RBM15 RNA-Seq in K562

General Information


RBP	RBM15
Cell_Line	K562
Method	shRNA
Exp_Name	RBM15-BGKLV08-K562
ENCODE_series_ID
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR627NVU
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	RBM15-LV08-43
Rep2	RBM15-LV08-44
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	67.3
Rep2_qPCR	81.2
Rep1_WB	14.0
Rep2_WB	14.2
Antibody Cat#	A300-821A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB626AJI
Status	Archived
Project	ENCODE3
ID	298

Experiment Information (Status: Released)

	BGKLV08-43	BGKLV08-44
idx	44	45
TRCN#_or_BGC#	TRCN0000074704	TRCN0000074704
shRNA_or_gRNA_sequence	CCCAATGGTTATGCCATTCTT	CCCAATGGTTATGCCATTCTT
PAM
Name	RBM15	RBM15
Sample_ID	BGKLV08-43	BGKLV08-44
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	RBM15	RBM15
qPCR_result	67.3	81.2
Ave_qPCR	74.3
RT-qPCR_primer-F	TCCCACCTTGTGAGTTCTCC
RT-qPCR_primer-R	ATCCGCTGTTCAACCAGTTT
protein_conc	2647	2786
WB_result	14.0	14.2
Ave_WB	14.1
WB_DONE_date	6/24/2015
MW	107kDa
IP	1	1
antibody_Cat#	A300-821A	GTX109899
Antibody DCC ID	better
submitted_to_DCC_date
Rep1_TPM	5.73247007	0
Rep2_TPM	7.46767413	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note		4
ID	47	48

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-43	BGKLV08-44
Sample_ID	BGKLV08-43	BGKLV08-44
Sample Name	RBM15-LV08-43	RBM15-LV08-44
Sample Name	RBM15-LV08-43	RBM15-LV08-44
RBP	RBM15	RBM15
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	308	309

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-43	BGKLV08-44
Sample #
Sample Name	RBM15-BGKLV08-43	RBM15-BGKLV08-44
Sample_Name_Alias	RBM15-LV08-43	RBM15-LV08-44
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set4/B2.png	DNA_Library_LV08/set4/C2.png
RIN	8.9	9.0
libSample_RNA_Well	RNA_Library_LV08/set3/C2.png	RNA_Library_LV08/set3/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-43	BGKLV08-44
RBP	RBM15	RBM15
Batch_ID	BGKLV08	BGKLV08
WB_result	14.000	14.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1928	1929

Sequencing Information

	BGKLV08-43	BGKLV08-44
Sample_ID	BGKLV08-43	BGKLV08-44
Sample Name	RBM15-LV08-43	RBM15-LV08-44
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	42,780,000	37,050,000
total_aligned_reads	39,060,978	33,747,146
unique_aligned_reads	36,027,686	30,994,864
percent_uniqueAligned	0.84216	0.83657
correlation_replicates	0.992924	0.992924
spikein_reads	414,754	292,040
percent_spikeins	0.00970	0.00788
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	628	629

Data Submission Information

	BGKLV08-43
ENCODE_alias	brenton-graveley:RBM15-LV08
ENCODE_accession	ENCSR627NVU
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV08-43
Sample Name	RBM15-LV08-43
Selected	Yes
Status	Released
Status_Date	2014-08-13
Project	ENCODE3

protocol_URL
ID	2703

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-LV08-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	628					GRCh38	V40	RBM15-LV08-43_GTCCGC_L006_R1_001.fastq.gz,RBM15-LV08-43_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	12015
RBM15-LV08-43_GTCCGC_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	628	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12071
RBM15-LV08-43_GTCCGC_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	628	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12127
RBM15-LV08-43_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	628					GRCh38	V40	RBM15-LV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	12183
RBM15-LV08-43_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	628					GRCh38	V40	RBM15-LV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	12239
RBM15-LV08-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	628					GRCh38	V40	RBM15-LV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	12295
RBM15-LV08-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	628					GRCh38	V40	RBM15-LV08-43/Aligned.sortedByCoord.out.bam		ENCORE2	12351
RBM15-LV08-43_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	628					GRCh38	V40	RBM15-LV08-43_GTCCGC_L006_R1_001.fastq.gz,RBM15-LV08-43_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	13350
RBM15-LV08-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	629					GRCh38	V40	RBM15-LV08-44_GTGAAA_L006_R1_001.fastq.gz,RBM15-LV08-44_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	12016
RBM15-LV08-44_GTGAAA_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	629	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12072
RBM15-LV08-44_GTGAAA_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	629	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12128
RBM15-LV08-44_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	629					GRCh38	V40	RBM15-LV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	12184
RBM15-LV08-44_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	629					GRCh38	V40	RBM15-LV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	12240
RBM15-LV08-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	629					GRCh38	V40	RBM15-LV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	12296
RBM15-LV08-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	629					GRCh38	V40	RBM15-LV08-44/Aligned.sortedByCoord.out.bam		ENCORE2	12352
RBM15-LV08-44_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	629					GRCh38	V40	RBM15-LV08-44_GTGAAA_L006_R1_001.fastq.gz,RBM15-LV08-44_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	13351