title: B1H assay using CCTA as bait, replicate 1


title: B1H assay using CCGG as bait, replicate 1

status: Public on Feb 17 2015

type: SRA

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Reads were trimmed at the 3’ end, so that for each read the minimum Phred quality score of any base of the remaining part was 12, there were no more than 10 bases with Phred quality scores <20, and the reads, after removing the constant vector region and amplification adapters, were not longer than 80 bases. The trimmed reads were further filtered to remove those shorter than 50 bases.
Reads were mapped to the library using Bowtie, allowing a maximum of 2 mismatches at the first 28 bases and a maximum of 70 for the sum of quality values at all mismatched read positions, retaining only reads that were uniquely mapped. The number of reads that mapped to each Egr1 variant was recorded.
*count.txt contains unique ID given to each sequence in the library and its abundance count. The 'OLS.info.xlsx' file contains the mapping of these IDs to different sequences.
Genome_build: Custom library
Supplementary_files_format_and_content: Text files containing the number of reads that were uniquely mapped to each Egr1 variant

molecule: genomic DNA

organism: synthetic construct

source_name: B1H assay using CCGG as bait

growth_protocol: We performed B1H screens essentially as described before (PMID 17406209), with the modification that we first transformed the bacterial selection strain with the bait plasmid, then made electrocompetent cells, then transformed these with the prey library of C2H2 variants.  We plated ~10^7 transformants on three μM medium plates (150 mm) containing 1 mM 3-Amino-1,2,4-triazole (3-AT), 100 μg/ml ampicillin, 25 μg/ml kanamycin, 10 μM IPTG, no histidine, and 0.2 mM uracil.  We incubated the plates at 37C for 2 days, or more if needed to obtain colonies (typically hundreds to thousands of visible colonies of varying size).

extract_protocol:
We scraped the colonies from the plates, and prepared plasmid DNA.
We PCR-amplified F3 from the plasmid DNA using Illumina barcoded primers.

tag: bait

value: CCGG

tag: ols

tag: molecule type

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using CCGC as bait, replicate 2

source_name: B1H assay using CCGC as bait

value: CCGC


title: B1H assay using CCTG as bait, replicate 1

source_name: B1H assay using CCTG as bait

value: CCTG


title: B1H assay using CGTA as bait, replicate 2

source_name: B1H assay using CGTA as bait

value: CGTA


title: B1H assay using CCGG as bait, replicate 2


title: B1H assay using CCCT as bait, replicate 1

source_name: B1H assay using CCCT as bait

value: CCCT


title: rno.br.3

city: Seoul

first: Alexey

last: Fushan

state: Seodaemun-gu

address: 52, Ewhayeodae-gil

country: South Korea

institute: EWHA

description: biological replicate 3

library_source: transcriptomic

data_processing:
The RNA-seq libraries were each sequenced (76 cycles) in at least one lane of the Illumina Genome Analyser IIx platform.
Samples were demultiplexed and the indexed adapter sequences were trimmed using the CASAVA v1.8.2 software (Illumina, Inc.).
The fluorophore intensity files were analyzed with the standard Illumina base-calling algorithms.
51-bp paired-end reads that passed the chastity filter threshold were mapped using TopHat4 2.0 with default parameter values, except for distance between mature pairs (r=200) and the number of allowable mismatches between read and genomic sequences (n=3) to ensure possible genetic heterogeneity between populations. The anchor size (i.e. the minimum aligned length spanning each of the two exons that deﬁne a splice junction) was set at 8 bp, and we allowed 1 mismatch on the anchor region. The transcript isoform abundance and averaged gene expression levels were calculated and FPKM normalized using Cufflinks.
Genome_build: Bos taurus Ensembl genome build 62,
Capra hircus de novo transcriptome assembly (PRJNA182763); see GSE43013_chi.rna.gtf.
Sus scrofa Ensembl genome build 62
Canis familiaris Ensembl genome build 62
Felis catus Ensembl genome build 62
Meles meles de novo transcriptome assembly (PRJNA182767)
Ursus americanus de novo transcriptome assembly (PRJNA182773)
Murina leucogaster de novo transcriptome assembly (PRJNA182766)
Tadarida brasiliensis de novo transcriptome assembly (PRJNA182772)
Petaurus breviceps de novo transcriptome assembly (PRJNA182769)
Erinaceus europaeus Ensembl genome build 62
Oryctolagus cuniculus Ensembl genome build 62
Equus caballus Ensembl genome build 62
Chlorocebus aethiops de novo transcriptome assembly (PRJNA182762)
Acomys cahirinus de novo transcriptome assembly (PRJNA182705)
Cavia porcellus Ensembl genome build 62
Mesocricetus auratus de novo transcriptome assembly (PRJNA182765)
Meriones unguiculatus de novo transcriptome assembly (PRJNA182768)
Mus musculus Ensembl genome build 62
Peromyscus leucopus de novo transcriptome assembly (PRJNA182770)
Rattus norvegicus Ensembl genome build 62
Tamias sibiricus de novo transcriptome assembly (PRJNA183188)
Suncus murinus de novo transcriptome assembly (PRJNA182771).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: Rattus norvegicus_brain

extract_protocol:
Total RNA was extracted using RNAeasy (Qiagen) purification kit according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina, Inc.) in accordance with the manufacturer' instructions. Polyadenylated RNA was isolated using a poly-dT bead procedure, chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 300-bp fragments were excised and then PCR-amplified (20 cycles). After column purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalysers.

tag: strain (source)

value: brown rat

tag: genotype/variation

value: wild type

tag: age

value: adult

tag: tissue

value: normal brain

tag: organ part

value: frontal parts of brain


title: B1H assay using CCGC as bait, replicate 1


title: rno.br.2

description: biological replicate 2


title: B1H assay using CCCT as bait, replicate 2


title: rno.br.1

description: biological replicate 1


title: B1H assay using CCCA as bait, replicate 2

source_name: B1H assay using CCCA as bait

value: CCCA


title: B1H assay using CCCA as bait, replicate 1


title: B1H assay using CCAT as bait, replicate 2

source_name: B1H assay using CCAT as bait

value: CCAT


title: rno.kd.3

description: biological replicate 3

source_name: Rattus norvegicus_kidney

value: normal kidney

value: whole kidney


title: rno.kd.2

description: biological replicate 2


title: rno.kd.1

description: biological replicate 1


title: B1H assay using CCAT as bait, replicate 1


title: B1H assay using CCAA as bait, replicate 2

source_name: B1H assay using CCAA as bait

value: CCAA


title: B1H assay using CCTC as bait, replicate 2

source_name: B1H assay using CCTC as bait

value: CCTC


title: rno.lv.3

description: biological replicate 3

source_name: Rattus norvegicus_liver

value: normal liver

value: whole liver


title: rno.lv.2

description: biological replicate 2


title: rno.lv.1

description: biological replicate 1


title: bta.br.1

description: biological replicate 1

organism: Bos taurus

source_name: Bos taurus_brain

value: in-house colony


title: B1H assay using CATT as bait, replicate 2

source_name: B1H assay using CATT as bait

value: CATT

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using CATG as bait, replicate 1

source_name: B1H assay using CATG as bait

value: CATG


title: B1H assay using CCAA as bait, replicate 1


title: bta.kd.1

description: biological replicate 1

source_name: Bos taurus_kidney


title: B1H assay using CATG as bait, replicate 2


title: bta.kd.2

description: biological replicate 2


title: bta.lv.2

description: biological replicate 2

source_name: Bos taurus_liver


title: B1H assay using CATC as bait, replicate 1

source_name: B1H assay using CATC as bait

value: CATC


title: B1H assay using CATA as bait, replicate 2

source_name: B1H assay using CATA as bait

value: CATA


title: bta.lv.1

description: biological replicate 1

value: wild type

value: adult


title: ssc.br.2

description: biological replicate 2

organism: Sus scrofa

source_name: Sus scrofa_brain

value: normal brain

value: frontal parts of brain


title: B1H assay using CAGT as bait, replicate 2

source_name: B1H assay using CAGT as bait

value: CAGT


title: B1H assay using CAGT as bait, replicate 1


title: ssc.kd.2

description: biological replicate 2

source_name: Sus scrofa_kidney

value: normal kidney


title: ssc.br.1

description: biological replicate 1


title: ssc.kd.1

description: biological replicate 1

value: whole kidney


title: ssc.lv.1

description: biological replicate 1

source_name: Sus scrofa_liver


title: bta.br.2

description: biological replicate 2


title: B1H assay using CACT as bait, replicate 1

source_name: B1H assay using CACT as bait

value: CACT


title: B1H assay using CATA as bait, replicate 1


title: B1H assay using CATT as bait, replicate 1


title: B1H assay using CAAT as bait, replicate 2

source_name: B1H assay using CAAT as bait

value: CAAT


title: B1H assay using CACT as bait, replicate 2


title: B1H assay using CACC as bait, replicate 1

source_name: B1H assay using CACC as bait

value: CACC


title: B1H assay using CACC as bait, replicate 2


title: mle.br.1

description: biological replicate 1

organism: Meles meles

source_name: Meles meles_brain


title: B1H assay using CAAT as bait, replicate 1


title: mle.kd.2

description: biological replicate 2

source_name: Meles meles_kidney


title: mle.kd.1

description: biological replicate 1


title: B1H assay using CAAC as bait, replicate 2

source_name: B1H assay using CAAC as bait

value: CAAC


title: B1H assay using CATC as bait, replicate 2


title: B1H assay using CAAC as bait, replicate 1


title: B1H assay using CAAA as bait, replicate 2

source_name: B1H assay using CAAA as bait

value: CAAA


title: mle.lv.2

description: biological replicate 2

source_name: Meles meles_liver

value: in-house colony

value: normal liver

value: whole liver


title: mhi.br.2

description: biological replicate 2

organism: Murina leucogaster

source_name: Murina leucogaster_brain

value: wild colony


title: mle.lv.1

description: biological replicate 1


title: mhi.br.1

description: biological replicate 1


title: B1H assay using ATTT as bait, replicate 2

source_name: B1H assay using ATTT as bait

value: ATTT

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using CAAA as bait, replicate 1


title: B1H assay using ATTT as bait, replicate 1


title: ssc.lv.2

description: biological replicate 2

value: wild type

value: adult


title: mhi.kd.1

description: biological replicate 1

source_name: Murina leucogaster_kidney


title: B1H assay using ATTA as bait, replicate 2

source_name: B1H assay using ATTA as bait

value: ATTA


title: B1H assay using ATTA as bait, replicate 1


title: mhi.lv.2

description: biological replicate 2

source_name: Murina leucogaster_liver


title: B1H assay using ATGG as bait, replicate 2

source_name: B1H assay using ATGG as bait

value: ATGG


title: mhi.lv.1

description: biological replicate 1


title: mle.br.2

description: biological replicate 2

value: normal brain

value: frontal parts of brain


title: mau.br.3

description: biological replicate 3

organism: Mesocricetus auratus

source_name: Mesocricetus auratus_brain


title: B1H assay using ATGG as bait, replicate 1


title: mau.br.2

description: biological replicate 2


title: mau.kd.3

description: biological replicate 3

source_name: Mesocricetus auratus_kidney

value: normal kidney

value: whole kidney


title: B1H assay using ATGA as bait, replicate 1

source_name: B1H assay using ATGA as bait

value: ATGA


title: B1H assay using ATGA as bait, replicate 2


title: B1H assay using ATGC as bait, replicate 1

source_name: B1H assay using ATGC as bait

value: ATGC


title: B1H assay using ATGC as bait, replicate 2


title: mau.br.1

description: biological replicate 1


title: mau.lv.3

description: biological replicate 3

source_name: Mesocricetus auratus_liver


title: mau.kd.1

description: biological replicate 1


title: mau.kd.2

description: biological replicate 2


title: mau.lv.2

description: biological replicate 2


title: B1H assay using ATAT as bait, replicate 2

source_name: B1H assay using ATAT as bait

value: ATAT


title: B1H assay using ATCC as bait, replicate 1

source_name: B1H assay using ATCC as bait

value: ATCC


title: B1H assay using ATAT as bait, replicate 1


title: mau.lv.1

description: biological replicate 1

value: in-house colony

value: normal liver


title: fca.br.3

description: biological replicate 3

organism: Felis catus

source_name: Felis catus_brain


title: B1H assay using ATAC as bait, replicate 1

source_name: B1H assay using ATAC as bait

value: ATAC


title: fca.br.2

description: biological replicate 2


title: fca.br.1

description: biological replicate 1


title: B1H assay using ATAC as bait, replicate 2


title: B1H assay using ATCC as bait, replicate 2


title: B1H assay using ATAA as bait, replicate 2

source_name: B1H assay using ATAA as bait

value: ATAA


title: fca.kd.2

description: biological replicate 2

source_name: Felis catus_kidney


title: B1H assay using AGTG as bait, replicate 2

source_name: B1H assay using AGTG as bait

value: AGTG

value: Plasmid extracted from bacteria after selection in B1H assay


title: fca.kd.1

description: biological replicate 1

value: wild type

value: adult


title: B1H assay using AGTG as bait, replicate 1


title: fca.lv.3

description: biological replicate 3

source_name: Felis catus_liver

value: whole liver


title: fca.lv.2

description: biological replicate 2


title: B1H assay using AGTA as bait, replicate 2

source_name: B1H assay using AGTA as bait

value: AGTA


title: fca.lv.1

description: biological replicate 1


title: B1H assay using AGTA as bait, replicate 1


title: B1H assay using AGGT as bait, replicate 1

source_name: B1H assay using AGGT as bait

value: AGGT


title: B1H assay using AGGT as bait, replicate 2


title: B1H assay using AGGG as bait, replicate 1

source_name: B1H assay using AGGG as bait

value: AGGG


title: B1H assay using AGGA as bait, replicate 1

source_name: B1H assay using AGGA as bait

value: AGGA


title: B1H assay using AGGA as bait, replicate 2


title: B1H assay using AGAG as bait, replicate 2

source_name: B1H assay using AGAG as bait

value: AGAG


title: B1H assay using AGAG as bait, replicate 1


title: B1H assay using ACTT as bait, replicate 2

source_name: B1H assay using ACTT as bait

value: ACTT


title: B1H assay using ACTC as bait, replicate 2

source_name: B1H assay using ACTC as bait

value: ACTC


title: B1H assay using ACTT as bait, replicate 1


title: B1H assay using ATAA as bait, replicate 1


title: B1H assay using ACTC as bait, replicate 1


title: B1H assay using ACTA as bait, replicate 1

source_name: B1H assay using ACTA as bait

value: ACTA


title: B1H assay using ACCT as bait, replicate 1

source_name: B1H assay using ACCT as bait

value: ACCT


title: B1H assay using ACTA as bait, replicate 2


title: B1H assay using ACCG as bait, replicate 2

source_name: B1H assay using ACCG as bait

value: ACCG


title: B1H assay using ACCG as bait, replicate 1


title: B1H assay using ACCT as bait, replicate 2


title: B1H assay using ACCC as bait, replicate 2

source_name: B1H assay using ACCC as bait

value: ACCC


title: B1H assay using ACCA as bait, replicate 2

source_name: B1H assay using ACCA as bait

value: ACCA


title: B1H assay using AGGG as bait, replicate 2


title: mus.br.3

description: biological replicate 3

organism: Mus musculus

source_name: Mus musculus_brain

value: normal brain

value: frontal parts of brain


title: mus.br.2

description: biological replicate 2

value: wild type


title: B1H assay using ACCA as bait, replicate 1

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using ACCC as bait, replicate 1


title: B1H assay using AGAA as bait, replicate 1

source_name: B1H assay using AGAA as bait

value: AGAA


title: B1H assay using AGAA as bait, replicate 2


title: B1H assay using ACAT as bait, replicate 2

source_name: B1H assay using ACAT as bait

value: ACAT


title: mus.kd.3

description: biological replicate 3

source_name: Mus musculus_kidney

value: adult

value: normal kidney

value: whole kidney


title: mus.kd.1

description: biological replicate 1


title: mus.kd.2

description: biological replicate 2


title: B1H assay using ACAC as bait, replicate 1

source_name: B1H assay using ACAC as bait

value: ACAC


title: B1H assay using ACAT as bait, replicate 1


title: B1H assay using ACAA as bait, replicate 2

source_name: B1H assay using ACAA as bait

value: ACAA


title: mus.lv.2

description: biological replicate 2

source_name: Mus musculus_liver

value: normal liver

value: whole liver


title: fca.kd.3

description: biological replicate 3

source_name: Felis catus_kidney

value: in-house colony


title: mus.lv.3

description: biological replicate 3


title: B1H assay using AATT as bait, replicate 1

source_name: B1H assay using AATT as bait

value: AATT


title: mus.lv.1

description: biological replicate 1


title: B1H assay using AATT as bait, replicate 2


title: B1H assay using ACAA as bait, replicate 1


title: B1H assay using AATC as bait, replicate 1

source_name: B1H assay using AATC as bait

value: AATC


title: B1H assay using AATC as bait, replicate 2


title: B1H assay using AAGT as bait, replicate 2

source_name: B1H assay using AAGT as bait

value: AAGT


title: B1H assay using AAGT as bait, replicate 1


title: B1H assay using AATA as bait, replicate 1

source_name: B1H assay using AATA as bait

value: AATA


title: B1H assay using AAGG as bait, replicate 2

source_name: B1H assay using AAGG as bait

value: AAGG


title: B1H assay using AAGG as bait, replicate 1


title: B1H assay using AAGC as bait, replicate 1

source_name: B1H assay using AAGC as bait

value: AAGC


title: mus.br.1

description: biological replicate 1

value: wild type

value: normal brain

value: frontal parts of brain


title: B1H assay using AACT as bait, replicate 1

source_name: B1H assay using AACT as bait

value: AACT

value: Plasmid extracted from bacteria after selection in B1H assay


title: B1H assay using AAGC as bait, replicate 2


title: B1H assay using AACT as bait, replicate 2


title: B1H assay using ACAC as bait, replicate 2


title: B1H assay using AACG as bait, replicate 2

source_name: B1H assay using AACG as bait

value: AACG


title: tsi.br.2

description: biological replicate 2

organism: Tamias sibiricus

source_name: Tamias sibiricus_brain

value: adult


title: tsi.br.1

description: biological replicate 1


title: B1H assay using AACG as bait, replicate 1


title: tsi.kd.1

description: biological replicate 1

source_name: Tamias sibiricus_kidney

value: normal kidney

value: whole kidney


title: B1H assay using AACA as bait, replicate 2

source_name: B1H assay using AACA as bait

value: AACA


title: tsi.kd.2

description: biological replicate 2

value: in-house colony


title: pbr.br.2

description: biological replicate 2

organism: Petaurus breviceps

source_name: Petaurus breviceps_brain


title: B1H assay using AAAG as bait, replicate 2

source_name: B1H assay using AAAG as bait

value: AAAG


title: B1H assay using AAAG as bait, replicate 1


title: pbr.br.1

description: biological replicate 1


title: B1H assay using AATA as bait, replicate 2


title: B1H assay using AAAC as bait, replicate 2

source_name: B1H assay using AAAC as bait

value: AAAC


title: pbr.kd.1

description: biological replicate 1

source_name: Petaurus breviceps_kidney


title: B1H assay using AAAC as bait, replicate 1


title: pbr.kd.2

description: biological replicate 2


title: B1H assay using AAAA as bait, replicate 2

source_name: B1H assay using AAAA as bait

value: AAAA


title: uam.br.2

description: biological replicate 2

organism: Ursus americanus

source_name: Ursus americanus_brain

value: captured in Alaska, USA


title: B1H assay using AAAA as bait, replicate 1


title: uam.br.1

description: biological replicate 1


title: Original B1H library, batch C

source_name: OLS Plasmid

value: OLS Plasmid


title: uam.kd.1

description: biological replicate 1

source_name: Ursus americanus_kidney


title: Original B1H library, batch B


title: uam.kd.2

description: biological replicate 2


title: uam.lv.2

description: biological replicate 3

source_name: Ursus americanus_liver

value: normal liver

value: whole liver


title: uam.lv.1

description: biological replicate 2

value: wild type


title: B1H assay using AACA as bait, replicate 1


title: Original B1H library, batch A


title: tbr.lv.3

description: biological replicate 3

organism: Tadarida brasiliensis

source_name: Tadarida brasiliensis_liver

value: wild colony


title: 1a

city: Cleveland

first: Helen

middle: Karen

last: Salz

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

country: USA

institute: Case Western Reserve University School of Medicine

data_processing:
reads aligned to Drosophila genome using TopHat(2.0.9) and reported as FPKM
differential expression analysis was done using cuffdiff program
reads mapping to 20 loci and less were retained
Genes with 0.05 or lower P values after adjusting to false discovery rate (FDR) with Benjamini and Hochberg (BH) method and a fold change of 2 or higher were considered significant
Genome_build: Drosophila UCSCdm3/Flybase r5.23
Supplementary_files_format_and_content: txt file containing list of upregulated and downregulated genes

organism: Drosophila melanogaster

source_name: snf mutant ovaries-1

extract_protocol:
total RNA isolated with Rneasy Kit (Qiagen), including on-column Dnase I digestion
Illumina Truseq Total stranded RNA kit,100 bp paired-end RNA seq on Illumina HiSeq 2500

value: 3 day adult

value: ovaries

tag: full genotype

value: y w snf[148] v


title: tbr.lv.2

description: biological replicate 2

value: adult


title: 1b

source_name: WT ovaries-1

value: 0-24 hour adult

value: y w


title: tbr.lv.1

description: biological replicate 1


title: 2a

source_name: snf mutant ovaries-2


title: 2b

source_name: WT ovaries-2


title: smu.lv.3

description: biological replicate 3

organism: Suncus murinus

source_name: Suncus murinus_liver


title: eca.br.2

description: biological replicate 2

organism: Equus caballus

source_name: Equus caballus_brain

value: normal brain

value: frontal parts of brain


title: eca.br.1

description: biological replicate 1

value: in-house colony


title: smu.lv.1

description: biological replicate 1


title: eca.kd.2

description: biological replicate 2

source_name: Equus caballus_kidney

value: normal kidney

value: whole kidney


title: eca.lv.2

description: biological replicate 2

source_name: Equus caballus_liver


title: eca.kd.3

description: biological replicate 3


title: eca.lv.1

description: biological replicate 1


title: eca.kd.1

description: biological replicate 1


title: p53 KO NPC

status: Public on Feb 16 2015

city: New Orleans

first: Yuwen

last: Li

address: 1430 Tulane Ave SL37 RM5534

department: Pediatrics

institute: Tulane University

data_processing:
PolyA-selection was done before 100bp/read paired-end Illumina TruSeq RNA-Seq on HiSeq 2000 system
Illumina Casava (1.8 or newer) software used for basecalling.
Sequence aligner Novoalign v2.08.02 aligned the raw reads to mouse genome assembly GRCm38/mm10.
The quality of raw reads was tested by FastQC (Babraham Bioinformatics) and p53 conditional knockout was confirmed by comparing RNA-Seq tracks in IGV 2.3 (Integrative Genomics Viewer).
The read quality codes (SamFlag codes “83”, “99”, “147” and “163”, which identified the reads that were paired and mapped in proper pair) were applied to control the quality for paired reads.
Read density (FPKM) quantification was done by GeneSpring NGS module
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read density (FPKM) for each genotype

source_name: embryonic kidney_p53_KO

extract_protocol:
~2ug total RNA extracted by Qiagen RNeasy Mini Kit from FACS-sorted cap mesenchymal cells for each genotypic (wild-type and conditional p53 knockout) nephron progenitor cells
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic day 15.5

tag: genotype

value: embryonic kidney

tag: cell type

value: Six2+ nephron progenitor cells

tag: strain

value: Mixed (CD1 & C57BL)


title: p53 WT NPC

source_name: embryonic kidney_p53_WT


title: siOXR1_NT

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
Libray preparison:mRNA is enriched by using the oligo(dT) magnetic beads, following to be fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.
Sequencing: The library products are ready for sequencing via Illumina HiSeqTM 2000.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to human reference sequences and/or reference gene set using SOAPaligner/SOAP2 (Li R., Yu C., Li Y., et al . 2009, Bioinformatics).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Genome_build: standard reference of human genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .The processed data contain 4 files: siCon_NT_Gene_rpkm.txt, siCon_R0h_Gene_rpkm.txt, siOXR1_NT_Gene_rpkm.txt and siOXR1_R0h_Gene_rpkm.txt.

organism: Homo sapiens

source_name: HeLa cell line

growth_protocol: The cells were cultured at 37°C with 5 % CO2 in growth medium: DMEM medium including 4.5% glucose (Biowhittaker, Cambrex Inc.) and supplemented with 10% fetal calf serum, 100 IU/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Total RNA was isolated from cell lines using RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were measured using a RNA Pico chip on an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hydrogen peroxide (H2O2 Sigma) was diluted freshly in growth medium immediately before use.

tag: cell line

value: HeLa S3

value: cervix

value: 31 years

value: hOXR1 knockdown

tag: treatment


title: siCon_R0h

value: wild type


title: siOXR1_R0h


title: siCon_NT


title: Sequencing analysis of input in 451Lu melanoma untreated cells

city: New York

first: Nikos

last: Kourtis

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
MACS version 1.4.2 was used for ChIP-sequencing peak discovery. GenomicTools version 2.7.2 was used for performing genomic interval mathematical operations, genomic interval annotation, ChIP-seq heatmap generation and ChIP-seq profile construction.
Genome_build: hg19
Supplementary_files_format_and_content: bed format containg relative enrichments

growth_protocol: attached cells, growing in TU2% medium containing 80% (v/v) MCDB153, 20% (v/v) Leibovitz's L-15 (Invitrogen), 2% (v/v) FBS, 5 μg/ml bovine insulin, 1.68 mM CaCl2 and 1% (v/v) penicillin/streptomycin

extract_protocol:
Twenty million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: Untreated cells

value: melanoma

tag: chip antibody


title: ChIP-Seq analysis of HSF1 in 451Lu melanoma untreated cells replicate2

value: HSF1 (Cell Signaling, catalog# 4356, lot# 2)


title: ChIP-Seq analysis of HSF1 in 451Lu melanoma untreated cells replicate1


title: ChIP-Seq analysis of HSF1 in HCT116 WT untreated cells replicate1

source_name: HCT116 WT

growth_protocol: attached cells, growing in McCoy's 5A

extract_protocol:
Five million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: HCT116 WT and FBXW7 KO colon cancer cells untreated or exposed to heat shock 42oC for 1 hour

value: human colon cancer cells

value: HSF1:Cell Signaling, 4356


title: Sequencing analysis of input in HCT116 WT cells upon heat shock treatment


title: ChIP-Seq analysis of HSF1 in HCT116 WT cells upon heat shock treatment replicate2


title: smu.lv.2

description: biological replicate 2

value: adult

value: normal liver

value: whole liver


title: Sequencing analysis of input in HCT116 FBXW7 KO untreated cells

source_name: HCT116 FBXW7 KO


title: ChIP-Seq analysis of HSF1 in HCT116 FBXW7 KO cells upon heat shock treatment replicate2


title: RNA-Seq analysis in HCT116 WT cells after recovery from heat shock treatment replicate 2

data_processing:
Basecalls performed using CASAVA
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Differential gene expression analysis was performed for each matched recovery vs heat-shock pairs, separately in each biological replicate and cell line (WT or KO). Two types of comparisons were tested: (a) WT recovery vs heat shock and (b) FBXW7 KO recovery vs heat shock. Analysis was performed using the DEGseq25 package.
Two types of comparisons were tested: (a) WT recovery vs heat shock and (b) FBXW7 KO recovery vs heat shock. Analysis was performed using the DEGseq25 package.
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text, Degexp output containing normalized expression values

extract_protocol:
RNeasy kit (Qiagen)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

treatment_protocol: cells were heat shocked for 1 hour at 42 °C followed by recovery at 37°C for 2 hours


title: ChIP-Seq analysis of HSF1 in HCT116 FBXW7 KO cells upon heat shock treatment replicate1


title: Sequencing analysis of input in HCT116 FBXW7 KO cells upon heat shock treatment


title: ChIP-Seq analysis of HSF1 in HCT116 FBXW7 KO untreated cells replicate1


title: RNA-Seq analysis in HCT116  WT cells after recovery from heat shock treatment replicate 1


title: RNA-Seq analysis in HCT116 WT cells upon heat shock treatment replicate 1


title: eca.lv.3

description: biological replicate 3

value: in-house colony


title: RNA-Seq analysis in HCT116 FBXW7 KO cells upon heat shock treatment replicate 2


title: RNA-Seq analysis in HCT116 FBXW7 KO cells after recovery from heat shock treatment replicate 2


title: Δhns (OD 2.0) rep1

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

description:
Table S2. Genes differentially expressed in hns mutant in early stationary phase.xlsx
Stationary V cholerae TopHat stats Rep1,2

data_processing:
Paired end 2X50bp sequencing read data were converted to the FASTQ Sanger format using FASTQ Groomer.  TopHat was used to align RNA-Seq reads to the reference genome using the short read aligner Bowtie.  Cufflinks was used to assemble transcripts from the TopHat aligned reads, to estimate their abundances and test for differential expression and regulation.  Cuffcompare, which is part of Cufflinks was used to compare the assembled transcripts to a reference annotation.  Finally, Cuffdiff was used to find significant changes in transcript expression. Genes exhibiting a fold change ≥ ±2.0 and q-value < 0.05) were considered differentially expressed in the Δhns mutant
Genome_build: NCBI Reference Sequences: NC_002505.1 and NC_002506.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, mutant to Wt fold-change ration, statistical significance, etc. Text Files describing the FastQC metrics of each sequencing run

organism: Vibrio cholerae

source_name: LB liquid medium planktonic cells

growth_protocol: V. cholerae cells were grown in 50 mL LB medium at 37°C with agitation (225 rpm) to optical densities at 600 nm (OD600) of 0.5 and 2.0. Culture media were supplemented for hns mutant cells with kanamycin (Km, 25 µg/mL).

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). To this end, the cell pellets were resuspended in 200 uL of bacterial lysis buffer [30 mM Tris-HCl pH 8.0, 1 mM EDTA, 15 mg/mL lysozyme (Sigma-Aldrich)], supplemented with  15 uL of proteinase K (20 mg/mL, Qiagen), and the samples were incubated at room temperature for 10 min with vortexing every 2 min. Qiagen RLT Plus buffer (750 uL) containing 1 % v/v 2-mercaptoethanol was added to each sample and the tubes were briefly vortexed. The bacterial lysates were homogenized using QIAshredder spin columns (Qiagen) and genomic DNA removed using gDNA Eliminator spin columns (Qiagen). Finally, total RNA was recovered using the RNeasy spin column method (Qiagen) following the manufacturer's protocol. RNA integrity was determined by formaldehyde agarose gel electrophoresis and RNA was stored at -80°C. Contamination with DNA was further eliminated using the TURBO DNA-free kit (Invitrogen), which involves a second treatment with DNase for 30 min at 37°C. Reactions were terminated by addition of 0.2 volumes of the DNase inactivation reagent and RNA was purified using the Agencourt RNAClean XP kit (Beckman) following the manufacturer's instructions. Total RNA was eluted in 60 uL of RNase-free water. The absence of DNA contamination was confirmed by PCR with 16S RNA sequence-specific primers. Next, rRNA was removed using Ribo-Zero Magnetic Kit (Epicentre) following the manufacturer's instructions. Briefly, 6 ug of total RNA sample and 20 uL of Ribo-Zero rRNA Removal Solution were combined in a final reaction volume of 80 uL. Samples in Ribo-Zero rRNA removal solution were incubated at 68°C for 10 min followed by a 5 min incubation at room temperature. To remove the rRNA molecules from the mRNA, reactions mixtures were incubated with the magnetic beads provided in the kit, mixed and placed at room temperature for 5 min and then at 50°C for 5 min. The rRNA bound to the beads was then removed by magnetic separation. Finally, mRNA was purified using Agencourt RNAClean XP kit and eluted in 15 uL of RNase-free water.
RNA-seq was performed on the Illumina HiSeq2000 using the latest versions of sequencing reagents and flow cells providing up to 300 Gb of sequence information per cell. Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer and samples were subsequently converted to cDNA. Libraries were constructed using the TruSeq library generation kits as per the manufacturer's instructions (Illumina, San Diego, CA). The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725K - 825K clusters/mm2

treatment_protocol: Each culture was divided into 5 mL aliquots and the cells were harvested by centrifugation at 4,000 × g for 10 min at room temperature. The pellets were resuspended in 5 mL of RNAlater (Invitrogen) and agitated on a rotator for 10 min at room temperature.  Then, cell pellets corresponding to 1 mL aliquots were collected by centrifugation 10 min at 4,000 × g.

tag: od600 nm

tag: phenotype


title: Wt (OD 2.0) rep2

value: Wt/ΔlacZ


title: Sequencing analysis of input in HCT116 WT untreated cells


title: Δhns (OD 2.0) rep2


title: Wt (OD 2.0) rep1


title: Δhns (OD 0.5) rep1

description:
Table S1. Genes differentially expressed in hns mutant in mid-exponential phase.xlsx
Exponential - TopHat stats Rep1


title: Wt (OD 0.5) rep1


title: RNA-Seq analysis in HCT116 FBXW7 KO cells upon heat shock treatment replicate 1


title: Δhns (OD 0.5) rep2

description:
Table S1. Genes differentially expressed in hns mutant in mid-exponential phase.xlsx
Exponential - TopHat stats Rep2


title: Wt (OD 0.5) rep2


title: ChIP-Seq analysis of HSF1 in HCT116 WT cells upon heat shock treatment replicate1


title: RNA-Seq analysis in HCT116 WT cells upon heat shock treatment replicate 2


title: F_FSB_culture2_RNAseq

status: Public on Feb 15 2015

city: Houston

first: Naoki

last: Nakayama

state: Texas

address: 7000 Fannin, Suite 1200

department: Institute of Molecular Medicine

institute: the University of Texas Health Science Center at Houston

data_processing:
Sequenced reads were mapped against the human reference genome (GRCh37), using TopHat v2.0.12
Expression levels were calculated as fragments per kilobase of exon per million mapped fragments (FPKMs) using Cufflinks v2.1.1
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM

source_name: Neural crest-like progeny

growth_protocol: H9 hESCs were treated with collagenase to generate clumps, which were plated onto gelatin-coated dishes. The clumps were cultured for 6 days in Differentiation medium: CDM supplemented with 10 µM SB431542 at 37oC under 5% CO2/5% O2. The CDM (chemically defined medium) is Iscove modified Dulbecco’s Medium: Ham’s F12 (1:1), 5 mg/ml fatty acid-free bovine serum albumin, 2% (v/v) chemically defined lipid concentrate, 2 mM GlutaMax, 100  μg/ml holo-transferrin, 20 μg/ml insulin, 0.17 mM ascorbic acid-2-phosphate, and 0.4 mM monothioglycerol. On the day of harvest, a suspension of single cells was prepared by treatment of the culture with TrypLE Select diluted 2.5 fold with 0.5% (w/v) EDTA in PBS, and the CD271hiCD73- neural crest-like progeny were isolated by FACS, which were then plated onto fibronectin-coated dishes and cultured in CDM supplemented with FGF2 at 5-10 ng/ml and/or SB431542 at 3-5 µM (FSB or F) at 37oC under 5% CO2/5% O2. Generated cells were passaged every 3-4 days by the diluted TrypLE Select.

extract_protocol:
AT passage 6-7, cultures were havested and RNAs were extracted using RNAeasy mini kit from Qiagen.
RNA-sequencing libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent technologies, Santa Clara, CA).

treatment_protocol: The neural crest cells expanded under FSB for 4 passages were divided in half.  Then one was continuously manintained in FSB, and the other was culrured under F for 3 more passages.

value: ES-derived CD271+CD73+ neural crest-like progeny

tag: passages

value: 6 to 7

value: Nodal/Activin/TGFb inhibitor and FGF2 then FGF2 alone


title: FSB_culture3_RNAseq

value: Nodal/Activin/TGFb inhibitor and FGF2


title: NoRnt1p_rep1

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

description: incubated with cleavage buffer only

data_processing:
The IonTorrent sequencing data were generated using Ion 318™ Chip Kit and acquired using Ion PGM System and Torrent Suite 2.2 software.
5' adapter sequences were trimmed using cutadapt 1.2rc2.
Sequences shorter than 16 nts were removed and the remaining reads aligned to S. cerevisiae reference genome sequence using subread 1.3.5p4
Sequences with multiple matching positions were removed and reads ranging between 32 and 38 nucleotides were considered for further analysis.
Reads clusters consisting of 14 or more identical reads found in the cleaved and not the control samples were considered enriched.
Genome_build: R64-1-1
Supplementary_files_format_and_content: BED file were generated using bamToBed and further processed to remove reads aligned to duplicated genome regions and unaligned terminal nucleotides. Scores represent alignment quality. Text files contain count for reads between 32 and 38 nt.

organism: Saccharomyces cerevisiae

source_name: rnt1d yeast cells

growth_protocol: Yeast cells were grown and manipulated using standard procedures in YEP media supplemented with 2% dextrose at 26°C

extract_protocol:
Cells were lysed by vortexing in presence of glass beads and phenol and the total RNA extracted using standard phenol:chloroform extraction. 150 µg of total rnt1∆ RNA was incubated with 50 pmol of purified Rnt1p (Lamontagne Methods 2001) for 30 min at 30 °C in 500 ml of reaction buffer [30mM Tris–HCl (pH 7.5), 5mM spermidine, 0.1mM DTT, 0.1mM EDTA (pH7.5), 10mM MgCl2, 150mM KCl]. The reactions were stopped by Phenol phenol : Chloroform chloroform extraction, and the RNA recuperated using 95% salted ethanol precipitation.
Hundred µg of RNA cleaved with Rnt1p were purified using the mirVana™ miRNA Isolation Kit (Ambion, Life Technologies, Burlington, ON) to isolate RNA shorter than ~150 nucleotides. The cDNA libraries were generated from 500 ng of size selected RNA using the Ion Total RNA-Seq Kit v2.

treatment_protocol: Exponentially growing yeast cells were collected


title: F_FSB_culture3_RNAseq


title: F_culture1_RNAseq


title: F_culture2_RNAseq


title: FSB_culture1_RNAseq


title: F_culture3_RNAseq


title: DKONR_MEF2

status: Public on Feb 14 2015

city: Berkeley

first: Terry

middle: E

last: Machen

state: CA

address: 231 LSA

department: Molec/Cell Bio

institute: Univ California-Berkeley

data_processing:
Illumina Casava v1.8.0 software was used for basecalling.
Sequnced reads were mapped to mm9 whole genome using TopHat v2.0.9 with parameters -g 1 --no-novel-juncs --no-novel-indels
Gene level counts were measured using htseq-counts with parameters -m intersection-strict
Gene level counts were normalized across samples using DESeq package for R.
Differential expression between individual samples were measured using DESeq package for R, with padj < 0.01 as threshold.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample
Supplementary_files_format_and_content: normalized_readcounts.txt: abundance measurements
Supplementary_files_format_and_content: raw_readcounts.txt: abundance measurements
Supplementary_files_format_and_content: WTvsDKOr_diffexp.txt: DESeq output
Supplementary_files_format_and_content: WTvsDKOnr_diffexp.txt: DESeq output
Supplementary_files_format_and_content: DKOrvsDKOnr_diffexp.txt: DESeq output

source_name: Mouse embryo fibroblast

growth_protocol: Cells were grown in a humidified 95/5% air/CO2 incubator at 37°C. The cells were passaged at 1:5–1:10 dilutions and the remaining cell suspension was seeded directly onto a 12-well tissue culture plate.

extract_protocol:
Cells were grown to confluency in 12-well plates. Two wells of each cell line were used for library construction. Total RNA was isolated using Trizol reagent.
1 microgram of total RNA was used for library construction following standard Illumina protocols.

value: Mouse embryo fibroblast

value: Bak−/− Bax−/− (C12 non-reponsive)


title: F_FSB_culture1_RNAseq


title: DKOR_MEF2

value: Bak−/− Bax−/− (C12 responsive)


title: DKONR_MEF1


title: RNA-Seq analysis in HCT116 FBXW7 KO cells after recovery from heat shock treatment replicate 1


title: DKOR_MEF1


title: WT_MEF1

value: WT


title: WithRnt1p_rep1

description: incubated with purified Rnt1p and cleavage buffer


title: GM12892_Rep2_PolyARNA

city: Stanford

first: Can

last: Cenik

address: 300 Pasteur Dr, Alway Building Rm M344

department: Genetics

institute: Stanford University

data_processing:
Where applicable, 3’ adaptors were removed using cutadapt v.1.2.1 with the following parameters: --overlap=2 --minimum-length=21 --quality-cutoff=33.
Reads were aligned using Bowtie2 v.2.0.5 with a sequential strategy. Human rRNA and tRNA sequences were downloaded from UCSC Genome Browser (hg19) repeatmasker track. All reads mapping to these sequences were filtered out. The remaining reads were aligned using parameters “-L 18 --norc” to APPRIS principal transcripts (release 12) from the GENCODE mRNA annotation v.15. This step was followed by alignment to all GENCODE transcripts and finally to the human genome (hg19).
Alignments with a mapping quality greater than two were used for subsequent analyses. Reads mapping to coding regions, 5’UTRs, and 3’UTRs were counted separately using bedtools and custom scripts. For all transcript level analyses, reads that map only to coding regions were used.
The cell line identity for all ribosomal profiling libraries were verified by comparing empirically generated genotype calls to the reference genotypes. Specifically, we utilized samtools mpileup utility in combination with bcftools to generate genotype calls from the ribosomal profiling read alignments. Genotypes that were supported by at least 10 reads were retained using ‘vcfutils.pl varFilter -d10’. Finally, a custom perl script was used to compare the number of perfect matches between empirically called genotypes and the reference genotype that was available from HapMap and 1K Genomes.
Genome_build: hg19
Supplementary_files_format_and_content: Two processed data files are provided. These files contain the number of reads that map to the coding region of each APPRIS transcript. The column names specify the cell line identity and the replicate number.

molecule: polyA RNA

source_name: EBV-transformed lymphoblastoid cells

growth_protocol: Human lymphoblastoid cell lines (LCLs) were obtained from Coriell Cell Repository and grown in 15% fetal bovine serum and 1% Pen-Strep. For replicate experiments, cells were grown separately to a density of 0.8-1.0 x 10^6 cells/mL. Approximately 20 million cells were pelleted at 250g at 4C and washed with PBS.

extract_protocol:
For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies).
For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096).

value: EBV-transformed lymphoblastoid

tag: rna type

value: polyA RNA


title: GM19238_Rep3_PolyARNA


title: GM19239_Rep3_PolyARNA


title: GM12892_Rep1_PolyARNA


title: GM19240_Rep3_PolyARNA


title: GM19239_Rep2_PolyARNA


title: GM19240_Rep2_PolyARNA


title: GM19238_Rep2_PolyARNA


title: GM12891_Rep2_PolyARNA


title: GM12891_Rep3_PolyARNA


title: GM18526_Rep2

data_processing:
Library strategy: ribosome profiling
Where applicable, 3’ adaptors were removed using cutadapt v.1.2.1 with the following parameters: --overlap=2 --minimum-length=21 --quality-cutoff=33.
Reads were aligned using Bowtie2 v.2.0.5 with a sequential strategy. Human rRNA and tRNA sequences were downloaded from UCSC Genome Browser (hg19) repeatmasker track. All reads mapping to these sequences were filtered out. The remaining reads were aligned using parameters “-L 18 --norc” to APPRIS principal transcripts (release 12) from the GENCODE mRNA annotation v.15. This step was followed by alignment to all GENCODE transcripts and finally to the human genome (hg19).
Alignments with a mapping quality greater than two were used for subsequent analyses. Reads mapping to coding regions, 5’UTRs, and 3’UTRs were counted separately using bedtools and custom scripts. For all transcript level analyses, reads that map only to coding regions were used.
The cell line identity for all ribosomal profiling libraries were verified by comparing empirically generated genotype calls to the reference genotypes. Specifically, we utilized samtools mpileup utility in combination with bcftools to generate genotype calls from the ribosomal profiling read alignments. Genotypes that were supported by at least 10 reads were retained using ‘vcfutils.pl varFilter -d10’. Finally, a custom perl script was used to compare the number of perfect matches between empirically called genotypes and the reference genotype that was available from HapMap and 1K Genomes.
Genome_build: hg19
Supplementary_files_format_and_content: Two processed data files are provided. These files contain the number of reads that map to the coding region of each APPRIS transcript. The column names specify the cell line identity and the replicate number.

molecule: cytoplasmic RNA

extract_protocol:
For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm.
For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions.

treatment_protocol: For ribosome profiling experiments, the cell pellets were frozen in liquid nitrogen prior to cell lysis. Cells were lysed in 150ul of lysis buffer (20 mM Tris-HCl pH 7.5; 150 mM NaCl; 5mM MgCl2; 1mM DTT; 100 μg.ml-1 Cycloheximide; 1% Triton X-100; 25U.ml-1 Turbo DNase I). Lysate was homogenized using a P1000 pipettor and gently pipetting up and down. Lysate was then incubated at 4ºC for 10 minutes before centrifugation at 1300g for 10 minutes at 4ºC. The supernatant was recovered and absorbance at 260nm measured.

tag: adapter

value: AGATCGGAAGAGCACACGTCT

value: ribosome protected fragment


title: GM12878_Rep1_PolyARNA


title: WT_MEF2


title: GM18507_Rep1


title: GM19240_Rep1_PolyARNA


title: GM19240_Rep3


title: GM18526_Rep3


title: GM12878_Rep2_PolyARNA


title: GM19239_Rep1


title: GM19238_Rep3


title: GM19239_Rep2


title: GM19239_Rep1_PolyARNA


title: GM12878_Rep3_PolyARNA


title: GM19240_Rep1


title: GM19238_Rep1_PolyARNA


title: GM12892_Rep3_PolyARNA


title: GM12891_Rep1_PolyARNA


title: GM19238_Rep1


title: GM19240_Rep2


title: GM19200_Rep2


title: GM19201_Rep1


title: GM19139_Rep2


title: GM19193_Rep1


title: GM19138_Rep1


title: GM19137_Rep2


title: GM19099_Rep1


title: GM19098_Rep2


title: GM19098_Rep1


title: GM19137_Rep1


title: FSB_culture2_RNAseq


title: GM18951_Rep1


title: GM18526_Rep1


title: GM18519_Rep1


title: GM18951_Rep3


title: GM18951_Rep2


title: GM18523_Rep3


title: GM18870_Rep2


title: GM18522_Rep1


title: GM18522_Rep2


title: GM18511_Rep1


title: Mdo Ut Pregant

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

institute: The University of Chicago

data_processing:
Alignment: Sequence reads were obtained and mapped to the opossum genome (monDom5) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Genome_build: monDom5
Supplementary_files_format_and_content: Txt file containing the read counts mapped to genome. Data is shown as mapped bases per gene.

organism: Monodelphis domestica

source_name: Endometrium

extract_protocol:
Qiagen RNEasy kit with Dnase digestion
For RNA extraction we used a Qiagen RNeasy midi kit following the manufacturers protocol with an on-column DNase treatment. Libraries were prepared according to Illumina's instructions for mRNA-Seq using 75bp reads.

value: Endometrium


title: GM18504_Rep2


title: GM18504_Rep3


title: GM18502_Rep1


title: GM18501_Rep1


title: GM18501_Rep2


title: GM19138_Rep2


title: ko4

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: mm10
Supplementary_files_format_and_content: counts data

source_name: pancreatic islets

growth_protocol: Pancreatic islets were isolated as previously described by Shimomura et al. (2009) from 6 mice in each genotype. Briefly, mice were executed by cervical dislocation and the islets isolated by collagenase digestion (Sigma, final concentration 1 mg/mL). The inflated pancreas was dissected out and incubated in a 37°C water bath for 13 minutes. The tissue was washed twice with 0.2% BSA (Sigma) and HBSS (Sigma) solution. The islets were handpicked under stereomicroscope in 0.2% BSA and HBSS solution. Finally, the islets were picked into high glucose (4.5 g/L) DMEM/Ham's F12 media (PAA), containing 10% FBS (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco) and 20 mM L-glutamine (Invitrogen). Islets were incubated overnight at 37°C before insulin secretion assay or RNA isolation.

extract_protocol:
RNeasy Mini Kit
RNA-sequencing was used for transcriptome analysis. Pancreatic islets from 4 animals were used in each genotype group. Total RNA was isolated from islets using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol and cDNA for sequencing was synthesized using Ovation RNA-Seq System V2 (NuGEN Technologies, Inc.), 10 ng of total RNA was used. SOLiD DNA Fragment library kit (cDNA input 2 µg) was used to generate libraries and quality was controlled with the Agilent Bioanalyzer 2100 (Agilent Technologies) before sequencing. The libraries were marked with different barcodes and pooled together for the following template preparation. The automated SOLiD EZ Bead System and SOLiD EZ Bead E80 System Consumables (Life Technologies) were applied for the template preparation. For sequencing the SOLiD 5500xl System and paired end (75 bp forward and 35 bp reverse) chemistry for DNA sequencing was applied (Life Technologies).

value: pancreatic islets

value: wfs1 homozygous


title: ko3


title: ko2


title: GM18499_Rep2


title: GM18499_Rep1


title: GM18523_Rep1


title: GM12892_Rep2


title: ko1


title: hz1

value: wfs1 heterozygous


title: hz2


title: GM12891_Rep2


title: GM12892_Rep1


title: GM18505_Rep1


title: hz3


title: hz4


title: GM12890_Rep2


title: GM12891_Rep1


title: wt2

value: wild-type


title: GM12878_Rep2


title: wt1


title: wt3


title: GM12890_Rep1


title: GM10847_Rep1


title: wt4


title: GM12878_Rep1


title: HuR iCLIP_B cells 2

status: Public on Feb 13 2015

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: HuR-bound RNA molecules

data_processing:
See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Raw sequence reads were trimmed to remove both barcodes and adapters.
Remaining sequences were mapped to the mouse mm9_ensembl59 genome using Bowtie (Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).). Deduplication and identification of unique cDNA counts was performed based on the 4 random bases present in the barcode.
Position -1 of uniquely annotated reads to the genome was annotated as the HuR crosslink site.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: Bed files contain the annotation of unique individual-nucleotide HuR crosslinks to the genome.

source_name: Splenic B cells

growth_protocol: C57BL/6 mice were used for B cell isolation. They were maintained under Babraham Institute AWEEC and UK home Office regulation.

extract_protocol:
Prior extraction, cells were UV irradiated (150 mJ/cm2). Total protein lysis performed with RIPA buffer + sonication.
See Konig et al. (Nature Structural & Molecular Biology 17, 909–915 (2010))
Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP). Samples were multiplexed based on a 7 bases barcode (annotated in the raw file)

treatment_protocol: After isolation, splenic B cells were cultured in RPMI 1640 Medium (Dutch Modification) plus 5% FCS, antibiotics, 2 mM L-glutamine and Beta-mercaptoethanol (5 microMolar) at a density of 5x10^5 cells/ml. They were activated with LPS (10 micrograms/ml) for 48 hours.

value: Primary splenic B cells

tag: cell isolation

value: Negative selection using a cocktail of biotin-conjugated antibodies against CD43, CD4 , and Ter-119 (Mylteni 130-090-862)

tag: condition

value: LPS activated for 48 hours

value: Total cell extracts


title: HuR iCLIP_B cells 3

description: HuR-bound RNA molecules


title: HuR KO_LPS3 [Ribo-Seq]

data_processing:
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
Remaining sequences were mapped to the mouse GRCm38 genome using Tophat (Bioinformatics. 2009 May 1;25(9):1105-11. and http://ccb.jhu.edu/software/tophat/index.shtml). Read counting was performed using HTSeq. Ensembl annotation GRCm38.72 was used.
Differential gene expression analysis was performed using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2.” bioRxiv). Ensembl annotation GRCm38.72 was used for differential analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Files contain the report generated by DESeq2 after differential expression analysis.

growth_protocol: HuRflox/flox x mb1wt and HuRflox/flox x mb1cre mice were littermates. This mouse line was maintained under Babraham Institute AWEEC and UK home Office regulation.

extract_protocol:
ARTseq™ Ribosome Profiling Kit - Mammalian (Epicentre, RPHMR12126)
ARTseq™ Ribosome Profiling Kit - Mammalian (Epicentre, RPHMR12126). ScriptMiner™ Index PCR Primers used for sample multiplexing (Epicentre, Cat. No. SMIP2124)

value: HuRflox/flox x mb1cre

value: HuR KO

value: Splenic B cells negative selection using a cocktail of biotin-conjugated antibodies against CD43, CD4 , and Ter-119 (Mylteni 130-090-862)

value: LPS (48 hours)

tag: scriptminer index

value: CTTGTA


title: HuR KO_LPS2 [Ribo-Seq]

value: ACTTGA


title: HuR iCLIP_B cells 1

description: HuR-bound RNA molecules


title: GM18489_Rep1

value: EBV-transformed lymphoblastoid

value: AGATCGGAAGAGCACACGTCT


title: CD8 T cells CA-RIT-NFAT1-transduced BR2 RNA-Seq

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
The sequencing reads given in color-space were mapped to the mm9 genome and exon-exon junctions using Tophat. The exon-exon junctions were derived from the RefSeq gene annotations downloaded on June 16, 2012.
The number of reads falling into each RefSeq gene was quantified using the HTSeq-count script.
The RPKM values were calculated based on the read counts using a custom script.
Genome_build: mm9
Supplementary_files_format_and_content: The estimated gene expression values (RPKM, txt)

source_name: CD8 T cells transduced in vitro

growth_protocol: Naïve CD8 or CD4 T cells were stimulated, retrovirally transduced, expanded with IL-2 in vitro

extract_protocol:
RNA extraction was performed using Qiagen kit
SOLID library preparation protocol was followed

treatment_protocol: Transcution with empty vector or CA-RIT-NFAT1

value: CD8 T cells


title: CD8 T cells CA-RIT-NFAT1-transduced BR1 RNA-Seq


title: CD8 T cells Mock-transduced BR2 RNA-Seq


title: CD8 T cells Mock-transduced BR1 RNA-Seq


title: HuR KO_Ex vivo3 [Ribo-Seq]

value: Ex-vivo

value: GATCAG


title: WT_LPS3 [Ribo-Seq]

value: HuRflox/flox x mb1wt

value: Wild type

value: GCCAAT


title: WT_LPS2 [Ribo-Seq]


title: CD4 T cells CA-RIT-NFAT1-transduced BR2 RNA-Seq

source_name: CD4 T cells transduced in vitro

value: CD4 T cells


title: WT_Ex vivo3 [Ribo-Seq]

value: CGATGT


title: HuR KO_Ex vivo2 [Ribo-Seq]


title: HuR KO_Ex vivo1 [Ribo-Seq]


title: CD4 T cells CA-RIT-NFAT1-transduced BR1 RNA-Seq


title: CD4 T cells Mock-transduced BR2 RNA-Seq


title: WT_Ex vivo2 [Ribo-Seq]


title: HuR KO_LPS3

description:
supplementary file: RNAseq Analysis_DESeq_LPS_B_cells.txt
supplementary file: DEXSeq_Exon centric analysis.txt
supplementary file: DEXSeq_Intron centric analysis.txt

data_processing:
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
Remaining sequences were mapped to the mouse GRCm38 genome using Tophat (Bioinformatics. 2009 May 1;25(9):1105-11. and http://ccb.jhu.edu/software/tophat/index.shtml). Read counting was performed using HTSeq. Ensembl annotation GRCm38.72 was used for gene or exon annotation. Intron definition from Ensembl exon annotation was performed using custom scripts.
Differential gene expression analysis was performed using DESeq (Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome biology 11, R106). Ensembl annotation GRCm38.72 was used for differential analysis.
Differential exon usage analysis was performed using DEXSeq (Anders, S., Reyes, A., and Huber, W. (2012). Detecting differential usage of exons from RNA-seq data. Genome research 22, 2008-2017). Libraries generated from LPS-activated B cells were used. Ensembl annotation GRCm38.72 was used for differential analysis.
Differential intron usage analysis was performed using DEXSeq (Anders, S., Reyes, A., and Huber, W. (2012). Detecting differential usage of exons from RNA-seq data. Genome research 22, 2008-2017). Libraries generated from LPS-activated B cells were used. Ensembl annotation GRCm38.72 was used for differential analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Files contain the report generated by DESeq and DEXSeq after differential expression analysis.

extract_protocol:
RNA extraction using TriZol (life Technologies)
Illumina TruSeq mRNA sample prep kit (Barcodes used for sample multiplexing: ATGTCA, CAGATC, CGATGT, GTGAAA, TGACCA, CCGTCC, ACAGTG, GCCAAT, CTTGTA, AGTCAA)

tag: illumina barcode

value: ATGTCA


title: WT_Ex vivo1 [Ribo-Seq]


title: WT Mock P+I 1h NFAT1 IP

data_processing:
The custom barcodes were removed from the reads using a custom script.
The ChIP-seq sequencing libraries were mapped against mm9 using Bowtie.
Reads with identical sequences were filtered and only one was retained for subsequent analysis.
The coverage tracks (RPM normalized) were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The RPM normalized coverage tracks (bigWig)

source_name: Memory-like CTLs

growth_protocol: Naïve CD8 T cells were stimulated, retrovirally transduced, expanded with IL-2. On day 6, cells were restimulated with PMA/ionomycin

extract_protocol:
Sonicated chromatin was obtained and incubated with anti-NFAT1/proteinG beads
SOLID

treatment_protocol: Restimulation with PMA/Ionomycin

tag: antibody

value: anti-mouse NFAT1 (67.1)


title: CD4 T cells Mock-transduced BR1 RNA-Seq


title: NFAT1 KO Mock P+I 1h NFAT1 IP


title: NFAT1 KO CA-RIT-RV P+I 1h NFAT1 IP


title: NFAT1 KO Mock None NFAT1 IP


title: HuR KO_LPS1

value: HuRflox/flox x mb1cre

value: HuR KO


title: HuR KO_LPS1 [Ribo-Seq]

value: Splenic B cells negative selection using a cocktail of biotin-conjugated antibodies against CD43, CD4 , and Ter-119 (Mylteni 130-090-862)

value: LPS (48 hours)


title: WT_LPS1 [Ribo-Seq]

value: ATCACG


title: WT Mock None NFAT1 IP


title: NFAT1 KO CA-RIT-RV P+I 1h input

value: none (input)


title: WT_LPS4

value: CAGATC


title: WT_LPS3


title: NFAT1 KO Mock P+I 1h input

value: CD8 T cells


title: WT_LPS2

value: TGACCA


title: WT Mock P+I 1h input


title: WT_LPS1


title: NFAT1 KO Mock None input


title: NFAT1 KO CA-RIT-RV None input


title: NFAT1 KO CA-RIT-RV None NFAT1 IP


title: HuR KO_LPS5 [Ribo-Seq]

value: ACTTGA


title: WT Mock None input


title: HuR KO_Ex vivo3

description: supplementary file: RNAseq Analysis_DESeq_Ex vivo_B_cells.txt

value: Ex-vivo

value: GTGAAA


title: HuR KO_LPS2


title: HuR KO_Ex vivo2

value: AGTCAA


title: WT_Ex vivo4

value: HuRflox/flox x mb1wt

value: Wild type


title: WT_LPS4 [Ribo-Seq]


title: HuR KO_Ex vivo1

value: CTTGTA


title: HuR KO_Ex vivo4 [Ribo-Seq]


title: WT_LPS5 [Ribo-Seq]


title: WT_Ex vivo2

value: ACAGTG


title: WT_Ex vivo4 [Ribo-Seq]

value: GCCAAT


title: WT_Ex vivo3


title: WT_Ex vivo1

value: CGATGT


title: Input_DNA_Treatment

city: Bronx

first: Maria-Paz

last: Ramos

state: New York

address: 1301 Morris Park Ave, Price 314

institute: Albert Einstein College of Medicine

data_processing:
ChIP-seq reads were aligned by the WASP Pipeline version 3.1.5
MACS version 1.4.2 was used for peak finder and bowtie version 0.12.7 as aligner
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing information on called peaks (IP vs INPUT)

source_name: HEK 293T cells_input_treatment

growth_protocol: HEK 293T cells were grown in triplicates, in DMEM supplemented with 10% fetal bovine serum and 2 mM Penicillin-Streptomycin at 37°C in 5% CO2. Cells were passaged only when reaching 80-90% confluence, for a total period of one month.

extract_protocol:
3 million cells crosslinked in 1% formaldehyde were lysed with Farnham and RIPA cold lysis buffers. Following collection, the crude nuclear preparation was processed in a Bioruptor at the high setting for a total of 15 minutes, in cycles of 30 seconds on/30 seconds off. The chromatin was collected by centrifugation and incubated with 5 µg of RNAPII-Ser5(P) antibody overnight
The immunoprecipitated samples were end-filled using a combination of  T4 DNA polymerase and T4  polynucleotide kinase , 3’ -terminal-A extended with Klenow 5'-3' exo minus, and ligated to pre-annealed TruSeq indexed Illumina adapters. Libraries were amplified using Illumina primers and gel extracted for size selection and primer-dimer removal.  Before sequencing, libraries were tested using the BioAnalyzer to test quality in terms of size and primer-dimer depletion.

treatment_protocol: HEK 293T cells were treated for three days with 1.0 µM of 5-aza-CdR. Cells with no drug were grown as controls. Tissue culture medium was changed every day for both control and treated cells, to maintain the drug stability during treatment. After collection, treated cells were remained in culture for a further 30 days.

value: HEK 293T

value: non-malignant cell line

value: cells treated for three days with 1.0 µM of 5-aza-CdR


title: Input_DNA_Control

source_name: HEK 293T cells_input_control

value: control cells with no drug


title: RNAPII-Ser5(P)_ChIPSeq_Treatment

source_name: HEK 293T cells_IP_treatment

value: RNAPII-Ser5(P) (Active Motif, 61085)


title: HpaII_1.0R

data_processing:
Library strategy: HELP-tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).  Initial data processing was performed using the default read length of 36 bp.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: The wig files were generated using in house pipeline; Scores represent degree of unmethylation

source_name: HEK 293T cells, cells allowed to recover for one month after the 5-aza-CdR treatment

extract_protocol:
HEK 293T cells were collected by washing and trypsinizing for three minutes. The same procedure was performed with cells allowed to remain in culture for 30 days without the drug. Genomic DNA samples were extracted using standard protocols.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  One micrograms of genomic DNA were digested with HpaII and MspI in separate 50 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 1 μg of MspI/HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 98°C for 2 minutes, then 18 cycles of 98°C for 15 seconds, 60°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  The product then underwent gel extraction (Qiagen).


title: HuR KO_Ex vivo4

value: HuRflox/flox x mb1cre

value: HuR KO

value: Splenic B cells negative selection using a cocktail of biotin-conjugated antibodies against CD43, CD4 , and Ter-119 (Mylteni 130-090-862)


title: MRE_6hpf

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

data_processing:
Base-calls performed using CASAVA.
Raw sequencing reads were aligned to the danRer7 genome assembly using novoalign (V2.08.02) with the following parameter: -o SAM -r random -a -H.
The aligned reads were further processed using homemade perl scripts. These include bed sorting, MRE site filtering and calculating normalized score.
Genome_build: Zv9

organism: Danio rerio

source_name: embryo

extract_protocol:
Wild-type embryos were obtained through in vitro fertilization, grown in 28.5 °C egg water to develop and harvested at the desired stages. Chorions were removed with pronase and yolk was removed with ice-cold deyolking buffer (55 mM NaCl, 1.8mM KCl, 1.25 mM NaHCO3). Embryos were snap-frozen in liquid nitrogen and stored at -80 °C until time of use. The genomic DNA was isolated by incubating embryos in genomic DNA extraction uffer (50 mM Tris, 1 mM EDTA, 0.5 % SDS, 1 mg/mL Proteinase K) followed by phenol-chloroform extraction.
5 parallel digests (HpaII, Hin6I, SsiI, BstUI and HpyCH4IV; New England Biolabs) were performed, each with 200 ng of DNA. Digested DNA was combined, size-selected, end-processed, and ligated to single-end adapters. After the second size-selection, DNA was amplified by 15 cycles of PCR and size-selected by agarose gel electrophoresis.

tag: developmental stage

value: shield

tag: hours post fertilization

value: sjA


title: MRE_24hpf


title: HpaII_1.0T

source_name: HEK 293T cells, cells treated for three days with 1.0 µM of 5-aza-CdR

tag: cell type


title: MRE_3.5hpf

value: high

tag: strain


title: MRE_4.5hpf

value: dome


title: MRE_2.5hpf


title: HuR KO_LPS4 [Ribo-Seq]

tag: genotype

value: LPS (48 hours)

value: ACTTGA


title: MRE_sperm

source_name: sperm

value: sperm


title: MeDIP_24hpf

data_processing:
Base-calls performed using CASAVA.
Raw sequencing reads were aligned to the danRer7 genome assembly using novoalign (V2.08.02) with the following parameter: -o SAM -r random -a -H.
The aligned reads were further processed using homemade perl script. These include removing duplicated reads, bed sorting.
Genome_build: Zv9
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Wild-type embryos were obtained through in vitro fertilization, grown in 28.5 °C egg water to develop and harvested at the desired stages. Chorions were removed with pronase and yolk was removed with ice-cold deyolking buffer (55 mM NaCl, 1.8mM KCl, 1.25 mM NaHCO3). Embryos were snap-frozen in liquid nitrogen and stored at -80 °C until time of use. The genomic DNA was isolated by incubating embryos in genomic DNA extraction uffer (50 mM Tris, 1 mM EDTA, 0.5 % SDS, 1 mg/mL Proteinase K) followed by phenol-chloroform extraction.
500 ng of DNA isolated was sonicated, end-processed, and ligated to paired-end adapters. After agarose gel size-selection, DNA was immunoprecipitated using a mouse monoclonal anti-methylcytidine antibody. Immunoprecipitated DNA was washed, amplified by 12 cycles of PCR, and size-selected by agarose gel electrophoresis.


title: HpaII_Ct_repB

source_name: HEK 293T cells, control cells with no drug

tag: cell line


title: HpaII_Ct_repA


title: MeDIP_6hpf


title: 1.0_Recovery

description: DNase-treated, rRNA-depleted mRNA

data_processing:
sequencing reads were aligned by the WASP pipeline version 3.1.3 (rev. 6589), using gsnap (2012-07-20)
FASTQ files incorperate Phred quality scores. NOTE: In the raw sequence data fastq file reads failing Illumina's purity filter are removed automatically
Cuffflinks was performed for each sample to calculate FPKM values, specifying the strand of the reads (fr-fisrtstrand), performing an initial estimation of the number of reads mapping in multiple locations in the genome (-u), and normalizing by the upper quartile of the number of fragments mapping to individual loci (-N). To calculate differences in expression between samples, the cufflinks results were merged by cuffmerge using a mm9 GTF file obtained from the UCSC Genome Browser as a reference genome, and then used by cuffdiff to calculate differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: tables containing all RefSeq and lncRNA Genes, analyzed by Cufflinks (Cuffdiff) in order to calculate FKPM values.

extract_protocol:
HEK 293T cells were collected by washing and trypsinizing for three minutes. The same procedure was performed with cells allowed to remain in culture for 30 days without the drug. Total RNA was extracted with Trizol (Invitrogen) and rRNA depleted with Ribozero (Epicentre).
cDNA synthesis was performed by using oligo-dT as well as random hexamers.  Actinomycin D was added to the reaction to prevent any possible amplification from contaminating genomic DNA.  During second strand synthesis, a dU/VTP mix was used to create directional libraries.   Before library preparation, cDNA samples were Covaris-fragmented to 300 bp fragments.  The samples were then end-filled, 3’ terminal A-extended and ligated to pre-annealed TruSeq indexed Illumina adapters.  Uracil-DNA-glycosylase (UDG) treatment preceded the PCR reaction to cleave the uridine-containing strand and therefore identify the orientation of each transcript


title: MeDIP_4.5hpf


title: 1.0_5azaCdR_repB

description: DNase-treated, rRNA-depleted mRNA


title: 1.0_5azaCdR_repA

description: DNase-treated, rRNA-depleted mRNA


title: Control_repB

description: DNase-treated, rRNA-depleted mRNA


title: MeDIP_3.5hpf


title: RNAPII-Ser5(P)_ChIPSeq_Control

source_name: HEK 293T cells_IP_control

tag: treatment

tag: chip antibody


title: 8DAP PED

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

description: amplified poly-A RNA

data_processing:
Illumina HiSeq 2000 System
Raw reads were trimmed using the Trimmomatic program to remove adapter sequences and low-quality bases.
Trimmed high-quality reads were aligned to the maize reference genome using TopHat v2.0.9. Intron length was set to 30 to 8000 nt while maximum number of mismatches per read was set to 3.
Reads mapped to exonic regions were extracted using the intersect function of BEDTools v2.17.0, and were normalized using Cufflinks v2.1.1 to quantify the reproducibility of data between the biological triplicates.
Based on the high correlation of gene expression profiles between the biological replicates, exonic reads were merged to create a union of each triplicate and FPKM were recalculated for the merged samples.
Genome_build: B73_RefGen_v3 (Release 5b+)
Tab-delimited text files include FPKM, and the lower and upper bound FPKM values (i.e., FPKM_conf_lo and FPKM_conf_hi, respectively) for the 95% confidence interval of each gene as normalized by Cufflinks.

organism: Zea mays

source_name: Kernel

growth_protocol: Plants of the reference maize genotype, B73, were grown under greenhouse conditions (16-h day) at the University of Arizona during April-July 2012, and self-pollinated to obtain 8-DAP kernels for laser-capture microdissection.

extract_protocol:
RNA was extracted following manufacturer?s suggested protocol (ARCTURUS PicoPure kit, Applied Biosystems), checked for quality, DNase treated using TURBO DNase (Life Technologies), and further purified using the ARCTURUS PicoPure columns (Applied Biosystems). For each of the 22 sequenced samples, 10 ng purified RNA was used for cDNA synthesis and amplification. cDNA synthesis with oligo(dT) and random primers, and cDNA amplification were carried out using an Ovation RNA-Seq System V2 kit (Nugen Technologies Inc.) following manufacturer?s protocols with minor modifications.
Using an Illumina TruSeq DNA Sample Preparation Kit v2 (Part # 15026486 Rev. A, Illumina, Inc.), nearly 1 µg amplified cDNA for each of the 22 samples was used to generate multiplexed RNA-Seq libraries (mean size 350-380 bp, including 120-bp adapters) by following the manufacturer?s suggested procedures.

tag: tissues

value: vascular region of the pedicel

tag: age

value: 8 DAP


title: MeDIP_sperm


title: 8DAP PE

description: amplified poly-A RNA

value: pericarp


title: Control_repA

description: DNase-treated, rRNA-depleted mRNA

value: HEK 293T

value: non-malignant cell line


title: 8DAP PC

description: amplified poly-A RNA

value: placento-chalazal region


title: MeDIP_2.5hpf


title: INPUT_CTCF_ChIP-Seq

city: Leuven

first: Kristofer

last: Davie

state: Flemish-Brabant

address: Herestraat 49 Bus 602

department: Center for Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

description: Cells/Nuclei fixed

data_processing:
Basecalls were performed using CASAVA version 1.8.2
All samples were trimmed for adapter sequences using fastq-mcf and aligned to the dm3 (r5.53) genome using bowtie2 with the default configuration - samples were filtered using samtools for reads passing the command '-q 4'
ATAC-Seq reads were adjusted to create reads centered on the transposase binding site ( +4 bp Forward reads, -5 bp reverse reads) and extended 5 bp either way to better identify the open regions
Peaks were called using macs2 - ATAC-Seq and FAIRE-Seq parameters = '-g dm --nomodel --shiftsize 50 -q 0.01 -t (Sample)', ChIP parameters = '-g dm -q 0.01 -c (Input_Sample) -t (Sample)'
All peaks from ATAC-Seq and FAIRE-Seq samples were merged and htseq-count was used to quantify reads in each region. Peaks in heterochromatin and the mitochondrial genome were disregarded
Scales were determined by the ‘sizeFactors()’ command from DESeq2 on the matrix of all samples with all peaks, these scales were used to create normalized bigWig files for visualization using genomeCoverageBed (using the –scale option) and bedGraphToBigWig
Genome_build: dm3 Flybase r5.53
Supplementary_files_format_and_content: rawCounts for all merged peaks from all samples, merged bed files with final (merged) peaks, bed files with peaks for each individual sample, bigWig coverage data - created with genomeCoverageBed and bedGraphToBigWig (FAIRE-Seq and ATAC-Seq samples are scaled)

source_name: Eye-Antennal disc

growth_protocol: Larvae were grown on a regular yeast based media

extract_protocol:
ATAC-Seq - Nuclei were extracted from 10 eye-antennal discs . FAIRE-Seq - 150 Head complexes were first dissected,  fixed and lysed. 200 eye-antennal discs were the uncrosslinked and sonicated, phenol chloroform extraction was used for DNA purification.  ChIP-Seq - 750 Head complexes were first fixed, 1000 eye-antennal discs were then dissected and sonicated. Sonicated chromatin was then immunoprecipitated and purified using magnetic beads
ATAC-Seq libraries were prepared using a simple PCR reaction with adapters based against the transpon sequence. FAIRE-Seq and ChIP-Seq libraries were prepared using standard Illumina Protocols.

treatment_protocol: Eye-antennal discs were manually dissected from wandering third instar larvae in 1xPBS

value: CantonS

tag: sample type

value: ChIP Input

tag: Stage

value: Wandering third instar larvae

tag: tissue

value: Eye-Antennal disc

value: input


title: CTCF_ChIP-Seq

description: Cells/Nuclei fixed

value: CTCF Immunoprecipitated

value: CTCF


title: RasScrib-Late_FAIRE-Seq

description: Cells/Nuclei fixed

value: (y,w,eyFlp; act>y+>Gal4, UAS-GFP; FRT82,Tub-Gal80) x (y,w;UAS-RasV12;FRT82,scrib2)

value: Ras/Scrib Late


title: RasScrib-Early_FAIRE-Seq

description: Cells/Nuclei fixed

value: Ras/Scrib Early


title: 8DAP NU

description: amplified poly-A RNA

value: nucellus


title: 8DAP ESR rep3

description: amplified poly-A RNA

value: embryo-surrounding region


title: 8DAP ESR rep2

description: amplified poly-A RNA

value: 8 DAP


title: CantonS_FAIRE-Seq

description: Cells/Nuclei fixed

value: Control


title: RasScrib-Late_ATAC-Seq

description: Cells/Nuclei non-fixed


title: UPD-Overexpression-Rep2_ATAC-Seq

description: Cells/Nuclei non-fixed

value: (GMR-gal4) x (UAS-UPD:GFP)

value: UPD-Overexpression


title: UPD-Overexpression-Rep1_ATAC-Seq

description: Cells/Nuclei non-fixed


title: RasScrib-Early_ATAC-Seq

description: Cells/Nuclei non-fixed


title: FRT82_FAIRE-Seq

description: Cells/Nuclei fixed


title: 8DAP EMB rep3

description: amplified poly-A RNA

value: embryo


title: 8DAP EMB rep2

description: amplified poly-A RNA


title: 8DAP CZ rep2

description: amplified poly-A RNA

value: conducting zone


title: 8DAP CZ rep1

description: amplified poly-A RNA


title: RAL-208_ATAC-Seq

description: Cells/Nuclei non-fixed


title: Optix-GFP_ATAC-Seq

description: Cells/Nuclei non-fixed

value: Optix-GFP


title: FRT82_ATAC-Seq

description: Cells/Nuclei non-fixed

value: Wandering third instar larvae


title: 8DAP CSE rep2

description: amplified poly-A RNA

value: central starchy endosperm


title: 8DAP CSE rep3

description: amplified poly-A RNA


title: 8DAP BETL rep3

description: amplified poly-A RNA

value: basal endosperm transfer layer


title: 8DAP CSE rep1

description: amplified poly-A RNA


title: 8DAP BETL rep2

description: amplified poly-A RNA


title: 8DAP BETL rep1

description: amplified poly-A RNA


title: SigX_wildtype_sample3

status: Public on Feb 12 2015

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description: deletion control rep3

data_processing:
The untrimmed RNA-seq reads were mapped to the PA14 genome using the stampy aligner with default settings.
Differential expression was estimated using the DESeq R library using a pre-filtering step. The overexpressing samples were used together with the empty vector controls for negative binomial test. Similarly, the relevant controls for the knockout mutant were the wildtype samples.
For detection of differentially expressed genes, both replicates for each condition were used, thus the corresponding data were generated on the basis of 4 samples for each comparison. Details can be found in the supplementary table and in the quality control file.
Quality control of the replicates and a summary of the samples used in the different comparisons are provided as supplementary information.
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: DESeq output in CSV format presenting the differential gene expression after discarding rRNA/tRNA genes and the bottom 40% genes sorted by decreasing variance

organism: Pseudomonas aeruginosa

growth_protocol: Sigma factor hyper-expressing strains harboring the sigma factor gene in trans under control of the araBAD promoter and sigma factor deletion mutants were constructed. Under optimal conditions regarding sigma factor activity and optional induction of sigma factor expression, bacteria were harvested and total RNA was extracted.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, rRNA depletion using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmentation by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

tag: strain background

tag: genotype/variation

value: PA14 bacterial culture


title: 8DAP AL rep1

description: amplified poly-A RNA

value: aleurone


title: 8DAP AL rep2

description: amplified poly-A RNA


title: 8DAP EMB rep1

description: amplified poly-A RNA


title: 8DAP ESR rep1

description: amplified poly-A RNA


title: SigX_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: SigX_overexpression_vs_empty_vector.csv


title: SigX_wildtype_sample2

description: deletion control rep2


title: SigX_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: SigX_overexpression_vs_empty_vector.csv


title: SigX_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: SigX_knockout_vs_wild_type.csv


title: 8DAP CZ rep3

description: amplified poly-A RNA


title: RpoS_wildtype_sample1

description: deletion control rep1


title: SigX_empty_vector_sample1

description: overexpressing control rep1


title: SigX_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: SigX_knockout_vs_wild_type.csv


title: RpoS_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: RpoS_knockout_vs_wild_type.csv


title: RpoS_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: RpoS_overexpression_vs_empty_vector.csv


title: RpoS_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: RpoS_overexpression_vs_empty_vector.csv


title: RpoS_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: RpoS_knockout_vs_wild_type.csv


title: RpoS_empty_vector_sample1

description: overexpressing control rep1


title: RpoN_wildtype_sample1

description: deletion control rep1


title: RpoN_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: RpoN_overexpression_vs_empty_vector.csv


title: 8DAP AL rep3

description: amplified poly-A RNA


title: RpoN_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: RpoN_knockout_vs_wild_type.csv


title: RpoN_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: RpoN_knockout_vs_wild_type.csv


title: RpoN_empty_vector_sample2

description: overexpressing control rep2


title: PvdS_wildtype_sample1

description: deletion control rep1


title: PvdS_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: PvdS_overexpression_vs_empty_vector.csv


title: RpoN_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: RpoN_overexpression_vs_empty_vector.csv


title: RpoN_empty_vector_sample1

description: overexpressing control rep1


title: PvdS_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: PvdS_overexpression_vs_empty_vector.csv


title: RpoS_wildtype_sample2

description: deletion control rep2


title: FpvI_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: FpvI_overexpression_vs_empty_vector.csv


title: FpvI_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: FpvI_overexpression_vs_empty_vector.csv


title: FpvI_wildtype_sample1

description: deletion control rep1


title: PvdS_empty_vector_sample1

description: overexpressing control rep1


title: SigX_empty_vector_sample2

description: overexpressing control rep2


title: PvdS_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: PvdS_knockout_vs_wild_type.csv


title: FliA_wildtype_sample2

description: deletion control rep2


title: FpvI_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: FpvI_knockout_vs_wildtype.csv


title: FliA_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: FliA_overexpression_vs_empty_vector.csv


title: FpvI_empty_vector_sample1

description: overexpressing control rep1


title: FpvI_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: FpvI_knockout_vs_wildtype.csv


title: FliA_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: FliA_overexpression_vs_empty_vector.csv


title: FliA_empty_vector_sample2

description: overexpressing control rep2


title: FliA_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: FliA_knockout_vs_wild_type.csv


title: FliA_wildtype_sample1

description: deletion control rep1


title: FliA_empty_vector_sample1

description: overexpressing control rep1


title: FliA_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: FliA_knockout_vs_wild_type.csv


title: FecI2_wildtype_sample1

description: deletion control rep1


title: FecI2_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: FecI2_overexpression_vs_empty_vector.csv


title: FecI2_empty_vector_sample1

description: overexpressing control rep1


title: FecI2_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: FecI2_overexpression_vs_empty_vector.csv


title: FecI_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: FecI_overexpression_vs_empty_vector.csv


title: FecI_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: FecI_knockout_vs_wild_type.csv


title: FecI_empty_vector_sample1

description: overexpressing control rep1


title: AlgU_wildtype_sample2

description: deletion control rep2


title: PvdS_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: PvdS_knockout_vs_wild_type.csv


title: AlgU_wildtype_sample1

description: deletion control rep1


title: AlgU_overexpressed_sample2

description:
overexpressing wildtype rep2
processed data file: AlgU_overexpression_vs_empty_vector.csv


title: AlgU_knockout_mutant_sample2

description:
deletion mutant rep2
processed data file: AlgU_knockout_vs_wild_type.csv


title: AlgU_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: AlgU_overexpression_vs_empty_vector.csv


title: RpoH_control_sample1

description: ChIP-seq control rep1

data_processing:
Sequenced ChIP-seq reads were trimmed for adaptor sequence allowing for a minimal quality of 10 at their ends, then mapped to the PA14 genome using bowtie v0.12.7 with default parameters
ChIP-seq peaks were called using the SAM files and the MACS algorithm with the following options: -g 5200000 –nomodel --shiftsize=30 -p 0.05
Comparisons were performed in the following way: sample1 vs control1; sample2 vs control2
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: The MACS output files contain the coordinates of the enriched genomic regions as well as their P-values, false discovery rate (FDR) and fold enrichment

growth_protocol: PA14 wild type harboring a plasmid encoding for the polyhistidine-tagged sigma factor gene was cultivated under optimal conditions regarding sigma factor activity. In addition, sigma factor expression was strongly induced by adding L-arabinose (0.5%) to the culture for at least 45 minutes prior to formaldehyde-mediated cross-linking.

extract_protocol:
Polyhistidine-tagged sigma-factors were isolated by using anti6Xhis-antibodies (abcam) and magnetic beads coupled with protein-G (Invitrogen) on a rotator.
Immunoprecipitated DNA was linear amplified similar to the LinDA-ChIP-seq protocol published by Shankaranarayanan et al., Nature potocols, 2012. Library was constructed using the TruSeq DNA sample preparation kit according to the low-throughput protocol (Illumina).

treatment_protocol: DNA-protein crosslinking was performed by addition of formaldehyde to a final concentration of 0.5% for 5 minutes at ambient temperature. Reaction was quenched by addition of glycine to a final concentration of 137 mM. Cells were lysed in lysis buffer containing EDTA and lysozyme. Cells were disrupted and DNA was sheared by sonication.

tag: genotype/background

value: Anti-6X His tag  antibody - ChIP Grade

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: AlgU_empty_vector_sample2

description: overexpressing control rep2


title: AlgU_empty_vector_sample1

description: overexpressing control rep1


title: SigX_control_sample1

description: ChIP-seq control rep1

value: harboring a plasmid encoding for the polyhistidine-tagged sigma factor gene


title: AlgU_knockout_mutant_sample1

description:
deletion mutant rep1
processed data file: AlgU_knockout_vs_wild_type.csv


title: RpoH_chip_sample1

description: ChIP-seq treated rep1


title: RpoN_chip_sample1

description: ChIP-seq treated rep1


title: RpoS_chip_sample1

description: ChIP-seq treated rep1


title: SigX_chip_sample1

description: ChIP-seq treated rep1


title: RpoD_FliA_control_sample1

description: ChIP-seq control rep1


title: PvdS_chip_sample1

description: ChIP-seq treated rep1


title: FecI_overexpressed_sample1

description:
overexpressing wildtype rep1
processed data file: FecI_overexpression_vs_empty_vector.csv


title: PvdS_control_sample1

description: ChIP-seq control rep1


title: RpoD_chip_sample1

description: ChIP-seq treated rep1


title: FliA_chip_sample1

description: ChIP-seq treated rep1


title: AlgU_control_sample1

description: ChIP-seq control rep1


title: AlgU_chip_sample1

description: ChIP-seq treated rep1