title: M32022110333_MCC13_RT

description: Library name: M32022110333


title: Pmc4_depletion

status: Public on Jan 27 2026

type: SRA

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

description: Library name: pmc4_60_v_HiC_Double-MHM

library_source: genomic

data_processing:
In situ Hi-C data were processed using the rfy_hic2 package (https://github.com/rafysta/rfy_hic2)
Processed HiC data were converted to juicer format using the pre command of JUICER program (version 1.22.01)
Assembly: S.pombe (2018)
Supplementary files format and content: Juicer format

molecule: genomic DNA

organism: Schizosaccharomyces pombe

extract_protocol:
Fission yeast cells (approximately 5 x 108 cells at OD595 = 0.5) were fixed with 3% pFA at 26°C for 10 minutes and disrupted with glass beads using Mini-Beadbeater-16 (BioSpec Products) in lysis buffer [50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM PMSF, and EDTA-free Protease Inhibitor Cocktail (Roche)].  After washing with 1 ml PBS solution, the cells were further fixed with 3 mM disuccinimidyl glutarate (Thermo Fisher Scientific) in 2.5 ml PBS solution at 30°C for 40 minutes.  The fixed cells were incubated at 62°C for 7 minutes with 0.1% SDS and subsequently with 1% Triton-X 100.  The permeabilized cells were incubated with 25 units of MboI, HinfI, and MluCI at 37°C overnight.  The pellet containing restriction enzyme-digested DNA fragments was treated with 150 μM biotin-14-dATP, dCTP, dGTP, and dTTP and incubated with 20 units of Klenow fragment (NEB) at 37°C for 45 minutes, followed by proximity ligation using 2,500 units of T4 DNA ligase (NEB) at room temperature for 4 hours with a gentle rotation.  After ligation, the pellet was subjected to proteinase K treatment at 68°C overnight in the presence of 0.5 M NaCl.
DNA was purified by phenol/chloroform extraction and ethanol precipitation.  The purified DNA was sheared into 100–500 bp fragments by Bioruptor UCD-200 (Diagenode).  Biotin-labeled DNA was purified using Dynabeads MyOne Streptavidin T1 (Thermo Fisher Scientific).  Sequencing adapters were ligated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) while DNA was bound to the beads.  Sequencing libraries were amplified by PCR using the NEBNext Ultra II Q5 Master Mix (NEB) with NEBNext Multiplex Oligos for Illumina (NEB).

tag: strain

tag: restriction enzyme

value: MboI, HinfI, MluCI


title: Mus musculus placenta, rep 1

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description: Library name: Placenta_musculus_RNA-1

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed using Trim_galore, with default settings.
Mapping was done with Hisat2 v2.0.5 with --no-softclip.
Reads with MAPQ < 2 were removed.
Raw read counts per gene were extracted using Seqmonk.
Assembly: mm10 (Mus musculus); GCF_900095145 (Mus pahari)
Supplementary files format and content: txt, table of raw counts

molecule: total RNA

organism: Mus musculus

source_name: Placenta

growth_protocol: TS conditioned medium (TS-CM) was prepared by incubating TS base medium (TS-BM; RMPI 1640 supplemented with 20% FBS, 1X antibiotic-antimycotic, 1 mM sodium pyruvate and 50 µM 2-mercaptoethanol) on confluent, mitomycin-treated primary mouse embryonic fibroblast (PMEF) feeders for 72 h, followed by filtration through a 0.45 µm PES membrane. Blastocysts from C57BL/6 mice were plated individually onto gelatin-coated wells containing mitomycin-treated PMEF feeders in medium consisting of 70% TS-CM and 30% TS-BM, supplemented with 50 ng/ml bFGF, 2 μg/ml heparin and 100 µM Y-27632 (ROCK inhibitor). Following hatching, once 3-4 layers of TSCs formed around the blastocyst, outgrowths were dissociated using 0.5% trypsin-EDTA. TSCs were passaged at sub-confluency until feeder cells were eliminated and subsequently cryopreserved in liquid nitrogen in freezing medium containing 90% culture medium and 10% DMSO. For regular passaging of established lines (B6 TSCs, GFP TSCs and Rs26 TSCs), medium with no ROCK inhibitor and reduced bFGF (25 ng/ml) and heparin (1 µg/ml) was used. Cells were kept in humidified atmosphere with 5% CO2 at 37 ˚C.

extract_protocol:
Total RNA was isolated using a commercial RNA extraction kit (Qiagen) and treated with DNase I (Ambion) to remove residual genomic DNA.
500 ng of total RNA was subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2. Strand-specific libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Rs26 KRAB sgIAP TSCs were treated with 8 µg/ml doxycycline hydrochloride to induce CRISPR interference.

tag: tissue

value: Placenta


title: EA-15

type: RNA

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

country: USA

institute: University of Illinois at Chicago

description: European-Amercian Stroma -15

hyb_protocol: Affymetrix Human Gene 1.0 ST Array fluidics script FS450-0001

scan_protocol: GenChipTM Scanner 3000 System

data_processing: Bioconductor Affy package

label: biotin

organism: Homo sapiens

source_name: Laser-capture microdissected prostate stroma

label_protocol: Ensore Biotin Module (NuGEN)

growth_protocol: not applicable

extract_protocol: RNAaqueous-Micro Kit (Thermo Fisher AM1931) and Affymetrix Gene Chip Pico Reagent Kit (Thermo Fisher 902622)

treatment_protocol: not applicable

value: Stroma around benign epithelium

tag: ethnicity

value: EA


title: B6 mTSC IgG

description: Library name: IgG_bTSCs_musculus

data_processing:
Sequencing reads were trimmed using Trim_galore, with default settings.
Mapping was done with Bowtie2, with default settings.
Reads with MAPQ < 2 were removed.
Peak detection was performed using GoPeaks with -r set to the number of million reads mapped; -t 200 was used for H3K4me3 and H3K27ac, and -t 2000 -l 200 for the broader H3K4me1 signal.
Assembly: mm10 (Mus musculus); GCF_900095145 (Mus pahari)
Supplementary files format and content: bed, genomic coordinates of peaks
Library strategy: CUT&Tag

source_name: B6 mTSCs

extract_protocol:
CUT&Tag was performed using either 50,000 cells or 5 mg of tissue per antibody. Cells were harvested fresh using TrypLE Express and centrifuged at 600 × g for 5 min at room temperature (RT). Placentas were homogenised in 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X protease inhibitor cocktail (PIC), 0.1% BSA) with a Dounce homogeniser using a tight pestle 30 times. Dounced tissue was transferred to a 1.5 ml tube and centrifuged at 600 × g for 5 min at RT. Pellet was resuspended in 500 µl ice-cold nuclei extraction buffer (20 mM HEPES pH 7.5, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, 20% glycerol, 1X PIC) and incubated on ice for 10 minutes. Nuclei were pelleted by centrifugation at 1,300 × g for 5 min at 4 ˚C. Pelleted cells or nuclei were washed twice with 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X PIC) by gentle pipetting. BioMagPlus Concanavalin A-coated magnetic beads (Generon) were activated by washing and resuspension in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂). Activated beads (10 µL per sample) were added to the cells and incubated for 10 min at RT. Bead-bound cells were isolated using a magnetic stand, the supernatant was removed, and cells were resuspended in 100 µl antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X PIC, 0.05% digitonin, 2 mM EDTA, 0.1% BSA). Primary antibodies (H3K4me1 [Abcam ab8895], H3K4me3 [Active Motif 39060], H3K27ac [Abcam ab4729], or IgG [Santa Cruz sc-2027]) were added at a 1:100 dilution, and samples were incubated overnight at 4 °C on a nutator. Cells were incubated with secondary antibody (guinea pig anti-rabbit IgG [ABIN101961]) diluted 1:100 in 100 µl Dig-Wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X PIC, 0.05% digitonin) for 1 h at RT on a nutator. Cells were washed three times with 800 µl Dig-Wash buffer before incubation with Protein A-Tn5 transposase fusion protein (pA-Tn5), pre-loaded with Illumina Nextera adapters (kind gift from the Henikoff laboratory via the Madapura laboratory). pA-Tn5 was diluted 1:250 in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1X PIC, 0.05% digitonin), and 100 µl was added per sample followed by incubation for 1 h at RT on a nutator. Unbound pA-Tn5 was removed by three washes with 800 µL Dig-300 buffer. Cells were then resuspended in 300 µl tagmentation buffer (10 mM MgCl₂ in Dig-300 buffer) and incubated at 37 °C for 1 h on a nutator. Tagmentation was stopped by the addition of 10 µl 0.5 M EDTA, 3 µl 10% SDS, and 2.5 µl Proteinase K (20 mg/ml), followed by overnight incubation at 37 °C. DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1, v/v; Sigma-Aldrich) and Phase Lock Gel Heavy tubes (5 PRIME), followed by chloroform extraction and ethanol precipitation. DNA pellets were washed with 100% ethanol, air-dried, and resuspended in 30 µl TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) containing RNase A (1:400).
Libraries were amplified using 8 µl DNA per sample with NEBNext HiFi 2X PCR Master Mix, universal i5 primer, and uniquely indexed i7 primers (0.5 µM each). PCR conditions were 72 °C for 5 min, 98 °C for 30 s, followed by 12 cycles of 98 °C for 10 s and 63 °C for 10 s, with a final extension at 72 °C for 1 min. Libraries were purified using AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions.

tag: cell line

value: B6 mTSCs

tag: antibody

value: IgG [Santa Cruz sc-2027]


title: B6 mTSC H3K4me3

description: Library name: H3K4me3_bTSCs_musculus

value: H3K4me3 [Active Motif 39060]


title: M32022110329_MCC13_ATRi

city: Seattle

first: Daniel

last: Jones

state: WA

institute: Fred Hutchinson Cancer Center

description: Library name: M32022110329

data_processing:
Reads aligned with Bowtie 2
Genes with counts less than 10 across all samples were filtered out
The subsequent raw RNA-Seq count data were normalized using TMM-FPKM, followed by log2 transformation with a pseudocount of 2, as implemented in the edgeR R/Bioconductor package
Assembly: GRCh38
Supplementary files format and content: Log FPKM expression estimates in csv format

molecule: polyA RNA

extract_protocol:
Sample QC was performed with Agilent Tapestation 4200 to identify samples with RIN>7. 200ng qualified RNA from each sample was processed for library preparation. In brief, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads.
RNA fragment and reverse transcription: Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP.  End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments.   PCR amplification: Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer.  Single strand separation and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.  DNA nanoball synthesis.

tag: treatment

value: ATRi


title: EA-16

description: European-Amercian Stroma -16


title: EA-17

description: European-Amercian Stroma -17


title: PolII_ChIP_noHD

description: Library name: PolII_mitosis

data_processing:
ChIP-seq reads were aligned to S.pombe genome (2018) using Bowtie2 version 2.4.4
bigWig files were generated using deeptools version 3.5.1 with subcommand "bamCoverage" and the options --ignoreForNormalization III --normalizeUsing RPGC --effectiveGenomeSize 10118937 or --scaleFactor for spike-in normalization.
Spike-in normalization was performed
Scores represent subtraction of control read density from treatment read density.
Assembly: S.pombe (2018)
Supplementary files format and content: bigWig

extract_protocol:
Fission yeast cells (approximately 5 x 108 cells at OD595 = 0.5) were fixed with 3% pFA at 26°C for 30 minutes, washed twice with 1´ PBS, and further fixed with 10 mM dimethyl adipimidate (Sigma Aldrich) at room temperature for 45 minutes.  After two washes with 1´ PBS, the cells were disrupted with glass beads using Mini-Beadbeater-16 (BioSpec Products) in ChIP lysis buffer [50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM PMSF, and EDTA-free Protease Inhibitor Cocktail (Roche)].  Chromatin DNA was sheared into 100–500 bp fragments by Bioruptor UCD-200 (Diagenode), and the soluble fraction was collected by centrifugation at 13,000 rpm for 15 minutes.  A total of 50 μl ChIP lysis buffer containing 5 µl antibody and 15 µl Dynabeads protein G (Thermo Fisher Scientific) was added to the soluble fraction, and the bead suspension was incubated at 4°C for 2 hours with a gentle rotation.  The beads were washed twice with ChIP lysis buffer, once with ChIP lysis buffer containing 0.65 M NaCl, once with washing buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, and 1 mM EDTA), and once with TE (10 mM Tris-HCl pH 8.0, and 1 mM EDTA) for 5 minutes each with a gentle rotation.  The protein-DNA mixture was eluted by incubating the beads with TES (10 mM Tris-HCl pH 8.0, 1 mM EDTA, and 1% SDS) at 65°C for 30 minutes with harsh agitation at 1,000 rpm using ThermoMixer (Eppendorf) and subjected to reverse crosslinking at 68°C overnight in the presence of 0.5 M NaCl.  DNA was purified using QIAquick PCR purification kit (Qiagen)
The recovered DNA was subjected to library construction using NEBNext Ultra DNA library prep kit (NEB).  The sequencing libraries were amplified by PCR using the NEBNext Ultra II Q5 Master Mix (NEB) with NEBNext Multiplex Oligos for Illumina (NEB).  The libraries were sequenced by NextSeq 2000 (Illumina) to obtain paired-end reads.

tag: chip antibody

value: Abcam Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody; ab5408


title: M32022110328_MCC13_ATRi

description: Library name: M32022110328


title: Pmc4_Pk_ChIP_5%_HD

description: Library name: Pmc4_pk_mitosis_HD

value: Bio-rad, V5-Tag antibody, SV5-Pk1


title: Cnd2_Pk_ChIP_5%_HD

description: Library name: Cnd2_pk_mitosis_HD


title: B6 mTSC H3K4me1

description: Library name: H3K4me1_bTSCs_musculus

value: H3K4me1 [Abcam ab8895]


title: M32022110331_MCC13_RT

description: Library name: M32022110331

value: Radiation


title: EA-19

description: European-Amercian Stroma -19


title: B6 mTSC H3K27ac

description: Library name: H3K27ac_bTSCs_musculus

value: H3K27ac [Abcam ab4729]


title: M32022110330_MCC13_ATRi

description: Library name: M32022110330


title: Mus musculus trophoblast IgG, rep 2

description: Library name: IgG_trophoblast_musculus-4

source_name: Trophoblast

value: Trophoblast


title: AA-13

description: African-American Stroma -13

value: AA


title: AA-14

description: African-American Stroma -14


title: Pmc4_Pk_ChIP_noHD

description: Library name: Pmc4_pk_mitosis


title: Mus musculus trophoblast IgG, rep 1

description: Library name: IgG_trophoblast_musculus-3


title: Cnd2_Pk_ChIP_noHD

description: Library name: Cnd2_pk_mitosis


title: M32022110325_MCC13_Untx

description: Library name: M32022110325

value: Untreated


title: Mus musculus trophoblast H3K4me3, rep 2

description: Library name: H3K4me3_trophoblast_musculus-4


title: AA-11

description: African-American Stroma -11


title: AA-10

description: African-American Stroma -10


title: M32022110326_MCC13_Untx

description: Library name: M32022110326


title: AA-12

description: African-American Stroma -12


title: Cnd1_Pk_ChIP_Cnd1_depletion

description: Library name: Cnd1_deg_ vector_Pk_ChIP


title: AA-9

description: African-American Stroma -9


title: M22022110323_MKL2_Combo

description: Library name: M22022110323

value: ATRi + Radiation


title: M22022110322_MKL2_Combo

description: Library name: M22022110322


title: Mus musculus trophoblast H3K4me3, rep 1

description: Library name: H3K4me3_trophoblast_musculus-3


title: M22022110324_MKL2_Combo

description: Library name: M22022110324


title: AA-7

description: African-American Stroma -7


title: Mus musculus trophoblast H3K4me1, rep 2

description: Library name: H3K4me1_trophoblast_musculus-4


title: Cnd1_WT_Myc_ChIP

description: Library name: Cnd1_WT_Myc_ChIP_R2

value: Takara, Myc antibody, 9E10


title: AA-8

description: African-American Stroma -8


title: Cnd1_WT1

description: Library name: Cnd1_WT_Myc_R1

value: MboI, HinfI, MluCI


title: M32022110327_MCC13_Untx

description: Library name: M32022110327


title: Cnd1_Pk_ChIP_Pmc4_depletion

description: Library name: Cnd1_pk_pmc4deg_vector


title: AA-3

description: African-American Stroma -3

value: Stroma around benign epithelium


title: alg3/4_PD_3

city: Montreal

first: Sabih

last: Rashid

state: Quebec

address: 3611 Rue Sainte Famille, Unit 11

department: Biology

country: Canada

institute: McGill University

description:
Library name: Sample 18
alg3/4_PD_3

data_processing:
Reference genome assembly and DESeq2. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference C. elegans genome version WBcel235 (gene annotation from Ensembl version 104) using STAR version 2.7.1a. Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression, either in TPM or FPKM values, for these stranded RNA libraries. DESeq2 version 1.48.2 was then used to normalize gene readcounts and obtain pairwise comparisons following filtering of low-readcount genes.
Assembly: WBcel235 (gene annotation from Ensembl version 104)
Supplementary files format and content: "daf2_aak_alg34_normalized_counts.csv" contains read counts, pairwise comparisons in separate files for fold change calculations.

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Bleach-synchronized worms were put onto large NGM plates and grown at 25 °C. Dauer animals were collected after 96 hours (i.e. Day 2 in dauer) and washed with M9, post-dauer animals collected after 192 hours. Animals were immediately subjected to Trizol RNA extraction after collection.

extract_protocol:
Standard Trizol RNA extraction was carried out, approximately 200 ul per 20 ul packed worms. Freeze-thawing with liquid nitrogen was carried out to separate RNA, followed by heavy centrifugation. Two rounds of chloform extraction were carried out (50 ul per 200 ul Trizol). Samples were washed with isopropanol followed by 70% EtoH, and air-dryed before dissolving in ultrapure water. Sample concentration was measured using Nanodrop, and run on agarose gels to verify integrity of RNA. RNA was stored at -80 °C for up to 3 days before being sent for sequencing. Minimum of 100 ng/ul RNA was sent for sequencing.
mRNA-Seq with PolyA selection, 150 cycles Paired-End (maximum 2x80nt), 400M fragments, using KAPA mRNA Hyper Prep Hyperprep library per manufacturer instructions

value: Whole animal

tag: developmental stage

value: Post-dauer

tag: time

value: 192 hrs

tag: genotype

value: Trizol

tag: batch


title: Cnd2_Flag_ChIP_Cnd2_depletion

description: Library name: Cnd2_deg_vector_FLAG_ChIP

value: Sigma, FLAG antibody, M2


title: EA-5

description: European-Amercian Stroma -5

value: EA


title: Cnd1_Pk_ChIP_Pmc4_WT

description: Library name: Cnd1_pk_pmc4deg_pPmc4WT

value: Bio-rad, V5-Tag antibody, SV5-Pk1


title: M22022110319_MKL2_RT

description: Library name: M22022110319


title: M22022110317_MKL2_ATRi

description: Library name: M22022110317

value: ATRi


title: alg3/4_PD_2

description:
Library name: Sample 17
alg3/4_PD_2


title: Mus musculus ex. mesoderm H3K4me3, rep 3

description: Library name: H3K4me3_endothelial_musculus-5

source_name: Extraembryonic mesoderm

value: Extraembryonic mesoderm

value: H3K4me3 [Active Motif 39060]


title: Mus musculus ex. mesoderm H3K4me3, rep 2

description: Library name: H3K4me3_endothelial_musculus-4


title: M22022110321_MKL2_RT

description: Library name: M22022110321

value: Radiation


title: Mus musculus ex. mesoderm IgG, rep 3

description: Library name: IgG_endothelial_musculus-5

value: IgG [Santa Cruz sc-2027]


title: Cnd1_Pk_ChIP

description: Library name: Cnd1_pk_R1


title: Mus musculus trophoblast H3K4me1, rep 1

description: Library name: H3K4me1_trophoblast_musculus-3

value: Trophoblast

value: H3K4me1 [Abcam ab8895]


title: M22022110318_MKL2_ATRi

description: Library name: M22022110318


title: M22022110316_MKL2_ATRi

description: Library name: M22022110316


title: Mus musculus ex. mesoderm IgG, rep 1

description: Library name: IgG_endothelial_musculus-3


title: alg3/4_PD_1

description:
Library name: Sample 16
alg3/4_PD_1


title: M22022110320_MKL2_RT

description: Library name: M22022110320


title: alg3/4_Dauer_1

description:
Library name: Sample 13
alg3/4_Dauer_1

value: Dauer

value: 96 hrs


title: alg3/4_Dauer_3

description:
Library name: Sample 15
alg3/4_Dauer_3


title: Mus musculus ex. mesoderm H3K4me1

description: Library name: H3K4me1_endothelial_musculus-5


title: M22022110315_MKL2_Untx

description: Library name: M22022110315

value: Untreated


title: notag_Pk_ChIP

description: Library name: notag_pk_R1


title: Cnd1_K658E_Myc_ChIP

description: Library name: Cnd1_K658E_Myc_ChIP_R2

value: Takara, Myc antibody, 9E10


title: Cnd1_mutant_mitosis_Proseq

data_processing:
RNA-seq reads were aligned to S.pombe (2018) using STAR version 2.7.6.
Reads assigned to exons were estimated by the RSEM program version 1.3.3.
bigWig files were generated using deeptools version 3.5.1 with subcommand "bamCoverage" and the options --ignoreForNormalization III --normalizeUsing RPGC --effectiveGenomeSize 10118937.
Assembly: S.pombe (2018)
Supplementary files format and content: bigWig

extract_protocol:
RNA was extracted using Rneasy Mini kit (Qiagen)
Libraries were constructed using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB) by following the manufacture's protocol


title: Mus musculus ex. mesoderm H3K4me3, rep 1

description: Library name: H3K4me3_endothelial_musculus-3


title: M22022110314_MKL2_Untx

description: Library name: M22022110314


title: Pmc4_depletion_mitosis_Proseq


title: Cnd1_WT_mitosis_Proseq


title: Mus musculus placenta IgG, rep 2

description: Library name: IgG_placenta_musculus-2

value: Placenta


title: Mus musculus ex. mesoderm IgG, rep 2

description: Library name: IgG_endothelial_musculus-4


title: daf2_PD_3

description:
Library name: Sample 6
daf2_PD_3

value: Whole animal

value: Post-dauer

value: 192 hrs


title: Mus musculus placenta IgG, rep 3

description: Library name: IgG_placenta_musculus-3


title: M22022110313_MKL2_Untx

description: Library name: M22022110313


title: Cnd1_depletion_mitosis_Proseq


title: Cnd2_WT

value: MboI, HinfI, MluCI


title: aak_Dauer_3

description:
Library name: Sample 9
aak_Dauer_3

value: daf-2; aak(0)

value: Trizol


title: alg3/4_Dauer_2

description:
Library name: Sample 14
alg3/4_Dauer_2


title: Mus musculus placenta H3K4me3, rep 3

description: Library name: H3K4me3_placenta_musculus-3


title: M12022110310_WaGa_Combo

description: Library name: M12022110310

source_name: WaGa

value: WaGa

value: ATRi + Radiation


title: Mus musculus placenta IgG, rep 1

description: Library name: IgG_placenta_musculus-1


title: M12022110311_WaGa_Combo

description: Library name: M12022110311


title: Cnd2_depletion


title: aak_PD_3

description:
Library name: Sample 12
aak_PD_3


title: Pmc4_WT_mitosis_Proseq


title: daf2_Dauer_3

description:
Library name: Sample 3
daf2_Dauer_3


title: M1202211039_WaGa_RT

description: Library name: M1202211039

value: Radiation


title: Mus musculus placenta H3K4me3, rep 1

description: Library name: H3K4me3_placenta_musculus-1

value: H3K4me3 [Active Motif 39060]


title: M12022110312_WaGa_Combo

description: Library name: M12022110312


title: M1202211037_WaGa_RT

description: Library name: M1202211037


title: M1202211035_WaGa_ATRi

description: Library name: M1202211035

value: ATRi


title: Radiated+Treated rat intestinal tissue RNA-seq_1

city: Nanning

first: Lingzhang

last: Meng

state: Guangxi

address: Qingxiu District

country: China

institute: Guangxi Academy of Medical Sciences

description:
Library name: Radiated+Treated_1
Intestinal tissue collected from untreated Sprague–Dawley rats.
TG_1

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Low-quality reads and adapter sequences were removed using fastp.
Clean reads were aligned to the Rattus norvegicus reference genome using STAR.
Aligned reads were sorted and indexed using SAMtools.
Gene-level read counts were generated using featureCounts.
Assembly: mRatBN7.2
Supplementary files format and content: gene_counts.txt is a tab-delimited text file containing gene-level raw read counts for all samples, with rows representing Ensembl gene IDs and columns representing individual samples.

organism: Rattus norvegicus

source_name: Intestine

growth_protocol: Sprague–Dawley rats were housed under specific pathogen-free conditions with controlled temperature, humidity, and a 12 h light/dark cycle, and had free access to food and water.

extract_protocol:
Total RNA was extracted from intestinal tissue samples using standard RNA extraction procedures. RNA purity was assessed using NanoDrop spectrophotometry, and RNA integrity was evaluated using the Agilent 5400 Bioanalyzer.
Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads and fragmented. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand synthesis. After end repair, A-tailing, and adaptor ligation, fragments of approximately 250–300 bp were selected and amplified by PCR to generate the final sequencing libraries.

treatment_protocol: Rats in the model and treatment groups were exposed to a single dose of 10 Gy X-ray irradiation to induce radiation-induced intestinal injury. Rats in the treatment group subsequently received Changbing Formula intervention.

value: Intestine

value: wild type

value: 10 Gy X-ray irradiation + Changbing Formula


title: {delta}srb11


title: {delta}med13


title: Mus musculus placenta H3K4me1, rep 1

description: Library name: H3K4me1_placenta_musculus-1

value: H3K4me1 [Abcam ab8895]


title: Mus musculus placenta H3K27ac, rep 2

description: Library name: H3K27ac_placenta_musculus-2

value: H3K27ac [Abcam ab4729]


title: {delta}pmc3


title: M1202211036_WaGa_ATRi

description: Library name: M1202211036


title: Radiated+Treated rat intestinal tissue RNA-seq_3

description:
Library name: Radiated+Treated_3
Intestinal tissue collected from untreated Sprague–Dawley rats.
TG_3


title: Cnd2_C703R


title: {delta}srb10


title: M1202211033_WaGa_Untx

description: Library name: M1202211033

value: Untreated


title: M1202211034_WaGa_ATRi

description: Library name: M1202211034


title: Radiated rat intestinal tissue RNA-seq_5

description:
Library name: Radiated_5
Intestinal tissue collected from untreated Sprague–Dawley rats.
Model_5

value: 10 Gy X-ray irradiation


title: Radiated+Treated rat intestinal tissue RNA-seq_5

description:
Library name: Radiated+Treated_5
Intestinal tissue collected from untreated Sprague–Dawley rats.
TG_5


title: {delta}rox3


title: Radiated rat intestinal tissue RNA-seq_6

description:
Library name: Radiated_6
Intestinal tissue collected from untreated Sprague–Dawley rats.
Model_6


title: Radiated+Treated rat intestinal tissue RNA-seq_6

description:
Library name: Radiated+Treated_6
Intestinal tissue collected from untreated Sprague–Dawley rats.
TG_6


title: {delta}med20


title: Radiated+Treated rat intestinal tissue RNA-seq_4

description:
Library name: Radiated+Treated_4
Intestinal tissue collected from untreated Sprague–Dawley rats.
TG_4


title: {delta}med1


title: Mus musculus placenta H3K4me1, rep 2

description: Library name: H3K4me1_placenta_musculus-2

value: Placenta


title: Mus musculus placenta H3K4me3, rep 2

description: Library name: H3K4me3_placenta_musculus-2


title: M1202211032_WaGa_Untx

description: Library name: M1202211032


title: {delta}med10


title: Radiated+Treated rat intestinal tissue RNA-seq_2

description:
Library name: Radiated+Treated_2
Intestinal tissue collected from untreated Sprague–Dawley rats.
TG_2


title: Radiated rat intestinal tissue RNA-seq_3

description:
Library name: Radiated_3
Intestinal tissue collected from untreated Sprague–Dawley rats.
Model_3


title: M1202211038_WaGa_RT

description: Library name: M1202211038


title: Mus musculus placenta H3K4me1, rep 3

description: Library name: H3K4me1_placenta_musculus-3


title: Mus musculus placenta H3K27ac, rep 1

description: Library name: H3K27ac_placenta_musculus-1


title: Radiated rat intestinal tissue RNA-seq_2

description:
Library name: Radiated_2
Intestinal tissue collected from untreated Sprague–Dawley rats.
Model_2


title: Sample10,CHB_prolonged,scRNAseq

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

description:
Library name: Sample10
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
The FASTQ files from the sequences were processed using the BD Rhapsody Targeted Analysis Pipeline (Revision 10) (Becton Dickinson) in the Seven Bridges Platform.
Assembly: GRCh38
Supplementary files format and content: matrix file

source_name: peripheral blood mononuclear cells

extract_protocol:
For peripheral blood mononuclear cells (PBMCs) isolation, 10 mL of heparinized blood was diluted 1:1 with PBS, gently layered over an equal volume of lymphocyte separation medium (Nacalai tesque, Japan), and centrifuged at 740 × g for 30 minutes; the mononuclear cell layer was then harvested.
Isolated PBMCs were freshly subjected to the single-cell RNA sequencing, using the BD Rhapsody platform (BD Biosciences). Cell capture and library preparation were performed with the BD Rhapsody™ Human Immune Response Targeted Panel including 397 immune related genes following the manufacturer’s instructions, and libraries were sequenced on an MGI DNBSEQ-G400RS.

value: peripheral blood mononuclear cells

value: NAs


title: Mus musculus placenta H3K27ac, rep 3

description: Library name: H3K27ac_placenta_musculus-3


title: Sample9,HC,scRNAseq

description:
Library name: Sample9
BD Rhapsody


title: Cnd1_K658E

value: MboI, HinfI, MluCI


title: Extraembryonic mesoderm, rep 2

description: Library name: ATAC_endothelial_musculus-2

data_processing:
Sequencing reads were trimmed using Trim_galore, with default settings.
Mapping was done with Bowtie2, with default settings.
Reads with MAPQ < 2 were removed.
Peak detection was performed using MACS2 with -q 0.05.
Assembly: mm10
Supplementary files format and content: bed, genomic coordinates of peaks

extract_protocol:
Cells were centrifuged at 500 × g for 5 min at 4 ˚C. Pellet was resuspended in 50 µl ice-cold resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20). Nuclei were centrifuged at 500 × g for 10 min at 4 ˚C. Pellet was resuspended in 50 µl transposition buffer (10 mM Tris-HCl pH 7.6, 5 mM MgCl₂, 10% dimethyl formamide, 100 nM transposase, 0.01% digitonin, 0.1% Tween-20, 33% PBS) and incubated at 37 ˚C for 30 min in a thermomixer set to 1000 rpm. DNA was eluted in 20 µl elution buffer using a commercial DNA purification kit (Zymo Research).
Libraries were amplified using 20 µl DNA with NEBNext HiFi 2X PCR Master Mix, universal i5 primer, and uniquely indexed i7 primers (1.25 µM each). PCR conditions were 72 °C for 5 min, 98 °C for 30 s, followed by 5 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. Libraries were eluted in 20 µl elution buffer using the same DNA purification kit.

value: Extraembryonic mesoderm


title: Extraembryonic mesoderm, rep 1

description: Library name: ATAC_endothelial_musculus-1


title: Cnd2_Flag_ChIP_Cnd2_mutant

data_processing:
ChIP-seq reads were aligned to S.pombe genome (2018) using Bowtie2 version 2.4.4
bigWig files were generated using deeptools version 3.5.1 with subcommand "bamCoverage" and the options --ignoreForNormalization III --normalizeUsing RPGC --effectiveGenomeSize 10118937 or --scaleFactor for spike-in normalization.
Spike-in normalization was performed so that the total number of the human genome was same among samples.
Scores represent subtraction of control read density from treatment read density.
Assembly: S.pombe (2018)
Supplementary files format and content: bigWig

extract_protocol:
Fission yeast cells (approximately 5 x 108 cells at OD595 = 0.5) were fixed with 3% pFA at 26°C for 30 minutes, washed twice with 1´ PBS, and further fixed with 10 mM dimethyl adipimidate (Sigma Aldrich) at room temperature for 45 minutes.  After two washes with 1´ PBS, the cells were disrupted with glass beads using Mini-Beadbeater-16 (BioSpec Products) in ChIP lysis buffer [50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM PMSF, and EDTA-free Protease Inhibitor Cocktail (Roche)].  Chromatin DNA was sheared into 100–500 bp fragments by Bioruptor UCD-200 (Diagenode), and the soluble fraction was collected by centrifugation at 13,000 rpm for 15 minutes.  A total of 50 μl ChIP lysis buffer containing 5 µl antibody and 15 µl Dynabeads protein G (Thermo Fisher Scientific) was added to the soluble fraction, and the bead suspension was incubated at 4°C for 2 hours with a gentle rotation.  The beads were washed twice with ChIP lysis buffer, once with ChIP lysis buffer containing 0.65 M NaCl, once with washing buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, and 1 mM EDTA), and once with TE (10 mM Tris-HCl pH 8.0, and 1 mM EDTA) for 5 minutes each with a gentle rotation.  The protein-DNA mixture was eluted by incubating the beads with TES (10 mM Tris-HCl pH 8.0, 1 mM EDTA, and 1% SDS) at 65°C for 30 minutes with harsh agitation at 1,000 rpm using ThermoMixer (Eppendorf) and subjected to reverse crosslinking at 68°C overnight in the presence of 0.5 M NaCl.  DNA was purified using QIAquick PCR purification kit (Qiagen)
The recovered DNA was subjected to library construction using NEBNext Ultra DNA library prep kit (NEB).  The sequencing libraries were amplified by PCR using the NEBNext Ultra II Q5 Master Mix (NEB) with NEBNext Multiplex Oligos for Illumina (NEB).  The libraries were sequenced by the NextSeq 500, NextSeq 2000, or NovaSeq 6000 (Illumina) to obtain paired-end reads.

value: Sigma, FLAG antibody, M2


title: WT

value: WT


title: {delta}med18


title: Radiated rat intestinal tissue RNA-seq_1

description:
Library name: Radiated_1
Intestinal tissue collected from untreated Sprague–Dawley rats.
Model_1


title: Trophoblast, rep 2

description: Library name: ATAC_trophoblast_musculus-2

value: Trophoblast


title: Sample11,CHB_decline,scRNAseq

description:
Library name: Sample11
BD Rhapsody


title: Trophoblast, rep 1

description: Library name: ATAC_trophoblast_musculus-1


title: Control rat intestinal tissue RNA-seq_3

description:
Library name: Control_3
Intestinal tissue collected from untreated Sprague–Dawley rats.
Control_3


title: Cnd1_WT


title: estrus female MACS-DPN biological replicate 3, H3K4me3

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample 45

data_processing:
Adapter sequences were trimmed using BBduk
Trimmed reads were aligned to the mm10 reference genome using Bowtie2
Uniquely mapped reads with a quality score >20 were retained using SAMtools
Duplicate reads were removed using the MarkDuplicates command in Picard
H3K27me3 and H3K4me3 deduplicated reads were size-selected for fragments between 150–500 bp using SAMtools
Read alignments were normalized to total mapped reads using deepTools.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using the deepTools bamCoverage command.
Library strategy: CUT&Run

source_name: Hippocampus

extract_protocol:
Nuclei pellets were split and incubated with either H3K27me3 antibody (Active Motif, 39055) or H3K4me3 antibody (Abcam, Ab8580). A modified Cut&Run protocol based on Henikoff and Epicypher methods was used to extract chromatin fragments.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: A selective ERβ agonist (DPN, 0.04 pmol/hemisphere) or vehicle (1% DMSO in saline) was injected into the hippocampus of estrus females. MACS estrus females experienced stress, whereas controls were not subjected to MACS.

value: Hippocampus

tag: group

value: Estrus female MACS-DPN

value: H3K4me3 (Abcam, Ab8580)


title: Sample6,CHB_prolonged,scRNAseq

description:
Library name: Sample6
BD Rhapsody


title: Control rat intestinal tissue RNA-seq_6

description:
Library name: Control_6
Intestinal tissue collected from untreated Sprague–Dawley rats.
Control_6

value: Intestine

value: wild type


title: Sample5,CHB_decline,scRNAseq

description:
Library name: Sample5
BD Rhapsody


title: Cnd1_Pk_ChIP_Cnd1_mutant

description: Cnd1_deg_ pcnd1_Cnd1mutant_Pk_ChIP

value: Bio-rad, V5-Tag antibody, SV5-Pk1


title: M1202211031_WaGa_Untx

description: Library name: M1202211031

value: WaGa


title: Sample8,CHB_decline,scRNAseq

description:
Library name: Sample8
BD Rhapsody


title: Control rat intestinal tissue RNA-seq_1

description:
Library name: Control_1
Intestinal tissue collected from untreated Sprague–Dawley rats.
Control_1


title: estrus female control-DPN biological replicate 3, H3K4me3

description: Library name: Sample 41

value: Estrus female control-DPN


title: estrus female control-DPN biological replicate 2, H3K4me3

description: Library name: Sample 40


title: estrus female MACS-DPN biological replicate 2, H3K4me3

description: Library name: Sample 44


title: Cnd2_Flag_ChIP_Cnd2_WT


title: Radiated rat intestinal tissue RNA-seq_4

description:
Library name: Radiated_4
Intestinal tissue collected from untreated Sprague–Dawley rats.
Model_4

value: 10 Gy X-ray irradiation


title: estrus female MACS-DPN biological replicate 1, H3K4me3

description: Library name: Sample 43


title: F_D2_Di_ket_IP_40

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

description: Library name: 40

data_processing:
Raw reads were first processed for quality filtering and adapter trimming with fastp (v0.23.4) using the following options: --detect_adapter_for_pe, base correction in overlapped regions (-c), polyX tail trimming (-x), and polyG tail trimming (-g). The final quality of reads was then verified using FastQC (v0.12.1).
Filtered reads were then pseudo-aligned and quantified using Salmon (v1.10.2) with --numBootstraps 1000, --validateMappings, --rangeFactorizationBins 4, --seqBias, --gcBias, and --recoverOrphans parameters.
Quantifications were thus summarized at the gene level using the R package tximport (v1.30.0) and then processed for differential expression analysis using DESeq2 (v1.42.1).
Assembly: mRatBN7.2 Ensembl Release 110
Supplementary files format and content: Matrix of reads counts (not normalized) for each gene in each sample as computed by DESeq2 (tab-delimited txt file).

source_name: Nucleus accumbens

extract_protocol:
Tissue punches (2mm) collected from 200 µm sections of the nucleus accumbens of individual rats were used for subsequent processing. Immunoprecipitation of polyribosomes from D1- and D2-Cre rats was performed as follows: frozen bilateral tissue punches were homogenized by douncing in a homogenization buffer (2.5-4% w/v) containing 50 mM Tris-HCl (pH 7.4), 100 mM KCl, 12mM MgCl2, and 1% NP-40 Substitute supplemented with 1 mM DTT, 100 µg/mL cycloheximide, 200 U/mL RNasin Plus (Promega), 1 mg/mL heparin, and EDTA-free protease inhibitor (ApexBio). Homogenate was spun at 10,000 x g at 4°C for 10 min and cleared lysate transferred to new tubes. Approximately 6-8% of lysate was retained as input and frozen at -80°C until further processing. The remaining lysate was incubated overnight at 4°C with an anti-HA antibody (BioLegend, Anti-HA.11; 1:200 v/v) with gentle end-over-end rotation, followed by an overnight incubation at 4°C with magnetic beads (Pierce; Protein A/G). The following day, beads were washed at 4°C 3 times with a high-salt buffer containing 50 mM Tris-HCl (pH 7.4), 300 mM KCl, 12 mM MgCl2, 1% NP-40 Substitute, 0.5 mM DTT, and 100 µg/mL cycloheximide. Finally, genomic DNA removal and RNA purification were carried out using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol.
Stranded RNA-seq libraries were prepared by the Florida State University NGS Library Facility following poly(A) mRNA purification from total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers (New England Biolabs, Ipswich, MA, USA). The resulting barcoded and stranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) and the absence of adapters or primers contamination was verified on an Agilent TapeStation (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: All treatment were administered in the context of a behavioral sensitization paradigm. All drug administration and locomotor activity assessments occurred during the dark cycle in the behavioral testing context following a 30-min habituation period. All groups of D1-Cre and D2-Cre rats first underwent a 1-h test session in circular chambers immediately following a single injection of 0.9% saline (i.p.). Then, every fourth day thereafter female rats in either proestrus or diestrus received either Saline, or 10 mg/kg racemic ketamine hydrochloride (i.p., 1 mL/kg volume; Dechra) and locomotor activity immediately recorded for 1 h. A total of 6 ketamine treatments were administered. On occasion, females exhibiting 5 d cycles were instead injected every fifth day in the appropriate cycle stage. Four days following the final treatment session, rats were placed back into the behavioral testing environment and terminated 30 min later under non-stressful conditions. Brains were quickly extracted, snap-frozen in 2-methylbutane at -25°C, and stored at -80°C until further processing.

value: Nucleus accumbens

value: Het

tag: Sex

value: Female

tag: estrous cycle

value: Diestrus

value: ketamine


title: Control rat intestinal tissue RNA-seq_5

description:
Library name: Control_5
Intestinal tissue collected from untreated Sprague–Dawley rats.
Control_5


title: estrus female control-DPN biological replicate 1, H3K4me3

description: Library name: Sample 39


title: Sample2,CHB_prolonged,scRNAseq

description:
Library name: Sample2
BD Rhapsody

value: peripheral blood mononuclear cells

value: NAs


title: estrus female control-DPN biological replicate 4, H3K4me3

description: Library name: Sample 42


title: Control rat intestinal tissue RNA-seq_4

description:
Library name: Control_4
Intestinal tissue collected from untreated Sprague–Dawley rats.
Control_4


title: Sample3,HC,scRNAseq

description:
Library name: Sample3
BD Rhapsody


title: Cnd1_depletion

value: MboI, HinfI, MluCI


title: Sample7,CHB_decline,scRNAseq

description:
Library name: Sample7
BD Rhapsody


title: Cnd2_Pk_ChIP_Pmc4_depletion


title: Sample4,CHB_prolonged,scRNAseq

description:
Library name: Sample4
BD Rhapsody


title: Control rat intestinal tissue RNA-seq_2

description:
Library name: Control_2
Intestinal tissue collected from untreated Sprague–Dawley rats.
Control_2


title: R3

city: Shenyang

first: Yongfeng

last: Yang

address: No. 120, Dongling Road, Shenhe District

institute: Shenyang Agricultural University

description: Library name: Sample 6

data_processing:
CLC Genormice workbench v 11.0.1
Assembly: Custom assembly (unique_transcripts)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Larix kaempferi

source_name: plant tissue cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocds

value: plant tissue cells

value: Neofusicoccum laricinum


title: Pmc4_Pk_ChIP


title: R2

description: Library name: Sample 5


title: Cnd2_Pk_ChIP_Pmc4_WT


title: Rad21_Myc_ChIP

value: Takara, Myc antibody, 9E10


title: estrus female control-vehicle biological replicate 4, H3K4me3

description: Library name: Sample 35

value: Hippocampus

value: Estrus female control-vehicle

value: H3K4me3 (Abcam, Ab8580)


title: F_D1_Di_sal_IP_35

description: Library name: 35

value: saline


title: Sample1,HC,scRNAseq

description:
Library name: Sampla1
BD Rhapsody


title: estrus female control-vehicle biological replicate 3, H3K4me3

description: Library name: Sample 34


title: F_D2_Pro_ket_IP_38

description: Library name: 38

value: Proestrus


title: F_D1_Pro_sal_IP_33

description: Library name: 33


title: Tbp1_Pk_ChIP

value: Bio-rad, V5-Tag antibody, SV5-Pk1


title: F_D2_Di_sal_IP_39

description: Library name: 39

value: Nucleus accumbens


title: RNAseq_LIM1215_Resistant_2_Rep2

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample008

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using STAR (star/2.7.9a). Reverse (sense strand) reads were quantified using htseq-count (htseq/0.9.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: LIM1215 cells were maintained in RPMI with 10% FBS and 1% Pen-Strep in a humidified 5% CO2 incubator at 37C.

extract_protocol:
Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and isolated using the miRNeasy Mini Kit (217004, Qiagen) according to the manufacturer’s instructions. Before RNA-sequencing, RNA integrity was validated by gel electrophoresis and libraries were prepped using 1 µg of RNA with the Illumina Stranded mRNA Prep Ligation Kit (1000000124518 v03, Illumina, CA, USA), following the manufacturer’s protocol. The library fragment size was determined by TapeStation.
cDNA_oligo_dT

tag: cell type

value: Colorectal cancer


title: estrus female MACS-vehicle biological replicate 3, H3K4me3

description: Library name: Sample 38

value: Estrus female MACS-vehicle


title: RNAseq_LIM1215_Resistant_2_Rep3

description: Library name: Sample009


title: Cut14_Pk_ChIP


title: Cnd1_Pk_ChIP_Cnd1_WT

description: Cnd1_deg_ pcnd1_Cnd1WT_Pk_ChIP


title: CK3

description: Library name: Sample 3

value: control


title: estrus female MACS-DPN biological replicate 3, H3K27me3

description: Library name: Sample 31

value: Estrus female MACS-DPN

value: H3K27me3 (Active Motif, 39055)


title: F_D2_Pro_sal_IP_37

description: Library name: 37

value: Het

value: Female


title: RNAseq_LIM1215_Resistant_1_Rep3

description: Library name: Sample006


title: estrus female control-vehicle biological replicate 2, H3K4me3

description: Library name: Sample 33


title: estrus female MACS-vehicle biological replicate 1, H3K4me3

description: Library name: Sample 36


title: RNAseq_LIM1215_Resistant_2_Rep1

description: Library name: Sample007


title: CK2

description: Library name: Sample 2

value: plant tissue cells


title: estrus female MACS-vehicle biological replicate 2, H3K4me3

description: Library name: Sample 37


title: F_D2_Pro_ket_IP_30

description: Library name: 30

value: ketamine


title: 1296_PZS_RNAi_nadk2_1

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

description: Library name: 49_1296_PZS_RNAi_nadk2_1

data_processing:
Small RNA libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using FASTQ/A Clipper (options: -Q33 -l 17 -c -n -a TGGAATTCTCGGGTGCCAAGG) and quality filtered using the FASTQ Quality Filter (options: -Q33 -q 27 -p 65) from the FASTX-Toolkit
Filtered reads were mapped to the C. elegans genome WS258 using Bowtie2 v. 2.5.0 (default parameters)
Reads were assigned to genomic features using featureCounts (options: -t exon -g gene_id -O --fraction –largestOverlap) which is part of the Subread v. 2.0.1 package.
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.

source_name: whole worm

growth_protocol: Sychronized animals were grown on enriched peptone plates seeded with E. coli at 15°or 20°C until 1-day-old adults.

extract_protocol:
For RNA extraction, synchronized gravid adult animals (~68 h at 20 °C after L1 arrest) were washed off plates with water three times and then settled on ice to clear bacteria. Worm pellet was resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by chloroform extraction and isopropanol precipitation.
40 ng of total RNA was used for total small RNA library preparation. Small RNAs (18 to 30-nt) were size selected on homemade 10% Urea-polyacrylamide gels. Small RNAs were treated with 5’ RNA polyphosphatase (Epicenter RP8092H) and ligated to 3’ pre-adenylated adapters with Truncated T4 RNA ligase (NEB M0373L). Small RNAs were then hybridized to the reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase (NEB M0204L), and reverse transcribed with Superscript III (Thermo Fisher 18080–051). Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase (NEB M0491L) and size selected on a homemade 10% polyacrylamide gel. Library concentration was determined using the Qubit 1 X dsDNA HS Assay kit (Thermo Fisher Q33231) and quality was assessed using the Agilent BioAnalyzer. Libraries were sequenced on the Illumina NextSeq2000 (SE 75 bp reads) platform.

treatment_protocol: RNAi treated animals were grown on RNAi plates seeded with HT115 bacteria.

value: whole worm

value: USC1296 - simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV

value: 1-day-old adult

tag: experimental temperature

tag: treatment- bacterial

value: nadk2 HT115 RNAi


title: F_D1_Pro_ket_IP_34

description: Library name: 34

tag: strain


title: CK1

description: Library name: Sample 1

tag: tissue


title: estrus female MACS-DPN biological replicate 1, H3K27me3

description: Library name: Sample 29

value: Hippocampus


title: F_D2_Pro_sal_IP_29

description: Library name: 29

value: Proestrus

value: saline


title: RNAseq_LIM1215_Parental_Rep3

description: Library name: Sample003


title: estrus female control-vehicle biological replicate 1, H3K4me3

description: Library name: Sample 32

value: Estrus female control-vehicle

value: H3K4me3 (Abcam, Ab8580)


title: estrus female control-DPN biological replicate 2, H3K27me3

description: Library name: Sample 26

value: Estrus female control-DPN


title: 1757_mom4_15C_2

description: Library name: 46_1757_mom4_15C_2


title: F_D2_Di_ket_IP_32

description: Library name: 32

value: Nucleus accumbens

value: Diestrus


title: F_D1_Di_ket_IP_36

description: Library name: 36


title: 1296_PZS_RNAi_nadk2_2

description: Library name: 50_1296_PZS_RNAi_nadk2_2


title: RNAseq_LIM1215_Resistant_1_Rep2

description: Library name: Sample005

value: Colorectal cancer


title: F_D1_Di_sal_IP_27

description: Library name: 27

value: Het


title: RNAseq_LIM1215_Parental_Rep2

description: Library name: Sample002


title: estrus female control-DPN biological replicate 4, H3K27me3

description: Library name: Sample 28

value: H3K27me3 (Active Motif, 39055)


title: 1296_PZS_RNAi_L4440_2

description: Library name: 48_1296_PZS_RNAi_L4440_2


title: RNAseq_LIM1215_Parental_Rep1

description: Library name: Sample001


title: R1

description: Library name: Sample 4

value: plant tissue cells

value: Neofusicoccum laricinum


title: 1296_PZS_RNAi_L4440_1

description: Library name: 47_1296_PZS_RNAi_L4440_1

value: whole worm


title: estrus female control-DPN biological replicate 1, H3K27me3

description: Library name: Sample 25


title: estrus female control-DPN biological replicate 3, H3K27me3

description: Library name: Sample 27


title: estrus female MACS-DPN biological replicate 2, H3K27me3

description: Library name: Sample 30

value: Estrus female MACS-DPN


title: 1757_mom4_15C_1

description: Library name: 45_1757_mom4_15C_1

value: 1-day-old adult


title: F_D1_Di_ket_IP_28

description: Library name: 28

value: Female

value: ketamine


title: F_D2_Di_ket_IP_24

description: Library name: 24


title: F_D1_Pro_sal_IP_25

description: Library name: 25

value: Proestrus


title: Stiff EV miRNA biol rep 2

city: Cincinnati

first: Claire

last: Chougnet

state: OH

address: 240 Albert Sabin Way

department: Immunobiology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: miMS5
miMS5_stiff_rep2

data_processing:
The exceRpt pipeline was utilized for Quality Control of small RNA samples. Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database. Raw counts were normalized as transcripts per million (TPM).
Assembly: Hg38
Supplementary files format and content: tab seperated file with raw count numbers generated from the exceRpt pipeline.

extract_protocol:
EVs were isolated from culture media samples using an insulator-based dielectrophoresis approach. Total RNA was extracted from purified EVs using the miRNeasy Micro kit as per the manufacturer’s suggested protocol. Size distribution and estimated RNA concentration were measured using the Agilent 6000 Pico Kit using Bioanalyzer.
For library preparation, NEBNext Small RNA Sample Library Preparation kit was used with a modified approach for precise miRNA library size selection, which makes it possible for the kit to process low input (ng level) and low-quality (Bioanalyzer RIN value <3) RNA with better library recovery and miRNA reads alignment. Specifically, using ~8 ng total RNA as input, after 15 cycles of final PCR, libraries with unique indices were first equal-10 µl pooled, column cleaned up, and mixed with a custom-designed DNA ladder that contains 135 and 146 bp purified PCR amplicons. This size range corresponds to a miRNA library with 16-27 nt insert that covers all miRNAs. After high-resolution agarose gel electrophoresis and gel excision, the library pool ranging from 135 to 146 bp, including the DNA marker, was purified and quantified by NEBNext Library Quant kit (NEB) using QuantStudio 5 Real-Time PCR System. The first round of sequencing was performed on NextSeq 2000 sequencer to generate a few million reads to quantify the relative concentration of each library. The volume of each library was then adjusted to generate the expected number of equal reads [~4.5M read clusters] from each sample for final data analysis.

value: Squamous epithelial

value: Day 14

value: Stiff ECM


title: Soft EV miRNA biol rep 3

description:
Library name: miMS3
miMS3_soft_rep3

value: Soft ECM


title: Stiff EV miRNA biol rep 3

description:
Library name: miMS6
miMS6_stiff_rep3


title: F_D2_Di_sal_IP_31

description: Library name: 31

value: Nucleus accumbens

value: saline


title: estrus female control-vehicle biological replicate 4, H3K27me3

description: Library name: Sample 22

value: Hippocampus

value: Estrus female control-vehicle


title: 1765_F55A125_PZS_2

description: Library name: 40_1765_F55A125_PZS_2

value: USC1765 - F55A12.5 mutant (cmp399) I; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: Soft EV miRNA biol rep 2

description:
Library name: miMS2
miMS2_soft_rep2


title: 1751_daf18_15C_2

description: Library name: 44_1751_daf18_15C_2


title: RNAseq_LIM1215_Resistant_1_Rep1

description: Library name: Sample004

value: Colorectal cancer


title: estrus female control-vehicle biological replicate 3, H3K27me3

description: Library name: Sample 21

value: H3K27me3 (Active Motif, 39055)


title: 1765_F55A125_PZS_1

description: Library name: 39_1765_F55A125_PZS_1

value: whole worm


title: estrus female MACS-vehicle biological replicate 1, H3K27me3

description: Library name: Sample 23

value: Estrus female MACS-vehicle


title: estrus female control-vehicle biological replicate 2, H3K27me3

description: Library name: Sample 20


title: F_D1_Pro_ket_IP_26

description: Library name: 26

value: Het


title: F_D2_Di_sal_IP_23

description: Library name: 23

value: Female

value: Diestrus


title: estrus female MACS-vehicle biological replicate 2, H3K27me3

description: Library name: Sample 24


title: N2_15C_2

description: Library name: 42_N2_15C_2

value: N2 - wild-type

value: 1-day-old adult


title: 1751_daf18_15C_1

description: Library name: 43_1751_daf18_15C_1


title: 1762_Y39A3CL4_PZS_1

description: Library name: 37_1762_Y39A3CL4_PZS_1

value: USC1762 - Y39A3CL.4 mutant (cmp397) III; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: N2_15C_1

description: Library name: 41_N2_15C_1


title: Stiff EV mRNA biol rep 3

description:
Library name: MS6
MS6_stiff_rep3

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1. The trimmed reads were aligned to the reference human genome version hg38 with the program STAR v2.6.1e. Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8. Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database. Read counting was done with the program featureCounts v1.6.2 from the Rsubread package. Raw counts were normalized as transcripts per million (TPM). Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0. Gene list and log2 fold change are used for GSEA analysis using GO pathway dataset.
Assembly: Hg38
Supplementary files format and content: tab seperated file with raw count numbers generated from the START aligner and FeatureCounts.

extract_protocol:
EVs were isolated from culture media samples using an insulator-based dielectrophoresis approach. Total RNA was extracted from purified EVs using the miRNeasy Micro kit as per the manufacturer’s suggested protocol. Size distribution and estimated RNA concentration were measured using the Agilent 6000 Pico Kit using Bioanalyzer.
Directional whole exosome RNA-seq was performed by the Genomics, Epigenomics and Sequencing Core (GESC) at the University of Cincinnati. To summarize, the quality of total RNA was quality control analyzed by Bioanalyzer. A total of ~10 ng RNA was input for library preparation using NEBNext Ultra II Directional RNA Library Prep kit under PCR cycle number 9. Library quality control and quantification were performed via Qubit quantification, and individually indexed libraries were proportionally pooled and sequenced using NextSeq 2000 Sequencer under the PE 2x61 bp setting to generate about 44M reads. Upon sequencing completion, fastq files were generated via Illumina BaseSpace Sequence Hub for downstream data analysis.

value: Squamous epithelial

value: Day 14

value: Stiff ECM


title: Soft EV miRNA biol rep 1

description:
Library name: miMS1
miMS1_soft_rep1

value: Soft ECM


title: F_D1_Di_sal_IP_19

description: Library name: 19

value: Nucleus accumbens

value: saline


title: F_D2_Pro_ket_IP_22

description: Library name: 22

value: Proestrus

value: ketamine


title: Stiff EV mRNA biol rep 2

description:
Library name: MS5
MS5_stiff_rep2


title: F_D1_Pro_sal_IP_17

description: Library name: 17


title: estrus female control-vehicle biological replicate 1, H3K27me3

description: Library name: Sample 19

value: Hippocampus

value: Estrus female control-vehicle

value: H3K27me3 (Active Motif, 39055)


title: Stiff EV mRNA biol rep 1

description:
Library name: MS4
MS4_stiff_rep2


title: 1762_Y39A3CL4_PZS_2

description: Library name: 38_1762_Y39A3CL4_PZS_2

value: whole worm


title: 1760_W06B41_PZS_2

description: Library name: 36_1760_W06B41_PZS_2

value: USC1760 - W06B4.1 mutant (cmp395) II; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: naive male biological replicate 1, H3K4me3

description: Library name: Sample 16

value: Naive Male

value: H3K4me3 (Abcam, Ab8580)


title: naive male biological replicate 2, H3K4me3

description: Library name: Sample 17


title: F_D2_Di_ket_IP_16

description: Library name: 16

value: Het

value: Female

value: Diestrus


title: F_D2_Pro_sal_IP_21

description: Library name: 21


title: Stiff EV miRNA biol rep 1

description:
Library name: miMS4
miMS4_stiff_rep1

value: Squamous epithelial

value: Day 14


title: naive male biological replicate 3, H3K4me3

description: Library name: Sample 18


title: Soft EV mRNA biol rep 2

description:
Library name: MS2
MS2_soft_rep2

value: Soft ECM


title: naive estrus female biological replicate 3, H3K4me3

description: Library name: Sample 15

value: Naive Estrus female


title: F_D1_Di_ket_IP_20

description: Library name: 20

value: Nucleus accumbens


title: Soft EV mRNA biol rep 3

description:
Library name: MS3
MS3_soft_rep3


title: Soft EV mRNA biol rep 1

description:
Library name: MS1
MS1_soft_rep1


title: F_D2_Pro_sal_IP_13

description: Library name: 13

value: Proestrus

value: saline


title: 1759_mask1_PZS_1

description: Library name: 33_1759_mask1_PZS_1

value: USC1759 - mask-1( cmp392[short isoform mutant],  cmp394[long isoform mutant]) IV; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV

value: 1-day-old adult


title: naive estrus female biological replicate 2, H3K4me3

description: Library name: Sample 14

value: Hippocampus


title: 1759_mask1_PZS_2

description: Library name: 34_1759_mask1_PZS_2

value: whole worm


title: F_D1_Pro_ket_IP_18

description: Library name: 18

value: ketamine


title: F_D2_Di_sal_IP_15

description: Library name: 15


title: naive estrus female biological replicate 1, H3K4me3

description: Library name: Sample 13


title: 121719 F22 Thy1.1/GFP double positive

city: Birmingham

first: Rob

last: Welner

state: AL

address: 1824 6th Ave S

department: Medicine - Hem/Onc

institute: University of Alabama at Birmingham

description:
Library name: F22 DP
F22 DP

data_processing:
RNA-seq data were mapped to mouse mm10 genome using STAR aligner
Mapped reads number of each gene were used to identify gene expression by feature Counts.
Gene expression counts were further normalized among samples based on the total numbers of all mapped reads, and subsequently log2-tranformed. Normalized data were further employed to identify differentially expressed genes with the cutoff values: 2 for the average fold change between the comparing two groups and 0.05 for the p value of t-test cross the replicated samples.
Assembly: mm10
Supplementary files format and content: P14.IFN-g.Thy1.1 IL-2.GFP_counts text file with normalized counts

source_name: Spleen

growth_protocol: Splenocytes were harvested and either left untreated or stimulated with GP33 peptide for 20 hours.

extract_protocol:
Cells were sorted directly into TRIzol LS (Invitrogen) using a BD FACS Aria IIIu cell sorter.  RNA was isolated using a Direct-zol RNA isolation kit (Zymo Research, Irvine, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2

treatment_protocol: Stimulated and control unstimulated splenocytes were stained with anti-CD8 (53-6.7), anti-CD69 (H1.2F3), and anti-Thy1.1 (OX-7)

value: Spleen

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: female

value: stimulated


title: naive proestrus female biological replicate 3, H3K4me3

description: Library name: Sample 12

value: Naive Proestrus female

value: H3K4me3 (Abcam, Ab8580)


title: 1752_alfa1_2

description: Library name: 30_1752_alfa1_2


title: 1760_W06B41_PZS_1

description: Library name: 35_1760_W06B41_PZS_1

value: USC1760 - W06B4.1 mutant (cmp395) II; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: F_D1_Di_ket_IP_12

description: Library name: 12

value: Het

value: Female

value: Diestrus


title: naive proestrus female biological replicate 2, H3K4me3

description: Library name: Sample 11


title: 121719 F22 Thy1.1/GFP double negative

description:
Library name: F22 DN
F22 DN


title: F_D2_Di_sal_IP_7

description: Library name: 7

value: Nucleus accumbens


title: 121719 M30 Thy1.1/GFP double negative

description:
Library name: M30 DN
M30 DN

value: male


title: 1749_gtbp1_1

description: Library name: 27_1749_gtbp1_1


title: F_D2_Pro_ket_IP_6

description: Library name: 6

value: Proestrus


title: F_D1_Di_sal_IP_11

description: Library name: 11

value: saline


title: 1755_Y71F9AL12midiso_PZS_2

description: Library name: 32_1755_Y71F9AL12midiso_PZS_2

value: USC1755 - Y71F9AL.12 middle isoform mutant (cmp391) I; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV

value: 1-day-old adult


title: naive estrus female biological replicate 3, H3K27me3

description: Library name: Sample 6

value: Hippocampus

value: Naive Estrus female

value: H3K27me3 (Active Motif, 39055)


title: 1755_Y71F9AL12midiso_PZS_1

description: Library name: 31_1755_Y71F9AL12midiso_PZS_1

value: whole worm


title: 121719 F22 GFP single positive

description:
Library name: F22 GFP
F22 GFP

value: Spleen

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: female

value: stimulated


title: 1748_tiar1_1

description: Library name: 25_1748_tiar1_1

value: DG3929 - tiar-1(tn1543[loxP::Cbr-unc-119(+)::loxP]) II (tiar-1 mutant)


title: naive estrus female biological replicate 2, H3K27me3

description: Library name: Sample 5


title: 121719 F22 Thy1.1 single positive

description:
Library name: F22 Thy1.1
F22 Thy1.1


title: 121719 M30 Thy1.1/GFP double positive

description:
Library name: M30 DP
M30 DP


title: 121019 M1 Thy1.1/GFP double positive

description:
Library name: M1 DP
M1 DP


title: F_D1_Pro_ket_IP_2

description: Library name: 2

value: Het

value: Female

value: ketamine


title: 121719 F22 Unstimulated

description:
Library name: F22 UN
F22 UN

value: unstimulated


title: F_D1_Di_sal_IP_3

description: Library name: 3

value: Nucleus accumbens

value: Diestrus


title: F_D1_Pro_ket_IP_10

description: Library name: 10

value: Proestrus


title: naive male biological replicate 1, H3K27me3

description: Library name: Sample 7

value: Naive Male


title: naive proestrus female biological replicate 3, H3K27me3

description: Library name: Sample 3

value: Hippocampus

value: Naive Proestrus female


title: 1741_F01G44_PZS_2

description: Library name: 22_1741_F01G44_PZS_2

value: USC1741 - F01G4.4 mutant (cmp384) IV; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV

value: 1-day-old adult


title: naive estrus female biological replicate 1, H3K27me3

description: Library name: Sample 4

value: Naive Estrus female

value: H3K27me3 (Active Motif, 39055)


title: 1752_alfa1_1

description: Library name: 29_1752_alfa1_1

value: whole worm


title: F_D2_Pro_sal_IP_5

description: Library name: 5

value: saline


title: naive proestrus female biological replicate 1, H3K4me3

description: Library name: Sample 10

value: H3K4me3 (Abcam, Ab8580)


title: naive male biological replicate 3, H3K27me3

description: Library name: Sample 9


title: naive proestrus female biological replicate 2, H3K27me3

description: Library name: Sample 2


title: naive male biological replicate 2, H3K27me3

description: Library name: Sample 8


title: F_D2_Di_ket_IP_8

description: Library name: 8

value: Het


title: F_D1_Pro_sal_IP_9

description: Library name: 9

value: Female


title: 1749_gtbp1_2

description: Library name: 28_1749_gtbp1_2


title: 1744_Y71F9AL9_PZS_2

description: Library name: 24_1744_Y71F9AL9_PZS_2

value: USC1744 - Y71F9AL.9 mutant (cmp387) I; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: F_D1_Di_ket_IP_4

description: Library name: 4

value: ketamine


title: 1741_F01G44_PZS_1

description: Library name: 21_1741_F01G44_PZS_1


title: 1748_tiar1_2

description: Library name: 26_1748_tiar1_2

value: DG3929 - tiar-1(tn1543[loxP::Cbr-unc-119(+)::loxP]) II (tiar-1 mutant)


title: naive proestrus female biological replicate 1, H3K27me3

description: Library name: Sample 1


title: 1744_Y71F9AL9_PZS_1

description: Library name: 23_1744_Y71F9AL9_PZS_1


title: 121019 M1 GFP single positive

description:
Library name: M1 GFP
M1 GFP

value: Spleen

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: male

value: stimulated


title: 121719 M30 Thy1.1 single positive

description:
Library name: M30 Thy1.1
M30 Thy1.1


title: naive male biological replicate 2, RNA

description: Library name: Sample 8

data_processing:
Reads were pseudo-aligned and quantified using kallisto (v0.46.2) with default parameters. Transcript-level abundances (TPM) were generated using the kallisto index built from the Mus musculus (mm10) reference transcriptome.
Assembly: mm10
Supplementary files format and content: Kallisto abundance files.

molecule: cytoplasmic RNA

extract_protocol:
RNA was extracted using RNAeasy micro kit (Quiagen).
RNA libraries were prepared by Azenta Life Sciences using their standard total RNA-seq library preparation workflow.

value: Hippocampus

value: Naive Male


title: 1736_gyf1_2

description: Library name: 18_1736_gyf1_2

value: 1-day-old adult


title: 1736_gyf1_1

description: Library name: 17_1736_gyf1_1


title: IAV_T12

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

description:
Library name: IAV_T12
IAV infected KP mice at weeks 12 after tumor induction

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Multi v7.0.1. Paired-end sequencing was performed on the DNBSEQ-G400 platform in rapid-run mode. Sequencing reads were aligned and quantified using the 10x Genomics Cell Ranger pipeline. Doublets were identified and removed using the scDblFinder R package. Data analysis was conducted using Seurat (v4.1.1), with quality filtering criteria of >200 detected genes, >1000 UMIs, and <5% mitochondrial gene content per cell.
Assembly: Mouse (GRCm39) 2024-A
Supplementary files format and content: matrix files

source_name: Lung

extract_protocol:
KP mice infected with IAV for 3 weeks were i.t. administered Ad5-SPC-Cre virus to initiate lung tumorigenesis. Lung single-cell suspensions were generated at weeks 6 (early-stage) and 12 (late-stage) after tumor induction for scRNA-Seq analysis. Tumor free PBS- and IAV-treated mice served as controls. Each group was representing pooled samples from 3-5 mice. Single-cell libraries were prepared using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) following the manufacturer’s protocol
KP mice infected with IAV for 3 weeks were i.t. administered Ad5-SPC-Cre virus to initiate lung tumorigenesis. Lung single-cell suspensions were generated at weeks 6 (early-stage) and 12 (late-stage) after tumor induction for scRNA-Seq analysis. Tumor free PBS- and IAV-treated mice served as controls. Each group was representing pooled samples from 3-5 mice. Single-cell libraries were prepared using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) following the manufacturer’s protocol

value: Lung

value: tissue


title: PBS_T12

description:
Library name: PBS_T12
PBS treated KP mice at weeks 12 after tumor induction


title: 121719 M30 Unstimulated

description:
Library name: M30 UN
M30 UN

value: unstimulated


title: PBS_T6

description:
Library name: PBS_T6
PBS treated KP mice at weeks 6 after tumor induction


title: 121019 M1 Thy1.1/GFP double negative

description:
Library name: M1 DN
M1 DN


title: 1740_Y110A7A15_PZS_1

description: Library name: 19_1740_Y110A7A15_PZS_1

value: whole worm

value: USC1740 - Y110A7A.15 (cmp383) I; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: 1740_Y110A7A15_PZS_2

description: Library name: 20_1740_Y110A7A15_PZS_2


title: naive male biological replicate 1, RNA

description: Library name: Sample 7


title: 1734_H05C051_PZS_2

description: Library name: 16_1734_H05C051_PZS_2

value: USC1734 - H05C05.1 (cmp378) III; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: naive estrus female biological replicate 2, RNA

description: Library name: Sample 5

value: Naive Estrus female


title: IAV_T6

description:
Library name: IAV_T6
IAV infected KP mice at weeks 6 after tumor induction


title: 121019 M1 Thy1.1 single positive

description:
Library name: M1 Thy1.1
M1 Thy1.1


title: 121719 M30 GFP single positive

description:
Library name: M30 GFP
M30 GFP


title: 1728_D20054_PZS_2

description: Library name: 14_1728_D20054_PZS_2

value: USC1728 - D2005.4 (cmp372) I; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: naive estrus female biological replicate 3, RNA

description: Library name: Sample 6

value: Niave Estrus female


title: CD8+ T cell, S1P treated, biol rep 3

city: KOLKATA

first: Puspendu

last: Ghosh

state: WEST BENGAL

address: CNO6,SECTOR V, BIDHANNAGAR

department: CBID

country: India

institute: CSIR-IICB

description:
Library name: S1P_rep3
S1P

data_processing:
Reads were quality-controlled and filtered using TrimGalore. The filtered reads were then aligned to the reference genome using STAR, and FeatureCounts was used to generate the count table from the alignment files. The raw count table was imported into R, where differential expression analysis was performed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Purified naïve CD8+ T cells from total splenocytes of B6 mice were activated with plate-bound anti-CD3 (5 mg/ml) and anti-CD28 (2 mg/ml) in the presence of rIL2 (100 U/ml) for three days. After 24hr of activation the culture was supplemented either with vehicle control or S1P (5 µM). Complete RMPI-1640 media supplemented with 10% FCS, 4 mmol/L L-glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, 55 mmol/L beta-mercaptoethanol was used for T-cell culture.

extract_protocol:
RNA was extracted using RNeasy Mini kit (Cat no: 74106) and quantified accordingly. Concentrations of RNA were measured with the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and Qubit 4 Fluorometer (Thermo Fisher Scientific – IN) while RNA quality was assessed with the Tapestation 4200TM (Agilent Technologies, Santa Clara, US).
RNA-seq libraries were prepared from 500 ng of total RNA using the KAPA mRNA Capture and KAPA RNA HyperPrep kits. Poly(A)+ RNA was selected, fragmented, reverse-transcribed, and converted into strand-specific cDNA libraries, followed by adapter ligation and PCR amplification.

value: CD8+ T cell

value: S1P treated


title: 1728_D20054_PZS_1

description: Library name: 13_1728_D20054_PZS_1


title: F_D1_Pro_sal_IP_1

description: Library name: 1

value: Nucleus accumbens

value: Het

value: Female

value: Proestrus

value: saline


title: proto_in_vitro_symbiotic, replicate 3

city: Gdańsk

first: Marcin

last: Jakalski

address: Wita Stwosza 59

department: Center for Applied Genomics and Bioinformatics

country: Poland

institute: University of Gdansk

description:
Library name: e97_S1
Column name in count_protoDM.csv: Frags_e97_S1_noribo_clean

data_processing:
FastQC (v 0.11.7), Trimmomatic (v 0.38), SortMeRNA (v 2.1), BBMap (v 38.22), DiCoExpress
Sequences were inspected for quality with FastQC, and subsequently subjected for quality trimming with Trimmomatic
SortMeRNA was used to filter the residual ribosomal RNAs against the SILVA databases
Sequencing read libraries were mapped to the reference transcriptome (unigene set) using BBmap. The software was run with the additional “rpkm” parameter, which yields per-contig raw counts directly along the standard SAM/BAM output files.
Read count filtering and normalization (TMM) was performed using DiCoExpress R package
Assembly: de novo assebmled transcriptome of Dactylorhiza majalis
Supplementary files format and content: tab-delimited file including raw counts for each sample

organism: Dactylorhiza majalis

source_name: protocorm (seed)

extract_protocol:
The samples were homogenized in liquid nitrogen using TissueLyser II (Qiagen) in 2 mL Eppendorf tubes containing ceramic beads. Homogenized material was subjected to the NucleoZol (Macherey-Nagel, Dueren, Germany) reagent extraction process following the manufacturer’s protocol. RNAs were further purified using Agencourt RNAClean XP (Beckman Coulter, Brea, CA, United States) magnetic beads following the manufacturer’s instructions.
The libraries were constructed using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, United States).

value: protocorm (seed)

value: in vitro, symbiotic


title: 1734_H05C051_PZS_1

description: Library name: 15_1734_H05C051_PZS_1

value: 1-day-old adult


title: CD8+ T cell, vehicle control, biol rep 3

description:
Library name: Control_rep3
Control

value: Spleen

value: Vehicle control


title: naive male biological replicate 3, RNA

description: Library name: Sample 9

value: Hippocampus

value: Naive Male


title: naive proestrus female biological replicate 3, RNA

description: Library name: Sample 3

value: Naive Proestrus female


title: naive proestrus female biological replicate 1, RNA

description: Library name: Sample 1


title: 1726_F56C96_PZS_2

description: Library name: 12_1726_F56C96_PZS_2

value: whole worm

value: USC1726 - F56C9.6 (cmp370) III; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: AEG-1 floxed mice (AEG-1fl/fl).

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

description:
Library name: AEG-1fl_500
FFPE tissue sequencing
slide id: V12Y31-095

data_processing:
Raw reads obtained from the 10x Visium library were processed using Space Ranger v2.0.1, which aligned the sequencing reads to the Gex-mm10-2020-A reference genome and probe set to generate gene-count matrices.
1. Filtered feature-barcode matrices and spatial coordinates were imported into R using the Seurat package (v4.3.0).
2. SCTransformation was applied to normalize gene expression data.
3. Samples were then merged into a single object for joint dimensional reduction and clustering.
4. Clustering.
Assembly: Gex-mm10-2020-A
Supplementary files format and content: filtered gene expression data (barcodes, features, and matrix files)
Supplementary files format and content: spatial TIFF images
Library strategy: Spatial Transcriptomics

source_name: Liver

growth_protocol: 27 wks old mice livers were used

extract_protocol:
Samples were prepared using 10X Genomics kit Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome (PN-1000339)
Spatial transcriptomics sequencing libraries were prepared using 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instruction

treatment_protocol: Mice were fed HF/HSD from 7 wks until the end of the experiment

value: Liver

value: HF/HSD feeding


title: CD8+ T cell, S1P treated biol rep 1

description:
Library name: S1P_rep1
S1P

value: CD8+ T cell

value: S1P treated


title: proto_in_vitro_symbiotic, replicate 2

description:
Library name: e22_S4
Column name in count_protoDM.csv: Frags_e22_S4_noribo_clean


title: proto_in_vitro_symbiotic, replicate 4

description:
Library name: i10_S2
Column name in count_protoDM.csv: Frags_i10_S2_noribo_clean


title: 121019 M1 Unstimulated

description:
Library name: M1 UN
M1 UN

value: P14 IFN-g.Thy1.1 IL-2.GFP

value: male

value: unstimulated


title: CD8+ T cell, vehicle control, biol  rep 2

description:
Library name: Control_rep2
Control


title: naive proestrus female biological replicate 2, RNA

description: Library name: Sample 2


title: CD8+ T cell, S1P treated, biol rep 2

description:
Library name: S1P_rep2
S1P


title: CD8+ T cell, vehicle control, biol rep 1

description:
Library name: Control_rep1
Control


title: naive estrus female biological replicate 1, RNA

description: Library name: Sample 4

value: Naive Estrus female


title: proto_in_vitro_symbiotic, replicate 1

description:
Library name: e21_S3
Column name in count_protoDM.csv: Frags_e21_S3_noribo_clean

value: protocorm (seed)

value: in vitro, symbiotic


title: Myeloid cell-specific AEG-1 knockout mice (AEG-1DMAC).

description:
Library name: LC_AEG-1_499
FFPE tissue sequencing
slide id: V12Y31-095


title: Tumor-free-S

description:
Library name: Tumor-free-S
Multiplexing Tumor free PBS- and IAV- treated mice

value: Lung

value: tissue


title: 1726_F56C96_PZS_1

description: Library name: 11_1726_F56C96_PZS_1

value: 1-day-old adult


title: Tumor-free

description:
Library name: Tumor-free
Tumor free PBS- and IAV- treated mice


title: Head, 3xFLAG-Da, Input, rep2

city: Tallinn

first: Tõnis

last: Timmusk

address: Akadeemia tee 15

department: Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

data_processing:
Demultiplexing and basecalling of all libraries for each sequencing lane by using the Illumina bcl2fastq 2.17.1.14.
ChIP-seq adapter and quality trimming were performed using BBDuk (part of BBMap version 38.90) with the following parameters: ktrim=r k=23 mink=11 hdist=1 tbo qtrim=lr trimq=10 maq=10 minlen=50.
ChIP-seq reads were mapped to the Ensembl BDGP6.32 genome using Bowtie2 (version 2.5.1). Resulting SAM files were processed using Samtools version 1.12 as follows: quality filtered (-q 20), sorted, removed duplicates (-s), and converted to BAM and indexed.
bigWig files from BAMs were generated using deepTools version 3.5.0 bamCoverage command with the following parameters: --normalizeUsing CPM --exactScaling -bs 10 --extendReads 220.
Peaks were called using MACS version 2.2.7.1 using the following parameters: -B -q 0.05 -s 75. narrowPeak files were generated using default parameters. bedGraph files were converted to bigWig format using ucsc-bedgraphtobigwig version 377.
Assembly: BDGP6.32
Supplementary files format and content: bigWig files (from all BAMs)
Supplementary files format and content: bigWig and narrowPeak files from MACS (except for input samples)

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Drosophila lines were fed with malt and semolina-based food with 12 h light and dark daily rhythms at 25°C with 60% humidity.

extract_protocol:
Chromatin preparations were carried out as described in Chanas et al. 2004 and Tamberg et al. 2020.
Indexed Illumina libraries were prepared using Ovation Rapid DR Multiplex System 1-96 (NuGEN) according to the manual.
Libraries were amplified for 10 cycles using MyTaq (Bioline) and standard Illumina primers.
Illumina libraries were pooled and size selection was done by preparative gel electrophoresis selecting a range between 300 and 500bp.
Final library purification step and quality control of DNA libraries via Fragmentanalyzer (Agilent) and Qubit.
Sequencing was done on an Illumina NextSeq 500/550 - 1x75 bp read length (Illumina) -followed manufacturer's instructions.

treatment_protocol: Flies were reared and collected as follows: 1-3 days old 3xFLAG-Da adult heads were used, as a control white* Drosophila line was used with no FLAG sequence in the genome.

value: Head

tag: age

value: 1 to 3 day old


title: Myeloid cell-specific AEG-1 knockout mice (AEG-1DMAC)

description:
Library name: M683
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were using the Cell Ranger software v7.1.0
Single cell RNA-seq data analysis using Seurat version v4.0.4; 1. Quality control on the gene count matrices of samples
2. Samples integration and feature selection
3. Dimension reduction and clustering
4. Cell type identification 5. Differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: filtered gene expression data (barcodes, features, and matrix files)

extract_protocol:
Samples were prepared using 10X Genomics Next GEM Single Cell Fixed RNA Sample Preparation Kit
Library was constructed using 10X Genomics kits: Chromium Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe kit (PN 1000490) and Chromium Fixed RNA kit, Mouse Transcriptome (PN1000495)


title: 1725_Y66D12A19_PZS_1

description: Library name: 9_1725_Y66D12A19_PZS_1

value: whole worm

value: USC1725 - Y66D12A.19 (cmp369) III; simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: AEG-1 floxed mice (AEG-1fl/fl)

description:
Library name: M684
10x Genomics

value: Liver


title: 1725_Y66D12A19_PZS_2

description: Library name: 10_1725_Y66D12A19_PZS_2


title: proto_in_vitro_asymbiotic, replicate 4

description:
Library name: e20_S6
Column name in count_protoDM.csv: Frags_e20_S6_noribo_clean

value: in vitro, asymbiotic


title: Head, 3xFLAG-Da, IP, rep2

value: anti-FLAG (F1804)


title: 1693_ddx19_2

description: Library name: 8_1693_ddx19_2


title: proto_in_vitro_asymbiotic, replicate 3

description:
Library name: e18_S8
Column name in count_protoDM.csv: Frags_e18_S8_noribo_clean


title: Head, Control, IP, rep2

value: White


title: J-Lat, JQ1 Replicate 2

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description:
Library name: Sample 6
JQ1-2

data_processing:
The sequencing reads were mapped to human reference genome hg38 using STAR v2.7.5c
using recommended ENCODE parameters
Differential gene expression analysis was performed using Bioconductor DESeq 2 package
Assembly: human reference genome hg38
Supplementary files format and content: xlsx file containing sample raw counts

source_name: J-Lat cell line

growth_protocol: J-Lat cells were culture complete RMPI medium.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen)
RNA-Seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation module (E7490) and NEBNext Ultra II Directional RNA Library Prep kit for illumina (E7760)

treatment_protocol: J-Lat cells (10.6) were treated with DMSO (as negative control), ZL0580 (5 uM), or JQ1 (5 uM) for 24 hours

value: J-Lat cell line

tag: cell line

value: Transformed lymphocytes

value: WT

value: JQ1 (5 uM)


title: Head, Control, Input, rep2


title: 1693_ddx19_1

description: Library name: 7_1693_ddx19_1


title: J-Lat, ZL0580 Replicate 2

description:
Library name: Sample 4
B48-2


title: J-Lat, JQ1 Replicate 1

description:
Library name: Sample 5
JQ1-1


title: Head, 3xFLAG-Da, Input, rep1


title: proto_field_symbiotic, replicate 3

description:
Library name: 1004_S12
Column name in count_protoDM.csv: Frags_1004_S12_noribo_clean

value: protocorm (seed)

value: field, symbiotic


title: 1296_PZS_2

description: Library name: 4_1296_PZS_2

value: USC1296 - simr-1(cmp112[simr-1::GFP + loxP + 3xFLAG]) I; znfx-1(gg634[HA::tagRFP::znfx-1]) II; pgl-1 (cmp226[pgl-1::BFP +loxP + 3xFLAG]) IV


title: proto_in_vitro_asymbiotic, replicate 1

description:
Library name: e16_S5
Column name in count_protoDM.csv: Frags_e16_S5_noribo_clean


title: J-Lat, NC Replicate 2

description:
Library name: Sample 2
NC-2

value: DMSO (NC)


title: 1688_m01h93_2

description: Library name: 6_1688_m01h93_2

value: 1-day-old adult


title: proto_field_symbiotic, replicate 4

description:
Library name: TA10_S9
Column name in count_protoDM.csv: Frags_TA10_S9_noribo_clean


title: Head, Control, IP, rep1

value: Head


title: Head, Control, Input, rep1

value: 1 to 3 day old


title: J-Lat, ZL0580 Replicate 1

description:
Library name: Sample 3
B48-1


title: proto_in_vitro_asymbiotic, replicate 2

description:
Library name: e17_S7
Column name in count_protoDM.csv: Frags_e17_S7_noribo_clean


title: Head, 3xFLAG-Da, IP, rep1


title: proto_field_symbiotic, replicate 1

description:
Library name: 1001_S10
Column name in count_protoDM.csv: Frags_1001_S10_noribo_clean


title: Thymus epithelial cells, NOD.AireWT/R249C, 4 to 8 weeks, biol rep 5

city: Aurora

first: Jordan

middle: Keith

last: Abbott

state: CO

department: Allergy and Immunology

institute: University of Colorado School of Medicine

description:
Library name: WT/R249C 5
4_S5_L005

data_processing:
Reads were demultiplexed into individual FASTQ files. Each FASTQ file was trimmed to remove adaptor sequences, empty reads, and long stretches of homopolymer. Timmed FASTQ files were evaluated with FASTQC for quality control. FASTQ files that passed QC were mapped to mm39 using a pre-built genome index (https://zenodo.org/records/7457660) in HISAT2 with splice-aware setting. Transcriptomes were assembled and quantified using Stringtie using the reference gencode.vM30. Raw counts were extracted in R using txImport.
Assembly: mm39
Supplementary files format and content: gene_count_matrix.csv containing raw gene counts

source_name: Thymus

extract_protocol:
Mouse thymus was surgically harvested and digested into single-cell suspensions. CD45-expressing cells were depleted using magnetic beads. Cells were sorted for EpCAM expression using a Sony MA900 cell sorter. RNA was isolated using the Qiagen RNeasy micro kit.
cDNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1).

value: Thymus

value: Thymus epithelium

value: B


title: 1296_PZS_1

description: Library name: 3_1296_PZS_1

value: whole worm


title: N2_2

description: Library name: 2_N2_2

value: N2 - wild-type


title: 1688_m01h93_1

description: Library name: 5_1688_m01h93_1


title: Cavia porcellus cochlear, with cisplatin plus STB treatment, rep3

city: Shanghai

first: Ziwen

last: Gao

address: Fenyang Road

department: ENT Institute and Department of Otorhinolaryngology

institute: Eye & ENT Hospital, Fudan University

description:
Library name: Sample11
Column name in RNAseq_raw data.txt: Treatment2-3

data_processing:
Raw sequencing reads in FASTQ format were processed using Cutadapt (v1.9.1) 1o remove technicalsequences and low-quality bases.
Clean reads were aligned to the reference genome (Species_name, assembly version) using HISAT2(v2.2.1), a splice-aware aligner. The reference genome and annotation files were obtainedfrom ENSEMBL, NCBI or other databases.
Genc-level counts were quanilicd using HTSeq (v0.6.1).
Assembly: mm20
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Cavia porcellus

source_name: cochlear

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1ug of total RNA was used for the construction of sequencing libraries
For mRNA enrichmcnt, poly(A) mRNA isolation was performed using Oligo(dT) beads. Alternatively, when the sample quality or experimental design necessitated, ribosomal RNA was depleted using rRNA removal methods to enrich for coding and non-polyadenylated transcripts. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA synthcsis was carricd out using reverse transcriptase, followed by second-strand cDNA synthesis. For strand-specific library construction, during the second-strand synthesis the standard dTTP was replaced with dUTP; subsequent treatment with USER enzymc selectively degrades the second strand prior to PCR amplification, thereby preserving strand information. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tail in a single reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and thc PCR products werc validated. Finally, libraries with different indexes were multiplexed and loaded on an Illumina HiSeg/ Illumina Novaseq/ MG12000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to the manufacturer's instructions.

value: cochlear


title: E150009253_L01_T1

city: wenzhou

first: bin

last: zhou

address: Nanbaixiang, Ouhai District, Wenzhou, Zhejiang Province

institute: Affiliated Hospital of Weifang Medical University

description: Library name: Sample 3

data_processing:
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Read count extraction and normalization were performed using CLC genomic benchwork
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: csv files include RPKM values for each Sample

source_name: cell line

growth_protocol: Human relapsed and refractory (R/R) AML samples were xenografted into mice to assess the anti-leukemic effects of HF in vivo

extract_protocol:
centrifuge to remove supernatant, add about 2ML PBS (2% FBS), with a total amount of about 2.5mL, Add cells to trizol
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Comparative gene expression profiling analysis of RNA-seq data for stem  cells treated with halofuginone  .

value: cell line

value: stem cell

value: adipogenic differentiation

value: Separate ribosomal RNA

value: Day 0


title: N2_1

description: Library name: 1_N2_1


title: J-Lat, NC Replicate 1

description:
Library name: Sample 1
NC-1

value: J-Lat cell line

value: Transformed lymphocytes

value: WT


title: Thymus epithelial cells, NOD.AireWT/R249C, 4 to 8 weeks, biol rep 4

description:
Library name: WT/R249C 4
3_S4_L005


title: Cavia porcellus cochlear, with cisplatin plus STB treatment, rep2

description:
Library name: Sample10
Column name in RNAseq_raw data.txt: Treatment2-2


title: Cavia porcellus cochlear, with cisplatin plus STB treatment, rep1

description:
Library name: Sample9
Column name in RNAseq_raw data.txt: Treatment2-1


title: proto_field_symbiotic, replicate 2

description:
Library name: 1002_S11
Column name in count_protoDM.csv: Frags_1002_S11_noribo_clean

value: protocorm (seed)

value: field, symbiotic


title: Thymus epithelial cells, NOD.AireWT/WT, 4 to 8 weeks, biol rep 3

description:
Library name: WT/WT 5
2_S3_L005

value: WT/WT


title: E150009242_L01_T2

description: Library name: Sample 4


title: Cavia porcellus cochlear, with cisplatin treatment, rep4

description:
Library name: Sample8
Column name in RNAseq_raw data.txt: Treatment1-4


title: E150009242_L01_C2

description: Library name: Sample 2