IGF2BP1 RNA-Seq in HepG2

General Information


RBP	IGF2BP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	IGF2BP1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR552BRA
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR708GKW
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	IGF2BP1_BGHLV14-27
Rep2	IGF2BP1_BGHLV14-28
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	65.1
Rep2_qPCR	69.6
Rep1_WB	73.6
Rep2_WB	60.0
Antibody Cat#	RN007P
Antibody Lot#	RN007P
Antibody DCC ID	ENCAB108MXA
Status	Archived
Project	ENCODE3
ID	396

Experiment Information (Status: Released)

	BGHLV14-27	BGHLV14-28
idx	123	124
TRCN#_or_BGC#	TRCN0000075149	TRCN0000075149
shRNA_or_gRNA_sequence	GCAGTGGTGAATGTCACCTAT	GCAGTGGTGAATGTCACCTAT
PAM
Name	IGF2BP1	IGF2BP1
Sample_ID	BGHLV14-27	BGHLV14-28
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	IGF2BP1	IGF2BP1
qPCR_result	65.1	69.6
Ave_qPCR	67.4
RT-qPCR_primer-F	acagcctgctggctcagtat
RT-qPCR_primer-R	ccggttggaataggtgacat
protein_conc	3659	3548
WB_result	73.6	60.0
Ave_WB	66.8
WB_DONE_date	1/20/2015
MW
IP	0.5MB	0.5MB
antibody_Cat#	RN007P	RN007P
Antibody DCC ID	ENCAB108MXA	ENCAB108MXA
submitted_to_DCC_date	5/6/2015
Rep1_TPM	19.6	0
Rep2_TPM	17.8	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2184	2185

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

	BGHLV14-27	BGHLV14-28
Sample_ID	BGHLV14-27	BGHLV14-28
Sample Name	IGF2BP1_BGHLV14-27	IGF2BP1_BGHLV14-28
Sample Name	IGF2BP1_BGHLV14-27	IGF2BP1_BGHLV14-28
RBP	IGF2BP1	IGF2BP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	514	515

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-27	BGHLV14-28
Sample #
Sample Name	IGF2BP1-BGHLV14-27	IGF2BP1-BGHLV14-28
Sample_Name_Alias	IGF2BP1_BGHLV14-27	IGF2BP1_BGHLV14-28
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B11.png	DNA_Library_LV13-14/set1/C11.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C7.png	RNA_Library_LV13-14-16/set1/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-27	BGHLV14-28
RBP	IGF2BP1	IGF2BP1
Batch_ID	BGHLV14	BGHLV14
WB_result	73.600	60.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2200	2201

Sequencing Information

	BGHLV14-27	BGHLV14-28
Sample_ID	BGHLV14-27	BGHLV14-28
Sample Name	IGF2BP1_BGHLV14-27	IGF2BP1_BGHLV14-28
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	59,940,000	58,660,000
total_aligned_reads	55,212,692	53,579,204
unique_aligned_reads	52,445,986	50,850,254
percent_uniqueAligned	0.87497	0.86686
correlation_replicates	0.997931	0.997931
spikein_reads	960,854	396,616
percent_spikeins	0.01603	0.00676
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	842	843

Data Submission Information

	BGHLV14-27	BGHLV14-27
ENCODE_alias	brenton-graveley:IGF2BP1_BGHLV14	brenton-graveley:IGF2BP1-BGHLV14-HepG2
ENCODE_accession	ENCSR708GKW	ENCSR552BRA
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-27	BGHLV14-27
Sample Name	IGF2BP1_BGHLV14-27	IGF2BP1_BGHLV14-27
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2807	6776

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_BGHLV14-27_GATCAG_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	842	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13806
IGF2BP1_BGHLV14-27_GATCAG_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	842	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13868
IGF2BP1_BGHLV14-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	842					GRCh38	V40	IGF2BP1_BGHLV14-27_GATCAG_L003_R1_001.fastq.gz,IGF2BP1_BGHLV14-27_GATCAG_L003_R2_001.fastq.gz		ENCORE2	13930
IGF2BP1_BGHLV14-27_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	842					GRCh38	V40	IGF2BP1_BGHLV14-27/Aligned.sortedByCoord.out.bam		ENCORE2	13992
IGF2BP1_BGHLV14-27_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	842					GRCh38	V40	IGF2BP1_BGHLV14-27/Aligned.sortedByCoord.out.bam		ENCORE2	14054
IGF2BP1_BGHLV14-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	842					GRCh38	V40	IGF2BP1_BGHLV14-27/Aligned.sortedByCoord.out.bam		ENCORE2	14116
IGF2BP1_BGHLV14-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	842					GRCh38	V40	IGF2BP1_BGHLV14-27/Aligned.sortedByCoord.out.bam		ENCORE2	14178
IGF2BP1_BGHLV14-27_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	842					GRCh38	V40	IGF2BP1_BGHLV14-27_GATCAG_L003_R1_001.fastq.gz,IGF2BP1_BGHLV14-27_GATCAG_L003_R2_001.fastq.gz		ENCORE2	14240
IGF2BP1_BGHLV14-28_TAGCTT_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	843	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13807
IGF2BP1_BGHLV14-28_TAGCTT_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	843	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13869
IGF2BP1_BGHLV14-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	843					GRCh38	V40	IGF2BP1_BGHLV14-28_TAGCTT_L004_R1_001.fastq.gz,IGF2BP1_BGHLV14-28_TAGCTT_L004_R2_001.fastq.gz		ENCORE2	13931
IGF2BP1_BGHLV14-28_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	843					GRCh38	V40	IGF2BP1_BGHLV14-28/Aligned.sortedByCoord.out.bam		ENCORE2	13993
IGF2BP1_BGHLV14-28_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	843					GRCh38	V40	IGF2BP1_BGHLV14-28/Aligned.sortedByCoord.out.bam		ENCORE2	14055
IGF2BP1_BGHLV14-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	843					GRCh38	V40	IGF2BP1_BGHLV14-28/Aligned.sortedByCoord.out.bam		ENCORE2	14117
IGF2BP1_BGHLV14-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	843					GRCh38	V40	IGF2BP1_BGHLV14-28/Aligned.sortedByCoord.out.bam		ENCORE2	14179
IGF2BP1_BGHLV14-28_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	843					GRCh38	V40	IGF2BP1_BGHLV14-28_TAGCTT_L004_R1_001.fastq.gz,IGF2BP1_BGHLV14-28_TAGCTT_L004_R2_001.fastq.gz		ENCORE2	14241