DKC1 RNA-Seq in HepG2

General Information


RBP	DKC1
Cell_Line	HepG2
Method	shRNA
Exp_Name	DKC1-BGHLV31-HepG2
ENCODE_series_ID	ENCSR502RXV
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR118KUN
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	DKC1_BGHLV31-33
Rep2	DKC1_BGHLV31-34
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	49.6
Rep2_qPCR	54.8
Rep1_WB	93.2
Rep2_WB	88.3
Antibody Cat#	GTX109000
Antibody Lot#	GTX109000
Antibody DCC ID	ENCAB174DOV
Status	Released
Project	ENCODE3
ID	695

Experiment Information (Status: Released)

	BGHLV31-33	BGHLV31-34
idx	781	782
TRCN#_or_BGC#	TRCN0000039738	TRCN0000039738
shRNA_or_gRNA_sequence	GCTCAGTGAAATGCTGTAGAA	GCTCAGTGAAATGCTGTAGAA
PAM
Name	DKC1	DKC1
Sample_ID	BGHLV31-33	BGHLV31-34
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	DKC1	DKC1
qPCR_result	49.6	54.8
Ave_qPCR	52.2
RT-qPCR_primer-F	ctggagatggggacagtgat
RT-qPCR_primer-R	cagcttcaagtggccttcac
protein_conc	2925	3488
WB_result	93.2	88.3
Ave_WB	90.8
WB_DONE_date	11/18/2015
MW	58kDa
IP	1	1
antibody_Cat#	GTX109000	GTX109000
Antibody DCC ID	ENCAB174DOV	ENCAB174DOV
submitted_to_DCC_date	12/7/2015
Rep1_TPM	54.4	0
Rep2_TPM	55.6	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2870	2871

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DKC1	Product_ID: GTX109000 Lot_ID: 40583 Source: GeneTex Target Name: DKC1-human

Experiment Status

	BGHLV31-33	BGHLV31-34
Sample_ID	BGHLV31-33	BGHLV31-34
Sample Name	DKC1_BGHLV31-33	DKC1_BGHLV31-34
Sample Name	DKC1_BGHLV31-33	DKC1_BGHLV31-34
RBP	DKC1	DKC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1117	1118

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-33	BGHLV31-34
Sample #
Sample Name	DKC1-BGHLV31-33	DKC1-BGHLV31-34
Sample_Name_Alias	DKC1_BGHLV31-33	DKC1_BGHLV31-34
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/C6.png	DNA_Library_LV31-21B/set1/D6.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C9.png	RNA_Library_LV29-30-31-32/set1/D9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-33	BGHLV31-34
RBP	DKC1	DKC1
Batch_ID	BGHLV31	BGHLV31
WB_result	93.200	88.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2814	2815

Sequencing Information

	BGHLV31-33	BGHLV31-34
Sample_ID	BGHLV31-33	BGHLV31-34
Sample Name	DKC1_BGHLV31-33	DKC1_BGHLV31-34
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	59,338,114	63,705,344
total_aligned_reads	53,768,580	56,440,752
unique_aligned_reads	50,537,178	53,053,702
percent_uniqueAligned	0.85168	0.83280
correlation_replicates	0.997704	0.997704
spikein_reads	297,546	280,610
percent_spikeins	0.00501	0.00440
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1463	1464

Data Submission Information

	BGHLV31-33	BGHLV31-33
ENCODE_alias	brenton-graveley:DKC1_BGHLV31	brenton-graveley:DKC1-BGHLV31-HepG2
ENCODE_accession	ENCSR118KUN	ENCSR502RXV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-33	BGHLV31-33
Sample Name	DKC1_BGHLV31-33	DKC1_BGHLV31-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3091	6666

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
DKC1_BGHLV31-33_GTGGCC_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1463	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20978
DKC1_BGHLV31-33_GTGGCC_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1463	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21004
DKC1_BGHLV31-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1463					GRCh38	V40	DKC1_BGHLV31-33_GTGGCC_L006_001.R1.fastq.gz,DKC1_BGHLV31-33_GTGGCC_L006_001.R2.fastq.gz		ENCORE2	21038
DKC1_BGHLV31-33_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1463					GRCh38	V40	DKC1_BGHLV31-33/Aligned.sortedByCoord.out.bam		ENCORE2	21064
DKC1_BGHLV31-33_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1463					GRCh38	V40	DKC1_BGHLV31-33/Aligned.sortedByCoord.out.bam		ENCORE2	21090
DKC1_BGHLV31-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1463					GRCh38	V40	DKC1_BGHLV31-33/Aligned.sortedByCoord.out.bam		ENCORE2	21116
DKC1_BGHLV31-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1463					GRCh38	V40	DKC1_BGHLV31-33/Aligned.sortedByCoord.out.bam		ENCORE2	21142
DKC1_BGHLV31-33_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1463					GRCh38	V40	DKC1_BGHLV31-33_GTGGCC_L006_001.R1.fastq.gz,DKC1_BGHLV31-33_GTGGCC_L006_001.R2.fastq.gz		ENCORE2	21168
DKC1_BGHLV31-34_GTTTCG_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1464	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20979
DKC1_BGHLV31-34_GTTTCG_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1464	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21005
DKC1_BGHLV31-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1464					GRCh38	V40	DKC1_BGHLV31-34_GTTTCG_L006_001.R1.fastq.gz,DKC1_BGHLV31-34_GTTTCG_L006_001.R2.fastq.gz		ENCORE2	21039
DKC1_BGHLV31-34_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1464					GRCh38	V40	DKC1_BGHLV31-34/Aligned.sortedByCoord.out.bam		ENCORE2	21065
DKC1_BGHLV31-34_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1464					GRCh38	V40	DKC1_BGHLV31-34/Aligned.sortedByCoord.out.bam		ENCORE2	21091
DKC1_BGHLV31-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1464					GRCh38	V40	DKC1_BGHLV31-34/Aligned.sortedByCoord.out.bam		ENCORE2	21117
DKC1_BGHLV31-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1464					GRCh38	V40	DKC1_BGHLV31-34/Aligned.sortedByCoord.out.bam		ENCORE2	21143
DKC1_BGHLV31-34_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1464					GRCh38	V40	DKC1_BGHLV31-34_GTTTCG_L006_001.R1.fastq.gz,DKC1_BGHLV31-34_GTTTCG_L006_001.R2.fastq.gz		ENCORE2	21169