CSE1L RNA-Seq in HepG2

General Information


RBP	CSE1L
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CSE1L-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CSE1L-BGHcLV34-15
Rep2	CSE1L-BGHcLV34-16
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR	60.6
Rep2_qPCR	69.2
Rep1_WB	52.0
Rep2_WB	60.8
Antibody Cat#	A300-473A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB024AVF
Status	Submitted
Project	ENCORE2
ID	942

Experiment Information (Status: Submitting)

	BGHcLV34-15	BGHcLV34-16
idx	1085	1086
TRCN#_or_BGC#	BGC#0000719	BGC#0000719
shRNA_or_gRNA_sequence	ATAATGAATGTGCTGTACGG	ATAATGAATGTGCTGTACGG
PAM	agg	agg
Name	CSE1L_93	CSE1L_93
Sample_ID	BGHcLV34-15	BGHcLV34-16
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	CSE1L	CSE1L
qPCR_result	60.6	69.2
Ave_qPCR	64.9
RT-qPCR_primer-F	aaaaagatctgtgcggttgg
RT-qPCR_primer-R	tcgggtaactcaaaaagacca
protein_conc	3440	3694
WB_result	52.0	60.8
Ave_WB	56.4
WB_DONE_date	4/5/22	JESS
MW	110KD
IP	Rabbit / I
antibody_Cat#	A300-473A	LOT #2
Antibody DCC ID	ENCAB024AVF
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	7264	7265

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSE1L	Product_ID: A300-473A Lot_ID: 2 Source: Bethyl Labs Target Name: CSE1L-human

Experiment Status

	BGHcLV34-15	BGHcLV34-16
Sample_ID	BGHcLV34-15	BGHcLV34-16
Sample Name
Sample Name	CSE1L-BGHcLV34-15	CSE1L-BGHcLV34-16
RBP	CSE1L	CSE1L
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10801	10802

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-15	BGHcLV34-16
Sample #	5	6
Sample Name	CSE1L-BGHcLV34-15	CSE1L-BGHcLV34-16
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	284	278
Peak_Molarity	37.00	64.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/E5.png	DNA_Library_set54-56/set3/F5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/E1.png	RNA_Library_set54-56/set2/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-15	BGHcLV34-16
RBP	CSE1L	CSE1L
Batch_ID	BGHcLV34	BGHcLV34
WB_result	52.000	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3322	3323

Sequencing Information

	BGHcLV34-15	BGHcLV34-16
Sample_ID	BGHcLV34-15	BGHcLV34-16
Sample Name	CSE1L-BGHcLV34-15	CSE1L-BGHcLV34-16
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	60,119,402	52,738,962
total_aligned_reads	49,491,960	41,359,528
unique_aligned_reads	46,606,416	38,961,594
percent_uniqueAligned	0.77523	0.73876
correlation_replicates	0.996482	0.996482
spikein_reads	5,662	5,476
percent_spikeins	0.00009	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2199	2200

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
CSE1L-BGHcLV34-15_S5_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2199	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8488
CSE1L-BGHcLV34-15_S5_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2199	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8538
CSE1L-BGHcLV34-15_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2199					GRCh38	V40	CSE1L-BGHcLV34-15/Aligned.sortedByCoord.out.bam		ENCORE2	17734
CSE1L-BGHcLV34-15_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2199					GRCh38	V40	CSE1L-BGHcLV34-15/Aligned.sortedByCoord.out.bam		ENCORE2	17784
CSE1L-BGHcLV34-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2199					GRCh38	V40	CSE1L-BGHcLV34-15/Aligned.sortedByCoord.out.bam		ENCORE2	17834
CSE1L-BGHcLV34-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2199					GRCh38	V40	CSE1L-BGHcLV34-15/Aligned.sortedByCoord.out.bam		ENCORE2	17884
CSE1L-BGHcLV34-15_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2199					GRCh38	V40	CSE1L-BGHcLV34-15_S5_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGHcLV34-15_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17934
CSE1L-BGHcLV34-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2199					GRCh38	V40	CSE1L-BGHcLV34-15_S5_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGHcLV34-15_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29275
CSE1L-BGHcLV34-16_S6_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2200	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8489
CSE1L-BGHcLV34-16_S6_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2200	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8539
CSE1L-BGHcLV34-16_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2200					GRCh38	V40	CSE1L-BGHcLV34-16/Aligned.sortedByCoord.out.bam		ENCORE2	17735
CSE1L-BGHcLV34-16_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2200					GRCh38	V40	CSE1L-BGHcLV34-16/Aligned.sortedByCoord.out.bam		ENCORE2	17785
CSE1L-BGHcLV34-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2200					GRCh38	V40	CSE1L-BGHcLV34-16/Aligned.sortedByCoord.out.bam		ENCORE2	17835
CSE1L-BGHcLV34-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2200					GRCh38	V40	CSE1L-BGHcLV34-16/Aligned.sortedByCoord.out.bam		ENCORE2	17885
CSE1L-BGHcLV34-16_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2200					GRCh38	V40	CSE1L-BGHcLV34-16_S6_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGHcLV34-16_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17935
CSE1L-BGHcLV34-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2200					GRCh38	V40	CSE1L-BGHcLV34-16_S6_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGHcLV34-16_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29276