RBM25 RNA-Seq in HepG2

General Information


RBP	RBM25
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM25-BGHLV12-HepG2
ENCODE_series_ID	ENCSR934EHD
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR610AEI
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	RBM25-BGHLV12-65
Rep2	RBM25-BGHLV12-66
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	78.0
Rep2_qPCR	82.9
Rep1_WB	85.5
Rep2_WB	78.3
Antibody Cat#	A301-068A
Antibody Lot#	A301-068A
Antibody DCC ID	ENCAB626AJI
Status	Released
Project	ENCODE3
ID	350

Experiment Information (Status: Released)

	BGHLV12-65	BGHLV12-66
idx	65	66
TRCN#_or_BGC#	TRCN0000074750	TRCN0000074750
shRNA_or_gRNA_sequence	GCGCCTTAAGAATTGGGAAAT	GCGCCTTAAGAATTGGGAAAT
PAM
Name	RBM25	RBM25
Sample_ID	BGHLV12-65	BGHLV12-66
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	RBM25	RBM25
qPCR_result	78.0	82.9
Ave_qPCR	80.5
RT-qPCR_primer-F	GAATTCTTAGAAGACTATGATGATGA
RT-qPCR_primer-R	TTTCTCTATCACGCAACCTTT
protein_conc	4123	4647
WB_result	85.5	78.3
Ave_WB	81.9
WB_DONE_date	2/22/2016
MW	100kDa	WES
IP	1	fu's
antibody_Cat#	A301-068A	A301-068A
Antibody DCC ID	ENCAB626AJI	ENCAB626AJI
submitted_to_DCC_date	3/8/2016
Rep1_TPM	31.8	0
Rep2_TPM	28.4	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2118	2119

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM25	Product_ID: A301-068A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM25-human

Experiment Status

	BGHLV12-65	BGHLV12-66
Sample_ID	BGHLV12-65	BGHLV12-66
Sample Name	RBM25-BGHLV12-65	RBM25-BGHLV12-66
Sample Name	RBM25-BGHLV12-65	RBM25-BGHLV12-66
RBP	RBM25	RBM25
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	420	421

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-65	BGHLV12-66
Sample #
Sample Name	RBM25-BGHLV12-65	RBM25-BGHLV12-66
Sample_Name_Alias	RBM25-BGHLV12-65	RBM25-BGHLV12-66
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/A3.png	DNA_Library_LV12/set3/B3.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV12/set1/A7.png	RNA_Library_LV12/set1/B7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-65	BGHLV12-66
RBP	RBM25	RBM25
Batch_ID	BGHLV12	BGHLV12
WB_result	85.500	78.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2044	2045

Sequencing Information

	BGHLV12-65	BGHLV12-66
Sample_ID	BGHLV12-65	BGHLV12-66
Sample Name	RBM25-BGHLV12-65	RBM25-BGHLV12-66
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	70,290,000	70,200,000
total_aligned_reads	63,929,668	62,096,234
unique_aligned_reads	60,767,356	58,937,904
percent_uniqueAligned	0.86452	0.83957
correlation_replicates	0.996529	0.996529
spikein_reads	655,214	614,418
percent_spikeins	0.00932	0.00875
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	742	743

Data Submission Information

	BGHLV12-65	BGHLV12-65
ENCODE_alias	brenton-graveley:RBM25-BGHLV12	brenton-graveley:RBM25-BGHLV12-HepG2
ENCODE_accession	ENCSR610AEI	ENCSR934EHD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-65	BGHLV12-65
Sample Name	RBM25-BGHLV12-65	RBM25-BGHLV12-65
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2759	6898

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
RBM25-BGHLV12-65_ATCACG_L007_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	742	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12803
RBM25-BGHLV12-65_ATCACG_L007_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	742	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12872
RBM25-BGHLV12-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	742					GRCh38	V40	RBM25-BGHLV12-65_ATCACG_L007_R1_001.fastq.gz,RBM25-BGHLV12-65_ATCACG_L007_R2_001.fastq.gz		ENCORE2	12942
RBM25-BGHLV12-65_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	742					GRCh38	V40	RBM25-BGHLV12-65/Aligned.sortedByCoord.out.bam		ENCORE2	13012
RBM25-BGHLV12-65_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	742					GRCh38	V40	RBM25-BGHLV12-65/Aligned.sortedByCoord.out.bam		ENCORE2	13082
RBM25-BGHLV12-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	742					GRCh38	V40	RBM25-BGHLV12-65/Aligned.sortedByCoord.out.bam		ENCORE2	13152
RBM25-BGHLV12-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	742					GRCh38	V40	RBM25-BGHLV12-65/Aligned.sortedByCoord.out.bam		ENCORE2	13222
RBM25-BGHLV12-65_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	742					GRCh38	V40	RBM25-BGHLV12-65_ATCACG_L007_R1_001.fastq.gz,RBM25-BGHLV12-65_ATCACG_L007_R2_001.fastq.gz		ENCORE2	13292
RBM25-BGHLV12-66_CGATGT_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	743	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12804
RBM25-BGHLV12-66_CGATGT_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	743	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12873
RBM25-BGHLV12-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	743					GRCh38	V40	RBM25-BGHLV12-66_CGATGT_L008_R1_001.fastq.gz,RBM25-BGHLV12-66_CGATGT_L008_R2_001.fastq.gz		ENCORE2	12943
RBM25-BGHLV12-66_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	743					GRCh38	V40	RBM25-BGHLV12-66/Aligned.sortedByCoord.out.bam		ENCORE2	13013
RBM25-BGHLV12-66_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	743					GRCh38	V40	RBM25-BGHLV12-66/Aligned.sortedByCoord.out.bam		ENCORE2	13083
RBM25-BGHLV12-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	743					GRCh38	V40	RBM25-BGHLV12-66/Aligned.sortedByCoord.out.bam		ENCORE2	13153
RBM25-BGHLV12-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	743					GRCh38	V40	RBM25-BGHLV12-66/Aligned.sortedByCoord.out.bam		ENCORE2	13223
RBM25-BGHLV12-66_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	743					GRCh38	V40	RBM25-BGHLV12-66_CGATGT_L008_R1_001.fastq.gz,RBM25-BGHLV12-66_CGATGT_L008_R2_001.fastq.gz		ENCORE2	13293