ELAC2 RNA-Seq in HepG2

General Information


RBP	ELAC2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ELAC2-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR546QKI
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR511EKJ
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	ELAC2-BGHcLV24-31
Rep2	ELAC2-BGHcLV24-32
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	81.0
Rep2_WB	83.0
Antibody Cat#	PA5-78553
Antibody Lot#	LOT# UK2881508
Antibody DCC ID	ENCAB519QXK
Status	Released
Project	ENCODE4
ID	8

Experiment Information (Status: Released)

	BGHcLV24-31	BGHcLV24-32
idx	689	690
TRCN#_or_BGC#	BGC#0000575	BGC#0000575
shRNA_or_gRNA_sequence	GCAGGGGGAAGATGTCCGGG	GCAGGGGGAAGATGTCCGGG
PAM	TGG	TGG
Name	ELAC2_73	ELAC2_73
Sample_ID	BGHcLV24-31	BGHcLV24-32
transduction_Date	10/30/20	10/30/20
days	D6	D6
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	4905	5465
WB_result	81.0	83.0
Ave_WB	82.0
WB_DONE_date	11/12/20	JESS
MW	92kd
IP	Rabbit / I
antibody_Cat#	PA5-78553	LOT# UK2881508
Antibody DCC ID	ENCAB519QXK
submitted_to_DCC_date	12/09/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6844	6845

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

	BGHcLV24-31	BGHcLV24-32
Sample_ID	BGHcLV24-31	BGHcLV24-32
Sample Name
Sample Name	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-32
RBP	ELAC2	ELAC2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7795	7796

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-31	BGHcLV24-32
Sample #	17	18
Sample Name	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-32
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	302	312
Peak_Molarity	81.50	72.80
libSampleQC_DNA_Well	DNA_Library_set47/set1/A6.png	DNA_Library_set47/set1/B6.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set47/set1/A3.png	RNA_Library_set47/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-31	BGHcLV24-32
RBP	ELAC2	ELAC2
Batch_ID	BGHcLV24	BGHcLV24
WB_result	81.000	83.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1480	1481

Sequencing Information

	BGHcLV24-31	BGHcLV24-32
Sample_ID	BGHcLV24-31	BGHcLV24-32
Sample Name	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-32
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	112,262,918	100,354,166
total_aligned_reads	99,161,190	91,265,010
unique_aligned_reads	93,487,536	86,102,276
percent_uniqueAligned	0.83276	0.85798
correlation_replicates	0.998831	0.998831
spikein_reads	70,440	48,114
percent_spikeins	0.00063	0.00048
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	562	563

Data Submission Information

	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-32	BGHcLV24-32	BGHcLV24-32	BGHcLV24-32
ENCODE_alias	brenton-graveley:ELAC2-BGHcLV24	brenton-graveley:ELAC2-BGHcLV24-31	brenton-graveley:L-ELAC2-BGHcLV24-31	brenton-graveley:ELAC2-BGHcLV24-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAC2-BGHcLV24-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAC2-BGHcLV24-HepG2	brenton-graveley:ELAC2-BGHcLV24-32	brenton-graveley:L-ELAC2-BGHcLV24-32	brenton-graveley:ELAC2-BGHcLV24-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ELAC2-BGHcLV24-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR511EKJ	ENCBS167JZF	ENCLB510VMT	ENCFF141OEO	ENCFF281MBH	ENCSR546QKI	ENCBS626EZN	ENCLB034NYK	ENCFF342LJN	ENCFF819QKQ
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	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-31	BGHcLV24-32	BGHcLV24-32	BGHcLV24-32	BGHcLV24-32
Sample Name	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-31	ELAC2-BGHcLV24-32	ELAC2-BGHcLV24-32	ELAC2-BGHcLV24-32	ELAC2-BGHcLV24-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		ELAC2-BGHcLV24-31.pdf	L-ELAC2-BGHcLV24-31.pdf				ELAC2-BGHcLV24-32.pdf	L-ELAC2-BGHcLV24-32.pdf
ID	3243	3273	3317	3361	3405	7207	3274	3318	3362	3406

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-BGHcLV24-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	562	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3720
ELAC2-BGHcLV24-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	562	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3766
ELAC2-BGHcLV24-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	562					GRCh38	V40	ELAC2-BGHcLV24-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGHcLV24-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25409
ELAC2-BGHcLV24-31_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	562					GRCh38	V40	ELAC2-BGHcLV24-31_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGHcLV24-31_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25453
ELAC2-BGHcLV24-31_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	562					GRCh38	V40	ELAC2-BGHcLV24-31/Aligned.sortedByCoord.out.bam		ENCORE2	26285
ELAC2-BGHcLV24-31_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	562					GRCh38	V40	ELAC2-BGHcLV24-31/Aligned.sortedByCoord.out.bam		ENCORE2	26329
ELAC2-BGHcLV24-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	562					GRCh38	V40	ELAC2-BGHcLV24-31/Aligned.sortedByCoord.out.bam		ENCORE2	26373
ELAC2-BGHcLV24-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	562					GRCh38	V40	ELAC2-BGHcLV24-31/Aligned.sortedByCoord.out.bam		ENCORE2	26417
ELAC2-BGHcLV24-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	563	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3721
ELAC2-BGHcLV24-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	563	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3767
ELAC2-BGHcLV24-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	563					GRCh38	V40	ELAC2-BGHcLV24-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGHcLV24-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25410
ELAC2-BGHcLV24-32_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	563					GRCh38	V40	ELAC2-BGHcLV24-32_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,ELAC2-BGHcLV24-32_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25454
ELAC2-BGHcLV24-32_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	563					GRCh38	V40	ELAC2-BGHcLV24-32/Aligned.sortedByCoord.out.bam		ENCORE2	26286
ELAC2-BGHcLV24-32_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	563					GRCh38	V40	ELAC2-BGHcLV24-32/Aligned.sortedByCoord.out.bam		ENCORE2	26330
ELAC2-BGHcLV24-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	563					GRCh38	V40	ELAC2-BGHcLV24-32/Aligned.sortedByCoord.out.bam		ENCORE2	26374
ELAC2-BGHcLV24-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	563					GRCh38	V40	ELAC2-BGHcLV24-32/Aligned.sortedByCoord.out.bam		ENCORE2	26418