RBM15 RNA-Seq in HepG2

General Information


RBP	RBM15
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM15-BGHLV31-HepG2
ENCODE_series_ID	ENCSR000OWF
Batch_ID	BGHLV31
Pool ID	Pool-160425
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR599PXD
ENCODE_CN_Exp_ID	ENCSR585KOJ
Rep1	RBM15_BGHLV31-53B
Rep2	RBM15_BGHLV31-54B
CN1	NT_BGHLV31-1B
CN2	NT_BGHLV31-2B
Rep1_qPCR	74.6
Rep2_qPCR	63.3
Rep1_WB	70.0
Rep2_WB	71.8
Antibody Cat#	A300-821A
Antibody Lot#	A300-821A
Antibody DCC ID	ENCAB626AJI
Status	Released
Project	ENCODE3
ID	701

Experiment Information (Status: Released)

	BGHLV31-53	BGHLV31-54
idx	801	802
TRCN#_or_BGC#	TRCN0000074707	TRCN0000074707
shRNA_or_gRNA_sequence	GATCGTTACAACAGCGACAAT	GATCGTTACAACAGCGACAAT
PAM
Name	RBM15	RBM15
Sample_ID	BGHLV31-53	BGHLV31-54
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	RBM15	RBM15
qPCR_result	74.6	63.3
Ave_qPCR	68.9
RT-qPCR_primer-F	TGAGTTCTCCCAGCAGTTCCT
RT-qPCR_primer-R	GCTGTTCAACCAGTTTTGCAC
protein_conc	4873	4280
WB_result	70.0	71.8
Ave_WB	70.9
WB_DONE_date	2/8/2016
MW	107kDa	WES
IP	1	1
antibody_Cat#	A300-821A	A300-821A
Antibody DCC ID	ENCAB626AJI	ENCAB626AJI
submitted_to_DCC_date	3/8/2016
Rep1_TPM	2.1	0
Rep2_TPM	3.4	0
Action
Library_start_date	3/10/2016	3/10/2016
repeat_library
Note
ID	2890	2891

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM15	Product_ID: A300-821A Lot_ID: 2 Source: Bethyl Labs Target Name: RBM15-human

Experiment Status

	BGHLV31-53	BGHLV31-54
Sample_ID	BGHLV31-53	BGHLV31-54
Sample Name	RBM15_BGHLV31-53B	RBM15_BGHLV31-54B
Sample Name	RBM15_BGHLV31-53B	RBM15_BGHLV31-54B
RBP	RBM15	RBM15
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1185	1186

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-53	BGHLV31-54
Sample #
Sample Name	RBM15-BGHLV31-53B	RBM15-BGHLV31-54B
Sample_Name_Alias	RBM15_BGHLV31-53B	RBM15_BGHLV31-54B
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/G12.png	DNA_Library_LV33-34-25B-32/set1/H12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G10.png	RNA_Library_LV29-30-31-32/set1/H10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-53	BGHLV31-54
RBP	RBM15	RBM15
Batch_ID	BGHLV31	BGHLV31
WB_result	70.000	71.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2870	2871

Sequencing Information

	BGHLV31-53	BGHLV31-54
Sample_ID	BGHLV31-53	BGHLV31-54
Sample Name	RBM15_BGHLV31-53B	RBM15_BGHLV31-54B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set31	set31
total_reads	85,176,022	157,845,610
total_aligned_reads	62,643,500	115,872,934
unique_aligned_reads	58,957,506	108,712,464
percent_uniqueAligned	0.69218	0.68873
correlation_replicates	0.998219	0.998219
spikein_reads	125,416	262,592
percent_spikeins	0.00147	0.00166
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1519	1520

Data Submission Information

	BGHLV31-53	BGHLV31-53
ENCODE_alias	brenton-graveley:RBM15_BGHLV31	brenton-graveley:RBM15-BGHLV31-HepG2
ENCODE_accession	ENCSR599PXD	ENCSR000OWF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-53	BGHLV31-53
Sample Name	RBM15_BGHLV31-53B	RBM15_BGHLV31-53B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3132	6892

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
RBM15_BGHLV31-53B_CGTACG_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1519	HiSeq2500	100	paired-ended	1				NT_BGHLV31-1B_GTGGCC_L007_001.R1.fastq.gz,NT_BGHLV31-2B_GTTTCG_L007_001.R1.fastq.gz	ENCODE3	20994
RBM15_BGHLV31-53B_CGTACG_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1519	HiSeq2500	100	paired-ended	2				NT_BGHLV31-1B_GTGGCC_L007_001.R2.fastq.gz,NT_BGHLV31-2B_GTTTCG_L007_001.R2.fastq.gz	ENCODE3	21020
RBM15_BGHLV31-53B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1519					GRCh38	V40	RBM15_BGHLV31-53B_CGTACG_L007_001.R1.fastq.gz,RBM15_BGHLV31-53B_CGTACG_L007_001.R2.fastq.gz		ENCORE2	21054
RBM15_BGHLV31-53B_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1519					GRCh38	V40	RBM15_BGHLV31-53B/Aligned.sortedByCoord.out.bam		ENCORE2	21080
RBM15_BGHLV31-53B_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1519					GRCh38	V40	RBM15_BGHLV31-53B/Aligned.sortedByCoord.out.bam		ENCORE2	21106
RBM15_BGHLV31-53B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1519					GRCh38	V40	RBM15_BGHLV31-53B/Aligned.sortedByCoord.out.bam		ENCORE2	21132
RBM15_BGHLV31-53B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1519					GRCh38	V40	RBM15_BGHLV31-53B/Aligned.sortedByCoord.out.bam		ENCORE2	21158
RBM15_BGHLV31-53B_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1519					GRCh38	V40	RBM15_BGHLV31-53B_CGTACG_L007_001.R1.fastq.gz,RBM15_BGHLV31-53B_CGTACG_L007_001.R2.fastq.gz		ENCORE2	21184
RBM15_BGHLV31-54B_GAGTGG_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1520	HiSeq2500	100	paired-ended	1				NT_BGHLV31-1B_GTGGCC_L007_001.R1.fastq.gz,NT_BGHLV31-2B_GTTTCG_L007_001.R1.fastq.gz	ENCODE3	20995
RBM15_BGHLV31-54B_GAGTGG_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1520	HiSeq2500	100	paired-ended	2				NT_BGHLV31-1B_GTGGCC_L007_001.R2.fastq.gz,NT_BGHLV31-2B_GTTTCG_L007_001.R2.fastq.gz	ENCODE3	21021
RBM15_BGHLV31-54B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1520					GRCh38	V40	RBM15_BGHLV31-54B_GAGTGG_L007_001.R1.fastq.gz,RBM15_BGHLV31-54B_GAGTGG_L007_001.R2.fastq.gz		ENCORE2	21055
RBM15_BGHLV31-54B_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1520					GRCh38	V40	RBM15_BGHLV31-54B/Aligned.sortedByCoord.out.bam		ENCORE2	21081
RBM15_BGHLV31-54B_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1520					GRCh38	V40	RBM15_BGHLV31-54B/Aligned.sortedByCoord.out.bam		ENCORE2	21107
RBM15_BGHLV31-54B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1520					GRCh38	V40	RBM15_BGHLV31-54B/Aligned.sortedByCoord.out.bam		ENCORE2	21133
RBM15_BGHLV31-54B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1520					GRCh38	V40	RBM15_BGHLV31-54B/Aligned.sortedByCoord.out.bam		ENCORE2	21159
RBM15_BGHLV31-54B_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1520					GRCh38	V40	RBM15_BGHLV31-54B_GAGTGG_L007_001.R1.fastq.gz,RBM15_BGHLV31-54B_GAGTGG_L007_001.R2.fastq.gz		ENCORE2	21185