GRSF1 RNA-Seq in K562

General Information


RBP	GRSF1
Cell_Line	K562
Method	shRNA
Exp_Name	GRSF1-BGKLV29-K562
ENCODE_series_ID	ENCSR423WRJ
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR835RMN
ENCODE_CN_Exp_ID	ENCSR118EFE
Rep1	GRSF1_BGKLV29-37B
Rep2	GRSF1_BGKLV29-38B
CN1	NTB_BGKLV29-1
CN2	NTB_BGKLV29-2
Rep1_qPCR	78.2
Rep2_qPCR	77.9
Rep1_WB	80.5
Rep2_WB	76.4
Antibody Cat#	RN050PW
Antibody Lot#	RN050PW
Antibody DCC ID	ENCAB438AYW
Status	Released
Project	ENCODE3
ID	674

Experiment Information (Status: Released)

	BGKLV29-37	BGKLV29-38
idx	572	573
TRCN#_or_BGC#	TRCN0000075044	TRCN0000075044
shRNA_or_gRNA_sequence	CGGTGAGAATGGAATACATTT	CGGTGAGAATGGAATACATTT
PAM
Name	GRSF1	GRSF1
Sample_ID	BGKLV29-37	BGKLV29-38
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	GRSF1	GRSF1
qPCR_result	78.2	77.9
Ave_qPCR	78.1
RT-qPCR_primer-F	TTCCTGAATTCATGTCCAAA
RT-qPCR_primer-R	CCAAGTCCAAGAAAGATGTGC
protein_conc	2849	2433
WB_result	80.5	76.4
Ave_WB	78.4
WB_DONE_date	9/23/2015
MW	53kDa
IP	1	1
antibody_Cat#	RN050PW	RN050PW
Antibody DCC ID	ENCAB438AYW	ENCAB438AYW
submitted_to_DCC_date	12/7/2015
Rep1_TPM	21.6468749	0
Rep2_TPM	14.0849471	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	651	652

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GRSF1	Product_ID: RN050PW Lot_ID: 1 Source: MBLI Target Name: GRSF1-human

Experiment Status

	BGKLV29-37	BGKLV29-38
Sample_ID	BGKLV29-37	BGKLV29-38
Sample Name	GRSF1_BGKLV29-37B	GRSF1_BGKLV29-38B
Sample Name	GRSF1_BGKLV29-37B	GRSF1_BGKLV29-38B
RBP	GRSF1	GRSF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1022	1023

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-37	BGKLV29-38
Sample #
Sample Name	GRSF1-BGKLV29-37B	GRSF1-BGKLV29-38B
Sample_Name_Alias	GRSF1_BGKLV29-37B	GRSF1_BGKLV29-38B
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-03	2015-11-03
Lib_ID	Lib-151103	Lib-151103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set2/B2.png	DNA_Library_LV28-29-30/set1/F6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A2.png	RNA_Library_LV29-30-31-32/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-37	BGKLV29-38
RBP	GRSF1	GRSF1
Batch_ID	BGKLV29	BGKLV29
WB_result	80.500	76.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2728	2729

Sequencing Information

	BGKLV29-37	BGKLV29-38
Sample_ID	BGKLV29-37	BGKLV29-38
Sample Name	GRSF1_BGKLV29-37B	GRSF1_BGKLV29-38B
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	138,110,872	91,349,912
total_aligned_reads	126,805,482	83,356,698
unique_aligned_reads	114,226,138	75,146,712
percent_uniqueAligned	0.82706	0.82262
correlation_replicates	0.997428	0.997428
spikein_reads	852,332	431,948
percent_spikeins	0.00617	0.00473
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1391	1392

Data Submission Information

	BGKLV29-37	BGKLV29-37
ENCODE_alias	brenton-graveley:GRSF1_BGKLV29-B	brenton-graveley:GRSF1-BGKLV29-K562
ENCODE_accession	ENCSR835RMN	ENCSR423WRJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-37	BGKLV29-37
Sample Name	GRSF1_BGKLV29-37B	GRSF1_BGKLV29-37B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3060	6738

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
GRSF1_BGKLV29-37B_ACAGTG_L008_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1391	HiSeq2500	100	paired-ended	1				NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE3	20424
GRSF1_BGKLV29-37B_ACAGTG_L008_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1391	HiSeq2500	100	paired-ended	2				NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE3	20454
GRSF1_BGKLV29-37B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1391					GRCh38	V40	GRSF1_BGKLV29-37B_ACAGTG_L008_001.R1.fastq.gz,GRSF1_BGKLV29-37B_ACAGTG_L008_001.R2.fastq.gz		ENCORE2	20484
GRSF1_BGKLV29-37B_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1391					GRCh38	V40	GRSF1_BGKLV29-37B/Aligned.sortedByCoord.out.bam		ENCORE2	20514
GRSF1_BGKLV29-37B_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1391					GRCh38	V40	GRSF1_BGKLV29-37B/Aligned.sortedByCoord.out.bam		ENCORE2	20544
GRSF1_BGKLV29-37B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1391					GRCh38	V40	GRSF1_BGKLV29-37B/Aligned.sortedByCoord.out.bam		ENCORE2	20574
GRSF1_BGKLV29-37B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1391					GRCh38	V40	GRSF1_BGKLV29-37B/Aligned.sortedByCoord.out.bam		ENCORE2	20604
GRSF1_BGKLV29-37B_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1391					GRCh38	V40	GRSF1_BGKLV29-37B_ACAGTG_L008_001.R1.fastq.gz,GRSF1_BGKLV29-37B_ACAGTG_L008_001.R2.fastq.gz		ENCORE2	20634
GRSF1_BGKLV29-38B_GCCAAT_L008_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1392	HiSeq2500	100	paired-ended	1				NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE3	20425
GRSF1_BGKLV29-38B_GCCAAT_L008_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1392	HiSeq2500	100	paired-ended	2				NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE3	20455
GRSF1_BGKLV29-38B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1392					GRCh38	V40	GRSF1_BGKLV29-38B_GCCAAT_L008_001.R1.fastq.gz,GRSF1_BGKLV29-38B_GCCAAT_L008_001.R2.fastq.gz		ENCORE2	20485
GRSF1_BGKLV29-38B_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1392					GRCh38	V40	GRSF1_BGKLV29-38B/Aligned.sortedByCoord.out.bam		ENCORE2	20515
GRSF1_BGKLV29-38B_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1392					GRCh38	V40	GRSF1_BGKLV29-38B/Aligned.sortedByCoord.out.bam		ENCORE2	20545
GRSF1_BGKLV29-38B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1392					GRCh38	V40	GRSF1_BGKLV29-38B/Aligned.sortedByCoord.out.bam		ENCORE2	20575
GRSF1_BGKLV29-38B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1392					GRCh38	V40	GRSF1_BGKLV29-38B/Aligned.sortedByCoord.out.bam		ENCORE2	20605
GRSF1_BGKLV29-38B_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1392					GRCh38	V40	GRSF1_BGKLV29-38B_GCCAAT_L008_001.R1.fastq.gz,GRSF1_BGKLV29-38B_GCCAAT_L008_001.R2.fastq.gz		ENCORE2	20635