title: IgG

city: Bunkyo-ku

first: Kosei

last: Nagata

department: Graduate School of Medicine

institute: the University of Tokyo

data_processing:
The library was sequenced on HiSeq2000 (Illumina, San Diego, CA, USA) platforms.
DNA sequence information was aligned to the unmasked mouse genome reference sequence mm9 by a bowtie1.2.2 aligner.
Peak calling was performed by two-sample analysis in CisGenome software v2.0 with a P-value cut-off of 1 × 10−5 compared with the input control.
Genome_build: mm9

source_name: SFZ chondrocytes

growth_protocol: SFZ cells were isolated as previously described (Lab Invest 2011;91(12):1739-52.).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The construction of ChIP-seq libraries was performed with a ThruPLEXFD Prep Kit (Takara Bio, Kusatsu, Japan), according to the manufacturer’s instructions.

treatment_protocol: SFZ chondrocytes were treated by lipofection (Lipofectamine 2000; Thermo Fisher Scientific) with vectors expressing 3xFLAG-tagged Runx3.

value: SFZ chondrocytes

tag: strain

tag: chip antibody

value: antimouse-IgG; Promega

tag: treatment

value: Lipofection with vectors expressing 3xFLAG-tagged Runx3


title: input

status: Public on Sep 03 2020

type: SRA

state: Tokyo

country: Japan

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type


title: MCF7 LY500_1

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: MCF7-2_M453_M468_DMSOvsAbema_7d_RNA-seq_readcounts.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using the VIPER pipeline; tab delimited text files of gene counts from STAR alignment

molecule: total RNA

organism: Homo sapiens

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of RNA-seq was between 60-70%.

extract_protocol:
Total RNA was isolated from cell lines using a Nucleospin RNA Plus kit (Macherey-Nagel).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: Abemaciclib (500 nM) or DMSO for 7 days for all cell lines.

tag: cell line

value: MCF7 breast carcinoma cell line

tag: treamtent

value: abemaciclib

tag: treatment length

value: 7 days


title: RUNX3-FLAG

value: FLAG, Clone M2; Sigma-Aldrich


title: MCF7 DMSO_2

value: DMSO


title: CHC1744T [hepatocellular carcinoma]

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: SAMPLE 113

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Standard Illumina protocol. Beta values exported from Illumina Beadstudio software.
(provide the normalization method) Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

growth_protocol: Not applicable

extract_protocol: DNA was extracted from 3 mm3 frozen tumor samples using high salt precipitation (as described in PMID: 3344216).

treatment_protocol: Not applicable

tag: age at sampling

tag: gender

value: M

tag: disease

value: hepatocellular carcinoma


title: CHC1205T [hepatocellular carcinoma]

description: SAMPLE 115


title: MCF7 DMSO_3


title: MCF7 DMSO_1


title: CHC1616T [hepatocellular carcinoma]

description: SAMPLE 116

value: F


title: CHC1152T [hepatocellular carcinoma]

description: SAMPLE 114


title: CHC1148T [hepatocellular carcinoma]

description: SAMPLE 112


title: MDA-MB-453 Abemaciclib 7 days (replicate 3)

value: MDA-MB-453 breast carcinoma cell line


title: CHC1763T [hepatocellular carcinoma]

description: SAMPLE 110


title: CHC097T [hepatocellular carcinoma]

description: SAMPLE 111


title: MDA-MB-453 DMSO 7 days (replicate 3)


title: MDA-MB-453 Abemaciclib 7 days (replicate 2)


title: ATATCT_AML393_M55783_LRC_2000

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

description:
sample name:
AATACA

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the concatenated Human (hg38) and Mouse (mm10) Genome with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

source_name: LRC

growth_protocol: AML PDX cells were isolated from a donor mouse, stained with CFSE, and 1E7 cells were re-injected into four recipient mice per sample. Ten (AML-393) or 14 (AML-491) days later, AML PDX cells were re-isolated from bone marrow.

extract_protocol:
AML PDX cells were re-isolated from murine bone marrow using a mortar and pistil, washed once in PBS. Murine cells were depleted using mouse cell depletion kit from Miltenyi. PDX cells were dissolved in PBS, and sorted according to the CFSE content as LRC or nLRC population (see Figure 1 for details of cell harvesting).
Libraries were constructed using a bulk adjusted SCRB-seq protocol.

treatment_protocol: AML PDX cells were stained with CFSE before injection into experimental mice.

tag: tissue

value: acute myeloid leukemia

tag: pdx

tag: mouse

value: LRC

tag: cell number


title: MDA-MB-453 DMSO 7 days (replicate 2)


title: MDA-MB-453 Abemaciclib 7 days (replicate 1)


title: CHC1717T [hepatocellular carcinoma]

description: SAMPLE 109


title: CHC1604T [hepatocellular carcinoma]

description: SAMPLE 108


title: MDA-MB-453 DMSO 7 days (replicate 1)


title: CHC1568T [hepatocellular carcinoma]

description: SAMPLE 107


title: CHC1137T [hepatocellular carcinoma]

description: SAMPLE 106


title: Organoids_6_p4

city: Buffalo

first: Vincent

middle: J.

last: Lynch

state: NY

address: 551 Cooke Hall

department: Department of Biological Sciences

country: USA

institute: University at Buffalo, SUNY

description: rRNA depleted total RNA

data_processing:
All sequencing data were uploaded and analyzed on the Galaxy platform (public server https://usegalaxy.org, Version 19.05; Afgan et al., 2018), converted using FASTQ Groomer (v1.1.1; Blankenberg et al., 2010) and aligned using HISAT2 (v2.1.0+galaxy4; Kim, Langmead and Salzberg, 2015). We assembled transcripts using StringTie (v1.3.4; Pertea et al., 2015), with reference GTF file and “Reference Transcripts Only” option, followed by DESeq2 (v2.11.40.2; Love, Huber and Anders, 2014) to calculate differential gene expression. The reference GTF file for guided assembly was done by StringTie merge (v1.3.4) of separately generated String Tie (v1.3.4) files (this time without “Reference Transcripts Only” option) and ensGene table from “Ensembl Genes” track from UCSC Genome Browser (GRC37/hg19 assembly).
Genome_build: hg38
Supplementary_files_format_and_content: Unmodified DESeq2 output

source_name: Endometrial gland organoids

growth_protocol:
Isolated decidua were treated as described in Burton et al., 2017. In short, decidua were minced in a dish, followed by digestion in collagenase V (0.4mg/ml)/dispase II (1.25U/ml) solution (Sigma, C9263 and D4693) in RPMI-1640 (Thermo Fisher Scientific, 1
Added for each subgroup of samples in the SAMPLES section above.

extract_protocol:
RNA was isolated from: unprocessed gland elements (small aliquot collected from the sieve after filtering the initial digest of decidua), growing organoids and endometrial stromal fibroblasts isolated from the same samples and established as primary cell cultures using RNeasy Plus Mini kit (QIAGEN, 74134) following manufacturer’s protocol, followed by DNase treatment using TURBO DNA-free Kit (Thermo Fisher Scientific, AM1907).
RNA quality and quantity were assessed on 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA-Seq libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human (RS-122-2201, Illumina Inc.) and following manufacturer’s protocol. Library quality and quantity were checked on 2100 Bioanalyzer and the pool of libraries was sequenced on Illumina HiSEQ4000 (single-end 50bp) using manufacturer’s reagents and protocols. DNase treatment, quality control, Ribo-Zero library preparation and Illumina sequencing were performed at the Genomics Facility at The University of Chicago.

tag: sample type

value: Non-hormone treated

tag: sample number

value: Sample #6, passage 4


title: Organoids_3_p8

description: rRNA depleted total RNA

value: Sample #3, passage 8


title: CHC060T [hepatocellular carcinoma]

description: SAMPLE 105


title: patient 90, primary tumor

type: RNA

city: Heidelberg

first: Peter

last: Sinn

address: Im Neuenheimer Feld 224

department: Pathology

institute: University of Heidelberg

description: nCounter® Technology

hyb_protocol: RNAs were  hybridized for 16h at 65°C to a capture/reporter probe pair equipped with a fluorescent barcode

scan_protocol: nCounter Digital Analyzer

data_processing: nSolver version 4.0 and R 3.6.1

label: molecular barcoding

source_name: Breast primary

label_protocol: Samples were labelled using a custom panel of 269 breast cancer related genes and 11 housekeeping genes supplied by Nanostring

growth_protocol: FFPE tissue

extract_protocol: The Promega Maxwell 16 Sytem was used to extract total RNA from the samples, according to manufacture's instructions.  A minimum of approximately 20 ng of total RNA was used.

treatment_protocol: For selection of tumor tissue for RNA extraction, FFPE tissue blocks from primary breast cancer and metastasis were selected after reviewing all original tissue slides, and re-cut for H&E sections, to be used for reference and to determine tumor cell content (tumor surface area). RNA was extracted using between 5 - 10 unstained FFPE slides for each tumor. Microdissection was performed in most cases to avoid normal breast tissue contamination.

tag: age at biopsy

tag: Sex

value: female

tag: histology

value: invasive ductal carcinoma

tag: tumor grade

tag: pt

tag: pn

value: pNX


title: patient 90, metastasis

description: nCounter® Technology

source_name: Pleura metastasis


title: patient 88, metastasis

description: nCounter® Technology

source_name: Lung metastasis


title: patient 88, primary tumor

description: nCounter® Technology


title: Organoids_3_p5

description: rRNA depleted total RNA

growth_protocol:
Isolated decidua were treated as described in Burton et al., 2017. In short, decidua were minced in a dish, followed by digestion in collagenase V (0.4mg/ml)/dispase II (1.25U/ml) solution (Sigma, C9263 and D4693) in RPMI-1640 (Thermo Fisher Scientific, 11875093) with 10% Fetal Bovine Serum (FBS; Thermo Fisher Scientific, 26140-079) for at least 20 minutes at 37°C with shaking. The digestion length is critical, in order for the stromal cells to be separated from gland elements, but without over-digesting the glands. Presence of significant mucous and greater thickness of the tissue samples usually requires longer digestion time. The digestion was stopped by dilution with RPMI-1640 and the digest was filtered through several 100μm sieves. After rinsing the sieves with RPMI-1640, gland elements were collected by inverting the sieves over the Petri dish and washing them off. They were pooled into low binding tubes (Eppendorf, 022431081) and pelleted by centrifugation at 600g for 6 minutes, re-suspended in Advanced DMEM/F12 (Thermo Fisher Scientific, 12634010) and pelleted again. After removing the supernatant, gland elements were placed on ice and mixed with 20x volume of Matrigel (Corning, 356231). 20-25μl droplets were plated per well of a 48-well plate (Thomas Scientific, 1156F01). They were put in the humidified cell culture incubator at 37°C and 5% CO2 to solidify for 15 minutes, overlaid with 250μl of Expansion Medium (ExM, see below) and returned to the incubator. ExM was exchanged every 3 days. First spherical structures start appearing about 10-14 days post-plating. After subsequent passaging, it takes them about 2-3 days to appear.  Expansion Medium (ExM) composition, as in Burton et al., 2017:   Advanced DMEM/F12 (Thermo Fisher Scientific, 12634010)   L-glutamine, 2mM (Thermo Fisher Scientific, 25030-081)  B27 minus vitamin A supplement, 1x final (Thermo Fisher Scientific, 12587010)  N2 supplement, 1x final (Thermo Fisher Scientific, 17502048)  Nicotinamide, 10nM (Sigma, N0636)  N-acetyl-L-cysteine, 1.25mM (Sigma, A9165)  Primocin 100μg/ml (Invivogen, ant-pm-1)  ALK-4, -5, -7 inhibitor, 500nM (StemRD, A8-002)  Recombinant human R-spondin-1, 500ng/ml (Peprotech, 120-38)  Recombinant human Noggin, 100ng/ml (Peprotech, 120-10C)  Recombinant human FGF-10, 100ng/ml (Peprotech, 100-26)  Recombinant human EGF, 50ng/ml (Peprotech, AF-100-15)  Recombinant human HGF, 50ng/ml (Peprotech, 100-39)  Y-27632, 10μM (Stemcell, 72302), added to ExM only for the first 3 days after thawing and re-plating the organoids.
Added for each subgroup of samples in the SAMPLES section above.

value: Sample #3, passage 5


title: patient 86, metastasis

description: nCounter® Technology


title: CHC961T [hepatocellular carcinoma]

description: SAMPLE 104


title: Glands_6

description: rRNA depleted total RNA

source_name: Endometrial gland elements (unprocessed)

growth_protocol:
After decidua digest was filtered through a 100μm sieve but before gland elements were collected by inverting the sieves over the Petri dish, some of the gland elements were collected from the sieve using a pipet tip, transferred to a centrifuge tube cont
Added for each subgroup of samples in the SAMPLES section above.

value: Sample #6


title: CHC798T [hepatocellular carcinoma]

description: SAMPLE 103


title: Glands_4

description: rRNA depleted total RNA

growth_protocol:
After decidua digest was filtered through a 100μm sieve but before gland elements were collected by inverting the sieves over the Petri dish, some of the gland elements were collected from the sieve using a pipet tip, transferred to a centrifuge tube containing 350μl RLT buffer from RNeasy Plus Mini kit (QIAGEN, 74134) and placed to the -20°C until RNA extraction.
Added for each subgroup of samples in the SAMPLES section above.

value: Sample #4


title: patient 86, primary tumor

description: nCounter® Technology


title: CHC794T [hepatocellular carcinoma]

description: SAMPLE 102


title: patient 84, metastasis

description: nCounter® Technology


title: patient 84, primary tumor

description: nCounter® Technology


title: RNA pooled from 5 larvae fed on Gomphocarpus physocarpus replicate 3 [sGP-3]

city: irapuato

first: Pablo M.

last: Gonzalez-De-la-Rosa

state: guanajuato

address: Km. 9.6 Libramiento Norte Carr. Irapuato-León

department: Langebio

country: Mexico

institute: Cinvestav

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/GP-3/GP-3.bam

data_processing:
All libraries were quality checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
reaper v16-098 (https://www.ebi.ac.uk/~stijn/reaper/reaper.html) was used to remove the Illumina small RNA Adapter sequence ("TGGAATTCTCGGGTGCCAAG") from sRNA-seq reads with the following parameters: -3p-global 14/2/1/0, -3p-prefix 8/2/0/2, -dust-suffix-late 20
RNA-seq paired-end reads were quality filtered and trimmed from adapter sequence with Trimmomatic v0.32 (http://www.usadellab.org/cms/?page=trimmomatic) with the following parameters: ILLUMINACLIP:TruSeq2-PE.fa:2:30:10, SLIDINGWINDOW:4:15, MINLEN:30
sRNA-seq reads were aligned with the alignment component of ShortStack 3.8.3 with parameters: --nostitch, --mismatches 1, --mmap u, --bowtie_m 500 and --ranmax 3.
RNA-seq paired-end reads were aligned with HISAT v2.1  with the following parameters: --max-intronlen 15000, -k 100
sRNA-seq read counts per gene were summarized with featureCounts v1.5.1 with "-s 1" and "-M" parameters.
RNA-seq read counts per gene were summarized with featureCounts v1.5.1 using "-p" and "-o" parameters.
Genome_build: The reference genome assembly for D. plexippus genome was Dpv3 from http://download.lepbase.org/archive/v2/sequence/Danaus_plexippus_v3_-_scaffolds.softmasked.fa.gz
Supplementary_files_format_and_content: Contain summarized counts from either protein coding genes (merge_Quan_OGS2.counts.tsv) or mature miRNAs (mature_miRNAannot.counts.tsv) as annotated in the supplementary files. One row per gene and one column per library.

organism: Danaus plexippus

source_name: 5 whole body second instar D. plexippus larvae fed on Gomphocarpus physocarpus

growth_protocol: Monarch eggs were collected from leaves of A. curassavica wild plants and kept in the laboratory on the same leaves, in petri dishes, until larvae emerged. Once the larvae emerged we transferred them to fresh A. curassavica leaves until they achieved the 2nd instar stage.

extract_protocol:
Larvae were collected after 24 hours, frozen immediately in liquid nitrogen and stored at -80C until the total RNA extractions were performed. Triplicates of five whole larvae for each treatment were homogenized using a Tissue Lyzer. Total RNA was extracted using the Direct-zol kit (Zymo), using the same total RNA to prepare mRNA and sRNA libraries.
The mRNA libraries were created using TruSeq RNA kit. The small RNA libraries were created using the Illumina TruSeq small RNA kit.

treatment_protocol: Early 2nd instar larvae were transferred to fresh leaves of the three different Asclepias species (A. curassavica, A. linaria and G. physocarpus) and allowed them to feed for 24 hrs.

tag: developmental stage

value: second instar

tag: host

value: Gomphocarpus physocarpus

value: whole body


title: CHC433T [hepatocellular carcinoma]

description: SAMPLE 101

tag: age at sampling

value: M

value: hepatocellular carcinoma


title: ESF_6_p3

description: rRNA depleted total RNA

source_name: Endometrial Stromal Fibroblasts

growth_protocol:
Decidua digest was filtered through a 100μm sieve, a 6ml aliquot from the flow-through was directly pipetted into a T25 cell culture flask and placed in a humidified cell culture incubator at 37°C and 5% CO2. The next day, the remaining floating blood cells were washed away with Dulbecco’s Phosphate Buffered Saline (DPBS; Thermo Fisher Scientific, 14190250) and the ESF medium was added (see below). Medium was exchanged every 3 days and the expansion of few initially attached endometrial stromal fibroblasts (ESFs) was observed. It took about 2 weeks for the cells to become confluent. From then on, ESFs were expanded by passaging every 2-3 days. ESF medium composition: Phenol Red-free DMEM (Thermo Fisher Scientific, 31053-028) supplemented with 10% FBS (Thermo Fisher Scientific, 26140-079), 1% L-glutamine (Thermo Fisher Scientific, 25030-081), 1% sodium pyruvate (Thermo Fisher Scientific, 11360070) and 1x insulin-transferrin-selenium (ITS; Thermo Fisher Scientific, 41400045).
Added for each subgroup of samples in the SAMPLES section above.

value: Sample #6, passage 3


title: ESF_5_p2

description: rRNA depleted total RNA

value: Sample #5, passage 2


title: CHC322T [hepatocellular carcinoma]

description: SAMPLE 100

tag: gender


title: patient 80, metastasis

description: nCounter® Technology


title: RNA pooled from 5 larvae fed on Gomphocarpus physocarpus replicate 1 [sGP-1]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/GP-1/GP-1.bam


title: RNA pooled from 5 larvae fed on Asclepias linaria replicate 3 [sAL-3]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/AL-3/AL-3.bam

source_name: 5 whole body second instar D. plexippus larvae fed on Asclepias linaria

value: Asclepias linaria


title: ESF_4_p1

description: rRNA depleted total RNA

value: Non-hormone treated

value: Sample #4, passage 1


title: patient 78, metastasis

description: nCounter® Technology


title: CHC314T [hepatocellular carcinoma]

description: SAMPLE 99

tag: disease


title: patient 80, primary tumor

description: nCounter® Technology

value: pTX


title: CHC313T [hepatocellular carcinoma]

description: SAMPLE 98

value: F


title: RNA pooled from 5 larvae fed on Asclepias linaria replicate 2 [sAL-2]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/AL-2/AL-2.bam

tag: tissue


title: RNA pooled from 5 larvae fed on Asclepias linaria replicate 1 [sAL-1]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/AL-1/AL-1.bam


title: ESF_3_p7

description: rRNA depleted total RNA

value: Sample #3, passage 3


title: CHC304T [hepatocellular carcinoma]

description: SAMPLE 97


title: Glands_5

description: rRNA depleted total RNA

value: Sample #5


title: CHC197T [hepatocellular carcinoma]

description: SAMPLE 96


title: RNA pooled from 5 larvae fed on Asclepias curassavica replicate 3 [sAC-3]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/AC-3/AC-3.bam

source_name: 5 whole body second instar D. plexippus larvae fed on Asclepias curassavica

value: Asclepias curassavica


title: 30_4006ER6_3

city: Houston

first: Lixia

last: Diao

state: TX

address: 1400 Pressler Steet

department: Bioinfomatics and Computational Biology

institute: University of Texa MD Anderson

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to hg19 genome using tophat v2.0.13
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq/miRNAseq reads count were calculated using HTSeq 0.6.1p1

source_name: HCC4006 ER6

growth_protocol: Tumor cells were grown in RPMI containing 10% FBS

extract_protocol:
RNA was extracted using a Qiagen RNase mini Kit
Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.

treatment_protocol: Tumor cells were untreated.

tag: treatment

value: untreated

tag: egfr tki sensitivity

value: resistant

tag: cell type

value: NSCLC

tag: cell line

value: HCC4006 ER6


title: patient 77, metastasis

description: nCounter® Technology

value: female


title: patient 78, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma


title: RNA pooled from 5 larvae fed on Gomphocarpus physocarpus replicate 2 [sGP-2]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/GP-2/GP-2.bam

value: second instar

value: Gomphocarpus physocarpus

value: whole body


title: CHC609T [hepatocellular carcinoma]

description: SAMPLE 95

value: M

value: hepatocellular carcinoma


title: 29_4006ER6_2


title: patient 76, metastasis

description: nCounter® Technology


title: 28_4006ER6_1


title: RNA pooled from 5 larvae fed on Asclepias curassavica replicate 1 [sAC-1]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/AC-1/AC-1.bam


title: CHC327T [hepatocellular carcinoma]

description: SAMPLE 93


title: 27_4006ER5_3

source_name: HCC4006 ER5

value: HCC4006 ER5


title: patient 76, primary tumor

description: nCounter® Technology

value: invasive lobular carcinoma


title: 26_4006ER5_2


title: CHC326T [early hepatocellular carcinoma]

description: SAMPLE 92

value: early hepatocellular carcinoma


title: patient 75, metastasis

description: nCounter® Technology


title: RNA pooled from 5 larvae fed on Gomphocarpus physocarpus replicate 1 [GP-1]

description:
processed data file: merge_Quan_OGS2.counts.tsv
GP-1.sorted.bam


title: patient 75, primary tumor

description: nCounter® Technology


title: patient 77, primary tumor

description: nCounter® Technology


title: RNA pooled from 5 larvae fed on Asclepias linaria replicate 3 [AL-3]

description:
processed data file: merge_Quan_OGS2.counts.tsv
AL-3.sorted.bam

value: Asclepias linaria


title: 23_4006ER3_2

source_name: HCC4006 ER3

value: HCC4006 ER3


title: RNA pooled from 5 larvae fed on Asclepias linaria replicate 2 [AL-2]

description:
processed data file: merge_Quan_OGS2.counts.tsv
AL-2.sorted.bam


title: CHC307T [hepatocellular carcinoma]

description: SAMPLE 91


title: RNA pooled from 5 larvae fed on Asclepias curassavica replicate 2 [sAC-2]

description:
processed data file: mature_miRNAannot.counts.tsv
output/ncRNA/ShortStack/sBowtie/AC-2/AC-2.bam

value: Asclepias curassavica


title: patient 74, primary tumor

description: nCounter® Technology


title: CHC306T [hepatocellular carcinoma]

description: SAMPLE 90


title: RNA pooled from 5 larvae fed on Asclepias linaria replicate 1 [AL-1]

description:
processed data file: merge_Quan_OGS2.counts.tsv
AL-1.sorted.bam


title: 25_4006ER5_1

value: untreated


title: RNA pooled from 5 larvae fed on Gomphocarpus physocarpus replicate 3 [GP-3]

description:
processed data file: merge_Quan_OGS2.counts.tsv
GP-3.sorted.bam


title: 21_4006ER2_3

source_name: HCC4006 ER2

value: resistant

value: HCC4006 ER2


title: CHC302T [hepatocellular carcinoma]

description: SAMPLE 88


title: CHC434T [hepatocellular carcinoma]

description: SAMPLE 94

value: F


title: RNA pooled from 5 larvae fed on Asclepias curassavica replicate 3 [AC-3]

description:
processed data file: merge_Quan_OGS2.counts.tsv
AC-3.sorted.bam


title: patient 70, metastasis

description: nCounter® Technology

value: female


title: 20_4006ER2_2

value: NSCLC


title: patient 72, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma


title: RNA pooled from 5 larvae fed on Gomphocarpus physocarpus replicate 2 [GP-2]

description:
processed data file: merge_Quan_OGS2.counts.tsv
GP-2.sorted.bam

value: second instar

value: Gomphocarpus physocarpus


title: patient 70, primary tumor

description: nCounter® Technology


title: 22_4006ER3_1


title: 24_4006ER3_3


title: RNA pooled from 5 larvae fed on Asclepias curassavica replicate 2 [AC-2]

description:
processed data file: merge_Quan_OGS2.counts.tsv
AC-2.sorted.bam

value: whole body


title: patient 74, metastasis

description: nCounter® Technology


title: 19_4006ER2_1


title: CHC303T [hepatocellular carcinoma]

description: SAMPLE 89

value: M

value: hepatocellular carcinoma


title: 18_4006ER1_3

source_name: HCC4006 ER1

value: HCC4006 ER1


title: CHC155T [hepatocellular carcinoma]

description: SAMPLE 85


title: RNA pooled from 5 larvae fed on Asclepias curassavica replicate 1 [AC-1]

description:
processed data file: merge_Quan_OGS2.counts.tsv
AC-1.sorted.bam


title: CHC121T [hepatocellular carcinoma]

description: SAMPLE 84


title: CHC301T [hepatocellular carcinoma]

description: SAMPLE 87


title: patient 67, metastasis

description: nCounter® Technology


title: SB-3CT+IFN-γ 3

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
All reads were aligned to the mouse reference genome (hg19) using hisat2 version 2.0.5 with the default setting.
Stringtie v1.3.3 was used to calculate the transcriptional expression level as fragments per kilobase per million (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file included FPKM for each gene

source_name: malignant melanoma

growth_protocol: We collected  samples from SB-3CT treated A375 human melanoma cell lines with or without induced by IFN-γ

extract_protocol:
Total RNA was extracted used the TRizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells divided into three parts when grow logarithmically. After co-treated by SB-3CT and vehicle with or without IFN-γ for 24 hours. The supernatant medium was removed and total RNA was extracted by TRizol reagent.

value: A375 melanoma

value: skin

tag: treated

value: SB-3CT + IFN-γ


title: 17_4006ER1_2


title: SB-3CT+IFN-γ 2


title: CHC051T [hepatocellular carcinoma]

description: SAMPLE 83


title: CHC983T [hepatocellular carcinoma]

description: SAMPLE 82


title: 16_4006ER1_1


title: 15_4006Parental_3

value: sensitive


title: CHC912T [hepatocellular carcinoma]

description: SAMPLE 81


title: patient 66, metastasis

description: nCounter® Technology

tag: age at biopsy


title: patient 66, primary tumor

description: nCounter® Technology

tag: Sex


title: SB-3CT+IFN-γ 1


title: CHC258T [hepatocellular carcinoma]

description: SAMPLE 86


title: 14_4006Parental_2

value: untreated


title: IFN-γ 2

value: IFN-γ


title: 13_4006Parental_1


title: CHC909T [hepatocellular carcinoma]

description: SAMPLE 80


title: IFN-γ 1


title: patient 64, primary tumor

description: nCounter® Technology

tag: histology


title: patient 63, metastasis

description: nCounter® Technology


title: CHC898T [hepatocellular carcinoma]

description: SAMPLE 79


title: SB-3CT 3


title: CHC896T [hepatocellular carcinoma]

description: SAMPLE 78


title: 12_827ER6_2

source_name: HCC827 ER6

value: resistant

value: HCC827 ER6


title: SB-3CT 2


title: patient 63, primary tumor

description: nCounter® Technology

value: female

tag: tumor grade


title: patient 67, primary tumor

description: nCounter® Technology

value: invasive lobular carcinoma

tag: pt


title: CHC892T [hepatocellular carcinoma]

description: SAMPLE 77

value: F


title: 10_827ER6_1

value: NSCLC


title: CHC891T [hepatocellular carcinoma]

description: SAMPLE 76


title: IFN-γ 3


title: SB-3CT 1


title: CHC889T [hepatocellular carcinoma]

description: SAMPLE 75


title: patient 64, metastasis

description: nCounter® Technology


title: Control 3


title: Control 2


title: CHC884T [hepatocellular carcinoma]

description: SAMPLE 74


title: patient 62, primary tumor

description: nCounter® Technology

tag: pn


title: 8_827ER3_2

source_name: HCC827 ER3

value: HCC827 ER3


title: patient 59, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma

value: pNX


title: patient 59, metastasis

description: nCounter® Technology


title: CHC805T [hepatocellular carcinoma]

description: SAMPLE 73

value: M

value: hepatocellular carcinoma


title: patient 57, metastasis

description: nCounter® Technology


title: 6_827ER1_3

source_name: HCC827 ER1

value: HCC827 ER1


title: 11_827ER6_2


title: CHC799T [hepatocellular carcinoma]

description: SAMPLE 72


title: MCF7 Abemaciclib (replicate 1)

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of ChIP-seq was between 60-70%.

extract_protocol:
Cells were washed in phosphate-buffered saline (PBS), cross-linked with DSG for 45 minutes followed by fixation with 1% formaldehyde (methanol-free) for 10 minutes at room temperature, quenched with 0.125 M glycine for 5 min at room temperature and washed with PBS complete. Cells were resuspended in lysis buffer (1%SDS, 50 mM Tris-HCl pH8, 10 mM EDTA) containing protease and deacetylase inhibitors, and incubated on ice for 15 min. Lysed cells were sonicated for 5 minutes with a Covaris E220 sonicator (PIP140, DF5%, 200cpb), in 1ml AFA Fiber milliTUBEs. 5 µg of soluble chromatin were immunoprecipitated overnight with 10 μg of c-JUN antibody (CST 9165) on protein A and G magnetic beads; and finally washed, eluted and DNA purified.
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences for c-Jun ChIP-seq.

treatment_protocol: Abemaciclib concentration 500 nM or equal volume of DMSO (control) for 7 days for all cell lines.

value: MCF7 breast carcinoma cell line

value: abemaciclib

tag: treatment length

value: 7 days

tag: chip antibody

value: c-Jun (Cell Signaling Technologies, Cat# 9165)


title: patient 57, primary tumor

description: nCounter® Technology

source_name: Breast primary


title: 5_827ER1_2

value: untreated


title: CHC796T [hepatocellular carcinoma]

description: SAMPLE 71

tag: age at sampling


title: patient 62, metastasis

description: nCounter® Technology

source_name: Pleura metastasis


title: PDX input DNA

data_processing:
Library strategy: FiTAc-seq
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Human PDX 14-07

growth_protocol: Breast cancer liver metastasis PDX 14-07 tumors were transplanted into nude mice.

extract_protocol:
For H3K27ac FiTAc-seq, FFPE sections containing >80% tumor cell enrichment were used and processed as previously described (Cejas P et al, Nat. Methods, 2019; Font-Tello A et al, Nat. Protocols, 2020). Briefly, chromatin was prepared from 5-10 sections (10 ?m each) per case. Sections were washed with xylenes to remove paraffin, rehydrated in an ethanol/water series and incubated overnight with lysis buffer (1%SDS, 50 mM Tris-HCl pH8, 10 mM EDTA) on a thermomixer at 65C, 1000rpm). Samples were put on ice,  suplemented with protease and deacetylase inhibitors and sonicated with Covaris E220 instrument for 10 min (PIP105, 5%DF, 200cbp) in 1mL AFA Fiber milliTUBEs. 2.5?g -5?g of chromatin were pre-cleared, immunoprecipitated overnight with 3 ?g of H3K27ac antibody (Diagenode, cat#A1723-0041D, lot#C15410196) on protein A and G magnetic beads and finally washed, eluted and DNA purified.
FiTAc-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences.

treatment_protocol: Mice were treated with 90 mg/kg abemaciclib or control for 21-28 days (PDX)

value: Patient-derived breast cancer liver metastasis


title: patient 56, metastasis

description: nCounter® Technology


title: MCF7 DMSO (replicate 1)

value: DMSO


title: 3_827Parental3

value: sensitive


title: CHC793T [hepatocellular carcinoma]

description: SAMPLE 70

tag: gender


title: 9_827ER3_3

value: resistant


title: 7_827ER3_1


title: Control 1

value: A375 melanoma

value: skin


title: PDX Abemaciclib 3

value: H3K27ac (Diagenode C15410196, polyclonal, lot # A1723-0041D)


title: patient 55, metastasis

description: nCounter® Technology

source_name: Lung metastasis

value: female


title: PDX Abemaciclib 2


title: 2_827Parental2

value: NSCLC


title: patient 55, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma

value: pNX


title: PDX Abemaciclib 1


title: 1_827Parental1


title: CHC614T [hepatocellular carcinoma]

description: SAMPLE 66

value: M

tag: disease

value: hepatocellular carcinoma


title: PDX Control 4

value: control

tag: tissue


title: CHC703T [hepatocellular carcinoma]

description: SAMPLE 67


title: F2S3

city: OMAHA

first: Sowmya

middle: V

last: Yelamanchili

state: Nebraska

address: 984455 Nebraska Medical Center

department: Anesthesiology

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

data_processing:
Preparation of clean sequence reads: Constructed sequencing libraries were subject to sequencing with Illumina Novaseq 6000 platform (paired-end, 150 bp). Prior to assembly, reads containing sequencing adaptors, reads containing sequencing primers, and sequences with q quality score lower than 20 were removed.
Alignment of reads: The cleaned sequencing reads were aligned to reference genome [Rattus norvegicus] using HISAT2 package. Multiple alignments were allowed for each read sequence (up to 20 by default), with a maximum of two mismatches allowed. HISAT2 also built a database of potential splice junctions.
Transcript abundance estimation and differential expression analysis: Aligned reads of individual samples were assembled using StringTie. Transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome using a proprietary Perl script of LC Sciences (Houston, Texas, U.S.A.). Following transcriptome reconstruction, FPKM reads were evaluated by StringTie, and differential expressed genes were evaluated by edgeR. The differentially expressed mRNAs and genes were selected with log2 (fold change) ≥1 or log2 (fold change) ≤-1, and with p values < 0.05.
Single-nucleotide Polymorphism (SNP) Analysis: The samtools software was used for calling variants of transcripts, and ANNOVAR was used for SNP/InDel annotation. The function, genome site and type of variation SNPs were also analyzed.
Alternative Splicing Analysis: The software ASprofile was used to identify alternative used to identify alternative splicing events and analyze differential alternative splicing events between samples.   The classification of alternative splicing is as follows: SKIP and MSKIP：skipped exon; IR and MIR：intron retained; AE：alternative 5’ or 3’ splice site; TSS：alternative transcription start site; TTS：alternative transcription termination site
Genome_build: GCA_000001895.4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Nucleus accumbens

extract_protocol:
Using a brain matrix, nucleus accumbens sections were removed from the P14 brains of each group from both generations. Tissues were frozen on dry ice. Total RNA was isolated from each sample using the Zymo Direct-Zol RNA kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the in utero exposure animals (IUO), an ascending dosing procedure was used wherein doses of 10 mg/kg/day oxycodone (oxy) were orally gavaged for 5 days followed by 0.5 mg/kg/day escalation for 10 days to a final dose of 15 mg/kg/day, after which F0 females were mated with proven male breeders, and the treatment regimen continued throughout mating, gestation, and parturition until weaning. For post-natal exposure (PNO), F0 dams were orally gavaged with 15 mg/kg/day of oxy after parturition until weaning. F1 pups were randomly selected from the litters and bred with males to produce the F2 generation. F1 animals were not dosed with oxy prior to/post breeding; they were only exposed in utero or via the breastmilk.

tag: age

value: post-natal day 14

tag: strain

value: Sprague Dawley Rat

value: Nucleus accumbens

tag: generation

tag: treatment

value: saline control


title: 4_827ER1_1

value: untreated

tag: egfr tki sensitivity

tag: cell type

tag: cell line

value: HCC827 ER1


title: PDX Control 3

value: Patient-derived breast cancer liver metastasis


title: F2S4


title: patient 53, primary tumor

description: nCounter® Technology

tag: age at biopsy

tag: Sex

tag: histology


title: CHC736T [hepatocellular carcinoma]

description: SAMPLE 69


title: CHC613T [hepatocellular carcinoma]

description: SAMPLE 65


title: patient 56, primary tumor

description: nCounter® Technology

tag: tumor grade

tag: pt

tag: pn


title: PDX Control 2

tag: chip antibody


title: patient 50, metastasis

description: nCounter® Technology


title: CHC442T [fibrolamellar carcinoma]

description: SAMPLE 63

tag: age at sampling

tag: gender

value: F

value: fibrolamellar carcinoma


title: PDX Control 1

value: H3K27ac (Diagenode C15410196, polyclonal, lot # A1723-0041D)

tag: tissue


title: CHC451T [hepatocellular carcinoma]

description: SAMPLE 64

tag: disease


title: F2S1

tag: age

tag: strain


title: CHC734T [hepatocellular carcinoma]

description: SAMPLE 68


title: patient 50, primary tumor

description: nCounter® Technology

value: female


title: patient 48, metastasis

description: nCounter® Technology


title: F2S2

tag: generation

tag: treatment


title: F1S4


title: patient 53, metastasis

description: nCounter® Technology


title: patient 48, primary tumor

description: nCounter® Technology


title: F1S3


title: F1S2


title: patient 47, metastasis

description: nCounter® Technology


title: CHC334T [fibrolamellar carcinoma]

description: SAMPLE 60


title: CHC412T [fibrolamellar carcinoma]

description: SAMPLE 61


title: CHC429T [hepatocellular carcinoma]

description: SAMPLE 62


title: F1S1


title: F2NO4

value: post-natal oxycodone exposure


title: F2NO3


title: CHC320T [hepatocellular carcinoma]

description: SAMPLE 59


title: CHC255T [fibrolamellar carcinoma]

description: SAMPLE 58


title: patient 46, metastasis

description: nCounter® Technology


title: patient 46, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma


title: F2NO2


title: CHC1192T [hepatocellular carcinoma]

description: SAMPLE 55


title: CHC1201T [hepatocellular carcinoma]

description: SAMPLE 57


title: F2NO1


title: CHC1199T [hepatocellular carcinoma]

description: SAMPLE 56


title: CHC1162T [hepatocellular carcinoma]

description: SAMPLE 54


title: patient 44, metastasis

description: nCounter® Technology


title: F1NO3


title: F1NO4


title: CHC1154T [hepatocellular carcinoma]

description: SAMPLE 53


title: patient 47, primary tumor

description: nCounter® Technology


title: F1NO2


title: CHC1146T [hepatocellular carcinoma]

description: SAMPLE 52


title: CHC1065T [hepatocellular carcinoma]

description: SAMPLE 51


title: F1NO1


title: F2AO4

value: in utero oxycodone exposure


title: patient 44, primary tumor

description: nCounter® Technology


title: CHC1062T [hepatocellular carcinoma]

description: SAMPLE 50

value: M


title: patient 43, metastasis

description: nCounter® Technology


title: F2AO2


title: F2AO3


title: patient 43, primary tumor

description: nCounter® Technology


title: patient 42, primary tumor

description: nCounter® Technology


title: patient 42, metastasis

description: nCounter® Technology


title: patient 41, metastasis

description: nCounter® Technology


title: CHC1061T [hepatocellular carcinoma]

description: SAMPLE 49

value: hepatocellular carcinoma


title: CHC1055T [hepatocellular carcinoma]

description: SAMPLE 47


title: F2AO1


title: CHC1060T [hepatocellular carcinoma]

description: SAMPLE 48


title: patient 40, metastasis

description: nCounter® Technology


title: patient 40, primary tumor

description: nCounter® Technology


title: patient 41, primary tumor

description: nCounter® Technology

value: invasive lobular carcinoma


title: CHC1044T [hepatocellular carcinoma]

description: SAMPLE 45


title: CHC1052T [hepatocellular carcinoma]

description: SAMPLE 46


title: patient 72, metastasis

description: nCounter® Technology


title: F1AO4

value: post-natal day 14


title: F1AO2

value: Sprague Dawley Rat


title: F1AO3

value: Nucleus accumbens


title: CHC1041T [hepatocellular carcinoma]

description: SAMPLE 44


title: F1AO1


title: patient 35, metastasis

description: nCounter® Technology


title: patient 38, primary tumor

description: nCounter® Technology


title: patient 38, metastasis

description: nCounter® Technology


title: Single-end RBM4 KO Clone

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
Reads were mapped to genome (hg38) using STAR (version 2.5.2a) (62), allowing for multi-mapping (parameters --outFilterMultimapNmax 100  --winAnchorMultimapNmax 100
STAR alignment BAM files were passed to the TEToolkit (Jin et al., Bioinformatics 2015), along with transcriptome and TE GTFs to be processed for gene and TE counts
TEToolkit parameters for paired-end samples:  --mode uniq --GTF Homo_sapiens.GRCh38.85.gtf --TE GRCh38_rmsk_TE.gtf --strand reverse
TEToolkit parameters for single-end samples: --mode multi --stranded=no  --GTF Homo_sapiens.GRCh38.85.gtf --TE GRCh38_rmsk_TE.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Read count tables per sample/gene are provided separately for paired-end and single-end sample as tab-delimited text (.tsv) files.

source_name: KBM-7 derived near-haploid cell line

growth_protocol: The cell lines were cultured in IMDM medium (Quality Biological)  supplemented with 10% (v/v) Tet System Approved fetal calf serum (Takara Bio/previously Clontech), 100 U/mL penicillin, 100 µg/mL streptomycin (Pen/Strep) (Thermo Fisher Scientific), at 37°C in an incubator containing 5% CO2

extract_protocol:
Total RNA was isolated from the HAP1 cells (WT and RBM4 KO) using the RNAzol®RT (Molecular Research Center) per manufacturer’s instruction. RNA was quantified with Qubit® RNA HS Assay Kit according to the manufacturer’s recommendation (Thermo Fisher Scientific). RNA integrity was verified with Agilent RNA 6000 Nano kit on the 2100 Bioanalyzer (Agilent Technologies) or HS RNA Kit (15 nt) on the Fragment Analyzer (Agilent Technologies) according to the manufacturers’ protocol.
RNA-Seq libraries were prepared from 65 ng of total RNA and 1 μL of 1:5000 (v/v) dilution of ERCC ExFold RNA Spike-In Mix 1 (Thermo Fisher Scientific) with TruSeq® Stranded mRNA Library Prep for NeoPrepTM instrument as per the NeoPrep Library Prep System Guide on the instrument (Illumina). Libraries were diluted 1:5 (v/v) and 1 μL was used to check the expected size (~300 bp) and the purify was verified with the Agilent High Sensitivity DNA Kit as manufacturer’s recommendation (Agilent Technologies). One μL of the diluted libraries were used to quantify as recommended in the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) with standard range from 0 to 14 ng/ well. Libraries were normalized with molecular grade water to 2 nM with the above expected size and quantification. Pooled libraries of 2 nM were denatured and diluted as per the Standard Normalization Method for the NextSeq® System (Illumina). Final loading concentration of 1.8 pM and 1% PhiX (v/v) was used with the NextSeq® 500/550 High Output Kit v2 (150 cycles) (Illumina). Samples were sequenced paired-end with 75 cycles and single index of 6 cycles.

tag: genotype

value: RBM4 KO


title: RBM4 KO Clone 2 replicate 2

tag: cell line


title: SA29498_IRI 3

city: Columbus

first: NavjotSingh

last: Pabla

state: OH

address: 496 w 12th ave

department: Pharmaceutics and Pharmacology

institute: Ohio State University

data_processing:
Sequencing data quality checks were performed by using FastQC followed by read alignments using Bowtie2 version 2.1.0 with alignment to the mouse Ensembl genome (GRCm38/mm10). The overall mapping rate of more than 80% and rRNA percentage less than 5% was considered as good quality mapping data. The reads were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0) and the gene expression level was estimated using RSEM v1.2.15. Differentially expressed genes were called for each time point with Bioconductor edgeR. TMM (trimmed mean of M-values) method in edgeR package was used to normalize the gene expression results. For all the analyses, we only kept genes with (a) FDR-transformed P values below 0.05, (b) fold change of at least 1.5, and (c) TMM above 1 in three distinct AKI and/or control samples. These values of fold change and TMM thresholds were chosen to enable experimental validation of our differential-expression calls. We used the fold changes calculated by edgeR to create a pre-ranked gene-list.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Data Matrix

source_name: kidney

extract_protocol:
Renal mRNA profiles of 8-week-old C57BL/6J mice challenged with ischemia-reperfusion (24 hours), cisplatin (72 hours), and rhabdomyolysis (24 hours) were generated by RNAseq analysis. Total RNA was isolated from harvested renal cortical tissues using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s protocols. Total RNA samples used for library construction and sequencing (Quick Biology, Pasadena, CA). RNA integrity, quality and purity were analyzed by Agilent 2100 Bioanalyzer.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit (KAPA Biosystems, Wilmington, MA) according to the manufacturer’s protocols. The workflow consisted of mRNA enrichment using bead capture for poly-A selection, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification of library fragments. Final Library size distribution was determined by using an Agilent 2100 Bioanalyzer using the High-Sensitivity DNA Kit and its quantity was analyzed by Life Technologies Qubit 3.0 Fluorometer. Libraries were pooled and sequenced on the Illumina HiSeq 4000 platform to obtain 150-bp paired-end reads, 20 million reads (10 million reads pairs) per sample.

value: kidney

value: IRI

value: WT


title: SA29499_IRI 4


title: Single-end Wild Type

value: wild type


title: CHC1035T [hepatocellular carcinoma]

description: SAMPLE 42


title: CHC398T [hepatocellular carcinoma]

description: SAMPLE 40


title: CHC1010T [hepatocellular carcinoma]

description: SAMPLE 41

value: F


title: patient 35, primary tumor

description: nCounter® Technology

tag: age at biopsy


title: RBM4 KO Clone 1 replicate 3


title: SA29497_IRI 2


title: RBM4 KO Clone 1 replicate 2


title: patient 34, metastasis

description: nCounter® Technology

tag: Sex


title: RBM4 KO Clone 2 replicate 1


title: CHC195T [hepatocellular carcinoma]

description: SAMPLE 38


title: patient 34, primary tumor

description: nCounter® Technology

tag: histology


title: SA29496_IRI 1


title: SA27110_Cisplatin 4

value: Cisplatin


title: SA27109_Cisplatin 3


title: CHC1040T [hepatocellular carcinoma]

description: SAMPLE 43


title: CHC317T [hepatocellular carcinoma]

description: SAMPLE 36


title: CHC1196T [hepatocellular carcinoma]

description: SAMPLE 39


title: Wild Type replicate 2


title: CHC789T [hepatocellular carcinoma]

description: SAMPLE 37


title: patient 33, metastasis

description: nCounter® Technology

value: female


title: CHC725T [hepatocellular carcinoma]

description: SAMPLE 35


title: SA27108_Cisplatin 2


title: patient 33, primary tumor

description: nCounter® Technology

tag: tumor grade


title: SA27106_Rhabdomyolysis 4

value: Rhabdomyolysis


title: patient 30, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma

tag: pt


title: patient 29, metastasis

description: nCounter® Technology


title: patient 31, metastasis

description: nCounter® Technology


title: patient 30, metastasis

description: nCounter® Technology


title: SA27107_Cisplatin 1


title: CHC437T [hepatocellular carcinoma]

description: SAMPLE 34


title: patient 31, primary tumor

description: nCounter® Technology

tag: pn


title: Wild Type replicate 1


title: SA27105_Rhabdomyolysis 3


title: patient 29, primary tumor

description: nCounter® Technology


title: CHC046T [hepatocellular carcinoma]

description: SAMPLE 32


title: RBM4 KO Clone 1 replicate 1


title: patient 28, metastasis

description: nCounter® Technology


title: SA27103_Rhabdomyolysis 1


title: SA27104_Rhabdomyolysis 2


title: CHC211T [hepatocellular carcinoma]

description: SAMPLE 33


title: Wild Type replicate 3


title: patient 26, metastasis

description: nCounter® Technology


title: CHC152T [hepatocellular carcinoma]

description: SAMPLE 31


title: SA27102_Control 8

value: mock


title: CHC206T [hepatocellular carcinoma]

description: SAMPLE 30

value: M


title: patient 28, primary tumor

description: nCounter® Technology


title: CHC220T [hepatocellular carcinoma]

description: SAMPLE 29

value: hepatocellular carcinoma


title: SA27101_Control 7


title: SA27100_Control 6


title: patient 26, primary tumor

description: nCounter® Technology


title: CHC059T [hepatocellular carcinoma]

description: SAMPLE 28


title: SA27099_Control 5


title: SA29495_Control 4


title: CHC242T [hepatocellular carcinoma]

description: SAMPLE 27


title: patient 25, metastasis

description: nCounter® Technology


title: patient 25, primary tumor

description: nCounter® Technology


title: patient 24, primary tumor

description: nCounter® Technology


title: CHC031T [hepatocellular carcinoma]

description: SAMPLE 26


title: SA29493_Control 2


title: patient 23, metastasis

description: nCounter® Technology


title: SA29494_Control 3


title: CHC081T [hepatocellular carcinoma]

description: SAMPLE 25


title: SA29492_Control 1


title: CHC218T [hepatocellular carcinoma]

description: SAMPLE 24


title: CHC205T [hepatocellular carcinoma]

description: SAMPLE 23


title: MOLM-13 Kevetrin 48h 3

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

description: Gene expression data from Kevetrin-treated (340 microM) MOLM-13 cells after 48h of culture

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard Affymetrix protocol. Washing and staining was performed on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip scanner 3000.

data_processing: The data were analyzed with Expression Console software (Affymetrix). Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA).

label: biotin

label_protocol: ss-cDNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: Cells were cultured in RPM1 1640 medium supplemented with 20% fetal bovine serum,  2 mM L-glutamine, 100 U/ml of penicillin, 100 μg/ml of streptomycin and 0.2% Mycozap.

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

treatment_protocol: Cells were treated with 340 microM Kevetrin for 6h or 48h before harvesting.

value: Kevetrin-treated (340 microM) cells after 48h of culture

tag: tp53 status

value: wildtype


title: patient 24, metastasis

description: nCounter® Technology


title: FigS3CK27010WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description:
75 mins after release from G1 (alpha factor) in the presence nocodazole.
FigS3CK27010IP.bw

data_processing:
Library sequencing was carried out on the Ion Torrent Proton.
The quality of the raw sequence data was examined using FastQC and trimming of reads was carried out using fastx_trimmer.
Any reads smaller than 50bp were removed using ‘Filter FASTQ’.
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, Genolevures) using Bowtie2 with the default (--sensitive) parameters.
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: bigWig files

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNase A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270.

tag: sac_cer strain

tag: can_gla strain

tag: chip antibody

value: none (input)


title: patient 23, primary tumor

description: nCounter® Technology


title: patient 22, metastasis

description: nCounter® Technology


title: CHC137T [hepatocellular carcinoma]

description: SAMPLE 22

tag: age at sampling

tag: gender

tag: disease


title: MOLM-13 CNTRL 48h 2

description: Gene expression data from untreated MOLM-13 cells after 48h of culture

value: Untreated cells after 48h of culture


title: FigS3CK27010IP

value: anti-PK antibody (Bio-Rad)


title: patient 22, primary tumor

description: nCounter® Technology

value: invasive mucinous carcinoma


title: KASUMI-1 Kevetrin 48h 3

description: Gene expression data from Kevetrin-treated (340 microM) KASUMI-1 cells after 48h of culture

value: mutated


title: MOLM-13 Kevetrin 48h 2


title: MOLM-13 CNTRL 48h 3


title: CHC010T [hepatocellular carcinoma]

description: SAMPLE 21


title: patient 20, metastasis

description: nCounter® Technology


title: FigS3CK24185WCE

description:
75 mins after release from G1 (alpha factor) in the presence nocodazole.
FigS3CK24185IP.bw


title: KASUMI-1 Kevetrin 48h 2


title: CHC228T [hepatocellular carcinoma]

description: SAMPLE 20


title: MOLM-13 CNTRL 48h 1


title: FigS3CK24185IP


title: KASUMI-1 Kevetrin 48h 1


title: KASUMI-1 CNTRL 48h 2

description: Gene expression data from untreated KASUMI-1 cells after 48h of culture


title: patient 20, primary tumor

description: nCounter® Technology

value: invasive lobular carcinoma


title: CHC230T [hepatocellular carcinoma]

description: SAMPLE 19


title: CHC335T [hepatocellular carcinoma]

description: SAMPLE 18


title: patient 19, metastasis

description: nCounter® Technology


title: KASUMI-1 CNTRL 48h 3


title: CHC080T [hepatocellular carcinoma]

description: SAMPLE 17


title: FigS3CK22390IP

description:
75 mins after release from G1 (alpha factor) in the presence nocodazole.
FigS3CK22390IP.bw


title: FigS3CK22390WCE


title: FigS2FK20785WCE

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
FigS2FK20785IP.bw


title: FigS2FK20785IP

value: anti-HA antibody (Roche)


title: patient 19, primary tumor

description: nCounter® Technology

value: pTX

value: pNX


title: patient 17, primary tumor

description: nCounter® Technology

value: female


title: CHC445T [hepatocellular carcinoma]

description: SAMPLE 16


title: CHC158T [hepatocellular carcinoma]

description: SAMPLE 15


title: patient 16, metastasis

description: nCounter® Technology


title: CHC253T [hepatocellular carcinoma]

description: SAMPLE 14


title: KASUMI-1 CNTRL 48h 1


title: patient 16, primary tumor

description: nCounter® Technology


title: FigS2FK20783IP

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
FigS2FK20783IP.bw


title: CHC245T [hepatocellular carcinoma]

description: SAMPLE 13


title: MOLM-13 Kevetrin 6h 1

description: Gene expression data from Kevetrin-treated (340 microM) MOLM-13 cells after 6h of culture

value: Kevetrin-treated (340 microM) cells after 6h of culture


title: patient 14, metastasis

description: nCounter® Technology


title: FigS2DK27697PKWCE

description:
Exponentially growing.
FigS2DK27697PKIP.bw


title: KASUMI-1 Kevetrin 6h 3

description: Gene expression data from Kevetrin-treated (340 microM) KASUMI-1 cells after 6h of culture


title: MOLM-13 CNTRL 6h 1

description: Gene expression data from untreated MOLM-13 cells after 6h of culture

value: Untreated cells after 6h of culture


title: MOLM-13 CNTRL 6h 3


title: patient 17, metastasis

description: nCounter® Technology


title: MOLM-13 Kevetrin 6h 2


title: MOLM-13 Kevetrin 6h 3


title: CHC339T [hepatocellular carcinoma]

description: SAMPLE 12

value: F


title: CHC037T [hepatocellular carcinoma]

description: SAMPLE 11

value: M


title: FigS2FK20783WCE


title: patient 14, primary tumor

description: nCounter® Technology


title: FigS2DK27697PKIP


title: FigS2CK27547WCE

description:
Exponentially growing.
FigS2CK27547IP.bw


title: FigS2CK27547IP


title: CHC043T [hepatocellular carcinoma]

description: SAMPLE 10

value: hepatocellular carcinoma


title: patient 13, metastasis

description: nCounter® Technology


title: ChIPSeq_HUVEC_H3K27me3_INPUT_set2

city: Kuopio

first: Oscar Hsin-Fu

last: Liu

state: Finland

address: P.O.Box 1627 (Neulaniementie 2)

department: Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation.
For RNA-Seq and ChIP-Seq libraries, the poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
RNA-Seq reads were aligned to the hg19 genome using Tophat. ChIP-Seq reads were aligned to hg19 genome using bowtie.
HOMER v 4.9 tool was used to generate RPKM table and bedGraphs.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

source_name: Human umbilical vein endothelial cell

growth_protocol: HUVECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich).

extract_protocol:
ChIP-Seq: Formaldehyde (37% liquid stock solution) was added drop by drop to the culture medium on 10cm plates to a final concentration of 1% and incubated at room temperature for 10 min. Glycine was added to a final concentration of 125mM at room temperature for 5 min to stop cross-linking. The culture medium was removed, and cells were washed twice with ice-cold 0.1% BSA in PBS. Cells were scraped and collected in MNase buffer (10mM Tris pH 7.4, 10mM NaCl, 5mM MgCl2, 0.5% IGEPAL NP-40, 1x protease inhibitor cocktail PIC, Roche), 1 mM PMSF) and incubated on ice for 10 min. Cells were spun down, washed with 1mL MNase buffer, and spun down again. The supernatant was removed and the pellet was suspended to 300µL of SDS lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1, 1x PIC, 1x PMSF). Samples were sonicated usign Bioruptor for 26 cycles.
RNA-Seq: RNA was purified using RNeasy Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
ChIP-Seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with H3K27me3 Ab (Millipore #07-449). DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors and library fragments were size-selected (150-250bp) from a 2% agarose gel.
RNA-Seq: The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: HUVECs were treated for 8h under hypoxia in 1%FBS EGM (Lonza).

tag: cell type

value: Human umbilical vein endothelial cell

value: normoxia/hypoxia

tag: antibory

value: input


title: patient 13, primary tumor

description: nCounter® Technology


title: patient 8, metastasis

description: nCounter® Technology


title: CHC014T [hepatocellular carcinoma]

description: SAMPLE 9

growth_protocol: Not applicable


title: KASUMI-1 Kevetrin 6h 2

tag: treatment


title: MOLM-13 CNTRL 6h 2

value: wildtype


title: FigS2CDK27542IP

description:
Exponentially growing.
FigS2CDK27542IP.bw

value: anti-PK antibody (Bio-Rad)


title: patient 8, primary tumor

description: nCounter® Technology

value: invasive ductal carcinoma


title: CHC239T [hepatocellular carcinoma]

description: SAMPLE 7


title: KASUMI-1 Kevetrin 6h 1

value: mutated


title: ChIPSeq_HUVEC_H3K27me3_VH298_rep2_set2

value: normoxia; inhibitor VH298


title: patient 7, metastasis

description: nCounter® Technology


title: KASUMI-1 CNTRL 6h 3

description: Gene expression data from untreated KASUMI-1 cells after 6h of culture


title: ChIPSeq_HUVEC_H3K27me3_VH298_rep1_set2


title: KASUMI-1 CNTRL 6h 2


title: MOLM-13 Kevetrin 48h 1

value: Kevetrin-treated (340 microM) cells after 48h of culture


title: CHC333T [hepatocellular carcinoma]

description: SAMPLE 6


title: KASUMI-1 CNTRL 6h 1


title: FigS2CDK27542WCE

value: none (input)


title: ChIPSeq_HUVEC_H3K27me3_VH298_rep3_set2


title: Fig3EK28287IP

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
Fig3EK28287IP.bw


title: patient 7, primary tumor

description: nCounter® Technology


title: CHC441T [hepatocellular carcinoma]

description: SAMPLE 5


title: CHC013T [hepatocellular carcinoma]

description: SAMPLE 4


title: Fig3EK28075IP

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
Fig3EK28075IP.bw


title: Fig3EK28075WCE


title: CHC399T [hepatocellular carcinoma]

description: SAMPLE 8


title: patient 6, primary tumor

description: nCounter® Technology

value: pNX


title: CHC231T [hepatocellular carcinoma]

description: SAMPLE 3


title: Fig3DK27802WCE

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
Fig3DK27802IP.bw


title: Fig3EK28287WCE


title: ChIPSeq_HUVEC_H3K27me3_Hox_rep1_set2

value: hypoxia


title: CHC229T [hepatocellular carcinoma]

description: SAMPLE 2


title: ChIPSeq_HUVEC_H3K27me3_Nox_rep3_set2

value: normoxia


title: ChIPSeq_HUVEC_H3K27me3_Nox_rep2_set2


title: ChIPSeq_HUVEC_H3K27me3_Hox_rep2_set2


title: CHC018T [hepatocellular carcinoma]

description: SAMPLE 1


title: patient 6, metastasis

description: nCounter® Technology

value: female


title: ChIPSeq_HUVEC_H3K27me3_Nox_rep1_set2


title: patient 5, primary tumor

description: nCounter® Technology


title: Fig3DK27796WCE

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
Fig3DK27796IP.bw


title: ChIPSeq_HUVEC_H3K27me3_INPUT_set1


title: patient 4, metastasis

description: nCounter® Technology


title: Fig3DK27796IP

value: anti-HA antibody (Roche)


title: ChIPSeq_HUVEC_H3K27me3_Hox_rep1_set1


title: patient 5, metastasis

description: nCounter® Technology


title: Fig3CK27821WCE

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
Fig3CK27821IP.bw


title: patient 4, primary tumor

description: nCounter® Technology


title: patient 2, metastasis

description: nCounter® Technology


title: patient 2, primary tumor

description: nCounter® Technology


title: patient 1, metastasis

description: nCounter® Technology


title: RNASeq_HUVEC_siKDM6B_Hox_rep2

molecule: polyA RNA

tag: sirna


title: Fig3CK27804WCE

description:
60 mins after release from G1 (alpha factor) in the presence of auxin and nocodazole.
Fig3CK27804IP.bw


title: patient 1, primary tumor

description: nCounter® Technology

tag: age at biopsy


title: Fig3CK27804IP


title: RNASeq_HUVEC_siKDM4B_Hox_rep2


title: Fig3DK27802IP


title: RNASeq_HUVEC_siCTL_Hox_rep2

value: control


title: set-2(bn129) rep3

city: Lyon

first: Marion

last: Herbette

address: 46 allée d'Italie

department: Laboratoire de Biologie et Modélisation de la Cellule

institute: ENS de Lyon

description: Replicate 3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Mapping & QC-mapped with rna-STAR (2.4.1d) & Samtools (0.1.19)
Gene expression analysis with HTSeq-count (Version 0.7.2) & package DESeq2 (1.16.1 using R version 3.4.4)
Genome_build: WS254
Supplementary_files_format_and_content: 1 CSV files containing genes differentially (set-2 vs WT) and raw counts

organism: Caenorhabditis elegans

source_name: dissected gonads from C.elegans adult worms

growth_protocol: Nematode strain maintenance was as described previously (Brenner, 1974).

extract_protocol:
RNAs were extracted with Arcturus PicoPure [Life Technology, #12204-01] according to manufacturer’s instructions and treated with DNAse [Qiagen, #79254]. Integrity of RNA was assessed on Tape Station 4200 [Agilent].
Library prep for total RNA-seq Ribozero/standard quantity. With this protocol, reads originate from to the first cDNA strand. Sequencing type: Single-Read Read length: 50

treatment_protocol: Germline of young adult were dissected and placed in extraction buffer (Arcturus PicoPure, Life Technology, #12204-01) and snap frozen in liquid nitrogen

tag: tissue

value: germline

tag: development stage

value: Young Adult

tag: strain


title: Columbia0_Pakerine_3

city: Wageningen

first: Tom

last: van der Meer

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

description: Gene expression data of Arabidopsis thaliana whole plants after 24 hours Pakerine treatment

hyb_protocol: Following fragmentation, 10 ng of labelled aRNA was hybridized for 16 hours to the Arabidopsis ATH1 Genome Array at 45 oC. The Genome Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The Genome Arrays were scanned using the GeneChip scanner 3000

data_processing: primary analysis was carry out using the R-package 'Affy'. Fold‐change differences and p values adjusted for false discovery rate were obtained with the R packages limma and qvalue, respectively

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 (7 day) treated with Pakerine for 24 hours

label_protocol: Biotin labelled aRNA (start 100ng) was prepared using the 3' IVT express kit (GeneChip) according to the manufacturer's protocol.

growth_protocol: Arabidopsis thaliana Col-0 plants were grown in liquid 1/2 MS media in translucent 96 well plates (5 plants per well) for 7 days at long day conditions (16h light/8h dark, 100 µmol m-2 s-1 light intensity, 21 oC, 70% relative humidity). After 7 days the original media was replaced by 1/2 MS media containing pakerine (5 μM) or DMSO (mock) and grown for 24 hours at long day conditions prior to harvesting.

extract_protocol: RNA was extracted using RNeasy plant Mini Kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: 7 days no treatment followed by 24 hours chemical treatment consisting of pakerine (5 μM final concentration) or equal amounts of DMSO (mock).

value: Whole plant

tag: ecotype


title: Fig3CK27821IP


title: set-2(bn129) rep1

description: Replicate 1


title: set-2(bn129) rep2

description: Replicate 2


title: T8: healthy subject

city: Zhengzhou

first: Baijun

last: Fang

address: 127 Dongming Road, Jinshui District

institute: Affiliated Tumor Hospital of Zhengzhou University

description: miRNA expression data from healthy subject

hyb_protocol: After the chip hybridization, Fluidics Station 450 instrument was used for washing and dyeing.

scan_protocol: GeneChip® Scanner 3000 scan chip results.

data_processing: The chip scanned images and raw data are generated by the AGCC operating system.

source_name: healthy subject

label_protocol: RNA was tailed by Poly(A) RNA polymerase. RNA ligase was used to connect biotin-labeled signal molecules with the RNA, and the ligands and chips were hybridized.

growth_protocol: Bone marrow fluids were collected with anticoagulant EDTA-containing tubes.

treatment_protocol: CD138+ cells in bone marrow samples were enriched with whole blood sorting magnetic beads from Miltenyi Biotec, Germany.

tag: disease state

value: healthy

value: bone marrow


title: RNASeq_HUVEC_siKDM4B_Nox_rep2

value: Human umbilical vein endothelial cell


title: R1

first: Jinshui

last: Wang

state: Henan

address: No. 100 Lianhua street

institute: Henan university of technology

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of sample G1, G2, G3,Z1,Z2,Z3,R1,R2 and R3 to the (ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gtf/triticum_aestivum/) Triticum aestivum L. reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: v36
Supplementary_files_format_and_content: text file include RPKM values for each Sample

organism: Triticum aestivum

source_name: Seed_low gluten content

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following of the merchant's recommended protocol.

treatment_protocol: Strong  (G),  middle  (Z)  and  weak  (R)  gluten  wheat  were  used  as  the  experimental material in this study, and were purchased from Henan province Xinxiang academy of agricultural sciences and Henan huang fan qu dishen seeds agricultural science institute

tag: gluten level

value: R (low)

value: seed


title: R2


title: T6: healthy subject


title: ChIPSeq_HUVEC_H3K27me3_Nox_rep1_set1


title: Columbia0_Pakerine_2


title: R3


title: Columbia0_DMSO_3

description: Gene expression data of Arabidopsis thaliana whole plants after 24 hours DMSO (mock) treatment

source_name: Arabidopsis Col-0 (7 day) treated with DMSO for 24 hours


title: T5: healthy subject


title: Columbia0_DMSO_2


title: Z3

source_name: Seed_medium gluten content

value: Z (medium)


title: WT (N2) rep2

description: Replicate 2


title: T7: healthy subject


title: T4: multiple myeloma patient

description: miRNA expression data from newly diagnosed multiple myeloma patient

value: multiple myeloma


title: RNASeq_HUVEC_siKDM6B_Nox_rep2


title: Z2


title: Z1


title: RNASeq_HUVEC_siKDM4B_Hox_rep1


title: RNASeq_HUVEC_siCTL_Hox_rep1


title: T3: multiple myeloma patient

source_name: newly diagnosed multiple myeloma patient


title: T2: multiple myeloma patient


title: WT (N2) rep3

description: Replicate 3


title: Columbia0_Pakerine_1


title: RNASeq_HUVEC_siCTL_Nox_rep2


title: G3

source_name: Seed_high gluten content

value: G (high)


title: MCF7 DMSO

city: Melbourne

first: Shom

last: Goel

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
performed the mapping and pre-processing using the default settings of HiC-Pro 2.9.048 and bowtie 1.1.266 as the base mapper
Interactions were called by fitHiChIP (6.0)
Genome_build: hg19
Supplementary_files_format_and_content: BED files of DNA regions of contact called by fitHiChIP

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of collection for sequencing was between 60-70%.

extract_protocol:
Nuclear isolation and in situ Hi-C contact generation were performed by proximity ligation on 5x10^6 crosslinked cells per condition using biotin-dATP. The isolated nuclei were then lysed and sonicated prior to chromatin immunoprecipitation against the epitope of interest (H3K27ac, Diagenode Cat# C15410196, Lot# A1723-0041D). Next, reverse crosslinking and DNA purification were performed on the immunoprecipitated DNA prior to biotin capture of the Hi-C contacts.
The HiChIP libraries were prepared as previously described (Mumbach et al Nature methods 2016), which consists of on-bead library prep with Illumina transposase (Tn5), adjusting enzyme amount linearly according to the amount of post-ChIP DNA (i.e. 1.25ul Tn5 for 25ng of DNA).

treatment_protocol: Abemaciclib 500 nM or DMSO for 7 days for all cell lines.

tag: cell line

value: MCF7 breast carcinoma cell line

value: DMSO

tag: treatment length

value: 7 days

tag: antibody

value: H3K27ac (Diagenode C15410196, polyclonal, lot # A1723-0041D)


title: MDA-MB-453 Abemaciclib

value: MDA-MB-453 breast carcinoma cell line

value: abemaciclib


title: T1: multiple myeloma patient


title: G2


title: G1


title: RNASeq_HUVEC_siKDM6B_Hox_rep1

value: hypoxia


title: Columbia0_DMSO_1


title: MDA-MB-453 DMSO


title: Sample_27_GCB_WT_repl2_HiC

status: Public on Sep 02 2020

city: New York

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
Hi-C reads were aligned to mm10 using bowtie2 2.2.3 (special paramters: --very-sensitive-local --local).
Hi-C aligned reads were filtered with GenomicTools "gtools-hic filter", discarding read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<10 kb).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited

source_name: GC B cell

extract_protocol: Hi-C libraries were prepared using the KAPA Hyper prep kit following Arima's manufacturer's instructions.

treatment_protocol: Included as additional column of SAMPLES section

tag: genotype

value: WT littermate control


title: Sample_29_GCB_H1_DKO_repl2_HiC

value: Constitutive H1c-/-;H1e-/-


title: Sample_26_GCB_WT_repl1_HiC


title: Sample_28_GCB_H1_DKO_repl1_HiC


title: RNASeq_HUVEC_siCTL_Nox_rep1

value: normoxia

value: control


title: MCF7 Abemaciclib


title: RNASeq_HUVEC_siKDM6B_Nox_rep1

value: Human umbilical vein endothelial cell


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A2_AD001_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male

tag: age


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_D4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_A3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A10_AD004_indexed


title: RNASeq_HUVEC_siKDM4B_Nox_rep1

tag: cell type


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD012_indexed


title: WT (N2) rep1

description: Replicate 1

value: germline

value: Young Adult


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H1_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H1_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_H10_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G7_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G3_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G3_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G3_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_E1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G11_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_G10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F9_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F9_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F9_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F8_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F7_AD001_indexed


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title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_3_CEMBA180612_5D_4_F5_AD001_indexed