TFRC RNA-Seq in K562

General Information


RBP	TFRC
Cell_Line	K562
Method	CRISPR
Exp_Name	TFRC-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	TFRC-BGKcLV46-107
Rep2	TFRC-BGKcLV46-108
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	19.6
Rep2_qPCR	40.8
Rep1_WB	87.5
Rep2_WB	86.4
Antibody Cat#	13113S
Antibody Lot#	lot# 4
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1655

Experiment Information (Status: Submitting)

	BGKcLV46-107	BGKcLV46-107	BGKcLV46-108	BGKcLV46-108
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001279	BGC#0001279	BGC#0001279	BGC#0001279
shRNA_or_gRNA_sequence	AGGTGAAGCATCCGGTTACT	AGGTGAAGCATCCGGTTACT	AGGTGAAGCATCCGGTTACT	AGGTGAAGCATCCGGTTACT
PAM	GGG	GGG	GGG	GGG
Name	TFRC_94	TFRC_94	TFRC_94	TFRC_94
Sample_ID	BGKcLV46-107	BGKcLV46-107	BGKcLV46-108	BGKcLV46-108
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	TFRC	TFRC	TFRC	TFRC
qPCR_result	19.6	19.6	40.8	40.8
Ave_qPCR	30.2	30.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4431	4431	4110	4110
WB_result	56.1	84.0	61.2	79.6
Ave_WB
WB_DONE_date	1/23/25	1/31/25
MW
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	check result befor release		check result befor release
ID	6128	6130	6129	6131

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

	BGKcLV46-107	BGKcLV46-107	BGKcLV46-108	BGKcLV46-108
Sample_ID	BGKcLV46-107	BGKcLV46-107	BGKcLV46-108	BGKcLV46-108
Sample Name
Sample Name	TFRC-BGKcLV46-107		TFRC-BGKcLV46-108
RBP	TFRC	TFRC	TFRC	TFRC
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2025-02-10	2025-04-21	2025-02-10
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14066	14138	14067	14139

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-107	BGKcLV46-108
Sample #	45	46
Sample Name	TFRC-BGKcLV46-107	TFRC-BGKcLV46-108
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	294	310
Peak_Molarity	77.90	85.80
libSampleQC_DNA_Well	DNA_Library_set77/set1/E12.png	DNA_Library_set77/set1/F12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/E6.png	RNA_Library_set77/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-107	BGKcLV46-108
RBP	TFRC	TFRC
Batch_ID	BGKcLV46	BGKcLV46
WB_result	87.500	86.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4704	4705

Sequencing Information

	BGKcLV46-107	BGKcLV46-108
Sample_ID	BGKcLV46-107	BGKcLV46-108
Sample Name	TFRC-BGKcLV46-107	TFRC-BGKcLV46-108
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	56,776,045	58,625,161
total_aligned_reads	53,545,788	55,416,735
unique_aligned_reads	49,710,180	51,096,677
percent_uniqueAligned	0.87555	0.87158
correlation_replicates	0.993436	0.993436
spikein_reads	11,836	51,260
percent_spikeins	0.00021	0.00087
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3407	3408

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-BGKcLV46-107_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3407	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32194
TFRC-BGKcLV46-107_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3407	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32244
TFRC-BGKcLV46-107_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3407					GRCh38	V40	TFRC-BGKcLV46-107_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGKcLV46-107_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32294
TFRC-BGKcLV46-107_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3407					GRCh38	V40	TFRC-BGKcLV46-107_Aligned.sortedByCoord.out.bam		ENCORE2	32344
TFRC-BGKcLV46-107_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3407					GRCh38	V40	TFRC-BGKcLV46-107_Aligned.sortedByCoord.out.bam		ENCORE2	32394
TFRC-BGKcLV46-107_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3407					GRCh38	V40	TFRC-BGKcLV46-107_Aligned.sortedByCoord.out.bam		ENCORE2	32444
TFRC-BGKcLV46-107_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3407					GRCh38	V40	TFRC-BGKcLV46-107_Aligned.sortedByCoord.out.bam		ENCORE2	32494
TFRC-BGKcLV46-107_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3407					GRCh38	V40	TFRC-BGKcLV46-107_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGKcLV46-107_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32544
TFRC-BGKcLV46-108_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3408	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32195
TFRC-BGKcLV46-108_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3408	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32245
TFRC-BGKcLV46-108_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3408					GRCh38	V40	TFRC-BGKcLV46-108_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGKcLV46-108_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32295
TFRC-BGKcLV46-108_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3408					GRCh38	V40	TFRC-BGKcLV46-108_Aligned.sortedByCoord.out.bam		ENCORE2	32345
TFRC-BGKcLV46-108_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3408					GRCh38	V40	TFRC-BGKcLV46-108_Aligned.sortedByCoord.out.bam		ENCORE2	32395
TFRC-BGKcLV46-108_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3408					GRCh38	V40	TFRC-BGKcLV46-108_Aligned.sortedByCoord.out.bam		ENCORE2	32445
TFRC-BGKcLV46-108_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3408					GRCh38	V40	TFRC-BGKcLV46-108_Aligned.sortedByCoord.out.bam		ENCORE2	32495
TFRC-BGKcLV46-108_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3408					GRCh38	V40	TFRC-BGKcLV46-108_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,TFRC-BGKcLV46-108_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32545