title: p03_08


title: C4_4C_76_0109_2

status: Public on Dec 31 2015

type: SRA

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

country: USA

institute: UCSC

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 RefSeq using Bowtie software in a sequencial manner first to rRNA, snRNA and miRNAs to eliminate any reads coming from them and then alinged to the genome
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet with normalized gene counts

molecule: total RNA

organism: Mus musculus

source_name: 4C embryo

growth_protocol: Zygotes, generated by IVF using sperm from mice fed on control diet and oocytes from females on control diet, were microinjected 2 hours after IVF and then allowed to develop until late 2C stage in KSOM media. 32 hours post IVF the microinjected embryos were collected and frozen at -80C.

extract_protocol:
2C embryos positive for GFP signal were individually collected at 2C or 4C stage in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit

treatment_protocol: Zygotes were injected with either tRF-GlyGCC oligo with modified bases (tRF-GlyGCC), tRF-Gly-GCC antisense oligo (tRF-GlyGCC Antisense), H3.3-GFP mRNA(GFP), tRF-GluCTC (tRF-GluCTC) or sperm small RNA from control or low protein animals.

tag: strain

value: FVB

tag: rna injected

value: GFP


title: C4_4C_52_0318


title: C4_4C_64_0109


title: p03_07

source_name: embryo

growth_protocol: Zygote were generated by IVF using sperm from mice fed control diet or Low protein diet and oocytes from females on control diet.The embryos were then allowed to develop iin KSOM media until different developmental stages when they were collected and frozen at -80C.

extract_protocol:
Embryos were collected in 5ul of buffer TCL with 1% beta mercaptoethanol and frozen at -80C.
single-cell RNA-seq/Nextera kit

tag: development stage

value: B

tag: diet of males

value: Low Protein


title: p03_06


title: C4_4C_42_0325


title: p03_05

value: Control


title: C4_4C_13_0126


title: p03_03


title: C3_4C_87_0313


title: p03_04


title: p02_96

value: M


title: p03_72


title: C3_4C_75_0109_2


title: C3_4C_63_0109


title: p03_65


title: p02_93


title: p02_94


title: p02_92


title: C3_4C_12_0126


title: C3_4C_41_0325


title: C2_4C_9_0119


title: p02_88


title: p02_87


title: p02_86


title: C2_4C_86_0313


title: C2_4C_74_0109_2


title: C2_4C_62_0109


title: p02_85


title: p02_84


title: C2_4C_40_0325


title: p02_83


title: C2_4C_38_0311


title: C1_4C_8_0119


title: p02_95


title: p02_82


title: C1_4C_85_0313


title: C3_4C_51_0318


title: p02_79


title: p02_80


title: C1_4C_73_0109_2


title: p02_73


title: p02_74


title: C1_4C_39_0325


title: p02_72


title: C1_4C_37_0311


title: p02_69


title: p02_71


title: C1_4C_10_0126


title: C2_4C_50_0318


title: p02_68


title: p02_67


title: p02_66


title: p02_65


title: p02_27


title: p02_28


title: p02_26


title: p02_25


title: p02_23


title: p02_24


title: C1_4C_49_0318


title: p02_21


title: p02_16


title: p02_15


title: p02_17


title: p02_19


title: p02_12


title: p02_11


title: p02_20


title: p02_10


title: p02_07


title: p02_08


title: p02_06


title: p02_05


title: p02_70


title: p02_09


title: p01_84


title: p02_03


title: p01_82


title: p01_81


title: p02_22


title: p01_80


title: p01_78


title: p02_14


title: p02_18


title: p01_79


title: p02_13


title: p01_76


title: p01_77


title: p01_72


title: p01_70


title: p01_68


title: p01_75


title: p01_74


title: p01_69


title: p01_73


title: p01_67


title: p01_71


title: p01_66


title: p01_65


title: p01_83


title: p01_63


title: p01_58


title: p01_56


title: p01_55


title: p01_60


title: p01_54


title: p01_62


title: p01_52


title: p01_61


title: p01_64


title: p01_53


title: p01_57


title: p01_46


title: p01_59


title: p01_51


title: p01_41


title: p01_49


title: p01_40


title: p01_44


title: p01_50


title: p01_42


title: p01_39


title: p01_38


title: p01_45


title: p01_37


title: p01_48


title: p01_47


title: p01_35


title: p01_31


title: p01_33


title: p01_36


title: p01_30


title: p01_32


title: p01_26


title: p01_34


title: p01_29


title: p01_25


title: p01_24


title: p01_23


title: p01_20


title: p01_18


title: p01_16


title: p01_17


title: p01_15


title: p01_21


title: p01_28


title: p01_22


title: p01_14


title: p01_13


title: p01_11


title: p01_09


title: p01_27


title: col_16h_wl replicate 2

city: La Jolla

first: Joanne

last: Chory

address: 10010 N Torrey Pines RD

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build using Tophat2 v2.0.8b (Kim et al. 2013 Genome Biology) on a Linux platform
FPKM were calculated for each sample using Cufflinks 2.1.1 (Trapnell et al. 2012 Nature Protocols) with parameters -u --compatible-hits-norm -G parameters on a Linux platform
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seeds of the indicated genotype was stratified for 2 days in the cold and then was grown on 0.5x Linsmaier and Skoog medium under continous white light at 22°C.

extract_protocol:
Spectrum Plant Total RNA kit (Sigma, MO)
Truseq RNA Sample prep kit v2 Cat# RS-122-2001 and RS-122-2002 (Illumina, CA)

treatment_protocol: 5 day old white light grown seedlings were treated (low blue) or mock treated (white light) for indicated times

tag: tissue

value: seedling

tag: ecotype

value: Columbia

tag: genotype

value: wild type

tag: treatment

value: white light

tag: time


title: p01_08


title: p01_19


title: B1_RNASeq

city: Lin’an

first: Yunxiang

last: Zang

address: Huanchengbei Road 88#

country: China

institute: Zhejiang A & F university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Chinese cabbage whole genome using SOAPaligner/soap2, allowing up to 2 bases mismatch in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Chinese cabbage genome (http://www.brassica.info/resource/sequencing.php)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Brassica rapa subsp. pekinensis

source_name: leaf

growth_protocol: Seeds of Chinese cabbage (Brassica rapa ssp. pekinensis, cv. ZSN5) were germinated in vermiculite in the greenhouse. The average temperature was 22-28°C/15-20°C (day/night) under natural light. Relative humidity fluctuated between 60%~70%.  Seedlings with one fully expanded true leaf were transferred into trough with 20L of full-strength nutrient solution (Japanese Garden formula), aerated continuously with an air bubbler. The nutrient solutions were renewed every week.

extract_protocol:
Total RNA was isolated using Trizol reagent according to the manufacturer’s protocol (Sigma-Aldrich, Inc., USA) and treated with RNase-free DNase to remove any genomic DNA contaminants. The purity of extracted RNA were assessed by ratio of absorbance A260 to A280, using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientiﬁc Inc., Waltham, MA, USA).
mRNA is enriched by using the oligo(dT) magnetic beads from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.

treatment_protocol: Chinese cabbage plants with about 8-10 leaves were sprayed with 0.2 mM MeJA or pure water as control. After 24 hours, the newly expanded leaves from mock or MeJA treated plants were harvested and immediately frozen in liquid nitrogen. They were then brought to laboratory for RNA extraction.

tag: cultivar

value: cv. ZSN5

tag: age

value: plants with about 8-10 leaves

value: leaf

tag: sprayed with

value: pure water (non-treated control)

tag: time point

value: 24hr after treatment


title: col_16h_lbl replicate 2

value: low blue


title: p01_06


title: col_16h_wl replicate 1


title: p01_05


title: p5ox_16h_wl replicate 2


title: p01_01


title: p01_04


title: p5ox_16h_lbl replicate 2


title: T17

description:
Sharma_Rando_TableS1.xlsx
Sharma_Rando_TableS2.xlsx

data_processing:
For each small RNA library, rRNA-mapping reads (which were highly abundant in testis and epididymis samples, but rare in epididymosome and sperm samples) were removed. Remaining reads were mapped to murine tRNAs, to the unique sequences present in the 467 defined pachytene piRNA clusters, to Repeatmasker (tRNA entries from Repeatmasker were deleted to avoid duplicating tRNA-mapping reads), to miRbase, and to Refseq, yielding 27385 data points for each library
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet

source_name: Testis

growth_protocol: Mice were fed control or low protein diet and various tissue samples were collected from mice at age 10-12 weeks old.

extract_protocol:
Total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (<40nts).
Small RNA cloning was carried out as in Gu et al, Cell 151, 1488-1500 (2013)

value: 10-12 weeks

tag: diet

value: low protein


title: col_16h_lbl replicate 1


title: p01_03

value: FVB


title: p5ox_16h_wl replicate 1


title: p4ox_16h_wl replicate 1


title: T18

tag: notes

value: Pool


title: p01_02


title: p4ox_16h_wl replicate 2


title: p4ox_16h_lbl replicate 2


title: p01_12


title: T16


title: p4ox_16h_lbl replicate 1


title: p01_07

value: Low Protein


title: ChIPSeq-PIF5_IgG_Rep2

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
antibody: IgG mock control IP
processed data file: P5_FLAG_set2_optimal_narrowPeak.bed

library_source: genomic

data_processing:
Base calling was done by RTA 1.17.20 (Illumina, CA).
Demultiplexing was done by CASAVA 1.8.2 (Illumina, CA).
Reads were aligned by bowtie2 version 2.1.0 against the Arabidopsis TAIR10 genome assembly with default parameters.
After filtering out reads mapped to chloroplast and mitochondria chromosomes, peaks were called by the Irreproducible Discovery Rate (IDR) pipeline using initial peak calls from MACS2 version 2.0.10, with q-value thresholds of 0.05, 0.01, and 0.001 for replicate consistency.  The resulting optimal set of peaks are uploaded.
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by MACS2 followed by the IDR pipeline.

molecule: genomic DNA

extract_protocol:
Please see accompanying publication for detailed protocol. Briefly, ChIP-seq experiments for PIF4, PIF5 and CRY2 were performed as described (Kaufmann et al., 2010) using 5 day-old seedlings harboring either a PIF4-Flash, PIF5-Flash (Thines et al., 2014) or UBQ10pro::Flash-CRY2 transgene. A monoclonal anti-FLAG antibody (Sigma) was used in all experiments. The CRY2 ChIP experiment was performed with two modifications. Instead of 2g starting material that we used to precipitate PIF4 or PIF5, 18g starting material was used for CRY2. Moreover, we conducted a dual cross-linking procedure for CRY2 using the additional cross-linker ethylene glycol bis-succinimidylsuccinate.
ChIP DNA was used to generate sequencing libraries as per Illumina protocol (Illumina, CA).
Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions

treatment_protocol: 5 day old white light grown seedlings were treated with low blue for 16 hours.

value: low blue 16h


title: T13


title: ChIPSeq-PIF5_FLAG_Rep2

description:
antibody: Flag antibody IP (Sigma Cat# F1804)
processed data file: P5_FLAG_set2_optimal_narrowPeak.bed


title: T14


title: T12


title: T11


title: ChIPSeq-PIF5_FLAG_Rep1


title: ChIPSeq-PIF4_IgG_Rep2

description:
antibody: IgG mock control IP
processed data file: P4_FLAG_set2_optimal_narrowPeak.bed


title: T10


title: T7

value: control


title: T6


title: T9


title: T8


title: ChIPSeq-CRY2_IgG_Rep2

description:
antibody: IgG mock control IP
processed data file: C2_FLAG_set2_optimal_narrowPeak.bed


title: ChIPSeq-PIF4_FLAG_Rep3

description:
antibody: Flag antibody IP (Sigma Cat# F1804)
processed data file: P4_FLAG_set2_optimal_narrowPeak.bed


title: T4


title: ChIPSeq-CRY2_IgG_Rep1


title: T5


title: T15


title: T3


title: ChIPSeq-CRY2_FLAG_Rep2

description:
antibody: Flag antibody IP (Sigma Cat# F1804)
processed data file: C2_FLAG_set2_optimal_narrowPeak.bed


title: ChIPSeq-CRY2_FLAG_Rep1


title: T2


title: ChIPSeq-PIF5_IgG_Rep1


title: T1


title: ChIPSeq-PIF4_IgG_Rep1


title: p4p5_24h_wl replicate 1

value: seedling


title: p4p5_24h_lbl replicate 1

value: Columbia


title: p4p5_24h_lbl replicate 2


title: p4p5_24h_wl replicate 2


title: ChIPSeq-PIF4_FLAG_Rep1


title: p5ox_16h_lbl replicate 1


title: SPTB3

source_name: Spermatid


title: col_24h_wl replicate 2

value: wild type


title: col_24h_wl replicate 1

value: white light


title: ChIPSeq-PIF4_FLAG_Rep2


title: col_24h_lbl replicate 2


title: SPTB2


title: col_24h_lbl replicate 1


title: p4p5_6h_wl replicate 2


title: p4p5_6h_wl replicate 1


title: p4p5_6h_lbl replicate 2


title: SPTA1


title: SPTA2


title: SPC4

source_name: Spermatocyte


title: SPTA3


title: SPC2


title: SPTB4


title: col_6h_wl replicate 2


title: p4p5_6h_lbl replicate 1


title: SPC1


title: SpCP11

source_name: Sperm

tag: location in epididymis

value: Caput


title: col_6h_lbl replicate 1


title: SPTB1


title: col_6h_wl replicate 1


title: col_6h_lbl replicate 2


title: SPTA4


title: SpCP9


title: SpCP10


title: SpCP7


title: SpCP8


title: p4p5_1h_lbl replicate 2


title: p4p5_1h_wl replicate 2


title: p4p5_1h_lbl replicate 1


title: p4p5_1h_wl replicate 1


title: col_1h_wl replicate 2


title: SPC3


title: SpCP4


title: SpCP5


title: col_1h_wl replicate 1


title: B2_RNASeq

value: cv. ZSN5

value: plants with about 8-10 leaves

value: 0.2 mM MeJA


title: SpCP3


title: SpCP2


title: SpCP1


title: col_1h_lbl replicate 2


title: col_1h_lbl replicate 1


title: SpCA17

value: Cauda


title: SpCA16


title: SpCA15


title: SpCA12


title: SpCA11


title: SpCA10


title: SpCA13


title: SpCA9


title: SpCP6


title: SpCA14


title: SpCA3


title: SpCA6


title: SpCA4


title: SpCA5


title: SpCA7


title: M4

source_name: Muscle


title: p01_43


title: M2


title: SpCA1


title: L4

source_name: Liver


title: M3


title: M1


title: L3


title: SpCA2


title: L2


title: L1


title: ES8

source_name: Embryonic stem cells

value: tRF


title: ES6

value: 10-12 weeks


title: ES5

value: LNA


title: ES4


title: SpCA8


title: ES3


title: ES1

value: GFP


title: EMCA11

source_name: Epididymosomes

value: low protein


title: EMCA10


title: EMCA13


title: EMCA12


title: ES2


title: EMCA7

value: high fat


title: EMCA4


title: EMCA5


title: EMCA8


title: EMCA6


title: EMCA3


title: EMCA1


title: EMCA2


title: ECP12

source_name: Epididymis


title: ECP10


title: ECP8


title: ECP11


title: EMF2

value: Fusion


title: ES7


title: ECP9


title: ECP6

value: control


title: ECP3


title: ECP2


title: ECP4


title: ECP5


title: ECP1

value: Pool


title: EMCA9


title: ECA10


title: ECA9


title: ECA8


title: ECA5


title: ECA6


title: ECA1


title: ECA2


title: ECA4


title: ECA7


title: ECA3


title: B4

source_name: Blood


title: EMF1


title: B2


title: B3


title: ECP7


title: B1


title: islet-ND-tsRNA [RRBS-seq]

city: Riverside

first: Junchao

last: Shi

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

data_processing:
Clean data is obtained by BGI standard data processing procedue.
Wiggle format files are generated by perl script bam2wig.pl
Genome_build: mm10
Supplementary_files_format_and_content: standard wiggle format files display of dense, continuous data

source_name: mouse_ND_ islet

growth_protocol: All animal experiments obey the rules and guidelines of the local animal ethical committee and the Institutional Animal Care and Use Committee of the Institute of Zoology, Chinese Academy of Sciences. 5 week old male C57BL/6J mice were purchased from Charles River Laboratories China Inc. These male C57BL/6J mice were housed in cages at a temperature of 22-24 °C and randomly divided into two diet groups, one group receiving a highDfat diet (HFD, D12492; Research Diets Inc., New Brunswick, NJ) and the other group received a normal diet (Diet 1415, BEIJING HFK BIOSCIENCE CO.,LTD).

extract_protocol:
Genomic DNA was extracted from islet cells using salt-out extraction method.
1) Genome DNA were cut by Restriction Enzyme; 2) DNA-end repair, 3’-dA overhang and adapter ligation; 3) Select the 40-110bp and 110bp-220bp insert fragments; 4) Bisulfite treatment by ZYMO EZ DNA MethylationDGold kit; 5) PCR amplification; 6) Qualified library for sequencing.

treatment_protocol: F1 offspring islet after ND or HFD sperm 30-40nt RNA fragments injection was isolation from mouse pancreas after 6h fasting.

value: ICR

tag: generation

value: F1 offspring

value: Normal-diet (ND)

value: islet


title: islet-HFD-tsRNA [RRBS-seq]

tag: strain

value: High-fat-diet (HFD)


title: islet-HFD-tsRNA_rep1 [RNA-seq]

data_processing:
Clean data is obtained by BGI standard data processing procedue. Briefly, filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
Map the clean reads to genome by TopHat v2.0.8b with default parameters except --b2-very-sensitive --no-convert-bam.
Fpkm are calculated based on bam files from tophat result.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene id, gene locus, FPKM value and mapping status

source_name: islet-HFD-tsRNA

extract_protocol:
Islet total RNAs are extracted by Trizol (Invitrogen).
Transcriptome libraries were constructed according to TruSeq Stranded mRNA Library Prep Kit (Illumina).


title: islet-ND-tsRNA_rep3 [RNA-seq]

source_name: islet-ND-tsRNA


title: islet-ND-tsRNA_rep2 [RNA-seq]


title: islet-ND-tsRNA_rep1 [RNA-seq]


title: sperm fragment 30-40nt high fat diet [ncRNA-seq]

data_processing:
The raw data is processed by the following steps to get clean reads: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt.
Clean data is produced using software developed by BGI.
Supplementary_files_format_and_content: tab-delimited text files include reads length, reads counts and reads sequence

source_name: mouse mature sperm

extract_protocol:
Sperm total RNAs are extracted by Trizol (Invitrogen). 1-2 μg total sperm RNAs were separated by denatured 15% PAGE with 7M urea. The gel was stained with SYBR Green I solution (Invitrogen). Small RNAs sized at 30-40 nt were excised from the gel and then each of these RNA fragments were extracted.
Small RNA libraries were constructed according to TruSeq Small RNA Sample Pre Kit (Illumina).

treatment_protocol: Sperm were released from cauda epididymis into 5ml phosphate-buffered saline (PBS) maintained at 37℃ for 15 min incubation, after which were then filtered with 40um cell strainer to rid of the tissue debris. The sperm were then treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 40 min on ice to eliminate somatic cell contamination, after which the sperm be pelleted by centrifugation at 600g for 5 minutes. after removal of suspension, the sperm pellet was resuspended and washed twice in 10mL of phosphate-buffered saline (PBS) then pelleted at 600g for 5 minutes. the sperm pellet were added with TRIzol reagent, homogenated,  followed by RNA extraction.

tag: gender

value: male

value: mature sperm


title: sperm fragment 30-40nt normal diet [ncRNA-seq]


title: sperm high fat diet  [ncRNA-seq]

data_processing:
The raw data is processed by the following steps to get clean reads: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt.
Clean data is produced using software developed by BGI.
Supplementary_files_format_and_content: tab-delimited text files include reads length, reads counts and reads sequence.

source_name: high fat diet_mature sperm

extract_protocol:
Sperm total RNAs are extracted by Trizol (Invitrogen).
Small RNA libraries were constructed according to TruSeq Small RNA Sample Pre Kit (Illumina).


title: sperm normal diet [ncRNA-seq]

source_name: normal diet_mature sperm


title: EBF2 replicate3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Hight-throught sequencing was performed using an Illumina HiSeq 2000 by the Functional Genomics Core at the University of Pennsylvania.
Sequencing reads were processed and aligned to mouse genome mm9 using RUM pipeline.
Differential gene expression analysis was performed using edgeR package.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing gene expression level & differential analysis results. Gene expression information is in two formats, 1) log2-transformed quantile-normalized values and 2) raw read counts.

molecule: polyA RNA

source_name: Inguinal white adipose tissue_Fabp4-Ebf2

growth_protocol: Mice were maintained on normal chow at room temperature

extract_protocol:
Inguinal white adipose tissue was harvested from adult (~6 week old mice). Lymph nodes were removed and tissue was homogenized in TRIzol. RNA was isolated using the TRIzol method (Invitrogen) combined with Ambion PURElink RNA purification.
RNA-seq libraries were prepared using Illumina Truseq RNA Sample Preparation Kit.

tag: background strain

value: mixed

value: Inguinal White Adipose

value: ~6 weeks


title: EBF2 replicate2


title: WT replicate4

source_name: Inguinal white adipose tissue_wildtype


title: WT replicate1


title: WT replicate3


title: EBF2 replicate1


title: EBF2 replicate4


title: WT replicate2


title: islet-HFD-tsRNA_rep3 [RNA-seq]


title: islet-HFD-tsRNA_rep2 [RNA-seq]


title: p53ko_Inp_rep1

city: Goettingen

first: Magdalena

last: Wienken

address: Justus-von-Liebig-Weg 11

country: Germany

institute: University Medical Center Goettingen

data_processing:
demultiplexed to fastq files with CASAVA (version 1.8.2)
Resulting reads were mapped to the mouse genome (UCSC mm9) using Bowtie 2 (Galaxy Tool Version 0.4)
peak calling was performed using MACS (Galaxy Tool Version 1.0.1)
Coverage was determined by normalizing the total number of mapped reads per hundred million.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

source_name: Mouse embryonic fibroblast

growth_protocol: Cells were cultured in DMEM (Gibco/Life Technologies) supplemented with 10 % fetal calf serum (FCS) and antibiotics

extract_protocol:
Chromatin immunoprecipitation (ChIP) was done according to the protocol published by Denissov and colleagues (Denissov et al., 2007). Briefly, cells were fixed in 1.1 % of PFA for 20 min, quenched with 0.125M glycine and lysed in 1% Triton X-100, 0,15 M NaCl, 1 mM EDTA, 0.3 % SDS and additional protease inhibitor. The cell lysate was sonicated as desired and used for antibody (2µg) and Protein A/G PLUS-Agarose incubation (Santa Cruz) over night. Bead interaction was released via 20 min rotation incubation in 1% SDS and 0.1 M NaHCO3 and DNA-protein crosslink was reversed via the addition of 0.2 M NaCl and shaking at 65 °C. DNA was purified by the MinElute PCR Purification Kit (Quiagen) and either used for targeted PCR (see primer table) or sequencing.
For sequencing, DNA was sonicated again to reach fragment sizes less than 200 bp, and libraries were prepared with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB). The size range of final libraries was determined with the Bioanalyzer 2100 from Agilent (290-310 bp). Libraries were amplified and sequenced by using cBot.

tag: cell type

value: MEF

tag: genotype/variation

value: p53 single knock out

tag: chip antibody


title: p53Mdm2ko_Inp_rep2

value: p53/Mdm2 double knock out


title: p53ko_Inp_rep2


title: p53ko_H2Ak119ub1 rep4

value: H2AK119ub (Diagenode, C15410002)


title: p53Mdm2ko_H2Ak119ub1 rep4


title: p53Mdm2ko_H2Ak119ub1 rep3


title: p53Mdm2ko_H2Ak119ub1 rep2


title: p53Mdm2ko_H2Ak119ub1 rep1


title: p53ko_H2Ak119ub1 rep3


title: p53ko_H2Ak119ub1 rep1


title: p53ko_H2Ak119ub1 rep2


title: p53Mdm2ko_H3K27me3 rep4

value: H3K27me3 (Diagenode, pAb-069-050)


title: p53Mdm2ko_H3K27me3 rep3


title: p53Mdm2ko_H3K27me3 rep1


title: p53Mdm2ko_H3K27me3 rep2


title: p53ko_H3K27me3 rep3


title: p53ko_H3K27me3 rep1


title: p53ko_H3K27me3 rep2


title: p53ko_H3K27me3 rep4


title: p53Mdm2ko_Inp_rep1


title: p53 ko MEF rep3

description: normalizedreads.txt

data_processing:
demultiplexed to fastq files with CASAVA (version 1.8.2)
mapped to the mouse reference transcriptome (UCSC mm9) using Bowtie 2 (version 2.1.0)
Read counts for each sample and each gene were aggregated using a custom Ruby script
DESeq (version 1.14.0) was used for measuring differential expression
Genome_build: mm9
Supplementary_files_format_and_content: [normalizedreads.txt] tab-delimited text file includes RPKM values for each Sample

source_name: p53 ko MEF

extract_protocol:
Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies).
For RNA-sequencing, the quality of total RNA was determined using the bioanalyzer 2100 from Agilent. All samples analyzed exhibited a RIN>8. Library preparation was conducted using the TruSeq RNA LT SamplePrep Kit (Illumina) starting from 1000 ng of total RNA. Barcodes used for sample preparation were used according to the indications given by the protocol. Accurate library quantitation of cDNA libraries was performed with the QuantiFluor™dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (290-310 bp). cDNA libraries were amplified and sequenced via cBot and HiSeq 2000 from Illumina (SR, 1×50 bp, 6 Gb/sample ca. 30 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA (version 1.8.2).

value: p53 KO


title: p53ko Mdm2 C462A ki rep1

description: normalizedreads.txt

source_name: p53ko Mdm2 C462A ki

value: p53KO Mdm2(C462A) KI


title: p53Mdm2 ko MEF rep2

description: normalizedreads.txt

source_name: p53Mdm2 ko MEF

value: p53Mdm2 KO


title: p53ko Mdm2 C462A ki rep2

description: normalizedreads.txt


title: cobsfr1

city: BERKELEY

first: Nadav

last: Sorek

state: CALIFORNIA

address: 2151 BERKELEY WAT

department: PMB

institute: UC BERKELEY

data_processing:
Analysis was done using CLC, all details can be found at :http://www.clcbio.com/support/tutorials/
Genome_build: Arabidopsis genome data was obtained from TAIR
Supplementary_files_format_and_content: counts

extract_protocol:
RNeasy Plant Mini Kit by Qiagen
http://qb3.berkeley.edu/qb3/gsl/services-lp.cfm
100 PE

tag: tissue

value: seedling

tag: genotype


title: cobsfr2


title: p53 ko MEF rep2

description: normalizedreads.txt


title: cob2


title: sfr1


title: sfr2


title: p53 ko MEF rep1

description: normalizedreads.txt


title: SCN_CT58

city: Philadelphia

first: Heather

last: Ballance

state: PA

address: 3400 Civic Center Blvd. Building 421

institute: University of Pennsylvania

data_processing:
RNA-Seq Mapping: The raw reads were mapped to the mm9 genome build provided on UCSC using the RNAseq aligner STAR (version STAR-2.3.0e) (Kent et al., 2002; Waterston et al., 2002; Dobin et al., 2013). The algorithm was given known gene models (provided by RefSeq) to achieve higher mapping accuracy (Pruitt et al., 2014).
Normalization: To normalize the read counts from each time point we used PORT. PORT is an in house developed algorithm that is not yet published but can be found at https://github.com/itmat/Normalization. We used release v0.6.3-beta 2/2/2015 and the normalization was conducted on the gene, exon, intron and junction level. We used the gene models provided from UCSC (Kent et al., 2002), as well as the ones available from ENSEMBL (Flicek et al., 2014).
Alternative-splicing analysis: During alignment, STAR identifies intronic regions from those reads with splice alignments to the reference genome. First, we filtered out all intronic regions that were present in less than four time points, to ensure that all introns and junctions analyzed were present in at least half of profiled time points. We identified alternative splicing events by searching for cases where introns shared the same start coordinates, but had different stop coordinates (or vice versa). We refer to these sets of introns representing alternative-splicing events as alternatively-splice loci. Next, we merged any alternative-spliced loci with overlapping genomic genomic coordinates, if they were present on the same strand. Lastly, we assigned annotation information to each junction and alternatively-splice locus using the Ensembl gene annotation (Flicek et al., 2014). Having assembled this list of alternatively-splice junctions, we then assigned read counts to all of them from the PORT-normalized SCN RNA-seq data. Next, we identified the major and minor spliceforms at each of these alternatively-spliced loci using the Ensembl annotation information. We only considered those junctions that could be assigned to a minimal set of spliceforms. We then analyzed these junction counts for oscillating patterns using JTK_CYCLE (parameters set to search for rhythms with periods of exactly 24 hours; oscillators defined as p < 0.05). For ease of visualization, read counts of each splice junction were median normalized across all CTs, and expressed with a loess value of 0.75 in ggplot2() in R (Wickham, 2009).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized gene, exon, intron and junction level counts.

source_name: suprachiasmatic nucleus

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for three weeks. Mice were then transferred to complete darkness prior to collection. Collection began at CT18.

extract_protocol:
SCN samples were homogenized in Trizol reagent (Invitrogen) using a Tissuelyser (Qiagen). RNA was extracted using RNeasy columns (Qiagen) as per manufacturer’s protocol, with the modification that 1.5 volumes of 100% ethanol were added to the aqueous phase following centrifugation. Samples were resuspended in 25 uL of RNase free H2O. RNA was quantified by QUBIT (Invitrogen). Equal amounts of SCN RNA from three mice were pooled for each time point.
Prepared using Illumina TruSeq Stranded mRNA HT Sample Preparation Kit as per manufacturer’s protocol. Briefly, 0.1 ug of total RNA was polyA-selected, fragmented by metal-ion hydrolysis, and converted into double-stranded cDNA using Invitrogen Superscript II. The cDNA fragments were subjected to end-repair, adenylation, ligation of Illumina sequencing adapters, and PCR amplification.

value: suprachiasmatic nucleus


title: SCN_CT52


title: WT2

source_name: Col-0 (WT)

value: Col-0 (WT)


title: SCN_CT40


title: MOT2D

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using TOPHATv2.0.8 for RNA sequencing with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: In RNA-seq, read counts for genes (TAIR10) was provided.

source_name: The first-pair rosette leaves

growth_protocol: Arabidopsis seedlings were first cultured on 1/2 MS medium at 22 ◦C with a 16-h light and 8-h dark photoperiod. Leaf explants from 12-day-old seedlings  were cultured on B5 medium  without carbohydrate under a photoperiod with 16 h light and 8 h dark

extract_protocol: none provided by theh submitter

tag: development stage

value: 12 days after sowing

tag: ecotype

value: The first-pair rosette leaves

tag: treatment

value: 2 d control


title: SCN_CT46


title: T0

value: control


title: WT1


title: SCN_CT28


title: SCN_CT22


title: DM

growth_protocol: Arabidopsis seedlings were first cultured on 1/2 MS medium at 22 ◦C with a 16-h light and 8-h dark photoperiod.

extract_protocol: none provided by submitter

treatment_protocol: The leaf explants from Samp1e(DM) were cultured on the B5 medium containing β-estradiol /DMSO,while the Sample(ER) were cultured on the B5 medium containing DMSO only.

value: estradiol


title: s8_GATCAG_4_Hif2aKO

first: M. Celeste

last: Simon

address: 421 Curie Blvd.

data_processing:
Basecalls performed using CASAVA version 1.8.2, and allowed 1 mismatch of barcodes for demultiplexing
Raw sequence and quality files were aligned to the mouse genome (GRCm38) using the RNA alignment tool STAR (version 2.4, https://code.google.com/p/rna-star/)
Unique transcript alignments were counted for each sample using htseq-count (version 0.6.1, http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) against the RefSeq transcripts for GRCm38
Normalized, log2-transformed expression values were generated with DESeq2 (version 1.6, http://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Genome_build: GRCm38
Supplementary_files_format_and_content: rawCounts.txt: unnormalized counts per gene, generated by htseq-count
Supplementary_files_format_and_content: deseq rLogNorm 8 samp.txt: Normalized (Deseq2 rlog normalized) counts
Supplementary_files_format_and_content: deseq rLogNorm 7 samp.txt: Normalized (Deseq2 rlog normalized) counts

source_name: UPS tumor derived from KPH2 mouse

extract_protocol:
UPS tumors were removed, and preserved in 4% PFA. Tumors were subsequently dehydrated, and embedded in parafin. Rna was extracted using the Qiagen miRNeasy FFPE Kit.
Libraries were prepared from RNA samples according to standard protocols for TruSeq Stranded Kit and the Ribo-Zero Gold Kit.

value: Mixed 129/C57BL/6

tag: tumor type

value: UPS

value: Epas1 -/-


title: p53Mdm2 ko MEF rep1

description: normalizedreads.txt

value: MEF


title: ER


title: s8_ACTTGA_3_Hif2aKO


title: s8_TTAGGC_2_Hif2aKO


title: s8_ATCACG_1_Hif2aKO


title: s8_GTTTCG_8_WT

source_name: UPS tumor derived from KP mouse

value: Wild type


title: SCN_CT64

tag: time point


title: -Pit Root 16 dat EXP

city: Irapuato

first: Luis Rafael

middle: Herrera

last: Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: LANGEBIO

country: Mexico

institute: LANGEBIO CINVESTAV

description:
MeP16DR in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Root16dat.csv

data_processing:
Basecalls for MethylC-Seq performed using illumina basecalling pipeline (SolexaPipeline 1.0). Short Methyl C-Seq reads with 90-nt reads from each end generated by Illumina sequencing were aligned to the Arabidopsis thaliana reference genome sequences downloaded from TAIR.
To align MethylC-Seq Reads we used the software named SOAPaligner2, allowing up to four mismatches for 90-nt pair-end reads to map the computationally transformed reads to the alignment target sequences.
Multiple reads mapped to the same start position were regarded as clonal duplication, which might be generated during PCR process, and only one of them was kept.For mC detection, we transformed each aligned read and the two strands of the Arabidopsi thaliana genome back to their original forms to build an alignment between the original forms. Cytosines in the MethylCseq reads that are also matched to the corresponding cytosines in the plus (Watson) strand, or otherwise guanines in the MethylC-seq reads that are also matched to the corresponding guanines in the minus (Crick) strand were regarded as potential mCs.
Basecalls for RNA-Seq were performed using illumina basecalling pipeline (SolexaPipeline 1.0). ShortRNA-Seq reads with 75-nt reads from each end generated by Illumina sequencing were aligned to the Arabidopsis thaliana reference genome sequences were downloaded from TAIR.
Alignment of RNA-Seq reads was performed using Bowtie2
Genome_build: TAIR 10
Supplementary_files_format_and_content: [MethylC-Seq] The cout file is a vertical arrangement format of each cytosine, the file provides the exact methylation of each cytosine. Each cout file row contains 9 columns, the headers for each column are: 1. Chromosome ID, 2. Position (position in chromosome), 3.  +/- (Strand orientation), 4. Cytosine pattern (CG/CHH/CHG), 5. Cytosine sequence context, 6. Copynumber, 7. Methyl-reads num (number of methylated reads), 8. Non-methyl-reads num (number of non-methylated reads) and 9. Binomial distribution expected values.
Supplementary_files_format_and_content: [RNA-Seq] The csv file contains processed information of differential expression, headers for each column are: 1. IDE (Arabidopsis locus ID), 2. Descript (gene description as given in TAIR), 3. Fold-Change (positive for induction, negative for repression; given as induced/expressed in response to Low Phosphate conditions, 4. FDR.  Pi_Starvation_RNASeq_counts_Total.txt reports total counts for all 8 samples.

source_name: Root

growth_protocol: Briefly, seeds were germinated and grown for 7 days in 0.1X MS liquid media (1mM Pi, HP), then seedlings were transferred to fresh HP (HP to HP treatment, +Pit) or to LP (HP to LP treatment, -Pit) liquid media and samples collected 7 or 16 days after transference (dat)

extract_protocol:
For RNA-Seq total RNA was isolated using the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions and further purificated using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions.
For preparation of mRNA-Seq Libraries, total RNA was isolated from frozen shoot and root powder using the TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions for isolation of total RNA from plant tissue and further purified using Plant RNeasy kit (Qiagen) according to the manufacturer’s instructions for RNA purification. Non–strand-specific mRNA-seq libraries were generated from 5 μg of total RNA (Plant RNeasy kit) and prepared by using the TruSeq RNA Sample Prep kit (Illumina) according to the manufacturer’s instructions.

value: root

value: Low Phosphate

tag: duration of treatment

value: Long term (16 dat)


title: -Pit Shoot 16 dat EXP

description:
MeP16DH in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Shoot16dat.csv

source_name: Shoot

value: shoot


title: +Pit Shoot 16 dat EXP

description:
MaP16DH in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Shoot16dat.csv

value: High Phosphate


title: s8_GTGGCC_7_WT


title: +Pit Root 16 dat EXP

description:
MaP16DR in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Root16dat.csv


title: SCN_CT34

value: suprachiasmatic nucleus


title: cob1

value: seedling


title: s8_GGCTAC_6_WT


title: EXP2D

value: 12 days after sowing

value: 2 d wounding


title: s8_TAGCTT_5_WT


title: -Pit Root 7 dat EXP

description:
MeP7DR in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Root7dat.csv

value: Short Term (7 dat)


title: -Pit Shoot 7 dat EXP

description:
MeP7DH in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Shoot7dat.csv


title: +Pit Root 7 dat EXP

description:
MaP7DR in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Root7dat.csv


title: RNAPII_ChipSeq_ipsc

first: Min

last: Li

address: 1239 Siping Road, Yangpu District

institute: Tongji University

description: RNAPII

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations:bowtie -v 2 -m1
Only these uniquely mapped reads were kept with the following command: samtools view -b -q 255 data.bam >uniquely_data.bam
peaks were called using macs2 version 2.1.0 with the default parameters plus --broad: macs2 -t treatment.bam -c input.bam --broad. H3K4me1, H3K27ac, H3K4me3, H3K27me3 and RNAPII peaks were called using macs version 1.4.1 with the following setting: macs14 -t treatment.bam -c input.bam --keep-dup auto -w -S --space 30 --fe-step=10.
Genome_build: mm9
Supplementary_files_format_and_content: broadPeak, bed

source_name: the corresponding 2nd iPS cell line

growth_protocol: The 2nd mouse embyronic fibroblast were derived from E13.5 tetraploid complementated all-iPS embryos and cultured with Feeder Medium. On passages 4, MEFs were plated on gelatin-coated dishes at appropriate density and the culture medium was changed to ES Medium supplemented with 1µg/ml Doxcycline and 50µg/ml Vitamin C to induce iPS cells. After 15days of induction, majority of cells were reprogrammed into Oct4-GFP+ ES-like colonies and we withrew Doxcycline and Vc from the medium. 3days later, the remaining dox-indenpent iPS cells were collected as day18 sample. The 2nd iPS cell line was established and maintained in ES medium supplemented with 2i(Gsk3i+Meki) with/without feeder. Feeder Medium contains DMEM supplemented with 10% (v/v) fetal bovine serum and 1 mM L-glutamine; ES Medium contains DMEM supplemented with 15% (v/v) fetal bovine serum , 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock,1% penicillin/streptomycin stock,1% nucleosides stock and 1000 U/ml LIF.

extract_protocol:
Reprogramming cells at different time point were trypsinized and washed twice with PBS. Cells were resuspended in PBS at a density of 107/ml and then chemically crosslinked by the addition of final 1% formaldehyde for 10 min at room temperature with gently rotation. Crosslinking was stopped by addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with cold PBS and lysed in Lysis Buffer(10 mM Tris-HCl, pH 7.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40; freshly added complete proteinase inhibitor cocktail (Roche)) at 4℃ for 15 min. Nuclei was collected by centrifugation and washed again with Lysis Buffer. Pellet was resuspended in ChIP Buffer I (300 mM NaCl, 3 mM EDTA, 1% NP40, 0.5% sodium deoxycholate, 0.1% SDS, 100 μg /ml BSA, 50 mM Tris, pH 8.0; freshly added proteinase inhibitor cocktail) and sheared by sonication to reduce the average DNA fragment size to 200-500 bp for analysis by q-PCR or 100-300 bp for analysis by sequencing. Antibodies were pre-coupled to protein G dynabeads. Generally, we used 10 μl protein G Dynabeads for 1 μg antibody. For transcription factor ChIP, we generally used 3 μg antibody for 30 μg chromatin per reaction; for histone ChIP, we used 1-2 μg antibody for 10-20 μg chromatin per reaction. After sonication, 1/10 of sheared chromatin was saved as input. The remaining chromatin was incubated with antibody-coupled dynabeads at 4℃ overnight. Beads were washed twice by ChIP Buffer I, four times by ChIP buffer II (100 mM Tris, pH 8.0, 500 mM LiCl, 1% NP40, 1% sodium deoxycholate) at 4℃ for 5 min with gently rotation. Beads were finally washed once by TE (10 mM Tris-HCl pH 8.0, 0.1 mM Na2EDTA) and transferred to a new tube for elution. Bound complexes were eluted twice in 100 μl Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS; 0.25 mg/mL proteinase K added freshly) at 55℃ for 1 hr with shaking. The eluted chromatin was further reverse-crosslinked by overnight incubation at 65℃.Input chromatin was also treated to reverse crosslinking. Immunoprecipitated DNA and input DNA was extracted by phenol: chloroform: isoamyl alcohol (25:24:1, pH 8.0) and precipitated by ethonal with 100 μg /ml LPA as co-precipitant.
For the following sequencing analysis, 10-100 ng DNA mixed from two or three independent ChIP reactions was used to prepare ChIP-seq library following the NEB protocol with minor modifications. Briefly, DNA was end-repaired, dA-tailed and ligated with NEBNext adaptors. Following USER enzyme treatment, DNA was purified and size selected with 0.8X\0.4X AMpureXP beads (Beckman). Selected DNA was PCR amplified using Phusion (NEB) or Q5 (NEB) DNA polymerase for 12-14 cycles. PCR primers were from NEBNext Multiplex Oligos for Illumina kit (NEB). Different samples were tagged with different indexes and 3-4 ChIP-libraries were mixed as one lane sample in HiSeq 2000/HiSeq 2500.

value: established iPS cell line

value: RNAPII-GFP/ Rosa26-M2rtTA transgenic background

tag: chip-antibody

value: anti-RNAP II(8WG16), Covance(MMS-126R)


title: RNAPII_ChipSeq_day18

description: RNAPII

source_name: reprogrammed cells after 15days induction and 3days dox-withdrawl treatment

value: reprogrammed dox-independent cell


title: RNAPII_ChipSeq_day15

description: RNAPII

source_name: reprogramming intermediate after 15days of induction

value: reprogramming intermediate


title: +Pit Shoot 7 dat EXP

description:
MaP7DH in Pi_Starvation_RNASeq_counts_Total.txt
Plusvsminus_Shoot7dat.csv


title: RNAPII_ChipSeq_day11

description: RNAPII

source_name: reprogramming intermediate after 11days of induction


title: -Pit Root 16 dat Meth

description: MethylC-Seq

extract_protocol:
For Bisulfite-Seq Arabidopsis thaliana genomic DNA from two biological replicates was extracted using the DNeasy system (Qiagen, Valencia, CA, USA).
For Bisulfite sequencing libraries,DNA was fragmented by sonication with a Sonicator to a mean size of approximately 250 bp, the preparation of MethylC-Seq libraries was carried out using Pico Methyl-Seq Library Prep Kit (Zymo Research) according to manufacturer instructions. Ultra-high-throughput pair-end sequencing was carried out using the Illumina HiSeq 2000 according to manufacturer instructions.


title: -Pit Shoot 16 dat Meth

description: MethylC-Seq


title: +Pit Shoot 16 dat Meth

description: MethylC-Seq


title: RNAPII_ChipSeq_day7

description: RNAPII

source_name: reprogramming intermediate after 7days of induction


title: +Pit Root 16 dat Meth

description: MethylC-Seq


title: RNAPII_ChipSeq_day3

description: RNAPII

source_name: reprogramming intermediate after 3days of induction


title: -Pit Shoot 7 dat Meth

description: MethylC-Seq


title: RNAPII_ChipSeq_day5

description: RNAPII

source_name: reprogramming intermediate after 5days of induction


title: -Pit Root 7 dat Meth

description: MethylC-Seq


title: RNAPII_ChipSeq_day1

description: RNAPII

source_name: reprogramming intermediate after 24hour of induction


title: H3K27me3_ChipSeq_ipsc

value: H3K27me3-GFP/ Rosa26-M2rtTA transgenic background

value: anti-H3K27me3, Millipore(07-449)


title: RNAPII_ChipSeq_day0

description: RNAPII

source_name: 2nd mouse embryonic fibroblasts prior to induction

value: primary mouse embryonic fibroblast isolated from E13.5 tetraploid blastocyst complementation embryo,P4


title: +Pit Shoot 7 dat Meth

description: MethylC-Seq


title: H3K27me3_ChipSeq_day18


title: H3K27me3_ChipSeq_day7


title: +Pit Root 7 dat Meth

description: MethylC-Seq

value: root


title: H3K27me3_ChipSeq_day15


title: H3K27me3_ChipSeq_day3


title: H3K4me3_ChipSeq_ipsc

value: H3K4me3-GFP/ Rosa26-M2rtTA transgenic background

value: anti-H3K4me3, Abcam(Ab8580)


title: H3K4me3_ChipSeq_day18


title: H3K27me3_ChipSeq_day5


title: H3K27me3_ChipSeq_day11


title: H3K27me3_ChipSeq_day1


title: H3K27me3_ChipSeq_day0


title: H3K4me3_ChipSeq_day7


title: H3K4me3_ChipSeq_day1


title: H3K4me3_ChipSeq_day15


title: H3K4me3_ChipSeq_day11


title: H3K27ac_ChipSeq_day15

value: H3K27ac-GFP/ Rosa26-M2rtTA transgenic background

value: anti-H3K27ac, Abcam(Ab4729)


title: H3K4me3_ChipSeq_day0


title: H3K27ac_ChipSeq_day18


title: H3K27ac_ChipSeq_day0


title: H3K27ac_ChipSeq_day3


title: H3K27ac_ChipSeq_day11


title: H3K4me3_ChipSeq_day3


title: H3K4me3_ChipSeq_day5


title: H3K4me1_ChipSeq_day18

value: H3K4me1-GFP/ Rosa26-M2rtTA transgenic background

value: anti-H3K4me1, Abcam(Ab8895)


title: H3K27ac_ChipSeq_day1


title: H3K4me1_ChipSeq_day7


title: H3K4me1_ChipSeq_day15


title: H3K4me1_ChipSeq_day11


title: H3K4me1_ChipSeq_day5


title: H3K4me1_ChipSeq_day3


title: input_DNA_ipsc

description: input

value: Oct4-GFP/ Rosa26-M2rtTA transgenic background


title: H3K4me1_ChipSeq_day1


title: H3K4me1_ChipSeq_day0


title: input_DNA_day7

description: input


title: input_DNA_day5

description: input


title: H3K27ac_ChipSeq_day7


title: input_DNA_day11

description: input


title: input_DNA_day3

description: input


title: input_DNA_day15

description: input


title: input_DNA_day1

description: input


title: total_Oct4_ChipSeq_day15

description: total Oct4 binding

value: anti-Oct4, Santa Cruz(Sc-8628X)


title: input_DNA_day0

description: input


title: total_Oct4_ChipSeq_day7

description: total Oct4 binding


title: total_Oct4_ChipSeq_day11

description: total Oct4 binding


title: total_Oct4_ChipSeq_day5

description: total Oct4 binding


title: total_Oct4_ChipSeq_ipsc

description: total Oct4 binding

value: established iPS cell line


title: H3K4me1_ChipSeq_ipsc


title: total_Oct4_ChipSeq_day3

description: total Oct4 binding


title: total_Oct4_ChipSeq_day0

description: total Oct4 binding


title: flag_Oct4_ChipSeq_day18

description: exogenous Oct4 binding

value: anti-Flag-M2, Sigma(F1804)


title: flag_Oct4_ChipSeq_day5

description: exogenous Oct4 binding


title: flag_Oct4_ChipSeq_day15

description: exogenous Oct4 binding


title: flag_Oct4_ChipSeq_day7

description: exogenous Oct4 binding


title: flag_Oct4_ChipSeq_day3

description: exogenous Oct4 binding


title: flag_Oct4_ChipSeq_day11

description: exogenous Oct4 binding


title: flag_Oct4_ChipSeq_day0

description: exogenous Oct4 binding


title: 24hr_R2

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

data_processing:
For all the sequenced samples  reads were aligned to Mouse genome (mm9) using TopHat with default parameters.  RNASeq data the aligned reads were then provided as an input to HTSeq_count utility from HTSeq package.  The raw read counts were normalized for library size differences using using DESeq package estimateSizeFactors function from DESeq package.
Genome_build: mm9
Supplementary_files_format_and_content: Processed file contain normalized read count for each genes. Column headers represent the sample name while each row show gene names.

extract_protocol:
RNA from harvested cells were column purified with Purelink RNA Mini kit (12183025, life technologies).
Standard illumina library for single end reads was used for library preparation.

treatment_protocol: NIH3T3 cells were synchronized with 100 nM Dexamethasone for 2 hours, then medium was changed to normal culture medium (0h). Every 4 hours cells were harvested, RNA isolated and RNAseq performed.

tag: cell line


title: 28hr_R2


title: 32hr_R2


title: 16hr_R2


title: 20hr_R2


title: total_Oct4_ChipSeq_day18

description: total Oct4 binding


title: input_DNA_day18

description: input


title: 12hr_R2


title: 4hr_R2


title: 0hr_R2


title: total_Oct4_ChipSeq_day1

description: total Oct4 binding


title: flag_Oct4_ChipSeq_day1

description: exogenous Oct4 binding


title: 8hr_R2


title: 28hr_R1


title: 32hr_R1


title: 24hr_R1


title: 12hr_R1


title: 16hr_R1


title: 8hr_R1


title: 4hr_R1


title: 0hr_R1


title: I/11 cells 96 h after infection with a scrambled shRNA (scr); 24h on differentiation medium

city: Heidelberg

first: Daniel

middle: B.

last: Lipka

address: INF 280

department: Epigenomics and Cancer Risk Factors

institute: German Cancer Research Center

description:
small hairpin RNA with no target in the corresponding genome
I/11 cells is a murine erythroblast cell line established from p53-deficient mouse fetal liver cells (day E12.5)

data_processing:
Sequence reads were aligned to the mouse genome assembly mm10 using BWA with default parameters and only uniquely aligned reads were kept for further analysis.
PCR-duplicates were identified and removed using picard and samtools with default parameters.
Peak calling was done with the Homer software package with a fixed window size of 150 bp and otherwise default settings using the scrambled shRNA as a reference.
Genome_build: mm10
Supplementary_files_format_and_content: Peak file (BED format)

source_name: murine erythroblast cell line

growth_protocol: The expanding erythroid progenitors (I/11) were maintained in serum-free medium (StemPro®34 plus nutrient supplement) supplemented with 1 U/ml of human recombinant Erythropoietin (Epo), 100 ng/ml SCF, 1 µM dexamethasone and 1% penicillin/streptomycin. For differentiation induction I/11 cells were seeded in StemPro34® medium containing 10 U/ml Epo, 0.5 mg/ml human holo-transferrin  and 1% penicillin/streptomycin.

extract_protocol:
Genomic DNA was isolated using Qiagen DNA mini kit. 3 μg of genomic DNA were sonicated in a Covaris S sonicator. DNA fragments which were about 150  bp in size were then subjected to enrichment with 60 μg MBD2-Fc protein in the presence of a salt gradient. The DNA fractions highly enriched for methylated DNA (eluted with 1 M NaCl) were subjected to next-generation sequencing.
NEBNext ChIP-seq Library Prep Reagent Set for Illumina

treatment_protocol: For methylome analysis, I/11 cells were infected with lentiviral particles (by spinfection; 2000 rpm for 1.5 hours at 33°C) containing either control or Plcγ1-specific shRNAs. After 24 hours of infection cells were cultured in serum-free medium (StemPro®34) supplemented with 1 U/ml of human recombinant Erythropoietin (Epo), 100 ng/ml SCF, 1 µM dexamethasone and 1% penicillin/streptomycin for 24 hours, followed by selection with puromycin (1 µg/ml) for 48 hours. For differentiation induction, I/11 were seeded 72 hours after infection in StemPro34® medium containing 10 U/ml Epo, 0.5 mg/ml human holo-transferrin and 1% penicillin/streptomycin. Cells were harvested at the indicated time points (0h on differentiation; 24h on differentiation).


title: I/11 cells 96 h after infection with anti-Plcg1 shRNA #133; 24h on differentiation medium

description:
small hairpin RNA against Plcg1
I/11 cells is a murine erythroblast cell line established from p53-deficient mouse fetal liver cells (day E12.5)


title: I/11 cells 96 h after infection with anti-Plcg1 shRNA #14; 24h on differentiation medium


title: Day 15 MPP+ EC

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: Sample 3

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg19 using TopHat with default parameters
RNAseq: FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

organism: Macaca nemestrina

source_name: MniPSC-CD34+ cells after induction with cytokines and EC

extract_protocol:
RNA was harvested using Trizol treatment
Illumina TruSeq PE 51x2 (RNA-seq)

value: MnIPSC line-7


title: Day 15 MPP + Cytokines

description: Sample 2

source_name: MniPSC-CD34+ cells after induction with cytokines alone


title: I/11 cells 72 h after infection with a scrambled shRNA (scr; 0h on differentiation medium)


title: MUVEC

description: Sample 5

source_name: monkey umbilical vein endothelial cells

value: umbilical vein endothelial cells


title: Day 8 EB

description: Sample 1

source_name: MniPSC-CD34+ cells before induction


title: 20hr_R1


title: Soleus rep3

city: Worcester

first: Yongxu

last: Wang

state: MA

address: 364 Plantation Street

department: Program in Gene Function and Expression

institute: UMass Medical School

description: soleus muscle replicate 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using tophat v1.4.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.0.1, and exported by R/Bioconductor package cummeRbund
Genome_build: mm9
Supplementary_files_format_and_content: csv files include RPKM values for each Sample

source_name: soleus muscle

extract_protocol:
Tissues were obtained from 3-month old C57BL/6J male mice (n=3 mice).  Total RNA were extracted using TRIzol Reagent.
Illumina TrueSeq RNA Sample Preparation v2 Guide.

value: Soleus

tag: age

value: 3 month

value: male


title: WAT rep2

description: white fat replicate 2

source_name: white fat

value: WAT

tag: strain


title: Soleus rep2

description: soleus muscle replicate 2

tag: gender


title: BAT rep2

description: brown fat replicate 2

source_name: brown fat

value: BAT


title: BAT rep1

description: brown fat replicate 1


title: WAT rep1

description: white fat replicate 1


title: WAT rep3

description: white fat replicate 3


title: BAT rep3

description: brown fat replicate 3


title: preadipocytes H3K27me3

data_processing:
Barcodes were removed from ChIP-seq reads. Barcodes: H3K27me3, ACGT-insert-ACGT…inputs: AGCT-insert-AGCT…
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 0.12.9 with configurations as -v 2 -m 1 --best --strata -p 8.
Peaks were called using MACS version 1.4.1 with the following setting: -g mm -f BOWTIE -s 20 --bw=150 --shiftsize=75 --nomodel --wig.
Genome_build: GRCm38
Supplementary_files_format_and_content: wig files were generated using MACS and converted to bigwig by wigToBigWig.

source_name: brown preadipocytes, H3K27me3 ChIP

extract_protocol:
Antibody against H3K27me3 (Millipore, Cat# 07-449, Lot# 2194165). 7.5 milllion cells were used for each ChIP.
Illumina's ChIP-seq Sample Prep kit.

tag: strain/background

value: immortalized brown preadipocytes

tag: passages


title: preadipocytes input

source_name: brown preadipocytes, input

tag: cell type


title: adipocytes H3K27me3

source_name: mature brown adipocytes, H3K27me3 ChIP

value: immortalized mature brown adipocytes

tag: chip antibody


title: YW3,YW7 m6A-seq

first: Yue

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

description: 2 biological replicates

data_processing: To account for PCR artefacts, only reads aligned to the distinct genome coordinates were retained. This post-alignment filtering was achieved using samtools rmdup from Samtools (0.1.18) and MarkDuplicates from Picard (1.74). As a result, the final processed alignments in each library comprises of distinct reads each mapped to a unique location in the mm10 reference genome.

source_name: Undifferentiated embryonic stem cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen). RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination. PolyA RNA was purified using GenEluteª mRNA Miniprep Kit (Sigma Aldrich) per manufacturer's instruction. PolyA RNA was fragmented using RNA fragmentation kit (Ambion). Two ug fragmented RNA was saved as input. Two hundred ug fragmented RNA was incubated with 3 ug anti-m6A antibody (Synaptic Systems) in RIP buffer (150mM NaCl, 10mM Tris, 0.1% NP40) for 2 hrs at 4 oC, followed by the addition of washed protein A/G magnetic beads (Millipore) and incubation at 4 oC for additional 2 hrs. Beads were washed 6 times in RIP buffer and incubated with 50 ul IP buffer containing 0.5mg/mL to elute RNA. IP'ed RNA was extracted with phenol/chloroform.
The Scriptseq v.2 RNA-seq Library Preparation method was performed on 40 ng of RNA for each sample. We followed the protocol given in the Scriptseq v.2 RNA-seq Library Preparation manual (Epicentre, an Illumina company), except DNA Clean & Concentratorª-5 - PCR/DNA clean columns (Zymo Research) were used to isolate the cDNA prior to PCR step. 15 cycles of PCR were performed on the cDNA and the resulting DNA products were purified on 2% E-Gel¨ EX Agarose Gels (Invitrogen). The products were visualized using a blue light transluminator and selected regions of the gel were excised corresponding to 200-400 bp products. The gel slices were dissolved in agarose dissolving buffer and the DNA was isolated on DNA Clean & Concentratorª-5 - PCR/DNA clean columns. The isolated DNA products were then analyzed and quantitated on an Agilent Bioanalyzer 2100.  Samples were pooled and loaded into one lane of a HiSeq2000 v3 flowcell (Illumina) and sequenced for 100 bases with separate 7 base indexing read.

value: Undifferentiated embryonic stem cell

tag: genotype/variation

value: Wild type

tag: antibody

value: anti-m6A antibody


title: YW1,YW5 Input RNA

description: 2 biological replicates


title: YW7 Input RNA

source_name: Input RNA


title: YW8 m6A-seq

value: Differentiated embryonic stem cell


title: I/11 cells 72 h after infection with anti-Plcg1 shRNA #14; 0h on differentiation medium


title: YW6 m6A-seq


title: YW5 Input RNA


title: Soleus rep1

description: soleus muscle replicate 1

tag: tissue


title: YW3 Input RNA


title: YW2 m6A-seq


title: Input_chromatin_control

status: Public on Dec 30 2015

city: Boulder

first: Jennifer

middle: F

last: Kugel

state: CO

address: 596 UCB

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
Read quality was assessed using FastQC.
Reads were mapped to the mouse mm10 genome using Bowtie (version 1.0.0) in the -v alignment mode, allowing one to three mismatches per read and reporting only reads with unique alignments.
Analysis of mapped reads was performed using the suite of tools available in HOMER, including making tag directories, generating bedGraph files, tag counting across RefSeq genes, generating histograms of factor occupancy flanking regions of interest, and generating heatmaps.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bedGraph files generated using the default makeUCSCfile command in HOMER.

source_name: embryonic fibroblasts, input

growth_protocol: NIH 3T3 cells were maintained in 5% CO2 at 37ºC in DMEM containing 10% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, and 2 mM L-glutamate. Cells were subcultured at least twice per week at 80% confluencey or less.

extract_protocol:
Chromatin was prepared from sonicated nuclei and specific protein-DNA complexes were isolated by immunoprecipitation.
Libraries for Illumina sequencing were prepared using the TruSeq ChIP Sample Prep kit (Illumina) for the input chromatin samples.

value: NIH 3T3

value: embryonic fibroblast


title: adipocytes input

source_name: mature brown adipocytes, input


title: I/11 cells 72 h after infection with anti-Plcg1 shRNA #133; 0h on differentiation medium


title: YW2,YW6 Input RNA

description: 2 biological replicates

source_name: Differentiated embryonic stem cell


title: ChIPSeq Input

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Input control

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8
Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts. BED files are generated using CASAVA pipeline 1.8 and samtools
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser. For RNA-Seq, read counts per transcript were calculated using Cuffnorm 2.2.0 and then R package edgeR was used for differential gene expression analysis.
Genome_build: mm9
Supplementary_files_format_and_content: MACS 1.4.2 peak file and read counts

source_name: gastric epithelial cells

growth_protocol: The mouse GEC cell line GSM06 was cultured in DMEM/F12 medium supplemented with 10% FBS, 1% ITES, 1% pen/strep antibiotics and 100 ng/ml of EGF. 90% of confluent cells were used for experiment.

extract_protocol: For ChIP-Seq, chromatin from 1 × 108 cells was sonicated for 20 cycles of 12 sec on/48 sec off, into 200-500 bp fragments, DNA ends were repaired using polynucleotide kinase and Klenow enzyme, and treated with Taq polymerase to generate a protruding 3’ “A” nucleotide. DNA fragments of ~250-450 bp were purified from agarose gels and used for cluster generation and sequencing. Antibodies against IRF8 were used (Santa Cruz Biotechnology, Cat# sc-6058x). For RNA-Seq,  Total RNA was isolated, and 5 μg per sample were used for mRNA purification using Dynal oligo(dT) beads (Invitrogen).  Double-stranded cDNA was synthesized with random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (Invitrogen) and fragmented by Bioraptor.  After end repair (Epicentre DNA END-Repair kit) and the addition of an “A” nucleotide to the 3’ ends with Taq DNA polymerase, two mixed Solexa adaptors (Illumina) were ligated to DNA ends using T4 DNA ligase (New England Biolabs).  250-450 bp fragments were isolated on 2% E-Gels (Invitrogen) and amplified for 18 cycles using PE 1.0 and 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).  PCR products were run on a gel, and 250-450 bp fragments were purified

treatment_protocol: Cells cultured at 70% confluence were stimulated with IFN-g at 10 ng/ml for 2 days. Non-stimulated cells were used as control.

value: stomach

value: Input control


title: ChIPSeq none IRF8

description: ChIP against IRF8

value: ICSBP/IRF8 (Santa Cruz, sc-6058, Lot C2713)


title: RNASeq noIFNg

description: -IFNg


title: Hi-C Neuron-NcoI

city: Montreal

first: Josee

last: Dostie

state: Quebec

address: 3655 Prom. Sir-William-Osler

country: Canada

institute: McGill University

data_processing:
Library strategy: Hi-C
The paired end Hi-C reads were mapped and filtered with the hiclib pipeline (Imakaev et al., 2012, Downloaded November 2013) using default parameters. Data was binned at 50kb or 100kb, depending on the application.
Hi-C matrices were corrected using Iterative Correction (Imakaev et al., 2012) and further processed with custom code to generate normalized heatmaps (See associated publication for details).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are tab-delimited text files that contain raw or normalized interaction scores between genomic loci for a given chromosome. The coordinates of each loci are marked in the first row and first column of the table.

source_name: Mouse Neuron cells

extract_protocol: Hi-C libraries were generated as previously published (Lieberman-Aiden et al, 2009), with modifications to increase DNA yield. See associated publication for details.

value: midbrain-like neurons

tag: restriction enzyme

value: NcoI


title: input_chromatin_heatshock

data_processing:
read quality was assessed using FastQC
Reads were mapped to the mouse genome (mm10 assembly) using Bowtie (version 1.0.0) in the -v alignment mode, allowing one to three mismatches per read and reporting only reads with unique alignments
Analysis of mapped reads was performed using the suite of tools available in HOMER, including making tag directories, generating bedGraph files, tag counting across RefSeq genes, generating histograms of factor occupancy flanking regions of interest, and generating heatmaps
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files generated using the default makeUCSCfile command in HOMER

source_name: embryonic fibroblast

growth_protocol: NIH 3T3 cells were maintained in 5% CO2 at 37ºC in DMEM containing 10% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, and 2 mM L-glutamate.  Cells were subcultured at least twice per week at 80% confluencey or less.

extract_protocol:
Chromatin was prepared from sonicated nuclei and specific protein-DNA complexes were isolated by immunoprecipitation.
Libraries for Illumina sequencing were prepared using the Ovation Ultralow System V2 (NuGEN) for Ser5-P samples, the TruSeq ChIP Sample Prep kit (Illumina) for the H2A.Z and input chromatin samples, and the ChIP Seq Sample Preparation Kit (Illumina) for the Pol II samples.

treatment_protocol: For heat shock, cells were grown to a confluency of 50% in T175 flasks and placed in a 45C water bath for 15-20 min then placed back at 37C for 45-60 min.

tag: exposed to

value: heat shock (45C water bath) for 15-20 min

tag: chip antibody vendor


title: Hi-C NPC-HindIII

source_name: Mouse NPC cells

value: neural progenitor cells

value: HindIII


title: Hi-C NPC-NcoI


title: YW4,YW8 m6A-seq

description: 2 biological replicates


title: input_chromatin_control

value: none (control)


title: Hi-C ESC-HindIII

source_name: Mouse 46C ES cells

value: embryonic stem cells


title: Hi-C ESC-NcoI


title: SW 2-week-cold rep3

city: Beltsville

first: Sunchung

last: Park

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

description: SW grown at 22°C on soil under a photoperiod of 12 h for 18 days, two weeks at 4C, sampled at ZT4

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the Arabidopsis reference genome (TAIR10) using Tophat version 1.4.1 in default mode with minimum and maxmum intron lengths being set to 10 and 15,000 bp, respectively. The transcript abundance (FPKM) was estimated using Cufflinks (version 2.1.1). Cuffdiff was run using default parameters with inputs of the TAIR10 genome and transcript annotations.
Genome_build: TAIR v10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

source_name: aerial part

growth_protocol: Plants were grown on soil at 22⁰C under a 12 h photoperiod with 100-120 μmol m-2 s-1 light intensity

extract_protocol:
Cold treated and control samples (all samples) were collected at ZT4
RNA was extracted using the RNeasy plant mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cold treatment was for 1 or 2 weeks at 4⁰C under a 12 h photoperiod of ~35 µmol m-2 sec-1

value: entire aerial part

value: 18 days after germination, 2 weeks at cold

tag: ecotype

value: Swedish


title: SW 2-week-cold rep2


title: SW 2-week-cold rep1


title: YW1 Input RNA

value: Undifferentiated embryonic stem cell

value: Wild type


title: PolII_ChIPSeq_mock

data_processing:
Read quality was assessed using FastQC.
Reads were mapped to the mouse mm10 genome using Bowtie (version 1.0.0) in the -v alignment mode, allowing one mismatch per read and reporting only reads with unique alignments.
Analysis of mapped reads was performed using the suite of tools available in HOMER, including making tag directories, generating bedGraph files, tag counting across RefSeq genes, generating histograms of Pol II occupancy flanking regions of interest, and peak calling.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bedGraph files generated using the default makeUCSCfile command in HOMER.

source_name: embryonic fibroblasts, mock infection, Pol II ChIP

extract_protocol:
Chromatin was prepared from sonicated nuclei and Pol II-DNA complexes were isolated by immunoprecipitation.
Libraries were prepared using the Ovation Ultralow System V2 from NuGEN. Libraries were sequenced on an Illumina HiSeq 2000.

treatment_protocol: For infection, cells were grown to a confluency of 70% and treated with HSV-1 strain KOS at a multiplicity of infection of 3 pfu/cell for 4 hr. Mock and infected cells were crosslinked with 1% formaldehyde for 10 min.

value: NIH 3T3

tag: treatment

value: anti-Pol II (sc899-x, Santa Cruz Biotechnology)


title: Hi-C Neuron-HindIII


title: SW 1-week-cold rep3

description: SW grown at 22°C on soil under a photoperiod of 12 h for 18 days, one week at 4C, sampled at ZT4

value: 18 days after germination, 1 week at cold


title: YW4 m6A-seq

value: Differentiated embryonic stem cell

value: anti-m6A antibody


title: SW 1-week-cold rep1


title: RNASeq withIFNg

description: +IFNg

value: stomach


title: SW warm rep3

description: SW grown at 22°C on soil under a photoperiod of 12 h for 18 days, sampled at ZT4

value: 18 days after germination


title: SW warm rep2


title: SW warm rep1


title: MT, rep1

city: wuhan

first: Fei

last: Guo

address: shizishan

institute: Huazhong Agricultural Univesity

description:
Citrus grandis
MT1

data_processing:
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and then mapped to the citrus sinensis whole genome using bowtie2 version 2.1.0.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Citrus sinensis whole genome (2014 version 2.1; http://citrus.hzau.edu.cn/orange/).
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each Sample. The geneIDs represent the gene IDs for Citrus sinensis.

organism: Citrus maxima

source_name: pericarp, mutant

extract_protocol:
Total RNA was extracted by the Trizol method.
20 mg total RNA was prepared to enrich mRNA by using oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with the QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.

treatment_protocol: No treatment.

tag: cultivar

value: "Guanxi" pummelo

value: orange-pericarp mutant

tag: developmental stage

value: ripe

value: pericarp


title: MT, rep2

description:
Citrus grandis
MT2


title: IT 2-week-cold rep3

description: IT grown at 22°C on soil under a photoperiod of 12 h for 18 days, two weeks at 4C, sampled at ZT4

tag: age

value: Italian


title: IT 2-week-cold rep2

value: entire aerial part


title: WT, rep2

description:
Citrus grandis
WT2

source_name: pericarp, WT

value: WT


title: WT, rep3

description:
Citrus grandis
WT3


title: IT 1-week-cold rep3

description: IT grown at 22°C on soil under a photoperiod of 12 h for 18 days, one week at 4C, sampled at ZT4


title: IT 2-week-cold rep1

value: 18 days after germination, 2 weeks at cold


title: IT 1-week-cold rep1


title: IT warm rep3

description: IT grown at 22°C on soil under a photoperiod of 12 h for 18 days, sampled at ZT4


title: IT warm rep2


title: WT, rep1

description:
Citrus grandis
WT1


title: IT warm rep1


title: Sox21a EB2

city: Lausanne

first: ZongZhao

last: Zhai

address: EPFL-SV-GHI-UPLEM station 19

country: Switzerland

institute: EPFL

description:
total RNA, but selected for mRNA, and amplified subsequently
a456_vs_a123_sig.txt
a456_vs_a123.txt

data_processing:
Mapping: Bowtie2
Expression quantification: Count reads in Exon (Own script)
Differentially gene expression: Published Method (check reference)
Genome_build: Drosophila Melanogaster Version 6.02
Supplementary_files_format_and_content: Text files, using Flybase ID use row id, mean expression in different conditions,variance in difference condition, fold change, pval and adjusted pvalues

organism: Drosophila melanogaster

source_name: enteroblast from the anterior midgut of adult fly

growth_protocol: 25 degree

extract_protocol:
Arcturus PicoPure RNA Isolation Kit
TruSeq RNA Sample Prep Kit-v2

treatment_protocol: FACS sorted

value: adult midgut

value: enteroblast

value: 16-18 days adult

value: female

tag: biomarker

value: Su(H)GBE-Gal4, UAS-CD8::GFP

value: Sox21a mutant


title: control EB3

tag: gender

value: wild-type


title: Sox21a EB1


title: MT, rep3

description:
Citrus grandis
MT3


title: Sox21a EB3


title: control EB2


title: SW 1-week-cold rep2

value: 18 days after germination, 1 week at cold

value: Swedish


title: control EB1


title: Usp16 KO

city: Richmond

first: Hengbin

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm10 with TopHat. Duplicate reads were removed with Picard.
Cufflinks was used to determine transcript abundance.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm

source_name: ckit and sca1 positive cells

extract_protocol:
ckit and sca1 positive cells were isolated from the bone marrow of Mx1 Cre:Usp16loxp/loxp mice treated with pIpC (Usp16 deleted bone marros) or saline (Control).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hematopoietic stem and progenitor cells from mouse bone marrow

tag: genotype

value: Usp16 KO


title: IgG ChIP

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to mm10 with Bowtie.  Duplicate reads were removed with Picard.  Peaks were called with MACS.
Genome_build: mm10
Supplementary_files_format_and_content: peak

extract_protocol:
ckit and sca1 positive cells were isolated from the bone marrow of Mx1 Cre:Usp16loxp/loxp mice. DNA was sheared into approximately 200bp fragments by sonication.  Usp16 bound DNA was immunoprecipitated by standard protocols.
Libraries were prepared for sequencing using standard Illumina protocols

value: IgG


title: Control

value: control


title: anti-Usp16 ChIP


title: PolII_ChIPSeq_HSV1

description: Genomic DNA (host cell and viral).

data_processing:
Read quality was assessed using FastQC.
Reads were mapped to the mouse mm10 genome using Bowtie (version 1.0.0) in the -v alignment mode, allowing one mismatch per read and reporting only reads with unique alignments.
Analysis of mapped reads was performed using the suite of tools available in HOMER, including making tag directories, generating bedGraph files, tag counting across RefSeq genes, generating histograms of Pol II occupancy flanking regions of interest, and peak calling.
Reads were mapped to the HSV-1 genome after building a custom index in Bowtie 1.0.0 using the HSV-1 strain KOS complete genome sequence GenBank JQ673480.1. Mapping was performed in the -v alignment mode, allowing one mismatch and reporting the best alignment per read.
HOMER was used to generate a bedGraph file of the HSV-1 mapped ChIP-seq reads, and to histogram reads using custom files to designate HSV-1 gene features.
Genome_build: Mouse: GRCm38 (mm10)
Genome_build: HIV-1: JQ673480.1
Supplementary_files_format_and_content: bedGraph files generated using the default makeUCSCfile command in HOMER.

organism:
Mus musculus
Human alphaherpesvirus 1 strain KOS

source_name: embryonic fibroblasts, HSV-1 infection, Pol II ChIP

tag: cell line

value: NIH 3T3

value: embryonic fibroblast

value: HSV1 strain KOS infection

value: anti-Pol II (sc899-x, Santa Cruz Biotechnology)


title: ChIPseq-mES-Input

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: Input control for mouse ES cell

data_processing:
The sequenced tags were aligned to mouse genome (mm8) and the peak detection was done using MACS.
Genome Build:
CME087-Input-mm8-tags.bed: mm8

source_name: E14 mouse embryonic stem cells

growth_protocol: E14 mouse ES cells were cultured without feeders on 0.1% gelatin-coated plates, in ES medium containing DMEM supplemented with 15% ES FBS (Invitrogen), 2 mM L-glutamine (Invitrogen), 0.1 mM MEM nonessential amino acid (Invitrogen), 0.1 mM beta-mercaptoethanol (Invitrogen), and Chinese hamster ovary Leukaemia Inhibitory Factor (CHO-LIF) (1000 U/ml).

extract_protocol: Standard Illumina single end read library was prepared as per as manufacturer's instruction to be sequenced on a GAII sequencer (14 round amplification cycle was used)

value: Embryonic stem cell


title: ChIPseq-mES-Zic3

description: ChIP-seq of Zic3 in mouse ES cell

data_processing:
The sequenced tags were aligned to mouse genome (mm8) and the peak detection was done using MACS.
Genome Build:
CME086-Zic3-mm8-tags.bed: mm8
Zic3Mouse_peaks-mm8.xls: mm8


title: Input DNA

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

description: Growing MCF10Asi-ER cells

data_processing:
Alignments were performed with BWA (Li and Durbin 2009) to hg18 using default parameters.
The peaks were identified from uniquely mapped reads without duplicates using MACS and the p-value cutoff used for peak detection was 1e-5.
Genome_build: hg18
Supplementary_files_format_and_content: SAMtools and BEDtools were used for filtering steps and file formats conversion.

organism: Homo sapiens

source_name: MCF10Asi-ER cells

growth_protocol: MCF10A were cultured in 1:1 mixture DMEM-F12 supplemented with 5% horse serum, 10 µg/ml insulin, 0,5 µg/ml hydrocortisone, 100 ng/ml cholera enterotoxin, and 20 ng/ml epidermal growth factor, and incubated at 37°C in humidified atmosphere with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 10 ng of ChIP (or Input) DNA with TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions. 50bp single-end sequencing was performed using Illumina HiSeq 2000 platform (Genomix4life S.R.L., Baronissi, Salerno, Italy) according to standard operating procedures.

treatment_protocol: MCF10A-AsiSI cells were arrested in G0 by growth in minimal medium (1:1 mixture DMEM-F12 supplemented with 5% horse serum) for two days. To induce re-entry into cell cycle, the GO arrested cells were cultured in complete medium. DNA damage was induced by treatment with 4-OHT.


title: ChIPSeq IFNg IRF8

description: ChIP against IRF8

tag: strain

value: stomach

value: ICSBP/IRF8 (Santa Cruz, sc-6058, Lot C2713)


title: gH2AX ChIP-seq_G0_4OHT

description: G0 MCF10Asi-ER cells treated with 4OHT

tag: chip antibody

value: gH2AX (ab81299, Abcam)


title: IT 1-week-cold rep2

value: entire aerial part

value: Italian


title: gH2AX ChIP-seq_grow_4OHT

description: Growing MCF10Asi-ER cells treated with 4OHT

treatment_protocol: DNA damage was induced by treatment with 4-OHT.


title: Landrace 7 dpi

city: Beijing

first: Ning

state: Beijing

address: Yuanmingyuan West Rd. 2,Haidian District

institute: China Agriculture University

description: three pigs total RNA were pooled at equal quantities

data_processing:
Illumina Casava1.7 software used for basecalling.
Abondon reads with >50% bases have a quality < 20
The clean reads were mapped using BOWTIE2 (default set)
RPKM was used to measure the expression level of genes in different samples
Genome_build: Ssc3
Supplementary_files_format_and_content: tab-delimited files include RPKM values for each sample

organism: Sus scrofa

source_name: lungs

extract_protocol:
Pigs were dissected and the lung tissue samples were stored in liquid nitrogen. The total RNA were extracted using Trizol reagents.
Standard Illumina protocols were used to prepare the RNA libraries

tag: hp-prrsv infection

value: 7 dpi

value: lung

value: 35 days old

tag: breed

value: Landrace

value: WT type


title: Landrace 3 dpi

value: 3 dpi

tag: tissue


title: Landrace 0 dpi

value: 0 dpi


title: Tongcheng 3 dpi

value: Tongcheng


title: Tongcheng 0 dpi


title: Landrace 5 dpi

value: 5 dpi


title: Tongcheng 7 dpi


title: cKO_REV-ERBa_ChIPSeq

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Road, Room 4537

department: Case Cardiovascular Research Institute

institute: Case Western Reserve University

description: genomic DNA

data_processing:
Base call was performed using Bcl2fastq-1.8.3
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.7.5a-r405 with default settings
Data were filtered with base quality >=33
peaks were called using MACS version 1.4.2 with the following setting: p<10-5
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS; Scores represent -10*log10pvalue of peak region

extract_protocol:
Hearts were harvest at ZT10, 3 hearts were pooled for chromatin extraction.
Libraries were prepared according to Illumina's instructions accompanying the Truseq ChIPseq Sample Preparation Kit (IP-202-1012).

treatment_protocol: Mice were kept on a 12/12 light/dark facility with ad lib access to food.

tag: genotype/variation

value: KLF15 knockout

value: heart

value: REV-ERBa (Cell Signaling, E1Y6D, #13418)


title: Tongcheng 5 dpi


title: Flox_input DNA

description: genomic DNA

source_name: input DNA

value: KLF15 wildtype


title: PolII_ChIPSeq_heatshock

value: NIH 3T3

tag: cell type

value: embryonic fibroblast

tag: exposed to

value: heat shock (45C water bath) for 15-20 min

value: Pol II Antibody (N-20)

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: cTG1_Flag_ChIPSeq

description: genomic DNA

value: FLAG tagged

value: FLAG (Sigma, F3165)


title: PolII_ChIPSeq_control

value: none (control)

tag: chip antibody vendor


title: cKO_input DNA

description: genomic DNA


title: P28-2dpi-1

first: Fan

last: Zhang

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

description:
replicate 1
CP3-E

data_processing:
Primary data analysis and base calling was performed by the Illumina instrument software.
The raw reads were first filtered by removing adaptor sequences and low-quality sequences by using in-house perl script. Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed, and the retained high quality pair-end reads of rice for each sample were mapped to the rice genome of RGAP at MSU (Kawahara et al., 2013) by tophat (Trapnell et al., 2009) and then assembled with Cufflinks (Trapnellet al., 2010) to construct unique transcipts sequences, using the parameter:-g -b -u -o.
The retained high quality pair-end reads of each sample were mapped to the rice genome using Tophat2(v2.0.11) with default parameters. Then gene expression abundance was quantified by FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks(v2.1.1), and differentially-expressed genes (DEGs) between samples were identified by Cuffdiff, a component of the Cufflinks package.
Genome_build: MSU Release 7.0 (Os-Nipponbare-Reference-IRGSP-1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: leaves

growth_protocol: Seeds of H471, HHZ, and P28 were sown in a seedling nursery and 30-day-old seedlings were transplanted into a screenhouse of the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. There were nine plants in each row, with a spacing of 20 × 17 cm.

extract_protocol:
For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Philippine’s representative strain of Xoo, PXO349, was used to artificially inoculate H471 and its parents. The strain was incubated on peptone sucrose agar at 30°C for 2 days, and the inoculum was prepared by suspending the bacterial mass in sterile water at a concentration of 108 cells mL-1. Five plants of each line were inoculated with PXO349 in the four to five uppermost leaves of each plant using the leaf-clipping method in three replications at the tillering stage (plant age of 65 days). LLs were measured on all inoculated leaves at 14 dpi when the lesions were stable.

value: donor parent

value: tillering phase

tag: time point

value: 2 days post-inoculation

tag: treatment

value: Xoo Philippinesâ€™ race 9b


title: E2F8 in HeLa cells

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using BWA package
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling. Cisgenome was used for peak-calling from the ChIP-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: peak coordinates file : number_chromosome_start_end_length_fold-enrichment

growth_protocol: Cells were synchronized by serum starvation followed by hydroxyurea block as following: first near-confluent cells were cultured for 36h in serum-deprived medium (0.5% FBS). Then, cells were subcultured, and allowed to attach to the culture dishes in DMEM containing 10% FBS for three hours. Subsequently, 2mM hydroxyurea (Sigma Aldrich) was added to the medium for 16 hours to arrest cells at the onset of S phase. Cells were released from the HU block by washing three times with PBS and adding fresh medium containing 10% FBS.

extract_protocol: Immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD/AB sequencer in multiplexed way.

treatment_protocol: ChIP was performed according the Millipore's EZ ChIP protocol, with the following specifications: cells were crosslinked for 10 minutes by 1% freshly made formaldehyde. Crosslinking was stopped by 5 minutes of 100mM glycine. Cells were then washed twice with PBS, and scraped in 1 mL of ChIP lysis buffer. Lysates were sonicated for 8 minutes at maximum power on a Covaris S2 (Covaris). For ChIP-qPCR 1 million cells were used for each reaction; for ChIP-seq, 25 million cells were used for each reaction. IPs were performed using BSA-blocked Fast Flow Agarose G beads (Millipore, 16-266). An Abcam ab 109596 was used. To improve signal-to-noise ratios in the ChIP-seq experiments, a double-IP protocol was used. Antibody-chromatin complexes were eluted from the beads using 200 uL of buffer containing 1% SDS and 100mM NaHCO3, and dissolved in 10 mL of ChIP dilution buffer. The I.P. was then repeated with 5 ug antibody, and processed according to the EZ ChIP protocol.

value: HeLa

tag: timepoint

value: mid to late S-phase

tag: antibody

value: E2F8, Abcam ab109596


title: H471_3d

data_processing:
Primary data analysis and base calling was performed by the Illumina instrument software.
Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed using an in-house Perl script.
High quality reads were mapped to the MSU Rice Genome Annotation Project (MSU RGAP; ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0), and to Xoo strain PXO99A genome reference information downloaded from the NCBI (http://www.ncbi.nlm.nih.gov/nuccore/NC_010717.1) using Bowtie. To avoid contamination of reads from interaction partners, reads were also mapped against the reference genome of the interaction partner.
Retained high quality pair-end reads of rice for each sample were mapped to the rice genome of MSU RGAP using TopHat, and assembled with Cufflinks to construct unique transcripts sequences using the parameter –g –b –u –o. Cuffcompare was used to compare the assembled transfrags of each sample to the reference annotation, and to build up a non-redundant transcript dataset among the samples. Next, Cuffdiff was used to identify DEGs, and genes with a P value ≤ 0.05 marked as significantly different between the two samples.
Similar to credibility interval approaches reported for the analysis of SAGE data, we employed IDEG6  to identify genes showing statistically significant difference in relative abundance (as reflected by total count of individual sequence reads) between the two samples.A general Chi2 test was employed, as this has proved to be an efficient test. Finally, genes with P value ≤ 0.05 were determined to be significantly different between the two samples.
Genome_build: Nipponbare and PXO99A
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism:
Oryza sativa
Xanthomonas oryzae pv. oryzae

source_name: inoculated leaves

extract_protocol:
For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled. Ribosomal RNA (rRNA) was removed from 8 μg of total RNA using a RiboMinus™ Plant Kit (Invitrogen) followed by a Ribo-Zero Gram-Negative Bacteria kit (Epicentre, Madison, Wisconsin, USA) in accordance with manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rice genotype

value: introgression line

tag: xanthomonas oryzae race

tag: host-pathogen compatibility status

value: incompatible

tag: Stage

value: inoculated by Xoo for 3 days

tag: rice strain number


title: Flox_REV-ERBa_ChIPSeq

description: genomic DNA

tag: strain

value: KLF15 wildtype

value: heart

tag: chip antibody

value: REV-ERBa (Cell Signaling, E1Y6D, #13418)


title: H471_1d

value: inoculated by Xoo for 1 day


title: HHZ_3d

value: recurrent parent

value: compatible


title: H471-2dpi-1

description:
replicate 1
CP16-E

tag: genotype

tag: developmental stage


title: P28-2dpi-2

description:
replicate 2
CP3-E


title: H471-2dpi-2

description:
replicate 2
CP16-E


title: HHZ-1dpi-2

description:
replicate 2
CP1-C

value: 1 day post-inoculation


title: HHZ-2dpi-2

description:
replicate 2
CP1-E


title: HHZ-2dpi-1

description:
replicate 1
CP1-E


title: HHZ-1dpi-1

description:
replicate 1
CP1-C


title: H471-1dpi-2

description:
replicate 2
CP16-C


title: H471-1dpi-1

description:
replicate 1
CP16-C


title: pH 4.0

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: RPKM=10^6C/(NL/10^3). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text files containing RPKM values for each Sample

organism: Candida albicans

source_name: candida albicans_pH4.0

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: P28-ck-1

description:
replicate 1
CP3

value: donor parent

value: tillering phase

value: normal condition


title: cTG1_input DNA

description: genomic DNA

tag: genotype/variation

value: FLAG tagged

tag: tissue


title: P28_1d


title: HHZ_1d


title: P28-1dpi-2

description:
replicate 2
CP3-C

value: Xoo Philippinesâ€™ race 9b


title: P28-1dpi-1

description:
replicate 1
CP3-C