SRRT RNA-Seq in K562

General Information


RBP	SRRT
Cell_Line	K562
Method	CRISPR
Exp_Name	SRRT-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SRRT-BGKcLV44-63
Rep2	SRRT-BGKcLV44-64
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	10.3
Rep2_qPCR	8.2
Rep1_WB	62.8
Rep2_WB	63.9053
Antibody Cat#	A304-551A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1609

Experiment Information (Status: Submitting)

	BGKcLV44-63	BGKcLV44-64
idx	0	0
TRCN#_or_BGC#	BGC#0001062	BGC#0001062
shRNA_or_gRNA_sequence	GAGAGATGAAAGACGTCGAG	GAGAGATGAAAGACGTCGAG
PAM	GGG	GGG
Name	SRRT_93	SRRT_93
Sample_ID	BGKcLV44-63	BGKcLV44-64
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	SRRT	SRRT
qPCR_result	10.3	8.2
Ave_qPCR	9.3
RT-qPCR_primer-F	gaggcaacagatgcaggatt
RT-qPCR_primer-R	tccatgagggacaggaagac
protein_conc	4974	4870
WB_result	62.8	63.9053
Ave_WB	63.4
WB_DONE_date	8/14/24,8/19/24,8/27
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	5946	5947

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

	BGKcLV44-63	BGKcLV44-64
Sample_ID	BGKcLV44-63	BGKcLV44-64
Sample Name
Sample Name	SRRT-BGKcLV44-63	SRRT-BGKcLV44-64
RBP	SRRT	SRRT
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13610	13611

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-63	BGKcLV44-64
Sample #	39	40
Sample Name	SRRT-BGKcLV44-63	SRRT-BGKcLV44-64
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	288	297
Peak_Molarity	81.30	60.10
libSampleQC_DNA_Well	DNA_Library_set75/set1/G10.png	DNA_Library_set75/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/G4.png	RNA_Library_set75/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-63	BGKcLV44-64
RBP	SRRT	SRRT
Batch_ID	BGKcLV44	BGKcLV44
WB_result	62.800	63.905
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4598	4599

Sequencing Information

	BGKcLV44-63	BGKcLV44-64
Sample_ID	BGKcLV44-63	BGKcLV44-64
Sample Name	SRRT-BGKcLV44-63	SRRT-BGKcLV44-64
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	54,399,235	77,979,107
total_aligned_reads	52,357,293	74,859,298
unique_aligned_reads	47,688,797	69,290,333
percent_uniqueAligned	0.87664	0.88858
correlation_replicates	0.996067	0.996067
spikein_reads	67,884	141,766
percent_spikeins	0.00125	0.00182
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3309	3310

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-BGKcLV44-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3309	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30968
SRRT-BGKcLV44-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3309	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31010
SRRT-BGKcLV44-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3309					GRCh38	V40	SRRT-BGKcLV44-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGKcLV44-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31052
SRRT-BGKcLV44-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3309					GRCh38	V40	SRRT-BGKcLV44-63_Aligned.sortedByCoord.out.bam		ENCORE2	31094
SRRT-BGKcLV44-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3309					GRCh38	V40	SRRT-BGKcLV44-63_Aligned.sortedByCoord.out.bam		ENCORE2	31136
SRRT-BGKcLV44-63_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3309					GRCh38	V40	SRRT-BGKcLV44-63_Aligned.sortedByCoord.out.bam		ENCORE2	31178
SRRT-BGKcLV44-63_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3309					GRCh38	V40	SRRT-BGKcLV44-63_Aligned.sortedByCoord.out.bam		ENCORE2	31220
SRRT-BGKcLV44-63_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3309					GRCh38	V40	SRRT-BGKcLV44-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGKcLV44-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31262
SRRT-BGKcLV44-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3310	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30969
SRRT-BGKcLV44-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3310	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31011
SRRT-BGKcLV44-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3310					GRCh38	V40	SRRT-BGKcLV44-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGKcLV44-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31053
SRRT-BGKcLV44-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3310					GRCh38	V40	SRRT-BGKcLV44-64_Aligned.sortedByCoord.out.bam		ENCORE2	31095
SRRT-BGKcLV44-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3310					GRCh38	V40	SRRT-BGKcLV44-64_Aligned.sortedByCoord.out.bam		ENCORE2	31137
SRRT-BGKcLV44-64_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3310					GRCh38	V40	SRRT-BGKcLV44-64_Aligned.sortedByCoord.out.bam		ENCORE2	31179
SRRT-BGKcLV44-64_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3310					GRCh38	V40	SRRT-BGKcLV44-64_Aligned.sortedByCoord.out.bam		ENCORE2	31221
SRRT-BGKcLV44-64_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3310					GRCh38	V40	SRRT-BGKcLV44-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,SRRT-BGKcLV44-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31263