GRSF1 RNA-Seq in HepG2

General Information


RBP	GRSF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	GRSF1-BGHLV22-HepG2
ENCODE_series_ID	ENCSR373VUD
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR674KDQ
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	GRSF1-BGHLV22-17_17754
Rep2	GRSF1-BGHLV22-18_17755
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	47.7
Rep2_qPCR	52.2
Rep1_WB	59.1
Rep2_WB	48.4
Antibody Cat#	RN050PW
Antibody Lot#	RN050PW
Antibody DCC ID	ENCAB438AYW
Status	Released
Project	ENCODE3
ID	535

Experiment Information (Status: Released)

	BGHLV22-17	BGHLV22-18
idx	445	446
TRCN#_or_BGC#	TRCN0000075044	TRCN0000075044
shRNA_or_gRNA_sequence	CGGTGAGAATGGAATACATTT	CGGTGAGAATGGAATACATTT
PAM
Name	GRSF1	GRSF1
Sample_ID	BGHLV22-17	BGHLV22-18
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	GRSF1	GRSF1
qPCR_result	47.7	52.2
Ave_qPCR	49.9
RT-qPCR_primer-F	TTCCTGAATTCATGTCCAAA
RT-qPCR_primer-R	CCAAGTCCAAGAAAGATGTGC
protein_conc	6713	6401
WB_result	59.1	48.4
Ave_WB	53.8
WB_DONE_date	5/20/2015
MW	53kDa
IP	1	1
antibody_Cat#	RN050PW	RN050PW
Antibody DCC ID	ENCAB438AYW	ENCAB438AYW
submitted_to_DCC_date	8/6/2015
Rep1_TPM	12.7	0
Rep2_TPM	10.9	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2518	2519

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

	BGHLV22-17	BGHLV22-18
Sample_ID	BGHLV22-17	BGHLV22-18
Sample Name	GRSF1-BGHLV22-17_17754	GRSF1-BGHLV22-18_17755
Sample Name	GRSF1-BGHLV22-17_17754	GRSF1-BGHLV22-18_17755
RBP	GRSF1	GRSF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	784	785

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-17	BGHLV22-18
Sample #
Sample Name	GRSF1-BGHLV22-17	GRSF1-BGHLV22-18
Sample_Name_Alias	GRSF1-BGHLV22-17_17754	GRSF1-BGHLV22-18_17755
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A7.png	DNA_Library_LV20-22-23/set1/B7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/F4.png	RNA_Library_LV19-21-24/set2/G4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-17	BGHLV22-18
RBP	GRSF1	GRSF1
Batch_ID	BGHLV22	BGHLV22
WB_result	59.100	48.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2470	2471

Sequencing Information

	BGHLV22-17	BGHLV22-18
Sample_ID	BGHLV22-17	BGHLV22-18
Sample Name	GRSF1-BGHLV22-17_17754	GRSF1-BGHLV22-18_17755
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	48,960,000	50,080,000
total_aligned_reads	44,714,122	45,340,292
unique_aligned_reads	41,998,370	42,537,864
percent_uniqueAligned	0.85781	0.84940
correlation_replicates	0.988752	0.988752
spikein_reads	309,708	331,466
percent_spikeins	0.00633	0.00662
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1204	1205

Data Submission Information

	BGHLV22-17	BGHLV22-17
ENCODE_alias	brenton-graveley:GRSF1-BGHLV22	brenton-graveley:GRSF1-BGHLV22-HepG2
ENCODE_accession	ENCSR674KDQ	ENCSR373VUD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-17	BGHLV22-17
Sample Name	GRSF1-BGHLV22-17_17754	GRSF1-BGHLV22-17_17754
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2924	6737

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-BGHLV22-17_17754_GATCAG_L007_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1204	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16280
GRSF1-BGHLV22-17_17754_GATCAG_L007_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1204	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16320
GRSF1-BGHLV22-17_17754_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1204					GRCh38	V40	GRSF1-BGHLV22-17_17754_GATCAG_L007_R1_001.fastq.gz,GRSF1-BGHLV22-17_17754_GATCAG_L007_R2_001.fastq.gz		ENCORE2	16418
GRSF1-BGHLV22-17_17754_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1204					GRCh38	V40	GRSF1-BGHLV22-17_17754/Aligned.sortedByCoord.out.bam		ENCORE2	16458
GRSF1-BGHLV22-17_17754_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1204					GRCh38	V40	GRSF1-BGHLV22-17_17754/Aligned.sortedByCoord.out.bam		ENCORE2	16498
GRSF1-BGHLV22-17_17754_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1204					GRCh38	V40	GRSF1-BGHLV22-17_17754/Aligned.sortedByCoord.out.bam		ENCORE2	16538
GRSF1-BGHLV22-17_17754_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1204					GRCh38	V40	GRSF1-BGHLV22-17_17754/Aligned.sortedByCoord.out.bam		ENCORE2	16578
GRSF1-BGHLV22-17_17754_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1204					GRCh38	V40	GRSF1-BGHLV22-17_17754_GATCAG_L007_R1_001.fastq.gz,GRSF1-BGHLV22-17_17754_GATCAG_L007_R2_001.fastq.gz		ENCORE2	16618
GRSF1-BGHLV22-18_17755_TAGCTT_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1205	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16281
GRSF1-BGHLV22-18_17755_TAGCTT_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1205	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16321
GRSF1-BGHLV22-18_17755_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1205					GRCh38	V40	GRSF1-BGHLV22-18_17755_TAGCTT_L008_R1_001.fastq.gz,GRSF1-BGHLV22-18_17755_TAGCTT_L008_R2_001.fastq.gz		ENCORE2	16419
GRSF1-BGHLV22-18_17755_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1205					GRCh38	V40	GRSF1-BGHLV22-18_17755/Aligned.sortedByCoord.out.bam		ENCORE2	16459
GRSF1-BGHLV22-18_17755_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1205					GRCh38	V40	GRSF1-BGHLV22-18_17755/Aligned.sortedByCoord.out.bam		ENCORE2	16499
GRSF1-BGHLV22-18_17755_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1205					GRCh38	V40	GRSF1-BGHLV22-18_17755/Aligned.sortedByCoord.out.bam		ENCORE2	16539
GRSF1-BGHLV22-18_17755_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1205					GRCh38	V40	GRSF1-BGHLV22-18_17755/Aligned.sortedByCoord.out.bam		ENCORE2	16579
GRSF1-BGHLV22-18_17755_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1205					GRCh38	V40	GRSF1-BGHLV22-18_17755_TAGCTT_L008_R1_001.fastq.gz,GRSF1-BGHLV22-18_17755_TAGCTT_L008_R2_001.fastq.gz		ENCORE2	16619