SFPQ RNA-Seq in K562

General Information


RBP	SFPQ
Cell_Line	K562
Method	shRNA
Exp_Name	SFPQ-BGKLV28-K562
ENCODE_series_ID	ENCSR627JUE
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR535YPK
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	SFPQ_BGKLV28-51
Rep2	SFPQ_BGKLV28-52
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	63.1
Rep2_qPCR	46.9
Rep1_WB	50.0
Rep2_WB	60.7
Antibody Cat#	A301-321A
Antibody Lot#	A301-321A
Antibody DCC ID	ENCAB692IKS
Status	Released
Project	ENCODE3
ID	657

Experiment Information (Status: Released)

	BGKLV28-51	BGKLV28-51	BGKLV28-52	BGKLV28-52
idx	520	520	521	521
TRCN#_or_BGC#	TRCN0000001084	TRCN0000001084	TRCN0000001084	TRCN0000001084
shRNA_or_gRNA_sequence	GCGCCAAAGAGAGGAAAGTTA	GCGCCAAAGAGAGGAAAGTTA	GCGCCAAAGAGAGGAAAGTTA	GCGCCAAAGAGAGGAAAGTTA
PAM
Name	SFPQ_84	SFPQ_84	SFPQ_84	SFPQ_84
Sample_ID	BGKLV28-51	BGKLV28-51	BGKLV28-52	BGKLV28-52
transduction_Date	6/16/2015	6/16/2015	6/16/2015	6/16/2015
days
RBP_name	SFPQ	SFPQ	SFPQ	SFPQ
qPCR_result	63.1	63.1	46.9	46.9
Ave_qPCR	55.0	55.0
RT-qPCR_primer-F	taagccagcagcaagaaagg	taagccagcagcaagaaagg
RT-qPCR_primer-R	gttccacaatgactggacga	gttccacaatgactggacga
protein_conc	2552	2552	2769	2769
WB_result	50.0	52.2	60.7	55.8
Ave_WB	55.4	54.0
WB_DONE_date	7/15/2015	6/27/2023
MW	76kDa	76KD
IP	1		1
antibody_Cat#	A301-321A	71992S	A301-321A
Antibody DCC ID	ENCAB692IKS		ENCAB692IKS
submitted_to_DCC_date	8/6/2015	1/8/2024
Rep1_TPM	265.084878	0	0	0
Rep2_TPM	181.077159	0	0	0
Action
Library_start_date	10/28/2015		10/28/2015
repeat_library
Note	x		x
ID	597	599	598	600

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
SFPQ	Product_ID: 71992S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SFPQ-human

Experiment Status

	BGKLV28-51	BGKLV28-52
Sample_ID	BGKLV28-51	BGKLV28-52
Sample Name	SFPQ_BGKLV28-51	SFPQ_BGKLV28-52
Sample Name	SFPQ_BGKLV28-51	SFPQ_BGKLV28-52
RBP	SFPQ	SFPQ
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1000	1001

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-51	BGKLV28-52
Sample #
Sample Name	SFPQ-BGKLV28-51	SFPQ-BGKLV28-52
Sample_Name_Alias	SFPQ_BGKLV28-51	SFPQ_BGKLV28-52
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E3.png	DNA_Library_LV28-29-30/set1/F3.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/A9.png	RNA_Library_LV26-27-28-29/set1/B9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-51	BGKLV28-52
RBP	SFPQ	SFPQ
Batch_ID	BGKLV28	BGKLV28
WB_result	50.000	60.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2692	2693

Sequencing Information

	BGKLV28-51	BGKLV28-52
Sample_ID	BGKLV28-51	BGKLV28-52
Sample Name	SFPQ_BGKLV28-51	SFPQ_BGKLV28-52
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	66,511,090	62,020,426
total_aligned_reads	60,625,616	54,702,256
unique_aligned_reads	55,487,774	50,003,832
percent_uniqueAligned	0.83426	0.80625
correlation_replicates	0.993686	0.993686
spikein_reads	224,512	190,968
percent_spikeins	0.00338	0.00308
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1334	1335

Data Submission Information

	BGKLV28-51	BGKLV28-51
ENCODE_alias	brenton-graveley:SFPQ_BGKLV28	brenton-graveley:SFPQ-BGKLV28-K562
ENCODE_accession	ENCSR535YPK	ENCSR627JUE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-51	BGKLV28-51
Sample Name	SFPQ_BGKLV28-51	SFPQ_BGKLV28-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3049	6947

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_BGKLV28-51_CGTACG_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1334	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20178
SFPQ_BGKLV28-51_CGTACG_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1334	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20210
SFPQ_BGKLV28-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1334					GRCh38	V40	SFPQ_BGKLV28-51_CGTACG_L001_001.R1.fastq.gz,SFPQ_BGKLV28-51_CGTACG_L001_001.R2.fastq.gz		ENCORE2	20242
SFPQ_BGKLV28-51_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1334					GRCh38	V40	SFPQ_BGKLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	20274
SFPQ_BGKLV28-51_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1334					GRCh38	V40	SFPQ_BGKLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	20306
SFPQ_BGKLV28-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1334					GRCh38	V40	SFPQ_BGKLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	20338
SFPQ_BGKLV28-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1334					GRCh38	V40	SFPQ_BGKLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	20370
SFPQ_BGKLV28-51_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1334					GRCh38	V40	SFPQ_BGKLV28-51_CGTACG_L001_001.R1.fastq.gz,SFPQ_BGKLV28-51_CGTACG_L001_001.R2.fastq.gz		ENCORE2	20402
SFPQ_BGKLV28-52_GAGTGG_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1335	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20179
SFPQ_BGKLV28-52_GAGTGG_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1335	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20211
SFPQ_BGKLV28-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1335					GRCh38	V40	SFPQ_BGKLV28-52_GAGTGG_L001_001.R1.fastq.gz,SFPQ_BGKLV28-52_GAGTGG_L001_001.R2.fastq.gz		ENCORE2	20243
SFPQ_BGKLV28-52_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1335					GRCh38	V40	SFPQ_BGKLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	20275
SFPQ_BGKLV28-52_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1335					GRCh38	V40	SFPQ_BGKLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	20307
SFPQ_BGKLV28-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1335					GRCh38	V40	SFPQ_BGKLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	20339
SFPQ_BGKLV28-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1335					GRCh38	V40	SFPQ_BGKLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	20371
SFPQ_BGKLV28-52_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1335					GRCh38	V40	SFPQ_BGKLV28-52_GAGTGG_L001_001.R1.fastq.gz,SFPQ_BGKLV28-52_GAGTGG_L001_001.R2.fastq.gz		ENCORE2	20403