title: BSSR0779

description: Library name: BSSR0779_RNAseq

value: ER-positive

tag: gender

tag: clinical stage

value: IA

tag: nseas aesthetic_quality_score


title: HZ62_1h_RNA_rep3

status: Public on Aug 15 2025

type: SRA

city: Wuhan

first: Junlin

last: Chen

address: No.1, Shizishan Street

country: China

institute: Huazhong Agricultural University

description: Library name: Sample90

library_source: transcriptomic

data_processing:
RNA-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using hisat2.
ATAC-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bowtie2.
Bisulfite sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using BatMeth2.
Whole-Genome sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bwa.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: bw files for each Sample

molecule: polyA RNA

organism: Brassica napus

growth_protocol: growth in Hoagland nutrient solution

extract_protocol:
Toal RNA was extracted by using Eastep® Super Total RNA Extraction Kit (Promega) from cotyledon with three replications. For ATAC-seq, the extracted nuclei were incubated with Tn5 transposase and tagmentation buffer following the manufacturer’s instructions (Vazyme, TD501-01).
mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads, and mRNAs were obtained by removing ribosomal RNAs from the total RNAs. For ATAC-seq, DNA was purified using the MinElute PCR Purification Kit (QIAGEN, 28004). Genomic DNA for was extracted using the DNeasy Plant Mini Kit (QIAGEN, 69104). Bisulfite-treated DNA libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) following the manufacturer’s instructions.

treatment_protocol: under 0 mM/L NaCl or 220 mM/L NaCl condition.

tag: tissue

tag: genotype

tag: treatment

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: HZ62_1h_RNA_rep2

description: Library name: Sample89


title: BiRi2D1_FB, CITE-seq

city: Birmingham

first: Kyle

middle: Hartley

last: Moore

state: Alabama

department: Division of Nephrology

country: USA

institute: University of Alabama at Birmingham

description:
Library name: BiRi2D1_FB
CITE-seq_CD45+ cells
BiRi2D1_filtered_feature_bc_matrix.h5

data_processing:
10x Genomics Cell Ranger version 6.0
10x Genomics Space Ranger version 1.2.2
Assembly: mm10
Supplementary files format and content: .h5
Library strategy: CITE-seq

organism: Mus musculus

source_name: kidney

extract_protocol:
RNA was isolated according to manufacturer's instructions for 3' Chromium gene expression
RNA-seq, CITE-seq

value: kidney

tag: time--added

value: Day1 post-BIRI

tag: library type

value: feature barcode

value: BIRI

tag: batch


title: BSSR0738

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

description: Library name: BSSR0738_RNAseq

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m10
Reads were mapped on the GRCh37 human genome with STAR (v. 2.7.1a)
Gene expression profiles were extracted with RSEM (v. 1.2.28) using Ensembl v75 for gene annotations
Assembly: GRCh37
Supplementary files format and content: Table with counts and FPKM values per gene

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor

extract_protocol:
RNA was extracted with Thermo MagMAX mirVana Total RNA Isolation kit (A27828) on a Thermo Kingfisher Apex
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold (RS-122-2303)

value: Breast tumor

tag: age

tag: race

value: White

tag: ethnicity

value: Hispanic or Latino

tag: er

value: Female

value: No

value: IIB

tag: adi (state_decile)

tag: nseas composite_score

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: eeds discrimination_score


title: HZ62_1h_RNA_rep1

description: Library name: Sample88


title: BiRi2D1_GEX, CITE-seq

description:
Library name: BiRi2D1_GEX
CITE-seq_CD45+ cells
BiRi2D1_filtered_feature_bc_matrix.h5

value: mRNA


title: HZ62_0h_RNA_rep3

description: Library name: Sample87

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: BSSR0680

description: Library name: BSSR0680_RNAseq

tag: gender

tag: clinical stage

value: IIA


title: HZ62_0h_RNA_rep1

description: Library name: Sample85

tag: tissue


title: BiRi1D1_FB, CITE-seq

description:
Library name: BiRi1D1_FB
CITE-seq_CD45+ cells
BiRi1D1_filtered_feature_bc_matrix.h5


title: HZ62_0h_RNA_rep2

description: Library name: Sample86

tag: genotype


title: BiRi1D1_GEX, CITE-seq

description:
Library name: BiRi1D1_GEX
CITE-seq_CD45+ cells
BiRi1D1_filtered_feature_bc_matrix.h5

tag: treatment


title: B409_48h_RNA_rep3

description: Library name: Sample84

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: BSSR0558

description: Library name: BSSR0558_RNAseq

value: ER-positive

tag: nseas aesthetic_quality_score


title: BSSR0567

description: Library name: BSSR0567_RNAseq


title: BSSR0551

description: Library name: BSSR0551_RNAseq


title: HZ62_3h_RNA_rep1

description: Library name: Sample91

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: B409_24h_RNA_rep1

description: Library name: Sample79

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 24 h.


title: B409_24h_RNA_rep2

description: Library name: Sample80


title: BSSR0634

description: Library name: BSSR0634_RNAseq


title: day6mouse3_GEX, scRNA-seq

description:
Library name: day6mouse3_GEX
3' gene expression of CD11b+ cells

library_source: transcriptomic single cell

data_processing:
10x Genomics Cell Ranger version 6.0
10x Genomics Space Ranger version 1.2.2
Assembly: mm10
Supplementary files format and content: .h5

value: kidney

tag: time--added

value: Day6 post-BIRI

tag: library type


title: B409_24h_RNA_rep3

description: Library name: Sample81


title: B409_12h_RNA_rep2

description: Library name: Sample77

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 12 h.


title: quiescentmouse3_GEX, scRNA-seq

description:
Library name: quiescentmouse3_R1_GEX
3' gene expression of CD11b+ cells

value: Uninjured

value: quiescent/uninjured

tag: batch


title: B409_12h_RNA_rep3

description: Library name: Sample78


title: B409_48h_RNA_rep1

description: Library name: Sample82


title: B409_12h_RNA_rep1

description: Library name: Sample76


title: BSSR0743

description: Library name: BSSR0743_RNAseq

value: Breast tumor

tag: age

tag: race

value: White


title: BSSR0754

description: Library name: BSSR0754_RNAseq

tag: ethnicity

value: Hispanic or Latino

tag: er

value: Female

value: IIIB


title: B409_6h_RNA_rep2

description: Library name: Sample74

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 6 h.


title: quiescentmouse2_GEX, scRNA-seq

description:
Library name: quiescentmouse2_R1_GEX
3' gene expression of CD11b+ cells

value: mRNA


title: day6mouse2_GEX, scRNA-seq

description:
Library name: day6mouse1_GEX
3' gene expression of CD11b+ cells

value: Day 6 post-BIRI

value: BIRI


title: BSSR0727

description: Library name: BSSR0727_RNAseq

value: ER-positive

value: No

value: IA

tag: adi (state_decile)

tag: nseas composite_score


title: quiescentmouse1_GEX, scRNA-seq

description:
Library name: quiescentmouse1_R1_GEX
3' gene expression of CD11b+ cells

value: kidney


title: B409_6h_RNA_rep3

description: Library name: Sample75


title: B409_6h_RNA_rep1

description: Library name: Sample73


title: G4_blood neutrophils_with MSC treatment_S24

city: Bucharest

first: Laudy

last: Cherry

state: Sector 5

address: Strada B.P.Hasdeu nr.8, sector 5, Bucuresti

department: Biology

country: Romania

institute: Institute of cellular biology and pathology

description: Library name: G4_Blood_MSC_S24

data_processing:
Data processing was performed in-house; adaptor trimming and PCR duplicate removal were done with Trimmomatic and Picard, respectively.
Trimmed reads were mapped to mouse genome GRCm39 P110 using STAR
Stranded quantification was performed with featureCounts.
To address the high percentage of mitochondrial RNA in the dataset and reduce the risk of bias in downstream analysis, reads mapping to mitochondrial regions were excluded. Differential expression analysis was then performed using DESeq2.
Details are provided in the materials and methods section
Assembly: Mouse genome GRCm39 P110
Supplementary files format and content: tab-delimited text file includes Normalized counts from obtained from DEseq2
Supplementary files format and content: csv text file includes raw counts after depleting Mitochondrial RNA

source_name: Blood

extract_protocol:
Cardiac tissues  were processed using the gentleMAC Octo Dissociator protocol, involving tissue dissociation, enzyme digestion, and centrifugation performed in single sessions under standardized conditions.
Neutrophils were isolated  using anti-Ly6G microbeads and MACS column separation. Ly6G-positive cells were collected, centrifuged, resuspended in Trizol, and stored at -80°C.
Total RNA was purified from samples using the PureLink RNA Mini Kit
Details are provided in the materials and methods section

value: Blood

tag: cell line

value: Neutrophils

tag: cell type

value: Hematopoietic

tag: strain

value: With MSC treatment


title: B409_3h_RNA_rep2

description: Library name: Sample71

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: BSSR0740

description: Library name: BSSR0740_RNAseq

value: Breast tumor

value: White

tag: gender

tag: clinical stage

value: IIA

tag: nseas safety_score

tag: nseas social_cohesion_score

tag: eeds discrimination_score


title: B409_48h_RNA_rep2

description: Library name: Sample83

tag: tissue

tag: genotype

tag: treatment

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: B409_3h_RNA_rep3

description: Library name: Sample72


title: B409_3h_RNA_rep1

description: Library name: Sample70


title: G4_blood neutrophils_with MSC treatment_S23

description: Library name: G4_Blood_MSC_S23

growth_protocol: Details are provided in the materials and methods section

tag: batch


title: B409_1h_RNA_rep3

description: Library name: Sample69

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: BSSR0624

description: Library name: BSSR0624_RNAseq

tag: age

tag: race

value: Hispanic or Latino

value: Female

tag: nseas aesthetic_quality_score


title: G3_blood neutrophils_without MSC treatment_S22

description: Library name: G3_Blood_S22

treatment_protocol: Details are provided in the materials and methods section

value: Without MSC treatment


title: BSSR0542

description: Library name: BSSR0542_RNAseq

tag: ethnicity

tag: er

value: ER-positive

tag: adi (state_decile)


title: B409_0h_RNA_rep2

description: Library name: Sample65

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: BSSR0553

description: Library name: BSSR0553_RNAseq

value: No

value: IIB

tag: nseas composite_score


title: B409_0h_RNA_rep1

description: Library name: Sample64


title: 2063A_48h_RNA_rep3

description: Library name: Sample63


title: id49

city: Los Angeles

first: Hiroshi

last: Kumagai

state: CA

address: 3715 McClintock Ave

institute: University of Southern California

data_processing:
The qualities of  the fastq files were checked and trimmed using FastQC and fastp.
Sequencef reads were mapped to the Human reference genome (GRCh38) using STAR.
Count matrices were generated using the summarizeOverlaps function of the GenomicAlignemnts.
Comparison of the gene expression levels between groups were performed using the DESeq2.
Assembly: Human reference genome (GRCh38)
Supplementary files format and content: The tab-delimited text file includes nomalized read counts of all samples

source_name: Vastus lateralis muscle

extract_protocol:
RNA was extracted from skeletal muscle by using TRIzol (Thermo Scientific).
High quality RNA was used for library preparation (NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina).

value: Vastus lateralis muscle

tag: Sex

value: female


title: G2_cardiac neutrophils_with MSC treatment_S17

description: Library name: G2_MI_MSC_S17

source_name: Cardiac tissue

value: Cardiac tissue

tag: cell line

value: Neutrophils

tag: cell type

value: Hematopoietic

tag: strain


title: 2063A_24h_RNA_rep3

description: Library name: Sample60

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 24 h.


title: G2_cardiac neutrophils_with MSC treatment_S15

description: Library name: G2_MI_MSC_S15

value: With MSC treatment


title: 2063A_24h_RNA_rep2

description: Library name: Sample59


title: id47


title: 2063A_12h_RNA_rep3

description: Library name: Sample57

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 12 h.


title: 2063A_24h_RNA_rep1

description: Library name: Sample58


title: GI_cardiac neutrophils_without MSC treatment_S20

description: Library name: G1_MI_S20


title: id46


title: id48

value: male


title: B409_1h_RNA_rep2

description: Library name: Sample68

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: GI_cardiac neutrophils_without MSC treatment_S19

description: Library name: G1_MI_S19


title: 2063A_12h_RNA_rep2

description: Library name: Sample56


title: 2063A_6h_RNA_rep3

description: Library name: Sample54

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 6 h.


title: B409_1h_RNA_rep1

description: Library name: Sample67


title: B409_0h_RNA_rep3

description: Library name: Sample66


title: 2063A_6h_RNA_rep2

description: Library name: Sample53


title: G3_blood neutrophils_without MSC treatment_S21

description: Library name: G3_Blood_S21

value: Blood


title: id44


title: 2063A_12h_RNA_rep1

description: Library name: Sample55


title: G2_cardiac neutrophils_with MSC treatment_S18

description: Library name: G2_MI_MSC_S18


title: Immobilization K14Q MOTS-c, rep8

data_processing:
The qualities of  the fastq files were checked and trimmed using FastQC and fastp.
Sequencef reads were mapped to mouse reference genome (GRCm38.p6) using STAR.
Count matrices were generated using the summarizeOverlaps function of the GenomicAlignemnts.
Assembly: Mouse genome (GRCm38.p6)
Supplementary files format and content: The tab-delimited text file includes nomalized read counts of all samples

extract_protocol:
RNA was extracted from frozen skeletal muscle by using TRIzol (Thermo Scientific), followed by the Quick-RNA Miniprep Kit (Zymo Research).
High quality RNA was used for library preparation (mRNA-Seq Nu Quant), which captured poly-adenylated RNA.

value: Male

value: 10 weeks old

value: K14Q MOTS-c

tag: disease state

value: Immobilization


title: 2063A_6h_RNA_rep1

description: Library name: Sample52


title: 2063A_48h_RNA_rep2

description: Library name: Sample62

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: ko_day15

city: Hannover

first: Dirk

last: Schlüter

address: Carl-Neuberg-Str. 1

department: Institute for Medical Microbiology and Hospital Hygiene

country: Germany

institute: Medizinische Hochschule Hannover

description: Library name: Sample 4

data_processing:
Sequence reads were trimmed for adaptor sequence/ low-quality sequence
Trimmed sequence reads were mapped to GrCM38/mm10
Read count extraction and normalization were performed
Assembly: mm10
Supplementary files format and content: csv file include raw counts for each sample

source_name: Spinal cord

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen)
RNA Library was created using a NEBNext® UltraTM II Directional RNA Library Prep Kit following manufacturer's protocol.

value: Spinal cord

value: Astrocyte

value: GFAP-Cre Otud7bfl/fl

value: MOG peptide+ complete freund's adjuvant+800ug of killed Mycobacterium tuberclosis

tag: time

value: day 15


title: 2063A_48h_RNA_rep1

description: Library name: Sample61

tag: tissue


title: Immobilization K14Q MOTS-c, rep7

value: Vastus lateralis muscle


title: ko_day0

description: Library name: Sample 3

tag: genotype

value: Näive

value: day 0


title: 2063A_3h_RNA_rep3

description: Library name: Sample51

tag: treatment

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: Immobilization K14Q MOTS-c, rep6


title: id41

value: male


title: id42


title: wt_day15

description: Library name: Sample 2


title: 2063A_3h_RNA_rep1

description: Library name: Sample49


title: 2063A_3h_RNA_rep2

description: Library name: Sample50


title: YAMCcells_Control _3

city: Nashville

first: Fang

last: Yan

state: TN

address: 2215 Garland Ave., Light hall, Lab No.  1035

institute: Vanderbilt University Medical Center

data_processing:
Guppy, Illumina's bcl2fastq version, 5.0.11
FastQC version 0.11.9
Bowtie2 version 2.7.3a
Assembly: GRCh38
Supplementary files format and content: TXT

source_name: colon

growth_protocol: A young adult mouse colonic epithelium (YAMC) cell line was generated using a mouse harboring thermolabile mutation (tsA58) under the control of an interferon (IFN)-Y-inducible H-2Kb promoter and a temperature-sensitive simian virus 40 large T antigen. YAMC cells was grown at 33°C in the presence of IFN-Y

extract_protocol:
Total RNA was extracted from YAMC cells by using the Qiagen RNeasy mini kit (Cat#74104; Qiagen).
Illumina sequencing libraries were made using the NEBNext Ultra II RNA Library Prep Kit (NEB #E7775)

treatment_protocol: 2FL-treatment for 6hours on YAMC cells

value: colon

value: YAMC

value: Young adult mouse colonic epithelium

value: WT

value: No treatment control


title: GI_cardiac neutrophils_without MSC treatment_S13

description: Library name: G1_MI_S13

value: Cardiac tissue

value: Neutrophils

value: Hematopoietic

value: Without MSC treatment

tag: batch


title: 2063A_1h_RNA_rep2

description: Library name: Sample47

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: YAMCcells_Control _2


title: Immobilization K14Q MOTS-c, rep3

value: Male

tag: age

value: 10 weeks old

value: K14Q MOTS-c

value: Immobilization


title: id39

value: Vastus lateralis muscle


title: wt_day0

description: Library name: Sample 1

value: Spinal cord

value: Astrocyte

value: Näive

value: day 0


title: id45

value: male


title: id40

value: female


title: YAMCcells_Control_1

value: colon

value: YAMC

value: Young adult mouse colonic epithelium

value: WT

value: No treatment control


title: id43


title: id38


title: id37


title: Immobilization K14Q MOTS-c, rep1


title: Immobilization K14Q MOTS-c, rep5


title: YAMCcells_2FLtreatment_6h _3

value: 2FLtreatment for 6h on YAMC cells


title: 2063A_0h_RNA_rep3

description: Library name: Sample45

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: id36


title: YAMCcells_2FLtreatment_6h _2


title: 2063A_0h_RNA_rep2

description: Library name: Sample44


title: id35


title: Immobilization K14Q MOTS-c, rep4

value: Male

value: 10 weeks old


title: YAMCcells_2FLtreatment_6h_1


title: 2063A_1h_RNA_rep3

description: Library name: Sample48

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: id34

value: Vastus lateralis muscle


title: mRNA3-4

city: Shinagawa-ku

first: Kunio

last: Kawanishi

state: Tokyo

address: 1-5-8 Hatanodai

country: Japan

institute: Showa Medical University

data_processing:
SevenBridges using the BD Rhapsody Targeted Analysis Pipeline
the Seurat v3.2.0 package
Mouse Molecular Signatures Database (MSigDB)
Immunological Genome Project (ImmGen)
Enrichr-KG
Assembly: MetaCore software
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast primary tumor

growth_protocol: Female BALB/c mice (8 weeks of age) were injected with 5 × 1044T1 cells

extract_protocol:
the suspension cells isolated from primary tumor were loaded into the BD Rhapsody TM Cartridge along with the enhanced cell capture beads. After cell lysis, the beads were retrieved with single-cell mRNA products
following the Rhapsody™ System mRNA Targeted and Sample Tag Library Preparation Protocol
Center for Medical Genomics for sequencing using an Illumina NovaSeq 6000 SP with a 200-cycle kit using BD Rhapsody Mouse Immune Response Targeted Panel gene list

treatment_protocol: Isotype control antibody (Rat IgG2a Isotype Control – Purified in vivo GOLD™ Functional Grade, I-1177, Leinco Technologies), anti Siglec-E antibody (Ultra-LEAF™ Purified anti-mouse Siglec-E Antibody, 934404, BioLegend), anti PD-1 antibody (Anti-Mouse CD279 (PD-1) (Clone RMP1-14) – Purified in vivo GOLD™ Functional Grade, P362, Leinco Technologies) and combination treatment of anti Siglec-E antibody and anti PD-1 antibody, were injectied to the mice.

value: Breast primary tumor

value: 4T1 cells and cells from Balb/c

value: 1 EPCAM-positive (epithelial) :4 EPCAM-negative (immune)

value: Anti-PD1 antibody and Combination Anti-Siglec E + anti-PD1


title: mRNA1-2

value: Isotype antibody and Anti-Siglec E antibody


title: K562 cells, N+11 CTCF-dCas9-EGFP, Input

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

description: Library name: N+11_input

library_source: genomic

data_processing:
[ChIP-seq] ChIP-seq raw reads were mapped (hg38 human genome assembly) using bwa (version 0.7.18-r1243-dirty), sorted and deduplicated using samtools (version 1.21). Deduplicated files were transformed to BigWig format using deepTools (version 3.5.5).
Assembly: hg38
Supplementary files format and content: ChIP-seq profiles in BigWig format

molecule: genomic DNA

growth_protocol: The K562 cell line was maintained in high-glucose DMEM medium with 10% fetal bovine serum (FBS), 1000 units/ml penicillin and 1000 units/ml streptomycin.

extract_protocol:
DNA for ChIP-seq/C-TALE and RNA for RNA-seq was extracted as discrabed in MATERIALS AND METHODS section in original manuscript and availible upon request.
All libraries were prepared as discrabed in MATERIALS AND METHODS section in original manuscript and availible upon request.

treatment_protocol: K562 cell line with deletion of CTCF binding site in HOXD locus was obtained by electroporation of plasmids encoding the Cas9 protein and two gRNAs (see original manuscript).

value: lymphoblast cells

value: Electroparion with N+11 CTCF-dCas9-EGFP plasmid


title: HZ62_48h_ATAC_rep2

description: Library name: Sample42

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: 2063A_1h_RNA_rep1

description: Library name: Sample46


title: HZ62_48h_ATAC_rep1

description: Library name: Sample41


title: K562 cells, N+2 CTCF-dCas9-EGFP, Input

description: Library name: N+2_input

value: Electroparion with N+2 CTCF-dCas9-EGFP plasmid


title: id33

value: female


title: K562 cells, N+7 CTCF-dCas9-EGFP, Input

description: Library name: N+7_input

value: Electroparion with N+7 CTCF-dCas9-EGFP plasmid


title: id31

value: male


title: HZ62_24h_ATAC_rep2

description: Library name: Sample40

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 24 h.


title: K562 cells, CTCF-dCas9-EGFP, Input

description: Library name: Full_H3K27me3_input

value: Electroparion with full CTCF-dCas9-EGFP plasmid


title: crizotinib, replicate 1

city: Hachioji

first: Hiroki

last: Kobayashi

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
FASTQ files were processed in AltAnalyze version 2.1.0.
Transcript per million (TPM) estimates were calculated via a built-in call to Kallisto for read pseudoalignment and transcript quantification.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include TPM values for each sample

source_name: bone marrow

extract_protocol:
Total RNA was isolated  using the Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs).

value: bone marrow

value: hematopoietic stem and progenitor cells

value: crizotinib


title: id32

value: Vastus lateralis muscle


title: K562 cells, dCas9-EGFP, Input

description: Library name: dCas9_input

value: Electroparion with dCas9-EGFP plasmid


title: HZ62_24h_ATAC_rep1

description: Library name: Sample39


title: K562 cells, N CTCF-dCas9-EGFP,Input

description: Library name: N_input

value: Electroparion with N CTCF-dCas9-EGFP plasmid


title: K562 cells, WT, Input

description: Library name: K562_input

value: No treatment


title: crizotinib, replicate 2


title: id30


title: DMSO, replicate 2

value: DMSO


title: HZ62_12h_ATAC_rep2

description: Library name: Sample38

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 12 h.


title: K562 cells, restored CBS + N+2 CTCF-dCas9-EGFP, Input

description: Library name: DEL-N+2_input

value: lymphoblast cells

value: K562 cell line with CBS deletion with electroporated N+2 CTCF-dCas9-EGFP plasmid


title: DMSO, replicate 1


title: id28


title: HZ62_12h_ATAC_rep1

description: Library name: Sample37


title: Immobilization K14Q MOTS-c, rep2

value: Male

value: 10 weeks old

value: K14Q MOTS-c

value: Immobilization


title: P2rx4KO Fib + Mac 2

city: San Francisco

first: Javier

last: Gomez Ortega

address: 513 Parnassus Ave.

institute: UCSF

data_processing:
The demultiplexed FASTQ files were aligned to mouse genome (mm10) using PIPseeker 1.0.0 (Fluent Biosciences) indicating that the samples were obtained with a v4 chemistry kit. After sequence alignment, we observed around 50% of input cells being called when PIPseeker sensitivity level was set to 3, which was near the inflection point of the barcode rank plot.
Assembly: mm10

source_name: Lung

extract_protocol:
For lung injury, mice anesthetized with isoflurane were instilled with bleomycin (Fresenius, 3U/Kg) by oropharyngeal aspiration, and lungs were isolated after 7 days after injury. After mincing with scissors, the tissue was resuspended in RPMI with 0.2% Collagenase (10103586001, Roche), 2000 U/ml DNase I (4716728001, Roche) and 0.1 mg/ml Dispase II (4942078001, Sigma). The suspension was incubated for 1 hour at 37oC and passed through a 70 mm filter (130-110-916, MACS SmartStrainers) to obtain single cells. The cells were washed twice with 1X PBS pH 7.4 (10010023, Gibco). For macrophage isolation, a total of 107 cells were resuspended in 80ml PBS buffer supplemented with 0.5% BSA (0332, VWR Life Science) and 2mM EDTA (E57040, Research Products International). 20ml CD11b microbeads were used per 107 cells.  Macrophages were obtained by positive selection by binding to CD11b microbeads and passing through MACS columns (130-049-601, Miltenyi Biotech). Isolated CD11b+ macrophages were cultured in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, and 20 ng/ml M-CSF (315-02, Peprotech) for 2 days. Primary mouse lung fibroblasts were freshly isolated after magnetic bead-based negative selection of epithelial cells (118204, Biotin anti-mouse CD326 Epcam, Clone: G8.8, BioLegend), endothelial cells (102404, Biotin anti-mouse CD31, clone: 390), immune cells (103104, Biotin anti-mouse CD45, clone: 30-F11, BioLegend), pericytes and smooth muscle cells (134716, Biotin anti-mouse CD146, clone: ME-9F1, BioLegend), and red blood cells (116204, Biotin anti-mouse Ter119, clone: TER-119, BioLegend) with biotinylated antibodies and Dynabeads (MyOne Streptavidin T1, 65601, Thermo Fisher Scientific) as previously described1. Fibroblasts were cultured for 5 days prior to trypsinization and addition to macrophages for coculture at a 1:1 ratio in DMEM complete media for 5 further days.
PIPseq T2 3ʹ Single Cell RNA Kit (v4.0 – cultured cells) was used for pre-templated instant partitioning (PIP) to capture single-cell mRNA transcripts with PIP beads according to manufacturer’s protocol (Fluent Biosciences). In the case of cocultures, 7 days after bleomycin lung injury, mice were sacrificed and lungs were harvested followed by cell isolation as above. After 5 days of coculture, single cell suspension of cells was obtained by trypsinization followed by washing in 1X PBS. Cells were washed in ice-cold PIPseq Cell Suspension Buffer. Cells were counted and stained with Trypan blue to confirm >90% viability. Cell concentration was adjusted to around 1,000 cells/mL with Cell Suspension Buffer. Five mL of ice-cold cell suspension from each co-culture group were loaded (around 5,000 cells) into individual PIPseq tubes. PIP beads and cells were vortexed droplet encapsulation. Emulsified lysis reagents were mixed and incubated with PIP droplets to lyse cells and release mRNA at 37° C. PIP droplets were cooled down to 4C for mRNA annealing to the PIP beads. After emulsion breakage and bead washing, the captured transcripts on PIP beads were converted into cDNAs with reverse transcription and template-switching reagents. The beads were washed again and then mixed with whole transcriptome amplification (WTA) reagents, which amplified the library from cDNAs on the PIP beads. The WTA library was purified with Solid Phase Reversible Immobilization (SPRI) beads before library fragmentation, end-repair, and A-tailing reactions. The fragmented library was then ligated with indexing adapters. Finally, sequencing adapters and dual-indices were attached to the library through indexing PCR. The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform, with a target yield of 100 million reads per sample, or 20,000 reads per input cell.

value: Lung

value: Fibroblasts and Cd11b+ Macrophages

value: WT Macrophages and P2rx4KO fibroblasts

value: Bleomycin


title: K562 cells, CBS deletion, Input

description: Library name: DEL-K562_input

value: K562 cell line with CBS deletion


title: Fib + Mac 2

description: The sequencing libraries were submitted to Novogene for 150-bp pair-end sequencing on the NovaSeq PE150 platform

value: WT


title: id26

value: Vastus lateralis muscle

value: female


title: Fib alone 2

value: Fibroblasts


title: HZ62_6h_ATAC_rep1

description: Library name: Sample35

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 6 h.


title: HZ62_6h_ATAC_rep2

description: Library name: Sample36


title: HZ62_3h_ATAC_rep1

description: Library name: Sample33

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: id23


title: HZ62_1h_ATAC_rep2

description: Library name: Sample32

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: K562 cells, restored CBS + N+2 CTCF-dCas9-EGFP, ChIP, H3K27me3

description: Library name: DEL-N+2_H3K27me3_chip

value: lymphoblast cells

value: K562 cell line with CBS deletion with electroporated N+2 CTCF-dCas9-EGFP plasmid


title: K562 cells, restored CBS + dCas9-EGFP, ChIP, H3K27me3

description: Library name: DEL-dCas9_H3K27me3_chip

value: K562 cell line with CBS deletion with electroporated dCas9-EGFP plasmid


title: P2rx4KO Fib + Mac 1


title: Fib + Mac 1


title: K562 cells, Full CTCF-dCas9-EGFP, ChIP, EGFP

description: Library name: Full_EGFP_chip

value: Electroparion with full CTCF-dCas9-EGFP plasmid


title: id29

value: male


title: id27


title: HZ62_1h_ATAC_rep1

description: Library name: Sample31


title: id24


title: Fib alone 1

value: Lung


title: id25


title: K562 cells, restored CBS + dCas9-EGFP, Input

description: Library name: DEL-dCas9_input


title: K562 cells, Full CTCF-dCas9-EGFP, ChIP, H3K27me3

description: Library name: Full_H3K27me3_chip


title: id22


title: Skin, IR-9D-3

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

description:
IR9D3
fpkm.anno.txt

data_processing:
For the data analysis, firstly clean reads were aligned to mouse genome (version mm10) using HISAT2 (version 2.2.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

source_name: skin

extract_protocol:
Total RNA of skin tissue was extracted using TRIzol as described previously. Aliquots of mRNA in each group were extracted and purified by the NucleoSpin RNA Plus XS Kit (Macherey-Nagel).
Libraries were constructed using the Smart-Seq2 method as previously described and sequenced with 10G depth and paired-end reads on an Illumina NovaSeq 6000, performed by Annoroad Gene Technology.

value: skin

value: Ionizing radiation

value: 9 days


title: HZ62_0h_ATAC_rep2

description: Library name: Sample30

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: id21


title: K562 cells, N+11 CTCF-dCas9-EGFP, ChIP, H3K27me3

description: Library name: N+11_H3K27me3_chip

value: Electroparion with N+11 CTCF-dCas9-EGFP plasmid


title: Skin, IR-9D-2

description:
IR9D2
fpkm.anno.txt


title: HZ62_0h_ATAC_rep1

description: Library name: Sample29


title: Skin, IR-9D-1

description:
IR9D1
fpkm.anno.txt


title: K562 cells, CBS deletion, ChIP, H3K27me3

description: Library name: DEL-K562_H3K27me3_chip

value: K562 cell line with CBS deletion


title: id20

value: Vastus lateralis muscle


title: B409_48h_ATAC_rep2

description: Library name: Sample28

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: id19

value: female


title: K562 cells, N+7 CTCF-dCas9-EGFP, ChIP, H3K27me3

description: Library name: N+7_H3K27me3_chip

value: Electroparion with N+7 CTCF-dCas9-EGFP plasmid


title: Skin, IR-6D-3

description:
IR6D3
fpkm.anno.txt

value: 6 days


title: B409_48h_ATAC_rep1

description: Library name: Sample27


title: K562 cells, N+2 CTCF-dCas9-EGFP, ChIP,SMC3

description: Library name: N+2_SMC3_chip

value: lymphoblast cells

value: Electroparion with N+2 CTCF-dCas9-EGFP plasmid


title: Skin, IR-6D-1

description:
IR6D1
fpkm.anno.txt


title: K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, EGFP

description: Library name: N+2_EGFP_chip


title: HZ62_3h_ATAC_rep2

description: Library name: Sample34

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: B409_24h_ATAC_rep2

description: Library name: Sample26

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 24 h.


title: K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, H3K27me3, rep 2

description: Library name: N+2_H3K27me3_chip_replicate_2


title: id18


title: B409_24h_ATAC_rep1

description: Library name: Sample25


title: id16

value: male


title: id17


title: Skin, IR-3D-2

description:
IR3D2
fpkm.anno.txt

value: 3 days


title: B409_12h_ATAC_rep2

description: Library name: Sample24

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 12 h.


title: id15


title: K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, H3K27me3, rep 1

description: Library name: N+2_H3K27me3_chip_replicate_1


title: K562 cells, N CTCF-dCas9-EGFP, ChIP, H3K27me3

description: Library name: N_H3K27me3_chip

value: Electroparion with N CTCF-dCas9-EGFP plasmid


title: id14


title: Skin, IR-3D-1

description:
IR3D1
fpkm.anno.txt

value: skin

value: Ionizing radiation


title: B409_12h_ATAC_rep1

description: Library name: Sample23


title: 2063A_0h_RNA_rep1

description: Library name: Sample43

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: Skin, Control-9D-3

description:
C9D3
fpkm.anno.txt

value: Control

value: 9 days


title: Skin, Control-9D-2

description:
C9D2
fpkm.anno.txt


title: B409_6h_ATAC_rep2

description: Library name: Sample22

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 6 h.


title: id13

value: Vastus lateralis muscle


title: B409_6h_ATAC_rep1

description: Library name: Sample21


title: K562 cells, dCas9-EGFP, ChIP, H3K27me3

description: Library name: dCas9_H3K27me3_chip

value: Electroparion with dCas9-EGFP plasmid


title: K562 cells, WT, ChIP, H3K27me3

description: Library name: K562_H3K27me3_chip

value: No treatment


title: K562 cells, dCas9-EGFP, ChIP, SMC3

description: Library name: dCas9_SMC3_chip

value: lymphoblast cells


title: id12

value: female


title: Skin, Control-9D-1

description:
C9D1
fpkm.anno.txt


title: K562 cells, WT, ChIP, SMC3

description: Library name: K562_SMC3_chip


title: B409_3h_ATAC_rep1

description: Library name: Sample19

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: B409_3h_ATAC_rep2

description: Library name: Sample20


title: Skin, IR-3D-3

description:
IR3D3
fpkm.anno.txt


title: Skin, Control-6D-1

description:
C6D1
fpkm.anno.txt

value: 6 days


title: id11

value: male


title: id8


title: id9


title: K562 cells, restored CBS, RNA-seq, replicate 2

description:
Library name: DEL-dCas9_RNAseq_replicate_2
Read counts in txt format

data_processing:
[RNA-seq] Raw reads were processed using STAR aligner (v.2.7.11b), samtools (version 1.21) and featureCounts (v2.0.1). Counted reads were processed and normalized in DEseq2 (v.1.42.1) [25516281] using RStudio working environment with custom R script (R version 4.3.2).
Assembly: hg38
Supplementary files format and content: Genes with counted transcripts in txt format

value: K562 cell line with CBS deletion with electroporated dCas9-EGFP plasmid


title: Skin, Control-6D-2

description:
C6D2
fpkm.anno.txt


title: K562 cells, WT, ChIP, CTCF

description: Library name: K562_CTCF_chip


title: Skin, Control-3D-3

description:
C3D3
fpkm.anno.txt

value: 3 days


title: B409_1h_ATAC_rep1

description: Library name: Sample17

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: id7


title: Skin, Control-3D-1

description:
C3D1
fpkm.anno.txt

value: skin


title: K562 cells, restored CBS, RNA-seq, replicate 1

description:
Library name: DEL-dCas9_RNAseq_replicate_1
Read counts in txt format


title: id6


title: B409_0h_ATAC_rep2

description: Library name: Sample16


title: K562 cells, restored CBS, N+2, RNA-seq, replicate 2

description:
Library name: DEL-N+2_RNAseq_replicate_2
Read counts in txt format

value: K562 cell line with CBS deletion with electroporated N+2 CTCF-dCas9-EGFP plasmid


title: Skin, Control-0D-2

description:
C0d2
fpkm.anno.txt

value: 0 days


title: B409_0h_ATAC_rep1

description: Library name: Sample15

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: id5


title: K562 cells, restored CBS, N+2, RNA-seq, replicate 1

description:
Library name: DEL-N+2_RNAseq_replicate_1
Read counts in txt format


title: Skin, Control-0D-1

description:
C0d1
fpkm.anno.txt

value: Control


title: 2063A_48h_ATAC_rep2

description: Library name: Sample14

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 48 h.


title: id3

value: Vastus lateralis muscle


title: S12

city: Indianapolis

first: Santhosh Kumar

last: Pasupuleti

state: Indiana

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE M22 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s0 –p –Q 10”.
Assembly: mm10
Supplementary files format and content: count

source_name: Bone Marrow Tissue

growth_protocol: The Shp2E76K/+;LysM-Cre+ mice were in C57BL/6 background, generated from Indiana University School of Medicine core facility (~12 to 14 weeks old, both males and females were used in this study). Mice husbandry and care were performed under 21-24°C temperature- and 12-hour light,12-hour dark cycle; group-housed according to age, sex, and genotype; and fed ad libitum. All experiments were matched for age and sex for each experiment. We did not observe any difference in function or phenotypes between males and females.

extract_protocol:
Total RNA was isolated from the BM cells of 4 different drug treatment groups (Group 1: Vehicle, Group 2: PD-901, Group 3: 5-azacitidine, and Group 4: Combo) using Qiagen RNeasy Plus Micro Kit. RNA with Agilent Bioanalyzer RIN of > 7 were selected for library preparation.
Library preparation was performed using New England Biolabs Single Cell/Low Input RNA Library Prep Kit for Illumina. Paired-end RNA-sequencing (RNA-seq) was performed on Illumina HiSeq4000 by Novogene (project number: Davis-US-IU-12-mouse-EukmRNAseq-6G-WOBI-NVUS2022042753). Each group/condition consists of three matched biological replicates and ~30 million reads were obtained per sample.

treatment_protocol: The Shp2E76K/+ mice were randomly assigned to cohorts that received either single or combination of PD-901 (5 mg/kg, via oral gavage for 5 days per week for 4 consecutive weeks for a total of 20 doses in 4 weeks) and 5-azacitidine (5 mg/kg, via intraperitoneal injection for 5 days given every other day per 4 weeks for a total of 5 doses in 4 weeks). Mice were harvested after 20 doses of PD0325901 and 5 doses of 5-azacitidine treatment.

tag: agent

value: Combo


title: B409_1h_ATAC_rep2

description: Library name: Sample18


title: S11


title: id4


title: K562 cells, CBS deletion, RNA-seq, replicate 2

description:
Library name: DEL-K562_RNAseq_replicate_2
Read counts in txt format

value: K562 cell line with CBS deletion


title: 2063A_48h_ATAC_rep1

description: Library name: Sample13


title: id2


title: 2063A_24h_ATAC_rep1

description: Library name: Sample11

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 24 h.


title: id1


title: 2063A_24h_ATAC_rep2

description: Library name: Sample12


title: K562 cells, dCas9-EGFP, RNA-seq, replicate 1

description:
Library name: dCas9_RNAseq_replicate_1
Read counts in txt format

value: lymphoblast cells

value: Electroparion with dCas9-EGFP plasmid


title: S9


title: S10


title: K562 cells, dCas9-EGFP, RNA-seq, replicate 2

description:
Library name: dCas9_RNAseq_replicate_2
Read counts in txt format


title: 2063A_12h_ATAC_rep1

description: Library name: Sample9

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 12 h.


title: S8


title: 2063A_12h_ATAC_rep2

description: Library name: Sample10


title: K562 cells, N+2 CTCF-dCas9-EGFP, RNA-seq, replicate 2

description:
Library name: N+2_RNAseq_replicate_2
Read counts in txt format

value: Electroparion with N+2 CTCF-dCas9-EGFP plasmid


title: K562 cells, N+2 CTCF-dCas9-EGFP, RNA-seq, replicate 1

description:
Library name: N+2_RNAseq_replicate_1
Read counts in txt format


title: Ri01_5m, scRNAseq

city: Lausanne

first: Renaud

last: Du Pasquier

address: Rue Du Bugnon 46

department: Department of Clinical Neurosciences

country: Switzerland

institute: Lausanne University Hospital - CHUV

description: 10x Genomics

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina) and primary data analysis performed with the Cell Ranger Gene Expression pipeline (version 7.1.0, 10X Genomics).
Assembly: hg38
Supplementary files format and content: Comma-Separated Values files (all contig, filtered contig, consensus and clonotypes), Hierarchical Data Format version 5 files (raw and filtered features and molecule info) and Tab-separated values files (Adaptive Immune Receptor Repertoire rearrangements).

source_name: CD8+  T cells

extract_protocol:
A Chromium Next GEM Chip N (10X genomics) was loaded with the appropriate number of cells, and the sequencing libraries prepared with the Chromium Next GEM Single Cell 5’ HT Reagent Kits v2 dual index following the manufacturer’s recommendations. Briefly, an emulsion encapsulating single cells, reverse transcription reagents and cell barcoding oligonucleotides was generated. After the actual reverse transcription step, the emulsion was broken, and double stranded cDNA generated and amplified in a bulk reaction. For V(D)J sequencing, a similar approach was followed except that 2 steps of PCR based V(D)J target enrichment were performed prior to fragmentation.
This cDNA was fragmented, a P7 sequencing adaptor ligated, and a 5’ gene expression library generated by PCR amplification.

value: CD8+  T cells


title: 2063A_6h_ATAC_rep2

description: Library name: Sample8

data_processing:
RNA-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using hisat2.
ATAC-seq Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bowtie2.
Bisulfite sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using BatMeth2.
Whole-Genome sequencing Reads were aligned to brassica napus reference genome (Brassica napus.ZS11.v0.genome.fa) using bwa.
FeatureCounts was used to count the number of paired mapping reads for each gene.
Assembly: Brassica_napus.ZS11.v0.genome.fa
Supplementary files format and content: bw files for each Sample

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 6 h.


title: Ri01_dis, scRNAseq

description: 10x Genomics


title: S6


title: K562 cells, CBS deletion, RNA-seq, replicate 1

description:
Library name: DEL-K562_RNAseq_replicate_1
Read counts in txt format


title: 2063A_3h_ATAC_rep2

description: Library name: Sample6

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 3 h.


title: K562 cells, restored CBS, replicate 2

description:
Library name: Deletion+N+2_restorage_CTALE_replicate_2
Contact map in cooler format

data_processing:
[C-TALE] Quality control of the reads were performed using FastQC (Version 0.11.8). The raw reads were mapped to the 175,634,800-176,937,632 bp DNA sequence from the human hg38 assembly using hiclib (https://bitbucket.org/mirnylab/hiclib). Same tool was used to filter out reads that mapped in close proximity to the DpnII restriction sites (5 bp), reads from the same restriction fragment, and possible PCR duplicates. Resulted contact maps were iteratively corrected using cooler (v 0.8.11) (https://github.com/mirnylab/cooler).
Assembly: hg38
Supplementary files format and content: Raw and corrected contact maps of HoxD locus in K562 in cooler format.


title: 2063A_3h_ATAC_rep1

description: Library name: Sample5


title: Nuclear  Thymus Gland Extract treatment replicate 3

city: Kannapolis

first: Robert

last: Reid

state: NC

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

institute: UNC Charlotte

data_processing:
Trimming (Trimmomatic)
STAR alignment
Featurecount
Deseq2
PATHVIEW & GAGE
Assembly: GCF_000002985.6
Supplementary files format and content: tab delimted text file of featurecounts for each gene

molecule: nuclear RNA

organism: Caenorhabditis elegans

source_name: Whole tissue

growth_protocol: Worms were raised in standard media of NGM buffer and live OPS0 from hatching until the L4 stage. (Prepared by Nemalife)

extract_protocol:
Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal micro kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Treatment with ThymusFD, Thymex, and ThymusPMG diets begin on the 1st day of adulthood. On the first day of adulthood (day four of animal life), the worms in each chip are imaged to record the population size and then exchange their media (NGM).

value: Whole tissue

value: Nuclear Thymus Gland Extract treatment


title: K562 cells, WT, RNA-seq, replicate 1

description:
Library name: K562_RNAseq_replicate_1
Read counts in txt format

value: No treatment


title: 2063A_6h_ATAC_rep1

description: Library name: Sample7


title: Nuclear Thymus Gland Extract treatment replicate 1


title: 2063A_1h_ATAC_rep2

description: Library name: Sample4

value: growth in Hoagland nutrient solution with 220 mM/L NaCl condition for 1 h.


title: Cytoplamsic Thymus Gland Extract treatment replicate 3


title: S4


title: Ri02, scRNAseq

description: 10x Genomics

value: mycophenolate mofetil, prednisone


title: K562 cells, CBS deletion, replicate 2

description:
Library name: Deletion_CTALE_replicate_2
Contact map in cooler format


title: 2063A_1h_ATAC_rep1

description: Library name: Sample3


title: S5


title: S3

value: Vehicle


title: S2


title: Nuclear Thymus Gland Extract treatment replicate 2


title: K562 cells, CBS deletion, replicate 1

description:
Library name: Deletion_CTALE_replicate_1
Contact map in cooler format


title: Cytoplamsic Thymus Gland Extract treatment replicate 2


title: S1


title: S7


title: 2063A_0h_ATAC_rep2

description: Library name: Sample2

value: growth in Hoagland nutrient solution with 0 mM/L NaCl condition.


title: F

city: CHANDIGARH

first: KHUSHBOO

last: MEHTA

address: SECTOR 39A

country: India

institute: CSIR IMTECH

description: Library name: SAMPLE 6

data_processing:
Basecalling, demultiplication and adaptor trimming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (Mycobacterium tuberculosis H37Rv accession number NC_000962.3) using Hisat2.
Differential gene expression analysis of samples with respect to control was performed using Cuffdiff program (v2.2.1).
Assembly: NC_000962.3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Mycobacterium tuberculosis

growth_protocol: 2851 knockdown strain with and without ATC strains were grown at 37°C .

extract_protocol:
RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown  to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen).
Total RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research Corporation), the purity of isolated RNA was determined using the NanoDrop (Thermo Scientific), quantified using Qubit (Invitrogen), and RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies).  Library construction, RNA-sequencing and data analysis have been carried out by medgenome Labs Private Limited (Cochin), India. Briefly, The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was carried out using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated. Thereads that passed quality control were mapped onto the reference genome of M. tuberculosis H37Rv using Hisat2 (version-2.0.5).  The abundance of transcripts in individual samples was estimated using Cufflinks (v2.2.1).

treatment_protocol: Cultures were grown till mid log phase. RNA was isolated and processed for RNA sequencing.

value: strain

value: RNA-Seq

value: WITH ATC


title: K562 cells, WT, RNA-seq, replicate 2

description:
Library name: K562_RNAseq_replicate_2
Read counts in txt format

value: lymphoblast cells


title: K562 cells, WT, replicate 2

description:
Library name: K562_CTALE_replicate_2
Contact map in cooler format


title: 2063A_0h_ATAC_rep1

description: Library name: Sample1

extract_protocol:
Toal RNA was extracted by using Eastep® Super Total RNA Extraction Kit (Promega) from cotyledon with three replications. For ATAC-seq, the extracted nuclei were incubated with Tn5 transposase and tagmentation buffer following the manufacturer’s instructions (Vazyme, TD501-01).
mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads, and mRNAs were obtained by removing ribosomal RNAs from the total RNAs. For ATAC-seq, DNA was purified using the MinElute PCR Purification Kit (QIAGEN, 28004). Genomic DNA for was extracted using the DNeasy Plant Mini Kit (QIAGEN, 69104). Bisulfite-treated DNA libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) following the manufacturer’s instructions.


title: Dessicated Thymus treatment  replicate 3

value: Dessicated Thymus treatment


title: K562 cells, WT, replicate 1

description:
Library name: K562_CTALE_replicate_1
Contact map in cooler format


title: K562 cells, restored CBS, replicate 1

description:
Library name: Deletion+N+2_restorage_CTALE_replicate_1
Contact map in cooler format

value: K562 cell line with CBS deletion with electroporated N+2 CTCF-dCas9-EGFP plasmid


title: E

description: Library name: SAMPLE 5

value: WITHOUT ATC


title: K562 cells, dCas9-EGFP

description:
Library name: dCas9_ne_novo_CTALE
Contact map in cooler format

value: Electroparion with dCas9-EGFP plasmid


title: Dessicated Thymus treatment  replicate 2


title: D

description: Library name: SAMPLE 4


title: NSC_fy/cre_3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

description: Library name: Sample 12

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 23.0.5. (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 23.0.5. (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Primary neurosphere

extract_protocol:
Total RNA was extracted from whole brain and primary neurospheres using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Primary neurosphere

tag: developmental stage

value: Primary neural stem cells from forebrain regions (E16)

value: male


title: Singel cell RNAseq of sorted Blimp1 KO and WT GCBC

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description:
Library name: Sample 1
10x Genomics; germinal centers sorted from 50/50 mixed bone marrow chimera (Prdm1 flox/flox CD19 Cre/+ CD45.2/2 and Prdm1 wt/wt CD19 Cre/+ CD45.1/1) day 12 post immunization with NP-CGG in alum

data_processing:
The 10x raw data from each sample were demultiplexed and FASTQ files were generated using the “mkfastq” Cell Ranger pipeline (v5.0.0, 10X Genomics).
Cell Ranger “count” was used to align reads to the mm10 reference genome, and mRNA transcript, and HTO unique molecular identifier (UMI) quantification tables were generated.
The raw barcode matrix files generated from the Cell Ranger pipeline were further utilized for downstream analysis using the Seurat package (v4.0.0) in R (v3.4.3).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: Raw count output file from Cellranger.

source_name: spleen

extract_protocol:
Cells were loaded into the 10x Chromium system and RNA was isolated using the Chromium Next GEM Single Cell V(D)J Reagent Kit v1
Libraries were normalized and pooled at a ratio of 1 part BCR and 1 part HTO library to 4 parts GEX library and sequenced on the Illumina HiSeq platform

value: spleen

value: Germinal Center B cells

value: CD19 Cre/+ or Prdm1 flox/flox CD19 Cre/+


title: K562 cells, N CTCF-dCas9-EGFP

description:
Library name: N_de_novo_CTALE
Contact map in cooler format

value: Electroparion with N CTCF-dCas9-EGFP plasmid


title: Control Sample replicate 3

value: Whole tissue

value: Control


title: NSC_fy/cre_1

description: Library name: Sample 10


title: B

description: Library name: SAMPLE 2

value: strain


title: NSC_fy/cre_2

description: Library name: Sample 11


title: Control Sample replicate 2


title: K562 cells, N+2 CTCF-dCas9-EGFP

description:
Library name: N+2_de_novo_CTALE
Contact map in cooler format

value: Electroparion with N+2 CTCF-dCas9-EGFP plasmid


title: C

description: Library name: SAMPLE 3

value: RNA-Seq


title: A

description: Library name: SAMPLE 1


title: Control Sample replicate 1


title: NSC_fy/-_3

description: Library name: Sample 9

value: Wildtype


title: NSC_fy/-_2

description: Library name: Sample 8


title: K562 cells, N+7 CTCF-dCas9-EGFP

description:
Library name: N+7_de_novo_CTALE
Contact map in cooler format

value: lymphoblast cells

value: Electroparion with N+7 CTCF-dCas9-EGFP plasmid


title: Cytoplamsic Thymus Gland Extract treatment replicate 1


title: K562 cells, N+11 CTCF-dCas9-EGFP

description:
Library name: N+11_de_novo_CTALE
Contact map in cooler format

value: Electroparion with N+11 CTCF-dCas9-EGFP plasmid


title: K562 cells, CTCF-dCas9-EGFP

description:
Library name: Full_de_novo_CTALE
Contact map in cooler format

value: Electroparion with full CTCF-dCas9-EGFP plasmid


title: U

address: SECTOR 39 A CHANDIGARH

description: Library name: SAMPLE 6

data_processing:
Basecalling, demultiplication and adaptor trimming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (Mycobacterium tuberculosis H37Rv accession number NC_000962.3) using Hisat2.
Differential gene expression analysis of samples with respect to control was performed using Cuffdiff program (v2.2.1).
Assembly: NC_000962.3
Supplementary files format and content: Differential Exp (Comparison )

source_name: Mycobacterium tuberculosis

growth_protocol: M. tuberculosis H37Rv strains were grown at 37°C in glycerol and acetate as  carbon source  at acidic pH(5.5)

extract_protocol:
RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown (in the indicated pH) to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen).
Total RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research Corporation), the purity of isolated RNA was determined using the NanoDrop (Thermo Scientific), quantified using Qubit (Invitrogen), and RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies).  Library construction, RNA-sequencing and data analysis have been carried out by medgenome Labs Private Limited (Cochin), India. Briefly, The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was carried out using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated. Thereads that passed quality control were mapped onto the reference genome of M. tuberculosis H37Rv using Hisat2 (version-2.0.5).  The abundance of transcripts in individual samples was estimated using Cufflinks (v2.2.1).

treatment_protocol: Cultures were grown till mid log phase in glycerol and acetate as carbon source  acidic stress (pH 5.5). RNA was isolated and processed for RNA sequencing.

value: Mycobacterium tuberculosis

value: acetate  5.5-C

value: acidic PH


title: T

description: Library name: SAMPLE 5

value: acetate  5.5-B


title: shALKBH1 #2 IP

city: Chicago

first: Emma

last: Wilkinson

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: University of Chicago

description: Library name: EW-8

data_processing:
The raw fastq data of different lanes for the same sample were first merged for R1 and R2, respectively. Then, Trim Galore was used to trim the adapters. FastQC was used for quality control. The trimmed reads were processed by using the easym6A pipeline (https://github.com/shunliubio/easym6A) to generate bam and bigwig files.
Assembly: hg38
Supplementary files format and content: .bw for processed data

source_name: Skin

growth_protocol: Arsenic-transformed keratinocytes maintained in DMEM with 10% FBS and antibiotics in 5% CO2 incubator at 37C

extract_protocol:
100μg total RNA was extracted from cells using TRIzol following the manufacturer’s protocol (phenol-choloroform extraction). These samples are extracted from human cancer cells. RNA was then purified and treated with DNAse using the Zymo RNA Clean and Concentrator Kit. mRNA was purified using a Dynabeads mRNA DIRECT Kit (Thermo Fisher, # 61012). Samples went through the mRNA extraction protocol twice to eliminate rRNA contamination. 1ug of RNA was then fragmented using the NEB RNA Fragmentation Module to 200nt. 5% of the fragmented mRNA was saved as input. mRNA fragments containing m6A were enriched with an EpiMark N6-Methyladenosine Enrichment Kit (NEB, E1610S) and then extracted using RNA Clean and Concentrator (Zymo Research). 2 biological replicates per each condition were used.
Oligo-dT mRNA directional

value: Skin

value: Arsenic-transformed keratinocytes


title: NSC_fy/-_1

description: Library name: Sample 7

value: Primary neurosphere

value: Primary neural stem cells from forebrain regions (E16)

value: male


title: Dessicated Thymus treatment replicate 1

value: Whole tissue

value: Dessicated Thymus treatment


title: shALKBH1 #1 IP

description: Library name: EW-7


title: Brain_fy/cre_3

description: Library name: Sample 6

source_name: Whole brain

value: Whole brain

value: Embryonic day (e):E15


title: S

description: Library name: SAMPLE 4

value: acetate 5.5-A


title: shNC #2 IP

description: Library name: EW-6


title: Exosomes derived from 3D cultured human umbilical cord mesenchymal stem cells

city: Beijing

first: Yu

last: Chen

state: Select...

address: NO.8,xitoutiao road,youwai street,fengtai district

institute: 1.	Fourth Department of Liver Disease, Beijing Youan Hospital, Capital Medical University

description: Library name: Ex3

data_processing:
The small RNA sequencing library adopted the PE150 sequencing scheme, and the quality value of the sequencing library was evaluated using FastQC. FastP was utilized for the removal of N bases at both ends of the sequence, Q20 filtering, and adaptor removal. Using the Ensembl release 102 Homo sapiens genome as a reference, the bowtie short sequence alignment tool was employed to align the Rfam library and remove ncRNAs such as rRNA and tRNA. miRDeep2 was used for quantitative statistics of small RNA, and DESeq2 (with replicate samples) or EdgeR (without replicate samples) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: csv format file containing differently expressed miRNA and target genes for differently expressed miRNA

source_name: Human umbilical cord mesenchymal stem 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: 3D cultured


title: R

description: Library name: SAMPLE 3

value: glycerol 5.5-C


title: Brain_fy/cre_2

description: Library name: Sample 5


title: shNC #1 IP

description: Library name: EW-5


title: Q

description: Library name: SAMPLE 2

value: glycerol 5.5-B


title: Brain_fy/cre_1

description: Library name: Sample 4


title: D25organoids-GEX

city: Clayton

first: Laura

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
all details of data processing are in the github repository: https://github.com/MonashBioinformaticsPlatform/scRNA-seq_Hypoxic_Kidney_Organoids
Supplementary files format and content: h5

source_name: kidney organoid

growth_protocol: Cell Culture  Human iPSC lines 522.3 (16-year-old female, derived from GM04522 fibroblasts - NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research), D4C4 (32-year-old female derived from human gingival tissue) and 808.5 (GM21808 fibroblasts - NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research) were used in this study. Cells were maintained on Essential 8 (E8) medium (Thermo Fisher Scientific) supplemented with 1% Penicillin/Streptomycin (Pen/Strep) (Thermo Fisher Scientific) in Matrigel-coated plate (Corning, cat no. FAL35427). Cells were passaged at 70-80% confluency at 1:3 ratio using 0.5 mM EDTA (Thermo Fisher Scientific).  Generation of Kidney Organoids Directed differentiation of human iPSC into kidney organoids was conducted as previously described (1, 2), with minor modifications. Briefly, iPSC were seeded on a Matrigel-coated 6-well plate (Corning, cat no. FAL35427) (refer to Table S1 for specific cell number) using E8 media (Thermo Fisher Scientific) supplemented with 10 M of ROCK inhibitor Y-27632 (In Vitro Technologies) and 1% Pen/Strep (Thermo Fisher Scientific). The next day (d0), the media was changed and cells cultured with Essential 6 (E6) medium (Thermo Fisher Scientific) supplemented with CHIR99021 (In Vitro Technologies) (refer to Table S1 for CHIR99021 concentration) and 1% Pen/Strep (Thermo Fisher Scientific). On day 4, 200 ng/ml of FGF9 (In Vitro Technologies) and 1 µg/ml of Heparin (Sigma-Aldrich) were added to the media. On day 7, cells were dissociated with TrypLE Select Enzyme (1X) (Thermo Fisher Scientific) and 150,000 cells were used to generate each 3D organoid. To achieve similar conditions between the wells, a total of four organoids were seeded onto each of the transwells of the 6-well plates (Sigma-Aldrich). After seeding, one-hour CHIR99021 treatment in E6 medium (refer to Table S1 for CHIR99021 concentration) was performed before changing the media to E6 supplemented with 200 ng/ml of FGF9, 1 µg/ml of Heparin and 1 % Pen/Strep. A media changed was performed every second day until d13, when organoids were cultured in E6 medium with 1 % Pen/Strep only.

extract_protocol:
The 12 samples from iPSC-derived kidney organoids were labelled with Cell Plex (10x Genomics) Cell Modified Oligonucleotides (CMO) for multiplexing. Libraries were prepared using 10X Genomics Chromium Single Cell 5' V3.1 chemistry, for GEX and FB/CellPlex libraries (10X Genomics; San Francisco CA, USA), prepared according to the manufacturer’s instructions and sequenced on MGITech MGISEQ2000RS hardware using MGIEasy V3 chemistry for 100 bp paired-end sequencing.
Multiplexed sample pool 1: Day 20 Normoxia (3 reps) of a pool of 3 organoids/rep and Day 20 Hypoxia (3 reps) of a pool of 3 organoids/rep  Multiplexed sample pool 2: Day 25 Normoxia (3 reps) of a pool of 3 organoids/rep and Day 25 Hypoxia (3 reps) of a pool of 3 organoids/rep   All samples come from a single differentiation to limit batch effects ·Individual samples are made up of cells from three organoids ·Replicate samples represent wells of 3 organoids differentiated in parallel ·Replicate samples from normoxic and hypoxic experimental groups were individually barcoded with Cell Plex barcodes prior to pooling ·Each sample pool was captured in a single well of a 10x chip on two separate days (one for the day 20 pool, the other for the day 25 pool) LMO (Cell Plex 10x genomics)

treatment_protocol: Hypoxic Injury Quality control measures on 18-day-old kidney organoids was performed to limit batch-to-batch variation. Immunostaining of LTL, GATA3, UMOD, NPHS1, MEIS2 and CDH1 were confirmed in all batches. Due to batch heterogeneity, only batches of organoids displaying homogenous tubular structures, observed under bright field microscope, were used for this study, suboptimal organoid batches were discontinued between day 12-18. In this study, 18-day old kidney organoids were placed in hypoxic incubators (1 % O2) for 48h. In parallel, organoids derived from the same batch were kept in normoxic conditions in routine incubators. After two days, some organoids from the experiment and control groups were harvested for analysis. The rest of organoids from the batch were placed in normoxic incubators for 5 days (recovery period) and harvested at d25. For bulk RNA-sequencing, quantitative PCR, proteomics and metabolomics studies, organoids were snap-frozen at d20 and d25. For this study, we maintain a rigorous number of 4 organoids per transwell to minimize variability regarding nutrient/oxygen diffusion.

value: kidney organoid

value: mulitplexed Normoxia/Hypoxia


title: shALKBH1 #2 Input

description: Library name: EW-4


title: Brain_fy/-_3

description: Library name: Sample 3

value: Wildtype


title: P

description: Library name: SAMPLE 1

value: Mycobacterium tuberculosis

value: glycerol 5.5-A

value: acidic PH


title: shALKBH1 #1 Input

description: Library name: EW-3

value: Skin

value: Arsenic-transformed keratinocytes


title: Brain_fy/-_2

description: Library name: Sample 2

value: male


title: D25organoids-FB

description: Libraries were prepared using 10X Genomics Chromium Single Cell 5' V3.1 chemistry, for GEX and FB/CellPlex libraries (10X Genomics; San Francisco CA, USA), prepared according to the manufacturer’s instructions and sequenced on MGITech MGISEQ2000RS hardware using MGIEasy V3 chemistry for 100 bp paired-end sequencing


title: D20organoids-FB


title: shNC #2 Input

description: Library name: EW-2


title: Smad1/5 dKO mESCs, scRNA-seq

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

institute: Teikyo University

description: 10X Genomics

data_processing:
The libraries were sequenced on the Illumina HiSeq X Ten platform in paired-end read mode with 150 bp per read. Raw sequencing data were processed using Cell Ranger software (version 3.0.2) with mm10 reference genome (provided by 10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse ESCs (E14)

growth_protocol: Feeder-free E14 mouse ESCs were maintained in serum-containing conditions, and Smad1/5 double knockout mESCs (S1/5 dKO) was generated using CRISPR-Cas9 system (Morikawa et al., 2016). These cells were cultured at 37°C in 5% CO2 and were maintained on gelatin (Millipore, Merck, Darmstadt, Germany, or FUJIFILM Wako, Tokyo, Japan)-coated dishes in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), with 15% ES-qualified fetal bovine serum (FBS) (Millipore, Merck), 0.1 mM β-mercaptoethanol (FUJIFILM Wako), 2 mM L-glutamine, 1×MEM nonessential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco), and 1000 U/ml LIF (Millipore).

extract_protocol:
The cells were gently digested into single cells using 0.05% trypsin-EDTA (Gibco) and were resuspended at ~1000 cells/uL.
The libraries were generated using the Chromium Single Cell 3' Reagent Kit v3 chemistry (10X Genomics) with a target of 3,000 cells per sample, according to manufacturer's protocol.

treatment_protocol: FBS and LIF

value: mouse ESCs (E14)

value: mouse embryonic stem cells

value: Smad1/5 dKO

value: FBS and LIF


title: D20organoids-GEX


title: wild-type mESCs, scRNA-seq

description: 10X Genomics

value: wild-type


title: Brain_fy/-_1

description: Library name: Sample 1

value: Whole brain

value: Embryonic day (e):E15


title: shNC #1 Input

description: Library name: EW-1


title: SCC15 cells, AOH1996

status: Public on Aug 14 2025

first: Yujia

last: Wang

address: 22 Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

description:
Library name: Sample 2
Column name in SCC15_All_Samples.xlsx

data_processing:
The fold changes were calculated.
The different categories of KEGG pathways were analyzed using the DAVID Bioinformatics website.
The heatmap was created using GraphPad Prism 9.0 for Windows (GraphPad Software Inc., La Jolla, CA, USA).
Assembly: GRCh38/hg38
Supplementary files format and content: The format is xlsx.
Supplementary files format and content: The content include the transcriptome alteration of SCC15 cells after treatment with AOH1996.

growth_protocol: SCC15 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS)  at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNAs were isolated from SCC15 cells using TRIzol Reagent.
The Illumina TruSeq RNA sample preparation Kit was used to prepare for the RNA-sequencing library construction.

treatment_protocol: After reaching 70%-80% confluence, the SCC15 cells were treated with 1 μM DMSO or AOH1996.

value: Squamous epithelial cells


title: dKO - BCR

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
Library name: SHE6920A4
single cell RNA sequencing, 10X genomics

data_processing:
CellRanger multi run with chemistry = SC5P-R2
Single cell BCR sequencing analysis. B-cell receptor (BCR) repertoire analysis was conducted with the Immcantation framework, implemented in a Python environment (v.3.11.10)
Assembly: mm10-2020
Supplementary files format and content: CellRanger verison 7.0.1 outputs file for expression, HTO and BCR .
Supplementary files format and content: Only B-1 cells from peritoneal cavity labelled with hashtag antibodies (C0303, C0304, C0306, Biolegend) are used for the further VDJ and diversity analysis
Library strategy: scBCR-Seq

source_name: foetal liver, bone marrow, spleen and peritoneal cavity

extract_protocol: B-1 progenitor cells (Lin-CD93+IgM-CD19+B220neg-lo) from E18.5 foetal livers (three foetal livers were pooled together as one replicate) or bone marrow from three 8 weeks mice, B-1 cells (CD19+B220neg-lo ) from peritoneal cavity and spleen from three 8 weeks old mice were sorted by the FACS Aria II cell sorting system (BD Immunocytometry Systems, San Jose, CA, USA)

value: B-1 progenitor cells and B-1 cells

value: dKO

value: E18.5 and 8 weeks old


title: WT - GEX

description:
Library name: SHE6920A7
single cell RNA sequencing, 10X genomics

data_processing:
CellRanger multi run with chemistry = SC5P-R2
Single cell BCR sequencing analysis. B-cell receptor (BCR) repertoire analysis was conducted with the Immcantation framework, implemented in a Python environment (v.3.11.10)
Assembly: mm10-2020
Supplementary files format and content: CellRanger verison 7.0.1 outputs file for expression, HTO and BCR .
Supplementary files format and content: Only B-1 cells from peritoneal cavity labelled with hashtag antibodies (C0303, C0304, C0306, Biolegend) are used for the further VDJ and diversity analysis

value: foetal liver, bone marrow, spleen and peritoneal cavity

value: WT


title: WT - BCR

description:
Library name: SHE6920A8
single cell RNA sequencing, 10X genomics


title: Alkali_burn-3,  alkali-injured

city: Columbia

first: Rajiv

middle: R

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

description: Library name: Sample 6

data_processing:
FastQC was used to generates quality metrics for sequencing reads.
Sequence data was aligned using bowtie2  and Samtools was used  to convert the SAM format into a compressed BAM file
MASC2 was used to identify peaks
Assembly: OryCun2.0
Supplementary files format and content: .narrowPeak files cotaining called peaks

organism: Oryctolagus cuniculus

source_name: Cornea

extract_protocol:
After clinical evaluation and on day14 post-injury, corneal tissue was collected and subjected to ATAC sequencing commercially by Activ Motif. 30-50mg flash frozen tissue was manually disassociated to isolate nuclei. Approx. 100,000 nuclei were tagmented via the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif)
The fragmented DNA was then purified via a DNA extraction method and amplified with PCR. The resulting libraries were purified via SPRI beads.

treatment_protocol: Corneas were exposed to alkali injury via topical application of 8mm filter discs soaked in alkali (0.5 N NaOH) for 30sec. Only one eye of each rabbit was exposed to alkali injury, while, the unexposed contralateral eye served as naïve control

value: Cornea

value: Female

value: NAOH, 1 N, 30s

value: Day 14


title: Naïve-3, untreated

description: Library name: Sample 3


title: Exosomes derived from 2D cultured human umbilical cord mesenchymal stem cells

description: Library name: Ex2

value: Human umbilical cord mesenchymal stem cells

value: 2D cultured


title: Naïve-2, untreated

description: Library name: Sample 2


title: Naïve-1, untreated

description: Library name: Sample 1


title: ADN_4h_S_Palb_0h_4h

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

data_processing:
library strategy: EdUseq
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17, retaining only the reads with the highest quality score.
CSV processed files have been generated as described in the section "Sequence alignment and calculation of sigma values" of Methods published in https://doi.org/10.1038/nature25507
Assembly: Human GRCh37/hg19
Supplementary files format and content: csv

source_name: RPE CDC6d CDT1d clone #1

growth_protocol: RPE CDC6d CDT1d clone #1 cells were cultured in an ambient-controlled incubator at 37°C and 5% CO2 and maintained using DMEM-F12 GlutaMAX (ThermoScientific, 31331093) supplemented with 1% Pen/Strep (ThermoScientific, 15140122) and 10% heat-inactivated fetal bovine serum (Sigma, F7524).

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina HiSeq 4000 sequencer.

treatment_protocol: EdU-seq samples were treated with nocodazole for 8hrs and mitotic cells were obtained with mitotic shake-off. They were then released in medium containing HU and EdU for 14 or 16h.

value: RPE CDC6d CDT1d clone #1

value: Human retinal pigment epithelial cells

tag: genetic modification

value: Integrationf of DOX-inducible OsTIR and ARF16-PB1 co-expression construct at the human Rosa26 locus and tagging of both alleles of CDC6 and CDT1 by a mAID_SMASh double degron


title: ADN_4h_S_Palb_4h_14h


title: ADN_M_4h_Palb_0h_4h


title: ADN_M_4h_no_Palb_Ctrl


title: no_ADN_Ctrl_Palb_0h_4h


title: ADN_M_4h_Palb_4h_14h


title: Alkali_burn-1, alkali-injured

description: Library name: Sample 4


title: Alkali_burn-2,  alkali-injured

description: Library name: Sample 5


title: ADN_M_8h


title: no_ADN_Ctrl_no_Palb_Ctrl


title: ADN_8h_S


title: ADN_4h_S


title: no_ADN_Ctrl_Palb_4h_14h


title: SCC15 cells, DMSO

description:
Library name: Sample 1
Column name in SCC15_All_Samples.xlsx

value: DMSO


title: ADN_M_4h


title: ADN_M_12h


title: no_ADN_Ctrl


title: NC-ADAR,Input,rep1

city: Shanghai

first: Zhibo

last: Shao

institute: Fudan University Shanghai Cancer Center

data_processing:
For Ribo-seq data analysis, Cutadapt was used to trim low-quality reads and remove adaptors. Then reads were mapped to rRNA and tRNA sequences to remove rRNA and tRNA reads using bowtie2 software. STAR aligner was applied to aligned clean reads to human genome (GRCh38) and genecode genes (gencode.v44.annotation.gtf). FeatureCounts was used to quantify the aligned reads with the parameter -t exon. For downstream analysis, TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was used. The translation efficiency was calculated as the following ratio: (TPM of Ribo-seq)/(TPM of RNA-seq). Only the genes with TPM ≥ 1(including both the Ribo-seq and input RNA-seq) were selected for further analysis. TE < 0.5 or > 2 were considered as translation-downregulated or translation-upregulated genes.
Assembly: hg38

source_name: Breast

extract_protocol:
Cells (4 x 10^6) were harvested and lysed in lysis buffer (20mM HEPES pH 7.4, 100mM KCl, 5mM MgCl2, 0.5mM NaF, 0.5% NP-40) with added protease inhibitor and 1mM dithiothreitol (DTT) before use. After 30 minutes on ice, cell debris was removed by centrifuging at 16,200g for 15 minutes at 4°C. Supernatants were then loaded onto 11.4 mL of 10% to 40% linear sucrose gradient in lysis buffer with polypropylene tubes (Beckman, 331372) and centrifuged at 39,000 rpm in a Beckman SW41Ti rotor at 4°C for 3 hours. RNA was quantified at optical density (OD) 260nm on a 2100 Bioanalyzer (Agilent Scientific Instruments, Santa Clara, CA).
For cDNA library construction and high-throughput sequencing, samples were then subjected to denaturing 15% polyacrylamide TBE-Urea gel, followed by excision and purification of 30 nt (ribo-seq) and 40-60 nt (input) RNAs. Desired RNA species were excised and soaked overnight in gel elution buffer (300 mM NaOAc, pH5.5, 1 mM EDTA, 0.1 U/mL SUPERase_In) followed by ethanol precipitation. Then, the purified RNA was processed for adding 3’ adapter by RNA Ligase 1 (NEB, M0437M) and reverse transcription afterward. Another adapter was also added with RNA Ligase 1. Eventually, PCR amplification was proceeded using Phusion highfidelity DNA polymerase (NEB M0530L). The quantification of PCR products was evaluated on Agilent Bioanalyzer 2100 system before being subjected to cluster generation, followed by deep sequencing on an Illumina Novaseq platform at Novogene

value: Breast

value: The triple-negative breast cancer cell line


title: Si-ADAR,Input,rep2


title: Si-ADAR,Ribo,rep2

library_source: other

data_processing:
For Ribo-seq data analysis, Cutadapt was used to trim low-quality reads and remove adaptors. Then reads were mapped to rRNA and tRNA sequences to remove rRNA and tRNA reads using bowtie2 software. STAR aligner was applied to aligned clean reads to human genome (GRCh38) and genecode genes (gencode.v44.annotation.gtf). FeatureCounts was used to quantify the aligned reads with the parameter -t exon. For downstream analysis, TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was used. The translation efficiency was calculated as the following ratio: (TPM of Ribo-seq)/(TPM of RNA-seq). Only the genes with TPM ≥ 1(including both the Ribo-seq and input RNA-seq) were selected for further analysis. TE < 0.5 or > 2 were considered as translation-downregulated or translation-upregulated genes.
Assembly: hg38
Library strategy: Ribo-seq

molecule: other


title: NC-ADAR,Input,rep2


title: Si-ADAR,Input,rep1


title: NC-ADAR,Ribo,rep2


title: NC-ADAR,Ribo,rep1


title: 2yr_All_M_M1

first: Aidan

last: Daly

state: SC

address: 2230 Rembert Street

institute: New York Genome Center

description: Library name: 2yr

data_processing:
CellRanger v3.0 was used for all initial data pre-processing. Fastq reads were first demultiplexed and then mapped to the reference mm10 transcriptome, augmented to allow for counting of all transcript tags in addition to counting exons as suggested by 10X Genomics. Each barcode was connected to a particular cell and UMIs were collapsed to account for duplicated transcripts. Filtered matrices reflecting digital gene expression (DGE) for each sample and cell were extracted from the pipeline.
Assembly: mm9
Supplementary files format and content: MTX-formatted file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file including annotation metadata for each cell (rows)
Supplementary files format and content: tab-delimited text file containing gene names and expression metadata (columns)
Supplementary files format and content: tab-delimited text file containing barcode names for each cell (rows)

source_name: All colon

growth_protocol: C57BL/6J mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and maintained in accordance with ethical guidelines monitored by the Institutional Animal Care and Use Committees (IACUC) established by the Division of Comparative Medicine at the Broad Institute of MIT and Harvard and Columbia University, and consistent with the Guide for Care and Use of Laboratory Animals, National Research Council, 1996 (institutional animal welfare assurance no. A4711-01), with protocols 0122-10-16 and AABI3617, respectively.

extract_protocol:
Frozen tissues were taken from 1.5ml tubes used for storage at −80°C and placed in pre-chilled 1 mL extraction buffer (0.03% Tween-20, 146mM NaCl, 10mM Tris pH 8.0, 1mMM CaCl2 and 21mM MgCl2; all from Sigma Aldrich, USA), supplemented with 400U RNasin Plus inhibitor (Promega Corporation, USA) and 200U SUPERaseIn RNase Inhibitor (ThermoFisher Scientific, USA). Tissues were disintegrated by chopping with tungsten Carbide Straight 11.5 cm Fine Scissors (14558-11, Fine Science Tools, Foster City, CA) for 10 minutes on ice. To avoid clogging, samples were filled through a 40 μm strainer (Falcon). To release any leftover material from the strainer, it was cleaned with the extraction buffer without the addition of Tween-20, followed by centrifugation to pellet the nuclei at 500g for 5 mins at 4°C. Supernatants were removed and nuclei were resuspended in a 100μL extraction buffer without the addition of Tween-20 before filtering through a 40 μm strainer-capped into a round bottom tube (Falcon). Nuclei were counted and ~8,000 nuclei were loaded per channel on the GemCode Single Cell Platform using the GemCode Gel Bead kit, Chip and Library Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol.
Nuclei were partitioned into Gel Beads in Emulsion (GEMs), lysed and barcoded using reverse transcription reactions, followed by amplification, shearing and 5′ adapter and library indexing. Libraries were sequenced on an Illumina NextSeq 550 (R1: 26 bases; R2: 55 bases) or a NovaSeq 6000 (R1: 28 bases; R2: 94 bases).

treatment_protocol: Colons were collected within 5 min of death and flushed using ice-cold 1x PBS (Gibco) using a straight gauge needle with a 2.4mm tip (Kent Scientific Corporation, USA) for mice >3 weeks of age or a newborn feeding needle (Cadence Science, USA) for mice ages 3 weeks. The rest of the mice were processed without colon flushing prior to freezing. Tissues were then dried and embedded in Optimal Cutting Temperature (OCT, Fisher Healthcare, USA) in large molds (VWR, USA). Samples were then plunged onto a metal plate pre-chilled and sitting on top of dry ice for 2min or until complete freezing. Samples were transferred and stored at -80°C until use. For nucleus extractions, colons were separated from the animals within 5 minutes of death and each colon was separately flushed similar to collecting tissue for ST. Approximately 0.5cm of tissue from three different colon regions was placed on a tissue and dried before transfer to a sterile dish to ensure all excess water was gently removed from the sample. Tissues were then placed in a 1.5 mL tube on dry ice and, upon freezing, transferred to −80°C until subsequent tissue processing.

value: All colon

value: male


title: ADN_4h_S_no_Palb_Ctrl


title: Si-ADAR,Ribo,rep1


title: 6m_All_M_M1

description: Library name: 6m


title: 8w_Middle_M_M2

description: Library name: 8w_v2_rep5

source_name: Middle colon

value: Middle colon


title: 8w_Distal_M_M5

description: Library name: 8w_v2_rep3

source_name: Distal colon

value: Distal colon


title: 8w_Distal_F_M3

description: Library name: 8w_v2_rep6

value: female


title: 4w_Proximal_F_M2

description: Library name: 4w_v2_rep3

source_name: Proximal colon

value: Proximal colon


title: 6w_All_M_M1

description: Library name: 6w


title: 4w_Middle_F_M2

description: Library name: 4w_v2_rep2


title: 8w_Distal_M_M2

description: Library name: 8w_v2_rep4


title: 4w_All_M_M1

description: Library name: 4w


title: 8w_All_F_M1

description: Library name: 8w


title: 4w_Distal_M_M4

description: Library name: 4w_v2_rep4


title: 1w_All_F_M1

description: Library name: 1w


title: 0d_All_M_M1

description: Library name: 0d


title: 3w_All_M_M1

description: Library name: 3w


title: 2w_All_M_M1

description: Library name: 2w


title: 8w_Middle_F_M3

description: Library name: 8w_v2_rep7