title: FLU MOCK CD45 2 biological replicate 2 (ATAC-seq)

value: Alveolar macrophages


title: Parr_spleen_3

status: Public on Jan 13 2020

type: RNA

city: Helsinki

first: Johanna

last: Kurko

state: --Please select--

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

hyb_protocol: First, CodeSet Master Mix was prepared by adding 70 µl of Hybridization Buffer to the Reporter Codeset tube and mixing. Then 8 µl of Master Mix was aliquoted to each well of a sample strip tube containing 100 ng (20 ng/ul) RNA, mixed and spinned gently. 2 µl of Capture ProbeSet was added to each well of a strip tube, mixed  and spinned gently. Next, tubes were immediately transferred to PCR cycler heated to 65 °C and incubated o/n.

scan_protocol: After hybridization, the sample strip was transferred to the nCounter Prep Station for purification and immobilization in a sample cartridge. After immobilization, the cartridge was analyzed with the nCounter Digital Analyzer by taking images of the immobilized fluorescent reporters. The number of images taken corresponded to the number of reporters counted. The raw count data was exported as a csv file.

data_processing: The raw count data was normalized by RNA content normalization factor for each sample calculated from geometric mean count values of six genes selected from the panel. These genes (ef1ac, prkar1aa, rps20, rxrbaa, vdraa and vdrab) were chosen as they exhibited a low coefficient of variation and average count values across samples. Genes included two (ef1ac and rps20) of the nine genes originally included in the panel as potential normalization candidates, as well as four additional genes (prkar1aa, rxrbaa, vdraa and vdrab). After normalization and quality control, two samples, N.4.M and I.1.L, were observed to have too high RNA content normalization factor values (> 3.0) and they were not used in the further analyses. Quality control and normalization of the data was performed using the nSolver Analysis Software (v3.0) (NanoString Technologies). Background correction was not performed, but in further analyses a normalized count value of 20 was set as a background signal threshold.

molecule: total RNA

organism: Salmo salar

source_name: Atlantic salmon developmental stages

extract_protocol: Dissected tissue samples or whole individuals (embryos, alevin, fry) were disrupted and homogenized in the presence of NucleoZOL (Macherey-Nagel, Düren, Germany) for lysis in 2 ml safe-lock tubes containing one 5 mm stainless steel bead (Qiagen) for 2.5-3 minutes at 30 Hz using TissueLyzer II (Qiagen). Total RNA was extracted from the lysate using NucleoSpin RNA Set for NucleoZOL (Macherey-Nagel) according to the manufacturer’s instructions. After the elution step, RNA was treated with rDNase using the rDNase Set (Macherey-Nagel) to remove any residual DNA and, subsequently, purified with either NucleoSpin RNA clean-up or NucleoSpin RNA clean-up XS kit (Macherey-Nagel) according to the RNA yield. Blood samples were lysed in the RNAprotect Animal Blood Tubes (Qiagen) and total RNA was extracted using the RNeasy Protect Animal Blood System kit (Qiagen) according to the manufacturer’s protocol followed by concentration of RNA using NucleoSpin RNA clean-up XS kit (Macherey-Nagel). The quantity and quality of RNA was determined using both NanoDrop Spectrophotometer ND-1000 (Thermo Scientific, Wilmington, DE, USA) and 2100 BioAnalyzer system (Agilent Technologies, Santa Clara, CA, USA).

tag: tissue

value: spleen

tag: Sex

value: F

tag: developmental stage

value: parr

tag: maturity stage

value: immature

tag: habitat

value: hatchery

tag: population origin

value: Neva

tag: diet

value: normal diet


title: A21F

type: SRA

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

country: China

institute: Shandong university

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: hg38
Supplementary_files_format_and_content: counts

organism: Homo sapiens

source_name: cell

growth_protocol: Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were
converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min
followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: Cells were treated  with F. nucleatum at a multiplicity of infection (MOI) of F. nucleatum : cell =10:1, and culured at 3d, 7d, 14d and 21d

tag: cell type

value: Human gingival-derived mesenchymal stem cells

tag: donor

value: donor 1

tag: culture time


title: circulating miRNA [66]

city: Lodz

first: Konrad

last: Pagacz

address: Mazowiecka 15

department: Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Sampled 7 days

data_processing:
No normalization was performed
matrix non-normalized values

label: SYBR

source_name: serum

label_protocol: Each microRNA sample was reverse transcribed into cDNA and run on the miRCURY LNA™ Universal RT miRNA PCR Human panel I and II. SYBR green was used to label PCR products according to the manufactturer's guidelines.

extract_protocol: miRNA was extracted from the samples usingmiRCURY RNA Isolation kit (Qiagen) according to the manufacturer's handbook.

tag: protocols

value: no irradiation


title: FLU MOCK CD45 1 biological replicate 2 (ATAC-seq)

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

library_source: genomic

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters “-a CTGTCTCTTATA -A CTGTCTCTTATA --minimum-length=25 –quality-cutoff=20 -u -50 -U -50”.
BWA (version 0.6.2) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the mouse mm10 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Read group addition, duplicate marking and insert size assessment was performed using the picard tools AddOrReplaceReadGroups, MarkDuplicates and CollectMultipleMetrics, respectively (version 2.1.1).
Reads mapped to mitochondrial DNA were removed using the pairToBed command from BEDTools (version 2.26.0) (Quinlan & Hall, 2010).
Additional filtering was performed to only include uniquely mapped, properly-paired reads with insert size <= 2kb, and mismatches <= 1 in both reads.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph coverage tracks representing the accessibility signal per million mapped paired-reads were generated using BEDTools genomeCoverageBed with the parameters “-bg -pc -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).

molecule: genomic DNA

organism: Mus musculus

source_name: FLU MOCK CD45 1

growth_protocol: Alveolar macrophages were enriched from whole lung using a postive selection using anti-Siglec F MACS selection. Enriched Ams were then FACS sorted based on Siglec F+ CD11c+ double positivity, and separated into resident and recruited using congenic markers (CD45.2 and CD45.1 respectively)

extract_protocol:
DNA was isolated as previously described (Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218, 2013).
50,000 cells were used for the transposition reaction, that was carried out for 4h at 37°C. Library fragments were amplified using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers. using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min - this was done for 13 cycles. Transposed DNA fragments were then PCR amplified for 13 cycles and purified by the ChargeSwitch PCR clean-up kit (Invitrogen)

treatment_protocol: 50,00 cells retrieved from FACs sorting were stimulated with 100ng/ml Pam3CSK4 (EnzoBiosciences) for 2 hours at 37°C and 5% CO2

tag: origin

value: Recruited AM - IAV d28 lung

tag: treatment

value: Mock stimulation


title: A21C


title: FLU MOCK CD45 1 biological replicate 1 (ATAC-seq)


title: FLU PAM CD45 1 biological replicate 2 (ATAC-seq)

source_name: FLU PAM CD45 1

value: Pam3CSK4 stimulation


title: A14F


title: Parr_skin_3

value: skin


title: Parr_pyloric caeca_3

value: pyloric caeca


title: PBS PAM CD45 2 biological replicate 2 (ATAC-seq)

source_name: PBS PAM CD45 2

value: Resident AM - PBS control lung


title: circulating miRNA [14]

description: Sampled 7 days


title: Parr_muscle_3

value: muscle


title: A14C


title: Parr_liver_3

value: liver


title: circulating miRNA [70]

description: Sampled 7 days


title: circulating miRNA [31]

description: Sampled 7 days


title: PBS MOCK CD45 2 biological replicate 2 (ATAC-seq)

source_name: PBS MOCK CD45 2

value: Alveolar macrophages


title: A7F


title: Parr_kidney_3

value: kidney

value: F

value: parr


title: A7C


title: A3F


title: circulating miRNA [22]

description: Sampled 7 days


title: PBS MOCK CD45 2 biological replicate 1 (ATAC-seq)


title: Parr_heart_3

value: heart

value: immature

value: hatchery

value: Neva


title: circulating miRNA [19]

description: Sampled 7 days

value: no irradiation


title: circulating miRNA [46]

description: Sampled 7 days


title: circulating miRNA [28]

description: Sampled 7 days


title: Parr_eye_3

value: eye

value: normal diet


title: circulating miRNA [44]

description: Sampled 7 days


title: Parr_gill_3

value: gill


title: PBS PAM CD45 2 biological replicate 1 (ATAC-seq)

value: Pam3CSK4 stimulation


title: Parr_gonad_3

value: gonad


title: Parr_brain_3

value: brain


title: Parr_adipose tissue_3

value: adipose


title: circulating miRNA [3]

description: Sampled 7 days


title: circulating miRNA [15]

description: Sampled 7 days


title: circulating miRNA [53]

description: Sampled 7 days


title: mammospheres_breast_cancer_cell_line_MDA_rep2

city: Lausanne

first: Nicolas

last: Mermod

address: Station 6, EPFL

department: Lab of Molecular Biotechnology

country: Switzerland

institute: University of Lausanne

hyb_protocol: The labeled RNA was hybridized to Agilent human miRNA microarrays for 20 hours at 55°C with rotation.

scan_protocol: After hybridization and washing the arrays were scanned with an Agilent microarray scanner G2505B using high dynamic range settings as specified by the manufacturer.

data_processing: Agilent Feature Extraction Software v 10.7.3.1 was used to extract the data. Quantile normalization was applied to the Total Gene Signal intensity values, using the function normalize.quantiles from the R Bioconductor package preprocessCore.

label_protocol: Each sample was prepared according to the Agilent’s miRNA Microarray System protocol. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH, Otelfingen, Switzerland), denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH, Otelfingen, Switzerland).

growth_protocol: Cells (4000 cells/cm2) were grown in ultralow attachment plates (Corning, USA) and in the MammoCult culture medium (Stemcells technologies, France).

extract_protocol: Cells were then harvested for RNA extraction. RNAs were extracted using TRIzol (Life Technologies, Fisher Scientific) following the manufacturer’s instructions, except that the volume of isopropanol used at the precipitation step was increased from 500 microL to 800 microL to enhance the recovery of small RNAs.

treatment_protocol: To generate chemoresistant mammospheres, cells were maintained in mammospheres growth conditions 3 days before a 48h-treatment with paclitaxel (100nM, treatment a) or 5-fluorouracil (50mg/ml, treatment b).

tag: cell line

value: MDA


title: mammospheres_MCF7_with_5FU_treatment


title: mammospheres_MCF7_with_paclitaxel_treatment


title: circulating miRNA [38]

description: Sampled 7 days


title: Parr_pyloric caeca_2

value: pyloric caeca

value: M


title: K8-HS142_stage-tm_rep1

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Four micrograms of labelled aRNA was hybridized to the array according to the manufacturer’s recommendations (http://www.combimatrix.com/support_docs.htm). Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS) using 4 μg of labelled aRNA. Hybridization washings were performed as following: wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20), wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20), 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

scan_protocol: Scanning was performed using Perkin Elmer ScanArray 4000XL microarray scanner and ScanArray Express 4.0 acquisition software. Laser was set at 60% of power. PMT gain was set at 60%.

data_processing: Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Data were quantile-normalized using Blist 0.6 software (Combimatrix).

molecule: polyA RNA

organism: Helianthus tuberosus

source_name: clone K8-HS142, growth stage tm

label_protocol: Total RNA (1 µg) was amplified and labelled using the RNA ampULSe kit (Kreatech)

growth_protocol: Field trials based on three replications for each clone grown under irrigation at 8 plants per m2 density on texture-balanced soil at the Experimental Farm of the University of Tuscia, Viterbo, Latium, Italy

extract_protocol: Total RNA isolation according to Chomczynski and Sacchi (1987) followed by a DNase I treatment (Ambion), starting from 500-800 mg of fresh frozen tuber tissue

treatment_protocol: Two experimental factors: clone (two levels: VR and K8-HS142), tuber develpmental stage (three levels: initial tuberization, maximum tuber growth elongation rate, tuber physiological maturation)

tag: clone

tag: growth stage

value: tm


title: K8-HS142_stage-tm_rep2


title: mammospheres_breast_cancer_cell_line_MDA_rep1


title: A3C

value: Human gingival-derived mesenchymal stem cells

value: donor 1


title: mammospheres_breast_cancer_cell_line MCF7_rep2


title: K8-HS142_stage-t3_rep3

source_name: clone K8-HS142, growth stage t3


title: K8-HS142_stage-t3_rep2


title: K8-HS142_stage-tm_rep3


title: circulating miRNA [37]

description: Sampled 7 days


title: K8-HS142_stage-t0_rep3

source_name: clone K8-HS142, growth stage t0


title: Parr_kidney_2

value: kidney

value: parr

value: immature


title: circulating miRNA [35]

description: Sampled 7 days

value: no irradiation


title: mammospheres_breast_cancer_cell_line_MCF7_rep1


title: K8-HS142_stage-t3_rep1


title: mammospheres_normal_breast_cells_rep2


title: Parr_heart_2

value: heart

value: hatchery

value: Neva


title: circulating miRNA [10]

description: Sampled 7 days


title: circulating miRNA [39]

description: Sampled 7 days


title: Parr_liver_2

value: liver

value: normal diet


title: mammospheres_normal_breast_cells_rep1


title: circulating miRNA [33]

description: Sampled 7 days


title: Parr_gonad_2

value: gonad


title: Brn1-6HA No tension IP

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

description: Reads mapped to saCer3 only/calibrated to s.pombe

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 30)
To obtain reads mapping only to sacCer3;
ChIP-Seq reads were first mapped with bwa (aln/samse) to pombe
Unmapped pombe reads were filtered using samtools
Unmapped pombe reads were then mapped to sacCer3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads)
chrMito was excluded using bedtools
To obtain reads mapping only to Pombe;
Reads were also mapped to sacCer3
Unmapped sacCer3 reads were filtered using samtools
Unmapped sacCer3 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization)
Genome_build: SacCer3, pombe ASM294v2.22
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to sacCer3 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (sacCer3))  calibrated sacCer3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: S. cerevisiae/S. pombe cells

growth_protocol: Cells were diluted to OD(600)=0.2 and arrested G1 with alpha factor for 3 hours, then released into a metaphase arrest by depletion of Cdc20 for 2 hours. "No tension" condition included addition of nocodazole and benomyl, "Tension" condition did not.

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds three times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with Roche 12CA5 anti-HA antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

treatment_protocol: Cells were fixed in 1% formaldehyde for 30 minutes before washing twice in TBS and once in FA lysis buffer with 0.1% SDS.

tag: chip antibody

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Scc1-6HA/Rad21-6HA

tag: target

tag: cell cycle stage

value: Metaphase

tag: tension/no tension

value: No tension (Nocodazole treatment)

tag: strain

value: Wild type Brn1-6HA


title: Parr_gill_2

tag: tissue

value: gill

tag: Sex

value: M

tag: developmental stage

tag: maturity stage

tag: habitat


title: Scc1-6HA No tension IP

description: Reads mapped to sacCer3 only/calibrated to S.pombe

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 65)
To obtain reads mapping only to sacCer3;
ChIP-Seq reads were first mapped with MiniMap2 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools
Unmapped pombe reads were then mapped to sacCer3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads)
chrMito was excluded using bedtools
To obtain reads mapping only to Pombe;
Reads were also mapped to sacCer3
Unmapped sacCer3 reads were filtered using samtools
Unmapped sacCer3 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Genome_build: sacCer3 + s.pombe ASM294v2.22
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to sacCer3 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (sacCer3)), calibrated sacCer3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

value: No tension (Nocodazol treatment)

value: WT


title: Scc1-6HA No tension Input

description: Reads mapped to sacCer3 only


title: Parr_eye_2

value: eye

value: parr

tag: population origin

tag: diet


title: Parr_brain_2

value: brain

value: immature


title: circulating miRNA [40]

description: Sampled 7 days

tag: protocols

value: no irradiation


title: Brn1-6HA No tension Input

description: Reads mapped to sacCer3 only


title: circulating miRNA [42]

description: Sampled 7 days


title: Violet-de-Rennes_stage-tm_rep1

source_name: clone Violet-de-Rennes, growth stage tm

value: Violet-de-Rennes

value: tm


title: K8-HS142_stage-t0_rep2


title: Violet-de-Rennes_stage-t3_rep3

source_name: clone Violet-de-Rennes, growth stage t3


title: circulating miRNA [49]

description: Sampled 7 days


title: circulating miRNA [26]

description: Sampled 7 days


title: Sgo1-6HA No tension IP

description: Reads mapped to sacCer3 only/calibrated to s.pombe

value: Wild type Sgo1-6HA


title: K8-HS142_stage-t0_rep1


title: Violet-de-Rennes_stage-tm_rep3


title: Violet-de-Rennes_stage-t0_rep3

source_name: clone Violet-de-Rennes, growth stage t0


title: Violet-de-Rennes_stage-t3_rep2


title: Scc1-6HA MED2-pURA3-URA3-PTC1 Input

description: Reads mapped to sacCer3 only

value: URA3 casette


title: Scc1-6HA MED2-pURA3-URA3-PTC1 IP

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Scc1-6HA/Rad21-6HA


title: Parr_skin_1

value: skin

value: hatchery

value: Neva

value: normal diet


title: Violet-de-Rennes_stage-tm_rep2


title: Parr_muscle_1

value: muscle

value: M


title: M_05_7d_500: Rv2549

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

country: USA

institute: Scitovation, LLC.

description: Rats were gavaged daily with acetamide in water vehicle

data_processing:
Illumina NextSeq 500 control software v2.1.0 with BCL files uploaded to Illumina BaseSpace for FASTQ file generation
Sequences trimmed from both based on QC (TRIMMOMATIC, min. retained read length 50bp), and mapped to Illumina iGenomes UCSC Rn6 using BOWTIE2
SAM files to BAM, and gene counts extracted from BAM files with HTSeq
Genome_build: UCSC Rn6 (Illumina iGenomes)
Supplementary_files_format_and_content: Tab delimited text files of gene counts

organism: Rattus norvegicus

source_name: Liver (left lobe)

extract_protocol:
Total RNA was isolated using the Maxwell RSC Simply RNA Tissue Kit (Promega, Cat No: AS1340).
Library preparation was accomplished using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, CatNo: RS-122-2103)

treatment_protocol: Rat were gavaged daily with water vehicle or acetamide, and the left lobe of the liver collected (at 7 or 28 days) for RNA-seq analysis.

value: Liver (left lobe)

value: Male

tag: age

tag: age unit

value: weeks

tag: treatment

value: Acetamide

tag: treatment cas

tag: dose

tag: dose unit

value: mg/kg/day

tag: treatment duration

tag: duration unit

value: days

tag: replicate

tag: exposure series

value: Exposure Experiment 2


title: circulating miRNA [64]

description: Sampled 7 days

value: no irradiation


title: circulating miRNA [34]

description: Sampled 7 days


title: Violet-de-Rennes_stage-t0_rep2

tag: clone

value: Violet-de-Rennes

tag: growth stage


title: circulating miRNA [59]

description: Sampled 7 days


title: Scc1-6HA PTC1-pURA3-URA3-MED2 IP

tag: chip antibody

tag: target

tag: cell cycle stage

value: Metaphase

tag: tension/no tension

value: No tension (Nocodazole treatment)

tag: strain

value: URA3 casette


title: Scc1-6HA PTC1-pURA3-URA3-MED2 Input

description: Reads mapped to sacCer3 only

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Scc1-6HA/Rad21-6HA


title: Violet-de-Rennes_stage-t3_rep1


title: Parr_liver_1

tag: tissue

value: liver

tag: Sex

tag: developmental stage

value: parr

tag: maturity stage

value: immature

tag: habitat

value: hatchery

tag: population origin

value: Neva

tag: diet


title: Scc1-6HA chl4Δ No tension IP

description:
3950_NT_IP_S4
Reads mapped to sacCer3 only/calibrated to S.pombe

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds three times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with Roche 12CA5 anti-HA antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.
ChIP-seq, barcoded

tag: treatment

tag: genotype

value: chl4 delete


title: Violet-de-Rennes_stage-t0_rep1


title: Parr_adipose tissue_2

value: adipose

value: M

value: normal diet


title: circulating miRNA [54]

description: Sampled 7 days

tag: protocols


title: Scc1-6HA chl4Δ Tension IP

description:
3950_T_IP_S3
Reads mapped to sacCer3 only/calibrated to S.pombe

value: Tension


title: circulating miRNA [41]

description: Sampled 7 days


title: Parr_heart_1

value: heart


title: Scc1-6HA chl4Δ No tension input

description:
3950_NT_input_S2
Reads mapped to sacCer3 only


title: Scc1-6HA chl4Δ Tension input

description:
3950_T_input_S1
Reads mapped to sacCer3 only


title: circulating miRNA [52]

description: Sampled 7 days

value: no irradiation


title: circulating miRNA [24]

description: Sampled 7 days


title: Parr_gill_1

value: gill


title: circulating miRNA [68]

description: Sampled 7 days


title: Parr_kidney_1

value: kidney


title: Parr_gonad_1

value: gonad


title: circulating miRNA [32]

description: Sampled 7 days


title: 1.8 M NaCl rep3

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

country: Germany

institute: Technische Universtität Braunschweig

description: 1.8 M_3

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Priestia megaterium DSM 319

source_name: DSM319, wt, grown at 1.8 M NaCl

label_protocol: RNA samples were labelled with Cy3 (stressed cells) and Cy5 (control) using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: Strains were aerobically grown at 37 °C om baffeled flasks in modified M9 minimal medium derived from Harwood and Cutting (Harwood and Cutting 1990) containing 5 g L-1 of glucose, 1 g L-1 of NH4Cl, 3 g L-1 of KH2PO4, 0.5 g L-1 NaCl, 6.7 g L-1 of Na2HPO4, 1 mg L-1 of MnCl2·4 H2O, 1.7 mg L-1 of ZnCl2, 430 µg L-1 of CuCl2·2 H2O, 328 µg L-1 of CoCl2, 600 µg L-1 of NaMoO4·2 H2O, 11.1 mg L-1 of CaCl2, 30 mg L-1 of 3,4-DHB, 13.5 mg L-1 of FeCl3 and 120 mg L-1 of MgSO4. In addition, up to 1.8 M NaCl was additionally supplemented to this medium where indicated.

extract_protocol: RNA extraction and purification were carried out following the protocols proposed by Biedendieck et al. (Biedendieck et al. 2011; Systems biology of recombinant protein production using Bacillus megaterium. Methods Enzymol 500:165-195)

treatment_protocol: Growth took place at 230 min-1 (Multitron, Infors AG, Bottmingen, Switzerland – 5 cm shaking diameter), Samples for transcriptome analyses were taken at an OD of 4 (exponential phase)

tag: salt stress

value: 1.8 M NaCl

source_name: DSM319, wt, grown without additional NaCl

tag: growth condition

value: control, without additional salt


title: 1.8 M NaCl rep4

description: 1.8 M_4


title: Parr_adipose fin_1

source_name: Atlantic salmon developmental stages

value: adipose fin


title: Scc1-6HA WT No tension IP

description:
1105_NT_IP_S4
Reads mapped to sacCer3 only/calibrated to S.pombe

tag: chip antibody

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Scc1-6HA/Rad21-6HA

value: Metaphase

value: No tension (Nocodazole treatment)

value: WT


title: 1.2 M NaCl rep4

description: 1.2 M_4

source_name: DSM319, wt, grown at 1.2 M NaCl

value: 1.2 M NaCl


title: 1.8 M NaCl rep1

description: 1.8 M_1


title: 1.8 M NaCl rep2

description: 1.8 M_2


title: Scc1-6HA WT Tension IP

description:
1105_T_IP_S3
Reads mapped to sacCer3 only/calibrated to S.pombe

tag: target


title: circulating miRNA [51]

description: Sampled 7 days

source_name: serum


title: 1.2 M NaCl rep3

description: 1.2 M_3


title: circulating miRNA [62]

description: Sampled 7 days


title: Parr_tail fin_1

value: tail fin

value: parr

value: immature

value: hatchery

value: Neva


title: Parr_eye_1

value: eye

value: M

value: normal diet


title: Parr_adipose tissue_1

value: adipose


title: Scc1-6HA WT No tension input

description:
1105_NT_input_S2
Reads mapped to sacCer3 only

tag: cell cycle stage


title: Scc1-6HA WT Tension input

description:
1105_T_input_S1
Reads mapped to sacCer3 only

value: Tension


title: Fry_blood_4

description: N.2212 °d fry.4.Bl

value: blood

value: fry

value: low fat diet


title: circulating miRNA [60]

description: Sampled 7 days

value: no irradiation


title: Brn1-6HIS-3FLAG No tension IP

description:
25379-IP_S4
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Mouse monoclonal M2 anti-FLAG (Sigma) against Brn1-6HIS-3FLAG/Rad21-6HIS-3FLAG

value: Metaphase

value: No tension (Nocodazole treatment)

value: Wild type Brn1-6HIS-3FLAG


title: Parr_brain_1

value: brain

value: parr


title: circulating miRNA [SE1S3]

description:
Sampled 7 days after 20Gy irradiation
SE1S3

value: 20Gy irradiation


title: Brn1-6HIS-3FLAG No tension Input

description:
25379-input_S3
Reads mapped to sacCer3 only


title: 1.2 M NaCl rep1

description: 1.2 M_1

value: 1.2 M NaCl

value: control, without additional salt


title: Sgo1-6HIS-3FLAG No tension Input

description:
25409-input_S3
Reads mapped to sacCer3 only

value: Wild type Sgo1-6HIS-3FLAG


title: circulating miRNA [65]

description: Sampled 7 days


title: circulating miRNA [BM2S3]

description:
Sampled 7 days after 20Gy irradiation
BM2S3


title: Fry_blood_3

description: N.2212 °d fry.3.Bl

value: immature

value: hatchery

value: Neva


title: Sgo1-6HIS-3FLAG No tension IP

description:
25409-IP_S4
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Mouse monoclonal M2 anti-FLAG (Sigma) against Sgo1-6HIS-3FLAG/Rad21-6HIS-3FLAG


title: Fry_blood_2

description: N.2212 °d fry.2.Bl

value: blood

value: fry

value: normal diet


title: 0.6 M NaCl rep3

description: 0.6 M_3

source_name: DSM319, wt, grown at 0.6 M NaCl

value: 0.6 M NaCl


title: 1.2 M NaCl rep2

description: 1.2 M_2


title: 0.6 M NaCl rep4

description: 0.6 M_4


title: 0.6 M NaCl rep2

description: 0.6 M_2


title: 0.6 M NaCl rep1

description: 0.6 M_1


title: circulating miRNA [GJ1S3]

description:
Sampled 7 days after 20Gy irradiation
GJ1S3


title: Whole fry_6

description: N.1320 °d fry.4

value: whole fry

value: low fat diet


title: circulating miRNA [SJ1S3]

description:
Sampled 7 days after 20Gy irradiation
SJ1S3


title: circulating miRNA [WJ1S3]

description:
Sampled 7 days after 20Gy irradiation
WJ1S3


title: Brn1-6HIS-3FLAG Reoriented No tension Input

description:
25299-input_S1
Reads mapped to sacCer3 only

value: Metaphase

value: No tension (Nocodazole treatment)

value: Reoriented borders


title: Sgo1-6HIS-3FLAG Reoriented No tension IP

description:
25298-IP_S2
Reads mapped to sacCer3 only/calibrated to S.pombe


title: circulating miRNA [PZ1S3]

description:
Sampled 7 days after 20Gy irradiation
PZ1S3

value: 20Gy irradiation


title: circulating miRNA [KE1S3]

description:
Sampled 7 days after 20Gy irradiation
KE1S3


title: Whole fry_5

description: N.1320 °d fry.3


title: Fry_blood_1

description: N.2212 °d fry.1.Bl


title: Sgo1-6HIS-3FLAG Reoriented No tension Input

description:
25298-input_S1
Reads mapped to sacCer3 only


title: Whole fry_3

description: N.1320 °d fry.1


title: Brn1-6HIS-3FLAG Reoriented No tension IP

description:
25299-IP_S2
Reads mapped to sacCer3 only/calibrated to S.pombe

value: Mouse monoclonal M2 anti-FLAG (Sigma) against Brn1-6HIS-3FLAG/Rad21-6HIS-3FLAG


title: Scc1-6HA Reoriented No tension IP

description:
22078_IP_S4_plus_tension
Reads mapped to sacCer3 only/calibrated to S.pombe

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Scc1-6HA/Rad21-6HA


title: Whole fry_4

description: N.1320 °d fry.2


title: circulating miRNA [PW1S3]

description:
Sampled 7 days after 20Gy irradiation
PW1S3


title: Whole fry_2

description: N.1119 °d fry.2


title: Whole fry_1

description: N.1119 °d fry.1


title: Scc1-6HA Reoriented Tension IP

description:
22078_IP_S2_plus_tension
Reads mapped to sacCer3 only/calibrated to S.pombe

value: Tension


title: circulating miRNA [PJ2S3]

description:
Sampled 7 days after 20Gy irradiation
PJ2S3


title: Scc1-6HA Reoriented No tension Input

description:
22078_input_S3_no_tension
Reads mapped to sacCer3 only


title: C3

type: genomic

city: Legnaro

first: Ginevra

last: Brocca

state: PD

address: Viale dell'Università 16

department: BCA

institute: University of Padova

description: Biological replicate 18

hyb_protocol: Oligo aCGH analysis was performed following the manufacturer’s recommendations, using  Oligo aCGH/ChIP-on-chip Hybridization Kit.

scan_protocol: Arrays were scanned at 3 µm resolution using an Agilent G2565CA scanner, and image data were processed using Feature Extraction version 11.5.

data_processing: Genomic Workbench version 7.0 was employed for data analysis, raw data were normalized using the centralization algorithm with a threshold of eight. Aberration filter was set as a minimum number of probes for amplification and deletion greater or equal to 3.

organism: Canis lupus familiaris

source_name: COM

label_protocol: Tumor and reference DNA samples were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively, using SureTag Complete DNA Labeling Kit.

extract_protocol: Genomic DNA was extracted from FFPE tumor sample and coexisting helthy tissue using the All-Prep DNA-RNA FFPE KIT (Qiagen®) according to the manufacturer's instructions.

value: tumor

source_name: normal

value: adjacent healthy tissue


title: C7

description: Biological replicate 19


title: C13

description: Biological replicate 17


title: C12

description: Biological replicate 16


title: Scc1-6HA Reoriented Tension Input

description:
22078_input_S1_plus_tension
Reads mapped to sacCer3 only


title: circulating miRNA [PJ1S3]

description:
Sampled 7 days after 20Gy irradiation
PJ1S3


title: C11

description: Biological replicate 15


title: Whole alevin_4

description: N.436 °d alevin.4

value: whole alevin

value: alevin

value: immature

value: hatchery

value: Neva


title: C1

description: Biological replicate 13


title: circulating miRNA [PC1S3]

description:
Sampled 7 days after 20Gy irradiation
PC1S3


title: B25

description: Biological replicate 12


title: circulating miRNA [LG1S3]

description:
Sampled 7 days after 20Gy irradiation
LG1S3


title: Scc1-6HA rad61Δ No tension IP

description:
26966_NT_IP_S4
Reads mapped to sacCer3 only/calibrated to S.pombe

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 30)
To obtain reads mapping only to sacCer3;
ChIP-Seq reads were first mapped with MiniMap2 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools
Unmapped pombe reads were then mapped to sacCer3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads)
chrMito was excluded using bedtools
To obtain reads mapping only to Pombe;
Reads were also mapped to sacCer3
Unmapped sacCer3 reads were filtered using samtools
Unmapped sacCer3 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Genome_build: sacCer3 + s.pombe ASM294v2.22
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to sacCer3 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (sacCer3)), calibrated sacCer3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

value: No tension (Nocodazol treatment)

value: rad61 delete


title: Whole alevin_3

description: N.436 °d alevin.3


title: circulating miRNA [DW1S3]

description:
Sampled 7 days after 20Gy irradiation
DW1S3


title: circulating miRNA [BW1S3]

description:
Sampled 7 days after 20Gy irradiation
BW1S3


title: Scc1-6HA rad61Δ Tension IP

description:
26966_T_IP_S3
Reads mapped to sacCer3 only/calibrated to S.pombe


title: Whole alevin_2

description: N.436 °d alevin.2


title: Whole alevin_1

description: N.436 °d alevin.1


title: Whole 258 °d embryo_4

description: N.258 °d embryo.4

value: whole embryo

value: 258 d embryo


title: Scc1-6HA rad61Δ No tension input

description:
26966_NT_input_S2
Reads mapped to sacCer3 only

value: Metaphase


title: circulating miRNA [GA1S3]

description:
Sampled 7 days after 20Gy irradiation
GA1S3


title: Sgo1-6HA No tension Input

description: Reads mapped to sacCer3 only

tag: tension/no tension

value: No tension (Nocodazole treatment)

value: Wild type Sgo1-6HA


title: Whole 258 °d embryo_3

description: N.258 °d embryo.3


title: Parr_pyloric caeca_1

value: pyloric caeca

value: M

value: parr

value: normal diet


title: MuTP05746_rep3

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

description:
total RNA was extracted from mycelia harvested at 12 h after a transfer from glucose into 1% (w/v) soluble corn starch (SCS)
MuTP05746 was constructed by knocking out TP05746 gene in the TPKu70

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of Talaromyces pinophilus wild type strain1-95 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Talaromyces pinophilus

source_name: Mycelium

extract_protocol:
the total RNA was extracted using TRIzol RNA Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
A cDNA library with 100 bp of length was constructed using the extracted total RNA, and assessed with the ABI StepOnePlus Real-Time PCR System and the Agilent 2100 Bioanalyzer. The eligible cDNA library was sequenced via the Illumina HiSeq 4000 system

tag: strain

value: TP05746 TpKu70 double KO


title: Scc1-6HA rad61Δ Tension input

description:
26966_T_input_S1
Reads mapped to sacCer3 only

value: Tension


title: A8

description: Biological replicate 10

tag: tissue

value: tumor

value: adjacent healthy tissue


title: A5

description: Biological replicate 9


title: B23

description: Biological replicate 11


title: A35

description: Biological replicate 8


title: circulating miRNA [MG1S3]

description:
Sampled 7 days after 20Gy irradiation
MG1S3

value: 20Gy irradiation


title: circulating miRNA [KM1S3]

description:
Sampled 7 days after 20Gy irradiation
KM1S3


title: MuTPKu70_rep3

description:
total RNA was extracted from mycelia harvested at 12 h after a transfer from glucose into 1% (w/v) soluble corn starch (SCS)
TPKu70 was constructed by knocking out TpKu70 gene in strain 1-95

value: TpKu70 KO


title: MuTP05746_rep1

growth_protocol: mycelia harvested at 12 h after a transfer from glucose into 1% (w/v) soluble corn starch (SCS)


title: MuTP05746_rep2


title: C10

description: Biological replicate 14


title: circulating miRNA [ZR1S3]

description:
Sampled 7 days after 20Gy irradiation
ZR1S3


title: MuTPKu70_rep2


title: MuTPKu70_rep1


title: Parr_spleen_1

value: spleen

tag: Sex

value: immature

value: hatchery

value: Neva


title: Whole 186 °d embryo_3

description: N.186 °d embryo.3

value: whole embryo

tag: developmental stage

value: 186 d embryo


title: Whole 186 °d embryo_4

description: N.186 °d embryo.4

tag: maturity stage


title: Whole 258 °d embryo_1

description: N.258 °d embryo.1

value: 258 d embryo

tag: habitat


title: Whole 258 °d embryo_2

description: N.258 °d embryo.2

tag: population origin


title: Whole 186 °d embryo_1

description: N.186 °d embryo.1

tag: diet


title: A34

description: Biological replicate 7


title: circulating miRNA [BM1S3]

description:
Sampled 7 days after 20Gy irradiation
BM1S3


title: A31

description: Biological replicate 6


title: A3

description: Biological replicate 5


title: A24

description: Biological replicate 2


title: A29

description: Biological replicate 4


title: A28

description: Biological replicate 3


title: circulating miRNA [RW1S3]

description:
Sampled 7 days after 20Gy irradiation
RW1S3


title: WTCHG_233110

status: Public on Jan 12 2020

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were mapped to the mouse genome (mm10, Genome Reference Consortium GRCm38) or to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated for the murine and human samples.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files contain htseq counts for each sample

extract_protocol:
Total RNA was extracted from frozen murine tumors and non-diseased omenta. The samples were transferred into RNAlater and homogenized with Miltenyi GentleMACS in RLT buffer and further processed using Qiagen RNeasy Mini kit with on-column DNAse digestion.
Library preparation and RNASeq were performed by the Wellcome Trust Oxford Genomics Centre (Oxford, UK) using RiboZero to deplete rRNA species.

tag: tissue type

value: ovarian tumour


title: WTCHG_230169


title: WTCHG_231181


title: WTCHG_205143


title: WTCHG_235134


title: WTCHG_238170


title: WTCHG_236146


title: WTCHG_295177


title: Whole 186 °d embryo_2

description: N.186 °d embryo.2


title: WTCHG_294165


title: WTCHG_234122


title: WTCHG_232193


title: WTCHG_240194


title: WTCHG_204155


title: WTCHG_228145


title: A1

description: Biological replicate 1


title: WTCHG_229157


title: WTCHG_201191

value: Normal Adipose


title: WTCHG_202179


title: WTCHG_207119


title: WTCHG_226121


title: WTCHG_257189


title: WTCHG_227133


title: WTCHG_254130


title: WTCHG_255118


title: WTCHG_206131


title: WTCHG_253142


title: WTCHG_252154


title: WTCHG_240108


title: WTCHG_259165


title: WTCHG_258177


title: WTCHG_203167


title: WTCHG_237158


title: WTCHG_260153


title: WTCHG_256106


title: siNTC_96hr_ER

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: ER ChIP-seq

data_processing:
Reads were aligned using Bowtie with the parameters: -m 1  -t –best -q -S -l 32 -e 80 -n 2
Peaks were called using MACS2 with a p-value cutoff of 1e-10 and the mfold parameter constrained between 15 and 100.
To determine read depth of peaks called, bedtools coverage was used to calculate the counts
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph, narrowpeaks

source_name: Endometrioid adenocarcinoma cell line

growth_protocol: Ishikawa cells (Sigma-Aldrich) were grown in full media (RPMI-1640 (Gibco), 10% fetal bovine serum (Gibco), and 1% penicillin-streptomycin (Gibco)).  Five days prior to induction, cells were moved to hormone-depleted media with phenol-red free RPMI-1640(Gibco), 10% charcoal-dextran treated fetal bovine serum (Sigma-Aldrich), and 1% penicillin-streptomycin(Gibco).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Crosslinking was stopped with 125mM Glycine and cells were washed and scraped in cold PBS. IP was done as described in Reddy et al 2009 using Santa Cruz ERα (HC-20) or Millipore ERα (06-935)
TruSeq library construction as described in Reddy et al 2009

treatment_protocol: Inductions involved treating cells with 10nM E2 (Sigma-Aldrich) for 1 hour. siRNAs were transfected either 72 or 96 hours before harvest.

tag: cell line

value: Ishikawa

value: Santa Cruz ERalpha (HC-20)

tag: treatment

value: 1 hr 10nM E2 and 96 hours non-targeting siRNA


title: siETV4_96hr_ER

description: ER ChIP-seq

value: 1 hr 10nM E2 and 96 hours ETV4 targeting siRNA


title: WTCHG_249190


title: WTCHG_251166


title: ph_RNAi_rep3

city: Montpellier

first: Vincent

last: Loubiere

state: FRANCE

address: 141 rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: UMR9002; CNRS-UM

data_processing:
After initial quality checks using fastqc, reads were aligned to the dm6 version (dmel_r6.15 annotation) of the Drosophila genome using STAR with default parameters (v2.4.0i). Then, the reads were counted using htseq-count and the differential expression analysis was performed using the “DESeq2” R package (v1.22.1).
genome build: dm6
Ouput file of differential expression analysis using the DESeq2 R package. 8 Columns: FBgn (FlyBase Gene ID); Symbol; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj. bw files correpond to the merged (4 replicates) RPKM-normalized bigwig binary files (10bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software.

organism: Drosophila melanogaster

source_name: ph RNAi ED from L3 wandering larvae (BL 64095 x VDRC50028)

extract_protocol:
About 150 ED were dissected from wandering larvae on ice and total RNA was extracted using TRIZOL reagent. Total RNA was purified using the RNeasy Mini Kit (Qiagen, 74104).
Poly-A RNAs were selected and libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit from Illumina.

value: ph RNAi

tag: develpmental stage

value: L3 wandering larvae

value: Eye Disc


title: WTCHG_250178


title: AR-V7-30ARD

city: Ann Arbor

first: Steven

last: Kregel

state: MI

address: 1500 E. Medical Center Drive, Room 5320 RCC

department: MCTP

institute: University of Michigan

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression treated with 100nM ARD-61 for 24 hours Clone-4
SI_25139

data_processing:
RNA-seq
Align to GRCh38 using version STAR 2.4.1
Count reads using featureCounts (default settings, strand specific mode)
FPKM - upper quartile normalized using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count

source_name: LNCaP AR-V7

extract_protocol:
cDNA samples were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).
RNA-seq using cDNA based on manufacturer's instructions (Illumina)

value: LNCaP AR-V7

tag: cell type

value: Prostate Adenocarcinoma

tag: passage

value: passage 30-50

tag: time

value: 24 hours


title: ph_RNAi_rep2


title: WTCHG_239120


title: w_RNAi_rep3

source_name: white RNAi ED from L3 wandering larvae (BL 64095 x BL33623)

value: white RNAi


title: ETV4KO1_MilliER_E2

description: ER ChIP-seq

value: Ishikawa ETV4 KO clone 1

tag: chip antibody

value: Millipore ERalpha (06-935)

value: 1 hr 10nM E2


title: WTCHG_247114

value: ovarian tumour


title: WTCHG_244150


title: WTCHG_246126


title: WTCHG_245138


title: w_RNAi_rep2


title: AR-V7-26DMSO

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression DMSO control Clone-3
SI_25136

value: no ARD-61


title: w_RNAi_rep1


title: WTCHG_243162


title: AR-V7-15DMSO

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression DMSO control Clone-2
SI_25134


title: AR-V7-13DMSO

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression DMSO control Clone-1
SI_25132


title: LNCaP EnzR 24h 100nM ARD 61b-3

description:
LNCaP 20uM enzalutamide Resistant Cells Treated immediately with 100nM ARD61b for 24 hours replicate 3
SI_22535

source_name: LNCaP-EnzR

value: LNCaP-EnzR


title: WTCHG_240103

value: Adjacent/Normal Adipose


title: WTCHG_242174


title: WTCHG_241186


title: LNCaP EnzR 24h 100nM ARD 61b-2

description:
LNCaP 20uM enzalutamide Resistant Cells Treated immediately with 100nM ARD61b for 24 hours replicate 2
SI_22534


title: siNTC_72hr_ER

description: ER ChIP-seq

value: Ishikawa

value: Santa Cruz ERalpha (HC-20)

value: 1 hr 10nM E2 and 72 hours non-targeting siRNA


title: ETV4KO2_MilliER_E2

description: ER ChIP-seq

value: Ishikawa ETV4 KO clone 2


title: HiC_ED_rep3_b

description:
processed data file: HiC_ED_scores.tar.gz
run2

data_processing:
Raw Hi-C sequencing data were processed using the “scHiC2” pipeline (Nagano et al., 2017). Construction of expected models, Hi-C contact scoring and Hi-C aggregate plots was performed using the “shaman” R package (https://bitbucket.org/tanaylab/shaman, Cohen et al., bioRxiv, 2017). Hi-C map visualization, segmented interaction frequencies and downstream analyses were conducted using in-house R scripts using the “misha” package (https://github.com/msauria/misha-package).
Raw sequencing data were processed using the HiC-Pro pipeline (version 2.11.1, REF: 26619908) with default parameters and the dm6 reference genome. Resulting raw data were normalized at 2, 5 and 10kb resolutions using the ice_norm flag. In parallel, the hicpro2juicebox utility was used to convert the allValidPairs output of the pipeline into the Juicebox .hic format at fragment resolution.
Supplementary_files_format_and_content:
bw files correpond to the merged (2 replicates) RPKM-normalized bigwig binary files (10bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software. NarrowPeak files correpond to the peaks that were called using the MACS2 software on separated replicates and on the merged replicates (10 columns: chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak). Summit file contains the summits of the peaks called from the merged replicates.
Compressed HiC tracks; Binary files of intrachromosomal pairwise interaction probabilities (score) computed using the "shaman" package in R.
Ouput file of differential expression analysis using the DESeq2 R package. 8 Columns: FBgn (FlyBase Gene ID); Symbol; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj.
The .hic binary files can be visualized using Juicer (https://github.com/aidenlab/juicer). The bins_ids.bed, iced.matrix.biases and iced.matrix files contain the genomic coordinates of the bins, the bin bias used to normalize the observed data and the normalized HiC matrices in plain text format, respectively.
Genome_build: dm6

extract_protocol:
Hi-C experiments from EDs and 16-18h embryos were conducted as previously described in Ogiyama, et al. 2018. For larval Hi-C triplicates, ~200 EDs were quickly dissected (<1h) from wandering larvae at R.T in Schneider’s insect medium before being directly processed. Briefly, formaldehyde was added to reach a 2% final concentration and the samples were homogenized for 3 minutes using a tight tenbrock at R.T and transferred on a rotating wheel (total time for fixation is 10min). Then, cell membrane was lysed on ice and nuclei were subjected to DpnII treatment O/N at 37°C. The next day, restriction sites were end-repaired and biotinylated using Klenow (NEB, M0210) and biotin-14-dATP (Life Tech., 19524-016) before being re-ligated in situ using T4 DNA ligase (NEB, M0202). Then, proteins were degraded with proteinase K before O/N de-crosslinking at 68°C and subsequent DNA purification using Phenol/chloroform and ethanol precipitation. Purified DNA was sheared with a LE220 Covaris sonicator (volume: 130µl, fill lvl: 10, duty cycle: 15, PIP: 500, cycles/burst: 200, time: 58s). Finally, sonication efficiency was checked on an agarose gel.
DNA fragments were size-selected using AMPure XP beads (300-500bp), and ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (Life Technologies, 65602). Biotin was removed from unligated ends, and pulled-down DNA fragments were end-repaired and a-tailed before NEXTflex (Bioo Scientific, 514101) adaptors ligation. Finally, libraries were PCR amplified (10-12 cycles) using NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs, M0544L) and DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.

value: W1118 Oregon-R

value: L3 wandering larvae

value: Eye Disc


title: LNCaP EnzR Cntl(w/MDV)-3

description:
LNCaP 20uM enzalutamide-Resistant Cells with 20uM enzalutamide replicate 3
SI_22526

value: Prostate Adenocarcinoma

value: passage 30-50


title: HiC_ED_rep2_a

description:
processed data file: HiC_ED_scores.tar.gz
run1


title: WTIshikawa_MilliER_E2

description: ER ChIP-seq


title: AR-V7-26ARD

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression treated with 100nM ARD-61 for 24 hours Clone-3
SI_25137

value: LNCaP AR-V7

value: 24 hours


title: ph_RNAi_rep4

value: ph RNAi


title: LNCap p.11 100nm ARD-61b 24h -2

description:
LNCaP Treated with 100nM ARD-61b Degrader for 24 hours replicate 2
SI_21511

source_name: LNCaP

value: LNCaP


title: AR-V7-13ARD

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression treated with 100nM ARD-61 for 24 hours Clone-1
SI_25133


title: w_RNAi_rep4

value: white RNAi


title: LNCaP p.11 DMSO 24h -3

description:
LNCaP Parental Cells Treated with DMSO Control for 24 hours replicate 3
SI_21488

value: no ARD-61


title: HiC_E1618_rep1_a

value: Whole 16-18h embryo

value: whole embryo


title: AR-V7-15ARD

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression treated with 100nM ARD-61 for 24 hours Clone-2
SI_25135


title: AR-V7-30DMSO

description:
LNCaP single cell clonal populations of Crispr-induced AR-V7 expression DMSO control Clone-4
SI_25138


title: siETV4_72hr_ER

description: ER ChIP-seq

value: Ishikawa

value: 1 hr 10nM E2 and 72 hours ETV4 targeting siRNA


title: Mutant_PcXT109_FRT2A_rep2

description: processed data file:FC_PcXT109.txt

data_processing:
After initial quality checks using fastqc, reads were aligned to the dm6 version (dmel_r6.15 annotation) of the Drosophila genome using STAR with default parameters (v2.4.0i). Then, the reads were counted using htseq-count and the differential expression analysis was performed using the “DESeq2” R package (v1.22.1).
Supplementary_files_format_and_content:
bw files correpond to the merged (2 replicates) RPKM-normalized bigwig binary files (10bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software. NarrowPeak files correpond to the peaks that were called using the MACS2 software on separated replicates and on the merged replicates (10 columns: chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak). Summit file contains the summits of the peaks called from the merged replicates.
Compressed HiC tracks; Binary files of intrachromosomal pairwise interaction probabilities (score) computed using the "shaman" package in R.
Ouput file of differential expression analysis using the DESeq2 R package. 8 Columns: FBgn (FlyBase Gene ID); Symbol; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj.
Genome_build: dm6

value: PCxt109 mutant


title: ChIP_SUZ12_ED_rep2

data_processing:
After initial quality checks using fastqc, paired-end and single-end .fastq files were aligned to the dm6 version of the Drosophila genome using bowtie 2 with default parameters (v2.1.0). Reads with low mapping quality (mapq<30) were discarded using samtools. Peak calling was performed on each replicate separately and on the merged replicates using MACS2 (v2.1.1.20160309) with the following parameters: -g dm --nomodel --keep-dup 1 --extsize 200. For the visualization and the quantification of ChIP-Seq tracks, RPKM-normalized bigwig binary files were generated using the bamCoverage function from Deeptools2 (v2.5.1) with the following parameters: -of=bigwig --samFlagExclude 128 --ignoreDuplicates -e 200 –normalizeUsingRPKM. Finally, replicates were merged using the bigWigMerge and bedGraphToBigWig tools from UCSC with default parameters.
Supplementary_files_format_and_content:
bw files correpond to the merged (2 replicates) RPKM-normalized bigwig binary files (10bp bins), which can be visualized using the Integrative Genomics Viewer (IGV) software. NarrowPeak files correpond to the peaks that were called using the MACS2 software on separated replicates and on the merged replicates (10 columns: chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak). Summit file contains the summits of the peaks called from the merged replicates.
Compressed HiC tracks; Binary files of intrachromosomal pairwise interaction probabilities (score) computed using the "shaman" package in R.
Ouput file of differential expression analysis using the DESeq2 R package. 8 Columns: FBgn (FlyBase Gene ID); Symbol; baseMean; log2FoldChange; lfcSE; stat; pvalue; padj.
Genome_build: dm6

extract_protocol:
ChIP from ED or whole 14-16h embryos were performed in duplicate as previously described in Loubiere et al., 2016. Briefly, ~200 ED from wandering larvae were used per replicate for PTM ChIP-Seq and ~500 for PSC and SU(Z)12 ChIP-Seq. For each replicate of PTM ChIP-Seq from 14-16h embryos, 2h collections were performed at 25°C with about 500 flies. When necessary, several batches of dissection/collection were snap-frozen in liquid nitrogen and stored at -80°C in order to collect enough material. Samples were then transferred into a tight Tenbrock and cross-linked for 15min at RT using 1.8% formaldehyde and continuous homogenization before being lysed on ice for 2h with 1% SDS Lysis Buffer 2 (see Loubiere et al., 2016). Chromatin was sonicated using a Bioruptor (Diagenode) for 18 cycles (settings 30s ON, 30s OFF, high power) and the quality of the sonication was checked on a 1.5% agarose gel (~300bp fragments). Then, samples were pre-cleared O/N using 15µL of protein A Dynabeads (ThermoFisher Scientific, 10001D) at 4°C and an aliquot was kept apart to constitute the INPUT. Antibodies were added (see Supplementary Table 7) 4h prior to the addition of 30µL of protein A dynabeads and O/N incubation at 4°C. Finally, beads were washed, and the precipitated chromatin was eluted before O/N decrosslinking at 65°C, Proteinase K treatment, Phenol/Chloroform purification and O/N ethanol precipitation.
Libraries were prepared using the TruSeq ChIP Sample Preparation kit from Illumina, following manufacturers’ instructions.

value: SU(Z)12 Ab (Polyclonal Rabbit, Loubiere et al., 2016)


title: ph_RNAi_rep1


title: LNCaP EnzR 24h 100nM ARD 61b-1

description:
LNCaP 20uM enzalutamide Resistant Cells Treated immediately with 100nM ARD61b for 24 hours replicate 1
SI_22533

value: LNCaP-EnzR


title: HiC_ED_rep3_a

value: W1118 Oregon-R

value: L3 wandering larvae


title: HiC_ED_rep2_b

value: Eye Disc


title: ChIP_INPUT_E1416_rep2

value: Whole 14-16h embryo

value: No Ab


title: LNCaP EnzR Cntl(w/MDV)-1

description:
LNCaP 20uM enzalutamide-Resistant Cells with 20uM enzalutamide replicate 1
SI_22524

value: Prostate Adenocarcinoma

value: passage 30-50

value: 24 hours


title: HiC_ED_rep1_b


title: Mutant_PcXT109_FRT2A_rep1


title: ChIP_INPUT_E1416_rep1


title: LNCap p.11 100nm ARD-61b 24h -3

description:
LNCaP Treated with 100nM ARD-61b Degrader for 24 hours replicate 3
SI_21512

value: LNCaP


title: HiC_ED_rep1_a


title: fog1_XX_youngadult_rep1

city: New York

first: Sarah

middle: Elizabeth

last: Albritton

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

description: mRNA-seq

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.0.12 using default parameters, specifying first strand alignment.
In parallel, resultant RNA-seq bam files were used to estimate transcript abundancies using cuffllinks version 2.2.0.
In parallel, resultant RNA-seq bam files were converted to sam files using samtools version 1.2. Sam files were used to generate count data using htseq-cout version 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: genes.fpkm_tracking files were generated using cufflinks version 2.2.0. This file contains the estimated gene-level expression values in the generic FPKM tracking format.
Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1. Files are in .txt format and contain 2 columns: (1) GeneName (2) Counts. Counts are not yet normalized.

organism: Caenorhabditis elegans

source_name: whole worms, XX

growth_protocol: Fog-1(q253)ts were maintained on NGM plates at 25C prior to collection/dissection.

extract_protocol:
Total RNA isolation protocol: Ten volumes of Trizol was added to worm collections. Total RNA was extracted by freeze cracking the samples (briefly, samples were flash frozen in liquid nitrogen and then thawed by placing in a 37C water bath) 3-5 times. Total RNA was isolated according to the manufacturer's (Invitrogen) Trizol protocol. Purified Total RNA was cleaned up on a Qiagen RNeasy column.
cDNA Synthesis Protocol: mRNA was isolated from 500ng-10ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). As in staging protocol: worms were synchronized by bleaching gravid adults from male-heavy plates. At least 750 young adult worms were hand picked for each replicate.  RNA isolation protocol: RNA was extracted by freeze cracking embryos by freezing in liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA was cleaned up through Qiagen RNeasy column.  cDNA synthesis protocol: mRNA was purified from 5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212, cDNA synthesis was performed in the presence of dUTP in order to prepare stranded mRNA-seq libraries.
cDNA was ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol:
Whole worms: At least 600 young adult worms were hand picked per replicate. Worms were picked directly into 1X M9. Ten volumes of Trizol was added. Samples were stored at -80C prior to Total RNA extraction.
Gonads: Gonadal tissue was dissected from young adult worms. At least 200 gonads were dissected per sample. Gonads were placed directly into 1X M9. Ten volumes of Trizol was added. Samples were stored at -80C prior to Total RNA extraction.

tag: strain/background

tag: genotype/variation

value: XX

value: young adult

value: whole body


title: HiC_E1618_rep1_b

description:
processed data file: HiC_E1618_scores.tar.gz
run2

tag: strain

value: Whole 16-18h embryo

tag: tissue

value: whole embryo


title: LNCap p.11 100nm ARD-61b 24h -1

description:
LNCaP Treated with 100nM ARD-61b Degrader for 24 hours replicate 1
SI_21510


title: fog1_XO_youngadult_rep2

description: mRNA-seq

source_name: whole worms, XO

value: XO

tag: developmental stage


title: LNCaP EnzR Cntl(w/MDV)-2

description:
LNCaP 20uM enzalutamide-Resistant Cells with 20uM enzalutamide replicate 2
SI_22525

value: no ARD-61


title: ChIP_PSC_ED_rep1

value: PSC Ab (Polyclonal Rabbit, Strutt et al., 1997)


title: ChIP_INPUTv_ED_rep1

value: W1118 Oregon-R


title: LNCaP p.11 DMSO 24h -2

description:
LNCaP Parental Cells Treated with DMSO Control for 24 hours replicate 2
SI_21487


title: ChIP_SUZ12_ED_rep1

value: L3 wandering larvae

value: SU(Z)12 Ab (Polyclonal Rabbit, Loubiere et al., 2016)


title: LNCaP p.11 DMSO 24h -1

description:
LNCaP Parental Cells Treated with DMSO Control for 24 hours replicate 1
SI_21486


title: fog1_XO_youngadult_rep1

description: mRNA-seq


title: ChIP_PSC_ED_rep2

value: Eye Disc


title: fog1_XX_dissectedgonad_rep2

description: mRNA-seq

source_name: dissected gonad, XX

value: gonad


title: fog1_XX_dissectedgonad_rep1

description: mRNA-seq


title: VCaP 100nM ARD-61b 6h-3

description:
VCaP Treated with 100nM ARD-61b Degrader for 6 hours replicate 3
SI_21482

source_name: VCaP

value: VCaP

value: Prostate Adenocarcinoma

value: 6 hours


title: 221_LPS_52

city: Basel

first: Diego

last: Kyburz

address: Petersplatz 4

department: Biomedicine

institute: University of Basel

data_processing:
Single-end 81-mers reads were obtained and their quality was assessed with the FastQC tool (version 0.11.3).
Reads were mapped to the human hg38 genome assembly with STAR (version 2.5.2a_modified) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Gene expression was quantified by the qCount function of the R Bioconductor package QuasR (version 1.18) as the number of reads that started within any annotated exon of a gene from the UCSC knownGenes annotation (downloaded on 2017-04-03).
Genome_build: hg38
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Entrez Gene ID, 2. gene length (exon union model), 3.-22. read counts per gene and sample.

source_name: in vitro derived M2 macrophages

growth_protocol: M2-macrophages from 5 HD were cultured in 12 well plates with 540’000 cells/well.

extract_protocol:
Total RNA for the 20 resulting samples was isolated using miRNeasy Micro kit (Qiagen).
RNA quality was assessed with a Fragment Analyzer (Advanced Analytical).
Library preparation was performed using the Illumina Truseq stranded kit.

treatment_protocol: miR-221-3p mimic was added 63.5 hours prior to stimulation with 100 ng/ml LPS for 8.5 hours.

value: M2 macrophages

tag: transfection

value: miR-221 mimic transfection

tag: stimulation

value: LPS-stimulated


title: ChIP_INPUTh_ED_rep1

value: No Ab


title: fog1_XO_dissectedgonad_rep2

description: mRNA-seq

source_name: dissected gonad, XO

value: young adult


title: VCaP 100nM ARD-61b 6h-2

description:
VCaP Treated with 100nM ARD-61b Degrader for 6 hours replicate 2
SI_21481

value: passage 30-50


title: VCaP 100nM ARD-61b 6h-1

description:
VCaP Treated with 100nM ARD-61b Degrader for 6 hours replicate 1
SI_21480


title: fog1_XX_youngadult_rep3

description: mRNA-seq

value: XX

value: whole body


title: 221_LPS_95


title: fog1_XO_dissectedgonad_rep1

description: mRNA-seq

value: XO


title: ChIP_H4K20me1_ED_rep2

value: W1118 Oregon-R

value: Abcam; Cat. N. ab9051


title: ChIP_INPUTh_ED_rep2

value: L3 wandering larvae


title: VCaP DMSO 6h -3

description:
VCaP Parental Cells Treated with DMSO Control for 6 hours replicate 3
SI_21479

value: no ARD-61


title: fog1_XO_youngadult_rep3

description: mRNA-seq


title: ChIP_H3K4me3_ED_rep2

value: Eye Disc

value: Millipore; Cat. N. 04-745; clone MC315


title: fog1_XX_youngadult_rep2

description: mRNA-seq


title: ChIP_INPUTv_ED_rep2


title: UCB-2 G-CSF

city: Leipzig

first: Gerhard

last: Behre

address: Johannisallee 32A

department: Division of Hematology and Oncology

institute: Leipzig University Hospital

data_processing:
Each library was indexed in order to multiplex sequencing runs on the Illumina HIScanSQ platform
50bp sequencing reads were collected and adaptor sequences were trimmed from raw sequences using cutadapt software
remaining read data for each sample were aligned to the most recent human (hsa-only) mature sequences of miRASE database v21 (miRBase.org) using bowtie aligner
Mapped reads for each miRNA were counted with R/Bioconductor programming environment by application of the ShortRead library
Supplementary_files_format_and_content: abundance measurements

source_name: huCD34+ HSPCs_G-CSF

growth_protocol: huCD34+ HSPCs were routinely isolated from umbilical cord blood using CD34 MicroBead Kit (Miltenyi). Typically 1x10^5 cells were seeded into 12well plates and grown in IMDM medium containing 10% FBS supplemented with IL-6 (50ng/ml), SCF (50ng/ml) and FLT3-L (50ng/ml). From day 4 on cells were cultured in IMDM supplemented with IL-3 (10ng/ml), SCF (25ng/ml) and FLT3-L (25ng/ml).

extract_protocol:
Total RNA was isolated using Trizol reagent.
TruSeq Small RNA Library Prep Kit v2 (Illumina) was used for the construction of sequencing libraries. smallRNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All cells were incubated at 37°C in 5%CO2. Freshly isolated huCD34+ HSPCs were split into 2 parts and seeded at a density of 1x10^5/ml. One part of cells (target) were immediately treated with G-CSF (100ng/ml) the other part of cells (control) was treated with vehicle. Addition of G-CSF or vehicle was repeated every 2nd day.

value: umbilical cord blood derived stem and progenitor cells (HSPCs)

tag: treated with

value: 100ng/ml G-CSF


title: VCaP DMSO 6h -2

description:
VCaP Parental Cells Treated with DMSO Control for 6 hours replicate 2
SI_21478

value: VCaP

value: Prostate Adenocarcinoma

value: 6 hours


title: UCB-3 control

source_name: huCD34+ HSPCs_control

value: vehicle (control)


title: fog1_XX_dissectedgonad_rep3

description: mRNA-seq

value: young adult

value: gonad


title: VCaP DMSO 6h -1

description:
VCaP Parental Cells Treated with DMSO Control for 6 hours replicate 1
SI_21477

value: passage 30-50


title: UCB-2 control


title: ctrl_LPS_50

value: M2 macrophages

value: control

value: LPS-stimulated


title: fog1_XO_dissectedgonad_rep3

description: mRNA-seq

value: XO


title: Candidate 16 75

city: Hong Kong

first: Mengge

last: Sun

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description: Sample name: 75

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.  a. The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min.  b. Then hybridized to the microarray for 16-20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).  c. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: The scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: Plasma, osteoporosis with vertebral fracture

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a. 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C.  b. The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C.  c. Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity were measured by using Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: Plasma

tag: disease state

value: Osteoporosis with vertebral fracture

tag: t-score

tag: age

value: 64 years

tag: Sex

value: Female


title: Candidate 17 90

description: Sample name: 90

value: 80 years


title: UCB-3 G-CSF

value: umbilical cord blood derived stem and progenitor cells (HSPCs)

value: 100ng/ml G-CSF


title: Candidate 14 72

description: Sample name: 72

value: 70 years


title: 221_LPS_85

value: miR-221 mimic transfection


title: 221_LPS_50


title: Candidate 18 91

description: Sample name: 91

value: 57 years


title: ChIP_H3K4me3_ED_rep1

value: W1118 Oregon-R

tag: develpmental stage

value: L3 wandering larvae

value: Eye Disc

value: Millipore; Cat. N. 04-745; clone MC315


title: 221_LPS_81

tag: cell type

value: M2 macrophages


title: UCB-1 control

tag: passage

value: vehicle (control)


title: ctrl_LPS_52

value: control

value: LPS-stimulated


title: K562-pLV-miR-143-3_AGO

description:
processed data file:
143 AGO.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence
reads were aligned to hg38 using TopHat
to assemlbe transcriptomes and analyze data from RNA-Seq we used Cufflinks suite (Trapnell, Rinn & Pachter)
Genome_build: hg38
Supplementary_files_format_and_content: text files include av. FPKM values for triplicates

growth_protocol: Cells were grown in RPMI-1640 medium without phenolred, 10% FBS, 1% Pen/Strep and 1µg/ml Puromycin

extract_protocol:
Total RNA was extracted using Trizol method according to the manufacturer's instructions
1µg of total RNA was subjected rRNA removal with Ribo-Zero Gold rRNA Removal Kit (Epicentre, RZG1224). RNA was enriched using random primer and reverse transcribed to double stranded cDNA (TargetAmp™-Nano Labeling Kit, Epicentre, TAN091096). The cDNA was end repaired, adenylated and ligated with PCR-indexes prior to 12 cycles of PCR. Sequencing was performed using 15pM hybridisation to a 2-100 paired end flow cell.

treatment_protocol: Cells were infected with pLV-miR-143 or control (Biosettia) PEG-concentrated viral particles followed by Puromycin selection. Purity of transduced cells was calculated using flow cytometry for expression of fluorescent markers. RNA Immunoprecipitation was performed according to the manufacturer's instructions (Sigma-Aldrich, RIP-12RXN)

tag: cell line

value: multipotential, hematopoietic malignant cells

tag: viral infection

value: pLV-miR-143 (Biosettia, mir-p114)


title: K562-pLV-miR-143-2_AGO

description:
processed data file:
143 AGO.txt


title: Candidate 15 73

description: Sample name: 73

value: Plasma

value: Osteoporosis with vertebral fracture

value: 71 years

value: Female


title: ChIP_H3K36me3_ED_rep2

tag: chip antibody

value: Abcam, Cat. N. ab9050


title: ChIP_H3K4me2_ED_rep1

value: Active motif; Cat. N. 39141


title: ChIP_H3K4me1_ED_rep1

value: Active motif; Cat. N. 39297


title: ctrl_LPS_95


title: UCB-1 G-CSF

value: umbilical cord blood derived stem and progenitor cells (HSPCs)

value: 100ng/ml G-CSF


title: ChIP_H3K4me1_ED_rep2

value: W1118 Oregon-R

value: L3 wandering larvae

value: Eye Disc


title: 221_52

value: M2 macrophages

value: miR-221 mimic transfection

value: non-stimulated


title: ctrl_LPS_85

value: control

value: LPS-stimulated


title: Candidate 10 67

description: Sample name: 67

source_name: Plasma, osteoporosis without vertebral fracture

value: Plasma

value: Osteoporosis without vertebral fracture

value: 61 years


title: Candidate 13 70

description: Sample name: 70

value: Osteoporosis with vertebral fracture

value: 76 years

value: Female


title: ChIP_H3K4me2_ED_rep2

value: Active motif; Cat. N. 39141


title: Candidate 12 79

description: Sample name: 79

value: 80 years


title: ChIP_H4K20me1_ED_rep1

value: Abcam; Cat. N. ab9051


title: ctrl_LPS_81


title: ChIP_H3K36me3_ED_rep1

value: W1118 Oregon-R

value: Abcam, Cat. N. ab9050


title: ChIP_H3K27me2_ED_rep2

value: L3 wandering larvae

value: Eye Disc

value: Cell Signaling Technology; Cat. N. 9728


title: Candidate 11 68

description: Sample name: 68

value: 77 years


title: K562-pLV-miR-143-1_AGO

description:
processed data file:
143 AGO.txt

value: multipotential, hematopoietic malignant cells

value: pLV-miR-143 (Biosettia, mir-p114)


title: 221_95

value: M2 macrophages

value: miR-221 mimic transfection

value: non-stimulated


title: ChIP_H3K27me1_ED_rep2

value: Upstate; Cat. N. 07-448


title: 221_81


title: 221_85


title: 221_50


title: ctrl_52

value: control


title: ChIP_H3K27me2_ED_rep1


title: ChIP_H3K27me1_ED_rep1


title: ChIP_H2AK118Ub_ED_rep2

value: Cell Signaling Technology; Cat. N. 8240S (D27C4)


title: K562-pLV-control-3_AGO

description:
processed data file:
control AGO.txt

value: pLV-control (Biosettia, mir-p000)


title: ctrl_50


title: K562-pLV-miR-143-3_IgG

description:
processed data file:
143 IgG.txt


title: K562-pLV-miR-143-1_IgG

description:
processed data file:
143 IgG.txt


title: Candidate 9 64

description: Sample name: 64

value: Plasma

value: Osteoporosis without vertebral fracture

value: 74 years

value: Female


title: K562-pLV-miR-143-2_IgG

description:
processed data file:
143 IgG.txt


title: ctrl_95


title: ChIP_H2AK118Ub_E1416_rep2

value: W1118 Oregon-R

value: Whole 14-16h embryo

value: whole embryo


title: K562-pLV-control-1_AGO

description:
processed data file:
control AGO.txt


title: ChIP_H2AK118Ub_ED_rep1

value: L3 wandering larvae

value: Eye Disc


title: K562-pLV-control-3_IgG

description:
processed data file:
control IgG.txt

value: multipotential, hematopoietic malignant cells


title: ctrl_85

value: M2 macrophages


title: K562-pLV-control-2_IgG

description:
processed data file:
control IgG.txt


title: Candidate 6 69

description: Sample name: 69

source_name: Plasma, healthy control

value: Healthy

value: 36 years


title: ChIP_H2AK118Ub_E1416_rep1


title: Candidate 5 63

description: Sample name: 63

value: 46 years


title: Candidate 7 49

description: Sample name: 49

value: 73 years


title: ctrl_81

value: control

value: non-stimulated


title: Candidate 4 59

description: Sample name: 59

value: Plasma

value: 48 years


title: K562-pLV-control-1_IgG

description:
processed data file:
control IgG.txt

value: pLV-control (Biosettia, mir-p000)


title: K562-pLV-control-2_AGO

description:
processed data file:
control AGO.txt


title: Candidate 3 58

description: Sample name: 58

value: 39 years

value: Female


title: Candidate 8 50

description: Sample name: 50

value: Osteoporosis without vertebral fracture

value: 43 years


title: aretIR IFM 24hAPF rep2

status: Public on Jan 11 2020

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

institute: University of Missouri Kansas City

description:
mRNA
aret24h_1
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

data_processing:
Basecalling and demultiplexing by IMP sequencing core facility (Vienna, Austria) using Illumina software.
Quality assessment of the raw data using fastqc.
Sequenced reads were mapped to the Ensembl BDGP6.80 whole genome using STAR.
Mapped reads were sorted and indexed using samtools.
Bam files were converted into bigwig for visualisation on the UCSC server.
Counting the mapped reads on the gene and exon level using featureCounts.
Run the differential gene expression analysis using the R package DESeq2.
Calculate the differential exon usage with the R package DEXSeq.
Genome_build: BDGP6.80 from ENSEMBL
Supplementary_files_format_and_content: Tab-delimited text files including raw counts calculated by featureCount for all libraries; wig files for positive and negative strand for all libraries.

source_name: indirect flight muscle

growth_protocol: Flies were grown on standard medium using standard fly husbandry protocol.

extract_protocol:
Total RNA isolated in Tri-Pure reagent (phenol-chloroform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP.
RNA libraries were prepared for sequencing by the IMP sequencing core facility (Vienna, Austria) using standard Illumina protocols.

treatment_protocol: Dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction.

value: indirect flight muscle

tag: muscle type

value: fibrillar

value: 24h APF

tag: genotype

value: Mef2-Gal4, UAS:GMA::GFP, UAS-T41568 (aretIR)

tag: growth protocol

value: grown at 27C, staged 0h white pre-pupae


title: WT leg 50h APF

description:
mRNA
leg50h
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: whole leg

tag: tissue

value: whole leg

value: tubular

tag: developmental stage

value: 50h APF

value: Mef2-Gal4, UAS:GMA::GFP


title: WT leg disc

description:
mRNA
leg_Myoblast
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

source_name: leg imaginal disc

value: leg imaginal disc

value: 3rd instar imaginal disc

value: grown at 27C, collected wandering 3rd instar larvae


title: aretIR IFM 24hAPF rep1

description:
mRNA
aret24h_2
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt


title: WT leg 30h APF

description:
mRNA
leg30h
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: 30h APF


title: Candidate 2 40

description: Sample name: 40

value: Plasma

value: Healthy

value: 59 years


title: H3-FLAG ChIP in rix1E414K cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: ChIP was performed using anti-FLAG M2 afffinity gel (Sigma-Aldrich A2220) followed by microarray analysis

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol. Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner. Scanned on an Agilent G2505B scanner.

data_processing:
Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.
Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: early log. growing cells

label_protocol:
ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).
ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol:
Cells carrying pINV1-H3.2-FLAG plasmid grown in EMM-Leu + 8% glucose media to OD 0.1- 0.15 were synchronized by adding 15 mM HU for 4 h before shifting the cells to EMM-Leu-glucose + 4% sucrose media containing 15mM HU for 2 h to induce the expression of H3-FLAG.
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) . Cultures were grown at 30˚C.

extract_protocol:
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with anti-FLAG M2 afffinity gel (Sigma-Aldrich A2220). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam, ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 20 min.
Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. DMA was also added to the fixation of cells to be used in Pds5 ChIPs. Prior fixation cells were incubated at 18˚C for 2h (Pds5 ChIPs).

value: rix1E414K cells

tag: fraction

value: H3-FLAG immunoprecipitated DNA

value: Whole-cell extract DNA


title: H3-FLAG ChIP in WT cells 1

value: Wild type cells


title: Candidate 1 37

description: Sample name: 37

value: Female


title: Caco-2 after EIEC invasion (3h), replicate 1

city: São Paulo

first: Hadassa Cristhina

middle: Azevedo Soares

last: Santos

state: São Paulo

address: Avenida Professor Lineu Prestes, 580

department: Department of Clinical Chemistry and Toxicology

country: Brazil

institute: University of São Paulo

description: Gene expression from Caco-2 cells after invasion of Escherichia coli strain O124:H- (EIEC FBC124/13)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering any NA per group and the expression values in Log (base 2).

source_name: Caco-2 cells, EIEC invasion

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA from Caco-2 cells invaded by Enteroinvasive Escherichia coli strain O124:H- (EIEC FBC124/13) was extracted using the RNeasy Mini Kit (Qiagen, cat no. 74104, MD, USA) according to the manufacturer’s instructions. RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: Caco-2 cells were cultivated in DMEM complemented with 10% fetal bovine serum (FBS), 1mM L-glutamine, penicillin (100U mL-1) and streptomycin (100mgmL-1) and 1% non-essential amino acids in a humidified 5% with CO2 atmosphere. The cells were grown until confluent monolayers in a six-well tissue culture plate at a density of 1x106 cells. To infection the cells were washed with phosphate-buffered saline (PBS). After washing, 900 μL of fresh DMEM with 10% FBS (D10) was added to each well with 100 μL of D10 plus bacterial (EIEC) culture (1x107 bacteria). The assay mixture was incubated for 1,5h at 37°C in 5% CO2. DMEM containing 10% FBS and 50 mg mL-1 gentamicin was added and cells were cultured for 30 min. The cells were then washed with a fresh medium containing 10% FBS, and re-incubated for up to 3h at 37°C in 5% CO2.

tag: sample type

value: Cellular culture


title: H3-FLAG ChIP in pob3D cells

value: pob3D cells


title: H3-FLAG ChIP in amo1D cells

value: amo1D cells


title: H3-FLAG ChIP in WT cells 3


title: Caco-2 after EIEC invasion (2h), replicate 2


title: Caco-2 after EIEC invasion (2h), replicate 1


title: Caco-2 after EIEC invasion (3h), replicate 2


title: Caco-2 after EIEC invasion (3h), replicate 3


title: Caco-2 after EIEC invasion (2h), replicate 3


title: Caco-2 after EIEC invasion (1h), replicate 3


title: WT leg 72h APF

description:
mRNA
leg72h
processed data file: featureCountsAll_exonLevel.txt
processed data file: featureCountsAll_geneLevel.txt

value: whole leg

value: tubular

value: 72h APF

value: grown at 27C, staged 0h white pre-pupae


title: Caco-2 after EIEC invasion (1h), replicate 2


title: Caco-2 after EIEC invasion (2h), replicate 4


title: Caco-2 after EIEC invasion (1h), replicate 4


title: H3-FLAG ChIP in WT cells 2


title: Caco-2 after EIEC invasion (0h), replicate 3


title: Caco-2 after EIEC invasion (1h), replicate 1


title: Caco-2 after EIEC invasion (0h), replicate 4


title: Caco-2 cell without interaction - control (3h), replicate 2

description: Gene expression from Caco-2 cells without interaction - control

source_name: Caco-2 cell, control

extract_protocol: Total RNA from Caco-2 cells (without any interaction) was extracted using the RNeasy Mini Kit (Qiagen, cat no. 74104, MD, USA) according to the manufacturer’s instructions. RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: Caco-2 cells (human intestinal epithelial cells) were cultivated in DMEM complemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA), 1mM L-glutamine (Sigma-Aldrich), penicillin (100U mL-1) (Sigma-Aldrich) and streptomycin (100mgmL-1) (Sigma-Aldrich) and 1% non-essential amino acids. All cell were cultivated in a humidified 5% CO2 atmosphere. The cells were grown until confluent monolayers in a six-well tissue culture plate at a density of 1x106 cells. This cells haven’t infection, but was incubated for 1,5h at 37°C in 5% CO2 as well as infected cells. DMEM containing 10% FBS and 50 mg mL-1 gentamicin was added and cells were cultured for 30 min. The cells were then washed with a fresh medium containing 10% FBS, and re-incubated for up to 3h at 37°C in 5% CO2.


title: Caco-2 after EIEC invasion (0h), replicate 2


title: Caco-2 cell without interaction - control (3h), replicate 4


title: Caco-2 after EIEC invasion (3h), replicate 4


title: Caco-2 cell without interaction - control (3h), replicate 1


title: Caco-2 after EIEC invasion (0h), replicate 1


title: MEFs

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing:
 Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.
gene expression analysis: high quality expression values (for example, where at least 1 out of 2 samples have values within cut-off, cut-off =100) will be selected for analysis. Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups. Hierarchical clustering was performed using R scripts. GO analysis and Pathway analysis were performed using the standard enrichment computation methods.

source_name: Wild-type MEFs

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Trizol

tag: strain background

tag: genotype/variation

value: Wild-type

value: mouse embryonic fibroblasts (MEFs)


title: Caco-2 cell without interaction - control (3h), replicate 3


title: Caco-2 cell without interaction - control (2h), replicate 1


title: Caco-2 cell without interaction - control (2h), replicate 4


title: Caco-2 cell without interaction - control (0h), replicate 1


title: Caco-2 cell without interaction - control (1h), replicate 3


title: Caco-2 cell without interaction - control (0h), replicate 4


title: Caco-2 cell without interaction - control (0h), replicate 3


title: Caco-2 cell without interaction - control (1h), replicate 1


title: Caco-2 cell without interaction - control (0h), replicate 2


title: Caco-2 cell without interaction - control (1h), replicate 4


title: Caco-2 after S. flexneri infection (3h), replicate 4

description: Gene expression from Caco-2 cells after infection of S. flexneri M90T strain 5a

source_name: Caco-2 cells, S. flexneri infection

extract_protocol: Total RNA from Caco-2 cells infected with Shigella flexneri strain 5a (S. flexneri M90T) was extracted using the RNeasy Mini Kit (Qiagen, cat no. 74104, MD, USA) according to the manufacturer’s instructions. RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA).

tag: infection time


title: Caco-2 after S. flexneri infection (3h), replicate 3


title: Caco-2 after S. flexneri infection (1h), replicate 4


title: Caco-2 after S. flexneri infection (3h), replicate 2


title: Caco-2 after S. flexneri infection (2h), replicate 2


title: Caco-2 after S. flexneri infection (3h), replicate 1


title: Caco-2 cell without interaction - control (2h), replicate 3


title: Caco-2 after S. flexneri infection (2h), replicate 4