title: 252162310325_b3 - 16_0Gy_24h_3 vs 19_20Gy_24h_3

hyb_protocol: 19_20Gy_24h_3 Cy5 / 16_0Gy_24h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample4

status: Public on Dec 01 2019

type: RNA

city: Singapore

first: Sarah

last: Daud

address: 1E Kent Ridge Road,NUHS Tower Blk,Lvl 12,

country: Singapore

institute: National University of Singapore

description: Cynomolgus macaque splenic CD27loCD11b+ NK subset

hyb_protocol: The hybridization cocktails containing 1µg of Cy3-labeled cDNA targets were heated at 95ºC for 3 minutes before hybridization. Equal volume of aliquots from each sample were hybridized onto Agilent SurePrint G3 custom-unrestricted GE microarray (8x60K format) at 65ºC for 17 hours at 20 rpm in a rotating hybridization oven. The slide was washed according to the gene expression was buffer pack protocol (Agilent Technologies) in the presence of 0.005% Triton X-102.

scan_protocol: The scanning of microarray slide was performed using Agilent DNA Microarray Scanner (Agilent Technologies) according to manufacturer’s instruction for AgilentG3_GX_1Color protocol. Assignment of grid template was performed based on AMADID 075606.

data_processing: Raw signal data extraction, spot intensities, grid measurements and removal of outlier pixels were performed using Feature Extraction Software v10.7.1.1 (Agilent Technologies). The Feature Extraction output file containing intensity and annotation information for each hybridized samples were transferred into Partek® Genomics Suite® software, version 7.0 (Partek Inc.) for data normalization.

molecule: total RNA

organism: Macaca fascicularis

source_name: Singapore

label_protocol: Purified total RNA of 50ng as input (4-5 biological replicates for each NK subset) was amplified using the Ovation® Pico WTA System V2 kit (NuGEN Technologies Inc.) that includes first-strand cDNA synthesis, second-strand cDNA synthesis and SPIA isothermal linear amplification. The purification of the final SPIA cDNA product was performed using MinElute® Reaction Cleanup Kit (Qiagen). For each sample, 400ng of amplified product was Cy3-labeled using the SureTag DNA Labeling kit (Agilent Technologies) with restriction digestion step based on Agilent’s recommended protocol for 8-pack microarrays. Dye incorporation, specific activity and cDNA yield were analyzed using MicroArray Measurement DNA-50 menu, NanoDrop ND-1000.

growth_protocol: Unstimulated NK cell subpopulations

extract_protocol: Total RNA was extracted from flow-sorted cells using TRIzol reagent (Invitrogen) method combined with RNeasy MinElute kit (Qiagen) purification steps.

treatment_protocol: Cryopreserved samples were thawed in a 37°C water bath, re-suspended in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum to wash away the freezing media. Macaque cells were stained for NK surface markers NKG2A/CD159a, CD8a, CD27, CD11b, NKp80 and lymphocyte lineage markers CD45, CD3, CD14, CD20, HLA-DR. After the addition of DAPI stain to distinguish dead cells, NK subsets were subjected to fluorescence-activated cell sorting using a four laser MoFlo® Astrios™ cell sorter(Beckman Coulter) and cells were flow sorted directly into TriZol solution. All NK subsets were derived from CD45+CD3-CD14-CD20-HLA-DR- live gate.

tag: tissue

value: Spleen

tag: gender

value: Male

tag: age

value: 5 years old


title: 252162310325_b2 - 12_20Gy_24h_2 vs 9_0Gy_24h_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Why radiation exposure on seeds at low doses causes stimulation of plant growth after germination?

hyb_protocol: 9_0Gy_24h_2 Cy5 / 12_20Gy_24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Hordeum vulgare

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: embryo - Media: ddWater Temperature: 20°C Light: dark

extract_protocol: 9_0Gy_24h_2:10mg. (Qiagenv1_RNeasy.pdf)

treatment_protocol: no treatment

tag: tissue = seeds

tag: barley (barley, nur variety)  - harvest date

treatment_protocol: Name:20 Gy (Gamma-irradiation) - gamma-irradiation - gamma-irradiation,gamma-irradiation:quantity 20 time 20min . Dry seeds of barley were placed in thin plastic bags and irradiated by gamma-rays source (cobalt-60) using dose rate 60 Gy/h.


title: NKG2A-CD8a-HLADR+CD20+ B cell_sample2

description: Cynomolgus macaque splenic CD20+ B cell

value: Female

value: 18 years old


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample4

description: Cynomolgus macaque splenic CD27+CD11b+ NK subset


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample5


title: GSTS_077: JRy12384_v5-ChIP-seq_arrested_dox_maintained_90m

type: SRA

city: Berkeley

first: Gavin

middle: Schwebs

last: Schlissel

state: CA

address: 440 Barker Hall

department: Molecular Cell Biology

country: USA

institute: UC Berkeley

description:
fig panel: 3c,e
GSTS_077

library_source: genomic

data_processing:
Raw reads were mapped to SacCer3 reference genome, modified to include the gal10::TetO sequence. Sequences were aligned using Bowtie2 with parameters -p 16 -N 1 -L 17, and raw reads were trimmed to 38bp for all experiments.
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, each base in the genome was counted for how often it appeared in the sequencing library (NOT how often the base was sequenced, but rather how often each base fell between the ends of a concordantly-aligned paired ned read).
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, read midpoints were extracted and stored as a bedGraph, corresponding to a histogram of read midpoints
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All proccessed data is a BedGraph

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 120m

extract_protocol:
Cells were mechanically disrupted, and chromatin was solubilized with Mnase. Chromatin was precipitated using either streptavidin-coupled magnetic beads or a V5 antibody agarose matrix.
NEBNext Ultra II library kit was used with dual index primers to prepare DNA for sequencing

tag: strain

tag: growth conditions

value: arrested with alpha factor, treated with doxycycline

tag: genotype

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) mcm2-3A dpb3<delta>::HIS3 gal10::TetO

tag: preciptation conditions

value: V5 (millipore #A7345)


title: FIB.D06

city: Yokoham

first: Joachim

middle: Felix

last: Luginbühl

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

organism: Homo sapiens

source_name: Fibroblasts

growth_protocol: Human dermal fibroblasts were purchased from Lonza (passages 4-8) and cultured in DMEM containing 10% FBS/L-glutamine/10% Penicilin&Streptomycin at 37°C 5% CO2 until virus infection. For TFi generation, a total of 6 MOI (~0.3 MOI per virus) were pooled into culture medium containing 8 mg*ml-1 Polybrene (SIGMA) to increase infection efficiency. The virus pool was infected and incubated overnight at 37°C 5% CO2. On the following day, virus-containing medium was removed and cells were incubated for an additional day in fresh culture medium at 37°C 5% CO2. For iN generation, infected cells were split onto Poly-d-lysine (100μg*ml-1) / Laminin (50μg*ml-1) (SIGMA)-coated culture plates and incubated overnight in culture medium at 37°C 5% CO2. On the following day, medium was changed to neuronal induction medium containing DMEM/F12 and Neurobasal-A (Thermo Fisher Scientific) mixed at a 1:1 ratio, 2% (vol/vol) B27 supplement and 0.5% N2 Supplement (GIBCO), 1x nonessential amino acids (Thermo Fisher Scientific), 1% GlutaMAX supplement, 10ng*ml-1 BDNF (GIBCO), 10ng*ml-1 NT3 (R&D Systems), 10ng*ml-1 GDNF (Thermo Fisher Scientific), VPA (0.5mM, WAKO), L-Ascorbic acid (200nM, SIGMA), Y-27632 (10μM, WAKO), dcAMP (0.5mM, SIGMA), 10% FBS and 10% Penicilin&Streptomycin (WAKO). The concentrations of small molecules used were as follows: CHIR99021 (2μM, Abcam), SB-431542 (10μM, SIGMA), LDN-193189 (0.5μM, Stemgent), Noggin (100ng*ml-1, SIGMA). Neuronal induction medium was changed every third day, during which the concentration of FBS was gradually reduced from 10% to 1%. After 2 weeks, neuronal induction medium was replaced with neuronal maturation medium without small molecules and 1% FBS and the medium was changed every third day until further analysis.

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

tag: cell type

value: Fibroblasts

tag: time

value: before induction

tag: passages

tag: treatment

value: No treatment

tag: batch


title: FIB.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_074: JRy12384_v5-ChIP-seq_arrested_dox

description:
fig panel: 3c,e
GSTS_074

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline

value: streptavidin (invitrogen #65001)


title: GSTS_075: JRy12384_input_arrested_dox

description:
fig panel: 3c,e
GSTS_075

source_name: input sample used for precipitation


title: GSTS_076: JRy12384_strepSeq_arrested_dox_maintained_90m

description:
fig panel: 3c,e
GSTS_076

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 120m


title: 252162310325_b1 - 9_0Gy_24h_2 vs 12_20Gy_24h_2

hyb_protocol: 12_20Gy_24h_2 Cy5 / 9_0Gy_24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GSTS_073: JRy12384_strepSeq_arrested_dox

description:
fig panel: 3c,e
GSTS_073

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline


title: NKG2A-CD8a-HLADR+CD20+ B cell_sample1

description: Cynomolgus macaque splenic CD20+ B cell


title: FIB.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_072: JRy12384_input_cycling

description:
fig panel: 3c,e
GSTS_072

value: cycling in YPD


title: 252162310324_b4 - 5_20Gy_24h_1 vs 2_0Gy_24h_1

hyb_protocol: 2_0Gy_24h_1 Cy5 / 5_20Gy_24h_1 Cy3 : 20pmol. (Hybridation_CAGE_proto.doc)

extract_protocol: 2_0Gy_24h_1:10mg. (Qiagenv1_RNeasy.pdf)


title: NKG2A+CD8a+CD27loCD11blo NK subset_sample4

description: Cynomolgus macaque splenic CD27loCD11blo NK subset


title: 252162310324_b3 - 2_0Gy_24h_1 vs 5_20Gy_24h_1

hyb_protocol: 5_20Gy_24h_1 Cy5 / 2_0Gy_24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: FIB.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 252162310324_b2 - 18_20Gy_2h_3 vs 15_0Gy_2h_3

hyb_protocol: 15_0Gy_2h_3 Cy5 / 18_20Gy_2h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 15_0Gy_2h_3:10mg. (Qiagenv1_RNeasy.pdf)


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample3

source_name: Vietnam

value: 11 years old


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample3

value: 12 years old


title: NKG2A+CD8a+CD27+CD11blo NK subset_sample4

description: Cynomolgus macaque splenic CD27+CD11blo NK subset


title: NKG2A+CD8a+CD27loCD11blo NK subset_sample3

value: 9 years old


title: FIB.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NKG2A+CD8a+CD27+CD11blo NK subset_sample3

value: 10 years old


title: 252162310324_b1 - 15_0Gy_2h_3 vs 18_20Gy_2h_3

hyb_protocol: 18_20Gy_2h_3 Cy5 / 15_0Gy_2h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 252162310323_b4 - 11_20Gy_2h_2 vs 8_0Gy_2h_2

hyb_protocol: 8_0Gy_2h_2 Cy5 / 11_20Gy_2h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8_0Gy_2h_2:10mg. (Qiagenv1_RNeasy.pdf)


title: GSTS_071: JRy12384_v5-ChIP-seq_cycling

description:
fig panel: 3c,e
GSTS_071

source_name: v5-precipitated chromatin from exponentially growing cells


title: FIB.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_069: JRy12383_input_arrested_dox_released_90m

description:
fig panel: 3b,e
GSTS_069

value: arrested with alpha factor, treated with doxycycline, synchronously released from arrest

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) dpb3<delta>::HIS3 gal10::TetO


title: 252162310323_b2 - 4_20Gy_2h_1 vs 1_0Gy_2h_1

hyb_protocol: 1_0Gy_2h_1 Cy5 / 4_20Gy_2h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1_0Gy_2h_1:10mg. (Qiagenv1_RNeasy.pdf)

extract_protocol: 4_20Gy_2h_1:10mg. (Qiagenv1_RNeasy.pdf)


title: GSTS_070: JRy12384_strepSeq_cycling

description:
fig panel: 3c,e
GSTS_070

source_name: streptavidin precipitated chromatin from exponentially growing cells


title: 20_P_4

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Reads were aligned with STAR aligner with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the featureCounts function
Genome_build: Canis_familiaris/Ensembl/CanFam3.1/Annotation/Version-2015-05-20
Supplementary_files_format_and_content: text files holding match counts per gene

organism: Canis lupus familiaris

source_name: Corpus luteum

extract_protocol:
Following surgical ovariectomy, corpora lutea were trimmed from surrounding tissue. Rinsed with phosphate-buffered saline (PBS) solution and immersed in RNA®later for 24h at 4oC. After 24h, tissue material was divided and stored in -80oC until further usage. RNA was isolated using Trizol reagent, following the manufacturer’s recommendations.
Illumina TruSeq RNA Sample Prep Kit v2 was used with 100-1000ng/per sample of total RNA for the construction of sequencing libraries.
RNA-seq polyA-selection

treatment_protocol: Starting at the day of ovulation (day 0), dogs were treated orally with 10mg/kg daily with firocoxib. Treatment was maintained for 5, 10, 20 and 30 days after ovulation. Control groups received for similar periods a placebo.

value: Corpus luteum

tag: day after ovulation

value: Day 20

value: firocoxib-treated


title: GSTS_066: JRy12383_input_arrested_dox_maintained_90m

description:
fig panel: 3b,e
GSTS_066

value: arrested with alpha factor, treated with doxycycline


title: GSTS_068: JRy12383_v5-ChIP-seq_arrested_dox_released_90m

description:
fig panel: 3b,e
GSTS_068

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, released for 1cc


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample2

value: Spleen

value: Male

value: unknown


title: DER006B

city: Oxford

first: Ling-Pei

last: Ho

address: Headley Way

department: MRC Human Immunology Unit

country: United Kingdom

institute: University of Oxford

data_processing:
QC analysis with the fastQC package
Reads were aligned using STAR against the  hg38 human genome assembly
After removing multi mapped reads with low-complexity reads, SAM files were generated from BAM files with SAMtools
Gene specific read counts were obtained by using the featureCounts function from the Subread package with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include featureCounts annotated read counts for each Sample

source_name: skin biopsy

extract_protocol:
Skin samples were collected directly into RNA Later reagent (Ambion) and frozen at -80°C until further use. Tissue disruption and homogenisation was carried out in RTL buffer (Qiagen) using TissueRuptor (Qiagen) on ice. RNA was extracted with RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions.
Next Generation Sequencing was carried out with Illumina reagents (TruSeq Targeted RNA Index Kit and TruSeq Targeted RNA Custom Panel Kit) at the Deep Seq Facility (The University of Nottingham).
Targeted RNAseq

treatment_protocol: Baseline full thickness punch biopsies were performed on the flank of healthy donors to create skin wounds. This was followed by larger biopsies, to encompass the original wounds, taken between one to four days later.

value: skin

tag: day post wounding


title: NKG2A+CD8a+CD27+CD11blo NK subset_sample2


title: DER009R


title: FIB.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction

value: No treatment


title: FIB.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 252162310323_b3 - 8_0Gy_2h_2 vs 11_20Gy_2h_2

hyb_protocol: 11_20Gy_2h_2 Cy5 / 8_0Gy_2h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GSTS_065: JRy12383_v5-ChIP-seq_arrested_dox_maintained_90m

description:
fig panel: 3b,e
GSTS_065

value: V5 (millipore #A7345)


title: FIB.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_067: JRy12383_strepSeq_arrested_dox_released_90m

description:
fig panel: 3b,e
GSTS_067

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, released for 1 cc


title: GSTS_064: JRy12383_strepSeq_arrested_dox_maintained_90m

description:
fig panel: 3b,e
GSTS_064

value: streptavidin (invitrogen #65001)


title: FIB.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample2


title: DER006L


title: DER010R


title: NKG2A+CD8a+CD27+CD11blo NK subset_sample1

source_name: Cambodia

value: 4 years old


title: DER006R


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample1


title: DER010B


title: 252162310323_b1 - 1_0Gy_2h_1 vs 4_20Gy_2h_1

hyb_protocol: 4_20Gy_2h_1 Cy5 / 1_0Gy_2h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GSTS_063: JRy12383_input_arrested_dox

description:
fig panel: 3b,e
GSTS_063


title: NKG2A+CD8a+CD27loCD11blo NK subset_sample2


title: GSTS_061: JRy12383_strepSeq_arrested_dox

description:
fig panel: 3b,e
GSTS_061


title: DER003L


title: FIB.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_062: JRy12383_v5-ChIP-seq_arrested_dox

description:
fig panel: 3b,e
GSTS_062


title: DER003B


title: FIB.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: DER010L


title: GSTS_058: JRy12383_strepSeq_cycling

description:
fig panel: 3b,e
GSTS_058

value: cycling in YPD


title: GSTS_060: JRy12383_input_cycling

description:
fig panel: 3b,e
GSTS_060


title: NKG2A+CD8a+CD27loCD11blo NK subset_sample1


title: FIB.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_059: JRy12383_v5-ChIP-seq_cycling

description:
fig panel: 3b,e
GSTS_059


title: DER011B


title: F7-350

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

country: Spain

institute: Institut de Ciencies del Mar

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to the array in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Dicentrarchus labrax

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: European sea bass were grown at the experimental aquarium facilities of the Institute of Marine Sciences (Barcelona) and general procedures of egg incubation, larval and juvenile rearing were according to Moretti et al. (1999).

extract_protocol: The mRNAs of a total of 42 gonad samples were individually extracted by RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's instructions. Quantity was determined by using a Nanodrop spectrophotometer (Nanodrop Technologies, USA) and quality (RNA integrity number, RIN) by using a Bioanalyzer (Agilent Technologies, USA). mRNA samples with a mean RIN of ≥8.4 were further processed for microarray analysis.

treatment_protocol: The set of samples consisted of six male (M) and six female (F) gonadal tissues at 110 dpf, six testes and six ovaries at 250 dpf and ten testes and ten ovaries at 350 dpf. Gonads were fully isolated in fish at 250 and 350 dpf

tag: Sex

value: female

tag: developmental stage

value: 350 dpf

value: gonad


title: DER011R

tag: tissue


title: GSTS_057: JRy12382_input_arrested_dox_released_90m

description:
fig panel: 3a,e
GSTS_057

value: arrested with alpha factor, treated with doxycycline, synchronously released from arrest

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) mcm2-3A gal10::TetO


title: F10-350


title: FIB.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: F8-350


title: M8-350

value: male


title: NKG2A+CD8a+CD27+CD11b+ NK subset_sample1

value: Spleen

tag: gender

tag: age


title: FIB.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.B10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: DER011L


title: F6-350


title: GSTS_056: JRy12382_v5-ChIP-seq_arrested_dox_released_90m

description:
fig panel: 3a,e
GSTS_056


title: M9-350


title: GSTS_054: JRy12382_input_arrested_dox_maintained_90m

description:
fig panel: 3a,e
GSTS_054

value: arrested with alpha factor, treated with doxycycline


title: F5-350


title: GSTS_055: JRy12382_strepSeq_arrested_dox_released_90m

description:
fig panel: 3a,e
GSTS_055


title: DER003R


title: FIB.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: M7-350


title: FIB.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: DER007B


title: DER007L


title: GSTS_052: JRy12382_strepSeq_arrested_dox_maintained_90m

description:
fig panel: 3a,e
GSTS_052

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 90m


title: FIB.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: DER005B


title: GSTS_053: JRy12382_v5-ChIP-seq_arrested_dox_maintained_90m

description:
fig panel: 3a,e
GSTS_053

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 90m


title: DER007R


title: GSTS_050: JRy12382_v5-ChIP-seq_arrested_dox

description:
fig panel: 3a,e
GSTS_050


title: FIB.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: F3-350


title: FIB.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_051: JRy12382_input_arrested_dox

description:
fig panel: 3a,e
GSTS_051


title: DER002B


title: M6-350


title: DER005R


title: F4-350


title: F2-350


title: M5-350


title: FIB.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_048: JRy12382_input_cycling

description:
fig panel: 3a,e
GSTS_048


title: F1-350


title: GSTS_047: JRy12382_v5-ChIP-seq_cycling

description:
fig panel: 3a,e
GSTS_047


title: FIB.D11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: DER002L


title: FIB.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: M4-350


title: DER002R


title: GSTS_049: JRy12382_strepSeq_arrested_dox

description:
fig panel: 3a,e
GSTS_049


title: FIB.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: M2-350


title: sh_0.5h

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

country: China

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

description: Brd4 knock down cells treatment for 0.5 hours

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), the reference genome using hg19, then put all the samples results together and normalized by EDAseq(1.99.1), genes expression fold change were calculated using normalized raw reads.
Genome_build: hg19
Supplementary_files_format_and_content: Each files contain Rsem output, including raw reads, TPM and RPKM, one extra file contains all the samples expression value after normalized.

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (Invitrogen). The cells were maintained in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Total RNA extraction was extracted with Trizol reagent.
RNA libraries performed by WuXi AppTec and Ribobio.

treatment_protocol: HeLaS3 cells stable expressing Ctrl shRNA and Brd4 shRNA were treated with 60 J/cm2 ultraviolet (UV) light. The cells were collected at 0.5, 1 and 2 hr after UV treatment, and Trizol was added for total RNA extraction. Then the sample was treated with DNase I (Ambion) to remove any potential contaminating DNA.

tag: cell line

value: HeLa

tag: expression

value: Brd4 shRNA

tag: uv treatment


title: GSTS_044: JRy12379_v5-ChIP-seq_arrested_dox_gal_90

description:
fig panel: 4b
GSTS_044

source_name: v5-precipitated precipitatd chromatin from cells arrested in YP + raf, treated with doscycline , with galactose added for 90m

tag: strain

tag: growth conditions

value: arrested with alpha factor in YP + raffinose, treated with doxycycline , galactose added for 90m

tag: genotype

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) gal10::TetO


title: sh_0h

description: Brd4 knock down cells treatment for 0 hours


title: M3-350


title: DER005L

value: skin


title: GSTS_043: JRy12379_strepSeq_arrested_dox_gal_90

description:
fig panel: 4b
GSTS_043

source_name: streptavidin precipitatd chromatin from cells arrested in YP + raf, treated with doxycycline, with galactose added for 90m

tag: preciptation conditions

value: V5 (millipore #A7345)


title: FIB.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Fibroblasts

tag: cell type

value: Fibroblasts

tag: time

value: before induction

tag: passages

value: No treatment


title: GSTS_046: JRy12382_strepSeq_cycling

description:
fig panel: 3a,e
GSTS_046

value: cycling in YPD

value: streptavidin (invitrogen #65001)


title: sh_2h

description: Brd4 knock down cells treatment for 2 hours


title: GSTS_041: JRy12379_v5-ChIP-seq_arrested_dox_dex_90

description:
fig panel: 4b
GSTS_041

source_name: v5-precipitated precipitatd chromatin from cells arrested in YP + raf, treated with doscycline , with dextrose added for 90m

value: arrested with alpha factor in YP + raffinose, treated with doxycycline , dextrose added for 90m


title: FIB.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: treatment

tag: batch


title: GSTS_045: JRy12379_input_arrested_dox_gal_90

description:
fig panel: 4b
GSTS_045

source_name: input sample used for precipitation


title: FIB.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_040: JRy12379_strepSeq_arrested_dox_dex_90

description:
fig panel: 4b
GSTS_040

source_name: streptavidin precipitatd chromatin from cells arrested in YP + raf, treated with doxycycline, with dextrose added for 90m


title: FIB.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: nc_2h

description: wide type cells UV treatment for 2 hours

value: Ctrl shRNA


title: GSTS_042: JRy12379_input_arrested_dox_dex_90

description:
fig panel: 4b
GSTS_042


title: FIB.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: nc_0.5h

description: wide type cells UV treatment for 0.5 hours


title: G11-250

tag: Sex

value: undifferentiated

value: 250 dpf

value: gonad


title: G12-250

tag: developmental stage


title: nc_0h

description: wide type cells UV treatment for 0 hours


title: G13-250

tag: tissue


title: M1-350

value: male

value: 350 dpf


title: TRKA-TGF-3

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

description: Biological replicate 3 of 4.

hyb_protocol: The corresponding Cy3 labeled cDNAs was hybridized overnight (17 hours, 65°C) to an Agilent SurePrint G3 Rat GE 8x60K Microarray using Agilent's recommended hybridization chamber and oven.

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5). Background was substracted and data were normalized by quantile.

organism: Rattus norvegicus

source_name: TGF stimulated cells

label_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure. The amplification is based on a global PCR protocol using mRNA-derived cDNA. 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec's undisclosed protocol. All samples are labeled with Cy3.

growth_protocol: CD90, P75 and TRKA cells were cultivated with the same protocol (A. Ramon-Cueto and M. Nieto-Sampedro, 1992). TGF-a induced TRKA (TRKA-TGF) were conditionned as described by Gueye et al. (2011).

extract_protocol: Cells samples were lysed using SuperAmp Lysis Buffer and strored appropriately according to the instructions of the SuperAmp Preparation Kit (Miltenyi Biotec). mRNA was isolated via magnetic bead technology.

treatment_protocol: CD90, p75, TRKA and TRKA-TGF cells were sorted using a FACSAria flow cytometer (BD Biosciences). Purification of each sorting experiments were assessed (93-97% purity).

value: Male fischer Rat


title: FIB.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: TRKA-TGF-4

description: Biological replicate 4 of 4.


title: FIB.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: G10-250


title: FIB.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_039: JRy12379_input_arrested_dox_gal_30

description:
fig panel: 4b
GSTS_039

value: arrested with alpha factor in YP + raffinose, treated with doxycycline , galactose added for 30m


title: GSTS_037: JRy12379_strepSeq_arrested_dox_gal_30

description:
fig panel: 4b
GSTS_037

source_name: streptavidin precipitatd chromatin from cells arrested in YP + raf, treated with doxycycline, with galactose added for 30m

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) gal10::TetO


title: FIB.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: G9-250


title: GSTS_038: JRy12379_v5-ChIP-seq_arrested_dox_gal_30

description:
fig panel: 4b
GSTS_038

source_name: v5-precipitated precipitatd chromatin from cells arrested in YP + raf, treated with doscycline , with galactose added for 30m


title: FIB.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: G6-250


title: FIB.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GSTS_036: JRy12379_input_arrested_dox_dex_30

description:
fig panel: 4b
GSTS_036

value: arrested with alpha factor in YP + raffinose, treated with doxycycline , dextrose added for 30m


title: GSTS_035: JRy12379_v5-ChIP-seq_arrested_dox_dex_30

description:
fig panel: 4b
GSTS_035

source_name: v5-precipitated precipitatd chromatin from cells arrested in YP + raf, treated with doscycline , with dextrose added for 30m

value: V5 (millipore #A7345)


title: G7-250


title: TRKA-TGF-1

description: Biological replicate 1 of 4.


title: GSTS_034: JRy12379_strepSeq_arrested_dox_dex_30

description:
fig panel: 4b
GSTS_034

source_name: streptavidin precipitatd chromatin from cells arrested in YP + raf, treated with doxycycline, with dextrose added for 30m


title: G8-250


title: TRKA-4

description: Biological replicate 4 of 4.

source_name: TRKA cells


title: FIB.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts


title: GSTS_033: JRy12379_input_arrested_dox_raf

description:
fig panel: 4b
GSTS_033

value: arrested with alpha factor in YP + raffinose, treated with doxycycline


title: Tissue from ADPKD kidney 4

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description: Sample name: ADPKD D

data_processing:
DNA from 7 RRBS libraries were sequenced in Illumina HiSeq Machines, Base-calling performed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment was done using Bismark program.
UNIX scripts and our in house developed tool DMAP (Chatterjee et al 2012, Nucleic Acids Research) was used for post processing of the data
DNA methylation analysis was performed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt files describing methylation status of significant MspI fragments (that were filtered based on high coverage)

source_name: Kidney tissue

extract_protocol:
Genomic DNA was extracted from fresh-frozen sections of kidney tissue using the QIAmp DNA Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Libraries prepared from Kidney E1, G2, H3, ADPKD 07 and 08 were prepared from 2.5µg of DNA. Due to improvements in the methodology, the subsequent preparation of libraries from ADPKD 05 and D only required an input of 500ng of DNA, and did not require size selection before bisulfite conversion. Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA), followed by end repair and the addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhand were then ligated to the generated fragments. Following adaptor ligation, fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG Agarose gel (Lonza, Basel, Switzerland), and were subsequently bisulfite modified using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) (ADPKD D was converted with the MethylCode Bisulfite Conversion kit (Invitrogen, Carlsbad, CA)) before selecting fragments between 40 and 220bp from NuSieve gel. This library was amplified by PCR, and the resulting library was sequenced on an Illumina platform with a single-ended 100bp run.

value: kidney

tag: diagnosis

value: Autosomal Dominant Polycystic Kidney Disease (ADPKD)


title: GSTS_032: JRy12379_v5-ChIP-seq_arrested_dox_raf

description:
fig panel: 4b
GSTS_032

source_name: v5-precipitated precipitatd chromatin from cells arrested in YP + raf, treated with doscycline

value: streptavidin (invitrogen #65001)


title: Tissue from ADPKD kidney 3

description: Sample name: ADPKD 08


title: Tissue from nonADPKD kidney 3

description: Sample name: Kidney H3

value: healthy


title: Tissue from ADPKD kidney 2

description: Sample name: ADPKD 07


title: GSTS_031: JRy12379_strepSeq_arrested_dox_raf

description:
fig panel: 4b
GSTS_031

source_name: streptavidin precipitatd chromatin from cells arrested in YP + raf, treated with doxycycline


title: GSTS_030: JRy12379_input_cycling_raf

description:
fig panel: 4b
GSTS_030

value: cycling in YP + raffinose


title: Tissue from ADPKD kidney 1

description: Sample name: ADPKD 05


title: GSTS_027: JRy12379_input_arrested_dox_released+180

description:
fig panel: 2b,3e
GSTS_027

value: arrested with alpha factor, treated with doxycycline, synchronously released from arrest


title: G5-250

value: undifferentiated

value: 250 dpf


title: Tissue from nonADPKD kidney 1

description: Sample name: Kidney E1


title: GSTS_029: JRy12379_v5-ChIP-seq_cycling_raf

description:
fig panel: 4b
GSTS_029

source_name: v5-precipitated precipitatd chromatin from cells cycling in YP + raf


title: GSTS_026: JRy12379_v5-ChIP-seq_arrested_dox_released+180

description:
fig panel: 2b,3e
GSTS_026

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, released for 2cc


title: Tissue from nonADPKD kidney 2

description: Sample name: Kidney G2


title: GSTS_028: JRy12379_strepSeq_cycling_raf

description:
fig panel: 4b
GSTS_028

source_name: streptavidin precipitatd chromatin from cells cycling in YP + raf


title: G4-250

value: gonad


title: TRKA-TGF-2

description: Biological replicate 2 of 4.


title: G3-250


title: G2-250


title: TRKA-2

description: Biological replicate 2 of 4.


title: G10-110

value: 110 dpf


title: TRKA-3

description: Biological replicate 3 of 4.

value: Male fischer Rat


title: G9-110


title: CD90-3

description: Biological replicate 3 of 4.

source_name: CD90 cells


title: p75-3

description: Biological replicate 3 of 4.

source_name: p75 cells


title: TRKA-1

description: Biological replicate 1 of 4.


title: G8-110


title: mock_3

first: Huichuan

last: Yu

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

data_processing:
Paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b).
Differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq2 R package (1.10.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt file generated showing raw counts and differential expression gene lists

source_name: mock, human colon cell line

extract_protocol:
The total RNA was extracted using RNeasy mini kit (Qiagen)
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: colon cell line KM12

tag: genotype/variation

value: control


title: G11-110


title: GSTS_025: JRy12379_strepSeq_arrested_dox_released+180

description:
fig panel: 2b,3e
GSTS_025

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, released for 2 cc

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) gal10::TetO


title: mock_2

tag: cell line


title: mock_1


title: p75-4

description: Biological replicate 4 of 4.


title: GSTS_024: JRy12379_input_arrested_dox_maintained+180

description:
fig panel: 2b,3e
GSTS_024

source_name: input sample used for precipitation

value: arrested with alpha factor, treated with doxycycline


title: CD90-4

description: Biological replicate 4 of 4.


title: p75-1

description: Biological replicate 1 of 4.


title: G12-110


title: G6-110


title: CDO1_3

source_name: CDO1, human colon cell line


title: p75-2

description: Biological replicate 2 of 4.


title: G13-110


title: DBSCC3

city: Berlin

first: Oliver

last: Nagel

address: Hindenburgdamm 30

department: Department of Gastroenterology, Rheumatology and Infectious Diseases

country: Germany

institute: Charité - Universitätsmedizin Berlin

data_processing:
Basecalling was performed using CASAVA version 1.8.
STAR aligner version 2.7.1a in two pass mode was used to map and sort the reads against the human genome GRCh38 release 97.
featureCounts function of Bioconductor package Rsubread was used to count reads on gene level
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file containing raw read counts of features (genes) of all samples

source_name: colonic epithelium

growth_protocol: Fresh HT-29/B6-GR/MR cells were cultured in RPMI medium (Sigma Aldrich, St. Louis, MO, USA) for one week at 37°C in humidified atmosphere (95% air / 5% CO2). RPMI media were supplemented with 10% fetal calf serum (FCS; Gibco Carlsbad, CA, USA), 1% penicillin/streptomycin (Gibco, Carlsbad, CA, USA), 500 IU/mL G418 (Merck Millipore, Billerica, MA, USA) and 200 μg/mL hygromycin B (Biochrom GmbH, Berlin, Germany). After one week, the trypsinized cells were seeded on Millicell PCF filters of 3 μm pore size (Merck Millipore, Billerica, MA, USA) and cultured for 7-10 days. Experiments were performed when the cell monolayers reached a transepithelial electrical resistance (TER) of 1500-2100 Ω * cmˆ2.

extract_protocol:
Total RNA was obtained from HT-29/B6-GR/MR cells using mirVanaTM miRNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA).
RNA sequencing was performed by the TrueSeq Stranded Total RNA method.

treatment_protocol: The cells were incubated with 10% hormone-free FCS (h-f FCS; Sigma-Aldrich, St. Louis, MO, USA) for 24 hours and stimulated with DBA (a combination of dexamethasone (D, 50 nM; Sigma-Aldrich, St. Louis, MO, USA), sodium butyrate (B,2 mM; Merck-Schuchardt, Hohenbrunn, Germany) and aldosterone (A, 3 nM; Sigma-Aldrich, St. Louis, MO, USA)) for four days. Three days following DBA stimulation, the cell monolayers were washed and incubated with heat-inactivated 10% h-f FCS without any antibiotic supplements for 24 hours.

value: colonic epithelium

value: colonic epithelium from cell culture


title: DBSCC2


title: GSTS_023: JRy12379_v5-ChIP-seq_arrested_dox_maintained+180

description:
fig panel: 2b,3e
GSTS_023

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 180m

value: V5 (millipore #A7345)


title: CDO1_2


title: G5-110


title: DBSCC1


title: G4-110


title: G3-110


title: CD90-1

description: Biological replicate 1 of 4.


title: CD90-2

description: Biological replicate 2 of 4.


title: GSTS_021: JRy12379_input_arrested_dox_released+90

description:
fig panel: 2b,3e
GSTS_021


title: CDO1_1


title: S Habrochaitis, FnyCMV

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v3.2
Supplementary_files_format_and_content: csv, raw abundances

organism: Solanum habrochaites

source_name: shoot apex

growth_protocol: the plants were grown in Conviron Chambers set at 28 and 22°C ( day and ngiht, respectively) with 16 hours of light

extract_protocol:
total RNA was extracted using Tri-reagent and 1.5 ug of total RNA was used for small RNA library construction using Illumina sRNA construction kit version 1.5
Illumina compatible method using standard Illumina adapters

treatment_protocol: the seedlings at 2-3 leaf stage were inoculated with viral RNA. The apical part of the plants were harvested at 9-10dpi.

tag: infection status

value: infected with Cucumber mosaic virus

value: shoot apex


title: DBS3


title: DBS2


title: SKOV3-Spheroid-3

city: Columbus

first: Qi-En

last: Wang

state: OH

address: 420 W.12th Avenue

department: Radiation Oncology

institute: The Ohio State University

hyb_protocol: Perofmed according to the manufacturer's instrutions (nanoString Technologies)

source_name: ovarian cancer cell line SKOV3

growth_protocol: For adherent growing, cells were cultured in regular dishes with RPMI1640 medium supplemented with 10% FBS. For spheroid growing, cells were cultured in ultra-low attachment dishes with serum-free DMEM-F12 medium supplemented with 10% KnockOut Serum Replacement, 20 ng/mL EGF, and 10 ng/mL bFGF.

extract_protocol: RNA was isolated using Trizol

value: ovarian cancer cell line


title: S Habrochaitis, FnyCMV-D

value: infected with Cucumber mosaic virus and D satellite RNA


title: GSTS_020: JRy12379_v5-ChIP-seq_arrested_dox_released+90

description:
fig panel: 2b,3e
GSTS_020

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, released for 1cc

extract_protocol:
Cells were mechanically disrupted, and chromatin was solubilized with Mnase. Chromatin was precipitated using either streptavidin-coupled magnetic beads or a V5 antibody agarose matrix.
NEBNext Ultra II library kit was used with dual index primers to prepare DNA for sequencing

value: arrested with alpha factor, treated with doxycycline, synchronously released from arrest

value: streptavidin (invitrogen #65001)


title: GSTS_019: JRy12379_strepSeq_arrested_dox_released+90

description:
fig panel: 2b,3e
GSTS_019

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, released for 1 cc


title: DBS1


title: S Habrochaitis, healthy

value: not infected (healthy)


title: GSTS_018: JRy12379_input_arrested_dox_maintained+90

description:
fig panel: 2b,3e
GSTS_018


title: GSTS_022: JRy12379_strepSeq_arrested_dox_maintained+180

description:
fig panel: 2b,3e
GSTS_022

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, rmaintained arrest for 180m


title: G2-110

value: undifferentiated

value: gonad


title: SKOV3-Spheroid-1

scan_protocol: Perofmed according to the manufacturer's instrutions (nanoString Technologies)


title: SKOV3-Adherent-3

data_processing: Perofmed according to the manufacturer's instrutions (nanoString Technologies)


title: Brg11* rep4 [I18R030d04_01]

city: Tuebingen

first: Dousheng

last: Wu

address: Auf der Morgenstelle 32

department: General Genetics

institute: Tuebingen University

data_processing:
Quality of raw RNA-seq data in FASTQ files was assessed using ReadQC (ngs-bits version 2018_06)
Reads were preprocessed with skewer (version 0.2.2)
Reads were aligned using STAR (version 2.5.4a)
Alignment quality was analyzed using MappingQC (ngs-bits version 2018_06) and visually inspected with Broad Integrative Genome Viewer (version 2.4.11)
Based on the genome annotation ITAG (version 3.20), read counts for all genes were obtained using subread (version 1.6.0)
Genome_build: Reference tomato genome (version SL3.0, International Tomato Genome Sequencing Project)
Supplementary_files_format_and_content: excel file with raw read counting and count per million (cpm)

organism: Solanum lycopersicum

source_name: Tomato leaf_Brg11*

growth_protocol: Tomato were grown at 25 degree in growth chambers for 5 weeks

extract_protocol:
Leaf discs were harvested and frozen in liquid nitrogen. Total RNA were extracted with a RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bacteria suspension were infiltrated into the tomato leaf with a blunt-end syringae

tag: ecotype

value: Moneymaker

tag: age

tag: infection

value: X. euvesicatoria Brg11*

value: Leaf


title: GSTS_009: JRy12379_strepSeq_cycling_dox

description:
fig panel: 1b,c
GSTS_009

source_name: streptavidin precipitated chromatin from exponentially growing cells

tag: strain

tag: growth conditions

value: cycling in YPD + doxycycline

tag: genotype

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) gal10::TetO


title: GSTS_008: JRy12379_strepSeq_cycling

description:
fig panel: 1b,c
GSTS_008

value: cycling in YPD

tag: preciptation conditions


title: SKOV3-Adherent-2

label_protocol: Perofmed according to the manufacturer's instrutions (nanoString Technologies)

tag: cell type


title: GSTS_017: JRy12379_v5-ChIP-seq_arrested_dox_maintained+90

description:
fig panel: 2b,3e
GSTS_017

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 90m

value: arrested with alpha factor, treated with doxycycline


title: GSTS_016: JRy12379_strepSeq_arrested_dox_maintained+90

description:
fig panel: 2b,3e
GSTS_016

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, maintained arrest for 90m


title: Brg11* rep3 [I18R030d03_01]


title: SKOV3-Adherent-1


title: GSTS_015: JRy12379_input_arrested_dox

description:
fig panel: 2b,3e
GSTS_015


title: GSTS_006: JRy12378_strepSeq_cycling

description:
fig panel: 1b,c
GSTS_006

value: H3-Avi TetR-BirA(G115S) gal10::TetO


title: GSTS_014: JRy12379_v5-ChIP-seq_arrested_dox

description:
fig panel: 2b,3e
GSTS_014

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline

value: V5 (millipore #A7345)


title: Brg11* rep2 [I18R030d02_01]


title: SKOV3-Spheroid-2


title: Kuramochi-Spheroid-2

source_name: ovarian cancer cell line Kuramochi


title: Brg11* rep1 [I18R030d01_01]


title: Kuramochi-Spheroid-3


title: GSTS_013: JRy12379_strepSeq_arrested_dox

description:
fig panel: 2b,3e
GSTS_013

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline


title: GSTS_004: JRy12392_v5-ChIP-seq_arrested_dox

description:
fig panel: 1a
GSTS_004

value: H3-Avi TetR-BirA(1-213); H3-Avi  TetR-BirA(214-320)

value: H3-Avi TetR-BirA gal10::TetO


title: GSTS_003: JRy12392_strepSeq_arrested_dox

description:
fig panel: 1a
GSTS_003


title: GSTS_012: JRy12379_input_cycling

description:
fig panel: 2b,3e
GSTS_012


title: GSTS_011: JRy12379_v5-ChIP-seq_cycling

description:
fig panel: 2b,3e
GSTS_011

source_name: v5-precipitated chromatin from exponentially growing cells


title: Brg11ΔDBD* rep2 [I18R030c02_01]

source_name: Tomato leaf_Brg11ΔDBD*

value: X. euvesicatoria Brg11ΔDBD*


title: Kuramochi-Spheroid-1

value: ovarian cancer cell line


title: Kuramochi-Adherent-3


title: Brg11ΔDBD* rep1 [I18R030c01_01]


title: Kuramochi-Adherent-2


title: GSTS_001: JRy12392_strepSeq_cycling

description:
fig panel: 1a,b,c
GSTS_001

value: streptavidin (invitrogen #65001)


title: GSTS_010: JRy12379_strepSeq_cycling

description:
fig panel: 2b,3e
GSTS_010


title: GSTS_007: JRy12378_strepSeq_cycling_dox

description:
fig panel: 1b,c
GSTS_007


title: GSTS_005: JRy12376-12377_mixed_strepSeq_cycling

description:
fig panel: 1b,c
GSTS_005

source_name: mixed cycling cultures of JRy12376, 12377 ex vivo and precipitated chromatin with streptavidin

value: fixed in exponential phase, mixed ex vivo

value: H3-Avi TetR-BirA(1-213); H3-Avi  TetR-BirA(214-320) gal10::TetO


title: Kuramochi-Adherent-1


title: Brg11ΔDBD* rep3 [I18R030c03_01]


title: Brg11ΔDBD* rep4 [I18R030c04_01]


title: GSTS_002: JRy12392_v5-ChIP-seq cycling

description:
fig panel: 1a,b,c
GSTS_002


title: WT_1

status: Public on Nov 30 2019

city: Cuernavaca

first: José

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autónoma de México

data_processing:
Ilumina adapter sequences were removed using Trimgalore
Reads were aligned to reference genome E. coli MG1655 (NC_000913.2) using Bowtie2 with two mismatches allowed per read alignment.
To estimate gene expression FPKM values Cufflinks was used.
Cuffdiff was used to estimate gene differential expression values
Genome_build: NC_000913.2
Supplementary_files_format_and_content: .txt files with fpkm values of each strain in duplicates, and total differential expression analysis

organism: Escherichia coli

growth_protocol: Cultures were grown in batch mode in M9 minimal media with glucose. Samples were taken from mid-log phase.

extract_protocol:
Cell pellets were incubated with lysozyme, SuperaseIn and protease K for 10 min at 37°C. Total RNA was isolated and purified using Zymo Research’s Quick-RNA kit according to the manufacturer’s specifications. All samples’ quality was inspected in a bioanalyzer RNA chip (Agilent).
Starting with 10ug of total RNA of each sample, the removal of ribosomal RNA was done with the kit Ribominus by Invitrogen. For the construction of the libraries, the TruSeq Stranded mRNA Sample Prep Kit by Illumina was used, following the HT protocol.

treatment_protocol: Samples were taken with 2 volumes of RNAprotect reagent (quiagen)

tag: strain background

value: wild type

value: suspension cells


title: PFC_1

source_name: BW25113 (ΔphoB,  ΔflhC, ΔcueR)

value: {delta}phoB,  {delta}flhC, {delta}cueR


title: WT_2


title: Sample_4753_L005

city: Boston

first: Camron

middle: D

last: Bryant

state: MA

address: 72 East Concord St

department: Pharmacology

institute: Boston University School of Medicine

description: Sample run across lanes 3,4,&5

data_processing:
Samples were run across four lanes on 3 different flow cells and reads for each sample were generated via the Illumina HiSeq 2500 (~25,000,000 reads per replicate, totalling ~100,000,000 per sample)
Fastq files are quality checked via FastQC (v0.10.1) and possessed Phred quality scores > 30 (i.e. less than 0.1% sequencing error)
We computed the read counts per gene using the HTSeq (v0.6.1p1) Python package. For spicesome analysis counts per exon bin were calculated using the dexseq_count.py Python script available through the DEXSeq (v1.12.2) R package.  Count normalization was carried out with weighted trimmed mean of M-values (TMM) using edgeR (v3.8.6) R package. Differential gene expression and splice variant analysis was carried out using the Limma (v3.22.7) R package.
Genome_build: mm10 (transcriptome); mm9 (splicesome)
Supplementary_files_format_and_content: htseq_gene_matrix.txt: HTseq output for each sample is in the form of a TXT (.txt) file that consists of a list of genes along side respective read counts per gene for each sample
Supplementary_files_format_and_content: htseq_exon_matrix.txt: HTseq output for each sample is in the form of a TXT (.txt) file that consists of a list of genes along side respective read counts per exon for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Wild-type (C57BL/6J) and 112kb congenic mice at about 50 days of age were decaptitate for brain retrieval. As mentioned before, 3mm strialtal punches (left and right hemispheres) were pooled per mouse, and collected tissue was immediately places into RNAlater (QIAGEN) for 24 hours. After incubation, RNA was extracted via miRNeasy Mini Kit and quality was assessed by Bioanalyzer analysis.
RNA that was deemed high quality was send to the University of Chicago Genomics Core Facility for cDNA library preparation. Libraries were prepared according to Illumina's detailed instructions accompanying the Illumina TruSeq Stranded mRNA LT (100bp; paired-end reads).  The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols

tag: brain area

value: Striatum

tag: sample id

value: B6 wild-type

value: female


title: Sample_4804_L003

description: Sample run across lanes 3,4,&5

value: 112kb congenic

tag: Sex


title: Sample_4806_L003

description: Sample run across lanes 3,4,&5


title: Sample_4753_L003

description: Sample run across lanes 3,4,&5


title: Sample_4804_L004

description: Sample run across lanes 3,4,&5


title: Sample_4739_L005

description: Sample run across lanes 3,4,&5


title: Sample_4739_L003

description: Sample run across lanes 3,4,&5


title: Sample_4804_L005

description: Sample run across lanes 3,4,&5


title: Sample_4806_L004

description: Sample run across lanes 3,4,&5


title: Sample_4806_L005

description: Sample run across lanes 3,4,&5


title: Sample_4739_L004

description: Sample run across lanes 3,4,&5


title: PFC_2


title: Mig-6 d/d Erbb2 d/d 2

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: Gene expression data from uterus at 2 weeks of age

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).

label: biotin

source_name: uteri of Mig-6 d/d Erbb2 d/d at GD 3.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Collect uteri from GD3.5 mice

extract_protocol: RNA was extracted from the uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA).

tag: developmental stage

tag: gender

value: Female

value: Mig-6 d/d Erbb2 d/d

tag: tissue

value: uterus


title: Mig-6 d/d Erbb2 d/d 3

tag: genotype/variation


title: control 2

source_name: uteri of control at GD3.5

value: control


title: Mig-6 d/d 3

source_name: uteri of Mig-6 d/d at GD 3.5

value: Mig-6 d/d


title: Mig-6 d/d 2


title: Mig-6 d/d Erbb2 d/d 1


title: control 3


title: Sample_4738_L005

description: Sample run across lanes 3,4,&5


title: control 1


title: Sample_4738_L004

description: Sample run across lanes 3,4,&5


title: Sample_4738_L003

description: Sample run across lanes 3,4,&5


title: Sample_4737_L005

description: Sample run across lanes 3,4,&5


title: Sample_4737_L004

description: Sample run across lanes 3,4,&5


title: Sample_4737_L003

description: Sample run across lanes 3,4,&5


title: Sample_4753_L004

description: Sample run across lanes 3,4,&5


title: Sample_4734_L004

description: Sample run across lanes 3,4,&5

value: male


title: Sample_4734_L003

description: Sample run across lanes 3,4,&5


title: Sample_4734_L005

description: Sample run across lanes 3,4,&5


title: Sample_4733_L003

description: Sample run across lanes 3,4,&5


title: Sample_4733_L005

description: Sample run across lanes 3,4,&5


title: Sample_4731_L005

description: Sample run across lanes 3,4,&5


title: Sample_4732_L003

description: Sample run across lanes 3,4,&5


title: Sample_4732_L005

description: Sample run across lanes 3,4,&5


title: Sample_4712_L005

description: Sample run across lanes 3,4,&5


title: Sample_4731_L003

description: Sample run across lanes 3,4,&5


title: Sample_4733_L004

description: Sample run across lanes 3,4,&5


title: Sample_4712_L004

description: Sample run across lanes 3,4,&5


title: Sample_4712_L003

description: Sample run across lanes 3,4,&5


title: Sample_4677_L004

description: Sample run across lanes 3,4,&5


title: Mig-6 d/d 1


title: Sample_4676_L005

description: Sample run across lanes 3,4,&5


title: Sample_4677_L003

description: Sample run across lanes 3,4,&5


title: Sample_4673_L005

description: Sample run across lanes 3,4,&5


title: Sample_4676_L003

description: Sample run across lanes 3,4,&5


title: Sample_4673_L004

description: Sample run across lanes 3,4,&5


title: Sample_4673_L003

description: Sample run across lanes 3,4,&5


title: Sample_4676_L004

description: Sample run across lanes 3,4,&5


title: Sample_4672_L005

description: Sample run across lanes 3,4,&5


title: Sample_4672_L004

description: Sample run across lanes 3,4,&5


title: Sample_4731_L004

description: Sample run across lanes 3,4,&5


title: Sample_4672_L003

description: Sample run across lanes 3,4,&5


title: Sample_4671_L005

description: Sample run across lanes 3,4,&5


title: Sample_4671_L004

description: Sample run across lanes 3,4,&5


title: Sample_4671_L003

description: Sample run across lanes 3,4,&5


title: Sample_4677_L005

description: Sample run across lanes 3,4,&5


title: rRNA_Exo10_GV_ctr_V1133_3

city: Ashburn

first: Di

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

description:
ribosomal RNA
plus ERCC spike-in mix #4456776

data_processing:
Raw sequence reads were trimmed with Cutadapt 2.5 to remove adapters while performing light quality trimming with parameters "-m 10 -q 20, 20".
Sequencing library quality was assessed with FastQC v0.11.8 with default parameters. Trimmed reads were mapped to the Mus musculus mm10 reference genome plus ERCC.fasta using STAR v2.7.2a.
Multi-mapping reads were filtered using samtools 1.9. Uniquely aligned reads were then mapped to gene features using HTseq v0.9.1 as an unstranded library with default parameters.
A gene/ERCC count was considered valid when present in at least 5 reads in at least 2 libraries. Differential expression between groups of samples was tested using R version 3.5.1 (2018-07-02) with DESeq2 v1.24.0. The oocyte libraries were normalized by ERCC counts by defining the ERCC genes as the controlGenes when estimating the sizeFactors in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated original counts of each gene

source_name: single mouse oocyte

growth_protocol: GV oocytes, 3 hr oocytes are cultured ex vivo in M2 medium. MII eggs are dissected from oviducts.

extract_protocol:
polyA RNAs: Each oocyte was lysed in RLT-plus buffer. The oligo-dT beads were used to isolate the polyA RNA. RiboMinus RNAs and ribosomal RNA: with Ovation Solo system.
For polyA RNAs: Single oocyte RNA-seq libraries were prepared according to a published single-cell RNA seq pipeline with subtle modifications (Macaulay et al., 2016). Briefly, the oocytes at desired stages were collected individually into 2.5 ml RLT plus and stocked at -80 °C until all samples were collected. In the beginning of RNA purification, ERCC RNA spike-in mix (ThermoFisher 4456740) was diluted 10^5 fold, and 1 ml of the diluted ERCC mix was added to each lysis. Poly(A) RNA were isolated by oligo (dT) beads, reverse transcribed, amplified and purified. The purified cDNAs were analyzed by Bioanalyzer 2100 to confirm successful amplification range and quality. cDNAs passing a quality test were further constructed into sequencing libraries by Nextera DNA Sample Preparation Kit. For RiboMinus RNAs: single oocyte libraries were prepared according to the Ovation Solo system, but random hexamer primer is used for reverse transcription.

value: single mouse oocyte

tag: Stage

value: GV


title: rRNA_Exo10_MII_ctr_V1145_3

description:
ribosomal RNA
plus ERCC spike-in mix #4456783

value: MII


title: rRNA_Exo10_MII_cKO_V1166_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456779

value: Exosc10 oocyte-specific knockout


title: rRNA_Exo10_MII_ctr_V1145_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456782


title: rRNA_Exo10_MII_ctr_V1145_4

description:
ribosomal RNA
plus ERCC spike-in mix #4456784


title: rRNA_Exo10_MII_cKO_V1167_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456781


title: rRNA_Exo10_GV_ctr_V1133_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456775


title: rRNA_Exo10_GV_ctr_V1133_4

description:
ribosomal RNA
plus ERCC spike-in mix #4456777


title: rRNA_Exo10_GV_ctr_V1133_1

description:
ribosomal RNA
plus ERCC spike-in mix #4456774


title: rRNA_Exo10_GV_ctr_V1132_4

description:
ribosomal RNA
plus ERCC spike-in mix #4456773


title: rRNA_Exo10_GV_ctr_V1132_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456771


title: rRNA_Exo10_GV_cKO_V1131_4

description:
ribosomal RNA
plus ERCC spike-in mix #4456769


title: rRNA_Exo10_GV_ctr_V1132_1

description:
ribosomal RNA
plus ERCC spike-in mix #4456770


title: rRNA_Exo10_GV_ctr_V1132_3

description:
ribosomal RNA
plus ERCC spike-in mix #4456772


title: rRNA_Exo10_GV_cKO_V1126_3

description:
ribosomal RNA
plus ERCC spike-in mix #4456764


title: rRNA_Exo10_GV_cKO_V1131_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456767


title: rRNA_Exo10_GV_cKO_V1131_1

description:
ribosomal RNA
plus ERCC spike-in mix #4456766


title: rRNA_Exo10_GV_cKO_V1126_2

description:
ribosomal RNA
plus ERCC spike-in mix #4456763


title: Exo10_MII_ctr_V1145_4_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456762


title: rRNA_Exo10_GV_cKO_V1131_3

description:
ribosomal RNA
plus ERCC spike-in mix #4456768


title: Exo10_MII_ctr_V1145_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456760


title: Exo10_MII_ctr_V1145_3_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456761


title: Exo10_MII_cKO_V1167_1_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456758


title: Exo10_MII_cKO_V1166_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456757


title: Exo10_MII_cKO_V1167_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456759


title: rRNA_Exo10_MII_cKO_V1167_1

description:
ribosomal RNA
plus ERCC spike-in mix #4456780


title: rRNA_Exo10_MII_cKO_V1166_1

description:
ribosomal RNA
plus ERCC spike-in mix #4456778


title: Sample_4732_L004

description: Sample run across lanes 3,4,&5


title: Exo10_MII_cKO_V1166_1_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456756


title: Exo10_GV_ctr_V1133_1_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456752


title: Exo10_GV_ctr_V1133_3_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456754


title: Exo10_GV_ctr_V1132_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456749


title: Exo10_GV_ctr_V1133_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456753


title: rRNA_Exo10_GV_cKO_V1126_4

description:
ribosomal RNA
plus ERCC spike-in mix #4456765


title: Exo10_GV_ctr_V1132_3_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456750


title: Exo10_GV_ctr_V1133_4_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456755


title: Exo10_GV_ctr_V1132_1_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456748


title: Exo10_GV_cKO_V1126_4_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456743


title: Exo10_GV_cKO_V1131_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456745


title: Exo10_GV_cKO_V1131_3_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456746


title: Exo10_GV_cKO_V1131_1_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456744


title: Exo10_GV_cKO_V1126_2_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456741


title: MII_ctr_V853_4

description:
polyA RNA
plus ERCC spike-in mix #4456740

molecule: polyA RNA


title: MII_ctr_V896_1


title: MII_ctr_V853_3


title: MII_ctr_V853_1


title: MII_ctr_V836_2


title: MII_ctr_V853_2


title: MII_ctr_V836_1


title: MII_cKO_V897_8


title: MII_cKO_V897_7


title: Exo10_GV_ctr_V1132_4_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456751


title: Exo10_GV_cKO_V1131_4_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456747


title: MII_cKO_V897_5


title: MII_cKO_V897_4


title: MII_cKO_V897_6


title: MII_cKO_V897_3


title: MII_ctr_V896_2


title: Exo10_GV_cKO_V1126_3_RiboMinus

description:
RiboMinus RNA
plus ERCC spike-in mix #4456742


title: MII_cKO_V842_1


title: MII_cKO_V897_10


title: MII_cKO_V897_11


title: MII_cKO_V842_2


title: MII_cKO_V897_1


title: MII_cKO_V841_1


title: MII_cKO_V841_2


title: GV3h_ctr_V995_4


title: MII_cKO_V897_9


title: GV3h_ctr_V995_2


title: GV3h_ctr_V995_3


title: GV3h_ctr_V982_1


title: GV3h_ctr_V982_2


title: GV3h_ctr_V995_1


title: MII_cKO_V897_2


title: GV3h_ctr_V951_2


title: GV3h_cKO_V993_3


title: GV3h_ctr_V951_1


title: FRI;flc-3 leaf 5 past full expansion, experiment 2, rep 3

city: Ithaca

first: Matthew

middle: R

last: Willmann

state: NY

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

institute: Cornell University

description: FRI;flc-3 Lf5L Expt 2 rep3

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

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

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

organism: Arabidopsis thaliana

source_name: FRI;flc-3 leaf 5 past full expansion_experiment 2

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

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

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

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

tag: genetic background

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

tag: days after plants put in the growth chamber

value: leaf 5 past full expansion

tag: leaf position

tag: experiment number

tag: day length

value: 16 hours (long day conditions)


title: GV3h_cKO_V993_2

tag: genotype


title: GV3h_cKO_V993_1


title: GV3h_cKO_V983_3


title: FRI;flc-3 leaf 5 past full expansion, experiment 2, rep 2

description: FRI;flc-3 Lf5L Expt 2 rep2


title: FRI;flc-3 leaf 7 past full expansion, experiment 2, rep 1

description: FRI;flc-3 Lf7L Expt 2 rep1

source_name: FRI;flc-3 leaf 7 past full expansion_experiment 2

value: leaf 7 past full expansion


title: GV3h_cKO_V983_2


title: H9_PrE_LN511_R2

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: DanStem

country: Denmark

institute: Copenhagen University

hyb_protocol: The labelled RNA was hybridised to a Human Gene Expression 8x60K v2 (Agilent; G4851B) for 17 hours.

scan_protocol: Microarrays were scanned on a Surescan G2600D scanner using Agilent Scan Control 9.1.7.1 software with default settings (GE 8x60k microarrays).

data_processing: All microarray expression data was analysed using ExAtlas (Sharov et al., 2015).

source_name: Human embryonic stem cells

label_protocol: Labelled with the LowInput QuickAmp Labeling Kit One-Color (Agilent; 5190–2305).

growth_protocol: Naïve pluripotent stem cells were cultured for 3 passages on either MEFs or LN511 in naïve medium (N2B27 supplemented with 10ng/mL LIF, 1µM CHIR99021, 1µM PD0325901 and 2µM Gö6983). These were then differentiated on either MEFs or LN511 in differentiation medium (RPMI GlutaMAX with B27 minus insulin supplemented with 10ng/mL LIF, 3µM CHIR and 100ng/mL Activin A) for 7 days.

extract_protocol: Total RNA was collected using the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by Dnase treatment (Qiagen).

tag: background

value: Extra-embryonic endoderm


title: FRI;flc-3 leaf7 past full expansion, experiment 2, rep 3

description: FRI;flc-3 Lf7L Expt 2 rep3

source_name: FRI;flc-3 leaf7 past full expansion_experiment 2


title: FRI;flc-3 leaf 5 past full expansion, experiment 2, rep 1

description: FRI;flc-3 Lf5L Expt 2 rep1


title: GV3h_cKO_V983_1


title: FRI;flc-3 leaf 3 past full expansion, experiment 2, rep 3

description: FRI;flc-3 Lf3L Expt 2 rep3

source_name: FRI;flc-3 leaf 3 past full expansion_experiment 2

value: leaf 3 past full expansion


title: H9_PrE_LN511_R1

tag: cell type


title: FRI;flc-3 leaf 3 past full expansion,, experiment 2, rep 2

description: FRI;flc-3 Lf3L Expt 2 rep2

source_name: FRI;flc-3 leaf 3 past full expansion,_experiment 2


title: FRI;flc-3 leaf7 past full expansion, experiment 2, rep 2

description: FRI;flc-3 Lf7L Expt 2 rep2


title: GV3h_cKO_V946_7


title: H9_PrE_MEF_R2


title: H9_PrE_MEF_R1


title: HNES1_PrE_MEF_R1


title: FRI;FLC leaf 7 past full expansion, experiment 2, rep 3

description: FRI;FLC Lf7L Expt 2 rep3

source_name: FRI;FLC leaf 7 past full expansion_experiment 2

value: FRI;FLC


title: H9_nES_LN511_R1

value: Naive pluripotent stem cells


title: FRI;flc-3 leaf 3 past full expansion, experiment 2, rep 1

description: FRI;flc-3 Lf3L Expt 2 rep1


title: GV3h_cKO_V993_4


title: GV3h_cKO_V946_5


title: FRI;FLC leaf 7 past full expansion, experiment 2, rep 2

description: FRI;FLC Lf7L Expt 2 rep2


title: GV3h_cKO_V946_3


title: H9_nES_LN511_R2


title: GV3h_cKO_V946_1


title: H9_nES_MEF_R3


title: GV_ctr_V889_3


title: GV_ctr_V889_4


title: GV_ctr_V889_2


title: GV_ctr_V856_4


title: GV_ctr_V856_2


title: GV_ctr_V856_1


title: GV_ctr_V889_1


title: GV_cKO_V888_9


title: GV_cKO_V888_8


title: GV_cKO_V888_7


title: GV_cKO_V888_6


title: GV_cKO_V888_4


title: H9_nES_MEF_R2


title: GV_cKO_V888_2


title: GV_cKO_V888_3


title: FRI;FLC leaf 5 past full expansion, experiment 2, rep 2

description: FRI;FLC Lf5L Expt 2 rep2

source_name: FRI;FLC leaf 5 past full expansion_experiment 2


title: FRI;FLC leaf 5 past full expansion, experiment 2, rep 3

description: FRI;FLC Lf5L Expt 2 rep3


title: GV_cKO_V888_11


title: FRI;FLC leaf 7 past full expansion, experiment 2, rep 1

description: FRI;FLC Lf7L Expt 2 rep1


title: FRI;FLC leaf 3 past full expansion, experiment 2, rep 3

description: FRI;FLC Lf3L Expt 2 rep3

source_name: FRI;FLC leaf 3 past full expansion_experiment 2


title: FRI;FLC leaf 5 past full expansion, experiment 2, rep 1

description: FRI;FLC Lf5L Expt 2 rep1


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

description: FRI;flc-3 Lf11 Expt 2 rep2

source_name: FRI;flc-3 fully-expanded leaf 11_experiment 2

value: fully-expanded leaf 11 (cauline leaf)


title: FRI;FLC leaf 3 past full expansion, experiment 2, rep 1

description: FRI;FLC Lf3L Expt 2 rep1


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

description: FRI;flc-3 Lf11 Expt 2 rep3


title: GV_cKO_V888_1


title: FRI;FLC leaf 3 past full expansion, experiment 2, rep 2

description: FRI;FLC Lf3L Expt 2 rep2


title: H9_nES_MEF_R1


title: PTX_CF_P8: MDA_MB_436_TREATED WITH  PTX

city: Montréal

first: isabelle

last: sirois

state: QC

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: McGill University

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

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

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

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

source_name: MDA_MB_436 treated with saline solution + PTX 0.01uM

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

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

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

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

value: female

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

tag: cell line

value: resistant DOXO-R cells


title: GV_cKO_V857_5


title: PTX_CF_P7: MDA_MB_436_TREATED WITH  PTX


title: GV_cKO_V857_3


title: PTX_CF_P6: MDA_MB_436_TREATED WITH  PTX


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

description: FRI;flc-3 Lf11 Expt 2 rep1


title: GV_cKO_V857_2


title: PTX_CD_P8: MDA_MB_436_TREATED WITH  PTX


title: GV_cKO_V888_10


title: GV_cKO_V857_1


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

description: FRI;flc-3 Lf9 Expt 2 rep2

source_name: FRI;flc-3 fully-expanded leaf 9_experiment 2

value: fully-expanded leaf 9 (rosette leaf)


title: PTX_CD_P7: MDA_MB_436_TREATED WITH  PTX


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

description: FRI;flc-3 Lf9 Expt 2 rep1


title: PTX_CD_P6: MDA_MB_436_TREATED WITH  PTX


title: scRNA-seq [N707-N508]

city: Tokyo

first: Daichi

last: Narushima

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

department: Department of Bioinformatics

institute: National Cancer Center Research Institute

description: 160120_Hiseq3B_l8_091_Dr_Okamoto_N707-N508_CTCTCTAC-CTAAGCCT_L008

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

source_name: colon tumor cells

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

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

tag: strain

value: ApcMin/+

tag: age

value: 12 weeks

value: male

value: colon

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


title: scRNA-seq [N710-N508]

description: 160120_Hiseq3B_l8_094_Dr_Okamoto_N710-N508_CGAGGCTG-CTAAGCCT_L008

tag: Sex


title: scRNA-seq [N708-N508]

description: 160120_Hiseq3B_l8_092_Dr_Okamoto_N708-N508_CAGAGAGG-CTAAGCCT_L008


title: scRNA-seq [N706-N508]

description: 160120_Hiseq3B_l8_090_Dr_Okamoto_N706-N508_TAGGCATG-CTAAGCCT_L008


title: scRNA-seq [N705-N508]

description: 160120_Hiseq3B_l8_089_Dr_Okamoto_N705-N508_GGACTCCT-CTAAGCCT_L008


title: PTX_CA_P11: MDA_MB_436_TREATED WITH  PTX


title: scRNA-seq [N710-N507]

description: 160120_Hiseq3B_l8_082_Dr_Okamoto_N710-N507_CGAGGCTG-AAGGAGTA_L008


title: scRNA-seq [N709-N507]

description: 160120_Hiseq3B_l8_081_Dr_Okamoto_N709-N507_GCTACGCT-AAGGAGTA_L008


title: GV_cKO_V857_4

value: single mouse oocyte

value: GV

value: Exosc10 oocyte-specific knockout


title: scRNA-seq [N704-N508]

description: 160120_Hiseq3B_l8_088_Dr_Okamoto_N704-N508_TCCTGAGC-CTAAGCCT_L008


title: PTX_CA_P10: MDA_MB_436_TREATED WITH  PTX


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

description: FRI;flc-3 Lf7 Expt 2 rep2

source_name: FRI;flc-3 fully-expanded leaf 7_experiment 2

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

value: fully-expanded leaf 7 (rosette leaf)

value: 16 hours (long day conditions)


title: PTX_CA_P9: MDA_MB_436_TREATED WITH  PTX


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

description: FRI;flc-3 Lf7 Expt 2 rep3


title: scRNA-seq [N708-N507]

description: 160120_Hiseq3B_l8_080_Dr_Okamoto_N708-N507_CAGAGAGG-AAGGAGTA_L008


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

description: FRI;flc-3 Lf9 Expt 2 rep3


title: scRNA-seq [N706-N507]

description: 160120_Hiseq3B_l8_078_Dr_Okamoto_N706-N507_TAGGCATG-AAGGAGTA_L008


title: scRNA-seq [N707-N507]

description: 160120_Hiseq3B_l8_079_Dr_Okamoto_N707-N507_CTCTCTAC-AAGGAGTA_L008


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

description: FRI;flc-3 Lf7 Expt 2 rep1


title: scRNA-seq [N709-N508]

description: 160120_Hiseq3B_l8_093_Dr_Okamoto_N709-N508_GCTACGCT-CTAAGCCT_L008


title: scRNA-seq [N705-N507]

description: 160120_Hiseq3B_l8_077_Dr_Okamoto_N705-N507_GGACTCCT-AAGGAGTA_L008


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

description: FRI;flc-3 Lf5 Expt 2 rep3

source_name: FRI;flc-3 fully-expanded leaf 5_experiment 2

value: fully-expanded leaf 5 (rosette leaf)


title: Saline CH18: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO AND VEHICLE FOR PTX

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

source_name: MDA_MB_436 PARENTAL TREATED WITH SALINE SOLUTION AND THEN WITH THE VEHICLE USED FOR PTX TREATMENT (CHREMOPHOR)

value: parental DOXO-S cells


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

description: FRI;flc-3 Lf5 Expt 2 rep2


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

description: FRI;flc-3 Lf5 Expt 2 rep1


title: scRNA-seq [N704-N507]

description: 160120_Hiseq3B_l8_076_Dr_Okamoto_N704-N507_TCCTGAGC-AAGGAGTA_L008


title: Saline CH17: MDA_MB_436_TREATED WITH VEHICLE FOR DOXO AND VEHICLE FOR PTX

value: female


title: scRNA-seq [N710-N506]

description: 160120_Hiseq3B_l8_070_Dr_Okamoto_N710-N506_CGAGGCTG-ACTGCATA_L008


title: Saline CH16 : MDA_MB_436_TREATED WITH VEHICLE FOR DOXO AND VEHICLE FOR PTX

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