EML4 RNA-Seq in K562

General Information


RBP	EML4
Cell_Line	K562
Method	CRISPR
Exp_Name	EML4-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EML4-BGKcLV40-21
Rep2	EML4-BGKcLV40-22
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	12.1
Rep2_qPCR	18.0
Rep1_WB	no cleared band on the position
Rep2_WB
Antibody Cat#	A301-909A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1360

Experiment Information (Status: Submitting)

	BGKcLV40-21	BGKcLV40-21	BGKcLV40-22	BGKcLV40-22
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000987	BGC#0000987	BGC#0000987	BGC#0000987
shRNA_or_gRNA_sequence	GCCGTACTCACCGAGACTGC	GCCGTACTCACCGAGACTGC	GCCGTACTCACCGAGACTGC	GCCGTACTCACCGAGACTGC
PAM	CGG	CGG	CGG	CGG
Name	EML4_93	EML4_93	EML4_93	EML4_93
Sample_ID	BGKcLV40-21	BGKcLV40-21	BGKcLV40-22	BGKcLV40-22
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	EML4	EML4	EML4	EML4
qPCR_result	12.1		18.0
Ave_qPCR	15.1
RT-qPCR_primer-F	tgacatcagaacggaactgc
RT-qPCR_primer-R	cggtcggaagaaggtaaaca
protein_conc	3616	3616	3940	3940
WB_result	67.2	need discussion	65.3
Ave_WB
WB_DONE_date	11/20/24	12/6/23
MW	109kd	109kd
IP
antibody_Cat#	A301-909A	A301-908A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date	12/2/24
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5690	5692	5691	5693

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EML4	Product_ID: A301-909A Lot_ID: 1 Source: Bethyl Labs Target Name: EML4-human

Experiment Status

	BGKcLV40-21	BGKcLV40-21	BGKcLV40-22	BGKcLV40-22
Sample_ID	BGKcLV40-21	BGKcLV40-21	BGKcLV40-22	BGKcLV40-22
Sample Name
Sample Name	EML4-BGKcLV40-21		EML4-BGKcLV40-22
RBP	EML4	EML4	EML4	EML4
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2024-02-16	2023-12-15	2024-02-16	2023-12-15
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12764	12810	12765	12811

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-21	BGKcLV40-22
Sample #	11	12
Sample Name	EML4-BGKcLV40-21	EML4-BGKcLV40-22
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	288	289
Peak_Molarity	88.50	68.70
libSampleQC_DNA_Well	DNA_Library_set67/set1/C8.png	DNA_Library_set67/set1/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/C2.png	RNA_Library_set67/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-21	BGKcLV40-22
RBP	EML4	EML4
Batch_ID	BGKcLV40	BGKcLV40
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4148	4149

Sequencing Information

	BGKcLV40-21	BGKcLV40-22
Sample_ID	BGKcLV40-21	BGKcLV40-22
Sample Name	EML4-BGKcLV40-21	EML4-BGKcLV40-22
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	35,970,319	34,183,289
total_aligned_reads	31,479,394	28,959,874
unique_aligned_reads	28,991,864	26,601,458
percent_uniqueAligned	0.80599	0.77820
correlation_replicates	0.996281	0.996281
spikein_reads	5,602	2,044
percent_spikeins	0.00016	0.00006
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2803	2804

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
EML4-BGKcLV40-21_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2803	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28149
EML4-BGKcLV40-21_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2803	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28193
EML4-BGKcLV40-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2803					GRCh38	V40	EML4-BGKcLV40-21_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EML4-BGKcLV40-21_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28237
EML4-BGKcLV40-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2803					GRCh38	V40	EML4-BGKcLV40-21/Aligned.sortedByCoord.out.bam		ENCORE2	28281
EML4-BGKcLV40-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2803					GRCh38	V40	EML4-BGKcLV40-21/Aligned.sortedByCoord.out.bam		ENCORE2	28325
EML4-BGKcLV40-21_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2803					GRCh38	V40	EML4-BGKcLV40-21/Aligned.sortedByCoord.out.bam		ENCORE2	28369
EML4-BGKcLV40-21_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2803					GRCh38	V40	EML4-BGKcLV40-21/Aligned.sortedByCoord.out.bam		ENCORE2	28413
EML4-BGKcLV40-21_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2803					GRCh38	V40	EML4-BGKcLV40-21_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EML4-BGKcLV40-21_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28457
EML4-BGKcLV40-22_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2804	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28150
EML4-BGKcLV40-22_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2804	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28194
EML4-BGKcLV40-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2804					GRCh38	V40	EML4-BGKcLV40-22_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EML4-BGKcLV40-22_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28238
EML4-BGKcLV40-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2804					GRCh38	V40	EML4-BGKcLV40-22/Aligned.sortedByCoord.out.bam		ENCORE2	28282
EML4-BGKcLV40-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2804					GRCh38	V40	EML4-BGKcLV40-22/Aligned.sortedByCoord.out.bam		ENCORE2	28326
EML4-BGKcLV40-22_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2804					GRCh38	V40	EML4-BGKcLV40-22/Aligned.sortedByCoord.out.bam		ENCORE2	28370
EML4-BGKcLV40-22_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2804					GRCh38	V40	EML4-BGKcLV40-22/Aligned.sortedByCoord.out.bam		ENCORE2	28414
EML4-BGKcLV40-22_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2804					GRCh38	V40	EML4-BGKcLV40-22_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EML4-BGKcLV40-22_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28458