NELFCD RNA-Seq in K562

General Information


RBP	NELFCD
Cell_Line	K562
Method	CRISPR
Exp_Name	NELFCD-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	NELFCD-BGKcLV42-57
Rep2	NELFCD-BGKcLV42-58
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	50.2
Rep2_qPCR	49.9
Rep1_WB	74.4
Rep2_WB	73.4
Antibody Cat#	12265S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1548

Experiment Information (Status: Submitting)

	BGKcLV42-57	BGKcLV42-58
idx	0	0
TRCN#_or_BGC#	BGC#0001159	BGC#0001159
shRNA_or_gRNA_sequence	ACTACGGGAGCGCGGCCGAG	ACTACGGGAGCGCGGCCGAG
PAM	TGG	TGG
Name	NELFCD_92	NELFCD_92
Sample_ID	BGKcLV42-57	BGKcLV42-58
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	NELFCD	NELFCD
qPCR_result	50.2	49.9
Ave_qPCR	50.0
RT-qPCR_primer-F	tggaaccctccatcttcaac
RT-qPCR_primer-R	ccacagcggtgtagttttca
protein_conc	2803	2893
WB_result	74.4	73.4
Ave_WB	73.9
WB_DONE_date	5/8/24
MW	66kd
IP
antibody_Cat#	12265S	lot # 1
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	5819	5820

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NELFCD	Product_ID: 12265S Lot_ID: 1 Source: Cell Signaling Technology Target Name: NELFCD-human

Experiment Status

	BGKcLV42-57	BGKcLV42-58
Sample_ID	BGKcLV42-57	BGKcLV42-58
Sample Name
Sample Name	NELFCD-BGKcLV42-57	NELFCD-BGKcLV42-58
RBP	NELFCD	NELFCD
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13090	13091

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-57	BGKcLV42-58
Sample #	47	48
Sample Name	NELFCD-BGKcLV42-57	NELFCD-BGKcLV42-58
Sample_Name_Alias
Index Well Position	G06	H06
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	292	283
Peak_Molarity	91.00	71.20
libSampleQC_DNA_Well	DNA_Library_set73/set1/G6.png	DNA_Library_set73/set1/H6.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set73/set1/G6.png	RNA_Library_set73/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-57	BGKcLV42-58
RBP	NELFCD	NELFCD
Batch_ID	BGKcLV42	BGKcLV42
WB_result	74.400	73.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4316	4317

Sequencing Information

	BGKcLV42-57	BGKcLV42-58
Sample_ID	BGKcLV42-57	BGKcLV42-58
Sample Name	NELFCD-BGKcLV42-57	NELFCD-BGKcLV42-58
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	57,085,869	54,786,964
total_aligned_reads	53,196,450	50,470,278
unique_aligned_reads	49,260,504	46,686,416
percent_uniqueAligned	0.86292	0.85214
correlation_replicates	0.998676	0.998676
spikein_reads	6,448	7,224
percent_spikeins	0.00011	0.00013
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3183	3184

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
NELFCD-BGKcLV42-57_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3183	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	30384
NELFCD-BGKcLV42-57_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3183	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	30474
NELFCD-BGKcLV42-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3183					GRCh38	V40	NELFCD-BGKcLV42-57_L001_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGKcLV42-57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31316
NELFCD-BGKcLV42-57_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	3183					GRCh38	V40	NELFCD-BGKcLV42-57_Aligned.sortedByCoord.out.bam		ENCORE2	31406
NELFCD-BGKcLV42-57_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	3183					GRCh38	V40	NELFCD-BGKcLV42-57_Aligned.sortedByCoord.out.bam		ENCORE2	31496
NELFCD-BGKcLV42-57_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	3183					GRCh38	V40	NELFCD-BGKcLV42-57_Aligned.sortedByCoord.out.bam		ENCORE2	31586
NELFCD-BGKcLV42-57_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	3183					GRCh38	V40	NELFCD-BGKcLV42-57_Aligned.sortedByCoord.out.bam		ENCORE2	31676
NELFCD-BGKcLV42-57_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3183					GRCh38	V40	NELFCD-BGKcLV42-57_L001_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGKcLV42-57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31766
NELFCD-BGKcLV42-58_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3184	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	30385
NELFCD-BGKcLV42-58_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3184	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	30475
NELFCD-BGKcLV42-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3184					GRCh38	V40	NELFCD-BGKcLV42-58_L001_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGKcLV42-58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31317
NELFCD-BGKcLV42-58_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	3184					GRCh38	V40	NELFCD-BGKcLV42-58_Aligned.sortedByCoord.out.bam		ENCORE2	31407
NELFCD-BGKcLV42-58_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	3184					GRCh38	V40	NELFCD-BGKcLV42-58_Aligned.sortedByCoord.out.bam		ENCORE2	31497
NELFCD-BGKcLV42-58_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	3184					GRCh38	V40	NELFCD-BGKcLV42-58_Aligned.sortedByCoord.out.bam		ENCORE2	31587
NELFCD-BGKcLV42-58_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	3184					GRCh38	V40	NELFCD-BGKcLV42-58_Aligned.sortedByCoord.out.bam		ENCORE2	31677
NELFCD-BGKcLV42-58_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3184					GRCh38	V40	NELFCD-BGKcLV42-58_L001_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGKcLV42-58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31767