SYMPK RNA-Seq in HepG2

General Information


RBP	SYMPK
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SYMPK-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SYMPK-BGHcLV45-73
Rep2	SYMPK-BGHcLV45-74
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	67.7
Rep2_WB	73.7
Antibody Cat#	13071S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1631

Experiment Information (Status: Submitting)

	BGHcLV45-73	BGHcLV45-74
idx	1217	0
TRCN#_or_BGC#	BGC#0001193	BGC#0001193
shRNA_or_gRNA_sequence	TGTCATCGGCTTCATCGAGG	TGTCATCGGCTTCATCGAGG
PAM	AGG	AGG
Name	SYMPK_91B	SYMPK_91B
Sample_ID	BGHcLV45-73	BGHcLV45-74
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	SYMPK	SYMPK
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CGAAAATTTGTCATCGGCTT
RT-qPCR_primer-R	TCACCACGTTCACATTCTCG
protein_conc	4479	3448
WB_result	67.7	73.7
Ave_WB
WB_DONE_date	10/15/24
MW	141kd
IP
antibody_Cat#	13071S	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	9763	9764

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SYMPK	Product_ID: 13071S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SYMPK-human

Experiment Status

	BGHcLV45-73	BGHcLV45-74
Sample_ID	BGHcLV45-73	BGHcLV45-74
Sample Name
Sample Name	SYMPK-BGHcLV45-73	SYMPK-BGHcLV45-74
RBP	SYMPK	SYMPK
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13720	13721

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-73	BGHcLV45-74
Sample #	35	36
Sample Name	SYMPK-BGHcLV45-73	SYMPK-BGHcLV45-74
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	296	292
Peak_Molarity	88.60	80.80
libSampleQC_DNA_Well	DNA_Library_set76/set1/C11.png	DNA_Library_set76/set1/D11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set76/set1/C5.png	RNA_Library_set76/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-73	BGHcLV45-74
RBP	SYMPK	SYMPK
Batch_ID	BGHcLV45	BGHcLV45
WB_result	67.700	73.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4644	4645

Sequencing Information

	BGHcLV45-73	BGHcLV45-74
Sample_ID	BGHcLV45-73	BGHcLV45-74
Sample Name	SYMPK-BGHcLV45-73	SYMPK-BGHcLV45-74
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	29,944,859	42,211,557
total_aligned_reads	27,903,650	37,731,819
unique_aligned_reads	26,300,147	35,470,426
percent_uniqueAligned	0.87829	0.84030
correlation_replicates	0.999314	0.999314
spikein_reads	16,940	17,808
percent_spikeins	0.00057	0.00042
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3355	3356

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
SYMPK-BGHcLV45-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3355	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31846
SYMPK-BGHcLV45-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3355	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31888
SYMPK-BGHcLV45-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3355					GRCh38	V40	SYMPK-BGHcLV45-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGHcLV45-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31930
SYMPK-BGHcLV45-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3355					GRCh38	V40	SYMPK-BGHcLV45-73_Aligned.sortedByCoord.out.bam		ENCORE2	31972
SYMPK-BGHcLV45-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3355					GRCh38	V40	SYMPK-BGHcLV45-73_Aligned.sortedByCoord.out.bam		ENCORE2	32014
SYMPK-BGHcLV45-73_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3355					GRCh38	V40	SYMPK-BGHcLV45-73_Aligned.sortedByCoord.out.bam		ENCORE2	32056
SYMPK-BGHcLV45-73_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3355					GRCh38	V40	SYMPK-BGHcLV45-73_Aligned.sortedByCoord.out.bam		ENCORE2	32098
SYMPK-BGHcLV45-73_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3355					GRCh38	V40	SYMPK-BGHcLV45-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGHcLV45-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32140
SYMPK-BGHcLV45-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3356	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31847
SYMPK-BGHcLV45-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3356	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31889
SYMPK-BGHcLV45-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3356					GRCh38	V40	SYMPK-BGHcLV45-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGHcLV45-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31931
SYMPK-BGHcLV45-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3356					GRCh38	V40	SYMPK-BGHcLV45-74_Aligned.sortedByCoord.out.bam		ENCORE2	31973
SYMPK-BGHcLV45-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3356					GRCh38	V40	SYMPK-BGHcLV45-74_Aligned.sortedByCoord.out.bam		ENCORE2	32015
SYMPK-BGHcLV45-74_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3356					GRCh38	V40	SYMPK-BGHcLV45-74_Aligned.sortedByCoord.out.bam		ENCORE2	32057
SYMPK-BGHcLV45-74_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3356					GRCh38	V40	SYMPK-BGHcLV45-74_Aligned.sortedByCoord.out.bam		ENCORE2	32099
SYMPK-BGHcLV45-74_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3356					GRCh38	V40	SYMPK-BGHcLV45-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,SYMPK-BGHcLV45-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32141