TFAM RNA-Seq in K562

General Information


RBP	TFAM
Cell_Line	K562
Method	CRISPR
Exp_Name	TFAM-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	TFAM-BGKcLV42-93
Rep2	TFAM-BGKcLV42-94
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	26.2
Rep2_qPCR	7.6
Rep1_WB	77.1
Rep2_WB	69.4
Antibody Cat#	8076S
Antibody Lot#	lot # 4
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1563

Experiment Information (Status: Submitting)

	BGKcLV42-93	BGKcLV42-94
idx	0	0
TRCN#_or_BGC#	BGC#0001192	BGC#0001192
shRNA_or_gRNA_sequence	GGCGTTTCTCCGAAGCATGT	GGCGTTTCTCCGAAGCATGT
PAM	GGG	GGG
Name	TFAM_93	TFAM_93
Sample_ID	BGKcLV42-93	BGKcLV42-94
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	TFAM	TFAM
qPCR_result	26.2	7.6
Ave_qPCR	16.9
RT-qPCR_primer-F	ccgaggtggttttcatctgt
RT-qPCR_primer-R	aacgctgggcaattcttcta
protein_conc	1802	1712
WB_result	77.1	69.4
Ave_WB	73.3
WB_DONE_date	5/8/24
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	5861	5862

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

	BGKcLV42-93	BGKcLV42-94
Sample_ID	BGKcLV42-93	BGKcLV42-94
Sample Name
Sample Name	TFAM-BGKcLV42-93	TFAM-BGKcLV42-94
RBP	TFAM	TFAM
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13120	13121

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-93	BGKcLV42-94
Sample #	77	78
Sample Name	TFAM-BGKcLV42-93	TFAM-BGKcLV42-94
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	334	325
Peak_Molarity	128.00	99.70
libSampleQC_DNA_Well	DNA_Library_set73/set1/E10.png	DNA_Library_set73/set1/F10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E10.png	RNA_Library_set73/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-93	BGKcLV42-94
RBP	TFAM	TFAM
Batch_ID	BGKcLV42	BGKcLV42
WB_result	77.100	69.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4346	4347

Sequencing Information

	BGKcLV42-93	BGKcLV42-94
Sample_ID	BGKcLV42-93	BGKcLV42-94
Sample Name	TFAM-BGKcLV42-93	TFAM-BGKcLV42-94
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	28,539,889	43,521,478
total_aligned_reads	27,009,192	40,441,719
unique_aligned_reads	25,039,474	37,419,002
percent_uniqueAligned	0.87735	0.85978
correlation_replicates	0.995396	0.995396
spikein_reads	2,024	752
percent_spikeins	0.00007	0.00002
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3213	3214

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-BGKcLV42-93_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3213	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30416
TFAM-BGKcLV42-93_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3213	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30506
TFAM-BGKcLV42-93_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3213					GRCh38	V40	TFAM-BGKcLV42-93_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGKcLV42-93_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31348
TFAM-BGKcLV42-93_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3213					GRCh38	V40	TFAM-BGKcLV42-93_Aligned.sortedByCoord.out.bam		ENCORE2	31438
TFAM-BGKcLV42-93_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3213					GRCh38	V40	TFAM-BGKcLV42-93_Aligned.sortedByCoord.out.bam		ENCORE2	31528
TFAM-BGKcLV42-93_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3213					GRCh38	V40	TFAM-BGKcLV42-93_Aligned.sortedByCoord.out.bam		ENCORE2	31618
TFAM-BGKcLV42-93_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3213					GRCh38	V40	TFAM-BGKcLV42-93_Aligned.sortedByCoord.out.bam		ENCORE2	31708
TFAM-BGKcLV42-93_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3213					GRCh38	V40	TFAM-BGKcLV42-93_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGKcLV42-93_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31798
TFAM-BGKcLV42-94_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3214	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30417
TFAM-BGKcLV42-94_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3214	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30507
TFAM-BGKcLV42-94_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3214					GRCh38	V40	TFAM-BGKcLV42-94_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGKcLV42-94_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31349
TFAM-BGKcLV42-94_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3214					GRCh38	V40	TFAM-BGKcLV42-94_Aligned.sortedByCoord.out.bam		ENCORE2	31439
TFAM-BGKcLV42-94_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3214					GRCh38	V40	TFAM-BGKcLV42-94_Aligned.sortedByCoord.out.bam		ENCORE2	31529
TFAM-BGKcLV42-94_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3214					GRCh38	V40	TFAM-BGKcLV42-94_Aligned.sortedByCoord.out.bam		ENCORE2	31619
TFAM-BGKcLV42-94_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3214					GRCh38	V40	TFAM-BGKcLV42-94_Aligned.sortedByCoord.out.bam		ENCORE2	31709
TFAM-BGKcLV42-94_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3214					GRCh38	V40	TFAM-BGKcLV42-94_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFAM-BGKcLV42-94_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31799