NELFCD RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-45	BGHcLV47-46
idx	1649	1650
TRCN#_or_BGC#	BGC#0001161	BGC#0001161
shRNA_or_gRNA_sequence	ACTACGGGAGCGCGGCCGAG	ACTACGGGAGCGCGGCCGAG
PAM	TGG	TGG
Name	NELFCD_92	NELFCD_92
Sample_ID	BGHcLV47-45	BGHcLV47-46
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	NELFCD	NELFCD
qPCR_result	54.3	55.8
Ave_qPCR	55.1
RT-qPCR_primer-F	tggaaccctccatcttcaac
RT-qPCR_primer-R	ccacagcggtgtagttttca
protein_conc	4979	4532
WB_result	96.2	96.5
Ave_WB
WB_DONE_date	3/24/25,3/11/25
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	9838	9839

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

	BGHcLV47-45	BGHcLV47-46
Sample_ID	BGHcLV47-45	BGHcLV47-46
Sample Name
Sample Name	NELFCD-BGHcLV47-45	NELFCD-BGHcLV47-46
RBP	NELFCD	NELFCD
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14166	14167

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-45	BGHcLV47-46
Sample #	19	20
Sample Name	NELFCD-BGHcLV47-45	NELFCD-BGHcLV47-46
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	269	270
Peak_Molarity	61.40	51.40
libSampleQC_DNA_Well	DNA_Library_set78/set1/C8.png	DNA_Library_set78/set1/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/C3.png	RNA_Library_set78/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-45	BGHcLV47-46
RBP	NELFCD	NELFCD
Batch_ID	BGHcLV47	BGHcLV47
WB_result	96.200	96.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4730	4731

Sequencing Information

	BGHcLV47-45	BGHcLV47-46
Sample_ID	BGHcLV47-45	BGHcLV47-46
Sample Name	NELFCD-BGHcLV47-45	NELFCD-BGHcLV47-46
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	13,986,414	20,027,712
total_aligned_reads	12,052,771	17,495,454
unique_aligned_reads	11,354,568	16,478,577
percent_uniqueAligned	0.81183	0.82279
correlation_replicates	0.993519	0.993519
spikein_reads	15,052	31,254
percent_spikeins	0.00108	0.00156
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3433	3434

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-BGHcLV47-45_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3433	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32564
NELFCD-BGHcLV47-45_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3433	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32598
NELFCD-BGHcLV47-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3433					GRCh38	V40	NELFCD-BGHcLV47-45_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGHcLV47-45_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32632
NELFCD-BGHcLV47-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3433					GRCh38	V40	NELFCD-BGHcLV47-45_Aligned.sortedByCoord.out.bam		ENCORE2	32666
NELFCD-BGHcLV47-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3433					GRCh38	V40	NELFCD-BGHcLV47-45_Aligned.sortedByCoord.out.bam		ENCORE2	32700
NELFCD-BGHcLV47-45_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3433					GRCh38	V40	NELFCD-BGHcLV47-45_Aligned.sortedByCoord.out.bam		ENCORE2	32734
NELFCD-BGHcLV47-45_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3433					GRCh38	V40	NELFCD-BGHcLV47-45_Aligned.sortedByCoord.out.bam		ENCORE2	32768
NELFCD-BGHcLV47-45_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3433					GRCh38	V40	NELFCD-BGHcLV47-45_S60_L002_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGHcLV47-45_S60_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32802
NELFCD-BGHcLV47-46_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3434	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32565
NELFCD-BGHcLV47-46_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3434	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32599
NELFCD-BGHcLV47-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3434					GRCh38	V40	NELFCD-BGHcLV47-46_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGHcLV47-46_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32633
NELFCD-BGHcLV47-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3434					GRCh38	V40	NELFCD-BGHcLV47-46_Aligned.sortedByCoord.out.bam		ENCORE2	32667
NELFCD-BGHcLV47-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3434					GRCh38	V40	NELFCD-BGHcLV47-46_Aligned.sortedByCoord.out.bam		ENCORE2	32701
NELFCD-BGHcLV47-46_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3434					GRCh38	V40	NELFCD-BGHcLV47-46_Aligned.sortedByCoord.out.bam		ENCORE2	32735
NELFCD-BGHcLV47-46_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3434					GRCh38	V40	NELFCD-BGHcLV47-46_Aligned.sortedByCoord.out.bam		ENCORE2	32769
NELFCD-BGHcLV47-46_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3434					GRCh38	V40	NELFCD-BGHcLV47-46_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NELFCD-BGHcLV47-46_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32803