RPL7 RNA-Seq in K562

General Information


RBP	RPL7
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL7-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	RPL7-BGKcLV46-65
Rep2	RPL7-BGKcLV46-66
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	68.3
Rep2_qPCR	64.0
Rep1_WB	52.6
Rep2_WB	54.6065
Antibody Cat#	A300-741A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1649

Experiment Information (Status: Submitting)

	BGKcLV46-65
idx	0
TRCN#_or_BGC#	BGC#0001259
shRNA_or_gRNA_sequence	TTCAGCTTCGAAAGGCAAGG
PAM	AGG
Name	RPL7-61
Sample_ID	BGKcLV46-65
transduction_Date	12/20/24
days	D6
RBP_name	RPL7
qPCR_result	68.3
Ave_qPCR	66.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3510
WB_result	52.6
Ave_WB
WB_DONE_date	1/2/24,1/6/25,1/17/2
MW	29kd
IP
antibody_Cat#	A300-741A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0
Rep2_TPM	0
Action	Ready
Library_start_date
repeat_library
Note
ID	6061

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL7	Product_ID: A300-741A Lot_ID: 3 Source: Bethyl Labs Target Name: RPL7-human

Experiment Status

	BGKcLV46-65	BGKcLV46-66
Sample_ID	BGKcLV46-65	BGKcLV46-66
Sample Name
Sample Name	RPL7-BGKcLV46-65	RPL7-BGKcLV46-66
RBP	RPL7	RPL7
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14052	14053

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-65	BGKcLV46-66
Sample #	31	32
Sample Name	RPL7-BGKcLV46-65	RPL7-BGKcLV46-66
Sample_Name_Alias
Index Well Position	G04	H04
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	298	302
Peak_Molarity	73.00	63.30
libSampleQC_DNA_Well	DNA_Library_set77/set1/G10.png	DNA_Library_set77/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/G4.png	RNA_Library_set77/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-65	BGKcLV46-66
RBP	RPL7	RPL7
Batch_ID	BGKcLV46	BGKcLV46
WB_result	52.600	54.607
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4690	4691

Sequencing Information

	BGKcLV46-65	BGKcLV46-66
Sample_ID	BGKcLV46-65	BGKcLV46-66
Sample Name	RPL7-BGKcLV46-65	RPL7-BGKcLV46-66
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	55,023,418	68,889,835
total_aligned_reads	51,257,187	64,602,312
unique_aligned_reads	47,254,069	59,646,025
percent_uniqueAligned	0.85880	0.86582
correlation_replicates	0.997692	0.997692
spikein_reads	57,004	132,214
percent_spikeins	0.00104	0.00192
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3395	3396

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
RPL7-BGKcLV46-65_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3395	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	32180
RPL7-BGKcLV46-65_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3395	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	32230
RPL7-BGKcLV46-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3395					GRCh38	V40	RPL7-BGKcLV46-65_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL7-BGKcLV46-65_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32280
RPL7-BGKcLV46-65_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	3395					GRCh38	V40	RPL7-BGKcLV46-65_Aligned.sortedByCoord.out.bam		ENCORE2	32330
RPL7-BGKcLV46-65_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	3395					GRCh38	V40	RPL7-BGKcLV46-65_Aligned.sortedByCoord.out.bam		ENCORE2	32380
RPL7-BGKcLV46-65_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	3395					GRCh38	V40	RPL7-BGKcLV46-65_Aligned.sortedByCoord.out.bam		ENCORE2	32430
RPL7-BGKcLV46-65_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	3395					GRCh38	V40	RPL7-BGKcLV46-65_Aligned.sortedByCoord.out.bam		ENCORE2	32480
RPL7-BGKcLV46-65_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3395					GRCh38	V40	RPL7-BGKcLV46-65_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL7-BGKcLV46-65_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32530
RPL7-BGKcLV46-66_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3396	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	32181
RPL7-BGKcLV46-66_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3396	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	32231
RPL7-BGKcLV46-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3396					GRCh38	V40	RPL7-BGKcLV46-66_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL7-BGKcLV46-66_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32281
RPL7-BGKcLV46-66_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	3396					GRCh38	V40	RPL7-BGKcLV46-66_Aligned.sortedByCoord.out.bam		ENCORE2	32331
RPL7-BGKcLV46-66_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	3396					GRCh38	V40	RPL7-BGKcLV46-66_Aligned.sortedByCoord.out.bam		ENCORE2	32381
RPL7-BGKcLV46-66_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	3396					GRCh38	V40	RPL7-BGKcLV46-66_Aligned.sortedByCoord.out.bam		ENCORE2	32431
RPL7-BGKcLV46-66_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	3396					GRCh38	V40	RPL7-BGKcLV46-66_Aligned.sortedByCoord.out.bam		ENCORE2	32481
RPL7-BGKcLV46-66_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3396					GRCh38	V40	RPL7-BGKcLV46-66_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL7-BGKcLV46-66_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32531