RBM15 RNA-Seq in K562

General Information


RBP	RBM15
Cell_Line	K562
Method	shRNA
Exp_Name	RBM15-BGKLV32-K562
ENCODE_series_ID	ENCSR676VUZ
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR385UPQ
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	RBM15_BGKLV32-53
Rep2	RBM15_BGKLV32-54
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	66.6
Rep2_qPCR	66.5
Rep1_WB	63.2
Rep2_WB	73.7
Antibody Cat#	A300-821A
Antibody Lot#	A300-821A
Antibody DCC ID	ENCAB626AJI
Status	Released
Project	ENCODE3
ID	714

Experiment Information (Status: Released)

	BGKLV32-53	BGKLV32-54
idx	652	653
TRCN#_or_BGC#	TRCN0000074707	TRCN0000074707
shRNA_or_gRNA_sequence	GATCGTTACAACAGCGACAAT	GATCGTTACAACAGCGACAAT
PAM
Name	RBM15	RBM15
Sample_ID	BGKLV32-53	BGKLV32-54
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	RBM15	RBM15
qPCR_result	66.6	66.5
Ave_qPCR	66.5
RT-qPCR_primer-F	TCCCACCTTGTGAGTTCTCC
RT-qPCR_primer-R	ATCCGCTGTTCAACCAGTTT
protein_conc	3069	3203
WB_result	63.2	73.7
Ave_WB	68.5
WB_DONE_date	11/9/2015
MW	107kDa
IP	1	1
antibody_Cat#	A300-821A	A300-821A
Antibody DCC ID	ENCAB626AJI	ENCAB626AJI
submitted_to_DCC_date	12/7/2015
Rep1_TPM	5.73247007	0
Rep2_TPM	7.46767413	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	737	738

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM15	Product_ID: A300-821A Lot_ID: 2 Source: Bethyl Labs Target Name: RBM15-human

Experiment Status

	BGKLV32-53	BGKLV32-54
Sample_ID	BGKLV32-53	BGKLV32-54
Sample Name	RBM15_BGKLV32-53	RBM15_BGKLV32-54
Sample Name	RBM15_BGKLV32-53	RBM15_BGKLV32-54
RBP	RBM15	RBM15
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1179	1180

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-53	BGKLV32-54
Sample #
Sample Name	RBM15-BGKLV32-53	RBM15-BGKLV32-54
Sample_Name_Alias	RBM15_BGKLV32-53	RBM15_BGKLV32-54
Index Well Position	S03	S04
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/C9.png	DNA_Library_LV33-34-25B-32/set1/D9.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/C2.png	RNA_Library_LV32-33-34/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-53	BGKLV32-54
RBP	RBM15	RBM15
Batch_ID	BGKLV32	BGKLV32
WB_result	63.200	73.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2864	2865

Sequencing Information

	BGKLV32-53	BGKLV32-54
Sample_ID	BGKLV32-53	BGKLV32-54
Sample Name	RBM15_BGKLV32-53	RBM15_BGKLV32-54
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	81,933,992	83,335,000
total_aligned_reads	70,072,614	71,580,550
unique_aligned_reads	63,655,732	64,741,384
percent_uniqueAligned	0.77691	0.77688
correlation_replicates	0.998156	0.998156
spikein_reads	305,918	291,672
percent_spikeins	0.00373	0.00350
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1513	1514

Data Submission Information

	BGKLV32-53	BGKLV32-53
ENCODE_alias	brenton-graveley:RBM15_BGKLV32	brenton-graveley:RBM15-BGKLV32-K562
ENCODE_accession	ENCSR385UPQ	ENCSR676VUZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-53	BGKLV32-53
Sample Name	RBM15_BGKLV32-53	RBM15_BGKLV32-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3129	6893

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
RBM15_BGKLV32-53_TTAGGC_L004_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1513	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21212
RBM15_BGKLV32-53_TTAGGC_L004_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1513	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21242
RBM15_BGKLV32-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1513					GRCh38	V40	RBM15_BGKLV32-53_TTAGGC_L004_001.R1.fastq.gz,RBM15_BGKLV32-53_TTAGGC_L004_001.R2.fastq.gz		ENCORE2	21272
RBM15_BGKLV32-53_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	1513					GRCh38	V40	RBM15_BGKLV32-53/Aligned.sortedByCoord.out.bam		ENCORE2	21302
RBM15_BGKLV32-53_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	1513					GRCh38	V40	RBM15_BGKLV32-53/Aligned.sortedByCoord.out.bam		ENCORE2	21332
RBM15_BGKLV32-53_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	1513					GRCh38	V40	RBM15_BGKLV32-53/Aligned.sortedByCoord.out.bam		ENCORE2	21362
RBM15_BGKLV32-53_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	1513					GRCh38	V40	RBM15_BGKLV32-53/Aligned.sortedByCoord.out.bam		ENCORE2	21392
RBM15_BGKLV32-53_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1513					GRCh38	V40	RBM15_BGKLV32-53_TTAGGC_L004_001.R1.fastq.gz,RBM15_BGKLV32-53_TTAGGC_L004_001.R2.fastq.gz		ENCORE2	21422
RBM15_BGKLV32-54_TGACCA_L004_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1514	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21213
RBM15_BGKLV32-54_TGACCA_L004_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1514	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21243
RBM15_BGKLV32-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1514					GRCh38	V40	RBM15_BGKLV32-54_TGACCA_L004_001.R1.fastq.gz,RBM15_BGKLV32-54_TGACCA_L004_001.R2.fastq.gz		ENCORE2	21273
RBM15_BGKLV32-54_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	1514					GRCh38	V40	RBM15_BGKLV32-54/Aligned.sortedByCoord.out.bam		ENCORE2	21303
RBM15_BGKLV32-54_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	1514					GRCh38	V40	RBM15_BGKLV32-54/Aligned.sortedByCoord.out.bam		ENCORE2	21333
RBM15_BGKLV32-54_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	1514					GRCh38	V40	RBM15_BGKLV32-54/Aligned.sortedByCoord.out.bam		ENCORE2	21363
RBM15_BGKLV32-54_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	1514					GRCh38	V40	RBM15_BGKLV32-54/Aligned.sortedByCoord.out.bam		ENCORE2	21393
RBM15_BGKLV32-54_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1514					GRCh38	V40	RBM15_BGKLV32-54_TGACCA_L004_001.R1.fastq.gz,RBM15_BGKLV32-54_TGACCA_L004_001.R2.fastq.gz		ENCORE2	21423