IGF2BP1 RNA-Seq in HepG2

General Information


RBP	IGF2BP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	IGF2BP1-BGHcLV03-HepG2
ENCODE_series_ID	ENCSR062UWG
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID	ENCSR268XHM
ENCODE_CN_Exp_ID	ENCSR105NML
Rep1	IGF2BP1_BGHcLV03-3
Rep2	IGF2BP1_BGHcLV03-4
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	47.3
Rep2_qPCR	49.0
Rep1_WB	91.5
Rep2_WB	90.8
Antibody Cat#	RN007P
Antibody Lot#	RN007P
Antibody DCC ID	ENCAB108MXA
Status	Released
Project	ENCODE3
ID	574

Experiment Information (Status: Released)

	BGHcLV03-3	BGHcLV03-4
idx	3	4
TRCN#_or_BGC#	BGC#0000002	BGC#0000002
shRNA_or_gRNA_sequence	CAAATCCGGCTACGCCTTCG	CAAATCCGGCTACGCCTTCG
PAM
Name	IGF2BP1-C2-A	IGF2BP1-C2-A
Sample_ID	BGHcLV03-3	BGHcLV03-4
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	IGF2BP1	IGF2BP1
qPCR_result	47.3	49.0
Ave_qPCR	48.2
RT-qPCR_primer-F	acagcctgctggctcagtat
RT-qPCR_primer-R	ccggttggaataggtgacat
protein_conc	2915	2391
WB_result	91.5	90.8
Ave_WB	91.2
WB_DONE_date	12/28/2015
MW	63kDa
IP	0.5MB	0.5MB
antibody_Cat#	RN007P	RN007P
Antibody DCC ID	ENCAB108MXA	ENCAB108MXA
submitted_to_DCC_date	9/28/16
Rep1_TPM	20	0
Rep2_TPM	18	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6144	6145

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV03-3	BGHcLV03-4
Sample_ID	BGHcLV03-3	BGHcLV03-4
Sample Name	IGF2BP1_BGHcLV03-3	IGF2BP1_BGHcLV03-4
Sample Name	IGF2BP1_BGHcLV03-3	IGF2BP1_BGHcLV03-4
RBP	IGF2BP1	IGF2BP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1101	1102

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-3	BGHcLV03-4
Sample #
Sample Name	IGF2BP1-BGHcLV03-3	IGF2BP1-BGHcLV03-4
Sample_Name_Alias	IGF2BP1_BGHcLV03-3	IGF2BP1_BGHcLV03-4
Index Well Position	S20	S21
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/C1.png	DNA_Library_cLV02/set1/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/E2.png	RNA_Library_cLV02/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-3	BGHcLV03-4
RBP	IGF2BP1	IGF2BP1
Batch_ID	BGHcLV03	BGHcLV03
WB_result	91.500	90.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2796	2797

Sequencing Information

	BGHcLV03-3	BGHcLV03-4
Sample_ID	BGHcLV03-3	BGHcLV03-4
Sample Name	IGF2BP1_BGHcLV03-3	IGF2BP1_BGHcLV03-4
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	51,977,560	57,170,554
total_aligned_reads	45,195,978	49,473,794
unique_aligned_reads	42,582,540	46,493,710
percent_uniqueAligned	0.81925	0.81325
correlation_replicates	0.993553	0.993553
spikein_reads	67,264	85,252
percent_spikeins	0.00129	0.00149
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1445	1446

Data Submission Information

	BGHcLV03-3	BGHcLV03-3
ENCODE_alias	brenton-graveley:IGF2BP1_BGHcLV03	brenton-graveley:IGF2BP1-BGHcLV03-HepG2
ENCODE_accession	ENCSR268XHM	ENCSR062UWG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV03-3	BGHcLV03-3
Sample Name	IGF2BP1_BGHcLV03-3	IGF2BP1_BGHcLV03-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3112	6775

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_BGHcLV03-3_GTGGCC_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1445	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22918
IGF2BP1_BGHcLV03-3_GTGGCC_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1445	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22936
IGF2BP1_BGHcLV03-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1445					GRCh38	V40	IGF2BP1_BGHcLV03-3_GTGGCC_L005_001.R1.fastq.gz,IGF2BP1_BGHcLV03-3_GTGGCC_L005_001.R2.fastq.gz		ENCORE2	22954
IGF2BP1_BGHcLV03-3_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1445					GRCh38	V40	IGF2BP1_BGHcLV03-3/Aligned.sortedByCoord.out.bam		ENCORE2	22972
IGF2BP1_BGHcLV03-3_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1445					GRCh38	V40	IGF2BP1_BGHcLV03-3/Aligned.sortedByCoord.out.bam		ENCORE2	22990
IGF2BP1_BGHcLV03-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1445					GRCh38	V40	IGF2BP1_BGHcLV03-3/Aligned.sortedByCoord.out.bam		ENCORE2	23008
IGF2BP1_BGHcLV03-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1445					GRCh38	V40	IGF2BP1_BGHcLV03-3/Aligned.sortedByCoord.out.bam		ENCORE2	23026
IGF2BP1_BGHcLV03-3_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1445					GRCh38	V40	IGF2BP1_BGHcLV03-3_GTGGCC_L005_001.R1.fastq.gz,IGF2BP1_BGHcLV03-3_GTGGCC_L005_001.R2.fastq.gz		ENCORE2	23044
IGF2BP1_BGHcLV03-4_GTTTCG_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1446	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22919
IGF2BP1_BGHcLV03-4_GTTTCG_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1446	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22937
IGF2BP1_BGHcLV03-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1446					GRCh38	V40	IGF2BP1_BGHcLV03-4_GTTTCG_L005_001.R1.fastq.gz,IGF2BP1_BGHcLV03-4_GTTTCG_L005_001.R2.fastq.gz		ENCORE2	22955
IGF2BP1_BGHcLV03-4_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1446					GRCh38	V40	IGF2BP1_BGHcLV03-4/Aligned.sortedByCoord.out.bam		ENCORE2	22973
IGF2BP1_BGHcLV03-4_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1446					GRCh38	V40	IGF2BP1_BGHcLV03-4/Aligned.sortedByCoord.out.bam		ENCORE2	22991
IGF2BP1_BGHcLV03-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1446					GRCh38	V40	IGF2BP1_BGHcLV03-4/Aligned.sortedByCoord.out.bam		ENCORE2	23009
IGF2BP1_BGHcLV03-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1446					GRCh38	V40	IGF2BP1_BGHcLV03-4/Aligned.sortedByCoord.out.bam		ENCORE2	23027
IGF2BP1_BGHcLV03-4_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1446					GRCh38	V40	IGF2BP1_BGHcLV03-4_GTTTCG_L005_001.R1.fastq.gz,IGF2BP1_BGHcLV03-4_GTTTCG_L005_001.R2.fastq.gz		ENCORE2	23045