title: +2 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AM_H2L_d2_p02h_B2


title: +1 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

status: Public on Dec 16 2025

type: SRA

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

country: USA

institute: UC Berkeley

description: Library name: Cr077_AL_H2L_d2_p01h_B2

library_source: transcriptomic

data_processing:
mapping to the C. reinhardtii reference assembly with STAR (v2.7.9a) with --alignIntronMax 3000 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outSAMmultNmax 1 --limitBAMsortRAM 2000000000 --outSAMunmapped Within
reads assigned to genes with featureCounts() function in R using annot.ext=annotations, isGTFAnnotationFile="SAF", useMetaFeatures=TRUE, allowMultiOverlap=TRUE, fracOverlap=0.5, minOverlap=30, largestOverlap=TRUE, countMultiMappingReads=TRUE, fraction=TRUE, minMQS=0, primaryOnly=TRUE, ignoreDup=FALSE, strandSpecific=2, genome=genome, isLongRead=FALSE, isPairedEnd=FALSE, countReadPairs=TRUE, checkFragLength=TRUE, minFragLength=50, maxFragLength=3000, countChimericFragments=FALSE, autosort=TRUE
reads per transcript normalized with DESeq2 (v1.45.0) using dds <- DESeqDataSetFromMatrix(), dds <- DESeq(dds)
transcript lengths added with mcols(dds)$basepairs <- transcriptLengths
transcript abundances calculated as Fragments Per Kb per Million mapped reads (FPKMs) with DESeq2 using fpkm(dds, robust = TRUE)
Assembly: Chlamydomonas reinhardtii reference v6.1 (from phytozome-next.jgi.doe.gov)
Supplementary files format and content: Cr077.FPKMs_all.csv contains normalized expression values for all samples and for all nuclear genes in a comma-delimited text file

molecule: total RNA

organism: Chlamydomonas reinhardtii

growth_protocol: Cultures were inoculated from TAP precultures at a starting optical density at 680 nm (OD680) of roughly 0.05 in HSM. Cultures were allowed to grow in turbidostat mode for at least 2 weeks prior to each experiment. The LL-acclimated population was first synchronized in diurnal ML (200 µmol photons m–2 s–1) for 1 week and then acclimated to diurnal LL for > 1 week. The HL-acclimated population was synchronized and acclimated in diurnal HL for > 1 week.

extract_protocol:
Roughly 17 mL of culture was collected by centrifugation at 2500 × g for 2 min at 4°C. Cell pellets were resuspended in 750 µL Zymo DNA/RNA Shield and transferred to ZR BashingBead Lysis Tubes containing 0.1 mm and 0.5 mm beads. Samples were subjected to bead beating for 2 min in a Mini-BeadBeater 16 Cell Disrupter in a 4°C room, and then were processed with the ZymoBIOMICS RNA Mini Kit according to the manufacturer's instructions.
Standard Illumina RNA-Seq kits.

treatment_protocol: At the start of the experiment (–12, t = 0 h), culture density was set to OD680 = 0.4 and medium flow was stopped. Then, the LL-acclimated populations were subjected to diurnal HL conditions, and the HL-acclimated populations were subjected to diurnal LL conditions. After the first 26 h (–10), experimental cultures were diluted back to OD680 = 0.4 and medium flow was stopped again before the second day of the experiment.

tag: cell line

tag: cell type

value: liquid culture

tag: genotype

value: WT

tag: treatment

value: HL to LL


title: +2 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AM_H2L_d2_p02h_B1


title: D1 biol rep2

city: Yuseong-gu, Daejeon-si

first: Taejun

last: Seol

address: 291, Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology (KAIST)

library_source: genomic

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (100bp reads)
ATAC-seq reads were trimmed using Trim Galore version 0.6.7 and aligned to the UCSC mm10 genome using Bowtie2 version 2.4.4
Duplicates were removed using Picard MarkDuplicates version 2.26.3.
Peaks were called using MACS3 version 3.0.0b1 with q-value cut-off 0.05.
BedGraph files were generated from -B parameter of MACS3 and loca bias-substracted files were converted to bigWig files.
Assembly: mm10
Supplementary files format and content: BED(narrowPeak) file of ATAC-seq peaks

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Nuclear suspensions obtained from 100,000 cells were treated with assembled Tn5 transposase for 30 min at 37°C. Tagmented DNA was cleaned up with a MinElute PCR Purification Kit (28006, Qiagen) before library preparation.
Library preparation for ATAC-seq was performed with the use of an ATAC-seq kit (AT53150, Active Motif) and the Omni-ATAC protocol (Corces et al. 2017)

treatment_protocol: For induction of adipocyte differentiation, confluent C3H10T1/2 cells were stimulated for 2 days with an adipogenic cocktail consisting of 1 μM dexamethasone (D4902, Sigma), insulin at 5 µg/ml (I0516, Sigma), 500 μM isobutylmethylxanthine (I5879, Sigma), and 1 μM rosiglitazone (R2408, Sigma). After 2 days, adipogenic medium was then changed to a maintenance medium (culture medium supplemented with insulin at 5 µg/ml). For activation of ERT2-TAZ, Cells were treated with 1 µM 4-OHT (H6278, Sigma) for 24 h.

value: mesenchymal stem cells

tag: condition

value: Adipogenic cocktail


title: D1 biol rep1


title: Bird 18, PR, retina

city: Tromsø

first: Jana

last: Kalinova

address: Postboks 6050 Stakkevollan

country: Norway

institute: UiT The Arctic University of Norway

description: Library name: 18_R

data_processing:
Long-read RNA-seq: Raw circular consensus sequences (CCS) were deconcatenated at segmentation adapter positions using skera split generating segmented reads (S-reads). Demultiplexing and primer removal were performed using lima (submited raw files have undergone these pre-processing steps). Isoseq refine was used to obtain full-length non-concatemer reads (FLNC-reads) and to trim poly(A) tails. FLNC-reads were clustered at the isoform level to generate high-quality transcript sequences using isoseq cluster2. Isoforms were aligned to a reference genome using minimap2. Identification and quantification of known and novel isoforms was performed using TALON.
Short-read RNA-seq: Raw sequences in fastq format were mapped to the Rock ptarmigan genome using STAR aligner. Reads for each exons were summarized via featureCounts using the Rock ptarmigan gff annotation file, manually modified to account for newly discovered VA opn exons. Raw exon counts were analyzed with edgeR separately for each tissue (hypothalamus, retina, pineal gland).
snRNAseq: Raw bcl files from each flow cell directory were demultiplexed into fastq files using cellranger mkfastq. Custom reference was created via cellranger mkref. The gtf file was filtered via cellranger mkgtf prior to creating the reference as per 10x Genomics instructions.  Furthermore, the gtf file was manually modified to (a) include newly discovered VA opn exons and (b) allow for counting of individual exons of the VA opn gene. The sequencing reads in fastq format were aligned to the reference via the cellranger count pipeline. Each library (n=4) was processed in a separate run of cellranger count. Subsequently, 2 libraries originating from the same sample (i.e., 1A+1B and 2A+2B) were combined via cellranger aggr. As a result, this pipeline outputted two filtered feature-barcode matrices (Sample1, Sample2).
Assembly: GCF_023343835.1
Supplementary files format and content: long-read RNA-seq: gtf file - annotation from the TALON database, tsv file - read counts for TALON isoforms
Supplementary files format and content: short-read RNA-seq: csv file - raw counts per exon for each sample
Supplementary files format and content: snRNAseq: tsv and mtx files

organism: Lagopus muta hyperborea

source_name: retina

extract_protocol:
RNA extraction: From hypothalamus and retina, total RNA was extracted using TRI Reagent (Invitrogen™). From the pineal gland, total RNA was extracted using RNeasy Plus Micro Kit (Qiagen™). Nuclei isolation was performed as described in Ayhan et al. (2021) with minor adjustmets.
long-read RNA-seq: Kinnex Full-Length RNA Kit; short-read RNA-seq: DNBSEQ Eukaryotic Strand-specific mRNA library; snRNAseq: 10x Chromium Single Cell 3’ Reagents Kit

tag: tissue

value: retina


title: PVH cells, female, sample 6, drop 1, RT-rxn A, lib. 1

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

description:
Library name: Mm PVH 6F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0). Read 1 was 20 bp (bases 1–12 cell barcode, bases 13–20 UMI), read 2 (paired end) was 60 bp, and index primer was 8bp.
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Reads from were aligned with STAR (version 2.7.7) against the GRCm38 mouse genome assembly. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 24 of the GENCODE mouse annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse gene count matrices.
Assembly: GRCm38
Supplementary files format and content: *.dge.tsv: tab-separated-values tables of gene x cell digital gene expression counts (DGEs)
Supplementary files format and content: *.dge_cellbender.tsv.gz: same as the DGEs, with specific gene counts reduced by CellBender (see data processing, above)

molecule: polyA RNA

source_name: paraventricular nucleus of the hypothalamus

extract_protocol:
C57BL/6J or Sim1-Cre::R26-LSL-EGFP-L10a mice aged 6-12 weeks were sacrificed between 9 am – 12 pm by rapid decapitation immediately after removal from the home cage. Brains were rapidly extracted and chilled in DMEM/F12 media slush. Next, brains were placed ventral side up in a chilled stainless steel brain matrix (Roboz Surgical Instrument Co.: SA-2165) and 1 mm coronal sections of the hypothalamus were collected. The PVH was then microdissected under a fluorescent stereoscope. For each sample preparation, 4-6 male or female mice were pooled.
Pooled tissue samples were digested in papain solution with DNAse for 1hr at 37C with gentle agitation, according to a published protocol (Saxena A, et al.) except that an entire vial of papain was used in a 1.6mL final reaction volume. Digestion was stopped by dilution with “EBSS #2” 56, with 10% fetal bovine serum used in place of the ovomucoid protease inhibitor. Tissue was centrifuged at 300×g for 5 min, re-suspended in the modified EBSS #2, then gently triturated using a series of 5 Pasteur pipettes with tips fire-polished to incrementally smaller openings. The resulting cell suspension was divided between two microfuge tubes, diluted with Drop-seq buffer (Macosko et al., 2015) to a volume of 1.5mL per tube. Cells were then washed twice by centrifugation at 300×g for 5 min, followed by re-suspension in Drop-seq buffer. Drop-seq buffer consisted of: 5% weight/volume trehalose; 1x Hank’s Buffered Salt Solution (magnesium- and calcium-free); 2.13mM MgCl2; 2mM MgSO4; 1.26mM CaCl2; 1mM glucose; 0.01% bovine serum albumin (molecular biology grade). Cells were filtered through a 20um mesh, diluted to 220 cells/uL based on cell concentration estimates from a hemacytometer, and then kept on ice until use. Drop-seq was performed as in the reference (Macosko et al., 2015) but with the following modifications: first, flow rates of 2.1 mL/hr were used for each aqueous suspension, and 12 mL/hr for the oil. Second, libraries were sequenced on the Illumina NextSeq 500, using 1.7 pM in a volume of 1.2 mL HT1 and 3 mL of 0.3 μM Read1CustSeqB.

treatment_protocol: No treatment

tag: Sex

value: female

tag: dietary condition/schedule

value: ad libitum feeding


title: D0 biol rep2


title: +4 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AN_H2L_d2_p04h_B1


title: +2 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AM_H2L_d2_p02h_B3


title: PVH cells, female, sample 7, drop 1, RT-rxn B, lib. 1

description:
Library name: Mm PVH 7F-1B-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript

value: paraventricular nucleus of the hypothalamus


title: PVH cells, female, sample 5, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 5F-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: +0.5 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AK_H2L_d2_p30m_B2


title: D6TAZ biol rep2 [CR24]

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (100bp reads)
Reads were mapped to the mouse transcriptome(mm10) and quantified using salmon v1.9.0 with option --numBootstraps 30.
Transcript-level quantification result from each samples were imported and summarized to gene-level using Tximeta v1.12.4.
Differential expression analysis was performed using DEseq2 v1.34.0 using lfcShrink function.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes transcript-level quantification results (TPM) for each samples

extract_protocol:
Total RNA was isolated using Hybrid-R Total RNA Kit (305-101, GeneAll Biotechnology).
Sequencing libraries were constructed with the use of a TruSeq stranded Total RNA Library Kit (Illumina).

value: Adipogenic cocktail + 4-OHT


title: Bird 15, BR, retina

description: Library name: 15_R


title: D6TAZ biol rep1 [CR23]


title: Bird 14, BR, retina

description: Library name: 14_R


title: Bird 12, PI, retina

description: Library name: 12_R


title: D6 biol rep2 [CR22]


title: –2 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AJ_H2L_n2_m02h_B3


title: +1 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AL_H2L_d2_p01h_B1


title: +0.5 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AK_H2L_d2_p30m_B1


title: Bird 13, PI, retina

description: Library name: 13_R


title: PVH cells, female, sample 5, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 5F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: D0 biol rep1


title: Bird 17, BR, retina

description: Library name: 17_R


title: D6 biol rep1 [CR21]


title: –2 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AJ_H2L_n2_m02h_B1


title: PVH cells, female, sample 5, drop 1, RT-rxn B, lib. 1

description:
Library name: Mm PVH 5F-1B-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, male, sample 4, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 4M-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript

value: male


title: –2 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AJ_H2L_n2_m02h_B2


title: Bird 11, PI, retina

description: Library name: 11_R


title: D1 biol rep1 [CR3]


title: –10 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AI_H2L_n1_m10h_B3


title: PVH cells, female, sample 4, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 4F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Bird 16, BR, retina

description: Library name: 16_R


title: D0 biol rep2 [CR2]


title: PVH cells, male, sample 3, drop 1, RT-rxn B, lib. 1

description:
Library name: Mm PVH 3M-1B-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Bird 10, PI, retina

description: Library name: 10_R


title: PVH cells, male, sample 3, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 3M-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Bird 8, PI, retina

description: Library name: 8_R


title: Bird 9, PI, retina

description: Library name: 9_R


title: –10 timepoint of the first day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AI_H2L_n1_m10h_B1


title: –10 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AI_H2L_n1_m10h_B2


title: PVH cells, male, sample 3, drop 1, RT-rxn A, lib. 2

description:
Library name: Mm PVH 3M-1A-2
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, male, sample 4, drop 1, RT-rxn B, lib. 1

description:
Library name: Mm PVH 4M-1B-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: D0 biol rep1 [CR1]


title: +12 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AH_H2L_d1_p12h_B3


title: Bird 6, SP, retina

description: Library name: 6_R


title: Mouse_Stomach_organoid_RZK_scMultiome RNA

city: Daejeon

first: Bon-Kyoung

last: Koo

state: Yuseong-gu

address: Expo-ro 55

department: Center for genome engineering

institute: Institute for Basic Science

description: 10x Genomics scMultiome

data_processing:
To generate count matrices consist of both gene expression and chromatin peaks for each organoid sample such as Rnf43/Znrf3 double knock-out (RZ), and Kras activated RZ-DKO (RZK), cellranger-ARC count (v6.1.1) was utilized with default option and mouse reference (‘refdata-cellranger-arc-mm10-2020-A-2.0.0’) provided in 10x Genomics. Based on both Signac (v1.8.0) and Seurat (v4.1.0) pipelines, we generated analytic objects from ‘filtered_feature_bc_matrix’ and ‘atac_fragments.tsv.gz’ of cellranger based on mouse genome which is output from ‘GetGRangesFromEnsDb’ with ‘EnsDb.Mmusculus.79’ for annotations. We filtered out poor-quality cell nuclei with unique molecular identifiers (UMIs) for RNA less than 1,000 and more than 25,000, and for ATAC less than 1,000 and more than 100,000, percent mitochondrial genes more than 15%, and nucleosome signal more than 3 for both samples. Using the selected nulei, we sequentially conducted NormalizeData (lognormalization) and FindVariableFeatures (‘vst’ method, 2,000 features) functions for RNA expression profiles. We also implemented FindTopFeatures with min.cutoff is ‘q0’, RunTFIDF, and RunSVD for both ATAC and macs2 assays for peak profiles from Signac package.
Assembly: mm10
Supplementary files format and content: hdf5: RNA+ATAC matrices
Supplementary files format and content: tsv: atac_fragments information

source_name: Stomach organoid

extract_protocol:
Single-cell dissociation was carried out by incubating mechanically disrupted organoids with TrypLE for 30 min at 37 o C. Nuclei from single cells were extracted.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits
scMultiome (RNA + ATAC)

value: Stomach organoid

value: multiple


title: PVH cells, male, sample 3, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 3M-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, female, sample 3, drop 1, RT-rxn B, lib. 2

description:
Library name: Mm PVH 3F-1B-2
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: +12 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AH_H2L_d1_p12h_B2


title: Bird 5, SP, retina

description: Library name: 5_R


title: D1 biol rep2 [CR4]


title: PVH cells, female, sample 3, drop 1, RT-rxn B, lib. 1

description:
Library name: Mm PVH 3F-1B-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: +12 timepoint of the first day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AH_H2L_d1_p12h_B1


title: Mouse_Stomach_organoid_RZ_scMultiome DNA

description: 10x Genomics scMultiome

value: Anxa10-CreERT2; Rnf43f/f; Znrf3f/f


title: Mouse_Stomach_organoid_RZK_scMultiome DNA

description: 10x Genomics scMultiome


title: +10 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AG_H2L_d1_p10h_B3


title: PVH cells, female, sample 3, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 3F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Mouse_Stomach_organoid_RZ_scMultiome RNA

description: 10x Genomics scMultiome


title: Bird 3, SP, retina

description: Library name: 3_R


title: +10 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AG_H2L_d1_p10h_B2


title: Bird 4, SP, retina

description: Library name: 4_R


title: +10 timepoint of the first day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AG_H2L_d1_p10h_B1


title: Hippo_High4

city: Warsaw

first: Katarzyna

last: Radwańska

state: Prowincja

address: ul. L. Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology (PAS)

data_processing:
mapping by STAR
MarkDuplicates
Counts features by Featurecounts
Assembly: mm10
Supplementary files format and content: tab separated text file with features assigned to genes

source_name: Hippocampus

extract_protocol: polyA+ KAPA Library kit

tag: strain

value: brain

value: Wild-type

tag: sample type

value: High drinkers

tag: transfection

tag: chip antibody


title: Hippo_High3


title: +8 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AF_H2L_d1_p08h_B3

value: liquid culture


title: Bird 1, SP, retina

description: Library name: 1_R


title: Bird 2, SP, retina

description: Library name: 2_R


title: Bird 7, PI, retina

description: Library name: 7_R


title: Bird 22, PR, hypothalamus

description: Library name: 22_H

source_name: brain (hypothalamus)

value: brain (hypothalamus)


title: PVH cells, male, sample 2, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 2M-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Hippo_Low4

value: Low drinkers


title: +8 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AF_H2L_d1_p08h_B2

value: WT

value: HL to LL


title: Bird 21, PR, hypothalamus

description: Library name: 21_H


title: +6 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AE_H2L_d1_p06h_B3


title: Hippo_High1


title: Bird 20, PR, hypothalamus

description: Library name: 20_H


title: PVH cells, female, sample 2, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 2F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Hippo_High2


title: Hippo_Low3


title: PVH cells, male, sample 1, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 1M-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, male, sample 1, drop 3, RT-rxn A, lib. 1

description:
Library name: Mm PVH 1M-3A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, male, sample 2, drop 3, RT-rxn A, lib. 1

description:
Library name: Mm PVH 2M-3A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Hippo_Low2


title: +8 timepoint of the first day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AF_H2L_d1_p08h_B1


title: PVH cells, male, sample 2, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 2M-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Bird 18, PR, hypothalamus

description: Library name: 18_H


title: +6 timepoint of the first day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AE_H2L_d1_p06h_B1


title: Hippo_Low1


title: Bird 17, BR, hypothalamus

description: Library name: 17_H


title: +6 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AE_H2L_d1_p06h_B2


title: +4 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AD_H2L_d1_p04h_B3


title: +4 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AD_H2L_d1_p04h_B2


title: Amy_High4

source_name: Amygdala


title: Bird 19, PR, hypothalamus

description: Library name: 19_H


title: PVH cells, female, sample 1, drop-run 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 1F-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, male, sample 1, drop-run 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 1M-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Amy_High3


title: Bird 16, BR, hypothalamus

description: Library name: 16_H


title: PVH cells, female, sample 1, drop-run 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 1F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Ctx 5XFAD; Idol; Camk2a-cre cKO Rep 5

city: Indianapolis

first: Jungsu

last: Kim

state: IN

address: 320 W. 15th Street

institute: Indiana University School of Medicine

description: Library name: Ctx_5XFAD_Idol_Neu-cKO_5

data_processing:
Base calling done by Illumina Real-Time Analysis v2
Adapters and polyA tails removed by bbduk from bbtools/38.72 using references files polyA/polyT (poly(A) sequence of 18 As, and a poly(T) sequence of 18 Ts) & truseq_rna.fa (from the BBTools suite: https://sourceforge.net/projects/bbmap/) and parameters k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
Alignment done by STAR/2.7.3a using parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD
Gene counts done by htseq-count from htseq/0.9.1-py13 using parameters htseq-count -m intersection-nonempty -s yes -f bam -r pos
Assembly: GRCm39
Supplementary files format and content: Matrix table of raw gene counts for each gene and each sample in experimental design

source_name: Brain cortex

extract_protocol:
Total RNA was extracted from mouse cortical tissues using phenol/chloroform & TRI reagent® (Molecular Research Center, Inc) and was quantified using the NanoDrop 2000 spectrophotometer (Thermo Scientific).
Isolated RNA was shipped to Lexogen for library preparation and sequencing. Libraries were prepared manually according to the manufacturer’s instructions using QuantSeq 3' mRNA-Seq FWD Library Prep Kit (Lexogen, UG Version 015UG009V0252). Briefly, 50 ng total RNA was denatured for 3 minutes at 85°C with oligo(dT) primers containing an Illumina-compatible sequence at its 5’ end followed by reverse transcription at 42°C for 15 minutes. After RNA removal, the second strand of the cDNA was synthesized by a random primer containing an Illumina-compatible linker sequence at its 5’ end, and the end product was purified by a magnetic bead-based method to remove all reaction components. Finally, individual sample barcodes (dual indexing) for multiplexing were introduced via PCR (cycle number determined by qPCR) and the leftover reaction components were removed by a magnetic bead-based purification method. All libraries were analyzed for adapter dimers, size distribution and concentration on a Fragment Analyzer System using the DNF-474 HS NGS Fragment kit (1-6,000 bp) (Agilent). After pooling the libraries in an equimolar ratio, the concentration and the size distribution of the lane mix was analyzed by Qubit dsDNA HS assay (Thermo Fisher Scientific) and by 2100 Bioanalyzer device using the HS-DNA assay (Agilent), respectively. A 2 nM dilution of the lane mix was denatured and diluted to loading concentration for sequencing on a NextSeq 500 instrument with SR75 High Output Kit (Illumina). Seventy-six-base-pair single-end reads were generated at Lexogen Services.

value: Brain cortex

value: Ctx 5XFAD; Idol; Camk2a-cre cKO

tag: batch

value: single-end


title: +2 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AC_H2L_d1_p02h_B3


title: PVH cells, female, sample 2, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 2F-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript

value: female

value: paraventricular nucleus of the hypothalamus

value: ad libitum feeding


title: Bird 14, BR, hypothalamus

description: Library name: 14_H


title: Amy_High2


title: Ctx 5XFAD; Idol; Camk2a-cre cKO Rep 4

description: Library name: Ctx_5XFAD_Idol_Neu-cKO_4


title: +1 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AB_H2L_d1_p01h_B3


title: Ctx 5XFAD; Idol; Camk2a-cre cKO Rep 3

description: Library name: Ctx_5XFAD_Idol_Neu-cKO_3


title: +2 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AC_H2L_d1_p02h_B2


title: Amy_High1


title: Bird 15, BR, hypothalamus

description: Library name: 15_H


title: Bird 12, PI, hypothalamus

description: Library name: 12_H


title: Amy_Low3


title: Ctx 5XFAD; Idol; Camk2a-cre cKO Rep 2

description: Library name: Ctx_5XFAD_Idol_Neu-cKO_2


title: +1 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AB_H2L_d1_p01h_B2


title: Bird 11, PI, hypothalamus

description: Library name: 11_H


title: Amy_Low2


title: Ctx 5XFAD; Idol; Camk2a-cre cKO Rep 1

description: Library name: Ctx_5XFAD_Idol_Neu-cKO_1


title: Bird 10, PI, hypothalamus

description: Library name: 10_H


title: +0.5 timepoint of the first day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AA_H2L_d1_p30m_B2


title: +0.5 timepoint of the first day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AA_H2L_d1_p30m_B3


title: +0.5 timepoint of the first day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AA_H2L_d1_p30m_B1


title: Amy_Low1


title: Bird 9, PI, hypothalamus

description: Library name: 9_H


title: Ctx 5XFAD; Idol; Camk2a-cre WT Rep 4

description: Library name: Ctx_5XFAD_Idol_Neu-WT_4

value: Ctx 5XFAD; Idol; Camk2a-cre WT


title: Ctx 5XFAD; Idol; Camk2a-cre WT Rep 5

description: Library name: Ctx_5XFAD_Idol_Neu-WT_5


title: Hippo_water4

value: Alcohol-naive


title: Bird 8, PI, hypothalamus

description: Library name: 8_H


title: Bird 13, PI, hypothalamus

description: Library name: 13_H


title: Bird 25, PI, hypothalamus, Sample 2B

description: Library name: 2B


title: Amy_Low4


title: Hippo_water3


title: Ctx 5XFAD; Idol; Camk2a-cre WT Rep 3

description: Library name: Ctx_5XFAD_Idol_Neu-WT_3


title: Bird 25, PI, hypothalamus, Sample 2A

description: Library name: 2A


title: Bird 7, PI, hypothalamus

description: Library name: 7_H


title: Ctx 5XFAD; Idol; Camk2a-cre WT Rep 2

description: Library name: Ctx_5XFAD_Idol_Neu-WT_2


title: Bird 6, SP, hypothalamus

description: Library name: 6_H


title: Bird 24, PI, hypothalamus, Sample 1B

description: Library name: 1B


title: Hippo_water1


title: Hippo_water2


title: Bird 24, PI, hypothalamus, Sample 1A

description: Library name: 1A


title: Ctx 5XFAD; Idol; Camk2a-cre WT Rep 1

description: Library name: Ctx_5XFAD_Idol_Neu-WT_1


title: Bird 5, SP, hypothalamus

description: Library name: 5_H


title: Bird 4, SP, pineal gland, long-read

description: Library name: 4_P_PB

source_name: pineal gland

value: pineal gland


title: Bird 3, SP, hypothalamus

description: Library name: 3_H


title: P2_28dpa scRNAseq

city: Boston

first: Jessica

middle: A

last: Lehoczky

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital

description: Library name: P2_28dpa_BRI2282

data_processing:
Base-calling and raw read files generated with Illumina platform
10x Genomics Cell Ranger software v7.1.0 was used to convert raw BCL files to FASTQ files, align read to mouse mm10-2020-A transcriptome, filter low quality cells, and count barcodes and unique molecular identifiers (UMIs)
Assembly: mm10-2020-A
Supplementary files format and content: cellranger output files: matrix.mtx, features.tsv, and barcodes.tsv

source_name: fibrosing P2 digit

extract_protocol:
Mid-digital, P2, fibrosing digit tissues were manually dissected, followed by trypsin and collagenase I enzymatic digestion. Red blood cells were lysed with ACK lysis buffer. Dissociated single cells were washed, filtered and resuspended in 0.4% BSA in PBS then FACS sorted with 1ug/mL propidium iodide. Live cells were collected and adjusted to concentration of 1000 cells/uL for single cell RNAseq library construction.
All samples used the 10x Chromium transcriptomics platform (10x Genomics) implemented by the Brigham and Women's Hospital Center for Cellular Profiling. 10x Chromium Single Cell 3' v3 chemistry was used per manufacturer's protocol.

value: fibrosing P2 digit

value: FVB/NJ

value: wild-type

value: pooled male and female

tag: age

value: 8 weeks old


title: Amy_water3

value: brain

value: Wild-type


title: Bird 1, SP, retina, long-read

description: Library name: 1_R_PB

value: retina


title: Bird 4, SP, hypothalamus

description: Library name: 4_H

value: brain (hypothalamus)


title: Bird 2, SP, hypothalamus

description: Library name: 2_H


title: Amy_water1


title: Bird 23, declining photoperiod (L:D 7:17), hypothalamus

description: Library name: 23_H_PB


title: Bird 1, SP, hypothalamus

description: Library name: 1_H


title: P2_unamp scRNAseq

description: Library name: P2_UA_BRI2263

source_name: homeostatic P2 digit

value: homeostatic P2 digit


title: P2_12dpa scRNAseq

description: Library name: P2_12dpa_BRI2450


title: Amy_water4


title: P22_Epi_Zone4_Replicate1

status: Public on Dec 15 2025

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description:
Library name: Epi_Z4_Rep1
column name in P22_RPKM_Table.xlsx: Epi_Z4_Rep1

data_processing:
Raw RNA-seq reads were aligned to the mm10 mouse genome using STAR v2.4.0 with default parameters.
Transcriptomes were assembled and gene expression levels quantified using featureCounts.
Data was further processed with limma, edgeR and DESeq2.
Assembly: mm10 mouse genome
Supplementary files format and content: P22_All_RPKM.xlxs; Tab separated file for all sequencing libraries combined, listing all genes (rows) and the number of reads per kilobase per million (RPKM) reads mapped for all samples. Columns show all samples and indicate the sorted cell type, anatomical zone and biological replicate. The first column lists the official gene symbol.

source_name: Dorsal skin

extract_protocol:
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
100ng of amplified cDNA was used to generate sequencing libraries with 56 unique barcoded adapters (Biological duplicates for 28 samples from K14-H2BGFP;Crabp1-GFP;Lef1-RFP, 7 populations from 4 zones) via the Ovation Ultralow DR Library System (NuGEN). Library concentration and quality was assessed by Qbit (invitrogen) and Bioanalyzer (Agilent).

treatment_protocol: Samples are FACS isolated cells.

value: Dorsal skin

value: Epidermis

value: Epidermal Cell

value: FACS sorted

value: Zone 4


title: P22_Epi_Zone4_Replicate2

description:
Library name: Epi_Z4_Rep2
column name in P22_RPKM_Table.xlsx: Epi_Z4_Rep2


title: P22_Epi_Zone3_Replicate2

description:
Library name: Epi_Z3_Rep2
column name in P22_RPKM_Table.xlsx: Epi_Z3_Rep2

value: Zone 3


title: P2_17dpa scRNAseq

description: Library name: P2_17dpa_BRI2272


title: Amy_water2

value: Alcohol-naive


title: P22_Epi_Zone2_Replicate1

description:
Library name: Epi_Z2_Rep1
column name in P22_RPKM_Table.xlsx: Epi_Z2_Rep1

value: Zone 2


title: P22_Epi_Zone1_Replicate2

description:
Library name: Epi_Z1_Rep2
column name in P22_RPKM_Table.xlsx: Epi_Z1_Rep2

value: Zone 1


title: P22_Epi_Zone1_Replicate1

description:
Library name: Epi_Z1_Rep1
column name in P22_RPKM_Table.xlsx: Epi_Z1_Rep1


title: P22_Epi_Zone2_Replicate2

description:
Library name: Epi_Z2_Rep2
column name in P22_RPKM_Table.xlsx: Epi_Z2_Rep2


title: P22_HGSC_Zone4_Replicate2

description:
Library name: HGSC_Z4_Rep2
column name in P22_RPKM_Table.xlsx: HGSC_Z4_Rep2

value: Epithelial Stem Cells

value: Germ Stem Cell


title: P22_HGSC_Zone2_Replicate2

description:
Library name: HGSC_Z2_Rep2
column name in P22_RPKM_Table.xlsx: HGSC_Z2_Rep2


title: P22_HGSC_Zone3_Replicate2

description:
Library name: HGSC_Z3_Rep2
column name in P22_RPKM_Table.xlsx: HGSC_Z3_Rep2


title: P22_HGSC_Zone3_Replicate1

description:
Library name: HGSC_Z3_Rep1
column name in P22_RPKM_Table.xlsx: HGSC_Z3_Rep1


title: P22_HGSC_Zone1_Replicate2

description:
Library name: HGSC_Z1_Rep2
column name in P22_RPKM_Table.xlsx: HGSC_Z1_Rep2


title: MTX-24h, biological rep3

type: RNA

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description: Gene expression from 24h treatment

hyb_protocol: Hybridaztion was performed using GeneChip HT 3’IVT Express Kit

scan_protocol: GeneChips were scanned using Genechip scanner 3000(Affymetrix)

data_processing:
Data was processed using Genespring v13 software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale, using a baseline transformation to the median of control samples
Affymetrix.ExonExprChip.HuGene-1_0-st-v1_na31_hg19_2010-09-03

label: Biotin

organism: Homo sapiens

source_name: HT29 Colon cancer cell line

label_protocol: RNA samples were processed in the automated  Biomek FX System (Beckman Coulter), where  cRNA was produced, and labeled with Biotin

growth_protocol: HT29 human colon cancer cells (250.000) were seeded in 100 mm plates, grown in F12 + 7%FBS

extract_protocol: RNAeasy mini kit, extraction performed according to user's protocol.

treatment_protocol: Incubation with 70 nM MTX for 0,8,24 and 48 h

value: methotrexate

tag: time


title: MTX-48h, biological rep1

description: Gene expression from 48h treatment


title: Control, biological rep1

description: Gene expression from untreated control

value: control


title: MTX-24h, biological rep1

description: Gene expression from 24h treatment


title: MTX-8h, biological rep1

description: Gene expression from 8h treatment

value: 8 h


title: MTX-24h, biological rep2

description: Gene expression from 24h treatment


title: P22_BuSC_Zone4_Replicate2

description:
Library name: BuSC_Z4_Rep2
column name in P22_RPKM_Table.xlsx: BuSC_Z4_Rep2

value: Bulge Stem Cell


title: Control, biological rep2

description: Gene expression from untreated control


title: MTX-48h, biological rep3

description: Gene expression from 48h treatment


title: MTX-48h, biological rep2

description: Gene expression from 48h treatment


title: P22_HGSC_Zone1_Replicate1

description:
Library name: HGSC_Z1_Rep1
column name in P22_RPKM_Table.xlsx: HGSC_Z1_Rep1


title: P22_Epi_Zone3_Replicate1

description:
Library name: Epi_Z3_Rep1
column name in P22_RPKM_Table.xlsx: Epi_Z3_Rep1


title: P22_BuSC_Zone3_Replicate2

description:
Library name: BuSC_Z3_Rep2
column name in P22_RPKM_Table.xlsx: BuSC_Z3_Rep2


title: P22_BuSC_Zone3_Replicate1

description:
Library name: BuSC_Z3_Rep1
column name in P22_RPKM_Table.xlsx: BuSC_Z3_Rep1


title: MTX-8h, biological rep2

description: Gene expression from 8h treatment


title: P22_BuSC_Zone2_Replicate1

description:
Library name: BuSC_Z2_Rep1
column name in P22_RPKM_Table.xlsx: BuSC_Z2_Rep1


title: P22_BuSC_Zone1_Replicate2

description:
Library name: BuSC_Z1_Rep2
column name in P22_RPKM_Table.xlsx: BuSC_Z1_Rep2


title: P22_BuSC_Zone1_Replicate1

description:
Library name: BuSC_Z1_Rep1
column name in P22_RPKM_Table.xlsx: BuSC_Z1_Rep1


title: P22_Foll_Zone4_Replicate1

description:
Library name: Foll_Z4_Rep1
column name in P22_RPKM_Table.xlsx: Foll_Z4_Rep1

value: Epithelial Cells

value: upper Hair Follicle


title: Control, biological rep3

description: Gene expression from untreated control


title: P22_Foll_Zone4_Replicate2

description:
Library name: Foll_Z4_Rep2
column name in P22_RPKM_Table.xlsx: Foll_Z4_Rep2

value: Dorsal skin


title: P22_BuSC_Zone2_Replicate2

description:
Library name: BuSC_Z2_Rep2
column name in P22_RPKM_Table.xlsx: BuSC_Z2_Rep2


title: MTX-8h, biological rep3

description: Gene expression from 8h treatment


title: P22_Foll_Zone3_Replicate2

description:
Library name: Foll_Z3_Rep2
column name in P22_RPKM_Table.xlsx: Foll_Z3_Rep2


title: P22_HGSC_Zone2_Replicate1

description:
Library name: HGSC_Z2_Rep1
column name in P22_RPKM_Table.xlsx: HGSC_Z2_Rep1


title: P22_Foll_Zone2_Replicate2

description:
Library name: Foll_Z2_Rep2
column name in P22_RPKM_Table.xlsx: Foll_Z2_Rep2


title: P22_HGSC_Zone4_Replicate1

description:
Library name: HGSC_Z4_Rep1
column name in P22_RPKM_Table.xlsx: HGSC_Z4_Rep1


title: P22_Foll_Zone2_Replicate1

description:
Library name: Foll_Z2_Rep1
column name in P22_RPKM_Table.xlsx: Foll_Z2_Rep1


title: P22_Foll_Zone1_Replicate2

description:
Library name: Foll_Z1_Rep2
column name in P22_RPKM_Table.xlsx: Foll_Z1_Rep2


title: P22_Foll_Zone1_Replicate1

description:
Library name: Foll_Z1_Rep1
column name in P22_RPKM_Table.xlsx: Foll_Z1_Rep1


title: P22_DP_Zone3_Replicate2

description:
Library name: DP_Z3_Rep2
column name in P22_RPKM_Table.xlsx: DP_Z3_Rep2

value: Mesenchymal Cells

value: Dermal Papilla


title: P22_DP_Zone4_Replicate2

description:
Library name: DP_Z4_Rep2
column name in P22_RPKM_Table.xlsx: DP_Z4_Rep2

value: FACS sorted


title: P22_DP_Zone4_Replicate1

description:
Library name: DP_Z4_Rep1
column name in P22_RPKM_Table.xlsx: DP_Z4_Rep1

value: Zone 4


title: P22_DP_Zone3_Replicate1

description:
Library name: DP_Z3_Rep1
column name in P22_RPKM_Table.xlsx: DP_Z3_Rep1

value: Zone 3


title: P22_BuSC_Zone4_Replicate1

description:
Library name: BuSC_Z4_Rep1
column name in P22_RPKM_Table.xlsx: BuSC_Z4_Rep1


title: P22_DP_Zone1_Replicate1

description:
Library name: DP_Z1_Rep1
column name in P22_RPKM_Table.xlsx: DP_Z1_Rep1


title: P22_DP_Zone2_Replicate2

description:
Library name: DP_Z2_Rep2
column name in P22_RPKM_Table.xlsx: DP_Z2_Rep2


title: P22_DP_Zone1_Replicate2

description:
Library name: DP_Z1_Rep2
column name in P22_RPKM_Table.xlsx: DP_Z1_Rep2


title: P22_DF_Zone4_Replicate2

description:
Library name: DF_Z4_Rep2
column name in P22_RPKM_Table.xlsx: DF_Z4_Rep2

value: Dermal Fibroblasts


title: P22_DP_Zone2_Replicate1

description:
Library name: DP_Z2_Rep1
column name in P22_RPKM_Table.xlsx: DP_Z2_Rep1

value: Zone 2


title: P22_DF_Zone3_Replicate1

description:
Library name: DF_Z3_Rep1
column name in P22_RPKM_Table.xlsx: DF_Z3_Rep1


title: P22_DF_Zone2_Replicate2

description:
Library name: DF_Z2_Rep2
column name in P22_RPKM_Table.xlsx: DF_Z2_Rep2


title: P22_DF_Zone1_Replicate2

description:
Library name: DF_Z1_Rep2
column name in P22_RPKM_Table.xlsx: DF_Z1_Rep2

value: Zone 1


title: P22_DF_Zone4_Replicate1

description:
Library name: DF_Z4_Rep1
column name in P22_RPKM_Table.xlsx: DF_Z4_Rep1


title: P22_DF_Zone2_Replicate1

description:
Library name: DF_Z2_Rep1
column name in P22_RPKM_Table.xlsx: DF_Z2_Rep1


title: P22_Neg_Zone4_Replicate1

description:
Library name: Neg_Z4_Rep1
column name in P22_RPKM_Table.xlsx: Neg_Z4_Rep1

value: mixed


title: P22_Neg_Zone3_Replicate1

description:
Library name: Neg_Z3_Rep1
column name in P22_RPKM_Table.xlsx: Neg_Z3_Rep1


title: P22_Neg_Zone4_Replicate2

description:
Library name: Neg_Z4_Rep2
column name in P22_RPKM_Table.xlsx: Neg_Z4_Rep2


title: P22_Foll_Zone3_Replicate1

description:
Library name: Foll_Z3_Rep1
column name in P22_RPKM_Table.xlsx: Foll_Z3_Rep1


title: P22_DF_Zone1_Replicate1

description:
Library name: DF_Z1_Rep1
column name in P22_RPKM_Table.xlsx: DF_Z1_Rep1


title: P22_Neg_Zone3_Replicate2

description:
Library name: Neg_Z3_Rep2
column name in P22_RPKM_Table.xlsx: Neg_Z3_Rep2


title: P22_Neg_Zone2_Replicate2

description:
Library name: Neg_Z2_Rep2
column name in P22_RPKM_Table.xlsx: Neg_Z2_Rep2


title: P22_Neg_Zone1_Replicate2

description:
Library name: Neg_Z1_Rep2
column name in P22_RPKM_Table.xlsx: Neg_Z1_Rep2


title: E2_2

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

data_processing:
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS v2.2.58 data collection software.
Base-calling is performed using Illumina’s RTA version 1.18.64.
FASTq files are mapped to mouse reference mm10 with STAR aligner.
Unique gene hit counts were calcultated using feature Counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: eosinophil

growth_protocol: Eosinophils were isolated from the blood of IL-5 Tg mice (NJ.1638) by miltneyi negative selection using CD90 and B220 beads and checked by cytospin and HE stain for >97% purity. Eosinophils were cultured at 4-5 million cells per ml in standard RPMI-1640+10% FBS + 1X streptomycin-penacllin-glutamine at 37C and 5% CO2 for 18 hrs under different conditions.

extract_protocol:
Trixol Extraction
TruSeq Stranded mRNA Sample Prep Kit v2  (Illumina, San Diego, CA).
Libraries were loaded following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3.

treatment_protocol: One experiment included duplicates of control eosinophils (CN) has no cytokines added conducted at the same time as eosinophils (E1) were cultured with 15ng/mL IFN-gamma and TNF-alpha. A second experiment included duplicates of IL-5 eosinophils (E0) were cultured with IL-5 10 ng/mL and eosinophils  (E2) were cultured with 10ng/ml of IL-5, GM-CSF, IL-4 and 30ng/mL IL-33.

value: eosinophil

value: WT

value: IL-5, IL-4, GM-CSF, IL-33

value: 18 hrs


title: E0_2


title: E0_1


title: E2_1


title: CN_2


title: E1_2

value: IFNg+TNFa


title: CN_1


title: P22_DF_Zone3_Replicate2

description:
Library name: DF_Z3_Rep2
column name in P22_RPKM_Table.xlsx: DF_Z3_Rep2


title: E1_1


title: SUM149 CRISPR screen -DOX rep4 in vivo

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Library name: SUM149_UN_4_invivo

data_processing:
The MAGeCK software package version 0.5.4 was used to statistically identify RBP candidates with a Wald P value < 0.05 and bet score < 0
Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: csv file includes beta score, Wald P value, and FDR for each RBP, essential gene, and non-targeting sgRNA with respect to each cell line the screen was performed in
Library strategy: CRISPR Screen

extract_protocol:
Qiagen DNeasy blood and tissue kit
genomic DNA libraries were prepared using a targeted enrichment approach and constructed with illumina sequencing adapters. Genomic libraries were sequenced to 6 million reads in single-end 55bp mode

treatment_protocol: RBP library was lentivirally infected at MOI 0.3 into MCF10As, MDAMB231s, MDAMB436s, and SUM149 cells. Dox was then administered to cultured cells stably expressing the library or cells transplanted subcutaneously into mice.


title: TIG-3 cells, DXR-Sen cells, Vehicle(DMSO), day7_2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: TD2_Vec

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 sequencer in 151-base paired-end mode.
Generated reads were mapped to the human (hg19) reference genome using TopHat ver. 2.1.1.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using cuffdiff of Cufflinks 2.2.1.
The raw count was calculated using featureCounts of subread 2.0.0.
Assembly: hg19
Supplementary files format and content: FPKM file: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: raw_count file: tab-delimited text files include raw count values for each sample

growth_protocol: TIG-3 cells were maintained in Dulbecco's Modified Eagle's medium supplumented with 10% fetal bovine serum and 100 U ml^-1 penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol.
Library preparation was performed using a TruSeq stranded mRNA Library Prep kit according to the manufacturer’s instructions.

treatment_protocol: For induction of cellular senescence, TIG-3 cells were incubated with doxorubicin at 250 ngper ml for 10 days. DXR-Sen TIG-3 cells were incubated with ABT263 (0.5µM) or ARV825 (25 nM) for 7 days.

value: fibroblast

value: DMSO


title: TIG-3 cells, DXR-Sen cells, ABT263, day7_2

description: Library name: TD2_A


title: TIG-3 cells, DXR-Sen cells, ARV825, day7_1

description: Library name: TD1_8


title: TIG-3 cells, DXR-Sen cells, ABT263, day7_1

description: Library name: TD1_A


title: TIG-3 cells, DXR-Sen cells, Vehicle(DMSO), day7_1

description: Library name: TD1_Vec


title: TIG-3 cells, DXR-Sen cells, ARV825, day7_2

description: Library name: TD2_8


title: SUM149 CRISPR screen -DOX rep1 in vivo

description: Library name: SUM149_UN_1_invivo


title: SUM149 CRISPR screen -DOX rep3 in vivo

description: Library name: SUM149_UN_3_invivo


title: SUM149 CRISPR screen +DOX rep5 in vivo

description: Library name: SUM149_DOX_5_invivo


title: SUM149 CRISPR screen +DOX rep3 in vivo

description: Library name: SUM149_DOX_3_invivo


title: SUM149 CRISPR screen -DOX rep2 in vivo

description: Library name: SUM149_UN_2_invivo


title: SUM149 CRISPR screen -DOX rep5 in vivo

description: Library name: SUM149_UN_5_invivo


title: SUM149 CRISPR screen +DOX rep4 in vivo

description: Library name: SUM149_DOX_4_invivo


title: SUM149 CRISPR screen +DOX rep2 in vivo

description: Library name: SUM149_DOX_2_invivo


title: P22_Neg_Zone2_Replicate1

description:
Library name: Neg_Z2_Rep1
column name in P22_RPKM_Table.xlsx: Neg_Z2_Rep1

value: Dorsal skin


title: MDAMB436 CRISPR screen -DOX rep5 in vivo

description: Library name: MDAMB436_UN_5_invivo


title: P22_Neg_Zone1_Replicate1

description:
Library name: Neg_Z1_Rep1
column name in P22_RPKM_Table.xlsx: Neg_Z1_Rep1


title: MDAMB436 CRISPR screen -DOX rep4 in vivo

description: Library name: MDAMB436_UN_4_invivo


title: MDAMB436 CRISPR screen -DOX rep3 in vivo

description: Library name: MDAMB436_UN_3_invivo


title: MDAMB436 CRISPR screen -DOX rep2 in vivo

description: Library name: MDAMB436_UN_2_invivo


title: SUM149 CRISPR screen +DOX rep1 in vivo

description: Library name: SUM149_DOX_1_invivo


title: MDAMB436 CRISPR screen +DOX rep5 in vivo

description: Library name: MDAMB436_DOX_5_invivo


title: MDAMB436 CRISPR screen +DOX rep2 in vivo

description: Library name: MDAMB436_DOX_2_invivo


title: circD-KO

city: Beijing

first: He

last: Luyun

address: 15 DaTun Road, Chaoyang District

country: China

institute: IBP

description: This is circD-deleted  liver CSCs

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data was processed following NimbleGen Systems standard operating protocol.

source_name: circD-deleted  liver CSCs

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: All these cell  were cultured in DMEM medium supplemented with 10% FBS, 100 g/ml penicillin, and 100 U/ml streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: We use CD13 and CD133 to sort  liver CSCs.

value: HCC

value: circD knockout


title: MDAMB436 CRISPR screen +DOX rep1 in vivo

description: Library name: MDAMB436_DOX_1_invivo


title: MDAMB231 CRISPR screen -DOX rep3 in vivo

description: Library name: MDAMB231_UN_3_invivo


title: MDAMB231 CRISPR screen -DOX rep5 in vivo

description: Library name: MDAMB231_UN_5_invivo


title: MDAMB231 CRISPR screen -DOX rep2 in vivo

description: Library name: MDAMB231_UN_2_invivo


title: MDAMB231 CRISPR screen -DOX rep1 in vivo

description: Library name: MDAMB231_UN_1_invivo


title: MDAMB231 CRISPR screen -DOX rep4 in vivo

description: Library name: MDAMB231_UN_4_invivo


title: VEC

description: This is control liver CSCs

source_name: control liver CSCs


title: MDAMB231 CRISPR screen +DOX rep5 in vivo

description: Library name: MDAMB231_DOX_5_invivo


title: MDAMB231 CRISPR screen +DOX rep4 in vivo

description: Library name: MDAMB231_DOX_4_invivo


title: MDAMB231 CRISPR screen +DOX rep3 in vivo

description: Library name: MDAMB231_DOX_3_invivo


title: SUM149 CRISPR screen -DOX rep2 in vitro

description: Library name: SUM149_UN_2_invitro


title: SUM149 CRISPR screen -DOX rep1 in vitro

description: Library name: SUM149_UN_1_invitro


title: SUM149 CRISPR screen +DOX rep2 in vitro

description: Library name: SUM149_DOX_2_invitro


title: MDAMB436 CRISPR screen -DOX rep2 in vitro

description: Library name: MDAMB436_UN_2_invitro


title: SUM149 CRISPR screen +DOX rep1 in vitro

description: Library name: SUM149_DOX_1_invitro


title: MDAMB231 CRISPR screen +DOX rep1 in vivo

description: Library name: MDAMB231_DOX_1_invivo


title: MDAMB231 CRISPR screen +DOX rep2 in vivo

description: Library name: MDAMB231_DOX_2_invivo


title: MDAMB436 CRISPR screen -DOX rep1 in vivo

description: Library name: MDAMB436_UN_1_invivo


title: MDAMB436 CRISPR screen +DOX rep2 in vitro

description: Library name: MDAMB436_DOX_2_invitro


title: MDAMB231 CRISPR screen -DOX rep2 in vitro

description: Library name: MDAMB231_UN_2_invitro


title: MDAMB436 CRISPR screen +DOX rep1 in vitro

description: Library name: MDAMB436_DOX_1_invitro


title: MDAMB231 CRISPR screen -DOX rep1 in vitro

description: Library name: MDAMB231_UN_1_invitro


title: MDAMB436 CRISPR screen -DOX rep1 in vitro

description: Library name: MDAMB436_UN_1_invitro


title: MDAMB231 CRISPR screen +DOX rep2 in vitro

description: Library name: MDAMB231_DOX_2_invitro


title: MDAMB436 CRISPR screen +DOX rep4 in vivo

description: Library name: MDAMB436_DOX_4_invivo


title: MDAMB231 CRISPR screen +DOX rep1 in vitro

description: Library name: MDAMB231_DOX_1_invitro


title: MCF10A CRISPR screen -DOX rep2 in vitro

description: Library name: MCF10A_UN_2_invitro


title: MDAMB436 CRISPR screen +DOX rep3 in vivo

description: Library name: MDAMB436_DOX_3_invivo


title: MCF10A CRISPR screen +DOX rep2 in vitro

description: Library name: MCF10A_DOX_2_invitro


title: MCF10A CRISPR screen -DOX rep1 in vitro

description: Library name: MCF10A_UN_1_invitro


title: MCF10A CRISPR screen +DOX rep1 in vitro

description: Library name: MCF10A_DOX_1_invitro


title: Pancreatic cancer, patient 3917, exome capture

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: 450 West Dr, CB7295

institute: University of North Carolina at Chapel Hill

description: Library name: tempus_3917

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 conversion software 2.20.0
Salmon (v1.5.2) was used to derive normalized counts (TPM)
For samples sequenced at Tempus, kallisto (v0.44.0) was used to derive normalized counts (TPM)
Assembly: GENCODE Release 38 (GRCh38.p13) for whole transcriptome; GENCODE Release 37 (GRCh37) for exome capture
Supplementary files format and content: csv files include TPM values per sample

source_name: PDAC

extract_protocol:
Total RNA was extracted from FFPE samples using Rneasy FFPE Kit (Qiagen, 73504).
KAPA RNA HyperPrep Kit with RiboErase (Roche) per manufacturer protocol for whole-transcriptome RNA-seq; sequencing done at Tempus for exome capture

value: PDAC

tag: individual

value: patient 3917


title: Pancreatic cancer, patient 3976, exome capture

description: Library name: tempus_3976

value: patient 3976


title: Pancreatic cancer, patient 4090, exome capture

description: Library name: tempus_4090

value: patient 4090


title: Pancreatic cancer, patient 4169, exome capture

description: Library name: tempus_4169

value: patient 4169


title: Pancreatic cancer, patient 4130, exome capture

description: Library name: tempus_4130

value: patient 4130


title: Pancreatic cancer, patient 3831, exome capture

description: Library name: tempus_3831

value: patient 3831


title: Pancreatic cancer, patient 3856, exome capture

description: Library name: tempus_3856

value: patient 3856


title: Pancreatic cancer, patient 3969, exome capture

description: Library name: tempus_3969

value: patient 3969


title: Pancreatic cancer, patient 3689, exome capture

description: Library name: tempus_3689

value: patient 3689


title: Pancreatic cancer, patient 3837, exome capture

description: Library name: tempus_3837

value: patient 3837


title: Pancreatic cancer, patient 3766, exome capture

description: Library name: tempus_3766

value: patient 3766


title: Pancreatic cancer, patient 3924, exome capture

description: Library name: tempus_3924

value: patient 3924


title: Pancreatic cancer, patient 3730, exome capture

description: Library name: tempus_3730

value: patient 3730


title: Pancreatic cancer, patient 3676, exome capture

description: Library name: tempus_3676

value: patient 3676


title: Pancreatic cancer, patient 3770, exome capture

description: Library name: tempus_3770

value: patient 3770


title: Pancreatic cancer, patient 3606, exome capture

description: Library name: tempus_3606

value: patient 3606


title: Pancreatic cancer, patient 3599, exome capture

description: Library name: tempus_3599

value: PDAC

value: patient 3599


title: Pancreatic cancer, patient 3665, exome capture

description: Library name: tempus_3665

value: patient 3665


title: Pancreatic cancer, patient 3594, exome capture

description: Library name: tempus_3594

value: patient 3594


title: Pancreatic cancer, patient 3620, exome capture

description: Library name: tempus_3620

value: patient 3620


title: Pancreatic cancer, patient 3562, exome capture

description: Library name: tempus_3562

value: patient 3562


title: Pancreatic cancer, patient 3613, exome capture

description: Library name: tempus_3613

value: patient 3613


title: Pancreatic cancer, patient 3656, exome capture

description: Library name: tempus_3656

value: patient 3656


title: Pancreatic cancer, patient 3592, exome capture

description: Library name: tempus_3592

value: patient 3592


title: Pancreatic cancer, patient 3577, exome capture

description: Library name: tempus_3577

value: patient 3577


title: Pancreatic cancer, patient 3571, exome capture

description: Library name: tempus_3571

value: patient 3571


title: Pancreatic cancer, patient 3776, exome capture

description: Library name: tempus_3776

value: patient 3776


title: Pancreatic cancer, patient 3836, exome capture

description: Library name: tempus_3836

value: patient 3836


title: Pancreatic cancer, patient 3659, exome capture

description: Library name: tempus_3659

value: patient 3659


title: Pancreatic cancer, patient 3515, exome capture

description: Library name: tempus_3515

value: patient 3515


title: Pancreatic cancer, patient 3510, exome capture

description: Library name: tempus_3510

value: patient 3510


title: Pancreatic cancer, patient 3496, exome capture

description: Library name: tempus_3496

value: patient 3496


title: Pancreatic cancer, patient 3497, exome capture

description: Library name: tempus_3497

value: PDAC

value: patient 3497


title: Pancreatic cancer, patient 3487, exome capture

description: Library name: tempus_3487

value: patient 3487


title: Pancreatic cancer, patient 3544, exome capture

description: Library name: tempus_3544

value: patient 3544


title: Pancreatic cancer, patient 3549, exome capture

description: Library name: tempus_3549

value: patient 3549


title: Pancreatic cancer, patient 3454, exome capture

description: Library name: tempus_3454

value: patient 3454


title: Pancreatic cancer, patient 3495, exome capture

description: Library name: tempus_3495

value: patient 3495


title: Pancreatic cancer, patient 3493, exome capture

description: Library name: tempus_3493

value: patient 3493


title: Pancreatic cancer, patient 3469, exome capture

description: Library name: tempus_3469

value: patient 3469


title: Pancreatic cancer, patient 3408, exome capture

description: Library name: tempus_3408

value: patient 3408


title: Pancreatic cancer, patient 3428, exome capture

description: Library name: tempus_3428

value: patient 3428


title: Pancreatic cancer, patient 3362, exome capture

description: Library name: tempus_3362

value: patient 3362


title: Pancreatic cancer, patient 3444, exome capture

description: Library name: tempus_3444

value: patient 3444


title: Pancreatic cancer, patient 3343, exome capture

description: Library name: tempus_3343

value: patient 3343


title: Pancreatic cancer, patient 3353, exome capture

description: Library name: tempus_3353

value: patient 3353


title: Pancreatic cancer, patient 3402, exome capture

description: Library name: tempus_3402

value: patient 3402


title: Pancreatic cancer, patient 3554, exome capture

description: Library name: tempus_3354

value: patient 3554


title: Pancreatic cancer, patient 3559, exome capture

description: Library name: tempus_3559

value: PDAC

value: patient 3559


title: Pancreatic cancer, patient 3337, exome capture

description: Library name: tempus_3337

value: patient 3337


title: Pancreatic cancer, patient 3328, exome capture

description: Library name: tempus_3328

value: patient 3328


title: Pancreatic cancer, patient 3282, exome capture

description: Library name: tempus_3282

value: patient 3282


title: Pancreatic cancer, patient 3253, exome capture

description: Library name: tempus_3253

value: patient 3253


title: Pancreatic cancer, patient 3235, exome capture

description: Library name: tempus_3235

value: patient 3235


title: Pancreatic cancer, patient 3250, exome capture

description: Library name: tempus_3250

value: patient 3250


title: Pancreatic cancer, patient 3232, exome capture

description: Library name: tempus_3232

value: patient 3232


title: Pancreatic cancer, patient 3434, exome capture

description: Library name: tempus_3434

value: patient 3434


title: Pancreatic cancer, patient 3220, exome capture

description: Library name: tempus_3220

value: patient 3220


title: Pancreatic cancer, patient 3165, exome capture

description: Library name: tempus_3165

value: patient 3165


title: Pancreatic cancer, patient 3196, exome capture

description: Library name: tempus_3196

value: patient 3196


title: Pancreatic cancer, patient 3144, exome capture

description: Library name: tempus_3144

value: patient 3144


title: Pancreatic cancer, patient 3127, exome capture

description: Library name: tempus_3127

value: patient 3127


title: Pancreatic cancer, patient 3109, exome capture

description: Library name: tempus_3109

value: patient 3109


title: Pancreatic cancer, patient 3030, exome capture

description: Library name: tempus_3030

value: patient 3030


title: Pancreatic cancer, patient 2924, exome capture

description: Library name: tempus_2924

value: PDAC

value: patient 2924


title: Pancreatic cancer, patient 2977, exome capture

description: Library name: tempus_2977

value: patient 2977


title: Pancreatic cancer, patient 3212, exome capture

description: Library name: tempus_3212

value: patient 3212


title: Pancreatic cancer, patient 3199, exome capture

description: Library name: tempus_3199

value: patient 3199


title: Pancreatic cancer, patient 3172, exome capture

description: Library name: tempus_3172

value: patient 3172


title: Pancreatic cancer, patient 3193, exome capture

description: Library name: tempus_3193

value: patient 3193


title: Pancreatic cancer, patient 2447, exome capture

description: Library name: tempus_2447

value: patient 2447


title: Pancreatic cancer, patient 3071, exome capture

description: Library name: tempus_3071

value: patient 3071


title: Pancreatic cancer, patient 3009, exome capture

description: Library name: tempus_3009

value: patient 3009


title: Pancreatic cancer, patient 3027, exome capture

description: Library name: tempus_3027

value: patient 3027


title: Pancreatic cancer, patient 3252, exome capture

description: Library name: tempus_3252

value: patient 3252


title: Pancreatic cancer, patient 2236, exome capture

description: Library name: tempus_2236

value: patient 2236


title: Pancreatic cancer, patient 3275, exome capture

description: Library name: tempus_3275

value: patient 3275


title: Pancreatic cancer, patient 2976, exome capture

description: Library name: tempus_2976

value: patient 2976


title: M3_g2_rep1

city: TORONTO

first: Xin

last: Xu

state: Ontario

address: 101 COLLEGE ST EAST TOWER 11-601D

country: Canada

institute: Princess Margaret Cancer Center

description:
Library name: 22Rv1 M3 writing g2 rep1
g2-1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to hg38 by using STAR
Read counts were generated by STAR and the differential analysis was done by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts

growth_protocol: 22Rv1 dCasRx-METTL3 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Lentivirus-mediated sgRNAs were transduced into cells prior to selection by 10 μg/mL blasticidin.

extract_protocol:
The total RNA was extracted from the cells by using the RNeasy Mini Kit (74106) following the manufacturer's protocol.
RNA-Seq of the sgRNA-mediated m6A installation onto CHD9 was performed by Geneseeq using NovaSeq paired-end 150 bp.

value: human prostate cancer

value: no treatment


title: M3_g2_rep3

description:
Library name: 22Rv1 M3 writing g2 rep3
g2-3


title: M3_g1_rep3

description:
Library name: 22Rv1 M3 writing g1 rep3
g1-3


title: M3_g2_rep2

description:
Library name: 22Rv1 M3 writing g2 rep2
g2-2


title: M3_g1_rep2

description:
Library name: 22Rv1 M3 writing g1 rep2
g1-2


title: M3_gNT_rep3

description:
Library name: 22Rv1 M3 writing gNT rep3
gNT-3

value: non-targeting


title: M3_g1_rep1

description:
Library name: 22Rv1 M3 writing g1 rep1
g1-1


title: M3_gNT_rep2

description:
Library name: 22Rv1 M3 writing gNT rep2
gNT-2


title: Pancreatic cancer, patient 3039, exome capture

description: Library name: tempus_3039

value: PDAC

value: patient 3039


title: M3_gNT_rep1

description:
Library name: 22Rv1 M3 writing gNT rep1
gNT-1


title: EPD210, Control, 72 hrs, rep 3

city: Aarhus

first: Lasse

middle: Sommer

last: Kristensen

address: Wilhelm Meyers Allé 4

department: Biomedicine

country: Denmark

institute: Aarhus University

description:
Library name: EPDC172
NC_72h_rep3
EPDC172_N482-0034_S88

data_processing:
Raw sequencing data were demultiplexed and preprocessed using Trim Galore (v0.6.10) to remove adapter sequences and low-quality bases (Phred score < 33). Filtered reads were aligned to the human reference genome (hg19/GRCh37) using STAR (v2.7.10b). Gene expression quantification was performed with FeatureCounts (v2.0.3), using annotations from Gencode release 37 (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV37lift37). Transcript expression levels were normalized with DeSeq2 (v1.44.0)
Assembly: GRCh37
Supplementary files format and content: csv file including raw read counts for all samples

source_name: ependymoma, posterior fossa

growth_protocol: EPD210 is a semi-attaching cell line, and a laminin (Sigma) coating (0.65 μg/cm2 laminin coating) was used to propagate the cells. EPD210 cells were cultured in neurobasal media (Gibco) containing 2% B27 (without vitamin A) (Gibco), 1% L-glutamine (Gibco), 1% penicillin-streptomycin (Gibco), 20 ng/ml recombinant human EGF (Gibco) and 20 ng/ml recombinant human FGF (Gibco) and cells were kept in a humidified atmosphere at 37°C and with 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen) and measured using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific)
Libraries for high-throughput RNA-seq analyses were generated using the SMARTer stranded total RNA-seq pico input mammalian kit (Takara Bio) with an input of 10 ng total RNA. The rRNA removal step was followed by a purification step using AMPure XP Beads (Beckman Coulter) and 10 PCR cycles were used for amplification. The final libraries were quality controlled and quantified using the high sensitivity DNA kit on 2100 Bioanalyzer (Agilent Technologies) and the high sensitivity double stranded DNA kit on Qubit 4 Fluorometer (Thermo Fisher Scientific). The libraries were pooled at equimolar concentrations and sequenced on a HiSeq 4000 platform (Illumina) to generate 150 bp paired-end reads

treatment_protocol: Transient circRMST knockdown of circRMST in EPD210 cells was achieved using two different Dicer-substrate small interfering RNAs (DsiRNAs) 24h and 72h post transfection

value: ependymoma, posterior fossa

value: cancer stem-like

value: NC

value: batch 1


title: EPD210, KD1, 24 hrs, rep 3

description:
Library name: EPDC224
circRMST-KD1_24h_rep3
EPDC224_N482-0032_S86


title: EPD210, Control, 24 hrs, rep 2

description:
Library name: EPDB124
NC_24h_rep2
EPDB124_N482-0025_S79

value: Control


title: EPD210, Control, 72 hrs, rep 1

description:
Library name: EPDA172
NC_72h_rep1
EPDA172_N482-0022_S76


title: EPD210, KD2, 24 hrs, rep 1

description:
Library name: EPDA324
circRMST-KD2_24h_rep1
EPDA324_N482-0021_S75


title: EPD210, KD2, 72 hrs, rep 3

description:
Library name: EPDC372
circRMST-KD2_72h_rep3
EPDC372_N482-0036_S90


title: EPD210, KD1, 24 hrs, rep 1

description:
Library name: EPDA224
circRMST-KD1_24h_rep1
EPDA224_N482-0020_S74


title: EPD210, Control, 24 hrs, rep 3

description:
Library name: EPDC124
NC_24h_rep3
EPDC124_N482-0031_S85


title: EPD210, KD2, 24 hrs, rep 3

description:
Library name: EPDC324
circRMST-KD2_24h_rep3
EPDC324_N482-0033_S87


title: EPD210, KD1, 24 hrs, rep 2

description:
Library name: EPDB224
circRMST-KD1_24h_rep2
EPDB224_N482-0026_S80


title: EPD210, KD2, 72 hrs, rep 1

description:
Library name: EPDA372
circRMST-KD2_72h_rep1
EPDA372_N482-0024_S78


title: EPD210, KD1, 72 hrs, rep 3

description:
Library name: EPDC272
circRMST-KD1_72h_rep3
EPDC272_N482-0035_S89


title: EPD210, KD1, 72 hrs, rep 1

description:
Library name: EPDA272
circRMST-KD1_72h_rep1
EPDA272_N482-0023_S77


title: P7,Abd

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: P7-Abd
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  cellranger-7.0.0
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous adipose tissues

extract_protocol:
Paired samples of subcubataneous adipose tissues were sampled from the abdomen and anterior thigh using mini  liposuction.  Single nuclei were extracted after dounce homogenication and single nuclei prepared using minor modifications of the procedures of Mandrup (pmid (34189477) and Rajbhandari (PMID: 31644425)
Library was performed according to the manufacter’s instructions(Chromium Next GEM Single Cell 3’ Reagent Kits v3.3, 10X Genomics).

treatment_protocol: Adipose samples were removed from overnight fasted women in the follicullar phase of their menstrual cycle .

value: subcutaneous adipose tissues

tag: tissue location

value: Abd

tag: subject id


title: P6,Thi

description:
Library name: P6-Thi
10x Genomics

value: Thi


title: EPD210, Control, 24 hrs, rep 1

description:
Library name: EPDA124
NC_24h_rep1
EPDA124_N482-0019_S73

tag: cell line

tag: cell type


title: P4,Thi

description:
Library name: P4-Thi
10x Genomics


title: Experiment group

city: Los Angeles

first: Youcheng

last: Yang

address: 430 Westwood Plaza, 5121 Engineering V, Box 951600, Attn (PI NAME): Li Lab

department: Bioengineering

institute: UCLA

description: Library name: Sample1

data_processing:
Use seurat package in R to Remove cells with extreme mitochondria counts, RNA counts, or RNA features, then normalize the data for further analysis
Assembly: GRCh38
Supplementary files format and content: HDF5 files with the filtered feature-barcode matrix

source_name: PBMC

extract_protocol:
Were conducted by UCLA TCGB core facility
Library preparation was accomplished using the Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: PBMC

tag: treatment

value: Our device


title: Control group

description: Library name: Sample 2

value: Clinical device


title: P7,Thi

description:
Library name: P7-Thi
10x Genomics


title: P6,Abd

description:
Library name: P6-Abd
10x Genomics


title: P5,Abd

description:
Library name: P5-Abd
10x Genomics


title: EPD210, KD1, 72 hrs, rep 2

description:
Library name: EPDB272
circRMST-KD1_72h_rep2
EPDB272_N482-0029_S83

tag: genotype


title: EPD210, KD2, 24 hrs, rep 2

description:
Library name: EPDB324
circRMST-KD2_24h_rep2
EPDB324_N482-0027_S81

tag: tissue


title: EPD210, KD2, 72 hrs, rep 2

description:
Library name: EPDB372
circRMST-KD2_72h_rep2
EPDB372_N482-0030_S84


title: P5,Thi

description:
Library name: P5-Thi
10x Genomics


title: EPD210, Control, 72 hrs, rep 2

description:
Library name: EPDB172
NC_72h_rep2
EPDB172_N482-0028_S82


title: P3,Thi

description:
Library name: P3-Thi
10x Genomics


title: P4,Abd

description:
Library name: P4-Abd
10x Genomics


title: 18 ATAC

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Library name: 18 ATAC

library_source: genomic single cell

data_processing:
Raw reads were demultiplexed and single-nucleus gene expression and peak enrichment were quantified simultaneously using CellRanger-arc count (10X Genomics). Single cells were filtered to ensure data used in the downstream analysis is high quality: cells with >10% mitochondrial expression, indicative of dead or dying cells; cells with low numbers of genes expressed (<1000 genes) or low total UMI RNA counts (<2000 UMI counts); and cells with low peak numbers (<200 peaks) or total ATAC counts (<500 counts) were removed. Clustering was performed on the RNA-seq data, anticipating that gene expression would have a higher dynamic range than open chromatin, using the Seurat package in R. Single - droplet multiplets were detected using the union of two independent methods: Scrublet (https://doi.org/10.1016/j.cels.2018.11.005) and DoubletDetection (http://doi.org/10.5281/zenodo.2678041). Following determination of cell types, we re-called peaks separately for each cell type using Seurat, merging peaks across all cell types to obtain a more complete measurement of the open chromatin peaks for rarer cell types.
Assembly: hg38
Supplementary files format and content: Aggregated_atac_fragments.tsv.gz: gzipped tab-separated text file, ATAC-seq fragment alignments
Supplementary files format and content: barcodes.tsv.gz: gzipped tab-separated text file, barcodes for combined multi-sample and multi-omics matrix.
Supplementary files format and content: features.tsv.gz: gzipped tab-separated text file, feature names for combined multi-sample and multi-omics matrix.
Supplementary files format and content: matrix.mtx.gz: gzipped tab-separated text file, Matrix Market format, expression matrix for combined multi-sample and multi-omics matrix.
Supplementary files format and content: recall_peaks.bed: peak coordinates of re-analyzed peak calls
Supplementary files format and content: sample_numbering_manifest.txt: manifest matching cell barcode suffixes in Aggregated_atac_fragments.tsv.gz and barcodes.tsv.gz to sample IDs
Supplementary files format and content: seurat_object.rds: Seurat object with analyzed data

source_name: Dentate gyrus

extract_protocol:
The dentate gyrus was isolated from Fresh Frozen blocks of 36 participants representing 5 diagnostic groups (YA, NCI, MCI, AD and SA). Tissue was then immediately moved to homogenization; For each sample, a separate homogenizer and douncing pestles (loose and tight) were used. Each sample was homogenized in 1ml pre-chilled lysis buffer (0.1% NP-40 Alternative (or NP-40), 10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 40U/mL of RNAse inhibitor) by mechanical douncing for 20 times with the loose pestle followed by 20 times with the tight pestle to obtain a single cell suspension. Cell suspensions were then incubated on ice for 5 minutes. The homogenate was then filtered through 70 µm filters (Milentyi Biotec 130-041-407) and 40 µm filters (Milentyi Biotec 130-041-406), moved to 1.5 ml tubes and centrifuged at 4C for 5 minutes at 500 RCF.   Supernatants were removed and the nuclei pellet was washed 3 times with wash buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2), 0.01% BSA, 40U/mL of RNAse inhibitor). After the last wash, supernatants were removed, and the nuclei pellet was resuspended in resuspension buffer and mixed with 900 µl of Sucrose Cushion buffer. To remove the additional debris, resuspended nuclei were then loaded above a 3 Sucrose Cushion gradient (2.7 ml Nuclei PURE 2M Sucrose Cushion Solution with 300 μl Nuclei PURE Sucrose Cushion Buffer) and the sucrose gradient containing the nuclei was Centrifuged at 13,000 rcf for 45 min at 4°C. The supernatant was then carefully removed and the samples were immediately processed following the Single Cell protocol from 10x Genomics.
The 10X Genomics Multiome library preparation and sequencing was done at Northwestern University NUseq facility core with the support of NIH Grant (1S10OD025120). Nuclei number was analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. The nuclei were first undergone transposition with ATAC enzyme for one hour at 37°C.  we loaded 16,000 transposed nuclei into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip J (10X Genomics, PN-1000230), and according to the manufacturer’s protocol, single cell gel beads were generated in the emulsion (GEM). Barcoded DNA and cDNA were PCR amplified and subjected to library construction. The single nuclei ATAC-seq library was generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene expression kit (10X Genomics, PN-1000281) and single Index Kit N Set A (10X Genomics, PN-1000212) according to the manufacturer’s manual. In addition, the amplified cDNA was used for the gene expression library using dual Index Kit TT Set A (10X Genomics, PN-1000215). Quality control for the constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. For the snATAC-seq library, the multiplexed libraries were pooled and sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 50 bp Read1 and 49 bp Read2. For the snRNA-seq library, the libraries were sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 28 bp Read 1 for cell barcode and UMI and 90 bp Read 2 for transcript expression. The targeted sequencing depth for snATAC-seq and snRNA-seq is 25,000 and 20,000 reads per cell, respectively.

value: Dentate gyrus

tag: diagnosis

value: SA

tag: age at_death

tag: pmi


title: P1,Thi

description:
Library name: P1-Thi
10x Genomics


title: 18 RNA

description: Library name: 18 RNA


title: 16 ATAC

description: Library name: 16 ATAC


title: 16 RNA

description: Library name: 16 RNA


title: P2,Thi

description:
Library name: P2-Thi
10x Genomics


title: 17 ATAC

description: Library name: 17 ATAC


title: P3,Abd

description:
Library name: P3-Abd
10x Genomics


title: 15 ATAC

description: Library name: 15 ATAC


title: S7,Time0,Rep1

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: Library name: S7_Time0_Rep1

data_processing:
Samples were demultiplexed based on the index sequence identified in Read 2. To isolate the sgRNA, fastx_trimmer from FASTX-Toolkit v0.0.14 was used to extract the first 20 bp from Read 1. The trimmed reads were then aligned to the reference library FASTA file using Bowtie v1.3.1. Read counts for each sgRNA in each sample were then extracted from SAM files generated by Bowtie using custom Python scripts.
Significant changes in sgRNA abundance between different conditions were determined using MAGeCK-RRA algorithm v0.5.9.5
Assembly: sgRNA library fasta
Supplementary files format and content: Tab delimited files with the counts for each sgRNA
Library strategy: CRISPR Screen

growth_protocol: Cas9-expressing LN229 cells were maintained in 5% CO2, 20% O2, and humidified in a 37°C incubator and grown in complete DMEM (DMEM (Gibco) + 10% fetal bovine serum.

extract_protocol:
Multiple pellets consisting of 3 million cells were collected for each sample and washed with PBS. PBS was aspirated and cells were flash-frozen and stored at -80°C. gDNA was extracted with Blood and Tissue kit (QIAGEN) according to the manufacturer's protocol.
sgRNA sequences were amplified using NGS Prep Kits from CELLECTA according to the manufacturer's protocol (NGS Prep Kit for sgRNA, shRNA, and DNA Barcode Libraries; version 1).

treatment_protocol: Cells were plated at desired coverage and then immediately treated with the chemical agent or vehicle control while still in suspension. Each condition was performed in duplicate. After 3 days, cells were trypsinized, counted with a hemocytometer (BioRad), replated at desired coverage and retreated. This procedure was repeated on Days 6 and 9. On Day 12, cells were trypsinized and counted.

value: glioma

value: WT (Cas9-expressing)

value: Screen 7


title: S7,MitomycinC_Dose3,Rep1

description: Library name: S7_MitomycinC_Dose3_Rep1

value: Mitomycin C


title: S7,Time0,Rep2

description: Library name: S7_Time0_Rep2


title: S7,MitomycinC_Dose3,Rep2

description: Library name: S7_MitomycinC_Dose3_Rep2


title: S7,MitomycinC_Dose2,Rep2

description: Library name: S7_MitomycinC_Dose2_Rep2


title: P2,Abd

description:
Library name: P2-Abd
10x Genomics


title: S7,Control,Rep1

description: Library name: S7_Control_Rep1

value: DMSO


title: S7,MitomycinC_Dose2,Rep1

description: Library name: S7_MitomycinC_Dose2_Rep1


title: S6,Time0,Rep2

description: Library name: S6_Time0_Rep2

value: Screen 6


title: S6,Time0,Rep1

description: Library name: S6_Time0_Rep1


title: S6,BRACO_19,Rep1

description: Library name: S6_BRACO_19_Rep1


title: S6,BRACO_19,Rep2

description: Library name: S6_BRACO_19_Rep2


title: S6,Control,Rep4

description: Library name: S6_Control_Rep4


title: S6,Control,Rep3

description: Library name: S6_Control_Rep3


title: S6,AflatoxinB1,Rep2

description: Library name: S6_AflatoxinB1_Rep2

value: Aflatoxin B1


title: P1,Abd

description:
Library name: P1-Abd
10x Genomics


title: 17 RNA

description: Library name: 17 RNA


title: S6,AflatoxinB1,Rep1

description: Library name: S6_AflatoxinB1_Rep1


title: S6,Control,Rep2

description: Library name: S6_Control_Rep2


title: S6,Control,Rep1

description: Library name: S6_Control_Rep1


title: S5,Time0,Rep1

description: Library name: S5_Time0_Rep1

value: Screen 5


title: S5,Time0,Rep2

description: Library name: S5_Time0_Rep2


title: S5,IlludinS,Rep2

description: Library name: S5_IlludinS_Rep2

value: IlludinS


title: 15 RNA

description: Library name: 15 RNA


title: S5,IlludinS,Rep1

description: Library name: S5_IlludinS_Rep1


title: S4,Time0,Rep2

description: Library name: S4_Time0_Rep2

value: Screen 4


title: S5,Control,Rep1

description: Library name: S5_Control_Rep1


title: S4,Time0,Rep1

description: Library name: S4_Time0_Rep1


title: S5,Control,Rep2

description: Library name: S5_Control_Rep2


title: S4,Chlorambucil,Rep2

description: Library name: S4_Chlorambucil_Rep2

value: Chlorambucil


title: S4,Chlorambucil,Rep1

description: Library name: S4_Chlorambucil_Rep1


title: S4,Control,Rep2

description: Library name: S4_Control_Rep2


title: S7,Control,Rep2

description: Library name: S7_Control_Rep2


title: S3,Time0,Rep2

description: Library name: S3_Time0_Rep2

value: Screen 3


title: S4,Control,Rep1

description: Library name: S4_Control_Rep1


title: S3,SJG_136_Dose3,Rep2

description: Library name: S3_SJG_136_Dose3_Rep2


title: S3,SJG_136_Dose3,Rep1

description: Library name: S3_SJG_136_Dose3_Rep1


title: S3,SJG_136_Dose2,Rep2

description: Library name: S3_SJG_136_Dose2_Rep2


title: S3,SJG_136_Dose2,Rep1

description: Library name: S3_SJG_136_Dose2_Rep1


title: S3,SJG_136_Dose1,Rep2

description: Library name: S3_SJG_136_Dose1_Rep2


title: S3,SJG_136_Dose1,Rep1

description: Library name: S3_SJG_136_Dose1_Rep1


title: S3,Control,Rep2

description: Library name: S3_Control_Rep2


title: S3,Control,Rep1

description: Library name: S3_Control_Rep1


title: S2,Time0,Rep2

description: Library name: S2_Time0_Rep2

value: Screen 2


title: S2,Time0,Rep1

description: Library name: S2_Time0_Rep1


title: S2,MTZ,Rep1

description: Library name: S2_MTZ_Rep1

value: MTZ


title: S2,KL50,Rep2

description: Library name: S2_KL50_Rep2


title: S2,MTZ,Rep2

description: Library name: S2_MTZ_Rep2


title: S2,KL50,Rep1

description: Library name: S2_KL50_Rep1


title: S2,TMZ,Rep2

description: Library name: S2_TMZ_Rep2

value: TMZ


title: S2,Control,Rep1

description: Library name: S2_Control_Rep1


title: S2,Control,Rep2

description: Library name: S2_Control_Rep2


title: S3,Time0,Rep1

description: Library name: S3_Time0_Rep1


title: RMG1 cell shHIF2A_2 biological replicate3

city: kyoto

first: MENGXIN

last: JIANG

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University

description:
Library name: shHIF2A_2_3
Column in readcounts.csv: shHIF2A_2_3

data_processing:
Raw reads were trimmed and quality-filtered using fastp v0.23.2.
Human reads were aligned to the GRCh38 reference genome using STAR v2.7.10a.
Transcript abundance was quantified using RSEM v1.3.1.
Differential expression analysis was performed using DESeq2 v1.36.0.
Assembly: GRCh38
Supplementary files format and content: The file "readcounts.csv" contains raw read counts for each gene (rows) across all samples (columns). The first column lists Hugo_symbol gene IDs, and each subsequent column represents a sample-specific read count.
Supplementary files format and content: Column names match the library names listed in the metadata table.

growth_protocol: RMG-I was cultured in F-12 supplemented with 10%FBS and antibiotics under 1.5%O2 condition for 24 hours with 5%CO2.

extract_protocol:
Total RNA was extracted from cultured cells using the RNeasy Micro Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA extracted from cultured cells using standard protocols. Libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

value: epithelial cell

value: HIF2A knockdown


title: PDX ID6 xenograft tumor biological replicate1

description:
Library name: ID6_1
Column in readcounts.csv: ID6_1

data_processing:
Raw reads were trimmed and quality-filtered using fastp v0.23.2.
Mouse contamination was removed by separating human reads from mouse reads using BBSplit.
The processed reads were aligned to the human reference genome GRCh38 or the mouse reference genome GRCm39 using STAR (version 2.7.10a) and quantified with RSEM (version 1.3.1).
Differential expression analysis was performed using DESeq2 v1.36.0.
Assembly: GRCh38,GRCm39
Supplementary files format and content: The file "pdxreadcounts.csv" contains raw read counts for each gene (rows) across all samples (columns). The first column lists Hugo_symbol gene IDs, and each subsequent column represents a sample-specific read count.
Supplementary files format and content: Column names match the library names.

source_name: xenograft tumor

growth_protocol: PDX tumors were established by subcutaneous implantation of human ovarian clear cell carcinoma tissues into immunodeficient mice. Mice were maintained under standard housing conditions in accordance with institutional animal care and use guidelines. Tumors were harvested when they reached experimental endpoint size.

extract_protocol:
Total RNA was extracted from xenograft tumor using the RNeasy Micro Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA extracted from xenograft tumors using standard protocols. Libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

value: xenograft tumor


title: PDX ID5 xenograft tumor biological replicate1

description:
Library name: ID5_1
Column in readcounts.csv: ID5_1


title: PDX ID40 xenograft tumor biological replicate3

description:
Library name: ID40_3
Column in readcounts.csv: ID40_3


title: PDX ID5 xenograft tumor biological replicate3

description:
Library name: ID5_3
Column in readcounts.csv: ID5_3


title: PDX ID40 xenograft tumor biological replicate1

description:
Library name: ID40_1
Column in readcounts.csv: ID40_1


title: PDX ID5 xenograft tumor biological replicate2

description:
Library name: ID5_2
Column in readcounts.csv: ID5_2


title: RMG1 cell shHIF2A_2 biological replicate2

description:
Library name: shHIF2A_2_2
Column in readcounts.csv: shHIF2A_2_2


title: RMG1 cell shHIF2A_2 biological replicate1

description:
Library name: shHIF2A_2_1
Column in readcounts.csv: shHIF2A_2_1


title: PDX ID6 xenograft tumor biological replicate3

description:
Library name: ID6_3
Column in readcounts.csv: ID6_3


title: RMG1 cell shHIF2A_1 biological replicate3

description:
Library name: shHIF2A_1_3
Column in readcounts.csv: shHIF2A_1_3


title: RMG1 cell shHIF2A_1 biological replicate2

description:
Library name: shHIF2A_1_2
Column in readcounts.csv: shHIF2A_1_2


title: RMG1 cell shHIF2A_1 biological replicate1

description:
Library name: shHIF2A_1_1
Column in readcounts.csv: shHIF2A_1_1


title: RMG1 cell shcontrol biological replicate3

description:
Library name: shcontrol_3
Column in readcounts.csv: shcontrol_3

value: shcontrol


title: RMG1 cell shcontrol biological replicate2

description:
Library name: shcontrol_2
Column in readcounts.csv: shcontrol_2


title: PDX ID40 xenograft tumor biological replicate2

description:
Library name: ID40_2
Column in readcounts.csv: ID40_2


title: Control 5

city: Shanghai

first: Chuqing

last: He

address: No. 910, Hengshan Rd

department: Department of Obstetrics and Gynecology

institute: School of Medicine, Shanghai Jiaotong University

description:
Library name: sample 10
10x Genomics

data_processing:
Single-cell analysis was conducted using Seurat (version 4.3.0). Potential doublets in the single-cell data were identified and removed using DoubleFinder (version 2.0) (available from https://github.com/chris-mcginnis-ucsf/DoubletFinder).
Genes included in the analysis were required to be expressed in a minimum of three cells, with the total number of expressed cells that expressed >200 genes and <5000 genes. Cells with a high percentage of mitochondrial genes to total genes (> 20%) and hemoglobin genes (> 2%) were filtered out.
Qualified cells from Adjacent tissues (n = 3),Control tissues (n = 4), and Niche tissues (n = 3) were used for scRNA-seq analysis.Using Seurat, the top 2000 most variable genes were identified as highly variable genes (HVG) based on their average expression and dispersion. The dimensionality of the data was reduced using principal component analysis (PCA) on HVG. The Louvain modularity optimization algorithm was used to cluster the cells in the graph, and the clustering results were visualized using Uniform Manifold Approximation and Projection (UMAP).
Differential expression and enrichment analysis were performed to explore the cellular heterogeneity of fibroblasts and endothelial cells.
Trajectory analysis was performed to explore endothelial cells transition.
Assembly: hg38
Supplementary files format and content: *cellranger_barcodes.tsv
Supplementary files format and content: *cellranger_matrix.mtx
Supplementary files format and content: *cellranger_features.tsv

source_name: well-healed cesarean scar

extract_protocol:
Adjacent myometrium tissue of uterine niche (Adjacent3,Adjacent4&Adjacent5), well-healed cesarean scar tissue (Control2,Control3,Control4&Control5) and uterine niche tissue (Niche3,,Niche4 & Niche5) were harvested. These tissues were cut into small pieces with scissors and then incubated in DMEM medium containing collagenase I (Gibco, 17100017) and collagenase II (Gibco, 17101015) at 37°C with gentle shaking for 40-60 minutes. The digested suspension was filtered through a 100-µm cell strainer (CSS-013-100, BIOFIL). Then, the enzymatic reaction was stopped by adding 10% fetal bovine serum (FBS). The cells were pelleted by centrifugation at 350 × g for 5 minutes at 4°C. Red blood cell lysis buffer (Beyotime Biotech, C3702) was used to remove red blood cells. After removing the supernatant, the cells were resuspended in 100 μL of DMEM medium. Cell analysis was conducted using a Trypan blue cell counter, and the cell viability was consistently above 80%. The cell concentration for loading onto the 10x Genomics Chromium™ machine ranged from 700 cells/μL to 1200 cells/μL. Cells were counted and loaded onto the Chromium Controller (10X Genomics) to recover a target of 8000 single cells. The process involved the generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction. Library quantification was performed using Qubit before pooling. The final library pool was sequenced on an Illumina Nova6000 platform using 150-base-pair paired-end reads. Aligning to the GRCh38 human genome, Cell Ranger software (version 6.0.3) was used for quality control and read counting of Ensembl genes
The cell concentration for loading onto the 10x Genomics Chromium™ machine ranged from 700 cells/μL to 1200 cells/μL. Cells were counted and loaded onto the Chromium Controller (10X Genomics) to recover a target of 8000 single cells. The process involved the generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction. Library quantification was performed using Qubit before pooling. The final library pool was sequenced on an Illumina Nova6000 platform using 150-base-pair paired-end reads.Aligning to the GRCh38 human genome, Cell Ranger software (version 6.0.3) was used for quality control and read counting of Ensemble genes.

value: well-healed cesarean scar


title: Control 4

description:
Library name: sample 9
10x Genomics


title: Adjacent 4

description:
Library name: sample 5
10x Genomics

source_name: adjacent myometrium of uterine niche

value: adjacent myometrium of uterine niche


title: Control 2

description:
Library name: sample 7
10x Genomics


title: PDX ID6 xenograft tumor biological replicate2

description:
Library name: ID6_2
Column in readcounts.csv: ID6_2


title: RMG1 cell shcontrol biological replicate1

description:
Library name: shcontrol_1
Column in readcounts.csv: shcontrol_1


title: Control 3

description:
Library name: sample 8
10x Genomics


title: S2,TMZ,Rep1

description: Library name: S2_TMZ_Rep1

value: glioma

value: WT (Cas9-expressing)


title: Adjacent 5

description:
Library name: sample 6
10x Genomics


title: Adjacent 3

description:
Library name: sample 4
10x Genomics


title: Niche 5

description:
Library name: sample 3
10x Genomics

source_name: uterine niche

value: uterine niche