IGF2BP2 RNA-Seq in HepG2

General Information


RBP	IGF2BP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	IGF2BP2-BGHLV12-HepG2
ENCODE_series_ID	ENCSR663TDN
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR478FJK
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	IGF2BP2-BGHLV12-41
Rep2	IGF2BP2-BGHLV12-42
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	80.4
Rep2_qPCR	79.7
Rep1_WB	93.5
Rep2_WB	91.7
Antibody Cat#	RN008P
Antibody Lot#	RN008P
Antibody DCC ID	ENCAB597TIV
Status	Released
Project	ENCODE3
ID	341

Experiment Information (Status: Released)

	BGHLV12-41	BGHLV12-42
idx	41	42
TRCN#_or_BGC#	TRCN0000255468	TRCN0000255468
shRNA_or_gRNA_sequence	GTTGGCCCAGGGCGTTAAATT	GTTGGCCCAGGGCGTTAAATT
PAM
Name	IGF2BP2	IGF2BP2
Sample_ID	BGHLV12-41	BGHLV12-42
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	IGF2BP2	IGF2BP2
qPCR_result	80.4	79.7
Ave_qPCR	80.1
RT-qPCR_primer-F	cgtcagaattatcgggcact
RT-qPCR_primer-R	gggtatttctgctcctgctg
protein_conc	1144	1935
WB_result	93.5	91.7
Ave_WB	92.6
WB_DONE_date
MW
IP	1MB	1MB
antibody_Cat#	RN008P	RN008P
Antibody DCC ID	ENCAB597TIV	ENCAB597TIV
submitted_to_DCC_date	5/6/2015
Rep1_TPM	68.9	0
Rep2_TPM	82	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2088	2089

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

	BGHLV12-41	BGHLV12-42
Sample_ID	BGHLV12-41	BGHLV12-42
Sample Name	IGF2BP2-BGHLV12-41	IGF2BP2-BGHLV12-42
Sample Name	IGF2BP2-BGHLV12-41	IGF2BP2-BGHLV12-42
RBP	IGF2BP2	IGF2BP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	396	397

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-41	BGHLV12-42
Sample #
Sample Name	IGF2BP2-BGHLV12-41	IGF2BP2-BGHLV12-42
Sample_Name_Alias	IGF2BP2-BGHLV12-41	IGF2BP2-BGHLV12-42
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/F4.png	DNA_Library_LV12/set2/G2.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_LV12/set1/E4.png	RNA_Library_LV12/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-41	BGHLV12-42
RBP	IGF2BP2	IGF2BP2
Batch_ID	BGHLV12	BGHLV12
WB_result	93.500	91.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2020	2021

Sequencing Information

	BGHLV12-41	BGHLV12-42
Sample_ID	BGHLV12-41	BGHLV12-42
Sample Name	IGF2BP2-BGHLV12-41	IGF2BP2-BGHLV12-42
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	60,710,000	73,750,000
total_aligned_reads	55,864,042	67,980,614
unique_aligned_reads	53,062,160	64,568,764
percent_uniqueAligned	0.87403	0.87551
correlation_replicates	0.999344	0.999344
spikein_reads	459,664	937,528
percent_spikeins	0.00757	0.01271
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	720	721

Data Submission Information

	BGHLV12-41	BGHLV12-41
ENCODE_alias	brenton-graveley:IGF2BP2-BGHLV12	brenton-graveley:IGF2BP2-BGHLV12-HepG2
ENCODE_accession	ENCSR478FJK	ENCSR663TDN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-41	BGHLV12-41
Sample Name	IGF2BP2-BGHLV12-41	IGF2BP2-BGHLV12-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2747	6779

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-BGHLV12-41_ACAGTG_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	720	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12777
IGF2BP2-BGHLV12-41_ACAGTG_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	720	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12846
IGF2BP2-BGHLV12-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	720					GRCh38	V40	IGF2BP2-BGHLV12-41_ACAGTG_L005_R1_001.fastq.gz,IGF2BP2-BGHLV12-41_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	12916
IGF2BP2-BGHLV12-41_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	720					GRCh38	V40	IGF2BP2-BGHLV12-41/Aligned.sortedByCoord.out.bam		ENCORE2	12986
IGF2BP2-BGHLV12-41_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	720					GRCh38	V40	IGF2BP2-BGHLV12-41/Aligned.sortedByCoord.out.bam		ENCORE2	13056
IGF2BP2-BGHLV12-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	720					GRCh38	V40	IGF2BP2-BGHLV12-41/Aligned.sortedByCoord.out.bam		ENCORE2	13126
IGF2BP2-BGHLV12-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	720					GRCh38	V40	IGF2BP2-BGHLV12-41/Aligned.sortedByCoord.out.bam		ENCORE2	13196
IGF2BP2-BGHLV12-41_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	720					GRCh38	V40	IGF2BP2-BGHLV12-41_ACAGTG_L005_R1_001.fastq.gz,IGF2BP2-BGHLV12-41_ACAGTG_L005_R2_001.fastq.gz		ENCORE2	13266
IGF2BP2-BGHLV12-42_GCCAAT_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	721	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12778
IGF2BP2-BGHLV12-42_GCCAAT_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	721	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12847
IGF2BP2-BGHLV12-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	721					GRCh38	V40	IGF2BP2-BGHLV12-42_GCCAAT_L005_R1_001.fastq.gz,IGF2BP2-BGHLV12-42_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	12917
IGF2BP2-BGHLV12-42_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	721					GRCh38	V40	IGF2BP2-BGHLV12-42/Aligned.sortedByCoord.out.bam		ENCORE2	12987
IGF2BP2-BGHLV12-42_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	721					GRCh38	V40	IGF2BP2-BGHLV12-42/Aligned.sortedByCoord.out.bam		ENCORE2	13057
IGF2BP2-BGHLV12-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	721					GRCh38	V40	IGF2BP2-BGHLV12-42/Aligned.sortedByCoord.out.bam		ENCORE2	13127
IGF2BP2-BGHLV12-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	721					GRCh38	V40	IGF2BP2-BGHLV12-42/Aligned.sortedByCoord.out.bam		ENCORE2	13197
IGF2BP2-BGHLV12-42_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	721					GRCh38	V40	IGF2BP2-BGHLV12-42_GCCAAT_L005_R1_001.fastq.gz,IGF2BP2-BGHLV12-42_GCCAAT_L005_R2_001.fastq.gz		ENCORE2	13267