DCP1B RNA-Seq in HepG2

General Information


RBP	DCP1B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DCP1B-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	DCP1B-BGHcLV45-15
Rep2	DCP1B-BGHcLV45-16
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	87.7
Rep2_WB	84.8
Antibody Cat#	A303-641A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1620

Experiment Information (Status: Submitting)

	BGHcLV45-15	BGHcLV45-16
idx	1448	1449
TRCN#_or_BGC#	BGC#0001086	BGC#0001086
shRNA_or_gRNA_sequence	AGGTCTGCTTCTCCAAAGCA	AGGTCTGCTTCTCCAAAGCA
PAM	TGG	TGG
Name	DCP1B	DCP1B
Sample_ID	BGHcLV45-15	BGHcLV45-16
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	DCP1B	DCP1B
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3940	4395
WB_result	87.7	84.8
Ave_WB
WB_DONE_date	10/9/24,10/18/24
MW	68kd
IP
antibody_Cat#	A303-641A	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	9703	9704

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV45-15	BGHcLV45-16
Sample_ID	BGHcLV45-15	BGHcLV45-16
Sample Name
Sample Name	DCP1B-BGHcLV45-15	DCP1B-BGHcLV45-16
RBP	DCP1B	DCP1B
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13698	13699

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-15	BGHcLV45-16
Sample #	13	14
Sample Name	DCP1B-BGHcLV45-15	DCP1B-BGHcLV45-16
Sample_Name_Alias
Index Well Position	E08	F08
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	290	304
Peak_Molarity	54.50	76.30
libSampleQC_DNA_Well	DNA_Library_set76/set1/E8.png	DNA_Library_set76/set1/F8.png
RIN	8.4	10.0
libSample_RNA_Well	RNA_Library_set76/set1/E2.png	RNA_Library_set76/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-15	BGHcLV45-16
RBP	DCP1B	DCP1B
Batch_ID	BGHcLV45	BGHcLV45
WB_result	87.700	84.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4622	4623

Sequencing Information

	BGHcLV45-15	BGHcLV45-16
Sample_ID	BGHcLV45-15	BGHcLV45-16
Sample Name	DCP1B-BGHcLV45-15	DCP1B-BGHcLV45-16
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	20,186,585	34,418,624
total_aligned_reads	17,312,953	30,713,761
unique_aligned_reads	16,192,782	28,860,858
percent_uniqueAligned	0.80216	0.83852
correlation_replicates	0.966056	0.966056
spikein_reads	23,082	23,000
percent_spikeins	0.00114	0.00067
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3333	3334

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
DCP1B-BGHcLV45-15_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3333	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	31822
DCP1B-BGHcLV45-15_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3333	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	31864
DCP1B-BGHcLV45-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3333					GRCh38	V40	DCP1B-BGHcLV45-15_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCP1B-BGHcLV45-15_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31906
DCP1B-BGHcLV45-15_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	3333					GRCh38	V40	DCP1B-BGHcLV45-15_Aligned.sortedByCoord.out.bam		ENCORE2	31948
DCP1B-BGHcLV45-15_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	3333					GRCh38	V40	DCP1B-BGHcLV45-15_Aligned.sortedByCoord.out.bam		ENCORE2	31990
DCP1B-BGHcLV45-15_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	3333					GRCh38	V40	DCP1B-BGHcLV45-15_Aligned.sortedByCoord.out.bam		ENCORE2	32032
DCP1B-BGHcLV45-15_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	3333					GRCh38	V40	DCP1B-BGHcLV45-15_Aligned.sortedByCoord.out.bam		ENCORE2	32074
DCP1B-BGHcLV45-15_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3333					GRCh38	V40	DCP1B-BGHcLV45-15_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCP1B-BGHcLV45-15_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32116
DCP1B-BGHcLV45-16_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3334	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	31823
DCP1B-BGHcLV45-16_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3334	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	31865
DCP1B-BGHcLV45-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3334					GRCh38	V40	DCP1B-BGHcLV45-16_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCP1B-BGHcLV45-16_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31907
DCP1B-BGHcLV45-16_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	3334					GRCh38	V40	DCP1B-BGHcLV45-16_Aligned.sortedByCoord.out.bam		ENCORE2	31949
DCP1B-BGHcLV45-16_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	3334					GRCh38	V40	DCP1B-BGHcLV45-16_Aligned.sortedByCoord.out.bam		ENCORE2	31991
DCP1B-BGHcLV45-16_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	3334					GRCh38	V40	DCP1B-BGHcLV45-16_Aligned.sortedByCoord.out.bam		ENCORE2	32033
DCP1B-BGHcLV45-16_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	3334					GRCh38	V40	DCP1B-BGHcLV45-16_Aligned.sortedByCoord.out.bam		ENCORE2	32075
DCP1B-BGHcLV45-16_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3334					GRCh38	V40	DCP1B-BGHcLV45-16_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCP1B-BGHcLV45-16_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32117