title: MYB_tnt.MYB77_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB74_colamp_a

status: Public on May 25 2016

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: A. thaliana Col-0 input DNA library was PCR amplifed (ampDAP-Seq library) before affinity purification.

library_source: genomic

data_processing:
library strategy: DAP-seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Reads were aligned by bowtie2 version 2.0.0-beta7 against the Arabidopsis TAIR10 genome assembly or Zea mays genome assembly B73 with default parameters, and additionally filter for highest scoring MAPQ alignments only (score=254).
Peaks were called using GEM peak caller version 2.3 with the default version 2.3 read distribution, TAIR10 genome sequences and parameters " --k_min 6 --k_max 20 --k_seqs 250 --outNP --k_neg_dinu_shuffle".
Genome_build: Arabidopsis TAIR10 or maize B73
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: young leaf

extract_protocol:
Genomic DNA is extracted from Arabidopsis young leaves by phenol:chloroform:isoamyl alchohol (25:24:1) followed by a chloroform  extraction, ethanol precipitation and resuspension in Tris/EDTA buffer.  The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  Separately, a construct containing an affinity-tagged transcription factor (GST or HALO) is translated by either heterologous (E. coli) or in vitro (wheat germ) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina HiSeq 2500.

tag: protein

tag: gene id

tag: protein family

value: MYB

tag: protein source

value: Arabidopsis thaliana

tag: protein affinity tag

value: Halo

tag: expression system

value: tnt

tag: dna source

value: colamp

tag: replicate

value: a

tag: subset

value: motif+TFBS


title: MYB_tnt.MYB77_colamp_a

value: motif


title: MYB_tnt.MYB70_col_a

description: A. thaliana Col-0 input DNA library

value: col


title: MYB_tnt.MYB67_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB62_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB65_colamp_a


title: MYB_tnt.MYB61_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB63_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB61_colamp_a


title: MYB_tnt.MYB58_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB58_colamp_a


title: MYB_tnt.MYB57_colamp_a


title: MYB_tnt.MYB56_colamp_a


title: MYB_tnt.MYB57_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB51_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB49_colamp_a


title: MYB_tnt.MYB44_colamp_a


title: MYB_tnt.MYB52_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB49_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB43_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB73_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB40_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB4_col200_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB65_col200_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB41_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB3R5_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB62_colamp_a


title: MYB_tnt.MYB3R4_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB3R1_colamp_a


title: MYB_tnt.MYB39_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB33_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB3R1_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB30_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB56_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB30_colamp_a


title: MYB_tnt.MYB27_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB23_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB55_colamp_a


title: MYB_tnt.MYB13_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB27_colamp_a


title: MYB_tnt.MYB17_colamp_a


title: MYB_tnt.MYB116_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB121_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB118_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB119_colamp_a


title: MYB_tnt.MYB116_colamp_a


title: MYB_tnt.MYB118_colamp_a


title: MYB_tnt.MYB13_colamp_a


title: MYB_tnt.MYB119_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB39_colamp_a


title: MYB_tnt.MYB105_colamp_a


title: MYB_tnt.MYB105_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB101_colamp_a


title: MYB_tnt.MYB101_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB107_colamp_a


title: MYB_tnt.MYB1_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MS188_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB113_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB10_colamp_a


title: MYB_tnt.BOS1_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.ATY19_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB10_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.ATY13_colamp_a


title: MADS_tnt.FEM111_col_a

description: A. thaliana Col-0 input DNA library

value: MADS


title: MADS_tnt.AGL63_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.SVP_colamp_v3b

value: SVP


title: MADS_tnt.SVP_col_v3b

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB107_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.AGL25_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.AGL25_colamp_a


title: MADS_tnt.AGL15_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.AGL6_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.AGL15_colamp_a


title: MADS_tnt.AGL55_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.AGL13_col_b

description: A. thaliana Col-0 input DNA library

value: b


title: MYB_tnt.MS188_colamp_a


title: LOBAS2_tnt.LBD23_colamp_a


title: LOBAS2_tnt.LBD23_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LBD19_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LBD2_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LBD18_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LBD2_colamp_a


title: LOBAS2_tnt.LBD13_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LBD19_colamp_a


title: MADS_tnt.AGL16_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.ATY13_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LBD13_colamp_a


title: MADS_tnt.AGL42_col_a

description: A. thaliana Col-0 input DNA library


title: LIM_tnt.WLIM2A_col_a

description: A. thaliana Col-0 input DNA library

value: LIM


title: LOBAS2_tnt.ASL18_colamp_a


title: LOBAS2_tnt.LBD18_colamp_a


title: LOBAS2_tnt.AS2_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.WUS1_col_a

description: A. thaliana Col-0 input DNA library

value: Homeobox


title: Homeobox_tnt.WUS1_colamp_a


title: Homeobox_tnt.HAT5_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.HAT5_colamp_a


title: Homeobox_tnt.HDG1_col100_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.LOB_col_a

description: A. thaliana Col-0 input DNA library

value: LOB


title: Homeobox_tnt.HAT2_colamp_a


title: Homeobox_tnt.HAT22_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.HAT1_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.HAT1_colamp_a


title: Homeobox_ecoli.HAT2_col_v31

description: A. thaliana Col-0 input DNA library

value: GST

value: ecoli


title: Homeobox_tnt.ATHB7_col_a

description: A. thaliana Col-0 input DNA library


title: LOBAS2_tnt.ASL18_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.ATHB6_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.ATHB6_colamp_a


title: Homeobox_tnt.ATHB20_colamp_a


title: Homeobox_tnt.ATHB20_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.HDG1_colamp_a


title: Homeobox_tnt.ATHB18_colamp_a


title: Homeobox_tnt.ATHB18_col_a

description: A. thaliana Col-0 input DNA library


title: Homeobox_tnt.ATHB13_col_a

description: A. thaliana Col-0 input DNA library


title: HSF_tnt.HSFB3_col_a

description: A. thaliana Col-0 input DNA library

value: HSF


title: HSF_tnt.HSFB4_col_a

description: A. thaliana Col-0 input DNA library

value: Arabidopsis thaliana


title: HSF_tnt.HSFC1_colamp_a

value: Halo


title: Homeobox_tnt.ATHB13_colamp_a

value: tnt


title: HSF_tnt.HSFB3_colamp_a

value: colamp


title: HSF_tnt.HSFA1E_col_a

description: A. thaliana Col-0 input DNA library

value: a


title: HSF_tnt.HSFC1_col_a

description: A. thaliana Col-0 input DNA library

value: motif+TFBS


title: HSF_tnt.HSFA6A_colamp_a

value: motif


title: HSF_tnt.HSFA6A_col_a

description: A. thaliana Col-0 input DNA library

value: col


title: HSF_tnt.HSF7_col_a

description: A. thaliana Col-0 input DNA library


title: HSF_tnt.HSF7_colamp_a


title: HSF_tnt.HSFA1E_colamp_a


title: HSF_tnt.HSF3_col_a

description: A. thaliana Col-0 input DNA library


title: HSF_tnt.HSF21_col_a

description: A. thaliana Col-0 input DNA library


title: MYB_tnt.MYB99_colamp_a

value: MYB


title: HMG_tnt.3XHMGBOX1_col_a

description: A. thaliana Col-0 input DNA library

value: HMG


title: HSF_tnt.HSF3_colamp_a


title: HB_tnt.WOX11_col_a

description: A. thaliana Col-0 input DNA library

value: HB


title: HB_tnt.LMI1_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.LMI1_colamp_a


title: HSF_tnt.HSFA6B_colamp_a


title: HB_tnt.ATHB53_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.ATHB53_colamp_a


title: HB_tnt.ATHB5_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.ATHB5_colamp_a


title: HB_tnt.ATHB40_colamp_a


title: HB_tnt.ATHB40_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.ATHB21_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.ANL2_col_a

description: A. thaliana Col-0 input DNA library


title: HSF_tnt.HSF6_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.ANL2_colamp_a


title: GeBP_tnt.AT1G66420_col_a

description: A. thaliana Col-0 input DNA library

value: GeBP


title: GeBP_tnt.AT4G00250_col_a

description: A. thaliana Col-0 input DNA library


title: GRF_tnt.GRF9_col_a

description: A. thaliana Col-0 input DNA library

value: GRF


title: HB_tnt.ATHB15_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At5g29000_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.KAN2_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.KAN2_colamp_a


title: HB_tnt.ATHB21_colamp_a


title: HB_tnt.PHV_col_a

description: A. thaliana Col-0 input DNA library

value: PHV


title: GRF_tnt.GRF9_colamp_a


title: G2like_tnt.At3g24120_col_a

description: A. thaliana Col-0 input DNA library


title: HB_tnt.HDG7_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At3g24120_colamp_a


title: G2like_tnt.At3g13040_col_b

description: A. thaliana Col-0 input DNA library

value: b


title: G2like_tnt.At3g12730_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At3g12730_colamp_a


title: G2like_tnt.At3g04030_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At2g03500_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At3g04030_colamp_a


title: G2like_tnt.AT5G45580_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At2g01060_colamp_a


title: G2like_tnt.At1g13300_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At1g68670_colamp_a


title: G2like_tnt.AT5G45580_colamp_a


title: G2like_tnt.AT4G37180_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.At1g25550_colamp_a


title: GRF_tnt.AtGRF6_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.AT4G37180_colamp_a


title: G2like_tnt.AT2G40260_colamp_a


title: G2like_tnt.At2g03500_colamp_a


title: G2like_tnt.AT2G40260_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.AT2G38300_col_a

description: A. thaliana Col-0 input DNA library


title: MADS_tnt.AGL16_colamp_a

value: MADS


title: G2like_tnt.AT2G20400_col_a

description: A. thaliana Col-0 input DNA library


title: G2like_tnt.AT2G20400_colamp_a


title: FAR1_tnt.FAR1_col_a

description: A. thaliana Col-0 input DNA library


title: FAR1_tnt.FAR1_colamp_a


title: G2like_tnt.AT1G49560_colamp_a


title: G2like_tnt.AT1G49560_col_a

description: A. thaliana Col-0 input DNA library


title: EIL_tnt.EIN3_col_a

description: A. thaliana Col-0 input DNA library

value: EIL


title: FHA_tnt.FHA2_col_b

description: A. thaliana Col-0 input DNA library

value: FHA

value: Arabidopsis thaliana


title: EIL_tnt.EIL3_col_b

description: A. thaliana Col-0 input DNA library

value: Halo

value: tnt


title: E2FDP_tnt.E2FC_col_a

description: A. thaliana Col-0 input DNA library

value: a


title: E2FDP_tnt.E2FA_col_a

description: A. thaliana Col-0 input DNA library

value: motif+TFBS


title: E2FDP_tnt.E2FA_colamp_a

value: colamp


title: EIL_tnt.EIN3_colamp_a

value: motif


title: E2FDP_tnt.DEL2_col_a

description: A. thaliana Col-0 input DNA library

value: col


title: E2FDP_tnt.DEL1_colamp_a


title: DBP_tnt.AT3G51470_col_a

description: A. thaliana Col-0 input DNA library

value: DBP


title: E2FDP_tnt.DEL1_col_a

description: A. thaliana Col-0 input DNA library


title: CPP_tnt.TCX2_col_a

description: A. thaliana Col-0 input DNA library

value: CPP


title: CPP_tnt.AT2G20110_colamp_a


title: CCAATHAP3_tnt.NFYB4_col_a

description: A. thaliana Col-0 input DNA library


title: CPP_tnt.SOL1_colamp_a


title: CPP_tnt.AT2G20110_col_a

description: A. thaliana Col-0 input DNA library


title: CAMTA_tnt.CAMTA5_col_a

description: A. thaliana Col-0 input DNA library

value: CAMTA


title: C3H_tnt.TZF9_col_a

description: A. thaliana Col-0 input DNA library


title: CPP_tnt.TSO1_col_a

description: A. thaliana Col-0 input DNA library


title: CAMTA_tnt.CAMTA1_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.EMB1789_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.U2AF35B_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.CDM1_colamp_a


title: HMG_tnt.3XHMGBOX1_colamp_a

value: HMG


title: CCAATHAP3_tnt.HAP3_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.At5g08750_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.At1g70910_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.AT5G63260_col_a

description: A. thaliana Col-0 input DNA library


title: C3H_tnt.AT5G63260_colamp_a


title: C3H_tnt.AT3G12130_colamp_a


title: C3H_tnt.At1g74370_col_a

description: A. thaliana Col-0 input DNA library


title: CPP_tnt.TCX2_colamp_a


title: C2H2_tnt.WIP5_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.WIP5_colamp_a


title: C2H2_tnt.STZ_colamp_a

value: STZ


title: C2H2_tnt.TF3A_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.STOP1_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.STOP1_colamp_a


title: C2H2_tnt.MGP_col_a

description: A. thaliana Col-0 input DNA library

value: MGP


title: C2H2_tnt.SGR5_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.NUC_colamp_a

value: NUC


title: C2H2_tnt.NUC_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.JKD_col_a

description: A. thaliana Col-0 input DNA library

value: JKD


title: C2H2_tnt.MGP_colamp_a


title: C2H2_tnt.JGL_col_a

description: A. thaliana Col-0 input DNA library

value: JGL


title: C2H2_tnt.IDD2_col_a

description: A. thaliana Col-0 input DNA library

value: Arabidopsis thaliana


title: C2H2_tnt.IDD4_col_a

description: A. thaliana Col-0 input DNA library

value: Halo


title: C2H2_tnt.IDD7_col_a

description: A. thaliana Col-0 input DNA library

value: tnt


title: C2H2_tnt.IDD5_colamp_a

value: a


title: C2H2_tnt.At2g48100_col_b

description: A. thaliana Col-0 input DNA library

value: b


title: C2H2_tnt.At5g66730_colamp_a

value: colamp

value: motif+TFBS


title: C2H2_tnt.At3g60580_col_a

description: A. thaliana Col-0 input DNA library

value: col


title: C2H2_tnt.AtIDD11_colamp_a


title: C2H2_tnt.IDD2_colamp_a

value: motif


title: C2H2_tnt.At1g14580_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.At5g04390_col200_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.AtIDD11_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.At2g41835_col_b

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.SGR5_colamp_a


title: C2H2_tnt.AZF1_colamp_a


title: C2H2_tnt.At1g14580_colamp_a


title: C2H2_tnt.AT3G49930_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.AT2G15740_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.AT4G26030_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.ZML2_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.ZML1_colamp_a


title: C2C2gata_tnt.GATA6_col200_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.ZML1_col_a

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.At5g22890_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.ZIM_col_a

description: A. thaliana Col-0 input DNA library

value: ZIM


title: C2C2gata_tnt.GATA4_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA20_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA19_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA20_colamp_a


title: C2C2gata_tnt.GATA19_colamp_a


title: C2H2_tnt.AT3G46070_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA15_col_b

description: A. thaliana Col-0 input DNA library


title: C2H2_tnt.AT5G22990_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA1_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA12_colamp_a


title: C2C2gata_tnt.GATA11_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA1_colamp_a


title: C2C2gata_tnt.GATA12_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.dof24_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.dof42_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.dof43_colamp_a


title: C2C2dof_tnt.dof45_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.dof43_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.dof45_colamp_a


title: C2C2dof_tnt.OBP4_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA16_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2gata_tnt.GATA14_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.OBP4_colamp_a


title: C2C2dof_tnt.OBP1_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.COG1_colamp_a


title: C2C2dof_tnt.CDF3_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.DAG2_colamp_a


title: C2C2dof_tnt.DAG2_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.CDF3_colamp_a


title: C2C2dof_tnt.OBP3_colamp_a


title: C2C2dof_tnt.OBP3_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.At4g38000_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.At4g38000_colamp_a


title: C2C2dof_tnt.dof24_colamp_a


title: C2C2dof_tnt.At3g45610_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.At1g64620_colamp_a


title: C2C2dof_tnt.Adof1_colamp_a


title: C2C2dof_tnt.At1g64620_100ng20cy_b

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT5G66940_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.At5g62940_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.At3g45610_colamp_a


title: C2C2dof_tnt.COG1_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT2G28810_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT5G02460_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.Adof1_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT5G66940_colamp_a


title: C2C2dof_tnt.AT5G02460_colamp_a


title: C2C2dof_tnt.AT3G52440_colamp_a


title: C2C2dof_tnt.AT3G52440_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT1G69570_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT2G28810_colamp_a


title: C2C2dof_tnt.AT1G47655_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2YABBY_tnt.CRC_col_a

description: A. thaliana Col-0 input DNA library

value: CRC


title: C2C2YABBY_tnt.CRC_colamp_a


title: C2C2COlike_tnt.AT5G59990_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT1G47655_colamp_a


title: C2C2COlike_tnt.AT5G59990_colamp_a


title: BBRBPC_tnt.BPC6_col_a

description: A. thaliana Col-0 input DNA library

value: BBRBPC


title: BZR_tnt.BZR1_col_a

description: A. thaliana Col-0 input DNA library

value: BZR


title: BZR_tnt.At4g18890_colamp_a


title: BES1_tnt.BAM8_col_a

description: A. thaliana Col-0 input DNA library


title: BZR_tnt.At1g78700_col_a

description: A. thaliana Col-0 input DNA library


title: BSD_tnt.AT1G10720_col_a

description: A. thaliana Col-0 input DNA library

value: BSD


title: BZR_tnt.At4g18890_col_a

description: A. thaliana Col-0 input DNA library


title: BZR_tnt.At4g36780_colamp_a


title: BZR_tnt.At4g36780_col_a

description: A. thaliana Col-0 input DNA library


title: ARID_tnt.At1g76110_colamp_a

value: ARID


title: ARID_tnt.At3g13350_col_a

description: A. thaliana Col-0 input DNA library


title: BBRBPC_tnt.BPC5_col_a

description: A. thaliana Col-0 input DNA library


title: BZR_tnt.At1g78700_colamp_a


title: C2C2COlike_tnt.AT4G27900_col_a

description: A. thaliana Col-0 input DNA library


title: BBRBPC_tnt.BPC5_colamp_a


title: ARID_tnt.At1g76110_col_a

description: A. thaliana Col-0 input DNA library


title: C2C2dof_tnt.AT1G69570_colamp_a


title: ARID_tnt.AT1G20910_col_a

description: A. thaliana Col-0 input DNA library


title: ARID_tnt.AT2G17410_col_a

description: A. thaliana Col-0 input DNA library


title: ARID_tnt.AT1G04880_col_a

description: A. thaliana Col-0 input DNA library


title: ARID_tnt.AT1G04880_colamp_a


title: BES1_tnt.BAM8_colamp_a


title: BBRBPC_tnt.BPC1_col_a

description: A. thaliana Col-0 input DNA library


title: BBRBPC_tnt.BPC1_colamp_a


title: AP2EREBP_tnt.TINY_col_a

description: A. thaliana Col-0 input DNA library

value: TINY


title: ARF_tnt.ARF16_col_b

description: A. thaliana Col-0 input DNA library

value: ARF


title: AP2EREBP_tnt.Rap210_colamp_a

value: Arabidopsis thaliana


title: AP2EREBP_tnt.RAP26_col_a

description: A. thaliana Col-0 input DNA library

value: Halo


title: AP2EREBP_tnt.SHN3_col_a

description: A. thaliana Col-0 input DNA library

value: tnt


title: AP2EREBP_tnt.RAP212_col_a

description: A. thaliana Col-0 input DNA library

value: a


title: AP2EREBP_tnt.RAP21_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.RRTF1_colamp_a


title: AP2EREBP_tnt.PUCHI_colamp_a

value: PUCHI


title: AP2EREBP_tnt.RAP211_colamp_a

value: colamp


title: AP2EREBP_tnt.RAP211_col_a

description: A. thaliana Col-0 input DNA library

value: motif+TFBS


title: AP2EREBP_tnt.RAP21_colamp_a


title: AP2EREBP_tnt.PLT1_col_a

description: A. thaliana Col-0 input DNA library

value: col


title: E2FDP_tnt.DEL2_colamp_a

value: motif


title: AP2EREBP_tnt.PLT1_colamp_a


title: AP2EREBP_tnt.ESE3_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.PUCHI_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.PLT3_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.LEP_col_a

description: A. thaliana Col-0 input DNA library

value: LEP


title: AP2EREBP_tnt.ESE1_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ESE3_colamp_a


title: AP2EREBP_tnt.ESE1_colamp_a


title: AP2EREBP_tnt.ERF9_colamp_a


title: ARF_tnt.ARF2_col_v31

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF9_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.Rap210_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.RRTF1_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF8_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.RAP26_colamp_a


title: CsrA +CL rep3

city: Irvine

first: Lei

last: Li

address: University of California, Irvine

institute: University of California, Irvine

description: signal sample

library_source: transcriptomic

data_processing:
library strategy:CLIP-seq
Demultiplexing
Fastq quality trimming using FastX version 0.0.13 and a cut-off value of 20
Adapter trimming using cutadapt (Martin, 2011) version 1.7.1 (R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, R2: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT), discard empty reads
Filtering of reads without mate via cmpfastq (http://compbio.brc.iop.kcl.ac.uk/software/cmpfastq.php)
Collapsing of identical reads and conversion to FASTA format using FastUniq (Xu et al. 2012)
Size filtering: discard read pairs with  at least one read shorter than 25 nt
Size filtering: discard read pairs with at least one read shorter than 12 nt (READemption 0.3.5, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 (READemption 0.3.5, Förstner et al., 2014)
Coverage calculation based on uniquely mapped reads (READemption 0.3.5, Förstner et al., 2014)
Coverage normalization based on DESeq2 (Love et al. 2014) size factors calculated during peak calling
Genome_build: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: wiggle

molecule: total RNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: Salmonella Thyphimurium strain SL1344 containing either a hfq::3xflag allele (strain JVS-1338) or a csrA::3xflag allele (strain JVS-4317) was grown from single colonies in 10 ml LB medium at 37°C for 16 hours. The cultures were diluted 1:100 into 200 ml fresh LB medium and continued to grow at 37°C until an OD600 of 2.0 was reached.

extract_protocol:
Bacteria were lysed and the FLAG-tagged proteins was immunoprecipitated using a monoclonal anti-FLAG antibody. The samples were treated with benzonase nuclease, calf intestine phophorylase, and polynucleotide kinase in the presence of radioactive gamma-ATP. Samples were separated with SDS-PAGE and followed by transfer to nitrocellulose membranes. Radioactively labelled RNA-protein complexes were eluted from membranes and treated with Proteinase K. RNA was purified with phenol:chloroform extraction and ethanol precipitation.
Purified RNA was used as input for library preparation using the NEB Next Small RNA Library kit according to the manufacturer’s instructions.

treatment_protocol: When the cultures reached an OD600 of 2.0, half of each culture was irradiated with UV light (254 nm, 800 mJ/cm2) while the other half was left untreated.

tag: strain

tag: genotype/variation

tag: treated with

value: UV light (254 nm, 800 mJ/cm2) irradiation

tag: clip antibody

value: M2 anti-FLAG monoclonal antibody attached to superparamagnetic iron impregnated agarose beads

tag: clip antibody vendor

value: Sigma-Aldrich

tag: clip antibody cat.#

tag: molecule subtype

value: CsrA-bound RNA


title: AP2EREBP_tnt.ERF8_colamp_a


title: CsrA +CL rep1

description: signal sample


title: AP2EREBP_tnt.ERF73_col_a

description: A. thaliana Col-0 input DNA library


title: CsrA +CL rep2

description: signal sample


title: AP2EREBP_tnt.ERF7_col_a

description: A. thaliana Col-0 input DNA library


title: Hfq +CL rep3

description: signal sample

value: Hfq-bound RNA


title: CsrA -CL rep1

description: background control sample

value: none (untreated control)


title: Hfq +CL rep2

description: signal sample


title: AP2EREBP_tnt.ERF48_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF5_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF5_colamp_a


title: CsrA -CL rep2

description: background control sample


title: Hfq -CL rep1

description: background control sample


title: AP2EREBP_tnt.ERF38_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF4_colamp_a


title: AP2EREBP_tnt.ERF7_colamp_a


title: AP2EREBP_tnt.ERF4_col_a

description: A. thaliana Col-0 input DNA library


title: Hfq -CL rep3

description: background control sample


title: AP2EREBP_tnt.ERF3_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF3_colamp_a


title: Hfq -CL rep2

description: background control sample


title: AP2EREBP_tnt.ERF2_colamp_a


title: AP2EREBP_tnt.ERF15_colamp_a


title: AP2EREBP_tnt.ERF73_colamp_a


title: AP2EREBP_tnt.ERF13_col_b

description: A. thaliana Col-0 input DNA library

value: b


title: AP2EREBP_tnt.ERF13_colamp_a

value: Arabidopsis thaliana


title: AP2EREBP_tnt.ERF115_col_a

description: A. thaliana Col-0 input DNA library

value: Halo


title: CsrA -CL rep3

description: background control sample


title: AP2EREBP_tnt.ERF115_colamp_a

value: tnt


title: AP2EREBP_tnt.ERF105_colamp_a

value: a


title: Hfq +CL rep1

description: signal sample


title: AP2EREBP_tnt.ERF11_colamp_a


title: AP2EREBP_tnt.ERF104_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF10_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DREB19_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DREB26_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DREB2_colamp_a


title: AP2EREBP_tnt.ERF1_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DREB19_colamp_a


title: AP2EREBP_tnt.DREB2_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DEAR3_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF10_colamp_a


title: AP2EREBP_tnt.DEAR5_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DEAR3_colamp_a


title: AP2EREBP_tnt.DEAR5_colamp_a


title: AP2EREBP_tnt.CRF4_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DDF1_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DDF2_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF11_col_b

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DDF1_colamp_a


title: AP2EREBP_tnt.CEJ1_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.CEJ1_colamp_a


title: AP2EREBP_tnt.CRF10_col100_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.DEAR2_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF2_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ERF1_colamp_a


title: AP2EREBP_tnt.CBF3_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.CRF10_colamp_a


title: AP2EREBP_tnt.ERF104_colamp_a


title: AP2EREBP_tnt.CBF4_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.CBF1_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.CBF2_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.CBF3_colamp_a


title: AP2EREBP_tnt.CBF2_colamp_a


title: AP2EREBP_tnt.CBF1_colamp_a


title: AP2EREBP_tnt.DEAR2_colamp_a


title: AP2EREBP_tnt.At5g18450_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At5g67000_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At5g65130_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At4g32800_colamp_a


title: AP2EREBP_tnt.At5g65130_colamp_a


title: AP2EREBP_tnt.At4g31060_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At4g31060_colamp_a


title: AP2EREBP_tnt.At4g28140_colamp_a


title: AP2EREBP_tnt.At4g16750_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At4g28140_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.CBF4_colamp_a


title: AP2EREBP_tnt.At4g16750_colamp_a


title: AP2EREBP_tnt.At2g44940_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At2g33710_colamp_a


title: AP2EREBP_tnt.At1g75490_colamp_a


title: AP2EREBP_tnt.At1g77640_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At1g75490_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At1g36060_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At1g19210_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At1g19210_colamp_a


title: AP2EREBP_tnt.At1g22810_colamp_a


title: AP2EREBP_tnt.AT3G60490_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT3G60490_colamp_a


title: AP2EREBP_tnt.At1g36060_colamp_a


title: AP2EREBP_tnt.AT4G18450_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT3G16280_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT3G57600_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT3G16280_colamp_a


title: AP2EREBP_tnt.AT1G77200_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT1G77200_colamp_a


title: AP2EREBP_tnt.AT1G28160_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT1G71450_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT1G44830_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT1G12630_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.At2g44940_colamp_a


title: AP2EREBP_tnt.AT1G01250_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AIL7_colamp_a


title: AP2EREBP_tnt.AIL7_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.ABR1_col_a

description: A. thaliana Col-0 input DNA library


title: ABI3VP1_tnt.VRN1_col_a

description: A. thaliana Col-0 input DNA library


title: ABI3VP1_tnt.VRN1_colamp_a


title: AP2EREBP_tnt.ABR1_colamp_a


title: ABI3VP1_tnt.NGA4_col_a

description: A. thaliana Col-0 input DNA library


title: ABI3VP1_tnt.FUS3_col_a

description: A. thaliana Col-0 input DNA library


title: AP2EREBP_tnt.AT1G28160_colamp_a


title: ABI3VP1_tnt.AT5G60130_colamp_a


title: control_none.beads_col_v3a

description: A. thaliana Col-0 input DNA library

value: beads

value: control


title: control_tnt-pixhalo_colamp_v3a

value: pixhalo

value: colamp


title: ABI3VP1_tnt.AT5G25475_col_a

description: A. thaliana Col-0 input DNA library

value: col

value: motif


title: ABI3VP1_tnt.AT5G18090_col_a

description: A. thaliana Col-0 input DNA library


title: ChIPSeq-ABI5_Ab

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.

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: tissue

value: whole seedlings

tag: age

value: 1.5 day

tag: light condition

value: long day

tag: treatment

value: 5 uM abscisic acid, 4 hours

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot#


title: ChIPSeq-IgG_mock

value: rabbit IgG


title: Sca1Set7KD_LG_rep2

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
[Base calling] Illumina RTA base calling software version 1.8 was used
[Data filtering] Illumina fastq files were loaded into Galaxy and converted to Sanger fastq with FastqGroomer v1.0.4
[Read alignment] BWA ALN v0.5.9 was used to map to the mouse RefSeq transcriptome database with default parameters.
[Abundance measurement] Samtools v0.1.17 was used to count mapped reads.
Custom script called “bams2mx” was used to count overlapping reads (Authors Antony Kaspi & Ross Lazarus)
edgeR v0.19 was used with the following parameters. Bottom 30% expressed transcripts excluded from DGE analysis. prior.df=4.
Genome_build: Mouse Refseq transcriptome Accessed 6th March 2012 [RefSeq-release52]
Supplementary_files_format_and_content: [.txt] count matrix in tabular format

organism: Mus musculus

growth_protocol:
Cell Culture: Mouse ES cells (a gift from Dr. Mark Denham, University of Melbourne) were maintained in stem cell medium containing Dulbecco’s modified Eagles medium (DMEM) supplemented with ES qualified fetal bovine serum (FBS), knockout serum replacement (KSR), non-essential amino acids (NEAA), antibiotics (penicillin/streptomycin), β-mercaptoethanol (Gibco) and 103 units/ml LIF (ESGRO, Millipore). 293FT cells (Invitrogen) were cultured in DMEM supplemented with FBS, Lglutamine and antibiotics. Alkaline phosphatase staining of the cells was performed using Alkaline Phosphatase Detection Kit (Millipore). Colonies expressing alkaline phosphatase were counted under phase-ontrast microscope. All cells were maintained at 37˚C with 5% CO2 incubator.
Cell Differentiation:  mESCs were cultured in gelatin-coated flasks with stem cell medium lacking LIF for 4 days. Sca1 positive (Sca1+) cells were sorted from 1x10e7  of differentiated mESCs by magnetic activated cell sorting (MACS) with anti-Sca1 microbeads (Miltenyi Biotech) as described previously [1]. To determine the purity of Sca1+ cells, the isolated cells were evaluated at >80% by flow cytometry and grown in culture without LIF for 2-8 population doublings. For smooth muscle cell (SMC) differentiation, Sca1+ cells were plated on collagen IV (Sigma) coated dishes and cultured in differentiation media; α-MEM (Gibco) supplemented with 10% FBS, penicillin/streptomycin and β-mercaptoethanol, stimulated with 10ng/ml of PDGF-BB (Sigma) for 14 days.

extract_protocol:
RNA was extracted using Trizol reagent and purified with RNAeasy columns (Qiagen). RNA was reverse transcribed with the high capacity cDNA kit (Applied Biosystems).
NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB) was used to isolate mRNA derived from 2 µg total RNA. Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (NEB). Libraries were quantified on MultiNA capillary electrophoresis system (Shimadzu Biotech) and sequenced at a concentration of 12 pM on the Genome Analyzer IIx (Illumina Inc,).

treatment_protocol: Knockdown of Set7 was performed in Sca1+ cells by MISSION shRNA expressing lentivirus vector (Sigma) as described previously [2]. The targeting sequence to Set7 knockdown corresponds to 5’-CCGTGTTCAGAGATACCAAAT-3’. Cells transduced with MISSION Non-target shRNA control vector (Sigma) was used as a control. Following transduction, cells were selected with 1µg/ml of puromycin (Sigma) for at least one week. For over-expression experiments, 10µg of plasmids (pLVX-hSet7, pLVX-hOct4, or pLVX-hSox2) were transfected with FuGENE® HD (Promega) into Sca1+ cells cultured in the stem cell medium without LIF. For siRNA knockdown, 25nM of siRNA Smart pool against mouse Oct4 (Dharmacon Research Inc) were transfected into mESC using Lipofectamine RNAiMax (Invitrogen). After transfection, cells were incubated for 72 h at 37˚C with 5% CO2 and harvested for RNA and protein analysis. Cells transfected with pLVXEF1α-IRES-Puro vector or Non-Target control siRNA were used as controls. All knockdown and over-expression of target proteins were verified by qRT-PCR and immunoblotting using anti-Flag M2 (Sigma), anti-HA (Roche), anti-OCT4 (abcam), anti-SOX2 and anti-Set7 (CST) antibodies.

tag: cell type

value: Sca1 cell

tag: plasmid construct

value: Set7 shRNA knock-down

tag: glucose concentration


title: ChIPSeq-ABI5_Ypet_1

description: processed data file: ChIPSeq-ABI5_YPet.chr1-5_macs02_peaks.narrowPeak

tag: genotype/variation

value: GFP

value: Life Technologies


title: Sca1Set7KD_LG_rep1

tag: strain


title: AP2EREBP_tnt.AT1G71450_colamp_a

tag: protein

tag: gene id

tag: protein family

tag: protein source

value: Arabidopsis thaliana

tag: protein affinity tag

value: Halo

tag: expression system

value: tnt

tag: dna source

tag: replicate

value: a

tag: subset


title: ChIPSeq-ABI5_Ypet_2

tag: accession

tag: tissue

tag: age

tag: light condition

tag: treatment

tag: chip antibody

tag: chip antibody vendor


title: Sca1NTC_LG_rep1

tag: strain

tag: cell type

tag: plasmid construct

value: Non target shRNA control

tag: glucose concentration


title: Sca1wt_LG_rep2


title: Sca1NTC_LG_rep2


title: Sca1wt_LG_rep1


title: mESC_LG_rep2

value: mESC


title: AP2EREBP_tnt.AT1G01250_colamp_a

tag: protein

tag: gene id

tag: protein family

tag: protein source

value: colamp

value: motif


title: mESC_LG_rep1


title: AP2EREBP_tnt.AT1G12630_colamp_a

tag: protein affinity tag

tag: expression system

tag: dna source

tag: replicate

value: motif+TFBS


title: ABI3VP1_tnt.REM16_col_a

description: A. thaliana Col-0 input DNA library

value: col

tag: subset


title: GFP-TTP-AA LPS 4h iCLIP Replicate 2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
RNA-TTP complex
Used Primer RCLIPE; 5'barcode GGGNNNN (reverse complement in each the 5; end of each read is CCCNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_4h_mm10--ensembl75.bed

data_processing:
See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Raw sequence reads were trimmed to remove both barcodes and adapters. Barcode sequence in the read is the reverse complement of the one in the RT-CLIP primer (i.e. If primer RCLIPA (5'barcode GTTNNNN), the reverse complement sequence in each read will be AACNNN
Remaining sequences were mapped to the mouse GRCm38 genome (Ensembl75 genome annotation) using Bowtie (Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).).
Deduplication and identification of unique cDNA counts was performed based on the 4 random bases present in the barcode.
Position -1 of uniquely annotated reads to the genome was annotated as the TTP crosslink site.
Peak enrichment analysis of TTP binding sites was performed in iCount with the sum of unique TTP crosslink sites identified in the different number of independent experiments as previously described (See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Briefly, 15 nucleotide windows flanking the crosslink site were generated, 100 permutations were allowed and multiple test correction of p-values (Benjamini-Hochberg) was performed to calculate FDR.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bed files contain the annotation of unique individual-nucleotide crosslinks to the genome in TTP binding peaks (FDR<0.05)

source_name: macrophages

growth_protocol: TTP-deficient primary bone marrow-derived macrophages (BMDMs) (10 days 10ng/ml M-CSF) were immortalized by transducing cells with a combination of hcmyc and hRasG12V ongogenes. CD11b and F4/80 positive cells were further transduced with all-in-one tet-inducible vectors expressing GFP, GFP-TTP or GFP-TTP-AA mutant

extract_protocol:
1 x 10E7 cells were treated as indicated. Afterwards cells were flushed on ice with 1x PBS and irradiated in 7.5ml 1x PBS with 300mJ/cm2 UV-C light in a Stratalinker, RNA-protein complexes were purified using a GFP-Nanotrap upon sonication of the cell pellets
See König et al, 2010 Nature Structural and Molecular Biology, 17, 909-915. Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP). Samples were multiplexed based on a 7 bases barcode (annotated under sample description)

treatment_protocol: BMDM cell lines were grown on 15 cm plates DMEM containing 2 mM L-glutamine, 10% (v/v) FCS, 100 U penicillin G/ml, 100 mg/ml streptomycin and non-essential amino acids, treatment with doxycycline (1µg/ml) and/or LPS (1µg/ml) occured as indicated

value: bone marrow-derived macrophages (BMDMs)

value: immortalized primary cells

tag: stimulation

value: 6h Doxycycline/4h LPS

tag: ip antibody

value: GFP-Nanotrap/GFP-binder


title: ABI3VP1_tnt.AT5G60130_col_a

description: A. thaliana Col-0 input DNA library


title: GFP-TTP-AA LPS 4h iCLIP Replicate 1

description:
RNA-TTP complex
Used Primer RCLIPA; 5'barcode GTTNNNN (reverse complement in each the 5; end of each read is AACNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_4h_mm10--ensembl75.bed


title: ChIPSeq-ABI5_mock_1

tag: accession

tag: genotype/variation

tag: tissue

value: whole seedlings

tag: age

value: 1.5 day

tag: light condition

value: long day

tag: treatment

value: 5 uM abscisic acid, 4 hours

tag: chip antibody

tag: chip antibody cat. #

tag: chip antibody lot#


title: GFP-TTP LPS 4h iCLIP Replicate 2

description:
RNA-TTP complex
Used Primer RCLIPC; 5'barcode ATCNNNN (reverse complement in each the 5; end of each read is GATNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_4h_mm10--ensembl75.bed

tag: cell type

tag: strain


title: CTR rep 3

city: Barcelona

first: Manuel

last: Serrano

state: Barcelona

address: Parc Científic de Barcelona, C/ Baldiri Reixac 10

department: Molecular Medicine

country: Spain

institute: IRB

description: Isolation of poly A+ RNA from total RNA

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (GRCm38/mm10) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used were Mus musculus GRCm38/mm10 from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

source_name: papilloma was obtained from a DMBA/TPA treated control C57Bl/6 background mice

extract_protocol:
Total RNA was extracted combining the Trizol reagent (Life Technologies) with the RNeasy Mini kit (Qiagen).
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 7.2 to 8.9 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by 8 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules of known strand origin was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Doxycycline treatment in their drinking water (2 mg/ml) throughout the entire DMBA/TPA protocol

value: skin

tag: mouse id number

tag: genotype

value: Control mice contain the tetO-Nanog transgene and lack the transactivator


title: CTR rep 2

description: Isolation of poly A+ RNA from total RNA


title: TG for Nanog rep 2

description: Isolation of poly A+ RNA from total RNA

source_name: papilloma was obtained from a DMBA/TPA treated Nanog-overexpressing C57Bl/6 background mice

value: Transgenic mice contain the trasactivator under the control of the K5 promoter (K5-rtTA) and the tetO-Nanog transgene


title: TG for Nanog rep 3

description: Isolation of poly A+ RNA from total RNA


title: TG for Nanog rep 1

description: Isolation of poly A+ RNA from total RNA


title: CTR rep 1

description: Isolation of poly A+ RNA from total RNA


title: GFP-TTP LPS 4h iCLIP Replicate 1

description:
RNA-TTP complex
Used Primer RCLIPH; 5'barcode AAGNNNN (reverse complement in each the 5; end of each read is CTTNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_4h_mm10--ensembl75.bed


title: GFP-TTP Non stimulated iCLIP Replicate 2

description:
RNA-TTP complex
Used Primer RCLIPB; 5'barcode GCCNNNN (reverse complement in each the 5; end of each read is GGCNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_0h_mm10--ensembl75.bed

value: 6h Doxycycline


title: GFP-TTP-AA Non stimulated iCLIP Replicate 2

description:
RNA-TTP complex
Used Primer RCLIPD; 5'barcode ACTNNNN (reverse complement in each the 5; end of each read is AGTNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_0h_mm10--ensembl75.bed


title: GFP-TTP Non stimulated iCLIP Replicate 1

description:
RNA-TTP complex
Used Primer RCLIPA; 5'barcode GTTNNNN (reverse complement in each the 5; end of each read is AACNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_0h_mm10--ensembl75.bed


title: GFP-TTP-AA LPS 1h iCLIP Replicate 3

description:
RNA-TTP complex
Used Primer RCLIPE; 5'barcode GGGNNNN (reverse complement in each the 5; end of each read is CCCNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_1h_mm10--ensembl75.bed

value: 6h Doxycycline/1h LPS


title: GFP-TTP-AA LPS 1h iCLIP Replicate 2

description:
RNA-TTP complex
Used Primer RCLIPD; 5'barcode ACTNNNN (reverse complement in each the 5; end of each read is AGTNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_1h_mm10--ensembl75.bed


title: GFP-TTP LPS 1h iCLIP Replicate 4

description:
RNA-TTP complex
Used Primer RCLIPH; 5'barcode AAGNNNN (reverse complement in each the 5; end of each read is CTTNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_1h_mm10--ensembl75.bed


title: GFP-TTP-AA LPS 1h iCLIP Replicate 1

description:
RNA-TTP complex
Used Primer RCLIPC; 5'barcode ATCNNNN (reverse complement in each the 5; end of each read is GATNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_1h_mm10--ensembl75.bed


title: GFP-TTP LPS 1h iCLIP Replicate 2

description:
RNA-TTP complex
Used Primer RCLIPB; 5'barcode GCCNNNN (reverse complement in each the 5; end of each read is GGCNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_1h_mm10--ensembl75.bed


title: GFP-TTP LPS 1h iCLIP Replicate 1

description:
RNA-TTP complex
Used Primer RCLIPA; 5'barcode GTTNNNN (reverse complement in each the 5; end of each read is AACNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_1h_mm10--ensembl75.bed


title: CTR rep 4

description: Isolation of poly A+ RNA from total RNA


title: GFP-TTP-AA RiboSeq Replicate 3

description:
DE_RiboSeq_analysis_DESeq_TTP-AAvsGFP.csv
DE_RiboSeq_analysis_DESeq_TTP-AAvsTTP.csv
Norm_counts_RiboSeq_DESeq.csv

data_processing:
Library strategy: Ribo-seq
Two FastQ files from each samples were generated and merged prior to processing.
Raw sequence reads were trimmed to remove adapters and poor quality scores using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.8, default parameters). Trimming mode: single-end. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default)
Remaining sequences were mapped to the mouse GRCm38 genome build (gene models Ensembl version 70) with TopHat (v2.0.12) using parameters -g 2 (non-primary alignments were then removed from the file, see https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/).
Read counting was performed using HTSeq (Mus_musculus.GRCm38.78.gtf annotation)
Differential gene expression analysis was performed using DESeq2_1.6.3 package. (DeSeq2 parameters: design(dds) <- formula(~ Library_date + Condition); nbinomWaldTest and Cooks filter off). NA omit.
Genome_build: mm10
Supplementary_files_format_and_content: csv files: DESeq2 results (NAomit applies) and DESeq2 normalised gene counts

extract_protocol:
Ribosome protected fragments were isolated by size exclusion chromatography (SEC) after ARTseq nuclease digestion; rRNA depletion using magnetic Ribo-zero Gold beads
ARTseq ribosome profiling kit (Epicentre/Illumina)
Ribosome protected footprinting libraries (Ribo-Seq)  were prepared as described in the ARTseq ribosome profiling kit (Epicentre/Illumina). Scriptminer Illumina compatible indexes were used for sample multiplexing (scriptminer_Index_id: 1 (CGTGAT), 2 (ACATCG), 6 (ATTGGC), 7 (GATCTG), 8 (TCAAGT), 9 (CTGATC), 10 (AAGCTA), 11 (GTAGCC), 12 (TACAAG)). 6 samples were multiplexed and sequenced in two lanes of a HiSeq2500 Illumina sequencer; RapidRun mode 50bp Single End.

treatment_protocol: BMDM cell lines were grown on 15 cm plates DMEM containing 2 mM L-glutamine, 10% (v/v) FCS, 100 U penicillin G/ml, 100 mg/ml streptomycin and non-essential amino acids, treatment with doxycycline (1µg/ml) for a total of 6h and with LPS (1µg/ml) for 1h.

tag: transduced

value: GFP-TTP-AA vector


title: GFP-TTP LPS 1h iCLIP Replicate 3

description:
RNA-TTP complex
Used Primer RCLIPG; 5'barcode AGANNNN (reverse complement in each the 5; end of each read is TCTNNNN)
peaks_lowFDR_Group_TTPGFP-LPS_1h_mm10--ensembl75.bed


title: GFP-TTP RiboSeq Replicate 2

description:
DE_RiboSeq_analysis_DESeq_TTPvsGFP.csv
DE_RiboSeq_analysis_DESeq_TTP-AAvsTTP.csv
Norm_counts_RiboSeq_DESeq.csv

value: GFP-TTP vector


title: GFP-TTP-AA RiboSeq Replicate 1


title: GFP-TTP-AA RiboSeq Replicate 2


title: GFP-TTP RiboSeq Replicate 3


title: GFP-TTP RiboSeq Replicate 1


title: GFP/EV RiboSeq Replicate 1

description:
DE_RiboSeq_analysis_DESeq_TTPvsGFP.csv
DE_RiboSeq_analysis_DESeq_TTP-AAvsGFP.csv
Norm_counts_RiboSeq_DESeq.csv

value: GFP vector


title: GFP-TTP-AA Non stimulated iCLIP Replicate 1

description:
RNA-TTP complex
Used Primer RCLIPC; 5'barcode ATCNNNN (reverse complement in each the 5; end of each read is GATNNNN)
peaks_lowFDR_Group_TTPAAGFP-LPS_0h_mm10--ensembl75.bed


title: GFP/EV RiboSeq Replicate 3


title: GFP/EV RiboSeq Replicate 2


title: GFP-TTP-AA RNASeq Replicate 1

description:
DE_RNAseq_analysis_DESeq_TTP-AAvsGFP.csv
DE_RNAseq_analysis_DESeq_TTP-AAvsTTP.csv
Norm_counts_RNAseq_DESeq.csv

data_processing:
Two Fastq files from each samples were generated and merged prior to processing.
Raw sequence reads were trimmed to remove adapters and poor qualities using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.8, default parameters). Trimming mode: single-end. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default)
Remaining sequences were mapped to the GRCm38 genome (guided by Ensembl version 70 gene models) with TopHat (v2.0.12) using tophat -g 2 parameters and subsequently filtered to just keep the primary alignment.
Read counting was performed using HTSeq (Mus_musculus.GRCm38.78.gtf annotation)
Differential gene expression analysis was performed using DESeq2_1.6.3 package. (DeSeq2 parameters: design(dds) <- formula(~ Library_date + Condition); nbinomWaldTest and Cooks filter off). NA omit.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files. DESeq2 results (NAomit applies) and DESeq2 normalised gene counts

extract_protocol:
rRNA-depleted total RNAs were generated using magnetic Ribo-zero Gold beads, heat fragmentation of rRNA-depleted total RNA prior library construction
ARTseq ribosome profiling kit (Epicentre/Illumina)
RNA-Seq libraries were prepared as described in the ARTseq ribosome profiling kit (Epicentre/Illumina). Scriptminer Illumina compatible indexes were used for sample multiplexing (scriptminer_Index_id:  5 (CACTGT), 6 (ATTGGC), 7 (GATCTG), 8 (TCAAGT), 9 (CTGATC), 10 (AAGCTA), 11 (GTAGCC), 12 (TACAAG)). 6 samples were multiplexed and sequenced in two lanes of a HiSeq2500 Illumina sequencer; RapidRun mode 50bp Single End.


title: GFP-TTP RNASeq Replicate 3

description:
DE_RNAseq_analysis_DESeq_TTPvsGFP.csv
DE_RNAseq_analysis_DESeq_TTP-AAvsTTP.csv
Norm_counts_RNAseq_DESeq.csv


title: GFP-TTP-AA RNASeq Replicate 3


title: GFP-TTP-AA RNASeq Replicate 2


title: GFP/EV RNASeq Replicate 3

description:
DE_RNAseq_analysis_DESeq_TTPvsGFP.csv
DE_RNAseq_analysis_DESeq_TTP-AAvsGFP.csv
Norm_counts_RNAseq_DESeq.csv


title: GFP/EV RNASeq Replicate 1


title: ARF_ecoli-ZmARF5_Zm_2

description: Zea mays input DNA library

data_processing:
Library strategy: DAP-Seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Reads were aligned by bowtie2 version 2.0.0-beta7 against the Arabidopsis TAIR10 genome assembly or Zea mays genome assembly B73 with default parameters, and additionally filter for highest scoring MAPQ alignments only (score=254).
Peaks were called using GEM peak caller version 2.3 with the default version 2.3 read distribution, TAIR10 genome sequences and parameters " --k_min 6 --k_max 20 --k_seqs 250 --outNP --k_neg_dinu_shuffle".
Genome_build: Arabidopsis TAIR10 or maize B73
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.

organism: Zea mays

tag: protein

tag: gene id

tag: protein family

value: ARF

tag: protein source

value: Zea mays

tag: protein affinity tag

value: GST

tag: expression system

value: ecoli

tag: dna source

value: zm

tag: replicate

tag: subset

value: motif+TFBS


title: GFP-TTP RNASeq Replicate 2

value: bone marrow-derived macrophages (BMDMs)

value: immortalized primary cells

tag: stimulation


title: GFP-TTP RNASeq Replicate 1


title: CC2

city: Wuhan

first: Chen

last: Tan

address: Huazhong Agricultural University

country: China

institute: College of Plant Science and Technology, Huazhong Agricultural University

description: normal type

data_processing:
100bp paired-end reads were generated via Illumina HiSeqTM 2000
The clean reads were directly aligned to the reference genome of Brassica napus using HISAT (HISAT version 0.1.6-beta) with the default parameters.
The genes were assembled with Cufflinks according to a reference-guided method.
The differentially expressed genes between three different samples were computed on RNA-seq data by using CuffDiff2.
Genome_build: Brassica_napus.annotation_v5.gff3
Supplementary_files_format_and_content: text files include the gene id, gene location,coverage of each reference gene and expression of gene(FPKM).

organism: Brassica oleracea

source_name: The newly expanded third leaves without petioles

growth_protocol: All of the samples were established in green house for transcriptomic analyses.

extract_protocol:
Using TRIzol reagent (Invitrogen, Life Technologies) according the manufacturer’s protocol, total RNA was extracted from two biological replicates (three plants per replicate) for each genotype.
NanoDrop ND 1000 (NanoDrop technologies) was used to initially calculate the quality and quantity of the extracted RNA, and then the RNA Integrity Number (RIN) value was assessed by Agilent Technologies 2100 Bioanalyzer (Agilent). Only when the value of RIN was higher than 8, the RNA was used to prepare the c-DNA library according to the TruSeq RNA Sample Prep v2 protocol

tag: tissue

value: Leaf

tag: subgenome composition

value: CC

tag: phenotype

value: normal


title: CC1

description: normal type


title: CCAA1

description: normal type

organism: Brassica napus

value: CCAA


title: CCA2

description: biased to B. oleracea

value: CCA

value: biased to B. oleracea


title: AAC2

description: biased to B. rapa

value: AAC

value: biased to B. rapa


title: CCAA2

description: normal type


title: AAC1

description: biased to B. rapa


title: AC2

description: normal type

value: AC


title: GFP/EV RNASeq Replicate 2

tag: cell type

value: 6h Doxycycline/1h LPS

value: GFP vector


title: AA2

description: normal type

organism: Brassica rapa

value: AA


title: AA1

description: normal type


title: AP2EREBP_tnt.CRF4_colamp_a

description: A. thaliana Col-0 input DNA library was PCR amplifed (ampDAP-Seq library) before affinity purification.

value: Arabidopsis thaliana

value: Halo

value: tnt

value: colamp

value: a


title: CCA1

description: biased to B. oleracea

value: Leaf


title: Colonospheres

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

data_processing:
After filtering contaminant (aligned) reads, sequenced reads were then mapped to hg19 genome, RefSeq exons, splicing junctions using BWA v0.7.3 alignment algorithm
The filtered reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were then counted as expression level for a corresponding transcript and was further subjected to log2 transformation  and global median normalization
hg19
Genome_build: tab-delimited text files include normalized values for each transcript in each sample

organism: Homo sapiens

source_name: colon carcinoma

extract_protocol:
Total RNA extraction was performed with Rneasy mini kit (Qiagen). 1 ug of total RNA was treated with RNAse free DNAseI (Roche) and used for the construction of the sequencing libraries as per manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: growth

value: suspension; serum-free medium

value: colon carcinoma

value: colonospheres


title: Input CaCo-2

data_processing:
Basecalls performed using CASAVA version 1.4
Raw RIP-seq reads are aligned against the aforementioned custom contaminant list (including mitochondria genome, ribosomal RNA and Illumina adapter) using bowtie2 to filter contaminant (aligned) reads
RIP-seq reads were aligned to the hg19 genome assembly using TopHat (version 2.0.8)
Cufflinks/Cuffdiff was used to compute FPKM values for each Ensembl transcript and fold-change difference of gene expression between the RIP and control libraries.
Genome_build: hg19

source_name: colon cancer

extract_protocol:
Cell nuclei were isolated, nuclear lysate was prepared and incubated overnight with 5 µg of beta-catenin antibody (Bethyl A302-012A) .Afterwards, the RNA-protein complexes were immunoprecipitated with protein G magnetic beads and the RNA fraction was extracted using Trizol reagent.
Library construction was prepared following the manufacturer's recommendation (TruSeq RNA Sample Preparation kit, Illumina RS-122-2001)

value: human adenocarcinoma

tag: treatment

value: no treatment

tag: rip antibody

value: no antibody


title: Beta-Catenin CaCo2

value: B-catenin (Bethyl A302-012A)


title: CCICs

description: POS

value: adherence


title: Non-CCICs

description: NEG


title: Input HT-29


title: BT474 cells control

city: Illkirch Cedex

first: Cecile

last: Rochette-Egly

address: 1 rue Laurent Fries

department: functional genomics and cancer

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using CASAVA v1.7.0.
Reads were mapped onto the hg19 assembly of the human genome by using Tophat v1.2.0 and the bowtie v0.12.7 aligner.
Gene expression was quantified using Cufflinks v1.0.1 and gene annotations from Ensembl release 62
Genome_build: hg19
Supplementary_files_format_and_content: tabulated text file containing RPKM for all samples

source_name: breast tumor_BT474_control

growth_protocol: MCF-7 and BT474 human breast cancer cell lines were purchased from the American Type Culture Collection (ATCC) and cultured as monolayers under standard conditions.

extract_protocol:
Total RNA was extracted using the GenElute miniprep kit (Sigma)
After isolation of total cellular RNA, a library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “Truseq RNA sample preparation low throughput” protocol with some modifications. Briefly, mRNA was purified from 4 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit (ref A84801, Beckman Coulter, Inc) with the SPRI-TE instrument (Beckman Coulter, Inc). Briefly, in this system double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7pM concentration and clusters generated and sequenced in the Illumina Genome Analyzer IIX as single-end 54 base reads.

treatment_protocol: When cells were 80-90 % confluent, all-trans RA (10-6 M) (Sigma Aldrich)was added to two dishes and vehicle (0.1% ethanol) to the two others, after 24h in low (1%) serum medium conditions, without insulin and phenol red. Then the cells were scrapped for RNA extraction

value: epithelial

value: ethanol 4 hours


title: BJAB BirA OCT2 T223A

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: No additional information.

data_processing:
ChIP-Seq Analysis
Calculation Method: Sequencing was performed on a GA2x (Illumina) sequencer, with single reads (SRs) of 36-bp length. Reads were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. To perform peak calling, the genome was divided into "bins" of 25 bp. Each sequencing tag was associated with the bin of its start site and an additional extension of seven bins (for a total of 200 bp) along the direction of its read to match the average library size. For a given experiment, the number of "hits" in a bin was defined as the number of extended tags associated with that bin. Bins with fewer than three hits were removed. Peaks were formed by merging consecutive significant bins. The height of the peak was defined as the largest number of hits in any of the bins forming the peak. The "apex" of the peak was defined as the bin that had this largest number of hits. In the case of ties, the earliest such peak was chosen as the apex.
Genome_build: hg18

source_name: BJAB BirA OCT2 T223A

extract_protocol:
Streptavidin DynaBeads
Other: Exponentially growing cells were cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 mins at RT and cells were washed twice with ice-cold PBS.  Cells were lysed in ice-cold RIPA buffer (10 mM Tris HCl, pH 8, 140 mM NaCl, 1 mM EDTA, pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.3% SDS, and 0.1% sodium deoxycholate) and DNA was sheared with a Misonix XL sonicator to an average fragment size of 300 nt.  For each immunoprecipitation reaction, 2.5 × 10(7) chromatin cell equivalents were incubated overnight with 50 ul of Streptavidin Dynal Beads (Invitrogen). Beads were washed four times with RIPA buffer, once with LiCl buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxy- cholate, 1 mM EDTA), once with TE, pH 8.0, and finally re-suspended in 100 uL of TE, pH 8, containing RNase A (0.2 ug/uL). Reverse cross-linking was performed overnight at 65 C, followed by treatment with 20 ug of proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIA- quick PCR purification columns (Qiagen).
ChIP DNA was used to generate ChIP-Seq libraries using the TruSeq ChIP library preparation kit from Illumina according to the manufacturer's instructions.

treatment_protocol:
Treatment type: Transduction
In-vitro treatment: BJAB cells that stably expressed the BirA enzyme were transduced with N-terminally tagged OCT2 T223A (pRCMV/TPO_Flag-Bio-OCT2_T223A). Selection was carried out with puromycin and expression was induced with Doxycycline.

value: BJAB

value: GCB DLBCL cells

tag: disease state

value: germinal center B cell (GCB) subtype of diffuse large B cell lymphoma (DLBCL)


title: HBL1 OCA-B - repeat 1

description: No additional information.

source_name: HBL1 OCA-B

extract_protocol:
OCA-B (SC955) Antibody Extraction
Other: 2.5 x 10(7) exponentially growing cells were cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 mins at RT and cells were washed twice with ice-cold PBS. Cells were lysed in ice-cold RIPA buffer (10 mM Tris HCl, pH 8, 140 mM NaCl, 1 mM EDTA, pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.3% SDS, and 0.1% sodium deoxycholate) and DNA was sheared with a Misonix XL sonicator to an average fragment size of 300 nt. For each immunoprecipitation reaction, 2.5 x 10(7) chromatin cell equivalents were incubated overnight with 10 ug of OCA-B (SC955). The following day, chromatin/antibody complexes were incubated with 50 uL of protein G magnetic beads (Invitrogen) for 4 h at 4 C. Beads were washed four times with RIPA buffer, once with LiCl buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxy- cholate, 1 mM EDTA), once with TE, pH 8.0, and finally re-suspended in 100 uL of TE, pH 8, containing RNase A (0.2 ug/uL). Reverse cross-linking was performed overnight at 65 C, followed by treatment with 20 ug of proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIA-quick PCR purification columns (Qiagen).
ChIP DNA was used to generate ChIP-Seq libraries using the TruSeq ChIP library preparation kit from Illumina according to the manufacturer's instructions.

value: ABC DLBCL cells

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)


title: BT474 cells RA-treated

source_name: breast tumor_BT474_RA_4h

value: retinoic acid 10-7M 4hours


title: HBL1 OCT2 - repeat 2

description: No additional information.

source_name: HBL1 OCT2

extract_protocol:
OCT2 (SC233) Antibody Extraction
Other: 2.5 x 10(7) exponentially growing cells were cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 mins at RT and cells were washed twice with ice-cold PBS. Cells were lysed in ice-cold RIPA buffer (10 mM Tris HCl, pH 8, 140 mM NaCl, 1 mM EDTA, pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.3% SDS, and 0.1% sodium deoxycholate) and DNA was sheared with a Misonix XL sonicator to an average fragment size of 300 nt. For each immunoprecipitation reaction, 2.5 x 10(7) chromatin cell equivalents were incubated overnight with 10 ug of OCT2 (SC233). The following day, chromatin/antibody complexes were incubated with 50 uL of protein G magnetic beads (Invitrogen) for 4 h at 4 C. Beads were washed four times with RIPA buffer, once with LiCl buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxy- cholate, 1 mM EDTA), once with TE, pH 8.0, and finally re-suspended in 100 uL of TE, pH 8, containing RNase A (0.2 ug/uL). Reverse cross-linking was performed overnight at 65 C, followed by treatment with 20 ug of proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIA-quick PCR purification columns (Qiagen).
ChIP DNA was used to generate ChIP-Seq libraries using the TruSeq ChIP library preparation kit from Illumina according to the manufacturer's instructions.


title: HBL1 IgG Control - repeat 1

description: No additional information.

source_name: HBL1 IgG Control

extract_protocol:
anti-Flag-M2 (Sigma) Extraction
Other: 2.5 x 10(7) exponentially growing cells were cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 mins at RT and cells were washed twice with ice-cold PBS. Cells were lysed in ice-cold RIPA buffer (10 mM Tris HCl, pH 8, 140 mM NaCl, 1 mM EDTA, pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.3% SDS, and 0.1% sodium deoxycholate) and DNA was sheared with a Misonix XL sonicator to an average fragment size of 300 nt. For each immunoprecipitation reaction, 2.5 x 10(7) chromatin cell equivalents were incubated overnight with 10 ug of negative control antibody (anti-Flag-M2; Sigma). The following day, chromatin/antibody complexes were incubated with 50 uL of protein G magnetic beads (Invitrogen) for 4 h at 4 C. Beads were washed four times with RIPA buffer, once with LiCl buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxy- cholate, 1 mM EDTA), once with TE, pH 8.0, and finally re-suspended in 100 uL of TE, pH 8, containing RNase A (0.2 ug/uL). Reverse cross-linking was performed overnight at 65 C, followed by treatment with 20 ug of proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIA-quick PCR purification columns (Qiagen).
ChIP DNA was used to generate ChIP-Seq libraries using the TruSeq ChIP library preparation kit from Illumina according to the manufacturer's instructions.


title: BJAB BirA OCT2 WT

description: No additional information.

source_name: BJAB BirA OCT2 WT

treatment_protocol:
Treatment type: Transduction
In-vitro treatment: BJAB cells that stably expressed the BirA enzyme were transduced with N-terminally tagged OCT2 WT (pRCMV/TPO_Flag-Bio-OCT2_WT). Selection was carried out with puromycin and expression was induced with Doxycycline.


title: BJAB BirA Empty Control

description: No additional information.

source_name: BJAB BirA Empty Control

treatment_protocol:
Treatment type: Transduction
In-vitro treatment: BJAB cells that stably expressed the BirA enzyme were transduced with the empty BioTag vector (pRCMV/TPO_Flag-Bio). Selection was carried out with puromycin and expression was induced with Doxycycline.


title: HBL1 OCT2 - repeat 1

description: No additional information.


title: BB_5

city: College Station

first: Cole

middle: M

last: McQueeen

address: 4467 VMRB

institute: Texas A&M University

data_processing:
Reads were mapped and aligned with Tophat 2.0.14
HT-Seq was used to generate read count tables for each sample using the equCab2 Ensembl annotation, HT-Seq intersection non-empty, and merged in counts.txt
counts.txt loaded in to edgeR to identify differentially expressed genes (AAvsABBB_TopTags.txt)
cufflinks was used to generate transcripts.gtf
cuffdiff generated AA_ABBB_gene_exp.diff to identify differentially expressed genes
Genome_build: EquCab2.0
Supplementary_files_format_and_content: abundance measurements and differentially expressed genes

organism: Equus caballus

source_name: BB, whole blood

extract_protocol:
Life Technologies MagMax RNA isolation kit
Illumina true seq

value: whole blood

value: circulating leukocytes

tag: snp allelic state

value: BB


title: HBL1 OCA-B - repeat 2

description: No additional information.


title: HBL1 IgG Control - repeat 2

description: No additional information.


title: BB_4


title: AC1

description: normal type

value: Leaf

value: AC

value: normal


title: Beta-catenin HT-29

value: human adenocarcinoma

value: no treatment


title: BB_3


title: AA_3

source_name: AA, whole blood

value: AA


title: AB_4

source_name: AB, whole blood

value: AB


title: MCF7 cells RA treated

source_name: breast tumor_MCF7_RA_4h

value: epithelial


title: BB_2


title: BB_1


title: AB_1


title: AA_1


title: AB_2


title: AB_3


title: PMM [miRNA-seq]

status: Public on May 24 2016

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
The reads were then subjected to a series of additional filters with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 21.0: not sequencing adapters; containing no more than 80% A, C, G, or T; containing no more than two N (undetermined bases); containing not only A and C or G and T, being longer than 14 nt or shorter than 27 nt; not containing 10 repeats of any dimer; not originating from porcine known classes of RNAs (i.e. mRNA in NCBI database; rRNA,tRNA, snRNA and snoRNA in Rfam database)
Then the high-quality reads were mapped to the pig genome (Sscrofa10.2) using NCBI Local BLAST following three steps in order: (1) map the high-quality reads to the precursor miRNAs of pig and 24 other mammals in miRBase 19.0; (2) map the mapped high-quality reads to pig genome (Sscrofa10.2) to obtain their genomic locations and annotations using NCBI Local BLAST; (3) cluster the unmapped sequences in step 1 that mapped to the pig genome as putative novel miRNAs, and predict their hairpin RNA structures from the adjacent 60 nt sequences in either direction from the pig genome using UNAFold
The expression of miRNAs in the two samples was normalized by total mappable reads, and the program IDEG6 was employed to detected DE miRNAs among the two libraries. A unique miRNA is considered to be differentially expressed when it simultaneously obtained p < 0.001 under three statistical tests
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: normalized counts

organism: Sus scrofa

source_name: psoas major

growth_protocol: Three female Landrace pigs, no direct and collateral blood relationship within the last 3 generations, were uesd in this study. All pigs were housed in some environment and fed twice a day with the some diet from weaning (28-day-old) to slaughter (210-day-old). The diets formulas meet the National Research Council (NRC 1998) recommendations for the different growth phase. During experiment preiods, the animals were allowed access to feed and water ad libitum and lived under the same normal conditions

extract_protocol:
Total RNA was extracted from adipose tissues using TRIzol (Invitrogen) and further purified with RNeasy columns (Qiagen) according to the manufacturer’s protocol.
About 45 μg of total RNA from the two tissues were used for miRNA transcriptome library preparation and sequencing. In briefly, only about 10–40 nt short RNAs were isolated from polyacrylamide gel electrophoresis (PAGE) was combined with adaptors (Illumina, San Diego, CA, USA) and converted to cDNA by RT-PCR. Then the cDNA was single-end sequencing in 36 bp on the Genome Analyzer GA-2 (Illumina) following the recommended protocol for small RNA sequencing.

treatment_protocol: When being slaughtered, the pigs were kept off feed but given free  access to water for 24 h, and then electrically stunned, exsanguinated, scalded and rinsed. Samples were obtained from the intermediate section of the longissimus dorsi and psoas major immediately after exsanguination, and rapidly frozen in liquid nitrogen for sequencing analysis

tag: breed

value: Landrace

tag: gender

value: female

tag: age

value: 210 days old

value: psoas major muscle


title: LDM [miRNA-seq]

source_name: longissimus dorsi

value: longissimus dorsi muscle


title: MCF7 cells control

source_name: breast tumor_MCF7_control

value: ethanol 4 hours


title: PMM rep3 [MeDIP-seq]

data_processing:
After filtering out low quality reads that contained more than 5 ‘N’s and over 50% of the sequence with low quality value (Phred score < 5), the MeDIP-seq data were aligned to pig reference genome (Sscrofa 10.2), allowing up to four mismatches using SOAP2 software (Version 2.21)
The reads mapping to multiple genomic location were regarded as duplicates and just choosen one read. To avoid stochastic sampling drift, we filtered out CpG sites that were covered by less than a 10 read depth.
The DMRs identification method was used our previous description, the normality and equal variance of the read depth at each CpG in LDM and PMM were tested using Bartlett's test (passing if P > 0.05, failed for p < 0.05).
Subsequently, a parametric (passing Bartlett's test) or non-parametric test (failing Bartlett's test) was used to select highly variable CpGs (P < 0.01) as seed sites for candidate DMRs. Then a 3’ downstream adjacent the CpG wes incorporated into the seed CpGs (up to 200 bp), and the new seed CpGs would repeatedly adjacent the next CpG until appearing a low-variance CpG (P > 0.01), which was allowed to be up to 2 kb from the seed CpG.
If five or more CpGs in a genomic region demonstrated significant different (P < 0.01) read depths between LBF and RBF, then taken this as a DMR. The P values for the DMRs were also corrected using the Benjamini-Hochberg method (FDR < 0.01, 1,000 permutations).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: methylation levels

extract_protocol:
Genomic DNA extracted using the DNeasy Blood & Tissue Kit (Qiagen) according as the manufacturer’s instructions.
Genomic DNA sonicated to approximately 100-500 bp fragments with a Bioruptor sonicator (Diagenode, NJ, USA). Then, libraries were constructed using a Paired-End DNA Sample Prep kit (Illumina, CA, USA) according as the manufacturer’s instructions. The fragments were ligated with adaptor and immunoprecipitated by monoclonal anti-methylcytidine antibody (Diagenode, NJ, USA). The enriched fragments with methylation and 10% input DNA were purified (DNA Clean & Concentrator-5 columns) and amplified by adaptor-mediated PCR. Then the MeDIP libraries were subjected to paired-end sequencing using Illumina HiSeq 2000 and a 50 bp read length.


title: PMM rep1 [MeDIP-seq]


title: LDM rep3 [MeDIP-seq]


title: PMM rep2 [MeDIP-seq]


title: LDM rep2 [MeDIP-seq]


title: LDM rep1 [MeDIP-seq]


title: SULINDAC 3

city: San Francisco

first: Dvir

last: Aran

institute: University of California San Francisco

description: Adenomatous polyps of APCmin/+ mice, treated them with the NSAID Sulindac

data_processing:
RSEM (RNA-Seq by Expectation-Maximization) software package was used for the analysis of the organoids RNA-seq experiments.
Bowtie2-2.2.4 was used for the alignment.
The mm9 gtf file was used for reference.
Genome_build: mm9
Supplementary_files_format_and_content: Raw counts

source_name: Gut epithelium

growth_protocol: Organoids were produced from WT and APCmin/+ mice as previously described (Sato et al. Nature 2009). For adenoma and APCmin/+ organoids, adenomas and normal adjacent tissue were separated and processed accordingly. All organoids were grown in Advanced DMEM/F12 culture medium (Gibco) supplemented with Noggin, EGF, bFGF (Peprotech, 1:1000), R-spondin1 (Peprotech, 1:500) and B27 (Gibco, 1:50). For staining, organoids were fixed in 4% PFA and incubated overnight with the primary antibody (IFITM2/3 - 1:200, Abcam). Secondary antibody was Alexa fluor-647 donkey anti-rabbit (1:1000, Molecular Probes). Hoechst (1µg/ml, Molecular Probes) was used to stain nuclei.

extract_protocol:
RNA was extracted using the QIAGEN mirNEASY kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adenomatous polyps of APCmin/+

tag: growth protocol

value: organoid culture

value: NSAID Sulindac


title: SULINDAC 1


title: ADENOMA 3

description: Adenomatous polyps of APCmin/+


title: ADENOMA 2

description: Adenomatous polyps of APCmin/+


title: ADENOMA 1

description: Adenomatous polyps of APCmin/+


title: SULINDAC 2


title: NKT Input

city: Chicago

first: Aiping

last: Mao

state: IL

address: 929 East 57th street

department: Pathology

institute: University of Chicago

data_processing:
Base calling was performed using Illumina software pipeline
ChIP-seq reads were aligned to mm10 genome using bowtie with the following parameters: --sam --best -m 1 -n 2 --chunkmbs 300
Duplicate reads were removed using picard tools
Peaks were called using MACS with P value 1e-5
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using HOMER; bed files contained the peaks called by MACS

source_name: NKT Input

growth_protocol: Mouse thymus from C57BL/6J background

extract_protocol:
Lysates were clarified from sonicated nuclei and PLZF-DNA complexes were isolated with magnetic Streptavidin beads.
Libraries were prepared according to Illumina TruSeq DNA Sample Preparation Guide (Part# 15026486).

treatment_protocol: Not applicable

tag: strain background

tag: genotype/variation

value: PLZF tg/BirA tg/Valpha14 tg mice

value: Thymocytes

tag: chip beads/antibody


title: Tg thy Input

source_name: Tg thy Input

value: PLZF tg/BirA tg mice


title: MIN 3

description: APC-mutated normal gut epithelium (MIN)

tag: tissue

value: APC-mutated normal gut epithelium


title: Tg thy Streptavidin ChIP-seq

source_name: Tg thy Streptavidin ChIP-seq

value: Streptavidin beads (Invitrogen; 14204)


title: NKT Streptavidin ChIP-seq

source_name: NKT Streptavidin ChIP-seq


title: MIN 2

description: APC-mutated normal gut epithelium (MIN)


title: MIN 1

description: APC-mutated normal gut epithelium (MIN)


title: AA_2

value: whole blood

value: circulating leukocytes

value: AA


title: HT10801b_Input_X2_(20151015_7)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: HT1080-1b cross-linked ChIP input, biological replicate 2

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).

source_name: Input

extract_protocol: The HT1080-1b fibrosarcoma cell  line was grown in DMEM media  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 Micrococcal nuclease (MNase, Sigma, Cat # N3755) at 37°C for 45 min. Reactions were stopped by addition of EGTA to a final concentration of 20 mM and EDTA to 10 mM. The MNase digested chromatin was sonicated as described before (PMID: 24737864). 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.

value: fibrosarcoma

tag: chip antibody


title: ht10801b_input_x1_(20151015_1)

description: ht1080-1b cross-linked chip input, biological replicate 1

source_name: input

extract_protocol: the ht1080-1b fibrosarcoma cell  line was grown in dmem media  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 micrococcal nuclease (mnase, sigma, cat # n3755) at 37°c for 45 min. reactions were stopped by addition of egta to a final concentration of 20 mm and edta to 10 mm. the mnase digested chromatin was sonicated as described before (pmid: 24737864). 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: HT10801b_CenpA_GFP_X_(20151015_6)

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

source_name: Sequential immunoprecipitated DNA

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-GFP(Abcam, Cat# Ab290)antibodies.Solexa library construction was performed as described previously (PMID:22025700) and PCR-amplified using Phusion polymerase.

tag: chip antibodies

value: Anti-FLAG M2 magnetic beads (Signa Cat # M8823) and Anti-GFP (Abcam Cat #Ab290)


title: HT10801b_CenpA_CenpT_X2_(20151015_12)

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

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-T (Abcam, Cat# Ab114120)antibodies.Solexa library construction was performed as described previously (PMID:22025700) and PCR-amplified using Phusion polymerase.

tag: cell type

value: Anti-FLAG M2 magnetic beads (Signa Cat # M8823) and Anti-CENP-T (Abcam Cat #Ab114120)


title: mESCs_shRing1b_rep3

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

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

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: cell line

value: embryonic stem cell, blastocyst derived

tag: celll subtype

value: pluripotent embryonic stem cells

tag: transfected with


title: mESCs_shRing1b_rep2


title: HT10801b_CenpA_CenpC_X2_(20151015_11)

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

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# Ab33034)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-C (Abcam Cat #Ab33034)


title: HT10801b_CenpA_CenpC_X1_(20151015_4)

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


title: mESCs_shNMC_rep2

value: shNMC


title: HT10801b_CenpA_CenpT_X1_(20151015_5)

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


title: mESCs_shMed12_rep3