HSPA9 RNA-Seq in HepG2

General Information


RBP	HSPA9
Cell_Line	HepG2
Method	CRISPR
Exp_Name	HSPA9-BGHcLV47-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV47
Pool ID	Pool-250422
Local_Set_Name	set78
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	HSPA9-BGHcLV47-41
Rep2	HSPA9-BGHcLV47-42
CN1	NT-BGHcLV47-1
CN2	NT-BGHcLV47-2
Rep1_qPCR	44.6
Rep2_qPCR	43.6
Rep1_WB	71.4
Rep2_WB	82.9
Antibody Cat#	3593S
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1664

Experiment Information (Status: Sequenced)

	BGHcLV47-41	BGHcLV47-42
idx	1645	1646
TRCN#_or_BGC#	BGC#0001148	BGC#0001148
shRNA_or_gRNA_sequence	TGGGGATACCTTCTTAGGTG	TGGGGATACCTTCTTAGGTG
PAM	GGG	GGG
Name	HSPA9_82	HSPA9_82
Sample_ID	BGHcLV47-41	BGHcLV47-42
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	HSPA9	HSPA9
qPCR_result	44.6	43.6
Ave_qPCR	44.1
RT-qPCR_primer-F	aattacttggggcacacagc
RT-qPCR_primer-R	cgaagcacattcagtccaga
protein_conc	3088	3951
WB_result	71.4	82.9
Ave_WB
WB_DONE_date	3/18/25
MW	75kd
IP
antibody_Cat#	3593S	lot # 2
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	9834	9835

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HSPA9	Product_ID: 3593S Lot_ID: 2 Source: Cell Signaling Technology Target Name: HSPA9-human

Experiment Status

	BGHcLV47-41	BGHcLV47-42
Sample_ID	BGHcLV47-41	BGHcLV47-42
Sample Name
Sample Name	HSPA9-BGHcLV47-41	HSPA9-BGHcLV47-42
RBP	HSPA9	HSPA9
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14162	14163

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-41	BGHcLV47-42
Sample #	15	16
Sample Name	HSPA9-BGHcLV47-41	HSPA9-BGHcLV47-42
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	251	259
Peak_Molarity	38.00	42.20
libSampleQC_DNA_Well	DNA_Library_set78/set1/G7.png	DNA_Library_set78/set1/H7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/G2.png	RNA_Library_set78/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-41	BGHcLV47-42
RBP	HSPA9	HSPA9
Batch_ID	BGHcLV47	BGHcLV47
WB_result	71.400	82.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4726	4727

Sequencing Information

	BGHcLV47-41	BGHcLV47-42
Sample_ID	BGHcLV47-41	BGHcLV47-42
Sample Name	HSPA9-BGHcLV47-41	HSPA9-BGHcLV47-42
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	21,064,881	21,004,656
total_aligned_reads	17,841,778	17,534,792
unique_aligned_reads	16,730,580	16,482,238
percent_uniqueAligned	0.79424	0.78469
correlation_replicates	0.996536	0.996536
spikein_reads	19,852	26,582
percent_spikeins	0.00094	0.00127
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3429	3430

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
HSPA9-BGHcLV47-41_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3429	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32560
HSPA9-BGHcLV47-41_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3429	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32594
HSPA9-BGHcLV47-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3429					GRCh38	V40	HSPA9-BGHcLV47-41_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz,HSPA9-BGHcLV47-41_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32628
HSPA9-BGHcLV47-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3429					GRCh38	V40	HSPA9-BGHcLV47-41_Aligned.sortedByCoord.out.bam		ENCORE2	32662
HSPA9-BGHcLV47-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3429					GRCh38	V40	HSPA9-BGHcLV47-41_Aligned.sortedByCoord.out.bam		ENCORE2	32696
HSPA9-BGHcLV47-41_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3429					GRCh38	V40	HSPA9-BGHcLV47-41_Aligned.sortedByCoord.out.bam		ENCORE2	32730
HSPA9-BGHcLV47-41_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3429					GRCh38	V40	HSPA9-BGHcLV47-41_Aligned.sortedByCoord.out.bam		ENCORE2	32764
HSPA9-BGHcLV47-41_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3429					GRCh38	V40	HSPA9-BGHcLV47-41_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz,HSPA9-BGHcLV47-41_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32798
HSPA9-BGHcLV47-42_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3430	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32561
HSPA9-BGHcLV47-42_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3430	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32595
HSPA9-BGHcLV47-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3430					GRCh38	V40	HSPA9-BGHcLV47-42_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,HSPA9-BGHcLV47-42_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32629
HSPA9-BGHcLV47-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3430					GRCh38	V40	HSPA9-BGHcLV47-42_Aligned.sortedByCoord.out.bam		ENCORE2	32663
HSPA9-BGHcLV47-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3430					GRCh38	V40	HSPA9-BGHcLV47-42_Aligned.sortedByCoord.out.bam		ENCORE2	32697
HSPA9-BGHcLV47-42_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3430					GRCh38	V40	HSPA9-BGHcLV47-42_Aligned.sortedByCoord.out.bam		ENCORE2	32731
HSPA9-BGHcLV47-42_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3430					GRCh38	V40	HSPA9-BGHcLV47-42_Aligned.sortedByCoord.out.bam		ENCORE2	32765
HSPA9-BGHcLV47-42_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3430					GRCh38	V40	HSPA9-BGHcLV47-42_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,HSPA9-BGHcLV47-42_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32799