ILF3 RNA-Seq in K562

General Information


RBP	ILF3
Cell_Line	K562
Method	shRNA
Exp_Name	ILF3-BGKLV24-K562
ENCODE_series_ID	ENCSR801WSO
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR269HQA
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	ILF3_BGKLV24_37_17617
Rep2	ILF3_BGKLV24_38_17618
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	60.6
Rep2_qPCR	59.3
Rep1_WB	70.1
Rep2_WB	66.5
Antibody Cat#	A303-651A
Antibody Lot#
Antibody DCC ID	ENCAB198ZHJ
Status	Released
Project	ENCODE3
ID	565

Experiment Information (Status: Released)

	BGKLV24-37	BGKLV24-38
idx	374	375
TRCN#_or_BGC#	TRCN0000329787	TRCN0000329787
shRNA_or_gRNA_sequence	CCTTCCAAGATGCCCAAGAAA	CCTTCCAAGATGCCCAAGAAA
PAM
Name	ILF3	ILF3
Sample_ID	BGKLV24-37	BGKLV24-38
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	ILF3	ILF3
qPCR_result	60.6	59.3
Ave_qPCR	59.9
RT-qPCR_primer-F	CGTTCTGGACAGGCAGAAAT
RT-qPCR_primer-R	CCGGATCACAATGACACAAG
protein_conc	3962	3466
WB_result	70.1	66.5
Ave_WB	68.3
WB_DONE_date	4/7/2015
MW
IP	1	1
antibody_Cat#	A303-651A
Antibody DCC ID	ENCAB198ZHJ	ENCAB198ZHJ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	61.8422174	0
Rep2_TPM	45.6865377	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	431	432

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

	BGKLV24-37	BGKLV24-38
Sample_ID	BGKLV24-37	BGKLV24-38
Sample Name	ILF3_BGKLV24_37_17617	ILF3_BGKLV24_38_17618
Sample Name	ILF3_BGKLV24_37_17617	ILF3_BGKLV24_38_17618
RBP	ILF3	ILF3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	868	869

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-37	BGKLV24-38
Sample #
Sample Name	ILF3-BGKLV24-37	ILF3-BGKLV24-38
Sample_Name_Alias	ILF3_BGKLV24_37_17617	ILF3_BGKLV24_38_17618
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/G3.png	DNA_Library_LV21-24/set1/H3.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/D3.png	RNA_Library_LV20-22-24/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-37	BGKLV24-38
RBP	ILF3	ILF3
Batch_ID	BGKLV24	BGKLV24
WB_result	70.100	66.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2556	2557

Sequencing Information

	BGKLV24-37	BGKLV24-38
Sample_ID	BGKLV24-37	BGKLV24-38
Sample Name	ILF3_BGKLV24_37_17617	ILF3_BGKLV24_38_17618
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	37,320,000	31,570,000
total_aligned_reads	35,482,342	30,010,432
unique_aligned_reads	32,403,992	27,537,386
percent_uniqueAligned	0.86827	0.87226
correlation_replicates	0.995331	0.995331
spikein_reads	188,802	153,032
percent_spikeins	0.00506	0.00485
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1090	1091

Data Submission Information

	BGKLV24-37	BGKLV24-37
ENCODE_alias	brenton-graveley:ILF3_BGKLV24	brenton-graveley:ILF3-BGKLV24-K562
ENCODE_accession	ENCSR269HQA	ENCSR801WSO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-37	BGKLV24-37
Sample Name	ILF3_BGKLV24_37_17617	ILF3_BGKLV24_37_17617
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2985	6786

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_BGKLV24_37_17617_ATGTCA_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1090	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17202
ILF3_BGKLV24_37_17617_ATGTCA_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1090	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17238
ILF3_BGKLV24_37_17617_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1090					GRCh38	V40	ILF3_BGKLV24_37_17617_ATGTCA_L007_R1_001.fastq.gz,ILF3_BGKLV24_37_17617_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	17274
ILF3_BGKLV24_37_17617_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1090					GRCh38	V40	ILF3_BGKLV24_37_17617/Aligned.sortedByCoord.out.bam		ENCORE2	17310
ILF3_BGKLV24_37_17617_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1090					GRCh38	V40	ILF3_BGKLV24_37_17617/Aligned.sortedByCoord.out.bam		ENCORE2	17346
ILF3_BGKLV24_37_17617_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1090					GRCh38	V40	ILF3_BGKLV24_37_17617/Aligned.sortedByCoord.out.bam		ENCORE2	17382
ILF3_BGKLV24_37_17617_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1090					GRCh38	V40	ILF3_BGKLV24_37_17617/Aligned.sortedByCoord.out.bam		ENCORE2	17418
ILF3_BGKLV24_37_17617_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1090					GRCh38	V40	ILF3_BGKLV24_37_17617_ATGTCA_L007_R1_001.fastq.gz,ILF3_BGKLV24_37_17617_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	17454
ILF3_BGKLV24_38_17618_CCGTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1091	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17203
ILF3_BGKLV24_38_17618_CCGTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1091	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17239
ILF3_BGKLV24_38_17618_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1091					GRCh38	V40	ILF3_BGKLV24_38_17618_CCGTCC_L007_R1_001.fastq.gz,ILF3_BGKLV24_38_17618_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	17275
ILF3_BGKLV24_38_17618_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1091					GRCh38	V40	ILF3_BGKLV24_38_17618/Aligned.sortedByCoord.out.bam		ENCORE2	17311
ILF3_BGKLV24_38_17618_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1091					GRCh38	V40	ILF3_BGKLV24_38_17618/Aligned.sortedByCoord.out.bam		ENCORE2	17347
ILF3_BGKLV24_38_17618_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1091					GRCh38	V40	ILF3_BGKLV24_38_17618/Aligned.sortedByCoord.out.bam		ENCORE2	17383
ILF3_BGKLV24_38_17618_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1091					GRCh38	V40	ILF3_BGKLV24_38_17618/Aligned.sortedByCoord.out.bam		ENCORE2	17419
ILF3_BGKLV24_38_17618_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1091					GRCh38	V40	ILF3_BGKLV24_38_17618_CCGTCC_L007_R1_001.fastq.gz,ILF3_BGKLV24_38_17618_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	17455