title: P5,CD-1,VLMC-1

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing was performed with the 10X Chromium cellranger pipline version 1.3 using default settings
The Unique Molecular Identifier and cellular barcode corresponding to each read have been appended to the read id separated by an underscore.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecules per gene in each cell

source_name: dentate gyrus

extract_protocol:
Mice were sacrificed by an overdose of Isoflurane or Ketamin/Xylazine, followed by perfusion through the left ventricle with artificial cerebrospinal fluid (aCSF), equilibrated in 95%O2/5%CO2 on ice or 4°C. The dentate gyrus was then microdissected from 300 μm vibratome brain sections. Single-cell suspensions were prepared using the Papain kit (Worthington) with 25-35min enzymatic digestion followed by manual trituration using a BSA-coated p1000 pipette or fire-polished Pasteur pipettes. For hGFAP-GFP mice, GFP-positive cells were sorted on a BD FACSAria II  into oxygenated aCSF at 4°C.
1000 cells/  μl were resuspended in artificial cerebrospinal fluid and added to the   Reverse transcription mix to aim for sampling of around 3500 cells. All downstream cDNA synthesis (13 PCR   cycles), library preparation and sequencing were carried   out as instructed by the manufacturer   (10X Genomics Chromium Single Cell Kit Version 2).

tag: cell cluster

value: VLMC


title: P5,CD-1,nIPC-1

status: Public on Dec 12 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

value: nIPC


title: P5,CD-1,nIPC-perin-1


title: Liver_15M_50

city: Toronto

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

country: Canada

institute: Centre for Addiction and Mental Health

description:
P1_D4_JV_L_15M_ZT56-29878933
technical_replicate1
sequencing_replicate2

library_source: genomic

data_processing:
The libraries were sequenced on the HiSeq 2500 platform (Illumina) using custom sequencing primers.
The FASTQ reads were quality trimmed using Trimmomatic (24695404) for trailing base with phred score < 30 and all reads with post-trimming length < 50 bp.
The trimmed reads were then aligned using Bismark version 0.14 (21493656) and Bowtie 2 version 2.2.2 (22388286).
The aligned reads were further filtered to only include reads that have start and end positions that match the padlock probe annealing arm sequence with no more than 1 mismatch.
The filtered reads were subsequently PCR de-duplicated using unique molecular identifiers.
The filtered read pairs were then converted to methylation calls using the Bismark methylation extractor tool (21493656).
Genome_build: mm10
Supplementary_files_format_and_content: Each txt file contain the following information in order: chrosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

molecule: genomic DNA

source_name: Liver

growth_protocol: The mice had ad libitum access to food and water

extract_protocol:
DNA isolation was performed using standard phenol chloroform methods.
Bisulfite padlock probes were designed using the ppDesigner 2.0 software (22306810) for mouse chromosome 7 (mm10).  The probe and library preparation was performed based on previously published protocol (ibid).

tag: tissue

value: Liver

tag: age (in months)

tag: Sex

value: male

tag: treatment (bisulfite/oxybisulfite)

value: bisulfite


title: Liver_15M_52

description:
P1_D5_JV_L_15M_ZT8-29863931
technical_replicate1
sequencing_replicate2


title: P5,CD-1,OPC-1

value: OPC


title: P5,CD-1,PVM-1

value: PVM


title: P5,CD-1,RGL_young-2


title: Liver_15M_46

description:
P1_D2_JV_L_15M_ZT32-29876955
technical_replicate1
sequencing_replicate2


title: P5,CD-1,RGL_young-1


title: Liver_15M_49

description:
P1_D4_JV_L_15M_ZT56-29870929
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Neuroblast-3

value: Neuroblast


title: Liver_15M_47

description:
P1_D3_JV_L_15M_ZT10-29874936
technical_replicate1
sequencing_replicate1


title: Liver_15M_44

description:
P1_D11_JV_L_15M_ZT40-29871945
technical_replicate1
sequencing_replicate2


title: Liver_15M_42

description:
P1_D10_JV_L_15M_ZT12-29872922
technical_replicate1
sequencing_replicate2


title: Liver_15M_43

description:
P1_D11_JV_L_15M_ZT40-29864915
technical_replicate1
sequencing_replicate1


title: Liver_15M_45

description:
P1_D2_JV_L_15M_ZT32-29872913
technical_replicate1
sequencing_replicate1


title: Liver_15M_41

description:
P1_D10_JV_L_15M_ZT12-29872914
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Neuroblast-2


title: Liver_15M_40

description:
P1_C9_JV_L_15M_ZT58-29877948
technical_replicate1
sequencing_replicate2


title: P5,CD-1,MiCajal-Retziusoglia-1

value: MiCajal


title: P5,CD-1,Immature-Pyr-4

value: Immature


title: P5,CD-1,Immature-Pyr-2


title: P5,CD-1,Immature-Pyr-3


title: Liver_15M_48

description:
P1_D3_JV_L_15M_ZT10-29874942
technical_replicate1
sequencing_replicate2


title: P5,CD-1,Immature-GC-6


title: Liver_15M_35

description:
P1_C7_JV_L_15M_ZT34-29860919
technical_replicate1
sequencing_replicate1


title: Liver_15M_34

description:
P1_C6_JV_L_15M_ZT50-29871944
technical_replicate1
sequencing_replicate2


title: Liver_15M_36

description:
P1_C7_JV_L_15M_ZT34-29869914
technical_replicate1
sequencing_replicate2


title: Liver_15M_37

description:
P1_C8_JV_L_15M_ZT18-29856924
technical_replicate1
sequencing_replicate1


title: Liver_15M_38

description:
P1_C8_JV_L_15M_ZT18-29870924
technical_replicate1
sequencing_replicate2


title: P5,CD-1,Immature-Pyr-1


title: Liver_15M_39

description:
P1_C9_JV_L_15M_ZT58-29862922
technical_replicate1
sequencing_replicate1


title: Liver_15M_33

description:
P1_C6_JV_L_15M_ZT50-29856916
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Neuroblast-1


title: P5,CD-1,Immature-GC-5


title: Liver_15M_32

description:
P1_C5_JV_L_15M_ZT44-29872912
technical_replicate1
sequencing_replicate2


title: P5,CD-1,NFOL-1

value: NFOL


title: P5,CD-1,MOL-1

value: MOL


title: P5,CD-1,Immature-GC-3


title: Liver_15M_31

description:
P1_C5_JV_L_15M_ZT44-29852911
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Immature-GABA-2


title: Liver_15M_30

description:
P1_C4_JV_L_15M_ZT30-29858926
technical_replicate1
sequencing_replicate2


title: Liver_15M_29

description:
P1_C4_JV_L_15M_ZT30-29858920
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Immature-GC-2


title: Liver_15M_28

description:
P1_C3_JV_L_15M_ZT24-29873931
technical_replicate1
sequencing_replicate2


title: P5,CD-1,Immature-GC-7


title: P5,CD-1,Immature-GABA-1


title: Liver_15M_27

description:
P1_C3_JV_L_15M_ZT24-29867924
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Immature-GC-1


title: P5,CD-1,Immature-Astro-1


title: P5,CD-1,Immature-Astro-2


title: P5,CD-1,Ependymal-1

value: Ependymal


title: P5,CD-1,Immature-GC-4


title: Liver_15M_25

description:
P1_C2_JV_L_15M_ZT46-29878937
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Immature-Astro-3


title: Liver_15M_21

description:
P1_C10_JV_L_15M_ZT0-29861901
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Endothelial-1

value: Endothelial


title: Liver_15M_26

description:
P1_C2_JV_L_15M_ZT46-29879930
technical_replicate1
sequencing_replicate2


title: Liver_15M_23

description:
P1_C11_JV_L_15M_ZT4-29873932
technical_replicate1
sequencing_replicate1


title: Liver_15M_24

description:
P1_C11_JV_L_15M_ZT4-29876944
technical_replicate1
sequencing_replicate2


title: Liver_15M_22

description:
P1_C10_JV_L_15M_ZT0-29863936
technical_replicate1
sequencing_replicate2


title: P5,CD-1,GABA-1

value: GABA


title: P5,CD-1,GC-juv-1

value: GC


title: Liver_15M_20

description:
P1_B9_JV_L_15M_ZT20-29864923
technical_replicate1
sequencing_replicate2


title: P5,CD-1,CA3-Pyr-1


title: Liver_15M_18

description:
P1_B8_JV_L_15M_ZT52-29874941
technical_replicate1
sequencing_replicate2


title: Liver_15M_19

description:
P1_B9_JV_L_15M_ZT20-29862910
technical_replicate1
sequencing_replicate1


title: P23,CD-1,nIPC-perin-1


title: Liver_15M_17

description:
P1_B8_JV_L_15M_ZT52-29874934
technical_replicate1
sequencing_replicate1


title: Liver_15M_16

description:
P1_B7_JV_L_15M_ZT48-29868931
technical_replicate1
sequencing_replicate2


title: P23,CD-1,nIPC-1


title: P23,CD-1,VLMC-1


title: Liver_15M_15

description:
P1_B7_JV_L_15M_ZT48-29860911
technical_replicate1
sequencing_replicate1


title: Liver_15M_14

description:
P1_B6_JV_L_15M_ZT14-29867931
technical_replicate1
sequencing_replicate2


title: Liver_15M_12

description:
P1_B5_JV_L_15M_ZT36-29877946
technical_replicate1
sequencing_replicate2


title: P23,CD-1,PVM-1


title: Liver_15M_13

description:
P1_B6_JV_L_15M_ZT14-29866915
technical_replicate1
sequencing_replicate1


title: P5,CD-1,Cajal-Retzius-1

value: Cajal


title: P23,CD-1,Neuroblast-1


title: Liver_15M_10

description:
P1_B4_JV_L_15M_ZT42-29866926
technical_replicate1
sequencing_replicate2


title: Liver_15M_9

description:
P1_B4_JV_L_15M_ZT42-29866914
technical_replicate1
sequencing_replicate1


title: Liver_15M_7

description:
P1_B3_JV_L_15M_ZT38-29872911
technical_replicate1
sequencing_replicate1


title: Liver_15M_5

description:
P1_B2_JV_L_15M_ZT2-29858919
technical_replicate1
sequencing_replicate1


title: P23,CD-1,NFOL-1


title: P23,CD-1,Immature-GC-2


title: Liver_15M_11

description:
P1_B5_JV_L_15M_ZT36-29863935
technical_replicate1
sequencing_replicate1


title: P23,CD-1,Immature-Pyr-1


title: Liver_15M_8

description:
P1_B3_JV_L_15M_ZT38-29876954
technical_replicate1
sequencing_replicate2


title: P23,CD-1,MiCajal-Retziusoglia-1


title: Liver_15M_4

description:
P1_B11_JV_L_15M_ZT26-29877947
technical_replicate1
sequencing_replicate2


title: P23,CD-1,Immature-GC-1


title: P23,CD-1,MOL-1


title: P23,CD-1,RGL_young-1


title: Liver_15M_2

description:
P1_B10_JV_L_15M_ZT28-29875943
technical_replicate1
sequencing_replicate2


title: P23,CD-1,Immature-Astro-1


title: P23,CD-1,Immature-GABA-1


title: Liver_15M_3

description:
P1_B11_JV_L_15M_ZT26-29852910
technical_replicate1
sequencing_replicate1


title: P23,CD-1,RGL-1

value: RGL


title: P23,CD-1,GC-juv-6


title: P23,CD-1,OPC-1


title: Long-term hypoxia microRNA

city: Kaohsiung

first: Po-Lin

last: Kuo

address: 100, Shih-Chuan 1st Road

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
processed data files format and content: excel files include miRNA name, raw read counts and normalized values
Genome_build: Human genome from Genome Reference Consortium Human GRCh38.p10

organism: Homo sapiens

source_name: Renal cell carcinoma cell line

growth_protocol: The RCC cell line, 786-O cells were grown in RPMI-1640, supplemented with 10% fetal bovine serum, and 10.000 U penicillin/10 μg streptomycin/25 μg amphotericin B per mL.

extract_protocol:
Total RNA lysates were harvested using Trizol® Reagent (Invitrogen, USA) according to the manufacturer’s instructions.
Small RNA library construction and deep sequencing was carried out using Illumina sample preparation kit, according to the TruSeq Small RNA Sample Preparation Guide.

treatment_protocol: For normoxia, the cells were incubated at 37oC, with 20% O2, and 5% CO2. For hypoxia, the cells were incubated and passaged in a Physiological Oxygen Workstations InvivO2 400 at 37oC, with 1% O2, and 5% CO2 for 3 months.

value: Kidney

tag: gender

tag: cell line

tag: cell type

value: Renal cell carcinoma


title: P23,CD-1,GC-juv-3


title: P23,CD-1,GC-juv-4


title: Liver_15M_6

description:
P1_B2_JV_L_15M_ZT2-29875942
technical_replicate1
sequencing_replicate2

value: Liver

value: male


title: Short-term hypoxia microRNA


title: Normoxia microRNA


title: P23,CD-1,GC-juv-2


title: Short-term hypoxia mRNA

data_processing:
The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit.
Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0
Trimmomatics was implemented to trim or remove the reads according to the quality score
Qualified reads were analyzed using TopHat/Cufflinks for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
CummeRbund was employed to perform statistical analyses of gene expression profiles.
processed data files format and content: excel files include gene ID, gene type, associated gene name, description, EntrezGene ID, locus and FPKM values
Genome_build: Human genome from Genome Reference Consortium Human GRCh38.p10

extract_protocol:
Total RNA lysates were harvested using Trizol® Reagent (Invitrogen, USA) according to the manufacturer’s instructions.
RNA library construction was carried out according to the manufacture’s protocol from Illumina, using Agilent's SureSelect Strand Specific RNA Library Preparation Kit for 75 Single-End sequencing on Solexa platform.


title: Long-term hypoxia mRNA


title: Liver_15M_1

description:
P1_B10_JV_L_15M_ZT28-29874935
technical_replicate1
sequencing_replicate1

value: bisulfite


title: P23,CD-1,GC-adult-1


title: P23,CD-1,Astro-juv-2

value: Astro


title: P23,CD-1,GC-juv-1


title: Normoxia mRNA


title: P23,CD-1,GABA-1


title: P23,CD-1,Ependymal-1


title: P23,CD-1,Cajal-Retzius-1


title: P23,CD-1,CA3-Pyr-1


title: P19,C57Bl/6,NFOL-1


title: P19,C57Bl/6,MiCajal-Retziusoglia-1


title: P23,CD-1,Astro-juv-1


title: P23,CD-1,Astro-adult-1


title: P19,C57Bl/6,MOL-1


title: P19,C57Bl/6,Immature-GC-1


title: P19,C57Bl/6,GC-juv-4


title: P19,C57Bl/6,GC-juv-3


title: P19,C57Bl/6,nIPC-1

value: nIPC


title: P19,C57Bl/6,VLMC-1

value: VLMC


title: A. thaliana not inoculated rep 1

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

data_processing:
HiSeq control software 2.2.38, RTA 1.18.61.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: TAIR10 (A. thaliana) - version 3 (S. lycopersicum)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 4-week old plants mature leaves

growth_protocol: Plants were grown in Jiffy pots under controlled conditions at 22°C, with a 9 hour light period and a light intensity of 120 µmol/m2/s 4 weeks prior to infection

extract_protocol:
The edge of developed necrotic lesions (15 to 30 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mature leaves of 4 week-old Arabidopsis thaliana and Solanum lycopersicum (Heinz genotype) were inoculated or not with the S. sclerotiorum strain 1980. An agar plug (5mm in diameter) containing actively growing S. sclerotiorum mycelium was placed on the adaxial surface of leaves and plants were maintained at 80% humidity

tag: genotype/variation

value: Col-0 ecotype

tag: treatment

value: healthy


title: P19,C57Bl/6,PVM-1

value: PVM


title: P19,C57Bl/6,nIPC-perin-1


title: P19,C57Bl/6,RGL-1


title: x01_Col_03_AvrRpt2_20h_rep03

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

description:
M366
This sample was not part of the publication analysis involving 348 samples.

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each of 18 samples (ReadCountTable_M349_366.txt).

source_name: Fully-expanded leaves of 30 to 33 day-old plants

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
Total RNAs were extracted using TRIzol (Invitrogen), followed by Dnase I (Roche) treatment.
RNA libraries were prepared from 1 μg of total RNA. Poly A enrichment and library preparation were performed with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Fully-expanded leaves were syringe-infiltrated with mock (water) or bacterial suspensions at the OD600 of 0.001.

tag: genotype

value: Pto AvrRpt2

tag: replicate

tag: time

value: 20 hpi

value: Leaves


title: x01_Col_01_mock_20h_rep03

description:
M364
This sample was not part of the publication analysis involving 348 samples.

value: Mock


title: x01_Col_02_EV_20h_rep03

description:
M365
This sample was not part of the publication analysis involving 348 samples.

value: Pto DC3000


title: P19,C57Bl/6,GC-juv-2

value: GC


title: P23,CD-1,GC-juv-5


title: P19,C57Bl/6,OPC-1

value: OPC


title: x01_Col_03_AvrRpt2_20h_rep02

description:
M363
This sample was not part of the publication analysis involving 348 samples.


title: P19,C57Bl/6,Neuroblast-1

value: Neuroblast


title: x01_Col_02_EV_20h_rep01

description:
M359
This sample was not part of the publication analysis involving 348 samples.


title: A. thaliana not inoculated rep 3


title: A. thaliana not inoculated rep 2


title: P23,CD-1,Endothelial-1

value: Endothelial


title: P19,C57Bl/6,GC-juv-1


title: P19,C57Bl/6,Cajal-Retzius-1

value: Cajal


title: x01_Col_03_AvrRpt2_02h_rep03

description:
M357
This sample was not part of the publication analysis involving 348 samples.

value: 2 hpi


title: x01_Col_02_EV_20h_rep02

description:
M362
This sample was not part of the publication analysis involving 348 samples.


title: x01_Col_01_mock_20h_rep02

description:
M361
This sample was not part of the publication analysis involving 348 samples.


title: P19,C57Bl/6,CA3-Pyr-1


title: x01_Col_03_AvrRpt2_20h_rep01

description:
M360
This sample was not part of the publication analysis involving 348 samples.


title: P19,C57Bl/6,GABA-1

value: GABA


title: x01_Col_01_mock_20h_rep01

description:
M358
This sample was not part of the publication analysis involving 348 samples.


title: P19,C57Bl/6,Astro-adult-1

value: Astro


title: x01_Col_03_AvrRpt2_02h_rep02

description:
M354
This sample was not part of the publication analysis involving 348 samples.


title: x01_Col_02_EV_02h_rep03

description:
M356
This sample was not part of the publication analysis involving 348 samples.


title: P19,C57Bl/6,Endothelial-1


title: P19,C57Bl/6,GC-adult-1


title: x01_Col_01_mock_02h_rep02

description:
M352
This sample was not part of the publication analysis involving 348 samples.


title: P18,CD-1,VLMC-1

value: VLMC


title: P19,C57Bl/6,Astro-juv-1


title: x01_Col_02_EV_02h_rep02

description:
M353
This sample was not part of the publication analysis involving 348 samples.


title: P18,CD-1,RGL_young-1


title: x01_Col_01_mock_02h_rep03

description:
M355
This sample was not part of the publication analysis involving 348 samples.


title: x01_Col_02_EV_02h_rep01

description:
M350
This sample was not part of the publication analysis involving 348 samples.


title: P18,CD-1,nIPC-1

value: nIPC


title: P18,CD-1,nIPC-perin-1


title: P19,C57Bl/6,Ependymal-1

value: Ependymal


title: x01_Col_03_AvrRpt2_02h_rep01

description:
M351
This sample was not part of the publication analysis involving 348 samples.


title: P18,CD-1,RGL-1

value: RGL


title: P19,C57Bl/6,GC-adult-2


title: x01_Col_01_mock_02h_rep01

description:
M349
This sample was not part of the publication analysis involving 348 samples.


title: P18,CD-1,PVM-1

value: PVM


title: x17_rr_04_AvrRpm1_04h_rep03

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each of 348 samples (ReadCountTable_M001_348.txt).

value: Pto AvrRpm1

value: 4 hpi


title: x17_rr_03_AvrRpt2_04h_rep03

value: Pto AvrRpt2

value: Leaves


title: x17_rr_04_AvrRpm1_04h_rep02


title: P18,CD-1,NFOL-1

value: NFOL


title: P18,CD-1,Neuroblast-1


title: P18,CD-1,MOL-1

value: MOL


title: x17_rr_04_AvrRpm1_04h_rep01


title: x17_rr_01_mock_04h_rep02

value: Mock


title: x17_rr_03_AvrRpt2_04h_rep02


title: P18,CD-1,Immature-GC-2

value: Immature


title: x17_rr_04_AvrRpm1_01h_rep03

value: 1 hpi


title: P18,CD-1,Immature-Pyr-1


title: P18,CD-1,Immature-Astro-1


title: x17_rr_03_AvrRpt2_04h_rep01


title: P18,CD-1,Immature-GC-1


title: P18,CD-1,GC-juv-7

value: GC


title: x17_rr_04_AvrRpm1_01h_rep02


title: P18,CD-1,GC-juv-8


title: x17_rr_03_AvrRpt2_01h_rep03


title: x17_rr_03_AvrRpt2_01h_rep02


title: x17_rr_01_mock_01h_rep03


title: P18,CD-1,GC-juv-5


title: x17_rr_01_mock_01h_rep02


title: x17_rr_01_mock_04h_rep01


title: P18,CD-1,OPC-1

value: OPC


title: x17_rr_04_AvrRpm1_01h_rep01


title: x17_rr_01_mock_04h_rep03


title: P18,CD-1,GC-juv-3


title: P18,CD-1,GC-juv-4


title: P18,CD-1,MiCajal-Retziusoglia-1

value: MiCajal


title: x17_rr_03_AvrRpt2_01h_rep01


title: x17_rr_01_mock_01h_rep01


title: P18,CD-1,GC-juv-2


title: P18,CD-1,GC-juv-6


title: P18,CD-1,GC-juv-1


title: x16_deps_04_AvrRpm1_24h_rep03

value: dde2-2 ein2-1 pad4-1 sid2-2

value: 24 hpi


title: x16_deps_04_AvrRpm1_24h_rep02


title: P18,CD-1,GC-adult-1


title: P18,CD-1,Endothelial-1

value: Endothelial


title: P18,CD-1,GABA-1

value: GABA


title: P18,CD-1,Cajal-Retzius-1

value: Cajal


title: x16_deps_04_AvrRpm1_16h_rep02

value: Pto AvrRpm1

value: 16 hpi


title: P18,CD-1,CA3-Pyr-1


title: x16_deps_04_AvrRpm1_16h_rep03


title: x16_deps_04_AvrRpm1_12h_rep03

value: 12 hpi


title: x16_deps_04_AvrRpm1_12h_rep02

value: Leaves


title: x16_deps_04_AvrRpm1_24h_rep01


title: x16_deps_04_AvrRpm1_16h_rep01


title: P18,CD-1,Astro-juv-1

value: Astro


title: P132,hGFAP-GFP,nIPC-1

value: hGFAP-GFP

value: nIPC


title: P18,CD-1,Astro-adult-1


title: x16_deps_04_AvrRpm1_12h_rep01


title: x16_deps_04_AvrRpm1_09h_rep03

value: 9 hpi


title: x16_deps_04_AvrRpm1_09h_rep02


title: P132,hGFAP-GFP,VLMC-1

value: VLMC


title: P132,hGFAP-GFP,RGL_young-1


title: x16_deps_04_AvrRpm1_09h_rep01


title: x16_deps_04_AvrRpm1_06h_rep03

value: 6 hpi


title: P132,hGFAP-GFP,PVM-1

value: PVM


title: P132,hGFAP-GFP,Neuroblast-1

value: Neuroblast


title: P132,hGFAP-GFP,RGL-1

value: RGL


title: x16_deps_04_AvrRpm1_04h_rep03

value: dde2-2 ein2-1 pad4-1 sid2-2

value: 4 hpi


title: P132,hGFAP-GFP,NFOL-1

value: NFOL


title: x16_deps_04_AvrRpm1_06h_rep01


title: x16_deps_04_AvrRpm1_04h_rep02


title: P18,CD-1,Ependymal-1

value: Ependymal


title: P132,hGFAP-GFP,MOL-1

value: MOL


title: x16_deps_04_AvrRpm1_04h_rep01

value: Pto AvrRpm1


title: x01_Col_04_AvrRpm1_24h_rep03

value: 24 hpi


title: P132,hGFAP-GFP,MiCajal-Retziusoglia-1

value: MiCajal


title: x01_Col_04_AvrRpm1_24h_rep02

value: Leaves


title: x01_Col_04_AvrRpm1_24h_rep01


title: P132,hGFAP-GFP,Immature-Pyr-1

value: hGFAP-GFP

value: Immature


title: P132,hGFAP-GFP,GC-juv-1

value: GC


title: P132,hGFAP-GFP,GC-adult-9


title: x01_Col_04_AvrRpm1_16h_rep03

value: 16 hpi


title: P132,hGFAP-GFP,GC-adult-7


title: x01_Col_04_AvrRpm1_16h_rep02


title: x01_Col_04_AvrRpm1_16h_rep01


title: P132,hGFAP-GFP,GC-adult-6


title: x01_Col_04_AvrRpm1_12h_rep02

value: 12 hpi


title: x01_Col_04_AvrRpm1_12h_rep03


title: P132,hGFAP-GFP,OPC-1

value: OPC


title: x16_deps_04_AvrRpm1_06h_rep02

value: 6 hpi


title: x01_Col_04_AvrRpm1_12h_rep01


title: x01_Col_04_AvrRpm1_09h_rep03

value: 9 hpi


title: P132,hGFAP-GFP,GC-adult-3


title: x01_Col_04_AvrRpm1_09h_rep01


title: P132,hGFAP-GFP,GC-adult-2


title: P132,hGFAP-GFP,GC-adult-11


title: P132,hGFAP-GFP,Immature-GC-1


title: x01_Col_04_AvrRpm1_06h_rep03


title: P132,hGFAP-GFP,GC-adult-10


title: x01_Col_04_AvrRpm1_06h_rep02


title: P132,hGFAP-GFP,GC-adult-1


title: P132,hGFAP-GFP,Ependymal-1


title: x01_Col_04_AvrRpm1_04h_rep03


title: x01_Col_04_AvrRpm1_06h_rep01


title: x01_Col_04_AvrRpm1_04h_rep01


title: x01_Col_04_AvrRpm1_03h_rep03

value: 3 hpi


title: P132,hGFAP-GFP,CA3-Pyr-1


title: x01_Col_04_AvrRpm1_03h_rep02


title: x01_Col_04_AvrRpm1_03h_rep01


title: P132,hGFAP-GFP,GC-adult-8


title: P132,hGFAP-GFP,Astro-juv-1

value: Astro


title: P132,hGFAP-GFP,Cajal-Retzius-1

value: Cajal


title: P132,hGFAP-GFP,Astro-adult-4


title: x01_Col_04_AvrRpm1_01h_rep03

value: 1 hpi


title: P132,hGFAP-GFP,GC-adult-4


title: x01_Col_04_AvrRpm1_09h_rep02


title: P132,hGFAP-GFP,Astro-adult-3


title: P132,hGFAP-GFP,GC-adult-5


title: P132,hGFAP-GFP,Astro-adult-2


title: x01_Col_04_AvrRpm1_01h_rep01


title: x11_ps_02_EV_04h_rep03

value: pad4-1 sid2-2

value: Pto DC3000

value: 4 hpi


title: P132,hGFAP-GFP,GABA-1

value: GABA


title: P132,hGFAP-GFP,Astro-adult-1


title: x11_ps_03_AvrRpt2_04h_rep03

value: Pto AvrRpt2

value: Leaves


title: P120,hGFAP-GFP,nIPC-perin-1

value: hGFAP-GFP

value: nIPC


title: x01_Col_04_AvrRpm1_04h_rep02

value: Pto AvrRpm1


title: P120,hGFAP-GFP,RGL-1

value: RGL


title: P120,hGFAP-GFP,nIPC-1


title: x11_ps_01_mock_04h_rep03

value: Mock


title: P132,hGFAP-GFP,Endothelial-1

value: Endothelial


title: P120,hGFAP-GFP,PVM-1

value: PVM


title: x04_pad4_03_AvrRpt2_04h_rep03


title: x04_pad4_02_EV_04h_rep03


title: P120,hGFAP-GFP,OPC-2

value: OPC


title: P120,hGFAP-GFP,OPC-1


title: x04_pad4_01_mock_04h_rep03


title: x11_ps_03_AvrRpt2_04h_rep02


title: P120,hGFAP-GFP,Neuroblast-1

value: Neuroblast


title: P120,hGFAP-GFP,MiCajal-Retziusoglia-1

value: MiCajal


title: x11_ps_02_EV_04h_rep02


title: P120,hGFAP-GFP,NFOL-1

value: NFOL


title: x04_pad4_03_AvrRpt2_04h_rep02


title: P120,hGFAP-GFP,MOL-1

value: MOL


title: x11_ps_01_mock_04h_rep02

value: pad4-1 sid2-2


title: P120,hGFAP-GFP,Immature-GC-1

value: Immature


title: x01_Col_04_AvrRpm1_01h_rep02

value: 1 hpi


title: x04_pad4_02_EV_04h_rep02

value: Pto DC3000

value: 4 hpi


title: x04_pad4_01_mock_04h_rep02

value: Leaves


title: P120,hGFAP-GFP,Immature-GABA-1

value: hGFAP-GFP


title: x11_ps_03_AvrRpt2_04h_rep01

value: Pto AvrRpt2


title: x11_ps_02_EV_04h_rep01


title: P120,hGFAP-GFP,GABA-1

value: GABA


title: P120,hGFAP-GFP,GC-juv-1

value: GC


title: P120,hGFAP-GFP,GC-adult-1


title: P120,hGFAP-GFP,Ependymal-1

value: Ependymal


title: x04_pad4_02_EV_04h_rep01


title: x11_ps_01_mock_04h_rep01

value: Mock


title: x04_pad4_03_AvrRpt2_04h_rep01


title: P120,hGFAP-GFP,Endothelial-1

value: Endothelial


title: x04_pad4_01_mock_04h_rep01


title: P120,hGFAP-GFP,Cajal-Retzius-1

value: Cajal


title: P120,hGFAP-GFP,CA3-Pyr-1


title: P120,hGFAP-GFP,Astro-adult-2

value: Astro


title: P120,hGFAP-GFP,Astro-juv-1


title: P120,hGFAP-GFP,Astro-adult-1


title: P0,CD-1,nIPC-perin-1

value: nIPC


title: x04_pad4_03_AvrRpt2_16h_rep03

value: 16 hpi


title: x04_pad4_01_mock_16h_rep03


title: P0,CD-1,nIPC-1


title: x11_ps_01_mock_16h_rep03

value: pad4-1 sid2-2


title: x04_pad4_02_EV_16h_rep03


title: P0,CD-1,VLMC-1

value: VLMC


title: x11_ps_02_EV_16h_rep02


title: P0,CD-1,RGL_young-2


title: x11_ps_01_mock_16h_rep02


title: x04_pad4_03_AvrRpt2_16h_rep02


title: P0,CD-1,PVM-1

value: PVM


title: x04_pad4_02_EV_16h_rep02

value: Pto DC3000


title: x04_pad4_01_mock_16h_rep02


title: P0,CD-1,OPC-1

value: OPC


title: P0,CD-1,Neuroblast-2

value: Neuroblast


title: P0,CD-1,Neuroblast-3


title: x11_ps_02_EV_16h_rep03

value: Leaves


title: x11_ps_03_AvrRpt2_16h_rep03

value: Pto AvrRpt2


title: P0,CD-1,MiCajal-Retziusoglia-1

value: MiCajal


title: P0,CD-1,Neuroblast-1


title: x11_ps_03_AvrRpt2_16h_rep01


title: x11_ps_02_EV_16h_rep01


title: x11_ps_01_mock_16h_rep01


title: x11_ps_03_AvrRpt2_16h_rep02


title: P0,CD-1,Immature-Pyr-8

value: Immature


title: P0,CD-1,Immature-Pyr-9


title: x04_pad4_01_mock_16h_rep01


title: P0,CD-1,Immature-Pyr-7


title: x11_ps_03_AvrRpt2_12h_rep03

value: 12 hpi


title: P0,CD-1,Immature-Pyr-5


title: x11_ps_02_EV_12h_rep03


title: P0,CD-1,RGL_young-1


title: x11_ps_01_mock_12h_rep03

value: Mock


title: P0,CD-1,Immature-Pyr-3


title: x04_pad4_02_EV_12h_rep03


title: P0,CD-1,Immature-Pyr-2


title: x04_pad4_01_mock_12h_rep03


title: P0,CD-1,Immature-Pyr-12


title: P0,CD-1,Immature-Pyr-11


title: P0,CD-1,Immature-Pyr-10


title: x11_ps_03_AvrRpt2_12h_rep02


title: x04_pad4_03_AvrRpt2_16h_rep01


title: x11_ps_01_mock_12h_rep02


title: x04_pad4_02_EV_16h_rep01


title: P0,CD-1,Immature-Pyr-1


title: x04_pad4_02_EV_12h_rep02


title: x04_pad4_03_AvrRpt2_12h_rep02


title: P0,CD-1,Immature-GC-1


title: x04_pad4_01_mock_12h_rep02


title: P0,CD-1,Immature-GC-2


title: x11_ps_03_AvrRpt2_12h_rep01


title: x11_ps_02_EV_12h_rep01


title: P0,CD-1,Immature-GC-3


title: x04_pad4_03_AvrRpt2_12h_rep03


title: P0,CD-1,Immature-GABA-2


title: P0,CD-1,Immature-Astro-1


title: x04_pad4_03_AvrRpt2_12h_rep01


title: P0,CD-1,Immature-GABA-3


title: x11_ps_01_mock_12h_rep01


title: P0,CD-1,Immature-GABA-1


title: x04_pad4_02_EV_12h_rep01


title: P0,CD-1,Immature-Pyr-4


title: x04_pad4_01_mock_12h_rep01


title: P0,CD-1,Ependymal-1

value: Ependymal


title: P0,CD-1,Endothelial-1

value: Endothelial


title: x11_ps_02_EV_06h_rep03

value: 6 hpi


title: E16.5,CD-1,nIPC-perin-1

value: nIPC


title: E16.5,CD-1,nIPC-1


title: E16.5,CD-1,VLMC-1


title: x11_ps_02_EV_12h_rep02


title: x04_pad4_03_AvrRpt2_06h_rep03


title: x04_pad4_02_EV_06h_rep03


title: x04_pad4_01_mock_06h_rep03


title: E16.5,CD-1,PVM-1


title: x11_ps_03_AvrRpt2_06h_rep02


title: E16.5,CD-1,OPC-1


title: x11_ps_02_EV_06h_rep02


title: x04_pad4_02_EV_06h_rep02


title: x04_pad4_03_AvrRpt2_06h_rep02


title: E16.5,CD-1,Immature-Pyr-8


title: E16.5,CD-1,MiCajal-Retziusoglia-1


title: E16.5,CD-1,Immature-Pyr-7


title: x11_ps_01_mock_06h_rep02


title: x04_pad4_01_mock_06h_rep02


title: E16.5,CD-1,Neuroblast-1


title: x11_ps_03_AvrRpt2_06h_rep01


title: x11_ps_03_AvrRpt2_06h_rep03


title: x11_ps_02_EV_06h_rep01


title: E16.5,CD-1,Immature-Pyr-6


title: x11_ps_01_mock_06h_rep01


title: P0,CD-1,Cajal-Retzius-1

value: Cajal


title: E16.5,CD-1,Immature-Pyr-5


title: E16.5,CD-1,Immature-Pyr-4


title: x04_pad4_03_AvrRpt2_06h_rep01


title: E16.5,CD-1,RGL_young-1


title: E16.5,CD-1,Immature-Pyr-2


title: E16.5,CD-1,Neuroblast-2


title: x04_pad4_02_EV_06h_rep01


title: x04_pad4_01_mock_06h_rep01


title: E16.5,CD-1,Immature-Pyr-1


title: x16_deps_03_AvrRpt2_16h_rep03

value: dde2-2 ein2-1 pad4-1 sid2-2

value: 16 hpi


title: E16.5,CD-1,Immature-GC-1


title: x16_deps_02_EV_16h_rep03


title: E16.5,CD-1,Ependymal-1


title: x16_deps_03_AvrRpt2_16h_rep02


title: E16.5,CD-1,Endothelial-1


title: x16_deps_01_mock_16h_rep02


title: E16.5,CD-1,Cajal-Retzius-1


title: rel-, mock

city: Cambridge

first: Anna

middle: M

last: Puszynska

state: MA

address: 455 Main street

country: USA

institute: Whitehead Institute for Biomedical Research

description: Stalling index, column O

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Reads were counted, extended by 50 bp (the sequence tag length), and normalized between samples. The RNA polymerase pausing index was calculated as the ratio between the maximum enrichment at the start of the transcription unit and the mean RNA polymerase enrichment within the open reading frame (300 bp from the start of the transcription unit to the end of it). Transcription units with a proximally paused polymerase were defined as transcription units characterized by the RNA polymerase pausing index greater than 3. Transcription units used in the analysis are at least 1000 bp long and include operons listed in OperomeDB database (Chetal and Janga, 2015) and single genes (Vijayan et al., 2011).
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with  polymerase pausing index values

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: cells

growth_protocol: Cell cultures were grown in tissue culture flasks in 12 h light/ 12 h dark conditions  in BG11 medium at 30 °C. During light periods cells were under illumination with cool fluorescent light at 40 μE m-2 s-1 (μmoles photons m-2 s-1).

extract_protocol:
Samples were resuspended in 500 μl phosphate-buffered saline and pelleted for 5 min at 3,000 x g. The pellets were flash frozen and stored at -80 °C. Samples were thawed and resuspended in 270 μl of lysis buffer (50 mM HEPES-NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1x Roche Complete EDTA-free Protease Inhibitors). Cells were disrupted by 10 cycles of 30 sec bead-beating at 4 °C with 0.1 mm glass beads with periodic cooling on ice. Chromatin was sheared by sonication to a median length of ~300 bp. Lysates were then clarified by two rounds of centrifugation at 21,000 x g for 15 min at 4 °C. Protein concentration was determined by BCA assay (Pierce Biotechnology) with a standard curve prepared with Bovine Serum Albumin. 750 μg of lysate from each time point (prepared in 500 ul of the lysis buffer) were mixed with 18 μg of purified anti-E. coli RNA polymerase β monoclonal antibody (BioLegend). Samples were incubated overnight at 4 °C with continuous rotation. 70 μl of 1:1 mix of rProtein A Sepharose and Protein G Sepharose Fast Flow beads (GE Healthcare; 50% slurry in the lysis buffer) were added to each sample.  After 2 h of incubation, beads were isolated by centrifugation for 1 min at 1000 g, washed twice with lysis buffer, once with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.1% sodium deoxycholate) and once with TE pH 7.5 (10 mM Tris-HCl pH 7.5, 1 mM EDTA). Elution of protein-DNA complexes was performed with 250 μl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) for 1 h at 65 °C. Crosslinks were reversed by incubation of samples at 65 °C for 12 h. Proteins were digested with proteinase K for 2 h at 37 °C, and samples were extracted with phenol/chloroform/isoamyl alcohol. Nucleic acids were precipitated with ethanol overnight and RNA was digested in 50 μl of TE containing 20 ng/μl of DNase-free RNase (Fermentas). Samples were extracted again with phenol/chloroform/isoamyl alcohol, precipitated with ethanol and resuspended in 50 μl 10 mM Tris-HCl pH 8.0.
Libraries for Illumina sequencing of ChIP DNA were prepared following a protocol developed by Ethan Ford (http://ethanomics.files.wordpress.com) with modifications as described in Markson et al., 2013.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment. After entrainment cells continued to be grown under light dark conditions and at the respective time points fixed with 1% formaldehyde for 15 min and quenched with 125 mM glycine for 5 min.

value: rel-

tag: time point

value: combined

tag: chip antibody

value: Mouse IgG whole molecule (Jackson ImmunoResearch, cat. 015-000-003 , Lot 111338)


title: x11_ps_01_mock_06h_rep03

value: pad4-1 sid2-2


title: x16_deps_02_EV_16h_rep01

value: Pto DC3000

value: Leaves


title: E16.5,CD-1,Immature-Pyr-3

tag: cell cluster


title: x16_deps_01_mock_16h_rep03


title: rel-, 12h dark

description: Stalling index, column L

value: darkness, 12 h

value: anti-E. coli RNA polymerase β monoclonal antibody (BioLegend, cat. 663905, Lot B194049)


title: x16_deps_03_AvrRpt2_12h_rep03

value: Pto AvrRpt2

value: 12 hpi


title: x16_deps_01_mock_16h_rep01

value: Mock


title: rel-, dawn

description: Stalling index, column M

value: darkness, dawn


title: rel-, 8h dark

description: Stalling index, column K

value: darkness, 8 h


title: x16_deps_03_AvrRpt2_16h_rep01


title: x16_deps_02_EV_12h_rep03


title: x16_deps_03_AvrRpt2_12h_rep02


title: E16.5,CD-1,Immature-GABA-1

tag: strain

value: Immature


title: rel-, dusk

description: Stalling index, column I

value: dusk


title: wild type, dawn

description: Stalling index, column H

value: wild type


title: wild type, 8h dark

description: Stalling index, column F


title: x16_deps_01_mock_12h_rep02

value: dde2-2 ein2-1 pad4-1 sid2-2


title: x16_deps_02_EV_16h_rep02

value: 16 hpi


title: wild type, 12h dark

description: Stalling index, column G


title: rel-, 4h dark

description: Stalling index, column J

value: rel-

value: darkness, 4 h


title: x16_deps_02_EV_12h_rep02


title: x16_deps_01_mock_12h_rep03


title: wild type, 4h dark

description: Stalling index, column E


title: x16_deps_03_AvrRpt2_12h_rep01


title: x16_deps_02_EV_12h_rep01


title: x16_deps_01_mock_12h_rep01


title: x16_deps_03_AvrRpt2_06h_rep03

value: 6 hpi


title: x16_deps_02_EV_06h_rep03

value: Pto DC3000


title: rel- relAE335Q replicate 2_dark_4 h

description: processed data: Expression.xls, column AJ

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Gene expression quantification: the alignment output from Bowtie was analyzed in Matlab using custom code as described in Markson et al., 2013. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene (Markson et al., 2013).
Gene expression normalization: We performed normalization with external RNA standards.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with  gene expression values (normalized with external RNA standards and cell number used in the experiment)

source_name: rel- relAE335Q_dark_4 h

extract_protocol:
Frozen cells were resuspended in the AE buffer with external RNA standards and lysed at 65° C with phenol/SDS by vortexing. Total RNA was extracted with phenol/chloroform followed by isopropanol precipitation. Then, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. To assess integrity total RNA was analyzed on an agarose gel.
Ribosomal RNA was depleted from total RNA using the Ribo-Zero rRNA removal Gram-negative bacteria kit (Illumina), following the protocol provided by the manufacturer. RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) from rRNA-depleted RNA. Samples were multiplexed and sequenced on an Illumina HiSeq 2000 platform by the Bauer Core Facility at the Harvard FAS Center for Systems Biology.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment. After entrainment cells continued to be grown under light dark conditions and were harvested at dusk and during darkness.

value: rel- relAE335Q


title: x16_deps_01_mock_06h_rep03

value: Leaves


title: rel- relAE335Q replicate 2_dark_12 h

description: processed data: Expression.xls, column AL.

source_name: rel- relAE335Q_dark_12 h

value: darkness, 12 h


title: rel- relAE335Q replicate 2_dark_2 h

description: processed data: Expression.xls, column AI

source_name: rel- relAE335Q_dark_2 h

value: darkness, 2 h


title: x16_deps_03_AvrRpt2_06h_rep02

value: Pto AvrRpt2


title: x16_deps_01_mock_06h_rep02

value: Mock


title: wild type, mock

description: Stalling index, column N

value: combined

value: Mouse IgG whole molecule (Jackson ImmunoResearch, cat. 015-000-003 , Lot 111338)


title: rel- relAE335Q replicate 2_dark_1 h

description: processed data: Expression.xls, column AH

source_name: rel- relAE335Q_dark_1 h

value: darkness, 1 h


title: x16_deps_02_EV_06h_rep02


title: rel- relAE335Q replicate 2_dark_30 min

description: processed data: Expression.xls, column AG

source_name: rel- relAE335Q_dark_30 min

value: darkness, 30 min


title: x16_deps_03_AvrRpt2_06h_rep01


title: rel- relAE335Q replicate 2_dark_5 min

description: processed data: Expression.xls, column AE

source_name: rel- relAE335Q_dark_5 min

value: darkness, 5 min


title: x16_deps_01_mock_06h_rep01

value: dde2-2 ein2-1 pad4-1 sid2-2


title: rel- relA+ replicate 2_dark_12 h

description: processed data: Expression.xls, column AC

source_name: rel- relA+_dark_12 h

value: rel- relA+


title: x16_deps_03_AvrRpt2_04h_rep03

value: 4 hpi


title: x16_deps_02_EV_06h_rep01


title: rel- relA+ replicate 2_dark_8 h

description: processed data: Expression.xls, column AB

source_name: rel- relA+_dark_8 h

value: darkness, 8 h


title: rel- relAE335Q replicate 2_dark_15 min

description: processed data: Expression.xls, column AF

source_name: rel- relAE335Q_dark_15 min

value: darkness, 15 min


title: rel- relA+ replicate 2_dark_4 h

description: processed data: Expression.xls, column AA

source_name: rel- relA+_dark_4 h

value: darkness, 4 h


title: x05_sid2_03_AvrRpt2_04h_rep03


title: x16_deps_02_EV_04h_rep03

value: Pto DC3000


title: x05_sid2_02_EV_04h_rep03

value: Leaves


title: rel- relAE335Q replicate 2_dark_8 h

description: processed data: Expression.xls, column AK

source_name: rel- relAE335Q_dark_8 h

value: rel- relAE335Q


title: x16_deps_01_mock_04h_rep03


title: rel- relA+ replicate 2_dark_1 h

description: processed data: Expression.xls, column Y

source_name: rel- relA+_dark_1 h


title: rel- relA+ replicate 2_dark_30 min

description: processed data: Expression.xls, column X

source_name: rel- relA+_dark_30 min


title: x16_deps_03_AvrRpt2_04h_rep02


title: wild type, dusk

description: Stalling index, column D

value: wild type

value: dusk

value: anti-E. coli RNA polymerase β monoclonal antibody (BioLegend, cat. 663905, Lot B194049)


title: rel- relA+ replicate 2_dark_5 min

description: processed data: Expression.xls, column V

source_name: rel- relA+_dark_5 min


title: x05_sid2_03_AvrRpt2_04h_rep02

value: Pto AvrRpt2


title: rel- relA+ replicate 2_dark_15 min

description: processed data: Expression.xls, column W

source_name: rel- relA+_dark_15 min


title: rel- relA+ replicate 2_dusk

description: processed data: Expression.xls, column U

source_name: rel- relA+_dusk


title: rel- relAE335Q replicate 1_dark_12 h

description: processed data: Expression.xls, column T

value: darkness, 12 h


title: rel- relAE335Q replicate 2_dusk

description: processed data: Expression.xls, column AD

source_name: rel- relAE335Q_dusk


title: x05_sid2_02_EV_04h_rep02

source_name: Fully-expanded leaves of 30 to 33 day-old plants


title: rel- relAE335Q replicate 1_dark_8 h

description: processed data: Expression.xls, column S


title: x16_deps_01_mock_04h_rep02

value: Mock


title: x16_deps_02_EV_04h_rep02


title: x05_sid2_01_mock_04h_rep02


title: rel- relA+ replicate 2_dark_2 h

description: processed data: Expression.xls, column Z

source_name: rel- relA+_dark_2 h

value: darkness, 2 h


title: rel- relAE335Q replicate 1_dark_4 h

description: processed data: Expression.xls, column R

source_name: rel- relAE335Q_dark_4 h


title: rel- relAE335Q replicate 1_dark_2 h

description: processed data: Expression.xls, column Q

source_name: rel- relAE335Q_dark_2 h


title: rel- relAE335Q replicate 1_dark_30 min

description: processed data: Expression.xls, column O

source_name: rel- relAE335Q_dark_30 min

value: darkness, 30 min


title: rel- relAE335Q replicate 1_dark_1 h

description: processed data: Expression.xls, column P

source_name: rel- relAE335Q_dark_1 h

value: darkness, 1 h


title: x05_sid2_03_AvrRpt2_04h_rep01


title: x16_deps_02_EV_04h_rep01

value: dde2-2 ein2-1 pad4-1 sid2-2


title: rel- relAE335Q replicate 1_dark_15 min

description: processed data: Expression.xls, column N


title: x16_deps_03_AvrRpt2_04h_rep01

value: 4 hpi


title: x05_sid2_02_EV_04h_rep01


title: x16_deps_01_mock_04h_rep01


title: x11_ps_03_AvrRpt2_24h_rep03

value: pad4-1 sid2-2

value: 24 hpi


title: x05_sid2_01_mock_04h_rep01


title: rel- relAE335Q replicate 1_dusk

description: processed data: Expression.xls, column L


title: rel- relAE335Q replicate 1_dark_5 min

description: processed data: Expression.xls, column M

source_name: rel- relAE335Q_dark_5 min

value: darkness, 5 min


title: rel- relA+ replicate 1_dark_12 h

description: processed data: Expression.xls, column K

source_name: rel- relA+_dark_12 h

value: rel- relA+


title: rel- relA+ replicate 1_dark_4 h

description: processed data: Expression.xls, column I

value: darkness, 4 h


title: rel- relA+ replicate 1_dark_2 h

description: processed data: Expression.xls, column H


title: rel- relA+ replicate 1_dark_8 h

description: processed data: Expression.xls, column J

source_name: rel- relA+_dark_8 h

value: darkness, 8 h


title: x05_sid2_01_mock_04h_rep03

value: Leaves


title: rel- relA+ replicate 1_dark_1 h

description: processed data: Expression.xls, column G


title: x11_ps_02_EV_24h_rep03

value: Pto DC3000


title: x11_ps_01_mock_24h_rep03


title: x04_pad4_01_mock_24h_rep03


title: x04_pad4_03_AvrRpt2_24h_rep03


title: rel- relA+ replicate 1_dark_30 min

description: processed data: Expression.xls, column F


title: rel- relA+ replicate 1_dark_15 min

description: processed data: Expression.xls, column E

value: darkness, 15 min


title: x11_ps_03_AvrRpt2_24h_rep02

value: Pto AvrRpt2


title: rel- replicate 2, dark, 12 h (light dark conditions)

description: Expression, column AL.

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Gene expression quantification: the alignment output from Bowtie was analyzed in Matlab using custom code as described in Markson et al., 2013. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene (Markson et al., 2013).
Gene expression normalization: We performed normalization with external RNA standards.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with  gene expression values (normalized with external RNA standards)

source_name: cells

value: rel- replicate 2

value: darkness, 12 h


title: rel- replicate 2, dark, 8 h (light dark conditions)

description: Expression, column AK


title: rel- relA+ replicate 1_dusk

description: processed data: Expression.xls, column C

value: dusk


title: rel- relA+ replicate 1_dark_5 min

description: processed data: Expression.xls, column D


title: x11_ps_02_EV_24h_rep02


title: x11_ps_01_mock_24h_rep02

value: Mock


title: rel- replicate 2, dark, 4 h (light dark conditions)

description: Expression, column AJ


title: x04_pad4_03_AvrRpt2_24h_rep02


title: x04_pad4_02_EV_24h_rep03


title: x04_pad4_01_mock_24h_rep02


title: rel- replicate 2, dark, 1 h (light dark conditions)

description: Expression, column AH

value: darkness, 1 h


title: x04_pad4_03_AvrRpt2_24h_rep01


title: x11_ps_02_EV_24h_rep01


title: rel- replicate 2, dark, 15 min (light dark conditions)

description: Expression, column AF


title: rel- replicate 2, dusk (light dark conditions)

description: Expression, column AD


title: x04_pad4_02_EV_24h_rep01


title: rel- replicate 2, dark, 30 min (light dark conditions)

description: Expression, column AG

value: darkness, 30 min


title: wild type replicate 2, dark, 8 h (light dark conditions)

description: Expression, column AB

value: wild type replicate 2


title: x11_ps_02_EV_09h_rep03

value: pad4-1 sid2-2

value: 9 hpi


title: x11_ps_03_AvrRpt2_09h_rep03


title: x11_ps_01_mock_24h_rep01

value: 24 hpi


title: wild type replicate 2, dark, 4 h (light dark conditions)

description: Expression, column AA


title: wild type replicate 2, dark, 12 h (light dark conditions)

description: Expression, column AC


title: x11_ps_01_mock_09h_rep03


title: x04_pad4_03_AvrRpt2_09h_rep03


title: wild type replicate 2, dark, 1 h (light dark conditions)

description: Expression, column Y


title: wild type replicate 2, dark, 2 h (light dark conditions)

description: Expression, column Z

value: darkness, 2 h


title: x04_pad4_02_EV_24h_rep02


title: x04_pad4_02_EV_09h_rep03


title: x04_pad4_01_mock_09h_rep03


title: x11_ps_03_AvrRpt2_09h_rep02


title: wild type replicate 2, dark, 30 min (light dark conditions)

description: Expression, column X


title: wild type replicate 2, dark, 15 min (light dark conditions)

description: Expression, column W


title: x11_ps_03_AvrRpt2_24h_rep01


title: x04_pad4_01_mock_24h_rep01


title: wild type replicate 2, dark, 5 min (light dark conditions)

description: Expression, column V

value: darkness, 5 min


title: rel- replicate 1, dark, 12 h (light dark conditions)

description: Expression, column T

value: rel- replicate 1


title: x04_pad4_03_AvrRpt2_09h_rep02

value: Leaves


title: rel- replicate 1, dark, 8 h (light dark conditions)

description: Expression, column S

value: darkness, 8 h


title: x04_pad4_02_EV_09h_rep02

value: Pto DC3000


title: rel- replicate 1, dark, 4 h (light dark conditions)

description: Expression, column R

value: darkness, 4 h


title: wild type replicate 2, dusk (light dark conditions)

description: Expression, column U


title: rel- replicate 1, dark, 2 h (light dark conditions)

description: Expression, column Q


title: x11_ps_03_AvrRpt2_09h_rep01

value: Pto AvrRpt2


title: x11_ps_02_EV_09h_rep01


title: rel- replicate 1, dark, 30 min (light dark conditions)

description: Expression, column O


title: rel- replicate 1, dark, 1 h (light dark conditions)

description: Expression, column P


title: x04_pad4_02_EV_09h_rep01


title: rel- replicate 1, dark, 15 min (light dark conditions)

description: Expression, column N

value: darkness, 15 min


title: rel- replicate 1, dusk (light dark conditions)

description: Expression, column L

value: dusk


title: x16_deps_03_AvrRpt2_24h_rep03

value: dde2-2 ein2-1 pad4-1 sid2-2


title: wild type replicate 1, dark, 12 h (light dark conditions)

description: Expression, column K

value: wild type replicate 1

value: darkness, 12 h


title: x04_pad4_01_mock_09h_rep01

value: Mock


title: rel- replicate 2, dark, 2 h (light dark conditions)

description: Expression, column AI

value: rel- replicate 2


title: wild type replicate 1, dark, 8 h (light dark conditions)

description: Expression, column J


title: x05_sid2_03_AvrRpt2_24h_rep03


title: x11_ps_02_EV_09h_rep02

value: pad4-1 sid2-2

value: 9 hpi


title: wild type replicate 1, dark, 4 h (light dark conditions)

description: Expression, column I


title: x01_Col_03_AvrRpt2_24h_rep03

value: 24 hpi


title: wild type replicate 1, dark, 2 h (light dark conditions)

description: Expression, column H

value: darkness, 2 h


title: wild type replicate 1, dark, 1 h (light dark conditions)

description: Expression, column G

value: darkness, 1 h


title: x16_deps_02_EV_24h_rep03

value: Leaves


title: rel- replicate 2, dark, 5 min (light dark conditions)

description: Expression, column AE

value: darkness, 5 min


title: x05_sid2_02_EV_24h_rep03

value: Pto DC3000


title: x11_ps_01_mock_09h_rep01


title: x01_Col_02_EV_24h_rep03


title: wild type replicate 1, dark, 30 min (light dark conditions)

description: Expression, column F

value: darkness, 30 min


title: wild type replicate 1, dark, 15 min (light dark conditions)

description: Expression, column E


title: wild type replicate 1, dusk (light dark conditions)

description: Expression, column C


title: x16_deps_01_mock_24h_rep03


title: rel- replicate 1, dark, 5 min (light dark conditions)

description: Expression, column M

value: rel- replicate 1


title: x04_pad4_03_AvrRpt2_09h_rep01

value: Pto AvrRpt2


title: x05_sid2_01_mock_24h_rep03


title: wild type + relAE335Q time = 1 h

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Gene expression quantification: the alignment output from Bowtie was analyzed in Matlab using custom code as described in Markson et al., 2013. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene (Markson et al., 2013).
Gene expression normalization: We performed RPM normalization.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with  gene expression values (RPM normalized)

growth_protocol: Cell cultures were grown in tissue culture flasks under illumination with cool fluorescent light at 40 μE m-2 s-1 (μmoles photons m-2 s-1) in BG11 medium at 30 °C.

extract_protocol:
Frozen cells were resuspended in the AE buffer and lysed at 65° C with phenol/SDS by vortexing. Total RNA was extracted with phenol/chloroform followed by isopropanol precipitation. Then, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. To assess integrity total RNA was analyzed on an agarose gel.
Ribosomal RNA was depleted from total RNA using the Ribo-Zero rRNA removal Gram-negative bacteria kit (Illumina), following the protocol provided by the manufacturer. RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) from rRNA-depleted RNA. Samples were multiplexed and sequenced on an Illumina HiSeq 2000 platform by the Bauer Core Facility at the Harvard FAS Center for Systems Biology.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment. Cells were released into constant light, induced with 1.6 mM theophylline at subjective dusk (CT = 12 h) and harvested by filtering and freezing in liquid-nitrogen at time = 0, 30 min and 1h after induction; and stored in -80º C.

value: wild type + relAE335Q

value: 1 h


title: wild type replicate 1, dark, 5 min (light dark conditions)

description: Expression, column D

value: wild type replicate 1


title: x16_deps_03_AvrRpt2_24h_rep02

value: dde2-2 ein2-1 pad4-1 sid2-2


title: x01_Col_01_mock_24h_rep03

value: Mock


title: wild type + relAE335Q time = 0

value: 0 (pre-induction)


title: x05_sid2_03_AvrRpt2_24h_rep02


title: wild type + relAE335Q time = 30 min

value: 30 min


title: x16_deps_02_EV_24h_rep02


title: x01_Col_03_AvrRpt2_24h_rep02


title: wild type + relA+ time = 1 h

value: wild type + relA+


title: x11_ps_01_mock_09h_rep02

value: pad4-1 sid2-2

value: 9 hpi


title: wild type + relA+ time = 30 min


title: x05_sid2_02_EV_24h_rep02

value: 24 hpi


title: wild type + relA+ time = 0


title: x01_Col_02_EV_24h_rep02

value: Leaves


title: x05_sid2_01_mock_24h_rep02


title: x01_Col_01_mock_24h_rep02


title: rel- + relAE335Q replicate 1 dawn

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Gene expression quantification: the alignment output from Bowtie was analyzed in Matlab using custom code as described in Markson et al., 2013. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene (Markson et al., 2013).
Gene expression normalization: We performed normalization using the external RNA standards added during extraction
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with  gene expression values (normalized with external RNA standards)

extract_protocol:
Extraction was performed with external RNA standards for normalization. Briefly, frozen cells were resuspended in the buffer containing external RNA standards and lysed at 65° C with phenol/SDS by vortexing. Total RNA was extracted with phenol/chloroform followed by isopropanol precipitation. Then, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. To assess integrity total RNA was analyzed on an agarose gel.
Ribosomal RNA was depleted from total RNA using the Ribo-Zero rRNA removal Gram-negative bacteria kit (Illumina), following the protocol provided by the manufacturer. RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) from rRNA-depleted RNA. Samples were multiplexed and sequenced on an Illumina HiSeq 2000 platform by the Bauer Core Facility at the Harvard FAS Center for Systems Biology.

treatment_protocol: Cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment. Cells were released into constant light and harvested by filtering and freezing in liquid-nitrogen at subjective dawn and subjective dusk, and stored in -80º C.

value: rel- + relAE335Q

value: subjective dawn (CT=0)


title: rel- + relAE335Q replicate 2 dawn


title: rel- + relAE335Q replicate 2 dusk

value: subjective dusk (CT=12h)


title: x05_sid2_03_AvrRpt2_24h_rep01


title: x16_deps_02_EV_24h_rep01

value: Pto DC3000


title: x01_Col_03_AvrRpt2_24h_rep01

value: Pto AvrRpt2


title: rel- + relA+ replicate 1 dusk

value: rel- + relA+


title: rel- + relA+ replicate 1 dawn


title: rel- + relA+ replicate 2 dusk


title: rel- + relAE335Q replicate 1 dusk


title: rel- replicate 1 dusk

value: rel-


title: x01_Col_02_EV_24h_rep01


title: x16_deps_01_mock_24h_rep01


title: x05_sid2_02_EV_24h_rep01


title: rel- + relA+ replicate 2 dawn


title: rel- replicate 2 dusk


title: x05_sid2_01_mock_24h_rep01


title: x01_Col_01_mock_24h_rep01


title: wild type replicate 2 dusk

value: wild type


title: wild type replicate 1 dusk


title: x16_deps_01_mock_24h_rep02

value: dde2-2 ein2-1 pad4-1 sid2-2


title: x05_sid2_03_AvrRpt2_16h_rep03

value: 16 hpi


title: x16_deps_03_AvrRpt2_24h_rep01


title: rel- replicate 2 dawn


title: x01_Col_03_AvrRpt2_16h_rep03


title: wild type replicate 2 dawn


title: x05_sid2_02_EV_16h_rep03


title: x01_Col_02_EV_16h_rep03


title: x01_Col_03_AvrRpt2_16h_rep02


title: x05_sid2_01_mock_16h_rep03

value: Mock


title: x05_sid2_01_mock_16h_rep02


title: x01_Col_02_EV_16h_rep02


title: x04_pad4_01_mock_09h_rep02


title: embryo_A-_8h

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description:
total mRNA of MPRA reporters
processed data file: seq1022.00A.txt

data_processing:
Library strategy: UTR-Seq
data (160nt reads) was filtered to retain only sequences that contained both terminal adapter sequences (with up to 10 mismatches) and an insert of 90nt or longer.
data (100nt reads) was filtered to retain only sequences that contained the 5’ terminal adapter sequence (with up to 10 mismatches) and an insert of 62nt or longer.
Bowtie2 was used to align retained reads to a reference set of all 90,000 synthetic oligonucleotide sequences
The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample.
A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2-fold increments (highest 50fg, lowest 3.125fg), and the resulting linear transformation was used to normalize UMI counts.
Genome_build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record.
Supplementary_files_format_and_content: tab delimited files of normalized mRNA levels

organism: Danio rerio

source_name: zebrafish embryos

growth_protocol: Fertilized zebrafish eggs or oocytes were collected at 28C, and kept in culture medium (5.03mM NaCl, 0.17mM KCl, 0.33mM CaCl2, 0.33mM MgSo4, 0.1% Methylene blue).  A total of 20-40 injected embryos/oocytes were randomly collected per sample after ensuring that all embryos were at the same expected developmental stage.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen), after adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step.
In the first step, total-RNA was reverse-transcribed with Maxima RT (Thermo Fisher) and a gene-specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step, resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors

treatment_protocol: Embryos/oocytes were removed from their chorion and injected with 50-80pg of reporter mRNAs at the one-cell stage.

tag: developmental stage

value: embryo


title: embryo_A-_10h

tag: tissue


title: x05_sid2_03_AvrRpt2_16h_rep01


title: x01_Col_01_mock_16h_rep03


title: embryo_A-_6h


title: x05_sid2_02_EV_16h_rep02


title: x01_Col_01_mock_16h_rep02


title: embryo_A-_7h


title: embryo_A-_5h


title: x01_Col_03_AvrRpt2_16h_rep01


title: rel- replicate 1 dawn


title: x05_sid2_02_EV_16h_rep01


title: x01_Col_02_EV_16h_rep01


title: x05_sid2_01_mock_16h_rep01


title: embryo_A-_2h


title: wild type replicate 1 dawn


title: embryo_A-_1h


title: x05_sid2_03_AvrRpt2_16h_rep02


title: x01_Col_01_mock_16h_rep01


title: embryo_A+_10h

description:
total mRNA of MPRA reporters
processed data file: seq1022.40A.txt


title: embryo_A-_uninjected


title: x01_Col_03_AvrRpt2_12h_rep03

value: 12 hpi


title: embryo_A+_8h


title: x01_Col_02_EV_12h_rep03


title: x05_sid2_02_EV_12h_rep03


title: embryo_A+_4h


title: embryo_A+_3h


title: embryo_A+_6h


title: x01_Col_01_mock_12h_rep03


title: x05_sid2_01_mock_12h_rep03


title: embryo_A+_7h


title: embryo_A+_5h


title: embryo_A-_4h


title: x05_sid2_03_AvrRpt2_12h_rep02


title: x05_sid2_02_EV_12h_rep02


title: embryo_A+_2h


title: embryo_A+_1h


title: embryo_A+_uninjected


title: x05_sid2_01_mock_12h_rep02


title: x01_Col_02_EV_12h_rep02


title: Sperm_RRBS_Rep2

city: Rochester

first: Patrick

last: Murphy

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Processed data file: Sperm_RRBS_Fraction_DNAme.bw

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) in bisulfite mode using the following options: -h 120 -t 240 -b 2 -R 3
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline (version 8.8.8) was then used to generate fraction DNA methylation scores for all CpGs with more than 6 reads and p-value for confidence of less than 0.01. Programs used included (in order of application): NovoalignBisulfiteParser, ParsePointDataContexts, BisStat
Useq Useq2UCSCBig was used to generate bigwigs.
Genome_build: Zv10
Supplementary_files_format_and_content: bigwigs for merged fraction DNA methylation

source_name: Sperm

growth_protocol: Standard zebrafish growth conditions.

extract_protocol:
DNA was extracted for sphere staged embryos or sperm by RIPA lysis, phenol extraction, and alcohol precipitation.
Libraries were generating using the BioO NEXTflex™ Bisulfite Library Prep protocol for Reduced Representation Bisulfite Sequencing.

treatment_protocol: Protein or embryo injections were according to standard methods

value: Sperm

value: Tu

tag: injection

tag: mutation


title: x01_Col_01_mock_12h_rep02


title: x05_sid2_03_AvrRpt2_12h_rep03


title: Sperm_RRBS_Rep1


title: x05_sid2_03_AvrRpt2_12h_rep01


title: PostZGA_RRBS_Rep1

description: Processed data file: Sphere_RRBS_Fraction_DNAme.bw

source_name: Sphere Stage

value: Sphere Stage


title: x01_Col_03_AvrRpt2_12h_rep01

value: Leaves


title: Haploid_PostZGA_RRBS_Rep2

description: Processed data file: Haploid_RRBS_Fraction_DNAme.bw

value: Gynogenetic Haploid


title: x01_Col_03_AvrRpt2_12h_rep02


title: x05_sid2_02_EV_12h_rep01


title: x01_Col_02_EV_12h_rep01


title: x01_Col_01_mock_12h_rep01


title: Haploid_PostZGA_Input_ChIP-Seq

description: Processed data file: Haploid_H2AZ_Corrected_LogFE_lambda.bw

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -r Random -k -Q 13 -o SAM
Sam files were then combined due to high correlation between technical and biological replicates.
Macs2 was then used to generate read count normalized genome wide pileup tracks and lambda tracks for precipitated samples and input. (callpeak --nomodel --extsize 150 --SPMR)
Pileup tracks were then Input corrected using the Macs2 subtract function (bdgcmp -m subtract).
Log10 Fold enrichment was then calculated for each sample comparing input corrected pileups to input lambda. (bdgcmp -m logFE).
Peaks were then called as regions with greater than 3 fold enrichment over lambda using the Macs2 bdgpeakcall function. (bdgpeakcall -c 0.477 -l 100 -g 100)
Useq Useq2UCSCBig was used to generate bigwigs.
Genome_build: Zv10
Supplementary_files_format_and_content: bigwig files

extract_protocol:
Whole embryos were cross-linked with 2.2% formaldehyde, then nuclei were extracted as described in Potok et al. Cell 2013. Nuclei preps were then combined and sonicated using a Branson Sonicator. Antibodies were then added to each lysate to bind overnight. The following day protein A/G dynabeads were then used to precipitate antibody bound chromatin (bead binding was for 4 hours at 4C). Bead bound chromatin was then washed and eluted using standard ChIP techniques.
NEBNext ChIP-Seq Library Prep Reagents


title: Etv2KOiETV2_MES_SCL

city: Los Angeles

first: Dan

last: Duan

state: CA

address: 615 Charles E. Young Dr, Los Angeles, 90095

institute: UCLA

data_processing:
Debarcoding of the multiplex runs was performed using Fastx toolkit or Unix shell scripts.
Tags were mapped to the mouse genome (mm9) using bowtie v0.12.7 with parameters -v 2 -m 1 -S --best --strata
Peak identification was performed with MACS v1.3.7.1 using default parameters
bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks
Scl peaks were mapped to nearby genes within 200kb range from TSS using Genomic Regions Enrichment of Annotations Tool (GREAT) (McLean et al., 2010). Peak intersections and overlaps with differentially expressed genes were performed using Galaxy (Blankenberg et al., 2010) and in house Ubix shell scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks

source_name: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain WT and Gata1&2KO ES cells. MEL cells were grown in RPMI 1640 with L-Glutamine plus10% of FBS,1% of penicillin and streptomycine. HPC7 cells were grown in  Iscove´s modified Dulbecco´s media (IMDM) (Gibco), supplemented with NaHCO3, 1.5 x 10-4 M MTG (Sigma),1% of penicillin and streptomycine, 10% of FBS and mouse Stem cell factor (SCF) at 100ng/mL (R&D systems).

extract_protocol:
Cells were trypsinized, washed with PBS and crosslinked with 1% formaldehyde in PBS for 10 min at RT. After PBS washing, cells were resuspended in 400 μl of lysis buffer (1% SDS, 20 mM EDTA and 50 mM Tris-HCl (pH 8.0)) containing protease inhibitors (Roche, Indianapolis, IN), incubated for 10 min on ice and sonicated using Misonix cup-horn sonicator to achieve, on average, 200bp fragments for ChIP-seq and 500bp fragments for ChIP-PCR. The lysate was diluted 10 times with ChIP dilution buffer containing 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA and 16.7 mM Tris-HCl (pH 8.1) and immunoprecipitatied with 3 ug of anti-PR or IgG antibody overnight at 4 degrees. 20 μl of the lysates were used as input. The complexes were captured using protein A Dynabeads (Invitrogen, Grand Island, NY) and washed twice with the following buffers: low-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1); high-salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl); LiCl wash buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and TE (10 mM Tris-HCl and 1 mM EDTA (pH 8.0)). After elution with 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 1% SDS, crosslinks were reversed by overnight incubation at 65°C. Samples were then treated with RNase A for 30 min at 37°C and proteinase K for 2 h at 56°C. DNA was subsequently purified using Qiagen MinElute Columns according to manufacturers instructions. DNA concentration was measured using a Qubit (Invitrogen, Grand Island, NY).
The library for sequencing was constructed using Ovation Ultralow IL Multiplex System 1-8 according to manufacturer's instructions (Nugen, San Carlos CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days.

value: Flk1+ mesodermal cells

tag: cell-line

value: Etv2KOiETV2 ES

value: EB formation, enrichment for Flk1+ cells at day 4


title: x16_deps_03_AvrRpt2_09h_rep03

value: Pto AvrRpt2

value: 9 hpi


title: Haploid_PostZGA_H2AFV_ChIP-Seq_Rep2


title: Haploid_PostZGA_H2AFV_ChIP-Seq_Rep3


title: Etv2KOiETV2_MES_INP


title: Haploid_PostZGA_H2AFV_ChIP-Seq_Rep1


title: Etv2KOiSCL_MES_SCL

source_name: ES cell derived day4 Etv2KOiSCL EB (embryoid body) Flk1+ mesodermal cells

value: Etv2KOiSCL ES


title: Anp32e_Null_PostZGA_H3K4me1_ChIP-Seq_Rep2

description: Processed data file: Anp32e_postZGA_H3K4me1_Corrected_LogFE_lambda.bw

value: Anp32e Null


title: x01_Col_03_AvrRpt2_09h_rep03


title: Etv2KOiSCL_d7EB_r2

data_processing:
Debarcoding of the multiplex runs was performed using in house shell script
Reads were then processed and aligned to the mouse genome (mm9) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.
The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate FPKM values. Assemblies  were merged using CuffMerge and differential expression was determined using Cuffdiff.Genes with a q-value less than 0.05 where considered as differentially expressed
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and Excel table wiith differential expression analysis results

source_name: Etv2KOiSCL_d7EB mES cell derived day 7 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

growth_protocol: Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain WT, SclKO (Porcher et al., 1996),Etv2KOiSCL and Etv2KOiETV2 ES cells.

extract_protocol:
Cells were digested by collagenase-dispase treatment, stained with CD31, Tie2 and CD41 antibodies and FACS sorted for Tie2+CD31+CD41- endothelial cell population.
The library for sequencing was constructed using Ovation RNA-seq System 1-16 for Model Organisms (0348, Nugen). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads.

treatment_protocol: ES cells were differentiated into endothelial cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4.75 days or 7 days.

value: endothelial cells

value: Etv2KOiSCL mESC

value: EB formation, FACS sorting for Tie2+CD31+CD41- endothelial cells at day 4.75


title: PostZGA_RRBS_Rep2


title: x05_sid2_03_AvrRpt2_09h_rep03


title: x16_deps_02_EV_09h_rep03

value: dde2-2 ein2-1 pad4-1 sid2-2

value: Pto DC3000


title: Etv2KOiETV2_d7EB_r2

source_name: Etv2KOiETV2_d7EB mES cell derived day 7 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

value: Etv2KOiETV2 mESC


title: SclKO_d7EB_r2

source_name: SclKO mES cell derived day 7 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

value: SclKO mESC


title: Anp32e_Null_PostZGA_H3K4me1_ChIP-Seq_Rep1

value: Sphere Stage

value: Tu


title: Anp32e_Null_Sperm_RNA-Seq_Rep2

description: Processed data file: RNASeq_geneCount_minimum10.xlsx

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.

source_name: Sperm Stage

extract_protocol:
Embryos were lysed using Trizol with the addition of 2% SDS, then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification.
Illumina TruSeq Stranded RNA kit with Rib-Zero Gold

value: Sperm Stage


title: WT_d7EB_r2

source_name: WT mES cell derived day 7 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

value: WT J1 mESC


title: Haploid_PostZGA_RRBS_Rep1

value: Gynogenetic Haploid


title: x05_sid2_01_mock_12h_rep01

source_name: Fully-expanded leaves of 30 to 33 day-old plants

value: Mock

value: 12 hpi

value: Leaves


title: x01_Col_02_EV_09h_rep03

value: 9 hpi


title: x05_sid2_02_EV_09h_rep03


title: Etv2KOiETV2_d7EB_r1


title: x16_deps_01_mock_09h_rep03


title: Anp32e_Null_Sperm_RNA-Seq_Rep1

value: Anp32e Null


title: Etv2KOiSCL_MES_INP

value: Flk1+ mesodermal cells

value: Etv2KOiSCL ES

value: EB formation, enrichment for Flk1+ cells at day 4


title: Etv2KOiSCL_d7EB_r1

value: endothelial cells

value: Etv2KOiSCL mESC

value: EB formation, FACS sorting for Tie2+CD31+CD41- endothelial cells at day 4.75


title: SclKO_d7EB_r1

value: SclKO mESC


title: Anp32e_INJ_PostZGA_RNA-Seq_Rep1

value: Sphere Stage

value: Anp32e Protein Injected


title: SRCAP_MO_INJ_RRBS_Rep2

description: Processed data file: SRCAP_MO_2_RRBS_fraction_DNAme.bw

extract_protocol:
DNA was extracted for sphere staged embryos or sperm by RIPA lysis, phenol extraction, and alcohol precipitation.
Libraries were generating using the BioO NEXTflex™ Bisulfite Library Prep protocol for Reduced Representation Bisulfite Sequencing. All libraries were sequenced on an Illumina HiSeq 2500 instrument.

value: Tu

value: SRCAP Morpholino


title: WT_d7EB_r1

value: WT J1 mESC


title: x16_deps_03_AvrRpt2_09h_rep02

value: dde2-2 ein2-1 pad4-1 sid2-2

value: Pto AvrRpt2


title: x05_sid2_03_AvrRpt2_09h_rep02

value: Leaves


title: Rcmb_Anp32e_INJ_RRBS_Rep4

description: Processed data file: Rcmb_Anp32e_INJ_merged_RRBS_fraction_DNAme.bw

value: Recombinant Anp32e Protein


title: Etv2KOiETV2_d475EB_r2

source_name: Etv2KOiETV2_d475EB mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells

value: Etv2KOiETV2 mESC


title: Etv2KOiSCL_d475EB_r2

source_name: Etv2KOiSCL_d475EB mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells


title: SRCAP_MO_INJ_RRBS_Rep1

description: Processed data file: SRCAP_MO_1_RRBS_fraction_DNAme.bw


title: x01_Col_03_AvrRpt2_09h_rep02

value: 9 hpi


title: Rcmb_Anp32e_INJ_RRBS_Rep3


title: SclKO_d475EB_r2

source_name: SclKO mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells


title: x16_deps_02_EV_09h_rep02

value: Pto DC3000


title: x05_sid2_02_EV_09h_rep02


title: Rcmb_Anp32e_INJ_RRBS_Rep2


title: WT_d475EB_r2

source_name: WT mES cell derived day 4.75 EB  EB (embryoid body) Tie2+CD31+CD41- endothelial cells


title: Rcmb_Anp32e_INJ_RRBS_Rep1


title: Anp32e_INJ_PostZGA_RNA-Seq_Rep2


title: Anp32e_postZGA_RRBS_Rep3

description: Processed data file: Anp32e_Sphere_merged_RRBS_fraction_DNAme.bw

value: NHGRI

value: Anp32e Null


title: Anp32e_postZGA_RRBS_Rep2


title: x01_Col_02_EV_09h_rep02


title: x05_sid2_01_mock_09h_rep03

value: Mock


title: x16_deps_01_mock_09h_rep02


title: Etv2KOiSCL_d475EB_r1

value: endothelial cells

value: Etv2KOiSCL mESC

value: EB formation, FACS sorting for Tie2+CD31+CD41- endothelial cells at day 4.75


title: x01_Col_01_mock_09h_rep03


title: Anp32e_postZGA_RRBS_Rep1

value: Sphere Stage


title: Etv2KOiETV2_d475EB_r1


title: x05_sid2_01_mock_09h_rep02


title: SclKO_d475EB_r1

value: SclKO mESC


title: Anp32e_Sperm_RRBS_Rep3

description: Processed data file: Anp32e_Sperm_merged_RRBS_fraction_DNAme.bw

value: Sperm


title: WT_d475EB_r1

value: WT J1 mESC


title: x01_Col_01_mock_09h_rep02


title: x05_sid2_03_AvrRpt2_09h_rep01


title: WT_leaf_RNASeq_Rep3

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNASeq: Tophat-2.0.10 followed by Cufflinks-2.2.1 were used to highlight differentially expressed genes between samples.
Genome_build: TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

growth_protocol: A. thaliana plants of Col-0 ecotype were grown under 16h light/ 8h dark in a growth chamber.

extract_protocol:
Stage 9 flower buds were collected and gently squeezed between a glass slide and coverslip. The released meiocytes (of meiotic prophase I) were examined carefully under a microscope. Clean meiocytes free from any somatic cell debris were transferred to a new slide using capillary glass pipettes, washed by 1 x PBS buffer 3 times, and frozen in liquid nitrogen. Sperm cells and vegetative cell nuclei were isolated by  Fluorescence-activated cell sorting (FACS)
Single-end bisulfite sequencing libraries for Illumina sequencing were constructed using the Ovation Ultralow Methyl-Seq Library Systems (Nugen, #0336) and EpiTect Fast Bisulfite Conversion (Qiagen, #59802) kits according to the kit protocols, except the incorporation of two rounds of bisulfite conversion.Strand-specific RNA sequencing libraries were prepared using ScriptSeq v2 RNA-Seq (Illumina, #SSV21106) Library Preparation and Ovation RNA-Seq Systems for Model Organisms Arabidopsis (Nugen, #0351) kits

tag: ecotype background

value: wild type

tag: age

value: 40 day

tag: tissue/cell type

value: rosette leaf


title: Etv2KOiSCL_d475endo_ATAC

data_processing:
Debarcoding of the multiplex runs was performed using Fastx toolkit or Unix shell scripts.
Tags were mapped to the mouse genome (mm9) using bowtie v0.12.7 with parameters -v 2 -m 1 -S --best --strata
Peak identification was performed with MACS v1.3.7.1 using default parameters
bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were created using Homer (Heinz et al., 2010) using -auto parameter converted into bigwig (bedGraphToBigWig) and visualized on UCSC (Kent et al., 2002) genome browser as custom tracks

tag: cell type


title: Etv2KOiETV2_d475endo_ATAC

tag: treatment


title: embryo_A-_3h

value: embryo


title: x16_deps_03_AvrRpt2_09h_rep01

tag: genotype

value: dde2-2 ein2-1 pad4-1 sid2-2

value: Pto AvrRpt2

value: Leaves


title: Anp32e_Sperm_RRBS_Rep2

value: NHGRI


title: Anp32e_Sperm_RRBS_Rep1

value: Anp32e Null


title: x01_Col_03_AvrRpt2_09h_rep01

tag: replicate

value: 9 hpi


title: WT_d475endo_ATAC

value: endothelial cells

value: WT mESC


title: Anp32e_Pat_Null_RRBS_Rep3

description: Processed data file: Anp32e_Pat-Null_merged_RRBS_fraction_DNAme.bw

value: Tu X NHGRI

value: Anp32e Paternal Null


title: drm1drm2_leaf_RNASeq_rep1

tag: genotype/variation


title: x16_deps_02_EV_09h_rep01

value: Pto DC3000

tag: time


title: Anp32e_Pat_Null_RRBS_Rep2

value: Sphere Stage


title: GF7

city: Corvallis

first: Jay

middle: R

last: Reichman

state: OR

address: 200 SW 35th St.

department: Office of Research and Development

institute: US Environmental Protection Agency

description: DECe Gas Phase

data_processing:
Base calls were made with Illumina Casava version 1.8.2
Illumina reads were auto trimmed and aligned to the psme_transcriptome_v203 template using SeqMan NGen v13.1 (DNASTAR, Inc., Madison, WI)
Gene expression levels were quantified using QSeq/ArrayStar v13.1 (DNASTAR, Inc.) with Reads Assigned per Kilobase of target per Million mapped reads (RPKM) normalization. All values were capped to an auto-calculated minimum value. The averaging method for biological replicates was Mean. Sets of regulated transcripts in treated samples were identified by filtering for those with means ≥2-fold change and 95% confidence across biological replicates compared to Air Controls. The confidence was based on Student’s t-test (P ≤ 0.05) with Benjamini & Hochberg Multiple Testing Correction (FDR ≤ 0.05).
Mapping, annotation and gene ontology enrichment analyses were performed with Blast2Go v3.3 (BioBam, Inc. Valencia, Spain).
Pathway enrichment analyses of regulated transcripts were performed with MapMan v3.5.1R2.
Genome_build: TSA: Pseudotsuga menziesii, transcriptome shotgun assembly; GenBank: GFFY00000000.1
Supplementary_files_format_and_content: Text files of raw counts and linear total RPKM generated with Qseq/ArrayStar v13.1

molecule: polyA RNA

organism: Pseudotsuga menziesii

source_name: DECe Gas Phase

growth_protocol: Half-sibling Douglas-fir seedlings were planted in square 4-inch pots and the pots were placed in shared trays. Trays were positioned in Hazelton 1000 (984 L) exposure chambers (one each for DE, DECe, DECe Gas Phase, and Air Control) outfitted with two LED grow lights that supplied 280 µmol/s/m2 photosynthetically active radiation (PAR) at tray level to plants during the exposures. LED Grow Light banks were set on a 16-hour light:8-hour dark cycle.  Seedlings were re-distributed within the exposure chambers mid-way through the exposure period to minimize potential edge effects. Chamber experiments were run during the month of December when needle growth was dormant.

extract_protocol:
Total RNA was extracted from needles using PureLink Plant RNA Reagent per the manufacturer’s protocol (Ambion, Life Technologies, Inc. Austin, TX).  Messenger RNA was purified from total RNA samples with FastTrack MAG mRNA Isolation Kits (Ambion, Inc.).
RNA-sequencing libraries were prepared with PrepX RNA-Seq for Illumina Library Kits using an Apollo 324 automated system (Wafergen Biosystems, Inc, Freemont, CA). Clusters were amplified from pooled libraries with TruSeq PE Cluster Kit v3-cBot-HS kits on a cBot System (Illumina Inc., San Diego, CA).

treatment_protocol: Douglas-fir seedlings were randomly assigned to one of four groups: 1) Charcoal / Purafil HEPA filtered air (Air Control); 2) Emissions released from combustion of diesel fuel containing engineered CeO2 nanoparticle catalysts (DECe); 3) Emissions released from combustion of diesel fuel (DE); or 4) HEPA filtered DECe (DECe Gas Phase). The overall exposure regime was 6 hours/day X 5 days/week X 2 weeks. Filtered air was pumped through all chambers during the times between the exposures.

tag: growth year

tag: sampling year

value: needles

tag: needle location

value: on lateral stem

tag: stem position

value: proximal to most recent bud scar


title: drm1drm2_meiocyte_RNASeq_Rep3

value: 5-6 week

value: male meiocyte


title: x05_sid2_02_EV_09h_rep01

tag: tissue


title: drm1drm2_meiocyte_RNASeq_Rep2


title: GF5

description: DECe Gas Phase


title: GF4

description: DECe Gas Phase


title: Anp32e_Mat_Null_RRBS_Rep4

description: Processed data file: Anp32e_Mat-Null_merged_RRBS_fraction_DNAme.bw

tag: developmental stage

tag: strain

tag: injection

value: Anp32e Maternal Null


title: GF3

description: DECe Gas Phase


title: x01_Col_02_EV_09h_rep01


title: Anp32e_Mat_Null_RRBS_Rep3

tag: mutation


title: x16_deps_01_mock_09h_rep01

value: dde2-2 ein2-1 pad4-1 sid2-2

value: Mock


title: Anp32e_Pat_Null_RRBS_Rep1


title: GF2

description: DECe Gas Phase


title: x05_sid2_01_mock_09h_rep01

value: Leaves


title: Anp32e_Mat_Null_RRBS_Rep2


title: WT_meiocyte_RNASeq_Rep2

tag: ecotype background

value: wild type

tag: age


title: Anp32e_Mat_Null_RRBS_Rep1


title: WT_meiocyte_RNASeq_Rep1

tag: tissue/cell type


title: x01_Col_01_mock_09h_rep01

tag: treatment

value: 9 hpi


title: DF8

description: DE

source_name: DE


title: GF10

description: DECe Gas Phase


title: x05_sid2_03_AvrRpt2_06h_rep03

tag: genotype

value: Pto AvrRpt2

value: 6 hpi


title: PostZGA_Pat-Null_6hpf_RNA-Seq_Rep2

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Anp32e_Pat_Null_RNA-Seq_2.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.

source_name: Shield Stage

value: Shield Stage

value: Tu X NHGRI


title: PostZGA_Pat-Null_6hpf_RNA-Seq_Rep1

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Anp32e_Pat_Null_RNA-Seq_1.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.

value: Anp32e Paternal Null


title: x01_Col_03_AvrRpt2_06h_rep03

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each of 348 samples (ReadCountTable_M001_348.txt).

tag: replicate


title: DF5

description: DE


title: biorep_A+_10h.1

description:
total mRNA of MPRA reporters
processed data file: seq0312.40A.1.txt

source_name: zebrafish embryos

value: embryo


title: x05_sid2_02_EV_06h_rep03

value: Pto DC3000


title: drm1drm2_meiocyte_RNASeq_Rep1

tag: genotype/variation


title: x01_Col_02_EV_06h_rep03

tag: time


title: biorep_A+_8h.1


title: biorep_A+_6h.1


title: biorep_A+_4h.1


title: PostZGA_Mat-Null_6hpf_RNA-Seq_Rep2

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Anp32e_Mat_Null_RNA-Seq_2.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.


title: DF4

description: DE

tag: growth year

value: needles

value: on lateral stem


title: WT_meiocyte_RNASeq_Rep3

value: 5-6 week


title: PostZGA_Mat-Null_6hpf_RNA-Seq_Rep1

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Anp32e_Mat_Null_RNA-Seq_1.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.


title: biorep_A+_2h.1


title: x05_sid2_01_mock_06h_rep03


title: PostZGA_Anp32e_Null_6hpf_RNA-Seq_Rep2

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Anp32e_Null_RNA-Seq_2.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.

value: NHGRI

value: Anp32e Null


title: DF12

description: DE

tag: sampling year

value: proximal to most recent bud scar


title: x01_Col_01_mock_06h_rep03

value: Mock


title: PostZGA_Anp32e_Null_6hpf_RNA-Seq_Rep1

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Anp32e_Null_RNA-Seq_1.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.


title: biorep_A+_uninjected


title: DF1

description: DE

tag: needle location


title: PostZGA_6hpf_RNA-Seq_Rep2

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -o SAM -r All 50
Sam files were then combined due to high correlation between technical and biological replicates.
The Useq Pipeline was utilized - Sam parsed using the SAMTranscriptomeParser, followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values.
Genome_build: Zv10
PostZGA_Control_RNA-Seq.bam
Supplementary_files_format_and_content: RNASeq_geneCount_minimum10.xlsx: Excel file contains gene count table.

value: Tu

value: Wild Type


title: x05_sid2_03_AvrRpt2_06h_rep02

value: Leaves


title: DF6

description: DE

tag: stem position


title: CF5

description: DECe

source_name: DECe

tag: tissue


title: oocyte_A+_7h

description:
total mRNA of MPRA reporters
Mature oocytes were collected at 28C by squeezing the belly of adult female zebrafish under anesthesia with tricaine solution (0.15  mg/ml).
processed data file: seq0514.40A.txt

data_processing:
Library strategy: UTR-Seq
data (160nt reads) was filtered to retain only sequences that contained both terminal adapter sequences (with up to 10 mismatches) and an insert of 90nt or longer.
data (100nt reads) was filtered to retain only sequences that contained the 5’ terminal adapter sequence (with up to 10 mismatches) and an insert of 62nt or longer.
Bowtie2 was used to align retained reads to a reference set of all 90,000 synthetic oligonucleotide sequences
The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample.
A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2-fold increments (highest 50fg, lowest 3.125fg), and the resulting linear transformation was used to normalize UMI counts.
Genome_build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record.
Supplementary_files_format_and_content: tab delimited files of normalized mRNA levels

source_name: zebrafish oocyte

tag: developmental stage

value: oocyte


title: x01_Col_03_AvrRpt2_06h_rep02

value: Pto AvrRpt2

value: 6 hpi


title: CF4

description: DECe


title: PostZGA_6hpf_RNA-Seq_Rep1

value: Shield Stage

tag: strain


title: oocyte_A+_4h


title: x05_sid2_02_EV_06h_rep02


title: DF2

description: DE


title: CF2

description: DECe


title: oocyte_A-_7h

description:
total mRNA of MPRA reporters
Mature oocytes were collected at 28C by squeezing the belly of adult female zebrafish under anesthesia with tricaine solution (0.15  mg/ml).
processed data file: seq0514.00A.txt


title: CF3

description: DECe


title: x01_Col_02_EV_06h_rep02


title: oocyte_A+_1h


title: Sperm_Input_ChIP-Seq

description:
Precipitated Genomic DNA from Chromatin
Processed data file: none

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -r Random -k -Q 13 -o SAM
Sam files were then combined due to high correlation between technical and biological replicates.
Macs2 was then used to generate read count normalized genome wide pileup tracks and lambda tracks for precipitated samples and input. (callpeak --nomodel --extsize 150 --SPMR)
Pileup tracks were then Input corrected using the Macs2 subtract function (bdgcmp -m subtract).
Log10 Fold enrichment was then calculated for each sample comparing input corrected pileups to input lambda. (bdgcmp -m logFE).
Peaks were then called as regions with greater than 3 fold enrichment over lambda using the Macs2 bdgpeakcall function. (bdgpeakcall -c 0.477 -l 100 -g 100)
Genome_build: Zv10
Supplementary_files_format_and_content: bed and bigWig files

source_name: Sperm

value: Sperm

tag: injection


title: Sperm_H3K4me3_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K4me3_Sperm_Log10FE_over_Input_Lambda.bw; H3K4me3_Sperm_Peaks_Log10FE_3fold.bed

tag: mutation