DGCR8 RNA-Seq in HepG2

General Information


RBP	DGCR8
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DGCR8-BGHcLV03-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DGCR8_BGHcLV03-15
Rep2	DGCR8_BGHcLV03-16
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	no band
Rep2_WB
Antibody Cat#	A302-468A
Antibody Lot#	A302-468A
Antibody DCC ID
Status	NotSatisfied
Project	ENCODE3
ID	572

Experiment Information (Status: NotSatisfied)

	BGHcLV03-15	BGHcLV03-16
idx	15	16
TRCN#_or_BGC#	BGC#0000017	BGC#0000017
shRNA_or_gRNA_sequence	GACAGCGACCATCCGTCCGA	GACAGCGACCATCCGTCCGA
PAM
Name	DGCR8-Z1-B	DGCR8-Z1-B
Sample_ID	BGHcLV03-15	BGHcLV03-16
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	DGCR8	DGCR8
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	cctccacgagtgccttaaaa
RT-qPCR_primer-R	cacgccatgacgtattcact
protein_conc	2284	1793
WB_result	no band
Ave_WB
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	6	0
Rep2_TPM	6	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6156	6157

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV03-15	BGHcLV03-16
Sample_ID	BGHcLV03-15	BGHcLV03-16
Sample Name	DGCR8_BGHcLV03-15	DGCR8_BGHcLV03-16
Sample Name	DGCR8_BGHcLV03-15	DGCR8_BGHcLV03-16
RBP	DGCR8	DGCR8
Cell_Line	HepG2	HepG2
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	36	37

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-15	BGHcLV03-16
Sample #
Sample Name	DGCR8-BGHcLV03-15	DGCR8-BGHcLV03-16
Sample_Name_Alias	DGCR8_BGHcLV03-15	DGCR8_BGHcLV03-16
Index Well Position	S07	S08
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/G2.png	DNA_Library_cLV02/set1/H2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/A4.png	RNA_Library_cLV02/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-15	BGHcLV03-16
RBP	DGCR8	DGCR8
Batch_ID	BGHcLV03	BGHcLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2792	2793

Sequencing Information

	BGHcLV03-15	BGHcLV03-16
Sample_ID	BGHcLV03-15	BGHcLV03-16
Sample Name	DGCR8_BGHcLV03-15	DGCR8_BGHcLV03-16
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	77,500,196	54,819,802
total_aligned_reads	68,686,640	49,197,852
unique_aligned_reads	64,478,922	46,334,930
percent_uniqueAligned	0.83198	0.84522
correlation_replicates	0.997026	0.997026
spikein_reads	125,162	103,216
percent_spikeins	0.00161	0.00188
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1441	1442

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_BGHcLV03-15_CAGATC_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1441	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22914
DGCR8_BGHcLV03-15_CAGATC_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1441	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22932
DGCR8_BGHcLV03-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1441					GRCh38	V40	DGCR8_BGHcLV03-15_CAGATC_L006_001.R1.fastq.gz,DGCR8_BGHcLV03-15_CAGATC_L006_001.R2.fastq.gz		ENCORE2	22950
DGCR8_BGHcLV03-15_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1441					GRCh38	V40	DGCR8_BGHcLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	22968
DGCR8_BGHcLV03-15_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1441					GRCh38	V40	DGCR8_BGHcLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	22986
DGCR8_BGHcLV03-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1441					GRCh38	V40	DGCR8_BGHcLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	23004
DGCR8_BGHcLV03-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1441					GRCh38	V40	DGCR8_BGHcLV03-15/Aligned.sortedByCoord.out.bam		ENCORE2	23022
DGCR8_BGHcLV03-15_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1441					GRCh38	V40	DGCR8_BGHcLV03-15_CAGATC_L006_001.R1.fastq.gz,DGCR8_BGHcLV03-15_CAGATC_L006_001.R2.fastq.gz		ENCORE2	23040
DGCR8_BGHcLV03-16_ACTTGA_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1442	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22915
DGCR8_BGHcLV03-16_ACTTGA_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1442	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22933
DGCR8_BGHcLV03-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1442					GRCh38	V40	DGCR8_BGHcLV03-16_ACTTGA_L006_001.R1.fastq.gz,DGCR8_BGHcLV03-16_ACTTGA_L006_001.R2.fastq.gz		ENCORE2	22951
DGCR8_BGHcLV03-16_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1442					GRCh38	V40	DGCR8_BGHcLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	22969
DGCR8_BGHcLV03-16_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1442					GRCh38	V40	DGCR8_BGHcLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	22987
DGCR8_BGHcLV03-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1442					GRCh38	V40	DGCR8_BGHcLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	23005
DGCR8_BGHcLV03-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1442					GRCh38	V40	DGCR8_BGHcLV03-16/Aligned.sortedByCoord.out.bam		ENCORE2	23023
DGCR8_BGHcLV03-16_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1442					GRCh38	V40	DGCR8_BGHcLV03-16_ACTTGA_L006_001.R1.fastq.gz,DGCR8_BGHcLV03-16_ACTTGA_L006_001.R2.fastq.gz		ENCORE2	23041