title: CKD2

city: Ann Arbor

first: Jie Ren Gerald

last: Har

state: MI

address: 1011 N University Ave

institute: University of Michigan School of Dentistry

description:
Library name: CKD2
Column name in gene_fpkm.xls: CKD2

data_processing:
Performed by Novogene
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2were set as the threshold for significantly differential expression.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: xls file: FPKM of each sample

source_name: Tibia cortex, flushed

growth_protocol: Mice were housed within dedicated animal care facilities prior to diet induction.

extract_protocol:
Following euthanasia, tibiae were quickly cleaned of connective tissue and flash frozen. Prior to RNA extraction, the ends of tibiae were cut and marrow was flushed with 1X PBS (no Ca/Mg) quickly, and cryo-pulverized. Pulverized cortical bone of tibiae was transferred into Trizol reagent. RNA was then extracted following the Trizol protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: At 8 weeks of age, mice were randomly assigned to the control diet or the adenine diet (0.2% w/w) for 4 weeks.

value: Tibia cortex, flushed

value: Bone

value: Wildtype

value: Adenine diet (0.2% w/w)


title: RA2d_2

status: Public on Nov 24 2025

type: SRA

city: Beijing

first: Cheng

last: Li

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
low-quality bases and adapters were removed through Trim Galore (v0.6.7)
The reads were mapped to human genome hg19 using hisat2(v2.1.0).
Mapped reads were then processed by htseq-count (v1.99.2) to calculate the read count of all genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count value for each gene

molecule: total RNA

organism: Homo sapiens

source_name: RNA-seq, HL-60, RA 2d

growth_protocol: HL-60 cell was cultured in a 5% CO2 incubator at 37 °C . The complete medium consist of ATCCformulated Iscove's Modified Dulbecco's Medium with 20% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol: RNA-Seq protocol

treatment_protocol: 1 μM all-trans-Retinoic acid (ATRA ) was applied to induce neutrophil differentiation

tag: cell line

tag: treatment

value: RA 2d


title: MEP_4977-01_34+_F_28

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

library_source: genomic

data_processing:
Aligned to hg38 using BWA with default parameters
Duplicates removed using PICARD. All ENCODE hg38 blacklist regions removed, as well as reads from outside autosomes/sex chromosomes.
MACS2 used to call peaks, and Bedtools used to compute maximum signal over background from MACS2 data over catalogue of all called peaks, which was then subjected to quantile normalizartion.
Assembly: hg38
Supplementary files format and content: bed files of called narrowPeaks from MACS2
Supplementary files format and content: tsv file of max signal over background from MACS2 data over catalogue of called peaks (quantile normalized)

molecule: genomic DNA

source_name: Bone Marrow

growth_protocol: Cells were freshly sorted from bone marrow samples and resuspended in lysis buffer. They were stored at -20C until processing.

extract_protocol:
DNA purification following Buenrostro et al. 2013 protocol
Nextera DNA Sample Preparation kit (Illumina) following Buenrostro et al. 2013 protocol
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

tag: tissue

value: Bone Marrow

value: Primary

tag: cell type

value: MEP

tag: Sex

value: female

tag: age


title: CKD1

country: USA

description:
Library name: CKD1
Column name in gene_fpkm.xls: CKD1

molecule: polyA RNA

organism: Mus musculus

tag: genotype


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, 5-Ph-IAA, 3hr, Hi-C_rep1

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

country: South Korea

institute: KAIST

description: Library name: Hi-C_RBD_del_IAA_3hr_rep1

data_processing:
In situ Hi-C sequencing data were analyzed using HiC-Pro. FASTQ files were aligned to the human reference genome (hg38), and low-quality and duplicate reads were removed. Valid paired-end reads were used to construct contact matrices, which were subsequently normalized using the Iterative Correction and Eigenvector decomposition (ICE) method.
Assembly: GRCh38
Supplementary files format and content: bedGraph files of eigenvalue

extract_protocol:
After cross-link reversal, 1μl of RNase A was added to each sample, followed by incubation at 37 ℃ for 30 min. DNA was purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v/v), followed by ethanol precipitation. The pellet was resuspended in 90 μl of TLE buffer (10 mM Tris-HCl pH 8.0, 0.1mM EDTA). Biotin removal was performed in a 100μl reaction containing 1x NEBuffer 2.1, 25μM each of dATP and dGTP, and 30 units of T5 DNA polymerase. The reaction was incubated at 20 ℃ for 4 h, then heat-inactivated at 75 ℃ for 20 min. DNA was fragmented using a Covaris S220 sonicator to an average fragment size of ~400 bp (peak power: 140W; duty factor: 10%; cycles per burst: 200; duration: 55 s). Fragment size selection was performed using a dual-sided AMPure XP bead cleanup: 0.6x bead volume for initial selection and 0.25x for secondary purification. Biotinylated fragments were captured using 10μl of MyOne C1 streptavidin beads per sample. The beads were washed with Tween wash buffer (5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and resuspended in 400μl of 2x binding buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). DNA diluted in TLE (400μl) was added to beads and incubated for 15 min at RT on a nutator. The beads were sequentially washed with 400μl of 1x binding buffer and 100 μl of 0.1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA), resuspended in 50μl of 0.1x TE, and transferred to 0.2 ml PCR tubes.
Library preparation was conducted using the NEBNext Ultra II DNA library Prep Kit (NEB, #E7645L), with slight modifications to the standard protocol. Following adaptor ligation, the beads were transferred to DNA LoBind tubes and washed twice with 400μl of Tween wash buffer for 5 min at RT on a nutator, then with 200μl of 1x binding buffer and 200μl of 0.1x TE. Final elution was performed in 15μl of 0.1x TE by heating at 98 ℃ for 10 min. Supernatants were collected and subjected to PCR amplification for 10 cycles. Amplified libraries were purified using 0.9x AMPure XP beads and sequenced on an Illumina Novaseq X platform (150bp paired-end reads).


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, 5-Ph-IAA, 3hr, Hi-C_rep2

description: Library name: Hi-C_RBD_del_IAA_3hr_rep2


title: RA4h_3

source_name: RNA-seq, HL-60, RA 4h

value: RA 4h


title: RA2d_1


title: MEP_07-18_34+_F_52


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, DMSO, Hi-C_rep2

description: Library name: Hi-C_RBD_del_DMSO_rep2


title: Ctrl2

description:
Library name: Ctrl2
Column name in gene_fpkm.xls: Ctrl2

value: Control diet


title: MEP_16_18_F_79


title: MLP_8F5042_34+_F_21

value: MLP


title: RA4h_2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, DMSO, Hi-C_rep1

description: Library name: Hi-C_RBD_del_DMSO_rep1


title: RA4h_1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(RBD del)-SNAP, dox, 24hr, 5-Ph-IAA, 3hr, Hi-C_rep2

description: Library name: Hi-C_RBD_del_IAA_3hr_dox_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, dox, 24hr, 5-Ph-IAA, 12hr, Hi-C_rep2

description: Library name: Hi-C_WT_IAA_12hr_dox_rep2


title: CKD3

description:
Library name: CKD3
Column name in gene_fpkm.xls: CKD3


title: RA0h_3

source_name: RNA-seq, HL-60, RA 0h

value: RA 0h


title: MLP_4977-01_34+_F_28

value: Male


title: Ctrl1

description:
Library name: Ctrl1
Column name in gene_fpkm.xls: Ctrl1


title: MLP_07-18_34+_F_52


title: primary cardiomyocyte, BMP2+DM, rep1

city: Shanghai

first: Qi

last: Tang

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science

description: Library name: BMP2DM_1

data_processing:
Raw sequencing data were quality-checked using FastQC, and adapter trimming and low-quality read removal were performed using Trimmomatic.
Clean reads were aligned to the mm10 genome using STAR.
Gene-level quantification was performed with HTSeq-count using the GENCODE gene annotation.
Differential gene expression analysis was conducted using the DESeq2 package in R.
Genes with |log2(FC)| > 1 and -log10 (p-value) > 1 were considered significantly differentially expressed. Gene Ontology (GO) enrichment analyses were performed using the clusterProfiler package.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: heart

extract_protocol:
Total RNA was extracted from primary cardiomyocyte using TRIzol reagent following the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
RNA library for RNA-seq was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library. After library preparation and pooling of different samples, the samples were subjected for NGS platform by Berry Genomics Co., Ltd (Beijing, China).

value: heart

value: primary cardiomyocyte

value: wild type


title: primary cardiomyocyte, BMP2+DM, rep2

description: Library name: BMP2DM_2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, 5-Ph-IAA, 12hr, Hi-C_rep2

description: Library name: Hi-C_WT_IAA_12hr_rep2


title: RA0h_2


title: primary cardiomyocyte, BMP2, rep2

description: Library name: BMP2_2


title: Ctrl3

description:
Library name: Ctrl3
Column name in gene_fpkm.xls: Ctrl3

value: Tibia cortex, flushed


title: GMP_8F5042_34+_F_21

value: GMP


title: RA0h_1


title: primary cardiomyocyte, BMP2, rep1

description: Library name: BMP2_1


title: RPS26dC_dC_3_HAR

city: Rehovot

first: Ariel

last: Ogran

address: 234 Herzl Street

department: Bimolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
Library name: HAR_dC_3
NextSeq High Output - 75 cycles

data_processing:
For the Ribo-seq and TIS-seq data analysis, the different samples were demultiplexed according to the given index, and the adaptor sequence was removed. rRNA was removed by aligning sequences to rRNA database from RNAcentral using bowtie2. Next, sequences were filtered to include only 28-32nt long sequences using cutadapt. Sequences were aligned to human transcriptome using STAR aligner (with parameters: –outFilterMultimaoNmax 1) while transcriptome data hg38 filtered by MANEv108 (UCSC) was selected for the alignment. The number of reads per sample (CPM) was calculated for normalization. For quality control, we checked if similar samples clustered together. Metagene plot was prepared using ribo-waltz R-package and TE for each gene was calculated by dividing each gene reads with its total RNA reads.
Assembly: hg38 filtered by MANEv108 (UCSC)
Supplementary files format and content: CSV files includes raw counts of CDS and 5'UTR per transcript
Library strategy: Ribo-Seq

source_name: kidney

growth_protocol: Both, WT and RPS26dC HEK293T cells grown at 37º C in a humidified incubator with 5% CO2 in Dulbecco’s modified Eagle’s medium (Gibco, Life Technologies, Thermo Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 units/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
Cells were scraped, washed with ice-cold PBS, and pelleted by centrifugation at 900 rpm for 10 min. Cell pellets were resuspended in ice-cold PBS and repelleted via centrifugation. Cells are then lysed in freshly prepared lysis buffer A containing 30 mM Tris, pH 7.5, 2% TritonX-100, 20 mM MgCl2, 300 mM NaCl, RNAsin (Promega) and 1X CoMplete Mini protease inhibitor cocktail. Cells were mixed gently by multiple inversions of the culture tube and incubated on ice for 10 min to complete lysis. Cell lysates were cleared of debris and nuclei via centrifugation at 9500 rpm at 4° C for 10 min. The supernatant was loaded on 1.1M sucrose cushion prepared in buffer B (45 mM HEPES KOH, pH 7.5, 150 mM KOAc, 10 mM Mg(OAc)2, and 2mM DTT) and centrifuged for 16 h at 55000 rpm to get the crude ribosomal pellet. Sucrose cushion buffer was treated with bentonite after preparation to inhibit ribonucleases. The pellet was resuspended in Buffer C (20 mM Tris pH 7.5, 150 mM KOAc, 10 mM Mg(OAc)2, RNAsin, and 2mM DTT) to homogeneity, and particles were removed by short centrifugation (10 min at 9500 rpm) and the supernatant was loaded on a linear gradient of 10-40% sucrose. The sucrose buffer was treated with bentonite after preparation to inhibit ribonucleases. The samples were centrifuged at 22,000 rpm for 11 h in a SW-28 rotor, fractions were collected and absorbance (A260) was measured for each. Fractions corresponding 80S peak were pooled together and further centrifuged at 56,000 rpm for 16h at 4˚C. The pellet was suspended in Buffer D [20 mM Tris pH 7.5, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc and 1 mM DTT], centrifuged for 2.5 h at 75,000 rpm (Ti100 rotor, Beckman). The pellet was dissolved in Buffer D overnight without shaking. The dissolved pellets were flash frozen in aliquots and stored at -800C.
Ribo-seq and TIS-seq protocols were adapted from Ingolia, N.T., et al., Nat Protoc, 2012. 7(8): p. 1534-50.

treatment_protocol: For the Ribo-seq, three biological replicates of HEK293 WT and Rps26dC cells were grown to 90% confluency on standard conditions and treated with Cycloheximide (CHX) for 5 minutes at 37 degrees. For the TIS-seq, three biological replicates were treated with CHX for 5 minutes and Harringtonine (HAR) for 2 minutes at 37 degrees.

value: kidney

value: human embryonic kidney cells

value: Harringtonine (HAR) + Cycloheximide (CHX)

tag: batch


title: GMP_19_16_F_61

value: Bone Marrow


title: GMP_4977-01_34+_F_28

value: Primary


title: primary cardiomyocyte, PBS, rep2

description: Library name: PBS_2

value: PBS


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, 5-Ph-IAA, 12hr, Hi-C_rep1

description: Library name: Hi-C_WT_IAA_12hr_rep1


title: RPS26dC_dC_2_HAR

description:
Library name: HAR_dC_2
NextSeq High Output - 75 cycles


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, dox, 24hr, 5-Ph-IAA, 3hr, Hi-C_rep1

description: Library name: Hi-C_WT_IAA_3hr_dox_rep1


title: primary cardiomyocyte, PBS, rep1

description: Library name: PBS_1


title: GMP_17_18_F_52

value: female


title: GMP_16_18_F_79


title: GMP_12-17_34+_F_58


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, 5-Ph-IAA, 3hr, Hi-C_rep2

description: Library name: Hi-C_WT_IAA_3hr_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, dox, 24hr, 5-Ph-IAA, 12hr, Hi-C_rep1

description: Library name: Hi-C_WT_IAA_12hr_dox_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, 5-Ph-IAA, 3hr, Hi-C_rep1

description: Library name: Hi-C_WT_IAA_3hr_rep1


title: HEK293T_WT_3_HAR

description:
Library name: HAR_WT_3
NextSeq High Output - 75 cycles

value: WT


title: HEK293T_WT_2_HAR

description:
Library name: HAR_WT_2
NextSeq High Output - 75 cycles


title: HiC_meristems_rep1

city: Amherst

first: Kirk

last: Amundson

state: MA

address: 240 Thatcher Rd

department: Biology

institute: University of Massachusetts Amherst

description: Library name: 22061Lip_DC2

data_processing:
ATAC-seq: ATAC-seq reads were trimmed with trimmomatic (Bolger et al. 2014) and aligned to Heinz SL4.0 reference genome (Hosmani et al. 2019) with BWA mem (Li 2013). Reads that mapped to either chloroplast or mitochondria were filtered out together with PCR duplicate reads (picard MarkDuplicates) and multiple position aligned reads. Finally, only high quality properly paired reads were retained for the analysis (samtools view -b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30). Hi-C: Raw sequencing reads were processed using HiC-Pro v3.1.0, mapping reads to the M82 genome (SollycM82_v1.0) with a MAPQ threshold >30 (Servant et al. 2015; Alonge et al. 2022).
ATAC-seq: For JBrowse visualization of the ATAC-seq, coverage was calculated with genomeCoverageBed followed by bedGraphToBigWig command. Hi-C: Valid read pairs were identified after filtering out invalid pairs and PCR duplicates, and both raw and normalized contact maps were generated at multiple bin sizes (5 kb, 10 kb, 20 kb, 40 kb, 150 kb, 500 kb, and 1 Mb).
ATAC-seq: ATAC-seq peak calling was done by Genrich V0.6 (https://github.com/jsh58/Genrich) using all six libraries with the following parameters: -j -r -v -q 0.5 -g 30. Hi-C: Contact matrices were converted to .mcool format with Cooler, and the reproducibility between replicates was evaluated using HiCRep (Yang et al. 2017; Abdennur and Mirny 2020).
Hi-C: HiC-Pro v3.1.0 was then used to merge valid read pairs from both replicates and generate contact matrices.
Hi-C: FitHiC2 was used to identify significant chromatin looping interactions at 5 kb resolution on the merged data (q-value 0.01, maximum loop distance of 1 Mb, minimum loop distance of 10 kb)
Assembly: ATAC-seq: Tomato SL4.0 ITAG4.0 Hi-C: Tomato M82 SollycM82_v1.0
Supplementary files format and content: ATAC-seq: ATAC-Leaf_Genrich_Rep_Final_09252020.bed - This file contain the ATAC-seq peaks called by Genrich using all six libraries to calculate q-value. Hi-C: BED3 (of loop edge midpoints)

organism: Solanum lycopersicum

source_name: inflorescences

growth_protocol: ATAC-seq: Tomato anantha-e1546 (Solyc02g081670) in M82 background seeds were directly sown into soil in 96-cell plastic flats and grown in a greenhouse under long-day conditions (16-hr light/8-hr dark) supplemented with artificial light from high-pressure sodium bulbs (~250 µmol m-2 s-1). The temperature ranged between 26-28˚C during the day to 18-20˚C during the night, with a relative humidity of 40-60%. One-month old seedlings were transplanted to a 4L pot and grown in the greenhouse at the same conditions. Hi-C: Solanum lycopersicum cv. M82 anantha (an) mutants were grown in pots under greenhouse conditions (Lippman et al. 2008).

extract_protocol:
ATAC-seq: Six biological replicates of 1g of freshly collected terminal leaflet of young M82 leaves were ground in ice-cold isolation buffer  (300 mM sucrose, 20 mM Tris pH 8.0, 5 mM MgCl2, 5 mM KCl, 5 mM beta-mercaptoethanol, 35% glycerol, 0.2% Triton X-100). After grinding, the suspension was filtered through a series of cell strainers (the smallest being 70 mm). Samples were further disrupted using a Dounce homogenizer, and then washed four times with ice-cold isolation buffer. The enriched nuclei samples were resuspended in Resuspension Buffer (50 mM Tris pH 8.0, 5 mM MgCl2, 5 mM beta-mercaptoethanol, 20% glycerol). Hi-C: The cauliflower-like tissue from young an inflorescences was harvested 10 weeks after sowing, with tissue collected from two different plants to obtain two biological replicates (3.3 g and 3.1 g, respectively). Hi-C data was generated using the Arima Hi-C 2.0 Kit (PN A410110) according to the manufacturer’s user guide for plant tissues (PN A160163 v00). Nuclei extraction was done using the CelLytic Plant Nuclei Isolation/Extraction Kit according to the manufacturer’s recommendations for cell lysis and semi-pure preparation of nuclei, with the addition of a Dounce homogenizer to increase nuclei yield (Sigma, CELLYTPN1). DNA fragmentation was performed with the Bioruptor Pico (Diagenode) using 4 cycles of 15 s sonication followed by 90 s rest.
ATAC-seq: For the transposase reaction 100,000 nuclei were resuspended  in 22.5 ml freezing buffer (5 mM MgCl2, 0.1 mM EDTA, 50 mM TRIS pH 8.0, 40% glycerol), and were mixed with  2X DMF Buffer (66 mM Tris-acetate (pH 7.8), 132 K-Acetate, 20 mM Mg-Acetate, 32% DMF) and 2.5ul Transposase enzyme from Illumina Nextera Kit (Catalog No. FC-121-1031), and incubated at 37°C for 30 min. Tagmented DNA was isolated using NEB Monarch PCR Purification kit (Catalog No. NEB #T1030). Next-generation sequencing (NGS) libraries were amplified in two steps (Buenrostro et al. 2015) using KAPA HiFi HotStart ReadyMix PCR kit (Catalog No. KK2601). NGS libraries were PE50 sequenced on an Illumina MiSeq SY-410-1003 instrument. Hi-C: Library preparation was performed using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit, Swift Biosciences Indexing Kit, KAPA Library Quantification Kit for Illumina Platforms, and KAPA Library Amplification Kit according to the Arima Hi-C 2.0 library preparation guide (PN A160164 v00). Each library was sequenced in paired-end mode (2 × 250 bp) on an Illumina NovaSeq 6000 SP flowcell, yielding 463,915,437 reads for replicate 1 and 461,940,842 reads for replicate 2.

value: inflorescences

value: anantha-e1546 mutant in M82 background


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, DMSO, Hi-C_rep2

description: Library name: Hi-C_WT_DMSO_rep2


title: GMP_07-18_34+_M_27


title: HEK293T_WT_1_HAR

description:
Library name: HAR_WT_1
NextSeq High Output - 75 cycles


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, DMSO, Hi-C_rep1

description: Library name: Hi-C_WT_DMSO_rep1


title: CMP_8F5042_34+_F_21

value: CMP


title: TITreg_EP2EP4cKO_4

city: Kyoto

first: Ryuma

last: Matsuura

address: 53 Kawara-cho, Shogoin, Sakyo-ku, Kyoto City,

country: Japan

institute: Kyoto University

data_processing:
Low quality bases and adapter sequences were removed from raw Fastq read sequences by Trim Galore.
Trimmed reads were aligned to mm10 using HISAT2.
The expression level of each gene was calculated from mapped read counts using Strintie and prepDE.py.
Assembly: mm10
Supplementary files format and content: tab-delimited text files of raw count

source_name: tumor

extract_protocol:
RNA was extracted from sorted cells using QIAGEN RNeasy plus micro kit.
cDNA was synthesized from isolated RNA, and RNA-seq libraries were constructed using SMART-Seq mRNA LP kit (Takara Bio) following the manufacturer's protocol.

treatment_protocol: Foxp3-GFP/CreERT2 and EP2/EP4 double-floxed Foxp3-GFP/CreERT2 mice were treated with tamoxifen (Sigma) for 5 days. One week after the final treatment, LLC1 tumor cells (3.0 x 10^5 cells/mouse) were injected subcutaneously into these mice. Eighteen days after injection, LLC1 tumors were dissected from the respective mice (n = 4 per group). Tumor-infiltrating Tregs (TI-Tregs) were FACS-sorted by GFP fluorescence following enrichment with TIL-CD4 microbeads (Miltenyi) and subjected to RNA sequencing.

value: tumor

value: primary cell

value: Tumor infirtrating Treg

value: EP2/EP4 double floxed Foxp3-GFP/CreERT2

tag: strain

value: EP2EP4 conditional KO


title: TITreg_EP2EP4cKO_3


title: CMP_4977-01_34+_F_28


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(wt)-SNAP, dox, 24hr, 5-Ph-IAA, 3hr, Hi-C_rep2

description: Library name: Hi-C_WT_IAA_3hr_dox_rep2


title: RPS26dC_dC_2_CHX

description:
Library name: CHX_dC_2
NextSeq High Output - 75 cycles

value: Cycloheximide (CHX)


title: HCT116, SAF-A, CLIP-seq (Pull down)_rep2

description: Library name: SAF-A_CLIP-seq_pull_down_rep2

data_processing:
PolyA and adaptor sequence of raw reads were trimmed and mapped y STAR. Read counts were quantified by FeatureCount.
Assembly: GRCh38
Supplementary files format and content: Aligned narrowpeak BED files.

extract_protocol:
HCT116 cells were rinsed with ice-cold PBS and cross-linked under UV light at 254 nm with a total E of 4000 J/m² using a UVP cross-linker CL-3000 (Analytik Jena). Cross-linked cells were lysed in CLIP lysis buffer (20.3 mM Na2HPO4, 3.5 mM KH2PO4, 6.8 mM KCl, 342.5 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, and 0.5% NP-40) and kept on ice for 10 min. The lysates were treated with RNase-free DNase I (Thermo Scientific; EN0523) at 37°C for 5 min, followed by the addition of 0.1 ng of RNase A (Thermo Scientific; EN0531) and incubation at 37°C for 10 min. After centrifugation at 13,000 g at 4°C for 20 min, the supernatants were divided for use as input or immunoprecipitation (IP) using mouse monoclonal SAF-A antibody (Santa Cruz Biotechnology; sc-32315) conjugated to Dynabeads™ Protein A (Invitrogen; 10002D). IP was carried out at 4°C for 3 h. The beads were washed twice with CLIP lysis buffer and subsequently with PNK buffer [50 mM Tris-HCl (pH 7.4), 10 mM MgCl2, and 0.5% NP-40]. To dephosphorylate the ends of RNA fragments, the beads were incubated with 40 U/mL alkaline phosphatase (Roche; 10108138001) at 37°C for 10 min. Next, the RNA 5’ ends were phosphorylated by incubation with 0.5 U/μl T4 polynucleotide kinase (New England Biolabs; M0201L) and 0.125 mM ATP at 37°C for 10 min. Ribonucleoprotein complexes were finally eluted from the beads using 4X lithium dodecyl sulfate sample buffer (Invitrogen; NP0008). For RNA isolation from both input and IP samples, the RNA-protein complex was separated by SDS-PAGE in a 7.5% Mini-PROTEAN® TGX™ Precast Protein Gels (BIO-RAD; 456-1024) and transferred to a 0.45 μm NC blotting membrane (Cytiva; 10600003). Membrane regions corresponding to the molecular weight of SAF-A plus ~20 kDa above was excised and incubated with PK buffer [100 mM Tris-HCl (pH 7.4), 50 mM NaCl, and 10 mM EDTA] containing 4 mg/mL proteinase K (Roche; 3115836001) at 37°C for 20 min, followed by an additional 20 min incubation with PK/Urea buffer [100 mM Tris-HCl (pH 7.4), 50 mM NaCl, 10 mM EDTA, and 7 M urea] at 37°C. Supernatants were then subjected to organic extraction and ethanol precipitation with GlycoBlue (Invitrogen; AM9515) for efficient recovery of RNA fragments.
CLIP libraries were constructed using the SMARTer® smRNA-Seq Kit for Illumina®.


title: TITreg_EP2EP4cKO_2


title: HCT116, SAF-A, CLIP-seq (Pull down)_rep1

description: Library name: SAF-A_CLIP-seq_pull_down_rep1


title: TITreg_EP2EP4cKO_1


title: RPS26dC_dC_1_HAR

description:
Library name: HAR_dC_1
NextSeq High Output - 75 cycles

value: kidney


title: CMP_17_18_F_52


title: HiC_meristems_rep2

description: Library name: 22061Lip_DC3


title: RPS26dC_dC_1_CHX

description:
Library name: CHX_dC_1
NextSeq High Output - 75 cycles

value: human embryonic kidney cells


title: CMP_19_16_F_61


title: HCT116, SAF-A, CLIP-seq (Input)_rep2

description: Library name: SAF-A_CLIP-seq_input_rep2


title: HEK293T_WT_2_CHX

description:
Library name: CHX_WT_2
NextSeq High Output - 75 cycles


title: HCT116, SAF-A, CLIP-seq (Input)_rep1

description: Library name: SAF-A_CLIP-seq_input_rep1


title: HEK293T_WT_3_CHX

description:
Library name: CHX_WT_3
NextSeq High Output - 75 cycles


title: TITreg_Control_4

value: Control


title: TITreg_Control_3


title: MPP_8F5042_34+_F_21

value: Bone Marrow

value: MPP


title: CMP_07-18_34+_M_27

value: Primary

value: Male


title: Citrine_total _30min(-)Glucose_post-ind_rep2

city: Zürich

first: Mostafa

last: Zedan

address: Otto-Stern-Weg 3

country: Switzerland

institute: ETH-Zurich

data_processing:
For ribosome profiling, total mRNA levels and polysomes enrichment analysis: adapter sequence was trimmed using cutadapt, reads were alligned to rRNA using bowtie, reads not mapping to rRNA were alligned to the yeast genome using tophat2, and the counts per gene was performed using featurecount.For SLAMseq, reads were mapped, fiiltered using multiple quality criteria, followed by quantification of labeled reads and bases using SLAM dunk.
Assembly: For ribosome profiling and total mRNA levels analysis,yeast genome was downloaded from SGD. For SLAMseq, yeast genome and annotations of transcripts 3'UTR was perfromed as described:  H. Alalam, J. A. Zepeda-Martínez, and P. Sunnerhagen, ‘Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets.’, RNA, vol. 28, no. 6, pp. 905–915, Jun. 2022, doi: 10.1261/rna.079077.121.
Supplementary files format and content: For ribosome profiling and total mRNA levels analysis, text file containing raw counts per gene. for SLAMseq anaysis, text file containing the SLAMSeq statistics

organism: Saccharomyces cerevisiae

extract_protocol:
For ribosome profiling and total mRNA levels analysis, total RNA was extracted from the total lysate using phenol-chlorofrom, and polyA selected using oligo-dT beads. Ribosome footprinting was performed by RNAaseI digestion of the total lysate, enrichment of the ribosomes using sucrose cushion, and phenol-chlorofrom extraction of the RNA. For polysomes enrichment analysis, RNA was extracted from the total lysate or from the polysomes fraction using phenol-chlorofrom, and polyA selected using oligo-dT beads. For SLAMseq analysis, total RNA was extracted from the total lysate using phenol-chlorofrom extraction, and alkylated using iodoacetamide.
For ribosome profiling and total mRNA levels analysis, library prepration was performed as described: A. Friedrich et al., ‘Nα-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae.’, Cell Rep, vol. 34, no. 5, p. 108711, Feb. 2021, doi: 10.1016/j.celrep.2021.108711.For polysomes enrichment analysis, library preparation was performed using  NextFlex directional RNA-sequencing kit. For SLAMseq, library preparation was performed using Quantseq for 3’end sequencing.


title: RPS26dC_dC_3_CHX

description:
Library name: CHX_dC_3
NextSeq High Output - 75 cycles


title: MPP_4977-01_34+_F_28

value: female


title: HEK293T_WT_1_CHX

description:
Library name: CHX_WT_1
NextSeq High Output - 75 cycles

value: WT


title: TITreg_Control_2


title: Citrine_total _30min(-)Glucose_post-ind_rep1


title: TITreg_Control_1


title: RNA-Seq_RPS26dC_dC_3_HAR

data_processing:
RNA-seq reads were aligned to the MANEv108 transcriptome using STAR (parameters: --outFilterMultimapNmax 1, --outSAMtype BAM SortedByCoordinate). BAM files were indexed with samtools, and read counts over transcript regions were generated in R using summarizeOverlaps from the GenomicAlignments package in “Union” mode. Transcripts were annotated using biomaRt, and transcript-level counts were computed.
Assembly: hg38 filtered by MANEv108 (UCSC)
Supplementary files format and content: CSV files includes raw counts of CDS and 5'UTR per transcript

extract_protocol:
Cells were scraped, washed with ice-cold PBS, and pelleted by centrifugation at 900 rpm for 10 min. Cell pellets were resuspended in ice-cold PBS and repelleted via centrifugation. Cells are then lysed in freshly prepared lysis buffer A containing 30 mM Tris, pH 7.5, 2% TritonX-100, 20 mM MgCl2, 300 mM NaCl, RNAsin (Promega) and 1X CoMplete Mini protease inhibitor cocktail. Cells were mixed gently by multiple inversions of the culture tube and incubated on ice for 10 min to complete lysis. Cell lysates were cleared of debris and nuclei via centrifugation at 9500 rpm at 4° C for 10 min. 10% of the lysate was kept and stored apart for the extraction of the total mRNA.
The RNAseq library of total mRNA was prepared with the TruSeq Stranded mRNA Library Prep (Illumina, 20020594) according to manufacturer’s protocol.

treatment_protocol: These RNA-seq libraries were generated as internal controls for translation efficiency (TE) calculations and therefore match the treatment conditions used in the corresponding Ribo-seq and TIS-seq experiments (see matched metadata). For Ribo-seq, three biological replicates of HEK293 wild-type (WT) and Rps26ΔC cells were cultured under standard conditions to ~90% confluency, then treated with 100 µg/mL cycloheximide (CHX) for 5 minutes at 37°C. For TIS-seq, three biological replicates were similarly treated with CHX for 5 minutes, followed by 2 minutes of treatment with 2 µg/mL harringtonine (HAR) at 37°C.

value: Harringtonine (HAR) + Cycloheximide (CHX)


title: RNA-Seq_RPS26dC_dC_2_HAR


title: VOM_Sh4d_3_mix23

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
Base-calling was performed with bcl2fastq program (v2.20).
By using the celseq2 pipeline (https://github.com/yanailab/celseq2), demultiplexing of the raw data was performed, and also UMI counts were calculated.
Using binomial statistics, the number of UMI was converted to transcript counts. The mathematical formula is described in "Validation of noise models for single-cell transcriptomics (PMID: 24747814)". In this calculation method, if the UMI is the maximum value of 4096, the transcriptome count diverges to infinity and cannot be converted, so 9genes (Fga, Mt-Rnr2, Mt-Nd4, Mt-Cytb, Mup14, Mup20, Mup8, Mup13, Mup15) with a UMI count of 4096 in at least one sample genes were excluded from the analysis.
Lowly expressed genes were filtered out, and batch correction of transcript counts was performed using Combat-Seq(PMID: 33015620). The numbers following the string “mix” at the end of each sample name are the same for the same batch, and this information was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Comma Separated Values files include Batch correlated transcript counts of all samples

source_name: Liver

growth_protocol: We bred wild-type C57BL/6 mice to ages of 11-14 weeks (young), 60 weeks (old), and 100 weeks (very old), and used them in the experiment.

extract_protocol:
Total RNA was extracted from mouse hepatocytes isolated from mouse livers using ISOGEN II (Nippongene), and purified using the RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of the total RNA was evaluated using a NanoDrop 2000 (Thermo Fisher Scientific), and only RNA with an A260/A280 ratio of 2 or higher was used.
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
OTHER: CEL-Seq2 (an RNA-seq protocol)

treatment_protocol: Detailed protocol of PH is described in "Partial hepatectomy in mice(PMID: 25835741)". The Sham surgery is performed under inhalation anesthesia with an abdominal median incision and suture closure. Hepatic cells were isolated from mouse livers by performing two-step collagenase digestion. Detailed protocol of hepatocyte isolation is described in "Hepatocyte suspensions and cultures as tools in experimental carcinogenesis (PMID: 224209)".

value: Liver

value: Primary Cells

value: Hepatocyte

value: Sham surgery

tag: time


title: Citrine_total _30min(-)Glucose_30min(pre-ind)_rep1


title: RNA-Seq_HEK293T_WT_3_HAR


title: OM_52h_3_mix23

value: PH


title: Citrine_total _30min(-)Glucose_30min(pre-ind)_rep2


title: MPP_17_18_F_52


title: RNA-Seq_RPS26dC_dC_1_HAR


title: Citrine_total _(+)Glucose_30min(ind)_rep2


title: OM_Sh2d_3_mix23


title: MPP_07-18_34+_M_27


title: VOM_Ctrl_1X_mix23


title: Citrine_total _(+)Glucose_30min(ind)_rep1


title: RNA-Seq_HEK293T_WT_2_HAR


title: HSC_19-16_34+_F_61

value: HSC


title: OF_Sh4d_3_mix22


title: HSC_8F5042_34+_F_21


title: VOF_4d_3_mix22


title: Citrine_polysomes _30min(-)Glucose_post-ind_rep2


title: Citrine_polysomes _30min(-)Glucose_post-ind_rep1


title: RNA-Seq_RPS26dC_dC_2_CHX

value: Cycloheximide (CHX)


title: Citrine_polysomes _30min(-)Glucose_30min(pre-ind)_rep1


title: HSC_12-17_34+_F_58


title: Citrine_polysomes _(+)Glucose_30min(ind)_rep2


title: OF_Sh2d_2_mix22


title: MPP_16_18_F_79


title: Citrine_polysomes _30min(-)Glucose_30min(pre-ind)_rep2


title: MPP_19-16_34+_F_61


title: HSC_16_18_F_79


title: YF_Sh2d_3_mix17


title: HSC_4977-01_34+_F_28


title: VOM_52h_3_mix22


title: RNA-Seq_RPS26dC_dC_1_CHX

value: kidney


title: RNA-Seq_HEK293T_WT_2_CHX

value: human embryonic kidney cells


title: HSC_07-18_34+_M_27


title: ATAC_seq_leaf_rep6

description: Library name: ATAC_seq_leaf_rep6

source_name: terminal leaflet of young leaf

value: terminal leaflet of young leaf


title: VOM_Sh4d_3X_mix17


title: RNA-Seq_HEK293T_WT_1_HAR


title: Citrine_polysomes_(+)Glucose_30min(ind)_rep1


title: GST_total _30min(-)Glucose_post-ind_rep2


title: RNA-Seq_RPS26dC_dC_3_CHX


title: OM_Sh2d_3X_mix17


title: ATAC_seq_leaf_rep5

description: Library name: ATAC_seq_leaf_rep5


title: GST_total _30min(-)Glucose_30min(pre-ind)_rep2


title: ATAC_seq_leaf_rep4

description: Library name: ATAC_seq_leaf_rep4


title: OM_Sh2d_2_mix17


title: RNA-Seq_HEK293T_WT_1_CHX


title: d15_vCM_H3K27ac_ZNF436kd_r3

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

description: Library name: d15_vCM_H3K27ac_ZNF436kd_r3

data_processing:
Libraries were sequenced with 75 bp paired-end reads on the Illumina NextSeq 500. Raw reads were mapped to the human genome (hg19) using the short-read aligner program Bowtie2 v2.4.5, with the sensitive local mode, retaining only the high-quality reads (MAPQ > 10). Bigwig coverage tracks were generated using bedtools v2.30.0. Histone mark coverage signal profiles were created using the computeMatrix function and plotHeatmap from deeptools 3.5.4 from the mean coverage of three replicates per condition.
Assembly: hg19
Supplementary files format and content: bigwig coverage files and read count tables on called peaks
Library strategy: CUT&Tag

source_name: H9 ESC

growth_protocol: Human embryonic stem cell (hESC) line H9 was grown at 37ºC in 95% air, 5% CO2 in mTeSR plus media (STEMCELL Technologies, 100-0276) on plates previously coated with Matrigel (Corning, 354277). Cells were differentiated into cardiomyocytes using a ventricular cardiomyocyte differentiation kit (STEMCELL Technologies, 05010) following the manufacturer’s protocol. At day 15 of differentiation, ventricular-like cardiomyocytes (vCMs) were dissociated using 0.25% trypsin (Thermo Fisher Scientific, 25300054) for 5 min at 37ºC, which was quenched using cardiomyocyte support media (STEMCELL Technologies, 05027).

extract_protocol:
Cleavage Under Targets and Tagmentation (CUT&Tag) was done by the original protocol with some modifications. For each mark, 100k cells were used per sample with the anti-H3K9me3 primary antibody (Diagenode, C15410056), anti-H3K4me3 primary antibody (Cell Signaling Technology, C42D8, 9751S), anti-H3K4me1 primary antibody (Diagenode, C15410194), anti-H3K27ac primary antibody (Active Motif, 39034), and the anti-rabbit IgG secondary antibody (antibodies, ABIN101961). A homemade purified pA-Tn5 protein (3XFlag-pA-Tn5-Fl) was produced by the Protein Production and Purification Facility (PTPSP) at EPFL and then coupled with MEDS oligos. The purified recombinant protein was used at a final concentration of 700 ng/μL (1:250 dilution from homemade stock).
CUT&Tag - Tn5 based

value: H9 ESC

value: cardiomyocyte differentiation


title: GST_total _30min(-)Glucose_post-ind_rep1


title: GST_total _30min(-)Glucose_30min(pre-ind)_rep1


title: OM_52h_2_mix17


title: GST_total _(+)Glucose_30min(ind)_rep2


title: RNA-Seq_HEK293T_WT_3_CHX


title: OF_Sh2d_3_mix21


title: OM_52h_3X_mix17


title: GST_total _(+)Glucose_30min(ind)_rep1


title: d15_vCM_H3K27ac_ZNF436kd_r2

description: Library name: d15_vCM_H3K27ac_ZNF436kd_r2


title: ATAC_seq_leaf_rep1

description: Library name: ATAC_seq_leaf_rep1


title: d15_vCM_H3K27ac_ctrl_r3

description: Library name: d15_vCM_H3K27ac_ctrl_r3


title: d15_vCM_H3K27ac_ctrl_r2

description: Library name: d15_vCM_H3K27ac_ctrl_r2


title: ATAC_seq_leaf_rep3

description: Library name: ATAC_seq_leaf_rep3


title: YM_Sh4d_2_mix21


title: d15_vCM_H3K27ac_ctrl_r1

description: Library name: d15_vCM_H3K27ac_ctrl_r1


title: GST_polysomes _30min(-)Glucose_post-ind_rep2


title: WT_WT_rep1

city: Piscataway

first: Ziyuan

last: Ma

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

data_processing:
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (version 0.6.10)
Trimmed sequence reads were mapped to GRCh38 reference genome and GENCODE v44 primary assembly using STAR (version 2.7.11a).
Read count extraction and normalization were performed using RSEM (version 1.3.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts, fragments per kilobase per million (FPKM), and transcripts per kilobase million (TPM) for each sample.

source_name: iPSC/ESC differentiated PMP cells

growth_protocol: PMPs were generated from the three pairs of Cont and DS hiPSC cell lines using a previously established protocol. The yolk sac embryoid bodies (YS-EBs) were generated by treating the YS-EBs with mTeSR 1 media (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To stimulate myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). At 4-6 weeks after plating, human PMPs emerged into the supernatant and were continuously produced for more than 3 months.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: No special treatment used after PMP differentiation.

value: iPSC/ESC differentiated PMP cells

value: WT iPSC from WT donor

value: Primitive macrophage progenitor (PMP)


title: GST_polysomes _30min(-)Glucose_post-ind_rep1


title: YM_4d_3_mix21

value: WT


title: d15_vCM_H3K4me1_ZNF436kd_r3

description: Library name: d15_vCM_H3K4me1_ZNF436kd_r3


title: ATAC_seq_leaf_rep2

description: Library name: ATAC_seq_leaf_rep2


title: d15_vCM_H3K27ac_ZNF436kd_r1

description: Library name: d15_vCM_H3K27ac_ZNF436kd_r1


title: GST_polysomes _30min(-)Glucose_30min(pre-ind)_rep2


title: WT_A455D_rep3

value: A455D iPSC from WT donor

value: CSF2RB A455D mutation


title: GST_polysomes _30min(-)Glucose_30min(pre-ind)_rep1


title: YM_Sh2d_3_mix21

value: Liver

value: Primary Cells


title: WT_A455D_rep1


title: WT_A455D_rep2


title: GST_polysomes _(+)Glucose_30min(ind)_rep2


title: YM_Sh4d_3_mix21

value: Hepatocyte

value: Sham surgery


title: d15_vCM_H3K4me1_ZNF436kd_r1

description: Library name: d15_vCM_H3K4me1_ZNF436kd_r1


title: d15_vCM_H3K4me1_ctrl_r3

description: Library name: d15_vCM_H3K4me1_ctrl_r3


title: GST_polysomes_(+)Glucose_30min(ind)_rep1


title: DS_WT_rep2

value: WT iPSC from DS donor


title: OM_Sh4d_3_mix20


title: VOM_52h_3X_mix20

value: PH


title: WT_WT_rep2


title: d15_vCM_H3K4me1_ctrl_r2

description: Library name: d15_vCM_H3K4me1_ctrl_r2


title: pat1delta_total_5min_(-)Glu_rep 2


title: DS_WT_rep1


title: DS_A455D_rep3

value: A455D iPSC from DS donor


title: OM_4d_3_mix20


title: d15_vCM_H3K4me1_ZNF436kd_r2

description: Library name: d15_vCM_H3K4me1_ZNF436kd_r2


title: YM_4d_2_mix21


title: pat1delta_total_(+)Glu_rep2


title: d15_vCM_H3K4me3_ZNF436kd_r3

description: Library name: d15_vCM_H3K4me3_ZNF436kd_r3


title: OM_4d_2_mix20


title: DS_A455D_rep2


title: OM_Sh4d_2_mix20


title: d15_vCM_H3K4me1_ctrl_r1

description: Library name: d15_vCM_H3K4me1_ctrl_r1


title: pat1delta_total_5min_(-)Glu_rep1


title: pat1delta_total_(+)Glu_rep1


title: d15_vCM_H3K4me3_ZNF436kd_r2

description: Library name: d15_vCM_H3K4me3_ZNF436kd_r2


title: DS_A455D_rep1


title: OM_Sh2d_1_mix20


title: pat1delta_footprint_5min_(-)Glu_rep 2


title: d15_vCM_H3K4me3_ZNF436kd_r1

description: Library name: d15_vCM_H3K4me3_ZNF436kd_r1


title: CAGG_WT_rep3

value: WT ESC from WT donor


title: VOM_Ctrl_1X_mix16


title: d15_vCM_H3K4me3_ctrl_r3

description: Library name: d15_vCM_H3K4me3_ctrl_r3


title: OM_4d_1_mix16


title: CAGG_WT_rep2


title: d15_vCM_H3K4me3_ctrl_r2

description: Library name: d15_vCM_H3K4me3_ctrl_r2


title: pat1delta_footprint_(+)Glu_rep2


title: CAGG_WT_rep1


title: OM_52h_1_mix16


title: d15_vCM_H3K4me3_ctrl_r1

description: Library name: d15_vCM_H3K4me3_ctrl_r1


title: pat1delta_footprint_(+)Glu_rep1


title: d15_vCM_H3K9me3_ZNF436kd_r2

description: Library name: d15_vCM_H3K9me3_ZNF436kd_r2


title: OM_Ctrl_2_mix16


title: dhh1tailless_total_5min_(-)Glu_rep 2


title: OM_Ctrl_3_mix16


title: total_(+)Glu_rep2


title: HCT116 CTR, replicate2

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence through in-house perl scripts
Short reads were aligned to the reference human genome GRCh38 using STAR
Gene expression in terms FPKM of genes overlapping with gene annotations in Ensembl release 75 was calculated by Cufflinks
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: HCT116 cells were maintained in RPMI1640 medium (Gibco, C11875500BT). Media were supplemented with 10% FBS with glutamine, penicillin, and streptomycin. Cells were incubated at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy kit (EZB, B0004DP).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit (NEB #E7775) for Illumina following manufacturer's protocols.

value: coloncancercellline

value: control


title: HCT116 shARID1A, replicate2

value: ARID1A knockdown


title: dhh1tailless_footprint_5min_(-)Glu_rep2


title: HCT116 CTR, replicate1


title: YF_Sh4d_3_mix19


title: CAGG_A455D

value: iPSC/ESC differentiated PMP cells

value: A455D ESC from WT donor


title: OF_52h_3_mix19


title: dhh1delta_total_5min_(-)Glu_rep 2


title: d15_vCM_H3K9me3_ctrl_r3

description: Library name: d15_vCM_H3K9me3_ctrl_r3

value: H9 ESC

value: cardiomyocyte differentiation


title: d15_vCM_H3K9me3_ctrl_r2

description: Library name: d15_vCM_H3K9me3_ctrl_r2


title: pat1delta_footprint_5min_(-)Glu_rep1


title: d15_vCM_H3K9me3_ctrl_r1

description: Library name: d15_vCM_H3K9me3_ctrl_r1


title: VOM_4d_3_mix19

value: WT


title: dhh1delta_total_5min_(-)Glu_rep1


title: endometrium, first trimester decidua, rep3

city: Newark

first: Nataki

middle: C.

last: Douglas

address: 185 S Orange Ave, MBS E569

department: Ob-Gyn and Women's Health

institute: Rutgers-New Jersey Medical School

description:
Library name: D 092
10X Genomics

library_source: transcriptomic single cell

data_processing:
For scRNA-seq, demultiplexed sequencing reads were processed and aligned to the Homo sapiens genome assembly GRCh38 (hg38) using STAR (v2.7.9a) with 10X Genomics Cell Ranger (v3.1.0, RRID:SCR_017344). Samples were merged using the integration anchors function of the Seurat package (v5.1.0, RRID:SCR_016341) in R (Hao, Hao et al. 2021). Genes expressed in fewer than three cells in a sample were excluded, as well as cells that expressed fewer than 200 genes and mitochondrial gene content >5% of the total unique molecular identifier count. Data were normalized using a global-scaling normalization method (Hao, Hao et al. 2021) that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000), and then log-transforms the results.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-seperated values files, barcodes and matrix files

source_name: decidua

extract_protocol:
Endometrial biopsies were performed with the Endocell®, a disposable endometrial cell sampler (Wallach Surgical Devices, Trumbull, CT, USA) in the secretory phase. For collection of endometrial deciduae, women scheduled for an elective termination of an uncomplicated pregnancy in the first trimester at 6-8 weeks estimated gestational age were eligible for inclusion. After dilation and curettage, tissue samples were floated in phosphate buffered saline (PBS, pH 7.2) and the endometrial decidua was isolated from the gestational sac and chorionic villi by mechanical separation using forceps. Endometrial tissue was placed in a tissue culture dish and rinsed with ice-cold PBS to remove blood and mucus. Using fine forceps, each sample was separated such that approximately 100 mg endometrial tissue was fixed in formalin and stored at room temperature for immunohistology; approximately 100 mg was preserved in RNAprotect (Qiagen, 76160) and was placed on ice, and the remainder minced and processed within one hour of collection for scRNA-seq. Cells were isolated from minced endometrial tissues for scRNA-seq by incubation at 37°C in digestion media (DMEM/F12, 3% charcoal-stripped fetal bovine serum (FBS), 1 mg/mL collagenase A (Roche, #11088793001), 0.1 mg/mL DNAse type I (Roche, #10104159001) with agitation on a benchtop shaker at 250 rpm for 15 minutes. The tissue was then further dissociated by repeatedly passing it through a 16G needle attached to a 10 mL syringe. The shaking and needle passage steps were repeated once more to ensure thorough dissociation. The cell suspension was centrifuged at 300 ×g for 5 minutes. The resulting pellet was resuspended in 1 mL of TrypLE Select Enzyme (Thermo Fisher #12563011) containing 0.1 mg/mL DNase I and incubated at 37°C on a shaker at 250 rpm for 15 minutes. 10 mL of ice-cold digestion media was added, and the cell suspension was filtered through a 40 µm cell strainer. Red blood cells (RBC) were lysed using RBC lysis buffer (ThermoFisher, #00-4333-57) and dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, #130-090-101). The resulting single-cell suspension was used for Chromium (10X Genomics) sequencing.
For scRNA-seq, libraries were generated and sequenced using the 10X Chromium Single Cell 3ʹ GEM kit (10X Genomics, v2). Paired end, 2 x 75 bp, sequencing was performed on an Illumina NextSeq 500 instrument (RRID:SCR_014983). Output was demultiplexed and converted to FASTQ format with Cell Ranger (10X Genomics, v3.1.0).

value: decidua

tag: cycle stage

value: first trimester


title: HCT116 shARID1A, replicate1


title: d15_vCM_H3K9me3_ZNF436kd_r3

description: Library name: d15_vCM_H3K9me3_ZNF436kd_r3


title: total_30min_(-)Glu_rep2


title: d15_vCM_H3K9me3_ZNF436kd_r1

description: Library name: d15_vCM_H3K9me3_ZNF436kd_r1


title: OM_Ctrl_1_mix16

value: Liver

value: Primary Cells


title: total_(+)Glu_rep1


title: total_15min_(-)Glu_rep2


title: YF_4d_3_mix19

value: Hepatocyte


title: total_30min_(-)Glu_rep1


title: endometrium, first trimester decidua, rep2-1

description:
Library name: D 079-1
10X Genomics


title: YM_Sh4d_1_mix19

value: Sham surgery


title: endometrium, first trimester decidua, rep2

description:
Library name: D 079
10X Genomics


title: OM_Sh4d_1_mix19


title: dhh1delta_total_(+)Glu_rep2


title: dhh1delta_total_(+)Glu_rep1


title: total_15min_(-)Glu_rep1


title: total_5min_(-)Glu_rep 2


title: dhh1tailless_total_5min_(-)Glu_rep1


title: dhh1tailless_total_(+)Glu_rep2


title: YF_52h_3_mix18

value: PH


title: endometrium, first trimester decidua, rep1

description:
Library name: D 076
10X Genomics


title: footprint_(+)Glu_rep2


title: endometrium, late secretory, rep3

description:
Library name: EMB 088
10X Genomics

source_name: endometrium

value: endometrium

value: late secretory


title: YM_Sh2d_2_mix18


title: endometrium, late secretory, rep2

description:
Library name: EMB 075
10X Genomics


title: total_5min_(-)Glu_rep1


title: footprint_(+)Glu_rep1


title: YM_Sh2d_1_mix18


title: wildtype_total_5min_(-)Glu_rep 2


title: wildtype_total_5min_(-)Glu_rep1


title: footprint_30min_(-)Glu_rep2


title: endometrium, late secretory, rep1

description:
Library name: EMB 066
10X Genomics


title: YM_52h_3_mix18


title: footprint_30min_(-)Glu_rep1


title: endometrium, mid secretory, rep4

description:
Library name: EMB 087
10X Genomics

value: mid secretory


title: wildtype_total_(+)Glu_rep2


title: footprint_15min_(-)Glu_rep2


title: YM_52h_2_mix18


title: YF_Ctrl_4_mix18


title: endometrium, mid secretory, rep2

description:
Library name: EMB 055
10X Genomics


title: VOF_Sh4d_3_mix15


title: wildtype_total_(+)Glu_rep1


title: footprint_5min_(-)Glu_rep 2


title: dhh1tailless_total_(+)Glu_rep1


title: footprint_15min_(-)Glu_rep1


title: endometrium, mid secretory, rep3

description:
Library name: EMB 057
10X Genomics


title: dhh1delta_footprint_(+)Glu_rep1


title: OF_Sh4d_2_mix15


title: dhh1delta_footprint_(+)Glu_rep2


title: endometrium, early secretory, rep4

description:
Library name: EMB 053
10X Genomics

value: early secretory


title: endometrium, mid secretory, rep1

description:
Library name: EMB 052
10X Genomics


title: footprint_5min_(-)Glu_rep1


title: Polysomes_30min(-)Glucose_(no 4TU)


title: dhh1delta_footprint_5min_(-)Glu_rep 2


title: OF_Sh4d_3X_mix15


title: OF_4d_2_mix15


title: dhh1delta_footprint_5min_(-)Glu_rep1


title: endometrium, early secretory, rep3

description:
Library name: EMB 051
10X Genomics


title: endometrium, early secretory, rep2

description:
Library name: EMB 050
10X Genomics


title: Polysomes_(+)Glucose (no 4TU)


title: dhh1tailless_footprint_(+)Glu_rep2


title: YM_4d_1_mix15


title: endometrium, early secretory, rep1

description:
Library name: EMB 044
10X Genomics


title: Total_30min(-)Glucose (no 4TU)


title: OF_4d_1_mix14


title: endometrium, late secretory, rep3

description: Library name: EMB088

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5)
Trimmed reads were mapped to Homo sapiens genome assembly GRCh38 (hg38) using STAR (version 2.7.9a)
Reads overlapping Ensembl annotations (version 110) were quantified with STAR
Genes with low counts per million (CPM) were removed using the filterByExpr function from edgeR
Assembly: GRCh38.p14
Supplementary files format and content: Tab-delimited Log2-transformed counts per million for all samples

extract_protocol:
Total RNA was isolated from tissue using a Qiagen RNeasy mini kit and stored at −80 °C in nuclease-free water
Libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase for Illumina Platforms (Kapa Biosystems #KK8483) with the addition of Ambion External RNA Controls Consortium (ERCC) spike-in controls (Invitrogen #4456740).

value: late seretory


title: dhh1tailless_footprint_(+)Glu_rep1


title: OF_4d_3_mix15


title: Total_(+)Glucose (no 4TU)


title: dhh1tailless_footprint_5min_(-)Glu_rep1


title: endometrium, late secretory, rep2

description: Library name: EMB075


title: endometrium, late secretory, rep1

description: Library name: EMB066


title: Polysomes_30min(-)Glucose_post-labeling(4TU)_rep2


title: Polysomes_30min(-)Glucose_post-labeling(4TU)_rep1


title: OF_Sh2d_1_mix14


title: OF_52h_1_mix14


title: wildtype_footprint_(+)Glu_rep2


title: wildtype_footprint_5min_(-)Glu_rep 2


title: OF_52h_2_mix14


title: wildtype_footprint_5min_(-)Glu_rep1


title: endometrium, mid secretory, rep6

description: Library name: EMB055


title: Polysomes_(+)Glucose_30min(4TU)_rep1


title: wildtype_footprint_(+)Glu_rep1


title: Polysomes _(+)Glucose_30min(4TU)_rep2


title: endometrium, mid secretory, rep7

description: Library name: EMB057


title: endometrium, mid secretory, rep5

description: Library name: EMB052


title: VOF_Sh2d_3_mix13


title: YM_52h_1_mix14


title: endometrium, mid secretory, rep4

description: Library name: EMB038


title: Total ribosome profiling (uL16 loop mutant), rep3

city: Austin

first: Can

last: Cenik

state: Texas

address: 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas

description: Library name: RPL10_Total_3_Rep3

library_source: other

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”. After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/yeast_reference Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 15 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”.
After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy
Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/yeast_reference
Assembly: Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 15 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Supplementary files format and content: Ribo files
Library strategy: Ribo-Seq

molecule: other

source_name: yeast cells

growth_protocol: Cultures of yeast strain AJY2643 and AJY4638 harboring plasmids pAJ5507 or pAJ5509 were grown overnight to saturation in 50 mL of selective medium at 30 °C. The following day, cultures were diluted to an OD600 of 0.05 in 500 mL and grown to mid-log phase (OD600= 0.4-0.5).

extract_protocol:
For cell lysis, frozen pellets were mixed with frozen IP buffer (20 mM Tris·HCl, pH 7.5, 100 mM KCl, 10 mM MgCl2, 100 μg/mL cycloheximide,100 μg/mL Tigecyclin (Sigma), Pierce Protease Inhibitor Cocktail, EDTA-free [1 tablet/10 mL], 1 mM PMSF, 1 μM each of leupeptin and pepstatin, and 5 mM β-mercaptoethanol) at approximately 1 mL buffer per pellet. Samples were homogenized in a cryogenic mill (Retsch MM 300) for six cycles of 3 min each at 15 Hz, with samples submerged in liquid nitrogen for 3 min between cycles. The resulting cell powder was thawed on ice, additional IP buffer was added, and the lysate was clarified by centrifugation at 18,000 × g for 20 min at 4 °C. The clarified extract was supplemented with 0.1% (v/v) Igepal CA-630. The lysates were diluted to 150 A260 units/mL. One milliliter of lysate was treated with RNase I (Ambion) at a ratio of 3 U RNase I per 1 A260 unit for 1 h at 4 °C. A 50 μL aliquot of this extract was reserved as the total ribosome profiling sample. The remaining lysate was diluted to 50 A260 units/mL and incubated with 20 μL of pre-washed anti-FLAG magnetic beads (Sigma Millipore) per 1 mL of lysate for 2 h at 4 °C with rotation. Beads were washed three times with IP buffer containing 0.1% Igepal and transferred to a clean tube during the final wash. Bound ribosomes were eluted in 100 μL of IP buffer supplemented with 0.1% Igepal and 150 μg/mL 3×FLAG peptide (Sigma Millipore) for 30 min at 4 °C. Eluted ribosomes were digested with RNase I (1 U/μg RNA; Ambion) for 45 min at room temperature. Reactions were stopped by addition of QIAzol (Qiagen), and RNA was extracted using chloroform extraction followed by ethanol precipitation. Total ribosome profiling samples were processed in parallel by treating 50 μL of lysate with RNase I (1 U/μg RNA) in IP buffer supplemented with 0.1% Igepal for 45 min at room temperature. Digested lysates were layered onto 50 μL of 1 M sucrose cushions prepared in IP buffer, and ribosomes were pelleted by centrifugation at 165,000 × g for 30 min at 4 °C in a TLA 100 rotor (Beckman Coulter).
RNA was extracted from ribosome pellets using 700 μL of QIAzol, followed by chloroform extraction and ethanol precipitation. To isolate the ribosome-protected fragments (RPFs), the digested RNA   was run on a 15% TBE–urea polyacrylamide gel (Invitrogen).  A 19–35 nt fragments were excised and extracted by crushing the excised gel slice in 400 μL RNA extraction buffer (300 mM sodium acetate, pH 5.5, 5 mM MgCl2 followed by incubation at -20 C for 1h and overnight incubation at RT on a hula mixer.  The gel extract was passed through a Spin-X filter (Corning 8160), and RNA was recovered from the flow-through by ethanol precipitation (2.5X volume) with 1.5 μL GlycoBlue (Invitrogen AM9516). Ribosome profiling libraries were prepared as previously described60 using the D-Plex Small RNA-Seq Kit (Diagenode). cDNA was subjected to rRNA depletion, and the cleaned-up cDNA was amplified by PCR for 12 cycles. Libraries were purified with AMPure XP (Beckman Coulter) at a ratio of 1:1.8 (sample to bead ratio) and eluted in 50 μL of water. The library quality was assessed using a Bioanalyzer and the Agilent High Sensitivity DNA Kit (Agilent). Final libraries were pooled in equimolar ratios and sequenced on the NovaSeqX Plus; PE 150 (Illumina).

treatment_protocol: Cells were harvested by vacuum filtration using a 0.2 μm aPES membrane bottle-top filter (Fisherbrand), immediately scraped from the filter, and flash-frozen in liquid nitrogen. Frozen cell pellets were stored at -80 °C until further use.

value: yeast cells

value: uL16 loop mutant bypass

value: Cycloheximide + Tigecyclin


title: Total _30min(-)Glucose_post-labeling(4TU)_rep2


title: OF_Sh2d_2X_mix14


title: OF_Sh4d_1_mix13


title: Total _(+)Glucose_30min(4TU)_rep2


title: Total ribosome profiling (uL16 loop mutant), rep2

description: Library name: RPL10_Total_2_Rep2


title: VOM_Sh4d_2_mix13


title: endometrium, mid secretory, rep2

description: Library name: EMB013


title: uL16 loop mutant-bound ribosomes profiling, rep3

description: Library name: RPL10_IP_3_Rep3


title: Total _(+)Glucose_30min(4TU)_rep1


title: VOM_Sh4d_1_mix13


title: decay_(-)Glu_rep2_t45


title: uL16 loop mutant-bound ribosomes profiling, rep2

description: Library name: RPL10_IP_2_Rep2


title: endometrium, mid secretory, rep1

description: Library name: EMB006


title: VOM_4d_2_mix13


title: endometrium, early secretory, rep10

description: Library name: EMB053


title: uL16 loop mutant-bound ribosomes profiling, rep1

description: Library name: RPL10_IP_1_Rep1


title: decay_(-)Glu_rep2_t20


title: endometrium, early secretory, rep9

description: Library name: EMB051


title: OF_Ctrl_1X_mix10


title: decay_(-)Glu_rep2_t30


title: pACT1-HYF1 37 C

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: Library name: HYF1_37C_S35

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of [PMID:26177267 Gilmore et al]).  Relative abundances (reported as TPM values [PMID:21816040 Li and Dewey]) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2 [PMID:27043002 Bray et al].  Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least three samples.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.46.0 [PMID:16646809 Symth, PMID:25605792 Ritchie et al].  Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 1.5x (absolute log2 fold change ≥ 0.585) for a given contrast.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: The results of the LIMMA analysis are in processed data file Table_QUO1018505.txt, an Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the ucsf_hc.01_1.G217B systematic gene name. The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. The next 9 columns give KALLISTO estimated counts for each transcript in each sample.  The next columns give LIMMA BH-adjusted p-values for differential expression in each of the 2 contrasts, and the corresponding LIMMA-fit log2 ratios are given in the final 2 columns.  Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), and HcG217B_acc (UCSF1 gene accessions [PMID:35089059]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_C (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  UCSF2_acc and UCSF3_acc give gene accessions from the G217B assemblies of [bioRxiv: 2025.05.05.652209v1].  CR is "critical_region" for genes in the critical region, "chr7" for genes on chromosome 7 but outside of the critical region, and blank for all other genes.  GWEIGHT is a place-holder column for JavaTreeView compatibility.  The estimated counts in this file are sufficient to recapitulate the LIMMA analysis.

organism: Histoplasma ohiense

source_name: fungal cell

growth_protocol: pACT1-HYF1 and control empty vector samples for RNA sequencing were collected from yeast cultures started at OD600 of 0.2 then grown for 2 days at either 37°C or 25°C in standard yeast conditions in HMM media not supplemented with GlcNAc.

extract_protocol:
Cells were collected by filtration, flash frozen in liquid nitrogen, and stored at -80°C prior to RNA extraction.
Library preparation and sequencing was performed at SeqCenter as follows: Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded mRNA prep and 10bp unique dual indices (UDI).  Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4).

tag: temperature

tag: replicate

value: C

value: fungal cell


title: YM_Ctrl_1X_mix10

value: WT


title: endometrium, early secretory, rep8

description: Library name: EMB050


title: endometrium, mid secretory, rep3

description: Library name: EMB022


title: endometrium, early secretory, rep7

description: Library name: EMB044


title: pACT1-HYF1 37 B

description: Library name: HYF1_37B_S34

value: B


title: decay_(-)Glu_rep2_t10


title: Total _30min(-)Glucose_post-labeling(4TU)_rep1


title: YF_Sh4d_2X_mix10

value: Liver


title: endometrium, early secretory, rep6

description: Library name: EMB037


title: decay_(-)Glu_rep2_t15


title: Total ribosome profiling (uL16 loop mutant), rep1

description: Library name: RPL10_Total_1_Rep1


title: decay_(-)Glu_rep2_t5


title: pACT1-HYF1 25 C

description: Library name: HYF1_25C_S29


title: OF_Ctrl_3_mix12

value: Primary Cells


title: pACT1-HYF1 37 A

description: Library name: HYF1_37A_S33

value: A


title: VOM_4d_1_mix13

value: Hepatocyte


title: decay_(-)Glu_rep2_t0


title: pACT1-HYF1 25 B

description: Library name: HYF1_25B_S28


title: endometrium, early secretory, rep5

description: Library name: EMB035


title: decay_(-)Glu_rep1_t45


title: OF_Ctrl_1_mix12


title: OF_Ctrl_2_mix12


title: Control 37 C

description: Library name: EV_37C_S32

value: Control


title: pACT1-HYF1 25 A

description: Library name: HYF1_25A_S27


title: endometrium, early secretory, rep3

description: Library name: EMB028

value: endometrium


title: VOF_4d_3X_mix11

value: PH


title: decay_(-)Glu_rep1_t30


title: decay_(-)Glu_rep1_t20


title: VOF_52h_3_mix11


title: decay_(-)Glu_rep1_t15


title: endometrium, early secretory, rep1

description: Library name: EMB020


title: YF_Sh4d_1X_mix11

value: Sham surgery


title: endometrium, proliferative, rep6

description: Library name: EMB077

value: proliferative


title: decay_(-)Glu_rep1_t10


title: Control 37 A

description: Library name: EV_37A_S30


title: YF_Sh2d_1X_mix11


title: Control 25 B

description: Library name: EV_25B_S25


title: YF_Sh2d_2X_mix10


title: endometrium, proliferative, rep4

description: Library name: EMB068


title: endometrium, early secretory, rep4

description: Library name: EMB029

value: early secretory


title: endometrium, proliferative, rep5

description: Library name: EMB070


title: decay_(-)Glu_rep1_t5


title: decay_(-)Glu_rep1_t0


title: endometrium, proliferative, rep3

description: Library name: EMB067


title: endometrium, early secretory, rep2

description: Library name: EMB027


title: VOM_Sh2d_3_mix9


title: WT_10DAG_rep2

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

institute: Pusan National University

description:
Library name: WT_2
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using trimmomatic-0.39 and cutadapt 2.8), then mapped to ath(mirBase V22) whole genome using STAR-2.5.3a
The quantification of reads was processed using COMPSRA.
Assembly: ath(mirBase V22)
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 2 d at 4℃. The seeds were sown on 0.7% (w/v) agar plates containing on-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22℃ under SD conditions (8-h-light/16-h-dark cycle).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: No treatment

value: whole seedlings

value: WT (Col-0)

value: no treatment


title: decay_(+)Glu_rep2_t45


title: Control 25 A

description: Library name: EV_25A_S24


title: Control 37 B

description: Library name: EV_37B_S31


title: decay_(+)Glu_rep2_t30


title: WT_10DAG_rep1

description:
Library name: WT_1
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.


title: VOM_Sh2d_1_mix9


title: VOM_Sh2d_2_mix9


title: decay_(+)Glu_rep2_t20


title: endometrium, proliferative, rep1

description: Library name: EMB059


title: endometrium, proliferative, rep2

description: Library name: EMB065


title: VOM_52h_3X_mix9


title: decay_(+)Glu_rep2_t15


title: AtC3H26OX_10DAG_rep1

description:
Library name: C3H26_OX_1
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

value: AtC3H26 overexpressing (Col-0)


title: Control 25 C

description: Library name: EV_25C_S26

value: C

value: fungal cell


title: VOM_52h_2_mix9

value: WT


title: ProteinA_control

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Library name: InputA

data_processing:
The nf-core/chipseq pipeline (v2.0.0) was utilized to process ChIP-seq data. Preprocessed reads were aligned to the GRCm38 reference genome using bowtie2; the rest of the pipeline was run using default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Enrichment tracks of bound-TFs or histone marks in BigWig format.
Supplementary files format and content: MACS2 called peaks in BED-like narrowPeak or broadPeak format.
Supplementary files format and content: HOMER peak annotations: tab-delimited text file.

growth_protocol: Stably transduced LβT2-FLAG-mFoxL2 cells were seeded in 15 cm tissue culture plates in DMEM supplemented with 10% FBS.

extract_protocol:
Cross-linking was achieved by the addition of a formaldehyde solution directly to the culture medium to a final concentration of 1%.  Cross-linked complexes suitable for ChIP studies were prepared.  Duplicate samples for each of vehicle or activin A treatment group consisted of pooled samples from three 15 cm plates.  Target-specific antibodies were added to enrich for either SMAD2/3-, FLAG-FOXL2- or H3K27ac-bound complexes.  Antibody-bound complexes were enriched with Protein-A or Protein-G magnetic DYNA beads.
Sequencing libraries appropriate for Illumina platforms were prepared for ChIP DNA fragments using NEXTFlex DNA sequencing kits (Bioo Scientific, Austin, TX). Briefly, fragments were blunted using the Klenow fragment followed by the addition of 3’-overhangs and ligation of barcoded adapters, with intervening cleanup steps with magnetic beads/PEG. After PCR amplification with adapter-specific primers, 300-400 bp fragments were size-selected by differential PEG precipitation onto magnetic beads. ChIP-seq libraries were sequenced for 51 cycles to a depth of 20 million reads on an Illumina HiSeq2500 sequencer using single-end 50 bp reads.

treatment_protocol: After a recovery period of 24h, DOX-induction was initiated by addition to a fresh medium of DOX to a final concentration of 2% (w/v) for 48 h. After 48 h, the cells were washed and equilibrated for 2 h in DMEM supplemented with 2% FBS before adding vehicle or 1 nM activin A for 1 h.

value: gonadotrope

value: Vehicle

tag: chip antibody

value: Protein-A (Abcam, ab214288)


title: activin_SMAD2_3_IP_REP2

description: Library name: D-anti-hSmad2-3-IP

value: Activin A

value: IgG-purified rabbit anti-SMAD2/3 (Wylie Vale lab; Salk Institute)


title: decay_(+)Glu_rep2_t10


title: decay_(+)Glu_rep2_t5


title: AtC3H3OX_10DAG_rep2

description:
Library name: C3H3_OX_2
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

value: AtC3H3 overexpressing (Col-0)


title: activin_H3K27_IP_REP2

description: Library name: D-anti-H3K27-IP

value: anti-H3K27ac (Abcam, ab4729, RRID:AB_2118291)


title: VOM_52h_1_mix9

value: Liver

value: Primary Cells

value: Hepatocyte

value: PH


title: VOM_Ctrl_3_mix8


title: activin_FLAG_IP_REP2

description: Library name: D-anti-Flag-IP

value: M2-anti-FLAG MAb (Sigma-Aldrich, F1804, RRID:AB_262044)


title: decay_(+)Glu_rep2_t0


title: activin_SMAD2_3_IP_REP1

description: Library name: C-anti-hSmad2-3-IP


title: decay_(+)Glu_rep1_t45


title: Xenium in situ spatial transcriptomics of heart_P5

type: RNA

first: Abdelahhad

last: Barbour

address: 124 Edward st

institute: University of Toronto

description: 10x Genomics Xenium Analyzer

data_processing:
Raw Xenium imaging data were processed with Xenium Onboard Analysis to detect fluorescent puncta and decode transcripts using the panel codebook.
Decoded transcripts were quality-filtered (Q-score ≥20), deduplicated across overlapping FOVs, and registered to global x–y–z coordinates relative to the morphology image.
Nuclei were segmented from DAPI; cell boundaries were defined by multimodal cell-segmentation staining, and transcripts were assigned to cells.
barcodes.tsv.gz: Cell IDs matching columns of counts.
features.tsv.gz: Feature (gene) IDs/names matching rows.
matrix.mtx.gz: Sparse counts matrix (features × cells).
cell_feature_matrix.h5: HDF5 per-cell counts (MEX equivalent).
cells.parquet: Per-cell metadata and centroids (µm).
cell_boundaries.parquet: Cell boundary polygons (global µm coords).
transcripts.parquet: One row per decoded transcript with coords/Q.
gene_panel.json — Probe panel/codebook metadata.
Morphology.ome.tif — Stitched morphology image (OME-TIFF).

extract_protocol:
Fresh heart tissue was formalin-fixed and paraffin-embedded (FFPE); 10 µm sections were cut and mounted on Xenium-compatible slides for in situ processing.
Spatial Transcriptomics library were prepared with 10x Genomics Xenium V1, with slides, reagents and kits according to manufacturer's construction.

value: Heart

tag: tissue type

value: Mixed Tissue


title: VOM_Ctrl_2_mix8


title: Xenium in situ spatial transcriptomics of heart_P4

description: 10x Genomics Xenium Analyzer


title: activin_H3K27_IP_REP1

description: Library name: C-anti-H3K27-IP


title: YM_Ctrl_3_mix7


title: Xenium in situ spatial transcriptomics of heart_P3

description: 10x Genomics Xenium Analyzer


title: AtC3H26OX_10DAG_rep2

description:
Library name: C3H26_OX_2
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

value: whole seedlings

value: AtC3H26 overexpressing (Col-0)

value: no treatment


title: decay_(+)Glu_rep1_t30


title: decay_(+)Glu_rep1_t20


title: activin_FLAG_IP_REP1

description: Library name: C-anti-Flag-IP

value: gonadotrope


title: YM_Ctrl_2_mix7

value: WT


title: decay_(+)Glu_rep1_t15


title: YM_Ctrl_1_mix7


title: Xenium in situ spatial transcriptomics of heart_P1

description: 10x Genomics Xenium Analyzer


title: vehicle_SMAD2_3_IP_REP2

description: Library name: B-anti-hSmad2-3-IP

value: Vehicle


title: vehicle_H3K27_IP_REP2

description: Library name: B-anti-H3K27-IP


title: AtC3H3OX_10DAG_rep1

description:
Library name: C3H3_OX_1
Gene expression in 10-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.


title: VOF_Sh4d_2_mix6

value: Sham surgery


title: decay_(+)Glu_rep1_t10


title: vehicle_FLAG_IP_REP2

description: Library name: B-anti-Flag-IP


title: decay_(+)Glu_rep1_t5


title: VOM_Ctrl_1_mix8


title: Xenium in situ spatial transcriptomics of heart_S3

description: 10x Genomics Xenium Analyzer


title: Xenium in situ spatial transcriptomics of heart_S2

description: 10x Genomics Xenium Analyzer


title: VOF_Sh4d_1_mix6


title: Xenium in situ spatial transcriptomics of heart_S1

description: 10x Genomics Xenium Analyzer


title: vehicle_SMAD2_3_IP_REP1

description: Library name: A-anti-hSmad2-3-IP

value: IgG-purified rabbit anti-SMAD2/3 (Wylie Vale lab; Salk Institute)


title: Cas9 Positif sans guide

city: Marseille

first: Eduardo

last: GASCON

address: 27 bd Jean Moulin

country: France

institute: INT Timone

description:
Library name: Cas9_Positif_sans_guide
Comma separated tabular count file of mutation

data_processing:
bcl2fastq, cutaDAPT, blastn
Supplementary files format and content: comma separated tabular file of mutations for the alignments

source_name: brain

extract_protocol:
FANS isolated nuclei were lysed using Thermo direct lysis buffer and used for gDNA downstream applications
QIAseq 1-Step Amplicon Library Kit (Qiagen, ref. 180419)

value: brain

value: neural cells


title: VOF_4d_1_mix6

value: Liver


title: vehicle_H3K27_IP_REP1

description: Library name: A-anti-H3K27-IP

value: anti-H3K27ac (Abcam, ab4729, RRID:AB_2118291)


title: C1qtnf6-KO, gd19.5, RNA-seq, replicate 5

city: Yangzhou

first: Yuchen

state: Jiangsu

address: Wenhui Road Yangzhou Citr No.48

institute: College of Veterinary Medicine Yangzhou University

description: Library name: C1qtnf6-KO gd19.5, RNA-seq, replicate 3

data_processing:
RNA-seq reads were trimmed with Trim Galore v0.6.4., and then aligned to the mouse reference genome (GRCm38) using STAR v2.7.3a. Gene-level read counts were calculated by using the featureCount function of subread v2.0.0.
Assembly: GRCm38
Supplementary files format and content: tab-delimited table, gene-level read counts

source_name: maternal-fetal interface

extract_protocol:
Total RNA was extracted using Trizol reagent (Qiagen, 74004) with on-column DNase digestion.
RNA-seq libraries were construction by using TruSeq stranded mRNA sample preparation kit (Illumina), and sequenced as 150 bp paired-end reads with HiSeq2500 (Illumina) platform.

value: maternal-fetal interface


title: Xenium in situ spatial transcriptomics of heart_P2

city: Toronto

description: 10x Genomics Xenium Analyzer


title: Skin, SspA/HDM-treated (SH)

city: Charlestown

first: Jin Mo

last: Park

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description: Xenium In Situ

hyb_protocol: The processed slides were subjected to probe hybridization and imaging in the Xenium Analyzer and post-run H&E staining.

scan_protocol: Raw image data were captured by the Xenium Analyzer.

data_processing:
Data were processed for spatial analysis using the Xenium Onboard Analysis pipeline.
Decoded transcripts with assigned Phred-scaled Q-Scores and high-resolution morphology images

source_name: Whole dorsal skin

label_protocol: 5-µm mouse skin sections sliced from formalin-fixed paraffin-embedded blocks were mounted onto Xenium slides and processed for deparaffinization and decrosslinking.

treatment_protocol: Shaved and depilated mouse dorsal skin was treated with epicutaneous PBS or epicutaneous SspA and HDM.

value: Epicutaneous SspA+HDM


title: vehicle_FLAG_IP_REP1

description: Library name: A-anti-Flag-IP

value: M2-anti-FLAG MAb (Sigma-Aldrich, F1804, RRID:AB_262044)


title: Cas9 Positif guide Sa4

description:
Library name: Cas9_Positif_guide_Sa4
Comma separated tabular count file of mutation


title: VOF_Sh2d_2_mix5

value: Primary Cells

value: Hepatocyte


title: Cas9 Positif guide Sa2

description:
Library name: Cas9_Positif_guide_Sa2
Comma separated tabular count file of mutation


title: C1qtnf6-KO, gd19.5, RNA-seq, replicate 4

last: Tang

description: Library name: C1qtnf6-KO gd19.5, RNA-seq, replicate 2


title: VOF_Sh2d_1_mix5


title: Cas9 Positif guide Sa1

description:
Library name: Cas9_Positif_guide_Sa1
Comma separated tabular count file of mutation


title: Bimagrumab-treated_Mouse15

description:
Library name: 040125-15-Bima3-B6-A
10X Genomics sc-ATAC assay

library_source: genomic single cell

data_processing:
Single Nuclei ATAC-seq sequencing data were processed using the CellRanger-ATAC pipeline version 2.2.0 with the provided mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Peak-associated cut-site count matrices for cell-called barcodes in Hierarchical Data Format (HDF5)
Supplementary files format and content: Motif-overlapping cut-site count matrices for cell-called barcodes in Hierarchical Data Format (HDF5)
Supplementary files format and content: Lists of barcode-associated DNA fragments in BED-like tabular format
Supplementary files format and content: Peak to-gene annotations in tabular format
Supplementary files format and content: Peak to-motif associations in BED format
Supplementary files format and content: Lists of called-peaks in BED format
Supplementary files format and content: Per barcode QC and summary metrics in CSV format

source_name: pituitary

growth_protocol: Animals were on a 12-hour on, 12-hour off light cycle, with lights on at 7 AM and off at 7 PM. Pituitaries were collected from male mice aged 8 weeks of C57BL/6 background strains.

extract_protocol:
Snap-frozen pituitaries were thawed on ice. For nuclei isolation, a modified protocol from Mathys et al Nat 2019 was followed, all on ice. RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCL2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized with 10 strokes (loose pestle) in an individual autoclaved dounce glass homogenizer (1ml, VWR cat# 71000-514). The homogenate was filtered through a 40-micrometer cell strainer. The volume was measured and an equal volume of 50% OptiPrep was added. The gradient was centrifuged using an SW41 rotor at 9200 rpm and at 4C for 25 min. Nuclei were collected from the interphase between 30% and 35% OptiPrep. The nuclei were washed, resuspended either in 1x nuclei dilution buffer for snATACseq (10X Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted on an Invitrogen Countess II cell counter. ii) Dissociated pituitary cells were cryopreserved in 90% FBS/10% DMSO and shipped to New York on dry-ice. Upon arrival, cells were stored in liquid nitrogen. On the day of an experiment, the vial was removed from liquid nitrogen on dry-ice, thawed quickly in a 37C waterbath, and cells were serially diluted with 10% FBS /DMEM until a minimum volume of 8ml was reached. Cells were centrifuged at 300xg for 5min, resuspended in 1ml of medium and counted. Nuclei were isolated from all cells remaining after the scGEM Drop-seq RNA-seq assay was done. Cells were centrifuged at 500g for 5min at 4C. The supernatant was carefully removed and 0.1X lysis buffer (1x: 10mM Tris-HCL pH 7.5, 10mM NaCl, 3mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 5min incubation on ice, 1ml of wash buffer was added. The nuclei were pelleted at 500xg for 5min at RT, resuspended either in 1X PBS/0.04% BSA for scGEM Drop-seq RNA-seq or in diluted nuclei buffer for snATAC-seq. Nuclei were counted and the concentration adjusted to run the given assay.
snATACseq was performed as described (10x Genomics), following the Chromium Single Cell ATAC Reagent Kits V1.1 User Guide. Nuclei were counted on a Nexclome instrument, and the final concentration was used to calculate the volume of nuclei stock to use. Transposition was performed in 10 microliter at 37C for 60min. Then the Chromium Chip E (PN-2000121) was loaded to target up to 10,000 nuclei. Barcoding was performed in the emulsion for 12 cycles following the Chromium protocol. Each library was tagged with a different index for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262). Quality control and quantification of the libraries were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the Cedars-Sinai Core on Illumina Novaseq X using 98+26 paired-end reads.

treatment_protocol: Nine-week-old male C57BL6/N mice were injected with a single dose of 20 mg/kg of IgG or Bimagrumab subcutaneously. Pituitary glands were flash-frozen in liquid N2 and subjected to snATAC-seq.

value: pituitary

value: all pituitary cells

value: Male

value: 9 weeks

tag: genetic modification

value: wild-type

value: Bimagrumab


title: VOF_52h_2_mix5

value: WT

value: PH


title: Bimagrumab-treated_Mouse14

description:
Library name: 040125-14-Bima2-B6-A
10X Genomics sc-ATAC assay


title: C1qtnf6-KO, gd19.5, RNA-seq, replicate 3

description: Library name: C1qtnf6-KO gd19.5, RNA-seq, replicate 1


title: VOF_52h_1_mix5


title: Cas9 Negatif sans guide

description:
Library name: Cas9_Negatif_sans_guide
Comma separated tabular count file of mutation

value: brain


title: decay_(+)Glu_rep1_t0

data_processing:
For ribosome profiling, total mRNA levels and polysomes enrichment analysis: adapter sequence was trimmed using cutadapt, reads were alligned to rRNA using bowtie, reads not mapping to rRNA were alligned to the yeast genome using tophat2, and the counts per gene was performed using featurecount.For SLAMseq, reads were mapped, fiiltered using multiple quality criteria, followed by quantification of labeled reads and bases using SLAM dunk.
Assembly: For ribosome profiling and total mRNA levels analysis,yeast genome was downloaded from SGD. For SLAMseq, yeast genome and annotations of transcripts 3'UTR was perfromed as described:  H. Alalam, J. A. Zepeda-Martínez, and P. Sunnerhagen, ‘Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets.’, RNA, vol. 28, no. 6, pp. 905–915, Jun. 2022, doi: 10.1261/rna.079077.121.
Supplementary files format and content: For ribosome profiling and total mRNA levels analysis, text file containing raw counts per gene. for SLAMseq anaysis, text file containing the SLAMSeq statistics


title: Bimagrumab-treated_Mouse13

description:
Library name: 033125-13-Bima1-B6-A
10X Genomics sc-ATAC assay


title: VOF_4d_2_mix6


title: Wild-type, gd19.5, RNA-seq, replicate 3

description: Library name: wild-type gd19.5, RNA-seq, replicate 3


title: Skin, mock-treated (mock)

description: Xenium In Situ

value: Mock (epicutaneous PBS)


title: VOF_Ctrl_3_mix2

value: Liver


title: IgG-treated_Mouse12

description:
Library name: 040125-12-IgG3-B6-A
10X Genomics sc-ATAC assay

value: IgG


title: Cas9 Negatif guide Sa2

description:
Library name: Cas9_Negatif_guide_Sa2
Comma separated tabular count file of mutation

value: neural cells


title: VOF_Ctrl_2_mix2


title: Wild-type, gd19.5, RNA-seq, replicate 1

description: Library name: wild-type gd19.5, RNA-seq, replicate 1

value: maternal-fetal interface


title: IgG-treated_Mouse11

description:
Library name: 033125-11-IgG2-B6-A
10X Genomics sc-ATAC assay


title: Cas9 Negatif guide Sa1

description:
Library name: Cas9_Negatif_guide_Sa1
Comma separated tabular count file of mutation


title: C1qtnf6-KO, gd16.5, RNA-seq, replicate 5

description: Library name: C1qtnf6-KO gd16.5, RNA-seq, replicate 3


title: tropicalis NF33 fg mesendo Rfx6 LOF rep3

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

description:
Library name: tropicalis_NF33_fg_mesendo_Rfx6_LOF_rep3
tropicalis_NF33_fg_mesendo_Rfx6_LOF_rep3

data_processing:
Quality of reads was asessed with factqc
Quality trimmed reads in fastq format were mapped and quantified using RSEM (v1.3.0)  with bowtie2
Assembly: Xenopus Tropicalis v10
Supplementary files format and content: raw counts and TPM files in .txt format

organism: Xenopus tropicalis

source_name: embryo

growth_protocol: embryos incubated at room temperature

extract_protocol:
RNA was extracted using the Macherey-Nagel Nucleospin RNA extraction kit according to manufacturer's insructions.
Library prep was performed using Illumina’s TruSeq stranded mRNA library preparation kit according to manufacturer's instructions.

treatment_protocol: 40uM cyclopamine (Tocris #1623), 100nM BMS493 (Tocris #3509) treatment from NF15-33.   1ng total Rfx6 ,morpholino oligo or 5bp mismatch oligo  (500pg per cell) injected at 2-cell stage.

value: embryo

value: Xenopus Tropicalis, NXR_1018, Xtr.NigerianSt549

value: dissected NF33 foregut tissue

value: wild type

value: DMSO 0.1% + 1ng rfx6 MO


title: OF_Ctrl_3X_mix1

data_processing:
Base-calling was performed with bcl2fastq program (v2.20).
By using the celseq2 pipeline (https://github.com/yanailab/celseq2), demultiplexing of the raw data was performed, and also UMI counts were calculated.
Using binomial statistics, the number of UMI was converted to transcript counts. The mathematical formula is described in "Validation of noise models for single-cell transcriptomics (PMID: 24747814)". In this calculation method, if the UMI is the maximum value of 4096, the transcriptome count diverges to infinity and cannot be converted, so 9genes (Fga, Mt-Rnr2, Mt-Nd4, Mt-Cytb, Mup14, Mup20, Mup8, Mup13, Mup15) with a UMI count of 4096 in at least one sample genes were excluded from the analysis.
Lowly expressed genes were filtered out, and batch correction of transcript counts was performed using Combat-Seq(PMID: 33015620). The numbers following the string “mix” at the end of each sample name are the same for the same batch, and this information was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Comma Separated Values files include Batch correlated transcript counts of all samples

value: Primary Cells

value: Hepatocyte


title: tropicalis NF33 fg mesendo Rfx6 LOF rep2

description:
Library name: tropicalis_NF33_fg_mesendo_Rfx6_LOF_rep2
tropicalis_NF33_fg_mesendo_Rfx6_LOF_rep2


title: Fshb-Enh2-KO_Mouse5

description:
Library name: 040125-5-A6-2-4-KO-A
10X Genomics sc-ATAC assay

value: pituitary

value: all pituitary cells

value: Male

value: 8 weeks

value: KO of Fshb-Enhancer2


title: tropicalis NF33 fg mesendo Rfx6 LOF rep1

description:
Library name: tropicalis_NF33_fg_mesendo_Rfx6_LOF_rep1
tropicalis_NF33_fg_mesendo_Rfx6_LOF_rep1


title: C1qtnf6-KO, gd16.5, RNA-seq, replicate 4

description: Library name: C1qtnf6-KO gd16.5, RNA-seq, replicate 2


title: OF_Ctrl_2X_mix1

value: WT


title: C1qtnf6-KO, gd16.5, RNA-seq, replicate 3

description: Library name: C1qtnf6-KO gd16.5, RNA-seq, replicate 1


title: OF_Ctrl_1X_mix1

value: Liver


title: Cas9 Negatif guide Sa4

description:
Library name: Cas9_Negatif_guide_Sa4
Comma separated tabular count file of mutation

value: brain


title: Fshb-Enh2-KO_Mouse2

description:
Library name: 033125-2-A7-4-9-KO-A
10X Genomics sc-ATAC assay


title: YM_Ctrl_3X_mix1


title: tropicalis NF33 fg mesendo RA LOF rep3

description:
Library name: tropicalis_NF33_fg_mesendo_RA_LOF_rep3
tropicalis_NF33_fg_mesendo_RA_LOF_rep1


title: Wild-type, gd16.5, RNA-seq, replicate 3

description: Library name: wild-type gd16.5, RNA-seq, replicate 3

value: wild-type


title: Wild-type, gd16.5, RNA-seq, replicate 2

description: Library name: wild-type gd16.5, RNA-seq, replicate 2

value: maternal-fetal interface


title: Wild-type, gd19.5, RNA-seq, replicate 2

description: Library name: wild-type gd19.5, RNA-seq, replicate 2


title: WildType_Mouse1

description:
Library name: 032525-1-A7-4-2-WT-A
10X Genomics sc-ATAC assay