RBFOX2 RNA-Seq in K562

General Information


RBP	RBFOX2
Cell_Line	K562
Method	shRNA
Exp_Name	RBFOX2-BGKLV24-K562
ENCODE_series_ID	ENCSR541DSO
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR336DFS
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	RBFOX2_BGKLV24_47_17624
Rep2	RBFOX2_BGKLV24_48_17625
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	52.6
Rep2_qPCR	62.1
Rep1_WB	87.8
Rep2_WB	93.3
Antibody Cat#	A300-864A
Antibody Lot#	A300-864A
Antibody DCC ID	ENCAB592TEY
Status	Released
Project	ENCODE3
ID	568

Experiment Information (Status: Released)

	BGKLV24-47	BGKLV24-48
idx	384	385
TRCN#_or_BGC#	TRCN0000074544	TRCN0000074544
shRNA_or_gRNA_sequence	CGGGTTCGTAACTTTCGAGAA	CGGGTTCGTAACTTTCGAGAA
PAM
Name	RBFOX2	RBFOX2
Sample_ID	BGKLV24-47	BGKLV24-48
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	RBFOX2	RBFOX2
qPCR_result	52.6	62.1
Ave_qPCR	57.3
RT-qPCR_primer-F	ggtggatatgcagcctacag
RT-qPCR_primer-R	gctgtgtacaccctgccata
protein_conc	4016	3474
WB_result	87.8	93.3
Ave_WB	90.6
WB_DONE_date	3/30/2015
MW	41kDa
IP	1IP	1IP
antibody_Cat#	A300-864A	A300-864A
Antibody DCC ID	ENCAB592TEY	ENCAB592TEY
submitted_to_DCC_date	5/4/2015
Rep1_TPM	3.98592955	0
Rep2_TPM	4.022439	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	441	442

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBFOX2	Product_ID: A300-864A Lot_ID: 2 Source: Bethyl Labs Target Name: RBFOX2-human

Experiment Status

	BGKLV24-47	BGKLV24-48
Sample_ID	BGKLV24-47	BGKLV24-48
Sample Name	RBFOX2_BGKLV24_47_17624	RBFOX2_BGKLV24_48_17625
Sample Name	RBFOX2_BGKLV24_47_17624	RBFOX2_BGKLV24_48_17625
RBP	RBFOX2	RBFOX2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	876	877

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-47	BGKLV24-48
Sample #
Sample Name	RBFOX2-BGKLV24-47	RBFOX2-BGKLV24-48
Sample_Name_Alias	RBFOX2_BGKLV24_47_17624	RBFOX2_BGKLV24_48_17625
Index Well Position	S22	S23
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/E4.png	DNA_Library_LV21-24/set1/F4.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E5.png	RNA_Library_LV20-22-24/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-47	BGKLV24-48
RBP	RBFOX2	RBFOX2
Batch_ID	BGKLV24	BGKLV24
WB_result	87.800	93.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2564	2565

Sequencing Information

	BGKLV24-47	BGKLV24-48
Sample_ID	BGKLV24-47	BGKLV24-48
Sample Name	RBFOX2_BGKLV24_47_17624	RBFOX2_BGKLV24_48_17625
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	42,360,000	34,950,000
total_aligned_reads	40,315,164	32,691,784
unique_aligned_reads	36,867,072	29,812,886
percent_uniqueAligned	0.87033	0.85302
correlation_replicates	0.953237	0.953237
spikein_reads	203,198	127,278
percent_spikeins	0.00480	0.00364
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1098	1099

Data Submission Information

	BGKLV24-47	BGKLV24-47
ENCODE_alias	brenton-graveley:RBFOX2_BGKLV24	brenton-graveley:RBFOX2-BGKLV24-K562
ENCODE_accession	ENCSR336DFS	ENCSR541DSO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-47	BGKLV24-47
Sample Name	RBFOX2_BGKLV24_47_17624	RBFOX2_BGKLV24_47_17624
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2989	6890

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
RBFOX2_BGKLV24_47_17624_CGTACG_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1098	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	17212
RBFOX2_BGKLV24_47_17624_CGTACG_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1098	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	17248
RBFOX2_BGKLV24_47_17624_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1098					GRCh38	V40	RBFOX2_BGKLV24_47_17624_CGTACG_L008_R1_001.fastq.gz,RBFOX2_BGKLV24_47_17624_CGTACG_L008_R2_001.fastq.gz		ENCORE2	17284
RBFOX2_BGKLV24_47_17624_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	1098					GRCh38	V40	RBFOX2_BGKLV24_47_17624/Aligned.sortedByCoord.out.bam		ENCORE2	17320
RBFOX2_BGKLV24_47_17624_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	1098					GRCh38	V40	RBFOX2_BGKLV24_47_17624/Aligned.sortedByCoord.out.bam		ENCORE2	17356
RBFOX2_BGKLV24_47_17624_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	1098					GRCh38	V40	RBFOX2_BGKLV24_47_17624/Aligned.sortedByCoord.out.bam		ENCORE2	17392
RBFOX2_BGKLV24_47_17624_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	1098					GRCh38	V40	RBFOX2_BGKLV24_47_17624/Aligned.sortedByCoord.out.bam		ENCORE2	17428
RBFOX2_BGKLV24_47_17624_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1098					GRCh38	V40	RBFOX2_BGKLV24_47_17624_CGTACG_L008_R1_001.fastq.gz,RBFOX2_BGKLV24_47_17624_CGTACG_L008_R2_001.fastq.gz		ENCORE2	17464
RBFOX2_BGKLV24_48_17625_GAGTGG_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1099	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	17213
RBFOX2_BGKLV24_48_17625_GAGTGG_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1099	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	17249
RBFOX2_BGKLV24_48_17625_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1099					GRCh38	V40	RBFOX2_BGKLV24_48_17625_GAGTGG_L008_R1_001.fastq.gz,RBFOX2_BGKLV24_48_17625_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	17285
RBFOX2_BGKLV24_48_17625_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	1099					GRCh38	V40	RBFOX2_BGKLV24_48_17625/Aligned.sortedByCoord.out.bam		ENCORE2	17321
RBFOX2_BGKLV24_48_17625_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	1099					GRCh38	V40	RBFOX2_BGKLV24_48_17625/Aligned.sortedByCoord.out.bam		ENCORE2	17357
RBFOX2_BGKLV24_48_17625_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	1099					GRCh38	V40	RBFOX2_BGKLV24_48_17625/Aligned.sortedByCoord.out.bam		ENCORE2	17393
RBFOX2_BGKLV24_48_17625_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	1099					GRCh38	V40	RBFOX2_BGKLV24_48_17625/Aligned.sortedByCoord.out.bam		ENCORE2	17429
RBFOX2_BGKLV24_48_17625_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1099					GRCh38	V40	RBFOX2_BGKLV24_48_17625_GAGTGG_L008_R1_001.fastq.gz,RBFOX2_BGKLV24_48_17625_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	17465