EIF3J RNA-Seq in K562

General Information


RBP	EIF3J
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF3J-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	EIF3J-BGKcLV38-53
Rep2	EIF3J-BGKcLV38-54
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	17.4
Rep2_qPCR	17.6
Rep1_WB	74.4
Rep2_WB	82.3
Antibody Cat#	A301-746A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1037

Experiment Information (Status: Submitting)

	BGKcLV38-53	BGKcLV38-54
idx	1470	1471
TRCN#_or_BGC#	BGC#0000969	BGC#0000969
shRNA_or_gRNA_sequence	TCACACCCGGCTCGAGATGG	TCACACCCGGCTCGAGATGG
PAM	CGG	CGG
Name	EIF3J_90	EIF3J_90
Sample_ID	BGKcLV38-53	BGKcLV38-54
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EIF3J	EIF3J
qPCR_result	17.4	17.6
Ave_qPCR	17.5
RT-qPCR_primer-F	tgactgtgctttgcagtgaa
RT-qPCR_primer-R	tttaatccccctccaggaac
protein_conc	3270	2951
WB_result	74.4	82.3
Ave_WB	78.3
WB_DONE_date	12/12/22
MW	29KD
IP
antibody_Cat#	A301-746A	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	5652	5653

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3J	Product_ID: A301-746A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3J-human

Experiment Status

	BGKcLV38-53	BGKcLV38-54
Sample_ID	BGKcLV38-53	BGKcLV38-54
Sample Name
Sample Name	EIF3J-BGKcLV38-53	EIF3J-BGKcLV38-54
RBP	EIF3J	EIF3J
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11048	11049

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-53	BGKcLV38-54
Sample #	83	84
Sample Name	EIF3J-BGKcLV38-53	EIF3J-BGKcLV38-54
Sample_Name_Alias
Index Well Position	A12	B12
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	297	299
Peak_Molarity	52.90	58.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/A12.png	DNA_Library_set54-56/set2/B12.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/C11.png	RNA_Library_set54-56/set1/D11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-53	BGKcLV38-54
RBP	EIF3J	EIF3J
Batch_ID	BGKcLV38	BGKcLV38
WB_result	74.400	82.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3454	3455

Sequencing Information

	BGKcLV38-53	BGKcLV38-54
Sample_ID	BGKcLV38-53	BGKcLV38-54
Sample Name	EIF3J-BGKcLV38-53	EIF3J-BGKcLV38-54
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	91,901,635	96,049,073
total_aligned_reads	85,928,634	88,127,912
unique_aligned_reads	79,775,489	81,649,657
percent_uniqueAligned	0.86805	0.85008
correlation_replicates	0.994547	0.994547
spikein_reads	33,288	20,550
percent_spikeins	0.00036	0.00021
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2325	2326

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
EIF3J-BGKcLV38-53_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2325	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	8330
EIF3J-BGKcLV38-53_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2325	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	8368
EIF3J-BGKcLV38-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2325					GRCh38	V40	EIF3J-BGKcLV38-53_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3J-BGKcLV38-53_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16982
EIF3J-BGKcLV38-53_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	2325					GRCh38	V40	EIF3J-BGKcLV38-53/Aligned.sortedByCoord.out.bam		ENCORE2	17020
EIF3J-BGKcLV38-53_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	2325					GRCh38	V40	EIF3J-BGKcLV38-53/Aligned.sortedByCoord.out.bam		ENCORE2	17058
EIF3J-BGKcLV38-53_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	2325					GRCh38	V40	EIF3J-BGKcLV38-53/Aligned.sortedByCoord.out.bam		ENCORE2	17096
EIF3J-BGKcLV38-53_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	2325					GRCh38	V40	EIF3J-BGKcLV38-53/Aligned.sortedByCoord.out.bam		ENCORE2	17134
EIF3J-BGKcLV38-53_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2325					GRCh38	V40	EIF3J-BGKcLV38-53_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3J-BGKcLV38-53_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17172
EIF3J-BGKcLV38-54_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2326	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	8331
EIF3J-BGKcLV38-54_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2326	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	8369
EIF3J-BGKcLV38-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2326					GRCh38	V40	EIF3J-BGKcLV38-54_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3J-BGKcLV38-54_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16983
EIF3J-BGKcLV38-54_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	2326					GRCh38	V40	EIF3J-BGKcLV38-54/Aligned.sortedByCoord.out.bam		ENCORE2	17021
EIF3J-BGKcLV38-54_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	2326					GRCh38	V40	EIF3J-BGKcLV38-54/Aligned.sortedByCoord.out.bam		ENCORE2	17059
EIF3J-BGKcLV38-54_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	2326					GRCh38	V40	EIF3J-BGKcLV38-54/Aligned.sortedByCoord.out.bam		ENCORE2	17097
EIF3J-BGKcLV38-54_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	2326					GRCh38	V40	EIF3J-BGKcLV38-54/Aligned.sortedByCoord.out.bam		ENCORE2	17135
EIF3J-BGKcLV38-54_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2326					GRCh38	V40	EIF3J-BGKcLV38-54_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3J-BGKcLV38-54_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17173