RBM5 RNA-Seq in HepG2

General Information


RBP	RBM5
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM5-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR610FMR
Batch_ID	BGHcLV05
Pool ID	Pool-161129
Local_Set_Name	BGHcLV05
ENCODE_KD_Exp_ID	ENCSR606PVX
ENCODE_CN_Exp_ID	ENCSR481WJH
Rep1	RBM5_BGHcLV05-23
Rep2	RBM5_BGHcLV05-24
CN1	NT_BGHcLV05-1
CN2	NT_BGHcLV05-2
Rep1_qPCR	47.8
Rep2_qPCR	59.7
Rep1_WB	95.0
Rep2_WB	81.9
Antibody Cat#	A302-228A
Antibody Lot#	A302-228A
Antibody DCC ID	ENCAB815XYC
Status	Released
Project	ENCODE3
ID	580

Experiment Information (Status: Released)

	BGHcLV05-23	BGHcLV05-23	BGHcLV05-24	BGHcLV05-24
idx	59	98	60	99
TRCN#_or_BGC#	BGC#0000042	BGC#0000042	BGC#0000042	BGC#0000042
shRNA_or_gRNA_sequence	ACTATGGTGAGCACGACTAT	ACTATGGTGAGCACGACTAT	ACTATGGTGAGCACGACTAT	ACTATGGTGAGCACGACTAT
PAM
Name	RBM5_4	RBM5_4	RBM5_4	RBM5_4
Sample_ID	BGHcLV05-23	BGHcLV05-23	BGHcLV05-24	BGHcLV05-24
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	RBM5	RBM5	RBM5	RBM5
qPCR_result	47.8		59.7
Ave_qPCR	53.8
RT-qPCR_primer-F	CCTTAGCTGAAAGGCAGCAG
RT-qPCR_primer-R	CACCAGCTCCTCCTCATTGT
protein_conc	3971	0	4067	0
WB_result	95.0		81.9
Ave_WB	88.4
WB_DONE_date	7/18/16		wes
MW	92kDa
IP	1
antibody_Cat#	A302-228A		A302-228A
Antibody DCC ID	ENCAB815XYC		ENCAB815XYC
submitted_to_DCC_date	10/26/16
Rep1_TPM	35	0	0	0
Rep2_TPM	28	0	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library
Note
ID	6202	6239	6203	6240

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM5	Product_ID: A302-228A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM5-human

Experiment Status

	BGHcLV05-23	BGHcLV05-24
Sample_ID	BGHcLV05-23	BGHcLV05-24
Sample Name	RBM5_BGHcLV05-23	RBM5_BGHcLV05-24
Sample Name	RBM5_BGHcLV05-23	RBM5_BGHcLV05-24
RBP	RBM5	RBM5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1329	1330

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-23	BGHcLV05-24
Sample #
Sample Name	RBM5-BGHcLV05-23	RBM5-BGHcLV05-24
Sample_Name_Alias	RBM5_BGHcLV05-23	RBM5_BGHcLV05-24
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-08-15	2016-08-15
Lib_ID	Lib-160815	Lib-160815
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/A2.png	DNA_Library_LV37-38/set1/B2.png
RIN	8.9	9.0
libSample_RNA_Well	RNA_Library_cLV04-05/set1/C8.png	RNA_Library_cLV04-05/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV05-23	BGHcLV05-24
RBP	RBM5	RBM5
Batch_ID	BGHcLV05	BGHcLV05
WB_result	95.000	81.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3022	3023

Sequencing Information

	BGHcLV05-23	BGHcLV05-24
Sample_ID	BGHcLV05-23	BGHcLV05-24
Sample Name	RBM5_BGHcLV05-23	RBM5_BGHcLV05-24
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	BGHcLV05	BGHcLV05
total_reads	29,291,728	36,153,226
total_aligned_reads	20,093,240	26,253,392
unique_aligned_reads	18,732,636	24,724,318
percent_uniqueAligned	0.63952	0.68388
correlation_replicates	0.986132	0.986132
spikein_reads	26,334	51,290
percent_spikeins	0.00090	0.00142
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1675	1676

Data Submission Information

	BGHcLV05-23	BGHcLV05-23
ENCODE_alias	brenton-graveley:RBM5_BGHcLV05	brenton-graveley:RBM5-BGHcLV05-HepG2
ENCODE_accession	ENCSR606PVX	ENCSR610FMR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV05-23	BGHcLV05-23
Sample Name	RBM5_BGHcLV05-23	RBM5_BGHcLV05-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-12	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3204	6906

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
RBM5_BGHcLV05-23_ATCACG_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1675	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23144
RBM5_BGHcLV05-23_ATCACG_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1675	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23156
RBM5_BGHcLV05-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1675					GRCh38	V40	RBM5_BGHcLV05-23_ATCACG_L003_001.R1.fastq.gz,RBM5_BGHcLV05-23_ATCACG_L003_001.R2.fastq.gz		ENCORE2	23168
RBM5_BGHcLV05-23_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1675					GRCh38	V40	RBM5_BGHcLV05-23/Aligned.sortedByCoord.out.bam		ENCORE2	23180
RBM5_BGHcLV05-23_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1675					GRCh38	V40	RBM5_BGHcLV05-23/Aligned.sortedByCoord.out.bam		ENCORE2	23192
RBM5_BGHcLV05-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1675					GRCh38	V40	RBM5_BGHcLV05-23/Aligned.sortedByCoord.out.bam		ENCORE2	23204
RBM5_BGHcLV05-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1675					GRCh38	V40	RBM5_BGHcLV05-23/Aligned.sortedByCoord.out.bam		ENCORE2	23216
RBM5_BGHcLV05-23_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1675					GRCh38	V40	RBM5_BGHcLV05-23_ATCACG_L003_001.R1.fastq.gz,RBM5_BGHcLV05-23_ATCACG_L003_001.R2.fastq.gz		ENCORE2	23228
RBM5_BGHcLV05-24_CGATGT_L003_001.R1.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1676	HiSeq2500	100	paired-ended	1				NT_BGHcLV05-1_GATCAG_L002_001.R1.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R1.fastq.gz	ENCODE3	23145
RBM5_BGHcLV05-24_CGATGT_L003_001.R2.fastq.gz	ENCODE_DATA/BGHcLV05/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1676	HiSeq2500	100	paired-ended	2				NT_BGHcLV05-1_GATCAG_L002_001.R2.fastq.gz,NT_BGHcLV05-2_TAGCTT_L002_001.R2.fastq.gz	ENCODE3	23157
RBM5_BGHcLV05-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1676					GRCh38	V40	RBM5_BGHcLV05-24_CGATGT_L003_001.R1.fastq.gz,RBM5_BGHcLV05-24_CGATGT_L003_001.R2.fastq.gz		ENCORE2	23169
RBM5_BGHcLV05-24_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1676					GRCh38	V40	RBM5_BGHcLV05-24/Aligned.sortedByCoord.out.bam		ENCORE2	23181
RBM5_BGHcLV05-24_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1676					GRCh38	V40	RBM5_BGHcLV05-24/Aligned.sortedByCoord.out.bam		ENCORE2	23193
RBM5_BGHcLV05-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1676					GRCh38	V40	RBM5_BGHcLV05-24/Aligned.sortedByCoord.out.bam		ENCORE2	23205
RBM5_BGHcLV05-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV05/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1676					GRCh38	V40	RBM5_BGHcLV05-24/Aligned.sortedByCoord.out.bam		ENCORE2	23217
RBM5_BGHcLV05-24_quant.sf	ENCODE_DATA/BGHcLV05/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1676					GRCh38	V40	RBM5_BGHcLV05-24_CGATGT_L003_001.R1.fastq.gz,RBM5_BGHcLV05-24_CGATGT_L003_001.R2.fastq.gz		ENCORE2	23229