EIF4H RNA-Seq in K562

General Information


RBP	EIF4H
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF4H-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF4H-BGKcLV42-35
Rep2	EIF4H-BGKcLV42-36
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	0.0
Rep2_qPCR	9.0
Rep1_WB	91.3
Rep2_WB	90.5
Antibody Cat#	3469S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1540

Experiment Information (Status: Submitting)

	BGKcLV42-35	BGKcLV42-36
idx	0	0
TRCN#_or_BGC#	BGC#0001137	BGC#0001137
shRNA_or_gRNA_sequence	AATCCATGTTGGATCCACGG	AATCCATGTTGGATCCACGG
PAM	AGG	AGG
Name	EIF4H_74	EIF4H_74
Sample_ID	BGKcLV42-35	BGKcLV42-36
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	EIF4H	EIF4H
qPCR_result	0.0	9.0
Ave_qPCR	4.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3859	3474
WB_result	91.3	90.5
Ave_WB	90.9
WB_DONE_date	5/2/24
MW	25,27kd
IP
antibody_Cat#	3469S	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	5797	5798

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4H	Product_ID: 3469S Lot_ID: 1 Source: Cell Signaling Technology Target Name: EIF4H-human

Experiment Status

	BGKcLV42-35	BGKcLV42-36
Sample_ID	BGKcLV42-35	BGKcLV42-36
Sample Name
Sample Name	EIF4H-BGKcLV42-35	EIF4H-BGKcLV42-36
RBP	EIF4H	EIF4H
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13074	13075

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-35	BGKcLV42-36
Sample #	31	32
Sample Name	EIF4H-BGKcLV42-35	EIF4H-BGKcLV42-36
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	287	300
Peak_Molarity	84.90	92.50
libSampleQC_DNA_Well	DNA_Library_set73/set1/G4.png	DNA_Library_set73/set1/H4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G4.png	RNA_Library_set73/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-35	BGKcLV42-36
RBP	EIF4H	EIF4H
Batch_ID	BGKcLV42	BGKcLV42
WB_result	91.300	90.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4300	4301

Sequencing Information

	BGKcLV42-35	BGKcLV42-36
Sample_ID	BGKcLV42-35	BGKcLV42-36
Sample Name	EIF4H-BGKcLV42-35	EIF4H-BGKcLV42-36
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	50,701,907	49,352,977
total_aligned_reads	47,417,860	43,940,279
unique_aligned_reads	43,712,958	40,438,834
percent_uniqueAligned	0.86216	0.81938
correlation_replicates	0.994071	0.994071
spikein_reads	6,230	8,670
percent_spikeins	0.00012	0.00018
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3167	3168

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
EIF4H-BGKcLV42-35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3167	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30368
EIF4H-BGKcLV42-35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3167	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30458
EIF4H-BGKcLV42-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3167					GRCh38	V40	EIF4H-BGKcLV42-35_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGKcLV42-35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31300
EIF4H-BGKcLV42-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3167					GRCh38	V40	EIF4H-BGKcLV42-35_Aligned.sortedByCoord.out.bam		ENCORE2	31390
EIF4H-BGKcLV42-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3167					GRCh38	V40	EIF4H-BGKcLV42-35_Aligned.sortedByCoord.out.bam		ENCORE2	31480
EIF4H-BGKcLV42-35_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3167					GRCh38	V40	EIF4H-BGKcLV42-35_Aligned.sortedByCoord.out.bam		ENCORE2	31570
EIF4H-BGKcLV42-35_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3167					GRCh38	V40	EIF4H-BGKcLV42-35_Aligned.sortedByCoord.out.bam		ENCORE2	31660
EIF4H-BGKcLV42-35_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3167					GRCh38	V40	EIF4H-BGKcLV42-35_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGKcLV42-35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31750
EIF4H-BGKcLV42-36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3168	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30369
EIF4H-BGKcLV42-36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3168	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30459
EIF4H-BGKcLV42-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3168					GRCh38	V40	EIF4H-BGKcLV42-36_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGKcLV42-36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31301
EIF4H-BGKcLV42-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3168					GRCh38	V40	EIF4H-BGKcLV42-36_Aligned.sortedByCoord.out.bam		ENCORE2	31391
EIF4H-BGKcLV42-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3168					GRCh38	V40	EIF4H-BGKcLV42-36_Aligned.sortedByCoord.out.bam		ENCORE2	31481
EIF4H-BGKcLV42-36_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3168					GRCh38	V40	EIF4H-BGKcLV42-36_Aligned.sortedByCoord.out.bam		ENCORE2	31571
EIF4H-BGKcLV42-36_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3168					GRCh38	V40	EIF4H-BGKcLV42-36_Aligned.sortedByCoord.out.bam		ENCORE2	31661
EIF4H-BGKcLV42-36_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3168					GRCh38	V40	EIF4H-BGKcLV42-36_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGKcLV42-36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31751