SRA1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-109	BGHcLV49-110
idx	1814	1815
TRCN#_or_BGC#	BGC#0000887	BGC#0000887
shRNA_or_gRNA_sequence	GCGCTCGCTGCTTACCAAGA	GCGCTCGCTGCTTACCAAGA
PAM	GGG	GGG
Name	SRA1_93	SRA1_93
Sample_ID	BGHcLV49-109	BGHcLV49-110
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	SRA1	SRA1
qPCR_result	57.7	49.1
Ave_qPCR	53.4
RT-qPCR_primer-F	atggaggatgtgctgagacc
RT-qPCR_primer-R	actttcctccagcccactgt
protein_conc	4470	4732
WB_result	71.6	83.1
Ave_WB
WB_DONE_date	7/3/25
MW	26kd
IP
antibody_Cat#	A300-743A	LOT #1
Antibody DCC ID	ENCAB874LTS
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	10003	10004

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRA1	Product_ID: A300-743A Lot_ID: 1 Source: Bethyl Labs Target Name: SRA1-human

Experiment Status

	BGHcLV49-109	BGHcLV49-110
Sample_ID	BGHcLV49-109	BGHcLV49-110
Sample Name
Sample Name	SRA1-BGHcLV49-109	SRA1-BGHcLV49-110
RBP	SRA1	SRA1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14368	14369

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-109	BGHcLV49-110
Sample #	65	66
Sample Name	SRA1-BGHcLV49-109	SRA1-BGHcLV49-110
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	260	252
Peak_Molarity	94.10	76.70
libSampleQC_DNA_Well	DNA_Library_set81/set1/C6.png	DNA_Library_set81/set1/D6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/C9.png	RNA_Library_set81/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-109	BGHcLV49-110
RBP	SRA1	SRA1
Batch_ID	BGHcLV49	BGHcLV49
WB_result	71.600	83.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4810	4811

Sequencing Information

	BGHcLV49-109	BGHcLV49-110
Sample_ID	BGHcLV49-109	BGHcLV49-110
Sample Name	SRA1-BGHcLV49-109	SRA1-BGHcLV49-110
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	34,553,112	35,355,552
total_aligned_reads	29,008,595	30,001,725
unique_aligned_reads	27,324,046	28,237,676
percent_uniqueAligned	0.79078	0.79868
correlation_replicates	0.997726	0.997726
spikein_reads	62,566	23,690
percent_spikeins	0.00181	0.00067
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3535	3536

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
SRA1-BGHcLV49-109_S148_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3535	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33210
SRA1-BGHcLV49-109_S148_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3535	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33256
SRA1-BGHcLV49-109_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3535					GRCh38	V40	SRA1-BGHcLV49-109_S148_L008_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGHcLV49-109_S148_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33302
SRA1-BGHcLV49-109_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3535					GRCh38	V40	SRA1-BGHcLV49-109_Aligned.sortedByCoord.out.bam		ENCORE2	33348
SRA1-BGHcLV49-109_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3535					GRCh38	V40	SRA1-BGHcLV49-109_Aligned.sortedByCoord.out.bam		ENCORE2	33394
SRA1-BGHcLV49-109_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3535					GRCh38	V40	SRA1-BGHcLV49-109_Aligned.sortedByCoord.out.bam		ENCORE2	33440
SRA1-BGHcLV49-109_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3535					GRCh38	V40	SRA1-BGHcLV49-109_Aligned.sortedByCoord.out.bam		ENCORE2	33486
SRA1-BGHcLV49-109_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3535					GRCh38	V40	SRA1-BGHcLV49-109_S148_L008_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGHcLV49-109_S148_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33532
SRA1-BGHcLV49-110_S137_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3536	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33211
SRA1-BGHcLV49-110_S137_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3536	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33257
SRA1-BGHcLV49-110_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3536					GRCh38	V40	SRA1-BGHcLV49-110_S137_L008_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGHcLV49-110_S137_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33303
SRA1-BGHcLV49-110_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3536					GRCh38	V40	SRA1-BGHcLV49-110_Aligned.sortedByCoord.out.bam		ENCORE2	33349
SRA1-BGHcLV49-110_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3536					GRCh38	V40	SRA1-BGHcLV49-110_Aligned.sortedByCoord.out.bam		ENCORE2	33395
SRA1-BGHcLV49-110_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3536					GRCh38	V40	SRA1-BGHcLV49-110_Aligned.sortedByCoord.out.bam		ENCORE2	33441
SRA1-BGHcLV49-110_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3536					GRCh38	V40	SRA1-BGHcLV49-110_Aligned.sortedByCoord.out.bam		ENCORE2	33487
SRA1-BGHcLV49-110_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3536					GRCh38	V40	SRA1-BGHcLV49-110_S137_L008_R1_001.filtered.trimmed.paired.fastq.gz,SRA1-BGHcLV49-110_S137_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33533