IGF2BP3 RNA-Seq in K562

General Information


RBP	IGF2BP3
Cell_Line	K562
Method	shRNA
Exp_Name	IGF2BP3-BGKLV11-K562
ENCODE_series_ID	ENCSR397RZP
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR302JQA
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	IGF2BP3-LV11-19
Rep2	IGF2BP3-LV11-20
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	73.3
Rep2_qPCR	76.1
Rep1_WB	87.9
Rep2_WB	86.2
Antibody Cat#	RN009P
Antibody Lot#	RN009P
Antibody DCC ID	ENCAB934MDN
Status	Released
Project	ENCODE3
ID	312

Experiment Information (Status: Released)

	BGKLV11-19	BGKLV11-19	BGKLV11-20	BGKLV11-20
idx	88	88	89	89
TRCN#_or_BGC#	TRCN0000074675	TRCN0000074675	TRCN0000074675	TRCN0000074675
shRNA_or_gRNA_sequence	CGGTGAATGAACTTCAGAATT	CGGTGAATGAACTTCAGAATT	CGGTGAATGAACTTCAGAATT	CGGTGAATGAACTTCAGAATT
PAM
Name	IGF2BP3	IGF2BP3	IGF2BP3	IGF2BP3
Sample_ID	BGKLV11-19	BGKLV11-19	BGKLV11-20	BGKLV11-20
transduction_Date	5/1/2014	5/1/2014	5/1/2014	5/1/2014
days
RBP_name	IGF2BP3	IGF2BP3	IGF2BP3	IGF2BP3
qPCR_result	73.3	73.3	76.1	76.1
Ave_qPCR	74.7	74.7
RT-qPCR_primer-F	GAATGACCAAGTGGTTGTCAAA	GAATGACCAAGTGGTTGTCAAA
RT-qPCR_primer-R	TTGGTGCTGCTTTACCTGAG	TTGGTGCTGCTTTACCTGAG
protein_conc	2130	2130	2221	2221
WB_result	87.9		86.2
Ave_WB	87.1	no clear band
WB_DONE_date		7/28/16		wes
MW	64kDa	64kDa		fu's
IP	1		1
antibody_Cat#	RN009P	#200898	RN009P	#200898
Antibody DCC ID	ENCAB934MDN		ENCAB934MDN
submitted_to_DCC_date	5/6/2015
Rep1_TPM	10.2377366	0	0	0
Rep2_TPM	10.7414275	0	0	0
Action	Ready		Ready
Library_start_date	5/19/2014		5/19/2014
repeat_library
Note
ID	97	99	98	100

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
IGF2BP3	Product_ID: RN009P Lot_ID: 2 Source: MBLI Target Name: IGF2BP3-human

Experiment Status

	BGKLV11-19	BGKLV11-20
Sample_ID	BGKLV11-19	BGKLV11-20
Sample Name	IGF2BP3-LV11-19	IGF2BP3-LV11-20
Sample Name	IGF2BP3-LV11-19	IGF2BP3-LV11-20
RBP	IGF2BP3	IGF2BP3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	336	337

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-19	BGKLV11-20
Sample #
Sample Name	IGF2BP3-BGKLV11-19	IGF2BP3-BGKLV11-20
Sample_Name_Alias	IGF2BP3-LV11-19	IGF2BP3-LV11-20
Index Well Position	S13	S14
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/F2.png	DNA_Library_LV11/set1/G2.png
RIN	9.3	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/E2.png	RNA_Library_LV11/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-19	BGKLV11-20
RBP	IGF2BP3	IGF2BP3
Batch_ID	BGKLV11	BGKLV11
WB_result	87.900	86.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1958	1959

Sequencing Information

	BGKLV11-19	BGKLV11-20
Sample_ID	BGKLV11-19	BGKLV11-20
Sample Name	IGF2BP3-LV11-19	IGF2BP3-LV11-20
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	61,210,000	65,220,000
total_aligned_reads	48,835,914	51,786,494
unique_aligned_reads	44,703,746	47,244,464
percent_uniqueAligned	0.73033	0.72439
correlation_replicates	0.998069	0.998069
spikein_reads	324,142	334,860
percent_spikeins	0.00530	0.00513
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	658	659

Data Submission Information

	BGKLV11-19	BGKLV11-19
ENCODE_alias	brenton-graveley:IGF2BP3-LV11	brenton-graveley:IGF2BP3-BGKLV11-K562
ENCODE_accession	ENCSR302JQA	ENCSR397RZP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-19	BGKLV11-19
Sample Name	IGF2BP3-LV11-19	IGF2BP3-LV11-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2717	6782

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
IGF2BP3-LV11-19_AGTCAA_L003_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	658	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12379
IGF2BP3-LV11-19_AGTCAA_L003_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	658	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12427
IGF2BP3-LV11-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	658					GRCh38	V40	IGF2BP3-LV11-19_AGTCAA_L003_R1_001.fastq.gz,IGF2BP3-LV11-19_AGTCAA_L003_R2_001.fastq.gz		ENCORE2	12475
IGF2BP3-LV11-19_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	658					GRCh38	V40	IGF2BP3-LV11-19/Aligned.sortedByCoord.out.bam		ENCORE2	12523
IGF2BP3-LV11-19_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	658					GRCh38	V40	IGF2BP3-LV11-19/Aligned.sortedByCoord.out.bam		ENCORE2	12571
IGF2BP3-LV11-19_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	658					GRCh38	V40	IGF2BP3-LV11-19/Aligned.sortedByCoord.out.bam		ENCORE2	12619
IGF2BP3-LV11-19_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	658					GRCh38	V40	IGF2BP3-LV11-19/Aligned.sortedByCoord.out.bam		ENCORE2	12667
IGF2BP3-LV11-19_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	658					GRCh38	V40	IGF2BP3-LV11-19_AGTCAA_L003_R1_001.fastq.gz,IGF2BP3-LV11-19_AGTCAA_L003_R2_001.fastq.gz		ENCORE2	12715
IGF2BP3-LV11-20_AGTTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	659	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12380
IGF2BP3-LV11-20_AGTTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	659	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12428
IGF2BP3-LV11-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	659					GRCh38	V40	IGF2BP3-LV11-20_AGTTCC_L003_R1_001.fastq.gz,IGF2BP3-LV11-20_AGTTCC_L003_R2_001.fastq.gz		ENCORE2	12476
IGF2BP3-LV11-20_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	659					GRCh38	V40	IGF2BP3-LV11-20/Aligned.sortedByCoord.out.bam		ENCORE2	12524
IGF2BP3-LV11-20_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	659					GRCh38	V40	IGF2BP3-LV11-20/Aligned.sortedByCoord.out.bam		ENCORE2	12572
IGF2BP3-LV11-20_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	659					GRCh38	V40	IGF2BP3-LV11-20/Aligned.sortedByCoord.out.bam		ENCORE2	12620
IGF2BP3-LV11-20_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	659					GRCh38	V40	IGF2BP3-LV11-20/Aligned.sortedByCoord.out.bam		ENCORE2	12668
IGF2BP3-LV11-20_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	659					GRCh38	V40	IGF2BP3-LV11-20_AGTTCC_L003_R1_001.fastq.gz,IGF2BP3-LV11-20_AGTTCC_L003_R2_001.fastq.gz		ENCORE2	12716