ELAVL1 RNA-Seq in HepG2

General Information


RBP	ELAVL1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ELAVL1-BGHcLV14-HepG2
ENCODE_series_ID	ENCSR993BQJ
Batch_ID	BGHcLV14
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR659DRE
ENCODE_CN_Exp_ID	ENCSR750CPT
Rep1	ELAVL1-BGHcLV14-39
Rep2	ELAVL1-BGHcLV14-40
CN1	NT-BGHcLV14-1
CN2	NT-BGHcLV14-2
Rep1_qPCR	65.6
Rep2_qPCR	63.8
Rep1_WB	57.3
Rep2_WB	57.8
Antibody Cat#	MA1-167
Antibody Lot#	Lot ID SJ260797
Antibody DCC ID	ENCAB443AAH
Status	Released
Project	ENCODE4
ID	170

Experiment Information (Status: Released)

	BGHcLV14-39	BGHcLV14-40
idx	394	395
TRCN#_or_BGC#	BGC#0000322	BGC#0000322
shRNA_or_gRNA_sequence	TGTGAACTACGTGACCGCGA	TGTGAACTACGTGACCGCGA
PAM	agg	agg
Name	ELAVL1_98	ELAVL1_98
Sample_ID	BGHcLV14-39	BGHcLV14-40
transduction_Date	12/5/18	12/5/18
days	D6	D6
RBP_name	ELAVL1	ELAVL1
qPCR_result	65.6	63.8
Ave_qPCR	64.7
RT-qPCR_primer-F	gaggctccagtcaaaaacca
RT-qPCR_primer-R	agcccgctgatgtacaagtt
protein_conc	3288	3131
WB_result	57.3	57.8
Ave_WB	57.5
WB_DONE_date	1/10/19	wes
MW	36KD
IP	mouse
antibody_Cat#	MA1-167	Lot ID SJ260797
Antibody DCC ID	ENCAB443AAH
submitted_to_DCC_date	3/11/19
Rep1_TPM	85	0
Rep2_TPM	70	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	8587	8588

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ELAVL1	Product_ID: MA1-167 Lot_ID: SJ260797 Source: Thermo Fisher Target Name: ELAVL1-human

Experiment Status

	BGHcLV14-39	BGHcLV14-40
Sample_ID	BGHcLV14-39	BGHcLV14-40
Sample Name	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-40
Sample Name	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-40
RBP	ELAVL1	ELAVL1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2981	2982

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV14-39	BGHcLV14-40
Sample #	75	76
Sample Name	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-40
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	2-C2	2-D2
Tecan	60.97	68.88
Tecan_date	2019-03-18	2019-03-18
Size_bp	284	283
Peak_Molarity	53.60	65.30
libSampleQC_DNA_Well	DNA_Library_set42/set1/C10.png	DNA_Library_set42/set1/D10.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set42/set1/C10.png	RNA_Library_set42/set1/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGHcLV14-39	BGHcLV14-40
RBP	ELAVL1	ELAVL1
Batch_ID	BGHcLV14	BGHcLV14
WB_result	57.300	57.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	75	76

Sequencing Information

	BGHcLV14-39	BGHcLV14-40
Sample_ID	BGHcLV14-39	BGHcLV14-40
Sample Name	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-40
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	56,419,676	42,304,756
total_aligned_reads	52,852,316	39,004,286
unique_aligned_reads	49,717,260	36,731,482
percent_uniqueAligned	0.88120	0.86826
correlation_replicates	0.999195	0.999195
spikein_reads	45,850	43,188
percent_spikeins	0.00081	0.00102
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	19	20

Data Submission Information

	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-40	BGHcLV14-40	BGHcLV14-40	BGHcLV14-40
ENCODE_alias	brenton-graveley:ELAVL1-BGHcLV14	brenton-graveley:ELAVL1-BGHcLV14-39	brenton-graveley:L-ELAVL1-BGHcLV14-39	brenton-graveley:ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAVL1-BGHcLV14-HepG2	brenton-graveley:ELAVL1-BGHcLV14-40	brenton-graveley:L-ELAVL1-BGHcLV14-40	brenton-graveley:ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR659DRE	ENCBS834AUG	ENCLB607GKN	ENCFF381BKH	ENCFF782BGX	ENCSR993BQJ	ENCBS777RCK	ENCLB195DSL	ENCFF746EGR	ENCFF674ZLX
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-39	BGHcLV14-40	BGHcLV14-40	BGHcLV14-40	BGHcLV14-40
Sample Name	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-39	ELAVL1-BGHcLV14-40	ELAVL1-BGHcLV14-40	ELAVL1-BGHcLV14-40	ELAVL1-BGHcLV14-40
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		ELAVL1-BGHcLV14-39.pdf	L-ELAVL1-BGHcLV14-39.pdf				ELAVL1-BGHcLV14-40.pdf	L-ELAVL1-BGHcLV14-40.pdf
ID	756	807	889	969	1051	7209	808	890	970	1052

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
ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	19	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	351
ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	19	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	433
ELAVL1-BGHcLV14-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	19					GRCh38	V40	ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23690
ELAVL1-BGHcLV14-39_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	19					GRCh38	V40	ELAVL1-BGHcLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	23772
ELAVL1-BGHcLV14-39_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	19					GRCh38	V40	ELAVL1-BGHcLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	23854
ELAVL1-BGHcLV14-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	19					GRCh38	V40	ELAVL1-BGHcLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	23936
ELAVL1-BGHcLV14-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	19					GRCh38	V40	ELAVL1-BGHcLV14-39/Aligned.sortedByCoord.out.bam		ENCORE2	24018
ELAVL1-BGHcLV14-39_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	19					GRCh38	V40	ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGHcLV14-39_AGTACTCC+AACCTGTT_HK3H2DSXX_S75_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24100
ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	20	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	352
ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	20	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	434
ELAVL1-BGHcLV14-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	20					GRCh38	V40	ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23691
ELAVL1-BGHcLV14-40_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	20					GRCh38	V40	ELAVL1-BGHcLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	23773
ELAVL1-BGHcLV14-40_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	20					GRCh38	V40	ELAVL1-BGHcLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	23855
ELAVL1-BGHcLV14-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	20					GRCh38	V40	ELAVL1-BGHcLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	23937
ELAVL1-BGHcLV14-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	20					GRCh38	V40	ELAVL1-BGHcLV14-40/Aligned.sortedByCoord.out.bam		ENCORE2	24019
ELAVL1-BGHcLV14-40_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	20					GRCh38	V40	ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGHcLV14-40_GACGTCTT+GGTTCACC_HK3H2DSXX_S76_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24101