IGF2BP1 RNA-Seq in K562

General Information


RBP	IGF2BP1
Cell_Line	K562
Method	CRISPR
Exp_Name	IGF2BP1-BGKcLV02-K562
ENCODE_series_ID	ENCSR405TAI
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID	ENCSR543LCG
ENCODE_CN_Exp_ID	ENCSR163JUC
Rep1	IGF2BP1_BGKcLV02-3
Rep2	IGF2BP1_BGKcLV02-4
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	79.1
Rep2_qPCR	77.8
Rep1_WB	92.2
Rep2_WB	91.2
Antibody Cat#	RN007P
Antibody Lot#	RN007P
Antibody DCC ID	ENCAB108MXA
Status	Released
Project	ENCODE3
ID	586

Experiment Information (Status: Released)

	BGKcLV02-3	BGKcLV02-4
idx	3	4
TRCN#_or_BGC#	BGC#0000001	BGC#0000001
shRNA_or_gRNA_sequence	CAACGAGAGCGTGACCCCCG	CAACGAGAGCGTGACCCCCG
PAM
Name	IGF2BP1-C1-A	IGF2BP1-C1-A
Sample_ID	BGKcLV02-3	BGKcLV02-4
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	IGF2BP1	IGF2BP1
qPCR_result	79.1	77.8
Ave_qPCR	78.5
RT-qPCR_primer-F	acagcctgctggctcagtat
RT-qPCR_primer-R	ccggttggaataggtgacat
protein_conc	3279	3716
WB_result	92.2	91.2
Ave_WB	91.7
WB_DONE_date	12/28/2015
MW	63kDa
IP	0.5MB
antibody_Cat#	RN007P	RN007P
Antibody DCC ID	ENCAB108MXA	ENCAB108MXA
submitted_to_DCC_date	9/28/16
Rep1_TPM	35.2	0
Rep2_TPM	22.6	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4097	4098

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
IGF2BP1	Product_ID: RN007P Lot_ID: 3 Source: MBLI Target Name: IGF2BP1-human

Experiment Status

	BGKcLV02-3	BGKcLV02-4
Sample_ID	BGKcLV02-3	BGKcLV02-4
Sample Name	IGF2BP1_BGKcLV02-3	IGF2BP1_BGKcLV02-4
Sample Name	IGF2BP1_BGKcLV02-3	IGF2BP1_BGKcLV02-4
RBP	IGF2BP1	IGF2BP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1089	1090

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-3	BGKcLV02-4
Sample #
Sample Name	IGF2BP1-BGKcLV02-3	IGF2BP1-BGKcLV02-4
Sample_Name_Alias	IGF2BP1_BGKcLV02-3	IGF2BP1_BGKcLV02-4
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/E3.png	DNA_Library_cLV02/set1/F3.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/G4.png	RNA_Library_cLV02/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-3	BGKcLV02-4
RBP	IGF2BP1	IGF2BP1
Batch_ID	BGKcLV02	BGKcLV02
WB_result	92.200	91.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2778	2779

Sequencing Information

	BGKcLV02-3	BGKcLV02-4
Sample_ID	BGKcLV02-3	BGKcLV02-4
Sample Name	IGF2BP1_BGKcLV02-3	IGF2BP1_BGKcLV02-4
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	59,971,118	89,107,378
total_aligned_reads	54,585,656	81,624,496
unique_aligned_reads	49,864,118	74,168,042
percent_uniqueAligned	0.83147	0.83234
correlation_replicates	0.997056	0.997056
spikein_reads	125,790	152,424
percent_spikeins	0.00210	0.00171
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1427	1428

Data Submission Information

	BGKcLV02-3	BGKcLV02-3
ENCODE_alias	brenton-graveley:IGF2BP1_BGKcLV02	brenton-graveley:IGF2BP1-BGKcLV02-K562
ENCODE_accession	ENCSR543LCG	ENCSR405TAI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-3	BGKcLV02-3
Sample Name	IGF2BP1_BGKcLV02-3	IGF2BP1_BGKcLV02-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3106	6777

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
IGF2BP1_BGKcLV02-3_AGTCAA_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1427	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22760
IGF2BP1_BGKcLV02-3_AGTCAA_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1427	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22780
IGF2BP1_BGKcLV02-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1427					GRCh38	V40	IGF2BP1_BGKcLV02-3_AGTCAA_L007_001.R1.fastq.gz,IGF2BP1_BGKcLV02-3_AGTCAA_L007_001.R2.fastq.gz		ENCORE2	22800
IGF2BP1_BGKcLV02-3_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1427					GRCh38	V40	IGF2BP1_BGKcLV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	22820
IGF2BP1_BGKcLV02-3_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1427					GRCh38	V40	IGF2BP1_BGKcLV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	22840
IGF2BP1_BGKcLV02-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1427					GRCh38	V40	IGF2BP1_BGKcLV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	22860
IGF2BP1_BGKcLV02-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1427					GRCh38	V40	IGF2BP1_BGKcLV02-3/Aligned.sortedByCoord.out.bam		ENCORE2	22880
IGF2BP1_BGKcLV02-3_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1427					GRCh38	V40	IGF2BP1_BGKcLV02-3_AGTCAA_L007_001.R1.fastq.gz,IGF2BP1_BGKcLV02-3_AGTCAA_L007_001.R2.fastq.gz		ENCORE2	22900
IGF2BP1_BGKcLV02-4_AGTTCC_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1428	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22761
IGF2BP1_BGKcLV02-4_AGTTCC_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1428	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22781
IGF2BP1_BGKcLV02-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1428					GRCh38	V40	IGF2BP1_BGKcLV02-4_AGTTCC_L007_001.R1.fastq.gz,IGF2BP1_BGKcLV02-4_AGTTCC_L007_001.R2.fastq.gz		ENCORE2	22801
IGF2BP1_BGKcLV02-4_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1428					GRCh38	V40	IGF2BP1_BGKcLV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	22821
IGF2BP1_BGKcLV02-4_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1428					GRCh38	V40	IGF2BP1_BGKcLV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	22841
IGF2BP1_BGKcLV02-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1428					GRCh38	V40	IGF2BP1_BGKcLV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	22861
IGF2BP1_BGKcLV02-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1428					GRCh38	V40	IGF2BP1_BGKcLV02-4/Aligned.sortedByCoord.out.bam		ENCORE2	22881
IGF2BP1_BGKcLV02-4_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1428					GRCh38	V40	IGF2BP1_BGKcLV02-4_AGTTCC_L007_001.R1.fastq.gz,IGF2BP1_BGKcLV02-4_AGTTCC_L007_001.R2.fastq.gz		ENCORE2	22901