DEAF1 RNA-Seq in K562

General Information


RBP	DEAF1
Cell_Line	K562
Method	CRISPR
Exp_Name	DEAF1-BGKcLV02-K562
ENCODE_series_ID
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DEAF1_BGKcLV02-17
Rep2	DEAF1_BGKcLV02-18
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	54.3
Rep2_qPCR	2.0
Rep1_WB	46.3
Rep2_WB	54.3
Antibody Cat#	A303-187A
Antibody Lot#	A303-187A
Antibody DCC ID
Status	NotSatisfied
Project	ENCODE3
ID	583

Experiment Information (Status: NotSatisfied)

	BGKcLV02-17	BGKcLV02-18
idx	19	20
TRCN#_or_BGC#	BGC#0000015	BGC#0000015
shRNA_or_gRNA_sequence	GACCTTTGACCGAGCGTCCA	GACCTTTGACCGAGCGTCCA
PAM
Name	DEAF1-Z1-A	DEAF1-Z1-A
Sample_ID	BGKcLV02-17	BGKcLV02-18
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	DEAF1	DEAF1
qPCR_result	54.3	2.0
Ave_qPCR	28.2
RT-qPCR_primer-F	aggacagctgccagatcg
RT-qPCR_primer-R	caggcagggatgtcaacac
protein_conc	2915	3895
WB_result	46.3	54.3
Ave_WB	50.3
WB_DONE_date	12/28/2015
MW	59kDa
IP	1
antibody_Cat#	A303-187A	A303-187A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	24.4	0
Rep2_TPM	17.7	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4117	4118

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV02-17	BGKcLV02-18
Sample_ID	BGKcLV02-17	BGKcLV02-18
Sample Name	DEAF1_BGKcLV02-17	DEAF1_BGKcLV02-18
Sample Name	DEAF1_BGKcLV02-17	DEAF1_BGKcLV02-18
RBP	DEAF1	DEAF1
Cell_Line	K562	K562
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2016-03-16	2016-03-16
Project	ENCODE3	ENCODE3
Note
ID	28	29

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-17	BGKcLV02-18
Sample #
Sample Name	DEAF1-BGKcLV02-17	DEAF1-BGKcLV02-18
Sample_Name_Alias	DEAF1_BGKcLV02-17	DEAF1_BGKcLV02-18
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/C5.png	DNA_Library_cLV02/set1/D5.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/E6.png	RNA_Library_cLV02/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-17	BGKcLV02-18
RBP	DEAF1	DEAF1
Batch_ID	BGKcLV02	BGKcLV02
WB_result	46.300	54.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2772	2773

Sequencing Information

	BGKcLV02-17	BGKcLV02-18
Sample_ID	BGKcLV02-17	BGKcLV02-18
Sample Name	DEAF1_BGKcLV02-17	DEAF1_BGKcLV02-18
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	58,421,122	59,354,242
total_aligned_reads	53,840,526	54,354,588
unique_aligned_reads	49,275,180	49,509,372
percent_uniqueAligned	0.84345	0.83413
correlation_replicates	0.987183	0.987183
spikein_reads	79,110	149,546
percent_spikeins	0.00135	0.00252
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1421	1422

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DEAF1_BGKcLV02-17_TTAGGC_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1421	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22754
DEAF1_BGKcLV02-17_TTAGGC_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1421	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22774
DEAF1_BGKcLV02-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1421					GRCh38	V40	DEAF1_BGKcLV02-17_TTAGGC_L008_001.R1.fastq.gz,DEAF1_BGKcLV02-17_TTAGGC_L008_001.R2.fastq.gz		ENCORE2	22794
DEAF1_BGKcLV02-17_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1421					GRCh38	V40	DEAF1_BGKcLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	22814
DEAF1_BGKcLV02-17_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1421					GRCh38	V40	DEAF1_BGKcLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	22834
DEAF1_BGKcLV02-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1421					GRCh38	V40	DEAF1_BGKcLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	22854
DEAF1_BGKcLV02-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1421					GRCh38	V40	DEAF1_BGKcLV02-17/Aligned.sortedByCoord.out.bam		ENCORE2	22874
DEAF1_BGKcLV02-17_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1421					GRCh38	V40	DEAF1_BGKcLV02-17_TTAGGC_L008_001.R1.fastq.gz,DEAF1_BGKcLV02-17_TTAGGC_L008_001.R2.fastq.gz		ENCORE2	22894
DEAF1_BGKcLV02-18_TGACCA_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1422	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22755
DEAF1_BGKcLV02-18_TGACCA_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1422	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22775
DEAF1_BGKcLV02-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1422					GRCh38	V40	DEAF1_BGKcLV02-18_TGACCA_L008_001.R1.fastq.gz,DEAF1_BGKcLV02-18_TGACCA_L008_001.R2.fastq.gz		ENCORE2	22795
DEAF1_BGKcLV02-18_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1422					GRCh38	V40	DEAF1_BGKcLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	22815
DEAF1_BGKcLV02-18_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1422					GRCh38	V40	DEAF1_BGKcLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	22835
DEAF1_BGKcLV02-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1422					GRCh38	V40	DEAF1_BGKcLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	22855
DEAF1_BGKcLV02-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1422					GRCh38	V40	DEAF1_BGKcLV02-18/Aligned.sortedByCoord.out.bam		ENCORE2	22875
DEAF1_BGKcLV02-18_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1422					GRCh38	V40	DEAF1_BGKcLV02-18_TGACCA_L008_001.R1.fastq.gz,DEAF1_BGKcLV02-18_TGACCA_L008_001.R2.fastq.gz		ENCORE2	22895