SSU72 RNA-Seq in K562

General Information


RBP	SSU72
Cell_Line	K562
Method	CRISPR
Exp_Name	SSU72-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	SSU72-BGKcLV42-89
Rep2	SSU72-BGKcLV42-90
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	81.0
Rep2_qPCR	80.3
Rep1_WB	78.0
Rep2_WB	82.6
Antibody Cat#	12816S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1561

Experiment Information (Status: Submitting)

	BGKcLV42-89	BGKcLV42-90
idx	0	0
TRCN#_or_BGC#	BGC#0001189	BGC#0001189
shRNA_or_gRNA_sequence	GCGTCCGATCCTTTGGAACA	GCGTCCGATCCTTTGGAACA
PAM	GGG	GGG
Name	SSU72_91	SSU72_91
Sample_ID	BGKcLV42-89	BGKcLV42-90
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	SSU72	SSU72
qPCR_result	81.0	80.3
Ave_qPCR	80.7
RT-qPCR_primer-F	caaccagaaccggagcat
RT-qPCR_primer-R	agcttcacgtgagtccctgt
protein_conc	2156	1987
WB_result	78.0	82.6
Ave_WB	80.3
WB_DONE_date	5/8/24
MW	27kd
IP
antibody_Cat#	12816S	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	5857	5858

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SSU72	Product_ID: 12816S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SSU72-human

Experiment Status

	BGKcLV42-89	BGKcLV42-90
Sample_ID	BGKcLV42-89	BGKcLV42-90
Sample Name
Sample Name	SSU72-BGKcLV42-89	SSU72-BGKcLV42-90
RBP	SSU72	SSU72
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13116	13117

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-89	BGKcLV42-90
Sample #	73	74
Sample Name	SSU72-BGKcLV42-89	SSU72-BGKcLV42-90
Sample_Name_Alias
Index Well Position	A10	B10
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	333	317
Peak_Molarity	71.50	87.60
libSampleQC_DNA_Well	DNA_Library_set73/set1/A10.png	DNA_Library_set73/set1/B10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A10.png	RNA_Library_set73/set1/B10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-89	BGKcLV42-90
RBP	SSU72	SSU72
Batch_ID	BGKcLV42	BGKcLV42
WB_result	78.000	82.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4342	4343

Sequencing Information

	BGKcLV42-89	BGKcLV42-90
Sample_ID	BGKcLV42-89	BGKcLV42-90
Sample Name	SSU72-BGKcLV42-89	SSU72-BGKcLV42-90
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	50,601,511	38,363,790
total_aligned_reads	47,832,064	33,621,773
unique_aligned_reads	44,089,258	31,011,311
percent_uniqueAligned	0.87130	0.80835
correlation_replicates	0.994244	0.994244
spikein_reads	6,904	1,394
percent_spikeins	0.00014	0.00004
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3209	3210

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
SSU72-BGKcLV42-89_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3209	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	30412
SSU72-BGKcLV42-89_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3209	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	30502
SSU72-BGKcLV42-89_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3209					GRCh38	V40	SSU72-BGKcLV42-89_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSU72-BGKcLV42-89_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31344
SSU72-BGKcLV42-89_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	3209					GRCh38	V40	SSU72-BGKcLV42-89_Aligned.sortedByCoord.out.bam		ENCORE2	31434
SSU72-BGKcLV42-89_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	3209					GRCh38	V40	SSU72-BGKcLV42-89_Aligned.sortedByCoord.out.bam		ENCORE2	31524
SSU72-BGKcLV42-89_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	3209					GRCh38	V40	SSU72-BGKcLV42-89_Aligned.sortedByCoord.out.bam		ENCORE2	31614
SSU72-BGKcLV42-89_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	3209					GRCh38	V40	SSU72-BGKcLV42-89_Aligned.sortedByCoord.out.bam		ENCORE2	31704
SSU72-BGKcLV42-89_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3209					GRCh38	V40	SSU72-BGKcLV42-89_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSU72-BGKcLV42-89_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31794
SSU72-BGKcLV42-90_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3210	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	30413
SSU72-BGKcLV42-90_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3210	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	30503
SSU72-BGKcLV42-90_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3210					GRCh38	V40	SSU72-BGKcLV42-90_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSU72-BGKcLV42-90_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31345
SSU72-BGKcLV42-90_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	3210					GRCh38	V40	SSU72-BGKcLV42-90_Aligned.sortedByCoord.out.bam		ENCORE2	31435
SSU72-BGKcLV42-90_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	3210					GRCh38	V40	SSU72-BGKcLV42-90_Aligned.sortedByCoord.out.bam		ENCORE2	31525
SSU72-BGKcLV42-90_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	3210					GRCh38	V40	SSU72-BGKcLV42-90_Aligned.sortedByCoord.out.bam		ENCORE2	31615
SSU72-BGKcLV42-90_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	3210					GRCh38	V40	SSU72-BGKcLV42-90_Aligned.sortedByCoord.out.bam		ENCORE2	31705
SSU72-BGKcLV42-90_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3210					GRCh38	V40	SSU72-BGKcLV42-90_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSU72-BGKcLV42-90_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31795