TFRC RNA-Seq in HepG2

General Information


RBP	TFRC
Cell_Line	HepG2
Method	CRISPR
Exp_Name	TFRC-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	TFRC-BGHcLV45-77
Rep2	TFRC-BGHcLV45-78
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	95.5
Rep2_qPCR	97.0
Rep1_WB	90.1
Rep2_WB	85.8
Antibody Cat#	13113S
Antibody Lot#	lot # 4
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1632

Experiment Information (Status: Submitting)

	BGHcLV45-77	BGHcLV45-77	BGHcLV45-78	BGHcLV45-78
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001197	BGC#0001197	BGC#0001197	BGC#0001197
shRNA_or_gRNA_sequence	GGCAATCCTGATGACCGAGA	GGCAATCCTGATGACCGAGA	GGCAATCCTGATGACCGAGA	GGCAATCCTGATGACCGAGA
PAM	TGG	TGG	TGG	TGG
Name	TFRC_86	TFRC_86	TFRC_86	TFRC_86
Sample_ID	BGHcLV45-77	BGHcLV45-77	BGHcLV45-78	BGHcLV45-78
transduction_Date	10/1/24	10/1/24	10/1/24	10/1/24
days	D6	D6	D6	D6
RBP_name	TFRC	TFRC	TFRC	TFRC
qPCR_result	95.5		97.0
Ave_qPCR	96.3
RT-qPCR_primer-F	tttcccattgttaacgcaga
RT-qPCR_primer-R	gcaatcctgatgaccgagat
protein_conc	2933	2933	2514	2514
WB_result	90.1	no clear band on the position	85.8
Ave_WB
WB_DONE_date	10/25/24	11/7/24
MW	90kd	90kd
IP
antibody_Cat#	13113S	13208S	lot # 4	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	9767	9769	9768	9770

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TFRC	Product_ID: 13113S Lot_ID: 4 Source: Cell Signaling Technology Target Name: TFRC-human

Experiment Status

	BGHcLV45-77	BGHcLV45-77	BGHcLV45-78	BGHcLV45-78
Sample_ID	BGHcLV45-77	BGHcLV45-77	BGHcLV45-78	BGHcLV45-78
Sample Name
Sample Name	TFRC-BGHcLV45-77		TFRC-BGHcLV45-78
RBP	TFRC	TFRC	TFRC	TFRC
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2024-11-25	2025-04-21	2024-11-25
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13722	13770	13723	13771

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-77	BGHcLV45-78
Sample #	37	38
Sample Name	TFRC-BGHcLV45-77	TFRC-BGHcLV45-78
Sample_Name_Alias
Index Well Position	E11	F11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	290	287
Peak_Molarity	77.30	79.20
libSampleQC_DNA_Well	DNA_Library_set76/set1/E11.png	DNA_Library_set76/set1/F11.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set76/set1/E5.png	RNA_Library_set76/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-77	BGHcLV45-78
RBP	TFRC	TFRC
Batch_ID	BGHcLV45	BGHcLV45
WB_result	90.100	85.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4646	4647

Sequencing Information

	BGHcLV45-77	BGHcLV45-78
Sample_ID	BGHcLV45-77	BGHcLV45-78
Sample Name	TFRC-BGHcLV45-77	TFRC-BGHcLV45-78
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	36,033,452	28,788,423
total_aligned_reads	33,081,215	25,046,241
unique_aligned_reads	31,188,105	23,594,977
percent_uniqueAligned	0.86553	0.81960
correlation_replicates	0.998543	0.998543
spikein_reads	12,356	11,518
percent_spikeins	0.00034	0.00040
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3357	3358

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
TFRC-BGHcLV45-77_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3357	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31848
TFRC-BGHcLV45-77_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3357	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31890
TFRC-BGHcLV45-77_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3357					GRCh38	V40	TFRC-BGHcLV45-77_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGHcLV45-77_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31932
TFRC-BGHcLV45-77_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3357					GRCh38	V40	TFRC-BGHcLV45-77_Aligned.sortedByCoord.out.bam		ENCORE2	31974
TFRC-BGHcLV45-77_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3357					GRCh38	V40	TFRC-BGHcLV45-77_Aligned.sortedByCoord.out.bam		ENCORE2	32016
TFRC-BGHcLV45-77_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3357					GRCh38	V40	TFRC-BGHcLV45-77_Aligned.sortedByCoord.out.bam		ENCORE2	32058
TFRC-BGHcLV45-77_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3357					GRCh38	V40	TFRC-BGHcLV45-77_Aligned.sortedByCoord.out.bam		ENCORE2	32100
TFRC-BGHcLV45-77_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3357					GRCh38	V40	TFRC-BGHcLV45-77_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGHcLV45-77_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32142
TFRC-BGHcLV45-78_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3358	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31849
TFRC-BGHcLV45-78_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3358	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31891
TFRC-BGHcLV45-78_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3358					GRCh38	V40	TFRC-BGHcLV45-78_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGHcLV45-78_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31933
TFRC-BGHcLV45-78_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3358					GRCh38	V40	TFRC-BGHcLV45-78_Aligned.sortedByCoord.out.bam		ENCORE2	31975
TFRC-BGHcLV45-78_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3358					GRCh38	V40	TFRC-BGHcLV45-78_Aligned.sortedByCoord.out.bam		ENCORE2	32017
TFRC-BGHcLV45-78_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3358					GRCh38	V40	TFRC-BGHcLV45-78_Aligned.sortedByCoord.out.bam		ENCORE2	32059
TFRC-BGHcLV45-78_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3358					GRCh38	V40	TFRC-BGHcLV45-78_Aligned.sortedByCoord.out.bam		ENCORE2	32101
TFRC-BGHcLV45-78_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3358					GRCh38	V40	TFRC-BGHcLV45-78_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGHcLV45-78_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32143