RBM47 RNA-Seq in HepG2

General Information


RBP	RBM47
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM47-BGHLV22-HepG2
ENCODE_series_ID	ENCSR974NRI
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR711ZJQ
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	RBM47-BGHLV22-39
Rep2	RBM47-BGHLV22-40
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	85.9
Rep2_qPCR	87.5
Rep1_WB	no AB
Rep2_WB	no AB
Antibody Cat#	no AB
Antibody Lot#	no AB
Antibody DCC ID
Status	Released
Project	ENCODE3
ID	526

Experiment Information (Status: Released)

	BGHLV22-39	BGHLV22-40
idx	467	468
TRCN#_or_BGC#	TRCN0000074563	TRCN0000074563
shRNA_or_gRNA_sequence	CGCTTGACTATTTATGAAGAA	CGCTTGACTATTTATGAAGAA
PAM
Name	RBM47	RBM47
Sample_ID	BGHLV22-39	BGHLV22-40
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	RBM47	RBM47
qPCR_result	85.9	87.5
Ave_qPCR	86.7
RT-qPCR_primer-F	gctgtcattcccactgtgtc
RT-qPCR_primer-R	gtagatcccggcagtaggaa
protein_conc	7736	6544
WB_result	no AB	no AB
Ave_WB
WB_DONE_date
MW
IP	1	1
antibody_Cat#	no AB	no AB
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	1.1	0
Rep2_TPM	1.1	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2536	2537

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-39	BGHLV22-40
Sample_ID	BGHLV22-39	BGHLV22-40
Sample Name	RBM47-BGHLV22-39	RBM47-BGHLV22-40
Sample Name	RBM47-BGHLV22-39	RBM47-BGHLV22-40
RBP	RBM47	RBM47
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	802	803

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-39	BGHLV22-40
Sample #
Sample Name	RBM47-BGHLV22-39	RBM47-BGHLV22-40
Sample_Name_Alias	RBM47-BGHLV22-39	RBM47-BGHLV22-40
Index Well Position	S01	S02
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/A9.png	DNA_Library_LV20-22-23/set1/B9.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A3.png	RNA_Library_LV22-23-25/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-39	BGHLV22-40
RBP	RBM47	RBM47
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2488	2489

Sequencing Information

	BGHLV22-39	BGHLV22-40
Sample_ID	BGHLV22-39	BGHLV22-40
Sample Name	RBM47-BGHLV22-39	RBM47-BGHLV22-40
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	57,610,000	57,710,000
total_aligned_reads	52,647,852	53,414,476
unique_aligned_reads	49,481,670	50,258,198
percent_uniqueAligned	0.85891	0.87088
correlation_replicates	0.996724	0.996724
spikein_reads	324,404	305,876
percent_spikeins	0.00563	0.00530
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1110	1111

Data Submission Information

	BGHLV22-39	BGHLV22-39
ENCODE_alias	brenton-graveley:RBM47-BGHLV22	brenton-graveley:RBM47-BGHLV22-HepG2
ENCODE_accession	ENCSR711ZJQ	ENCSR974NRI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-39	BGHLV22-39
Sample Name	RBM47-BGHLV22-39	RBM47-BGHLV22-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2933	6905

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
RBM47-BGHLV22-39_ATCACG_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1110	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	16300
RBM47-BGHLV22-39_ATCACG_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1110	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	16340
RBM47-BGHLV22-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1110					GRCh38	V40	RBM47-BGHLV22-39_ATCACG_L002_R1_001.fastq.gz,RBM47-BGHLV22-39_ATCACG_L002_R2_001.fastq.gz		ENCORE2	16438
RBM47-BGHLV22-39_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	1110					GRCh38	V40	RBM47-BGHLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	16478
RBM47-BGHLV22-39_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	1110					GRCh38	V40	RBM47-BGHLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	16518
RBM47-BGHLV22-39_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	1110					GRCh38	V40	RBM47-BGHLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	16558
RBM47-BGHLV22-39_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	1110					GRCh38	V40	RBM47-BGHLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	16598
RBM47-BGHLV22-39_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1110					GRCh38	V40	RBM47-BGHLV22-39_ATCACG_L002_R1_001.fastq.gz,RBM47-BGHLV22-39_ATCACG_L002_R2_001.fastq.gz		ENCORE2	16638
RBM47-BGHLV22-40_CGATGT_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1111	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	16301
RBM47-BGHLV22-40_CGATGT_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1111	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	16341
RBM47-BGHLV22-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1111					GRCh38	V40	RBM47-BGHLV22-40_CGATGT_L002_R1_001.fastq.gz,RBM47-BGHLV22-40_CGATGT_L002_R2_001.fastq.gz		ENCORE2	16439
RBM47-BGHLV22-40_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	1111					GRCh38	V40	RBM47-BGHLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	16479
RBM47-BGHLV22-40_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	1111					GRCh38	V40	RBM47-BGHLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	16519
RBM47-BGHLV22-40_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	1111					GRCh38	V40	RBM47-BGHLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	16559
RBM47-BGHLV22-40_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	1111					GRCh38	V40	RBM47-BGHLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	16599
RBM47-BGHLV22-40_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1111					GRCh38	V40	RBM47-BGHLV22-40_CGATGT_L002_R1_001.fastq.gz,RBM47-BGHLV22-40_CGATGT_L002_R2_001.fastq.gz		ENCORE2	16639