DGCR8 RNA-Seq in K562

General Information


RBP	DGCR8
Cell_Line	K562
Method	CRISPR
Exp_Name	DGCR8-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	DGCR8_BGKcLV02-19
Rep2	DGCR8_BGKcLV02-20
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	28.9
Rep2_qPCR	14.4
Rep1_WB	3.3
Rep2_WB	0.0
Antibody Cat#	A302-468A
Antibody Lot#	A302-468A
Antibody DCC ID
Status	NotSatisfied
Project	ENCODE3
ID	584

Experiment Information (Status: NotSatisfied)

	BGKcLV02-19	BGKcLV02-20
idx	21	22
TRCN#_or_BGC#	BGC#0000018	BGC#0000018
shRNA_or_gRNA_sequence	CGCGACGTGCGGGCGGAGTG	CGCGACGTGCGGGCGGAGTG
PAM
Name	DGCR8-C1-A	DGCR8-C1-A
Sample_ID	BGKcLV02-19	BGKcLV02-20
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	DGCR8	DGCR8
qPCR_result	28.9	14.4
Ave_qPCR	21.7
RT-qPCR_primer-F	ccagccaatcagaagctcat
RT-qPCR_primer-R	tactcgtgcaggatgcagac
protein_conc	3302	3743
WB_result	3.3	0.0
Ave_WB	1.7
WB_DONE_date	1/4/2016
MW	86kDa
IP	1
antibody_Cat#	A302-468A	A302-468A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	40.2	0
Rep2_TPM	38.4	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4119	4120

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV02-19	BGKcLV02-20
Sample_ID	BGKcLV02-19	BGKcLV02-20
Sample Name	DGCR8_BGKcLV02-19	DGCR8_BGKcLV02-20
Sample Name	DGCR8_BGKcLV02-19	DGCR8_BGKcLV02-20
RBP	DGCR8	DGCR8
Cell_Line	K562	K562
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2016-03-16	2016-03-16
Project	ENCODE3	ENCODE3
Note
ID	30	31

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-19	BGKcLV02-20
Sample #
Sample Name	DGCR8-BGKcLV02-19	DGCR8-BGKcLV02-20
Sample_Name_Alias	DGCR8_BGKcLV02-19	DGCR8_BGKcLV02-20
Index Well Position	S05	S06
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/E5.png	DNA_Library_cLV02/set1/F5.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/G6.png	RNA_Library_cLV02/set1/H6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-19	BGKcLV02-20
RBP	DGCR8	DGCR8
Batch_ID	BGKcLV02	BGKcLV02
WB_result	3.300	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2774	2775

Sequencing Information

	BGKcLV02-19	BGKcLV02-20
Sample_ID	BGKcLV02-19	BGKcLV02-20
Sample Name	DGCR8_BGKcLV02-19	DGCR8_BGKcLV02-20
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	119,680,590	55,678,050
total_aligned_reads	110,522,664	51,846,916
unique_aligned_reads	100,506,300	47,299,210
percent_uniqueAligned	0.83979	0.84951
correlation_replicates	0.997807	0.997807
spikein_reads	159,768	872
percent_spikeins	0.00133	0.00002
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1423	1424

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
DGCR8_BGKcLV02-19_ACAGTG_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1423	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22756
DGCR8_BGKcLV02-19_ACAGTG_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1423	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22776
DGCR8_BGKcLV02-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1423					GRCh38	V40	DGCR8_BGKcLV02-19_ACAGTG_L008_001.R1.fastq.gz,DGCR8_BGKcLV02-19_ACAGTG_L008_001.R2.fastq.gz		ENCORE2	22796
DGCR8_BGKcLV02-19_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	1423					GRCh38	V40	DGCR8_BGKcLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	22816
DGCR8_BGKcLV02-19_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	1423					GRCh38	V40	DGCR8_BGKcLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	22836
DGCR8_BGKcLV02-19_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	1423					GRCh38	V40	DGCR8_BGKcLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	22856
DGCR8_BGKcLV02-19_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	1423					GRCh38	V40	DGCR8_BGKcLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	22876
DGCR8_BGKcLV02-19_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1423					GRCh38	V40	DGCR8_BGKcLV02-19_ACAGTG_L008_001.R1.fastq.gz,DGCR8_BGKcLV02-19_ACAGTG_L008_001.R2.fastq.gz		ENCORE2	22896
DGCR8_BGKcLV02-20_GCCAAT_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1424	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22757
DGCR8_BGKcLV02-20_GCCAAT_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1424	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22777
DGCR8_BGKcLV02-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1424					GRCh38	V40	DGCR8_BGKcLV02-20_GCCAAT_L008_001.R1.fastq.gz,DGCR8_BGKcLV02-20_GCCAAT_L008_001.R2.fastq.gz		ENCORE2	22797
DGCR8_BGKcLV02-20_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	1424					GRCh38	V40	DGCR8_BGKcLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	22817
DGCR8_BGKcLV02-20_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	1424					GRCh38	V40	DGCR8_BGKcLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	22837
DGCR8_BGKcLV02-20_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	1424					GRCh38	V40	DGCR8_BGKcLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	22857
DGCR8_BGKcLV02-20_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	1424					GRCh38	V40	DGCR8_BGKcLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	22877
DGCR8_BGKcLV02-20_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1424					GRCh38	V40	DGCR8_BGKcLV02-20_GCCAAT_L008_001.R1.fastq.gz,DGCR8_BGKcLV02-20_GCCAAT_L008_001.R2.fastq.gz		ENCORE2	22897