title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB303QWL)

description:
https://www.encodeproject.org/experiments/ENCSR168QRY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR168QRY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB303QWL

value: primary cell

tag: biosample encode accession

value: female

value: adult

value: 34 year

value: ENCBS057CUG at ENCODE; https://www.encodeproject.org/ENCBS057CUG/


title: gavage vehicle control 4

status: Public on Jul 24 2026

type: SRA

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

country: USA

institute: Baylor College of Medicine

description: Library name: LL11_105_gav_con_veh

library_source: transcriptomic

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Raw count and Differentially expressed gene list

molecule: total RNA

organism: Mus musculus

source_name: colon

growth_protocol: SPF and GF C57BL/6J mice were obtained from The Jackson Laboratory or the Center for Comparative Medicine at Baylor College of Medicine. Dams with 8-day-old pups were randomized to receive either a triple-irradiated control chow diet (20% kcal from protein, 15% kcal from fat, 65% kcal from carbohydrate; Research Diets #D21012505-1.5Viii) or a triple-irradiated low-protein, low-fat diet (LPLFD; 7% kcal from protein, 5% kcal from fat, 88% kcal from carbohydrate; Research Diets # D21012506-1.5Viii), both formulated to be isocaloric. Offspring were weaned at postnatal day 21 (DOL 21) onto the same diet as their dams and maintained ad libitum on these diets for an additional 5 weeks.

extract_protocol:
Colonic tissue was excised, opened longitudinally, and rinsed in ice-cold Ca2+ and Mg2+ free DPBS (Gibco) to remove luminal contents. Tissues were kept on ice until all samples were collected. Tissues were incubated in a chelation buffer (30 mM EDTA, 1.5 mM DTT in DPBS) on ice for 20 minutes, followed by transfer to a second EDTA-based dissociation solution (30 mM EDTA in DPBS) pre-warmed to 37°C and incubated for 10 minutes. Samples were shaken vigorously for ~30 seconds to detach the epithelium and the resulting suspension was collected while excluding residual tissue fragments. Cells were pelleted (800 × g, 4°C, 5 minutes) and either reconstituted in Trizol (Zymo Research) for RNA extraction, and submitted to Novogene (Sacramento, CA) for poly(A)-based mRNA enrichment, library preparation, and NovaSeq PE150 sequencing (~6 Gb raw reads/sample).
Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq X Plus  for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample.

treatment_protocol: At DOL 56, mice received 114 mM of either leucine or alanine (Millipore Sigma) by oral gavage twice daily for 2.5 days. Sterile water was used as vehicle control. In separate experiments, 100 mM sodium isovalerate (Pfaltz & Bauer) pH- and osmolality-matched saline was administered daily via rectal enema for 3 days. For enemas, mice were anesthetized with isoflurane, solutions were instilled via a flexible catheter, and animals were maintained in a head-down position for 1 minute to facilitate retention.

tag: tissue

value: colon

tag: strain

tag: cell type

value: epithelium

tag: disease state

value: gavage vehicle control

tag: Sex

value: male


title: total RNA-seq from suppressor macrophage (ENCLB216NDQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR127IQP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR127IQP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB216NDQ

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male adult (24 years) suppressor macrophage primary cell

value: suppressor macrophage

tag: encode accession

tag: dev stage

tag: age

value: 24 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Shelly Heimfeld

tag: link

value: ENCBS355BHK at ENCODE; https://www.encodeproject.org/ENCBS355BHK/


title: mock, rep1

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

description:
Library name: Mock.1
column name in the processed files: num_Mock.1

data_processing:
RNAseq and splicing analysis were described earlier using DEDseq (https:// github.com/liwc01/DEDSeq, REF) with minor modifications.
RNA sequencing reads were mapped to human genome (hg19) using STAR (version 2.7.10b) (REF; PMID: 34911927); only uniquely mapped reads (with MAPQ > 10) with <5nt/100nt mismatches and properly paired reads were used.
For splicing analysis, all junction reads (read with a gap in alignment indicating splicing) were used, including the ones mapped to unannotated splice sites. Reads were counted for different exons (for cassette exon [CE]) or exonic regions (for A5′ss or A3′ss). For each splicing event, a percent-spliced-in (PSI) value was calculated using the percent of average read number supporting the inclusion among all reads supporting either the inclusion or the exclusion. A minimum of 10 for the denominator of PSI calculation was required. Otherwise, a ‘NA’ value would be generated. PSI values for biological replicates were averaged, and the PSI difference between the two treatment groups was calculated. For a statistical test, a 2 × 2 read counts table was made for each event, with rows for reads supporting inclusion or exclusion, and columns for the two comparing sample groups. Fisher’s exact test was used for the statistical tests. For biological replicates, each pair of the testing and control sample was analyzed by Fisher’s exact test and the geometric mean of all P-values was reported as a final P-value.  PSI change (deltaPSI) of >10% (or < −10%) and P < 0.001 was used to select splicing events being regulated by the treatment. PSI calculation, Fisher’s exact test, were performed using R (4.0.5).
Assembly: hg19
Supplementary files format and content: U1CKD_2CpdDR_293RNAseq.junction.counts.txt.gz: tab-delimited text file with rows representing splice junctions (from a 5'ss to a 3'ss) and columns representing the read counts in different RNAseq samples
Supplementary files format and content: U1CKD_2CpdDR_293RNAseq.Gene.counts.txt.gz: a tab-delimited text file with rows representing genes and columns representing read counts in RNAseq
Supplementary files format and content: U1_HelixH_GA_variants.junction.counts.txt.gz: tab-delimited text file with rows representing splice junctions (from a 5'ss to a 3'ss) and columns representing the read counts in different RNAseq samples

molecule: polyA RNA

growth_protocol: HEK293T cells were grown in DMEM media with 10% FBS. 500,000 cells in 1.75mL of media were plated into a 6 well plate for approximately 6 hours.

extract_protocol:
RNA was isolated using KingFisherTM Apex instrument and the MagMAX™ mirVana™ Total RNA Isolation Kit (A27828) by Thermo Fisher according to manufacturer’s protocol.
Isolated RNA was submitted to Admera Health for library preparation (polyA selected, stranded) and mRNA-sequencing and >20M 150bp pair-end reads were returned.

treatment_protocol: Either siRNA negative control (ThermoFisher SilencerTM Negative control #2, AM4613) or U1C siRNA (ThermoFisher SilencerTM Select Pre-designed siRNA, S13225) were transfected for a final concentration of 25nM using Invitrogen Lipofectamine RNAiMax (13778-150). In brief, 10 uL 5uM siRNA was added to 115 uL of OptiMEM while 5 uL Lipofectamine added to 120 uL OptiMEM for 5 minutes before mixing the solutions and incubating for 20 minutes. 250uL of Lipofectamine:siRNA solution was gentle added to the 1.75mL cells. After 24 hours post-transfection, cells were treated with 10uL compound resuspended in DMSO. Final concentrations of branaplam were 1.2mM, 400nM, 100nM, 25nM, and 5nM. Final concentrations of risdiplam were 3.6mM, 1.2mM, 400nM, 200nM, and 50nM. Each compound treated experimental condition was treated and collected in duplicate while four DMSO only treated samples per siRNA transfection were collected. Synthesize of the U1 variants constructs, growth of HEK293 cells, transfection and RNA isolation were described in Bhattacharyya, et al 2021.

tag: cell line

tag: treatment

value: mock, rep1

tag: batch


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB791KWO)

description:
https://www.encodeproject.org/experiments/ENCSR146SOA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146SOA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB791KWO

source_name: Homo sapiens female adult (33 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: 33 year

value: AllCells

value: ENCBS418QMX at ENCODE; https://www.encodeproject.org/ENCBS418QMX/


title: SCAF2858_22929

city: Bethesda

first: Huaitian

last: Liu

state: MD

address: Building 37, Room 3050

department: CCR

institute: NCI

library_source: transcriptomic single cell

data_processing:
The demultiplexing, the primary analysis output, gene counting and TCR and BCR counting were performed by Cell Ranger Software. Base calling was performed using RTA 3.9.2, demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.1 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided human reference sequence (refdata-gex-GRCh38-2020-A).
PBMCs from the 59 patients yielded ≥ 3 cells per isolation with a total of 322897 cells that were merged using the Merge() function. After merging, cells with less than 200 nFeature RNA or more than 10% mitochondrial reads were excluded using Seurat v4.3.0
The V(D)J sequencing data were analyzed with the djvdj R package for single-cell V(D)J data.
Assembly: GRCh38
Supplementary files format and content: H5 file containing per-molecule information for all molecules that contain a valid barcode, a valid UMI, and were assigned with high confidence to a gene or Feature Barcode.
Supplementary files format and content: Filtered_contig_annotations.csv contains annotations of each high-confidence cell barcode.

source_name: Prostate cancer patient

extract_protocol:
Whole blood was collected and Lymphocyte separation medium was added and then the samples were centrifuged at 1400 rpm for 30 min. The lymphocyte layer was transferred to a new tube, 1X phosphate-buffered saline (PBS) was added and then centrifuged.The supernatant was discarded and the remaining sample was resuspended in PBS and centrifuged at 800 rpm for 8 mins. The supernatant was again discarded and the sample was then resuspend in freezing media: RPMI + 20% human AB serum.The cells in the samples were counted and frozen in 900 µl of freezing media and 100 µl of DMSO per cryovial.Vials were stored in liquid nitrogen.
Library construction was performed at the Single Cell Analysis Facility, a core service with the Center for Cancer Research at the NCI, Bethesda, MD. scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 5’Reagent Kits V2 (10X Genomics; PN-1000263, PN-1000265, PN-1000190, PN-1000252, PN-1000253) following the manufacturer’s instruction. Briefly, cells were partitioned into nanoliter-scale Gel-beads-in-Emulsion (GEMs), generated by combining barcoded Gel Beads, a Master Mix containing  cells, and Partitioning Oil onto Chromium Next GEM Chip K. After successful completion of uniform emulsion consistency, the reverse transcription was run overnight to amplify full length cDNA. Simplified cDNA was then used to amplify full-length V(D)J segments, followed V(D)J library construction and 5' gene expression library construction. All the steps including TCR and BCR enrichment libraries and QC steps were performed as described in the 10X Genomics 5’ v2 Single Cell User Guide.

value: Blood

tag: race

value: African American (AA)

tag: lethal prostate_cancer_group

value: Nonlethal


title: total RNA-seq from T-helper 1 cell (ENCLB132NPC)

description:
https://www.encodeproject.org/experiments/ENCSR124FVF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR124FVF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB132NPC

source_name: Homo sapiens male adult (38 years) T-helper 1 primary cell

value: T-helper 1 cell

value: primary cell

tag: biosample encode accession

value: adult

value: 38 year

value: ENCBS895MZS at ENCODE; https://www.encodeproject.org/ENCBS895MZS/


title: gavage vehicle control 3

description: Library name: LL11_104_gav_con_veh

tag: tissue

value: colon

value: epithelium

value: gavage vehicle control

value: male


title: SCAF2824_24574


title: gavage vehicle control 2

description: Library name: LL11_103_gav_con_veh

tag: strain


title: U1C siRNA, + branaplam 5nM, rep2

description:
Library name: U1C.P905.5nM.2
column name in the processed files: num_U1C.P905.5nM.2

value: U1C siRNA, + branaplam 5nM, rep2


title: total RNA-seq from T-cell (ENCLB839ARP)

description:
https://www.encodeproject.org/experiments/ENCSR144LNR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR144LNR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB839ARP

source_name: Homo sapiens female adult (33 years) T-cell primary cell

value: T-cell

value: female

value: John Stamatoyannopoulos, UW

value: ENCBS352YLF at ENCODE; https://www.encodeproject.org/ENCBS352YLF/


title: SCAF2823_24397

value: Blood

value: European American (EA)


title: U1C siRNA, + branaplam 5nM, rep1

description:
Library name: U1C.P905.5nM.1
column name in the processed files: num_U1C.P905.5nM.1

value: U1C siRNA, + branaplam 5nM, rep1


title: U1 GA and HelixH G12C/C122G variant

description:
Library name: U1.GA.HelixH.ID2
column name in the processed files: num_U1.GA.HelixH.ID2

value: U1 GA and HelixH G12C/C122G variant


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB083CQQ)

description:
https://www.encodeproject.org/experiments/ENCSR119OKW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR119OKW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB083CQQ

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 42 year

value: AllCells

value: ENCBS934EUK at ENCODE; https://www.encodeproject.org/ENCBS934EUK/


title: gavage vehicle control 1

description: Library name: LL11_102_gav_con_veh

value: colon

tag: cell type

value: epithelium


title: SCAF2822_24392


title: U1C siRNA, + branaplam 400nM, rep2

description:
Library name: U1C.P905.400nM.2
column name in the processed files: num_U1C.P905.400nM.2

value: U1C siRNA, + branaplam 400nM, rep2


title: gavage alanine LPLFD 5

description: Library name: LL11_101_gav_lpl_ala

tag: disease state

value: gavage alanine LPLFD

value: male


title: gavage vehicle LPLFD 5

description: Library name: LL11_111_gav_lpl_veh

value: gavage vehicle LPLFD

tag: Sex


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB923BUK)

description:
https://www.encodeproject.org/experiments/ENCSR118GLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR118GLJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB923BUK

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

tag: encode accession

value: female

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: ENCBS327CJZ at ENCODE; https://www.encodeproject.org/ENCBS327CJZ/


title: SCAF2821_23198

value: Blood

value: European American (EA)

value: Lethal


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB870GEA)

description:
https://www.encodeproject.org/experiments/ENCSR117NBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR117NBV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB870GEA

source_name: Homo sapiens female adult (33 years) stimulated activated CD4-positive, alpha-beta T primary cell

value: primary cell

tag: dev stage

value: 33 year

value: ENCBS723MHK at ENCODE; https://www.encodeproject.org/ENCBS723MHK/


title: gavage vehicle LPLFD 4

description: Library name: LL11_110_gav_lpl_veh

value: colon


title: U1C siRNA, + branaplam 400nM, rep1

description:
Library name: U1C.P905.400nM.1
column name in the processed files: num_U1C.P905.400nM.1

value: U1C siRNA, + branaplam 400nM, rep1


title: gavage alanine LPLFD 4

description: Library name: LL11_100_gav_lpl_ala

value: epithelium


title: total RNA-seq from T-cell (ENCLB022FQB)

description:
https://www.encodeproject.org/experiments/ENCSR116HHQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR116HHQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB022FQB

source_name: Homo sapiens male adult (38 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: T-cell

tag: age

value: 38 year

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS205PTS at ENCODE; https://www.encodeproject.org/ENCBS205PTS/


title: SCAF2875_26352

value: African American (AA)

value: Nonlethal


title: SCAF2820_22915


title: U1C siRNA, + branaplam 25nM, rep2

description:
Library name: U1C.P905.25nM.2
column name in the processed files: num_U1C.P905.25nM.2

value: U1C siRNA, + branaplam 25nM, rep2


title: gavage alanine LPLFD 3

description: Library name: LL11_099_gav_lpl_ala

value: gavage alanine LPLFD

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB080OJR)

description:
https://www.encodeproject.org/experiments/ENCSR111UMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR111UMO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB080OJR

value: CD4-positive, alpha-beta T cell

value: adult

value: 42 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: ENCBS833KUX at ENCODE; https://www.encodeproject.org/ENCBS833KUX/


title: SCAF2819_22010

value: Blood

value: European American (EA)


title: U1 GA and HelixH G12C variant

description:
Library name: U1.GA.HelixH.Break1
column name in the processed files: num_U1.GA.HelixH.Break1

tag: cell line

value: U1 GA and HelixH G12C variant


title: gavage alanine LPLFD 2

description: Library name: LL11_098_gav_lpl_ala

value: colon

value: epithelium


title: U1C siRNA, + branaplam 25nM, rep1

description:
Library name: U1C.P905.25nM.1
column name in the processed files: num_U1C.P905.25nM.1

tag: treatment

value: U1C siRNA, + branaplam 25nM, rep1


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB648WMF)

description:
https://www.encodeproject.org/experiments/ENCSR110EAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR110EAN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB648WMF

value: primary cell

value: female

value: 34 year

value: AllCells

tag: link

value: ENCBS730BCY at ENCODE; https://www.encodeproject.org/ENCBS730BCY/


title: SCAF2818_21943

tag: race

value: African American (AA)

value: Nonlethal


title: gavage alanine LPLFD 1

description: Library name: LL11_097_gav_lpl_ala

value: gavage alanine LPLFD

value: male


title: U1C siRNA, + branaplam 1.2uM, rep2

description:
Library name: U1C.P905.1.2uM.2
column name in the processed files: num_U1C.P905.1.2uM.2

value: U1C siRNA, + branaplam 1.2uM, rep2

tag: batch


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB069LVL)

description:
https://www.encodeproject.org/experiments/ENCSR108VOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR108VOF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB069LVL

source_name: Homo sapiens male adult (42 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

tag: biosample encode accession

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: ENCBS559UUZ at ENCODE; https://www.encodeproject.org/ENCBS559UUZ/


title: SCAF2817_21365

tag: tissue

value: Blood

tag: lethal prostate_cancer_group


title: U1C siRNA, + branaplam 1.2uM, rep1

description:
Library name: U1C.P905.1.2uM.1
column name in the processed files: num_U1C.P905.1.2uM.1

value: U1C siRNA, + branaplam 1.2uM, rep1


title: gavage alanine control 5

description: Library name: LL11_096_gav_con_ala

value: colon

tag: strain

tag: cell type

value: epithelium

value: gavage alanine control


title: gavage alanine control 4

description: Library name: LL11_095_gav_con_ala

tag: disease state

tag: Sex


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB482KQA)

description:
https://www.encodeproject.org/experiments/ENCSR104XPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR104XPI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB482KQA

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

value: female

tag: dev stage

value: 34 year

value: AllCells

value: ENCBS502AJM at ENCODE; https://www.encodeproject.org/ENCBS502AJM/


title: SCAF2811_26136

value: African American (AA)


title: U1C siRNA, + branaplam 100nM, rep1

description:
Library name: U1C.P905.100nM.1
column name in the processed files: num_U1C.P905.100nM.1

value: U1C siRNA, + branaplam 100nM, rep1


title: total RNA-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB904JJZ)

description:
https://www.encodeproject.org/experiments/ENCSR108HJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR108HJO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB904JJZ

source_name: Homo sapiens male adult (42 years) stimulated activated CD4-positive, alpha-beta T primary cell

value: male

value: adult

tag: age

value: ENCBS683MCZ at ENCODE; https://www.encodeproject.org/ENCBS683MCZ/


title: gavage alanine control 3

description: Library name: LL11_094_gav_con_ala


title: SCAF2810_26003

value: Lethal


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB068HXL)

description:
https://www.encodeproject.org/experiments/ENCSR099JHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR099JHK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB068HXL

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: ENCBS979XBL at ENCODE; https://www.encodeproject.org/ENCBS979XBL/


title: U1C siRNA, + risdiplam 50nM, rep2

description:
Library name: U1C.P683.50nM.2
column name in the processed files: num_U1C.P683.50nM.2

value: U1C siRNA, + risdiplam 50nM, rep2


title: gavage alanine control 2

description: Library name: LL11_093_gav_con_ala

value: colon

value: epithelium

value: gavage alanine control


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB560YXD)

description:
https://www.encodeproject.org/experiments/ENCSR098KNC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR098KNC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB560YXD

source_name: Homo sapiens female adult (33 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: female

value: 33 year

tag: source

value: ENCBS311GAO at ENCODE; https://www.encodeproject.org/ENCBS311GAO/


title: SCAF2809_25015

value: Blood

value: European American (EA)


title: U1C siRNA, + risdiplam 50nM, rep1

description:
Library name: U1C.P683.50nM.1
column name in the processed files: num_U1C.P683.50nM.1

tag: cell line

value: U1C siRNA, + risdiplam 50nM, rep1


title: gavage alanine control 1

description: Library name: LL11_092_gav_con_ala

value: male


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB122GUP)

description:
https://www.encodeproject.org/experiments/ENCSR094IXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR094IXV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB122GUP

source_name: Homo sapiens male adult (38 years) CD8-positive, alpha-beta T primary cell

value: adult

value: AllCells

value: ENCBS845SVP at ENCODE; https://www.encodeproject.org/ENCBS845SVP/


title: SCAF2808_22573

value: African American (AA)

value: Nonlethal


title: gavage leucine LPLFD 5

description: Library name: LL11_091_gav_lpl_leu

value: colon

value: gavage leucine LPLFD


title: U1C siRNA, + risdiplam 400nM, rep2

description:
Library name: U1C.P683.400nM.2
column name in the processed files: num_U1C.P683.400nM.2

tag: treatment

value: U1C siRNA, + risdiplam 400nM, rep2


title: SCAF2807_22213

value: Lethal


title: U1C siRNA, + risdiplam 400nM, rep1

description:
Library name: U1C.P683.400nM.1
column name in the processed files: num_U1C.P683.400nM.1

value: U1C siRNA, + risdiplam 400nM, rep1


title: gavage leucine LPLFD 4

description: Library name: LL11_090_gav_lpl_leu

value: epithelium


title: SCAF2806_22135


title: U1C siRNA, + risdiplam 3.6uM, rep2

description:
Library name: U1C.P683.3.6uM.2
column name in the processed files: num_U1C.P683.3.6uM.2

value: U1C siRNA, + risdiplam 3.6uM, rep2


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB082MTP)

description:
https://www.encodeproject.org/experiments/ENCSR092TIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092TIL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB082MTP

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 38 year

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS796BUO at ENCODE; https://www.encodeproject.org/ENCBS796BUO/


title: SCAF2786_25509

value: Blood

tag: race

value: European American (EA)


title: U1C siRNA, + risdiplam 3.6uM, rep1

description:
Library name: U1C.P683.3.6uM.1
column name in the processed files: num_U1C.P683.3.6uM.1

value: U1C siRNA, + risdiplam 3.6uM, rep1

tag: batch


title: U1C siRNA, + risdiplam 200nM, rep2

description:
Library name: U1C.P683.200nM.2
column name in the processed files: num_U1C.P683.200nM.2

value: U1C siRNA, + risdiplam 200nM, rep2


title: total RNA-seq from T-helper 9 cell (ENCLB584LPX)

description:
https://www.encodeproject.org/experiments/ENCSR092PHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092PHJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB584LPX

source_name: Homo sapiens female adult (33 years) T-helper 9 primary cell

value: T-helper 9 cell

tag: biosample encode accession

value: female

value: adult

value: 33 year

value: AllCells

value: ENCBS694IFA at ENCODE; https://www.encodeproject.org/ENCBS694IFA/


title: gavage leucine LPLFD 1

description: Library name: LL11_087_gav_lpl_leu

tag: tissue

value: colon

value: epithelium

value: gavage leucine LPLFD

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB297YIO)

description:
https://www.encodeproject.org/experiments/ENCSR083GNI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR083GNI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB297YIO

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 42 year

value: ENCBS680ZTG at ENCODE; https://www.encodeproject.org/ENCBS680ZTG/


title: SCAF2785_25265

value: Blood

value: European American (EA)

tag: lethal prostate_cancer_group

value: Lethal


title: U1C siRNA, + risdiplam 200nM, rep1

description:
Library name: U1C.P683.200nM.1
column name in the processed files: num_U1C.P683.200nM.1

value: U1C siRNA, + risdiplam 200nM, rep1


title: gavage leucine control 5

description: Library name: LL11_086_gav_con_leu

tag: strain

value: gavage leucine control


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB062JMU)

description:
https://www.encodeproject.org/experiments/ENCSR080BPH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR080BPH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB062JMU

value: female

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS140HEW at ENCODE; https://www.encodeproject.org/ENCBS140HEW/


title: SCAF2784_24520

value: African American (AA)


title: U1C siRNA, + risdiplam 1.2uM, rep2

description:
Library name: U1C.P683.1.2uM.2
column name in the processed files: num_U1C.P683.1.2uM.2

value: U1C siRNA, + risdiplam 1.2uM, rep2


title: gavage leucine control 4

description: Library name: LL11_085_gav_con_leu

value: colon

tag: cell type

value: epithelium


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB931PMN)

description:
https://www.encodeproject.org/experiments/ENCSR075FPQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075FPQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB931PMN

value: CD4-positive, alpha-beta T cell

value: male

value: AllCells

value: ENCBS800BVN at ENCODE; https://www.encodeproject.org/ENCBS800BVN/


title: SCAF2783_24358

value: Blood


title: gavage leucine control 3

description: Library name: LL11_084_gav_con_leu

tag: disease state


title: U1C siRNA, + risdiplam 1.2uM, rep1

description:
Library name: U1C.P683.1.2uM.1
column name in the processed files: num_U1C.P683.1.2uM.1

value: U1C siRNA, + risdiplam 1.2uM, rep1


title: SCAF2782_23995


title: U1C siRNA, + DMSO, rep4

description:
Library name: U1C.DMSO.4
column name in the processed files: num_U1C.DMSO.4

value: U1C siRNA, + DMSO, rep4


title: gavage leucine control 2

description: Library name: LL11_083_gav_con_leu

tag: Sex


title: total RNA-seq from inflammatory macrophage (ENCLB503MJF)

description:
https://www.encodeproject.org/experiments/ENCSR072XZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR072XZF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB503MJF

source_name: Homo sapiens male adult (24 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: primary cell

tag: encode accession

value: 24 year

value: Shelly Heimfeld

value: ENCBS955QJR at ENCODE; https://www.encodeproject.org/ENCBS955QJR/


title: SCAF2781_22152

value: Nonlethal


title: U1C siRNA, + DMSO, rep3

description:
Library name: U1C.DMSO.3
column name in the processed files: num_U1C.DMSO.3

value: U1C siRNA, + DMSO, rep3


title: gavage leucine control 1

description: Library name: LL11_082_gav_con_leu

source_name: colon

value: gavage leucine control


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB795HNU)

description:
https://www.encodeproject.org/experiments/ENCSR068SXL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR068SXL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB795HNU

source_name: Homo sapiens male adult (38 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

tag: dev stage

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: ENCBS678PDM at ENCODE; https://www.encodeproject.org/ENCBS678PDM/


title: SCAF2812_27281

value: European American (EA)

value: Lethal


title: U1C siRNA, + branaplam 100nM, rep2

description:
Library name: U1C.P905.100nM.2
column name in the processed files: num_U1C.P905.100nM.2

value: U1C siRNA, + branaplam 100nM, rep2


title: U1C siRNA, + DMSO, rep2

description:
Library name: U1C.DMSO.2
column name in the processed files: num_U1C.DMSO.2

value: U1C siRNA, + DMSO, rep2


title: SCAF2780_22105

value: Blood

value: African American (AA)


title: enema isovalerate LPLFD 5

description: Library name: LL11_081_ene_lpl_iso

value: colon

value: epithelium

value: enema isovalerate LPLFD

value: male


title: SCAF2779_21906

value: Nonlethal


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB810OSZ)

description:
https://www.encodeproject.org/experiments/ENCSR058NWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR058NWZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB810OSZ

source_name: Homo sapiens male adult (42 years) effector memory CD8-positive, alpha-beta T primary cell

value: primary cell

tag: age

value: 42 year

value: AllCells

value: ENCBS406EPP at ENCODE; https://www.encodeproject.org/ENCBS406EPP/


title: U1C siRNA, + DMSO, rep1

description:
Library name: U1C.DMSO.1
column name in the processed files: num_U1C.DMSO.1

value: U1C siRNA, + DMSO, rep1


title: enema isovalerate LPLFD 4

description: Library name: LL11_080_ene_lpl_iso


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB081UAW)

description:
https://www.encodeproject.org/experiments/ENCSR056RVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR056RVQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB081UAW

source_name: Homo sapiens male adult (38 years) effector memory CD8-positive, alpha-beta T primary cell

value: adult

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: ENCBS831GIE at ENCODE; https://www.encodeproject.org/ENCBS831GIE/


title: SCAF2318_5-28070

source_name: Prostate cancer patient


title: control siRNA, + branaplam 5nM, rep2

description:
Library name: Neg.P905.5nM.2
column name in the processed files: num_Neg.P905.5nM.2

value: control siRNA, + branaplam 5nM, rep2


title: enema isovalerate control 5

description: Library name: LL11_079_ene_con_iso

value: enema isovalerate control


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB437GFT)

description:
https://www.encodeproject.org/experiments/ENCSR053ZUQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR053ZUQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB437GFT

value: CD4-positive, alpha-beta T cell

tag: source

value: ENCBS166RRJ at ENCODE; https://www.encodeproject.org/ENCBS166RRJ/


title: SCAF2317_3-27997

value: Blood

value: African American (AA)


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB997IEO)

description:
https://www.encodeproject.org/experiments/ENCSR093FXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR093FXB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB997IEO

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: female

value: 40 year

value: ENCBS519MDA at ENCODE; https://www.encodeproject.org/ENCBS519MDA/


title: control siRNA, + branaplam 5nM, rep1

description:
Library name: Neg.P905.5nM.1
column name in the processed files: num_Neg.P905.5nM.1

tag: cell line

value: control siRNA, + branaplam 5nM, rep1


title: enema isovalerate control 4

description: Library name: LL11_078_ene_con_iso

value: colon

value: epithelium

value: male


title: gavage leucine LPLFD 3

description: Library name: LL11_089_gav_lpl_leu

value: gavage leucine LPLFD


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB024GUL)

description:
https://www.encodeproject.org/experiments/ENCSR092ZRN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092ZRN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB024GUL

value: primary cell

value: adult

value: 34 year

value: AllCells

value: ENCBS783KHW at ENCODE; https://www.encodeproject.org/ENCBS783KHW/


title: SCAF2316_6-28066

value: Nonlethal


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB585AOV)

description:
https://www.encodeproject.org/experiments/ENCSR053TWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR053TWA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB585AOV

source_name: Homo sapiens male adult (56 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: 56 year

value: John Stamatoyannopoulos, UW

value: ENCBS374RUK at ENCODE; https://www.encodeproject.org/ENCBS374RUK/


title: control siRNA, + branaplam 400nM, rep2

description:
Library name: Neg.P905.400nM.2
column name in the processed files: num_Neg.P905.400nM.2

tag: treatment

value: control siRNA, + branaplam 400nM, rep2


title: SCAF2805_21570

value: Blood

value: European American (EA)


title: enema isovalerate control 3

description: Library name: LL11_077_ene_con_iso

value: enema isovalerate control


title: gavage leucine LPLFD 2

description: Library name: LL11_088_gav_lpl_leu

value: colon


title: total RNA-seq from T-cell (ENCLB634JSQ)

description:
https://www.encodeproject.org/experiments/ENCSR051QDS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR051QDS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB634JSQ

source_name: Homo sapiens male adult (42 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours

value: T-cell

value: 42 year

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour;

tag: link

value: ENCBS338MHP at ENCODE; https://www.encodeproject.org/ENCBS338MHP/


title: SCAF2314_4-27693

tag: race


title: enema isovalerate control 2

description: Library name: LL11_076_ene_con_iso

value: epithelium

value: male


title: control siRNA, + branaplam 400nM, rep1

description:
Library name: Neg.P905.400nM.1
column name in the processed files: num_Neg.P905.400nM.1

value: control siRNA, + branaplam 400nM, rep1

tag: batch


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB667RUG)

description:
https://www.encodeproject.org/experiments/ENCSR051IEG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR051IEG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB667RUG

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

value: adult

value: 38 year

value: AllCells

value: ENCBS441MQE at ENCODE; https://www.encodeproject.org/ENCBS441MQE/


title: control siRNA, + branaplam 25nM, rep2

description:
Library name: Neg.P905.25nM.2
column name in the processed files: num_Neg.P905.25nM.2

value: control siRNA, + branaplam 25nM, rep2


title: SCAF2312_2-27446

tag: tissue

value: Blood

value: European American (EA)

tag: lethal prostate_cancer_group

value: Nonlethal


title: enema isovalerate control 1

description: Library name: LL11_075_ene_con_iso

value: colon

tag: strain

tag: cell type

value: enema isovalerate control


title: SCAF2311_1-28019


title: control siRNA, + branaplam 25nM, rep1

description:
Library name: Neg.P905.25nM.1
column name in the processed files: num_Neg.P905.25nM.1

value: control siRNA, + branaplam 25nM, rep1


title: total RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB562XZN)

description:
https://www.encodeproject.org/experiments/ENCSR049VKA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049VKA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB562XZN

source_name: Homo sapiens female adult (25 years) CD4-positive, CD25-positive, alpha-beta regulatory T primary cell

tag: Sex

value: female

value: 25 year

value: John Stamatoyannopoulos, UW

value: ENCBS616WAY at ENCODE; https://www.encodeproject.org/ENCBS616WAY/


title: enema vehicle LPLFD 5

description: Library name: LL11_074_ene_lpl_veh

value: epithelium

tag: disease state

value: enema vehicle LPLFD

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB758PUA)

description:
https://www.encodeproject.org/experiments/ENCSR045PKU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR045PKU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB758PUA

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

tag: dev stage

value: adult

value: 42 year

value: ENCBS034GVO at ENCODE; https://www.encodeproject.org/ENCBS034GVO/


title: lung, ILC2s, scRNA-seq

city: Beijing

first: Hongjie

last: Chen

address: No.5 Yiheyuan Road

country: China

institute: Peking University

description: multiplexed

data_processing:
The demultiplexing, barcoded processing, gene counting were made using  the STAR software (v2.7.9a)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix file

source_name: lung

extract_protocol:
Freshly collected human lung tissues were cut into small pieces. The tissues were digested at 37°C for 30 min in RPMI 1640 medium containing Liberase (0.1 mg/ml)/deoxyribonuclease I (20 μg/ml)/10 mM Hepes/3% heat-inactivated fetal bovine serum and then mashed through 70-μm cell strainers. The cells were stained with intended FACS antibodies and processed on the BD FACSAria Fusion
single cell lysis to release RNA, reverse transcription, amplification, pooling and purification, quality control, DNA fragmentation, construction of sequencing library

value: lung

value: type 2 innate lymphoid cells


title: control siRNA, + branaplam 1.2uM, rep2

description:
Library name: Neg.P905.1.2uM.2
column name in the processed files: num_Neg.P905.1.2uM.2

value: control siRNA, + branaplam 1.2uM, rep2


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB932HHO)

description:
https://www.encodeproject.org/experiments/ENCSR044ICH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR044ICH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB932HHO

tag: age

tag: lab

value: AllCells

value: ENCBS305ZCU at ENCODE; https://www.encodeproject.org/ENCBS305ZCU/


title: MIAML-090-Re

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description: human leukemic blood PBMCs single cell Drop-seq

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.13.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2a.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.13.
Gene expression matrix was generated using Drop-seq tools v1.13.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: leukemic blood (AML)

growth_protocol: Cryo-preserved bone marrow mononuclear cells or peripheral blood mononuclear cells from AML patients or healthy donors (STEMCELL Technologies) were thawed in a 37 °C water bath, dissociated by DNase I solution (New England Biolabs) treatment at a final concentration of 0.1 mg/mL and filtered through 40 μm cell strainers (Corning Life Sciences) to remove clumped cells. Isolated single cells were transferred into warm culture media (RPMI1640 supplemented with 10% FBS) and incubated at 37 °C for 2 hours. Then dead cells in the culture were eliminated using a dead cell removal kit from Miltenyi Biotec following the manufacturer’s protocol. The remaining viable single cells were counted and resuspended at 100 cells/ μl in a PBS-BSA solution.

extract_protocol:
Single-cell RNA sequencing was performed following the Drop-seq Online Protocol by Macosko et al (http://mccarrolllab.com/dropseq/) with minor modifications. Briefly, single cell suspension were loaded into the microfluidic device (FlowJEM) together with droplet-generating oil (Bio-Rad) and barcoded beads (MACOSKO-2011-10, Chemgenes) suspended in lysis buffer supplemented with RNase inhibitor (Lucigen) at a final concentration of 1 U/µL. Emulsions were incubated on ice for 30 minutes before droplet breakage and bead collection. Beads were subject to reverse transcription (Maxima H Minus Reverse Transcriptase: ThermoFisher; Template switch oligo: IDT) and Exo I (New England Biolabs) digestion. Next, 4000 beads were aliquoted into one PCR tube for amplification (KAPA HotStart ReadyMix: Kapa Biosystems). Products from multiple parallel PCRs were pooled together and purified using AMPure XP Beads (Beckman Coulter Life Sciences).
For each sample, 1 ng high quality cDNA was used for tagmentation and NGS library preparation using a Nextera XT kit (Illumina). High quality NGS libraries were sequenced on an Illumina NextSeq 550 (75-cycle kit) or NovaSeq 6000 (100-cycle kit) sequencers. All paired AML samples were processed and sequenced together to minimize batch effects.

tag: ex vivo treatment

value: untreated

value: blood

value: AML

tag: time point

value: at relapse


title: enema vehicle control 5

description: Library name: LL11_072_ene_con_veh

value: colon

value: epithelium

value: enema vehicle control


title: enema vehicle LPLFD 4

description: Library name: LL11_073_ene_lpl_veh

value: enema vehicle LPLFD

value: male


title: control siRNA, + branaplam 100nM, rep2

description:
Library name: Neg.P905.100nM.2
column name in the processed files: num_Neg.P905.100nM.2

tag: cell line

tag: treatment

value: control siRNA, + branaplam 100nM, rep2


title: MIAML-090-Dx

value: at diagnosis


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB646DTW)

description:
https://www.encodeproject.org/experiments/ENCSR043DGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR043DGB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB646DTW

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

tag: source

tag: link

value: ENCBS594VSR at ENCODE; https://www.encodeproject.org/ENCBS594VSR/


title: enema vehicle control 4

description: Library name: LL11_071_ene_con_veh


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB028PVE)

description:
https://www.encodeproject.org/experiments/ENCSR074DPH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR074DPH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB028PVE

source_name: Homo sapiens female adult (33 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

tag: biosample encode accession

value: 33 year

value: AllCells

value: ENCBS481PMZ at ENCODE; https://www.encodeproject.org/ENCBS481PMZ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB941JHU)

description:
https://www.encodeproject.org/experiments/ENCSR040XOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR040XOI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB941JHU

value: 42 year

value: ENCBS848DBI at ENCODE; https://www.encodeproject.org/ENCBS848DBI/


title: control siRNA, + branaplam 100nM, rep1

description:
Library name: Neg.P905.100nM.1
column name in the processed files: num_Neg.P905.100nM.1

value: control siRNA, + branaplam 100nM, rep1

tag: batch


title: enema isovalerate LPLFD 3

description: Library name: LL11_070_ene_lpl_iso

tag: tissue

value: colon

value: epithelium

value: enema isovalerate LPLFD

value: male


title: AMLMRD041-Re

value: untreated

value: blood

value: AML

value: at relapse


title: AMLMRD041-Dx

value: at diagnosis


title: total RNA-seq from effector CD4-positive, alpha-beta T cell (ENCLB344JMS)

description:
https://www.encodeproject.org/experiments/ENCSR039LCP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR039LCP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB344JMS

source_name: Homo sapiens male adult (38 years) effector CD4-positive, alpha-beta T primary cell

value: primary cell

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: ENCBS442UIQ at ENCODE; https://www.encodeproject.org/ENCBS442UIQ/


title: control siRNA, + risdiplam 50nM, rep2

description:
Library name: Neg.P683.50nM.2
column name in the processed files: num_Neg.P683.50nM.2

value: control siRNA, + risdiplam 50nM, rep2


title: enema isovalerate LPLFD 2

description: Library name: LL11_069_ene_lpl_iso

tag: strain


title: AMLMRD032-Re


title: control siRNA, + risdiplam 50nM, rep1

description:
Library name: Neg.P683.50nM.1
column name in the processed files: num_Neg.P683.50nM.1

value: control siRNA, + risdiplam 50nM, rep1


title: snATAC-seq from MCF 10A (ENCLB134FTS)

description:
https://www.encodeproject.org/experiments/ENCSR037XNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR037XNN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB134FTS
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens MCF 10A cell line nuclear fraction

tag: line

value: MCF 10A

value: cell line

value: female

tag: health state

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

tag: subcellular fraction term name

value: nucleus

value: ATCC

value: ENCBS201MSR at ENCODE; https://www.encodeproject.org/ENCBS201MSR/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: enema isovalerate LPLFD 1

description: Library name: LL11_068_ene_lpl_iso

value: colon

tag: cell type

value: epithelium

tag: disease state

value: enema isovalerate LPLFD

tag: Sex

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB590CIQ)

description:
https://www.encodeproject.org/experiments/ENCSR030BLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR030BLB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB590CIQ

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

tag: dev stage

value: adult

tag: age

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS917HMW at ENCODE; https://www.encodeproject.org/ENCBS917HMW/


title: AMLMRD032-Dx

tag: ex vivo treatment

value: untreated

value: blood

value: AML

tag: time point

value: at diagnosis


title: control siRNA, + risdiplam 400nM, rep2

description:
Library name: Neg.P683.400nM.2
column name in the processed files: num_Neg.P683.400nM.2

tag: cell line

tag: treatment

value: control siRNA, + risdiplam 400nM, rep2


title: wilt-type strain T=30 min (pH 8.0), replicate B

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description: Library name: W_T30_B

data_processing:
Raw reads (fastq format) were transformed into clean reads through fastp  (Chen et al., 2018, PMID: 30423086). The HISAT2 (v2.2.1) was used to align paired-end clean reads to the K. phaffii GS115 reference genome (assembly GCA_000027005.1) to generate BAM files.
Differential gene expression analysis was carried out with the BAM files using DESeq2 (Love et al., 2014, PMID:25516281) and stablishing a |log2(FoldChange)| >= 1 and a p-value <= 0.01, unless otherwise stated.
Assembly: GCA_000027005.1
Supplementary files format and content: File "All_data_FPKM.xlsx" excel file with "Fragment per kilobase Million" data for each sample.
Supplementary files format and content: File "LowvsHigh Pi.xlsx", excel file with diverse comparisons for the low vs high phosphate experiments
Supplementary files format and content: File "Alkali_stress.xlsx", Excel file with diverse comparisons of the pH 5.5 to pH 8.0 time-course experiments

organism: Komagataella phaffii GS115

source_name: whole cell

growth_protocol: For evaluation of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YPGly medium. Cultures were then diluted in 100 ml of fresh medium at OD600=0.2 (~ 107 cells/ml) and grown until an OD600 around 0.6. At this point, two 50 ml-aliquots were centrifuged (5 min at 1000xg). For assessment of the effects of phosphate starvation, cells were grown for ~40 h on 20 ml of synthetic medium prepared with Formedium premade mix (ref. CYN0803, Yeast Nitrogen Base without Amino Acids and Phosphate) supplemented with 15 mM KCl, 2% glycerol and 7.35 mM KH2PO4, and adjusted to pH 5.8.

extract_protocol:
Total RNA extraction was carried out as described in (Albacar et al., 2023, PMID: 37013612 ) from three independent cultures of wild-type, pho4(A) (strain PJA-004), pho4(B) (strain PJA-021) and pho4(A) pho4(B) (PJA-026) cells. RNA concentration was assessed by Qubit assay (ThermoFisher) and its integrity with an Agilent 5400 Fragment Analyzer System.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, synthesis of the first strand cDNA was achieved by means of random hexamer primers, followed by the second strand cDNA synthesis using dTTP. After end repair, A-tailing, and adapter ligation, fragments were size selected, PCR amplified, and purified. Libraries were then pooled and subjected to sequencing in a NovaSeq X Plus equipment (Illumina) by Novogene Co., Ltd.

treatment_protocol: For alkalinization experiments, two 50 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of fresh YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (T=0) and, for each stressed culture, after 15, 30 and 60 min, placed on ice and immediately centrifuged (5 min at 1000 xg) at 4 °C. Then one ml of cold H2O was added, and cells were transferred to pre-cooled 1.5 ml screw cap tubes and centrifuged (2 min at 1000 xg) at 4 °C. Finally, the supernatant was removed, and samples were frozen with liquid N2 and stored at -80 ºC. For cultures to be subjected to Pi starvation (low Pi), cells (10 OD600) were centrifuged and washed twice with medium without KH2PO4, whereas for control cultures (high Pi) 2.5 OD600 were taken and washed twice with medium containing 7.35 mM KH2PO4. In all cases, cells were resuspended in 50 ml the appropriate medium and growth resumed for 24 h.  Then, ~5 OD600 of each culture was collected and processed as described above.

value: whole cell

tag: genotype

value: wild-type


title: enema vehicle LPLFD 3

description: Library name: LL11_067_ene_lpl_veh

source_name: colon

tag: tissue

value: colon

value: epithelium

value: enema vehicle LPLFD


title: total RNA-seq from central memory CD4-positive, alpha-beta T cell (ENCLB236JBG)

description:
https://www.encodeproject.org/experiments/ENCSR029MBZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029MBZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB236JBG

source_name: Homo sapiens male adult (42 years) central memory CD4-positive, alpha-beta T primary cell

tag: biosample encode accession

value: male

value: 42 year

tag: source

tag: link

value: ENCBS533NCZ at ENCODE; https://www.encodeproject.org/ENCBS533NCZ/


title: enema vehicle LPLFD 2

description: Library name: LL11_066_ene_lpl_veh

tag: strain


title: AMLMRD022-Re

description: human leukemic bone marrow mononuclear cells single cell Drop-seq

source_name: leukemic bone marrow (AML)

value: bone marrow

value: at relapse


title: control siRNA, + risdiplam 400nM, rep1

description:
Library name: Neg.P683.400nM.1
column name in the processed files: num_Neg.P683.400nM.1

value: control siRNA, + risdiplam 400nM, rep1

tag: batch


title: AMLMRD022-Dx

tag: disease state


title: total RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB296TGY)

description:
https://www.encodeproject.org/experiments/ENCSR029LAA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029LAA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB296TGY

source_name: Homo sapiens male adult (56 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

tag: Sex

value: adult

value: 56 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS090TXI at ENCODE; https://www.encodeproject.org/ENCBS090TXI/


title: control siRNA, + risdiplam 3.6uM, rep2

description:
Library name: Neg.P683.3.6uM.2
column name in the processed files: num_Neg.P683.3.6uM.2

value: control siRNA, + risdiplam 3.6uM, rep2


title: enema vehicle LPLFD 1

description: Library name: LL11_065_ene_lpl_veh

tag: cell type


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB832CXI)

description:
https://www.encodeproject.org/experiments/ENCSR025QHQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025QHQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB832CXI

value: CD4-positive, alpha-beta T cell

tag: encode accession

value: female

tag: dev stage

value: 34 year

value: ENCBS902ZQZ at ENCODE; https://www.encodeproject.org/ENCBS902ZQZ/


title: control siRNA, + risdiplam 3.6uM, rep1

description:
Library name: Neg.P683.3.6uM.1
column name in the processed files: num_Neg.P683.3.6uM.1

value: control siRNA, + risdiplam 3.6uM, rep1


title: enema vehicle control 3

description: Library name: LL11_064_ene_con_veh

value: colon

value: epithelium

value: enema vehicle control

value: male


title: AMLMRD010-Re

description: human leukemic blood PBMCs single cell Drop-seq

value: untreated

value: blood

value: AML

value: at relapse


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB243OGG)

description:
https://www.encodeproject.org/experiments/ENCSR022BIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR022BIB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB243OGG

value: primary cell

value: adult

tag: age

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

value: ENCBS541RGT at ENCODE; https://www.encodeproject.org/ENCBS541RGT/


title: AMLMRD010-Dx

tag: ex vivo treatment

tag: time point

value: at diagnosis


title: enema vehicle control 2

description: Library name: LL11_063_ene_con_veh


title: control siRNA, + risdiplam 200nM, rep2

description:
Library name: Neg.P683.200nM.2
column name in the processed files: num_Neg.P683.200nM.2

tag: cell line

tag: treatment

value: control siRNA, + risdiplam 200nM, rep2


title: AMLMRD008-Re

tag: tissue


title: enema vehicle control 1

description: Library name: LL11_062_ene_con_veh


title: control siRNA, + risdiplam 200nM, rep1

description:
Library name: Neg.P683.200nM.1
column name in the processed files: num_Neg.P683.200nM.1

value: control siRNA, + risdiplam 200nM, rep1


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB796PDP)

description:
https://www.encodeproject.org/experiments/ENCSR014SGQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014SGQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB796PDP

value: CD4-positive, alpha-beta T cell

tag: biosample encode accession

value: AllCells

value: ENCBS930HAB at ENCODE; https://www.encodeproject.org/ENCBS930HAB/


title: control siRNA, + risdiplam 1.2uM, rep2

description:
Library name: Neg.P683.1.2uM.2
column name in the processed files: num_Neg.P683.1.2uM.2

value: control siRNA, + risdiplam 1.2uM, rep2


title: AMLMRD008-Dx


title: Spatial co-profiling,mouse embryo E11.5, RNA

city: philadelphia

first: Pengfei

last: Guo

state: PA

address: 422 Curie Boulevard, Stellar Chance Labs, 711-712 (lab), philadelphia

institute: University of Pennsylvania

description:
Library name: mouse_embryo_E11.5_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes

data_processing:
Raw reads (fastq file) were aligned to the mouse or human genome using BWA (ATAC), BWA (Hi-C) or STAR (RNA). RNA counts were generated with featureCounts, ATAC  fragments were created with Sinto, and Hi-C pairs were generated with Pairtools.
Assembly: mm10 for mouse embryo and adult brain; hg38 for human melanoma
Supplementary files format and content: RNA.tar.gz: gene expression count matrix in mtx, tsv format
Supplementary files format and content: Image.tar.gz: spatial related images in tif, png, json, csv format
Supplementary files format and content: HIC.nodups.pairs.gz: Hi-C pairs in pairs format
Supplementary files format and content: HIC_RNA.h5ad.gz: HIC_RNA processing data in h5ad format
Supplementary files format and content: ATAC.bed.gz: ATAC fragments in bed format

source_name: Mouse embryo

extract_protocol:
Frozen tissue sections were cryosectioned at 10 µm thickness, and processed for spatial Hi-C-RNA or ATAC library preparation using DBiT-seq.   Spatial barcoding was performed on cryosections using DBiT-seq.
Barcoded gDNA/cDNA (or ATAC fragments) were converted into Illumina-compatible sequencing libraries following standard protocols.

value: Mouse embryo


title: AMLMRD004-Re

value: untreated

value: bone marrow


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB321VYE)

description:
https://www.encodeproject.org/experiments/ENCSR008FVJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008FVJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB321VYE

value: CD8-positive, alpha-beta T cell

value: female

value: 33 year

tag: source

value: ENCBS568UDE at ENCODE; https://www.encodeproject.org/ENCBS568UDE/


title: control siRNA, + risdiplam 1.2uM, rep1

description:
Library name: Neg.P683.1.2uM.1
column name in the processed files: num_Neg.P683.1.2uM.1

value: control siRNA, + risdiplam 1.2uM, rep1


title: Spatial co-profiling,mouse embryo E11.5, Hi-C

description:
Library name: mouse_embryo_E11.5_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes


title: total RNA-seq from T-helper 1 cell (ENCLB034MOS)

description:
https://www.encodeproject.org/experiments/ENCSR008FFS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008FFS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034MOS

source_name: Homo sapiens female adult (25 years) T-helper 1 primary cell

value: T-helper 1 cell

value: primary cell

value: adult

value: 25 year

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS524NFO at ENCODE; https://www.encodeproject.org/ENCBS524NFO/


title: AMLMRD004-Dx

description: human leukemic bone marrow mononuclear cells single cell Drop-seq

value: AML

value: at diagnosis


title: control siRNA, + DMSO, rep4

description:
Library name: Neg.DMSO.4
column name in the processed files: num_Neg.DMSO.4

value: control siRNA, + DMSO, rep4


title: Spatial co-profiling,mouse brain_r2, RNA

description:
Library name: mouse_brain_r2_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes

source_name: Mouse brain

value: Mouse brain


title: AMLMRD002-Re2

value: untreated

value: at relapse


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB452YFK)

description:
https://www.encodeproject.org/experiments/ENCSR007YPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007YPV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB452YFK

value: CD4-positive, alpha-beta T cell

value: male

value: 42 year

value: AllCells

value: ENCBS481MXL at ENCODE; https://www.encodeproject.org/ENCBS481MXL/


title: control siRNA, + DMSO, rep3

description:
Library name: Neg.DMSO.3
column name in the processed files: num_Neg.DMSO.3

value: control siRNA, + DMSO, rep3


title: Spatial co-profiling,mouse brain_r2, Hi-C

description:
Library name: mouse_brain_r2_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB964GKL)

description:
https://www.encodeproject.org/experiments/ENCSR006DUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR006DUH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB964GKL

source_name: Homo sapiens female adult (33 years) CD4-positive, alpha-beta T primary cell

value: primary cell

value: female

value: 33 year

value: ENCBS088XVA at ENCODE; https://www.encodeproject.org/ENCBS088XVA/


title: AMLMRD002-Re

value: bone marrow


title: Spatial co-profiling,mouse brain_r1, RNA

description:
Library name: mouse_brain_r1_RNA
3'mRNA: read 1 contains transcript sequence; read 2 contains barcodes


title: control siRNA, + DMSO, rep2

description:
Library name: Neg.DMSO.2
column name in the processed files: num_Neg.DMSO.2

value: control siRNA, + DMSO, rep2


title: control siRNA, + DMSO, rep1

description:
Library name: Neg.DMSO.1
column name in the processed files: num_Neg.DMSO.1

value: control siRNA, + DMSO, rep1


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB428APE)

description:
https://www.encodeproject.org/experiments/ENCSR004XRD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004XRD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB428APE

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: ENCBS878AHO at ENCODE; https://www.encodeproject.org/ENCBS878AHO/


title: AMLMRD002-Dx

value: untreated

value: AML

value: at diagnosis


title: Spatial co-profiling,mouse brain_r1, Hi-C

description:
Library name: mouse_brain_r1_HiC
Hi-C: read 1 contains genome sequence; read 2 contains barcodes

value: Mouse brain


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB772ATO)

description:
https://www.encodeproject.org/experiments/ENCSR003JNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR003JNT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB772ATO

value: CD4-positive, alpha-beta T cell

value: AllCells

value: ENCBS012TBD at ENCODE; https://www.encodeproject.org/ENCBS012TBD/


title: Batch4_Urate1

status: Public on Jul 23 2026

first: Meenakshi

last: Chakraborty

address: 269 Campus Drive

institute: Stanford University

description: Library name: Batch4_Urate1

data_processing:
TrimGalore v0.6.10
Kallisto 0.48.0
Assembly: GRCh38
Supplementary files format and content: h5 files are outputs from kallisto
Supplementary files format and content: tsv files are outputs from kallisto

source_name: brain

extract_protocol:
Cells were frozen in TRIzol, and chloroform was added after the samples were thawed. Following centrifugation, RNA was isolated from the aqueous phase using the Qiagen RNeasy Mini Kit. Samples were then treated with TURBO DNase (Fisher Scientific), followed by RNA cleanup according to the "RNA Cleanup" protocol in the RNeasy Mini Kit handbook and subsequent ethanol precipitation.
mRNA libraries were prepared by Novogene from the extracted RNA, using a polyA enrichment strategy.

value: brain


title: Batch4_Urate2

description: Library name: Batch4_Urate2


title: Batch4_PA3

description: Library name: Batch4_PA3


title: Batch4_Urate3

description: Library name: Batch4_Urate3


title: Batch4_PA2

description: Library name: Batch4_PA2


title: Batch4_PA1

description: Library name: Batch4_PA1


title: Batch4_NAcAla3

description: Library name: Batch4_NAcAla3


title: Batch4_NAcAla2

description: Library name: Batch4_NAcAla2


title: Batch4_NAcAla1

description: Library name: Batch4_NAcAla1


title: Batch4_Methyl_IAA3

description: Library name: Batch4_Methyl_IAA3


title: Batch4_Methyl_IAA2

description: Library name: Batch4_Methyl_IAA2


title: Batch4_Methyl_IAA1

description: Library name: Batch4_Methyl_IAA1


title: Batch4_Lys3

description: Library name: Batch4_Lys3


title: Batch4_Lys1

description: Library name: Batch4_Lys1


title: Batch4_Lys2

description: Library name: Batch4_Lys2


title: Batch4_LPS1

description: Library name: Batch4_LPS1


title: Batch4_LPS2

description: Library name: Batch4_LPS2


title: Batch4_ILA3

description: Library name: Batch4_ILA3


title: Batch4_LPS3

description: Library name: Batch4_LPS3


title: Batch4_ILA2

description: Library name: Batch4_ILA2


title: Batch4_Hypoxanthine2

description: Library name: Batch4_Hypoxanthine2


title: Batch4_ILA1

description: Library name: Batch4_ILA1


title: Batch4_Hypoxanthine3

description: Library name: Batch4_Hypoxanthine3


title: Batch4_Hypoxanthine1

description: Library name: Batch4_Hypoxanthine1


title: Batch4_H2O3

description: Library name: Batch4_H2O3


title: Batch4_DMSO6

description: Library name: Batch4_DMSO6


title: Batch4_H2O2

description: Library name: Batch4_H2O2


title: Batch4_H2O1

description: Library name: Batch4_H2O1


title: Batch4_DMSO5

description: Library name: Batch4_DMSO5


title: Batch4_DMSO2

description: Library name: Batch4_DMSO2


title: Batch4_DMSO4

description: Library name: Batch4_DMSO4


title: Batch4_DMSO3

description: Library name: Batch4_DMSO3


title: Batch4_Allantoin2

description: Library name: Batch4_Allantoin2


title: Batch4_DMSO1

description: Library name: Batch4_DMSO1


title: Batch4_Allantoin3

description: Library name: Batch4_Allantoin3


title: Batch4_Allantoin1

description: Library name: Batch4_Allantoin1


title: Batch3_TMAO1

description: Library name: Batch3_TMAO1


title: Batch3_TMAO3

description: Library name: Batch3_TMAO3


title: Batch3_TMAO2

description: Library name: Batch3_TMAO2


title: Batch3_Quin3

description: Library name: Batch3_Quin3


title: Batch3_Quin2

description: Library name: Batch3_Quin2


title: Batch3_Quin1

description: Library name: Batch3_Quin1


title: Batch3_Panto3

description: Library name: Batch3_Panto3


title: Batch3_NAM3

description: Library name: Batch3_NAM3


title: Batch3_Panto1

description: Library name: Batch3_Panto1


title: Batch3_NAM2

description: Library name: Batch3_NAM2


title: Batch3_NAM1

description: Library name: Batch3_NAM1


title: Batch3_MA3

description: Library name: Batch3_MA3


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB019WWP)

description:
https://www.encodeproject.org/experiments/ENCSR015AOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR015AOP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB019WWP

value: primary cell

value: female

value: ENCBS614DHT at ENCODE; https://www.encodeproject.org/ENCBS614DHT/


title: Batch3_MA1

description: Library name: Batch3_MA1


title: Batch3_LPS2

description: Library name: Batch3_LPS2


title: Batch3_LPS1

description: Library name: Batch3_LPS1


title: Batch3_H2O9

description: Library name: Batch3_H2O9


title: Batch3_H2O8

description: Library name: Batch3_H2O8


title: Batch3_LPS3

description: Library name: Batch3_LPS3


title: Batch3_H2O7

description: Library name: Batch3_H2O7


title: Batch3_H2O6

description: Library name: Batch3_H2O6


title: Batch3_H2O4

description: Library name: Batch3_H2O4


title: Batch3_H2O5

description: Library name: Batch3_H2O5


title: Batch3_H2O3

description: Library name: Batch3_H2O3


title: Batch3_H2O1

description: Library name: Batch3_H2O1


title: Batch3_H2O2

description: Library name: Batch3_H2O2


title: Batch3_GDCA2

description: Library name: Batch3_GDCA2


title: Batch3_GDCA1

description: Library name: Batch3_GDCA1


title: Batch3_GDCA3

description: Library name: Batch3_GDCA3


title: Batch3_Citrulline3

description: Library name: Batch3_Citrulline3


title: Batch3_Citrulline1

description: Library name: Batch3_Citrulline1


title: Batch3_Choline3

description: Library name: Batch3_Choline3


title: Batch3_Citrulline2

description: Library name: Batch3_Citrulline2


title: Batch3_Choline2

description: Library name: Batch3_Choline2


title: Batch3_Choline1

description: Library name: Batch3_Choline1


title: Batch2_Val3

description: Library name: Batch2_Val3


title: Batch2_Oxalate3

description: Library name: Batch2_Oxalate3


title: Batch2_Val1

description: Library name: Batch2_Val1


title: Batch2_Val2

description: Library name: Batch2_Val2


title: Batch2_Oxalate2

description: Library name: Batch2_Oxalate2


title: Batch2_Oxalate1

description: Library name: Batch2_Oxalate1


title: Batch2_LPS1

description: Library name: Batch2_LPS1


title: Batch2_Ile3

description: Library name: Batch2_Ile3


title: Batch2_LPS2

description: Library name: Batch2_LPS2


title: Batch2_LPS3

description: Library name: Batch2_LPS3


title: Batch2_Ile2

description: Library name: Batch2_Ile2


title: Batch2_Ile1

description: Library name: Batch2_Ile1


title: Batch2_H2O9

description: Library name: Batch2_H2O9


title: Batch2_H2O8

description: Library name: Batch2_H2O8


title: Batch2_H2O7

description: Library name: Batch2_H2O7


title: Batch2_H2O6

description: Library name: Batch2_H2O6


title: Batch2_H2O5

description: Library name: Batch2_H2O5


title: Batch2_H2O4

description: Library name: Batch2_H2O4


title: Batch2_H2O3

description: Library name: Batch2_H2O3


title: Batch2_H2O2

description: Library name: Batch2_H2O2


title: Batch2_H2O1

description: Library name: Batch2_H2O1


title: Batch2_Glycerate2

description: Library name: Batch2_Glycerate2


title: Batch2_Gly3

description: Library name: Batch2_Gly3


title: Batch2_Glycerate1

description: Library name: Batch2_Glycerate1


title: Batch2_Gly2

description: Library name: Batch2_Gly2


title: Batch2_Glycerate3

description: Library name: Batch2_Glycerate3


title: Batch2_Gly1

description: Library name: Batch2_Gly1


title: Batch2_Carnitine3

description: Library name: Batch2_Carnitine3


title: Batch2_Carnitine1

description: Library name: Batch2_Carnitine1


title: Batch2_Carnitine2

description: Library name: Batch2_Carnitine2


title: Batch2_BHBA3

description: Library name: Batch2_BHBA3


title: Batch2_BHBA2

description: Library name: Batch2_BHBA2


title: Batch2_BHBA1

description: Library name: Batch2_BHBA1


title: Batch2_AKG3

description: Library name: Batch2_AKG3


title: Batch2_AKG2

description: Library name: Batch2_AKG2


title: Batch1_pCS3

description: Library name: Batch1_pCS3


title: Batch1_pCS2

description: Library name: Batch1_pCS2


title: Batch1_PAGln3

description: Library name: Batch1_PAGln3


title: Batch1_PAGln1

description: Library name: Batch1_PAGln1


title: Batch1_LPS3

description: Library name: Batch1_LPS3


title: Batch1_PAGln2

description: Library name: Batch1_PAGln2


title: Batch1_pCS1

description: Library name: Batch1_pCS1


title: Batch1_LPS2

description: Library name: Batch1_LPS2


title: Batch1_ImP3

description: Library name: Batch1_ImP3


title: Batch1_ImP2

description: Library name: Batch1_ImP2


title: Batch1_ImP1

description: Library name: Batch1_ImP1


title: Batch1_LPS1

description: Library name: Batch1_LPS1


title: Batch1_IAA3

description: Library name: Batch1_IAA3


title: Batch1_IAA2

description: Library name: Batch1_IAA2


title: Batch1_IAA1

description: Library name: Batch1_IAA1


title: Batch1_HA3

description: Library name: Batch1_HA3


title: Batch1_HA2

description: Library name: Batch1_HA2


title: Batch1_HA1

description: Library name: Batch1_HA1


title: Batch1_H2O5

description: Library name: Batch1_H2O5


title: Batch1_H2O3

description: Library name: Batch1_H2O3


title: Batch1_H2O4

description: Library name: Batch1_H2O4


title: Batch1_H2O1

description: Library name: Batch1_H2O1


title: Batch1_H2O6

description: Library name: Batch1_H2O6


title: Batch1_Cholate3

description: Library name: Batch1_Cholate3


title: Batch1_DMSO2

description: Library name: Batch1_DMSO2


title: Batch1_DMSO1

description: Library name: Batch1_DMSO1


title: Batch1_H2O2

description: Library name: Batch1_H2O2


title: Batch1_Cholate2

description: Library name: Batch1_Cholate2


title: Batch1_Cholate1

description: Library name: Batch1_Cholate1


title: hiPSC-derived liver organoid 47 n2  fasted-refeed

city: Nantes

first: Antoine

last: Rimbert

address: 8 quai moncousu

country: France

institute: institut du thorax

description: Library name: O47_R2_S36

data_processing:
Read mapping was performed using Bowtie2 with the paired-end settings and the “-X 2000” parameter on the GRCh38 reference genome. Only the properly mapped reads were kept and duplicates were filtered using Samblaster.
The BAM files were then converted to BEDPE format and coordinate-shifted using DeepTools50 (--ATACshift option).
Broad peak calling was performed using MACS2 with the bedpe options and the default p-value and q-value for the broad cutoff.
Quality control was performed by calculating the fraction of reads in peaks (FrIP) using the subread feature counts, with the peaks having been called using MACS2 narrowPeak. The complexity of the library was evaluated according to the standards defined by the ENCODE consortium, with the NRF (non-redundant fraction), PCB1 and PCB2 (PCR bottleneck 1 and 2) being computed for all samples.
ATAC-seq signal alignment files (BAM and corresponding BAI) from human liver, hiPSCs, and liver organoids were converted into genome coverage tracks. The sequencing depth was normalized using deepTools (bamCoverage, bin size 10 bp, normalization by BPM) with the GRCh38 effective genome size.
The resulting BigWig files were used to calculate the average read depth across the samples, which were then visualized using a UCSC Genome Browser track hub.
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: cell with deprivated medium follow by  1 hour basal medium

growth_protocol: (1) Human induced pluripotent stemcells (hiPSCs) were cultured under hypoxia (4% O2, 5% CO2) on plates coated with 0.05 mg/mL Matrigel® (Corning) in StemMACSTM iPS-Brew medium XF (Miltenyi) and passaged using the Gentle Dissociation reagent (STEMCELLTM Technologies). Control hiPSCs (ITXi001-A) were generated and characterized as previously described.                                                                                (2) In-suspension liver organoids were generated from hiPSCs using a dedicated protocol (Harrison et al., 2020).  We adapted this protocol slightly, by adding the following steps: hiPSCs were dissociated and seeded at a density of 1000 cells/microwell in 24-well AggreWell™ 400 plates (STEMCELLTM Technologies), as recommended by the manufacturer. The cells were cultured in StemMACS™ iPS-Brew XF medium supplemented with 10 µM Y27632 (Cell Guidance Systems) to form aggregates (day -2). The next day, the medium was carefully replaced with StemMACS iPS-Brew XF medium without disturbing the aggregates. On day 0, the aggregates were collected using a 37 µm reversible strainer (STEMCELLTM Technologies) and washed with complete RPMI 1640 medium supplemented with 1X insulin, B27, NEAA and GlutaMAX™-I (all from Life Technologies). The aggregates were resuspended in a vented Erlenmeyer flask containing complete RPMI medium supplemented with 4 µM 99021 (BOC Sciences) to induce mesendoderm formation, before being incubated at 37 °C with agitation. All subsequent steps were performed under orbital shaking at 70 rpm. On day 1 after the differentiation process was initiated, the medium was changed to complete RPMI medium without any additional molecules to direct the aggregates towards definitive endoderm. From days 2 to 6, the aggregates were directed towards hepatic endoderm, with the medium being changed every two days. The medium used was knockout DMEM, supplemented with 20% knockout serum replacement (KSR), 1x NEAA, 1x GlutaMAX™-I (Life Technologies), 1% DMSO, and 100 µM 2-mercaptoethanol (Sigma). From days 7 to 19, the liver organoids were cultured in a maturation medium for liver tissue, with the medium being changed every two to three days. This medium was a hepatocyte culture medium (HCM) from Lonza, supplemented with 100nM dexamethasone (from Sigma) and 100nM N-hexanoic-Tyr-Ile-(6)-aminohexanoic amide (from Active Peptide). The organoids were harvested on day 20 for further analysis.

extract_protocol:
(1) hiPSCs were dissociated using an accutase solution (Sigma, #A6964) for 5 min at 37 °C, followed by the addition of 10 mg/mL collagenase IV (Sigma) in TrypLE dissociation reagent (Thermo Fisher) for a further 20 min. A total of 50,000 live cells were collected.                                                  (2) Liver organoids at day 20 were manually picked using a microscope (Vision Engineering) and transferred into an ultra-low-binding 6-well plate (BD Falcon) at a density of 200 organoids/well for 1 day before ATAC experiment. The day after, the cell supernatant was removed and kept for further analysis, and organoids were processed for single-cell dissociation. Liver organoids  were dissociated using enzymatic digestion with Ca2+Mg2+-free phosphate buffer and dissociated for 5 min at 37 °C using first 2 mL TrypLE dissociation reagent animal-free (Thermo Fisher) followed by the addition of 10 mg/mL collagenase IV (Sigma) solution for 20 min. When complete, the dissociation was blocked using Ca2+Mg2+-containing HBSS buffer supplemented with 1% BSA (Thermo Fisher) and the cell suspension was passed through a 37 µm strainer to remove possible cell aggregates. 50 000 single living cells were collected and centrifuged for 10 min at 500 G at 4 °C. The pelleted cells were resuspended in a transposase reaction mix containing digitonin (25 µL of 2x TD buffer, 5 µL of TDE1 (Illumina), 1 µL of 0.5% digitonin (Promega) and 19 µL of nuclease-free water). The transposition reaction was then carried out for 30 min at 37 °C. The samples were then purified immediately using a DNA Clean and Concentrator-5 kit (Zymo Research).
Following purification, each sample was dual indexed using i7 and i5 primers from the Nextera Index Kit (Illumina), then amplified using the Nextera DNA Library Prep Kit (Illumina) under the following PCR conditions: 72 °C for 3 min, 98 °C for 30 sec, followed by 11 cycles of 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 3 min. Libraries were double size-selected using Beckman Coulter™ Agencourt AMPure XP beads at 0.5x and 1.3x ratios. The quality of the libraries was assessed using a TapeStation, and the libraries were quantified using a NEBNext® Library Quant Kit for Illumina® (New England Biolabs). Sequencing was performed on an Illumina NovaSeq 6000 platform in 2 × 51 paired-end mode. Trimming and demultiplexing were performed using Illumina bcl2fastq2.

treatment_protocol: Liver organoids received 3 different mediums on the 21st day: (A) Basal: hepatocyte culture medium (HCM) from Lonza, supplemented with 100nM dexamethasone (from Sigma) and 100nM N-hexanoic-Tyr-Ile-(6)-aminohexanoic amide (from Active Peptide). (B) Starved:  hepatocyte culture medium (HCM) from Lonza only. (C) Sarved-Refeed: hepatocyte culture medium (HCM) from Lonza only during the 24h then Basal mdium (hepatocyte culture medium (HCM) from Lonza, supplemented with 100nM dexamethasone (from Sigma) and 100nM N-hexanoic-Tyr-Ile-(6)-aminohexanoic amide (from Active Peptide)) 1 hour before dissociation.

value: hiPSC-derived liver organoid

value: liver cell lines

tag: genotype

value: WT

value: fasted-refeed


title: hiPSC-derived liver organoid 47 n1  fasted

description: Library name: O47_S1_S33

source_name: cell with deprivated medium

value: fasted

tag: batch


title: hiPSC-derived liver organoid 47 n2  fasted

description: Library name: O47_S2_S34


title: hiPSC-derived liver organoid 47 n1  fasted-refeed

description: Library name: O47_R1_S35


title: hiPSC-derived liver organoid 47 n2  feed

description: Library name: O47_B2_S32

source_name: cell with basal medium

value: feed


title: hiPSC-derived liver organoid 47 n1  feed

description: Library name: O47_B1_S31


title: hiPSC-derived liver organoid 46 n2  fasted-refeed

description: Library name: O46_R2_S30


title: hiPSC-derived liver organoid 46 n1  fasted-refeed

description: Library name: O46_R1_S29


title: hiPSC-derived liver organoid 46 n2  fasted

description: Library name: O46_S2_S28


title: hiPSC-derived liver organoid 46 n1  fasted

description: Library name: O46_S1_S27


title: hiPSC-derived liver organoid 46 n2 feed

description: Library name: O46_B2_S26


title: hiPSC 2 feed

description: Library name: i_MSB01_C39

value: hiPSC


title: hiPSC-derived liver organoid 46 n1 feed

description: Library name: O46_B1_S25


title: hiPSC 1 feed

description: Library name: i_MSB01_C38


title: A549 cells with SLC7A5 knocked down by specific siRNA rep5

city: Nanchang

first: Penghui

state: Jiangxi

address: No. 17 Yongwaizheng Street

institute: First Affiliated Hospital of Nanchang University

description: Library name: SLC7A5_KD_5

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include genecount values for each Sample

source_name: A549 cells

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: A549 cells


title: A549 cells with SLC7A5 knocked down by specific siRNA rep2

description: Library name: SLC7A5_KD_2


title: A549 cells with SLC7A5 knocked down by specific siRNA rep1

description: Library name: SLC7A5_KD_1


title: A549 cells with SLC7A5 knocked down by specific siRNA rep4

description: Library name: SLC7A5_KD_4


title: A549 cells with SLC7A5 knocked down by specific siRNA rep3

description: Library name: SLC7A5_KD_3


title: A549 cells with SLC7A5 knocked down by specific siRNA rep6

description: Library name: SLC7A5_KD_6


title: A549 cells transfected with non-target scrambled siRNA rep6

description: Library name: Control_6


title: A549 cells transfected with non-target scrambled siRNA rep4

description: Library name: Control_4


title: A549 cells transfected with non-target scrambled siRNA rep3

description: Library name: Control_3


title: A549 cells transfected with non-target scrambled siRNA rep5

description: Library name: Control_5


title: A549 cells transfected with non-target scrambled siRNA rep2

description: Library name: Control_2


title: A549 cells transfected with non-target scrambled siRNA rep1

description: Library name: Control_1