EIF2B5 RNA-Seq in HepG2

General Information


RBP	EIF2B5
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF2B5-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	EIF2B5-BGHcLV41-25B
Rep2	EIF2B5-BGHcLV41-26B
CN1	NT-BGHcLV41-1B
CN2	NT-BGHcLV41-2B
Rep1_qPCR	42.6
Rep2_qPCR	38.0
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A302-557A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1449

Experiment Information (Status: NotSatisfied)

	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26
idx	1292	1294	1293	1295
TRCN#_or_BGC#	BGC#0000959	BGC#0000959	BGC#0000959	BGC#0000959
shRNA_or_gRNA_sequence	AGTCGGGCTAACAAGCGCAG	AGTCGGGCTAACAAGCGCAG	AGTCGGGCTAACAAGCGCAG	AGTCGGGCTAACAAGCGCAG
PAM	CGG	CGG	CGG	CGG
Name	EIF2B5_93	EIF2B5_93	EIF2B5_93	EIF2B5_93
Sample_ID	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26
transduction_Date	1/12/24	1/12/24	1/12/24	1/12/24
days	D6	D6	D6	D6
RBP_name	EIF2B5	EIF2B5	EIF2B5	EIF2B5
qPCR_result	42.6	42.6	38.0	38.0
Ave_qPCR	40.3	40.3
RT-qPCR_primer-F	gctggaaagctgctcaaatc	gctggaaagctgctcaaatc
RT-qPCR_primer-R	aggacatctcccagtgatcg	aggacatctcccagtgatcg
protein_conc	3085	3085	2919	2919
WB_result	0.0		0.0
Ave_WB	0.0
WB_DONE_date	2/5/24
MW	80KD	80KD
IP
antibody_Cat#	A302-557A	A302-556A	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	7483	7485	7484	7486

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV41-25	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26	BGHcLV41-26
Sample_ID	BGHcLV41-25	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26	BGHcLV41-26
Sample Name	EIF2B5-BGHcLV41-25			EIF2B5-BGHcLV41-26
Sample Name	EIF2B5-BGHcLV41-25		EIF2B5-BGHcLV41-25B	EIF2B5-BGHcLV41-26		EIF2B5-BGHcLV41-26B
RBP	EIF2B5	EIF2B5	EIF2B5	EIF2B5	EIF2B5	EIF2B5
Cell_Line	HepG2	HepG2	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	NotSatisfied	NotSatisfied	Submitting	NotSatisfied	NotSatisfied	Submitting
Status_date	2024-07-24	2024-03-01	2024-09-20	2024-07-24	2024-03-01	2024-09-20
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12958	13006	13306	12959	13007	13307

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26
Sample #	11	3	12	4
Sample Name	EIF2B5-BGHcLV41-25	EIF2B5-BGHcLV41-25B	EIF2B5-BGHcLV41-26	EIF2B5-BGHcLV41-26B
Sample_Name_Alias
Index Well Position	C02	C02	D02	D02
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	294	286	292	290
Peak_Molarity	96.90	50.90	29.50	80.00
libSampleQC_DNA_Well	DNA_Library_set70/set1/C2.png	DNA_Library_set70/set2/C9.png	DNA_Library_set70/set1/D2.png	DNA_Library_set70/set2/D9.png
RIN	9.8	9.8	9.9	9.9
libSample_RNA_Well	RNA_Library_set70/set1/G7.png	RNA_Library_set70/set1/G7.png	RNA_Library_set70/set1/H7.png	RNA_Library_set70/set1/H7.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	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26
RBP	EIF2B5	EIF2B5	EIF2B5	EIF2B5
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	4236	4420	4237	4421

Sequencing Information

	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26
Sample_ID	BGHcLV41-25	BGHcLV41-25	BGHcLV41-26	BGHcLV41-26
Sample Name	EIF2B5-BGHcLV41-25	EIF2B5-BGHcLV41-25B	EIF2B5-BGHcLV41-26	EIF2B5-BGHcLV41-26B
Pool ID	Pool-240314	Pool-240822	Pool-240314	Pool-240822
LocalServer_folder	set70	set70	set70	set70
total_reads	27,523,277	52,923,208	31,348,930	70,265,007
total_aligned_reads	23,875,042	44,785,157	29,083,407	60,036,773
unique_aligned_reads	22,577,554	42,161,444	26,382,702	56,370,921
percent_uniqueAligned	0.82031	0.79665	0.84158	0.80226
correlation_replicates	0.503705	0.998854	0.503705	0.998854
spikein_reads	5,046	109,362	7,084	62,190
percent_spikeins	0.00018	0.00207	0.00023	0.00089
original_ReadLength	151	100	151	100
QC_Status	BadCorrelation	Submitting	BadCorrelation	Submitting
ID	2955	2991	2956	2992

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
EIF2B5-BGHcLV41-25B_S3_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2991	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	28905
EIF2B5-BGHcLV41-25B_S3_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2991	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	28951
EIF2B5-BGHcLV41-25B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2991					GRCh38	V40	EIF2B5-BGHcLV41-25B_S3_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B5-BGHcLV41-25B_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28997
EIF2B5-BGHcLV41-25B_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	2991					GRCh38	V40	EIF2B5-BGHcLV41-25B/Aligned.sortedByCoord.out.bam		ENCORE2	29043
EIF2B5-BGHcLV41-25B_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	2991					GRCh38	V40	EIF2B5-BGHcLV41-25B/Aligned.sortedByCoord.out.bam		ENCORE2	29089
EIF2B5-BGHcLV41-25B_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	2991					GRCh38	V40	EIF2B5-BGHcLV41-25B/Aligned.sortedByCoord.out.bam		ENCORE2	29135
EIF2B5-BGHcLV41-25B_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	2991					GRCh38	V40	EIF2B5-BGHcLV41-25B/Aligned.sortedByCoord.out.bam		ENCORE2	29181
EIF2B5-BGHcLV41-25B_quant.sf	ENCODE_DATA/set70/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2991					GRCh38	V40	EFL1-BGHcLV41-23/Signal.Unique.strand-.bw,EIF2B5-BGHcLV41-26B/Signal.Unique.strand+.bw		ENCORE2	29227
EIF2B5-BGHcLV41-26B_S4_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2992	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	28906
EIF2B5-BGHcLV41-26B_S4_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set70/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2992	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	28952
EIF2B5-BGHcLV41-26B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2992					GRCh38	V40	EIF2B5-BGHcLV41-26B_S4_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B5-BGHcLV41-26B_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28998
EIF2B5-BGHcLV41-26B_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	2992					GRCh38	V40	EIF2B5-BGHcLV41-26B/Aligned.sortedByCoord.out.bam		ENCORE2	29044
EIF2B5-BGHcLV41-26B_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	2992					GRCh38	V40	EIF2B5-BGHcLV41-26B/Aligned.sortedByCoord.out.bam		ENCORE2	29090
EIF2B5-BGHcLV41-26B_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	2992					GRCh38	V40	EIF2B5-BGHcLV41-26B/Aligned.sortedByCoord.out.bam		ENCORE2	29136
EIF2B5-BGHcLV41-26B_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	2992					GRCh38	V40	EIF2B5-BGHcLV41-26B/Aligned.sortedByCoord.out.bam		ENCORE2	29182
EIF2B5-BGHcLV41-26B_quant.sf	ENCODE_DATA/set70/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2992					GRCh38	V40	EFL1-BGHcLV41-24/Signal.Unique.strand-.bw,EIF3E-BGHcLV41-29/Signal.Unique.strand+.bw		ENCORE2	29228