title: HCT116_Hyp_24hr_rep2

city: Cambridge

first: Danish

last: Memon

address: Robinson Way

institute: CRUK Cambridge Institute, University of Cambridge

description:
Hyp24r2
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt

data_processing:
Basecalling was performed using Illumina CASAVA version 1.8.2.
27~58 million paired-end sequencing reads (101 nt) were obtained from all sequencing libraries and aligned to the human reference genome hg19 using the splice alignment software Mapsplice (version 2.1.6) with default parameters, except for options specifying library type (fr-firststrand). Gene annotation was taken from Ensembl release 74.
The expression of a gene or feature was measured by the Fragment Per Kilobase Per Million Mapped (FPKM) score, which was estimated using Cufflinks.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Cufflinks_FPKM_values.txt: Cufflinks FPKM values for all samples (normalized abundance measurements for transcripts).
Supplementary_files_format_and_content: Isoforms.attr_table.txt: Isoform attributes (Ensembl v74) derived from the transcriptome assembly process.

source_name: Colorectal cancer cells, hypoxia, 24hr

extract_protocol:
RNA was extracted using the Qiagen QIAshredder kit (79654) and the Qiagen RNeasy Mini Kit (74104) as per the manufacturer's instructions. The RNA was DNase treated following the protocol in the RNeasy Mini Kit with Qiagen RNase-free DNase I (79254).
Indexed PolyA libraries were prepared using 1ug of Total RNA and 13 cycles of amplification in the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc., Cat No: E7420S). Libraries were quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems Inc., Cat No: KK4835). Pooled libraries were clustered at 15pM on the cBot and 2 x 100bp sequencing was carried out using the High Throughput mode of a HiSeq 2500 using TruSeq SBS Kit v3 chemistry (Illumina Inc.)

treatment_protocol: HCT116 were cultured in RPMI-1640 media (Life Technologies) supplemented with 10% FBS (Biowest). All cells were maintained in a humidified atmosphere at 37°C and 5% CO2. For hypoxia treatment, the HCT116 cell line was cultured in 1% O2 in an Invivo2 hypoxia workstation 4000 (Biotrace, Fred Baker Ltd.) for the given time course 24 hours after plating.

value: colorectal cancer cell line

value: 1% oxygen

tag: time-point

tag: replicate


title: shr 0h photorespiratory stress rep1

status: Public on Jul 28 2016

type: SRA

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description:
shr-0H-I_S7
Control sample shr
Three-week-old seedlings (shoot tissue)

library_source: transcriptomic

data_processing:
Adapter sequences and low quality base-pairs (Q < 20) were trimmed using Trim Galore (v0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp length.
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 (v2.1.0)
The number of reads per gene was quantified using featureCounts function as implemented in the Subread package v1.4.6
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 24 samples as delivered by featureCounts

molecule: total RNA

organism: Arabidopsis thaliana

source_name: shr 0h photorespiratory stress

growth_protocol: Plants were grown in Petri dishes (150×25 mm; Becton-Dickinson) on full-strength MS agar-solidified medium supplemented with 1% (w/v) sucrose, 100 mg/L myo-inositol, 0.5 mg L‑1 nicotinic acid, 0.5 mg/L pyridoxine, and 1 mg/L thiamine at 21°C and LD conditions (16 h light [100 μmol m−2 s−1]/8 h dark).

extract_protocol:
RNA was extracted using a combination of TRIzol and RNeasy Kit (Qiagen) according to the manufacturers’ instructions.
Library preparation and sequencing was performed at the VIB Nucleomics Core (www.nucleomics.be). Sequencing libraries were constructed with using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

treatment_protocol: After 21 days of growth, the MicroporeTM surgical tape (3M) that sealed the plates was replaced by two layers of Parafilm M (Bemis) to restrict gas exchange. Plants were transferred to a continuous light regime.

tag: developmental stage

value: seedling

tag: age

tag: tissue

value: shoot

tag: ecotype

tag: genotype/variation

value: shr

tag: stress

value: control


title: HCT116_Hyp_24hr_rep3

country: United Kingdom

description:
Hyp24r3
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: cat2shr 0h photorespiratory stress rep1

description:
catshr-0H-I_S10
Control sample cat2xshr
Three-week-old seedlings (shoot tissue)

source_name: cat2shr 0h photorespiratory stress


title: cat2 24h photorespiratory stress rep1

description:
cat-24H-I_S16
Stress (24h photorespiratory stress) sample cat2
Three-week-old seedlings (shoot tissue)

source_name: cat2 24h photorespiratory stress

value: photorespiratory stress


title: H3K27me3_ChIP-Seq

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

country: USA

institute: St Jude Children's Research Hospital

description: Processed data file: H3K27me3.bgsub.Fnor.wig

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Total read numbers of ChIP-Seq samples without spike-in control are normalized to be 25 million, and ChIP-Seq samples with spiked-in Control are normalized according to the number of spiked-in Drosophila melanogaster chromatin.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with parameters -p 8 -m 1 --chunkmbs 512 --best
ChIP-Seq peaks were called using DANPOS2 v2.2.2 with the following parameters: --smooth_width 0 -e 1 --frsz 200 --extend 200 --pheight 1e-50 --extend_pheight 1e-20
RNA-Seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome assembly using tophat v2.0.12 with parameters --mate-std-dev 200 -p 8 -r 203
The number of fragments that originated from each gene in each sample is estimated using cuffdiff with default parameters. Then, the differentially expressed genes based on read counts are inferred using edgeR R package v3.12.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text file (genes.count_tracking.txt) includes raw counts of reads, RPKM values for each gene of each sample.
Supplementary_files_format_and_content: For ChIP-Seq data, wig files showing the average signal density across genome are generated using DANPOS2 v2.2.2.

molecule: genomic DNA

source_name: DU145 cells, untreated, H3K27me3 ChIP

growth_protocol: DU145 were cultured in High Glucose Dulbecco's Modified Eagle's Medium supplemented with L-glutamine, sodium bicarbonate, pyridoxine.HCI, sodium pyruvate and 10% fetal bovine serum.

extract_protocol:
DU145 prostate cells were cross-linked with 1% formaldehyde at room temperature for 10 min and then lysed and sonicated to fragment genomic DNA sizes to 200-500 bp. Chromatin samples were incubated with specific antibodies overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads. The bound fractions were washed with low salt, high salt, LiCI wash buffer and TE buffer. Reverse-crosslinking of the eluted DNA were carried out at 67℃ for 8 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR purification kit.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Normal DU145 cells.

value: prostate cancer cell line

tag: tissue derivation

value: prostate; derived from brain metastatic site

tag: chip antibody


title: HCT116_Hyp_2hr_rep1

description:
Hyp2r1
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt

source_name: Colorectal cancer cells, hypoxia, 2hr


title: cat2 0h photorespiratory stress rep3

description:
cat-0H-III_S6
Control sample cat2
Three-week-old seedlings (shoot tissue)

source_name: cat2 0h photorespiratory stress


title: HCT116_Hyp_1hr_rep3

description:
Hyp1r3
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt

source_name: Colorectal cancer cells, hypoxia, 1hr


title: HCT116_Hyp_24hr_rep1

description:
Hyp24r1
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: cat2 0h photorespiratory stress rep2

description:
cat-0H-II_S5
Control sample cat2
Three-week-old seedlings (shoot tissue)


title: Col-0 0h photorespiratory stress rep3

description:
Col-0H-III_S3
Control sample Col-0
Three-week-old seedlings (shoot tissue)

source_name: Col-0 0h photorespiratory stress

value: wt


title: HCT116_Hyp_2hr_rep2

description:
Hyp2r2
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: HCT116_Hyp_2hr_rep3

description:
Hyp2r3
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: cat2 0h photorespiratory stress rep1

description:
cat-0H-I_S4
Control sample cat2
Three-week-old seedlings (shoot tissue)


title: HCT116_Hyp_1hr_rep2

description:
Hyp1r2
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: Col-0 0h photorespiratory stress rep2

description:
Col-0H-II_S2
Control sample Col-0
Three-week-old seedlings (shoot tissue)


title: HCT116_Hyp_0hr_rep1

description:
Norm0r1
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt

source_name: Colorectal cancer cells, hypoxia, 0hr

value: 21% oxygen


title: cat2shr 24h photorespiratory stress rep3

description:
catshr-24H-III_S24
Stress (24h photorespiratory stress) sample cat2xshr
Three-week-old seedlings (shoot tissue)

source_name: cat2shr 24h photorespiratory stress


title: Epi352

status: Public on Jul 27 2016

city: Stockholm

first: Qiaolin

last: Deng

address: Berzelius väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina Casava1.7 software used for basecalling
RNA-seq reads of each cell were mapped to the mouse reference genome (mm10) using STAR (version 2.4.1) with parameter --outSAMstrandField intronMotif.
Expression  of genes for each sample was quantified and normalized using Cufflinks and Cuffnorm (version 2.2.1) with parameter -library-norm-method geometric.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: embryo

growth_protocol: This female Epistem cell line was  generated from female mESCs by culturing them with Activin A and FGF2 for seven passages.

extract_protocol:
Cells are directly picked after dissociation and deposited into lyssis buffer. No RNA extraction is conducted.The cell lysis is proceed directly to library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation

tag: strain

value: male CAST/EiJ x female C57BL/6J

value: Epi

tag: Sex

value: Female


title: H3K14ac_ChIP-Seq

description: Processed data file: H3K14ac.bgsub.Fnor.wig

source_name: DU145 cells, untreated, H3K14ac ChIP

value: H3K14ac (Millipore, MABE351, lot 2298448)


title: Epi349


title: Epi342


title: Epi344


title: Epi336


title: Epi348


title: Epi330


title: Epi338


title: Epi347


title: Epi325


title: Epi340


title: Epi329


title: Epi326


title: Epi322


title: Epi328


title: Epi317


title: HCT116_Hyp_1hr_rep1

description:
Hyp1r1
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: Epi316


title: Epi315


title: Col-0 0h photorespiratory stress rep1

description:
Col-0H-I_S1
Control sample Col-0
Three-week-old seedlings (shoot tissue)


title: HCT116_Hyp_0hr_rep3

description:
Norm0r3
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: HCT116_Hyp_0hr_rep2

description:
Norm0r2
Strand-specific RNA-seq
PolyA RNA
Processed data file: Cufflinks_FPKM_values.txt


title: Epi320


title: Epi341


title: Epi312


title: Epi313


title: Epi314


title: Epi311


title: Epi310


title: Epi308


title: Epi305


title: Epi301


title: Epi307


title: Epi306


title: Epi295


title: Epi323


title: Epi299


title: Epi324


title: Epi297


title: Epi289


title: Epi292


title: Epi294


title: Epi293


title: Epi303


title: Epi290


title: lateblast_9_3

data_processing:
Illumina Casava1.7 software used for basecalling
RNA-seq reads of each cell were mapped to the mouse reference genome (mm10) using STAR (version 2.4.1)
Expression  of genes for each sample was quantified and normalized using Cufflinks and Cuffnorm (version 2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

growth_protocol: mESCs were cultured in 2i and LIF as the ground state condition or in serum and LIF as the conventional condition. Epistem cell lines were also generated from the two lines by culturing them with Activin A and FGF2. In order to study more advanced development, we differentiated the two mESC lines through embryonic body formation to postmitotic motor neurons using retinoic acid and the smoothened agonist SAG. This differentiation process also results in the derivation of several types of interneurons.

extract_protocol: Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation

value: E4.5 Epiblast


title: lateblast_9_2


title: lateblast_10_9


title: lateblast_4_1


title: lateblast_4_21


title: lateblast_9_19


title: lateblast_10_10


title: lateblast_9_16


title: lateblast_9_15


title: lateblast_9_4


title: lateblast_9_13


title: lateblast_8_7


title: lateblast_8_3


title: lateblast_7_3


title: lateblast_7_6


title: lateblast_10_11


title: lateblast_5-4_707_506

value: E3.5 ICM


title: lateblast_5-6_701_507


title: lateblast_6_10


title: lateblast_5_3


title: lateblast_5_2


title: lateblast_4-2_702_505


title: lateblast_3-15_708_504


title: lateblast_7_5


title: lateblast_6_8


title: lateblast_3-1_702_503


title: lateblast_4-11_703_506


title: lateblast_3-12_705_504


title: lateblast_3-5_706_503


title: lateblast_1-7_704_501


title: lateblast_1-6_703_501


title: lateblast_5-3_706_506


title: lateblast_8_8


title: lateblast_3-13_706_504


title: lateblast_3-6_707_503


title: lateblast_5-2_705_506


title: lateblast_5-7_702_507


title: lateblast_1-9_701_502


title: lateblast_7_2


title: lateblast_1-1_701_501


title: lateblast_1-13_705_502


title: lateblast_4-8_708_505


title: EB_125

value: male C57BL/6J x female C57BL/6J

value: E5.5 Epilbast


title: EB_124


title: EB_126


title: lateblast_4-10_702_506


title: lateblast_3-11_704_504


title: EB_123


title: EB_117


title: EB_121


title: EB_116


title: EB_114


title: EB_120


title: EB_115


title: EB_112


title: EB_122


title: EB_113


title: EB_111


title: EB_102


title: EB_104


title: EB_109


title: EB_106


title: EB_100


title: lateblast_1-4_702_501


title: lateblast_1-14_706_502


title: EB_99


title: EB_93

value: Male


title: EB_94


title: EB_92


title: EB_87


title: EB_91


title: EB_86


title: EB_85


title: EB_81


title: EB_79


title: EB_83


title: EB_77


title: EB_74


title: EB_78


title: EB_68


title: EB_69


title: EB_71


title: EB_73


title: EB_96


title: EB_65


title: EB_67


title: EB_63


title: EB_82


title: EB_59


title: EB_62


title: EB_61


title: EB_58


title: EB_57


title: EB_56


title: EB_55


title: EB_75


title: EB_50


title: EB_54


title: EB_46


title: EB_44


title: EB_49


title: EB_48


title: EB_40


title: EB_47


title: EB_9


title: EB_36


title: EB_38


title: EB_37


title: EB_76


title: EB_33


title: EB_35


title: EB_34


title: EB_39


title: EB_70


title: EB_20


title: EB_28


title: EB_19


title: EB_24


title: EB_22


title: EB_14


title: EB_15


title: EB_18


title: EB_13


title: EB_12


title: M85

value: Motor neuron


title: M88


title: M86


title: M91


title: EB_25


title: EB_10


title: M94


title: EB_26


title: M84


title: M78


title: M82


title: M81


title: M83


title: M48


title: M75


title: M76


title: M47


title: M74


title: M45


title: M80


title: M77


title: M42


title: M73


title: M43


title: EB_23


title: M41


title: M89


title: M40


title: M37


title: M39


title: M38


title: M36


title: M33


title: M32


title: M34


title: M35


title: M28


title: M31


title: M29


title: M72


title: M25


title: M70


title: M68


title: M44


title: M67


title: M26


title: M66


title: M65


title: M57


title: M60


title: M56


title: M54


title: M52


title: M51


title: M50


title: EB_17


title: M22


title: M24


title: M27


title: M21


title: M20


title: M18


title: M14


title: M16


title: M15


title: M13


title: M3


title: M12


title: M9


title: M5


title: M10


title: Epi_96


title: M49


title: M19


title: M11


title: Epi_91


title: Epi_94


title: M17


title: M1


title: Epi_95


title: Epi_89


title: Epi_88


title: M23


title: Epi_85


title: Epi_83


title: M8


title: Epi_80


title: Epi_79


title: Epi_82


title: Epi_74


title: Epi_71


title: Epi_70


title: Epi_76


title: Epi_69


title: Epi_67


title: Epi_92


title: Epi_66


title: Epi_64


title: Epi_90


title: Epi_63


title: Epi_59


title: Epi_62


title: M59


title: Epi_53


title: Epi_84


title: Epi_52


title: Epi_50


title: Epi_49


title: Epi_192


title: Epi_86


title: Epi_191


title: Epi_78


title: Epi_58


title: Epi_190


title: Epi_189


title: Epi_73


title: Epi_187


title: Epi_184


title: Epi_185


title: Epi_188


title: Epi_182


title: Epi_183


title: Epi_77


title: Epi_181


title: Epi_180


title: Epi_178


title: Epi_176


title: Epi_177


title: Epi_179


title: Epi_174


title: Epi_172


title: Epi_169


title: Epi_173


title: Epi_170


title: Epi_171


title: Epi_162


title: Epi_167


title: Epi_166


title: Epi_168


title: Epi_186


title: Epi_165


title: Epi_161


title: Epi_160


title: Epi_158


title: Epi_156


title: Epi_152


title: Epi_151


title: Epi_153


title: Epi_175


title: Epi_159


title: Epi_148


title: Epi_149


title: Epi_150


title: Epi_164


title: Epi_145


title: Epi_98


title: Epi_99


title: Epi_8


title: Epi_6


title: Epi_4


title: Epi_45


title: Epi_48


title: Epi_41


title: Epi_44


title: Epi_154


title: Epi_5


title: Epi_47


title: Epi_37


title: Epi_155


title: Epi_39


title: Epi_42


title: Epi_97


title: Epi_26


title: Epi_1


title: Epi_24


title: Epi_30


title: Epi_20


title: Epi_35


title: Epi_29


title: Epi_18


title: Epi_32


title: Epi_31


title: Epi_17


title: Epi_19


title: Epi_13


title: Epi_133


title: Epi_134


title: Epi_132


title: Epi_131


title: Epi_130


title: Epi_12


title: Epi_125


title: Epi_136


title: Epi_128


title: Epi_124


title: Epi_127


title: Epi_11


title: Epi_122


title: Epi_15


title: Epi_117


title: Epi_118


title: Epi_119


title: Epi_123


title: Epi_14


title: Epi_116


title: Epi_120


title: Epi_115


title: Epi_113


title: Epi_163


title: Epi_111


title: Epi_22


title: Epi_10


title: Epi_110


title: Epi_103


title: Epi_104


title: Epi_100


title: Epi_101


title: Epi_109


title: ES_99

value: ES


title: ES_97


title: Epi_102


title: ES_98


title: ES_96


title: Epi_114


title: ES_94


title: ES_95


title: ES_93


title: ES_91


title: ES_92


title: ES_88


title: ES_84


title: ES_87


title: ES_83


title: ES_86


title: Epi_135


title: ES_81


title: ES_79


title: ES_80


title: ES_77


title: ES_73


title: ES_75


title: ES_78


title: ES_72


title: ES_74


title: ES_71


title: ES_68


title: ES_76


title: ES_69


title: ES_67


title: ES_66


title: ES_90


title: ES_89


title: ES_82


title: ES_135


title: ES_134


title: ES_136


title: ES_85


title: ES_133


title: ES_132


title: ES_131


title: ES_130


title: ES_126


title: ES_124


title: ES_123


title: ES_122


title: ES_129


title: ES_121


title: ES_120


title: ES_114


title: ES_116


title: ES_119


title: ES_115


title: ES_112


title: ES_125


title: ES_128


title: ES_110


title: ES_127


title: ES_111


title: ES_104


title: ES_101


title: ES_109


title: ES_113


title: ES_108


title: ES_100


title: ES_102


title: ES_106


title: ES_9


title: ES_103


title: ES_4


title: ES_7


title: ES_6


title: ES_118


title: ES_117


title: ES_1


title: ES_3


title: ES_183


title: ES_181


title: ES_179


title: ES_177


title: ES_182


title: ES_180


title: ES_175


title: ES_170


title: ES_172


title: ES_176


title: ES_165


title: ES_167


title: ES_169


title: ES_173


title: ES_174


title: ES_164


title: ES_168


title: ES_5


title: ES_157


title: ES_166


title: ES_158


title: ES_163


title: ES_155


title: ES_156


title: ES_160


title: ES_15


title: ES_159


title: ES_184


title: ES_152


title: ES_153


title: ES_147


title: ES_162


title: ES_14


title: ES_146


title: ES_161


title: ES_141


title: ES_145


title: ES_12


title: ES_142


title: ES_143


title: ES_13


title: ES_11


title: ES_2i_99


title: ES_139


title: ES_10


title: ES_2i_288


title: ES_2i_97


title: ES_2i_98


title: ES_2i_286


title: ES_2i_285


title: ES_2i_284


title: ES_154


title: ES_2i_281


title: ES_2i_283


title: ES_2i_278


title: ES_2i_280


title: ES_2i_275


title: ES_2i_274


title: ES_2i_270


title: ES_2i_277


title: ES_2i_279


title: ES_138


title: ES_2i_273


title: ES_2i_271


title: ES_2i_269


title: ES_2i_268


title: ES_2i_276


title: ES_2i_266


title: ES_2i_264


title: ES_2i_263


title: ES_2i_265


title: ES_2i_262


title: ES_2i_261


title: ES_2i_260


title: ES_2i_258


title: ES_2i_282


title: ES_2i_257


title: ES_2i_259


title: ES_2i_128


title: ES_2i_124


title: ES_2i_123


title: ES_2i_122


title: ES_2i_117


title: ES_2i_116


title: ES_2i_114


title: ES_2i_113


title: ES_2i_119


title: ES_2i_118


title: ES_2i_120


title: ES_2i_115


title: ES_2i_112


title: ES_2i_267


title: ES_2i_111


title: ES_2i_121


title: ES_2i_125


title: ES_2i_104


title: ES_2i_105


title: ES_2i_106


title: ES_2i_109


title: ES_2i_103


title: ES_2i_127


title: ES_2i_102


title: ES_2i_256


title: ES_2i_254


title: ES_2i_108


title: ES_2i_101


title: ES_2i_100


title: ES_2i_253


title: ES_2i_251


title: ES_2i_110


title: ES_2i_248


title: ES_2i_247


title: ES_2i_245


title: ES_2i_246


title: ES_2i_244


title: ES_2i_242


title: ES_2i_243


title: ES_2i_238


title: ES_2i_240


title: ES_2i_239


title: ES_2i_241


title: ES_2i_236


title: ES_2i_235


title: ES_2i_228


title: ES_2i_225


title: ES_2i_229


title: ES_2i_234


title: ES_2i_237


title: ES_2i_231


title: ES_2i_152


title: ES_2i_151


title: ES_2i_230


title: ES_2i_150


title: ES_2i_226


title: ES_2i_252


title: ES_2i_227


title: ES_2i_250


title: ES_2i_249


title: ES_2i_149


title: ES_2i_143


title: ES_2i_146


title: ES_2i_147


title: ES_2i_141


title: ES_2i_138


title: ES_2i_142


title: ES_2i_136


title: ES_2i_137


title: ES_2i_140


title: ES_2i_139


title: ES_2i_135


title: ES_2i_131


title: ES_2i_134


title: ES_2i_133


title: ES_2i_130


title: X43 Pre-NACT

city: London

first: Oliver

last: Pearce

address: Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description: RNA-Seq

data_processing: Alignments were performed to human RefSeq genes archived in the Illumina iGenomes resource using RSEM (version 1.2.4; Li and Dewey 2011)

source_name: OMENTAL TISSUE

extract_protocol:
Total RNA was isolated from frozen whole tissue using the RNeasy kit (Qiagen) following the manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: omental

value: PRE-NACT


title: X54 Pre-NACT

description: RNA-Seq


title: X76 Pre-NACT

description: RNA-Seq


title: ES_2i_132


title: X30 Pre-NACT

description: RNA-Seq


title: X51 Post-NACT CRS2

description: RNA-Seq

value: POST-NACT


title: X69 Pre-NACT

description: RNA-Seq


title: X36 Pre-NACT

description: RNA-Seq


title: X57 Post-NACT CRS2

description: RNA-Seq


title: N8D-30SIC

city: Beijing

first: Xiao-Dong

last: Su

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Science

country: China

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.
Using in-house python script, trim microRNA adapter sequence from reads, then filter out reads who have low quality scores.
Use a given sequence according to the experiment designment as an anchor, trim fixed sequences with in-house script, only keep the 'N' part.
For each sample's filted fasta file, summarize nucleotide occurance at each base, showed in Nucleotide_Statistic_Analysis.xlsx file. Base number means the position of the base in the randomized region from 5' end to 3' end.
Supplementary_files_format_and_content: Fasta format files of translational initiation region sequences.

organism: Escherichia coli

source_name: in vitro transcription

extract_protocol:
Randomized mRNAs were recruited on ribosome at the different initiation complex by incubation of the initiation reaction at 37oC for 30 min until initiation complex to reach equilibrium.  Initiation complexes were collected using Ni-NTA chromatography to capture the his-tagged ribosomal protein followed by phenol:chloroform treatment to remove all the ribosomal proteins.  Finally, the pools of RNAs were precipitated by ethanol, resuspended in distilled H2O, and used directly for sequencing library preparation.  The RNA pools include both the ribosomal RNAs and the selected mRNAs binding to initiation complex.
The sequencing library was prepared by following the procedure described in NEBNext MultiplexSmall RNA Library Prep Set for Illumina.

tag: sample type

value: mRNAs N8D captured by ribosome 30S initiation complex


title: N8D-70SIC

value: mRNAs N8D captured by ribosome 70S initiation complex


title: ES_2i_145


title: N8D-30S

value: mRNAs N8D captured by ribosome 30S subunit alone


title: ES_2i_144

value: male CAST/EiJ x female C57BL/6J


title: N8D-Blank

value: blank control of mRNA N8D


title: PRE-NACT-NORMAL [X93]


title: PRE-NACT-NORMAL [X94]


title: N8M-70SIC

value: mRNAs N8M captured by ribosome 70S initiation complex


title: PRE-NACT-NORMAL [X88]


title: PRE-NACT-NORMAL [X42]


title: N8M-Blank

value: blank control of mRNA N8M


title: N8M-30SIC

value: mRNAs N8M captured by ribosome 30S initiation complex


title: N8M-30S

value: mRNAs N8M captured by ribosome 30S subunit alone


title: PRE-NACT-NORMAL [X45]


title: X72 Pre-NACT

description: RNA-Seq


title: N8U-70SIC

value: mRNAs N8U captured by ribosome 70S initiation complex


title: N8U-30S

value: mRNAs N8U captured by ribosome 30S subunit alone


title: N8U-Blank

value: blank control of mRNA N8U


title: N20D’-70SIC

value: mRNAs N20D captured by ribosome 70S initiation complex (repeated)


title: N8U-30SIC

value: mRNAs N8U captured by ribosome 30S initiation complex


title: N20D’-Blank

value: blank control of mRNA N20D (repeated)


title: N20D’-30S

value: mRNAs N20D captured by ribosome 30S subunit alone (repeated)


title: N20D’-30SIC

value: mRNAs N20D captured by ribosome 30S initiation complex (repeated)


title: N20U’-70SIC

value: mRNAs N20U captured by ribosome 70S initiation complex (repeated)


title: khES3 with 4 ng/ml bFGF

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: ATAC-seq

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Methyl-seq: Methyl-seq data were aligned using Bismark(v0.14.1) with Bowtie2 (version 2.2.5) allowing up to 1 mismatches (-N 1). The methylation calls at CpG sites were performed by bismark_methylation_extractor in the Bismark (v0.14.1) software. Methylation calls are deposited in processed data files. We used CpGs represented by at least 10 sequencing reads.
ATAC-seq: Mapping was performed by BWA (version 0.6.2) , allowing up to 2 mismatches, using the reference human genome, NCBI build 37 (hg19) .
ChIP-seq: Mapping was performed by BWA (version 0.6.2) , allowing up to 2 mismatches, using the reference human genome, NCBI build 37 (hg19) .
Genome_build: hg19

source_name: embryonic stem cells

extract_protocol: ChIP-seq: The sequencing library preparation including barcoding was conducted using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN). The Illumina libraries were sequenced with the TruSeq SBS kit v3 (Illumina) in 51-cycle Single-End mode of HiSeq 2500 (Illumina).

treatment_protocol: Human iPSC/ESCs were culture on mitomycin C-treated SNL feeder cells in Primate ES cell medium (ReproCELL) containing 4 ng/mL recombinant bFGF (Wako) unless mentioned otherwise. One ESC sample (sample name: SAMPLE 28, khES3 with 100 ng/ml bFGF) was cultured with increased concentration of bFGF (100 ng/ml) for 1 week. The human fibroblasts were cultured with Dulbecco's Modified Eagle Medium with 10% fetal bovine serum. The peripheral blood were freshly drawn from a volunteer, and subject to the analysis. The keratinocyte was purchased from ATCC, and cultured with Keratinocyte-SFM (1X), Liquid (Life Technologies).

value: undifferentiated embryonic stem cells cultured with our normal culture condition (4 ng/ml basic FGF (bFGF))


title: 409B2

source_name: induced pluripotent stem cells

value: undifferentiated induced pluripotent stem cells


title: 246G1


title: khES3 with 100 ng/ml bFGF

description: ATAC-seq

value: undifferentiated embryonic stem cells cultured with increased concentration of basic FGF (100 ng/ml) for 1 week


title: 692D2


title: N20U’-30SIC

value: mRNAs N20U captured by ribosome 30S initiation complex (repeated)


title: 201B6


title: khES1

value: undifferentiated embryonic stem cells

tag: antibody

value: anti-CTCF polyclonal antibody (ab070303, Abcam)


title: PRE-NACT-NORMAL [X144]

value: omental

value: PRE-NACT


title: Peripheral blood-SF91

source_name: Peripheral blood

value: Peripheral blood


title: 784D1 atac

description: ATAC-seq


title: N20U’-30S

value: mRNAs N20U captured by ribosome 30S subunit alone (repeated)


title: N20U’-Blank

value: blank control of mRNA N20U (repeated)


title: N20D-30SIC

value: mRNAs N20D captured by ribosome 30S initiation complex


title: N20D-30S

value: mRNAs N20D captured by ribosome 30S subunit alone


title: 7KE2 atac

description: ATAC-seq


title: 253G1


title: HDF-TIG120

source_name: human dermal fibroblasts

value: human dermal fibroblasts (HDF)


title: Keratinocyte-#1

source_name: keratinocytes

value: keratinocytes


title: N20D-Blank

value: blank control of mRNA N20D


title: 427F1


title: N20U-70SIC

value: mRNAs N20U captured by ribosome 70S initiation complex


title: 253G4


title: Kep1


title: 606A1


title: N20U-30S

value: mRNAs N20U captured by ribosome 30S subunit alone


title: N20U-30SIC

value: mRNAs N20U captured by ribosome 30S initiation complex


title: N20U-Blank

value: blank control of mRNA N20U


title: Sample 112: AMY_susceptible_imipramine_non_responder

city: New York

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Bowtie2, version 2.1.0, parameters: default
TopHat2, version 2.0.9, parameters --no-novel-juncs --b2-very-sensitive
HTSeq, version 0.6.0, parameters -s no
Genome_build: NCBIM37
Supplementary_files_format_and_content: HT-seq counts

source_name: Brain tissue

extract_protocol:
Mice were euthanized; brains were removed, coronally sliced and NAC, PFC, HIP and AMY tissues were rapidly dissected and frozen on dry ice. Tissue from 2 mice were pooled for each sample for n=3-5 biological replicates for each brain region and phenotype. RNA was isolated with TriZol reagent (Invitrogen) and purified with RNAeasy micro kits from Qiagen.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 protocol  with 1ug RNA (Illumina, San Diego, CA). Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with   sequencing adaptors. The libraries were size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer or Tape Station (Life Technologies, Grand Island, NY) before sequencing. Libraries were sequenced on the Illumina HiSeq 2500 System utilizing V3 chemistry with 50 base pair paired-end reads at the Mount Sinai Genomics Core Facility.

tag: brain region

value: Basolateral Amygdala

tag: group


title: 610B1

value: undifferentiated induced pluripotent stem cells


title: 751A3


title: Sample 111: AMY_susceptible_ketamine_non_responder


title: Sample 110: AMY_resilient_saline

value: Resilient, saline-treated


title: 784D1 bs


title: 751B4


title: TIG120-4F1


title: N20D-70SIC

value: mRNAs N20D captured by ribosome 70S initiation complex


title: 201B7


title: 744A2


title: Sample 108: HIP_susceptible_saline

value: Ventral Hippocampus

value: Susceptible, saline-treated


title: Sample 105: HIP_susceptible_saline


title: Sample 106: HIP_susceptible_ketamine_responder


title: Sample 107: HIP_susceptible_imipramine_responder


title: Sample 104: HIP_resilient_saline


title: Sample 103: HIP_control_saline

value: Control, saline-treated


title: Sample 109: AMY_control_saline


title: 585B1


title: 648B1


title: POST-NACT CRS2 X77

description:
RNA-Seq
X77

value: omental

value: POST-NACT


title: POST-NACT CRS2 X79

description:
RNA-Seq
X79


title: POST-NACT CRS2 X75

description:
RNA-Seq
X75


title: Sample 101: NAC_susceptible_imipramine_non_responder

value: Nucleus Accumbens


title: 404C2


title: Sample 102: NAC_susceptible_ketamine_non_responder


title: Sample 100: NAC_susceptible_ketamine_responder


title: POST-NACT CRS2 X33

description:
RNA-Seq
X33


title: POST-NACT CRS2 X17

description:
RNA-Seq
X17


title: Sample 99: NAC_susceptible_saline


title: POST-NACT CRS2 X15

description:
RNA-Seq
X15


title: 7KE2 bs


title: Sample 97: PFC_susceptible_imipramine_non_responder

value: Prefrontal Cortex


title: Sample 98: NAC_control_saline


title: POST-NACT CRS2 X11

description:
RNA-Seq
X11


title: POST-NACT CRS3 X102

description:
RNA-Seq
X102


title: Sample 95: PFC_resilient_saline


title: Sample 96: PFC_susceptible_ketamine_non_responder


title: POST-NACT CRS3 X92

description:
RNA-Seq
X92


title: Sample 94: PFC_control_saline


title: POST-NACT CRS3 X85

description:
RNA-Seq
X85


title: POST-NACT CRS3 X81

description:
RNA-Seq
X81


title: POST-NACT CRS3 X67

description:
RNA-Seq
X67


title: Sample 88: AMY_susceptible_imipramine_non_responder


title: POST-NACT CRS3 X58

description:
RNA-Seq
X58


title: Sample 90: AMY_susceptible_imipramine_responder


title: POST-NACT CRS3 X10

description:
RNA-Seq
X10


title: Sample 87: AMY_susceptible_ketamine_non_responder


title: 585A1


title: POST-NACT CRS3 X8

description:
RNA-Seq
X8


title: Sample 85: AMY_control_saline


title: Sample 84: HIP_susceptible_imipramine_responder


title: PRE-NACT X138

description:
RNA-Seq
X138

value: PRE-NACT


title: Sample 83: HIP_susceptible_imipramine_non_responder


title: POST-NACT CRS3 X29

description:
RNA-Seq
X29


title: Sample 81: HIP_resilient_saline


title: Sample 80: HIP_control_saline


title: PRE-NACT X124

description:
RNA-Seq
X124


title: PRE-NACT X82

description:
RNA-Seq
X82


title: Mouse DC 5-prime 4h rep2

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description:
exo-CAGE RNA
4 hours post LPS stimulation
processed data file: 5end_ESAT.gene.txt, 5end_ESAT.window.txt

data_processing:
mouse 3' and 5' alignments: Tophat v2.0.9, mm10, single-ended, default parameters to produce genome alignments (only R2 reads)
mouse 3' ESAT analysis parameters: wLen=100, wOlap=50, wExt=5000, sigTest=0.05, multimap=ignore, task=score3p, geneMapping:(mm10, only NM annotations). Produced output files 3end_ESAT.gene.txt and 3end_ESAT.window.txt.
mouse 5' ESAT analysis parameters: wLen=100, wOlap=50, wExt=5000, sigTest=0.05, multimap=ignore, task=score5p, geneMapping:(mm10, only NM annotations). Produced output files 5end_ESAT.gene.txt and 5end_ESAT.window.txt.
genome build: mm10
processed data files format and content: ESAT gene-level: tab-delimited text files containing gene/transcript ID, genomic location, and ESAT-quantified read counts for each gene/transcript, one data column per experiment or cell
processed data files format and content: ESAT window-level: tab-delimited text files containing window genomic location, and ESAT-quantified read counts for eachwindow, one data column per experiment or cell

source_name: 4 hours post LPS stimulation

extract_protocol:
Qiagen RNeasy
ExoCAGE

value: bone marrow

value: dendritic cell

tag: time

value: 4 hours


title: Mouse DC 5-prime 4h rep1


title: Sample 89: AMY_resilient_saline


title: Mouse DC 5-prime 2h rep2

description:
exo-CAGE RNA
2 hours post LPS stimulation
processed data file: 5end_ESAT.gene.txt, 5end_ESAT.window.txt

source_name: 2 hours post LPS stimulation

value: 2 hours


title: Mouse DC 5-prime 0h rep2

description:
exo-CAGE RNA
unstimulated
processed data file: 5end_ESAT.gene.txt, 5end_ESAT.window.txt

source_name: unstimulated

value: 0 hours


title: Sample 79: NAC_resilient_saline


title: Sample 86: AMY_susceptible_saline

value: Basolateral Amygdala


title: Mouse DC 5-prime 0h rep1


title: Sample 74: PFC_susceptible_imipramine_non_responder


title: Sample 73: PFC_susceptible_ketamine_non_responder


title: Sample 72: PFC_susceptible_saline


title: PRE-NACT X136

description:
RNA-Seq
X136


title: Sample 77: NAC_susceptible_ketamine_responder


title: Mouse DC 3-prime 4h rep2

description:
polyA RNA
4 hours post LPS stimulation
processed data file: 3end_ESAT.gene.txt, 3end_ESAT.window.txt

molecule: polyA RNA

extract_protocol:
Qiagen RNeasy
polyA selection


title: Mouse DC 3-prime 4h rep1


title: Sample 82: HIP_susceptible_ketamine_non_responder


title: Mouse DC 3-prime 6h rep2

description:
polyA RNA
6 hours post LPS stimulation
processed data file: 3end_ESAT.gene.txt, 3end_ESAT.window.txt

source_name: 6 hours post LPS stimulation

value: 6 hours


title: Sample 71: PFC_control_saline


title: Sample 78: NAC_susceptible_imipramine_responder


title: Mouse DC 3-prime 2h rep2

description:
polyA RNA
2 hours post LPS stimulation
processed data file: 3end_ESAT.gene.txt, 3end_ESAT.window.txt


title: Mouse DC 3-prime 0h rep2

description:
polyA RNA
unstimulated
processed data file: 3end_ESAT.gene.txt, 3end_ESAT.window.txt


title: Sample 65: AMY_susceptible_imipramine_non_responder


title: Mouse DC 5-prime 2h rep1


title: Sample 63: AMY_resilient_saline

value: Resilient, saline-treated


title: Sample 66: AMY_susceptible_imipramine_responder


title: Sample 64: AMY_susceptible_ketamine_non_responder


title: inDrop SC BBDR rat islet cells

description:
polyA RNA
non-diabetic inDrop SC sample

data_processing:
rat islet SC analysis: step 1 - select reads with valid or correctable cell barcodes and UMIs with no Ns from R1 reads. Concatenate ":<cell barcode>:<UMI>" to the corresponding R2 read name and save into a modified version of the R2 reads file contaning only reads with valid barcodes and UMIs. (Custom Python script. Also produces barcode counts file contining the number of reads from each barcode.)
rat islet SC analysis step 1 detail:  The cell and transcript barcoding methodology is described in detail in Supplemental information of "Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells", Klein, et al., Cell 161, 1187–1201 (2015), Table S5. Briefly, the custom Python script processes the R1 and R2 fastq files in parallel, one read at a time. It first locates the two 8-base barcode segments (bc1 and bc2) in the R1 read, and applies error-correction if necessary to determine if the barcodes are valid. If they are valid (or correctable) they are concatenated into a single BC. The unique molecular identifier (UMI) is then located and checked to ensure that it doesn't contain any Ns. If the barcode is not valid (or correctable) or the UMI contains Ns, the read pair is discarded. Otherwise, the barcode and UMI are appended to the corresponding R2 read name with the colon-separated format ":<BC>:<UMI>". Only reads with valid barcodes and UMIs are saved, and the resulting R2 (sequence) file is treated as single-ended, carrying the cell barcode an UMI with the read name for the remainder of the analysis. The script also keeps a count of the number of reads from each cell barcode and writes a 'barcode counts' file after processing all reads.
rat islet SC analysis: step 2 - process step 1 output with Tophat v2.0.9, rn5, single-ended, default parameters to produce genome alignment file.
rat islet SC analysis: step 3 - filter alignments from step 2 to remove any reads from barcodes with too few reads (fewer than 13,000 reads for this analysis) using barcode counts file generated in step 1 (custom Python script). This step reduces both the memory requirements and processing time for ESAT.
rat islet SC analysis: step 4 - ESAT analysis parameters: wLen=100, wOlap=50, wExt=5000, sigTest=0.05, multimap=ignore, task=score3p, -scPrep, geneMapping:(rn5, only NM annotations). Produced output files RatIsletInDrop_ESAT.gene.txt and RatIsletInDrop_ESAT.window.txt output files.
rat islet SC analysis: step 5 - ICA/t-SNE/clustering analysis of ESAT output (custom R script). Produced the Heatmap_GeneList.xlsx file.
genome build: rn5
processed data files format and content: ESAT gene-level: tab-delimited text files containing gene/transcript ID, genomic location, and ESAT-quantified read counts for each gene/transcript, one data column per experiment or cell
processed data files format and content: ESAT window-level: tab-delimited text files containing window genomic location, and ESAT-quantified read counts for eachwindow, one data column per experiment or cell

organism: Rattus norvegicus

source_name: non-diabetic inDrop SC sample

extract_protocol:
cells lysed in droplets
modified CEL-Seq

value: pancreas

value: pancreatic islets


title: Sample 62: AMY_control_saline


title: Sample 76: NAC_resilient_saline


title: Sample 75: PFC_resilient_saline


title: Sample 61: HIP_control_saline

value: Ventral Hippocampus


title: Sample 60: HIP_susceptible_imipramine_responder


title: Fore wing Input chromatin rep2

first: Shreeharsha

last: Tarikere

address: 16 Divinity Avenue, Biolabs

department: Organismic and Evolutionary Biology

institute: Harvard University

description: FW rep 2 Input control

data_processing:
The fastq files obtained were aligned to the silkworm genome ver 2.0 (SilkDB) using bowtie 0.12.7 valentine. Using the command line " ./bowtie silk_index -q ChIP_reads_file.fastq -M 1 -S -5 3 -v 3 aligned_output_file.sam -p3"
Aligned BAM files were used to call peaks with MACS ver1.4.2. Both the anti Ubx pulldown experiment or the Normal sera negative control were normalized against the Input bam files. The following parameters were used in Peak calling "macs14 -t aligned_output_experiment/negative_control-file.bam -c aligned_input_control-file.bam -g 3.11e+08 --keep-dup=2 -nNameofpeaksfile_exp_vs_input"
The peaks common to Negative and anti Ubx datasets were deleted. An FDR cutoff of 15% was used to select the final set of peaks.
The common peaks between replicate 1 and 2 were selected through bedtools intersect tool with a minimum intersect of 1 nucleotide overlap.
Genes were allocated to a peak using Galaxy tool "fetch both up and downstream " and also intersecting the peak file with Bombyx gtf annotation file (SilkDB v2.0) to obtain all genes corresponding to a peak spanning 10Kb up and downstream.
Genome_build: SilkDB ver 2.0 silkworm genome. (ftp://silkdb.org/pub/current/Genome/silkworm_genome_v2.0.fa)
Supplementary_files_format_and_content: Excel sheets with peak locations (chr (scaffold), start, end, length, summit, tags, MACS_peak_#, -10*log10(pvalue), fold enrichment, FDR(%)).
Supplementary_files_format_and_content: Bed file header- chr, start, end, MACS_peak_#, -10*log10(pvalue), fold enrichment, FDR(%)

organism: Bombyx mori

source_name: Fore Wing buds

growth_protocol: Larvae were maintained at 25C and fed on Morus alba leaves.

extract_protocol:
Fore and Hind wing buds (80 each) were isolated from second and third thoracic segments of the fourth instar larvae after temporarily aneasthetizing them on ice.The buds were isolated in cold PBS with Roche Protease inhibitor cocktail. The Wing buds were subjected to quick hypotonic lysis to obtain nuclei.
Chromatin Immunoprecipitation was carried out on equal volumes of wing bud Chromatin for experiment and negative control, while retaining 10% for input normalization control.The experimental pulldown was carried out using anti Bombyx N terminal Ubx antibodies generated by us. The antibodies against the 19 KDa N terminal region of Ubx protein that are specific to Bombyx Ubx were raised in Rabbit and the resultant antiserum obtained was purified against Milipore Prosep Protein A column to isolate the IgG fraction that was used for the anti Ubx ChIP pulldown. The negative control experiment was carried out using the Normal Rabbit IgG antibodies supplied with the Invitrogen Magnify Chromatin Immunoprecipitation kit, this dataset was used to eliminate non specific peaks from the anti Ubx pulldown set. Libraries for ChIP sequencing were constructed according to a modification of the Illumina ChIP Seq library protocol outlined in “Preparing Samples for ChIP Sequencing of DNA” (Part # 11257047, Rev. A, 2007). Briefly, DNA was subjected to a series of enzymatic reactions that repair frayed ends, phosphorylate the fragments, add a single nucleotide A overhang and ligate adaptors (Illumina ChIP Seq Library preparation kit). The libraries were enriched using PCR (18 cycles), post PCR cleanup was performed using Agencourt AMPURE XP beads (Beckman Coulter #A63881). The enriched PCR fragments were size selected using a 2 % Low melting agarose gel and purified using MinElute Gel Extraction Kit (QIAGEN). The prepared libraries were quantified using Nanodrop Spectrophotometer and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent).

treatment_protocol: Nuclei were isolated from wing buds and fixed with 1% formaldehyde (in PBS) for 12 mins.The fixing was stopped by adding Glycine to a final concentration of 1.25 M for 5 minutes. Sonication of the lysed nuclei was done on Diagenode® Bioruptor XL for a total time of 15 minutes with 55 sec on /60 sec off cycle at high power.

value: Daizo

tag: developmental stage

value: larval

tag: larval instar

value: IV

value: Fore Wing buds

value: none (input)


title: Mouse DC 3-prime 6h rep1

tag: tissue


title: Fore wing anti Ubx ChIP pulldown rep2

description: FW rep 2 Experiment

value: anti-Ubx (made in-house)


title: Fore wing negative IgG control rep2

description: FW rep 2 IgG control

value: anti-IgG (supplied with the Invitrogen Magnify Chromatin Immunoprecipitation kit)


title: Sample 58: HIP_resilient_saline


title: Hind wing negative IgG control rep2

description: HW rep 2 IgG control

source_name: Hind Wing buds

value: Hind Wing buds


title: Sample 59: HIP_susceptible_ketamine_responder


title: Hind wing anti Ubx ChIP pulldown rep2

description: HW rep 2 Experiment


title: Mouse DC 3-prime 2h rep1

value: bone marrow

value: dendritic cell


title: Fore wing negative IgG control rep1

description: FW rep 1 IgG control


title: Sample 56: NAC_susceptible_imipramine_non_responder

value: Nucleus Accumbens


title: Sample 57: NAC_control_saline

value: Control, saline-treated


title: Sample 55: NAC_susceptible_ketamine_non_responder


title: Fore wing Input chromatin rep1

description: FW rep 1 Input control


title: Fore wing anti Ubx ChIP pulldown rep1

description: FW rep 1 Experiment


title: Hind wing Input chromatin rep1

description: HW rep 1 Input control


title: Hind wing anti Ubx ChIP pulldown rep1

description: HW rep 1 Experiment


title: Sample 53: NAC_control_saline


title: Sample 51: PFC_susceptible_imipramine_non_responder

value: Prefrontal Cortex


title: Sample 50: PFC_susceptible_ketamine_non_responder


title: Hind wing negative IgG control rep1

description: HW rep 1 IgG control


title: Sample 52: PFC_susceptible_imipramine_responder


title: Hind wing bud RNA sequence left and right reads

data_processing:
Both fore and hind wing reads were trimmed by 10 bases at start and end of the read to remove low quality reads using the tool seqtk. "seqtk trimfq -b 10 -e 10 input.fastq > output.fastq"
The fastq files obtained were aligned to the silkworm genome ver 2.0 (SilkDB) using Tophat2.0.8b /Bowtie2.1.0 using default parameters.
The aligned reads were assembled using Cufflinks v2.1.1 using default parameters.
Cuffdiff was used to calculate the differential expression between HW (q2) and FW (q1) paired datasets using default parameters.
Genes were allocated to a peak using Galaxy tool "fetch both up and downstream " and also intersecting the peak file with Bombyx gtf annotation file (SilkDB v2.0) to obtain all genes corresponding to a peak spanning 10Kb up and downstream.
Genome_build: SilkDB ver 2.0 silkworm genome. (ftp://silkdb.org/pub/current/Genome/silkworm_genome_v2.0.fa.tar.gz)
Supplementary_files_format_and_content: transcript.gtf files include transcripts identified for fore wing and hind wing samples.
Supplementary_files_format_and_content: Gene_exp.diff is a tab seperated value file containing the differential expression between fore and hind wing bam files obtained from cuffdiff. A q-value based significance is indicated as 'yes' or 'no' in the last column.

extract_protocol:
Fore and Hind wing buds were isolated from second and third thoracic segments of the fourth instar larvae after temporarily aneasthetizing them on ice. The Wing buds were plunged directly into liquid Nitrogen and stored at -80C prior to trizol extraction of the RNA. The extracted RNA was processed through Agen court purification before proceedng for library preperation.
Transcriptome library for sequencing was constructed according to the Illumina TruSeq RNA library protocol outlined in “TruSeq RNA Sample Preparation Guide” (Part # 15008136; Rev. A; Nov 2010). Briefly, the Total RNA was fragmented for 4 minutes at elevated temperature (94oC) in the presence of divalent cations and reverse transcribed with Superscript II Reverse transcriptase by priming with Random Hexamers. Second strand cDNA was synthesized in the presence of DNA Polymerase I and RnaseH. The cDNA was cleaned up using Agencourt Ampure XP SPRI beads (Beckman Coulter). Illumina Adapters were ligated to the cDNA molecules after end repair and addition of “A”- base. SPRI cleanup was performed after ligation. The library was amplified using 11 cycles of PCR for enrichment of adapter ligated fragments. The prepared library was quantified using Nanodrop and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent)

treatment_protocol: The Larval wing buds (80) were isolated and plunged directly into liquid nitrogen before trizol extraction.


title: Sample 48: PFC_control_saline


title: Fore wing bud RNA sequence left and right reads

data_processing:
Both fore and hind wing reads were trimmed by 10 bases at start and end of the read to remove low quality reads using the tool seqtk. "seqtk trimfq -b 10 -e 10 input.fastq > output.fastq"
The fastq files obtained were aligned to the silkworm genome ver 2.0 (SilkDB) using Tophat2.0.8b /Bowtie2.1.0 using default parameters.
The aligned reads were assembled using Cufflinks v2.1.1 using default parameters.
Cuffdiff was used to calculate the differential expression between HW(q2) and FW (q1) paired datasets using default parameters.
Genes were allocated to a peak using Galaxy tool "fetch both up and downstream " and also intersecting the peak file with Bombyx gtf annotation file (SilkDB v2.0) to obtain all genes corresponding to a peak spanning 10Kb up and downstream.
Genome_build: SilkDB ver 2.0 silkworm genome. (ftp://silkdb.org/pub/current/Genome/silkworm_genome_v2.0.fa.tar.gz)
Supplementary_files_format_and_content: transcript.gtf files include transcripts identified for fore wing and hind wing samples.
Supplementary_files_format_and_content: Gene_exp.diff is a tab seperated value file containing the differential expression between fore and hind wing bam files obtained from cuffdiff. A q-value based significance is indicated as 'yes' or 'no' in the last column.


title: Sample 42: AMY_susceptible_ketamine_responder

value: Basolateral Amygdala


title: Sample 40: AMY_control_saline


title: Hind wing Input chromatin rep2

description: HW rep 2 Input control


title: Sample 43: AMY_susceptible_imipramine_non_responder


title: Sample 41: AMY_susceptible_saline

value: Susceptible, saline-treated


title: Sample 38: HIP_susceptible_imipramine_non_responder


title: Sample 39: HIP_susceptible_imipramine_non_responder


title: Sample 36: HIP_resilient_saline

value: Resilient, saline-treated


title: Sample 37: HIP_susceptible_ketamine_non_responder

value: Ventral Hippocampus


title: Sample 54: NAC_susceptible_saline


title: Sample 33: NAC_susceptible_ketamine_responder


title: Sample 35: NAC_susceptible_imipramine_non_responder


title: Sample 31: NAC_resilient_saline


title: Sample 30: NAC_control_saline


title: Sample 32: NAC_susceptible_saline


title: Sample 49: PFC_resilient_saline


title: Sample 27: PFC_susceptible_ketamine_responder


title: Sample 26: PFC_susceptible_saline


title: Sample 25: PFC_control_saline


title: Sample 21: AMY_susceptible_imipramine_responder


title: Sample 29: PFC_susceptible_ketamine_responder


title: Sample 17: AMY_control_saline


title: Sample 28: PFC_susceptible_imipramine_non_responder


title: Sample 44: AMY_susceptible_ketamine_responder


title: Sample 19: AMY_susceptible_saline


title: Sample 15: HIP_susceptible_imipramine_non_responder


title: Sample 16: HIP_susceptible_ketamine_non_responder


title: Sample 14: HIP_susceptible_ketamine_responder


title: Sample 12: HIP_control_saline


title: Sample 13: HIP_susceptible_saline


title: Sample 18: AMY_resilient_saline


title: Sample 11: NAC_susceptible_imipramine_responder


title: Sample 20: AMY_susceptible_ketamine_responder


title: Sample 10: NAC_susceptible_imipramine_non_responder


title: Sample 7: NAC_control_saline


title: Sample 6: PFC_susceptible_imipramine_responder


title: Sample 9: NAC_susceptible_ketamine_non_responder


title: Sample 5: PFC_susceptible_imipramine_responder


title: Sample 8: NAC_resilient_saline


title: Sample 34: NAC_susceptible_imipramine_responder


title: Sample 3: PFC_susceptible_saline


title: Sample 4: PFC_susceptible_ketamine_responder


title: Sample 1: PFC_control_saline


title: Sample 2: PFC_resilient_saline


title: CTRLT3C_study2

city: Ste-Anne-de-Bellevue

first: Timothy

middle: G.

last: Geary

state: Quebec

address: 21,111 Lakeshore Rd

department: Parasitology

country: Canada

institute: McGill University

data_processing:
unaligned fastq files were groomed using Fastq Groomer (v 1.0.4)
quality control statistics were verified using FastQC: Reads QC (version 0.52).
Quality and adapter trimming was performed using Fastq Quality Trimmer (v 1.0.0) and Trim Galore (v 0.2.8.1)
Tophat2 (v 0.6) was used for mapping gapped reads to the B. malayi reference genome (Bmalayi V3 243 reference)
HTSeq-count (version 1.0.0) was used to count the number of reads per transcript
edgeR (version 3.10.5)  was used to perform differential expression analysis between time points
Genome_build: Bmalayi V3 243 reference
Supplementary_files_format_and_content: txt files containing read counts matrix (First Study and Second Study)

organism: Brugia malayi

source_name: adult female worms

growth_protocol: Groups were incubated 1 worm per well of a 12-well plate (Costar) containing 6 ml RPMI 1640 (Sigma-Aldrich, St. Louis MO) supplemented with 10% v/v heat-inactivated fetal bovine serum (Sigma-Aldrich, F1051), 5% penicillin/streptomycin (Sigma–Aldrich) and 2% gentamycin (Gibco, 15750-060)

extract_protocol:
RNA extracted using Trizol method.
Messenger RNA (mRNA) was enriched with a NEBNext® Poly (A) mRNA Magnetic Isolation Module (NEB, E7490, Ipswich, MA). Using the enriched mRNA as template, cDNA libraries were constructed using the NEBNext® Ultra RNA Library Prep Kit Illumina (NEB, E7530, Ipswich, MA) and NEBNext® Multiplex Oligos for Illumina (Index Primer 1-12) (NEB, E7600, Ipswich, MA) following the manufacturer’s instructions. To verify the quality, DNA concentration and product size of the cDNA libraries, a Qubit® 2.0 Fluorometer (Life Technologies, Q32866), Qubit® dsDNA BR assay kit (Life Technologies, Q32850), High Sensitivity DNA Analysis Kit (Agilent, 5067-4626) and Bioanalyzer were used. cDNA libraries were sequenced on an Illumina MiSeq® Platform employing a 150 base pair single-end NGS setting.

treatment_protocol: Groups were either untreated or exposed to 100 nM IVM for up to 72 hours, 300 nM for up to 5 days, or 1 uM for up to 5 days

tag: gender

value: female

value: adult

tag: study number

value: Study 2

tag: ivm concentration

tag: time point

value: RNA extraction at 5 d


title: IVM1T3A_study2


title: IVM2T3A_study2

value: 1 uM


title: IVM1T3C_study2


title: IVM1T3B_study2


title: IVM2T2B_study2

value: RNA extraction at 48 h


title: IVM2T2C_study2


title: IVM2T2A_study2


title: CTRLT3A_study2


title: IVM1T2B_study2


title: IVM1T2C_study2


title: CTRLT2C_study2


title: CTRLT2B_study2


title: 794F

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

description:
RNA purification method: EtOH precip.
no processed data; removed as outlier

data_processing:
Reads were filtered with Trim Galore v.0.3.1 with the following parameters: --q 20 --l 25 --s 3
Reads were mapped to the Canis lups familiaris genome (Ensembl CanFam3.1.74, unmasked) using Tophat2 v.2.0.10. We allowed up to 3 mismatches, a total of 3 bp length of gaps, and an edit distance no more than 3 bp between the reads and the ref sequence.
The expression level of each gene was quantified using the union mode of the python script htseq-count (HTSeq 0.6.1)
Genes were filtered to only include protein-coding genes with at least 10 reads in at least 75% of cDNA libraries (N = 13,558 protein-coding genes).
We used conditional quantile normalization (cqn package in R) to normalize for sequencing depth (TMM), GC-content, and gene length (averaged from the transcripts in the canFam3.1.74 gtf file).
Supplementary_files_format_and_content: Tab-delimited text file containing gene transcript abundance measurements. The unit of measure is the log2 transformed read counts controlling for library size, GC content, and gene length, as produced by CQN (R package) and analagous to RPKM.

organism: Canis lupus

source_name: Whole blood

extract_protocol:
Whole blood was preserved in PAXgeneTM Blood RNA tubes. Total RNA was extracted using the PAXgene Blood RNA kit.Total RNA was treated with the Globin-Zero kit and purified with the Qiagen RNeasy MinElute® column cleanup procedure or ethanol precipitation (listed in description column).
cDNA libraries were synthesized using a strand-specific kit from Epicentre (ScriptSeqTM v2 Library Prep kit, Illumina) with ScriptSeq Indexes PCR primers.

tag: age (years)

tag: social rank

value: Alpha


title: 871M

description: RNA purification method: Column

value: male


title: 869M

description: RNA purification method: Column

value: Subordinate


title: T1B_study2

value: RNA extraction upon arrival at McGill


title: T1C_study2


title: 641M


title: 829F

description: RNA purification method: Column


title: 832F

description: RNA purification method: EtOH precip.


title: T1A_study2


title: pkm2_p53_3

city: Bad Nauheim

middle: Andrew

last: Stone

address: Ludwigstr 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute

description: si-PKM2 and sip53

data_processing:
Read quality trimming with Reaper 13-100 (-geom no-bc -3pa -clean-length 30 -qqq-check 53/20 -trim-length 150)
Mapping of reads versus human genome version GRCh37.p5 hg19 using STAR 2.4.0a (--outFilterMismatchNoverLmax 0.1)
Read counting per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters
Differentially expressed genes were identified using DESeq2 version 1.62
Raw gene counts were normalized with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all genes

source_name: HUVEC, si-PKM2 and sip53

growth_protocol: Primary Human Umbilical Vein Endothelial Cells were grown in EGM-2 media (Lonza)

extract_protocol:
Total RNA was extracted and DNase treated using the Rneasy mini kit (Qiagen)
RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 2µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina)

treatment_protocol: siRNA duplexes were transfected into subconfluent cells using RNAi Max and cells were collected for RNA extraction 48 hrs after transfection

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: passages

tag: sirna treatment

value: si-PKM2 and sip53


title: CTRLT3B_study2


title: 828M

description: RNA purification method: Column

tag: Sex


title: IVMT4B_study1

value: Study 1

value: RNA extraction at 72 h


title: pkm2_p53_2

description: si-PKM2 and sip53


title: 825F

description: RNA purification method: Column


title: pkm2_p53_1

description: si-PKM2 and sip53


title: pkm2_3

source_name: HUVEC, si-PKM2


title: 823F

description: RNA purification method: EtOH precip.


title: CTRLT4B_study1


title: CTRLT2A_study2


title: IVMT4A_study1


title: pkm2_2


title: IVMT3B_study1


title: 870F

description: RNA purification method: Column


title: CTRLT4A_study1


title: 820F

description: RNA purification method: Column


title: scr_p53_3

source_name: HUVEC, si-p53


title: IVMT3A_study1


title: IVM2T3B_study2


title: 818F

description: RNA purification method: Column


title: scr_p53_2


title: 819F

description: RNA purification method: EtOH precip.


title: 779F

description: RNA purification method: EtOH precip.


title: IVMT2B_study1

value: RNA extraction at 24 h


title: CTRLT3A_study1


title: scr_p53_1


title: 778M

description: RNA purification method: EtOH precip.


title: scr_3

description: scrambled

source_name: HUVEC, scrambled

value: scrambled


title: 824M

description: RNA purification method: EtOH precip.


title: IVMT2A_study1


title: 777M

description: RNA purification method: EtOH precip.


title: 776F

description: RNA purification method: EtOH precip.


title: pkm2_1


title: CTRLT2A_study1


title: 775M

description: RNA purification method: EtOH precip.


title: scr_1

description: scrambled


title: CTRLT2B_study1


title: T1A_study1


title: IVM1T2A_study2


title: T1B_study1


title: sw763M

description: RNA purification method: Column

value: Beta


title: 661M

description: RNA purification method: Column


title: 759F

description: RNA purification method: Column

value: female


title: 822F

description: RNA purification method: Column


title: 712M

description: RNA purification method: EtOH precip.


title: 471F

description: RNA purification method: EtOH precip.


title: hg19_shMLL1_RNA_150410_rep3

status: Public on Jul 26 2016

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Cells lentiviral infected with MLL1 specific shRNA vector

data_processing:
Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
RNA-seq reads were aligned to UCSC hg19 and dm3 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: hg19
processed data files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit.
Stranded Total RNA Preparation Kit with

treatment_protocol: Treatment with GSK126[5uM] or DMSO was administrated at 0- and 48-hour; harvesting cells at 96-hours.

tag: cell type

value: Human colorectal tumor

value: Low passages (6-10)

tag: cell line

tag: chip antibody


title: 586M

description: RNA purification method: EtOH precip.


title: hg19_shMLL1_RNA_150331_rep1


title: hg19_shMLL1_RNA_150408_rep2


title: hg19_shMLL1_H3K4me3_150727_rep2

data_processing:
Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 and dm3 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: hg19
processed data files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

extract_protocol:
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: H3K4me3 (homemade)


title: hg19_shMLL1_Input_150331


title: hg19_shMLL1_Input_150727


title: scr_2

description: scrambled


title: hg19_shMLL1_H3K4me3_150408_rep1


title: hg19_shMLL1_Input_150408


title: hg19_shMLL1_H3K4me2_150727_rep2

value: H3K4me2 (homemade)


title: hg19_shMLL1_H3K4me2_150408_rep1


title: hg19_shMLL1_H3K4me1_150727_rep2

value: H3K4me1 (homemade)


title: hg19_shMLL1_H3K27me3_150331_rep1

value: H3K27me3 (homemade)


title: hg19_shMLL1_H3K4me1_150408_rep1


title: 636M

description: RNA purification method: EtOH precip.

value: male

value: Alpha


title: hg19_shMLL1_H3K27me3_150408_rep2


title: hg19_shGFP_RNA_150331_rep1

description: Cells lentiviral infected with non-targeting shRNA vector


title: hg19_shMLL1_H3K27ac_150408_rep2


title: hg19_shGFP_RNA_150408_rep2


title: hg19_shGFP_Input_150408


title: hg19_shGFP_RNA_150410_rep3


title: hg19_shGFP_Input_150331


title: hg19_shGFP_H3K4me3_150727_rep2


title: hg19_shGFP_Input_150727


title: hg19_shGFP_H3K4me2_150408_rep1


title: hg19_shGFP_H3K4me3_150408_rep1


title: hg19_shGFP_H3K4me1_150408_rep1


title: hg19_shGFP_H3K4me1_150727_rep2


title: hg19_shGFP_H3K27me3_150408_rep2


title: hg19_deltaMLL1_GSK_RNA_160219_rep2

description: Cells treated with GSK126 [5uM] for 4 days

source_name: HCT116 (MLL1-null)

value: Human colorectal tumor (MLL1-null)


title: hg19_shGFP_H3K27ac_150331_rep1


title: hg19_shGFP_H3K27me3_150331_rep1


title: hg19_shGFP_H3K27ac_150408_rep2


title: CTRLT3B_study1

value: adult

value: RNA extraction at 48 h


title: hg19_deltaMLL1_DMSO_RNA_160219_rep2

description: Cells treated with DMSO for 4 days


title: hg19_deltaMLL1_GSK_RNA_160219_rep1


title: hg19_WT_GSK_RNA_160219_rep2


title: hg19_deltaMLL1_DMSO_RNA_160219_rep1

description: Cells treated with DMSO for 4 days


title: hg19_WT_GSK_RNA_160219_rep1


title: hg19_shMLL1_H3K27ac_150331_rep1


title: hg19_WT_DMSO_RNA_160219_rep2

description: Cells treated with DMSO for 4 days


title: hg19_WT_DMSO_RNA_160219_rep1

description: Cells treated with DMSO for 4 days


title: hg19_MLL1_WT_Input_160121


title: hg19_MLL1_WT_Input_160322


title: hg19_MLL1_NULL_Input_160121

extract_protocol:
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
1000 Kit


title: Ly5.2 macrophages rep2

city: Madrid

first: Francisco

last: Sanchez-Madrid

address: Diego de Leon 62

country: Spain

institute: Hospital Universitario de la Princesa

data_processing:
Bcl files were generated with RTA  v1.8 (Illumina, San Diego, CA). Demultiplexed fastQ files were generated with CASAVA  v1.8 (Illumina, San Diego, CA)
Reads were pre-processed with Cutadapt 1.2.1, to remove both TruSeq adaptor and SMARTer primer sequences.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) and genome, using RSEM v1.2.3 and Bowtie2 v2.0.6. The observation that a significant fraction of reads could be mapped on the genome, but not on the transcriptome, in close proximity to dA/dT-rich sequences, suggested that traces of contaminant genomic DNA could  have  been artifactually amplified by poly(A) priming.
Read clusters mapped on the genome at less than 50 bp downstream of dT-rich or upstream dA-rich regions were discarded, to avoid overestimation of transcript read counts.
Filtered reads were mapped again on the transcriptome, and quantified, with RSEM v1.2.3.
Genome_build: GRCm38
Supplementary_files_format_and_content: OB_fpkm_table.csv file contains ENSEMBL gene IDs and FPKM counts for each sample.

source_name: Skin-resident macrophages

extract_protocol:
Skin samples were digested with 2mg/ml crude collagenase type IA (Gibco) in PBS for 2h at 37ºC. Samples were then mechanically disrupted, washed and filtered. Flow cytometry staining was performed to isolate skin macrophages from donor (CD45.1, F4/80 high, CD11b+, CD11c-, MHC-II int) and host (CD45.2, F4/80 high, CD11b+, CD11c-, MHC-II low) by sorting.
cDNA synthesis and amplification were performed directly from cells using the Smarter Ultra Low RNA kit (Clontech). Amplified cDNAs (10ng) were fragmented using Covaris E220 (Covaris) to an average fragment size of approximately 150pb
Barcode-tagged sequencing libraries were generated from the fragmented cDNAs using the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA), starting from the End Repair step, followed by A tailing, adaptor ligation and PCR enrichment. The following barcodes were used: TTAGGC (Q1_5_2); ATCACG (Q2_5_1); TGACCA (Q2_5_2); CGATGT (Q4_5_1)

treatment_protocol: Chimeric mice of C57BL/6 background expressing the CD45 haplotype Ly5.2 were lethally irradiated and reconstituted with bone marrow from B6SJL

tag: strain

value: macrophages

value: skin


title: hg19_MLL1_WT_H3K27me3_160322


title: hg19_MLL1_NULL_H3K4me2_160121

extract_protocol:
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
of total RNA was used as starting material. Libraries were validated using the Agilent DNA


title: Ly5.1 macrophages rep2


title: hg19_MLL1_NULL_H3K27me3_160322

extract_protocol:
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg


title: Ly5.1 macrophages rep1


title: hg19_shGFP_H3K4me2_150727_rep2


title: WT

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

data_processing:
ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads after filtering low-quality data 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). For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene ID, transcript ID, gene name, gene description, expression level

source_name: Cerebral cortex

extract_protocol:
Total RNA was extracted from mouse cerebral cortex or hippocampus using NucleoSpin® miRNA (Macherey-Nagel, 740971).
SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies)


title: dm3_dsTrx_2_Input_140226

description: Cells treated with Trx-specific dsRNA

data_processing:
Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 and dm3 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: dm3
processed data files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

organism: Drosophila melanogaster

value: embryo-derived


title: dm3_dsTrx_2_H3K4me3_130821_rep1

description: Cells treated with Trx-specific dsRNA


title: hg19_MLL1_WT_H3K4me2_160121


title: dm3_dsTrx_2_RNA_130808_rep2

description: Cells treated with Trx-specific dsRNA

data_processing:
Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
RNA-seq reads were aligned to UCSC hg19 and dm3 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: dm3
processed data files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.


title: dm3_dsTrx_2_H3K4me2_130821_rep1

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_1_H3K27me3_151208_rep2

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_2_H3K27ac_140226_rep1

description: Cells treated with Trx-specific dsRNA

value: H3K27ac (homemade)


title: dm3_dsTrx_2_H3K4me1_130821_rep1

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_1_Input_140127

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_1_H3K27ac_151208_rep2

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_1_RNA_130718_rep1

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_2_H3K27me3_140226_rep1

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_1_H3K4me3_140127_rep2

description: Cells treated with Trx-specific dsRNA


title: dm3_dsTrx_1_H3K4me2_140127_rep2

description: Cells treated with Trx-specific dsRNA


title: dm3_dsLacZ_H3K27me3_151208_rep2

description: Cells treated with non-targeting dsRNA


title: dm3_dsTrx_1_H3K4me1_140127_rep2

description: Cells treated with Trx-specific dsRNA


title: dm3_dsLacZ_H3K27ac_151208_rep2

description: Cells treated with non-targeting dsRNA


title: Ly5.2 macrophages rep1


title: dm3_dsTrr_2_Input_140127

description: Cells treated with Trr-specific dsRNA


title: F16_rep2

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

data_processing:
QC with FastQC (defaults)
Trimming with Trimmomatic (defaults)
Mapping with Tophat (defaults)
Exp analysis using Cufflinks (cufflinks-2.1.1.Linux_x86_64) (defaults)
DE genes were visualized in MapMan software
Genome_build: Transcripts combined from two other papers as mentioned in the manuscript was used as reference (see Ali_alfalfa_reference_split.fasta linked as supplementary file on the Series record).
Supplementary_files_format_and_content: [gene_exp.diff] file reports FPKMs

organism: Medicago sativa

growth_protocol: Alfalfa forage samples were grown in hydroponic sand tanks situated in a greenhouse facility at the Canadian Salt Lab at Swift Current, SK, Canada. Seeds for each population were placed 13 mm deep into the sand bed and positioned 40 mm apart within and between the rows, resulting in 641 seed m-2. Upon completion of emergence (after 1 month), the surviving plants were thinned to 25 genotypes (individuals have unique genotypes within the overall population) per tank quadrant. Each tank held three randomly chosen salinity-tolerant populations (i.e., three quadrants) and the remaining quadrant (randomized for within-tank position) held 25 genotypes of a more salt-sensitive AC Rangelander population.

extract_protocol:
RNA was extracted using Qiagen Rneasy Plant mini kit.  RNA quantity and quality was assessed using a Qubit fluorometry assay (Invitrogen Corp., Carlsbad, CA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), respectively.
Libraries were prepared using a Truseq stranded mRNA kit (Illumina, San Diego, USA) following the manufacturer’s instructions.

treatment_protocol: Three electrical conductivity (EC) test levels formulated together with hydroponic growth solutions were used to irrigate the tanks: 1.53 dSm-1 as the no-salt control solution, and 8.03 and 15.61 dSm-1 as salt-supplemented solutions containing increased concentrations of sulphate-based sodium, calcium, and magnesium salts (composition fully defined in Steppuhn et al., 2012). Each EC level was replicated three times, and the two salinity-tolerant populations were replicated four times among the tanks, such that a total of 100 genotypes per salt-tolerant population were in the experiment. This covered the entire genotypic variation within each outcrossed alfalfa population at each EC level, and the salt-sensitive Rangelander genotypes were included in every tank as a population and tank control (Figure 1D). Since growth was retarded in all populations irrigated at 15.61 dSm-1, high-EC tanks were also positioned at an outer edge so that small plants would not be over-shadowed by vigorously  growing plants at the other EC levels (Figure 1D). Sand tanks were irrigated 4 times (for 5 min each) over a 24 h cycle with the hydroponic solutions. Harvest date was determined when the 4th-regrowth forage was at 10% flowering in populations growing at 1.53 dSm-1.

tag: growth protocol

value: grown under 15.61 dS/m salt condition

value: leaf and stem


title: F16_rep3


title: KO


title: dm3_dsTrr_2_H3K4me2_140127_rep2

description: Cells treated with Trr-specific dsRNA


title: dm3_dsTrr_1_H3K4me2_130915_rep1

description: Cells treated with Trr-specific dsRNA


title: dm3_dsLacZ_dSet1_131016_rep2

description: Cells treated with non-targeting dsRNA

value: dSet1 (homemade)


title: F16_rep1


title: dm3_dsLacZ_TrxNT_131016_rep2

description: Cells treated with non-targeting dsRNA

value: Low passages (6-10)

value: TrxNT (homemade)


title: dm3_dsLacZ_dSet1_130915_rep1

description: Cells treated with non-targeting dsRNA


title: F8_rep2

value: grown under 8 dS/m salt condition


title: F8_rep1


title: dm3_dsLacZ_TrxCT_131016_rep2

description: Cells treated with non-targeting dsRNA

value: TrxCT (homemade)


title: F1_rep2

value: grown under 1.53 dS/m salt condition


title: F1_rep3


title: C16_rep3

value: Bridgeview


title: F1_rep1


title: C16_rep2


title: dm3_dsLacZ_Input_140226

description: Cells treated with non-targeting dsRNA


title: dm3_dsLacZ_TrxCT_130915_rep1

description: Cells treated with non-targeting dsRNA


title: C16_rep1


title: dm3_dsLacZ_Input_140127

description: Cells treated with non-targeting dsRNA


title: C8_rep2


title: dm3_dsLacZ_RNA_130808_rep2

description: Cells treated with non-targeting dsRNA


title: dm3_dsLacZ_RNA_130718_rep1

description: Cells treated with non-targeting dsRNA


title: C1_rep3


title: dm3_dsLacZ_Input_131016

description: Cells treated with non-targeting dsRNA


title: dm3_dsLacZ_Input_130915

description: Cells treated with non-targeting dsRNA


title: C8_rep1


title: F8_rep3


title: C1_rep1


title: dm3_dsLacZ_TrxNT_130915_rep1

description: Cells treated with non-targeting dsRNA


title: dm3_dsLacZ_H3K4me3_130821_rep1

description: Cells treated with non-targeting dsRNA

value: H3K4me3 (homemade)


title: dm3_dsLacZ_Trr_131016_rep2

description: Cells treated with non-targeting dsRNA

value: Trr (homemade)


title: C1_rep2


title: M88R2

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

institute: CCHMC

description: Diaphragmatic hernia with subsequent tracheal occlusion

data_processing:
reads were aligned to reference genome using kallisto v0.42.2.1, with the ‘—bias’ parameter and all others default
cpm were computed using edgeR
genes with cpm>1 in at least 3 samples were retained
Genome_build: OryCun2.0 build in Ensembl
Supplementary_files_format_and_content: tab-delimited text file include CPM values for each Sample

organism: Oryctolagus cuniculus

extract_protocol:
After DNase treatment (30 units, PureLink DNASE Kit, ThermoFisher) RNA was isolated using the RNEasy Mini kit per manufacturer protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Left diaphragmatic hernia was surgically created at E25 in DH fetuses Tracheal occlusion was performed at E27 in TO fetuses.

value: New Zealand

value: Lateral Left Upper Lobe


title: dm3_dsLacZ_H3K4me3_140127_rep2

description: Cells treated with non-targeting dsRNA


title: dm3_dsLacZ_H3K4me2_140127_rep2

description: Cells treated with non-targeting dsRNA

value: H3K4me2 (homemade)


title: A16_rep2

value: Rangelander


title: dm3_dsLacZ_H3K4me2_130821_rep1

description: Cells treated with non-targeting dsRNA

value: embryo-derived


title: M83_L1

source_name: Diaphragmatic hernia with subsequent tracheal occlusion


title: M87R1


title: dm3_dsLacZ_H3K4me1_140127_rep2

description: Cells treated with non-targeting dsRNA

value: H3K4me1 (homemade)


title: A16_rep3

value: grown under 15.61 dS/m salt condition


title: C8_rep3

value: leaf and stem


title: M88_R3

description: Tracheal occlusion

source_name: Tracheal occlusion


title: A16_rep1


title: M86R3

description: Tracheal occlusion


title: A8_rep3


title: dm3_dsLacZ_H3K4me1_130821_rep1

description: Cells treated with non-targeting dsRNA


title: M39L2

description: Diaphragmatic hernia

source_name: Diaphragmatic hernia


title: dm3_dsLacZ_H3K27ac_140226_rep1

description: Cells treated with non-targeting dsRNA

value: H3K27ac (homemade)


title: A8_rep2


title: A8_rep1


title: dm3_dsLacZ_H3K27me3_140226_rep1

description: Cells treated with non-targeting dsRNA

value: Low passages (6-10)

value: H3K27me3 (homemade)


title: M38_R1

description: Diaphragmatic hernia


title: A1_rep3


title: M98_L3

description: Control

source_name: Control


title: A1_rep2


title: M83_L3

description: Control


title: M85_L3

description: Control


title: CCR6–Foxp3EGFP+ Il4raR576 Treg 3

status: Public on Jul 25 2016

city: Los Angeles

first: Matteo

last: Pellegrini

state: CA

address: 610 Charles Young Drive East

institute: UCLA

data_processing:
Reads aligned with STAR (version 2.5.1b)
Raw counts quantified with htseq-count (version 0.6.1p1)
Normalized counts generated with DESeq2 (version 1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of normalized counts

source_name: CCR6–Foxp3EGFP+ Il4raR576 Treg

extract_protocol:
We purified CCR6+Foxp3EGFP+ Il4raR576 and CCR6–Foxp3EGFP+ Il4raR576 Treg cells from total lung digests of OVA-sensitized and challenged mice, using FACS (Fluorescence Activated Cell Sorting).
RNA was first converted to cDNA using ClonetechÕs SMART-Seq v4 Ultra Low Input RNA kit following standard procedure. After cDNA was measured with Nanodrop, 250 ng in a 50 ul volume was then fragmented to 200-300 bp size using the Covaris M220. All the fragmented DNA was then used with the KAPA Hyper Prep Kit (Illumina platform) to make cDNA libraries. Libraries were quantified using HS DNA Qubit and Agilent HS DNA Bioanalyzer.

treatment_protocol: 5- 5-7 week-old female mice were sensitized to ovalbumin (OVA) by intraperitoneal injection of 100 μg of OVA in 100 μL of PBS and then boosted 2 weeks later with a second intraperitoneal injection of OVA in PBS. Starting on day 29, OVA-sensitized mice were challenged with aerosolized OVA at 1% delivered through a Schuco 2000 nebulizer (Allied Health Care Products) for 30 minutes daily for 3 days. Mice were euthanized on day 32 post sensitization and analyzed.

tag: age

value: 5-7 weeks

value: female

tag: sensitized and challenged with

value: ovalbumin (OVA)

value: lung; total lung digest

tag: genotype

value: CCR6-Foxp3EGFP+ Il4raR576

value: regulatory T (Treg) cells


title: CCR6–Foxp3EGFP+ Il4raR576 Treg 4

tag: gender

tag: tissue


title: CCR6+Foxp3EGFP+ Il4raR576 Treg 3

source_name: CCR6+Foxp3EGFP+ Il4raR576 Treg

value: CCR6+Foxp3EGFP+ Il4raR576


title: CCR6+Foxp3EGFP+ Il4raR576 Treg 1


title: CCR6–Foxp3EGFP+ Il4raR576 Treg 2


title: Non-infected cecum repeat 1

city: Tian'an

first: XIANYAO

last: LI

address: No. 61  Daizong Street,

department: Department of Animal Science

institute: Shandong Agricultural University

data_processing:
The raw reads were obtained using the Solexa deep-sequencing analyzer, then removing the low-quality reads and eliminating reads with5’ primer contaminants, without 3’ primer and insert tag, reads with poly(A) and shorter than 18nt, the clean reads were obtained and were used for further analysis.
The small RNA sequence reads were pre-processed using FASTX-Toolkit, excluding low-quality reads (ambiguous N, quality<10 nt, and length<18 nt) as well as 3′ adapter, 5′ adapter and poly(A) sequences.
Further annotation analyses were performed using the commercial software CLC Genomic Workbench 5.5
Genome_build: galGal4
Supplementary_files_format_and_content: Sequence and Count

organism: Gallus gallus

source_name: cecum

growth_protocol: The infeced and non-infected SPF Leghorn chickens were raised in separate incubator

extract_protocol:
Cecum was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent
The smaller RNA fraction (<100KDa) was further fractioned on a 15% tris-borate-EDTA (TBE) urea polyacrylamide gel and the 18-38 nt fraction was obtained. Subsequently, 5′ and 3′ RNA adapters were ligated to the small RNA by T4 RNA ligase (Promega), followed by reverse transcription and PCR product purification. Purified products were quantified on the Qubit® 2.0 fluorometer (Invitrogen) using QubitTM dsDNA HS  array kit(Invitrogen), then were diluted to 2 nM to finish cluster generation

treatment_protocol: The chickens in treated group were inoculated with 10^8 cfu C. jejuni per chicken

tag: breed

value: SPF leghorn

value: cecum

tag: infectious agent

value: non-infected


title: Infected cecum repeat 1

value: Campylobacter jejuni


title: Non-infected cecum repeat 2


title: Infected cecum repeat 2


title: A1_rep1

value: Rangelander

value: grown under 1.53 dS/m salt condition


title: nf-ycT_PAC_1

city: Guangzhou

first: Xu

last: Liu

state: Guangdong

address: No.723, Xingke Road, Tianhe District

department: South China Botanical Garden

institute: Chinese Academy of Sciences

description: PAC  treatment

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, to abtian the Clean tags, then mapped to TAIR10 whole genome (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas) acorrding to standard protocol.
Transcript Per Million clean tags (TPM) were calculated using a protocol (Peter A.C.'t Hoen, Ariyurek, et al. 2008; Morrissy, Morin, et al. 2009).
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: Tab-delimited excel files include TPM values and FDR-adjusted P-values for each differentially expressed genes

source_name: Seed

growth_protocol: The seeds used for germination comparison were harvested in same batch of plants grown at 22°C under long days (16 h light/8 h dark). Dry seeds were obtained and stored in a dry condition (25% humidity, 25°C) for at least 4 weeks of after-ripening.

extract_protocol:
Total RNA was extracted from the treated seeds by Plant RNA Kit (R6827, Omega)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The after-ripened seeds were sterilized and washed with 75% (v/v) ethanol with 0.5% (v/v) Triton X-100 (Sigma-Aldrich) for 1 min, and washed twice with absolute ethanol, then were plated on sterile filter paper for air drying. Subsequently, the sterilized seeds were sown on half-strength MS medium (0.025% MES, pH 5.7) containing 0.8% (w/v) Bacto Agar (Difco/BD) supplemented with 0.01% (w/v) ethanol (Mock), or 5 µM PAC (Sigma-Aldrich) under light for 12 h.

value: seed

tag: cultivar

tag: treatment

value: PAC

value: nf-ycT


title: nf-ycT_PAC_3

description: PAC  treatment


title: Col_PAC_1

description: PAC  treatment

value: wild type


title: Col_PAC_3

description: PAC  treatment


title: Col_Mock_3

description:
Mock treatment
processed data file for this sample is available on GSM2249730

value: Mock


title: rgl2_PAC_2

description: PAC  treatment


title: Ss rep 3

city: Winnipeg

first: Kelly

last: Duke

address: 410 Buller Bldg, 100 Chancellors Circle

department: Microbiology

institute: University of Manitoba

description:
Processed data files:
gene_exp.diff
genes.fpkm_tracking
cuffdiff_genes_nossl.txt

data_processing:
Sequenced reads were analyzed to remove barcode adapters and low quality reads using the Trimmomatic tool. The parameters for Trimmomatic which maximized mapping efficiency to the B. napus genome [B. napus: v.4.1, Chalhoub et al. was determined using FastQC reports for quality control (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) followed by alignment using Tophat2 v.2.1.0.
Alignment was completed using Tophat2 v.2.1.0. Alignment of reads to these genomes was performed in high-sensitivity mode using B. napus reference annotation v5 from Chalhoub et al. as guides.
The cufflinks and cuffmerge tools within the Cufflinks v.2.2.1 suite were used construct a transcriptome from the reads and identify novel transcripts.
Transdecoder was used to identify open reading frames (ORFs) within transcript sequences. Genes were identified by aligning translated ORF sequences with proteins in the Arabidopsis TAIR10, NCBI and Uniprot databases using BLAST.
Read counts were normalized to FPKM values using the cuffquant and cuffdiff tools in the Cufflinks package with default settings.
Genome_build: B. napus: v.4.1, Chalhoub et al.
Supplementary_files_format_and_content: Cuffdiff output files (gene_exp.diff; genes.fpkm_tracking) were used for FPKM values and significant log2 fold change values. Cuffdiff_genes_nossl.txt matches mapped sequence XLOC identifiers to corresponding Bna gene identifiers determined via BLAST search.

organism: Brassica napus

source_name: Ss, leaf

growth_protocol: Brassica napus cv. Westar plants were grown in Sunshine Mix #1 soil in growth chambers at 21ºC with a light/dark photoperiod of 16h/8h and 0% humidity

extract_protocol:
Total RNA was extracted using PureLink® Plant RNA Reagent (Invitrogen). DNA contamination was removed using Turbo DNA-freeTM kit (Ambion), following the manufacturer’s instructions. RNA concentration was verified using a NanoVue spectrophotometer (GE Healthcare), and quality was measured using an Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico and Nano Chips (Agilent Technologies; Santa Clara, CA, USA).
RNA-seq libraries were prepared according to the alternative HTR protocol (C2) described by Kumar with the exception of PCR enrichment of the libraries, where the number of cycles was adjusted to 11. Libraries were validated using the Agilent Bioanalyzer High Sensitivity DNA Assay with DNA chips (Agilent Technologies). The desired fragment sizes of sheared cDNA with ligated adapters were isolated using the E-Gel® electrophoresis system (Invitrogen). 100 bp single-end RNA sequencing was carried out at Génome Québec (Montreal, Canada) on the Illumina HiSeq 2000 platform.

treatment_protocol: One day prior to fungal pathogen exposure, B. napus plants at the 30% flowering stage were sprayed until dripping with a 2x108 cfu/mL solution of PA23 resuspended in sterile water supplemented with 0.02% Tween 20 as a surfactant. Plants not receiving biocontrol treatment (water control and Ss only groups) were sprayed with sterile water (0.02% Tween 20). Plants were sealed in clear bags to preserve relative humidity and returned to the growth chamber for 24 hours. The following day, bags were removed and plants receiving the pathogen treatment were sprayed with an 8x104 spores/mL solution of S. sclerotiorum ascospores resuspended in sterile water (0.02% Tween 20). Control plants and plants to be exposed only to PA23 were sprayed with sterile water (0.02% Tween 20). Plants were transferred to a humidity chamber with humidity levels of 70-90% for 72 hours. During this time, plants were gently shaken at the base twice to encourage petals to detach and fall into the plant canopy. Three leaves per plant and three plants per treatment group were used for each biological replicate. Leaves upon which petals had landed were used for collection, as these are sites of potential infection. The petal was removed from the leaf and approximately 1cm2 area of leaf tissue surrounding the site was collected with a scalpel. For S. sclerotiorum-infected leaves, green tissue immediately surrounding the lesion was collected. Cuttings were flash frozen in liquid nitrogen, and stored at -80℃ for no more than 2 days before processing.

value: leaf

tag: developmental stage

value: 30% flowering

value: S. sclerotiorum ascospores


title: rgl2_PAC_3

description: PAC  treatment


title: Col_Mock_1

description:
Mock treatment
processed data file for this sample is available on GSM2249728


title: PA23+Ss rep 3

source_name: PA23+Ss, leaf

value: PA23 and S. sclerotiorum


title: PA23+Ss rep 1


title: PA23+Ss rep 2


title: Ss rep 2


title: PA23 rep 3

source_name: PA23, leaf

value: P. chlororaphis PA23 (biocontrol)


title: CCR6+Foxp3EGFP+ Il4raR576 Treg 2

value: 5-7 weeks

value: female

value: ovalbumin (OVA)

value: lung; total lung digest

value: CCR6+Foxp3EGFP+ Il4raR576

value: regulatory T (Treg) cells


title: PA23 rep 2


title: Water rep 3

source_name: Water, leaf

value: water


title: Water rep 2


title: rgl2_PAC_1

description: PAC  treatment

value: seed


title: nf-ycT_PAC_2

description: PAC  treatment

value: PAC


title: PA23 rep 1


title: Col_PAC_2

description: PAC  treatment


title: Col_Mock_2

description:
Mock treatment
processed data file for this sample is available on GSM2249729