title: miR_MSC_P4_REP3 [P4413]

source_name: Bone marrow_miR_MSC_P4

value: Expansion in vitro to passage 4


title: L7-F14_S314

status: Public on Jun 21 2021

type: SRA

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description:
L8-E17_S221
L8-E18_S222
L8-E19_S223
L8-E20_S224

library_source: transcriptomic

data_processing:
To confirm quality of the raw reads, a FastQC analysis was performed. Reads were aligned to the mouse mm10 genome using STAR with default options. A count table was generated from the alignments using Subread/FeatureCounts 1.5.1.
The count matrix was analyzed with Seurat 2.3.1, using the following workflow: Cells with less than 200 genes or more than 6,000 genes (likely doublets) were removed, as well as cells whose mitochondrial gene expression accounted for more than 20% of the total gene expression of that cell. Genes found in less than 0.5% of cells were also excluded. Following this filtering, 709 of the original 768 cells remained (with a median read depth of 630,131 reads per cell and median of 2,646 genes per cell).
Data was log-normalized and scaled by a factor of 10,000.
The normalized count data was subsequently regressed on the number of reads.
The first 30 PCAs were used to identify clusters (using default parameters).
Cluster markers were determined by a differential expression analysis of each cluster versus all other clusters combined. Seurat’s “AddModuleScore” function, with default parameters, was used to calculate gene set scores of cell type-specific markers extracted from previous studies. Boxplots of these scores were used to assign each cluster to a cell type. We confirmed these assignments by comparing our cluster markers to unique markers of cell type defined by the aforementioned studies to ensure that there was no ambiguity in the assignment of cell types.
Gene differential expression between experimental (miR-132 overexpression) and control conditions (within each cell population) was performed. Differential expression (for analysis of cluster markers and for analysis between controls and experimental conditions) was performed as follows: p-values were calculated using a Wilcoxon rank-sum test (using Seurat’s “FindMarkers” function), and corrected for multiple testing using a Bonferroni correction. Log fold changes were calculated using the natural logarithm. Genes with adjusted p-values of < 0.05 were considered significantly differentially expressed.
Functional enrichment analysis was performed by using Ingenuity Pathway Analysis. By convention, the 150 transcripts with the most negative (‘Downregulated Transcripts’) or most positive (‘Upregulated Transcripts’) log fold changes after differential gene expression (comparing miR-132-overexpression to control samples) were selected per cluster for analysis.
Genome_build: mm10 genome (Ensembl Version 88)
Supplementary_files_format_and_content: Raw count matrix: neurogenesis_mirOE_raw_counts.tsv.gz

molecule: total RNA

organism: Mus musculus

source_name: Dentate gyrus

extract_protocol:
For FACS isolation of single cells, four miR-132-injected and four control-injected Nestin:GFP male mice were used and 94 cells were initially sorted per mouse.
FACS-sorted cells were processed using the Smart-seq2 protocol. Briefly, RNA was reverse-transcribed using biotinylated oligo-dT primers and biotinylated template-switching (TSO) oligonucleotides and subsequently cDNA was preamplified using the KAPA HiFi Hot Start DNA Polymerase and biotinylated ISPCR primers. cDNA was purified using AMPURE XP Agencourt beads, concentration was calculated with the Quantifluor dsDNA kit and adjusted on an Echo 525 Liquid Handler. 100 pg cDNA per cell were used for library preparation with Nextera XT DNA Library Preparation Kit. Finally, following purification on magnetic beads the libraries were multiplexed and sequenced using the Illumina NextSeq500 platform.

treatment_protocol: For miR‐132 overexpression, 2 month-old Nestin:GFP mice received either a miR‐132 mimic or a negative control oligonucleotide in a 3 μl mix with lipofectamine 2000 (at a 1:1 volume ratio). Injections of 150 pmol oligo each were performed once a week for 5 weeks in total

tag: isolation

tag: mouse id

tag: date

tag: treatment

value: Control


title: miR_MSC_P4_REP2 [P4411]

city: Shenzhen

first: Ziming

last: Wang

state: Guangdong

address: 3025 Shennan Zhong Lu

department: Department of Orthopedics

country: China

institute: the eighth affiliated hospital of Sun Yat-sen University

data_processing:
After RNA integrity evaluation (Agilent Technologies, USA), rRNA remove, cDNA synthesis and PCR amplification, the sequencing database was built at BGI (Beijing Genomic Institute in Shenzhen) using the IlluminaHiSeq 3000 platform. Then the data was filtered with SOAPnuke (v1.5.2) to obtain clean reads.
The clean reads were obtained and stored in FASTQ format. HISAT2 (v2.0.4) and Bowtie2 (v2.2.5) were applied to align the clean reads to the reference gene set.
Expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)15 with a Q value ≤ 0.05
Genome_build: Grch38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

growth_protocol: Cells were seeded in 12-well plates and cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) containing 10% fetal bovine serum (FBS; Gibco) at 37°C in a 5% CO2 atmosphere. The medium was replaced every 3 days.

extract_protocol:
MSCs total RNA samples of P4, P6 and P12 were separately treated with TRIzol (TAKARA).
The extracted total RNA was first removed using a biotin-labeled specific probe (Ribo-Zero™ rRNA Removal Kit) to remove the ribosomal rRNA.After purification, the RNA is fragmented at a certain temperature and ionic environment.A cDNA strand was then synthesized using a random primer and reverse transcriptase in the TruSeq® Stranded kit, and then a double-stranded cDNA was synthesized using DNA polymerase I and RNaseH.During cDNA two-strand synthesis, the RNA template is removed and dTTP is replaced by dUTP.The involvement of dUTP prevents the two strands of cDNA from being amplified in the subsequent process because the polymerase cannot cross the dUTP site on the template as it extends.The double-stranded cDNA product is then linked with an "A" base and connector.The ligation products will be amplified and purified to produce the final cDNA library.Finally, the constructed sequencing library was sequenced.
For miRNAs, Experiment Pipeline Steps for Small RNA Sequencing 1) Filter small RNA: separate 18-30nt RNA segment by PAGE gel. 2) 3' adaptor ligation: link 5-adenylated, 3-blocked single-stranded DNA adapter to 3'  end of selected small RNAs from step 1. 3) Reverse primer annealing: the RT primer is added to the solution from step 2, and is cross-linked to the 3' adapter of RNAs and excessive free 3' adapter. 4) 5' adaptor ligation: the 5' adaptor is linked to the 5' end of the product from step 3. The connection (5鈥 adaptor) will be attached to the 5鈥 end only, but it is not c onnected to the 3' adaptor or RT primer hybrid chain. This greatly reduces self-ligation.  5) Strand cDNA synthesis: reverse extend the RT primer in step 3 to synthetize strand cDNA. 6) PCR amplification: use high-ping polymerase to amplify cDNA, enrich cDNA with both 3' and 5' adaptor. 7) Library fragment selection: separate the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other products.  8) Library quantitative and pooling cyclization.

treatment_protocol: MSCs were digested with 0.25% trypsin supplemented with 0.53mM EDTA (Gibco) to passaging cells to generation 4, 6, 12, respectively.

tag: cell type

value: Bone marrow-derived mesenchymal stem cells

tag: generation

value: Generation 6


title: L7-F12_S132

description:
L8-E9_S33
L8-E10_S34
L8-E11_S35
L8-E12_S36


title: L7-E2_S218

description:
L8-C17_S209
L8-C18_S210
L8-C19_S211
L8-C20_S212


title: L7-F11_S131

description:
L8-E5_S29
L8-E6_S30
L8-E7_S31
L8-E8_S32


title: L7-E23_S35

description:
L8-C9_S21
L8-C10_S22
L8-C11_S23
L8-C12_S24


title: L7-E24_S36

description:
L8-C13_S205
L8-C14_S206
L8-C15_S207
L8-C16_S208


title: miR_MSC_P4_REP1 [P4393]

value: Generation 4


title: MSC_P12_REP2 [P12411]

source_name: Bone marrow_MSC_P12

value: Expansion in vitro to passage 12


title: L7-E9_S225

description:
L8-D21_S309
L8-D22_S310
L8-D23_S311
L8-D24_S312


title: MSC_P12_REP3 [P12413]

value: Generation 12


title: L7-E22_S34

description:
L8-C5_S17
L8-C6_S18
L8-C7_S19
L8-C8_S20


title: L7-E21_S33

description:
L8-C1_S13
L8-C2_S14
L8-C3_S15
L8-C4_S16


title: L7-E20_S32

description:
L8-B21_S297
L8-B22_S298
L8-B23_S299
L8-B24_S300


title: MSC_P12_REP1 [P12393]


title: L7-E1_S217

description:
L8-B17_S293
L8-B18_S294
L8-B19_S295
L8-B20_S296


title: MSC_P6_REP3 [P6413]

source_name: Bone marrow_MSC_P6

value: Expansion in vitro to passage 6


title: MSC_P6_REP2 [P6411]


title: L7-E19_S31

description:
L8-B13_S289
L8-B14_S290
L8-B15_S291
L8-B16_S292


title: L7-E18_S30

description:
L8-B9_S105
L8-B10_S106
L8-B11_S107
L8-B12_S108


title: MSC_P4_REP1 [P4393]

source_name: Bone marrow_MSC_P4


title: MSC_P4_REP2 [P4411]


title: L7-E3_S219

description:
L8-C21_S213
L8-C22_S214
L8-C23_S215
L8-C24_S216


title: MSC_P6_REP1 [P6393]


title: MSC_P4_REP3 [P4413]


title: L7-E15_S27

description:
L8-A21_S201
L8-A22_S202
L8-A23_S203
L8-A24_S204


title: L7-E14_S26

description:
L8-A17_S197
L8-A18_S198
L8-A19_S199
L8-A20_S200


title: L7-E16_S28

description:
L8-B1_S97
L8-B2_S98
L8-B3_S99
L8-B4_S100


title: L7-E13_S25

description:
L8-A13_S193
L8-A14_S194
L8-A15_S195
L8-A16_S196


title: L7-E17_S29

description:
L8-B5_S101
L8-B6_S102
L8-B7_S103
L8-B8_S104


title: L7-E12_S228

description:
L8-A9_S9
L8-A10_S10
L8-A11_S11
L8-A12_S12


title: L7-D9_S117

description:
L7-P21_S381
L7-P22_S382
L7-P23_S383
L7-P24_S384


title: L7-E11_S227

description:
L8-A5_S5
L8-A6_S6
L8-A7_S7
L8-A8_S8


title: L7-E10_S226

description:
L8-A1_S1
L8-A2_S2
L8-A3_S3
L8-A4_S4


title: GC1459_rep3

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

country: USA

institute: University of Oregon

data_processing:
Bowtie version 1.2.2 was used to map reads with the following settings: bowtie -I 0 -X 500 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset (file name c_elegans.PRJNA13758.WS273.canonical_geneset.gtf downloaded from Wormbase)
edgeR version 3.24.4 was used for differential expression analysis. Count data was restricted to include protein-coding genes, and further restricted to include only genes with counts-per-million (CPM) greater than one in at least four libraries.
In edgeR, the "calcNormFactors" function was used to normalize for RNA composition and the tagwise dispersion estimate was used for differential expression analysis. The exact test was implemented for pairwise comparison of GC1171 to GC1459.
Genome_build: WS273
Supplementary_files_format_and_content: Count files for each library; these are the non-normalized input into edgeR for differential expression analysis. An excel final with all edgeR differential expression output, normalized CPMs, and additional analysis is also included.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: C. elegans adult hermaphrodites were selected to 10cm high peptone agar plates seeded with OP50 E. coli (4-6 plates per strain, 40-60 animals per plate), and grown for 5 days at 20°C. Gravid hermaphrodites and all embryos were then washed from plates and treated with sodium hypochlorite solution to obtain pure embryo preparations free of bacteria. Embryos hatched for 2 hours in 20-30mL of M9 buffer containing 0.08% ethanol, with rocking. Resulting L1 stage larvae were separated from embryos using 10mm mesh Pluristrainer and pelleted in 10mL or less of buffer, then flash frozen in liquid nitrogen.

extract_protocol:
RNA was isolated using TRIzol following the manufacturer's protocol with notable exceptions. Only 100 uL of Trizol was used, and 5 ug linear polyacrylamide (Sigma Aldrich) was included as a neutral carrier for RNA precipitation. RNA was eluted in nuclease-free water and incubated at 55C for approximately four minutes to resuspend the pellet.
140 ng of total RNA was used for each library prep. NEBNext Ultra II RNA Library Prep kit was used to perform polyA selection and prepare libraries for sequencing. The libraries were enriched with 11 cycles of PCR.

tag: tissue

value: whole animal

tag: developmental stage

tag: strain


title: GC1171_rep5


title: GC1459_rep5


title: GC1171_rep4


title: GC1171_rep3


title: GC1459_rep4


title: L7-D8_S116

description:
L7-P17_S377
L7-P18_S378
L7-P19_S379
L7-P20_S380


title: GC1171_rep1


title: L7-D7_S115

description:
L7-P13_S373
L7-P14_S374
L7-P15_S375
L7-P16_S376


title: L7-D5_S113

description:
L7-P5_S185
L7-P6_S186
L7-P7_S187
L7-P8_S188


title: L7-D4_S112

description:
L7-P1_S181
L7-P2_S182
L7-P3_S183
L7-P4_S184


title: Young Wild Type 1

city: Albany

first: Patrick

last: Blatt

address: 1400 Washington Ave

institute: SUNY Albany

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSCdm6 and FlyBase R6.01) using HISAT2 v2.0.5. Unambiguously mapping reads RefSeq annotated mRNA and lincRNA were quantified using featureCounts v1.5.1 default parameters. Genes with >=0.5 reads per million (RPM) in one of WT ovaries, tst mutant ovaries, tst RNAi ovaries, or young ovaries were retained for further analysis (N=9251 genes). Tst regulated mRNAs were classified as genes whose transcript-per-million (TPM) expression levels were >4-fold increased in the tst RNAi samples; a subset of these that are additionally >2-fold increased in the tst mutant samples were considered to be strong Tst regulated mRNAs (N=207 genes). To curate a set of non-target genes to serve as a background set, we identified genes that differed <1.25 fold between WT and tst RNAi and selected the 3 non-targets with the most similar tst RNAi expression level to each Tst regulated mRNA, to yield a set of 621 non-targets. For polysome profiling samples, normalized ribosome occupancy was calculated as log2(polysome TPM / input TPM). To compare ribosome occupancy of Tst regulated mRNAs across different conditions relative to the global differences observed, we normalized Tst regulated mRNA ribosome occupancy by mean non-target occupancy, i.e. log2((polysome_target TPM) / (input_target TPM) / average (polysome_non-target TPM / input_non-target TPM)). Codon optimality index (CAI) was calculated for each gene relative to the codon frequencies in the top 100 expressed genes in WT ovaries according to Sharp & Li, 1987.
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: D. melanogaster UCSC dm6, Flybase R6.01
Supplementary_files_format_and_content: Tab-delimited log2 transcripts per million (TPM) per gene

organism: Drosophila melanogaster

source_name: Whole Ovaries

growth_protocol: Ovaries dissected in 1x PBS.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026) or phenol-chloroform treatment, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907), and then run on a 1% agarose gel to check integrity of the RNA. To generate mRNA-enriched libraries total RNA was treated with poly(A)tail selection beads and then following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes.
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

treatment_protocol: For samples titled "Psome" samples were loaded onto polysome gradients prior to RNA isolation. Samples titled "Input" are the corresponding total mRNA for the polysome samples.

value: ovary

tag: genotype

tag: age

value: dissected 0-3 hours post-closion

tag: rna population

value: PolyA RNA Enriched

tag: strand specificity


title: L7-D2_S110

description:
L7-O17_S89
L7-O18_S90
L7-O19_S91
L7-O20_S92


title: L7-D3_S111

description:
L7-O21_S93
L7-O22_S94
L7-O23_S95
L7-O24_S96


title: tst RNAi 1

value: UAS-Dcr2;nosGAL4>tst RNAi

value: dissected 1-3 days post-eclosion


title: L7-D24_S312

description:
L7-O13_S85
L7-O14_S86
L7-O15_S87
L7-O16_S88


title: tst Mutant 1


title: L7-D23_S311

description:
L7-O9_S285
L7-O10_S286
L7-O11_S287
L7-O12_S288


title: Adult Wild Type 1


title: bam

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSCdm6 and FlyBase R6.01) using HISAT2 v2.0.5. Unambiguously mapping reads RefSeq annotated mRNA and lincRNA were quantified using featureCounts v1.5.1 default parameters. Genes with >=0.5 reads per million (RPM) in one of WT ovaries, tst mutant ovaries, tst RNAi ovaries, or young ovaries were retained for further analysis (N=9251 genes).
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: D. melanogaster UCSC dm6, Flybase R6.01
Supplementary_files_format_and_content: Tab-delimited log2 transcripts per million (TPM) per gene

value: Whole Ovaries

tag: processing

value: Strand-specific (reverse)


title: L7-D20_S308

description:
L7-N21_S369
L7-N22_S370
L7-N23_S371
L7-N24_S372


title: L7-D21_S309

description:
L7-O1_S277
L7-O2_S278
L7-O3_S279
L7-O4_S280


title: GC1459_rep1


title: L7-D22_S310

description:
L7-O5_S281
L7-O6_S282
L7-O7_S283
L7-O8_S284


title: bam RNAi Polysome

data_processing:
Library strategy: RNA-seq of polysome associated RNA
Sequenced reads were aligned to the D. melanogaster genome (UCSCdm6 and FlyBase R6.01) using HISAT2 v2.0.5. Unambiguously mapping reads RefSeq annotated mRNA and lincRNA were quantified using featureCounts v1.5.1 default parameters. Genes with >=0.5 reads per million (RPM) in one of WT ovaries, tst mutant ovaries, tst RNAi ovaries, or young ovaries were retained for further analysis (N=9251 genes). Tst regulated mRNAs were classified as genes whose transcript-per-million (TPM) expression levels were >4-fold increased in the tst RNAi samples; a subset of these that are additionally >2-fold increased in the tst mutant samples were considered to be strong Tst regulated mRNAs (N=207 genes). To curate a set of non-target genes to serve as a background set, we identified genes that differed <1.25 fold between WT and tst RNAi and selected the 3 non-targets with the most similar tst RNAi expression level to each Tst regulated mRNA, to yield a set of 621 non-targets. For polysome profiling samples, normalized ribosome occupancy was calculated as log2(polysome TPM / input TPM). To compare ribosome occupancy of Tst regulated mRNAs across different conditions relative to the global differences observed, we normalized Tst regulated mRNA ribosome occupancy by mean non-target occupancy, i.e. log2((polysome_target TPM) / (input_target TPM) / average (polysome_non-target TPM / input_non-target TPM)). Codon optimality index (CAI) was calculated for each gene relative to the codon frequencies in the top 100 expressed genes in WT ovaries according to Sharp & Li, 1987.
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: D. melanogaster UCSC dm6, Flybase R6.01
Supplementary_files_format_and_content: Tab-delimited log2 transcripts per million (TPM) per gene

value: nosGAL4>bam RNAi

value: Polysome


title: L7-D6_S114

description:
L7-P9_S189
L7-P10_S190
L7-P11_S191
L7-P12_S192


title: L7-D1_S109

description:
L7-N17_S365
L7-N18_S366
L7-N19_S367
L7-N20_S368


title: bam RNAi Input

value: Input


title: tst RNAi Polysome 2


title: L7-D18_S306

description:
L7-N9_S177
L7-N10_S178
L7-N11_S179
L7-N12_S180


title: tst RNAi Input 2


title: Control Replicate 3

type: RNA

city: Fuzhou

first: Qi

last: Lin

state: Fujian

address: No. 1 Xuefu North Road

institute: The School of Public Health,Fujian Medical University

description: Biological replicate 3 of 3. Control, exposed by NS, archived after 90days exposure.

hyb_protocol: hybridized with lncRNA microarray (Agilent, p/n G2545A) and washed twice.

scan_protocol: Scanned on an Agilent Microarray Scanner (Agilent, p/n G2565BA)

data_processing: Agilent feature extraction software (version 11.0.1.1) was used to analyze acquired array images

label: Agilent quick amp labeling kit

organism: Rattus norvegicus

source_name: Control

label_protocol: 10 µg of total RNA were labeled by Quick Amp Labeling Kit (Agilent, p/n 5190-0042)

growth_protocol: Wistar rats (male, 6-8w) divided into 3 group randomly, PMM group: PM2.5 exposure for 90 days; CSM group: CS exposure for 90 days; Ctrl group: NS inhaled for 90 days.

extract_protocol: The whole lung tissue was cryopulyerized by using the Biopulyerizer and total RNA extracted with TRIzol Reagent following manufacturer's instructions

value: NS inhaled for 90 days

tag: gender

value: male

value: Wistar

value: Lung


title: L7-D17_S305

description:
L7-N5_S173
L7-N6_S174
L7-N7_S175
L7-N8_S176


title: L7-D16_S304

description:
L7-N1_S169
L7-N2_S170
L7-N3_S171
L7-N4_S172


title: tst RNAi Polysome 1


title: Control Replicate 1

description: Biological replicate 1 of 3. Control, exposed by NS, archived after 90days exposure.


title: mRNA-20K-exp2

city: RTP

first: ruifang

last: li

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
ATACseq processing: Raw reads were filtered to exclude pairs with average base quality <20.  Adapters removed by Cutadapt with parameters "a CTGTCTCTTATA -O 5 -q 0”, then reads were filtered to exclude fragments with length <30bp.  Filtered, trimmed read pairs were mapped against  mm10  via Bowtie2 v2.1.0 with parameters “-X 2000 --fr --end-to-end --very-sensitive”, followed by filtering with samtools v1.3.1 at MAPQ5.  Reads mapped to chrM were filtered out.  Duplicate mapped read pairs were removed by Picard tools MarkDuplicates.jar v1.110.  Only the 9bp at the 5’ end of each read was retained for downstream analysis.
ATACseq signal tracks: Coverage tracks for genome browser views were generated with BEDtools v2.24.0 genomeCoverageBed, depth-normalized to 10 million read ends per sample, then converted to bigWig format with UCSC utility bedGraphToBigWig.
ATACseq peaks: Peak calls per sample were made by MACS2 v2.1.1 with parameters “callpeak -g mm -q 0.0001 --keep-dup=all --nomodel --extsize 9", then BEDtools v2.24.0 mergeBed was used to merge neighboring peaks within 200bp.  One single set of unified peaks was generated by collapsing called peaks and identifying only peak regions that overlap from at least 3 of 8 samples via BEDtools v2.24.0 unionBedGraphs, followed by merging neighboring peaks within 200bp with BEDtools v2.24.0 mergeBed.  Unified peaks less than 50bp in width were discarded.  Unified peaks not within canonical chromosomes (chr1-19, X, Y) were also discarded.
RNAseq processing: Raw reads were filtered to exclude pairs with average base quality <20.  Filtered reads pairs were mapped against  mm10 by STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".  Counts per gene per sample were collected by featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p".
RNAseq signal tracks:  Coverage tracks were generated by STAR v2.5 with parameters “--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Unstranded --outWigNorm RPM”, then converted to bigWig format with UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: coverage tracks in bigWig format; peaks in BED format; RNAseq counts-per-gene in tab-delimited text format

source_name: E14 mouse embryonic stem cells

growth_protocol: Mouse E14 embryonic stem cells (129/Ola background) were maintained in Glasgow Minimum Essential Medium (GMEM, Sigma) containing 15% fetal bovine serum, supplemented with 1× Pen-Strep (Gibco), 2 mM Glutamax (Gibco), 50 µM β-mercaptoethanol (Gibco), 0.1 mM nonessential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), and Leukemia Inhibitory Factor (LIF, 1000U/ml, Millipore).

extract_protocol:
For low-input ATAC&mRNA-seq, harvested cells were washed and then permeabilized with mild detergent to facilitate the entry of Tn5 into the nuclei to tagment open chromatin regions. Tagmented cells were then lysed and Dynabeads Oligo (dT)25 were added into the cell lysate to capture mRNA. After magnetic separation, tagmented genomic DNA in the supernatant was purified and further amplified with indexed PCR to construct ATAC-seq library, while mRNA captured on beads was reverse transcribed using the bead-bound oligo (dT) as primer. The mRNA/cDNA hybrids were then directly tagmented by Tn5, and after initial end extension, the tagmented cDNA was amplified with indexed PCR to prepare mRNA-seq library using Nextera XT DNA Library Preparation Kit. Omni-ATAC-seq was performed following the Omni-ATAC protocol (Corces et al., 2017).
Open chromatin regions and mRNA/cDNA hybrids were tagmented with Tn5 and then amplified with indexed PCR to prepare ATAC-seq and RNA-seq libraries.

tag: cell line

value: E14 mouse embryonic stem cells

tag: cell numbers

tag: library protocol

value: low-input ATAC&mRNA-seq


title: L7-D14_S302

description:
L7-M17_S77
L7-M18_S78
L7-M19_S79
L7-M20_S80

tag: isolation

tag: mouse id

value: Control


title: L7-D19_S307

description:
L7-N13_S361
L7-N14_S362
L7-N15_S363
L7-N16_S364

tag: date

tag: treatment


title: tst RNAi Input 1

value: ovary


title: COPD model exposed by PM2.5 replicate 3

description: Biological replicate 3 of 3. rat model of COPD, exposed by PM2.5, archived after 92days exposure.

source_name: Rats model of COPD exposed by PM2.5

value: PM2.5 exposure for 90 days


title: Control Replicate 2

description: Biological replicate 2 of 3. Control, exposed by NS, archived after 90days exposure.


title: Adult Control Polysome 1

value: PolyA RNA Enriched


title: mRNA-10K-exp2


title: L7-D12_S120

description:
L7-M9_S273
L7-M10_S274
L7-M11_S275
L7-M12_S276


title: Adult Control Input 1


title: mRNA-10K-exp1


title: mouse_897_Rep2

city: Houston

first: Abhinav

last: Jain

state: TX

address: 1515 Holcombe Blvd

department: Epigenetics and Molecular Carcinogenesis

institute: The UT MD Anderson Cancer Center

library_source: genomic

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
Adapter sequences were removed from 3’ends of reads by Trim Galore! (version 0.4.1) and cutadapt (version 1.9.1).
Then the reads were mapped to the mouse genome (mm10) using Bowtie (version 1.1.2) with parameters "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, for multiple pairs of reads that were mapped to the same genomic position, only one copy was retained for further analysis.
For each fragment (e.g. a pair of reads), the 5’ end was offset by +4 bp and the 3’ end was offset by -5 bp to adjust both ends to represent the center of a transposon binding event.
To generate the signal landscape, binding events (i.e. ends of fragments) were smoothed by 73 bp (i.e. extended 36 bp upstream and 36 bp downstream), piled up and normalized to 10M total binding events. The resulting values were averaged over every 10bp window and written in bigWig files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files, representing normalized pileup of transposon binding events.

molecule: genomic DNA

source_name: TRIM24-driven primary carcinosarcoma cells

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 100U/mL penicillin/streptomycin.

extract_protocol:
The cells were extracted using Trypsin when 80% confluency reached. Around 50K cells were counted and used for ATAC-Seq.
ATAC-seq in replicates was performed following the Omni-ATAC protocol as previously described (M. R. Corces et al., An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959-962 (2017)).

treatment_protocol: The cells were not treated.

tag: cell type

value: TRIM24-overexpressing primary carcinosarcoma cells

tag: passage


title: mouse_897_Rep1


title: L7-D11_S119

description:
L7-M5_S269
L7-M6_S270
L7-M7_S271
L7-M8_S272


title: mRNA-5K-exp2


title: L7-D15_S303

description:
L7-M21_S81
L7-M22_S82
L7-M23_S83
L7-M24_S84


title: COPD model exposed by PM2.5 replicate 1

description: Biological replicate 1 of 3. rat model of COPD, exposed by PM2.5, archived after 90days exposure.

tag: tissue


title: COPD model exposed by CS replicate 2

description: Biological replicate 2 of 3. rat model of COPD, exposed by CS, archived after 91days exposure.

source_name: Rats model of COPD exposed by CS

value: CS exposure for 90 days

tag: strain


title: COPD model exposed by PM2.5 replicate 2

description: Biological replicate 2 of 3. rat model of COPD, exposed by PM2.5, archived after 91days exposure.


title: COPD model exposed by CS replicate 3

description: Biological replicate 3 of 3. rat model of COPD, exposed by CS, archived after 92days exposure.


title: mRNA-20K-exp1


title: mouse_823_Rep2

source_name: MMTV-Cre expressing immortalized primary cells


title: L7-D10_S118

description:
L7-M1_S265
L7-M2_S266
L7-M3_S267
L7-M4_S268


title: Omni-ATAC-50K

value: Omni-ATAC-seq


title: L7-D13_S301

description:
L7-M13_S73
L7-M14_S74
L7-M15_S75
L7-M16_S76


title: pelo Mutant Input 2

tag: genotype

value: dissected 1-3 days post-eclosion

value: Strand-specific (reverse)


title: mouse_823_Rep1

value: MMTV-Cre expressing immortalized primary cells


title: Adult Control Polysome 2

value: Polysome

tag: age


title: L7-C8_S212

description:
L7-L17_S353
L7-L18_S354
L7-L19_S355
L7-L20_S356


title: Adult Control Input 2

value: Input

tag: rna population


title: COPD model exposed by CS replicate 1

description: Biological replicate 1 of 3. rat model of COPD, exposed by CS, archived after 90days exposure.

value: male


title: Omni-ATAC-10K


title: L7-C9_S213

description:
L7-L21_S357
L7-L22_S358
L7-L23_S359
L7-L24_S360


title: pelo Mutant Polysome 2

tag: strand specificity


title: ATAC-20K-exp2


title: pelo Mutant Polysome 1


title: ATAC-20K-exp1


title: Omni-ATAC-5K


title: L7-C5_S209

description:
L7-L5_S161
L7-L6_S162
L7-L7_S163
L7-L8_S164


title: ATAC-10K-exp2


title: L7-C6_S210

description:
L7-L9_S165
L7-L10_S166
L7-L11_S167
L7-L12_S168


title: pelo Mutant Input 1


title: L7-C7_S211

description:
L7-L13_S349
L7-L14_S350
L7-L15_S351
L7-L16_S352


title: L7-C4_S208

description:
L7-L1_S157
L7-L2_S158
L7-L3_S159
L7-L4_S160


title: hfp Mutant 1


title: hfp Het Control 1


title: ATAC-5K-exp2


title: L7-C3_S207

description:
L7-K21_S69
L7-K22_S70
L7-K23_S71
L7-K24_S72


title: pelo Mutant 1


title: ATAC-10K-exp1


title: L7-C2_S206

description:
L7-K17_S65
L7-K18_S66
L7-K19_S67
L7-K20_S68


title: L7-C24_S24

description:
L7-K13_S61
L7-K14_S62
L7-K15_S63
L7-K16_S64


title: WAT preadipocyte differentiation day 0 replicate1

city: Xinyang

first: pengpeng

last: Zhang

state: Henan

address: No.237 Nanhu Road Shihe District

institute: Xinayang Normal University

description:
cW01
circRNA

data_processing:
Quality control of sequences was examined with FastQC version 0.11.9. The clean data were obtained using the Fastp version 0.20.1 to remove reads with adapters, reads containing ploy-N and reads with low quality.
The clean reads were subjected to mapping with Mus musculus mm9 reference genome by HISAT2 version 2.2.0.
circRNA was indentified by CIRI2
Supplementary_files_format_and_content: mm9
Supplementary_files_format_and_content: Matrix table with raw circRNA counts for every gene and every sample

source_name: WAT preadipocyte

growth_protocol: Primary WAT SVF cells were isolated using collagenase digestion as we previously described. Briefly, the inguinal WAT were collected from 6-week-old mice. Adipose tissue was cut into small pieces and digested with 1.5 mg ml-1 collagenase at 37 ℃ for 30-50 min. The digestions were terminated with DMEM containing 20% FBS, and filtered through 100-μm and 70-μm cells trainer to remove tissue debris. Cells were then centrifuged at 450g for 8 min and SVF cells pellet was resuspend. SVF cells were cultured in growth medium containing 20 % FBS, high glucose DMEM, at 37 ℃ with 5% CO2, culture medium was changed every 2 days.

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’ instructions.  To enrich circRNA, the rRNA and linear RNA were removed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the cells reached 90 % confluence, they were induced to adipogenic differentiation with induction medium, which contains DMEM, 10% FBS, 2.85 mM insulin, 0.3 mM dexamethasone and 0.63mM 3-isobutyl-methylxanthine for 4 days. Then the medium was switched to differentiation medium which contains DMEM, 10% FBS, 200 nM insulin and 10 nM T3 for another 4 days to induce the mature of adipocytes.

value: WAT preadipocyte

tag: time

value: proliferation


title: pelo Het Control 1


title: WAT preadipocyte differentiation day 0 replicate2

description:
cW02
circRNA


title: L7-C23_S23

description:
L7-K9_S261
L7-K10_S262
L7-K11_S263
L7-K12_S264


title: hfp Het Control 2


title: L7-C22_S22

description:
L7-K5_S257
L7-K6_S258
L7-K7_S259
L7-K8_S260


title: WAT preadipocyte differentiation day 8 replicate1

description:
cW81
circRNA

value: post differentiation day8


title: WAT preadipocyte differentiation day 4 replicate2

description:
cW42
circRNA

value: post differentiation day4


title: L7-C21_S21

description:
L7-K1_S253
L7-K2_S254
L7-K3_S255
L7-K4_S256

value: Control


title: pelo Het Control 2

value: ovary


title: WAT preadipocyte differentiation day 4 replicate1

description:
cW41
circRNA


title: L7-C20_S20

description:
L7-J21_S345
L7-J22_S346
L7-J23_S347
L7-J24_S348


title: L7-C1_S205

description:
L7-J17_S341
L7-J18_S342
L7-J19_S343
L7-J20_S344


title: 4_11

city: Lübeck

first: Henrik

last: Oster

address: Ratzeburger Allee 160

department: Institute of Neurobiology

country: Germany

institute: University Lübeck

data_processing:
Basecalling and demultiplexing to fastq files using bcl2fastq (version 2.17.1.14)
sequence alignments using STAR (version 2.5.2a)
read counting using featureCounts (version 1.5.0-p1)
processing and analysis were done in R (version 3.6.3), specifically with R package DESeq2 (version 1.24.0)
additional filtering: include only genes expressed in at least all replicates of one time point in either sham or VSG
rhythmicity analysis JTK_CYCLEv3
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts after additional filtering for JTK

source_name: subcutanous WAT

extract_protocol:
WAT biopsies were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Library Preparation Kit (version 2, set A, 48 samples, 12 indexes) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: e.g. Chambers et al. 2013 (Gastroenterology); presurgery mice received liquid diet as a choice 3 days prior, exclusively 2 days prior, and fasted ON; postsurgery liquid diet exclusively until day 3, as a choice against HFD on day 4

tag: zt

tag: surgery

value: VSG

tag: weight loss

value: subcutanous WAT


title: tst RNAi 2

value: UAS-Dcr2;nosGAL4>tst RNAi

value: PolyA RNA Enriched


title: C8861_RNA

city: Chicago

first: Michelle

middle: C

last: Ward

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
Paired-end RNA-seq reads from each species were trimmed and mapped to each genome (hg19 or panTro3) using Tophat2 (version 2.0.13) (Kim et al. 2013). Only properly-paired reads were used for further analysis.
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac3 (Blekhman et al. 2010) was determined using featureCounts within subread (version 1.5.0) (Liao et al. 2014).
Only autosomal genes are retained.
Genome_build: hg19 & panTro3
Supplementary_files_format_and_content: RNA-seq counts for orthologous autosomal genes for all individuals

organism: Pan troglodytes

source_name: induced pluripotent stem cells

growth_protocol: Human and chimpanzee feeder-independent induced pluripotent stem cell lines were maintained at 70% confluence on Matrigel hESC-qualified Matrix (354277, Corning, Bedford, MA, USA) at a 1:00 dilution. Cells were cultured in Essential 8 Medium (A1517001, ThermoFisher Scientific, Waltham, MA, USA) at 37°C with 5% (vol/vol) CO2 with daily media changes. Cells were passaged by enzyme-free dissociation (0.5 mM EDTA, 300 mM NaCl in PBS), and seeded with ROCK inhibitor Y-27632 (ab120129, Abcam, Cambridge, MA, USA).

extract_protocol:
RNA was extracted from ~3 million cells using the ZR-Duet DNA/RNA extraction kit (D7001, Zymo, Irvine, CA, USA) in two species-balanced batches. All RNA samples were of good quality: RIN scores of 10 were obtained for all samples except C40280 (9.7).
All 17 samples were pooled together for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit.  Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: cell line

value: induced pluripotent stem cells

tag: Sex

value: Male

tag: population

value: Chimpanzee


title: L7-C19_S19

description:
L7-J13_S337
L7-J14_S338
L7-J15_S339
L7-J16_S340

tag: isolation

tag: mouse id

tag: date


title: WAT preadipocyte differentiation day 8 replicate2

description:
cW82
circRNA

tag: cell type


title: tst Mutant 2

tag: tissue

tag: treatment

value: dissected 1-3 days post-eclosion

value: Strand-specific (reverse)


title: hfp Mutant 2

tag: genotype


title: C40280_RNA

value: Female


title: 4_9

tag: strain

value: sham


title: C4955_RNA


title: L7-C18_S18

description:
L7-J9_S153
L7-J10_S154
L7-J11_S155
L7-J12_S156


title: C40210_RNA


title: 4_8


title: Adult Wild Type 2

tag: age

tag: rna population


title: 4_10


title: pelo Mutant 2

tag: strand specificity


title: L7-C16_S16

description:
L7-J1_S145
L7-J2_S146
L7-J3_S147
L7-J4_S148


title: Young Wild Type 2

value: dissected 0-3 hours post-closion


title: C3651_RNA


title: L7-C17_S17

description:
L7-J5_S149
L7-J6_S150
L7-J7_S151
L7-J8_S152


title: 4_7

tag: zt


title: 4_6

tag: surgery


title: L7-C15_S15

description:
L7-I21_S57
L7-I22_S58
L7-I23_S59
L7-I24_S60


title: OsRR6ox , Biological replicate 2

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of 10-days-old seedlings overexpressing OsRR6

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: The data were analyzed with Bioconductor packages-affy and rma in R version 3.4.0.

label: Biotin

organism: Arabidopsis thaliana

source_name: 10 days old transgenic seedlings

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: The Arabidopsis seeds were grown in 1/2MS medium  under white light (50-60µmol m-2 s -1) at 22+C and 16h-light : 8h-dark cycle after 72 hrs of stratification. 10 days old seedlings (equivalent to 100mg fresh weight) were harvested and snap frozen in liquid nitrogen.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The quality check of total RNA was done using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: No special treatment was given to plants before harvesting.

value: whole seedlings

value: OsRR6 overexpression transgenic

tag: ecotype


title: C3647_RNA

tag: cell line


title: L7-C14_S14

description:
L7-I17_S53
L7-I18_S54
L7-I19_S55
L7-I20_S56


title: 4_2

tag: weight loss


title: C3649_RNA

tag: Sex

tag: population


title: 3_10


title: L7-C13_S13

description:
L7-I13_S49
L7-I14_S50
L7-I15_S51
L7-I16_S52

tag: isolation

tag: mouse id


title: FEC + oHSV-1_rep10

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St. West

department: Department of Pathology

country: Canada

institute: McMaster University

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the UCSC/mm10 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.

source_name: E0771 Tumors

growth_protocol: 5 million E0771 cells were implanted subcutaneously on the left flank and allowed to grow for 12 days prior to the start of treatment

extract_protocol:
Subcutaneous tumors were harvested and extracted in Trizol using the Qiagen RNA Extraction Kit
Libraries were generated using an Illumina TruSeq Stranded RNA kit

treatment_protocol: Day 1 - Chemotherapy or Vehicle. Day 2, 3, 4 - Virus or Vehicle

value: C57/Bl6 Mouse

value: Wildtype

tag: virus

value: Chemotherapy + Virus


title: 4_1

tag: tissue


title: HIV YTHDC1 PAR-CLIP

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Genome_build: NL4-3 genome: 551-9626nt of GenBank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to HIV-1 NL4-3 genome

organism:
Homo sapiens
Human immunodeficiency virus 1

extract_protocol:
PAR-CLIP
All samples were processed with the Illumina Truseq small RNA-seq library prep kit

tag: virus strain

value: HIV-1 NL4-3

tag: technique

value: PAR-CLIP

tag: pulldown antibody

value: anti-Flag, clone M2, Sigma, Cat No F1804


title: HIV YTHDC1 PAR-CLIP repeat


title: HIV GFP PAR-CLIP


title: 3_9

tag: strain

value: subcutanous WAT


title: L7-C10_S214

description:
L7-I1_S241
L7-I2_S242
L7-I3_S243
L7-I4_S244

source_name: Dentate gyrus

tag: date

tag: treatment

value: Control


title: L7-C12_S216

description:
L7-I9_S249
L7-I10_S250
L7-I11_S251
L7-I12_S252


title: OsRR6ox , Biological replicate 1

tag: genotype

tag: age


title: FEC + oHSV-1_rep9


title: L7-C11_S215

description:
L7-I5_S245
L7-I6_S246
L7-I7_S247
L7-I8_S248


title: 3_8

tag: zt

tag: surgery


title: FEC + oHSV-1_rep8


title: L7-B9_S105

description:
L7-H21_S333
L7-H22_S334
L7-H23_S335
L7-H24_S336


title: L7-B8_S104

description:
L7-H17_S329
L7-H18_S330
L7-H19_S331
L7-H20_S332


title: Wild type, Biological replicate 2

description: Gene expression data of control 10-days-old seedlings

source_name: 10 days old wild type seedlings

value: wild type

tag: ecotype


title: Wild type, Biological replicate 1


title: GIST-T1 AP replicate2

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: GIST-T1 cells treated with 5-aza-dC plus 4-PBA replicate2

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: GIST-T1 cells were maintained in DMEM supplemented with 10% fatal bovine serum.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen).

treatment_protocol: GIST-T1 cells were treated with 2 μM 5-aza-2’-deoxycytidine (5-aza-dC; Sigma-Aldrich) for 72 hours and then treated with or without 3 mM 4-phenylbutyric acid (4-PBA; Sigma-Aldrich) for an additional 48 hour, replacing drug and medium every 24 hours.

value: 5-aza-dC + 4-PBA


title: 3_4

value: VSG

tag: weight loss


title: FEC + oHSV-1_rep6


title: L7-B7_S103

description:
L7-H13_S325
L7-H14_S326
L7-H15_S327
L7-H16_S328


title: GIST-T1 AP replicate1

description: GIST-T1 cells treated with 5-aza-dC plus 4-PBA replicate1


title: 3_3


title: FEC + oHSV-1_rep5


title: 3_2


title: L7-B6_S102

description:
L7-H9_S141
L7-H10_S142
L7-H11_S143
L7-H12_S144


title: FEC + oHSV-1_rep4


title: 3_5


title: 3_1


title: FEC + oHSV-1_rep3


title: 2_11


title: H508_LSD1_KD

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

data_processing:
FASTQ files were processed using Cell Ranger v3.1.0 using the genome index GRCh38-3.0.0 from 10X Genomics and --expect-cells 10000.
Features, cell barcodes, and counts were compiled into a feature count matrix using the Seurat v3.9.9.9014 function Read10X.
Genome_build: GRCh38
Supplementary_files_format_and_content: Feature count matrix.

source_name: NCI-H508 Cells

growth_protocol: HT29 and NCI-H508 cells were culturing under standard growth conditions in McCoys 5A (HT29) or RPMI (NCI-H508) media

extract_protocol:
Cells were partitioned and barcoded using the Chromium Controller
Chromium Next GEM Single Cell 3′ Kit v3.1

tag: cell line

tag: condition

value: LSD1 knockdown


title: H508_EV

value: empty vector


title: FEC + oHSV-1_rep7


title: FEC + oHSV-1_rep2


title: 2_9

value: sham


title: FEC + oHSV-1_rep1


title: L7-B3_S99

description:
L7-G21_S45
L7-G22_S46
L7-G23_S47
L7-G24_S48

data_processing:
To confirm quality of the raw reads, a FastQC analysis was performed. Reads were aligned to the mouse mm10 genome using STAR with default options. A count table was generated from the alignments using Subread/FeatureCounts 1.5.1.
The count matrix was analyzed with Seurat 2.3.1, using the following workflow: Cells with less than 200 genes or more than 6,000 genes (likely doublets) were removed, as well as cells whose mitochondrial gene expression accounted for more than 20% of the total gene expression of that cell. Genes found in less than 0.5% of cells were also excluded. Following this filtering, 709 of the original 768 cells remained (with a median read depth of 630,131 reads per cell and median of 2,646 genes per cell).
Data was log-normalized and scaled by a factor of 10,000.
The normalized count data was subsequently regressed on the number of reads.
The first 30 PCAs were used to identify clusters (using default parameters).
Cluster markers were determined by a differential expression analysis of each cluster versus all other clusters combined. Seurat’s “AddModuleScore” function, with default parameters, was used to calculate gene set scores of cell type-specific markers extracted from previous studies. Boxplots of these scores were used to assign each cluster to a cell type. We confirmed these assignments by comparing our cluster markers to unique markers of cell type defined by the aforementioned studies to ensure that there was no ambiguity in the assignment of cell types.
Gene differential expression between experimental (miR-132 overexpression) and control conditions (within each cell population) was performed. Differential expression (for analysis of cluster markers and for analysis between controls and experimental conditions) was performed as follows: p-values were calculated using a Wilcoxon rank-sum test (using Seurat’s “FindMarkers” function), and corrected for multiple testing using a Bonferroni correction. Log fold changes were calculated using the natural logarithm. Genes with adjusted p-values of < 0.05 were considered significantly differentially expressed.
Functional enrichment analysis was performed by using Ingenuity Pathway Analysis. By convention, the 150 transcripts with the most negative (‘Downregulated Transcripts’) or most positive (‘Upregulated Transcripts’) log fold changes after differential gene expression (comparing miR-132-overexpression to control samples) were selected per cluster for analysis.
Genome_build: mm10 genome (Ensembl Version 88)
Supplementary_files_format_and_content: Raw count matrix: neurogenesis_mirOE_raw_counts.tsv.gz

tag: isolation

tag: mouse id


title: L7-B4_S100

description:
L7-H1_S133
L7-H2_S134
L7-H3_S135
L7-H4_S136


title: L7-B5_S101

description:
L7-H5_S137
L7-H6_S138
L7-H7_S139
L7-H8_S140


title: GIST-T1 Aza replicate1

description: GIST-T1 cells treated with 5-aza-dC replicate1


title: GIST-T1 Aza replicate2

description: GIST-T1 cells treated with 5-aza-dC replicate2


title: L7-B2_S98

description:
L7-G17_S41
L7-G18_S42
L7-G19_S43
L7-G20_S44


title: HT29_LSD1_KD

source_name: HT29 Cells


title: oHSV-1_rep5

tag: virus

value: Virus


title: GIST-T1 replicate1

description: GIST-T1 cells replicate1

value: untreated


title: GIST-T1 replicate2

description: GIST-T1 cells replicate2


title: HT29_EV


title: RNA_p17_Treated, AML

city: Miami

first: Ramin

last: Shiekhattar

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: University of Miami - Sylvester Comprehensive Cancer Center

description:
Patients_treated_raw_counts_gene_expression.txt
Patients_treated_normalized_gene_expression_RPKM.txt

data_processing:
RNA-seq: FASTQ data were processed with Trimmomatic v0.38 to remove adapters and low-quality reads.
RNA-seq: reads were aligned to the hg38 human genome using STAR aligner v 2.5.3a with default parameters and RSEM v1.2.28 to obtain expected gene counts against the human Ensembl (release 97).
Genome_build: hg38
Supplementary_files_format_and_content: The processed data files are in txt format : Total RNA-seq raw counts per gene and gene expression normalized by Reads Per Kilobase of transcript, per Million mapped reads (RPKM) using Deseq2.

source_name: CD34+ leukemic blasts

extract_protocol:
Cells were isolated by Miltenyi CD34 microbead kit according to the manufacturer’s instructions. In brief, selection was performed immediately after defrosting the cryopreserved bone marrow patient samples. Samples were thawed in 37°C and DNase-I (Sigma D4513) was added to the samples to prevent cells clumping. Cells were resuspended in 2% FBS + IMDM medium. Cell pellets were resuspended in FcR blocking reagent and CD34 microbeads; incubated for 30 minutes. Positive selection of CD34+ cells were performed on MACS MS columns (Miltenyi Biotec 130-042-201). Cells were lysed with Trizol reagent (Invitrogen) and total RNA was extracted using miRNeasy Micro Kit (Qiagen) following manufacturer's protocol.
Preparation of total RNA for sequencing on the Illumina NovaSeq 6000 NGS platform was carried out at the University of Miami’s Hussman Institute for Human Genomics (http://hihg.med.miami.edu/cgt). Briefly, 1ng of total RNA was ribo-depleted and library construction was performed using the ‘Nugen Ovation SoLo RNA-Seq (Human) (Rev. M01406 v3) with AnyDeplete Probe Standard Human/Mouse (rRNA)’ according to manufacturer’s protocol. Samples were barcoded to allow for multiplexing. Cluster generation and sequencing took place on the Illumina NovaSeq 6000 using the reagents provided in the Illumina NovaSeq 6000 S1 Reagent Kit (200 cycle) with >60M paired-end 100 reads per sample

tag: disease state

value: AML

tag: tissue

value: bone marrow

tag: cell source

value: Cryopreserved patient sample

value: ATRA+TCP Treated end of study


title: 2_6

tag: strain


title: oHSV-1_rep4

value: C57/Bl6 Mouse

value: Wildtype


title: GIST-T1

type: genomic

description: GIST-T1 cells

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

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

data_processing: BeadStudio software V2011.1

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the standard phenol-chloroform method.

treatment_protocol: GIST-T1 cells were cultured in growth medium without drug treatment.


title: 2_4


title: L7-B23_S299

description:
L7-G9_S237
L7-G10_S238
L7-G11_S239
L7-G12_S240

extract_protocol:
For FACS isolation of single cells, four miR-132-injected and four control-injected Nestin:GFP male mice were used and 94 cells were initially sorted per mouse.
FACS-sorted cells were processed using the Smart-seq2 protocol. Briefly, RNA was reverse-transcribed using biotinylated oligo-dT primers and biotinylated template-switching (TSO) oligonucleotides and subsequently cDNA was preamplified using the KAPA HiFi Hot Start DNA Polymerase and biotinylated ISPCR primers. cDNA was purified using AMPURE XP Agencourt beads, concentration was calculated with the Quantifluor dsDNA kit and adjusted on an Echo 525 Liquid Handler. 100 pg cDNA per cell were used for library preparation with Nextera XT DNA Library Preparation Kit. Finally, following purification on magnetic beads the libraries were multiplexed and sequenced using the Illumina NextSeq500 platform.

tag: date


title: oHSV-1_rep3


title: 2_7


title: L7-B24_S300

description:
L7-G13_S37
L7-G14_S38
L7-G15_S39
L7-G16_S40

tag: treatment


title: 2_8


title: 2_3


title: L7-B21_S297

description:
L7-G1_S229
L7-G2_S230
L7-G3_S231
L7-G4_S232


title: RNA_p11_Treated, AML

value: ATRA+TCP Treated cycle3 day15


title: oHSV-1_rep1

tag: genotype


title: RNA_p7_Treated, MDS

value: MDS

value: ATRA+TCP Treated cycle6


title: RNA_p10_Treated, AML

value: ATRA+TCP Treated cycle9 day15


title: 2_1

value: subcutanous WAT


title: L7-B22_S298

description:
L7-G5_S233
L7-G6_S234
L7-G7_S235
L7-G8_S236

value: Control


title: RNA_p8_Treated, MDS

value: ATRA+TCP Treated cycle3 day1


title: L7-B1_S97

description:
L7-F17_S317
L7-F18_S318
L7-F19_S319
L7-F20_S320


title: FEC_rep9

value: Chemotherapy


title: 1_11

value: sham


title: RNA_p4_Treated, AML

value: ATRA+TCP Treated cycle2 day1


title: 1_10

value: VSG


title: L7-B19_S295

description:
L7-F13_S313
L7-F14_S314
L7-F15_S315
L7-F16_S316


title: FEC_rep8


title: oHSV-1_rep2

value: Virus


title: L7-B18_S294

description:
L7-F9_S129
L7-F10_S130
L7-F11_S131
L7-F12_S132


title: L7-B20_S296

description:
L7-F21_S321
L7-F22_S322
L7-F23_S323
L7-F24_S324


title: 1_9


title: RNA_U937_ATRA_TCP_rep2

description:
U937_raw_counts_gene_expression_treatments.txt
AML_cells_normalized_gene_expression_RPKM.txt

growth_protocol: U-937 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin (P/S).

extract_protocol:
Total RNA was isolated from fresh U-937 cell pellets using Trizol reagent (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen) following the manufacturer's protocol.
1 μg of the RNA samples were processed with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat #. RS-122-2301), following the manufacturer’s instructions. Cluster generation and sequencing took place on the Illumina NovaSeq 6000 using the reagents provided in the Illumina NovaSeq 6000 S1 Reagent Kit (200 cycle) with >30M paired-end 100 reads per sample

treatment_protocol: Cells treated with ATRA (1μM) + TCP (10μM)  for 4 days.

tag: cell type

value: AML cells

value: ATRA+TCP


title: FEC_rep7


title: FEC_rep10


title: FEC_rep6


title: RNA_U937_ATRA_TCP_rep1


title: RNA_U937_TCP_rep2

treatment_protocol: Cells treated with TCP  (1μM)  for 4 days.

value: TCP


title: 1_8

tag: zt


title: L7-B17_S293

description:
L7-F5_S125
L7-F6_S126
L7-F7_S127
L7-F8_S128


title: L7-B16_S292

description:
L7-F1_S121
L7-F2_S122
L7-F3_S123
L7-F4_S124


title: 1_7

tag: surgery


title: L7-B15_S291

description:
L7-E21_S33
L7-E22_S34
L7-E23_S35
L7-E24_S36


title: RNA_U937_TCP_rep1

treatment_protocol: Cells treated with TCP  (10μM)  for 4 days.


title: 1_6


title: FEC_rep4

value: C57/Bl6 Mouse


title: FEC_rep5

value: Wildtype


title: 1_5


title: RNA_U937_ATRA_rep2

treatment_protocol: Cells treated with ATRA (1μM)  for 4 days.

value: ATRA


title: RNA_U937_ATRA_rep1


title: 1_4


title: FEC_rep3


title: L7-B13_S289

description:
L7-E13_S25
L7-E14_S26
L7-E15_S27
L7-E16_S28


title: FEC_rep2


title: L7-B12_S108

description:
L7-E9_S225
L7-E10_S226
L7-E11_S227
L7-E12_S228


title: H19101_RNA

value: induced pluripotent stem cells

tag: Sex

value: Male

tag: population

value: Yoruba


title: RNA_U937_Ctrl_rep2

treatment_protocol: Cells treated with vehicle control (DMSO) for 4 days.

tag: cell line


title: H19098_RNA


title: RNA_U937_Ctrl_rep1


title: FEC_rep1


title: Saline_rep5

value: Vehicle


title: L7-B11_S107

description:
L7-E5_S221
L7-E6_S222
L7-E7_S223
L7-E8_S224

value: Control


title: L7-B10_S106

description:
L7-E1_S217
L7-E2_S218
L7-E3_S219
L7-E4_S220


title: Saline_rep4


title: Saline_rep3


title: H18511_RNA

value: Female


title: L7-A9_S201

description:
L7-D21_S309
L7-D22_S310
L7-D23_S311
L7-D24_S312


title: RNA_SKNO1_ATRA_TCP_rep1

description:
SKNO1_raw_counts_gene_expression_treatments.txt
AML_cells_normalized_gene_expression_RPKM.txt

growth_protocol: SKNO-1 cells were cultured in 90% RPMI 1640, 10% FBS, 10 ng/ml GM-CSF and 1% P/S and incubated at 37oC, 5% CO2.

extract_protocol:
Total RNA was isolated from fresh SKNO-1 cell pellets using Trizol reagent (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen) following the manufacturer's protocol.
1 μg of the RNA samples were processed with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat #. RS-122-2301), following the manufacturer’s instructions. Cluster generation and sequencing took place on the Illumina NovaSeq 6000 using the reagents provided in the Illumina NovaSeq 6000 S1 Reagent Kit (200 cycle) with >30M paired-end 100 reads per sample


title: L7-B14_S290

description:
L7-E17_S29
L7-E18_S30
L7-E19_S31
L7-E20_S32


title: H18489_RNA


title: Saline_rep2


title: L7-A8_S200

description:
L7-D17_S305
L7-D18_S306
L7-D19_S307
L7-D20_S308


title: L7-A7_S199

description:
L7-D13_S301
L7-D14_S302
L7-D15_S303
L7-D16_S304


title: H28815_RNA

value: Caucasian


title: H28126_RNA


title: RNA_SKNO1_ATRA_rep2


title: Saline_rep1


title: RNA_SKNO1_TCP_rep1


title: H21792_RNA


title: L7-A5_S197

description:
L7-D5_S113
L7-D6_S114
L7-D7_S115
L7-D8_S116


title: RNA_SKNO1_ATRA_rep1


title: H21194_RNA


title: RNA_SKNO1_ATRA_TCP_rep2


title: RNA_SKNO1_TCP_rep2


title: H20961_RNA


title: L7-A3_S195

description:
L7-C21_S21
L7-C22_S22
L7-C23_S23
L7-C24_S24


title: L7-A6_S198

description:
L7-D9_S117
L7-D10_S118
L7-D11_S119
L7-D12_S120


title: L7-A2_S194

description:
L7-C17_S17
L7-C18_S18
L7-C19_S19
L7-C20_S20


title: RNA_p17_Baseline, AML

description:
Patients_baseline_raw_counts_gene_expression.txt
Patients_baseline_normalized_gene_expression_RPKM.txt

value: AML

value: bone marrow

value: Cryopreserved patient sample

value: Baseline


title: RNA_p13_Baseline, MDS

value: MDS


title: RNA_SKNO1_Ctrl_rep1

value: AML cells


title: case9_Ventral_Tegmental_area

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

data_processing:
Base-calling using Illumina Cassava 1.7
Alignment to the human genome (hg38) performed using STAR with default parameters. RPKM were estimated using ¨rpkmforgenes¨ (Ramsköld et al., 2009).
For cases having more than 1 replicate per group, corresponding samples were averaged before the analysis so that each Case have only 1 SNc and 1 VTA.
Differential gene expression analysis was performed on the read counts using DESeq version 1.16.1. Only genes with reads in at least one third of the samples or more were considered in the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: One processed data file is added providing abundance measurements (RPKM) organized as a matrix for all samples (tab-delimited txt).

source_name: midbrain dopamine neurons

extract_protocol:
Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.

tag: case number (refer to table in paper)

tag: disease status

tag: neurons

value: VTA


title: RNA_p18_Baseline, AML


title: case8_Ventral_Tegmental_area


title: case9_Substantia_Nigra_compacta

value: SNc


title: L7-A22_S10

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

institute: KULeuven

description:
L7-C5_S209
L7-C6_S210
L7-C7_S211
L7-C8_S212

tag: isolation

tag: mouse id


title: RNA_SKNO1_Ctrl_rep2


title: L7-A24_S12

description:
L7-C13_S13
L7-C14_S14
L7-C15_S15
L7-C16_S16


title: siRAB38 1

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from LN229 cells treated with RAB38-specific siRNA.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.60.0), using R version 3.5.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

label: biotin

source_name: LN229 cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium with primocin (DMEM, Corning, Manassas, VA), containing 1% Primocin (Invivogen, San Diego, CA) and 10% fetal bovine serum unless otherwise noted (FBS; Hyclone, Logan, UT). Cells were kept in an incubator (37 °C in a humidified 5% CO2, 95% air environment) on uncoated petri dishes and monitored regularly for density and doubling time.

extract_protocol: RNA has been extracted using RNeasy® Mini Kit (Qiagen, Cat. No. 74104).

treatment_protocol: LN229 human glioblastoma cell line was transfected with non-targeting (NT) or RAB38 specific siRNA (siRAB38) for 48h. Transfection was performed according to the provided kit protocol without fetal bovine serum and without antibiotics (Dharmacon ON-TARGETplus Non-targeting Pool, #D-001810-10-05, Human RAB38, #L-010059-00-0010). 24 hours following transfection, fetal bovine serum was added for a total concentration of 1.5%. 48 hours following transfection, cells were subjected to RNA extraction and submitted for microarray and GSEA analysis

tag: sirna

value: RAB38-specific siRNA


title: siRAB38 2


title: NT 1

description: Gene expression data from LN229 cells treated with non-targeting siRNA.

value: non-targeting siRNA


title: Transduced with shRNA targeting PML for 3 days, then treated with IFNα (600 IU/ml) for 18 hours, 3

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

description:
shPML_INF1-3
600 IU/ml IFNα

data_processing:
Reads were checked for quality using FASTQC (v0.11.8).
Trimmed using BBMAP (v3.8.16b).
Aligned to the mouse genome with GENCODE (vM22) annotations using STAR (v2.7.1a) with ENCODE parameters.
Transcripts per million calculations were performed by RSEM (v1.3.1).
Genome_build: GENCODE vM22
Supplementary_files_format_and_content: *_mm.vM22.genes.results.txt: TPM files are tab-delimited files as outputted by RSEM for each sample.
Supplementary_files_format_and_content: *_mm.vM22_ReadsPerGene.out.tab: Count files are tab-delimited files as outputted by STAR for each sample.

source_name: Postnatal (P6) SCG sympathetic neurons

growth_protocol:
Sympathetic neurons were maintained in CM1 (Neurobasal® Medium supplemented with PRIME-XV IS21 Neuronal Supplement (Irvine Scientific), 50 ng/mL Mouse NGF 2.5S, 2 mM L-Glutamine, and Primocin).
Neurons cultured in vitro for 6 days prior to treatment.

extract_protocol:
RNA was extracted from approximately 5.0x10^4 neurons using the Quick-RNA™ Miniprep Kit (Zymo Research) with an on-column DNase I digestion.
Sequencing libraries were sent to a service provider (Novogene) for library preparation, where the provider created nonstranded libraries.

treatment_protocol: Sympathetic neurons were transduced overnight in neuronal media containing 8mg/ml protamine with either control non-targeting shRNA or shRNA targeting PML for 3 days, then treated with IFNα (600 IU/ml) for 18 hours.

tag: age

tag: tissue

value: Superior Cervical Ganglia

value: Sympathetic neurons

tag: lentiviral-mediated shrna

value: shRNA PML (TRCN0000314605)

value: 600 IU/ml IFNalpha


title: Transduced with shRNA targeting PML for 3 days, then mock treated for 18 hours, 2

tag: strain

tag: treatment

value: Mock


title: Transduced with shRNA targeting PML for 3 days, then mock treated for 18 hours, 1

tag: cell type


title: NT 2


title: RNA_p12_Baseline, AML

tag: disease state

tag: cell source


title: L7-A4_S196

description:
L7-D1_S109
L7-D2_S110
L7-D3_S111
L7-D4_S112

treatment_protocol: For miR‐132 overexpression, 2 month-old Nestin:GFP mice received either a miR‐132 mimic or a negative control oligonucleotide in a 3 μl mix with lipofectamine 2000 (at a 1:1 volume ratio). Injections of 150 pmol oligo each were performed once a week for 5 weeks in total

tag: date


title: L7-A23_S11

description:
L7-C9_S213
L7-C10_S214
L7-C11_S215
L7-C12_S216

value: Control


title: L7-A20_S8

description:
L7-B21_S297
L7-B22_S298
L7-B23_S299
L7-B24_S300


title: H20682_RNA

value: induced pluripotent stem cells

tag: Sex

value: Female

tag: population

value: Caucasian


title: case7_Ventral_Tegmental_area

tag: case number (refer to table in paper)


title: case7_Substantia_Nigra_compacta

tag: disease status


title: case8_Substantia_Nigra_compacta

tag: neurons


title: L7-A21_S9

description:
L7-C1_S205
L7-C2_S206
L7-C3_S207
L7-C4_S208

tag: isolation


title: RNA_p11_Baseline, AML

value: AML

value: bone marrow

value: Cryopreserved patient sample


title: Transduced with shRNA targeting PML for 3 days, then mock treated for 18 hours, 3


title: case6_Ventral_Tegmental_area


title: RNA_p1_Baseline, AML

value: Baseline


title: RNA_p7_Baseline, MDS

value: MDS


title: Transduced with shRNA targeting PML for 3 days, then treated with IFNα (600 IU/ml) for 18 hours, 2

description:
shPML_INF1-2
600 IU/ml IFNα


title: L7-A1_S193

description:
L7-B17_S293
L7-B18_S294
L7-B19_S295
L7-B20_S296

tag: mouse id


title: Transduced with shRNA targeting PML for 3 days, then treated with IFNα (600 IU/ml) for 18 hours, 1

description:
shPML_INF1-1
600 IU/ml IFNα


title: L7-A18_S6

description:
L7-B9_S105
L7-B10_S106
L7-B11_S107
L7-B12_S108


title: case3_Ventral_Tegmental_area_rep2

value: VTA


title: PD_5_VTA

data_processing:
reads aligned to human genome with transcriptome annotation (GRCh38, ensemble 93) using STAR (version 2.6.0a).
the count number was calculated by htseq-count (version 0.10.0),
the TPM was calculated by stringtie (version 1.3.4d)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

source_name: ventral tegmental area

value: midbrain

tag: brain region

value: ventral tegmental area

value: Parkinson disease

tag: age group


title: RNA_p2_Baseline, AML

tag: tissue


title: L7-A19_S7

description:
L7-B13_S289
L7-B14_S290
L7-B15_S291
L7-B16_S292


title: Transduced with control non-targeting shRNA for 3 days, then mock treated for 18 hours, 3

tag: age

value: Superior Cervical Ganglia

value: Sympathetic neurons

tag: lentiviral-mediated shrna

value: non-targeting control (shCtrl)


title: PD_3_VTA


title: Transduced with control non-targeting shRNA for 3 days, then mock treated for 18 hours, 1

tag: strain

tag: treatment

value: Mock


title: Transduced with control non-targeting shRNA for 3 days, then mock treated for 18 hours, 2

tag: cell type


title: PD_1_VTA


title: case1_Substantia_Nigra_compacta

value: Control

value: SNc


title: case6_Substantia_Nigra_compacta_rep2


title: case3_Substantia_Nigra_compacta_rep2


title: L7-A16_S4

description:
L7-B1_S97
L7-B2_S98
L7-B3_S99
L7-B4_S100


title: L7-A17_S5

description:
L7-B5_S101
L7-B6_S102
L7-B7_S103
L7-B8_S104


title: Transduced with control non-targeting shRNA for 3 days, then treated with IFNα (600 IU/ml) for 18 hours, 2

description:
shCtrl_INF1-2
600 IU/ml IFNα

value: 600 IU/ml IFNalpha


title: PD_4_VTA


title: L7-A14_S2

description:
L7-A17_S5
L7-A18_S6
L7-A19_S7
L7-A20_S8


title: case16_Ventral_Tegmental_area


title: PD_4_SNc

source_name: substantia nigra pars compacta

value: substantia nigra pars compacta


title: PD_5_SNc


title: L7-A13_S1

description:
L7-A13_S1
L7-A14_S2
L7-A15_S3
L7-A16_S4


title: case2_Ventral_Tegmental_area


title: case16_Substantia_Nigra_compacta


title: Transduced with control non-targeting shRNA for 3 days, then treated with IFNα (600 IU/ml) for 18 hours, 3

description:
shCtrl_INF1-3
600 IU/ml IFNα


title: Transduced with control non-targeting shRNA for 3 days, then treated with IFNα (600 IU/ml) for 18 hours, 1

description:
shCtrl_INF1-1
600 IU/ml IFNα


title: PD_3_SNc


title: case14_Ventral_Tegmental_area


title: L7-A12_S204

description:
L7-A9_S201
L7-A10_S202
L7-A11_S203
L7-A12_S204


title: L7-A15_S3

description:
L7-A21_S9
L7-A22_S10
L7-A23_S11
L7-A24_S12


title: ESC C3G-KO rep2 [C3GK03_S58]

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

institute: CSIR Centre for Cellular and Molecular biology

data_processing:
bcl2fastq v2.20 software used for basecalling
Read quality was checked for each sample using FastQC v0.11.7
Sequenced reads were mapped to mm10 whole genome using STAR v2.5.1b with the following command:  STAR --runThreadN 16 --runMode alignReads --sjdbGTFfile ./Mus_musculus.GRCm38.99.gtf --limitBAMsortRAM 120416916151 --quantMode TranscriptomeSAM GeneCounts --genomeDir  star_index/  --readFilesCommand zcat --outSAMstrandField intronMotif --readFilesIn file.1.fastq.gz file.2.fastq.gz --outSAMtype BAM SortedByCoordinate  --outFileNamePrefix
Quantification of trancripts using RSEM v1.2.31
Genome_build: mm10(GRCm38.99)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: ESC C3G-KO

growth_protocol: WT and C3G-/- E14Tg2a cells (5x10^4) were seeded on to each well gelatin coated tissue culture plates. GMEM  Serum+LIF media was changed after every 24hr.

extract_protocol:
Total RNA was extracted by Trizol RNA extraction protocol. DNA was removed by Turbo DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: cell line

value: Embryonic Stem cells

tag: genotype/variation


title: ESC WT rep3 [E14TG2A3_S64]

source_name: ESC WT

value: wild type


title: ESC C3G-KO rep1 [C3GK01_S57]


title: case14_Substantia_Nigra_compacta


title: case12_Substantia_Nigra_compacta_rep3


title: L7-A10_S202

description:
L7-A1_S193
L7-A2_S194
L7-A3_S195
L7-A4_S196

tag: date


title: PD_1_SNc


title: ESC WT rep2 [E14TG2A2_S63]


title: ESC WT rep1 [E14TG2A1_S62]


title: Murine vagal sensory ganglia_IAV 12 [AM326]

status: Public on Jun 20 2021

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Rsubread package (version 1.24.0) was used for read mapping and summarisation.
Sequenced reads were mapped to the Mus musculus genome (GRCm38) using Subread.
Gene-level summarisation was carried out using the featureCounts function and in-built mm10 annotation to get gene counts.
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing Entrez gene identifiers (GeneID) and gene counts for each sample.

source_name: IAV_female_vagal ganglia

extract_protocol:
Experiments were performed using vagal sensory ganglia from mice infected with 105 PFU PR8 or mock, euthanized 4 days post-infection with (100 mg/ kg) sodium pentobarbital and exsanguinated.  Bilateral vagal sensory ganglia were excised and placed in 250 ml TRIzol reagent (ThermoFisher Scientific, Australia) and homogenized.  RNA was extracted and concentrated from vagal ganglia using the RNeasy MinElute Cleanup kit (Qiagen, Australia).
RNAseq libraries were generated using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, RS-122-2101/RS-122-2102). RNA was subjected to a heat fragmentation to produce fragments between 120-210 bp (average 155 bp).  cDNA was synthesized using SuperScript II Reverse Transcriptase (ThermoFisher Scientific, Australia) and random primers. The cDNA was converted into dsDNA in the presence of dUTP to prevent subsequent amplification of the second strand and thus maintaining the ‘strandedness’ of the library. Following 3’ adenylation and adaptor ligation, libraries were subjected to 15 cycles of PCR to produce libraries ready for sequencing.  Libraries were quantified on Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit (Perkin Elmer, CLS760672). Libraries were pooled in equimolar ratios, and the pool was quantified by qPCR using the KAPA Library Quantification Kit - Illumina/Universal (KAPA Biosystems, Part no. KK4824) in combination with the Life Technologies Viia 7 real time PCR instrument.

treatment_protocol: Experiments were done using pathogen-free C57BL/6 mice (8 - 10 weeks, male and female).  Mice were housed in temperature (21 °C) controlled, individually ventilated cages on a 12 hour light/ dark cycle, with access to food and water ad libitum in groups of up to five.  105 plaque forming units (PFU) of the PR8 (A/Puerto Rico/8/1934 H1N1 ) virus was prepared in phosphate buffered saline (PBS) (Invitrogen, Carlsbad, U.S.A.) with PBS alone being used for mock infections.  Mice were infected intranasally with either virus or mock (50 μl) under isoflurane-induced anesthesia (1-3 L/ min).

tag: Sex

value: female

value: 8 - 10 weeks

value: Intranasal influenza A (PR8 strain) inoculation

value: vagal sensory ganglia

tag: experiment

value: experiment 2


title: Murine vagal sensory ganglia_Mock 11 [AM322]

source_name: Mock_female_vagal ganglia

value: Intranasal mock inoculation


title: Murine vagal sensory ganglia_IAV 13 [AM327]


title: Murine vagal sensory ganglia_IAV 10 [AM324]


title: PD_2_SNc

tag: case number (refer to table in paper)

value: midbrain

tag: disease status

value: Parkinson disease


title: Murine vagal sensory ganglia_Mock 8 [AM319]


title: Murine vagal sensory ganglia_Mock 7 [AM318]


title: Murine vagal sensory ganglia_Mock 6 [AM317]

source_name: Mock_male_vagal ganglia

value: male


title: Murine vagal sensory ganglia_Mock 9 [AM320]


title: Murine vagal sensory ganglia_IAV 9 [AM323]


title: L7-A11_S203

description:
L7-A5_S197
L7-A6_S198
L7-A7_S199
L7-A8_S200

tag: isolation


title: Murine vagal sensory ganglia_Mock 5 [AM316]


title: Murine vagal sensory ganglia_Mock 4 [AM315]


title: L7-G21_S45

description:
L8-K1_S61
L8-K2_S62
L8-K3_S63
L8-K4_S64

tag: mouse id


title: Murine vagal sensory ganglia_IAV 8 [AM314D]

source_name: IAV_male_vagal ganglia


title: Murine vagal sensory ganglia_IAV 6 [AM312D]


title: Murine vagal sensory ganglia_IAV 4 [AM313]

value: experiment 1


title: Murine vagal sensory ganglia_IAV 2 [AM311]


title: Murine vagal sensory ganglia_IAV 1 [AM310]


title: Murine vagal sensory ganglia_IAV 3 [AM312]


title: Murine vagal sensory ganglia_Mock 3 [AM309]


title: Murine vagal sensory ganglia_IAV 11 [AM325]


title: Murine vagal sensory ganglia_Mock 1 [AM307]


title: Murine vagal sensory ganglia_Mock 2 [AM308]


title: Murine vagal sensory ganglia_Mock 10 [AM321]


title: WT

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

data_processing:
BS-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
BS-seq reads were aligned to the TAIR10 genome using BS Seeker2
If multiple alignments mapped to the same location only one is kept.
Calling methylation levels and removing BS-seq reads with incomplete bisulfite conversion (#(mCH sites)/#(all CH sites)>0.8 and #(mCH sites)>5 for one read) by using BS-Seeker2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

source_name: 20 days old seeding

growth_protocol: Arabidopsis plants were grown in a growth chamber under long-day conditions (LD, 22°C, 16 h light/8 h dark).

extract_protocol:
Total DNA were extracted by grinding in liquid nitrogen followed by purification with Dneasy Plant Mini Kit (Qiagen)
For whole-genome bisulfite sequencing, 1 μg of fragmented DNA was first ligated with premethylated TruSeq DNA adapters (Illumina). The DNA fragments were then converted using the EZ DNA Methylation-Gold kit (Zymo Research) using the manufacturer’s protocol.

tag: genotype


title: swi3b mutant

value: swi3b mutant


title: Murine vagal sensory ganglia_IAV 5 [AM314]


title: Murine vagal sensory ganglia_IAV 7 [AM313D]


title: NHDF Pre-Red 4h - 3

city: Goyang-si

first: Young Rok

last: Seo

address: Dongguk-ro 32

department: Life science

country: South Korea

institute: Dongguk University

description: Processed data_NHDF RNAseq_2 (Post 4h).xlsx

data_processing:
FASTQC for quality check
Trimmomatic 0.32 for trimming
HISAT2 ver 2.0.5 and Bowtie2 2.2.6 for reference mapping
StringTie ver 1.3.3b for transcript assembling
Genome_build: USCS hg19
Supplementary_files_format_and_content: Excel file include fold change, p-value, FPKM values of each groups

source_name: Normal Human Dermal Fibroblast Cells

growth_protocol: Normal Human Dermal Fibroblasts (NHDFs) were purchased from Lonza (Basel, Switzerland). NHDFs were cultured in Dulbecco's modified Eagle medium with 4.5 g/L glucose and L-glutamine (DMEM) (Lonza) supplemented with 10% fetal bovine serum (FBS) (Invitrogen-Gibco, Grand Island, NY, USA) and 1% antibiotics (Invitrogen-Gibco) at 37°C and 5% CO2.

extract_protocol:
NHDF cells were harvested and extracted mRNA using RNeasy mini kits (Qiagen, USA) in accordance with manufacturer’s instructions. Quality of extracted mRNA was evaluated using Agilent Bioanalyzer Nano Chip 2100 (Agilent Technologies, USA).
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: The LED system, which emits a narrow bandwidth inside a CO2 incubator, was provided by HanaroTR (Suwon, Korea). Internal LED arrays, which emit red light (620-690 nm, λmax: 660 nm), could be adjusted from intensities of 1 to 60 mW/㎠ and cells were 50 mm away from the LED arrays at 27.8 mW/㎠. UVB light (312nm) was applied at the 0.1 J/㎠ with a Stratalinker 2400UV crosslinker (Stratagene, La Jolla, CA, USA) with bulbs emitting UVB (λmax 312 nm). Cells were exposed to visible light for 1 hour (60 J/㎠) for Red light treated group, and exposed to UVB 0.1J/㎠ for UV treated group. After the light treatment, the post-incubation with fresh DMEM media. (PMID 27729279)

tag: passage #

value: Normal Human Dermal Fibroblasts


title: NHDF Pre-Red 4h - 2


title: NHDF Pre-Red 4h - 1


title: NHDF Control 2 - 3


title: NHDF Red 2-  3


title: NHDF Red 2 - 1


title: sil1 mutant

value: sil1 mutant


title: NHDF Control 2 - 2


title: NHDF Red 2 - 2


title: NHDF UV 4h - 1


title: NHDF UV 4h - 2


title: NHDF Control 2 - 1


title: NHDF Pre-Red 1h - 3

description: Processed data_NHDF RNAseq_1 (post 1h).xlsx


title: Testes_26dpp_KO_rep 1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description:
Gene expression in replicate 1 of 26dpp Ip6k1-/- testes
M71 K0-26dpp

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed

source_name: 26dpp Ip6k1-/- testes biological replicate 1

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The mice were kept in individually ventilated cages where humidity was maintained at 55-60% and temperature was kept at 21-22°C, with ad-libitum water and diet containing 20% protein. Ip6k1+/+ and Ip6k1-/- littermates were produced by breeding Ip6k1+/- mice. Pre-weaned pups at 17dpp, and post-weaning juvenile mice at 26dpp were euthanised with CO2, and testes were dissected.

extract_protocol: RNA was extracted using TRIZOL method  as per the manufacturer’s protocol.

tag: tissue

value: Testes


title: Testes_26dpp_WT_rep 1

description:
Gene expression in replicate 1 of 26dpp Ip6k1+/+ testes
M73 WT- 26dpp

source_name: 26dpp Ip6k1+/+ testes biological replicate 1

value: WT

tag: age


title: Testes_26dpp_KO_rep 2

description:
Gene expression in replicate 2 of 26dpp Ip6k1-/- testes
M01 K0 26dpp

source_name: 26dpp Ip6k1-/- testes biological replicate 2


title: NHDF Pre-Red 1h - 2


title: Testes_26dpp_WT_rep 2

description:
Gene expression in replicate 2 of 26dpp Ip6k1+/+ testes
M92 WT-26dpp

source_name: 26dpp Ip6k1+/+ testes biological replicate 2


title: NHDF UV 1h - 1


title: NHDF Pre-Red 1h - 1


title: Testes_17dpp_KO_rep 2

description:
Gene expression in replicate 2 of 17dpp Ip6k1-/- testes
M85 K0-17dpp

source_name: 17dpp Ip6k1-/- testes biological replicate 2


title: Testes_17dpp_WT_rep 2

description:
Gene expression in replicate 2 of 17dpp Ip6k1+/+ testes
M79 WT-17dpp

source_name: 17dpp Ip6k1+/+ testes biological replicate 2


title: NHDF Red 1 - 3


title: NHDF UV 4h - 3


title: NHDF Red 1 - 2


title: NHDF UV 1h - 3


title: Testes_17dpp_KO_rep 1

description:
Gene expression in replicate 1 of 17dpp Ip6k1-/- testes
M82 K0-17dpp

source_name: 17dpp Ip6k1-/- testes biological replicate 1


title: NHDF Red 1 - 1


title: NHDF Control 1 - 3


title: NHDF Control 1 - 1


title: Testes_17dpp_WT_rep 1

description:
Gene expression in replicate 1 of 17dpp Ip6k1+/+ testes
M78 WT-17dpp

source_name: 17dpp Ip6k1+/+ testes biological replicate 1


title: NHDF Control 1 - 2


title: 20150624_MatterCancerRun12_N11_11

city: Basel

first: Matthias

middle: Sebastian

last: Matter

state: BS

address: Schönbeinstrasse 40

department: Institute of Pathology

country: Switzerland

institute: University of Basel

hyb_protocol: The samples were hybridized with a panel of mRNA:tag-specific nCounter capture and barcoded reporter probes identifying mRNA associated with cancer development.  Sample preparation was done according to the nCounter® mRNA Expression Assay User Manual. After the hybridization protocol, the samples were processed on the Prep Station from NanoString.

scan_protocol: Scan protocol was performed according to the nCounter® mRNA Expression Assay User Manual for the nCounter® PanCancer Pathways Panel. 12 samples per plate/cartridge were processed and scanned. From each patient the 1st and 2nd biopsy was always run on the same plate. Scanning was done using the Digital Analyzer.

data_processing: The raw data was normalized as described in the manual using Nsolver Software 3.0 by using the following genes as housekeeping genes: C10orf76, PIAS1, DNAJC14, TTC31, SFSA3, and ERCC3. Because additional samples of a related project were run at the same time on the some arrays,  these additional samples were included in the normalization process, however not analyzed for the present study. These samples are labelled as "Used for normalization" in the raw data section. Samples, which did not fulfill quality criteria as described in the user manual, were excluded from further analysis. No background subtraction was performed with the NSolver Software 3.0. Data analysis was performed using the Qlucore software (Lund, Sweden). All values were log transformed. Data was always analyzed paired between 1st and 2nd biopsy of the same patient (which were always run on the same plate/cartridge) using patient identification as an eliminating factor to remove batch effects between runs. Statistically significant difference between 1st and 2nd biopsy was calculated using a paired t-test.

label: nCounter

source_name: Tumor-free 1st Biopsy

label_protocol: 100 ng total RNA was prepared for mRNA expression analysis according to the nCounter® mRNA Expression Assay User Manual

extract_protocol: On average 5 sections at 10um thickness were cut from a paraffin block. Afterwards, total RNA extraction was performed using Qiagen FFPE total RNA/DNA extraction kit (Cat No./ID: 80234).

value: Liver tissue

tag: fibrosis stage

tag: liver disease


title: 20150624_MatterCancerRun12_N12_12

source_name: Tumor-free 2nd Biopsy


title: 20140917MMf1_F MC 62 08_08

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Sample preparation was done according to the nCounter® miRNA Expression Assay User Manual. After the hybridization protocol the samples were processed on the Prep Station from NanoString.

scan_protocol: Scan protocol was performed according to the nCounter® miRNA Expression Assay User Manual. 12 samples per plate/cartridge were processed and scanned. From each patient the 1st and 2nd biopsy was always run on the same plate. Scanning was done using the Digital Analyzer.

data_processing: The raw data was normalized as described in the manual using Nsolver Software 3.0 by using the geometric mean of the top 50 most expressed miRNAs as described in the user manual and described before (e.g. Valeri N Cancer Cell 2016). Because additional samples of a related project were run at the same time on the some arrays,  these additional samples were included in the normalization process, however not analyzed for the present study. These samples are labelled as "Used for normalization" in the raw data section. Samples, which did not fulfill quality criteria as described in the user manual, were excluded from further analysis. No background subtraction was performed with the NSolver Software 3.0. Data analysis was performed using the Qlucore software (Lund, Sweden). For analysis a threshold of 64 was set and all values were log transformed. Data was always analyzed paired between 1st and 2nd biopsy of the same patient (which were always run on the same plate/cartridge) using patient identification as an eliminating factor to remove batch effects between runs. Statistically significant difference between 1st and 2nd biopsy was calculated using a paired t-test.

source_name: HCC 2nd Biopsy

label_protocol: 100 ng total RNA was prepared for miRNA expression analysis according to the nCounter® miRNA Expression Assay User Manual


title: 20140917MMf1_F MC 61 06_06


title: NHDF UV 1h - 2


title: 20140917MMf1_F MC 60 04_04


title: 20160330_MatterCancerRun16_R9_09


title: 20140917MMf1_F MC 63 10_10


title: 20150624_MatterCancerRun11_M1_01

source_name: HCC 1st Biopsy


title: 20150624_MatterCancerRun11_M2_02


title: 20160330_MatterCancerRun16_R4_04


title: 20150527_MatterCancerRun1_A5_05


title: 20140917MMd_D MC 51 10_10


title: 20140917MMe_E MC 58 12_12


title: 20140917MMe_E MC 53 02_02


title: 20140917MMe_E MC 57 10_10


title: 20140917MMe_E MC 54 04_04


title: 20150527_MatterCancerRun1_A4_04


title: 20140917MMe_E MC 55 06_06


title: 20140917MMd_D MC 50 08_08


title: 20160330_MatterCancerRun16_R3_03


title: 20150625_MatterCancerRun114_P11_11


title: 20160330_MatterCancerRun15_Q7_07


title: 20160330_MatterCancerRun15_Q8_08


title: 20150625_MatterCancerRun114_P12_12


title: 20140917MMd_D MC 49 06_06


title: 20150625_MatterCancerRun114_P10_10


title: 20140917MMd_D MC 48 04_04


title: 20150625_MatterCancerRun114_P9_09


title: 20140917MMd_D MC 46 02_02


title: 20140916MMc_C MC 45_12


title: 20150623_MatterCancerRun9_I1_01


title: 20140916MMc_C MC 42_06


title: 20150625_MatterCancerRun13_O4_04


title: 20140916MMc_C MC 41_04


title: 20150625_MatterCancerRun13_O3_03


title: 20150624_MatterCancerRun12_N9_09


title: 20150624_MatterCancerRun12_N8_08


title: 20150624_MatterCancerRun12_N10_10


title: 20140918MMg_74 G MC 101 02_02


title: 20150624_MatterCancerRun12_N6_06


title: 20150624_MatterCancerRun12_N7_07


title: 20150624_MatterCancerRun12_N5_05


title: 20140919MMk_130 K MC 129 10_10


title: 20140919MMk_129 K MC 93 09_09


title: AML12_UNC0638_2

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

description: Replicate 2 of 2 UNC0638 treated AML12 cells

hyb_protocol: Hybridized to Agilent-027414 arrays.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. we also smoothed the probe signals using a moving average approach with a window size of 40k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.

label_protocol: Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol: 5×10^5 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam-only or Dam-Lamin B1 for 48 hours before harvest. gDNA was isolated with Phenol-chloroform-isopropanol method. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.

treatment_protocol: AML12 cells were treated with 8 μM of UNC0638 (Selleck) for five days, and the same amount of DMSO (Sigma) was used as the control.

value: AML12 cells

tag: lenti-virus expression

value: Dam-only


title: AML12_UNC0638_1

description: Replicate 1 of 2 UNC0638 treated AML12 cells


title: 20140917MMf1_F MC 31 09_09


title: AML12_DMSO_1

description: Replicate 1 of 2 DMSO treated AML12 cells


title: 20140916MMc_C MC 9_03


title: 20150624_MatterCancerRun11_M10_10


title: 20150623_MatterCancerRun9_I2_02


title: 20150624_MatterCancerRun11_M12_12


title: 20150624_MatterCancerRun12_N2_02


title: 20160330_MatterCancerRun16_R8_08


title: 20140916MMc_C MC 44_10


title: 20150624_MatterCancerRun12_N1_01


title: 20140917MMe_E MC 25 09_09


title: 20140918MMg_73 G MC 65 01_01


title: 20140917MMe_E MC 23 05_05


title: 20150623_MatterCancerRun10_L11_11


title: 20150624_MatterCancerRun11_M9_09


title: 20140917MMe_E MC 22 03_03


title: 20150623_MatterCancerRun10_L10_10


title: 20140917MMe_E MC 21 01_01


title: 20150623_MatterCancerRun10_L9_09


title: AML12_DMSO_2

description: Replicate 2 of 2 DMSO treated AML12 cells


title: 20140917MMf1_F MC 29 05_05


title: 20140917MMf1_F MC 30 07_07


title: 20150624_MatterCancerRun11_M8_08


title: 20150623_MatterCancerRun10_L12_12


title: 20150624_MatterCancerRun11_M7_07


title: 20140917MMf1_F MC 28 03_03


title: 20140917MMd_D MC 17 05_05


title: 20140917MMe_E MC 26 11_11


title: 20140917MMd_D MC 18 07_07


title: 20150624_MatterCancerRun11_M11_11


title: 20140917MMd_D MC 19 09_09


title: 20150623_MatterCancerRun9_I12_12


title: 20150618_MatterCancerRun8postBo_H10_10


title: 20140917MMd_D MC 16 03_03


title: 20140916MMc_C MC 13_11


title: 20140917MMd_D MC 14 01_01


title: 20150623_MatterCancerRun9_I9_09


title: 20140916MMc_C MC 40_02


title: 20150623_MatterCancerRun9_I10_10


title: 20150618_MatterCancerRun8postBo_H9_09


title: 20150618_MatterCancerRun7postBo_G8_08


title: 20150623_MatterCancerRun9_I11_11


title: 20150618_MatterCancerRun7postBo_G7_07


title: 20140916MMc_C MC 12_09


title: 20140916MMc_C MC 10_05


title: 20150603_MatterCancerRun6_F12_12


title: 20150603_MatterCancerRun6_F4_04


title: 20140916MMc_C MC 43_08


title: 20140916MMc_C MC 11_07


title: 20150603_MatterCancerRun6_F3_03


title: 20150603_MatterCancerRun6_F11_11


title: 20150603_MatterCancerRun6_F2_02


title: 20150528_MatterCancerRun3_C12_12


title: 20140919MMl_L MC 133 06_06


title: 20140919MMl_L MC 134 08_08


title: 20150603_MatterCancerRun6_F1_01


title: 20140919MMl_L MC 135 10_10


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