RBM34 RNA-Seq in K562

General Information


RBP	RBM34
Cell_Line	K562
Method	shRNA
Exp_Name	RBM34-BGKLV11-K562
ENCODE_series_ID	ENCSR930UCY
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR560AYQ
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	RBM34-LV11-43
Rep2	RBM34-LV11-44
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	83.3
Rep2_qPCR	81.6
Rep1_WB	91.4
Rep2_WB	90.4
Antibody Cat#	A302-293A
Antibody Lot#	A302-293A
Antibody DCC ID	ENCAB594ZFC
Status	Released
Project	ENCODE3
ID	320

Experiment Information (Status: Released)

	BGKLV11-43	BGKLV11-44
idx	112	113
TRCN#_or_BGC#	TRCN0000147509	TRCN0000147509
shRNA_or_gRNA_sequence	GCTATGTGCTCTTTGAGAATA	GCTATGTGCTCTTTGAGAATA
PAM
Name	RBM34	RBM34
Sample_ID	BGKLV11-43	BGKLV11-44
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	RBM34	RBM34
qPCR_result	83.3	81.6
Ave_qPCR	82.5
RT-qPCR_primer-F	ATGACAGGCATCGGCAAAG
RT-qPCR_primer-R	TCAGAATTATTTAATTTCAGAGCAAGA
protein_conc	1880	1973
WB_result	91.4	90.4
Ave_WB	90.9
WB_DONE_date	3/19/2015
MW	48kDa
IP	1	1
antibody_Cat#	A302-293A	A302-293A
Antibody DCC ID	ENCAB594ZFC	ENCAB594ZFC
submitted_to_DCC_date	4/2/2015
Rep1_TPM	73.9831258	0
Rep2_TPM	67.2432532	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	125	126

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM34	Product_ID: A302-293A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM34-human

Experiment Status

	BGKLV11-43	BGKLV11-44
Sample_ID	BGKLV11-43	BGKLV11-44
Sample Name	RBM34-LV11-43	RBM34-LV11-44
Sample Name	RBM34-LV11-43	RBM34-LV11-44
RBP	RBM34	RBM34
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	354	355

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-43	BGKLV11-44
Sample #
Sample Name	RBM34-BGKLV11-43	RBM34-BGKLV11-44
Sample_Name_Alias	RBM34-LV11-43	RBM34-LV11-44
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set3/B1.png	DNA_Library_LV11/set3/C1.png
RIN	9.4	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/G4.png	RNA_Library_LV11/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-43	BGKLV11-44
RBP	RBM34	RBM34
Batch_ID	BGKLV11	BGKLV11
WB_result	91.400	90.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1976	1977

Sequencing Information

	BGKLV11-43	BGKLV11-44
Sample_ID	BGKLV11-43	BGKLV11-44
Sample Name	RBM34-LV11-43	RBM34-LV11-44
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	61,110,000	56,910,000
total_aligned_reads	49,944,294	46,204,618
unique_aligned_reads	45,807,778	42,537,280
percent_uniqueAligned	0.74960	0.74745
correlation_replicates	0.995716	0.995716
spikein_reads	299,612	354,898
percent_spikeins	0.00490	0.00624
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	676	677

Data Submission Information

	BGKLV11-43	BGKLV11-43
ENCODE_alias	brenton-graveley:RBM34-LV11	brenton-graveley:RBM34-BGKLV11-K562
ENCODE_accession	ENCSR560AYQ	ENCSR930UCY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-43	BGKLV11-43
Sample Name	RBM34-LV11-43	RBM34-LV11-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2726	6902

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
RBM34-LV11-43_CAGATC_L006_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	676	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12397
RBM34-LV11-43_CAGATC_L006_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	676	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12445
RBM34-LV11-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	676					GRCh38	V40	RBM34-LV11-43_CAGATC_L006_R1_001.fastq.gz,RBM34-LV11-43_CAGATC_L006_R2_001.fastq.gz		ENCORE2	12493
RBM34-LV11-43_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	676					GRCh38	V40	RBM34-LV11-43/Aligned.sortedByCoord.out.bam		ENCORE2	12541
RBM34-LV11-43_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	676					GRCh38	V40	RBM34-LV11-43/Aligned.sortedByCoord.out.bam		ENCORE2	12589
RBM34-LV11-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	676					GRCh38	V40	RBM34-LV11-43/Aligned.sortedByCoord.out.bam		ENCORE2	12637
RBM34-LV11-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	676					GRCh38	V40	RBM34-LV11-43/Aligned.sortedByCoord.out.bam		ENCORE2	12685
RBM34-LV11-43_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	676					GRCh38	V40	RBM34-LV11-43_CAGATC_L006_R1_001.fastq.gz,RBM34-LV11-43_CAGATC_L006_R2_001.fastq.gz		ENCORE2	12733
RBM34-LV11-44_ACTTGA_L006_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	677	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12398
RBM34-LV11-44_ACTTGA_L006_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	677	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12446
RBM34-LV11-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	677					GRCh38	V40	RBM34-LV11-44_ACTTGA_L006_R1_001.fastq.gz,RBM34-LV11-44_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	12494
RBM34-LV11-44_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	677					GRCh38	V40	RBM34-LV11-44/Aligned.sortedByCoord.out.bam		ENCORE2	12542
RBM34-LV11-44_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	677					GRCh38	V40	RBM34-LV11-44/Aligned.sortedByCoord.out.bam		ENCORE2	12590
RBM34-LV11-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	677					GRCh38	V40	RBM34-LV11-44/Aligned.sortedByCoord.out.bam		ENCORE2	12638
RBM34-LV11-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	677					GRCh38	V40	RBM34-LV11-44/Aligned.sortedByCoord.out.bam		ENCORE2	12686
RBM34-LV11-44_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	677					GRCh38	V40	RBM34-LV11-44_ACTTGA_L006_R1_001.fastq.gz,RBM34-LV11-44_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	12734