ILF2 RNA-Seq in HepG2

General Information


RBP	ILF2
Cell_Line	HepG2
Method	shRNA
Exp_Name	ILF2-BGHLV20-HepG2
ENCODE_series_ID	ENCSR502GKB
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR366FFV
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	ILF2-BGHLV20-39_17728
Rep2	ILF2-BGHLV20-40_17729
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	90.3
Rep2_qPCR	83.0
Rep1_WB	63.7
Rep2_WB	65.3
Antibody Cat#	A303-147A
Antibody Lot#	A303-147A
Antibody DCC ID	ENCAB709CSJ
Status	Released
Project	ENCODE3
ID	499

Experiment Information (Status: Released)

	BGHLV20-39	BGHLV20-40
idx	403	404
TRCN#_or_BGC#	TRCN0000014556	TRCN0000014556
shRNA_or_gRNA_sequence	CCAACGAAACTGGCTTTGAAA	CCAACGAAACTGGCTTTGAAA
PAM
Name	ILF2	ILF2
Sample_ID	BGHLV20-39	BGHLV20-40
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	ILF2	ILF2
qPCR_result	90.3	83.0
Ave_qPCR	86.7
RT-qPCR_primer-F	aggccttgctgaagaggaat
RT-qPCR_primer-R	atgtccctggagccacaat
protein_conc	6510	6306
WB_result	63.7	65.3
Ave_WB	64.5
WB_DONE_date	4/16/2015
MW
IP	1	1
antibody_Cat#	A303-147A	A303-147A
Antibody DCC ID	ENCAB709CSJ	ENCAB709CSJ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	31.9	0
Rep2_TPM	24.3	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2468	2469

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ILF2	Product_ID: A303-147A Lot_ID: 1 Source: Bethyl Labs Target Name: ILF2-human

Experiment Status

	BGHLV20-39	BGHLV20-40
Sample_ID	BGHLV20-39	BGHLV20-40
Sample Name	ILF2-BGHLV20-39_17728	ILF2-BGHLV20-40_17729
Sample Name	ILF2-BGHLV20-39_17728	ILF2-BGHLV20-40_17729
RBP	ILF2	ILF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	728	729

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-39	BGHLV20-40
Sample #
Sample Name	ILF2-BGHLV20-39	ILF2-BGHLV20-40
Sample_Name_Alias	ILF2-BGHLV20-39_17728	ILF2-BGHLV20-40_17729
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G3.png	DNA_Library_LV20-22-23/set1/H3.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A10.png	RNA_Library_LV20-22-24/set1/B10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-39	BGHLV20-40
RBP	ILF2	ILF2
Batch_ID	BGHLV20	BGHLV20
WB_result	63.700	65.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2414	2415

Sequencing Information

	BGHLV20-39	BGHLV20-40
Sample_ID	BGHLV20-39	BGHLV20-40
Sample Name	ILF2-BGHLV20-39_17728	ILF2-BGHLV20-40_17729
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	66,360,000	43,770,000
total_aligned_reads	58,633,814	38,721,310
unique_aligned_reads	55,194,038	36,448,144
percent_uniqueAligned	0.83174	0.83272
correlation_replicates	0.995634	0.995634
spikein_reads	303,152	191,922
percent_spikeins	0.00457	0.00438
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1182	1183

Data Submission Information

	BGHLV20-39	BGHLV20-39
ENCODE_alias	brenton-graveley:ILF2-BGHLV20	brenton-graveley:ILF2-BGHLV20-HepG2
ENCODE_accession	ENCSR366FFV	ENCSR502GKB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-39	BGHLV20-39
Sample Name	ILF2-BGHLV20-39_17728	ILF2-BGHLV20-39_17728
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2913	6783

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
ILF2-BGHLV20-39_17728_ACTGAT_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1182	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15606
ILF2-BGHLV20-39_17728_ACTGAT_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1182	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15648
ILF2-BGHLV20-39_17728_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1182					GRCh38	V40	ILF2-BGHLV20-39_17728_ACTGAT_L004_R1_001.fastq.gz,ILF2-BGHLV20-39_17728_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	15690
ILF2-BGHLV20-39_17728_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1182					GRCh38	V40	ILF2-BGHLV20-39_17728/Aligned.sortedByCoord.out.bam		ENCORE2	15732
ILF2-BGHLV20-39_17728_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1182					GRCh38	V40	ILF2-BGHLV20-39_17728/Aligned.sortedByCoord.out.bam		ENCORE2	15774
ILF2-BGHLV20-39_17728_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1182					GRCh38	V40	ILF2-BGHLV20-39_17728/Aligned.sortedByCoord.out.bam		ENCORE2	15816
ILF2-BGHLV20-39_17728_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1182					GRCh38	V40	ILF2-BGHLV20-39_17728/Aligned.sortedByCoord.out.bam		ENCORE2	15858
ILF2-BGHLV20-39_17728_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1182					GRCh38	V40	ILF2-BGHLV20-39_17728_ACTGAT_L004_R1_001.fastq.gz,ILF2-BGHLV20-39_17728_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	15900
ILF2-BGHLV20-40_17729_ATTCCT_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1183	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15607
ILF2-BGHLV20-40_17729_ATTCCT_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1183	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15649
ILF2-BGHLV20-40_17729_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1183					GRCh38	V40	ILF2-BGHLV20-40_17729_ATTCCT_L004_R1_001.fastq.gz,ILF2-BGHLV20-40_17729_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	15691
ILF2-BGHLV20-40_17729_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1183					GRCh38	V40	ILF2-BGHLV20-40_17729/Aligned.sortedByCoord.out.bam		ENCORE2	15733
ILF2-BGHLV20-40_17729_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1183					GRCh38	V40	ILF2-BGHLV20-40_17729/Aligned.sortedByCoord.out.bam		ENCORE2	15775
ILF2-BGHLV20-40_17729_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1183					GRCh38	V40	ILF2-BGHLV20-40_17729/Aligned.sortedByCoord.out.bam		ENCORE2	15817
ILF2-BGHLV20-40_17729_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1183					GRCh38	V40	ILF2-BGHLV20-40_17729/Aligned.sortedByCoord.out.bam		ENCORE2	15859
ILF2-BGHLV20-40_17729_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1183					GRCh38	V40	ILF2-BGHLV20-40_17729_ATTCCT_L004_R1_001.fastq.gz,ILF2-BGHLV20-40_17729_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	15901