EIF2D RNA-Seq in K562

General Information


RBP	EIF2D
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2D-BGKcLV38-K562
ENCODE_series_ID
Batch_ID	BGKcLV38
Pool ID	Pool-230127C
Local_Set_Name	set56
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF2D-BGKcLV38-45
Rep2	EIF2D-BGKcLV38-46
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	25.8
Rep2_qPCR	22.2
Rep1_WB	53.0
Rep2_WB	56.0
Antibody Cat#	A303-006A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1035

Experiment Information (Status: Submitting)

	BGKcLV38-45	BGKcLV38-46
idx	0	0
TRCN#_or_BGC#	BGC#0000961	BGC#0000961
shRNA_or_gRNA_sequence	CTTTCGGGTCAAGTCCAACA	CTTTCGGGTCAAGTCCAACA
PAM	CGG	CGG
Name	EIF2D_91	EIF2D_91
Sample_ID	BGKcLV38-45	BGKcLV38-46
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EIF2D	EIF2D
qPCR_result	25.8	22.2
Ave_qPCR	24.0
RT-qPCR_primer-F	cctgctcttccaggagtctg
RT-qPCR_primer-R	ttgtctgcatcaaccaggtc
protein_conc	0	0
WB_result	53.0	56.0
Ave_WB
WB_DONE_date
MW	65kd
IP
antibody_Cat#	A303-006A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5644	5645

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

	BGKcLV38-45	BGKcLV38-46
Sample_ID	BGKcLV38-45	BGKcLV38-46
Sample Name
Sample Name	EIF2D-BGKcLV38-45	EIF2D-BGKcLV38-46
RBP	EIF2D	EIF2D
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11044	11045

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-45	BGKcLV38-46
Sample #	79	80
Sample Name	EIF2D-BGKcLV38-45	EIF2D-BGKcLV38-46
Sample_Name_Alias
Index Well Position	E11	F11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-19	2023-01-19
Lib_ID	Lib-230119	Lib-230119
Tecan_Location
Tecan
Tecan_date
Size_bp	285	277
Peak_Molarity	86.90	67.00
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/E11.png	DNA_Library_set54-56/set2/F11.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/G10.png	RNA_Library_set54-56/set1/H10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-45	BGKcLV38-46
RBP	EIF2D	EIF2D
Batch_ID	BGKcLV38	BGKcLV38
WB_result	52.700	55.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3450	3451

Sequencing Information

	BGKcLV38-45	BGKcLV38-46
Sample_ID	BGKcLV38-45	BGKcLV38-46
Sample Name	EIF2D-BGKcLV38-45	EIF2D-BGKcLV38-46
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	70,171,498	94,105,306
total_aligned_reads	66,202,790	86,645,951
unique_aligned_reads	61,720,618	80,603,275
percent_uniqueAligned	0.87957	0.85652
correlation_replicates	0.998041	0.998041
spikein_reads	5,610	9,372
percent_spikeins	0.00008	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2321	2322

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-BGKcLV38-45_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2321	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8326
EIF2D-BGKcLV38-45_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2321	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8364
EIF2D-BGKcLV38-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2321					GRCh38	V40	EIF2D-BGKcLV38-45_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGKcLV38-45_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16978
EIF2D-BGKcLV38-45_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2321					GRCh38	V40	EIF2D-BGKcLV38-45/Aligned.sortedByCoord.out.bam		ENCORE2	17016
EIF2D-BGKcLV38-45_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2321					GRCh38	V40	EIF2D-BGKcLV38-45/Aligned.sortedByCoord.out.bam		ENCORE2	17054
EIF2D-BGKcLV38-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2321					GRCh38	V40	EIF2D-BGKcLV38-45/Aligned.sortedByCoord.out.bam		ENCORE2	17092
EIF2D-BGKcLV38-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2321					GRCh38	V40	EIF2D-BGKcLV38-45/Aligned.sortedByCoord.out.bam		ENCORE2	17130
EIF2D-BGKcLV38-45_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2321					GRCh38	V40	EIF2D-BGKcLV38-45_S77_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGKcLV38-45_S77_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17168
EIF2D-BGKcLV38-46_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2322	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8327
EIF2D-BGKcLV38-46_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2322	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8365
EIF2D-BGKcLV38-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2322					GRCh38	V40	EIF2D-BGKcLV38-46_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGKcLV38-46_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16979
EIF2D-BGKcLV38-46_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2322					GRCh38	V40	EIF2D-BGKcLV38-46/Aligned.sortedByCoord.out.bam		ENCORE2	17017
EIF2D-BGKcLV38-46_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2322					GRCh38	V40	EIF2D-BGKcLV38-46/Aligned.sortedByCoord.out.bam		ENCORE2	17055
EIF2D-BGKcLV38-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2322					GRCh38	V40	EIF2D-BGKcLV38-46/Aligned.sortedByCoord.out.bam		ENCORE2	17093
EIF2D-BGKcLV38-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2322					GRCh38	V40	EIF2D-BGKcLV38-46/Aligned.sortedByCoord.out.bam		ENCORE2	17131
EIF2D-BGKcLV38-46_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2322					GRCh38	V40	EIF2D-BGKcLV38-46_S78_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF2D-BGKcLV38-46_S78_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17169