title: 3044_M0

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform, with the 30 samples pooled and then sequenced across 8 consecutive lanes of a flow cell. Reads from all lanes were then combined for each sample.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the human GRCh38 genome assembly including ERCC spike-ins using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.45.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
GRCm38
Read count quantitation file was generated by counting reads using Rsubread, followed by vsd normalised using ‘varianceStabilzingTransformation’ within DESeq2 package. Row names are Ensembl_IDs, with each sample included as columns

source_name: Blood

extract_protocol:
PBMCs were isolated at the Ifakara Health Institute by density gradient centrifugation, cryopreserved in liquid nitrogen and shipped to the Babraham Institute where the PBMC were thawed and rested for 2 hours at 37 degrees C. Cell number and viability were measured using a Nucleocounter (NC-3000, Chemometec). Samples with low viability (<50% live cells) were discarded.
Peripheral blood mononuclear cells from Tanzanian children at B0 and B32 post thaw were stored in RNA-later. RNA from samples with high viability (>90%), sufficient cell number (>3x10^6 cells) were isolated using RNeasy plus Mini kit (Qiagen). Samples with high RNA quality (RIIN >7) were used
Libraries were generated from samples with high RNA quality (RIIN >7) using TruSeq Stranded mRNA Library prep (Illumina) by Eurofins.

tag: timepoint

value: peripheral blood mononuclear cells

value: Blood


title: HCC1954_HiC

status: Public on Feb 05 2020

type: SRA

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
library strategy: HiC-seq
Hi-C libraries were sequenced on a NextSeq 500 or a HiSeq 4000. Reads were aligned to the hg19 reference genome using BWA-MEM, and PCR duplicates were removed with Picard.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C interaction matrices were generated using 40kb as window size, and matrices were normalized using the iterative correction method (Imakaev et al., 2012). Sparse matrices represent the normalized contact frequency between two interacting genomic loci. Genomic coordinates of the bin numbers can be found in hg19_40kb.txt file.

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast cancer cell line

extract_protocol:
Hi-C was performed using the in situ Hi-C protocol as previously described in Rao et al., 2014, using 2-5 million cells per experiment digested with the MboI restriction enzyme.
The libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq LT adaptors.

tag: cell line

tag: cell type

value: Breast cancer cell line


title: 3085_M0

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: CXCR2 KOPit C Rep3

city: Montpellier

first: Gwendal

last: Lazennec

address: 1682 rue de la valsiere

country: France

institute: CNRS

data_processing:
Raw sequencing data was quality-controlled with the FastQC program. Low quality reads were trimmed or removed using Trimmomatic (minimum length: 40 bp).
Reads were aligned to the mouse reference genome (mm10 build) with the TopHat2 tool (option for no multihits).
Mapping results were quality-checked using RNA-SeQC. Gene counts were obtained by read counting software featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: csv files

organism: Mus musculus

source_name: Pituitary

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

tag: strain

value: BALB/c

tag: age

value: 12 weeks

tag: genotype

value: CXCR2 KO

tag: housing

value: Conventional


title: Tet-hammerhead-13, 25 uM Tetracycline, rep 5

city: Biberach an der Riß

first: Holger

last: Klein

state: Baden-Württemberg

address: Birkendorfer Straße 65

department: Global Computational Biology and Data Sciences

country: Germany

institute: Boehringer-Ingelheim Pharma GmbH & Co KG

data_processing:
Basecalls performed using bcl2fastq2/2.17.1.14
Reads were search for the expected amplicon patterns
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample. Fields represent: [abundance] [amplicon_sequence_name] [amplicon_variable_part1] [amplicon_variable_part2]

source_name: HEK293 cell line

growth_protocol: HEK-293 cells were grown in DMEM + 10 % FCS at 37°C in an incubator. 24 h prior to transfection, 310.000 cells were seeded per well of a 12-well plate.

extract_protocol:
RNA was extracted using the Qiagen RNeasy 96 kit.
Following random priming-based reverse transcription to cDNA, sequence amplicons of interest were generated by non-saturating PCR and PCR amplicons were purified. DNA concentration was determined on the Fragment Analyzer with NGS StandardSensitivity according to manufacturer’s instructions. Subsequently, end repair was carried out using the Ovation Library System for Low Complexity Samples kit (NuGEN) with the manufacturer’s protocol, followed by adaptor ligation from the same kit. The libraries underwent cleanup again using the MagMAX Express-96 Magnetic Particle processor and the Agencourt RNAClean XP beads (Beckmann Coulter) following the manufacturer’s protocol. Subsequently, library amplification was carried out using the Ovation Library System for Low Complexity Samples kit (NuGEN) with manufacturer’s protocol, followed by a clean-up step with Agencourt AMPure XP Beads (Beckmann Coulter). The libraries were quantified with a Quant-iT PicoGreen dsDNA Assay kit (Invitrogen) according to manufacturer’s instructions and fragment size was determined with NGS Standard Sensitivity Kit (Advanced Analytical) on a Fragment Analyzer. Based on the concentrations obtained from the PicoGreen measurement, a 2 nM dilution of the libraries in Illumina Resuspension Buffer + 0.1% Tween20 preparation (Sigma) was prepared and in the following 10 µl of each sample were mixed with a unique reverse adaptor from the 2 nM dilution. Libraries were denatured by consecutive addition of 10 µl 0.2 N NaOH, µl of 200 mM Tris-HCl, pH 7.0 and 970 µl of prechilled HT1 buffer. In a new prechilled tube, 1183 µl of prechilled HT1 buffer were added. Subsequently 117 µl of the library pool dilution and 2 µl of 20 pM PhiX control were added. Finally, the libraries were sequenced on an Illumina NextSeq 500, using 10 million single-end reads of 154 bp length  per sample, using the NextSeq 500/550 High Output Kit v2.

treatment_protocol: Cells were transfected with 600 ng of DNA (plasmid library) per well, using Lipofectamine-3000 and incubated for 48 h. Cells were then stimulated with Tetracycline or Guanine at indicated doses for 3 h, before being lysed for RNA extraction.

tag: sample type

value: HEK293 cell lysate

tag: treatment

value: 25 uM Tetracycline


title: CXCR2 KO Pit S Rep3

value: SOPF


title: WT Pit C Rep3

value: WT


title: CXCR2 KO Pit C Rep2


title: WT Pit C Rep2


title: WT Pit S Rep3


title: Tet-hammerhead-4, untreated, rep 4

value: untreated


title: 2982_M0


title: CXCR2 KO Pit S Rep1


title: Tet-hammerhead-5, untreated, rep 5


title: 2965_M32


title: 2989_M0


title: WT Pit S Rep1


title: WT Pit S Rep2


title: WT Pit C Rep1


title: 2943_M32


title: CXCR2 KOGM C Rep3

source_name: Mammary gland


title: 2936_M0


title: CXCR2 KO GM C Rep2


title: CXCR2 KO GM C Rep1


title: 3025_M32


title: 2893_M32


title: 2895_M32


title: 2898_M0


title: WT GM C Rep2


title: CXCR2 KO Pit S Rep2


title: 2895_M0


title: 2893_M0


title: 2880_M0


title: WT GM C Rep1


title: WT GM C Rep3


title: CXCR2 KO GM S Rep3


title: CXCR2 KO GM S Rep2


title: 2873_M0


title: CXCR2 KO GM S Rep1


title: CXCR2 KO Pit C Rep1


title: 2876_M0


title: WT GM S Rep1


title: WT GM S Rep2


title: WT GM S Rep3


title: 2863_M32


title: 2849_M0


title: 2856_M0


title: 2817_M32


title: 2826_M32


title: 2764_M0


title: Pooled Gua-HDV and Gua-hammerhead-screen-8, untreated, rep 8


title: 2758_M0


title: 2758_M32


title: 2718_M0


title: 2750_M0


title: 2715_M0


title: 2852_M0


title: High ARID3A and High ARID3B 2

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
The raw RNA Seq data were mapped to Human HG19 genome using STARv2.0 at default parameters
Expression abundances were measured in FPKM (Fragments per Kilo base per Million reads) was done in Cufflinks program
Differential expression analysis was done using DESEQ
Genome_build: HG19
Supplementary_files_format_and_content: FPKM and DESEQ results in xls format

source_name: OVCA433 cells

growth_protocol: OVCA433 cells were grown at 37°C with 5% CO2 in Minimal Essential Medium (MEM);. Media was supplemented with 10% fetal bovine serum (FBS) (Atlas, Ft. Collins, CO), 0.1 mM L-glutamine, 1mM sodium pyruvate, 50 U/mL penicillin, and 50 μg/mL streptomycin.

extract_protocol:
RNA was collected using RNAeasy kit (Qiagen) according to manufacturer's instructions.
RNA-seq libraries were prepared at the University of Notre Dame Genomics and Bioinformatics Core Facility. Total RNA samples were diluted 5 times prior to analysis.  Sample concentration was measured using Qubit RNA HS Assay Kit (PN: Q32855; Invitrogen, Carlsbad, CA, USA). Total RNA evaluate with Agilent Bioanlayzer 2100 System and Agilent RNA 6000 Nano Kit (PN: 5067-1511; Agilent Technologies, Santa Clara, CA, USA). Samples with an RNA Integrity Number (RIN) of 7 or higher were qualified for library preparation. Sample 2 and Sample 4 with RIN of 6.9 were included in the study. Total RNA input was normalized to 150 ng. Polyadendylated RNA molecules were selected for using NEBNext Poly(A) mRNA Magnetic Isolation Module (PN: E7490S/L; New England BioLabs, Ipswich, MA, USA).  Enriched polyadendylated RNA was converted into an Illumina library using NEBNext Ultra II RNA Library Prep with Sample Purification Beads (PN: E7775S/L; New England BioLabs, Ipswich, MA, USA) and barcoded with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (PN: E7335S/L; New England BioLabs, Ipswich, MA, USA) or NEBNext Multiplex Oligos for Illumina (Index Primers Set 2) (PN: E7500S/L; New England BioLabs, Ipswich, MA, USA). Indexed libraries were quantitated with Qubit dsDNA HS Assay Kit (PN: Q32854; Invitrogen, Carlsbad, CA, USA). Library quality assessment with Agilent DNA 7500 Kit (PN: 5067-1506; Agilent Technologies, Santa Clara, CA, USA). The individual libraries were normalized, and equal molar amounts were multiplexed into a single pool.  Molar concentration of the multiplex pool was determined with KAPA Library Quantification Kits for Illumina (PN: KK4824; KAPA Biosystems, Boston, MA, USA). Materials used:
NEBNext Ultra II RNA Library Prep with Sample Purification Beads (PN: E7775S/L; New England BioLabs, Ipswich, MA, USA), NEBNext Poly(A) mRNA Magnetic Isolation Module (PN: E7490S/L; New England BioLabs, Ipswich, MA, USA), NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (PN: E7335S/L; New England BioLabs, Ipswich, MA, USA), NEBNext Multiplex Oligos for Illumina (Index Primers Set 2) (PN: E7500S/L; New England BioLabs, Ipswich, MA, USA), Agilent RNA 6000 Nano Kit (PN: 5067-1511; Agilent Technologies, Santa Clara, CA, USA). Agilent DNA 7500 Kit (PN: 5067-1506; Agilent Technologies, Santa Clara, CA, USA), Qubit RNA HS Assay Kit (PN: Q32855; Invitrogen, Carlsbad, CA, USA), Qubit dsDNA HS Assay Kit (PN: Q32854; Invitrogen, Carlsbad, CA, USA), and KAPA Library Quantification Kits for Illumina (PN: KK4824; KAPA Biosystems, Boston, MA, USA).

treatment_protocol: Cells were lentivirally transduced with ARID3A-GFP (Genecopia, Rockville, MD), ARID3B (Genetarget), both ARID3A and ARID3B, GFP (Gentarget), Red Fluorescent Protein (RFP) (Gentarget), or both RFP and GFP.   Fluorescence activated cell sorting (FACS) was conducted to isolate GFP, RFP, or cells with both RFP and GFP.

value: OVCA433 cells

value: Ovarian cancer cell line

tag: genotype/variation

value: High ARID3A and High ARID3B


title: High ARID3A and High ARID3B 3


title: High ARID3A and High ARID3B 1


title: High ARID3A and Low ARID3B 2

value: High ARID3A and Low ARID3B


title: 2776_M0


title: High ARID3A and Low ARID3B 1


title: Low ARID3A and High ARID3B 3

value: Low ARID3A and High ARID3B


title: 2708_M0

value: peripheral blood mononuclear cells


title: Low ARID3A and High ARID3B 2


title: Low ARID3A and High ARID3B 1


title: ARID3B + RFP 3

value: ARID3B + RFP


title: ARID3B + RFP 2


title: High ARID3A and Low ARID3B 3


title: ARID3B + RFP 1


title: ARID3A - GFP 3

value: ARID3A - GFP


title: ARID3A - GFP 2


title: B16-OVA tumor_4570_MEKi+CD40-3

type: RNA

city: Heidelberg

first: Michael

last: Volkmar

state: BW

address: Im Neuenheimer Feld 280

department: D200 Molecular Oncology of Gastrointestinal Tumors

institute: German Cancer Research Center (DKFZ)

description: Gene expression data from tumor biopsy

hyb_protocol: After fragmentation, 11ug of cRNA were hybridized for 16h to the Affymetrix mouse 430 2.0 Gene Chip® array (GPL1261).

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data was exported as cell intensity (CEL) files and analyzed using Chipster (Kallio et al., 2011; BMC Genomics 12, 507, doi:19.1186/1471-2164-12-507). After quality control, samples were normalized by applying the Robust Multichip Averaging (RMA) normalization method.

label: biotin

source_name: B16-OVA whole tumor, snap frozen, RNA isolated from tumor

label_protocol: Labeling was performed by the DKFZ's Genomics and Proteomics Core Facility using 200ng total RNA (RIN=>8.0) with  a GeneChip™ 3’IVT Plus Reagent Kit (Affymetrix).

growth_protocol: Murine tumor cell lines were passaged at least four times after thawing and grown as a monolayer with a maximal confluency of 70-80%. Cells were detached using 0.25% trypsin-EDTA solutions, centrifuged and washed once with cell culture medium. 0.5 x 10^5 B16-OVA tumor cells were injected in PBS/Matrigel (1:1, Corning) subcutaneously into the flank of six to twelve weeks old C57BL/6-Ly5.1 mice. Tumor growth was measured twice a week with a caliper. The tumor volume was calculated by multiplying length by width by height.

extract_protocol: Tumor material was homogenized in RLT buffer (Qiagen) supplemented with beta-mercaptoethanol with 2.8 mm steel beads (Precellys) using a tissue homogenizer (TissueLyzer sample disrupter, Qiagen) at 30 Hz, 30 sec for 3 times. Subsequent RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions with on-column DNase I digestion. Amount of isolated RNA was measured using a Nanodrop spectrophotometer, while RNA quality was determined using a Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated daily with 30 mg/kg GDC-0623 or vehicle solution (MCT) for approximately two weeks. Anti-CD40 and control Ab were administered intraperitoneally on treatment days 3, 5, 7 as well as 1 day prior to biomarker analyses. Four mice per treatment group were sacrificed at the end of the MEK inhibitor treatment and subjected to whole transcriptome analyses (day 18 after tumor inoculation).

value: Whole tumor

tag: treatment groups

value: MEKi+CD40 mIgG1

tag: treatment period

value: Mice were treated daily with 30 mg/kg GDC-0623 or vehicle solution (MCT) for two weeks. Anti-CD40 and control Ab were administered intraperitoneally on treatment days 3, 5, 7 as well as 1 day prior to biomarker analyses. Four mice per treatment group were sacrificed at the end of the MEK inhibitor treatment and subjected to whole transcriptome analyses (day 18 after tumor inoculation).


title: B16-OVA tumor_3137_MEKi+CD40-2

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4586_MEKi-2

description: Gene expression data from tumor biopsy

value: MEKi+control IgG


title: ARID3A - GFP 1


title: B16-OVA tumor_4594_CD40-2

description: Gene expression data from tumor biopsy

value: Vehicle+CD40 mIgG1


title: B16-OVA tumor_1332_MEKi+CD40-1

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4619_MEKi-3

description: Gene expression data from tumor biopsy


title: RFP + GFP 3

value: RFP + GFP


title: RFP + GFP 2


title: B16-OVA tumor_4582_MEKi+CD40-4

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4608_Ctrl-3

description: Gene expression data from tumor biopsy

value: Vehicle+control IgG


title: B16-OVA tumor_4622_MEKi-4

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_3133_MEKi-1

description: Gene expression data from tumor biopsy


title: B16-OVA tumor 4593_Ctrl-2

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4573_Ctrl-1

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4584_CD40-1

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4632_CD40-4

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4609_Ctrl-4

description: Gene expression data from tumor biopsy


title: B16-OVA tumor_4621_CD40-3

description: Gene expression data from tumor biopsy


title: 16_ATVr1

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the Fluidic Station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing:
The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.
RMA normalization is performed using Partek software with Affymetrix CDF file.

source_name: ATVr Treatment

label_protocol: 600 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

extract_protocol: RNA kit Macherey Nagel

treatment_protocol: Cells were treated with/without DMSO 0.1% or with the drugs dissolved in DMSO for 15 days.

value: Coronary endothelial cells

value: ATVr


title: 17_ATVr2


title: RFP + GFP 1

value: OVCA433 cells


title: EFO-21_prexasertib_resistant, biological rep2

city: Indianapolis

first: Ricardo

last: Martinez

state: IN

address: 307 E Merrill St

institute: Eli Lilly and Company

data_processing:
The sequencing and basecalling was performed by WuXi NextCode Genomics Inc. (China).
RNAseq data were subjected to an alignment and QC pipeline developed at Eli Lilly and Company. Briefly, pre-processed FASTQ files were aligned to GRCh37/hg19 human reference genome using the GSNP alignment algorithm. Then base quality/base composition, heterologous organism contamination, adapter content, mapping rate/mapped read counts, 3′ bias, template length, and rRNA/mitochondrial content were checked.
The aligned data were subjected to a “rollup” pipeline developed at Eli Lilly and Company for gene expression measurement. First, exon reads of multiple assays from the same libraries were aggregated. Then exons with less than 10 reads in more than 80% of samples were excluded. The gene expression was determined using a robust linear model based on all exon and junction reads. Last, quantile normalization was performed for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file includes quantile-normalized Log2 gene expression values from "rollup" pipeline for each sample.

extract_protocol:
Total RNA was extracted using Direct-zol RNA kit (Zymo Research)according to the manufacturer's instructions.
The cDNA library was generated using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA)

treatment_protocol: The prexasertib resistant lines were generated through a long-term drug concentration escalation protocol.

value: Ovarian cancer cell line

tag: phenotype


title: EFO-21_prexasertib_resistant, biological rep3


title: EFO-21_prexasertib_resistant, biological rep1


title: 13_DRVr1

source_name: DRVr Treatment

value: DRVr


title: 15_DRVr3


title: OVSAHO_prexasertib_resistant, biological rep2

value: OVSAHO


title: OVSAHO_prexasertib_resistant, biologica rep3


title: 14_DRVr2


title: Kuramochi_prexasertib_resistant, biological rep3

value: Kuramochi


title: Kuramochi_prexasertib_resistant, biological rep2


title: OVSAHO_prexasertib_resistant, biological rep1


title: 12_DTGMVC3

source_name: DTG + MVC Treatment

value: DTG + MVC


title: OV-90_prexasertib_resistant, biological rep3


title: 11_DTGMVC2


title: OV-90_prexasertib_resistant, biological rep2


title: OV-90_prexasertib_resistant, biological rep1


title: EFO-21_parental, biological rep3

value: parental


title: 9_Control_HEV_N503_N701 Ctrl HEV 36 35.9 1.98 1.21355964424034

city: South San Francisco

first: Shannon

last: Turley

state: California

address: 1 DNA Way, Building 15, MS 231b

department: Cancer Immunology

institute: Genentech

data_processing: Reads were aligned to the mm9 reference genome using Genentech internal alignment tool, GSNAP. Gene models were from our internal database. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: libraries were generated after FRC and HEV were FACS sorted from murine peyers patches from unperturbed animals or those in which PEG was administered to mice through ad libitum through drinking at a concentration of 10% (w/v).

extract_protocol: For each mouse, 1,000 PP FRCs or HEV ECs were sorted into 5 ml/well of TCL (Qiagen #1031576) buffer containing 1% 2-mercaptoethanol. RNA was isolated using RNAClean XP beads (Agencourt A63987). Template switching, cDNA synthesis and cDNA amplification were adapted from previous studies41. Libraries were prepared using the Nextera kit (Illumina).  Libraries were sequenced using an Illumina HiSeq yielding, on average, 27.5 million reads pairs per sample. RNA-sequencing data were analyzed using HTSeqGenie package in BioConductor42 as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed. The reads that passed were then aligned to the reference genome GRCh37 using GSNAP43. 1.6 - 4.3 % reads were of low quality and were removed. The percentage rRNA contamination ranged from 1.16 - 4.64 %. These were also removed. Reads that were uniquely mapped were used for subsequent analysis.

tag: samid

value: Ctrl

value: HEV


title: EFO-21_parental, biological rep2


title: 9_MVC3

source_name: MVC Treatment

value: MVC


title: 10_DTGMVC1


title: 6_DTG3

source_name: DTG Treatment

value: DTG


title: 5_DTG2


title: 1_Ctrl1

source_name: DMSO Treatment

value: DMSO


title: 8_MVC2


title: 7_PEG_HEV_N504_N703 PEG HEV 35.8 34.6 5.01 0.862407809526633

value: PEG


title: 7_MVC1


title: 2_Ctrl2


title: 3_Ctrl3


title: 6_Control_FRC_N504_N702 Ctrl FRC 35.8 34.5 5.41 0.867229286124785

value: FRC


title: Kuramochi_prexasertib_resistant, biological rep1


title: OVSAHO_parental, biological rep3


title: EFO-21_parental, biological rep1


title: OVSAHO_parental, biological rep1


title: OVSAHO_parental, biological rep2


title: 2_PEG_FRC_N503_N702 PEG FRC 36.1 36 1.6 1.31144937859286


title: 4_Control_FRC_N503_N704 Ctrl FRC 36.1 36.1 1.41 1.20725495768112


title: Kuramochi_parental, biological rep3


title: Kuramochi_parental, biological rep1


title: Kuramochi_parental, biological rep2


title: 8_Control_HEV_N504_N704 Ctrl HEV 35.8 35 3.87 1.09671291835454


title: OV-90_parental, biological rep2


title: 4_DTG1


title: 5_Control_FRC_N504_N701 Ctrl FRC 35.8 34.7 4.53 0.996325441554236


title: 23_PEG_HEV_N504_N703 PEG HEV 36.3 35.2 3.64 1.0274412262192


title: 24_Control_HEV_N504_N704 Ctrl HEV 36.3 35.3 3.5 1.02788710231373


title: 22_PEG_HEV_N504_N702 PEG HEV 36.3 35.2 3.86 0.89128673667776


title: OV-90_parental, biological rep1


title: 21_Control_FRC_N504_N701 Ctrl FRC 36.3 35.3 3.45 1.16121577318446


title: 3_PEG_FRC_N503_N703 PEG FRC 36.1 36 1.51 1.14447381228495


title: 20_Control_FRC_N503_N704 Ctrl FRC 36.1 36.1 1.86 1.07828463020377


title: 1_PEG_FRC_N503_N701 PEG FRC 36 36 1.5 1.50036304627581


title: 18_PEG_FRC_N503_N702 PEG FRC 36.1 36 2.07 1.21297140652186


title: Adult_heart_1

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

country: China

institute: Peking University

description: PolyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling. Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the human reference genome (hg19) using Tophat software.
We quantified the relative expression level as log2(FPKM + 1) to perform PCA analysis and hierarchical clustering. Uniquely mapped reads counted by HTSeq were used to conduct differential-expression analysis in DEseq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_expression_FPKM.txt: Tab-delimited text files include the FPKM values of RefSeq genes.

source_name: Adult normal heart

growth_protocol: Human iPSCs 253G1 derived cardiomyocytes cultured in medium.

extract_protocol:
Total RNA in tissue was harvested using Trizol reagent (Life Technologies) according to manufacturer instructions. The purified mRNAs were used to construct the cDNA library with the NEB RNA library construct kit. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.
A total of 1.5 μg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using a NEBNext UltraTM RNA library prep kit Illumina (New England Biolabs, Ipswich, MA, USA) according to manufacturer instructions, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and fragmentation was performed using divalent cations under an elevated temperature in NEBNext First Strand Synthesis reaction buffer (5×; New England Biolabs). First-strand cDNA was synthesized using a random hexamer primer and M-MuLV reverse transcriptase (RNase H−; New England Biolabs). Second-strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptor (New England Biolabs) with a hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of the correct length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, MA, USA), after which 3 µL USER enzyme (New England Biolabs) was incubated with size-selected, adaptor-ligated cDNA at 37°C for 15 min, followed by 5 min at 95°C. PCR was performed using a Phusion high-fidelity DNA polymerase, universal PCR primers, and an Index (X) primer (New England Biolabs). Products were purified (AMPure XP; Beckman Coulter), and library quality was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies).

treatment_protocol: The cardiomyocytes were cultured for 14 day with or without traveling wave.

value: Adult normal heart (R1234122-P)


title: 16_PEG_HEV_N504_N704 PEG HEV 36.1 35.2 3.88 0.214978289435977


title: 14_PEG_HEV_N504_N702 PEG HEV 36.1 35 3.84 1.35346526240881


title: OE33_HiC

source_name: Esophegeal adenocarcinoma cell line

value: Esophegeal adenocarcinoma cell line


title: 12_Control_FRC_N503_N704 Ctrl FRC 36 36 1.91 1.28576659524935


title: SW480_HiC-Rep2

data_processing:
Hi-C libraries were sequenced on a NextSeq 500 or a HiSeq 4000. Reads were aligned to the hg19 reference genome using BWA-MEM, and PCR duplicates were removed with Picard.
Hi-C interaction matrices were generated using 40kb as window size, and matrices were normalized using the iterative correction method (Imakaev et al., 2012). Sparse matrices represent the normalized contact frequency between two interacting genomic loci. Genomic coordinates of the bin numbers can be found in hg19_40kb.txt file.
Genome_build: hg19
Supplementary_files_format_and_content: the normalized contact frequency between two interacting genomic loci.

value: Colon cancer cell line


title: 11_PEG_FRC_N503_N703 PEG FRC 36 35.9 1.95 1.14857164866475


title: perfect_cured_T14_rep2

city: Stanford

first: Anupam

middle: K.

last: Chakravarty

state: CA

address: 269 Campus Dr, CCSR3120

department: Chemical & Systems Biology

institute: Stanford University

description:
oligo dT enrichment
12Perfect-cured-diploid-C-CTTGTA_S12

data_processing:
fastq files were pseudo-aligned to version (S288C_reference_genome_R64-2-1_2015011) of budding yeast reference genome using kallisto package and default settings.
Genome_build: S288C_reference_genome_R64-2-1_20150113
Supplementary_files_format_and_content: tab-delimited text files include counts and transcripts per million (tPM) values for each gene in each Sample

organism: Saccharomyces cerevisiae

source_name: culture in SPO media for 14h

growth_protocol: 10 ml of cells were grown to saturation in preSPO medium for 48 hours; 5 ml culture was harvested as preSPO sample; rest 5 ml was put into SPO medium and harvested afrer 14 h for SPO sample.

extract_protocol:
RNA extraction was performed using standard kits.
Library construction was performed using standard kits (oligo dT based mRNA  was conducted).

treatment_protocol: preSPO and SPO samples were collected as specified. selective curing was as decribed in citation.

tag: strain background

value: wild-type

value: selective curing of [SMAUG+] (SPO medium)


title: SW480_HiC

source_name: Colon cancer cell line


title: SW480_HiC-Rep1


title: 18_ATVr3

value: Coronary endothelial cells

value: ATVr


title: 15_PEG_HEV_N504_N703 PEG HEV 36.2 35.1 3.51 1.4373851801718


title: 13_Control_FRC_N504_N701 Ctrl FRC 36.1 35.1 3.77 1.33824020767593


title: 17_Control_HEV_N503_N701 Ctrl HEV 36.1 36 1.93 1.0029051360583


title: natSMAUG+_T14_rep2

description:
oligo dT enrichment
9BY4743-C-GATCAG_S9

value: untreated (SPO medium)


title: perfect_cured_T0_rep2

description:
oligo dT enrichment
6Perfect-cured-diploid-C-GCCAAT_S6

source_name: culture in preSPO media for 48h

value: selective curing of [SMAUG+] (preSPO medium)


title: 10_PEG_FRC_N503_N702 PEG FRC 36.1 35.9 2.08 1.21504841282204


title: perfect_cured_T0_rep1

description:
oligo dT enrichment
4Perfect-cured-diploid-A-TGACCA_S4


title: perfect_cured_T14_rep1

description:
oligo dT enrichment
10Perfect-cured-diploid-A-TAGCTT_S10


title: natSMAUG+_T14_rep1

description:
oligo dT enrichment
7BY4743-A-CAGATC_S7


title: KO_SIorg_3

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.0.3 (no soft clipping,--no-mixed --no-discordant)
BAM files were imported into Seqmonk v1.42.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

source_name: small intestine

growth_protocol:
organoid generation protocol: Small intestinal crypts were derived from mice where Smarcad1 had been deleted in very early development in all cells using ZP3-cre and control litter mates as described by Kuehbacher, T. et al. (2008) with minor modifications. Small intestines were collected and opened longitudinally. The villus content was removed by scraping the intestine with a coverslip and by shaking the samples vigorously in cold PBS. The intestines were then incubated at 4ᵒC in PBS containing EDTA 2 mM for 30 min and in PBS with 5 mM EDTA for another 30 minutes, shaking the samples in between to separate the crypts from the connective tissue. Large material was removed by passing the supernatant through a 40 μm cell strainer. 100-200 small intestinal crypts were suspended in cold liquid Matrigel and incubated at 37ᵒC for 15 minutes for Matrigel polymerization. After that, complete ENR medium containing advanced DMEM/F12 (Sigma), 2 mM Glutamax (Invitrogen), 10 mM HEPES (Gibco), 100 U ml-1 penicillin/streptomycin (Invitrogen), 1 mM N-acetyl-cystein (Sigma), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 50 ng ml-1 mouse EGF (Peprotech), 100 ng ml-1 mouse Noggin (Peprotech) and 10% human R-spondin-1-conditioned medium from R-spondin-1-transfected HEK 293T cells was added to the cultures.
Media was replaced every 2 days. For the organoid passages, after 7 days of culture, Matrigel was mechanically disrupted with a P1000 pipette tip and cold media was added to help it to depolymerize. The organoids were broken into small fragments by pipetting them up and down several times using a P200 pipette. Organoid fragments were pelleted using centrifugation at 1500 rpm for 5 minutes at 4ᵒC to wash away the old Matrigel and debris. The organoid fragments were re-suspended in cold liquid Matrigel (50% Matrigel and 50% complete ENR medium) and reseeded as described above.

extract_protocol:
After 5 days, organoids were collected for RNA extraction. For RNA sequencing, total RNA was extracted from approximately 600 organoids per condition using TRIzol Reagent (Invitrogen), following the manufactorer’s directions. DNA contamination was removed using the DNA-free DNA Removal kit (ThermoFisher). From the total RNA, poly(A)+ RNA was selected using NEBNext Oligo d(T)25 beads (NEB) according to the manufactorer’s. All RNA samples were precipitated and resuspended in water in order to increase the purity.
Directional libraries were generated from 500 ng total RNA according to NEBNext Ultra directional RNA library Prep kit for Illumina. Libraries were sequenced on an Illumina HiSeq as 50 bp Paired End reads.

value: Vil-Cre mediated KO

value: organoid culture


title: natSMAUG+_T0_rep2

description:
oligo dT enrichment
3BY4743-C-TTAGGC_S3

value: untreated (preSPO medium)


title: KO_SIorg_2


title: 19_PEG_FRC_N503_N703 PEG FRC 36.1 36.1 1.61 1.16291164693046


title: KO_SIorg_1


title: WT_SIorg_2

value: wild type


title: WT_SIorg_3


title: 48hr control 4

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description:
Bulk_seq
DT_Bulk_umitab.txt.gz

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2))
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached). Pooled samples analyzed with laser capture microdissection were demultiplexed once based once to separate the pooled samples.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Jejunum epithelial cells

growth_protocol: C57bl6 male mice were fed regular chow ad libitum

extract_protocol:
Isolation of telocytes was performed as previously decribed (Shoshkes-Carmel, M. et al. Nature 2018).
for scRNAseq, 3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014). For bulk analysis, mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018). For LCM bulk analysis SMARTseq v4 Ultra Low Input RNA Kit (Clontech, 634888) was used

treatment_protocol: Mice were sacrificed by cervical dislocation

value: post natal four months

value: Jejunum

tag: sequencing protocol

value: mcSCRBseq

tag: barcode

value: Read 1 contains UMI (bp 1-10)


title: KO_enriched_08

description:
16S_Amplicon_OTU_shared_by_cohort.xls
16S_Amplicon_OTU_shared_by_sample.xls
16S_Amplicon_OTU_taxonomy.xls
16S_Amplicon_report.pdf

data_processing:
Libraries were sequenced on the Illumina HiSeq platform by BGI Hong Kong.
low-quality, N-rich or adaptor-polluted reads prefiltered according to BGI Hong Kong standard procedure
paired-end merging to tags
Tags were assigned to operational taxonomic units (OTU) at 97% similarity threshold
Taxonomic ranks were assigned with the Ribosomal Database Project (RDP) Naïve Bayesian Classifier v.2.2
α- and β-diversity were analysed based on OTUs and their taxonomic ranks
Supplementary_files_format_and_content: OTU-overlap tables by sample/cohort, OTU taxonomic information, detailed bioinformatic report

source_name: murine stool

extract_protocol:
Fresh stool samples were collected and frozen on dry ice.
16S-Amplicon libraries were generated from stool samples by BGI Hong Kong. Libraries were sequenced on the Illumina HiSeq platform as 250bp Paired End reads.

treatment_protocol: microbiome enrichment: Enriched microbiota was provided for 28 days by bedding transfer and co-ventilation with the donor C57BL/6 females obtained from an SPF facility in York.

value: stool sample

tag: molecule

value: metagenome DNA, 16S Amplicon


title: 48hr control 2

description:
Bulk_seq
DT_Bulk_umitab.txt.gz

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2))
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached). Pooled samples analyzed with laser capture microdissection were demultiplexed once based once to separate the pooled samples.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Telocytes_sc_umitab.zip: single cell expression matrix; column header includes cell#_cell_BC_plate_name in the column headers
LCM_tpm_gene.zip: LCM_expression matrix
DT_Bulk_umitab.zip: expression matrix of DT bulk experiment
marsseq_cell_barcodes.txt: list of barcodes used for demultiplexing the cells in the single cell RNAseq experiment
mcSCRBseq_samples_barcodes.txt: list of barcods used for demultiplexing the pooled expereiment from the mcSCRBseq


title: 48hr DT 4

description:
Bulk_seq
DT_Bulk_umitab.txt.gz


title: 48hr DT 2

description:
Bulk_seq
DT_Bulk_umitab.txt.gz


title: KO_enriched_04

tag: cell type


title: 48hr control 1

description:
Bulk_seq
DT_Bulk_umitab.txt.gz

tag: tissue


title: KO_enriched_09

tag: strain


title: KO_enriched_10


title: WT_enriched_10


title: WT_SIorg_1


title: 48hr DT 3

description:
Bulk_seq
DT_Bulk_umitab.txt.gz

tag: age


title: Sort301218_m2_PdgfraEpcamDoublets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz

source_name: Jejunum single cells

value: post natal three months

value: MARSseq

value: Read 2 contains the cell barcode (bp 1-7) and UMI (bp 8-15).


title: KO_enriched_03


title: Sort301218_m1_PdgfraSinglets_P7

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort301218_m2_CD45Singlets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: 48hr control 3

description:
Bulk_seq
DT_Bulk_umitab.txt.gz


title: KO_enriched_07


title: KO_enriched_02


title: Sort301218_m2_EpcamSinglets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort301218_m1_TripleNeg_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort301218_m1_PdgfraSinglets_P3

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_enriched_09


title: WT_enriched_08


title: KO_enriched_01


title: natSMAUG+_T0_rep1

description:
oligo dT enrichment
1BY4743-A-ATCACG_S1

value: wild-type


title: Sort301218_m1_PdgfraSinglets_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_enriched_06


title: Sort301218_m2_PdgfraEpcamDoublets_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_enriched_05


title: 48hr DT 1

description:
Bulk_seq
DT_Bulk_umitab.txt.gz


title: WT_enriched_07


title: Sort301218_m1_PdgfraSinglets_P10

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_enriched_06


title: WT_enriched_05


title: Sort301218_m1_CD45Singlets_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort301218_m1_PdgfraSinglets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort250319_m1_PdgfraSingletsPop3_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_enriched_04


title: sort181118_m1_PDGFRaSmall_p1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_enriched_02


title: KO_initial_10


title: Sort250319_m1_PdgfraSingletsPop3_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: sort181118_m1_PDGFRaBig_p4

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_enriched_01


title: KO_initial_09


title: sort181118_m1_PDGFRaBig_p1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort130119_m1_PdgfraSinglets_P3

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_initial_08


title: sort181118_m1_PDGFRaBig_p2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_initial_07


title: Sort130119_m2_PdgfraSinglets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_initial_05


title: sort181118_m1_PDGFRaBig_p3

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort130119_m1_PdgfraSinglets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_initial_04


title: KO_initial_06


title: Sort110219_m1_TripleNeg_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort110219_m1_TripleNeg_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_initial_03


title: WT_enriched_03


title: KO_initial_01


title: WT_initial_09


title: WT_initial_10


title: Sort110219_m1_PdgfraSingletsPop3_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort110219_m1_PdgfraSingletsPop3_P3

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_initial_08


title: WT_initial_07


title: WT_initial_05


title: Sort061218_m1_PdgfraSinglets_P4

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_initial_06


title: Sort061218_m1_PdgfraSinglets_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort061218_m1_PdgfraSinglets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_initial_04


title: Sort061218_m1_Nt5ePdgfraDoublets_P2

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort061218_m1_PdgfraSinglets_P3

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort061218_m1_EpcamPdgfraDoublets_P5

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_initial_01


title: Sort061218_m1_EpcamPdgfraDoublets_P3

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: WT_initial_02


title: donor_3


title: donor_2


title: Sort061218_m1_EpcamPdgfraDoublets_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_initial_02


title: donor_1


title: Sort110219_m1_PdgfraSingletsPop6_P4

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: mouse 5 villus top - rep 8

description:
LCM mouse #5 tip S1
LCM_tpm_gene.txt

source_name: Jejunum-LCM

value: SMARTseq


title: mouse 5 villus center - rep 7

description:
LCM mouse #5 mid S1
LCM_tpm_gene.txt


title: Sort110219_m1_PdgfraSingletsPop3_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: Sort110219_m1_CD31_P1

description:
single_cell
Telocytes_sc_umitab.txt.gz


title: KO_COcr_2

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
They were mapped to the mouse GRCm38 genome assembly using Hisat2 2.0.1 (no soft clipping)
BAM files were imported into Seqmonk v1.42.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

source_name: colon crypt

extract_protocol:
cell isolation protocol: Colons were dissected as described by Kazakevych et al., Nucleic Acids Res. 2017 with extended PBS-EDTA incubation (30 min) and crypt shaking extraction (5 min).
RNA-isolation with the RNeasy Micro kit (Qiagen 74004)
Libraries were generated from 500 ng total RNA according to NEB Ultra Directional RNA Library Preparation Kit for Illumina.

value: CO

tag: isolation type

value: whole crypt


title: mouse 5 villus bottom - rep 8

description:
LCM mouse #5 bottom S1
LCM_tpm_gene.txt


title: KO_COcr_3

value: Vil-Cre mediated KO


title: mouse 4 villus top - rep 7

description:
LCM mouse #4 tip S1
LCM_tpm_gene.txt


title: WT_initial_03


title: mouse 4 villus center - rep 6

description:
LCM mouse #4 mid S1
LCM_tpm_gene.txt


title: WT_COcr_2


title: mouse 4 villus bottom - rep 7

description:
LCM mouse #4 bottom S1
LCM_tpm_gene.txt


title: WT_COcr_1


title: mouse 3 villus center - rep 5

description:
LCM mouse #3 mid S1
LCM_tpm_gene.txt


title: KO_wSI_4

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence and poor quality base calls.
They were mapped to the mouse GRCm38 genome assembly using Hisat2 2.0.1 (no soft clipping)
BAM files were imported to Seqmonk v1.42.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

extract_protocol: 25-100 mg frozen tissue was ground to powder with dry ice in a precooled mortar. After addition of 1ml Trizol, the sample was collected and incubated 5 min at RT. 200 µl Chloroform were added prior vigorous vortexing and centrifugation 20 min at 16,000 g, 4 °C. The upper phase was transferred to 500 µl isopropanol, vortexed and incubated 15 min at RT before centrifuging 10 min at 16,000g, 4°C and removal of supernatant. Next, the RNA was precipitated with 20 µl 3M NaAc pH 5.2 and 400 µl 100% EtOH for 30 min incubation at -20 °C. After centrifugation, the pellet was washed once in 70% EtOH and dried on ice before resuspending in ice cold H2O.

treatment_protocol: cell isolation protocol: The small intestine was cut open longitudionally, washed in PBS to remove faeces and snap frozen in liquid nitrogen.

value: whole tissue


title: mouse 3 villus top - rep 6

description:
LCM mouse #3 tip S2
LCM_tpm_gene.txt


title: WT_COcr_3


title: mouse 3 crypt - rep 5

description:
LCM mouse #3 crypt S1
LCM_tpm_gene.txt


title: mouse 3 crypt - rep 6

description:
LCM mouse #3 crypt S2
LCM_tpm_gene.txt


title: mouse 3 villus bottom - rep 6

description:
LCM mouse #3 bottom S2
LCM_tpm_gene.txt


title: mouse 3 villus bottom - rep 5

description:
LCM mouse #3 bottom S1
LCM_tpm_gene.txt


title: KO_wSI_3


title: KO_wSI_2


title: KO_COcr_1


title: KO_wSI_1


title: WT_wSI_4


title: WT_wSI_1


title: WT_wSI_3


title: WT_wSI_2


title: mouse 2 villus top - rep 4

description:
LCM mouse #2 tip S2
LCM_tpm_gene.txt


title: mouse 2 villus top - rep 3

description:
LCM mouse #2 tip S1
LCM_tpm_gene.txt


title: mouse 2 villus center - rep 4

description:
LCM mouse #2 mid S2
LCM_tpm_gene.txt


title: KO_CO_3

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
They were mapped to the mouse GRCm38 genome assembly using Hisat2 2.1.0 (no soft clipping)
BAM files were imported into Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

extract_protocol:
1-80 thousand ISC, 1-135 thousand TA, 100 thousand AE and 75-100 thousand colon epithelial cells (CO) were sorted per sample into RLT buffer for subsequent RNA-isolation with the RNeasy Micro kit (Qiagen 74004) with on-column DNA digestion.
Libraries were generated from 10 ng total RNA according to NEB Ultra II Directional RNA Library Preparation Kit for Illumina (E7760), Poly(A) mRNA magnetic isolation module (E7490) and multiplex oligos (E7335, 7500) manuals with the following modifications: RNA was fragmented for 20 min. Adaptor stock was diluted 150x.  15 PCR-amplification cycles were performed. SPRI select beads were substituted with Seramag Speedbeads (Thermo scientific 65152105050250) for size selection steps. Seramag beads were washed with TE buffer and resuspended in 50 volumes of PEG 8000 (Sigma 1546605) with 2.5M NaCl, 10mM Tris-Cl pH 8.0, 1mM EDTA, 0.05% Tween 20. PEG 8000 amounts used were corresponding to 10 and 12 % final PEG concentrations on sample addition. Size selection steps were performed at room temperature, adding the sample topped up to 100 µl with nuclease free water to 80 µl of bead suspension, followed by resuspension by pipetting, incubation for 10 min and precipitation on a magnetic rack. After removal of supernatant (SN), the beads were washed twice with 80% ethanol and moderately dried before elution with TE buffer. The size selection after second strand DNA-synthesis was performed with 12% PEG concentration, the remaining size selections with 10 % PEG. After PCR-amplification the size selection was performed twice (10 % PEG).  Libraries were sequenced on an Illumina HiSeq2500 as HiSeq 50 bp Single End reads.

treatment_protocol:
cell isolation protocol: Small intestines were dissected as described by Kazakevych et al., Nucleic Acids Res. 2017. Colons were dissected by the same protocol with extended PBS-EDTA incubation (30 min) and crypt shaking extraction (5 min).  Single cell material was derived from intestinal crypts by digestion with Dispase II (Sigma D4693, 0.05 mg/ml final concentration), DNase (Qiagen 79254, 20 Kunitz U/ml final concentration) and Collagenase (Sigma C7657, 0.15 mg/ml final concentration), while villus single cells were derived without digestion, by vigorous pipetting only.
flow-sorting protocol: Cell suspensions for RNA-seq were stained and flow-sorted: Small intestinal villus- and colon crypt-derived cells were stained in 2 % fetal bovine serum (FBS)/PBS with 1:200 APC-conjugated Epcam antibody (CD326, eBioscience 17-5791-82), 1:1000 AF488-conjugated CD45 antibody (Biolegend 103122) and 1:1000 AF488-conjugated CD31 antibody (Biolegend 102414) for 15 minutes at room temperature, washed 3 times and resuspended in 2 % FBS/PBS with 3.2 µg/ml ROCK-inhibitor (Y-27632, Sigma). All cell preparations were stained with 4’,6-diamidino-2-phenylindole (DAPI) prior to sorting. Epcam-high CD31- CD45- DAPI- cells were sorted on BD Aria III SORP cell sorter with a 100 µM nozzle. RNA from ISC (GFP-high DAPI-) and transit amplifying cells (TA, GFP-medium DAPI-) was isolated from single cell crypt suspensions of Lgr5-GFP+ mice and processed as above except the antibody staining step.

value: C57BL/6 Lgr5-GFP


title: KO_CO_2


title: mouse 3 villus top - rep 5

description:
LCM mouse #3 tip S1
LCM_tpm_gene.txt


title: mouse 2 villus center - rep 3

description:
LCM mouse #2 mid S1
LCM_tpm_gene.txt


title: mouse 2 crypt - rep 4

description:
LCM mouse #2 crypt S2
LCM_tpm_gene.txt


title: KO_CO_1


title: mouse 2 crypt - rep 3

description:
LCM mouse #2 crypt S1
LCM_tpm_gene.txt


title: KO_AE_3

source_name: small intestinal villus

value: AE


title: mouse 2 villus bottom - rep 4

description:
LCM mouse #2 bottom S2
LCM_tpm_gene.txt


title: KO_AE_2


title: KO_AE_1


title: mouse 2 villus bottom - rep 3

description:
LCM mouse #2 bottom S1
LCM_tpm_gene.txt


title: KO_TA_3

source_name: small intestinal crypt

value: TA


title: mouse 1 villus center - rep 1

description:
LCM mouse #1 mid S1
LCM_tpm_gene.txt

value: Jejunum


title: KO_ISC_3

value: ISC


title: mouse 1 villus center - rep 2

description:
LCM mouse #1 mid S2
LCM_tpm_gene.txt


title: KO_ISC_2


title: KO_TA_1


title: KO_ISC_1


title: mouse 1 villus bottom - rep 2

description:
LCM mouse #1 bottom S2
LCM_tpm_gene.txt


title: WT_CO_3

value: wild type


title: mouse 1 villus bottom - rep 1

description:
LCM mouse #1 bottom S1
LCM_tpm_gene.txt


title: WT_CO_2


title: AI_wt3 WT, replicate3

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

institute: The Weizmann Institute

description:
WT, replicate3
wild type

data_processing:
Reads were trimmed from their adapter with cutadapt
Alignment to the genome (NCIB 3610, NZ_CM000488.1) was done with Bowtie2 version 2.3.4.1
The number of uniquely mapped reads per gene was calculated with HT-seq
Genome_build: NZ_CM000488.1
Supplementary_files_format_and_content: bam files

organism: Bacillus subtilis

source_name: Biofilms colony

growth_protocol: Biofilms colonies were grown on MSgg solid medium for 24 hours, and colonies (n=3) were collected for RNA extraction.

extract_protocol:
The samples were snap-frozen in liquid nitrogen and stored at -80°C until extraction. Frozen pellets were lysed by incubation with lysozyme (20 mg/ml) for 10 min at 37°C, and RNA was extracted using TRI Reagent (Sigma-Aldrich, T9424) according to the manufacturer’s instructions. RNA levels and integrity were determined by Qubit RNA BR Assay Kit (Life Technologies, Q10210) and Tapestation, respectively.
A total of 5 ug RNA was treated with RiboMinus™ Transcriptome Isolation Kit  (Invitrogen, K155004), according to the manufacturers’ protocols. RNA quantity and quality post-depletion was assessed as described above. RNA-seq libraries were contracted with TruSeq RNA Library Preparation Kit v2 (Illumina RS-122-2001) according to the manufacturer’s instructions. Libraries concentrations and sizes were evaluated as above, and were sequenced as multiplex indexes in one lane using the Illumina NovaSeq1500 platform.
RNA-seq, paired-end


title: mouse 1 crypt - rep 2

description:
LCM mouse #1 crypt S2
LCM_tpm_gene.txt


title: WT_CO_1


title: AI_wt1 WT, replicate1

description:
WT, replicate1
wild type


title: AI_sipW3 delSipW3, replicate2

description:
delSipW3, replicate2
SIPW gene deletion


title: WT_AE_3


title: AI_wt2 WT, replicate2

description:
WT, replicate2
wild type


title: AI_sipW1 delSipW1, replicate1

description:
delSipW1, replicate1
SIPW gene deletion


title: WT_AE_1


title: WT_AE_2


title: WT_TA_3


title: Cd_N_3

city: Chengdu

first: Jinliang

last: Huang

state: Sichuan

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
genome build: http://www.mbkbase.org/Pinku1/
processed data files format and content: tab-delimited text files include FPKM values for each Sample

organism: Populus yunnanensis

source_name: Leaves

growth_protocol: The cutting Yunnan poplar (Populus yunnanensis) plants were selected as the experimental materials in the study.  The P. yunnanensis were obtained from native habitats in Butuo county of Liangshan prefecture Sichuan province in China.Seventy-two healthy cuttings out 15 cm long were sampled from 15 different trees of the wide Yunnan poplar，After sampling, these 72 cuttings were replanted into 24 plastic pots (3 cuttings per pot), and each pot was filled with 15kg of dry soil. A polyethylene disc was placed under each pot to avoid run-off. When the plants reached 20 cm height with average 10-15 leaves, the 24 pots were divided into 3 sets.

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

treatment_protocol: The first one acted as control, the second set was treated with Cd up to a final concentration of 480 mg· kg-1 (480 mg Cd2+·kg -1 dry weight soil) and the third set was treated with Cd and N (up to a final concentration of 480 mg Cd2+·kg-1 and 360 mg N·kg-1 dry weight soil). The method of cadmium treatment was based on the phenomenon of the gradual infiltration of cadmium into soil in nature. A 1.22g CdCl2?2.5H2O and 1.69 g NH4HCO3 (equal to 40 mg Cd2+·kg -1 and 30 mg N·kg-1 dry weight soil) was added to each pot every 5 days. The fourth, fifth and sixth from the apex of each seedling was harvested and immediately kept frozen in -80 °C for subsequent RNA extraction and analysis after 60 d of treatment.

tag: agent

value: leaves

tag: developmental stage

value: 4months seedlings


title: mouse 1 villus top - rep 2

description:
LCM mouse #1 tip S2
LCM_tpm_gene.txt

value: post natal three months


title: mouse 1 villus top - rep 1

description:
LCM mouse #1 tip S1
LCM_tpm_gene.txt


title: WT_TA_2


title: Cd_N_2

value: Cd and N (up to a final concentration of 480 mg Cd2+·kg-1 and 360 mg N·kg-1 dry weight soil).


title: mouse 1 crypt - rep 1

description:
LCM mouse #1 crypt S1
LCM_tpm_gene.txt


title: Cd_N_1


title: WT_ISC_3


title: WT_ISC_2


title: WT_ISC_1


title: Cd_2

value: Cd up to a final concentration of 480 mg· kg-1 (480 mg Cd2+·kg -1 dry weight soil).


title: Cd_3


title: pGAS1:FT ft-10 tsf-1 replicate 4

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

description: 9_020209.pGAS1:FT ft-10 tsf-1

hyb_protocol: After fragmentation, 7.5 ug of ds-cDNA was hybridized for 16 hr at 45C on GeneChip Arabidopsis Tiling 1.0R Array. GeneChips were washed and stained with Fluidics Script FS450_0001 in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing:
Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94. Probe-level data were pre-processed using the RMA algorithm (Irizarry et al., 2003), which involves three steps: (i) background correction – where an error component of the intensities is estimated and eliminated; (ii) quantile normalization – where every slide is normalized to have the same cumulative frequency distribution; and (iii) summarization, using the median polish algorithm – where the median values per probe set, adjusted for slide differences, are calculated. RMA ignores the MM probes. On the basis of an empirical Bayes moderated t-statistic for the contrasts (Smyth, 2004), as implemented in the Bioconductor package limma, P values were calculated and then transformed into false-discovery rates, or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue.
Log2 RMA signals included in processed data

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlins

label_protocol: 1 μg of total RNA was reverse transcribed into cDNA using an oligo(dT)-T7 primer, and was then converted into cRNA and linearly amplified by T7 in vitro transcription reaction using the standard Ambion protocol (MessageAmp aRNA Kit, Ambion). cRNA was then reverse transcribed with random primers to dUTP-containing ds cDNA (WT ds cDNA Synthesis Kit, catalog no. 900813; Affymetrix). Fragmentation and labeling was performed with the GeneChip WT double-stranded DNA Terminal Labeling Kit (catalog no. 900812, Affymetrix)

growth_protocol: Plants were grown under under long day conditions for 9 days and leaves were harvested at ZT16.

extract_protocol: RNA was extracted using the RNA Plant Mini kit, QIAGEN (www1.qiagen.com/). (The amount of total RNA was quantified by NanoDrop).

tag: genotype

value: pGAS1:FT ft-10 tsf-1

value: leaf

value: 9 days old


title: pGAS1:FT ft-10 tsf-1 replicate 3

description: 8_020209.pGAS1:FT ft-10 tsf-1


title: Cd_1


title: Ck_3

value: none, control


title: pGAS1:FT ft-10 tsf-1 replicate 2

description: 7_020209.pGAS1:FT ft-10 tsf-1


title: H3K9me3 KO_input

description:
ChIP-seq_H3K9me3_MACS_peaks_SI
ChIP-seq_H3K9me3_EdgeR_MACS_peaks_SI

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
Reads were mapped to the mouse GRCm38 genome assembly using Bowtie2 (v2.3.2; --no-mixed --no-discordant -X 1200)
BAM files were imported into Seqmonk v1.44.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: MACS peaks (300 bp fragment size, significance threshold 0.00001) annotated with closest gene (distance cutoff 5 kbp). All read counts quantitated as log(2) with a lower limit of 1.0 transformed by matching distributions.
Supplementary_files_format_and_content: Sublist of EdgeR probes with FDR<0.05 KO vs WT, Benjamini-Hochberg correction. MACS peaks (300 bp fragment size, significance threshold 0.00001) annotated with closest gene (distance cutoff 5 kbp). All read counts quantitated as log(2) with a lower limit of 1.0 transformed by matching distributions.

extract_protocol:
Sonication was performed in 180 μl of lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA,1% SDS and protein inhibitors cocktail) in a water-cooled Bioruptor (Diagenode), high power, with 14 cycles with 30 seconds on and 30 seconds off each. The sonicated chromatin was diluted in 810 ul of RIPA buffer containing 0.1% SDS and incubated overnight with protein A/G sepharose Dynabeads previously incubated with the specific antibody for ChIP (H3K9me2 - ab1220 and H3K9me3 - ab8898 Abcam) for 2 hours. For the inputs 3% of the volume for each sample was used. Following incubation, the material was washed 2 times with RIPA buffer low salt (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton-X-100, 0.1 % SDS ) and 2 times with RIPA buffer high salt (containing 500 mM NaCl) and once with TE buffer (10 mM Tris-HCl, 1 mM EDTA). Samples were diluted in 200 μl of elution buffer (20 mM Tris-HCl pH 7.5, 5 mM EDTA and 50 mM NaCl) and treated with 2 μl of RNase (20 mg/ml) for 30 minutes at 37 °C. After, samples was incubated with protein k for 2 hours at 65 °C at 300 rpm. The DNA was extracted with phenol-chloroform protocol.
Libraries were generated from 5 ng total chromatin according to NEBNext UltraII DNA Library Prep kit for Illumina. Libraries were sequenced on an Illumina HiSeq as 100 bp Paired End reads.

treatment_protocol:
Crypt isolation protocol: Small intestines were dissected as described by Kazakevych et al., Nucleic Acids Res. 2017. Whole crypt suspensions were used for further processing.
fixation protocol: The pellet containing crypt cells was resuspended in 1 ml of PBS-1% formaldehyde and fixated for 10 minutes with gentle shaking at room temperature. The reaction was quenched with glycine at a final concentration of 0.125 M for 5 minutes. Cells were pelleted at 2400 g 4 °C for 2 minutes and washed three times with 1 ml of PBS.

tag: genotype/variation

value: Vil-Cre mediated KO of Smarcad1

tag: antibody

value: whole crypt isolate


title: ft-10 tsf-1 replicate 4

description: 6_020209.ft-10 tsf-1

value: ft-10 tsf-1


title: ft-10 tsf-1 replicate 2

description: 4_020209.ft-10 tsf-1


title: wildtype replicate 4

value: Col-0 wild type


title: H3K9me3 KO3

value: H3K9me3 - ab8898 Abcam


title: wildtype replicate 3


title: Ck_1


title: H3K9me3 KO2


title: WT_TA_1

value: C57BL/6 Lgr5-GFP

value: TA


title: H3K9me3 KO1


title: Ck_2


title: wildtype replicate 2


title: H3K9me3 WT3

value: wild type


title: H3K9me3 WT2


title: H3K9me3 WT_input


title: ft-10 tsf-1 replicate 3

description: 5_020209.ft-10 tsf-1


title: H3K9me3 WT1


title: mps1-3 GLC7-24 32°C InPut

first: Giorgia

last: Benzi

address: 1919 route de mende

institute: CRBM-CNRS

data_processing:
DROMPA software (Nakato and Shirahige, 2018).
Genome_build: Saccer3
Supplementary_files_format_and_content: bedGraph

source_name: yeast

growth_protocol: cells grown at 25°C in YEPD, synchronised with alpha factor and then released either at 32°C or 34°C (as indicated in the sample section) in presence of Nocodazole . Samples taken at 90min from release in Nocodazole

extract_protocol:
100 mL of cells (concentration 107cells/mL) were fixed in 1% formaldehyde for 30’ at RT with shaking and then transferred ON at 4°C. Cells were then spun down 3min at 3000 rpm at 4°C and washed three times with TBS. Cells were resuspended in 0.4 mL of 50mM Hepes-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate containing a cocktail of protease inhibitors (Complete EDTA-free Roche) and 1mM PMSF, followed by cell breakage through a Multi-beads shaker (Yasui-Kikai) at 0°C. Lysates were eluted in 15mL Falcon tubes (centrifuged twice at 3000 rpm for 1 min at 4°C), transferred in 1.5 Eppendorf tube, centrifuged at 5000 rpm 1 min at 4°C and sonicated through a Sonifyer Branson 2508 (5-7 cycles of 15sec, tune 1.5 with centrifugation of 5000 rpm for 1 min between each cycle). Sonicated lysates were then centrifuged for 5 min at 15000 rpm at 4°C. Supernatants were recovered. 10 µL of lysates were withdrawn at this stage (=Inputs). For immunoprecipitations (IPs), 60 µL of Protein G-dynabeads pre-washed twice with PBS containing 5 mg/mL BSA and pre-adsorbed with 3 µg Babco 16B12 anti-HA antibody were added to each lysate and incubated ON at 4°C on a nutator. IPs were then washed twice with ice-cold 50mM Hepes-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate, twice with ice-cold 50mM Hepes-KOH pH7.5, 500mM NaCl, 1mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate, twice with ice-cold 10mM Tris-Cl pH8, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA and once with ice-cold TE (50mM Tris-Cl pH8, 1mM EDTA pH8). IPs were eluted at 65°C for 15min with 50µL of 50mM Tris-Cl pH8, 10mM EDTA, 1% SDS, resuspended in 50 µL of TE/1% SDS and incubated overnight at 65°C to reverse crosslinking. IPs were then incubated at 37°C for 1 hour with 100 µL of TE containing 10 µg of RNAseA and 2 hours at 37°C with 2 µL of ProteinaseK 50 mg/mL. DNA was then purified with the Qiagen PCR purification kit
Libraries for Illumina sequencing have been prepared following the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Nocodazole 15ug/mL was used for 90 minutes at the reported temperatures

tag: antibodies

value: Babco 16B12 anti-HA


title: mps1-3 GLC7-24 32°C IP


title: H3K9me2 WT_input

description:
ChIP-seq_H3K9me2_MACS_peaks_SI
ChIP-seq_H3K9me2_EdgeR_MACS_peaks_SI


title: H3K9me2 KO_input


title: mps1-3 spc105-18 32°C InPut


title: mps1-3 spc105-18 32°C IP


title: cdc28-4_2h + αF

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: 300ng each of labeled standard and sample cRNA, as well as 10x Blocking agent, were mixed and fragmented: (60°C for 30min), followed by hybridization (65 °C for 18h in rotating hybridization chamber), followed by sequential wash.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used and Dye-Normalized Signal was used to calculate log2 ratios between control and sample. Log2 ratios for each SUID were averaged for Table S1 of the publication.

organism: Saccharomyces cerevisiae W303

source_name: Standard (cdc28-4, 2h 35°C)

label_protocol: 500ng of RNA were labeled using Agilent Quick Amp Labeling Kit (two-color) as directed.

growth_protocol: Yeast strains were grown in yeast extract/peptone (YEP) supplemented with adenine (0.055mg/mL) and tryptophan (0.8 mg/mL) and 2% glucose (YEPD) at 25 °C.

extract_protocol: Acid Phenol Extraction, EtOH precipitation followed by RNeasy mini-kit (Qiagen).

treatment_protocol: Cells were shifted to 35 °C for varying amounts of time to arrest cells in G2 phase. This allowed the generation of differently sized cells. One culture was treated with 100ng/mL cycloheximide during the arrest to attenuate cell growth. After this treatment regime, cells were transferred to fresh medium and treated with alpha factor for 40 minutes. Cells were collected on a filter and snap frozen.

tag: strain/background

tag: time at 35 °c

source_name: cdc28-4, 2h 35°C + alpha factor

tag: alpha factor

value: 40 minutes alpha factor

tag: cyclohexamide


title: wt + αF

source_name: wild type, 6h 35°C + alpha factor


title: cdc28-4_6h_CHX + αF

source_name: cdc28-4, 6h 35°C + 100ng/mL cycloheximide + alpha factor

value: 100ng/mL cycloheximide


title: H3K9me2 KO3

first: Felix

last: Krueger

institute: Altos Labs


title: cdc28-4_6h + αF

source_name: cdc28-4, 6h 35°C + alpha factor


title: mps1-3_32°C_IP


title: cdc28-4_6h


title: H3K9me2 KO2

source_name: small intestine


title: mps1-3_32°C_InPut


title: wt

source_name: wild type, 6h 35°C


title: MPS1_32°C_InPut


title: ht_7

city: Québec

first: Valerie

last: Langlios

address: 490, rue de la Couronne

country: Canada

institute: Institut national de la recherche scientifique

description: gene expression medaka high temperature

hyb_protocol: Microarray hybridizations were performed according to the Agilent One-Color Microarray Based G2.4 Expression analysis protocol using cyanine 3 (Cy3) dye and 100 ng total RNA per sample. The RNA samples were used to synthesize cDNA and labeled/amplified to cRNA as per the Agilent Low RNA Input Fluorescent Amplification kit. Hybridization was then carried out at 65 °C for 17 h. Intensity signals were collected using an Agilent High Resolution DNA Microarray Scanner (Agilent, ON, Canada).

scan_protocol: High Resolution DNA Microarray Scanne

data_processing: The raw signals were normalized using quantile normalization and log2 transformation. Probes with a signal value less than 10% of the 95% percentile of the negative control signals were considered as low expression and removed.

organism: Oryzias latipes

label_protocol: according to the treatment group and sex

extract_protocol: RNA isolation was carried out on individual embryos using the All Prep DNA/RNA Micro Kit (Qiagen, 80284) following manufacturer’s instruction. Concentrations and integrity of RNA extracts were determined using the NanoDrop-1000 spectrophotometer (NanoDrop Technologies, Inc.) and a Bioanalyzer (Agilent Technologies), respectively.

treatment_protocol: Control temperature is 24 °C, high temperature is 32°C. High temperature was given first day of fertilization until hatching. Embryos for this study were collected at stage 39.

value: HNI strain ID:MT835

value: individual embryo

value: stage 39

tag: Sex

value: male

tag: treatment

value: high temperature


title: ht_8

description: gene expression medaka high temperature


title: ht_4

description: gene expression medaka high temperature

value: famale


title: ht_1

description: gene expression medaka high temperature


title: cdc28-4_2h


title: ht_5

description: gene expression medaka high temperature


title: ht_6

description: gene expression medaka high temperature


title: mps1-3_34°C_InPut


title: H3K9me2 WT3

address: Granta Park

tag: cell type


title: H3K9me2 KO1

value: Vil-Cre mediated KO of Smarcad1


title: mps1-3_34°C_IP


title: cntl_8

description: gene expression medaka control

tag: tissue

value: control


title: cdc28-4_6h_CHX

source_name: cdc28-4, 6h 35°C + 100ng/mL cycloheximide


title: ht_2

description: gene expression medaka high temperature

tag: strain


title: MPS1_34°C_IP


title: MPS1_34°C_InPut


title: BW-cic2

city: Busan

first: Kwang-sun

last: Kim

address: 63 beon-gil 2, Jangjeon-dng, Geumjeong-gu

department: Chemistry

country: South Korea

institute: Pusan National University

description: Growth in the presence of 12.5 ug/mL ciclopirox (replicate 2)

data_processing:
CLRNASeq V.1.00 (From ChunLab, Inc.)
Trimmed Mean of M-value of library size were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Elimination of <100 reads with or without treatment of ciclopirox
Supplementary_files_format_and_content: excel files include (Relative Log Expression) normalized values for each sample.

organism: Escherichia coli

source_name: growth in the presence of 12.5 ug/mL ciclopirox (replicate 2)

growth_protocol: Growth in LB media to OD600=1.0 at 37C with vigorous shaking

extract_protocol:
RNA was extracted from OD600=1.0 using RNA Protect Bacteria (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ciclopirox (0 or 12.5 ug/mL) in LB media was prepaed and used for growing cells


title: BW25113

description: growth in the absence of ciclopirox (Control for replicates)

source_name: growth in the absence of ciclopirox

growth_protocol: Growth in LB media to OD600=1.0 at 37C with vigourous shaking.

treatment_protocol: Ciclopirox (0 or 12.5 ug/mL) in LB media was prepared and used for the cell growth.


title: ht_3

description: gene expression medaka high temperature

tag: age


title: H3K9me2 WT1

value: whole crypt isolate


title: ATAC KO3

description:
ATAC-seq_MACS_peaks_small_intestine
ATAC-seq_EdgeR_MACS_peaks_small_intestine

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.1 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
They were mapped to the mouse GRCm38 genome assembly using Bowtie 2 (v2.2.5)
BAM files were imported into Seqmonk v1.44.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: MACS peaks (300 bp fragment size, significance threshold 0.00001) annotated with closest gene (distance cutoff 5 kbp), read counts quantitated as log(2) using all reads with normalization to largest data store.
Supplementary_files_format_and_content: Sublist of EdgeR probes with FDR<0.05 KO vs WT, Benjamini-Hochberg correction. MACS peaks (300 bp fragment size, significance threshold 0.00001) annotated with closest gene (distance cutoff 5 kbp), read counts quantitated as log(2) using all reads with normalization to largest data store.

extract_protocol:
Nuclei isolation protocol: The crypts were resuspended in 2 ml TrypLE Express with 10 μM Y-27632 and 0.5 mM N-acetylcysteine, pipetted carefully through a 1 ml pipet for dissociation at room temperature. The suspension was then topped up with 20 ml 10% fetal bovine serum (FBS) in PBS and the cells were filtered through a 40 μm cell strainer. The cell suspension was then pelleted at 465 x g, 4 °C for 5 min. The cells were then resuspended in 5 ml ice cold HBSS and re-pelleted and this step was repeated to remove the TrypLE and FBS. The cells were the re-supended in 2 ml 1 % containing N-buffer (15 mM HEPES, pH 7.5, 10% sucrose, 60 mM KCl, 15 mM NaCl, 0.5 mM EGTA, 0.2 mM PMSF, 1 x CompleteTM [Roche] protease inhibitor, 50 mM sodiumbutyrate) and incubated 15 min on ice. This mix was then overlayed on a 5 ml sucrose cushion (30% sucrose in N-buffer) and nuclei were pelleted for 15 min at 1300 x g, 4 °C. Nuclei were taken up in 100 μl ice cold nuclei storage (25 mM Tris-HCl, pH 7.5, 100 mM potassium acetate, 10 mM MgCl2, 2 mM Spermidine) and counted.
ATAC-seq Libraries were generated from 50 000 cells as described by Buenostro using the Nextera kit from Illumina and TruSeq primers. Libraries were sequenced on an Illumina HiSeq as 50 bp Paired End reads.

treatment_protocol: Crypt isolation protocol: Mice were culled and small intestines extracted, immediately flushed with ice cold PBS and cut open longitudially. They were then rinsed 3 x 10 sec with HBSS (Hank’s balanced salt solution) without Ca2+/Mg2+. The intestines were incubated 10 min in 30 mM EDTA/ HBSS on ice, shaken vigorously by hand for 5 sec and the supernatant removed. They were incubated a further 20 min in 30 mM EDTA/ HBSS on ice and then shaken vigorously for 5 min. Villi and mucus was removed by consecutive filtering the material through a 100 and 70 μm strainers. Crypts were pelleted at 170 x g at 4 °C for 10 min and supernatant removed. The crypts were washed with 10 ml ice cold PBS, re-pelleted and the supernatant removed twice.

value: whole crypt nuclei


title: cntl_6

description: gene expression medaka control


title: Git1-CWT2

city: Nanjing

first: Hao

last: Liu

address: 300 guangzhou road, gulou district, Nanjing, China

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Genome_build: gencode v27
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Macrophages

growth_protocol: To obtain primary bone marrow-derived macrophages, bone marrow cells first underwent lysis of red blood cells and were then resuspended in complete RPMI-1640 medium consisting of 25 ng/ml macrophage colony-stimulating factor (M-CSF) and cultured for 7 days.

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 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). 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).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.

treatment_protocol: Further, macrophages from GIT1 CKO or CWT mice were treated with 100 ng/ml LPS

value: BMM derived macrophages


title: ATAC KO2

city: Cambridge


title: H3K9me2 WT2


title: Git1-CKO1


title: Git1-CKO3


title: Git1-CWT3


title: cntl_5

description: gene expression medaka control


title: Git1-CKO2


title: ATAC WT3


title: non-KO_replicate2

city: nanning

first: wang

last: jun

state: guangxi

address: DaXue road100

institute: guangxi university

description:
RR195(non-KO_replicate2)
Rice_N462-01-T17

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. These clean reads were then mapped to the reference genome sequence (Os-Nipponbare-Reference-IRGSP-1.0: http://rapdb.dna.affrc.go.jp/download/irgsp1.html). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools soft were used to map with reference genome (Kim et al 2015). Differential expression analysis of two groups (KO samples and Non-KO samples) was performed using the DESeq2 (Love et al 2014). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with FDR (false discovery rate) < 0.01 found by DESeq2 & absolute log2FC (Fold Change) > 1 were assigned as differentially expressed.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0: http://rapdb.dna.affrc.go.jp/download/irgsp1.html
Supplementary_files_format_and_content: fpkm

organism: Oryza sativa

source_name: non-KO_mature leaves

growth_protocol: Rice (Oryza sativa L.) plants were grown in the greenhouse at 30°C for days and 25°C for night.

extract_protocol:
Mature leaves (60 days after germination) from a single plant were collected, total RNA was extracted using a Plant RNA Purification Kit: RNeasy Plant Mini Kit (74904, QIAGEN, Germany) following the manufacturer’s instructions. RNA degradation and contamination were monitored on 1% agarose gels.
Library construction and RNA-seq were performed at Beijing BioMarker Technologies (Beijing, China) in accordance with the institute’s protocols and briefly described here. RNA concentration was measured using NanoDrop 2000 (Thermo). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNaseH. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on Illumina Hiseq Xten PE150 platform (paired end 150 bp) and paired-end reads were generated.

value: control (non-KO)

value: mature leaves


title: ATAC WT2

value: wild type


title: non-KO_replicate1

description:
RR194(non-KO_replicate1)
Rice_N462-01-T16


title: non-KO_replicate3

description:
RR196(non-KO_replicate3)
Rice_N462-01-T18


title: Git1-CWT1


title: ATAC WT1


title: cntl_2

description: gene expression medaka control


title: RNA-seq P3

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

data_processing:
RNA-seq: Raw data (raw reads) of fastq format were filtered by CUTADAPT
RNA-seq: Files were then processed by FASTQC
RNA-seq: Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR
RNA-seq: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene
RNA-seq: Differential expression analysis was performed using the DESeq2 R package. Genes with an adjusted P-value≤0.05 and │FoldChange│> 1.2 found by DESeq were assigned as differentially expressed
Genome_build: Sparassis latifolia (assembly ASM260774v1)

organism: Sparassis latifolia

source_name: primordia

growth_protocol: Samples of fungi in three different groups (mycelia, light induced mycelia，and primordia) were harvested in the cultivation bags used in industry.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

value: primordia

tag: time

value: SP-C


title: RNA-seq P2


title: cntl_4

description: gene expression medaka control


title: cntl_3

description: gene expression medaka control


title: srl1-KO_replicate2

description:
RR192(srl1-KO_replicate2)
Rice_N462-01-T14

source_name: srl1-KO_mature leaves

value: SRL1 knockout mutants srl1-KO


title: KO_wCO_colitis_5

description:
RNA-seq_DESeq2_FDR_005 wCO colitisVScontrol KO
RNA-seq_DESeq2_FDR_005 wCO KOvsWT colitis

data_processing:
Libraries were sequenced on the BGISEQ500 platform by BGI Hong Kong.
low-quality, N-rich or adaptor-polluted reads prefiltered according to BGI Hong Kong standard procedure
Reads were mapped to the mouse GRCm38 genome assembly using Hisat2 2.1.0 (no soft clipping, --no-mixed --no-dicscordant)
BAM files were imported into Seqmonk v1.42.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
rRNA reads were removed using the attached custom rRNA annotation track (downloaded from the UCSC table browser)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

source_name: colon

extract_protocol:
The colon was cut open longitudionally, washed in PBS to remove faeces and snap frozen in liquid nitrogen.
25-100 mg frozen tissue was ground to powder with dry ice in a precooled mortar. After addition of 1ml Trizol, the sample was collected and incubated 5 min at RT. 200 µl Chloroform were added prior vigorous vortexing and centrifugation 20 min at 16,000 g, 4 °C. The upper phase was transferred to 500 µl isopropanol, vortexed and incubated 15 min at RT before centrifuging 10 min at 16,000g, 4°C. To deplete DSS, after discarding the supernatant, LiCl-precipitation was performed at 4 °C by dissolving the pellet in 120 µl H2O and addition of 80 µl 2M LiCl and 2h incubation prior to centrifugation for 30 min at 14,000 g. LiCl-precipitation was repeated once more and the pellet dissolved in 200 µl H2O. Next, the RNA was precipitated substituting LiCl with 20 µl 3M NaAc pH 5.2 and 400 µl 100% EtOH for 30 min incubation at -20 °C. After centrifugation, the pellet was washed once in 70% EtOH and dried on ice before resuspending in ice cold H2O.
Libraries were generated from total RNA by BGI Hong Kong. Libraries were sequenced on the BGISEQ500 platform as 100bp Single End reads.

treatment_protocol:
microbiome enrichment: Enriched microbiota was provided starting 2 weeks before colitis induction by bedding transfer and co-ventilation with the donor C57BL/6 females obtained from an SPF facility in York.
DSS-induced colitis: 1% DSS (Dextran sulphate sodium salt, Sigma Aldrich 42867) was continuously administered with drinking water and exchanged every 3 days.Tissue was harvested after 15 days DSS-administraton.

value: Vil-Cre mediated KO

value: whole tissue

tag: isolation type

value: whole tissue, DSS depletion


title: ATAC KO1


title: cntl_1

description: gene expression medaka control

value: HNI strain ID:MT835

value: individual embryo

value: stage 39


title: RNA-seq P1


title: srl1-KO_replicate3

description:
RR193(srl1-KO_replicate3)
Rice_N462-01-T15


title: cntl_7

description: gene expression medaka control

value: male


title: pif45_wl3

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description:
processed data file: rawcounts.txt
processed data file: normcounts.txt

data_processing:
Illumina Casava2.2 software used for basecalling.
Quality control was performed with FastQC v.0.11.5.
Reads were mapped to Arabidopsis TAIR-10 genome using STAR v2.5.3a software.
Biological quality control was done with the PicardTools v2.9.0.
The gene features were counted with HTSeq v.0.9.1 (htseq-count).
Normalization and differential expression analysis were performed with the statistical analysis R/Bioconductor package edgeR v.3.22.3 for the genes annotated in TAIR10.
Genome_build: TAIR10
Supplementary_files_format_and_content: rawcounts.txt: Tab-delimited text file includes raw count values for each Sample.
Supplementary_files_format_and_content: normcounts.txt: Tab-delimited text file includes normalized expression values (cpm = count per millions) for each Sample.

source_name: seedlings

growth_protocol: Arabidopsis seeds were surface sterilized with sodium hypochlorite and sown on half-strength Murashige and Skoog basal salt medium (MS; Duchefa) containing 1% (wt/vol) agar (Applichem) and 1% (wt/vol) sucrose. Seeds were germinated aseptically at 22°C in a white light field under continuous irradiation provided by Osram L18W/30 tubes (3.6 μmol m−2 s−1; measured with an LI-250 Light Meter). UV-B was supplemented for the indicated times with Philips TL20W/01RS narrowband UV-B tubes (0.06 mW cm−2 s-1; measured with a VLX-3W Ultraviolet Light Meter equipped with a CX-312 sensor, Vilber Lourmat). The UV-B range was modulated by the use of 3-mm transmission cut-off filters of the WG series (Schott Glaswerke) with half-maximal transmission at the indicated wavelength (WG304 for UV-B-treated and WG368 for non-UV-B-treated controls).

extract_protocol:
Whole seedlings material of 30 seedlings per sample were collected in 1.5ml eppendorf tubes. Plant materials were ground using silamat and RNA was isolated with Plant RNeasy kit (Qiagen) and treated with DNaseI according to the manufacturer’s instructions. DNase was heat inactivated in the presence of 2 mM EDTA. The libraries were prepared with 400 ng of total RNA as starting material and processed with the TruSeqUD Stranded mRNA (Illumina), and sequencing on an Illumina HiSeq 4000 System using 100 bp single-end reads protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: On day 4, half plates remained in white light (3.6 μmol m−2 s−1) and the other half transferred to white light supplemented with narrowband UV-B (0.06 mW cm−2 s-1) under WG304 filters.

tag: ecotype/background

value: Whole seedlings

value: 4 days

tag: light treatment

value: low white light


title: KO_wCO_colitis_4

tag: genotype/variation


title: KO_wCO_colitis_3


title: pif45_wl2


title: srl1-KO_replicate1

description:
RR191(srl1-KO_replicate1)
Rice_N462-01-T13


title: RNA-seq L3

source_name: mycelia

value: light induced mycelia


title: KO_wCO_colitis_2


title: RNA-seq L1


title: pif45_wl1


title: KO_wCO_colitis_1


title: WT_wCO_colitis_5

description:
RNA-seq_DESeq2_FDR_005 wCO colitisVScontrol WT
RNA-seq_DESeq2_FDR_005 wCO KOvsWT colitis


title: uvr8-6_6h3

value: 6h acclimation-level UV-B


title: RNA-seq D3

value: mycelia under dark


title: WT_wCO_colitis_4

value: wild type


title: RNA-seq D1


title: uvr8-6_6h1


title: gastrocnemius_anti210lna_non-diabetic_rep9

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: LNA oligonucleotides against miR-210

hyb_protocol: The obtained cRNAs were hybridized on a MouseWG-6 v2 BeadChip Array according to the Standard Illumina hybridization protocol.

scan_protocol: Hybridized chips were then scanned and intensities were generated by GenomeStudio Software, according to the standard Illumina scanning protocol.

data_processing: GenomStudio’s bead summary probe level data, not normalized and not background corrected, were analyzed using Bioconductor. Quality was assessed by plotting the intensities of regular and control probes and the correct clustering of biological replicates was checked by PCA (Principal Component Analysis). Sample intensities were quantile normalized and filtered for expression and probe quality using the beadarray R package: only probes with Detection P-value<0.05 in at least one condition and whose quality categories was defined “Perfect” or “Good” were kept.

source_name: gastrocnemius muscle

label_protocol: Biotinylated cRNA was generated starting from 200ng total RNA per sample using the Ambion Illumina RNA amplification kit.

growth_protocol: C57BL/6N male mice (8-12 weeks old, Charles River laboratories) underwent hind limb ischemia and then they were randomized in two groups.

extract_protocol: RNA samples were extracted from gastrocnemius muscles (n= 11/group), using TRIzol (Invitrogen) and the TissueLyser system (Qiagen), according to the manufacturer's instructions. Following extraction, RNA integrity was checked with Agilent RNA Nano Kit and all samples had a RIN (RNA Integrity Number) >7.

treatment_protocol: After 5 days of ischemia, intraperitoneal injection of LNA oligonucleotides (In vivo LNAmicroRNA Inhibitors; Exiqon) against miR-210 (ANTI-210) or a scrambled control sequence (SCR) was carried out.

tag: experiment group

value: ANTI-210 LNA


title: gastrocnemius_anti210lna_non-diabetic_rep10

description: LNA oligonucleotides against miR-210


title: WT_wCO_colitis_3


title: RNA-seq L2

value: SP-C


title: gastrocnemius_anti210lna_non-diabetic_rep8

description: LNA oligonucleotides against miR-210


title: SMGX75-16

city: Swords

first: Shannon

last: Nelson

state: Dublin

address: Glasnevin

department: NICB

country: Ireland

institute: DCU

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

data_processing:
Raw sequencing files were merged for each sample to generate a single fastq file per sample. Cutadapt was used to remove adapter sequences.
Trimmed reads were aligned against the Homo sapiens Ch37 genome (hg19) with hisat2 with the following paramaters hisat2 --no-mixed --summary-file hg19/Align_stats -p 8 -x /home/Indexes/hg19/ -1 reads1List -2 reads2List --no-unal | samtools view -Sb | samtools sort -o
The resulting sam file was piped into samtools for bam conversion and sorting. The resulting featureCounts object can easily be manipulated to generate a counts matrix for DESeq2. This counts generation is written to counts.tsv for further analysis.
Up/down regulated genes: differential expression genes (p < 0.001 and |log2 fold-change| ≧ 2) are detected using DESeq2 after filtering out reads count less than 10. Compare CLOs with CLs; compare PT127 PDX, CLO with CL; compare PT291 organoids, CLO with CL. The correlation of paired groups - for each sample, reads count is normalised to TPM. Median is applied if there is more than one sample in a group. Linear regression was performed to identify the relationship of paired groups: PT291 ORG and PT127 PDX; PT127 PDX and PT127 CLO; PT291 ORG and PT291 CLO, (p < 0.05).
Genome_build: Homo sapiens Ch37 genome (hg19)
Supplementary_files_format_and_content: Excel spreadsheet, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj

source_name: PT127 PDX

growth_protocol:
Cell lines - PDX tumours were dissociated to single cells, and infiltrating mouse cells were removed using a Mouse Cell Removal Kit (Miltenyi Biotec). Cells were seeded in 1mg/mL matrigel until cells attached to plate. Cells were scaled up, and were grown in a T75 tissue culture flask, cells were maintained with Gibco DMEM-High glucose Glutamax media with 10% FBS, and placed in a 5% CO2 37 °C incubator for until they reached 80% confluency.
Organoids –PDX tumours were dissociated to single cells, and infiltrating mouse cells were removed using a Mouse Cell Removal Kit (Miltenyi Biotec). Cell were seeded in 8-12 mg/mL ECM Gel from Engelbreth-Holm-Swarm murine sarcoma, and maintained using media containing 50% L-WRN conditioned media 50% DMEM-high glucose Glutamax, and A83-01, hFGF10, Gastrin I, N-acetylcysteine, Nicotinammide, B-27 Supplement. Cells were also supplemented with Y-27632 when dissociated to single cells. Cells were grown for a 14 days before RNA extraction.
Cell line organoids - a cell lines were trypsinised, and cells were seeded at 5x10^4 cells/well in 8-12 mg/mL ECM Gel from Engelbreth-Holm-Swarm murine sarcoma, and maintained using media containing 50% L-WRN conditioned media 50% DMEM-high glucose Glutamax, and A83-01, hFGF10, Gastrin I, N-acetylcysteine, Nicotinammide, B-27 Supplement. Cells were also supplemented with Y-27632 when dissociated to single cells. Cells were grown for a 14 days before passaging. Fourteen days after passaging, RNA was extracted.

extract_protocol:
TRI-reagent® (Sigma) was used to lyse cells, and RNA isolation was performed using Direct-zol RNA Miniprep Plus Kit (Zymo Research, R2072).
RNA samples were quality controlled with an RNA Screen Tape (Agilent) and quantified with Qubit RNA HS Assay kit. Sequencing libraries were prepared with 200 ng of total RNA for all samples. The Nugen Universal Plus mRNA protocol was followed as recommended by the manufacturer. Libraries were amplified by 15 cycles of PCR. Libraries were sequenced in one NextSeq 550 run with the NextSeq 500/550 High Output Kit v2.5 (300 cycles), sequencing was done with Paired End 150 nt reads and 8 nt indexes. Libraries were loaded at 1.4 pM, 5% PhiX control was used.

tag: model type

value: Pancreatic cancer

tag: culture method

value: PDX

tag: source

value: Patient tumour