RBM34 RNA-Seq in HepG2

General Information


RBP	RBM34
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM34-BGHLV14-HepG2
ENCODE_series_ID	ENCSR070SVE
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR318HAT
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	RBM34_BGHLV14-39
Rep2	RBM34_BGHLV14-40
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	87.3
Rep2_qPCR	83.7
Rep1_WB	99.5
Rep2_WB	99.2
Antibody Cat#	A302-293A
Antibody Lot#	A302-293A
Antibody DCC ID	ENCAB594ZFC
Status	Released
Project	ENCODE3
ID	400

Experiment Information (Status: Released)

	BGHLV14-39	BGHLV14-40
idx	135	136
TRCN#_or_BGC#	TRCN0000147509	TRCN0000147509
shRNA_or_gRNA_sequence	GCTATGTGCTCTTTGAGAATA	GCTATGTGCTCTTTGAGAATA
PAM
Name	RBM34	RBM34
Sample_ID	BGHLV14-39	BGHLV14-40
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	RBM34	RBM34
qPCR_result	87.3	83.7
Ave_qPCR	85.5
RT-qPCR_primer-F	ATGACAGGCATCGGCAAAG
RT-qPCR_primer-R	TCAGAATTATTTAATTTCAGAGCAAGA
protein_conc	4585	3528
WB_result	99.5	99.2
Ave_WB	99.4
WB_DONE_date	3/19/2015
MW	48kDa
IP	1	1
antibody_Cat#	A302-293A	A302-293A
Antibody DCC ID	ENCAB594ZFC	ENCAB594ZFC
submitted_to_DCC_date	4/2/2015
Rep1_TPM	52.8	0
Rep2_TPM	44.2	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2194	2195

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM34	Product_ID: A302-293A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM34-human

Experiment Status

	BGHLV14-39	BGHLV14-40
Sample_ID	BGHLV14-39	BGHLV14-40
Sample Name	RBM34_BGHLV14-39	RBM34_BGHLV14-40
Sample Name	RBM34_BGHLV14-39	RBM34_BGHLV14-40
RBP	RBM34	RBM34
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	526	527

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-39	BGHLV14-40
Sample #
Sample Name	RBM34-BGHLV14-39	RBM34-BGHLV14-40
Sample_Name_Alias	RBM34_BGHLV14-39	RBM34_BGHLV14-40
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B12.png	DNA_Library_LV13-14/set1/C12.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C8.png	RNA_Library_LV13-14-16/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-39	BGHLV14-40
RBP	RBM34	RBM34
Batch_ID	BGHLV14	BGHLV14
WB_result	99.500	99.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2208	2209

Sequencing Information

	BGHLV14-39	BGHLV14-40
Sample_ID	BGHLV14-39	BGHLV14-40
Sample Name	RBM34_BGHLV14-39	RBM34_BGHLV14-40
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	52,080,000	49,110,000
total_aligned_reads	47,983,592	45,074,600
unique_aligned_reads	45,327,918	42,559,982
percent_uniqueAligned	0.87035	0.86663
correlation_replicates	0.998075	0.998075
spikein_reads	258,718	420,000
percent_spikeins	0.00497	0.00855
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	850	851

Data Submission Information

	BGHLV14-39	BGHLV14-39
ENCODE_alias	brenton-graveley:RBM34_BGHLV14	brenton-graveley:RBM34-BGHLV14-HepG2
ENCODE_accession	ENCSR318HAT	ENCSR070SVE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-39	BGHLV14-39
Sample Name	RBM34_BGHLV14-39	RBM34_BGHLV14-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2812	6901

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
RBM34_BGHLV14-39_GTCCGC_L005_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	850	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13818
RBM34_BGHLV14-39_GTCCGC_L005_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	850	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13880
RBM34_BGHLV14-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	850					GRCh38	V40	RBM34_BGHLV14-39_GTCCGC_L005_R1_001.fastq.gz,RBM34_BGHLV14-39_GTCCGC_L005_R2_001.fastq.gz		ENCORE2	13942
RBM34_BGHLV14-39_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	850					GRCh38	V40	RBM34_BGHLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	14004
RBM34_BGHLV14-39_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	850					GRCh38	V40	RBM34_BGHLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	14066
RBM34_BGHLV14-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	850					GRCh38	V40	RBM34_BGHLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	14128
RBM34_BGHLV14-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	850					GRCh38	V40	RBM34_BGHLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	14190
RBM34_BGHLV14-39_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	850					GRCh38	V40	RBM34_BGHLV14-39_GTCCGC_L005_R1_001.fastq.gz,RBM34_BGHLV14-39_GTCCGC_L005_R2_001.fastq.gz		ENCORE2	14252
RBM34_BGHLV14-40_GTGAAA_L005_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	851	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13819
RBM34_BGHLV14-40_GTGAAA_L005_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	851	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13881
RBM34_BGHLV14-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	851					GRCh38	V40	RBM34_BGHLV14-40_GTGAAA_L005_R1_001.fastq.gz,RBM34_BGHLV14-40_GTGAAA_L005_R2_001.fastq.gz		ENCORE2	13943
RBM34_BGHLV14-40_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	851					GRCh38	V40	RBM34_BGHLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	14005
RBM34_BGHLV14-40_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	851					GRCh38	V40	RBM34_BGHLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	14067
RBM34_BGHLV14-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	851					GRCh38	V40	RBM34_BGHLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	14129
RBM34_BGHLV14-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	851					GRCh38	V40	RBM34_BGHLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	14191
RBM34_BGHLV14-40_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	851					GRCh38	V40	RBM34_BGHLV14-40_GTGAAA_L005_R1_001.fastq.gz,RBM34_BGHLV14-40_GTGAAA_L005_R2_001.fastq.gz		ENCORE2	14253