title: ECBM13_a9_sdc-2-y93-RNAi-embryo_SDC3-IP

data_processing:
50 base single end Illumina sequences were sorted by the bar code in the first 4 or 6 sequenced bases, then  bar codes were removed
alignment to reference C. elegans genome WS230 with BOWTIE
pileup files were made using SamTools
the number of reads at each base was normalized by the total number of reads per million, then the average normalized read value for 50 bp windows was calculated and formatted into gff3
Genome_build: WS230
Supplementary_files_format_and_content: the processed data only contains reads for chromosome X

extract_protocol:
The frozen embryos were ground under liquid nitrogen by mortar and pestle. Chromatin was sheared by the Covaris S2 (20% duty factor, power level 8, 200 cycles per burst) for a total of 30 min processing time (60 sec ON, 45 sec OFF, 30 cycles). To perform the ChIP reactions, extract containing approximately 2 mg of protein was incubated in a microfuge tube with 5 ug of anti-SDC-3 or random IgG antibodies overnight at 4°C. A 25 ul bed volume of protein A sepharose beads was added to the ChIP for 2 hr. ChIPs were washed for 5 min at room temperature twice with FA Buffer (150 mM NaCl), once with FA Buffer (1 M NaCl), once with FA Buffer (500 mM NaCl), once with TEL buffer (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE Buffer. Protein and DNA were eluted twice with 1% SDS, 250 mM NaCl, 1mM EDTA at 65°C for 15 min.
Sequencing libraries were prepared as published in Zhong et al. (2010) with minor changes: sequencing adapters were as described in Lefrancois et al. (2009) and adapters were ligated using NEB Quick Ligation Kit (M2200).

treatment_protocol: Embryos were cross-linked with 2% formaldehyde for 30 min. Cross-linked embryos were resuspended in 1 ml of FA Buffer (150 mM NaCl, 50 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM DTT, protease inhibitor cocktail) for every 1 gram of embryos. This mixture was frozen in small droplets in liquid nitrogen.


title: BSW008i5

status: Public on Jun 03 2015

type: SRA

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

country: USA

institute: HHMI/UCB

library_source: transcriptomic

data_processing:
100 base single end Illumina sequences were trimmed to remove reads that failed quality control, barcodes were trimmed off reads using cutadapt version 0.9.5
Reads were aligned to the transcriptome using GSNAP version 2012-01-11
Uniquely mapping reads were assigned to genes using HTSeq version 0.5.4p3 using the union mode
Changes in gene expression were determined by analysis with DESeq
Genome_build: WormBase WS220
Supplementary_files_format_and_content: csv file with averaged FPKM values for N2 and sdc-2(y93).

molecule: total RNA

organism: Caenorhabditis elegans

source_name: mixed stage embryos

growth_protocol: Wild-type N2 worms were grown at 20°C on NG agar plates with concentrated HB101 bacteria. For DC-mutant embryos, 10 ml of packed synchronous sdc-2(y93) L1 worms were placed onto 10 cm RNAi plates (NG agar with 1 mM IPTG and 100 mg/ml Carbenicillin) seeded with 2-3 ml of concentrated HT115 (DE3) bacteria carrying the Ahringer feeding library plasmid expressing the coding region of sdc-2. The RNAi plates were incubated at 25°C overnight before L1s were added.  Mixed-stage embryos were harvested from gravid hermaphrodites.

extract_protocol:
RNA was extracted using a the protocol described in Baugh, Hunter Development 2002 except that 10 µL of a 20 mg/mL glycogen solution was used as a carrier.
Libraries were prepared from 10 µg of total RNA. PolyA RNA was purified using the Dynabeads mRNA purification kit (Ambion) and fragmented using Fragmentation Reagent (Ambion). First strand cDNA was synthesized from polyA RNA using the SuperScript III Reverse Transcriptase Kit with random primers (Invitrogen). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNAse H (Invitrogen). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina).

tag: strain

value: sdc-2(y93) with RNAi against sdc-2

tag: genotype

value: sdc-2 mutant

tag: developmental stage

value: embryo


title: lincenc1_RNA-seq_JR778

city: Cambridge

first: Abbie

last: Groff

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
processed data files format and content: the DiffTable output from cummeRbund, or essentially a tab-delimited file with all of the expression values and differential expression test statistics as called by cuffdiff for each gene in the transcriptome for each wt-v-ko comparison.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
E14.5 whole brains were harvested and homogenized in TRIzol. Adult brains were harvested immediately after euthanasia, snap frozen in liquid nitrogen, and stored at -80C. These brains were pulverized in liquid nitrogen and homogenized in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

tag: genotype/variation

value: WT

tag: lncrna previous name

tag: Sex

value: male

tag: timepoint

value: Adult

tag: litter

tag: tissue

value: whole brain


title: M_PGC_7W_embryo3_sc12

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

country: China

institute: Liangzhu Laboratory

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
For RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings (Trapnell et al., 2009). And for WGBS, bisulfite-converted reads were aligned to the human refference genome (hg19) using Bismark software (v0.7.6).
For RNA-seq, Cufflinks (v2.2.1) with default parameters was further used to assemble the transcripts and quantify transcription levels (FPKM, fragments per kilobase of transcript per million mapped reads) of annotated genes (Trapnell et al., 2010). And for WGBS, CpG methylation level of covered cytosines was estimated using comstomized Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the FPKM values of RefSeq genes, and the bed files which include the methylation level of cytosines in CpG, CHH and CHG context.

organism: Homo sapiens

source_name: Primordial Germ Cells

extract_protocol:
For single cell transcriptome analysis, the protocol for single-cell RNA-Seq has been published previously (Tang et al., 2010; Tang et al., 2009). Briefly, after a MACS or FACS procedure, a single PGC or somatic cell was randomly picked by using a mouth pipette and transferred into lysate buffer. And for DNA methylome analysis, the KIT-positive PGCs that were obtained by FACS were further washed with DPBS, and then DNA was isolated from the cell pellets using DNeasy Blood & Tissue Kits (Qiagen).
For single cell RNA-seq library construction, a total of 20–100 ng of cDNA was sheared into 150 bp to 350 bp by Covaris S2 after the generation of cDNA from a single cell, and the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, Inc.) was used to prepare the sequencing library following the manufacturer’s protocol. Briefly, the fragmented cDNA was end-repaired, dA tailed, adapter ligated and then subjected to 10–12 cycles of PCR amplification. Libraries were pooled and sequenced on Illumina HiSeq2500 sequencers for 100-bp paired-end sequencing. And for whole genome bisulfite sequencing (WGBS) library construction, samples of 5–100 ng of genomic DNA were used to construct the PBAT library, as previously described with minor modifications (Miura et al., 2012; Smallwood et al., 2014). Briefly, the isolated genomic DNAs, together with 1% unmethylated lambda DNA (Thermo Scientific), were subjected to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions. The bisulfite-converted templates were then annealed using random nonamer primers with a 5’ biotin tag and a truncated Illumina P5 adapter (5’-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) supplemented with 50 units of klenow polymerase (3’ to 5’ exo-, NEB). The excess primers were removed using 40 U exonuclease I (NEB) before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter). Then, the newly synthesized DNA strands were immobilized using the Dynabeads M280 Streptavidin (Invitrogen) and the original bisulfite-treated DNA templates were removed via two rounds of 0.1 N NaOH washes. The second strands were synthesized using 50 units klenow polymerase (3’ to 5’ exo-, NEB) with random nonamer primers containing a truncated P7 Illumina adapter (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads were further collected and were washed several times, and the library was finally amplified with 4–6 cycles of PCR using 1 U Kapa HiFi HS DNA Polymerase (Kapa Biosystems) together with 0.4 µM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 µM pre-indexed Illumina Reversed primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates index sequences). Amplified libraries were purified with 0.8× Agencourt Ampure XP beads twice and were assessed on the Agilent Bioanalyzer 2100 platform and quantified with a standard curve-based qPCR assay (Kapa Biosystems). The final quality-ensured libraries were pooled and sequenced on the Illumina HiSeq2000/2500 sequencer for 100 bp or 150 bp paired-end sequencing.

value: 7 week gestation

tag: gender


title: M_PGC_7W_embryo3_sc11

description: polyA RNA


title: M_PGC_7W_embryo3_sc10

description: polyA RNA


title: ECBM13_a6_sdc-2-y93-RNAi-embryo_IgG-IP

library_source: genomic

molecule: genomic DNA


title: ECMB09_w4_N2-embryo_SDC3-IP

value: wild type

tag: antibody


title: Eldr_RNA-seq_JR777

value: lincRNA knockout (KO)

value: linc-Egfr


title: M_PGC_10W_embryo1_sc4

description: polyA RNA

value: 10 week gestation


title: ECMB09_a8_N2-embryo_IgG-IP


title: Kantr_RNA-seq_JR775

value: linc-Jarid1c_L12-8 ***


title: M_PGC_7W_embryo3_sc9

description: polyA RNA


title: Ptgs2os2_RNA-seq_JR776


title: Kantr_RNA-seq_JR774


title: Celrr_RNA-seq_JR773

value: female


title: M_PGC_7W_embryo3_sc8

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR781

source_name: Trp53cor1 _RNA-seq_WT_Adult


title: Mannr_RNA-seq_JR772


title: M_PGC_7W_embryo3_sc5

description: polyA RNA


title: Mannr_RNA-seq_JR771


title: M_PGC_7W_embryo3_sc3

description: polyA RNA


title: M_PGC_7W_embryo3_sc4

description: polyA RNA


title: M_PGC_7W_embryo3_sc2

description: polyA RNA


title: Halr1_RNA-seq_JR768


title: lincenc1_RNA-seq_JR770


title: M_PGC_7W_embryo3_sc1

description: polyA RNA


title: Halr1_RNA-seq_JR767


title: Pantr2_RNA-seq_JR764


title: Kantr_RNA-seq_JR762

value: linc-Jarid1c_L12-1 ***


title: M_PGC_7W_embryo2_sc9

description: polyA RNA


title: M_PGC_7W_embryo2_sc10

description: polyA RNA


title: Celrr_RNA-seq_JR761


title: M_PGC_7W_embryo2_sc7

description: polyA RNA


title: BSW007i4


title: M_PGC_7W_embryo2_sc8

description: polyA RNA


title: Celrr_RNA-seq_JR760


title: Halr1_RNA-seq_JR759


title: M_PGC_7W_embryo2_sc6

description: polyA RNA


title: M_PGC_7W_embryo3_sc7

description: polyA RNA


title: Tug1_RNA-seq_JR757


title: M_PGC_7W_embryo2_sc5

description: polyA RNA


title: Pantr2_RNA-seq_JR758


title: M_PGC_7W_embryo3_sc6

description: polyA RNA


title: M_PGC_7W_embryo2_sc3

description: polyA RNA


title: M_PGC_7W_embryo2_sc4

description: polyA RNA


title: peloPB60/1 pep1

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

description: 18-30nt small RNA

data_processing: Reads which passed filter were mapped to rRNA, tRNA, snoRNA, miRNA, transposon, nonLTR, LTR, TRF and Drosophila melanogaster whole genome (BDGP5.25) using bowtie v0.12.7 with parameters -q -p 20 -m 1 -v 2, respectively. The miRNA reference was download from miRBase, and other resource were downloaded from Repbase.

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
Ovaries were manually dissected in ice-cold PBS. Total RNA were isolated using Trizol. 18-30nt RNAs were purified according to RNA oligo markers.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: age

value: 3-5 days old


title: Halr1_RNA-seq_JR755


title: Halr1_RNA-seq_JR754


title: lincenc1_RNA-seq_JR753


title: M_PGC_7W_embryo2_sc1

description: polyA RNA


title: M_PGC_7W_embryo1_sc15

description: polyA RNA


title: M_PGC_7W_embryo1_sc16

description: polyA RNA


title: lincenc1_RNA-seq_JR752


title: Mannr_RNA-seq_JR751


title: M_PGC_7W_embryo1_sc14

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR749

source_name: Trp53cor1 _RNA-seq_KO_E14.5


title: Mannr_RNA-seq_JR750


title: M_PGC_7W_embryo1_sc12

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR748

source_name: Trp53cor1 _RNA-seq_WT_E14.5


title: Kantr_RNA-seq_JR747

value: linc-Jarid1c_L13-2 ***


title: M_PGC_7W_embryo1_sc10

description: polyA RNA


title: Kantr_RNA-seq_JR746

value: linc-Jarid1c_L12-7 ***


title: Peril_RNA-seq_JR744


title: M_PGC_7W_embryo1_sc9

description: polyA RNA


title: Tug1_RNA-seq_JR745


title: M_PGC_7W_embryo1_sc8

description: polyA RNA


title: Tug1_RNA-seq_JR756


title: pelo1/+ rep1

description: 18-30nt small RNA


title: M_PGC_7W_embryo2_sc2

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR743

source_name: Trp53cor1 _RNA-seq_KO_Adult


title: M_PGC_7W_embryo1_sc6

description: polyA RNA


title: M_PGC_7W_embryo1_sc5

description: polyA RNA


title: Crnde_RNA-seq_JR741


title: Kantr_RNA-seq_JR742


title: M_PGC_7W_embryo1_sc4

description: polyA RNA


title: Eldr_RNA-seq_JR740


title: Celrr_RNA-seq_JR739


title: M_PGC_7W_embryo1_sc13

description: polyA RNA


title: M_PGC_7W_embryo1_sc2

description: polyA RNA


title: Mannr_RNA-seq_JR737


title: M_PGC_7W_embryo1_sc11

description: polyA RNA


title: lincenc1_RNA-seq_JR736


title: M_PGC_4W_embryo3_sc6

description: polyA RNA

value: 4 week gestation


title: Halr1_RNA-seq_JR735

value: WT


title: M_PGC_7W_embryo1_sc1

description: polyA RNA

value: male


title: Mannr_RNA-seq_JR734

value: Adult


title: M_PGC_4W_embryo3_sc4

description: polyA RNA


title: Pantr2_RNA-seq_JR731

value: whole brain


title: M_PGC_4W_embryo3_sc5

description: polyA RNA


title: M_PGC_7W_embryo1_sc7

description: polyA RNA

value: 7 week gestation


title: Ptgs2os2_RNA-seq_JR732


title: M_PGC_4W_embryo3_sc2

description: polyA RNA


title: M_PGC_4W_embryo3_sc3

description: polyA RNA


title: Peril_RNA-seq_JR721


title: Pantr1_RNA-seq_JR728


title: Pantr1_RNA-seq_JR729


title: Peril_RNA-seq_JR720


title: Pantr1_RNA-seq_JR730


title: Peril_RNA-seq_JR718


title: Peril_RNA-seq_JR719


title: M_PGC_4W_embryo3_sc1

description: polyA RNA


title: Halr1_RNA-seq_JR738


title: M_PGC_7W_embryo1_sc3

description: polyA RNA


title: Peril_RNA-seq_JR717


title: RAL-229-Challenged

status: Public on Jun 02 2015

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

description: Sample 14

data_processing:
Post processing was done using Illumina Casava 1.82
Reads were aligned to the DGRP line-specific transcriptomes that were obtained based on the Drosophila melanogaster reference genome release 5.45, DGRP freeze 2 variant information, and the RefSeq annotation.
Count data was converted to Count Per Million (cpm) using the Voom function in the R limma package.
RPKM values were calculated for each transcript based on annotation data from Refseq tables extracted from UCSC genome browser.
Genome_build: Dm3 R5.45
Supplementary_files_format_and_content: Text files with log2(RPKM) values

source_name: Whole gut from adult female

extract_protocol:
Guts were dissected and put in Trizol on ice. RNA was harvested using Trizol reagent.
Illumina TruSeq Stranded mRNA LT kit (cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: treatment

value: Challenged

tag: dgrp line

tag: resistance

value: Susceptible

value: adult


title: RAL-280-Challenged

description: Sample 16


title: RAL-502-Challenged

description: Sample 13


title: RAL-908-Challenged

description: Sample 15


title: RAL-486-Challenged

description: Sample 12

value: Resistant


title: RAL-857-Challenged

description: Sample 10


title: RAL-502-Unchallenged

description: Sample 5

value: Unchallenged


title: RAL-486-Unchallenged

description: Sample 4

value: female


title: RAL-908-Unchallenged

description: Sample 7


title: RAL-208-Challenged

description: Sample 11


title: RAL-280-Unchallenged

description: Sample 8


title: RAL-208-Unchallenged

description: Sample 3


title: RAL-802-Unchallenged

description: Sample 1


title: RAL-857-Unchallenged

description: Sample 2


title: Peril_RNA-seq_JR716


title: Arabidopsis Fsc infiltrated 2day [Sample_SC-23_009]

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing:
Bowtie for alignment, v1, default parameter
Cufflink for expression profiling, v2.1.0, default paremeter
Genome_build: TAIR10
Supplementary_files_format_and_content: tabulat, table head : test_id gene_id gene    locus   sample_1        sample_2        status  value_1 value_2 log2(fold_change)       test_stat       p_value q_value significant

organism: Arabidopsis thaliana

source_name: Arabidopsis Fsc infiltrated 2day

growth_protocol: Plants were grown on Murashige and Skoog plates containing 1% Suc at 22 ºC under white light (100 μmol m-2 s-1) conditions (8 h light/16 h dark). Leaves from 4-week-old plants were used for various assays

extract_protocol:
RNAeasy Kit
stander Illumina mRNA-seq protocol

treatment_protocol: Leaves from 4-week-old plants collected at different time points were infiltrated with Pst DC3000 (1×105 cfu/ml).

value: leaves


title: Arabidopsis Fsc infiltrated 2day [Sample_SC-22_006]


title: Arabidopsis Fsc infiltrated 1day [Sample_SC-11_001]

source_name: Arabidopsis Fsc infiltrated 1day


title: Arabidopsis Fsc infiltrated 2day [Sample_SC-21_002]


title: Arabidopsis Fsc infiltrated 1day [Sample_SC-13_012]


title: Arabidopsis Fsc infiltrated 3day [Sample_SC-32_007]

source_name: Arabidopsis Fsc infiltrated 3day


title: Arabidopsis Fsc infiltrated 3day [Sample_SC-33_012]


title: Arabidopsis Sei-0 infiltrated 3day [Sample_S-33_004]

source_name: Arabidopsis Sei-0 infiltrated 3day


title: Arabidopsis Fsc infiltrated 1day [Sample_SC-12_006]


title: Arabidopsis Sei-0 infiltrated 3day [Sample_S-31_007]


title: Arabidopsis Fsc infiltrated 3day [Sample_SC-31_004]


title: Arabidopsis Sei-0 infiltrated 3day [Sample_S-32_012]


title: Arabidopsis Sei-0 infiltrated 2day [Sample_S-22_009]

source_name: Arabidopsis Sei-0 infiltrated 2day


title: Arabidopsis Sei-0 infiltrated 1day [Sample_S-13_001]

source_name: Arabidopsis Sei-0 infiltrated 1day


title: Arabidopsis Sei-0 infiltrated 2day [Sample_S-21_006]


title: Arabidopsis Sei-0 infiltrated 1day [Sample_S-11_001]


title: Arabidopsis Sei-0 infiltrated 1day [Sample_S-12_004]


title: RAL-802-Challenged

description: Sample 9


title: RAL-229-Unchallenged

description: Sample 6


title: Arabidopsis Fcs infiltrated 3day [Sample_CS-33_007]

source_name: Arabidopsis Fcs infiltrated 3day


title: Arabidopsis Fcs infiltrated 3day [Sample_CS-32_004]


title: Arabidopsis Fcs infiltrated 2day [Sample_CS-22_002]

source_name: Arabidopsis Fcs infiltrated 2day


title: Arabidopsis Fcs infiltrated 3day [Sample_CS-31_012]


title: Arabidopsis Fcs infiltrated 1day [Sample_CS-13_009]

source_name: Arabidopsis Fcs infiltrated 1day


title: Arabidopsis Fcs infiltrated 1day [Sample_CS-11_002]


title: Arabidopsis Fcs infiltrated 1day [Sample_CS-12_001]


title: Arabidopsis Col-0 infiltrated 3day [Sample_C-33_012]

source_name: Arabidopsis Col-0 infiltrated 3day


title: Arabidopsis Col-0 infiltrated 3day [Sample_C-31_004]


title: Arabidopsis Col-0 infiltrated 2day [Sample_C-22_006]

source_name: Arabidopsis Col-0 infiltrated 2day


title: Arabidopsis Col-0 infiltrated 2day [Sample_C-23_009]


title: Arabidopsis Col-0 infiltrated 2day [Sample_C-21_002]


title: WT3

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis.    Filter steps:    Remove reads with adaptors;  Remove reads in which unknown bases are more than 10%;   Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. 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).
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/).
Supplementary_files_format_and_content: xls files were generated by Microsoft Excel,RPKM represent the expression of genes.

organism: Citrus sinensis

source_name: fruit

growth_protocol: The WT ‘Fengjie 72-1’ orange (C. sinensis L. Osbeck) and its spontaneous  late-ripening mutant (MT) ‘Fengwan’ were both cultivated  in the same orchard (Fengjie, Chongqing City, China).

extract_protocol:
Approximate 2 to 3 g of  powdered material was subjected to each RNA extraction, including 10 mL buffer  extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol  precipitation, 5 mL 75% ethanol cleaning and RNA purification as described  by Camacho-Villasana YM et al.
mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads. 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 sythsize 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

treatment_protocol: No treatment

value: pulp

tag: development stage

value: 210 days after flowering

tag: cultivar

value: Fengjie 72-1' navel orange


title: Arabidopsis Col-0 infiltrated 1day [Sample_C-13_007]

source_name: Arabidopsis Col-0 infiltrated 1day


title: wild-type

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
25F58F
Contains two raw files that are technical replicates (separate preparations of the same biological sample). Wig files composed of combination of two technical replicates (25F and 58F).

data_processing:
Base calling was performed at UC Riverside or Johns Hopkins sequencing facilities with CASAVA 1.8
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence (or trimmed to 35 nt for RNA-Seq samples). Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009) and the  parameters: -y -a -m 1 --best --strata. Reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all 4 of these alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

molecule: cytoplasmic RNA

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome or disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

tag: strain

value: wild-type (BY4741)

tag: cell culture treatment

value: Grown 8 hours after switch from galactose to glucose


title: rli1 depletion_1

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
26Fc
Contains two raw files that represent two sequencing runs of the same sample. Wig files 26Fc composed of combination of two lanes. Wig files 26Fc57F are composition of 2 biological replicates, which are available on the series record.

value: rli1 degron


title: Arabidopsis Sei-0 infiltrated 2day [Sample_S-23_002]


title: WT2

value: 190 days after flowering


title: Arabidopsis Col-0 infiltrated 1day [Sample_C-12_003]


title: WT1

value: 170 days after flowering


title: MT3

value: Fengwan' navel orange


title: Arabidopsis Col-0 infiltrated 1day [Sample_C-11_001]


title: MT1


title: MT2


title: Arabidopsis Fcs infiltrated 2day [Sample_CS-23_006]


title: rli1-depletion/dom34Δ_2

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
59F
Biological replicate of 41F. Wig files 41F59F are composition of 2 biological replicates (41F and 59F), which are available on the series record.


title: wild-type mRNA-Seq


title: Arabidopsis Fcs infiltrated 2day [Sample_CS-21_009]


title: rli1 depletion mRNA-Seq

value: rli1 degron mRNA-Seq


title: rli1 depletion +3-AT

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
44Fc
Contains two raw files that represent two sequencing runs of the same sample. Wig files composed of combination of two lanes.

value: rli1 degron +3-AT

value: 3-AT added. Grown 8 hours after switch from galactose to glucose.


title: wild-type +3-AT

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
43Fc
Contains two raw files that represent two sequencing runs of the same sample. Wig files composed of combination of two lanes.

value: wild-type +3-AT


title: Arabidopsis Col-0 infiltrated 3day [Sample_C-32_007]


title: rli1-depletion/dom34Δ_1

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
41F
Wig files 41F59F are composition of 2 biological replicates (41F and 59F), which are available on the series record.

value: rli1 degron/dom34delta


title: RLI1 high-copy / dom34Δ

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
42F

value: RLI1 high-copy / dom34delta


title: PT11-123-5_450

status: Public on Jun 01 2015

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reads were trimmed by finding longest subsequence with all bases>=Phred20. PolyA tail was removed and reads with minimum length of 50 bp were mapped with TopHat2 (version 2.0.5) taking into account strand specificity (forward strand).
Mapped read counts were collected within 16667 predicted gene models. Only unique mappings were accepted.
Genewise read counts were normalized using TMM method in R package edgeR. Genes were required to have min.10 reads from min.10 individuals which resulted in 8258 genes.
Genome_build: GenBank APLT01000000
Supplementary_files_format_and_content: Text files include unnormalized read counts of 16667 genes separately for two libraries with different insertsizes. Supplementary file normalizedCounts8258Genes.txt contains TMM-normalized counts where two libraries have been combined for each individual.

organism: Melitaea cinxia

source_name: Thorax

extract_protocol:
Total RNA was extracted from frozen butterfly thorax with Trizol (Life Technologies Corporation, CA, USA) followed by chloroform, phenol-chloroform-isoamylalcohol and second chloroform purification. RNA was precipitated with isopropanol and washed with ethanol. RNA quality was verified with NanoDrop measurement (Thermo Fischer Scientific Inc., MA, USA) and Bioanalyzer run (Agilent Technologies, CA, USA).
An in-house strand-specific library construction protocol based on polyA-anchoring. Two libraries with average insertsizes 450nt and 650nt were constructed for each individual.

treatment_protocol: Butterflies in treatment group F1 were flash frozen in liquid nitrogen 1 h (average: 62 min, range: 56-69 min) after the beginning of the flight treatment, while butterflies in treatment group F20 were kept overnight in individual 10 x 30 cm cages (08-10 Light/24°C, 10-15 Light/28°C, 15-17 Light/24°C, 17-08 Dark/18°C) with food, and were flash frozen in liquid nitrogen in the following morning, 17-24 hrs (average: 20.5 hrs) after the beginning of the flight treatment. The whole body of the butterfly was preserved, but RNA was extracted only from the thorax. The control group butterflies were treated similarly to the experimental butterflies, with the exception of not experiencing the flight treatment, and were flash frozen 1 hr (C1) or 17-24 hrs (C20) after being moved to the flight treatment conditions. All samples were stored in -80°C until RNA extraction.

tag: population

value: PT

value: Male


title: PT11-119-2_450


title: PT11-119-2_650


title: PT11-136-3_450


title: PT11-88-5_650

value: Female


title: PT11-94-4_650


title: PT11-90-1_650


title: PT11-88-5_450


title: PT11-94-4_450


title: PT11-76-5_650


title: PT11-123-5_650


title: PT11-90-1_450


title: rli1 depletion_2

description:
Ribosome profiling
Ribosome-protected RNA 25-34 nt
57F
Biological replicate of 26F/26F1. Wig files 26Fc57F are composition of 2 biological replicates (26Fc and 57F), which are available on the series record.


title: PT11-68-1_450


title: PT11-54-5_450


title: PT11-68-1_650


title: PT11-49-5_650


title: PT11-51-4_650


title: PT11-49-5_450


title: PT11-41-4_450


title: PT11-51-4_450


title: PT11-41-4_650


title: PT11-54-5_650


title: PT11-25-4_450


title: PT11-76-5_450


title: PT11-18-2_650


title: PT11-16-4_650


title: PT11-18-2_450


title: PT11-16-4_450


title: PT11-132-2_450


title: PT11-151-1_450


title: PT11-146-5_650


title: PT11-151-1_650


title: PT11-146-5_450


title: PT11-127-2_450


title: PT11-125-4_450


title: PT11-25-4_650


title: PT11-148-3_650


title: PT11-148-3_450


title: PT11-120-3_450


title: PT11-117-4_650


title: PT11-125-4_650


title: PT11-127-2_650


title: PT11-111-3_450


title: PT11-115-1_450


title: PT11-109-4_450


title: PT11-107-3_650


title: PT11-111-3_650


title: PT11-120-3_650


title: PT11-107-3_450


title: PT11-103-5_650


title: PT11-115-1_650


title: PT11-117-4_450


title: PT11-106-1_450


title: PT11-106-1_650


title: PT11-109-4_650


title: PT11-103-5_450


title: PT11-132-2_650


title: PT11-102-5_650


title: AF11-7345_650

value: AL


title: PT11-101-4_450


title: PT11-101-4_650


title: AF11-6874_650


title: AF11-6874_450


title: AF11-5308_450


title: AF11-5308_650


title: AF11-3227_650


title: AF11-7345_450


title: AF11-5171_650


title: AF11-5171_450


title: AF11-1888_450


title: AF11-17767_450


title: AF11-17767_650


title: AF11-3227_450


title: AF11-16146_450


title: AF11-16018_650


title: AF11-16113_650


title: AF11-16113_450


title: AF11-16018_450


title: AF11-1342_650


title: AF11-13957_650


title: AF11-13957_450


title: AF11-12984_450


title: AF11-12984_650


title: AF11-1342_450


title: PT11-102-5_450


title: AF11-1888_650


title: AF11-12747_650


title: AF11-12747_450


title: AF11-16146_650


title: AF11-11245_450


title: AF11-948_650


title: AF11-9102_450


title: AF11-8940_650


title: AF11-9052_450


title: AF11-9052_650


title: AF11-8757_650


title: AF11-8387_450


title: Mutant CshA-full-deletion, RNA decay assay at 600s, replicate 1

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

data_processing:
mRNA-seq sequences were trimmed to an uniform length of 50bp
reads were aligned with the software BWA v0.7.7-r441 to N315 genome. Command line: bwa mem -t8 -M N315.fasta reads.fastq
reads aligning to mutiple positions on the genome are filtered out (i.e. reads with a BWA mapping quality of 0). Command line: samtools -q1 …
count the number of read overlapping each gene using the function summarizeOverlaps(ignore.strand=FALSE,inter.feature=FALSE), from the Bioconductor package GenomicAlignments
normalize the counts according to the number of read aligning on HU gene
RNA decay halflife is estimated for each gene by fitting a weighted linear model on log2 transformed counts (normalized ones) with an R script calling the function lm(normalizedCounts~timepoint,weights=c(256,64,16,1))
Data are manually processed by a biological expert with excel to annotate the genes with the operons and select stabilized and destabilized candidates genes
Genome_build: NC_002745.2
Supplementary_files_format_and_content: N315_CshA_raw.txt.gz: tab-delimited text file giving the number of read mapping onto each gene for all the samples
Supplementary_files_format_and_content: N315_CshA_normalized.txt.gz: tab delimited text file giving the HU-normalized number of read mapping onto each gene for all the samples
Supplementary_files_format_and_content: N315_CshA_RNA-decay.txt.gz: tab-delimited text file with the manually curated and annotated list of genes that are stabilized and destabilized in CshA/CTA strain as compared to WT strain

organism: Staphylococcus aureus

source_name: Liquid culture

growth_protocol: Mueller-Hinton medium, 37°C

extract_protocol: Silica-column based RNA isolation, DNase treatment, followed by ribo depletion

treatment_protocol: rifampicin at t=0

tag: genotype/variation

value: PR01 + full deletion of CshA

tag: decay delay

value: rifampicin at t=0


title: Mutant CshA-full-deletion, RNA decay assay at 600s, replicate 2


title: Mutant CshA-full-deletion, RNA decay assay at 150s, replicate 2


title: AF11-7361_650

tag: Sex


title: AF11-827_650


title: AF11-9102_650


title: AF11-8387_650


title: Mutant CshA-full-deletion, RNA decay assay at 150s, replicate 1


title: AF11-8757_450


title: AF11-11245_650


title: Mutant CshA-full-deletion, RNA decay assay at 300s, replicate 1


title: AF11-827_450


title: AF11-7658_650


title: Mutant CshA-full-deletion, RNA decay assay at 300s, replicate 2


title: AF11-8940_450


title: AF11-7361_450


title: AF11-948_450


title: Mutant CshA-full-deletion, RNA decay assay at 0s (steady state), replicate 1


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 600s, replicate 2

value: PR01 + C-terminal deletion of CshA


title: AF11-7658_450


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 300s, replicate 2


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 300s, replicate 1


title: WT, RNA decay assay at 600s, replicate 2


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 0s (steady state), replicate 2


title: AF11-658_450


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 150s, replicate 2


title: AF11-4728_650


title: WT, RNA decay assay at 300s, replicate 2


title: AF11-3372_650


title: AF11-3228_450


title: AF11-3009_450


title: Mutant CshA-full-deletion, RNA decay assay at 0s (steady state), replicate 2


title: AF11-6979_650


title: AF11-6979_450


title: AF11-658_650


title: WT, RNA decay assay at 600s, replicate 1


title: AF11-3372_450


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 600s, replicate 1


title: WT, RNA decay assay at 300s, replicate 1


title: AF11-5917_450


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 0s (steady state), replicate 1


title: AF11-3009_650


title: AF11-19683_650


title: WT, RNA decay assay at 0s (steady state), replicate 2


title: Mutant CshA-C-terminal-deletion, RNA decay assay at 150s, replicate 1


title: AF11-4728_450


title: WT, RNA decay assay at 150s, replicate 1


title: WT, RNA decay assay at 150s, replicate 2


title: AF11-3228_650


title: AF11-5917_650


title: AF11-19682_450


title: INPUT

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 9.1) with a complete match within 60 bp using in-house scripts.
The mapping data were analyzed with the MACS2 peak-calling algorithm using .5 × 107 reads. Conditions for peak calling included an FDR < 0.01 and fold enrichments > 5 in both the analyses.
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: Text file with peak positions called by MACS2

organism: Plasmodium berghei

source_name: Plasmodium berghei_AP2-O-GFP_input

growth_protocol: Balb/c mice were pre-treated with phenylhydrazine and then infected with P. berghei expressing GFP-fused AP2-O.

extract_protocol:
Erythrocytes in the fixed culture were removed by lysis in 0.84% NH4Cl, and the remaining ookinetes were subjected to ChIP. ChIP was performed using the ChIP Assay Kit (Millipore, USA) according to the manufacturer’s protocol. Briefly, samples in the lysis buffer were sonicated with a Bioruptor (Tosho Denki, Yokohama, Japan) until chromatin DNA was fragmented to 150 bp for sequencing with a SOLID 5500 system (Life Technologies). Immunoprecipitation (IP) was performed with anti-GFP antibodies, and the harvested DNA fragments were subjected to sequencing. Input DNAs were obtained from the chromatin without IP. Anti-GFP antibodies used for ChIP were purchased from Abcam (Cambridge, MA).
Single read - SOLiD 5500 (ABI)

treatment_protocol: Sulfadiazine was added to their drinking water (10 mg/L) in order to deplete asexual blood-stage parasites. When the exflagellation of the male gametes reached approximately 300 per 1 μL of blood, the blood was harvested and cultured in an ookinete culture medium for 16 h, and then fixed with 1% paraformaldehyde.

tag: host

value: mus musculus strain Balb/c

tag: Stage

value: ookinete

value: ANKA

tag: genotype

value: GFP-fused AP2-O expressing

value: none (input)


title: IP

source_name: Plasmodium berghei_AP2-O-GFP_IP

value: anti-GFP

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: AF11-19683_450

tag: treatment


title: WT, RNA decay assay at 0s (steady state), replicate 1


title: AF11-1890_650


title: AF11-1890_450


title: AF11-19682_650


title: AF11-16875_650


title: AF11-1884_450


title: AF11-16376_650


title: AF11-16875_450


title: AF11-16376_450


title: AF11-13001_650


title: PT11-97-4_650


title: AF11-13001_450


title: AF11-1884_650


title: AF11-10770_450


title: ookinete transcriptome

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 9.1) with a complete match within 60 bp using in-house scripts.
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: Text file containing Tag number and RPKM value

source_name: ookinetes cultured for 24 h

growth_protocol: Ookinetes were obtained from asexual parasite-depleted infected mouse blood that had been cultured for 24 h in an ookinete culture medium.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols.mRNA was purified using Oligotex-dT30mRNA Purification Kit TAKARA, Bio, japan) according to the manufacturer’s protocols.
Libraries were prepared according to a version of ABI's mRNA-Seq protocol [single read - SOLiD 5500 (ABI)].

value: wild type


title: PT11-83-3_650


title: PT11-97-4_450


title: PT11-76-3_450


title: AF11-104_450


title: AF11-104_650


title: PT11-73-5_650


title: PT11-56-3_450


title: PT11-56-3_650


title: PT11-67-3_450


title: PT11-74-4_650


title: PT11-74-4_450


title: PT11-83-3_450


title: PT11-76-3_650


title: AF11-10770_650


title: PT11-60-3_650


title: PT11-60-3_450


title: PT11-5-3_450


title: PT11-73-5_450


title: PT11-67-3_650


title: PT11-5-3_650


title: PT11-26-3_650


title: PT11-28-5_450


title: PT11-28-5_650


title: PT11-26-3_450


title: PT11-159-2_450


title: PT11-15-3_650


title: PT11-15-3_450


title: PT11-147-3_450


title: PT11-147-3_650


title: DMEmb_AGTTC_L001_R1_001

city: Chapel Hill

first: William

middle: F

last: Marzluff

state: NC

address: 207 Fordham Hall

institute: The University of North Carolina at Chapel Hill

description: Fly Embryo

data_processing:
Basecalls performed using CASAVA v. 1.8.2
Reads were aligned to hg19 or dm3 (including custom chromosome containing histone genes) using Bowtie2
The AppEnD algorithm was used to identify 3' tails
Genome_build: hg19, dm3
Supplementary_files_format_and_content: tab-delimited text files containing 3' tails generated using AppEnD

source_name: Fly Embryo

growth_protocol: HeLa cells were plated at 2X10^5 cells per 10 cm dish and synchronized by double thymidine block.  Cells were treated with HU for 15 minutes 3 hrs after release into S-phase and RNA prepared.

extract_protocol:
Total RNA was extracted with Trizol.
Libraries were prepared with Illumina sequences using two limited rounds of PCR after ligation of a custom linker to the 3' end of the RNA; cDNA was synthesized either with a primer to the custom linker (Sample2), or the same primer with 3 A's added to the 3' end (Sample1). Sample3 was prepared using only the H2A primer; Samples 4 and 5 were prepared using primers for H2A, H2B, H3, and H4.

treatment_protocol: Cells were treated with hydroxyurea at 5 mM  for 15 min[C].

tag: 3' linker

value: NEB+Ext

tag: tissue

value: embryo


title: DM_CTTGT_L001_R1_001

description: Fly Ovary

source_name: Fly Ovary

value: ovary


title: Run1_Combined_data_5_files

description: Hydroxyurea-treated sample, dA priming

source_name: HeLa cells

value: SOLID Reverse

tag: cell line

value: HeLa


title: sample_666 (validation)

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

description: validation sample

data_processing:
Genomic DNA from the above 20 samples were extracted and were subjected to RRBS library preparation.
Libraries were then subjected to paired-end 50bp multiplex sequencing on the Hiseq 2000 platform.
Raw sequencing data were processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 30% ‘N’s or more than 10% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the UCSC human reference genome (hg18, NCBI build 36) using the Short Oligonucleotide Alignment Program 2(SOAP2), to identify methylcytosine (mC).
The uniquely mapped reads that contained at least one enzyme digestion site in the ends were used for further analysis.
Genome_build: hg18
Supplementary_files_format_and_content: count files report cytosine methylation detected data
count.txt file format (test samples):
(1)Chromosome ID
(2)Cytosine position
(3)+/- Watson/Crick chain
(4)Type (CG/CHH/CHG)
(5)Base pattern
(6)Copynum: the same value as repeat rate
(7)Methy reads num
(8)Nonmethy reads num
(9)Binomial distribution expected values
count.txt file format (validation samples):
(1)Test region ID
(2)CpG coordinate
(3)chain +/-
(4)Cytosine type
(5)Basic pattern
(6)CpG methylation level (the value is calculated by the number methylated reads and non-methylated reads)
(7)Methylated reads number
(8)Non-methylated reads number

source_name: conceptus

growth_protocol: Samples were chosen on the basis of the karyotype (46, XX), parental origin (P1P1) of the mole genome and the gestational age at evacuation between 9 and 12 weeks

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen). 1µg of genomic DNA was fragmented into approximately 200-300bp using a Covarias sonication system (Covarias). After purification, the fragmented fractions were treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair blunt and phosphorylate ends.
Reduced representation bisulfite sequencing (RRBS) libraries with single MspI digestion  were constructed for all samples. 1.5 µg of genomic DNA was digested with 500U of MspI  enzymes (NEB) in 100µl reactions at 37°C for 16h. After that MspI was inactivated at 65°C for  20 min. After digestion the Ilumina Paired-End protocol was used to construct the libraries  including end-repair, dA addition and methylated-adaptor ligation. MspI-digested DNA was  purified and size-selected on a 2% agarose gel. To obtain DNA fragments of 40-120 bp and  120-220 bp of length, adaptor-ligated fragments of 160-240 bp and 240-340 bp were excised,  respectively. Subsequently bisulfite conversion was conducted by ZYMO EZ DNA  Methylation-Gold KitTM (ZYMO) following the manufacturer’s instructions. The final libraries  were generated by PCR in a final reaction volume of 50 µl, comprising 20 µl purified DNA, 4  µl 2.5 mM dNTP, 1 µl PCR primer PE 1.0, 1 µl Index primer, 5 µl 10×buffer, 0.5 µl JumpStartTM  TaqDNA polymerase and 28.5 µl UltraPureTM Water. The PCR program was as follows: 94 ◦C  for 60 s, 13/15 cycles (13 cycles for 160–240 bp, 15 cycles for 240–340 bp) of 94 ◦C for 30 s,  58 ◦C for 30 s and 72 ◦C for 30 s. finally 72 ◦C for 5 min and products were then hold at 12 ◦C.  Between each step in the above mentioned process the DNA was purified using MinElute og  QIAquick columns according to protocols from Qiagen. Libraries were then subjected to  paired-end multiplex sequencing on Hiseq 2000 platform after quality control.

tag: karyotype

tag: gestational age

tag: disease state

value: PTD


title: sample_550 (validation)

description: validation sample


title: sample_325 (validation)

description: validation sample


title: sample_437 (validation)

description: validation sample


title: sample_491 (validation)

description: validation sample


title: sample_607 (validation)

description: validation sample

value: non-PTD


title: sample_594 (validation)

description: validation sample


title: sample_631 (validation)

description: validation sample


title: 3189

city: Hefei

first: Lei

last: Sheng

state: Anhui

address: Changjiang Road

department: School of Life Sciences

institute: Anhui Agricultural University

data_processing:
The filtered small RNA sequences were compared with known miRNAs in miRBase 20.0 [http://www.mirbase.org [41], allowing for a 0-2 nucleotide mismatch, and compared with ZmB73_4a.53 (ZmB73_AGPv1) [42] using BLASTn with no mismatches permitted. To identify potential novel miRNAs, ESTs that contained small RNA sequences were selected, and their secondary structures were predicted using MFOLD (http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form). Based on the criteria for miRNA definition previously described [43], small RNAs with corresponding star (miRNA*) sequences were deemed to be novel miRNAs, while those without star sequences were regarded as potential miRNAs.
Genome_build: ZmB73_AGPv1

organism: Zea mays

source_name: maize leaves

growth_protocol: Drought-tolerant (Hz4) and drought-sensitive (3189) maize inbred lines were germinated in a greenhouse and grown under standard conditions until seedlings had developed three leaves.

extract_protocol:
To construct small RNA libraries, total RNA was extracted from leaves using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol as modified by LC Sciences (Houston, USA).
The small RNA fraction (10-40 nt) was isolated by polyacrylamide gel electrophoresis and ligated with proprietary adaptors (Illumina). Short RNAs were then reverse-transcribed into cDNA by RT-PCR. Small RNA libraries were constructed for each maize line and sequenced using a Hiseq 2000 (Illumina) following the manufacturer’s instructions. Small RNA sequencing data was processed with the in-house program ACGT101-miR (LC Sciences, USA). Program parameters were set as previously described [40] with modifications to adapt the program for plant miRNA prediction.

treatment_protocol: Seedlings were then subjected to drought conditions. Specifically, the soil water content was reduced from 90% to 70%, and approximately 5 g of leaves was collected from each seedling and immediately frozen in liquid nitrogen.

value: leaves

tag: line

value: drought-sensitive (3189)


title: Run2_Combined_data_5_files

description: Hydroxyurea-treated sample, no dA priming


title: sample_595 (validation)

description: validation sample


title: HZS

value: drought-tolerant (Hz4)


title: sample_571 (validation)

description: validation sample


title: sample_558 (validation)

description: validation sample


title: sample_180 (validation)

description: validation sample


title: sample_136 (validation)

description: validation sample


title: PT11-159-2_650

tag: population

value: PT

value: Male


title: PT11-136-3_650


title: DMOvary_AGTCA_L001_R1_001

description: Fly Ovary


title: sample_545 (validation)

description: validation sample


title: sample_517 (validation)

description: validation sample


title: sample_644 (validation)

description: validation sample


title: sample_458 (validation)

description: validation sample


title: sample_246 (validation)

description: validation sample


title: sample_534 (validation)

description: validation sample


title: INPUT_SC_seq_MEF

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: mapped reads (mm10) were binned across 200bp windows.

data_processing:
Reads mapped to mm10 mouse build in the cloud using TMAP software
Data binned into 200bp windows across the genome
Data converted into mm9 build and into a wiggle (.wig) file
data normalised by read count
enriched (5hmC) datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: mm10
Supplementary_files_format_and_content: .wig file

source_name: MEF

growth_protocol: Liver samples extracted from C57BL/6 mice aged ~120 days. MEFs cultured in standard media. iPSC were dervied followign establisehd protocols outlined by Yusa et al 2013 [PMID: 24071911]

extract_protocol:
Sheared gDNA was enriched using Active motif rabbit polyclonal against hydroxymethylation (cat#39769). prior to enrichment through magnetic IgG beads (Dynabeads protein G (Invitrogen #100-03D). Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 10 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5hmc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an hmc-DIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

value: Mouse embryonic fibroblast

tag: strain/cell type

value: P53 null MEFs

tag: antibody


title: sample_143 (validation)

description: validation sample


title: INPUT_SC_seq_iPSC

source_name: iPSC

value: mouse induced pluripotent stem cells

value: P53 null MEFs reprogrammed to iPSCs


title: 5hmC_SC_seq_iPSC

value: Active motif rabbit polyclonal against 5hmC:cat#39769


title: 5hmC_SC_seq_MEF


title: sample_112 (validation)

description: validation sample


title: INPUT_SC_seq_mus_liver_B

source_name: Liver B

value: Liver


title: IP

data_processing:
Mapping was performed with Bowtie. Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 9.1) allowing one mismatch within 35 bp.
The mapping data were analyzed with the MACS2 peak-calling algorithm using .5 × 107 reads. Conditions for peak calling included an FDR < 0.01 and fold enrichments > 5 .
Genome_build: PlasmoDB, version 9.1
Supplementary_files_format_and_content: text file with peak positions called by MACS2

source_name: whole cell

extract_protocol:
Erythrocytes in the fixed culture were removed by lysis in 0.84% NH4Cl, and the remaining ookinetes were subjected to ChIP. ChIP was performed using the ChIP Assay Kit (Millipore, USA) according to the manufacturer’s protocol. Briefly, samples in the lysis buffer were sonicated with a Bioruptor (Tosho Denki, Yokohama, Japan) until chromatin DNA was fragmented to 300 bp. Immunoprecipitation (IP) was performed with anti-GFP antibodies, and the harvested DNA fragments were subjected to sequencing. Input DNAs were obtained from the chromatin without IP.
Single read - Illumina

tag: host

value: mus musculus strain Balb/c

value: ookinete

tag: strain

value: ANKA

value: GFP-fused AP2-O expressing

value: anti-GFP

value: Clontech


title: sample_240 (validation)

description: validation sample

value: non-PTD


title: 5hmC_SC_seq_mus_liver_A

source_name: Liver A


title: XIP_15_I

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
fastQ-mcf was used to clip adapter sequences and bases with a quality score below 20 from the raw reads
Rockhopper version 2.0.2 (http://cs.wellesley.edu/~btjaden/Rockhopper/index.html) was used to map the clipped reads to the genome of S. Mutans UA159 using the default parameters.
Genome_build: NC_004350.2
Supplementary_files_format_and_content: tab-delimited textfile including mapped reads per ORF

organism: Streptococcus mutans UA159

source_name: bacterial culture

extract_protocol:
Pelleted bacteria were washed with 500 µl nuclease free water and centrifuged for 2 min at 13.000 rpm. The supernatant was removed and the pellet resuspended in LM-lysis buffer containing 2.5 mg lysozyme and 100 U mutanolysin (pH=7.4). The resuspension was shaken in a heating block at 25°C and 1400 rpm for 45 min. 700 µl of Qiazol Lysis solution (Qiagen, Germany) was added and the mixture transferred to a falcon tube containing sterile 0.1 µm glass beads (Carl Roth, Germany). The falcon tubes were vortexed for 3 min and centrifuged at 6000 rpm at RT to pellet the glass beads. The supernatant was transferred to a new tube and 200 µl of chloroform was added. Samples were vortexed for 15 sec, incubated for 2 min at RT and centrifuged for 20 min at 13.000 rpm and 4°C. The upper aqueous phase (approximately 550 µl) was transferred to a new tube and 870 µl of ethanol was added and mixed thoroughly. RNA extraction was carried out using the MiRNeasy Kit (Qiagen, Germany) according to the manufacturer’s instructions. To remove genomic DNA the optional on-column DNAseI digestion using the DNAse I Kit (Qiagen, Germany) was performed for 45 min. After the washing steps the RNA was eluted in 50 µl of nuclease free water supplied with the kit. To test the integrity of the isolated total RNA and the enriched mRNA, samples were analyzed using the Agilent 2100 Bioanalyzer and the RNA 6000 Pico Kit (Agilent, Germany).
The Illumina ScriptSeq™ v2 RNA-Seq Library Preparation Kit was used according to the manufacturers protocol

treatment_protocol: Overnight cultures of the S. mutans UA 159 wildtype grown in THBY were diluted to an OD of 0.1 in CDM and cultivated at 37°C and 5% CO2 until the culture had reached an OD of 0.175. Subsequently the culture was divided into three equal parts, one part was treated with 2 µM synthetic XIP, one with 2 µM synthetic CSP and the third part was used as an uninduced control. Samples were taken at 5, 15, 30, 60 and 120 min post addition of the synthetic peptides. The samples were immediately transferred into an equal volume of RNA Protect and incubated for 5 min at RT. Subsequently the bacteria were pelleted (13000 rpm, 2 min, RT), the supernatant was removed and the pellet was frozen at -70°C.

value: XIP

tag: time after treatment (min)

tag: replicate


title: 5hmC_SC_seq_mus_liver_B


title: XIP_15_II


title: K5_I


title: INPUT_SC_seq_mus_liver_A


title: K5_II


title: K30_II


title: K15_II


title: K30_I


title: K15_I


title: K0_II


title: K0_I


title: CSP_5_II

value: CSP


title: CSP_30_II


title: XIP_5_I


title: XIP_30_II


title: MYB3R3-GFP_9d_seedlings_ChIP

city: Nagoya

first: Norihito

last: Nakamichi

state: Aichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

institute: Nagoya University

data_processing:
Basecalls was performed by Illumina Genome Analyzer Pipeline.
Sequence reads were mapped against to a Arabidopsis reference genome (TAIR10) by Bowtie 0.12.7 (Langmead et al., Genome Biol., 2009), generating Sequence Alignment/Map (SAM) files.
SAM files were converted into Binary Alignment/Map (BAM) format files by Samtools 0.1.18 (Li et al., Bioinformatics 2009).
Peak-calling of ChIP.bam compared with input.bam files was performed by MACS2 (Zhang et al., Genome Biol., 2008), generating a bed file (MYB3R3-GFP_ChIP_peaks.bed).
Genome_build: TAIR10
Supplementary_files_format_and_content: bed

source_name: MYB3R3-GFP Col-0, 9d whole seedlings

growth_protocol: Seedlings were grown in liquid half strength of MS  medium with 2% sucrose in continuous light at 22 Celcius degree.

extract_protocol:
Nuclei isolated from fixed plnats, were sonicated and immunoprecipitated with anti-GFP antibody (ab290, Abcam), according to the method (Nakamichi et al., PNAS,109:17123-17128, 2012).
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq Sample Prep Kit (Part# IP-102-1001)

tag: chip antibody

value: GFP

tag: ecotype

value: Whole seedlings

tag: age

value: 9 days after germination


title: CSP_30_I

tag: treatment


title: CSP_15_II


title: Hopx E9.5 Hearts -EGS, Input

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using option of --best -v 2 --strata -m 1
Peaks were called using Homer with a FDR cutoff=0.01 and p-value=0.001. The peaks from two samples were merged when they overlap within 200bps
Genome_build: mm9
Supplementary_files_format_and_content: a merged bed file was generated after peak calling

source_name: E9.5 hearts

growth_protocol: E9.5 embryonic hearts were harvested

extract_protocol:
10 μg of DNA was used to incubate with anti-Flag antibody (Sigma M2) or with same amount of mouse IgG as the negative control. BSA coated protein A agarous beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65°C ~16hours, and DNA was purified by Qiagen PCR purification kit.
After wash steps, cells were resuspended in lysis buffer and proceeded to the sonication with Diagenode Bioruptor (High power, 30 second cycles, 7.5 min total length X 3). Cell debris was removed by 10 min centrifuge, 15,000 rpm at 4°C. Extracted chromatin supernatant was used for the following chromatin immunoprecipitation or frozen in -80°C for storage.
To generate the library from ChIP experiements, ChIP-Seq Library Protocol with multiplexing was used. This protocol was developed before Illumina released its multiplex truSeq ChIP-seq kit, and the details can be found on http://ngsc.med.upenn.edu/. 10 ng of ChIP DNA product was used to start the library construction.

treatment_protocol: Hearts from Hopx3Xflag/+ mouse embryos (E9.5) were harvested, pooled and fixed in 1% formaldehye, 10 min. Glycine was added to final 140mM to quench the fixation. Cells were pelleted and washed with PBS and wash buffers. After wash steps, cells were resuspended in lysis buffer and proceeded to the sonication with Diagenode Bioruptor (High power, 30 second cycles, 7.5 min total length X 3). Cell debris was removed by 10 min centrifuge, 15,000 rpm at 4°C. Extracted chromatin supernatant was used for the following chromatin immunoprecipitation or frozen in -80°C for storage. A portion of the chromatin supernatant was reverse crosslinked and total DNA was purified by PCR purification kit. According to the measurement from this pilot DNA quantification, 10 μg of DNA was used to incubate with anti-Flag antibody (Sigma M2) or with same amount of mouse IgG as the negative control. BSA coated protein A agarous beads were used to obtain the ChIP product. Chromatin was reverse crosslinked at 65°C ~16hours, and DNA was purified by Qiagen PCR purification kit.

tag: tissue

value: embryonic heart

value: Input


title: Hopx E9.5 Hearts -EGS, Flag, Sigma M2

value: Flag, Sigma M2


title: Input DNA (p53)

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
Base-calling and quality-control was performed using the Illumina pipeline Casava
ChIP-Seq reads were aligned to the human hg19 using Bowtie 1.0.1
Peak calling was done by MACS 2 The setting for peak calling was tsize=36, bw=200, mfold=10,30, p-value at least 1e-5.
Genome_build: hg19

source_name: HCT 116

extract_protocol: 10 ng of the immunoprecipitated chromatin was used to prepare the libraries for sequencing following the manufacturer’s instructions including DNA end repairing, adaptor ligation, and amplification

tag: cell type

value: colorectal carcinoma cells

tag: cell line

value: HCT 116


title: iChe_P53

value: Anti-p53 AB7 (Calbiochem)


title: CSP_5_I


title: IR P53


title: STHSC_KO2

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

institute: STANFORD UNIVERSITY

description: STHSC_KO2 SMART-seq2

data_processing:
base calling: Casava1.8
read alignment, RNA-seq data: TopHat 2.0.8
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

extract_protocol:
LT-HSCs (LSK CD150+ CD48-), ST-HSCs (LSK CD150- CD48-) and MPPs (LSK CD150- CD48+) from WT and miR-212/132-/- were sorted as follows. Cells were then spun down, resuspended in MACS separating buffer (Phosphate buffered saline, pH7.2, with 0.5% BSA and 2mM EDTA) and filtered through a 70uM cell-strainer. These cells were then blocked with FcBlock (Becton Dickinson) and depleted of mature cells on a magnetic column using biotin-conjugated mouse antibodies for CD3e, CD8, CD4, CD19, B220, CD11b, Gr-1, IL-7Ra, and Ter119 (BioLegend) and streptavidin magnetic beads (Miltenyi), as suggested by the manufacturer (Miltenyi). Cells were subsequently  stained with fluorophore-conjugated antibodies for lineage markers (CD3, CD19, CD11b, Gr-1, Ter119, Nk1.1), cKit, Sca1, CD150, CD48 and with 7-AAD, and several  populations were sorted for analysis including HSCs (Lineage- cKit+ Sca1+ CD150+ CD48-), LSK cells (Lineage- cKit+ Sca1+), and other progenitor subsets. Cells  were sorted on a FACSAria IIu cell sorter (Becton Dickinson) at Caltech. the Caltech Flow Cytometry Core Facility. Mature cell populations were sorted using a  magnetic column using positive-selection for the respective surface marker.
Cells were sorted directly into cell lysis buffer and processed using an RNAeasy kit (Qiagen) with DNAseI digestion (Qiagen) as per manufacturer’s protocol.  Libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2013) modified to use Maxima H Minus enzyme for reverse transcription (Thermo Scientific). Amplified cDNA products were purified using AMPure XP SPRI beads (Beckman Coulter) and eluted in TE buffer (Teknova). Cleaned-up amplified cDNA was used for library construction using the Nextera XT DNA Sample Preparation Kit and Nextera XT Index Kit (Illumina). Libraries were then pooled and cleaned-up using AMPure XP SPRI beads (Beckman Coulter Genomics). Final library quality and quantity were assessed using a DNA High Sensitivity chip (Agilent)

value: ST-HSCs

tag: cell markers

value: LSK CD150- CD48-

tag: genotype


title: LTHSC_KO2

description: LTHSC_KO2 SMART-seq2

value: LT-HSCs

value: LSK CD150+ CD48-


title: CSP_15_I


title: XIP_5_II


title: MPP_WT1

description: MPP_WT1 SMART-seq2

value: MPP

value: LSK CD150- CD48+

value: wildtype


title: MPP_KO2

description: MPP_KO2 SMART-seq2


title: MPP_WT2

description: MPP_WT2 SMART-seq2


title: STHSC_WT2

description: STHSC_WT2 SMART-seq2


title: Hopx E9.5 Hearts +EGS, Flag, Sigma M2


title: MPP_KO1

description: MPP_KO1 SMART-seq2


title: LTHSC_KO1

description: LTHSC_KO1 SMART-seq2


title: MYB3R3-GFP_9d_seedlings_input

value: input


title: STHSC_WT1

description: STHSC_WT1 SMART-seq2


title: LTHSC_WT1

description: LTHSC_WT1 SMART-seq2


title: STHSC_KO1

description: STHSC_KO1 SMART-seq2


title: Hopx E9.5 Hearts +EGS, Input


title: MDP_57

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

data_processing:
Reads were mapped against the MM9 reference genome using STAR with intronMotif option. The reference genome was generated with UCSC known gene annotation and the –sjdbOverhang 50 option.
The number of reads mapped to each UCSC known gene was quantified using htseq-count and normalized by calculating reads per kilobase of exon model per million mapped reads (RPKM) values
Genome_build: MM9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: mouse bone marrow

growth_protocol: primary mpuse bone marrow cells

extract_protocol:
magnetic bead enrichment, FACS sorting, IFC capture, on-chip lysis & rt-pcr
Nextera_XT Kit (Illumina, PN FC-131-1096) with dual indices (Illumina, PN FC-131-1002) was used to prepare single-cell multiplexed libraries

treatment_protocol: no treatment

tag: mouse strain

tag: gender

value: male

tag: cell population

tag: mouse status

value: steady state


title: MDP_59


title: MDP_58


title: MDP_56


title: MDP_55


title: MDP_54


title: MDP_53


title: MDP_51


title: MDP_49


title: LTHSC_WT2

description: LTHSC_WT2 SMART-seq2


title: MDP_52


title: MDP_48


title: MDP_47


title: MDP_46


title: MDP_45


title: MDP_44


title: MDP_38


title: MDP_36


title: MDP_41


title: MDP_42


title: MDP_37


title: MDP_33


title: MDP_32


title: MDP_34


title: MDP_50


title: MDP_30


title: MDP_29


title: LN-REP1_ChIPSeq

city: San Antonio

first: Zhenqing

last: Ye

state: Texas

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: The University of Texas Health Science Center at San Antonio

description: Sample 1

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using the Bowtie aligner with default parameters.
Peaks were called using MACS with a threshold p-value < 1E-8 on the combined alignment of the two replicate samples.
Genome_build: hg19
Supplementary_files_format_and_content: bed file of peak calling by MACS

growth_protocol: LNCaP cells were routinely cutured in RPMI medium supplemented with 10% FBS.

extract_protocol: Lysates were clarified from sonicated nuclei and GATA2-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 11257074). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~225 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 3 days before ChIP assay, the full medium was changed to RPMI medium supplied with 5% charcal treated FBS.

value: LNCaP

value: prostate cancer cells

tag: passages

tag: chip antibody vendor

value: Santa cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: MDP_39


title: MDP_35


title: INPUT

tag: host

value: mus musculus strain Balb/c

tag: Stage

value: ookinete

tag: strain

value: ANKA

value: GFP-fused AP2-O expressing

tag: antibody

value: none (input)


title: MDP_26


title: MDP_40


title: MDP_43


title: LN-REP2_ChIPSeq

description: Sample 2

tag: chip antibody


title: MDP_24


title: MDP_25


title: MDP_27


title: MDP_23


title: MDP_22


title: MDP_19


title: MDP_20


title: MDP_14


title: MDP_21


title: MDP_16


title: MDP_17


title: MDP_13


title: MDP_15


title: MDP_28


title: MDP_18


title: MDP_12


title: MDP_10


title: MDP_31


title: MDP_11


title: MDP_8


title: MDP_9


title: MDP_7


title: XIP_30_I

tag: treatment

value: XIP

tag: time after treatment (min)

tag: replicate


title: MDP_4


title: MDP_5


title: MDP_3


title: MDP_1


title: MDP_2


title: PreDC_96


title: MDP_6


title: PreDC_93


title: PreDC_94


title: PreDC_91


title: PreDC_95


title: PreDC_92


title: PreDC_90


title: PreDC_89


title: PreDC_88


title: PreDC_87


title: PreDC_84


title: PreDC_74


title: PreDC_75


title: PreDC_85


title: PreDC_86


title: PreDC_83


title: PreDC_77


title: PreDC_58


title: PreDC_82


title: PreDC_60


title: PreDC_76


title: PreDC_69


title: PreDC_70


title: PreDC_62


title: PreDC_78


title: PreDC_68


title: PreDC_80


title: PreDC_66


title: PreDC_79


title: PreDC_67


title: PreDC_71


title: PreDC_59


title: PreDC_81


title: PreDC_64


title: PreDC_63


title: PreDC_73


title: PreDC_65


title: PreDC_72


title: PreDC_61


title: PreDC_57


title: PreDC_56


title: PreDC_53


title: PreDC_55


title: PreDC_51


title: PreDC_54


title: PreDC_52


title: PreDC_50


title: PreDC_41


title: PreDC_48


title: PreDC_46


title: PreDC_47


title: PreDC_49


title: PreDC_43


title: PreDC_45


title: PreDC_38


title: PreDC_33


title: PreDC_40


title: PreDC_44


title: PreDC_29


title: PreDC_34


title: PreDC_37


title: PreDC_42


title: PreDC_30


title: PreDC_35


title: PreDC_28


title: PreDC_36


title: PreDC_27


title: PreDC_39


title: PreDC_25


title: PreDC_22


title: PreDC_24


title: PreDC_26


title: PreDC_23


title: PreDC_31


title: PreDC_32


title: PreDC_20


title: PreDC_19


title: PreDC_17


title: PreDC_18


title: PreDC_15


title: PreDC_14


title: PreDC_13


title: PreDC_11


title: PreDC_16


title: PreDC_10


title: PreDC_2


title: PreDC_8


title: PreDC_7


title: PreDC_21


title: PreDC_5


title: PreDC_3


title: CDP_96


title: PreDC_12


title: PreDC_6


title: PreDC_1


title: CDP_94


title: CDP_95


title: CDP_90


title: CDP_92


title: CDP_91


title: CDP_88


title: CDP_89


title: CDP_87


title: CDP_86


title: CDP_85


title: CDP_84


title: PreDC_9


title: PreDC_4


title: CDP_83


title: CDP_82


title: CDP_80


title: CDP_81


title: CDP_79


title: CDP_76


title: CDP_75


title: CDP_93


title: CDP_78


title: CDP_77


title: CDP_74


title: CDP_72


title: CDP_73


title: saiLC-RZ small RNA-seq

city: Shanghai

first: Fengjuan

last: Zhang

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Small RNA-seq raw fastq reads were filtered low quality sequences, trimmed for adaptor sequence. Redundant sequences were collapsed as useful reads for further analysis. Reads that could not be clipped or with lengths shorter than 19 bp were removed. Useful reads were mapped into hg19 whole genome and shRNA or saiRNA sequences using Bowtie (version 0.12.7) without allowing any mismatches. The mapped genome reads were further categorized as miRNA, tRNA, rRNA and snoRNA as the written sequence.
For small RNA-seq, tab-delimited text files include read count of sequence, and read_sequence represents read sequence, read_count represents sequenced number of read.
Illumina Casava1.7 software used for basecalling.
Genome_build: hg19

source_name: HEK293 cells total RNA

growth_protocol: HEK293 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) supplemented with 10% FBS.

extract_protocol:
Small RNA libraries were prepared for sequencing using standard Illumina protocols.
HEK293 cells were washed once with PBS and then treated with Trizol reagent for total RNA extracting.

treatment_protocol: HEK293 cells in 6-well plate were transiently transfected with 400 ng plasmids of control, shRNA, shRNA-LC, saiRNA-RZ for 48 hr.

tag: cell type

tag: transfection time

value: 48 hours

tag: plasmids used

tag: transfection dosage

value: 400 ng plasmids per well in 6-well cell culture plate


title: CDP_70

tag: mouse strain

tag: gender

tag: cell population

tag: mouse status


title: CDP_69


title: shLC small RNA-seq


title: CDP_67


title: CDP_68


title: CDP_66


title: saiGP-RZ small RNA-seq


title: shGP-LC small RNA-seq


title: shGP small RNA-seq


title: con small RNA-seq


title: CDP_63


title: CDP_64


title: CDP_65


title: CDP_62


title: saiGP-RZ RNA-seq

data_processing:
RNA-seq raw fastq reads were uniquely mapped to hg19 whole human genome using Tophat with up to 2 nt mismatches and assembled into transcripts using cufflinks with known transcriptome annotation. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated for each known genes.
For RNA-seq, tab-delimited text files include FPKM values of known genes, and gene_name represents known gene name, FPKM represents gene expression.
Illumina Casava1.7 software used for basecalling.
Genome_build: hg19

extract_protocol:
RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) according to the manufacturer’s protocol.
HEK293 cells were washed once with PBS and then treated with Trizol reagent for total RNA extracting.


title: CDP_61


title: shGP RNA-seq


title: CDP_60


title: CDP_71


title: shLC-LC small RNA-seq


title: con RNA-seq


title: CDP_58


title: CDP_59


title: shGP-LC RNA-seq


title: MCF7_Sample 2

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

description: Replicate 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and for low-quality sequence, then mapped to hg19 whole genome using TopHat2 v2.0.10 with parameters: -p 8 -N 2 -g 10 -r 200 -a 15 -m 1 -i 100 --library-type fr-unstranded --segment-mismatches 3 --read-edit-dist 2 -G
Gene expression and alternative splicing were analyzed using Cufflinks v2.1.1 and a computational procedure described in Scarpato et al., 2014
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are provided in tab delimited text format and consist of normalized counts (FPKM);

source_name: MCF7 breast-cancer cell line

extract_protocol:
Total RNA was extracted using TRIzol. The integrity and quantity of RNAs were assessed by Experion.
RNA libraries were prepared for sequencing using standard Illumina protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used  for the construction of sequencing libraries.
RNA-Seq paired-end (75+75 bp)

tag: cell line

value: MCF7 breast tumor cell line


title: CDP_57


title: MCF7_Sample 1

description: Replicate 1


title: CDP_56


title: CDP_54


title: CDP_53


title: CDP_52


title: sample_101

city: Shenzhen

description: the karyotype (46, XX), contained cells with biparental genomes and the gestational age at evacuation between 10 and 15 weeks

data_processing:
Genomic DNA from the above 12 samples were extracted and were subjected to RRBS library preparation.
The libraries were sequenced using an Illumina Hiseq2000 analyzer according to the manufacturer’s instructions.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads containing more than 30% ‘N’s or with more than 10% of the sequence having a low quality value (quality value <20) per read, were omitted from the data analysis.
The sequencing reads were aligned to the human genomic reference sequence (Hg18, NCBI Build 36) in an unbiased way for bisulfite sequencing data: (1) all the observed cytosines were replaced by thymines and the guanines were replaced by adenosines in silico, forming two “alignment form” references; (2) observed cytosines on the forward read of each read pair were replaced by thymines, and observed guanines on the reverse read of each read pair were replaced by adenosines, in silico; (3) the “alignment form” reads were then mapped to the “alignment form” reference using the Short Oligonucleotide Alignment Program (SOAP) (http://soap.genomics.org.cn).
The uniquely mapped reads that contained at least one enzyme digestion site in the ends were used for further analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Count files include the following column headers:
(1) Chromosome ID
(2) Cytosine position
(3) +/- Watson/Crick chain
(4) Type (CG/CHH/CHG)
(5) Base pattern
(6) Copynum: the same value as repeat rate
(7) Methy reads num
(8) Nonmethy reads num
(9) Binomial distribution expected values

source_name: HMs/HM-like placentas

growth_protocol: Samples were chosen on the basis of the karyotype (46, XX), nine normal placentas and  three diploid biparental HMs/HM-like placentas.

extract_protocol:
In the Danish Mole Project, samples from conceptuses presenting with vesicular villi on ultrasound or by visual inspection of the aborted tissue, are collected consecutively. The histopathology is revised blindly with respect to the results of the genetic analyses. The Danish Mole Biobank contains 309 samples collected in the period April 1986-June 2003. At the histopathological revision 270 were classified as originating from hydatidiform moles. The genetic constitution was analyzed by karyotyping, flow cytometric assessment of the nuclear DNA contents, and analysis of polymorphic DNA markers. 162 HMs were diploid, of which 151 were diploid androgenetic (AnHM) whereas 11 showed biparental DNA markers. Eight of the diploid moles with biparental markers were mosaics, in that two different cell lines were identified, a biparental cell line and an androgenetic cell line (AnHM/BiHM), whereas three of the 11 moles contained cells with biparental genomes, only (BiHM) (20,21).
RRBS libraries based on single MspI digestion were constructed for the normal placentas and the HMs/HM-like placentas described above. Briefly, 100 ng of genomic DNA was digested with 300U of MspI enzyme (NEB) in 100 μl reactions at 37°C for 16–19 h. The digested DNA was purified by MiniElute PCR Purification Kit (Qiagen). To prepare the samples for the ligation of 5-methylcytosine modified adapters, the overhangs generated by digestion were repaired in 100 μl reactions containing 15 units of T4 DNA polymerase, 2 units of Klenow fragment, 60 units of T4 polynucleotide Kinase, 0.6 mM of dNTP and 1× polynucleotide kinase buffer. Reactions were incubated at 20°C for 30 min, followed by purification. The blunt ended DNA fragments were 3’ adenylated using 15 units of Klenow (3’→5’ exo-) (Enzymatics) and 0.2 mM of dATP in 50 μl reactions with 1× blue buffer (Enzymatics) at 37°C for 30 min.   Purification using a MiniElute PCR Purification Kit (Qiagen) was performed and the products were resolved in 50 μl reaction mixture containing 360 units of T4 DNA ligase, 0.12 μM of 5-methylcytosine modified adapter oligo mix (5’GATCGGAAGAGCACACGTCTGAACTCCAGTCAC and 5’ TACACTCTTTCCCTACACGACGCTCTTCCGATCT) in 1× Rapid ligation buffer, and incubated at 20°C for 15 min, then 65°C for 15 min. A 2% of agarose gel was used to separate the fractions of adapter-ligated fragments. To obtain DNA fragments of 40-120 bp and 120-220 bp genomic DNA, 160-240 bp and 240-340 bp adapter ligated fragments were excised from the gel and purified using a QIAquick gel extraction kit (Qiagen). Bisulfite conversion was conducted using a ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO), following the manufacturer’s instructions. Finally, the libraries were generated by PCR amplification in a reaction volume of 50 μl consisting of 10 μl of bisulfite converted fragments, 4 μl of 2.5 mM dNTP, 5 μl of 10× PCR buffer, 0.5 μl of JumpStart™ Taq DNA Polymerase (Sigma), 2 μl of PCR primers and 28.5 μl of water. The following thermal cycling program was used: 94°C/1 min; 11 to 15 cycles of 94°C/10 s, 58°C/30 s and 72°C/30 s; extention for 5 min at 72°C and the products were kept at 12°C. The PCR products were size-selected and purified using a QIAquick gel extraction kit (Qiagen). To assess the C-T conversion rate of the bisulfite treatment, 50 pg of ummethylated lambda DNA was added to the genomic DNA samples. The libraries were analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: karyotype

value: contained cells with biparental genomes

tag: gestational age

value: 10 and 15 weeks

tag: tissue

value: HMs/HM-like placenta


title: sample_131


title: sample_635


title: sample_I

description: the karyotype (46, XX), biparental origin and the gestational age at evacuation between 10 and 11 weeks

source_name: normal placentas

value: biparental origin

value: 10 and 11 weeks

value: normal placenta


title: sample_J


title: CDP_51

value: male

value: steady state


title: sample_G


title: sample_H


title: CDP_49


title: CDP_50


title: CDP_48


title: CDP_47


title: sample_E


title: CDP_46


title: sample_D


title: CDP_45


title: sample_A


title: sample_B


title: CDP_55


title: CDP_44


title: CDP_42


title: sample_508 (test)

description: researching sample

tag: disease state

value: non-PTD


title: CDP_43


title: CDP_41


title: sample_268 (test)

description: researching sample


title: sample_262 (test)

description: researching sample


title: sample_271 (test)

description: researching sample


title: CDP_39


title: sample_196 (test)

description: researching sample


title: CDP_38


title: sample_186 (test)

description: researching sample


title: CDP_36


title: CDP_35


title: sample_C


title: CDP_34


title: sample_177 (test)

description: researching sample


title: sample_133 (test)

description: researching sample


title: sample_570 (test)

description: researching sample


title: CDP_33


title: CDP_32


title: CDP_30


title: sample_512 (test)

description: researching sample

value: PTD


title: sample_563 (test)

description: researching sample


title: sample_454 (test)

description: researching sample


title: CDP_29


title: sample_592 (test)

description: researching sample


title: CDP_28


title: sample_427 (test)

description: researching sample


title: sample_409 (test)

description: researching sample


title: CDP_40


title: CDP_37


title: CDP_27


title: sample_236 (test)

description: researching sample


title: CDP_26


title: sample_158 (test)

description: researching sample


title: CDP_25


title: CDP_24


title: CDP_23


title: sample_111 (test)

description: researching sample


title: sample_605 (test)

description: researching sample


title: CDP_22


title: CDP_21


title: CDP_31


title: S371 Control siRNA

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Control 1

data_processing:
Initial processing of data was done by the Illumina Sequence Control Software (SCS) and Pipeline 1.n software packages. These software components perform the functions of image analysis (Firecrest), base-calling (Bustard) and alignment of sequence tags to the Appropriate reference genome (ELAND), sorting samples by the index sequences (up to 4 per lane). Differential expression analysis between samples was performed by edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file available on the series records include normalized gene expression for each sample

source_name: 786-0 human RCC cells were transfected with control siRNA

extract_protocol:
One microgram of total RNA was used to prepare RNA-seq library (poly A selection based) using Illumina TruSeq technology.
An adaptor ligated cDNA library was prepared from the sample RNAs using Illumina® TruSeq® RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA). The resulting libraries were sequenced using Illumina HiSeq 2500 sequencer (single-end reads).

value: renal cell carcinoma


title: S374 Slfn5 siRNA

description: SLFN5 KD2

source_name: 786-0 human RCC cells were transfected with siRNA specifically targeting SLFN5


title: S374 Control siRNA

description: Control 2


title: S371 Slfn5 siRNA

description: SLFN5 KD1


title: CDP_20


title: CDP_18


title: CDP_19


title: sample_230 (test)

description: researching sample

source_name: conceptus


title: CDP_16


title: CDP_17


title: DC_MTB (TAB-Seq)

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped in bisulfite mode to human reference genome (GRCh37/hg19) and control sequences and PCR duplicates were removed.
Hydroxymethylation levels for each CpG site were estimated by counting the number of reported C (‘hydroxymethylated’ reads) divided by the total number of reported C and T (‘non-hydroxymethylated’ reads) at the same position of the reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include hydroxymethylation levels for each covered CpG site for each sample.

source_name: Monocyte-derived dendritic cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by Ficoll-Paque centrifugation. Blood monocytes were then purified from PBMCs by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech). Pure monocytes were cultured for 5 days in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned. Before infection, we systematically checked the differentiation/activation status of the monocyte-derived DCs by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR. Only samples presenting the expected phenotype for non-activated DCs – CD1a+, CD14-, CD83-, and HLA-DRlow – were used in downstream experiments.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
Genomic DNA was spiked with 0.25% of M. SsI methylated lambda DNA and 0.25% of 5hmC spike-in control II (where all cytosines were 5hmC) and then sonicated to 200-500bp with a Covaris ultrasonicator. Next,  b-glucosyltransferase (bGT) was used to introduce a glucose onto 5hmC, generating b-glucosyl-5-hydroxymethylcytosine (5gmC) to protect 5hmC from further TET oxidation. After blocking of 5hmC, all 5mC is converted to 5caC by oxidation with an excess of recombinant Tet1 protein. Bisulfite treatment of the resulting DNA then converts all C and 5caC (derived from 5mC) to uracil or 5caU, respectively, whereas the original 5hmC bases remain protected as 5gmC. Thus, following sequencing, only the 5hmC that were protected from bisulfite conversion will be read as cytosine bases. After the treatment, bisulfite conversion and library preparation were performed following a protocol identical to that for MethylC-Seq libraries.

treatment_protocol: Dendritic cells (DCs) were infected with a Mycobacterium tuberculosis (MTB) strain expressing green-fluorescent protein (H37Rv) for 18 h at a multiplicity of infection of 1-to-1. Full details can be found in Barreiro et al. (2012).

tag: condition

value: MTB-infected


title: DC_NI_rep6 (Bisulfite-Seq)

data_processing:
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped in bisulfite mode to human reference genome (GRCh37/hg19) and control sequences and PCR duplicates were removed.
Methylation levels for each CpG site were estimated by counting the number of reported C (‘methylated’ reads) divided by the total number of reported C and T (‘unmethylated’ reads) at the same position of the reference genome using Bismark’s methylation extractor tool. The same strategy was also applied for non-CpG methylation (CHG context, where H is either an A, T, or C nucleotide).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include methylation levels for each covered CpG site for each sample.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
DNA from infected and non-infected DCs (6ug) was spiked with 30ng of unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI) and further sonicated to an average length of ~100bp using a Covaris ultrasonicator under the following settings for 16 cycles: Duty cycle: 10%; Intensity: 5; Cycles/burst: 100. The sonicated product was further subjected to repair of 3’ and 5’ ends followed by the addition of a non-templated dA-tail before ligation to cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) as per manufacturerʼs instructions for genomic DNA library construction. Adapter-ligated DNA of 100-200 bp was isolated by 2% agarose gel electrophoresis, and sodium bisulfite conversion was performed on the resulting sample using the MethylCode™ Bisulfite Conversion Kit (Invitrogen) as per manufacturer’s instructions. Half of the bisulfite-converted, adapter-ligated DNA molecules were enriched by six cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Agilent), 5 μl 10X PfuTurbo reaction buffer, 25 μM dNTPs, 1 μl PE Primer 1.0 (Illumina), 1 μl PE Primer 2.0 (Illumina) (50 μl final volume). The thermocycling parameters were: 95 ̊C 2 min, 98 ̊C 30 sec, then 6 cycles of 98 ̊C 15 sec, 60 ̊C 30 sec and 72 ̊C 4 min, ending with one 72 ̊C 10 min step. The reaction products were purified using the QIAquick PCR spin column (Qiagen). Two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding two independent libraries from the same biological sample.  The quality of the libraries was checked on a Bioanalyzer followed by quantification of the libraries by qPCR using the KAPA Library Quantification Kit prior to sequencing.  Samples were sequenced on an Illumina HiSeq 2000 using 50- and 59-bp single-end reads.

treatment_protocol: We infected dendritic cells (DCs) with a Mycobacterium tuberculosis (MTB) strain expressing green-fluorescent protein (H37Rv). Importantly, previous studies have shown that the presence of GFP in this strain does not alter the growth rate or the virulence of the bacilli under axenic conditions, relative to wild-type MTB. M. tuberculosis H37Rv was grown from a frozen stock to midlog phase in 7H9 medium (BD) supplemented with albumin-dextrose-catalase (ADC; Difco).

value: Non-infected


title: DC_MTB_rep6 (Bisulfite-Seq)


title: CDP_14


title: DC_NI_rep4 (Bisulfite-Seq)


title: DC_MTB_rep5 (Bisulfite-Seq)


title: CDP_13


title: DC_MTB_rep4 (Bisulfite-Seq)


title: CDP_11


title: DC_NI_rep3 (Bisulfite-Seq)


title: DC_MTB_rep3 (Bisulfite-Seq)


title: CDP_10


title: CDP_9


title: DC_NI_rep2 (Bisulfite-Seq)


title: DC_MTB_rep2 (Bisulfite-Seq)


title: DC_NI (TAB-Seq)


title: CDP_8


title: DC_MTB_rep1 (Bisulfite-Seq)


title: DC_NI_rep1 (Bisulfite-Seq)


title: CDP_7


title: CDP_6


title: CDP_15


title: DC_NI_rep5 (Bisulfite-Seq)


title: CDP_5


title: CDP_12


title: DC_NI_Input_rep2 (ChIP-Seq)

data_processing:
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped in bisulfite mode to human reference genome (GRCh37/hg19) and control sequences and PCR duplicates were removed.
genome build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files using bedGraphToBigWig (UCSC); Scores represent the number of reads that mapped within a genomic region.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
Samples from infected and non-infected DCs from two individuals were crosslinked with 1% w/v formaldehyde for 10 min at RT and immediately quenched for 5 min with 125mM Glycine at RT. The formaldehyde fixed samples were then sonicated to 100-400 bp using a Bioruptor (Diagenode) and then ChIP-DNA prepared using the IP-Star Compact (Diagenode) Indirect method with an Antibody-Antigen incubation of 10 hr, Bead incubation of 2 hr, and 4x 20 min wash steps. Approximately 1 million cells were used for each ChIP and ~50,000 cells for the input. The following antibodies were used: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1), H3K4me3 (CST, 9751BC, 7), H3K9me3 (MABI, 0318, 13001), H3K27me3 (MABI, 0323, 13001), H3K27ac (Abcam, Ab4729, GR119051), and H3K36me3 (MABI, 0333, 12003). ChIP and Input libraries were prepared using the Illumina Truseq Nano DNA kit, with alterations including: PCR enrichment (14 cycles) prior to size selection and utilizing the PippinPrep method (SAGE Science) instead of the SPRI method for size selection (200-400 bp).

tag: chip anitbody


title: DC_NI_H3K9me3_rep2 (ChIP-Seq)


title: CDP_4


title: CDP_3


title: CDP_1


title: DC_NI_H3K36me3_rep2 (ChIP-Seq)


title: CDP_2


title: DC_NI_H3K4me1_rep2 (ChIP-Seq)

value: H3K4me1 (Company:CST, Cat. No.:5326P, Lot No.:1)


title: DC_NI_H3K27ac_rep2 (ChIP-Seq)


title: DC_MTB_Input_rep2 (ChIP-Seq)


title: DC_NI_H3K27me3_rep2 (ChIP-Seq)


title: Med1-Med12-Input

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

institute: University of Geneva Medical School

data_processing:
reads generated from the sequencing were mapped against the mouse genome (mm9) using the BWA (Burrows-Wheeler Aligner)(Li and Durbin 2009) alignment program with the default parameters (allowing 2 mismatches).
Mapped reads were submitted to the HOMER (Hypergeometric Optimization of Motif EnRichment) software for the identification of DNA binding sites
HOMER was used with the default parameters after removing of the duplicated reads.
peak finding was done by comparing the tags to the input tags (background removal)
Genome_build: mm9
Supplementary_files_format_and_content: text file: peak ID, chromosome, start, end, strand, Normalized Tag Count, Focus ratio, FindPeaks score, Total tags, control tags, Fold change vs control, p-value vs control, Fold change vs local, p-value vs local, Clonal fold change

source_name: mouse embryonic stem cells

growth_protocol: mES cells were grown on 0.1% gelatin (Sigma #G1890) coated dishes in DMEM high glucose medium (Life technologies #41965) supplemented with 15% Fetal Bovine Serum (FBS HyClone, Thermo Scientific #SH30070), 2mM L-glutamine (Life technologies #25030), 1mM Sodium pyruvate (Life technologies #11360), 100units/ml penicillin/streptomycin (Bioconcept #4-01F00-H), 0.1mM 2-mercaptoethanol (Life technologies #31350), 1000units/ml Leukemia Inhibitory Factor (LIF, Millipore #ESG1107) and 1μg/ml tetracycline (Sigma #T7660). Cells were incubated at 37°C in a 5% CO2 atmosphere. Medium was changed every day and cells were passed every 1 or 2 days using 1X Trypsin-EDTA (Sigma #T4174).

extract_protocol:
ChIP was performed using the SimpleChIPTM Enzymatic Chromatin IP Kit (Cell Signaling #9003) according to manufacturer’s instructions.
Preparation of the libraries for high throughput sequencing was performed using the ChIP-Seq DNA sample Prep Kit (Illumina #IP-102-1001), following the manufacturer’s instructions

treatment_protocol: Induction of Sim2 expression was performed by culturing the cells in  tetracycline-free medium for 26h

value: Sim2-expressing cells

tag: clone

tag: antibody


title: Sox2-Input


title: Med1-ChIP

value: anti-Med1 (CRSP1/TRAP220) (Bethyl #A300-793A)


title: Med12-ChIP

value: anti-Med12 (Bethyl #A300-774A)


title: Oct4-Nanog-Input


title: DC_MTB_H3K4me3_rep2 (ChIP-Seq)