RBFOX2 RNA-Seq in HepG2

General Information


RBP	RBFOX2
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBFOX2-BGHLV26-HepG2
ENCODE_series_ID	ENCSR322ACH
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR767LLP
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	RBFOX2_BGHLV26_35
Rep2	RBFOX2_BGHLV26_36
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	73.9
Rep2_qPCR	73.7
Rep1_WB	87.3
Rep2_WB	90.5
Antibody Cat#	A300-864A
Antibody Lot#	A300-864A
Antibody DCC ID	ENCAB592TEY
Status	Released
Project	ENCODE3
ID	632

Experiment Information (Status: Released)

	BGHLV26-35	BGHLV26-36
idx	591	592
TRCN#_or_BGC#	TRCN0000074544	TRCN0000074544
shRNA_or_gRNA_sequence	CGGGTTCGTAACTTTCGAGAA	CGGGTTCGTAACTTTCGAGAA
PAM
Name	RBFOX2	RBFOX2
Sample_ID	BGHLV26-35	BGHLV26-36
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	RBFOX2	RBFOX2
qPCR_result	73.9	73.7
Ave_qPCR	73.8
RT-qPCR_primer-F	ggtggatatgcagcctacag
RT-qPCR_primer-R	gctgtgtacaccctgccata
protein_conc	3359	4017
WB_result	87.3	90.5
Ave_WB	88.9
WB_DONE_date	6/30/2015
MW	41kDa
IP	1IP	1IP
antibody_Cat#	A300-864A	A300-864A
Antibody DCC ID	ENCAB592TEY	ENCAB592TEY
submitted_to_DCC_date	8/6/2015
Rep1_TPM	6.8	0
Rep2_TPM	7.6	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note	x	x
ID	2674	2675

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

	BGHLV26-35	BGHLV26-36
Sample_ID	BGHLV26-35	BGHLV26-36
Sample Name	RBFOX2_BGHLV26_35	RBFOX2_BGHLV26_36
Sample Name	RBFOX2_BGHLV26_35	RBFOX2_BGHLV26_36
RBP	RBFOX2	RBFOX2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	948	949

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-35	BGHLV26-36
Sample #
Sample Name	RBFOX2-BGHLV26-35	RBFOX2-BGHLV26-36
Sample_Name_Alias	RBFOX2_BGHLV26_35	RBFOX2_BGHLV26_36
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A9.png	DNA_Library_LV24-25-26/set1/B9.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV25-26/set1/C2.png	RNA_Library_LV25-26/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-35	BGHLV26-36
RBP	RBFOX2	RBFOX2
Batch_ID	BGHLV26	BGHLV26
WB_result	87.300	90.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2636	2637

Sequencing Information

	BGHLV26-35	BGHLV26-36
Sample_ID	BGHLV26-35	BGHLV26-36
Sample Name	RBFOX2_BGHLV26_35	RBFOX2_BGHLV26_36
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	93,239,712	80,320,976
total_aligned_reads	68,352,122	63,378,566
unique_aligned_reads	63,571,048	59,411,788
percent_uniqueAligned	0.68180	0.73968
correlation_replicates	0.976712	0.976712
spikein_reads	187,010	157,468
percent_spikeins	0.00201	0.00196
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1278	1279

Data Submission Information

	BGHLV26-35	BGHLV26-35
ENCODE_alias	brenton-graveley:RBFOX2_BGHLV26	brenton-graveley:RBFOX2-BGHLV26-HepG2
ENCODE_accession	ENCSR767LLP	ENCSR322ACH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-35	BGHLV26-35
Sample Name	RBFOX2_BGHLV26_35	RBFOX2_BGHLV26_35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3021	6889

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_BGHLV26_35_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1278	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19822
RBFOX2_BGHLV26_35_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1278	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19844
RBFOX2_BGHLV26_35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1278					GRCh38	V40	RBFOX2_BGHLV26_35_1.fastq.gz,RBFOX2_BGHLV26_35_2.fastq.gz		ENCORE2	19866
RBFOX2_BGHLV26_35_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1278					GRCh38	V40	RBFOX2_BGHLV26_35/Aligned.sortedByCoord.out.bam		ENCORE2	19888
RBFOX2_BGHLV26_35_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1278					GRCh38	V40	RBFOX2_BGHLV26_35/Aligned.sortedByCoord.out.bam		ENCORE2	19910
RBFOX2_BGHLV26_35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1278					GRCh38	V40	RBFOX2_BGHLV26_35/Aligned.sortedByCoord.out.bam		ENCORE2	19932
RBFOX2_BGHLV26_35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1278					GRCh38	V40	RBFOX2_BGHLV26_35/Aligned.sortedByCoord.out.bam		ENCORE2	19954
RBFOX2_BGHLV26_35_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1278					GRCh38	V40	RBFOX2_BGHLV26_35_1.fastq.gz,RBFOX2_BGHLV26_35_2.fastq.gz		ENCORE2	20662
RBFOX2_BGHLV26_36_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1279	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19823
RBFOX2_BGHLV26_36_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1279	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19845
RBFOX2_BGHLV26_36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1279					GRCh38	V40	RBFOX2_BGHLV26_36_1.fastq.gz,RBFOX2_BGHLV26_36_2.fastq.gz		ENCORE2	19867
RBFOX2_BGHLV26_36_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1279					GRCh38	V40	RBFOX2_BGHLV26_36/Aligned.sortedByCoord.out.bam		ENCORE2	19889
RBFOX2_BGHLV26_36_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1279					GRCh38	V40	RBFOX2_BGHLV26_36/Aligned.sortedByCoord.out.bam		ENCORE2	19911
RBFOX2_BGHLV26_36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1279					GRCh38	V40	RBFOX2_BGHLV26_36/Aligned.sortedByCoord.out.bam		ENCORE2	19933
RBFOX2_BGHLV26_36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1279					GRCh38	V40	RBFOX2_BGHLV26_36/Aligned.sortedByCoord.out.bam		ENCORE2	19955
RBFOX2_BGHLV26_36_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1279					GRCh38	V40	RBFOX2_BGHLV26_36_1.fastq.gz,RBFOX2_BGHLV26_36_2.fastq.gz		ENCORE2	20663