SFPQ RNA-Seq in HepG2

General Information


RBP	SFPQ
Cell_Line	HepG2
Method	shRNA
Exp_Name	SFPQ-BGHLV26-HepG2
ENCODE_series_ID	ENCSR165RVO
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR782MXN
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	SFPQ_BGHLV26_55
Rep2	SFPQ_BGHLV26_56
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	48.7
Rep2_qPCR	55.7
Rep1_WB	52.3
Rep2_WB	62.1
Antibody Cat#	A301-321A
Antibody Lot#	A301-321A
Antibody DCC ID	ENCAB692IKS
Status	Released
Project	ENCODE3
ID	636

Experiment Information (Status: Released)

	BGHLV26-55	BGHLV26-56
idx	611	612
TRCN#_or_BGC#	TRCN0000001084	TRCN0000001084
shRNA_or_gRNA_sequence	GCGCCAAAGAGAGGAAAGTTA	GCGCCAAAGAGAGGAAAGTTA
PAM
Name	SFPQ	SFPQ
Sample_ID	BGHLV26-55	BGHLV26-56
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	SFPQ	SFPQ
qPCR_result	48.7	55.7
Ave_qPCR	52.2
RT-qPCR_primer-F	taagccagcagcaagaaagg
RT-qPCR_primer-R	gttccacaatgactggacga
protein_conc	3091	3778
WB_result	52.3	62.1
Ave_WB	57.2
WB_DONE_date	7/6/2015
MW	76kDa
IP	1	1
antibody_Cat#	A301-321A	A301-321A
Antibody DCC ID	ENCAB692IKS	ENCAB692IKS
submitted_to_DCC_date	8/6/2015
Rep1_TPM	110.9	0
Rep2_TPM	94.1	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note	x	x
ID	2698	2699

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SFPQ	Product_ID: A301-321A Lot_ID: 1 Source: Bethyl Labs Target Name: SFPQ-human

Experiment Status

	BGHLV26-55	BGHLV26-56
Sample_ID	BGHLV26-55	BGHLV26-56
Sample Name	SFPQ_BGHLV26_55	SFPQ_BGHLV26_56
Sample Name	SFPQ_BGHLV26_55	SFPQ_BGHLV26_56
RBP	SFPQ	SFPQ
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	956	957

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-55	BGHLV26-56
Sample #
Sample Name	SFPQ-BGHLV26-55	SFPQ-BGHLV26-56
Sample_Name_Alias	SFPQ_BGHLV26_55	SFPQ_BGHLV26_56
Index Well Position	S18	S19
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/A10.png	DNA_Library_LV24-25-26/set1/B10.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C3.png	RNA_Library_LV26-27-28-29/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-55	BGHLV26-56
RBP	SFPQ	SFPQ
Batch_ID	BGHLV26	BGHLV26
WB_result	52.300	62.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2644	2645

Sequencing Information

	BGHLV26-55	BGHLV26-56
Sample_ID	BGHLV26-55	BGHLV26-56
Sample Name	SFPQ_BGHLV26_55	SFPQ_BGHLV26_56
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	72,667,458	72,279,686
total_aligned_reads	59,523,544	63,135,232
unique_aligned_reads	55,354,640	59,012,692
percent_uniqueAligned	0.76175	0.81645
correlation_replicates	0.996402	0.996402
spikein_reads	155,926	184,548
percent_spikeins	0.00215	0.00255
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1286	1287

Data Submission Information

	BGHLV26-55	BGHLV26-55
ENCODE_alias	brenton-graveley:SFPQ_BGHLV26	brenton-graveley:SFPQ-BGHLV26-HepG2
ENCODE_accession	ENCSR782MXN	ENCSR165RVO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-55	BGHLV26-55
Sample Name	SFPQ_BGHLV26_55	SFPQ_BGHLV26_55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3025	6946

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
SFPQ_BGHLV26_55_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1286	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19830
SFPQ_BGHLV26_55_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1286	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19852
SFPQ_BGHLV26_55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1286					GRCh38	V40	SFPQ_BGHLV26_55_1.fastq.gz,SFPQ_BGHLV26_55_2.fastq.gz		ENCORE2	19874
SFPQ_BGHLV26_55_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	1286					GRCh38	V40	SFPQ_BGHLV26_55/Aligned.sortedByCoord.out.bam		ENCORE2	19896
SFPQ_BGHLV26_55_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	1286					GRCh38	V40	SFPQ_BGHLV26_55/Aligned.sortedByCoord.out.bam		ENCORE2	19918
SFPQ_BGHLV26_55_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	1286					GRCh38	V40	SFPQ_BGHLV26_55/Aligned.sortedByCoord.out.bam		ENCORE2	19940
SFPQ_BGHLV26_55_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	1286					GRCh38	V40	SFPQ_BGHLV26_55/Aligned.sortedByCoord.out.bam		ENCORE2	19962
SFPQ_BGHLV26_55_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1286					GRCh38	V40	SFPQ_BGHLV26_55_1.fastq.gz,SFPQ_BGHLV26_55_2.fastq.gz		ENCORE2	20670
SFPQ_BGHLV26_56_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1287	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19831
SFPQ_BGHLV26_56_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1287	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19853
SFPQ_BGHLV26_56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1287					GRCh38	V40	SFPQ_BGHLV26_56_1.fastq.gz,SFPQ_BGHLV26_56_2.fastq.gz		ENCORE2	19875
SFPQ_BGHLV26_56_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	1287					GRCh38	V40	SFPQ_BGHLV26_56/Aligned.sortedByCoord.out.bam		ENCORE2	19897
SFPQ_BGHLV26_56_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	1287					GRCh38	V40	SFPQ_BGHLV26_56/Aligned.sortedByCoord.out.bam		ENCORE2	19919
SFPQ_BGHLV26_56_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	1287					GRCh38	V40	SFPQ_BGHLV26_56/Aligned.sortedByCoord.out.bam		ENCORE2	19941
SFPQ_BGHLV26_56_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	1287					GRCh38	V40	SFPQ_BGHLV26_56/Aligned.sortedByCoord.out.bam		ENCORE2	19963
SFPQ_BGHLV26_56_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1287					GRCh38	V40	SFPQ_BGHLV26_56_1.fastq.gz,SFPQ_BGHLV26_56_2.fastq.gz		ENCORE2	20671