HNRNPD RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV48-31	BGKcLV48-32
idx	0	0
TRCN#_or_BGC#	BGC#0000192	BGC#0000192
shRNA_or_gRNA_sequence	GTCGGAGGAGCAGTTCGGCG	GTCGGAGGAGCAGTTCGGCG
PAM	GGG	GGG
Name	HNRNPD-93F	HNRNPD-93F
Sample_ID	BGKcLV48-31	BGKcLV48-32
transduction_Date	4/15/25	4/15/25
days	D6	D6
RBP_name	HNRNPD	HNRNPD
qPCR_result	38.0	26.7
Ave_qPCR	32.4
RT-qPCR_primer-F	CTCCAGATACACCTGAAGAGAAA
RT-qPCR_primer-R	CGCCTCTTATTGGTCTTGTTG
protein_conc	2399	2552
WB_result	84.8	86.3
Ave_WB
WB_DONE_date	5/1/25
MW	38kd	TUBULIN
IP		fu's #18
antibody_Cat#	#12382	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	6177	6178

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPD	Product_ID: 12382 Lot_ID: 1 Source: Cell Signaling Technology Target Name: HNRNPD-human

Experiment Status

	BGKcLV48-31	BGKcLV48-32
Sample_ID	BGKcLV48-31	BGKcLV48-32
Sample Name
Sample Name	HNRNPD-BGKcLV48-31	HNRNPD-BGKcLV48-32
RBP	HNRNPD	HNRNPD
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-02	2025-10-02
Project	ENCORE2	ENCORE2
Note
ID	14242	14243

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV48-31	BGKcLV48-32
Sample #	5	6
Sample Name	HNRNPD-BGKcLV48-31	HNRNPD-BGKcLV48-32
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-18	2025-08-18
Lib_ID	Lib-250818	Lib-250818
Tecan_Location
Tecan
Tecan_date
Size_bp	264	248
Peak_Molarity	85.90	92.10
libSampleQC_DNA_Well	DNA_Library_set79/set1/E1.png	DNA_Library_set79/set1/F1.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set79/set1/E10.png	RNA_Library_set79/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-08-19	2025-08-19
Sample_ID	BGKcLV48-31	BGKcLV48-32
RBP	HNRNPD	HNRNPD
Batch_ID	BGKcLV48	BGKcLV48
WB_result	84.800	86.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4750	4751

Sequencing Information

	BGKcLV48-31	BGKcLV48-32
Sample_ID	BGKcLV48-31	BGKcLV48-32
Sample Name	HNRNPD-BGKcLV48-31	HNRNPD-BGKcLV48-32
Pool ID	Pool-250822	Pool-250822
LocalServer_folder	set79	set79
total_reads	35,225,594	29,875,845
total_aligned_reads	28,692,639	21,911,235
unique_aligned_reads	26,365,512	20,052,398
percent_uniqueAligned	0.74848	0.67119
correlation_replicates	0.995547	0.995547
spikein_reads	73,000	45,280
percent_spikeins	0.00207	0.00152
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3453	3454

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
HNRNPD-BGKcLV48-31_S169_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3453	NovaSeq6000	100	paired-ended	1				NT-BGKcLV48-1_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32822
HNRNPD-BGKcLV48-31_S169_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3453	NovaSeq6000	100	paired-ended	2				NT-BGKcLV48-1_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32844
HNRNPD-BGKcLV48-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3453					GRCh38	V40	HNRNPD-BGKcLV48-31_S169_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPD-BGKcLV48-31_S169_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32866
HNRNPD-BGKcLV48-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3453					GRCh38	V40	HNRNPD-BGKcLV48-31_Aligned.sortedByCoord.out.bam		ENCORE2	32888
HNRNPD-BGKcLV48-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3453					GRCh38	V40	HNRNPD-BGKcLV48-31_Aligned.sortedByCoord.out.bam		ENCORE2	32910
HNRNPD-BGKcLV48-31_Signal.Unique.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3453					GRCh38	V40	HNRNPD-BGKcLV48-31_Aligned.sortedByCoord.out.bam		ENCORE2	32932
HNRNPD-BGKcLV48-31_Signal.Unique.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3453					GRCh38	V40	HNRNPD-BGKcLV48-31_Aligned.sortedByCoord.out.bam		ENCORE2	32954
HNRNPD-BGKcLV48-32_S170_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3454	NovaSeq6000	100	paired-ended	1				NT-BGKcLV48-1_S165_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32823
HNRNPD-BGKcLV48-32_S170_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set79/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3454	NovaSeq6000	100	paired-ended	2				NT-BGKcLV48-1_S165_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV48-2_S166_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32845
HNRNPD-BGKcLV48-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3454					GRCh38	V40	HNRNPD-BGKcLV48-32_S170_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPD-BGKcLV48-32_S170_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32867
HNRNPD-BGKcLV48-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3454					GRCh38	V40	HNRNPD-BGKcLV48-32_Aligned.sortedByCoord.out.bam		ENCORE2	32889
HNRNPD-BGKcLV48-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3454					GRCh38	V40	HNRNPD-BGKcLV48-32_Aligned.sortedByCoord.out.bam		ENCORE2	32911
HNRNPD-BGKcLV48-32_Signal.Unique.strand-.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3454					GRCh38	V40	HNRNPD-BGKcLV48-32_Aligned.sortedByCoord.out.bam		ENCORE2	32933
HNRNPD-BGKcLV48-32_Signal.Unique.strand+.bw	ENCODE_DATA/set79/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3454					GRCh38	V40	HNRNPD-BGKcLV48-32_Aligned.sortedByCoord.out.bam		ENCORE2	32955