title: Bleo Female 4 RNA

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

institute: University of Nebraska Medical Center

description: Library name: Sample Female 9

data_processing:
Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Assembly: Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Supplementary files format and content: CSV file including FPKM values for each sample

source_name: Lung tissue

extract_protocol:
Paired mRNA and miRNA sequencing utilized services offered by LC Sciences (Houston, TX, USA).  Total lung RNA was extracted from the BW-matched cohort only (five sham-male, five sham-female, five bleomycin-male, five bleomycin-female) with TRIzol (Invitrogen) and randomized for downstream processing. Integrity was verified on a Bioanalyzer 2100 (Agilent); every sample showed RIN ≥ 7.0. Two complementary libraries were prepared from the same RNA aliquot for each animal.
mRNA (poly-A) libraries were generated with the TruSeq-Stranded mRNA kit (Illumina). Poly-A RNA was captured with two rounds of oligo-dT magnetic-bead purification, chemically fragmented, converted to cDNA, end-repaired, A-tailed, ligated to indexed adapters, and amplified (15 cycles). Paired-end 150-bp reads were produced on an Illumina NovaSeq 6000 at LC Sciences (Houston, TX, USA), yielding a median of 7.9 G bases per sample with ≥97 % valid reads and Q30 > 98 %. Adapters and low-quality bases were removed with Cutadapt 1.10; quality was confirmed with FastQC 0.10.1. Clean reads were aligned to the Rattus norvegicus genome (Ensembl v112, Rnor_6.0) using HISAT2 2.0. Transcript assembly and gene-level quantification (FPKM) were performed with StringTie 1.3.4; counts were imported into DESeq2 and edgeR for differential expression. Genes with |log₂ fold-change| ≥ 1 and FDR < 0.05 were considered significant. Downstream GO and KEGG enrichment used clusterProfiler with Benjamini–Hochberg correction.

treatment_protocol: sham and Bleomycin-induced acute lung injury

value: Lung tissue

value: Sprague Dawley

value: Bleomycin


title: VTA_130

status: Public on Apr 01 2026

type: SRA

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 190
Illumina Stranded mRNA Prep

library_source: transcriptomic

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 and Illumina Stranded mRNA Prep

tag: tissue

value: Brain

tag: region

value: VTA

tag: group

value: NP

tag: virus

tag: ruvs k_value

tag: batch


title: skin, biopsy, HDM+SEB, vehicle, animal 51

city: San Diego

first: Joshua

last: Wollam

address: 9761 W. Canyon Ter. Unit 1

institute: Escient Pharmaceuticals

description: Library name: An_51_Skin_20220823_S50

data_processing:
Partek Flow Software, version 7.0
Alignment was performed using STAR with mouse reference genome GRCm39. Ensembl Transcripts release 107 was used for gene feature annotation.
For normalization of transcript counts, CPM (Counts per million of reads) and add 0.0001 normalization method was applied.
Data was filtered by “Lowest average coverage = 1”, before applying differential expression algorithm.
Partek-based GSA was used to determine differentially expressed genes between sample set comparisons.  Different P-value cutoffs were used to filter for significantly differentially expressed genes between different sample set comparisons.
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: Annotated excel of CPM plus 0.0001

molecule: total RNA

source_name: skin

extract_protocol:
RNA was harvested using RNAeasy Mini Plus Kits (Qiagen).  1 ug total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kits (Roche) following manufacturer's protocols.

value: skin

tag: genetic background

tag: genotype

value: MRGPRX2 Knock-in

tag: Sex

value: Male

tag: treatment (topical)

value: HDM+SEB

tag: treatment (oral)

value: vehicle


title: VTA_117

description:
Library name: Sample 186
Illumina Stranded mRNA Prep

value: PP


title: Bleo Female 5 RNA

description: Library name: Sample Female 10

tag: treatment


title: HAESC spheroids maintained in Placental Epithelial Cell Basal Medium_rep2

type: RNA

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from HAESC 3D spheroids maintained in PromoCell Placental Epithelial Cell Basal Medium for 7 days

hyb_protocol: The samples were hybridized on human genome array strips (HG-U219) for 16 hours, followed by washing, staining, and scanning using the GeneAtlas® Hybridization, Wash, and Stain Kit.

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing: The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.5 (in linear space)

label: biotin

organism: Homo sapiens

source_name: HAESCs, Placental Epithelial Cell Basal Medium, 7 days

label_protocol: Total RNA (250 ng) was extracted from three replicates of the control and treated hAESC samples. Amplified and biotin-labeled complementary RNA (cRNA) was generated, fragmented, and labeled

growth_protocol: Human amniotic epithelial cells (hAESCs) were extracted. After incubation, the  cells were detached, centrifuged, and filtered. Cells with >90% viability were cultured a Placental Epithelial Cell Basal Medium. Spheroids were formed by seeding 1 × 10⁶ hAESCs per well in  3D culture plates  and maintained for 24 hours.

extract_protocol: Total RNA was isolated using ISOGEN (Nippon Gene, Tokyo, Japan), according to the manufacturer’s instructions, and evaluated for quantity and quality using the NanoDrop 2000 spectrophotometer (ThermoScientific, Tokyo, Japan).

treatment_protocol: 20 μM of each compound was administered to each sample for a span of seven days with replacing the compound-containing medium every 48 hours. Control samples were maintained in the basal medium, which was also replaced every 48 hours. Duplicates were tested per compound, and eleven total conditions for the ten compounds and control were performed.

tag: cell type

value: Human Amniotic Epithelial Stem Cells


title: skin, biopsy, HDM+SEB, vehicle, animal 50

description: Library name: An_50_Skin_20220823_S49


title: skin, biopsy, HDM+SEB, vehicle, animal 49

description: Library name: An_49_Skin_20220823_S48


title: VTA_125

description:
Library name: Sample 188
Illumina Stranded mRNA Prep


title: HAESC spheroids maintained in Placental Epithelial Cell Basal Medium_rep3


title: HAESC spheroids maintained in Placental Epithelial Cell Basal Medium_rep1


title: VTA_114

description:
Library name: Sample 184
Illumina Stranded mRNA Prep


title: VTA_116

description:
Library name: Sample 185
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, vehicle, animal 12

description: Library name: An_12_Skin_20220823_S12


title: Bleo Female 3 RNA

description: Library name: Sample Female 8


title: Bleo Female 2 RNA

description: Library name: Sample Female 7


title: skin, biopsy, vehicle, vehicle, animal 11

description: Library name: An_11_Skin_20220823_S11


title: skin, biopsy, vehicle, vehicle, animal 10

description: Library name: An_10_Skin_20220823_S10


title: Sham Female 5 RNA

description: Library name: Sample Female 5

value: Sham


title: Bleo Female 1 RNA

description: Library name: Sample Female 6


title: VTA_111

description:
Library name: Sample 183
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with M3CQA_rep3

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Methyl tricaffeoylquinate  for 7 days

source_name: HAESCs, 20 uM  M3CQA, 7 days


title: skin, biopsy, vehicle, vehicle, animal 9

description: Library name: An_9_Skin_20220823_S9


title: VTA_107

description:
Library name: Sample 182
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, vehicle, animal 8

description: Library name: An_8_Skin_20220823_S8


title: OB_23

description:
Library name: Sample 181
Illumina Stranded mRNA Prep

value: OB


title: Sham Female 4 RNA

description: Library name: Sample Female 4


title: skin, biopsy, vehicle, vehicle, animal 7

description: Library name: An_7_Skin_20220823_S7


title: HAESC spheroids treated with M3CQA_rep1


title: HAESC spheroids treated with M4FQA_rep3

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Methyl tetraferuloylquinate  for 7 days

source_name: HAESCs, 20 uM  M4FQA, 7 days


title: Sham Female 3 RNA

description: Library name: Sample Female 3


title: Sham Female 2 RNA

description: Library name: Sample Female 2


title: OB_17

description:
Library name: Sample 179
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with M3CQA_rep2


title: HAESC spheroids treated with M4FQA_rep2


title: skin, biopsy, vehicle, vehicle, animal 6

description: Library name: An_6_Skin_20220823_S6


title: HAESC spheroids treated with M4CQA_rep2

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Methyl tetracaffeoylquinate  for 7 days

source_name: HAESCs, 20 uM  M4CQA, 7 days


title: HAESC spheroids treated with M4FQA_rep1


title: Sham Female 1 RNA

description: Library name: Sample Female 1


title: OB_20

description:
Library name: Sample 180
Illumina Stranded mRNA Prep


title: OB_10

description:
Library name: Sample 178
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with M4CQA_rep3


title: skin, biopsy, vehicle, vehicle, animal 5

description: Library name: An_5_Skin_20220823_S5


title: OB_9

description:
Library name: Sample 177
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, vehicle, animal 4

description: Library name: An_4_Skin_20220823_S4


title: Bleo Male 5 RNA

description: Library name: Sample Male 10


title: OB_8

description:
Library name: Sample 176
Illumina Stranded mRNA Prep


title: Bleo Male 3 RNA

description: Library name: Sample Male 8


title: OB_7

description:
Library name: Sample 175
Illumina Stranded mRNA Prep


title: Bleo Male 4 RNA

description: Library name: Sample Male 9


title: skin, biopsy, vehicle, vehicle, animal 3

description: Library name: An_3_Skin_20220823_S3


title: HAESC spheroids treated with M4CQA_rep1


title: skin, biopsy, vehicle, vehicle, animal 2

description: Library name: An_2_Skin_20220823_S2


title: OB_4

description:
Library name: Sample 174
Illumina Stranded mRNA Prep


title: Bleo Male 2 RNA

description: Library name: Sample Male 7


title: skin, biopsy, vehicle, vehicle, animal 1

description: Library name: An_1_Skin_20220823_S1


title: HAESC spheroids treated with M3DQA_rep3

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Methyl Tri(dimethoxycinnamoyl)quinate for 7 days

source_name: HAESCs, 20 uM  M3DQA, 7 days


title: skin, biopsy, HDM+SEB, animal 28

description: Library name: An_28_Skin_IL4_20220614_S37


title: Bleo Male 1 RNA

description: Library name: Sample Male 6


title: Sham Male 5 RNA

description: Library name: Sample Male 5


title: OB_2

description:
Library name: Sample 173
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, animal 27

description: Library name: An_27_Skin_IL4_20220614_S36


title: OB_1

description:
Library name: Sample 172
Illumina Stranded mRNA Prep


title: Sham Male 4 RNA

description: Library name: Sample Male 4


title: HAESC spheroids treated with 3FQA_rep1

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Triferuloylquinic acid for 7 days

source_name: HAESCs, 20 uM  3FQA, 7 days


title: HAESC spheroids treated with M3DQA_rep1


title: HAESC spheroids treated with M3DQA_rep2


title: HAESC spheroids treated with 4CQA_rep3

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Tetracaffeoylquinic acid for 7 days

source_name: HAESCs, 20 uM  4CQA, 7 days


title: skin, biopsy, HDM+SEB, animal 26

description: Library name: An_26_Skin_IL4_20220614_S35


title: HAESC spheroids treated with 3FQA_rep2


title: HAESC spheroids treated with 3FQA_rep3


title: LC_24

description:
Library name: Sample 171
Illumina Stranded mRNA Prep

value: LC


title: skin, biopsy, HDM+SEB, animal 24

description: Library name: An_24_Skin_IL4_20220614_S34


title: Sham Male 3 RNA

description: Library name: Sample Male 3


title: LC_7

description:
Library name: Sample 168
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, animal 23

description: Library name: An_23_Skin_IL4_20220614_S33


title: Bleo Female 5

description: Library name: Sample Female 10

data_processing:
Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Assembly: Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Supplementary files format and content: CSV file including gene counts for each sample

extract_protocol:
Paired mRNA and miRNA sequencing utilized services offered by LC Sciences (Houston, TX, USA).  Total lung RNA was extracted from the BW-matched cohort only (five sham-male, five sham-female, five bleomycin-male, five bleomycin-female) with TRIzol (Invitrogen) and randomized for downstream processing. Integrity was verified on a Bioanalyzer 2100 (Agilent); every sample showed RIN ≥ 7.0. Two complementary libraries were prepared from the same RNA aliquot for each animal.
miRNA libraries were built from the remaining 1 µg RNA using the TruSeq Small-RNA kit (Illumina). Size-selected libraries (18–26 nt inserts) were single-end-sequenced (50 bp) on an Illumina HiSeq 2500, producing a median 9.2 million raw reads per sample. Filtering (adapter, low-quality, rRNA/tRNA/snoRNA) and mapping to miRBase v22 rat precursors were performed with ACGT101-miR v2023.1, allowing one mismatch in the mature region. Unmapped reads were BLASTed to Rnor_6.0; hairpins that met LC Sciences structural criteria (≥16 stem pairs, ΔG ≤ −15 kcal mol⁻¹, loop ≤ 20 nt) were annotated as novel miRNAs. Normalization used the median-ratio (DESeq) method; edgeR identified differentially expressed miRNAs (p < 0.05, |log₂ FC| ≥ 1). Putative targets were predicted by the intersection of miRanda and TargetScan-Rat


title: LC_16

description:
Library name: Sample 170
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, animal 20

description: Library name: An_20_Skin_IL4_20220614_S31


title: LC_6

description:
Library name: Sample 167
Illumina Stranded mRNA Prep


title: LC_4

description:
Library name: Sample 166
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with 4CQA_rep1


title: Sham Male 1 RNA

description: Library name: Sample Male 1


title: skin, biopsy, HDM+SEB, animal 19

description: Library name: An_19_Skin_IL4_20220614_S30


title: Bleo Female 3

description: Library name: Sample Female 8


title: LC_8

description:
Library name: Sample 169
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with 3DMQA_rep2

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Tri(dimethoxycinnamoyl)quinic acid for 7 days

source_name: HAESCs, 20 uM  3DMQA, 7 days


title: LC_2

description:
Library name: Sample 165
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with 3DMQA_rep3


title: Bleo Female 4

description: Library name: Sample Female 9


title: skin, biopsy, vehicle, animal 16

description: Library name: An_16_Skin_IL4_20220614_S29


title: Bleo Female 2

description: Library name: Sample Female 7


title: LC_1

description:
Library name: Sample 164
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, animal 15

description: Library name: An_15_Skin_IL4_20220614_S28


title: HAESC spheroids treated with 4CQA_rep2

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Tetracaffeoylquinic acid for 7 days


title: skin, biopsy, vehicle, animal 13

description: Library name: An_13_Skin_IL4_20220614_S27


title: DRN_17

description:
Library name: Sample 162
Illumina Stranded mRNA Prep

value: DRN


title: Sham Female 5

description: Library name: Sample Female 5

value: Lung tissue


title: HAESC spheroids treated with 3DMQA_rep1


title: DRN_16

description:
Library name: Sample 161
Illumina Stranded mRNA Prep


title: Sham Female 4

description: Library name: Sample Female 4

value: Sprague Dawley


title: HAESC spheroids treated with 3CUQA_rep2

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Tricoumaroylquinic acid for 7 days

source_name: HAESCs, 20 uM  3CUQA, 7 days


title: Bleo Female 1

description: Library name: Sample Female 6

value: Bleomycin


title: skin, biopsy, vehicle, animal 12

description: Library name: An_12_Skin_IL4_20220614_S26


title: DRN_23

description:
Library name: Sample 163
Illumina Stranded mRNA Prep

value: Brain


title: HAESC spheroids treated with 3CUQA_rep3


title: HAESC spheroids treated with 3CUQA_rep1


title: Sham Female 3

description: Library name: Sample Female 3


title: DRN_14

description:
Library name: Sample 160
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, animal 5

description: Library name: An_5_Skin_IL4_20220614_S24


title: DRN_11

description:
Library name: Sample 159
Illumina Stranded mRNA Prep


title: HAESC spheroids treated with 3CQA_rep3

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Tricaffeoylquinic acid for 7 days

source_name: HAESCs, 20 uM  3CQA, 7 days


title: DRN_10

description:
Library name: Sample 158
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, animal 4

description: Library name: An_4_Skin_IL4_20220614_S23


title: Sham Female 1

description: Library name: Sample Female 1


title: HAESC spheroids treated with 4FQA_rep3

description: Gene expression data from HAESC 3D spheroids treated with 20 uM Tetraferuloylquinic acid for 7 days

source_name: HAESCs, 20 uM  4FQA, 7 days


title: skin, biopsy, vehicle, animal 1

description: Library name: An_1_Skin_IL4_20220614_S22


title: HAESC spheroids treated with 4FQA_rep2


title: HAESC spheroids treated with 4FQA_rep1


title: DRN_7

description:
Library name: Sample 156
Illumina Stranded mRNA Prep


title: skin, biopsy, vehicle, animal 7

description: Library name: An_7_Skin_IL4_20220614_S25


title: Tl1a-tg_3

city: Los Angeles

first: Kathrin

last: Michelsen

address: 110 George Burns Rd

department: Medicine/GI

institute: Cedars-Sinai Medical Center

description:
tg_young_3
Deseq2_results_from_rawcounts

data_processing:
FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases.
After adapter clipping, leading and trailing ambiguous or low-quality bases were removed. The reads were then mapped to the latest UCSC latest transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
DESeq2 was used to find differentially expressed genes

source_name: ileum

extract_protocol:
Ileal tissue sections were fixed in Methacarn and paraffin-embedded. Well-oriented crypts were obtained through Leica LMD7000 Laser Microdissection Cell Capture System. RNA was extracted using Arcturus PicoPure® RNA Isolation Kits (ThermoFisher Scientific, Waltham, MA)
RNA-Seq libraries were created using the Kapa stranded mRNA-seq kit (Roche, Indianapolis, IN).

value: ileum

value: crypts

tag: strain

tag: age

value: 3 months old


title: Bleo Male 3

description: Library name: Sample Male 8


title: Bleo Male 4

description: Library name: Sample Male 9


title: Tl1a-tg_2

description:
tg_young_2
Deseq2_results_from_rawcounts


title: Bleo Male 5

description: Library name: Sample Male 10


title: left ventricle_4086/4087

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

description: Left ventricle tissue of a 2 month old female donor

hyb_protocol: Each Cy3-labeled sample was mixed with an equal amount of Cy5-labeled reference and hybridized to the microarrays

scan_protocol: Hybridized arrays were scanned by fluorescence confocal microscopy (Scan array 4000XL, GSI-Lumonics). Fluorescence signal measurements were obtained separately for each fluorochrome at 10 µm/pixel resolution. Hybridization signal intensities were measured using GenePix Pro 5.0 (Axon).

data_processing: A lowess normalization procedure was applied channel-by-channel. For each microarray, Cy3- and Cy5-signal intensities were separately normalized to a prototype defined as the median profile of all Cy3- or Cy5-signal intensities.

source_name: left ventricle

label_protocol: Cy3- and Cy5 labeled cDNA was prepared using the CyScribe cDNA Post Labeling Kit (Amersham Pharmacia Biotech). Each sample was labeled individually with Cy3. A reference-pool was created from equal quantities of all samples and labeled with Cy5.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and treated with Amplification-grade Dnase I (Invitrogen), followed by purification using the GenElute Mammalian Total RNA Isolation Kit (Sigma)

value: female

value: 2 months

value: left ventricle

source_name: pooled total RNA from all samples


title: Tl1a-tg_1

description:
tg_young_1
Deseq2_results_from_rawcounts


title: DRN_8

description:
Library name: Sample 157
Illumina Stranded mRNA Prep

value: NP


title: Bleo Male 2

description: Library name: Sample Male 7

source_name: Lung tissue


title: HAESC spheroids treated with 3CQA_rep2


title: left ventricle_4062

description: Left ventricle tissue of a 55 year old male donor

value: male

value: 55 years


title: DRN_2

description:
Library name: Sample 155
Illumina Stranded mRNA Prep

source_name: Brain

value: PP


title: DRN_1

description:
Library name: Sample 154
Illumina Stranded mRNA Prep


title: Bleo Male 1

description: Library name: Sample Male 6


title: Nac_24

description:
Library name: Sample 153
Illumina Stranded mRNA Prep

value: NAc


title: HAESC spheroids treated with 3CQA_rep1

value: Human Amniotic Epithelial Stem Cells


title: WT_3

description:
wt_young_3
Deseq2_results_from_rawcounts

value: WT


title: WT_2

description:
wt_young_2
Deseq2_results_from_rawcounts


title: WT_1

description:
wt_young_1
Deseq2_results_from_rawcounts


title: left ventricle_3145

description: Left ventricle tissue of a 39 year old male donor

value: 39 years


title: left ventricle_2035

description: Left ventricle tissue of a 37 year old male donor

value: 37 years


title: Sham Male 3

description: Library name: Sample Male 3

value: Lung tissue

value: Sprague Dawley

value: Sham


title: E32_B

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 53
Illumina

library_source: transcriptomic single cell

data_processing:
We aligned scRNA-seq reads to the GRCh38 human genome reference and quantified them using a Cellranger (version 5.0). DoubletDetection was used to filter out doublets (Gayoso and Shor, 2025) Cells with high mitochondrial read proportion (>20%) and more than 6,000 detected genes were filtered out . Data from each sample was normalized and scaled using the Scanpy (v1.9.8) pp.log1p function and principal components were calculated using the Scanpy (v1.9.8) tl.pca function. Uniform Manifold Approximation and Projection (UMAP) was calculated on the data using the by calculating nearest principal component neighbors with the Scanpy (v1.9.8) pp.neighbors function and embedding using Scanpy (v1.9.8) tl.umap function. Leiden clusters were determined using the Scanpy (v1.9.8) tl.leiden function. Differentially expressed genes determined using Mast, in addition to canonical marker genes, were used to annotate clusters (Finak et al., Genome Bio. 2015). Clusters were initially annotated as epithelial, immune and stromal before each of these populations was subclustered for further annotation. In some subclusterings where batch effects were evident in the clustering, Harmony was employed to generate a batch-corrected dimensionally-reduced space using Scanpy’s (v1.9.8) external.pp.harmony_integrate function.
Assembly: Human GRCh38
Supplementary files format and content: h5ad files

source_name: Primary gastric tumor

extract_protocol:
Tissue samples were collected from the patients who had biopsies one day prior to cycle 1, one day before cycle 2 and 1 day before cycle 7. All tissue samples were from the primary gastric tumor which was endoscopically mapped so the same region of the tumor was sampled at each biopsy.
For tissue samples, if tumor purity was estimated to be more than 40% after pathological reviews, tumor DNA and RNA were extracted by using a QIAamp Mini Kit (Qiagen, Hilden, Germany) according to the manufactures’ instructions for transcriptome sequencing. Concentration, 260/280 and 260/230nm ratios were measured with ND1000 spectrophotometer (Nanodrop Technologies, Thermo-Fisher Scientific) and then DNA/RNA was quantified using a Qubit fluorometer (Life Technologies).

value: Primary gastric tumor


title: Sham Male 4

description: Library name: Sample Male 4


title: Nac_16

description:
Library name: Sample 150
Illumina Stranded mRNA Prep

value: Brain


title: Sham Male 5

description: Library name: Sample Male 5


title: Nac_17

description:
Library name: Sample 151
Illumina Stranded mRNA Prep


title: left ventricle_3091

description: Left ventricle tissue of a 31 year old female donor

value: female

value: 31 years


title: E31_F2

description:
Library name: Sample 52
Illumina


title: Nac_23

description:
Library name: Sample 152
Illumina Stranded mRNA Prep


title: Sham Female 2

description: Library name: Sample Female 2


title: Sham Male 2

description: Library name: Sample Male 2


title: E31_F1

description:
Library name: Sample 51
Illumina


title: E31_B

description:
Library name: Sample 50
Illumina


title: left ventricle_XXXI

description: Left ventricle tissue of a 24 year old female donor

value: 24 years

value: left ventricle


title: Nac_10

description:
Library name: Sample 148
Illumina Stranded mRNA Prep

value: NP


title: left ventricle_3109

description: Left ventricle tissue of a 8 year old male donor

value: male

value: 8 years


title: Nac_7

description:
Library name: Sample 147
Illumina Stranded mRNA Prep

value: NAc


title: left ventricle_3108

description: Left ventricle tissue of a 37 year old female donor


title: left ventricle_VIII

description: Left ventricle tissue of a 52 year old male donor

value: 52 years


title: Sham Male 1

description: Library name: Sample Male 1


title: Nac_11

description:
Library name: Sample 149
Illumina Stranded mRNA Prep

value: PP


title: E30_F2

description:
Library name: Sample 49
Illumina


title: E30_F1

description:
Library name: Sample 48
Illumina


title: Nac_6

description:
Library name: Sample 146
Illumina Stranded mRNA Prep


title: KO-SRT4

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: Johnston Centre for Cancer Research

country: United Kingdom

institute: Queen's University Belfast

description: Library name: KO-SRT4

library_source: genomic

data_processing:
Samples were sequenced using Illumina HiSeq 2500 sequencer [dual-indexed 150–base pair (bp) paired-end reads. FASTQ read were mapped against the mm9 reference genome using Bowtie2. High quality reads were filtered using SAMtools q > 15. Followed by PCR duplicate removal using PicardTools. Next, SAM files were converted to BAM using SAMTools. BAM files were converted to BED files using BEDTools, reads were extended to 200bp and converted to BedGraph using BEDTools. BedGraphs were converted into BigWig files using bedGraphToBigWig for visualization. Peak calling was performed using MACS2 and pvalue e-8. H3K4me3 read counts were computed using BedTools and the MACS2-identified peaks. For library size normalization and differential peak analysis, DESeq2 was performed. Differential peaks between conditions were defined using the following criteria: fold change > 1.5, p-value < 0.05 and minimum normalized reads per peak > 40.
Assembly: mm9
Supplementary files format and content: Count_table_H3K4me3
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Hippocampus

extract_protocol:
Samples were fixed with 1% paraformaldehyde followed by 0.125M glycine to stop crosslinking. Samples were lysed in freshly made sonication buffer (20mM Hepes, 1% SDS, 0.25 protease inhibitor cocktail (Sigma Aldrich)) and sonicated using the Bioraptor Pico (Diagenode). Fragmented chromatin was precleared using bovine serum albumin (BSA)- blocked protein A/G beads (Invitrogen) and 1.7ug of H3K4me3 antibody (Diagenode) was added. Following overnight incubation, immune complexes were captured by incubation with BSA-blocked protein A/G beads for 1 hour at 4C on a rotating wheel. Beads were washed with wash buffer 1 (2mM EDTA, 20mM tris (pH8), 150mM NaCl, 1 Triton X- 100, and 0.1% SDS), buffer 2 (2 mM EDTA, 20 mM tris (pH 8), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, and 500 mM NaCl), and buffer 3 (1 mM EDTA and 10 mM tris (pH 8)) for 5 mins at 4C on a rotating wheel. Samples were eluted for 20 mins at room temperature in 0.1 M NaHCO3 and 1% SDS. Eluted chromatin was de-crosslinked overnight at 65C using 10mg/ml proteinase K and 5M NaCL. De-crosslinked DNA was purified using MiniElute PCR Purification Kit (QIAGEN)
library preparation was performed using the KAPA HyperPrep kit (Roche) according to manufacturer’s instructions.

treatment_protocol: Our experiments were conducted using C57BL/6 mice with a targeted knockout of the Mtr gene (Mtr- cKO) specifically in the central nervous system. The knockout was achieved using the Cre/Lox system, targeting exons 4 and 5, essential for MS activity. Female mice carried "floxed Mtr exons," while male mice expressed the Cre recombinase under the control of the Thy-1.2 promoter. Recombination efficiency was validated using qPCR on floxed exons, and MS protein loss was confirmed by Western blot in brain tissues.   The treatment protocol with SRT2104 or Vehicle (DMSO-PEG) began on 28 day 15 (D15) for the treated group until day 36 (D36), continuing for a total of 9 administrations at a frequency of three gavages per week, at a dosage of 50 mg/kg. SRT2104 was diluted using a stock solution in 20% DMSO-PEG

value: Hippocampus


title: KO-SRT3

description: Library name: KO-SRT3


title: KO-SRT2

description: Library name: KO-SRT2


title: Nac_4

description:
Library name: Sample 145
Illumina Stranded mRNA Prep


title: E30_B

description:
Library name: Sample 47
Illumina


title: Nac_2

description:
Library name: Sample 144
Illumina Stranded mRNA Prep


title: KO-SRT1

description: Library name: KO-SRT1


title: E29_F1

description:
Library name: Sample 45
Illumina


title: KO-2

description: Library name: KO-2

value: not-treated


title: Nac_1

description:
Library name: Sample 143
Illumina Stranded mRNA Prep


title: E29_F2

description:
Library name: Sample 46
Illumina


title: KO-1

description: Library name: KO-1


title: left ventricle_IV

description: Left ventricle tissue of a 49 year old male donor

value: 49 years


title: left ventricle_3164

description: Left ventricle tissue of a 61 year old male donor

value: 61 years


title: Sham Male 2 RNA

description: Library name: Sample Male 2

value: Lung tissue

value: Sprague Dawley

value: Sham


title: WT-VEH4

description: Library name: WT-VEH4

value: MLML-WT

value: Vehicle


title: mPOA_22

description:
Library name: Sample 141
Illumina Stranded mRNA Prep

value: Brain

value: mPOA


title: E29_B

description:
Library name: Sample 44
Illumina

value: Primary gastric tumor


title: left ventricle_2054

description: Left ventricle tissue of a 39 year old male donor

value: male

value: 39 years

value: left ventricle


title: left ventricle_3149

description: Left ventricle tissue of a 56 year old male donor

value: 56 years


title: left ventricle_XVII

description: Left ventricle tissue of a 52 year old female donor

value: female

value: 52 years


title: E27_F2

description:
Library name: Sample 43
Illumina


title: left ventricle_III

description: Left ventricle tissue of a 48 year old male donor

value: 48 years


title: mPOA_23

description:
Library name: Sample 142
Illumina Stranded mRNA Prep

value: NP


title: E27_F1

description:
Library name: Sample 42
Illumina


title: mPOA_20

description:
Library name: Sample 140
Illumina Stranded mRNA Prep

value: PP


title: WT-VEH3

description: Library name: WT-VEH3

value: Hippocampus


title: WT-VEH2

description: Library name: WT-VEH2


title: mPOA_17

description:
Library name: Sample 139
Illumina Stranded mRNA Prep


title: E27_B

description:
Library name: Sample 41
Illumina


title: left ventricle_5054

description: Left ventricle tissue of a 27 year old male donor

value: 27 years


title: E26_F2

description:
Library name: Sample 40
Illumina


title: left ventricle_3064

description: Left ventricle tissue of a 54 year old male donor

value: 54 years


title: E26_F1

description:
Library name: Sample 39
Illumina


title: WT-VEH1

description: Library name: WT-VEH1

value: MLML-WT


title: WT-SRT3

description: Library name: WT-SRT3


title: mPOA_7

description:
Library name: Sample 136
Illumina Stranded mRNA Prep


title: mPOA_9

description:
Library name: Sample 137
Illumina Stranded mRNA Prep


title: WT-SRT2

description: Library name: WT-SRT2


title: E26_B

description:
Library name: Sample 38
Illumina


title: WT-SRT1

description: Library name: WT-SRT1


title: mPOA_10

description:
Library name: Sample 138
Illumina Stranded mRNA Prep


title: mPOA_6

description:
Library name: Sample 135
Illumina Stranded mRNA Prep


title: left ventricle_XXIV


title: JRH_6_S6

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

description: Library name: KO_UVB_JRH_6_S6

data_processing:
Bioinformatics processing and data interpretation were carried out in consultation with the Bioinformatics Core at the NCSU Center for Human Health and the Environment.  The quality of the sequenced data was evaluated using the fastqc application and 12 poor quality bases were trimmed from the 5’-end. The remaining good quality reads were aligned to the Mouse reference genome (mm39) downloaded from the Ensembl database using the STAR aligner (41).  Per-gene counts of uniquely mapped reads for each replicate were calculated using the htseq count script from the HTSeq Python package. The count matrix was imported to the R statistical computing environment for further analysis. Initially, genes that had no count in most replicate samples were discarded. The remaining count data were normalized for sequencing depth and distortion, and the dispersion was estimated using the DESeq2 Bioconductor package in the R statistical computing environment (42). We fitted a leaner model using treatment levels, and differentially expressed genes were identified after applying multiple testing corrections using the Benjamini-Hochberg procedure (43). The final significant genes were generated using an adj p-value<0.05.
Assembly: GRCm39
Supplementary files format and content: resultDATA_COUNT_countcombined_formated.csv

source_name: primary keratinocyte

growth_protocol: Mouse primary epidermis was isolated from 1-2 day old wild type and C/EBPβ knockout C57BL/6J:129 hybrid mouse skin by flotation in Hanks’ Balanced Salt Solution (H9394, Sigma-Aldrich) and 0.25% trypsin (15090-046, Life Technologies) (38, 40). Isolated keratinocytes were plated at 1 x 106 cells per 35 mm cell culture dish in calcium-free EMEM (06-174 G, Lonza), 10% Chelex 100-treated FBS (F2442, Sigma-Aldrich), 10 ng/mL human EGF (PHG0311, Life Technologies), 1% antibiotic/antimycotic (15240, Life Technologies), and 0.05 mM CaCl2 for 24 hours. Cells were then washed in PBS and cultured in Keratinocyte serum free medium (SFM, 10725-018, Life Technologies) containing 5 ng/mL human EGF and 50 ng/mL bovine pituitary extract (37000-015, Life Technologies), 10 mg/mL gentamycin (15710-064, Life Technologies), and 0.05 mM CaCl2. Media was replaced every other day; treatment began 5 days post-plating.

extract_protocol:
Total RNA was isolated from wild type and C/EBPβ -/- B6J129 primary keratinocytes collected in QIAzol lysis reagent (79306, Qiagen). Following chloroform extraction, the RNA Clean and Concentrator-25 kit (R1018, Zymo Research) was used following the manufacturer’s protocol for total RNA clean-up, DNase I treatment (E1010, Zymo Research) was performed during clean-up.
Illumina RNA library preparation and sequencing were performed at the NC State Genomic Sciences Laboratory (Raleigh, NC). Total RNA was assessed for quality, concentration, and integrity using RIN > 9) an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, Cary, NC). Following Illumina RNA library preperation sequencing was performed using Illumina NovaSeq generating 100M 150bp paired end reads per sample.

treatment_protocol: Cells were exposed to UVB using an EB 280C 312 nm UVB lamp (Spectronics). The light intensity was measured with the IL-1700 Research Radiometer (International Light) equipped with an SED 240 sensor. The UVB lamp was positioned above the cells, cell culture medium was removed, cells were washed in PBS, and cells were irradiated in PBS for the amount of time corresponding to the indicated UVB dose

value: primary keratinocyte

value: CEBPB KO

value: 10 mJ/cm2 UVB light

tag: time

value: 8h post exposure


title: mPOA_2

description:
Library name: Sample 134
Illumina Stranded mRNA Prep

value: Brain

value: mPOA


title: E25_F1

description:
Library name: Sample 36
Illumina

value: Primary gastric tumor


title: E25_F2

description:
Library name: Sample 37
Illumina


title: JRH_5_S5

description: Library name: KO_UVB_JRH_5_S5


title: left ventricle_XXVII

description: Left ventricle tissue of a 49 year old female donor

value: 49 years

value: left ventricle


title: left ventricle_XXVIII

description: Left ventricle tissue of a 65 year old female donor

value: female

value: 65 years


title: mPOA_1

description:
Library name: Sample 133
Illumina Stranded mRNA Prep


title: E25_B

description:
Library name: Sample 35
Illumina


title: JRH_4_S4

description: Library name: KO_UVB_JRH_4_S4


title: left ventricle_XII

description: Left ventricle tissue of a 50 year old male donor

value: male

value: 50 years


title: left ventricle_XIX

value: 52 years


title: left ventricle_XXIII

description: Left ventricle tissue of a 60 year old female donor

value: 60 years


title: BLA_24

description:
Library name: Sample 132
Illumina Stranded mRNA Prep

value: BLA

value: NP


title: E24_F2

description:
Library name: Sample 34
Illumina


title: JRH_3_S3

description: Library name: CNT_UVB_JRH_3_S3

value: primary keratinocyte

value: wt


title: BLA_23

description:
Library name: Sample 131
Illumina Stranded mRNA Prep


title: E24_F1

description:
Library name: Sample 33
Illumina


title: JRH_2_S2

description: Library name: CNT_UVB_JRH_2_S2

value: 10 mJ/cm2 UVB light


title: BLA_17

description:
Library name: Sample 130
Illumina Stranded mRNA Prep

value: PP


title: E23_F2

description:
Library name: Sample 31
Illumina


title: left ventricle_XX

description: Left ventricle tissue of a 53 year old male donor

value: 53 years


title: E24_B

description:
Library name: Sample 32
Illumina


title: left ventricle_XXVI

description: Left ventricle tissue of a 52 year old male donor


title: BLA_11

description:
Library name: Sample 128
Illumina Stranded mRNA Prep

value: Brain


title: JRH_1_S1

description: Library name: CNT_UVB_JRH_1_S1

value: 8h post exposure


title: BLA_16

description:
Library name: Sample 129
Illumina Stranded mRNA Prep


title: left ventricle_XVI

description: Left ventricle tissue of a 50 year old female donor


title: E23_F1

description:
Library name: Sample 30
Illumina

value: Primary gastric tumor


title: left ventricle_3061

description: Left ventricle tissue of a 34 year old female donor

value: 34 years

value: left ventricle


title: left ventricle_4095

description: Left ventricle tissue of a 48 year old female donor

value: female

value: 48 years


title: E23_B

description:
Library name: Sample 29
Illumina


title: E22_F2

description:
Library name: Sample 28
Illumina


title: ductal_24D

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

data_processing:
The quality of the sequenced reads was assessed with FastQC v0.11.8 and QoRTs v1.3.6.
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.9a.
. Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M25).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: Adult Pancreas

extract_protocol:
tdTomato+ acinar cells were FACS sorted into 1.5 mL Eppendorf tubes containing Trizol. Total RNA was purified using a standard phenol-chloroform extraction method.
Sequencing libraries were constructed using Illumina TruSeq Library Prep Kit (Non-Stranded and Poly-A selection) and sequenced on either Illumina HiSeq 2500 or NovaSeq 6000 (2x50 cycles paired-end run)

value: Adult Pancreas

value: KrasWT


title: BLA_10

description:
Library name: Sample 127
Illumina Stranded mRNA Prep


title: E22_F1

description:
Library name: Sample 27
Illumina


title: BLA_7

description:
Library name: Sample 125
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, animal 21

description: Library name: An_21_Skin_IL4_20220614_S32

source_name: skin

value: skin

value: MRGPRX2 Knock-in

value: Male

value: HDM+SEB


title: BLA_8

description:
Library name: Sample 126
Illumina Stranded mRNA Prep

value: BLA

value: NP


title: ductal1

data_processing:
Reads were processed with the ENCODE ATAC-seq pipeline v2.2.2 (https://github.com/ENCODE-DCC/atac-seq-pipeline/) and were aligned to the human genome build mm10
Briefly, adapters were trimmed with cutadapt v2.5 and aligned to Encode mm10 with Bowtie2 v2.3.4.3.
Duplicate reads and reads mapping to the mitochondrial chromosome were removed.
Signal files and peak calls were generated using MACS2 v2.2.4.
Peaks overlapping ENCODE blacklisted regions (ENCFF547MET.bed) were excluded.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
tdTomato+ acinar cells, tdTomato+ progenitor cells or CD133+ CD49f+ ductal cells were FACS sorted as applicable. Standard ATAC-seq protocol was followed (Buenrostro et al. 2013).
Illumina Nextera kit


title: BLA_6

description:
Library name: Sample 124
Illumina Stranded mRNA Prep


title: BLA_4

description:
Library name: Sample 123
Illumina Stranded mRNA Prep

value: PP


title: E21_F2

description:
Library name: Sample 25
Illumina


title: ductal2


title: AAV6-CMV-shThbs2-2

city: Beijing

first: Wei

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

country: China

institute: Capital Medical University

data_processing:
Illumina HiSeq2500: Clean reads were obtained by Perl script.
Illumina HiSeq2500: Clean reads were mapped to the mouse reference genome GRCm38 using Bowtie2 and HISAT algorithms.
Illumina HiSeq2500: Gene expression levels were measured using FPKM values by Cufflinks software.
DNBSEQ-T7: SOAPnuke (V2.1.0) was used to filter the sequencing data.
DNBSEQ-T7: HISAT2 (V2.1.0) was used to compare clean reads with the reference genome, and Bowtie2 (V2.3.5) was used to align the quality controlled sequence to the reference transcription sequence.
DNBSEQ-T7: FPKM conversion was performed as reported by Nat Biotechnol, 2010,28(5):511-515.
Assembly: GRCm38
Supplementary files format and content: Excel file includes FPKM values for AAV-CMV-shThbs2-NC mice.xlsx
Supplementary files format and content: Excel file includes FPKM values for AAV-αSMA-shThbs2-NC mice.xlsx

source_name: liver

extract_protocol:
Illumina HiSeq2500: Poly(A) mRNAs were enriched using magnetic oligo (dT) beads (Invitrogen, Carlsbad, CA), followed by RNA-seq library preparation using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s instructions.
DNBSEQ-T7: Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis and purified using AMPure XP Beads. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end cDNA repair. The cDNA fragments obtained from previous steps were amplified by PCR, and products were purified by Ampure XP Bead, get the final library.

value: liver


title: left ventricle_I

description: Left ventricle tissue of a 49 year old female donor

value: 49 years


title: ductal_23D


title: left ventricle_33830

description: Left ventricle tissue of a 65 year old female donor

value: 65 years


title: left ventricle_VI

description: Left ventricle tissue of a 49 year old male donor

value: male


title: ductal_1


title: BLA_2

description:
Library name: Sample 122
Illumina Stranded mRNA Prep

value: Brain


title: E22_B

description:
Library name: Sample 26
Illumina

value: Primary gastric tumor


title: E21_F1

description:
Library name: Sample 24
Illumina


title: left ventricle_4152

description: Left ventricle tissue of a 4 year old male donor

value: 4 years

value: left ventricle


title: left ventricle_2158

description: Left ventricle tissue of a 17 year old male donor

value: 17 years


title: left ventricle_3131

description: Left ventricle tissue of a 51 year old female donor

value: female

value: 51 years


title: AAV6-CMV-shThbs2-1

description: Excel file includes FPKM values for AAV-CMV-shThbs2-NC mice.xlsx


title: AAV6-CMV-NC-2


title: BLA_1

description:
Library name: Sample 121
Illumina Stranded mRNA Prep


title: E21_B

description:
Library name: Sample 23
Illumina


title: AAV6-CMV-NC-1


title: E20_F2

description:
Library name: Sample 22
Illumina


title: PVN_9

description:
Library name: Sample 120
Illumina Stranded mRNA Prep

value: PVN


title: E20_F1

description:
Library name: Sample 21
Illumina


title: left ventricle_3122

description: Left ventricle tissue of a 44 year old male donor

value: 44 years


title: left ventricle_5033

description: Left ventricle tissue of a 48 year old female donor

value: 48 years


title: mTSC_siMETTL3 RNA-seq rep 3

city: Shanghai

first: Junpeng

last: Dong

address: 145 Guangyuan Rd, Xuhui District

department: School of Medicine, Shanghai Jiao Tong University

institute: The International Peace Maternity and Child Health Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads containing poly-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to mm10 using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
DESeq2 was used to count reads for each gene and to perform differential expression analysis.
Assembly: mm10
Supplementary files format and content: FPKMs

source_name: mTSC

growth_protocol: Mouse trophoblast stem cells (mTSCs)  were cultured in stem cell medium (SCM): 30% standard medium (Roswell Park Memorial Institute (RPMI) 1640 supplemented with 20% fetal bovine serum, 100 mM 2-mercaptoethanol, 2 mM L-glutamine, 2 mM sodium pyruvate), 25 ng/ml FGF4, 1 mg/ml heparin, and 70% mouse embryonic fibroblast‑feeder condition medium (FCM). Differentiation medium (DM) consisted of unconditioned SCM without FGF4 and heparin.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyze. RNA libraries were prepared for sequencing using standard Illumina protocols.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit according to the manufacturer’ s instructions.

treatment_protocol: The transfection reagent was combined with OptiMEM media. Transfection was performed using Lipofectamine RNAiMAX Transfection Reagent for siRNAs in  stem cell medium.

tag: cell line

value: mTSC

value: trophoblast stem cells

value: METTL3 knockdown


title: mTSC_siMETTL3 RNA-seq rep 1


title: mTSC_siMETTL3 RNA-seq rep 2


title: PVN_4

description:
Library name: Sample 117
Illumina Stranded mRNA Prep

tag: tissue

value: PP


title: PVN_7

description:
Library name: Sample 118
Illumina Stranded mRNA Prep

tag: region

value: NP


title: PVN_8

description:
Library name: Sample 119
Illumina Stranded mRNA Prep

tag: group


title: mTSC_siNC RNA-seq rep 3

value: WT


title: left ventricle_2152

description: Left ventricle tissue of a 23 year old male donor

value: male

value: 23 years


title: E19_F1

description:
Library name: Sample 19
Illumina

value: Primary gastric tumor


title: PVN_24

description:
Library name: Sample 116
Illumina Stranded mRNA Prep

value: Brain

tag: virus


title: E20_B

description:
Library name: Sample 20
Illumina


title: mTSC_siNC RNA-seq rep 2


title: E18_F2

description:
Library name: Sample 17
Illumina


title: left ventricle_4015

description: Left ventricle tissue of a 19 year old male donor

value: 19 years

value: left ventricle


title: PVN_23

description:
Library name: Sample 115
Illumina Stranded mRNA Prep

tag: ruvs k_value


title: left ventricle_2089

description: Left ventricle tissue of a 36 year old female donor

value: female

value: 36 years


title: PVN_20

description:
Library name: Sample 114
Illumina Stranded mRNA Prep

value: PVN

tag: batch


title: E18_F1

description:
Library name: Sample 16
Illumina


title: D2.OR shSLX4IP Biological Rep 3

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd.

department: Case Comprehensive Cancer Center

institute: Case Western Reserve University

data_processing:
Read quality filtering and adapter trimming were carried out using fastp (v0.19.5; qualified quality phred = 20, overrepresented sequence analysis enabled, all other parameters default)
Remaining reads were aligned to the most recent Mus musculus genome assembly (GRCm38/mm10) using STAR (v2.7.7)
Transcript-level counts were subsequently tabulated using StringTie (v2.1.7; all parameters default except --rf -e)
Differential expression analysis was performed using DESeq2 (v1.22.1; prepDE.py -length=100 to generate read counts from coverage values estimated by StringTie)
Assembly: mm10
Supplementary files format and content: matrix table (as a tab-delimited text file) that includes normalized count values per gene (with Ensembl IDs) for each sample

growth_protocol: Longitudinal 3D-outgrowth was carried out by plating cells (31,500 cells/cm2) atop solidified Cultrex cushion (300 µL/well; 12-well plate) and grown in DMEM supplemented with 10% fetal bovine serum and 5% Cultrex for 7 days.

extract_protocol:
Cells were non-enzymatically isolated using Cultrex 3D-Culture Cell Harvesting Kit (Trevigen), and RNA was isolated using an RNeasy Mini RNA Extraction Kit (QIAGEN) according to the manufacturer's instructions.
1 μg total RNA was used to construct sequencing libraries using the Tru-Seq Stranded mRNA library prep kit (Illumina)

treatment_protocol: D2.OR cells were transduced with lentiviral vectors containing either a scrambled (i.e., non-targeting) shRNA (Scram) or an shRNA targeting SLX4IP (shSLX4IP). Successfully transduced cells were selected with puromycin.

value: Murine breast cancer


title: E19_B

description:
Library name: Sample 18
Illumina


title: left ventricle_2073

description: Left ventricle tissue of a 55 year old female donor

value: 55 years


title: E18_B

description:
Library name: Sample 15
Illumina


title: D2.OR shSLX4IP Biological Rep 2


title: E17_F2

description:
Library name: Sample 14
Illumina


title: mTSC_siNC RNA-seq rep 1

value: mTSC


title: left ventricle_5048

description: Left ventricle tissue of a 25 year old female donor

value: 25 years


title: left ventricle_5003

description: Left ventricle tissue of a 37 year old male donor

value: 37 years


title: D2.OR shSLX4IP Biological Rep 1


title: PVN_17

description:
Library name: Sample 112
Illumina Stranded mRNA Prep

value: PP


title: PVN_16

description:
Library name: Sample 111
Illumina Stranded mRNA Prep


title: E17_F1

description:
Library name: Sample 13
Illumina


title: D2.OR Scram Biological Rep 3

value: shScram


title: left ventricle_3069

description: Left ventricle tissue of a 40 year old female donor

value: 40 years


title: PVN_10

description:
Library name: Sample 110
Illumina Stranded mRNA Prep

value: NP


title: PVN_2

description:
Library name: Sample 113
Illumina Stranded mRNA Prep


title: D2.OR Scram Biological Rep 2


title: PVN_1

description:
Library name: Sample 109
Illumina Stranded mRNA Prep


title: E16_F2

description:
Library name: Sample 11
Illumina


title: left ventricle_2090

description: Left ventricle tissue of an 8 year old male donor

value: male

value: 8 years


title: E17_B

description:
Library name: Sample 12
Illumina

value: Primary gastric tumor


title: left ventricle_5041

description: Left ventricle tissue of a 42 year old female donor

value: 42 years


title: D2.OR Scram Biological Rep 1


title: left ventricle_4049

description: Left ventricle tissue of a 65 year old female donor

value: 65 years

value: left ventricle


title: left ventricle_4013

description: Left ventricle tissue of a 23 year old male donor

value: 23 years


title: E16_F1

description:
Library name: Sample 10
Illumina


title: mPFC_9

description:
Library name: Sample 107
Illumina Stranded mRNA Prep

value: Brain

value: mPFC


title: E15_F2

description:
Library name: Sample 8
Illumina


title: vHipp_9

description:
Library name: Sample 108
Illumina Stranded mRNA Prep

value: vHpc


title: E16_B

description:
Library name: Sample 9
Illumina


title: vHipp_8

description:
Library name: Sample 105
Illumina Stranded mRNA Prep


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 2

first: Wen-Wei

last: Liang

address: 101 Avenue of the Americas

institute: New York Genome Center

description: Library name: THP1_Day07_R2

data_processing:
Quality of the raw fastq files was assessed using MultiQC .We processed reads from pooled Cas13d screens following established pipelines. In brief, reads were de-multiplexed based on Illumina i7 barcodes and custom i5 barcodes. We trimmed reads to the expected gRNA length by identifying known anchor sequences relative to the guide sequence. We did this using Cutadapt (v.1.13) with the following parameters: -g CTGGTCGGGGTTTGAAAC -e 0.2 -O 5 --discard-untrimmed and -a TTTTTGAATTCGCTAGCT -e 0.1 -O 5 --minimum-length 15 --discard-untrimmed. We aligned processed reads to the designed crRNA reference using bowtie (v.1.1.2) allowing for up to three mismatches (parameters: -v 1 -m 3 –best -q). The raw gRNA counts were normalized using median-of-ratios (geometric mean), similar to DESeq2, and batch correction was applied using combat from the SVA R package (v.3.34.0). We removed nonreproducible technical outliers by pair-wise linear regression for each sample, collecting residuals, and taking the median value for each gRNA across biological replicates.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for each sample.

source_name: peripheral blood

growth_protocol: HEK293FT and MDA-MB-231 cells were cultured in D10 medium:  Dulbecco’s Modified Eagle Medium with high glucose and stabilized L-glutamine (Cytiva SH30022.01) supplemented with 10% Serum Plus II (Sigma-Aldrich 14009C) and 5 µg/ml blasticidin. HAP1 and K562 cells were cultured in I10 medium: Iscove’s Modified Dulbecco’s Medium with L-glutamine (Cytiva SH30228.FS) supplemented with 10% Serum Plus II and 5 µg/ml blasticidin. THP-1 cells were cultured in R10 medium: HyClone RPMI 1640 Medium (Cytiva SH30255.FS) supplemented with 10% Serum Plus II and 5 µg/ml blasticidin. All cells were incubated at 37 °C with 5% carbon dioxide.

extract_protocol:
Genomic DNA was isolated from cell pellets via a modified salting out procedure. For that, 12 ml of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) and 60 µl of 20 mg/ml Proteinase K (QIAGEN 19131) were added to 80 million cells and incubated at 55 °C overnight. The next day, 6 µl of 100 mg/ml RNase A (A.G. Scientific R-2000) was added to the lysed sample, which was then inverted 25 times and incubated at 37 °C for 30 min. Samples were cooled on ice before addition of 4 ml of pre-chilled 7.5M ammonium acetate (Sigma A1542) to precipitate proteins. After adding ammonium acetate, the samples were vortexed and centrifuged at 4,000 × g for 10 minutes. After the spin, 12 ml isopropanol was added to the collected supernatant, inverted 50 times and centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, 12 ml of freshly prepared 70% ethanol was added, the tube was inverted 10 times, and then centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, and remaining ethanol was removed. After air drying for 30 minutes, 500 µl of 0.2× TE buffer (Sigma 93283) was added, the tube was incubated at 65 °C for 1 hour and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly. The gDNA concentration was measured using a Nanodrop (Thermo). We excluded one biological replicate (K562 day 0) due to low recovery after gDNA extraction.
We amplified gRNA cassettes and prepared them for sequencing using a two-step PCR. PCR1 was performed to amplify a region containing the crRNA cassette in the lentiviral genomic integrant using TaqB polymerase (Enzymatics P7250L). We performed 70 PCR1 reactions for each gDNA sample using 5 μg gDNA per 100 μl PCR1 reaction as follows: 94 °C for 3 min, 20× (94 °C for 10 s, 55 °C for 30 s, 68 °C for 45 s), 68 °C for 5 min. We then combined PCR1 products for the same sample together before PCR2, which was done to incorporate Illumina adaptors using Q5 High-Fidelity DNA Polymerase (NEB M0491). We performed 10 PCR2 reactions for each sample using 10 μl unpurified PCR1 product per 50 μl reaction as follows: 98 °C for 30 s, 6-10× (98 °C for 10 s, 63 °C for 30 s, 72 °C for 45 s), 72 °C for 5 min. The resulting amplicons from PCR2 (~270 bp) were pooled and then purified using double-sided SPRI beads clean up (Beckman B23317) or gel extracted using a QiaQuick Gel Extraction kit (Qiagen 28704). For double-sided SPRI clean up, the amplicon was first incubated with 0.6× SPRI to remove larger fragments (>350 bp bound to beads and removed), the supernatant was then transferred and further incubated with 0.8× SPRI beads (<200 bp in supernatant and removed).

treatment_protocol: Cas13d-expressing cells were transduced with the library lentivirus through separate infection replicates by spinfection at 1000 rpm for 1 hour at 37 °C, followed by overnight incubation. After 24 hours, new media with 1 μg/ml puromycin (Invivogen ant-pr-1) was added. Puromycin selection was completed within 48 hours for all cell lines, except for THP1. Because THP1 required an extended selection time, we maintained it in R10 but with 10% Tet-system approved serum (Gibco A4736201) substituted for Serum Plus II and with 1 μg/ml puromycin. THP1 cells took approximately two weeks for full selection. Following puromycin selection, RfxCas13d expression was induced by replenishing the growth medium containing 1 μg/ml puromycin, 5 μg/ml blasticidin and 1 μg/ml doxycycline. Cells were passaged every 2 to 4 days and split as needed, ensuring a guide representation of >1,000×. Samples with a guide abundance of 1,000-fold were harvested at 0, 7, and 14 days post-Cas13d induction.

value: peripheral blood

value: cancer cells

value: lncRNAs knockdown

value: doxycycline induction


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 1

description: Library name: THP1_Day07_R1


title: dHipp_9

description:
Library name: Sample 106
Illumina Stranded mRNA Prep

value: dHpc


title: E15_F1

description:
Library name: Sample 7
Illumina


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 1

description: Library name: THP1_Day14_R1


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 2

description: Library name: THP1_Day14_R2


title: mPFC_8

description:
Library name: Sample 104
Illumina Stranded mRNA Prep


title: E15_B

description:
Library name: Sample 6
Illumina


title: left ventricle_4021

description: Left ventricle tissue of a 53 year old female donor

value: female

value: 53 years


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, before doxycycline induction, replicate 2

description: Library name: THP1_Day00_R2


title: dHipp_8

description:
Library name: Sample 103
Illumina Stranded mRNA Prep


title: left ventricle_3168

description: Left ventricle tissue of a 19 year old female donor

value: 19 years


title: left ventricle_3135

description: Left ventricle tissue of a 26 year old male donor

value: male

value: 26 years


title: vHipp_71

description:
Library name: Sample 102
Illumina Stranded mRNA Prep


title: left ventricle_3141

description: Left ventricle tissue of a 52 year old male donor

value: 52 years


title: mPFC_71

description:
Library name: Sample 101
Illumina Stranded mRNA Prep


title: E14_F1

description:
Library name: Sample 5
Illumina

value: Primary gastric tumor


title: left ventricle_3160

description: Left ventricle tissue of a 21 year old male donor

value: 21 years

value: left ventricle


title: E12_F2

description:
Library name: Sample 3
Illumina


title: left ventricle_3056

description: Left ventricle tissue of a 45 year old female donor

value: 45 years


title: E12_F1

description:
Library name: Sample 2
Illumina


title: RfxCas13d expressing THP1 cells, pooled lncRNA library, before doxycycline induction, replicate 1

description: Library name: THP1_Day00_R1


title: dHipp_71

description:
Library name: Sample 100
Illumina Stranded mRNA Prep

value: Brain


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 2

description: Library name: MDA-MB-231_Day07_R2

source_name: breast

value: breast


title: vHipp_7

description:
Library name: Sample 99
Illumina Stranded mRNA Prep

value: vHpc


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 1

description: Library name: MDA-MB-231_Day14_R1

value: cancer cells


title: E12_B

description:
Library name: Sample 1
Illumina


title: left ventricle_4084

description: Left ventricle tissue of a 50 year old male donor

value: 50 years


title: left ventricle_4103

description: Left ventricle tissue of a 47 year old female donor

value: 47 years


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 2

description: Library name: MDA-MB-231_Day14_R2

value: lncRNAs knockdown

value: doxycycline induction


title: E14_B

description:
Library name: Sample 4
Illumina


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 1

description: Library name: MDA-MB-231_Day07_R1


title: left ventricle_3165

description: Left ventricle tissue of a 39 year old female donor

value: female

value: 39 years


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, before doxycycline induction, replicate 2

description: Library name: MDA-MB-231_Day00_R2


title: mPFC_7

description:
Library name: Sample 98
Illumina Stranded mRNA Prep

value: mPFC


title: EC_4

city: Belgrade

first: Mila

last: Ljujic

address: Vojvode Stepe 444a

department: Human Molecular Genetics and Genomics

country: Serbia

institute: IMGGE

description: Library name: T4

data_processing:
Preprocessing and quality control of raw data (fastq files) were performed by fastp v_0.23.4 with default parameters.
Filtered reads were mapped to the GRCh38.p12 human reference genome utilizing STAR v_2.7.11b.
Gene expression quantification was accomplished using featuresCounts tool from subread v2.0.4 with exon feature type specified and GTF annotation file format (Homo_sapiens.GRCh38.111.chr.gtf). Multi-mapping and multi-overlapping reads were ignored.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung; Bronchus

growth_protocol: BEAS-2B cells were cultured in Dulbecco's Modified Eagle Medium (Sigma) supplemented with 10% (v/v) Fetal Bovine Serum (Gibco) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit (Qiagen) according to the manufacturer’s recommended guidelines
RNA Library was constructed according to the following workflow: messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: BEAS-2B cells were exposed to e-cigarette aerosol condensate generated from carrier liquid (propylene glycol and vegetable glycerine – PG/VG) and from e-cigarette (18mg/ml nicotine and Virginia tobacco flavor – EC) for 24h. Untreated cells were used as control.

value: Lung; Bronchus

value: epithelial cell

value: treated with electronic cigarette vapour


title: dHipp_7

description:
Library name: Sample 97
Illumina Stranded mRNA Prep

value: dHpc


title: left atrium_3099

description: Left atrium tissue of a 46 year old female donor

source_name: left atrium

value: 46 years

value: left atrium


title: RfxCas13d expressing MDA-MB-231 cells, pooled lncRNA library, before doxycycline induction, replicate 1

description: Library name: MDA-MB-231_Day00_R1


title: EC_3

description: Library name: T3


title: vHipp_66

description:
Library name: Sample 96
Illumina Stranded mRNA Prep

value: Brain


title: left atrium_4152

description: Left atrium tissue of a 4 year old male donor

value: male

value: 4 years


title: RfxCas13d expressing K562 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 2

description: Library name: K562_Day14_R2

source_name: bone marrow

value: bone marrow

value: cancer cells


title: RfxCas13d expressing K562 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 1

description: Library name: K562_Day14_R1


title: mPFC_66

description:
Library name: Sample 95
Illumina Stranded mRNA Prep


title: PG/VG_4

description: Library name: B4

value: treated with PG/VG


title: left atrium_5003

description: Left atrium tissue of a 37 year old male donor

value: 37 years


title: dHipp_66

description:
Library name: Sample 94
Illumina Stranded mRNA Prep


title: EC_2

description: Library name: T2


title: left ventricle_3113

description: Left ventricle tissue of a 41 year old male donor

value: 41 years

value: left ventricle


title: PG/VG_3

description: Library name: B3


title: left atrium_3057

description: Left atrium tissue of a 32 year old male donor

value: 32 years


title: vHipp_65

description:
Library name: Sample 93
Illumina Stranded mRNA Prep

value: vHpc


title: RfxCas13d expressing K562 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 1

description: Library name: K562_Day07_R1

value: lncRNAs knockdown

value: doxycycline induction


title: mPFC_65

description:
Library name: Sample 92
Illumina Stranded mRNA Prep

value: mPFC


title: left atrium_XVI

description: Left atrium tissue of a 50 year old female donor

value: female

value: 50 years


title: RfxCas13d expressing K562 cells, pooled lncRNA library, before doxycycline induction, replicate 2

description: Library name: K562_Day00_R2


title: Control_4

description: Library name: C4

value: Lung; Bronchus

value: epithelial cell

value: untreated


title: left atrium_3083

description: Left atrium tissue of a 27 year old female donor

value: 27 years

value: left atrium


title: RfxCas13d expressing K562 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 2

description: Library name: K562_Day07_R2

value: bone marrow

value: cancer cells


title: dHipp_65

description:
Library name: Sample 91
Illumina Stranded mRNA Prep

value: Brain

value: dHpc


title: Control_3

description: Library name: C3


title: left atrium_3056

description: Left atrium tissue of a 45 year old female donor

value: 45 years


title: left atrium_3127

description: Left atrium tissue of a 19 year old female donor

value: 19 years


title: PG/VG_2

description: Library name: B2

value: treated with PG/VG


title: Inr region HARPE (14nt, Inr only) - replicate 3 in vitro

city: La Jolla

first: James

middle: T.

last: Kadonaga

state: California

address: 9500 Gilman Dr

department: Molecular Biology

institute: University of California, San Diego

description:
Library name: HARPE_Inr14-only_inVitro_rep3
reporter RNA and plasmid DNA

library_source: other

data_processing:
Paired-end (PE100) sequences were required to have a perfect match to the 10-nt sequences immediately upstream and downstream of the randomized Inr region, which was required to be exactly 10 nt or 14 nt (for experiments with the 10-nt or 14-nt randomized Inr libraries, respectively). Sequences were also required to have a perfect match to the 10-nt sequences immediately upstream and downstream of the randomized barcode region, which was required to be exactly 15 nt or 17 nt (for experiments with the 10-nt or 14-nt randomized Inr libraries, respectively). All reads containing a match to the selection pattern were deemed usable and trimmed for sequences outside the randomized region.
Conversion tables from barcode to Inr variant were built by paired-end sequencing of amplicons from the starting plasmid libraries. Both read 1 and read 2 were required to pass the above screening criteria. Barcodes that were associated with multiple Inr variants were discarded (this was rare given the complexity of the 15-nt and 17-nt regions used). DNA and RNA datasets for all Inr HARPE experiments were matched to their corresponding barcode-to-Inr conversion tables.
For the DNA datasets, we only used sequences with a minimum absolute read count of 10 and a minimum relative count of 0.2 or 0.75 reads per million (RPM; for experiments with the 10-nt or 14-nt randomized Inr libraries, respectively) so that low-confidence variants would not be included in the analyses. RNA dataset sequences were then matched to their corresponding DNA dataset.
The transcription strength for each Inr sequence variant was defined as the RNA read count (in RPMs) divided by the DNA read count (in RPMs). Inr variants associated with multiple barcodes were combined, and their transcription strengths were computed as the average transcription strength across multiple barcodes.
Supplementary files format and content: txt files (15) containing the processed sequencing data [each Inr region variant and its corresponding barcode, DNA and RNA read counts, and the computed transcription strengths ("score")] for each sample
Supplementary files format and content: SVR model files (7)
Supplementary files format and content: Python script for use of the SVR models

molecule: other

source_name: HeLa S3

growth_protocol: HeLa cells were maintained at 37°C and 5% CO2 in DMEM (ATCC) supplemented with 10% FBS (ATCC), 50 U/mL penicillin (Thermo Fisher Scientific), and 50 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
HARPE DNA/RNA extraction and processing: RNA transcripts from cells or from in vitro transcription reactions were extracted with Trizol or Trizol LS (Thermo Fisher Scientific), respectively. Total RNA (120 μg per condition for cell transfection experiments, or the entirety of each condition for in vitro transcription experiments) was processed as described in Vo ngoc et al. (2020, 2023). Briefly, the following steps were performed. First, contaminating plasmid DNA was removed with the TURBO DNA-free Kit (Thermo Fisher Scientific). Next, the RNA was subjected to reverse transcription with SuperScript III Reverse Transcriptase (Thermo Fisher Scientific) and treatment with RNase H (New England Biolabs). The resulting cDNA was size-selected on a 6% (w/v) polyacrylamide-8 M urea gel with fluorescently-labeled size markers. The size-selected cDNAs and HARPE plasmid DNAs were used as templates to generate DNA amplicons for Illumina sequencing (RNA and DNA datasets, respectively). In the cell-based HARPE experiments, the DNA datasets were obtained with plasmid DNA samples that were extracted post-transfection as described in van Arensbergen et al. (2017). Briefly, cells were treated with trypsin, washed with PBS, and then incubated in 500 µL nuclear extraction buffer [10 mM NaCl, 2 mM MgCl2, 10 mM Tris-HCl (pH 7.8), 5 mM DTT, 0.5% NP40] on ice for 5 min. Nuclei were pelleted at 7,000 x g and washed twice with 1 mL nuclear extraction buffer. DNA was then extracted with ZymoPURE Plasmid Miniprep Kit (Zymo Research).
HARPE library construction: Custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequences corresponding to nucleotides +19 to +34 (relative to the SCP1 +1 TSS; the SCP1 DPR and mutDPR promoter backbones required different primers) were used to amplify the randomized barcode regions. Custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequences corresponding to nucleotides −44 to −23 or −40 to −23 (relative to the SCP1 +1 TSS; the SCP1 TATA and mutTATA promoter backbones required different primers) were used to pair each barcode with its corresponding Inr variant. Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (New England Biolabs), which match the Illumina Read2-primer sequence present on the HARPE plasmid and corresponding cDNA. NGS PCR amplicons were size-selected on native 6% (w/v) polyacrylamide gels prior to Illumina sequencing.

treatment_protocol: Transcription of HARPE libraries: HeLa cells were transfected with HARPE libraries using Lipofectamine 3000 (Thermo Fisher Scientific) as recommended by the manufacturer. For HARPE experiments performed in vitro, the products from 6 or 12 (for the 14-nt or 10-nt Inr libraries, respectively; the reactions were scaled according to to the number of independent transformants in each library) standard in vitro transcription reactions were combined. Standard reactions were performed as follows. DNA template (500 ng) was incubated with HeLa nuclear extract (prepared as described in Dignam et al. 1983) for preinitiation complex assembly at 30 °C for 1 hour in 46 μL of transcription buffer [20 mM HEPES-K+ (pH 7.6), 50 mM KCl, 6 mM MgCl2, 1.25% (w/v) polyvinyl alcohol, 1.25% (w/v) polyethylene glycol, 0.5 mM DTT, 3 mM ATP, 0.02 mM EDTA, and 2% (v/v) glycerol]. rNTPs (4 μL; 0.4 mM final concentration of each rNTP) were added to initiate transcription. The reaction was incubated at 30 °C for 20 min and terminated by the addition of 150 μL of Stop Mix [20 mM EDTA, 200 mM NaCl, 1% (w/v) SDS, 0.3 mg/mL glycogen]. Proteinase K (5 μL; 2.5 mg/mL) was added, and the mixture was incubated at 30 °C for 15 min. All HARPE experiments were performed independently at least two times to ensure reproducibility of the data.

value: HeLa S3

tag: biosource type

value: HeLa nuclear extract


title: mPFC_62

description:
Library name: Sample 89
Illumina Stranded mRNA Prep

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 and Illumina Stranded mRNA Prep

value: mPFC


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 2

description: Library name: HEK293FT_Day14_R2

source_name: kidney

value: kidney

value: embryonic kidney cells

tag: genotype

value: lncRNAs knockdown

value: doxycycline induction


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 1

description: Library name: HEK293FT_Day07_R1


title: Control_2

description: Library name: C2

value: Lung; Bronchus

value: epithelial cell

value: untreated


title: RfxCas13d expressing K562 cells, pooled lncRNA library, before doxycycline induction, replicate 1

description: Library name: K562_Day00_R1

value: bone marrow


title: Inr region HARPE (14nt, with TATA) - replicate 2 in vitro

description:
Library name: HARPE_Inr14-TATA_inVitro_rep2
reporter RNA and plasmid DNA


title: left atrium_5054

description: Left atrium tissue of a 27 year old male donor

tag: Sex

value: male

value: 27 years

value: left atrium

source_name: pooled total RNA from all samples


title: Inr region HARPE (14nt, Inr only) - replicate 2 in vitro

description:
Library name: HARPE_Inr14-only_inVitro_rep2
reporter RNA and plasmid DNA


title: vHipp_62

description:
Library name: Sample 90
Illumina Stranded mRNA Prep

value: Brain

value: vHpc


title: Inr region HARPE (14nt, Inr only) - replicate 1 in vitro

description:
Library name: HARPE_Inr14-only_inVitro_rep1
reporter RNA and plasmid DNA


title: mPFC_61

description:
Library name: Sample 86
Illumina Stranded mRNA Prep


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 1

description: Library name: HEK293FT_Day14_R1


title: vHipp_61

description:
Library name: Sample 87
Illumina Stranded mRNA Prep


title: Inr region HARPE (14nt, with TATA) - replicate 1 in vitro

description:
Library name: HARPE_Inr14-TATA_inVitro_rep1
reporter RNA and plasmid DNA


title: RfxCas13d expressing HEK293FT cells, pooled lncRNA library, before doxycycline induction, replicate 2

description: Library name: HEK293FT_Day00_R2


title: left atrium_3020

description: Left atrium tissue of a 29 year old male donor

value: 29 years


title: dHipp_61

description:
Library name: Sample 85
Illumina Stranded mRNA Prep

value: dHpc


title: left atrium_4155

description: Left atrium tissue of a 19 year old male donor

value: 19 years


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 2

description: Library name: HAP1_Day14_R2

value: cancer cells


title: Inr region HARPE (14nt, with DPR) - replicate 2 in vitro

description:
Library name: HARPE_Inr14-DPR_inVitro_rep2
reporter RNA and plasmid DNA

value: HeLa S3

value: HeLa nuclear extract


title: mPFC_60

description:
Library name: Sample 83
Illumina Stranded mRNA Prep

value: mPFC


title: left atrium_3131

description: Left atrium tissue of a 51 year old female donor

value: female

value: 51 years


title: left atrium_3095

description: Left atrium tissue of a 17 year old male donor

value: 17 years


title: left atrium_XXIII

description: Left atrium tissue of a 60 year old female donor

value: 60 years


title: left atrium_2090

description: Left atrium tissue of an 8 year old male donor

value: 8 years


title: vHipp_60

description:
Library name: Sample 84
Illumina Stranded mRNA Prep


title: left atrium_3109

value: male


title: dHipp_60

description:
Library name: Sample 82
Illumina Stranded mRNA Prep


title: Inr region HARPE (14nt, with DPR) - replicate 1 in vitro

description:
Library name: HARPE_Inr14-DPR_inVitro_rep1
reporter RNA and plasmid DNA


title: left atrium_4084

description: Left atrium tissue of a 50 year old male donor

value: 50 years


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 1

description: Library name: HAP1_Day07_R1

value: bone marrow

value: lncRNAs knockdown

value: doxycycline induction


title: vHipp_56

description:
Library name: Sample 81
Illumina Stranded mRNA Prep

value: Brain

value: vHpc


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, 7 days after doxycycline induction, replicate 2

description: Library name: HAP1_Day07_R2


title: left atrium_5041

description: Left atrium tissue of a 42 year old female donor

value: 42 years

value: left atrium


title: mPFC_56

description:
Library name: Sample 80
Illumina Stranded mRNA Prep


title: mix_JHH390Org

city: Baltimore

first: Jacquelyn

last: Zimmerman

state: MD

address: 1650 Orleans St

institute: Johns Hopkins

description:
Library name: mix_JHH390Org
Orgnanoid Patient 390, Monoculture

data_processing:
Salmon v.1.9.0
Alignment was performed utilizing Salmon v1.9.0 on the Joint High-Performance Computing Exchange (JHPCE). “salmon_partial_sa_index__default.tgz” was used as the index for alignment for the HG38 genome, which was premade and available on refgenie (http://refgenomes.databio.org/v3/genomes/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4). Salmon quantification, [salmon quant], was completed in mapping-based mode (--validateMappings) with automatic library detection. Salmon quantifications were the imported into R using tximport v1.20.0, with the use of the “tgMap.tsv” file also provided in the HG38 refgenie repository for accurate gene-level summarization.
We evaluated sample quality from the distribution of reads as visualized in a boxplot of log counts. We observed no samples with zero median expression, reflective of a low read count, so samples were not of low quality. We used principal component analysis (PCA) of the variance stabilization transform (vst) RNA-seq data to evaluate sample clustering. Projection of the discovered CoGAPS Pattern 7 onto the VST data was completed using ProjectR (V1.8.0). The bulk-seq normalized data and CoGAPs feature loadings were run through the projectR function of the package(14). The projection results were combined with the bulk-seq metadata and plotted using ggplot2 (V3.3.5) and paired t-test results added using ggpubr (V0.4.0)(14).
Analysis completed using DESeq2
Assembly: HG38
Supplementary files format and content: tab-separated values

source_name: pancreas

extract_protocol:
Cells that were coculture were sorted by FACS and immediately underwent RNA extraction (Qiagen RNeasy kit 74004) per manufacturers protocol. RNA was quantified at 260nm using NanoDrop1000 (Thermo Fisher Scientific) and 200ug of RNA was sent to Novogene Corporation Inc. RNA integrity (RIN) was measured at Novogene with Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). All samples were required to demonstrate RIN > 6.8 and ranged from 7.2 to 10.0.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: pancreas

value: Patient-derived organoid

value: epithelium

value: monoculture


title: mix_JHH387CoCAF

description:
Library name: mix_JHH387CoCAF
CAF Patient 387, Coculture

value: CAF

value: coculture


title: JHH390CAF

description:
Library name: JHH390CAF
CAF Patient 390, Monoculture


title: mix_JHH390CoCAF

description:
Library name: mix_JHH390CoCAF
CAF Patient 390, Coculture


title: dHipp_56

description:
Library name: Sample 79
Illumina Stranded mRNA Prep

source_name: Brain

value: dHpc


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, before doxycycline induction, replicate 1

description: Library name: HAP1_Day00_R1

value: cancer cells


title: vHipp_54

description:
Library name: Sample 78
Illumina Stranded mRNA Prep


title: left atrium_3113

description: Left atrium tissue of a 41 year old male donor

value: male

value: 41 years


title: left atrium_1064

description: Left atrium tissue of a 35 year old male donor

value: 35 years


title: JHH387CAF

description:
Library name: JHH387CAF
CAF Patient 387, Monoculture


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, before doxycycline induction, replicate 2

description: Library name: HAP1_Day00_R2

value: bone marrow

value: lncRNAs knockdown


title: JHH387CoOrg

description:
Library name: JHH387CoOrg
Orgnanoid Patient 387, Coculture


title: left atrium_3069

description: Left atrium tissue of a 40 year old female donor

value: female

value: 40 years


title: left atrium_4062

description: Left atrium tissue of a 55 year old male donor

value: 55 years


title: mPFC_54

description:
Library name: Sample 77
Illumina Stranded mRNA Prep

value: Brain

value: mPFC


title: MDA-MB-468, 72h EGF, biol rep 3

city: Trondheim

first: Ellen Marie

middle: Botne

last: Quinsgaard

address: Erling Skjalgsons gate 1

country: Norway

institute: Norwegian University of Science and Technology

description: Library name: RS272h3

data_processing:
Gene normalization and differential analysis was performed using the DESeq2 and Bioconductor packages in R according to the SARTools pipeline.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing gene name, gene ID, raw counts, normalized counts, fold change, log2 fold change, wald statistic (in stat), raw and adjusted p-values, estimated dispersion parameter from feature counts (dispGeneEst), dispersion parameter estimated from model (dispFit), dispersion parameter estimated from Maximum A Posteriori model (dispMAP), final dispersion parameter used to perform test (disp), convergence of model coefficients (betaConv), maximum Cooks distance of feature (maxCooks)

growth_protocol: MDA-MB-468 cells were maintained in DMEM:F12 supplemented with 5% Fetal Bovine Serum and 50U/mL Penicillin-Streptomycin. Cells were cultured in an incubator at 37 degrees celsius and 5% CO2.

extract_protocol:
RNA was harvested using the RNeasy Mini kit (Qiagen, 74104) according to the manufacturer's instructions.
Library preparation was performed using the Lexogen Corall mRNA protocol.

treatment_protocol: Cells were seeded, cultured for 24 hours then serum-starved for 24 hours before EMT was induced using 50ng/mL EGF. All treatment groups were seeded and harvested together, with timing of EGF-supplementation the only differentiating factor.

value: Epithelial, triple negative breast cancer

value: 72h EGF


title: dHipp_54

first: Jennifer

address: 1470 Madison Ave 9-201

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 76
Illumina Stranded mRNA Prep


title: MDA-MB-468, 72h EGF, biol rep 4

description: Library name: RS272h4


title: JHH387Org

description:
Library name: JHH387Org
Orgnanoid Patient 387, Monoculture

value: pancreas

value: Patient-derived organoid

value: epithelium

value: monoculture


title: mix_JHH383CoCAF

description:
Library name: mix_JHH383CoCAF
CAF Patient 383, Coculture

value: CAF

value: coculture


title: mPFC_53

description:
Library name: Sample 74
Illumina Stranded mRNA Prep


title: vHipp_53

description:
Library name: Sample 75
Illumina Stranded mRNA Prep

value: vHpc


title: MDA-MB-468, 72h EGF, biol rep 1

description: Library name: RS272h1


title: left atrium_3168

description: Left atrium tissue of a 19 year old female donor

value: 19 years

value: left atrium


title: MDA-MB-468, 72h EGF, biol rep 2

description: Library name: RS272h2


title: MDA-MB-468, 48h EGF, biol rep 4

description: Library name: RS248h4

value: 48h EGF


title: left atrium_3135

description: Left atrium tissue of a 26 year old male donor

value: male

value: 26 years


title: left atrium_3164

description: Left atrium tissue of a 61 year old male donor

value: 61 years


title: mix_JHH383CoOrg

description:
Library name: mix_JHH383CoOrg
Orgnanoid Patient 383, Coculture


title: JHH383CAF

description:
Library name: JHH383CAF
CAF Patient 383, Monoculture


title: MDA-MB-468, 48h EGF, biol rep 3

description: Library name: RS248h3


title: dHipp_53

description:
Library name: Sample 73
Illumina Stranded mRNA Prep

value: Brain

value: dHpc


title: vHipp_51

description:
Library name: Sample 72
Illumina Stranded mRNA Prep


title: left atrium_2152

description: Left atrium tissue of a 23 year old male donor

value: 23 years


title: mix_JHH383Org

description:
Library name: mix_JHH383Org
Orgnanoid Patient 383, Monoculture


title: mPFC_51

description:
Library name: Sample 71
Illumina Stranded mRNA Prep

value: mPFC


title: MDA-MB-468, 48h EGF, biol rep 2

description: Library name: RS248h2

value: Epithelial, triple negative breast cancer


title: JHH372CoCAF

description:
Library name: JHH372CoCAF
CAF Patient 372, Coculture

value: pancreas

value: Patient-derived organoid


title: left atrium_3140

description: Left atrium tissue of a 39 year old male donor

value: 39 years


title: MDA-MB-468, 48h EGF, biol rep 1

description: Library name: RS248h1


title: RfxCas13d expressing HAP1 cells, pooled lncRNA library, 14 days after doxycycline induction, replicate 1

description: Library name: HAP1_Day14_R1

value: bone marrow

value: cancer cells

value: lncRNAs knockdown

value: doxycycline induction


title: left atrium_XIX

description: Left atrium tissue of a 52 year old female donor

value: female

value: 52 years

value: left atrium


title: dHipp_51

description:
Library name: Sample 70
Illumina Stranded mRNA Prep


title: mix_JHH372CoOrg

description:
Library name: mix_JHH372CoOrg
Orgnanoid Patient 372, Coculture

value: epithelium

value: coculture


title: JHH372CAF

description:
Library name: JHH372CAF
CAF Patient 372, Monoculture

value: CAF

value: monoculture


title: MDA-MB-468, 24h EGF, biol rep 3

description: Library name: RS224h3

value: 24h EGF


title: mPFC_45

description:
Library name: Sample 68
Illumina Stranded mRNA Prep

value: Brain

value: mPFC


title: vHipp_45

description:
Library name: Sample 69
Illumina Stranded mRNA Prep

value: vHpc


title: dHipp_45

description:
Library name: Sample 67
Illumina Stranded mRNA Prep

value: dHpc


title: MDA-MB-468, 24h EGF, biol rep 2

description: Library name: RS224h2

value: Epithelial, triple negative breast cancer


title: MDA-MB-468, 24h EGF, biol rep 4

description: Library name: RS224h4


title: JHH369CoCAF

description:
Library name: JHH369CoCAF
CAF Patient 369 Coculture

value: pancreas

value: Patient-derived organoid


title: JHH372Org

description:
Library name: JHH372Org
Orgnanoid Patient 372, Monoculture


title: vHipp_44

description:
Library name: Sample 66
Illumina Stranded mRNA Prep


title: MDA-MB-468, 24h EGF, biol rep 1

description: Library name: RS224h1


title: left atrium_5033

description: Left atrium tissue of a 48 year old female donor

value: 48 years


title: JHH369CAF

description:
Library name: JHH369CAF
CAF Patient 369, Monoculture


title: mPFC_44

description:
Library name: Sample 65
Illumina Stranded mRNA Prep


title: left atrium_2056

description: Left atrium tissue of a 34 year old female donor

value: 34 years


title: MDA-MB-468, 12h EGF, biol rep 4

description: Library name: RS212h4

value: 12h EGF


title: left atrium_XXVI

description: Left atrium tissue of a 52 year old male donor

value: male

value: 52 years


title: left atrium_XXV

description: Left atrium tissue of a 50 year old male donor

value: 50 years

value: left atrium


title: left atrium_4086/4087

description: Left atrium tissue of a 2 month old female donor

value: female

value: 2 months


title: mix_JHH369CoOrg

description:
Library name: mix_JHH369CoOrg
Orgnanoid Patient 369, Coculture

value: epithelium

value: coculture


title: MDA-MB-468, 12h EGF, biol rep 3

description: Library name: RS212h3


title: left atrium_XXXII

description: Left atrium tissue of a 28 year old female donor

value: 28 years


title: JHH369Org

description:
Library name: JHH369Org
Orgnanoid Patient 369, Monoculture

value: monoculture


title: JHH368CoCAF

description:
Library name: JHH368CoCAF
CAF Patient 368, Coculture

value: CAF


title: vHipp_43

description:
Library name: Sample 63
Illumina Stranded mRNA Prep

value: Brain

value: vHpc


title: MDA-MB-468, 12h EGF, biol rep 2

description: Library name: RS212h2

value: Epithelial, triple negative breast cancer


title: MDA-MB-468, 12h EGF, biol rep 1

description: Library name: RS212h1


title: mPFC_43

description:
Library name: Sample 62
Illumina Stranded mRNA Prep

value: mPFC


title: JHH368CAF

description:
Library name: JHH368CAF
CAF Patient 368, Monoculture

value: pancreas

value: Patient-derived organoid


title: left atrium_3145

description: Left atrium tissue of a 39 year old male donor

value: male

value: 39 years


title: left atrium_XXVII

description: Left atrium tissue of a 49 year old female donor

value: 49 years


title: MDA-MB-468, untreated ctr, biol rep 4

description: Library name: RS2ctr4

value: control


title: dHipp_44

description:
Library name: Sample 64
Illumina Stranded mRNA Prep

value: dHpc


title: dHipp_43

description:
Library name: Sample 61
Illumina Stranded mRNA Prep


title: mix_JHH368CoOrg

description:
Library name: mix_JHH368CoOrg
Orgnanoid Patient 368, Coculture


title: left atrium_3073

description: Left atrium tissue of a 41 year old female donor

value: female

value: 41 years

value: left atrium


title: vHipp_40

description:
Library name: Sample 60
Illumina Stranded mRNA Prep


title: MDA-MB-468, untreated ctr, biol rep 2

description: Library name: RS2ctr2


title: mix_JHH368Org

description:
Library name: mix_JHH368Org
Orgnanoid Patient 368, Monoculture

value: epithelium


title: JHH357CoCAF

description:
Library name: JHH357CoCAF
CAF Patient 357, Coculture

value: coculture


title: mPFC_40

description:
Library name: Sample 59
Illumina Stranded mRNA Prep


title: dHipp_40

description:
Library name: Sample 58
Illumina Stranded mRNA Prep


title: MDA-MB-468, untreated ctr, biol rep 3

description: Library name: RS2ctr3


title: JHH357CAF

description:
Library name: JHH357CAF
CAF Patient 357, Monoculture

value: CAF

value: monoculture


title: MDA-MB-468, untreated ctr, biol rep 1

description: Library name: RS2ctr1


title: left atrium_4043

description: Left atrium tissue of a 13 year old male donor

value: 13 years


title: left atrium_3085

description: Left atrium tissue of a 40 year old male donor

value: 40 years


title: E16-ISX9

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku

institute: Hokkaido University

description: Library name: DK21266_05

data_processing:
Illumina adapters and polyA sequences were removed from the reads.
Low-quality bases were trimmed from the 3' end, and 6 bp were removed from the 5' end.
Following these steps, reads shorter than 25 bp were excluded from further analysis.
The remaining reads were mapped to the human reference genome.
Normalization was performed using the DESeq method.
Assembly: hg38
Supplementary files format and content: xlsx

source_name: brain

growth_protocol: GICs were cultured in 50% of NSC medium containing bFGF and EGF+50% of DMEM-10% FCS.

extract_protocol:
RNA was prepared using RNeasy kit (QIAGEN).
RNA libraries for RNA seq were prepared using QuantSeq 3’mRNA-Seq Library Prep Kit following manufacture’s procols.

treatment_protocol: GICs were cultured in either DMSO alone or ISX9 for ? Days.

value: brain

value: glioblastoma


title: left atrium_3134

description: Left atrium tissue of a 17 year old male donor

value: 17 years


title: mix_JHH357CoOrg

description:
Library name: mix_JHH357CoOrg
Orgnanoid Patient 357, Coculture

value: pancreas

value: Patient-derived organoid


title: left atrium_XXIV

description: Left atrium tissue of a 56 year old male donor

value: male

value: 56 years


title: E16-control

description: Library name: DK21266_04

value: DMSO


title: vHipp_4

last: Chan

description:
Library name: Sample 57
Illumina Stranded mRNA Prep

value: Brain

value: vHpc


title: mPFC_4

description:
Library name: Sample 56
Illumina Stranded mRNA Prep

value: mPFC


title: mix_JHH357Org

description:
Library name: mix_JHH357Org
Orgnanoid Patient 357, Monoculture

value: epithelium


title: left atrium_XXVIII

description: Left atrium tissue of a 65 year old female donor

value: female

value: 65 years

value: left atrium


title: dHipp_4

description:
Library name: Sample 55
Illumina Stranded mRNA Prep

value: dHpc


title: E6-ISX9

description: Library name: DK21266_02


title: E6-control

description: Library name: DK21266_01


title: vHipp_39

description:
Library name: Sample 54
Illumina Stranded mRNA Prep


title: JHH352CAF

description:
Library name: JHH352CAF
CAF Patient 352, Monoculture

value: CAF

value: monoculture


title: JHH352CoCAF

description:
Library name: JHH352CoCAF
CAF Patient 352, Coculture

value: coculture


title: mix_JHH352CoOrg

description:
Library name: mix_JHH352CoOrg
Orgnanoid Patient 352, Coculture


title: mPFC_39

description:
Library name: Sample 53
Illumina Stranded mRNA Prep