title: PSPPH_3170_cycle4_Rep1

value: exponential phase


title: PSPPH_1580_cycle3_Rep1

status: Public on Aug 18 2020

type: SRA

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt

library_source: genomic

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A  (GCF_000012205.01)
Supplementary_files_format_and_content: xls file was summary of position weight matrix for all motifs; txt file was genome wide target sites result of TFs.

molecule: genomic DNA

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary TableX and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary TableX, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer.

treatment_protocol: 1 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce each TF expression at 16 °C for 16 h.

tag: genotype

value: wide type

tag: growth phase


title: Kupffer cells derived from mice fed a western diet for 12 weeks, 4

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

library_source: transcriptomic

data_processing:
FastQC v0.11.9 is used to check the quality of the samples
Sequenced reads were then mapped to mm10 transcriptome using HiSat2 v2.2.0 with default parameters and --max-intronlen 1000000
The mapping files were converted into bam files using samtools v1.10 with parameters -l 9
Reads were counted using FeatureCounts v2.0.0 with parameters -s 0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output FeatureCounts, only column 1 and 7) for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol: All Methods listed in Remmerie et al.  Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in MAFLD.. Immunity. 2020.

tag: strain

tag: diet

value: standard diet

tag: time point

value: 12 weeks


title: PSPPH_3170_cycle3_Rep1

organism: Pseudomonas savastanoi pv. phaseolicola 1448A


title: PSPPH_1651_cycle2_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject LD21

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

label: biotin

organism: Homo sapiens

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject LD21

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Experimental procedures of the 12 week combined exercise training intervention study have been previously published (PMID: 20028948)  Eighteen healthy middle-aged male subjects (mean age 59.0 ± 0.8, mean BMI 29.7 ± 0.8 kg/m2; average ± SD) participated in this study.

extract_protocol: Total RNA was isolated using Trizol and further purified using Rneasy columns. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Eighteen healthy middle-aged male subjects performed 12 weeks of combined exercise training. Combined exercise training consisted of 2 endurance exercise sessions and 1 resistance exercise session per week. See Meex et al. (Diabetes. 2010;59(3):572-9. doi: 10.2337/db09-1322 , PMID:  20028948) for more details.

tag: subject id

tag: disease

value: healthy

value: after training intervention period

tag: Sex

value: male


title: PSPPH_3170_cycle2_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject GS25

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject GS25

value: before training intervention period


title: PSPPH_1580_cycle1_Rep1


title: Kupffer cells derived from mice fed a western diet for 12 weeks, 3


title: Kupffer cells derived from mice fed a western diet for 12 weeks, 2


title: PSPPH_1580_cycle2_Rep1


title: Kupffer cells derived from mice fed a western diet for 24 weeks, 1

value: western diet

value: 24 weeks


title: PSPPH_3233_cycle1_Rep1


title: PSPPH_3170_cycle1_Rep1


title: Kupffer cells derived from mice fed a western diet for 12 weeks, 1


title: PSPPH_3022_cycle4_Rep2


title: PSPPH_1460_cycle3_Rep1


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 7


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject HE24

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject HE24


title: PSPPH_1460_cycle4_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject JW34

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject JW34


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject LD21

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject LD21


title: PSPPH_1460_cycle2_Rep1


title: PSPPH_3022_cycle3_Rep2


title: PSPPH_3022_cycle2_Rep2


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 6


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 5


title: PSPPH_1460_cycle1_Rep1


title: PSPPH_3022_cycle1_Rep2


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 4


title: PSPPH_1187_cycle4_Rep2


title: PSPPH_2921_cycle4_Rep2


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 3


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 2


title: PSPPH_2921_cycle3_Rep2


title: PSPPH_1187_cycle2_Rep2


title: PSPPH_1187_cycle3_Rep2


title: Kupffer cells derived from mice fed a standard diet for 12 weeks, 1


title: PSPPH_1187_cycle1_Rep2


title: PSPPH_2921_cycle1_Rep2


title: PSPPH_1179_cycle4_Rep1


title: PSPPH_2800_cycle4_Rep1


title: PSPPH_1179_cycle3_Rep1


title: PSPPH_2800_cycle3_Rep1


title: IL34-KO striatum rep 3

city: New York

first: Ana

last: Badimon

state: NY

address: 1 Gustave L Levy PLace

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: D1 rpkms.txt

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Sequences were mapped using the TopHat2 package (v2.1.0)71.
Reads were counted using HTSeq-count (v0.6.0) against the Ensembl v67 annotation.
The read alignment, read counting, and quality assessment were done using SPEctRA.
The raw counts were processed through VST procedure using the DESeq2 package.
genome build: mm9

source_name: Striatal tissue from Drd1-eGFPL10a; Drd1-Cre; Il34-/- mice

extract_protocol:
RNA was isolated from the unbound portion of TRAP from the striatum
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

tag: cell type

value: striatal tissue


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject JW34

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject JW34


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject HE24

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject HE24


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject RP12

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject RP12


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject RP12

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject RP12


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject RJ28

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject RJ28


title: HelaUV1

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Genome_build: Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Supplementary_files_format_and_content: Ribosome codon occpuancy for untreated compared to UV-irradiated

source_name: HelaUV

growth_protocol: Cells were grown to 75% confluency

extract_protocol:
Fragments ranging from 15-34 nt  were gel purified for monosome or disome footprints, respectively.
rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription (TGIRT) as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Monosomes were isolated by sucrose pelleting after RNaseI treatment

tag: cell line

value: HeLa

tag: plasmid(s)

value: ZAK-FLAG

tag: treatment

value: UV-irradiated

tag: sample type

value: Isolated monosomes

tag: molecule subtype

value: Ribosome Protected mRNA (15-34 nt)


title: HelaUnt2

source_name: HelaUnt

value: untreated


title: PSPPH_1179_cycle2_Rep1

value: exponential phase


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject RJ28

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject RJ28


title: PSPPH_2800_cycle2_Rep1

value: wide type


title: IL34-KO striatum rep 1

description: D1 rpkms.txt

value: Striatal tissue


title: PSPPH_1179_cycle1_Rep1


title: IL34-KO striatum rep 2

description: D1 rpkms.txt


title: PSPPH_2921_cycle2_Rep2


title: muscly biopsy, healthy overweight middle-aged male subject, after training intervention, subject GL23

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, after a 12 week combined exercise training intervention, subject GL23


title: PSPPH_1160_cycle4_Rep1


title: muscly biopsy, healthy overweight middle-aged male subject, before training intervention, subject GL23

source_name: biopsy from the vastus lateralis muscle, taken from healthy overweight middle-aged male subject, before a 12 week combined exercise training intervention, subject GL23


title: IL34-KO striatum rep 4

description: D1 rpkms.txt


title: HelaUV2


title: PSPPH_2677_cycle4_Rep1


title: IL34-KO D1 neuron rep 3

description: D1 rpkms.txt

source_name: Striatal D1 neurons from Drd1-eGFPL10a; Drd1-Cre; Il34-/- mice

extract_protocol:
D1 neuron RNA was isolated from striatum using TRAP.
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Striatal D1 neurons


title: IL34-KO D1 neuron rep 2

description: D1 rpkms.txt


title: Ubiq_Proteasome_Inh

city: Houston

first: Andre

last: Catic

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using Basespace.
Alignments: sequences were aligned to the human reference genome hg19 with bowtie using default parameters
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm (http://liulab.dfci.harvard.edu/MACS/), version 2
Genome_build: hg19
Supplementary_files_format_and_content: The SAM file with the alignments was converted to BAM format and then sorted using samtools. Sorted alignments were converted to WIG format using a perl script.

source_name: 3F-Ubiquitin ChIP with Proteasome Inhibitor

growth_protocol: HeLa cells were obtained by ATCC and cultured following standard recommendations. 10-15 Mio cells were processed for an average ChIP-seq run.

extract_protocol:
After fixation in PBS/1% para-Formaldehyde (37ºC, 10 min), nuclei were isolated by lysis in Triton-X100 buffer and sonicated to 200-500 bp length. DNA was co-immunoprecipitated with the M2 anti-Flag antibody over night.
Samples were size-selected with AMPure XP Beads (Beckman #A63880) and libraries were synthesized with the Ultra Next DNA Library Prep kit for Illumina (New England Biolabs #E7370S) according to recommended protocols. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols for ChIP-seq with HiSeq2500 and NexSeq500 using the High Output v2.5 flow cell.

treatment_protocol: Treatment was performed with 25 microM lactacystin as proteasome inhibitor (Cayman Chemical, # 70980) or 0.1% DMSO (mock) for three hours for the anti-3F-Ubiquitin ChIP.

value: HeLa cells (ATCC # CCL-2)

tag: tagged protein

tag: antibody

value: M2 (Sigma Aldrich)


title: PSPPH_1160_cycle3_Rep1


title: IL34-KO D1 neuron rep 1

description: D1 rpkms.txt


title: CUL1_rep1

source_name: 3F-Cullin-1 ChIP


title: Control striatum rep 4

description: D1 rpkms.txt

source_name: Striatal tissue from Drd1-eGFPL10a; Il34-/- mice

value: control


title: Ubiq_DMSO

source_name: 3F-Ubiquitin ChIP, mock treated


title: input_rep2

source_name: Genomic background


title: Tricho_WGBS_750-3_7years

city: Los Angeles

first: Eric

middle: Alva

last: Webb

state: CA

address: 3616 Trousdale Parkway

institute: University of Southern California

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 7 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750_3_7years

data_processing:
Raw read files were downloaded from the USC Epigenome server upon completion
Reads were quality processed, filtered, and mapped onto the respective reference genomes using the MethPipe pipeline with default settings (http://smithlabresearch.org/software/methpipe/)
Bisulfite conversion rates and methylation levels were estimated using MethPipe
A cytosine was deemed methylated if the residue had a combined coverage of at least 5 reads with at least 20% of total reads being methylated in at least 1 treatment.
Supplementary_files_format_and_content: The All_methylation_levels.txt file contains Smet methylation levels (# of reads with a methylated cytosine/ total # of reads mapping to that cytosine) with each row representing a methylated cytosine that satisfied the above thresholds with columns being 1 replicate each.

organism: Trichodesmium erythraeum IMS101

source_name: cell population

growth_protocol: See description in the SAMPLES section. The Tricho_WGBS_ancestral.fastq.gz file contains the methylome of the founding ancestral population of all other cell lines (replicates). Every sample that has "7years" in the name are samples taken at the 7-year mark of the experiment. Every other Tricho_WGBS* file (other than the ancestral file) without "7years" means samples were taken at the 4.5 year mark.

extract_protocol:
Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction.
DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol.
Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina).

tag: environment

value: cell culture

tag: co2 concentration

value: 750 microatm

tag: medium

value: Aquil medium w/o fixed nitrogen

tag: location

value: University of Southern California


title: Tricho_WGBS_750-2_7years

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 7 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750_2_7years


title: PSPPH_2677_cycle3_Rep1

tag: genotype

tag: growth phase


title: HelaUnt1

value: HeLa


title: PSPPH_2800_cycle1_Rep1


title: Control striatum rep 2

description: D1 rpkms.txt

value: striatal tissue


title: PSPPH_2677_cycle1_Rep1


title: PSPPH_2128_cycle4_Rep1


title: input_rep1


title: Tricho_WGBS_380-3_7years

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 7 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380_3_7years

value: 380 microatm


title: PSPPH_2128_cycle3_Rep1


title: ZAK_IP2

description: Ribosome Protected mRNA (24-90 nt)

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Genome_build: Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Supplementary_files_format_and_content: Metagene plots for stop codons

source_name: Immunoprecipitated sample

extract_protocol:
Monosomes or disomes were isolated by sucrose gradient centrifugation after RNaseI treatment and subjected to immunoprecipitation
Fragments ranging from 24-90 nt  were gel purified for monosome or disome footprints, respectively. rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Expression of ZAK-FLAG was induced by addition of Doxycycline for 24 hr.

value: ZAK-FLAG


title: PSPPH_2128_cycle2_Rep1


title: Tricho_WGBS_380-2_7years

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 7 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380_2_7years


title: Mock_IP2

description: Ribosome Protected mRNA (24-90 nt)


title: ZAK_IP1

description: Ribosome Protected mRNA (24-90 nt)


title: Control D1 neuron rep 4

description: D1 rpkms.txt

source_name: Striatal D1 neurons from Drd1-eGFPL10a; Il34-/- mice


title: PSPPH_2128_cycle1_Rep1


title: Tricho_WGBS_380-1_7years

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 7 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380_1_7years


title: Tricho_WGBS_750-380-3

description:
Cells growing semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years were transferred to the same medium but now under 380 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750-380_3


title: Control D1 neuron rep 3

description: D1 rpkms.txt


title: PSPPH_2677_cycle2_Rep1


title: Mock_IP1

description: Ribosome Protected mRNA (24-90 nt)


title: Tricho_WGBS_750-380-2

description:
Cells growing semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years were transferred to the same medium but now under 380 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750-380_2


title: PSPPH_2095_cycle3_Rep1


title: Tricho_WGBS_750-1_7years

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 7 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750_1_7years


title: PSPPH_2095_cycle4_Rep1


title: Tricho_WGBS_750-380-1

description:
Cells growing semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years were transferred to the same medium but now under 380 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750-380_1


title: Control striatum rep 3

description: D1 rpkms.txt


title: Control D1 neuron rep 2

description: D1 rpkms.txt


title: Control striatum rep 1

description: D1 rpkms.txt


title: PSPPH_2095_cycle1_Rep1


title: Control D1 neuron rep 1

description: D1 rpkms.txt


title: PSPPH_2095_cycle2_Rep1


title: Liver CD45- cells derived from mice fed a standard diet for 24 weeks

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 3.1.0 mkfastq
Demultiplexed data was then processed using the Cell Ranger 3.1.0 count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: h5 files including raw counts (output CellRanger Count) for each sample

source_name: Liver

tag: strain

tag: diet

value: standard diet

value: CD45- cells

tag: time point

tag: platform

value: 10x Genomics – v3

tag: number of cells


description:
Liver CD45+ cells derived from mice fed a standard diet for 36 weeks
aggrCd45pos_filtered_feature_bc_matrix.h5

tag: cell type

value: CD45+ cells


title: PSPPH_1960_cycle4_Rep1

value: wide type

value: exponential phase


description:
Liver CD45+ cells derived from mice fed a western diet for 24 weeks
aggrCd45pos_filtered_feature_bc_matrix.h5

value: western diet


title: Tricho_WGBS_750-2

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750_2


title: Tricho_WGBS_750-1

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750_1


title: Tricho_WGBS_380-750-3

description:
Cells growing semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 4.5 years were transferred to the same medium but now under 750 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380-750_3


title: PSPPH_1960_cycle2_Rep1


title: PSPPH_1960_cycle3_Rep1


description:
Liver CD45+ cells derived from mice fed a standard diet for 24 weeks
aggrCd45pos_filtered_feature_bc_matrix.h5


title: Liver CD45- cells derived from mice fed a western diet for 24 weeks


title: 48 hours after HCV infection in Huh7 cells

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 human miRNA database and human genome.
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Huh7 cell line

growth_protocol: Human hepatoma Huh7 and Huh7.5.1 cells were cultured in Dulbecco’s modified Eagle medium (DMEM, Life Technologies, USA) supplemented with 10% fetal bovine serum (FBS), 1× nonessential amino acids, 100 IU/ml streptomycin and penicillin, and 2 mM L-glutamine (Gibco, Invitrogen). Cells were incubated under an atmosphere with 5% CO2 at 37℃ for subsequent use in experimental procedures.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
smallRNA libraries were prepared for sequencing using standard Ion  Proton Protocols

treatment_protocol: The Japanese fulminant hepatitis type 1 (JFH-1) plasmid was linearized and transcribed in vitro to produce HCV RNA using a MEGAscript kit (Promega, Madison, WI, USA). Then, 106 hepatoma cells were transfected with 10 ng of viral RNA by electroporation. The cells were moved to culture plates for further viral amplification, and the medium was changed for fresh medium 4 h later. The supernatant was collected 96 h after transfection and filtered through a 0.45-μm membrane. HCVcc was then concentrated and purified by ultracentrifugation, and viral titers were determined for later experiments.

tag: tissue

value: Hepatoma cell

tag: passage

value: Passage 4


title: None infected Huh7.5.1 cells

source_name: Huh7.5.1 cell line


title: PSPPH_1960_cycle1_Rep1


title: 24 hours after HCV infection in Huh7.5.1 cells


description:
Liver CD45+ cells derived from mice fed a western diet for 12 weeks
aggrCd45pos_filtered_feature_bc_matrix.h5


title: 48 hours after HCV infection in Huh7.5.1 cells


title: Tricho_WGBS_750-3

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
750_3

value: cell culture


description:
Liver CD45+ cells derived from mice fed a standard diet for 12 weeks
aggrCd45pos_filtered_feature_bc_matrix.h5


description:
Liver CD45+ cells derived from mice fed a western diet for 36 weeks
aggrCd45pos_filtered_feature_bc_matrix.h5


title: Tricho_WGBS_380-750-1

description:
Cells growing semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 4.5 years were transferred to the same medium but now under 750 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380-750_1

value: 750 microatm


title: 24 hours after HCV infection in Huh7 cells


title: PSPPH_1011_cycle4_Rep1

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt


title: Tricho_WGBS_380-3

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 4.5 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380_3

value: Aquil medium w/o fixed nitrogen


title: None infected Huh7 cells


title: 6 hours after HCV infection in Huh7.5.1 cells


title: PSPPH_1011_cycle3_Rep1


title: Tricho_WGBS_380-2

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 4.5 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380_2

value: University of Southern California


title: PSPPH_1011_cycle2_Rep1


title: Mef2cTdT_neg_Ad2.7

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

country: France

institute: INSERM U1251

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Raw ATAC-Seq reads were aligned with the SNAP aligner
Deduplicated reads were marked and, following ENCODE specifications [], umapped, not primarily aligned, failing platform and duplicated reads were removed using samtools4 (-F 1804). Properly paired reads were kept (samtools -f 2)
Reads mapping blacklisted regions for mouse genome mm10 provided by ENCODE [] were excluded from the analysis
Irreproducible Discovery Rate5 (IDR) methodology from ENCODE was used to evaluate the reproducibility between replicates.
Narrow peaks were called with MACS 2.1.1
Differential peaks between Hoxb1GFP and Mef2cTdT cell lines were identified using a bed file containing selected peaks from IDR methodology and the DiffBind R package Peaks with a FDR (False Discovery Rate) at 10% were kept.
Genome_build: mm10
Supplementary_files_format_and_content: List of narrow peaks is the standad output of MACS2. The both List of annotated selected peaks were obtained after IDR analysis and annotated with Homer. The differential observed peaks is obtained with the DiffBind Package

source_name: murine FACS sorted cardiac cells

extract_protocol: Hoxb1GFP progenitor cells and Mef2c-Cre;RosatdT progenitor cells were dissected, pooled and digested for FACS sorting.

value: second heart field region

tag: Stage


title: Tricho_WGBS_380-1

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 4.5 years. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380_1


title: Mef2cTdT_Ad2.6


title: CUL1_rep2

tag: cell line

value: HeLa cells (ATCC # CCL-2)

tag: tagged protein

value: M2 (Sigma Aldrich)


title: PSPPH_1011_cycle1_Rep1


title: Tricho_WGBS_380-750-2

description:
Cells growing semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 for 4.5 years were transferred to the same medium but now under 750 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380-750_2

tag: environment


title: Tricho_WGBS_ancestral

description:
This is the founding ancestral population from which all other samples originated. Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)
380-ancestral

tag: co2 concentration

value: 379 microatm


title: Human_436_20C_UNC_d4_3

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Reads were aligned to hg19 using tophat (2.0.8) with default parameters
Transcripts were merged using cufflinks (2.1.1) and differential expression computed for all relevant contrasts with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: mean FPKM value for all identified transcripts

growth_protocol: MDA-MB-436 and HS 578T cells were grown in DMSO supplemented with 10%FBS and Penicilin/Streptomycin (100 U/mL Penicilium and 100 μg/mL. Streptomycin). Taxane-resistant cells were generated upon long-term exposure to increasing concentrations of paclitaxel at a starting concentration 0.05 nM with increments (dose and time adjusted to the growth and survival of adapting cells), until the cytotoxic concentration of 10 to 20 nM was reached with the resistant cells growing at a similar rate than the parental cells (>6 months).

extract_protocol:
RNA was extracted using the qiaquick purification kit
RNA samples were quantified by qubit (Life Technologies) and quality by Agilent Bioananlyzer. Two hundred nanograms Total RNA from 42 samples were library prepared using TruSeq Stranded Total RNA kit (Illumina). RNA samples were ribosomal RNA depleted using Ribo-zero Gold rRNA beads, following purification the RNA was fragmented. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” based were added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries.
Final cDNA libraries were size validated using Agilent Bioanalyzer and concentration validated by qPCR (Kapa Biosystems/Roche). All libraries were normalized to 10nM and pooled together, denatured with 0.2N NaOH and diluted to a final concentration of 1.4pM.  1.3ml of 1.4pM pooled libraries were loaded onto an Illumina NextSeq cartridge for cluster generation and sequencing on an Illumina Nextseq500 instrument (Illumina) using Paired-end 75bp protocol to achieve ~ 40 million reads per sample

treatment_protocol: Taxol-resistant cells were grown in presence of 20nM of Paclitaxel at all time. Parental cells (MDA-MB-436 and Hs 578T) were grown in DMEM with 1:1000 DMSO at all time.

value: TNBC

tag: paclitaxel sensitivity

value: Taxol-resistant

tag: treatment

tag: replicate

value: GD_RNA_73 and 59


title: PSPPH_0146_cycle4_Rep1

tag: genotype

tag: growth phase


title: 6 hours after HCV infection in Huh7 cells


title: Human_436_20C_UNC_d0_3

value: GD_RNA_71 and 57


title: PSPPH_0146_cycle2_Rep1

value: wide type


title: GFP_neg_Ad2.2


title: Human_436_20B_UNC_d4_3

value: parental taxol-sensitive  treated with paclitaxel 72h

value: GD_RNA_70 and 56


title: Hoxb1GFP_Ad2.3


title: PSPPH_0146_cycle1_Rep1

value: exponential phase


title: Mef2cTdT_Ad2.8


title: PSPPH_0146_cycle3_Rep1


title: Human_436_20A_UNC_d4_3

value: GD_RNA_67 and 53


title: Human_436_20B_UNC_d0_3

value: parental taxol-sensitive

value: GD_RNA_68 and 54


title: GFP_neg_Ad2.1


title: PSPPH_0037_cycle4_Rep1


title: mRNA_Blade_S5_rep2

city: Wuhan

first: Chang

last: Liu

address: Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
After removing low-quality reads, the clean reads were trimmed with Trimmomatic-0.36 and then mapped to the rice reference genome rice IRGSP-1.0 with TopHat v2.1.1(defaut parameters)
The uniquely mapped reads were used to calculate FPKM (fragments per kilobase of transcript per million reads) values for the genes with Cufflinks v2.2.1 (Trapnell et al., 2012) to estimate their expression levels in different samples.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample of RNA-seq

organism: Oryza sativa

source_name: blade

growth_protocol: The seeds were soaked in distilled water at room temperature for 1 day and imbibed for 2 days in water at 37°C in a constant temperature incubator (referred to as the first and second day after germination, respectively). The water was changed twice daily. The germinated seeds were transferred to 96-well plates with cut bottoms and grown in water under a 16 h (light, 28°C)/8 h (dark, 25°C) cycle.

extract_protocol:
LJ and blade tissue form the first complete leaves of seedlings were separately cut and collected on the 4th, 5th, 6th, 7th, and 9th day after germination, the length of LJ were less than 1 mm, and the length of blade was less than 10 mm. The collected tissues were immediately frozen in liquid nitrogen and subjected to total RNA extraction with TRIzol (Invitrogen). The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA per sample to constructed RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blade

tag: developmental stage


title: mRNA_Blade_S4_rep2


title: mRNA_Blade_S4_rep1


title: mRNA_Blade_S5_rep1


title: Human_436_20A_UNC_d0_3

value: GD_RNA_65 and 51


title: mRNA_Blade_S3_rep2


title: PRMT1-p53_si_TGFB_2

city: New Orleans

first: Olan

last: Jackson-Weaver

state: Louisiana

address: 1430 Tulane Ave, Department of Surgery

department: Surgery

institute: Tulane University

data_processing:
Sequencing was performed on a HiSeq 4000 (Illumina) with paired end reads of 100 bp.
Analysis was performed using Partek Flow software (Partek Inc.).
Reads were first trimmed to remove adaptor sequences and then mapped to the mouse genome (mm10) TopHat2 (--sensitive) (Kim et. al. 2013).
Aligned reads were then quantified using Partek E/M.
Raw read counts were filtered for low expression features (gene with <= 10 raw read counts in all samples) and normalized (add 1 raw read then upper quartile normalization)
Differential expressed genes in each condition were identified using GSA
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw read counts

source_name: Epicardial cell line MEC1

extract_protocol:
Total RNA from MEC1 cells was extracted using TRIzol (Thermo Fisher Scientific). Total RNA was enriched for poly(A) RNA and fragmented for library construction.
RNA fragments were reverse transcribed followed by A-tailing and and index adapter ligation, then denatured and amplified on cBot. Library analysis and quality checks were performed on a LabChip GX.

tag: sirna treatment

value: PRMT1 and p53 siRNA

tag: tgfbeta treatment

value: yes


title: PRMT1-p53_si_TGFB_1


title: PSPPH_0037_cycle3_Rep1


title: Human_436DMSO_UNC_d4_3

value: GD_RNA_62 and 48


title: mRNA_Blade_S3_rep1


title: Hoxb1GFP_Ad2.4

value: second heart field region


title: PRMT1-p53_si_2

value: no


title: PSPPH_0037_cycle2_Rep1


title: Human_436DMSO_UNC_d0_3

value: TNBC

value: GD_RNA_60 and 46


title: mRNA_Blade_S2_rep2


title: PRMT1-p53_si_1


title: PSPPH_0037_cycle1_Rep1


title: Human_436_20C_UNC_d4_2

value: GD_RNA_73 and 87


title: PSPPH_4062_cycle4_Rep1

value: wide type


title: p53_si_TGFB_2

value: p53 siRNA


title: PSPPH_4062_cycle3_Rep1


title: p53_si_TGFB_1


title: mRNA_Blade_S1_rep1


title: Human_436_20B_UNC_d4_2

value: Taxol-resistant

value: GD_RNA_70 and 84


title: mRNA_Blade_S1_rep2


title: PSPPH_4062_cycle1_Rep1

value: exponential phase


title: p53_si_2


title: p53_si_1


title: PRMT1_si_TGFB_2

value: PRMT1 siRNA


title: mRNA_LJ_S5_rep2

source_name: lamina joint

value: lamina joint


title: mRNA_LJ_S5_rep1


title: Human_436_20B_UNC_d0_2

value: GD_RNA_68 and 82


title: PSPPH_4062_cycle2_Rep1


title: Human_436_20A_UNC_d4_2

value: parental taxol-sensitive  treated with paclitaxel 72h

value: GD_RNA_67 and 81


title: Human_436_20A_UNC_d0_2

value: parental taxol-sensitive

value: GD_RNA_65 and 79


title: PRMT1_si_TGFB_1

value: yes


title: mRNA_LJ_S4_rep2


title: Human_436DMSO_UNC_d4_2

value: GD_RNA_62 and 76


title: PRMT1_si_2

value: no


title: PSPPH_3990_cycle3_Rep1


title: mRNA_LJ_S4_rep1


title: PSPPH_3990_cycle2_Rep1


title: mRNA_Blade_S2_rep1

value: blade


title: mRNA_LJ_S3_rep2


title: Human_436DMSO_UNC_d0_2

value: TNBC

value: GD_RNA_60 and 74


title: PRMT1_si_1


title: Human_436_20C_UNC_d0_2

value: GD_RNA_71 and 85


title: PSPPH_3990_cycle1_Rep1

value: wide type


title: PSPPH_3990_cycle4_Rep1


title: Cont_si_TGFB_2

value: Control siRNA


title: mRNA_LJ_S2_rep2


title: PSPPH_3907_cycle4_Rep1

value: exponential phase


title: Human_436_20C_UNC_d4_1

value: Taxol-resistant

value: GD_RNA_73 and 87


title: Human_436_20C_UNC_d0_1


title: mRNA_LJ_S3_rep1

value: lamina joint


title: Cont_si_TGFB_1


title: Human_436_20B_UNC_d4_1

value: GD_RNA_70 and 84


title: Cont_si_2


title: Human_436_20B_UNC_d0_1

value: GD_RNA_68 and 82


title: PSPPH_3907_cycle2_Rep1


title: Cont_si_1


title: PSPPH_3907_cycle3_Rep1


title: Human_436_20A_UNC_d4_1

value: GD_RNA_67 and 81


title: mRNA_LJ_S1_rep1


title: mRNA_LJ_S2_rep1


title: PSPPH_3645_cycle4_Rep1-2


title: PSPPH_3645_cycle3_Rep1-2


title: PSPPH_3907_cycle1_Rep1


title: Human_436DMSO_UNC_d4_1

value: parental taxol-sensitive  treated with paclitaxel 72h


title: ∆lsd1 N5555 H3K4me3 ChIP-seq

city: Eugene

middle: U

last: Selker

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are tdf or bigwig files generated using IGV or DeepTools (Ramirez et al., 2016) respectively, using a window size of 25bp.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and H3K9me3 antibody was added (3µL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4˚C, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65˚C.  Samples (IP and input) were decrosslinked at 65˚C overnight.  The next day, samples were proteinase K treated for 2 hours at 50˚C, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98˚C for 30 sec, 10 cycles at 98˚C for 10 sec, 60˚C for 30 sec and 72˚C for 30 sec and a final extension at 72˚C for 5 min.

value: germinated conidia

tag: chip antibody

value: mat a delta_lsd1::hph


title: Human_436_20A_UNC_d0_1

tag: cell type

value: GD_RNA_65 and 79


title: ∆lsd1 N5555 RNA-seq rep2

description:
lsd1_sig_DOWNregulated_genes.txt
lsd1_sig_UPregulated_genes.txt

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy (Afgan et al., 2018) were used to map mRNA-sequencing reads (intron size < 1kb) (Dobin et al, 2012) against the corrected N. crassa OR74A (NC12) genome (Galazka et al., 2016), count the number of reads per gene (Dobin et al., 2012) and determine differentially expressed genes with DESeq2 (Love et al, 2014).
Bisulfite-seq processing: The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping. BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged. The average 5mC level was determined for 25bp step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/). The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp.
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 replicates each of wild type (Klocko et al. 2016; GSE82222) and ∆lsd1 and the output file from DESeq2 (Love et al., 2014) with pairwise comparisons of 2 biological replicates from each genotype.
Supplementary_files_format_and_content: Bisulfite-seq processed data files are .igv files displaying the % methylation over 25bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region.  Values in between 0 and 1.0 represent partial methylation of a region.

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32˚C. Mycelia were harvested and added to a tube containing ~350µL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350µL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350µL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350µL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650µL cold 100% EtOH.  Samples were precipitated at -20˚C, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNAseI, amplification grade (Thermo Fisher Scientific), cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter), and RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems).

tag: tissue


title: WT N3752 H3K4me3 ChIP-seq

value: mat A


title: Human_436DMSO_UNC_d0_1

value: TNBC

value: parental taxol-sensitive


title: PSPPH_3645_cycle2_Rep1-2


title: PSPPH_3645_cycle1_Rep1-2


title: KO4.S6

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
Quality check of raw reads by FastQC
STAR v2.5.2b for reads alignment and counts summary
Reads count data were processed using R/Bioconductor "RSubread", "edgeR" and "limma" packages
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for reads count

source_name: Mus Musculus

growth_protocol: clinical demographics: Patients were recruited for the prospective SHARE study at University of Chicago Medical Center and Mayo Clinic Rochester.  Ulcerative colitis patients who underwent total proctocolectomy with IPAA and over the age of 18 were eligible for the study.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7.
RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit.

treatment_protocol: sample collection: biopsy via pouchoscopy

value: Bone marrow

tag: prognosis

value: LT-HSCs

tag: age

tag: Sex

value: female

tag: genotype/variation


title: ∆lsd1 N5555 RNA-seq rep1


title: mRNA_LJ_S1_rep2


title: ∆lsd1 N5555 H3K9me3 ChIP-seq


title: PSPPH_3618_cycle4_Rep1

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A  (GCF_000012205.01)
Supplementary_files_format_and_content: xls file was summary of position weight matrix for all motifs; txt file was genome wide target sites result of TFs.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary TableX and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary TableX, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer.

value: wide type

value: exponential phase


title: KO1.S4


title: KO3.S5


title: PSPPH_3618_cycle1_Rep1


title: PSPPH_3618_cycle2_Rep1


title: WT3.S2

value: c-Mycfl/+


title: PSPPH_3471_cycle4_Rep1


title: WT1.S1


title: PSPPH_3618_cycle3_Rep1


title: WT4.S3


title: PSPPH_3471_cycle2_Rep1


title: PSPPH_3471_cycle1_Rep1


title: PSPPH_3471_cycle3_Rep1


title: Chrm4 stMg CNO UB rep 1

description: DREADD rpkms.xlsx

source_name: Striatal tissue from Camk2a-tTA; TetO-Chrm4; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with CNO

treatment_protocol: Mice were ravaged with Tamoxifen at 4-6 weeks of age, mice were injected with CNO 2 hours prior to the experiment

value: striatal tissue

value: injected with CNO


title: PSPPH_3031_cycle4_Rep1


title: Chrm3 stMg CNO UB rep 3

description: DREADD rpkms.xlsx

source_name: Striatal tissue from Camk2a-tTA; TetO-Chrm3; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with CNO


title: PSPPH_3031_cycle3_Rep1


title: PSPPH_3031_cycle2_Rep1


title: PSPPH_3031_cycle1_Rep1


title: Chrm4 stMg Control UB rep 1

description: DREADD rpkms.xlsx

source_name: Striatal tissue from Camk2a-tTA; TetO-Chrm4; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with saline

treatment_protocol: Mice were ravaged with Tamoxifen at 4-6 weeks of age, mice were injected with saline 2 hours prior to the experiment

value: injected with saline


title: PSPPH_3022_cycle4_Rep1


title: Chrm3 stMg CNO UB rep 1

description: DREADD rpkms.xlsx

value: Camk2a-tTA; TetO-Chrm3; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice


title: Chrm3 stMg CNO UB rep 2

description: DREADD rpkms.xlsx


title: Chrm4 stMg CNO UB rep 2

description: DREADD rpkms.xlsx

value: Camk2a-tTA; TetO-Chrm4; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice


title: HEK293T_IP_OE:TOB1_rep2

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

data_processing:
library strategy: CLIP-seq
Reads were processed essentially as described (Van Nostrand et al., 2016b).
Brifely, reads were adapter-trimmed and mapped to human-specific repetitive elements from RepBase (version 18.04) by STAR. Repeat-mapping reads were removed and remaining reads mapped to the human genome assembly hg19 with STAR. PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5’ adapter and remaining reads retained as ‘usable reads’.
Peaks were called on the usable reads by CLIPper ,and assigned to gene regions annotated in Gencode (v19)
Each peak was normalized to the size-matched input (SMInput)
Genome_build: Homo sapiens UCSC hg19

extract_protocol:
Cell lysates were prepared by sonication in 1 ml iCLIP lysis buffer, treated with RNase I (40 U, LifeTech).
Enhanced crosslinking and immunoprecipitation (eCLIP) was performed on HEK293T cells, and immunoprecipitated overnight at 4 °C with 10 µg affinity-purified antibody pre-coupled to Dynabeads sheep M-280 anti-IgG beads (LifeTech). Prior to IP, a 20 µl aliquot of extract was removed and stored at 4 °C for preparation of the size-matched input (SMInput) control. After washing, immunoprecipitated protein-RNA complexes were dephosphorylated and 3’-linker ligated on-bead to a custom oligonucleotide adapter. All samples (IPs and SMInputs) were heated in LDS Sample Buffer (LifeTech) containing 0.1 M DTT for 10 min at 70° and run on 4-12% NuPAGE Bis-Tris polyacrylamide gels in MOPS running buffer (LifeTech). Complexes were wet-transferred to iBLOT nitrocellulose membranes in NuPAGE transfer buffer (all LifeTech) containing 10% methanol (overnight, 4 °C, 30V). Successful immunoprecipitation was confirmed by performing standard western blotting on fractions (10%) of each sample. RNA-protein complexes in the range from expected molecular mass to 75 kDa above expected molecular mass (corresponding to the RBP crosslinked to RNAs of ~220 nucleotides in length) were excised from the membrane. RNAs were released by proteinase K treatment in the presence of urea and recovered by phenol/chloroform extraction and column purification (RNA Clean-Up kit; Zymo Research). Input samples were dephosphorylated and 3’-linker ligated to a custom oligonucleotide primer. All samples (IPs and SMInputs) were then reverse transcribed using AffinityScript reverse transcriptase (Agilent). After treatment with ExoSAP-IT (Affymetrix) and alkali, cDNAs were recovered by purification on Dynabeads MyONE Silane beads (LifeTech), 5’-linker ligated on-bead to a custom oligonucleotide primer, and again purified. cDNAs were quantified by qPCR analysis of a fraction of each sample using custom oligonucleotide primers specific to the 5’ and 3’ adapters. Half of the recovered cDNA was PCR-amplified (Q5 polymerase, NEB) using custom sequence-indexed oligonucleotide primers. PCR products were purified (Agencourt AMPure XP beads; Beckman Coulter), size-selected to 175-350 bp on 2% agarose gels, extracted (MinElute Gel Extraction kit; Qiagen), and quantified on a TapeStation using D1000 ScreenTape (Agilent). Libraries were sequenced on a HiSeq 4000 instrument (Illumina) in single-end 75 bp mode.

treatment_protocol: 20 million cells were UV-crosslinked (254 nm, 400 mJ/cm2)

tag: clip-seq antibody

value: Bethyl, A190-120A

tag: barcode


title: Chrm3 stMg Control UB rep 3

description: DREADD rpkms.xlsx

source_name: Striatal tissue from Camk2a-tTA; TetO-Chrm3; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with saline


title: CRC_Tumor_Patient2

city: Zhuhai

first: Hong-Wei

last: Sun

address: 79 Kangning Road

department: The Affiliated Hospital of Beijing Institute of Technology (Zhuhai People's Hospital)

institute: Beijing Institute of Technology

description: Gene expression in tumor tissue from colorectal cancer patients

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

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

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

source_name: Tumor tissue, CRC Patient 2

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

extract_protocol: Total RNA was prepared using the TRIzol® Reagent (Cat#15596-026, Life Technologies) following the manufacturer's recommendations. Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: tissue type

value: Tumor


title: Chrm4 stMg Control UB rep 2

description: DREADD rpkms.xlsx

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Sequences were mapped using the TopHat2 package (v2.1.0)71.
Reads were counted using HTSeq-count (v0.6.0) against the Ensembl v67 annotation.
The read alignment, read counting, and quality assessment were done using SPEctRA.
The raw counts were processed through VST procedure using the DESeq2 package.
genome build: mm9

extract_protocol:
RNA was isolated from the unbound portion of TRAP from the striatum
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

tag: treatment


title: CRC_Tumor_Patient4

source_name: Tumor tissue, CRC Patient 4


title: CRC_Tumor_Patient6

source_name: Tumor tissue, CRC Patient 6


title: HEK293T_Input_OE:TOB1_rep1


title: CRC_Tumor_Patient3

source_name: Tumor tissue, CRC Patient 3


title: CRC_Tumor_Patient5

source_name: Tumor tissue, CRC Patient 5


title: HEK293T_IP_OE:TOB1_rep1


title: CRC_Tumor_Patient1

source_name: Tumor tissue, CRC Patient 1


title: PSPPH_3022_cycle2_Rep1


title: CRC_Normal_Patient5

description: Gene expression in adjacent normal colonic tissue from colorectal cancer patients

source_name: Normal colon tissue, CRC Patient 5

value: Normal


title: CRC_Normal_Patient1

source_name: Normal colon tissue, CRC Patient 1


title: Chrm3 stMg Control UB rep 2

description: DREADD rpkms.xlsx


title: Chrm3 stMg Control UB rep 1

description: DREADD rpkms.xlsx


title: CRC_Normal_Patient3

source_name: Normal colon tissue, CRC Patient 3


title: CRC_Normal_Patient6

source_name: Normal colon tissue, CRC Patient 6


title: Chrm4 stMg CNO TRAP rep 2

description: DREADD rpkms.xlsx

source_name: Striatal microglia from Camk2a-tTA; TetO-Chrm4; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with CNO

extract_protocol:
Microglial RNA was isolated from striatum using TRAP.
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Striatal microglia


title: PSPPH_3022_cycle3_Rep1


title: PSPPH_2921_cycle4_Rep1


title: Chrm4 stMg CNO TRAP rep 1

description: DREADD rpkms.xlsx


title: Single nuclei prepared from striatal tissue

data_processing:
Demultiplexed fastq files were generated from raw Illumina BCL files using Cellranger (version 2.1.0) with default parameters (cellranger mkfastq).
Two samples’s expression matrices were determined and merged using Cellranger with default parameters (cellranger count and cellranger aggr).
10X refdata-cellranger-1.2.0 mm10, genome-build GRCm38.p4
genome build: mm10

extract_protocol:
Microglial nuclei were isolated. RNA was obtained from 10X Chromium
The 3’ GEX snRNASeq v2 protocol by 10X Genomics

value: wild type


title: HEK293T_Input_OE:TOB1


title: PSPPH_2921_cycle2_Rep1


title: HEK293T_Input_OE:NANOS3_rep2


title: Chrm4 stMg Control TRAP rep 2

description: DREADD rpkms.xlsx

source_name: Striatal microglia from Camk2a-tTA; TetO-Chrm4; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with saline


title: PSPPH_2921_cycle1_Rep1


title: HEK293T_Input_OE:NANOS3_rep1


title: HEK293T_IP_OE:NANOS3_rep1


title: PSPPH_3022_cycle1_Rep1


title: Chrm3 stMg CNO TRAP rep 2

description: DREADD rpkms.xlsx

source_name: Striatal microglia from Camk2a-tTA; TetO-Chrm3; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with CNO


title: PSPPH_2772_cycle4_Rep1


title: Chrm3 stMg CNO TRAP rep 3

description: DREADD rpkms.xlsx


title: HEK293T_Input_OE:IFIT2_rep2


title: HEK293T_IP_OE:NANOS3_rep2


title: PSPPH_2772_cycle2_Rep1


title: Chrm3 stMg Control TRAP rep 3

description: DREADD rpkms.xlsx

source_name: Striatal microglia from Camk2a-tTA; TetO-Chrm3; Cx3cr1CreErt2/+(Litt);Eef1a1LSL.eGFPL10a/+ mice injected with saline


title: Chrm3 stMg CNO TRAP rep 1

description: DREADD rpkms.xlsx


title: Chrm3 stMg Control TRAP rep 2

description: DREADD rpkms.xlsx


title: PSPPH_2921_cycle3_Rep1


title: PSPPH_2772_cycle3_Rep1


title: HEK293T_IP_OE:IFIT2_rep1


title: PSPPH_2720_cycle4_Rep2


title: PSPPH_2772_cycle1_Rep1


title: HEK293T_IP_OE:BOLL_rep2


title: PSPPH_2720_cycle3_Rep2


title: HEK293T_IP_OE:IFIT2_rep2


title: CRC_Normal_Patient2

source_name: Normal colon tissue, CRC Patient 2


title: CRC_Normal_Patient4

source_name: Normal colon tissue, CRC Patient 4


title: Chrm3 stMg Control TRAP rep 1

description: DREADD rpkms.xlsx


title: PSPPH_2720_cycle2_Rep2


title: Chrm4 stMg Control TRAP rep 1

description: DREADD rpkms.xlsx


title: TBL3_3

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
The strand-specific reads were mapped on to Bovine genome (bosTau7; Btau_4.6.1; GCF_000003205.5) using Tophat2 (-g 1 --library-type fr-firststrand). The samples with respective replicates were analyzed further for differential gene expression by three different tools, baySeq, DESeq2 (fitType ="local") and CuffDiff2 with default parameters unless mentioned specifically. The count values for DESeq2 and baySeq were calculated from BAM files using HTSeq-count tool.  The transcriptome quality plots were generated by cummeRbund package (v2.14.0).
Genome_build: Bos taurus4.6.1 (bosTau7)

organism: Bos taurus

growth_protocol: Bovine BL3, TBL3, BL20, TBL20  B lymphocytes, and Ode macrophages were cultured in RPMI 1640 medium supplemented with 2 mM of L-glutamine (Lonza, catalogue number 12-702F) and 10 mM Hepes (Lonza, catalogue number 17-737E), 10 % heat-inactivated FBS (Gibco, catalogue number 10082147), 100 units/ml of Penicillin and 100 μg/ml of streptomycin (Lonza, catalogue number 17-602E) and 10mM beta-mercaptoethanol (Sigma-Aldrich, catalogue number M6250) for BL3/TBL3 and BL20/TBL20. The virulent (Vir) hyper-disseminating Ode cell line was used at low passage (53-71), while its attenuated (Att) poorly disseminating vaccine counterpart corresponded to passages 309-317. The OCI-LY19 cell line (DSMZ, ACC 528) was cultured in Minimum Essential Medium Eagle - Alpha Modification (Gibco, catalog number 12000063) supplemented with 2.2g/L of sodium bicarbonate (Thermofisher Scientific, catalog number 25080094), 20% FBS, 10 mM Hepes and 100 units/ml of Penicillin and 100 μg/ml of streptomycin. The RI-1 cell line (DSMZ, ACC 585) was cultured in RPMI1640 and supplemented with 10% FBS, 100 units/ml of Penicillin and 100 μg/ml of streptomycin and 10 mM Hepes. All cell lines were incubated at 37°C with 5% CO2 and were regularly tested for mycoplasma contamination.

extract_protocol:
Cells were seeded in 3 biological replicates at a density of 2.5x105 cell/ml. RNA extraction was performed using the PureLink RNA Mini Kit (Life technologies, catalogue number 12183018A) following the manufacturer’s instructions. Briefly, cells were pelleted, lysed and homogenized using a 21-gauge needle, then 70% ethanol was added to cell lysates and samples loaded onto spin cartridges to bind RNA. After 3 washes RNA was eluted in RNase-free water. The quality of extracted RNA was verified using a Bioanalyzer 2100 and quantification carried using Qubit (Invitrogen, catalogue number Q10210).
Strand-specific RNA-sequencing (ssRNA-seq) libraries were prepared using the Illumina Truseq Stranded mRNA Sample Preparation Kit (Illumina, catalogue number RS-122-2101) following the manufacturer’s instructions. Briefly, 1ug of total RNA was used to purify mRNA using poly-T oligo-attached magnetic beads. mRNA was then fragmented and cDNA was synthesized using SuperScript III reverse transcriptase (Thermofisher, catalogue number 18080044), followed by adenylation of the 3’-end, barcoding and adapter ligation. The adapter ligated cDNA fragments were then enriched and cleaned with Agencourt Ampure XP beads (Agencourt, catalogue number A63880). Libraries validation was conducted using the 1000 DNA kit on 2100 Bioanalyzer (Agilent Technologies, catalogue number 5067-1504) and quantified using qubit (Thermofisher, catalogue number Q32850). ssRNA libraries were sequenced on Illumina Hiseq2000 and Hiseq4000.

value: B lymphocytes


title: HEK293T_Input_OE:IFIT2_rep1


title: HEK293T_IP_OE:BOLL_rep1


title: TBL3_2


title: HEK293T_Input_OE:BOLL_rep1


title: PSPPH_2688_cycle4_Rep1

city: Hong Kong

last: Yan

institute: City University of Hong Kong


title: PSPPH_2720_cycle1_Rep2


title: TBL3_1


title: HEK293T_IP_TOB2_rep2

value: Abnova, 8141


title: BL3_rep3


title: HEK293T_Input_TOB2_rep2


title: PSPPH_2688_cycle3_Rep1


title: PSPPH_2688_cycle2_Rep1


title: HEK293T_Input_OE:BOLL_rep2


title: PSPPH_2688_cycle1_Rep1


title: BL3_rep1


title: BL3_rep2


title: PSPPH_2491_cycle4_Rep1


title: TBL20_rep3


title: TBL20_rep2


title: HEK293T_Input_TOB2_rep1


title: HEK293T_IP_SNRPA_rep2

value: Genetex, GTX101664


title: PSPPH_2491_cycle2_Rep1


title: TBL20_rep1


title: HEK293T_Input_SNRPA_rep2


title: HEK293T_IP_SNRPA_rep1


title: PSPPH_2491_cycle1_Rep1


title: HEK293T_IP_TOB2_rep1


title: PSPPH_2473_cycle4_Rep1


title: HEK293T_Input_SNRPA_rep1


title: HEK293T_IP_PARN_rep2

value: Genetex, GTX115020


title: PSPPH_2473_cycle3_Rep1

value: wide type


title: BL20_rep2


title: BL20_rep1


title: PSPPH_2473_cycle2_Rep1

value: exponential phase


title: HEK293T_Input_PARN_rep2


title: BL20_rep3


title: PSPPH_2473_cycle1_Rep1


title: MDA-MB-231 co-culture, exosomes (Replicate 2)

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description:
microRNA
NEB-Next multiplex small RNA
DEG_miRNAs.xlsx

data_processing:
Cutadapt, Fastx toolkit, for quality control using FastQC software.
Clean data were obtained by filtering out low-quality reads and bases with less than 18 and more than 26 nucleotides prior to mapping miRNA read sequences to the human genome.
Reads were aligned to the human reference genome (UCSC 38) using Mapper and precursor mature miRNA reference (miRBase 21) using miRDeep2 version 2.0.0.8.
Statistical analysis: Bonferroni and FDR corrected.
Filtering: Significant, above 2; Kalz test: FDR pvalue <0.05; Kalz test: FC abs value>2.
Genome_build: GRCh38, miRBase 21
Supplementary_files_format_and_content: DEG_miRNAs.xlsx: Excel file containing Fold change values of miRNAs of co-culture normalized against parental control.

source_name: Exosomes

growth_protocol: The parental and co-culture of Breast cancer cells were cultured with or without adipose MSC in indirect-transwell insert. All cells were maintained in 5% CO2 humidified incubator in exosomes depleted serum.

extract_protocol:
Total RNA with retention of small RNAs from the cells were extracted using miRNeasy.
RNA libraries were prepared for sequencing using standard NEB-Next multiplex small RNA protocols.

treatment_protocol: Cells were co-cultured for 48 hours prior to exosomes and cells collection and extraction.

tag: cell source

value: Basal human breast adenocarcinoma

tag: culture condition

value: Co-culture

tag: culture dimension


title: MDA-MB-231 co-culture, exosomes (Replicate 3)


title: PSPPH_2491_cycle3_Rep1

first: Jian

address: 83 Tat Chee Avenue, Kowloon

tag: genotype

tag: growth phase


title: PSPPH_2295_cycle3_Rep1


title: MDA-MB-231 co-culture, exosomes (Replicate 1)


title: HEK293T_Input_PARN_rep1


title: PSPPH_2295_cycle4_Rep1


title: HEK293T_IP_MEX3C_rep2

value: ProSci, 4857


title: MCF-7 co-culture, exosomes (Replicate 3)

value: Luminal A human breast adenocarcinoma


title: HEK293T_Input_MEX3C_rep2


title: HEK293T_IP_MEX3C_rep1


title: PSPPH_2295_cycle1_Rep1


title: MCF-7 co-culture, exosomes (Replicate 1)


title: MCF-7 co-culture, exosomes (Replicate 2)


title: HEK293T_Input_MEX3C_rep1


title: PSPPH_2055_cycle4_Rep1


title: Adipose MSC Exo, exosomes (Replicate 3)

value: Human Mesenchymal stem cell

value: Monolayer


title: HEK293T_IP_DDX6_rep2

value: Genetex, GTX102795


title: HEK293T_Input_DDX6_rep2


title: PSPPH_2055_cycle2_Rep1


title: Adipose MSC Exo, exosomes (Replicate 2)


title: Adipose MSC Exo, exosomes (Replicate 1)


title: PSPPH_2055_cycle3_Rep1


title: HEK293T_IP_PARN_rep1


title: MDA-MB-231 parental, exosomes (Replicate 3)

tag: cell line


title: HEK293T_IP_DDX6_rep1


title: HEK293T_Input_DDX6_rep1


title: PSPPH_1800_cycle4_Rep1


title: MDA-MB-231 parental, exosomes (Replicate 2)


title: PSPPH_1800_cycle3_Rep1


title: PSPPH_2295_cycle2_Rep1


title: MDA-MB-231 parental, exosomes (Replicate 1)


title: PSPPH_1800_cycle2_Rep1


title: MCF-7 parental, exosomes (Replicate 3)


title: PSPPH_1800_cycle1_Rep1


title: HEK293T_Input_CLK3_rep2


title: HEK293T_IP_CLK3_rep1

value: Abgent, AT1558a


title: HEK293T_IP_CLK3_rep2


title: PSPPH_1771_cycle4_Rep1


title: MCF-7 parental, exosomes (Replicate 1)


title: MCF-7 parental, exosomes (Replicate 2)


title: PSPPH_1771_cycle3_Rep1


title: HEK293T_Input_CLK3_rep1


title: HEK293T_IP_UBAP2L_rep2

value: Bethyl, A300-533A


title: MDA-MB-231 co-culture, cells (Replicate 3)

source_name: Cells


title: MDA-MB-231 co-culture, cells (Replicate 2)


title: PSPPH_2055_cycle1_Rep1


title: PSPPH_1771_cycle1_Rep1


title: MDA-MB-231 co-culture, cells (Replicate 1)


title: MCF-7 co-culture, cells (Replicate 3)


title: PSPPH_1308_cycle4_Rep1


title: HEK293T_Input_UBAP2L_rep1


title: PSPPH_1308_cycle3_Rep1


title: MCF-7 co-culture, cells (Replicate 2)


title: HEK293T_IP_MTDH_rep2

value: Bethyl, A303-144A


title: PSPPH_1308_cycle2_Rep1


title: MCF-7 co-culture, cells (Replicate 1)


title: HEK293T_Input_MTDH_rep2


title: HEK293T_IP_MTDH_rep1


title: HEK293T_IP_UBAP2L_rep1


title: Adipose MSC, cells (Replicate 2)


title: Adipose MSC, cells (Replicate 3)


title: PSPPH_1259_cycle4_Rep1


title: HEK293T_IP_AIMP1_rep2

value: MBL, RN055PW


title: Adipose MSC, cells (Replicate 1)


title: MDA-MB-231 parental, cells (Replicate 3)


title: PSPPH_1259_cycle2_Rep1


title: HEK293T_Input_UBAP2L_rep2


title: PSPPH_1259_cycle3_Rep1


title: HEK293T_Input_MTDH _rep1


title: HEK293T_Input_AIMP1_rep2


title: PSPPH_1771_cycle2_Rep1


title: PSPPH_1259_cycle1_Rep1


title: PSPPH_0442_cycle4_Rep1


title: HEK293T_Input_AIMP1_rep1


title: MDA-MB-231 parental, cells (Replicate 2)


title: MDA-MB-231 parental, cells (Replicate 1)


title: HEK293T_IP_CNOT7_R1_rep2

value: MBL, RN110PW


title: PSPPH_0442_cycle3_Rep1


title: PSPPH_0442_cycle2_Rep1


title: MCF-7 parental, cells (Replicate 3)


title: MCF-7 parental, cells (Replicate 2)


title: HEK293T_Input_CNOT7_rep2


title: PSPPH_1308_cycle1_Rep1


title: PSPPH_0442_cycle1_Rep1


title: HEK293T_IP_CNOT7_rep1


title: PSPPH_5087_cycle4_Rep1


title: HEK293T_IP_AIMP1_rep1


title: HEK293T_Input_CNOT7_rep1


title: SK-N-AS_siPrp19c_fpkm

first: Yuanxia

last: Cai

address: No.1665, Kongjiang Road, Yangpu District

institute: Xinhua Hospital

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.
Reference genome and gene model annotation files were downloaded from genome website directly. 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM values for each Sample

growth_protocol: Human neuroblastoma cell lines SK-N-AS was kindly provided by Stem Cell Bank, Chinese Academy of Sciences and maintained in MEM/F12 with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent.RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: To generate Prp19 knockdown cells, we used siRNA to transfect the neuroblastoma cells for 72h.

value: SK-N-AS

value: neuroblastoma cell line

tag: replicate


title: OE_TOB2-1

description:
processed data file: RNAseq_set4_RPKM.csv
The control samples are OE-FLAG-1/ OE-FLAG-2

data_processing:
RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i). Reads did not map to repetitive elements were then mapped to the human genome (hg19). Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
Differential expression was calculated using DESeq2 version 1.10.1
The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.
Genome_build: Homo sapiens UCSC hg19

growth_protocol: HEK293T cells were grown in standard cell culture in 10% FBS in DMEM

extract_protocol:
Total and polysome derived RNA were extracted using Trizol reagent
Strand-specific RNA sequencing libraries were prepared from 0.5-3 µg total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina).

treatment_protocol: Polysome cells were treated with cycloheximide (CHX) at 100 µg/ml for 5 min at 37°C.

value: HEK293T cells


title: OE_TOB1-2


title: PSPPH_5087_cycle3_Rep1

value: wide type


title: PSPPH_5087_cycle2_Rep1

value: exponential phase


title: SK-N-AS_NCc_fpkm

description: NCc

tag: cell type

value: NC


title: SK-N-AS_NCb_fpkm

description: NCb


title: PSPPH_5087_cycle1_Rep1


title: PSPPH_4870_cycle4_Rep1


title: SK-N-AS_siPrp19a_fpkm


title: SAMPLE_04_01

city: Fuzhou

first: Shenglong

last: Lin

state: Fujian

address: No. 312, Xi-hong Road, Gu-lou District

department: Hepatology

institute: Mengchao Hepatobiliary Hospital of Fujian Medical University

description: microRNA

hyb_protocol: The labeled samples were hybridized on miRNA arrays for 18 h at 48˚C. Arrays were washed to remove non-specifically bound nucleic acids and stained on Fluidics Station 450s (Affymetrix).

scan_protocol: GeneChip Scanner 3000 7G system (Affymetrix).

data_processing: Data were processed by Affymetrix GeneChip Command Console 6.0+ software (Thermo Fisher Scientific).

label: FlashTag™ Biotin

source_name: Healthy control

label_protocol: Total RNA (1 µg) from each sample was labeled using the FlashTag™ Biotin HSR RNA labeling kit.

extract_protocol: Total RNA was extracted from 200 μl serum using the miRNeasy MicroKit (Qiagen). Purity and concentration of isolated total RNA were tested with a NanoDrop® ND-2000 spectrophotometer (NanoDrop Technologies) through absorbance measurements at 260 and 280 nm.

tag: disease state

value: Healthy control

tag: tissue

value: serum

tag: gender

value: Male


title: OE_SNRPA-2


title: SK-N-AS_NCa_fpkm

description: NCa


title: MCF-7 parental, cells (Replicate 1)

value: Luminal A human breast adenocarcinoma


title: SAMPLE_04_02

description: microRNA

value: Female


title: PSPPH_4870_cycle3_Rep1


title: PSPPH_4870_cycle2_Rep1


title: SAMPLE_04_03

description: microRNA


title: OE_TOB2-2


title: SK-N-AS_siPrp19b_fpkm


title: OE_NANOS3-2


title: siPrp19c_fpkm

description:
rep3
none

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.
Reference genome and gene model annotation files were downloaded from genome website directly. 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: neuroblastoma cell line

growth_protocol: Human neuroblastoma cell lines SK-N-BE(2) was kindly provided by Stem Cell Bank, Chinese Academy of Sciences and maintained in MEM/F12 with 10% fetal bovine serum.


title: SAMPLE_04_04

description: microRNA


title: OE_SNRPA-1


title: NCc_fpkm

description:
rep3
none


title: OE_NANOS3-1


title: PSPPH_4853_cycle4_Rep1


title: OE_IFIT2-2


title: OE_TOB1-1


title: PSPPH_4853_cycle3_Rep1


title: SAMPLE_03_03

description: microRNA

source_name: Chronic hepatitis B

value: Chronic hepatitis B


title: SAMPLE_03_04

description: microRNA


title: SAMPLE_03_02

description: microRNA


title: OE_IFIT2-1


title: PSPPH_4853_cycle2_Rep1


title: siPrp19a_fpkm

description:
rep1
none


title: NCa_fpkm

description:
rep1
none


title: PSPPH_4870_cycle1_Rep1


title: OE_FLAG-1

description: processed data file: RNAseq_set4_RPKM.csv


title: PSPPH_4853_cycle1_Rep1


title: SAMPLE_03_01

description: microRNA


title: siPrp19b_fpkm

description:
rep2
none


title: SAMPLE_02_04

description: microRNA

source_name: Cirrhosis without bacterial infection

value: Cirrhosis without bacterial infection


title: Human HS_20C_PAC-3

city: Montreal

first: Genevieve

last: Deblois

state: Quebec

address: 2950, chemin de Polytechnique

institute: Université de Montréal

data_processing:
Reads were aligned to hg19 using tophat (2.0.8) with default parameters
Transcripts were merged using cufflinks (2.1.1) and differential expression computed for all relevant contrasts with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: csv file showing mean FPKM value for all identified transcripts

source_name: HS 578T

extract_protocol:
RNA was extracted using the qiaquick purification kit according to manufacturer's protocol
RNA samples were quantified by qubit (Life Technologies) and quality by Agilent Bioananlyzer. All samples had RIN score >8 were library prepared using TruSeq Stranded mRNA kit (Illumina). Two hundred nanograms total RNa from  30 RNA samples were purified for polyA tail containing mRNA molecules using poly-T oligo attached magnetic beads , following purification the RNA was fragmented. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” based were added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries.
Final cDNA libraries were size validated using Agilent Bioanalyzer and concentration validated by qPCR (Kapa Biosystems/Roche). All libraries were normalized to 10nM and pooled together, denatured with 0.2N NaOH and diluted to a final concentration of 8 pM. Pooled libraries were loaded onto cBot (Illumina) for cluster generation. Clustered flow cell was then sequenced Paired-end 100 cycles V3 using Illumina Hiseq2000 to achieve ~30 million reads per sample.

value: TNBC

tag: paclitaxel sensitivity

value: Taxol-resistant

value: GD_RNA_20 and 10

tag: agent

value: 20nM Paclitaxel


title: PSPPH_4448_cycle3_Rep1


title: PSPPH_4448_cycle4_Rep1


title: NCb_fpkm

description:
rep2
none


title: SAMPLE_02_02

description: microRNA


title: Human HS_20A_PAC-3

value: GD_RNA_18 and 8


title: Human HS_20B_PAC-3

value: GD_RNA_19 and 9


title: SAMPLE_02_03

description: microRNA


title: PSPPH_4448_cycle2_Rep1


title: SAMPLE_01_04

description: microRNA

source_name: Cirrhosis with bacterial infection

value: Cirrhosis with bacterial infection


title: SAMPLE_02_01

description: microRNA


title: OE_FLAG-2

value: HEK293T cells


title: PARN-sh2-2

description:
processed data file: RNAseq_set3_RPKM.csv
The control samples are Control-3-1/ Control-3-2


title: OE_BOLL-1


title: PARN-sh2-1


title: Human HS_PAC-3

value: parental taxol-sensitive  treated with paclitaxel 72h

value: GD_RNA_17 and 7

value: 20nM Paclitaxel, 72h


title: Gdpd3 KO CML_7

city: Hiroshima

first: Kazuhito

last: Naka

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description:
KO_S7
processed data file: gene-FPKM_name.txt
processed data file: gene-WT-Gdpd3-KO_DESeq2.txt

data_processing:
Fastq files from the Illumina sequencer were filtered for low quality reads by using a sliding window (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic (version is unknown, probably, 0.39). Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptors, polyA, polyT, polyG, and polyC sequences were removed using Trim Galore! (version is unknown, probably, ver. 0.6.5) and cutadapt (ver. 1.16).
Trimmed reads were then mapped to the mouse genome (mm9) using STAR (version 2.6.1a). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript length.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: gene-WT-Gdpd3-KO_DESeq2.txt: Tab-delimited text file including FPKM values for each sample.

source_name: CML stem cells

extract_protocol:
LT CML stem cells isolated from Gdpd3+/+ tet-CML-affected mice and Gdpd3-/- tet-CML-affected mice were directly sorted by FACS Aria III cell sorter (BD Biosciences) into 500μl Isogene solution (Nippon Gene, Co. Ltd., Toyama, Japan). RNA extraction and sequencing were performed by DNAform (Yokohama, Japan). The RNA quality was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies). All RNA samples had an RNA integrity number of >7.5 and exceeded the quality threshold for RNA sequencing.
Libraries were constructed from total RNA using the SMART-Seq® v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech, Kusatsu, Shiga, Japan). Full-length double-stranded cDNA libraries were fragmented by transposase using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, USA). Paired-end reads of 150 bases were generated using HiSeq (Illumina).

tag: strain

tag: genotype/variation

value: murine bone marrow long-term CML stem cells

tag: time point

value: post 5 wks from CML induction


title: SAMPLE_01_03

description: microRNA

value: serum

value: Male


title: SAMPLE_01_02

description: microRNA


title: PSPPH_4448_cycle1_Rep1

value: wide type

value: exponential phase


title: Gdpd3 KO CML_6

description:
KO_S6
processed data file: gene-FPKM_name.txt
processed data file: gene-WT-Gdpd3-KO_DESeq2.txt


title: PSPPH_3962_cycle4_Rep1


title: SAMPLE_01_01

description: microRNA


title: PARN-sh1-2


title: Human HS_DMSO-3

value: TNBC

value: parental taxol-sensitive

value: GD_RNA_16 and 6


title: OE_BOLL-2


title: Human 436_20C_PAC-3

value: Taxol-resistant

value: GD_RNA_15 and 5

value: 20nM Paclitaxel


title: Gdpd3 KO CML_5

description:
KO_S5
processed data file: gene-FPKM_name.txt
processed data file: gene-WT-Gdpd3-KO_DESeq2.txt


title: PSPPH_3962_cycle2_Rep1


title: Human 436_20B_PAC-3

value: GD_RNA_14 and 4


title: WT CML_3

description:
WT_S3
processed data file: gene-FPKM_name.txt
processed data file: gene-WT-Gdpd3-KO_DESeq2.txt


title: PARN-sh1-1

value: HEK293T cells


title: PSPPH_3962_cycle1_Rep1

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt


title: WT CML_2

description:
WT_S2
processed data file: gene-FPKM_name.txt
processed data file: gene-WT-Gdpd3-KO_DESeq2.txt


title: MTDH-sh2-2


title: Human 436_20A_PAC-3

value: GD_RNA_13 and 3


title: PSPPH_3479_cycle4_Rep1


title: Human 436_PAC-3

value: parental taxol-sensitive  treated with paclitaxel 72h

value: GD_RNA_12 and 2


title: MTDH-sh1-2


title: WT CML_1

description:
WT_S1
processed data file: gene-FPKM_name.txt
processed data file: gene-WT-Gdpd3-KO_DESeq2.txt

value: murine bone marrow long-term CML stem cells


title: PSPPH_3479_cycle3_Rep1


title: Human 436_DMSO-3

value: GD_RNA_11 and 1


title: PSPPH_3962_cycle3_Rep1


title: E6_C1_3: H1_KO_NGN2_3

city: Singapore

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: Lee Kong Chian School of Medicine - NTU

description: D50 NGN2-induced WT H1 hESC batch3

data_processing:
Adapter sequences were then trimmed using trimmomatic v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, adapter sequences are AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

molecule: polyA RNA

source_name: H1 hESC

extract_protocol:
Human neuron-rat astrocyte co-cultures at day 40 were directly lysed in TRIzol (Thermofisher) and total RNAs were extracted with Direct-zol RNA miniPrep kit (Zymo Research)
Truseq Stranded mRNA (Poly A selection) kit

value: UBE3A KO

value: human embryonic stem cell (hESC)

tag: batch


title: E5_H1_3: H1_WT_NGN2_3

description: D50 NGN2-induced WT H1 hESC batch 3

value: WT


title: MTDH-sh1-1


title: Control-3-2

description: processed data file: RNAseq_set3_RPKM.csv


title: PSPPH_3479_cycle1_Rep1

value: wide type

value: exponential phase


title: Human HS_20B_PAC-2

value: TNBC

value: GD_RNA_9 and 29


title: Control-3-1


title: E4_C30_2: H9_KO_NGN2_2

description: D50 NGN2-induced KO H9 hESC batch 1

source_name: H9 hESC


title: Human HS_20C_PAC-2

value: Taxol-resistant

value: GD_RNA_10 and 30


title: E3_Ha_2: H9_WT_NGN2_1

description: D50 NGN2-induced WT H9 hESC batch 1


title: PSPPH_3297_cycle4_Rep1


title: Human HS_20A_PAC-2

value: GD_RNA_8 and 28

value: 20nM Paclitaxel


title: MEX3C-sh2-2

description:
processed data file: RNAseq_set2_RPKM.csv
The control samples are Control-2-1/ Control-2-2

value: HEK293T cells


title: MEX3C-sh2-1


title: E2_C30_1: H9_KO_NGN2_2

description: D50 NGN2-induced KO H9 hESC batch 1


title: MTDH-sh2-1


title: Human HS_PAC-2

value: GD_RNA_7 and 27

value: 20nM Paclitaxel, 72h


title: Human HS_DMSO-2

value: parental taxol-sensitive

value: GD_RNA_6 and 26


title: PSPPH_3297_cycle3_Rep1


title: PSPPH_3297_cycle2_Rep1


title: E1_Ha_1: H9_WT_NGN2_1

description: D50 NGN2-induced WT H9 hESC batch 1


title: PSPPH_3479_cycle2_Rep1


title: LnCaP_Combination_Replicate2

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Two biological replicates of each condition were used for the assay
Samples were multiplexed and paired-end sequenced with 150bp read length
Sequencing reads were aligned to Hg19 (GRCh37) using STAR
Raw counts of reads were mapped to genes using HTSeq counts
Normalised counts were generated using DESeq2
Genome_build: Hg19 (GRCh37)

source_name: LnCaP Cell Line

extract_protocol:
RNA was isolated with Illustra RNAspin Minikit (GE healthcare, cat num. 25-0500-72)
Libraries for sequencing were prepared by the Norwegian High Throughput Sequencing Centre using Strand-specific TruSeq RNA-seq library prep kit.

treatment_protocol: LNCaP cells were treated with control, 40mM OSMI-2-only, 0.5mM AT7519-only and 0.5mM AT7519+40mM OSMI-2, for 4 hours prior to harvesting

value: LnCaP

tag: treatment

value: OSMI2 & AT7519 treated


title: MEX3C-sh1-1


title: MEX3C-sh1-2


title: Human 436_20C_PAC-2

value: GD_RNA_5 and 25


title: PSPPH_3278_cycle4_Rep1


title: LnCaP_Combination_Replicate1


title: Human 436_20A_PAC-2

value: GD_RNA_3 and 23


title: DDX6-sh2-2


title: DDX6-sh2-1


title: PSPPH_3278_cycle2_Rep1

value: wide type


title: Human 436_PAC-2

value: parental taxol-sensitive  treated with paclitaxel 72h

value: GD_RNA_2 and 22


title: PSPPH_3278_cycle3_Rep1

value: exponential phase


title: LnCaP_AT7519_Replicate2

value: AT7519 treated


title: DDX6-sh1-2


title: LnCaP_AT7519_Replicate1


title: Human 436_DMSO-2

value: TNBC

value: GD_RNA_1 and 21


title: PSPPH_3278_cycle1_Rep1


title: Human HS_20C_PAC-1

value: Taxol-resistant

value: GD_RNA_20 and 30

value: 20nM Paclitaxel


title: PSPPH_3241_cycle4_Rep1


title: PSPPH_3297_cycle1_Rep1


title: LnCaP_OSMI2_Replicate1

value: OSMI2 treated


title: Control-2-2

description: processed data file: RNAseq_set2_RPKM.csv

value: HEK293T cells


title: Human HS_20B_PAC-1

value: GD_RNA_19 and 29


title: Human 436_20B_PAC-2

value: GD_RNA_4 and 24