title: 3h-lo-420_S18_L001_R1_001_AF_SOL_547

status: Public on Nov 14 2014

last: Fire

address: 300 Pasteur Drive Lane building L302

institute: Stanford

data_processing:
turn fastq to fasta
Computational Methods: Calculation of retention and normalization: We use the log2 of retention in the PCR pool as a measure of target cleavage by Cas9, with a retention score calculated for each sequence in each experiment.
For each sequence 'X': Retention[X]=
log2(RepresentationX[Cleaved Library]/RepresentationX[Uncleaved Library])
Representationx in a library gives the ratio between:
[Instances of sequence X in the library]/[Instances of a reference population in the library]
As reference populations we used either an aggregate of all sequences with 4-7 mismatches to the original trigger, or (for the unc-22A library) an "internal control" population comprising a subset of plasmids from the protospacer 4 library. Comparable results were obtained with these two references for normalization.
Each line of the fasta file is a read of a sequence from the library experiments. First unique sequences were identified then each unique sequence and only sequences with a 50 count minimum in the control experiment from the sequencing run was considered in the library analysis. The numbers are normalized and the retention score is calculated (see above).
Supplementary_files_format_and_content: Each .dat file is a tab-delimited file of all considered sequences in each experiment. The names of the files and the AF_SOL_# run number can be found in the associated publication (Supplementary Materials) with the details of the conditions. Each filename starts with the type of gRNA used (either unc-22WT or the mutant version unc22C11G). The next number (#min) is indication of the time of incubation for the experiment and this is either followed by #pcr_AF_SOL_# or just AF_SOL_#. If followed by #pcr, that is the indication of the number of PCR cycles used in the experiments. Finally, AF_SOL_# denotes the sequencing run ID number.

organism: synthetic construct

source_name: unc-22 RVL library

extract_protocol:
Cas9 in vitro assays and sequencing: Cas9 in vitro assays were performed in 10 ul reactions with Cas9 protein pre-incubated with gRNA, 1X NEB ThermoPol Taq buffer, dH2O, and random variant target library. Following incubation at 37° C, reactions were stopped by flash freezing in dry ice, addition of 200 ul of proteinase K buffer (0.1M NaCl, 0.1M TRIS pH 8.4, 0.1M EDTA, 1% SDS), addition of 20 ul of proteinase K (20 mg/ml), and incubation at 3 hours at 60° C. After adding 190 ul TE, 1 ul 1.5 ug of GlycoBlue, 2.5ug of yeast tRNA, and 40 ul of saturated ammonium acetate samples were extracted with phenol/ chloroform (1:1) and chloroform, ethanol precipitated, and resuspended in 10 ul of TE. PCR for a total of 26 cycles was used to amplify the retained sequences and prepare for sequencing. This included a first round (20 cycles) with short primers AF-KLA-136 and AF-KLA-140, and a second round (6 cycles) with longer primers bearing index sequences and flow cell anchors for sequencing and subsequent analysis (Table S1-2). All libraries were sequenced using the 50 cycle Illumina Miseq (100 cycle single-read) platforms. A list of experiments, experimental conditions, sequencing run IDs, and SRA accession numbers is reported in the supplemental material (Table S2). Samples that are controls are either with 0 Cas9 or have Cas9 and with a 0 time point.
Generation of random variant target library: The random variant target library was generated using the pHRL-TK vector (Promega). Customized variant primers for the target library were extended and cloned into the NotI and Acc65I digested pHRL-TK vector (see Generation of random variant target library). The variant sequence was designed to be 35 nt (6 nt flanking on each side of a 23 nt target sequence). The 12 nt of flanking sequence and the N in the PAM sequence of the target were synthesized with custom mixes that were made up of 25% adenine (A), 25% thymine (T), 25% cytosine (C), or 25% guanine (G). The 22 bps sequence of unc-22A and ps4 were synthesized with custom mixes designed to produce a 10% variant rate at each position (3.3% of each variant base), although, the ps4 library has a unexpectedly high variant rate at two positions.The initial oligonucleotide library preparations were extended using NEB ThermoPol Taq polymerase and primer AF-KLA-87. Reaction tubes with 100 pM of each primer in 25 ul dH2O and 2.5 ul of 10X Taq ThermoPol buffer (20 mM Tris-HCl, 10 mM KCl, 2 mM MgSO4, 10mM (NH4)2SO4 , 0.1% Triton® X-100, pH 8.8) is put in a beaker of boiling water for 5 minutes and removed from heat and allowed to cool at 45° C. The primer mix is then diluted by adding 5ul of 25 mM dNTPs, 210 ul of 1X Taq buffer, and 10 ul of NEB Taq polymerase. Extension is then allowed for 15 minutes at 72° C, with extension stopped by adding 180 ul of (1.9 NH4OAc, 19 mM EDTA, 0.38% SDS), and 1.5 ug of GlycoBlue. Following extractions with phenol/chloroform (1:1) and chloroform, and ethanol precipitation, the resulting material was resuspsended in 40 ul of TE, digested with NEB NotI+Acc65I purified following electrophoresis on a 1.5% agarose gel, and ligated into the NotI and AccI65 digested recipient vector using NEB Quick ligation. Following transformation of library efficiency DH5α cells (Invitrogen), plating on pre-warmed 15 cm plates, colonies were grown overnight at 37° C then moved and incubated at 30° C for 24 hrs. Approximately 5000 colonies were scraped off of agar plates into 10 mls of 2XTY. The 10 mls of cells were pelleted and prepped using Qiagen Midi plasmid prep kit.

tag: random variant target

value: unc-22 RVL

tag: molecule subtype

value: library DNA


title: 3f-lo-420_S16_L001_R1_001_AF_SOL_547

type: SRA

city: Stanford

first: Andrew

state: California

department: Genetics

country: USA

library_source: genomic

molecule: genomic DNA


title: 3e-lo-420_S15_L001_R1_001_AF_SOL_547


title: 2f-con_S14_L001_R1_001_AF_SOL_551


title: 2e-con_S13_L001_R1_001_AF_SOL_551


title: 2d-lo-420_S12_L001_R1_001_AF_SOL_547


title: 2d-lo-420_S12_L001_R1_001_AF_SOL_550


title: 2c-lo-420_S11_L001_R1_001_AF_SOL_550


title: 2c-lo-420_S11_L001_R1_001_AF_SOL_547


title: 2c-con_S11_L001_R1_001_AF_SOL_551


title: 2d-con_S12_L001_R1_001_AF_SOL_551


title: 2b-lo-420_S10_L001_R1_001_AF_SOL_550


title: 2b-lo-420_S10_L001_R1_001_AF_SOL_547


title: 2a-con_S9_L001_R1_001_AF_SOL_551


title: 2a-lo-420_S9_L001_R1_001_AF_SOL_547


title: 1h-lo-420_S8_L001_R1_001_AF_SOL_551


title: 2b-con_S10_L001_R1_001_AF_SOL_551


title: 2a-lo-420_S9_L001_R1_001_AF_SOL_550


title: 1h-lo-420_S8_L001_R1_001_AF_SOL_547


title: 1h-lo-420_S8_L001_R1_001_AF_SOL_550


title: 1g-lo-420_S7_L001_R1_001_AF_SOL_551


title: 3g-lo-420_S17_L001_R1_001_AF_SOL_547


title: 1g-lo-420_S7_L001_R1_001_AF_SOL_547


title: 1g-lo-420_S7_L001_R1_001_AF_SOL_550


title: 1f-lo-420_S6_L001_R1_001_AF_SOL_551


title: 1f-lo-420_S6_L001_R1_001_AF_SOL_550


title: 1e-lo-420_S5_L001_R1_001_AF_SOL_550


title: 1e-lo-420_S5_L001_R1_001_AF_SOL_551


title: 1d-lo-420_S4_L001_R1_001_AF_SOL_551


title: 1d-lo-420_S4_L001_R1_001_AF_SOL_550


title: 1a-lo-420_S1_L001_R1_001_AF_SOL_551


title: 1c-lo-420_S3_L001_R1_001_AF_SOL_551


title: 1b-lo-420_S2_L001_R1_001_AF_SOL_551


title: 1c-lo-420_S3_L001_R1_001_AF_SOL_550


title: 1a-lo-420_S1_L001_R1_001_AF_SOL_550


title: 3h-con_S24_L001_R1_001_AF_SOL_513

data_processing:
turn fastq to fasta
Computational Methods: Calculation of retention and normalization: We use the log2 of retention in the PCR pool as a measure of target cleavage by Cas9, with a retention score calculated for each sequence in each experiment.
For each sequence 'X': Retention[X]=
log2(RepresentationX[Cleaved Library]/RepresentationX[Uncleaved Library])
Representationx in a library gives the ratio between:
[Instances of sequence X in the library]/[Instances of a reference population in the library]
As reference populations we used either an aggregate of all sequences with 4-7 mismatches to the original trigger, or (for the unc-22A library) an "internal control" population comprising a subset of plasmids from the protospacer 4 library.  Comparable results were obtained with these two references for normalization.
Each line of the fasta file is a read of a sequence from the library experiments. First unique sequences were identified then each unique sequence and only sequences with a 50 count minimum in the control experiment from the sequencing run was considered in the library analysis. The numbers are normalized and the retention score is calculated (see above).
Processed data 'dat' files contain the calculated final retentions for each experiment. Each experiment labeled: 'AF_SOL_###_t###'. 'AF_SOL_###' corresponds to the experiment run ID and 't###' corresponds to the incubation time of the experiment. For example AF_SOL_513_t360, corresponds to experiment 513 on the protospacer 4 guide and DNA target and the incubation time was 360 mins. The experimental conditions and ID can be found in the associated publication.

Supplementary_files_format_and_content: 'dat' files containing the calculated final retentions for each experiment

source_name: protospacer 4 (ps4) library

extract_protocol:
Cas9 in vitro assays and sequencing: Cas9 in vitro assays were performed in 10 ul reactions with Cas9 protein pre-incubated with gRNA, 1X NEB ThermoPol Taq buffer, dH2O, and random variant target library. Following incubation at 37° C, reactions were stopped by flash freezing in dry ice, addition of 200 ul of proteinase K buffer (0.1M NaCl, 0.1M TRIS pH 8.4, 0.1M EDTA, 1% SDS), addition of 20 ul of proteinase K (20 mg/ml), and incubation at 3 hours at 60° C.  After adding 190 ul TE, 1 ul 1.5 ug of GlycoBlue, 2.5ug of yeast tRNA, and 40 ul of saturated ammonium acetate samples were extracted with phenol/ chloroform (1:1) and chloroform, ethanol precipitated, and resuspended in 10 ul of TE. PCR for a total of 26 cycles was used to amplify the retained sequences and prepare for sequencing.  This included a first round (20 cycles) with short primers AF-KLA-136 and AF-KLA-140, and a second round (6 cycles) with longer primers bearing index sequences and flow cell anchors for sequencing and subsequent analysis (Table S1-2). All libraries were sequenced using the 50 cycle Illumina Miseq (100 cycle single-read) platforms.  A list of experiments, experimental conditions, sequencing run IDs, and SRA accession numbers is reported in the supplemental material (Table S2). Samples that are controls are either with 0 Cas9 or have Cas9 and with a 0 time point.
Generation of random variant target library: The random variant target library was generated using the pHRL-TK vector (Promega). Customized variant primers for the target library were extended and cloned into the NotI and Acc65I digested pHRL-TK vector (see Generation of random variant target library). The variant sequence was designed to be 35 nt  (6 nt flanking on each side of a 23 nt target sequence). The 12 nt of flanking sequence and the N in the PAM sequence of the target were synthesized with custom mixes that were made up of 25% adenine (A), 25% thymine (T), 25% cytosine (C), or 25% guanine (G). The 22 bps sequence of unc-22A and ps4 were synthesized with custom mixes designed to produce a 10% variant rate at each position (3.3% of each variant base), although, the ps4 library has a unexpectedly high variant rate at two positions.The initial oligonucleotide library preparations were extended using NEB ThermoPol Taq polymerase and primer AF-KLA-87. Reaction tubes with 100 pM of each primer in 25 ul dH2O and 2.5 ul of 10X Taq ThermoPol buffer (20 mM Tris-HCl, 10 mM KCl, 2 mM MgSO4, 10mM (NH4)2SO4 , 0.1% Triton® X-100, pH 8.8) is put in a beaker of boiling water for 5 minutes and removed from heat and allowed to cool at 45° C. The primer mix is then diluted by adding 5ul of 25 mM dNTPs, 210 ul of 1X Taq buffer, and 10 ul of NEB Taq polymerase. Extension is then allowed for 15 minutes at 72° C, with extension stopped by adding 180 ul of (1.9 NH4OAc, 19 mM EDTA, 0.38% SDS), and 1.5 ug of GlycoBlue. Following extractions with phenol/chloroform (1:1) and chloroform, and ethanol precipitation, the resulting material was resuspsended in 40 ul of TE, digested with NEB NotI+Acc65I purified following electrophoresis on a 1.5% agarose gel, and ligated into the NotI and AccI65 digested recipient vector using NEB Quick ligation. Following transformation of library efficiency DH5α cells (Invitrogen), plating on pre-warmed 15 cm plates, colonies were grown overnight at 37° C then moved and incubated at 30° C for 24 hrs. Approximately 5000 colonies were scraped off of agar plates into 10 mls of 2XTY. The 10 mls of cells were pelleted and prepped using Qiagen Midi plasmid prep kit.


title: 3g-con_S23_L001_R1_001_AF_SOL_513


title: 3e-con_S21_L001_R1_001_AF_SOL_513


title: 3d-con_S20_L001_R1_001_AF_SOL_513


title: 3f-con_S22_L001_R1_001_AF_SOL_513


title: 2d-lo_S12_L001_R1_001_AF_SOL_513


title: 2c-lo_S11_L001_R1_001_AF_SOL_513


title: 3c-con_S19_L001_R1_001_AF_SOL_513


title: Suz12GTd5-1_RRBS

status: Public on Nov 17 2014

city: Cambridge

first: Laurie

middle: A

last: Boyer

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
The sequencing data were analyzed as previously described (Gu et al., 2011).
Reads were mapped against an in-silico modified mouse genome (UCSC mm9, with inferred MspI restriction and genome-wide conversion of C to T and G to A) using maq (v 0.7.1-9) with the parameters  -D -s 0 -M c -e 100 C.
Read pileups were obtained using samtools mpileup, and for each CpG position, the number of reads bearing a modified or unmodified read was tallied and summed across the dinucleotide, and the fraction methylated was used for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: For each CpG position with at least one sample with 10x coverage, # of methylated C / number of bases are reported, summed over the CpG motif on both strands. The file is organized as chromosome, position, dinucleotide, and for each sample #modified Cs:coverage

organism: Mus musculus

source_name: in vitro differentiated cells

growth_protocol: ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates.  Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Before collection or in vitro differentiation, cells were briefly plated on non-gelatinized tissue culture plates to remove MEFs.

extract_protocol: Reduced representation bisulfite sequencing was performed as published (Gu et al., 2011) and sequenced on an Illumina Hi-Seq.

tag: cell line

tag: cell type

value: day 5 of Spinal Motor Neuron in vitro directed differentiation

tag: background

tag: replicate number

tag: differentiation

value: ESCs were subjected to Spinal motor Neuron in vitro directed differentiation as previously described (Wichterle and Peljto, 2008). Cells were collected at day 5.


title: 2a-lo_S9_L001_R1_001_AF_SOL_513


title: 2b-lo_S10_L001_R1_001_AF_SOL_513


title: 1h-lo_S8_L001_R1_001_AF_SOL_513


title: 9h-con-lin_S60_L001_R1_001_AF_SOL_515

source_name: unc-22A library RML-1


title: 1g-lo_S7_L001_R1_001_AF_SOL_513


title: 9g-con-lin_S59_L001_R1_001_AF_SOL_515


title: 9a-lo-180-lin_S55_L001_R1_001_AF_SOL_515


title: 1b-lo-420_S2_L001_R1_001_AF_SOL_550


title: 9b-lo-180-lin_S56_L001_R1_001_AF_SOL_515


title: 8d-lo-12-lin_S52_L001_R1_001_AF_SOL_515


title: 8e-lo-48-lin_S53_L001_R1_001_AF_SOL_515


title: 8f-lo-48-lin_S54_L001_R1_001_AF_SOL_515


title: 8b-lo-12-lin_S50_L001_R1_001_AF_SOL_515


title: 8c-lo-12-lin_S51_L001_R1_001_AF_SOL_515


title: 8a-lo-12-lin_S49_L001_R1_001_AF_SOL_515


title: 7h-lo-3-lin_S48_L001_R1_001_AF_SOL_515


title: 7g-lo-3-lin_S47_L001_R1_001_AF_SOL_515


title: 7e-lo-3-lin_S45_L001_R1_001_AF_SOL_515


title: 6d-lo-1-lin_S36_L001_R1_001_AF_SOL_515


title: 6c-lo-1-lin_S35_L001_R1_001_AF_SOL_515


title: 5h-lo-0-lin_S34_L001_R1_001_AF_SOL_515


title: 5g-lo-0-lin_S33_L001_R1_001_AF_SOL_515


title: E14d5-1_RRBS

value: E14 wild type


title: 5g-lo-48_S39_L001_R1_001_AF_SOL_514

source_name: unc-22A library RML-A


title: 6b-lo-48_S42_L001_R1_001_AF_SOL_514


title: 5h-lo-48_S40_L001_R1_001_AF_SOL_514


title: 6c-lo-12_S43_L001_R1_001_AF_SOL_514


title: 6d-lo-12_S44_L001_R1_001_AF_SOL_514


title: 5e-lo-48_S37_L001_R1_001_AF_SOL_514


title: 5f-lo-48_S38_L001_R1_001_AF_SOL_514


title: 7f-lo-3-lin_S46_L001_R1_001_AF_SOL_515


title: 5a-lo-12_S33_L001_R1_001_AF_SOL_514


title: 4h-lo-3_S32_L001_R1_001_AF_SOL_514


title: 4g-lo-3_S31_L001_R1_001_AF_SOL_514


title: 4d-lo-3_S28_L001_R1_001_AF_SOL_514


title: 4e-lo-3_S29_L001_R1_001_AF_SOL_514


title: 4f-lo-3_S30_L001_R1_001_AF_SOL_514


title: 4a-con_S25_L001_R1_001_AF_SOL_514


title: 4b-con_S26_L001_R1_001_AF_SOL_514


title: 3h-con_S24_L001_R1_001_AF_SOL_514


title: 3g-con_S23_L001_R1_001_AF_SOL_514


title: 3f-con_S22_L001_R1_001_AF_SOL_514


title: 3e-con_S21_L001_R1_001_AF_SOL_514


title: 5c-lo-12_S35_L001_R1_001_AF_SOL_514


title: 6a-lo-48_S41_L001_R1_001_AF_SOL_514


title: 3d-con_S20_L001_R1_001_AF_SOL_514


title: 3c-con_S19_L001_R1_001_AF_SOL_514


title: 5b-lo-12_S34_L001_R1_001_AF_SOL_514


title: 9b-con-9ng_S60_L001_R1_001_AF_SOL_516


title: 5d-lo-12_S36_L001_R1_001_AF_SOL_514


title: 7g-con-40ng_S51_L001_R1_001_AF_SOL_516


title: 7h-con-40ng_S52_L001_R1_001_AF_SOL_516


title: 5d-lo-180-40ng_S34_L001_R1_001_AF_SOL_516


title: 7e-con-40ng_S49_L001_R1_001_AF_SOL_516


title: 7f-con-40ng_S50_L001_R1_001_AF_SOL_516


title: 4h-lo-180-40ng_S30_L001_R1_001_AF_SOL_516


title: 5c-lo-180-40ng_S33_L001_R1_001_AF_SOL_516


title: 9a-con-9ng_S59_L001_R1_001_AF_SOL_516


title: 4f-lo-360-9ng_S28_L001_R1_001_AF_SOL_516


title: 4e-lo-360-9ng_S27_L001_R1_001_AF_SOL_516


title: 4b-lo-360-9ng_S26_L001_R1_001_AF_SOL_516


title: 3b-lo-180-9ng_S18_L001_R1_001_AF_SOL_516


title: 4a-lo-360-9ng_S25_L001_R1_001_AF_SOL_516


title: 4c-lo-3_S27_L001_R1_001_AF_SOL_514


title: 9c-con-9ng_S61_L001_R1_001_AF_SOL_516


title: 2f-lo-180-9ng_S14_L001_R1_001_AF_SOL_516


title: 3a-lo-180-9ng_S17_L001_R1_001_AF_SOL_516


title: 2g-lo-180-9ng_S15_L001_R1_001_AF_SOL_516


title: 2e-lo-180-9ng_S13_L001_R1_001_AF_SOL_516


title: 1f-lo-3-9ng_S6_L001_R1_001_AF_SOL_516


title: 2c-lo-3-40ng_S11_L001_R1_001_AF_SOL_516


title: 2d-lo-3-40ng_S12_L001_R1_001_AF_SOL_516


title: 1e-lo-3-9ng_S5_L001_R1_001_AF_SOL_516


title: Prmt5 KO4

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description: Sample 8

library_source: transcriptomic

data_processing:
Reads were processed and aligned with the Lifescope 2.5 genomic analysis software (http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/ngs-data-analysis-software/lifescope.html).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Read counts per ENSEMBL transcript (ENSEMBL 74)

molecule: total RNA

source_name: Prmordial germ cell (E11.5)

extract_protocol:
Primordial germ cells from E11.5 dpc control and prmt5 germ cell specific knockout embryo that harbors dPE_Oct4 GFP reporter were sorted by FACs and total RNA was extracted using picopure RNA extraction kit.
RNA libraries prepared from 50 pg of total RNA using published protocol (Tang F et al.,2010, Nat Protoc 5:516-35)

tag: strain

value: C57BL/6 &129 mixed background

value: primordial germ cells

tag: age

value: E11.5 dpc

tag: genotype


title: 1d-lo-3-9ng_S4_L001_R1_001_AF_SOL_516

data_processing:
turn fastq to fasta
Computational Methods: Calculation of retention and normalization: We use the log2 of retention in the PCR pool as a measure of target cleavage by Cas9, with a retention score calculated for each sequence in each experiment.
For each sequence 'X': Retention[X]=
log2(RepresentationX[Cleaved Library]/RepresentationX[Uncleaved Library])
Representationx in a library gives the ratio between:
[Instances of sequence X in the library]/[Instances of a reference population in the library]
As reference populations we used either an aggregate of all sequences with 4-7 mismatches to the original trigger, or (for the unc-22A library) an "internal control" population comprising a subset of plasmids from the protospacer 4 library.  Comparable results were obtained with these two references for normalization.
Each line of the fasta file is a read of a sequence from the library experiments. First unique sequences were identified then each unique sequence and only sequences with a 50 count minimum in the control experiment from the sequencing run was considered in the library analysis. The numbers are normalized and the retention score is calculated (see above).
Processed data 'dat' files contain the calculated final retentions for each experiment. Each experiment labeled:'AF_SOL_###_t###'. 'AF_SOL_###' corresponds to the experiment run ID and 't###' corresponds to the incubation time of the experiment. For example AF_SOL_513_t360, corresponds to experiment 513 on the protospacer 4 guide and DNA target and the incubation time was 360 mins. The experimental conditions and ID can be found in the associated publication.

Supplementary_files_format_and_content: 'dat' files containing the calculated final retentions for each experiment


title: Prmt5 KO1

description: Sample 5


title: Prmt5 KO2

description: Sample 6


title: Prmt5 KO3

description: Sample 7


title: Control2

description: Sample 2


title: MacLowKit+Sca1+ replicate 4

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

description: Sample name: R_Kit+Sca1+

data_processing:
Illumina 1.5 software used for basecalling.
RNA-seq reads were mapped to mm10 using TopHat version 2.0.4.
FPKMs were calculated by Cuffdiff, minimum alignment count = 10, false discovery rate = 0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: NRASG12V/Mll-AF9 AML cells

extract_protocol:
Rneasy from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

value: (FVB/n X C57/BL/6J) F1

tag: genotype/variation

value: AML cells

tag: cell sorting


title: MacLowKit+Sca1+ replicate 3

description: Sample name: 26_Kit+Sca1+


title: MacLowKit+Sca1+ replicate 2

description: Sample name: 12_Kit+Sca1+


title: Control4

description: Sample 4


title: MacLowKit+Sca1+ replicate 1

description: Sample name: 11_Kit+Sca1+


title: MacLowKit+Sca1- replicate 2

description: Sample name: 26_Kit+Sca1-


title: MacLowKit-Sca1- replicate 5

description: Sample name: R_Kit-Sca1-


title: MacLowKit+Sca1- replicate 3

description: Sample name: L_Kit+Sca1-


title: MacLowKit-Sca1- replicate 4

description: Sample name: L_Kit-Sca1-


title: MacLowKit+Sca1- replicate 5

description: Sample name: R_Kit+Sca1-


title: MacLowKit-Sca1- replicate 1

description: Sample name: 11_Kit-Sca1-


title: 4g-lo-180-40ng_S29_L001_R1_001_AF_SOL_516


title: MacLowKit-Sca1- replicate 3

description: Sample name: 26_Kit-Sca1-


title: MacHigh replicate 3

description: Sample name: L_MacHigh

value: MacHigh


title: MacHigh replicate 2

description: Sample name: 26_MacHigh


title: MacHigh replicate 5

description: Sample name: R_MacHigh


title: MacHigh replicate 1

description: Sample name: 11_MacHigh


title: unsorted replicate 5

description: Sample name: R_unsorted

value: unsorted


title: MacHigh replicate 4

description: Sample name: N_MacHigh


title: unsorted replicate 4

description: Sample name: N_unsorted


title: Control3

description: Sample 3


title: Control1

description: Sample 1


title: unsorted replicate 1

description: Sample name: 12_unsorted


title: unsorted replicate 3

description: Sample name: L_unsorted


title: unsorted replicate 2

description: Sample name: 26_unsorted


title: 2h-lo-180-9ng_S16_L001_R1_001_AF_SOL_516


title: RNA-Seq WT-Rep2

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

data_processing:
We aligned reads to the mouse mm10 genome with TopHat2 v2.0.12 using default parameters.
We calculated raw read counts in mouse RefSeq genes from the BAM files with HTseq-count v0.6.0 using default parameters.
We then used DESeq2 v1.4.5 to identify differentially expressed genes between WT and KO samples using default parameters. Normalized counts were calculated with the ‘counts’ function of DESeq2.
sample_supplementary_files_format_and_content: We provide a tab-delimited matrix table that contains raw read counts in RefSeq genes calculated by HTseq-count, as well as normalized read counts, fold change of expression and adjusted p-values calculated by DESeq2.
Genome_build: mm10

source_name: E8.5 whole embryos

extract_protocol:
Total RNA was extracted from the embryos with the RNeasy Protect Mini Kit (Qiagen).
RNA-Seq libraries were prepared from 500 ng of total RNA using ribosomal RNA depletion with the Ribo-Zero Gold kit (Epicentre) and the TruSeq Stranded Total RNA Sample preparation kit (Illumina) according to the manufacturer’s instructions.

tag: embryo stage

value: wild type


title: RNA-Seq 3BKO-Rep3


title: RNA-Seq 3BKO-Rep2


title: RNA-Seq WT-Rep3


title: MacLowKit+Sca1- replicate 1

description: Sample name: 11_Kit+Sca1-


title: MacLowKit+Sca1- replicate 4

description: Sample name: N_Kit+Sca1-


title: RNA-Seq 3BKO-Rep1


title: MacLowKit-Sca1- replicate 2

description: Sample name: 12_Kit-Sca1-


title: RRBS E11.5_3BKO-Rep2

data_processing:
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired.
We aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
sample_supplementary_files_format_and_content: We provide .igv files containing methylation scores calculated for all CGs with at least 8x sequencing depth.
Genome_build: mm10

source_name: E11.5 limbs

extract_protocol:
Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction.
We prepared RRBS libraries using a published protocol (Gu et al., Nat Protoc 6:468-81, 2011) with some modifications. Briefly, we digested 25-100 ng of genomic DNA 5 hours with MspI (Fermentas), followed by end-repair and A-tailing (Klenow fragment, Fermentas), and ligation to methylated adapters (T4 DNA ligase, Fermentas) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR.

tag: gender

value: female


title: RRBS E11.5_WT-Rep2


title: RRBS E11.5_WT-Rep1


title: DKO H3K4me3 (at 24 month age) rep3

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description:
technical replicate of biological replicate 2
dko_H3K4me3.peaks.bed

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using SOAP with 2 mismatches allowed; H3K4me3 and H3K36me3 are processed by MACS and H3K27me3 are processed by SICER for peak calling. Different replicates are accepted by the peak calling programs to generate one set of peaks for each condition.
Genome_build: mm9
Supplementary_files_format_and_content: BED format with 1-3 columns as chromosome, start, end. The 4th column for sicer.bed is read count. The 4th and 5th columns for peaks.bed are MACS peak id and pvalue.

source_name: Hematopoietic stem cells (HSC)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipittaion with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)

value: Murine bone marrow derived primary HSCs

tag: cell surface marker

tag: chip antibody

value: Millipore 07-473


title: SKO H3K36me3 (at 24 month age) rep2

description:
technical replicate of biological replicate 1
sko_H3K36me3.peaks.bed

value: Millipore 07-549


title: DKO H3K4me3 (at 24 month age) rep1

description:
technical replicate of biological replicate 1
dko_H3K4me3.peaks.bed


title: DKO H3K27me3 (at 24 month age) rep2

description:
technical replicate of biological replicate 2
dko_H3K27me3.sicer.bed

value: Millipore 07-449


title: DKO H3K27me3 (at 24 month age) rep3


title: DKO H3K4me3 (at 24 month age) rep2


title: SKO H3K27me3 (at 24 month age) rep1

description:
technical replicate of biological replicate 2
sko_H3K27me3.sicer.bed


title: DKO H3K27me3 (at 24 month age) rep1

description:
technical replicate of biological replicate 1
dko_H3K27me3.sicer.bed


title: IDGSW3_PTH_rep3_d35

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
TopHat with default settings and sample type "fr-secondstrand" for directional libraries
ArrayStar (DNASTAR) with default RNA sequencing settings.  Imported BAM files from TopHat output.
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated text files include RPKM values for each sample

Vehicle (control) data were submitted previously and are available in:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1323967
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1323968
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1323969

source_name: IDG-SW3 cell line (osteocytic)

growth_protocol: Custom αMEM powdered tissue culture medium was purchased from Cellgro (Manassas, VA) and supplemented with 2.20g/L NaHCO3 (S233-3) (Fisher Scientific, Waltham, MA). Fetal Bovine Serum (FBS) (SH30396) was purchased from HyClone (Logan, Utah) and heat inactivated by incubation at 55°C for 30 minutes. Penicillin-Streptomycin Solution (SV30010) was purchased from Fisher Scientific, (Waltham, MA) and recombinant mouse interferon-gamma (rmIFN-γ) from Gibco/Invitrogen (Camarillo, CA). 10cm and 6 well collagen IV coated plates were purchased from BD Biosciences (San Jose, CA). IDG-SW3 cells (6) were expanded in 10cm collagen coated at 33°C in αMEM with 10% heat inactivated FBS, 100 units/mL penicillin/streptomycin, and 50U/mL IFNγ.  Cells were harvested with 0.05% Trypsin/0.53mM EDTA (Fisher Scientific, Waltham, MA) and plated in 6 well collagen coated plates at 40,000 cells/cm2. To induce osteocytogenesis, two days after plating, cells were transferred to 37°C and media was changed to osteogenic media (αMEM with 10% heat inactivated FBS, 100 units/mL penicillin/streptomycin, 50μg/mL ascorbic acid (A4034, Sigma, St. Louis, MO) and 4mM β-glycerol phosphate (G9422, Sigma, St. Louis, MO) without IFNγ. Osteogenic media was changed three times weekly.

extract_protocol:
RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH) with an additional LiCl extraction. Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions
Directional RNA-seq libraries were prepared with the Epicentre (Madison, WI) ScriptSeq v2 RNA-seq Library Preparation Kit per manufacturer’s instructions.  Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Cells were treated with 100nM of PTH for 24 hours prior to RNA harvesting.

value: osteocytic cells

tag: differentiation day


title: RNA-Seq WT-Rep1


title: pCREB_Fsk_rep1_MC3T3-E1

description: ChIP-DNA

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: fastq files are the raw sequence files [barcoded lanes (4 each) were concatenated for each sample for simplicity, no other modification was made], bedGraph files are for display in the UCSC genome browser, ChIP-seq peak files are the *.bed files
Supplementary_files_format_and_content: Input data was submitted previously and is available in GSM1027508 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1027508)

source_name: MC3T3-E1 (pre-osteoblast)

growth_protocol: MC3T3-E1 cells were cultured in alpha MEM with 10% heat-inactivated fetal bovine serum from Hyclone (Logan, UT) and 1% penicillin-streptomycin.

extract_protocol: Chromatin immunoprecipitation was performed as described previously (Meyer MB. Mol Endo. 2012).  Briefly, MC3T3-E1 cells were treated for 1 hour with vehicle or 100nM forskolin.  Samples were subjected to immunoprecipitation using either a control IgG antibody or the indicated experimental antibody. For ChIP protocol, please see Meyer MB. Mol Endo. 2012.  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.  ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols. ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina GAIIx [for all samples sequenced before June, 2011] or the Illumina HiSeq2000 [after June, 2011] sequencers by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver. 3) on an Illumina cBot (Illumina) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver. 3).  Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  Each ChIP sample was repeated in biological replicate in the same manner (minimum of 2 replicates).  Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Cells were treated with 100nM fsk or with DMSO vehicle [Veh] for 1 hours prior to ChIP assay

value: pre-osteoblast

tag: antibody

value: pCREB (Millipore, Ser 133, 06-519)


title: IDGSW3_PTH_rep1_d35


title: pCREB_Fsk_rep2_MC3T3-E1

description: ChIP-DNA


title: pCREB_Veh_rep1_MC3T3-E1

description: ChIP-DNA


title: RRBS E10.5-Rep1

data_processing:
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired.
We aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: We provide .igv files containing methylation scores calculated for all CGs with at least 8x sequencing depth.

source_name: E10.5 whole embryos

value: mixed

value: WT


title: RRBS E8.5_3BKO-Rep2


title: RRBS_Sperm-Rep1

source_name: Sperm

value: Adult

value: male


title: RRBS_Sperm-Rep2


title: RRBS E10.5-Rep2


title: RRBS_Ad Liver

source_name: Adult liver


title: RRBS E11.5_3BKO-Rep1


title: RRBS E8.5_3AKO-Rep2


title: RRBS E8.5_WT-Rep1


title: IDGSW3_PTH_rep2_d35


title: RRBS E7.5

source_name: E7.5 epiblasts


title: RRBS E8.5_3AKO-Rep1


title: RRBS E5.5

source_name: E5.5 epiblasts


title: RRBS E8.5_WT-Rep2


title: RRBS E8.5_3BKO-Rep1


title: Run1 Sepsis T0 n37

city: Camperdown

first: David

middle: Graeme

last: Hancock

state: NSW

address: Building 93, RPAH, Missenden Road

country: Australia

institute: Centenary Institute

data_processing:
Raw basecall data was converted to FASTQ sequence files using Off-Line Basecaller 1.9.4 (Ilumina) and a custom Perl script.
Reads were aligned to the hg19 human genome with TopHat version 2.06 and Bowtie2 2.0.0-beta6
Reads were initially mapped to Ensembl transcripts with the search for novel junctions disabled. Genomic coordinates were then transformed into counts of protein-coding Ensembl genes. To do this, a chimeric gene-model was first defined by merging all protein-coding transcripts for a given gene. Transcripts that had reads in less than 50% of their exons in all samples were defined as not expressed and were excluded from the chimeric transcriptome.
Reads that overlapped the chimeric genes were counted using the htseq-count script in the intersection-nonempty mode (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). The script discards multi-mapped reads as well as reads that overlap multiple distinct genes, to generate a file of uniquely mapped gene counts.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited csv files includes mapped count values for each Sample

organism: Homo sapiens

source_name: whole blood_Sepsis T0

extract_protocol:
Blood was collected in EDTA tubes at the time of initial blood culture, and immediately placed on ice. Plasma and buffy coat were separated and two 1-ml aliquots transferred into bar-coded cryovials at -20oC until they were transferred to a secure, alarmed -80oC freezer.
cDNA libraries were prepared from total RNA according to the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero sample preparation guide (Illumina). Unique adapter indexes (Illumina) were attached during sample prep and samples were run pooled and loaded into a single flow cell lane to reduce technical variability.

tag: tissue

value: whole blood

tag: group

value: Sepsis T0

tag: organ failure count

tag: cardiovascular failure

value: Yes

tag: liver failure

value: No

tag: aki

tag: coagulation failure

tag: respiratory failure

tag: sirs signs

tag: culture positive


title: RRBS E8.5_WT-Rep3

tag: genotype/variation

tag: strain


title: RRBS E4.5

source_name: E4.5 blastocysts

tag: embryo stage

tag: gender


title: SKO H3K4me3 (at 24 month age) rep3

description:
technical replicate of biological replicate 1
sko_H3K4me3.peaks.bed

tag: cell type

tag: cell surface marker

tag: chip antibody


title: Run1 Control n10

source_name: whole blood_Control T0

tag: tissue

value: Control T0


title: Run1 Control n11

tag: group


title: Run1 No Sepsis T0 n32

source_name: whole blood_No Sepsis T0

value: No Sepsis T0

tag: organ failure count


title: Run1 No Sepsis T0 n33

tag: cardiovascular failure


title: Run1 Sepsis T0 n36

tag: liver failure


title: Run1 No Sepsis T0 n34

tag: aki


title: Run1 Sepsis T0 n31

tag: coagulation failure


title: Run1 No Sepsis T0 n35

tag: respiratory failure


title: Run1 Sepsis T0 n34

tag: sirs signs


title: Run1 Sepsis T0 n33

tag: culture positive


title: Run1 Sepsis T0 n30


title: Run1 No Sepsis T0 n31


title: RRBS E6.5

source_name: E6.5 epiblasts

tag: genotype/variation


title: Run1 Sepsis T0 n35


title: Run1 Sepsis T0 n29


title: Run1 No Sepsis T0 n30


title: Run1 Sepsis T0 n27


title: RRBS E3.5

source_name: E3.5 blastocysts

tag: strain


title: Run1 Sepsis T0 n28


title: Run1 No Sepsis T0 n29


title: Run1 Control n8


title: Run1 Sepsis T0 n23


title: Run1 Sepsis T0 n25


title: Run1 Control n9


title: Run1 Sepsis T0 n26


title: Run1 No Sepsis T0 n28


title: Run1 Sepsis T0 n22


title: Run1 Sepsis T0 n24


title: Run1 No Sepsis T0 n27


title: Run1 Sepsis T0 n32


title: Run1 Sepsis T0 n20


title: Run1 Sepsis T0 n21


title: Run1 No Sepsis T0 n25


title: Run1 Sepsis T0 n19


title: Run1 No Sepsis T0 n26


title: Run1 Control n7


title: Run1 Control n6


title: Run1 Control n4


title: Run1 No Sepsis T0 n24


title: Run1 Control n5


title: Run1 No Sepsis T0 n23


title: Run1 No Sepsis T0 n22


title: Run1 No Sepsis T0 n21


title: Run1 Sepsis T0 n16


title: Run1 Sepsis T0 n13


title: Run1 Sepsis T0 n15


title: Run1 Sepsis T0 n14


title: Run1 No Sepsis T0 n19


title: Run1 Control n3


title: Run1 No Sepsis T0 n18


title: Run1 No Sepsis T0 n15


title: Run1 No Sepsis T0 n16


title: Run1 No Sepsis T0 n20


title: Run1 No Sepsis T0 n17


title: Run1 Sepsis T0 n18


title: Run1 No Sepsis T0 n12


title: Run1 No Sepsis T0 n10


title: Run1 No Sepsis T0 n11


title: Run1 Control n1


title: Run1 Sepsis T0 n11


title: Run1 No Sepsis T0 n14


title: Run1 Control n2


title: Run1 No Sepsis T0 n9


title: Run1 Sepsis T0 n17


title: Run1 No Sepsis T0 n7


title: Run1 Sepsis T0 n9


title: Run1 No Sepsis T0 n8


title: Run1 Sepsis T0 n8


title: Run1 No Sepsis T0 n5


title: Run1 No Sepsis T0 n13


title: Run1 Sepsis T0 n6


title: Run1 Sepsis T0 n5


title: Run1 Sepsis T0 n4


title: Run1 No Sepsis T0 n4


title: Run1 Sepsis T0 n2


title: Run1 Sepsis T0 n12


title: Run1 Sepsis T0 n3


title: Run1 No Sepsis T0 n2


title: Run1 No Sepsis T0 n1


title: Run1 Sepsis T0 n10


title: Run1 Sepsis T0 n1


title: Run1 Sepsis T0 n7


title: lncap_siFOXA1_dht10nM_24h_AR

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description: Sample 29

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.16.
Signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5)
Genome_build: hg18
Supplementary_files_format_and_content: Bed files reporting peaks can be visualized by Integrative genomic viewer ver 2.2 (IGV ver 2.2)

source_name: prostate cancer cells

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS. VCaP cells were cultures in DMEM containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free DMEM/RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.  Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).  The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: LNCaP or VCaP cells were treated with vehicle or DHT 10 nM for 24 h or 1h.

tag: cell line

value: LNCaP

tag: treatment

value: FOXA1 K.D/DHT 10 nM

value: AR (Santa Cruz, catalog # H-280)


title: lncap_24h_input4

description: Sample 30

value: DHT 10 nM

value: none (input)


title: vcap_24h_input_DHT2

description: Sample 25

value: VCaP

value: ethanol (Vehicle)


title: lncap_et_24h_FOXA1

description: Sample 28

value: FOXA1 (Abcam, catalog # ab23738)


title: lncap_24h_input3

description: Sample 22


title: vcap_Ethanol_10nM_24h_AR

description: Sample 24


title: lncap_dht10nM_24h_AR

description: Sample 21


title: lncap_dht10nM_24h_K4me3

description: Sample 20

value: K4me3 (Millipore, catalog# 17-614)


title: lncap_dht10nM_24h_K4me1

description: Sample 19

value: K4me1 (Abcam, catalog# ab8895)


title: lncap_24h_input2

description: Sample 18


title: pCREB_Veh_rep2_MC3T3-E1

description: ChIP-DNA

tag: cell type

value: pre-osteoblast

tag: antibody

value: pCREB (Millipore, Ser 133, 06-519)


title: lncap_dht10nM_24h_AcH3

description: Sample 17

tag: chip antibody

value: AcH3 (Millipore, catalog # 06-599)


title: Run1 No Sepsis T0 n3

tag: tissue

value: whole blood

value: Yes


title: Run1 No Sepsis T0 n6

tag: group

value: No


title: UPF1b

city: PARIS

first: Herve

last: LE HIR

address: 46 rue d'Ulm

department: Functional Genomics

institute: IBENS

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads that do not pass the Illumina quality filter were firstly discarded. The remaining mRNA-seq reads were mapped to the human genome (hg19) using TopHat v.2.08. Ensembl65 annotations were provided to TopHat (-G option). Alignments with reads that matches multiple positions on the genome were removed
From the mapped reads and the GTF annotation files (Ensembl65), we counted the number of reads for each gene using htseq-count. To normalize the read counts and perform differential gene expression analysis, we used the DESeq package.
We used two different softwares to perform differential exon usage analysis: MISO and DiffSplice. See methods from Wang et al. Genome Biology for details.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include differential expression results from DESeq and differential exon usage from MISO and DiffSplice

source_name: HeLa Cervical cancer cells

growth_protocol: HeLa cells were grown in DMEM with 10% FCS

extract_protocol:
Total RNAs are extracted using TRI-reagent following manufactuer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA treatment with 10nM siRNA using RNAimax for 2 days before collecting.

value: HeLa

tag: condition

value: UPF1 siRNA


title: MLNb

value: MLN51 siRNA


title: MLNa


title: eIF4A3b

value: eIF4A3 siRNA


title: Y14a

value: Y14 siRNA


title: Y14b


title: eIF4A3a


title: lncap_dht10nM_24h_AR_-2

description: Sample 26

value: LNCaP

value: DHT 10 nM

value: AR (Santa Cruz, catalog # H-280)


title: GFPb

value: GFP siRNA


title: GFPa


title: vcap_24h_input_Et

description: Sample 16

value: VCaP

value: ethanol (Vehicle)

value: none (input)


title: vcap_dht10nM_24h_FOXA1

description: Sample 14

value: FOXA1 (Abcam, catalog # ab23738)


title: vcap_et_24h_FOXA1

description: Sample 15


title: vcap_DHT_10nM_24h_AR-2

description: Sample 23


title: lncap_dht10nM_24h_FOXA1

description: Sample 27


title: vcap-siFOXP1_dht10nM_24h_AR

description: Sample 12

value: FOXP1 K.D/DHT 10 nM


title: vcap-siRUNX1_dht10nM_24h_AR

description: Sample 13

value: RUNX1 K.D/DHT 10 nM


title: vcap_dht10nM_24h_RUNX1

description: Sample 10

value: RUNX1 (Abcam, catalog# ab23980)


title: lncap_1h_input

description: Sample 5


title: lncap_24h_input

description: Sample 6


title: vcap_24h_input_DHT

description: Sample 8


title: lncap_EtOH_24h_CTBP2

description: Sample 4

value: CTBP2 (Abcam, catalog # 96107)


title: vcap_dht10nM_24h_FOXP1

description: Sample 9

value: FOXP1 (Antibody produced in our laboratory)


title: lncap_dht10nM_24h_CTBP2

description: Sample 2


title: lncap_EtOH_1h_CTBP1

description: Sample 3

value: CTBP1 (BD bioscience, catalog #612942)


title: vcap_dht10nM_24h_AR

description: Sample 7


title: vcap-siFOXA1_dht10nM_24h_AR

description: Sample 11

value: FOXA1 K.D/DHT 10 nM


title: UPF1a

value: HeLa

value: UPF1 siRNA


title: lncap_dht10nM_1h_CTBP1

description: Sample 1

value: LNCaP


title: CR4 FA2 long p5

city: Stony Brook

first: Yuanhao

last: Zhang

address: AMS Department,Stony Brook University

department: Applied Mathematics and Statistics

institute: Stony Brook University

data_processing:
Image processing and basecalling were performed as the runs progressed with Illumina’s Real Time Analysis (RTA) software.
The sequences were filtered using FASTX-Toolkit to remove sequences with low Phred scores
First 3 base pairs of each read were trimmed
Alignment is done by tophat on hg19.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) was obtained with software cufflinks. The genome annotation files were downloaded from ncbi ftp in gff format.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with FPKM value

source_name: CR tumor specimens were obtained from SBU patients

growth_protocol: Dissociated human cancer cells were grown either as adherent to type I collagen or as floating spheroids in 3D cultures the Ultra-Low Attachment (ULA) 6-well plate (Corning, Lowell, MA) in serum-free Mesenchymal Stem Cell Growth Medium (MSCGM; Lonza) or Stemline Pluripotent Culture Medium (SPCM; Sigma-Aldrich).  The FA-depleted cell suspensions were resuspended in standard McCoy medium supplemented with 10% fetal bovine serum (Gibco, USA) and placed either on regular culture dishes or on the type I collagen-coated ones. The CD133high/CD44high cells (4-5 × 103 cells/well were seeded onto the type I collagen-coated 6-well plates, and the experiments were initiated 24 h later, upon sub-confluency.

extract_protocol:
RNA was isolated according to the manufacturer protocol (Qiagen)
Libraries for NGS were generated using 1 microgram of total RNA. The RNA quality was assessed with an Agilent Bioanalyzer. All RNA samples had a RIN above 8. Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA LT kit according to manufacturer recommendations. The quality of each library was evaluated with the Agilent bioanalyzer high sensitivity assay, and quantified by qPCR (Kappa Biosystem, CT). The libraries were pooled together based on the qPCR results, and then the pool was quantified again by qPCR.

value: colorectal cancer tumor

tag: source

value: SBU patients


title: CR4L FA2 long p6


title: CR4 small


title: HMLER_UBF1/2 ChIP-seq

city: East Melbourne

first: Elaine

last: Sanij

state: VIC

address: 1 St Andrews Place

department: Research

institute: Peter MacCallum Cancer Centre

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the mm9 and hg19 genome assemblies using BWA with default parameters
Duplicates were removed using Picard MarkDuplicates
peaks were called using MACS1.4 using default parameters except keep.dup=T
Genome_build: mm9, hg19
Supplementary_files_format_and_content: peak file (txt) generated by MACS

source_name: HMLER

growth_protocol:
NIH3T3 were growin in DMEM supplemented in 10% FBS. HMEC and HMLER cells were growin in HuMEC ready medium (12752010, life technologies).  10 million of exponentially growing cells were harvested for ChIP.
HMEC and HMLER cells were growin in HuMEC ready medium (12752010, life technologies) . 10 million of exponentially growing cells were harvested for ChIP

extract_protocol:
Standard ChIP protocol as reported in Sanij et al, J Cell Biol, 2008
Libraries were prepared using Illumina ChIP-seq DNA sample preparation kit as per manufacturer's instruction

value: HMLER

value: HMLER, an isogenic HMEC-derived cell line expressing the SV40 large-T, TERT, and an oncogenic allele of the HRAS gene (expressing HRASV12G)

value: anti-UBF1/2 rabbit polyclonal

tag: chip antibody ref.

value: Sanij et al., J Cell Biol, 2008


title: DMS_averages_3

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description: purified 18S ribosomal RNA

data_processing:
Base-calling by Illumina
Raw data processing was carried out using tools described in the pyCRAC software package (Webb, Hector, Kudla and Granneman, submitted; https://bitbucket.org/sgrann/pycrac)
The pyBarcodeFilter tool was used to split reads based on barcoded indexes
PyFastqDuplicateRemover was used to remove potential PCR duplicates using random nucleotide information in the 5’ adapter sequence
pyPileup was used to generate count data for the genes of interest
Genome_build: Reads were mapped to the Saccharomyces cerevisiae 35S gene (RDN37-1) using Novoalign version 2.07
Supplementary_files_format_and_content: The Average_drop_off_rates.txt file is a tab-delimited file of average sample drop-off rates at each nucleotide in the yeast 18S rRNA. The drop-off rate is defined as  the total number of reads that stop at a nucleotide divided by the total number of reads covering that nucleotide.

organism: Saccharomyces cerevisiae

source_name: total RNA isolated from culture

growth_protocol: S.cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) or YPG/R (YP with 2% Galactose and 2% Raffinose) at 30ºC.

extract_protocol:
Immunoprecipitations with HTP-and TAP-tagged proteins were performed with TNM150 buffer (50 mM Tris-HCl pH 7.8, 1.5 mM MgCl2, 150 mM NaCl, 0.1% NP-40 and 5 mM b-mercaptoethanol), essentially as previously described (Granneman et al., 2009). RNA was extracted using a GTC phenol solution (4 M guanidine thiocyanate, 0.05 M Tris at pH 8.0, 0.01 M EDTA, 2% sarcosyl, 1% β-mercaptoethanol, 50% [v/v] phenol) as previously described (Sambrook, 1989).
cDNA libraries were generated from purified ribosomal RNA using an RT oligonucteotide containing random hexamers (SuperScript III, Invitrogen). 5' adapters were ligated on (CircLigase II, EpiCentre) and 3' adaptors generated during PCR amplification.

value: BY4741 with fun12-TAP::K.I.HIS3

value: DMS

tag: sample type

value: purified 18S ribosomal RNA


title: Control_averages_3

description: purified 18S ribosomal RNA

value: control


title: DMS_averages_2

description: purified 18S ribosomal RNA


title: DMS_averages_1

description: purified 18S ribosomal RNA


title: spheroids


title: Control_averages_2

description: purified 18S ribosomal RNA


title: Control_averages_1

description: purified 18S ribosomal RNA


title: gamma8-Notch

city: Fukuoka city

first: Masataka

last: Nakamura

state: Fukuoka prefecture

address: 3-1-1 Maidashi

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
HiSeq control software (HCS) version 2.0.10 was used for basecalling.
ChIP-seq reads were aligned with the mouse reference geneme (mm10) using the bowtie program (v1.0.0) with the following parameters: -m 1 -n 3.
Duplicate reads were removed using the samtools program (v0.1.18).
Peaks were called using the MACS program (v1.4.2) with the following setting: -p 1e-5 --to-large.
Genome_build: mm10
Supplementary_files_format_and_content: Bed files were generated for processed data containing chromosome, regions in which peaks were located and scores calculated with MACS program.

source_name: Primary gd T cells

extract_protocol:
Cellular lysate was prepared by sonication in detergent-containing buffer after fixation with 0.5% formaldehyde at room temperature for 5min, and then DNA/protein complex was obtained by enzymatic digestion.
To repair ChIP-DNA and input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with NEB Next Multiplex Oligos for Illumina (Index Primers Set1).

value: thymus

tag: age

value: post natal day 0-3

tag: genotype

value: wild type

value: Rabbit Notch1 mAb (D1E11, Cell Signaling Technology)

value: gamma delta T cells


title: m6

city: jinan

first: liu

middle: gui

last: fen

state: shandong

address: sangyuan road 8

country: China

institute: Institute of animal science and veterinary medicine Shandong academy of agricultural sciences

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity
or low quality sequence, then mapped to cattle whole genome using SOAPaligner/soap2.
Mismatches no more than 2 bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following PMID: 19528076.
In short, exons from all isoforms of a gene were merged to create one meta-transcript.
The number of reads falling in the exons of this meta-transcript were counted and
normalized by the size of the meta-transcript and by the size of the library.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: txt file includes mRNA name, length, reads number, RPKM, significance analysis

organism: Bos taurus

extract_protocol:
Muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Illumina HiSeq2000 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Angus beef cattle

value: eighteen months

value: muscle


title: 80S_18S_NAI_1

description: purified 18S ribosomal RNA

value: NAI


title: Rio1_20S_NAI_1

description: purified 20S ribosomal RNA

value: BY4741 with rio1-HTP::K.I.URA3

value: purified 20S ribosomal RNA


title: m5


title: 80S_18S_NAI_2

description: purified 18S ribosomal RNA


title: gamma8-input


title: m4


title: m3

value: Chinese Luxi cattle


title: m2


title: m1

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity
or low quality sequence, then mapped to cattle whole genome using SOAPaligner/soap2.
Mismatches no more than 2 bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following PMID: 19528076.
In short, exons from all isoforms of a gene were merged to create one meta-transcript.
The number of reads falling in the exons of this meta-transcript were counted and
normalized by the size of the meta-transcript and by the size of the library.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: txt file includes mRNA name, length, reads number, RPKM, significance analysis


title: Tsr1_20S_DMSO_2

description: purified 20S ribosomal RNA

value: BY4741 with tsr1-HTP::K.I.URA3

value: DMSO


title: Tsr1_20S_DMSO_1

description: purified 20S ribosomal RNA


title: Tsr1_20S_NAI_1

description: purified 20S ribosomal RNA


title: 80S_18S_DMSO_2

description: purified 18S ribosomal RNA

value: BY4741 with fun12-TAP::K.I.HIS3


title: hRetnTg+ Infected 4

city: Riverside

first: Meera

last: Nair

address: 301 SOM Research Building, 900 University Ave.

department: Biomedical Sciences Department

institute: University of California, Riverside

data_processing:
Sequencing, base calling and demultiplexing was done using HiSeq2500 Control Software v2.0.12.0, RTA 1.17.21.3 and CASAVA v1.8.2
Sequenced maps were aligned using QuasR and Rbowtie v1.0.2
RPKM values were measured by taking the (transcript count/width of exon * 1000)/total counts *1e6)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files including raw counts and rpkm values for each sample

source_name: Lung

extract_protocol:
RNA extracted from whole lung tissue using Trizol
RNA-seq libraries were generated using NEBnext Ultra Directional Kit for Illumina

treatment_protocol: Mice were infected with the helminth Nippostrongylus brasiliensis and sacrificed at day 7 for RNA extraction

tag: agent

value: Nippostrongylus brasiliensis

value: hRetnTg+


title: hRetnTg+ Infected 3


title: 80S_3

description: purified 18S ribosomal RNA

value: purified 18S ribosomal RNA


title: 80S_18S_DMSO_1

description: purified 18S ribosomal RNA


title: hRetnTg+ Infected 2


title: hRetnTg+ Infected 1


title: 80S_2

description: purified 18S ribosomal RNA


title: hRetnTg- Infected 4

value: hRetnTg-


title: AtDEK3 OE17-4 input

city: Vienna

first: Sascha

last: Waidmann

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
Sequenced reads were aligned with mismatch cost set to 1 and limit to 7 using CLC Genomics Workbench 5.1. As reference genome, TAIR 10 was used.
Significant binding regions were identified using CLC Genomics Workbench 5.1 with the following settings: window size 150 nt; maximum false discovery rate 10%; shift reads based on fragment length 300 nt.
Peak boundaries were refined and candidate peaks were filtered using two filtering criteria: based on difference in read orientation count 0.4 and on probability of identical locations of forward and reverse reads 0.1.
Peaks were annotated using information from TAIR 10.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Peaks were annotated using information from TAIR 10.

organism: Arabidopsis thaliana

source_name: Arabidopis nuclei

growth_protocol: Arabidopsis seedlings were grown on soil and cultivated in a 16-h-light/8-h-dark regime at 150 µmol m-2 s-1 light intensity and 60% relative humidity for 14 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The libraries were constructed using KAPA Library Preparation Kit Illumina series (#KK8201, KAPA Biosystems). To summarize, 5-10 ng DNA was end-repaired, A bases were added to the 3’ end of the DNA fragments and adapters ligated. The libraries were validated using Agilent Bioanalyzer and DNA concentration was determined by qPCR. Library DNA was captured on an Illumina flowcell for cluster generation and 36-bp single-end sequencing was achieved on a Genome Analyzer IIx (Illumina) following Illumina’s protocol. Each library was sequenced in one lane of the flow cell.

value: AtDEK3 overexpressor

value: seedling

tag: protein tagged

value: CFP-tag

value: input

tag: ecotype


title: 80S_like_2

description: purified 20S ribosomal RNA

tag: strain

value: BY4741 with fun12-TAP::K.I.HIS3 and GAL::3HA-fap7::kanMX4


title: Tsr1_20S_NAI_2

description: purified 20S ribosomal RNA

tag: treatment


title: hRetnTg- Infected 2


title: hRetnTg- Infected 3


title: AtDEK3 OE17-4

value: GFP antibdoy (abcam #290)


title: 80S_like_1

description: purified 20S ribosomal RNA


title: hRetnTg+ Naïve (pooled)

value: none, Naïve


title: 80S_1

description: purified 18S ribosomal RNA


title: AtDEK3 OE3-1 input


title: Rio1_2

description: purified 20S ribosomal RNA

value: BY4741 with rio1-HTP::K.I.URA3


title: hRetnTg- Naïve (pooled)


title: AtDEK3 OE9-1 inout


title: hRetnTg- Infected 1


title: Rio1_3

description: purified 20S ribosomal RNA

value: purified 20S ribosomal RNA


title: AtDEK3 OE3-1


title: AtDEK3 OE9-1


title: Rio1_1

description: purified 20S ribosomal RNA


title: dms4-1 sdr1-1

city: Cold Spring Harbor

first: Wen-Wei

last: Liao

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
BS-seq reads were aligned to the TAIR10 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data (CGmap) is in text format containing methylation level per cytosine.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

source_name: Arabidopsis mature leaves

extract_protocol:
Genomic DNA was isolated with DNeasy Plant Mini Kit (QIAGEN) from mature leaves
Briefly, sonicated DNA was end repaired with NEBnext End Repair module (New England Biolabs), adenylated, and ligated to TruSeq barcoded adaptors (illumina) with T4 DNA ligase. Following purification, samples were bisulfite converted with MethylCode Kit (Invitrogen) and then PCR amplified using Pfu Cx Turbo (Agilent) using the following PCR conditions (2 min at 95°C, 4 cycles of 15sec at 98°C, 30sec at 60°C, 4 min at 72°C and 10min at 72°C).

tag: genotype/variation

value: dms4-1 sdr1-1 mutant

value: mature leaves


title: sdr1-1

value: sdr1-1 mutant


title: Nob1_1

description: purified 20S ribosomal RNA

value: BY4741 with nob1-TAP::K.I.URA3


title: dms4-1

value: dms4-1 mutant


title: NIH3T3_H3K9me3 ChIP-seq

tag: cell line

tag: cell type

value: immortalized fibroblasts

value: Anti-Histone H3 (tri methyl K9) antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Tsr1_3

description: purified 20S ribosomal RNA

value: BY4741 with tsr1-HTP::K.I.URA3


title: NIH3T3_H4 hyperacetylation ChIP-seq

tag: chip antibody

value: Anti-hyperacetylated Histone H4 (Penta) Antibody

value: Millipore


title: NIH3T3_H3K4me3 ChIP-seq

value: Anti-Histone H3 (tri methyl K4) antibody


title: ago6_Spiked_FLAGAGO6_FLAG-IP_Replicate_A

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: in vitro binding control: FLAG-IP in an ago6 plant complemented with the FLAG-AGO6 protein. The lysate was spiked with 20ug of purified small RNAs from a ddm1 mutant plant to determine if the  siRNAs produced in a ddm1 plant would be incorperated into FLAG-AGO6 in vitro.

data_processing:
Illumina software was used for basecalling. Sequenced reads de-multiplexed and were trimmed for adaptor sequence. Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, tRNA and rRNA-matching reads were removed, and only small RNAs that perfectly match the genome are reported (UEA small RNA tool v 2.5.0 used).
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced

growth_protocol: Plants were grown on soil in 18 hour long days at 23C.

extract_protocol:
For the total RNA libraries, total RNA was extracted using Trizol reagent and enriched using the MirVana microRNA isolation kit. For the IP libraries, mock and IPs were performed as in MuCue et al (in preparation). Small RNAs were extracted from proteins using Trizol LS.
Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit

tag: ecotype background

value: ago6 mutant

tag: tissue

value: unopened flower buds

tag: ip antibody

value: FLAG Antibody

tag: ip antibody vendor

value: Sigma

tag: molecule subtype

value: Immunoprecipitated small RNA


title: Tsr1_2

description: purified 20S ribosomal RNA

tag: sample type

value: purified 20S ribosomal RNA


title: NIH3T3_Pol II ChIP-seq

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody [4H8]


title: ddm1_AGO6-IP_Replicate_A

description: AGO6-IP from a sample with the AGO6 antigen

value: ddm1 mutant

value: AGO6 polyclonal

value: Agrisera


title: NIH3T3_Pol I (POLR1A/ RPA194) ChIP-seq

value: immortalized fibroblasts

value: rabbit polyclonal antibodies targetting the largest subunit of the Pol I complex

tag: chip antibody ref.

value: Sanij et al., J Cell Biol, 2008


title: Tsr1_1

description: purified 20S ribosomal RNA

value: BY4741 with tsr1-HTP::K.I.URA3


title: Rio2_2

description: purified 20S ribosomal RNA

value: BY4741 with rio2-HTP::K.I.URA3


title: HMEC_UBF1/2 ChIP-seq

source_name: HMEC

value: HMEC

value: Primary mammary epithelial cells immortalized by TERT

value: anti-UBF1/2 rabbit polyclonal


title: ddm1-ago6_FLAGAGO6_FLAG-IP_Replicate_B

description: FLAG-IP from a sample with the FLAG antigen

value: ddm1-ago6 mutant

value: unopened flower buds


title: HMEC_Pol I (POLR1A) ChIP-seq


title: Ltv1_2

description: purified 20S ribosomal RNA

value: BY4741 with ltv1-HTP::K.I.URA3


title: VDR ChIP-seq for calcitriol-stimulated, LPS-polarized THP-1 cells

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against VDR

data_processing:
Alignment to hg19 using Bowtie v1.0.0 with the following essential command line arguments: bowtie -n 1 -m 1 -k 1 -e 70 --best, and adjusting the seed length (argument -l) as appropriate per data set
Conversion to sorted BAM format using samtools
Peak calling using MACS2 with the following essential command line arguments: macs2 callpeak –bw 150 –keep-dup 1 –g hs --qvalue=0.01 –m 5 50 --bdg
Identification of consensus VDR ChIP-seq summit locations over all data sets using the R density function with triangular smoothing and bandwidth of 20. After converting all densities under 1.0e-15 to zero, local density maxima, identified with a span of 100, were considered as the consensus summits. For each consensus summit, FEs and q-values were extracted from the score tracks generated by the MACS2 bdgcmp tool, using a pseucocount of 1 for FEs.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak: standard ENCODE-style narrowPeak format (the .encodePeak files from MACS2)

source_name: THP-1 cells polarized towards M1-macrophages using LPS

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air / 5% CO2 incubator. For polarization towards M1-type macrophages, THP-1 cells were grown in a density of 500,000 cells/ml in phenol red-free RPMI 1640 medium supplemented with 5% charcoal-stripped fetal calf serum and incubated for 24 h with 100 ng/ml LPS (Sigma-Aldrich).

extract_protocol:
see PMID: 21846776
Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany.

treatment_protocol: Prior to chromatin extraction, the cells were exposed for 80 min with 10 nM 1,25(OH)2D3 or were left unstimulated.

tag: antibody

value: VDR


title: Rio2_1

description: purified 20S ribosomal RNA

value: purified 20S ribosomal RNA


title: ddm1-ago6_mock_FLAG-IP_Replicate_B

description: mock control: FLAG-IP without the FLAG antigen

value: FLAG Antibody

value: Sigma

value: Immunoprecipitated small RNA


title: Enp1_2

description: purified 20S ribosomal RNA

value: BY4741 with enp1-HTP::K.I.URA3


title: NIH3T3_UBF1/2 ChIP-seq

value: immortalized fibroblasts


title: Nob1_2

description: purified 20S ribosomal RNA

value: BY4741 with nob1-TAP::K.I.URA3


title: NIH3T3_H3k9ac

value: Anti-acetyl-Histone H3 (Lys9) Antibody

value: Millipore


title: Enp1_1

description: purified 20S ribosomal RNA


title: VDR ChIP-seq for unstimulated, LPS-polarized THP-1 cells

description: Chromatin IP against VDR

value: unstimulated


title: ago6_mock_AGO6-IP_Replicate_A

description: mock control: AGO6-IP without the AGO6 antigen

value: ago6 mutant

value: AGO6 polyclonal

value: Agrisera


title: ago6_FLAGAGO6_FLAG-IP_Replicate_B


title: ago6_mock_FLAG-IP_Replicate_B


title: ddm1-ago6_mock_AGO6-IP_Replicate_A

value: ddm1-ago6 mutant


title: late_controls_3

description: purified 18S ribosomal RNA

value: BY4741 with fun12-TAP::K.I.HIS3

value: control

value: purified 18S ribosomal RNA


title: ddm1-ago6_FLAGAGO6_FLAG-IP_Replicate_A

value: unopened flower buds


title: late_controls_1

description: purified 18S ribosomal RNA


title: Col_AGO6-IP_Replicate_A

value: wild ypte


title: ago6_FLAGAGO6_FLAG-IP_Replicate_A

value: FLAG Antibody

value: Sigma


title: H3K4me3 ChIP LCL Doxo

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations
Uniquely mapped reads with mis-match <= 2 were used for peak detection
Peaks were called using QuEST (version 2.4) using the “Transcription factor binding site” setting (bandwidth of 30 bp, region size of 300 bp) and the “stringent peak calling” parameters (corresponding to 50-fold ChIP to input enrichment for seeding the regions, and 3-fold ChIP enrichment for extending the regions).
Peaks with FDR q <= 0.05
Genome_build: hg19
Supplementary_files_format_and_content: NARROWPEAK file reports peaks with FDR q <= 0.05

source_name: lymphoblastoid cells

growth_protocol: human lymphoblastoid cells were grown as recommended by Coriell

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K4me3-DNA complexes were isolated with rabbit polyclonalanti-trimethyl-Histone H3 (Lys4) antibody (Millipore, cat# 07-473). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.
Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 0.5 μM doxorubicin (Sigma) or water as a vehicle control for 18 hours

tag: agent

value: doxorubicin

value: rabbit polyclonal anti-trimethyl-Histone H3 (Lys4) antibody (Millipore, cat# 07-473)


title: H3K4me3 ChIP LCL NT

value: control (vehicle)


title: Ltv1_1

description: purified 20S ribosomal RNA

tag: strain

value: BY4741 with ltv1-HTP::K.I.URA3

value: purified 20S ribosomal RNA


title: mid_early_controls_4

description: purified 20S ribosomal RNA

value: BY4741 with rio2-HTP::K.I.URA3

tag: treatment


title: mid_early_controls_2

description: purified 20S ribosomal RNA


title: mid_early_controls_3

description: purified 20S ribosomal RNA

value: BY4741 with tsr1-HTP::K.I.URA3


title: mid_early_controls_1

description: purified 20S ribosomal RNA

value: BY4741 with enp1-HTP::K.I.URA3


title: ddm1-pol4-rdr6_Replicate_A

source_name: ddm1-pol4-rdr6_small RNA-seq

tag: genotype/variation

value: ddm1-pol4-rdr6 mutant

value: small RNA


title: ddm1-ago6_Replicate_A

source_name: ddm1-ago6_small RNA-seq

value: ddm1-ago6 mutant


title: ddm1-pol4-rdr6_Replicate_B


title: ddm1-ago6_Replicate_B


title: ddm1-dcl3_Replicate_A

source_name: ddm1-dcl3_small RNA-seq

value: ddm1-dcl3 mutant


title: ddm1-dcl3_Replicate_B


title: ddm1_Replicate_B

source_name: ddm1_small RNA-seq

value: ddm1 mutant


title: pol4_Replicate_A

source_name: pol4_small RNA-seq

value: pol4 mutant

value: unopened flower buds


title: Col_Replicate_B

source_name: Col_small RNA-seq

value: wild type


title: TAL1 ChIP-seq in HSPC rep1 05062009_427E3AAXX_B3

status: Public on Nov 13 2014

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against TAL1 in HSPC

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples, reads were aligned with bowtie 0.12.9 to the mm9 genome.  Aligned sequences were processed with MACS 1.4.2 with parameters -w -S --space=50 --keep-dup=auto -p 1e-9. Counts were normalized to reads per million.

source_name: Hematopoietic Stem & Progenitor Cells

growth_protocol: Human CD133-positive Umbilical Cord Blood (UCB) cells were purchased from AllCells, Emeryville, CA. Cells were expanded for 10-11 days using Lodish conditions (Zhang et al Blood 2008 PMID: 18202223) in StemSpan serum-free medium (StemCell Technologies,Vancouver, BC) supplemented with 10 Âµg/mL heparin (Sigma-Aldrich, St Louis, MO), 10 ng/mL mouse SCF, 20 ng/mL mouse TPO, 100 ng/mL human IGFBP2 (all from R&D Systems, Minneapolis, MN), and 10 ng/mL human FGF-1 (Invitrogen, Frederick, MD) and 500 ng/ul human Angptl5 (Abnova, Taipei City, Taiwan). At the end of culture cells were positively selected for CD133 using an immunomagnetic MicroBead labeling system (StemCell Technologies). Cell purity was determined by FACS for CD34 and CD133 to be 75-90% double positive. For location analysis, cells were cross-linked with formaldehyde for 20 min.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: Santa Cruz SC-12984

value: CD133+ expanded UCB

tag: cell number

value: 1 million

tag: library prep protocol

value: Illumina ChIP-seq

tag: replicate


title: 3815

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

data_processing:
Basecalls using CASAVA 1.4
Alignment; STAR, Dobin et al doi:10.1093/bioinformatics/bts635, version 2.2.0; default run except --outFilterMismatchNmax 2; only first fastq files usd in case of paired-end data
Count generation; HTSeq-count, version 0.3p7; -m union -t exon -i gene_id -s no
Filtering by RPKM; removal of bottom 25% of lowest abundance genes ranked by RPKM calculated as ((10^9*count)/(total counts in sample*length of gene)) following TMM normalisation of the library using edgeR; bottom 25% per condition removed, excluding E_5 of Fert-; 15,524 bovine genes retained
Genome_build: UMD3.1.69
Supplementary_files_format_and_content: Format: tab separated; content: column1=bovine gene ID, column2=number of sequence reads overlapping bovine gene ID as defined by GTF, using the HTSeq-count 'union' method

molecule: polyA RNA

source_name: endometrium

growth_protocol: See Cummins et al doi:10.3168/jds.2011-4742

extract_protocol:
Standard trizol extraction see Chomczynski doi:10.1016/0003-2697(87)90021-2
Illumina TruSeq v1 kit

treatment_protocol: Washed in PBS, connective tissue removed, snap-frozen in liquid nitrogen, stored -80 freezer

value: ipsilateral uterine horn

tag: timepoint

value: day 7 oestrus

tag: fertility group

value: Fert+ ('high fertility')


title: 965

tag: tissue


title: 3445


title: TAL1 ChIP-seq in HSPC rep2 04102009_3139VAAXX_B1

description: Chromatin IP against TAL1 in HSPC

tag: chip antibody

tag: cell type


title: H3K27Ac ChIP RPMI-8402_ChipSeq 11132012_64WVDAAXX_4

description: Chromatin IP against H3K27Ac ChIP RPMI-8402

source_name: T-ALL cell line

growth_protocol: Human RPMI-8402 cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Abcam AB4729

tag: cell line


title: ddm1-ago6_mock_FLAG-IP_Replicate_A

tag: ecotype background

tag: ip antibody

value: FLAG Antibody

tag: ip antibody vendor

value: Sigma

tag: molecule subtype

value: Immunoprecipitated small RNA


title: 781


title: late_controls_2

description: purified 18S ribosomal RNA

source_name: total RNA isolated from culture

tag: strain

value: BY4741 with fun12-TAP::K.I.HIS3

value: control

tag: sample type

value: purified 18S ribosomal RNA


title: 33


title: 3434


title: 782


title: 984

value: Fert- ('low fertility')


title: 150


title: 1153


title: 1411


title: 996


title: CPL7

city: Tianjin

first: Pengli

last: Cai

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, CAS

data_processing:
Illumina HiSeq™ 2000 used for sequencing
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 12) with Tophat.
The alignment results were stored in SAM format files for subsequent analysis.
The counts of reads counts uniquely mapped to only one gene for each gene were calculated by HTseq-count using SAM files and genome annotation as input.
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM).
Genome_build: GCA_000182925.2
Supplementary_files_format_and_content: Excel files include GeneID, gene_length, reads, RPKM values for each Sample

organism: Neurospora crassa OR74A

growth_protocol: All the strains were innoculated at 106 conidia/mL and grown 16 hours in sucrose media.

extract_protocol:
Total RNA was isolated from frozen mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA). Total RNA was then treated with DNase I (RNeasy Mini Kit, QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were Washed and transferred to fresh media with 2% cellobiose for 4 hours inducing cultivation.

tag: induce condition

value: 4 hours on 2% cellobiose

value: mycelia


title: 997


title: 179


title: Δ3β

source_name: Δ3βG

value: Δ3βG


title: CPL4


title: GFP_Sus_B15

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
name: cutadapt; version: 1.4.2; parameters: "-m 16 -q 20 -n 2 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
name: groupReads.pl (script in miRanalyzer package); version: 0.3; parameters: "input=input.fastq output=output.rc.txt"
Genome_build: mm9
Supplementary_files_format_and_content: read count table for adapter-trimmed small RNA

source_name: Nucleus accumbens tissue

extract_protocol:
Small RNA (<200bp) was first isolated and enriched with Qiagen RNeasy mini kit (Cat# 74104)
Epicentre Scriptminer small RNA library kit (Cat# SMSP10908)
the di-tagged cDNA was amplified and individually barcoded with nine cycle PCR cycles using indices and PCR primers provided in the kit. The library was then purified with Zymo DNA Clean & Concentrator kit (Cat# D4003) and size selected with Pippin

treatment_protocol: 10 day chronic social defeat stress

tag: treatment

value: AAV GFP, Susceptible


title: GFP_Sus_A15


title: GFP_Res_B24

value: AAV GFP, Resilient


title: GFP_Res_B23


title: GFP_Res_B22


title: GFP_Res_B20


title: GFP_Res_A22


title: GFP_Res_B19


title: GFP_Res_A21


title: GFP_Res_A19


title: GFP_Res_A20


title: GFP_Con_B06

value: AAV GFP, no social defeat


title: GFP_Con_B05


title: GFP_Con_B03


title: GFP_Con_B01


title: GFP_Con_B04


title: GFP_Con_B02


title: GFP_Con_A06


title: GFP_Sus_B14


title: GFP_Sus_A14


title: CRE_Sus_B30

value: AAV Cre, Susceptible


title: GFP_Con_A05


title: CRE_Sus_B27


title: GFP_Con_A02


title: GFP_Res_A24


title: GFP_Res_B21


title: GFP_Con_A01


title: GFP_Con_A04


title: CRE_Sus_A29


title: CRE_Sus_A30


title: CRE_Sus_A27


title: CRE_Con_B12

value: AAV Cre, no social defeat


title: CRE_Con_B11


title: CRE_Con_B10


title: CRE_Con_B09


title: CRE_Con_B07


title: CRE_Con_A12


title: CRE_Con_A11


title: CRE_Con_A09


title: CRE_Con_B08


title: GFP_Con_A03


title: CRE_Con_A08


title: CRE_Sus_B29


title: CRE_Con_A07


title: Resilient_E

data_processing:
name: CASAVA Suite; version: 1.8; parameters: defaults
name: IGVTOOLS; version: 2.3.3; parameters: defaults
name: samtools merge; version: 0.1.19; parameters: defaults
Genome_build: mm9

extract_protocol:
Following fixation, Nac punches were sonicated with a desktop sonicator and then underwent high power sonication in a Bioruptor for 30 cycles of 30 s on/30 sec of. The machine was cooled before one more round of 10 cycles. Beta-catenin AB (ChIP validated, Cell Signaling 4176) was used for IP. IPed DNA was reverse cross-linked at 65 degrees overnight and purified.  Each replicate was 15 mice pooled, 4 14 gauge NAc punches/animal
Libraries were prepared for sequencing with standard Illumina Protocol. 200-400 bp fragments were selected for sequencing.

value: Resilient

tag: antibody (company, cat#, lot#)

value: beta Catenin antiboy (Cell Signaling 4176, various lot)


title: CRE_Con_A10


title: CRE_Sus_B28


title: Input_H

value: Input

value: no antibody


title: Defeat_A

value: Defeat


title: Defeat_B


title: Resilient_D


title: Control_F

value: Control


title: CRE_Sus_A28


title: Control_G


title: GFP_Res_A23


title: E11.5 embryo endothelial cells #2

city: Madison

first: David

last: Vereide

address: 330 North Orchard Street

department: Regenerative Biology

institute: Morgridge Institute for Research

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
TPMs renormalized to transcripts per million non-mitochondrial transcripts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: E11.5 embryo primary endothelial cells

growth_protocol: Not cultured. Lysed immediately upon isolation.

extract_protocol:
Cells were lysed in Trizol (Life Technology), and total RNA was purified from the lysates using RNeasy columns (Qiagen) with on-column DNAse treatment.
Total RNAs were converted to cDNAs and otherwise prepared for sequencing using the Tru-seq RNA Sample Prep Kit v2 (Illumina), as described by the manufacturer.

tag: facs purification

value: E11.5 embryo primary endothelial cells


title: E11.5 yolk sac endothelial cells #2

source_name: E11.5 yolk sac primary endothelial cells


title: Day 3 endothelial cells derived from M5

source_name: Endothelial progeny of eHB cells

growth_protocol: Derived from eHB cells (line M5). Differentiated three days on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, and 12.5 ng/mL human FGF2.

value: Endothelial progeny of eHB cells


title: E11.5 yolk sac endothelial cells #1

source_name: E11.5 yolk sac endothelial cells

value: E11.5 yolk sac endothelial cells


title: Day 3 blood cells derived from RB4.6.9

source_name: VE-cadherin-positive, CD45-positive blood progeny of eHB cells

growth_protocol: Derived from eHB cells (line RB4.6.9). Differentiated three days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 3 endothelial cells derived from FL10

growth_protocol: Derived from eHB cells (line FL10). Differentiated three days on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, and 12.5 ng/mL human FGF2.


title: Day 3 endothelial cells derived from FL4

growth_protocol: Derived from eHB cells (line FL4). Differentiated three days on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, and 12.5 ng/mL human FGF2.


title: Day 3 blood cells derived from M5

growth_protocol: Derived from eHB cells (line M5). Differentiated three days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.

value: VE-cadherin-positive, CD45-positive blood progeny of eHB cells


title: Day 3 blood cells derived from FL4

growth_protocol: Derived from eHB cells (line FL4). Differentiated three days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 3 blood cells derived from FL10

growth_protocol: Derived from eHB cells (line FL10). Differentiated three days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 3 blood cells derived from RB3.6.5

growth_protocol: Derived from eHB cells (line RB3.6.5). Differentiated three days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 2 blood cells derived from FL4

source_name: VE-cadherin-positive, CD45-negative blood progeny of eHB cells

growth_protocol: Derived from eHB cells (line FL4). Differentiated two days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 2 blood cells derived from M5

growth_protocol: Derived from eHB cells (line M5). Differentiated two days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.

value: VE-cadherin-positive, CD45-negative blood progeny of eHB cells


title: Day 2 blood cells derived from RB3.6.5

growth_protocol: Derived from eHB cells (line RB3.6.5). Differentiated two days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 2 blood cells derived from FL10

growth_protocol: Derived from eHB cells (line FL10). Differentiated two days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Day 2 blood cells derived from RB4.6.9

growth_protocol: Derived from eHB cells (line RB4.6.9). Differentiated two days on Matrigel in N2B27 medium supplemented with 3 μM CHIR99021, 100 ng/mL murine SCF, 100 ng/mL murine IL-3, and 100 ng/mL murine Flt3L in 1.5% atmospheric oxygen.


title: Kdr-positive mesoderm cells derived from RB3

source_name: Kdr-positive mesoderm cells

growth_protocol: Derived from ES cells (line RB3). Differentiated four days on Matrigel in N2B27 medium, supplemented after the first two days with 4 ng/mL Activin A, 3 μM CHIR99021, 5 ng/mL human BMP4, and 12.5 ng/mL human FGF2

value: Kdr-positive cells

value: Kdr-positive mesoderm cells


title: Kdr-positive mesoderm cells derived from RB2

growth_protocol: Derived from ES cells (line RB2). Differentiated four days on Matrigel in N2B27 medium, supplemented after the first two days with 4 ng/mL Activin A, 3 μM CHIR99021, 5 ng/mL human BMP4, and 12.5 ng/mL human FGF2


title: eHB line FL10

source_name: Fetal liver-derived eHB cells

growth_protocol: Passage 6 eHB cells (line FL10), growing on Matrigel in N2B27 medium supplemented with 12.5 ng/mL human FGF2 and 2 μg/mL doxycycline.

value: eHB line FL10


title: Kdr-positive mesoderm cells derived from RB4

growth_protocol: Derived from ES cells (line RB4). Differentiated four days on Matrigel in N2B27 medium, supplemented after the first two days with 4 ng/mL Activin A, 3 μM CHIR99021, 5 ng/mL human BMP4, and 12.5 ng/mL human FGF2


title: E11.5 embryo endothelial cells #1

source_name: E11.5 embryo endothelial cells

growth_protocol: Not cultured. Lysed immediately upon isolation.

value: E11.5 embryo endothelial cells


title: eHB line FL4

growth_protocol: Passage 6 eHB cells (line FL4), growing on Matrigel in N2B27 medium supplemented with 12.5 ng/mL human FGF2 and 2 μg/mL doxycycline.

value: eHB line FL4


title: eHB line M5

source_name: Embryonic fibroblast-derived eHB cells

growth_protocol: Passage 7 eHB cells (line M5), growing on Matrigel in N2B27 medium supplemented with 12.5 ng/mL human FGF2 and 2 μg/mL doxycycline.

value: eHB line M5


title: Day 3 endothelial cells derived from RB4.6.9

growth_protocol: Derived from eHB cells (line RB4.6.9). Differentiated three days on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, and 12.5 ng/mL human FGF2.


title: eHB line RB3.6.5

source_name: ES-derived eHB cells

growth_protocol: Passage 6 eHB cells (line RB3.6.5), growing on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, 12.5 ng/mL human FGF2, and 2 μg/mL doxycycline.

value: eHB line RB3.6.5


title: E14.5 hematopoietic stem cells

source_name: E14.5 hematopoietic stem cells

value: CD45-positive, CD201-positive, CD150-positive, CD48-negative cells

value: E14.5 hematopoietic stem cells


title: eHB line RB4.6.9

growth_protocol: Passage 5 eHB cells (line RB4.6.9), growing on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, 12.5 ng/mL human FGF2, and 2 μg/mL doxycycline.

value: eHB line RB4.6.9