CIRBP RNA-Seq in K562

General Information


RBP	CIRBP
Cell_Line	K562
Method	shRNA
Exp_Name	CIRBP-BGKLV11-K562
ENCODE_series_ID	ENCSR360LED
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR056QEW
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	CIRBP-LV11-3
Rep2	CIRBP-LV11-4
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	73.1
Rep2_qPCR	64.3
Rep1_WB
Rep2_WB
Antibody Cat#	RN032P
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB000BFF
Status	Archived
Project	ENCODE3
ID	306

Experiment Information (Status: Released)

	BGKLV11-3	BGKLV11-4
idx	72	73
TRCN#_or_BGC#	TRCN0000017265	TRCN0000017265
shRNA_or_gRNA_sequence	GCCATGAATGGGAAGTCTGTA	GCCATGAATGGGAAGTCTGTA
PAM
Name	CIRBP	CIRBP
Sample_ID	BGKLV11-3	BGKLV11-4
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	CIRBP	CIRBP
qPCR_result	73.1	64.3
Ave_qPCR	68.7
RT-qPCR_primer-F	TGTGGTGCGCTGTCTTCC
RT-qPCR_primer-R	AAACTCAGCCCTCCAACAAA
protein_conc	1933	1859
WB_result
Ave_WB	No good signal	No good signal
WB_DONE_date	1/20/15
MW	19kDa
IP	1	1
antibody_Cat#	RN032P	RN032P
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	25.7581204	0
Rep2_TPM	39.2223346	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	77	78

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV11-3	BGKLV11-4
Sample_ID	BGKLV11-3	BGKLV11-4
Sample Name	CIRBP-LV11-3	CIRBP-LV11-4
Sample Name	CIRBP-LV11-3	CIRBP-LV11-4
RBP	CIRBP	CIRBP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	324	325

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-3	BGKLV11-4
Sample #
Sample Name	CIRBP-BGKLV11-3	CIRBP-BGKLV11-4
Sample_Name_Alias	CIRBP-LV11-3	CIRBP-LV11-4
Index Well Position	S03	S04
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/set1/D1.png	DNA_Library_LV11/set1/E1.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/C1.png	RNA_Library_LV11/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-3	BGKLV11-4
RBP	CIRBP	CIRBP
Batch_ID	BGKLV11	BGKLV11
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1946	1947

Sequencing Information

	BGKLV11-3	BGKLV11-4
Sample_ID	BGKLV11-3	BGKLV11-4
Sample Name	CIRBP-LV11-3	CIRBP-LV11-4
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	69,730,000	74,780,000
total_aligned_reads	56,139,876	58,447,792
unique_aligned_reads	51,307,872	53,383,848
percent_uniqueAligned	0.73581	0.71388
correlation_replicates	0.998284	0.998284
spikein_reads	519,592	527,826
percent_spikeins	0.00745	0.00706
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	646	647

Data Submission Information

	BGKLV11-3	BGKLV11-3
ENCODE_alias	brenton-graveley:CIRBP-LV11	brenton-graveley:CIRBP-BGKLV11-K562
ENCODE_accession	ENCSR056QEW	ENCSR360LED
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-3	BGKLV11-3
Sample Name	CIRBP-LV11-3	CIRBP-LV11-3
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2711	6620

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
CIRBP-LV11-3_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	646	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12367
CIRBP-LV11-3_TTAGGC_L001_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	646	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12415
CIRBP-LV11-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	646					GRCh38	V40	CIRBP-LV11-3_TTAGGC_L001_R1_001.fastq.gz,CIRBP-LV11-3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	12463
CIRBP-LV11-3_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	646					GRCh38	V40	CIRBP-LV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	12511
CIRBP-LV11-3_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	646					GRCh38	V40	CIRBP-LV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	12559
CIRBP-LV11-3_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	646					GRCh38	V40	CIRBP-LV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	12607
CIRBP-LV11-3_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	646					GRCh38	V40	CIRBP-LV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	12655
CIRBP-LV11-3_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	646					GRCh38	V40	CIRBP-LV11-3_TTAGGC_L001_R1_001.fastq.gz,CIRBP-LV11-3_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	12703
CIRBP-LV11-4_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	647	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12368
CIRBP-LV11-4_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	647	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12416
CIRBP-LV11-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	647					GRCh38	V40	CIRBP-LV11-4_TGACCA_L001_R1_001.fastq.gz,CIRBP-LV11-4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	12464
CIRBP-LV11-4_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	647					GRCh38	V40	CIRBP-LV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	12512
CIRBP-LV11-4_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	647					GRCh38	V40	CIRBP-LV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	12560
CIRBP-LV11-4_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	647					GRCh38	V40	CIRBP-LV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	12608
CIRBP-LV11-4_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	647					GRCh38	V40	CIRBP-LV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	12656
CIRBP-LV11-4_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	647					GRCh38	V40	CIRBP-LV11-4_TGACCA_L001_R1_001.fastq.gz,CIRBP-LV11-4_TGACCA_L001_R2_001.fastq.gz		ENCORE2	12704