title: ShortDay_ZT20_Rep_B

city: New Haven

first: Chun Chung

last: Leung

state: CT

address: YSB 424, 260 Whitney Avenue

department: MCDB

institute: Yale University

data_processing:
Adaptor sequence and low-quality sequence were removed with Trimmomatic (v.0.39) with the parameters -phred33 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:8 TRUE SLIDINGWINDOW:4:20 LEADING:5 TRAILING:5 MINLEN:36
The trimmed sequences were aligned to the TAIR10 genome (version 47) with HISAT2 (v.2.1.0) using the parameters: --rna-strandness FR --no-mixed -I 100 -X 800 -x -p 10
Mapped reads were annotated with stringtie (v.2.1.2) using -v -e -B -G
Assembly: TAIR10 EnsemblPlants release 47
Supplementary files format and content: comma-delimited text files include gene count values for each sample

organism: Arabidopsis thaliana

source_name: Whole 12-day old seedling

growth_protocol: Seeds were surface sterilized for 20 minutes in 70% ethanol and 0.01% Triton X-100. Seeds were then sown onto ½ Murashige and Skoog medium (Cassion Laboratories, cat. #MSP01) plates lined with autoclaved filter papers. Seeds were put into dark at 4oC for 48 hours before transferring to equinox photoperiod (12 hours light and 12 hours dark) at 22oC and 130 μmol m-2 s-1 light intensity. After germination, seedings were grown in the same condition for 10 days.

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher) according to manufacturer's instructions.
Library was prepared at the Yale Center for Genome Analysis using Illumina's mRNA Sample preparation Kit (Part# 1004814) following manufactuer's protocol with the modification that 5 - 20 nanograms of total RNA was used as starting material

treatment_protocol: Seedlings were transferred to equinox (12 hours light and 12 hours dark), long day (16 hours light and 8 hours dark) and short day (8 hours light and 16 hours dark) photoperiod at 22oC and 130 μmol m-2 s-1 light intensity for 48 hours before harvest

value: Whole 12-day old seedling

value: Columbia 0

value: Short day (8 hours light and 16 hours dark) photoperiod at 20 hours after dawn in the dark


title: ShortDay_ZT20_Rep_C

status: Public on Aug 15 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment


title: Stage E7.5 embryo 3 section 3 region R1

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

description:
E7.5_3.txt
E7.5_3_3R1

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Textfile includes FPKM values for each embryo

organism: Mus musculus

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit.

treatment_protocol: Sample from each location was laser-microdissected and collected for single-cell based RNA sequencing. For the single cells isolated from known positions, embryos were dissected from the decidua in 10% FBS-DMEM medium, and cells were isolated from a specific position of the embryo by mouth pipetting guided by microscopy, then subject to Smart-seq2.

tag: developmental stage

tag: strain

value: embryo


title: ShortDay_ZT20_Rep_A


title: Dand5 mutant stage E7.5 embryo 1 section 8 region A

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8A

data_processing:
Raw reads were mapped to mm10 version of the mouse genome using the Tophat2 v2.0.4 program.
We calculated fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters.
Genes with the FPKM value > 1.0 in at least one sample across all samples were retained for further analysis.
The expression levels were transformed to logarithmic space by using log2(FPKM+1).
Batch effects were corrected using ComBat function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Text file includes FPKM values for each embryo


title: Dand5 mutant stage E7.5 embryo 1 section 8 region L1

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8L1


title: Stage E7.5 embryo 3 section 3 region P

description:
E7.5_3.txt
E7.5_3_3P


title: Dand5 mutant stage E7.5 embryo 1 section 4 region P

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4P


title: ShortDay_ZT16_Rep_C

value: Short day (8 hours light and 16 hours dark) photoperiod at 16 hours after dawn in the dark


title: Stage E7.5 embryo 3 section 3 region MP

description:
E7.5_3.txt
E7.5_3_3MP


title: Dand5 mutant stage E7.5 embryo 1 section 4 region MPR

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4MPR


title: Dand5 mutant stage E7.5 embryo 1 section 4 region MPL

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4MPL


title: ShortDay_ZT16_Rep_B


title: Dand5 mutant stage E7.5 embryo 1 section 8 region L2

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_8L2


title: Stage E7.5 embryo 3 section 3 region MA

description:
E7.5_3.txt
E7.5_3_3MA


title: Stage E7.5 embryo 3 section 3 region L2

description:
E7.5_3.txt
E7.5_3_3L2


title: ShortDay_ZT16_Rep_A


title: Dand5 mutant stage E7.5 embryo 1 section 4 region MAR

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4MAR


title: Dand5 mutant stage E7.5 embryo 1 section 4 region L2

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4L2


title: Dand5 mutant stage E7.5 embryo 1 section 4 region L1

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4L1


title: Stage E7.5 embryo 3 section 3 region R2

description:
E7.5_3.txt
E7.5_3_3R2


title: Dand5 mutant stage E7.5 embryo 1 section 4 region MAL

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4MAL


title: ShortDay_ZT12_Rep_C

value: Short day (8 hours light and 16 hours dark) photoperiod at 12 hours after dawn in the dark


title: Dand5 mutant stage E7.5 embryo 1 section 4 region R2

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4R2


title: Stage E7.5 embryo 3 section 3 region L1

description:
E7.5_3.txt
E7.5_3_3L1


title: Dand5 mutant stage E7.5 embryo 1 section 4 region R1

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4R1


title: Dand5 mutant stage E7.5 embryo 1 section 4 region EA

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4EA


title: Dand5 mutant stage E7.5 embryo 1 section 4 region EP

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4EP


title: Dand5 mutant stage E7.5 embryo 1 section 4 region A

description:
Dand5_mutant_1_FPKM_Filter_Log2.txt
Dand5_mutant_E7.5_1_4A


title: Stage E7.5 embryo 3 section 3 region EP

description:
E7.5_3.txt
E7.5_3_3EP


title: ShortDay_ZT12_Rep_B


title: Stage E7.5 embryo 3 section 3 region EA

description:
E7.5_3.txt
E7.5_3_3EA


title: LDN193189-treated  section 3 region R

description:
Inhibitor.txt
LDN_S3_R


title: LDN193189-treated  section 3 region MR

description:
Inhibitor.txt
LDN_S3_MR


title: Stage E7.5 embryo 3 section 3 region A

description:
E7.5_3.txt
E7.5_3_3A


title: LDN193189-treated  section 3 region P

description:
Inhibitor.txt
LDN_S3_P


title: LDN193189-treated  section 3 region L

description:
Inhibitor.txt
LDN_S3_L


title: ShortDay_ZT08_Rep_B

value: Short day (8 hours light and 16 hours dark) photoperiod at 8 hours after dawn in the light


title: Stage E7.5 embryo 3 section 2 region P

description:
E7.5_3.txt
E7.5_3_2P


title: LDN193189-treated  section 3 region A

description:
Inhibitor.txt
LDN_S3_A


title: ShortDay_ZT08_Rep_A


title: LDN193189-treated  section 2 region MR

description:
Inhibitor.txt
LDN_S2_MR


title: LDN193189-treated  section 2 region ML

description:
Inhibitor.txt
LDN_S2_ML


title: ShortDay_ZT04_Rep_C

value: Short day (8 hours light and 16 hours dark) photoperiod at 4 hours after dawn in the light


title: Stage E7.5 embryo 3 section 2 region MA

description:
E7.5_3.txt
E7.5_3_2MA


title: ShortDay_ZT12_Rep_A


title: Stage E7.5 embryo 3 section 2 region EP

description:
E7.5_3.txt
E7.5_3_2EP


title: ShortDay_ZT04_Rep_B


title: LDN193189-treated  section 2 region R

description:
Inhibitor.txt
LDN_S2_R


title: ShortDay_ZT08_Rep_C


title: LDN193189-treated  section 3 region ML

description:
Inhibitor.txt
LDN_S3_ML


title: ShortDay_ZT04_Rep_A


title: Stage E7.5 embryo 3 section 2 region EA

description:
E7.5_3.txt
E7.5_3_2EA


title: LDN193189-treated  section 2 region A

description:
Inhibitor.txt
LDN_S2_A


title: LDN193189-treated  section 1 region P

description:
Inhibitor.txt
LDN_S1_P


title: Stage E7.5 embryo 3 section 1 region P

description:
E7.5_3.txt
E7.5_3_1P


title: LDN193189-treated  section 2 region P

description:
Inhibitor.txt
LDN_S2_P


title: LDN193189-treated  section 1 region R

description:
Inhibitor.txt
LDN_S1_R


title: ShortDay_ZT00_Rep_A

value: Short day (8 hours light and 16 hours dark) photoperiod at 0 hour after dawn in the dark


title: Stage E7.5 embryo 3 section 2 region MP

description:
E7.5_3.txt
E7.5_3_2MP


title: ShortDay_ZT00_Rep_B


title: Stage E7.5 embryo 3 section 1 region EAP

description:
E7.5_3.txt
E7.5_3_1EAP


title: LDN193189-treated  section 1 region ML

description:
Inhibitor.txt
LDN_S1_ML


title: Stage E7.5 embryo 2 section 9 region R2

description:
E7.5_2.txt
E7.5_2_9R2


title: LDN193189-treated  section 2 region L

description:
Inhibitor.txt
LDN_S2_L


title: LDN193189-treated  section 1 region L

description:
Inhibitor.txt
LDN_S1_L


title: LongDay_ZT20_Rep_C

value: Long day (16 hours light and 8 hours dark) photoperiod at 20 hours after dawn in the dark


title: LongDay_ZT20_Rep_B


title: Stage E7.5 embryo 2 section 9 region R1

description:
E7.5_2.txt
E7.5_2_9R1


title: ShortDay_ZT00_Rep_C


title: PYR1_CA_3

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

description:
ODED30
mRNA

data_processing:
Trimmed the raw reads using Trimmomatic version 0.38.
Reads were mapped using Salmon version 1.3.0.
Trimmed-mean normalized using edgeR (3.28.0).
Genome_build: TAIR10
Supplementary_files_format_and_content: allOdedRaw.csv: Comma-separated text file includes TMM normalized data for all samples.

source_name: Whole seedling 10 DAG

growth_protocol: T3 lines of expressing PYLCA, Col-0 and aba2-1 were grown for seven days on MS plates.

extract_protocol:
Following treatment, seedlings were frozen in liquid nitrogen and stored in -80°C. RNA was extracted using RNeasy Plant Mini Kit (QIAGEN, Germany) followed by DNase treatment using an AMBION DNA-free™ Kit (Life Technologies, CA, USA) according to manufacturers' instructions.
Libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit and sequenced with Illumina® NextSeq® 500.

treatment_protocol: Seedlings were then incubated in liquid MS for three hours. The media contained mock for PYLCA, and mock, ABA 10nM or ABA 50nM for Col-0 and aba2-1.

tag: line

tag: age

value: 10 DAG

value: Whole seedling

value: Mock


title: LDN193189-treated  section 1 region A

description:
Inhibitor.txt
LDN_S1_A


title: PYR1_CA_2

description:
ODED29
mRNA


title: Stage E7.5 embryo 2 section 9 region P

description:
E7.5_2.txt
E7.5_2_9P


title: LongDay_ZT20_Rep_A


title: Stage E7.5 embryo 2 section 9 region L2

description:
E7.5_2.txt
E7.5_2_9L2


title: PYR1_CA_1

description:
ODED28
mRNA


title: LongDay_ZT16_Rep_C

value: Long day (16 hours light and 8 hours dark) photoperiod at 16 hours after dawn in the light


title: Ctrl section 2 region R

description:
Inhibitor.txt
Ctrl_S2_R


title: LDN193189-treated  section 1 region MR

description:
Inhibitor.txt
LDN_S1_MR


title: Ctrl section 2 region P

description:
Inhibitor.txt
Ctrl_S2_P


title: LongDay_ZT16_Rep_B


title: MDA231_shEGR1_TNF_24h

type: RNA

city: Seoul

first: Soon Young

last: Shin

address: 120, Neungdong-ro, Gwangjin-gu

department: Department of Biological Sciences

country: South Korea

institute: Konkuk University

description: Gene expression of TNF-α-treated MSCs

hyb_protocol: Hybridization and washing steps were performed using Agilent’s Gene Expression Hybridization Kit and Agilent’s Gene Expression Wash Buffer Kit, respectively.

scan_protocol: Microarrays were scanned using Agilent’s DNA microarray scanner and Feature Extraction Software.

data_processing: Raw data were processed and normalized using Agilent's GeneSpring Software. First, noise data with signal intensity less than 0.01 were adjusted to 0.01. For normalization, Each probes are divided by the 50th percentile (median) value of all probes. To optain reliable genes, spots with signal intensity lower than the background or insignificant standard deviation of each pixel value were removed by applying flag values.

organism: Homo sapiens

label_protocol: Amplification and babeling were performed using Agilent’s Low RNA Input Linear Amplification kit PLUS.

growth_protocol: MDA-MB-231 cells were cultured in DMEM containing 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated using NucleoZOL (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: MDA-MB-231 cells were transfected with shCT (control) or shEGR1 and splited into two groups. Cells were then serum-starved (0.5% FBS) and treated with vehicle or 10 ng/mL TNF-a for 24 h.

value: TNBC

tag: cell line

tag: shRNA

value: TNFα, 10ng/mL, 24h


title: MDA231_shCT_TNF_24h

description: Gene expression of TNF-α-treated MSCs

value: shCT


title: Ctrl section 2 region MR

description:
Inhibitor.txt
Ctrl_S2_MR


title: Stage E7.5 embryo 2 section 9 region A

description:
E7.5_2.txt
E7.5_2_9A


title: Stage E7.5 embryo 2 section 9 region L1

description:
E7.5_2.txt
E7.5_2_9L1


title: MDA231_shEGR1_NT

description: Gene expression of nontreated MSCs

value: nontreated


title: PYL6_CA_2

description:
ODED26
mRNA


title: MDA231_shCT_NT

description: Gene expression of nontreated MSCs


title: LongDay_ZT16_Rep_A

value: Whole 12-day old seedling

value: Columbia 0


title: Ctrl section 2 region ML

description:
Inhibitor.txt
Ctrl_S2_ML

value: embryo


title: Stage E7.5 embryo 2 section 8 region P

description:
E7.5_2.txt
E7.5_2_8P


title: PYL6_CA_1

description:
ODED25
mRNA


title: Ctrl section 2 region L

description:
Inhibitor.txt
Ctrl_S2_L


title: PYL5_CA_3

description:
ODED24
mRNA


title: Stage E7.5 embryo 2 section 7 region P

description:
E7.5_2.txt
E7.5_2_7P


title: Ctrl section 2 region A

description:
Inhibitor.txt
Ctrl_S2_A


title: PYL6_CA_3

description:
ODED27
mRNA


title: LongDay_ZT12_Rep_B

value: Long day (16 hours light and 8 hours dark) photoperiod at 12 hours after dawn in the light


title: Stage E7.5 embryo 2 section 6 region R2

description:
E7.5_2.txt
E7.5_2_6R2


title: LongDay_ZT12_Rep_C


title: LongDay_ZT12_Rep_A


title: PYL5_CA_2

description:
ODED23
mRNA


title: Stage E7.5 embryo 2 section 6 region R1

description:
E7.5_2.txt
E7.5_2_6R1


title: PYL5_CA_1

description:
ODED22
mRNA


title: Ctrl section 1 region R

description:
Inhibitor.txt
Ctrl_S1_R


title: Ctrl section 1 region P

description:
Inhibitor.txt
Ctrl_S1_P


title: PYL4_CA_3

description:
ODED21
mRNA


title: Stage E7.5 embryo 2 section 6 region P

description:
E7.5_2.txt
E7.5_2_6P


title: Ctrl section 1 region MR

description:
Inhibitor.txt
Ctrl_S1_MR


title: LongDay_ZT08_Rep_C

value: Long day (16 hours light and 8 hours dark) photoperiod at 8 hours after dawn in the light


title: Stage E7.5 embryo 2 section 6 region L2

description:
E7.5_2.txt
E7.5_2_6L2


title: Ctrl section 1 region ML

description:
Inhibitor.txt
Ctrl_S1_ML


title: LongDay_ZT08_Rep_B


title: LongDay_ZT08_Rep_A


title: PYL4_CA_2

description:
ODED20
mRNA


title: PYL4_CA_1

description:
ODED19
mRNA


title: Stage E7.5 embryo 2 section 6 region L1

description:
E7.5_2.txt
E7.5_2_6L1


title: LongDay_ZT04_Rep_C

value: Long day (16 hours light and 8 hours dark) photoperiod at 4 hours after dawn in the light


title: Ctrl section 1 region L

description:
Inhibitor.txt
Ctrl_S1_L


title: LongDay_ZT04_Rep_B


title: Stage E7.5 embryo 2 section 6 region A

description:
E7.5_2.txt
E7.5_2_6A


title: aba2_1_50nM_2

description:
ODED17
mRNA

value: 50nM ABA


title: Stage E7.5 embryo 2 section 5 region P

description:
E7.5_2.txt
E7.5_2_5P


title: LongDay_ZT04_Rep_A


title: aba2_1_50nM_1

description:
ODED16
mRNA


title: Stage E7.5 with L/R sections embryo 3 section 9 region R2

description:
E7.5_LR_3.txt
E7.5_LR_3_9R2


title: LongDay_ZT00_Rep_C

value: Long day (16 hours light and 8 hours dark) photoperiod at 0 hour after dawn in the dark


title: Stage E7.5 embryo 2 section 4 region P

description:
E7.5_2.txt
E7.5_2_4P


title: Stage E7.5 embryo 2 section 3 region R2

description:
E7.5_2.txt
E7.5_2_3R2


title: aba2_1_10nM_3

description:
ODED15
mRNA

value: 10nM ABA


title: LongDay_ZT00_Rep_B


title: Stage E7.5 with L/R sections embryo 3 section 9 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_9P


title: Stage E7.5 embryo 2 section 3 region R1

description:
E7.5_2.txt
E7.5_2_3R1


title: aba2_1_10nM_2

description:
ODED14
mRNA

value: 10 DAG


title: LongDay_ZT00_Rep_A


title: aba2_1_10nM_1

description:
ODED13
mRNA

value: Whole seedling


title: Stage E7.5 with L/R sections embryo 3 section 9 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_9MPR


title: Equinox_ZT20_Rep_C

value: Equinox (12 hours light and 12 hours dark) photoperiod at 20 hours after dawn in the dark


title: aba2_1_50nM_3

description:
ODED18
mRNA


title: Stage E7.5 with L/R sections embryo 3 section 9 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_9MPL


title: Ctrl section 1 region A

description:
Inhibitor.txt
Ctrl_S1_A


title: Equinox_ZT20_Rep_B


title: Stage E7.5 embryo 2 section 3 region L2

description:
E7.5_2.txt
E7.5_2_3L2


title: Stage E7.5 with L/R sections embryo 3 section 9 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_9MAR


title: aba2_1_mock_3

description:
ODED12
mRNA

value: Mock


title: Stage E7.5 embryo 2 section 3 region L1

description:
E7.5_2.txt
E7.5_2_3L1


title: Stage E7.5 with L/R sections embryo 3 section 9 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_9MAL


title: aba2_1_mock_2

description:
ODED11
mRNA


title: Equinox_ZT20_Rep_A


title: Stage E7.5 embryo 2 section 3 region A

description:
E7.5_2.txt
E7.5_2_3A


title: Stage E7.5 with L/R sections embryo 3 section 9 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_9R1


title: Equinox_ZT16_Rep_C

value: Equinox (12 hours light and 12 hours dark) photoperiod at 16 hours after dawn in the dark


title: aba2_1_mock_1

description:
ODED10
mRNA


title: Stage E7.5 embryo 2 section 2 region P

description:
E7.5_2.txt
E7.5_2_2P


title: Equinox_ZT16_Rep_B


title: Stage E7.5 with L/R sections embryo 3 section 9 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_9L2


title: Col_0_50nM_3

description:
ODED9
mRNA


title: Stage E7.5 with L/R sections embryo 3 section 9 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_9L1


title: Col_0_50nM_2

description:
ODED8
mRNA


title: Stage E7.5 embryo 2 section 3 region P

description:
E7.5_2.txt
E7.5_2_3P


title: Stage E7.5 embryo 2 section 1 region P

description:
E7.5_2.txt
E7.5_2_1P


title: Stage E7.5 with L/R sections embryo 3 section 9 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_9EP


title: Equinox_ZT16_Rep_A


title: Stage E7.5 embryo 1 section 9 region R

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9R


title: Stage E7.5 with L/R sections embryo 3 section 9 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_9EA


title: Col_0_50nM_1

description:
ODED7
mRNA


title: Stage E7.5 embryo 1 section 9 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9P


title: Equinox_ZT12_Rep_C

value: Equinox (12 hours light and 12 hours dark) photoperiod at 12 hours after dawn in the light


title: Equinox_ZT12_Rep_B


title: Stage E7.5 with L/R sections embryo 3 section 9 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_9A


title: Stage E7.5 with L/R sections embryo 3 section 8 region R2

description:
E7.5_LR_3.txt
E7.5_LR_3_8R2


title: Stage E7.5 embryo 1 section 9 region L

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9L


title: Equinox_ZT12_Rep_A


title: Stage E7.5 embryo 1 section 9 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9A


title: Col_0_mock_2

description:
ODED2
mRNA


title: Col_0_10nM_3

description:
ODED6
mRNA


title: Stage E7.5 with L/R sections embryo 3 section 8 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_8R1


title: Equinox_ZT08_Rep_C

value: Equinox (12 hours light and 12 hours dark) photoperiod at 8 hours after dawn in the light


title: Stage E7.5 embryo 1 section 8 region R2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8R2


title: Col_0_mock_1

description:
ODED1
mRNA


title: Equinox_ZT08_Rep_B


title: Stage E7.5 embryo 1 section 8 region R1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8R1


title: Equinox_ZT08_Rep_A


title: Stage E7.5 with L/R sections embryo 3 section 8 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_8MPR


title: Stage E7.5 with L/R sections embryo 3 section 8 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_8P


title: Stage E7.5 with L/R sections embryo 3 section 8 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_8MPL


title: Stage E7.5 embryo 1 section 8 region L2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8L2


title: Equinox_ZT04_Rep_C

value: Equinox (12 hours light and 12 hours dark) photoperiod at 4 hours after dawn in the light


title: Equinox_ZT04_Rep_B

value: Whole 12-day old seedling


title: Stage E7.5 embryo 1 section 8 region L1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8L1


title: Equinox_ZT04_Rep_A

value: Columbia 0


title: Col_0_10nM_2

description:
ODED5
mRNA


title: Stage E7.5 embryo 1 section 8 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8A

value: embryo


title: Stage E7.5 with L/R sections embryo 3 section 8 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_8MAL


title: Stage E7.5 with L/R sections embryo 3 section 8 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_8L2


title: Stage E7.5 embryo 1 section 7 region R2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7R2


title: Equinox_ZT00_Rep_B

value: Equinox (12 hours light and 12 hours dark) photoperiod at 0 hour after dawn in the dark


title: Stage E7.5 with L/R sections embryo 3 section 8 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_8L1


title: Stage E7.5 embryo 1 section 7 region R1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7R1


title: Stage E7.5 embryo 1 section 8 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8P


title: Equinox_ZT00_Rep_A


title: Stage E7.5 embryo 1 section 7 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7P


title: Bud, WT, sorted cells (S phase), replicate 4

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

description:
Bud_WT_S_4
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

library_source: genomic

data_processing:
Raw reads were trimmed with fastp.
Trimmed reads were aligned to the zebrafish genome with BWA-MEM.
Duplicate reads were marked with Picard MarkDuplicates.
Properly-paired and non-duplicated reads with MapQ scores of at least 20 were filtered with Bamtools.
Alignments were read into GenomicRanges for downstream analysis in R.
Reads were removed if they were within a set of 100 bp windows with anomalously high read counts (exceeding 1.5 times the interquartile range in at least 4 out of 65 whole genome sequencing runs from this study and previously published work). Genomic windows for calculating RT were defined as regions with a minimum of 400 reads in every sample. An S/G1 quotient was calculated for each window, and quotients were smoothed and Log2 transformed
Assembly: GRCz11
Supplementary files format and content: Counts.csv has read counts in replication timing windows for all samples.
Supplementary files format and content: Quotients.csv has S/G1 Quotients calculated from read counts in replication timing windows for all samples.
Supplementary files format and content: Smoothed.csv  has smoothed quotients.
Supplementary files format and content: Log2Ratios.csv has Log2 transformations of all smoothed S/G1 Quotients
Supplementary files format and content: ZScores.csv has Z Scores of all smoothed S/G1 Quotients
Library strategy: DNA-seq

molecule: genomic DNA

organism: Danio rerio

source_name: whole organism

growth_protocol: Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10-hour light and 14-hour dark cycles.

extract_protocol:
Genomic DNA was prepared from whole embryo pellets or sorted nuclei using the Quick-DNA Miniprep Plus Kit (D4069; Zymo Research). mRNA was prepared from whole embryos using the RNeasy Mini Kit (74104; Qiagen).
For whole-genome sequencing, 50ng - 2μg of gDNA was sheared to approximately 300 bp fragments using a sonicator (Covaris). The gDNA libraries were prepared using the KAPA Hyper Prep Kit (Roche) with SeqCap (Roche) or Illumina TruSeq (Illumina) adapters. Genomic DNA libraries were sequenced in 150bp paired-end read fragments on an Illumina HiSeq 2500 or NovaSeq 6000.

treatment_protocol: Zebrafish were spawned, and cohorts of embryos were collected within 10 minutes of fertilization. Embryos were incubated at 28.5°C. Before collection, clutches were visually inspected to ensure that all embryos were developing synchronously. Unfertilized or morphologically abnormal embryos were removed before collection. Pools of >100 whole embryos at preMBT, dome, or shield stage were treated as S-phase samples, since a high percentage cells at these stages are in S phase. Nuclei from bud or 24 hpf embryos were sorted based on DNA content to isolate G1 and S-phase fractions. Whole embryo pools to be used for gDNA were rapidly frozen and stored at −80°C for later processing. For DNA content FACS-sorting of cells, bud stage or 24 hpf embryos were dechorionated with Pronase, deyolked, and then triturated to a single cell suspension in Phosphate Buffered Saline. Nuclei were prepared from the cells were incubated in DNA staining solution (PBS; 1% Bovine Serum Albumin; 50 ug/ml Propidium iodide P4170-25mg Sigma-Aldrich; 100 ug/ml RNAse A 12091039 Invitrogen) on ice for at least one hour before sorting. The nuclei were then filtered through a 40μm mesh before analysis on a BD LSRII (shield and bud), BD Biosciences FACSAria IIIu (28hpf) or BD Biosciences FACSCalibur.

value: whole organism

tag: time

value: 10 hpf

value: WT

tag: cell cycle_phase

value: S


title: Stage E7.5 with L/R sections embryo 3 section 8 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_8EA


title: TP plus GH-treated TXOX rat replicate 2

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernández-Pérez

state: Las Palmas

address: Blas Cabrera Felipe s/n

department: Clinical Sciences

country: Spain

institute: University of Las Palmas de Gran Canaria (ULPGC-IUIBS)

description: Biological replicate 2 of 4.TPGH-treated TXOX rat

hyb_protocol: Hybridized following the manufacturer’s protocol (ProntoTM Plus System, Promega).

scan_protocol: After 16 h of hybridization, the slides were washed and scanned using the GenePix Microarray Scanner (Axon Instruments, CA).

data_processing: Four independent hybridizations were performed comparing individual animals from the different experimental groups (INTACT, TXOXGH, TXOXTP and TXOXTPGH) with the references TXOX for a total of 4 analyses (4 biological replicates). The LOWESS method was used to normalize the raw intensity data. If the measured probe sets were not present in at least 3 of the 4 chips, they were assumed to contain no information and therefore were eliminated to reduce data complexity. Differentially expressed genes were identified by using the SAM statistical technique. A q value was assigned for each of the detectable genes in the array. This value is similar to a P-value, measuring the lowest false discovery rate (FDR) at which differential expression of a gene is considered significant. A minimal FDR of 0.05 was assigned for each gene. An additional selection requirement was added to FDR based on absolute changes in the gene expression ratios. A value of 1.5 (50%) (log2 ratio ≥ |0.57|) was chosen to describe ratios as up- or down-regulated.

organism: Rattus norvegicus

source_name: TPGH-treated TXOX rat

label_protocol: Five μg of high-quality total RNA from the liver were reversed-transcribed and labeled with Cy5 (test samples) or Cy3 (TXOX referecence samples)

growth_protocol: A microarray containing 27000 rat 70-mer oligo probe sets produced at the KTH Microarray Center (www.biotech.kth.se) was used to evaluate the effects of hypothyroidism and hormonal replacement in TXOX rats on liver gene expression.

extract_protocol: Total RNA was isolated with TriReagent (Sigma, St. Louis, MO) according to the protocol supplied by the manufacturer. RNA yields were measured by UV absorbance and the quality of total RNA was analyzed by using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The goitrogenic drug methimazole (MMI; 0.05%) was added to the drinking water for 5 weeks starting on postnatal day (PND) 59 until sacrifice on PND94. Two weeks after starting MMI administration (TX), rats were orchidectomized (OX) or sham–operated to make TXOX rats or testis-intact controls (TX), respectively. Six rats were not treated with MMI and were subjected to sham-surgery to provide euthyroid testis-intact controls (INTACT). Four days after OX, we began hormonal replacement with TP (50 μg/kg; sc; 5 days per week) (TXOXTP) or vehicle (0.20 ml corn oil) (TXOX) to TXOX rats for 20 days before hormonal replacement with GH for 7 days. GH (0.3 mg/kg/day) (TXOXGH or TXOXTPGH) was administered as two daily sc injections at 12-h intervals (08:00h and 20:00h) to mimic the male-specific GH secretion. Adult hypothyroid control animals received equivalent amounts of the vehicle alone. On PND94,  liver was snap frozen in liquid nitrogen and stored at -80ºC until processed for mRNA analysis.

tag: gender

value: male

value: Sprague Dawley

value: Liver

tag: condition

value: TP plus GH-treated TXOX

source_name: hypothyroid-orquidectomized rats

value: hypothyroid-orquidectomized rats

value: liver


title: TP plus GH-treated TXOX rat replicate 1

description: Biological replicate 1 of 4.TPGH-treated TXOX rat


title: TP plus GH-treated TXOX rat replicate 3

description: Biological replicate 3 of 4.TPGH-treated TXOX rat


title: TP plus GH-treated TXOX rat replicate 4

description: Biological replicate 4 of 4.TPGH-treated TXOX rat


title: Stage E7.5 embryo 1 section 7 region L2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7L2


title: Stage E7.5 with L/R sections embryo 3 section 8 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_8MAR


title: Bud, WT, sorted cells (S phase), replicate 3

description:
Bud_WT_S_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: TP-treated TXOX rat replicate 4

description: Biological replicate 4 of 4.TP-treated TXOX rat

source_name: TP-treated TXOX rat

value: Testosterone Propionate-treated TXOX


title: TP-treated TXOX rat replicate 2

description: Biological replicate 2 of 4.TP-treated TXOX rat


title: TP-treated TXOX rat replicate 1

description: Biological replicate 1 of 4.TP-treated TXOX rat


title: Equinox_ZT00_Rep_C


title: Stage E7.5 embryo 1 section 7 region L1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7L1


title: GH-treated TXOX rat replicate 4

description: Biological replicate 4 of 4.GH-treated TXOX rat

source_name: GH-treated TXOX rat

value: GH-treated TXOX


title: Bud, WT, sorted cells (S phase), replicate 2

description:
Bud_WT_S_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 embryo 1 section 7 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7A


title: Stage E7.5 with L/R sections embryo 3 section 8 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_8EP


title: Stage E7.5 with L/R sections embryo 3 section 7 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_7R1


title: Bud, WT, sorted cells (S phase), replicate 1

description:
Bud_WT_S_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: GH-treated TXOX rat replicate 3

description: Biological replicate 3 of 4.GH-treated TXOX rat


title: Stage E7.5 with L/R sections embryo 3 section 7 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_7P


title: Stage E7.5 embryo 1 section 6 region R2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6R2


title: TP-treated TXOX rat replicate 3

description: Biological replicate 3 of 4.TP-treated TXOX rat


title: GH-treated TXOX rat replicate 2

description: Biological replicate 2 of 4.GH-treated TXOX rat


title: Bud, omf201, sorted cells (S phase), replicate 4

description:
Bud_omf201_S_4
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

value: rif1 omf201/omf201


title: Stage E7.5 with L/R sections embryo 3 section 7 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_7MPR


title: Stage E7.5 embryo 1 section 6 region R1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6R1


title: Stage E7.5 with L/R sections embryo 3 section 7 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_7MPL


title: Bud, omf201, sorted cells (S phase), replicate 3

description:
Bud_omf201_S_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 embryo 1 section 6 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6P


title: GH-treated TXOX rat replicate 1

description: Biological replicate 1 of 4.GH-treated TXOX rat


title: Stage E7.5 embryo 1 section 6 region L2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6L2


title: Stage E7.5 with L/R sections embryo 3 section 8 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_8A


title: Bud, omf201, sorted cells (S phase), replicate 1

description:
Bud_omf201_S_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Bud, omf201, sorted cells (S phase), replicate 2

description:
Bud_omf201_S_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 3 section 7 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_7MAR


title: Vehicle-treated INTACT rat replicate 4

description: Biological replicate 4 of 4.Vehicle-treated INTACT rat

source_name: Euthyroid testis-intact adult rat

value: vehicle treated euthyroid testis-intact


title: Stage E7.5 with L/R sections embryo 3 section 7 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_7MAL


title: Stage E7.5 embryo 1 section 6 region L1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6L1


title: Stage E7.5 with L/R sections embryo 3 section 7 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_7L2


title: 24hpf, WT, sorted cells (S phase), replicate 4

description:
24hpf_WT_S_4
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

value: 24 hpf


title: 24hpf, WT, sorted cells (S phase), replicate 3

description:
24hpf_WT_S_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 3 section 7 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_7L1

value: embryo


title: Stage E7.5 embryo 1 section 6 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6A


title: Stage E7.5 embryo 1 section 5 region R2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5R2


title: Vehicle-treated INTACT rat replicate 3

description: Biological replicate 3 of 4.Vehicle-treated INTACT rat


title: Stage E7.5 with L/R sections embryo 3 section 7 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_7EP


title: Vehicle-treated INTACT rat replicate 2

description: Biological replicate 2 of 4.Vehicle-treated INTACT rat


title: 24hpf, WT, sorted cells (S phase), replicate 2

description:
24hpf_WT_S_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 embryo 1 section 5 region R1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5R1


title: Vehicle-treated INTACT rat replicate 1

description: Biological replicate 1 of 4.Vehicle-treated INTACT rat


title: 544 cells, with shRX3-4, biol rep-3

city: Tokyo

first: Takehiro

last: Yasukawa

address: 2-1-1 Hongo, Bunkyo-ku

country: Japan

institute: Juntendo University

description:
2.txt
4.txt

data_processing:
Adaptor sequences were removed using TrimGalore (ver. 0.6.6).
Low-quality reads (Q < 20) were trimmed and resulting reads shorter than 20 bases were removed using FastqPuri ver. 1.0 for (1). Siimilar quality filtering was performed using fastp (ver. 0.6.6) for (2).
Reads were aligned against GRCh38.105 human genome using HISAT2 (version 2.2.1) by RSEM (ver. 1.3.3).
Differential gene expression analysis was performed using DESeq2 (ver. 1.34.0).
Culture 1 and 2 in each biol rep in (1) were averaged for analysis.
Assembly: GRCh38.105
Supplementary files format and content: Tab-delimited text files (3.txt, 4.txt) contain results of raw counts.
Supplementary files format and content: Tab-delimited text files (1.txt, 2.txt) contain results of DESeq2 analysis with log2 FC | > 1 and padj <0.05.

source_name: 544 cells

extract_protocol:
RNA was prepared using NucleoSpin RNA (TaKaRa).
Libraries for RNA-seq were prepared using an MGIEasy RNA Directional Library Prep Set.

value: 544 cells

tag: cell type

value: mammary fibroblasts


title: 544 cells, with shRX3-5, biol rep-3

description:
2.txt
4.txt


title: 544 cells, with shCtrl, biol rep-3

description:
2.txt
4.txt

value: shCtrl


title: Stage E7.5 with L/R sections embryo 3 section 7 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_7EA


title: Stage E7.5 embryo 1 section 5 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5P


title: 24hpf, WT, sorted cells (S phase), replicate 1

description:
24hpf_WT_S_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

value: whole organism

value: WT


title: 544 cells, with shGFP, biol rep-3

description:
2.txt
4.txt

value: shGFP


title: 24hpf, omf201, sorted cells (S phase), replicate 4

description:
24hpf_omf201_S_4
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

value: S


title: Stage E7.5 with L/R sections embryo 3 section 7 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_7A


title: 24hpf, omf201, sorted cells (S phase), replicate 3

description:
24hpf_omf201_S_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 embryo 1 section 5 region L1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5L1


title: 24hpf, omf201, sorted cells (S phase), replicate 2

description:
24hpf_omf201_S_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: 544 cells, with shRX3-5, biol rep-2

description:
2.txt
4.txt


title: 544 cells, with shRX3-4, biol rep-2

description:
2.txt
4.txt


title: Stage E7.5 with L/R sections embryo 3 section 6 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_6P


title: Stage E7.5 embryo 1 section 5 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5A


title: 24hpf, omf201, sorted cells (S phase), replicate 1

description:
24hpf_omf201_S_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 3 section 6 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_6MPR


title: 544 cells, with shCtrl, biol rep-2

description:
2.txt
4.txt


title: Bud, WT, sorted cells (G1 phase), replicate 4

description:
Bud_WT_G1_4
Counts.csv

value: 10 hpf


title: 544 cells, with shGFP, biol rep-2

description:
2.txt
4.txt


title: Stage E7.5 embryo 1 section 4 region R2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4R2


title: Bud, WT, sorted cells (G1 phase), replicate 3

description:
Bud_WT_G1_3
Counts.csv


title: 544 cells, with shRX3-5, biol rep-1

description:
2.txt
4.txt


title: Stage E7.5 with L/R sections embryo 3 section 6 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_6MAR


title: Stage E7.5 embryo 1 section 5 region L2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5L2


title: Stage E7.5 embryo 1 section 4 region R1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4R1


title: 544 cells, with shRX3-4, biol rep-1

description:
2.txt
4.txt


title: Stage E7.5 with L/R sections embryo 3 section 6 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_6MAL


title: Stage E7.5 embryo 1 section 4 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4P


title: Stage E7.5 embryo 1 section 4 region L2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4L2


title: Stage E7.5 with L/R sections embryo 3 section 6 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_6L2


title: Stage E7.5 with L/R sections embryo 3 section 6 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_6R1


title: 544 cells, with shCtrl, biol rep-1

description:
2.txt
4.txt


title: Bud, WT, sorted cells (G1 phase), replicate 1

description:
Bud_WT_G1_1
Counts.csv


title: Bud, omf201, sorted cells (G1 phase), replicate 4

description:
Bud_omf201_G1_4
Counts.csv


title: Stage E7.5 with L/R sections embryo 3 section 6 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_6L1


title: Stage E7.5 embryo 1 section 4 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4A


title: 544 cells, untreated, biol rep3- culture 2

description:
1.txt
3.txt

value: untreated


title: Bud, omf201, sorted cells (G1 phase), replicate 3

description:
Bud_omf201_G1_3
Counts.csv


title: Stage E7.5 embryo 1 section 3 region R2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3R2


title: Stage E7.5 with L/R sections embryo 3 section 6 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_6EP


title: Stage E7.5 with L/R sections embryo 3 section 6 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_6MPL


title: 544 cells, untreated, biol rep3- culture 1

description:
1.txt
3.txt


title: Bud, omf201, sorted cells (G1 phase), replicate 2

description:
Bud_omf201_G1_2
Counts.csv


title: Stage E7.5 with L/R sections embryo 3 section 6 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_6EA


title: 544 cells, untreated, biol rep2- culture 2

description:
1.txt
3.txt


title: Stage E7.5 embryo 1 section 3 region R1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3R1


title: Bud, WT, sorted cells (G1 phase), replicate 2

description:
Bud_WT_G1_2
Counts.csv


title: Stage E7.5 with L/R sections embryo 3 section 6 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_6A


title: Bud, omf201, sorted cells (G1 phase), replicate 1

description:
Bud_omf201_G1_1
Counts.csv


title: 544 cells, with shGFP, biol rep-1

description:
2.txt
4.txt


title: 544 cells, untreated, biol rep2- culture 1

description:
1.txt
3.txt


title: Stage E7.5 embryo 1 section 3 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3P


title: 24hpf, WT, sorted cells (G1 phase), replicate 4

description:
24hpf_WT_G1_4
Counts.csv


title: Stage E7.5 with L/R sections embryo 3 section 5 region R2

description:
E7.5_LR_3.txt
E7.5_LR_3_5R2


title: Stage E7.5 with L/R sections embryo 3 section 5 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_5R1


title: 24hpf, WT, sorted cells (G1 phase), replicate 3

description:
24hpf_WT_G1_3
Counts.csv


title: 544 cells, untreated, biol rep1- culture 1

description:
1.txt
3.txt


title: Stage E7.5 embryo 1 section 3 region L1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3L1


title: 522 cells, untreated, biol rep3- culture 2

description:
1.txt
3.txt

source_name: 522 cells

value: 522 cells


title: Stage E7.5 embryo 1 section 3 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3A


title: Stage E7.5 with L/R sections embryo 3 section 5 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_5MPR


title: Stage E7.5 embryo 1 section 4 region L1

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4L1


title: Stage E7.5 with L/R sections embryo 3 section 5 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_5P


title: 24hpf, omf201, sorted cells (G1 phase), replicate 4

description:
24hpf_omf201_G1_4
Counts.csv


title: 24hpf, WT, sorted cells (G1 phase), replicate 2

description:
24hpf_WT_G1_2
Counts.csv


title: Stage E7.5 with L/R sections embryo 3 section 5 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_5MPL


title: 522 cells, untreated, biol rep2- culture 2

description:
1.txt
3.txt


title: Stage E7.5 with L/R sections embryo 3 section 5 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_5MAR


title: Stage E7.5 embryo 1 section 2 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2P


title: 24hpf, omf201, sorted cells (G1 phase), replicate 3

description:
24hpf_omf201_G1_3
Counts.csv


title: 522 cells, untreated, biol rep2- culture 1

description:
1.txt
3.txt


title: Stage E7.5 embryo 1 section 3 region L2

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3L2


title: 24hpf, omf201, sorted cells (G1 phase), replicate 2

description:
24hpf_omf201_G1_2
Counts.csv


title: Stage E7.5 with L/R sections embryo 3 section 5 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_5MAL


title: 544 cells, untreated, biol rep1- culture 2

description:
1.txt
3.txt


title: 522 cells, untreated, biol rep1- culture 2

description:
1.txt
3.txt


title: Stage E7.5 with L/R sections embryo 3 section 5 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_5L2


title: Stage E7.5 embryo 1 section 2 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2A


title: Stage E7.5 embryo 1 section 1 region P

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_1P


title: 24hpf, WT, sorted cells (G1 phase), replicate 1

description:
24hpf_WT_G1_1
Counts.csv


title: 522 cells, untreated, biol rep1- culture 1

description:
1.txt
3.txt


title: Stage E7.5 with L/R sections embryo 3 section 5 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_5L1


title: 24hpf, omf201, sorted cells (G1 phase), replicate 1

description:
24hpf_omf201_G1_1
Counts.csv


title: preMBT, WT, whole embryo, replicate 3

description:
preMBT_WT_WE_3
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

value: Asynchronous


title: Stage E7.5 embryo 1 section 1 region A

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_1A


title: Stage E7.5 embryo 1 section 2 region R

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2R


title: Stage E7.5 embryo 1 section 9 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9MP


title: Stage E7.5 with L/R sections embryo 3 section 5 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_5EP


title: MT3

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mm9) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count.

source_name: trigeminal ganglion (TG) neurons

growth_protocol: 3.5 x 10^5 oral squamous cell carcinoma cells; HSC3 cells were injected in tongue of male and female Balb/c athymic nude mice. Normal control group received no cells. Tissues were harvest at day 15 post cell inoculation

extract_protocol:
Total RNA was isolated from harvested tumors using the Qiagen RNeasy micro kit (Qiagen; Valencia, CA) according to the manufacturer’s recommendation. After quantification with Nanodrop (Thermo Scientific; Rockford, IL), RNA was stored at -80ºC.
RNA-seq libraries were prepared according to SMART-seq2 protocol, with the following modifications: PCR preamplification to 10-12 cycles, two rounds beads cleanup with 1:1 ratio after cDNA synthesis, and 0.6-0.8 dual beads cleanup for Nextera XT DNA-seq library purification.

treatment_protocol: At day 13 post cell inoculation, animals were injected with 0.5% WGA-488 (retrolabeled dye) in the tongue. At day 15, trigeminal ganglia were harvested and subjected to single-cell preparation. Each sample was prepared by pooling 4 TGs from 2 animals for normal groups and 4 animals for tumor-bearing groups as only ipsilateral TGs were collected from this group. A total of 3 samples per group was prepared. TG tissues were dissected and collected in cold 1X HBSS buffer, washed three times with 1X HBSS and incubated with 5ul of 50ng/ml dispase (type 2, Sigma) and 75ul of 2.5mg/ml liberase (Roche) for 60 mins at 37°C for enzymatic digestion. Following this, tissues were centrifuged at 2min at 1000rpm and washed with 5mls of DMEM containing 5% FBS and resuspended in 1.5ml DMEM with 5% FBS and triturated with a Pasteur pipette to breakdown the tissues and prepare a homogenous solution. The solution was then strained with a 100um strainer to remove all debris, supernatant collected in an eppendorf tube and subjected to flow sorting. Flow sorting was performed using FACSAria III (BD Biosciences; San Jose, CA) using 130 μm nozzle. Consecutive gates were used to isolate WGA-AF488 labeled TG neurons. First, debris was excluded by forward scatter area (FSC-A) and side scatter area (SSC-A) gating. Second, duplets and clumps were excluded by side scatter width (SSC-W) and side scatter area gate (SSC-A) gate. Third, WGA-AF488+ bright cells were gated compared to unstained TG control and sorted directly to RLT buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma) to be able to use for RNA extraction.

value: athymic nude mice

value: male

value: trigeminal ganglion (TG) neurons

value: mouse tongue tumor induced by human oral squamous cell carcinoma cell lines HSC3


title: 522 cells, untreated, biol rep3- culture 1

description:
1.txt
3.txt


title: preMBT, WT, whole embryo, replicate 2

description:
preMBT_WT_WE_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 embryo 1 section 2 region L

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2L


title: MT2


title: MT1


title: Stage E7.5 embryo 1 section 9 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9MA


title: Stage E7.5 with L/R sections embryo 3 section 5 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_5A


title: HSJD-DIPG-007-DMSO-3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5 was used to align the reads to the hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 96
Assembly: hg38 gene version 96
Supplementary files format and content: Tab-delimited gene counts

source_name: DIPG tumor

growth_protocol: gliomashere culture

extract_protocol: Cells were pelleted by centrifugation, subsequently resuspended in TRIzol reagent (Ambion) and stored at -80°C

value: DIPG tumor

value: gliomashpere

value: DMSO


title: Stage E7.5 with L/R sections embryo 3 section 5 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_5EA

value: embryo


title: HSJD-DIPG-007-AKBA-2

value: AKBA 10 microM


title: Stage E7.5 with L/R sections embryo 3 section 4 region R2

description:
E7.5_LR_3.txt
E7.5_LR_3_4R2


title: MN3

value: normal trigeminal ganglia (TG) tissues


title: Stage E7.5 with L/R sections embryo 3 section 4 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_4R1


title: MN2


title: HSJD-DIPG-007-DMSO-2


title: Stage E7.5 with L/R sections embryo 3 section 4 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_4P


title: Stage E7.5 embryo 1 section 8 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8MP


title: Stage E7.5 embryo 1 section 8 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8MA


title: Stage E7.5 embryo 1 section 9 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9EA


title: HSJD-DIPG-007-DMSO-1


title: Stage E7.5 embryo 1 section 8 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8EP


title: FT3

value: female


title: HSJD-DIPG-007-AKBA-1


title: FT2


title: Stage E7.5 embryo 1 section 8 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_8EA


title: HSJD-DIPG-007-AKBA-3


title: Stage E7.5 with L/R sections embryo 3 section 4 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_4MPL


title: iPSC Line 3 GENtoniK Replicate 3

city: New York

first: Emiliano

last: Hergenreder

state: NY

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality.
Transcripts were quantified directly from trimmed FASTQ files using Salmon referenced to GENCODE Release 36 transcripts
TPM values from Salmon were used for differential expression analysis using DESeq2
Assembly: GRCh38.p13
Supplementary files format and content: DESeq2 results (csv files)

source_name: iPSC-cortical neurons

growth_protocol: hPSC-derived cortical neurons were plated at a density of 150,000/cm2 on poly-L-ornithine and laminin-coated 6-well plates, and maintained in Neurobasal medium supplemented with B27 and GlutaMAX.

extract_protocol:
Directly lysed in Trizol reagent. RNA was isolated using Zymo RNA miniprep kit.
RNA was sent to GENEWIZ for sequencing. Standard Illumina protocols were used for library preparation.

treatment_protocol: Treatment was initiated 7 days after plating and maintained for 7 days. Cells were collected 7 days after treatment withdrawal and washout.

value: 1 uM GSK2869552, 1 uM EPZ5676, 1 uM NMDA, 1 uM Bay K 8644


title: Stage E7.5 embryo 1 section 9 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_9EP


title: FT1


title: iPSC Line 3 GENtoniK Replicate 2


title: Stage E7.5 with L/R sections embryo 3 section 4 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_4MAR


title: Stage E7.5 embryo 1 section 7 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7MP


title: FN3


title: MN1


title: Stage E7.5 embryo 1 section 7 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7MA


title: Stage E7.5 with L/R sections embryo 3 section 4 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_4MAL


title: iPSC Line 3 DMSO Replicate 3


title: FN2


title: Stage E7.5 with L/R sections embryo 3 section 4 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_4MPR


title: Stage E7.5 with L/R sections embryo 3 section 4 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_4L2


title: Stage E7.5 embryo 1 section 7 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7EP


title: iPSC Line 3 DMSO Replicate 2


title: Stage E7.5 embryo 1 section 7 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_7EA


title: FN1


title: HN_swthr4

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

institute: Georg-Speyer-Haus

data_processing:
50 million unique mapped reads were obtained from each RNA-seq experiment. The reads were aligned using STAR aligner.
Read count was calculated with GenomicFeatures Bioconductor package.
Calculation and normalization of “transcripts per kilobase million (TPM)” accounting for reads per kilobase (RPK) was performed as described elsewhere
Assembly: mm10
Supplementary files format and content: Data represented TPM values to ENSMBLIDs for each time point and replicate

source_name: Heart

growth_protocol: 8 week old adult mice were sacrificed via cervical dislocation to harvest hearts and prepare heart slices

extract_protocol:
TRIreagent according the manufactures protocol
TruSeq RNA Library Prep Kit v2
mRNA with Paired-End sequencing

treatment_protocol: Heart slices were incubated under hypoxic conditions (3% O2) for one week followed by normoxic conditions (21% O2) for one week

value: Heart

value: ex vivo treated

value: mutant


title: Stage E7.5 with L/R sections embryo 3 section 4 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_4L1


title: Stage E7.5 with L/R sections embryo 3 section 4 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_4EP


title: Stage E7.5 embryo 1 section 6 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6MP


title: iPSC Line 2 GENtoniK Replicate 3


title: HN_swthr3


title: iPSC Line 3 DMSO Replicate 1


title: HN_swthr2


title: Stage E7.5 embryo 1 section 6 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6MA


title: Stage E7.5 with L/R sections embryo 3 section 4 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_4A


title: Stage E7.5 with L/R sections embryo 3 section 4 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_4EA


title: HN_swthr1


title: Stage E7.5 embryo 1 section 6 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6EP


title: iPSC Line 2 GENtoniK Replicate 1


title: Stage E7.5 with L/R sections embryo 3 section 3 region R2

description:
E7.5_LR_3.txt
E7.5_LR_3_3R2


title: iPSC Line 3 GENtoniK Replicate 1


title: Stage E7.5 embryo 1 section 6 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_6EA


title: HN_WT4

value: wild type


title: Stage E7.5 embryo 1 section 5 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5MP


title: iPSC Line 2 DMSO Replicate 3


title: iPSC Line 2 DMSO Replicate 2


title: Stage E7.5 with L/R sections embryo 3 section 3 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_3P


title: Stage E7.5 embryo 1 section 5 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5MA


title: HN_WT3


title: Stage E7.5 with L/R sections embryo 3 section 3 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_3MPR


title: HN_WT2


title: HN_WT1


title: iPSC Line 2 GENtoniK Replicate 2


title: iPSC Line 2 DMSO Replicate 1


title: ctrl_swthr4

value: ex vivo untreated


title: Stage E7.5 embryo 1 section 5 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5EA


title: Stage E7.5 embryo 1 section 5 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_5EP


title: Stage E7.5 with L/R sections embryo 3 section 3 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_3MAL


title: Stage E7.5 with L/R sections embryo 3 section 3 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_3MAR


title: ctrl_swthr3


title: Stage E7.5 embryo 1 section 4 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4MP


title: Stage E7.5 embryo 1 section 4 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4MA


title: Stage E7.5 embryo 1 section 4 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4EP


title: ctrl_swthr2


title: Stage E7.5 with L/R sections embryo 3 section 3 region R1

description:
E7.5_LR_3.txt
E7.5_LR_3_3R1


title: Stage E7.5 with L/R sections embryo 3 section 3 region L2

description:
E7.5_LR_3.txt
E7.5_LR_3_3L2


title: ctrl_swthr1


title: Stage E7.5 embryo 1 section 4 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_4EA


title: Stage E7.5 with L/R sections embryo 3 section 3 region L1

description:
E7.5_LR_3.txt
E7.5_LR_3_3L1


title: Stage E7.5 with L/R sections embryo 3 section 3 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_3MPL


title: ctrl_WT4


title: Stage E7.5 with L/R sections embryo 3 section 3 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_3EP


title: ctrl_WT3


title: Stage E7.5 with L/R sections embryo 3 section 3 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_3EA


title: Stage E7.5 embryo 1 section 3 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3MA


title: ctrl_WT2


title: Stage E7.5 embryo 1 section 3 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3EP


title: Stage E7.5 with L/R sections embryo 3 section 3 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_3A


title: Progressing MGUS patient_036

city: Little Rock

first: Fumou

last: Sun

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description:
P036
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

hyb_protocol: Double-stranded complementary DNA (cDNA) and biotinylated complementary RNA (cRNA) were hybridized to GeneChip microarrays (Affymetrix, Santa Clara, CA), which were washed and scanned according to procedures developed by the manufacturer.

scan_protocol: The arrays were scanned using Hewlett Packard confocal laser scanner and visualized using Affymetrix 3.3 software (Affymetrix).

data_processing: The data were processed using Microarray Suite version 5.0 (MAS 5.0) with Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was standardized to a value of 100 as a reference point.

label: Biotin

source_name: Bone marrow Progressing MGUS patient

label_protocol: Double-stranded cDNA is synthesized from 6 ug total RNA. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization. The protocol according to the manufacturer's instructions Expression Analysis Technical Manual, 2001, Affymetrix.

growth_protocol: Plasma cells were enriched by anti-CD138 immunomagnetic bead selection of mononuclear cell fractions from bone marrow aspirates in a central laboratory. All samples analyzed by microarray contained more than 85% plasma cells as determined by 2-color flow cytometry (CD38+ and CD45–/dim) performed after selection.

extract_protocol:
Fresh plasma cells were used directly for RNA extraction.
Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: Bone marrow plasma cells

tag: disease state

value: Progressing MGUS


title: Progressing MGUS patient_037

description:
P037
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_038

description:
P038
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 embryo 1 section 3 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3EA


title: Progressing MGUS patient_034

description:
P034
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: ctrl_WT1


title: Stage E7.5 with L/R sections embryo 3 section 2 region R

description:
E7.5_LR_3.txt
E7.5_LR_3_2R


title: Stage E7.5 with L/R sections embryo 3 section 2 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_2P


title: Stage E7.5 embryo 1 section 2 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2MP


title: Progressing MGUS patient_039

description:
P039
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 embryo 1 section 2 region MA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2MA


title: Progressing MGUS patient_035

description:
P035
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 3 section 2 region MPL

description:
E7.5_LR_3.txt
E7.5_LR_3_2MPL


title: Progressing MGUS patient_033

description:
P033
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 16 weeks male Mice 9

city: gainesville

first: Kesavalu

middle: Lakshmyya

last: Naidu

state: Florida

address: 1600 SW Archer Road

department: Dentistry

institute: University of Florida

hyb_protocol: We used high-throughput nCounter® miRNA Expression Panels (Nanostring Technologies, Seattle, WA, USA) to effectively identify the DE of miRNA in both sexes. Nanos-  Int. J. Mol. Sci. 2022, 23, 5107 14 of 18  tring nCounter® analysis can identify 577 miRNAs in any sample, and by using molecular  barcodes, it can detect even a low number of miRNAs without the need for reverse transcription or amplification.  miRNA expression profiling was performed using the Nanostring nCounter® Mouse  miRNA Assay kit v1.5 (Nanostring Technologies). This assay is a highly sensitive multiplexed method that detects miRNAs using molecular barcodes called nCounter reporter  probes without the need for reverse transcription. Sample preparation involved annealing,  ligation, and purification. These steps were carried out based on the experimental procedure described in the nCounter® miRNA assay panel kit. Briefly, the annealing master  mix was prepared by combining 13 µL of annealing buffer, 26 µL of nCounter miRNA Tag  reagent, and 6.5 of diluted (1:500) miRNA assay controls. Next, 3.5 µL of the annealing master mix was aliquoted into each tube of the strip tube and 100 ng of the total RNA from six  left mandibles from each group (maximum 3-µL volume) with 260/280 and 260/230 ratios  of greater than 2 was added to the respective tubes. The strip tube was placed in the  Thermal Cycler with the following conditions: 94 ◦C for 1 min, 65 ◦C for 1 min, 45 ◦C for  1 min, and 48 ◦C for hold.  After annealing, 2.5 µL of the ligation master mix (19.5 µL of polyethylene glycol (PEG)  and 13 µL of ligation buffer) was added to all the tubes in the strip tube. The strip tube  was incubated at 48 ◦C for 5 min, followed by the addition of 1 µL of ligase into each tube  without removing the strip tubes from the Thermal Cycler. Ligation was performed with  the following conditions: 48 ◦C for 3 min, 47 ◦C for 3 min, 46 ◦C for 3 min, 45 ◦C for 3 min,  65 ◦C for 10 min, and 4 ◦C for hold. To remove the unligated tags, a purification step was  performed after adding 1 µL of ligation cleanup enzyme to all the tubes and incubating the  tubes at 37 ◦C for 1 h, 70 ◦C for 10 min, and 4 ◦C for hold. Forty microliters of RNase-free  water were added to each tube in the strip tube and the sample was ready for hybridization  with the nCounter reporter and capture probes. After denaturation at 85 ◦C for 5 min, a  5-µL aliquot from the miRNA sample preparation tube was taken along with the 10 µL of  miRNA reporter code, 10 µL of hybridization buffer, and 5 µL miRNA capture probe. The  strip tubes were incubated at 65 ◦C for 18 h in the Thermal cycler, and the samples were  immediately processed for post-hybridization with the nCounter analysis system at the  Molecular Pathology Core at the University of Florida.  The nCounter® Mouse miRNA Assay kit v1.5 provided six positive hybridization controls and eight negative control probes to monitor hybridization efficiency. All components  and reagents needed for sample preparation at the reparation station were taken from  the nCounter master kit (Nanostring Technologies). Twelve samples per cartridge were  processed in a single run, which took 3 h. This was followed by digital analysis, which  involved the transfer of the cartridge to the multichannel epifluorescence digital analyzer.  A cartridge definition file with a maximum fields of view (FOV) count of 555 per flow cell  was taken for digital analysis. The number of images taken per scan corresponded to the  number of immobilized reporter probes on the cartridge. A separate Reporter Code Count  (RCC) file for each sample containing the count for each probe was downloaded and used  for data analysis.

data_processing: Initial data analysis was performed using nSolver 4.0. Initially, RCC files were imported into nSolver and imaging quality control (QC), binding density QC, positive control linearity QC, and positive control limit of detection QC were carried out as recommended in the system QC parameters. The lanes were flagged when the percent FOV registration was less than 75% for imaging QC. Binding density was outside the range from 0.1 to 2.25 for binding density QC, and the positive control R2 value was less than 0.95. All 24 samples passed the QC, and no flag lanes were observed. Raw data were generated after passing the QC. To reduce the background signal/noise, the background threshold count value was set to 52 and calculated by taking an average of eight negative control probe counts from all 24 samples. Codeset content normalization parameters were chosen, and the normalization was performed based on the top 100 miRNA genes expressed. The normalized factor was calculated based on the geometric mean values of the miRNA genes expressed in each sample. Fold changes in the genes were calculated based on the ratio of the difference in the means of the log-transformed normalized data to the square root of the sum of the variances of the samples in the two groups. The limma R library was used to calculate fold changes. Clustering of miRNA for the final heatmap of DE miRNA was done using the Partitioning Around Medoids method with the fpc R library.

source_name: Streptococcus gordonii

growth_protocol: S. gordonii DL1 was grown in Brucella Blood Agar with Hemin, and Vitamin K, Hardy Diagnostics - A30, 15×100 mm, Brucella Blood Agar with Hemin, and Vitamin K for three days in anaerobic growth chamber.

extract_protocol: Total RNA isolated from the mandible tissue using mirVana miRNA isolation kit (Ambion, Austin, TX, USA). mandibles from each mouse were entirely homogenized using the handheld rotor-stator homogenizer with sterile individual TissueRuptor disposable probes (Qiagen; Germantown, MD, USA) for each sample. After homogenization, each sample was lysed in a denaturing lysis solution that stabilized RNAs and inactivated RNases. The samples were subjected to an acid-phenol:chloroform extraction that removed all the cellular components such as protein, DNA, and other cellular products. The aqueous phase was removed, transferred to the fresh nuclease-free microcentrifuge tube, and 1.25 volume of 100% ethanol was added. This mixture was transferred to the filter cartridge placed into the collection tube and centrifuged for 15 s at 10,000× g. The filter cartridge was washed with 700 µL of wash solution-1 followed by washing with wash solution-2/3. After washing, the total RNA was eluted from the filter cartridge with 100 µL of nuclease-free water. RNA yield and purity were determined using a Take3 micro-volume plate in Epoch Microplate Spectrophotometer (BioTek), and quantification was performed in technical duplicates for each sample.

treatment_protocol: 100 million bacterial cells suspended in reduced transport fluid is mixed with equal volume of 6% carboxymethylcellulose (CMC) and administed orally. 0.1 ml cell suspension/mice.

tag: Sex

value: male

value: Left Mandibles

value: Streptococcus gordonii infected 16 weeks


title: Streptococcus gordonii infection 16 weeks male Mice 10

description: miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).


title: Stage E7.5 embryo 1 section 3 region MP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_3MP


title: Stage E7.5 with L/R sections embryo 3 section 2 region MPR

description:
E7.5_LR_3.txt
E7.5_LR_3_2MPR


title: Progressing MGUS patient_032

description:
P032
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 16 weeks male Mice 8


title: Stage E7.5 embryo 1 section 2 region EP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2EP


title: Stage E7.5 with L/R sections embryo 3 section 2 region MAR

description:
E7.5_LR_3.txt
E7.5_LR_3_2MAR


title: Stage E7.5 embryo 1 section 2 region EA

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_2EA


title: Streptococcus gordonii infection 16 weeks male Mice 7


title: Progressing MGUS patient_030

description:
P030
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 embryo 1 section 1 region EAP

description:
E7.5_1_FPKM_Filter_Log2.txt
E7.5_1_1EAP


title: Stage E7.5 with L/R sections embryo 3 section 2 region MAL

description:
E7.5_LR_3.txt
E7.5_LR_3_2MAL


title: Streptococcus gordonii infection 16 weeks male Mice 6


title: Progressing MGUS patient_031

description:
P031
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_029

description:
P029
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 16 weeks male Mice 5


title: Stage E7.5 with L/R sections embryo 3 section 2 region L

description:
E7.5_LR_3.txt
E7.5_LR_3_2L


title: Streptococcus gordonii infection 16 weeks male Mice 4


title: Stage E7.5 with L/R sections embryo 3 section 2 region EA

description:
E7.5_LR_3.txt
E7.5_LR_3_2EA


title: Streptococcus gordonii infection 16 weeks male Mice 3


title: Stage E7.5 with L/R sections embryo 3 section 2 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_2A


title: Stage E7.0 embryo 1 section 9 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9R


title: Stage E7.0 embryo 1 section 9 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9L


title: Stage E7.0 embryo 1 section 9 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9A


title: Streptococcus gordonii infection 16 weeks male Mice 2


title: Stage E7.5 with L/R sections embryo 3 section 1 region P

description:
E7.5_LR_3.txt
E7.5_LR_3_1P


title: Progressing MGUS patient_027

description:
P027
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 16 weeks male Mice 1


title: Stage E7.5 with L/R sections embryo 3 section 2 region EP

description:
E7.5_LR_3.txt
E7.5_LR_3_2EP


title: Stage E7.0 embryo 1 section 8 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8R


title: Progressing MGUS patient_023

description:
P023
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_028

description:
P028
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_026

description:
P026
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_024

description:
P024
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 8 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8P


title: Stage E7.0 embryo 1 section 9 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_9P


title: Streptococcus gordonii infection 8 weeks male Mice 10

value: Streptococcus gordonii infected 8 weeks


title: Stage E7.5 with L/R sections embryo 3 section 1 region A

description:
E7.5_LR_3.txt
E7.5_LR_3_1A


title: Progressing MGUS patient_021

description:
P021
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_025

description:
P025
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 8 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8L


title: Progressing MGUS patient_022

description:
P022
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 8 weeks male Mice 9


title: Stage E7.0 embryo 1 section 8 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_8A


title: Stage E7.5 with L/R sections embryo 2 section 9 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_9R2


title: Stage E7.0 embryo 1 section 7 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7R


title: Stage E7.5 with L/R sections embryo 3 section 1 region EAP

description:
E7.5_LR_3.txt
E7.5_LR_3_1EAP


title: Progressing MGUS patient_020

description:
P020
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 8 weeks male Mice 8


title: Progressing MGUS patient_019

description:
P019
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 8 weeks male Mice 7


title: Progressing MGUS patient_018

description:
P018
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 7 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7P


title: Stage E7.5 with L/R sections embryo 2 section 9 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_9P


title: Streptococcus gordonii infection 8 weeks male Mice 6


title: Stage E7.0 embryo 1 section 7 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7L


title: Progressing MGUS patient_017

description:
P017
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Streptococcus gordonii infection 8 weeks male Mice 5

description: miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).


title: Stage E7.5 with L/R sections embryo 2 section 9 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_9MAR


title: Stage E7.0 embryo 1 section 7 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_7A


title: Stage E7.5 with L/R sections embryo 2 section 9 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_9R1


title: Stage E7.0 embryo 1 section 6 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6R


title: Streptococcus gordonii infection 8 weeks male Mice 4


title: Stage E7.5 with L/R sections embryo 2 section 9 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_9MAL


title: Streptococcus gordonii infection 8 weeks male Mice 3


title: Streptococcus gordonii infection 8 weeks male Mice 2


title: Progressing MGUS patient_014

description:
P014
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 6 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6P


title: Progressing MGUS patient_015

description:
P015
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 6 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6L


title: Streptococcus gordonii infection 8 weeks male Mice 1


title: Stage E7.5 with L/R sections embryo 2 section 9 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_9MPL


title: Stage E7.0 embryo 1 section 6 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_6A


title: Stage E7.5 with L/R sections embryo 2 section 9 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_9L2


title: Progressing MGUS patient_016

description:
P016
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_011

description:
P011
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 9 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_9L1


title: Progressing MGUS patient_012

description:
P012
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 16 weeks female Mice 10

source_name: Sterile reduced transport Fluid and 6% CMC (1:1 ratio).

value: SHAM 16 WEEKS


title: Stage E7.0 embryo 1 section 5 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5R

source_name: Mouse embryonic cells

value: embryo


title: Stage E7.5 with L/R sections embryo 2 section 9 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_9EA


title: Stage E7.0 embryo 1 section 5 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5P


title: Stage E7.0 embryo 1 section 5 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5L


title: Stage E7.5 with L/R sections embryo 2 section 9 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_9A


title: Progressing MGUS patient_013

description:
P013
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_010

description:
P010
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 16 weeks female Mice 7


title: Stage E7.5 with L/R sections embryo 2 section 8 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_8R2


title: Stage E7.0 embryo 1 section 5 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_5A


title: SHAM 16 weeks female Mice 8


title: Progressing MGUS patient_009

description:
P009
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 16 weeks male Mice 5


title: SHAM 16 weeks female Mice 6


title: Stage E7.0 embryo 1 section 4 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4R


title: Stage E7.5 with L/R sections embryo 2 section 9 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_9EP


title: Stage E7.5 with L/R sections embryo 2 section 9 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_9MPR


title: Progressing MGUS patient_007

description:
P007
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 8 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_8R1


title: SHAM 16 weeks female Mice 9


title: SHAM 16 weeks male Mice 4


title: Progressing MGUS patient_008

description:
P008
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 8 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_8P


title: Stage E7.0 embryo 1 section 4 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4P


title: Stage E7.5 with L/R sections embryo 2 section 8 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_8MPR


title: Progressing MGUS patient_006

description:
P006
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_005

description:
P005
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 16 weeks male Mice 3


title: Stage E7.0 embryo 1 section 4 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4L


title: Stage E7.0 embryo 1 section 4 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_4A


title: Stage E7.5 with L/R sections embryo 2 section 8 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_8MAL


title: Stage E7.0 embryo 1 section 3 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_3R


title: Stage E7.5 with L/R sections embryo 2 section 8 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_8MPL


title: Progressing MGUS patient_004

description:
P004
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 8 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_8MAR


title: SHAM 16 weeks male Mice 2


title: SHAM 16 weeks male Mice 1


title: Stage E7.0 embryo 1 section 3 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_3P


title: SHAM 8 weeks female Mice 10

value: SHAM 8 WEEKS


title: Stage E7.5 with L/R sections embryo 2 section 8 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_8L2


title: Stage E7.5 with L/R sections embryo 2 section 8 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_8L1


title: Progressing MGUS patient_003

description:
P003
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 3 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_3L


title: Stage E7.0 embryo 1 section 2 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2R


title: Progressing MGUS patient_002

description:
P002
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Progressing MGUS patient_001

description:
P001
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 8 weeks female Mice 8

description: miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).


title: SHAM 8 weeks female Mice 7


title: Stable MGUS patient_319

description:
S319
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).

source_name: Bone marrow Stable MGUS patient

value: Stable MGUS


title: Stage E7.0 embryo 1 section 2 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2P


title: Stage E7.0 embryo 1 section 2 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2L


title: Stage E7.5 with L/R sections embryo 2 section 8 region EP

description:
E7.5_LR_2.txt
E7.5_LR_2_8EP


title: Stage E7.5 with L/R sections embryo 2 section 8 region EA

description:
E7.5_LR_2.txt
E7.5_LR_2_8EA


title: SHAM 8 weeks female Mice 6

value: female


title: Stable MGUS patient_318

description:
S318
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 8 region A

description:
E7.5_LR_2.txt
E7.5_LR_2_8A


title: Stable MGUS patient_316

description:
S316
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 8 weeks male Mice 5


title: Stable MGUS patient_315

description:
S315
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 8 weeks female Mice 9


title: Stage E7.0 embryo 1 section 1 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_1P


title: Stage E7.0 embryo 1 section 2 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_2A


title: Stage E7.5 with L/R sections embryo 2 section 7 region R1

description:
E7.5_LR_2.txt
E7.5_LR_2_7R1


title: Stage E7.0 embryo 1 section 1 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_1A


title: SHAM 8 weeks male Mice 4


title: Stable MGUS patient_314

description:
S314
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: SHAM 8 weeks male Mice 3


title: SHAM 8 weeks male Mice 2


title: Stable MGUS patient_317

description:
S317
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 11 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11R


title: Stable MGUS patient_313

description:
S313
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.5 with L/R sections embryo 2 section 7 region P

description:
E7.5_LR_2.txt
E7.5_LR_2_7P


title: Stage E7.5 with L/R sections embryo 2 section 7 region MPR

description:
E7.5_LR_2.txt
E7.5_LR_2_7MPR


title: Stage E7.0 embryo 1 section 11 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11P


title: SHAM 8 weeks male Mice 1


title: Stage E7.5 with L/R sections embryo 2 section 7 region MPL

description:
E7.5_LR_2.txt
E7.5_LR_2_7MPL


title: Stage E7.0 embryo 1 section 11 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11L


title: Stage E7.5 with L/R sections embryo 2 section 7 region R2

description:
E7.5_LR_2.txt
E7.5_LR_2_7R2


title: Shield, WT, whole embryo, replicate 5

description:
Shield_WT_WE_5
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv

source_name: whole organism

value: whole organism

value: 6 hpf

value: WT

value: Asynchronous


title: Stage E7.5 with L/R sections embryo 2 section 7 region MAR

description:
E7.5_LR_2.txt
E7.5_LR_2_7MAR


title: Stage E7.0 embryo 1 section 11 region A

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_11A


title: Stable MGUS patient_311

description:
S311
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Shield, WT, whole embryo, replicate 4

description:
Shield_WT_WE_4
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.5 with L/R sections embryo 2 section 7 region MAL

description:
E7.5_LR_2.txt
E7.5_LR_2_7MAL


title: Stable MGUS patient_310

description:
S310
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 10 region R

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10R


title: Stage E7.5 with L/R sections embryo 2 section 7 region L2

description:
E7.5_LR_2.txt
E7.5_LR_2_7L2


title: Shield, WT, whole embryo, replicate 2

description:
Shield_WT_WE_2
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stage E7.0 embryo 1 section 10 region P

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10P


title: Stable MGUS patient_308

description:
S308
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Shield, WT, whole embryo, replicate 6

description:
Shield_WT_WE_6
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stable MGUS patient_309

description:
S309
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stage E7.0 embryo 1 section 10 region L

description:
E7.0_1_FPKM_Filter_Log2.txt
E7.0_1_10L


title: Stage E7.5 with L/R sections embryo 2 section 7 region L1

description:
E7.5_LR_2.txt
E7.5_LR_2_7L1


title: Stable MGUS patient_312

description:
S312
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Shield, WT, whole embryo, replicate 1

description:
Shield_WT_WE_1
Counts.csv
Smoothed.csv
ZScores.csv
Log2Ratios.csv
Quotients.csv


title: Stable MGUS patient_307

description:
S307
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).


title: Stable MGUS patient_306

description:
S306
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).