SRRT RNA-Seq in HepG2

General Information


RBP	SRRT
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRRT-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	SRRT-BGHcLV45-63
Rep2	SRRT-BGHcLV45-64
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	93.9
Rep2_WB	91.2
Antibody Cat#	A304-551A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1628

Experiment Information (Status: Submitting)

	BGHcLV45-63	BGHcLV45-64
idx	1217	1217
TRCN#_or_BGC#	BGC#0001062	BGC#0001062
shRNA_or_gRNA_sequence	GAGAGATGAAAGACGTCGAG	GAGAGATGAAAGACGTCGAG
PAM	GGG	GGG
Name	SRRT_93	SRRT_93
Sample_ID	BGHcLV45-63	BGHcLV45-64
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	SRRT	SRRT
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gaggcaacagatgcaggatt
RT-qPCR_primer-R	tccatgagggacaggaagac
protein_conc	3125	2276
WB_result	93.9	91.2
Ave_WB
WB_DONE_date	10/25/24
MW	101kd
IP
antibody_Cat#	A304-551A	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	9753	9754

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRRT	Product_ID: A304-551A Lot_ID: 1 Source: Bethyl Labs Target Name: SRRT-human

Experiment Status

	BGHcLV45-63	BGHcLV45-64
Sample_ID	BGHcLV45-63	BGHcLV45-64
Sample Name
Sample Name	SRRT-BGHcLV45-63	SRRT-BGHcLV45-64
RBP	SRRT	SRRT
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13714	13715

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-63	BGHcLV45-64
Sample #	29	30
Sample Name	SRRT-BGHcLV45-63	SRRT-BGHcLV45-64
Sample_Name_Alias
Index Well Position	E10	F10
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	284	296
Peak_Molarity	66.90	77.60
libSampleQC_DNA_Well	DNA_Library_set76/set1/E10.png	DNA_Library_set76/set1/F10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set76/set1/E4.png	RNA_Library_set76/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-63	BGHcLV45-64
RBP	SRRT	SRRT
Batch_ID	BGHcLV45	BGHcLV45
WB_result	93.900	91.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4638	4639

Sequencing Information

	BGHcLV45-63	BGHcLV45-64
Sample_ID	BGHcLV45-63	BGHcLV45-64
Sample Name	SRRT-BGHcLV45-63	SRRT-BGHcLV45-64
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	28,595,813	42,896,352
total_aligned_reads	24,546,570	39,118,046
unique_aligned_reads	23,101,919	36,923,530
percent_uniqueAligned	0.80788	0.86076
correlation_replicates	0.996209	0.996209
spikein_reads	11,432	16,416
percent_spikeins	0.00040	0.00038
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3349	3350

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
SRRT-BGHcLV45-63_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3349	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	31840
SRRT-BGHcLV45-63_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3349	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	31882
SRRT-BGHcLV45-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3349					GRCh38	V40	SRRT-BGHcLV45-63_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGHcLV45-63_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31924
SRRT-BGHcLV45-63_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	3349					GRCh38	V40	SRRT-BGHcLV45-63_Aligned.sortedByCoord.out.bam		ENCORE2	31966
SRRT-BGHcLV45-63_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	3349					GRCh38	V40	SRRT-BGHcLV45-63_Aligned.sortedByCoord.out.bam		ENCORE2	32008
SRRT-BGHcLV45-63_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	3349					GRCh38	V40	SRRT-BGHcLV45-63_Aligned.sortedByCoord.out.bam		ENCORE2	32050
SRRT-BGHcLV45-63_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	3349					GRCh38	V40	SRRT-BGHcLV45-63_Aligned.sortedByCoord.out.bam		ENCORE2	32092
SRRT-BGHcLV45-63_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3349					GRCh38	V40	SRRT-BGHcLV45-63_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGHcLV45-63_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32134
SRRT-BGHcLV45-64_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3350	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	31841
SRRT-BGHcLV45-64_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3350	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	31883
SRRT-BGHcLV45-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3350					GRCh38	V40	SRRT-BGHcLV45-64_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGHcLV45-64_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31925
SRRT-BGHcLV45-64_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	3350					GRCh38	V40	SRRT-BGHcLV45-64_Aligned.sortedByCoord.out.bam		ENCORE2	31967
SRRT-BGHcLV45-64_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	3350					GRCh38	V40	SRRT-BGHcLV45-64_Aligned.sortedByCoord.out.bam		ENCORE2	32009
SRRT-BGHcLV45-64_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	3350					GRCh38	V40	SRRT-BGHcLV45-64_Aligned.sortedByCoord.out.bam		ENCORE2	32051
SRRT-BGHcLV45-64_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	3350					GRCh38	V40	SRRT-BGHcLV45-64_Aligned.sortedByCoord.out.bam		ENCORE2	32093
SRRT-BGHcLV45-64_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3350					GRCh38	V40	SRRT-BGHcLV45-64_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGHcLV45-64_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32135