EPB41L2 RNA-Seq in HepG2

General Information


RBP	EPB41L2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EPB41L2-BGHcLV41-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV41
Pool ID	Pool-240822
Local_Set_Name	set70
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EPB41L2-BGHcLV41-43B
Rep2	EPB41L2-BGHcLV41-44B
CN1	NT-BGHcLV41-1B
CN2	NT-BGHcLV41-2B
Rep1_qPCR	42.7
Rep2_qPCR	20.3
Rep1_WB	NEED DISCUSSION
Rep2_WB
Antibody Cat#	A301-425A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1455

Experiment Information (Status: NotSatisfied)

	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
idx	1314	1316	1315	1317
TRCN#_or_BGC#	BGC#0000989	BGC#0000989	BGC#0000989	BGC#0000989
shRNA_or_gRNA_sequence	CATGTCGGTCACAAGAGTGG	CATGTCGGTCACAAGAGTGG	CATGTCGGTCACAAGAGTGG	CATGTCGGTCACAAGAGTGG
PAM	TGG	TGG	TGG	TGG
Name	EPB41L2-87	EPB41L2-87	EPB41L2-87	EPB41L2-87
Sample_ID	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
transduction_Date	1/12/24	1/12/24	1/12/24	1/12/24
days	D6	D6	D6	D6
RBP_name	EPB41L2	EPB41L2	EPB41L2	EPB41L2
qPCR_result	42.7	42.7	20.3	20.3
Ave_qPCR	31.5	31.5
RT-qPCR_primer-F	ccagtttgcccctactcaga	ccagtttgcccctactcaga
RT-qPCR_primer-R	actgggaatcagcttgtgct	actgggaatcagcttgtgct
protein_conc	3396	3396	3035	3035
WB_result	NEED DISCUSSION	NEED DISCUSSION
Ave_WB
WB_DONE_date	2/1/24	2/29/24
MW	113kd	113kd
IP
antibody_Cat#	A301-425A	A301-424A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note	check result befor release		check result befor release
ID	7509	7511	7510	7512

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
Sample_ID	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
Sample Name	EPB41L2-BGHcLV41-43		EPB41L2-BGHcLV41-44
Sample Name	EPB41L2-BGHcLV41-43	EPB41L2-BGHcLV41-43B	EPB41L2-BGHcLV41-44	EPB41L2-BGHcLV41-44B
RBP	EPB41L2	EPB41L2	EPB41L2	EPB41L2
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	NotSatisfied	Submitting	NotSatisfied	Submitting
Status_date	2024-07-24	2024-09-20	2024-07-24	2024-09-20
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12970	13308	12971	13309

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
Sample #	23	5	24	6
Sample Name	EPB41L2-BGHcLV41-43	EPB41L2-BGHcLV41-43B	EPB41L2-BGHcLV41-44	EPB41L2-BGHcLV41-44B
Sample_Name_Alias
Index Well Position	G03	G03	H03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-03-01	2024-08-22	2024-03-01	2024-08-22
Lib_ID	Lib-240301	Lib-240822	Lib-240301	Lib-240822
Tecan_Location
Tecan
Tecan_date
Size_bp	293	275	338	273
Peak_Molarity	72.80	61.00	57.90	73.00
libSampleQC_DNA_Well	DNA_Library_set70/set1/G3.png	DNA_Library_set70/set2/E9.png	DNA_Library_set70/set1/H3.png	DNA_Library_set70/set2/F9.png
RIN	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_set70/set1/C9.png	RNA_Library_set70/set1/C9.png	RNA_Library_set70/set1/D9.png	RNA_Library_set70/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-03-14	2024-08-22	2024-03-14	2024-08-22
Sample_ID	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
RBP	EPB41L2	EPB41L2	EPB41L2	EPB41L2
Batch_ID	BGHcLV41	BGHcLV41	BGHcLV41	BGHcLV41
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	4248	4422	4249	4423

Sequencing Information

	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
Sample_ID	BGHcLV41-43	BGHcLV41-43	BGHcLV41-44	BGHcLV41-44
Sample Name	EPB41L2-BGHcLV41-43	EPB41L2-BGHcLV41-43B	EPB41L2-BGHcLV41-44	EPB41L2-BGHcLV41-44B
Pool ID	Pool-240314	Pool-240822	Pool-240314	Pool-240822
LocalServer_folder	set70	set70	set70	set70
total_reads	36,310,053	89,380,813	31,954,300	88,801,607
total_aligned_reads	34,060,643	77,599,944	29,905,689	77,609,952
unique_aligned_reads	32,221,289	73,028,901	28,523,003	72,894,020
percent_uniqueAligned	0.88739	0.81705	0.89262	0.82086
correlation_replicates	0.805957	0.998470	0.805957	0.998470
spikein_reads	5,714	99,788	11,626	43,306
percent_spikeins	0.00016	0.00112	0.00036	0.00049
original_ReadLength	151	100	151	100
QC_Status	BadCorrelation	Submitting	BadCorrelation	Submitting
ID	2967	2993	2968	2994

Data Submission Information DCC submission information was not avaliable

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
EPB41L2-BGHcLV41-43B_S5_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2993	NovaSeq6000	100	paired-ended	1				NT-BGHcLV41-1B_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-2B_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28917
EPB41L2-BGHcLV41-43B_S5_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2993	NovaSeq6000	100	paired-ended	2				NT-BGHcLV41-1B_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-2B_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28963
EPB41L2-BGHcLV41-43B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2993					GRCh38	V40	EPB41L2-BGHcLV41-43B_S5_R1_001.filtered.trimmed.paired.fastq.gz,EPB41L2-BGHcLV41-43B_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29009
EPB41L2-BGHcLV41-43B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2993					GRCh38	V40	EPB41L2-BGHcLV41-43B/Aligned.sortedByCoord.out.bam		ENCORE2	29055
EPB41L2-BGHcLV41-43B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2993					GRCh38	V40	EPB41L2-BGHcLV41-43B/Aligned.sortedByCoord.out.bam		ENCORE2	29101
EPB41L2-BGHcLV41-43B_Signal.Unique.strand-.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2993					GRCh38	V40	EPB41L2-BGHcLV41-43B/Aligned.sortedByCoord.out.bam		ENCORE2	29147
EPB41L2-BGHcLV41-43B_Signal.Unique.strand+.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2993					GRCh38	V40	EPB41L2-BGHcLV41-43B/Aligned.sortedByCoord.out.bam		ENCORE2	29193
EPB41L2-BGHcLV41-43B_quant.sf	ENCODE_DATA/set70/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2993					GRCh38	V40	EML4-BGHcLV41-41/Signal.Unique.strand-.bw,EPB41L2-BGHcLV41-44B/Signal.Unique.strand+.bw		ENCORE2	29239
EPB41L2-BGHcLV41-44B_S6_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2994	NovaSeq6000	100	paired-ended	1				NT-BGHcLV41-1B_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-2B_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28918
EPB41L2-BGHcLV41-44B_S6_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2994	NovaSeq6000	100	paired-ended	2				NT-BGHcLV41-1B_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-2B_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28964
EPB41L2-BGHcLV41-44B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2994					GRCh38	V40	EPB41L2-BGHcLV41-44B_S6_R1_001.filtered.trimmed.paired.fastq.gz,EPB41L2-BGHcLV41-44B_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29010
EPB41L2-BGHcLV41-44B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2994					GRCh38	V40	EPB41L2-BGHcLV41-44B/Aligned.sortedByCoord.out.bam		ENCORE2	29056
EPB41L2-BGHcLV41-44B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2994					GRCh38	V40	EPB41L2-BGHcLV41-44B/Aligned.sortedByCoord.out.bam		ENCORE2	29102
EPB41L2-BGHcLV41-44B_Signal.Unique.strand-.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2994					GRCh38	V40	EPB41L2-BGHcLV41-44B/Aligned.sortedByCoord.out.bam		ENCORE2	29148
EPB41L2-BGHcLV41-44B_Signal.Unique.strand+.bw	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2994					GRCh38	V40	EPB41L2-BGHcLV41-44B/Aligned.sortedByCoord.out.bam		ENCORE2	29194
EPB41L2-BGHcLV41-44B_quant.sf	ENCODE_DATA/set70/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2994					GRCh38	V40	EML4-BGHcLV41-42/Signal.Unique.strand-.bw,EXOSC9-BGHcLV41-59/Signal.Unique.strand+.bw		ENCORE2	29240