BUD13 RNA-Seq in K562

General Information


RBP	BUD13
Cell_Line	K562
Method	shRNA
Exp_Name	BUD13-BGKLV29-K562
ENCODE_series_ID	ENCSR136SIX
Batch_ID	BGKLV29
Pool ID	Pool-151215C
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR267RHP
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	BUD13_BGKLV29-15
Rep2	BUD13_BGKLV29-16
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	76.7
Rep2_qPCR	68.6
Rep1_WB	82.7
Rep2_WB	85.7
Antibody Cat#	A303-320A
Antibody Lot#	A303-320A
Antibody DCC ID	ENCAB673IND
Status	Released
Project	ENCODE3
ID	664

Experiment Information (Status: Released)

	BGKLV29-15	BGKLV29-16
idx	548	549
TRCN#_or_BGC#	TRCN0000074896	TRCN0000074896
shRNA_or_gRNA_sequence	CGAGTATCTGAAGCGTTACTT	CGAGTATCTGAAGCGTTACTT
PAM
Name	BUD13	BUD13
Sample_ID	BGKLV29-15	BGKLV29-16
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	BUD13	BUD13
qPCR_result	76.7	68.6
Ave_qPCR	72.7
RT-qPCR_primer-F	ctttcgttccagtgccaaat
RT-qPCR_primer-R	aggagatgaatccggggtat
protein_conc	3031	3442
WB_result	82.7	85.7
Ave_WB	84.2
WB_DONE_date	9/4/2015
MW	71kd
IP	1	1
antibody_Cat#	A303-320A	A303-320A
Antibody DCC ID	ENCAB673IND	ENCAB673IND
submitted_to_DCC_date	12/7/2015
Rep1_TPM	21.8489328	0
Rep2_TPM	15.4837705	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	627	628

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BUD13	Product_ID: A303-320A Lot_ID: 1 Source: Bethyl Labs Target Name: BUD13-human

Experiment Status

	BGKLV29-15	BGKLV29-16
Sample_ID	BGKLV29-15	BGKLV29-16
Sample Name	BUD13_BGKLV29-15	BUD13_BGKLV29-16
Sample Name	BUD13_BGKLV29-15	BUD13_BGKLV29-16
RBP	BUD13	BUD13
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1014	1015

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-15	BGKLV29-16
Sample #
Sample Name	BUD13-BGKLV29-15	BUD13-BGKLV29-16
Sample_Name_Alias	BUD13_BGKLV29-15	BUD13_BGKLV29-16
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E5.png	DNA_Library_LV28-29-30/set1/F5.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A1.png	RNA_Library_LV29-30-31-32/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-15	BGKLV29-16
RBP	BUD13	BUD13
Batch_ID	BGKLV29	BGKLV29
WB_result	82.700	85.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2706	2707

Sequencing Information

	BGKLV29-15	BGKLV29-16
Sample_ID	BGKLV29-15	BGKLV29-16
Sample Name	BUD13_BGKLV29-15	BUD13_BGKLV29-16
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set29	set29
total_reads	60,512,024	60,819,878
total_aligned_reads	47,301,854	46,529,046
unique_aligned_reads	43,281,060	42,750,836
percent_uniqueAligned	0.71525	0.70291
correlation_replicates	0.998883	0.998883
spikein_reads	225,672	202,202
percent_spikeins	0.00373	0.00332
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1348	1349

Data Submission Information

	BGKLV29-15	BGKLV29-15
ENCODE_alias	brenton-graveley:BUD13_BGKLV29	brenton-graveley:BUD13-BGKLV29-K562
ENCODE_accession	ENCSR267RHP	ENCSR136SIX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-15	BGKLV29-15
Sample Name	BUD13_BGKLV29-15	BUD13_BGKLV29-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3056	6607

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
BUD13_BGKLV29-15_AGTCAA_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1348	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20416
BUD13_BGKLV29-15_AGTCAA_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1348	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20446
BUD13_BGKLV29-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1348					GRCh38	V40	BUD13_BGKLV29-15_AGTCAA_L005_001.R1.fastq.gz,BUD13_BGKLV29-15_AGTCAA_L005_001.R2.fastq.gz		ENCORE2	20476
BUD13_BGKLV29-15_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1348					GRCh38	V40	BUD13_BGKLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	20506
BUD13_BGKLV29-15_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1348					GRCh38	V40	BUD13_BGKLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	20536
BUD13_BGKLV29-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1348					GRCh38	V40	BUD13_BGKLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	20566
BUD13_BGKLV29-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1348					GRCh38	V40	BUD13_BGKLV29-15/Aligned.sortedByCoord.out.bam		ENCORE2	20596
BUD13_BGKLV29-15_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1348					GRCh38	V40	BUD13_BGKLV29-15_AGTCAA_L005_001.R1.fastq.gz,BUD13_BGKLV29-15_AGTCAA_L005_001.R2.fastq.gz		ENCORE2	20626
BUD13_BGKLV29-16_AGTTCC_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1349	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20417
BUD13_BGKLV29-16_AGTTCC_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1349	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20447
BUD13_BGKLV29-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1349					GRCh38	V40	BUD13_BGKLV29-16_AGTTCC_L005_001.R1.fastq.gz,BUD13_BGKLV29-16_AGTTCC_L005_001.R2.fastq.gz		ENCORE2	20477
BUD13_BGKLV29-16_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1349					GRCh38	V40	BUD13_BGKLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	20507
BUD13_BGKLV29-16_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1349					GRCh38	V40	BUD13_BGKLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	20537
BUD13_BGKLV29-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1349					GRCh38	V40	BUD13_BGKLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	20567
BUD13_BGKLV29-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1349					GRCh38	V40	BUD13_BGKLV29-16/Aligned.sortedByCoord.out.bam		ENCORE2	20597
BUD13_BGKLV29-16_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1349					GRCh38	V40	BUD13_BGKLV29-16_AGTTCC_L005_001.R1.fastq.gz,BUD13_BGKLV29-16_AGTTCC_L005_001.R2.fastq.gz		ENCORE2	20627