ELAC2 RNA-Seq in K562

General Information


RBP	ELAC2
Cell_Line	K562
Method	CRISPR
Exp_Name	ELAC2-BGKcLV23-K562
ENCODE_series_ID	ENCSR064KZR
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR715GSX
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	ELAC2-BGKcLV23-41
Rep2	ELAC2-BGKcLV23-42
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	86.3
Rep2_WB	83.5
Antibody Cat#	PA5-78553
Antibody Lot#	LOT# UK2881508
Antibody DCC ID	ENCAB519QXK
Status	Released
Project	ENCODE4
ID	30

Experiment Information (Status: Released)

	BGKcLV23-41	BGKcLV23-42
idx	827	828
TRCN#_or_BGC#	BGC#0000575	BGC#0000575
shRNA_or_gRNA_sequence	GCAGGGGGAAGATGTCCGGG	GCAGGGGGAAGATGTCCGGG
PAM	TGG	TGG
Name	ELAC2_73	ELAC2_73
Sample_ID	BGKcLV23-41	BGKcLV23-42
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	ELAC2	ELAC2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GCAGAGCGTGCAGGAGTACA
RT-qPCR_primer-R	CATTTCGAATCTTCATCGGG
protein_conc	2019	2521
WB_result	86.3	83.5
Ave_WB	84.9
WB_DONE_date	9/24/20	jess
MW	92kd
IP	Rabbit / I
antibody_Cat#	PA5-78553	LOT# UK2881508
Antibody DCC ID	ENCAB519QXK
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4951	4952

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ELAC2	Product_ID: PA5-78553 Lot_ID: UK2881508 Source: Thermo Fisher Target Name: ELAC2-human

Experiment Status

	BGKcLV23-41	BGKcLV23-42
Sample_ID	BGKcLV23-41	BGKcLV23-42
Sample Name
Sample Name	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-42
RBP	ELAC2	ELAC2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7449	7450

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-41	BGKcLV23-42
Sample #	51	52
Sample Name	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-42
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	290	293
Peak_Molarity	105.00	98.70
libSampleQC_DNA_Well	DNA_Library_set46/set1/C7.png	DNA_Library_set46/set1/D7.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_set46/set2/C11.png	RNA_Library_set46/set2/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-41	BGKcLV23-42
RBP	ELAC2	ELAC2
Batch_ID	BGKcLV23	BGKcLV23
WB_result	86.300	83.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1426	1427

Sequencing Information

	BGKcLV23-41	BGKcLV23-42
Sample_ID	BGKcLV23-41	BGKcLV23-42
Sample Name	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-42
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	175,374,264	160,536,422
total_aligned_reads	161,354,824	149,553,500
unique_aligned_reads	145,747,918	135,359,392
percent_uniqueAligned	0.83107	0.84317
correlation_replicates	0.997951	0.997951
spikein_reads	84,602	42,950
percent_spikeins	0.00048	0.00027
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	532	533

Data Submission Information

	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-42	BGKcLV23-42	BGKcLV23-42	BGKcLV23-42
ENCODE_alias	brenton-graveley:ELAC2-BGKcLV23	brenton-graveley:ELAC2-BGKcLV23-41	brenton-graveley:L-ELAC2-BGKcLV23-41	brenton-graveley:ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAC2-BGKcLV23-K562	brenton-graveley:ELAC2-BGKcLV23-42	brenton-graveley:L-ELAC2-BGKcLV23-42	brenton-graveley:ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR715GSX	ENCBS669IHM	ENCLB940PEV	ENCFF930LSL	ENCFF241JFB	ENCSR064KZR	ENCBS813KFP	ENCLB515PZV	ENCFF596OXV	ENCFF884TLM
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	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-41	BGKcLV23-42	BGKcLV23-42	BGKcLV23-42	BGKcLV23-42
Sample Name	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-41	ELAC2-BGKcLV23-42	ELAC2-BGKcLV23-42	ELAC2-BGKcLV23-42	ELAC2-BGKcLV23-42
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		ELAC2-BGKcLV23-41.pdf	L-ELAC2-BGKcLV23-41.pdf				ELAC2-BGKcLV23-42.pdf	L-ELAC2-BGKcLV23-42.pdf
ID	2420	2477	2541	2635	2669	7208	2478	2542	2636	2670

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
ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	532	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1396
ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	532	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1460
ELAC2-BGKcLV23-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	532					GRCh38	V40	ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25299
ELAC2-BGKcLV23-41_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	532					GRCh38	V40	ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGKcLV23-41_AACAGGTT+CTTGGTAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25333
ELAC2-BGKcLV23-41_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	532					GRCh38	V40	ELAC2-BGKcLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	26137
ELAC2-BGKcLV23-41_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	532					GRCh38	V40	ELAC2-BGKcLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	26171
ELAC2-BGKcLV23-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	532					GRCh38	V40	ELAC2-BGKcLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	26205
ELAC2-BGKcLV23-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	532					GRCh38	V40	ELAC2-BGKcLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	26239
ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	533	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1397
ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	533	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1461
ELAC2-BGKcLV23-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	533					GRCh38	V40	ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25300
ELAC2-BGKcLV23-42_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	533					GRCh38	V40	ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGKcLV23-42_GGTGAACC+TCCAACGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25334
ELAC2-BGKcLV23-42_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	533					GRCh38	V40	ELAC2-BGKcLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	26138
ELAC2-BGKcLV23-42_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	533					GRCh38	V40	ELAC2-BGKcLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	26172
ELAC2-BGKcLV23-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	533					GRCh38	V40	ELAC2-BGKcLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	26206
ELAC2-BGKcLV23-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	533					GRCh38	V40	ELAC2-BGKcLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	26240