EIF2D RNA-Seq in HepG2

General Information


RBP	EIF2D
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF2D-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF2D-BGHcLV39-53
Rep2	EIF2D-BGHcLV39-54
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	0.0
Rep2_qPCR	26.0
Rep1_WB	89.4
Rep2_WB	94.1
Antibody Cat#	A303-006A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1251

Experiment Information (Status: Submitting)

	BGHcLV39-53	BGHcLV39-54
idx	1255	1256
TRCN#_or_BGC#	BGC#0000961	BGC#0000961
shRNA_or_gRNA_sequence	CTTTCGGGTCAAGTCCAACA	CTTTCGGGTCAAGTCCAACA
PAM	CGG	CGG
Name	EIF2D_91	EIF2D_91
Sample_ID	BGHcLV39-53	BGHcLV39-54
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	EIF2D	EIF2D
qPCR_result	0.0	26.0
Ave_qPCR	13.0
RT-qPCR_primer-F	cctgctcttccaggagtctg
RT-qPCR_primer-R	ttgtctgcatcaaccaggtc
protein_conc	1124	2108
WB_result	89.4	94.1
Ave_WB	91.8
WB_DONE_date	7/5/23
MW	65KD
IP
antibody_Cat#	A303-006A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7446	7447

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2D	Product_ID: A303-006A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2D-human

Experiment Status

	BGHcLV39-53	BGHcLV39-54
Sample_ID	BGHcLV39-53	BGHcLV39-54
Sample Name
Sample Name	EIF2D-BGHcLV39-53	EIF2D-BGHcLV39-54
RBP	EIF2D	EIF2D
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11994	11995

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-53	BGHcLV39-54
Sample #	21	22
Sample Name	EIF2D-BGHcLV39-53	EIF2D-BGHcLV39-54
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	278	277
Peak_Molarity	55.90	54.20
libSampleQC_DNA_Well	DNA_Library_set63/set1/E11.png	DNA_Library_set63/set1/F11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/E11.png	RNA_Library_set63/set1/F11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-53	BGHcLV39-54
RBP	EIF2D	EIF2D
Batch_ID	BGHcLV39	BGHcLV39
WB_result	89.400	94.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3764	3765

Sequencing Information

	BGHcLV39-53	BGHcLV39-54
Sample_ID	BGHcLV39-53	BGHcLV39-54
Sample Name	EIF2D-BGHcLV39-53	EIF2D-BGHcLV39-54
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	68,886,393	54,425,824
total_aligned_reads	54,013,637	45,039,585
unique_aligned_reads	50,987,753	42,473,064
percent_uniqueAligned	0.74017	0.78038
correlation_replicates	0.999620	0.999620
spikein_reads	53,204	26,564
percent_spikeins	0.00077	0.00049
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2663	2664

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
EIF2D-BGHcLV39-53_S15_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2663	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8648
EIF2D-BGHcLV39-53_S15_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2663	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8674
EIF2D-BGHcLV39-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2663					GRCh38	V40	EIF2D-BGHcLV39-53_S15_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGHcLV39-53_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9945
EIF2D-BGHcLV39-53_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2663					GRCh38	V40	EIF2D-BGHcLV39-53/Aligned.sortedByCoord.out.bam		ENCORE2	9971
EIF2D-BGHcLV39-53_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2663					GRCh38	V40	EIF2D-BGHcLV39-53/Aligned.sortedByCoord.out.bam		ENCORE2	9997
EIF2D-BGHcLV39-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2663					GRCh38	V40	EIF2D-BGHcLV39-53/Aligned.sortedByCoord.out.bam		ENCORE2	10023
EIF2D-BGHcLV39-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2663					GRCh38	V40	EIF2D-BGHcLV39-53/Aligned.sortedByCoord.out.bam		ENCORE2	10049
EIF2D-BGHcLV39-53_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2663					GRCh38	V40	EIF2D-BGHcLV39-53_S15_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGHcLV39-53_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10075
EIF2D-BGHcLV39-54_S16_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2664	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8649
EIF2D-BGHcLV39-54_S16_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2664	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8675
EIF2D-BGHcLV39-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2664					GRCh38	V40	EIF2D-BGHcLV39-54_S16_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGHcLV39-54_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9946
EIF2D-BGHcLV39-54_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2664					GRCh38	V40	EIF2D-BGHcLV39-54/Aligned.sortedByCoord.out.bam		ENCORE2	9972
EIF2D-BGHcLV39-54_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2664					GRCh38	V40	EIF2D-BGHcLV39-54/Aligned.sortedByCoord.out.bam		ENCORE2	9998
EIF2D-BGHcLV39-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2664					GRCh38	V40	EIF2D-BGHcLV39-54/Aligned.sortedByCoord.out.bam		ENCORE2	10024
EIF2D-BGHcLV39-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2664					GRCh38	V40	EIF2D-BGHcLV39-54/Aligned.sortedByCoord.out.bam		ENCORE2	10050
EIF2D-BGHcLV39-54_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2664					GRCh38	V40	EIF2D-BGHcLV39-54_S16_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGHcLV39-54_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10076