DKC1 RNA-Seq in K562

General Information


RBP	DKC1
Cell_Line	K562
Method	shRNA
Exp_Name	DKC1-BGKLV32-K562
ENCODE_series_ID	ENCSR329ZWP
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR494UDF
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	DKC1_BGKLV32-29
Rep2	DKC1_BGKLV32-30
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	87.2
Rep2_WB	89.9
Antibody Cat#	GTX109000
Antibody Lot#	GTX109000
Antibody DCC ID	ENCAB174DOV
Status	Released
Project	ENCODE3
ID	708

Experiment Information (Status: Released)

	BGKLV32-29	BGKLV32-30
idx	628	629
TRCN#_or_BGC#	TRCN0000039738	TRCN0000039738
shRNA_or_gRNA_sequence	GCTCAGTGAAATGCTGTAGAA	GCTCAGTGAAATGCTGTAGAA
PAM
Name	DKC1	DKC1
Sample_ID	BGKLV32-29	BGKLV32-30
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	DKC1	DKC1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ggcgagttgtttaccctttg
RT-qPCR_primer-R	taatcttggccccatagcag
protein_conc	2781	2679
WB_result	87.2	89.9
Ave_WB	88.5
WB_DONE_date	11/18/2015
MW	58kDa
IP	1	1
antibody_Cat#	GTX109000	GTX109000
Antibody DCC ID	ENCAB174DOV	ENCAB174DOV
submitted_to_DCC_date	10/26/16
Rep1_TPM	136.7534529	0
Rep2_TPM	98.59522831	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	711	712

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

	BGKLV32-29	BGKLV32-30
Sample_ID	BGKLV32-29	BGKLV32-30
Sample Name	DKC1_BGKLV32-29	DKC1_BGKLV32-30
Sample Name	DKC1_BGKLV32-29	DKC1_BGKLV32-30
RBP	DKC1	DKC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1165	1166

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-29	BGKLV32-30
Sample #
Sample Name	DKC1-BGKLV32-29	DKC1-BGKLV32-30
Sample_Name_Alias	DKC1_BGKLV32-29	DKC1_BGKLV32-30
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/G7.png	DNA_Library_LV33-34-25B-32/set1/H7.png
RIN	10.0	9.5
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G12.png	RNA_Library_LV29-30-31-32/set1/H12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-29	BGKLV32-30
RBP	DKC1	DKC1
Batch_ID	BGKLV32	BGKLV32
WB_result	87.200	89.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2850	2851

Sequencing Information

	BGKLV32-29	BGKLV32-30
Sample_ID	BGKLV32-29	BGKLV32-30
Sample Name	DKC1_BGKLV32-29	DKC1_BGKLV32-30
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	93,625,812	81,754,738
total_aligned_reads	80,190,584	69,687,008
unique_aligned_reads	73,421,636	63,874,560
percent_uniqueAligned	0.78420	0.78129
correlation_replicates	0.997764	0.997764
spikein_reads	358,052	318,754
percent_spikeins	0.00382	0.00390
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1499	1500

Data Submission Information

	BGKLV32-29	BGKLV32-29
ENCODE_alias	brenton-graveley:DKC1_BGKLV32	brenton-graveley:DKC1-BGKLV32-K562
ENCODE_accession	ENCSR494UDF	ENCSR329ZWP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-29	BGKLV32-29
Sample Name	DKC1_BGKLV32-29	DKC1_BGKLV32-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3122	6667

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_BGKLV32-29_ATGTCA_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1499	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21198
DKC1_BGKLV32-29_ATGTCA_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1499	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21228
DKC1_BGKLV32-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1499					GRCh38	V40	DKC1_BGKLV32-29_ATGTCA_L002_001.R1.fastq.gz,DKC1_BGKLV32-29_ATGTCA_L002_001.R2.fastq.gz		ENCORE2	21258
DKC1_BGKLV32-29_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1499					GRCh38	V40	DKC1_BGKLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	21288
DKC1_BGKLV32-29_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1499					GRCh38	V40	DKC1_BGKLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	21318
DKC1_BGKLV32-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1499					GRCh38	V40	DKC1_BGKLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	21348
DKC1_BGKLV32-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1499					GRCh38	V40	DKC1_BGKLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	21378
DKC1_BGKLV32-29_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1499					GRCh38	V40	DKC1_BGKLV32-29_ATGTCA_L002_001.R1.fastq.gz,DKC1_BGKLV32-29_ATGTCA_L002_001.R2.fastq.gz		ENCORE2	21408
DKC1_BGKLV32-30_CCGTCC_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1500	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21199
DKC1_BGKLV32-30_CCGTCC_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1500	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21229
DKC1_BGKLV32-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1500					GRCh38	V40	DKC1_BGKLV32-30_CCGTCC_L002_001.R1.fastq.gz,DKC1_BGKLV32-30_CCGTCC_L002_001.R2.fastq.gz		ENCORE2	21259
DKC1_BGKLV32-30_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1500					GRCh38	V40	DKC1_BGKLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	21289
DKC1_BGKLV32-30_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1500					GRCh38	V40	DKC1_BGKLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	21319
DKC1_BGKLV32-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1500					GRCh38	V40	DKC1_BGKLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	21349
DKC1_BGKLV32-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1500					GRCh38	V40	DKC1_BGKLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	21379
DKC1_BGKLV32-30_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1500					GRCh38	V40	DKC1_BGKLV32-30_CCGTCC_L002_001.R1.fastq.gz,DKC1_BGKLV32-30_CCGTCC_L002_001.R2.fastq.gz		ENCORE2	21409