TFAM RNA-Seq in HepG2

General Information


RBP	TFAM
Cell_Line	HepG2
Method	CRISPR
Exp_Name	TFAM-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	TFAM-BGHcLV43-55
Rep2	TFAM-BGHcLV43-56
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	88.4
Rep2_qPCR	83.2
Rep1_WB	57.6
Rep2_WB	68.0
Antibody Cat#	8076S
Antibody Lot#	lot # 4
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1590

Experiment Information (Status: Submitting)

	BGHcLV43-55	BGHcLV43-56
idx	1423	1424
TRCN#_or_BGC#	BGC#0001195	BGC#0001195
shRNA_or_gRNA_sequence	AGGAAGTTCCCTCCAACGCT	AGGAAGTTCCCTCCAACGCT
PAM	GGG	GGG
Name	TFAM_91	TFAM_91
Sample_ID	BGHcLV43-55	BGHcLV43-56
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	TFAM	TFAM
qPCR_result	88.4	83.2
Ave_qPCR	85.8
RT-qPCR_primer-F	ccgaggtggttttcatctgt
RT-qPCR_primer-R	acgctgggcaattcttctaa
protein_conc	4441	3992
WB_result	57.6	68.0
Ave_WB	62.8
WB_DONE_date	6/25/24
MW	24kd
IP
antibody_Cat#	8076S	lot # 4
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	9678	9679

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TFAM	Product_ID: 8076S Lot_ID: 4 Source: Cell Signaling Technology Target Name: TFAM-human

Experiment Status

	BGHcLV43-55	BGHcLV43-56
Sample_ID	BGHcLV43-55	BGHcLV43-56
Sample Name
Sample Name	TFAM-BGHcLV43-55	TFAM-BGHcLV43-56
RBP	TFAM	TFAM
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13270	13271

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-55	BGHcLV43-56
Sample #	43	44
Sample Name	TFAM-BGHcLV43-55	TFAM-BGHcLV43-56
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	302	273
Peak_Molarity	85.50	99.80
libSampleQC_DNA_Well	DNA_Library_set74/set1/C6.png	DNA_Library_set74/set1/D6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/G11.png	RNA_Library_set74/set1/H11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-55	BGHcLV43-56
RBP	TFAM	TFAM
Batch_ID	BGHcLV43	BGHcLV43
WB_result	57.600	68.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4402	4403

Sequencing Information

	BGHcLV43-55	BGHcLV43-56
Sample_ID	BGHcLV43-55	BGHcLV43-56
Sample Name	TFAM-BGHcLV43-55	TFAM-BGHcLV43-56
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	43,192,477	52,326,803
total_aligned_reads	38,301,378	50,498,911
unique_aligned_reads	35,913,603	47,484,799
percent_uniqueAligned	0.83148	0.90747
correlation_replicates	0.993386	0.993386
spikein_reads	36,930	19,326
percent_spikeins	0.00086	0.00037
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3269	3270

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
TFAM-BGHcLV43-55_S133_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3269	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30562
TFAM-BGHcLV43-55_S133_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3269	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30614
TFAM-BGHcLV43-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3269					GRCh38	V40	TFAM-BGHcLV43-55_S133_L003_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGHcLV43-55_S133_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30666
TFAM-BGHcLV43-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3269					GRCh38	V40	TFAM-BGHcLV43-55_Aligned.sortedByCoord.out.bam		ENCORE2	30718
TFAM-BGHcLV43-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3269					GRCh38	V40	TFAM-BGHcLV43-55_Aligned.sortedByCoord.out.bam		ENCORE2	30770
TFAM-BGHcLV43-55_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3269					GRCh38	V40	TFAM-BGHcLV43-55_Aligned.sortedByCoord.out.bam		ENCORE2	30822
TFAM-BGHcLV43-55_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3269					GRCh38	V40	TFAM-BGHcLV43-55_Aligned.sortedByCoord.out.bam		ENCORE2	30874
TFAM-BGHcLV43-55_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3269					GRCh38	V40	TFAM-BGHcLV43-55_S133_L003_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGHcLV43-55_S133_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30926
TFAM-BGHcLV43-56_S134_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3270	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30563
TFAM-BGHcLV43-56_S134_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3270	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30615
TFAM-BGHcLV43-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3270					GRCh38	V40	TFAM-BGHcLV43-56_S134_L003_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGHcLV43-56_S134_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30667
TFAM-BGHcLV43-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3270					GRCh38	V40	TFAM-BGHcLV43-56_Aligned.sortedByCoord.out.bam		ENCORE2	30719
TFAM-BGHcLV43-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3270					GRCh38	V40	TFAM-BGHcLV43-56_Aligned.sortedByCoord.out.bam		ENCORE2	30771
TFAM-BGHcLV43-56_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3270					GRCh38	V40	TFAM-BGHcLV43-56_Aligned.sortedByCoord.out.bam		ENCORE2	30823
TFAM-BGHcLV43-56_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3270					GRCh38	V40	TFAM-BGHcLV43-56_Aligned.sortedByCoord.out.bam		ENCORE2	30875
TFAM-BGHcLV43-56_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3270					GRCh38	V40	TFAM-BGHcLV43-56_S134_L003_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGHcLV43-56_S134_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30927