P3L


title: ADSCD6P3L


title: Burkitt's Lymphoma patient BL_050

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: According to affymetrix protocol

scan_protocol: According to affymetrix protocol

data_processing: Raw cel files were RMA normalized using the ExpressionFileCreator module of GenePattern31, and quality checked for batch effects by unsupervised clustering of the 3,000 most variably expressed genes across the dataset.

source_name: biopsy

label_protocol: According to affymetrix protocol

extract_protocol: Trizol or Qiagen RNA extraction kit

tag: diagnosis

value: Burkitt's Lymphoma

tag: tissue

value: tumor specimen


title: Burkitt's Lymphoma patient BL_048


title: Burkitt's Lymphoma patient BL_057


title: Burkitt's Lymphoma patient BL_051


title: Burkitt's Lymphoma patient BL_056


title: Burkitt's Lymphoma patient BL_058


title: Burkitt's Lymphoma patient BL_043


title: Burkitt's Lymphoma patient BL_055


title: Burkitt's Lymphoma patient BL_054


title: Burkitt's Lymphoma patient BL_052


title: Burkitt's Lymphoma patient BL_059


title: Burkitt's Lymphoma patient BL_047


title: Burkitt's Lymphoma patient BL_042


title: Burkitt's Lymphoma patient BL_041


title: Burkitt's Lymphoma patient BL_053


title: Burkitt's Lymphoma patient BL_045


title: Diffuse Large B-cell Lymphoma patient DLBCL_136

value: Diffuse Large B-cell Lymphoma


title: ADSCD6P3


title: Burkitt's Lymphoma patient BL_044


title: Burkitt's Lymphoma patient BL_049


title: Burkitt's Lymphoma patient BL_037


title: Burkitt's Lymphoma patient BL_039


title: Burkitt's Lymphoma patient BL_038


title: Burkitt's Lymphoma patient BL_046


title: High-grade B-cell Lymphoma Not Otherwise Specified patient HGBL-NOS_019


title: ADSCD4P3L


title: ADSCD5P3L


title: ADSCD4P3


title: ADSCD3P3


title: ADSCD5P3


title: Burkitt's Lymphoma patient BL_040


title: ADSCD3P3L


title: ADSCD22P3L


title: ADSCD22P3


title: ADSCD21P3L


title: Burkitt's Lymphoma patient BL_034


title: Burkitt's Lymphoma patient BL_033


title: Burkitt's Lymphoma patient BL_036


title: Burkitt's Lymphoma patient BL_035


title: ADSCD10P3L


title: ADSCD14P3


title: Burkitt's Lymphoma patient BL_030


title: ADSCD14P3L


title: Burkitt's Lymphoma patient BL_027


title: Burkitt's Lymphoma patient BL_025


title: ADSCD21P3


title: Burkitt's Lymphoma patient BL_032


title: Burkitt's Lymphoma patient BL_026


title: Burkitt's Lymphoma patient BL_029


title: Burkitt's Lymphoma patient BL_018


title: Burkitt's Lymphoma patient BL_017


title: Burkitt's Lymphoma patient BL_028


title: Burkitt's Lymphoma patient BL_023


title: Burkitt's Lymphoma patient BL_022


title: Burkitt's Lymphoma patient BL_021


title: Burkitt's Lymphoma patient BL_020


title: Burkitt's Lymphoma patient BL_024


title: MHCC-97H Cell overexpressed ROCK2 Replicate 2

city: Shanghai

first: HeMing

state: Shanghai

address: No.100 Haining Road

department: Clinical Pharmacy

institute: Shanghai General Hospital

description:
lncRNA & mRNA expression when ROCK2 was overexpressed
MHCC-97H ROCK2 rep-2

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_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: MHCC-97H cells overexpressed ROCK2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Dulbecco's modified eagle medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: MHCC-97H hepatocellular carcinoma cell line

value: ROCK2 overexpression

tag: growth phase

value: exponential phase


title: Burkitt's Lymphoma patient BL_015


title: Burkitt's Lymphoma patient BL_019


title: Burkitt's Lymphoma patient BL_031


title: Burkitt's Lymphoma patient BL_016


title: MHCC-97H Cell overexpressed ROCK1 Replicate 3

description:
lncRNA & mRNA expression when ROCK1 was overexpressed
MHCC-97H ROCK1 rep-3

source_name: MHCC-97H cells overexpressed ROCK1

value: ROCK1 overexpression


title: MHCC-97H Cell overexpressed ROCK2 Replicate 3

description:
lncRNA & mRNA expression when ROCK2 was overexpressed
MHCC-97H ROCK2 rep-3


title: Root_Salt_input

data_processing:
The reads from ChIP-seq were aligned to rice genome (TIGR release 7) with  one mismatch allowed using bowtie2 program. Only the reads mapped to a unique position of rice genome were included in the analysis.
macs14(version 1.4.2) is the software for peak calling, parameter -s SAM, -t, -c,--wig, --single, -g 3.8e+8  --bw 200 were used
Genome_build: rice (release 7)
Supplementary_files_format_and_content: wig files were generated using macs14,variableStep format andfixedStep format are included

growth_protocol: Rice cultivar ‘Nipponbare’ seedlings grown in green house for two weeks

extract_protocol:
Six commercial ChIP-grade antibodies, H3K9ac (Millipore, 07-352), H3K27ac (Abcam, ab4729), H3K27me3 (Millipore, 07-449), H3K36me3 (Abcam, ab9050), H4K12ac (Millipore, 07-595) and H3K4me3 (Abcam, ab8580), were used for ChIP experiments with leaf and root tissues,
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Leaves and root of two-week old rice cultivar ‘Nipponbare’ seedlings grown in green house were collected and ground into fine powder in liquid nitrogen. The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation.

value: two weeks

tag: cultivar

value: Nipponbare

tag: chip antibody

value: none, input_rootsalt

value: shoot

value: salt


title: Burkitt's Lymphoma patient BL_014


title: Root_CK_input

tag: age

value: none, input_rootck

tag: treatment

value: control


title: Leaf_Salt_input

value: none, input_leafsalt

value: seedling


title: Leaf_CK_input

value: none, input_leafck


title: Control MHCC-97H Cell Replicate 2

description:
lncRNA & mRNA expression
MHCC-97H rep-2

source_name: MHCC-97H control cell lines

tag: genotype


title: MHCC-97H Cell overexpressed ROCK2 Replicate 1

description:
lncRNA & mRNA expression when ROCK2 was overexpressed
MHCC-97H ROCK2 rep-1


title: MHCC-97H Cell overexpressed ROCK1 Replicate 1

description:
lncRNA & mRNA expression when ROCK1 was overexpressed
MHCC-97H ROCK1 rep-1


title: Root_Salt_H3K27me3


title: Root_Salt_H4K12ac


title: Root_Salt_H3K9ac


title: Burkitt's Lymphoma patient BL_012

value: Burkitt's Lymphoma


title: Burkitt's Lymphoma patient BL_010

value: tumor specimen


title: Root_Salt_H3K27ac


title: MHCC-97H Cell overexpressed ROCK1 Replicate 2

description:
lncRNA & mRNA expression when ROCK1 was overexpressed
MHCC-97H ROCK1 rep-2


title: Root_Salt_H3K36me3


title: Burkitt's Lymphoma patient BL_011


title: Control MHCC-97H Cell Replicate 3

description:
lncRNA & mRNA expression
MHCC-97H rep-3


title: Control MHCC-97H Cell Replicate 1

description:
lncRNA & mRNA expression
MHCC-97H rep-1


title: Burkitt's Lymphoma patient BL_008


title: High-grade B-cell Lymphoma Not Otherwise Specified patient HGBL-NOS_018


title: Burkitt's Lymphoma patient BL_009


title: Burkitt's Lymphoma patient BL_013


title: Root_CK_H3K27me3


title: Root_CK_H4K12ac


title: Burkitt's Lymphoma patient BL_007


title: Spleen Ly6c+ monocytes, replicate 1

city: Denver

first: Claudia

last: Jakubzick

state: Colorado

address: 1400 Jackson St

department: Pediatrics

institute: National Jewish Health

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 4.4.
Sequence reads of at least 30 nt length were mapped to the canonical chromosomes of the mm10 mouse genome release using STAR (version 2.4.0j [Dcs] or 2.4.1d [monocytes]) with splice site data from the Ensembl annotation release 78.
Reads mapping unambiguously to each gene in the Ensembl 75 annotation were quantified using the featureCounts program from the Subread software package (v1.5.2) with options “-s 0 -O --fracOverlap 0.5 ”.
Transcripts per million (TPM) were calculated using the sum of all bases covered by any transcript for a given gene as its length.
Genome_build: mm10
Supplementary_files_format_and_content: read counts and transcripts per million (TPM) assigned to each gene of the mouse Ensembl 75 annotation and sample, as tab-separated text tables: 1) output from subread featureCounts (2 subread_* files), separated by sequencing run, 2) aggregated by adding different sequencing runs for each sample (counts and TPM)

source_name: Spleen digest

extract_protocol:
Single cell suspensions were obtained by enzymatic digestion with 2.5 mg/ml collagenase D (Roche via Sigma Aldrich) of the applicable organ from different cohorts of naïve C57Bl/6 mice (NCI/Charles River). Whole digests were magnetically enriched with Miltenyi microbeads for cells of interest before FACS sorting to purify (BD FACS Aria Fusion). Resulting cells were lysed with RLT buffer and total RNA was extracted using the Qiagen RNeasy micro or mini kits.
A modified Clontech SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Mountain View, CA, USA) and modified Kapa Biosystems (Wilmington, MA, USA) KAPA Hyper Prep Kit was used to primarily target all polyA RNA. Library construction started from isolation of total RNA species, followed by mRNA (poly-A) isolation, 1st and 2nd strand cDNA synthesis, adapter ligation, amplification and bead templating.

tag: strain

value: spleen

value: 6-8 weeks

tag: cell type

value: Monocyte

tag: identifying markers

value: Ly6C+, CD11b+


title: Spleen Ly6c+ monocytes, replicate 2


title: Lung Lymph node CD11b+ dendritic cells, replicate 2

source_name: Lung lymph node digest

value: lung lymph node

value: Dendritic cell

value: CD11b+, CD11c+, MHCII+


title: Root_Salt_H3K4me3

value: two weeks

value: Nipponbare


title: Burkitt's Lymphoma patient BL_006


title: Lung Lymph node CD103+ dendritic cells, replicate 3

value: CD103+, CD11c+, MHCII+


title: Burkitt's Lymphoma patient BL_005


title: Root_CK_H3K9ac

value: shoot


title: Lung Lymph node CD11b+ dendritic cells, replicate 3


title: Burkitt's Lymphoma patient BL_003


title: Root_CK_H3K27ac

value: control


title: Lung Lymph node CD103+ dendritic cells, replicate 2


title: Spleen CD4+ dendritic cells, replicate 3

value: CD4+, CD11c+, MHCII+


title: Lung Lymph node CD103+ dendritic cells, replicate 1


title: Burkitt's Lymphoma patient BL_002


title: Root_CK_H3K36me3


title: Lung Lymph node CD11b+ dendritic cells, replicate 1


title: Spleen CD4+ dendritic cells, replicate 2


title: Diffuse Large B-cell Lymphoma patient DLBCL_135

value: Diffuse Large B-cell Lymphoma


title: Spleen CD8+ dendritic cells, replicate 3

value: CD8+, CD11c+, MHCII+


title: Spleen CD8+ dendritic cells, replicate 2


title: Spleen CD4+ dendritic cells, replicate 1


title: Root_CK_H3K4me3


title: P33T-PP_PDX1_Lane2_CTTGTA

description: P33T_PDX1_Multi-Condidtion_GEM_events.bed

data_processing:
Fastq files were preprocessed with Trimmomatic (0.35) with parameters CROP:50 ILLUMINACLIP:path/to/adapter.fa:2:30:10:1 LEADING:0 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Preprocessed Fastq files were aligned to hg19 genome using bowtie2 (2.2.6) with very-sensitive option.
SAM files were converted to BAM and duplicate reads were removed using samtools (1.3).
Deduplicated BAM files from PDX1P33T/+ PDX1 and H3H27ac were subsampled to match the read depth of the corresponding experiments in XM001 cells (GSE106949)
Binding sites for PDX1 were then called using GEM (3.2) in multicondition mode using data from XM001 (GSE106949) and PDX1P33T/+ (this study) PPs. Bindingsites were filtered, after visual inspection, using a Q-value cut-off of 10^-4 (XM001) and 10^-4.05 (PDX1P33T/+). Overlapping regions were merged and peaks overlapping blacklist regions were removed using bedtools (2.26.0).
Regions of H3K27ac enrichment were called using HOMER (4.10) on the merged data from XM001 (GSE106949) and PDX1P33T/+ (this study) cells using parameters -style histone -size 500 -minDist 2000. Regions overlapping blacklist-regions were discarded.
Regions and binding sites within 20 kb of a TSS or within a gene body were annotated with the respective gene using bedtools (2.26.0).
Genome_build: hg19
Supplementary_files_format_and_content: BED file containing peak locations

source_name: PDX1P33T/+ iPS derived pancreatic precursor cells

growth_protocol: PDX1P33T/+ iPSCs were cultured on 1:100 diluted Matrigel (BD Biosciences) in mTeSR™1 medium (Stem Cell Technologies). At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) followed by incubation with 1× TrypLE Select Enzyme (Life Technology) for 3–5 min at 37 °C. Single cells were rinsed with mTeSR™1 medium, and spun at 1,000 rpm for 3 min. The resulting cell pellet was resuspended in mTeSR™1 medium supplemented with 10 μM Y-27632 (Sigma-Aldrich) and the single cell suspension was seeded at ~1.0 × 105 cells/cm² on Matrigel-coated surfaces. Cultures were fed every day with mTeSR™1 medium and differentiation was initiated 48 h following seeding, resulting in ~90% starting confluency.

extract_protocol:
PDX1P33T/+ PP cells (2 × 106 cells) were cross-linked in 1% formaldehyde in culture medium for 10 min at room temperature. The cross-linking reaction was stopped by the addition of glycine to a final concentration of 125 mM. For chromatin fragmentation, cells were resuspended in lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.5% SDS) and sonicated in a Covaris S220 sonicator with a duty cycle of 2%, a peak incident power of 105 W and 200 cycles per burst for 20 min. The fragmented chromatin was diluted 1:5 in IP-Buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-Desoxycholate, 140 mM NaCl, H2O, Protease Inhibitors) and directly used for immunoprecipitation. For PDX1 ChIP, 60% of the chromatin (equivalent of 1.2 × 106 cells) was processed in two parallel ChIPs using magnetic beads, preloaded with 3 µl goat anti PDX1 antibody (kindly provided by C. Wright), for each ChIP. For H3K27ac ChIP, 40% of the chromatin (equivalent 0.4 × 106 cells) was processed in three parallel IPs using magnetic beads, preloaded with 3 µg anti H3K27ac antibody (Diagenode, pAb-174-050). For all ChIPs, antibody incubation was performed at 4 °C for 5 h. Beads were then washed 5 times using (1.) IP-Buffer, (2.) Washing-Buffer 1 (500 mM NaCl, 50 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% NP-40), (3.) Washing-Buffer 2 (250 mM LiCl, 50 mM Tris-HCl (pH 8.0), 0.5% Na-Deoxycholate, 1% NP-40) and (4. & 5.) Washing-Buffer 3 (10 mM Tris-HCl (pH 8.0), 10 mM EDTA). Subsequently, protein-DNA complexes were eluted from the beads in Elution-Buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS) at 65 °C for 20 min. Cross-links were reversed at 65 °C overnight and DNA was purified by ethanol precipitation.
Libraries were constructed using the MicroPlex kit (Diagenode, C05010010). Library construction, purification and size selection using AMPureXP (Beckman Coulter) were performed according to the MicroPlex kit instruction manual (version 4 / 03.09.14)

treatment_protocol: PDX1P33T/+ iPSCs plated on 1:100 diluted Matrigel were first rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) and then cultured in RPMI 1640 medium (Invitrogen) further supplemented with 1.2 g/L sodium bicarbonate (Sigma), 0.2% ESC-qualified FBS (Life Technologies), 100 ng/mL Activin-A (R&D Systems), and 20 ng/mL of Wnt3A (R&D Systems) for day 1 only. For the next 2 days, cells were cultured in RPMI with 0.5% FBS, 1.2g/L sodium bicarbonate and 100 ng/mL Activin-A ; Cells were rinsed with 1× DPBS (without Mg2+ and Ca2+) once and then exposed to DMEM-F12 (Life Technologies) medium further supplemented with 2 g/L sodium bicarbonate, 2% FBS and 50 ng/mL of FGF7 (R&D Systems) for 3 days; Cultures were maintained for 4 days in DMEM-HG medium (Life Technologies) supplemented with 0.25 µM SANT-1 (Sigma-Aldrich), 2 µM retinoic acid (RA; Sigma-Aldrich), 100 ng/mL of Noggin (R&D Systems), and 1% B27 (Invitrogen).

tag: assay

tag: lane

tag: antibody

value: Goat anit PDX1 (Christopher V. E., Wright)


title: Spleen CD8+ dendritic cells, replicate 1


title: Spleen Ly6c+ monocytes, replicate 3


title: Leaf_Salt_H4K12ac

value: seedling

value: salt


title: Leaf_Salt_H3K27me3


title: P33T-PP_PDX1_Lane1_CTTGTA


title: Diffuse Large B-cell Lymphoma patient DLBCL_134

value: tumor specimen


title: P33T-PP_H3K27ac_Lane2_TAGCTT

value: Rabbit anti H3K27ac, Diagenode, C15410175


title: Diffuse Large B-cell Lymphoma patient DLBCL_133


title: Burkitt's Lymphoma patient BL_001

value: Burkitt's Lymphoma


title: Leaf_Salt_H3K9ac


title: Burkitt's Lymphoma patient BL_004


title: Leaf_Salt_H3K27ac


title: P33T-PP_H3K27ac_Lane1_TAGCTT

value: Rabbit anti H3K27ac, Diagenode, C15410174


title: U2OS SM3 R2

city: Leicester

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
The raw files were processed with LifeTechnologies LifeScope (v2.5.1) Whole Transcriptome Pipeline
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the deepTools 2.5.3 bamCoverage tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: U2OS SM3

growth_protocol: U2OS cells were maintained in DMEM with 10% fetal bovine serum and antibiotics.

extract_protocol:
RNA extracted with the High Pure RNA isolation kit (Roche Applied Science), following manufacturer's instructions
Libraries were prepared using Solid Total RNASeq protocol (Life tech, 4445374) according to manufacturer's instructions

tag: cell line

value: expressing SM3


title: Diffuse Large B-cell Lymphoma patient DLBCL_132


title: U2OS SM3 R1


title: U2OS SM2 R2

source_name: U2OS SM2

value: expressing SM2


title: Leaf_Salt_H3K4me3

source_name: seedling

value: two weeks


title: U2OS SM2 R1


title: U2OS SM1 R1

source_name: U2OS SM1

value: expressing SM1


title: P33T-PP_H3K27ac_Lane3_TAGCTT

value: Rabbit anti H3K27ac, Diagenode, C15410176


title: Leaf_CK_H3K27me3

value: Nipponbare


title: Leaf_Salt_H3K36me3


title: U2OS SM1 R2


title: High-grade B-cell Lymphoma Not Otherwise Specified patient HGBL-NOS_017


title: Leaf_CK_H4K12ac

value: control


title: Diffuse Large B-cell Lymphoma patient DLBCL_131


title: Diffuse Large B-cell Lymphoma patient DLBCL_130


title: H3K27me3_DCA_ChIP_rep2

description:
H3K27me3_DCA2
H3K27me3_DCA2_GTGAAA

value: 6-8 weeks old

value: Dorsal Root Ganglia (DRG)

value: H3K27me3 Diagenode C15410195

tag: index sequence

value: GTGAAA


title: U2OS Control R1

source_name: U2OS Control

value: Control


title: Double Hit Lymphoma patient DHL_001

value: Double Hit Lymphoma


title: Leaf_CK_H3K9ac

value: seedling


title: H3K27me3_Lam_ChIP_rep2

description:
H3K27me3_Lam2
H3K27me3_Lam2_ACTTGA

value: ACTTGA


title: H3K27me3_DCA_ChIP_rep1

description:
H3K27me3_DCA1
H3K27me3_DCA1_GATCAG

value: GATCAG


title: Leaf_CK_H3K27ac


title: H3K27me3_Lam_ChIP_rep1

description:
H3K27me3_Lam1
H3K27me3_Lam1_CTTGTA

value: CTTGTA


title: Diffuse Large B-cell Lymphoma patient DLBCL_088

value: Diffuse Large B-cell Lymphoma

value: tumor specimen


title: Chimpanzee_Hi-C

city: Pittsburgh

first: Yang

last: Yang

state: PA

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
Hi-C contacts based on the corresponding genome assembly of each species were calculated from the Hi-C sequencing reads of the corresponding species using the processing pipeline of the software Juicer Tools, with the command: bash juicer.sh -g genomeID -s HindIII -D Juicer scripts directory -z reference genome file -p chromosome sizes path -y restriction site file -x. For each species, we merged the paired-end Hi-C sequencing reads from different lanes.
The genomic loci of Hi-C contacts in each species were mapped to the reference genome (human genome assembly hg38) using the tool liftOver with reciprocal mapping, with command: liftOver oldFile map.chain newFile unMapped -minMatch=0.5.
The .hic file of each species which stores the Hi-C contact matrix information of the species was obtained from the Hi-C contacts that were mapped to the human genome, using the software Juicer Tools, with the command: java -Xmx16g -jar path of juicer_tools.jar pre Hi-C contact file output_file genomeID.
Hi-C contact maps of each species were generated at the resolution of 50Kb using Juicer Tools with the normalization by Knight-Ruiz matrix balancing applied. The command is: java -jar path of juicer_tools.jar dump observed KR .hic file chromID1 chromID2 BP 50000 output_file.
Median filtering was performed to interpolate the missing values in the Hi-C contact map of each species in each synteny block. For each node without signal value in the Hi-C contact map, the median of Hi-C contact frequencies of the 8-connected neighbors was used as the value assigned to the node.
Anisotropic diffusion filtering was applied to the Hi-C contact map of each species in each synteny block to smooth the signals, using the function in the MedPy package.
The Hi-C contact frequencies of each species were normalized to the same scale over all the autosomes for all the species.
Genome_build: panTro5
Genome_build: panPan2
Genome_build: gorGor4
Supplementary_files_format_and_content: The .hic file of each species is compressed binary file that stores Hi-C contact matrices from multiple resolutions. The .hic files of non-human species are based on the human genome coordinates (human genome assembly hg38), as the Hi-C contacts in each species have been mapped to human genome. The files named by *_contact50K_norm.txt are the smoothed and normalized Hi-C contact frequencies of each species on all the autosomes based on the human genome coordinates, which include intra-chromosome contacts only. The first column is the chromosome ID. The second column is the starting position of the first locus in a Hi-C contact. The third column is the starting position of the second locus in a Hi-C contact. The paired genomic loci in a Hi-C contact are both 50Kb in length. The third column is the smoothed and normalized Hi-C contact frequency between the paired genomic loci.

organism: Pan troglodytes

source_name: Chompanzee lymphocyte

growth_protocol: The cell lines were a gift from the laboratory of Dr. Ajit Varki. Cells were grown as suspension cultures RPMI-1640 media supplemented with 15% Fetal bovine serum and Penicillin/Streptomycin. Cells were fixed in suspension culture at density of 1 million cells/mL with %1 formaldehyde for 10 minutes at room temperature. Fixation was quenched with glycine, and cells were harvested by centrifugation, washed with 1X DPBS, and frozen in aliquots of 5 million cells until ready for further processing.

extract_protocol:
Hi-C libraries were prepared using the original dilution Hi-C protocol and using the HindIII restriction enzyme. In brief, nuclei were isolated by performing gentle cell lysis on ice followed by 10 strokes with a Dounce homogenizer. Nuclei were washed in lysis buffer and resuspended in NEB Buffer 2, and digested with 400U of HindIII restriction enzyme and digested overnight. The following day the restriction enzyme was heat inactivated and ends were filled in with nucleotides including a biotin-14-dCTP and blunt end ligated for 4 hours. The samples were then subject to overnight proteinase K treatment and reverse cross linking. DNA was purified using phenol:chloroform extraction and ethanol precipitation. Libraries were prepared using Illumina TruSeq adaptors, and biotin containing fragments were isolated using streptavidin coated beads. Libraries were amplified using on-bead PCR amplification and purified using SPRI beads.
Illumina TruSeq paired end

value: lymphocyte


title: Leaf_CK_H3K36me3

value: two weeks


title: H3K27me3_SNA_ChIP_rep1

description:
H3K27me3_SNA1
H3K27me3_SNA1_CAGATC

value: CAGATC


title: U2OS Control R2


title: Leaf_CK_H3K4me3

value: Nipponbare


title: Diffuse Large B-cell Lymphoma patient DLBCL_087


title: H3K27me3_SNA_ChIP_rep2

description:
H3K27me3_SNA2
H3K27me3_SNA2_GTCCGC

value: GTCCGC


title: High-grade B-cell Lymphoma Not Otherwise Specified patient HGBL-NOS_016


title: Diffuse Large B-cell Lymphoma patient DLBCL_086


title: H3K27me3_DCA_Input_rep1

description:
H3K27me3_DCAI1
H3K27me3_DCAI1_TTAGGC

value: 6-8 weeks old

value: TTAGGC


title: H3K27me3_Sham_ChIP_rep1

description:
H3K27me3_Sham1
H3K27me3_Sham1_GCCAAT

value: Dorsal Root Ganglia (DRG)

value: H3K27me3 Diagenode C15410195

value: GCCAAT


title: H3K27me3_Lam_Input_rep1

description:
H3K27me3_LamI1
H3K27me3_LamI1_ACAGTG

value: ACAGTG


title: H3K27me3_SNA_Input_rep2

description:
H3K27me3_SNAI2
H3K27me3_SNAI2_AGTTCC

value: AGTTCC


title: H3K27me3_Sham_Input_rep2

description:
H3K27me3_ShamI2
H3K27me3_ShamI2_AGTCAA

value: AGTCAA


title: H3K27me3_Sham_ChIP_rep2

description:
H3K27me3_Sham2
H3K27me3_Sham2_CCGTCC

value: CCGTCC


title: H3K27me3_DCA_Input_rep2

description:
H3K27me3_DCAI2
H3K27me3_DCAI2_ATGTCA

value: ATGTCA


title: H3K27ac_DCA_ChIP_rep2

description:
H3K27ac_DCA2
H3K27ac_DCA2_GTGAAA

value: H3K27ac Abcam Ab4729

value: GTGAAA


title: H3K27me3_Sham_Input_rep1

description:
H3K27me3_ShamI1
H3K27me3_ShamI1_CGATGT

value: CGATGT


title: H3K27ac_Lam_ChIP_rep2

description:
H3K27ac_Lam2
H3K27ac_Lam2_ACTTGA

value: ACTTGA


title: Pdx1_p33tpp_09: p33t_pp_rep2

hyb_protocol: According to the Affymetrix expression protocol

data_processing:
Expression data were RMA normalized using the oligo package (version 1.38.0) together with expression data from GSE106813
Normalized expression data was filtered to retain only the 30562 probe sets with highest expression values

source_name: PDX1P33T/+ iPS derived pancreatic precursor cells, biological replicate 2

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

extract_protocol: miRNeasy Mini Kit (Qiagen)


title: iPSPdx1_p33t_05: p33t_iPS_rep1

scan_protocol: According to the Affymetrix expression protocol

source_name: PDX1P33T/+ iPS cells, biological replicate 1

value: PDX1P33T/+ iPS cells


title: KO1

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to GRCh38 with Bismark
Genome_build: GRCh38

source_name: liver

extract_protocol:
Mouse liver tissue lysate was enriched for mitochondria. RNA was treated with Ribo Zero Gold and DNase. Bisulfite treatment (Epigentek, three cycles of 90°C for 5 min and 60°C for 1h)
Illumina TruSeq small RNA

value: liver

tag: molecule subtype

value: mitochondrial enriched RNA


title: KO2


title: H3K27me3_Lam_Input_rep2

description:
H3K27me3_LamI2
H3K27me3_LamI2_ATCACG

value: 6-8 weeks old

value: ATCACG


title: Diffuse Large B-cell Lymphoma patient DLBCL_082

tag: diagnosis

value: Diffuse Large B-cell Lymphoma

value: tumor specimen


title: H3K27ac_Lam_ChIP_rep1

description:
H3K27ac_Lam1
H3K27ac_Lam1_CTTGTA

tag: tissue

value: Dorsal Root Ganglia (DRG)

value: CTTGTA


title: Diffuse Large B-cell Lymphoma patient DLBCL_083


title: H3K27ac_DCA_ChIP_rep1

description:
H3K27ac_DCA1
H3K27ac_DCA1_GATCAG

value: GATCAG


title: H3K27ac_SNA_ChIP_rep2

description:
H3K27ac_SNA2
H3K27ac_SNA2_GTCCGC

value: GTCCGC


title: Diffuse Large B-cell Lymphoma patient DLBCL_084


title: Diffuse Large B-cell Lymphoma patient DLBCL_081


title: WT2

value: wild type