ILF3 RNA-Seq in HepG2

General Information


RBP	ILF3
Cell_Line	HepG2
Method	shRNA
Exp_Name	ILF3-BGHLV22-HepG2
ENCODE_series_ID	ENCSR405LHE
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR942MBU
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	ILF3-BGHLV22-29
Rep2	ILF3-BGHLV22-30
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	66.7
Rep2_qPCR	57.0
Rep1_WB	62.3
Rep2_WB	43.4
Antibody Cat#	A303-651A
Antibody Lot#	A303-651A
Antibody DCC ID	ENCAB198ZHJ
Status	Released
Project	ENCODE3
ID	522

Experiment Information (Status: Released)

	BGHLV22-29	BGHLV22-30
idx	457	458
TRCN#_or_BGC#	>TRCN0000329787	>TRCN0000329787
shRNA_or_gRNA_sequence	CCTTCCAAGATGCCCAAGAAA	CCTTCCAAGATGCCCAAGAAA
PAM
Name	ILF3	ILF3
Sample_ID	BGHLV22-29	BGHLV22-30
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	ILF3	ILF3
qPCR_result	66.7	57.0
Ave_qPCR	61.9
RT-qPCR_primer-F	CGTTCTGGACAGGCAGAAAT
RT-qPCR_primer-R	CCGGATCACAATGACACAAG
protein_conc	6434	7184
WB_result	62.3	43.4
Ave_WB	52.9
WB_DONE_date	4/7/2015
MW
IP	1	1
antibody_Cat#	A303-651A	A303-651A
Antibody DCC ID	ENCAB198ZHJ	ENCAB198ZHJ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	37.4	0
Rep2_TPM	41.7	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2526	2527

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ILF3	Product_ID: A303-651A Lot_ID: 1 Source: Bethyl Labs Target Name: ILF3-human

Experiment Status

	BGHLV22-29	BGHLV22-30
Sample_ID	BGHLV22-29	BGHLV22-30
Sample Name	ILF3-BGHLV22-29	ILF3-BGHLV22-30
Sample Name	ILF3-BGHLV22-29	ILF3-BGHLV22-30
RBP	ILF3	ILF3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	792	793

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-29	BGHLV22-30
Sample #
Sample Name	ILF3-BGHLV22-29	ILF3-BGHLV22-30
Sample_Name_Alias	ILF3-BGHLV22-29	ILF3-BGHLV22-30
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A8.png	DNA_Library_LV20-22-23/set2/D1.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A2.png	RNA_Library_LV22-23-25/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-29	BGHLV22-30
RBP	ILF3	ILF3
Batch_ID	BGHLV22	BGHLV22
WB_result	62.300	43.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2478	2479

Sequencing Information

	BGHLV22-29	BGHLV22-30
Sample_ID	BGHLV22-29	BGHLV22-30
Sample Name	ILF3-BGHLV22-29	ILF3-BGHLV22-30
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	59,670,000	52,950,000
total_aligned_reads	55,132,620	48,983,524
unique_aligned_reads	51,927,000	46,115,744
percent_uniqueAligned	0.87024	0.87093
correlation_replicates	0.996516	0.996516
spikein_reads	282,070	274,020
percent_spikeins	0.00473	0.00518
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1102	1103

Data Submission Information

	BGHLV22-29	BGHLV22-29
ENCODE_alias	brenton-graveley:ILF3-BGHLV22	brenton-graveley:ILF3-BGHLV22-HepG2
ENCODE_accession	ENCSR942MBU	ENCSR405LHE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-29	BGHLV22-29
Sample Name	ILF3-BGHLV22-29	ILF3-BGHLV22-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2928	6785

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
ILF3-BGHLV22-29_GTCCGC_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1102	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16288
ILF3-BGHLV22-29_GTCCGC_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1102	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16328
ILF3-BGHLV22-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1102					GRCh38	V40	ILF3-BGHLV22-29_GTCCGC_L001_R1_001.fastq.gz,ILF3-BGHLV22-29_GTCCGC_L001_R2_001.fastq.gz		ENCORE2	16426
ILF3-BGHLV22-29_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1102					GRCh38	V40	ILF3-BGHLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	16466
ILF3-BGHLV22-29_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1102					GRCh38	V40	ILF3-BGHLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	16506
ILF3-BGHLV22-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1102					GRCh38	V40	ILF3-BGHLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	16546
ILF3-BGHLV22-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1102					GRCh38	V40	ILF3-BGHLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	16586
ILF3-BGHLV22-29_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1102					GRCh38	V40	ILF3-BGHLV22-29_GTCCGC_L001_R1_001.fastq.gz,ILF3-BGHLV22-29_GTCCGC_L001_R2_001.fastq.gz		ENCORE2	16626
ILF3-BGHLV22-30_GTGAAA_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1103	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16289
ILF3-BGHLV22-30_GTGAAA_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1103	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16329
ILF3-BGHLV22-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1103					GRCh38	V40	ILF3-BGHLV22-30_GTGAAA_L001_R1_001.fastq.gz,ILF3-BGHLV22-30_GTGAAA_L001_R2_001.fastq.gz		ENCORE2	16427
ILF3-BGHLV22-30_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1103					GRCh38	V40	ILF3-BGHLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	16467
ILF3-BGHLV22-30_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1103					GRCh38	V40	ILF3-BGHLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	16507
ILF3-BGHLV22-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1103					GRCh38	V40	ILF3-BGHLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	16547
ILF3-BGHLV22-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1103					GRCh38	V40	ILF3-BGHLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	16587
ILF3-BGHLV22-30_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1103					GRCh38	V40	ILF3-BGHLV22-30_GTGAAA_L001_R1_001.fastq.gz,ILF3-BGHLV22-30_GTGAAA_L001_R2_001.fastq.gz		ENCORE2	16627