RBM22 RNA-Seq in K562

General Information


RBP	RBM22
Cell_Line	K562
Method	shRNA
Exp_Name	RBM22-BGKLV11-K562
ENCODE_series_ID	ENCSR071HSS
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR947OIM
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	RBM22-LV11-41
Rep2	RBM22-LV11-42
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	52.1
Rep2_qPCR	59.3
Rep1_WB	88.6
Rep2_WB	84.0
Antibody Cat#	A303-923A
Antibody Lot#	A303-923A
Antibody DCC ID	ENCAB476CFS
Status	Released
Project	ENCODE3
ID	319

Experiment Information (Status: Released)

	BGKLV11-41	BGKLV11-42
idx	110	111
TRCN#_or_BGC#	TRCN0000008650	TRCN0000008650
shRNA_or_gRNA_sequence	GCCGCAGACTGAATGTGAAAT	GCCGCAGACTGAATGTGAAAT
PAM
Name	RBM22	RBM22
Sample_ID	BGKLV11-41	BGKLV11-42
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	RBM22	RBM22
qPCR_result	52.1	59.3
Ave_qPCR	55.7
RT-qPCR_primer-F	TCCAGCTGTGGTGAACATTG
RT-qPCR_primer-R	GTCCCATTGGGTGGAACA
protein_conc	1976	1932
WB_result	88.6	84.0
Ave_WB	86.3
WB_DONE_date	6/4/2015
MW	47kDa
IP	1	1
antibody_Cat#	A303-923A	A303-923A
Antibody DCC ID	ENCAB476CFS	ENCAB476CFS
submitted_to_DCC_date	8/6/2015
Rep1_TPM	19.8626769	0
Rep2_TPM	18.0613345	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	123	124

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM22	Product_ID: A303-923A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM22-human

Experiment Status

	BGKLV11-41	BGKLV11-42
Sample_ID	BGKLV11-41	BGKLV11-42
Sample Name	RBM22-LV11-41	RBM22-LV11-42
Sample Name	RBM22-LV11-41	RBM22-LV11-42
RBP	RBM22	RBM22
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	352	353

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-41	BGKLV11-42
Sample #
Sample Name	RBM22-BGKLV11-41	RBM22-BGKLV11-42
Sample_Name_Alias	RBM22-LV11-41	RBM22-LV11-42
Index Well Position	S05	S06
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/set2/G2.png	DNA_Library_LV11/set2/H2.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/E4.png	RNA_Library_LV11/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-41	BGKLV11-42
RBP	RBM22	RBM22
Batch_ID	BGKLV11	BGKLV11
WB_result	88.600	84.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1974	1975

Sequencing Information

	BGKLV11-41	BGKLV11-42
Sample_ID	BGKLV11-41	BGKLV11-42
Sample Name	RBM22-LV11-41	RBM22-LV11-42
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	61,520,000	63,440,000
total_aligned_reads	49,720,728	50,248,500
unique_aligned_reads	45,663,596	45,832,786
percent_uniqueAligned	0.74226	0.72246
correlation_replicates	0.992895	0.992895
spikein_reads	451,180	344,806
percent_spikeins	0.00733	0.00544
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	674	675

Data Submission Information

	BGKLV11-41	BGKLV11-41
ENCODE_alias	brenton-graveley:RBM22-LV11	brenton-graveley:RBM22-BGKLV11-K562
ENCODE_accession	ENCSR947OIM	ENCSR071HSS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-41	BGKLV11-41
Sample Name	RBM22-LV11-41	RBM22-LV11-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2725	6897

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
RBM22-LV11-41_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	674	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12395
RBM22-LV11-41_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	674	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12443
RBM22-LV11-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	674					GRCh38	V40	RBM22-LV11-41_ACAGTG_L005_R1_001.fastq.gz,RBM22-LV11-41_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	12491
RBM22-LV11-41_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	674					GRCh38	V40	RBM22-LV11-41/Aligned.sortedByCoord.out.bam		ENCORE2	12539
RBM22-LV11-41_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	674					GRCh38	V40	RBM22-LV11-41/Aligned.sortedByCoord.out.bam		ENCORE2	12587
RBM22-LV11-41_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	674					GRCh38	V40	RBM22-LV11-41/Aligned.sortedByCoord.out.bam		ENCORE2	12635
RBM22-LV11-41_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	674					GRCh38	V40	RBM22-LV11-41/Aligned.sortedByCoord.out.bam		ENCORE2	12683
RBM22-LV11-41_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	674					GRCh38	V40	RBM22-LV11-41_ACAGTG_L005_R1_001.fastq.gz,RBM22-LV11-41_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	12731
RBM22-LV11-42_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	675	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12396
RBM22-LV11-42_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	675	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12444
RBM22-LV11-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	675					GRCh38	V40	RBM22-LV11-42_GCCAAT_L005_R1_001.fastq.gz,RBM22-LV11-42_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	12492
RBM22-LV11-42_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	675					GRCh38	V40	RBM22-LV11-42/Aligned.sortedByCoord.out.bam		ENCORE2	12540
RBM22-LV11-42_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	675					GRCh38	V40	RBM22-LV11-42/Aligned.sortedByCoord.out.bam		ENCORE2	12588
RBM22-LV11-42_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	675					GRCh38	V40	RBM22-LV11-42/Aligned.sortedByCoord.out.bam		ENCORE2	12636
RBM22-LV11-42_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	675					GRCh38	V40	RBM22-LV11-42/Aligned.sortedByCoord.out.bam		ENCORE2	12684
RBM22-LV11-42_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	675					GRCh38	V40	RBM22-LV11-42_GCCAAT_L005_R1_001.fastq.gz,RBM22-LV11-42_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	12732