title: Cyto_HCT_WT_SOG_seq_rep2


title: CAR22/CD28/CD3z-short linker, end of manufacturing, rep 1

status: Public on Dec 08 2025

type: SRA

city: St. Louis

first: Nathan

last: Singh

address: 660 S Euclid Ave

country: USA

institute: Washington University School of Medicine in St Louis

description: Library name: M_28s-1

library_source: genomic

data_processing:
In brief, paired-end reads were trimmed for adapters and low-quality bases and aligned to hg38 using Bowtie version 2.5.4. PCR duplicates were removed and for CUT&RUN fragments were truncated to 120 base pairs to enrich mononucleosome-sized fragments.  Sorted BAM files were used for peak calling with MACS2, and resulting narrow peaks were filtered against the ENCODE blacklist. Peak sequences were extracted for downstream motif and footprinting analyses. Differential binding analysis was performed using DiffBind (v3.18.0) with DESeq2 (1.48.2) framework and default settings after resizing peaks to 500 bp around summits. Genomic annotation of peaks and nearest-gene mapping were performed using ChIPseeker (v1.44.0) with the default settings.
Assembly: hg38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

growth_protocol: Primary Human T cells  were grown in RPMI media with 10% FBS, 1% Pen/Strep, 1% HEPES, 1% L-glutamine in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
ATAC library preparation was done by standard methods(45). 50,000 CAR T cells were used per reaction and index primers for sequencing acquired were from IDT for Illumina DNA/RNA UD Indexes plate A (Illumina 20027213), then size selection of fragments (< 600bp) was done using SPRIselect Beads (Beckman Coulter, Inc.).
ATAC library preparation was done by standard methods(45). 50,000 CAR T cells were used per reaction and index primers for sequencing acquired were from IDT for Illumina DNA/RNA UD Indexes plate A (Illumina 20027213), then size selection of fragments (< 600bp) was done using SPRIselect Beads (Beckman Coulter, Inc.).

treatment_protocol: Cells were stimulated on CD3/CD28 dynabeads at a ratio of 3 beads : 1 T cell. The following day, different lentiviral vectors encoding CAR or BACH2 were co-transduced into T cells. Beads were removed on day 6 after bead stimulation and cells were expanded for 8 more days prior to collection for genomic DNA purification. For chronic stimulation, CAR+ T cells with truncated CD34 were magnetically sorted with CD34-PE and anti-PE microbeads, and BACH2-overexpressed CAR+ T cells with truncated EGFR were magnetically sorted with EGFR-PE and anti-PE microbeads. Absolute count of CD34+ T cells and GFP+ Nalm6 were evaluated by flow cytometry and combined with an targeted E:T ratio. The absolute count of T cell and Nalm6 in this co-culture were re-evaluated every 2-3 days by flow cytometry and fresh cancer cells were added to maintain an targeted E:T ratio. On day 7 after co-culture, dead cells were removed, then CAR+ T cells were magnetically sorted again.

tag: tissue

value: Peripheral blood mononuclear cells

tag: cell type

value: primary human T cells

tag: genotype

value: WT

tag: treatment

value: CAR22-short linker/CD28/CD3z


title: RPF_HCT_Optogranule_rep1

city: Boston

first: Jarrett

last: Smith

state: MA

address: 455 Main st, Room 627

institute: Whitehead Institute

description:
ribo-seq (RPFs)
cts_riboseq.csv

library_source: transcriptomic

data_processing:
DESeq2
Assembly: hg38
Supplementary files format and content: Comma-delimited files containing read counts for all samples.
Supplementary files format and content: Supplemental Excel tables that summarize the sequencing data.

molecule: total RNA

growth_protocol: All cells were cultured at 37°C with 5% CO2 using McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine

extract_protocol:
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.

treatment_protocol: Cells were either treated with 500 μM IAA (depletion), 500 μM sodium arsenite for 1 hr (oxidative stress), or 45°C incubation for 25 min (heatshock)

value: dox; blue light


title: RPF_HCT_blue_control_rep2

description:
ribo-seq (RPFs)
cts_riboseq.csv

value: blue light


title: RPF_HCT_Optogranule_rep2

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: CAR22/41BB/CD3z-short linker, end of manufacturing, rep 1

description: Library name: M_BBs-1

value: CAR22-short linker/41BB/CD3z


title: RPF_HCT_blue_control_rep1

description:
ribo-seq (RPFs)
cts_riboseq.csv


title: ∆Ste12, None, 0hs, Rep4, batch_2

city: Bethesda

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

description: Library name: AY37

data_processing:
Fastq files from sequencing were trimmed of remaining sequencing adaptors and low-quality sequences using bbtools.
The resulting fastq files were aligned to the sacCer3 reference genome using STAR
Duplicate reads were removed and a table of read counts per gene per sample were generated using featureCounts
Assembly: sacCer3
Supplementary files format and content: Tabulated file with read counts per sample per gene

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown overnight at 30ºC in YPGal (1% yeast extract, 2% peptone, and 2% galactose) to mid-log phase and then centrifuged and resuspended in YPD (1% yeast extract, 2% peptone, and 2% glucose) for 3 hours in order to arrest cells in G1 (Figure 1A).

extract_protocol:
Total RNA was prepared using SDS, hot acid phenol, and chloroform
Libraries for RNA-sequencing were prepared using "Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus" kits (with 50-nt sequencing) from total RNA. During the reverse-transcription step of library preparation, removal of cytoplasmic and mitochondrial rRNA was done using the QIAseq FastSelect -rRNA Yeast Kit.

treatment_protocol: After the 3-hour synchronization, half of the culture was pelleted, the YPD was removed, and the pellet was flash frozen in liquid nitrogen for RNA extraction. To the second half of the culture, alpha-factor (10mM in 0.1 M sodium acetate pH 5.2, Zymo Research) was added at a 1:500 ratio (20 µM final concentration) for 60 minutes before the same freezing process was done.

tag: cell line

value: MATa

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3 ste12::KanMX

tag: batch


title: ∆Ste12, None, 0hs, Rep3, batch_2

description: Library name: AY35


title: RNA_HCT_Optogranule_rep2

description: matched RNA seq


title: RNA_HCT_blue_control_rep2

description: matched RNA seq


title: SG_HCT_SOG_Control_seq_rep1

description:
RNA seq of SG purified fraction
cts_SGseq.csv

value: oxidative stress


title: CAR22/CD28/CD3z-long linker, end of manufacturing, rep 2

description: Library name: M_28L-2

value: CAR22-long linker/CD28/CD3z


title: RNA_HCT_blue_control_rep1

description: matched RNA seq


title: RNA_HCT_Optogranule_rep1

description: matched RNA seq


title: ∆Kar4, alpha-factor, 1hs, Rep4, batch_2

description: Library name: AY34

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3 kar4::KanMX

value: alpha-factor


title: B16F10 shRNA Ctrl replicat3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: Library name: CTRLN2

data_processing:
Sequencing data from total RNA sequencing were pre-processed and aligned using the nf-core/rnaseq workflow (v.3.0).
Assembly: Pre-processed reads were aligned to the Mus musculus (GRCm38) reference genome using STAR aligner (v.2.6.1d) and quantification was performed by Salmon (v.1.4.0)
Supplementary files format and content: Differential expression analysis was performed on the triplicates of two groups (shCTR and shOSGEP) using the packages edgeR (v.3.14) [3] and DESeq2 (v.1.30) [4] in the R environment. To identify the Differentially Expressed Genes (DEGs), the Log2 Fold-Change (log2FC) and p-values were calculated, shCTR was used as the reference. DEGs were considered up or down-regulated according to the sign of the log2FC

molecule: polyA RNA

organism: Mus musculus

source_name: Cell

growth_protocol: B16F10 were cultured in a humidified incubator at 37°C with 5% CO2, grown in Dulbecco’s modified Eagle’s medium (DMEM, LONZA) supplemented with 1% glutamine and 1% penicillin-streptomycin and 10% FBS (GIBCO)

extract_protocol:
Total RNAs from three independent infections were extracted using TRIzol (Life Technologies) following the manufacturer’s protocol
Libraries were prepared from 500 ng of total RNA using the Illumina Truseq RNA Sample Preparation kit V2. PolyA RNAs were purified with polyT-coated magnetic beads, chemically fragmented, and used as templates for cDNA synthesis with random hexamers. The cDNA ends were then end-blunted, adenylated at the 3′OH ends, and ligated to indexed adaptors. The adaptor-ligated library fragments were enriched by PCR according to Illumina’s protocol and purified. Libraries were validated on the Bioanalyser DNA 1000 chip and quantified by qPCR using the KAPA library quantification kit. Sequencing was performed on a HiSeq2000 with a paired-end 2 × 100 base protocol

value: Cell

value: melanoma


title: ∆Kar4, None, 0hs, Rep4, batch_2

description: Library name: AY33


title: B16F10 shRNA OSGEP#2 replicat3

description: Library name: O2N2

value: KD OSGEP


title: ∆Kar4, alpha-factor, 1hs, Rep3, batch_2

description: Library name: AY32


title: CAR22/CD28/CD3z-short linker, end of manufacturing, rep 2

description: Library name: M_28s-2


title: B16F10 shRNA OSGEP#2 replicat1

description: Library name: O2AR8


title: B16F10 shRNA Ctrl replicat2

description: Library name: CTRLN1


title: CAR22/CD28/CD3z-long linker, end of manufacturing, rep 1

description: Library name: M_28L-1


title: ∆Kar4, None, 0hs, Rep3, batch_2

description: Library name: AY31


title: CAR22/41BB/CD3z-short linker, D7 chronic stimulation, rep 2

description: Library name: CUTnRUN_BBs_cJUN-2

data_processing:
In brief, paired-end reads were trimmed for adapters and low-quality bases and aligned to hg38 using Bowtie version 2.5.4. PCR duplicates were removed and for CUT&RUN fragments were truncated to 120 base pairs to enrich mononucleosome-sized fragments.  Sorted BAM files were used for peak calling with MACS2, and resulting narrow peaks were filtered against the ENCODE blacklist. Peak sequences were extracted for downstream motif and footprinting analyses. Differential binding analysis was performed using DiffBind (v3.18.0) with DESeq2 (1.48.2) framework and default settings after resizing peaks to 500 bp around summits. Genomic annotation of peaks and nearest-gene mapping were performed using ChIPseeker (v1.44.0) with the default settings.
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Run

extract_protocol:
CUT&RUN sample preparation was performed using the CUTANA CUT&RUN kit (Epicypher 14-1048). Briefly, 500,000 nuclei per reaction were extracted from thawed CAR T cells using nuclei extraction buffer (EpiCypher 21-1026). 1ug of antibody (control IgG, H3K4Me3 or cJUN) was used to pull down fragments. Sequencing libraries were prepared using the CUTANA Library Prep Kit (Epicypher 14-1001 & 14-1002) and following manufacturer instructions.
CUT&RUN sample preparation was performed using the CUTANA CUT&RUN kit (Epicypher 14-1048). Briefly, 500,000 nuclei per reaction were extracted from thawed CAR T cells using nuclei extraction buffer (EpiCypher 21-1026). 1ug of antibody (control IgG, H3K4Me3 or cJUN) was used to pull down fragments. Sequencing libraries were prepared using the CUTANA Library Prep Kit (Epicypher 14-1001 & 14-1002) and following manufacturer instructions.

value: CAR22-short linker/41BB/CD3z, cJUN antibody pull down


title: CAR22/41BB/CD3z-short linker, D7 chronic stimulation, rep 1

description: Library name: CUTnRUN_BBs_cJUN-1

value: Peripheral blood mononuclear cells


title: B16F10 shRNA Ctrl replicat1

description: Library name: CTRLAR8


title: CAR22/CD28/CD3z-long linker, end of manufacturing, rep 3

description: Library name: M_28L-3

value: primary human T cells


title: Zap_K2

city: Novosibirsk

first: Nikita

last: Torgunakov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics

description:
Library name: Zap_K2
Raw data are not provided due to patient privacy concerns.

data_processing:
Fastq files from different sequencing runs of the same DNA library were merged by zcat and gzip and processed using the Juicer program (https://github.com/genomech/juicer1.6_compact) to generate duplicate-removed alignment files (merged_nodups.txt). Finally, the Juicer Tools utility from Juicer was used to produce hic files filtered for blacklist regions.
Reads in fastq format were aligned to the T2T genome using BWA (v 0.7.18)33, and stored as coordinate-sorted bam files via samtools (v 1.20)34. Subsequently, bam files were resorted by picard (v3.2.0) (https://broadinstitute.github.io/picard/) AddOrReplaceReadGroups using query name, assigning all reads to a single group. Then duplicates were removed with picard MarkDuplicates, after which files were coordinate-sorted and indexed with samtools. Finally, coverage files in BigWig format were generated using bamCoverage (v 3.5.5)3 with the options --Offset 1 1 --binSize 1 --minMappingQuality 30).
Assembly: T2T
Supplementary files format and content: .hic files as the primary output of Juicer, containing the processed Hi-C contact matrices data.
Supplementary files format and content: .bw files in BigWig format containing sequencing coverage data.

source_name: Trophectoderm

extract_protocol:
1. Crosslinking Trophectoderm biopsies were fixed by incubating sample in 2% formaldehyde (Sigma-Aldrich) drop for 15 min at room temperature. Crosslinking was quenched by transferring the sample into a 0.125M glycine solution drop and incubating for 10 min at room temperature. The samples were then transferred to 0.2 ml tubes containing 4 μl of PBS, snap-frozen, and stored at -80°C.  2. Lysis and agarose embedding 1 μl of 2% SDS in 4x NEB 3.1 buffer (New England Biolabs) was added to each sample, followed by incubation for 1 h at 37°C. SDS was quenched with Triton X-100 (final concentration 3%) for 20 min. Subsequently, the samples were embedded into 10 μl of low melting point agarose (ThermoFisher Scientific), incubation for 30 min at 4°C.  3. Fragmentation The reaction volume was 20 µL: 2 µL of 10x NEB 3.1 buffer, 4 µL of 10% Triton X-100, 0.5 µL of DpnII (25 U/µL, New England Biolabs), and 13.5 µL of H2O. The samples were incubated overnight at 37°C. After incubation, the samples were washed sequentially with 30 µL of NEB 3.1 buffer containing 0.1% SDS, 50 µL of NEB 3.1 buffer with 2% Triton X-100, and finally with 60 µL of NEB 3.1 buffer. 4. Biotin labelling The reaction volume was 6 µL, consisting of 0.6 µL of 10x NEB 3.1 buffer, 0.15 µL each of 10 mM dTTP, dATP, dGTP, 1.5 µL of 1 mM biotin-15-dCTP (DNA-Synthesis), and 1 µL of Klenow fragment (5000 U/µL, SibEnzym). The reaction was incubated for 4 h at 22°C. 5. Ligation The reaction volume was 50 µL: 5 µL of 10x T4 ligase buffer (New England Biolabs), 0.5 µL of 100 mM ATP, 0.5 µL of 100 mg/mL BSA (SibEnzyme), 5 µL of 10% Triton X-100, 5 µL of T4 DNA ligase (DNA Technologies), and H2O to a final volume of 44 µL. The reaction was incubated overnight at 16°C. 6. Agarose removal The liquid was removed, and the samples were washed with 50 µL of 10 mM Tris-HCl, pH 8.0. Incubation followed for 20 minutes at 65°C, then for 20 minutes at 42°C. Subsequently, 2.2 µL of 10 mM Tris-HCl, pH 8.0, and 0.8 µL of agarase (0.4 U/µL, ThermoFisher Scientific) were added, and the incubation continued for 40 minutes at 42°C. 7. Cross-link reversal 0.5 µL of proteinase K (800 U/mL, NEB) and 0.5 µL of 10 mM Tris-HCl, pH 8.0 were added, and the reaction was incubated overnight at 65°C. 8. Sample Purification Samples were purified using two volumes of VAHTS DNA Clean Beads (Vazyme) and eluted in 16 µL of H2O.
1. NGS library preparation Library preparation was performed using the KAPA HyperPLus Kit (Roche) following the manufacturer's instructions with modifications. The reaction volumes were adjusted: enzymatic fragmentation was performed in 20 µL for 10 min, end-repair and A-tailing in 24 µL, adapter ligation in 44 µL. The adapters (KAPA Single-Indexed Adapter Kit, Roche) were diluted to 300 nM, and the ligation time was extended to 2 h at 20°C. Post-ligation cleanup was performed using 35 µL VAHTS DNA Clean Beads, then samples were eluted in 20 µL of H2O. 2. Biotin pulldown For enrichment, 25 µL of streptavidin beads (Hydrophilic Streptavidin Magnetic Beads, NEB) were used. Enrichment occurred after adapter ligation for sequencing and before amplification. 3. Amplification 20 cycles of amplification were performed in a 25 µL reaction, followed by purification of the reaction with one volume of VAHTS DNA Clean Beads.

value: Trophectoderm

value: Trophectoderm cells


title: Zap_e3

description:
Library name: Zap_e3
Raw data are not provided due to patient privacy concerns.

source_name: Blastocyst

value: Blastocyst

value: Whole-blastocyst cell population


title: Zap_e2

description:
Library name: Zap_e2
Raw data are not provided due to patient privacy concerns.


title: YAK_e4

description:
Library name: YAK_e4
Raw data are not provided due to patient privacy concerns.


title: WT, alpha-factor, 1hs, Rep3, batch_2

description: Library name: AY40

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3


title: ∆Ste12, alpha-factor, 1hs, Rep3, batch_2

description: Library name: AY36

value: MATa


title: CAR22/CD28/CD3z-short linker, D7 chronic stimulation, rep 2

description: Library name: CUTnRUN_28s_cJUN-2

value: WT

value: CAR22-short linker/CD28/CD3z, cJUN antibody pull down


title: XAH_K13

description:
Library name: XAH_K13
Raw data are not provided due to patient privacy concerns.


title: XAH_e13

description:
Library name: XAH_e13
Raw data are not provided due to patient privacy concerns.


title: WT, None, 0hs, Rep4, batch_2

description: Library name: AY41


title: CAR22/41BB/CD3z-short linker, D7 chronic stimulation, rep 3

description: Library name: CUTnRUN_BBs_cJUN-3


title: CAR22/CD28/CD3z-short linker, D7 chronic stimulation, rep 1

description: Library name: CUTnRUN_28s_cJUN-1


title: Vor1_K

description:
Library name: Vor1_K
Raw data are not provided due to patient privacy concerns.


title: Vla9_e

description:
Library name: Vla9_e
Raw data are not provided due to patient privacy concerns.


title: WT, None, 0hs, Rep3, batch_2

description: Library name: AY39


title: CAR22/CD28/CD3z-short linker+BACH2 overexpression, D7 chronic stimulation, rep 3

description: Library name: CUTnRUN_28s+BACH2_cJUN-3

value: CAR22-short linker/CD28/CD3z+BACH2 overexpression, cJUN antibody pull down


title: Vla6_K

description:
Library name: Vla6_K
Raw data are not provided due to patient privacy concerns.


title: CAR22/CD28/CD3z-short linker+BACH2 overexpression, D7 chronic stimulation, rep 2

description: Library name: CUTnRUN_28s+BACH2_cJUN-2


title: WT, alpha-factor, 1hs, Rep4, batch_2

description: Library name: AY42


title: Vla4_K

description:
Library name: Vla4_K
Raw data are not provided due to patient privacy concerns.


title: ∆Ste12, alpha-factor, 1hs, Rep2, batch_1

description: Library name: AY8

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3 ste12::KanMX


title: B16F10 shRNA OSGEP#2 replicat2

description: Library name: O2N1


title: Vla2_e

description:
Library name: Vla2_e
Raw data are not provided due to patient privacy concerns.


title: ∆Ste12, alpha-factor, 1hs, Rep1, batch_1

description: Library name: AY7

value: alpha-factor


title: Vla2_K_0705

description:
Library name: Vla2_K_0705
Raw data are not provided due to patient privacy concerns.


title: CAR22/CD28/CD3z-short linker, D7 chronic stimulation, rep 3

description: Library name: CUTnRUN_28s_cJUN-3


title: ∆Ste12, None, 0hs, Rep2, batch_1

description: Library name: AY6


title: Vla1_K_0705

description:
Library name: Vla1_K_0705
Raw data are not provided due to patient privacy concerns.


title: CAR22/CD28/CD3z-short linker+BACH2 overexpression, D7 chronic stimulation, rep 1

description: Library name: CUTnRUN_28s+BACH2_cJUN-1


title: Vla1_e

description:
Library name: Vla1_e
Raw data are not provided due to patient privacy concerns.


title: Ton1_e

description:
Library name: Ton1_e
Raw data are not provided due to patient privacy concerns.


title: ∆Ste12, None, 0hs, Rep1, batch_1

description: Library name: AY5


title: Tok1_K

description:
Library name: Tok1_K
Raw data are not provided due to patient privacy concerns.


title: MII_occyte3_IP

city: Hefei

first: TC

last: H

address: 130 Changjiang West Road

country: China

institute: AAU

description: Library name: Sample12

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: ARE-UCD1.2
Supplementary files format and content: GV_oocyte_IPVSGV_oocyte_input_peak.xlsx,MII_oocyte_IPVSMII_oocyte_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: MII_oocyteVSGV_oocyte_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: 1_genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)
Library strategy: MeRIP-Seq

organism: Bos taurus

source_name: oocyte

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: oocyte


title: ∆Kar4, alpha-factor, 1hs, Rep2, batch_1

description: Library name: AY4

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3 kar4::KanMX


title: Shur3_K

description:
Library name: Shur3_K
Raw data are not provided due to patient privacy concerns.


title: MII_occyte3_input

description: Library name: Sample11


title: Vla7_K

description:
Library name: Vla7_K
Raw data are not provided due to patient privacy concerns.


title: Shur2_K

description:
Library name: Shur2_K
Raw data are not provided due to patient privacy concerns.


title: Shur1_K_2205

description:
Library name: Shur1_K_2205
Raw data are not provided due to patient privacy concerns.


title: ∆Kar4, alpha-factor, 1hs, Rep1, batch_1

description: Library name: AY3


title: Shen3_e

description:
Library name: Shen3_e
Raw data are not provided due to patient privacy concerns.


title: ∆Kar4, None, 0hs, Rep2, batch_1

description: Library name: AY2


title: MII_occyte1_IP

description: Library name: Sample8


title: MII_occyte2_input

description: Library name: Sample9


title: Shen3_K

description:
Library name: Shen3_K
Raw data are not provided due to patient privacy concerns.


title: Shen2_e

description:
Library name: Shen2_e
Raw data are not provided due to patient privacy concerns.


title: Shen2_K

description:
Library name: Shen2_K
Raw data are not provided due to patient privacy concerns.


title: ∆Kar4, None, 0hs, Rep1, batch_1

description: Library name: AY1


title: Shen1_e

description:
Library name: Shen1_e
Raw data are not provided due to patient privacy concerns.


title: Shen1_K

description:
Library name: Shen1_K
Raw data are not provided due to patient privacy concerns.


title: Sheg1_K2

description:
Library name: Sheg1_K2
Raw data are not provided due to patient privacy concerns.


title: WT, alpha-factor, 1hs, Rep2, batch_1

description: Library name: AY12


title: Sheg1_e

description:
Library name: Sheg1_e
Raw data are not provided due to patient privacy concerns.


title: Early AVF resection 2

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description:
Library name: T668
10X Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2).
The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger human reference package (version 2020-A), from GRCh38 Ensembl build 98/GENCODE v32 gene annotations.
Assembly: GRCh38 Ensembl build 98
Supplementary files format and content: barcodes.tsv.gz is a gzipped text file listing individual cell barcodes included in the sample analysis
Supplementary files format and content: features.tsv.gz is a gzipped tab-delimited file of the gene features included in the gene quantification for each sample
Supplementary files format and content: matrix.mtx.gz is a gzipped tab-delimited file of the counts per feature per cell barcode for each sample

source_name: AVF

extract_protocol:
Upper arm veins or venous AVF segments 0.5-1 cm in length were cut longitudinally with a sterile scalpel and then into 1-2 mm square sections. Samples were enzymatically digested for 90 minutes at 37°C with shaking using a combination of collagenase type II, soybean trypsin inhibitor, elastase, Dispase, DNAse I, collagenase type XI, hyaluronidase type I, and HEPES in HBSS with Ca2+ and Mg2+. After 90 minutes, an equal volume of Accumax was added to the dissociation mix and incubated for an additional 5 minutes. Single cells were filtered through a 40 μM strainer, washed with HBSS twice, and incubated with red blood cell lysis buffer for 5-10 min. Cells were washed once again with HBSS and resuspended in 0.1% BSA in PBS for counting and RNA sequencing.
Samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and subsequently run on a thermocycler (Eppendorf). Sequencing libraries were evaluated for quality on the Agilent Tape Station (Agilent Technologies, Palo Alto, CA) and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and qPCR before sequencing on the Illumina NovaSeq 6000.

value: AVF

tag: Sex

value: Male

tag: age

tag: race/ethnicity

value: Hispanic


title: WT, None, 0hs, Rep2, batch_1

description: Library name: AY10


title: MII_occyte1_input

description: Library name: Sample7


title: Say3_K

description:
Library name: Say3_K
Raw data are not provided due to patient privacy concerns.


title: Sav4_K

description:
Library name: Sav4_K
Raw data are not provided due to patient privacy concerns.


title: Sav4_eB

description:
Library name: Sav4_eB
Raw data are not provided due to patient privacy concerns.


title: Sav4_e

description:
Library name: Sav4_e
Raw data are not provided due to patient privacy concerns.


title: WT, None, 0hs, Rep1, batch_1

description: Library name: AY9


title: Sach2_K

description:
Library name: Sach2_K
Raw data are not provided due to patient privacy concerns.


title: MII_occyte2_IP

description: Library name: Sample10


title: Sach1_K_2110

description:
Library name: Sach1_K_2110
Raw data are not provided due to patient privacy concerns.


title: GV_occyte2_IP

description: Library name: Sample4


title: DMSO + Antigen + Carvacrol 4

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: 28

data_processing:
RNAseq data were quality filtered using Trim-galore
Alignment using Salmon v 1.4
DEG analysis with DESEQ2
Assembly: Equine genome Ensembl110
Supplementary files format and content: Read counts table with gene symbol and raw read count

organism: Equus caballus

source_name: Primary monocytes

extract_protocol:
RNA extracted with Qiagen RNeasy® Plus Mini kit (Qiagen 74134)
Standard Illumina

treatment_protocol: Cells were treated for six hours with LPS (125 ng/mL), Helminth antigen (50 µg/mL),  or antoigen combined with either carvacrol or cinnamaldehyde (both 5 µg/mL)

value: Primary monocytes


title: GV_occyte2_input

description: Library name: Sample3


title: Sach1_e

description:
Library name: Sach1_e
Raw data are not provided due to patient privacy concerns.


title: DMSO + Antigen + Cinnamaldehyde 4

description: Library name: 27


title: Pash_K2

description:
Library name: Pash_K2
Raw data are not provided due to patient privacy concerns.

value: Trophectoderm


title: DMSO + LPS 4

description: Library name: 26


title: GV_occyte1_input

description: Library name: Sample1


title: GV_occyte1_IP

description: Library name: Sample2


title: Water + Antigen 4

description: Library name: 25


title: GV_occyte3_IP

description: Library name: Sample6


title: Pet1_K

description:
Library name: Pet1_K
Raw data are not provided due to patient privacy concerns.

value: Trophectoderm cells


title: Pash_K3

description:
Library name: Pash_K3
Raw data are not provided due to patient privacy concerns.


title: WT, alpha-factor, 1hs, Rep1, batch_1

description: Library name: AY11


title: Pash_e3

description:
Library name: Pash_e3
Raw data are not provided due to patient privacy concerns.

value: Blastocyst


title: GV_occyte3_input

description: Library name: Sample5


title: Pash_e2

description:
Library name: Pash_e2
Raw data are not provided due to patient privacy concerns.

value: Whole-blastocyst cell population


title: Pan1_K

description:
Library name: Pan1_K
Raw data are not provided due to patient privacy concerns.


title: GliomaxSlo-RNAi sample

city: LLEIDA

first: Judit

last: Herreros

address: Rovira Roure 80 (lab 2.11)

department: Basic Medical Sciences

country: Spain

institute: University of Lleida-IRBLleida

description:
Library name: GliomaxSlo-RNAi
glioma flies with the RFP expression in glial membranes and Slo-RNAi expression in glia

data_processing:
Reads were assessed for quality using FastQC v0.11.7.
Adapter sequences and low-quality bases were removed using Trimmomatic v0.38.
Reads were aligned to the Drosophila melanogaster genome (dm6, FlyBase r6.32) using HISAT2 v2.1.0.
Transcript assembly and expression quantification were performed using StringTie v2.1.3b. Expression values were calculated as raw counts, TPM, and FPKM.
Differential expression analysis was conducted using edgeR (Bioconductor R package) with genes filtered by log2 fold change ≥ 2 and p-value < 0.05.
Assembly: Drosophila melanogaster dm6 (FlyBase release r6.32)
Supplementary files format and content: The processed data is provided in a single file named Drosophila_Glioma_RNAseq_Expression.tsv, which contains gene expression values for all experimental conditions. The file includes the following columns: Gene and transcript information: Gene_ID, Transcript_ID, Gene_Symbol, Description, gene_biotype, Protein_ID, FLYBASE, locus_tag, old_locus_tag. Expression values: FPKM and TPM for each condition (Control, Glioma, GliomaxCa-α1T-RNAi, GliomaxSlo-RNAi). Differential expression analysis: Fold-change (fc), logCPM, raw p-values, and adjusted p-values (Benjamini-Hochberg correction) for comparisons between conditions. Summary statistics: Mean expression values and sample sizes (N) for each condition. Read count data: Raw read counts for each condition. The data is formatted as a tab-separated values (TSV) file.

organism: Drosophila melanogaster

source_name: Larval head

growth_protocol: Flies were bred in conventional fly food at 25°C. Parental flies were crossed and kept at 25°C for 3 days for egg laying. Then, larvae were transferred to 29°C for 5 days to activate the Gal80[ts]-Gal4 expression system. Dissections were performed on the fifth day at 29°C

extract_protocol:
Total RNA was extracted from Drosophila larval heads using the EZNA Total RNA Kit I (VWR, R6834-01) following the manufacturer’s instructions. Samples were treated with DNase to eliminate potential DNA contamination.
RNA quality was assessed using Bioanalyzer (Agilent Technologies). Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina), and poly-A mRNA was enriched using oligo-dT beads.

treatment_protocol: No additional treatment was applied beyond the genetic manipulation and temperature shift for Gal80[ts]-Gal4 activation.

value: Larval head

value: UAS-dEGFR[L], UAS-dp110[CAAX]; tub-Gal80[ts]; UAS-Slo-RNAi; repo-Gal4, UAS-myrRFP

value: untreated


title: Ore1_K

description:
Library name: Ore1_K
Raw data are not provided due to patient privacy concerns.


title: GliomaxCa-alpha1T-RNAi

description:
Library name: GliomaxCa-alpha1T-RNAi
glioma flies with the RFP expression in glial membranes and Ca-α1T-RNAi expression in glia

value: UAS-dEGFR[L], UAS-dp110[CAAX]; tub-Gal80[ts]; UAS-Ca-alpha1T-RNAi; repo-Gal4, UAS-myrRFP


title: Water + LPS 4

description: Library name: 24


title: Ore1_e27

description:
Library name: Ore1_e27
Raw data are not provided due to patient privacy concerns.


title: Water Control 4

description: Library name: 23


title: Glioma sample

description:
Library name: Glioma
glioma flies with the RFP expression in glial membranes

value: UAS-dEGFR[L], UAS-dp110[CAAX]; tub-Gal80[ts]; repo-Gal4, UAS-myrRFP


title: Mog1_e

description:
Library name: Mog1_e
Raw data are not provided due to patient privacy concerns.


title: DMSO + Antigen + Carvacrol 3

description: Library name: 22


title: Mel6_K

description:
Library name: Mel6_K
Raw data are not provided due to patient privacy concerns.


title: Mat2_K

description:
Library name: Mat2_K
Raw data are not provided due to patient privacy concerns.


title: Control sample

description:
Library name: Control
control flies with the RFP expression in glial membranes

value: tub>Gal80[ts]; repo>Gal4, UAS-myrRFP


title: Mar1_K

description:
Library name: Mar1_K
Raw data are not provided due to patient privacy concerns.


title: Mal3_K

description:
Library name: Mal3_K
Raw data are not provided due to patient privacy concerns.


title: DMSO + Antigen + Cinnamaldehyde 3

description: Library name: 21


title: MAD_K3

description:
Library name: MAD_K3
Raw data are not provided due to patient privacy concerns.


title: GE_Screen_Tcell

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

description: Library name: GE_Screen_Tcell

data_processing:
Trimmed sequences were aligned to libraries using Bowtie, with zero mismatches tolerated and all alignments from multi-mapped reads included. Guide composition and comparisons across each cellular fraction were analyzed using CasTLE version 1.040. Briefly, enrichment of individual sgRNAs was then calculated as a median-normalized log ratio of the fraction of counts. For each gene, a maximum likelihood estimator was used to identify the most likely effect size and associated log-likelihood ratio (confidence score) by comparing the distribution of gene-targeting guides to a background of nontargeting and safe-targeting guides. P-values were then estimated by permuting gene-targeting guides, and hits were called using FDR thresholds calculated via the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: .bam, .bw, .broadPeak
Library strategy: CRISPR Screen

source_name: Bone marrow

extract_protocol:
After 3-week ex vivo expansion of c-Kit+ bone marrow HSPCs, ~50 million cells were transduced overnight with lentivirus generated from one of 10 Bassik mouse CRISPR knockout sub-libraries40 (a kind gift from the Bassik lab; Addgene 1000000121-1000000130). Each sub-library contained ~20,000 elements. Lentivirus was generated using helper plasmids pCMV-VSV-G-RSV-Rev and pMDLg/pRRE. To reduce multiple integrations per cell, we used a transduction efficiency of 20-30%, to achieve 500-750x coverage (10-15 million transduced HSPCs per sub-library). Two days later, transduced HSPCs were selected for using puromycin for 72 hours. HSPCs were recovered and expanded in culture for another 9 days. For ex vivo timepoints, 20 million HSPCs were harvested for DNA extraction. At day-14 post-transduction, HSPCs were transplanted into lethally-irradiated (10Gy) C57BL/6-CD45.1 recipients (1-2 million HSPCs per recipient; >10 million per sub-library across 6-8 mice). A total of 65 mice were transplanted for the genome-wide screen, while 24 mice were transplanted for the Gene Expression-focused screen. After 10-12-weeks, whole bone marrow and spleen were harvested. From the whole bone marrow, c-Kit+Sca-1+Lineage- or c-Kit+Lineage- cells were isolated by FACS. The remaining bone marrow and spleen cells were pooled and CD45R+ B cells, CD4/CD8+ T cells, Mac1/Gr1+ myeloid cells, and Ter119+ erythroid cells were isolated via MACS columns. Genomic DNA was extracted for all screen populations separately according to the protocol included with QIAGEN Blood Mini or Midi Kit.
Using known universal sequences present in the lentivirally incorporated DNA (oMCB 1562 and oMCB 1563), sgRNA sequences were amplified and prepared for sequencing by two sequential polymerase chain PCR reactions as previously described. Products were sequenced using an Illumina Nextseq to monitor library composition (20–40 million reads per sample).

value: Bone marrow

value: HSPC


title: Lam1_K

description:
Library name: Lam1_K
Raw data are not provided due to patient privacy concerns.


title: Lim1_K

description:
Library name: Lim1_K
Raw data are not provided due to patient privacy concerns.


title: DMSO + LPS 3

description: Library name: 20


title: GE_Screen_HSPC

description: Library name: GE_Screen_HSPC


title: MAD_e3

description:
Library name: MAD_e3
Raw data are not provided due to patient privacy concerns.


title: GE_Screen_Myeloid

description: Library name: GE_Screen_Myeloid


title: Water + Antigen 3

description: Library name: 19


title: Kus1_K

description:
Library name: Kus1_K
Raw data are not provided due to patient privacy concerns.


title: Kur3_e

description:
Library name: Kur3_e
Raw data are not provided due to patient privacy concerns.


title: Water + LPS 3

description: Library name: 18


title: Kur3_K

description:
Library name: Kur3_K
Raw data are not provided due to patient privacy concerns.


title: Water Control 3

description: Library name: 17


title: Kra3_K

description:
Library name: Kra3_K
Raw data are not provided due to patient privacy concerns.


title: GE_Screen_Eryth

description: Library name: GE_Screen_Eryth


title: Kul2_K

description:
Library name: Kul2_K
Raw data are not provided due to patient privacy concerns.


title: DMSO + Antigen + Carvacrol 2

description: Library name: 16


title: GE_Screen_Bcell

description: Library name: GE_Screen_Bcell


title: GE_Screen_All_Lineage

description: Library name: GE_Screen_All_Lineage


title: Kra1_e

description:
Library name: Kra1_e
Raw data are not provided due to patient privacy concerns.


title: Kul_K

description:
Library name: Kul_K
Raw data are not provided due to patient privacy concerns.


title: DMSO + Antigen + Cinnamaldehyde 2

description: Library name: 15


title: Kov2_e

description:
Library name: Kov2_e
Raw data are not provided due to patient privacy concerns.


title: Kra_e

description:
Library name: Kra_e
Raw data are not provided due to patient privacy concerns.


title: DMSO + LPS 2

description: Library name: 12


title: Kond5_K

description:
Library name: Kond5_K
Raw data are not provided due to patient privacy concerns.


title: Water + Antigen 2

description: Library name: 11


title: U2_HSPC

description: Library name: U2_HSPC


title: Kond3_K

description:
Library name: Kond3_K
Raw data are not provided due to patient privacy concerns.


title: Kira1_K2

description:
Library name: Kira1_K2
Raw data are not provided due to patient privacy concerns.


title: Water + LPS 2

description: Library name: 10


title: U2_Eryth

description: Library name: U2_Eryth


title: Water Control 2

description: Library name: 9


title: Kira1_K1

description:
Library name: Kira1_K1
Raw data are not provided due to patient privacy concerns.


title: Kaz3_K

description:
Library name: Kaz3_K
Raw data are not provided due to patient privacy concerns.


title: Kaz1_e

description:
Library name: Kaz1_e
Raw data are not provided due to patient privacy concerns.


title: K8

description:
Library name: K8
Raw data are not provided due to patient privacy concerns.


title: K13

description:
Library name: K13
Raw data are not provided due to patient privacy concerns.


title: U2_All_Lineage

description: Library name: U2_All_Lineage


title: K11

description:
Library name: K11
Raw data are not provided due to patient privacy concerns.


title: DMSO + Antigen + Carvacrol 1

description: Library name: 8


title: Isa1_e

description:
Library name: Isa1_e
Raw data are not provided due to patient privacy concerns.


title: DMSO + LPS 1

description: Library name: 4


title: U1_Tcell

description: Library name: U1_Tcell


title: U2_Tcell

description: Library name: U2_Tcell


title: IlI_K3

description:
Library name: IlI_K3
Raw data are not provided due to patient privacy concerns.


title: U1_Myeloid

description: Library name: U1_Myeloid


title: IlI_e4

description:
Library name: IlI_e4
Raw data are not provided due to patient privacy concerns.


title: Kov1_e

description:
Library name: Kov1_e
Raw data are not provided due to patient privacy concerns.


title: U2_Myeloid

description: Library name: U2_Myeloid


title: Kond4_K

description:
Library name: Kond4_K
Raw data are not provided due to patient privacy concerns.


title: HAN_K5

description:
Library name: HAN_K5
Raw data are not provided due to patient privacy concerns.


title: HAN_e5

description:
Library name: HAN_e5
Raw data are not provided due to patient privacy concerns.


title: U1_HSPC

description: Library name: U1_HSPC


title: Water + LPS 1

description: Library name: 2


title: U1_Eryth

description: Library name: U1_Eryth


title: Gri2_e

description:
Library name: Gri2_e
Raw data are not provided due to patient privacy concerns.


title: Fuks2_K1

description:
Library name: Fuks2_K1
Raw data are not provided due to patient privacy concerns.


title: Water Control 1

description: Library name: 1


title: Fuks1_K

description:
Library name: Fuks1_K
Raw data are not provided due to patient privacy concerns.


title: U2_Bcell

description: Library name: U2_Bcell


title: DMSO + Antigen + Cinnamaldehyde 1

description: Library name: 7


title: Fisher1_K

description:
Library name: Fisher1_K
Raw data are not provided due to patient privacy concerns.


title: U1_Bcell

description: Library name: U1_Bcell


title: Fed1_e

description:
Library name: Fed1_e
Raw data are not provided due to patient privacy concerns.


title: U1_All_Lineage

description: Library name: U1_All_Lineage


title: Pig P3 Skin, scRNA-seq

city: Pullman

first: Sean

last: Thompson

state: WA

address: BLS 240

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: P3_Pig_scRNA
Pig P3 scRNA-seq

data_processing:
scRNA-seq Analysis: Fastq files were aligned to the Sscrofa.11.1 genome assembly (NCBI RefSeq GCF_000003025.6) using 10x Genomics Cellranger (v6.0.0). Cellranger outputs were used in downstream analyses in R using the Seurat package. We used standard quality control metrics to filter out low quality cells, normalized/scaled data using SCTransform, and performed dimensional reduction using UMAP with the SLM algorithm to identify clusters.
Stereo-seq Analysis: The pig reference genome for SAW (8.1.1) was prepared using the Sscrofa11.1.112 release from Ensembl and the makeRef function. Next, we used SAW count to generate gene expression matrix files. We manually aligned the gene expression matrix onto the tissue mask using Stereo Map 4 and slightly cropped the tissue mask area of each dataset to enable downstream analysis on our local hardware. Then, we ran SAW realign on the cropped tissue mask image and previous SAW count outputs to obtain the processed Stereo-seq tissue mask image and gene expression files used in downstream analysis. SAW realign Visualization output .gef  files were loaded into Stereopy (1.5.0) in Python (3.8.20) using read_gef() and bin_size=20. Data underwent QC filtration and was normalized using sctransform. Clustering was performed using the Leiden algorithm with resolutions of 1.2 (P3), 1.0 (P10), and 1.0 (6mo).
Assembly: Sscrofa.11.1
Supplementary files format and content: scRNA-seq: Cellranger output .h5 files encode a gene by cell matrix representing the number of reads per gene within each sequenced cell. These .h5 files contain all the information required to create a SeuratObject and analyze scRNA-seq data in R using the Seurat package. Saved SeuratObjects are available as processed data (.RData). Stereo-seq: SAW output ssDNA_regist.tif (tissue image mask) and .tissue.gef (gene expression matrix) were analyzed in Python using the Stereopy package. Saved Stereopy objects are available as processed data (.stereo.h5ad)

organism: Sus scrofa

source_name: Dorsal skin

extract_protocol:
scRNA-seq: Epidermal and dermal cells were isolated from E90, P3, P10, or 6-month old pig skin as previously described (Jensen et al., 2010), with the addition of Elastase (Worthington Biosciences), Hyaluronidase (Sigma-Aldritch), and Collagenase IV (Worthington Biosciences) enzymes to the dermal digestion solution to obtain single-cell suspensions of unsorted epidermal and dermal cells. Stereo-seq: Fixed-frozen cryo skin samples from P3, P10, and 6-month old pigs were sectioned at 10um for use with Complete Genomics Stereo-seq T FF V1.2 kit.
scRNA-seq: Epidermal and dermal single-cell suspensions were mixed 1:1 and processed for 10x Genomics scRNA-seq 3’ V3 Kit to generate scRNA-seq libraries. Libraries were sequenced on an Illumina NovaSeq PE150. Stereo-seq: libraries from the Complete Genomics Stereo-seq T FF V1.2 kit were sequenced using a DNBSEQ-T7.

value: Dorsal skin

value: WT


title: Ezh1_K

description:
Library name: Ezh1_K
Raw data are not provided due to patient privacy concerns.


title: Ezh3_K

description:
Library name: Ezh3_K
Raw data are not provided due to patient privacy concerns.


title: Esh2_K

description:
Library name: Esh2_K
Raw data are not provided due to patient privacy concerns.


title: Pig P10 Skin, scRNA-seq

description:
Library name: P10_Pig_scRNA
Pig P10 scRNA-seq


title: Pig 6mo Skin, scRNA-seq

description:
Library name: 6mo_Pig_scRNA
Pig 6mo scRNA-seq


title: TMM_Tcell

description: Library name: TMM_Tcell


title: embryo6

description:
Library name: embryo6
Raw data are not provided due to patient privacy concerns.


title: Pig E90 Skin, scRNA-seq

description:
Library name: E90_Pig_scRNA
Pig E90 scRNA-seq


title: Droz_2_K

description:
Library name: Droz_2_K
Raw data are not provided due to patient privacy concerns.


title: Water + Antigen 1

description: Library name: 3


title: Ezh2_K3110

description:
Library name: Ezh2_K3110
Raw data are not provided due to patient privacy concerns.


title: Dik_K1

description:
Library name: Dik_K1
Raw data are not provided due to patient privacy concerns.


title: TMM_Eryth

description: Library name: TMM_Eryth


title: D12

city: Santa Cruz

first: Vikas

last: Peddu

email: vpeddu@ucsc.edu, dkim142@ucsc.edu

state: CA

address: 1156 High Street

department: Biomolecular engineering

institute: University of California Santa Cruz

data_processing:
Transcripts assembled using Isoquant version 3.3.1
Assembly: HG38
Supplementary files format and content: Counts matrix

source_name: Plasma

extract_protocol:
Norgen Biotek Plasma/Serum Circulating and Exosomal RNA purification slurry format kit
Barcoded nanopore sequencing libraries were created using a custom low-input protocol for the Oxford Nanopore Technologies SQK-NBD-114.24 and LSK-114 kits. Briefly, cDNA was end-repaired and A-tailed as specified, but incubated for 30 minutes, followed by a 30 minute deactivation. Barcodes from the SQK-NBD-114.24 kit were incubated at 20C for 4.5 hours. Ligation was terminated by the addition of 2ul of EDTA to each reaction. Barcoded samples were pooled and subject to a 1.8x Ampure Bead cleanup, and then used as input for the LSK-114 protocol.
Here, we modified all bead cleanups to use a 1.8x ratio, and performed all bead washes at 37C. Adapter ligation was performed as specified, but incubated for 20 minutes to increase ligation efficiency. Short fragment buffer was used to capture the full gamut of cDNA lengths. The final library was eluted into 25ul of elution buffer, and loaded onto an R10.4 Promethion flow cell.

value: Plasma

value: cell-free RNA

value: control


title: Dik_K2

description:
Library name: Dik_K2
Raw data are not provided due to patient privacy concerns.

value: Trophectoderm


title: TMM_Myeloid

description: Library name: TMM_Myeloid


title: TMM_HSPC

description: Library name: TMM_HSPC


title: Dik_e

description:
Library name: Dik_e
Raw data are not provided due to patient privacy concerns.


title: Dik_e1

description:
Library name: Dik_e1
Raw data are not provided due to patient privacy concerns.


title: CHR_K1

description:
Library name: CHR_K1
Raw data are not provided due to patient privacy concerns.

value: Trophectoderm cells


title: TMM_Bcell

description: Library name: TMM_Bcell


title: CHR_e1

description:
Library name: CHR_e1
Raw data are not provided due to patient privacy concerns.

value: Blastocyst


title: TMM_All_Lineage

description: Library name: TMM_All_Lineage


title: Ch-D_e

description:
Library name: Ch-D_e
Raw data are not provided due to patient privacy concerns.

value: Whole-blastocyst cell population


title: D10


title: D09


title: Chal2_e

description:
Library name: Chal2_e
Raw data are not provided due to patient privacy concerns.


title: D08

value: Barrett's Esophagus (BE)


title: Chal_K2

description:
Library name: Chal_K2
Raw data are not provided due to patient privacy concerns.


title: STP_Tcell

description: Library name: STP_Tcell


title: Chal_K1

description:
Library name: Chal_K1
Raw data are not provided due to patient privacy concerns.


title: D07


title: STP_Myeloid

description: Library name: STP_Myeloid


title: BTR_e9

description:
Library name: BTR_e9
Raw data are not provided due to patient privacy concerns.


title: BTR_e3

description:
Library name: BTR_e3
Raw data are not provided due to patient privacy concerns.


title: STP_HSPC

description: Library name: STP_HSPC


title: Boc_K4

description:
Library name: Boc_K4
Raw data are not provided due to patient privacy concerns.


title: D06


title: D11


title: BOC_K1

description:
Library name: BOC_K1
Raw data are not provided due to patient privacy concerns.


title: BOC_e1

description:
Library name: BOC_e1
Raw data are not provided due to patient privacy concerns.


title: D05

value: adenocarcinoma


title: STP_Bcell

description: Library name: STP_Bcell


title: STP_All_Lineage

description: Library name: STP_All_Lineage


title: Bal1_K

description:
Library name: Bal1_K
Raw data are not provided due to patient privacy concerns.


title: Bal3_e

description:
Library name: Bal3_e
Raw data are not provided due to patient privacy concerns.


title: D03


title: Bal1_eB

description:
Library name: Bal1_eB
Raw data are not provided due to patient privacy concerns.


title: Bag3_K

description:
Library name: Bag3_K
Raw data are not provided due to patient privacy concerns.


title: MU2_Tcell

description: Library name: MU2_Tcell


title: Chal_e

description:
Library name: Chal_e
Raw data are not provided due to patient privacy concerns.


title: MU2_Myeloid

description: Library name: MU2_Myeloid


title: Aks_K

description:
Library name: Aks_K
Raw data are not provided due to patient privacy concerns.


title: D02


title: D01


title: Ani_e

description:
Library name: Ani_e
Raw data are not provided due to patient privacy concerns.


title: 8388_3_K

description:
Library name: 8388_3_K
Raw data are not provided due to patient privacy concerns.


title: MU2_HSPC

description: Library name: MU2_HSPC


title: C12


title: 8388_1_K

description:
Library name: 8388_1_K
Raw data are not provided due to patient privacy concerns.


title: STP_Eryth

description: Library name: STP_Eryth


title: C11


title: MU2_Eryth

description: Library name: MU2_Eryth


title: Boc_e4

description:
Library name: Boc_e4
Raw data are not provided due to patient privacy concerns.


title: 6069_plus

description:
Library name: 6069_plus
Raw data are not provided due to patient privacy concerns.


title: D04


title: MU2_Bcell

description: Library name: MU2_Bcell


title: 6069_1_K

description:
Library name: 6069_1_K
Raw data are not provided due to patient privacy concerns.


title: 5Sachk3_eB

description:
Library name: 5Sachk3_eB
Raw data are not provided due to patient privacy concerns.


title: C10


title: 3Bal2_eB

description:
Library name: 3Bal2_eB
Raw data are not provided due to patient privacy concerns.


title: C09


title: 11425_K

description:
Library name: 11425_K
Raw data are not provided due to patient privacy concerns.


title: MU2_All_Lineage

description: Library name: MU2_All_Lineage


title: MU1_Tcell

description: Library name: MU1_Tcell


title: Aks1_K

description:
Library name: Aks1_K
Raw data are not provided due to patient privacy concerns.


title: C08


title: C07


title: 7493_K

description:
Library name: 7493_K
Raw data are not provided due to patient privacy concerns.


title: MU1_HSPC

description: Library name: MU1_HSPC


title: MU1_Eryth

description: Library name: MU1_Eryth


title: C04


title: C03


title: MU1_Bcell

description: Library name: MU1_Bcell


title: FARIE-Seq, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 2

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

institute: Institute of Gene Biology RAS

description: Library name: 35_FAIRE_20E1h_SKi_2

data_processing:
ChIP-Seq, RNA-Seq, FAIRE-Seq sequencing
Adapter sequences were removed from the raw files by Cutadapt. ChIP-seq, FAIRE-Seq and RNA-Seq reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
Aligned reads were sorted to have MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library.
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: Bigwig files were generated using bamCoverage 3.0.2

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider cell line 2 (S2) cells were maintained at 25°C in ecdysone-free Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated with the NEBNext UltraTM II Directional RNA Library Prep Kit. FAIRE-Seq protocol was perfomed exactly as previously described in Simon et al (2012) Nat protocols, 7:256-267.
DNA and RNA-Seq libraries were prepared for sequencing using standard Illumina NEBNext protocols

treatment_protocol: S2 Schneider cells were treated with SRP dsRNA or sham dsRNA (SKi) for 5 days prior to 20E treatment (30ug of dsRNA were taken per 2 mln of cells). The treatment of S2 cells with 20-hydroxyecdysone (20E) (H5142, Sigma-Aldrich) was performed at a final concentration of 0.3 μM for 1 hour. Control treatment was performed with DMSO.

value: S2 Schneider cells

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment

tag: chip antibody

value: no abs


title: FAIRE-Seq, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 36_FAIRE_20E1h_SRPi_1

value: with SRP dsRNA (corresponding to 1020-1525 bp of mRNA-SRP-H NM_001382083) for 5 days prior to 20E treatment


title: MU1_All_Lineage

description: Library name: MU1_All_Lineage

value: Bone marrow

value: HSPC


title: FAIRE-Seq, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 42_FAIRE_20E1h_SRPi_2


title: C02


title: FAIRE-Seq, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 34_FAIRE_20E1h_SKi_1


title: MP_Tcell

description: Library name: MP_Tcell


title: C01


title: Dp16_placenta_euploid_Dam33_embryo3

type: RNA

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH

description: Gene expression data from mouse E18.5 placenta

hyb_protocol: Arrays were washed and stained using the GeneTitan Hybridization, Wash, and Stain kit with streptavidin-phycoerythrin protocol according to the manufacturer's instructions.           Arrays were scanned using the GeneTitan automated microarray system.

data_processing: Microarray data were analyzed using Transcriptome Analysis Console (TAC) software (version 4.0.0) (Thermo Fisher Scientific) using RMA normalization

label: biotin

source_name: Mouse E18.5 placenta

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate using Mouse Clariom S HT arrays (Cat. No. 902970, Thermo Fisher Scientific) and the GeneTitan automated microarray system.

growth_protocol: Mouse placentas were collected at E18.5 (late gestation), snap frozen, and stored at -80°C until RNA extraction.

extract_protocol: RNA was processed and hybridized on Mouse Clariom S HT 96-array plates (902970; ThermoFisher Scientific) using GeneChip WT Plus Reagent Kits following the manufacturer’s protocol (902281; ThermoFisher Scientific).

value: EUP

tag: model

value: Female


title: MU1_Myeloid

description: Library name: MU1_Myeloid


title: MP_Myeloid

description: Library name: MP_Myeloid


title: Arabidopsis, hira-1_H3.3_3xFlag, 12DAG,H3,Rep2

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

description: Library name: 12DAG_hira-1_H3.3_3xFlag_Rep2,H3,ChIP

data_processing:
ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of 20 for the final base.Reads shorter than 35 bp after trimming were discarded.
Assembly: TAIR 10
Supplementary files format and content: BigWig files were generated by using the Deeptools  (version 3.5.2).

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Plants were grown on GM in a growth chamber under long-day conditions supplemented with 1% sucrose under long-day photoperiod and ~21°C. Seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
Tissue was fixed with 1% formaldehyde for 12mins and stopped by adding glycine to a final concentration of 0.125M and incubating for 6 extra mins.After nuclear lysis,chromatin was sonicated using using Bioruptor® Pico with the following conditions: 14 cycles,10 sec ON/30 sec OFF at 4°C.
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

value: 12DAG seedling


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 33_ChIP_K27Ac_20E1h_SRPi_2

value: Active motif antibodies against Histone H3K27Ac (39133)


title: Arabidopsis, hira-1_H3.3_3xFlag, 12DAG,H3,Rep1

description: Library name: 12DAG_hira-1_H3.3_3xFlag_Rep1,H3,ChIP


title: Arabidopsis, input, 12DAG,H3,Rep2

description: Library name: 12DAG_input,H3,ChIP


title: Dp16_placenta_trisomic_Dam33_embryo1

scan_protocol: Arrays were scanned using the GeneTitan automated microarray system.

value: TS

value: Male


title: Dp16_placenta_trisomic_Dam2_embryo4


title: B12

value: Plasma

value: cell-free RNA

value: control


title: Dp16_placenta_trisomic_Dam33_embryo2


title: C06

value: adenocarcinoma


title: Dp16_placenta_euploid_Dam2_embryo3


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 32_ChIP_K27Ac_20E1h_SRPi_1

value: S2 Schneider cells


title: Dp16_placenta_euploid_Dam2_embryo2


title: Dp16_placenta_trisomic_Dam2_embryo1


title: Arabidopsis, fas2-4_H3.3_3xFlag, 12DAG,H3,Rep2

description: Library name: 12DAG_fas2-4_H3.3_3xFlag_Rep2,H3,ChIP


title: B11


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 31_ChIP_K27Ac_20E1h_SKi_2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour


title: MP_Eryth

description: Library name: MP_Eryth


title: MP_Bcell

description: Library name: MP_Bcell


title: B10


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 29_ChIP_K27Ac_20E1h_SKi_1

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment


title: Arabidopsis, fas2-4_H3.3_3xFlag, 12DAG,H3,Rep1

description: Library name: 12DAG_fas2-4_H3.3_3xFlag_Rep1,H3,ChIP


title: B09


title: Arabidopsis, Columbia-0_H3.3_3xFlag, 12DAG,H3,Rep1

description: Library name: 12DAG_Columbia-0_H3.3_3xFlag_Rep1,H3,ChIP


title: MP_All_Lineage

description: Library name: MP_All_Lineage


title: GE_Tcell

description: Library name: GE_Tcell


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 27_ChIP_K27Ac_DMSO_SRPi_1

value: sham-treated (DMSO) for 1 hour


title: B08

value: Barrett's Esophagus (BE)


title: Arabidopsis, hira-1_H3.1_3xFlag, 12DAG,H3,Rep2

description: Library name: 12DAG_hira-1_H3.1_3xFlag_Rep2,H3,ChIP


title: GE_Myeloid

description: Library name: GE_Myeloid

value: Bone marrow


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 26_ChIP_K27Ac_DMSO_SKi_2


title: B06


title: B07


title: GE_HSPC

description: Library name: GE_HSPC

value: HSPC


title: MP_HSPC

description: Library name: MP_HSPC


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 25_ChIP_K27Ac_DMSO_SKi_1


title: B05


title: GE_Eryth

description: Library name: GE_Eryth


title: Arabidopsis, fas2-4_H3.1_3xFlag, 12DAG,H3,Rep2

description: Library name: 12DAG_fas2-4_H3.1_3xFlag_Rep2,H3,ChIP


title: Arabidopsis, fas2-4_H3.1_3xFlag, 12DAG,H3,Rep1

description: Library name: 12DAG_fas2-4_H3.1_3xFlag_Rep1,H3,ChIP


title: ChIP-Seq, EcR abs, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 23_ChIP_EcR_20E1h_SRPi_1

value: with SRP dsRNA (corresponding to 1020-1525 bp of mRNA-SRP-H NM_001382083) for 5 days prior to 20E treatment

value: EcR-full antibodies against full-length EcR-A isoform NM_165461 were obtained in our lab and described in Evdokimova AA et al (2025) Nucleic Acids Research. Apr 24;53(7):gkaf284.


title: Arabidopsis, Columbia-0_H3.3_3xFlag, 12DAG,H3,Rep2

description: Library name: 12DAG_Columbia-0_H3.3_3xFlag_Rep2,H3,ChIP

value: 12DAG seedling


title: ChIP-Seq, EcR abs, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 24_ChIP_EcR_20E1h_SRPi_2


title: B03


title: B04


title: ChIP-Seq, EcR abs, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 22_ChIP_EcR_20E1h_SKi_2


title: GE_Bcell

description: Library name: GE_Bcell


title: Arabidopsis, Columbia-0_H3.1_3xFlag, 12DAG,H3,Rep1

description: Library name: 12DAG_Columbia-0_H3.1_3xFlag_Rep1,H3,ChIP


title: B02


title: ChIP-Seq, EcR abs, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 21_ChIP_EcR_20E1h_SKi_1


title: ChIP-Seq, H3K27Ac abs, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 28_ChIP_K27Ac_DMSO_SRPi_2

value: Active motif antibodies against Histone H3K27Ac (39133)


title: Arabidopsis, hira-1_H3.1_3xFlag, 12DAG,H3,Rep1

description: Library name: 12DAG_hira-1_H3.1_3xFlag_Rep1,H3,ChIP


title: E6 Rep2 Dox (14d) - washout (14d)

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

description: Library name: E614dDox14dWOR2

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). For the E6, CL30.7/CL30.7.7 and CL31/CL31.16, the mm10 genome was used  (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

organism: Mus

growth_protocol: NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
RNA was extracted from > 1M NPCs using the RNeasy kit and on-column DNAse digestion (Qiagen). RNA integrity was measured using the Bioanalyzer Nano Kit.
Only high-quality RNA was used for subsequent library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; and the pools were loaded on the Illumina sequencer NextSeq 500 or NextSeq 2000 and sequenced bi-directionally, generating ~500 million paired-end reads, each 75 bases long.

treatment_protocol: Xist expression in TX1072 was induced by addition of doxycycline (1 µg/mL) to the NPC media. Culture media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media. Auxin-mediated depletion of SPEN was achieved by supplementing the culture media with Auxin (Sigma) at the concentration of 500 µM, as previously described [Dossin et al. 2020]. Auxin-containing media was renewed every 24h.

tag: strain

value: C57BL6/J x CAST/EiJ

value: neural progenitor cell

value: Xptet / R26rtTA

value: Dox (14d) - washout (14d)

tag: experiment


title: DTKP_Tcell

description: Library name: DTKP_Tcell


title: B01

value: Plasma

value: cell-free RNA


title: E6 Rep2 Dox (7d) - washout (14d)

description: Library name: E67dDox14dWOR2

value: Dox (7d) - washout (14d)


title: DTKP_Myeloid

description: Library name: DTKP_Myeloid


title: ChIP-Seq, EcR abs, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 20_ChIP_EcR_DMSO_SRPi_2

value: S2 Schneider cells


title: CL31.16 Rep2 Dox (7d)

description: Library name: CL317dDoxR2

value: Xptet / R26rtTA / SPEN-AID

value: Dox (7d)


title: A11

value: control


title: DTKP_HSPC

description: Library name: DTKP_HSPC

value: Bone marrow


title: ChIP-Seq, EcR abs, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 18_ChIP_EcR_DMSO_SKi_2

value: sham-treated (DMSO) for 1 hour

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment


title: DTKP_Eryth

description: Library name: DTKP_Eryth

value: HSPC


title: ChIP-Seq, EcR abs, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 19_ChIP_EcR_DMSO_SRPi_1

value: with SRP dsRNA (corresponding to 1020-1525 bp of mRNA-SRP-H NM_001382083) for 5 days prior to 20E treatment

value: EcR-full antibodies against full-length EcR-A isoform NM_165461 were obtained in our lab and described in Evdokimova AA et al (2025) Nucleic Acids Research. Apr 24;53(7):gkaf284.


title: CL31.16 Rep2 Dox (7d) - washout (7d)

description: Library name: CL317dDox7dWOR2

value: C57BL6/J x CAST/EiJ

value: Dox (7d) - washout (7d)


title: A10


title: GE_All_Lineage

description: Library name: GE_All_Lineage


title: Arabidopsis, Columbia-0_H3.1_3xFlag, 12DAG,H3,Rep2

description: Library name: 12DAG_Columbia-0_H3.1_3xFlag_Rep2,H3,ChIP

value: 12DAG seedling


title: DTKP_Bcell

description: Library name: DTKP_Bcell


title: ChIP-Seq, EcR abs, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 17_ChIP_EcR_DMSO_SKi_1


title: CL31.16 Rep2 Dox (7d) - washout (14d)

description: Library name: CL317dDox14dWOR2

value: neural progenitor cell


title: A09

value: Plasma


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 16_ChIP_SRP_20E1h_SRPi_2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: SRP/dGATAb antibodies against 946-1264 a.a. of NP_732100.2 isoform were obtained in our lab and described in this manuscript for the first time


title: CL31.16 Rep2 Dox (21d)

description: Library name: CL3121dDoxR2

value: Dox (21d)


title: DTKP_All_Lineage

description: Library name: DTKP_All_Lineage


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 15_ChIP_SRP_20E1h_SRPi_1

value: S2 Schneider cells


title: A08

value: cell-free RNA

value: Barrett's Esophagus (BE)


title: ACOC_Tcell

description: Library name: ACOC_Tcell

value: Bone marrow


title: A12

value: control


title: CL31.16 Rep2 Dox (21d) - washout (7d)

description: Library name: CL3121dDox7dWOR2

value: Xptet / R26rtTA / SPEN-AID

value: Dox (21d) - washout (7d)


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 14_ChIP_SRP_20E1h_SKi_2

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 13_ChIP_SRP_20E1h_SKi_1


title: ACOC_Myeloid

description: Library name: ACOC_Myeloid

value: HSPC


title: CL31.16 Rep2 Dox (14d) - washout (7d)

description: Library name: CL3114dDox7dWOR2

value: C57BL6/J x CAST/EiJ

value: Dox (14d) - washout (7d)


title: A05


title: CL31.16 Rep2 Dox (14d)

description: Library name: CL3114dDoxR2

value: Dox (14d)


title: ACOC_Eryth

description: Library name: ACOC_Eryth


title: CL31.16 Rep2 Dox (14d) - washout (14d)

description: Library name: CL3114dDox14dWOR2

value: neural progenitor cell

value: Dox (14d) - washout (14d)


title: ACOC_Bcell

description: Library name: ACOC_Bcell


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 12_ChIP_SRP_DMSO_SRPi_2

value: sham-treated (DMSO) for 1 hour

value: with SRP dsRNA (corresponding to 1020-1525 bp of mRNA-SRP-H NM_001382083) for 5 days prior to 20E treatment


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 11_ChIP_SRP_DMSO_SRPi_1

value: SRP/dGATAb antibodies against 946-1264 a.a. of NP_732100.2 isoform were obtained in our lab and described in this manuscript for the first time


title: A03

value: Plasma

value: adenocarcinoma


title: CL31.16 Rep2 Control

description: Library name: CL310dDoxR2

value: Control


title: ACOC_All_Lineage

description: Library name: ACOC_All_Lineage

value: Bone marrow


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 10_ChIP_SRP_DMSO_SKi_2

value: S2 Schneider cells


title: A02

value: cell-free RNA


title: CL30.7 Rep2 Dox (7d)

description: Library name: CL307dDoxR2

value: Xptet / R26rtTA / SPEN-AID

value: Dox (7d)


title: ChIP-Seq, SRP/dGATAb abs, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 9_ChIP_SRP_DMSO_SKi_1

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment


title: E6 Dox (7d) Kdm5c

data_processing:
Library strategy: Capture Hi-C
Allele-specific Capture Hi-C analysis was performed using the Hi-C Pro pipeline (v2.11.4). Paired-end reads were first independently aligned using bowtie2 to the same N-masked genome reference. Read pairs were then assigned to either C57BL-6J or CAST-EiJ genomes and allele-specific BAM files for downstream analysis are generated. Low-quality reads, multiple hits, singletons and read pairs which do not map to the same genotype were then removed. Further filtering for valid interactions, which excludes reads outside of the captured region, was performed and only valid pairs were used to build the normalized contact maps at a 10kb resolution with the cooler package (v0.8.9)
Assembly: mm10
Supplementary files format and content: mcool files contains the contact maps at various resolution for visualization

source_name: neural progenitor cell

growth_protocol: ESCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in 2i-containing ESC media (DMEM, 15% FBS, 0.1 mM β-mercaptoethanol, 1,000 U/mL−1 leukaemia inhibitory factor (LIF), CHIR99021 (3 µM), and PD0325901 (1 µM)). NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
Capture Hi-C was performed as described in Hauth et. al 2022. Three arrays of biotinylated RNA probes were designed to tile 3 Mb targets on the mouse X chromosome (Hcfc1-Mecp2 cluster; ChrX:72,590,000 - 75,430,000; Kdm5c cluster; ChrX:150,210,000 - 153,045,000, Kdm6a cluster: ChrX:15,725,000-18,725,000).
Capture Hi-C libraries were constructed using the SureSelect XT Library Prep Kit

treatment_protocol: Xist expression was induced by addition of doxycycline (1 µg/mL) to the media. Culture media supplemented with doxycycline was renewed every 24h if applicable. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media. Auxin-mediated depletion of SPEN was achieved by supplementing the culture media with Auxin (Sigma) at the concentration of 500 µM, as previously described [Dossin et al. 2020]. Auxin-containing media was renewed every 24h.

value: C57BL6/J x CAST/EiJ

value: Xptet / R26rtTA


title: A01


title: CL30.7 Rep2 Dox (7d) - washout (14d)

description: Library name: CL307dDox14dWOR2

value: Dox (7d) - washout (14d)


title: A06

value: Barrett's Esophagus (BE)


title: CL30.7 Rep2 Dox (21d)

description: Library name: CL3021dDoxR2

value: neural progenitor cell

value: Dox (21d)


title: RNA-Seq, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 7_RNA_20E1h_SRPi_1

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: with SRP dsRNA (corresponding to 1020-1525 bp of mRNA-SRP-H NM_001382083) for 5 days prior to 20E treatment


title: E14_CP cells, Foxf1 KO, Rep 2

city: Nanjing

first: Jingjing

last: He

state: 2 Sipailou

address: 2 Sipailou

department: School of Life Science and Technology

institute: Southeast University

data_processing:
Fastq files were checked for quality using fastqc (v0.11.5) .Fastq files were mapped to mouse genome using Hisat2 (v2.2.1.0).Read counts were generated using featureCounts  for coding genes from genomes.
Assembly: mm10
Supplementary files format and content: *.bw: bigWig files

growth_protocol: Mouse E14 ESCs were differentiated into embryoid bodies (EBs) at a density of 75,000 cells/ml in 6 cm dishes for 48 h in serum-free media (DMEM (Hyclone, SH30243.01), DMEM/F12 (1:1) (Gibco, 11320-033), 0.05% BSA (Sigma, A1933), 1 × GlutaMax (Gibco, 35050-061), B27 supplement (Gibco, 12587010), N2 supplement (Gibco, 17502048), supplemented with 50 mg/ml ascorbic acid (Alfa Aesar, 50-81-7) and 4.5×10-4 M monothioglycerol). EBs were dissociated into single cells and re-aggregated as MES cells for 40 h at 50,000 cells/ml in the presence of 5 ng/mL human VEGF (Novoprotein, C083) and 10 ng/ml human Activin A (Peprotech, 96-120-14-10) and 0.3 ng/ml human BMP4 (R&D, 5020-BP-010). MES cells were dissociated and plated as a monolayer in gelatin-coated 12-well plate at 50,000 cells/ml in StemPro-34 (Gibco, 10639011) supplemented with 5 ng/mL VEGF (Novoprotein, C083), 10 ng/mL human basic FGF (Gibco, PMG0035) and 25 ng/mL FGF10 (R&D, 345-FG-250). CP cells were harvested after differentiation for 32 h.

extract_protocol:
For RNA-seq, 1 × 106 MES or CP cells were harvested and RNA extraction was performed using Rneasy mini plus kit (Qiagen). 1 ?g of total RNA was used for the construction of sequencing libraries and sequencing.RNA library for RNA-seq was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3? ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3? ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: Mouse Embryonic stem cells

value: Foxf1 knockout

value: CP differentiation

tag: time

value: Day 5


title: A07

value: Plasma


title: ACOC_HSPC

description: Library name: ACOC_HSPC

value: Bone marrow

value: HSPC


title: CL30.7 Rep2 Dox (21d) - washout (7d)

description: Library name: CL3021dDox7dWOR2

value: Xptet / R26rtTA / SPEN-AID

value: Dox (21d) - washout (7d)


title: A04

value: cell-free RNA

value: adenocarcinoma


title: E14_CP cells, Foxf1 KO, Rep 1


title: E6 Ctrl  Mecp2

value: C57BL6/J x CAST/EiJ

value: Xptet / R26rtTA

value: Control


title: RNA-Seq, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 6_RNA_20E1h_SKi_2

value: S2 Schneider cells

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment


title: E6 October2021 Dox (3d)

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). For the E6, CL30/CL30.7 and CL31/CL31.16, the mm10 genome was used (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

value: neural progenitor cell

value: Dox (3d)

tag: experiment id


title: CL30.7 Rep2 Dox (14d) - washout (7d)

description: Library name: CL3014dDox7dWOR2

value: Dox (14d) - washout (7d)


title: CL30.7 Rep2 Dox (14d)

description: Library name: CL3014dDoxR2

value: Dox (14d)


title: E14_CP cells, WT, Rep 2

value: Mouse Embryonic stem cells

value: WT

value: CP differentiation

value: Day 5


title: RNA-Seq, S2 Schneider cells, 20E 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 5_RNA_20E1h_SKi_1

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour


title: E6 October2021 Dox (7d)

value: Dox (7d)


title: E14_CP cells, WT, Rep 1


title: E14_MES cells, Foxf1 KO, Rep 2

value: Foxf1 knockout

value: MES differentiation

value: Day 3.7


title: RNA-Seq, S2 Schneider cells, 20E 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 8_RNA_20E1h_SRPi_2

value: with SRP dsRNA (corresponding to 1020-1525 bp of mRNA-SRP-H NM_001382083) for 5 days prior to 20E treatment


title: E6 October2021 Control

value: C57BL6/J x CAST/EiJ

value: Xptet / R26rtTA

value: Control


title: CL30.7 Rep2 Dox (14d) - washout (14d)

description: Library name: CL3014dDox14dWOR2

value: neural progenitor cell

value: Xptet / R26rtTA / SPEN-AID

value: Dox (7d) - washout (14d)


title: RNA-Seq, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 2

description: Library name: 4_RNA_DMSO_SRPi_2

value: S2 Schneider cells

value: sham-treated (DMSO) for 1 hour


title: CL30.7 Rep2 Control

description: Library name: CL300dDoxR2


title: RNA-Seq, S2 Schneider cells, DMSO 1 hour, SRP dsRNA (SRPi) 5 days, rep 1

description: Library name: 3_RNA_DMSO_SRPi_1


title: E14_MES cells, Foxf1 KO, Rep 1

value: Mouse Embryonic stem cells


title: E6 Ctrl Kdm5c


title: RNA-Seq, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 2

description: Library name: 2_RNA_DMSO_SKi_2

value: with sham dsRNA (against pSK plasmid fragment) for 5 days prior to 20E treatment


title: E6 Dox (7d) Mecp2


title: E6 October2021 Dox (7d) - washout (4d)

value: Dox (7d) - washout (4d)


title: Adiopicyte, OO, biol rep 1

city: Berkeley

first: Yuchen

state: California

address:
344 Morgan Hall, University of California
 Berkeley

department: Department of Nutritional Science and Toxicology

institute: University of California Berkeley

description:
OO1
counts_heterochronic_WAT_MPS.xlsx

data_processing:
FASTQ file generation was performed by Novogene using Illumina NovaSeq 6000
Original image data file from the high-throughput sequencing platform was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
Alignment were performed with HISAT2
Gene expression level analysis, including PCA, hierarchical clustering
Differential expression analysis using pyDESeq2
Assembly: Homo_sapiens_Ensembl_94
Supplementary files format and content: .xlsx files includes raw gene counts info
Supplementary files format and content: .xlsx files includes sample metadata of each batch of experiments

source_name: G15.AO iPSC

extract_protocol:
Cells were exposed by cutting and exfoliating the cell chamber slab off the device then lysed in Trizol (#15596026, Invitrogen)
Library construction was performed by Novogene. The polyA enrichment library preparation procedure was used and resulted in the construction of 250-300 bp insert cDNA library.

value: G15.AO iPSC

value: Adipocyte

value: WT

value: MSC and adipogenic differentiation, PPARG lentivius transduction

tag: group

value: OO


title: CL31.16 Rep4 Dox (7d)

description: Library name: CL317dDoxR4

value: Dox (7d)


title: E14_MES cells, WT, Rep 4

value: MES differentiation

value: Day 3.7


title: RNA-Seq, S2 Schneider cells, DMSO 1 hour, sham dsRNA (SKi) 5 days, rep 1

description: Library name: 1_RNA_DMSO_SKi_1


title: E6_rep2

data_processing:
All steps for the preprocessing of ATAC-seq data can be reproduced using a nextflow pipeline available at https://github.com/yuviaapr/allele-specific_ATAC-seq. Briefly, initial quality checks of the raw FASTQ files were performed using FastQC (v0.11.9). Reads were trimmed using Trim Galore (v0.6.3). Reference genome for allele-specific mapping, was constructed as described for the allele-specific RNA-seq analysis, and  used to generate a bowtie index. Paired-end reads were aligned using bowtie2 (v2.3.4.1) to the N-masked genome index with the following parameters: --very-sensitive -X 2000. Duplicates were removed using Picard Tools (v2.20.8) before downstream analyses. Peaks were called using MACS2 (v2.2.7.1) using the following parameters: -g mm --buffer-size 100 -q 0.01 --keep-dup all --min-length 100 --format BAMPE --nomodel. Consensus peaks were generated using the “dba.peakset” function from the DiffBind Bioconductor R package (v3.8.4), with the requirement that peaks should be present in at least two BAM files. Blacklist regions (from ENCODE for BSgenome.Mmusculus.UCSC.mm10) were removed using the dba.blacklist function, and the raw counts for the resulting consensus peak set were generated using the dba.count function using summits=FALSE. Peak counts were normalised using the dba.normalize function, with default settings. Differential accessibility analysis between the split BAM files coming from the Xi and Xa was performed using the dba.analyze function with methods=DBA_DESEQ2 (calling the DESeq2 Bioconductor R package (v1.38.3) in the background). Peaks were annotated to their nearest gene using the ChIPseeker Bioconductor R package (v1.34.1) using the mm10 genome from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor R package (v3.10.0).
Assembly: GRCm38
Supplementary files format and content: delimited text file; Genome 1 is C57B6/J, genome 2 is CAST/EiJ

source_name: C57BL6/J x CAST/EiJ

extract_protocol:
ATAC-seq was performed following the Omni-ATAC protocol (Corces et al. 2017), that has been shown to reduce the number of mitochondrial reads while increasing the signal-to-noise ratio. 25,000 cells were collected, lysed for 3 min on ice in lysis buffer (10mM Tris-HCL pH.5, 5M NaCl, 1M MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin), washed in wash buffer (10mM Tris-HCL pH.5, 5M NaCl, 1M MgCl2, 0.1% Tween-20), and spun down at 500 RCF at 4°C for 10 min. Pellets were resuspended in 50 µL of transposition reaction (2X TD buffer, 1X PBS, 0.1% Tween-20, 0.1% Digitonin, 5µL of Illumina Tn5 transposase) and incubated for 30 min at 37°C with 1,000 rpm agitation. DNA was isolated with Zymo DCC5 kit and eluted in 21 µL of elution buffer.
DNA samples were initially amplified by 5 cycles of PCR, followed by a variable number of additional amplification cycles estimated by qPCR for each sample. PCR products were purified using the Zymo DCC5 kit and eluted in 20 µL of H2O. A two-size selection of fragments was performed using 0.5x and 1.3x volume of AMPure XP beads (Beckman Coulter). Libraries were quantified and analyzed using Qubit and Tapestation assays, before preparing equimolar dilutions. Paired-end sequencing was performed on NextSeq 500 (Illumina).

value: C57BL6/J x CAST/EiJ

value: Xptet / R26rtTA

value: Control


title: E6_rep1

value: neural progenitor cell


title: CL31.16 Rep4 Dox (3d)

description: Library name: CL313dDoxR4

value: Xptet / R26rtTA / SPEN-AID

value: Dox (3d)


title: Pig 6mo Skin, Stereo-seq

description:
Library name: 6mo_Pig_Stereo
Pig 6mo Stereo-seq

data_processing:
scRNA-seq Analysis: Fastq files were aligned to the Sscrofa.11.1 genome assembly (NCBI RefSeq GCF_000003025.6) using 10x Genomics Cellranger (v6.0.0). Cellranger outputs were used in downstream analyses in R using the Seurat package. We used standard quality control metrics to filter out low quality cells, normalized/scaled data using SCTransform, and performed dimensional reduction using UMAP with the SLM algorithm to identify clusters.
Stereo-seq Analysis: The pig reference genome for SAW (8.1.1) was prepared using the Sscrofa11.1.112 release from Ensembl and the makeRef function. Next, we used SAW count to generate gene expression matrix files. We manually aligned the gene expression matrix onto the tissue mask using Stereo Map 4 and slightly cropped the tissue mask area of each dataset to enable downstream analysis on our local hardware. Then, we ran SAW realign on the cropped tissue mask image and previous SAW count outputs to obtain the processed Stereo-seq tissue mask image and gene expression files used in downstream analysis. SAW realign Visualization output .gef  files were loaded into Stereopy (1.5.0) in Python (3.8.20) using read_gef() and bin_size=20. Data underwent QC filtration and was normalized using sctransform. Clustering was performed using the Leiden algorithm with resolutions of 1.2 (P3), 1.0 (P10), and 1.0 (6mo).
Assembly: Sscrofa.11.1
Supplementary files format and content: scRNA-seq: Cellranger output .h5 files encode a gene by cell matrix representing the number of reads per gene within each sequenced cell. These .h5 files contain all the information required to create a SeuratObject and analyze scRNA-seq data in R using the Seurat package. Saved SeuratObjects are available as processed data (.RData). Stereo-seq: SAW output ssDNA_regist.tif (tissue image mask) and .tissue.gef (gene expression matrix) were analyzed in Python using the Stereopy package. Saved Stereopy objects are available as processed data (.stereo.h5ad)
Library strategy: Spatial Transcriptomics

value: Dorsal skin


title: E14_MES cells, Hand1 KO, Rep 2

source_name: Mouse Embryonic stem cells

extract_protocol:
For RNA-seq, 1 × 106 MES or CP cells were harvested and RNA extraction was performed using Rneasy mini plus kit (Qiagen). 1 ?g of total RNA was used for the construction of sequencing libraries and sequencing.RNA library for RNA-seq was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3? ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.
RNA library for RNA-seq was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3? ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: Mouse Embryonic stem cells

value: Hand1 knockout


title: E14_MES cells, WT, Rep 3


title: Pig P10 Skin, Stereo-seq

description:
Library name: P10_Pig_Stereo
Pig P10 Stereo-seq


title: SG_HCT_WT_SG_seq_rep2

first: Jarrett

address: 455 Main st, Room 627

institute: Whitehead Institute

description:
RNA seq of SG purified fraction
cts_SGseq.csv

data_processing:
DESeq2
Assembly: hg38
Supplementary files format and content: Comma-delimited files containing read counts for all samples.
Supplementary files format and content: Supplemental Excel tables that summarize the sequencing data.

extract_protocol:
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.

value: oxidative stress; wt


title: CL31.16 Rep4 Dox (3d), Aux (5d)

description: Library name: CL313dDox5dAuxR4

value: Dox (3d), Aux (5d)


title: E14_MES cells, Hand1 KO, Rep 1


title: Pig P3 Skin, Stereo-seq

description:
Library name: P3_Pig_Stereo
Pig P3 Stereo-seq

value: WT


title: CL31.16 Rep4 Aux (2d)

description: Library name: CL3102dAuxR4

value: Aux (2d)


title: Cyto_HCT_WT_SG_seq_rep2

description:
RNA seq of total cytoplasmic RNA
cts_SGseq.csv


title: SG_HCT_WT_SG_seq_rep1


title: CL31.16 Rep4 Control

description: Library name: CL3100R4


title: E14_MES cells, WT, Rep 2


title: E14_MES cells, WT, Rep 1


title: CL30.7 Rep4 Dox (7d)

description: Library name: CL307dDoxR4