ILF2 RNA-Seq in K562

General Information


RBP	ILF2
Cell_Line	K562
Method	shRNA
Exp_Name	ILF2-BGKLV24-K562
ENCODE_series_ID	ENCSR212NEC
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR126ARZ
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	ILF2_BGKLV24_35B
Rep2	ILF2_BGKLV24_36B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	77.7
Rep2_qPCR	71.9
Rep1_WB	35.0
Rep2_WB	36.8
Antibody Cat#	A303-147A
Antibody Lot#
Antibody DCC ID	ENCAB709CSJ
Status	Released
Project	ENCODE3
ID	605

Experiment Information (Status: Released)

	BGKLV24-35	BGKLV24-36
idx	372	373
TRCN#_or_BGC#	TRCN0000014556	TRCN0000014556
shRNA_or_gRNA_sequence	CCAACGAAACTGGCTTTGAAA	CCAACGAAACTGGCTTTGAAA
PAM
Name	ILF2	ILF2
Sample_ID	BGKLV24-35	BGKLV24-36
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	ILF2	ILF2
qPCR_result	77.7	71.9
Ave_qPCR	74.8
RT-qPCR_primer-F	aggccttgctgaagaggaat
RT-qPCR_primer-R	atgtccctggagccacaat
protein_conc	3862	4123
WB_result	35.0	36.8
Ave_WB	35.9
WB_DONE_date	4/16/2015
MW
IP	1	1
antibody_Cat#	A303-147A
Antibody DCC ID	ENCAB709CSJ	ENCAB709CSJ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	117.625688	0
Rep2_TPM	86.6702746	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x?	x
ID	429	430

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

	BGKLV24-35	BGKLV24-36
Sample_ID	BGKLV24-35	BGKLV24-36
Sample Name	ILF2_BGKLV24_35B	ILF2_BGKLV24_36B
Sample Name	ILF2_BGKLV24_35B	ILF2_BGKLV24_36B
RBP	ILF2	ILF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	890	891

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-35	BGKLV24-36
Sample #
Sample Name	ILF2-BGKLV24-35B	ILF2-BGKLV24-36B
Sample_Name_Alias	ILF2_BGKLV24_35B	ILF2_BGKLV24_36B
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A6.png	DNA_Library_LV24-25-26/set1/B6.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A4.png	RNA_Library_LV20-22-24/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-35	BGKLV24-36
RBP	ILF2	ILF2
Batch_ID	BGKLV24	BGKLV24
WB_result	35.000	36.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2578	2579

Sequencing Information

	BGKLV24-35	BGKLV24-36
Sample_ID	BGKLV24-35	BGKLV24-36
Sample Name	ILF2_BGKLV24_35B	ILF2_BGKLV24_36B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	74,018,994	83,566,566
total_aligned_reads	69,092,678	80,988,244
unique_aligned_reads	62,357,672	73,805,824
percent_uniqueAligned	0.84246	0.88320
correlation_replicates	0.997421	0.997421
spikein_reads	256,870	272,360
percent_spikeins	0.00347	0.00326
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1220	1221

Data Submission Information

	BGKLV24-35	BGKLV24-35
ENCODE_alias	brenton-graveley:ILF2_BGKLV24_B	brenton-graveley:ILF2-BGKLV24-K562
ENCODE_accession	ENCSR126ARZ	ENCSR212NEC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-35	BGKLV24-35
Sample Name	ILF2_BGKLV24_35B	ILF2_BGKLV24_35B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2994	6784

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_BGKLV24_35B_GATCAG_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1220	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17476
ILF2_BGKLV24_35B_GATCAG_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1220	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17500
ILF2_BGKLV24_35B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1220					GRCh38	V40	ILF2_BGKLV24_35B_GATCAG_L002_001.R1.fastq.gz,ILF2_BGKLV24_35B_GATCAG_L002_001.R2.fastq.gz		ENCORE2	17524
ILF2_BGKLV24_35B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1220					GRCh38	V40	ILF2_BGKLV24_35B/Aligned.sortedByCoord.out.bam		ENCORE2	17548
ILF2_BGKLV24_35B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1220					GRCh38	V40	ILF2_BGKLV24_35B/Aligned.sortedByCoord.out.bam		ENCORE2	17572
ILF2_BGKLV24_35B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1220					GRCh38	V40	ILF2_BGKLV24_35B/Aligned.sortedByCoord.out.bam		ENCORE2	17596
ILF2_BGKLV24_35B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1220					GRCh38	V40	ILF2_BGKLV24_35B/Aligned.sortedByCoord.out.bam		ENCORE2	17620
ILF2_BGKLV24_35B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1220					GRCh38	V40	ILF2_BGKLV24_35B_GATCAG_L002_001.R1.fastq.gz,ILF2_BGKLV24_35B_GATCAG_L002_001.R2.fastq.gz		ENCORE2	17644
ILF2_BGKLV24_36B_TAGCTT_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1221	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17477
ILF2_BGKLV24_36B_TAGCTT_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1221	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17501
ILF2_BGKLV24_36B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1221					GRCh38	V40	ILF2_BGKLV24_36B_TAGCTT_L002_001.R1.fastq.gz,ILF2_BGKLV24_36B_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	17525
ILF2_BGKLV24_36B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1221					GRCh38	V40	ILF2_BGKLV24_36B/Aligned.sortedByCoord.out.bam		ENCORE2	17549
ILF2_BGKLV24_36B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1221					GRCh38	V40	ILF2_BGKLV24_36B/Aligned.sortedByCoord.out.bam		ENCORE2	17573
ILF2_BGKLV24_36B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1221					GRCh38	V40	ILF2_BGKLV24_36B/Aligned.sortedByCoord.out.bam		ENCORE2	17597
ILF2_BGKLV24_36B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1221					GRCh38	V40	ILF2_BGKLV24_36B/Aligned.sortedByCoord.out.bam		ENCORE2	17621
ILF2_BGKLV24_36B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1221					GRCh38	V40	ILF2_BGKLV24_36B_TAGCTT_L002_001.R1.fastq.gz,ILF2_BGKLV24_36B_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	17645