MAPK1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-43	BGHcLV47-44
idx	1647	1648
TRCN#_or_BGC#	BGC#0001155	BGC#0001155
shRNA_or_gRNA_sequence	TGGAGCCCTGTACCAACGTG	TGGAGCCCTGTACCAACGTG
PAM	TGG	TGG
Name	MAPK1_91	MAPK1_91
Sample_ID	BGHcLV47-43	BGHcLV47-44
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	MAPK1	MAPK1
qPCR_result	68.3	72.4
Ave_qPCR	70.4
RT-qPCR_primer-F	gtgacctcaagccttccaac
RT-qPCR_primer-R	cctgtgtgatcatggtctgg
protein_conc	4265	4905
WB_result	66.2	61.3
Ave_WB
WB_DONE_date	3/25/25
MW	42,44kd
IP
antibody_Cat#	4695S	lot # 28
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	9836	9837

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MAPK1	Product_ID: 4695S Lot_ID: 28 Source: Cell Signaling Technology Target Name: MAPK1-human

Experiment Status

	BGHcLV47-43	BGHcLV47-44
Sample_ID	BGHcLV47-43	BGHcLV47-44
Sample Name
Sample Name	MAPK1-BGHcLV47-43	MAPK1-BGHcLV47-44
RBP	MAPK1	MAPK1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14164	14165

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-43	BGHcLV47-44
Sample #	17	18
Sample Name	MAPK1-BGHcLV47-43	MAPK1-BGHcLV47-44
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	265	266
Peak_Molarity	83.30	53.30
libSampleQC_DNA_Well	DNA_Library_set78/set1/A8.png	DNA_Library_set78/set1/B8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set78/set1/A3.png	RNA_Library_set78/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-43	BGHcLV47-44
RBP	MAPK1	MAPK1
Batch_ID	BGHcLV47	BGHcLV47
WB_result	66.200	61.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4728	4729

Sequencing Information

	BGHcLV47-43	BGHcLV47-44
Sample_ID	BGHcLV47-43	BGHcLV47-44
Sample Name	MAPK1-BGHcLV47-43	MAPK1-BGHcLV47-44
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	12,572,682	17,494,858
total_aligned_reads	10,922,744	15,291,958
unique_aligned_reads	10,272,971	14,415,503
percent_uniqueAligned	0.81709	0.82399
correlation_replicates	0.998479	0.998479
spikein_reads	4,614	31,532
percent_spikeins	0.00037	0.00180
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3431	3432

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
MAPK1-BGHcLV47-43_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3431	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32562
MAPK1-BGHcLV47-43_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3431	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32596
MAPK1-BGHcLV47-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3431					GRCh38	V40	MAPK1-BGHcLV47-43_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,MAPK1-BGHcLV47-43_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32630
MAPK1-BGHcLV47-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3431					GRCh38	V40	MAPK1-BGHcLV47-43_Aligned.sortedByCoord.out.bam		ENCORE2	32664
MAPK1-BGHcLV47-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3431					GRCh38	V40	MAPK1-BGHcLV47-43_Aligned.sortedByCoord.out.bam		ENCORE2	32698
MAPK1-BGHcLV47-43_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3431					GRCh38	V40	MAPK1-BGHcLV47-43_Aligned.sortedByCoord.out.bam		ENCORE2	32732
MAPK1-BGHcLV47-43_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3431					GRCh38	V40	MAPK1-BGHcLV47-43_Aligned.sortedByCoord.out.bam		ENCORE2	32766
MAPK1-BGHcLV47-43_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3431					GRCh38	V40	MAPK1-BGHcLV47-43_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,MAPK1-BGHcLV47-43_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32800
MAPK1-BGHcLV47-44_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3432	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32563
MAPK1-BGHcLV47-44_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3432	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32597
MAPK1-BGHcLV47-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3432					GRCh38	V40	MAPK1-BGHcLV47-44_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,MAPK1-BGHcLV47-44_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32631
MAPK1-BGHcLV47-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3432					GRCh38	V40	MAPK1-BGHcLV47-44_Aligned.sortedByCoord.out.bam		ENCORE2	32665
MAPK1-BGHcLV47-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3432					GRCh38	V40	MAPK1-BGHcLV47-44_Aligned.sortedByCoord.out.bam		ENCORE2	32699
MAPK1-BGHcLV47-44_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3432					GRCh38	V40	MAPK1-BGHcLV47-44_Aligned.sortedByCoord.out.bam		ENCORE2	32733
MAPK1-BGHcLV47-44_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3432					GRCh38	V40	MAPK1-BGHcLV47-44_Aligned.sortedByCoord.out.bam		ENCORE2	32767
MAPK1-BGHcLV47-44_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3432					GRCh38	V40	MAPK1-BGHcLV47-44_S59_L002_R1_001.filtered.trimmed.paired.fastq.gz,MAPK1-BGHcLV47-44_S59_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32801