ESS2 RNA-Seq in K562

General Information


RBP	ESS2
Cell_Line	K562
Method	CRISPR
Exp_Name	ESS2-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	ESS2-BGKcLV44-19
Rep2	ESS2-BGKcLV44-20
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	63.8
Rep2_WB	57.5
Antibody Cat#	A304-566A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1598

Experiment Information (Status: Submitting)

	BGKcLV44-19	BGKcLV44-20
idx	0	0
TRCN#_or_BGC#	BGC#0000909	BGC#0000909
shRNA_or_gRNA_sequence	CAGGCCCCCGAGGAAGCGCG	CAGGCCCCCGAGGAAGCGCG
PAM	agg	agg
Name	DGCR14_82	DGCR14_82
Sample_ID	BGKcLV44-19	BGKcLV44-20
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	ESS2	ESS2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tccaaatgaatttgcaaaacttac
RT-qPCR_primer-R	tctcctcttcttcccctgct
protein_conc	4212	4516
WB_result	63.8	57.5
Ave_WB	60.7
WB_DONE_date	8/8/24
MW	53kd
IP
antibody_Cat#	A304-566A	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	5896	5897

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ESS2	Product_ID: A304-566A Lot_ID: 1 Source: Bethyl Labs Target Name: ESS2-human

Experiment Status

	BGKcLV44-19	BGKcLV44-20
Sample_ID	BGKcLV44-19	BGKcLV44-20
Sample Name
Sample Name	ESS2-BGKcLV44-19	ESS2-BGKcLV44-20
RBP	ESS2	ESS2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13588	13589

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-19	BGKcLV44-20
Sample #	17	18
Sample Name	ESS2-BGKcLV44-19	ESS2-BGKcLV44-20
Sample_Name_Alias
Index Well Position	A08	B08
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	288	296
Peak_Molarity	72.70	80.70
libSampleQC_DNA_Well	DNA_Library_set75/set1/A8.png	DNA_Library_set75/set1/B8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/A2.png	RNA_Library_set75/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-19	BGKcLV44-20
RBP	ESS2	ESS2
Batch_ID	BGKcLV44	BGKcLV44
WB_result	63.800	57.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4576	4577

Sequencing Information

	BGKcLV44-19	BGKcLV44-20
Sample_ID	BGKcLV44-19	BGKcLV44-20
Sample Name	ESS2-BGKcLV44-19	ESS2-BGKcLV44-20
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	68,710,742	56,112,441
total_aligned_reads	64,893,453	53,015,652
unique_aligned_reads	59,730,658	49,084,278
percent_uniqueAligned	0.86931	0.87475
correlation_replicates	0.993615	0.993615
spikein_reads	173,094	146,510
percent_spikeins	0.00252	0.00261
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3287	3288

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
ESS2-BGKcLV44-19_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3287	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	30946
ESS2-BGKcLV44-19_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3287	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	30988
ESS2-BGKcLV44-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3287					GRCh38	V40	ESS2-BGKcLV44-19_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,ESS2-BGKcLV44-19_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31030
ESS2-BGKcLV44-19_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	3287					GRCh38	V40	ESS2-BGKcLV44-19_Aligned.sortedByCoord.out.bam		ENCORE2	31072
ESS2-BGKcLV44-19_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	3287					GRCh38	V40	ESS2-BGKcLV44-19_Aligned.sortedByCoord.out.bam		ENCORE2	31114
ESS2-BGKcLV44-19_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	3287					GRCh38	V40	ESS2-BGKcLV44-19_Aligned.sortedByCoord.out.bam		ENCORE2	31156
ESS2-BGKcLV44-19_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	3287					GRCh38	V40	ESS2-BGKcLV44-19_Aligned.sortedByCoord.out.bam		ENCORE2	31198
ESS2-BGKcLV44-19_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3287					GRCh38	V40	ESS2-BGKcLV44-19_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,ESS2-BGKcLV44-19_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31240
ESS2-BGKcLV44-20_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3288	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	30947
ESS2-BGKcLV44-20_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3288	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	30989
ESS2-BGKcLV44-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3288					GRCh38	V40	ESS2-BGKcLV44-20_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,ESS2-BGKcLV44-20_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31031
ESS2-BGKcLV44-20_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	3288					GRCh38	V40	ESS2-BGKcLV44-20_Aligned.sortedByCoord.out.bam		ENCORE2	31073
ESS2-BGKcLV44-20_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	3288					GRCh38	V40	ESS2-BGKcLV44-20_Aligned.sortedByCoord.out.bam		ENCORE2	31115
ESS2-BGKcLV44-20_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	3288					GRCh38	V40	ESS2-BGKcLV44-20_Aligned.sortedByCoord.out.bam		ENCORE2	31157
ESS2-BGKcLV44-20_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	3288					GRCh38	V40	ESS2-BGKcLV44-20_Aligned.sortedByCoord.out.bam		ENCORE2	31199
ESS2-BGKcLV44-20_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3288					GRCh38	V40	ESS2-BGKcLV44-20_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,ESS2-BGKcLV44-20_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31241