title: HT10801b_CenpA_CenpA_X1_(20151015_3)

description: HT1080-1b cross-linked CENP-A/CENP-A Sequential ChIP, biological replicate 1

extract_protocol: The HT1080-1b fibrosarcoma cell  line was grown in DMEM media  using standard protocols. Antibodies used in this study were purchased from Abcam (Cambridge MA). Primary cross-linking ChIP was performed as described previously (PMID: 24737864) with few modifications. Briefly, for each IP 200 million cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) and digested with Micrococcal nuclease (MNase, Sigma, Cat # N3755) at 37°C for 45 min. MNase digested chromatin was sonicated as described before ( PMID: 24737864)and  solubilized chromatin was precleared using protein A sepharose beads for 30 minutes at 4 °C. The precleared chromatin was incubated with Anti-FLAG-M2 magnetic beads (Sigma Cat # M8823) for 4 hrs at 4 °C . The FLAG-M2 magnetic beads were washed  once with buffer I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), and 150 mM NaCl), four times with buffer II 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 150 mM NaCl), 2 times with buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and once with 1X TE. Protein complexes were eluted from magnetic beads using FLAG peptide in HE buffer (10 mM HEPES, 0.25 mM EDTA, 0.5 mM PMSF). The eluent was subjected to subsequent ChIP reaction with Anti-CENP-A (Abcam cat #Ab13939)antibodies.Solexa library construction was performed as described previously (PMID:22025700) and PCR-amplified using Phusion polymerase.

value: Anti-FLAG M2 magnetic beads (Signa Cat # M8823) and Anti-CENP-A (Abcam cat #Ab13939)


title: HT10801b_CenpA_CenpA_X2_(20151015_9)

status: Public on May 24 2016

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: HT1080-1b cross-linked CENP-A/CENP-A Sequential ChIP, biological replicate 2

library_source: genomic

data_processing: 250bp single end reads were trimmed with trim-galore version 0.3.7 with parameters --quality 20 --adapter AGATCGGAAGAGC --stringency 3 --phred33 --length 25 and then aligned with various human alpha-satellite sequences using BWA 0.7.10 aln and sampe functions saving up to 10 alignments per pair, otherwise with default options. Trimmed reads mapped to two consensus sequences representing 20 human centromere sequences are included as supplementary bed files (Cen1-like and Cen13-like).

molecule: genomic DNA

organism: Homo sapiens

source_name: Sequential immunoprecipitated DNA

tag: cell type

value: fibrosarcoma

tag: cell line

tag: chip antibodies


title: HuRef_Input_(20141219_2)

description: HuRef native ChIP input

data_processing: Paired-end 25bp reads were merged using SeqPrep (https://github.com/jstjohn/SeqPrep) with parameters -q 30 (quality) and -L 25 (minimum merged pair length). SeqPrep also removed adaptors and low-quality reads.. Merged pairs were aligned with various human BACs using the aln/samse functions of BWA version 0.7.5 saving up to 10 alignments per read (-n 10), otherwise with default options. Merged pairs mapped to two consensus sequences representing 20 human centromere sequences are included as supplementary bed files (Cen1-like and Cen13-like).

source_name: Input

extract_protocol: The HuRef lymphoblastoid cell  line was grown in RPMI media  using standard protocols. Antibodies used in this study were purchased from Abcam (Cambridge MA). Nuclei were prepared following a previously published protocol (PMID: 23644596). Briefly, for each IP 40-60 million cells were collected and washed with 1X PBS. Cells were re-suspended in ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) at a density equal to ~25 million cells/ml. An equal volume of ice-cold buffer I supplemented with 0.1% NP40 was added and samples were incubated on ice for 10 min. Nuclei solution was layered on ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) and centrifuged at 10,000g for 20 min at 4 °C. The pellet was re-suspended in buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF and protease inhibitor, 3mM Cacl2) at density equal to ~ 32.5 million cells/ml.Micrococcal nuclease (MNase, Sigma, Cat # N3755) was added to ~2.5 units/ml, and digestion was carried out at 37°C for 5 min. Reactions were stopped by addition of EGTA to a final concentration of 20 mM and EDTA to 10 mM. The final NaCl concentration was adjusted to 215 mM and needle extraction was performed as described previously (PMID: 22184235) to enhance the solubility of kinetochore complex. The resulting solution was incubated overnight at 4 °C on nutator. Soluble chromatin was collected by centrifuging the mixture at 12000rpm at 4 °C for 8 min. An aliquot containing 1/20th of the entire chromatin solution was subjected to DNA extraction.

tag: cell part

value: nuclei

value: Lymphoblastoid

value: HuRef

tag: chip antibody


title: HuRef_CenpA_(20141219_1)

description: HuRef native ChIP CENP-A

source_name: Immunoprecipitated DNA

extract_protocol: The HuRef lymphoblastoid cell  line was grown in RPMI media  using standard protocols. Antibodies used in this study were purchased from Abcam (Cambridge MA). Nuclei were prepared following a previously published protocol (PMID: 23644596). Briefly, for each IP 40-60 million cells were collected and washed with 1X PBS. Cells were re-suspended in ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) at a density equal to ~25 million cells/ml. An equal volume of ice-cold buffer I supplemented with 0.1% NP40 was added and samples were incubated on ice for 10 min. Nuclei solution was layered on ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) and centrifuged at 10,000g for 20 min at 4 °C. The pellet was re-suspended in buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF and protease inhibitor, 3mM Cacl2) at density equal to ~ 32.5 million cells/ml.Micrococcal nuclease (MNase, Sigma, Cat # N3755) was added to ~2.5 units/ml, and digestion was carried out at 37°C for 5 min. Reactions were stopped by addition of EGTA to a final concentration of 20 mM and EDTA to 10 mM. The final NaCl concentration was adjusted to 215 mM and needle extraction was performed as described previously (PMID: 22184235) to enhance the solubility of kinetochore complex. The resulting solution was incubated overnight at 4 °C on nutator. Soluble chromatin was collected by centrifuging the mixture at 12000rpm at 4 °C for 8 min. Soluble chromatin was diluted 3X with 20 mM Tris, pH 8.0, 5 mM EDTA and 200 mM NaCl, and Triton-X was added at a final concentration of 0.1% (v/v). Next, the chromatin solution was pre-cleared using Protein A/G fast flow Sepharose beads for 20 min at 4 °C, and 15 µg of antibody (Abcam anti-CENP-A Ab13939) was added per ChIP sample and incubated overnight at 4 °C. Dynabeads were added to the samples and incubated at 4°C for 2 hrs. Immunoprecipitated complexes were washed 6 times with 50mM Phosphate buffer pH 7.4, 5mM EDTA, 200mM NaCl, and DNA was extracted from Dynabeads.

value: Anti-CENP-A (Abcam anti-CENP-A Ab13939)


title: mESCs_shMed12_rep1

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

library_source: transcriptomic

data_processing:
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.3.1z13_r470 onto the iGenomes mm9 reference
Secondary alignments were filtered with samtools 1.2
Counts for every gene were calculated with HTSeq-0.6.1p1 using the gene model provided with the iGenomes mm9 reference from 2013-03-06
Counts were normalized and modeled with DESeq2_1.6.3
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file containing counts per gene

molecule: polyA RNA

organism: Mus musculus

growth_protocol: E14TG2a ES cells were cultured in feeder layer-free conditions in the presence of serum and LIF

extract_protocol:
RNA was extracted from frozen cell pellets with Trizol reagent and purified with Rneasy Columbs (Qiagen)
Libraries were prepared for sequencing using standard Illumina protocols
Strand-specific mRNA-seq with Poly-A selection, Read length 50 bp

treatment_protocol: For differentiation, LIF was removed from the culture medium and all-trans- Retinoic Acid was added at a concentration of 10^-6 M

tag: strain

tag: tissue

value: embryonic stem cell, blastocyst derived

tag: celll subtype

value: pluripotent embryonic stem cells

tag: transfected with


title: mESCs_shRing1b_rep1


title: mESCs_shCdk8_rep3


title: mESCs_shCdk8_rep1


title: mESCs_shCdk8_rep2


title: HCT116 MYC 3' TBE1 (WT) - 2

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter masked fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using hg19 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used Gencode v19 gtf file as guided annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: xls files for FPKM values for each sample and result of differential gene expression analysis

source_name: colorectal carcinoma cell line

growth_protocol: HCT116 MYC 3' TBE1 (WT) and KO cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% FBS, 50 units/ml penicillin, 2 mM Glutamax, and 0.1 mg/ml streptomycin at 37°C in 5% CO2

extract_protocol:
RNA was extracted from two biological replicates of 7.5 x 105 MYC 3' TBE1 (WT) or KO cells using the mirVana kit (Ambion, AM1560).  The extracted RNAs were quantified using a NanoDrop apparatus (Thermo Scientific) which also ensured that the A260:A280 ratio was 1.9 or above.  The RNA integration number (RIN) for each sample was measured using an RNA 6000 Nano Kit (Agilent, 5067-1511), and a RIN value of above 7 was required to proceed.
The cDNA libraries were prepared using the NEXTflex™ Rapid RNA Sequencing Kit and NEXTflex™ RNA-Seq Barcodes – 24 Kit (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). The samples were sequenced using a HiSeq 2500 that was set to run for 50 cycles using a single-read recipe (TruSeq SBS Kit v3, FC-401-3002) according to the manufacturer’s instructions.

tag: genotype

value: wild type


title: HCT116 MYC 3' TBE1 (KO) - 1

value: MYC 3' TBE1 knockout


title: mESCs_control_rep3

value: control


title: HCT116 MYC 3' TBE1 (KO) - 2


title: HT10801b_CenpA_X_(20151015_2)

description: HT1080-1b cross-linked ChIP CENP-A

extract_protocol: The HT1080-1b fibrosarcoma cell line was grown in RPMI medium using standard protocols. Cross-linking ChIP was performed as described previously (PMID: 24737864) with few modifications. Briefly, for each IP 200 million cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) and digested with Micrococcal nuclease (MNase, Sigma, Cat # N3755) at 37°C for 45 min. MNase digested chromatin was sonicated as described before ( PMID: 24737864)and  solubilized chromatin was precleared using protein A sepharose beads for 30 minutes at 4 °C. The precleared chromatin was subjected to crosslinking immunoprecipitation using Anti-FLAG-M2 magnetic beads (Sigma Cat # M8823).

value: Anti-FLAG M2 magnetic beads (Signa Cat # M8823)


title: HCT116 MYC 3' TBE1 (WT) - 1


title: mESCs_shMed12_rep2


title: mESCs_control_rep2


title: HeLa_CenpT_X2_(20140710_1,2_8)

description: HeLa cross-linked (X-ChIP) CENP-T ChIP. Replicate with Bethyl antibody.

data_processing: Paired reads were merged using SeqPrep (https://github.com/jstjohn/SeqPrep) with parameters -q 30 (quality) and -L 25 (minimum merged pair length). SeqPrep also removed adaptors and low-quality reads. Merged pairs were aligned with various human BACs using the aln/samse functions of BWA version 0.7.5 saving up to 10 alignments per read (-n 10), otherwise with default options. Merged pairs mapped to two consensus sequences representing 20 human centromere sequences are included as supplementary files (Cen1-like and Cen13-like).

extract_protocol: The HeLa cell line was grown in DMEM media using standard protocols. Cross-linking ChIP was performed as described previously (PMID:24737864).

value: Epithelial carcinoma

value: HeLa

value: Anti-CENP-T (Bethyl, A302-313A)


title: mESCs_shNMC_rep1

value: shNMC


title: HT10801b_CenpA_CenpB_X_(20151015_10)

description: HT1080-1b cross-linked CENP-A/CENP-B Sequential ChIP

extract_protocol: The HT1080-1b fibrosarcoma cell  line was grown in DMEM media  using standard protocols. Antibodies used in this study were purchased from Abcam (Cambridge MA). Primary cross-linking ChIP was performed as described previously (PMID: 24737864) with few modifications. Briefly, for each IP 200 million cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) and digested with Micrococcal nuclease (MNase, Sigma, Cat # N3755) at 37°C for 45 min. MNase digested chromatin was sonicated as described before ( PMID: 24737864)and  solubilized chromatin was precleared using protein A sepharose beads for 30 minutes at 4 °C. The precleared chromatin was incubated with Anti-FLAG-M2 magnetic beads (Sigma Cat # M8823) for 4 hrs at 4 °C . The FLAG-M2 magnetic beads were washed  once with buffer I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), and 150 mM NaCl), four times with buffer II 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 150 mM NaCl), 2 times with buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and once with 1X TE. Protein complexes were eluted from magnetic beads using FLAG peptide in HE buffer (10 mM HEPES, 0.25 mM EDTA, 0.5 mM PMSF). The eluent was subjected to subsequent ChIP reaction with Anti-CENP-B (Abcam, Cat# Ab25734)antibodies.Solexa library construction was performed as described previously (PMID:22025700) and PCR-amplified using Phusion polymerase.

value: Anti-FLAG M2 magnetic beads (Signa Cat # M8823) and Anti-CENP-B (Abcam Cat #Ab25734)


title: HeLa_CenpT_X1_(20140710_1,2_1)

description: HeLa cross-linked (X-ChIP) CENP-T ChIP. Replicate with Abcam antibody

value: Anti-CENP-T (Abcam Ab114120)


title: mESCs_shNMC_rep3


title: HeLa_CenpC_X_(20140710_1,2_10)

description: HeLa cross-linked (X-ChIP) CENP-C ChIP

value: Anti-CENP-C (Abcam Ab33034)


title: 24hRA_shNMC_rep3

value: early differentiating embryonic stem cells

value: shNMC (Non Mammalian Control)

tag: treated with

value: Retinoic acid to induce differentiation


title: HeLa_Input_X_(20140710_1,2_11)

description: HeLa cross-linked (X-ChIP) input

source_name: HeLa input

extract_protocol: The HeLa cell line was grown in DMEM media using standard protocols. Input DNA was prepared from cross-linked cells as described previously (PMID:24737864).

value: nuclei


title: HuRef_M2_X_(20140710_1,2_6)

description: HuRef cross-linked (X-ChIP) mock IgG ChIP.

extract_protocol: The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) . MNase digestion, sonication, and chromatin immunoprecipitation steps were performed as described previously (PMID: 24737864) using antibodies.

value: Lymphoblastoid

value: HuRef

value: Anti-FLAG (Sigma F1804)


title: mESCs_control_rep1

value: embryonic stem cell, blastocyst derived

value: pluripotent embryonic stem cells


title: 24hRA_shNMC_rep2


title: 24hRA_shNMC_rep1


title: HuRef_CenpT_X4_(20140710_1,2_6)

description: HuRef cross-linked (X-ChIP) CENP-T ChIP. Replicate with Bethyl anti-body.

value: Anti-CENP-T (Bethyl A302-313A).


title: 24hRA_shMed12_rep2


title: 24hRA_shMed12_rep3


title: HuRef_CenpT_X2_(20140710_1,2_5)

description: HuRef cross-linked (X-ChIP) CENP-T ChIP. Replicate with Abcam antibody.

extract_protocol: The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) . MNase digestion, sonication and chromatin immunoprecipitation steps were performed as described previously (PMID: 24737864) using antibodies.


title: 24hRA_shMed12_rep1


title: HuRef_CenpT_X1_(20140417_1,2_3)


title: 24hRA_shCdk8_rep2


title: 24hRA_shCdk8_rep3


title: 24hRA_shCdk8_rep1


title: HuRef_CenpA_X_(20140417_1,2_4)

description: HuRef cross-linked (X-ChIP) CENP-A ChIP. Replicate with Abcam antibody.

value: Anti-CENP-A (Abcam Ab13939)


title: HuRef_CenpC_X2_(20140710_1,2_15)

description: HuRef cross-linked (X-ChIP) CENP-C ChIP. Replicate with Abcam antibody.


title: HuRef_CenpC_X1_(20140417_1,2_5)


title: HuRef_Input_X2_(20140710_1,2_2)

description: HuRef cross-linked (X-ChIP) ChIP input. Replicate.

source_name: HuRef input

extract_protocol: The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) and digested with MNase. An aliquot containing 100th of the entire chromatine solution was de-cross-linked at 65 degrees C overnight. De-cross-linked chromatin was subjected to RNase A and Proeinase K treatment followed by DNA extraction.


title: HuRef_Input_X1_(20140417_1,2_2)


title: HuRef_CenpT_3_(20150213_1_19)

description: HuRef native CENP-T ChIP. Replicate with Abcam antibody.

data_processing: Paired reads were aligned with various human BACs using BWA 0.7.10 aln and sampe functions saving up to 10 alignments per pair, otherwise with default options. Merged pairs were aligned with various human BACs using the aln/samse functions of BWA version 0.7.5 saving up to 10 alignments per read (-n 10), otherwise with default options. Merged pairs mapped to two consensus sequences representing 20 human centromere sequences are included as supplementary files (Cen1-like and Cen13-like).

extract_protocol: The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Antibodies used in this study were purchased from Abcam (Cambridge MA). Nuclei were prepared following a previously published protocol (PMID:23644596). Briefly, for each IP 40-60 million cells were collected and washed with 1X PBS. Cells were re-suspended in ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) at a density equal to ~25 million cells/ml. An equal volume of ice-cold buffer I supplemented with 0.1% NP40 was added and samples were incubated on ice for 10 min. Nuclei solution was layered on ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) and centrifuged at 10,000g for 20 min at 4 degrees C. The pellet was re-suspended in buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF and protease inhibitor, 3mM Cacl2) at density equal to ~ 32.5 million cell/ml.  Micrococcal nuclease (MNase, Sigma, Cat # N3755) was added to ~2.5 units/ml, and digestion was carried out at 37 degrees C for 5 min. Reactions were stopped by addition of EGTA to a final concentration of 20 mM and EDTA to 10 mM. The final NaCl concentration was adjusted to 215 mM and needle extraction was performed as described previously (PMID:22184235) to enhance the solubility of kinetochore complex. The resulting solution was incubated overnight at 4 degrees C on nutator. Soluble chromatin was collected by centrifuging the mixture at 12000rpm at 4 degrees C for 8 min. Soluble chromatin was diluted 3X with 20 mM Tris, pH 8.0, 5 mM EDTA and 200 mM NaCl, and Triton-X was added at a final concentration of 0.1% (v/v). Next, the chromatin solution was pre-cleared using Protein A/G fast flow Sepharose beads for 20 min at 4 degrees C, and 15 mcg of antibody was added per ChIP sample and incubated overnight at 4 degrees C. Dynabeads were added to the samples and incubated at 4 degrees C for 2 hrs. Immunoprecipitated complexes were washed 6 times with 50mM Phosphate buffer pH 7.4, 5mM EDTA, 200mM NaCl, and DNA was extracted from Dynabeads as described (PMID:22184235). Solexa library construction was performed as described previously (PMID:22025700) and PCR-amplified using Phusion polymerase.

value: Anti-CENP-T (Abcam cat #Ab114120)


title: HuRef_CenpT_2_(20150213_1_12)

extract_protocol: The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Antibodies used in this study were purchased from Abcam (Cambridge MA). Nuclei were prepared following a previously published protocol (PMID:23644596). Briefly, for each IP 40-60 million cells were collected and washed with 1X PBS. Cells were re-suspended in ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) at a density equal to ~25 million cells/ml. An equal volume of ice-cold buffer I supplemented with 0.1% NP40 was added and samples were incubated on ice for 10 min. Nuclei solution was layered on ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and protease inhibitor) and centrifuged at 10,000g for 20 min at 4 degrees C. The pellet was re-suspended in buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF and protease inhibitor, 3mM Cacl2) at density equal to ~ 32.5 million cell/ml.  Micrococcal nuclease (MNase, Sigma, Cat # N3755) was added to ~2.5 units/ml, and digestion was carried out at 37 degrees C for 5 min. Reactions were stopped by addition of EGTA to a final concentration of 20 mM and EDTA to 10 mM. The final NaCl concentration was adjusted to 215 mM and needle extraction was performed as described previously (PMID:22184235) to enhance the solubility of kinetochore complex. The resulting solution was incubated overnight at 4 degrees C on nutator. Soluble chromatin was collected by centrifuging the mixture at 12000rpm at 4 degrees C for 8 min. Soluble chromatin was diluted 3X with 20 mM Tris, pH 8.0, 5 mM EDTA and 200 mM NaCl, and Triton-X was added at a final concentration of 0.1% (v/v). Next, the chromatin solution was pre-cleared using Protein A/G fast flow Sepharose beads for 20 min at 4 degrees C, and 15 mcg of antibody was added per ChIP sample and incubated overnight at 4 degrees C. Dynabeads were added to the samples and incubated at 4 degrees C for 2 hrs. Immunoprecipitated complexes were washed 6 times with 50mM Phosphate buffer pH 7.4, 5mM EDTA, 200mM NaCl, and DNA was extracted from Dynabeads as described (PMID:22184235). Solexa library construction was performed as described previously (PMID:22025700) and PCR-amplified using KAPA polymerase.


title: 5mC D551 iPSC 29abcsp 255

city: New Haven

first: Eriona

last: Hysolli

state: CT

address: 10 Amistad Street

department: Genetics

institute: Yale University

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Bowtie2 (v2.1.0) with the parameter “--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1” .
Genome_build: hg19
Supplementary_files_format_and_content: wig files were created by 100bp sliding window

source_name: Detroit551-derived iPSC

growth_protocol: Fibroblasts were cultured with 10%FBS in DMEM. ESC and iPSC were cultured with hES medium containing KSR and bFGF in DMEM/F12.

extract_protocol:
gDNA was extracted by PureLink Kit from Life Technologies (cat# K1820-02) and applied for hMeDIP (Auto hMeDIP kit, cat#AF-Auto02-0016) or MeDIP (Auto-MeDIP kit, cat#AF-Auto01-0016).
Library was generated by Illumina Truseq DNA LT Sample Prep kit and sequenced by HiSeq2000

treatment_protocol: Cells were transfected with control and miR29a/b/c sponge.

value: D551-derived iPSC

tag: treatment

value: miR29a/b/c sponge


title: 5mC D551 iPSC 29abcsp 253


title: 5mC D551 iPSC 29abcsp 251


title: 5mC D551 iPSC Ctrlsp 254

value: Ctrl sponge


title: heart input

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

data_processing:
Basecalling is performed by Ion Suite version 5.0.4, with BaseCaller script: BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1
Reads are aligned to mouse genome mm9 with Ion Torrent Tmap aligner (v5.0.13): tmap mapall map4
Peak calling were performed by Homer v4.8.1, with findPeaks -style factor for fix-sized transcription factors binding peaks and -style histone for histone marks
Bedgraphs were generated by Homer v4.8.1, with makeUCSCfiles, by default, normalized to 10M reads.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, The bedGraph format allows display of continuous-valued ChIP-Seq data in track format.
Supplementary_files_format_and_content: bed, genomic interval of ChIP-Seq peaks.

source_name: heart

extract_protocol:
Monoclonal anti-Flag BioM2 antibody (Sigma-Aldrich) was used for pulling down Pitx2-Flag.
ChIP libraries were constructed using Kapa Library Preparation Kits for Ion Torrent (Kapa Biosystems)

treatment_protocol: For ChIP-Seq, P2 LAD-O was performed on Pitx2flag neonates, and 4 days later whole ventricles were collected and subjected to the ChIP-Seq.

tag: development stage

value: Postnatal day 6

tag: tissue compartment

value: ventricles


title: 5mC D551 iPSC Ctrlsp 253


title: 5mC D551 iPSC Ctrlsp 252


title: HuRef_CenpT_X3_(20140710_1,2_7)

description: HuRef cross-linked (X-ChIP) CENP-T ChIP. Replicate with Abcam antibody and pre-clearing.

extract_protocol: The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) . MNase digestion, sonication, pre-clearing and chromatin immunoprecipitation steps were performed as described previously (PMID: 24737864) using antibodies.

value: Anti-CENP-T (Abcam Ab114120)


title: Pitx2 4dpmi rep2

description: Chromatin-immunoprecipitated DNA

source_name: heart ventricels of wild type mouse at 5-day-post-resection


title: HuRef_CenpT_1_(20150213_1_6)


title: 5mC D551 iPSC Ctrlsp 251


title: Pitx2 4dpmi rep1

description: Chromatin-immunoprecipitated DNA


title: Nrf2 4dpmi

description: Chromatin-immunoprecipitated DNA


title: 5mC H1

source_name: ESC


title: 5mC D551 iPSC


title: ChIPSeq-ABI5_mock_2

status: Public on May 25 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Base-calling were performed by Illumina Real-Time Analysis software v1.13 or v1.17.
Reads were aligned by bowtie version 0.12.7 against the Arabidopsis TAIR10 genome assembly with parameters " -m 1 --best --strata -S --chunkmbs 200".
Peaks called with MACS2 version 2.0.10 with paramteers " --call-summits --nomodel --shiftsize 150 --keep-dup auto".
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by MACS2.

organism: Arabidopsis thaliana

growth_protocol: Recommending gene tagging of ABI5 (AT2G36270) was carried out as described previously (Zhou et al., The Plant Journal 2011; PMID 21294796).  Seedling were germinated and grown on nylon mesh in hydroponics for 36 hours under long day light conditions.

extract_protocol:
After nuclei isolation, chromatin was sonicated to 100-400 bp fragments. Native ABI5 in wild-type Col-0 plants was immunoprecipitated by a rabbit polyclonal ABI5 antibody (cat #ab98831 lot #GR24437-1, Abcam, USA). Tagged ABI5 proteins in the transgenic lines were immunoprecipitated by a rabbit polyclonal GFP antibody (cat #A11122 lot #1232939, Life Technologies, USA). Col-0 was immunoprecipitated with either rabbit IgG or the GFP antibody as mock IP for the native ABI5 and tagged ABI5, respectively.
Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions.

treatment_protocol: 5 uM ABA treatment for 4 hours.

tag: accession

tag: genotype/variation

value: whole seedlings

tag: age

value: 1.5 day

tag: light condition

value: long day

value: 5 uM abscisic acid, 4 hours

value: GFP

tag: chip antibody vendor

value: Life Technologies

tag: chip antibody cat. #

tag: chip antibody lot#


title: 5mC H9

tag: cell type


title: 5hmC Ctrli

source_name: Detroit551 fibroblast

value: control inhibitor


title: 5mC 29ai

value: miR29a inhibitor


title: 5hmC 29ai


title: 5mC D551 iPSC 29abcsp 252


title: 5mC Ctrli


title: input


title: H9 ESC

description: gene expression in ESC

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Tophat2 (v2.0.12) with SAMtools (v0.1.18) and Bowtie2 (v2.1.0).
RPKM value was calculated Cufflinks (v1.2.1) by using RefSeq genes as reference annotation with "-G" option
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and RPKM value for each sample

molecule: total RNA

extract_protocol:
Total RNA was extracted using TRIzol and miRNeasy Mini Kit (Qiagen cat# 217004).
library preparation was conducted using standard Tru-Seq Illumina kits.


title: H1 ESC

description: gene expression in ESC


title: iPSC Ctrli FM2

description: gene expression in iPSC

source_name: FM1-derived iPSC

value: FM1-derived iPSC


title: Nasonia_F1VG_24h_adult_female

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

data_processing:
Illumina CASAVA 1.8.2 software was used for HiSeq2000 basecalling.
Illumina read QC was performed using FastQC software. Adapter containing reads were trimmed by Trimmomatic.
We built C->T converted reference genomes for both the Watson (+) and Crick (-) strand for Nasonia vitripennis and Nasonia giraulti reference genomes, with all Cs in CpGs context remains Cs (meth_genome) and all CpG Cs converted to Ts (unmeth_genome).
Illumina sequencing reads were aligned to both converted genomes using BWA with a maximum of 4 mismatches for Nasonia vitripennis and 6 mismatches for Nasonia giraulti. 85% of all the reads were aligned to the converted genomes in both species and only 60% of those that uniquely mapped to the genome were kept for the methylation analysis.
To infer allele-specific methylation, we assigned the parental transmission direction for the WGBS-seq reads with an informative V-G SNP or a G-specific indel in them. Among the uniquely mapped reads, 36% do not contain any V-G fixed differences or indels and they were excluded from the allele-specific methylation analysis; 36% came from the Nasonia vitripennis parent and 28% came from the Nasonia giraulti parent. The unequal number of Nasonia vitripennis and Nasonia giraulti parental reads is due to reference genome mapping bias, which was corrected subsequently. To achieve accurate estimation nof allele-specific methylation, we restricted our analysis on the CpGs with at least 8X Nasonia vitripennis allele coverage and 8X Nasonia giraulti allele coverage (total coverage > 16X). Methylation percentage for the Nasonia vitripennis and Nasonia giraulti alleles were estimated separately in both reciprocal F1s. The total methylation percentage were also calculated.
Genome_build: Nvit_1.0; http://www.ncbi.nlm.nih.gov/assembly/GCF_000002325.1
Genome_build: Ngir_1.0; http://www.ncbi.nlm.nih.gov/assembly/GCA_000004775.1
Supplementary_files_format_and_content: gzipped tab-delimited text file includes the C and T counts at alignable CpG positions in both Nasonia vitripennis and Nasonia giraulti genomes. C/T counts for reads mapped with equal score to both genomes, V-specific reads and G-specific reads are summarized separately.

organism: Nasonia vitripennis x Nasonia giraulti

source_name: 24h adult Nasonia vitripennis x giraulti F1 female whole body

extract_protocol:
Genomic DNA samples were extracted from a pool of 50 adult whole-body samples 24 hour following eclosion from reciprocal F1 hybrids of Nasonia vitripennis (strain AsymCX) and Nasonia giraulti (strain R16A), using DNeasy Blood & Tissue Kit (Qiagen, CA).
WGBS-seq libraries were made with 20 µg of input genomic DNA according to Illumina protocols (WGBS for Methylation Analysis Guide, Part# 15021861 Rev. A) using Illumina TruSeq adapters.

tag: hybrid background

value: Nasonia vitripennis x Nasonia giraulti

tag: n. vitripennis strain

value: AsymCX

tag: n. giraulti strain

tag: Sex

value: female

tag: developmental stage

value: 24-hour adult

value: whole body


title: iPSC 29ai FM5

description: gene expression in iPSC


title: Nasonia_F1GV_24h_adult_female

source_name: 24h adult Nasonia giraulti x vitripennis F1 female whole body

value: Nasonia giraulti x Nasonia vitripennis

tag: tissue


title: Nasonia_F1GV_24h_adult_female_replicate3

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling.
Illumina reads QC was performed using FastQC software. Adapter containing reads were trimmed by Trimmomatic.
Illumina short reads were aligned to N.vit and N.gir reference genomes (v1.0) respectively using TopHat v2.0 and >90% of them were uniquely mapped to the genome scaffolds. Counts of aligned reads in Nasonia OGS2 (official gene set 2) transcripts were summarized by Cufflinks v2.1.0 and reads mapped to multiple places in the genome were weighted by the “-u” parameter. We also summarized the counts from uniquely mapped reads only to eliminate the problems caused by paralogs to extremely highly expressed genes. These read counts were fed into the edgeR package in Bioconductor. Normalization was performed and total expression level were calculated using edgeR. F1GV replicate 2 has a significant lower mapping percentage and it was excluded from the analysis.
Genome_build: Nvit_1.0; http://www.ncbi.nlm.nih.gov/assembly/GCF_000002325.1
Genome_build: Ngir_1.0; http://www.ncbi.nlm.nih.gov/assembly/GCA_000004775.1
Supplementary_files_format_and_content: gzipped tab-delimited text file includes the raw read counts for expressed nasonia OGS2 (Nasonia Official Gene Set 2) genes.
Supplementary_files_format_and_content: the gene models could be found at http://arthropods.eugenes.org/genes2/nasonia/genes/nvit2_evigenes_pub11u.good.gff.gz

extract_protocol:
Total RNA samples were extracted from a pool of 10 adult whole-body samples 24 hour after eclosion from reciprocal F1 hybrids of Nasonia vitripennis (strain AsymCX) and Nasonia giraulti (strain R16A), using Qiagen RNeasy Plus mini kit (Qiagen, CA). Three independent batches biological replicates were performed and collected for each direction.
RNA-Seq libraries were made from 2 ug total RNA input using TruSeq RNA Sample Preparation Kits v2 (Illumina Inc., CA)


title: iPSC 29ai FM4

description: gene expression in iPSC

tag: treatment


title: iPSC 29ai E7

description: gene expression in iPSC

value: D551-derived iPSC


title: Nasonia_F1GV_24h_adult_female_replicate2


title: H3k4me1 5dpr rep2

description: Chromatin-immunoprecipitated DNA

tag: development stage

value: Postnatal day 6

value: ventricles


title: Nasonia_F1VG_24h_adult_female_replicate3


title: iPSC 29ai E1

description: gene expression in iPSC


title: iPSC 29ai FM2

description: gene expression in iPSC


title: H3k4me1 5dpr rep1

description: Chromatin-immunoprecipitated DNA

tag: tissue compartment


title: iPSC 29ai E6

description: gene expression in iPSC


title: H3k4me1 sham rep2

description: Chromatin-immunoprecipitated DNA

source_name: heart ventricels of wild type mouse at 5-day-post sham surgery


title: H3k4me1 sham rep1

description: Chromatin-immunoprecipitated DNA


title: Nasonia_F1VG_24h_adult_female_replicate2


title: iPSC 29abc sp 1

description: gene expression in iPSC

value: miR29a/b/c sponge


title: iPSC 29abc sp 5

description: gene expression in iPSC


title: Nasonia_F1VG_24h_adult_female_replicate1


title: iPSC Ctrli F5

description: gene expression in iPSC


title: iPSC Ctrl sp 3

description: gene expression in iPSC

value: Ctrl sponge


title: Fib Ctrli

description: gene expression in fibroblast


title: Fib 29ai

description: gene expression in fibroblast


title: iPSC Ctrli F3

description: gene expression in iPSC


title: iPSC Ctrl sp 1

description: gene expression in iPSC


title: TED-120

city: Kingston upon Thames

first: Lori

last: Snyder

address: Penrhyn Road

department: School of Life Sciences, Pharmacy, and Chemistry

country: United Kingdom

institute: Kingston University

data_processing:
Base calling using Torrent Suite v4.2.1
Data filtering using Torrent Suite v4.2.1
Generation of BAM format file using Torrent Suite v4.2.1
Alignment of BAM file with strain NCCP11945 reference genome using NextGENe v2.3.4.2
Alignment generated expression reports (txt files) and the ability to manually assess transcript alignment against the genomic locations.
Genome_build: ASM2010v1

organism: Neisseria gonorrhoeae NCCP11945

source_name: Bacteria

growth_protocol: Neisseria gonorrhoeae strain NCCP11945 was grown on GC agar (Oxoid) at 40°C in an incubator in a candle tin.

extract_protocol:
Bacterial samples stored in RNALater were removed and extracted using Rneasy Kit (Qiagen).
Libraries were prepared using the Ion Torrent protocols for use with the Ion Torrent RNA-Seq Kit (Life Technologies).

treatment_protocol: treatment protocol

tag: strain


title: Fib 29abc sp

description: gene expression in fibroblast


title: Fib Ctrl sp

description: gene expression in fibroblast


title: Nasonia_F1GV_24h_adult_female_replicate1


title: BSA-8h

status: Public on May 23 2016

city: beijing

first: jianying

last: Liu

state: beijing

address: Room 4-305,Biotechnology building, Tsinghua University, Beij

country: China

institute: tsinghua university

description: 8h BSA-VS-NS1.GeneDiffExp.txt

data_processing:
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Genome_build: Aaegl3.3
Supplementary_files_format_and_content: .txt files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...

organism: Aedes aegypti

source_name: Midguts

growth_protocol: Aedes Aegypti was reared at 28℃ and 80% humidity.

extract_protocol:
Midguts were dissected from mosquitoes, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 days old mosquitos were blood fed BSA or DENV2 NS1, then treated after 4, 8,18 hours.

value: Liverpool

tag: gender

tag: protocol

value: blood fed BSA

tag: time

value: Midguts


title: BSA-4h

description: 4h BSA-VS-NS1.GeneDiffExp.txt

tag: age


title: NS1-18h

description: 18h BSA-VS-NS1.GeneDiffExp.txt

value: blood fed DENV2 NS1


title: NS1-8h

description: 8h BSA-VS-NS1.GeneDiffExp.txt


title: BSA-18h

description: 18h BSA-VS-NS1.GeneDiffExp.txt


title: RFX_ChIPSeq_WT_1

city: Boston

first: Thomas

middle: Andy

last: Nguyen

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Identifying sequence barcodes were extracted from sequencing reads from RNA-seq and DNA-seq
Barcodes not matching correct length are filtered out.
Barcodes without trailing common sequence TCTAGA are filtered out.
Barcode counts were totalled for each sample.
Supplementary_files_format_and_content: Excel files for each test tile library with barcode counts for each sample. Each file also contains a tab that explains the columns.
We aligned using Bowtie and called peaks as in (Kim et al., 2010).
We distinguished distal enhancers and gene promoters based on a distance threshold of 1 kb from RefSeq TSSs.
Genome_build: mm9
Supplementary_files_format_and_content: Bam files are the aligned reads from Bowtie used to call peaks. The combined_names files have peaks combined from two reps each. They indicate peak start and stop for the combined peak and the centers from each of the individual replicates. There is a -1 if a peak wasn't found in a particular replicate.

source_name: E16 cortical neurons

growth_protocol:
RNA-seq: Primary cultures were prepared from E16 CD-1 mouse embryos (Charles River Labs) and cultured on 15 cm dishes.
DNA-seq: Plasmid library cloning was performed in e. coli.
ChIP-seq: Primary cultures were prepared from E16 CD-1 mouse embryos (Charles River Labs) and cultured on 15 cm dishes.

extract_protocol:
RNA-seq: Samples were collected and stored in 15 ml Trizol Reagent (Invitrogen). RNA extraction was performed followed by DNase treatment, mRNA selection, a second DNase treatment, reaction cleanup, concentration, and conversion to cDNA.
RNA-seq: Barcode sequences were amplified from cDNA samples using primers to add Illumina sequencing adapters.
DNA-seq: Cultures were spun down and libraries were isolated using Qiagen CompactPrep Maxi Kit.
DNA-seq: Barcode sequences were amplified from plasmid DNA samples using primers to add Illumina sequencing adapters.
ChIP-seq: We performed ChIP-Seq in RFX-DN transduced neurons using an anti-MYC A14 antibody (Santa Cruz, sc-789) after 0 or 1 hour of depolarization in 55mM KCl as described in (Kim et al., 2010), except performing sonication on a Covaris.
ChIP-seq: As described in (Kim et al., 2010).

treatment_protocol:
RNA-seq: AAV transduction was performed on DIV4. For depolarization of neurons, DIV6 neurons were quieted overnight in 1mM tetrodotoxin (Tocris) and 100 mM DL-2-amino-5-phosphonopentanoic acid (Tocris). On DIV7, neurons were depolarized for 0 or 12 hours by removal of drugs and addition of 55 mM KCl.
DNA-seq: Transformed bacteria were incubated overnight at 30 C.
ChIP-seq: Lentiviral transduction with RFX dominant negative was performed on DIV2. For depolarization of neurons, DIV6 neurons were quieted overnight in 1mM tetrodotoxin (Tocris) and 100 mM DL-2-amino-5-phosphonopentanoic acid (Tocris). On DIV7, neurons were depolarized for 0 or 1 hour by removal of drugs and addition of 55 mM KCl.

tag: replicate


title: RFX_ChIPSeq_WT_2


title: RFX_ChIPSeq_input_2


title: TN05_P_DNA

data_processing:
Library strategy: DNA-seq
Identifying sequence barcodes were extracted from sequencing reads from RNA-seq and DNA-seq
Barcodes not matching correct length are filtered out.
Barcodes without trailing common sequence TCTAGA are filtered out.
Barcode counts were totalled for each sample.
Supplementary_files_format_and_content: Excel files for each test tile library with barcode counts for each sample. Each file also contains a tab that explains the columns.
We aligned using Bowtie and called peaks as in (Kim et al., 2010).
We distinguished distal enhancers and gene promoters based on a distance threshold of 1 kb from RefSeq TSSs.
Genome_build: mm9
Supplementary_files_format_and_content: Bam files are the aligned reads from Bowtie used to call peaks. The combined_names files have peaks combined from two reps each. They indicate peak start and stop for the combined peak and the centers from each of the individual replicates. There is a -1 if a peak wasn't found in a particular replicate.

organism: unidentified plasmid

source_name: Plasmid DNA library

tag: test tiles

value: genomic

tag: assay

value: promoter


title: RFX_ChIPSeq_input_1


title: RFX_ChIPSeq_1hr_1

value: KCl Depolarized 1 hour


title: RFX_ChIPSeq_1hr_2


title: TN04_E_DNA

value: artifical

value: enhancer


title: TN04_P_DNA


title: TN03_E_DNA


title: TN03_P_DNA


title: TN05_E_DNA


title: iPSC Ctrl sp 4

description: gene expression in iPSC

tag: cell type


title: RFX_ChIPSeq_0hr_2

value: unstimulated


title: OE12-2

city: Wuhan

first: Liu

last: Zheng

institute: Huazhong Agricultural University

data_processing:
After removal of low quality reads and/or adaptor sequences, the clean reads were aligned to the genomic DNA sequence of sweet orange (Citrus sinensis)
The gene expression level was calculated by using RPKM method.
Differentially expressed genes were analysed based on the poisson distribution method.
Gene ontology enrichment analysis and KEGG enrichment analysis of differentially expressed genes
Genome_build: citrus sinensis whole genome（http://www.ncbi.nlm.nih.gov/assembly/GCF_000317415.1）
Supplementary_files_format_and_content: 8 files includes RPKM values

organism: Citrus unshiu

source_name: CsFUS3 overexpression_12wk induction

growth_protocol: Callus of  ‘Guoqing No.1’ Satsuma mandarin  was preserved on MT medium.

extract_protocol:
Total RNA was extracted by Trizol method
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the degestion products are purified by magnetic beads. After that, the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primed reverse transcription. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads . End reparation is then performed. After the previous step, adaptors are ligated to the ends of these fragments. Next, ligation products were selected by size and purified on TAE-agarose gel. Finally, the fragments are enriched by PCR amplification, then purified by magnetic beads and dissolved in the appropriate amount of Epstein-Barr solution.

treatment_protocol: Overexpression CsFUS3 vector and empty vector were transferred into ‘Guoqing No.1’ Satsuma mandarin (G1) callus, respectively.

tag: strain/clone background

value: ‘Guoqing No.1’ Satsuma mandarin

tag: genotype/variation

value: overexpressing CsFUS3 vector

value: 12 weeks of glycerol induction

tag: time points during se

value: onset of the somatic embryo emergence

value: callus


title: NS1-4h

description: 4h BSA-VS-NS1.GeneDiffExp.txt

value: female


title: OE12-1


title: OE6-1

source_name: CsFUS3 overexpression_6wk induction

value: 6 weeks of glycerol induction

value: colour just beginning to change


title: OE6-2


title: EV12-2

source_name: empty vector_12wk induction

value: expressing empty vector

value: 12weeks of glycerol induction


title: RFX_ChIPSeq_0hr_1


title: TN05_DNA_Key_Development


title: TN03_DNA_Key_Development


title: EV12-1


title: TN05_P_Un2_DN

value: unstimulated and DN


title: TN05_P_KCl1_DN

value: genomic

value: KCl depolarized and DN


title: TN05_P_Un3_DN

value: promoter


title: EV6-2

source_name: empty vector_6wk induction


title: TN05_P_Un1_DN


title: TN05_P_KCl2

value: KCl depolarized


title: TN05_P_KCl3


title: TN05_P_Un2


title: TN05_P_Un1


title: TN05_P_KCl3_DN


title: TN05_P_KCl2_DN


title: Angus #3

city: Burlington

first: David

last: Kerr

state: VT

address: 570 Main Street

department: Animal and Veterinary Sciences

institute: University of Vermont

data_processing:
Library strategy: MIRA-Seq
Illumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the UMD v. 3.1 bovine genome. Only reads with a median q score above 20 were considered for mapping.
Genome_build: Bos taurus UMD 3.1/bosTau6
Supplementary_files_format_and_content: Tab-delimited text files include raw reads mapping to genomic location.

organism: Bos taurus

source_name: Bovine dermal fibroblasts, Angus

growth_protocol: Fibroblasts were grown in DMEM supplemented with 5% fetal bovine serum, 1X ITS, and 1X Pen/Strep antibiotic in a T75 culture flask.

extract_protocol:
gDNA was collected using the ArchivePure DNA Extraction kit (5 Prime, Gaithersburg, MD)
Libraries were constructed based upon manufacturer's instructions for the Active Motif MethylCollector Ultra-seq kit. Briefly, genomic DNA was fragmented by sonication, repaired, and ligated with Illumina sequencing adapters. Enrichment for methylated DNA was conducted using the kit's provided nickel-coated dual protein (methyl-binding domain proteins) pulldown. Sequencing of the enriched library was then conducted following recommendations from Illumina.

treatment_protocol: No treatment was imposed on the cells

tag: breed

value: Angus

value: dermal fibroblasts

tag: passage

tag: animal #


title: Holstein #2

source_name: Bovine dermal fibroblasts, Holstein

value: Holstein


title: Holstein #3


title: Angus #4


title: TN05_P_KCl1

tag: treatment


title: Angus #2


title: Holstein #1


title: Holstein #4


title: TN05_E_KCl2_DN

value: enhancer


title: Angus #1


title: TN05_E_KCl3_DN


title: HCT116 was treated by S2101

city: Guangzhou

first: Gong

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

data_processing:
Adapter sequences were trimmed from the reads.
High quality reads were mapped to human mRNA reference sequence (RefSeq) for GRCh38/hg38 (downloaded from UCSC genome browser on May 21st, 2014) using FANSe2 mapping algorithm with the options –L80 –S10 –I0 –E5 –B1.
Genome_build: Human mRNA reference sequence (RefSeq) for GRCh38/hg38 (downloaded from UCSC genome browser on May 21st, 2014)

growth_protocol: A549 and MHCC97H cells were cultured in the complete DMEM medium and epigenetically manipulation (1 μM TSA, 50 μM GSK126 and 100μM S2101 respectively); HCT116 cells were maintained in complete RPMI 1640 medium and epigenetically manipulation (1 μM TSA, 50 μM GSK126 and 100μM S2101 respectively). We detected and analyzed the miss protein with transcriptome and proteome.

extract_protocol:
Total RNA was extracted using Trizol method.
The polyA+mRNA was selected by NEBNext® Poly(A) mRNAMagnetic Isolation Module. We used NEBNext® Ultra™ RNA Library Prep Kit for Illumina to construct sequencing libraries.

tag: cell line


title: HCT116 was treated by TSA

source_name: HCT116, 1 μM TSA


title: TN05_E_KCl1_DN

tag: strain


title: EV6-1

value: ‘Guoqing No.1’ Satsuma mandarin

tag: tissue


title: HCT116 was treated by GSK126


title: NHEK LL-37 / Poly(I:C)

city: San Diego

first: Christopher

last: Adase

address: 2525 John Hopkins Ct

department: Dermatology

institute: UCSD

description: barcode: TATAGCCT

data_processing:
Reads aligned via Tophat2 2.0.8 to hg19, default parameter values used
Samples were quantified to RefSeq Transcripts - 2015-05-07
Gene analysis used Partek Gene Specific Analysis (GSA) run on the gene level with default values except for the following parameter changes, Lowest maximum coverage: 10, Poisson: True, and TMM normalization. Gene filters used were p < 0.05 and fold expression > 2
Values are reads per gene per condition
Genome_build: hg19
Supplementary_files_format_and_content: Adase_JBC_2016_GF_Paper_Processed_data_raw_count.txt

source_name: NHEK LL-37 / Poly(I:C)

growth_protocol: NHEKs grown in serum-free EpiLife cell culture media with EDGS, Ca2+, and Pen/Strep until passage 4 then plated at 70k cells per well in a 12 well plate (now P5). Cell media changed 24 hours after plating which was also 24 prior to treatment

extract_protocol:
RNA was isolated after 24 hours of treatment using a Ambion Purelink RNA Mini kit. Followed protocol to lyse cells. Cells were lysed with lysis buffer plus 1% Beta mercaptoethanol as in the protocol.
Libraries were prepared using a TruSeq HT library prep kit according to Illumina's instruction. Our samples are under index 2 (i5) adapters . Barcode: UNIQUE TO SAMPLE; common adapter: AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT

treatment_protocol: P6 NHEKs grown until 60 – 80% confluence in 12 well plate then treated with 0.1μg/ml Poly(I:C), 1.75 µM LL-37 for 24 hours before RNA isolation

value: Normal Human Epidermal Keratinocytes

value: 1.75uM LL-37 and 0.1ug/ml Poly(I:C)

value: treatment lasted 24 hours


title: Holstein #3, hour 8

data_processing:
Illumina Casava 1.7 software was used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the UMD v. 3.1 bovine genome. Only reads with a median q score above 20 were considered for mapping.
Genome_build: UMD 3.1/bosTau6
Supplementary_files_format_and_content: tab-delimited text files incude raw reads mapping to genomic location.

source_name: Bovine dermal fibroblasts, Holstein, 8 hrs post LPS

growth_protocol: Fibroblasts were grown in DMEM supplemented with 5% fetal bovine serum, 1X ITS, and 1X Pen/Strep antibiotic in a T75 culture flask and then challenged in a 6-well plate.

extract_protocol:
mRNA was collected following challenge with the 5 Prime RNA PerfectPure Extraction Kit. Cell lyaste from duplicate wells were pooled prior to RNA extraction.
Massively Parallel sequencing library preparation was performed in accordance to the Illumina TruSeq RNA Sample Prep LT version 2 (RS-122-2001/2002). Breifly, each sample was Poly-A enriched for mRNA followed by a reverse transcription step with SuperScript II (Invitrogen) to convert mRNA to cDNA, then fragmented, end repaired, and adenylated. Illumina indexed adaptors, which contain a universal PCR primer and flow cell binding site, were ligated onto each sample. Each index sequence was unique for the purpose of labelling each sample with its own sequence for individualization and demultiplexing purposes. An Illumina specific PCR master mix was used to perform PCR enrichment/amplification for a predetermined number of cycles using a standard PCR cycle titration in order to keep the number of cycles to a minimum and reduce potential for duplicate sequences in the final data. Generally, 6-10 cycles were required. The enriched PCR product is cleaned using AMPure Beads (Beckman Coulter) and the resulting product is quantified using a Qubit Spectrofluorometer and Aligent Bioanalyzer 2100 High sensitivity DNA chip.

treatment_protocol: Cells were treated with 100ng/ml of LPS (Sigma, St. Louis, MO)

value: lipopolysaccharide (LPS)

tag: hours post lps


title: NHEK Poly(I:C)

description: barcode: GTACTGAC

source_name: NHEK Poly(I:C)

value: 0.1ug/ml high molecular weight Poly(I:C)

tag: time


title: TN05_E_Un3_DN

tag: age


title: TN05_P_Un3

value: unstimulated

tag: replicate


title: HCT116 Normal condition

source_name: HCT116, Grown under normal condition


title: Holstein #2, hour 8


title: NHEK LL-37

description: barcode: CAGGACGT

source_name: NHEK LL-37


title: A549 was treated by TSA

source_name: A549, 1 μM TSA


title: TN05_E_Un2_DN

tag: test tiles


title: A549 was treated by S2101


title: TN05_E_Un1_DN

tag: assay


title: E14.5 WT medial cortex rep3

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina base calling
BWA mapping
STAR mapping
HTSEQ counting
Genome_build: mm9
Supplementary_files_format_and_content: raw read

source_name: WT embryonic mouse brain

growth_protocol: none, acquired by dissection

extract_protocol:
RNeasy Micro Kit (Qiagen).
polyA unstranded protocol

treatment_protocol: none, normal WT samples

tag: developmental stage

tag: strain background

value: mixed

tag: genotype

value: wildtype

value: brain

tag: tissue compartment

value: medial cortex


title: A549 was treated by GSK126


title: TN05_E_KCl3

value: genomic


title: Holstein #4, hour 8

tag: breed

tag: cell type


title: Holstein #1, hour 8


title: NHEK Control

description: barcode: TAATCTTA

source_name: NHEK Control

tag: passage

value: PBS


title: TN05_E_KCl2

source_name: E16 cortical neurons

tag: treatment

value: KCl depolarized


title: A549 Normal condition

source_name: A549, Grown under normal condition

tag: cell line


title: Holstein #3, hour 2

source_name: Bovine dermal fibroblasts, Holstein, 2 hrs post LPS

value: dermal fibroblasts


title: TN05_E_KCl1

tag: strain


title: E14.5 WT medial cortex rep2

tag: tissue


title: Holstein #2, hour 2

value: Holstein

tag: hours post lps


title: TN05_E_Un3

value: enhancer


title: Holstein #1, hour 2


title: E14.5 WT lateral cortex rep1

value: lateral cortex


title: MHCC97H was treated by S2101


title: E14.5 WT medial cortex rep1


title: MHCC97H was treated by TSA

source_name: MHCC97H, 1 μM TSA


title: MHCC97H was treated by GSK126

source_name: MHCC97H, 50 μM GSK126


title: Holstein #3, hour 0

source_name: Bovine dermal fibroblasts, Holstein, 0 hrs post LPS


title: TN05_E_Un2


title: Holstein #4, hour 2


title: Holstein #4, hour 0


title: TN05_E_Un1


title: E14.5 WT lateral cortex rep2


title: MHCC97H Normal condition

source_name: MHCC97H, Grown under normal condition


title: Holstein #2, hour 0


title: K12

city: Paris

first: Brice

last: Sperandio

address: 28, rue du Docteur Roux

department: Biologie Cellulaire et Infection

country: France

institute: Institut Pasteur

data_processing:
Reads were mapped to human genome hg19 (GRCh37) using TopHat 2.0.11, with Gencode 19 human genes as a transcriptome guide and maximum of 50 multihits
Reads mapping to Gencode genes were counted with the featureCounts software of the Subread package
Read counts were normalized uzing the DESeq 1.14 estimateSizeFactors function
Genes having less than 10 reads in any condition were filtered out, and remaining transcripts had a psendocount of 5 to down-weight poorly expressed transcripts in fold-change calculations
Genome_build: human genome hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include fold-change values for each conditions

source_name: Colon

growth_protocol: Cells were cultured with DME supplemented with 10% decomplemented Fetal Bovine Serum, 1% non-essential amino acids, 100 U/ml penicillin and 100 ug/ml streptomycin, at 37°C and 10% CO2. Cells were split two times per week using Versene solution

extract_protocol:
mRNA was isolated using the Rneasy Mini kit and the Rnase free Dnase kit from Qiagen
RNA libraries were created with Illumina TruSeq stranded PolyA+ mRNA kit

treatment_protocol: Cell were pretreated or not with 5 uM TSA for 16 hours, and challenged or not with E. coli (10 bacteria per cell) for 2 hours

value: TC7 cells (Caco-2)

tag: condition

value: Non treated cells infected with E. coli K12


title: K12+TSA

value: Cells treated with TSA and infected with E. coli K12


title: Angus #3, hour 8

source_name: Bovine dermal fibroblasts, Angus, 8 hrs post LPS

value: Angus

value: lipopolysaccharide (LPS)


title: TN04_P_KCl2

value: artifical

value: promoter

tag: age


title: Angus #4, hour 8


title: TN04_P_KCl1

tag: replicate


title: Angus #2, hour 8


title: LF82

value: Non treated cells infected with E. coli LF82


title: TN04_P_Un3

tag: test tiles

value: unstimulated


title: TN04_P_Un1

tag: assay


title: TN04_E_KCl3


title: Angus #1, hour 8


title: Angus #3, hour 2

source_name: Bovine dermal fibroblasts, Angus, 2 hrs post LPS


title: TN04_E_KCl2


title: NI

value: Non infected and non treated cells


title: NI+TSA

value: Non infected cells treated with TSA


title: TN04_P_KCl3


title: Whole kidney #2

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22367
GUDMAP ID: 22367

data_processing:
BAM files were processed to obtain RPKM expression values using the Partek Genomics Suite 6.6 software.
file format and content: Excel (xlsx) file with 2 sheets. Sheet 1 contains Cortex, Whole Kidney, and ROR2 data and Sheet 2 contains ITGA8 data. File contains Reads and RPKM values for each transcript.
Sequence files were aligned using TopHat v2.0.8b and Bowtie 2.1.0.0 by the USC Epigenome Center.

source_name: Human fetal whole kidney (representative slice) #2

extract_protocol:
RNA was isolated from FACS isolated cells, cortex, or whole kidney using the Qiagen RNeasy micro (cells) or mini (tissue) kit following the manufacturer’s instructions. Cells were resuspended and vortexed in buffer RLT and tissue homogenized in buffer RLT using a motorized pestle. Tissue was additionally centrifuged through a QIAshredder to shear genomic DNA and reduce viscosity. The lysates were centrifuged through the provided column to isolate RNA, and the columns subsequently washed, DNase treated, washed, and eluted with RNase-free H2O.
Libraries were constructed from 40-200ng of total RNA by the USC Epigenome Center with the Illumina TruSeq RNA Library Prep Kit V2 following the manufacturer’s instructions with following modifications:  End-IT repair from Epicentre was used instead of TruSeq end repair (more favorable volumes). Half of adapter-ligation was amplified for a variable number of cycles depending on input amounts. KAPA Biosystems PCR Master Mix was utilized in place of Illumina's.

treatment_protocol: Intact, unfixed human embryonic kidneys from 15-16 weeks gestation were obtained from Novogenix. The outer capsule was removed, kidneys washed several times in sterile PBS, and a representative slice of the kidney collected (from outer cortex to inner medulla). RNA was isolated using the Qiagen RNeasy mini kit. Libraries were constructed by the USC Epigenome Center with the Illumina mRNA-seq kit and sequenced on the Illumina HiSeq 2000.

value: wild type

value: outer renal medulla,inner renal medulla,renal cortex,renal medulla

value: 15 weeks 6 days

tag: Stage

value: Fetal 16wk

tag: Sex

value: unknown

tag: pooled sample

value: no


title: TN04_E_KCl1

value: enhancer

value: KCl depolarized


title: Angus #2, hour 2

value: dermal fibroblasts


title: LF82+TSA

value: TC7 cells (Caco-2)

value: Cells treated with TSA and infected with E. coli LF82


title: Holstein #1, hour 0

value: Holstein

value: lipopolysaccharide (LPS)


title: ROR2 positive cells

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22365
GUDMAP ID: 22365

source_name: ROR2+ FACS cells from fetal kidney outer cortex

treatment_protocol: Intact, unfixed human embryonic kidneys from fetal week 16 were obtained from Novogenix. The outer capsule was removed, kidneys washed several times in sterile PBS, and whole kidneys incubated with Liberase to remove only the outer cortical cell layers enriched for stromal and nephron progenitors. The dissociated cells were subsequently treated with red blood cell lysis buffer. In order to isolate a nephron progenitor specific population, cell suspensions were incubated with anti-ROR2 conjugated with Alexa Fluor 488 (R&D Systems, FAB20641G) to label the nephron progenitors. Labeled cells were treated with a viability marker and sorting performed on an Aria II Flow Cytometer. Nephron progenitors were isolated by selecting for the ROR2+ population. Collected cells were pelleted and RNA obtained using the Qiagen RNeasy Micro Kit. Libraries were constructed by the USC Epigenome Center with the Illumina mRNA-seq kit and sequenced on the Illumina HiSeq 2000.

tag: genotype

value: cap mesenchyme,pretubular aggregate

value: 16 weeks 4 days

value: Fetal 17wk


title: Whole kidney #1

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22366
GUDMAP ID: 22366

source_name: Human fetal whole kidney (representative slice) #1

value: inner renal medulla,renal cortex,renal medulla,outer renal medulla

value: 16 weeks 3 days


title: Angus #1, hour 2

tag: breed

value: Angus


title: Angus #4, hour 0

source_name: Bovine dermal fibroblasts, Angus, 0 hrs post LPS

tag: cell type


title: TN04_E_Un2

value: artifical

value: unstimulated


title: TN04_E_Un3


title: Angus #3, hour 0


title: TN04_E_Un1


title: Angus #2, hour 0


title: ITGA8 positive cells #2

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22362
GUDMAP ID: 22362

source_name: ITGA8+ FACS cells from fetal kidney outer cortex #2

treatment_protocol: Intact, unfixed human embryonic kidneys from fetal weeks 16-17 were obtained from Novogenix. The outer capsule was removed, kidneys washed several times in sterile PBS, and whole kidneys incubated with Liberase to remove only the outer cortical cell layers enriched for stromal and nephron progenitors. The dissociated cells were subsequently treated with red blood cell lysis buffer. In order to isolate a nephron progenitor specific population, cell suspensions were incubated with following antibodies: anti-integrin alpha 8 (ITGA8; R&D Systems, AF4076) to label the nephron progenitors, anti-podocalyxin (R&D Systems, MAB1556) to label contaminating ITGA8+ podocytes, and anti-F4/80 (Abcam, ab6640) to label contaminating macrophages. After primary labeling, cells were incubated with the appropriate fluorophore labeled secondary antibodies. Labeled cells were treated with a viability marker and sorting performed on an Aria II Flow Cytometer. Nephron progenitors were isolated by selecting for the ITGA8+ population and selecting against podocalyxin+ and F4/80+ populations. Collected cells were pelleted and RNA obtained using the Qiagen RNeasy Micro Kit. Libraries were constructed by the USC Epigenome Center with the Illumina mRNA-seq kit and sequenced on the Illumina HiSeq 2000.

value: wild type

value: 16 weeks 6 days

value: unknown


title: TN03_P_KCl2

value: genomic

value: promoter

value: KCl depolarized


title: ITGA8 positive cells #3

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22363
GUDMAP ID: 22363

source_name: ITGA8+ FACS cells from fetal kidney outer cortex #3

value: 17 weeks 2 days

value: Fetal 18wk

value: no


title: TN04_P_Un2


title: ITGA8 positive cells #1

description:
genome build: hg19
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22361
GUDMAP ID: 22361

source_name: ITGA8+ FACS cells from fetal kidney outer cortex #1

value: cap mesenchyme,pretubular aggregate


title: TN03_P_KCl1

source_name: E16 cortical neurons


title: ITGA8 negative cells #1

description:
genome build: hg19
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22359
GUDMAP ID: 22359

source_name: ITGA8- FACS cells from fetal kidney outer cortex #1

value: renal cortex,nephrogenic interstitium,renal cortical interstitium


title: ITGA8 negative cells #3

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22360
GUDMAP ID: 22360

source_name: ITGA8- FACS cells from fetal kidney outer cortex #3

value: renal cortex,renal cortical interstitium,nephrogenic interstitium


title: Angus #1, hour 0

value: dermal fibroblasts

value: lipopolysaccharide (LPS)


title: TN03_P_Un1


title: TN03_P_Un2


title: TN03_E_KCl1

value: enhancer


title: Cortex

description:
genome build: hg19
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22358
GUDMAP ID: 22358

source_name: Human fetal kidney cortex

treatment_protocol: Intact, unfixed human embryonic kidneys from 16 weeks gestation were obtained from Novogenix. The outer capsule was removed, kidneys washed several times in sterile PBS, and the outer cortex (~0.5 mm) micro-dissected. RNA was isolated using the Qiagen RNeasy mini kit. Libraries were constructed by the USC Epigenome Center with the Illumina mRNA-seq kit and sequenced on the Illumina HiSeq 2000.

value: renal cortex

value: 16 weeks 4 days

value: Fetal 17wk


title: ROR2 negative cells

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22364
GUDMAP ID: 22364

source_name: ROR2- FACS cells from fetal kidney outer cortex

value: wild type


title: TN03_E_Un2

value: unstimulated


title: TN03_E_KCl2

value: genomic


title: SIX2 ChIP w/specifc antibody (17 week #1)

description:
genome build: hg19
ChIP Antibody: SIX2, Polyclonal Antibody (MyBioscience, cat# MBS610128)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22357
GUDMAP ID: 22357

data_processing:
Mapped ChIP-seq and input data were analyzed using QuEST 2.4 software (Valouev et al., 2008; PMID: 19160518). QuEST peak calling parameters: We used a “transcription factor” setting (for SIX1 and SIX2); bandwidth of 30 bp, regions size of 300 bp) or a ‘histone’ setting (H3K27ac, P300); bandwidth of 100 bp, regions size of 1000 bp). Peak calling stringency was specified as following: a sample-dependent ChIP enrichment fold, 3-fold ChIP over input enrichment were used to seed the regions, and 3-fold ChIP enrichment was assigned for extending the regions. FDR for detecting the bound regions was evaluated by allocating the same number of mapped reads from a separate input library and performing QuEST analysis using the same parameters.
All ChIP-seq sequences were mapped to hg19 using Novoalign software (Novocraft). Novoalign alignment parameters: Single-end reads trimming of 10 bp, polyclonal read filter: 7,10 0.4,2,  maximum alignment score acceptable: 120.

source_name: Human kidney ChIP w/SIX2 specific antibody-17wk sample #1

extract_protocol:
Human fetal kidney tissue was microdissected to remove the cortex and incubated for 30 minutes at room temperature in crosslink buffer. Crosslinking was stopped by the addition of glycine. Tissue was washed with PBS containing protease inhibitors, homogenized, pelleted, and lysed in ChIP lysis buffer with the aid of a B dounce homogenizer. Processing of the samples from this point was carried forward using the mouse ChIP protocol (see Park et al 2012; PMID: 22902740 for experimental  conditions and buffer components).
Sequencing libraries were made using the ThruPLEX-FD Prep Kit (Rubicon Genomics) according to manufacturer’s instructions. In brief 10-50ng of DNA was end repaired, A-tailed and ligated with adapters, amplified with indexing reagents, and DNA libraries purified using Ampure magnetic beads. Libraries were submitted to the USC Epigenome Center for sequencing on the Illumina HiSeq 2000.

treatment_protocol: For ChIP-seq from 16-17 week human fetal kidneys, specimens were immediately incubated in 1% PFA crosslink buffer (PMID:22902740) and stored on ice for a maximum of 30 minutes. Samples were then microdissected to remove the cortex (~0.5 mm) and incubated for an additional 30 minutes at room temperature in fresh 1% PFA crosslink buffer. Crosslinking was stopped by the addition of glycine. Tissue was washed with PBS containing protease inhibitors (PI) and resuspended in fresh PBS+PI. Tissue was spread across 1.5 mL Eppendorf tubes and homogenized with a motorized pestle. Homogenized tissue was pelleted, resuspended in mouse ChIP lysis buffer (PMID:22902740), and recombined. The tissue was lysed with the aid of a B dounce homogenizer and incubated on ice for 20 minutes. Processing of the samples from this point was carried forward using the mouse ChIP protocol (PMID:22902740). Sequencing libraries were made using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were submitted to the USC Epigenome Center for sequencing on the Illumina HiSeq 2000.

value: unknown


title: SIX2 ChIP (17 week #1)

description:
genome build: hg19
ChIP Antibody: SIX2 Antibody (Proteintech, cat# 11562-1-AP)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22356
GUDMAP ID: 22356

source_name: Human kidney ChIP SIX2-17wk sample #1

extract_protocol:
Human fetal kidney tissue was microdissected to remove the cortex and incubated for 30 minutes at room temperature in crosslink buffer. Crosslinking was stopped by the addition of glycine. Tissue was washed with PBS containing protease inhibitors, homogenized, pelleted, and lysed in ChIP lysis buffer with the aid of a B dounce homogenizer. Processing of the samples from this point was carried forward using the mouse ChIP protocol (see Park et al, 2012; PMID: 22902740 for experimental  conditions and buffer components).
Sequencing libraries were made using the ThruPLEX-FD Prep Kit (Rubicon Genomics) according to manufacturer’s instructions. In brief 10-50ng of DNA was end repaired, A-tailed and ligated with adapters, amplified with indexing reagents, and DNA libraries purified using Ampure magnetic beads. Libraries were submitted to the USC Epigenome Center for sequencing on the Illumina HiSeq 2000.


title: SIX2 ChIP (17 week #2)

description:
genome build: hg19
ChIP Antibody: SIX2, Polyclonal Antibody (MyBioscience, cat# MBS610128)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22355
GUDMAP ID: 22355

source_name: Human kidney ChIP SIX2-17wk sample #2

value: 17 weeks 3 days


title: SIX2 ChIP (16 week)

description:
genome build: hg19
ChIP Antibody: SIX2 Antibody (Proteintech, cat# 11562-1-AP)
URL: ww.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22354
GUDMAP ID: 22354

source_name: Human kidney ChIP SIX2-16wk

value: 16 weeks 2 days


title: SIX1 ChIP (17 week #2)

description:
genome build: hg19
ChIP Antibody: SIX1 (D4A8K) Rabbit mAb (Cell Signalling, cat# 12891)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22352
GUDMAP ID: 22352

source_name: Human kidney ChIP SIX1-17wk sample #2

value: Fetal 18wk


title: SIX1 ChIP (17 week #1)

description:
genome build: hg19
ChIP Antibody: SIX1 (D4A8K) Rabbit mAb (Cell Signalling, cat# 12891)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22353
GUDMAP ID: 22353

source_name: Human kidney ChIP SIX1-17wk sample #1

value: 17 weeks 2 days

value: no


title: TN03_E_Un1


title: Input control (17 week #1)

description:
genome build: hg19
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22347
GUDMAP ID: 22347

data_processing: All ChIP-seq sequences were mapped to hg19 using Novoalign software (Novocraft). Novoalign alignment parameters: Single-end reads trimming of 10 bp, polyclonal read filter: 7,10 0.4,2,  maximum alignment score acceptable: 120.

source_name: Human kidney ChIP control-17wk sample #1


title: H3K27ac ChIP (17 week #1)

description:
genome build: hg19
ChIP Antibody: Anti-Histone H3 (acetyl K27) antibody (Abcam, cat# ab4729)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22349
GUDMAP ID: 22349

source_name: Human kidney ChIP H3K27ac-17wk sample #1


title: Input control (16 week)

description:
genome build: hg19
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22342
GUDMAP ID: 22342

source_name: Human kidney ChIP control-16wk

treatment_protocol: For ChIP-seq from 16-17 week human fetal kidneys, specimens were immediately incubated in 1% PFA cross-link buffer (PMID:22902740) and stored on ice for a maximum of 30 minutes. Samples were then micro-dissected to remove the cortex (~0.5 mm) and incubated for an additional 30 minutes at room temperature in fresh 1% PFA cross-link buffer. Cross-linking was stopped by the addition of glycine. Tissue was washed with PBS containing protease inhibitors (PI) and resuspended in fresh PBS+PI. Tissue was spread across 1.5 mL Eppendorf tubes and homogenized with a motorized pestle. Homogenized tissue was pelleted, resuspended in mouse ChIP lysis buffer (PMID:22902740), and recombined. The tissue was lysed with the aid of a B dounce homogenizer and incubated on ice for 20 minutes. Processing of the samples from this point was carried forward using the mouse ChIP protocol (PMID:22902740). Sequencing libraries were made using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were submitted to the USC Epigenome Center for sequencing on the Illumina HiSeq 2000.


title: Input control (17 week #2)

description:
genome build: hg19
http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22343
GUDMAP ID: 22343

source_name: Human kidney ChIP control-17wk sample #2


title: rN.SLE.3

status: Public on May 22 2016

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie version1.1.1 with the default parameters
reads per million normalized bigWig files were generated using the GenomicRanges R/Bioconductor package and UCSC tool bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: reads per million normalized bigWig

source_name: CD19+ B cells

extract_protocol:
Naïve B cells (CD19+IgD+CD3-CD27-Mtg-CD24+CD38-) were sorted by FACS
Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg.  Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C.  DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

tag: facs sorting markers

tag: fresh or biobanked

value: Biobanked

value: B cell


title: H3K27ac ChIP (16 week)

description:
genome build: hg19
ChIP Antibody: Anti-Histone H3 (acetyl K27) antibody (Abcam, cat# ab4729)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22348
GUDMAP ID: 22348

source_name: Human kidney ChIP H3K27ac-16wk

tag: genotype:


title: rN.SLE.1


title: rN.HC.3

value: Fresh


title: rN.HC.2


title: rN.HC.1


title: Frozen.1K

data_processing:
Library strategy: ATAC-seq
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie version1.1.1 with the default parameters
reads per million normalized bigWig files were generated using the GenomicRanges R/Bioconductor package and UCSC tool bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: reads per million normalized bigWig

extract_protocol:
The indicated number of naïve B cells (CD19+IgD+CD3-CD27-Mtg-CD24+CD38-) were sorted by FACS
Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg.  Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C.  DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: B cells

value: blood


title: Frozen.20K


title: Frozen.50K


title: Fresh.50K


title: Fresh.20K


title: P300 ChIP (16 week)

description:
genome build: hg19
ChIP Antibody: p300 Antibody (C-20) (Santa Cruz, cat# sc-585)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22350
GUDMAP ID: 22350

source_name: Human kidney ChIP P300-16wk

value: renal cortex


title: Fresh.1K


title: CTRL, rep2

status: Public on May 21 2016

city: Los Angeles

first: Yi

last: Xing

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

description: CTRL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 72) then mm10 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.1 with uniquely and properly mapped pairs.
Genome_build: mm10
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample

source_name: E18.5 mouse embryo

extract_protocol:
E18.5 embryonic kidney pairs isolated from individual embryos were placed in PBS on ice, then transferred into 500 μl of 0.03% collagenase (Sigma, Cat#C1889) in PBS for 10 minutes at 37ºC. Samples were transferred to ice and the kidneys were dissociated by trituration using an 18 gauge needle with 8-10 passes followed by a 25 gauge needle for 8-10 passes to homogenize to a single-cell slurry. Cells were transferred to a 15ml falcon tube containing 4-5mls 2% fetal bovine serum (FBS) in PBS to inhibit collagenase. The cells were pelleted for 5 minutes at 400xg (4ºC) and washed three times in  5 mls of 2% fetal bovine serum (FBS). The final cell pellet was resuspended in 60ul 2% FBS in PBS and transferred to an Eppendorf tube. Cell count and viability was measured using 5 μl of cells + 5 μl trypan blue and a Hemocytometer. 5 μl of the remaining cell volume from each sample was pooled to serve as an unstained control. The remaining 50ul was processed for labelled with FITC-DBA lectin. The cells were pelleted at 400xg for 5 min. and stained in a fresh 50 μl of staining solution on ice and in the dark with DBA-FITC (Vector Labs, Cat#FL-1031) 1:10 diluted in 2% FBS in PBS for 20min. The cells were washed in 1mL of 2% FBS in PBS and centrifuged at 400 x g (4ºC) for 5min. The cell pellet was resuspended in 300-400 μl of 2% FBS in PBS for FACS. GFP positive gated cells were isolated using the unstained cells as a negative control. GFP+ cells were collected directly into 500 μl of Trizol (ThermoFisher) and snap frozen on dry ice and stored at -80ºC.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (mRNA) (New England Biolabs)

value: Ureteric epithelial cells

value: Kidney

value: 18.5 days


title: SIX1 ChIP (16 week)

description:
genome build: hg19
ChIP Antibody: SIX1 (D4A8K) Rabbit mAb (Cell Signalling, cat# 12891)
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22351
GUDMAP ID: 22351

source_name: Human kidney ChIP SIX1-16wk

value: wild type

value: Fetal 17wk


title: CTRL, rep1

description: CTRL


title: Fresh.5K


title: Esrp1;Esrp2 KO, rep1

description: both Esrp1 and Esrp2 KO


title: rN.SLE.2


title: Esrp1;Esrp2 KO, rep2

description: both Esrp1 and Esrp2 KO


title: reversionlifMM401P2-rep1 #2

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

data_processing:
RNA-Seq reads were mapped to mm9 using TopHat2 with default parameters, only unique mapped reads used to subsequent analysis.
Read numbers for each gene was counted using Subread program.
Read counts were used to performed differentially gene expression analysis by DESeq program.
Genome_build: mm9
Supplementary_files_format_and_content: Read counts matrix table (tsv)

source_name: embryo

growth_protocol: 1) mESCs (CD1/JF1 background) were cultured in the presence of leukemia inhibitory factor (LIF, Millipore) in Glasgow modification of Eagles medium (GMEM) containing 15% KSR with feeder cells. 2) mEpiSCs were in EpiSC cell medium consisting of Knockout DMEM supplemented with 20% KSR, 10 ng/ml bFGF, 3) mEpiSCs were treate by MM401 supplemented with LIF/KSR/KO DMEM; 4) Established rESCs were cultured in LIF/KSR/KO DMEM medium with or without MM401.

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.
Single end RNA-Seq

treatment_protocol: 1) MM401 conversion on EpiSC at 100uM for 3 day or 6 day (passage 2) in LIF/KSR/KO-DMEM medium, 2) 25 uM MM401/LIF/KSR for rES lines maintaining after passage 3.

value: EpiSC treated by MM401


title: mESf-rep2 #2

value: embryonic stem cell , blastocyst derived


title: reversionlifMM401P2b-rep2 #2


title: rN.SLE.4


title: mESf-rep1 #2


title: reversionlifMM401D3-rep2 #2


title: rN.HC.4


title: reversionlifMM401D3-rep1 #2


title: 9FEpi-rep1 #2

value: Epiblast stem cell , blastocyst derived


title: 9FEpi-rep2 #2


title: rESp30-no-MM401-rep1 #2

value: rESC, reverted form EpiSC


title: rESp30-rep2 #2


title: rESp6-rep2 #2


title: EpiSC/MM401-H3K4me1-ChIP-seq

data_processing:
Reads were mapped to mm9 using BWA with default parameters, only unique mapped reads used to subsequent analysis.
Peaks were called using the MACS program.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file for coverage and bed file for called peaks

growth_protocol: mEpiSCs were maintained in the presence of bFGF in Knock out DMEM (KO-DMEM) containing 20% KSR with feeder cells.

extract_protocol:
ChIP experiments were performed using 3E6 cells and 4µg a-Mll1 antibody per ChIP (5E7 cells in total) ; 2.5ug a-H3K4me1 and 2.5ug H3K4me3 antibody per ChIP according to standard protocols. For Mll1-ChIP, crosslinking of the cells was performed with dimethyl pimelimidate dihydrochloride (DMP, Sigma-D8388) on the culture plates for 30 minutes. While ChIPed DNA was collected and purified by Qiaquick PCR purification Kit (Qiagen).
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: MM401 conversion on EpiSC at 100uM for 4 day in LIF/KSR/KO-DMEM medium

tag: chip antibody


title: rESp6-rep1 #2


title: rESp30-rep1 #2


title: EpiSC/MM401-input

value: input


title: EpiSC/MM401-H3K4me3-ChIP-seq


title: EpiSC-MLL1-ChIP-Seq


title: EpiSC-input

source_name: EpiSC-input


title: Endothelial_CD31_pos_KO2

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description: Cell population isolated by flow cytometry using indicated markers from animals with indicated genotypes

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Tumor bearing lungs from K-rasG12D/+; miR-143/145-/- mouse

growth_protocol: RNA was extracted from cell populations isolated in vivo from tumor-bearing lungs and subjected to flow cytometry with indicated surface markers

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.

treatment_protocol: No treatment

value: Lung endothelial cells (CD31+)


title: EpiSC/MM401-MLL1-ChIP-seq


title: Endothelial_CD31_pos_KO1


title: Endothelial_CD31_pos_KO3


title: Endothelial_CD31_pos_WT1

source_name: Tumor bearing lungs from K-rasG12D/+; miR-143/145+/+ mouse


title: rESp30-no-MM401-rep2 #2


title: Fibroblasts_Triple_neg_KO1

value: Triple-negative (Epcam-CD45-CD31-) includes fibroblasts, pericytes, neutrophils, etc


title: Fibroblasts_Triple_neg_KO3


title: Fibroblasts_Triple_neg_WT3


title: Endothelial_CD31_pos_WT2


title: Fibroblasts_Triple_neg_WT2


title: Epithelial_Epcam_pos_KO3

value: Lung epithelial cells (Epcam+)


title: Fibroblasts_Triple_neg_WT1


title: 30DAP_12h

city: Delhi

first: Manu

last: Agarwal

address: Chatra Marg, North campus

department: Department of Botany

country: India

institute: University of Delhi

description: paired end, illumina HiSeq platform

data_processing:
Paired end reads were quality filtered and pooled together to construct an assembly using Trinity at 25 K-mer.
Transcripts were quantified with the help of RSEM. Transcripts having less then 1 read count in all the libraries were removed.
Assembly were further annotated for functional characterisation using FastAnnotator
Differentially expressed transcript were identifed using edgeR.
Genome_build: n/a
Supplementary_files_format_and_content: Tab delimited text file
Supplementary_files_format_and_content: Assembly.fa: Assembly sequence
Supplementary_files_format_and_content: Assembly_Annotation: Assembly annotation

organism: Brassica juncea

source_name: Silique

growth_protocol: B. juncea plants were grown in field conditions in the month of october and self pollinated at the time of flowering initation.

extract_protocol:
Total RNA was extracted from stressed as well as control siliques using Qiagen’s plant RNA extraction kit as per the manufacturer’s protocol.
RNA-seq libraries were prepared utilizing TruSeq RNA sample preparation kit v2 (Illumina Inc., USA) as per the manufacturer’s protocol

treatment_protocol: Self-pollinated branches (5,10,15,20,25 and 30 DAP) were excised and placed in a beaker filled with water and subjected to cold treatment at 4°C for 6 h and 12 h followed by immediate harvesting. Self-pollinated branches placed in water under field conditions served as control.

tag: developmental stage

value: 30DAP silique

tag: stress duration

value: 12 hour


title: Epithelial_Epcam_pos_KO2


title: Fibroblasts_Triple_neg_KO2


title: Epithelial_Epcam_pos_KO1


title: Epithelial_Epcam_pos_WT2


title: 25DAP_12h

description: paired end, illumina HiSeq platform

value: 25DAP silique


title: Epithelial_Epcam_pos_WT1


title: Epithelial_Epcam_pos_WT3


title: 25DAP_6h

description: paired end, illumina HiSeq platform

value: 6 hour


title: 20DAP_12h

description: paired end, illumina HiSeq platform

value: 20DAP silique


title: 25DAP_C

description: paired end, illumina HiSeq platform

value: Control


title: 30DAP_C

description: paired end, illumina HiSeq platform


title: 20DAP_6h

description: paired end, illumina HiSeq platform


title: 20DAP_C

description: paired end, illumina HiSeq platform


title: 15DAP_C

description: paired end, illumina HiSeq platform

value: 15DAP silique


title: 15DAP_6h

description: paired end, illumina HiSeq platform


title: 10DAP_12h

description: paired end, illumina HiSeq platform

value: 10DAP silique


title: 10DAP_6h

description: paired end, illumina HiSeq platform


title: 5DAP_6h

description: paired end, illumina HiSeq platform

value: 5DAP silique


title: 10DAP_C

description: paired end, illumina HiSeq platform


title: 7158_308

city: Leiden

first: Nicolas

last: Davin

address: Darwingweg 4

department: Botany

country: Netherlands

institute: Naturalis

data_processing:
Low read quality filtering using Trimmomatic v0.0.3 (Illumina TruSeq adapters were filtered out, the first nine bases were removed, sliding window over four bases with quality threshold of Phred>20 was applied corresponding to base call accuracy>99%, only reads in pairs and with a minimum length of 45bp were retained)
Read mapping to the TAIR10 Arabisopsis thaliana genome using TopHat v2.0.8 (using default parameters)
Genome_build: Arabidopsis thaliana TAIR v10
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each samples and statistical differentially expression for each pairwise comparison

source_name: leaf soc1ful

growth_protocol: 16h light per day, 20C

extract_protocol: Total RNA was isolated from stems and leaves using EZNA Plant RNA Kit (Omega Bio-tek, VWR international) including DNAse I treatment on column (Qiagen, Netherlands) according to the manufacturers’ instructions. Poly A+ RNA purification and strand-specific cDNA library preparation for Illumina Hiseq 2000 were performed by Leiden Genome Technology Center (Leiden, the Netherlands) as described in Parkhomchuk et al. (2009).

treatment_protocol: Sample were flash frozen in liquid nitrogen and concerved at -80C until extraction

tag: tissue type

value: Leaf

tag: ecotype


title: 7159_309

source_name: Wood stem soc1ful

value: Stem


title: 7163_337


title: 7162_312


title: 30DAP_6h

description: paired end, illumina HiSeq platform


title: 7164_338

source_name: Cambium stem soc1ful


title: 5DAP_12h

description: paired end, illumina HiSeq platform


title: 7155_305


title: 15DAP_12h

description: paired end, illumina HiSeq platform


title: rpn10-1 No Treatment 2

city: Cold Spring Harbor

first: Nicholas

last: Gladman

state: NY

address: 1 Bungtown Rd

department: ARS

institute: USDA

data_processing:
Quality control (trimming of raw reads) was performed with Trimmomatic using the default parameters
Alignment was performed through Tophat-Bowtie 2 against the TAIR 10 genome using the Ensemble 2013 Arabidopsis.gtf file for annotations.  Parameters: -i 30 -I 5000 --min-segment-intron 30 --max-segment-intron 5000 --min-coverage-intron 30 --max-coverage-intron 5000 --no-convert-bam --b2-very-sensitive
Read counts were generated through HTSeq using TAIR10 .gtf file for annotations. Parameters:  -m intersection-nonempty -t exon -s no
Differential expression analysis was performed via the edgeR package (negative binomial normalization) using the Col-0 No treatment as the control comparison. Analysis was run as described in manual example using calcNormFactors and GLM dispersion options.
Genome_build: TAIR10

source_name: 5 DAG Arabidopsis seedling

growth_protocol: Seedlings were sterilized with 50% bleach and stratified for 2 days at 4 degrees C in the dark, then grown in liquid culture (1/2 MS salts, 1% Sucrose) under constant light at ~22 degrees C in 12-well plates.

extract_protocol:
Seedlings were pressed between paper towels to remove excess liquid and frozen immediately in liquid nitrogen, then pulverized and total RNA isolation was performed using Trizol Reagent.  mRNA was isolated via the TruSeq RNA library sample preparation kit v2 (Illumina).
TruSeq RNA library sample preparation kit v2 (Illumina).  This was performed by the University of Wisconsin-Madison Gene Expression Center (http://www.biotech.wisc.edu/services/gec).

treatment_protocol: After 5 days growth, fresh media was swapped out and either 0 or 100 uM or MG132 was added to each well.  Incubation time was either 3 or 24 hours for MG132-treated samples.  No-treatment samples were harvested immediately at the 5 day mark.

tag: treatment

value: No MG132


title: 7166_340


title: 7165_339

source_name: Herbaceous stem soc1ful


title: 7160_310


title: 7156_306