title: anti-GFP ASO 300pmol 24h, rep 1

city: Cambridge

first: Yang

middle: Eric

last: Guo

state: MA

address: 455 Main St

institute: Whitehead Institute MIT

description:
poly A RNA
Processed data file: H1_KD_WT.txt

data_processing:
Illumina Casava software 1.9 was used for basecalling.
The raw data were processed and mapped to the marmoset reference genome (version caljac 3.2) using Tophat on the Galaxy server (http://galaxy.psu.edu). Transcript levels were quantified by Cufflinks (Trapnell et al., 2010) using 55,137 transcripts annotated by Ensembl as a reference.
Genome_build: Callithrix jacchus-3.2
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values.

organism: Callithrix jacchus

source_name: T cells, anti-GFP ASO

growth_protocol: T cells from common marmoset (Callithrix jacchus) immortalized by wildtype HVS strain A11 (WT cells) or a deletion mutant lacking HSURs 1 and 2 (Δ2A cells) (Murthy et al., 1989) were cultured as described (Cook et al., 2004).

extract_protocol:
Total RNAs were extracted using Trizol reagent (Life Technology).
Poly A selection and RNA libraries were prepared for sequencing using standard Illumina protocols by the Yale Center for Genomic Analysis.

treatment_protocol: Ten million WT cells were transfected, as described in the EXPERIMENTAL PROCEDURES, with 300 pmol ASO against GFP (α-GFP) or HSUR 1 (α-H1). Two biological replicates were performed for each ASO transfection. Similarly, 10 million Δ2A cells were transfected with 300 pmol LNA against miR-27 or control (Exiqon), as described in the EXPERIMENTAL PROCEDURES. Two biological replicates were performed for each LNA transfection.

value: T cells

tag: viral infection

value: immortalized by WT herpesvirus saimiri (HVS) strain A11

tag: treatment

value: anti-GFP ASO


title: anti-GFP ASO 300pmol 24h, rep 2

status: Public on Sep 01 2014

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: cell type


title: anti-HSUR1 ASO 300pmol 24h, rep 2

source_name: T cells, anti-HSUR1 ASO

value: anti-HSUR1 ASO


title: 2A untreated mRNA-seq

description: poly A RNA

source_name: T cells, untreated

value: immortalized by Δ2A herpesvirus saimiri (HVS) strain A11


title: control LNA 300pmol 24h, rep 2

description:
poly A RNA
Processed data file: mR27_KD_2A.txt

source_name: T cells, control LNA

value: control LNA


title: P013

city: Tartu

first: Tauno

last: Metsalu

address: Liivi 2

country: Estonia

institute: University of Tartu

data_processing:
DESeq package in the R statistical language and environment (version 3.0.2) was used to calculate the reads per kilobase per million reads (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts and RPKM values for each sample

organism: Homo sapiens

source_name: placenta

extract_protocol:
mirVana™ miRNA  Isolation Kit (Ambion®, Life Technologies™) according to manufacturer’s instructions
Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) + SOLiD 5500 System; DNA fragment library kit (Life Technologies, Carlsbad, CA, USA), both according to manufacturer's instructions.
45 ng total RNA was used to consruct WT RNA seq library (cDNA synthesis, cDNA amplification, SOLiDi 5500 adaptor ligation and library amplification), barcoded adaptors were applied for multiplex sequencing

tag: person

value: child

tag: trio


title: anti-HSUR1 ASO 300pmol 24h, rep 1


title: control LNA 300pmol 24h, rep 1


title: miR27 LNA 300pmol 24h, rep 1

source_name: T cells, miR27 LNA

value: miR27 LNA


title: miR27 LNA 300pmol 24h, rep 2


title: SOX3 ChIP biological replicate 3

status: Public on Aug 31 2014

city: Adelaide

first: Dale

last: McAninch

state: SA

address: North Terrace

country: Australia

institute: The University of Adelaide

library_source: genomic

data_processing:
Reads were aligned by Bowtie (V1.0.0), with options -n 2 -m 1, against genome build mm9
Peaks were called using MACS V(1.4.2)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP peak files in BED file format, with mm9 genomic coordinates of each peak

molecule: genomic DNA

organism: Mus musculus

source_name: Neural Progenitor Cells

growth_protocol: Mouse ES-cells were differentiated with N2 and B27 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) for 4 days

extract_protocol:
Lysates were clarified from sonicated nuclei and SOX3-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit (1003473)

value: R1 ES cell derived neural progenitor cells

tag: chip antibody

value: R&D hSOX3 (AF2569)

tag: differentiation

value: ES cells were differentiated in N2B27 media for 4 days


title: SOX3 ChIP biological replicate 1


title: Esa1_ChIP-seq_t11

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

description: Same time points as other histone modifiers ChIP-Seq.

data_processing:
Sequence reads were mapped to the Saccharomyces.cerevisiae (sacCer2) using bowtie. In order to adjust sequencing depth difference, signals at each window were normalized by total number of mappable reads across 14 time points.
supplementary_files_format_and_content: .txt files show the sequencing read intensity across the sacCer2 genome in CisGenome browser. The first column in the txt file is the name of the chromosome. The second column is the start position of each of the continuous 100 bp windows in the chromosome. The third column is the intensity of reads in this window.
Genome_build: sacCer2

organism: Saccharomyces cerevisiae

source_name: YMC cycling cells

extract_protocol:
~50 OD cycling cells per time point were collected for ChIP 3 µg primary antibody was used per ChIP experiment. Briefly, cells were first fixed in 1% formaldehyde at 25℃ for 15 min and quenched in 125mM glycine at 25℃ for 10 min. Cells were pelleted and washed twice with buffer containing 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1 mM PMSF, 1 mM benzamidine•HCl before freezing. The frozen pellet was resuspended in 0.45 ml ChIP lysis buffer (50 mM HEPES•KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, Roche protease inhibitor cocktail) and lysed by bead beating. Lysate from 50 OD cells were split into two tubes each containing 280 µl lysate and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode, Denville, NJ or Tosho Denki, Japan). The supernatant of the sonicated lysate was pre-cleared. 50 µl lysate was saved as input. For ChIP with histone modifier proteins, 500 µl whole cell extract (WCE) was diluted 1:10 and used for each ChIP. After incubation overnight, 50 µl protein A Sepharose beads (GE Healthcare Life Sciences, Piscataway, NJ, 17-5280-01) resuspended in ChIP lysis buffer was added and incubated for 1.5 h at 4 ℃. Beads were washed twice with ChIP lysis buffer, twice with DOC buffer (10 mM Tris•Cl pH 8.0, 0.25 M LiCl, 0.5% deoxycholate, 0.5% NP-40, 1 mM EDTA) and twice with TE. 125 µl of TES buffer (TE pH8.0 with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) was added to resuspend the beads. Supernatant was collected after incubation at 65°C for 10 min. A second round of elution was performed and the eluates were combined. Reverse crosslinking was performed by incubation for 6 h at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K and 0.4 mg/ml glycogen was added to the samples after reverse crosslinking and samples were incubated for 2 h at 37°C. Samples were extracted twice with an equal volume of phenol and once with 25:1 chloroform:isoamyl alcohol. DNA was precipitated in 0.1 volume 3.0 M sodium acetate (PH 5.3) and 2.5 volume of 100% ice-cold ethanol at -20℃ overnight. Pellets were washed once with cold 70% ethanol and resuspended in 20 µl TE.
Library construction and sequencing were performed following the Illumina protocol. Briefly, DNA was end repaired and A-tailed. Barcoded adaptors were ligated and DNA was run in 2% agarose gel. DNA fragments from 150 bp to 300 bp long were excised from gel and used for PCR. PCR products were gel-extracted again and quantified on an Agilent Bioanalyzer.

tag: strain

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX44

tag: time

value: Esa1 [ab4466 (Abcam)]


title: Esa1_ChIP-seq_t14

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX47


title: Esa1_ChIP-seq_t6

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX39


title: Esa1_ChIP-seq_t13

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX46


title: NPC Input DNA


title: Esa1_ChIP-seq_t8

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX41


title: Esa1_ChIP-seq_t7

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX40


title: Esa1_ChIP-seq_t9

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX42


title: Esa1_ChIP-seq_t5

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX38


title: Esa1_ChIP-seq_t2

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX35


title: Esa1_ChIP-seq_t10

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX43


title: Esa1_ChIP-seq_t1

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX34


title: Esa1_ChIP-seq_t3

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX36


title: Esa1_ChIP-seq_t12

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX45


title: Set1_ChIP-seq_t13

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX32


title: Set1_ChIP-seq_t11

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX30


title: Set1_ChIP-seq_t10

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX29


title: Set1_ChIP-seq_t9

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX28


title: H3_ChIP-seq_t16

description: Same time points as other histone marks ChIP-Seq.

data_processing:
Sequence reads were mapped to the Saccharomyces.cerevisiae (sacCer2) using bowtie. In order to adjust sequencing depth difference, signals at each window were normalized by total number of mappable reads across 16 time points.
supplementary_files_format_and_content: .txt files show the sequencing read intensity across the sacCer2 genome in CisGenome browser. The first column in the txt file is the name of the chromosome. The second column is the start position of each of the continuous 100 bp windows in the chromosome. The third column is the intensity of reads in this window.
Genome_build: sacCer2

extract_protocol:
~50 OD cycling cells per time point were collected for ChIP 3 µg primary antibody was used per ChIP experiment. Briefly, cells were first fixed in 1% formaldehyde at 25℃ for 15 min and quenched in 125mM glycine at 25℃ for 10 min. Cells were pelleted and washed twice with buffer containing 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1 mM PMSF, 1 mM benzamidine•HCl before freezing. The frozen pellet was resuspended in 0.45 ml ChIP lysis buffer (50 mM HEPES•KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, Roche protease inhibitor cocktail) and lysed by bead beating. Lysate from 50 OD cells were split into two tubes each containing 280 µl lysate and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode, Denville, NJ or Tosho Denki, Japan). The supernatant of the sonicated lysate was pre-cleared. 50 µl lysate was saved as input. For ChIP with histone antibodies, 50 µl whole cell extract (WCE) was diluted 1:10 and used for each ChIP. After incubation overnight, 50 µl protein G magnetic beads (Invitrogen, Grand Island, NY, 10003D) resuspended in ChIP lysis buffer was added and incubated for 1.5 h at 4 ℃. Beads were washed twice with ChIP lysis buffer, twice with DOC buffer (10 mM Tris•Cl pH 8.0, 0.25 M LiCl, 0.5% deoxycholate, 0.5% NP-40, 1 mM EDTA) and twice with TE. 125 µl of TES buffer (TE pH8.0 with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) was added to resuspend the beads. Supernatant was collected after incubation at 65°C for 10 min. A second round of elution was performed and the eluates were combined. Reverse crosslinking was performed by incubation for 6 h at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K and 0.4 mg/ml glycogen was added to the samples after reverse crosslinking and samples were incubated for 2 h at 37°C. Samples were extracted twice with an equal volume of phenol and once with 25:1 chloroform:isoamyl alcohol. DNA was precipitated in 0.1 volume 3.0 M sodium acetate (PH 5.3) and 2.5 volume of 100% ice-cold ethanol at -20℃ overnight. Pellets were washed once with cold 70% ethanol and resuspended in 20 µl TE.
Library construction and sequencing were performed following the Illumina protocol. Briefly, DNA was end repaired and A-tailed. Barcoded adaptors were ligated and DNA was run in 2% agarose gel. DNA fragments from 150 bp to 300 bp long were excised from gel and used for PCR. PCR products were gel-extracted again and quantified on an Agilent Bioanalyzer.

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX


title: H3_ChIP-seq_t13


title: H3_ChIP-seq_t14


title: H3_ChIP-seq_t15


title: H3_ChIP-seq_t11


title: SOX3 ChIP biological replicate 2

value: R1 ES cell derived neural progenitor cells

value: R&D hSOX3 (AF2569)

value: ES cells were differentiated in N2B27 media for 4 days


title: H3_ChIP-seq_t12


title: Set1_ChIP-seq_t12

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX31


title: H3_ChIP-seq_t7


title: H3_ChIP-seq_t10


title: H3_ChIP-seq_t8


title: Set1_ChIP-seq_t8

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX27


title: H3_ChIP-seq_t6


title: Set1_ChIP-seq_t1

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX20


title: H3_ChIP-seq_t9


title: Set1_ChIP-seq_t4

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX23


title: H3_ChIP-seq_t5


title: Set1_ChIP-seq_t3

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX22


title: Set1_ChIP-seq_t5

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX24


title: H3_ChIP-seq_t4


title: H3_ChIP-seq_t3


title: Set1_ChIP-seq_t7

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX26


title: Set1_ChIP-seq_t6

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX25


title: H3_ChIP-seq_t1


title: H3_ChIP-seq_t2


title: Gcn5_ChIP-seq_t14

extract_protocol:
~50 OD cycling cells per time point were collected for ChIP 3 µg primary antibody was used per ChIP experiment. Briefly, cells were first fixed in 1% formaldehyde at 25℃ for 15 min and quenched in 125mM glycine at 25℃ for 10 min. Cells were pelleted and washed twice with buffer containing 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1 mM PMSF, 1 mM benzamidine•HCl before freezing. The frozen pellet was resuspended in 0.45 ml ChIP lysis buffer (50 mM HEPES•KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, Roche protease inhibitor cocktail) and lysed by bead beating. Lysate from 50 OD cells were split into two tubes each containing 280 µl lysate and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode, Denville, NJ or Tosho Denki, Japan). The supernatant of the sonicated lysate was pre-cleared. 50 µl lysate was saved as input. For ChIP with histone modifier proteins, 500 µl whole cell extract (WCE) was diluted 1:10 and used for each ChIP. After incubation overnight, 50 µl protein G magnetic beads (Invitrogen, Grand Island, NY, 10003D) resuspended in ChIP lysis buffer was added and incubated for 1.5 h at 4 ℃. Beads were washed twice with ChIP lysis buffer, twice with DOC buffer (10 mM Tris•Cl pH 8.0, 0.25 M LiCl, 0.5% deoxycholate, 0.5% NP-40, 1 mM EDTA) and twice with TE. 125 µl of TES buffer (TE pH8.0 with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) was added to resuspend the beads. Supernatant was collected after incubation at 65°C for 10 min. A second round of elution was performed and the eluates were combined. Reverse crosslinking was performed by incubation for 6 h at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K and 0.4 mg/ml glycogen was added to the samples after reverse crosslinking and samples were incubated for 2 h at 37°C. Samples were extracted twice with an equal volume of phenol and once with 25:1 chloroform:isoamyl alcohol. DNA was precipitated in 0.1 volume 3.0 M sodium acetate (PH 5.3) and 2.5 volume of 100% ice-cold ethanol at -20℃ overnight. Pellets were washed once with cold 70% ethanol and resuspended in 20 µl TE.
Library construction and sequencing were performed following the Illumina protocol. Briefly, DNA was end repaired and A-tailed. Barcoded adaptors were ligated and DNA was run in 2% agarose gel. DNA fragments from 150 bp to 300 bp long were excised from gel and used for PCR. PCR products were gel-extracted again and quantified on an Agilent Bioanalyzer.

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX19

value: FLAG M2 [F1804 (Sigma)]


title: Gcn5_ChIP-seq_t9

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX14


title: Gcn5_ChIP-seq_t10

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX15


title: Gcn5_ChIP-seq_t11

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX16


title: Set1_ChIP-seq_t14

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX33


title: H3K56ac_ChIP-seq_t15

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX

value: H3K56ac [07-677 (Millipore)]


title: Gcn5_ChIP-seq_t13

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX18


title: Set1_ChIP-seq_t2

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX21


title: H3K56ac_ChIP-seq_t14


title: H3K56ac_ChIP-seq_t16


title: H3K56ac_ChIP-seq_t13


title: Gcn5_ChIP-seq_t7

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX12


title: H3K56ac_ChIP-seq_t12


title: Gcn5_ChIP-seq_t12

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX17


title: Gcn5_ChIP-seq_t5

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX10


title: H3K56ac_ChIP-seq_t10


title: H3K56ac_ChIP-seq_t11


title: H3K56ac_ChIP-seq_t9


title: Gcn5_ChIP-seq_t4

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX9


title: H3K56ac_ChIP-seq_t5


title: Gcn5_ChIP-seq_t6

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX11


title: H3K56ac_ChIP-seq_t7


title: H3K56ac_ChIP-seq_t8


title: Gcn5_ChIP-seq_t3

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX8


title: H3K56ac_ChIP-seq_t6


title: Gcn5_ChIP-seq_t2

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX7


title: Gcn5_ChIP-seq_t1

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX6


title: H4K16ac_ChIP-seq_t16

extract_protocol:
~50 OD cycling cells per time point were collected for ChIP 3 µg primary antibody was used per ChIP experiment. Briefly, cells were first fixed in 1% formaldehyde at 25℃ for 15 min and quenched in 125mM glycine at 25℃ for 10 min. Cells were pelleted and washed twice with buffer containing 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1 mM PMSF, 1 mM benzamidine•HCl before freezing. The frozen pellet was resuspended in 0.45 ml ChIP lysis buffer (50 mM HEPES•KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, Roche protease inhibitor cocktail) and lysed by bead beating. Lysate from 50 OD cells were split into two tubes each containing 280 µl lysate and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode, Denville, NJ or Tosho Denki, Japan). The supernatant of the sonicated lysate was pre-cleared. 50 µl lysate was saved as input. For ChIP with histone antibodies, 50 µl whole cell extract (WCE) was diluted 1:10 and used for each ChIP. After incubation overnight, 50 µl protein A Sepharose beads (GE Healthcare Life Sciences, Piscataway, NJ, 17-5280-01) resuspended in ChIP lysis buffer was added and incubated for 1.5 h at 4 ℃. Beads were washed twice with ChIP lysis buffer, twice with DOC buffer (10 mM Tris•Cl pH 8.0, 0.25 M LiCl, 0.5% deoxycholate, 0.5% NP-40, 1 mM EDTA) and twice with TE. 125 µl of TES buffer (TE pH8.0 with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) was added to resuspend the beads. Supernatant was collected after incubation at 65°C for 10 min. A second round of elution was performed and the eluates were combined. Reverse crosslinking was performed by incubation for 6 h at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K and 0.4 mg/ml glycogen was added to the samples after reverse crosslinking and samples were incubated for 2 h at 37°C. Samples were extracted twice with an equal volume of phenol and once with 25:1 chloroform:isoamyl alcohol. DNA was precipitated in 0.1 volume 3.0 M sodium acetate (PH 5.3) and 2.5 volume of 100% ice-cold ethanol at -20℃ overnight. Pellets were washed once with cold 70% ethanol and resuspended in 20 µl TE.
Library construction and sequencing were performed following the Illumina protocol. Briefly, DNA was end repaired and A-tailed. Barcoded adaptors were ligated and DNA was run in 2% agarose gel. DNA fragments from 150 bp to 300 bp long were excised from gel and used for PCR. PCR products were gel-extracted again and quantified on an Agilent Bioanalyzer.

value: H4K16ac [07-329 (Millipore)]


title: H4K16ac_ChIP-seq_t15


title: H3K56ac_ChIP-seq_t4


title: H3K56ac_ChIP-seq_t3


title: Esa1_ChIP-seq_t4

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX37

value: Esa1 [ab4466 (Abcam)]


title: H4K16ac_ChIP-seq_t14


title: H4K16ac_ChIP-seq_t13


title: H4K16ac_ChIP-seq_t12


title: H3K56ac_ChIP-seq_t2


title: H3K56ac_ChIP-seq_t1


title: H4K16ac_ChIP-seq_t11


title: Gcn5_ChIP-seq_t8

value: ZKY428:CEN.PK MATa GCN5-FLAG::natMX, SET1-3HA::KanMX13

value: FLAG M2 [F1804 (Sigma)]


title: H4K16ac_ChIP-seq_t10

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX


title: H3K9ac_ChIP-seq_t15

value: H3K9ac [06-942 (Millipore)]


title: H3K9ac_ChIP-seq_t16


title: H3K9ac_ChIP-seq_t14


title: H4K16ac_ChIP-seq_t9


title: H3K9ac_ChIP-seq_t13


title: H4K16ac_ChIP-seq_t7


title: H3K9ac_ChIP-seq_t12


title: H4K16ac_ChIP-seq_t6


title: H4K16ac_ChIP-seq_t8


title: H4K16ac_ChIP-seq_t5


title: H3K9ac_ChIP-seq_t11


title: H3K9ac_ChIP-seq_t10


title: H4K16ac_ChIP-seq_t2


title: H4K16ac_ChIP-seq_t3


title: H3K36me3_ChIP-seq_t14


title: H4K16ac_ChIP-seq_t1


title: H3K36me3_ChIP-seq_t11


title: H3K36me3_ChIP-seq_t13


title: H3K36me3_ChIP-seq_t10


title: H3K36me3_ChIP-seq_t7


title: H3K36me3_ChIP-seq_t9


title: H3K36me3_ChIP-seq_t5


title: H3K36me3_ChIP-seq_t8


title: H3K36me3_ChIP-seq_t2


title: H3K36me3_ChIP-seq_t1


title: H3K36me3_ChIP-seq_t3


title: H3K36me3_ChIP-seq_t6


title: H3K4me3_ChIP-seq_t16

value: H3K4me3 [CS200580 (Millipore)]


title: H3K4me3_ChIP-seq_t15


title: H3K36me3_ChIP-seq_t4


title: H4K16ac_ChIP-seq_t4


title: H3K4me3_ChIP-seq_t13


title: H3K36me3_ChIP-seq_t12


title: H3K4me3_ChIP-seq_t6


title: H3K4me3_ChIP-seq_t3


title: H3K4me3_ChIP-seq_t12


title: H3K36me3_ChIP-seq_t15


title: H3K36me3_ChIP-seq_t16


title: H3K4me3_ChIP-seq_t10


title: H3K4me3_ChIP-seq_t11


title: H3K4me3_ChIP-seq_t8


title: H3K4me3_ChIP-seq_t9


title: H3K4me3_ChIP-seq_t1


title: H3K4me3_ChIP-seq_t5


title: H4K5ac_ChIP-seq_t14

value: H4K5ac [07-327 (Millipore)]


title: H3K4me3_ChIP-seq_t7


title: H4K5ac_ChIP-seq_t15


title: H4K5ac_ChIP-seq_t13


title: H3K4me3_ChIP-seq_t2


title: H3K4me3_ChIP-seq_t4


title: H4K5ac_ChIP-seq_t10


title: H3K4me3_ChIP-seq_t14


title: H4K5ac_ChIP-seq_t11


title: H4K5ac_ChIP-seq_t16


title: H4K5ac_ChIP-seq_t8


title: H4K5ac_ChIP-seq_t7


title: H4K5ac_ChIP-seq_t5


title: H3K9ac_ChIP-seq_t9


title: H4K5ac_ChIP-seq_t12


title: H3K9ac_ChIP-seq_t8


title: H4K5ac_ChIP-seq_t4


title: H4K5ac_ChIP-seq_t6


title: H3K9ac_ChIP-seq_t6


title: H3K9ac_ChIP-seq_t5


title: H4K5ac_ChIP-seq_t3


title: H4K5ac_ChIP-seq_t1


title: H4K5ac_ChIP-seq_t2


title: H3K9ac_time alignment_ChIP-seq_t16

description: Same time points as RNA-Seq. Used for time alignment between RNA-Seq and histone modification ChIP-Seq experiments.

data_processing:
Sequence reads were mapped to the Saccharomyces.cerevisiae (sacCer2) using bowtie. In order to adjust sequencing depth difference, signals at each window were normalized by total number of mappable reads across 16 time points.
Genome_build: sacCer2

value: BY5765:CEN.PK MATalpha


title: H3K9ac_ChIP-seq_t3


title: H3K9ac_ChIP-seq_t1


title: H3K9ac_time alignment_ChIP-seq_t13


title: H3K9ac_time alignment_ChIP-seq_t14


title: H4K5ac_ChIP-seq_t9


title: H3K9ac_time alignment_ChIP-seq_t10


title: H3K9ac_ChIP-seq_t7


title: H3K9ac_time alignment_ChIP-seq_t12


title: H3K9ac_time alignment_ChIP-seq_t8


title: H3K9ac_time alignment_ChIP-seq_t7


title: H3K9ac_time alignment_ChIP-seq_t9


title: H3K9ac_time alignment_ChIP-seq_t6


title: H3K9ac_time alignment_ChIP-seq_t11


title: H3K9ac_time alignment_ChIP-seq_t5


title: H3K9ac_ChIP-seq_t4


title: RNA-seq_t15

description: Same time points as H3K9ac_time alignment

data_processing:
Sequence reads were mapped to the Saccharomyces.cerevisiae (sacCer2) using TopHat (--bowtie1 -i 40 --genome-read-mismatches 4 --no-coverage-search -G genes.gtf). FPKM counts were calculated by Cuffidff. Visulization signals at exons and introns was performed by bowtie and Cisgenome. In order to adjust sequencing depth difference, signals at each window were first normalized by total number of mappable reads across 16 time points and then displayed as the percentage of the maximum value of the 16 time points.
supplementary_files_format_and_content: FPKM file contains FPKM values for each gene at all 16 time points. .txt file show the sequencing read density across the sacCer2 genome at exons and introns separately. The first column in the txt file is the name of the chromosome. The second column is the start position of each of the continuous 20 bp windows in the chromosome. The third column is the intensity of reads in this window.
Genome_build: sacCer2

molecule: polyA RNA

extract_protocol:
1 mL BY5765 cells from the cycle (about 15 OD/mL) were collected and flash frozen. The pellet was resuspended in 200 µl RNA stat-60 (Tel-Test, Friendswood, TX) and disrupted in a Mini-Beadbeater-16 (Biospec, Bartlesville, OK) broken up three times with 100 µl glass beads in 1.5 ml conical screw cap tube (USA SCIENTIFIC, 1415-8700, Ocala, FL). Supernatant was collected into a new microcentrifuge tube and 800 µl RNA stat-60 was added to repeat bead beating one more time. The supernatants were combined and sit at room temperature for 10 min. 200 µl chloroform was then added and the tube was vortexed for 15 sec and left at room temperature for 10 min. The tubes were centrifuged at 4°C, 16000 rcf for 15 min and the supernatant was transferred to a new tube. 500 µl isopropanol was added and mixed by inverting the tube several times. The mixture was incubated at room temperature for 10 min and centrifuged at 4°C, 16000 rcf for 15 min. The pellet was washed with 70% ethanol twice, air dried and resuspended in 100 µl H2O.
Samples were run on the Agilent 2100 Bioanalyzer to ensure that high quality RNA was used. 4 µg total RNA was then prepared with the TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). mRNA was purified and fragmented before cDNA synthesis. cDNA was then end repaired and A-tailed. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads (Agencourt, A63880, Brea, CA), then validated again on the Agilent 2100 Bioanalyzer.


title: H3K9ac_time alignment_ChIP-seq_t1


title: H3K9ac_time alignment_ChIP-seq_t2


title: H3K9ac_time alignment_ChIP-seq_t15


title: RNA-seq_t16


title: H3K9ac_time alignment_ChIP-seq_t3


title: RNA-seq_t14


title: RNA-seq_t13


title: RNA-seq_t11


title: RNA-seq_t9


title: RNA-seq_t10


title: RNA-seq_t6


title: RNA-seq_t7


title: RNA-seq_t12


title: RNA-seq_t8


title: RNA-seq_t3


title: RNA-seq_t4


title: RNA-seq_t5


title: H3K9ac_ChIP-seq_t2


title: H3K9ac_time alignment_ChIP-seq_t4


title: H3K14ac_ChIP-seq_t16

value: H3K14ac [07-353 (Millipore)]


title: RNA-seq_t2


title: RNA-seq_t1


title: H3K14ac_ChIP-seq_t11


title: H3K14ac_ChIP-seq_t14


title: H3K14ac_ChIP-seq_t10


title: H3K14ac_ChIP-seq_t15


title: metastasized cancer AMC_23-3

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.
The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPFM values

source_name: metastasized cancer

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: tissue

value: metastatic colorectal cancer to the liver

tag: ajcc stage

value: Stage IV


title: H3K14ac_ChIP-seq_t9


title: H3K14ac_ChIP-seq_t13


title: H3K14ac_ChIP-seq_t7


title: metastasized cancer AMC_20-3


title: H3K14ac_ChIP-seq_t8


title: metastasized cancer AMC_22-3


title: metastasized cancer AMC_21-3


title: H3K14ac_ChIP-seq_t6


title: metastasized cancer AMC_19-3


title: H3K14ac_ChIP-seq_t4


title: metastasized cancer AMC_18-3


title: metastasized cancer AMC_17-3


title: metastasized cancer AMC_13-3


title: H3K14ac_ChIP-seq_t1


title: H3K14ac_ChIP-seq_t5


title: H3K14ac_ChIP-seq_t3


title: H3K14ac_ChIP-seq_t2


title: metastasized cancer AMC_10-3


title: metastasized cancer AMC_9-3


title: metastasized cancer AMC_24-3


title: H3K14ac_ChIP-seq_t12


title: metastasized cancer AMC_7-3


title: metastasized cancer AMC_8-3


title: metastasized cancer AMC_6-3


title: metastasized cancer AMC_5-3


title: metastasized cancer AMC_2-3


title: metastasized cancer AMC_3-3


title: normal colon AMC_23-2

source_name: normal colon

value: normal-looking surrounding colonic epithelium


title: normal colon AMC_24-2


title: normal colon AMC_21-2


title: normal colon AMC_22-2


title: normal colon AMC_19-2


title: normal colon AMC_18-2


title: normal colon AMC_12-2


title: normal colon AMC_10-2


title: normal colon AMC_8-2


title: normal colon AMC_9-2


title: metastasized cancer AMC_12-3


title: normal colon AMC_7-2


title: normal colon AMC_17-2


title: normal colon AMC_20-2


title: normal colon AMC_6-2


title: CML17 iCD34+ Imatinib

city: Madison

first: Scott

last: Swanson

state: WI

address: 330 N. Orchard St

institute: Morgridge Institute for Research

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Differential expression likelihoods obtained using EBSeq 1.1.6
GO analysis performed using DAVID on genes with 1.000 Posterior Probability of differential expression, and estimated TPM > 10 in at least one sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: induced pluripotent stem cell-derived hematopoietic cells

growth_protocol: Differentiated cells derived from Day 9th induced pluripotent stem cell/OP9 coculture were cultured in 10%FBS in αMEM supplemented with 200 ng/ml GM-CSF (expansion medium) for 2 days before FACs sorting for lin-CD34+CD45+

extract_protocol:
PureLink RNA micro kit (Life Technology) with on-column DNaseI digestion
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

treatment_protocol: DMSO or 5 μM for 16 hours in expansion medium supplemented with 200 ng/ml GM-CSF

tag: cell origin

value: 5 uM imatinib


title: CML15 iCD34+ Imatinib


title: normal colon AMC_5-2


title: normal colon AMC_3-2


title: BM9 iCD34+ Imatinib


title: normal colon AMC_2-2


title: CML17 iCD34+ Control

value: DMSO


title: CML15 iCD34+ Control


title: primary colorectal cancer AMC_24-1

source_name: primary colorectal cancer

value: primary colorectal cancer


title: BM1K iCD34+ Imatinib


title: primary colorectal cancer AMC_23-1


title: BM1K iCD34+ Control


title: primary colorectal cancer AMC_22-1


title: primary colorectal cancer AMC_21-1


title: normal colon AMC_13-2


title: Mt plus salt

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to soybean whole genome using software BWA (Burrows-Wheeler Alignment, bwa-0.7.4).
Reads per kilo bases per million reads (RPKM) were calculated.
Genome_build: Glycine max (http://www.plantgdb.org)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Glycine max

source_name: leaves

growth_protocol: The seedlings were grown at 25℃ under artificial light with a photoperiod of 16-h light and 8-h dark.

extract_protocol:
Total RNA was extracted using TRNzol Reagent (TIANGEN company).
Library were prepared according to the protocol of RNA-Seq RNA sample Prep Kit (Illumina)

treatment_protocol: Three-week old seedlings were treated with water, 100 µM melatonin, 1% NaCl or 100 µM melatonin plus 1% NaCl.

value: salt plus 100µM melatonin


title: Melatonin

value: 100µM melatonin


title: Salt

value: 1% NaCl


title: primary colorectal cancer AMC_18-1


title: primary colorectal cancer AMC_20-1


title: primary colorectal cancer AMC_19-1


title: H2O


title: primary colorectal cancer AMC_17-1


title: primary colorectal cancer AMC_13-1


title: primary colorectal cancer AMC_10-1


title: primary colorectal cancer AMC_8-1


title: primary colorectal cancer AMC_9-1


title: primary colorectal cancer AMC_7-1


title: primary colorectal cancer AMC_12-1


title: Input_ChIPSeq_Embryonic_Liver

city: Vancouver

first: Pamela

last: Hoodless

state: BC

address: 675 W 10th Ave

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency - Research Centre

description: Input chromatin (no IP)

data_processing:
base-calling Bustard
alignments Gerlad/Eland
peak calling FP4 with fixed read extension (200bp)
post processing using control - custom scripts
Genome_build: mm9

source_name: Dlk1+ hepatoblasts

growth_protocol: Hepatoblasts were isolated from pooled E14.5 livers, organs were disassociated in PBS containing 2% FBS, 1μg/ml DNase, 0.4 mM EDTA, 0.06% collagenase, and 0.6U/ml dispase for an hour at 37˚C. DLK1+  cells were enriched using magnetic cell sorting EasySep kits (Stem Cell Technologies) and PE conjugated anti-DLK1+ (MBL International), according to manufacturers instructions.

extract_protocol:
Cells were homogenized in 1% formaldehyde and incubated at room temperature (RT) for 10 min, prior to the addition of glycine to 0.125 M followed by incubation at RT for 5 min. Cells were pelleted, washed and resuspended in 5 volumes ChIP cell lysis buffer (10 mM Tris–Cl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) containing protease inhibitor cocktail tablets (Roche, Laval, QC, Canada). Cells were then rehomogenized, incubated on ice for 5 min and repelleted. The pellet was resuspended in 3 volumes ChIP nuclear lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris–Cl, pH 8.1) supplemented with protease inhibitor cocktail tablets (Roche). Cells were sonicated on ice-water (Sonicator 3000, Misonix, Farmingdale, NY, USA) for 20 cycles of 30 s on, 40 s off and 60 μg of chromatin was precleared with Protein G beads (100 μl, Active Motif), Protein Inhibitor Cocktail (0.5 μl, Active Motif) and ChIP dilution buffer (to 250 μl, 0.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 16.7 mM Tris–Cl, pH 8.1). Beads were precipitated and 3 μg of Foxa2 [HNF-3β (M-20): sc-6554] or HNF4a [sc-8987] antibody was added to supernatants. Fresh Protein G beads were also blocked with 1 mg/mg BSA and 0.1 mg/mg herring sperm DNA in ChIP dilution buffer. Following overnight incubation, rocking at 4°C, the samples were incubated with the blocked beads for 4 h rocking at 4°C. The beads were then precipitated and washed in low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–Cl, pH 8.1, 150 mM NaCl), high salt buffer (low salt buffer with 500 mM NaCl), lithium chloride buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris–Cl, pH 8.1) and twice with TE buffer. Bead complexes were eluted twice by addition of 125 μl elution buffer (1% SDS, 0.1 M NHCO3) and rotation for 15 min at RT. NaCl was added to 0.192 M to reverse crosslink and samples were incubated overnight at 65°C. Samples were then incubated with Proteinase K (Invitrogen, Carlsbad, CA, USA) and RNaseA (Sigma-Aldrich, Oakville, ON, Canada) for 2 h at 50°C. DNA was purified by two rounds of phenol–chloroform extraction and ethanol precipitation and resuspended in 50 μl dH2O.
ChIP DNA was run and size separated by PAGE (8%). The 100-300bp DNA fraction was excised and eluted from the gel slice overnight at 4°C in 300 μl of elution buffer (5:1, LoTE buffer (3 mM Tris-HCl, pH 7.5, 0.2 mM EDTA)-7.5 M ammonium acetate), and was purified using a Spin-X Filter Tube (Fisher Scientific), and by ethanol precipitation. The library was prepared by following the pair end library protocol (Illunima Inc., USA). Briefly, the DNA was subject to end-repair, and phosphorylation by T4 DNA polymerase, Klenow DNA Polymerase, and T4 polynucleotide kinase respectively in a single reaction, and then 3’ A overhangs generation by Klenow fragment (3’ to 5’ exo minus), and ligated to Illumina PE adapters, which contain 5’ T overhangs. The adapter-ligated products were purified on Qiaquick spin columns (Qiagen), then PCR-amplified with Phusion DNA Polymerase in 10-15 cycles using Illumina’s PE primer set (Illumina). PCR product of desired size range was purified using a 8% PAGE, and the DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay and Nanodrop 7500 spectrophotometer (Nanodrop, USA) and diluted to 10nM. The final concentration was double checked and determined by Quant-iT dsDNA HS Assay Kit using Qubit fluorometer (Invitrogen). Clusters were generated on the Illumina cluster station and sequence was run on Illumina Genome Analyzer following the manufacturer’s instructions.

tag: developmental stage

value: Embryonic day 14.5

tag: genotype

value: wildtype

value: MACs purified DLK1+ hepatoblasts


title: primary colorectal cancer AMC_6-1


title: BM9 iCD34+ Control


title: HNF4a_ChIPSeq_Embryonic_Liver

description: Chromatin IP against HNF4a

value: HNF4a SantaCruz H191 sc-8987 lot #J1003


title: primary colorectal cancer AMC_3-1


title: primary colorectal cancer AMC_2-1


title: primary colorectal cancer AMC_5-1


title: cabozantinib treated arm, patient-derived tumor xenograft CRC102

status: Public on Aug 30 2014

city: Aurora

first: John

last: Arcaroli

state: CO

address: 12801 E. 17th Avenue

department: Department of Medicine

institute: University of Colorado Denver

data_processing:
fastq reads were aligned against hg19 reference genome using tophat-2.0.6/bowtie 1.0.0
Aligned transcripts were assembled and their abundance was estimated using cufflinks-2.1.1
Transcripts were then merged using cuffmerge
Cuffdiff-2.1.1 was used for analyzing differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: patient-dervied tumor xenograft

growth_protocol: in vivo

extract_protocol:
Qiagen kit
RNA SEQ

treatment_protocol: XL184 daily 30 mg/kg

tag: host

value: mouse

tag: model

value: CRC PDTX Model

value: cabozantinib

value: patient-dervied tumor xenograft


title: AGO2IP_CMV-Δ2b

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

description: small RNAs (18-26nt)

data_processing:
18-26nt small RNA sequences were used for analysis, after removing the adaptor sequences.
Bowtie program (http://bowtie-bio.sourceforge.net/index.shtml) was used for aligning small RNAs to annotated Arabidopsis sequences in miRBase database (http://www.mirbase.org), and perfect matches were permitted.
Genome_build: TAIR9
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequences and reads number

organism: Arabidopsis thaliana

source_name: systemic leaves after virus infection

extract_protocol:
This study constructed and sequenced two independent small RNA libraries from the upper uninoculated leaves of (i) WT Arabidopsis plants 14 d after mock inoculation and of (ii) rdr1 rdr6 plants 14 d after infection with Fny CMV-Δ2b, and one library each from the upper uninoculated leaves of (iii) WT, (iv) rdr1, and (v) rdr6 plants 14 d after infection with TuMV-GFP. Coimmunoprecipitation with FLAG- and HA-specific antibodies was used to obtain (vi,vii) AGO1 and (viii,ix) AGO2 complexes, respectively, from the FLAG-AGO1/ago1-36 and HA-AGO2 plants 14 d after infection with Fny CMV-Δ2b for extracting total loaded small RNAs for the construction and sequencing of small RNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fny CMV-Δ2b

value: leaf

tag: antibody

value: anti-HA antibody (clone 12CA5, Roche)


title: rdr1_TuMV

description: small RNAs (18-26nt)

tag: viral infection

value: TuMV


title: AGO1IP_mock

description: small RNAs (18-26nt)

source_name: systemic leaves after mock infection

value: none (mock)

value: anti-FLAG M2 agarose beads (Sigma)


title: rdr6_TuMV

description: small RNAs (18-26nt)


title: AGO1IP_CMV-Δ2b

description: small RNAs (18-26nt)


title: Control arm, patient-derived tumor xenograft CRC102

tag: treatment

value: Control


title: rdr16_CMV-Δ2b

description: small RNAs (18-26nt)

value: rdr1; rdr6


title: Control arm, patient-derived tumor xenograft CRC020


title: cabozantinib treated arm, patient-derived tumor xenograft CRC020


title: WT_TuMV

description: small RNAs (18-26nt)


title: cabozantinib treated arm, patient-derived tumor xenograft CRC098


title: Control arm, patient-derived tumor xenograft CRC098


title: male ethanol non-enriched amygdala replicate 1 [miRNA-seq]

status: Public on Aug 29 2014

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mena_32

data_processing:
Partek Flow software was used for trimming, alignment and quantification
Reads were trimmed using a minimum phred score of 20
Reads were aligned using the Bowtie algorithm to the rat Rn5 genome
Quantified using miRBase 21 annotations for both precursor and mature miRNAs
Read counts converted to Reads per million (RPM) for each sample
Genome_build: Rn5
Supplementary_files_format_and_content: miRNA Reads per million (RPM) normalized counts for precursor and mature miRNAs

organism: Rattus norvegicus

source_name: male ethanol non-enriched amygdala

extract_protocol:
Qiagen total RNA
Illumna TruSeq Small RNA library preparation

tag: strain background

value: Long Evans

tag: age

value: postnatal day 42

tag: gender

value: male

tag: brain region

value: Amygdala

tag: prenatal exposure

value: Ethanol

tag: postnatal social treatment

value: Non-enriched


title: FOXA2_ChIPSeq_Embryonic_Liver

description: Chromatin IP against FOXA2

tag: strain

value: Embryonic day 14.5

value: wildtype

tag: chip antibody

value: FOXA2 Santa Cruz sc-6554

tag: cell type

value: MACs purified DLK1+ hepatoblasts


title: male ethanol non-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mena_52


title: male ethanol non-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mena_84


title: AGO2IP_mock

description: small RNAs (18-26nt)

tag: tissue

value: leaf


title: male saline socially-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcsa_56

source_name: male saline socially-enriched amygdala

value: Saline

value: Socially-enriched


title: female ethanol socially-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fesa_66

value: female


title: male saline socially-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcsa_46


title: male saline socially-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcsa_44


title: male saline non-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcna_36

source_name: male saline non-enriched amygdala


title: female saline socially-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcsa_26


title: male ethanol socially-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mesa_62

source_name: male ethanol socially-enriched amygdala


title: male ethanol socially-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mesa_86


title: male ethanol socially-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mesa_24


title: male saline non-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcna_16


title: male saline non-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcna_14


title: female ethanol socially-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fesa_60


title: male ethanol socially-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mesv_85

value: Ventral striatum


title: male ethanol socially-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mesv_61


title: male ethanol non-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
menv_83


title: male ethanol non-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
menv_31


title: male saline socially-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcsv_45


title: male saline non-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcnv_35


title: female ethanol non-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fena_74

source_name: female ethanol non-enriched amygdala


title: WT_mock

description: small RNAs (18-26nt)

value: none (mock)


title: female ethanol non-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fena_10


title: female ethanol socially-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fesa_40


title: female saline socially-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcsa_2


title: female saline socially-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcsa_6


title: female saline non-enriched amygdala replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcna_18

source_name: female saline non-enriched amygdala


title: male saline non-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcnv_15


title: female saline non-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcna_8


title: female saline non-enriched amygdala replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcna_34


title: male ethanol socially-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mesv_23


title: male ethanol non-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
menv_51


title: female ethanol non-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fenv_73


title: male saline socially-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcsv_43


title: male saline non-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcnv_13


title: female ethanol non-enriched amygdala replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fena_88


title: female ethanol socially-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fesv_65


title: female saline non-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcnv_33


title: male saline socially-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
mcsv_55


title: female ethanol socially-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fesv_39


title: female saline socially-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcsv_1


title: female ethanol non-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fenv_9


title: female saline socially-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcsv_25


title: female ethanol socially-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fesv_59


title: female ethanol non-enriched ventral striatum replicate 2 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fenv_87


title: female saline non-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcnv_7


title: female saline non-enriched ventral striatum replicate 1 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcnv_17


title: female saline socially-enriched ventral striatum replicate 3 [miRNA-seq]

description:
gene expression data from the brains of postnatal day 42 Long Evans rats that were exposed in utero to ethanol or saline and exposed postnatally to normal or enriched social environment
fcsv_5


title: NaOH_Sorghum_Shoot

city: Cold Spring Harbor

first: Andrew

middle: J

last: Olson

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequences were processed using Illumina’s CASAVA v1.5/1.6 software.
Sequences were aligned to the sorghum genome (sbi1.4 downloaded from ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v6.0/Sbicolor/assembly/) using Bowtie/Tophat (default settings; version 0.12.7 and 1.0.13, respectively) .
Cufflinks (version 0.8.1) was run on merged alignments using all default settings except "-F/--min-isoform-fraction 0.0" and returned genes and FPKMs in GTF format.
Cufflinks transcript fragments were processed by the Gramene/EnsEMBL evidence based gene builder
Cufflinks was rerun on each sample to quantify gene expression of Sbi1.4 and GeneBuilder models
genome_build:Sbi1.4
supplementary_files_format_and_content: GTF; assembled via Cufflinks using the standard GTF format. The 'ref' GTF files give expression levels of reference annotations (Sbi1.4) while the 'GB2' files give expression levels of GeneBuilder gene models.

organism: Sorghum bicolor

source_name: Shoots from 9d sorghum seedings treated with 0.2M NaOH for 27 hrs (control for ABA)

growth_protocol: Seeds of Sorghum bicolor genotype BTx623 were germinated by soaking in distilled, aerated water overnight and then transferred to moist germination paper for 3 days.  The seedlings were then transferred to 0.5x Hoagland’s solution and allowed to grow for an additional 5 days in a controlled environment chamber with a day length of 12 hrs, 50% humidity, and day and night temperatures of 31˚C and 22˚C, respectively.

extract_protocol: Following grinding of tissues in a mortar and pestle under liquid nitrogen, total RNA was extracted using miRNEasy kits (Qiagen, Valencia, CA). Each RNAseq library was prepared according to the manufacturer’s instructions (mRNA-Seq sample preparation kit, Illumina Inc., San Diego, CA) and quality control was conducted as previously described (Dugas et al., 2011 GSE30249). The libraries were run on the Illumina GAIIx Sequencer using version 4 reagents for single-end non-strand-specific read sequences of 51 bp in length.

treatment_protocol: At 8 days, the plants were treated with 0.2M NaOH for 27 hrs.  Three groups of 10 plant shoots each were harvested post-treatment.

tag: germplasm

value: Shoot

tag: replicate type

value: biological


title: H2O_Sorghum_Shoot

source_name: Shoots from untreated 9d sorghum seedings (control for PEG)

treatment_protocol: At 8 days, the plants were treated with H2O.  Three groups of 10 plant shoots each were harvested post-treatment.


title: ABA_Sorghum_Shoot

source_name: Shoots from 9d sorghum seedings treated with 20µM exogenous ABA for 27 hrs

treatment_protocol: At 8 days, the plants were treated with 20µM exogenous ABA for 27 hours  Three groups of 10 plant shoots each were harvested post-treatment.


title: NaOH_Sorghum_Root

source_name: Roots from 9d sorghum seedings treated with 0.2M NaOH for 27 hrs (control for ABA)

treatment_protocol: At 8 days, the plants were treated with 0.2M NaOH for 27 hrs.  Three groups of 10 plant roots each were harvested post-treatment.

value: Root


title: NaOH_Sorghum_Root_BS

data_processing:
BS-seq reads were trimmed for adaptor sequence and low quality base call, then aligned to sorghum genome assembly using rmap V2.03  with parameters -Q -v -m 4
Then the C/T counts from aligned BS-seq reads for each cytosine in reference genome were saved in CT count file
genome_build:Sbi1.4
supplementary_files_format_and_content: The CT count files have the first 6 columns the same as a bed file, the 7th col is count of C, the 8th col is count of T, the 9th col is the 3 nt in reference genome, the 10th col is the context of cytosine

extract_protocol: Flash-frozen root tissue was ground under liquid Nitrogen, and high-quality DNA was isolated utilizing the FastDNA SPIN Kit (MP Biomedicals, Santa Ana, CA USA). Library construction and bisulfite conversion were conducted as described previously (Regulski et al., 2013 GSE39232) and sequenced on Illumina GAIIx machines using PE50 protocol.

value: technical


title: BY4742_WT_input

city: Illkirch

first: Didier

last: Devys

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

data_processing:
FASTQ files have been generated using CASAVA v1.8.2.
ChIP-seq reads were aligned to the sacCer3 genome assembly using the Bowtie aligner 0.12.8.
Wig files were generated by WigMaker3, an in-house program developed by the microarray and sequencing platform of the IGBMC.
For each pair of H3K9ac ChIP-seq datasets that are compared in this study (WT vs gcn5∆), Wig files were generated from normalized BED files with the same number of aligned reads on mid-gene bodies (25%-75% of the coding region) of large genes (> 2 kb).
For the two H2Bub ChIP-seq datasets that are compared in this study (WT vs ubp8∆), the Wig file for H2Bub_ubp8∆ was generated from a normalized BED file containing 2.5 times more aligned reads than the H2Bub_WT BED file (this difference between the two strains was observed in three independent ChIP-qPCR experiments).
For each pair of RNA Pol II ChIP-seq datasets that are compared in this study (WT vs spt20∆), Wig files were generated from normalized BED files with the same number of aligned reads on 300 genes with background level of RNA Pol II signal and devoid of H3K4me3 and H3K9ac.
Genome_build: sacCer3
Supplementary_files_format_and_content: Wig files (for each sample, aligned sequences were extended to 200 bp from their 3' end, and allocated into 25 bp bins)

growth_protocol: Yeast cells were grown in YPD at 30˚C and harvested at the mid-log phase.

extract_protocol:
Yeasts were fixed with formaldehyde and lysed by glass beads with vigorous votexing. Chromatin extract was obtained after sonication. H3K9ac, H2Bub, H2B, H3K4me3 and RNA Pol II-DNA complexes were isolated with specific antibodies.
Libraries were prepared according to the Illumina ChIP-seq protocol.

tag: genotype/variation

value: wild type


title: Pol_II_BY4741_spt20D_ChIPseq

value: Pol II


title: BY4741_spt20D_input


title: Pol_II_BY4742_WT_rep2_ChIPseq


title: H2O_Sorghum_Root

source_name: Roots from untreated 9d sorghum seedings (control for PEG)

treatment_protocol: At 8 days, the plants were treated with H2O.  Three groups of 10 plant roots each were harvested post-treatment.


title: Pol_II_BY4742_WT_rep1_ChIPseq


title: PEG_Sorghum_Root

source_name: Roots from 9d sorghum seedings treated with 20% PEG-8000 for 27 hrs

treatment_protocol: At 8 days, the plants were treated with 20% PEG-8000 for 27 hrs.  Three groups of 10 plant roots each were harvested post-treatment.


title: H3K4me3_WT_hH2B_ChIPseq

tag: version of h2b

value: Flag-hHTB1 (R119K, S125T)


title: ABA_Sorghum_Root

source_name: Roots from 9d sorghum seedings treated with 20µM exogenous ABA for 27 hrs

treatment_protocol: At 8 days, the plants were treated with 20µM exogenous ABA for 27 hours.  Three groups of 10 plant roots each were harvested post-treatment.


title: H2Bub_WT_hH2B_ChIPseq


title: H2B_WT_hH2B_ChIPseq


title: H2Bub_ubp8∆_hH2B_ChIPseq


title: Floral_Meristem_Sorghum

source_name: Floral meristems excised after the meristem transitions.

growth_protocol: Seeds of Sorghum bicolor genotype BTx623 were surface sterilized and treated with Captan before being planted into pots filled with Sunshine MVP potting mix and transferred into the greenhouse. Plants were grown in 14-hours of daylight and the temperatures were kept as close to 31-35ºC as possible.

value: Floral meristem


title: H2Bub_WT_yH2B_ChIPseq


title: Vegetative_Meristem_Sorghum

source_name: Vegetative meristems collected by hand.

value: Vegetative meristem


title: Flowers_Sorghum

source_name: Immature (green) florets were harvested after panicle exsertion prior extruding pollen or anthers. Flowers were collected from 6-8 plants, pooled together, and flash frozen.

value: Flower


title: H3K9ac_gcn5∆_rep2_ChIPseq


title: H3K9ac_gcn5∆_rep1_ChIPseq


title: gcn5∆_input


title: Embryos_Sorghum

source_name: Embryos collected from maturing sorghum seeds

value: Embryo


title: H3K9ac_WT_rep2_ChIPseq


title: H3K9ac_WT_rep1_ChIPseq


title: PEG_Sorghum_Shoot

source_name: Shoots from 9d sorghum seedings treated with 20% PEG-8000 for 27 hrs

treatment_protocol: At 8 days, the plants were treated with 20% PEG-8000 for 27 hrs.  Three groups of 10 plant shoots each were harvested post-treatment.


title: H2Bub_HeLa_shATXN7L3_ChIPseq

data_processing:
FASTQ files have been generated using CASAVA v1.8.2.
ChIP-seq reads were aligned to the hg19 genome assembly using the Bowtie aligner 0.12.8.
Wig files were generated by WigMaker3, an in-house program developed by the microarray and sequencing platform of the IGBMC.
For each pair of ChIP-seq datasets that are compared in this study (shCtrl vs shATXN7L3 (H2Bub) and shCtrl vs shADA3 (H3K9ac)), Wig files were generated from normalized BED files with the same number of aligned reads in large intergenic regions.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files (for each sample, aligned sequences were extended to 200 bp from their 3' end, and allocated into 25 bp bins)

source_name: HeLa cells

growth_protocol: HeLa cells were grown in 15 cm Petri-dishes (medium: DMEM, 1g/l glucose + 5%FCS + Gentamicin).

extract_protocol:
HeLa cells were fixed with formaldehyde, chromatin was extracted after sonication of nuclei and H3K9ac or H2Bub-DNA complexes were isolated with specific antibodies.
Libraries were prepared according to the Illumina ChIP-seq protocol.

tag: cell line

value: HeLa

tag: stable expression of shrna


title: WT_hH2B_input


title: ubp8∆_hH2B_input


title: RNAPolII_WT_hH2B_ChIPseq


title: H2Bub_HeLa_shCtr_ChIPseq


title: WT_yH2B_input


title: CTCF ChIP-seq_TFII-1_KD_2

city: Montreal

first: Michael

last: Witcher

state: QC

address: 3755 Chemin de la Cote Ste-Catherine

institute: Lady Davis Institut

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using BWA with default parameters
Only sequence with MAPQ score ≥20 were kept for further analysis
Peak calling was performed using MACS with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: txt are direct output from MACS, bedgraph file were generated with HOMER after combining replicate to visualize result in UCSC genome browser.

source_name: Wehi-231-TFII-I KD

growth_protocol: WEHI-231 Control (CT) and TFII-I stable (TFII-1 KD) knockdown cells were cultured in DMEM 10% FBS. Cells were generated by re-planting 1mL of cells in suspension in 15 mL of cultured media in a T75 flask and were split every 2-3 days when they reach a density of about 75 to 80%. Cell cultures were maintained for up to 12 passages.

extract_protocol:
Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
Libraries were prepared according to  Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Libraries were sequenced on the Illumina Hiseq 2000 following the manufacturer's protocols.

value: B cell lymphoma

value: (BALB/c x NZB)F1

value: CTCF Millipore #07-729


title: CTCF ChIP-seq_CT_2


title: ChIPseq WT WCE

first: Jerry

last: Pelletier

state: Quebec

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

department: Department of Biochemistry

institute: McGill university

description: BARCODE ChIP-seq library. BARCODE adaptor was used for generating the each library. In raw data file, barcode seuquence was trimmed in first 4 bps in each sequence reads.

data_processing:
For BARCODE ChIP-sequencing library, we used the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/ (Version 0.0.13)) to split the reads according to the specific nucleotide barcode in first 4bp of sequence reads. Before mapping to the genome, we trimmed the first 4bps nucleotide of each reads. Low quality reads were trimmed to 25bps.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 (version 2.0.2) with default parameter. After mapping into genome, the duplicate reads were filtered using Picard (version 1.69) and samtools (0.1.19-96b5f2294a).
For peak calling, HOMER tools (http://http://homer.salk.edu/homer/chipseq/) were used.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated by HOMER program. Score was normalized to tags per 1e7 reads.

source_name: ChIPseq WT WCE

growth_protocol: Arf −/− MEFs cells were maintained in D-MEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin/streptomycin, and 100 U/mL Gln.

extract_protocol:
Protein-DNA complexes were immunoprecipitated from sonicated chromatin extract by the specific antibody.
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (E6200S, NEB) according to the manufacturer’s protocol. For BARCODE ChIP-seq library we used the BARCODE adaptor for generating the library (BARCODE adaptor: PMID 19159457).

treatment_protocol: Arf −/− MEFs cells were transduced with MSVC-based retrovirus expressing dmCas9-GFP and sgRNA (either p53-1 trgRNA: 5'-GTGTAATAGCTCCTGCATG-3', p53-3 trgRNA: 5'-GAAGTCACAGCACATGACGG-3') or dmCas9-GFP alone. Cells were enriched for GFP expression following flow cytometic sorting.

value: Arf −/− MEFs

value: mouse embryonic fibroblasts

tag: dmcas9 + triggerrna

value: Non

tag: antibody

value: No antibody


title: dmCas9-ChIPseq sgRNA p53-3 WCE

source_name: dmCas9-ChIPseq sgRNA p53-3 WCE

extract_protocol:
Protein-DNA complexes were immunoprecipitated from sonicated chromatin extract with anti-FLAG antibody.
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (E6200S, NEB) according to the manufacturer’s protocol. For BARCODE ChIP-seq library we used the BARCODE adaptor for generating the library (BARCODE adaptor: PMID 19159457).

treatment_protocol: Arf −/− MEFs cells were transduced with MSVC-based retrovirus expressing dmCas9-GFP and sgRNA (either p53-1 sgRNA: 5'-GTGTAATAGCTCCTGCATG-3', p53-3 sgRNA: 5'-GAAGTCACAGCACATGACGG-3') or dmCas9-GFP alone. Cells were enriched for GFP expression following flow cytometic sorting.

tag: dmcas9 + sgrna

value: dmCas9 + sgRNA p53-3


title: dmCas9-ChIPseq sgRNA p53-3 IP

source_name: dmCas9-ChIPseq sgRNA p53-3 IP

value: FLAG antibody F1804, SIGMA


title: dmCas9-ChIPseq sgRNA p53-1 WCE

source_name: dmCas9-ChIPseq sgRNA p53-1 WCE

value: dmCas9 + p53-1


title: dmCas9-ChIPseq No sgRNA IP

source_name: dmCas9-ChIPseq No trgRNA IP


title: T2h Blood

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

data_processing:
Basecalling was performed using Illumina CASAVA version1.8.2.
CLC genomics version 5.5.1 was used for alignment, Reads Per Kilobase of exon per Megabase of library size (RPKM) and for differential gene expression calculations
Baggerly’s statistical test (Baggerly et al. 2003 Bioinformatics) with false discovery rate (Pawitan et al., 2005 Bioinformatics) was applied to identify statistically significant changes in gene expression between the tested conditions.
Genes that were not detected (RPKM=0) and those with p values above 0.05 were discarded.
Venn diagrams (Oliveros JC 2007 http://bioinfogpcnbcsices/tools/venny/indexhtml) were used to identify the genes that were present in both replicates and then the fold changes of each run for each condition were avereged. Additionally, genes that were uniquely expressed in the presence of human blood were also identified.
Gene ontology enrichment was performed using STRING (version 9.05) (Franceschini et al., 2013 Nucleic Acids Research)
Genome_build: NC_002976.3
Supplementary_files_format_and_content: Tab-delimited text files including gene locus tag and fold change values (average of the both runs performed for each condition tested). The text files labeled as T2h/ T4h Blood only.txt were constructed crossing the list of genes expressed in biofilms incubated with TSB and Blood in order to identify the genes that transcripts were uniquely produced in the presence of human blood.

organism: Staphylococcus epidermidis

source_name: Bacterial biofilms

growth_protocol: One single colony of S. epidermidis was inoculated into 2 mL of TSB and grown overnigh at 37oC and 120 rpm. Overnight cultures were then diluted 1:600 in TSB supplemented with 1% glucose. One mL of the bacterial suspension was then distributed into 24-well tissue culture plates and incubated at 37oC and 120 rpm for 24 hours.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen) with some alterations in the bacterial cell lyses procedure. Lyses was performed as described in França et al., PLoS One 2012. In brief, biofilm pellets were suspended in 500 µL of in the lyses buffer provided by the kit plus 500 µL of phenol. This supension was then transfered into Lysing Matrix B tubes (MPBiomedicals) and using a FastPrep BioSavan101 (Therno Scientific) the cells were lysed. Finally, the tubes were centrifuged and the suspension transfered into a new tube. An equal volume of 70% of ethanol was added. The suspension was transfered to the RNeasy mini kit columns and following the manufacturer's instructions total RNA was isolated. Thereafter, total RNA was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to remove genomic DNA. Additionally total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) to remove eukaryotic RNA and bacterial ribosomal RNA, respectively.
Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2. Briefly, 400 ng of previosuly purified mRNA was fragmented and used for the synthesis of double stranded complementary DNA. Thereafter, end-repair, single ‘A’ nucleotide addition to the 3' end of the blunt fragments, adaptor ligation and DNA fragments enrichment was performed to complete libraries construction. Validation of the constructed libraries was assessed through quantitative PCR and Agilent 2200 TapeStation High SensitivityD1K ScreenTapes.

treatment_protocol: Twenty-four hour biofilms were washed once with phosphate buffered saline, and 1 mL of either TSB or whole human blood were added. Biofilms were then incubated at 37oC, 5% CO2 with sligh agitation for 2 or 4 hours. After incubation, both TSB and blood were carefully removed, biofilms washed twice with PBS supplemented with 0.05% Tween20 and with a tablet of protease inhibitor cocktail (Roche). Finally, biofilms were suspended in 1mL of RNA protect bacteria reagent (Qiagen) following manufacturer's instructions.

tag: incubation

value: human blood 2 hrs


title: T4h Blood

value: human blood 4 hrs


title: T4h TSB

value: tryptic soy broth 4 hrs


title: H3K9ac_HeLa_shADA3_ChIPseq


title: T2h TSB

value: tryptic soy broth 2hrs


title: T0h

value: control


title: dmCas9-ChIPseq sgRNA p53-1 IP

source_name: dmCas9-ChIPseq sgRNA p53-1 IP

value: dmCas9 + sgRNA p53-1


title: dormant_2

status: Public on Aug 28 2014

first: Virginia

last: Carvalhais

state: Braga

department: Centre of Biological Engeneering

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to Staphylococcus epidermidis whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench software (V.5.5.1, CLC Bio.).
Genome_build: S. epidermidis strain RP62A (GenBank accession number NC_002976)
Supplementary_files_format_and_content: Tab-delimited text files include transcript name and RPKM values for each Sample.

source_name: S. epidermidis biofilm

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit. To remove genomic DNA, Ambion® TURBO DNA-free™ kit was used followed by acid-phenol:chloroform precipitation,  both following the manufacturer’s instructions.  rRNA was depleted from total RNA samples using the Ribo-ZeroTM Magnetic kit for Gram-Positive bacteria.
Libraries were prepared according to Illumina's TruSeq RNA Sample Prep kit version 2, using standard Illumina protocols

tag: dormancy

value: dormant


title: non-dormant_3

value: non-dormant


title: dormant_3


title: dormant_1


title: H3K9ac_HeLa_shCtr_ChIPseq

value: HeLa


title: non-dormant_1


title: CTCF ChIP-seq_CT_1

value: B cell lymphoma

value: (BALB/c x NZB)F1

value: CTCF Millipore #07-729


title: AGSC_Thy1_BiSeq_Rep4

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Bisulfite reads were aligned using Novocraft novoalign in bisulfite mode with the following parameters: [-o SAM -rRandom -t240 -h120 -b2]
All downstream analysis and file manipulation were done using the USeq (http://useq.sourceforge.net/) suite.
Genome_build: mm9
Supplementary_files_format_and_content: Point methylation data files generated by useq viewable on IGB browser

source_name: Testis

extract_protocol:
DNA was extracted using Gentra PUREGENE DNA Isolation Kit and sheared on COVARIS to a median 400 bp fragment.
For all samples unmethylated lambda DNA was added to 1% final concentration (Promega Madison, WI 53711). Methylated paired-end adapters were ligated to sheared DNA according to the Illumina library preparation protocol. Sodium bisulfite conversion was performed using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA 91355) with an additional incubation step at 60C for 120 min to increase conversion rate. Bisulfite treated DNA was then PCR amplified with 16 cycles and sequenced. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

value: Spermatogonia (Thy1+)

tag: age

value: postnatal week 8


title: ChIPseq WT IP

source_name: ChIPseq WT IP

value: Arf −/− MEFs

value: mouse embryonic fibroblasts

value: Non


title: AGSC_Thy1_BiSeq_Rep7


title: AGSC_Thy1_BiSeq_Rep6


title: AGSC_Thy1_BiSeq_Rep3


title: AGSC_Thy1_BiSeq_Rep5


title: AGSC_Thy1_BiSeq_Rep2


title: AGSC_Thy1_BiSeq_Rep1


title: dmCas9-ChIPseq No sgRNA WCE

source_name: dmCas9-ChIPseq No sgRNA WCE

value: No antibody


title: D20C2

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

data_processing:
Normalize to CDS length, library size
Count reads  in CDS using Python script
Map to transcriptome with Bowtie: bowtie --best --strata -m 5 -n 2 --norc -l 20 -k 2 -3 15 -p 7 --chunkmbs 512 mouseRef readFile outFile
Genome_build: Refseq release 61
Supplementary_files_format_and_content: XLS spreadsheets indicating the RPKM for each gene

source_name: Mouse embryonic fibroblasts

extract_protocol:
ribosome profiling: nuclease digest, pellet ribosomes, isolate RNA, gel purify ribosome footpring; mRNA: GT/phenol extract, deplete rRNA with ribominus
ribosome profling: PNK treat, ligate adapters, amplify by PCR (used NEB small RNA kit); mRNA-seq: extract RNA with GT/phenol, deplete rRNA with ribominus, fragment, ligate adapters, PCR amplify (Illumina directional mRNA kit)

tag: treatment

value: 30 min DTT, 20 min recover

tag: genotype

tag: cell fraction

value: cyt

tag: replicate


title: D20C1


title: D20M2

value: ER


title: D10C2

value: 30 min DTT, 10 min recover


title: D10M2


title: D10C1


title: CTCF ChIP-seq_TFII-1_KD_1

tag: tissue

tag: strain

tag: chip antibody


title: D0C2

value: 30 min DTT


title: non-dormant_2


title: D10M1


title: D0C1


title: D0M2


title: mRNAW4M1

value: 4 h Tg


title: mRNAW4C1


title: fpW4C1


title: mRNAW4C2


title: D0M1


title: fpW4M2


title: fpW4M1


title: mRNAW2C1

value: 2 h Tg


title: mRNAW2C2


title: mRNAW2M2


title: mRNAW2M1


title: fpW2M2


title: fpW2C1


title: D20M1


title: fpW2M1


title: fpW2C2


title: mRNAW1C2

value: 1 h Tg


title: mRNAW1M1


title: mRNAW1M2


title: fpW1M1


title: fpW1C1


title: fpW1M2


title: mRNAW1C1


title: fpW4C2


title: mRNAW05C2

value: 0.5 h Tg


title: mRNAW4M2


title: mRNAW05M2


title: mRNAW05C1


title: fpW05C1


title: fpW05C2


title: fpW05M1


title: fpW05M2


title: mRNAW05M1


title: mRNAWNM2


title: mRNAWNM1


title: mRNAWNC2


title: mRNAWNC1


title: fpWNC2


title: fpWNC1


title: fpWNM2


title: fpWNM1


title: P28 OB 3

city: Marseille

first: christophe

last: beclin

state: Bouches du Rhone

address: campus de Luminy, case 907

department: Aix-Marseille université

institute: CNRS

data_processing:
Reads filtering against Adaptor and Barcode sequences in connection with the SOLiD technology, ribosomal RNA, mitochondrial ribosomal RNA, known repeat sequences including Alu sequences
Genome aligment using Bowtie aligner with the following parameters : Reads trimming at the adaptator position (trimming at 31 bases otherwise), 2 allowed mismatches over the total read length, Maximum best alignment hits included in the alignment result  le .bam is 10
Reads annotation using the following public databases : miRBase miRNAs database v16, tRNAs (UCSC), Rfam database, ncRNA.org database, UCSC refGene.
Size factor normalization between samples using DESeq package (Bioconductor)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads per molecule in each sample

source_name: dissected brain tissus

extract_protocol:
miRNeasy Mini Kit (Qiagen)
After reverse transcription, DNA fragments of 15-50 bp were gel purified for HTS on a SOLiD™ 5500XL (Applied Biosystem, Life technologies) machine according to  manufacturer instructions

value: OB


title: fpW1C2


title: P28 OB 2


title: P28 OB 1


title: P15 OB 3


title: P15 OB 1


title: P28 RMS 1

value: RMS


title: P28 RMS 2


title: Lateral P6 SVZ 3

value: Lateral SVZ


title: Lateral P6 SVZ 1


title: P15 RMS


title: P15 OB 2


title: Dorsal P1 SVZ 3

value: Dorsal SVZ


title: Dorsal P1 SVZ 2


title: Dorsal P1 SVZ 1


title: Dorsal P6 SVZ 3


title: Dorsal P6 SVZ 2


title: Lateral P1 SVZ 1


title: Lateral P6 SVZ 2


title: Lateral P1 SVZ 3


title: Patient 1_43P

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

data_processing:
Results were generated using the WASP system pipeline provided by Albert Einstein College of Medicine. Raw FASTQ files were trimmed for adapter sequences using quart. Alignment to the reference genome was performed using gsnap.Assignment of reads to genes was performed by htseq-count.
Genome_build: HG 19
Supplementary_files_format_and_content: A txt file format containing the Ensemble ID and the absolute number of counts per ID

source_name: B CD19 Lymphocytes

extract_protocol:
Trizol was used to extract Total RNA, following manufacturer's recommendations.
Bar-coded directional libraries were prepared using the dUTP/UNG system. More information about theprotocol can be found at WASP system from the Albert Einstein College of Medicine

treatment_protocol: Peripheral blood CD19+ B lymphocytes were isolated using immuno-magnetic procedures and FACS analysis was used to confirm the purity of the sorted cellular populations

tag: phenotype

value: House dust mite allergic

tag: cell type

value: B CD19 Lymphocytes


title: Patient 2_55P


title: Control 2_51C

value: Control


title: Patient 3_57P


title: Control 1_48C


title: HighVaccinated1

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

description: High elute concentration

data_processing:
Sequencing analyses in the Solexa 1G Genome Analyzer (Illumina)
Alignment with Bowtie
The peak-calling step was applied individually for each sample using Model Based Analysis of ChIP-Seq (MACS)
Identification of the Differentially Methylated Regions (DMRs) was accomplished implementing the DiffBind R package.It computes differentially bound sites using affinity data. The set of peaks identified by MACS and the bam files containing aligned reads for each sample, was the input for DiffBind. The program creates a matrix with the consensus peaks; for this case it was obtained with a “minimum overlap” of 2, determined by the number of replications in the experiment.  After creating a contrast between conditions and considering concentration as a block effect, DiffBind runs an edgeR analysis, which is an empirical Bayes method. For normalization, the default method TMM (Trimmed Mean of M-values) that subtracts the controls reads and considers the effective library size (reads in peaks), was applied.  The threshold utilized was 0.1, for False Discovery Rate (FDR).
For the genomic annotation of the DMRs, the software ChIPpeakAnno was used [60]. ChIPpeakAnno provides information about the overlaps, relative position and distances for the inquired feature.  The annotation information was obtained from biomart, using Ensembl 70 in the archive site. Dataset “ggallus_gene_ensembl” corresponds to WASHUC2 (galGal3), the genome used for alignment.
Genome_build: galGal3
Supplementary_files_format_and_content: Sequencing, fastq; alignment, sam; peak calling from MACS, bed; DMR, xls; annotation, xls

organism: Gallus gallus

source_name: Trachea scrape

growth_protocol: All chickens were obtained from Charles River Laboratories. They consist in ten, 15 day-old White Leghorn chickens that were randomly assigned to groups of five birds each.

extract_protocol:
Genomic DNA from five samples of each group was extracted using the Wizard Genomic DNA purification kit (Promega, A1120)
MethylCap kit (Diagenode, C02020010) was employed to obtain DNA containing methylated CpGs.

treatment_protocol: After 6 days, the control group received only sterile vaccine diluent (50 μl per nostril and 50 μl per eye, for a total dose of 200 μl per animal) and then allocated in a separated animal room. Later, the vaccine was prepared following the manufacturer’s recommendations and the vaccination was performed in the second group. The procedure was the same as for the control group, excepting for the viral load (3.3 x 103 pfu). The vaccinated birds were placed in an animal isolator in another suite.

tag: breed

value: Leghorn

tag: timepoint

value: 6 days post infection

tag: precipitation mol

value: MBD2 protein

tag: concentration

value: High elute viral load (3.3 x 103 pfu)


title: MediumVaccinated2

description: Medium elute concentration

value: Medium elute viral load (3.3 x 103 pfu)


title: LowVaccinated1

description: Low elute concentration

value: Low elute viral load (3.3 x 103 pfu)


title: HighControl2

description: High elute concentration

value: High elute sterile vaccine


title: MediumVaccinated1

description: Medium elute concentration


title: MediumControl2

description: Medium elute concentration

value: Medium elute sterile vaccine


title: HighVaccinated2

description: High elute concentration


title: MediumControl1

description: Medium elute concentration


title: LowControl2

description: Low elute concentration

value: Low elute sterile vaccine


title: LowControl1

description: Low elute concentration


title: Lateral P1 SVZ 2


title: Dorsal P6 SVZ 1


title: Control 3_56C


title: Shoot-Cold stress

status: Public on Aug 27 2014

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.3 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Genome_build: Chickpea genome v1.0 (http://nipgr.res.in/CGAP/download/genome_sequencing/genome_sequence/)
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

organism: Cicer arietinum

source_name: 10-day-old seedlings

growth_protocol: Seedlings were grown in a culture room

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol

treatment_protocol: Root and shoot tissues of 10-day-old seedlings were subjected to control (in water), desiccation (on folds of tissue paper), salinity (in 150 mM NaCl solution) and cold (in water at 4 ± 1°C) stress treatments for 5 h

value: 10 days

value: shoot


title: Shoot-Desiccation stress


title: Shoot-Control


title: Root-Cold stress

value: root


title: Root-Desiccation stress


title: Root-Salinity stress


title: LowVaccinated2

description: Low elute concentration


title: Root-Control


title: ELT-2 RNAi Hypoxia

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 240 E. Huron St.

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

data_processing:
After sequencing, the reads were demultiplexed by removing adapters and filtered by censoring the reads with poor quality.
Reads were aligned to the C. elegans reference genome (ce10 from UCSC) using TopHat (v2.0.8b) in conjunction with the ce10 gene annotation data obtained from UCSC.
After alignment, transcripts were quantified and a differential expression analysis was performed using Cufflinks (v2.1.1), which calculates gene expression as RPKM values.
Genome_build: WBcel215
Supplementary_files_format_and_content: Processed data file (.xls) reports RPKM values.

organism: Caenorhabditis elegans

source_name: C. elegans whole RNA extract

growth_protocol: Synchronized C. elegans were grown until day 1 of adulthood and then exposed to 36hrs of transient hypoxia or normoxia

extract_protocol:
RNA was isolated using TriZol extraction and isopropanol precipitation
RNA was evaluated for integrity using an Agilent Bioanalyzer 2100 and 100 bp paired-end cDNA sequencing libraries were prepared separately for each sample using indexed adapters.  All four samples were multiplexed onto a single lane of an Illumina HiSeq2000.

treatment_protocol: Animals were exposed to 36h 0.5% O2/bal N2 in an airthight chamber at room temperature

tag: developmental stage

value: adult

tag: stress

value: Hypoxia

tag: media

value: NGM modified RNAi media

value: fed ELT-2 RNAi

tag: temperature


title: HighControl1

description: High elute concentration


title: Foc4_48h

city: Shenzhen

first: Fan

middle: ding

last: ding

address: yantian shashen Road

institute: EasyATCG

description: infect Musa acuminata 48 hour

data_processing:
Used Fusarium oxysporum f. sp. cubense tropical race 1 and 4 genomes, PRJNA174275 and PRJNA174274, respectively. Sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 10 -I 10000  --segment-mismatches 3  --segment-length 24 --solexa1.3-quals
Cnnnnn identifiers found in the .wig files represent contigs.

organism: Fusarium oxysporum f. sp. cubense

extract_protocol: Total RNA is extracted by TRIzol Reagent. For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

tag: tropical race

tag: time point

tag: infection

value: Musa acuminata


title: Foc4_0h

description: infect Musa acuminata 0 hour


title: Foc1_0h

description: infect Musa acuminata 0 hour


title: E13_5_KO5

status: Public on Aug 26 2014

city: Montpellier

first: Brigitte

last: Boizet-Bonhoure

address: 141 rue de la Cardonille

department: Genetic and Development

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software (HCS 1.5.15) and Real-Time Analysis component (RTA 1.13.48).
Demultiplexing, alignment and RNA counting was performed using CASAVA 1.8.2 (Illumina). Alignment was made with eland_rna on the mm9 version of mouse genome and on several contaminants (the ribosomal RNA sequences 28S, Rn18s and Rn5s, the mitochondrial chromosome, the PhiX genome and the Illumina adaptors). The transcript annotation was retrieved from UCSC (refFlat file) on January 15, 2012.
Differentially expressed genes were identified using the Bioconductor package edgeR (v2.6.2). Genes with less than 15 reads (cumulating the two analysed samples) were filtered and thus removed from the analysis. Data were normalized using  Upper Quartile normalization factors. Genes with adjusted p-value less than 1% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Table with 5 columns for gene description. The next columns correspond to the normalized abundance measurements (Upper Quartile normalization using edgeR statistical package) for each sample

extract_protocol:
E13.5  gonads were dissected from staged embryos from 6 different WT and L/H-Pgds-/- littermates, were rapidly frozen on dry ice, and 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-Seq libraries were prepared the 'TruSeq RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

value: male gonad

tag: genotype

value: L/H-Pgds ko


title: E13_5_KO8

tag: tissue


title: Control RNAi Normoxia

tag: strain

value: Normoxia

tag: treatment

value: control


title: E13_5_WT4

value: wild type


title: Control RNAi Hypoxia


title: E13_5_WT3


title: E13_5_KO7