ALYREF RNA-Seq in K562

General Information


RBP	ALYREF
Cell_Line	K562
Method	CRISPR
Exp_Name	ALYREF-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ALYREF-BGKcLV44-3
Rep2	ALYREF-BGKcLV44-4
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	61.3
Rep2_qPCR	61.2
Rep1_WB	61.9
Rep2_WB	70.0
Antibody Cat#	12655S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1595

Experiment Information (Status: Submitting)

	BGKcLV44-3	BGKcLV44-4
idx	0	0
TRCN#_or_BGC#	BGC#0001108	BGC#0001108
shRNA_or_gRNA_sequence	GCCGCGCGAGTGAATCGAGG	GCCGCGCGAGTGAATCGAGG
PAM	CGG	CGG
Name	ALYREF_97	ALYREF_97
Sample_ID	BGKcLV44-3	BGKcLV44-4
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	ALYREF	ALYREF
qPCR_result	61.3	61.2
Ave_qPCR	61.2
RT-qPCR_primer-F	CTGAAGGCCATGAAGCAGTA
RT-qPCR_primer-R	TCTGTGACGTGACAAGCTGA
protein_conc	4981	5850
WB_result	61.9	70.0
Ave_WB	66.0
WB_DONE_date	8/13/24
MW	27KD
IP
antibody_Cat#	12655S	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	5880	5881

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ALYREF	Product_ID: 12655S Lot_ID: 1 Source: Cell Signaling Technology Target Name: ALYREF-human

Experiment Status

	BGKcLV44-3	BGKcLV44-4
Sample_ID	BGKcLV44-3	BGKcLV44-4
Sample Name
Sample Name	ALYREF-BGKcLV44-3	ALYREF-BGKcLV44-4
RBP	ALYREF	ALYREF
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13582	13583

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-3	BGKcLV44-4
Sample #	11	12
Sample Name	ALYREF-BGKcLV44-3	ALYREF-BGKcLV44-4
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	297	291
Peak_Molarity	96.90	81.70
libSampleQC_DNA_Well	DNA_Library_set75/set1/C7.png	DNA_Library_set75/set1/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/C1.png	RNA_Library_set75/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-3	BGKcLV44-4
RBP	ALYREF	ALYREF
Batch_ID	BGKcLV44	BGKcLV44
WB_result	61.900	70.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4570	4571

Sequencing Information

	BGKcLV44-3	BGKcLV44-4
Sample_ID	BGKcLV44-3	BGKcLV44-4
Sample Name	ALYREF-BGKcLV44-3	ALYREF-BGKcLV44-4
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	66,148,716	53,764,910
total_aligned_reads	62,662,185	50,836,462
unique_aligned_reads	57,701,604	46,763,766
percent_uniqueAligned	0.87230	0.86978
correlation_replicates	0.994222	0.994222
spikein_reads	135,558	99,790
percent_spikeins	0.00205	0.00186
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3281	3282

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
ALYREF-BGKcLV44-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3281	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30936
ALYREF-BGKcLV44-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3281	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30978
ALYREF-BGKcLV44-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3281					GRCh38	V40	ALYREF-BGKcLV44-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGKcLV44-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31020
ALYREF-BGKcLV44-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3281					GRCh38	V40	ALYREF-BGKcLV44-3_Aligned.sortedByCoord.out.bam		ENCORE2	31062
ALYREF-BGKcLV44-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3281					GRCh38	V40	ALYREF-BGKcLV44-3_Aligned.sortedByCoord.out.bam		ENCORE2	31104
ALYREF-BGKcLV44-3_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3281					GRCh38	V40	ALYREF-BGKcLV44-3_Aligned.sortedByCoord.out.bam		ENCORE2	31146
ALYREF-BGKcLV44-3_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3281					GRCh38	V40	ALYREF-BGKcLV44-3_Aligned.sortedByCoord.out.bam		ENCORE2	31188
ALYREF-BGKcLV44-3_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3281					GRCh38	V40	ALYREF-BGKcLV44-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGKcLV44-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31230
ALYREF-BGKcLV44-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3282	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30937
ALYREF-BGKcLV44-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3282	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30979
ALYREF-BGKcLV44-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3282					GRCh38	V40	ALYREF-BGKcLV44-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGKcLV44-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31021
ALYREF-BGKcLV44-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3282					GRCh38	V40	ALYREF-BGKcLV44-4_Aligned.sortedByCoord.out.bam		ENCORE2	31063
ALYREF-BGKcLV44-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3282					GRCh38	V40	ALYREF-BGKcLV44-4_Aligned.sortedByCoord.out.bam		ENCORE2	31105
ALYREF-BGKcLV44-4_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3282					GRCh38	V40	ALYREF-BGKcLV44-4_Aligned.sortedByCoord.out.bam		ENCORE2	31147
ALYREF-BGKcLV44-4_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3282					GRCh38	V40	ALYREF-BGKcLV44-4_Aligned.sortedByCoord.out.bam		ENCORE2	31189
ALYREF-BGKcLV44-4_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3282					GRCh38	V40	ALYREF-BGKcLV44-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGKcLV44-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31231