IGF2BP2 RNA-Seq in K562

General Information


RBP	IGF2BP2
Cell_Line	K562
Method	shRNA
Exp_Name	IGF2BP2-BGKLV11-K562
ENCODE_series_ID	ENCSR182YTG
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR952RRH
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	IGF2BP2-LV11-21
Rep2	IGF2BP2-LV11-22
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	83.9
Rep2_qPCR	81.7
Rep1_WB	80.2
Rep2_WB	79.2
Antibody Cat#	RN008P
Antibody Lot#	RN008P
Antibody DCC ID	ENCAB597TIV
Status	Released
Project	ENCODE3
ID	311

Experiment Information (Status: Released)

	BGKLV11-21	BGKLV11-22
idx	90	91
TRCN#_or_BGC#	TRCN0000255468	TRCN0000255468
shRNA_or_gRNA_sequence	GTTGGCCCAGGGCGTTAAATT	GTTGGCCCAGGGCGTTAAATT
PAM
Name	IGF2BP2	IGF2BP2
Sample_ID	BGKLV11-21	BGKLV11-22
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	IGF2BP2	IGF2BP2
qPCR_result	83.9	81.7
Ave_qPCR	82.8
RT-qPCR_primer-F	cgtcagaattatcgggcact
RT-qPCR_primer-R	gggtatttctgctcctgctg
protein_conc	2276	2316
WB_result	80.2	79.2
Ave_WB	79.7
WB_DONE_date
MW	66kDa
IP	1MB	1MB
antibody_Cat#	RN008P	RN008P
Antibody DCC ID	ENCAB597TIV	ENCAB597TIV
submitted_to_DCC_date	5/6/2015
Rep1_TPM	25.8436782	0
Rep2_TPM	22.2675988	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	101	102

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
IGF2BP2	Product_ID: RN008P Lot_ID: 2 Source: MBLI Target Name: IGF2BP2-human

Experiment Status

	BGKLV11-21	BGKLV11-22
Sample_ID	BGKLV11-21	BGKLV11-22
Sample Name	IGF2BP2-LV11-21	IGF2BP2-LV11-22
Sample Name	IGF2BP2-LV11-21	IGF2BP2-LV11-22
RBP	IGF2BP2	IGF2BP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	334	335

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-21	BGKLV11-22
Sample #
Sample Name	IGF2BP2-BGKLV11-21	IGF2BP2-BGKLV11-22
Sample_Name_Alias	IGF2BP2-LV11-21	IGF2BP2-LV11-22
Index Well Position	S15	S16
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/H2.png	DNA_Library_LV11/set2/B1.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_LV11/set1/G2.png	RNA_Library_LV11/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-21	BGKLV11-22
RBP	IGF2BP2	IGF2BP2
Batch_ID	BGKLV11	BGKLV11
WB_result	80.200	79.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1956	1957

Sequencing Information

	BGKLV11-21	BGKLV11-22
Sample_ID	BGKLV11-21	BGKLV11-22
Sample Name	IGF2BP2-LV11-21	IGF2BP2-LV11-22
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	70,490,000	61,620,000
total_aligned_reads	55,182,904	48,353,264
unique_aligned_reads	50,410,728	44,154,850
percent_uniqueAligned	0.71515	0.71657
correlation_replicates	0.994310	0.994310
spikein_reads	380,068	348,274
percent_spikeins	0.00539	0.00565
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	656	657

Data Submission Information

	BGKLV11-21	BGKLV11-21
ENCODE_alias	brenton-graveley:IGF2BP2-LV11	brenton-graveley:IGF2BP2-BGKLV11-K562
ENCODE_accession	ENCSR952RRH	ENCSR182YTG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-21	BGKLV11-21
Sample Name	IGF2BP2-LV11-21	IGF2BP2-LV11-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2716	6780

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
IGF2BP2-LV11-21_ATGTCA_L003_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	656	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12377
IGF2BP2-LV11-21_ATGTCA_L003_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	656	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12425
IGF2BP2-LV11-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	656					GRCh38	V40	IGF2BP2-LV11-21_ATGTCA_L003_R1_001.fastq.gz,IGF2BP2-LV11-21_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	12473
IGF2BP2-LV11-21_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	656					GRCh38	V40	IGF2BP2-LV11-21/Aligned.sortedByCoord.out.bam		ENCORE2	12521
IGF2BP2-LV11-21_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	656					GRCh38	V40	IGF2BP2-LV11-21/Aligned.sortedByCoord.out.bam		ENCORE2	12569
IGF2BP2-LV11-21_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	656					GRCh38	V40	IGF2BP2-LV11-21/Aligned.sortedByCoord.out.bam		ENCORE2	12617
IGF2BP2-LV11-21_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	656					GRCh38	V40	IGF2BP2-LV11-21/Aligned.sortedByCoord.out.bam		ENCORE2	12665
IGF2BP2-LV11-21_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	656					GRCh38	V40	IGF2BP2-LV11-21_ATGTCA_L003_R1_001.fastq.gz,IGF2BP2-LV11-21_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	12713
IGF2BP2-LV11-22_CCGTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	657	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12378
IGF2BP2-LV11-22_CCGTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	657	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12426
IGF2BP2-LV11-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	657					GRCh38	V40	IGF2BP2-LV11-22_CCGTCC_L003_R1_001.fastq.gz,IGF2BP2-LV11-22_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	12474
IGF2BP2-LV11-22_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	657					GRCh38	V40	IGF2BP2-LV11-22/Aligned.sortedByCoord.out.bam		ENCORE2	12522
IGF2BP2-LV11-22_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	657					GRCh38	V40	IGF2BP2-LV11-22/Aligned.sortedByCoord.out.bam		ENCORE2	12570
IGF2BP2-LV11-22_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	657					GRCh38	V40	IGF2BP2-LV11-22/Aligned.sortedByCoord.out.bam		ENCORE2	12618
IGF2BP2-LV11-22_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	657					GRCh38	V40	IGF2BP2-LV11-22/Aligned.sortedByCoord.out.bam		ENCORE2	12666
IGF2BP2-LV11-22_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	657					GRCh38	V40	IGF2BP2-LV11-22_CCGTCC_L003_R1_001.fastq.gz,IGF2BP2-LV11-22_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	12714