title: scRNA-seq [N708-N506]

description: 160120_Hiseq3B_l8_068_Dr_Okamoto_N708-N506_CAGAGAGG-ACTGCATA_L008


title: FRI;flc-3 fully-expanded leaf 3, experiment 2, rep 3

status: Public on Nov 30 2019

type: RNA

city: Ithaca

first: Matthew

middle: R

last: Willmann

state: NY

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

country: USA

institute: Cornell University

description: FRI;flc-3 Lf3 Expt 2 rep3

hyb_protocol: Affymetrix ATH1 GeneChips were hybridized with 3.75 ug of biotin-labeled cDNA at a concentration of 17 ng/ul in the hybridization coctail. Hybridization was carried out for 16-18 hours at 45oC. Washing and staining were done using a GeneChip Fluidics Station 450.

scan_protocol: The GeneChips were scanned using a 7G Affymetrix GeneChip Scanner.

data_processing: The data were gcRMA-normalized in R using the gcrma package and filtered to remove all probesets that did not have a MAS5.0 present call in at least three of the arrays.

label: biotin

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: FRI;flc-3 fully-expanded leaf 3_experiment 2

label_protocol: Biotin-labeled cDNA targets were made from 50 ng starting RNA that was reverse-transcribed and amplified using the OvationTM RNA Amplification SystemV2 and fragmented and labeled using the FL-OvationTM cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA) per the manufacturer’s instructions.

growth_protocol: Plants were sown in MetroMix360 (Sun Gro Horticulture, Vancouver, British Columbia, Canada) soil in 12-well (for the shoot apex and primordia collections) or 96-well flats (for the fully-expanded leaf collections) with wicks made from strips of batting extending into a water reservoir, allowing for a constant moisture level.  The flats were placed at 4oC for five days before being put in a Conviron growth chamber at a constant 23oC under a one-to-one ratio of T8 Sylvania Octron 4100K Ecologic and GroLite WS fluorescent lamps (Interlectric).  Plants were grown under long days conditions—16 hr light (100-125 mol m-2 s-1):8 hr dark. Flats were covered with a clear dome for the first 3-5 days in the growth chamber to aid germination.  Plants were fertilized twice—at planting and at 20 days—with Peters 15-16-17.  Plant age was measured from the date flats were transferred to the growth chamber.

extract_protocol: The tissue was ground in liquid nitrogen and then Trizol (Invitrogen, Carlsbad, CA) with a mortar and pestle or with pestle for a microcentrifuge tube. After extraction with chloroform (1/5th volume of the Trizol), per the manufacturer’s instructions, the aqueous phase was combined with ½ volume of 100% ethanol, mixed and passed over an RNeasy Mini (Qiagen, Valencia, CA) column. The RNA was further purified according to the RNeasy Mini directions, including an on-column DNA digestion with Qiagen’s RNase-Free DNase Set. The final RNA was eluted in the provided RNase-free water, and 1 ul of RNasin was added to increase stability. After RNA extraction, equal amounts of RNA from each of the three collection points were pooled to minimize the effects of circadian rhythms on the data. This mixed RNA sample counted as one replicate.

treatment_protocol: Collections were made at three different times in the day—4-5 hours, 8-9 hours, and 11.5-12.5 hours after the subjective dawn—and, after RNA extraction, equal amounts of RNA from each collection were pooled to minimize the effects of circadian rhythms on the data. To further minimize the effect of collection time, during each collection time, small batches of tissue were collected for a given sample before moving onto the next one, cycling between all tubes to be collected that day until the desired total number of samples was achieved in each tube. Tissue samples were collected using forceps and immediately placed in microcentrifuge or conical tubes in liquid nitrogen, one tube per replicate per collection time point. For shoot apices, 120 apices were collected for each replicate for days 4 and 6, 60 for day 9, and 30 for days 11 and 14. For primordia, 30 were collected for each replicate. For fully-expanded and leaves past full expansion, 9 leaves were collected per replicate of leaves 3, 5, 7, 9, and 11, and 18 leaves of leaves 1/2.

tag: genetic background

value: Col-0 with FRI introgressed from Sf-2

tag: genotype

tag: days after plants put in the growth chamber

tag: tissue

value: fully-expanded leaf 3 (rosette leaf)

tag: leaf position

tag: experiment number

tag: day length

value: 16 hours (long day conditions)


title: Clone_8_B: MDA_MB_436_TREATED WITH  DOXO

city: Montréal

first: isabelle

last: sirois

state: QC

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: McGill University

description: gene expression from DOXO-resistant colonies regrown after short treatment with DOXORUBICIN

hyb_protocol: The resulting labeled cRNA was purified using the RNeasy Mini Kit (Qiagen Sciences) according to the instructions of the manufacturer and hybridized to a Sure Print G3 Human GE 860 K Microarray (Agilent Technologies) for 17hrs at 65°C. The array was then washed and scanned on the Agilent DNA Microarray scanner

scan_protocol: We used the “read.maimages” function of the LIMMA R package to read the Agilent scanner output files

data_processing: First, we corrected the background intensities using the “backgroundCorrect” function in LIMMA and employing the “minimum” method to avoid zero or negative numbers after correction for background intensity. Then, we normalized the intensity values of each array using the “loess” method from the “normalizeWithinArrays” function of the LIMMA package.

molecule: total RNA

organism: Homo sapiens

source_name: MDA_MB_436 treated with 0.3 uM doxorubicin for 48hrs

label_protocol: one hundred nanograms of total RNA from each cell population was reverse and transcribed into cRNA, amplified and labeld with Cy3 dye.

growth_protocol: Cells were maintained in RPMI high glucose + 10% FBS

extract_protocol: Total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) and quantity and integrity were assed using a 2100 bioanalyzer.

treatment_protocol: MDA-MB-436 (parental cells) were plated (density = 1.6 x 104 cells/cm2) and treated the next day with DOX (0.3 μM) or PTX (0.01 μM) corresponding to their IC75. After 48hrs of drug exposure the media containing drug was removed and replaced with fresh medium. After 4-6 weeks, colonies that grew were isolated, expanded and kept in culture in absence of drug in complete medium

tag: gender

value: female

value: triple negative breast cancer (TNBC) cell line derived from ascites

tag: cell line

tag: genotype/variation

value: resistant DOXO-R cells


title: FRI;flc-3 fully-expanded leaf 3, experiment 2, rep 2

description: FRI;flc-3 Lf3 Expt 2 rep2


title: Clone_8_A: MDA_MB_436_TREATED WITH  DOXO


title: scRNA-seq [N704-N506]

type: SRA

city: Tokyo

first: Daichi

last: Narushima

address: 5-1-1 Tsukiji, Chuo-ku

department: Department of Bioinformatics

country: Japan

institute: National Cancer Center Research Institute

description: 160120_Hiseq3B_l8_064_Dr_Okamoto_N704-N506_TCCTGAGC-ACTGCATA_L008

library_source: transcriptomic

data_processing:
Basecalling was performed using configureBclToFastq.pl of bcl2fastq version 1.8.4 with the following arguments: --with-failed-reads --no-eamss --use-bases-mask Y*,I8,I8
Reference sequences for mapping were prepared using rsem-prepare-reference of RSEM version 1.2.31 and Bowtie2 version 2.2.9.
Reads were filtered and trimmed using prinseq-lite.pl of PRINSEQ version 0.20.4 with the following arguments: -min_len 30 -trim_tail_right 5 -trim_tail_left 5 -min_qual_mean 20 -trim_qual_right 20 -trim_qual_left 20
The processed reads were mapped to the reference sequences and TPM (Transcripts Per Million) were calculated using rsem-calculate-expression of RSEM version 1.2.31 and Bowtie2 version 2.2.9 with the default parameters.
Gene TPM values were extracted from TPM columns of RSEM gene result files.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file including TPM values; The column labels are single cell names, and the row labels are gene IDs.

organism: Mus musculus

source_name: colon tumor cells

extract_protocol:
DAPI-Cd31-Cd45-Epcam+Cd24+ cells were single-cell sorted.
FACS-sorted single cells were subjected to cDNA synthesis using Bead-seq method (DOI:10.1016/j.ab.2014.10.011, DOI:10.1038/s41598-017-04616-6). The processes from the production of cDNA libraries to their amplification and first purification were carried out automatically using a Caliper Zephyr compact liquid handler (Perkin Elmer, CA, USA).

treatment_protocol: Male ApcMin/+ mice between 10 weeks of age were given 2% (w/v) Dextran sulfate sodium salt (DSS) (MP Biomedicals, #0216011090) in drinking water for 5 days

tag: strain

value: ApcMin/+

tag: age

value: 12 weeks

tag: Sex

value: male

value: colon

tag: cell type

value: DAPI-Cd31-Cd45-Epcam+Cd24+ cells


title: scRNA-seq [N707-N506]

description: 160120_Hiseq3B_l8_067_Dr_Okamoto_N707-N506_CTCTCTAC-ACTGCATA_L008


title: scRNA-seq [N710-N505]

description: 160120_Hiseq3B_l8_058_Dr_Okamoto_N710-N505_CGAGGCTG-GTAAGGAG_L008


title: scRNA-seq [N705-N506]

description: 160120_Hiseq3B_l8_065_Dr_Okamoto_N705-N506_GGACTCCT-ACTGCATA_L008


title: Clone_8_D: MDA_MB_436_TREATED WITH  DOXO


title: scRNA-seq [N709-N505]

description: 160120_Hiseq3B_l8_057_Dr_Okamoto_N709-N505_GCTACGCT-GTAAGGAG_L008


title: scRNA-seq [N708-N505]

description: 160120_Hiseq3B_l8_056_Dr_Okamoto_N708-N505_CAGAGAGG-GTAAGGAG_L008


title: Clone_8_C: MDA_MB_436_TREATED WITH  DOXO


title: scRNA-seq [N709-N506]

description: 160120_Hiseq3B_l8_069_Dr_Okamoto_N709-N506_GCTACGCT-ACTGCATA_L008


title: Clone_1_B: MDA_MB_436_TREATED WITH  DOXO


title: FRI;flc-3 fully-expanded leaf 3, experiment 2, rep 1

description: FRI;flc-3 Lf3 Expt 2 rep1


title: scRNA-seq [N705-N505]

description: 160120_Hiseq3B_l8_053_Dr_Okamoto_N705-N505_GGACTCCT-GTAAGGAG_L008


title: scRNA-seq [N707-N505]

description: 160120_Hiseq3B_l8_055_Dr_Okamoto_N707-N505_CTCTCTAC-GTAAGGAG_L008


title: FRI;flc-3 fully-expanded leaves 1+2, experiment 2, rep 3

description: FRI;flc-3 Lf1/2 Expt 2 rep3

source_name: FRI;flc-3 fully-expanded leaves 1+2_experiment 2

value: fully-expanded leaves 1+2 (rosette leaf)


title: FRI;flc-3 fully-expanded leaves 1+2, experiment 2, rep 1

description: FRI;flc-3 Lf1/2 Expt 2 rep1


title: scRNA-seq [N706-N505]

description: 160120_Hiseq3B_l8_054_Dr_Okamoto_N706-N505_TAGGCATG-GTAAGGAG_L008


title: Clone_1_A: MDA_MB_436_TREATED WITH  DOXO


title: FRI;flc-3 fully-expanded leaves 1+2, experiment 2, rep 2

description: FRI;flc-3 Lf1/2 Expt 2 rep2


title: scRNA-seq [N710-N504]

description: 160120_Hiseq3B_l8_046_Dr_Okamoto_N710-N504_CGAGGCTG-AGAGTAGA_L008


title: FRI;FLC fully-expanded leaf 11, experiment 2, rep 3

description: FRI;FLC Lf11 Expt 2 rep3

source_name: FRI;FLC fully-expanded leaf 11_experiment 2

value: FRI;FLC

value: fully-expanded leaf 11 (rosette leaf)


title: scRNA-seq [N709-N504]

description: 160120_Hiseq3B_l8_045_Dr_Okamoto_N709-N504_GCTACGCT-AGAGTAGA_L008


title: Clone_1_C: MDA_MB_436_TREATED WITH  DOXO


title: scRNA-seq [N707-N504]

description: 160120_Hiseq3B_l8_043_Dr_Okamoto_N707-N504_CTCTCTAC-AGAGTAGA_L008


title: scRNA-seq [N708-N504]

description: 160120_Hiseq3B_l8_044_Dr_Okamoto_N708-N504_CAGAGAGG-AGAGTAGA_L008


title: scRNA-seq [N706-N504]

description: 160120_Hiseq3B_l8_042_Dr_Okamoto_N706-N504_TAGGCATG-AGAGTAGA_L008


title: Clone_1_D: MDA_MB_436_TREATED WITH  DOXO


title: Parental_A: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO

description: gene expression from DOXO-sensitive cells treated with DOXORUBICIN Vehicle (i.e. Saline)

source_name: MDA_MB_436 treated with saline solution

value: parental DOXO-S cells


title: scRNA-seq [N704-N504]

description: 160120_Hiseq3B_l8_040_Dr_Okamoto_N704-N504_TCCTGAGC-AGAGTAGA_L008


title: scRNA-seq [N710-N503]

description: 160120_Hiseq3B_l8_034_Dr_Okamoto_N710-N503_CGAGGCTG-TATCCTCT_L008


title: scRNA-seq [N705-N504]

description: 160120_Hiseq3B_l8_041_Dr_Okamoto_N705-N504_GGACTCCT-AGAGTAGA_L008


title: FRI;FLC fully-expanded leaf 9, experiment 2, rep 3

description: FRI;FLC Lf9 Expt 2 rep3

source_name: FRI;FLC fully-expanded leaf 9_experiment 2

value: fully-expanded leaf 9 (rosette leaf)


title: FRI;FLC fully-expanded leaf 11, experiment 2, rep 1

description: FRI;FLC Lf11 Expt 2 rep1


title: scRNA-seq [N704-N505]

description: 160120_Hiseq3B_l8_052_Dr_Okamoto_N704-N505_TCCTGAGC-GTAAGGAG_L008


title: scRNA-seq [N708-N503]

description: 160120_Hiseq3B_l8_032_Dr_Okamoto_N708-N503_CAGAGAGG-TATCCTCT_L008


title: Parental_B: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO


title: FRI;FLC fully-expanded leaf 9, experiment 2, rep 1

description: FRI;FLC Lf9 Expt 2 rep1


title: scRNA-seq [N707-N503]

description: 160120_Hiseq3B_l8_031_Dr_Okamoto_N707-N503_CTCTCTAC-TATCCTCT_L008


title: scRNA-seq [N709-N503]

description: 160120_Hiseq3B_l8_033_Dr_Okamoto_N709-N503_GCTACGCT-TATCCTCT_L008


title: Parental_C: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO


title: FRI;FLC fully-expanded leaf 9, experiment 2, rep 2

description: FRI;FLC Lf9 Expt 2 rep2


title: scRNA-seq [N706-N503]

description: 160120_Hiseq3B_l8_030_Dr_Okamoto_N706-N503_TAGGCATG-TATCCTCT_L008


title: scRNA-seq [N705-N503]

description: 160120_Hiseq3B_l8_029_Dr_Okamoto_N705-N503_GGACTCCT-TATCCTCT_L008


title: scRNA-seq [N709-N502]

description: 160120_Hiseq3B_l8_021_Dr_Okamoto_N709-N502_GCTACGCT-CTCTCTAT_L008


title: scRNA-seq [N710-N502]

description: 160120_Hiseq3B_l8_022_Dr_Okamoto_N710-N502_CGAGGCTG-CTCTCTAT_L008


title: FRI;FLC fully-expanded leaf 7, experiment 2, rep 2

description: FRI;FLC Lf7 Expt 2 rep2

source_name: FRI;FLC fully-expanded leaf 7_experiment 2

value: fully-expanded leaf 7 (rosette leaf)


title: FRI;FLC fully-expanded leaf 7, experiment 2, rep 3

description: FRI;FLC Lf7 Expt 2 rep3

value: Col-0 with FRI introgressed from Sf-2


title: scRNA-seq [N707-N502]

description: 160120_Hiseq3B_l8_019_Dr_Okamoto_N707-N502_CTCTCTAC-CTCTCTAT_L008


title: scRNA-seq [N706-N506]

description: 160120_Hiseq3B_l8_066_Dr_Okamoto_N706-N506_TAGGCATG-ACTGCATA_L008


title: scRNA-seq [N705-N502]

description: 160120_Hiseq3B_l8_017_Dr_Okamoto_N705-N502_GGACTCCT-CTCTCTAT_L008


title: Parental_D: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO


title: FRI;FLC fully-expanded leaf 5, experiment 2, rep 3

description: FRI;FLC Lf5 Expt 2 rep3

source_name: FRI;FLC fully-expanded leaf 5_experiment 2

value: fully-expanded leaf 5 (rosette leaf)


title: scRNA-seq [N706-N502]

description: 160120_Hiseq3B_l8_018_Dr_Okamoto_N706-N502_TAGGCATG-CTCTCTAT_L008


title: scRNA-seq [N704-N502]

description: 160120_Hiseq3B_l8_016_Dr_Okamoto_N704-N502_TCCTGAGC-CTCTCTAT_L008


title: scRNA-seq [N704-N503]

description: 160120_Hiseq3B_l8_028_Dr_Okamoto_N704-N503_TCCTGAGC-TATCCTCT_L008


title: FRI;FLC fully-expanded leaf 7, experiment 2, rep 1

description: FRI;FLC Lf7 Expt 2 rep1

value: 16 hours (long day conditions)


title: scRNA-seq [N709-N517]

description: 160120_Hiseq3B_l8_009_Dr_Okamoto_N709-N517_GCTACGCT-GCGTAAGA_L008


title: scRNA-seq [N708-N517]

description: 160120_Hiseq3B_l8_008_Dr_Okamoto_N708-N517_CAGAGAGG-GCGTAAGA_L008


title: scRNA-seq [N707-N517]

description: 160120_Hiseq3B_l8_007_Dr_Okamoto_N707-N517_CTCTCTAC-GCGTAAGA_L008


title: FRI;FLC fully-expanded leaf 5, experiment 2, rep 2

description: FRI;FLC Lf5 Expt 2 rep2


title: scRNA-seq [N710-N517]

description: 160120_Hiseq3B_l8_010_Dr_Okamoto_N710-N517_CGAGGCTG-GCGTAAGA_L008


title: FRI;FLC fully-expanded leaf 3, experiment 2, rep 3

description: FRI;FLC Lf3 Expt 2 rep3

source_name: FRI;FLC fully-expanded leaf 3_experiment 2

value: fully-expanded leaf 3 (rosette leaf)


title: FRI;FLC fully-expanded leaf 5, experiment 2, rep 1

description: FRI;FLC Lf5 Expt 2 rep1


title: scRNA-seq [N708-N502]

description: 160120_Hiseq3B_l8_020_Dr_Okamoto_N708-N502_CAGAGAGG-CTCTCTAT_L008


title: scRNA-seq [N706-N517]

description: 160120_Hiseq3B_l8_006_Dr_Okamoto_N706-N517_TAGGCATG-GCGTAAGA_L008


title: WT_2i_rep1

city: Nijmegen

first: Tianran

last: Peng

address: Geert Grooteplein Zuid  28

department: Molecular Life Science

country: Netherlands

institute: Radboud University

data_processing:
RNA sequencing reads were aligned to the mouse reference genome mm9 using STAR tool which could enumerate gene-level read counts at the same time. The differentially expressed genes were identified with the DESeq2 package by comparing knockout with wild-type groups. Only those genes greater than 1.5-fold changed at Benjamini-Hochberg-corrected P-value< 0.1 were considered significantly deregulated. The transcriptional levels of genes were estimated as Fragments Per Kilobase per Million aligned reads value (FPKM) values using by Cufflinks.
Genome_build: mm9

source_name: mESCs

growth_protocol: Mouse ESCs were cultured in either serum or 2i conditions

extract_protocol:
Total RNA were extracted using the RNeasy Mini Kit (Qiagen #74106) following the manufacturer’s protocol.
5 µg of extracted RNA was depleted from ribosomal RNA using Ribo-Zero Gold Kit (Epicentre Madison). After fragmentation of the rRNA-depleted RNA, 500ng was reverse-transcribed using SuperScript™ III Reverse Transcriptase and random primers (dN)6 following the manufacturer’s instructions. Next, libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit (KAPA #8400) following the manufacturer’s instructions.

treatment_protocol: G1 phase cells were isolated seperately by FACS sorting

value: embryonic stem cells

tag: Stage

value: G1 phase

tag: growth

value: WT


title: scRNA-seq [N705-N517]

description: 160120_Hiseq3B_l8_005_Dr_Okamoto_N705-N517_GGACTCCT-GCGTAAGA_L008

value: ApcMin/+

value: 12 weeks


title: WT_serum_rep2

value: serum


title: P53KO_2i_rep2

value: p53 KO


title: WT_2i_rep2


title: FRI;FLC fully-expanded leaf 3, experiment 2, rep 1

description: FRI;FLC Lf3 Expt 2 rep1


title: p53KO_2i_rep1


title: p53KO_serum_rep1


title: p53KO_serum_rep2


title: 2i_WT_rep1


title: WT_serum_rep1


title: 2i_WT_rep2


title: 2i_P21_KO_rep2

value: p21 KO


title: 2i_P21_KO_rep1


title: FRI;FLC fully-expanded leaves 1+2, experiment 2, rep 3

description: FRI;FLC Lf1/2 Expt 2 rep3

source_name: FRI;FLC fully-expanded leaves 1+2_experiment 2

value: FRI;FLC

value: fully-expanded leaves 1+2 (rosette leaf)


title: ChIP_P53_input

library_source: genomic

data_processing:
For each sample, all 42bp reads were mapped onto the mouse genome (mm9) using Burrows-Wheeler Aligner (BWA) aligner with default parameters. The mapped reads were regarded as input for Picard Mark Duplicates (http://broadinstitute.github.io/picard/) to remove potential PCR duplicates. MACS2 was used to call P53 peaks with a narrow q-value cut-off of 0.01. Read density profiles are displayed as fold enrichment track generated by normalizing ChIP data over input DNA pileup signal files using MACS2. These profiles were further visualized by deepTools.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file, scores represent the fold enrichment over input

molecule: genomic DNA

extract_protocol:
ESCs were fixed using 1% formaldehyde (Millipore #344198) for 10 min at room temperature then quenched by adding 1.25M glycine to a final concentration of 0.125M. Cell pellets were snap frozen and stored in -80℃. Every 10 million cells were lysed by 300μL 1% SDS include freshly made Protease Inhibitor (PI) cocktail (Roche #4693132001), sonicated with Diagenode Bioruptor Pico and diluted with 2.7mL PBA (1x PBS + 0.5% BSA) with fresh added PI cocktail. Dynabeads protein A+G (Invitrogen #10008D, 10009D) were washed and pre-blocked with cold PBA for 30 minutes. Diluted chromatin containing 30μg DNA was incubated with 15μg P53 antibody (Novocastra #CM5P) and 60μL pre-blocked beads and rotated at 4℃ overnight. After incubation, beads were washed subsequently with High-NaCl, Low-NaCl, LiCl, TE and TE washing buffers for 10 minutes and transferred to new eppendorf tube. Beads were eluted with 200µL elution buffer (1%SDS, 0.2M NaCl, 0.1μg/μL Proteinase K) at 65°C thermo shaker 1000rpm for 20 minutes. Supernatants were purified with MinElute PCR Purification Kit (QIAGEN #28006).
1-5ng of DNA was used for library construction with KAPA Hyper Prep Kit (KAPA #KK8504).

tag: chip antibody

value: input


title: FRI;FLC fully-expanded leaf 3, experiment 2, rep 2

description: FRI;FLC Lf3 Expt 2 rep2

tag: genetic background


title: FRI;FLC fully-expanded leaves 1+2, experiment 2, rep 2

description: FRI;FLC Lf1/2 Expt 2 rep2

tag: genotype


title: FRI;flc-3 fully-expanded leaf 11, experiment 1, rep 3

description: FRI;flc-3 Lf11 Expt 1 rep3

source_name: FRI;flc-3 fully-expanded leaf 11_experiment 1

tag: days after plants put in the growth chamber

value: fully-expanded leaf 11 (cauline leaf)


title: FRI;FLC fully-expanded leaves 1+2, experiment 2, rep 1

description: FRI;FLC Lf1/2 Expt 2 rep1

tag: tissue


title: FRI;flc-3 fully-expanded leaf 11, experiment 1, rep 2

description: FRI;flc-3 Lf11 Expt 1 rep2

tag: leaf position


title: scRNA-seq [N704-N517]

description: 160120_Hiseq3B_l8_004_Dr_Okamoto_N704-N517_TCCTGAGC-GCGTAAGA_L008

value: male

value: colon

value: DAPI-Cd31-Cd45-Epcam+Cd24+ cells


title: FRI;flc-3 fully-expanded leaf 11, experiment 1, rep 1

description: FRI;flc-3 Lf11 Expt 1 rep1

value: Col-0 with FRI introgressed from Sf-2

tag: experiment number

value: 16 hours (long day conditions)


title: ChIP_2i_P53_rep1

value: embryonic stem cells

value: Novocastra #CM5P


title: ChIP_serum_P53_rep3


title: ChIP_serum_P53_rep1


title: ChIP_serum_P53_rep2


title: FRI;FLC fully-expanded leaf 11, experiment 2, rep 2

description: FRI;FLC Lf11 Expt 2 rep2

value: fully-expanded leaf 11 (rosette leaf)

tag: day length


title: ChIP_2i_P53_rep3


title: FRI;flc-3 fully-expanded leaf 7, experiment 1, rep 1

description: FRI;flc-3 Lf7 Expt 1 rep1

source_name: FRI;flc-3 fully-expanded leaf 7_experiment 1

value: fully-expanded leaf 7 (rosette leaf)


title: FRI;flc-3 fully-expanded leaf 5, experiment 1, rep 2

description: FRI;flc-3 Lf5 Expt 1 rep2

source_name: FRI;flc-3 fully-expanded leaf 5_experiment 1

value: fully-expanded leaf 5 (rosette leaf)


title: FRI;flc-3 fully-expanded leaf 7, experiment 1, rep 3

description: FRI;flc-3 Lf7 Expt 1 rep3


title: FRI;flc-3 fully-expanded leaf 5, experiment 1, rep 1

description: FRI;flc-3 Lf5 Expt 1 rep1


title: FRI;flc-3 fully-expanded leaf 9, experiment 1, rep 2

description: FRI;flc-3 Lf9 Expt 1 rep2

source_name: FRI;flc-3 fully-expanded leaf 9_experiment 1

value: fully-expanded leaf 9 (rosette leaf)


title: FRI;flc-3 fully-expanded leaf 7, experiment 1, rep 2

description: FRI;flc-3 Lf7 Expt 1 rep2


title: FRI;flc-3 fully-expanded leaf 9, experiment 1, rep 3

description: FRI;flc-3 Lf9 Expt 1 rep3


title: FRI;flc-3 fully-expanded leaf 5, experiment 1, rep 3

description: FRI;flc-3 Lf5 Expt 1 rep3


title: FRI;flc-3 fully-expanded leaf 3, experiment 1, rep 1

description: FRI;flc-3 Lf3 Expt 1 rep1

source_name: FRI;flc-3 fully-expanded leaf 3_experiment 1

value: fully-expanded leaf 3 (rosette leaf)


title: FRI;flc-3 fully-expanded leaf 3, experiment 1, rep 3

description: FRI;flc-3 Lf3 Expt 1 rep3


title: FRI;flc-3 fully-expanded leaf 9, experiment 1, rep 1

description: FRI;flc-3 Lf9 Expt 1 rep1


title: FRI;FLC fully-expanded leaf 11, experiment 1, rep 2

description: FRI;FLC Lf11 Expt 1 rep2

source_name: FRI;FLC fully-expanded leaf 11_experiment 1


title: FRI;flc-3 fully-expanded leaves 1+2, experiment 1, rep 3

description: FRI;flc-3 Lf1/2 Expt 1 rep3

source_name: FRI;flc-3 fully-expanded leaves 1+2_experiment 1


title: FRI;FLC fully-expanded leaf 11, experiment 1, rep 3

description: FRI;FLC Lf11 Expt 1 rep3


title: FRI;flc-3 fully-expanded leaves 1+2, experiment 1, rep 2

description: FRI;flc-3 Lf1/2 Expt 1 rep2


title: FRI;flc-3 fully-expanded leaf 3, experiment 1, rep 2

description: FRI;flc-3 Lf3 Expt 1 rep2


title: FRI;FLC fully-expanded leaf 11, experiment 1, rep 1

description: FRI;FLC Lf11 Expt 1 rep1


title: FRI;FLC fully-expanded leaf 9, experiment 1, rep 3

description: FRI;FLC Lf9 Expt 1 rep3

source_name: FRI;FLC fully-expanded leaf 9_experiment 1


title: FRI;FLC fully-expanded leaf 9, experiment 1, rep 2

description: FRI;FLC Lf9 Expt 1 rep2


title: MSCs rep2

city: AUGUSTA

first: YAN

last: CUI

state: GA

address: 1410 Laney Walker Blvd, CN 4120

department: Georgia Cancer Center

institute: Augusta University

data_processing:
Illumina Casava1.8 software used for basecalling
High throughput RNA sequencing reads were mapped to the reference genome (NCBI, UCSC/mm10) using Tophat 2.0.11 and the relative gene expression was estimated using cufflinks 2.0.2.
Genome_build: mm10

source_name: Bone marrow

growth_protocol: DMEM medium

extract_protocol:
Total RNA was harvested from purified CAFs and MSCs using Trizol reagent (Thermo Fisher Scientific) followed with Purelink RNA mini kit (Thermo Fisher Scientific). RNA quality assessment, libraries preparation and RNA sequencing were all performed in the Genome Core of Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio.
RNA libraries were prepared for sequencing using standard Illumina protocols. Approximately 200-300ng Total RNA was used for RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cautions under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM).  These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final RNA-seq library. After RNA-seq libraries were subjected to quantification process, pooled for cBot amplification and subsequent 50bp single read sequencing run with Illumina HiSeq 3000 platform. After the sequencing run, demultiplexing with Bcl2fastq2 will be employed to generate the fastq file for each sample.

treatment_protocol: No treatment

value: cells

value: wild type


title: FRI;FLC fully-expanded leaf 7, experiment 1, rep 3

description: FRI;FLC Lf7 Expt 1 rep3

source_name: FRI;FLC fully-expanded leaf 7_experiment 1

value: FRI;FLC


title: MSCs rep3


title: FRI;FLC fully-expanded leaf 7, experiment 1, rep 2

description: FRI;FLC Lf7 Expt 1 rep2


title: FRI;FLC fully-expanded leaf 9, experiment 1, rep 1

description: FRI;FLC Lf9 Expt 1 rep1


title: FRI;FLC fully-expanded leaf 7, experiment 1, rep 1

description: FRI;FLC Lf7 Expt 1 rep1


title: FRI;flc-3 fully-expanded leaves 1+2, experiment 1, rep 1

description: FRI;flc-3 Lf1/2 Expt 1 rep1

value: fully-expanded leaves 1+2 (rosette leaf)


title: MSCs rep1


title: FRI;FLC fully-expanded leaf 5, experiment 1, rep 3

description: FRI;FLC Lf5 Expt 1 rep3

source_name: FRI;FLC fully-expanded leaf 5_experiment 1


title: CAFs rep3

source_name: EG7 tumor


title: FRI;FLC fully-expanded leaf 5, experiment 1, rep 2

description: FRI;FLC Lf5 Expt1 rep2


title: CAFs rep2


title: pearl sac_7D  after implantation

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

country: China

institute: Shanghai  University

description: 7D pearl sac after treated with implantation

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie0.12.5  with parameters default
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al,Nature methods 2008.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sinohyriopsis cumingii

source_name: pearl sac

growth_protocol: All mussels with similar size (2 years old, shell length ranging from 9-10 cm) were cultured in aeration tanks with recirculating water and fed daily with unicellular algae prior to processing.

extract_protocol: The library were prepareted by NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer's instructions: (1) Adding Random Primers and First Strand Synthesis Reaction Buffer (5X) to 100ng purified mRNA, incubation at 94°C for 15min and then immediately put it in the ice to break in the mRNA. (2) Adding Murine RNase Inhibitor and ProtoScript II Reverse Transcriptase for first strand synthesis; the reaction procedure list below: 25°C 10 minutes, 42°C 50 minutes, 70°C 15 minutes. (3) Adding Second Strand Synthesis Reaction Buffer (10X) and Second Strand Synthesis Enzyme Mix at 16°C for1h to synthesize the second strand. (4)  Adding 1.8 times volume AMPure XP Beads (Agencourt, USA) to purify reagent getting from the last step; Then adding End Repair Reaction Buffer (10X) and End Prep Enzyme Mix, reaction at 20°C for 30min, at 65°C for 30min for end repairing. (5) Adding NEBNext Adaptor and Blunt/TA Ligase Master Mix, incubation at 20°C for 15min for adaptor linkage, then adding USER Enzyme at 37°C for 15min to excise U in adaptor. (6) Adding 0.6 times volume AMPure XP Beads and mixing, and then put it on the Magnetic Grate for 5min after standing 5min. (7) Collecting supernatant, adding Adding 0.25 times volume AMPure XP Beads for purification, getting the 300~500bp length ligated cDNA. (8) Using Universal PCR Primer and Index (X) Primer for PCR amplification; After hot starting at 98°C for 10s, 12~15 cycles of amplification were performed using a cycle profile of denaturation at 98°C for 10 s, a primer-dependent annealing temperature at 65°C for 30 s, extension at 72°C for 30s. (9) Purified the Reagent by 1 times volume AMPure XP Beads, getting the library for sequencing.

value: pearl sac

tag: time point


title: pearl sac_14D after implantation

description: 14d pearl sac after treated with implantation


title: FRI;FLC fully-expanded leaf 5, experiment 1, rep 1

description: FRI;FLC Lf5 Expt1 rep1


title: FRI;FLC fully-expanded leaf 3, experiment 1, rep 2

description: FRI;FLC Lf3 Expt1 rep2

source_name: FRI;FLC fully-expanded leaf 3_experiment 1


title: FRI;FLC fully-expanded leaves 1+2, experiment 1, rep 2

description: FRI;FLC Lf1/2 Expt1 rep2

source_name: FRI;FLC fully-expanded leaves 1+2_experiment 1


title: H441 treated with TTF-1 siRNA #1

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description:
gene expression values are in the siTTF1#1_FPKM column of H441_TTF1KD_genes.fpkm_tracking file
H441_TTF1KD_genes.fpkm_tracking
H441_siTTF-1_1

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene expression levels in fragments per kilobase of exon per million fragments mapped (FPKM) were estimated using Tophat/Cufflinks (version 2.0.10 and 2.1.1, respectively) with the default parameter settings (Trapnell et al., 2012).
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
WIG to bigWig conversion was performed  using "samtools depth" combined with "UCSC wigToBigWig".
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM values of genes for each Sample, which was generated by Cufflinks; bigWig files were generated by Tophat and wigToBigWig.

source_name: A human lung adenocarcinoma cell line, NCI-H441

growth_protocol: NCI-H209 and NCI-H441 cells were obtained from ATCC, and maintained as reccomended. Briefly, Cells were cultured at 37°C and 5% CO2 in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (HyClone, GE Healthcare Life Sciences, Piscataway, NJ, USA) and 100 U/ml penicillin-streptomycin (Gibco).

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen) with the On-Column DNase Digestion Set (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using Dynabeads mRNA DIRECT Purification Kit and the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

treatment_protocol: Reverse transfection of Stealth Select siRNA (Thermo Fisher Scientific, Waltham, MA, USA) was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific).

tag: sirna

value: TTF-1 siRNA #1(HSS144277, Thermo Fisher Scientific), 48h

tag: cell line

tag: assay number

value: assay 3; TTF-1 knock down analysis, H441 cells


title: FRI;FLC fully-expanded leaf 3, experiment 1, rep 3

description: FRI;FLC Lf3 Expt1 rep3


title: H441 treated with TTF-1 siRNA #2

description:
gene expression values are in the siTTF1#2_FPKM column of H441_TTF1KD_genes.fpkm_tracking file
H441_TTF1KD_genes.fpkm_tracking
H441_siTTF-1_2

value: TTF-1 siRNA #2(HSS144278, Thermo Fisher Scientific), 48h


title: pearl sac_96h  after implantation

description: 96h pearl sac after treated with implantation


title: FRI;FLC fully-expanded leaves 1+2, experiment 1, rep 3

description: FRI;FLC Lf1/2 Expt1 rep3

value: Col-0 with FRI introgressed from Sf-2


title: FRI;FLC fully-expanded leaf 3, experiment 1, rep 1

description: FRI;FLC Lf3 Expt1 rep1

value: 16 hours (long day conditions)


title: pearl sac_30D  after implantation

description: 30D pearl sac after treated with implantation


title: pearl sac_24h  after implantation

description: 24h pearl sac after treated with implantation


title: pearl sac_12h  after implantation

description: 12h pearl sac after treated with implantation


title: FRI;FLC fully-expanded leaves 1+2, experiment 1, rep 1

description: FRI;FLC Lf1/2 Expt1 rep1


title: pearl sac_48h  after implantation

description: 48h pearl sac after treated with implantation


title: H209 treated with negative control siRNA (a control for TTF-1 depletion)

description:
gene expression values are in the siNC_FPKM column of H209_TTF1KD_genes.fpkm_tracking file
H209_TTF1KD_genes.fpkm_tracking
H209_siNC_2

source_name: A human small cell lung cancer cell line, NCI-H209

value: negative control siRNA (12935-112, Thermo Fisher Scientific), 48h

value: assay 2; TTF-1 knock down analysis, H209 cells


title: FRI;flc-3 primordia leaf 11, rep 3

description: FRI;flc-3 PRI11 rep3

source_name: FRI;flc-3 primordia leaf 11

value: 1 mm primordia of leaf 11


title: H441 treated with negative control siRNA

description:
gene expression values are in the siNC_FPKM column of H441_TTF1KD_genes.fpkm_tracking file
H441_TTF1KD_genes.fpkm_tracking
H441_siNC


title: H209 treated with TTF-1 siRNA #1

description:
gene expression values are in the siTTF1#1_FPKM column of H209_TTF1KD_genes.fpkm_tracking file
H209_TTF1KD_genes.fpkm_tracking
H209_siTTF-1_1


title: FRI;flc-3 primordia leaf 11, rep 2

description: FRI;flc-3 PRI11 rep2


title: H209 treated with ASCL1 siRNA #2

description:
gene expression values are in the siASCL1#2_FPKM column of H209_ASCL1KD_genes.fpkm_tracking file
H209_ASCL1KD_genes.fpkm_tracking
H209_siASCL1_2

value: ASCL1 siRNA #2(HSS181121, Thermo Fisher Scientific), 48h

value: assay 1; ASCL1 knock down analysis


title: H209 treated with TTF-1 siRNA #2

description:
gene expression values are in the siTTF1#2_FPKM column of H209_TTF1KD_genes.fpkm_tracking file
H209_TTF1KD_genes.fpkm_tracking
H209_siTTF-1_2


title: CAFs rep1

tag: strain


title: pearl sac_6h  after implantation

description: 6h pearl sac after treated with implantation


title: H209 treated with ASCL1 siRNA #1

description:
gene expression values are in the siASCL1#1_FPKM column of H209_ASCL1KD_genes.fpkm_tracking file
H209_ASCL1KD_genes.fpkm_tracking
H209_siASCL1_1

value: ASCL1 siRNA #1(HSS100745, Thermo Fisher Scientific), 48h


title: FRI;flc-3 primordia leaf 11, rep 1

description: FRI;flc-3 PRI11 rep1


title: pearl sac_2h after implantation

description: 2h pearl sac after treated with implantation


title: H209 treated with negative control siRNA (a control for ASCL1 depletion)

description:
gene expression values are in the siNC_FPKM column of H209_ASCL1KD_genes.fpkm_tracking file
H209_ASCL1KD_genes.fpkm_tracking
H209_siNC_1


title: pearl sac_0h after implantation

description: 0h pearl sac after treated with implantation


title: ASCL1 binding region in NCI-H209

description: anti-ASCL1 ChIP-seq

data_processing:
Reference files of the human reference sequence assembly (NCBI Build 37/hg19, February 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie (version 1.1.0) (Langmead et al., 2009) with the command “-S -a --best --strata -v 1 -m 1”.
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
TTF-1 or ASCL1 binding regions were identified using MACS2 software (Model based analysis of ChIP-seq) (version 2.0.9) (Zhang et al, 2008) with a default q-value threshold of 0.00001.
WIG to bigWig conversion was performed  using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED and WIG files were generated using MACS2 (version 2.0.9).

source_name: A small cell lung carcinoma cell line, NCI-H209

growth_protocol: NCI-H209 was obtained from ATCC, and maintained as reccomended. Briefly, H209 cells were cultured at 37℃ and 5% CO2 in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (HyClone, GE Healthcare Life Sciences, Piscataway, NJ, USA) and 100 U/ml penicillin-streptomycin (Gibco).

extract_protocol:
ChIP-seq of H209 cells were performed using 5 μg of anti-TTF-1 antibody (#MS-699-P, Lab Vision Corporation, Fremont, CA, USA) or anti-ASCL1 antibody (#556604, BD Biosciences, Franklin Lakes, NJ, USA) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: untreated

tag: small cell lung carcinoma subtype

value: classic type SCLC

tag: treatment

value: untreated

tag: antibody


title: FRI;flc-3 primordia leaf 9, rep 3

description: FRI;flc-3 PRI9 rep3

source_name: FRI;flc-3 primordia leaf 9

value: 1 mm primordia of leaf 9


title: TTF-1 binding region in NCI-H209

description: anti-TTF-1 ChIP-seq


title: CE17-CAp4

city: Beijing

first: Shu

last: Zhang

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: BIOPIC

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The first 8bp of read2 were used to split the mixed data into single cells according to the barcode sequences. The following 8bp were recorded and attached to the end of each read2 as unique molecular identifier (UMI). After that, reads1 were separated by the header of the corresponding read2 and then added UMI information. Hereafter, the split reads1 were trimmed off ploy(A) tail sequence and template switch oligo (TSO) sequence. Then we did quality control by removing out reads with adaptor contaminants (length < 37bp) and low-quality bases (N > 10%).
Subsequently, TopHat (version 2.0.12) was applied to align clean reads to the hg19 human transcriptome downloaded from UCSC.  Uniquely aligned reads were counted by the tool ‘htseq-count’ of HTSeq. According to the UMI information, transcripts with same UMI sequence of each gene were merged as one, thus the number of different UMIs for each gene was considered as the transcript counts of that gene without PCR bias for each sequenced cell.
The transcript counts of each cell were normalized to transcript per million (TPM), and the formula to calculate TPM is: the transcript counts of each gene divided by the sum of transcript counts of that cell, and multiplied by one million. TPM values were then normalized by log2(TPM/10 + 1) for the following analysis, since the sequencing depth of most single cell samples were less than 1,000,000 reads, we divided TPM values by 10.
Genome_build: Macaca_fascicularis_5.0 sourced from Ensemble
Supplementary_files_format_and_content: xls files which include the transcirptional counts of RefSeq genes.

organism: Macaca fascicularis

source_name: Artery of Cynomolgus Monkey

extract_protocol:
FACS protocol: To enrich for CD31+ endothelial cells, the cell suspension was incubated with anti- CD31 for 30 minutes, FACS was used to separate positive and negative cells.
Single cells were directly picked into 2.5ul cell lysis buffer the same as Smartseq2 except that we used barcoded reverse transcription primers instead of oligdT30VN primer. Further cell lysis, reverse transcription and amplification was referred to Smartseq2 with little modification.
Each cell was amplified for 18 cycles in total. The PCR product for each barcode 1 to barcode 96 was pooled together for purification and library construction. The libraries were sequenced on illumina platform for 1.8M 150bp pair-end reads per cell.

treatment_protocol: The tissues were rinsed in cold Krebs-Henseleit (leagene, c20079) solution. The left and right coronary arteries were branched from the root of the aortic artery and raised from the anterior and posterior aortic sinus, respectively.Both the aortic arch and coronary artery were isolated and sliced into small fragments separately. The aortic arch and coronary artery were first digested by collagenase I (Thermo, 17100017) for 10 minutes, followed by digestion with a mixture of collagenase I, dispase II (Thermo, 17105041), elastase (Sigma, E7885) and Dnase I (Worthington, LS006333) for 45 minutes. Then, the cell suspension was treated with Accumax (Thermo, 00-4666-56) for another 5 minutes to dissociate cell aggregate into single cells.

value: coronary artery

tag: age(years old)

tag: gender

value: Male


title: CE17-CAp2

description: polyA RNA


title: Control_PR8_rep1

city: Cambridge

first: Ang

last: Cui

state: MA

address: 415 Main St.

institute: Broad Institute

data_processing:
Short sequencing reads were aligned to the UCSC Hg19 reference genome using Bowtie
Transcript abundance was quantified using RSEM
Genome_build: Hg19
Supplementary_files_format_and_content: transcript counts txt file

source_name: Lung Epithelial Cell Line

extract_protocol:
RNA were extracted from A549 cells using Qia-gen RNA extraction kit
RNA libaries were prepared for sequencing using standard illumina protocols

value: Lung

tag: genotype/variation

value: WT

value: PR8 infection MOI=5


title: TMEM199_PR8_rep3


title: Control_PR8_rep2


title: Control_PR8_rep3


title: FRI;flc-3 primordia leaf 9, rep 2

description: FRI;flc-3 PRI9 rep2

tag: genetic background

tag: genotype


title: TMEM199_PR8_rep1

tag: tissue


title: FRI;flc-3 primordia leaf 9, rep 1

description: FRI;flc-3 PRI9 rep1

tag: days after plants put in the growth chamber

tag: leaf position


title: FRI;flc-3 primordia leaf 7, rep 3

description: FRI;flc-3 PRI7 rep3

source_name: FRI;flc-3 primordia leaf 7

value: 1 mm primordia of leaf 7

tag: experiment number

tag: day length


title: TMEM199_PR8_rep2


title: CE17-CAp1

description: polyA RNA


title: FRI;flc-3 primordia leaf 7, rep 1

description: FRI;flc-3 PRI7 rep1

value: Col-0 with FRI introgressed from Sf-2


title: FRI;flc-3 primordia leaf 5, rep 3

description: FRI;flc-3 PRI5 rep3

source_name: FRI;flc-3 primordia leaf 5

value: 1 mm primordia of leaf 5

value: 16 hours (long day conditions)


title: CCDC115_PR8_rep3


title: CCDC115_PR8_rep1


title: CCDC115_PR8_rep2


title: WDR7_PR8_rep3


title: CE17-CAp3

description: polyA RNA


title: CE17-CAn1

description: polyA RNA


title: WDR7_PR8_rep2


title: FRI;flc-3 primordia leaf 3, rep 3

description: FRI;flc-3 PRI3 rep3

source_name: FRI;flc-3 primordia leaf 3

value: 1 mm primordia of leaf 3


title: FRI;flc-3 primordia leaf 5, rep 1

description: FRI;flc-3 PRI5 rep1


title: FRI;flc-3 primordia leaf 5, rep 2

description: FRI;flc-3 PRI5 rep2


title: CE17-CAn2

description: polyA RNA


title: Control_uninfected_rep2

value: uninfected


title: Control_uninfected_rep3


title: FRI;flc-3 primordia leaf 3, rep 2

description: FRI;flc-3 PRI3 rep2


title: FRI;flc-3 primordia leaf 7, rep 2

description: FRI;flc-3 PRI7 rep2


title: Control_uninfected_rep1


title: CE17-AAp2

description: polyA RNA

value: aortic artery


title: TMEM199_uninfected_rep2


title: CE17-AAp1

description: polyA RNA


title: CCDC115_uninfected_rep2


title: CCDC115_uninfected_rep3


title: CE17-AAp4

description: polyA RNA


title: CE17-AAn2

description: polyA RNA


title: FRI;flc-3 primordia leaf 3, rep 1

description: FRI;flc-3 PRI3 rep1


title: WDR7_PR8_rep1


title: CCDC115_uninfected_rep1


title: WDR7_uninfected_rep3


title: FRI;flc-3 primordia leaves 1+2, rep 3

description: FRI;flc-3 PRI1/2 rep3

source_name: FRI;flc-3 primordia leaves 1+2

value: 1 mm primordia of leaves 1 + 2


title: CE16-CAp2

description: polyA RNA

value: Female


title: FRI;flc-3 primordia leaves 1+2, rep 2

description: FRI;flc-3 PRI1/2 rep2


title: CE17-AAp3

description: polyA RNA


title: TMEM199_uninfected_rep3


title: WDR7_uninfected_rep2


title: FRI;flc-3 primordia leaves 1+2, rep 1

description: FRI;flc-3 PRI1/2 rep1


title: CE16-CAp1

description: polyA RNA


title: Control_IFN_11302016_rep2

value: IFN treatment 200U/ml


title: WDR7_uninfected_rep1


title: Control_IFN_11302016_rep1


title: Control_IFN_11242016_rep3


title: Control_IFN_11302016_rep3


title: TMEM199_uninfected_rep1


title: FRI;FLC primordia leaf 11, rep 3

description: FRI;FLC PRI11 rep3

source_name: FRI;FLC primordia leaf 11

value: FRI;FLC

value: 1 mm primordia of leaf 11


title: CE17_AAn1

description: polyA RNA


title: Control_IFN_11242016_rep2


title: Control_IFN_11242016_rep1


title: CE16_CAn1

description: polyA RNA

value: coronary artery


title: CE16_AAp2

description: polyA RNA


title: CE16_AAp1

description: polyA RNA


title: FRI;FLC primordia leaf 11, rep 2

description: FRI;FLC PRI11 rep2


title: Control_IFN_07122016_rep3


title: Control_IFN_07122016_rep2


title: Control_IFN_07122016_rep1


title: Control_PR8_11302016_rep3


title: FRI;FLC primordia leaf 11, rep 1

description: FRI;FLC PRI11 rep1


title: FRI;FLC primordia leaf 9, rep 3

description: FRI;FLC PRI9 rep3

source_name: FRI;FLC primordia leaf 9

value: 1 mm primordia of leaf 9


title: ChIP_2i_P53_rep2

source_name: mESCs

tag: cell type

value: embryonic stem cells

tag: chip antibody

value: Novocastra #CM5P

tag: growth


title: CE16_AAn1

description: polyA RNA


title: Control_PR8_11302016_rep2

value: Lung

value: WT

value: PR8 infection MOI=5


title: CE15-CAp2

description: polyA RNA

value: Male


title: Control_PR8_11302016_rep1


title: CE15-CAp1

description: polyA RNA


title: Control_PR8_11242016_rep3


title: Control_PR8_11242016_rep2


title: CE15-CAn1

description: polyA RNA


title: Control_PR8_11242016_rep1


title: Control_PR8_07122016_rep3


title: CE15-AAp2

description: polyA RNA


title: Control_PR8_07122016_rep2


title: FRI;FLC primordia leaf 9, rep 2

description: FRI;FLC PRI9 rep2

value: Col-0 with FRI introgressed from Sf-2

value: 16 hours (long day conditions)


title: Control_PR8_07122016_rep1


title: FRI;FLC primordia leaf 9, rep 1

description: FRI;FLC PRI9 rep1


title: Control_uninfected_11302016_rep2

value: no treatment


title: CE15_AAp1

description: polyA RNA

value: aortic artery


title: Control_uninfected_11302016_rep1


title: Control_uninfected_11242016_rep3


title: CE15-AAn1

description: polyA RNA


title: CE14-CAp1

description: polyA RNA


title: FRI;FLC primordia leaf 7, rep 1

description: FRI;FLC PRI7 rep1

source_name: FRI;FLC primordia leaf 7

value: 1 mm primordia of leaf 7


title: FRI;FLC primordia leaf 7, rep 2

description: FRI;FLC PRI7 rep2


title: CE14-CAn2

description: polyA RNA

value: Female


title: Control_uninfected_11242016_rep2


title: Control_uninfected_11242016_rep1


title: FRI;FLC primordia leaf 5, rep 3

description: FRI;FLC PRI5 rep3

source_name: FRI;FLC primordia leaf 5

value: 1 mm primordia of leaf 5


title: Control_uninfected_07122016_rep2


title: Control_uninfected_07122016_rep1


title: CE14-CAn1

description: polyA RNA


title: Control_uninfected_11302016_rep3


title: FRI;FLC primordia leaf 5, rep 1

description: FRI;FLC PRI5 rep1

value: FRI;FLC


title: FRI;FLC primordia leaf 5, rep 2

description: FRI;FLC PRI5 rep2


title: FRI;FLC primordia leaf 7, rep 3

description: FRI;FLC PRI7 rep3


title: CMTR1 _IFN_11302016_rep3

value: IFN treatment 200U/ml


title: FRI;FLC primordia leaf 3, rep 1

description: FRI;FLC PRI3 rep1

source_name: FRI;FLC primordia leaf 3

value: 1 mm primordia of leaf 3


title: FRI;FLC primordia leaf 3, rep 2

description: FRI;FLC PRI3 rep2


title: CE14_AAp1

description: polyA RNA


title: FRI;FLC primordia leaves 1+2, rep 3

description: FRI;FLC PRI1/2 rep3

source_name: FRI;FLC primordia leaves 1+2

value: 1 mm primordia of leaves 1 + 2


title: CE14_AAp2

description: polyA RNA


title: CMTR1 _IFN_11302016_rep1


title: CMTR1 _IFN_11302016_rep2


title: FRI;FLC primordia leaves 1+2, rep 2

description: FRI;FLC PRI1/2 rep2


title: FRI;FLC primordia leaf 3, rep 3

description: FRI;FLC PRI3 rep3


title: CMTR1 _IFN_11242016_rep2


title: CMTR1 _IFN_07122016_rep3


title: CMTR1_PR8_11302016_rep3


title: CE14-AAn1

description: polyA RNA


title: FRI;FLC primordia leaves 1+2, rep 1

description: FRI;FLC PRI1/2 rep1


title: Control_uninfected_07122016_rep3


title: CMTR1 _IFN_11242016_rep1


title: CMTR1_IFN_07122016_rep1


title: CE13-CAp1

description: polyA RNA

value: coronary artery


title: CE13-CAn1

description: polyA RNA


title: CMTR1_PR8_11302016_rep2


title: CMTR1_PR8_11302016_rep1


title: CMTR1_PR8_11242016_rep3


title: CE13_CAp2

description: polyA RNA


title: FRI;FLC;35S::miR156mimic shoot apices, day 6, rep 1

description: FRI;FLC;35S::miR156mimic SA6 rep1

source_name: FRI;FLC;35S::miR156mimic shoot apices_day 6

value: FRI;FLC with 35S::miR156mimic transgene

value: shoot apices plus leaf primordia ≤ 1 mm


title: CMTR1 _IFN_11242016_rep3

value: Lung


title: FRI;FLC;35S::miR156mimic shoot apices, day 6, rep 3

description: FRI;FLC;35S::miR156mimic SA6 rep3


title: CMTR1_PR8_11242016_rep1

value: PR8 infection MOI=5


title: CMTR1_PR8_11242016_rep2


title: CMTR1_PR8_07122016_rep3


title: FRI;flc-3 shoot apices, day 11, rep 3

description: FRI;flc-3 SA11 rep3

source_name: FRI;flc-3 shoot apices_day 11


title: FRI;FLC;35S::miR156mimic shoot apices, day 6, rep 2

description: FRI;FLC;35S::miR156mimic SA6 rep2


title: CMTR1 _IFN_07122016_rep2


title: CMTR1_PR8_07122016_rep1


title: CMTR1_PR8_07122016_rep2


title: FRI;flc-3 shoot apices, day 11, rep 1

description: FRI;flc-3 SA11 rep1


title: CE13-AAp2

description: polyA RNA


title: CMTR1_uninfected_11302016_rep2


title: CMTR1_uninfected_11302016_rep3


title: CE12-CAp1

description: polyA RNA

value: Male


title: CMTR1_uninfected_11302016_rep1


title: CE13-AAn1

description: polyA RNA


title: CMTR1_uninfected_11242016_rep1


title: CMTR1_uninfected_11242016_rep3


title: CE12-AAp1

description: polyA RNA


title: CMTR1_uninfected_11242016_rep2


title: CE12-AAp2

description: polyA RNA


title: CMTR1_uninfected_07122016_rep2


title: CMTR1_uninfected_07122016_rep1


title: CE12-AAn1

description: polyA RNA


title: CE11-CAp1

description: polyA RNA


title: CE11-CAn1

description: polyA RNA


title: CE12-CAn1

description: polyA RNA


title: FRI;flc-3 shoot apices, day 9, rep 1

description: FRI;flc-3 SA9 rep1

source_name: FRI;flc-3 shoot apices_day 9

value: Col-0 with FRI introgressed from Sf-2


title: FRI;flc-3 shoot apices, day 11, rep 2

description: FRI;flc-3 SA11 rep2

value: 16 hours (long day conditions)


title: FRI;flc-3 shoot apices, day 9, rep 2

description: FRI;flc-3 SA9 rep2


title: FRI;flc-3 shoot apices, day 9, rep 3

description: FRI;flc-3 SA9 rep3


title: FRI;flc-3 shoot apices, day 4, rep 3

description: FRI;flc-3 SA4 rep3

source_name: FRI;flc-3 shoot apices_day 4


title: CMTR1_uninfected_07122016_rep3

value: no treatment


title: CE11-AAp2

description: polyA RNA

source_name: Artery of Cynomolgus Monkey

value: aortic artery


title: FRI;flc-3 shoot apices, day 4, rep 1

description: FRI;flc-3 SA4 rep1


title: FRI;flc-3 shoot apices, day 4, rep 2

description: FRI;flc-3 SA4 rep2


title: CE11-AAp1

description: polyA RNA


title: CE11-AAn1

description: polyA RNA


title: FRI;flc-3 shoot apices, day 6, rep 1

description: FRI;flc-3 SA6 rep1

source_name: FRI;flc-3 shoot apices_day 6


title: CE10_CAp2

description: polyA RNA


title: CE10_CAp1

description: polyA RNA


title: FRI;FLC shoot apices, day 21, rep 3

description: FRI;FLC SA21 rep3

source_name: FRI;FLC shoot apices_day 21


title: FRI;FLC shoot apices, day 21, rep 2

description: FRI;FLC SA21 rep2


title: FRI;FLC shoot apices, day 14, rep 3

description: FRI;FLC SA14 rep3

source_name: FRI;FLC shoot apices_day 14


title: FRI;FLC shoot apices, day 21, rep 1

description: FRI;FLC SA21 rep1


title: CE10_AAp2

description: polyA RNA


title: CE10_AAp1

description: polyA RNA


title: CE10-AAn1

description: polyA RNA


title: CE09-CAp2

description: polyA RNA


title: CE09-CAp1

description: polyA RNA


title: FRI;FLC shoot apices, day 14, rep 2

description: FRI;FLC SA14 rep2


title: FRI;FLC shoot apices, day 11, rep 1

description: FRI;FLC SA11 rep1

source_name: FRI;FLC shoot apices_day 11


title: CE09_CAn

description: polyA RNA


title: CE09-AAp2

description: polyA RNA


title: CE09_AAp1

description: polyA RNA


title: FRI;FLC shoot apices, day 11, rep 2

description: FRI;FLC SA11 rep2


title: CE09_AAn1

description: polyA RNA


title: FRI;FLC shoot apices, day 14, rep 1

description: FRI;FLC SA14 rep1


title: FRI;FLC shoot apices, day 11, rep 3

description: FRI;FLC SA11 rep3


title: CE10-CAn1

description: polyA RNA


title: FRI;FLC shoot apices, day 9, rep 3

description: FRI;FLC SA9 rep3

source_name: FRI;FLC shoot apices_day 9


title: FRI;FLC shoot apices, day 9, rep 2

description: FRI;FLC SA9 rep2


title: CE08_CAp2

description: polyA RNA


title: Exp-ERRγ-2

city: beijing

first: zhou

last: lei

address: No. 5, Summer Palace Road

institute: peking university

data_processing:
Basecalls performed using clc genomics workbench
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: pancreatic β cells

growth_protocol: NIT-1 pancreatic β cells were purchased from Bena Culture Collection in China and maintained in Ham’s F-12 Nutrient Mix (21700, Life Technologies) +10% fetal bovine serum (04-001-1ACS, Biological Industries) and were tested to exclude mycoplasma contamination.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen), and there were two biological replicates per sample. The RNA quality was assessed with an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and agarose gel electrophoresis (AGE). RNA-Seq library construction (151bp paired-end, PE) and sequencing reactions were performed at Novogene (China) using the Illumina-PE150 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded in a 25 cm2 flask at confluent of 2.6×106 per flask and transfected with 1000 μL serum-free Opti-MEM that contained 16 μL liposomal transfection reagent (HB-TRLF-1000, HANBIO) and 8.3 μg pRP[Exp]-CMVE>EGFP or pRP[Exp]-EGFP >ERRγ plasmid.

value: NIT-1 pancreatic beta cells

tag: transfection

value: pRP[Exp]-EGFP >ERR[gamma]

tag: passage

tag: strain

value: NOD/Lt


title: Exp-ERRγ-1


title: CE08_CAp1

description: polyA RNA

value: Female


title: Exp-ctrl-2

value: pRP[Exp]-CMVE>EGFP


title: CE08_CAn1

description: polyA RNA


title: Exp-ctrl-1


title: FRI;FLC shoot apices, day 6, rep 2

description: FRI;FLC SA6 rep2

source_name: FRI;FLC shoot apices_day 6

value: FRI;FLC


title: FRI;FLC shoot apices, day 4, rep 2

description: FRI;FLC SA4 rep2

source_name: FRI;FLC shoot apices_day 4


title: CE08_AAn1

description: polyA RNA


title: CE08_AAp1

description: polyA RNA


title: FRI;FLC shoot apices, day 4, rep 3

description: FRI;FLC SA4 rep3


title: CE07-CAp2

description: polyA RNA


title: CE07_CAp1

description: polyA RNA


title: FRI;FLC shoot apices, day 4, rep 1

description: FRI;FLC SA4 rep1


title: CE07-AAp2

description: polyA RNA


title: CE07-CAn1

description: polyA RNA


title: CE07_AAp1

description: polyA RNA


title: FRI;FLC shoot apices, day 6, rep 1

description: FRI;FLC SA6 rep1


title: FRI;FLC shoot apices, day 9, rep 1

description: FRI;FLC SA9 rep1


title: CE06-CAp1

description: polyA RNA


title: CE07-AAn1

description: polyA RNA


title: treatment-GC rep1 [401GC]

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the sequencing platform were cleaned with the Cutadapt program (Martin 2011) to trim off sequencing adaptors, low quality bases, and potential errors introduced during sequencing or library preparation. Reads with a quality Phred-like score < 20 and read length < 40 bases were excluded from RNAseq analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The transcripts of Bos taurus (76,341 sequences) retrieved from the NCBI genome database (GCF_002263795.1) were used as reference sequences for RNAseq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the bowtie2 mapper (v. 2.2.3) with a ‘3 mismatches a read’ allowance (Langmead and Salzberg 2012). The mapping results were processed with the SAMtools (Li et al. 2009), and scripts developed in-house by the Interdisciplinary Centre for Biotechnology Research to remove potential PCR duplicates and select uniquely-mapped reads for gene expression analysis, as described previously (Piersanti et al. 2019a). Gene expression was compared between the bacteria-infused and control animals by counting the number of mapped reads for each transcript (Yao and Yu 2011).
Ingenuity Pathway Analysis (Qiagen) was used to identify pathways, gene networks, and upstream regulators of DEGs affected by bacterial infusion (Krämer et al. 2014). Pathways were identified by -log P > 1.3 and log2FC ≤ −2 or ≥ 2, and corresponding z-scores were calculated to predict activation status. Gene networks were identified by assessing the number of DEGs in each network, and gene network scores were calculated by the software (a network score of ≥ 2 gives 99% confidence the network was not identified by chance). Upstream regulators of DEGs, and predicted diseases and functions were identified by z-scores ≥ 2 or ≤ −2, and were considered significant predictors of activation or inhibition of DEGs, respectively
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Bos taurus

source_name: treatment-GC

growth_protocol: To avoid confounding effects of periparturient problems, lactation and metabolic stress, we used virgin Holstein heifers, 11 to 13 months old.

extract_protocol:
Two weeks prior to slaughter, the oestrous cycles of all the animals were synchronized using the modified 5-d Co-synch protocol described above. Animals were slaughtered by captive bolt and exsanguination 94 days after infusion. Reproductive tracts were collected, transported on ice, and processed within 1 h of slaughter. Endometrial tissue was dissected away from underlying myometrium, and oviduct samples were collected by extrusion into a collection vessel. Granulosa cells were isolated from dominant follicles > 8 mm diameter by aspiration, using a sterile 20-gauge needle and syringe containing collection medium (0.5% BSA, 20 mM HEPES, 2 mM sodium pyruvate, 10 IU/ml heparin, 100 U/ml penicillin, 100 ug/ml streptomycin in Medium 199); the aspirates were centrifuged at 500 × g to isolate the granulosa cells. Samples of caruncular and intercaruncular endometrium, oviduct isthmus and ampulla, and granulosa cells were snap frozen in liquid nitrogen and stored at -80°C. Technical problems prevented collection of the oviduct from one bacteria-infused animal and the intercaruncular endometrium from another bacteria-infused animal
Samples were thawed, suspended in RLT buffer, and RNA extracted using the RNeasy Micro kit. To produce RNAseq libraries, 500 ng (endometrium and oviduct) or 200 ng (granulosa) total RNA was used for mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by RNA library construction with NEBNext Ultra II Directional Library Preparation (both New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s instructions. Briefly, extracted mRNA was fragmented in NEBNext first-strand synthesis buffer at 94°C, followed by first-strand cDNA synthesis using reverse transcriptase and random primers. Synthesis of double-stranded cDNA was performed using the second strand master mix provided with the kit. The resulting double-stranded cDNA was end-repaired, dA-tailed and ligated with NEBNext adaptors. Finally, libraries were enriched by amplification and purified by Meg-Bind RxnPure Plus beads (Omega Biotek, Norcross, GA, USA). Barcoded libraries were sized on a bioanalyzer, and quantified by Qubit and qPCR. All individual libraries were pooled, and equal molar concentrations were run on an Illumina HiSeq3000 sequencer. Both library construction and sequencing were performed at the ICBR of the University of Florida

treatment_protocol: The animals were clinically healthy prior to the experiment, tested negative for Brucella abortus, Neospora caninum and Leptospirosa, and had clear vaginal mucus. Estrous cycles were synchronized using a modified 5-d Co-synch protocol and were injected intramuscularly with 100 mg gonadotropin-releasing hormone (GnRH; gonadorelin diacetate tetrahydrate) followed by 25 mg prostaglandin F2α (dinoprost tromethamine) 5 and 6 days later, and 100 mg GnRH 8 days later. Starting the day after the final GnRH injection, animals were injected intramuscularly with 200 mg progesterone in corn oil (50 mg/mL) daily for 7 d to ensure elevated circulating progesterone concentrations at the time of intrauterine infusion. Three days after the final GnRH injection, animals were blocked by age and weight, and randomly assigned to intrauterine infusion of control sterile medium (n = 6), using 30 ml Luria-Bertani broth, or bacteria (n = 4), using 4.64 × 10^7 CFU/mL E. coli MS499 and 3.38 × 10^7 CFU/mL T. pyogenes MS249 in 30 mL Luria-Bertani broth. Vaginal mucus was collected daily using a Metricheck device from the day before until 7 days after infusion, and endometritis was graded as described previously; grade 0, clear or translucent mucus; grade 1, mucus containing flecks of pus; grade 2, mucus containing ≤ 50% pus; and grade 3, mucus containing > 50% pus. Clinical endometritis was induced 4 to 6 days after infusion in the bacterial-infusion animals but not in controls as evidenced by pus detectable in the vagina (median endometritis grade 3 vs. ≤ 1).

tag: breed

value: Holstein heifers

tag: age

value: 11-13 months

tag: Sex

value: female

tag: location

value: University of Florida Dairy Unit

tag: treatment

value: uterine infection with E. coli and T. pyogenes

value: granulosa


title: treatment-GC rep3 [436GC]


title: control-GC rep5 [437GC]

source_name: control-GC

value: control vehicle


title: CE08_AAp2

description: polyA RNA

tag: age(years old)

tag: gender


title: control-GC rep4 [431GC]

tag: tissue


title: control-GC rep6 [447GC]


title: CE06-CAn1

description: polyA RNA

value: coronary artery

value: Male


title: CE06-AAp2

description: polyA RNA


title: control-GC rep3 [397GC]


title: MDA-MB-231_siGpx1_rep2

city: Seoul

first: AHYOUNG

last: CHOI

address: 52, Ewhayeodae-gil

country: South Korea

institute: Ewha womans university

data_processing:
Raw read data was first run through quality control metrics using FastQC.
Sequenced reads were trimmed adapter sequence using sickle (v1.33).
Resulting reads were then aligned to the human genome (hg19) using mapsplice (v2.1.8) with default options.
Raw readcount and transcript abundance in FPKM (Fragments Per Kilobase of exon per Million mapped reads) was calculated by RSEM (v1.2.12) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expected count, TPM, and FPKM values for each Sample

source_name: Breast cancer cell line MDA-MB-234

extract_protocol:
The Illumina Qiagen RNeasy mini Kit (cat.No 74104) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Triple-negative breast cancer (TNBC) cell line MDA-MB-234

tag: cell line

value: mammary gland; breast

value: epithelial

tag: genotype/variation


title: CE06-AAp1

description: polyA RNA

value: aortic artery


title: MDA-MB-231_Control_rep1

source_name: Breast cancer cell line MDA-MB-231

value: Triple-negative breast cancer (TNBC) cell line MDA-MB-231

value: control


title: CE06-AAn1

description: polyA RNA


title: CE05_CAp2

description: polyA RNA


title: HS578T_siGpx1_rep2

source_name: Breast cancer cell line HS581T

value: Triple-negative breast cancer (TNBC) cell line HS581T


title: CE05_CAp1

description: polyA RNA


title: HS578T_siGpx1_rep1

source_name: Breast cancer cell line HS580T

value: Triple-negative breast cancer (TNBC) cell line HS580T


title: treatment-C rep4 [436C]

source_name: treatment-C

value: Holstein heifers

value: caruncular endometrium


title: treatment-C rep3 [408C]

value: 11-13 months

value: female


title: treatment-C rep2 [401C]

value: University of Florida Dairy Unit

value: uterine infection with E. coli and T. pyogenes


title: CE05_CAn1

description: polyA RNA


title: CE05_AAp2

description: polyA RNA


title: HS578T_Control_rep2

source_name: Breast cancer cell line HS579T

value: Triple-negative breast cancer (TNBC) cell line HS579T


title: HS578T_Control_rep1

source_name: Breast cancer cell line HS578T

value: Triple-negative breast cancer (TNBC) cell line HS578T


title: HEK-293 cells, treated with siADAR rep2

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

description:
Sample_5
Cells were transfected with siRNA against ADAR.

data_processing:
trim_fastqs: trimmomatic-0.36.jar PE -phred33 {input.fastq_1} {input.fastq_2} {output.trimmed_fastq_paired_1} {output.trimmed_fastq_unpaired_1} {output.trimmed_fastq_paired_2} {output.trimmed_fastq_unpaired_2} ILLUMINACLIP:all_fastq_primers.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
align_fastq_to_genome: Align trimmed fastq files to genome with  bwa aln -t {threads} -n {params.max_diff} -k {params.seed_diff} {params.reference_genome} {input} > {output}
convert_single_sai_to_sam: bwa sampe -r "{params.read_group_header}" -f {output} {params.reference_genome} {input.sai_1} {input.sai_2} {input.fastq_1} {input.fastq_2}
sam_to_bam:  samtools sort -@ {threads} -o {output} {input}
index_bam: samtools index {input} {output}
mark_PCR_duplicates: java -Xmx32G -Djava.io.tmpdir={params.tmp_path} -jar {params.picard_tools} INPUT={input} OUTPUT={output.marked_file} METRICS_FILE={output.pcr_metrics} VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true TMP_DIR={params.tmp_path}
identify_regions_for_realignment: java -Xmx32G -Djava.io.tmpdir={params.tmp_path} -jar {params.gatk} -nt {threads} -T RealignerTargetCreator -R {params.reference_genome} -I {input} -o {output} -l ERROR
perform_realignment: java -Xmx32G -Djava.io.tmpdir={params.tmp_path} -jar {params.gatk} -T IndelRealigner -R {params.reference_genome} -I {input.marked_file} -l ERROR -targetIntervals {input.interval_file} -o {output}
find_quality_score_recalibration_spots: java -Xmx32G -jar {params.gatk}   -T BaseRecalibrator   -l ERROR    -R {params.reference_genome}   -knownSites {params.snps}   -I {input.realigned_file}       -cov CycleCovariate      -cov ContextCovariate  -o {output.recalibrated_file}
quality_score_recalibration: java -Xmx32G -jar {params.gatk}  -T PrintReads -l ERROR   -R {params.reference_genome}   -I {input.realigned_file}   -BQSR {input.recalibrated_file}  -o {output}
StringTie_recalibration: stringtie -p 8 -G {params.ref_gtf} {input} -A {output.genes} -o {output.gtf}
remove_snps: python3 src/remove_annotated_snps_and_below_threshold.py {input} > {output}
remove_edge_mismatches: python3 src/remove_edge_mismatches.py --vcf {input.vcf} --bam {input.bam} --min_distance {params.min_distance} > {output}
get_repeat_region_snps: python3 src/remove_title.py {input} | vectools slice --keep-cols 0,1,1: - | vectools subtract -r --only-apply-on 0 --scalar 1 - | bedtools intersect -wa -a stdin -b {params.repeats_bed} | vectools slice --remove-cols 2 - > {output}
remove_non_editing_snps: vectools vrep --only-apply-on 3,4 {params.editing_types} {input} > {output}
get_non_alu_regions: python3 src/remove_title.py {input} | vectools slice --keep-cols 0,1,1: - | vectools subtract -r --only-apply-on 0 --scalar 1 - | bedtools intersect -v -wa -a stdin -b {params.repeats_bed} | vectools slice --remove-cols 1 - > {output}
remove_intron_splice_junctions: "python3 src/remove_title.py {input} | vectools slice --keep-cols 0,1,1: - | vectools subtract -r --only-apply-on 0 --scalar 1 - | bedtools intersect -v -wa -a stdin -b {params.splice_junctions} | vectools slice --remove-cols 1 - > {output}
remove_homopolymers: python3 src/remove_homopolymers.py --vcf {input} --reference-genome {params.reference_genome} --distance {params.distance} > {output}
generate_snp_overlap_fasta: python3 src/generate_fasta_from_vcf_and_bam.py --vcf {input.vcf} --bam {input.bam} > {output}
run_blat: blat -stepSize=5 -repMatch=2253 -minScore=20 -minIdentity=0 -noHead {params.ref_genome} {input} {output}
filter_psl: python3 src/filter_psl_file.py --vcf {input.vcf} --psl {input.psl} > {output}
remove_non_editing_snps_nonmismatches: vectools vrep --only-apply-on 3,4 {params.editing_types} {input} > {output}
combine_filtered_editing_sites: cat {input.repeats} {input.non_repeat} > {output}
Genome_build: GRCm38.87
Supplementary_files_format_and_content: Output files from RNAEditor for the detected RNA editing sites and islands.

source_name: HEK-293 cells

growth_protocol: HEK-293 cells were cultured in growth medium consisting of DMEM with low glucose and pyruvate (Thermo Fischer Scientific) supplemented with 10% FBS (Thermo Fischer Scientific), and antibiotics (100 units of penicillin and 100 μg of streptomycin per ml, Sigma-Aldrich). Cells were propagated under standard incubation conditions with 5% atmospheric CO2 at 37°C.

extract_protocol:
Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. Twenty-four hours after transfection, total RNA was isolated.
RNA-seq was performed by Novogene (California, U.S.A.). From total RNA, rRNA was removed using Ribo-Zero rRNA Removal kit (Illumina, #MRZH11124). Then, rRNA-depleted total RNA was subjected to the library preparation using  NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs, #E7770). The insert size of 250~300bp were sequenced in a directional manner using The HiSeq 4000 System Illumina (pair-end, 2 × 150 bp).

value: HEK-293 cells

tag: sirna


title: CE05_AAp1

description: polyA RNA

source_name: Artery of Cynomolgus Monkey

value: Male


title: control-C rep6 [447C]

source_name: control-C

value: control vehicle


title: control-GC rep2 [396GC]

value: granulosa


title: MDA-MB-231_siGpx1_rep1

source_name: Breast cancer cell line MDA-MB-233

value: Triple-negative breast cancer (TNBC) cell line MDA-MB-233

value: mammary gland; breast

tag: cell type

value: epithelial


title: HEK-293 cells, treated with siADAR rep1

description:
Sample_4
Cells were transfected with siRNA against ADAR.


title: treatment-C rep1 [385C]


title: CE05_AAn1

description: polyA RNA

value: aortic artery


title: control-C rep5 [437C]


title: control-C rep3 [397C]


title: control-C rep4 [431C]


title: control-C rep2 [396C]


title: control-GC rep1 [388GC]


title: MDA-MB-231_Control_rep2

source_name: Breast cancer cell line MDA-MB-232

value: Triple-negative breast cancer (TNBC) cell line MDA-MB-232

value: control


title: HEK-293 cells, treated with siScr (Ctrl.) rep1

description:
Sample_1
Cells were transfected with siRNA against scrambled sequence ("Ctrl.").

value: siScr


title: CE04_CAn1

description: polyA RNA

value: coronary artery


title: CE04_AAp2

description: polyA RNA


title: control-C rep1 [388C]

value: Holstein heifers

value: 11-13 months

value: female

value: caruncular endometrium


title: Quadriceps myofibers, daily prednisone 2

city: Chicago

first: Mattia

last: Quattrocelli

state: IL

address: 303 E. Superior St.

department: Center for Genetic Medicine

institute: Northwestern University

description:
H3K27ac ChIP-seq on myofiber DNA
D2

data_processing:
Reads were aligned to mm10 using bowtie2
Peak analysis was conducted using HOMER software (v4.10) and analyzing peaks in IP samples versus input controls
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files for all samples and inputs (UCSC genome browser-ready)

extract_protocol:
Input and IP chromatin was purified using Qiagen MinElute kit.
TrueSeq ChiP-seq library prep (Illumina)

treatment_protocol: Prednisone (Sigma #P6254) was injected for 4-week-long treatments as IP solution of 1mg/kg in 100ul PBS from a 5mg/kg stock solution in DMSO in male mdx mice (DBA/2J background) of approximately 6 months of age. 48hours after last injection quadriceps muscles were obtained from each mouse, the myofiber fraction from both muscles was obtained through collagenase digestion and filtration. Chromatin was then fixed, isolated, sonicated and immunoprecipitated.

tag: genotype

value: mdx model of DMD

value: daily prednisone

value: quadriceps myofibers

tag: chip-seq antibody

value: rabbit anti-H3K27ac polyclonal antibody (ActiveMotif #39133)


title: Quadriceps myofibers, daily prednisone 3

description:
H3K27ac ChIP-seq on myofiber DNA
D3


title: Quadriceps myofibers, pooled inputs for daily-prednisone samples

description:
H3K27ac ChIP-seq on myofiber DNA
D_input


title: treatment-IC rep1 [385IC]

source_name: treatment-IC

value: University of Florida Dairy Unit

value: uterine infection with E. coli and T. pyogenes

value: intercaruncular endometrium


title: CE04_AAp1

description: polyA RNA

value: Male


title: CE03_CAp1

description: polyA RNA


title: CE13-AAp1

description: polyA RNA

value: aortic artery

value: Female


title: Quadriceps myofibers, weekly prednisone 2

description:
H3K27ac ChIP-seq on myofiber DNA
W2

value: weekly prednisone


title: CE04_AAn1

description: polyA RNA


title: treatment-IC rep3 [436IC]


title: CE04_CAp2

description: polyA RNA


title: Quadriceps myofibers, daily prednisone 1

description:
H3K27ac ChIP-seq on myofiber DNA
D1


title: treatment-IC rep2 [401IC]


title: CE03_CAp2

description: polyA RNA


title: control-IC rep4 [431IC]

source_name: control-IC

value: control vehicle


title: CE03_AAn1

description: polyA RNA


title: HEK-293 cells, treated with siScr (Ctrl.) rep2

description:
Sample_2
Cells were transfected with siRNA against scrambled sequence ("Ctrl.").

value: HEK-293 cells

value: siScr


title: control-IC rep6 [447IC]

value: Holstein heifers

value: 11-13 months


title: Quadriceps myofibers, weekly prednisone 3

description:
H3K27ac ChIP-seq on myofiber DNA
W3


title: control-IC rep5 [437IC]

value: female


title: CE01_CAp2

description: polyA RNA

value: coronary artery


title: CE03_CAn1

description: polyA RNA


title: control-IC rep1 [388IC]


title: CE01_CAn2

description: polyA RNA


title: Quadriceps myofibers, weekly prednisone 1

description:
H3K27ac ChIP-seq on myofiber DNA
W1

value: mdx model of DMD


title: CE03_AAp1

description: polyA RNA


title: CE01_CAn1

description: polyA RNA


title: SB-EP, SB-2ilif and NatE45 (mixture of 6 samples)

first: Florian

last: Hollfelder

address: 80 tennis court road

country: United Kingdom

institute: University of Cambridge

description: 6 mixed samples: SB-EP1, SB-EP2, SB-EP3, SB-2ilif1, SB-2ilif2, NatE45

data_processing:
R1 is the biological read.
R2 carries the first half of the gel barcode.
R3 carries the library index.
R4 the second half of the gel barcode (8 cycles) and the UMI (6 cycles).
indropv3 filtering and demultiplexing
indropv3  identify abundant barcodes
indropv3 quantify expression
indropv3 sort
indropv3 aggregate
scrublet remove doublets
Genome_build: Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
Supplementary_files_format_and_content: indrop quantification matrices converted to 10x format

source_name: Cells extracted from the synthetic blastocyst (SB) built with extended pluripotent stem cells and trophoblast stem cells.  Cells extracted from the synthetic blastocyst (SB) built with conventional embryonic stem cells and trophoblast stem cells.

growth_protocol: Cell suspension seeded in aggregation plates. Grown in sequencial media.

extract_protocol:
Blastoids (n=100 per group) were  exposed to Tryple Express Select X10 (Thermofisher A1217701) for 15 mins in 37°C, and  subsequently dissected with glass capillaries of different diameters. For ESC-derived blastoid  group; total of 1,154 cells including 752 ESCs, 350 TSCs 52 PE-like cells extracted. For EPSCderived blastoid group; total of 2,350 cells including 1,087 EPSC, 1,140 TSCs 123 PE-like cells  extracted.
Indrop v3

treatment_protocol: no treatment was used.

value: mixed sample (non-demultiplexed) representing SB-EP, SB-2iLif and NatE45 cells


title: CE03_AAp2

description: polyA RNA


title: Quadriceps myofibers, vehicle 3

description:
H3K27ac ChIP-seq on myofiber DNA
V3

value: vehicle

value: quadriceps myofibers

value: rabbit anti-H3K27ac polyclonal antibody (ActiveMotif #39133)


title: control-IC rep3 [397IC]

value: University of Florida Dairy Unit

value: intercaruncular endometrium


title: Quadriceps myofibers, pooled inputs for weekly-prednisone samples

description:
H3K27ac ChIP-seq on myofiber DNA
W_input


title: CE01_AAp2

description: polyA RNA

value: aortic artery


title: CE01_AAp3

description: polyA RNA

value: Female


title: control-IC rep2 [396IC]


title: Quadriceps myofibers, vehicle 2

description:
H3K27ac ChIP-seq on myofiber DNA
V2


title: CE01_CAp1

description: polyA RNA


title: CE01_AAp1

description: polyA RNA


title: Quadriceps myofibers, pooled inputs for vehicle samples

description:
H3K27ac ChIP-seq on myofiber DNA
V_input


title: Quadriceps myofibers, vehicle 1

description:
H3K27ac ChIP-seq on myofiber DNA
V1


title: treatment-I rep3 [436I]

source_name: treatment-I

value: uterine infection with E. coli and T. pyogenes

value: isthmus


title: treatment-I rep2 [401I]


title: control-I rep3 [397I]

source_name: control-I

value: control vehicle


title: treatment-I rep1 [385I]


title: control-I rep1 [388I]


title: control-I rep5 [437I]


title: control-I rep6 [447I]


title: control-I rep4 [431I]


title: CE01_AAn2

description: polyA RNA


title: treatment-GC rep2 [408GC]

source_name: treatment-GC

value: granulosa


title: CE01_AAn1

description: polyA RNA


title: Cas9-Dam (-)/gRNA(+)

city: Los Angeles

first: Byoung San

last: Moon

state: California

address: 1425 San Pablo St. 409B

institute: University of Southern California

data_processing:
Library strategy: DNA-seq
Sequencing reads were checked for quality by FastQC before adaptor removal and Barrows Wheeler alignment.
Results summarized through visualization with Integrated Genome Browser.
UCSC Genome Browser mm9
Genome_build: mm9
Supplementary_files_format_and_content: bw files

source_name: E14 mouse embryonic stem cells

growth_protocol: E14 mouse ES cells were grown in ESC media containing GMEM with 15% FBS, 1% NEAA, 1% Sodium Pyruvate, 1% L-glutamine, 1% PenStrep, 1X B-mercaptoethanol, and 1000U LIF. Cells were passaged using 0.05% Trypsin in PBS solution. Primary mouse MEF cells were derived from E12.5 embryos and cultured in DMEM/10% FBS, 1% PenStrep, and 1% L-glutamine for two passages before use.

extract_protocol:
Genomic DNA from samples were extracted and purified using Genomic DNA Mini Kit (Bioland Scientific LLC, Paramount, CA).
For high throughput sequencing library preparation, DNA was digested for 24 hours with DpnI and ethanol precipitated before ligating PCR adaptors. DNA was then digested for 24 hours with DpnII to exclude amplification of fragments containing non-methylated sites. PCR was performed to enrich for fragments flanked by methylated GATC sites. Adaptors were removed via sonication and AluI digestion and cleaned up with AMPure XP beads (Beckman Coulter, Indianapolis, IN ). Library fragments were further processed using the NEBNext® Ultra™ DNA Library Prep Kit (NEB) and labeled with dual indexes prior to sequencing.

treatment_protocol: NmCRISPR-Dam cell lines were generated first through selection of rtTA containing E14 ESC clones using 200ug/ml Hygromycin B (VWR) and then gRNA selection with 1ug/ml of puromycin (Santa Cruz Biotechnology, Santa Cruz, CA) for 48 hours post transduction. Clones were manually selected and genotyped by PCR to confirm construct integration. NmCas9-Dam labeling performed using 5x106 cells and induced with a single pulse of 2ug/ml doxycycline (Sigma, St. Louis, MO).

value: pluripotent stem cell

tag: construct

value: Doxycycline inducible


title: treatment-A rep3 [436A]

source_name: treatment-A

value: Holstein heifers

value: 11-13 months

value: female

value: ampulla


title: Cas9-Dam (+)/gRNA(+)


title: treatment-A rep1 [385A]


title: Cas9-Dam (+)/gRNA(-)


title: control-A rep6 [447A]

source_name: control-A


title: control-A rep5 [437A]


title: control-A rep4 [431A]


title: control-A rep1 [388A]


title: control-I rep2 [396I]


title: control-A rep3 [397A]


title: siPDK1 2

city: Hong Kong

first: Michelle

middle: KY

last: Siu

address: Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: O&G

country: Hong Kong

institute: University of Hong Kong

data_processing:
Gene expression levels were quantified using RNA-Seq by Expectation Maximization (RSEM) (Li and Dewey, 2011). The DEseq2 method was applied to detect differentially expressed genes (DEG) between groups.
Genome_build: hg19
Supplementary_files_format_and_content: normalized signal with NBCI Gene IDs.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA preparation, library construction and sequencing with the BGISEQ-500 platform were performed at Beijing Genomics Institute (BGI, Shenzhen, China). 1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double- strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.

value: ovarian cancer cell line

tag: knockdown


title: treatment-A rep2 [401A]


title: siPDK1 1


title: Control 1

value: control siRNA


title: Control 2


title: exp4_10: HT29_2D_plastic

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from HT29 grpwth in 2D plastic

hyb_protocol: Following fragmentation and labelling,5.5 μg ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome Clariom S Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: HT-29 cells

label_protocol: Labeled and Fragmented ss-cDNA were prepared according to the standard GeneChip WT Plus protocol starting from 100 ng of Total RNA

growth_protocol: The human colon adenocarcinoma cell line HT29 ZsGreen/Luc+  was maintained in RPMI-1640 medium supplemented with 10 %fetal bovine serum, 1 % L-Glutamine and 1 % pen/strep antibiotic solution (growth medium) in humidified atmosphere at 37 °C in 5 % CO2. HC, CRC, HL and CRLM decellularized matrices were then injected with 2.5x105 HT-29 ZsGreen/Luc+ cells, resuspended in 10μL of Collagen I (diluted 2:3 with RPMI-1640). Complete medium was carefully added and changed every day

extract_protocol: Total RNA was extracted from cells, HL and CRLM recellularized matrices using TissueLyser (Qiagen) combined with Trizol in 3 independent experiments

value: human colon adenocarcinoma cell line

tag: type of culture

value: Cell line


title: exp4_05: HT29_3D_CRLM

description: Gene expression data from HT29 cell growth in 3D with a decellularized matrix derived form a CRLM

value: Decellularized matrix from Patient3


title: exp4_08: HT29_3D_HL

description: Gene expression data from HT29 cell growth in 3D with a decellularized matrix derived form a HL

value: Decellularized matrix from Patient4


title: L75

status: Public on Nov 29 2019

city: Chongqing

first: Yi

last: Shu

address: 136 2nd Zhongshan Rd

institute: Children's Hospital, Chongqing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: T-ALL

extract_protocol:
Total RNA was used for library preparation using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, USA). rRNA was removed and strand-specific RNA-seq libraries were prepared following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T cell


title: control-A rep2 [396A]

tag: breed

value: University of Florida Dairy Unit


title: N2

source_name: Normal T cell


title: N3


title: N4


title: L72


title: L71


title: exp4_09: HT29_2D_plastic


title: L62


title: exp4_07: HT29_3D_CRLM


title: exp4_02: HT29_3D_HL

value: Decellularized matrix from Patient1


title: L52


title: L74


title: exp4_01: HT29_3D_CRLM


title: exp4_06: HT29_3D_HL


title: L43


title: exp4_04: HT29_3D_HL

value: Decellularized matrix from Patient2


title: L10


title: L8


title: L4


title: N1


title: 045norm

status: Public on Nov 28 2019

city: Storrs

first: Sheida

last: Nabavi

address: 371 Fairfield Way

institute: University of Connecticut

description: RNA-seq of Homo sapiens: Normal breast

data_processing:
Quality Check: FASTQ file quality was checked using FASTQC v0.11.2. The summary reports showed no potential errors or warnings.
Alignment and Pre-processing: Reads were mapped using STAR Aligner tool v020201 to the human genome reference (Hg19) downloaded from UCSC genome browser.
Transcripts quantification: Gene expression levels were obtained from the RNA-seq dataset using RSEM v1.2.31 with Ensembl gene annotation database.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each Sample, obtained using RSEM V1.2.31.

source_name: Breast

extract_protocol:
Qiagen RNeasy FFPE kit is used for FFPE sample extraction.
Illumina library preparation for RNA-Seq is done using the TruSeq RNA Access library prep kit. The samples were sequenced on Illumina Nextseq 500 high output v2 platform (2x75).

tag: cancer type

value: Breast

tag: race

tag: ethnicity

value: Normal

value: FFPE

value: Female


title: L64


title: 047_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer

source_name: Overy

value: BRCA

value: Ovary

value: White

value: Tumor

value: Carrier

tag: Sex


title: 056_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer

value: SD


title: 065_EOS

description: RNA-seq of Homo sapiens: Breast cancer


title: 011Norm

description: RNA-seq of Homo sapiens: Normal breast


title: 038_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer

value: PR


title: 051_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer

value: Neg

value: Non-Carrier


title: 058_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer


title: 008Norm

description: RNA-seq of Homo sapiens: Normal breast


title: 017_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer


title: 043_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer


title: 031_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer

value: Unknown


title: 067_BC

description: RNA-seq of Homo sapiens: Breast cancer


title: 293T_Safb1/2_DKO_clone_3

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

description:
processed data file:
total reads_293T_all samples.txt

data_processing:
Basecalling by the Illumina Real-Time Analysis (RTA) software
De-multiplexing into sample specific BAM files using Picard tools
Trimming of Sequencing adapter with TrimGalore
Mapping against reference miRNA with HISAT2
Analysis of differential miRNA expression with edgeR
Genome_build: Reference: human miRNAs extracted from the miRBase 22 release
Supplementary_files_format_and_content: tab-delimited text files total reads_Ramos_all samples and total reads_293T_all samples include the number of reads aligned to the respective reference miRNAs; tab-delimited text files Ramos_edgeR_output and 293T_edgeR_output provide logFC, logCPM, F, PValue, FDR and -log10pvalue for the comparison of control vs. Safb1/2 ko cells

extract_protocol:
Cells were harvested, washed once with PBS and total RNA was isolated with the miRNEasy Kit (QIAGEN) according to the manufacturer's recommendation.
Libraries for Illumina sequencing were prepared with the Somagenics RealSeq-AC miRNA library Kit, using 100 ng total RNA as input.

value: 293T cell line; DSMZ #ACC635


title: 004_EOS

description: RNA-seq of Homo sapiens: Ovarian cancer


title: 064_BC

description: RNA-seq of Homo sapiens: Breast cancer


title: L50

value: T cell


title: 293T_control_clone_2

value: wild type; CRISPR control


title: 049_BC

description: RNA-seq of Homo sapiens: Breast cancer

value: Breast


title: 069_BC

description: RNA-seq of Homo sapiens: Breast cancer


title: 293T_Safb1/2_DKO_clone_2


title: L9


title: 293T_Safb1/2_DKO_clone_1


title: 062_BC

description: RNA-seq of Homo sapiens: Breast cancer


title: 012Norm

description: RNA-seq of Homo sapiens: Normal breast

value: Normal


title: 053_BC

description: RNA-seq of Homo sapiens: Breast cancer

value: FFPE


title: 016Norm

description: RNA-seq of Homo sapiens: Normal breast

value: Female


title: 293T_control_clone_1


title: Ramos_Safb1/2_DKO_clone_3

description:
processed data file:
total reads_Ramos_all samples.txt

value: Ramos cell line; DSMZ #ACC603


title: Ramos_Safb1/2_DKO_clone_2


title: Ramos_Safb1/2_DKO_clone_1


title: Ramos_control_clone_1


title: Ramos_control_clone_2


title: 044_BC

description: RNA-seq of Homo sapiens: Breast cancer

value: BRCA


title: Ramos_control_clone_3


title: 020_BC

description: RNA-seq of Homo sapiens: Breast cancer

value: White


title: PGC_Replicate2

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

data_processing:
Clean reads were mapped to the Mus musculus mm10 reference genome using Bowtie2 (population) or Hisat2 (a few cells).
Reads were assigned and counted to genes using the RSEM.
The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: expMatrix_Tpm_pESC.csv. This file contains all samples TPM value of all genes

source_name: PGC

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For the experiments by treatment with crotonic acid during induction, 7 mM crotonic acid (pH=7) was added into induction medium from 16D to 28D continuously; For the induced PGCLCs, ESCs or gSCs treated with 1%KSR, 1. ng/ml bFGF and 2ng/ml Activin A for 2 days can form EpiLCs, and further treated with 500 ng/ml BMP4, 100 ng/ml SCF, 50ng/ml EGF and 1000 IU mLif for 4 days to form PGCLCs.

tag: strain

value: PGC


title: ESC-PGCLC_Replicate2

source_name: Female ES cell line derived PGC-like cell


title: pESC-PGCLC_Replicate2

source_name: Parthenogenetic ES cell line derived PGC-like cell


title: pESC-PGCLC_Replicate1

value: Parthenogenetic ES cell line derived PGC-like cell


title: PGC_Replicate1


title: 293T_control_clone_3


title: ESC-PGCLC_Replicate1

value: Female ES cell line derived PGC-like cell


title: Female ESC_Replicate1

source_name: Female ES cell line

value: Female ES cell line


title: pESC_Replicate2

source_name: Parthenogenetic ES cell line

value: Parthenogenetic ES cell line


title: Female ESC_Replicate2


title: pESC_Replicate1


title: DSS day 39_WT intestinal macrophage-1

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

institute: CHA Bundang Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: colon

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: mice were orally administered 2.5% dextran sodium sulphate (DSS) in drinking water for 5 days

value: WT

value: colon

tag: marker


title: DSS day 39_Csf1r-EP4-/- intestinal macrophage-3

tag: tissue


title: DSS day 39_Csf1r-EP4-/- intestinal macrophage-2


title: DSS day 0_WT intestinal macrophage-1


title: DSS day 39_WT intestinal macrophage-3


title: DSS day 39_WT intestinal macrophage-2


title: DSS day 39_Csf1r-EP4-/- intestinal macrophage-1


title: exp4_03: HT29_3D_CRLM

tag: cell line

value: human colon adenocarcinoma cell line

value: Decellularized matrix from Patient2


title: 026_BC

description: RNA-seq of Homo sapiens: Breast cancer

value: Tumor

value: SD

value: Carrier