title: Placenta sample X31303.313

description:
Library name: X31303.313
Column name in counts_nhbcs.csv.gz : X31303.313


title: PABPC1-POND-293T-1h_rep2

status: Public on Jun 24 2026

type: SRA

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

description:
Library name: Sample54
fig4_36

library_source: transcriptomic

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: HEK293T cell line

growth_protocol: HEK293T, Huh-7, and A549 cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml). V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor. H1 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2.

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

tag: cell line

value: HEK293T cell line

tag: genotype

tag: treatment

value: 0.2 μM doxycycline


title: PABPC1-POND-293T-3h_rep1

description:
Library name: Sample55
fig4_37


title: Placenta sample X31303.317

city: New York

first: Corina

last: Lesseur

state: NY

address: 1 Gustave L. Levy Pl

country: USA

institute: Icahn School of Medicine

description:
Library name: X31303.317
Column name in counts_nhbcs.csv.gz : X31303.317

data_processing:
Reads aligned with Splice Transcripts Alignment to a Reference (STAR) with GENCODE v47 (GRCh38) and quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv gzipped file with raw counts for each sample

molecule: total RNA

source_name: Placenta villis fetal side

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany, cat. No. 74106), and the Norgen Tissue RNA Purification Kit (Norgen Biotek, Thorold, ON, Canada, Cat. No. 25700), following the manufacturer’s protocols.
Ribosomal RNA depletion was used to prepare RNA-sequencing (RNA-seq) libraries, transcriptome-wide RNA-sequencing was performed with paired-end 75 bp reads on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) .

tag: tissue

value: Placenta villis fetal side

tag: maternal smoking

value: Yes

tag: baby race

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

value: AGA

tag: delivery method

value: Vaginal delivery

tag: infant sex

value: Male

tag: maternal age

tag: rna integrity_number


title: PABPC1-POND-293T-1h_rep1

description:
Library name: Sample53
fig4_35


title: Placenta sample X31303.311

description:
Library name: X31303.311
Column name in counts_nhbcs.csv.gz : X31303.311

value: No

value: LGA


title: Placenta sample X31303.309

description:
Library name: X31303.309
Column name in counts_nhbcs.csv.gz : X31303.309


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1R3_rep2

description:
Library name: Sample90
fig4_72


title: Huh-7-Mock_supernatant_rep1

description:
Library name: Sample91
fig5_5

source_name: Huh-7 cell line

value: Huh-7 cell line

value: WT


title: Placenta sample X31303.308

description:
Library name: X31303.308
Column name in counts_nhbcs.csv.gz : X31303.308


title: PABPC1-POND-293T-0.5h_rep2

description:
Library name: Sample52
fig4_34


title: Placenta sample X31303.307

description:
Library name: X31303.307
Column name in counts_nhbcs.csv.gz : X31303.307

value: Female


title: PABPC1-POND-293T-0.5h_rep1

description:
Library name: Sample51
fig4_33


title: 293T-MMLV-gag_supernatant_rep2

description:
Library name: Sample50
fig4_14

value: OE-MMLV-gag


title: Placenta sample X31303.303

description:
Library name: X31303.303
Column name in counts_nhbcs.csv.gz : X31303.303


title: 293T-MMLV-gag_supernatant_rep1

description:
Library name: Sample49
fig4_13


title: Placenta sample X31303.300

description:
Library name: X31303.300
Column name in counts_nhbcs.csv.gz : X31303.300


title: 293T-HIV-gagZIP_supernatant_rep2

description:
Library name: Sample48
fig4_12

value: OE-HIV-gagZIP


title: 293T-HIV-gagZIP_supernatant_rep1

description:
Library name: Sample47
fig4_11


title: 293T-Mock_supernatant_rep2

description:
Library name: Sample46
fig4_10


title: Placenta sample X31303.297

description:
Library name: X31303.297
Column name in counts_nhbcs.csv.gz : X31303.297

value: C-section


title: Placenta sample X31303.298

description:
Library name: X31303.298
Column name in counts_nhbcs.csv.gz : X31303.298


title: Placenta sample X31303.295

description:
Library name: X31303.295
Column name in counts_nhbcs.csv.gz : X31303.295


title: 293T-Mock_supernatant_rep1

description:
Library name: Sample45
fig4_9


title: SRSF7-NLS-NES-NLS-POND_rep2

description:
Library name: Sample44
fig3_24


title: Placenta sample X31303.292

description:
Library name: X31303.292
Column name in counts_nhbcs.csv.gz : X31303.292


title: Placenta sample X31303.289

description:
Library name: X31303.289
Column name in counts_nhbcs.csv.gz : X31303.289


title: Placenta sample X31303.288

description:
Library name: X31303.288
Column name in counts_nhbcs.csv.gz : X31303.288


title: TDP43-NLS-NES-NLS-POND_rep2

description:
Library name: Sample42
fig3_22


title: Placenta sample X31303.287

description:
Library name: X31303.287
Column name in counts_nhbcs.csv.gz : X31303.287


title: Placenta sample X31303.284

description:
Library name: X31303.284
Column name in counts_nhbcs.csv.gz : X31303.284


title: PTBP1-NLS-NES-NLS-POND_rep2

description:
Library name: Sample40
fig3_20


title: PTBP1-NLS-NES-NLS-POND_rep1

description:
Library name: Sample39
fig3_19


title: Placenta sample X31303.283

description:
Library name: X31303.283
Column name in counts_nhbcs.csv.gz : X31303.283


title: TDP43-NLS-NES-NLS-POND_rep1

description:
Library name: Sample41
fig3_21


title: NOP56-NLS-NES-NLS-POND-smallRNA_rep2

description:
Library name: Sample38
fig3_18

library_source: other

molecule: other


title: Placenta sample X31303.280

description:
Library name: X31303.280
Column name in counts_nhbcs.csv.gz : X31303.280


title: Placenta sample X31303.277

description:
Library name: X31303.277
Column name in counts_nhbcs.csv.gz : X31303.277


title: NOP56-NLS-NES-NLS-POND-smallRNA_rep1

description:
Library name: Sample37
fig3_17


title: Placenta sample X31303.273

description:
Library name: X31303.273
Column name in counts_nhbcs.csv.gz : X31303.273


title: NOP10-NLS-NES-NLS-POND-smallRNA_rep1

description:
Library name: Sample35
fig3_15


title: Placenta sample X31303.271

description:
Library name: X31303.271
Column name in counts_nhbcs.csv.gz : X31303.271


title: EPN24-POND-smallRNA_rep1

description:
Library name: Sample33
fig3_13


title: EPN24-PONDforAGO2-RNA-rep2

description:
Library name: Sample32
fig3_12


title: Placenta sample X31303.270

description:
Library name: X31303.270
Column name in counts_nhbcs.csv.gz : X31303.270


title: EPN24-PONDforAGO2-RNA-rep1

description:
Library name: Sample31
fig3_11


title: Placenta sample X31303.266

description:
Library name: X31303.266
Column name in counts_nhbcs.csv.gz : X31303.266


title: Placenta sample X31303.264

description:
Library name: X31303.264
Column name in counts_nhbcs.csv.gz : X31303.264


title: AGO2-POND-RNA-rep2

description:
Library name: Sample30
fig3_10


title: AGO2-POND-RNA-rep1

description:
Library name: Sample29
fig3_9


title: Placenta sample X31303.263

description:
Library name: X31303.263
Column name in counts_nhbcs.csv.gz : X31303.263


title: EPN24-POND-smallRNA_rep2

description:
Library name: Sample34
fig3_14


title: Placenta sample X31303.262

description:
Library name: X31303.262
Column name in counts_nhbcs.csv.gz : X31303.262


title: 293T-EPN24-miRNA_celllysate_rep3

description:
Library name: Sample28
fig3_8


title: Placenta sample X31303.261

description:
Library name: X31303.261
Column name in counts_nhbcs.csv.gz : X31303.261


title: 293T-EPN24-miRNA_celllysate_rep2

description:
Library name: Sample27
fig3_7


title: Placenta sample X31303.260

description:
Library name: X31303.260
Column name in counts_nhbcs.csv.gz : X31303.260


title: 293T-EPN24-miRNA_celllysate_rep1

description:
Library name: Sample26
fig3_6


title: Placenta sample X31303.259

description:
Library name: X31303.259
Column name in counts_nhbcs.csv.gz : X31303.259


title: 293T-AGO2-miRNA_celllysate_rep2

description:
Library name: Sample24
fig3_4


title: 293T-AGO2-miRNA_celllysate_rep3

description:
Library name: Sample25
fig3_5


title: Placenta sample X31303.258

description:
Library name: X31303.258
Column name in counts_nhbcs.csv.gz : X31303.258


title: 293T-AGO2-miRNA_celllysate_rep1

description:
Library name: Sample23
fig3_3


title: Placenta sample X31303.257

description:
Library name: X31303.257
Column name in counts_nhbcs.csv.gz : X31303.257


title: AGO2-POND-miRNA-rep2

description:
Library name: Sample22
fig3_2


title: Placenta sample X31303.255

description:
Library name: X31303.255
Column name in counts_nhbcs.csv.gz : X31303.255


title: YTHDF2-POND-293T-T1R2_rep2

description:
Library name: Sample20
fig2_38


title: AGO2-POND-miRNA-rep1

description:
Library name: Sample21
fig3_1


title: Placenta sample X31303.252

description:
Library name: X31303.252
Column name in counts_nhbcs.csv.gz : X31303.252


title: YTHDF2-POND-293T-T1R2_rep1

description:
Library name: Sample19
fig2_37


title: YTHDF2-POND-293T-T1R1_rep2

description:
Library name: Sample18
fig2_36


title: Placenta sample X31303.251

description:
Library name: X31303.251
Column name in counts_nhbcs.csv.gz : X31303.251


title: YTHDF2-POND-293T-T1R1_rep1

description:
Library name: Sample17
fig2_35


title: Placenta sample X31303.249

description:
Library name: X31303.249
Column name in counts_nhbcs.csv.gz : X31303.249


title: Placenta sample X31303.294

description:
Library name: X31303.294
Column name in counts_nhbcs.csv.gz : X31303.294


title: SRSF7-NLS-NES-NLS-POND_rep1

description:
Library name: Sample43
fig3_23


title: YTHDF2-POND-293T-T1_rep2

description:
Library name: Sample16
fig2_34

value: 1mM DMOG plus 0.2 μM doxycycline


title: YTHDF2-POND-293T-T1_rep1

description:
Library name: Sample15
fig2_33

value: HEK293T cell line


title: YTHDF2-POND-293T-T0_rep2

description:
Library name: Sample14
fig2_32

value: 0.2 μM doxycycline


title: Placenta sample X31303.245

description:
Library name: X31303.245
Column name in counts_nhbcs.csv.gz : X31303.245

value: Placenta villis fetal side


title: Placenta sample X31303.247

description:
Library name: X31303.247
Column name in counts_nhbcs.csv.gz : X31303.247


title: YTHDF2-POND-293T-T0_rep1

description:
Library name: Sample13
fig2_31


title: Placenta sample X31303.248

description:
Library name: X31303.248
Column name in counts_nhbcs.csv.gz : X31303.248


title: Placenta sample X31303.243

description:
Library name: X31303.243
Column name in counts_nhbcs.csv.gz : X31303.243


title: FMR1-noGSlinker-POND_rep2

description:
Library name: Sample12
fig2_12


title: NOP10-NLS-NES-NLS-POND-smallRNA_rep2

description:
Library name: Sample36
fig3_16


title: Placenta sample X31303.275

description:
Library name: X31303.275
Column name in counts_nhbcs.csv.gz : X31303.275


title: Placenta sample X31303.242

description:
Library name: X31303.242
Column name in counts_nhbcs.csv.gz : X31303.242


title: FMR1-noGSlinker-POND_rep1

description:
Library name: Sample11
fig2_11


title: POND-IGF2BP1-Sucrose_rep2

description:
Library name: Sample10
fig1_32


title: Placenta sample X31303.241

description:
Library name: X31303.241
Column name in counts_nhbcs.csv.gz : X31303.241


title: Placenta sample X31303.240

description:
Library name: X31303.240
Column name in counts_nhbcs.csv.gz : X31303.240


title: POND-IGF2BP1-Sucrose_rep1

description:
Library name: Sample9
fig1_31


title: Placenta sample X31303.239

description:
Library name: X31303.239
Column name in counts_nhbcs.csv.gz : X31303.239


title: POND-EPN24-Sucrose_rep2

description:
Library name: Sample8
fig1_30


title: Placenta sample X31303.272

description:
Library name: X31303.272
Column name in counts_nhbcs.csv.gz : X31303.272


title: Placenta sample X31303.238

description:
Library name: X31303.238
Column name in counts_nhbcs.csv.gz : X31303.238

value: Yes


title: Placenta sample X31303.237

description:
Library name: X31303.237
Column name in counts_nhbcs.csv.gz : X31303.237

value: White


title: POND-EPN24-Sucrose_rep1

description:
Library name: Sample7
fig1_29


title: POND-IGF2BP1+Untreat_rep2

description:
Library name: Sample6
fig1_28


title: Placenta sample X31303.234

description:
Library name: X31303.234
Column name in counts_nhbcs.csv.gz : X31303.234

value: AGA


title: Placenta sample X31303.233

description:
Library name: X31303.233
Column name in counts_nhbcs.csv.gz : X31303.233

value: Vaginal delivery


title: POND-IGF2BP1+RNase+Detergent_rep2

description:
Library name: Sample4
fig1_26


title: Placenta sample X31303.231

description:
Library name: X31303.231
Column name in counts_nhbcs.csv.gz : X31303.231


title: POND-IGF2BP1+Untreat_rep1

description:
Library name: Sample5
fig1_27


title: POND-IGF2BP1+RNase+Detergent_rep1

description:
Library name: Sample3
fig1_25


title: POND-IGF2BP1+RNase_rep2

description:
Library name: Sample2
fig1_24


title: Placenta sample X31303.230

description:
Library name: X31303.230
Column name in counts_nhbcs.csv.gz : X31303.230


title: Placenta sample X31303.227

description:
Library name: X31303.227
Column name in counts_nhbcs.csv.gz : X31303.227


title: Placenta sample X31303.226

description:
Library name: X31303.226
Column name in counts_nhbcs.csv.gz : X31303.226


title: POND-IGF2BP1+RNase_rep1

description:
Library name: Sample1
fig1_23


title: POND-FMR1-manual-E280K_rep2


title: BG-4

city: Gainesville

first: Yangyi

middle: Edward

last: Luo

state: FL

address: 1864 Stadium Road

institute: University of Florida

description: Library name: BG-4

data_processing:
In the second analysis, raw sequence reads were quality checked and aligned to mm10 using HISAT2 (D. Kim et al., 2019). Gene-level counts were generated using FeatureCounts (Liao, Smyth, & Shi, 2014). Differential Gene Expression (DGE) analysis was performed in R using DESeq2 package (Love, Huber, & Anders, 2014).
Assembly: GRC39 Mus Musculus
Supplementary files format and content: csv file. Reads per sample

organism: Mus musculus

source_name: Muscle

extract_protocol:
Total RNA from TA muscle tissue was extracted using Trizol and Qiagen RNeasy Kit
Briefly, total RNA from the left TA muscles from three 13-month-old male mice in each strain was reverse-transcribed using an Oligo(dT) primer, and limited cDNA amplification was performed using the SMARTer® Ultra® Low Input RNA Kit for Sequencing – v4 (Takara Bio USA, Inc., Mountain View, CA, USA). The resulting full-length cDNA was fragmented and tagged, followed by limited PCR enrichment to generate the final cDNA sequencing library (Nextera® XT DNA Library Prep, Illumina, San Diego, CA, USA).

value: Muscle

value: Svil-Mut

tag: batch


title: Placenta sample X31303.224

description:
Library name: X31303.224
Column name in counts_nhbcs.csv.gz : X31303.224

value: Male


title: BG-2

description: Library name: BG-2


title: BG-1

description: Library name: BG-1


title: POND-FMR1-manual-E280K_rep1


title: Placenta sample X31303.223

description:
Library name: X31303.223
Column name in counts_nhbcs.csv.gz : X31303.223

value: No


title: POND-FMR1-manual-WT_rep2


title: Placenta sample X31303.220

description:
Library name: X31303.220
Column name in counts_nhbcs.csv.gz : X31303.220


title: KO1

description: Library name: KO1

value: Svil-KO


title: KO3

description: Library name: KO3


title: KO4

description: Library name: KO4


title: WT4

description: Library name: WT4

value: WT


title: POND-FMR1-manual-WT_rep1


title: Placenta sample X31303.219

description:
Library name: X31303.219
Column name in counts_nhbcs.csv.gz : X31303.219

value: Female


title: WT3

description: Library name: WT3


title: WT1

description: Library name: WT1


title: POND-FMR1-D619syn_rep2


title: Placenta sample X31303.217

description:
Library name: X31303.217
Column name in counts_nhbcs.csv.gz : X31303.217


title: Placenta sample X31303.254

description:
Library name: X31303.254
Column name in counts_nhbcs.csv.gz : X31303.254


title: T3_18_1_H3K4me3

city: Berkeley

first: Yibing

last: Chen

state: CA

address: Morgan Hall 335

department: Metabolic Biology & Nutrition

institute: University of California, Berkeley

description: Library name: T3_18_1_H3K4me3

library_source: genomic

data_processing:
Paired-end reads were trimmed using Trimmomatic (v0.38). Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2. PCR duplicates were removed using Picard. Peaks were called with MACS2 (v2.2.7.1) using a q-value cutoff of 0.01. Differential peak analysis was performed using DESeq2, and pathway enrichment analysis was carried out with GSEApy (v1.0.6) in Python.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: HSC

extract_protocol:
100,000 sorted HSC were used for H3K4me3 CUT&Tag sequencing. Sequencing libraries were prepared using the CUT&Tag-IT assay kit (Active Motif, 53160) following the manufacturer’s instructions.
In brief, sorted HSC were immobilized with Concanavalin A beads and permeabilized with digitonin-containing antibody buffer. HSCs underwent overnight incubation with anti-trimethyl-histone H3 (Lys4) rabbit mAb (Active Motif, 39159, 1:50) at 4°C, and then incubation with Guinea pig anti-rabbit secondary antibody at room temperature for 1 hour. Samples were incubated with pA-Tn5 transposomes at room temperature for 1 hour, followed by tagmentation at 37°C for 1 hour. The tagmented DNA was then purified and subjected to PCR amplification and SPRI bead clean-up for sequencing. Sequencing libraries were quantified by KAPA library quantification kit (Roche), and sequencing was performed on NextSeq 150 MID.

tag: cell type

value: HSC

tag: antibody


title: Placenta sample X31303.253

description:
Library name: X31303.253
Column name in counts_nhbcs.csv.gz : X31303.253


title: T3_15_8_H3K4me3

description: Library name: T3_15_8_H3K4me3

value: anti-trimethyl-histone H3 (Lys4) rabbit mAb (Active Motif, 39159, 1:50)


title: POND-FMR1-D619syn_rep1


title: T3_15_3_H3K4me3

description: Library name: T3_15_3_H3K4me3


title: Placenta sample X31303.215

description:
Library name: X31303.215
Column name in counts_nhbcs.csv.gz : X31303.215


title: WT_18_9_H3K4me3

description: Library name: WT_18_9_H3K4me3


title: Placenta sample X31303.214

description:
Library name: X31303.214
Column name in counts_nhbcs.csv.gz : X31303.214


title: POND-FMR1-R611L_rep2


title: WT_15_4_H3K4me3

description: Library name: WT_15_4_H3K4me3


title: WT_15_2_H3K4me3

description: Library name: WT_15_2_H3K4me3


title: POND-FMR1-R611L_rep1


title: 7FN

city: VILLEJUIF

first: Dominique

last: Bluteau

address: Gustave Roussy, PR2, 114, rue Edouard Vaillant

country: France

institute: EPHE, PSL Research university

description: Library name: 7FN

data_processing:
Sequencing reads were pseudo aligned to genome and genes quantified using Kallisto
Assembly: GRCm38v96
Supplementary files format and content: Tab delimited table containing gene symbol and sample normalized counts

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted using QIAGEN RNAeasy plus mini kit following manufacturer's instructions
CATS RNA-seq Kit v2

value: Bone Marrow

value: FancgKO


title: Placenta sample X31303.213

description:
Library name: X31303.213
Column name in counts_nhbcs.csv.gz : X31303.213

value: LGA

value: C-section


title: Placenta sample X31303.212

description:
Library name: X31303.212
Column name in counts_nhbcs.csv.gz : X31303.212

value: Placenta villis fetal side


title: POND-FMR1-R611C_rep2

value: HEK293T cell line


title: 6FN

description: Library name: 6FN


title: 5FN

description: Library name: 5FN


title: 3FN

description: Library name: 3FN


title: 4FN

description: Library name: 4FN


title: POND-FMR1-R611C_rep1


title: Placenta sample X31303.208

description:
Library name: X31303.208
Column name in counts_nhbcs.csv.gz : X31303.208

value: White

value: AGA


title: 2FN

description: Library name: 2FN


title: 7FP

description: Library name: 7FP


title: Placenta sample X31303.207

description:
Library name: X31303.207
Column name in counts_nhbcs.csv.gz : X31303.207

value: Yes

value: Vaginal delivery


title: POND-FMR1-D610G_rep2


title: 6FP

description: Library name: 6FP


title: 5FP

description: Library name: 5FP


title: 4FP

description: Library name: 4FP


title: Placenta sample X31303.206

description:
Library name: X31303.206
Column name in counts_nhbcs.csv.gz : X31303.206


title: POND-FMR1-T607M_rep2


title: 3FP

description: Library name: 3FP


title: Placenta sample X31303.204

description:
Library name: X31303.204
Column name in counts_nhbcs.csv.gz : X31303.204


title: Mx1Cre_2

city: BERKELEY

first: DANICA

last: CHEN

address: 119 Morgan Hall

department: NST

institute: UC BERKELEY

description: Library name: 80_8

extract_protocol:
100,000 sorted HSCs were used for H3K18la CUT&Tag sequencing. Sequencing libraries were prepared using the CUT&Tag-IT assay kit (Active Motif, 53160) following the manufacturer’s instructions.
In brief, sorted HSCs were immobilized with Concanavalin A beads and permeabilized with digitonin-containing antibody buffer. HSCs underwent overnight incubation with anti-L-lactyl-histone H3 (Lys18) rabbit mAb (PTMBIO, PTM-1406RM, 1:50) at 4°C, and then incubation with Guinea pig anti-rabbit secondary antibody at room temperature for 1 hour. Samples were incubated with pA-Tn5 transposomes at room temperature for 1 hour, followed by tagmentation at 37°C for 1 hour. The tagmented DNA was then purified and subjected to PCR amplification and SPRI bead clean-up for sequencing. Sequencing libraries were quantified by KAPA library quantification kit (Roche), and sequencing was performed on NextSeq 150 MID.

value: anti-L-lactyl-histone H3 (Lys18) rabbit mAb (PTMBIO, PTM-1406RM)


title: POND-FMR1-T607M_rep1


title: Placenta sample X31303.203

description:
Library name: X31303.203
Column name in counts_nhbcs.csv.gz : X31303.203

value: No


title: 2FP

description: Library name: 2FP


title: Mx1T3_2

description: Library name: 80_3


title: Mx1Cre_1

description: Library name: 77_8


title: Mx1T3_1

description: Library name: 80_1


title: Placenta sample X31303.201

description:
Library name: X31303.201
Column name in counts_nhbcs.csv.gz : X31303.201


title: POND-FMR1-R606C_rep2


title: POND-FMR1-D610G_rep1


title: POND-FMR1-R606C_rep1


title: 8FPI_d_2

description: Library name: 24

data_processing:
Sequencing reads were pseudo aligned to mouse mm10 genome using STAR with quantMode option
Assembly: GRCm38v96
Supplementary files format and content: Tab delimited table containing gene symbol and sample normalized counts

molecule: polyA RNA

value: Poly(IC)


title: 7FPI_d

description: Library name: 23

value: WT


title: Placenta sample X31303.200

description:
Library name: X31303.200
Column name in counts_nhbcs.csv.gz : X31303.200

value: Male


title: POND-FMR1-C584Y_rep2


title: 8FP_d_2

description: Library name: 21

value: PBS


title: Placenta sample X31303.198

description:
Library name: X31303.198
Column name in counts_nhbcs.csv.gz : X31303.198

value: Female


title: 6FPI_d

description: Library name: 22

value: Bone Marrow


title: POND-FMR1-C584Y_rep1


title: 7FP_d

description: Library name: 20


title: Placenta sample X31303.196

description:
Library name: X31303.196
Column name in counts_nhbcs.csv.gz : X31303.196


title: POND-FMR1-G576R_rep2


title: Placenta sample X31303.192

description:
Library name: X31303.192
Column name in counts_nhbcs.csv.gz : X31303.192


title: 6FP_d

description: Library name: 19


title: 8FPTI_d_2

description: Library name: 17


title: 2FP_d_2

description: Library name: 18


title: POND-FMR1-G576R_rep1


title: 7FPTI_d

description: Library name: 16


title: Placenta sample X31303.191

description:
Library name: X31303.191
Column name in counts_nhbcs.csv.gz : X31303.191


title: POND-FMR1-R564H_rep2


title: Placenta sample X31303.190

description:
Library name: X31303.190
Column name in counts_nhbcs.csv.gz : X31303.190


title: 8FPT_d_2

description: Library name: 15


title: 7FPT_d

description: Library name: 14


title: 2FPT_d_2

description: Library name: 13


title: 8FNI_d_2

description: Library name: 12

value: FancgKO


title: POND-FMR1-R564H_rep1


title: Placenta sample X31303.189

description:
Library name: X31303.189
Column name in counts_nhbcs.csv.gz : X31303.189


title: POND-FMR1-D555N_rep2


title: Placenta sample X31303.188

description:
Library name: X31303.188
Column name in counts_nhbcs.csv.gz : X31303.188


title: 8FNTI_d_2

description: Library name: 9


title: 7FNI_d

description: Library name: 11


title: 6FNI_d

description: Library name: 10


title: 7FNTI_d

description: Library name: 8


title: POND-FMR1-D555N_rep1


title: Placenta sample X31303.187

description:
Library name: X31303.187
Column name in counts_nhbcs.csv.gz : X31303.187


title: 7FNT_d

description: Library name: 6


title: 8FNT_d_2

description: Library name: 7


title: POND-FMR1-K551R_rep2


title: Placenta sample X31303.186

description:
Library name: X31303.186
Column name in counts_nhbcs.csv.gz : X31303.186

value: LGA


title: 2FNT_d_2

description: Library name: 5


title: POND-FMR1-K551R_rep1


title: Placenta sample X31303.182

description:
Library name: X31303.182
Column name in counts_nhbcs.csv.gz : X31303.182

value: C-section


title: 6FN_d

description: Library name: 3


title: POND-FMR1-G547syn_rep2


title: 4FN_d_2

description: Library name: 2


title: 2FN_d_2

description: Library name: 1


title: Placenta sample X31303.181

description:
Library name: X31303.181
Column name in counts_nhbcs.csv.gz : X31303.181

value: Placenta villis fetal side


title: POND-FMR1-G547syn_rep1

value: HEK293T cell line


title: M202_S12

city: Los Angeles

first: Ahmad

last: Besaratinia

address: 1450 Biggy Street

department: Population & Public Health Sciences

institute: University of Southern California

description: Library name: Sample 83

data_processing:
Data quality was evaluated with Illumina SAV, and demuliplexing was performed using Illumina Bcl2fastq2 v2.17. RNA-seq data were trimmed, aligned, and quantified using Partek Flow (Partek Inc., St. Louis, MO).
Sequenced reads were trimmed from both ends based on quality (Phred ≥ 20 and minimum read length = 25 nt). Trimmed reads were aligned to the human hg38 reference genome using STAR with default parameter settings. Gene and transcript abundances were estimated from aligned reads with Partek E/M method. Post-alignment processing, quantification, and differential expression analyses were performed in R. Lowly expressed genes were filtered using the filterByExpr() method in the edgeR package, with the experimental group specified and all other parameters left at their default values. This method retains genes with sufficient expression based on library sizes and study design, requiring no less than 10 reads in at least the minimum number of samples defined by the smallest group. In our study, this corresponded to retaining genes with a minimum of 10 reads in at least 24 samples.
Assembly: hg38
Supplementary files format and content: .txt file; raw counts

source_name: Oral epithelial cells

extract_protocol:
Total RNA was extracted from snap frozen oral epithelial cells using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). RNA quality was assessed in an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip kit (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were prepared from 300 ng of total RNA samples using the Kapa HyperPrep kit with RiboErase (Kapa Biosystems, Wilmington, DE, USA). The protocol involves rRNA depletion, cDNA generation, end repair, A-tailing, and adaptor ligation by polymerase chain reaction (PCR). Samples were multiplexed with unique adaptors and sequenced on an Illumina NextSeq 500 platform (75 base pair single-end reads). To minimize technical bias, library preparation and sequencing for samples from different groups were performed randomly and in a blinded manner.

value: Oral epithelial cells

tag: group

value: Vaper


title: Placenta sample X31303.178

description:
Library name: X31303.178
Column name in counts_nhbcs.csv.gz : X31303.178

value: White

value: AGA


title: Placenta sample X31303.177

description:
Library name: X31303.177
Column name in counts_nhbcs.csv.gz : X31303.177

value: Vaginal delivery


title: M200_S10

description: Library name: Sample 81

value: Non-user


title: M201_S11

description: Library name: Sample 82


title: M199_S9

description: Library name: Sample 80


title: 7FN_d

description: Library name: 4


title: M198_S8

description: Library name: Sample 79


title: POND-FMR1-R546C_rep1

tag: cell line


title: POND-FMR1-R546C_rep2

tag: genotype


title: Placenta sample X31303.176

description:
Library name: X31303.176
Column name in counts_nhbcs.csv.gz : X31303.176

value: No


title: M197_S7

description: Library name: Sample 78


title: POND-FMR1-Deletion_rep2

tag: treatment


title: Placenta sample X31303.174

description:
Library name: X31303.174
Column name in counts_nhbcs.csv.gz : X31303.174

tag: tissue


title: M195_S5

description: Library name: Sample 76


title: POND-FMR1-Deletion_rep1


title: M196_S6

description: Library name: Sample 77


title: M194_S4

description: Library name: Sample 75


title: Placenta sample X31303.173

description:
Library name: X31303.173
Column name in counts_nhbcs.csv.gz : X31303.173

tag: maternal smoking


title: M191_S1

description: Library name: Sample 74

value: Smoker


title: POND-FMR1-R527H_rep2


title: Placenta sample X31303.171

description:
Library name: X31303.171
Column name in counts_nhbcs.csv.gz : X31303.171

tag: baby race

value: SGA


title: M190_S12

description: Library name: Sample 73


title: POND-FMR1-R527H_rep1


title: M189_S11

description: Library name: Sample 72


title: Placenta sample X31303.170

description:
Library name: X31303.170
Column name in counts_nhbcs.csv.gz : X31303.170

tag: gestational age

value: Male


title: M188_S10

description: Library name: Sample 71


title: M187_S9

description: Library name: Sample 70


title: POND-FMR1-R527S_rep2


title: M186_S8

description: Library name: Sample 69


title: Placenta sample X31303.169

description:
Library name: X31303.169
Column name in counts_nhbcs.csv.gz : X31303.169

tag: birthweight percentile


title: M185_S7

description: Library name: Sample 68


title: POND-FMR1-R527S_rep1


title: M184_S6

description: Library name: Sample 67


title: Placenta sample X31303.168

description:
Library name: X31303.168
Column name in counts_nhbcs.csv.gz : X31303.168

tag: birthweight fenton_group

value: Female


title: M182_S5

description: Library name: Sample 65


title: Placenta sample X31303.167

description:
Library name: X31303.167
Column name in counts_nhbcs.csv.gz : X31303.167


title: M181_S11

description: Library name: Sample 64


title: POND-FMR1-L526M_rep2


title: M183_S12

description: Library name: Sample 66


title: Placenta sample X31303.166

description:
Library name: X31303.166
Column name in counts_nhbcs.csv.gz : X31303.166

tag: delivery method


title: POND-FMR1-S524syn_rep2


title: POND-FMR1-L526M_rep1


title: HCAEC, IR with Rapa, 55YO, Female

city: Didcot

first: christopher

last: Whiteman

address: UKHSA

country: United Kingdom

institute: UK Health Security Agency

description:
Library name: barcode24
Column name in RapavIRRapa_all_gene_counts.tsv: irrapa6_sum

data_processing:
wf-transcriptomes Nextflow workflow was used (Oxford Nanopore Technologies, https://github.com/nanoporetech/pipeline-transcriptome-de)
Assembly: GRCh38
Supplementary files format and content: .tsv, raw gene counts

source_name: Human coronary artery endothelial cell

growth_protocol: HCAECs were immortalised with the hTERT gene using retrovirus, cultured on fibronectin coated T-75 plates and maintained in MesoEndo cell growth medium in a humidified incubator at 37C with 5 % CO2

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, #72134) was used following the manufacturer’s instructions.
Barcoded cDNA libraries were created using the PCR-cDNA barcoding kit, following the manufacturer’s instructions (Oxford Nanopore Technologies, SQK-PCB111.24)

value: Human coronary artery endothelial cell

value: hTERT immortalised

value: 10 Gy X-ray with 5 days rapamycin,  harvest day 7


title: RNA-seq_293T-PABPC1-POND_celllysate-3h-T1R3_rep1

description:
Library name: Sample89
fig4_71

value: 0.2 μM doxycycline


title: HCAEC, IR, 55YO, Female

description:
Library name: barcode23
Column name in CvIR_all_gene_counts.tsv: IR6_sum

value: 10 Gy X-ray,  harvest day 7


title: M179_S9

description: Library name: Sample 62


title: M180_S10

description: Library name: Sample 63


title: POND-FMR1-S524syn_rep1

value: HEK293T cell line


title: Placenta sample X31303.164

description:
Library name: X31303.164
Column name in counts_nhbcs.csv.gz : X31303.164

value: Placenta villis fetal side

tag: infant sex


title: M177_S8

description: Library name: Sample 61

value: Oral epithelial cells

value: Vaper


title: Placenta sample X31303.163

description:
Library name: X31303.163
Column name in counts_nhbcs.csv.gz : X31303.163

value: Yes

value: White

value: AGA

value: C-section

tag: maternal age


title: POND-FMR1-Y488C_rep2


title: HCAEC, Rapa, 55YO, Female

description:
Library name: barcode22
Column name in RapavIRRapa_all_gene_counts.tsv: rapa6_sum

value: 5 days 10 nM Rapamycin,  harvest day 7


title: M175_S4

description: Library name: Sample 60

value: Smoker


title: Placenta sample X31303.162

description:
Library name: X31303.162
Column name in counts_nhbcs.csv.gz : X31303.162

tag: rna integrity_number


title: HCAEC, Ctrl, 55YO, Female

description:
Library name: barcode21
Column name in CvIR_all_gene_counts.tsv: CTRL6_sum

value: none, harvest day 7


title: POND-FMR1-Y488C_rep1


title: M174_S3

description: Library name: Sample 59


title: HCAEC, IR with Rapa, 54YO(2), Male

description:
Library name: barcode20
Column name in RapavIRRapa_all_gene_counts.tsv: irrapa5_sum


title: POND-FMR1-R484C_rep2


title: Placenta sample X31303.161

description:
Library name: X31303.161
Column name in counts_nhbcs.csv.gz : X31303.161

value: Male


title: Placenta sample X31303.160

description:
Library name: X31303.160
Column name in counts_nhbcs.csv.gz : X31303.160

value: No

value: Vaginal delivery


title: M173_S7

description: Library name: Sample 58


title: M172_S2

description: Library name: Sample 57


title: Placenta sample X31303.156

description:
Library name: X31303.156
Column name in counts_nhbcs.csv.gz : X31303.156

value: Female


title: POND-FMR1-R484C_rep1


title: HCAEC, IR, 54YO(2), Male

description:
Library name: barcode19
Column name in CvIR_all_gene_counts.tsv: IR5_sum

value: Human coronary artery endothelial cell

value: hTERT immortalised


title: M171_S6

description: Library name: Sample 56


title: POND-FMR1-G480E_rep2

value: HEK293T cell line


title: Placenta sample X31303.353

description:
Library name: X31303.353
Column name in counts_nhbcs.csv.gz : X31303.353

value: Placenta villis fetal side


title: Placenta sample X31303.155

description:
Library name: X31303.155
Column name in counts_nhbcs.csv.gz : X31303.155

value: LGA


title: HCAEC, Ctrl, 54YO(2), Male

description:
Library name: barcode17
Column name in CvIR_all_gene_counts.tsv: CTRL5_sum


title: HCAEC, Rapa, 54YO(2), Male

description:
Library name: barcode18
Column name in RapavIRRapa_all_gene_counts.tsv: rapa5_sum


title: M170_S1

description: Library name: Sample 55

value: Oral epithelial cells


title: POND-FMR1-G480E_rep1


title: Placenta sample X31303.153

description:
Library name: X31303.153
Column name in counts_nhbcs.csv.gz : X31303.153


title: HCAEC, IR with Rapa, 17YO, Female

description:
Library name: barcode16
Column name in RapavIRRapa_all_gene_counts.tsv: irrapa4_sum

value: 10 Gy X-ray with 5 days rapamycin,  harvest day 7


title: Placenta sample X31303.152

description:
Library name: X31303.152
Column name in counts_nhbcs.csv.gz : X31303.152

value: White


title: M169_S5

description: Library name: Sample 54


title: POND-FMR1-R471*_rep2


title: POND-FMR1-R471*_rep1


title: HCAEC, Rapa, 17YO, female

description:
Library name: barcode14
Column name in RapavIRRapa_all_gene_counts.tsv: rapa4_sum


title: M168_S4

description: Library name: Sample 53


title: Placenta sample X31303.151

description:
Library name: X31303.151
Column name in counts_nhbcs.csv.gz : X31303.151

value: AGA


title: HCAEC, Ctrl, 17YO,Female

description:
Library name: barcode13
Column name in CvIR_all_gene_counts.tsv: CTRL4_sum


title: M167_S3

description: Library name: Sample 52


title: POND-FMR1-G470S_rep1


title: POND-FMR1-G470S_rep2


title: HCAEC, IR with Rapa, 54YO, Male

description:
Library name: barcode12
Column name in RapavIRRapa_all_gene_counts.tsv: irrapa3_sum


title: Placenta sample X31303.149

description:
Library name: X31303.149
Column name in counts_nhbcs.csv.gz : X31303.149

value: Yes

value: C-section


title: M166_S2

description: Library name: Sample 51

value: Smoker


title: Placenta sample X31303.147

description:
Library name: X31303.147
Column name in counts_nhbcs.csv.gz : X31303.147


title: M165_S1

description: Library name: Sample 50

value: Non-user


title: POND-FMR1-T461C_rep2


title: Placenta sample X31303.146

description:
Library name: X31303.146
Column name in counts_nhbcs.csv.gz : X31303.146

value: Male


title: HCAEC, IR, 54YO, Male

description:
Library name: barcode11
Column name in CvIR_all_gene_counts.tsv: IR3_sum

value: 10 Gy X-ray,  harvest day 7


title: HCAEC, Rapa, 54YO, Male

description:
Library name: barcode10
Column name in RapavIRRapa_all_gene_counts.tsv: rapa3_sum

value: 5 days 10 nM Rapamycin,  harvest day 7


title: POND-FMR1-T461C_rep1


title: Placenta sample X31303.145

description:
Library name: X31303.145
Column name in counts_nhbcs.csv.gz : X31303.145

value: No

value: Vaginal delivery


title: 164_S15

description: Library name: Sample 49


title: 162_S13

description: Library name: Sample 48

value: Vaper


title: HCAEC, Ctrl, 54YO, Male

description:
Library name: barcode09
Column name in CvIR_all_gene_counts.tsv: CTRL3_sum

value: Human coronary artery endothelial cell

value: hTERT immortalised

value: none, harvest day 7


title: POND-FMR1-K459*_rep2

value: HEK293T cell line


title: HCAEC, IR with Rapa, 26YO, Male

description:
Library name: barcode08
Column name in RapavIRRapa_all_gene_counts.tsv: irrapa2_sum

value: 10 Gy X-ray with 5 days rapamycin,  harvest day 7


title: 161_S12

description: Library name: Sample 47

value: Oral epithelial cells


title: POND-FMR1-K459*_rep1


title: HCAEC, IR, 26YO, Male

description:
Library name: barcode07
Column name in CvIR_all_gene_counts.tsv: IR2_sum


title: POND-FMR1-K457syn_rep2


title: Placenta sample X31303.143

description:
Library name: X31303.143
Column name in counts_nhbcs.csv.gz : X31303.143

value: Placenta villis fetal side

value: White

value: AGA


title: 160_S11

description: Library name: Sample 46

value: Smoker


title: Placenta sample X31303.142

description:
Library name: X31303.142
Column name in counts_nhbcs.csv.gz : X31303.142

value: Female


title: patient infected with High-grade glioma, immunophenotype consistent with glioblastoma (WHO grade IV, IDH wild-type)

city: Wuhan

first: Haobin

last: Ren

state: Hubei

address: G9P7+CP8, Wuchang District

institute: Wuhan University

description: Library name: GBM102

data_processing:
FastQC for QC
Trim Galore for trimming
BWA-MEM for alignment
Circle-Map for ecDNA detection
Assembly: hg38
Supplementary files format and content: txt for identified ecDNA

source_name: Right temporal region

extract_protocol:
ecDNA purification was performed on DNA extracted from meningioma, glioblastoma, pituitary adenoma and vestibular schwannoma. After confirming the successful enrichment of ecDNA from total DNA samples, Phi29-assisted ecDNA rolling circle amplification was performed before DNA library preparation.
Amplicon was sonicated into DNA fragments with average size as 350bp using Bioruptor. Library preparation was performed using Vazyme DNA library preparation kit (Vazyme) following the standard protocol starting with 300 ng of sonicated DNA per sample. Library quality and fragment size distribution were assessed using the Qsep400 system (BiOptic).

value: Right temporal region

tag: infection


title: HCAEC, Rapa, 26YO, Male

description:
Library name: barcode06
Column name in RapavIRRapa_all_gene_counts.tsv: rapa2_sum

tag: cell type


title: HCAEC, Ctrl, 26YO, Male

description:
Library name: barcode05
Column name in CvIR_all_gene_counts.tsv: CTRL2_sum


title: Placenta sample X31303.141

description:
Library name: X31303.141
Column name in counts_nhbcs.csv.gz : X31303.141

value: C-section

value: Male


title: POND-FMR1-K457syn_rep1


title: POND-FMR1-I444syn_rep2


title: 159_S10

description: Library name: Sample 45


title: Placenta sample X31303.140

description:
Library name: X31303.140
Column name in counts_nhbcs.csv.gz : X31303.140

value: No


title: 157_S8

description: Library name: Sample 44

value: Non-user


title: HCAEC, IR with Rapa, 23YO, Male

description:
Library name: barcode04
Column name in RapavIRRapa_all_gene_counts.tsv: irrapa1_sum


title: Placenta sample X31303.144

description:
Library name: X31303.144
Column name in counts_nhbcs.csv.gz : X31303.144

value: Vaginal delivery


title: POND-FMR1-I444syn_rep1


title: Placenta sample X31303.139

description:
Library name: X31303.139
Column name in counts_nhbcs.csv.gz : X31303.139

value: SGA


title: 156_S7

description: Library name: Sample 43


title: HCAEC, IR, 23YO, Male

description:
Library name: barcode03
Column name in CvIR_all_gene_counts.tsv: IR1_sum

value: Human coronary artery endothelial cell

value: hTERT immortalised

value: 10 Gy X-ray,  harvest day 7


title: POND-FMR1-R442Q _rep2

value: HEK293T cell line


title: 155_S6

description: Library name: Sample 42

value: Oral epithelial cells

value: Vaper


title: Placenta sample X31303.137

description:
Library name: X31303.137
Column name in counts_nhbcs.csv.gz : X31303.137

value: Placenta villis fetal side

value: White


title: HCAEC, Rapa, 23YO, Male

description:
Library name: barcode02
Column name in RapavIRRapa_all_gene_counts.tsv: rapa1_sum

value: 5 days 10 nM Rapamycin,  harvest day 7


title: POND-FMR1-R442Q _rep1


title: 154_S5

description: Library name: Sample 41


title: Placenta sample X31303.133

description:
Library name: X31303.133
Column name in counts_nhbcs.csv.gz : X31303.133

value: AGA

value: Female


title: POND-FMR1-D428H_rep2


title: HCAEC, Ctrl, 23YO, Male

description:
Library name: barcode01
Column name in CvIR_all_gene_counts.tsv: CTRL1_sum

value: none, harvest day 7


title: Placenta sample X31303.131

description:
Library name: X31303.131
Column name in counts_nhbcs.csv.gz : X31303.131


title: 153_S4

description: Library name: Sample 40


title: POND-FMR1-D428H_rep1


title: In vitro implantation model

city: Hirakata

first: Toru

last: Matsu-ura

state: Osaka

address: 2-5-1 Shin-mach

department: Pathology

country: Japan

institute: Kansai Medical University

description:
Library name: sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw base call (BCL) files were converted to FASTQ files using Cell Ranger mkfastq (10x Genomics). FASTQ files were aligned to the mouse reference genome (mm10) using Cell Ranger pipeline.
Assembly: Mm10
Supplementary files format and content: Processed data are provided as sparse gene-by-cell count matrices generated by Cell Ranger. The dataset includes matrix.mtx, barcodes.tsv, and features.tsv files.

source_name: Endometrium and embryo

extract_protocol:
Co-cultured embryos and an artificial uterus were dissociated with TrypLE Express enzyme (Thermo Fisher). 7AAD-non stained viable cells were isolated by fluorescent activated cell sorter (Sony SH800).
Single-cell RNA libraries were generated using the Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics) according to the manufacturer’s instructions.

value: endometrium and embryo

tag: strain

value: C57BL/6 for endometrium, B6D2F1 for embryos

tag: Sex

value: female

tag: age

value: 8-12 weeks for endometrium


title: 151_S2

description: Library name: Sample 39

tag: group

value: Smoker


title: Placenta sample X31303.128

description:
Library name: X31303.128
Column name in counts_nhbcs.csv.gz : X31303.128

value: No

value: Vaginal delivery


title: POND-FMR1-Y423fs_rep2

tag: cell line

tag: genotype

tag: treatment


title: Placenta sample X31303.127

description:
Library name: X31303.127
Column name in counts_nhbcs.csv.gz : X31303.127

tag: tissue

tag: maternal smoking

tag: baby race

value: Male


title: 150_S1

description: Library name: Sample 38


title: SG6

city: Yufu City

first: Miho

last: Suzuki

address: 1-1 Idaigaoka, Hasama-Machi

department: Department of Endocrinology, Metabolism, Rheumatology and Nephrology, Faculty of Medicine

institute: Oita university

description:
Library name: Sample 12
canagliflozin 10mg/kg body weight/day for 8 weeks from 24 weeks of age.

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: rn6
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

organism: Rattus norvegicus

source_name: kidney cortex

extract_protocol:
The total RNA was isolated from kidney cortex using RNeasy kit (Qiagen, Germantown, MD, USA) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

value: kidney cortex

value: Zucker Fatty

value: 32 weeks old

value: SGLT2 inhibitor


title: SG4

description:
Library name: Sample 11
canagliflozin 10mg/kg body weight/day for 8 weeks from 24 weeks of age.


title: Placenta sample X31303.126

description:
Library name: X31303.126
Column name in counts_nhbcs.csv.gz : X31303.126

value: Placenta villis fetal side

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group


title: 149_S17

description: Library name: Sample 37

value: Oral epithelial cells

value: Vaper


title: POND-FMR1-Y423fs_rep1

value: HEK293T cell line


title: SG3

description:
Library name: Sample 10
canagliflozin 10mg/kg body weight/day for 8 weeks from 24 weeks of age.


title: 148_S16

description: Library name: Sample 36


title: POND-FMR1-Y419C_rep1


title: 146_S14

description: Library name: Sample 35

value: Non-user


title: SG2

description:
Library name: Sample 9
canagliflozin 10mg/kg body weight/day for 8 weeks from 24 weeks of age.


title: POND-FMR1-A411T_rep2


title: ZF5

description:
Library name: Sample 8
obesity control

value: obesity control


title: Placenta sample X31303.123

description:
Library name: X31303.123
Column name in counts_nhbcs.csv.gz : X31303.123

value: LGA

tag: delivery method

value: C-section

tag: infant sex

value: Female

tag: maternal age


title: 145_S13

description: Library name: Sample 34

tag: cell type

value: Smoker


title: Placenta sample X31303.122

description:
Library name: X31303.122
Column name in counts_nhbcs.csv.gz : X31303.122

value: No

value: AGA

value: Vaginal delivery

tag: rna integrity_number


title: ZF4

description:
Library name: Sample 7
obesity control

value: kidney cortex

tag: strain

value: Zucker Fatty


title: 144_S12

description: Library name: Sample 33


title: POND-FMR1-A411T_rep1


title: ZF3

description:
Library name: Sample 6
obesity control

tag: age

value: 32 weeks old


title: Placenta sample X31303.121

description:
Library name: X31303.121
Column name in counts_nhbcs.csv.gz : X31303.121

value: Placenta villis fetal side


title: POND-FMR1-D408G_rep2


title: 143_S11

description: Library name: Sample 32

tag: group


title: Placenta sample X31303.120

description:
Library name: X31303.120
Column name in counts_nhbcs.csv.gz : X31303.120

value: Yes

value: White

value: Male


title: POND-FMR1-Y419C_rep2

tag: cell line

value: HEK293T cell line


title: ZF2

description:
Library name: Sample 5
obesity control


title: POND-FMR1-D408G_rep1

tag: genotype


title: 142_S10

description: Library name: Sample 31

value: Oral epithelial cells

value: Vaper


title: Placenta sample X31303.119

description:
Library name: X31303.119
Column name in counts_nhbcs.csv.gz : X31303.119


title: POND-FMR1-G397S_rep2

tag: treatment


title: 141_S9

description: Library name: Sample 30

value: Non-user


title: C4

description:
Library name: Sample 4
control

tag: tissue

value: Zucker Lean

value: control


title: Placenta sample X31303.117

description:
Library name: X31303.117
Column name in counts_nhbcs.csv.gz : X31303.117

tag: maternal smoking

value: Female


title: C3

description:
Library name: Sample 3
control


title: POND-FMR1-G397S_rep1


title: 140_S8

description: Library name: Sample 29


title: Placenta sample X31303.116

description:
Library name: X31303.116
Column name in counts_nhbcs.csv.gz : X31303.116

value: No

tag: baby race

value: C-section


title: C2

description:
Library name: Sample 2
control


title: 139_S7

description: Library name: Sample 28


title: Placenta sample X31303.115

description:
Library name: X31303.115
Column name in counts_nhbcs.csv.gz : X31303.115

tag: gestational age

value: AGA

value: Vaginal delivery


title: POND-FMR1-W395*_rep2


title: POND-FMR1-W395*_rep1


title: 137_S18

description: Library name: Sample 27


title: Placenta sample X31303.114

description:
Library name: X31303.114
Column name in counts_nhbcs.csv.gz : X31303.114

tag: birthweight percentile


title: C1

description:
Library name: Sample 1
control

value: kidney cortex


title: POND-FMR1-R375M_rep2


title: Placenta sample X31303.112

description:
Library name: X31303.112
Column name in counts_nhbcs.csv.gz : X31303.112

tag: birthweight fenton_group

value: SGA


title: 136_S4

description: Library name: Sample 26


title: RNA-Seq data of lasermicrodissected PVN of hamster EH05-15 sampled at ZT07 on a TFD

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: Ulm University

data_processing:
FastQC 0.11.9
trim-galore 0.6.6
Trinity 2.8.5
Assembly: GRCm39, Mus musculus
blastx 2.5.0+
extract_hits_from_fasta.rb [https://sourceforge.net/projects/prepare-transcript-to-gene-map/]
hits_to_genemap.rb [https://sourceforge.net/projects/prepare-transcript-to-gene-map/]
bowtie 1.3.0
rsem 1.3.1
Supplementary files format and content: .results, non-normalized gene expression
Supplementary files format and content: Trinity_Phodopus_HT-NT_SCN-PVN_ZT01-ZT07_beforemapping.fasta: de novo assembly of transcriptomes
Supplementary files format and content: Trinity_Phodopus_HT-NT_SCN-PVN_ZT01-ZT07_aftermapping.fasta: assembly after mapping against Mus musculus (GRCm39, Annotation Release 109, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Mus_musculus/109/), protein table available here https://www.ncbi.nlm.nih.gov/genome/browse#!/proteins/52/992563%7CMus%20musculus/

organism: Cricetiscus sungorus

source_name: paraventricular nucleus (PVN)

growth_protocol: indoor breeding colony of Ulm University, Ulm, Germany

extract_protocol:
20 µm kryosections were prepared in a RNAse-poor environment on Poly-L-Lysine coated Carl Zeiss™ MembraneSlides 1.0 PEN (Fisher Scientific GmbH, Schwerte, Germany) using a cryostat “Microm HM 560” (Thermo Scientific, Walldorf, Germany). The sections were kresylviolett-stained to enable lasermicrodissection of the hypothalamic core areas SCN and PVN in Carl Zeiss™ adhesive-cap tube per sample (Fisher Scientific GmbH, Schwerte, Germany) on a PALM MicroBeam (Carl Zeiss Microscopy Deutschland GmbH, Oberkochen, Germany). Total RNA was purified using the RNeasy Plus Micro Kit with gDNA eliminator spin column (Qiagen GmbH, Hilden, Germany). Total RNA was checked for quality (Bioanalyzer, Agilent Technologies, Waldbronn, Germany) and quantity (RNA 6000 Pico Kit for very small RNA amounts of 50–5000pg/µL, Agilent Technologies, Waldbronn, Germany).
The mRNA were isolated, the library prepared (NEBNext® Single Cell / Low Input RNA library Prep Kit dual index), and the RNA-Seq performed on an Illumina NextSeq 500 (1 lane, 2x25 mio reads, 2 x 150 nt, 7.5 gb).

treatment_protocol: short photoperiod (8:16 hours light:darkness)

value: outbreed crossing scheme

value: own breeding colony

value: brain

value: paraventricular nucleus (PVN)

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum

tag: condition

value: torpor-free day (TFD)

tag: Sex

value: male


title: RNA-Seq data of lasermicrodissected PVN of hamster EH05-04 sampled at ZT07 on a TFD

value: female


title: POND-FMR1-R375M_rep1

value: HEK293T cell line


title: Placenta sample X31303.110

description:
Library name: X31303.110
Column name in counts_nhbcs.csv.gz : X31303.110

value: Placenta villis fetal side

value: White

tag: delivery method

tag: infant sex

value: Male

tag: maternal age


title: 135_S3

description: Library name: Sample 25

tag: cell type

value: Oral epithelial cells

value: Smoker


title: POND-FMR1-S370N_rep2


title: RNA-Seq data of lasermicrodissected PVN of hamster EH05-07 sampled at ZT07 on a TFD


title: Placenta sample X31303.108

description:
Library name: X31303.108
Column name in counts_nhbcs.csv.gz : X31303.108

value: No

value: AGA

value: Vaginal delivery

tag: rna integrity_number


title: POND-FMR1-S370N_rep1


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_11 sampled at ZT07 on a TFD

value: outbreed crossing scheme


title: 133_S1

description: Library name: Sample 23

tag: group


title: Placenta sample X31303.107

description:
Library name: X31303.107
Column name in counts_nhbcs.csv.gz : X31303.107


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_24 sampled at ZT07 on a TFD

tag: cell line

value: own breeding colony


title: 132_S11

description: Library name: Sample 22

value: Vaper


title: POND-FMR1-E352G_rep2

tag: genotype


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_20 sampled at ZT07 on a TFD

value: brain

value: paraventricular nucleus (PVN)

tag: treatment


title: POND-FMR1-E352G_rep1


title: 131_S11

description: Library name: Sample 21


title: Placenta sample X31303.104

description:
Library name: X31303.104
Column name in counts_nhbcs.csv.gz : X31303.104

tag: tissue

value: Yes


title: Placenta sample X31303.103

description:
Library name: X31303.103
Column name in counts_nhbcs.csv.gz : X31303.103

tag: maternal smoking

value: C-section


title: Placenta sample X31303.124

description:
Library name: X31303.124
Column name in counts_nhbcs.csv.gz : X31303.124

tag: baby race

value: LGA

value: Female


title: 130_S9

description: Library name: Sample 20

value: Non-user


title: RNA-Seq data of lasermicrodissected PVN of hamster EH05-12 sampled at ZT07 during torpor arousal on a TD

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum

value: torpor-day (TD)

value: female


title: POND-FMR1-G346E_rep2

value: HEK293T cell line


title: RNA-Seq data of lasermicrodissected PVN of hamster EH05-02 sampled at ZT07 during torpor arousal on a TD

value: male


title: Placenta sample X31303.101

description:
Library name: X31303.101
Column name in counts_nhbcs.csv.gz : X31303.101

value: Placenta villis fetal side

value: No

value: White

tag: gestational age

value: AGA

value: Male


title: POND-FMR1-G346E_rep1


title: 129_S8

description: Library name: Sample 19

value: Oral epithelial cells


title: Placenta sample X31303.102

description:
Library name: X31303.102
Column name in counts_nhbcs.csv.gz : X31303.102

tag: birthweight percentile

value: Vaginal delivery


description: RNA-Seq data of lasermicrodissected PVN of hamster EH05-10 sampled at ZT07 during torpor arousal on a TD (involved for assebly, not involved not in manuscript)

value: outbreed crossing scheme

value: own breeding colony

value: brain

value: paraventricular nucleus (PVN)


title: POND-FMR1-V345A_rep2


title: Placenta sample X31303.099

description:
Library name: X31303.099
Column name in counts_nhbcs.csv.gz : X31303.099

tag: birthweight fenton_group

value: LGA

value: C-section

value: Female


title: 128_S8

description: Library name: Sample 18

value: Non-user


title: RNA-Seq data of lasermicrodissected PVN of hamster EH05-03 sampled at ZT07 during torpor arousal on a TD

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum

tag: condition

value: torpor-day (TD)


title: POND-FMR1-V345A_rep1

value: HEK293T cell line


title: 127_S6

description: Library name: Sample 17


title: Placenta sample X31303.098

description:
Library name: X31303.098
Column name in counts_nhbcs.csv.gz : X31303.098

value: Placenta villis fetal side

value: No


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_01 sampled at ZT07 during torpor arousal on a TD

tag: Sex

value: male


title: Placenta sample X31303.097

description:
Library name: X31303.097
Column name in counts_nhbcs.csv.gz : X31303.097

value: Yes

value: White

value: AGA

tag: delivery method


title: POND-FMR1-R344S_rep2


title: M_126_Exp1_S9

description: Library name: Sample 16

value: Oral epithelial cells

value: Smoker


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_03 sampled at ZT07 during torpor arousal on a TD

value: outbreed crossing scheme

value: own breeding colony

value: brain

value: female


title: POND-FMR1-R344S_rep1


title: Placenta sample X31303.096

description:
Library name: X31303.096
Column name in counts_nhbcs.csv.gz : X31303.096

value: C-section

tag: infant sex

value: Male


title: 125_S6

description: Library name: Sample 15

value: Non-user


title: RNA-Seq data of lasermicrodissected SCN of hamster EH05-04 sampled at ZT07 on a TFD

source_name: suprachiasmatic nucleus (SCN)

value: suprachiasmatic nucleus (SCN)

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum

value: torpor-free day (TFD)


title: POND-FMR1-N341S_rep2

value: HEK293T cell line


title: Placenta sample X31303.095

description:
Library name: X31303.095
Column name in counts_nhbcs.csv.gz : X31303.095

value: Placenta villis fetal side

value: No

value: Vaginal delivery

tag: maternal age


title: M_124_Ctrl_S5

description: Library name: Sample 14

tag: cell type


title: RNA-Seq data of lasermicrodissected SCN of hamster EH05-15 sampled at ZT07 on a TFD

value: male


title: POND-FMR1-N341S_rep1


title: Placenta sample X31303.094

description:
Library name: X31303.094
Column name in counts_nhbcs.csv.gz : X31303.094

value: White

value: AGA

value: Female

tag: rna integrity_number


title: 123_S6

description: Library name: Sample 13

value: Oral epithelial cells

tag: group

value: Vaper


title: RNA-Seq data of lasermicrodissected SCN of hamster EH05-07 sampled at ZT07 on a TFD

value: outbreed crossing scheme

tag: cell line

value: own breeding colony

value: brain

value: female


title: POND-FMR1-L338P_rep2

tag: genotype


title: Placenta sample X31303.088

description:
Library name: X31303.088
Column name in counts_nhbcs.csv.gz : X31303.088

value: Male


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_11 sampled at ZT07 on a TFD

value: suprachiasmatic nucleus (SCN)

tag: treatment

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum


title: POND-FMR1-L338P_rep1

value: HEK293T cell line


title: M_121_Exp2_S13

description: Library name: Sample 11


title: Placenta sample X31303.085

description:
Library name: X31303.085
Column name in counts_nhbcs.csv.gz : X31303.085

tag: tissue

value: Placenta villis fetal side

value: LGA


title: M_122_Exp1_S8

description: Library name: Sample 12

value: Smoker


title: POND-FMR1-E323Q_rep2


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_24 sampled at ZT07 on a TFD

value: torpor-free day (TFD)


title: Placenta sample X31303.084

description:
Library name: X31303.084
Column name in counts_nhbcs.csv.gz : X31303.084

tag: maternal smoking

value: No

value: White

value: Vaginal delivery


title: POND-FMR1-E323Q_rep1


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_20 sampled at ZT07 on a TFD


title: Placenta sample X31303.080

description:
Library name: X31303.080
Column name in counts_nhbcs.csv.gz : X31303.080

tag: baby race

value: AGA

value: Female


title: 120_S4

description: Library name: Sample 10

value: Oral epithelial cells

value: Non-user


title: RNA-Seq data of lasermicrodissected SCN of hamster EH05-12 sampled at ZT07 during torpor arousal on a TD

value: outbreed crossing scheme

value: own breeding colony

value: brain

value: torpor-day (TD)


title: POND-FMR1-K310syn_rep2


title: M_118_Ctrl_S3

description: Library name: Sample 8


title: Placenta sample X31303.079

description:
Library name: X31303.079
Column name in counts_nhbcs.csv.gz : X31303.079

tag: gestational age

value: C-section

value: Male


title: RNA-Seq data of lasermicrodissected SCN of hamster EH05-02 sampled at ZT07 during torpor arousal on a TD

value: suprachiasmatic nucleus (SCN)

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum

value: male


title: Placenta sample X31303.078

description:
Library name: X31303.078
Column name in counts_nhbcs.csv.gz : X31303.078

value: Placenta villis fetal side

tag: birthweight percentile


title: POND-FMR1-K310syn_rep1

value: HEK293T cell line


title: POND-FMR1-I304N_rep2


title: RNA-Seq data of lasermicrodissected SCN of hamster EH05-03 sampled at ZT07 during torpor arousal on a TD


title: M_115_Exp1_S7

description: Library name: Sample 5

value: Smoker


title: Placenta sample X31303.074

description:
Library name: X31303.074
Column name in counts_nhbcs.csv.gz : X31303.074

value: No

value: White

tag: birthweight fenton_group

value: Vaginal delivery


title: M_116_Ctrl_S2

description: Library name: Sample 6

value: Oral epithelial cells


title: POND-FMR1-P289L_rep2


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_01 sampled at ZT07 during torpor arousal on a TD

tag: condition


title: Placenta sample X31303.073

description:
Library name: X31303.073
Column name in counts_nhbcs.csv.gz : X31303.073

value: AGA

value: Female


title: 134_S2

description: Library name: Sample 24


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_03 sampled at ZT07 during torpor arousal on a TD

value: outbreed crossing scheme

value: own breeding colony

tag: Sex

value: female


title: POND-FMR1-P289L_rep1


title: M_108_Exp2_S12

description: Library name: Sample 3

value: Vaper


title: Placenta sample X31303.071

description:
Library name: X31303.071
Column name in counts_nhbcs.csv.gz : X31303.071

tag: delivery method

value: C-section


title: M_107_Exp2_S11

description: Library name: Sample 2


title: POND-FMR1-E280K_rep1


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_08 normothermic on day of sampling

data_processing:
FastQC 0.11.9
trim-galore 0.6.6
Trinity 2.8.5
Genome_build: GRCm39, Mus musculus
blastx 2.5.0+
extract_hits_from_fasta.rb (https://sourceforge.net/projects/prepare-transcript-to-gene-map/)
hits_to_genemap.rb (https://sourceforge.net/projects/prepare-transcript-to-gene-map/)
bowtie 1.3.0
rsem 1.3.1
Supplementary_files_format_and_content: .results, non-normalized gene expression
Supplementary_files_format_and_content: Trinity_SCN-PVN_Phodopus-ZT01.fasta (de novo assembly of transcriptomes)
Supplementary_files_format_and_content: Trinity_SCN-PVN_Phodopus-ZT01_aftermapping.fasta (assembly after mapping against Mus musculus (GRCm39))

treatment_protocol: short photoperiod (8:16 L:D)

value: paraventricular nucleus (PVN)

tag: developmental stage

value: adult

tag: adapted to

value: short photoperiod (LD 8:16)

tag: time

value: normothermia


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_09 normothermic on day of sampling


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_05 normothermic on day of sampling

value: male


title: THP1_lenti-LINC01857l_LPS

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: Library name: Sample19

data_processing:
Fastq data were loaded into the CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed using the CLC workbench with quality score limit set to 0.05 and 25 nt minimal read length
Trimmed sequences were mapped to the GRCh38 human reference genome using the CLC workbench with the following parameters: Mismatch cost: 2. Insertion cost: 3. Deletion cost: 3. Length fraction: 0.8. Similarity fraction: 0.8. Max. hits for a read: 10. Strand specific: both.
Normalized expression values (e.g. RPKM) were calculated based on unique read counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, including gene identifiers and coordinates, read counts and RPKM values for each sample.

source_name: blood

growth_protocol: Primary macrophages were cultured in X-Vivo-15 medium (Lonza), supplemented with 5 % FCS.  THP1 cells were cultivated in RPMI Glutamax medium, supplemented with 5 % FCS. All cells were cultured at 37 °C with humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted with Trizol reagent and DNaseI-treated, using established protocols. PolyA RNA was selected using magnetic beads.
Libraries were generated using the TruSeq Stranded mRNA Kit (Illumina)

treatment_protocol:
Blood-derived monocytes (CD14 MACS purification) were differentiated into macrophages using 15 ng / ml recombinant GM-CSF or M-CSF for 7 days. THP1 cells were differentiated with PMA (20 nM) for two days.
Upon differentiation / attachment, cells were treated with different immune-stimuli at the following concentrations: LPS: 100 ng / ml. Salmonella Typhimurium: multiplicity of infection (MOI) = 10

value: blood

tag: cell type

value: monocytic

value: LINC01857_long lenti-vector

value: lipopolysaccharide

tag: batch


title: Placenta sample X31303.068

description:
Library name: X31303.068
Column name in counts_nhbcs.csv.gz : X31303.068

value: Placenta villis fetal side

value: No

value: White

tag: infant sex

tag: maternal age

tag: rna integrity_number


title: POND-FMR1-K273R_rep1

tag: cell line

value: HEK293T cell line

tag: genotype

tag: treatment


title: Placenta sample X31303.067

description:
Library name: X31303.067
Column name in counts_nhbcs.csv.gz : X31303.067

tag: tissue

tag: maternal smoking

tag: baby race

tag: gestational age

value: AGA

value: Female


title: THP1_lenti-LINC01857l_Salmonella

description: Library name: Sample18

value: Salmonella Typhimurium


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_29 normothermic on day of sampling

tag: Sex

value: female


title: POND-FMR1-G266E_rep2


title: Placenta sample X31303.066

description:
Library name: X31303.066
Column name in counts_nhbcs.csv.gz : X31303.066

value: Yes

tag: birthweight percentile

tag: birthweight fenton_group

tag: delivery method

value: Vaginal delivery

value: Male


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_05 normothermic on day of sampling

value: paraventricular nucleus (PVN)

tag: developmental stage

value: adult

tag: adapted to

value: short photoperiod (LD 8:16)

tag: time

value: normothermia


title: Placenta sample X31303.065

description:
Library name: X31303.065
Column name in counts_nhbcs.csv.gz : X31303.065

tag: infant sex


title: 117_S2

description: Library name: Sample 7

tag: cell type

value: Oral epithelial cells

tag: group

value: Non-user


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_06 in torpor entry

value: torpor entry


title: POND-FMR1-Y265syn_rep1

tag: cell line


title: THP1_lenti-ctrl_Salmonella

description: Library name: Sample14

value: blood

value: monocytic

tag: genotype

value: Control lenti-vector

tag: batch


title: Placenta sample X31303.062

description:
Library name: X31303.062
Column name in counts_nhbcs.csv.gz : X31303.062

tag: tissue

value: Placenta villis fetal side

value: No

value: White

value: SGA

value: C-section

tag: maternal age

tag: rna integrity_number


title: M_119_Ctrl_S4

description: Library name: Sample 9


description: RNA-Seq data of lasermicrodissected SCN of hamster EH05-10 sampled at ZT07 during torpor arousal on a TD (involved for assebly, not involved not in manuscript)

value: outbreed crossing scheme

value: own breeding colony

value: brain

value: suprachiasmatic nucleus (SCN)

tag: treatment

value: winter-like short photoperiod (8:16 light:darkness), food and water ad libitum

tag: condition

value: torpor-day (TD)

value: male


title: POND-FMR1-I304N_rep1

value: HEK293T cell line


title: M_114_Exp1_S6

description: Library name: Sample 4

value: Oral epithelial cells

value: Smoker


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_07 in torpor entry

value: paraventricular nucleus (PVN)

value: adult

value: short photoperiod (LD 8:16)

tag: Sex

value: torpor entry


title: Placenta sample X31303.075

description:
Library name: X31303.075
Column name in counts_nhbcs.csv.gz : X31303.075

value: Placenta villis fetal side

tag: maternal smoking

value: No

tag: baby race

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

value: AGA

value: Vaginal delivery

value: Female


title: POND-FMR1-F262L_rep2


title: Placenta sample X31303.072

description:
Library name: X31303.072
Column name in counts_nhbcs.csv.gz : X31303.072

tag: delivery method

tag: infant sex


title: POND-FMR1-E280K_rep2


title: Placenta sample X31303.058

description:
Library name: X31303.058
Column name in counts_nhbcs.csv.gz : X31303.058

value: C-section


title: THP1_lenti-ctrl_mock

description: Library name: Sample13

value: blood

tag: cell type

value: monocytic

value: Control lenti-vector

value: mock


title: BDM_siRNA_LINC010857_2_LPS_donor2

description: Library name: Sample12

tag: cell line

value: blood-derived macrophage

value: LINC01857 knockdown

value: lipopolysaccharide


title: POND-FMR1-F262L_rep1

value: HEK293T cell line

tag: genotype


title: Placenta sample X31303.069

description:
Library name: X31303.069
Column name in counts_nhbcs.csv.gz : X31303.069

value: Male


title: Placenta sample X31303.057

description:
Library name: X31303.057
Column name in counts_nhbcs.csv.gz : X31303.057


title: M_105_Exp2_S10

description: Library name: Sample 1

value: Oral epithelial cells

tag: group

value: Vaper


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_11 in torpor entry

tag: tissue

value: paraventricular nucleus (PVN)

tag: developmental stage

value: adult

tag: adapted to

value: short photoperiod (LD 8:16)

value: female

tag: time

value: torpor entry


title: POND-FMR1-K273R_rep2

tag: treatment


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_30 in torpor entry

tag: Sex

value: male


title: POND-FMR1-P248L_rep2


title: BDM_siRNA_LINC010857_2_mock_donor2

description: Library name: Sample11

value: blood

tag: batch


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_22 normothermic on day of sampling

value: normothermia


title: RNA-Seq data of lasermicrodissected PVN of hamster EH03_08 in torpor entry


title: POND-FMR1-P248L_rep1


title: Placenta sample X31303.056

description:
Library name: X31303.056
Column name in counts_nhbcs.csv.gz : X31303.056

value: Placenta villis fetal side

tag: maternal smoking

value: No

tag: baby race

value: White

value: AGA

value: Vaginal delivery

value: Female

tag: maternal age

tag: rna integrity_number


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_05 normothermic on day of sampling

value: suprachiasmatic nucleus (SCN)


title: BDM_siRNA_LINC010857_1_LPS_donor2

description: Library name: Sample10

value: blood-derived macrophage

value: LINC01857 knockdown

value: lipopolysaccharide


title: Placenta sample X31303.054

description:
Library name: X31303.054
Column name in counts_nhbcs.csv.gz : X31303.054

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

tag: delivery method

value: C-section

value: Male


title: POND-FMR1-K246R_rep2

tag: cell line

value: HEK293T cell line

tag: genotype


title: BDM_siRNA_LINC010857_1_mock_donor2

description: Library name: Sample9

tag: tissue

tag: cell type

value: mock


title: Placenta sample X31303.052

description:
Library name: X31303.052
Column name in counts_nhbcs.csv.gz : X31303.052

value: SGA

tag: infant sex


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_08 normothermic on day of sampling

tag: developmental stage

value: adult

tag: adapted to

value: short photoperiod (LD 8:16)

value: male

tag: time


title: THP1_lenti-LINC01857s_LPS

description: Library name: Sample17

value: blood

value: monocytic

value: LINC01857_short lenti-vector

tag: treatment

tag: batch


title: Placenta sample X31303.051

description:
Library name: X31303.051
Column name in counts_nhbcs.csv.gz : X31303.051

value: Placenta villis fetal side

tag: maternal smoking

value: No

tag: baby race

value: White

value: LGA


title: Placenta sample X31303.049

description:
Library name: X31303.049
Column name in counts_nhbcs.csv.gz : X31303.049

value: AGA

value: Female

tag: maternal age

tag: rna integrity_number


title: POND-FMR1-V225I_rep2


title: BDM_siRNA-ctrl_LPS_donor2

description: Library name: Sample8

value: blood-derived macrophage

value: WT

value: lipopolysaccharide


title: POND-FMR1-K246R_rep1

value: HEK293T cell line


title: POND-FMR1-V225I_rep1


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_09 normothermic on day of sampling

value: suprachiasmatic nucleus (SCN)

tag: Sex

value: female

value: normothermia


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_22 normothermic on day of sampling

value: adult

value: short photoperiod (LD 8:16)

value: male


title: BDM_siRNA-ctrl_mock_donor2

description: Library name: Sample7

value: blood

value: mock


title: THP1_lenti-LINC01857s_Salmonella

description: Library name: Sample16

value: monocytic

value: LINC01857_short lenti-vector

value: Salmonella Typhimurium


title: POND-FMR1-G266E_rep1


title: BDM_siRNA_LINC010857_2_LPS_donor1

description: Library name: Sample6

value: LINC01857 knockdown


title: Placenta sample X31303.048

description:
Library name: X31303.048
Column name in counts_nhbcs.csv.gz : X31303.048

value: Placenta villis fetal side

value: No

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

value: LGA

value: C-section

value: Female


title: POND-FMR1-E221fs_rep2

tag: cell line

value: HEK293T cell line

tag: genotype


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_29 normothermic on day of sampling

tag: tissue

value: suprachiasmatic nucleus (SCN)

value: female

value: normothermia


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_05 normothermic on day of sampling

value: adult

value: short photoperiod (LD 8:16)

value: male


title: BDM_siRNA_LINC010857_1_mock_donor1

description: Library name: Sample3

value: blood

tag: cell type

value: blood-derived macrophage

value: mock


title: POND-FMR1-E221fs_rep1


title: POND-FMR1-S217syn_rep2


title: Placenta sample X31303.046

description:
Library name: X31303.046
Column name in counts_nhbcs.csv.gz : X31303.046

value: AGA

tag: delivery method

value: Vaginal delivery

tag: infant sex

value: Male


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_10 in torpor entry

tag: developmental stage

tag: adapted to

tag: time

value: torpor entry


title: Placenta sample X31303.044

description:
Library name: X31303.044
Column name in counts_nhbcs.csv.gz : X31303.044

value: Placenta villis fetal side

tag: maternal smoking

value: No

value: White


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_06 in torpor entry


title: Placenta sample X31303.042

description:
Library name: X31303.042
Column name in counts_nhbcs.csv.gz : X31303.042

tag: baby race

value: C-section

value: Female


title: POND-FMR1-S217syn_rep1

value: HEK293T cell line

tag: treatment


title: Placenta sample X31303.041

description:
Library name: X31303.041
Column name in counts_nhbcs.csv.gz : X31303.041

tag: maternal age

tag: rna integrity_number


title: BDM_siRNA-ctrl_mock_donor1

description: Library name: Sample1

value: WT

tag: batch


title: POND-FMR1-E204del_rep2


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_11 in torpor entry

value: suprachiasmatic nucleus (SCN)

value: adult

tag: Sex

value: female


title: Placenta sample X31303.040

description:
Library name: X31303.040
Column name in counts_nhbcs.csv.gz : X31303.040

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_30 in torpor entry

tag: tissue

value: short photoperiod (LD 8:16)

value: male


title: POND-FMR1-R201T_rep2

tag: cell line

tag: genotype


title: Placenta sample X31303.034

description:
Library name: X31303.034
Column name in counts_nhbcs.csv.gz : X31303.034

tag: delivery method

tag: infant sex


title: RNA-Seq data of lasermicrodissected SCN of hamster EH03_08 in torpor entry

tag: developmental stage

tag: adapted to


title: preLSC, cDKO, rep3

city: Edinburgh

first: Yuka

last: Kabayama

address: Max Born Crescent

institute: University of Edinburgh

description: Library name: KO_3

data_processing:
Adapter was removed using cutadapt (1.17),
Trimmed reads were mapped to GRCm38 genome_tran (release 84) with HISAT2 (2.1.0).
Mapped reads per gene were counted with htseq-count (HTSeq 0.11.1).
Differentially expressed genes were analysed using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file which contains ensemble gene ID and raw read count.

source_name: preleukemic cells

growth_protocol: Meis1/Hoxa9 preleukemic cells were cultured at 200,000 cells/mL in IMDM supplemented with 10% FBS, Stem Cell Factor (40 ng/mL), IL-6 (20 ng/mL), IL-3 (20 ng/mL), Penicillin and Streptomycin, 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using QIAzol and teated with DNase I following QIAGEN RNA mini extraction kit's instructions.
Libraries were prepared from 1 ug of total RNA using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, cat. no. E7760) with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB, cat. no. E6310) following the manufacture’s protocol. Eight cycles of PCR was performed to amplify libraries and the pooled library was sequenced on Illumina NextSeq 550 with 85 bp single-end.

tag: cell type

value: preleukemic cells

value: Tut4/7 Vav-iCre cDKO


title: Placenta sample X31303.032

description:
Library name: X31303.032
Column name in counts_nhbcs.csv.gz : X31303.032

tag: maternal smoking

tag: baby race

value: AGA

value: Vaginal delivery


title: POND-FMR1-R193H_rep2

tag: treatment


title: Patient_8_pre

city: Southampton

first: Andres

middle: Felipe

last: Vallejo Pulido

address: University of Southampton

department: Medicine

institute: University of Southampton

description: FFPE

data_processing:
Fastq files were parsed on HTG Edge parser software and generated a gene expression count matrix.
Raw counts underwent processing using EdgeR R v4.3.2
Normalized using Trimmed Mean of M-values
Batch effect was corrected (batches 37 and 38)
Assembly: GRCh38
Supplementary files format and content: Raw counts

source_name: skin

extract_protocol:
Tissues were lysed using a lysis buffer from the HTG Molecular Diagnostics kit followed by the proteinase K digestion. Gene-specific nuclease protection probes with universal priming sites were then added. S1 nuclease was added to specifically digest non-hybridized molecules. The resulting DNA probes were quantitatively amplified using PCR, incorporating extended primers that included sequencing primer and sample barcode seqeunces for library preparation.
RNA sequencing of tissue with HTG EdgeSeq system's Precision Immuno-Oncology Panel was undertaked from all samples.

value: skin

value: pre


title: preLSC, cDKO, rep2

description: Library name: KO_2


title: POND-FMR1-R193H_rep1


title: Patient_7_post

description: FFPE

value: post


title: Placenta sample X31303.030

description:
Library name: X31303.030
Column name in counts_nhbcs.csv.gz : X31303.030

value: Placenta villis fetal side

value: No

value: White

tag: maternal age

tag: rna integrity_number


title: preLSC, cDKO, rep1

description: Library name: KO_1


title: POND-FMR1-I185T_rep2

value: HEK293T cell line


title: Patient_7_pre

description: FFPE


title: Placenta sample X31303.029

description:
Library name: X31303.029
Column name in counts_nhbcs.csv.gz : X31303.029

value: Yes

value: C-section

value: Female


title: Patient_6_post

description: FFPE


title: POND-FMR1-I185T_rep1


title: Placenta sample X31303.039

description:
Library name: X31303.039
Column name in counts_nhbcs.csv.gz : X31303.039


title: RNA-Seq data of lasermicrodissected SCN of hamster EH04_07 in torpor entry

value: suprachiasmatic nucleus (SCN)

value: adult

tag: Sex

tag: time

value: torpor entry


title: Patient_9_post

description: FFPE


title: Placenta sample X31303.028

description:
Library name: X31303.028
Column name in counts_nhbcs.csv.gz : X31303.028

tag: gestational age

tag: birthweight percentile


title: POND-FMR1-H182R_rep2


title: Patient_6_pre

description: FFPE

tag: tissue


title: preLSC, WT, rep2

description: Library name: Control_2

value: preleukemic cells

value: Control


title: POND-FMR1-H182R_rep1

tag: cell line


title: Patient_5_post

description: FFPE


title: Placenta sample X31303.359

description:
Library name: X31303.359
Column name in counts_nhbcs.csv.gz : X31303.359

tag: birthweight fenton_group

value: AGA

value: Male


title: preLSC, WT, rep1

description: Library name: Control_1

tag: genotype


title: Placenta sample X31303.360

description:
Library name: X31303.360
Column name in counts_nhbcs.csv.gz : X31303.360

tag: delivery method

value: Vaginal delivery

tag: infant sex


title: POND-FMR1-N174K_rep2


title: Placenta sample X31303.354

description:
Library name: X31303.354
Column name in counts_nhbcs.csv.gz : X31303.354


title: Patient_5_pre

description: FFPE

value: skin

value: pre


title: Placenta sample X31303.022

description:
Library name: X31303.022
Column name in counts_nhbcs.csv.gz : X31303.022

value: Placenta villis fetal side


title: preLSC, 540min, cDKO, rep3

description: Library name: T9_dko3

data_processing:
T to C conversion rates were obtained using the SlamDunk (v0.4.3).
Conversion rates across different time points were normalized to time 0 for each gene and were used to fit an exponential decay model to calculate half-lives.
Assembly: GRCm38
Supplementary files format and content: Output of slamdunk, tab-delimited text file.

extract_protocol:
Total RNA was extracted using QIAzol and alkylated in the dark room following manufactures protocol from Lexogen catabolic kit (cat. no. 062.24).
500 ng of total RNA was used for library preparation and 16 PCR cycles were performed using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (cat. no. 015.24).

treatment_protocol: Medium with 2.9 μM of 4-thiouridine (4SU) was used for labelling preleukemic cells for 12 hours and was later replaced with 4SU-free medium (T0, 0min). Cells were collected into QIAzol reagent immediately after changing medium and at 1, 3, and 9 hours and frozen on dry ice.

value: Tut4/7 Vav-iCre cDKO

tag: batch

value: 540 min


title: Patient_4_post

description: FFPE

value: post


title: POND-FMR1-N174K_rep1

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

value: HEK293T cell line


title: Placenta sample X31303.020

description:
Library name: X31303.020
Column name in counts_nhbcs.csv.gz : X31303.020

data_processing:
Reads aligned with Splice Transcripts Alignment to a Reference (STAR) with GENCODE v47 (GRCh38) and quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv gzipped file with raw counts for each sample

value: No

value: White

value: C-section


title: preLSC, 540min, cDKO, rep2

description: Library name: T9_dko2

tag: cell type


title: POND-FMR1-I170L_rep2


title: preLSC, 540min, cDKO, rep1

description: Library name: T9_dko1


title: Patient_4_pre

description: FFPE


title: Placenta sample X31303.016

description:
Library name: X31303.016
Column name in counts_nhbcs.csv.gz : X31303.016

tag: maternal smoking


title: POND-FMR1-I170L_rep1


title: Patient_2_post

description: FFPE


title: Placenta sample X31303.015

description:
Library name: X31303.015
Column name in counts_nhbcs.csv.gz : X31303.015

value: Yes

tag: baby race


title: preLSC, 180min, cDKO, rep3

description: Library name: T3_dko3

tag: treatment

value: 180 min


title: Patient_2_pre

description: FFPE


title: Placenta sample X31303.014

description:
Library name: X31303.014
Column name in counts_nhbcs.csv.gz : X31303.014

tag: maternal age


title: POND-FMR1-T160I_rep2


title: preLSC, WT, rep3

description: Library name: Control_3

value: preleukemic cells


title: preLSC, 180min, cDKO, rep2

description: Library name: T3_dko2


title: POND-FMR1-T160I_rep1


title: Placenta sample X31303.026

description:
Library name: X31303.026
Column name in counts_nhbcs.csv.gz : X31303.026

value: SGA

tag: rna integrity_number


title: Placenta sample X31303.012

description:
Library name: X31303.012
Column name in counts_nhbcs.csv.gz : X31303.012

value: AGA


title: Patient_1_post

description: FFPE


title: POND-FMR1-H147R_rep2


title: preLSC, 180min, cDKO, rep1

description: Library name: T3_dko1


title: Patient_1_pre

description: FFPE


title: preLSC, 60min, cDKO, rep3

description: Library name: T1_dko3

value: 60 min


title: POND-FMR1-H147R_rep1


title: Placenta sample X31303.010

description:
Library name: X31303.010
Column name in counts_nhbcs.csv.gz : X31303.010

value: Vaginal delivery

value: Male


title: Placenta sample X31303.025

description:
Library name: X31303.025
Column name in counts_nhbcs.csv.gz : X31303.025

value: Female


title: NEC_3d_hiPSC_rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic was employed to trim reads ends where average base calling qualities (in 5 bp windows) were below Q20. Only reads with minimum length of 30 bp were kept for further analyses.
We aligned all trimmed and filtered reads into human genome version hg38 (GRCh38) by using STAR version 2.7.1a.
Uniquely mapped reads were counted using featureCounts in Subread toolkit 1.6.473. By this approach, each read was only aligned and counted for the reference genome that had higher similarity to, and the reads with equal similarity to both genomes were excluded.
Counts normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2. Genes having absolute log2 fold-change higher than 1 and Benjamini-Hochberg adjusted P-value less than 0.05 were considered as significant differentially expressed genes (DEGs).
The shrinkage of log fold changes was performed using “ashr” shrinkage estimator. Visualization of the results was done by ggplot2, pheatmap and EnhancedVolcano packages. Overrepresentation analysis was performed in DAVID Bioinformatics Resources76. Gene set enrichment analysis was performed using Broad Institute GSEA software.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Txt file of raw counts

source_name: RiPS4-derived NEC

extract_protocol:
miRNeasy micro kit (Qiagen)
Libraries for cell and tissue samples were generated by SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takar Bio).

value: RiPS4-derived NEC

value: Neuroepithelial cells

value: WT

value: NEC differentiation


title: POND-FMR1-A145V_rep2

source_name: HEK293T cell line

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

value: HEK293T cell line


title: Placenta sample X31303.009

description:
Library name: X31303.009
Column name in counts_nhbcs.csv.gz : X31303.009

source_name: Placenta villis fetal side

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany, cat. No. 74106), and the Norgen Tissue RNA Purification Kit (Norgen Biotek, Thorold, ON, Canada, Cat. No. 25700), following the manufacturer’s protocols.
Ribosomal RNA depletion was used to prepare RNA-sequencing (RNA-seq) libraries, transcriptome-wide RNA-sequencing was performed with paired-end 75 bp reads on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) .

value: Placenta villis fetal side

value: No


title: NEC_3d_hiPSC_rep2


title: preLSC, 60min, cDKO, rep2

description: Library name: T1_dko2

value: Tut4/7 Vav-iCre cDKO


title: Placenta sample X31303.008

description:
Library name: X31303.008
Column name in counts_nhbcs.csv.gz : X31303.008

value: White


title: preLSC, 60min, cDKO, rep1

description: Library name: T1_dko1


title: NEC_3d_hiPSC_rep1


title: Placenta sample X31303.007

description:
Library name: X31303.007
Column name in counts_nhbcs.csv.gz : X31303.007

value: Yes


title: POND-FMR1-A145V_rep1


title: hiPSC_rep3

value: iPS cells

value: control


title: Placenta sample X31303.006

description:
Library name: X31303.006
Column name in counts_nhbcs.csv.gz : X31303.006

value: AGA


title: preLSC, 0min, cDKO, rep3

description: Library name: T0_dko3

value: preleukemic cells

value: 0 min


title: POND-FMR1-A145S_rep2


title: BDM_siRNA_LINC010857_1_LPS_donor1

description: Library name: Sample4

value: blood

value: blood-derived macrophage

value: LINC01857 knockdown

value: lipopolysaccharide


title: BDM_siRNA_LINC010857_2_mock_donor1

description: Library name: Sample5

value: mock


title: preLSC, 0min, cDKO, rep2

description: Library name: T0_dko2


title: Placenta sample X31303.005

description:
Library name: X31303.005
Column name in counts_nhbcs.csv.gz : X31303.005

value: Vaginal delivery

value: Female


title: hiPSC_rep2

value: WT


title: preLSC, 0min, cDKO, rep1

description: Library name: T0_dko1


title: POND-FMR1-R138syn_rep2

value: HEK293T cell line


title: hiPSC_rep1


title: BDM_siRNA-ctrl_LPS_donor1

description: Library name: Sample2


title: preLSC, 540min, control, rep3

description: Library name: T9_ctl3

value: 540 min