IGF2BP3 RNA-Seq in HepG2

General Information


RBP	IGF2BP3
Cell_Line	HepG2
Method	shRNA
Exp_Name	IGF2BP3-BGHLV12-HepG2
ENCODE_series_ID	ENCSR362BLN
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR710NWE
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	IGF2BP3-BGHLV12-43
Rep2	IGF2BP3-BGHLV12-44
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	54.8
Rep2_qPCR	45.7
Rep1_WB	78.1
Rep2_WB	81.6
Antibody Cat#	RN009P
Antibody Lot#	RN009P
Antibody DCC ID	ENCAB934MDN
Status	Released
Project	ENCODE3
ID	342

Experiment Information (Status: Released)

	BGHLV12-43	BGHLV12-44
idx	43	44
TRCN#_or_BGC#	TRCN0000074675	TRCN0000074675
shRNA_or_gRNA_sequence	CGGTGAATGAACTTCAGAATT	CGGTGAATGAACTTCAGAATT
PAM
Name	IGF2BP3	IGF2BP3
Sample_ID	BGHLV12-43	BGHLV12-44
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	IGF2BP3	IGF2BP3
qPCR_result	54.8	45.7
Ave_qPCR	50.3
RT-qPCR_primer-F	GAATGACCAAGTGGTTGTCAAA
RT-qPCR_primer-R	TTGGTGCTGCTTTACCTGAG
protein_conc	1824	2144
WB_result	78.1	81.6
Ave_WB	79.9
WB_DONE_date
MW	64kDa
IP	1	1
antibody_Cat#	RN009P	RN009P
Antibody DCC ID	ENCAB934MDN	ENCAB934MDN
submitted_to_DCC_date	5/6/2015
Rep1_TPM	9.3	0
Rep2_TPM	8.2	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2090	2091

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

	BGHLV12-43	BGHLV12-44
Sample_ID	BGHLV12-43	BGHLV12-44
Sample Name	IGF2BP3-BGHLV12-43	IGF2BP3-BGHLV12-44
Sample Name	IGF2BP3-BGHLV12-43	IGF2BP3-BGHLV12-44
RBP	IGF2BP3	IGF2BP3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	398	399

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-43	BGHLV12-44
Sample #
Sample Name	IGF2BP3-BGHLV12-43	IGF2BP3-BGHLV12-44
Sample_Name_Alias	IGF2BP3-BGHLV12-43	IGF2BP3-BGHLV12-44
Index Well Position	S07	S08
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/G4.png	DNA_Library_LV35/set1/H4.png
RIN	9.4	8.9
libSample_RNA_Well	RNA_Library_LV12/set1/G4.png	RNA_Library_LV12/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-43	BGHLV12-44
RBP	IGF2BP3	IGF2BP3
Batch_ID	BGHLV12	BGHLV12
WB_result	78.100	81.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2022	2023

Sequencing Information

	BGHLV12-43	BGHLV12-44
Sample_ID	BGHLV12-43	BGHLV12-44
Sample Name	IGF2BP3-BGHLV12-43	IGF2BP3-BGHLV12-44
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	70,640,000	41,700,000
total_aligned_reads	66,064,008	38,844,240
unique_aligned_reads	62,361,868	36,872,708
percent_uniqueAligned	0.88281	0.88424
correlation_replicates	0.993035	0.993035
spikein_reads	535,994	428,118
percent_spikeins	0.00759	0.01027
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	722	723

Data Submission Information

	BGHLV12-43	BGHLV12-43
ENCODE_alias	brenton-graveley:IGF2BP3-BGHLV12	brenton-graveley:IGF2BP3-BGHLV12-HepG2
ENCODE_accession	ENCSR710NWE	ENCSR362BLN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-43	BGHLV12-43
Sample Name	IGF2BP3-BGHLV12-43	IGF2BP3-BGHLV12-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2748	6781

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-BGHLV12-43_CAGATC_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	722	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12779
IGF2BP3-BGHLV12-43_CAGATC_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	722	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12848
IGF2BP3-BGHLV12-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	722					GRCh38	V40	IGF2BP3-BGHLV12-43_CAGATC_L005_R1_001.fastq.gz,IGF2BP3-BGHLV12-43_CAGATC_L005_R2_001.fastq.gz		ENCORE2	12918
IGF2BP3-BGHLV12-43_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	722					GRCh38	V40	IGF2BP3-BGHLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	12988
IGF2BP3-BGHLV12-43_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	722					GRCh38	V40	IGF2BP3-BGHLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	13058
IGF2BP3-BGHLV12-43_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	722					GRCh38	V40	IGF2BP3-BGHLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	13128
IGF2BP3-BGHLV12-43_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	722					GRCh38	V40	IGF2BP3-BGHLV12-43/Aligned.sortedByCoord.out.bam		ENCORE2	13198
IGF2BP3-BGHLV12-43_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	722					GRCh38	V40	IGF2BP3-BGHLV12-43_CAGATC_L005_R1_001.fastq.gz,IGF2BP3-BGHLV12-43_CAGATC_L005_R2_001.fastq.gz		ENCORE2	13268
IGF2BP3-BGHLV12-44_ACTTGA_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	723	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12780
IGF2BP3-BGHLV12-44_ACTTGA_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	723	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12849
IGF2BP3-BGHLV12-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	723					GRCh38	V40	IGF2BP3-BGHLV12-44_ACTTGA_L005_R1_001.fastq.gz,IGF2BP3-BGHLV12-44_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	12919
IGF2BP3-BGHLV12-44_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	723					GRCh38	V40	IGF2BP3-BGHLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	12989
IGF2BP3-BGHLV12-44_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	723					GRCh38	V40	IGF2BP3-BGHLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	13059
IGF2BP3-BGHLV12-44_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	723					GRCh38	V40	IGF2BP3-BGHLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	13129
IGF2BP3-BGHLV12-44_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	723					GRCh38	V40	IGF2BP3-BGHLV12-44/Aligned.sortedByCoord.out.bam		ENCORE2	13199
IGF2BP3-BGHLV12-44_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	723					GRCh38	V40	IGF2BP3-BGHLV12-44_ACTTGA_L005_R1_001.fastq.gz,IGF2BP3-BGHLV12-44_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	13269