title: CX3CR1 CTL

description:
tot_counts.txt.gz
CX3CR1_CTL_19844_ACAGTG


title: CD34_Neg_Basophil_23

status: Public on Oct 20 2020

type: SRA

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts(.txt)

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover.
Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer’s protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads).

tag: strain

tag: cell population

value: CD34 Neg Basophil

tag: sorting strategy

value: Live Lin- Sca1- FcεRI+ CD34- cells

tag: Sex

value: female


title: EY26

city: Barcelona

first: Anna

last: PLANAS

state: - If in U.S, Select a State -

address: Rossello 161 planta 6

country: Spain

institute: Spanish Research Council (CSIC)

description:
tot_counts.txt.gz
EY26_32445_CTCAGA

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5
and filtered using skewer (v0.2.2) for removing the low quality reads and trimming the Illumina adapter if necessary.
Reads were then aligned to the reference genome  using the annotation from Ensembl (version 88) with STAR aligner (v2.5.3a) using the option "--quantMode GeneCounts" for retrieving the gene counts.
Differential gene expression analysis was performed using DESEQ2 package
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with raw read counts (only unique mapping reads)

source_name: Brain Ipsilateral hemisphere (ischemic)

extract_protocol:
CD11c-eYFP+ cells and microglia were isolated from the brain of adult CD11c-eYFP mice, parabiotic WT/CD11c-eYFP mice or CX3CR1CreERT2-ROSA26 tdTomato mice respectively (13-16 weeks old) using Fluorescence Activated Cell Sorting. Brains were collected in cold HBSS buffer (w/o Ca2+ and Mg2+, Thermo Fisher Scientific #14175-053). The brain tissue was enzymatically dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec #130-092-628). The gentleMACS™ Dissociator with Heaters (Miltenyi Biotec #130-096-427) was used for mechanical dissociation steps following the Neural Tissue Dissociation Kit (P) for dissociation without heaters. The digested tissue was filtered twice with 70 µm and 40 µm filters washing with HBSS (w/ Ca2+ and Mg2+, Thermo Fisher Scientific #14025-092). Cells were separated from myelin and debris by 30% isotonic percoll gradient (GE Healthcare #17-0891-01) in Myelin Gradient Buffer (MGB). Samples were centrifuged at 950g for 30 min without acceleration nor brake. Cells were collected from the interface, washed once with FACS Stain Buffer (BD Biosciences #554656), and processed for FACS (no staining required) in a FACSAriaII sorter (BD Biosciences)
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (#634890, Clontech) and NEBNext Ultra DNA Library Prep kit (#E7370, New England) according to the manufacturer's protocol. Briefly, 1 or 5 ng of total RNA were converted to cDNA using the SMART-seq kit. Long distance PCR was performed for 9 (5 ng) or 11 (1 ng) cycles. Agilent 2100 Bioanalyzer (High Sensitivity DNA Chip) was used for quantification and validation of the obtained cDNA. Ten ng of the resultant cDNA was fragmented using the Covaris S2 instrument in a final volume of 55 l and adjusting the settings as follows: 10% duty cycle, intensity 5, and 200 cycles per burst for 5 minutes. The resultant fragments were used for the library synthesis using the NEBNext Ultra kit. Briefly, fragments were subjected to end repair and addition of “A” bases to 3′ ends, ligation of adapters and USER excision. Library amplification was performed through 10 cycles of PCR using different indexed primers for multiplexing. All purification steps were performed using AgenCourt AMPure XP beads.
Final libraries were analyzed using Agilent DNA High Sensitivity chip to estimate the quantity and to check the size distribution and were then quantified by qPCR using the KAPA Library Quantification Kit (#KK4835, KapaBiosystems). Sequencing was carried out using the Illumina HiSeq 2500, Single Reads, 50nts.

tag: tissue

value: Brain Ipsilateral hemisphere

tag: disease state

value: ischemic

tag: cell type

tag: age

value: 13-14 week old

tag: genotype


title: CD34_Neg_Basophil_21


title: EY24

description:
tot_counts.txt.gz
EY24_29389_GAGTGG


title: CD34_Neg_Basophil_1


title: CD34_Neg_Basophil_20


title: CD34_Neg_Basophil_19


title: EY23

description:
tot_counts.txt.gz
EY23_29388_GTTTCG


title: PA11

description:
tot_counts.txt.gz
PA11_29386_CCGTCC

value: C57BL/6 parabiotic with Tg(Itgax-Venus)1Mnz

value: 15-16 week old


title: CD34_Neg_Basophil_18


title: CD34_Neg_Basophil_28


title: PA03

description:
tot_counts.txt.gz
PA03_29385_CAGATC


title: CX40

description:
tot_counts.txt.gz
CX40_29383_TGACCA

value: CX3CR1+ microglia


title: CX41

description:
tot_counts.txt.gz
CX41_29384_ACAGTG


title: CD34_Neg_Basophil_17


title: CD34_Neg_Basophil_16


title: CD34_Neg_Basophil_15


title: CX39

description:
tot_counts.txt.gz
CX39_29382_CGATGT


title: Control_H3K27Ac_ChIP_A

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

country: USA

institute: Case Western Reserve University

description: CRISPR-Control OPCs

library_source: genomic

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to mm10 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWIG files were generated using Deeptools bamCoverage with reads per genome coverage normalization. BED files in a broadPeaks format from MACS2.

molecule: genomic DNA

source_name: Oligodendrocyte progenitor cells (OPCs)

growth_protocol: OPCs were grown in DMEM F12 supplemented with N2max and B27 and Fgf2 and Pdgfa.

extract_protocol: Nuclei isolation and chromatin shearing were performed using the Covaris TruChIP protocol following manufacturer’s instructions for the “high-cell” format. In brief, 5-20 million cells were crosslinked in “Fixing buffer A” supplemented with 1% fresh formaldehyde for 10 minutes at room temperature with oscillation and quenched for 5 minutes with “Quench buffer E.” These cells were then washed with PBS and either snap frozen and stored at -80, or immediately continued to nuclei extraction and shearing per the manufacturer protocol. The samples were sonicated with the Covaris S2 using the following settings: 5% Duty factor 4 intensity for four 60-second cycles. Sheared chromatin was cleared and incubated overnight at 4 degrees with antibody that was pre-incubated with protein G magnetic DynaBeads (ThermoFisher). Protein G dynabeads were then washed, eluted, reverse cross-linked and treated with RNase A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Aline Biosciences, C-1003-5) and then used to prepare illumina sequencing libraries.

treatment_protocol: Comparison between control and Vhl knockout OPCs.

value: epiblast stem cell derived OPCs

tag: antibody

value: H3K27Ac (abcam4729, 9ug per ChIP

tag: number of cells per chip

value: 5-20 million OPCs


title: CX3CR1 15 CTL

description:
tot_counts.txt.gz
CX3CR1_15_CTL_19845_GCCAAT

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5
Reads were then aligned to the reference genome using the annotation from Ensembl (version 88) with STAR aligner (v2.5.3a) using the option "--quantMode GeneCounts" for retrieving the gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with raw read counts (only unique mapping reads)

source_name: Brain Control

extract_protocol:
CD11c-eYFP+ cells and microglia were isolated from the brain of adult CD11c-eYFP mice or CX3CR1CreERT2-ROSA26 tdTomato mice respectively (13-14 weeks old) using Fluorescence Activated Cell Sorting. Brains were collected in cold HBSS buffer (w/o Ca2+ and Mg2+, Thermo Fisher Scientific #14175-053). The brain tissue was enzymatically dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec #130-092-628). The gentleMACS™ Dissociator with Heaters (Miltenyi Biotec #130-096-427) was used for mechanical dissociation steps following the Neural Tissue Dissociation Kit (P) for dissociation without heaters. The digested tissue was filtered twice with 70 µm and 40 µm filters washing with HBSS (w/ Ca2+ and Mg2+, Thermo Fisher Scientific #14025-092). Cells were separated from myelin and debris by 30% isotonic percoll gradient (GE Healthcare #17-0891-01) in Myelin Gradient Buffer (MGB). Samples were centrifuged at 950g for 30 min without acceleration nor brake. Cells were collected from the interface, washed once with FACS Stain Buffer (BD Biosciences #554656), and processed for FACS (no staining required) in a FACSAriaII sorter (BD Biosciences)
libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (Illumina, # RS-122-2101/2) according to the manufacturer's protocol. Briefly, from 2,4 to 147 ng of total RNA were used for poly(A)-mRNA selection using streptavidin-coated magnetic beads and were subsequently fragmented to approximately 300bp. cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen # 18064-014) and random primers. The second strand of the cDNA incorporated dUTP in place of dTTP. Double-stranded DNA was further used for library preparation. dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. All purification steps were performed with AMPure XP beads and eluted in 20 µl EB. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit.
Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems #KK4835) prior to amplification with Illumina’s cBot. Libraries were sequenced Single Reads, 50nts on the Illumina HiSeq 2500.

value: Brain

value: control

value: male


title: CD34_Neg_Basophil_14


title: CD34_Neg_Basophil_13


title: ESC_siTIP5_H3K27me3_spiked_in

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

description: Quantitative ChIPseq analysis

data_processing:
Quantitative ChIPseq experiments were performed by spike-in ESCs chromatin with 50ng of Drosophila chromatin in order to compare the differences in H3K27me3 levels. ChIP experiments were performed as described above. After sequencing, reads uniquely aligned were mapped to Drosophila genome (dm6) and an internal normalization factor was generated for each sample according to Active Motif spike-in normalization strategy. The number of reads for ESC ChIPs were normalized by down-sampling the reads based on the spike-in normalization factor using “bamCoverage” from deepTools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mouse embryonic stem cells (ESCs)

growth_protocol: mouse embryonic stem cells (E14) were either cultured in N2B27 medium with LIF/2i or in medium containing 15% fetal bovine serum with LIF

extract_protocol: ChIP analysis was performed as previously described (Leone et al., 2017). Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. For histone ChIPs, isolated nuclei were then lysed and sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris–HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed Sepharose beads for 2 h at 4°C. Pre-cleared chromatin was incubated overnight with the indicated antibodies. The next day, Dynabeads protein-A (or -G, Millipore) were added and incubated for 4 h at 4°C. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K digestion (50°C for 3 h) and reversion of cross-linking (65°C, overnight), DNA was purified with phenol/chloroform and ethanol precipitated. For TIP5 ChIPs, isolated and crosslinked nuclei were MNase digested in 400µl MNase digestion buffer (0.3M Sucrose, 50mM Tris pH 7.5, 30mM KCl, 7.5mM NaCl, 4mM MgCl2, 1mM CaCl2, 0.125% NP-40, 0.25% NaDeoxycholate, 2mM Na3VO4 supplemented with cOmplete™ Protease Inhibitor Cocktail (Roche)) with 100U MNase (Roche) at 37°C for 1h. The digestion was then stopped with 5mM EDTA and the digested chromatin was solubilized in 1% SDS and three pulses of 30sec sonication using a Bioruptor ultrasonic cell disruptor (Diagenode). 200µg of pre-cleared chromatin was immunopurified with incubation of 30µl of Anti-FLAG M2 Affinity Gel (Sigma) or 30µl Anti-HA magnetic beads (Pierce) over night. The samples were subsequently washed, eluted and the DNA was purified as for histone ChIPs.  For ChIPseq analyses, the quantity and quality of the isolated DNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The Nugen Ovation Ultra Low Library Systems (Nugen, Inc, California, USA) was used in the sfollowing steps. Briefly, ChIP samples (1 ng) was end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 2500 single end 126 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).

treatment_protocol: ESCs were transfected with the indicated siRNAs and collected 3 days post transfection

tag: sirna

tag: spiked in

value: spiked in Drosophila


title: EY27

description:
tot_counts.txt.gz
EY27_32446_GACGAC


title: CD34_Neg_Basophil_12


title: ESC_siCTL_1_H3K27me3_spiked_in

description: Quantitative ChIPseq analysis

value: siCTL


title: CD34_Neg_Basophil_10

value: CD34 Neg Basophil


title: Young rep5 L2

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

data_processing:
After demultiplexing, run quality was evaluated using FastQC 0.11.8
FASTQ files were merged for each sample
FASTQ files were aligned to the reference genome using STAR aligner 2.5.4b with standard arguments
In order to determine the strandness of the reads, piccard CollectRnaSeqMetrics 2.18.0 was used
Differently expressed analysis was done using edgeR 3.24.3
Genome_build: mm10 M13
Supplementary_files_format_and_content: normalized read counts and differently expressed genes of protein coding genes

molecule: total RNA

source_name: Hematopoietic Stem Cells

extract_protocol:
RNA was isolated from 15,000 HSC using the Nucleospin XS kit (Macherey Nagel) and quantified on Bionalyzer using RNA Pico 6000 Kit (Agilent)
300pg ribosomal-depleted RNA was used as input into TotalScript RNA-Seq Kit (Takara)

value: WT


title: CD34_Neg_Basophil_11

value: Live Lin- Sca1- FcεRI+ CD34- cells

value: female


title: Young rep4 L2


title: Young rep4 L1


title: MCP_9

source_name: Peritoneal cells

extract_protocol:
189 single cells were index-sorted into 2 x 96-well PCR plates containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton per well), vortexed and frozen at -70 °C. Sample preparation for RNA-sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) with minor modifications. Following brief centrifugation at 2000 rpm for 2 minutes to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 50 U/reaction SmartScribe Reverse Transcriptase (Takara ClonTech, 639537) without Betaine and MgCl2, and amplified using 23 PCR cycles. ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882) using BioMek FXP Dual Span Liquid Handler. Single cell cDNA library was eluted in 22 µl volume of EB Buffer (Qiagen, 19086) and 20 µl volume collected to ensure minimal bead carryover.
Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set A and D (Illumina, FC-121-2001 and FC-121-2004 respectively), following the manufacturer’s protocol using ¼ of the recommended volumes and 1.26 µl cDNA library. Single cell libraries labelled with Index Kit A and D were pooled separately and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 32.0 µl EB Buffer and 30.0 µl volume collected to ensure minimal bead carryover. Quantification was performed with KAPA Library Quant Kit (Roche, 07960140001); index kit A pooled libraries were mixed with equimolar concentration of index kit D pooled libraries and sequenced in one lane on the Illumina HiSeq4000 system (50 bp single-end reads).

value: basophil-mast cell progenitors

value: Live Lin- c-Kit+ FcεRI+ integrin β7hi SSClow cells

tag: gender


title: MCP_95


title: Young rep3 L2


title: MCP_94


title: Young rep2 L2


title: MCP_93


title: Young rep2 L1


title: MCP_91


title: MCP_92


title: Young rep1 L2


title: MCP_90


title: Old rep7 L2


title: Young rep1 L1


title: MCP_89


title: Old rep7 L1


title: MCP_88


title: MCP_8


title: Young rep5 L1


title: Old rep6 L2


title: Old rep5 L2


title: MCP_85


title: MCP_86


title: Old rep6 L1


title: MCP_87


title: Old rep5 L1


title: MCP_84


title: Old rep4 L2


title: MCP_83


title: Young rep3 L1


title: Old rep4 L1


title: Old rep3 L2


title: Old rep3 L1


title: MCP_80


title: MCP_82


title: Old rep2 L2


title: MCP_7


title: MCP_79


title: Old rep2 L1


title: Old rep1 L2


title: Old rep1 L1


title: MCP_78


title: MCP_77


title: Ezh2-cKO exostoses cells (1612295)

city: Xi'an

first: Feng

last: Zhang

address: Changle west Road

department: Department of Pathology

country: China

institute: Fourth Military Medical University

data_processing:
Basecalls performed using bcl2fastq version 1.8.4
Deleted adaptor, reads with N>3%,and low-quality sequence from sequenced reads, then mapped the reads to mm10 whole genome using Hisat2 with the default spliced mapping setting
Reads Per Kilobase of exon per Megabase of library size (RPKM) for each refseq genes were obtained using Stringtie and normalized using TMM method. Differentially expressed transcripts were identified by edgeR.
WT(1605272) vs Ezh2-cKO(1612295)
WT(1605272) vs Utx-cKO(1612297)
Genome_build: mm10
Supplementary_files_format_and_content: excel files generated by edgeR including fold changes and qvalues for each ensembl genes

source_name: Ezh2-cKO exostoses cells

extract_protocol:
RNA was extracted, purified, and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies)
Libraries were generated for sequencing using the TruSeq RNA sample preparation kit (Illumina). Libraries were sequenced using an Illumina HiSEq. 2500 sequencer.

treatment_protocol: These mice were intraperitoneally administrated tamoxifen (100 mg/kg) every other day for 8 days (a total of 4 injections) starting 4 weeks after birth

value: Ezh2-cKO exostoses cells

value: 8 weeks old


title: MCP_76


title: Wild type chondrocyte (1605272)

source_name: Chondrocytes

value: Articular cartilage from the same aged control mice


title: MCP_75


title: Utx-cKO exostoses cells (1612297)

source_name: Utx-cKO exostoses cells

value: Utx-cKO exostoses cells


title: MCP_73


title: MCP_74


title: MCP_81


title: MCP_6


title: MCP_70


title: MCP_71


title: MCP_69


title: MCP_68


title: MCP_67


title: MCP_66


title: input_serum_wt_MNase

data_processing:
ChIPseq reads were aligned to the mouse mm10 reference genome using Bowtie2 (version 2.2.5). Read counts were computed and normalized using “bamCoverage” from deepTools (version 2.0.1; (Ramirez et al., 2014)) using a bin size of 50bp. TIP5 bound regions were defined using SICER (version 1.1; (Zang et al., 2009)) by comparing the FLAG ChIPs of tagged vs non-tagged TIP5 ESCs in 2i and serum using the following arguments: W=1000 G=3000 FDR=0.00001.
Genome_build: GRCm38/mm10

extract_protocol:
ChIP analysis was performed as previously described (Leone et al., 2017). Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. For histone ChIPs, isolated nuclei were then lysed and sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted to a total volume of 500 μl with ChIP buffer (16.7 mM Tris–HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100) and pre-cleared with 10 μl packed Sepharose beads for 2 h at 4°C. Pre-cleared chromatin was incubated overnight with the indicated antibodies. The next day, Dynabeads protein-A (or -G, Millipore) were added and incubated for 4 h at 4°C. After washing, bound chromatin was eluted with the elution buffer (1% SDS, 100 mM NaHCO3). Upon proteinase K digestion (50°C for 3 h) and reversion of cross-linking (65°C, overnight), DNA was purified with phenol/chloroform and ethanol precipitated. For TIP5 ChIPs, isolated and crosslinked nuclei were MNase digested in 400µl MNase digestion buffer (0.3M Sucrose, 50mM Tris pH 7.5, 30mM KCl, 7.5mM NaCl, 4mM MgCl2, 1mM CaCl2, 0.125% NP-40, 0.25% NaDeoxycholate, 2mM Na3VO4 supplemented with cOmplete™ Protease Inhibitor Cocktail (Roche)) with 100U MNase (Roche) at 37°C for 1h. The digestion was then stopped with 5mM EDTA and the digested chromatin was solubilized in 1% SDS and three pulses of 30sec sonication using a Bioruptor ultrasonic cell disruptor (Diagenode). 200µg of pre-cleared chromatin was immunopurified with incubation of 30µl of Anti-FLAG M2 Affinity Gel (Sigma) or 30µl Anti-HA magnetic beads (Pierce) over night. The samples were subsequently washed, eluted and the DNA was purified as for histone ChIPs.
For ChIPseq analyses, the quantity and quality of the isolated DNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The Nugen Ovation Ultra Low Library Systems (Nugen, Inc, California, USA) was used in the sfollowing steps. Briefly, ChIP samples (1 ng) was end-repaired and polyadenylated before the ligation of Illumina compatible adapters. The adapters contain the index for multiplexing. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 2500 single end 126 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).

tag: treatment


title: ChIPseq_serum_FLAG_wt

tag: chip antibody

value: FLAG-ChIP


title: ChIPseq_2i_FLAG_wt


title: ChIPseq_serum_FLAG_FH-TIP5


title: input_wt_sonication


title: input_2i_FH-TIP5_MNase


title: input_2i_wt_MNase


title: MCP_65


title: ChIPseq_2i_FLAG_FH-TIP5


title: ChIPseq_2i_H3K27ac_siTIP5


title: MCP_64


title: MCP_63


title: ChIPseq_2i_H3K27ac_siCTRL

value: siCTRL


title: MCP_62


title: MCP_72


title: ChIPseq_serum_H3K27me3_siTIP5


title: input_serum_FH-TIP5_MNase


title: MCP_61


title: MCP_60


title: ChIPseq_2i_H3K27me3_siTIP5


title: ChIPseq_2i_HA_FH-TIP5

value: HA-ChIP


title: MCP_5


title: MCP_59


title: ChIPseq_2i_H3K27me3_siCTRL


title: ChIPseq_2i_H3K4me3_siTIP5


title: ChIPseq_2i_H3K4me3_siCTRL


title: MCP_58


title: MCP_57


title: Silence_RNASeq_Rep3

city: Nanjing

first: Rong

last: Yin

address: Baiziting 42

department: Thoracic Surgery

institute: Nanjing Medical University Affiliated Jiangsu Cancer Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to human  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Homo sapiens

source_name: A549 cell line

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: A549 cells were transfected with FAM83H-AS1 siRNA or control, respectively.

value: silence


title: Silence_RNASeq_Rep2


title: MCP_55


title: MCP_54


title: Silence_RNASeq_Rep1


title: Control_RNASeq_Rep2

value: control


title: PC3_4h_hemeTreated_replicate1

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
Raw fastq files first had optical duplicates removed using clumpify from the BBTools suite using the flag “dedupe spany addcount”.
Next, adaptor trimming was performed using bbduk, also from the BBTools suite using the flag “ktrim=l hdist=2”.
Next, reads were quality trimmed with Trimmomatic in paired end mode with the flags “ILLUMINACLIP: <adapter_path> Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25”.
Alignment was performed using STAR with the flags “--outFilterScoreMinOverLread 0.1 --outFilterMatchNminOverLread 0.1 --outFilterMultimapNmax 1“ with the resultant bam files sorted and indexed using samtools.  BamCoverage was used to generate coverage maps using default parameters.
HTSeqCount was used to generate gene counts values using the flags “--stranded=no  --mode=intersection-nonempty.
Genome_build: hg38
Supplementary_files_format_and_content: text files are contain gene x counts per sample

source_name: prostate cancer cell line

growth_protocol: PC3 cells were cultured in RPMI medium with 10% FBS and antibiotics

extract_protocol:
RNA was extracted with Trizol
Illumina TruSeq Kit

treatment_protocol: Heme at 50 uM was added to cell culture media for 2h or 4h.

value: prostate cancer cell line derived from bone metastases

value: heme (50 uM) for 4h


title: ChIPseq_serum_H3K27me3_siCTRL


title: PC3_4h_hemeTreated_replicate2


title: Control_RNASeq_Rep1


title: Control_RNASeq_Rep3


title: MCP_53


title: sample_cf_049T21_R1_XX_uCG

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

data_processing:
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a reference genome, minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files contain CG coverage for each sample

source_name: Cell-free DNA

extract_protocol:
Chorionic villi gDNA was purified using standard phenol-chloroform extraction. Cell-free DNA was isolated from blood plasma with "QIAamp MinElute ccfDNA kit" according to the manufacturer‘s instructions.
Libraries were constructed according to TOP-seq (Stasevskij et al., 2017) and hmTOP-seq (Gibas et al., 2020) protocols. Briefly, cfDNA and sonicated gDNA were labeled with azide moieties using Ado-6-azide (for uCG analysis) or UDP-6-azide-glucose (for 5hmCG analysis) cofactors. After ligation of adapters, the alkyne-bearing oligodeoxyribonucleotides (ODNs) with (5hmCG) or without (uCG) biotin were attached to the azide-modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads. Purified DNA after ODN conjugation (uCG) or biotin-enrichment (5hmC) was subsequently used in a DNA priming reaction. The products were amplified, size-selected and subjected to Ion Proton sequencing.

tag: sample type

value: Pregnant women carrying T21 positive fetus

tag: dna modification

value: Unmodified CG sites


title: sample_cf_068T21_R1_XX_uCG


title: PC3_2h_hemeTreated_replicate2

value: heme (50 uM) for 2h


title: PC3 control_replicate2


title: MCP_51

tag: strain

value: female


title: PC3_2h_hemeTreated_replicate1


title: MCP_50

value: basophil-mast cell progenitors

tag: sorting strategy


title: sample_cf_025T21_R1_XY_uCG


title: MCP_52

value: Live Lin- c-Kit+ FcεRI+ integrin β7hi SSClow cells


title: PC3 control_replicate1


title: MCP_4


title: sample_cf_016T21_R1_XX_uCG


title: MCP_49


title: MCP_56


title: sample_cf_004T21_R1_XY_uCG


title: MCP_48


title: MCP_47


title: Dry_ABA_0uM

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
The alignment was performed using hisat2 against the reference Punica granatum isolate: Tunisia-2019 RefSeq Genome (Assembly: GCA_007655135.2)
Gene counts were obtained using featureCounts.
Genome_build: Punica granatum isolate: Tunisia-2019 RefSeq Genome (Assembly: GCA_007655135.2)
Supplementary_files_format_and_content: tab-delimited text files containing raw count values for each sample

organism: Punica granatum

source_name: pomegranate

growth_protocol: Annual twigs of robust and disease- and insect pest-free pomegranate were selected as cuttings, and cut into 4-6 cm lengths (at least 2 buds were left in each branch). The upper end was cut flat 1 - 2.5 cm away from the bud or leaf, and the lower end (i.e., insertion end) was cut at a 45-degree bevel to the bud mouth. The lower end of cuttings was dipped in 500 mg/L IBA aqueous solution and then cut into a 20 cm x 20 cm nutrient pot for soil culture. Each pot was then filled with 4 kg of mixed soil (msoil: morganic fertilizer: msand = 6: 3: 1), with one plant in each pot. The plants were cultured in an artificial climate chamber (temperature of 26+/-2 ℃, light intensity of 5000 LX, light conditions of 12 h/12 h and relative humidity of 60 - 70%) for 90 days.

extract_protocol:
Total RNAs was extracted from the leaves of each plant using TRIzol.
Illumina libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: After 90 days growth, the healthy seedlings of the same growth condition (plant height 15+/-1 cm) were selected and transferred into an artificial incubator (temperature of 26 - 32℃, natural light conditions). Plants were subjected to drought stress by reducing the soil moisture content of the cultivation pot to 30% - 35% of the field water capacity. The weighing strategy was applied to control soil humidity in pots. In order to prevent evaporation or leakage of the soil moisture, we sealed the soil in pots with plastic bags, and tightened the top of at the base of the seedlings. At the same time of drought stress, the plants were assigned into four experimental groups, where three groups were then sprayed daily with 5 mL of 30, 60 and 90 μM ABA solutions concentrations, respectively, and the rest one group was treated with the same amount of distilled water (0 μM ABA solution) as control.

value: Hongmanao

value: leaf

value: 180 days

value: wt


title: Dry_ABA_30uM


title: sample_cf_041_R1_XX_uCG

value: Pregnant women carrying healthy fetus


title: sample_cf_083_R1_XX_uCG


title: Dry_ABA_90uM


title: sample_cf_031_R1_XX_uCG


title: sample_cf_137_R1_XY_uCG


title: MCP_45


title: Dry_ABA_60uM


title: MCP_44


title: sample_cf_022_R1_XY_uCG


title: MCP_43


title: sample_cf_006_R1_XY_uCG


title: MCP_42


title: sample_cf_002_R1_XY_uCG


title: control_cf_035_R1_XX_uCG

value: Non-pregnant controls


title: MCP_40


title: MCP_3


title: MCP_46


title: Female 3 Control corresponding to inulin intake

type: RNA

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 11 block 4_F3_Ctr2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides 8x15K were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mus musculus female control2 individual 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard chow and water ad libitum (Diet A04C-10, Scientific Animal Food and Engineering, Augy, France)

extract_protocol: Total RNA was extracted from hepatic tissues using RNAspin columns (Macherey-Nagel).

treatment_protocol: Mice were fed for 30 days with an aqueous decoction of the roots flour from two selected chicory genotypes (G12 and G35) and with an inulin (I2255 Sigma Aldrich, MO, USA).solution. Mice were fed with an aqueous decoction of the roots flour from two selected chicory genotypes (G12 and G35) and with an inulin (I2255 Sigma Aldrich, MO, USA) solution. The mice gavages consisted in a daily force-feeding of 500 µl of stemming solution decoctions of chicory flour or inulin water solution besides the standard chow. For the chicory flour, the decoction corresponded to 10 mg root powder/mouse/day. The administrated dose of inulin was calculated to correspond to the concentration of the inulin in the G35 roots at the daily consumption, and was respectively 6.9 mg/mouse/day. Controls will undergo an equivalent force-feeding with water.

value: liver

value: 8 weeks of age at D0


title: Female 2 Control corresponding to inulin intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 9 block 4_F2_Ctr2

source_name: Mus musculus female control2 individual 2


title: Female 2 gavage with inulin

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 9 block 2_F2_Inu

source_name: Mus musculus female force-fed with inulin individual 2

value: force-fed with inulin


title: Female 1 gavage with inulin

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 11 block 2_F1_Inu

source_name: Mus musculus female force-fed with inulin individual 1


title: Female 1 Control corresponding to inulin intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 10 block 1_F1_Ctr2

source_name: Mus musculus female control2 individual 1


title: Female 3 gavage with inulin

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 9 block 1_F3_Inu

source_name: Mus musculus female force-fed with inulin individual 3


title: control_cf_011_R1_XX_uCG


title: sample_tissue_6A_R1_XY_uCG

source_name: Chorionic villi tissue

value: Chorionic villi tissue sample


title: MCP_39


title: MCP_38


title: MCP_37


title: MCP_41


title: sample_tissue_22A_R1_XX_uCG


title: sample_tissue_23A_R1_XY_uCG


title: MCP_36


title: sample_tissue_20A_R1_XY_uCG


title: Male 3 gavage with inulin

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 7 block 2_M3_Inu

source_name: Mus musculus male force-fed with inulin individual 3

value: male


title: control_cf_017_R1_XX_uCG


title: sample_tissue_10A_R1_XX_uCG


title: Male 1 gavage with inulin

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 8 block 2_M1_Inu

source_name: Mus musculus male force-fed with inulin individual 1


title: Male 2 gavage with inulin

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 10 block 2_M2_Inu

source_name: Mus musculus male force-fed with inulin individual 2


title: MCP_34

source_name: Peritoneal cells


title: Male 2 Control corresponding to inulin intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 8 block 4_M2_Ctr2

source_name: Mus musculus male control2 individual 2


title: Male 3 Control corresponding to inulin intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 10 block 4_M3_Ctr2

source_name: Mus musculus male control2 individual 3


title: Male 1 Control corresponding to inulin intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 7 block 4_M1_Ctr2

source_name: Mus musculus male control2 individual 1


title: MCP_33


title: MCP_32


title: sample_cf_050T21_R1_XY_hmC

value: Pregnant women carrying T21 positive fetus


title: MCP_31


title: sample_cf_016T21_R3_XX_hmC_3MillionReads


title: Female 2 gavage with chicory G35

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 6 block 2_F2_G35

source_name: Mus musculus female force-fed with G35 individual 2

value: force-fed with G35


title: MCP_30


title: MCP_35


title: sample_cf_016T21_R1_XX_hmC

source_name: Cell-free DNA


title: MCP_2


title: Female 1 gavage with chicory G35

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 6 block 1_F1_G35

source_name: Mus musculus female force-fed with G35 individual 1


title: sample_cf_011T21_R1_XX_hmC


title: MCP_29


title: sample_cf_004T21_R1_XY_hmC


title: Female 3 gavage with chicory G35

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 2 block 3_F3_G35

source_name: Mus musculus female force-fed with G35 individual 3


title: Female 3 gavage with chicory G12

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 2 block 4_F3_G12

source_name: Mus musculus female force-fed with G12 individual 3

value: force-fed with G12


title: MCP_28

value: female


title: sample_cf_050T21_R3_XY_hmC_3MillionReads


title: MCP_27

value: basophil-mast cell progenitors


title: sample_cf_136_R1_XY_hmC


title: Female 2 gavage with chicory G12

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 4 block 1_F2_G12

source_name: Mus musculus female force-fed with G12 individual 2


title: sample_cf_130_R1_XY_hmC


title: MCP_25

value: Live Lin- c-Kit+ FcεRI+ integrin β7hi SSClow cells


title: sample_cf_050_seqR1_XX_hmC


title: MCP_24


title: Female 1 Control corresponding to chicory food intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 6 block 4_F1_Ctr1

source_name: Mus musculus female control1 individual 1


title: sample_cf_023_R2_XY_hmC_3MillionReads


title: Female 2 Control corresponding to chicory food intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 4 block 2_F2_Ctr1

source_name: Mus musculus female control1 individual 2


title: MCP_23


title: Male 3 gavage with chicory G35

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 1 block 2_M3_G35

source_name: Mus musculus male force-fed with G35 individual 3


title: Male 2 gavage with chicory G35

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 4 block 3_M2_G35

source_name: Mus musculus male force-fed with G35 individual 2


title: sample_cf_007_R2_XX_hmC_3MillionReads


title: MCP_22


title: Male 1 gavage with chicory G35

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 5 block 1_M1_G35

source_name: Mus musculus male force-fed with G35 individual 1


title: MCP_21


title: sample_cf_023_R1_XY_hmC


title: sample_cf_007_R1_XX_hmC


title: MCP_26


title: Female 1 gavage with chicory G12

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 6 block 3_F1_G12

source_name: Mus musculus female force-fed with G12 individual 1


title: MCP_1


title: Female 3 Control corresponding to chicory food intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 1 block 1_F3_Ctr1

source_name: Mus musculus female control1 individual 3


title: control_cf_005_R1_XX_hmC


title: control_cf_007_R1_XX_hmC


title: Male 3 gavage with chicory G12

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 1 block 3_M3_G12

source_name: Mus musculus male force-fed with G12 individual 3


title: control_cf_004_R1_XX_hmC


title: MCP_19

source_name: Peritoneal cells


title: MCP_20


title: Male 2 gavage with chicory G12

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 5 block 2_M2_G12

source_name: Mus musculus male force-fed with G12 individual 2


title: Male 2 Control corresponding to chicory food intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 4 block 4_M2_Ctr1

source_name: Mus musculus male control1 individual 2


title: Male 3 Control corresponding to chicory food intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 1 block 4_M3_Ctr1

source_name: Mus musculus male control1 individual 3


title: control_cf_001_R1_XX_hmC

source_name: Cell-free DNA


title: MCP_17


title: Male 1 Control corresponding to chicory food intake

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 5 block 4_M1_Ctr1

source_name: Mus musculus male control1 individual 1


title: sample_tissue_6A_R1_XY_hmC

source_name: Chorionic villi tissue


title: sample_tissue_22A_R1_XX_hmC


title: MCP_15


title: MCP_16


title: sample_tissue_10A_R1_XX_hmC


title: MCP_13


title: MCP_14


title: MCP_12


title: MCP_18


title: Male 1 gavage with chicory G12

description:
Gene expression after 30 days of gavage (D30)
raw data file: Slide 5 block 3_M1_G12

source_name: Mus musculus male force-fed with G12 individual 1


title: MCP_11


title: sample_cf_144_R1_XX_hmC


title: MCP_10


title: Mature_Mast_Cell_9

value: Mature mast cell

value: Live Lin- c-Kit+ FcεRI+ integrin β7low SSChi cells


title: MEG3_EC109_3_NS

city: Shantou

first: Li

middle: Ming

last: kai

address: Dong Xia

institute: Shantou University

description: EC109 cells harvested from the second dish were transfected with Lv-MEG3

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Affy packages in R.

label: biotin

source_name: human esophageal squamous cell carcinoma

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: EC109 cells were cultured in Dulbecco's  modified Eagle's medium (DMEM) containing 10% (v/v) fetal  bovine serum (FBS; Invitrogen Life Technologies, Carlsbad,  CA, USA), penicillin (final concentration, 100 U/ml), and strep-  tomycin (final concentration, 100 mg/ml), under a humidified  atmosphere with 5% CO 2 at 37˚C.

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

treatment_protocol: EC109 cells were cultured in 6-well plates at a density of 5 × 104 cells/well. When cells were approximately30-40% confluence,the cells were infected with Lv-MEG3 or Lv-NC under the condition that the multiplicity of infection(MOI) is 10 for 12 h.Then discarded lentivirus and continued to cultured the cell for 48h.Puromysin(final concentration 2ug/ml,Sigma, Germany) was added to original culture medium, and continued to culture for a week.Finally,obtained EC109 cells stably expressing MEG3.

tag: transfection


title: Mature_Mast_Cell_94


title: MEG3_EC109_1_NS

description: EC109 cells harvested from the third dish were transfected with Lv-MEG3


title: MEG3_EC109_2_NS

description: EC109 cells harvested from the first dish were transfected with Lv-MEG3


title: Field samples TRAC2 Clinical sample number 10

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 70°C in a rotating hybridization oven at 10rpm as described (Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923)

scan_protocol: Microarray scanning was done using PowerScanner (Tecan) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments) as described (Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391).

data_processing:
Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted.
Data was processed individually for each batch which was designed for testing one of the experimental factors at the time, namely: parasitemia, total RNA input amount, extraction method or field validation analyses with real field samples.
Local  background correction using normexp, followed by lowess normalization across all features within array and quantile normalization between arrays were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium falciparum

source_name: In vivo P. falciparum parasites obtained from venous blood in Southeast Asia Greater Mekong Subregion

label_protocol: Reverse transcription and cDNA synthesis were done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014)). Synthesis of aminoallyl-coupled cDNA and labeling of samples with Cy fluorophore (GE Healthcare) were carried out as described (Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211).

growth_protocol: P. falciparum strain 3D7 was obtained from BEI Resources (MRA-102) and cultured under standard conditions described before (William Trager, James B. Jensen, Human malaria parasites in continuous culture, Science, 193, 4254, 1976). Prior to the experiment, parasites were double-synchronized with 5% sorbitol solution to achieve a synchrony of +/- 4 hours and cultured under constant agitation. Parasite development was monitored by Giemsa staining and media change was performed every 24 hours to maintain parasite growth.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) with chloroform supplemantaiton (Merck) and Direct-Zol-96 kit (Zymo) or Direct-Zol_MagBeads where applicable following manufacturers' instructions.

tag: experimental factor

value: real field sample

source_name: P. falciparum 3D7 RNA reference pool

tag: culture

value: In vitro culture

tag: Stage

value: asexual blood stage

value: laboratory strain 3D7

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: Field samples TRAC2 Clinical sample number 9

value: In vivo P. falciparum parasites obtained from venous blood in Southeast Asia Greater Mekong Subregion


title: Kong_M_3_NS

description: EC109 cells harvested from the third dish were transfected with Lv-NC

tag: cell type

value: Lv-NC


title: Kong_M_2_NS

description: EC109 cells harvested from the second dish were transfected with Lv-NC


title: Field samples TRAC2 Clinical sample number 7


title: Mature_Mast_Cell_93


title: Kong_M_1_NS

description: EC109 cells harvested from the first dish were transfected with Lv-NC


title: Field samples TRAC2 Clinical sample number 8


title: Mature_Mast_Cell_92


title: Mature_Mast_Cell_91


title: Mature_Mast_Cell_8


title: Mature_Mast_Cell_90


title: Field samples TRAC2 Clinical sample number 4


title: Mature_Mast_Cell_89


title: Field samples TRAC2 Clinical sample number 6


title: Field samples TRAC2 Clinical sample number 5


title: Field samples TRAC2 Clinical sample number 3


title: Field samples TRAC2 Clinical sample number 1


title: Mature_Mast_Cell_87


title: Mature_Mast_Cell_88


title: DirecZolMagBeads_noChloroform

source_name: MagBeads Extractions P.falciparum 3D7 transcriptome with RNA extracted using Direct Zol MagBeads Method without Chloroform supplementation

value: In vitro culture, asexual stage, laboratory strain 3D7

value: extraction method


title: DirecZolMagBeads_Chloroform

source_name: MagBeads Extractions P.falciparum 3D7 transcriptome with RNA extracted using Direct Zol MagBeads Method with Chloroform supplementation


title: Field samples TRAC2 Clinical sample number 2


title: DirecZol_noChloroform

source_name: MagBeads Extractions P.falciparum 3D7 transcriptome with RNA extracted using Direct Zol Method without Chloroform supplementation


title: Mature_Mast_Cell_86


title: Mature_Mast_Cell_85


title: DirecZol_Chloroform

source_name: MagBeads Extractions P.falciparum 3D7 transcriptome with RNA extracted using Direct Zol Method with Chloroform supplementation


title: Mature_Mast_Cell_84


title: SAMPLE 24: Genomic DNA of N8 from Health control group

type: genomic

city: Changsha

first: Wei

last: Hao

state: Hunan

address: 139 Renmin Middle Road, Furong district

institute: The second xiangya hospital of Central South University

description: Health control

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: N8 from Health control group

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from blood samples using Qiagen DNeasy blood & tissue kits according to standard instructions.

value: Male

tag: tissue

value: Peripheral blood lymphocytes

tag: disease state

value: Health control


title: Mature_Mast_Cell_83

value: female


title: RNA input P.falciparum 3D7 transcriptome at 0.1% parasitemia (10ng total RNA)

source_name: In vitro culture, asexual stage, laboratory strain 3D7

value: RNA input amount


title: RNA input P.falciparum 3D7 transcriptome at 0.1% parasitemia (50ng total RNA)


title: RNA input P.falciparum 3D7 transcriptome at 0.1% parasitemia (250ng total RNA)


title: RNA input P.falciparum 3D7 transcriptome at 0.1% parasitemia (125ng total RNA)


title: Mature_Mast_Cell_82

source_name: Peritoneal cells


title: SAMPLE 22: Genomic DNA of N6 from Health control group

description: Health control

source_name: N6 from Health control group


title: SAMPLE 23: Genomic DNA of N7 from Health control group

description: Health control

source_name: N7 from Health control group


title: RNA input P.falciparum 3D7 transcriptome at 1% parasitemia (10ng total RNA)


title: RNA input P.falciparum 3D7 transcriptome at 1% parasitemia (50ng total RNA)


title: SAMPLE 21: Genomic DNA of N5 from Health control group

description: Health control

source_name: N5 from Health control group


title: Mature_Mast_Cell_81


title: SAMPLE 18: Genomic DNA of N2 from Health control group

description: Health control

source_name: N2 from Health control group


title: RNA input P.falciparum 3D7 transcriptome at 1% parasitemia (125ng total RNA)


title: Mature_Mast_Cell_80


title: SAMPLE 17: Genomic DNA of N1 from Health control group

description: Health control

source_name: N1 from Health control group


title: RNA input P.falciparum 3D7 transcriptome at 1% parasitemia (250ng total RNA)


title: Mature_Mast_Cell_7


title: Mature_Mast_Cell_79


title: SAMPLE 20: Genomic DNA of N4 from Health control group

description: Health control

source_name: N4 from Health control group


title: SAMPLE 19: Genomic DNA of N3 from Health control group

description: Health control

source_name: N3 from Health control group


title: Serial dilutions Uninfected Red Blood Cells

description: uninfected

value: parasitemia


title: Mature_Mast_Cell_78

value: Mature mast cell


title: Serial dilutions P.falciparum 3D7 transcriptome at 0.001% parasitemia


title: SAMPLE 12: Genomic DNA of B4 from LMAS group

description: Low MA addiction susceptibility

source_name: B4 from LMAS group

value: methamphetamine (MA) abuser


title: buffalo_muscle_2

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

data_processing:
Low-quality reads and those containing adapters were removed to obtain clean reads using Trim Galore. High-quality data were used for the subsequent analysis. Each read was aligned to the reference genome using STAR. Mapped reads were assembled using Cufflinks v2.2.1. These assemblies were merged to the reference gene model annotation by Cuffmerge.
For mRNAs and lncRNAs, fragments per kilobase of transcript per million mapped reads (FPKM) was used as index to calculate the expression level of each transcript in every library using Cuffdiff program.
For circRNA prediction, the CIRCexplorer2 was employed to identify the back-spliced junction of circRNAs. To calculate the expression levels of circRNAs, back-spliced reads per million mapped reads (BSRP) was used.
Genome_build: UMD3.1
Supplementary_files_format_and_content: (1) Tab-delimited text files include FPKM  values (mRNAs and lncRNAs) or BSRP values (circRNAs) for each sample. (2) The .fa files include sequences of lncRNAs and circRNAs predicted in this study.

organism: Bubalus bubalis

source_name: low IMF

growth_protocol: Three Xinyang buffalo and three Nanyang cattle were raised in the breeding farm of Xinyang Buffalo (Guangshan, Henan province, P.R. China) and the breeding center of Nanyang cattle (Nanyang, Henan province, P.R. China), respectively, with equivalent forage and feeding management conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, USA). The quality and concentration of total RNA were determined by the NanoDrop 2,000 (Nanodrop, Wilmington, DE) and 1% agarose gel.
Approximately 2 μg total RNA per sample was used for library construction according to protocol of the TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA).

treatment_protocol: Animals were weaned at three months of age, castrated at six months of age, started to fatten at 18 months of age, and slaughtered at 30 months of age.

tag: intramuscular fat

value: low IMF

value: muscle


title: Mature_Mast_Cell_75

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts(.txt)

value: Live Lin- c-Kit+ FcεRI+ integrin β7low SSChi cells


title: Mature_Mast_Cell_77


title: buffalo_muscle_3


title: Mature_Mast_Cell_74


title: SAMPLE 16: Genomic DNA of B8 from LMAS group

description: Low MA addiction susceptibility

source_name: B8 from LMAS group


title: SAMPLE 10: Genomic DNA of B2 from LMAS group

description: Low MA addiction susceptibility

source_name: B2 from LMAS group


title: Serial dilutions P.falciparum 3D7 transcriptome at 0.01% parasitemia

source_name: P. falciparum 3D7 RNA reference pool

value: In vitro culture

value: asexual blood stage

value: laboratory strain 3D7


title: Serial dilutions P.falciparum 3D7 transcriptome at 0.05% parasitemia

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: buffalo_muscle_1


title: Serial dilutions P.falciparum 3D7 transcriptome at 0.005% parasitemia

value: In vitro culture, asexual stage, laboratory strain 3D7


title: SAMPLE 13: Genomic DNA of B5 from LMAS group

description: Low MA addiction susceptibility

source_name: B5 from LMAS group


title: P.falciparum 3D7 transcriptome at time point 25

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 70°C in a rotating hybridization oven at 10rpm as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923:

scan_protocol: Microarray scanning was done using PowerScanner (Tecan) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing:
Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted.
Local  background correction using normexp, followed by lowess normalization across all features within array and quantile normalization between arrays were carried out to generate the normalized Log2 gene expression ratios.
The 9th time point was removed due to its big dissimilarity to all the other samples.

source_name: In vitro culture, asexual stage, laboratory strain 3D7,48h

label_protocol: Reverse transcription and cDNA synthesis were done following modifed Smart-Seq2 protocol (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014)). Synthesis of aminoallyl-coupled cDNA and labeling of samples with Cy fluorophore (GE Healthcare) were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: P. falciparum strain 3D7 was obtained from BEI Resources (MRA-102) and cultured under standard conditions as described in Trager and Jensen (1976) Human malaria parasites in continuous culture. Science. 1976;193(4254):673‐675. Prior to time-point experiment, parasites were double-synchronized with 5% sorbitol solution to achieve a synchrony of +/- 6 hours and cultured under constant agitation. For sampling of highly synchronous parasites during the asexual life cycle, the first time point was considered as the 0 h when >95% of early ring stage parasites (<6hr HPI) were present in the culture. To ensure a sufficient amount of mRNA for subsequent analysis, parasites were cultured in 25 individual flasks in 25 mL of medium at 2% haematocrit and 8% parasitemia for each time point. Starting from 0 h, parasites were collected every 2 hours for 25 successive time points. Parasite development was monitored by Giemsa staining and media change was performed once at 24 h time point to maintain parasite growth.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: time point

source_name: P. falciparum 3D7 asexual stage, RNA reference pool of equal amounts of RNA from each time point


title: SAMPLE 14: Genomic DNA of B6 from LMAS group

description: Low MA addiction susceptibility

source_name: B6 from LMAS group

tag: gender


title: Serial dilutions P.falciparum 3D7 transcriptome at 1% parasitemia

source_name: In vitro culture, asexual stage, laboratory strain 3D7


title: SAMPLE 15: Genomic DNA of B7 from LMAS group

description: Low MA addiction susceptibility

source_name: B7 from LMAS group


title: Mature_Mast_Cell_73

source_name: Peritoneal cells


title: induced 3

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

description: 5-aza induced iCDCs at passage 30

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 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
Genome_build: mm10

source_name: cardiosphere derived cells

extract_protocol:
Total RNA was extracted from 3 separate samples of control CDCs and 5-aza treated CDCs at passage 30 using Trizol(Life science)and DNA-free kit(Ambion).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: iCDC at passage 30 were treated with 10uM 5-aza for 3 days,following with culture in IMDM medium contained 2% FBS for 4 weeks.

value: heart ventricle


title: Mature_Mast_Cell_72


title: induced 2

description: 5-aza induced iCDCs at passage 30


title: SAMPLE 7: Genomic DNA of A7 from HMAS group

description: High MA addiction susceptibility

source_name: A7 from HMAS group

value: Male

value: methamphetamine (MA) dependence


title: SAMPLE 8: Genomic DNA of A8 from HMAS group

description: High MA addiction susceptibility

source_name: A8 from HMAS group

value: Peripheral blood lymphocytes


title: SAMPLE 5: Genomic DNA of A5 from HMAS group

description: High MA addiction susceptibility

source_name: A5 from HMAS group


title: P.falciparum 3D7 transcriptome at time point 24

source_name: In vitro culture, asexual stage, laboratory strain 3D7,46h


title: SAMPLE 9: Genomic DNA of B1 from LMAS group

description: Low MA addiction susceptibility

source_name: B1 from LMAS group


title: control 2

description: iCDCs at passage 30


title: SAMPLE 4: Genomic DNA of A4 from HMAS group

description: High MA addiction susceptibility

source_name: A4 from HMAS group


title: Mature_Mast_Cell_70

value: female


title: P.falciparum 3D7 transcriptome at time point 23

source_name: In vitro culture, asexual stage, laboratory strain 3D7,44h


title: SAMPLE 6: Genomic DNA of A6 from HMAS group

description: High MA addiction susceptibility

source_name: A6 from HMAS group


title: induced 1

description: 5-aza induced iCDCs at passage 30


title: Mature_Mast_Cell_69


title: Mature_Mast_Cell_68


title: Mature_Mast_Cell_76


title: P.falciparum 3D7 transcriptome at time point 22

source_name: In vitro culture, asexual stage, laboratory strain 3D7,42h


title: SAMPLE 11: Genomic DNA of B3 from LMAS group

description: Low MA addiction susceptibility

source_name: B3 from LMAS group


title: SAMPLE 2: Genomic DNA of A2 from HMAS group

description: High MA addiction susceptibility

source_name: A2 from HMAS group


title: control 3

description: iCDCs at passage 30


title: Mature_Mast_Cell_6


title: Mature_Mast_Cell_71


title: control 1

description: iCDCs at passage 30


title: SAMPLE 3: Genomic DNA of A3 from HMAS group

description: High MA addiction susceptibility

source_name: A3 from HMAS group


title: SAMPLE 1: Genomic DNA of A1 from HMAS group

description: High MA addiction susceptibility

source_name: A1 from HMAS group


title: Vhl_OPC_AZ_C

description:
CRISPR-Vhl OPCs
AZ_DMSO_VHL_EXPT.tpm_table.csv

data_processing:
Raw RNA sequencing reads were analyzed with salmon 0.14.1 (Patro et al. Nature Methods 2017) to quantify transcript abundance in transcripts per million (TPM) for the Gencode M22 release.
Transcripts were summarized as gene-level TPM abundances with tximport (Soneson et al. F1000Research 2015)
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values file of raw TPM expression values

source_name: Oligodendrocyte precursor cells (OPCs)

extract_protocol:
Phenol-chloroform with TRIzol.
Submitted RNA to Novogene for library construction and sequencing.

treatment_protocol: CRISPR-Control and CRISPR-Vhl OPCs were grown and then lysed for RNA. For drug treated samples, CRISPR-Control OPCs and CRISPR-Vhl OPCs were grown for a day and then media was switched to media containing either DMSO or 300nM AZD8330 for 14hrs and then lysed for RNA.

value: epiblast stem cell derived OPCs

tag: drug treatment

value: 300nM AZD8330 (Selleck chemicals, S2134)


title: Mature_Mast_Cell_67

value: Mature mast cell


title: Mature_Mast_Cell_66


title: Mature_Mast_Cell_65


title: LtfCreBrg1flfl_rep1

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: RNA library from sorted EPCAM+ endometrial epithelial cells of an individual 120-day old LtfCre^0/+; Brg1^fl/fl mouse biological replicate.

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file. Raw gene counts were combined with control cell data retrieved from GEO accession GSE129784.
Gene Ensembl IDs were converted to external gene names (symbols) via biomaRt. Low count genes were filtered (at least 1 count per sample on average) prior to normalization factor generation, dispersion estimation, negative binomial generalized linear model fitting, and hypothesis testing in DESeq2 for differential gene expression analysis. For linear modeling, the design matrix was constructed from a single “condition” variable with the inclusion of an intercept, in the form: ~ condition. Calculated differential gene expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including per-sample gene counts (STAR output) and non-thresholded DESeq2 differential gene expression analysis.

source_name: EPCAM+ endometrial epithelial cells

growth_protocol: Mice were housed at the Michigan State University Grand Rapids Research Center in accordance with protocols approved by Michigan State University.

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Directional mRNA-seq libraries were constructed from 500 ng of total RNA supplied to the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems). RNA was sheared to 300-400 bp. cDNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc.).

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).

tag: genotype

value: LtfCre^0/+; Brg1^fl/fl


title: P.falciparum 3D7 transcriptome at time point 21

source_name: In vitro culture, asexual stage, laboratory strain 3D7,40h

source_name: P. falciparum 3D7 asexual stage, RNA reference pool of equal amounts of RNA from each time point


title: LtfCreBrg1flfl_rep3


title: LtfCreBrg1flfl_rep4


title: Mature_Mast_Cell_64

city: Solna

first: Joakim

last: Dahlin

institute: Karolinska Institutet

source_name: Peritoneal cells


title: LtfCreBrg1flfl_rep2


title: Vhl_OPC_AZ_B


title: P.falciparum 3D7 transcriptome at time point 20

source_name: In vitro culture, asexual stage, laboratory strain 3D7,38h


title: Vhl_OPC_AZ_A


title: Vhl_OPC_D_C

value: DMSO


title: P.falciparum 3D7 transcriptome at time point 17

source_name: In vitro culture, asexual stage, laboratory strain 3D7,32h


title: P.falciparum 3D7 transcriptome at time point 16

source_name: In vitro culture, asexual stage, laboratory strain 3D7,30h


title: Mature_Mast_Cell_63


title: Mature_Mast_Cell_61


title: Mature_Mast_Cell_62


title: P.falciparum 3D7 transcriptome at time point 19

source_name: In vitro culture, asexual stage, laboratory strain 3D7,36h


title: P.falciparum 3D7 transcriptome at time point 18

source_name: In vitro culture, asexual stage, laboratory strain 3D7,34h


title: P.falciparum 3D7 transcriptome at time point 15

source_name: In vitro culture, asexual stage, laboratory strain 3D7,28h


title: P.falciparum 3D7 transcriptome at time point 14

source_name: In vitro culture, asexual stage, laboratory strain 3D7,26h


title: Mature_Mast_Cell_60


title: Mature_Mast_Cell_5


title: Vhl_OPC_D_A


title: P.falciparum 3D7 transcriptome at time point 13

source_name: In vitro culture, asexual stage, laboratory strain 3D7,24h


title: Mature_Mast_Cell_59


title: Control_OPC_AZ_B

description:
CRISPR-Control OPCs
AZ_DMSO_VHL_EXPT.tpm_table.csv


title: Control_OPC_AZ_A


title: P.falciparum 3D7 transcriptome at time point 12

source_name: In vitro culture, asexual stage, laboratory strain 3D7,22h


title: Mature_Mast_Cell_58


title: P.falciparum 3D7 transcriptome at time point 10

source_name: In vitro culture, asexual stage, laboratory strain 3D7,18h


title: P.falciparum 3D7 transcriptome at time point 11

source_name: In vitro culture, asexual stage, laboratory strain 3D7,20h


title: Mature_Mast_Cell_57


title: Mature_Mast_Cell_56


title: Vhl_OPC_D_B


title: P.falciparum 3D7 transcriptome at time point 8

source_name: In vitro culture, asexual stage, laboratory strain 3D7,14h


title: Control_OPC_D_C

source_name: Oligodendrocyte precursor cells (OPCs)


title: Control_OPC_D_A


title: Control_OPC_D_B


title: P.falciparum 3D7 transcriptome at time point 6

source_name: In vitro culture, asexual stage, laboratory strain 3D7,10h


title: Vhl_OPC_C

description:
CRISPR-Vhl OPCs
Control_Vhl_tpm_table.csv


title: P.falciparum 3D7 transcriptome at time point 7

source_name: In vitro culture, asexual stage, laboratory strain 3D7,12h


title: Mature_Mast_Cell_55


title: Mature_Mast_Cell_54


title: Mature_Mast_Cell_53


title: P.falciparum 3D7 transcriptome at time point 5

source_name: In vitro culture, asexual stage, laboratory strain 3D7,8hr

source_name: P. falciparum 3D7 asexual stage, RNA reference pool of equal amounts of RNA from each time point


title: Vhl_OPC_B


title: Control_OPC_AZ_C


title: SAHA_JQ1_RNA_Rep3

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
For H4ac ChIP, single end 50-bp reads were filtered using TagDust (Lassmann et al. 2009). ChIP-Rx normalization was performed as described in (Orlando et al. 2014). Briefly, reads were first aligned to the Drosophila dm3 genome using Bowtie (Langmead et al. 2009). Unmapped reads were then aligned to the human hg19 genome using Bowtie and reads were normalized to Drosophila mapped read counts.
To generate differential windows, input signal was subtracted from ChIP signal. Signal was then averaged across 300bp sliding windows offset by 100 bp. Differential windows were identified using DESEQ2 (Love et al. 2014). Windows with significant enrichment were merged and identified as a peak.
For BRD4 ChIP, single end 50-bp reads were filtered using TagDust (Lassmann et al. 2009) and aligned to hg19 using Bowtie (Langmead et al. 2009). Peaks were called with MACS2 (Zhang et al. 2008).
Sequencing reads were aligned to hg19 (STAR v2.5.2b, (Dobin et al. 2013). Differential genes were identified by DESEQ2 (Love et al. 2014) and count data was used to generate the MAplot using RStudio.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent spike-in normalized read depth genomic coverage
Excel files contain peak calls as determined by MACS2
DESeq2 differential gene files contain relevant data necessary to determine differential genes via DESeq2
ROSE super-enhancer files lists enhancer, super-enhancers, and signal associated with called enhancers
Differential window files contain differential H4ac peaks as determined by DESeq2
The combined expression matrix contains the TPMs (as calculated by Salmon) for each RefSeq isoform across all samples.

growth_protocol: Cells were grown in RPMI-1640 plus 20% FBS

extract_protocol:
RNA was extracted using TRIzol reagent. For H4ac ChIP, HL60 cells were cultured to a density of 7x10^5 cell/mL and treated with 1 µM SAHA or 0.01% DMSO for 1 h prior to ChIP protocol.
Sequencing libraries were generated from DNA enriched by ChIP following the manufacturer’s specification for the Tru-Seq library preparation kit (Illumina)

treatment_protocol: HL60 cells were treated with either DMSO or SAHA for 1hr or 2hr prior to collection

tag: cell line

value: leukemia cell line HL60

tag: treatment

value: SAHA and JQ1


title: Mature_Mast_Cell_52

source_name: Peritoneal cells

extract_protocol:
189 single cells were index-sorted into 2 x 96-well PCR plates containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton per well), vortexed and frozen at -70 °C. Sample preparation for RNA-sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) with minor modifications. Following brief centrifugation at 2000 rpm for 2 minutes to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 50 U/reaction SmartScribe Reverse Transcriptase (Takara ClonTech, 639537) without Betaine and MgCl2, and amplified using 23 PCR cycles. ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882) using BioMek FXP Dual Span Liquid Handler. Single cell cDNA library was eluted in 22 µl volume of EB Buffer (Qiagen, 19086) and 20 µl volume collected to ensure minimal bead carryover.
Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set A and D (Illumina, FC-121-2001 and FC-121-2004 respectively), following the manufacturer’s protocol using ¼ of the recommended volumes and 1.26 µl cDNA library. Single cell libraries labelled with Index Kit A and D were pooled separately and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 32.0 µl EB Buffer and 30.0 µl volume collected to ensure minimal bead carryover. Quantification was performed with KAPA Library Quant Kit (Roche, 07960140001); index kit A pooled libraries were mixed with equimolar concentration of index kit D pooled libraries and sequenced in one lane on the Illumina HiSeq4000 system (50 bp single-end reads).

tag: strain

value: Live Lin- c-Kit+ FcεRI+ integrin β7low SSChi cells


title: P.falciparum 3D7 transcriptome at time point 4

source_name: In vitro culture, asexual stage, laboratory strain 3D7,6hr


title: Vhl_OPC_A

city: Cleveland

first: Paul

last: Tesar

institute: Case Western Reserve University


title: P.falciparum 3D7 transcriptome at time point 2

source_name: In vitro culture, asexual stage, laboratory strain 3D7,2hr


title: SAHA_JQ1_RNA_Rep2


title: Control_OPC_C

description:
CRISPR-Control OPCs
Control_Vhl_tpm_table.csv


title: Mature_Mast_Cell_50

tag: sorting strategy


title: Mature_Mast_Cell_51


title: P.falciparum 3D7 transcriptome at time point 3

source_name: In vitro culture, asexual stage, laboratory strain 3D7,4hr


title: Control_OPC_B


title: P.falciparum 3D7 transcriptome at time point 1

source_name: In vitro culture, asexual stage, laboratory strain 3D7,0h


title: Mature_Mast_Cell_4


title: Mature_Mast_Cell_48


title: Mature_Mast_Cell_49


title: JQ1_RNA_Rep1


title: Control_OPC_A


title: JQ1_RNA_Rep2


title: JQ1_RNA_Rep3


title: Mature_Mast_Cell_46


title: SAHA_RNA_Rep3

value: SAHA


title: Mature_Mast_Cell_47


title: Mature_Mast_Cell_45


title: SAHA_RNA_Rep1


title: p20050_s054_7252_d14_BAL

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
p20050_s054_7252_d14_BAL_S54
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Composite reference was generated by concatenating sequence (.fa) and annotation (.gtf) files for host and viral genome references
Reads were mapped to the Composite (MacaM MN985325.1)  genomic reference with STAR (v2.7.3a) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized abundace was caluclated with DESeq2 R Package (version 1.26.0)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) (https://www.unmc.edu/rhesusgenechip/index.htm).
Genome_build: MN985325.1, SARS-CoV2 (strain MN985325.1) was downloaded from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/MN985325)
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Group III_d14_BAL

extract_protocol:
RNA was extracted from PAXgene RNA Blood Tubes using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit (ThermoFisher). RNA was extracted from BAL fluid stored in PAXgene RNA Blood Tubes using the PAXgene Blood RNA Kit IVD (Qiagen).
Globin transcripts in the blood RNA were blocked prior to library prep using the FastSelect Globin Reagent (Qiagen). Libraries were prepared using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) in combination with the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 25 million reads per sample.

tag: animalid

tag: timepoint

tag: group

value: BAL


title: DMSO_RNA_Rep3


title: p20050_s042_7244_d14_BAL

description:
p20050_s042_7244_d14_BAL_S42
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: C42B_Con_shC

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

data_processing:
Bowtie2 version 2.1.0 was used for mapping to the human genome hg19 transcript set.
RSEM v1.2.15 was used to calculate the count and estimate the gene expression level.
Trimmed Mean of M-values (TMM) method in the edgeR package was used for gene  expression normalization.
Genome_build: hg19
Supplementary_files_format_and_content: TMM

source_name: enzalutamide-sensitive (C4-2B Con)

growth_protocol:
C4-2B ENZR cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin and 20 µM ENZ, and cultured at 37°C in a humidified atmosphere containing 5% CO2 (v/v).
C4-2B Con cells were maintained in RPMI 1640 medium [supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin] containing DMSO in parallel with C4-2B ENZR cells, and at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
The total RNA of C4-2B Con and C4-2B ENZR cells was extracted by RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq was performed on an Illumina HiSeq 3000 for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

tag: cell line background

value: Derivative subline of human prostate cancer LNCaP-derived C4-2 cells

tag: phenotype

value: Enzalutamide-sensitive, castration-resistant prostate cancer cell line


title: C42B_EZ_shC

source_name: enzalutamide-resistant (C4-2B ENZR)

tag: cell type

value: Enzalutamide-resistant, castration-resistant prostate cancer cell line


title: DMSO_RNA_Rep2


title: SAHA_JQ1_RNA_Rep1


title: DMSO_RNA_Rep1


title: p20050_s036_7182_d14_BAL

description:
p20050_s036_7182_d14_BAL_S36
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group II_d14_BAL

tag: tissue


title: Mature_Mast_Cell_43

address: CMM, Visionsgatan 18


title: Mature_Mast_Cell_44


title: Mature_Mast_Cell_42


title: p20050_s030_7174_d14_BAL

description:
p20050_s030_7174_d14_BAL_S30
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: p20050_s024_7173_d14_BAL

description:
p20050_s024_7173_d14_BAL_S24
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: Mature_Mast_Cell_41


title: p20050_s018_7172_d14_BAL

description:
p20050_s018_7172_d14_BAL_S18
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group I_d14_BAL


title: p20050_s012_7165_d14_BAL

description:
p20050_s012_7165_d14_BAL_S12
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: MCC-polyA

city: Frankfurt

first: Tuna

last: Toptan

state: Hessen

address: Institute of Medical Virology, Paul-Ehrlich-Straße 40

country: Germany

institute: University Hospital Frankfurt

data_processing:
Fastq files were imported into CLC Genomics Workbench 20.0 software (Qiagen, Hilden, Germany), paired-end reads 1 and 2 were merged, and duplicate reads were removed. Reads were filtered for Q-scores above 30, trimmed for quality (limit = 0.05) and ambiguity (2-nt maximum), and the illumina and SMART adaptor sequence were removed. Reads below 20 nt were discarded and paired-end reads were aligned to combined reference index from GRCh38 (Hg38) and MCV (JF813003) or to individual reference genomes. The following alignment settings were applied: mismatch = 2, insertion = 3, deletion = 3, length fraction = 0.8, and similarity fraction = 0.8.
Genome_build: GRCh38 (Hg38) and MCV (JF813003)
Supplementary_files_format_and_content: transcript expression profiles exproted as txt files

source_name: Merkel cell carcinoma

extract_protocol:
Total RNA was isolated using TRIzol (Ambion Inc, Austin, TX, USA) and was treated with TURBO DNase (ThermoFisher Scientific). Libraries were prepared using the SMARTer PCR cDNA synthesis kit (Clontech, Mountain View, CA, USA)
RNA quality was examined by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) before and after ribosomal RNA depletion using RiboMinus Eukaryote kit (ThermoFisher).   Libraries were prepared using the SMARTer PCR cDNA synthesis kit (Clontech, Mountain View, CA, USA) according to the manufacturer’s recommendations with the following modifications: Switching Mechanism at 5' End of RNA Template (SMART) fusion primers were designed, which have the SMART sequence (5’-AAGCAGTGGTATCAACGCAGAGTAC-3’) added to the 5’ end of each dMS-identified MCV- or human-specific degenerate reverse primer listed in Supplementary Table 3. dMS-SMART-degenerate primer mix or a modified oligo(dT) primer (3’ SMART CDS primer IIA) were used to prime first strand cDNA synthesis.
Nextera DNA Flex kit was used to generate libraries from SMART-cDNA templates following the manufacturer’s instructions and sequencing was carried out on a NextSeq500 platform (Illumina Inc., San Diego, CA, USA) for 2x75 paired-end reads

tag: mcv status

value: positive (verified by CM2B4 immunohistochemistry staining.

tag: cdna library

value: modified oligo dT primed cDNA library

value: skin


title: Mature_Mast_Cell_40

value: female


title: MCC-LNAdeg

value: pool of LNA modified degenerate oligo primed cDNA library


title: SAHA_RNA_Rep2


title: p20050_s006_7162_d14_BAL

description:
p20050_s006_7162_d14_BAL_S6
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: MCC-deg

value: pool of degenerate oligo primed cDNA library


title: p20050_s053_7252_d10_BAL

description:
p20050_s053_7252_d10_BAL_S53
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group III_d10_BAL


title: Mature_Mast_Cell_39

value: Mature mast cell


title: CUT&RUN IgG

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
CUT&RUN library has been aligned to the hg19 genome using bowtie2 and normalized by the yeast (Saccharomyces cerevisiae) spikein reads.
Genome_build: hg19

source_name: Patient-derived colorectal cancer#92

extract_protocol:
Total RNA was extracted from 5-AZA-CdR or mock-treated samples using QIAGEN RNeasy mini kit. DNA was extracted for CUT&RUN using QIAGEN MinElute Kit.
For the MDA5 protection assay 100ng of RNA was used for the cDNA library construction using KAPA RNA Hyper-Prep with RiboErase library preparation kit from Roche. For the RNA sequencing on total RNA, libraries were prepared using TruSeq Stranded Total RNA Kit (Illumina) and 200ng of RNA underwent ribosomal RNA depletion using Ribo-zero Gold rRNA beads. For DNA-sequencing, libraries were prepared using NEB Ultra II library Preparation kit

value: Patient-derived colorectal cancer#92

tag: time


title: p20050_s048_7250_d14_BAL

description:
p20050_s048_7250_d14_BAL_S48
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: Mature_Mast_Cell_38

tag: gender


title: Mature_Mast_Cell_37


title: p20050_s047_7250_d10_BAL

description:
p20050_s047_7250_d10_BAL_S47
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: 12N3

description:
Reanalyzed sample GSM3721984; RNA library from 12Z cells after non-targeting siRNA control treatment
12N3

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned GRCh38.p12 genome assembly, indexed to GENCODE (v28) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file. Raw gene counts were combined with non-targeting siRNA (control) treated 12Z data retrieved from GEO accession GSE129782.
Gene Ensembl IDs were converted to external gene names (symbols) via biomaRt. Low count genes were filtered (at least 1 count per sample on average) prior to normalization factor generation, dispersion estimation, negative binomial generalized linear model fitting, and hypothesis testing in DESeq2 for differential gene expression analysis. For linear modeling, the design matrix was constructed from a single “condition” variable with the inclusion of an intercept, in the form: ~ condition. Calculated differential gene expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: GRCh38.p12 indexed to GENCODE (v28) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including per-sample gene counts (STAR output) and non-thresholded DESeq2 differential gene expression analysis.

source_name: 12Z cell line

growth_protocol: 12Z cells were cultured in DMEM/F12 media supplemented with 10% FBS, 1% L-glutamine, and 1% Penicllin-Streptomycin.

extract_protocol:
72 hours following siRNA transfection and 48 hours following drug or vehicle treatment, RNA was extracted using the Quick-RNA Miniprep Kit (Zymo Research).
Directional mRNA-seq libraries were constructed from 500 ng of total RNA supplied to the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems). RNA was sheared to 300-400 bp. cDNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc.).

treatment_protocol: Cells were transfected in the absence of antibiotic with 50 nM siRNA (Dharmacon, ON-TARGETplus) via RNAiMax (ThermoFisher) lipofectamine reagent in OptiMEM (Gibco). 24 hours following transfection, growth media was replaced. 48 hours following transfection, growth media was replaced again with 0.5% FBS.

tag: condition

value: non-targeting siRNA control


title: CUT&RUN H3K4me3 ADAR1WT_5-AZA-CdR_D5

description: CUTnRUN_ADAR1WT_5-AZA-CdR_H3K4me3.hg19.bw

data_processing:
Library strategy: CUT&RUN
RNAseq and MDA5-protection libraries have been aligned to the hg19 genome using the STAR aligner.
ADAR1 Editing had been called in the MDA5- protection library.
Inverted Repeats Alus have been detected in the MDA5-protected samples.
CUT&RUN library has been aligned to the hg19 genome using bowtie2 and normalized by the yeast (Saccharomyces cerevisiae)  spikein reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for the RNASeq and MDA5-protection libraries are separated for the forward strand (Positive) and reverse strand (Negative).  Editing tables includes editing/mismatches within Alu repeats. Each table includes the editing in the two replicates of each genotype/treatment condition. It includes the depth of the reference and alternative nucleotide in each replicate and the total depth in the two replicates.  Inverted repeat tables are the tables for 5-AZA-CdR treatment-induced IR list, baseline IR list and the ADAR1KD Mock-treated-induced IR list. 5-AZA-CdR treatment-induced IR list are listed in two tables, one includes their expression in the ADAR1WT 5-AZA-CdR and the other includes their expression in the ADAR1WT Mock-treated sample. Baseline IR are listed in three tables which include their expression in the ADAR1WT Mock-treated, ADAR1WT 5-AZA-CdR, and the ADAR1KD Mock-treated samples. ADAR1KD Mock-treated-induced IR are listed in two tables which include their expression in the ADAR1WT Mock-treated and ADAR1KD Mock-treated samples.
Supplementary_files_format_and_content: githup_data.tar: Metadata for use with githup script.

source_name: CUT&RUN H3K4me3 ADAR1WT_5-AZA-CdR_D5

growth_protocol: Patient-derived colorectal cancer cells #92 were cultured in DMEM/F12 medium, supplemented with L-glutamine (1%), penicillin/streptomycin (1%), Fungizone, Non-essential amino acids (1X), Sodium Pyruvate (1mM), Heparin (4ug/ml Sigma),Neurocult SM1(STEMCELL), N2 supplement (STEMCELL), Lipids (0.2%, Sigma), EGF (20ng/ml, Reprokine) and basic FGF (10ng/ml,Reprokine).

extract_protocol:
Total RNA was extracted from 5-AZA-CdR or mock-treated samples using  QIAGEN RNeasy mini kit.  DNA was extracted for CUT&RUN using QIAGEN MinElute Kit.
For the MDA5 protection assay 100ng of RNA was used for the cDNA library construction using KAPA RNA Hyper-Prep with RiboErase library preparation kit from Roche.  For the RNA sequencing on total RNA, libraries were prepared using TruSeq Stranded Total RNA Kit (Illumina) and 200ng of RNA underwent ribosomal RNA depletion using Ribo-zero Gold rRNA beads. For DNA-sequencing, libraries were prepared using NEB Ultra II library Preparation kit

treatment_protocol: Patient-derived colorectal cancer cells#92  were seeded as 50,000 cells/mL 6-24hrs prior to treatment, then they were treated with 300nM of 5-AZA-CdR or mock-treated, they were kept in culture for 5days and then were collected

tag: genotype

value: Wild type (LACZ)


title: 12N2

description:
Reanalyzed sample GSM3721983; RNA library from 12Z cells after non-targeting siRNA control treatment
12N2

tag: cell line


title: Mature_Mast_Cell_34


title: p20050_s035_7182_d10_BAL

description:
p20050_s035_7182_d10_BAL_S35
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group II_d10_BAL


title: p20050_s041_7244_d10_BAL

description:
p20050_s041_7244_d10_BAL_S41
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: Mature_Mast_Cell_36


title: p20050_s029_7174_d10_BAL

description:
p20050_s029_7174_d10_BAL_S29
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt


title: CUT&RUN H3K27ac ADAR1WT_5-AZA-CdR_D5

description: CUTnRUN_ADAR1WT_5-AZA-CdR_H3K27ac.hg19.bw

source_name: CUT&RUN H3K27ac ADAR1WT_5-AZA-CdR_D5

tag: treatment


title: Mature_Mast_Cell_35

source_name: Peritoneal cells

tag: strain


title: 12N1

description:
Reanalyzed sample GSM3721982; RNA library from 12Z cells after non-targeting siRNA control treatment
12N1


title: Mature_Mast_Cell_3

tag: sorting strategy


title: Mature_Mast_Cell_33


title: p20050_s023_7173_d10_BAL

description:
p20050_s023_7173_d10_BAL_S23
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

tag: animalid


title: Mature_Mast_Cell_32


title: CUT&RUN H3K4me3 ADAR1WT_Mock-Treated_D5

description: CUTnRUN_ADAR1WT_Mock-treated_H3K4me3.hg19.bw

source_name: CUT&RUN H3K4me3 ADAR1WT_Mock-Treated_D5

value: Mock-Treated


title: p20050_s011_7165_d10_BAL

description:
p20050_s011_7165_d10_BAL_S11
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

source_name: Group I_d10_BAL

tag: timepoint


title: p20050_s017_7172_d10_BAL

description:
p20050_s017_7172_d10_BAL_S17
processed data file:
p20050_MacaM_RawCount.txt
p20050_MacaM_DESeq2_NormCount.txt

tag: group