title: ATACseq_Donor3917_AAVS1

city: Philadelphia

first: Eugene

last: Khandros

state: PA

address: 3615 Civic Center Blvd.

department: Hematology

institute: The Children's Hospital of Philadelphia

description: Library name: 4267_ATACseq_Donor3917_AAVS1

data_processing:
ENCODE4 unreplicated ATAC-seq pipeline, version2.2.2, with parameter "atac.multimapping" : 4
Assembly: hg38
Supplementary files format and content: tab separated values, gene expression levels from RSEM

source_name: Human erythroid cells P3D3

growth_protocol: HSPCs were expanded for 5 days in hematopoietic expansion medium (HEM) medium containing StemSpan SFEM-II medium supplemented with 100 ng/ml stem cell factor (SCF), 100 ng/ml FMS-related tyrosine kinase 3 ligand (Flt3-L), 100 ng/ml thrombopoietin (TPO), 20 ng/ml interleukin-6 (IL-6), and 50 ng/ml interleukin-3 (IL-3), for 5 days. Subsequently, the expanded HSPCs were differentiated to the erythroid lineage using the erythroid progenitor medium (EPM) containing StemSpan SFEM-II medium supplemented with 50 ng/ml SCF, 3 U/ml erythropoietin (Epo), 20 ng/ml IL-3, and 40 ng/ml insulin growth factor-1 (IGF-1). The cells were terminally differentiated using Erythroid Differentiation Medium -I (EDM-I) consisting of IMDM Glutamax supplemented with 5% human AB serum, 2 IU/ml heparin, 10 μg/ml insulin, 5 U/ml Epo, 500 μg/ml holotransferrin and 1 μM mifepristone. After 4 days the cells were cultured in Erythroid Differentiation Medium-I (EDM-II), which consisted of EDM-I without SCF, with media change every other day until the end of differentiation.

extract_protocol:
DNA was extracted and purified using the QIAGEN MinElute Reaction Cleanup Kit.
For library preparation, fragmented DNA was amplified with Phusion High-Fidelity PCR Master Mix supplemented with HF Buffer (Thermo Fisher Scientific, catalog no. F531S) and indexed primers featuring unique dual barcodes. Libraries were purified with AMPure XP beads (Beckman Coulter, catalog no. A63881) at a 1:1 ratio, adhering to the manufacturer’s guidelines. Library quality assessment was performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 kit (catalog no. 5067-1504), and concentrations were determined through real-time PCR with the KAPA Library Quantification Kit for Illumina (KAPA Biosystems, catalog no. KK4835). Pooled libraries were sequenced in paired-end mode utilizing a P2 flow cell on the NextSeq 2000 platform, employing Illumina reagent kits as required.

treatment_protocol: Erythroid cells were targetted using a control guide RNA targetting the AAVS1 locus or BRD9 as described in the methods.

value: Primary erythroid cells

value: AAVS1 targetting

value: Erythroid differentiation


title: LN229 cells, LN2

status: Public on Nov 18 2025

type: SRA

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

country: China

institute: Jilin university

description: Library name: LN299 cells-LN2

library_source: transcriptomic

data_processing:
Raw data were processed with Cutadapt.
The clean reads were aligned to the reference Database of miRBase22.1, piRNABank and RfamV14.1
The UMI Counts of miRNA ,piRNA and SmallRNA were calculated by perl.
The expression of miRNA ,piRNA and SmallRNA was normalized to CPM
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes row counts for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Small RNAs were extracted from Ac4ManNAz-labeled U87, LN229, and Hela cells by using RNAzol RT kit (Molecular Research Center, RN-190). The extracted small RNAs were treated with DBCO-biotin and then purified through Zymo columns. The MyOne C1 Streptavidin magnetic beads (Thermo Fisher Scientific, REF: 65001) were utilized to enrich Ac4ManNAzlabeled glycoRNAs. MyOne C1 streptomycin avidin magnetic beads containing 50 ng/mL glycogen were incubated in 500 μL Biotin Wash Buffer at 25 ℃ for 1h, then centrifuged at 3000 rpm at 4℃ for 2 min, and the supernatant was discarded. The magnetic beads were re-suspended in 500 μL Biotin Wash Buffer, added into small RNAs, rotated and mixed at 4 ℃ for 2 h, and centrifuged at 3000 rpm for 2 min. The supernatant was collected, and purified using Zymo columns. The magnetic beads and the small RNAs bound to them were re-suspended in solution containing 0.75M NaCl, 10 mM EDTA, and 10 mM Tris-Cl (pH 7.4) and incubated at 22 °C for 5 min. The above mixture was mixed with 1× volume of 5% B-mercaptoethanol (BME) solution, incubated at 22 °C for 5 min, and centrifuged at 3000 rpm for 2 min. The glycoRNA-rich supernatant was collected and purified by Zymo columns.
RNA quality was checked using Agilent 4200 TapeStation (Agilenttechnologies, Santa Clara, CA, US) according to standard procedures. Sequencing libraries were constructed by QIAseq miRNA Library Kit for Illumina (Cat #331505, Qiagen) according to manufacturer's instructions. The sequencing was performed on an Illumina NovaSeq platform (Illumina, San Diego, CA, USA).

tag: cell line


title: MHU4_GC2_1G

type: RNA

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: The arrays were incubated for 16 h (60 rpm) at 45 °C in a GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientiﬁc) and washed with a GeneChip™ Fluidics Station 450 (Thermo Fisher Scientiﬁc) according to the manufacturer’s protocol.

scan_protocol: The samples were scanned using a GeneChip™ Scanner 3000 7G (Thermo Fisher Scientiﬁc). We analyzed the results via the Transcriptome Analysis Console (Thermo Fisher Scientiﬁc).

data_processing: The data was analyzed with Transcriptome Analysis Console (TAC) 4.0.3.

label: biotin

organism: Mus musculus

source_name: Mandible, C57BL/6J male, JAXA

label_protocol: We produced fragmented and labeled cDNA from 50 ng of total RNA with a GeneChip™ 3' IVT Pico Kit (Thermo Fisher Scientiﬁc).

growth_protocol: Six mice in the transportation cage unit (TCU) were launched aboard SpX-17 on May 7, 2019, from the NASA Kennedy Space Center (KSC) and were then transported to the ISS. To determine the effects of different gravitational forces on mice during spaceflight, the mice were maintained on the ISS for approximately one month.

extract_protocol: RNA was extracted from the samples via a miRNeasy® FFPE Kit (QIAGEN, Hilden, Germany), RNase Free DNase Set (QIAGEN), NanoDrop TM One (Thermo Fisher Scientific, MA, USA) and an Agilent RNA 6000 Nano Kit (Agilent Technologies, Inc., Santa Clara, California, USA), and the quality was assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, California, USA).

treatment_protocol: Gravity was set to 1/6G (0.167 g = lunar gravity = partial gravity) to mimic the gravity of the moon, as the most feasible future missions are to explore the moon. Habitat cage units (HCUs) were placed on the floor, each housing six mice, and a short radius centrifuge (MARS-S) was used to generate 1/6G. In contrast, the mice in the 1G group were housed on Earth and in the same MHU as those in the 1/6G group were.

tag: tissue

value: Mandible

tag: strain

tag: genotype

value: wild type

tag: Sex

value: male

tag: treatment


title: ATACseq_Donor3917_SMARCD1_4

country: USA

description: Library name: 4271_ATACseq_Donor3917_SMARCD1

library_source: genomic

molecule: genomic DNA

tag: cell type

value: SMARCD1 targetting


title: U87 cells, U1

description: Library name: U87 cells-U1


title: LynKO BMDMs, LPS-treated, Replicate 3

city: Minneapolis

first: Anders

middle: John

last: Lindstedt

state: MN

address: 2101 6th Street SE

department: Department of Pharmacology

institute: University of Minnesota

description: Library name: LynKO3_LPS

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36.
Trimmed sequence reads mapped to the Mus musculus GRCm38 reference genome on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were determined using featureCounts from the Subread package v.1.5.2, generating the raw_counts.csv file.
Pre-filtering was done in R to identify genes with at least 10 hit counts in at least 3 of 4 samples within a genotype-treatment group.
DESeq2 in R was used on pre-filtered hit counts and variance-stablizing transformation was applied on gene hit counts, generating the normalized expression values in vst_normalized_counts.csv file.
Assembly: GRCm38
Supplementary files format and content: The raw_counts.csv file includes the raw hit counts of all detected transcripts for every sample.
Supplementary files format and content: The vst_normalized_counts.csv file includes the variance-stablizing transformed hit counts for every sample.

molecule: polyA RNA

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow was isolated from femurs and tibiae of mice, and erythrocytes were lysed with a hypotonic solution of ammonium-chloride-potassium. For BMDM generation, 8x106 cells were seeded in 150mm untreated, polystyrene plates and cultured in 30mL of Dulbecco’s modified Eagle’s medium (DMEM) with a final concentration of 10% heat-inactivated fetal bovine serum (FBS), 1mM sodium pyruvate, 6mM L-glutamine, 1% Penicillin-Streptomycin (179mM-172mM), and 5% CMG14-12 cell-conditioned medium as a source of M-CSF, at 37 °C, 10% CO2.

extract_protocol:
Cell-culture supernatants were aspirated, cells were washed briefly in phosphate-buffered saline (PBS), and then lysed in TRIzol. RNA was isolated by chloroform extraction followed by the use of an RNeasy Mini Kit.
RNA samples were enriched for mRNA via poly-A tail selection and were sequenced with Illumina NovaSeq (2 x 150bp), generating paired-end reads, with a read depth ranging 17.5M to 27M reads per sample and a mean Q-score ranging from 37.92 to 38.64. Files labeled R1 are in the forward orientation and R2 are in the reverse-complement orientation.

treatment_protocol: BMDMs were resuspended in M-CSF-free DMEM containing 10% heat-inactivated FBS, plated at 1x106 cells/well in untreated, polystyrene 6-well plates, and rested overnight at 37 °C, 10% CO2. After resting, cells were treated 2h with M-CSF-free media alone (NT) or media containing 2 ng/mL LPS from S. Minnesota R595 or 20 ng/mL R848.

value: Bone marrow-derived macrophages

value: LynKO

value: LPS

value: Female


title: ATACseq_Donor3911_SMARCD1_4

description: Library name: 4263_ATACseq_Donor3911_SMARCD1


title: ATACseq_Donor3911_AAVS1

description: Library name: 4259_ATACseq_Donor3911_AAVS1


title: LN229 cells, LN1

description: Library name: LN229 cells-LN1


title: MHU4_FLT6_1/6G


title: MHU4_FLT5_1/6G


title: MHU4_GC3_1G


title: MHU4_FLT4_1/6G


title: RNAseq_Donor3917_SMARCD1_sg4

description: Library name: 4299_RNAseq_Donor3917_SMARCD1_sg4

data_processing:
ENCODE3 long RNA pipeline, using Gencode v43
Assembly: hg38
Supplementary files format and content: tab separated values, gene expression levels from RSEM

extract_protocol:
Total RNA was purified using an RNeasy Mini Kit (Qiagen, #74104). Genomic DNA was isolated after tagmentation using Qiagen MinElute Reaction Cleanup Kit (Qiagen #28204).
Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit (New England Biolabs, E6310L). RNA was then prepared with the Illumina Stranded Total kit (Illumina, 20040525).


title: LynKO BMDMs, R848-treated, Replicate 2

description: Library name: LynKO2_R848

value: Male


title: RNAseq_Donor3917_AAVS1

description: Library name: 4295_RNAseq_Donor3917_AAVS1


title: MHU4_GC1_1G


title: MHU4_FLT1_1/6G


title: MHU4_FLT2_1/6G


title: Hela cells, H2

description: Library name: Hela cells-H2

source_name: Hela

value: Hela


title: LynKO BMDMs, Non-treated, Replicate 2

description: Library name: LynKO2_NT

value: Non-treated


title: MHU4_FLT3_1/6G


title: MHU4_GC4_1G


title: Hela cells, H1

description: Library name: Hela cells-H1


title: RNAseq_Donor3911_AAVS1

description: Library name: 4287_RNAseq_Donor3911 _AAVS1


title: LynKO BMDMs, LPS-treated, Replicate 2

description: Library name: LynKO2_LPS


title: RNAseq_Donor3891_AAVS1

description: Library name: 4279_RNAseq_Donor3891_AAVS1


title: LynKO BMDMs, R848-treated, Replicate 1

description: Library name: LynKO1_R848


title: RNAseq_Donor3891_SMARCD1_sg4

description: Library name: 4283_RNAseq_Donor3891_SMARCD1_sg4


title: 4028_Input

description: Library name: 6076_4028_Input

data_processing:
Reads were aligned to the hg38 reference genome using Bowtie2 (2.4.5). Duplicate reads were filtered out using SAMtools (1.3.1) with MAPQ<20. We generated bigwig files for each replicate using deeptools (v3.5.1)bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig files in .bw format

source_name: Primary erythroid cells

extract_protocol:
DNA was extracted using Qiagen MinElute kit as described in the methods section.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit with NEBNext unique dual index primer pairs. Libraries were sequenced (2x50bp) on an Illumina NextSeq 2000 platform.

treatment_protocol: Erythroid cells were treated with DMSO or CFT8634 for 6hr following which they were harvested for ChIP seq.

value: Human erythroid cells P3D3

value: DMSO


title: LynKO BMDMs, Non-treated, Replicate 1

description: Library name: LynKO1_NT


title: D4017_Input

description: Library name: 6075_D4017_Input


title: U2OS, WT, Nascent Strand SEQ, Replicate 2

city: La Jolla

first: Xiaohua

last: Wu

state: CA

address: 10550 N Torrey Pines Rd

institute: Scripps Research

description: Library name: U2OS_NSSEQ_S36_S29

data_processing:
Raw bam files were generated from fastq files of NS-seq after QC, trimmimming, QC, aligned to hg19 with BWA.
Bigwig files were generated using BAMscale
Broad peaks were called with the MACS2 algorithm.
Peaks were filtered according to timing of replication
Assembly: hg19
Supplementary files format and content: Bed file format showing NS-seq peaks
Supplementary files format and content: BigWig file format of replication origin locations

source_name: bone

growth_protocol: U2OS are grown in RPMI medium with 10% FBS

extract_protocol:
For NS-seq DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).

treatment_protocol: U2OS cells were synchronized with a double thymidine block, arresting them at G1/S. After recovery and a second thymidine treatment, samples were collected at 2 hour point for analysis.

value: bone

value: osteosarcoma


title: C3277_c_1015

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

description: Library name: C3277_c_1015

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the combined reference genome (Gencode human GRCh38 and mouse GRCm38 concatenated) using TopHat2 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 1.6.3) in order to generate read count data on gene/feature level (parameters: -p -t exon -g gene_id -s 0)
Genes/features were annotated using the combined GTF file from Gencode human GRCh38 and mouse GRCm38 references
Only the reads that were mapped to the human genome were kept, whereas the reads mapped to the mouse genome were removed
Assembly: Human GRCh38 and mouse GRCm38
Supplementary files format and content: Raw read count data generated by featureCounts (Subread 1.6.3) for each sample

source_name: patient-derived xenograft

extract_protocol:
Total RNA was isolated from cell lysates using Trizol reagent (Ambion Life Technologies) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

value: patient-derived xenograft

value: BLU-222:60 mg/kg; BID, oral; palbociclib:50 mg/kg; QD, oral


title: C3277_c_1007

description: Library name: C3277_c_1007


title: D4009_Input

description: Library name: 6074_D4009_Input

value: Primary erythroid cells


title: C3277_B_1009

description: Library name: C3277_B_1009

value: BLU-222:60 mg/kg; BID, oral


title: RNAseq_Donor3911_SMARCD1_sg4

description: Library name: 4291_RNAseq_Donor3911 _SMARCD1_sg4

value: Erythroid differentiation


title: LynKO BMDMs, LPS-treated, Replicate 1

description: Library name: LynKO1_LPS


title: D4028_CFT8634_H3K27ac

description: Library name: 6071_D4028_CFT8634_H3K27ac


title: D4017_CFT8634_H3K27ac

description: Library name: 6069_D4017_CFT8634_H3K27ac


title: D4028_DMSO_H3K27ac

description: Library name: 6070_D4028_DMSO_H3K27ac


title: LynBKO BMDMs, R848-treated, Replicate 4

description: Library name: LynBKO4_R848

value: LynBKO


title: D4009_CFT8634_H3K27ac

description: Library name: 6067_D4009_CFT8634_H3K27ac


title: D4017_DMSO_H3K27ac

description: Library name: 6068_D4017_DMSO_H3K27ac


title: AR_T6

description: Library name: AR_T6

value: Vehicle:BID, oral


title: C3277_B_1004

description: Library name: C3277_B_1004


title: U2OS, WT, Nascent Strand SEQ, Replicate 1

description: Library name: U2OS_NSSEQ_S35_S28


title: C3277_c_1020

description: Library name: C3277_c_1020


title: D4009_DMSO_H3K27ac

description: Library name: 6066_D4009_DMSO_H3K27ac


title: D4028_CFT8634_BRD9

description: Library name: 6065_D4028_CFT8634_BRD9


title: LynBKO BMDMs, Non-treated, Replicate 4

description: Library name: LynBKO4_NT

value: Bone marrow-derived macrophages


title: D4017_CFT8634_BRD9

description: Library name: 6063_D4017_CFT8634_BRD9


title: D4028_DMSO_BRD9

description: Library name: 6064_D4028_DMSO_BRD9


title: LynBKO BMDMs, R848-treated, Replicate 3

description: Library name: LynBKO3_R848


title: AR_T5

description: Library name: AR_T5


title: LynBKO BMDMs, Non-treated, Replicate 3

description: Library name: LynBKO3_NT


title: AR_T4

description: Library name: AR_T4


title: AR_T3

description: Library name: AR_T3


title: LynBKO BMDMs, LPS-treated, Replicate 3

description: Library name: LynBKO3_LPS

value: LPS


title: LynBKO BMDMs, LPS-treated, Replicate 4

description: Library name: LynBKO4_LPS

value: Female


title: D4009_CFT8634_BRD9

description: Library name: 6061_D4009_CFT8634_BRD9


title: D4017_DMSO_BRD9

description: Library name: 6062_D4017_DMSO_BRD9


title: D4009_DMSO_BRD9

description: Library name: 6060_D4009_DMSO_BRD9


title: H2VS43_d2_CFT8634

description: Library name: 6084_H2VS43_d2_CFT8636

source_name: HUDEP-2 cells

growth_protocol: HUDEP-2 cells were grown at a density of 100,000/mL to 1 million/mL in StemSpan Serum Free Medium (SFEM, StemCell Technologies, Cat. #09650) containing 50 ng/ml human Stem Cell Factor (hSCF, Peprotech, Cat #300-07), 1 μM dexamethasone (Sigma, Cat #D4902), 1 μg/ml doxycycline (Sigma, Cat #D9891), 3 IU/ml erythropoietin (Amgen, Cat #55513-144-10), 1% penicillin/streptomycin (ThermoFisher, Cat #15140122), and 1 μg/ml puromycin. For differentiation, cells were washed and resuspended in IMDM (Mediatech, Cat #MT10016CV) supplemented with 3 IU/ml erythropoietin, 5% fetal bovine serum, 320 μg/ml holo-transferrin (Sigma, Cat # T4132), 1% penicillin/streptomycin, 10 g/ml (2 IU/mL) heparin (Sigma, Cat # H3149), 10 μg/ml insulin (Sigma, Cat # I9278), 1 μg/ml doxycycline, and 50 ng/ml hSCF for the first 2 days. Media was changed once at day 2 of differentiation to remove hSCF.

treatment_protocol: HUDEP-2 clones were either treated with DMSO or CFT8634 for 6h.

value: HUDEP-2 cells

value: Immortalized erythroid cells

value: CFT8634 treatment


title: AR_T2

description: Library name: AR_T2


title: H2VS43_d2_DMSO

description: Library name: 6083_H2VS43_d2_DMSO

value: DMSO treatment


title: LynBKO BMDMs, R848-treated, Replicate 2

description: Library name: LynBKO2_R848

value: Male


title: AR_T1

description: Library name: AR_T1


title: H2VS37_d2_CFT8634

description: Library name: 6082_H2VS37_d2_CFT8634


title: H2VS22_d2_CFT8634

description: Library name: 6080_H2VS22_d2_CFT8634


title: T141_c_2063

description: Library name: T141_c_2063

value: BLU-222:50 mg/kg; BID, oral; palbociclib:50 mg/kg; QD, oral


title: LynBKO BMDMs, LPS-treated, Replicate 2

description: Library name: LynBKO2_LPS


title: T141_c_2060

description: Library name: T141_c_2060


title: H2VS15_d2_CFT8634

description: Library name: 6078_H2VS15_d2_CFT8634


title: H2VS15_d2_DMSO

description: Library name: 6077_H2VS15_d2_DMSO

value: DMSO


title: LynBKO BMDMs, R848-treated, Replicate 1

description: Library name: LynBKO1_R848


title: RNAseq_Donor3_BRD9_KO

description: Library name: 5269_RNAseq_Donor3_BRD9_KO

value: Human erythroid cells P3D3

value: BRD9 knockout


title: T141_c_2056

description: Library name: T141_c_2056

value: patient-derived xenograft


title: T141_c_2038

description: Library name: T141_c_2038


title: RNAseq_Donor2_AAVS2

description: Library name: 5266_RNAseq_Donor2_AAVS1

value: Primary erythroid cells

value: AAVS1 targetting


title: LynBKO BMDMs, Non-treated, Replicate 1

description: Library name: LynBKO1_NT

value: LynBKO

value: Non-treated


title: T141_p_2075

description: Library name: T141_p_2075

value: Palbociclib:50 mg/kg; QD, oral


title: RNAseq_Donor2_BRD9_KO

description: Library name: 5267_RNAseq_Donor2_BRD9_KO

value: Erythroid differentiation


title: RNAseq_Donor1_BRD9_KO

description: Library name: 5265_RNAseq_Donor1_BRD9_KO


title: RNAseq_Donor3_AAVS1

description: Library name: 5268_RNAseq_Donor3_AAVS1


title: LynBKO BMDMs, LPS-treated, Replicate 1

description: Library name: LynBKO1_LPS

value: Bone marrow-derived macrophages

value: LPS


title: ATACseq_Donor3_CFT8634

description: Library name: 5275_ATACseq_Donor3_BRD9_KO

data_processing:
ENCODE4 unreplicated ATAC-seq pipeline, version2.2.2, with parameter "atac.multimapping" : 4
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
DNA was extracted using Qiagen MinElute kit as described in the methods section.
ATAC-seq was conducted following the Omni-ATAC protocol.


title: T141_p_2071

description: Library name: T141_p_2071


title: LynAKO BMDMs, R848-treated, Replicate 4

description: Library name: LynAKO4_R848

value: LynAKO

value: Female


title: LynBKO BMDMs, Non-treated, Replicate 2

description: Library name: LynBKO2_NT


title: ATACseq_Donor3_DMSO

description: Library name: 5274_ATACseq_Donor3_AAVS1


title: T141_p_2070

description: Library name: T141_p_2070


title: ATACseq_Donor2_CFT8634

description: Library name: 5273_ATACseq_Donor2_BRD9_KO


title: RNAseq_Donor1_AAVS1

description: Library name: 5264_RNAseq_Donor1_AAVS1


title: LynAKO BMDMs, Non-treated, Replicate 4

description: Library name: LynAKO4_NT


title: H2VS22_d2_DMSO

description: Library name: 6079_H2VS22_d2_DMSO

value: HUDEP-2 cells

value: Immortalized erythroid cells

value: DMSO treatment


title: ATACseq_Donor1_CFT8634

description: Library name: 5271_ATACseq_Donor1_BRD9_KO


title: LynAKO BMDMs, R848-treated, Replicate 3

description: Library name: LynAKO3_R848


title: ATACseq_Donor1_DMSO

description: Library name: 5270_ATACseq_Donor1_AAVS1


title: T141_p_2057

description: Library name: T141_p_2057


title: Muscle, exercised, placebo, P10

city: Liverpool

first: Daniel

last: Owens

address: Byrom Street

department: Research Institute for Sport and Exercise Science

country: United Kingdom

institute: Liverpool John Moores University

description: Library name: GC-DO-11238-10-2-PLA-40_S36

data_processing:
Partek® Flow® Genomic Analysis Software
Pre-alignment QA/QC was performed on all reads prior to read trimming. STAR alignment 4.4.1d was used to align trimmed reads to the hg38 - Ensembl Transcripts release 99
Aligned reads were then quantified to the Ensembl transcriptome annotation model associated with hg38 - Ensembl Transcripts release 99
Filtered raw counts were used for normalisation and differential analysis with DESeq2
Assembly: hg38 - Ensembl Transcripts release 99
Supplementary files format and content: Matrix table, raw counts (quantification)
Supplementary files format and content: Matrix table, normalized counts (normalization)

source_name: Skeletal muscle

extract_protocol:
Muscle biopsies were lysed with TRI reagent and mechanically disrupted with a Tissue Lyser. Lysates were then process with the Qiagen RNeasy kit (Qiagen Ltd). RNA was then extracted from  lysates using the RNeasy kit with proteinase K digestion, as per the manufacturer’s guidelines. Eluted RNA was stored at -80oC until required for determination of total RNA and library processing.
Libraries were constructed from 100 ng of total RNA with Poly-A tail enrichment of mRNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with Agencourt AMPureXP Sample Purification Beads (Beckman Coulter. Wycombe, UK) as per manufacturers guidelines, by Bart's and the London Genome Centre at Queen Mary, University of London.

value: Skeletal muscle

value: exercised

value: placebo

tag: subject id


title: LynAKO BMDMs, Non-treated, Replicate 3

description: Library name: LynAKO3_NT


title: LynAKO BMDMs, LPS-treated, Replicate 4

description: Library name: LynAKO4_LPS


title: ATACseq_Donor2_DMSO

description: Library name: 5272_ATACseq_Donor2_AAVS1

value: Human erythroid cells P3D3


title: Muscle, rest, placebo, P10

description: Library name: GC-DO-11238-10-2-PLA-39_S9

value: rest


title: T141_p_2037

description: Library name: T141_p_2037

value: patient-derived xenograft


title: Muscle, exercised, ketone ester, P10

description: Library name: GC-DO-11238-10-1-KET-38_S18

value: ketone ester


title: Muscle, exercised, ketone ester, P9

description: Library name: GC-DO-11238-9-2-KET-36_S33


title: Muscle, rest, ketone ester, P10

description: Library name: GC-DO-11238-10-1-KET-37_S8


title: T141_p_2036

description: Library name: T141_p_2036


title: LynAKO BMDMs, R848-treated, Replicate 2

description: Library name: LynAKO2_R848

value: Male


title: Muscle, exercised, placebo, P9

description: Library name: GC-DO-11238-9-1-PLA-34_S22


title: Muscle, rest, ketone ester, P9

description: Library name: GC-DO-11238-9-2-KET-35_S15


title: H2VS37_d2_DMSO

description: Library name: 6081_H2VS37_d2_DMSO

value: DMSO


title: Muscle, rest, placebo, P9

description: Library name: GC-DO-11238-9-1-PLA-33_S5


title: T141_hi_2061

description: Library name: T141_hi_2061

value: BLU-222:100 mg/kg; BID, oral


title: T141_hi_2049

description: Library name: T141_hi_2049


title: Muscle, exercised, placebo, P8

description: Library name: GC-DO-11238-8-2-PLA-32_S4


title: Muscle, exercised, ketone ester, P8

description: Library name: GC-DO-11238-8-1-KET-30_S39


title: T141_lo_2046

description: Library name: T141_lo_2046

value: BLU-222:50 mg/kg; BID, oral


title: Muscle, rest, placebo, P8

description: Library name: GC-DO-11238-8-2-PLA-31_S14


title: LynAKO BMDMs, Non-treated, Replicate 2

description: Library name: LynAKO2_NT

value: Bone marrow-derived macrophages

value: Non-treated


title: LynAKO BMDMs, LPS-treated, Replicate 2

description: Library name: LynAKO2_LPS

value: LynAKO

value: LPS


title: Muscle, rest, ketone ester, P8

description: Library name: GC-DO-11238-8-1-KET-29_S29


title: Muscle, exercised, placebo, P7

description: Library name: GC-DO-11238-7-2-PLA-28_S16


title: LynAKO BMDMs, LPS-treated, Replicate 3

description: Library name: LynAKO3_LPS

value: Female


title: LynAKO BMDMs, Non-treated, Replicate 1

description: Library name: LynAKO1_NT


title: T141_lo_2035

description: Library name: T141_lo_2035


title: Muscle, exercised, ketone ester, P7

description: Library name: GC-DO-11238-7-1-KET-26_S34


title: LynAKO BMDMs, LPS-treated, Replicate 1

description: Library name: LynAKO1_LPS


title: T141_v_2066

description: Library name: T141_v_2066

value: Vehicle:BID, oral


title: Muscle, rest, placebo, P6

description: Library name: GC-DO-11238-6-2-PLA-23_S12

value: Skeletal muscle


title: Muscle, exercised, placebo, P6

description: Library name: GC-DO-11238-6-2-PLA-24_S3

value: exercised


title: Muscle, exercised, ketone ester, P6

description: Library name: GC-DO-11238-6-1-KET-22_S21


title: Niacin Treated Mouse - Slide 1

city: Charlestown

first: Reid

last: Mcneil

state: MA

address: 149 13th Street

department: Cancer Research

institute: Mass General Hospital

description:
Library name: B9_S6
10x Genomics - fressh frozen tissue

data_processing:
Spatial transcriptomics data were processed using the 10x Genomics Space Ranger software. BCL files were converted to FASTQ files and processed using the spaceranger count pipeline, which performs demultiplexing, alignment, and gene counting. Reads were aligned to the mm10 mouse reference transcriptome using STAR. Tissue images were registered to the spatial barcode array using fiducial alignment and manual tissue detection. Expression matrices were generated for each capture area. When applicable, the spaceranger aggr pipeline was used to aggregate data from multiple samples into a single expression matrix, with the normalization option set to 'none' to retain raw sequencing depth per spot.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz - list of spatial barcodes
Supplementary files format and content: features.tsv.gz - list of gene IDs
Supplementary files format and content: matrix.mtx.gz - gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fluidics.jpg - aligned fluidics of tissue image
Supplementary files format and content: detected_tissue_image.jpeg - image of tissue and spots
Supplementary files format and content: scale_factors_json.json - scale factors in json format
Supplementary files format and content: tissue_hires_image.png - hires image of tissue
Supplementary files format and content: tissue_lowres_image.png - lowres image of tissue
Supplementary files format and content: tissue_position_list.csv - list of spatial barcodes and the coordinates specifiying spots
Library strategy: Spatial Transcriptomics

source_name: Brain

growth_protocol: In this study, all mice utilized were of C57BL/6 background and were sourced from Charles River as 6- to 8-week-old female wild-type mice. Ethical approval for all experiments involving animals was obtained from the Animal Care Committee at the University of Calgary, following the guidelines set forth by the Canadian Council of Animal Care.

extract_protocol:
The spatial transcriptomics analysis was conducted using the Visium Spatial Gene Expression platform by 10x Genomics. Brain tissues, collected 40 days after tumor implantation, were frozen and sectioned into 10-μm slices, following the manufacturer’s guidelines. Sections were placed on Visium slides and processed as per the user guide. Tissue optimization studies delineated an optimal permeabilization time of 12 mins. Brightfield images distinguishing tumor and non-tumor regions were captured using the EVOS FL Auto Imaging System.
The subsequent library preparation steps were performed as per the user guide (Visium Spatial Gene Expression Reagent Kit; CG000239). The libraries were then sequenced on an Illumina NovaSeq 6000 system, employing a NovaSeq 200 Cycle S1 flow cell and specific read cycles for sequencing.

treatment_protocol: In the niacin experiments, starting seven days after implantation, mice were treated with niacin at a dose of 100 mg/kg daily via intraperitoneal injection until the termination of the experiment. Control mice were injected with an identical vehicle (saline) solution.

value: Brain

tag: mouse strain

value: female

tag: age

value: treated


title: T141_hi_2034

description: Library name: T141_hi_2034

value: patient-derived xenograft


title: Niacin Treated Mouse 2

description:
Library name: N2_S4
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing depth obtained ranged from approximately 95,000-116,000 reads/cell. BCL files obtained were processed using the Cell Ranger version 3.1 pipeline. Briefly, the fastq files were processed with the cellranger count pipeline which uses STAR to align the reads to the mm10 mouse reference transcriptome. The cellranger aggregate pipeline was run to generate an expression matrix with all combined libraries with normalization setting set to ‘None’.
Assembly: mm10
Supplementary files format and content: tab-separated files and matrix files

extract_protocol:
Mice were euthanized four weeks post-tumor implantation, and brains were isolated. To enrich for tumor tissue, brains were hemisected, and a 2 mm section around the tumor injection site was collected into Hank’s Balanced Salt Solution (HBSS, Gibco). Four brain tissues were pooled together per sample to ensure an adequate number of cells for downstream scRNA-seq analysis (Control: 5 mice, one replicates; niacin injection: 10 mice, two replicates). Subsequently, brain tissues were homogenized using a Dounce homogenizer and filtered through a 40-µm cell strainer. The cell suspension underwent Percol gradient separation to remove myelin debris. After further filtration through a 35-µm cell strainer, cells were resuspended in PBS containing 1% heat-inactivated FBS (Sigma) and 0.1LJmM EDTA.
Once a single cell suspension was generated as described above, cells were labelled with SYTOX™ Red Dead Cell Stain (ThermoFisher, S34860) to discriminate between live/dead cells. Live cells were sorted on FACSAria III (BD) using a 100-µm nozzle. scRNA gene expression libraries were prepared using the Chromium Next GEM single cell 3’ reagent kits v3.1 from 10x Genomics. Appropriate volume of cells, as determined from the user guide for recovery of 3000 cells, was loaded on the Chromium single cell controller chip. Post cDNA amplification QC and quantification as well as library construction QC was done using an Agilent Bioanalyzer high sensitivity DNA chip for use with the Agilent 2100 Bioanalyzer. For sequencing, all libraries were pooled and loaded at 300pM on the NovaSeq Ilumina system using the NovaSeq S1 flowcell. A 28 base-pair Read 1 was used to sequence the cell barcode and UMI, an 8 bp i7 index read was used to sequence the sample index and a 91bp Read 2 was used to sequence the transcript using paired-end sequencing.


title: Muscle, rest, ketone ester, P6

description: Library name: GC-DO-11238-6-1-KET-21_S37

value: rest

value: ketone ester


title: Muscle, rest, placebo, P4

description: Library name: GC-DO-11238-4-2-PLA-15_S25

value: placebo


title: T141_v_2050

description: Library name: T141_v_2050


title: Muscle, exercised, placebo, P4

description: Library name: GC-DO-11238-4-2-PLA-16_S17


title: Niacin Treated Mouse 1

description:
Library name: N1_S3
10x Genomics


title: LynAKO BMDMs, R848-treated, Replicate 1

description: Library name: LynAKO1_R848

value: Male


title: T141_v_2048

description: Library name: T141_v_2048


title: Muscle, exercised, ketone ester, P4

description: Library name: GC-DO-11238-4-1-KET-14_S28


title: X517_c_2023

description: Library name: X517_c_2023

value: BLU-222:50 mg/kg; BID, oral; palbociclib:50 mg/kg; QD, oral


title: Control 2

description:
Library name: C2_S2
10x Genomics

value: control


title: T141_lo_2041

description: Library name: T141_lo_2041

value: BLU-222:50 mg/kg; BID, oral


title: Muscle, rest, placebo, P3

description: Library name: GC-DO-11238-3-2-PLA-11_S24


title: Muscle, rest, placebo, P7

description: Library name: GC-DO-11238-7-2-PLA-27_S10


title: R2, day12, rep2

city: Beijing

first: Shuo

last: Liu

address: 5 Dong Dan San Tiao

department: Department of Immunology

institute: Chinese Academy of Medical Sciences

description:
Library name: Resolution-2
Column name: R2

data_processing:
CRISPR sequencing data processing step included filtering and error rate distribution check. RNA-seq data processing step included filtering, error rate check, GC content distribution check.
Assembly: mm10
Supplementary files format and content: Excel table with sgRNA read count in screen and input sample.
Supplementary files format and content: Excel table with fpkm level of each gene in different samples.

source_name: lung

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen). Total RNA was extracted using Direct-zol RNA Microprep Kits (Zymo Research).
DNA templates underwent terminal repair and poly A tail addtion, and then adapters were connected to both ends of DNA fragments to prepare a PCR-free library.  mRNA were enriched by oligo(dT) beads and library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Mice were infected with IAV for different times before type 2 AEC isolation.

value: lung

value: Type 2 AEC


title: Muscle, rest, ketone ester, P7

description: Library name: GC-DO-11238-7-1-KET-25_S2


title: Muscle, exercised, ketone ester, P3

description: Library name: GC-DO-11238-3-1-KET-10_S38


title: X517_c_2022

description: Library name: X517_c_2022


title: R1, day12, rep1

description:
Library name: Resolution-1
Column name: R1


title: Muscle, rest, ketone ester, P3

description: Library name: GC-DO-11238-3-1-KET-9_S30


title: Muscle, exercised, placebo, P2

description: Library name: GC-DO-11238-2-2-PLA-8_S40


title: X517_c_2020

description: Library name: X517_c_2020


title: I2, day7, rep2

description:
Library name: Inflammation-2
Column name: I2


title: Muscle, exercised, ketone ester, P2

description: Library name: GC-DO-11238-2-1-KET-6_S27


title: X517_c_2019

description: Library name: X517_c_2019


title: Muscle, rest, ketone ester, P2

description: Library name: GC-DO-11238-2-1-KET-5_S35


title: T141_v_2032

description: Library name: T141_v_2032


title: X517_p_2009b

description: Library name: X517_p_2009b

value: Palbociclib:50 mg/kg; QD, oral


title: I1, day7, rep1

description:
Library name: Inflammation-1
Column name: I1


title: Muscle, rest, ketone ester, P1

description: Library name: GC-DO-11238-1-2-KET-3_S7


title: Muscle, exercised, ketone ester, P1

description: Library name: GC-DO-11238-1-2-KET-4_S20


title: C2, day0, rep2

description:
Library name: Ctrl-2
Column name: C2


title: Muscle, rest, ketone ester, P4

description: Library name: GC-DO-11238-4-1-KET-13_S11


title: Muscle, rest, placebo, P1

description: Library name: GC-DO-11238-1-1-PLA-1_S19


title: C1, day0, rep1

description:
Library name: Ctrl-1
Column name: C1


title: X517_p_2009

description: Library name: X517_p_2009


title: Muscle, exercised, placebo, P3

description: Library name: GC-DO-11238-3-2-PLA-12_S23


title: X517_hi_2029

description: Library name: X517_hi_2029

value: BLU-222:100 mg/kg; BID, oral


title: 48hr SAHA Treated RNA-seq Bio rep 2

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

description:
Library name: 2501_126
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T48vsUTR48.DESEQ.norm.csv

data_processing:
ATAC-seq libraries were sequenced as described above and analysis was performed as previously described (Roth et al., 2023; Venu et al., 2024). Twelve ATAC-seq libraries were sequenced to a median depth of 57 million read pairs per library. Briefly, raw reads were trimmed and filtered to remove Nextra adaptors and reads with repetitive sequences using Fastp (Chen et al., 2018) . Bases with low quality scores (q < 15) were removed. Processed reads were aligned to the telomere-to-telomere (T2T) human reference genome, version 2 (Nurk et al., 2022) via BWA (Li and Durbin, 2009). Duplicate sequenced pairs and mitochondrial reads were marked and removed from analysis via Samblaster (Faust and Hall, 2014). Samples were further filtered using samtools with the following flags:  -F 4 -F 256 -F 512 -F 1024 -F 2048 -q 30.  Samples were then passed to MACS2 in BAMPE mode. Loci displaying significant enrichment of paired-end reads were identified as peaks using MACS2 (Gaspar, 2018; Zhang et al., 2008). Replicate correlation was assessed using deepTools (Ramirez et al., 2016) -plotCorrelation function on SPMR normalized MACS2 output big wig files. Open chromatin regions (OCRs) were defined by MACS2-called peaks followed the BEDtools (Quinlan and Hall, 2010) merge function. OCR differential accessibility analysis was performed using the DESeq2 (Love et al., 2014) matrix design (~time + treatment).
We generated 12 RNA-seq libraries and sequenced to approximately 17 million read pairs per library. Raw read quality control was performed using FastQC (Andrews, 2010) and SeqMonk (Andrews, 2007) to verify library quality and degree of PCR duplication; all metrics are within the expected range. The human T2T reference genome and annotations were retrieved from NCBI. Annotations were converted to gtf format using the AGAT (Jacques Dainat, 2023) package function (agat_convert_sp_gff2gtf.pl). A splice junction aware reference index was generated for the combined genome and annotation files using STAR (Dobin et al., 2013) with the arguments (--runMode genomeGenerate --sjdbOverhang 149). Pre-alignment read trimming was not performed in favor of soft-clipping/quality filtering by the STAR aligner. Reads were aligned to the combined genome using STAR. Duplicate reads were marked but retained in downstream analysis per DESeq2 guidelines. Sense strand reads aligning to gene features were counted using htseq-count (Putri et al., 2022) with the arguments (--stranded=reverse). Differential expression analysis was performed using the DESeq2 (Love et al., 2014) matrix design (~time + treatment). For visualization, replicate alignment files were merged using samtools. bigWigs were then generated using the bamCoverage function from the deepTools (Ramirez et al., 2016) package with the arguments (--effectiveGenomeSize 3117292070 --normalizeUsing BPM –filterRNAstrand {forward/reverse/NULL} --binSize 1).
Assembly: T2T-CHM13v2.0
Supplementary files format and content: .bw files: contain signal track visualizable in any genome browser
Supplementary files format and content: DESeq2 result table includes timepoint specific DESeq output. This file is used to identify genes with significant difference in expression.

source_name: lung carcinomatous tissue

growth_protocol: A549 cells, isolated from the lung tissue of a 58-year-old Caucasian male with lung cancer, were obtained from ATCC (Cat. #CCL-185). Cells were maintained in Complete Medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 4 mM L-Glutamine (ATCC, Cat. #30-2002) and 10% (v/v) Fetal Bovine Serum (FBS, ATCC, Cat. #30-2020). Cells were incubated at 37°C with 5% CO2 and 95% relative humidity. Multiple vials were cryopreserved at passage #2 in liquid nitrogen vapor until needed for cell culture experiments. For cryopreservation, cells were resuspended to a density of 106 cells per mL in ice-cold Freezing Medium consisting of DMEM,  20% (v/v) FBS, and 5% (v/v) dimethylsulfoxide (DMSO, ATCC, Cat. # 4-X).

extract_protocol:
During cell harvest (at 24 and 48 hrs post-treatment), drug-treated and mock-treated culture flasks for each biological replicate were processed in parallel. Cells were washed once in 1X PBS, detached using 1X TrypLE Express Enzyme for 20 min, then resuspended in Complete Medium to create a uniform single-cell suspension. Cell suspensions were held at room temperature and counted using the Scepter 3.0 Handheld Cell Counter and 60 µm Counter Sensors, then immediately divided as needed for downstream processing.
For RNA-seq, 2x105 cells were cryopreserved in Freezing Medium into duplicate 1 mL aliquots 24 and 48 hrs after treatment. RNA was extracted using the RNeasy UCP Micro Kit protocol kit (Qiagen, Cat. #73934) as previously described (Venu et al., 2024). Aliquots were thawed in treatment pairs (mock-treated and SAHA-treated) in a 37°C water-bath, transferred to ice-cold Complete Medium, then centrifuged at 1000 rcf for 2 min. Cells were washed in 10 mL ice-cold 1X HBSS (Gibco, Cat. #14025092) and lysed in 350 µL ice-cold RULT Buffer containing 1% (v/v) b-mercaptoethanol (Sigma, Cat. #63689). RNA extractions, performed immediately after cell lysis, and included an on-column DNase I treatment step for 15 min to deplete DNA. RNA was eluted in 20 µL RNase-free water and total RNA was quantified with the Qubit RNA HS Assay Kit (Thermo Scientific, Cat. #Q32855). RNA quality was measured using the Bioanalyzer RNA 6000 Assay (Agilent, Cat. #5067-1511). Ribosomal RNA was depleted from 500 ng total RNA using the Ribo-Zero Plus rRNA Depletion Kit (Illumina, Cat. #20037135). Sequencing libraries were generated using the Illumina NextSeq 500 High Output Kit v2.5 (Cat. #20024908) and eluted in DNA Elution Buffer (Zymo Research, Cat. #D3004-4-10). Library concentration and average size was verified using the TapeStation DNA 5000 Assay Reagents and Screen Tapes (Agilent, Cat. #5067-5589 and #5067-5588). Libraries were normalized and pooled based on the TapeStation concentrations, then pooled libraries were quantified using the Illumina/Universal Library Quantification Kit (KAPA Biosystems, Cat. #KK4824). Libraries were sequenced on an entire lane of NextSeq 500 HO flow cell to generate paired-end 151 bp reads (300 cycles).

treatment_protocol: For cell culture experiments, A549 cells were propagated for at least two additional passages prior to seeding for HDACi drug treatments. Cells were washed once in 1X PBS (Gibco, Cat. # 10010049), detached using 1X TrypLE Express Enzyme (Thermo Scientific, Cat. # 12604021), resuspended into Complete Medium, and counted using the Scepter 3.0 Handheld Cell Counter and 60 µm Counter Sensors (Millipore, Cat. #PHCC360KIT). Cells were seeded for HDACi drug treatments at passage #7-8 into replicate tissue culture flasks (surface area = 175 cm2) in three biological replicates using 5x106 cells per flask. Seeded flasks were incubated for 72 hrs at 37°C, yielding a confluent monolayer (~10x106 cells per flask) at the time of drug treatment. Cell-seeding medium was removed after 72 hrs from replicate tissue culture flasks and replaced with Complete Medium containing 10 µM of the HDACi drug suberoylanilide hydroxamic acid (SAHA) or containing an equivalent volume of the drug vehicle only, DMSO (Pierce, Cat. #85190). Mock-treated (control) and drug-treated culture flasks were incubated in parallel for 24 or 48 hrs at 37°C.

value: lung carcinomatous tissue

value: Treated with 10 µM SAHA


title: Input

description:
Library name: Control
Column name: control_count

data_processing:
CRISPR sequencing data processing step included filtering and error rate distribution check. RNA-seq data processing step included filtering, error rate check, GC content distribution check.
Assembly: mm10
Supplementary files format and content: Excel table with sgRNA read count in screen and input sample.
Supplementary files format and content: Excel table with fpkm level of each gene in different samples.
Library strategy: CRISPR Screen


title: 48hr SAHA Treated RNA-seq Bio rep 1

description:
Library name: 2501_125
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T48vsUTR48.DESEQ.norm.csv


title: 48hr Control RNA-seq Bio rep 3

description:
Library name: 2501_124
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T48vsUTR48.DESEQ.norm.csv

value: Untreated


title: IAV_screen

description:
Library name: Screen
Column name: treatment_count


title: Muscle, rest, placebo, P2

description: Library name: GC-DO-11238-2-2-PLA-7_S31

value: Skeletal muscle


title: 48hr Control RNA-seq Bio rep 2

description:
Library name: 2501_123
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T48vsUTR48.DESEQ.norm.csv


title: X517_hi_2021

description: Library name: X517_hi_2021


title: 2312041_F_0116,the naphthalene-induce airway epithelial injury group

city: Tianjin

first: Xuan

last: Miao

address: No. 890 Jingu Road, Shuanggang Town, Tianjin, China

institute: Haihe Clinical School, Tianjin Medical University, Tianjin, China

description:
Library name: sample4
Filtered gene-barcode matrix generated by Cell Ranger v2.1.1. Contains UMI counts for high-quality cells from sample 2312041_F_0116.

data_processing:
Raw sequencing data were processed for quality control using fastp 0.23.1, removing low-quality reads, adapter sequences, and fragments shorter than 60 bp. Quality metrics, including Q20, Q30, and GC content, were assessed to obtain Clean Reads. The Clean Reads were subjected to single-cell library quality control using SeekSoul® Tools 1.0.0, aligned to the reference genome with STAR 2.7.1a, and gene expression was quantified using featureCounts. Reads with matching Barcodes and UMI values from the same cell were deduplicated to generate a cell-gene expression matrix. High-quality cells were identified using Cell Ranger and EmptyDrops methods based on UMI total and expression characteristics. Cell filtering was performed using Seurat 4.0.5, with criteria: cells with less than 300 UMIs were considered free RNA contamination, and cells with significantly higher mitochondrial gene expression were removed based on the MAD method.
Assembly: mm10
Supplementary files format and content: Processed data files include: 1. filtered_feature_bc_matrix.zip – Contains the filtered gene-barcode matrix generated by Cell Ranger v2.1.1 (10x Genomics), including:    - matrix.mtx.gz: Sparse UMI count matrix (genes x cells),    - barcodes.tsv.gz: List of cell barcodes,    - features.tsv.gz: List of gene names. 2. A/B/E/F_0116_seurat.rds – An RDS file containing the Seurat object for sample A_0116. This object includes the normalized expression matrix, dimensionality reduction results (PCA, UMAP), clustering assignments, and cell metadata. Generated using Seurat v4.1.1. 3. result.rds – An RDS file containing the integrated Seurat object from four samples. This object includes merged expression data, clustering results, UMAP coordinates, and marker gene analysis for each cluster. Generated using Seurat v4.1.1. These files represent processed single-cell RNA-seq data ready for downstream analysis and visualization.

source_name: Lung tissue

extract_protocol:
After sampling, tissue was washed in pre-chilled PBS and dissociated using the Tissue Dissociation Kit A Pro (K01801-30, SeekGene BioTech Co., Ltd., Shanghai, China). Red blood cells were removed using Red Blood Cell Lysis Buffer (R1010, Solarbio), followed by AO/PI staining. Cell quality was assessed using a fluorescence cell analyzer (Countstar®Rigel S2). Based on cell viability and nuclear integrity, dead cells (130-090-101, Miltenyi Biotec) and debris (130-109-398, Miltenyi) were removed. The cells were washed twice in RPMI1640 (11875119, Gibco) and resuspended in RPMI1640 with 2% FBS at a concentration of 1 × 10⁶ cells/mL.
scRNA-seq libraries were prepared using the SeekOne® Digital Droplet Single Cell 3’ Library Preparation Kit (No.K00202, SeekGene). Cells were mixed with reverse transcription reagents and loaded into sample wells of the SeekOne® chip. Barcoded Hydrogel Beads (BHB) and oil phase were then added to form emulsion droplets. Reverse transcription was performed at 42°C for 90 minutes, followed by 5 minutes of inactivation at 85°C. After emulsion breaking, cDNA was purified and PCR amplified. The amplified cDNA products were fragmented, end-repaired, and ligated with sequencing adapters, followed by purification. The library was purified using Vazyme N411-01 DNA purification beads and analyzed with Qubit (Q33226, Thermo Fisher Scientific) and a Bioptic Qsep400 Fragment Analyzer. Finally, libraries were sequenced on an Illumina NovaSeq 6000 platform with PE150 chemistry, and the raw data was saved in FASTQ format.

value: Lung tissue

tag: batch


title: X517_hi_2004

description: Library name: X517_hi_2004

value: patient-derived xenograft


title: 24hr SAHA Treated RNA-seq Bio rep 3

description:
Library name: 2501_121
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T24vsUTR24.DESEQ.norm.csv


title: Muscle, exercised, placebo, P1

description: Library name: GC-DO-11238-1-1-PLA-2_S32

value: exercised


title: 24hr SAHA Treated RNA-seq Bio rep 2

description:
Library name: 2501_120
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T24vsUTR24.DESEQ.norm.csv


title: X517_lo_2026

description: Library name: X517_lo_2026


title: X517_lo_2011

description: Library name: X517_lo_2011


title: 24hr Control RNA-seq Bio rep 1

description:
Library name: 2501_116
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T24vsUTR24.DESEQ.norm.csv


title: 2312041_B_0116,the H37Rv-infect group

description:
Library name: sample2
Filtered gene-barcode matrix generated by Cell Ranger v2.1.1. Contains UMI counts for high-quality cells from sample 2312041_B_0116.


title: 2312041_E_0116,the naphthalene-induce airway epithelial injury prior to infection with H37Rv group

description:
Library name: sample3
Filtered gene-barcode matrix generated by Cell Ranger v2.1.1. Contains UMI counts for high-quality cells from sample 2312041_E_0116.


title: X517_lo_2005

description: Library name: X517_lo_2005


title: 24hr SAHA Treated RNA-seq Bio rep 1

description:
Library name: 2501_119
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T24vsUTR24.DESEQ.norm.csv


title: 48hr SAHA Hi-C Bio rep 1

description:
Library name: 2501_054
Processed .hic files.

data_processing:
Paired Hi-C reads were analyzed via Juicer Hi-C pipeline (Durand et al., 2016) and aligned to the T2T reference genome (Nurk et al., 2022). Restriction sites were identified, and Hi-C (.hic) files were generated using Juicer default settings with a mapping quality threshold of ‘q = 30’. We detected at least 700 million valid Hi-C contacts per condition. Replicate Hi-C maps were merged via Juicer (“mega” function)
Assembly: T2T-CHM13v2.0
Supplementary files format and content: .hic files prvide contract matrices from multiple resolutions.

extract_protocol:
During cell harvest (at 24 and 48 hrs post-treatment), drug-treated and mock-treated culture flasks for each biological replicate were processed in parallel. Cells were washed once in 1X PBS, detached using 1X TrypLE Express Enzyme for 20 min, then resuspended in Complete Medium to create a uniform single-cell suspension. Cell suspensions were held at room temperature and counted using the Scepter 3.0 Handheld Cell Counter and 60 µm Counter Sensors, then immediately divided as needed for downstream processing.
For Hi-C analysis, 1x106 cells per aliquot were processed in triplicate 24 and 48 hrs after treatment as previously described (Venu et al., 2024). Briefly, cells were crosslinked with 37% (w/v) formaldehyde containing 10-15% (v/v) methanol (Sigma, Cat. #252549), treated with 200 mM glycine (Sigma, Cat. #G8790) and snap frozen for storage. As previously described, frozen crosslinked cells were processed into Hi-C libraries per the Arima Hi-C Kit manual (Cat. #A160134), the Arima-Hi-C Library Preparation user guide (Cat. # A160141), and the Accel-NGS® 2S Plus DNA Library Kit (IDT, Cat. #10009877). Libraries were sequenced on an Illumina NextSeq 2000 (PE 2x150bp) at the LANL Genome Center.


title: 24hr Control RNA-seq Bio rep 3

description:
Library name: 2501_118
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T24vsUTR24.DESEQ.norm.csv


title: 48hr SAHA Treated RNA-seq Bio rep 3

description:
Library name: 2501_127
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T48vsUTR48.DESEQ.norm.csv


title: 2312041_A_0116,the Control group

description:
Library name: sample1
Filtered gene-barcode matrix generated by Cell Ranger v2.1.1. Contains UMI counts for high-quality cells from sample 2312041_A_0116.


title: X517_hi_2028

description: Library name: X517_hi_2028


title: 48hr Control Hi-C Bio rep 2

description:
Library name: 2501_053
Processed .hic files.


title: 24hr Control RNA-seq Bio rep 2

description:
Library name: 2501_117
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T24vsUTR24.DESEQ.norm.csv


title: 48hr SAHA Hi-C Bio rep 2

description:
Library name: 2501_055
Processed .hic files.


title: 48hr Control Hi-C Bio rep 1

description:
Library name: 2501_052
Processed .hic files.


title: act_WT_4

city: Nanjing

first: Xiaoli

last: Min

address: No.4 Jiang Wang Temple Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: sample7

data_processing:
Illumina Novaseq was used for basecalling
The raw data were firstly processed through in-house perl scripts
The RNA-seq data were then mapped to the human reference genome hg38 with Hisat2 v2.0.5
The differential analysis was performed using DESeq
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol:
RNA was harvested using Trizol reagent.RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Cat#FC-122-1001) was used to 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were from SLE and healthy controls

value: spleen

value: CD4+T cells

value: WT


title: act_WT_5

description: Library name: sample8


title: X517_lo_2002

description: Library name: X517_lo_2002


title: X517_l_20171

description: Library name: X517_l_20171


title: 48hr Control RNA-seq Bio rep 1

description:
Library name: 2501_122
Processed stranded bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
T48vsUTR48.DESEQ.norm.csv


title: 24hr SAHA Hi-C Bio rep 1

description:
Library name: 2501_050
Processed .hic files.


title: 24hr SAHA Hi-C Bio rep 2

description:
Library name: 2501_051
Processed .hic files.


title: 24hr Control Hi-C Bio rep 2

description:
Library name: 2501_049
Processed .hic files.


title: X517_v_20301

description: Library name: X517_v_20301

value: Vehicle:BID, oral


title: 24hr Control Hi-C Bio rep 1

description:
Library name: 2501_048
Processed .hic files.


title: act_WT_2

description: Library name: sample5


title: 48hr SAHA Treated  H3K4me3 ChIP-seq Bio rep 3

description:
Library name: 2501_103
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
48hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt

data_processing:
Each ChIP-seq library was sequenced to approximately 23 million read pairs. Briefly, raw reads were trimmed and filtered to remove Nextra adaptors and reads with repetitive sequences using Fastp (Chen et al., 2018) . Bases with low quality scores (q < 15) were removed. Processed reads were aligned to the telomere-to-telomere (T2T) human reference genome, version 2 (Nurk et al., 2022) via BWA (Li and Durbin, 2009). Duplicate sequenced pairs and mitochondrial reads were marked and removed from analysis via Samblaster (Faust and Hall, 2014). Samples were further filtered using samtools with the following flags:  -F 4 -F 256 -F 512 -F 1024 -F 2048 -q 30.  Samples were then passed to MACS2 in BAMPE mode specifiying reads from corresponding input library as control (raw .fastq files for input libraries are provided in SRA). Loci displaying significant enrichment of paired-end reads were identified as peaks using MACS2 (Gaspar, 2018; Zhang et al., 2008).
MACS2 output treat pileup bedgraph files are converted to bigwig format using bedGraphToBigwig function from UCSC
Assembly: T2T-CHM13v2.0
Supplementary files format and content: .bw files: contain signal track visualizable in any genome browser
Supplementary files format and content: DESeq2 result table includes timepoint specific DESeq output. This file is used to identify genes with significant difference in expression.
Supplementary files format and content: .narrowPeak files: Peaks called uisng MACS2 as mentioned in the data processing tab

extract_protocol:
During cell harvest (at 24 and 48 hrs post-treatment), drug-treated and mock-treated culture flasks for each biological replicate were processed in parallel. Cells were washed once in 1X PBS, detached using 1X TrypLE Express Enzyme for 20 min, then resuspended in Complete Medium to create a uniform single-cell suspension. Cell suspensions were held at room temperature and counted using the Scepter 3.0 Handheld Cell Counter and 60 µm Counter Sensors, then immediately divided as needed for downstream processing.
For ChIP-seq, 10x106 cells per aliquot were processed in duplicate 24 and 48 hrs after treatment. Counted cells were resuspended in 1X PBS and crosslinked for 5 min using PierceTM 16% (w/v) methanol-free formaldehyde (ThermoScientific, Cat. #28906) at a final concentration of 1% (v/v). Formaldehyde was quenched with 125 mM glycine. Crosslinked cells were pelleted and washed twice in ice-cold 1X PBS (Gibco, Cat. #10010049). Chromatin was isolated and fragmented using the Diagenode Chromatin EasyShear Kit Ultra Low SDS (Cat. #C01020010) following the manufacturer’s protocol and Diagenode Bioruptor Pico (Cat. #B01080010) (30 sec on and 30 sec off settings for 17 cycles) to generate ~350 bp sized fragments. Fragmented chromatin was stored at -80°C until use. Frozen chromatin was thawed on ice, and the volume was brought to 500 µl by adding IP dilution buffer (16.7 mM Tris-HCl, 0.01% SDS, 1.1% Triton X 100, 1.2 mM EDTA, 167 mM NaCl) supplemented with 1X Halt™ Protease Inhibitor Cocktail (Thermo Scientific, Cat. #78430). Fragmented chromatin was precleared with 15 µl Pierce Protein A/G beads (Thermo Scientific, Cat. #88803) at 4°C for 1 hr with rotation; 50 µl of the precleared chromatin was saved as input and stored at -80°C until use. The following antibodies were used for ChIP experiments: H3ac (pan-acetyl) (Active Motif, Cat. #39139), H3K4me3 (Active Motif, Cat. #39060), and H3K27ac (Abcam, Cat. #ab4729). ChIP antibodies (4-5 µg) were prebound to 30 µl Protein A/G beads in 500 µl RIPA buffer (10mM Tris-HCl, 0.1% SDS, 1% Triton X 100, 1mM EDTA, 140mM NaCl, 0.1% Na deoxycholate) incubated for 2-4 hrs at 4°C with rotation. Conjugated beads were pulled down and washed 3X with RIPA buffer. Antibody-conjugated beads were added to precleared fragmented chromatin and incubated o/n at 4°C with rotation. Antibody-bound precleared fragmented chromatin was incubated with 30 µl Protein A/G beads for 2 hrs at 4°C with rotation. Complexes were pulled down, unbound lysate was removed, and beads were washed as follows for 10 min each at 4°C with rotation: RIPA; 2X RIPA 500 (RIPA buffer with 500 mM NaCl); LiCl buffer (10 mM Tris-HCl, 250 mM LiCl, 0.1% SDS, 1% NP40,1 mM EDTA, 0.5% Na deoxycholate); and TE buffer (10mM Tris pH 8, 1 mM EDTA). Chromatin was incubated in elution buffer (1% SDS, 0.1 M NaHCO3) at 65°C for 10 mins, incubated at RT for 10 min, and incubated o/n at 65°C. The input DNA was thawed and its volume brought to 300 µL with elution buffer. Both chromatin and input samples were treated with 40 µg/ml RNaseA (Qiagen, Cat. #19101) at 37°C for 30 min, followed by protein digestion with 80 µg/ml Proteinase K (ThermoScientific, Cat. #25530049). Samples were incubated with NaCl (100 mM final concentration) for 1 hr at 65°C in an Eppendorf thermomixer at 300 rpm. The DNA was purified using the Qiagen PCR cleanup kit (Qiagen, Cat. #28104), quantified via Qubit, and concentrated with Ampure beads (Beckman, Cat. #A63881) to remove any PCR inhibitors and meet library prep volume requirements. Libraries were generated via the Tecan Ovation V2 Ultra Low Kit with unique dual indexes (Tecan, Cat. #9149-A01) and sequenced on an Illumina HiSeq 2500 (PE 2x150bp) at the LANL Genome Center.


title: X517_v_2027

description: Library name: X517_v_2027


title: 48hr SAHA Treated  H3K4me3 ChIP-seq Bio rep 2

description:
Library name: 2501_102
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
48hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: 48hr Control H3K4me3 ChIP-seq Bio rep 3

description:
Library name: 2501_100
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
48hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: 48hr SAHA Treated  H3K4me3 ChIP-seq Bio rep 1

description:
Library name: 2501_101
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
48hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: act_KO_4

description: Library name: sample3

value: KO


title: 48hr Control H3K4me3 ChIP-seq Bio rep 2

description:
Library name: 2501_099
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
48hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: X517_v_2013

description: Library name: X517_v_2013


title: 48hr Control H3K4me3 ChIP-seq Bio rep 1

description:
Library name: 2501_098
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
48hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: 24hr SAHA Treated  H3K4me3 ChIP-seq Bio rep 3

description:
Library name: 2501_097
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
24hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: act_KO_3

description: Library name: sample2


title: X517_v_2006

description: Library name: X517_v_2006


title: act_KO_2

description: Library name: sample1


title: X517_v_20082

description: Library name: X517_v_20082


title: CH12F3_AID-KO_Valemetostat_2_R1

city: Boston

first: Roberto

last: Chiarle

state: Ma

address: Longwood 333

institute: Boston Childrens Hospital

library_source: other

data_processing:
aligned using Bowtie software default parameters
Uniquely mapped, non-redundant sequence reads were retained
HOMER software to count reads and calculate the nascent RNA expression levels as RPKM (reads per 1000bp per million mapped reads) in whole genes or in focal translocation clusters, and to identify transcripts from both strands of chromosomes
ConvT region was defined as sense and antisense transcription overlaps that were longer than 100 bp
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: GRO-seq

molecule: other

growth_protocol: Cells were cultured at 37 °C with 5% CO2

extract_protocol:
GRO-seq libraries were prepared as previously described in Zhang, X. et al, Nature 575, 385-389 (2019).
GRO-seq libraries were sequenced through Illumina NextSeq 550 (PE75)

treatment_protocol: GRO-seq libraries were prepared from CH12F3 AID-deficient cells stimulated with anti-CD40–IL-4–TGF-β for 24 h

value: Mouse B-lymphoma cells

value: AID-KO

value: anti-CD40–IL-4–TGF-β + Valemetostat_1


title: 24hr SAHA Treated  H3K4me3 ChIP-seq Bio rep 1

description:
Library name: 2501_095
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
24hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: act_WT_3

description: Library name: sample6


title: 24hr SAHA Treated  H3K4me3 ChIP-seq Bio rep 2

description:
Library name: 2501_096
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
24hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: CH12F3_AID-KO_Tazemetostat_2_R1

value: anti-CD40–IL-4–TGF-β + Tazemetostat_1


title: CH12F3_AID-KO_DMSO_2_R1

value: anti-CD40–IL-4–TGF-β + DMSO_1


title: BM-MMC replicat 2

city: Toulouse

last: Espinosa

state: France

address: IRSD  INSERM U1220 105 Avenue de Casselardit

department: IMMUNOLOGY

country: France

institute: INSERM

description:
Library name: sample5
column name in normalized_counts.txt = M3

data_processing:
The libraries were sequenced on a Novaseq 6000 (Illumina) platform in paired end sequencing 2 × 150 bp with 10bp-dual indexes. FastQ files were generated via llumina bcl2fastq2
Quality check of raw reads was performed with FastQC (v0.11.9) and transcript abundance was quantified using Salmon (v1.9.0) based on the transcript fasta files downloaded from Ensembl.org (Mus_musculus.GRCm39.cdna.all.fa). Salmon was run with the default settings using GC bias correction.Transcript abundances were aggregated to gene-level abundances using tximport function  (tximport package v1.32.0) and differential expression analysis was carried out by DESeq2 package (v1.44.0) in R (v4.4.1).
Assembly: Mus_musculus.GRCm39.cdna.all.fa
Supplementary files format and content: tab-delimited file includes normalized counts

source_name: primary BM-MMC

growth_protocol: PCMCs grown as described in Malbec et al., J Immunol 2007;178(10):6465-6475 BM-MMCs: Bone marrow cells were cultured in Opti-MEM Glutamine supplemented with 10% FBS, 100 IU/mL penicillin, 100 μg/mL streptomycin, 50 µM 2-Mercaptoethanol, MEM Non-Essential Amino Acids Solution + 70 ng/mLSCF and 5 ng/mL of recombinant murine IL-3 . Cells were diluted by half in fresh medium every 2 days to maintain a concentration of 5x105 to 1x106 cells/mL and the flasks were changed every 5 days to remove adherent cell for 4 weeks and then supplemented with 5 ng/mL of recombinant murine IL-9 and 1 ng/mL of recombinant murine TGF-β1 for one week.

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen) and purified on a RNeasy column (RNeasy Mini Kit Qiagen 79254)
Libraries were prepared using 418-500 ng of high-quality total RNA. Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and IDT for Illumina DNA/RNA UD Indexes (Illumina) are used according to the manufacturer protocol. Size selection was performed using SPRIselect beads (Beckman Coulter). Library size and quality were confirmed on HS NGS Fragment kit for Fragment Analyzer (Agilent). Libraries were quantified by qPCR using the KAPA Library quantification kit for Illumina platforms (Roche Sequencing Solution). Samples were pooled in equimolar fashion.

value: primary BM-MMC

value: mast cells


title: BM-MMC replicat 3

description:
Library name: sample6
column name in normalized_counts.txt = M4


title: B070_c_2106

description: Library name: B070_c_2106

value: BLU-222:50 mg/kg; BID, oral; palbociclib:50 mg/kg; QD, oral


title: B070_c_2105

description: Library name: B070_c_2105


title: 24hr Control H3K4me3 ChIP-seq Bio rep 2

description:
Library name: 2501_093
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
24hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt

value: lung carcinomatous tissue

value: Untreated


title: 24hr Control H3K4me3 ChIP-seq Bio rep 3

description:
Library name: 2501_094
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
24hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: BM-MMC replicat 1

description:
Library name: sample4
column name in normalized_counts.txt = M2


title: act_KO_5

description: Library name: sample4


title: CH12F3_AID-KO_Valemetostat_1_R1


title: B070_c_2100

description: Library name: B070_c_2100

value: patient-derived xenograft


title: X517_v_2025

description: Library name: X517_v_2025


title: PCMC replicat 3

description:
Library name: sample3
column name in normalized_counts.txt = C5

source_name: primary PCMC

value: primary PCMC


title: CH12F3_AID-KO_Tazemetostat_1_R1


title: B070_p_2116

description: Library name: B070_p_2116

value: Palbociclib:50 mg/kg; QD, oral


title: PCMC replicat 2

description:
Library name: sample2
column name in normalized_counts.txt = C2


title: 48hr SAHA Treated  H3K27ac ChIP-seq Bio rep 3

description:
Library name: 2501_091
processed .narrowPeak files
treat pileup bigwig files

value: Treated with 10 µM SAHA


title: CH12F3_AID-KO_DMSO_1_R1


title: B070_p_2114

description: Library name: B070_p_2114


title: PCMC replicat 1

description:
Library name: sample1
column name in normalized_counts.txt = C1

value: WT


title: Heart, Mdx/Utrn dKO 66, setanaxib 12 weeks

city: Tampa

first: Da-Zhi

last: Wang

state: FL

address: 560 Channelside Dr.

institute: University of South Florida

description: Library name: Sample 66

data_processing:
Raw reads were assessed for quality using FastQC v0.11.9 and processed to remove adapters and low-quality bases. Clean reads were aligned to the mouse reference genome (GRCm39) with STAR v2.5.4b  aligner and gene-level sequencing reads were counted using featureCounts v2.0.1.Differential expression analysis was performed with DESeq2 v1.42.0 (three biological replicates per condition) with default settings. Differentially expressed genes were identified as those with false discovery rate (FDR) < 0.05, base mean > 50, and log2 fold change > 0.8. Gene set enrichment analysis was assessed with GSEA v4.3.2 based on fold-changed-ranked gene list. Functional annotation and pathway enrichment were performed using DAVID tool suites.
Assembly: GRCm39
Supplementary files format and content: CSV. Gene counts

source_name: Heart

extract_protocol:
Total RNA was isolated from hearts using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. RNA quality and concentration were measured using Qubit RNA Assay Kit (Thermo Fisher Scientific).
One μg of total RNA was used for library preparation. The libraries were sequenced on an Illumina platform (paired-end, 2x150 bp, ≥ 60 million reads per sample) by GENEWIZ (Azenta Life Sciences).

value: Heart

value: heart tissue

value: Mdx Utrn dKO

value: Setanaxib (Nox4 inhibitor)


title: 48hr SAHA Treated  H3K27ac ChIP-seq Bio rep 2

description:
Library name: 2501_090
processed .narrowPeak files
treat pileup bigwig files


title: B070_p_2108

description: Library name: B070_p_2108


title: 48hr SAHA Treated  H3K27ac ChIP-seq Bio rep 1

description:
Library name: 2501_089
processed .narrowPeak files
treat pileup bigwig files


title: Heart, Mdx/Utrn dKO 453, setanaxib 12 weeks

description: Library name: Sample 453


title: Trancriptome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep6

first: Christina

last: Mayerhofer

address: 185 Cambridge St.

department: Center for Regenerative Medicine

institute: MGH, Simches building

description: Library name: RNA 25

data_processing:
RiboSeq data was processed according to the recommendation of the manufacturer (diagenode user guide C05030001) and the original RiboLite publication. First, the UMI was copied from the read to the read identifier with fumi tools (https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools) to allow subsequent deduplication. Trimming was performed by cutadapt with parameters --match-read-wildcards -u 16 -n 4 -a AGATCGGAAGAGCACACGTCTG -a AAAAAAAA -a GAACTCCAGTCAC -e 0.166666 --nextseq-trim 20 -m 18. The reads were then aligned to mouse rRNA (https://www.ncbi.nlm.nih.gov/nuccore/BK000964) using bowtie2 with --seedlen=23. Unaligned reads were aligned to GRCm38 release 102 reference genome using STAR with parameters  --sjdbOverhang 36 -outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. Deduplication of reads was performed using samtools and fumi_tools (https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools). Read distribution was calculated using read_distribution.py from RSeQC package, and metaplots were generated by RiboCode. Finally, featureCounts was used to detect exons in single-end forward stranded mode, and reads were summarized per gene.
Transcriptome RNASeq data was processed according to the recommendation of the manufacturer (Smart-Seq v4, Takara Bio USA) and the original RiboLite publication. Reads were trimmed with cutadapt in paired-end read mode with parameters: -j 4 --trim-n --match-read-wildcards -a CTGTCTCTTATACACATCT -a AAAAAAAAAAA -A CTGTCTCTTATACACATCT -A AAAAAAAAAAA --nextseq-trim 20 -m 10. Reads were then aligned using STAR to GRCm38 release 102 reference genome in paired-end read mode with parameters --sjdbOverhang 99. Finally, featureCounts was used to detect exons in paired-end unstranded mode, and reads were summarized per gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: bone marrow

growth_protocol: The MLL-AF9 leukemia cells express GFP under the control of the ubiquitin transporter.  Leukemic cells from a terminally ill mouse were harvested and expanded ex vivo in RPMI1640 medium (Lonza) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine (all from Corning), 20 ng/ml recombinant mouse SCF (rmSCF), 10 ng/ml recombinant mouse interleukin 3 (rmIL-3) and 10 ng/ml rmIL-6 (all from R&D Systems).

extract_protocol:
Mice were euthanized at the point of maximum response of chemotherapy and femurs, tibias, pelvis and humeri were isolated and cleaned to remove muscle. Bones were then crushed using a pre-cooled mortar and pestle in ice-cold flow buffer (PBS containing 2% FBS), and the obtained BM cell suspension was passed through a 70 μm cell strainer. Red blood cells were removed by incubating cells for 5 minutes in ACK lysing buffer (Gibco) on ice, the remaining BM cells were washed and resuspended in ice-cold flow buffer. Viable cells (AML cells GFP+) were sorted on a BD FACSAria II (BD Biosciences) with the sample collector cooled to 4°C. After centrifugation, samples were lysed in 20 μl ice-cold lysis buffer (20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 1% Triton X-100; 25 U/ml Turbo DNase) for 10 min on ice. For mRNA 2 μl of the lysate was subjected to the Smart-seq2 protocol. Following addition to 300 μl lysis buffer to the lysate, it was clarified for 10 min at 20,000g at 4°C, then treated with RNase 1 Ambion, AM2295, 1 μl for up to 50k cells, 2 μl for up to 200k cells) and incubated at room temperature for 45 min with gentle mixing. The digested extracts were stopped by the addition of 10 μl SUPERaseIn and were overlaid onto a 700 μl sucrose cushion of 1 M sucrose in 20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX and 20 U/ml SUPERaseIn for 4 h at 260,000g, 4°C in MLA-150 rotor in Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris pH 7.5 and 1% SDS). RPFs were extracted from pellet buffer by using 1 ml Trizol and 200 μl chloroform. The aqueous phase was precipitated by adding 750 μl isopropanol and 20 μg glycogen. Precipitation was carried out at −20 °C overnight, and RPFs were then pelleted by centrifugation for 40 min at 12,000 g, 4 °C. RPF was resuspended in 6 μl nuclease-free water and mixed with 6 μl Gel Loading Buffer II. The 15% (wt/vol) polyacrylamide TBE-urea gel was pre-run for 30 min at 200 V. The RNA samples were denatured for 90 s at 80°C. RPFs were separated by electrophoresis for 65 min at 200 V. To minimize contamination, each sample was run in a separate gel and the electrophoresis was run without RNA or DNA markers. The region from 26 to 34 nt for RPFs was excised according to the light-blue loading dye and further determined on the basis of the relative position of RNA oligo markers to the loading dye on a separate and parallel gel. Extract RNA from the polyacrylamide gel slices by adding 400 μl RNA extraction buffer (300 mM sodium acetate pH 5.5, 1 mM EDTA and 0.25% SDS), snap-frozen at −80°C for 20 min and thawed at 37°C for two rounds and then kept overnight at room temperature with gentle mixing. The liquid was transferred to a clean tube, and 500 μl isopropanol and 20 μg glycogen were added and precipitated overnight. The RPF sample was pelleted by centrifugation for 40 min at 12,000 g, 4°C and resuspended in 6 μl nuclease-free water. The sample was then subjected to sequencing library preparation by D-Plex Small RNA-seq Kit and DNA library was purified using AMPure XP. Barcoded libraries were pooled and sequenced on the Illumina platform with 2x 100bp reads.
For mRNA 2 μl of the lysate (10%) was subjected to the Smart-seq2 protocol. The Ribo-lite/RPF sample was then subjected to sequencing library preparation by D-Plex Small RNA-seq Kit and DNA library was purified using AMPure XP.

treatment_protocol: Recipient male mice (age 8-10 weeks) were injected intravenously (retro-orbital) with 1 million leukemia cells in 200 μl PBS.  Mice were treated with 5+3 (cytarabine, 100 mg/kg, once daily for 5 days and doxorubicin, 3 mg/kg, once daily for the first 3 days) or vehicle (PBS) delivered via i.p. injection.

value: bone marrow

value: MLL-AF9 AML

value: Acute myeloid leukemia

value: BCAA-free plus 5+3


title: B070_hi_2115

description: Library name: B070_hi_2115

value: BLU-222:100 mg/kg; BID, oral


title: Trancriptome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep5

description: Library name: RNA 24


title: Heart, Mdx/Utrn dKO 665, setanaxib 12 weeks

description: Library name: Sample 665


title: B070_hi_2113

description: Library name: B070_hi_2113


title: 48hr Control H3K27ac ChIP-seq Bio rep 2

description:
Library name: 2501_087
processed .narrowPeak files
treat pileup bigwig files


title: Heart, Mdx/Utrn dKO 1607, vehicle 12 weeks

description: Library name: Sample 1607

value: Corn Oil (Vehicle)


title: 48hr Control H3K27ac ChIP-seq Bio rep 3

description:
Library name: 2501_088
processed .narrowPeak files
treat pileup bigwig files

value: lung carcinomatous tissue


title: Trancriptome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep4

description: Library name: RNA 22


title: B070_hi_2111

description: Library name: B070_hi_2111


title: Heart, Mdx/Utrn dKO 1000, vehicle 12 weeks

description: Library name: Sample 1000


title: 48hr Control H3K27ac ChIP-seq Bio rep 1

description:
Library name: 2501_086
processed .narrowPeak files
treat pileup bigwig files

value: Untreated


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep7

description: Library name: RNA 21

value: sgScramble


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep6

description: Library name: RNA 20


title: 24hr Control H3K4me3 ChIP-seq Bio rep 1

description:
Library name: 2501_092
processed .narrowPeak files
treat pileup bigwig files
DESeq2 result files are provided. Single DESeq2 file present differential gene expression analysis across all samples at a given time point
24hr_untr_Vs_SAHA_differential_H3K4me3_peaks_DEseq2_result.txt


title: B070_hi_2110

description: Library name: B070_hi_2110

value: patient-derived xenograft


title: 24hr SAHA Treated  H3K27ac ChIP-seq Bio rep 3

description:
Library name: 2501_085
processed .narrowPeak files
treat pileup bigwig files


title: Heart, Mdx/Utrn dKO 670, vehicle 12 weeks

description: Library name: Sample 670


title: 24hr SAHA Treated  H3K27ac ChIP-seq Bio rep 2

description:
Library name: 2501_084
processed .narrowPeak files
treat pileup bigwig files


title: B070_lo_2109

description: Library name: B070_lo_2109

value: BLU-222:50 mg/kg; BID, oral


title: control HepG2-NTCP D2 biol rep 3

city: Neuherberg

first: Salih

last: Özer

address: Ingolstädter Landstraße 1

department: Institute of Virology

country: Germany

institute: Helmholtz Munich

description: Library name: Sample 6

data_processing:
Data was processed as described in Liang et al., 2024
Assembly: GRCh38
Supplementary files format and content: csv file includes log2foldchange and padj

source_name: liver

extract_protocol:
RNA was harvested using RNeasy mini Kit (Quiagen). 1.3 ug of total RNA was used for library preparation.
RNA library was constructed as described in Liang et al., 2024

value: liver

value: immortal

value: control HepG2-NTCP


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep5

description: Library name: RNA 19


title: HBV infected HepG2-NTCP D2 biol rep 3

description: Library name: Sample 5

value: HBV infected HepG2-NTCP


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep4

description: Library name: RNA 18


title: 24hr Control H3K27ac ChIP-seq Bio rep 3

description:
Library name: 2501_082
processed .narrowPeak files
treat pileup bigwig files


title: B070_lo_2104

description: Library name: B070_lo_2104

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the combined reference genome (Gencode human GRCh38 and mouse GRCm38 concatenated) using TopHat2 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 1.6.3) in order to generate read count data on gene/feature level (parameters: -p -t exon -g gene_id -s 0)
Genes/features were annotated using the combined GTF file from Gencode human GRCh38 and mouse GRCm38 references
Only the reads that were mapped to the human genome were kept, whereas the reads mapped to the mouse genome were removed
Assembly: Human GRCh38 and mouse GRCm38
Supplementary files format and content: Raw read count data generated by featureCounts (Subread 1.6.3) for each sample


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep3

description: Library name: RNA 17


title: control HepG2-NTCP D2 biol rep 2

description: Library name: Sample 4


title: 24hr Control H3K27ac ChIP-seq Bio rep 2

description:
Library name: 2501_081
processed .narrowPeak files
treat pileup bigwig files


title: Trancriptome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep3

description: Library name: RNA 15


title: HBV infected HepG2-NTCP D2 biol rep 2

description: Library name: Sample 3


title: B070_lo_2090

description: Library name: B070_lo_2090


title: 24hr Control H3K27ac ChIP-seq Bio rep 1

description:
Library name: 2501_080
processed .narrowPeak files
treat pileup bigwig files


title: Trancriptome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep2

description: Library name: RNA 14


title: HBV infected HepG2-NTCP D2 biol rep 1

description: Library name: Sample 1


title: B070_v_2107

description: Library name: B070_v_2107

value: Vehicle:BID, oral


title: 48hr SAHA Treated  H3ac ChIP-seq Bio rep 2

description:
Library name: 2501_078
processed .narrowPeak files
treat pileup bigwig files

value: Treated with 10 µM SAHA


title: B070_v_2112

description: Library name: B070_v_2112


title: control HepG2-NTCP D2 biol rep 1

description: Library name: Sample 2


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep2

description: Library name: RNA 12

value: bone marrow


title: B070_hi_2088

description: Library name: B070_hi_2088


title: B070_lo_2089

description: Library name: B070_lo_2089


title: Transcriptome BCAA-free plus 5+3 sgScramble AML cells biol rep1

description: Library name: RNA 11

value: MLL-AF9 AML


title: 24hr SAHA Treated  H3K27ac ChIP-seq Bio rep 1

description:
Library name: 2501_083
processed .narrowPeak files
treat pileup bigwig files


title: 48hr SAHA Treated  H3ac ChIP-seq Bio rep 1

description:
Library name: 2501_077
processed .narrowPeak files
treat pileup bigwig files


title: Trancriptome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep1

description: Library name: RNA 13

value: Acute myeloid leukemia


title: tsk_m_2

city: hangzhou

first: li

last: qi

address: xihu

institute: zhejiang university

description: Library name: tsk_m-rep2

data_processing:
The clean reads were aligned to the Arabidopsis reference genome using STAR software
Transcripts assembled from three independent biological replicates were included in the analysis, compared using DESeq2 (version 1.30.1) with default settings.
The R package DESeq2 (version 1.30.1) in v4.0.3 was employed to identify differentially expressed genes with at least a 1.5-fold change
Assembly: TAIR10
Supplementary files format and content: text files include genecounts for each files

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 7 d. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Seven-day-old seedlings grown on half-strength MS plates were harvested, flash-frozen in liquid nitrogen, and ground to a fine powder. Total RNA was isolated using the Plant RNA Kit (Omega, R6827). For RT-qPCR, 0.5 μg of total RNA was reverse-transcribed using the M5 Super plus qPCR RT Kit (Mei5bio, MF166-plus-01), and 1 μL of the resulting cDNA was used for qPCR on a Biorad CFX96 Touch system.
RNA sequencing was carried out using the Illumina NovaSeq 6000 with Hiseq-PE150 strategy, conducted by Novogene Corporation (Beijing, China).

value: leaves

value: Columbia

value: MMS


title: 48hr Control H3ac ChIP-seq Bio rep 3

description:
Library name: 2501_076
processed .narrowPeak files
treat pileup bigwig files

value: lung carcinomatous tissue


title: B070_v_2097

description: Library name: B070_v_2097

extract_protocol:
Total RNA was isolated from cell lysates using Trizol reagent (Ambion Life Technologies) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols


title: 48hr Control H3ac ChIP-seq Bio rep 2

description:
Library name: 2501_075
processed .narrowPeak files
treat pileup bigwig files

value: Untreated


title: B070_v_2094

description: Library name: B070_v_2094


title: 48hr Control H3ac ChIP-seq Bio rep 1

description:
Library name: 2501_074
processed .narrowPeak files
treat pileup bigwig files


title: XW_m_2

description: Library name: XW_m-rep2


title: NPC CISTR KO rep3

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
PM_NPC_CISTRKO_3_S11_L004
NPC_CISTR.GENCODEv32.RPKM.genPos.consensus

data_processing:
We aligned reads to hg38 using STAR aligner, version 2.7.0f. We used FeatureCounts to count reads aligning to genes in GENCODE v32 (human), vM33 (mouse).
Assembly: hg38, mm39
Supplementary files format and content: text files include RPKM values for each sample

source_name: NPC

extract_protocol:
RNA was harvested and purified using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocols.

value: NPC

value: ESC-derived NPC

value: [delta]CISTR


title: B070_lo_2091

description: Library name: B070_lo_2091

value: patient-derived xenograft

value: BLU-222:50 mg/kg; BID, oral


title: Transcriptome AA vehicle sgOgfod1 AML cells biol rep5

description: Library name: RNA 10

value: AA vehicle


title: Transcriptome AA vehicle sgOgfod1 AML cells biol rep4

description: Library name: RNA 9


title: XW_m_3

description: Library name: XW_m-rep3


title: tsk_m_1

description: Library name: tsk_m-rep1


title: Transcriptome AA vehicle sgOgfod1 AML cells biol rep3

description: Library name: RNA 8


title: tsk_m_3

description: Library name: tsk_m-rep3


title: 48hr SAHA Treated  H3ac ChIP-seq Bio rep 3

description:
Library name: 2501_079
processed .narrowPeak files
treat pileup bigwig files


title: XW_m_1

description: Library name: XW_m-rep1


title: NPC CISTR KO rep2

description:
PM_NPC_CISTRKO_2_S10_L004
NPC_CISTR.GENCODEv32.RPKM.genPos.consensus


title: W_m_3

description: Library name: W_m-rep3


title: Transcriptome AA vehicle sgOgfod1 AML cells biol rep1

description: Library name: RNA 6


title: 24hr SAHA Treated  H3ac ChIP-seq Bio rep 2

description:
Library name: 2501_072
processed .narrowPeak files
treat pileup bigwig files


title: B070_v_2095

description: Library name: B070_v_2095


title: NPC WT rep3

description:
PM_NPC_WT_3_S14_L004
NPC_CISTR.GENCODEv32.RPKM.genPos.consensus

value: WT


title: NPC WT rep2

description:
PM_NPC_WT_2_S13_L004
NPC_CISTR.GENCODEv32.RPKM.genPos.consensus


title: NPC CISTR KO rep1

description:
PM_NPC_CISTRKO_1_S9_L004
NPC_CISTR.GENCODEv32.RPKM.genPos.consensus


title: Transcriptome AA vehicle sgScramble AML cells biol rep4

description: Library name: RNA 4

value: sgScramble


title: Transcriptome AA vehicle sgScramble AML cells biol rep3

description: Library name: RNA 3


title: 24hr Control H3ac ChIP-seq Bio rep 3

description:
Library name: 2501_070
processed .narrowPeak files
treat pileup bigwig files


title: W_m_2

description: Library name: W_m-rep2


title: Transcriptome AA vehicle sgScramble AML cells biol rep5

description: Library name: RNA 5


title: 24hr SAHA Treated  H3ac ChIP-seq Bio rep 3

description:
Library name: 2501_073
processed .narrowPeak files
treat pileup bigwig files

value: Treated with 10 µM SAHA


title: 24hr SAHA Treated  H3ac ChIP-seq Bio rep 1

description:
Library name: 2501_071
processed .narrowPeak files
treat pileup bigwig files


title: 24hr Control H3ac ChIP-seq Bio rep 2

description:
Library name: 2501_069
processed .narrowPeak files
treat pileup bigwig files


title: W_m_1

description: Library name: W_m-rep1


title: NPC WT rep1

description:
PM_NPC_WT_1_S12_L004
NPC_CISTR.GENCODEv32.RPKM.genPos.consensus


title: Transcriptome AA vehicle sgScramble AML cells biol rep2

description: Library name: RNA 2

value: bone marrow


title: X_m_3

description: Library name: X_m-rep3


title: X_m_2

description: Library name: X_m-rep2


title: K562 CISTR KO 48h hemin rep2

description:
PM_K562_CISTRKO2_48h_hemin_S19_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus

value: erythropoietic precursors

value: K562 ΔCISTR cells treated with 50 µM hemin for 48 hours


title: 24hr Control H3ac ChIP-seq Bio rep 1

description:
Library name: 2501_068
processed .narrowPeak files
treat pileup bigwig files


title: Transcriptome AA vehicle sgScramble AML cells biol rep1

description: Library name: RNA 1

value: MLL-AF9 AML

value: Acute myeloid leukemia