ERP29 RNA-Seq in K562

General Information


RBP	ERP29
Cell_Line	K562
Method	CRISPR
Exp_Name	ERP29-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	ERP29-BGKcLV40-31
Rep2	ERP29-BGKcLV40-32
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	74.1
Rep2_qPCR	73.2
Rep1_WB	68.4
Rep2_WB	66.5
Antibody Cat#	A305-406A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1364

Experiment Information (Status: Submitting)

	BGKcLV40-31	BGKcLV40-32
idx	0	0
TRCN#_or_BGC#	BGC#0000997	BGC#0000997
shRNA_or_gRNA_sequence	GGGGAGAGAAATGCGGCGCG	GGGGAGAGAAATGCGGCGCG
PAM	GGG	GGG
Name	ERP29_88	ERP29_88
Sample_ID	BGKcLV40-31	BGKcLV40-32
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	ERP29	ERP29
qPCR_result	74.1	73.2
Ave_qPCR	73.7
RT-qPCR_primer-F	ggtgaagttcgacacccagt
RT-qPCR_primer-R	gctccatgttcagcttgtca
protein_conc	3394	3788
WB_result	68.4	66.5
Ave_WB	67.5
WB_DONE_date	11/8/23
MW	29kd
IP
antibody_Cat#	A305-406A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5706	5707

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ERP29	Product_ID: A305-406A Lot_ID: 1 Source: Bethyl Labs Target Name: ERP29-human

Experiment Status

	BGKcLV40-31	BGKcLV40-32
Sample_ID	BGKcLV40-31	BGKcLV40-32
Sample Name
Sample Name	ERP29-BGKcLV40-31	ERP29-BGKcLV40-32
RBP	ERP29	ERP29
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12772	12773

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-31	BGKcLV40-32
Sample #	19	20
Sample Name	ERP29-BGKcLV40-31	ERP29-BGKcLV40-32
Sample_Name_Alias
Index Well Position	C03	D03
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	294	294
Peak_Molarity	93.90	79.20
libSampleQC_DNA_Well	DNA_Library_set67/set1/C9.png	DNA_Library_set67/set1/D9.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set67/set1/C3.png	RNA_Library_set67/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-31	BGKcLV40-32
RBP	ERP29	ERP29
Batch_ID	BGKcLV40	BGKcLV40
WB_result	68.400	66.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4156	4157

Sequencing Information

	BGKcLV40-31	BGKcLV40-32
Sample_ID	BGKcLV40-31	BGKcLV40-32
Sample Name	ERP29-BGKcLV40-31	ERP29-BGKcLV40-32
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	42,898,489	28,631,899
total_aligned_reads	37,733,841	25,590,025
unique_aligned_reads	34,757,484	23,521,833
percent_uniqueAligned	0.81023	0.82153
correlation_replicates	0.995304	0.995304
spikein_reads	6,868	438
percent_spikeins	0.00016	0.00002
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2811	2812

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
ERP29-BGKcLV40-31_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2811	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	28157
ERP29-BGKcLV40-31_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2811	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	28201
ERP29-BGKcLV40-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2811					GRCh38	V40	ERP29-BGKcLV40-31_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,ERP29-BGKcLV40-31_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28245
ERP29-BGKcLV40-31_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	2811					GRCh38	V40	ERP29-BGKcLV40-31/Aligned.sortedByCoord.out.bam		ENCORE2	28289
ERP29-BGKcLV40-31_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	2811					GRCh38	V40	ERP29-BGKcLV40-31/Aligned.sortedByCoord.out.bam		ENCORE2	28333
ERP29-BGKcLV40-31_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	2811					GRCh38	V40	ERP29-BGKcLV40-31/Aligned.sortedByCoord.out.bam		ENCORE2	28377
ERP29-BGKcLV40-31_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	2811					GRCh38	V40	ERP29-BGKcLV40-31/Aligned.sortedByCoord.out.bam		ENCORE2	28421
ERP29-BGKcLV40-31_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2811					GRCh38	V40	ERP29-BGKcLV40-31_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,ERP29-BGKcLV40-31_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28465
ERP29-BGKcLV40-32_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2812	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	28158
ERP29-BGKcLV40-32_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2812	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	28202
ERP29-BGKcLV40-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2812					GRCh38	V40	ERP29-BGKcLV40-32_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,ERP29-BGKcLV40-32_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28246
ERP29-BGKcLV40-32_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	2812					GRCh38	V40	ERP29-BGKcLV40-32/Aligned.sortedByCoord.out.bam		ENCORE2	28290
ERP29-BGKcLV40-32_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	2812					GRCh38	V40	ERP29-BGKcLV40-32/Aligned.sortedByCoord.out.bam		ENCORE2	28334
ERP29-BGKcLV40-32_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	2812					GRCh38	V40	ERP29-BGKcLV40-32/Aligned.sortedByCoord.out.bam		ENCORE2	28378
ERP29-BGKcLV40-32_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	2812					GRCh38	V40	ERP29-BGKcLV40-32/Aligned.sortedByCoord.out.bam		ENCORE2	28422
ERP29-BGKcLV40-32_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2812					GRCh38	V40	ERP29-BGKcLV40-32_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,ERP29-BGKcLV40-32_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28466