title: HPr1AR_shCTL_DHT_0hr_R3

data_processing:
Sequenced reads were trimmed for adaptor sequences, and alignment was performed using tophat2
Aligned reads translated to expression counts using featurecounts
Expression normalized using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Expression counts provided as normalized expression counts

source_name: non-malignant prostate cell line infected with shRNA

growth_protocol: Cells were maintained in Keratinocyte Serum Free Medium supplemented with EGF and Bovine Pituitary Extract. shCTL and shRARG containing cells were maintained in 2ug/uL puromycin for selection.

extract_protocol:
total RNA was extracted using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exponentially growing cells were treated with 10nM DHT or EtOH vehicle, and samples collected at 0, 24 and 96 hours of exposure.

tag: shRNA

value: shCTL

value: untreated


title: HPr1AR_shCTL_DHT_96hr_R3

status: Public on Jul 20 2018

type: SRA

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

country: USA

institute: Roswell Park Comprehensive Cancer Center

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: gender

value: male

tag: cell line

tag: cell type

value: non-malignant prostate epithelial cell

tag: treatment

value: DHT

tag: treatment time


title: HPr1AR_shCTL_DHT_24hr_R3


title: HPr1AR_sh272_DHT_0hr_R2


title: HPr1AR_shCTL_DHT_96hr_R2


title: HPr1AR_shCTL_DHT_24hr_R2


title: HPr1AR_sh272_DHT_0hr_R3


title: HPr1AR_sh272_DHT_96hr_R2


title: HPr1AR_sh272_DHT_24hr_R2


title: HPr1AR_sh272_DHT_96hr_R3


title: HPr1AR_sh272_DHT_24hr_R3


title: HPr1AR_shCTL_DHT_0hr_R2


title: HPr1AR_shCTL_DHT_96hr_R1


title: HPr1AR_sh272_DHT_24hr_R1


title: HPr1AR_sh272_DHT_0hr_R1


title: HPr1AR_shCTL_DHT_24hr_R1


title: HPr1AR_sh272_DHT_96hr_R1


title: HPr1AR_shCTL_DHT_0hr_R1


title: C7_input_Rep2_For_Hdac1Mta2

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: Clone C7

library_source: genomic

data_processing:
The raw sequencing reads were mapped to the mm10 reference genome (conventional ChIP) or mm10 concatenated with dm6 genome (calibrated ChIP) using Bowtie, PCR duplicates were removed by ‘picard-tools MarkDuplicates’ program, and only unique read pairs were kept for further analysis.
MACS2 (2.0.10) was employed to call the ChIP-seq peaks with the default parameters except (-f BAMPE -g mm -q 0.01)
The metagene binding patterns and heatmap matrix were generated by DANPOS with the key parameters (--flank_up 5000 --flank_dn 5000 --region_size 10000 --bin_size 50 --excludeP 0.01)
The bigwig tracks shown in UCSC Genome Browser were generated using the custom script xbam2wig.py from https://github.com/guifengwei/glib , normalizing to one million mapped reads for PWWP2A and PWWP2B ChIP-seq, whereas 10 million mapped reads for the remaining calibrate ChIP-seq.
Genome_build: mm10 (GRCm38) or mm10+dm6
Supplementary_files_format_and_content: *.bw: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: E14 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 10% foetal calf serum (FCS, from Seralab), 2 mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50 g/mL penicillin/streptomycin (all from Invitrogen) and 1000 U/mL of LIF. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO. For cells stably expressing PWWP2A/B or PWWP2A truncations, ES cell medium were supplemented with 1.75 µg/ml Puromycin. SG4 Drosophila melanogaster cells were cultured at 27ºC with Schneider’s Drosophila Medium (ThermoFisher) supplemented with penicillin/streptomycin and 10% FCS.

extract_protocol:
For crosslinking-ChIP, 40-45 million ES cells were resuspended in 10ml PBS with 2 mM EGS for 45 min, followed by 1% formaldehyde for a further 10 minutes. The reactions were quenched by the addition of glycine to a final concentration of 125 mM. Cells were first lysed for 10 minutes on ice in LB1 (50 mM Hepes pH 7.9, 140 mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton). The nuclei was pelleted and washed for 5 minutes in LB2 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and pelleted again. The nuclei was suspended in 1 ml of LB3 (10 mM Tris pH 8.0, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a BioRuptor sonicator (Diagenode) with for 25 cycles 30 sec on and 30 sec off, followed by centrifugation at maximum speed for 15 min at 4 ºC, and either used freshly or snap freeze and stored at -80 ºC.
For calibrated ChIP-seq of HDAC1, MTA2, Pol II Ser5P, and Pol II Ser2P 40 million ES cells and 10 million Drosophila SG4 Cells were pooled in PBS prior to crosslinking. For each IP, 100 µl of chromatin was diluted with ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) prior to pre-clearing with protein A agarose beads or magnetic Dynabeads (Invitrogen) blocked with 1 mg/mL BSA and 1 mg/mL yeast tRNA at 4 ºC for 1 h. Precleared chromatin samples were further incubated overnight with relevant antibodies at 4 ºC with rotation.
For each calibrated ChIP sample, 5-8 μg antibody plus 2 μg Drosophila-specific H2Av antibody (Active Motif) were used. Antibody-bound chromatin was isolated on blocked protein A beads, and followed by washes with low salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer ((0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)), and twice with TE (10 mM Tris-HCl (pH 8.0), 1 mM EDTA) buffer. The DNA was eluted with 1% SDS and 100 mM NaHCO3, and reversed crosslinked at 65 ºC overnight in the presence of 200mM NaCl, following by treatment with RNaseA and Proteinase K. DNA was purified by ChIP DNA Clean and Concentrator kit (Zymo) and quantified by dsDNA Qubit reagents.
For calibrated native ChIP (H3K27ac and H3K9ac), 40 million ES cells and 10 million Drosophila SG4 Cells were pooled and lysed in RSB (10 mM Tris pH 8, 10 mM NaCl, 3 mM MgCl2) + 0.1% NP40 for 5 min on ice with gentle inversion. Nuclei was resuspended in 1 ml of RSB + 0.25 M sucrose + 3mM CaCl2, treated with 200U of MNase (Fermentas) for 5 minutes at 37ºC, quenched with 4 µl of 1M EDTA, then centrifuged at 5000 rpm for 5 minutes. The supernatant was transferred to a fresh tube as fraction S1. The chromatin pellet was incubated for 1 h in 300 µl of nucleosome release buffer (10 mM Tris pH 7.5, 10 mM NaCl, 0.2 mM EDTA), carefully passed 5 times through a 27G needle using a 1 ml syringe, then centrifuged at 5000 rpm for 5 minutes. The supernatant from this S2 fraction was combined with S1. For each ChIP reaction, 80 µl of chromatin was diluted in Native ChIP incubation buffer (10 mM Tris pH 7.5, 70 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton) to 1 ml and incubated with antibody overnight at 4ºC. Samples were incubated with 50 µl protein A agarose beads preblocked in Native ChIP incubation buffer with 1 mg/ml BSA and 1 mg/ml yeast tRNA, then washed for a total of 4 times in Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton) and once in TE. The DNA was eluted with 1% SDS and 100 mM NaHCO3, and was purified using ChIP DNA Clean and Concentrator kit (Zymo).
Approximately 5-20 ng of ChIPed DNA were used for library prep using NEBNext Ultra II DNA Library Prep Kit with NEBNext Single index, and then further quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems) and SensiMix SYBR (Bioline, UK). The libraries were pooled and 2 × 42 paired end sequencing was performed on the Illumina NextSeq500.

tag: genotype/variation

value: double PWWP2A/B knockout

value: embryonic stem cells

tag: chip antibody


title: E14_input_Rep2_For_Hdac1Mta2

value: wild-type


title: A1_input_Rep2_For_Hdac1Mta2

description: Clone A1


title: C7_Hdac1_Rep2

description: Clone C7

value: Hdac1 (Abcam #Ab7028) + H2Av (Active Motif #61686)


title: A1_Hdac1_Rep2

description: Clone A1


title: A1_Mta2_Rep1

description: Clone A1

value: Mta2 (Abcam #Ab8106) + H2Av (Active Motif #61686)


title: E14_Hdac1_Rep2


title: E14_Mta2_Rep1


title: E14_input_Rep1_For_Hdac1Mta2


title: A1_input_Rep1_For_Hdac1Mta2

description: Clone A1


title: C7_Mta2_Rep1

description: Clone C7


title: C7_input_Rep1_For_Hdac1Mta2

description: Clone C7


title: C7_Hdac1_Rep1

description: Clone C7


title: A1_Hdac1_Rep1

description: Clone A1


title: E14_Hdac1_Rep1


title: A1_H3K9ac_Rep1

description: Clone A1

value: H3K9ac (Millipore #07-352)


title: E14_Input_Rep2_For_acetylation


title: E14_H3K9ac_Rep1


title: C7_Input_Rep1_For_acetylation

description: Clone C7


title: C7_H3K27ac_Rep2

description: Clone C7

value: H3K27ac (Abcam #Ab4729)


title: A1_Input_Rep1_For_acetylation

description: Clone A1


title: C7_H3K9ac_Rep2

description: Clone C7


title: E14_H3K27ac_Rep2


title: A1_Input_Rep2_For_acetylation

description: Clone A1


title: C7_Input_Rep2_For_acetylation

description: Clone C7


title: A1_H3K27ac_Rep1

description: Clone A1


title: E14_H3K27ac_Rep1


title: C7_H3K27ac_Rep1

description: Clone C7


title: A1_H3K9ac_Rep2

description: Clone A1


title: E14_Input_Rep1_For_acetylation


title: E14_H3K9ac_Rep2


title: C7_Pol2SerP_Input_Rep1

description: Clone C7


title: A1_Pol2SerP_Input_Rep3

description: Clone A1


title: C7_Pol2SerP_Input_Rep2

description: Clone C7


title: A1_Pol2SerP_Input_Rep2

description: Clone A1


title: A1_H3K27ac_Rep2

description: Clone A1


title: C7_H3K9ac_Rep1

description: Clone C7


title: A1_Pol2SerP_Input_Rep1

description: Clone A1


title: E14_Pol2SerP_Input_Rep2


title: E14_Pol2SerP_Input_Rep3


title: C7_Pol2SerP_Input_Rep3

description: Clone C7


title: E14_Pol2SerP_Input_Rep1


title: C7_Pol2S5P_Rep1

description: Clone C7

value: Ser5P (Cell Signalling #13523)


title: C7_Pol2S2P_Rep3

description: Clone C7

value: Ser2P (Cell Signalling #13499)


title: A1_Pol2S5P_Rep1

description: Clone A1


title: E14_Pol2S5P_Rep1


title: C7_Pol2S2P_Rep1

description: Clone C7


title: Pol2_NTD_ChIP_A1_input_Rep2

description: Clone A1


title: C7_Pol2S2P_Rep2

description: Clone C7


title: A1_Pol2S2P_Rep3

description: Clone A1


title: A1_Pol2S2P_Rep1

description: Clone A1


title: Pol2_NTD_ChIP_C7_input_Rep2

description: Clone C7


title: A1_Pol2S2P_Rep2

description: Clone A1


title: Pol2_NTD_ChIP_A1_input_Rep1

description: Clone A1


title: E14_Pol2S2P_Rep1


title: Pol2_NTD_ChIP_E14_input_Rep2


title: Pol2_NTD_ChIP_E14_Rep2

description: processed data file: Pol2_E14.Merged.bw

value: NTD Pol2 (Cell Signalling #14958)


title: Pol2_NTD_ChIP_A1_Rep2

description: processed data file: Pol2_A1.Merged.bw


title: Pol2_NTD_ChIP_C7_Rep2

description: processed data file: Pol2_C7.Merged.bw


title: Pol2_NTD_ChIP_C7_input_Rep1

description: Clone C7


title: Pol2_NTD_ChIP_E14_input_Rep1


title: Pol2_NTD_ChIP_A1_Rep1

description: processed data file: Pol2_A1.Merged.bw


title: Input_FS2Vec

value: stably expressing FS2 vector


title: Pol2_NTD_ChIP_C7_Rep1

description: processed data file: Pol2_C7.Merged.bw


title: Pol2_NTD_ChIP_E14_Rep1

description: processed data file: Pol2_E14.Merged.bw


title: C7_Pol2S5P_Rep2

description: Clone C7


title: E14_Pol2S5P_Rep2


title: Input_FS2PWWP2A

value: stably expressing ectopic FS2PWWP2A


title: A1_Pol2S5P_Rep2

description: Clone A1


title: Hdac1_in_FS2Vec

value: Hdac1 (Abcam #Ab7028)


title: E14_Pol2S2P_Rep2


title: E14_Pol2S2P_Rep3


title: Hdac1_in_FS2PWWP2A


title: FS2PWWP2A_SI_Rep2

description: processed data file: Pwwp2a_SI_B4.bw

value: stably expressing ectopic short isoform of PWWP2A

value: FS2 (homemade)


title: FS2ChIP_in_FS2Vec


title: FS2PWWP2A_DelPWWP

value: stably expressing ectopic PWWP-deleted PWWP2A


title: FS2PWWP2A_SI_Rep1

description: processed data file: Pwwp2a_SI_B4.bw


title: FS2PWWP2B_Rep1

description: processed data file: Pwwp2b_E6.bw

value: stably expressing ectopic FS2PWWP2B


title: FS2PWWP2A_Rep3

description: processed data file: E14_FS2PWWP2A.bw


title: FS2PWWP2B_Rep2

description: processed data file: Pwwp2b_E6.bw


title: FS2PWWP2A_Rep2

description: processed data file: E14_FS2PWWP2A.bw


title: C7_4sU_seq_Rep3

description:
Clone C7
4sU-RNA
processed data file: C7_4su.Norm.bw

data_processing:
The raw reads from our 4sU-seq data were mapped to the mm10 reference genome with STAR70 under the default parameters apart from (--outFilterMultimapNmax 1  --outFilterMismatchNmax 8  --alignEndsType EndToEnd).
For visualization of RNA-seq data in UCSC genome browser, the coverage was generated by Bedtools (v2.17.0) (Quinlan and Hall, 2010) and was normalized to 10 million mapped reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_4su.Norm.bw: bigWig files

extract_protocol:
Total RNAs were extracted according to TRIzol manuals, followed by DNaseI treatment. For each μg of total RNA, 2μL of Biotin-HPDP (Pierce, 50mg EZ-Link Biotin-HPDP), previously dissolved in DMF at a concentration of 1mg/mL, and 1μL of 10x Biotinylation buffer (100mM Tris HCl pH 7.4, 10mM EDTA), were added. The reaction was incubated with rotation for 15 min at 25ºC. Biotinylated 4sU-RNA was recovered using the μMacs Streptavidin Kit.
NEBNext® Ultra™ II Directional RNA Library Prep Kit.

value: double PWWP2A/B knockout


title: FS2PWWP2A_Rep1

description: processed data file: E14_FS2PWWP2A.bw

value: embryonic stem cells


title: B8_4sU_seq_Rep2

description:
Clone B8
4sU-RNA
processed data file: B8_4su.Norm.bw

value: PWWP2A knockout


title: E14_4sU_seq_Rep2

description:
4sU-RNA
processed data file: E14_4su.Norm.bw

value: wild-type


title: E14_4sU_seq_Rep1


title: C7_4sU_seq_Rep2


title: C7_4sU_seq_Rep1


title: HUDEP2_HRI_sgRNA5_differentiated_rep2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing: The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/). In brief, reads were mapped to the human genome (hg19 assembly) using STAR, followed by RSEM for gene quantifications.

source_name: HUDEP2 cells

growth_protocol:
HUDEP2 cells were maintained in StemSpan™ Serum Free Medium (SFEM, StemCell Technologies, Cat. #09650) supplemented with 50ng/ml human Stem Cell Factor (hSCF, Peprotech, Cat. #300-07), 10uM dexamethasone (Sigma, Cat. #D4902), 1ug/ml doxycycline (Sigma, Cat. #D9891), 3IU/ml erythropoietin (Amgen, Cat. #55513-144-10), 1% penicillin/streptomycin (ThermoFisher, Cat. #15140122). Cells were kept at a density of less than 1.0 million/ml. Differentiation was achieved by growing cells for 7 days (one medium change at day 3 or 4) in IMDM (Mediatech, Cat. #MT10016CV) supplemented with 50ng/ml hSCF, 3IU/ml erythropoietin, 2.5% fetal bovine serum, 250ug/ml holo-transferrin (Sigma, Cat. #T4132), 1% penicillin/streptomycin, 10ng/ml heparin (Sigma, H3149), 10ug/ml insulin (Sigma, Cat. #I9278), 1ug/ml doxycycline.
Peripheral blood mononuclear cells (PBMCs) were obtained from the University of Pennsylvania Human Immunology Core. CD34+ cells were purified from using MACS MicroBead kit (Miltenyi, Cat #130-100-453) and cultured in three phases in IMDM supplemented with 3IU/ml erythropoietin, 2.5% human male AB serum (Sigma, Cat. #H4522), 10ng/ml heparin, 10ug/ml insulin. Phase-I medium was supplemented with 100ng/ml hSCF, 5ng/ml IL-3 (Peprotech, Cat. #200-03), 250ug/ml holo-transferrin. Phase-II medium was supplemented with 100ng/ml hSCF and 250ug/ml holo-transferrin.  Cells were maintained in Phase-I from the day of collection until day 8. Cells were spin-infected on day 8, incubated overnight with viral supernatant, and transitioned to Phase-II media on day 9. RNA samples for RT-qPCR were harvested on day 13 of culture.

extract_protocol:
RNA samples were harvested in TRIzol™ (ThermoFisher Scientific, Cat #15596018), and purified with the RNeasy Mini kit which included an on-column DNAse treatment to remove genomic DNA (Qiagen, Cat. #74106).
Sequencing libraries were then constructed from 100 ng of purified total RNA using the ScriptSeq Complete Kit (Illumina cat# BHMR1224) according to manufacturer’s specifications. In brief, the RNA was subjected to rRNA depletion using the Ribo-Zero removal reagents and fragmented. First strand cDNA was synthesized using a 5’ tagged random hexamer, and reversely transcribed, followed by annealing of a 5’ tagged, 3’-end blocked terminal-tagged oligo for second strand synthesis. The Di-tagged cDNA fragments were purified, barcoded, and PCR-amplified for 15 cycles. The size and quality of each library were then evaluated by Bioanalyzer 2100 (Agilent Techniologies, Santa Clara, CA), and quantified using qPCR.

value: HRI sgRNA5

tag: sample type

value: Differentiated


title: E14_4sU_seq_Rep3


title: B8_4sU_seq_Rep1


title: HUDEP2_nontargeting_sgRNA_differentiated_rep2

value: nontargeting sgRNA


title: CD34 shRNA HRI 2

source_name: CD34+ derived erythroid progrenitors

value: shRNA HRI 2


title: B8_4sU_seq_Rep3


title: HUDEP2_HRI_sgRNA5_differentiated_rep1


title: HUDEP2_HRI_sgRNA5_undifferentiated_rep1

value: Undifferentiated


title: HUDEP2_HRI_sgRNA5_undifferentiated_rep2


title: HUDEP2_nontargeting_sgRNA_undifferentiated_rep2


title: CD34 shRNA HRI 1

value: shRNA HRI 1


title: HUDEP2_nontargeting_sgRNA_undifferentiated_rep1


title: INPUT_muscle_DNA

city: Munich

first: Nina

middle: Henriette

last: Uhlenhaut

state: Bavaria

address: Ingolstädter Landstraße 1,  Neuherberg

department: Molecular Endocrinology

country: Germany

institute: HelmholtzZentrum München - IDC

data_processing:
Mapping against mm10 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsample Bmal and Reverb ~20 million reads and PolII ~ 13 million reads. Only reads with MAPQ >24 were kept.
Peak calling with macs2 version 2.1.1  using Input as control with p-value 0.05
Create peak universe
Genome_build: mm10
Supplementary_files_format_and_content: narrowpeak files were produced using macs2 representing peaks

source_name: gastrocnemius

extract_protocol:
ChIP was performed as previously described (Uhlenhaut et al. 2012) with minor modifications. Briefly, around 300 mg of frozen muscle was homogenized, filtered through a 70µm cell strainer, and pellet fixed in 1% Formaldehyde. Nuclei were purified and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies.
Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

tag: tissue

value: gastrocnemius

tag: strain

tag: time

value: Zeitgeber Time 4

value: male

tag: genotype

value: Wild Type

value: input DNA


title: X3seBACS_primed_BAC_RNA_1

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a BAC-STARR-seq library with DNA from three super-enhancer regions

data_processing:
Library strategy: STARR-Seq
Base-calling using default Illumina software by Edinburgh Genomics
Adapter contaminants trimmed using Skewer; 125bp reads were trimmed to 50bp for consistency
Reads aligned to GRCh37/h19 genome using Bowtie2 (default parameters + “--very-sensitive”)
Only properly paired, concordantly aligning and uniquely mapping fragments
Read counts summed up per unique (chromosome,start-read1,end-read2) coordinate
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated text file with read counts per coordinate

source_name: BAC

growth_protocol: H9 human embryonic stem cells were cultured on Matrigel coated cell culture plates, using mTesR1 medium (Stem Cell Technology, 05850). Cells were routinely split (ratio 1:3-1:4) using 0.5mM EDTA (Invitrogen, 15575020). For transfection, single cells were obtained by Accutase treatment (Invitrogen, A1110501), in the presence of Rock inhibitor, Y-27632 (10uM, Cambridge bioscience, SM02-10). For conversion to the naive state, cells were split on irradiated MEFs on gelatin coated plates and media was changed to NHSM media, as described by Gafni et al. (Gafni et al., 2013), containing knockout DMEM (Invitrogen ), 20% knockout serum (Invitrogen), human insulin (Sigma, 12.5ug ml-1 final concentration), 20 ng ml-1 recombinant human LIF (Millipore), 8 ng ml-1 recombinant bFGF (Peprotech) and 1 ng ml-1 recombinant TGF-beta1 (Peprotech), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Invitrogen), penicillin-streptomycin (Invitrogen) and small molecule inhibitors: PD0325901 (1uM, ERK1/2i, Axon Medchem); CHIR99021 (3uM, GSKbetai, Axon Medchem); SP600125 (10uM, JNKi, Abcam ab120065) and SB203580 (10 uM, p38i,Abcam ab120638) Y-27632 (5uM, ROCKi) and protein kinase C inhibitor G06983 (5 uM, PKCi, Abcam, ab144414). Cells were 1:10 passaged using TrypLETM (Invitrogen, 12604021) in the presence of Rock inhibitor and maintained for more than 10 passages in NHSM media prior to analysis. All cells were regularly karyotyped and checked for the presence of mycoplasm.

extract_protocol:
A minimum of 400,000 GFP-positive, sorted cells were used to isolate total RNA using Trizol (Thermo Fisher) according to manufacturer’s instructions.
The mRNA fraction was captured using Oligo (dT)25 beads (61002, Life Technologies) and DNAseI treated (18068-015, Life Technologies), followed by reverse transcription using 2 ul SuperscriptIII (18080-044, Life Technologies) using a GFP-mRNA specific primer (149 STARRseq rep RNA cDNA synth, CAAACTCATCAATGTATCTTATCATG) at 50ᴼC for 90 minutes, in a total reaction volume of 21 ul. To repress residual plasmid DNA contamination, cDNA was PCR amplified using a combination of primers (152 STARR reporter specific primer 2 fw, GGGCCAGCTGTTGGGGTG*T*C*C*A*C and 153 STARR reporter specific primer 2 rv, CTTATCATGTCTGCTCGA*A*G*C, where * represent phosphorothioate bonds) spanning a synthetic intron in the STARR-seq plasmid, as previously described (Arnold et al., 2013). PCR was performed with Phusion polymerase and High-fidelity buffer, in 6 x 50 ul reactions (cycling conditions: 98ᴼC 2 min, (98ᴼC 10 sec, 62ᴼC 30 sec, 72ᴼC 70 sec) x15, 72ᴼC 5 min, 4ᴼC hold). PCR reactions were pooled, purified using AMPureXP beads (1.0x) and eluted in 18 ul 0.1xTE. Absence of significant plasmid contamination in the PCR amplified cDNA was assessed by qPCR using a primer-set amplifying an amplicon from the STARR-seq plasmid backbone (161 STARRseq detect plasmid backbone qPCR fw, CATCATCGGGAATCGTTCTT, and 162 STARRSeq detect plasmid backbone qPCR rv, TGAAGATCAACTGGGTGCAA), relative to a primer-set amplifying GFP (154 STARRseq GFP fw, ACGGCCACAAGTTCTCTGTC, and 155 STARRseq GFP rv, GCAGTTTGCCAGTAGTGCAG). PCR amplified cDNA was then used in a second round of PCR to add Illumina index primers (7335, 7500, NEB) using priming on the adapter sequences added during the plasmid library generation. PCR was performed in 1-4x 50 ul reactions using Phusion polymerase and High-fidelity buffer (NEB)(cycling conditions: 98ᴼC 2 min, (98ᴼC 10 sec, 65ᴼC 30 sec, 72ᴼC 30 sec) x13, 72ᴼC 5 min, 4ᴼC hold), after which PCR reactions were pooled, purified using AMPureXP beads (1.0x) and eluted in 15 ul 0.1xTE. Quantity and quality of generated sequencing libraries was assessed on an Agilent Tapestation.

treatment_protocol: Primed and naive H9 hESCs were transfected using either Nucleofection (Lonza, VPH-5022), or using Lipofectamin3000 according to manufacturer’s instructions. For each transfection, six million cells were used and transfected with 8 ug of plasmid library DNA and 500 ng pmCherry-N1 plasmid (Clonetech) as transfection control. Cells were incubated in 10 cm dishes and 24h post-transfection, single cells were harvested and subjected to FACS. Non-transfected cells were used to set sorting gates, DAPI was used as a marker for dead cells.

tag: cell state source

value: Primed

tag: cell state target

tag: chip target

value: None (BAC)


title: X3seBACS_primed_BAC_RNA_2


title: HUDEP2_nontargeting_sgRNA_differentiated_rep1


title: primed_primed_Oct4_RNA_3

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a OCT4 ChIP-STARR-seq library generated in primed hESCs

source_name: embryonic stem cells


title: naive_primed_Oct4_RNA_3

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a OCT4 ChIP-STARR-seq library generated in naive hESCs

value: Naive


title: RNAP2_ZT4 control rep1

value: RNA Polymerase II (Biolegends #MMS-126R; clone 8WG1)


title: naive_primed_H3K4me1_RNA_1

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a H3K4me1 ChIP-STARR-seq library generated in naive hESCs


title: primed_primed_H3K27ac_RNA_4

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a H3K27ac ChIP-STARR-seq library generated in primed hESCs


title: naive_primed_H3K4me1_RNA_2


title: primed_primed_H3K4me1_RNA_3

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a H3K4me1 ChIP-STARR-seq library generated in primed hESCs


title: CD34 shRNA SC

value: shRNA SC


title: primed_primed_Oct4_RNA_4


title: primed_primed_H3K4me1_RNA_4


title: naive_primed_Oct4_RNA_4


title: primed_primed_H3K27ac_RNA_3


title: naive_primed_H3K27ac_RNA_2

description:
other RNA
STARR-RNA-seq for GFP-positive RNA from primed hESCs transfected with a H3K27ac ChIP-STARR-seq library generated in naive hESCs


title: Reverb⍺_ZT8 control REP2

value: Zeitgeber Time 8

value: Rev-erb⍺ (#23678 and #27401 produced by Ron Evans)


title: naive_primed_H3K27ac_RNA_1


title: Reverb⍺_ZT8 control REP1


title: Bmal1_ZT4 control rep2


title: RNAP2_ZT4 control rep2


title: HFDPC control

type: RNA

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

country: Japan

institute: Aomori University of Health and Welfare

description:
normal fibroblast from skin
TIG113 control

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

source_name: HFDPC control

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: HFDPC were purchased from TAKARA BIO INC. The HFDPC were routinely cultured in phenol red-free follicle dermal papilla cell growth medium at 37ºC in 5% CO2.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Then medium replace with phenol red-free follicle dermal papilla cell basal medium with or without BCE (1.0μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.

value: control

value: human fibroblasts from skin


title: ck1-alpha RNAi

city: Dallas

first: Rupali

last: Ugrankar

state: TX

address: 6000 Harry Hines Blvd

department: Cell Biology

institute: University of Texas Southwestern Medical Center

hyb_protocol: 15 µg of fragmented cRNA was hybridized in oven at 45°C for 16 h

scan_protocol: Array was scanned on GeneChip Scanner 3000

data_processing: Microarray Suite Version 5 (MAS5)

label: biotin

organism: Drosophila melanogaster

source_name: Drosphila mid-third instar larvae

label_protocol: GeneChip IVT Labeling Kit was used for labeling

growth_protocol: 20 Dcg-Gal4 females were crossed with 7 w1118 or UAS-Ck1alphaRNAi males in vials. Crosses were maintained at 25°C. After egg laying, larvae were cultured in medium to high-density conditions (75-150 larvae/vial) for 6 days before harvesting feeding mid-third instars.

extract_protocol: RNA was extracted from whole larvae (20 larva/sample) using Trizol reagent according to manufacturer's instuctions.

treatment_protocol: Larvae  were collected in 630 µm mesh fitted baskets, and washed with distilled water.

value: feeding, whole larvae

tag: age

value: mid-third instar

tag: Sex

value: female

value: Dcg-Gal4 X UAS-Ck1alphaRNAi


title: W1118

value: Dcg-Gal4 X w1118


title: HFDPC BCE

description:
normal fibroblast from skin
TIG113 blackcurrant

source_name: HFDPC blackcurrant extract

value: blackcurrant extract


title: Bmal1_ZT4 control rep1

value: gastrocnemius

value: Zeitgeber Time 4

tag: gender

value: male

value: Wild Type


title: tumor11

type: genomic

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

description: FFPE

hyb_protocol: Arrays were hybridized for 16 hours, then washed and stained in the GeneChip® Fluidics Station 450 according to manufacturer's instructions

scan_protocol: Stained arrays  were scanned on Genechip Scanner 3000 7G using AGCC Sofware according to manufacturer's instructions

data_processing:
Each sample has 2 CEL files since it is hybridized in two arrays(A/T array and G/C). Hence, ” _A” correspond to the CEL file for the A/T array,  and  “_C” correspond to the CEL file for the G/C array. Nexus Express for OncoScan analysis software (BioDiscovery, Hawthorne, CA) was used to obtain the OSCHP files
CEL files were added to the affymetrix OncoScan Console where resulting OSCHP files were generated and standard Central QC was completed.  B-allele frequency track was made available by Chromosome Analysis Suite (ChAS) Software 3.1 using OSCHP files. Nexus Express for OncoScan 3 software was also used to generate whole-genome view of copy number gains and losses, B-allele frequency, and copy number aberrations

source_name: genomic DNA

label_protocol: 80 ng of FFPE-DNA was Annealed to MIP probes,Gap filled, Linearized, PCR amplified, HaeIII- digested, Fragmented and hybridized to arrays with biotinylated oligos (for labeling) according to the standard OncoScan™ array protocol

growth_protocol: Samples were formamid-fixed paraffin-embedded tissue

extract_protocol: Manual DNA extraction protocol (QIAampDNA Mini Kit, Qiagen, Valencia, CA) was used for isolation of genomic DNA from the archived breast tumor specimens. DNA yield and purity was evaluated by Nanodrop and TapeStation

treatment_protocol: no treatment

tag: disease state

value: Neurofibromatosis type 1

value: breast tumor specimen

value: NF1 germline mutation

tag: age at diagnosis

tag: pathology

value: IDC, stage T2N3M0, grade III

tag: survival

value: 5-10 years


title: tumor10

description: FFPE

value: IDC, stage T3N3M2, grade 3/3


title: tumor09

description: FFPE

value: IDC, stage T1N0Mx, grade T3N2M1


title: Mixed_Rb_6.Oct22.07_CGH_UHNC

city: Chapel Hill

first: Charles

last: Perou

state: NC

address: 102 Mason Farm Road

institute: University of North Carolina at Chapel Hill

description: mammary tumor

hyb_protocol: hybridized to Agilent 244k CGH arrays (model G4415A)

scan_protocol: scanned on Agilent scanner (model G2505B)

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: DNA reference

label_protocol: labeled according to the direct incorporation method (Agilent)

extract_protocol: genomic DNA isolated using Dneasy kit (Qiagen)

tag: reference

value: DNA reference

extract_protocol: Qiagen Dneasy Kit

tag: tumor

value: mammary tumor


title: Mixed_Rb_3.oct22.07_CGH_UHNC

description: mammary tumor


title: Mixed_Rb_4.Oct22.07_CGH_UHNC

description: mammary tumor


title: tumor08

description: FFPE

value: stage n/a


title: FVB_Wap_Myc_117252_CGH_Biorep_cn_Perou

description: mammary tumor


title: Mixed_Rb_5.Oct22.07_CGH_UHNC

description: mammary tumor


title: Mixed_Brg1het_T160_CGH_Bultman

description: mammary tumor


title: tumor07

description: FFPE

value: IDC, stage T1aN0Mx, grade II

value: 10+ years


title: FVB_Wap_Myc_117318_CGH_Biorep_cn_Perou

description: mammary tumor


title: FVB_Wap_Myc_117254_CGH_biorep_cn_Perou

description: mammary tumor


title: Mixed_Rb_1.Oct22.07_CGH_UHNC

description: mammary tumor


title: Mixed_Brg1het_T2134_CGH_Bultman

description: mammary tumor


title: Mixed_Brg1het_T135_CGH_Bultman

description: mammary tumor


title: Mixed_Brg1het_T172_CGH_Bultman

description: mammary tumor


title: tumor05

description: FFPE

value: IDC, pT1aN0Mx, grade T3N3M2 (8/9)


title: tumor04

description: FFPE

value: IDC, stage pT1N1Mx, moderately differentiated


title: FVB_MMTV_Wnt1_iR2_5103_3L_CGH_Rosen

description: mammary tumor


title: FVB_MMTV_Wnt1_2494-2L_CGH_Rosen

description: mammary tumor


title: tumor03

description: FFPE

value: LCIS


title: tumor02

description: FFPE

value: IDC, positive nodes 6/29


title: Mixed_Brg1het_T2023_CGH_Bultman

description: mammary tumor


title: FVB_MMTV_Wnt1_2406-4R_CGH_Rosen

description: mammary tumor


title: FVB_Wap_Myc_117166_CGH_Biorep_cn_Perou

description: mammary tumor


title: FVB_MMTV_Pymt_116301_CGH_Perou

description: mammary tumor


title: SP_8

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

state: CA

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC v. 0.11.4
Reads with adapter contamination were trimmed using Trimmomatic v. 0.32
Reads aligned using STAR vs. 2.4.2a
FPKMs and differential expression tests calculated using the Cufflinks Suite v. 2.2.1.
Gene annotations obtained from RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: TXT file containing a matrix of FPKM values for all samples.

molecule: polyA RNA

source_name: Scalp psoriatic skin

extract_protocol:
RNA was extracted from one 4-mm punch biopsy specimen for bulk RNA sequencing with the Qiagen Allprep DNA/RNA mini kit.
Samples that passed quality control underwent library preparation using the Ovation RNA-Seq System V2 protocol (Nugen) or the Ribozero (Illumina) kits.

value: skin

value: scalp psoriasis


title: FVB_T11_x1_CGH_GMurrow

description: mammary tumor


title: tumor01

description: FFPE

value: Neurofibromatosis type 1

value: breast tumor specimen

value: IDC, stage pT1aN0Mx, grade T2N3M1 (6/9)


title: FVB_MMTV_Wnt1_iR2_5101_3L_CGH_Rosen

description: mammary tumor


title: FVB_MMTV_Wnt1_3065_CGH_Rosen

description: mammary tumor


title: FVB_WAP_Myc_117250_CGH_Perou

description: mammary tumor


title: FVB_MMTV_Pymt_103572-T2_CGH_cn_Perou

description: mammary tumor


title: SP_6


title: FVB_MMTV_Wnt1_2543-4L_CGH_Rosen

description: mammary tumor


title: FVB_MMTV_Wnt1_3718-3R_CGH_Rosen

description: mammary tumor


title: tumor06

description: FFPE

value: NF1 germline mutation

value: IDC, multifocal, stage T1N1Mx, grade II


title: SP_5


title: SP_7


title: CP_7

source_name: Conventional psoriatic skin

value: psoriasis


title: CP_6


title: CP_8


title: CP_5


title: FVB_MMTV_Pymt_103572-T1_CGH_cn_Perou

description: mammary tumor

value: DNA reference


title: FVB_MMTV_Neu_117391_CGH_cn_Perou

description: mammary tumor

value: mammary tumor


title: HF_3

source_name: Palmoplantar psoriatic skin

value: palmoplantar psoriasis


title: FVB_MMTV_Pymt_103571_CGH_cn_Perou

description: mammary tumor


title: FVB_MMTV_Neu_116922_CGH_cn_Perou

description: mammary tumor


title: RWPE1_sh268_DMSO_24hr_A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells maintained in Keratinocyte Serum Free Medium supplemented with EGF and Bovine Pituitary Extract. shCTL and shRARG containing cells were maintained in 2ug/uL puromycin for selection.

extract_protocol: RNA was extracted with TRIzol reagent

treatment_protocol: Exponentially growing cells were treated with 10nM CD437 or DMSO vehicle for 24 hours.

value: male

tag: cell line

tag: cell type

value: non-malignant prostate epithelial cell

tag: shRNA

tag: treatment

value: DMSO


title: RWPE1_sh268_10nMCD437_24hr_A


title: RWPE1_sh268_DMSO_24hr_B


title: RWPE1_sh268_10nMCD437_24hr_B


title: RWPE1_sh268_DMSO_24hr_C


title: RWPE1_sh268_10nMCD437_24hr_C


title: RWPE1_shC_10nMCD437_24hr_B

value: shCTL


title: RWPE1_shC_DMSO_24hr_B


title: RWPE1 bi-NC input M4

source_name: non-malignant prostate cell line transfected with biotin-miRNA

growth_protocol: Cells maintained in Keratinocyte Serum Free Medium supplemented with EGF and Bovine Pituitary Extract.

treatment_protocol: Exponentially growing cells were transfected with 30nM biotin-miR-96 or non-targeting control (bi-NC) for 24 hours.

tag: biotin-mirna

value: bi-NC

tag: rna source

value: Input


title: RWPE1_shC_10nMCD437_24hr_A


title: FVB_C3-Tag_117517-1_CGH_Perou

description: mammary tumor


title: RWPE1 bi-96 input M4


title: RWPE1_shC_DMSO_24hr_A


title: RWPE1 bi-NC PD M4

value: Pulldown


title: RWPE1_shC_DMSO_24hr_C


title: RWPE1 bi-96 input M3


title: RWPE1 bi-96 PD M3


title: RWPE1_shC_10nMCD437_24hr_C


title: RWPE1 bi-96 PD M4


title: RWPE1 bi-NC PD M3


title: RWPE1 bi-96 PD M2


title: RWPE1 bi-NC input M3


title: RWPE1 bi-NC input M2


title: RWPE1 bi-96 input M2


title: RWPE1 bi-NC PD M2


title: FVB_C3-Tag_116966_CGH_Perou

description: mammary tumor


title: LNCaP_sh268_250nMCD437_24hr_C

source_name: malignant prostate cell line infected with shRNA

growth_protocol: Cells maintained in RPMI 1640 Medium supplemented with 10% fetal bovine serum. shCTL and shRARG containing cells were maintained in 2ug/uL puromycin for selection.

treatment_protocol: Exponentially growing cells were treated with 250nM CD437 or DMSO vehicle for 24 hours.

value: LNCaP

value: malignant prostate epithelial cell


title: FVB_MMTV_Neu_110288_CGH_cn_Perou

description: mammary tumor


title: LNCaP_sh268_DMSO_24hr_C


title: LNCaP_sh268_250nMCD437_24hr_B


title: LNCaP_shC_250nMCD437_24hr_B


title: LNCaP_sh268_250nMCD437_24hr_A


title: Brain csf1ra-/-;b-/- #3

city: Rotterdam

first: Tjakko

middle: Jakob

last: Van Ham

address: Wytemaweg 80

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

data_processing:
Image analysis and base calling were done using the Illumina pipeline. Reads were aligned to the zebrafish genome (GRCz10 ) using HiSat2 aligner (Pertea et al., 2016).
The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges (Lawrence  et al. Plos Computational Biology, 2013).
Differential gene expression analysis was performed with Bioconductor package EdgeR (Robinson, et al., 2010).
Genome_build: GRCz10

organism: Danio rerio

source_name: Brain

extract_protocol:
Zebrafish were sacrificed with ice water. Then brains were taken out of the skull and trypsinized on ice for 2 hours. Brains were flash frozen in liquid nitrogen. Total RNA extraction was performed using Trizol.
cDNA libraries were created using reverse transcription, pre-aplification and Tn5 tagmentation. Illumina RNAseq libraries were prepared from cDNA using the Illumina TruSeq™ RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina Inc.). In all libraries 50 nucleotide single-end reads (SR50) were sequenced on an Illumina HiSeq2500 sequencer according to the manufacturer’s protocol, obtaining 10-20 million reads per sample library.

tag: genotype

tag: strain

value: TLF x AB

tag: tissue

value: brain

value: ~8 months

tag: line


title: LNCaP_shC_DMSO_24hr_C

tag: gender


title: LNCaP_shC_250nMCD437_24hr_C


title: FVB_C3-Tag_117338-1_CGH_Perou

description: mammary tumor


title: Non-Volar Passage 4

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Gene expression data from NHEK from the sole or dorsum

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: Normal cultured primary human epidermal keratinocytes

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: Normal human epidermal keratinocytes (NHEKs) were harvested from the volar or dorsal foot  of a human donor and cultured in KGM-GOLD to passage 4 before use.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells were not treated differently; only harvested from different locations

value: Normal Non-Volar keratinocyte

tag: passage

value: Passage 4


title: LNCaP_sh268_DMSO_24hr_A


title: FVB_MMTV_Neu_116843-2_CGH_cn_Perou

description: mammary tumor

value: DNA reference


title: FVB_MMTV_Neu_116913_CGH_cn_Perou

description: mammary tumor

value: mammary tumor


title: Brain csf1ra-/-;b-/- #2

tag: age


title: Balbc_Brca1het_p53het_IR_C0917_4_CGH_Koller

description: mammary tumor


title: Balbc_Brca1het_p53het_IR_B1129_4_CGH_Koller

description: mammary tumor


title: LNCaP_sh268_DMSO_24hr_B


title: LNCaP_shC_DMSO_24hr_B


title: Normal Volar Passage 4

description: Gene expression data from NHEK from the sole early or late passage

growth_protocol: Normal human epidermal keratinocytes (NHEKs) were harvested from the sole of a human donor and cultured in KGM-GOLD for either 4 or 8 passages before use.

treatment_protocol: Cells were not treated differently; only harvested at different passages

value: Normal Volar keratinocyte

tag: passage level


title: LNCaP_shC_250nMCD437_24hr_A

value: male


title: Brain csf1ra-/-;b-/- #1


title: Volar Passage 4


title: Brain csf1ra-/-;b+/- #3


title: Brain csf1ra-/-;b+/- #2


title: LNCaP_shC_DMSO_24hr_A


title: Normal Volar Passage 8

value: Passage 8


title: Brain csf1ra-/-;b+/- #1


title: FVB_C3(1)-Tag_120157_untreated_CGH_GMurrow

description: mammary tumor


title: Brain csf1ra-/- #2


title: Brain csf1ra-/- #1


title: Brain control #2

value: wild type


title: FVB_MMTV_Neu_116916_untreated_CGH_GMurrow

description: mammary tumor


title: Brain control #1


title: LNCaP bi-96 input M2

source_name: malignant prostate cell line transfected with biotin-miRNA

growth_protocol: Cells maintained in RPMI 1640 Medium supplemented with 10% fetal bovine serum.


title: LNCaP bi-NC PD M3


title: Microglia csf1ra-/-;b+/- #2

source_name: brain

extract_protocol:
Zebrafish were sacrificed with ice water. Then brains were taken out of the skull and trypsinized on ice for 2 hours. Percoll gradient centrifugation was used to enrich the cell population for microglia. FACS sorting based on GFP expressing was used to isolate microglia. Cells were spun down and pellet was flash frozen in liquid nitrogen. Total RNA extraction was performed using the Quiagen miRNeasy kit.
cDNA libraries were created using the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Clontech). Illumina RNAseq libraries were prepared from cDNA using the Illumina TruSeq™ RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina Inc.). In all libraries 50 nucleotide single-end reads (SR50) were sequenced on an Illumina HiSeq2500 sequencer according to the manufacturer’s protocol, obtaining 10-20 million reads per sample library.

value: Microglia

value: 9-12 months


title: LNCaP bi-96 PD M3


title: Brain csf1ra-/- #3


title: Microglia csf1ra-/-;b+/- #1


title: Microglia csf1ra-/- #2


title: Td35405_0_2

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

description:
Wild type and type strain of the species
Microorganism frequently isolated from lesion of chronic periodontitis.

hyb_protocol: 1. Fragmentation of Cy3 labeled cRNA was carried out at 60°C for 30 min. 2. Stop fragmentation. 3. Hybridization was performed at 65°C for 17 h with agitation in Hybrioven.

scan_protocol: Scanned by Agilent Technologies Microarray Scanner

data_processing:
Normalization: Shift to 75 percentile
Baseline Transformation: median of control samples
GeneSpring 13.1.1 software.

organism: Treponema denticola

label_protocol: Cy3 label with Input Quick-Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: T. denticola ATCC 35405 was inoculated into 100 mL 10% TYGVS and incubated at 37°C under anaerobic conditions for 2 d (to an absorbance at 660 nm of approximately 0.4). The cells were harvested and resuspended in TYGV, 1% TYGVS and 10% TYGVS and incubated under anaerobic conditions for 17 h.

extract_protocol: TRIzol reagent (Invitorogen, Carlsbad, CA)

treatment_protocol:
Td35405_10:    T. denticola ATCC 35405 grown in medium containing 10% serum
Td35405_1:    T. denticola ATCC 35405 grown in medium containing 1% serum
Td35405_0:    T. denticola ATCC 35405 grown in medium containing 0% serum

tag: culture condition

value: 0% serum


title: FVB_C3-Tag_117485_CGH_Perou

description: mammary tumor

tag: reference


title: Balbc_p53het_IR_C1201-4_spontaneous_CGH_GMurrow

description: mammary tumor

tag: tumor


title: CHML3

city: Isfahan

first: Aboozar

last: Soorni

address: Isfahan

department: Biotechnology

country: Iran

institute: Isfahan University of Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then RNA sequencing data were assembled using BinPacker software
The RNA-seq by Expectation Maximization (RSEM) package was used to estimate gene expression levels from the de novo assembled transcripts
Identification of differentially expressed genes was carried out using run_DE_analysis.pl, which involves the Bioconductor package EdgeR in the R statistical environment
Gene expression values were measured in FPKM (fragments per kilobase of transcript per million reads mapped)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Chelidonium majus

source_name: C. majus_leaf

extract_protocol:
Fresh leafs and roots were  frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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: ecotype

value: leaf


title: CHML4


title: LNCaP bi-NC PD M2

tag: cell line

value: LNCaP

tag: cell type

value: bi-NC

value: Pulldown


title: LNCaP bi-NC input M3

value: malignant prostate epithelial cell

value: Input


title: LNCaP bi-96 input M3


title: Td35405_0_1


title: LNCaP bi-NC input M1


title: LNCaP bi-96 PD M1


title: Td35405_1_1

value: 1% serum


title: Microglia control #2

value: TLF x AB

value: brain


title: Td35405_10_2

value: 10% serum


title: Td35405_1_2


title: Td35405_10_3


title: Microglia csf1ra-/- #1


title: LNCaP bi-96 input M1


title: CHMR2

source_name: C. majus_root

value: root


title: Microglia control #1


title: LNCaP bi-NC input M2

value: male


title: articular zone 4

status: Public on Jul 19 2018

city: New York

first: Christopher

middle: L

last: Ricupero

address: 630 West 168th Street VC12-2132

department: Center for Craniofacial Regeneration

institute: Columbia University Medical Center

data_processing:
Samples were sequenced using the Illumina HiSeq 2500
The RNA-Seq reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32)
Mapped to the Mus musculus genome (version mm10) with SHRiMP2.2.3
Differential expressed genes were identified using DESeq, with <0.05 false discovery rate (FDR).
Fragments 160 Per Kilobase of exon model per Million Mapped fragments (FPKM) were estimated for each gene in each sample. Hierarchical clustering was also performed on log2FPKM values with Cluster 3.0. Only genes with FDR<0.05 and ≥0.80 standard deviation were included.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mandibular condyle

extract_protocol:
Laser capture microdissection (LCM) protocol: LCM was performed using the PALM Microbeam system (Zeiss). The articular zone, mature zone and hypertrophic zone were readily identified on the basis of cell morphology under 10×microscope objective. A focused laser beam was activated to dissect the zone of interestinto Adhesive Cap tube caps (Zeiss). A total of 25-30 sections from each zone were microdissected and pooled to create single samples. A total of three independent biological replicates were tested.
The collected cell samples were immediately lysed in 50-μl Arcturus PicoPure RNA extraction buffer at 42°C for 30 min. Total RNA was extracted from cell lysates using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). To evaluate RNA quality, the RNA 6000 Pico kit and Bio-Analyzer 2100 (Agilent Biotechnologies) were used. RNA integrity number (RIN) ranging from 10 (intact) to 1 (totally degraded) was analyzed and only high-quality RNA samples (RIN value>6) were selected for RNA-sequencing.
RNA samples were subjected to RNA-sequencing at the University of Rochester Genomics Research Center. Briefly, total RNAs from each sample were polyA selected and single-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit (Illumina).

value: Mandibular condyle


title: articular zone 3


title: LNCaP bi-NC PD M1


title: LNCaP bi-96 PD M2


title: articular zone 2


title: Td35405_10_1


title: mature zone 4

description:
Middle_biorep4
That replicate did not map well so we left it out of further processing. No processed data.


title: mature zone 3


title: Bt_KO5_S11

city: Boston

first: Lina

last: Yao

state: Massachusetts

address: 250 Longwood Ave

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
Illumina bcl2fastq 2.19.1.403 software used for basecalling.
Reads were assessed for quality using FastQC and aggregated in MultiQC.
STAR aligner was used against mouse geneome GRCm38 revision 91.
The edgeR package was performed for the differential expression analysis, using the exacTest calculation and Benjamini-Hochberg correction (FDR). FDR <= 0.05, fold-change (FC) >= ± 1.5 were set as the threshold.
The goseq package, stating that significant differentially-expressed genes were subject to a probability weighting function, to account for gene length, in the goseq package, and run against Gene Ontology (GO) and KEGG pathways.
Genome_build: Mouse geneome GRCm38 revision 91 was downloaded and used.
Supplementary_files_format_and_content:
BtBSH_KO_vs_WT_differential_expressed_genes: normalized counts via TMM normalization; differential gene expression analysis result  with FDR <= 0.05 and fold-change of KO / WT >= 1.5 or <= -1.5.
goseq: Gene ontology (GO) enrichment analysis
kegg: Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis

source_name: mouse distal ileum_KO

growth_protocol: 8-9 weeks old male germ-free C57BL/6 mice were maintained in gnotobiotic isolators at the Massachusetts Host-Microbiome Center under a strict 12-hour light cycle and a constant temperature (21 ± 1∘ C) and humidity (55-65%).

extract_protocol:
Total RNA was extracted from frozen mouse distal ileum obtained from the first mono-colonization experiment using RNeasy Mini Kit (Qiagen) and DNA was removed by on-column DNase digestion using RNAse-free DNAse Set (Qiagen) (n=6).
RNA quality was checked on Bioanalyzer before proceeding to library preparation and RNA-sequencing (paired-end, 100 bp read length) on Illumina HiSeq 2500 platform by the Biopolymers Facility at Harvard Medical School. Illumina's Ribo Zero H/M/R kit was used to perform ribosomal reduction. Agilent Tapestation 4200 was used for post-prep QC with the High Sensitivity D1000 assay. The data from the Tapestation assay was combined with the data from KAPA library quantification qPCR on the Applied Biosystems QuantStudio 7 instrument. The libraries were pooled equimolar and were sequenced on the HiSeq 2500 at 8.0pM with 5% PhiX.

treatment_protocol: One group of mice were mono-colonized with either Bacteroides thetaiotaomicron VPI-5482 wild type (Bt WT) and the other group were mono-colonized with the bile salt hydrolase (D2086) knock out mutant (Bt KO) by oral gavage of overnight cultures. The mice were co-housed in their respective groups in germ-free isolators for the entire duration of the experiment. The mice were fed a standard diet containing 24% of calories from fat, 23% from protein, and 53% from carbohydrates (Autoclavable Mouse Breeder Diet 5021; LabDiet) for the first 4 days after gavage. After a 4 day acclimation period post-gavage, the mice were switched to a high fat diet (Research Diets) with 60 kcal% of fat sterilized by 10 -20 kGy of gamma-irradiation.

value: 8-9 weeks

tag: Sex

tag: monocolonized with

value: Bacteroides thetaiotaomicron VPI-5482 bile salt hydrolase knockout strain

value: distal ileum

tag: molecule subtype

value: total RNA with ribosomal depleted


title: Bt_KO4_S10


title: Bt_KO6_S12


title: Bt_KO2_S8


title: Bt_KO3_S9


title: Bt_WT5_S5

source_name: mouse distal ileum_WT

value: Bacteroides thetaiotaomicron VPI-5482 wild type strain


title: Bt_WT6_S6


title: Bt_WT4_S4


title: Bt_WT3_S3


title: Bt_KO1_S7


title: FVB_C3-Tag_117338-2_CGH_Perou

description: mammary tumor

value: DNA reference

value: mammary tumor


title: ED170916

first: Erin

middle: Elizabeth

last: Duffy

state: MA

address: 200 Longwood Ave, Goldenson 405

department: Neurobiology

description: no DRB enriched rep 2

data_processing:
Adapters were trimmed using cutadapt 1.10
Sequencing reads were aligned using STAR (version 2.4.2a) to a joint index of the H. sapiens and S. pombe genomes (GRCh38 and sp2) and transcriptomes (NCBI and Ensembl Fungi v22; respective) or to the Mus musculus genome and transcriptome (GRCm38, NCBI).
s4U Chase-seq and MTS-TT-seq: BedGraphs were normalized using values that were calculated in edgeR based on counts from the S. pombe spike-ins
Genome coverage tracks were generated using STAR (version 2.4.2a)
Genome_build: GrCh38, GrCm38
Supplementary_files_format_and_content: bedGraph files for forward and reverse strands for each sample are separated

source_name: Primary cortical neurons

growth_protocol: Immortalized K562s were cultured at 37 degrees C in high glucose RPMI media supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, and 1% (v/v) penicilin/streptamycin. Mouse cortical neurons were isolated at E18 as previously described (Kaech et al. (2006) Nat. Protocols). About 2x10^6 cells were plated per 6-well dish.

extract_protocol:
All samples: Cells were resuspended in TRIzol reagent, flash frozen, and stored overnight at -80°C. Cell lysates were chloroform extracted once and total RNA purified by isopropanol precipitation. Contaminating DNA was digested with Turbo DNase. Samples were purified by phenol:chloroform extraction followed by a second isopropanol precipitation and resuspension in RNase-free water. 1-5 μg RNA in 9 μL RNase-free water was mixed with 1.5 μL 10x binding buffer (1 M NaCl, 100 mM HEPES pH 7.4, 10 mM EDTA, 0.5% Tween), and 3 μL DMF, added to MTS resin (10 μL aliquot), and incubated at room temperature in the dark for 2 h with rotation. Beads were captured on a magnetic rack and supernatant removed. Beads were incubated for 5 min with the following wash buffers: once with 100 μL 1x binding buffer, twice with 100 μL high salt wash buffer (1M NaCl, 100 mM Tris pH 7.4, 10 mM EDTA, 0,05% Tween), twice with 100 μL denaturing buffer (8 M guanidinium chloride), and three times with 100 μL buffer TE (10 mM Tris pH 7.4, 1 mM EDTA) at 55°C. RNA was eluted with 10 μL elution buffer (100 mM NaCl, 10 mM Tris pH 7.4, 1 mM EDTA, 10 mM DTT, and 100 pg fragmented total RNA from S. pombe), and incubated at room temperature in the dark for 15 min with rotation. Eluent was ethanol precipitated with 5-10 μg glycoblue, and RNA concentration was assayed by Bioanalyzer RNA 6000 Pico Kit (Agilent) according to the manufacturer’s instructions. For s4U Chase-Seq and TT-Seq: total RNA was sheared prior to s4U-RNA enrichment with MgCl2 at 94℃ for 4 min.
10 ng input and enriched RNA were used for rRNA-depleted library preparation. Sequencing libraries were constructed using the Clontech RNA Pico Input mammalian kit.

treatment_protocol: s4U Chase-Seq: Cultured cells at 50% confluence were labeled with 1 mM s4U for 2h, followed by chase with 20 mM uridine in fresh media. After 0.5h or 18h, cells were harvested in TRIzol. TT-Seq: Cultured cells at 80% confluence were labeled with 1 mM s4U for 5 min, followed by harvest in TRIzol. s4U DRB-Seq: Cells were treated wtih 500 μM DRB or DMSO for 3h. During the last 30, 20, or 10 min of DRB treatment for t=0, t=10, or t=20 min samples, respectively, 500 μM s4U was added to media. Cells were washed with PBS and media containing 500 μM s4U was added. Cells were harvested after 0, 10, or 20 min of media replacement.

value: Primary cortical neurons

tag: experiment

value: 4sU DRB-Seq

tag: s4u feed + chemical treatment

value: 30 min s4U

tag: target molecule

value: biochemically enriched RNA


title: ED170915

description: no DRB enriched rep 1

tag: tissue


title: ED170914

description: DRB t=20 min enriched rep 2

value: 3h DRB, 30 min 500 uM s4U at 2h 50 min DRB, 20 min DRB release


title: ED170911

description: DRB t=10 min enriched rep 1

value: 3h DRB, 30 min 500 uM s4U at 2h 40 min DRB, 10 min DRB release


title: ED170910

description: DRB t=0 min enriched rep 2

value: 3h DRB, 30 min 500 uM s4U at 2.5h DRB, 0 min DRB release


title: ED170912

description: DRB t=10 min enriched rep 2


title: ED170909

description: DRB t=0 min enriched rep 1


title: ED170904

description: RNA-Seq

value: total RNA


title: mature zone 2

tag: strain


title: donor309pl7cell192

city: Heidelberg

first: Natalie

last: Romanov

address: Meyerhofstr. 1

department: Structural and Computational Biology

institute: EMBL

description:
single-cell RNA
1 out of 192 cells per donor

data_processing:
Alignments to Homo sapiens genome (hg38) was performed with Salmon v0.9.1 (Patro et al., 2017)
tximport used to produce gene count table (Soneson et al., 2015)
remove cells with less than 1000 genes at a minimum of 10 reads per gene, python 2.7.14
remove genes with less than 10 reads in at least 5 cells, python 2.7.14
processing with SimpleSingleCell version1.2.0 (Lun et al., 2016) for further filtering and normalization
Genome_build: hg38
Supplementary_files_format_and_content: HTMGNBGX3_Donor_302_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: HTMGNBGX3_Donor_304_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: HTMGNBGX3_Donor_305_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: HTMGNBGX3_Donor_309_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: donor302_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table
Supplementary_files_format_and_content: donor304_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table
Supplementary_files_format_and_content: donor305_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table
Supplementary_files_format_and_content: donor309_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table

source_name: Haematopoietic progenitor cells

growth_protocol: Bone marrow (BM) samples were harvested through puncture at the posterior iliac crest using a Yamshidi needle

extract_protocol:
Sequencing libraries from 192 single CD34+ cells per donor were produced based on the smart-seq2 protocol of Picelli et al. 2014 and the tagmentation procedure of Henning et al. 2018 with slight modifications as described in the publication.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BM aspirates were processed by FICOLL density fractionation for isolation of MNCs; stained with CD34-APC, CD45-FITC and CD14-PE; FACS-sorted and stored at -80°C

tag: donor

tag: donor age

value: 21.2 years

tag: gender

value: female

value: bone marrow


title: donor309pl7cell191


title: donor309pl7cell187


title: donor309pl7cell188


title: donor309pl7cell189


title: donor309pl7cell190


title: Bt_WT2_S2

tag: age

value: 8-9 weeks

value: male


title: Bt_WT1_S1

value: distal ileum

value: total RNA with ribosomal depleted


title: donor309pl7cell186


title: ED170913

description: DRB t=20 min enriched rep 1


title: donor309pl7cell184


title: donor309pl7cell182


title: donor309pl7cell183


title: donor309pl7cell176


title: donor309pl7cell177


title: donor309pl7cell178


title: donor309pl7cell179


title: donor309pl7cell171


title: donor309pl7cell174


title: donor309pl7cell172


title: donor309pl7cell170


title: donor309pl7cell175


title: donor309pl7cell167


title: donor309pl7cell168


title: donor309pl7cell169


title: donor309pl7cell166


title: donor309pl7cell164


title: donor309pl7cell162


title: donor309pl7cell180


title: donor309pl7cell160


title: donor309pl7cell161


title: donor309pl7cell163


title: donor309pl7cell165


title: donor309pl7cell181


title: donor309pl7cell185


title: donor309pl7cell156


title: donor309pl7cell155


title: donor309pl7cell159


title: donor309pl7cell157


title: donor309pl7cell154


title: donor309pl7cell158


title: donor309pl7cell173


title: donor309pl7cell153


title: donor309pl7cell151


title: donor309pl7cell150


title: donor309pl7cell148


title: donor309pl7cell146


title: donor309pl7cell145


title: donor309pl7cell147


title: donor309pl4cell143


title: donor309pl4cell144


title: donor309pl4cell140


title: donor309pl4cell141


title: donor309pl4cell139


title: donor309pl4cell137


title: donor309pl4cell138


title: donor309pl4cell135


title: donor309pl4cell134


title: donor309pl4cell136


title: donor309pl4cell133


title: donor309pl4cell132


title: donor309pl4cell129


title: donor309pl4cell127


title: donor309pl4cell131


title: donor309pl4cell128


title: donor309pl7cell149


title: donor309pl7cell152


title: donor309pl4cell125


title: donor309pl4cell130


title: donor309pl4cell124


title: donor309pl4cell123


title: donor309pl4cell122


title: donor309pl4cell119


title: donor309pl4cell121


title: donor309pl4cell120


title: donor309pl4cell142


title: donor309pl4cell117


title: donor309pl4cell116


title: donor309pl4cell126


title: donor309pl4cell110


title: donor309pl4cell106


title: donor309pl4cell109


title: donor309pl4cell112


title: donor309pl4cell107


title: donor309pl4cell111


title: donor309pl4cell105


title: donor309pl4cell100


title: donor309pl4cell104


title: donor309pl4cell101


title: donor309pl4cell118


title: donor309pl4cell102


title: donor309pl4cell099


title: donor309pl4cell097


title: donor309pl4cell098


title: donor309pl2cell096


title: donor309pl2cell093


title: donor309pl2cell091


title: donor309pl2cell094


title: donor309pl2cell095


title: donor309pl2cell092


title: donor309pl2cell089


title: donor309pl4cell113


title: donor309pl2cell090


title: donor309pl4cell114


title: donor309pl4cell108


title: donor309pl2cell087


title: donor309pl2cell085


title: donor309pl2cell084


title: donor309pl2cell083


title: donor309pl2cell082


title: donor309pl4cell103


title: donor309pl4cell115


title: donor309pl2cell088


title: donor309pl2cell086


title: donor309pl2cell080


title: donor309pl2cell077


title: donor309pl2cell076


title: donor309pl2cell075


title: donor309pl2cell079


title: donor309pl2cell072


title: donor309pl2cell074


title: donor309pl2cell073


title: donor309pl2cell081


title: donor309pl2cell071


title: donor309pl2cell069


title: donor309pl2cell068


title: donor309pl2cell070


title: donor309pl2cell066


title: donor309pl2cell065


title: donor309pl2cell064


title: donor309pl2cell063


title: donor309pl2cell062


title: donor309pl2cell061


title: donor309pl2cell060


title: donor309pl2cell059


title: donor309pl2cell056


title: donor309pl2cell057


title: donor309pl2cell055


title: donor309pl2cell054


title: donor309pl2cell053


title: donor309pl2cell051


title: donor309pl2cell050


title: donor309pl2cell052


title: CHMR4

value: root


title: donor309pl2cell049


title: donor309pl1cell047


title: donor309pl1cell048


title: donor309pl2cell067


title: donor309pl1cell043


title: donor309pl1cell046


title: donor309pl1cell042


title: donor309pl1cell044


title: donor309pl1cell041


title: donor309pl1cell039


title: donor309pl1cell037


title: donor309pl1cell038


title: donor309pl1cell040


title: donor309pl1cell036


title: donor309pl1cell035


title: donor309pl1cell033


title: donor309pl1cell032


title: donor309pl1cell031


title: donor309pl1cell030


title: donor309pl1cell028


title: donor309pl1cell029


title: donor309pl1cell027


title: donor309pl1cell045


title: donor309pl1cell026


title: donor309pl1cell025


title: donor309pl1cell023


title: donor309pl1cell024


title: donor309pl1cell021


title: donor309pl1cell018


title: donor309pl1cell022


title: donor309pl1cell019


title: donor309pl1cell017


title: donor309pl1cell014


title: donor309pl1cell012


title: donor309pl1cell015


title: donor309pl1cell011


title: donor309pl1cell010


title: donor309pl1cell016


title: donor309pl1cell013


title: donor309pl2cell058


title: donor309pl1cell009


title: donor309pl1cell034


title: donor309pl1cell008


title: donor309pl1cell006


title: donor309pl1cell005


title: donor309pl1cell004


title: donor309pl1cell002


title: donor309pl1cell003


title: donor309pl1cell001


title: donor305pl6cell192

value: 62.2 years


title: donor305pl6cell191


title: donor309pl1cell020


title: donor305pl6cell189


title: donor305pl6cell190


title: donor305pl6cell187


title: donor305pl6cell188


title: donor309pl1cell007


title: donor305pl6cell185


title: donor305pl6cell184


title: donor305pl6cell183


title: donor305pl6cell176


title: donor305pl6cell181


title: donor305pl6cell178


title: donor305pl6cell177


title: donor305pl6cell180


title: donor305pl6cell182


title: donor305pl6cell179


title: donor305pl6cell175


title: Jurkat Endpoint, Replicate 2

city: San Francsico

first: Max

middle: A

last: Horlbeck

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

institute: UCSF

data_processing:
Base-calling and demultiplexing with bcl2fastq v2.17.1.14; --barcode-mismatches 1 --minimum-trimmed-read-length 5 --mask-short-adapter-reads 5 --use-bases-mask y19,y19,i6nn,y38 (for triple sequencing)
Each sgRNA (R1 and R2) or barcode pair (R3) was aligned to the expected library allowing 1 mismatch each using custom scripts (github.com/mhorlbeck/Gimap_tools, tripleseq_fastqgz_to_counts.py). For full triple sequencing analysis, an sgRNA pair was counted if both sgRNAs and barcodes mapped to the expected library and if sgRNA A and B each matched the correct barcode. Reads were summed across all lanes for a given sample. Counts from each of sgRNA, barcode, and triple sequencing for each sample were calculated, except for K562 T0 where only barcode sequencing was available.
sgRNA pair phenotypes for each cell line and screen replicate were calculated using custom scripts (gitub.com/mhorlbeck/GImap_tools, Gimap_analysis.py) comparing counts from T0 and endpoint samples. Phenotypes were normalized to the number of cell doublings measured over the course of the screen (K562 Rep1: 6.91, K562 Rep2: 7.61, Jurkat Rep1: 6.151474054, Jurkat Rep2: 6.44). Phenotypes from each sequencing analysis method were calculated along with averages between replicates.
Further analysis, including the computation of sgRNA- and gene-level epistasis scores, was performed using GImap_analysis.py and can be found at Mendeley (doi:10.17632/rdzk59n6j4.1).
Genome_build: hg19
Supplementary_files_format_and_content:
tab-delimited text containg summed read counts, phenotypes, and reference library table
For read_counts.txt, the 20 columns refer to the 2 K562 T0 samples analyzed just with barcode sequencing plus the 6 other samples analyzed with three different methods (barcode, sgRNA, and triple sequencing).
For phenotypes.txt, the 18 columns refer to 2 screens x 3 different ways to analyze the data x (2 replicates + replicate average).

source_name: Jurkat Endpoint

growth_protocol: A pool of lentiviral vectors each encoding two sgRNAs and matching barcode sequences were packaged in HEK293T cells and then transduced into K562 or Jurkat cells expressing dCas9-KRAB. Infected cells were selected with puromycin and passaged for 15-16 days. Cells were harvested for genomic DNA at T0 (day 5 post-infection for K562 and 6 for Jurkat) and at screen endpoint 10 days later.

extract_protocol:
Genomic DNA was harvested from all samples using the Machery-Nagel Blood XL kit. DNA was digested with Mfe1 overnight at 37C, then run on 0.8% agarose big gels to enrich for the lentiviral fragment expected to run at 2158bp. The Machery-Nagel gel extraction kit was to isolate DNA from gel for library construction.
The sgRNA- and barcode-encoding regions were then amplified by PCR using custom primers (see Key Resources table in the associated manuscript).
Amplified sequences were sequenced on an Illumina HiSeq 2500 or 4000 using custom sequencing primer sets (see Key Resources table in the associated manuscript).

value: Jurkat

tag: timepoint

value: Endpoint

tag: replicate

tag: sequencing strategy

value: triple sequencing


title: Jurkat T0, Replicate 2

source_name: Jurkat T0

tag: cell line


title: Jurkat T0, Replicate 1


title: donor305pl6cell186


title: donor305pl6cell174


title: donor305pl6cell173


title: donor305pl6cell172


title: donor305pl6cell171


title: WTCHG_312640_708503

description:
donor_age59.9_male_MSC
sample extracted from cell population from given donor
countTable_MSC.txt

data_processing:
Reads were trimmed for Nextera, Smart-seq2 adapter sequences using skewer-v0.1.125
Trimmed read pairs were mapped to human genome hg38.ERCC using HISAT2 version 2.0.0-beta.
Uniquely mapped read pairs were counted using featureCounts, subread-1.5.0, using exons annotated in ENSEMBL annotations,release 75.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with raw read counts (featureCounts)

source_name: Mesenchymal stem/stromal cells(MSC)

extract_protocol:
RNA was extracted with trizol (Invitrogen) using a linear acrylamide carrier. RNA was then treated with DNase I (Life technologies) and purified using Agencourt RNAClean XP beads (Beckman Coulter). RNA quality and concentration were assessed by using an RNA 6000 bioanalyzer pico kit (Agilent). Samples with concentrations less than 30 pg/µl and/or an RNA integrity number (RIN) less than 6 were excluded from further analysis.
A cDNA library was produced using the Smart-Seq 2 protocol. Sequencing was performed on an Illumina HiSeq4000 with 75 bp paired-end reads with the aim to achieve coverage of 25 million reads per sample.

tag: cell type

value: Mesenchymal stem/stromal cells(MSC)

value: technical replicate 1


title: WTCHG_312085_706505

description:
donor_age59.9_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_312086_707517

description:
donor_age59.9_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt

source_name: Lymphocytes and precursors(LYM)

value: Lymphocytes and precursors(LYM)

value: technical replicate 2


title: WTCHG_312641_708503


title: WTCHG_312085_707517


title: WTCHG_312092_705506

description:
donor_age59.9_male_HPC
sample extracted from cell population from given donor
countTable_HPC.txt

source_name: Haematopoietic stem and progenitor cells(HPC)


title: WTCHG_312086_706505


title: Jurkat Endpoint, Replicate 1


title: donor305pl6cell168


title: donor305pl6cell166


title: donor305pl6cell167


title: donor305pl6cell169


title: donor305pl6cell165


title: donor305pl6cell164


title: WTCHG_312091_705506

value: Haematopoietic stem and progenitor cells(HPC)


title: WTCHG_312090_701517

description:
donor_age57.0_female_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: WTCHG_312342_702503

description:
donor_age59.9_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt

source_name: Erythroid precursors(ERP)

value: Erythroid precursors(ERP)


title: WTCHG_312342_704502

description:
donor_age57.0_female_MON
sample extracted from cell population from given donor
countTable_MON.txt

value: female


title: WTCHG_312089_701517

value: bone marrow


title: donor305pl6cell170


title: donor305pl6cell161


title: donor305pl6cell162


title: WTCHG_312086_705517

description:
donor_age57.0_female_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: donor305pl6cell163


title: donor305pl6cell160


title: WTCHG_312085_705517


title: WTCHG_312342_703506

description:
donor_age57.0_female_GRA
sample extracted from cell population from given donor
countTable_GRA.txt

source_name: Granulocytic precursors(GRA)

value: Granulocytic precursors(GRA)


title: WTCHG_312341_703506


title: donor305pl6cell159


title: WTCHG_312342_701517

description:
donor_age57.0_female_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: donor305pl6cell158


title: donor305pl6cell156


title: WTCHG_312341_701517


title: donor305pl6cell157


title: WTCHG_312641_703503

description:
donor_age56.6_male_MSC
sample extracted from cell population from given donor
countTable_MSC.txt

value: male


title: WTCHG_312341_704502


title: WTCHG_312341_702503


title: WTCHG_312092_708505

description:
donor_age56.6_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: donor305pl6cell155


title: WTCHG_312091_708505


title: donor305pl6cell154


title: WTCHG_312640_703503


title: donor305pl6cell153


title: WTCHG_312090_704503

description:
donor_age56.6_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: WTCHG_312092_706504

description:
donor_age56.6_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: donor305pl6cell152


title: donor305pl6cell150


title: WTCHG_312641_711504

description:
donor_age56.1_female_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: donor305pl6cell151


title: donor305pl6cell147


title: donor305pl6cell149


title: donor305pl6cell148


title: WTCHG_312640_711504


title: donor305pl6cell146


title: donor305pl6cell145


title: WTCHG_312090_702505

description:
donor_age56.1_female_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: donor305pl5cell143

description:
single-cell RNA
1 out of 192 cells per donor


title: WTCHG_312091_706504


title: donor305pl5cell142


title: WTCHG_319032_704503

description:
donor_age56.1_female_HPC
sample extracted from cell population from given donor
countTable_HPC.txt

value: technical replicate 6


title: WTCHG_320115_704503

value: technical replicate 7


title: WTCHG_312089_702505


title: WTCHG_284762_704503

value: technical replicate 5


title: WTCHG_284761_704503

value: technical replicate 4


title: WTCHG_284760_704503

value: technical replicate 3


title: WTCHG_284759_704503


title: donor305pl5cell144

value: 62.2 years


title: donor305pl5cell138


title: donor305pl5cell141


title: donor305pl5cell137


title: donor305pl5cell139


title: donor305pl5cell140


title: donor305pl5cell136


title: WTCHG_319032_707505

description:
donor_age56.1_female_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: WTCHG_320115_707505


title: WTCHG_284762_707505


title: WTCHG_284761_707505


title: donor305pl5cell134


title: donor305pl5cell133


title: WTCHG_284760_707505


title: donor309pl2cell078

value: 21.2 years


title: WTCHG_284759_707505


title: donor305pl5cell132


title: WTCHG_320115_708503

description:
donor_age56.1_female_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: WTCHG_282160_707505


title: donor305pl5cell131


title: WTCHG_282160_704503


title: donor305pl5cell130


title: donor305pl5cell127


title: WTCHG_284760_702503


title: WTCHG_319032_708503


title: WTCHG_284762_702503


title: donor305pl5cell124


title: donor305pl5cell126


title: WTCHG_284761_702503


title: donor305pl5cell123


title: donor305pl5cell125


title: donor305pl5cell135


title: WTCHG_312641_704505

description:
donor_age55.6_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_282160_702503


title: WTCHG_312640_704505


title: donor305pl5cell122


title: WTCHG_312638_709505

description:
donor_age55.6_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: WTCHG_312639_709505


title: donor305pl5cell120


title: donor305pl5cell121


title: WTCHG_312086_707505

description:
donor_age55.6_male_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: WTCHG_312085_707505


title: donor305pl5cell128


title: donor305pl5cell119


title: WTCHG_312086_707507

description:
donor_age55.6_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: WTCHG_284759_702503


title: donor305pl5cell129


title: donor305pl5cell116


title: donor305pl5cell115


title: donor305pl5cell114


title: donor305pl5cell113


title: WTCHG_312090_702504

description:
donor_age54.9_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_312085_707507


title: WTCHG_312641_705503

description:
donor_age54.9_male_MSC
sample extracted from cell population from given donor
countTable_MSC.txt

value: Mesenchymal stem/stromal cells(MSC)


title: WTCHG_312089_702504

value: technical replicate 1


title: WTCHG_312640_705503


title: WTCHG_312088_711505

description:
donor_age54.9_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt

value: Lymphocytes and precursors(LYM)


title: donor305pl5cell111


title: donor305pl5cell110


title: donor305pl5cell112


title: WTCHG_312090_703503

description:
donor_age54.9_male_HPC
sample extracted from cell population from given donor
countTable_HPC.txt

value: technical replicate 2


title: WTCHG_312087_711505


title: WTCHG_312089_703503

value: Haematopoietic stem and progenitor cells(HPC)


title: donor305pl5cell108


title: donor305pl5cell107


title: WTCHG_312341_702517

description:
donor_age54.0_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_312342_702517


title: donor305pl5cell117


title: donor305pl5cell106


title: donor305pl5cell118


title: donor305pl5cell105


title: donor305pl5cell104


title: donor305pl5cell103


title: WTCHG_312638_709504

description:
donor_age54.0_male_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: WTCHG_312639_709504


title: WTCHG_312087_710517

description:
donor_age54.0_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: donor305pl5cell102


title: WTCHG_312086_705507

description:
donor_age54.0_male_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: WTCHG_312085_705507


title: donor305pl5cell109


title: WTCHG_312342_704504

description:
donor_age54.0_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt

value: Erythroid precursors(ERP)


title: donor305pl5cell101

description:
single-cell RNA
1 out of 192 cells per donor

value: female


title: donor305pl5cell099

value: bone marrow


title: WTCHG_312641_711503

description:
donor_age50.5_male_MSC
sample extracted from cell population from given donor
countTable_MSC.txt


title: donor305pl5cell097


title: WTCHG_312088_710517


title: donor305pl4cell096


title: donor305pl4cell095


title: donor305pl4cell094


title: WTCHG_284762_707517

description:
donor_age50.5_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_312640_711503


title: donor305pl4cell093


title: WTCHG_284761_707517


title: WTCHG_284759_707517


title: donor305pl4cell092


title: donor305pl4cell091


title: WTCHG_282160_707517


title: donor305pl4cell090


title: donor305pl5cell100


title: donor305pl4cell088


title: WTCHG_312090_702507

description:
donor_age50.5_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: donor305pl4cell089


title: WTCHG_284762_708504

description:
donor_age50.5_male_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: WTCHG_312341_704504


title: WTCHG_312089_702507


title: donor305pl4cell087


title: donor305pl5cell098


title: WTCHG_284760_708504


title: WTCHG_282160_708504


title: donor305pl4cell085


title: donor305pl4cell086


title: donor305pl4cell084


title: WTCHG_284760_707517


title: WTCHG_320115_709503

description:
donor_age50.5_male_GRA
sample extracted from cell population from given donor
countTable_GRA.txt

value: Granulocytic precursors(GRA)


title: WTCHG_284762_706503

value: male


title: donor305pl4cell081


title: WTCHG_284761_706503


title: WTCHG_284760_706503


title: donor305pl4cell079


title: donor305pl4cell078


title: WTCHG_284759_706503


title: WTCHG_284761_708504


title: donor305pl4cell077


title: donor305pl4cell076


title: WTCHG_284759_708504


title: WTCHG_282160_706503


title: WTCHG_284761_709517

description:
donor_age50.5_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: WTCHG_284762_709517


title: WTCHG_282160_709517


title: WTCHG_284760_709517


title: donor305pl4cell073


title: donor305pl4cell074


title: donor305pl4cell072


title: WTCHG_284759_709517


title: donor305pl4cell075


title: donor305pl4cell083


title: donor305pl4cell082


title: WTCHG_319032_709503

value: technical replicate 6


title: WTCHG_312342_702506

description:
donor_age29.8_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: donor305pl4cell080


title: donor305pl4cell070


title: donor305pl4cell071


title: WTCHG_312092_705507

description:
donor_age29.8_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: donor305pl4cell069


title: donor305pl4cell068


title: WTCHG_312091_705507


title: WTCHG_312088_710508

description:
donor_age29.8_male_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: WTCHG_312341_702506


title: donor305pl4cell067


title: WTCHG_312087_710508


title: donor305pl4cell066


title: WTCHG_312342_704506

description:
donor_age29.8_male_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: donor305pl4cell065


title: donor305pl4cell064


title: WTCHG_312341_704506


title: WTCHG_312640_712503

description:
donor_age27.5_female_MSC
sample extracted from cell population from given donor
countTable_MSC.txt


title: donor305pl4cell061


title: WTCHG_312641_712503


title: donor305pl4cell060


title: donor305pl4cell062


title: WTCHG_312085_708505

description:
donor_age29.8_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: donor305pl4cell063


title: WTCHG_312086_708505


title: donor305pl4cell059


title: WTCHG_312090_703506

description:
donor_age27.5_female_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: WTCHG_312089_703506


title: WTCHG_284762_703517

description:
donor_age27.5_female_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: WTCHG_319032_702503


title: WTCHG_320115_702503


title: donor305pl4cell058


title: WTCHG_282160_703517


title: donor305pl4cell056


title: donor305pl4cell057


title: donor305pl4cell054


title: donor305pl4cell055


title: WTCHG_284760_703517


title: donor305pl4cell052


title: donor305pl4cell051


title: donor305pl4cell053


title: donor305pl4cell050


title: WTCHG_284761_709505

description:
donor_age27.5_female_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: WTCHG_284762_709505


title: donor305pl4cell049


title: WTCHG_284760_709505


title: donor305pl3cell048


title: WTCHG_284759_709505


title: WTCHG_282160_709505


title: donor305pl3cell047


title: WTCHG_284762_705505

description:
donor_age27.5_female_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: donor305pl3cell046

description:
single-cell RNA
1 out of 192 cells per donor


title: WTCHG_284761_705505


title: donor305pl3cell045


title: WTCHG_284760_705505


title: WTCHG_284759_703517


title: WTCHG_284759_705505


title: WTCHG_312641_703504

description:
donor_age24.7_female_MSC
sample extracted from cell population from given donor
countTable_MSC.txt


title: WTCHG_282160_705505


title: donor305pl3cell043


title: donor305pl3cell042


title: donor305pl3cell041


title: WTCHG_312640_703504


title: donor305pl3cell040


title: donor305pl3cell039


title: donor305pl3cell038


title: donor305pl3cell037


title: WTCHG_312086_707502

description:
donor_age24.7_female_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: WTCHG_312085_708508

description:
donor_age24.7_female_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_312085_707502


title: donor305pl3cell036


title: WTCHG_312088_712504

description:
donor_age24.7_female_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: donor305pl3cell035


title: WTCHG_312087_712504


title: donor305pl3cell033


title: donor305pl3cell034


title: donor305pl3cell032


title: WTCHG_312085_707504

description:
donor_age24.7_female_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: WTCHG_312086_705508

description:
donor_age24.7_female_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: WTCHG_312085_705508


title: donor305pl3cell031


title: donor305pl3cell044


title: donor305pl3cell030


title: WTCHG_312641_701504

description:
donor_age22.5_female_MSC
sample extracted from cell population from given donor
countTable_MSC.txt


title: donor305pl3cell029


title: WTCHG_312640_701504


title: donor305pl3cell028


title: WTCHG_312086_708508


title: donor305pl3cell027


title: WTCHG_312090_702506

description:
donor_age22.5_female_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: WTCHG_312089_702506


title: WTCHG_312342_702502

description:
donor_age22.5_female_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: donor305pl3cell024


title: donor305pl3cell026


title: WTCHG_312088_711504

description:
donor_age22.5_female_HPC
sample extracted from cell population from given donor
countTable_HPC.txt


title: WTCHG_312087_711504


title: donor305pl3cell023


title: WTCHG_312086_707504


title: donor305pl3cell021


title: WTCHG_312086_706517

description:
donor_age22.5_female_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: donor305pl3cell020


title: donor305pl3cell022


title: WTCHG_312085_706517


title: donor305pl3cell018


title: WTCHG_312641_705504

description:
donor_age19.9_male_MSC
sample extracted from cell population from given donor
countTable_MSC.txt


title: WTCHG_312342_704508

description:
donor_age22.5_female_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: donor305pl3cell019


title: WTCHG_312341_704508


title: donor305pl3cell017


title: donor305pl3cell016


title: WTCHG_312640_705504


title: donor305pl3cell015


title: WTCHG_312086_706508

description:
donor_age19.9_male_MON
sample extracted from cell population from given donor
countTable_MON.txt


title: donor305pl3cell014


title: donor305pl3cell025


title: donor305pl3cell013


title: WTCHG_312085_706508


title: WTCHG_312341_702502


title: WTCHG_312342_704503

description:
donor_age19.9_male_LYM
sample extracted from cell population from given donor
countTable_LYM.txt


title: WTCHG_312342_704507

description:
donor_age19.9_male_GRA
sample extracted from cell population from given donor
countTable_GRA.txt


title: WTCHG_312341_704503


title: WTCHG_312341_704507


title: WTCHG_312086_708506

description:
donor_age19.9_male_ERP
sample extracted from cell population from given donor
countTable_ERP.txt


title: WTCHG_312085_708506


title: donor305pl3cell005

description:
single-cell RNA
1 out of 192 cells per donor


title: donor304pl4cell192

value: 30.6 years


title: donor304pl4cell187


title: donor305pl3cell006


title: donor305pl3cell009


title: donor305pl3cell007


title: donor305pl3cell003


title: donor304pl4cell185


title: donor305pl3cell011


title: donor304pl4cell191


title: donor304pl4cell189


title: donor305pl3cell004


title: donor305pl3cell008


title: donor304pl4cell188


title: donor305pl3cell002


title: donor304pl4cell190


title: donor304pl4cell186


title: donor305pl3cell012


title: donor305pl3cell001


title: donor305pl3cell010


title: donor304pl4cell183


title: donor304pl4cell184


title: donor304pl4cell180


title: donor304pl4cell181


title: donor304pl4cell182


title: Sham operated animal_72h_repicate_1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Heart tissue from C57BL/6J animals, 24h after sham operation

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. Additional analysis was performed with R and HOMER (transcription factor binding motif finder)

source_name: Sham operated animal 72h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The study was performed with 8 weeks old C57BL/6J animals, exposed to either sham operation or occlusion of the medial cerebral artery. All mice had free access to food and water. Hearts were isolated 24h and 72h after occlusion of the medial cerebral artery.  As control, age matched sham operated C57BL/6J mice were used.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For the microarray study hearts were isolated from four study groups and their respective controls: 1) hearts from C57BL/6J animals 24h after occlusion of the middle cerebral artery, 2) hearts from C57BL/6J animals 72h after occlusion of the middle cerebral artery, 3) hearts from C57BL/6J animals, 24h after sham operation and 4) hearts from C57BL/6J 72h after sham operation.

tag: treatment

value: Sham

tag: time


title: Middle cerebral artery occlusion (MCAO)_72h_repicate_4

description: Heart tissue from C57BL/6J animals, 24h after ischemic stroke of the brain

source_name: Middle cerebral artery occlusion (MCAO) 72h

value: MCAO


title: Sham operated animal_24h_repicate_5

source_name: Sham operated animal 24h


title: Sham operated animal_72h_repicate_2


title: Sham operated animal_24h_repicate_1


title: C3

city: shannxi

first: TingLi

last: Liu

address: xinong load

department: Northwest A&F University

country: China

institute: College of Veterinary Medicine

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: The GeneSpring GX software and the Percentile 75 method was used to generate the normalized signals

source_name: Human colonic epithelial cells

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: 10% FBS for cell growth

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: HCT-8 cells were infectedby cryptosporidium parvum, and then the six samples from each well was rapidly sampled, washed with nuclease-free PBS. All instruments and reagents in the trial were treated with DEPC in advance and without RNase.

value: Human colonic epithelial cells

tag: infection

value: control

value: post infection (pi) 24hrs


title: donor304pl4cell174


title: donor304pl4cell176


title: donor304pl4cell179


title: Sham operated animal_72h_repicate_5


title: donor304pl4cell178


title: Sham operated animal_24h_repicate_2


title: donor304pl4cell177


title: donor304pl4cell173


title: donor304pl4cell175


title: donor304pl4cell172


title: Sham operated animal_24h_repicate_4


title: donor304pl4cell171


title: Sham operated animal_72h_repicate_4


title: O1

value: Cryptosporidium parvum


title: Sham operated animal_72h_repicate_3


title: Sham operated animal_24h_repicate_3


title: Sham operated animal_72h_repicate_6


title: donor304pl4cell170


title: Sham operated animal_24h_repicate_6


title: Middle cerebral artery occlusion (MCAO)_72h_repicate_3


title: Middle cerebral artery occlusion (MCAO)_72h_repicate_5


title: donor304pl4cell169


title: Middle cerebral artery occlusion (MCAO)_72h_repicate_6


title: C2


title: O2


title: O3


title: Middle cerebral artery occlusion (MCAO)_72h_repicate_2


title: C1


title: donor304pl4cell168


title: donor304pl4cell165


title: donor304pl4cell160


title: donor304pl4cell166


title: donor304pl4cell163


title: donor304pl4cell162


title: donor304pl4cell161


title: donor304pl4cell164


title: donor304pl4cell158


title: Middle cerebral artery occlusion (MCAO)_24h_repicate_6

source_name: Middle cerebral artery occlusion (MCAO) 24h


title: donor304pl4cell167


title: donor304pl4cell157


title: donor304pl4cell155


title: donor304pl4cell156


title: donor304pl4cell159


title: Middle cerebral artery occlusion (MCAO)_24h_repicate_5


title: Middle cerebral artery occlusion (MCAO)_72h_repicate_1