title: GD3_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203

value: GD


title: WT_Flow_2 (expt 1)

status: Public on Jun 01 2020

type: RNA

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in AFP-expressing MR-1 grown under an electrolyte-flow condition

hyb_protocol: For each array, 19 µL of the purified Cy3-labeled cRNA (600 ng) was mixed with 5 µL of 10× Blocking Agent, 1 µL of 25× Fragmentation Buffer, and 25 µL of 2× GE Hybridization Buffer HI-RPM. The resultant mixtures were hybridized to the arrays at 65ºC for 17 h. After hybridization, each microarray slide was washed with Gene Expression wash buffer 1 at room temperature for 1 min, followed by Gene Expression wash buffer 2 at 37ºC for 1min.

scan_protocol: Slides were air dried for 1 min and scanned using an Agilent DNA Microarray Scanner at 5-µm resolution.

data_processing: Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using the limma software package (version 3.36.2; https://www.bioconductor.org/packages/release/bioc/html/limma.html)

molecule: total RNA

organism: Shewanella oneidensis

source_name: AFP-expressing MR-1 grown under a flow condition replicate 2

label_protocol: Cyanine3 (Cy3)-labeled cRNA was synthesized from 25 ng of total RNA using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) and purified using a RNeasy Mini Kit (Qiagen). The labeled cRNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: An electrochemical flow cell (EFC) was filled with lactate minimal medium (LMM) containing gentamicin (Gm) and was purged with pure nitrogen gas (99.999%) for anaerobic operation. After inoculation with AFP-expressing MR-1 pregrown in LB medium supplemented with Gm, the electrodes were connected to a potentiostat (VMP3; Bio-Logic Science Instruments, Seyssinet-Pariset, France), and the potential of the working electrode (WE) was poised at +0.2 V (versus the standard hydrogen electrode). After inoculation, medium (electrolyte) was not supplied to the EFC for approximately 1 h, to allow MR-1 cells to attach to the WE. For operation under the electrolyte-flow conditions, LMM containing Gm was supplied to the EFC at a constant linear velocity of 5.5 mm min-1. The EFC was operated for 48 h (for the flow condition) or 78 h (for the non-flow condition) until the WE-associated cells reached the early stationary growth phase.

extract_protocol: Total RNA was extracted using a Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and subsequently purified using an RNeasy Mini Kit and an RNase-Free DNase Set (Qiagen, Valencia, CA). The quality of total RNA was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Pico reagents and RNA Pico Chips (Agilent Technologies) according to the manufacture’s instruction.

treatment_protocol: Cells associated with the WE were suspended in LMM with vigorous pipetting. After vortex-mixing, the cell suspension was centrifuged at 15,000 g for 5 min to precipitate the cells.

tag: strain

value: AFP-expressing MR-1

tag: genotype

value: WT

tag: growth protocol


title: RNA-seq of Col-0_L_2

type: SRA

city: Qingdao

first: Lingyan

last: Wang

address: No.72 Binhai Road Jimo

country: China

institute: Shandong University

description: biological replicate 2

library_source: transcriptomic

data_processing:
The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software, and differential gene expression was analyzed using Noiseq software.
Genome_build: tair 10
Supplementary_files_format_and_content: XLS file for two sample comparison testing if a gene is differentially expressed

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Hypocotyl

growth_protocol: The seedlings of wild type Col-0 and 35S:miR396a were grown on ½ MS medium containing 1% sucrose for 4 days in the dark, and treated with or without light for 3 hrs.

extract_protocol:
Total RNA was extracted with Trizaol RNA extraction kit (Transgene)
the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute(BGI)

treatment_protocol: The seedlings grown in the dark were treated with or without light for 3 hrs

tag: ecotype

value: Columbia

tag: tissue

value: hypocotyl

tag: development stage

value: 4day-dark growth seedling


title: WT425_YPD_2

city: San Francisco

first: Suzanne

middle: M

last: Noble

state: CA

address: 513 Parnassus Ave., Box 0414

country: USA

institute: UCSF

data_processing:
Reads In fastq files were aligned to C. albicans transcriptome using kallisto with default parameters
Estimated counts generated from kallisto for each fastq were extracted and pair-wise comparisons between biological conditions was performed with limma using growth condition and batch as parameters in the design matrix
Supplementary_files_format_and_content: White_opaque_regulator_RNA_expression.xlsx contains log2 fold changes and adjusted p-values of pair-wise comparisons performed in limma; White_opaque_regulator_estimated_counts.xlsx contains estimated counts generated by kallisto that were used as input to limma

organism: Candida albicans

source_name: in vitro culture

growth_protocol: Candida albicans strains were grown in YEPD media overnight, then diluted to OD=0.1 and grown for 4 hours to an OD=1. These log phase cultures were either pelleted and snap frozen or used for oral gavage of mice. For mouse colonization, mice were given autoclaved food and water with penicillin and streptomycin ad libitum throughout the colonization. C. albicans colonization in mice was maintained for 10 days until the euthanization of the animals.

extract_protocol:
Acid phenol extraction followed by phenol-chloroform extraction, isopropanol preciptation, followed by SPRI bead cleanup
Followed standard protocol for NEBNext Ultra Directional Library Preparation

tag: time post inoculation

value: 4 hours

tag: growth condition

value: YEPD, 30C


title: GD2_1

city: 天津市

first: peixia

last: wang

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203

institute: 天津大学

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to ControlSYN3_1 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: R64
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

organism: Saccharomyces cerevisiae

source_name: Fungus

extract_protocol:
Strains were quickly frozen on dry ice, ground to powder with liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using  oligo -dT beads


title: WT_Flow_1 (expt 1)

source_name: AFP-expressing MR-1 grown under a flow condition replicate 1

value: grown under an electrolyte-flow condition


title: WT425_YPD_1


title: WT_Batch_3 (expt 1)

description: Gene expression in AFP-expressing MR-1 grown under a non-flow condition

source_name: AFP-expressing MR-1 grown under a non-flow condition replicate 3

value: grown under a non-flow condition


title: WT_Batch_4 (expt 1)

source_name: AFP-expressing MR-1 grown under a non-flow condition replicate 4


title: wor1_YPD_2


title: control_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203

value: wild-type


title: RNA-seq of Col-0_D_3

description: biological replicate 3


title: WT250_YPD_2


title: WT250_YPD_3


title: RNA-seq of Col-0_D_2

description: biological replicate 2


title: GD1_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203


title: WT425_YPD_3


title: WT250_YPD_1


title: RNA-seq of Col-0_D_1

description: biological replicate 1


title: donor of TTYH2 editing complementary sequence

city: Stanford

first: Jin

last: Li

address: M341, 300 Pasteur Dr.

department: Genetics

institute: Stanford University

description:
targeted mutagenesis
TTYH2donorEDIT_counts

library_source: genomic

data_processing:
Library strategy: amplicon sequencing
genome with designed mutations was built using GMAP
alignment using GSNAP with parameter -m 12 -i 1000000
mutant isoforms with less than 50 reads were filtered out
RNA editing level were measured at target sits by calculating G in total reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including editing level, reads coverage of each isoform

molecule: genomic DNA

organism: synthetic construct

source_name: oligo chip

extract_protocol:
nuclear fraction was extracted using Cell Biolabs kit (AKR-171), DNA was extracted using Zymo kit (D3020) and RNA was extracted using Trizol reagent.
gene specific primers with partial Illumina adapter were used to amplify each targets and then a second round of PCR was included to add barcodes.

tag: cell type

value: synthesized oligo

tag: extraction

value: PCR from chip


title: donor of TTYH2 editing stem

description:
targeted mutagenesis
TTYH2donorECS_counts


title: ControlSYN3_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203


title: WT_Batch_1 (expt 1)

source_name: AFP-expressing MR-1 grown under a non-flow condition replicate 1


title: RNA-seq of Col-0_L_1

description: biological replicate 1


title: WT_Batch_2 (expt 1)

source_name: AFP-expressing MR-1 grown under a non-flow condition replicate 2


title: donor of AJUBA editing stem

description:
targeted mutagenesis
AJUBAdonorEDIT_counts


title: Thyroid_10mo_0 kBq_young/adult_rep4

status: Public on May 31 2020

city: Gothenburg

first: Malin

last: Larsson

address: Gula straket 2B

country: Sweden

institute: University of Gothenburg

description: Gene expression after 9/6mo in 0 kBq young/adult rat thyroid

hyb_protocol: Samples were hybridized to SurePrint G3 Rat GE 8x60K Microarrays and incubated under rotation at 65° C  for 17 h.  After hybridization, arrays were washed according to manufacturer's protocol.

scan_protocol: Slides were immediately scanned using Agilent DNA microarray scanner G2505C at 3 um resolution (Agilent Technologies).  The fluorescent intensities of the scanned images were extracted and preprocessed with the Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Data were quantile normalized using Partek software.Sample groups were compared using unpaired two-sided Student´s t-test. P-values were adjusted for multiple testing using Benjamini-Hochberg procedure.

organism: Rattus norvegicus

source_name: Thyroid, 10mo, 0 kBq, young/adult, replicate 4

label_protocol: For each sample, total RNA (200 ng) was labelled and amplified with Cy3-dCTP  using the Agilent Low Input Quick Amp Labelling kit according to the manufacturer's protocol.  Samples were spiked with Agilent One-Color Spike-Mix (1:10). The labelled and amplified cRNA was purified using the Qiagen RNease mini spin kit.  Purified cRNA was quantified using a NanoDrop spectrophotometer. All samples had cRNA yields > 0.825 ug  and Cy3 specific activity > 6.0

extract_protocol: Total RNA samples were extracted from flash-frozen thyroid tissue samples with the RNeasy Lipid Tissue Mini Kit (Qiagen; Hilden, Germany).

treatment_protocol: 52 Sprague Dawley male rats were divided into groups contianing 4 indivduals each, six groups were injected at an age of five weeks with four different doses (0.5-500 kBq) and three groups were injected with 50 kBq at an age of 17 weeks, remaingin four groups served as untreated controlls.  Animals were killed at 3,6 or 9 month after irradiation, and thyroid samples from each indvidual were flash-frozen and stored at -80C .

value: Thyroid

tag: gender

value: Male

tag: age


title: Thyroid_7mo_0 kBq_young/adult_rep3

description: Gene expression after 6/3mo in 0 kBq young/adult rat thyroid

source_name: Thyroid, 7mo, 0 kBq, young/adult, replicate 3


title: Thyroid_10mo_50kBq_adult_rep3

description: Gene expression after 6mo in 50 kBq adult rat thyroid

source_name: Thyroid, 10mo, 50 kBq, adult, replicate 3


title: Thyroid_10mo_0 kBq_young/adult_rep2

source_name: Thyroid, 10mo, 0 kBq, young/adult, replicate 2


title: Thyroid_7mo_50kBq_adult_rep3

description: Gene expression after 3mo in 50 kBq adult rat thyroid

source_name: Thyroid, 7mo, 50 kBq, adult, replicate 3


title: Thyroid_13mo_0 kBq_adult_rep3

description: Gene expression after 9mo in 0 kBq adult rat thyroid

source_name: Thyroid, 13mo, 0 kBq, adult, replicate 3


title: Thyroid_7mo_50kBq_adult_rep4

source_name: Thyroid, 7mo, 50 kBq, adult, replicate 4


title: Thyroid_7mo_0 kBq_young/adult_rep1

source_name: Thyroid, 7mo, 0 kBq, young/adult, replicate 1


title: Thyroid_4mo_0 kBq_young_rep1

description: Gene expression after 3mo in 0 kBq young rat thyroid

source_name: Thyroid, 4mo, 0 kBq, young, replicate 1


title: Thyroid_7mo_0 kBq_young/adult_rep2

source_name: Thyroid, 7mo, 0 kBq, young/adult, replicate 2


title: Thyroid_13mo_0 kBq_adult_rep1

source_name: Thyroid, 13mo, 0 kBq, adult, replicate 1


title: Thyroid_10mo_50kBq_adult_rep1

source_name: Thyroid, 10mo, 50 kBq, adult, replicate 1


title: Thyroid_4mo_0 kBq_young_rep2

source_name: Thyroid, 4mo, 0 kBq, young, replicate 2


title: Thyroid_13mo_50kBq_adult_rep3

description: Gene expression after 9mo in 50 kBq adult rat thyroid

source_name: Thyroid, 13mo, 50 kBq, adult, replicate 3


title: Thyroid_4mo_0 kBq_young_rep4

source_name: Thyroid, 4mo, 0 kBq, young, replicate 4


title: Thyroid_10mo_50kBq_adult_rep4

source_name: Thyroid, 10mo, 50 kBq, adult, replicate 4


title: Thyroid_7mo_50kBq_adult_rep2

source_name: Thyroid, 7mo, 50 kBq, adult, replicate 2


title: Thyroid_10mo_500kBq_young_rep2

description: Gene expression after 9mo in 500 kBq young rat thyroid

source_name: Thyroid, 10mo, 500 kBq, young, replicate 2


title: Thyroid_13mo_0 kBq_adult_rep2

source_name: Thyroid, 13mo, 0 kBq, adult, replicate 2


title: Thyroid_10mo_0 kBq_young/adult_rep3

source_name: Thyroid, 10mo, 0 kBq, young/adult, replicate 3


title: Thyroid_13mo_50kBq_adult_rep4

source_name: Thyroid, 13mo, 50 kBq, adult, replicate 4


title: Thyroid_10mo_0 kBq_young/adult_rep1

source_name: Thyroid, 10mo, 0 kBq, young/adult, replicate 1


title: Thyroid_13mo_50kBq_adult_rep2

source_name: Thyroid, 13mo, 50 kBq, adult, replicate 2


title: Thyroid_10mo_50kBq_adult_rep2

source_name: Thyroid, 10mo, 50 kBq, adult, replicate 2


title: Thyroid_7mo_50kBq_adult_rep1

source_name: Thyroid, 7mo, 50 kBq, adult, replicate 1


title: Thyroid_4mo_0 kBq_young_rep3

source_name: Thyroid, 4mo, 0 kBq, young, replicate 3


title: Thyroid_10mo_500kBq_young_rep3

source_name: Thyroid, 10mo, 500 kBq, young, replicate 3


title: Thyroid_10mo_500kBq_young_rep4

source_name: Thyroid, 10mo, 500 kBq, young, replicate 4


title: Thyroid_10mo_5kBq_young_rep3

description: Gene expression after 9mo in 5 kBq young rat thyroid

source_name: Thyroid, 10mo, 5 kBq, young, replicate 3


title: Thyroid_10mo_5kBq_young_rep2

source_name: Thyroid, 10mo, 5 kBq, young, replicate 2


title: Thyroid_10mo_5kBq_young_rep1

source_name: Thyroid, 10mo, 5 kBq, young, replicate 1


title: Thyroid_7mo_50kBq_young_rep4

description: Gene expression after 6mo in 50 kBq young rat thyroid

source_name: Thyroid, 7mo, 50kBq, young, replicate 4


title: Thyroid_7mo_50kBq_young_rep2

source_name: Thyroid, 7mo, 50kBq, young, replicate 2


title: Thyroid_10mo_50kBq_young_rep1

description: Gene expression after 9mo in 50 kBq young rat thyroid

source_name: Thyroid, 10mo, 50kBq, young, replicate 1


title: Thyroid_10mo_50kBq_young_rep4

source_name: Thyroid, 10mo, 50kBq, young, replicate 4


title: Thyroid_10mo_0.5kBq_young_rep1

description: Gene expression after 9mo in 0.5 kBq young rat thyroid

source_name: Thyroid, 10mo, 0.5 kBq, young, replicate 1


title: Thyroid_4mo_50kBq_young_rep4

description: Gene expression after 3mo in 50 kBq young rat thyroid

source_name: Thyroid, 4mo, 50kBq, young, replicate 4


title: Thyroid_10mo_0.5kBq_young_rep4

source_name: Thyroid, 10mo, 0.5 kBq, young, replicate 4


title: Thyroid_10mo_500kBq_young_rep1

source_name: Thyroid, 10mo, 500 kBq, young, replicate 1


title: Thyroid_13mo_50kBq_adult_rep1

source_name: Thyroid, 13mo, 50 kBq, adult, replicate 1


title: Thyroid_10mo_0.5kBq_young_rep3

source_name: Thyroid, 10mo, 0.5 kBq, young, replicate 3


title: Thyroid_10mo_50kBq_young_rep3

source_name: Thyroid, 10mo, 50kBq, young, replicate 3


title: Thyroid_10mo_50kBq_young_rep2

source_name: Thyroid, 10mo, 50kBq, young, replicate 2


title: Thyroid_10mo_0.5kBq_young_rep2

source_name: Thyroid, 10mo, 0.5 kBq, young, replicate 2


title: Thyroid_7mo_50kBq_young_rep3

source_name: Thyroid, 7mo, 50kBq, young, replicate 3


title: mvaS mutant time 2 replicat 1

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: S. aureus mvaS mutant strain grown in mlate-log phase in TSB versus pool DNA

hyb_protocol: A mixture of cDNA obtained from reverse transcription of RNA from WT or mutant strains were diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. Per chip and per spot normalisation wee performed in GeneSpring (7.3)

label: cyanine 3

organism: Staphylococcus aureus

source_name: mvaS mutant

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in TSB and extracted at middle exponential phase

extract_protocol: Briefly, bacteria were stabilized in RNA protect for 5 minutes, then harvested. Cells were lysed in the presence of 600 µg/ml lysostaphin and total RNA was extracted using the PrestoSpin R bug Kit including DNase I treatment (Molzym). Quantity and absence of contaminating DNA was measured by using the Nanodrop spectrophotometer (Nanodrop Technologies), and by qPCR, respectively.

treatment_protocol: RNAProtect (Qiagen)

value: mvaS

tag: growth phase

value: late-log phase in TSB

label: cyanine 5

source_name: Pooled DNA

tag: sample type

value: Purified DNA pool


title: mvaS mutant time 1 replicat 2

description: S. aureus mvaS mutant strain grown in mid-log phase in TSB versus pool DNA

value: mid-log phase in TSB


title: mvaS mutant time 1 replicat 3


title: DNA of NEIL1 mutants from double strand donor knockin rep2

description:
targeted mutagenesis
176Neilds2g_counts

organism: Homo sapiens

source_name: HEK293T cells

value: HEK293T cells

value: total genomic DNA


title: mvaS mutant time 1 replicat 1


title: mvaS mutant time 2 replicat 2


title: mvaS mutant time 2 replicat 3


title: WT time 2 replicat 3

description: S. aureus WT strain grown in late-log phase in TSB versus pool DNA

value: WT


title: Thyroid_4mo_50kBq_young_rep1

source_name: Thyroid, 4mo, 50kBq, young, replicate 1


title: Thyroid_7mo_50kBq_young_rep1

source_name: Thyroid, 7mo, 50kBq, young, replicate 1


title: WT time 2 replicat 2


title: Thyroid_4mo_50kBq_young_rep3

source_name: Thyroid, 4mo, 50kBq, young, replicate 3


title: Thyroid_4mo_50kBq_young_rep2

source_name: Thyroid, 4mo, 50kBq, young, replicate 2


title: control_16_S16

city: Boulder

first: Tom

last: Cech

state: CO

address: 3415 Colorado Avenue

department: BioFrontiers Institute

institute: University of Colorado Boulder, Boulder

description:
processed data file:
WTb_RNaseA_pos_RPB1.pooled.RPM.sorted.bw
WTb_RNaseApos_Rpb1_peaks.broadPeak

data_processing:
For ChIP-seq, Illumina sequencing adapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC was clipped by cutadapt. BWA was used for alignment with the following options: “-q 5 -l 32 -k 2”.  Samtools was used to keep only the primary alignments whose mapping score was greater than 30. Potential duplicates identified by Picard MarkDuplicates were removed. Coverage files (bigwig) were generated using bedtools and UCSC bedGraphToBigWig after pooling replicates for a given clone. Coverage is scaled as reads per million reads (RPM). Macs2 was used to call peaks with "--keep-dup all --nomodel --extsize X --bdg --broad" where X was found by SPP.
For fRIP-seq, STAR was used for alignment with GENCODE (v27) gene annotation. Samtools was used to keep only the primary alignments. Potential duplicates identified by Picard MarkDuplicates were removed. FeatureCounts were used to count reads in gene bodies (GENCODE v27) in a strand specific way.
For RNA-seq, STAR was used for alignment with GENCODE (v27) gene annotation. The number of reads were counted in a strand specific way for every gene annotated in GENCODE (v27) by featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: For fRIP-seq, comma seperated file has the read counts for every gene in the GENCODE (v27) gene annotation.
Supplementary_files_format_and_content: For RNA-seq, comma seperated file has the transcripts per million reads (TPM) for every gene in the GENCODE (v27) gene annotation.
Supplementary_files_format_and_content: For ChIP-seq, bigwigs and Macs2 peaks were provided for biologically independent clones.

source_name: iPSC

growth_protocol: Undifferentiated iPSCs were cultured in Essential 8 Flex medium on Vitronection-coated plates. Cardiomyocyte differentiation was induced using GSK3 inhibitor CHIR99021 and Wnt inhibitor IWP2 (GiWi protocol, Lian et al. Nature Protocol 2013)

extract_protocol:
Total RNA or RNA samples in fRIP-seq were extracted with Trizol following manufactuer's protocol. DNA samples in ChIP-seq was extracted using phenol-chloroform.
KAPA RNA Hyperprep kit with riboerase (RNA-seq and fRIP-seq), KAPA HyperPlus Kit (ChIP-seq)

treatment_protocol: For the RNase A treatment, 5 µg/mL of RNase A was added in pulldown step together with the primary antibody in the ChIP experiment; For the triptolide drug treatment, WT iPSC (two clones, two replicates each) grown to 80% confluency in Essential 8 flex media on vitronectin were treated with 10 µM triptolide (Sigma-Aldrich T3652) for 5 hours, after which cells were harvested and crosslinked for ChIP analysis.

tag: clone

tag: differentiation

value: Undifferentiated

tag: treatment

value: RNaseApos

tag: molecule subtype

value: DNA pulldown by RPB1


title: control_15_S15


title: control_14_S14

description:
processed data file:
WTa_RNaseA_pos_RPB1.pooled.RPM.sorted.bw
WTa_RNaseApos_Rpb1_peaks.broadPeak


title: control_13_S13


title: control_12_S12

description:
processed data file:
WTb_RNaseA_neg_RPB1.pooled.RPM.sorted.bw
WTb_RNaseAneg_Rpb1_peaks.broadPeak

value: RNaseAneg


title: control_10_S10

description:
processed data file:
WTa_RNaseA_neg_RPB1.pooled.RPM.sorted.bw
WTa_RNaseAneg_Rpb1_peaks.broadPeak


title: control_11_S11


title: control_8_S8

description:
processed data file:
WTb_RNaseA_pos_TBP.pooled.RPM.sorted.bw
WTb_RNaseApos_TBP_peaks.narrowPeak

value: DNA pulldown by TBP


title: control_7_S7


title: control_9_S9


title: WT time 2 replicat 1

tag: genotype


title: WT time 1 replicat 2

description: S. aureus WT strain grown in mid-log phase in TSB versus pool DNA


title: control_4_S4

description:
processed data file:
WTb_RNaseA_neg_TBP.pooled.RPM.sorted.bw
WTb_RNaseAneg_TBP_peaks.narrowPeak


title: control_3_S3


title: control_5_S5

description:
processed data file:
WTa_RNaseA_pos_TBP.pooled.RPM.sorted.bw
WTa_RNaseApos_TBP_peaks.narrowPeak


title: control_2_S2

description:
processed data file:
WTa_RNaseA_neg_TBP.pooled.RPM.sorted.bw
WTa_RNaseAneg_TBP_peaks.narrowPeak


title: 22_S22

description:
processed data file:
WTb_Triptolide.pooled.RPM.sorted.bw
WTb_Triptolide_peaks.broadPeak

value: Triptolide

value: DNA pulldown by EZH2


title: WTa_Triptolide_Input

description:
processed data file:
WTa_Triptolide_Input.dedupped.RPM.sorted.bw

value: DNA input


title: control_6_S6


title: 21_S21

description:
processed data file:
WTa_Triptolide.pooled.RPM.sorted.bw
WTa_Triptolide_peaks.broadPeak


title: WTb_Triptolide_Input

description:
processed data file:
WTb_Triptolide_Input.dedupped.RPM.sorted.bw


title: 16_S16

description:
processed data file:
WTb_RNaseA_pos_IP_SUZ12.pooled.RPM.sorted.bw
WTb_RNaseA_pos_SUZ12_peaks.broadPeak

value: RnaseA positive

value: DNA pulldown by SUZ12


title: 34_S34


title: 13_S13

description:
processed data file:
WTa_RNaseA_pos_IP_SUZ12.pooled.RPM.sorted.bw
WTa_RNaseA_pos_SUZ12_peaks.broadPeak


title: 14_S14


title: 33_S33


title: 12_S12

description:
processed data file:
WTb_RNaseA_neg_IP_SUZ12.pooled.RPM.sorted.bw
WTb_RNaseA_neg_SUZ12_peaks.broadPeak

value: RnaseA negative


title: 15_S15


title: 11_S11


title: 9_S9

description:
processed data file:
WTa_RNaseA_neg_IP_SUZ12.pooled.RPM.sorted.bw
WTa_RNaseA_neg_SUZ12_peaks.broadPeak


title: WT time 1 replicat 1


title: 7_S7

description:
processed data file:
WTb_RNaseA_pos_IP_EZH2.pooled.RPM.sorted.bw
WTb_RNaseA_pos_EZH2_peaks.broadPeak


title: 8_S8


title: control_1_S1


title: 2_S2

description:
processed data file:
WTa_RNaseA_neg_IP_EZH2.pooled.RPM.sorted.bw
WTa_RNaseA_neg_EZH2_peaks.broadPeak


title: 3_S3

description:
processed data file:
WTb_RNaseA_neg_IP_EZH2.pooled.RPM.sorted.bw
WTb_RNaseA_neg_EZH2_peaks.broadPeak


title: 6_S6

description:
processed data file:
WTa_RNaseA_pos_IP_EZH2.pooled.RPM.sorted.bw
WTa_RNaseA_pos_EZH2_peaks.broadPeak


title: 4_S4


title: 1_S1


title: 5_S5


title: SW620 dnLEF1 replicate 2

city: Irvine

first: Marian

last: Waterman

address: 224 Sprague Hall

institute: University of California Irvine

data_processing:
Standard Illumina software used for basecalling.
Sets of samples were trimmed and filtered with Trimmomatic to remove adapters with up to 2 mismatches, with a palindrome read alignment accuracy of 40 and a sequence match accuracy of 15. This program trimmed reads further by removing leading low-quality or N bases (below quality 3), removing trailing low-quality or N bases (below quality 3), and scanning each read with a 4-base-wide sliding window. The parameters were set for cutting when the average quality per base drops below 15 and then to drop any reads below 36 bases long
RNA-seq reads for each sample were mapped to the reference transcriptome using Tophat2.
Gene counts were then generated using HTSeq by inputing aligned .BAM files.
Statistical analysis for differential gene expression was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files created from HTSeq

molecule: polyA RNA

source_name: in vitro cell culture (colon cancer cell line)

growth_protocol: Cell lines were cultured in Dulbecco’s Modification of Eagle’s Medium (DMEM, Hyclone)

extract_protocol:
Cell culture monolayers were collected using trypsin/EDTA. Total RNA was isolated using TRIzol (Invitrogen) and DirectZol RNA Extraction Kit following the manufacturer’s instructions (Zymo Research). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable

tag: wnt activity

value: Wnt low (experimental)

tag: passage

tag: cell line

value: colon cancer


title: SW620 GFP replicate 4

value: Wnt high (mock/control)


title: SW620 GFP replicate 2


title: SW620 dnLEF1 replicate 4


title: SW620 dnLEF1 replicate 1


title: SW620 GFP replicate 3


title: SW620 GFP replicate 1


title: SW480 dnLEF1 replicate 2


title: SW480 dnLEF1 replicate 4


title: 10_S10


title: SW480 dnLEF1 replicate 1


title: SW480 GFP replicate 3


title: SW480 GFP replicate 4


title: SW480 GFP replicate 1


title: SW480 GFP replicate 2


title: MDA-MB-231-205-5p Rep2

city: Riyadh

first: Nehad

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

description: Gene expression in MDA-MB-231 breast cancer cell line transfected with has-miR-205-5p precursor replica 2.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2× Hi-RPM Hybridization Buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome GE 4x44K v2 Microarray chip for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Data were analyzed using Agilent GeneSpring X software.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: MDA-MB-231 cells were grown in DMEM supplemented with 10% fetal bovine serum, 1% NEAA, 1% L-glutamine, 100 mg/l penicillin, and 100 mg/l streptomycin.

extract_protocol: Total RNA were isolated from control and treated cells using Total RNA Purification Kit (Norgen-Biotek Corp., Canada) according to the manufacturer’s instructions. The concentrations of total RNA were measured using NanoDrop 2000 (Thermo-Scientific).

treatment_protocol: MDA-MB-231 cells (0.168 x 10e6 cells/ml) were transfected with the selected miRNA precursors (pre-miR–negative control, hsa-miR-205-5p and hsa-miR-214-3p) purchased from Ambion. Cell transfection was conducted employing a reverse transfection protocol.

value: Breast cancer cell line

tag: miRNA

value: has-miR-205-5p precursor


title: MDA-MB-231-SCR Rep2

description: Gene expression in MDA-MB-231 breast cancer cell line transfected with scrambled microRNA replica 2.

value: scrambled microRNA


title: MDA-MB-231-214-3p Rep1

description: Gene expression in MDA-MB-231 breast cancer cell line transfected with has-miR-214-3p precursor replica 1.

value: has-miR-214-3p precursor


title: MDA-MB-231-SCR Rep1

description: Gene expression in MDA-MB-231 breast cancer cell line transfected with scrambled microRNA replica 1.


title: MDA-MB-231-205-5p Rep1

description: Gene expression in MDA-MB-231 breast cancer cell line transfected with has-miR-205-5p precursor replica 1.


title: 3205_H3.3S31E_60_rep2

city: New York

first: Steven

middle: Zvi

last: Josefowicz

state: NY

address: 1300 York Ave, Box 69

department: Laboratory of Epigenetics and Immunity

institute: Weill Cornell Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence and quality control with Trim Galore v.0.5.0.
Resulting trimmed fastq files were aligned to GENCODE vM3 transcriptome in mm10 using STAR aligner v.2.4.2 with default settings and then name sorted using SAMtools v.1.5 with default parameters.
Utility featureCounts from Subread v.1.4.6 used to calculate raw counts reads per geen to be used as input for differential expression analysis following the DESeq2 workflow.
genome_build: mm10
processed data files format and content: .tdf (tiled data file) files were generated from bam files using igvtools v.2.3.98 count to compute the average feature density over a default-specified window size; bigWig files were generated from bam files using deeptools v.2.5.4 bamCoverage to obtain counts normalized to 1x depth of coverage as reads per genomic content (RPGC); .txt file contains an R v3.4.0 dataframe of statistics of differential analysis by DESeq2 for each gene (baseMean, log2FoldChange, pvalue, padj).

organism: Mus musculus

source_name: RAW264.7 (macrophage cell line)

growth_protocol: As previously described in Josefowicz et al., 2016

extract_protocol:
RNA was isolated using RNAeasy Kit (Qiagen).
Libraries were prepared using Illumina TruSeq protocol.

tag: tissue

value: macrophage (tumor ascites)

tag: stimulation time

tag: chip antibody


title: 3205_H3.3S31E_60_rep3

treatment_protocol: As previously described in Josefowicz et al., 2016


title: MDA-MB-231-214-3p Rep2

description: Gene expression in MDA-MB-231 breast cancer cell line transfected with has-miR-214-3p precursor replica 2.

tag: cell type


title: 3205_H3.3S31E_60_rep1


title: 3205_H3.3S31A_60_rep2


title: 3205_H3.3_60_rep3


title: SW620 dnLEF1 replicate 3


title: SW480 dnLEF1 replicate 3


title: 3205_H3.3_60_rep1


title: Zmynd11_IKKi_0

data_processing:
ChIP-seq reads were mapped to the mm10 genome using Bowtie2 v.2.3.4.1 with the following parameters: -p 8 -k 1 -N 1.
Aligned reads underwent three stages of filtering using SAMtools v.1.5. First, the unmapped, non-primary, qc failed, and multi-mapped reads were discarded. PCR duplicates were then marked by Picard Tools v.2.14.0 using 'VALIDATION_STRINGENCY=SILENT and REMOVE_DUPLICATES=false" options and removed by SAMtools (-F 1796). Then, chromosome M and scaffolds were removed to create the final filtered bam file.
genome_build: mm10
processed data files format and content: .tdf (tiled data file) files were generated from bam files using igvtools v.2.3.98 count to compute the average feature density over a default-specified window size; bigWig files were generated from bam files using deeptools v.2.5.4 bamCoverage to obtain counts normalized to 1x depth of coverage as reads per genomic content (RPGC); .txt file contains a tab-delimited file of read densities used for downstream analysis in R v.3.4.0.

source_name: Bone Marrow Derived Macrophage - unstimulated treated

extract_protocol: As previously described in Josefowicz et al., 2016

value: Bone Marrow Derived Macrophage


title: 3205_60_rep1


title: 3205_60_rep2


title: Zmynd11_60

source_name: Bone Marrow Derived Macrophage - stimulated/LPS


title: Zmynd11_0

source_name: Bone Marrow Derived Macrophage - unstimulated


title: Zmynd11_IKKi_60

source_name: Bone Marrow Derived Macrophage - stimulated/LPS treated


title: Zmynd11_DMSO_60


title: Zmynd11_DMSO_0


title: H3S31ph_CHK1_5_60


title: H3S31ph_CHK1_5_0


title: H3S31ph_shIKKa_60


title: aged dMCAO 5d 2

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

data_processing:
TopHat2 was used to align trimmed reads to mouse reference genome sequences (mm10) and transcript annotation from Gencode (v19).
HTSeq (v0.11.2) was used to quantify gene expression by the numbers of read counts.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include read counts for each sample

source_name: brain microglia

extract_protocol:
Single-cell suspensions were prepared from the mouse brain. Briefly, mice were deeply anesthetized and transcardially perfused with 0.9% NaCl. The ipsilesional brain hemisphere was harvested, and cell suspensions were prepared using the Neural Tissue Dissociation Kit and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). Suspensions were passed through a 70 μm cell strainer and fractionated on a 30% and 70% Percoll gradient at 500 g for 30 min to remove myelin and cell debris. Mononuclear cells at the interface were collected. Cells were then resuspended at 1×10^6 cells per mL, and stained with fluorophore-conjugated antibodies and the appropriate isotype controls. Fluorescence-activated cell sorting (FACS) was performed using an FACS Aria I sorter and FACS Diva software (BD Biosciences). Microglia were gated as CD11c–Ly6G–CD11b+CD45low and sorted for bulk RNA-seq. Each sample was pooled from 5 mouse brains to obtain enough cells.
Total RNA was extracted from FACS-sorted microglia using RNeasy Plus micro/mini kits (Qiagen). Libraries for RNA-seq were prepared from 300 ng of total RNA with the Clonetech SMARTer Stranded Total RNA-Seq (Pico) Kit.

tag: strain

tag: procedure

value: stroke

value: 18 months

tag: cell marker

value: CD11b+ CD45low


title: 3205_H3.3S31A_60_rep1


title: 3205_60_rep3


title: aged sham 2

value: sham

tag: age


title: H3S31ph_shSC_60


title: young dMCAO 5d 2

value: 10 weeks


title: H3S31ph_shSC_0


title: H3S31ph_IKKi_0


title: H3S31ph_shIKKa_0


title: young dMCAO 5d 1


title: H3S31ph_DMSO_60


title: aged sham 1


title: young sham 2


title: IKKa_60

value: IKKa


title: H3S31ph_DMSO_0


title: H3S31ph_ETO_60


title: young sham 1


title: 3205_H3.3_60_rep2


title: H3S31ph_FVP_60


title: H3S31ph_60


title: H3K27ac-60

data_processing:
RNAseq
Sequenced reads were trimmed for adaptor sequence and quality control with Trim Galore v.0.5.0.
Resulting trimmed fastq files were aligned to GENCODE vM3 transcriptome in mm10 using STAR aligner v.2.4.2 with default settings and then name sorted using SAMtools v.1.5 with default parameters.
Utility featureCounts from Subread v.1.4.6 used to calculate raw counts reads per geen to be used as input for differential expression analysis following the DESeq2 workflow.
Genome_build: mm10
Supplementary_files_format_and_content: .tdf (tiled data file) files were generated from bam files using igvtools v.2.3.98 count to compute the average feature density over a default-specified window size; bigWig files were generated from bam files using deeptools v.2.5.4 bamCoverage to obtain counts normalized to 1x depth of coverage as reads per genomic content (RPGC); .txt file contains an R v3.4.0 dataframe of statistics of differential analysis by DESeq2 for each gene (baseMean, log2FoldChange, pvalue, padj).
ChIPseq:
ChIP-seq reads were mapped to the mm10 genome using Bowtie2 v.2.3.4.1 with the following parameters: -p 8 -k 1 -N 1.
Aligned reads underwent three stages of filtering using SAMtools v.1.5. First, the unmapped, non-primary, qc failed, and multi-mapped reads were discarded. PCR duplicates were then marked by Picard Tools v.2.14.0 using 'VALIDATION_STRINGENCY=SILENT and REMOVE_DUPLICATES=false" options and removed by SAMtools (-F 1796). Then, chromosome M and scaffolds were removed to create the final filtered bam file.
Genome_build: mm10
Supplementary_files_format_and_content: .tdf (tiled data file) files were generated from bam files using igvtools v.2.3.98 count to compute the average feature density over a default-specified window size; bigWig files were generated from bam files using deeptools v.2.5.4 bamCoverage to obtain counts normalized to 1x depth of coverage as reads per genomic content (RPGC); .txt file contains a tab-delimited file of read densities used for downstream analysis in R v.3.4.0.
Regarding the chip_rna_lpsi120.txt file, it is the combined data frame of our ChIP analysis and our output from our differential DESEQ2 analysis for our RNAseq data from time 0 to time 120. The samples inputDNA-0_ChIPseq and inputDNA-60_ChIPseq were used for a type of normalization during processing.

extract_protocol:
RNAseq: RNA was isolated using RNAeasy Kit (Qiagen). Libraries were prepared using Illumina TruSeq protocol.
ChIP-seq:As previously described in Josefowicz et al., 2016


title: aged dMCAO 5d 1


title: H3S31ph_CPT_60


title: H3S28ph-0


title: H3S28ph-60


title: H3K27ac-0


title: H3S31ph_IKKi_60


title: LNM15

description: microRNA expression of lymph node metastatic breast cancer.

hyb_protocol: Labeled samples were hybridized to the Agilent 8 × 60k v16 miRNA microarray chip

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Data were analyzed using Agilent GeneSpring X software

label_protocol: Cyanine-3 (Cy3) as per Agilent one-color (Agilent) labeling kit.

extract_protocol: Total RNA was extracted from FFPE sections using the recover all total nucleic acid isolation kit (Ambion Inc., Life Technologies, USA) according to the manufacturer’s protocol.

value: Lymph node metastasis


title: BC15

description: microRNA expression of primary breast cancer.

value: Paired primary breast cancer


title: HCT/OHP1 Tumor

city: Nishinomiya

first: Tomoki

last: Yamano

state: Hyogo

address: 1-1 Mukogawa-cho

department: Department of Surgery

institute: Hyogo College of Medicine

description: Gene expression in tumor without drug treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Xenograft derived from HCT/OHP1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HCT116 cells, HCT/OHP1 cells, and HCT/OHP5 cells were subcutaneously inoculated in the frank of nude mice.

extract_protocol: RNA was extracted using TRIzol and TRIzol RNA Purification kit (Invitrogen) following the manufacture's instructions.

treatment_protocol: No drug treatment

value: Human colorectal cancer tumor in nude mouse

tag: tumor source


title: IKKa_0


title: HCT/OHP5 Tumor

source_name: Xenograft derived from HCT/OHP5


title: siz_SIM6d_r3

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: Riken

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 6d and SIM4d replicate 3

data_processing:
Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 1.2.1 with the following parameters: '-all -best -strata'.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-delimited data with transcript CPM (counts per million mapped reads) values for each sample

source_name: Excised hypocotyl from dark-grown seedlings

growth_protocol: 22°C constant temperature in the dark vertically grown on 1%Sucrose 1X MS medium containing 0.6% Gelzan CM growth 7 days

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column DNase digestion to eliminate genomic DNA.
Isolated RNA was subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) used as adapters and Agencourt AMPure XP (Beckman Coulter) beads used instead of KAPA Pure Beads.

treatment_protocol: Hypocotyl explants (around 10mm long) were excised using a razor blade and incubated on CIM (Gamborg B5 medium with 0.25% Gelzan supplemented with 0.5 μg/ml 2,4-dichlorophenoxyacetic acid [2,4-D] and 0.05 μg/ml kinetin) for 4 days under constant light. Hypocotyl or root explants were then transferred to SIM (Gamborg B5 medium 0.25% Gelzan,  0.15ug/ml IAA and 0.5 ug/ml 2-IPA)

tag: ecotype

value: Columbia (Col-0)

tag: time of sampling

value: After CIM 4 days and SIM 6 days


title: BC21


title: BC16


title: siz_SIM4d_r3

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d and SIM4d replicate 3

value: After CIM 4 days and SIM 4 days


title: siz_SIM6d_r1

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d and SIM6d replicate 1


title: siz_SIM4d_r2

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d and SIM4d replicate 2


title: siz_SIM6d_r2

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 6d and SIM4d replicate 2


title: LNM16


title: BC5


title: LNM1


title: siz_CIM4d_r3

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d replicate 3

value: After CIM 4 days


title: LNM5


title: siz_SIM4d_r1

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d and SIM4d replicate 1


title: BC19


title: LNM21


title: LNM8


title: BC1


title: BC8


title: BC10


title: BC11


title: LNM10


title: LNM11


title: LNM19


title: siz_CIM4d_r2

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d replicate 2


title: siz_CIM4d_r1

description: RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d replicate 1


title: siz_AfterCut_r3

description: RNA-seq for siz1-2  hypocotyl  after cut replicate 3

value: within 15 minutes after excision


title: siz_AfterCut_r2

description: RNA-seq for siz1-2 hypocotyl  after cut replicate 2


title: WT_SIM6d_r3

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 6d and SIM4d replicate 3

value: wild type


title: siz_AfterCut_r1

description: RNA-seq for siz1-2  hypocotyl  after cut replicate 1


title: WT_SIM6d_r2

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 6d and SIM4d replicate 2


title: WT_SIM6d_r1

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d and SIM6d replicate 1


title: WT_SIM4d_r3

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d and SIM4d replicate 3


title: WT_SIM4d_r2

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d and SIM4d replicate 2


title: 10 week immune profile

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

description: CD45+ cells pooled from mammary glands from 3 mice, lymph nodes removed, thoracic and inguinal

data_processing:
10x genomic CellRanger pipeline (version 3.1.0) was used to demultiplex, map and retrieve counts for all of the samples.
Analysis of sequencing data was performed using the Seurat R package (version 3.1.1).
Data was filtered to keep all genes expressed in >=5 cells and keep all cells with >=200 and <= 5000 genes expressed.
The global-scaling normalization method “LogNormalize” normalizes the gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000), and log-transforms the result.
Genome_build: GRCm38
Supplementary_files_format_and_content: Seurat global-scaling normalization method “LogNormalize”

source_name: macrophage

growth_protocol: Mammary glands were harvested from 10-week-old diestrus FVB/NJ mice (n=3). After removing the lymph nodes, thoracic (#3) and inguinal (#4) glands were pooled, minced and incubated in DMEM containing 2 mg/ml collagenase A (Roche) and 2 units/ml DNase (Sigma) at 37oC for 12 minutes, and single cells were purified as previously described. After red blood cell depletion with ACK lysis buffer (Thermo Fisher Scientific), single cells were incubated with mouse CD45 microbeads (Miltenyi Biotec) and CD45+ cells were enriched according to the manufacturer's protocol and prepared for scRNA-seq.

extract_protocol:
10X GEM Technology
Barcoding and library construction were performed using 10X GEM technology
Chromium single-cell 3' v2 library

value: FVB/NJ

value: CD45+ microbead enrichment


title: WT_CIM4d_r3

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d replicate 3


title: WT_SIM4d_r1

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d and SIM4d replicate 1


title: WT_CIM4d_r2

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d replicate 2


title: WT_CIM4d_r1

description: RNA-seq for wild-type hypocotyl explant incubated on CIM 4d replicate 1


title: BC14

description: microRNA expression of primary breast cancer.


title: BC12


title: LNM13

description: microRNA expression of lymph node metastatic breast cancer.


title: BC13


title: LNM14


title: WT_AfterCut_r3

description: RNA-seq for wild-type hypocotyl  after cut replicate 3


title: WT_AfterCut_r2

description: RNA-seq for wild-type hypocotyl  after cut replicate 2


title: HCT116 Tumor

description: Gene expression in tumor without drug treatment

source_name: Xenograft derived from HCT116


title: LNM12


title: H3.3-0

value: Bone Marrow Derived Macrophage


title: H3.3-60


title: IUGR2: Placental tissue, Intrauterine growth restriction, sample 2

city: Mexico City

first: Ivan

last: Salido-Guadarrama

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 8 x60k Human Gene expression  Microarrays (G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The glass slides were scanned using an Agilent G2565BA microarray scanner

data_processing: Relative target intensity was calculated using Agilent Feature Extraction Software version 11.5.1 and non-detected probes, as evaluated by the gIsGeneDetected parameter, were removed

source_name: Placental tissue,Intrauterine growth restriction, sample 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. All samples showed a yield ≧ 0.825 and a specific activity ≧ 6. all appropiate for the 8 pack format.

extract_protocol: RNA extraction was performed from 30-100 mg of fresh placental tissue, using RNeasy Fibrous Tissue Mini KitÒ (Qiagen) following manufactures instructions. Purity and concentration of total RNA was measured using a NanoDropÒ UV-Vis spectrophotometer (Thermo Fisher Scientific Inc) and RNA Integrity Number (RIN) was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Sampling and RNA extraction was performed by the same personnel using the same methodology

treatment_protocol: Full thickness placental tissue was collected immediately after C-sections taking samples from the middle region of the placenta, close to the umbilical cord and, right after collection samples were transported to the lab (at 4 ºC ) and within one hour, samples were rinsed with cold 1X Red Blood Cells Lysis buffer (RBC) and washed with cold 1X PBS in order to eliminate contamination with maternal blood

value: placental tissue

tag: gender

value: female

tag: disease state

value: Intrauterine growth restriction


title: IUGR5: Placental tissue, Intrauterine growth restriction, sample 5

source_name: Placental tissue,Intrauterine growth restriction, sample 5


title: IUGR9: Placental tissue, Intrauterine growth restriction, sample 9

source_name: Placental tissue,Intrauterine growth restriction, sample 9


title: IUGR10: Placental tissue, Intrauterine growth restriction, sample 10

source_name: Placental tissue,Intrauterine growth restriction, sample 10


title: NP1: Placental tissue, Control group, sample 1

source_name: Placental tissue,Control group, sample 1

value: Control group


title: CTRL 7

city: Messina

first: M'Hammed

last: Aguennouz

address: Piazza Pugliatti, 1

department: Department of Clinical and Experimental Medicine

country: Italy

institute: University of Messina

description: about 100ng RNA input

hyb_protocol: Purified and labeled target/probe complexes were hybridized to the manufactuer supplied cartridge, according to the manufactuer's instructions.

scan_protocol: The cartridges were digitally imaged and analyzed using the nCounter Digital Analyzer.

data_processing: Data analysis was performed using nSolver 3.0 software. Quality of raw data was assessed through an evaluation of imaging, binding density, positive control linearity and positive control limit of detection parameters. A code-set normalization was applied to minimize technical noise (variations in purification, binding, hybridization efficiency), according to the nSolver analysis software protocol.

label: not provided

source_name: serum

label_protocol: RNA were hybridized to color codes and washed using a two step-magnetic bead method, according to the manufactuer's instructions.

growth_protocol: not applicable

extract_protocol: Extraction of RNA was carried out from 800 μl of serum samples by using a Qiagen miRNeasy Mini Kit (Qiagen, GmbH, Hilden, Germany), according to Qiagen Supplementary Protocol for purification of total RNA (including small RNAs) from serum and plasma.

treatment_protocol: not applicable

value: CTRL

tag: Sex

value: F

value: serum


title: CTRL 10

description: about 100ng RNA input


title: NP13: Placental tissue, Control group, sample 13

source_name: Placental tissue,Control group, sample 13


title: CTRL 9

description: about 100ng RNA input

value: M


title: CTRL 8

description: about 100ng RNA input


title: IUGR11: Placental tissue, Intrauterine growth restriction, sample 11

source_name: Placental tissue,Intrauterine growth restriction, sample 11


title: CTRL 5

description: about 100ng RNA input


title: CTRL 4

description: about 100ng RNA input


title: H3K36me2-60


title: NP11: Placental tissue, Control group, sample 11

source_name: Placental tissue,Control group, sample 11


title: IUGR12: Placental tissue, Intrauterine growth restriction, sample 12

source_name: Placental tissue,Intrauterine growth restriction, sample 12


title: NP2: Placental tissue, Control group, sample 2

source_name: Placental tissue,Control group, sample 2


title: NP3: Placental tissue, Control group, sample 3

source_name: Placental tissue,Control group, sample 3


title: WT_AfterCut_r1

description: RNA-seq for wild-type hypocotyl  after cut replicate 1

value: Columbia (Col-0)

tag: genotype


title: PE-IUGR1: Placental tissue, Intrauterine growth restriction associated with severe preeclampsia, sample 1

source_name: Placental tissue,Intrauterine growth restriction associated with severe preeclampsia, sample 1


title: NP10: Placental tissue, Control group, sample 10

source_name: Placental tissue,Control group, sample 10


title: NP8: Placental tissue, Control group, sample 8

source_name: Placental tissue,Control group, sample 8


title: PE-IUGR2: Placental tissue, Intrauterine growth restriction associated with severe preeclampsia, sample 2

source_name: Placental tissue,Intrauterine growth restriction associated with severe preeclampsia, sample 2


title: IUGR8: Placental tissue, Intrauterine growth restriction, sample 8

source_name: Placental tissue,Intrauterine growth restriction, sample 8


title: NP4: Placental tissue, Control group, sample 4

source_name: Placental tissue,Control group, sample 4


title: CTRL 3

description: about 100ng RNA input


title: H3K36me2-0

source_name: Bone Marrow Derived Macrophage - unstimulated


title: PE-IUGR3: Placental tissue, Intrauterine growth restriction associated with severe preeclampsia, sample 3

source_name: Placental tissue,Intrauterine growth restriction associated with severe preeclampsia, sample 3


title: CTRL 6

description: about 100ng RNA input


title: H3K36me3-60

source_name: Bone Marrow Derived Macrophage - stimulated/LPS treated


title: H3K36me3-0


title: H3S31ph-60


title: CTRL 2

description: about 100ng RNA input


title: CTRL 1

description: about 100ng RNA input


title: CMT 10

description: about 100ng RNA input

value: CMT


title: CMT 8

description: about 100ng RNA input


title: CMT 9

description: about 100ng RNA input


title: CMT 7

description: about 100ng RNA input


title: inputDNA-0_ChIPSeq


title: inputDNA-60_ChIPSeq


title: CMT 6

description: about 100ng RNA input


title: PE-IUGR4: Placental tissue, Intrauterine growth restriction associated with severe preeclampsia, sample 4

source_name: Placental tissue,Intrauterine growth restriction associated with severe preeclampsia, sample 4


title: PE-IUGR5: Placental tissue, Intrauterine growth restriction associated with severe preeclampsia, sample 5

source_name: Placental tissue,Intrauterine growth restriction associated with severe preeclampsia, sample 5


title: 3205_120_rep1

source_name: RAW264.7 (macrophage cell line)


title: PE-IUGR6: Placental tissue, Intrauterine growth restriction associated with severe preeclampsia, sample 6

source_name: Placental tissue,Intrauterine growth restriction associated with severe preeclampsia, sample 6


title: 3205_60_rep2


title: PE12: Placental tissue, Preeclampsia with severe features, sample 12

source_name: Placental tissue,Preeclampsia with severe features, sample 12

value: Preeclampsia with severe features


title: PE11: Placental tissue, Preeclampsia with severe features, sample 11

source_name: Placental tissue,Preeclampsia with severe features, sample 11


title: CMT 5

description: about 100ng RNA input

source_name: serum


title: CMT 3

description: about 100ng RNA input


title: CMT 4

description: about 100ng RNA input


title: 3205_60_rep1


title: H3S31ph-0


title: PE3: Placental tissue, Preeclampsia with severe features, sample 3

source_name: Placental tissue,Preeclampsia with severe features, sample 3


title: PE9: Placental tissue, Preeclampsia with severe features, sample 9

source_name: Placental tissue,Preeclampsia with severe features, sample 9


title: PE7: Placental tissue, Preeclampsia with severe features, sample 7

source_name: Placental tissue,Preeclampsia with severe features, sample 7


title: CMT 2

description: about 100ng RNA input


title: 3205_120_rep2


title: PE6: Placental tissue, Preeclampsia with severe features, sample 6

source_name: Placental tissue,Preeclampsia with severe features, sample 6


title: PE10: Placental tissue, Preeclampsia with severe features, sample 10

source_name: Placental tissue,Preeclampsia with severe features, sample 10


title: 3205_0_rep1


title: CMT 1

description: about 100ng RNA input


title: Asympt_ATTR 10

description: about 100ng RNA input


title: 264_60_rep2


title: Asympt_ATTR 9

description: about 100ng RNA input


title: 264_60_rep1


title: 3205_0_rep2


title: 264_0_rep1


title: 264_0_rep2


title: 264_120_rep1


title: Asympt_ATTR 7

description: about 100ng RNA input


title: HL-60_SF4

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HG-U133-plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalisation of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

label: biotin

source_name: lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

tag: cell line

value: control


title: HL-60_SF3


title: HL-60_SF-NANOG1

value: NANOG overexpression


title: RAW_120_rep2


title: RAW_120_rep1


title: 264_120_rep2


title: Asympt_ATTR 5

description: about 100ng RNA input


title: Asympt_ATTR 6

description: about 100ng RNA input


title: RAW_60_rep2


title: EZH2-KO1-MYB-ChIP-seq

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: UCL

description:
ChIP of Myb protein in EZH2- cells
TL-1-EZH2-Myb_S2

data_processing:
Bam files were derived by ChIP sequencing data aligned to the hg19 human assembly using bwa-mem (v0.7.15).
BigWig files for viewing ChIP alignments were created using deeptools bamCoverage (v3.0.2) with bin height scaled to expected read counts using the Counts Per Million mapped reads (CPM) method
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Processed data file sare UCSCS Bigwig format

source_name: Jurkat cell line

growth_protocol: Cells were in culture in complete RPMI (10% FBS, 1% Pen/Strep).

extract_protocol:
Exponentially growing cells were washed and Chipmentation protocol adapted from (Schmidl C, et al, Nat Methods, 2015) was carried out.
DNA was amplified in the following conditions (25µl KAPA HiFi 2x master mix (pre-activated), 20µl ChIP DNA, Nextera primer Ad1/Ad2.x at 0.75 uM, were Ad2 primers were indexed per sample in a 50µl reaction volume) and cycled to the number of cycles judged from Q-PCR. Input controls were tagmented in the following conditions (2.5ng input DNA, 1µl tagmentation enzyme, 1µl 5x tagmentation buffer (Tris pH8.0 50mM, MgCl2 25mM) in a total volume of 5µl at 55C for 5 mins. Tagmentation was stopped by the addition of 1µl 0.6% SDS at room temperature for 5mins. Inputs were amplified in the following conditions (25µl KAPA HiFi 2x master mix (pre-activated), 1.5µl Ad1 primer, 1.5µl Ad2.x index primer, 25µl, 6µl tagmented DNA in a 50µl reaction) for 12 cycles as above. The resulting PCR products were purified using magnetic SPRI beads (Agencourt AMPure XP Beckman Coulter, Cat. A63881) and after two 80% ethanol washes were resuspended in 50µl water. Size separation was performed by incubation with  SPRI beads, transfer of supernatant to a new tube and then addition of 12.5µl fresh SPRI beads. Following two further 80% ethanol washes the size selected libraries were eluted into 15µl water. Libraries were checked and quantified by QubitTM (Invitrogen) and Tapestation (Agilent).
ChIP-seq normalised libraries were pooled and sequenced using a NextSeq® (Illumina) 75bp paired end short read sequencer using standard protocols.

value: Jurkat

value: T lymphocyte

tag: genotype/variation

value: CRISPR/Cas9- edited -EZH2-KO1

value: Anti-Myb clone 1-1 (Millipore, Cat. 05-175)


title: Asympt_ATTR 4

description: about 100ng RNA input

tag: tissue


title: RAW_0_rep2

value: Bone Marrow Derived Macrophage

tag: stimulation time


title: EZH2-WT-MYB-ChIP-seq

description:
ChIP of Myb protein
TL-1-PJ-Myb_S6

tag: chip antibody


title: RAW_60_rep1

data_processing:
RNAseq
Sequenced reads were trimmed for adaptor sequence and quality control with Trim Galore v.0.5.0.
Resulting trimmed fastq files were aligned to GENCODE vM3 transcriptome in mm10 using STAR aligner v.2.4.2 with default settings and then name sorted using SAMtools v.1.5 with default parameters.
Utility featureCounts from Subread v.1.4.6 used to calculate raw counts reads per geen to be used as input for differential expression analysis following the DESeq2 workflow.
Genome_build: mm10
Supplementary_files_format_and_content: .tdf (tiled data file) files were generated from bam files using igvtools v.2.3.98 count to compute the average feature density over a default-specified window size; bigWig files were generated from bam files using deeptools v.2.5.4 bamCoverage to obtain counts normalized to 1x depth of coverage as reads per genomic content (RPGC); .txt file contains an R v3.4.0 dataframe of statistics of differential analysis by DESeq2 for each gene (baseMean, log2FoldChange, pvalue, padj).
ChIPseq:
ChIP-seq reads were mapped to the mm10 genome using Bowtie2 v.2.3.4.1 with the following parameters: -p 8 -k 1 -N 1.
Aligned reads underwent three stages of filtering using SAMtools v.1.5. First, the unmapped, non-primary, qc failed, and multi-mapped reads were discarded. PCR duplicates were then marked by Picard Tools v.2.14.0 using 'VALIDATION_STRINGENCY=SILENT and REMOVE_DUPLICATES=false" options and removed by SAMtools (-F 1796). Then, chromosome M and scaffolds were removed to create the final filtered bam file.
Genome_build: mm10
Supplementary_files_format_and_content: .tdf (tiled data file) files were generated from bam files using igvtools v.2.3.98 count to compute the average feature density over a default-specified window size; bigWig files were generated from bam files using deeptools v.2.5.4 bamCoverage to obtain counts normalized to 1x depth of coverage as reads per genomic content (RPGC); .txt file contains a tab-delimited file of read densities used for downstream analysis in R v.3.4.0.
Regarding the chip_rna_lpsi120.txt file, it is the combined data frame of our ChIP analysis and our output from our differential DESEQ2 analysis for our RNAseq data from time 0 to time 120. The samples inputDNA-0_ChIPseq and inputDNA-60_ChIPseq were used for a type of normalization during processing.
Regarding the chip_rna_lpsi120.txt file, it is the combined data frame of our ChIP analysis and our output from our differential DESEQ2 analysis for our RNAseq data from time 0 to time 120. The samples inputDNA-0_ChIPseq and inputDNA-60_ChIPseq were used for a type of normalization during processing.


title: RAW_0_rep1


title: Asympt_ATTR 2

description: about 100ng RNA input


title: Asympt_ATTR 3

description: about 100ng RNA input


title: Asympt_ATTR 1

description: about 100ng RNA input


title: Asympt_ATTR 8

description: about 100ng RNA input


title: HL-60_SF-NANOG2


title: BMDM_LPS_DMSO_120_rep3

source_name: Bone Marrow Derived Macrophage - stimulated/DMSO treated


title: BMDM_LPS_DMSO_120_rep2


title: BMDM_LPS_DMSO_120_rep1


title: Sympt_ATTR 9

description: about 100ng RNA input


title: Sympt_ATTR 8

description: about 100ng RNA input


title: Sympt_ATTR 6

description: about 100ng RNA input


title: Sympt_ATTR 7

description: about 100ng RNA input


title: BMDM_LPS_DMSO_60_rep1


title: Sympt_ATTR 10

description: about 100ng RNA input


title: BMDM_LPS_DMSO_0_rep3

source_name: Bone Marrow Derived Macrophage - unstimulated/DMSO treated


title: BMDM_LPS_DMSO_0_rep2


title: Sympt_ATTR 3

description: about 100ng RNA input


title: BMDM_LPS_DMSO_0_rep1


title: BMDM_LPS_DMSO_60_rep3


title: Sympt_ATTR 4

description: about 100ng RNA input


title: Sympt_ATTR 5

description: about 100ng RNA input


title: Sympt_ATTR 1

description: about 100ng RNA input


title: Sympt_ATTR 2

description: about 100ng RNA input


title: BMDM_LPS_DMSO_60_rep2


title: AKS 4

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

description:
36_aks
ws190219_36
36_(Clariom_S_Mouse)

hyb_protocol: Fragmented cDNA was hybridized on mouse Clariom D pico assay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Normalisation was done using the affymetrix power tools RMA sketch, without filtering. Data were analysed using R2 Genomics analysis and visualization platform

label: Biotin

source_name: Small intestinal organoids from C57BL/6 Villin-Cre Apc fl/fl Kras wt/G12D mouse recombined ex vivo with 4-OH tamoxifen and transduced with shRNA against Smad4

label_protocol: 400 ng RNA was amplified and labeled using 3' IVT nano kit (ThermoFisher) and Ovation RNA amplification system v2 kit (Nugen) according to manufacturers protocol

growth_protocol: Organoids were grown in Matrigel and standard organoid growth medium ENR

extract_protocol: Bioline Isolate II RNA mini kit

tag: strain background

value: Loss of Apc, transgenic KrasG12D, loss of Smad4

tag: tissue/cell type

value: Small intestinal organoids


title: AK 3

description:
24_ak
ws190219_24
24_(Clariom_S_Mouse)

source_name: Small intestinal organoids from C57BL/6 Villin-Cre Apc fl/fl Kras wt/G12D mouse recombined ex vivo with 4-OH tamoxifen

value: Loss of Apc, transgenic KrasG12D


title: AKSP 1

description:
8_aksp
ws190219_08
8_(Clariom_S_Mouse)

source_name: Small intestinal organoids from C57BL/6 Villin-Cre Apc fl/fl Kras wt/G12D mouse recombined ex vivo with 4-OH tamoxifen and transduced with shRNAs against Smad4 and p53

value: Loss of Apc, transgenic KrasG12D, loss of Smad4, loss of p53


title: AKS 3

description:
26_aks
ws190219_26
26_(Clariom_S_Mouse)


title: AKS 2

description:
16_aks
ws190219_16
16_(Clariom_S_Mouse)


title: AKSP 3

description:
28_aksp
ws190219_28
28_(Clariom_S_Mouse)


title: AKS 1

description:
6_aks
ws190219_06
6_(Clariom_S_Mouse)


title: AKSP 4

description:
38_aksp
ws190219_38
38_(Clariom_S_Mouse)


title: MytilusHygallo18vs22 [12_5]

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Applied biosystems Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, global mean normalisation across microarray surfaces and local mean normalisation across element signal intensity. Data obtained from log2 of processed Ch2 signal / processed Ch1 signal.

organism: Mytilus edulis x Mytilus galloprovincialis

label_protocol: 5 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

growth_protocol: Microplate with oocytes and sperms were incubated in a temperature-controlled chamber al 18°C; 22°C for 48h in the dark.

extract_protocol: Total RNA extracted from 200.000 larvae from each experimental condition using Trizol following manufacturer's instructions

value: Mytilus galloprovincialis male

tag: temperature


title: KD_02

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
The raw FASTQ reads were quality trimmed using Trimmomatic (version 0.36) to trim low quality bases, systematic base calling errors, as well sequencing adapter contamination. FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) was used to assess the quality of the sequenced reads pre/post quality trimming. Only the reads that passed quality trimming in pairs were retained for downstream analysis. The quality trimmed RNAseq reads were aligned to the Homo sapiens GRch38.p4 genome using HISAT2 (version 2.0.4). The resulting SAM alignment files for each sequenced sample were then converted to BAM format and sorted by coordinate using SAMtools (version 0.1.19). The BAM alignment files were processed using HTseq-count using the reference annotation file to produce raw counts for each sample.
Genome_build: GRch38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read counts for each sample.

source_name: HeLa cells

growth_protocol: Full DMEM medium with 10%FBS and Pen/Strep.

extract_protocol:
TRIzol was used to isolate total RNA.
The RNA seq libraries were prepared with TruSeq RNA Library Prep kit v2 as per protocol instructions. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer with a dsDNA high sensitivity kit and on an Agilent 2100 bioanalyzer using a DNA 7500 kit. Then libraries were normalized, pooled and quantified with a KAPA Library quantification kit for Illumina platforms on a ABI StepOnePlus qPCR machine, then loaded on a high output flow cell and paired-end sequenced (2x75 bp) on an Illumina NextSeq 550 next generation sequencer (performed at the NYUAD Sequencing Center).

treatment_protocol: For MVI knock-down experiments, HeLa cell monolayers, seeded to 30 – 50 % confluency, were transfected with human myosin VI siRNA duplex (5′GGUUUAGGUGUUAAUGAAGtt-3′) (Ambion) or AllStars Negative Control siRNA duplex (Qiagen) at a concentration of 50 nM, using Lipofectamine 2000 (Invitrogen), according to the manufacturer’s guidelines. Cells were harvested after 48 h for further analysis.

value: HeLa

tag: cell type

value: cervical cancer cell line

tag: sirna

value: MyoVI


title: KD_03


title: KD_01


title: MytilusHygallo18vs22 [12_6]


title: A 3

description:
22_apc
ws190219_22
22_(Clariom_S_Mouse)

source_name: Small intestinal organoids from C57BL/6 Villin-Cre Apc fl/fl mouse recombined ex vivo with 4-OH tamoxifen

value: Loss of Apc


title: MytilusHyedulis18vs22 [12_2]

value: Mytilus edulis male


title: MytilusHyedulis18vs22 [12_3]


title: AK 2

description:
14_ak
ws190219_14
14_(Clariom_S_Mouse)


title: AK 1

description:
4_ak
ws190219_04
4_(Clariom_S_Mouse)


title: A 4

description:
32_apc
ws190219_32
32_(Clariom_S_Mouse)


title: AKSP 2

description:
18_aksp
ws190219_18
18_(Clariom_S_Mouse)


title: A 2

description:
12_apc
ws190219_12
12_(Clariom_S_Mouse)


title: A 1

description:
2_apc_
ws190219_02
2_(Clariom_S_Mouse)


title: WT 1

description:
1_wildtype_(apc_non-recombined)
ws190219_01
1_(Clariom_S_Mouse)

source_name: Small intestinal organoids from C57BL/6 Villin-Cre Apc fl/fl mouse unrecombined

value: Apc wildtype control


title: WT 3

description:
21_wildtype_(apc_non-recombined)
ws190219_21
21_(Clariom_S_Mouse)


title: MytilusHygallo18vs22 [12_7]


title: Mytilusedulis18vs22 [10_8]

organism: Mytilus edulis


title: scrWT_03

value: scrambled


title: scrWT_02


title: scrWT_01


title: WT 4

description:
31_wildtype_(apc_non-recombined)
ws190219_31
31_(Clariom_S_Mouse)


title: WT_03

value: untreated


title: Mytilusedulis18vs22 [10_7]


title: WT_02


title: MytilusHyedulis18vs22 [12_1]


title: WT_01


title: TY 13: ex vivo naïve B cells

status: Public on May 30 2020

city: Berlin

first: Thomas

last: Sommermann

address: Robert-Rossle-Str. 10

institute: Max Delbruck Center for Molecular Medicine

data_processing:
Adapters and low quality reads trimmed using trim-galore version 0.4.2
reads mapped to reference genome using STAR version 2.5.1b
used STAR with --quantMode GeneCounts to produce counts by genes
Genome_build: mm10 (GRCm38)

source_name: spleen

growth_protocol: ex vivo

extract_protocol:
FACS-sorted cells were pelleted and RNA was extracted using a Rneasy kit (Quiagen)
Illumina TruSeq RNA

tag: secondary host

tag: secondary host strain

value: naive B cells

tag: strain

tag: facs-sort

value: spleen


title: Mytilusgallo18vs22 [10_2]

organism: Mytilus galloprovincialis


title: Mytilusedulis18vs22 [10_5]


title: Mytilusgallo18vs22 [10_3]


title: TY 12: ex vivo naïve B cells


title: LASV_CAGE

first: Sook Yuin Jessica

last: Ho

state: New York

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
CAGE of LASV infected Vero Cells
CAGE of LASV infected Vero cells to identify cap-snatching events.

data_processing:
Library strategy: CAGE
Unique chimeric host-virus reads were extracted from the resulting FASTQ files by searching for a match to conserved nucleotides at the 5′ end of the LASV (Josiah Strain) mRNAs (GCAC[M]G[N]GGATCCT), allowing for a maximum of 1 mismatch, and removing all reads with ambiguously mapped nucleotides. The reference genome of LASV was obtained from UniProt (Accessions: J04324 and U73034). Reads were kept if at least 60 nucleotides could be mapped and assigned unambiguously to the viral reference sequences. Each read was then split into host derived or virus derived sequences based on the sequences of viral 5′ end (GCAC[M]G[N]GGATCCT).
Genome_build: The reference genome of LASV was obtained from UniProt (Accessions: J04324 and U73034)
Supplementary_files_format_and_content: Table of unique, unambiguously mapped LASV reads. Col1: Sequence of Cap-snatched event, Col2: Sequence of Viral Read, Col 3-6: Assigned viral mRNA  [SR=Reverse Sense, S segment; SF=Forward Sense, S Segment; LR=Reverse Sense, L Segment; LF=Forward Sense, L segment; 1=TRUE, 0=FALSE], Col 7: Percent Identity (PID) of read to the assigned segment

organism: Mammarenavirus lassaense

source_name: LASV (Josiah Strain)

growth_protocol: Vero Cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
2 days post infection, cells were lyzed in Trizol. Total RNA from Trizol Treated isolates were isolated and DNAse treated using the Purelink RNA Minikit (Invitrogen)
Purified RNA was submitted for CAGE sequencing at Kabushiki Kaisha DNAForm Japan.
Libraries were prepared as previously described (FANTOM Consortium et al, A promoter level mammalian expression atlas, Nature, 507(7493), 462-470 (2014))

treatment_protocol: Vero Cells were infected with LASV (Josiah Strain) at MOI 0.1

tag: moi

tag: host cell

value: Vero

tag: time post infection

value: 2 days


title: PRP8Aa prp8bb ovules rep2

city: Prague 6

first: Mila

last: Juricek

address: Rozvojova 313

country: Czech Republic

institute: Inst. Exp. Botany, Czech Acad Sci

description: mixed PRP8A;prp8b and prp8a;prp8b ovules

data_processing:
Basecalling by Illumina Casava1.8
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, adaptively trimmed by sickle and then mapped to TAIR10 whole genome with STAR aligner (Dobin et al.: Bioinformatics (2013) 29:15)
Counting for differential expression analysis was done with program featureCounts of the Subread package v1.6.0  with parameters -T 10 -p -P -a -G (Liao et al.: Nucleic Acids Res. (2013) 41: e108)
Counting for differential exone usage analysis was done with program featureCounts of the Subread package v1.6.0 with parameters set by dexseq_count.py script of the DEXSeq R package (Anderset al.: Genome Research (2014) 22:4025)
Intron retention analysis was performed with IRFinder according to Middleton et al.: Genome Biology (2017) 18:51
Differential expression analysis using DESeq2 as described in Love and Anders: Genome Biology (2014) 15:550
Differential exone usage analysis with DEXSeq according to Anderset al.: Genome Research (2014) 22:4025
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for differential expression analysis
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for differential exone usage analysis
Supplementary_files_format_and_content: Table with metrics for all measured introns from IRFinder
Supplementary_files_format_and_content: Table with differencialy expressed genes (p-value <0.05)
Supplementary_files_format_and_content: Tar archive with listof genes with differential exone usage in html format, including graphical representation

source_name: T-DNA insertion ovules

growth_protocol: Arabidopsis thaliana plants were grown at 22°C and 60% humidity in Conviron PGC Flex growth chambers under 16 h light/8 h dark conditions.

extract_protocol:
Ovules were isolated by dissecting flowers from stage 13-14 (FG7) containing a fully developed embryo sac (Christensen et al., 1997) from PRP8Aa;bb double mutant plants and wild-type control plants. RNA extracted from three biological replicates of each was used for Next Generation (NGS) RNA Sequencing. Total RNA was isolated from dissected ovules using Qiagen Plant RNA extraction kit (Qiagen). Total RNA was treated with DNase (Ambion) and RNA integrity (RIN) analyzed using a bioanalyzer. RNA (800 ng) with RIN >7 was processed using TrueSeq stranded total RNA library with RiboZero plant prep kit (Illumina, San Diego, CA, USA) as per the manufacturer’s protocol. Samples were run on HiSeq4000 2×100 bp paired-end run Illumina sequencing machine (Illumina, San Diego, CA, USA) by Macrogen (Geumcheon-gu, Seoul, S.Korea).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovules from stage 13-14 flowers

tag: development stage

value: 6-week old plants

tag: genotype

value: mixture of PRP8A;prp8b and prp8a;prp8b


title: Mytilusgallo18vs22 [10_1]


title: PRP8Aa prp8bb ovules rep3

tag: tissue


title: PRP8Aa prp8bb ovules rep1


title: Ovules WT rep1

description: wild type ovules

source_name: wild type ovules

value: wild type


title: Ovules WT rep2

description: wild type ovules


title: IP170_9

status: Public on May 29 2020

city: Boston

first: Jean-Pierre

last: Roussarie

state: MA

address: 72 E Concord Street

department: Anatomy & Neurobiology

institute: Boston University School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using STAR version 2.5.3a
Reads falling on each gene are counted by HT-Seq
Genome_build: mm10
Supplementary_files_format_and_content: rawcount
Supplementary_files_format_and_content: dexseq_count

source_name: brain

extract_protocol:
TRAP
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

tag: treatment

value: PTBP1 OE


title: IP170_10


title: IP170_8

value: control OE


title: IP170_6


title: IP170_3


title: IP170_2


title: IP170_1


title: IP162_8


title: IP162_7


title: WT_T 0_1, biological rep1

city: Brisbane

first: yong

middle: hua

last: sheng

state: QLD

address: 37 Kent St

department: Inflammatory Disease Biology

country: Australia

institute: Mater Research Institute – The University of Queensland

description: Gene expression data from WT stomach (sham ) mock -infected

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Log2- RMA -gene-default-Signal.

source_name: stomach of mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol:
H. pylori strain SS1(Lee et al., 1997), was initially cultured on horse blood agar plates. Prior to infection of mice, H. pylori were cultured in brain heart infusion broth (BHI; Oxoid) containing 5% horse serum (Sigma, Castle Hill, Australia), 0.02% Amphostat, and Skirrow’s Selective Supplements under microaerophilic conditions for 24 h at 37°C
Muc1−/− (derived and kindly provided by Sandra Gendler, Mayo Clinic (Spicer et al., 1995)) and  wild-type (WT) mice  were bred within the Veterinary Science animal house, University of Melbourne.

extract_protocol: RNA was extracted from each longitudinally bisected half stomach of each mouse using Trizol (Invitrogen) and further purified on RNeasy columns (Qiagen).

treatment_protocol: Mice were infected intragastrically once with 107 H. pylori SS1 suspended in 0.1 mL BHI and groups (n = 3 of each genotype) were euthanased after 8, 24 and 72 h for collection of gastric tissues to determine bacterial abundance and gastric gene expression. Control uninfected (sham) mice were mock-infected   with 0.1 mL sterile BHI and sampled after 8, 24 and 72 h mock-infection (n = 3 of each genotype).

tag: agent

value: sham

value: WT


title: Muc1-/- _T 72h_1, biological rep1

description: Gene expression data from Muc1-/- stomach at 72h -infection

value: H. pylori

tag: time point


title: Muc1-/- _T 8h_1, biological rep1

description: Gene expression data from Muc1-/- stomach at 8h -infection


title: Ovules WT rep3

description: wild type ovules


title: WT_T 8h_1, biological rep1

description: Gene expression data from WT stomach at 8h -infection


title: IP162_10


title: Muc1-/- _T 24h_1, biological rep1

description: Gene expression data from Muc1-/- stomach at 24h -infection


title: WT_T 72h_1, biological rep1

description: Gene expression data from WT stomach at 72h -infection


title: Muc1-/- _T 0_1, biological rep1

description: Gene expression data from Muc1-/- stomach (sham ) mock -infected


title: WT_T 24h_1 , biological rep1

description: Gene expression data from WT stomach at 24h -infection


title: IP162_6


title: IP162_5


title: IP162_3


title: IP162_4


title: IP162_2


title: IP162_1


title: IP170_7


title: MCL_40

status: Public on May 28 2020

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 40th St

institute: University of Nebraska Medical Center

description: Hybridized to U133 plus 2.0 array

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: As per manufacturer (Affymetrix)

data_processing: The data was analyzed using BRB Array-Tools (v4.6.0) via MAS 5.0 using Affymetrix default analysis setting and quartile normalization method. Gene filter to exclude if less than 10% of expression data values have at least 1.5 fold change in either direction of the gene's median value or if percent missing exceeds 60% at any gene was applied.

source_name: tumor biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix)

extract_protocol: Total RNA was extracted from cryopreserved lymphoma tissue using the Qiagen AllPrep DNA/RNA kit. RNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: diease state

value: lymphoma

tag: lymphoma type

value: MCL


title: MCL_41

description: Hybridized to U133 plus 2.0 array


title: MCL_35

description: Hybridized to U133 plus 2.0 array


title: MCL_36

description: Hybridized to U133 plus 2.0 array


title: MCL_33

description: Hybridized to U133 plus 2.0 array


title: MCL_43

description: Hybridized to U133 plus 2.0 array


title: MCL_37

description: Hybridized to U133 plus 2.0 array


title: MCL_34

description: Hybridized to U133 plus 2.0 array


title: MCL_38

description: Hybridized to U133 plus 2.0 array


title: MCL_26

description: Hybridized to U133 plus 2.0 array


title: MCL_27

description: Hybridized to U133 plus 2.0 array


title: MCL_30

description: Hybridized to U133 plus 2.0 array


title: MCL_28

description: Hybridized to U133 plus 2.0 array


title: MCL_39

description: Hybridized to U133 plus 2.0 array


title: MCL_19

description: Hybridized to U133 plus 2.0 array


title: MCL_31

description: Hybridized to U133 plus 2.0 array


title: MCL_29

description: Hybridized to U133 plus 2.0 array


title: MCL_22

description: Hybridized to U133 plus 2.0 array


title: MCL_20

description: Hybridized to U133 plus 2.0 array


title: MCL_17

description: Hybridized to U133 plus 2.0 array


title: MCL_18

description: Hybridized to U133 plus 2.0 array


title: MCL_23

description: Hybridized to U133 plus 2.0 array


title: MCL_32

description: Hybridized to U133 plus 2.0 array


title: MCL_24

description: Hybridized to U133 plus 2.0 array


title: IP170_5


title: MCL_21

description: Hybridized to U133 plus 2.0 array


title: MCL_25

description: Hybridized to U133 plus 2.0 array


title: MCL_42

description: Hybridized to U133 plus 2.0 array


title: MCL_12

description: Hybridized to U133 plus 2.0 array


title: MCL_11

description: Hybridized to U133 plus 2.0 array


title: MCL_3

description: Hybridized to U133 plus 2.0 array


title: MCL_4

description: Hybridized to U133 plus 2.0 array


title: MCL_5

description: Hybridized to U133 plus 2.0 array


title: MCL_16

description: Hybridized to U133 plus 2.0 array


title: MCL_15

description: Hybridized to U133 plus 2.0 array


title: MCL_8

description: Hybridized to U133 plus 2.0 array


title: MCL_7

description: Hybridized to U133 plus 2.0 array


title: MZL_21

description: Hybridized to U133 plus 2.0 array

value: NMZL


title: MCL_10

description: Hybridized to U133 plus 2.0 array


title: MZL_22

description: Hybridized to U133 plus 2.0 array

value: SMZL


title: MZL_19

description: Hybridized to U133 plus 2.0 array


title: MZL_16

description: Hybridized to U133 plus 2.0 array


title: MCL_2

description: Hybridized to U133 plus 2.0 array


title: MCL_14

description: Hybridized to U133 plus 2.0 array


title: MZL_18

description: Hybridized to U133 plus 2.0 array


title: MCL_13

description: Hybridized to U133 plus 2.0 array


title: MZL_13

description: Hybridized to U133 plus 2.0 array


title: MCL_9

description: Hybridized to U133 plus 2.0 array


title: MZL_14

description: Hybridized to U133 plus 2.0 array


title: MZL_20

description: Hybridized to U133 plus 2.0 array


title: MZL_12

description: Hybridized to U133 plus 2.0 array


title: MCL_1

description: Hybridized to U133 plus 2.0 array


title: MZL_15

description: Hybridized to U133 plus 2.0 array


title: lungORG_3: hBO_rep3

status: Public on May 26 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: human bronchial organoids_rep3

data_processing:
Sequencing was performed on an Illumina NextSeq500 or NovaSeq6000 platform in a 152 or 101-base single-end mode, respectively.
Illumina RTA 2.4.11 and Casava1.8.2 softwares were used for basecalling for an Illumina NextSeq500 or NovaSeq6000 platform, respectively.  .
Fastq files were generated using bcl2fastq2.
Adapter sequences were trimmed from raw reads by cutadapt ver 2.7 and then trimmed reads were mapped to the human reference genome sequences (hg19) using HISAT2 v2.1.0.
The raw counts were calculated using featureCounts v 2.0.0.
Genome_build: hg19

source_name: human bronchial organoids_rep3

growth_protocol: Normal human bronchial epithelial cells (hBEpC, Lonza) were suspended in 10 mg/ml cold Matrigel growth factor reduced (GFR) basement membrane matrix. 50 μL drops of cell suspension were solidify on pre-warmed Nunc cell-culture treated multidishes (24 well plate) at 37°C for 10 min, and then 500 μL of the expansion medium was added to each well. The expansion medium was changed every 2 days. HBO were passaged every 10-12 days. To passage the hBO, organoids were suspended in 1 mL 0.5 mM EDTA/PBS (Nacalai tesque) and mechanically sheared using P1000 pipette tip, and 2 mL TrypLE Select (Thermo Fisher Scientific) was added to the suspension. After incubating for 5 min at room temperature, organoids were mechanically sheared using P1000 pipette tip. 7 mL of the expansion medium was added, and the organoid suspension tubes were centrifuged at 400 rpm. Organoid fragments were re-suspended in the cold expansion medium and seeded as above. The hBO were passaged every 10 days. To maturate the hBO, the expanded hBO were cultured with the differentiation medium for 5 days.

extract_protocol:
Total RNA was isolated from hBO and A549 cells using ISOGENE II (NIPPON GENE).
Library preparation was performed using a NEBNext Ultra II Directional RNA Library Prep Kit for an Illumina NextSeq500 and a TruSeq stranded mRNA sample prep kit for NovaSeq6000 platform according to the manufacturer’s instructions.

treatment_protocol: Approximately 100 organoids were infected with 7.0×10^4 TCID50 of SARS-CoV-2 in 24 well plate containing 500 uL differentiation medium. The one-half of differentiation medium containing SARS-CoV-2 was replaced with fresh differentiation medium every day. After 5 days from the infection, the hBO and their supernatant were collected. In the drug treatment experiment, the infected hBO were cultured with the differentiation medium containing 10 μM camostat (Sigma-Aldrich) for 5 days.

value: Bronchi


title: lungORG_1: hBO_rep1

description: human bronchial organoids_rep1

source_name: human bronchial organoids_rep1


title: MCL_6

description: Hybridized to U133 plus 2.0 array


title: MZL_9

description: Hybridized to U133 plus 2.0 array


title: lungNHBE_3: hBEpC_rep3

description: primary human bronchial epithelial cells_rep3


title: MZL_8

description: Hybridized to U133 plus 2.0 array


title: MZL_11

description: Hybridized to U133 plus 2.0 array


title: MZL_3

description: Hybridized to U133 plus 2.0 array

value: EMZL


title: lungNHBE_2: hBEpC_rep2

description: primary human bronchial epithelial cells_rep2


title: A549_3: A549_rep3

description: A549 cells_rep3

source_name: A549 cells_rep3

value: lung tumor


title: MZL_1

description: Hybridized to U133 plus 2.0 array


title: MZL_5

description: Hybridized to U133 plus 2.0 array


title: MZL_6

description: Hybridized to U133 plus 2.0 array


title: MZL_4

description: Hybridized to U133 plus 2.0 array


title: MZL_2

description: Hybridized to U133 plus 2.0 array


title: WT 2

description:
11_wildtype_(apc_non-recombined)
ws190219_11
11_(Clariom_S_Mouse)

tag: strain background

tag: genotype/variation

value: Apc wildtype control

tag: tissue/cell type

value: Small intestinal organoids


title: A549_2: A549_rep2

description: A549 cells_rep2

source_name: A549 cells_rep2


title: MZL_10

description: Hybridized to U133 plus 2.0 array


title: lungORG_2: hBO_rep2

description: human bronchial organoids_rep2

source_name: human bronchial organoids_rep2


title: MZL_7

description: Hybridized to U133 plus 2.0 array


title: AK 4

description:
34_ak
ws190219_34
34_(Clariom_S_Mouse)

source_name: Small intestinal organoids from C57BL/6 Villin-Cre Apc fl/fl Kras wt/G12D mouse recombined ex vivo with 4-OH tamoxifen

value: Loss of Apc, transgenic KrasG12D


title: VC_3: SARS-CoV-2+camostat_rep3

description: SARS-CoV-2-infected human bronchial organoids treated with camostat_rep3


title: VC_1: SARS-CoV-2+camostat_rep1

description: SARS-CoV-2-infected human bronchial organoids treated with camostat_rep1


title: A549_1: A549_rep1

description: A549 cells_rep1

source_name: A549 cells_rep1


title: V_1: SARS-CoV-2_rep1

description: SARS-CoV-2-infected human bronchial organoids_rep1


title: V_3: SARS-CoV-2_rep3

description: SARS-CoV-2-infected human bronchial organoids_rep3


title: Ctl_3: uninfected hBP_rep3

description: uninfected human bronchial organoids_rep3


title: Ctl_1: uninfected hBP_rep1

description: uninfected human bronchial organoids_rep1


title: Ctl_2: uninfected hBP_rep2

description: uninfected human bronchial organoids_rep2


title: lungNHBE_1: hBEpC_rep1

description: primary human bronchial epithelial cells_rep1


title: MZL_17

description: Hybridized to U133 plus 2.0 array