ELAVL1 RNA-Seq in K562

General Information


RBP	ELAVL1
Cell_Line	K562
Method	CRISPR
Exp_Name	ELAVL1-BGKcLV13-K562
ENCODE_series_ID	ENCSR399DMA
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR356PRP
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	ELAVL1-BGKcLV13-39
Rep2	ELAVL1-BGKcLV13-40
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	57.6
Rep2_qPCR	68.9
Rep1_WB	79.6
Rep2_WB	82.3
Antibody Cat#	MA1-167
Antibody Lot#	Lot ID SJ260797
Antibody DCC ID	ENCAB443AAH
Status	Released
Project	ENCODE4
ID	171

Experiment Information (Status: Released)

	BGKcLV13-39	BGKcLV13-40
idx	484	485
TRCN#_or_BGC#	BGC#0000322	BGC#0000322
shRNA_or_gRNA_sequence	TGTGAACTACGTGACCGCGA	TGTGAACTACGTGACCGCGA
PAM	agg	agg
Name	ELAVL1_98	ELAVL1_98
Sample_ID	BGKcLV13-39	BGKcLV13-40
transduction_Date	11/28/18	11/28/18
days	Day 6	Day 6
RBP_name	ELAVL1	ELAVL1
qPCR_result	57.6	68.9
Ave_qPCR	63.3
RT-qPCR_primer-F	gaggctccagtcaaaaacca
RT-qPCR_primer-R	agcccgctgatgtacaagtt
protein_conc	3990	4648
WB_result	79.6	82.3
Ave_WB	80.9
WB_DONE_date	1/4/19
MW	36KD
IP	mouse
antibody_Cat#	MA1-167	Lot ID SJ260797
Antibody DCC ID	ENCAB443AAH
submitted_to_DCC_date	3/11/19
Rep1_TPM	108.9	0
Rep2_TPM	105.8	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	4588	4589

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

	BGKcLV13-39	BGKcLV13-40
Sample_ID	BGKcLV13-39	BGKcLV13-40
Sample Name	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-40
Sample Name	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-40
RBP	ELAVL1	ELAVL1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2901	2902

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-39	BGKcLV13-40
Sample #	55	56
Sample Name	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-40
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	1-G1	1-H1
Tecan	49.82	43.41
Tecan_date	2019-03-18	2019-03-18
Size_bp	291	294
Peak_Molarity	42.10	27.70
libSampleQC_DNA_Well	DNA_Library_set42/set1/G7.png	DNA_Library_set42/set1/H7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set42/set1/G7.png	RNA_Library_set42/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-39	BGKcLV13-40
RBP	ELAVL1	ELAVL1
Batch_ID	BGKcLV13	BGKcLV13
WB_result	79.600	82.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	55	56

Sequencing Information

	BGKcLV13-39	BGKcLV13-40
Sample_ID	BGKcLV13-39	BGKcLV13-40
Sample Name	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-40
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	63,948,178	74,614,470
total_aligned_reads	62,213,630	72,849,840
unique_aligned_reads	56,697,778	66,458,038
percent_uniqueAligned	0.88662	0.89069
correlation_replicates	0.997614	0.997614
spikein_reads	50,686	72,938
percent_spikeins	0.00079	0.00098
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	21	22

Data Submission Information

	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-40	BGKcLV13-40	BGKcLV13-40	BGKcLV13-40
ENCODE_alias	brenton-graveley:ELAVL1-BGKcLV13	brenton-graveley:ELAVL1-BGKcLV13-39	brenton-graveley:L-ELAVL1-BGKcLV13-39	brenton-graveley:ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAVL1-BGKcLV13-K562	brenton-graveley:ELAVL1-BGKcLV13-40	brenton-graveley:L-ELAVL1-BGKcLV13-40	brenton-graveley:ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR356PRP	ENCBS929OHW	ENCLB566GTR	ENCFF652FGN	ENCFF219IGA	ENCSR399DMA	ENCBS137LOR	ENCLB471ZZN	ENCFF748RMW	ENCFF126HTE
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	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-39	BGKcLV13-40	BGKcLV13-40	BGKcLV13-40	BGKcLV13-40
Sample Name	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-39	ELAVL1-BGKcLV13-40	ELAVL1-BGKcLV13-40	ELAVL1-BGKcLV13-40	ELAVL1-BGKcLV13-40
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-BGKcLV13-39.pdf	L-ELAVL1-BGKcLV13-39.pdf				ELAVL1-BGKcLV13-40.pdf	L-ELAVL1-BGKcLV13-40.pdf
ID	778	851	933	971	1053	7210	852	934	972	1054

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-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	21	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	353
ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	21	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	435
ELAVL1-BGKcLV13-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	21					GRCh38	V40	ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23692
ELAVL1-BGKcLV13-39_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	21					GRCh38	V40	ELAVL1-BGKcLV13-39/Aligned.sortedByCoord.out.bam		ENCORE2	23774
ELAVL1-BGKcLV13-39_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	21					GRCh38	V40	ELAVL1-BGKcLV13-39/Aligned.sortedByCoord.out.bam		ENCORE2	23856
ELAVL1-BGKcLV13-39_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	21					GRCh38	V40	ELAVL1-BGKcLV13-39/Aligned.sortedByCoord.out.bam		ENCORE2	23938
ELAVL1-BGKcLV13-39_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	21					GRCh38	V40	ELAVL1-BGKcLV13-39/Aligned.sortedByCoord.out.bam		ENCORE2	24020
ELAVL1-BGKcLV13-39_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	21					GRCh38	V40	ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGKcLV13-39_AGGCAGAG+AGAATGCC_HK3H2DSXX_S55_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24102
ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	22	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	354
ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	22	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	436
ELAVL1-BGKcLV13-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	22					GRCh38	V40	ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23693
ELAVL1-BGKcLV13-40_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	22					GRCh38	V40	ELAVL1-BGKcLV13-40/Aligned.sortedByCoord.out.bam		ENCORE2	23775
ELAVL1-BGKcLV13-40_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	22					GRCh38	V40	ELAVL1-BGKcLV13-40/Aligned.sortedByCoord.out.bam		ENCORE2	23857
ELAVL1-BGKcLV13-40_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	22					GRCh38	V40	ELAVL1-BGKcLV13-40/Aligned.sortedByCoord.out.bam		ENCORE2	23939
ELAVL1-BGKcLV13-40_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	22					GRCh38	V40	ELAVL1-BGKcLV13-40/Aligned.sortedByCoord.out.bam		ENCORE2	24021
ELAVL1-BGKcLV13-40_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	22					GRCh38	V40	ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R1_001.filtered.trimmed.paired.fastq.gz,ELAVL1-BGKcLV13-40_GAATGAGA+GAGGCATT_HK3H2DSXX_S56_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24103