SRP9 RNA-Seq in HepG2

General Information


RBP	SRP9
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRP9-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SRP9-BGHcLV36-35
Rep2	SRP9-BGHcLV36-36
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	65.8
Rep2_qPCR	60.4
Rep1_WB	75.7
Rep2_WB	84.7
Antibody Cat#	A305-455A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1043

Experiment Information (Status: Submitting)

	BGHcLV36-35	BGHcLV36-36
idx	1166	1167
TRCN#_or_BGC#	BGC#0001053	BGC#0001053
shRNA_or_gRNA_sequence	GCCAGCGATTTACCTTCATA	GCCAGCGATTTACCTTCATA
PAM	GGG	GGG
Name	SRP9_94	SRP9_94
Sample_ID	BGHcLV36-35	BGHcLV36-36
transduction_Date	8/2/22	8/2/22
days	D6	D6
RBP_name	SRP9	SRP9
qPCR_result	65.8	60.4
Ave_qPCR	63.1
RT-qPCR_primer-F	GGTGGTCTCTGCCTTCCTAAAG
RT-qPCR_primer-R	CGAGGAGTTGAAAGCCTTCTGC
protein_conc	4974	5752
WB_result	75.7	84.7
Ave_WB	80.2
WB_DONE_date	8/10/22
MW	10kd
IP
antibody_Cat#	A305-455A	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	7347	7348

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRP9	Product_ID: A305-455A Lot_ID: 1 Source: Bethyl Labs Target Name: SRP9-human

Experiment Status

	BGHcLV36-35	BGHcLV36-36
Sample_ID	BGHcLV36-35	BGHcLV36-36
Sample Name
Sample Name	SRP9-BGHcLV36-35	SRP9-BGHcLV36-36
RBP	SRP9	SRP9
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10948	10949

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-35	BGHcLV36-36
Sample #	7	8
Sample Name	SRP9-BGHcLV36-35	SRP9-BGHcLV36-36
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	301	302
Peak_Molarity	51.90	23.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/G1.png	DNA_Library_set54-56/set1/H1.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set54-56/set1/G1.png	RNA_Library_set54-56/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-35	BGHcLV36-36
RBP	SRP9	SRP9
Batch_ID	BGHcLV36	BGHcLV36
WB_result	75.700	84.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3378	3379

Sequencing Information

	BGHcLV36-35	BGHcLV36-36
Sample_ID	BGHcLV36-35	BGHcLV36-36
Sample Name	SRP9-BGHcLV36-35	SRP9-BGHcLV36-36
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	57,079,730	44,542,284
total_aligned_reads	51,857,380	38,889,342
unique_aligned_reads	48,945,498	36,902,014
percent_uniqueAligned	0.85749	0.82847
correlation_replicates	0.930602	0.930602
spikein_reads	9,034	14,408
percent_spikeins	0.00016	0.00032
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2251	2252

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
SRP9-BGHcLV36-35_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2251	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8404
SRP9-BGHcLV36-35_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2251	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8454
SRP9-BGHcLV36-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2251					GRCh38	V40	SRP9-BGHcLV36-35_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP9-BGHcLV36-35_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25645
SRP9-BGHcLV36-35_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2251					GRCh38	V40	SRP9-BGHcLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	25695
SRP9-BGHcLV36-35_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2251					GRCh38	V40	SRP9-BGHcLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	25745
SRP9-BGHcLV36-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2251					GRCh38	V40	SRP9-BGHcLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	25795
SRP9-BGHcLV36-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2251					GRCh38	V40	SRP9-BGHcLV36-35/Aligned.sortedByCoord.out.bam		ENCORE2	25845
SRP9-BGHcLV36-35_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2251					GRCh38	V40	SRP9-BGHcLV36-35_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP9-BGHcLV36-35_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25895
SRP9-BGHcLV36-36_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2252	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8405
SRP9-BGHcLV36-36_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2252	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8455
SRP9-BGHcLV36-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2252					GRCh38	V40	SRP9-BGHcLV36-36_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP9-BGHcLV36-36_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25646
SRP9-BGHcLV36-36_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2252					GRCh38	V40	SRP9-BGHcLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	25696
SRP9-BGHcLV36-36_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2252					GRCh38	V40	SRP9-BGHcLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	25746
SRP9-BGHcLV36-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2252					GRCh38	V40	SRP9-BGHcLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	25796
SRP9-BGHcLV36-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2252					GRCh38	V40	SRP9-BGHcLV36-36/Aligned.sortedByCoord.out.bam		ENCORE2	25846
SRP9-BGHcLV36-36_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2252					GRCh38	V40	SRP9-BGHcLV36-36_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRP9-BGHcLV36-36_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25896