title: KAI1-KD rep2

tag: cell type


title: MIRA-6553

status: Public on Mar 31 2016

type: SRA

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

country: USA

institute: Beckman Research Institute

description: DNA methylation with MIRA-seq

library_source: genomic

data_processing:
Bases were called using Illumina's CASAVA v1.8.2
Sequences were aligned to hg19 genome using Novoalign, only unique aligned reads were kept
Peaks were called using MACS 2.0 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: binary bedGraph files were generated using in house R scripts

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanoma

extract_protocol:
Genomic DNAs from human melanocytes were prepared using Quick-gDNA MiniPrep kit (Zymo Research, Cat# D3007) followed the manufacture's method.
For Methylated-CpG island recovery assay (MIRA), two micrograms of genomic DNA was sonicated to produce DNA fragments with a length distribution of 100 to 300 bp using a Covaris S220 sonicator. The sheared DNA was Illumina linker-ligated, and methylated DNA fragments were enriched using the methylated-CpG island recovery assay (MIRA) technique using recombinant MBD3L1 and MBD2b proteins. To prepare a sequencing library, the MIRA-enriched DNA fragments and input DNA were PCR-enriched with PE 1.0 primer and index primer (Illumina). Next, Ampure XP beads (Beckman Coulter; Brea, CA) was added to the PCR solution to remove DNA fragments smaller than 200 bp, and double bead selection (0.65x) was used to remove fragments larger than 500 bp according to the manufacturer’s instructions. The size-selected sequencing library was sequenced on an Illumina HiSeq instrument.
MIRA-Seq

value: tissue

tag: source tissue

value: skin

tag: sample diagnosis

value: Malignant melanoma

tag: gender

value: Male


title: MIRA-6551

description: DNA methylation with MIRA-seq


title: MIRA-6556-Melanocyte1

description: DNA methylation with MIRA-seq

source_name: Melanocyte

value: Cultured epidermal melanocytes


title: MIRA-6559-Input3

description: DNA methylation with MIRA-seq


title: MIRA-6559-Input1

description: DNA methylation with MIRA-seq


title: MIRA-6555

description: DNA methylation with MIRA-seq


title: MIRA-6554

description: DNA methylation with MIRA-seq


title: MIRA-6550

description: DNA methylation with MIRA-seq


title: MIRA-6556-Melanocyte2

description: DNA methylation with MIRA-seq


title: MIRA-6556-Melanocyte3

description: DNA methylation with MIRA-seq


title: ur89_BT_12h_rep2

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

country: Germany

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using tophat-2.0.8 with parameters --no-coverage-search  --b2-very-sensitive
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using cufflinks-2.0.2
Genome_build: WS235; GCF_000002985.6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Caenorhabditis elegans

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: Worms were exposed to PA and BT at the stage L4. The BT strains were diluted in 1:250 (E.coli OP50). PA14 was diluted in 4:1 (E.coli OP50). The experiments with BT were performed at 20°C and with PA14 at 25°C.

tag: strain background

tag: genotype/variation

tag: develpmental stage

tag: exposed to

tag: timepoint

tag: medium

value: PFM

tag: temperature

tag: tissue

value: whole body


title: N2_OP_12h_rep3

description:
Matched control of N2 to BT247 at 12h
B1758

value: Wide type


title: MIRA-6559-Input2

description: DNA methylation with MIRA-seq

value: Female


title: MIRA-6552

description: DNA methylation with MIRA-seq


title: N2_OP_12h_rep2

description:
Matched control of N2 to BT247 at 12h
B1678


title: MIRA-6548

description: DNA methylation with MIRA-seq


title: MIRA-6546

description: DNA methylation with MIRA-seq


title: MIRA-6544

description: DNA methylation with MIRA-seq


title: MIRA-6547

description: DNA methylation with MIRA-seq


title: 96 hpi INOC. FO40 1

city: Ames

first: Alessandra

last: Lanubile

state: Iowa

address: Seed Science Building

department: Plant Pathology

institute: Iowa State University

data_processing:
Illumina Casava 1.7 software used for basecalling
GSNAP version 2014-06-10 was used for aligning raw reads to the reference genome
HTSeq was used to get the raw counts for the genes
Quasi-seq was used to normalize (upper quarltile) and call DGE
Genome_build: soybean Williams 82 reference genome; F. oxysporum f. sp. pisi HDV247
Supplementary_files_format_and_content: Raw read counts for gene expression in text format

organism: Glycine max

source_name: Soybean

extract_protocol:
Soybean seedlings were collected, flash frozen on liquid nitrogen, and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: f. oxysporum isolate

value: FO40 pathogenic

value: Seedling

tag: hours post inoculation

value: 96 hpi


title: 96 hpi INOC. FO40 3


title: 72 hpi INOC. FO40 3

value: 72 hpi


title: MIRA-6543

description: DNA methylation with MIRA-seq


title: Experimental_3hr_45min

city: La Jolla

first: Miles

last: Wilkinson

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

description:
Cells treated with siRNA and then Actinomycin D
Experimental Sample1_3hr_45min (3hr45minutes_E1)
Experimental Sample2_3hr_45min (3hr45minutes_E2)

data_processing:
RNA-seq reads were mapped with Tophat2 pipeline against mm10 transcriptome hosted at SevenBridges Genomics.
Cufflinks was used to compare FPKM values across all timepoints.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Mus musculus

growth_protocol: P19 cells were grown in MEM-alpha (Invitrogen) and 10% fetal bovine serum

extract_protocol:
RNA was isolated with Trizol and total RNA quality was assessed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siControl or siUPF3A we used.  24 h after transfection, cells were treated with actinomycin D and RNA was isolated 0, 15, 105, and 225 minutes post-actinomycin D treatment.

tag: cell line

value: embryonic carcinoma cell line P19

value: loss of UPF3A

tag: treatment

value: Actinomycin D

tag: time (post-treatment)

value: 3hr 45minutes


title: MIRA-6545

description: DNA methylation with MIRA-seq

tag: cell type

value: tissue


title: MIRA-6542

description: DNA methylation with MIRA-seq

tag: source tissue

value: skin


title: MIRA-6541

description: DNA methylation with MIRA-seq

tag: sample diagnosis

value: Malignant melanoma


title: MIRA-6549

description: DNA methylation with MIRA-seq

tag: gender

value: Male


title: Experimental_1hr_45min

description:
Cells treated with siRNA and then Actinomycin D
Experimental Sample1_1hr_45min (1hr45minutes_E1)
Experimental Sample2_1hr_45min (1hr45minutes_E2)

value: 1hr 45minutes


title: Control_3hr_45min

description:
Cells treated with Control siRNA and then Actinomycin D
Control Sample 1_3hr_45min (3hr45minutes_C1)
Control Sample 2_3hr_45min (3hr45minutes_C2)

value: control


title: 96 hpi INOC. FO36 1

value: FO36 non-pathogenic


title: 72 hpi INOC. FO40 1


title: 96 hpi INOC. FO36 2


title: MIRA-6539

description: DNA methylation with MIRA-seq


title: MIRA-6540

description: DNA methylation with MIRA-seq


title: MIRA-6537

description: DNA methylation with MIRA-seq


title: Control_1hr_45min

description:
Cells treated with Control siRNA and then Actinomycin D
Control Sample 1_1hr_45min (1hr45minutes_C1)
Control Sample 2_1hr_45min (1hr45minutes_C2)


title: 96 hpi INOC. FO36 3


title: MIRA-6536

description: DNA methylation with MIRA-seq


title: Control_15min

description:
Cells treated with Control siRNA and then Actinomycin D
Control Sample 1_15min (15minutes_C1)
Control Sample 2_15min (15minutes_C2)


title: Experimental_15min

description:
Cells treated with siRNA and then Actinomycin D
Experimental Sample1_15min (15minutes_E1)
Experimental Sample2_15min (15minutes_E2)


title: 72 hpi INOC. FO36 3


title: Experimental_0min

description:
Cells treated with siRNA and then Actinomycin D
Experimental Sample1_0min (0minutes_E1)
Experimental Sample2_0min (0minutes_E2)


title: MIRA-6535

description: DNA methylation with MIRA-seq


title: 72 hpi INOC. FO36 2


title: 96 hpi INOC. FO40 2


title: Control_0min

description:
Cells treated with Control siRNA and then Actinomycin D
Control Sample 1_0min (0minutes_C1)
Control Sample 2_0min (0minutes_C2)


title: MIRA-6534

description: DNA methylation with MIRA-seq


title: 96 hpi CTRL 3

value: Control


title: 72 hpi INOC. FO40 2


title: MIRA-6533

description: DNA methylation with MIRA-seq


title: 96 hpi CTRL 2


title: MIRA-6532

description: DNA methylation with MIRA-seq


title: MIRA-6538

description: DNA methylation with MIRA-seq

value: Female


title: MP.srsf2_wt.vehicle.805

city: Madison

first: Heidi

last: Dvinge

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: UW-Madison

description: Srsf2 wildtype (Mx1-cre Srsf2+/+) and Srsf2 heterozygous P95H mutant (Mx1-Cre Srsf2P95H/+).

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the mm10 mouse genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: Text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
RNA was extracted from sorted mouse cell populations using Qiagen RNeasy columns
The Illumina TruSeq RNA Sample Prep Kit was used with 2-4 ug of total RNA for the construction of sequencing libraries. The protocol was modified to select DNA fragments in the 100-400bp range using bead selection. Samples were multiplexed using Illumina barcodes to run four samples per sequencing lane.

treatment_protocol: E7107 was dissolved in vehicle (10% ethanol (EtOH) and 4% Tween-80 in sterile PBS) and administered via IV injection at 4mg/kg/day. For RNA-seq analysis in murine MLL-AF9 leukemia model, 5 consecutive doses of E7107 were administered, and mice were sacrificed 3 hours after the last dose and bone marrow Mac1+ GFP+ cells were purified by flow cytometry.

value: Myeloid progenitor

value: vehicle

tag: mouse

tag: srsf2 genotype

value: Wildtype


title: 96 hpi CTRL 1

value: Seedling

value: 96 hpi


title: 72 hpi CTRL 3

value: 72 hpi


title: MP.srsf2_wt.e7107.809


title: MP.srsf2_wt.vehicle.804


title: MIRA-6531

description: DNA methylation with MIRA-seq


title: MP.srsf2_wt.e7107.808


title: MP.srsf2_wt.e7107.807


title: MP.srsf2_p95h.vehicle.796


title: MIRA-6529

description: DNA methylation with MIRA-seq


title: R30

description: Total RNA from Melanocytes

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v1.2.0 with default settings.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: hg19
Supplementary_files_format_and_content: Counts for each refseq genes

extract_protocol:
Total RNAs from human melanocytes were prepared using PureLink RNA Mini kit (Ambion, Cat# 12183018A). The cells were lysated by addition of lysis buffer, the lysate was then homogenized using QIAshredder (QIAGEN, cat# 79654) by centrifuge at 14,000 rpm for 2 min, and then followed the manufacture's method.
The RNA samples were used for RNA-seq with the range of the RIN value 8.50 ~ 10 at least. A cDNA library for deep sequencing was prepared using oligo d(T) primer, and followed the Illumina protocol (kit) for later steps.

value: Cultured epidermal melanocytes


title: 72 hpi CTRL 2


title: 72 hpi CTRL 1


title: MP.srsf2_p95h.vehicle.794


title: R29

description: Total RNA from Melanocytes


title: R25

description: Total RNA from Melanoma


title: MP.srsf2_p95h.vehicle.795


title: MP.srsf2_p95h.e7107.819


title: R23

description: Total RNA from Melanoma


title: MP.srsf2_p95h.e7107.818


title: 72 hpi INOC. FO36 1


title: MP.srsf2_p95h.e7107.817


title: R21

description: Total RNA from Melanoma


title: R22

description: Total RNA from Melanoma


title: R20

description: Total RNA from Melanoma


title: MIRA-6530

description: DNA methylation with MIRA-seq


title: R19

description: Total RNA from Melanoma


title: LSK.srsf2_wt-wt.I

description: Mx1-cre Srsf2fl/+ mice crossed to Srsf2P95H/+ mice to generate Srsf2 wildtype (Mx1-cre Srsf2+/+), Srsf2 heterozygous knockout (Mx1-Cre Srsf2+/-), Srsf2 heterozygous P95H mutant (Mx1-Cre Srsf2P95H/+), and Srsf2 hemizygous P95H mutant (Mx1-Cre Srsf2P95H/-) mice

value: LSK

value: I

value: Srsf2 +/+


title: LSK.srsf2_wt-ko.K

value: K

value: Srsf2 KO/+


title: R16

description: Total RNA from Melanoma

value: skin

value: Malignant melanoma


title: R13

description: Total RNA from Melanoma

value: Male


title: LSK.srsf2_wt-ko.J

value: J


title: MP.srsf2_wt.vehicle.806


title: R18

description: Total RNA from Melanoma


title: R28

description: Total RNA from Melanocytes


title: LSK.srsf2_wt-wt.J


title: LSK.srsf2_p95h-wt.K

value: Srsf2 P95H/+


title: R10

description: Total RNA from Melanoma

value: Female


title: LSK.srsf2_p95h-wt.I


title: LSK.srsf2_wt-ko.I


title: R11

description: Total RNA from Melanoma


title: LSK.srsf2_p95h-wt.J


title: R5

description: Total RNA from Melanoma


title: AML.srsf2_p95h.e7107.748

description: Isogenic murine leukemia model created by retroviral overexpression of the MLL-AF9 fusion oncogene in Vav-Cre Srsf2+/+ or Vav-Cre Srsf2P95H/+ BM cells followed by transplantation into lethally irradiated recipient mice.

value: GFP+ Cd11b+


title: R2

description: Total RNA from Melanoma


title: LSK.srsf2_p95h-ko.IJ

value: I+J (pooled)

value: Srsf2 KO/P95H


title: R4

description: Total RNA from Melanoma


title: LSK.srsf2_wt-wt.K


title: AML.srsf2_p95h.e7107.746


title: 99-In (7477)

description: Genomic DNA input

data_processing:
Bases were called using Illumina's CASAVA v1.8.2
Sequences were aligned to hg19 genome using Novoalign, only unique aligned reads were kept
Peaks were called using in house built R scripts and Bioconductor package "chipseq"
Genome_build: hg19
Supplementary_files_format_and_content: binary bedGraph files were generated using in house R scripts

extract_protocol:
Five million human melanocyte cells per ChIP reaction were cross-linked and lysed by incubation in lysis buffer containing 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.25 % Triton X-100, 10% glycerol, and 1x complete protease inhibitor cocktail (Roche) for 20 min on ice. After washing twice with cold washing buffer (10 mM Tris-HCl pH 8.1, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), the nuclear pellet was resuspended in 1 ml of cold shearing buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA, and 0.1% SDS) and then sheared to produce chromatin fragments with a length distribution of 100 to 300 bp using a Covaris S220 sonicator (Covaris) with the following settings: 12.5 min, 5% duty cycle, 140 Watts peak incident power, and 200 cycles per burst. After adding 1% Triton X-100 and 150 mM NaCl (final concentrations) to the sheared chromatin and mixing, the solution was cleared by centrifugation at 14,000xg for 10 min at 4°C. Chromatin fragments were incubated with 8 μg of polyclonal anti-H3K27me3 antibody (07-449; Millipore; Billerica, MA) overnight at 4°C with rotation, and then immunoprecipitated using Dynabeads Protein G (Invitrogen; Carlsbad, CA).
ChIP DNA fragments were end-repaired using NEB End Repair Enzyme mix (NEB) and A-tailed using NEB Klenow Fragment (3’→5’ exo-). After Illumina’s adapter ligation, DNA was PCR amplified with Illumina primers for 12 cycles, and the library fragments of 200 bp to 500 bp were size selected by using Ampure XP beads (Beckman Coulter; Brea, CA) according to the manufacturer’s instructions.

tag: chip antibody


title: AML.srsf2_p95h.e7107.745


title: 99-Ad (7476)

description: Chromatin IP against H3K27me3

value: H3K27me3 (Millipore, 07-449)


title: 09-Ad (7474)

description: Chromatin IP against H3K27me3


title: AML.srsf2_p95h.e7107.744


title: R7

description: Total RNA from Melanoma


title: LSK.srsf2_p95h-ko.K


title: 09-In (7475)

description: Genomic DNA input


title: AML.srsf2_p95h.vehicle.740

value: vehicle


title: AML.srsf2_wt.e7107.727

value: Wildtype


title: AML.srsf2_p95h.vehicle.741


title: R9

description: Total RNA from Melanoma


title: AML.srsf2_p95h.e7107.747


title: AML.srsf2_p95h.vehicle.743


title: AML.srsf2_p95h.vehicle.742


title: AML.srsf2_wt.e7107.725


title: AML.srsf2_wt.e7107.728


title: AML.srsf2_wt.vehicle.722


title: AML.srsf2_wt.vehicle.723


title: AML.srsf2_p95h.vehicle.739


title: AML.srsf2_wt.vehicle.721


title: CB MNC

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
The reads were mapped to targetd exon-exon junctions with Bowtie by allowing up to two mismatches, then the number of reads for each isoform was counted.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data are in csv format, containing the counts of isoforms on assayed alternative splicing events.

source_name: cord blood

growth_protocol: WAS patient derived B-lymphocyte line ID00003 (p.Glu133Lys) and a wile-type B-lymphocyte line GM11518 were cultured in triplicate in RPMI supplemented with 15% fetal bovine serum, penicillin/streptomycin. WAS-iPSC and cWAS-iPSC were differentiated on OP9 feeders and then culture in IMDM supplemented with 10% fetal bovine serum, 100 ng/ml GM-CSF and 50 ng/ml M-CSF. The differentiated macrophages were matured in the X-vivo 10 serum-free medium supplemented with 50 ng/ml M-CSF.

extract_protocol:
Total RNA was extracted from cells using Qiagen Rneasy micro kit
RASL library was constructed according to Li H, et al protocol published Current Protocols in Molecular Biology.
RASL-seq

value: macrophage

tag: genotype

value: wild type

tag: alternative name

value: CB-MP


title: AML.srsf2_wt.e7107.724


title: R12

description: Total RNA from Melanoma


title: cSC9N rep1

source_name: iPSC

value: ctrl-iMP


title: cSC9N rep2


title: WAS-B Y4-4N C18 neo6 rep3


title: WAS-B Y4-4N C18 neo6 rep2


title: WAS-B Y4-4N C18 neo6 rep1


title: AML.srsf2_wt.e7107.726


title: GM11518 rep3

source_name: blood

value: B lymphoblastoid cell line

value: GM


title: ID00003 rep1

value: ID


title: GM11518 rep1


title: treated sample #18 TT

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: treated sample #18 TT

data_processing:
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
The RNAseq read count quantification was performed using the HTSeq tool (version 0.6.1)
To identify the gene expression differences between the three pairs of HG3 pools, DESeq2 software was used. (Love, Huber et al. 2014)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each Sample.

source_name: lymphoblastoid cell line HG3

extract_protocol: Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.

tag: strain

value: lymphoblastoid cell line HG3

tag: sample type

value: fludarabine-resistant


title: treated sample #28 TT

description: treated sample #28 TT


title: control sample #28 TU

description: control sample #28 TU

value: control


title: ID00003 rep3


title: WAS-B Y4-4N rep1


title: AML.srsf2_wt.vehicle.720


title: GM11518 rep2


title: AML.srsf2_wt.vehicle.719


title: Columella root cap RNA-seq

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using tophat 1.3.1 implemented with bowtie  0.12.7 with parameters --solexa1.3-quals -F 0 -g 1
FPKM ( fragments per kilobase of exon per million fragments mapped) were quantified using Cufflinks 2.0.2 with parameters --library-type fr-unstranded
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM ( fragments per kilobase of exon per million fragments mapped) for all genes in the TAIR10 reference annotation as defined by Cufflinks

organism: Arabidopsis thaliana

source_name: Columella root cap

growth_protocol: Seedlings were grown vertically for 6 days after plating on 1x Murashige and Skoog media supplemented with 1% sucrose and 1% agar. All seedlings were grown under standard long day conditions (16 hours of light, 8 hrs of darkness, 22 °C).

extract_protocol:
Fluorescent Activated Cell Sorting (FACS) was performed using cell specific GFP lines. Sorted cells were collected directly into specific lysis buffers that were compatible with downstream applications. Cells used for bisulfite sequencing, mRNA-seq, smRNA-seq were lysed in Buffer AP1 (Qiagen), Buffer RLT (Qiagen), Trizol (Invitrogen). All samples were immediately stored at -80 °C until gDNA and RNA was extracted using DNeasy Plant mini kit (Qiagen) and RNeasy Plant mini kit (Qiagen) or Trizol, respectively.
RNA-seq library preparation was performed using the Illumina TruSeq RNA Library Prep kit from polyA+ selected mRNA as per manufacturer’s instructions.

value: FACSorted columella root cap cells

value: PET111 enhancer trap line

tag: tissue

value: root


title: treated sample #17 TT

description: treated sample #17 TT


title: control sample #17 TU

description: control sample #17 TU


title: Lower columella MethylC-seq

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

source_name: Lower columella

extract_protocol:
Fluorescent Activated Cell Sorting (FACS) was performed using cell specific GFP lines. Sorted cells were collected directly into specific lysis buffers that were compatible with downstream applications. Cells used for bisulfite sequencing, mRNA-seq, smRNA-seq were lysed in Buffer AP1 (Qiagen), Buffer RLT (Qiagen), Trizol (Invitrogen). All samples were immediately stored at -80 °C until gDNA and RNA was extracted using DNeasy Plant mini kit (Qiagen) and RNeasy Plant mini kit (Qiagen) or Trizol, respectively.
Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) or KAPA HIFI Uracil+ (KAPA Biosystems, Wilmington, MA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).

value: FACSorted lower columella cells


title: Endodermis line2 RNA-seq

source_name: Endodermis line2

value: FACSorted endodermis cells

value: ProSCR:GFP line2


title: Root tip (Col-0) MethylC-seq

source_name: Root tip (Col-0)

value: Root tip

value: Col-0 (wild type)


title: Stele RNA-seq

source_name: Stele

value: FACSorted stele cells


title: Endodermis line1 RNA-seq

source_name: Endodermis line1

value: ProSCR:GFP line1


title: ID00003 rep2


title: Columella root cap MethylC-seq


title: NR -N rep2

city: New Brunswick

first: Orly

last: Levitan

state: NJ

address: 71 Dudley Road

institute: Rutgers university

description:
NR minusN replicat 2
NR_Nplus_vs_NR_Nminus_DESeq_output.txt
wt_Nminus_vs_NR_Nminus_DESeq_output.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, then mapped to Phaeodactylum tricornutum's filtered models genes (10,402) using CLC genomic workbench v6.0.2 alowing a maximum of 3 mismatches. Only unique matching reads were counted for differential expression analysis.
The R package DESeq v1.10.1 was used for calling differentially expressed genes.
Genome_build: Phatr2 (http://genome.jgi.doe.gov/Phatr2/Phatr2.home.html)
Supplementary_files_format_and_content: tab-delimited text file, DESeq output with 8 columns: gene id, baseMean, baseMeanA,  baseMeanB ,  foldChange (B/A), log2FoldChange,  pval and padj (FDR).

organism: Phaeodactylum tricornutum

source_name: whole cells

growth_protocol: Axenic culture of the WT Phaeodactylum tricornutum (accession Pt1, 8.6) and our nitrate reductase transformant NR21 were maintained in sterile artificial sea water enriched with F/2 nutrients  . The nitrogen source used was 0.88 mM NaNO3. A set of three biologically independent cultures were maintained under exponential growth conditions at 18 °C and 200 µmol photons m-2s-1 continuous white LED light, and aerated through 0.2 µm filters. Cultures were cultivated using an exponentially growing inoculum to keep them optically thin and to make sure that the sampling is done during exponential growth phase.

extract_protocol:
Used oligo dt to extract mRNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exponentially grown cells were spun down for 5 minutes at 5,000 g  set to 18 °C, and the pellets were washed (re-suspended and centrifuged) twice using an nitrogen-free ASW-based F/2. Following the washes, each original culture was separated into two cultures with cell concentration of 2.5x105 cells/mL, one with 0.88 mM of NaNO3 (called nitrogen-replete) and one without any nitrogen source (nitrogen-stressed). Cultures were grown for 48 hours and then harvested for the different analysis.


title: NTC-human

description: It's a negative control reaction with no nucleic acid, but with the rest of reagents of the RASL reaction.

organism: unidentified plasmid

source_name: no template control


title: NR -N rep3

description:
NR minusN replicat 3
NR_Nplus_vs_NR_Nminus_DESeq_output.txt
wt_Nminus_vs_NR_Nminus_DESeq_output.txt


title: Epidermis RNA-seq

source_name: Epidermis

value: FACSorted epidermis cells


title: NR -N rep1

description:
NR minusN replicat 1
NR_Nplus_vs_NR_Nminus_DESeq_output.txt
wt_Nminus_vs_NR_Nminus_DESeq_output.txt


title: control sample #18 TU

description: control sample #18 TU


title: Cortex RNA-seq

source_name: Cortex

value: FACSorted cortex cells


title: NR +N rep3

description:
NR plusN replicat 3
NR_Nplus_vs_NR_Nminus_DESeq_output.txt
wt_Nplus_vs_NR_Nplus_DESeq_output.txt


title: Root tip (PET111) MethylC-seq

source_name: Root tip (PET111)


title: NR +N rep2

description:
NR plusN replicat 2
NR_Nplus_vs_NR_Nminus_DESeq_output.txt
wt_Nplus_vs_NR_Nplus_DESeq_output.txt


title: NR +N rep1

description:
NR plusN replicat 1
NR_Nplus_vs_NR_Nminus_DESeq_output.txt
wt_Nplus_vs_NR_Nplus_DESeq_output.txt


title: Endodermis line2 MethylC-seq


title: WT -N rep2

description:
WT minusN replicat 2
wt_Nplus_vs_wt_Nminus_DESeq_output.txt
wt_Nminus_vs_NR_Nminus_DESeq_output.txt


title: Epidermis MethylC-seq


title: WT +N rep3

description:
WT plusN replicat 3
wt_Nplus_vs_wt_Nminus_DESeq_output.txt
wt_Nplus_vs_NR_Nplus_DESeq_output.txt


title: WT -N rep1

description:
WT minusN replicat 1
wt_Nplus_vs_wt_Nminus_DESeq_output.txt
wt_Nminus_vs_NR_Nminus_DESeq_output.txt


title: Endodermis line1 MethylC-seq


title: WT -N rep3

description:
WT minusN replicat 3
wt_Nplus_vs_wt_Nminus_DESeq_output.txt
wt_Nminus_vs_NR_Nminus_DESeq_output.txt


title: Cortex MethylC-seq


title: rdr1/2/6_dry_smRNA rep2

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

data_processing:
Remove 3'end sequence (TGGAATTCTCGGGTGCCAAGGAACT) that invovled in adaptor sequence
The sequence was mapped to the Arabidopsis reference genome (TAIR10), using bowtie software (Langmead et al., 2009).
Genome_build: TAIR10
Supplementary_files_format_and_content: The sequences mapped on plus- and minus- strand on the genome were generated to wig files resistively

source_name: whole plant

growth_protocol: 2-week-old rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium.

extract_protocol:
small RNA fraction was extracted from whole plants using Ambion mirVana miRNA Isolation Kit (Life technologies). 10μg small RNA fractions wrere purified into 20-30nt RNA by 8M urea and 7.5% acrylamide gel electrophoresis and gel extraction.
20-30nt small RNAs were constructed to small RNA libraries, using TruSeq Small RNA Library Preparation Kits (Illumina)  The small RNA labraries were read by hi-seq 2000.

treatment_protocol: The plants were transferred from MS medium to plastic dish and kept for 2 hr.

tag: ecotype

tag: genotype/variation

value: drought stress

value: whole plant


title: rdr1/2/6_dry_smRNA rep3


title: rdr1/2/6_con_smRNA rep3


title: WT +N rep1

description:
WT plusN replicat 1
wt_Nplus_vs_wt_Nminus_DESeq_output.txt
wt_Nplus_vs_NR_Nplus_DESeq_output.txt


title: rdr1/2/6_con_smRNA rep2


title: WT_dry_smRNA rep2

value: wildtype


title: WT_dry_smRNA rep3


title: HN878 RIF-R mutant with RpoB:S531L, replicate 3

status: Public on Mar 30 2016

city: College Station

first: Thomas

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

description: processed data file column header: W-S531L_3

data_processing:
base-calling with Casava
custom C program to align reads to genome
custom script to count reads mapping to each ORF
Genome_build: NC_000962.2

organism: Mycobacterium tuberculosis HN878

source_name: bacteria

growth_protocol: The samples were first grown in a 15 ml starter culture with rich media until the OD reached .5.  The cells were then pelleted and washed twice with PBST, resuspended in 1 ml of the relevant media, then grown in a 100 ml culture of the same relevant media.  These cultures were grown in roller bottles to an OD of 0.5.

extract_protocol:
RNA was  extracted by bead beating in Trizol and then using the direct-zol kit (Zymo research) to purify RNA.
RIBOzero was used for rRNA depletion, followed by RIBOtag-seq protocol (Shishin et al., 2015; Nature Methods)

tag: replicate

tag: mutation


title: WT_con_smRNA rep2

tag: treatment


title: WT_con_smRNA rep3


title: -ARS2

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

data_processing:
Illumina Casava software used for basecalling.
Raw sequenced reads were trimmed for adaptor sequence using cutadapt, and then mapped to zebra finch whole genome, transcriptome (Ensembl annotations) and assembled golden-collared manakin genome using Bowtie version 0.12.9 with parameters --sam-nosq -S -k 80 –e 140 -n 3 -l 20 -q --phred33-quals -p 1 –y and BLAT version3.4 with parameters -minIdentity=75 -stepSize=75
Expression levels of genes, the RPKM (reads per kilobase of exon per million mapped reads) measure was calculated (MORTAZAVI et al. 2008)
Genome_build: taeGut1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Taeniopygia guttata

source_name: scapulohumeralis caudalis

extract_protocol:
Total RNA was extracted from zebra finch and golden-collared manakin muscle tissues using Trizol (Life Technologies). Additional column purification and DNaseI treatment were applied using Direct-zol RNA kit (Zymo Research).
The standard Illumina protocol was used to prepare strand-specific libraries for RNA-Seq (TruSeq mRNA library prep kit, with ribosomal RNA removal and polyA selection).

treatment_protocol: 1) golden-collared manakins: Each males were assigned at random to receive either a testosterone implant or a blank implant. Both testosterone-filled and control implants were inserted subcutaneously at the base of the neck according to standard procedures. 2) zebra finches: Each bird was assigned at random to receive either a flutamide implant or a blank implant. On the subsequent day, every male received an implant filled with testosterone.

value: scapulohumeralis caudalis

value: in the absence of testosterone


title: -ARS1


title: HN878 RIF-R mutant with RpoB:H526D, replicate 1

description: processed data file column header: W-H526D


title: MabATCC_rna_R1

city: Dublin

first: Brendan

last: Loftus

address: Conway Institute, Belfield, Dublin 4

department: School of Medicine & Medical Science

country: Ireland

institute: University College Dublin

description: RNAseq

data_processing:
Basecalls were performed using Illumina CASAVA (1.8) software.
Sequence reads were trimmed for adapter sequences, further filtered to preserve only higher quality reads, using Cutadapt (1.4.2),  and finally aligned to the M. abscessus ATCC19977 (NC_010397) genome, using Bowtie (1.1.1).
Samtools' (0.1.19) BAM/SAM functionality was applied to the trimmed sequences in order to produce corresponding BAM/SAM files for downstream processing.
Reads Per Kilobase per Million mapped reads (RPKM) analysis was performed on the aligned reads in order to quantify gene expression from sequencing data by normalizing for total read length and the number of sequencing reads (RNA-seq and ribo-seq). (Nat Methods, 5(7):621-628.)
Bedtools' (v2.22.0) genomecov function was applied to the data in order to quantify per-base read densities across the entire genome (RNA-seq and ribo-seq).
Bedtools' (v2.22.0) bamtobed function was applied to the data in order to generate BED files for read data (dRNA-seq).
Genome_build: NC_010397.1  GI:169627108
Supplementary_files_format_and_content: .rpkm.txt extended files are tab-delimited text files including RPKM values for each sample.
Supplementary_files_format_and_content: .forward.txt/.reverse.txt extended files are tab-delimited text files including per-base read densities for each sample.
Supplementary_files_format_and_content: .fastq.sam.bam.bed extended files are tab-delimited BED files containing information on read alignments for each sample and treatment.

organism: Mycobacteroides abscessus ATCC 19977

source_name: Whole cell

growth_protocol: Triplicate M. abscessus ATCC19977 cultures were grown in Middlebrook 7H9 medium (supplemented with 10% albumin-dextrose-catalase solution, 0.5% glycerol and 0.05 % Tween-80) with continuous shaking at 37 ᵒC. At OD600 = 0.8 each culture was split into three aliquots and processed for RNAseq, ribosome profiling and whole proteome analyses.

extract_protocol:
Bacteria were recovered by centrifugation (10 min at 4000 x g) and re-suspended in TRI-Reagent (Sigma Aldrich). Following physical disruption using 0.1 mm zirconia-silica beads in a MagNA Lyzer (Roche Diagnostics), RNA was isolated as previously described (doi: 10.1111/mmi.12387). Briefly, RNA was isolated using miRNeasy spin columns with an additional on-column DNase treatment, according to manufacturer’s instructions (Qiagen).
Total RNA was treated with RiboZero (Epicentre) to deplete ribosomal RNA. Sequencing libraries were generated with the TruSeq Stranded RNA kit according to manufacturer’s instructions (Illumina Inc.).

tag: growth phase

value: mid-log

value: Wild type

tag: detected molecule

value: Ribosome depleted total RNA


title: -ARS3


title: HN878 RIF-R mutant with RpoB:H526R, replicate 1

description: processed data file column header: W-H526R_1


title: HN878 RIF-R mutant with RpoB:S531L, replicate 1

description: processed data file column header: W-S531L_1


title: WT +N rep2

description:
WT plusN replicat 2
wt_Nplus_vs_wt_Nminus_DESeq_output.txt
wt_Nplus_vs_NR_Nplus_DESeq_output.txt


title: HN878 RIF-R mutant with RpoB:D516V, replicate 3

description: processed data file column header: W-D516V_3


title: Stele MethylC-seq

tag: cell type

value: root


title: HN878 RIF-R mutant with RpoB:H526R, replicate 2

description: processed data file column header: W-H526R_2


title: HN878 RIF-R mutant with RpoB:D516V, replicate 2

description: processed data file column header: W-D516V_2


title: HN878 Beijing strain, replicate 3

description: processed data file column header: W_3


title: HN878 Beijing strain, replicate 2

description: processed data file column header: W_2


title: HN878 Beijing strain, replicate 1

description: processed data file column header: W_1


title: HN878 RIF-R mutant with RpoB:H526R, replicate 3

description: processed data file column header: W-H526R_3


title: -ARP3

source_name: pectoralis

value: pectoralis


title: -ARP1


title: +ARS3

value: in the presence of testosterone


title: +ARS2


title: -TS1

organism: Manacus vitellinus


title: HN878 RIF-R mutant with RpoB:S531L, replicate 2

description: processed data file column header: W-S531L_2


title: +ARS1


title: -TP2


title: MabATCC_rna_R2

description: RNAseq


title: +ARP3


title: -TP3


title: +TS2


title: +TS3


title: +TP1


title: +ARP1


title: H3K4me2-KO rep3 input

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

country: China

institute: shanghai jiao tong university

data_processing:
Sequencing reads were aligned to mouse genome (mm10) by bowtie2 (version 2.2.3)
After mapping reads to mouse genome (mm10) by bowtie2 (version 2.2.3) with parameter “--sensitive”,perform filtering by (1) removing alignments with mapping quality less than 10, (2) removing duplicate reads identified by Picard Mark Duplicates (version 1.92, http://broadinstitute.github.io/picard).
The enriched regions (peaks) were identified using MACS2 (version 2.0.10.20131216), with a q-value cut-off of 0.05.For the occupancy-based analysis (Venn diagram results), common peaks of replicates were used. Peak regions was annotated by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, and peak file

source_name: perfused primary hepatocytes

extract_protocol:
liver were perfused and primary hepatocytes were isolated and performed for ChIP-seq.
ChIP-seq libraries were prepared using KAPA HTP Library Preparation Kit, and sequenced on Illumina HiSeq 2500 using 50SR SBS v3 reagents at McDermott Center Next Generation Sequencing Core at UT Southwestern.And for H3K4me2 chip-seq, library were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit, and sequenced on Illumina NEXTseq 500 using High  Output kit v2 reagents at CRI Sequencing Facility at UT Southwestern.

value: C57/B6 and 129 mix

value: liver

tag: age

value: postnatal day 90

value: Arid1a Fl/Fl; Alb-cre


title: -ARP2


title: +ARP2


title: -TP1


title: +TP2


title: HN878 RIF-R mutant with RpoB:D516V, replicate 1

description: processed data file column header: W-D516V_1


title: +TS1


title: +TP3


title: H3K4me2-WT rep3 input

value: Arid1a Fl/Fl


title: H3K4me2-KO rep3

description: ChIP DNA

value: H3K4me2 (Millipore, 07-030)


title: H3K4me2-KO rep2

description: ChIP DNA


title: H3K4me2-KO rep1 input


title: H3K4me2-WT rep2 input


title: H3K4me2-WT rep1

description: ChIP DNA


title: H3K4me2-KO rep1

description: ChIP DNA


title: H3K4me2-WT rep3

description: ChIP DNA


title: postPHX-H3K4me2-KO input

data_processing:
Sequencing reads were aligned to mouse genome (mm10) by bowtie2 (version 2.2.3)
After mapping reads to mouse genome (mm10) by bowtie2 (version 2.2.3) with parameter “--sensitive”,perform filtering by (1) removing alignments with mapping quality less than 10, (2) removing duplicate reads identified by Picard Mark Duplicates (version 1.92, http://broadinstitute.github.io/picard).
The enriched regions (peaks) were identified using MACS2 (version 2.0.10.20131216), with a q-value cut-off of 0.05.For the occupancy-based analysis, common peaks of replicates were used. Peak regions was annotated by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, and peak file

source_name: frozen post-hepatectomy liver tissue

extract_protocol:
Frozen liver tissues were minced quickly with a razorblade into small pieces which less than 0.5 cm3. Crosslink tissue in 1% formaldehyde for 20 min at room temperature.Dounce tissue in ice-cold PBS first with the loose and later with the tight pestle. Rinse tissue with PBS. hepatocytes were isolated and performed for ChIP-seq.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit, and sequenced on Illumina NEXTseq 500 using High  Output kit v2 reagents at CRI Sequencing Facility at UT Southwestern.

treatment_protocol: The mice were performed for two thirds partial hepatectomy and 40 hours later sack mice.Liver tissues were collected and frozen in -80.


title: postPHX-H3K4me2-WT input


title: postPHX-E2f4-KO rep2 input


title: postPHX-E2f4-KO rep1 input


title: H3K4me2-WT rep1 input


title: postPHX-H3K27ac-KO input


title: H3K4me2-KO rep2 input


title: postPHX-H3K27ac-WT input


title: postPHX-E2f4-WT rep2 input


title: postPHX-E2f4-WT rep1 input


title: postPHX-E2f4-WT rep2

value: E2f4 (Santa Cruz, sc-866x)


title: postPHX-H3K4me2-KO


title: postPHX-E2f4-WT rep1


title: postPHX-E2f4-KO rep2


title: postPHX-H3K27ac-KO

value: H3K27ac (Abcam, ab4729)


title: postPHX-H3K27ac-WT


title: postPHX-E2f4-KO rep1


title: RNAseq_postPHX_KO_rep3

description: processed data in Series supplementary file phx-40h-filtered.merged.genes.fpkm_tracking.txt

data_processing:
Sequence reads were aligned to mouse  genome version mm9(pre-phx) and mm10(post-phx) using TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads)
Differential gene expression analyses were performed using edgeR.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: text file of gene RPKM values

extract_protocol:
Frozen liver tissues RNA was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina or Nugen library protocols.


title: RNAseq_postPHX_WT_rep3


title: RNAseq_postPHX_WT_rep2


title: H3K4me2-WT rep2

description: ChIP DNA


title: RNAseq_postPHX_KO_rep2


title: RNAseq_postPHX_WT_rep1


title: 270 FLOW

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Remove outliers (9595, 791 & 814)
Normalization (TMM), quantitation (FPKM and adjFPKM) and differential expression analysis using EdgeR. For IP vs IP IP and Flow vs Flow, IP and flow samples were separately analyzed. All samples were included in normalization for IP vs Flow.
Genome_build: mm10

source_name: spinal cord

extract_protocol:
HA and FT samples underwent on-column DNA digestion using the RNase-Free Dnase Set (Qiagen) and RNA purified with the RNeasy Micro kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by RiboGreen RNA Assay kit (Life Technologies).
cDNA was generated from 5ng of IP or FT RNA using the Nugen Ovation® 2 RNA-Seq Sytstem V2 kit (Nugen). 1 ug of cDNA was fragmented using the Covaris M220. Paired-end libraries for multiplex sequencing were generated from 300 ng of fragmented cDNA using the Apollo 324 automated library preparation system (Wafergen Biosystems), enriched over 10 cycles of PCR cycles and purified with Agencourt AMPure XP beads (Beckman Coulter).

value: STAT3 KO

tag: rna sample type

value: flow through

tag: condition

value: Spinal cord injury

value: spinal cord


title: RNAseq_postPHX_KO_rep1


title: postPHX-H3K4me2-WT

tag: chip antibody


title: 186 FLOW

tag: genotype


title: 531 FLOW


title: 9596 HA

value: Wild type

value: HA IP


title: 9596 FLOW


title: 531 HA


title: 9935 HA


title: 186 HA


title: 65 FLOW

value: Uninjured


title: 9843 HA


title: 9874 FLOW


title: 154 HA


title: 9843 FLOW


title: 42 FLOW


title: 9935 FLOW


title: 154 FLOW


title: H37Rv grown in toloxapol, pH 5.5, replicate 2

description: processed data file column header: 37Rv_TOL_LpH_2

organism: Mycobacterium tuberculosis H37Rv


title: 65 HA


title: HeatShock1

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

description: rRNA depleted total RNA

data_processing:
QC was performed using FastQC v0.10.1
Reads were quality filtered, trimmed and adapter sequences were removed using Trimmomatic v0.3.0
Reads were aligned to the hg19 Homo sapiens genome using tophat2 using the default settings except for the following (-M -microexon-search -n 3 --genome-read-mismatches 3 --read-mismatches 3 --b2-sensitive)
Transcripts were assembled using Cufflinks v2.0.2 and the hg19 annotations were included. Transcripts across all replicates were merged using cuffmerge and differential expression analysis was performed pair-wise on the groups using cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: [Heat_shock_table.csv] standard cuffdiff output.
Supplementary_files_format_and_content: [.fpkm_tracking] isoform level read counts
Supplementary_files_format_and_content: [.gtf] Cufflinks output

source_name: HeatShock

growth_protocol: HEK293 cells were cultured in DMEM which was supplemented with 1% Penicillin-Streptomycin-Glutamine solution and 10% FBS. The cells were incubated at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions
Samples were rRNA depleted using ribominus and were prepared using the Truseq RNA prep kit according to manufacturer instructions.

treatment_protocol: During cell passaging, an aliquot of cells was taken and placed in a 15ml falcon tube. Heatshocked cells were placed in a water bath at 45°C for 30 minutes while control cells remained untreated.

tag: cell line

value: HEK293 cells

tag: stress

value: heat shock


title: HeatShock2

description: rRNA depleted total RNA


title: 79 FLOW


title: 42 HA


title: 79 HA


title: 270 HA


title: HeatShock3

description: rRNA depleted total RNA


title: Control3

description: rRNA depleted total RNA

source_name: Control

value: control


title: 9874 HA


title: H37Rv grown in toloxapol, pH 5.5, replicate 1

description: processed data file column header: 37Rv_TOL_LpH_1


title: Control2

description: rRNA depleted total RNA


title: Control1

description: rRNA depleted total RNA


title: H37Rv grown in toloxapol, pH 7.0, replicate 2

description: processed data file column header: 37Rv_TOL_2


title: H37Rv grown in toloxapol, pH 7.0, replicate 1

description: processed data file column header: 37Rv_TOL_1


title: RD64_f

city: Naples

first: Carmen

last: Bianco

address: Via P. Castellino 111

department: IBBR

country: Italy

institute: CNR

data_processing:
Prior to mapping, the 50nt single end reads  were trimmed by using the Mott’s trimming algorithm to reduce low quality base calls.
Sequencing reads from three biological replicates were processed using Bowtie2
Alignments reported from Bowtie were processed to count the number of reads that map to each gene in the S. meliloti genome using BEDTools
Count data were then used to assess the statistical significance of expression differences measured by using the software package DESeq
Genome_build: S. meliloti 1021 uid57603 (ASM696v1)
Supplementary_files_format_and_content: Tab-delimited txt files include raw counts and normalized counts of sequencing reads for each sample

organism: Sinorhizobium meliloti

source_name: Free-living cells

growth_protocol: Bacterial strains were grown in Tryptone Yeast extract for rhizobia or minimal medium

extract_protocol:
RNA was purified from cells up to exponential growth phase. MICROBExpress kit was tused to enrich bacterial mRNA from purified total RNA by removing the 16S and 23S ribosomal RNAs.The sequencing libraries were constructed using the TruSeq RNA-seq sample prep kit from Illumina skipping the first part of the protocol consisting in the purification of poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In some experiments glutamate 5 mM was used as nitrogen source. For the growth under low-oxygen condition the oxygen was excluded by flushing the headspaces with N2 and vials sealed and incubated for 4 h at 30° C on a shaker at 200 rpm.

tag: strain

tag: growth stage

value: cells in exponential growth phase

value: IAA-overproducing


title: 1021_a

data_processing:
Prior to mapping, the 50nt single end reads  were trimmed by using the Mott’s trimming algorithm to reduce low quality base calls.
Sequencing reads from three biological replicates were processed using Bowtie2
Alignments reported from Bowtie were processed to count the number of reads that map to each gene in the S. meliloti genome using BEDTools
Count data were then used to assess the statistical significance of expression differences measured by using the software package DESeq
Genome_build: S. meliloti 1021 uid57603
Supplementary_files_format_and_content: Tab-delimites txt file includes raw counts of sequencing reads for each sample

value: wild type


title: H37Rv grown in low iron, 1 week replicate 3

description: processed data file column header: 37Rv_LoFe_1W_3


title: H37Rv grown in low iron, 1 week replicate 1

description: processed data file column header: 37Rv_LoFe_1W_1


title: 1021_c


title: H1T_MDAMB231_ChIPseq

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

institute: Okayama University of Science

data_processing:
In this study, all of the data processing was performed by using Galaxy platform (https://usegalaxy.org/).
ChIP-seq reads were aligned to the hg19 or mm9 genome assembly using BWA (Galaxy Tool Version 1.2.3).
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: wig files were generated using MACS (ver1.0.1) with the following setting: Extend tag from its middle point to a wigextend size fragment (-1), Resolution for saving wiggle files (10).

growth_protocol: AGS cells were cultured in RPMI1640 (SIGMA), 2 mM L-Glutamine, 10% fetal bovine serum (FBS) (Cell Culture Bioscience). MDA-MB-231 cells were cultured in D-MEM (high glucose), 2 mM L-Glutamine, 10% FBS. mESCs (J1 line) were maintained the stemness in D-MEM (high glucose) (Wako) supplemented 15% KnockOut Serum Replacement (Invitrogen), 5% FBS, 2 mM L-glutamine (Wako), 1 mM Na-pyruvate (Wako), 100 µM 2-Mercaptoethanol (Wako), MEM Non-essential Amino Acids (Wako), 1500 U/ml leukemia inhibitory factor (ESGRO; Millipore) on the gelatin-coated dish.

extract_protocol:
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, Cat No. 53009) and anti-H1T rabbit polyclonal antibody
The libraries for massive parallel sequencing were prepared with the TruSeq DNA Sample Preparation v2 Kit (Illumina) according to the manufacturer's instructions. Briefly, 50 ng of immunoprecipiated DNA or input DNA were end repaired, 3’ adenylated and ligated with adapter oligos. DNA fragments within the range of 120~500 bp were purified using AMpure XP beads (Beckman Coulter) and amplified by PCR. Library DNA was electrophoresed in 2% agarose gel and subsequently purified with a Zymoclean Gel DNA Recovery Kit (Zymo Reserch). Libraries were quantified by BioAnalyzer2000 (Agilent). Sequencing was performed with Illumina HiSeq 2000 systems

value: Breast adenocarcinoma

tag: chip-antibody

value: anti-H1T (rabbit polyclonal antibody, prepared in-house)


title: Input_MDAMB231


title: Input_AGS

value: AGS

value: Gastric adenocarcinoma


title: RD64_e


title: H1T_AGS_ChIPseq


title: Myla_DMSO

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
Adapter trimming: trim_galore 0.3.7
Alignment: Bismark v0.13.1 -–bowtie2 -N 1 -L 20
deduplicate: Bismark v0.13.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files: CpG percent methylation

source_name: cell line

growth_protocol: MyLa CTCL cell lines were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), glutamine (2 mM) and streptomycin (100 μg/ml) at 37°C, 5% CO2 and 95% humidity. Patients’ peripheral blood was collected in EDTA tubes. PBMCs were separated from whole blood by Ficoll density gradient, then CD4+ T-cells were selected by MACS CD4+ negative selection kit (Miltenyi Biotec) per manufacture’s protocol. After negative cell selection, CD4+ T-cells were stimulated with CD3/CD28 Dynabeads (Life technologies) in addition in IL-2 30 Unit/ml.

extract_protocol:
DNA was isolated using TRIzol, according to manufacturer’s instructions
Total of 3ug of DNA was used as input amount in the Agilent SureSelectXTMethyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing protocol. Quality of the isolated DNA was assessed by an Agilent 2200 Tapestation. DNA was sheared using a S220 Focused-ultrasonicator (Covaris). Bisulfite conversion was done using EZ DNA Methylation Kit from Zymo Research according to manufacturer’s instructions.

treatment_protocol: MyLa cells were 48hrs treated with the romidepsin (1.25nM) and/or azacitidine (2.5uM) or DMSO only treated cells for 48hrs. Patient derived cells were treated with azacitidine 2.5uM for 4 days and romidepsin 2.5nM was added for the last 24 hours

tag: disease

value: CTCL

tag: origin

value: cell culture

value: DMSO


title: 1021_b


title: Myla_Romidepsin_Azacitidine

value: romidepsin (1.25nM) and azacitidine (2.5uM)


title: MabATCC_tss_R2

description: TSS-sequencing (single end, strand specific cDNA sequencing)

extract_protocol:
Following physical disruption using 0.1 mm zirconia-silica beads in a MagNA Lyzer (Roche Diagnostics), RNA was isolated as previously described (doi: 10.1111/mmi.12387). Briefly, RNA was isolated using miRNeasy spin columns with an additional on-column DNase treatment, according to manufacturer’s instructions (Qiagen).
Two types of strand specific libraries were prepared in parallel, mRNA enriched (TEX+) and not enriched (TEX-) libraries, and sequenced using the Illumina HiSeq 2000 instrument in a single read mode. Briefly, for mRNA enriched samples, monophosphorylated i.e. processed transcripts were removed from total RNA by a 1 h treatment at 30 °C with a terminator-5′-phosphate-dependent exonuclease (TEX+) (TEX, Epicentre Biotechnologies). The not enriched samples (TEX-) were incubated in the reaction buffer alone, without the enzyme. Obtained RNA samples were then treated with a tobacco acid pyrophosphatase (TAP, Epicentre Biotechnologies) at 37°C for 1 hour, followed by a 5’ linker ligation and synthesis of cDNA.

treatment_protocol: Bacteria were recovered by centrifugation (10 min at 4000 x g) and re-suspended in TRI-Reagent (Sigma Aldrich).

value: mid-log

value: Wild type

value: total RNA


title: H37Rv grown in low iron, 1 day, replicate 2

description: processed data file column header: 37Rv_LoFe_1D_2

tag: replicate


title: Myla_Romidepsin

tag: treatment

value: romidepsin (1.25nM)


title: Myla_Azacitidine

value: azacitidine (2.5uM)


title: H37Rv grown in low iron, 1 day, replicate 1

description: processed data file column header: 37Rv_LoFe_1D_1


title: MabATCC_ribo_R2

description: Ribosome Profiling

extract_protocol:
The bacterial pellets were re-suspended in lysis buffer (100 mg/mL chloramphenicol, 70 mM KCl, 10 mM MgCl2, 10 mM Tris-HCl [pH 7.4]) and physically disrupted by two passages through a French Press (10,000 psi), followed by centrifugation to remove intact cells and cellular debris. The clarified lysates were digested with MNase and RNaseI. Ribosome protected fragments were recovered by sedimentation through a 1 M sucrose cushion, size selected by gel purification and prepared for high throughput sequencing (doi: 10.1038/nprot.2012.086).
Briefly, 3’ termini of ribosome protected fragments were dephosphorylated with polynucleotide kinase (PNK, New England Biolabs) allowing for ligation of a 3’ RNA TruSeq small RNA adapter (Illumina Inc.). The 5’ termini were then phosphorylated by PNK and 5’ RNA TruSeq small RNA adapter was ligated. Following reverse transcription, the ribosome protected fragments were amplified by PCR and PCR products of expected size were purified from a Tris-Borate-EDTA gel.

treatment_protocol: To arrest translation bacterial cultures were treated with 100 mg/mL chloramphenicol and then spun down (10 min at 4000 x g).

tag: growth phase

value: Ribosome protected mRNA fragments


title: RD64_d

value: cells in exponential growth phase


title: H37Rv grown in low iron, 1 week replicate 2

description: processed data file column header: 37Rv_LoFe_1W_2


title: H37Rv grown in high iron, replicate 2

description: processed data file column header: 37Rv_HiFe_2


title: BSB_DMSO

source_name: peripheral blood

value: patient derived


title: H37Rv grown in high iron, replicate 3

description: processed data file column header: 37Rv_HiFe_3


title: BSB_Romidepsin_Azacitidine


title: H37Rv grown in high iron, replicate 1

description: processed data file column header: 37Rv_HiFe_1


title: MabATCC_ribo_R1

description: Ribosome Profiling

tag: detected molecule


title: H37Rv grown on 0.4% glucose, replicate 2

description: processed data file column header: 37Rv_4G_2

value: glucose


title: AR501_L3_RNAseq

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

data_processing:
Quality filtering: Sequenced reads were filtered for primer and adapter sequences using Tagdust (1.12) (Lassmann et al., 2009)
Alignment: High quality reads were aligned to the C. elegans ce10 genome using Tophat2 (2.0.14) (Kim et al., 2013). Resulting bam files were normalized to read depth and converted to bigwig format using bedtools genomecov (2.22.1) (Quinlan et al, 2010) followed by bedGraphToBigWig (UCSC Genome Browser). Replicate bigwig files were averaged using java-genomics-toolkit wigmath.Average (java/1.8.0_11), (http://palpant.us/java-genomics-toolkit/).
Genome_build: ce10
Supplementary_files_format_and_content: .bw files for individual samples; average_track.bw files merging ELT-2 or H3K4me3 ChIP-seq tracks (subtracted over IgG only tracks); bed files for significant peaks; bed files for significant peak summits.

source_name: L3 staged worms_RNA-seq

growth_protocol: N2 worms were grown in liquid culture (S-medium) at 25°C, fed with HB101 Escherichia coli bacteria, and harvested for ChIP-seq at the L3 stage of development (24 - 26 hrs post feeding).

extract_protocol:
Total RNA was prepared using TRIZOL and Qiagen RNeasy spin kit.
RNA-seq was performed using a standard protocol (NEBNext Poly(A) mRNA Magnetic Isolation Module E7490, NEBNext Ultra RNA Library Prep Kit E7530 or E7420, and Agencourt Ampure XP beads). The resulting fragmented cDNA was ligated to Illumina multiplexed adapters and sequenced on Hi-Seq2500 Illumina instruments as 50 bp single-end reads with 8 bp for multiplex adapter sequencing.

tag: developmental stage

value: L3 staged worms


title: AR138_rep3_input

data_processing:
Quality filtering: Sequenced reads were trimmed of barcodes (FASTX-Toolkit, 11sep2008, http://hannonlab.cshl.edu/fastx_toolkit/index.html) and filtered for primer and adapter sequences using Tagdust (1.12), (Lassmann et al., 2009).
Alignment: Resulting high quality reads were aligned to the C. elegans ce10 genome using Bowtie/1.1.0 (Langmead et al., 2009).  Resulting bam files were normalized to read depth and converted to bigwig format using bedtools genomecov (2.22.1), (Quinlan et al, 2010) followed by bedGraphToBigWig (UCSC Genome Browser) to create individual .bw tracks. The resulting ELT-2 and H3K4me3 ChIP-seq bigwig files were subtracted from IgG-only bigwig tracks and the resulting replicates were averaged using java-genomics-toolkit wigmath.Average (java/1.8.0_11), (http://palpant.us/java-genomics-toolkit/) to create average_track.bw files.
Peak Calling: Significant peaks were identified by MACS2 (2.0.9) using a concatenated set of ChIP-seq replicates as treatment and a concatenated set of input samples as a control (Zhang et al., 2008). Concatenated samples were downsampled to standardize the number of input reads per replicate. Peaks were filtered for a minimum threshold of -log10(q-value) ≥ 30. HOT regions (Chen et al., 2014), blacklisted regions (Araya et al., 2014) and IgG-only peaks were subtracted from the set of identified MACS2 peaks.
Genome_build: ce10
Supplementary_files_format_and_content: .bw files for individual samples; average_track.bw files merging ELT-2 or H3K4me3 ChIP-seq tracks (subtracted over IgG only tracks); bed files for significant peaks; bed files for significant peak summits.

source_name: L3 staged worms_input

extract_protocol:
Flash frozen larvae were physically homogenized in a mixer mill, fixed in 1 % formaldehyde for 10 minutes, quenched with 50 mM glycin for 5 min, sheared by sonication in a Bioruptor, and the resulting chromatin was extracted. Immunoprecipitation was performed using either 5 mg a-ELT-2 (455-2A4) antibody, 5 mg a-H3K4me3 antibody (WAKO 305-34819), or mock conditions (IgG only). The anti-ELT-2 monoclonal antibodies was produce by the Southern Alberta Cancer Research Institute Antibody Services by using a purified poly-histidine tagged full-length ELT-2 protein produced in E. coli as an antigen to produce anti-ELT-2 monoclonal antibody 455-2A4 (isotype IgG1). Antibodies concentrated from hybridoma supernatants concentrated ~10-fold by pressure filtration, dialyzed extensively against PBS and then concentrated a further 2-3 fold by dialysis against PBS-50 % glycerol.
ChIP-recovered DNA and input DNA were ligated to sequencing adapters using containing an eight-base multiplexing barcode sequence. DNA libraries were sequenced on either the Hi-Seq2000 or Hi-Seq2500 Illumina sequencers with 50 rounds of single-end sequencing, 8 cycles of which were used for multiplex barcode indices.


title: H37Rv grown in low iron, 1 day, replicate 3

description: processed data file column header: 37Rv_LoFe_1D_3


title: BSB_Romidepsin


title: AR505_L3_RNAseq


title: BSB_Azacitidine


title: EO037_rep2_ELT2

source_name: L3 staged worms_ELT2_ChIP-seq


title: AR137_rep3_IgG

source_name: L3 staged worms_IgG_ChIP-seq

value: IgG


title: EO041_rep2_input


title: MabATCC_tss_R1


title: H37Rv grown on 0.4% glucose, replicate 1

description: processed data file column header: 37Rv_4G_1


title: cebpa-KO rep2 input

description: ChIP DNA

value: C57/B6 and 129 mix

tag: tissue

value: liver

tag: age

value: postnatal day 90

value: Arid1a Fl/Fl; Alb-cre

value: C/ebpα (Santa Cruz, sc-61)


title: AR136_rep3_ELT2


title: cebpa-KO rep1 input

description: ChIP DNA


title: EO036_rep2_H3K4me3

source_name: L3 staged worms_H3K4me3_ChIP-seq


title: H37Rv grown on 0.2% glucose+0.1% butyrate, replicate 3

description: processed data file column header: 37Rv_2G1B_3

source_name: bacteria

tag: condition


title: AR135_rep3_H3K4me3

tag: chip antibody


title: EO028_rep1_input


title: H37Rv grown on 0.2% glucose+0.1% butyrate, replicate 1

description: processed data file column header: 37Rv_2G1B_1


title: cebpa-WT rep2 input

description: ChIP DNA

tag: genotype

value: Arid1a Fl/Fl


title: EO027_rep1_IgG


title: cebpa-WT rep1 input

description: ChIP DNA


title: H37Rv grown on 0.2% glucose+0.1% butyrate, replicate 2

description: processed data file column header: 37Rv_2G1B_2


title: EO025_rep1_ELT2


title: RNAseq_prePHX_KO_rep2

source_name: frozen pre-hepatectomy liver tissue


title: H37Rv grown on 0.4% glucose, replicate 3

description: processed data file column header: 37Rv_4G_3


title: Input_mESCs

tag: cell line

tag: cell type

value: Undifferentiated ESCs


title: RNAseq_prePHX_KO_rep1

tag: strain


title: H37Rv grown on 0.1% butyrate, replicate 2

description: processed data file column header: 37Rv_1B_2

value: butyrate


title: RNAseq_prePHX_WT_rep2


title: H37Rv grown on 0.1% butyrate, replicate 1

description: processed data file column header: 37Rv_1B_1


title: H37Rv grown on 0.1% butyrate, replicate 3

description: processed data file column header: 37Rv_1B_3


title: RNAseq_prePHX_WT_rep1


title: H1T_mESCs_ChIPseq

value: anti-H1T (rabbit polyclonal antibody, prepared in-house)


title: KO_clone_1_rep2_RNASeq

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

data_processing:
Tophat2 alignment to mouse genome, default
call differential genes with cuffdiff2
default setup
Genome_build: mm9
Supplementary_files_format_and_content: diff-gene table

source_name: Alkbh1 KO ESC

growth_protocol: standard mouse ES cell culture media and without feder

extract_protocol:
QIAGEN MiRNeasy kit, get total RNA
Illumina RNA strand specific mRNA TRUESeq kit protocol

tag: strain background

value: C57BL6 x CBA

tag: genotype/variation

value: Alkbh1 KO

tag: cell

value: ES cell

tag: passage

value: passage 5


title: WT_rep2_RNASeq

source_name: wildtype TT2 ESC

value: wildtype TT2


title: KO_clone_1_rep1_RNASeq


title: KO_clone_2_rep1_RNASeq


title: cebpa-WT rep2

data_processing:
Sequencing reads were aligned to mouse genome (mm10) by bowtie2 (version 2.2.3)
After mapping reads to mouse genome (mm10) by bowtie2 (version 2.2.3) with parameter “--sensitive”,perform filtering by (1) removing alignments with mapping quality less than 10, (2) removing duplicate reads identified by Picard Mark Duplicates (version 1.92, http://broadinstitute.github.io/picard).
The enriched regions (peaks) were identified using MACS2 (version 2.0.10.20131216), with a q-value cut-off of 0.05.For the occupancy-based analysis (Venn diagram results), common peaks of replicates were used. Peak regions was annotated by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, and peak bed file

source_name: perfused primary hepatocytes

extract_protocol:
liver were perfused and primary hepatocytes were isolated and performed for ChIP-seq.
ChIP-seq libraries were prepared using KAPA HTP Library Preparation Kit, and sequenced on Illumina HiSeq 2500 using 50SR SBS v3 reagents at McDermott Center Next Generation Sequencing Core at UT Southwestern.


title: cebpa-KO rep2


title: WT_rep1_RNASeq


title: cebpa-WT rep1


title: ChIP_KO_H2AX

data_processing:
Bowtie2.2.4 alignment to mouse genome, default
For the detection of  peaks in individual samples, use SICER
with  input DNA as control in SICER
FDR < 0.01
Genome_build: mm10
Supplementary_files_format_and_content: BED

growth_protocol: standard mouse ES cell culture media and without feeder

extract_protocol:
Native ChIP pulldown DNA fragments
Illumina ChIP TRUESeq kit protocol

tag: strain  background

value: passage 5 to 10

value: customize H2AX antibody


title: ChIP_WCE_genome_input


title: ChIP_KO_K4Me1

value: K4Me1 (Abcam, ab8895)


title: ChIP_KO_K27Ac

value: K27Ac (Abcam, ab4729)


title: H2A.X-N-ChIP-SMRTSeq_KO_S_rep2

description:
call DNA modification
processed data file: T8_S_Modification_N6mA.gff

data_processing:
Base modification was detected using SMRT Analysis 2.3.0
For the detection of modified bases in individual samples, the RS_Modification_Detection.1 protocol was used with the default parameters.
grep m6A modification sites
information to .gff file
Genome_build: mm10
Supplementary_files_format_and_content: The Gff file is  the PacBio standard analysis protocol result for DNA modification containing the N6-mA sites information, genome locus, IPD ratio, context sequence.

extract_protocol:
Native ChIP; QIAGEN DNeasy kit.
SMRT seq library; raw data files are in tar archive with each set 1 bas.h5 and 3 bax.h5 files; and sequence repeat twice

tag: antibody

value: customized H2A.X antibody


title: ChIP_WT_K4Me1


title: ChIP_WT_K9Me3

value: K9Me3 (Abcam, ab8898)


title: KO_clone_2_rep2_RNASeq


title: V5-Arid1a

value: C57/B6 and 129 mix

value: liver

value: postnatal day 90

value: V5 (Abcam ab15828)


title: ChIP_WT_H2AX


title: H2A.X-N-ChIP-SMRTSeq_KO_S_rep1


title: ChIP_KO_K9Me3


title: H2A.X-N-ChIP-SMRTSeq_WT_S_rep1

description:
call DNA modification
processed data file: T7_S_Modification_N6mA.gff

value: wild type


title: Input_control

description: ctrl

data_processing:
Bowtie2.2.4 alignment to mouse genome, default
For the detection of modification peaks in individual samples, use SICER
with sonicated input as control in SICER
FDR < 1.0E-15
For 5mC, use MACS2 generated wig to normalize, then transfer to bigwig file
Genome_build: mm10
Supplementary_files_format_and_content: BED

extract_protocol:
DNA IP
Follow ActiveMotif 5mC DNA IP kit protocol
single strand DNA pulldown then PCR

value: No antibody


title: AB5075_LB

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

description: total RNA, rRNA-depleted

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Expression values for Gene/CDS and Misc. RNA tracks were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The accession number for the Genbank genome files used as references is NZ_CP008706.1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

organism: Acinetobacter baumannii AB5075

source_name: Bacterial cells, pelleted

growth_protocol: Bacteria were grown in LB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: wild-type

tag: growth medium

value: LB

tag: growth conditions (time/temp/shaking)


title: H2A.X-N-ChIP-SMRTSeq_KO_L_rep2

description:
call DNA modification
processed data file: T8_L_Modification_N6mA.gff

value: C57BL6 x CBA

value: Alkbh1 KO

value: ES cell


title: H2A.X-N-ChIP-SMRTSeq_KO_L_rep1

value: passage 5 to 10


title: H2A.X-N-ChIP-SMRTSeq_WT_S_rep2


title: cebpa-KO rep1

value: Arid1a Fl/Fl; Alb-cre

value: C/ebpα (Santa Cruz, sc-61)


title: WT_5mC_DIP_Seq

description: call DNA modification peaks

value: wildtype

value: ActiveMotif kit 5mC antibody


title: KO_5mC_DIP_Seq

description: call DNA modification peaks


title: -TS2

data_processing:
Illumina Casava software used for basecalling.
Raw sequenced reads were trimmed for adaptor sequence using cutadapt, and then mapped to zebra finch whole genome, transcriptome (Ensembl annotations) and assembled golden-collared manakin genome using Bowtie version 0.12.9 with parameters --sam-nosq -S -k 80 –e 140 -n 3 -l 20 -q --phred33-quals -p 1 –y and BLAT version3.4 with parameters -minIdentity=75 -stepSize=75
Expression levels of genes, the RPKM (reads per kilobase of exon per million mapped reads) measure was calculated (MORTAZAVI et al. 2008)
Genome_build: taeGut1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: scapulohumeralis caudalis

extract_protocol:
Total RNA was extracted from zebra finch and golden-collared manakin muscle tissues using Trizol (Life Technologies). Additional column purification and DNaseI treatment were applied using Direct-zol RNA kit (Zymo Research).
The standard Illumina protocol was used to prepare strand-specific libraries for RNA-Seq (TruSeq mRNA library prep kit, with ribosomal RNA removal and polyA selection).

value: scapulohumeralis caudalis

tag: treatment

value: in the absence of testosterone


title: H2A.X-N-ChIP-SMRTSeq_WT_L_rep2

description:
call DNA modification
processed data file: T7_L_Modification_N6mA.gff

value: customized H2A.X antibody


title: WT_N6mA_DIP_Seq

description: call DNA modification peaks

value: SYSY 202-003 antibody


title: -TS3

tag: tissue


title: 4sU-seq of YRI individual (NA19257) [19257-60-1_C30NNACXX-6-19]

status: Public on Mar 29 2016

city: Stanford

first: Yang

middle: I

last: Li

state: CALIFORNIA

address: Department of Genetics

department: genetics

institute: Stanford University

description: processed data file: 4su_60_norm.txt

data_processing:
The reads were mapped to hg19 using STAR with option --outSAMstrandField intronMotif
The alignment were filtered to remove mapped reads with quality less than 10 using samtools -q 10
We used the WASP alignment strategy to filter read that may be mismapped owing to the human genome reference allele bias (pmid26366987)
We also used WASP to remove cofounding effect from sample-specific GC biases and read count differences to allow comparison between samples (4su_30_norm.txt, 4su_60_norm.txt).
We standardize the values by genes (row) and qqnorm by individuals (column) to get our final quantitative measurements (4su_30_qqnorm.txt, 4su_60_qqnorm.txt).
Genome_build: hg19

source_name: 4sU-seq of YRI individual NA19257_60min

growth_protocol: Cell lines were grown to log phase (6.5x10^6 - 8.5x10^6 viable cells/ml, with at least 70% cell viability) in RPMI 1640 (supplemented with 2 mM L-glutamine and 15% fetal bovine serum) using standard procedures (as recommended by Coriell).

extract_protocol:
RNA was isolated using QIAshredder columns (Qiagen) and the RNeasy mini kit (Qiagen), using the protocols provided. RNA concentration was measured using a NanoDrop spectrophotometer, and RNA quality was checked using an Agilent Bioanalyzer.
See PMID 21516085.

treatment_protocol: Culture volumes were sufficient to yield at least 6.4x10^6 viable cells, or enough to yield 300 ng of total RNA for the zero time point, and 300 ng of 4sU-labeled RNA for each of the 30' and 60' time points. At the designated “time 0,” cultures were divided into 10-ml aliquots, and 50 mM 4sU was added to each aliquot to obtain a final 4sU concentration of 2x10-7 uMoles/cell. Aliquots corresponding to the 0' time point were immediately washed in 5 mL PBS, pelleted, and frozen in liquid nitrogen. Aliquots corresponding to subsequent time points were returned to the incubator, and washed and frozen at the appropriate times.

value: lymphoblastoid cell line (LCL)

tag: cell line id

tag: incubated with 4su for


title: 4sU-seq of YRI individual (NA19257) [19257-60-1_C311JACXX-6-19]

description: processed data file: 4su_60_norm.txt


title: H2A.X-N-ChIP-SMRTSeq_WT_L_rep1

value: wild type


title: 4sU-seq of YRI individual (NA19239) [19239-60-1_D2775ACXX-4-19]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19239_60min


title: 4sU-seq of YRI individual (NA19257) [19257-30-1_C30BHACXX-6-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19257_30min


title: 4sU-seq of YRI individual (NA19257) [19257-60-1_C30BHACXX-6-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19257) [19257-30-1_C30NNACXX-6-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19238) [19238-30-1_D2775ACXX-7-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19238_30min


title: 4sU-seq of YRI individual (NA19238) [19238-60-1_D2775ACXX-7-08]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19238_60min


title: 4sU-seq of YRI individual (NA19225) [19225-60-1_D2775ACXX-5-04]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19225_60min


title: 4sU-seq of YRI individual (NA19225) [19225-30-1_D2775ACXX-5-03]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19225_30min


title: KO_N6mA_DIP_Seq

description: call DNA modification peaks


title: 4sU-seq of YRI individual (NA19223) [19223-60-1_C311JACXX-2-27]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19223_60min


title: 4sU-seq of YRI individual (NA19223) [19223-60-1_C30BHACXX-2-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19223) [19223-60-1_C30NNACXX-2-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19223) [19223-30-1_C30NNACXX-2-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19223_30min


title: 4sU-seq of YRI individual (NA19222) [19222-60-2_C30NNACXX-2-14]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19222_60min


title: 4sU-seq of YRI individual (NA19222) [19222-60-2_C311JACXX-2-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19222) [19222-60-2_C30BHACXX-2-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19222) [19222-60-1_D2775ACXX-5-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19257) [19257-30-1_C311JACXX-6-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19239) [19239-30-1_D2775ACXX-4-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19239_30min


title: 4sU-seq of YRI individual (NA19222) [19222-30-1_D2775ACXX-5-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19222_30min


title: 4sU-seq of YRI individual (NA19222) [19222-30-2_C30BHACXX-2-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19210) [19210-60-1_D2775ACXX-6-14]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19210_60min


title: 4sU-seq of YRI individual (NA19210) [19210-30-1_D2775ACXX-6-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19210_30min


title: 4sU-seq of YRI individual (NA19209) [19209-60-1_D2775ACXX-2-27]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19209_60min


title: 4sU-seq of YRI individual (NA19206) [19206-60-1_D2775ACXX-4-27]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19206_60min


title: 4sU-seq of YRI individual (NA19209) [19209-30-1_D2775ACXX-2-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19209_30min


title: 4sU-seq of YRI individual (NA19222) [19222-30-2_C30NNACXX-2-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19206) [19206-30-1_D2775ACXX-4-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19206_30min


title: 4sU-seq of YRI individual (NA19204) [19204-60-2_C311JACXX-5-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19204_60min


title: 4sU-seq of YRI individual (NA19223) [19223-30-1_C311JACXX-2-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19223) [19223-30-1_C30BHACXX-2-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19204) [19204-60-1_D2775ACXX-3-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19204) [19204-60-2_C30BHACXX-5-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19204) [19204-30-2_C30NNACXX-5-05]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19204_30min


title: 4sU-seq of YRI individual (NA19204) [19204-60-2_C30NNACXX-5-06]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-60-2_C30NNACXX-3-04]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19203_60min


title: 4sU-seq of YRI individual (NA19203) [19203-60-2_C30BHACXX-3-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19204) [19204-30-1_D2775ACXX-3-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19204) [19204-30-2_C311JACXX-5-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-60-1_C30NNACXX-5-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-30-2_C30NNACXX-3-10]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19203_30min


title: 4sU-seq of YRI individual (NA19204) [19204-30-2_C30BHACXX-5-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19222) [19222-30-2_C311JACXX-2-13]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-30-1_C311JACXX-5-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-30-2_C30BHACXX-3-10]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-30-1_C30NNACXX-5-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-30-1_C30BHACXX-5-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19201) [19201-30-2_D2775ACXX-2-22]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19201_30min


title: 4sU-seq of YRI individual (NA19200) [19200-60-2_D2775ACXX-6-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19200_60min


title: 4sU-seq of YRI individual (NA19201) [19201-60-1_D2775ACXX-8-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19201_60min


title: 4sU-seq of YRI individual (NA19201) [19201-30-1_D2775ACXX-8-15]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19201) [19201-60-2_D2775ACXX-2-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19200) [19200-60-1_D2775ACXX-2-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-60-2_C311JACXX-3-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19192) [19192-60-2_C311JACXX-5-08]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19192_60min


title: 4sU-seq of YRI individual (NA19200) [19200-30-1_D2775ACXX-2-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19200_30min


title: 4sU-seq of YRI individual (NA19203) [19203-30-2_C311JACXX-3-10]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-60-1_C30BHACXX-5-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19192) [19192-60-2_C30NNACXX-5-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19190) [19190-60-1_C311JACXX-1-08]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19190_60min


title: 4sU-seq of YRI individual (NA19192) [19192-60-2_C30BHACXX-5-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19192) [19192-30-2_C30NNACXX-5-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19192_30min


title: 4sU-seq of YRI individual (NA19192) [19192-30-2_C311JACXX-5-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19203) [19203-60-1_C311JACXX-5-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19190) [19190-60-1_C30BHACXX-1-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19190) [19190-30-1_C311JACXX-1-07]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19190_30min


title: 4sU-seq of YRI individual (NA19192) [19192-30-2_C30BHACXX-5-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19190) [19190-60-1_C30NNACXX-1-08]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19190) [19190-30-1_C30NNACXX-1-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19190) [19190-30-1_C30BHACXX-1-07]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19172) [19172-60-1_C30NNACXX-4-23]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19172_60min


title: 4sU-seq of YRI individual (NA19172) [19172-60-1_C30BHACXX-4-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19200) [19200-30-2_D2775ACXX-6-15]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19159) [19159-60-2_C30NNACXX-4-21]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19159_60min


title: 4sU-seq of YRI individual (NA19172) [19172-30-1_C30BHACXX-4-22]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19172_30min


title: 4sU-seq of YRI individual (NA19172) [19172-30-1_C30NNACXX-4-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19159) [19159-30-2_C30BHACXX-4-20]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19159_30min


title: 4sU-seq of YRI individual (NA19153) [19153-60-2_C30NNACXX-7-04]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19153_60min


title: 4sU-seq of YRI individual (NA19159) [19159-60-2_C30BHACXX-4-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19159) [19159-30-2_C30NNACXX-4-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19153) [19153-60-1_D2775ACXX-3-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19153) [19153-30-2_C311JACXX-7-03]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19153_30min


title: 4sU-seq of YRI individual (NA19153) [19153-30-2_C30NNACXX-7-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19153) [19153-60-2_C30BHACXX-7-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19153) [19153-30-2_C30BHACXX-7-03]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19153) [19153-30-1_D2775ACXX-3-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19152) [19152-60-1_C311JACXX-1-02]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19152_60min


title: 4sU-seq of YRI individual (NA19152) [19152-60-1_C30NNACXX-1-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19152) [19152-60-1_C30BHACXX-1-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19152) [19152-60-2_D2775ACXX-6-23]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19152) [19152-30-1_C311JACXX-1-01]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19152_30min


title: 4sU-seq of YRI individual (NA19152) [19152-30-1_C30NNACXX-1-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19152) [19152-30-2_D2775ACXX-6-22]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19144) [19144-60-2_D2775ACXX-6-27]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19144_60min


title: 4sU-seq of YRI individual (NA19143) [19143-60-2_C311JACXX-7-02]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19143_60min


title: 4sU-seq of YRI individual (NA19144) [19144-30-2_D2775ACXX-6-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19144_30min


title: 4sU-seq of YRI individual (NA19147) [19147-30-1_D2775ACXX-2-15]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19147_30min


title: 4sU-seq of YRI individual (NA19143) [19143-60-2_C30NNACXX-7-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19152) [19152-30-1_C30BHACXX-1-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19143) [19143-60-2_C30BHACXX-7-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19143) [19143-30-1_D2775ACXX-2-20]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19143_30min


title: 4sU-seq of YRI individual (NA19153) [19153-60-2_C311JACXX-7-04]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19141) [19141-60-2_C30NNACXX-6-27]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19141_60min


title: 4sU-seq of YRI individual (NA19143) [19143-30-2_C30NNACXX-7-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19141) [19141-60-2_C30BHACXX-6-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19141) [19141-30-2_C311JACXX-6-25]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19141_30min


title: 4sU-seq of YRI individual (NA19141) [19141-30-2_C30BHACXX-6-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19140) [19140-60-2_C30NNACXX-4-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19140_60min


title: 4sU-seq of YRI individual (NA19140) [19140-60-2_C30BHACXX-4-16]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19147) [19147-60-1_D2775ACXX-2-16]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19147_60min


title: 4sU-seq of YRI individual (NA19141) [19141-30-2_C30NNACXX-6-25]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19140) [19140-30-1_D2775ACXX-8-13]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19140_30min


title: 4sU-seq of YRI individual (NA19140) [19140-60-1_D2775ACXX-8-14]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19140) [19140-30-2_C30BHACXX-4-15]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19138) [19138-30-2_D2775ACXX-6-20]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19138_30min


title: 4sU-seq of YRI individual (NA19140) [19140-30-2_C30NNACXX-4-15]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19138) [19138-60-1_D2775ACXX-3-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19138_60min


title: 4sU-seq of YRI individual (NA19138) [19138-60-2_D2775ACXX-6-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-60-2_C30BHACXX-7-12]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19137_60min


title: 4sU-seq of YRI individual (NA19137) [19137-60-2_C30NNACXX-7-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19143) [19143-60-1_D2775ACXX-2-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19138) [19138-30-1_D2775ACXX-3-05]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19143) [19143-30-2_C311JACXX-7-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-60-1_C311JACXX-3-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-60-1_C30NNACXX-3-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19141) [19141-60-2_C311JACXX-6-27]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19143) [19143-30-2_C30BHACXX-7-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-60-2_C311JACXX-7-12]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-60-1_C30BHACXX-3-02]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-30-2_C311JACXX-7-11]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19137_30min


title: 4sU-seq of YRI individual (NA19137) [19137-30-2_C30NNACXX-7-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-30-2_C30BHACXX-7-11]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-30-1_C311JACXX-3-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-30-1_C30NNACXX-3-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19137) [19137-30-1_C30BHACXX-3-01]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19131) [19131-60-2_C30BHACXX-8-21]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19131_60min


title: 4sU-seq of YRI individual (NA19131) [19131-60-2_C30NNACXX-8-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19131) [19131-60-2_C311JACXX-8-21]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19131) [19131-30-2_C30BHACXX-8-20]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19131_30min


title: 4sU-seq of YRI individual (NA19131) [19131-30-2_C30NNACXX-8-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19131) [19131-30-2_C311JACXX-8-20]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19128) [19128-60-2_C30BHACXX-8-19]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19128_60min


title: 4sU-seq of YRI individual (NA19130) [19130-30-1_D2775ACXX-1-05]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19130_30min


title: 4sU-seq of YRI individual (NA19130) [19130-60-1_D2775ACXX-1-06]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19130_60min


title: 4sU-seq of YRI individual (NA19128) [19128-60-2_C30NNACXX-8-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19127) [19127-30-1_D2775ACXX-8-22]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19127_30min


title: 4sU-seq of YRI individual (NA19128) [19128-30-2_C311JACXX-8-18]

description: processed data file: 4su_30_norm.txt

source_name: 4sU-seq of YRI individual NA19128_30min


title: 4sU-seq of YRI individual (NA19128) [19128-60-2_C311JACXX-8-19]

description: processed data file: 4su_60_norm.txt


title: 4sU-seq of YRI individual (NA19127) [19127-60-1_D2775ACXX-8-23]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19127_60min


title: 4sU-seq of YRI individual (NA19128) [19128-30-2_C30BHACXX-8-18]

description: processed data file: 4su_30_norm.txt


title: 4sU-seq of YRI individual (NA19119) [19119-60-1_C30BHACXX-3-08]

description: processed data file: 4su_60_norm.txt

source_name: 4sU-seq of YRI individual NA19119_60min