title: ugpC KO rep2

status: Public on Sep 03 2016

city: davis

first: Ilias

last: Tagkopoulos

state: CALIFORNIA

address: 2063 kemper hall, 1 shields avenue

institute: university of california at davis

description:
ugpC_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

data_processing:
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample.
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most.
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings.
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0).
HTSeq is used to generate expression count for each gene.
Genome_build: RefSeq NC_000913.3
Supplementary_files_format_and_content: htcount : expression count for each gene and its name.

organism: Escherichia coli BW25113

source_name: Whole cell, ugpC KO, M9 and 0.4% glucose

growth_protocol: For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested.

extract_protocol:
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen).
Library constructed using KAPA Kit.

tag: strain/background

value: ugpC knockout

tag: media

value: 0.4% glucose


title: ugpC KO rep3

type: SRA

country: USA

description:
ugpC_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

library_source: transcriptomic

molecule: total RNA

tag: genotype/variation

tag: treatment


title: aspC KO rep2

description:
aspC_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, aspC KO, M9 and 0.4% glucose

value: aspC knockout


title: lplA KO rep3

description:
lplA_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, lplA KO, M9 and 0.4% glucose

value: lplA knockout


title: trpD KO rep2

description:
trpD_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, trpD KO, M9 and 0.4% glucose

value: trpD knockout


title: khc KO rep3

description:
khc_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, khc KO, M9 and 0.4% glucose

value: khc knockout


title: aspC KO rep1

description:
aspC_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: aspC KO rep3

description:
aspC_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: lplA KO rep2

description:
lplA_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: fliY KO rep1

description:
fliY_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, fliY KO, M9 and 0.4% glucose

value: fliY knockout


title: lplA KO rep1

description:
lplA_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: fliY KO rep2

description:
fliY_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: mhpD KO rep3

description:
mhpD_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, mhpD KO, M9 and 0.4% glucose

value: mhpD knockout


title: khc KO rep2

description:
khc_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: khc KO rep1

description:
khc_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: ugpC KO rep1

description:
ugpC_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: trpD KO rep3

description:
trpD_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: trpD KO rep1

description:
trpD_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: mhpD KO rep2

description:
mhpD_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: mhpD KO rep1

description:
mhpD_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: galE KO rep3

description:
galE_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, galE KO, M9 and 0.4% glucose

value: galE knockout


title: galE KO rep2

description:
galE_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: fliY KO rep3

description:
fliY_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: galE KO rep1

description:
galE_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: cysA KO rep2

description:
cysA_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, cysA KO, M9 and 0.4% glucose

value: cysA knockout


title: cysA KO rep1

description:
cysA_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: kefB KO rep3

description:
kefB_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, kefB KO, M9 and 0.4% glucose

value: kefB knockout


title: cysA KO rep3

description:
cysA_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: kefB KO rep2

description:
kefB_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: kefB KO rep1

description:
kefB_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: entF KO rep1

description:
entF_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, entF KO, M9 and 0.4% glucose

value: entF knockout


title: entF KO rep2

description:
entF_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: entF KO rep3

description:
entF_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: putP KO rep1

description:
putP_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, putP KO, M9 and 0.4% glucose

value: putP knockout


title: sdhC KO rep2

description:
sdhC_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, sdhC KO, M9 and 0.4% glucose

value: sdhC knockout


title: rfbA KO rep1

description:
rfbA_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, rfbA KO, M9 and 0.4% glucose

value: rfbA knockout


title: rfbA KO rep2

description:
rfbA_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: rfbA KO rep3

description:
rfbA_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: gabT KO rep3

description:
gabT_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, gabT KO, M9 and 0.4% glucose

value: gabT knockout


title: putP KO rep2

description:
putP_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: sdhC KO rep3

description:
sdhC_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: WT rep2

description:
WT_2
Parental strain.
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, WT, M9 and 0.4% glucose

value: WT


title: mgtA KO rep2

description:
mgtA_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

source_name: Whole cell, mgtA KO, M9 and 0.4% glucose

value: mgtA knockout


title: sdhC KO rep1

description:
sdhC_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.

value: 0.4% glucose


title: gabT KO rep2

description:
gabT_2
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: WT rep3

description:
WT_3
Parental strain.
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: gabT KO rep1

description:
gabT_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: mgtA KO rep1

description:
mgtA_1
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: fepA KO M9 rep2

description:
fepA_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, fepA KO, M9 and 0.3% glucose

value: fepA knockout

value: 0.3% glucose


title: lacA KO M9 rep2

description:
lacA_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, lacA KO, M9 and 0.3% glucose

value: lacA knockout


title: wzc KO M9 rep2

description:
wzc_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, wzc KO, M9 and 0.3% glucose

value: wzc knockout


title: wzc KO M9 rep1

description:
wzc_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: ppk KO M9 rep2

description:
ppk_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, ppk KO, M9 and 0.3% glucose

value: ppk knockout


title: putP KO rep3

description:
putP_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: ppk KO M9 rep1

description:
ppk_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: dcd KO M9 rep2

description:
dcd_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, dcd KO, M9 and 0.3% glucose

value: dcd knockout


title: mgtA KO rep3

description:
mgtA_3
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: fepA KO M9 rep1

description:
fepA_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: lacA KO M9 rep1

description:
lacA_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: fadr KO M9 rep1

description:
fadR_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, fadR KO, M9 and 0.3% glucose

value: fadR knockout


title: dcd KO M9 rep1

description:
dcd_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: WT rep1

description:
WT_1
Parental strain.
Batch 2
Bacteria grown for 8 h in M9 and 0.4% glucose.


title: Parent M9 rep1

description:
WT_M9_1
Parental strain.
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, WT, M9 and 0.3% glucose


title: lacA KO LB rep2

description:
lacA_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, lacA KO, LB and 0.3% glucose

value: LB


title: Parent M9 rep2

description:
WT_M9_2
Parental strain.
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: yghD KO LB rep2

description:
yghD_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, yghD KO, LB and 0.3% glucose

value: yghD knockout


title: cysH KO LB rep1

description:
cysH_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, cysH KO, LB and 0.3% glucose

value: cysH knockout


title: dcd KO LB rep2

description:
dcd_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, dcd KO, LB and 0.3% glucose


title: lacA KO LB rep1

description:
lacA_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: wzc KO LB rep2

description:
wzc_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, wzc KO, LB and 0.3% glucose


title: cysH KO LB rep2

description:
cysH_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: fepA KO LB rep2

description:
fepA_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, fepA KO, LB and 0.3% glucose


title: fadr KO M9 rep2

description:
fadR_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.


title: ppk KO LB rep2

description:
ppk_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, ppk KO, LB and 0.3% glucose


title: yghD KO M9 rep2

description:
yghD_M9_2
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

source_name: Whole cell, yghD KO, M9 and 0.3% glucose


title: cysG KO LB rep2

description:
cysG_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, cysG KO, LB and 0.3% glucose

value: cysG knockout


title: cysG KO LB rep1

description:
cysG_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: yghD KO LB rep1

description:
yghD_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: fepA KO LB rep1

description:
fepA_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: wzc KO LB rep1

description:
wzc_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: Parent LB rep1

description:
WT_LB_1
Parental strain.
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, WT, LB and 0.3% glucose


title: mouse OB_p11_control_no cre_rep1

city: Shanghai

first: Jiwen

last: Li

address: NO. 138 Yixueyuan Road

country: China

institute: Fudan University

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample.

organism: Mus musculus

source_name: mouse OB_p11_control_no cre

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The olfactory bulbs from P11 no cre littermate controls and Sp8/Sp9-DCKO mice were dissected in ice-cold HBSS. These tissues were flash frozen in the nitrogen and then stored into -80 oC

tag: strain

value: a mixed genetic background of C57BL/6J, 129S6 and CD1

tag: tissue

value: olfactory bulb

tag: age

value: postnatal day 11

value: control


title: mouse OB_p11_Sp8/Sp9-DCKO_Dlx5/6-CIE; Sp8 Flox/Flox; Sp9 Flox/Flox_rep2


title: fadr KO LB rep2

description:
fadR_LB_2
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

source_name: Whole cell, fadR KO, LB and 0.3% glucose


title: ppk KO LB rep1

description:
ppk_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: Control day 14 tibialis anterior muscle replicate 1

city: MELBOURNE

first: Jonathan

middle: Robert

last: Davey

state: VIC

address: 75 Commercial Rd

country: Australia

institute: Baker IDI Heart and Diabetes Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Transcriptome libraries were sequenced on an Illumina GAIIx instrument, with the resulting 36bp single-end reads mapped to the mouse genome (mm10 assembly) using TopHat
Gene transcript levels were determined via Cuffdiff in the form of FPKM (RPKM) values by correcting for multi reads and using geometric normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample with p-value and q-value for expression testing

molecule: polyA RNA

source_name: tibialis anterior muscle

extract_protocol:
Tibialis anterior muscles were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tibialis anterior muscle


title: Follistatin treated day 14 tibialis anterior muscle replicate 2

value: follistatin


title: Control day 7 tibialis anterior muscle replicate 2


title: Parent LB rep2

description:
WT_LB_2
Parental strain.
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.

value: WT


title: yghD KO M9 rep1

description:
yghD_M9_1
Batch 1
Bacteria grown for 12 h in M9 and 0.3% glucose.

value: 0.3% glucose


title: fadr KO LB rep1

description:
fadR_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: Control day 7 tibialis anterior muscle replicate 1


title: dcd KO LB rep1

description:
dcd_LB_1
Batch 1
Bacteria grown for 12 h in LB and 0.3% glucose.


title: Follistatin treated day 3 tibialis anterior muscle replicate 4


title: Control day 3 tibialis anterior muscle replicate 3


title: Control day 3 tibialis anterior muscle replicate 2


title: Follistatin treated day 3 tibialis anterior muscle replicate 3


title: mouse OB_p11_control_no cre_rep2


title: mouse OB_p11_Sp8/Sp9-DCKO_Dlx5/6-CIE; Sp8 Flox/Flox; Sp9 Flox/Flox_rep1


title: L_japonicus

status: Public on Sep 02 2016

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: Whole Genome Bisulphite Sequencing of L. japonicus

library_source: genomic

data_processing:
For MethylC-seq data: Reads were trimmed, aligned, and methylation called using the methylpy pipeline (Schultz et al. 2015). The genome is converted into a forward strand reference (all Cs to Ts) and a reverse strand reference (all Gs to As). Cutadapt (Martin et al. 2011) is used to trim adaptor sequences and then bowtie (Langmead et al. 2009) aligns reads to the two converted reference genomes. Only uniquely aligned reads are retained and the non-conversion rate calculated from unmethylated reads aligned to the chloroplast genome or spiked in unmethylated lambda DNA.
genome build: A. lyrata = v1.0; A. thaliana = TAIR10; A. trichopoda =  v1.0; B. distachyon = v2.1; B. oleracea = TO1000 v1.0; B. rapa = FPsc v1.3; B. vulgaris =  v1.1; C. clementina =  v1.0; C. rubella = v1.0; C. sativa =  canSat3; C. sativus =  v1.0; E. grandis =  v1.1; E. salsugineum = v1.0, F. vesca =  v1.1; G. max =  w82.a2.v1; G. raimondii =  v2.1; L. japonicus =  v2.5; M. domestica =  v1.0; M. esculenta =  v4.1; M. guttatus =  v2.0; M. truncatula =  Mt4.0v1; O. sativa =  v7.0; P. hallii = v0.5; P. persica =  v1.0; P trichocarpa =  v3.0; P. virgatum =  v1.1; P. vulgaris =  v1.0; R. communis =  v0.1; S. bicolor =  v2.1; S. lycopersicum =  iTAG2.3; S. viridis =  unpublished; T. cacao =  V1.1; V. vinifera =  GENOSCOPE.12X; Z. mays =  AGPv3.21 (6a)
processed data files format and content: MethylC-seq data (marked as “allc_total.tsv”) column 1 = chr = chromosome; column 2 = pos = coordinate for the cytosine position on the chromosome; column 3 = strand = + or - strand; column 4 = mc_class = context of the cytosine and the two following bases from the same strand; column 5 = mc_count = number of reads supporting a methylated cytosine; column 6 = total = total number of reads at that position; column 7 = methylated = cytosine is considered methylated if there is a 1 or unmethylated if there is a 0

molecule: genomic DNA

organism: Lotus japonicus

source_name: Lotus japonicus

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).

tag: accession

value: Gifu

value: leaf


title: M_domestica

description: Whole Genome Bisulphite Sequencing of M. domestica

organism: Malus domestica

source_name: Malus domestica

value: Borkh


title: yw embr AB+ 2

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: processed data file: ywAB_div_input_profile_in_10000bp_bins_1000bp_shift.wig.gz

data_processing:
The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample. Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment.
To build the whole genome profile, the data were smoothed using a 10kb sliding window, step 1kb.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing Log2 of the ChIP to input RPM ratio smoothed using a 10kb sliding window with 1000 bp step.

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were raised at 23°C

extract_protocol:
20 ul of 0-4h embryos were used as starting material. Abcam anti-H3K27me3 antibodies (6002) were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using Illumina Nextera protocol.

tag: genotype

value: yw

tag: chip antibody

value: Abcam anti-H3K27me3 (6002)

value: 0-4h embryos


title: SuUR embr input 2

description: processed data file: SUUR_AB_div_input_profile_in_10000bp_bins_1000bp_shift.wig.gz

value: SuUR mutant


title: Follistatin treated day 14 tibialis anterior muscle replicate 1


title: Follistatin treated day 7 tibialis anterior muscle replicate 1


title: yw embr input 1


title: Follistatin treated day 3 tibialis anterior muscle replicate 2


title: Control day 3 tibialis anterior muscle replicate 1


title: E_salsugineum_sRNA

description: small RNA sequencing of E. salsugineum

data_processing:
Small RNA-seq data: bed files of mapped sRNAs
genome build: A. lyrata = v1.0; A. thaliana = TAIR10; A. trichopoda =  v1.0; B. distachyon = v2.1; B. oleracea = TO1000 v1.0; B. rapa = FPsc v1.3; B. vulgaris =  v1.1; C. clementina =  v1.0; C. rubella = v1.0; C. sativa =  canSat3; C. sativus =  v1.0; E. grandis =  v1.1; E. salsugineum = v1.0, F. vesca =  v1.1; G. max =  w82.a2.v1; G. raimondii =  v2.1; L. japonicus =  v2.5; M. domestica =  v1.0; M. esculenta =  v4.1; M. guttatus =  v2.0; M. truncatula =  Mt4.0v1; O. sativa =  v7.0; P. hallii = v0.5; P. persica =  v1.0; P trichocarpa =  v3.0; P. virgatum =  v1.1; P. vulgaris =  v1.0; R. communis =  v0.1; S. bicolor =  v2.1; S. lycopersicum =  iTAG2.3; S. viridis =  unpublished; T. cacao =  V1.1; V. vinifera =  GENOSCOPE.12X; Z. mays =  AGPv3.21 (6a)
processed data files format and content: Small RNA-seq data: bed files of mapped sRNAs

organism: Eutrema salsugineum

source_name: Eutrema salsugineum sRNA

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
Small RNA-seq: Libraries were constructed using the TruSeq Small RNA Library Preparation Kit (Illumina Inc).

value: Shandong


title: Follistatin treated day 7 tibialis anterior muscle replicate 2


title: yw embr AB+ 1


title: Follistatin treated day 3 tibialis anterior muscle replicate 1


title: S_bicolor

description: Whole Genome Bisulphite Sequencing of S. bicolor

organism: Sorghum bicolor

source_name: Sorghum bicolor


title: SuUR embr input 1


title: M_guttatus

description: Whole Genome Bisulphite Sequencing of M. guttatus

organism: Erythranthe guttata

source_name: Mimulus guttatus


title: yw embr input 2


title: P_trichocarpa

description: Whole Genome Bisulphite Sequencing of P. trichocarpa

organism: Populus trichocarpa

source_name: Populus trichocarpa

value: Nisquilly


title: Wild-type, KLRG1-high [3d]

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and Illumina CASAVA sofware version 1.8.2.
Reads were aligned to the mouse genome with subread 1.4.4.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in RefSeq annotation.
Read counts from technical replicates of the same sample were summed.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: CD8+ T cells

extract_protocol:
Total RNA was prepared using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: P14 transgenic CD8+ T cells were isolated directly ex vivo from the spleen of naïve mice or those infected for eight days with LCMV-WE.

tag: background strain

value: Wild-type

tag: infection

value: Infected, KLRG1-high


title: SuUR embr AB+ 2


title: SuUR embr AB+ 1


title: H838 rep1

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

description: adapter sequence: CAGATCA

data_processing:
Instrument control: HiSeq Control Software v1.4.8
Base calling and quality scoring: Real Time Analysis v1.12.4.2
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8
Sequenced reads were mapped using the align function in the Rsubread package (version 1.16.1, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the in-built hg19 annotation in the reverse stranded mode.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with gene-level summarised read counts with columns representing samples and rows representing genes. The first column contains Entrez Gene IDs.

organism: Homo sapiens

source_name: H838 human lung cancer cell line

growth_protocol: Five lung adenocarcinoma cell lines (H2228, NCI-H1975, HCC827, H838 and A549) from a range of passages (2-4) were grown on 2 separate occasions in RPMI media (Gibco) supplemented with Glutamax and 10\% fetal calf serum to a 70\% confluence.

extract_protocol:
Total RNA was extracted from between half a million and million cells using Total RNA Purification Kit (Norgen Biotek) according to the kit instructions. RNA quality and concentration were assessed using Nanodrop and Tapestation RNA ScreenTape (Agilent) respectively.
1 ug of total RNA from each sample were used for RNA-seq library preparation using TruSeq Total Stranded RNA with Ribozero (Illumina) according to manufacturer's instructions. Completed libraries were sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility (AGRF), Melbourne.

treatment_protocol: To replicate common experimental conditions cell lines were treated with 0.01\% Dimethyl sulfoxide (Sigma), which is commonly used as a vehicle in drug treatment experiments. After 6 hours of treatment, cells were collected, snap-frozen on dry ice and stored at -80 degree C until required.

tag: cell line

tag: replicate


title: H838 rep2

description: adapter sequence: GCCAATA


title: H2228 rep1

description: adapter sequence: GATCAGA

source_name: H2228 human lung cancer cell line


title: A549 rep2

description: adapter sequence: TGACCAA

source_name: A549 human lung cancer cell line


title: HCC827 rep1

description: adapter sequence: ATCACGA

source_name: HCC827 human lung cancer cell line


title: Kat6a-KO, KLRG1-low [3a]

value: Kat6a knock-out

value: Infected, KLRG1-low


title: A549 rep1

description: adapter sequence: ACAGTGA


title: Wild-type, KLRG1-low [3c]


title: H2228 rep2

description: adapter sequence: ACTTGAA


title: HCC827 rep2

description: adapter sequence: TAGCTTA


title: Trdd2_3P_CBE KI rep3

city: Boston

first: Lijuan

last: Zhao

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: fragmentation by sonication

data_processing:
Library strategy: LAM-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils
Genome_build: Modified-mm9 genome, in which Tcra-Tcrd locus at positions chr14: 52971974-54848751 was replaced with a 1666365nt-long segment from the 129S1/SvImJ strain (NT_039614.1).
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of aligned prey junction, bait chromosome (B_Rname), beginning (B_Rstart) and end (B_Rend) nucleotide position of aligned bait junction, chromosome orientation of the bait junction (B_Strand), start (B_Qstart) and end (B_Qend) positions on the sequence read for the bait junction, start (Qstart) and end (Qend) position on the sequence read for the prey junction, the length of the sequence read (Qlen), the entire sequence read (Seq), sequence at the junction (J_Seq), and the experiment assocaited with the read (Library).

source_name: DN2/DN3 T cell precursors

growth_protocol: OP9-DL1 stromal cell lines were maintained in α-MEM (Invitrogen, 12571-071), supplemented with 20% FBS (Gibco, 10438-026). Flt3-L (R&D, 427FL), IL-7 (R&D, 407-ML) were purchased from R&D and used at concentration of 5ng/ml each in co-culture. After 14 days of monitoring of differentiation, stromal cells were excluded by staining with CD140a MicroBeads (Miltenyi Biotec, 130-101-547) and B cells were excluded by staining with an antibody to B220 (Miltenyi Biotec, 130-049-501). Genomic DNA was collected for LAM-HTGTS library preparation.

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using linear amplification-mediated HTGTS (LAM-HTGTS).

treatment_protocol: Genomic DNA was collected after 14 days of differentiation

tag: cell type

value: stromal cell line


title: Trdd2_3P_CBE KI rep2

description: fragmentation by sonication


title: H1975 rep1

description: adapter sequence: TTAGGCA

source_name: H1975 human lung cancer cell line


title: Kat6a-KO, KLRG1-high [2b]


title: Kat6a-KO, KLRG1-high [3b]


title: Kat6a-KO, KLRG1-low [2a]


title: Wild-type, KLRG1-high [2d]


title: Trdd2_3P_WT rep2

description: fragmentation by sonication


title: Trdd2_3P_WT rep3

description: fragmentation by sonication


title: Wild-type, KLRG1-low [2c]


title: Trdd2_5P_CBE KI rep2

description: fragmentation by sonication


title: Trdd2_5P_WT rep3

description: fragmentation by sonication


title: Trdd2_5P_CBE KI rep1

description: fragmentation by sonication


title: Kat6a-KO uninfected [282]

value: Uninfected


title: Wild-type uninfected [275]


title: Kat6a-KO uninfected [273]


title: H1975 rep2

description: adapter sequence: CGATGTA


title: Wild-type, KLRG1-high [1d]


title: Trdd2_3P_CBE KI rep1

description: fragmentation by sonication


title: Wild-type, KLRG1-low [1c]


title: Trdd2_3P_WT rep1

description: fragmentation by sonication

value: WT


title: P_persica

description: Whole Genome Bisulphite Sequencing of P. persica

organism: Prunus persica

source_name: Prunus persica

value: Lovell


title: Kat6a-KO, KLRG1-high [1b]


title: Trdd2_5P_WT rep1

description: fragmentation by sonication


title: Trdd2_5P_CBE KI rep3

description: fragmentation by sonication


title: Aldh+ KO_4

city: New York

first: Youngjung

middle: Rachel

last: Kim

state: NY

address: 1150 St. Nicholas Ave

department: Medicine

institute: Columbia University

data_processing:
RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
Tophat v2.0.4 to map the reads to a mm9 with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: FAC-sorted cells

extract_protocol:
Isolated primary islets from control (triple heterozygous for FoxO 1, 3, 4) or knockout (triple knockout for FoxO 1, 3, 4) mice, and isolated ALDH1A3-espressing cells from the islets. The cell-permeable fluorescent ALDH substrate BODIPY™-aminoacetaldehyde (aldeflour) is metabolized to the non-releasable derivative BODIPY™-aminoacetate (BAA), thus permanently labeling ALDH-expressing cells. We used RFP to label beta (or former beta) cells by cre-mediated recombination. Thereafter, we incubated cells with aldefluor, and selected for RFP (red) and aldefluor (green) fluorescence, yielding ALDH– and ALDH+ cells. The latter should include dysfunctional/dedifferentiating β cells. In wild-type mice, we obtained three sub-populations: RFP–ALDH– (non-beta cells), RFP+ALDH– (healthy beta cells), and RFP+ALDH+ (dysfunctional beta cells). We used the beta cell subpopulations from control or KO islets (RFP+ALDH- and RFP+ALDH+) and performed total RNA isolation using the RNeasy Mini Kit (QIAGEN).
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed to library preparation by using Illumina TruSeq RNA prep kit.

tag: foxo 1 genotype

value: KO

tag: foxo 3 genotype

tag: foxo4 genotype

tag: cre

value: Pdx-Cre

value: islet

tag: tissue genotype category

value: FoxO Triple KO

tag: aldh expression

value: sorted beta cells

tag: sorted cell type category

value: Aldh+ FoxO tKO

value: mixed 129JC57BL/6


title: Aldh+ KO_5

tag: tissue


title: Aldh+ KO_3

value: RIP-Cre


title: Aldh+ Ctrl_2

value: Het

value: FoxO Triple Heterozygous

value: Aldh+ FoxO Het


title: Aldh- KO_5

value: Aldh- FoxO tKO


title: Aldh- KO_4


title: B_distachyon_RNA

description: RNA sequencing of B. distachyon

data_processing:
For RNA-seq data: Raw FASTQ reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32 (Bolger et al. 2014). Reads were aligned using Tophat v2.0.13 (Trapnell et al. 2010) supplied with a reference GFF file and the following arguments: -I 50000 --b2-very-sensitive --b2-D 50. Transcripts were then quantified using Cufflinks v2.2.1 (Trapnell et al. 2012) supplied with a reference GFF file.
genome build: A. lyrata = v1.0; A. thaliana = TAIR10; A. trichopoda =  v1.0; B. distachyon = v2.1; B. oleracea = TO1000 v1.0; B. rapa = FPsc v1.3; B. vulgaris =  v1.1; C. clementina =  v1.0; C. rubella = v1.0; C. sativa =  canSat3; C. sativus =  v1.0; E. grandis =  v1.1; E. salsugineum = v1.0, F. vesca =  v1.1; G. max =  w82.a2.v1; G. raimondii =  v2.1; L. japonicus =  v2.5; M. domestica =  v1.0; M. esculenta =  v4.1; M. guttatus =  v2.0; M. truncatula =  Mt4.0v1; O. sativa =  v7.0; P. hallii = v0.5; P. persica =  v1.0; P trichocarpa =  v3.0; P. virgatum =  v1.1; P. vulgaris =  v1.0; R. communis =  v0.1; S. bicolor =  v2.1; S. lycopersicum =  iTAG2.3; S. viridis =  unpublished; T. cacao =  V1.1; V. vinifera =  GENOSCOPE.12X; Z. mays =  AGPv3.21 (6a)
processed data files format and content: RNA-seq data column 1 = gene_ID = gene identifier; column 2 = FPKM = gene expression in fragments per kilobase per million (FPKM)

organism: Brachypodium distachyon

source_name: B. distachyon RNA

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
RNA-seq: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

value: leaf


title: Aldh+ Ctrl_1


title: Aldh- KO_1


title: B_distachyon

description: Whole Genome Bisulphite Sequencing of B. distachyon (Bd21)

source_name: Brachypodium distachyon (Bd21)


title: Kat6a-KO, KLRG1-low [1a]

value: Kat6a knock-out

value: Infected, KLRG1-low


title: Aldh- Ctrl_3

value: Aldh- FoxO Het


title: input

city: Pasadena

first: Chun-Kan

last: Chen

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

data_processing:
Base-calling was performed using Illumina software
Sequenced paired-end reads were aligned to mm9 genome with Bowtie2 using the following parameters: -k 1 -p 12 --very-sensitive-local --maxins 2000 --fr --no-discordant --no-mixed no-unal
We identified protein binding sites on the Xist RNA by identifying regions that were enriched relative to the same region in the input control ("differential enrichment") and also was enriched relative to all other regions on the remainder of the Xist RNA ("local enrichment").
To compute significant enrichment, we computed the differential enrichment as IP/Input for each window (window size=100 nucleotides). We computed the local enrichment for each region by taking the normalized number of reads for each region (IP) and dividing it by the normalized number of reads over the entire Xist RNA.
To make these rates comparable, we divided each number by their respective region length prior to taking the ratio. We then generated 1,000 random permutations of the reads in the IP samples and paired input samples across the Xist RNA. For each permutation, we computed the differential and local enrichments and generated an empirical distribution of the maximum value observed for each permutation.
We assigned a multiple-testing corrected p-value to each region by comparing the observed differential and local enrichment values to these permutation distributions. We identified significant windows that had a differential p-value <0.01 and a local p-value<0.01.
We computed the enrichment for the Xist region by normalizing the number of reads upon immunoprecipitation with a specific protein relative to the number of reads in its input control (input sample). Specifically, we counted the total number of reads overlapping the Xist RNA region (negative strand in genomic alignments) in either the immunoprecipitation sample or the input control. To account for differences in read coverage between samples, each of these numbers was normalized to the total number of reads within the same experiment. This generates a normalized score, per region, within each sample. We then computed an enrichment metric by taking the ratio of these normalized values (IP/Input).
Genome_build: mm9
Supplementary_files_format_and_content: .bed files showing identified binding sites of SHARP, LBR, and PTBP1 on Xist transcript.

source_name: mouse ES cells

extract_protocol:
We crosslinked 6 hour doxycycline-induced pSM33 mouse male ES cells with 0.4 J/cm2 of UV254. Cells were lysed and RNA was digested with RNase I to achieve a size range of 100-500 nucleotides in length. For each CLIP sample, target proteins were immunoprecipitated from 20 million cells with antibody pre-coupled with Protein G beads. Samples were then washed and RNAs were eluted with NLS elution buffer with 100 mM DTT. Samples were then run through a standard SDS-PAGE gel and transferred to a nitrocellulose membrane, and a region 75 kDa above the molecular size of the protein of interest was isolated and treated with protease followed by phenol/chloroform/isoamyl alcohol extraction to isolate the RNAs.
The purified RNA in each sample was dephosphorylated and ligated to a mixture of barcoded adapters in which each adapter had a unique barcode identifier and Illumina sequencing libraries were generated according to our Massively Multiplexed RNA Sequencing method.

tag: treatment

value: doxycycline-induced

tag: gender

value: male


title: PTBP1 binding sites

tag: binding sites


title: Aldh- Ctrl_2


title: Aldh- Ctrl_1


title: Aldh+ KO_2

value: KO


title: SHARP binding sites

value: SHARP


title: LBR binding sites

value: LBR


title: Aldh+ KO_1

value: islet

value: FoxO Triple KO

value: sorted beta cells


title: C_clementina

description: Whole Genome Bisulphite Sequencing of C. clementina

organism: Citrus x clementina

source_name: C clementina

tag: accession

value: Clemenules (haploid)


title: 3077-SH-8_KO1_nonGC

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

data_processing:
Read alignment performed with TopHat (v.2.0.11)
Differential gene expression determined by Cuffdiff (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including RPKM values and log2 fold change in gene expression comparing Hdac3 knockout to wt samples and non-GC to GC samples

source_name: sorted splenic B cells

extract_protocol:
RNA was extracted by Trizol from sorted splenic B cell populations
libraries prepared from polyA enriched RNAs by standard Illumina protocols

treatment_protocol: 6-8 wk old mice were sacrificed 10 days following I.P. injection with sheep red blood cells.  Single cell suspensions were obtained from spleens and they were stained for surface B220 and GL7.

tag: strain

tag: genotype/variation

value: Hdac3 KO

tag: protocol

value: I.P. injection with sheep RBCs

value: spleen

value: B cell

tag: cell subpopulation


title: 3077-SH-9_KO2_GC

tag: cell type


title: 3077-SH-7_KO1_GC


title: Aldh- KO_3

tag: foxo 1 genotype

value: RIP-Cre

value: Aldh- FoxO tKO

tag: background strain

value: mixed 129JC57BL/6


title: S_viridis

description: Whole Genome Bisulphite Sequencing of S. viridis

organism: Setaria viridis

source_name: Setaria viridis

value: leaf


title: 3077-SH-6_WT2_nonGC

value: WT


title: 3077-SH-5_WT2_GC


title: 3077-SH-1_WT1_GC


title: WT H3K36me3_ChIPSeq

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

description: ChIPSeq_consensusPeaks_K36me3_normalizedReadCounts.xls

data_processing:
Basecalls performed using bcl2fastq version 2.16.0
data were filtered using Trimmomatic software version 0.32 with the following setting: TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 version 2.2.3
peaks were called using MACS2 version 2.1.0 with the following setting: callpeak -t <ChIP tag file> -c <control tag file> -f BED -g 'mm' --nomodel –extsize=250 --bdg –-broad -n <output peak file>
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and TMM normalized read counts were obtained using DiffBind library in R version 3.1.1. Consensus peaks were annotated using HOMER software.

source_name: Sorted neutrophils

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
libraries were prepared using the KAPA Hyper Prep Kit

value: neutrophil

tag: passages

value: ex vivo non-cultured

value: WT (C57BL6)

tag: chip antibody

value: Rabbit polyclonal to Histone H3 (tri methyl K36) - ChIP Grade ( Abcam ab9050)


title: WT input DNA

value: normal rabbit IgG _200 µg/0.5 ml  (Santa Cruz sc-2027)


title: 3077-SH-2_WT1_nonGC


title: WT H3K4me1_ChIPSeq

description: ChIPSeq_consensusPeaks_K4me1_normalizedReadCounts.xls

value: Rabbit polyclonal to Histone H3 (mono methyl K4) - ChIP Grade  (Abcam ab8895)


title: DA-EC8/Rrrc_Sample 2

city: Columbia

first: Elizabeth

middle: C

last: Bryda

state: MO

address: 4011 Discovery Ridge

institute: University of Missouri

data_processing:
Basecalls performed by Casava v1.8 using default settings
RNA-seq reads aligned to rn5 using TopHat (v1.4.0)
Bam files generated uploaded to Avadis NGS (v 1.3)
Alignment performed against RefSeq (10/20/2012) build
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: RPKM-Refseq.txt (supplementary file linked to Series record) reports RPKMs.

organism: Rattus norvegicus

source_name: Embryonic Stem Cell

growth_protocol: Cells grown according to Rat Resource Center (http://www.rrrc.us/ES_Cells___/) protocol using 2i media.

extract_protocol:
Total RNA extracted by Trizol (Invitrogen) followed by RNA cleanup protocol using Qiagen Rneasy following manufactor's protocol.  RNA integrity analyzed by RNA nano chip on Agilent 2100 Bioanalyzer as RNA integrity (RIN) number.
3.5 ng of total RNA using TruSeq RNA sample preparation kit v2 (Illumina, San Diego, CA)

tag: cell line

value: RRRC#464 DA-EC8/Rrrc cell line

tag: passage

tag: karyotype

value: Normal

value: Dark Agouti


title: KO input DNA

value: Morrbid deficient (Background - C57BL6)


title: KO H3K36me3_ChIPSeq


title: KO H3K4me3_ChIPSeq

description: ChIPSeq_consensusPeaks_K4me3_normalizedReadCounts.xls

value: Rabbit polyclonal to Histone H3 (tri methyl K4) - ChIP Grade  (Abcam ab8580)


title: DA-EC8/Rrrc_Sample 1


title: WT_2 ATAC-Seq

data_processing:
Basecalls performed using bcl2fastq version 2.16.0
Data were filtered using Trimmomatic software version 0.32 with the following setting: TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
ChIP-seq reads were aligned to the mm9 genome assembly using BWA with 'mem' option
Peaks were called using MACS2 version 2.1.0 with the following setting: callpeak -t <ATAC tag file> -f BAMPE -n <output peak file> -g 'mm' --nomodel -B
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and TMM normalized read counts were obtained using DiffBind library in R version 3.1.1. Consensus peaks were annotated using HOMER software.

source_name: Sorted Neutrophils

extract_protocol:
WT and KO cells were isolated and flow sorted from bone marrow and 50,000 of each geneotype were used for transposition in duplicate.
ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688

value: Neutrophils

value: non-cultured


title: Aldh- KO_2

value: KO

tag: foxo 3 genotype

tag: foxo4 genotype

tag: cre

value: RIP-Cre

tag: tissue

value: islet

tag: tissue genotype category

value: FoxO Triple KO

tag: aldh expression

value: sorted beta cells

tag: sorted cell type category

value: Aldh- FoxO tKO


title: KO H3K27ac_ChIPSeq

description: ChIPSeq_consensusPeaks_K27ac_normalizedReadCounts.xls

value: neutrophil

value: ex vivo non-cultured

tag: strain

value: Rabbit polyclonal to Histone H3 (acetyl K27) - ChIP Grade  (Abcam ab4729)


title: 3077-SH-10_KO2_nonGC

tag: genotype/variation

value: Hdac3 KO

tag: protocol

value: I.P. injection with sheep RBCs

value: spleen

value: B cell

tag: cell subpopulation


title: F_vesca

description: Whole Genome Bisulphite Sequencing of F. vesca

organism: Fragaria vesca

source_name: Fragaria vesca (Hawaii4) micropropagated

tag: accession

value: leaf


title: WT_1 ATAC-Seq

tag: cell type

tag: passages

value: WT (C57BL6)


title: M_esculenta

description: Whole Genome Bisulphite Sequencing of M. esculenta

organism: Manihot esculenta

source_name: Manihot esculenta


title: KO_2 ATAC-Seq

value: Neutrophils

value: Morrbid deficient (Background - C57BL6)

tag: chip antibody


title: KO H3K4me1_ChIPSeq

value: Rabbit polyclonal to Histone H3 (mono methyl K4) - ChIP Grade  (Abcam ab8895)


title: Cucumis_sativus

description: Whole Genome Bisulphite Sequencing of C. sativus

organism: Cucumis sativus

source_name: Cucumis sativus


title: E_grandis

description: Whole Genome Bisulphite Sequencing of E. grandis

organism: Eucalyptus grandis

source_name: Eucalyptus grandis


title: KO_1 ATAC-Seq

organism: Mus musculus

value: non-cultured


title: WT H3K27ac_ChIPSeq


title: WT H3K4me3_ChIPSeq

value: Rabbit polyclonal to Histone H3 (tri methyl K4) - ChIP Grade  (Abcam ab8580)


title: Cannabis_sativa

description: Whole Genome Bisulphite Sequencing of C. sativa

organism: Cannabis sativa

source_name: Cannabis sativa

value: Purple Kush


title: B6_thymocytes_input

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

data_processing:
Paired-end sequencing (101bp x2) was performed on the HiSeq1500 system (illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Reads from each sample were first trimmed by removing adapters and low quality bases at ends using Trimmomatic 0.22.
Approximately the same number of reads (30 ~ 60 million reads) for a pair of ChIP and corresponding input libraries were aligned to the mouse reference genome (mm9) using the Burrows-Wheeler Aligner 0.6.2.
Uniquely mapped reads were selected by a custom script, converted from sam to bam using SAMtools 0.1.18. Reads with mapping quality < 20 were removed using SAMtools 0.1.18.
The resultant bam files were visualized using the Integrative Genomics Viewer (IGV). The uniquely mapped reads were analysed using the MACS algorithm implemented in the Avadis NGS softwere (Agilent) to identify ChIPseq peaks using the matched input DNA reads as a control.
Genome_build: mm9
Supplementary_files_format_and_content: MACS peak calling output

source_name: Thymocytes

extract_protocol:
Thymocytes (1.5 × 10^8 cells) from 4 to 5-weeks-old C57BL/6, Zfatf/f or Zfatf/f-LckCre mice were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking reaction was quenched with 125 mM glycine for 5 min. The cells were rinsed with PBS twice and incubated in 600 µl of MNase treated buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% NP-40, 5 mM CaCl2) containing 375 unit MNase (Roche) for 0.5 h at 37°C. The MNase reaction was stopped by adding 600 µl of lysis buffer  (100 mM Tris-HCl, pH 8.0, 20 mM EDTA, 2% SDS, protease inhibitor cocktail (Roche)), and the lysate was sonicated using a Bioruptor (Cosmo Bio, Tokyo, Japan) for two cycles of one minute with 30 seconds on/off. The sonicated lysate was subjected to immunoprecipitation with a monoclonal antibody against ZFAT (prepared in Dr. Shirasawa's lab), H3K9me3 (MBL), or H3K9ac/K27ac (MBL).
The immunoprecipitated DNA was purified using MinElute Reaction Cleanup kit (Qiagen) according to the manufacturer’s instructions. ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set and Multiplex Oligos for Illumina (New England Biolabs) according to manufacturer's instructions. ChIP or input DNA (0.1 ~ 1 ng) was subjected to end repair, dA-tailing, and adaptor-ligation, and amplified by 6-13 cycles of PCR.

value: Thymus


title: F_vesca_seed

description: Whole Genome Bisulphite Sequencing of F. vesca (Hawaii4) propagated from seed

source_name: Fragaria vesca (Hawaii4) grown from seed


title: B_rapa_RNA

description: RNA sequencing of B. rapa

organism: Brassica rapa

source_name: B. rapa RNA

value: FPsc


title: B6_thymocytes_ZFAT_ChIPseq


title: Cucumis_sativus_RNA

description: RNA sequencing of C. sativus

source_name: C. sativus RNA


title: M_truncatula

description: Whole Genome Bisulphite Sequencing of M. truncatula

organism: Medicago truncatula

source_name: Medicago truncatula


title: B6_thymocytes_IgG_ChIPseq


title: C_sativus_sRNA

description: small RNA sequencing of C. sativus

source_name: Cucumis sativus sRNA


title: R_communis_sRNA

description: small RNA sequencing of R. communis

organism: Ricinus communis

source_name: Ricinus communis sRNA


title: M_esculenta_seed

description: Whole Genome Bisulphite Sequencing of M. esculenta offspring from grown from seed

source_name: Manihot esculenta grown from seed


title: E_grandis_sRNA

description: small RNA sequencing of E. grandis

source_name: Eucalyptus grandis sRNA


title: V_vinifera

description: Whole Genome Bisulphite Sequencing of V. vinifera

organism: Vitis vinifera

source_name: Vitis vinifera

value: Pinot Noir


title: B_vulgaris

description: Whole Genome Bisulphite Sequencing of B. vulgaris

organism: Beta vulgaris

source_name: Beta vulgaris


title: R_communis

description: Whole Genome Bisulphite Sequencing of R. communis

source_name: Ricinus communis


title: M_esculenta_parent

description: Whole Genome Bisulphite Sequencing of M. eculenta clonally propagated parent

source_name: Manihot esculenta clonal propagated


title: Cucumis_sativus_rep2

description: Whole Genome Bisulphite Sequencing of C. sativus 2nd rep

source_name: Cucumis sativus rep2


title: tl10b_h3k27ac_4

status: Public on Sep 01 2016

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute for Medical Research

description: ChIP-seq for H3K27ac in Toll10b (replicate 3)

data_processing:
RNA-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to FlyBase r5.57 genome and gene annotations using Tophat v2.0.14.
Differential gene expression was determined using cuffdiff (Cufflinks v2.2.1) between the three mutant genotypes (Toll10b, Toll rm9/rm10, gd7)
----------------------------------------------
ATAC-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 25 bp each and aligned to the UCSC Drosophila melanogaster dm3 genome with Bowtie 1.1.2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
Genome_build: UCSC dm3
BigWig files contain per-base coverage of all aligned read pairs
----------------------------------------------
ChIP-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

organism: Drosophila melanogaster

source_name: tl10b embryos

growth_protocol: Adult flies were used in population cages for embryo collections and embryos were collected on apple juice plates for 2 h at 25°C in cages and then matured at 25°C for another 2 h (2-4 h after egg deposition (AED)).

extract_protocol:
ChIP-seq experiments were performed as described (He et al 2011, Nature Genet, He et al 2015, Nature Biotech) with the following differences: ~100 mg embryos were used per IP. After incubation of magnetic beads with antibodies, H3K27ac IP samples were washed 3 times by rotating tubes for 3 min at 4°C to reduce background.
Several different methods were used for library construction, please refer to the supplemental material of Koenecke et al 2016, Genome Research or Koenecke and Johnston, 2016, Genome Biol

treatment_protocol: Embryos were dechorionated for 1 min with 100% bleach and then cross-linked for 15 min with 1.8% formaldehyde (final concentration in water phase).

tag: developmental stage

value: 2-4 hr after egg deposition

tag: barcode-kit

value: H3K27ac (Active Motif Carlsbad, CA, #39133)

tag: library-kit

value: NEB-next-ChIP


title: P_hallii

description: Whole Genome Bisulphite Sequencing of P. hallii

organism: Panicum hallii

source_name: Panicum hallii


title: orer_nej_1

description: ChIP-seq for Nejire in OregonR

source_name: Oregon-R embryos

value: Custom GenScript CBP (aa 2528-2872)


title: orer_atac_2

description: Oregon-R ATAC-seq replicate 2

growth_protocol: Oregon-r fly cages were set up. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).

extract_protocol:
Nuclei were isolated from  Oregon-R embryos 2-4h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). Isolated nuclie were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.

treatment_protocol: Embryos were dechorionated in 100% bleach for ~1 min and washed with water. Embryos were not fixed

value: Illumina Nextera


title: P_hallii_sRNA

description: small RNA sequencing of P. hallii

source_name: Panicum hallii sRNA


title: mRNA-seq Toll10b replicate 2

source_name: Toll10b embryos

extract_protocol:
Total mRNA was extracted from 20-100 mg non-cross-linked 2-4 h AED in duplicates using the Maxwell Total mRNA purification kit (Promega, #AS1225) according to manufacturer’s instructions. PolyA-mRNA was isolated using DynaI oligo(dT) beads (Life Technologies, #61002).
Libraries were prepared following the instructions of the TruSeq DNA Sample Preparation Kit (Illumina, #FC-121-2001)

value: Illumina TRU-Seq


title: orer_atac_1

description: Oregon-R ATAC-seq replicate 1


title: P_virgatum

description: Whole Genome Bisulphite Sequencing of P. virgatum

organism: Panicum virgatum

source_name: Panicum virgatum

extract_protocol:
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al. 2015).

value: Kanlow

value: leaf


title: M_truncatula_sRNA

description: small RNA sequencing of M. truncatula

source_name: Medicago truncatula sRNA


title: mRNA-seq Toll10b replicate 1


title: T_cacao

description: Whole Genome Bisulphite Sequencing of T. cacao

organism: Theobroma cacao

source_name: Theobroma cacao

value: Matina


title: tl10b_twi_2

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

growth_protocol: Fly stocks Toll10b (Meso) and gd7 (Ecto) were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males, and Toll10b, e /TM3, Sb, Ser, e females were crossed to Toll10b, e/TM3, Sb, Ser, e males. Offspring of these crosses were used for embryo collections. For Trl, Sna, Pc ChIPs wild type embryos (Oregon-R) were used. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).

extract_protocol: ChIP-seq was performed according to He et al. (2011) with whole cell extract (WCE) derived from 100 mg embryos per ChIP

treatment_protocol: Embryos were dechorionated in 100% bleach for ~1 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.

value: Custom Covance Twi (aa 340-490)

tag: barcode kit

tag: library kit


title: tl10b_twi_1


title: tl10b_h3k27me3_2

value: H3K27me3 (Active Motif Carlsbad, CA, catalog #39155)


title: tl10b_wce_5


title: tl10b_h3k27me3_1


title: tl10b_h3k4me1_3

value: H3K4me1 (Active Motif Carlsbad, CA, catalog #39635)


title: gd7_zen_2

source_name: gd7 embryos

value: Custom GenScript Zen (full length)


title: orer_wce_1

source_name: orer embryos

value: wild type


title: orer_sna_1

value: Custom GenScript Sna (Full length) 134626-2


title: gd7_zen_1


title: gd7_wce_4


title: orer_gaf_1

value: Custom GenScript Trl (N-term) 163185-42


title: gd7_mad_2

value: Custom GenScript Mad (aa 147-455)


title: gd7_h3k4me1_2

value: 2-4 hr after egg deposition


title: gd7_h3k27me3_2


title: Aero_pln_rep2

city: Midreshet Ben Gurion

first: Bihter

last: Bayramoglu

address: Albert Katz International School, Jacob Blaustein Institute

department: Aquatic and Environmental Microbiology

country: Israel

institute: Ben Gurion University of the Negev

data_processing:
All reads were alligned to E.coli genome using Rockhopper software
Genome_build: U00096.2
Supplementary_files_format_and_content: excel file containing expression levels for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655, Planktonic, Aerobic

growth_protocol: E.coli cells were cultivated in ambient temperature in planktonic and biofilm cultures in the presence and absence of oxygen

extract_protocol:
Total RNA was extracted using Epicentre MasterPure kit. rRNA was depleted using Epicentre RiboZero rRNA removal (gram-negative) kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture type

value: Planktonic

tag: oxygen availability

value: Aerobic


title: Anaero_bio_rep1

source_name: Escherichia coli MG1655, Biofilm, Anaerobic

value: Biofilm

value: Anaerobic


title: Aero_bio_rep1

source_name: Escherichia coli MG1655, Biofilm, Aerobic


title: gd7_h3k27me3_1

value: NEB-next-ChIP


title: gd7_mad_1


title: gd7_h3k27ac_2

value: H3K27ac (Active Motif Carlsbad, CA, catalog #39133)


title: MN_T1SA_A

city: Nottingham

first: Michaela

last: Novodvorska

address: University Park

department: School of Life Sciences

country: United Kingdom

institute: Nottingham University

data_processing:
Sequencing was performed on a SOLiD 5500xl ABi sequencer according to the manufacturer’s instructions to generate 75bp reads in colour space. Reads from each sequencing library were mapped to the annotated genome assembly of the A. niger CBS 588.13 (AspGD version s01_m06_r10) using the LifeScope 2.5.1 Whole Transcriptome Pipeline (LifeTechnologies). Reads were initially quality checked and then subsequently filtered against the sequences of library adaptors and A. niger rRNA. LifeScope then mapped the reads to the sequence of the entire genome as well as a library of all exon junctions, derived from the genome annotation information, thereby accounting for spliced reads. The primary read alignment position of each mapped read was recorded in BAM format for further downstream analysis. Read counts per gene were calculated from each sample BAM file using HTseq-count with read alignments with a minimum mapping quality score of 20 (MAPQ20) (PMID: 25260700). Normalised gene expression values (RPKM) (Reads Per Kilobase of gene model per Million mapped reads) (Mortazavi et al. 2008) were also calculated using a custom Perl script. Differential gene expression analysis was achieved using the R package DEseq using the read counts per gene for each sample according to replicate grouping. Significantly differentially expressed genes were determined according to an adjusted p-value of 0.05.
Genome_build: Aspergillus niger CBS.588.13
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each sample

organism: Aspergillus niger

source_name: conidia germinated with 1mm sorbic acid in growth media for 1h

growth_protocol: Aspergillus niger strain N402, a cpsA1 derivative of A. niger N400 (Bos et al. 1988) was grown on Aspergillus complete medium (ACM) (containing per litre: NaNO3 6g, KCl, 0.52 g; MgSO4.7H2O, 0.52 g; KH2PO4, 1.52 g; Na2B4O7.10H2O, 0.008 mg; CuSO4.5H2O, 0.16 mg; FePO4.H2O, 0.16 mg; MnSO4.4H2O, 0.16 mg; NaMoO4.2H2O, 0.16 mg; ZnSO4, 1.6 mg, Bacto casamino acids, 1g, yeast extract, 1g, Bacto peptone, 2g, glucose, 10g, vitamins: p-aminobenzoic acid, 4mg, thiamine HCl, 0.5mg, D-biotin, 0.02mg, nicotinic acid, 1mg,  pyridoxine hydrochloride, 2.5mg, choline chloride, 0.014g, riboflavin, 1mg, agar 20g where applicable  ) at pH4 at 28oC. Conidia were collected by washing the agar slopes using 0.01% (w/v) Tween 80, filtered through sterile synthetic wool and counted using a haemocytometer. Germinated conidia were recovered by filtration into 0.5 ml RNA extraction buffer (0.6M NaCl, 0.2M sodium acetate, 0.1M EDTA, 4% w/v SDS) and snap frozen in liquid nitrogen. Frozen dormant or germinated conidia were mixed with 0.5ml glass beads and disintegrated in a Sartorius dismembranator (4 min, 2000rpm).

extract_protocol:
Total RNA was extracted using the Plant/Fungi total RNA Purification Kit (Norgen Biotek, Canada) including the on-column DNAase treatment step.
SOLiD whole transcriptome libraries were made as outlined in the SOLiD Total RNA-Seq kit protocol (Applied Biosystems).  Libraries were quantified by qPCR using a KAPA library quantification kit for Applied Biosystems SOLiD platform and pooled in equimolar amounts.  Pooled libraries were gel-purified using 2% size-select E-gels to 200-300 bp (Invitrogen). Emulsion PCR and bead-based enrichment was carried out using the SOLiD EZ bead system.

treatment_protocol: 1mM sorbic acid in growth media


title: MN_T1A

source_name: conidia germinated for 1h

value: conidia germinated for 1h


title: Anaero_bio_rep2


title: WT_2

first: Chris

middle: W

last: Seidel

department: Genomics

institute: Stowers Institute

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.

organism: Schmidtea mediterranea

source_name: Whole Worm Tissue

growth_protocol: The CIW4 clonal line of S. mediterranea was maintained at 20 C in 1X Montjuic salts (Cebrià and Newmark, 2005) supplemented with 50 ug/mL gentamicin sulfate, and fed homogenized calf liver paste once per week.

extract_protocol:
Isolated RNA from whole worm tissue was treated with RNase-free DNase on QIagen RNeasy columns and eluted in nuclease-free water.
500ng-1μg RNA per whole worm sample or 100ng of sorted cell RNA was used for generation of RNAseq libraries using the Illumina TruSeq kit.

treatment_protocol: Planarians 2-3 mm in length were starved for at least 1 week before use. Irradiation was done with a GammaCell 40 Exactor irradiator at a dose rate of 85 Rad/minute.

tag: time point

value: 0 hours

tag: gamma radiation

value: 0 rads

tag: replicate


title: Cm_Darkness_Rep1

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

description: Total cells

data_processing:
The purified cDNA library was sequenced on Illumina's MiSeq sequencing platform following vendor's instruction for running the instrument.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cyanidioschyzon merolae 10D reference genome (assembly ID:ASM9120v1) using TopHat (v2.0.5).
Differential expression analysis was conducted by using cuffdiff tool in cufflink suite (v2.2)
Genome_build: ASM9120v1
Supplementary_files_format_and_content: Excel spreadsheet includes FPKM values for Darkness and Blue-Light exposed samples with p and q values of cuffdiff output.

organism: Cyanidioschyzon merolae strain 10D

growth_protocol: Cyanidioschyzon merolae cells were grown in 2xMA media

extract_protocol:
Dark kept and blue-light exposed C.merolae cells were removed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were exposed to blue-light (15 µmole m-2s-1) for 30 minutes

tag: genotype/variation

value: Darkness


title: WT_1


title: tl10b_h3k27ac_3


title: Cm_Darkness_Rep2

description: Total cells

tag: protocol


title: IR96_1

value: 96 hours

value: 6000 rads


title: IR96_3


title: MN_T1B

tag: strain


title: Cm_BlueLight_Rep1

description: Total cells

value: wild type

value: Blue Light Induction


title: Cm_BlueLight_Rep2

description: Total cells


title: Trdd2_5P_WT rep2

description: fragmentation by sonication

source_name: DN2/DN3 T cell precursors

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using linear amplification-mediated HTGTS (LAM-HTGTS).

tag: genotype

value: WT

tag: cell line

value: stromal cell line


title: IR48_2

value: 48 hours


title: Anaero_pln_rep2

source_name: Escherichia coli MG1655, Planktonic, Anaerobic

value: Planktonic


title: IR24_3

value: 24 hours


title: Anaero_pln_rep1


title: Aero_pln_rep1

value: Aerobic


title: Animal8_Female_Cerebellum_Sequencing batch 2

city: Indianapolis

first: Aaron

middle: Thomas

last: Smith

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly

description:
Sequencing batch 2 from sample Animal8_Female_Cerebellum
US-1456472_AD1GBMACXX_US-1456472_CATGGC_L002_R1_001

data_processing:
FastQ files were processed to remove adaptor sequence and discard reads < 17bp in length with cutadapt v. 1.4.1 [23] with options –a TGGAATTCTCGGGTGCCAAGG –quality-base 33 –q 20 –match-read-wildcards –m 17. All trimmed reads that contained an ‘N’ were discarded. Identical sequences from the same sample were combined into a single sequence in the form expected by miRDeep2
Quantifier.pl from the mirdeep2 package [v. 2.0.0.5 ] was used to generate miR alignment files (.mrd files) against known miRs from miRbase 20 with options –P –p <org>_hairpin.fa –m <org>_mature.fa –r trimmed_reads.fa –d. This was done separately for rat, mouse, human, and C. elegans known miRs.
The .mrd files were then parsed with a custom Perl script as follows. Each isomiR sequence in an alignment was associated with the corresponding mature miR identifier. If it aligned to a miRNA precursor, but not with an expected mature miR sequence, it was identified as <miR>-pre to indicate this. Usually these correspond with reverse strand miRs that have not yet been annotated as alternate mature forms. Sometimes these appear to be microRNA offset RNAs [25] and sometimes they appear to represent incompletely processed sequence. If a given sequence was identified as aligning with more than one precursor, it was associated with all potential names as a composite name. That is, a sequence that aligned to both let-7a-5p and let-7f-5p was assigned to the composite mature miR let-7a-5p;let-7f-5p to indicate for subsequent analyses that this identification was ambiguous. All sequences that had not yet been identified against known rat miRs were then looked for in the analysis with respect to known mouse miRs, and so on against human and finally C. elegans miRs. This process allows for identification of conserved rodent miRs that have not yet been annotated in rat, and against conserved mammalian miRs that have not yet been annotated in rat and mouse. The comparison with C. elegans was to identify spiked in C. elegans miRs (not used in this data set).
In parallel to the above identification of known miRs, we used miRDeep2’s novel miR identification process as well. We aligned all the unique trimmed fasta reads to the RN5 reference rat genome with miRDeep2’s mapper.pl script with default parameters and then used the miRDeep2.pl script to generate novel miR predictions and .mrd files. The .mrd files were parsed as above to assign miR names to each unique read. We then attempted to identify and merge novel predictions that were identical to known miRs as follows. If the same read sequence identified a miR in the novel analysis and in the known analysis and the known miR appeared in miRDeep’s .mrd file, we assumed that this was a duplicate identification and changed the miR name from that reported by miRDeep (chr# followed by a unique ID) to that of the known miR. Otherwise, we assumed that the novel prediction might be different from the known miR identification and added it to the list of potential identifications for the sequence. So, for example, a sequence which was aligned by miRDeep2 to a predicted miR on chrX and also identified as miR-450a is identified as “chrX_48156-5p;miR-450a-5p” because miRDeep2 does not show miR-450a as aligned to this predicted miR, indicating that these are two potentially distinctsources of this sequence. Finally, the counts associated with each unique sequence are summed for each named miR (including complex, multi-named miRs) for each sample and these are reported as the miR level counts.
Genome_build: Rn5 for novel miR identification, mirbase 20 for known miR identification
Supplementary_files_format_and_content: Tab delimited text files with raw count information at either the mature miR level or isomiR level. Both files also contain the source of the predictiion that the indicated counts go with the indicated miR or isomiR.

organism: Rattus norvegicus

growth_protocol: Naïve Sprague Dawley rats ,12-13 weeks old, were used for organ isolation.

extract_protocol:
RNA was purified using the miRNAeasy protocol from Qiagen (Kit cat# 217004).
Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Cataloge # RS-200-0048) using a HiSeq2000.  Briefly, RNA was extracted from tissues using the miRNeasy protocol. Libraries were constructed using the Illumina TruSeq small RNA preparation guide which entails ligation of adapters on the 3' and 5' ends of the RNA molecules.  The libraries were quantitated using RiboGreen and were size selected through gel electrophoresis and libraries consistent with the size of miRNAs were gel purified.  Sequencing was performed with each sample receiving 4-5 million, 30bp, single-end reads. generated

value: Sprague Dawley

tag: animal id

tag: age

value: 12-13 weeks

tag: gender

value: female

tag: tissue

value: Cerebellum

tag: rin


title: Animal9_Female_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Heart
US-1466231_AD1GBMACXX_US-1466231_CAAAAG_L006_R1_001

value: Heart


title: Aero_bio_rep2

value: Biofilm


title: Wild-type uninfected [276]

data_processing:
FASTQ files were output using standard Illumina protocols and Illumina CASAVA sofware version 1.8.2.
Reads were aligned to the mouse genome with subread 1.4.4.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in RefSeq annotation.
Read counts from technical replicates of the same sample were summed.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: CD8+ T cells

extract_protocol:
Total RNA was prepared using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: background strain

value: Wild-type

tag: infection

value: Uninfected


title: Animal6_Male_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Cortex
US-1456448_AD1GBMACXX_US-1456448_GTGAAA_L005_R1_001

value: male

value: Cortex


title: MN_T0B

source_name: dormant conidia

tag: developmental stage

value: dormant conidia


title: Animal7_Female_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Duodenum
US-1459905_AD1GBMACXX_US-1459905_CTATAC_L002_R1_001

value: Duodenum


title: Animal8_Female_Uterus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Uterus
US-1454058_BC2BUMACXX_US-1454058_GTTTCG_L004_R1_001

value: Uterus


title: WT_3

value: 0 hours

value: 0 rads


title: IR24_2

value: 24 hours

value: 6000 rads


title: IR96_2

value: 96 hours


title: Animal10_Female_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Heart
US-1466195_AD1GBMACXX_US-1466195_AGTTCC_L006_R1_001

value: Sprague Dawley

value: 12-13 weeks


title: MN_T1SA_B

value: conidia germinated with 1mm sorbic acid in growth media for 1h


title: MN_T0A


title: IR72_3

value: 72 hours


title: Animal11_Female_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_WholeBlood
US-1459951_AD1GBMACXX_US-1459951_CTCAGA_L003_R1_001

value: female

value: WholeBlood


title: Animal2_Male_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Heart
US-1458627_AD2C4RACXX_US-1458627_GATCAG_L004_R1_001

value: Heart


title: IR72_2


title: Animal2_Male_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Hippocampus
US-1454082_AD1GBMACXX_US-1454082_ATGTCA_L003_R1_001

value: male

value: Hippocampus


title: IR72_1


title: IR48_3

value: 48 hours


title: IR48_1


title: Animal5_Male_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Medulla
US-1458837_AD2C4RACXX_US-1458837_ATGTCA_L008_R1_001

value: Medulla


title: Animal8_Female_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Muscle_Soleus
US-1459955_BC2BUMACXX_US-1459955_TAATCG_L008_R1_001

value: Muscle - Soleus


title: Animal10_Female_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Duodenum
US-1456498_AD1GBMACXX_US-1456498_CAGATC_L002_R1_001

value: Duodenum


title: Animal3_Male_Cerebellum_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal3_Male_Cerebellum
US-1456436_BC2BUMACXX_US-1456436_TAGCTT_L006_R1_001

value: Cerebellum


title: Animal5_Male_Liver_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Liver
US-1454092_AD1GBMACXX_US-1454092_TAATCG_L005_R1_001

value: Liver


title: Animal7_Female_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Stomach_Non-Glandular
US-1458858_AD1GBMACXX_US-1458858_GTGGCC_L006_R1_001


title: Animal9_Female_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Jejunum
US-1458713_AD1GBMACXX_US-1458713_CGTACG_L002_R1_001

value: Jejunum


title: Animal2_Male_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Brainstem
US-1466193_AD1GBMACXX_US-1466193_CAGGCG_L004_R1_001

value: Brainstem


title: Animal5_Male_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Medulla
US-1458837_AD1GBMACXX_US-1458837_ATGTCA_L005_R1_001

value: Sprague Dawley


title: Animal8_Female_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Stomach_Non-Glandular
US-1466238_AD1GBMACXX_US-1466238_CACGAT_L005_R1_001

value: 12-13 weeks


title: Animal2_Male_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Ileum
US-1458865_AD1GBMACXX_US-1458865_TACAGC_L002_R1_001

value: Ileum


title: IR24_1

value: 24 hours

value: 6000 rads


title: Animal3_Male_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Brainstem
US-1459943_BC2BUMACXX_US-1459943_GTGGCC_L004_R1_001


title: 1004_Sequencing batch 2

description:
Sequencing batch 2 from sample 1004
US-1459915_AD1GBMACXX_US-1459915_GTAGAG_L002_R1_001

value: DRG


title: Animal10_Female_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Brainstem
US-1459933_AD1GBMACXX_US-1459933_GATCAG_L003_R1_001

value: female


title: Animal8_Female_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Brainstem
US-1459880_AD2C4RACXX_US-1459880_ACAGTG_L007_R1_001


title: Animal7_Female_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Heart
US-1458709_BC2BUMACXX_US-1458709_GTGGCC_L007_R1_001

value: Heart


title: Animal4_Male_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_WholeBlood
US-1459904_BC2BUMACXX_US-1459904_AGTTCC_L006_R1_001

value: male

value: WholeBlood


title: Animal5_Male_Duodenum_Homogenate_re-extract_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal5_Male_Duodenum_Homogenate_re-extract
US-1462953_BC2BUMACXX_US-1462953_CAAAAG_L004_R1_001


title: Animal7_Female_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_WholeBlood
US-1462736_AD1GBMACXX_US-1462736_CAACTA_L005_R1_001


title: Animal6_Male_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Jejunum
US-1458707_BC2BUMACXX_US-1458707_CGGAAT_L005_R1_001


title: Animal8_Female_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Jejunum
US-1458710_BC2BUMACXX_US-1458710_CGATGT_L002_R1_001


title: Animal9_Female_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Cerebrum
US-1466207_BC2BUMACXX_US-1466207_CATGGC_L008_R1_001

value: Cerebrum


title: Animal11_Female_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Duodenum
US-1454094_AD2C4RACXX_US-1454094_GCCAAT_L004_R1_001


title: Animal7_Female_Muscle_Biceps_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Muscle_Biceps
US-1459935_AD1GBMACXX_US-1459935_CAAAAG_L003_R1_001

value: Muscle - Biceps


title: Animal10_Female_Liver_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Liver_Homogenate_re-extract
US-1462936_AD2C4RACXX_US-1462936_ATTCCT_L002_R1_001


title: Animal11_Female_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Muscle_Soleus
US-1463120_BC2BUMACXX_US-1463120_CAGGCG_L001_R1_001

value: Muscle - Soleus


title: Animal11_Female_Ovary_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Ovary
US-1454030_AD1GBMACXX_US-1454030_ACAGTG_L006_R1_001

value: Ovary


title: Animal8_Female_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Hippocampus
US-1458649_AD1GBMACXX_US-1458649_CCGTCC_L002_R1_001

value: Hippocampus


title: Animal7_Female_Uterus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Uterus
US-1456454_AD1GBMACXX_US-1456454_TGACCA_L003_R1_001

value: Uterus


title: Animal10_Female_Jejunum_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Jejunum_Homogenate_re-extract
US-1462920_AD2C4RACXX_US-1462920_ATCACG_L007_R1_001

value: Jejunum


title: Animal2_Male_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Cerebellum
US-1456481_BC2BUMACXX_US-1456481_TAGCTT_L003_R1_001

value: Sprague Dawley

value: Cerebellum


title: Animal8_Female_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Muscle_Biceps_Homogenate_re-extract
US-1459950_AD1GBMACXX_US-1459950_CTTGTA_L002_R1_001

value: 12-13 weeks


title: Animal2_Male_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Ileum
US-1458865_AD2C4RACXX_US-1458865_TACAGC_L007_R1_001

value: Ileum


title: Animal11_Female_Liver_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Liver_Homogenate_re-extract
US-1462928_AD1GBMACXX_US-1462928_GTCCGC_L005_R1_001

value: Liver


title: Animal10_Female_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Cerebellum
US-1456494_AD1GBMACXX_US-1456494_AGTCAA_L003_R1_001


title: Animal11_Female_Jejunum_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Jejunum_Homogenate_re-extract
US-1462922_AD1GBMACXX_US-1462922_GGCTAC_L002_R1_001


title: Animal2_Male_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Jejunum
US-1458623_AD1GBMACXX_US-1458623_CACTCA_L002_R1_001


title: Animal7_Female_Kidney_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Kidney_Homogenate_re-extract
US-1462986_AD1GBMACXX_US-1462986_CTCAGA_L004_R1_001

value: Kidney


title: Animal4_Male_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Adrenal
US-1458848_AD2C4RACXX_US-1458848_GTGAAA_L002_R1_001

value: Adrenal


title: Animal4_Male_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Muscle_Soleus
US-1466220_AD1GBMACXX_US-1466220_ACTGAT_L004_R1_001


title: Animal7_Female_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Ileum
US-1458863_AD1GBMACXX_US-1458863_GACGAC_L002_R1_001

value: female


title: Animal3_Male_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Muscle_Soleus_Homogenate_re-extract
US-1462968_BC2BUMACXX_US-1462968_TAATCG_L002_R1_001

value: male


title: Animal3_Male_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Adrenal
US-1458835_AD1GBMACXX_US-1458835_GCCAAT_L006_R1_001


title: Animal9_Female_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Cortex
US-1456509_AD2C4RACXX_US-1456509_CATGGC_L006_R1_001

value: Cortex


title: Animal11_Female_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Adrenal
US-1458844_BC2BUMACXX_US-1458844_GAGTGG_L004_R1_001


title: Animal4_Male_Muscle_Biceps_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Muscle_Biceps
US-1459894_BC2BUMACXX_US-1459894_CCGTCC_L006_R1_001


title: Animal8_Female_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Cerebrum
US-1458895_BC2BUMACXX_US-1458895_ACTGAT_L004_R1_001

value: Cerebrum


title: Animal5_Male_Liver_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Liver
US-1454092_AD2C4RACXX_US-1454092_TAATCG_L004_R1_001


title: Animal8_Female_Ovary_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Ovary
US-1458901_AD1GBMACXX_US-1458901_GTCCGC_L004_R1_001


title: Animal6_Male_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Adrenal
US-1458836_AD1GBMACXX_US-1458836_CAACTA_L006_R1_001


title: CTCF ChIP

city: Shanghai

first: Bo

last: Zhu

address: Institute of Cancer, Xinqiao Hospital, Third Military Medical University

department: Institute of Cancer, Xinqiao Hospital

institute: Third Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with the defaut configurations
Couverage track are generated using Deeptools'function BamCompare
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is gerated using Deeptools

organism: Homo sapiens

growth_protocol: SKOV3 cells were cultured in DMEM/H (Hyclone) containing 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Beyotime Biotechnology) and incubated at 37℃ in a humidified atmosphere with 5% CO2.Then harvest typically 2–3 × 106 cells per sample.

extract_protocol:
Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

tag: chip antibody

value: Anti-CTCF antibody - ChIP Grade,ab70303


title: Animal7_Female_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Jejunum
US-1458704_BC2BUMACXX_US-1458704_GATCAG_L003_R1_001


title: CTCF input


title: Animal3_Male_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Jejunum
US-1458656_AD1GBMACXX_US-1458656_ACAGTG_L002_R1_001


title: Animal9_Female_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Stomach_Glandular
US-1456516_AD1GBMACXX_US-1456516_ATTCCT_L006_R1_001


title: WT_1

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

data_processing:
default parameters to Torrent Suite Software version 4.0.2
Mapping with Bowties2 on messager RNA TAIR 10 reference (parameters : no MultiHit, local reads mapping, TAIR 10 refrence with one gene model)
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: our processed data files contain 3 comment lines corresponding to the time of processing, the number of reads parsed and the number of reads mapped. An example is shown below: #sam2pkm :2014-02-14 11:16:22.632693 # total read parsed : 34170794 # total read mapped : 28674853. Then the column headers #id    len    nb_single : "id" corresponds to the locus identifier (Arabidopsis Genome Initiative code); "len" corresponds to the length of the gene model in nt;"nb_single" corresponds to the number of reads mapped on the gene model

organism: Arabidopsis thaliana

growth_protocol: Media_soil/Hygrometry_65%/Temperature_21°C/Light_Short day conditions (8h light -16h dark)

extract_protocol:
extraction-MirVana_fm_1560.pdf
RNA libraries were prepared for sequencing using standard LifeTechnologies protocols for Ion Torrent Proton (4476286_Ion Total RNA-Seq Kit v2_UG_RevE.pdf)
RNA Seq in Stranded Single End, sizing 230bp, messager RNA selection (DynabeadsmRNADIRECTMicro_UG_Rev004.pdf)

treatment_protocol: no treatment

tag: organ

value: aerial

value: 21 days

tag: ecotype

value: WT


title: WT_2


title: WT_3


title: Animal9_Female_Pancreas_Reextract_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal9_Female_Pancreas_Reextract
US-1459554_SEA055491C:299:D2C4RACXX:5

value: Pancreas


title: Animal11_Female_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Stomach_Glandular
US-1458903_AD1GBMACXX_US-1458903_CCGTCC_L006_R1_001


title: Animal4_Male_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Brainstem
US-1459907_AD1GBMACXX_US-1459907_GTTTCG_L002_R1_001

value: Brainstem


title: Animal6_Male_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Adrenal
US-1458836_AD2C4RACXX_US-1458836_CAACTA_L003_R1_001

value: Sprague Dawley


title: cuc2-3_3


title: Animal11_Female_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Heart
US-1458660_BC2BUMACXX_US-1458660_CCAACA_L005_R1_001

value: Heart


title: 117_3


title: Animal6_Male_Duodenum_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Duodenum_Homogenate_re-extract
US-1462960_AD1GBMACXX_US-1462960_ATGAGC_L003_R1_001

value: 12-13 weeks

value: Duodenum


title: 117_2


title: cuc2-3_1


title: Animal11_Female_Uterus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Uterus
US-1466217_AD1GBMACXX_US-1466217_CTCAGA_L006_R1_001

value: Uterus


title: Animal7_Female_Liver_Homogenate_re-extract_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal7_Female_Liver_Homogenate_re-extract
US-1462955_SEA062401C:142:C2BUMACXX:2

value: Liver


title: W3

city: Hangzhou

first: Chun-Fang

last: Li

state: Zhejiang

address: 9 South Meiling Road

department: Key Laboratory of Tea Biology and Resources Utilization

institute: Tea Research Institute of the Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: de novo transcriptome assembly. FASTA file of assembled transcripts is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Camellia sinensis

source_name: Anji Baicha

growth_protocol: The tea plant [Camellia sinensis (L.) O. Kuntze cv. ‘Anji Baicha’] was grown in the China National Germplasm Hangzhou Tea Repository (CNGHTR) of the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRICAAS). Leaf samples from different albescent stages of the four years old tea plant were used in this study.

extract_protocol:
Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Leaf samples from yellow green stage, white stage and green stage were used in this study

value: Leaf

tag: leaf stage

value: White color

tag: cultivar

value: Anji Baicha


title: Animal2_Male_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Stomach_Glandular
US-1456450_AD1GBMACXX_US-1456450_CTTGTA_L006_R1_001

tag: strain

value: male


title: YG2

value: Yellow green color


title: W2


title: Animal8_Female_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Hippocampus
US-1458649_AD2C4RACXX_US-1458649_CCGTCC_L002_R1_001

value: female

value: Hippocampus


title: YG1


title: YG3


title: Animal8_Female_Uterus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Uterus
US-1454058_AD1GBMACXX_US-1454058_GTTTCG_L005_R1_001


title: Animal10_Female_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Stomach_Glandular
US-1456512_AD1GBMACXX_US-1456512_ATGTCA_L006_R1_001


title: W1


title: Animal7_Female_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Pancreas_Reextract
US-1459556_AD2C4RACXX_US-1459556_ATGAGC_L002_R1_001


title: Animal5_Male_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Muscle_Biceps_Homogenate_re-extract
US-1459909_AD1GBMACXX_US-1459909_GTGAAA_L003_R1_001

value: Muscle - Biceps


title: G1

value: Green color


title: Animal3_Male_Kidney_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Kidney_Homogenate_re-extract
US-1462965_AD1GBMACXX_US-1462965_CCGTCC_L005_R1_001

value: Kidney


title: Animal8_Female_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Ileum
US-1458914_AD1GBMACXX_US-1458914_GGTAGC_L002_R1_001

value: Ileum


title: Animal5_Male_Kidney_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Kidney_Homogenate_re-extract
US-1462988_AD1GBMACXX_US-1462988_AGTCAA_L006_R1_001

value: Sprague Dawley


title: Animal3_Male_Kidney_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Kidney_Homogenate_re-extract
US-1462965_BC2BUMACXX_US-1462965_CCGTCC_L003_R1_001


title: Animal9_Female_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Brainstem
US-1466199_AD1GBMACXX_US-1466199_CTAGCT_L004_R1_001

value: Brainstem


title: G3


title: G2


title: 117_1

value: aerial

value: 21 days

tag: genotype


title: Animal10_Female_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Heart
US-1466195_AD2C4RACXX_US-1466195_AGTTCC_L008_R1_001

value: 12-13 weeks

value: Heart


title: Animal9_Female_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Hippocampus
US-1459925_BC2BUMACXX_US-1459925_ATTCCT_L004_R1_001


title: Histone3-K27me3 ChIPSeq 2

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

description: anti-Histone3-K27me3 antibody

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.9 with parameters -m 1 -v 2 --best --strata
Peaks were called using HOMER through "findpeaks" function with -style factor and default parameters for K ChIP sample and -F 3 -P 0.01 -L 3 -fdr 0.05 -style factor for J ChIP sample
Common peaks between K ChIP and J ChIP samples were found using BedTools v2.25.0 "intersectBed" command using default settings
for Heat Map Figure 4E.  Macs2 command line macs2 callpeak -t *.bam -c input.bam --gsize=1.87e9 --broad --broad-cutoff 0.1 -B
Genome_build: mm9

organism: Mus musculus

source_name: pancreas

extract_protocol:
Lysates were clarified from sonicated nuclei and MIST1-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina True-seq protocols

value: pancreas