RBM25 RNA-Seq in K562

General Information


RBP	RBM25
Cell_Line	K562
Method	shRNA
Exp_Name	RBM25-BGKLV08-K562
ENCODE_series_ID	ENCSR849SUF
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR149DMY
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	RBM25-LV08-45
Rep2	RBM25-LV08-46
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	67.8
Rep2_qPCR	66.4
Rep1_WB	30.9
Rep2_WB	42.6
Antibody Cat#	A301-068A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB401CSY
Status	Archived
Project	ENCODE3
ID	299

Experiment Information (Status: Released)

	BGKLV08-45	BGKLV08-46
idx	46	47
TRCN#_or_BGC#	TRCN0000074750	TRCN0000074750
shRNA_or_gRNA_sequence	GCGCCTTAAGAATTGGGAAAT	GCGCCTTAAGAATTGGGAAAT
PAM
Name	RBM25	RBM25
Sample_ID	BGKLV08-45	BGKLV08-46
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	RBM25	RBM25
qPCR_result	67.8	66.4
Ave_qPCR	67.1
RT-qPCR_primer-F	GAATTCTTAGAAGACTATGATGATGA
RT-qPCR_primer-R	TTTCTCTATCACGCAACCTTT
protein_conc	2840	2792
WB_result	30.9	42.6
Ave_WB	36.8
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A301-068A	A301-068A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	32.3531997	0
Rep2_TPM	23.0787827	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	49	50

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-45	BGKLV08-46
Sample_ID	BGKLV08-45	BGKLV08-46
Sample Name	RBM25-LV08-45	RBM25-LV08-46
Sample Name	RBM25-LV08-45	RBM25-LV08-46
RBP	RBM25	RBM25
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	310	311

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-45	BGKLV08-46
Sample #
Sample Name	RBM25-BGKLV08-45	RBM25-BGKLV08-46
Sample_Name_Alias	RBM25-LV08-45	RBM25-LV08-46
Index Well Position	S20	S21
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/D2.png	DNA_Library_LV08/set4/E2.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV08/set3/E2.png	RNA_Library_LV08/set3/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-45	BGKLV08-46
RBP	RBM25	RBM25
Batch_ID	BGKLV08	BGKLV08
WB_result	30.900	42.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1930	1931

Sequencing Information

	BGKLV08-45	BGKLV08-46
Sample_ID	BGKLV08-45	BGKLV08-46
Sample Name	RBM25-LV08-45	RBM25-LV08-46
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	39,200,000	46,210,000
total_aligned_reads	34,703,696	41,712,800
unique_aligned_reads	31,692,060	37,988,170
percent_uniqueAligned	0.80847	0.82208
correlation_replicates	0.997491	0.997491
spikein_reads	266,854	292,670
percent_spikeins	0.00681	0.00633
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	630	631

Data Submission Information

	BGKLV08-45	BGKLV08-45
ENCODE_alias	brenton-graveley:RBM25-LV08	brenton-graveley:RBM25-BGKLV08-K562
ENCODE_accession	ENCSR149DMY	ENCSR849SUF
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-45	BGKLV08-45
Sample Name	RBM25-LV08-45	RBM25-LV08-45
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2704	6899

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
RBM25-LV08-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	630					GRCh38	V40	RBM25-LV08-45_GTGGCC_L007_R1_001.fastq.gz,RBM25-LV08-45_GTGGCC_L007_R2_001.fastq.gz		ENCORE2	12017
RBM25-LV08-45_GTGGCC_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	630	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	12073
RBM25-LV08-45_GTGGCC_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	630	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	12129
RBM25-LV08-45_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	630					GRCh38	V40	RBM25-LV08-45/Aligned.sortedByCoord.out.bam		ENCORE2	12185
RBM25-LV08-45_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	630					GRCh38	V40	RBM25-LV08-45/Aligned.sortedByCoord.out.bam		ENCORE2	12241
RBM25-LV08-45_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	630					GRCh38	V40	RBM25-LV08-45/Aligned.sortedByCoord.out.bam		ENCORE2	12297
RBM25-LV08-45_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	630					GRCh38	V40	RBM25-LV08-45/Aligned.sortedByCoord.out.bam		ENCORE2	12353
RBM25-LV08-45_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	630					GRCh38	V40	RBM25-LV08-45_GTGGCC_L007_R1_001.fastq.gz,RBM25-LV08-45_GTGGCC_L007_R2_001.fastq.gz		ENCORE2	13352
RBM25-LV08-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	631					GRCh38	V40	RBM25-LV08-46_GTTTCG_L007_R1_001.fastq.gz,RBM25-LV08-46_GTTTCG_L007_R2_001.fastq.gz		ENCORE2	12018
RBM25-LV08-46_GTTTCG_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	631	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	12074
RBM25-LV08-46_GTTTCG_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	631	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	12130
RBM25-LV08-46_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	631					GRCh38	V40	RBM25-LV08-46/Aligned.sortedByCoord.out.bam		ENCORE2	12186
RBM25-LV08-46_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	631					GRCh38	V40	RBM25-LV08-46/Aligned.sortedByCoord.out.bam		ENCORE2	12242
RBM25-LV08-46_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	631					GRCh38	V40	RBM25-LV08-46/Aligned.sortedByCoord.out.bam		ENCORE2	12298
RBM25-LV08-46_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	631					GRCh38	V40	RBM25-LV08-46/Aligned.sortedByCoord.out.bam		ENCORE2	12354
RBM25-LV08-46_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	631					GRCh38	V40	RBM25-LV08-46_GTTTCG_L007_R1_001.fastq.gz,RBM25-LV08-46_GTTTCG_L007_R2_001.fastq.gz		ENCORE2	13353