title: S-1076_F_0.1_0.7_perc_meoh rep1

description: Library name: d1239.S-1076_F_0.1_0.7_perc_meoh


title: ABS-CSF-C05

status: Public on Mar 11 2026

type: SRA

city: New York

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

description: Library name: ABS-CSF-C05

library_source: transcriptomic

data_processing:
Raw sequencing files was demultiplexed with bcl2fastq
Samples were uniformly processed using RAPiD-nf, an efficient RNA-Seq processing pipeline implemented in the NextFlow framework(Di Tommaso et al. 2017). Following adapter trimming with Trimmomatic (version 0.36)(Bolduc, n.d.), all samples were aligned to the hg38 build (GRCh38.primary_assembly) of the human reference genome using STAR (2.7.2a)(Dobin et al. 2013), with indexes created from GENCODE, version 30(Harrow et al. 2012). Gene expression was quantified using RSEM (1.3.1)(B. Li and Dewey 2011). Quality control was performed using SAMtools(H. Li et al. 2009) and Picard, and the results were collated using MultiQC(Ewels et al. 2016).
Assembly: hg38
Supplementary files format and content: csv files contatining count and tpm data

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA extraction from fresh frozen tissue or cells – starting material is homogenized in TRIzol reagent using a series of needles for trituration. The homogenized sample undergoes phase separation with the addition of chloroform,  the upper aqueous phase of the mixture then follows the RNeasy Mini procedure (Qiagen, 74106). A series of washes will purify the final eluted total RNA. The RNeasy Mini portion of the protocol is processed on the QIAcube Connect automated platform (Qiagen, 9002864) for higher throughput.
RNA sequencing libraries are prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche 07962304001) in accordance with the manufacturer’s instructions. Samples are normalized to 500ng and undergo rRNA depletion through oligo hybridization and RNase H treatment. DNase treatment removes DNA oligos. Samples are fragmented to 350bp inserts and undergo cDNA generation. Samples undergo A-tailing and are ligated to Illumina sequencing adapters and amplified. Final libraries are quantified using the Qubit Fluorometer (Life Technologies) or Spectramax M2 (Molecular Devices) and Fragment Analyzer (Agilent). Libraries are sequenced on an Illumina sequencer.

tag: tissue

tag: genotype

value: CTL

tag: subject id

tag: gender

value: female

tag: age

value: Not Applicable


title: MT_rep1

city: Jatai

first: Bruna

middle: Tereza Thomazini

last: Zanella

state: Goias

country: Brazil

institute: Federal University of Jatai (UFJ)

description: Library name: MT1

data_processing:
Transcriptome was obtained through the NovaSeq 6000 platform (Illumina) with 150 base pairs, paired-end, and 6 GB data per sample
Quality of the sequencing was evaluated through the software FastQC version 0.11.8
Adapters were removed, and the reads were filtered using the software Trimmomatic using a phred score >33
De novo transcriptome assembly was performed using Trinity software
Contigs were mapped and annotated based on the proteome data of Danio rerio (GRcz11), Pygocentrus nattereri (Pygocentrus_nattereri-1.0.2), and Astyanax mexicanus (Astyanax_mexicanus-2.0) using the Bowtie2 aligner
Counts were normalized by the median of ratios method, with the counts divided by sample-specific size factors, using DESeq2 package in R environment. Only genes with counts mean >10 between samples were maintained.
Assembly: A. mexicanus (Astyanax_mexicanus-2.0), D. rerio (GRcz11) and P. nattereri (Pygocentrus_nattereri-1.0.2)
Supplementary files format and content: tab-delimited file with normalized gene counts for every gene and every sample

organism: Piaractus mesopotamicus

source_name: Fast-twitch muscle

growth_protocol: Fish were fed ad libitum once a day with commercial food. Cells were cultured in completed growth medium (DMEM supplemented with 10% fetal bovine serum and 1% antiobiotics)

extract_protocol:
The total RNA was extracted using TRIzol® Reagent (Thermo Fisher Scientific), following the manufacturer's protocol guidelines.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol

value: Fast-twitch muscle

value: WT

tag: treatment

value: Ad libitum feeding with commercial food


title: S-1076_F_std_0.7_perc_meoh rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: Library name: d1235.S-1076_F_std_0.7_perc_meoh

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.1.1645, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Komagataella phaffi transcripts and exogenous transgenes were quantified using salmon 1.6.0
Gene-level summaries created with tximport 1.24.0
Assembly: Komagataella phaffi WT (strain Y11430) with transcriptome phaffi_plus_240125Lov_transgenes
Supplementary files format and content: phaffi_plus_240125Lov_transgenes.fa.gz is fasta format transcriptome used in salmon quantitation
Supplementary files format and content: 240125Lov_transcript2gene.txt.gz is a tab-delimited file that associates transcript and gene identifiers
Supplementary files format and content: 240125Lov_annotation.txt.gz is a tab-delimited annotation file associating gene names with gene IDs.
Supplementary files format and content: 240125Lov_intCt.txt.gz is a tab delimited file of integrer count data
Supplementary files format and content: 240125Lov_l2tpm.txt.gz is a tab-delimited file of log2 TPM data with a +1 offset.

molecule: polyA RNA

organism: Komagataella phaffii

source_name: K. phaffii S-1076

growth_protocol: Strains were grown in 3 mL cultures in 24-deep well plates (toom temperature, 600 RPM, 3 mm orbit). Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone). Cultures were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and cells resuspended in fresh media with the described quantity of methanol and corresponding co-feed. Supernatant samples were collected after 18 hrs and 24 hrs of production for the co-feed screen and the knockout screen respectively, and analyzed.

extract_protocol:
Qiagen RNeasy 96 kit
Nextera XT DNA Library Preparation Kit with the Illumina DNA/RNA UD Indexes

tag: strain

tag: carbon cofeed

value: Rhamnose

tag: cofeed concentration_(m)

tag: meoh concentration_(v/v_%)


title: S-1076_F_std_0.7_perc_meoh rep1

description: Library name: d1233.S-1076_F_std_0.7_perc_meoh


title: S-1076_E_0.1_0.7_perc_meoh rep2

description: Library name: d1230.S-1076_E_0.1_0.7_perc_meoh

value: Sucrose


title: MC_rep3

description: Library name: MC3

tag: cell type

value: Primary muscle cell culture

value: Complete growth medium


title: ABS-CSF-C14

description: Library name: ABS-CSF-C14

value: male


title: MC_rep2

description: Library name: MC2


title: S-1076_E_0.1_0.7_perc_meoh rep3

description: Library name: d1231.S-1076_E_0.1_0.7_perc_meoh


title: S-1076_F_std_0.7_perc_meoh rep2

description: Library name: d1234.S-1076_F_std_0.7_perc_meoh


title: NEUXU870-AJT

description: Library name: NEUXU870-AJT

value: ALS


title: NEUJZ071-VTN

description: Library name: NEUJZ071-VTN


title: S-1076_E_0.5_0.7_perc_meoh rep2

description: Library name: d1227.S-1076_E_0.5_0.7_perc_meoh


title: S-1076_E_0.5_0.7_perc_meoh rep3

description: Library name: d1228.S-1076_E_0.5_0.7_perc_meoh


title: MC_rep1

description: Library name: MC1


title: S-1076_E_0.5_0.7_perc_meoh rep1

description: Library name: d1226.S-1076_E_0.5_0.7_perc_meoh


title: S-1076_E_0.1_0.7_perc_meoh rep1

description: Library name: d1229.S-1076_E_0.1_0.7_perc_meoh


title: S-1076_E_std_0.7_perc_meoh rep2

description: Library name: d1224.S-1076_E_std_0.7_perc_meoh


title: S-1076_D_std_0.7_perc_meoh rep3

description: Library name: d1222.S-1076_D_std_0.7_perc_meoh

value: NoCofeed


title: Primary microglia, cKO, biol rep1

city: Suzhou

first: Lele

last: Liu

state: Jiangsu

address: No. 199, Ren'ai Road

department: college of pharmacy

country: China

institute: Soochow University

description: Library name: cKO1

data_processing:
Quality analysis: Dr.TOM II (v2)
Quality control: SOAPnuke (v2.2.1, proportion of N: 0.05, quality limit:0.2)
Alignment: Bowtie2 (v2.4.5) default parameters
Expression analysis: DESeq2 (v1.34.0)
Assembly: mm39
Supplementary files format and content: Microsoft Excel file include raw counts and FPKM values for each sample

organism: Mus musculus

source_name: Brain

growth_protocol: Primary microglia were maintained in DMEM/F12 supplement with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol Reagent (invitrogen). 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Tamoxifen was administered to mice via intraperitoneal injection (i.p., 100 mg/kg) for 5 consecutive days at postnatal day 28 (P28). Thirty days after the final injection, cardiac perfusion was performed to harvest mouse brains, followed by microglial isolation via flow cytometry.

value: Brain

tag: cell line

value: primary microglia

value: microglia


title: Primary microglia, cKO, biol rep2

description: Library name: cKO2


title: S-1076_E_std_0.7_perc_meoh rep3

description: Library name: d1225.S-1076_E_std_0.7_perc_meoh


title: NEUUA448-AXH

description: Library name: NEUUA448-AXH


title: S-1076_D_std_0.7_perc_meoh rep2

description: Library name: d1221.S-1076_D_std_0.7_perc_meoh


title: NEUJC660-UUD

description: Library name: NEUJC660-UUD


title: NEUJB115-NN8

description: Library name: NEUJB115-NN8


title: S-1076_C_0.1_0.7_perc_meoh rep2

description: Library name: d1218.S-1076_C_0.1_0.7_perc_meoh

value: Citrate


title: Primary microglia, Ctrl, biol rep2

description: Library name: Ctrl2


title: Primary microglia, Ctrl, biol rep3

description: Library name: Ctrl3


title: S-1076_C_0.1_0.7_perc_meoh rep1

description: Library name: d1217.S-1076_C_0.1_0.7_perc_meoh


title: S-1076_C_0.1_0.7_perc_meoh rep3

description: Library name: d1219.S-1076_C_0.1_0.7_perc_meoh


title: Primary microglia, cKO, biol rep3

description: Library name: cKO3


title: NEUKZ419-MJ5

description: Library name: NEUKZ419-MJ5


title: Primary microglia, Ctrl, biol rep1

description: Library name: Ctrl1


title: S-1076_C_0.5_0.7_perc_meoh rep3

description: Library name: d1216.S-1076_C_0.5_0.7_perc_meoh


title: S-1076_C_0.5_0.7_perc_meoh rep2

description: Library name: d1215.S-1076_C_0.5_0.7_perc_meoh


title: NEUZA939-NER

description: Library name: NEUZA939-NER


title: S-1076_C_0.5_0.7_perc_meoh rep1

description: Library name: d1214.S-1076_C_0.5_0.7_perc_meoh


title: S-1076_C_std_0.7_perc_meoh rep3

description: Library name: d1213.S-1076_C_std_0.7_perc_meoh


title: S-1076_C_std_0.7_perc_meoh rep2

description: Library name: d1212.S-1076_C_std_0.7_perc_meoh


title: S-1076_E_std_0.7_perc_meoh rep1

description: Library name: d1223.S-1076_E_std_0.7_perc_meoh


title: S-1076_C_std_0.7_perc_meoh rep1

description: Library name: d1211.S-1076_C_std_0.7_perc_meoh


title: NEUAT073-FD5

description: Library name: NEUAT073-FD5


title: S-1076_B_0.1_0.7_perc_meoh rep3

description: Library name: d1210.S-1076_B_0.1_0.7_perc_meoh

value: Galactose


title: S-1076_B_0.1_0.7_perc_meoh rep2

description: Library name: d1209.S-1076_B_0.1_0.7_perc_meoh


title: BV2 cells, knockdown878, biol rep1

description: Library name: knockdown878_1

growth_protocol: BV2 cells were maintained in DMEM supplement with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

treatment_protocol: siRNA was mixed with RNAiMAX in OMEM and incubated for 30 minutes, following which the mixture was added to pre-inoculated cell culture plates for a 24-hour treatment. Subsequently, the medium was replaced with fresh DMEM supplement with 10% FBS and antibiotics, and the cells were cultured for an additional 24 hours.

value: BV2 cells

value: Microglia

value: Nus1 knockdown


title: BV2 cells, knockdown878, biol rep2

description: Library name: knockdown878_2


title: NEAYE577-YEJ

description: Library name: NEAYE577-YEJ

value: Not Applicable


title: ABS-CSF-C06

description: Library name: ABS-CSF-C06

value: CTL

value: female


title: ABS-CSF-C13

description: Library name: ABS-CSF-C13


title: NEUZR978-PZB

description: Library name: NEUZR978-PZB


title: BV2 cells, knockdown644, biol rep3

description: Library name: knockdown644_3


title: S-1076_D_std_0.7_perc_meoh rep1

description: Library name: d1220.S-1076_D_std_0.7_perc_meoh


title: S-1076_B_0.1_0.7_perc_meoh rep1

description: Library name: d1208.S-1076_B_0.1_0.7_perc_meoh


title: S-1076_B_0.5_0.7_perc_meoh rep3

description: Library name: d1207.S-1076_B_0.5_0.7_perc_meoh


title: S-1076_B_0.5_0.7_perc_meoh rep1

description: Library name: d1205.S-1076_B_0.5_0.7_perc_meoh


title: SBU-ABS-003

description: Library name: SBU-ABS-003


title: BV2 cells, knockdown644, biol rep2

description: Library name: knockdown644_2


title: BV2 cells, knockdown878, biol rep3

description: Library name: knockdown878_3


title: S-1076_B_0.5_0.7_perc_meoh rep2

description: Library name: d1206.S-1076_B_0.5_0.7_perc_meoh


title: S-1076_B_std_0.7_perc_meoh rep3

description: Library name: d1204.S-1076_B_std_0.7_perc_meoh


title: S-1076_B_std_0.7_perc_meoh rep2

description: Library name: d1203.S-1076_B_std_0.7_perc_meoh


title: S-1076_B_std_0.7_perc_meoh rep1

description: Library name: d1202.S-1076_B_std_0.7_perc_meoh


title: BV2 cells, NC, biol rep3

description: Library name: NC_3

value: WT


title: NEUX902-YNL

description: Library name: NEUX902-YNL


title: S-1076_J_0.1_1_perc_meoh rep3

description: Library name: d1201.S-1076_J_0.1_1_perc_meoh

value: Xylose


title: NEUYF683-DW9

description: Library name: NEUYF683-DW9


title: Yoda1-treated mouse3

city: Jinan

first: Qinghao

last: Yuan

state: Shandong

address: wenhuaxilu 44

institute: Qilu hospital

description: Library name: Sample6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: skin

growth_protocol: Mice were housed under specific pathogen–free (SPF) conditions (23 ± 2 °C, 12 h light/dark cycle) with ad libitum access to food and water. They were randomly assigned to treatment groups.

extract_protocol:
operation
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: give treatmen drugs in a form of gels via skin

value: skin

value: keratinocytes

value: skin cell


title: S-1076_J_std_1_perc_meoh rep3

description: Library name: d1195.S-1076_J_std_1_perc_meoh


title: S-1076_J_0.1_1_perc_meoh rep1

description: Library name: d1199.S-1076_J_0.1_1_perc_meoh


title: B-shNC-R2

city: Shanghai

first: Xin

last: Xin

address: 320 Yueyang Road, Shanghai 200031, China

institute: University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS)

description: Library name: B-shNC-R2

library_source: other

data_processing:
Raw reads were adapter-trimmed (cutadapt) and size-filtered (25-35 bp). rRNA and tRNA reads were removed (bowtie alignment). Clean reads were aligned to the reference genome and transcriptome (Ensembl v91; HISAT2 and bowtie software). Ribosome periodicity and codon usage were assessed (riboWaltz package), ORFs identified (Price software), and gene-level counts obtained (featureCounts software). Counts were RPKM-normalized (DESeq2 package). Translational efficiency (TE) was calculated as (Ribo-RPKM)/(RNA-seq-RPKM) as previously reported.15 Differential TE was identified (DESeq2 package; fold change (FC)>2, p<0.05, regarded as significant) with GO/KEGG enrichment (clusterProfiler package) and heatmaps (pheatmap package) in R.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM  values for each sample
Library strategy: Ribo-Seq

molecule: other

source_name: not applicable for B-shNC-R2

growth_protocol: Both shNC and shAldh2 AC16 cells were seeded in 10 cm dishes.

extract_protocol:
Total RNA Extraction with TRIzol, Ribosome Isolation via Sucrose Density Gradient Centrifugation.
Raw reads were adapter-trimmed (cutadapt) and size-filtered (25-35 bp). rRNA and tRNA reads were removed (bowtie alignment). Clean reads were aligned to the reference genome and transcriptome (Ensembl v91; HISAT2 and bowtie software). Ribosome periodicity and codon usage were assessed (riboWaltz package), ORFs identified (Price software), and gene-level counts obtained (featureCounts software). Counts were RPKM-normalized (DESeq2 package). Translational efficiency (TE) was calculated as (Ribo-RPKM)/(RNA-seq-RPKM) as previously reported.15 Differential TE was identified (DESeq2 package; fold change (FC)>2, p<0.05, regarded as significant) with GO/KEGG enrichment (clusterProfiler package) and heatmaps (pheatmap package) in R.

treatment_protocol: Cells were treated with 100 μg/mL cycloheximide (CHX) in medium for 3 to 5 minutes after 1 μM RSL3 treated for 12 hours to induce ferroptosis at 37°C. For Ribo-seq analysis, 1 x 107 cells were rinsed with ice-cold PBS containing 100 μg/mL CHX, pelleted (1000g, 10 minutes, 4°C), and saved at -80°C in nuclease-free tubes.

value: not applicable for B-shNC-R2

value: AC16 cells

value: Human hybrid cardiomyocyte


title: S-1076_J_0.5_1_perc_meoh rep1

description: Library name: d1196.S-1076_J_0.5_1_perc_meoh


title: S-1076_J_0.1_1_perc_meoh rep2

description: Library name: d1200.S-1076_J_0.1_1_perc_meoh


title: B-shNC-R1

description: Library name: B-shNC-R1

source_name: not applicable for B-shNC-R1

value: not applicable for B-shNC-R1


title: S-1076_H_0.1_1_perc_meoh rep3

description: Library name: d1192.S-1076_H_0.1_1_perc_meoh

value: Sorbitol


title: S-1076_J_std_1_perc_meoh rep1

description: Library name: d1193.S-1076_J_std_1_perc_meoh


title: Yoda1-treated mouse2

description: Library name: Sample5


title: S-1076_J_std_1_perc_meoh rep2

description: Library name: d1194.S-1076_J_std_1_perc_meoh


title: Yoda1-treated mouse1

description: Library name: Sample4


title: S-1076_H_0.1_1_perc_meoh rep2

description: Library name: d1191.S-1076_H_0.1_1_perc_meoh


title: S-1076_J_0.5_1_perc_meoh rep2

description: Library name: d1197.S-1076_J_0.5_1_perc_meoh


title: NEUCW759-LRC

description: Library name: NEUCW759-LRC

value: ALS

value: male


title: S-1076_H_0.5_1_perc_meoh rep3

description: Library name: d1189.S-1076_H_0.5_1_perc_meoh


title: BV2 cells, NC, biol rep2

description: Library name: NC_2

value: Brain

value: BV2 cells

value: Microglia


title: CST-treated mouse 3

description: Library name: Sample3

value: CST


title: A-shAldh2-R1

description: Library name: A-shAldh2-R1

source_name: not applicable for A-shAldh2-R1

value: not applicable for A-shAldh2-R1


title: A-shAldh2-R2

description: Library name: A-shAldh2-R2

source_name: not applicable for A-shAldh2-R2

value: not applicable for A-shAldh2-R2


title: S-1076_J_0.5_1_perc_meoh rep3

description: Library name: d1198.S-1076_J_0.5_1_perc_meoh

value: Xylose


title: B-shNC-R2-m

description: Library name: B-shNC-R2-m

data_processing:
Raw reads were adapter-trimmed (cutadapt) and size-filtered (25-35 bp). rRNA and tRNA reads were removed (bowtie alignment). Clean reads were aligned to the reference genome and transcriptome (Ensembl v91; HISAT2 and bowtie software). Ribosome periodicity and codon usage were assessed (riboWaltz package), ORFs identified (Price software), and gene-level counts obtained (featureCounts software). Counts were RPKM-normalized (DESeq2 package). Translational efficiency (TE) was calculated as (Ribo-RPKM)/(RNA-seq-RPKM) as previously reported.15 Differential TE was identified (DESeq2 package; fold change (FC)>2, p<0.05, regarded as significant) with GO/KEGG enrichment (clusterProfiler package) and heatmaps (pheatmap package) in R.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM  values for each sample

source_name: not applicable for B-shNC-R2-m

value: not applicable for B-shNC-R2-m


title: S-1076_H_0.5_1_perc_meoh rep2

description: Library name: d1188.S-1076_H_0.5_1_perc_meoh


title: B-shNC-R1-m

description: Library name: B-shNC-R1-m

source_name: not applicable for B-shNC-R1-m

value: not applicable for B-shNC-R1-m


title: CST-treated mouse 2

description: Library name: Sample2

value: skin

value: keratinocytes

value: skin cell

value: WT


title: S-1076_H_std_1_perc_meoh rep3

description: Library name: d1186.S-1076_H_std_1_perc_meoh


title: S-1076_H_0.5_1_perc_meoh rep1

description: Library name: d1187.S-1076_H_0.5_1_perc_meoh


title: S-1076_H_0.1_1_perc_meoh rep1

description: Library name: d1190.S-1076_H_0.1_1_perc_meoh


title: S-1076_H_std_1_perc_meoh rep2

description: Library name: d1185.S-1076_H_std_1_perc_meoh


title: S-1076_H_std_1_perc_meoh rep1

description: Library name: d1184.S-1076_H_std_1_perc_meoh


title: S-1076_G_0.1_1_perc_meoh rep3

description: Library name: d1183.S-1076_G_0.1_1_perc_meoh

value: D-Arabinose


title: WT mESC RNA-seq rep2

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: MES_CDX2_rnaseq_featureCount_10samples_rep2.txt

data_processing:
STAR (v2.7.0d) was used to align the RNA-seq reads to mouse genome (mm10) with gene annotation. FeatuerCounts (v1.5.3) was used to count the read number of each gene (with parameters -T 12 -s 2 -p -g gene_name).
Fastp (v0.19.5) was first used to trimmed and removed low quality ATAC-seq reads and adapter sequences (-a CTGTCTCTTATA --detect_adapter_for_pe -w 12 --length_required 20 -q 30). Reads were aligned to mouse reference genome (hg38) using Bowtie2 v2.3.4.3 with parameters (-p 12 -X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom scripts. Sambamba (v0.7.0) was then used to sort the reads and remove duplicates. MACS2 was used to call peaks
paired-end ChIP-seq reads were first trimmed to remove adapter sequences using cutadapt v2.6 (-a AGATCGGAAGAG -A AGATCGGAAGAG -m 20 -q 30). Reads were aligned to mouse reference genome (mm10) using Bowtie2 v2.3.4.3 with parameters (-X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom script. Picard (v2.6.0, http://broadinstitute.github.io/picard/) was then used to sort the reads and remove duplicates.  MACS2 was used to call peaks (-g mm --keep-dup all -q 0.05 -B).
Genome_build: mm10
Supplementary_files_format_and_content: txt, read count

source_name: mESC

extract_protocol:
(a) Total RNA were extracted from all the treated cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).; (b) For ATAC-seq, samples were washed and then lysed in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501).; (c) The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST, 56383)
(a) Truseq Stranded mRNA sequencing libraries were prepared with 2 μg total RNA according to the manufacturer’s protocol (Yeasen 12300ES24). (b) For ATAC-seq, PCR was then performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411). (c) ChIP-seq libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607)

value: mESC

tag: genotype/variation


title: CST-treated mouse 1

description: Library name: Sample1


title: S-1076_G_0.1_1_perc_meoh rep1

description: Library name: d1181.S-1076_G_0.1_1_perc_meoh


title: rCDX2_R123 OE in mESC RNA-seq

description:
rCDX2_R123 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

data_processing:
STAR (v2.7.0d) was used to align the RNA-seq reads to mouse genome (mm10) with gene annotation. FeatuerCounts (v1.5.3) was used to count the read number of each gene (with parameters -T 12 -s 2 -p -g gene_name).
Fastp (v0.19.5) was first used to trimmed and removed low quality ATAC-seq reads and adapter sequences (-a CTGTCTCTTATA --detect_adapter_for_pe -w 12 --length_required 20 -q 30). Reads were aligned to mouse reference genome (hg38) using Bowtie2 v2.3.4.3 with parameters (-p 12 -X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom scripts. Sambamba (v0.7.0) was then used to sort the reads and remove duplicates. MACS2 was used to call peaks
paired-end ChIP-seq reads were first trimmed to remove adapter sequences using cutadapt v2.6 (-a AGATCGGAAGAG -A AGATCGGAAGAG -m 20 -q 30). Reads were aligned to mouse reference genome (mm10) using Bowtie2 v2.3.4.3 with parameters (-X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom script. Picard (v2.6.0, http://broadinstitute.github.io/picard/) was then used to sort the reads and remove duplicates.  MACS2 was used to call peaks (-g mm --keep-dup all -q 0.05 -B).
Genome_build: mm10 or rn6
Supplementary_files_format_and_content: txt, read count

extract_protocol:
(a) Total RNA were extracted from all the treated cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).; (b) For ATAC-seq, samples were washed and then lysed in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501).; (c) The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST, 56383)
(a) Truseq Stranded mRNA sequencing libraries were prepared with 2 μg total RNA according to the manufacturer’s protocol (Yeasen  12300ES24). (b) For ATAC-seq, PCR was then performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411). (c) ChIP-seq libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607)

value: rCDX2_R123 OE


title: A-shAldh2-R2-m

description: Library name: A-shAldh2-R2-m

source_name: not applicable for A-shAldh2-R2-m

value: not applicable for A-shAldh2-R2-m

value: AC16 cells

value: Human hybrid cardiomyocyte


title: A-shAldh2-R1-m

description: Library name: A-shAldh2-R1-m

source_name: not applicable for A-shAldh2-R1-m

value: not applicable for A-shAldh2-R1-m


title: rCDX2_R23 OE in mESC RNA-seq

description:
rCDX2_R23 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: rCDX2_R23 OE


title: S-1076_G_0.5_1_perc_meoh rep3

description: Library name: d1180.S-1076_G_0.5_1_perc_meoh


title: BV2 cells, knockdown644, biol rep1

description: Library name: knockdown644_1

value: Brain

value: BV2 cells

value: Microglia

value: Nus1 knockdown


title: M5_W83

city: Krakow

first: Jan

last: Potempa

address: Gołębia 24

department: Microbiology

country: Poland

institute: Jagiellonian University

description: Library name: M5_W83

data_processing:
Single-end reads were aligned with STAR v2.7.0f. Gene counts were quantified using featureCounts v2.0.0 with no strand specificity parameter.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human blood using density gradient centrifugation. Monocytes were isolated from the PBMC fraction using magnetic sorting beads (Miltenyi Biotec). Monocytes were differentiated to monocyte-derived macrophages (MDMs) by culturing for 1 week in RPMI 1640 10% FBS with 50 ng/ml human recombinant GM-CSF (Biolegend).

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Prior to infection, the culture medium was replaced with RPMI 1640 2% FBS. MDMs were infected for 24 h at 20 MOI with the P. gingivalis  ATCC 33277 WT strain (ATCC WT) and its isogenic PPAD (delPPAD) and fimbriae: main FimA subunit (delFimA) and accessory subunits - FimE (K04) and FimC (OZ5001C) – mutants or W83 WT (W83) strain. Cells obtained from 5 different donors were used for this analysis.

value: Monocyte-derived macrophages

value: Pg W83 WT infection


title: S-1076_G_0.5_1_perc_meoh rep1

description: Library name: d1178.S-1076_G_0.5_1_perc_meoh


title: M5_OZ5001C

description: Library name: M5_OZ5001C

value: Pg ATCC 33277-derived FimC mutant infection


title: S-1076_G_0.5_1_perc_meoh rep2

description: Library name: d1179.S-1076_G_0.5_1_perc_meoh


title: S-1076_G_0.1_1_perc_meoh rep2

description: Library name: d1182.S-1076_G_0.1_1_perc_meoh


title: M5_K04

description: Library name: M5_K04

value: Pg ATCC 33277-derived FimE mutant infection


title: rCDX2_R13 OE in mESC RNA-seq

description:
rCDX2_R13 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: rCDX2_R13 OE


title: S-1076_F_0.1_1_perc_meoh rep3

description: Library name: d1174.S-1076_F_0.1_1_perc_meoh

value: Rhamnose


title: S-1076_G_std_1_perc_meoh rep3

description: Library name: d1177.S-1076_G_std_1_perc_meoh

value: D-Arabinose


title: S-1076_F_0.1_1_perc_meoh rep2

description: Library name: d1173.S-1076_F_0.1_1_perc_meoh


title: S-1076_G_std_1_perc_meoh rep1

description: Library name: d1175.S-1076_G_std_1_perc_meoh


title: M5_delFimA

description: Library name: M5_delFimA

value: Pg ATCC 33277-derived FimA mutant infection


title: M5_delPPAD

description: Library name: M5_delPPAD

value: Pg ATCC 33277-derived PPAD mutant infection


title: rCDX2_R3 OE in mESC RNA-seq

description:
rCDX2_R3 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: mESC

value: rCDX2_R3 OE


title: S-1076_F_0.1_1_perc_meoh rep1

description: Library name: d1172.S-1076_F_0.1_1_perc_meoh


title: rCDX2_R2 OE in mESC RNA-seq

description:
rCDX2_R2 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: rCDX2_R2 OE


title: S-1076_G_std_1_perc_meoh rep2

description: Library name: d1176.S-1076_G_std_1_perc_meoh


title: rCDX2_R1 OE in mESC RNA-seq

description:
rCDX2_R1 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: rCDX2_R1 OE


title: M5_ATCC_WT

description: Library name: M5_ATCC_WT

value: Pg ATCC 33277 WT infection


title: S-1076_F_0.5_1_perc_meoh rep1

description: Library name: d1169.S-1076_F_0.5_1_perc_meoh


title: S-1076_F_0.5_1_perc_meoh rep3

description: Library name: d1171.S-1076_F_0.5_1_perc_meoh


title: S-1076_F_std_1_perc_meoh rep2

description: Library name: d1167.S-1076_F_std_1_perc_meoh


title: rCDX2_R12 OE in mESC RNA-seq

description:
rCDX2_R12 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: rCDX2_R12 OE


title: S-1076_F_0.5_1_perc_meoh rep2

description: Library name: d1170.S-1076_F_0.5_1_perc_meoh


title: M4_W83

description: Library name: M4_W83


title: rCDX2 OE in mESC RNA-seq

description:
rCDX2 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt

value: rCDX2 OE


title: S-1076_E_0.1_1_perc_meoh rep2

description: Library name: d1164.S-1076_E_0.1_1_perc_meoh

value: Sucrose


title: S-1076_E_0.1_1_perc_meoh rep3

description: Library name: d1165.S-1076_E_0.1_1_perc_meoh


title: M4_OZ5001C

description: Library name: M4_OZ5001C

value: Monocyte-derived macrophages


title: S-1076_E_0.1_1_perc_meoh rep1

description: Library name: d1163.S-1076_E_0.1_1_perc_meoh


title: S-1076_F_std_1_perc_meoh rep1

description: Library name: d1166.S-1076_F_std_1_perc_meoh


title: mCDX2 OE in mESC ChIP-seq

description:
mCDX2 OE in mESC, mCDX2 ChIP-seq
merge_MR_cdx2.flt4.SAF.featureCounts.txt

library_source: genomic

molecule: genomic DNA

value: mCDX2 OE


title: M5_control

description: Library name: M5_control

value: non infected control cells


title: S-1076_F_std_1_perc_meoh rep3

description: Library name: d1168.S-1076_F_std_1_perc_meoh


title: S-1076_E_0.5_1_perc_meoh rep2

description: Library name: d1161.S-1076_E_0.5_1_perc_meoh


title: S-1076_E_0.5_1_perc_meoh rep3

description: Library name: d1162.S-1076_E_0.5_1_perc_meoh


title: M4_K04

description: Library name: M4_K04

value: Pg ATCC 33277-derived FimE mutant infection


title: S-1076_E_0.5_1_perc_meoh rep1

description: Library name: d1160.S-1076_E_0.5_1_perc_meoh


title: M4_delPPAD

description: Library name: M4_delPPAD


title: S-1076_E_std_1_perc_meoh rep3

description: Library name: d1159.S-1076_E_std_1_perc_meoh


title: M4_delFimA

description: Library name: M4_delFimA


title: rCDX2 OE in mESC ChIP-seq

description:
rCDX2 OE in mESC, mCDX2 ChIP-seq
merge_MR_cdx2.flt4.SAF.featureCounts.txt


title: WT mESC ATAC-seq

description:
WT mESC ATAC-seq
mes_WT_mCdx2_compare_ATAC_202011_featureCounts_2samples.txt

value: WT


title: S-1076_E_std_1_perc_meoh rep2

description: Library name: d1158.S-1076_E_std_1_perc_meoh


title: mCDX2 OE in mESC RNA-seq

description:
mCDX2 OE in mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt


title: S-1076_E_std_1_perc_meoh rep1

description: Library name: d1157.S-1076_E_std_1_perc_meoh


title: S-1076_D_std_1_perc_meoh rep1

description: Library name: d1154.S-1076_D_std_1_perc_meoh

value: NoCofeed


title: M4_ATCC_WT

description: Library name: M4_ATCC_WT


title: S-1076_D_std_1_perc_meoh rep3

description: Library name: d1156.S-1076_D_std_1_perc_meoh


title: M4_control

description: Library name: M4_control


title: WT mESC RNA-seq

description:
WT mESC RNA-seq
MES_CDX2_rnaseq_featureCount_10samples.txt


title: S-1076_C_0.1_1_perc_meoh rep3

description: Library name: d1153.S-1076_C_0.1_1_perc_meoh

value: Citrate


title: S-1076_C_0.1_1_perc_meoh rep2

description: Library name: d1152.S-1076_C_0.1_1_perc_meoh


title: mCDX2 OE in mESC ATAC-seq

description:
mCDX2 OE in mESC ATAC-seq
mes_WT_mCdx2_compare_ATAC_202011_featureCounts_2samples.txt


title: S-1076_C_0.5_1_perc_meoh rep3

description: Library name: d1150.S-1076_C_0.5_1_perc_meoh


title: ag1-3

city: Moscow

first: Andrey

last: Zaraisky

address: Miklukho-Maklaya str. 16/10

country: Russia

institute: Institute of Bioorganic Chemistry (RAS)

description: Library name: ag1-3

data_processing:
FASTQ files were processed using the ROSALIND platform (https://rosalind.bio/, San Diego, CA). Adapter trimming was carried out with Cutadapt, and reads were aligned to the Mus musculus reference genome build GRCm39 using STAR.
Read counts were obtained with HTSeq4 and normalized by Relative Log Expression (RLE) with the DESeq2 R package. DESeq2 was also used to calculate fold changes, p-values, and perform optional covariate correction.
Assembly: Mus musculus reference genome build GRCm39
Supplementary files format and content: excel file (.xlsx) containing output from DESeq2;  log2-transformed, normalized read counts

source_name: tissues of healing skin wound

growth_protocol: Mice were housed with ad libitum access to food and water, under a 12 h light/12 h dark cycle, at 23 ± 1°C and 42 ± 5% humidity. All animal procedures were approved by the Committee for the Control of the Care and Use of Laboratory Animals of the Pirogov Russian National Research Medical University.

extract_protocol:
Total RNA was extracted on NucleoSpin RNA columns (Macherey-Nagel).The obtained RNA samples were tested on integrity on Aligent 4200 TapeStation instrument.
For preparation for sequencing, the samples were processed with TruSeq Stranded mRNA Library Prep Kit (Illumina) according to a manufacturer’s protocol. The resulted libraries were tested by qPCR and Aligent 4200 TapeStation.

treatment_protocol: Transgenic mice carrying the ag1 cassette were produced by pronuclear microinjection of the pKB2-ag1 plasmid into fertilized C57BL/6 eggs. Founder males were crossed with wild-type C57BL/6 femalese. In parallel, B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J (R26-CreERT2, Stock No. 008463) mice were crossed with B6.Cg-Gt(ROSA)26Sortm2(CAG-rtTA3,-mKate2)Slowe/J (rtTA, Stock No. 029633) mice, generating a double-transgenic Cre/rtTA line that carries both regulatory elements required to activate ag1 expression. To generate Cre/rtTA/ag1 triple-transgenic animals for conditional induction experiments, the target transgenic line, F1 ag1-positive mice were then crossed with Cre/rtTA mice, which resulted in individuals carrying all three transgenes (Cre, rtTA, and ag1 with excised STOP-cassette). Expression of ag1 was induced with doxycycline (Sigma-Aldrich, D9891) in drinking water (200 μg/ml) for 7 days. Mice with confirmed ag1 expression on day 7 were used for subsequent experiments.

value: tissues of healing skin wound

tag: sample group


title: S-1076_C_0.1_1_perc_meoh rep1

description: Library name: d1151.S-1076_C_0.1_1_perc_meoh


title: M3_OZ5001C

description: Library name: M3_OZ5001C

value: Pg ATCC 33277-derived FimC mutant infection


title: shcaf1-Hindgut-Nanopore

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

description: Library name: sample1

data_processing:
Sequencing data were aligned to Drosophila melanogaster reference genome dm6 and corresponding transposon sequences via Minimap2 (v 2.17-r941). After mapping, two files, "dm6 PAF file" and "TE PAF file", were generated. The alignments with mapping quality less than 30 or target sequence length less than 200bp were filtered. Python script was written to process two filtered PAF files to find insertions.
Assembly: dm6 and Drosophila TE consensus sequence
Supplementary files format and content: bed Columns 1–3: Chromosomal location of the TE insertion (200bp window) Column 4: TE insertion information (exact genomic site of insertion, strand, TE name, inserted TE locus) Columns 5–6: Number of supporting reads for spanning insertion / partial insertion Column 7: Supporting reads (names starting with p_ indicate partial insertions, s_ indicate spanning insertions)

organism: Drosophila melanogaster

source_name: Adult hindgut

extract_protocol:
Genomic DNA from fly samples was extracted using Buffer A (100 mM Tris-HCl pH7.5, 100 mM EDTA, 100 mM NaCl, 0.5% SDS) and Buffer B (28.6% 5 M potassium acetate and 71.4% 6 M lithium chloride) reagents. Genomic DNA from fetal livers was extracted by using lysis buffer (100 mM Tris-HCl pH7.5, 50 mM NaCl, 5 mM EDTA, 0.2% SDS) with Protease K.
Genomic DNA extracted from Drosophila hindguts was sent toBenagen for quality control and Nanopore Sequencing.

value: Adult hindgut


title: M3_K04

description: Library name: M3_K04


title: S-1076_C_0.5_1_perc_meoh rep2

description: Library name: d1149.S-1076_C_0.5_1_perc_meoh


title: S-1076_C_0.5_1_perc_meoh rep1

description: Library name: d1148.S-1076_C_0.5_1_perc_meoh


title: S-1076_D_std_1_perc_meoh rep2

description: Library name: d1155.S-1076_D_std_1_perc_meoh


title: ag1-2

description: Library name: ag1-2


title: shwhite-Hindgut-Nanopore

description: Library name: sample2

value: sh-white


title: S-1076_C_std_1_perc_meoh rep1

description: Library name: d1145.S-1076_C_std_1_perc_meoh


title: M3_W83

description: Library name: M3_W83

value: Pg W83 WT infection


title: M3_control

description: Library name: M3_control


title: M2_OZ5001C

description: Library name: M2_OZ5001C


title: S-1076_B_std_1_perc_Meoh rep2

description: Library name: d1137.S-1076_B_std_1_perc_Meoh

value: Galactose


title: M3_delPPAD

description: Library name: M3_delPPAD

value: Pg ATCC 33277-derived PPAD mutant infection


title: S-1076_C_std_1_perc_meoh rep3

description: Library name: d1147.S-1076_C_std_1_perc_meoh


title: S-1076_B_std_1_perc_Meoh rep1

description: Library name: d1136.S-1076_B_std_1_perc_Meoh


title: M2_K04

description: Library name: M2_K04


title: Control-2 wt+DOX

description: Library name: Control-2 wt+DOX

value: Control wt+DOX


title: S953_J_std_0.3 rep3

description: Library name: d5539.S953_J_std_0.3

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.1.1645, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Komagataella phaffi transcripts and exogenous transgenes were quantified using salmon 1.6.0
Gene-level summaries created with tximport 1.24.0
Assembly: Komagataella phaffi WT (strain Y11430) with transcriptome phaffi_plus_240408Lov_transgenes
Supplementary files format and content: phaffi_plus_240408Lov_transgenes.fa.gz is fasta format transcriptome used in salmon quantitation
Supplementary files format and content: 240408Lov_transcript2gene.txt.gz is a tab-delimited file that associates transcript and gene identifiers
Supplementary files format and content: 240408Lov_annotation.txt.gz is a tab-delimited annotation file associating gene names with gene IDs.
Supplementary files format and content: 240408Lov_intCt.txt.gz is a tab delimited file of integrer count data
Supplementary files format and content: 240408Lov_l2tpm.txt.gz is a tab-delimited file of log2 TPM data with a +1 offset.

source_name: K. phaffii S-953

growth_protocol: Strains were grown in 3 mL cultures in 24-deep well plates (toom temperature, 600 RPM, 3 mm orbit). Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone). Cultures were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and cells resuspended in fresh media with the described quantity of methanol and corresponding co-feed, with 10 mM glutathione. Supernatant samples were collected after 18 hrs and 24 hrs of production for the co-feed screen and the knockout screen respectively, and analyzed.

tag: co-feed

value: Xylose


title: S953_J_std_0.3 rep1

description: Library name: d5537.S953_J_std_0.3


title: S953_J_std_0.3 rep2

description: Library name: d5538.S953_J_std_0.3


title: Control-1 wt+DOX

description: Library name: Control-1 wt+DOX


title: M2_delPPAD

description: Library name: M2_delPPAD


title: S953_H_0.1_0.3 rep3

description: Library name: d5536.S953_H_0.1_0.3

value: Sorbitol


title: S953_H_0.1_0.3 rep2

description: Library name: d5535.S953_H_0.1_0.3


title: PREP0070_AShar11187A_H02v1_N2_D8_Fast_4_S16_combined

city: Boston

first: William

middle: B.

last: Mair

address: 677 Huntington Ave, Boston,

institute: Harvard School of Public Health

description:
Library name: Sample 16
wild-type, old, fasted

data_processing:
DEseq differential expression analysis
Assembly: WBcel235
Supplementary files format and content: .xlsx gene counts

organism: Caenorhabditis elegans

source_name: whole nematodes

growth_protocol: C elegans were maintained on NGM plates at 20 degree celsius

extract_protocol:
Animals were snap frozen in Qiazol lysis reagent and RNA was extracted using Qiagen RNAeasy Mini Kit
Kapa mRNA Hyperprep

treatment_protocol: Animals at respective ages were ad lib fed or fasted for 6 hours

value: whole nematodes

value: N2 Bristol

value: Old (D8), Fasted


title: M2_delFimA

description: Library name: M2_delFimA

value: Monocyte-derived macrophages

value: Pg ATCC 33277-derived FimA mutant infection


title: S953_H_0.1_0.3 rep1

description: Library name: d5534.S953_H_0.1_0.3


title: PREP0070_AShar11187A_G02v1_N2_D8_Fast_3_S15_combined

description:
Library name: Sample 15
wild-type, old, fasted


title: S953_H_0.5_0.3 rep3

description: Library name: d5533.S953_H_0.5_0.3


title: M2_control

description: Library name: M2_control

value: non infected control cells


title: PREP0070_AShar11187A_F02v1_N2_D8_Fast_2_S14_combined

description:
Library name: Sample 14
wild-type, old, fasted


title: S953_H_0.5_0.3 rep2

description: Library name: d5532.S953_H_0.5_0.3


title: S953_H_0.5_0.3 rep1

description: Library name: d5531.S953_H_0.5_0.3


title: S-1076_B_0.1_1_perc_meoh rep2

description: Library name: d1143.S-1076_B_0.1_1_perc_meoh

source_name: K. phaffii S-1076


title: S953_H_std_0.3 rep3

description: Library name: d5530.S953_H_std_0.3


title: PREP0070_AShar11187A_E02v1_N2_D8_Fast_1_S13_combined

description:
Library name: Sample 13
wild-type, old, fasted


title: S-1076_C_std_1_perc_meoh rep2

description: Library name: d1146.S-1076_C_std_1_perc_meoh

value: Citrate


title: M3_delFimA

description: Library name: M3_delFimA


title: S953_H_std_0.3 rep1

description: Library name: d5528.S953_H_std_0.3


title: M1_W83

description: Library name: M1_W83


title: M2_ATCC_WT

description: Library name: M2_ATCC_WT

value: Pg ATCC 33277 WT infection


title: ag1-1

description: Library name: ag1-1

value: tissues of healing skin wound


title: PREP0070_AShar11187A_C02v1_N2_D8_Fed_3_S11_combined

description:
Library name: Sample 11
wild-type, old, fed

value: Old (D8), Fed


title: S953_G_0.1_0.3 rep3

description: Library name: d5527.S953_G_0.1_0.3

value: D-Arabinose


title: M1_OZ5001C

description: Library name: M1_OZ5001C

value: Pg ATCC 33277-derived FimC mutant infection


title: S953_G_0.1_0.3 rep1

description: Library name: d5525.S953_G_0.1_0.3


title: M3_ATCC_WT

description: Library name: M3_ATCC_WT


title: S953_H_std_0.3 rep2

description: Library name: d5529.S953_H_std_0.3


title: S953_G_0.1_0.3 rep2

description: Library name: d5526.S953_G_0.1_0.3


title: S953_G_0.5_0.3 rep3

description: Library name: d5524.S953_G_0.5_0.3


title: S953_G_0.5_0.3 rep1

description: Library name: d5522.S953_G_0.5_0.3


title: PREP0070_AShar11187A_D02v1_N2_D8_Fed_4_S12_combined

description:
Library name: Sample 12
wild-type, old, fed


title: S953_G_0.5_0.3 rep2

description: Library name: d5523.S953_G_0.5_0.3


title: PREP0070_AShar11187A_A02v1_N2_D8_Fed_1_S9_combined

description:
Library name: Sample 9
wild-type, old, fed


title: M1_K04

description: Library name: M1_K04

value: Pg ATCC 33277-derived FimE mutant infection


title: M1_delPPAD

description: Library name: M1_delPPAD

value: Pg ATCC 33277-derived PPAD mutant infection


title: PREP0070_AShar11187A_B02v1_N2_D8_Fed_2_S10_combined

description:
Library name: Sample 10
wild-type, old, fed


title: S953_G_std_0.3 rep2

description: Library name: d5520.S953_G_std_0.3


title: S953_G_std_0.3 rep3

description: Library name: d5521.S953_G_std_0.3


title: M1_delFimA

description: Library name: M1_delFimA


title: Control-6 ag1-DOX

description: Library name: Control-6 ag1-DOX

value: Control ag1-DOX


title: S953_F_0.1_0.3 rep3

description: Library name: d5518.S953_F_0.1_0.3

value: Rhamnose


title: S953_G_std_0.3 rep1

description: Library name: d5519.S953_G_std_0.3


title: M1_control

description: Library name: M1_control


title: S-1076_B_0.1_1_perc_meoh rep1

description: Library name: d1142.S-1076_B_0.1_1_perc_meoh

value: Galactose


title: PREP0070_AShar11187A_H01v1_N2_YA_Fast_4_S8_combined

description:
Library name: Sample 8
wild-type, young, fasted

value: whole nematodes

value: Young (YA), Fasted


title: S-1076_B_0.5_1_perc_meoh rep3

description: Library name: d1141.S-1076_B_0.5_1_perc_meoh


title: PREP0070_AShar11187A_G01v1_N2_YA_Fast_3_S7_combined

description:
Library name: Sample 7
wild-type, young, fasted

value: N2 Bristol


title: S953_F_0.1_0.3 rep2

description: Library name: d5517.S953_F_0.1_0.3


title: M1_ATCC_WT

description: Library name: M1_ATCC_WT

value: Monocyte-derived macrophages


title: S953_F_0.5_0.3 rep3

description: Library name: d5515.S953_F_0.5_0.3


title: S953_F_0.1_0.3 rep1

description: Library name: d5516.S953_F_0.1_0.3


title: iNeuron, SMN shRNA, rep 3

city: Stanford

first: Yi

last: Zeng

address: 300 Pasteur Drive

institute: Stanford University

description: Library name: iN_SMN_3

data_processing:
For RNA-seq data, adaptors in FASTQ files were removed using fastp. For differential gene expression analysis, the adapter trimmed FASTQ files were analyzed using Salmon and DESeq2. The normalized gene counts were calculated  in DESeq2 and exported. For splicing analysis, the adapter trimmed FASTQ files were first mapped to human geneom using STAR following the ENCODE recommended settings. The unique-mapping, properly paired reads were then used for splicing analysis using leafcutter
Assembly: hg38
Supplementary files format and content: Files' formart is csv and files contain gene expression differences between two conditions of DESeq2 analysis output
Supplementary files format and content: bw

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) combined with DNase I treatment according to the manufacturer's protocol.
Total RNA from cells treated with scrambled shRNA or SMN1/2-targeting shRNA was used to construct RNA-sequencing libraries using a ribosomal RNA depletion protocol (RiboErase), performed by the Stanford Genomics Core Facility. The resulting libraries were quantified, pooled, and sequenced on an Illumina NovaSeq 6000 using an S2 flow cell with 150 bp paired-end reads.

value: SMN shRNA

value: cortical neuron


title: S953_F_0.5_0.3 rep2

description: Library name: d5514.S953_F_0.5_0.3


title: S953_F_std_0.3 rep2

description: Library name: d5511.S953_F_std_0.3


title: PREP0070_AShar11187A_D01v1_N2_YA_Fed_4_S4_combined

description:
Library name: Sample 4
wild-type, young, fed

value: Young (YA), Fed


title: PREP0070_AShar11187A_E01v1_N2_YA_Fast_1_S5_combined

description:
Library name: Sample 5
wild-type, young, fasted


title: S953_F_0.5_0.3 rep1

description: Library name: d5513.S953_F_0.5_0.3


title: iNeuron, SMN shRNA, rep 2

description: Library name: iN_SMN_2


title: iNeuron, SMN shRNA, rep 1

description: Library name: iN_SMN_1


title: PREP0070_AShar11187A_F01v1_N2_YA_Fast_2_S6_combined

description:
Library name: Sample 6
wild-type, young, fasted


title: iNeuron, Scramble shRNA, rep 3

description: Library name: iN_Scramble_3

value: Scramble shRNA


title: S953_F_std_0.3 rep3

description: Library name: d5512.S953_F_std_0.3


title: S953_E_0.1_0.3 rep3

description: Library name: d5509.S953_E_0.1_0.3

value: Sucrose


title: S953_E_0.1_0.3 rep2

description: Library name: d5508.S953_E_0.1_0.3


title: S953_E_0.1_0.3 rep1

description: Library name: d5507.S953_E_0.1_0.3


title: S-1076_B_0.1_1_perc_meoh rep3

description: Library name: d1144.S-1076_B_0.1_1_perc_meoh


title: iNeuron, Scramble shRNA, rep 2

description: Library name: iN_Scramble_2


title: PREP0070_AShar11187A_B01v1_N2_YA_Fed_2_S2_combined

description:
Library name: Sample 2
wild-type, young, fed


title: S953_E_0.5_0.3 rep3

description: Library name: d5506.S953_E_0.5_0.3


title: PREP0070_AShar11187A_C01v1_N2_YA_Fed_3_S3_combined

description:
Library name: Sample 3
wild-type, young, fed


title: S953_F_std_0.3 rep1

description: Library name: d5510.S953_F_std_0.3


title: GFI1-KO, scATAC

status: Public on Mar 13 2026

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

description:
Library name: GFI1-KO-scATAC
BD Rhapsody ATAC + WTA

library_source: genomic single cell

data_processing:
RNA and ATAC raw reads were processed using BD Rhapsody sequence analysis pipeline to map RNA transcripts and ATAC peaks to mm39 reference genome.
Assembly: mm39
Supplementary files format and content: Tab separated matrix files for scRNA andFragments bed files for scATAC data

source_name: spleen

extract_protocol:
Cells were pelleted for 5 mins at 300 × g followed by nuclei isolation by incubating cells with chilled cell lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% tween-20, 0.1% IGEPAL CA-630, 0.01% digitonin, 1mM dithiothreitol, 1 U/μL RNase inhibitor and 1% BSA) for 3 min. Nuclei were washed twice in 1 ml of wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1 mM dithiothreitol and 1 U/µL RNase inhibitor and 1% BSA) by centrifuging at 500 × g for 5 min. After centrifugation, cells were resuspended in chilled Nuclei Buffer (1× Nuclei Buffer, 1 mM dithiothreitol and 1 U/µL RNase inhibitor).
Nuclei were incubated in transposition mix according to the BD Rhapsody single-cell ATAC-seq and mRNA whole transcriptome analysis protocol version 23-24474(01). Following tagmentation, cells were loaded onto BD Rhapsody cartridge. Library preparation was performed according to the BD Rhapsody single-cell ATAC-seq and mRNA whole transcriptome analysis protocol version 23-24474(01).

treatment_protocol: NK cells were FAC-sorted from spleen of naïve NcriCreT/+, NcriCreT/+Gfi1fl/fl, NcriCreT/+Foxo1fl/fl and NcriCreT/+Gfi1fl/flFoxo1fl/fl mice. NK cells were pooled from 3-5 mice and ~1×105 cells were used for nuclei isolation.

value: spleen

value: NK cells


title: PREP0070_AShar11187A_A01v1_N2_YA_Fed_1_S1_combined

description:
Library name: Sample 1
wild-type, young, fed


title: S-1076_B_0.5_1_perc_meoh rep2

description: Library name: d1140.S-1076_B_0.5_1_perc_meoh


title: iNeuron, Scramble shRNA, rep 1

description: Library name: iN_Scramble_1


title: S953_E_0.5_0.3 rep1

description: Library name: d5504.S953_E_0.5_0.3


title: S953_E_0.5_0.3 rep2

description: Library name: d5505.S953_E_0.5_0.3


title: Pzg-GFP ovary Input 2

city: Stuttgart

first: Lea

last: Hüttinger

address: Garbenstr. 30

department: Molecular Genetics (190g)

country: Germany

institute: University of Hohenheim

description: Library name: Pzg-ovary_Input2

data_processing:
The ChIP-seq raw data were first subjected to quality control and trimming in Trim Galore (0.6.10; setting: --quality 20), whereby adapter sequences and all bases with a Phred quality score below 20 were removed. The sequences were then filtered for low-complexity regions using BBMap (39.19; tool: BBduk.sh, settings: entropy=0.35 entropywindow=18 entropyk=4), using an entropy threshold of 0.35. To remove mitochondrial sequences, the reads were aligned to the corresponding sequences  using Bowtie2 (2.5.4) and only non-aligned reads were used. Bowtie2 (2.5.4; settings: -k 1, --very-sensitive) was used for alignment to the Drosophila genome. Duplicates were removed with Picard (3.3.0; tool: MarkDuplicates) and blacklist regions were removed by intersection with Bedtools (2.31.0; tool: intersect). The final alignments were converted into Bigwig files using deepTools (3.5.6; tool: bamCoverage; setting: --normaliseUsing RPKM) and normalised to the number of reads.
Assembly: dm6
Supplementary files format and content: bigwig for each sample

source_name: ovary

extract_protocol:
100 ovaries from 3 to 5 days old Pzg-GFP females were prepared in PBS. Crosslinking was performed in 500 µl of 1% formaldehyde for exactly 10 min at RT, which was stopped by adding 500 µl 50 mM glycine. After five minutes of gentle rotation at RT, the samples were placed on ice. The ovaries were then washed three times with PBS and twice with Farnham buffer [5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40, 1 tablet of protease inhibitor cocktail, 10 mM NaF, 0.2 mM Na3VO4 in ddH2O] for 5 minutes each at 4°C. The ovaries were then homogenised in 100 µl RIPA-2 buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 % sodium deoxycholate (SAC), 0.1 % SDS, 1 tablet of protease inhibitor cocktail, 10 mM NaF, 0.2 mM Na3VO4 in ddH2O] in a glass homogenizer with a size B pestle on ice and sonicated in 12 cycles (30s on, 90s off) with a Branson Sonifier Cell Disruptor B15. After centrifugation at 20.000 x g for 10 min at 4°C, 100 µl of lysate per IP were used and 5% input control was removed from each lysate. Incubation with 10 µg rabbit ⍺-GFP antibody was carried out overnight at 4°C. The following day, the lysate-antibody mixture was added to 50 µl of Dynabeads™ Protein G and incubated for 5 hours at 4°C. While the Dynabeads™ were washed five times for 10 minutes at 4°C, the input control was digested for 1 hour at 37°C with 1 µl 10 mg/ml RNase. After adding 713 µl PK buffer [200 mM TRIS-HCl pH 7.4, 25 mM EDTA, 300 mM NaCl, 2 % SDS, 100 µg Proteinase K] and 277 µl ddH2O to the input and 713 µl PK buffer and 267 µl ddH2O to the Dynabeads™, the samples were incubated for 3 hours in a 55°C water bath. Reverse crosslinking was performed overnight in an oven at 65°C. The following day, the DNA was extracted using phenol-chloroform, precipitated with ethanol and dissolved in 10 µl TE.
All samples were sequenced using Illumina's NextSeq 500 System and NextSeq 500/550 Mid-Output v2.5 Kit, generating single-end reads with a length of 150 bp.

value: ovary

value: Pzg-GFP


title: HB9-iMN, SMN shRNA, rep 3

description: Library name: Hb9-iMN_SMN_3

source_name: NINDS (NH50286)

value: NINDS (NH50286)

value: Motor neuron


title: S953_E_std_0.3 rep2

description: Library name: d5502.S953_E_std_0.3


title: Pzg-GFP ovary Input 1

description: Library name: Pzg-ovary_Input1


title: S953_E_std_0.3 rep1

description: Library name: d5501.S953_E_std_0.3


title: S953_D_std_0.3 rep3

description: Library name: d5500.S953_D_std_0.3

value: NoCofeed


title: HB9-iMN, SMN shRNA, rep 2

description: Library name: Hb9-iMN_SMN_2


title: Pzg-GFP ovary GFP-ChIP rep2-2

description: Library name: Pzg-ovary_IP2-2


title: S953_D_std_0.3 rep2

description: Library name: d5499.S953_D_std_0.3


title: Control-4 ag1-DOX

description: Library name: Control-4 ag1-DOX

value: tissues of healing skin wound

value: Control ag1-DOX


title: S953_C_0.1_0.3 rep3

description: Library name: d5497.S953_C_0.1_0.3

value: Citrate


title: HB9-iMN, SMN shRNA, rep 1

description: Library name: Hb9-iMN_SMN_1


title: S953_E_std_0.3 rep3

description: Library name: d5503.S953_E_std_0.3


title: Pzg-GFP ovary GFP-ChIP rep2-1

description: Library name: Pzg-ovary_IP2-1


title: S953_C_0.1_0.3 rep2

description: Library name: d5496.S953_C_0.1_0.3


title: S-1076_B_0.5_1_perc_meoh rep1

description: Library name: d1139.S-1076_B_0.5_1_perc_meoh

value: Galactose


title: HB9-iMN, Scramble shRNA, rep 3

description: Library name: Hb9-iMN_Scramble_3


title: Pzg-GFP ovary GFP-ChIP rep1

description: Library name: Pzg-ovary_IP1


title: TU_6hr.3

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

description:
Library name: Sample 17
column name in gene_count.AO.csv TU_6hr.3

data_processing:
Seuqnce reads were assessed for quality and trimmed as necessary using Cutadapt
Reads were then aligned to the Drosophila melanogaster genome (dm6) using the STAR aligner
HT-seq was used to assigns aligned reads to genomic features
DESeq2 was used for differential gene expression analysis
Assembly: dm6
Supplementary files format and content: csv file include raw read count for each sample

source_name: Ovary

growth_protocol: All fly stocks were raised on standard fly food.Nutrient restriction was accomplished by placing flies in collection cages on grape juice plates.

extract_protocol:
RNA was isolated, and TU tagged RNA from starved, 3, 6, or 24 hr fed flies was biotinylated and immunoprecipitated by streptavidin beads
TruSeq stranded mRNA kit

treatment_protocol: Re-feeding during the 24-h timecourse was done by adding a water-based paste of baker's yeast in water to grape juice plates

value: Ovary

value: in vivo labeling

value: follicle stem cell

value: wild type

tag: time

value: Hour 6


title: Control-5 ag1-DOX

description: Library name: Control-5 ag1-DOX


title: HB9-iMN, Scramble shRNA, rep 2

description: Library name: Hb9-iMN_Scramble_2

value: Scramble shRNA


title: S953_C_0.5_0.3 rep3

description: Library name: d5494.S953_C_0.5_0.3


title: S953_C_0.5_0.3 rep2

description: Library name: d5493.S953_C_0.5_0.3


title: S953_C_std_0.3 rep3

description: Library name: d5491.S953_C_std_0.3


title: TU_3hr.3

description:
Library name: Sample 16
column name in gene_count.AO.csv TU_3hr.3

value: Hour 3


title: S953_C_0.5_0.3 rep1

description: Library name: d5492.S953_C_0.5_0.3


title: S953_C_std_0.3 rep2

description: Library name: d5490.S953_C_std_0.3


title: S953_C_std_0.3 rep1

description: Library name: d5489.S953_C_std_0.3


title: HB9-iMN, Scramble shRNA, rep 1

description: Library name: Hb9-iMN_Scramble_1


title: S953_D_std_0.3 rep1

description: Library name: d5498.S953_D_std_0.3


title: M2_W83

description: Library name: M2_W83

value: Monocyte-derived macrophages

value: Pg W83 WT infection


title: S953_B_0.1_0.3 rep3

description: Library name: d5488.S953_B_0.1_0.3


title: TU_6hr.2

description:
Library name: Sample 14
column name in gene_count.AO.csv TU_6hr.2


title: S953_B_0.1_0.3 rep1

description: Library name: d5486.S953_B_0.1_0.3


title: His-FLAG, CRAC - Background, Replicate 2

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

description: Library name: His-FLAG_2

data_processing:
Paired-end reads were merged using PEAR (v0.9.6) with the arguments: -p 0.05 -n 4 -v 6
Assembled reads were adapter- and quality-trimmed using Flexbar (v3.5.0) with the parameters: -qf i1.8 -qt 13 -u 0 -m 15 -n 23 -at RIGHT -z GZ -o -ao 2 -ae 0.1 -as TGGAATTCTCGGGTGCCAAGG
Reads were demultiplexed and deduplicated using pyCRAC tools: barcode filtering with pyBarcodeFilter.py (v3.1) and PCR duplicate removal with pyFastqDuplicateRemover.py (v0.0.5)
Filtered reads were aligned to the human genome supplemented with a custom pre-rRNA reference  using STAR (v2.7.11a) with following arguments --outFilterMultimapNmax 80 ,--winAnchorMultimapNmax 80 --outFilterMismatchNmax 4 --outSAMmultNmax -1 --scoreDelOpen -2 --scoreDelBase -2 --outFilterMismatchNoverReadLmax 0.04 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1--outSJfilterOverhangMin -1 -1 -1 -1 --outSJfilterCountTotalMin -1 -1 -1 -1 --outSAMattributes NH HI AS MD nM --alignEndsType Local --seedSearchStartLmax 30 --outFilterScoreMinOverLread 0--outFilterMatchNminOverLread 0 --outFilterMatchNmin 13.
Peak calling was performed with PEAKachu (v0.2.0) in adaptive mode (default settings). Peaks with adjusted p-value ≤ 0.05 and log₂FC ≥ 1 were considered significant.
Significant peaks were exported as BED files and used to filter BAM files via samtools view (v1.21). Bigwig files were generated using bamCoverage function from deeptools (v 3.5.6).
Assembly: GENCODE release 47 (GRCh38.p14) supplemented with a custom pre-rRNA reference (GenBank accession U13369) as chr25
Supplementary files format and content: GNL3L-His-FLAG significant peaks in BigWig format

source_name: Flp-in-T-Rex 293

growth_protocol: HEK293 Flp-In cells  were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin, 10 μg/mL blasticidin, and 100 μg/mL hygromycin B. Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
HEK293 Flp-In cells expressing GNL3L-His₆-2xFLAG or the His₆-2xFLAG tag control were UV crosslinked (254 nm, 800 mJ/cm²), lysed by sonication in TMN150 buffer, and subjected to anti-FLAG and Ni-NTA affinity purification. After SDS-PAGE and transfer to nitrocellulose, labeled protein–RNA complexes were visualized by autoradiography. Membrane regions containing crosslinked material were excised and treated with Proteinase K (Roche). RNA was extracted using TRI-Reagent LS (Sigma-Aldrich) according to the manufacturer’s instructions.
Crosslinked protein–RNA complexes were partially digested with RNace-IT and purified via anti-FLAG and Ni-NTA affinity. RNA fragments were dephosphorylated with FastAP (Thermo Fisher) and ligated to a pre-adenylated Illumina RA3 3′ adapter (5′-/5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/-3′) using RNA ligase II (truncated KQ mutant, NEB). 5′ ends were labeled with [γ-32P] ATP and ligated to a 5′ adapter containing a 5-nt Unique Molecular Identifier (UMI) (5′-/InvddT/ACACrGrUrUrCrArGrArGrUrUrCrUrArCrArGUrCrCrGrArCrGrArUrCrNrNrNrNrNrArGrC-3′) using T4 ssRNA Ligase I (NEB). RNA  extracted from excised nitrocellulose membrane regions was reverse transcribed with SuperScript III (Thermo Fisher), PCR-amplified with Phusion Hot Start II DNA Polymerase and gel purified. Libraries were sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Expression of GNL3L-His₆-2xFLAG or the His₆-2xFLAG tag was induced by treatment with 1 μg/mL tetracycline for 24 h prior to UV crosslinking.

value: Flp-in-T-Rex 293

value: Epithelial Cells

tag: crac antibody

value: anti-FLAG®

value: 1 µg/mL Tetracycline

tag: batch


title: S953_C_0.1_0.3 rep1

description: Library name: d5495.S953_C_0.1_0.3


title: S953_B_0.1_0.3 rep2

description: Library name: d5487.S953_B_0.1_0.3


title: His-FLAG, CRAC - Background, Replicate 1

description: Library name: His-FLAG_1


title: TU_3hr.2

description:
Library name: Sample 13
column name in gene_count.AO.csv TU_3hr.2

tag: tissue

tag: genotype


title: S953_B_0.5_0.3 rep3

description: Library name: d5485.S953_B_0.5_0.3


title: Control-3 wt+DOX

description: Library name: Control-3 wt+DOX

value: tissues of healing skin wound

value: Control wt+DOX


title: GNL3L-His-FLAG, CRAC - Protein of interest, Replicate 2

description: Library name: GNL3L-His-FLAG_2


title: GNL3L-His-FLAG, CRAC - Protein of interest, Replicate 1

description: Library name: GNL3L-His-FLAG_1


title: TU_0hr.3

description:
Library name: Sample 15
column name in gene_count.AO.csv TU_0hr.3

value: Hour 0


title: S-1076_B_std_1_perc_Meoh rep3

description: Library name: d1138.S-1076_B_std_1_perc_Meoh

data_processing:
Sequencing using v3 chemistry. Software: Control v2.2.1.1645, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Komagataella phaffi transcripts and exogenous transgenes were quantified using salmon 1.6.0
Gene-level summaries created with tximport 1.24.0
Assembly: Komagataella phaffi WT (strain Y11430) with transcriptome phaffi_plus_240125Lov_transgenes
Supplementary files format and content: phaffi_plus_240125Lov_transgenes.fa.gz is fasta format transcriptome used in salmon quantitation
Supplementary files format and content: 240125Lov_transcript2gene.txt.gz is a tab-delimited file that associates transcript and gene identifiers
Supplementary files format and content: 240125Lov_annotation.txt.gz is a tab-delimited annotation file associating gene names with gene IDs.
Supplementary files format and content: 240125Lov_intCt.txt.gz is a tab delimited file of integrer count data
Supplementary files format and content: 240125Lov_l2tpm.txt.gz is a tab-delimited file of log2 TPM data with a +1 offset.

value: Galactose


title: S953_B_0.5_0.3 rep2

description: Library name: d5484.S953_B_0.5_0.3


title: TU_0hr.2

description:
Library name: Sample 12
column name in gene_count.AO.csv TU_0hr.2

value: Ovary


title: S953_B_0.5_0.3 rep1

description: Library name: d5483.S953_B_0.5_0.3


title: S953_B_std_0.3 rep3

description: Library name: d5482.S953_B_std_0.3


title: TU_6hr.1

description:
Library name: Sample 11
column name in gene_count.AO.csv TU_6hr.1

value: in vivo labeling


title: S953_B_std_0.3 rep2

description: Library name: d5481.S953_B_std_0.3


title: CD56pos_NU4

city: Nagoya

first: Takahiko

last: Sato

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Department of Hematology

country: Japan

institute: Nagoya University Graduate School of Medicine

description: Library name: CD56pos_NU4

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 platform in 101-base paired-end mode.
Assembly: GRCh38
Supplementary files format and content: Comma separated value (csv) file includes estimated raw counts for all samples.

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA samples were extracted using RNeasy Micro Kit (QIAGEN) accroding to manufacturer's instruction.
The cDNA libraries were constructed according to the manufacturer's instructions using the TruSeq Stranded mRNA Library Prep (Illumina, Inc., San Diego, CA).

value: Peripheral blood mononuclear cells

value: CD56 positive monocytes


title: TU_3hr.1

description:
Library name: Sample 10
column name in gene_count.AO.csv TU_3hr.1

value: follicle stem cell

value: wild type


title: S953_J_0.1_0.7 rep3

description: Library name: d5479.S953_J_0.1_0.7

value: Xylose


title: CD56pos_NU2

description: Library name: CD56pos_NU2


title: CD56pos_NU1

description: Library name: CD56pos_NU1


title: S953_J_0.1_0.7 rep2

description: Library name: d5478.S953_J_0.1_0.7


title: S953_B_std_0.3 rep1

description: Library name: d5480.S953_B_std_0.3


title: S953_J_0.1_0.7 rep1

description: Library name: d5477.S953_J_0.1_0.7


title: TU_0hr.1

description:
Library name: Sample 9
column name in gene_count.AO.csv TU_0hr.1


title: S953_J_0.5_0.7 rep3

description: Library name: d5476.S953_J_0.5_0.7


title: Input_6hr.3

description:
Library name: Sample 8
column name in gene_count.AO.csv Input_6hr.3

value: Hour 6


title: S953_J_std_0.7 rep2

description: Library name: d5472.S953_J_std_0.7


title: Input_3hr.2

description:
Library name: Sample 7
column name in gene_count.AO.csv Input_3hr.2

value: Hour 3


title: S953_H_0.1_0.7 rep3

description: Library name: d5470.S953_H_0.1_0.7

value: Sorbitol


title: Input_6hr.2

description:
Library name: Sample 5
column name in gene_count.AO.csv Input_6hr.2


title: S953_J_0.5_0.7 rep1

description: Library name: d5474.S953_J_0.5_0.7


title: CD56neg_NU4

description: Library name: CD56neg_NU4

value: CD56 negative monocytes


title: S953_J_0.5_0.7 rep2

description: Library name: d5475.S953_J_0.5_0.7


title: CD56neg_NU2

description: Library name: CD56neg_NU2


title: Input_0hr.3

description:
Library name: Sample 6
column name in gene_count.AO.csv Input_0hr.3


title: S953_J_std_0.7 rep3

description: Library name: d5473.S953_J_std_0.7


title: CD56neg_NU3

description: Library name: CD56neg_NU3


title: S953_H_0.1_0.7 rep2

description: Library name: d5469.S953_H_0.1_0.7


title: S953_J_std_0.7 rep1

description: Library name: d5471.S953_J_std_0.7


title: CD56pos_NU3

description: Library name: CD56pos_NU3


title: S953_H_0.1_0.7 rep1

description: Library name: d5468.S953_H_0.1_0.7


title: CD56neg_NU1

description: Library name: CD56neg_NU1


title: Input_3hr.1

description:
Library name: Sample 4
column name in gene_count.AO.csv Input_3hr.1


title: S953_H_0.5_0.7 rep3

description: Library name: d5467.S953_H_0.5_0.7


title: CMK-CTNNB-2

first: Fang

last: Fang

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description:
Library name: Sample 2
CUT&Tag DNA

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS3 (v3.0.2)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

source_name: CMK

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: CMK

value: WT

tag: antibody

value: CTNNB1 (CST,#8480S)


title: CMK-CTNNB-1

description:
Library name: Sample 1
CUT&Tag DNA


title: S953_H_0.5_0.7 rep2

description: Library name: d5466.S953_H_0.5_0.7

extract_protocol:
Qiagen RNeasy 96 kit
Nextera XT DNA Library Preparation Kit with the Illumina DNA/RNA UD Indexes


title: Input_6hr.1

description:
Library name: Sample 2
column name in gene_count.AO.csv Input_6hr.1


title: S953_H_std_0.7 rep2

description: Library name: d5463.S953_H_std_0.7


title: S953_H_0.5_0.7 rep1

description: Library name: d5465.S953_H_0.5_0.7


title: Input_0hr.2

description:
Library name: Sample 3
column name in gene_count.AO.csv Input_0hr.2


title: S953_H_std_0.7 rep1

description: Library name: d5462.S953_H_std_0.7


title: S953_G_0.1_0.7 rep3

description: Library name: d5461.S953_G_0.1_0.7

value: D-Arabinose


title: S953_G_0.1_0.7 rep1

description: Library name: d5459.S953_G_0.1_0.7


title: Zfrp8 GKD Polysomes #1

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 19_Polysomes_Zfrp8_1_S18

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: dm6
Supplementary files format and content: .csv, salmon raw gene counts and median-ratios normalized gene counts

source_name: Ovary tissue

extract_protocol:
Polysome profiling of ovaries was carried out with modifications based on established protocols (44). In brief, we dissected ovaries from approximately 100 YWT flies (UAS-Dcr2; nosGAL4) or around 275 pairs of ovaries from zfrp8 experimental flies using PBS. The dissected ovaries were immediately flash-frozen in liquid nitrogen. The frozen tissue was then homogenized in lysis buffer using a motorized pestle, with 20% of the lysate reserved for mRNA extraction and library preparation as previously described. The remaining lysate was loaded onto sucrose gradients (10–45%) supplemented with cycloheximide, using Beckman Coulter 9 of 16 × 3.5 PA tubes (#331372), and centrifuged at 35,000g in an SW41 rotor for 3 hours at 4°C. After centrifugation, the gradients were fractionated using a density gradient fractionation system.
RNA was extracted from the fractions with acid phenol–chloroform, precipitated overnight, and the resulting pellet was resuspended in 20 μl of water, treated with TURBO DNase, and used for library preparation as outlined above

value: Ovary tissue

value: nosGAL4; Zfrp8 RNAi

tag: dissection

value: dissected 1-3 days post-eclosion

tag: developmental stage

value: Adult


title: S953_G_0.1_0.7 rep2

first: Charles

last: Whittaker

institute: Koch Institute

description: Library name: d5460.S953_G_0.1_0.7

tag: strain


title: Zfrp8 GKD Polysomes #2

description: Library name: 20_Polysomes_Zfrp8_2_S19


title: S953_G_0.5_0.7 rep1

description: Library name: d5456.S953_G_0.5_0.7


title: MINO control rep1

city: Napels

first: Wout

last: Megchelenbrink

address: Vico de Crecchio 7

department: Precision Medicine

country: Italy

institute: University of Campania "Luigi Vanvitelli”

description: Library name: RNAseq_MINO_CTR_rep1

data_processing:
Paired-end FASTQ files were aligned with STAR version 2.7.10b against the GRCh38 human reference genome (Gencode version 39) with parameter "--quantMode GeneCounts".
Assembly: Gencode v39 (GRCh38)
Supplementary files format and content: Processed data contains the raw counts per gene as output by the STAR aligner. The relevant colums are column 1 (ensembl_id) and column 4 (counts for the 2nd read strand aligned with RNA). Column 2 and 3 can be ignored.

source_name: peripheral blood mononuclear cells

growth_protocol: Mec-1 and Mino cell lines were grown in RPMI 1640 medium (EuroClone) supplemented with 10% and 20% of heat inactivated FBS (EuroClone ECS5000L) respectively, 1% glutamine (MicroGem TCL012), 1% penicillin/streptomycin (EuroClone ECB3001D) and 0.01% amphotericin (EuroClone ECM0009D). Granta 519 was grown in DMEM (EuroClone) supplemented with 10% of heat inactivated FBS (EuroClone ECS5000L), 1% glutamine (MicroGem TCL012), 1% penicillin/streptomycin (EuroClone ECB3001D) and 0.01% amphotericin (EuroClone ECM0009D).

extract_protocol:
Total RNAs were extracted using TRIZOL reagent. 500 ng of total RNA was used fot the construction of sequencing libraries.
Samples with an RIN of 7 or higher were processed to generate libraries for mRNA sequencing following the Illumina® TruSeq Stranded mRNA Sample Preparation Guide, starting from a defined concentration of 500 ng of material per sample

treatment_protocol: Cells were treated with uvi5008 at 5 μm concentration for 24 h.

value: peripheral blood mononuclear cells

value: Mino

value: B cell lymphoma

value: wt

tag: treatment

value: CTR


title: S953_G_0.5_0.7 rep3

description: Library name: d5458.S953_G_0.5_0.7

tag: cofeed concentration_(m)


title: MINO control rep2

description: Library name: RNAseq_MINO_CTR_rep2


title: S953_G_std_0.7 rep3

description: Library name: d5455.S953_G_std_0.7

tag: meoh concentration_(v/v_%)


title: MINO treated with UVI 5008 5 µM 24h rep2

description: Library name: RNAseq_MINO_5008_rep2

tag: cell type


title: WT Polysomes #1

city: New York

description: Library name: 17_Polysomes_WT_1_S16

value: nos gal4; m/t


title: MEC1 control rep2

description: Library name: RNAseq_MEC1_CTR_rep2

tag: cell line

value: chronic B cell leukemia


title: MINO treated with UVI 5008 5 µM 24h rep1

description: Library name: RNAseq_MINO_5008_rep1


title: S953_F_0.1_0.7 rep2

description: Library name: d5451.S953_F_0.1_0.7

value: Rhamnose


title: S953_G_0.5_0.7 rep2

description: Library name: d5457.S953_G_0.5_0.7


title: Zfrp8 GKD Input #2

description: Library name: 16_Input_Zfrp8_2_S15


title: S953_F_0.1_0.7 rep3

description: Library name: d5452.S953_F_0.1_0.7


title: S953_G_std_0.7 rep2

description: Library name: d5454.S953_G_std_0.7


title: MEC1 control rep1

description: Library name: RNAseq_MEC1_CTR_rep1


title: S953_F_0.1_0.7 rep1

description: Library name: d5450.S953_F_0.1_0.7


title: WT Polysomes #2

description: Library name: 18_Polysomes_WT_2_S17


title: S953_G_std_0.7 rep1

description: Library name: d5453.S953_G_std_0.7


title: Zfrp8 GKD Input #1

description: Library name: 15_Input_Zfrp8_1_S14


title: S953_H_std_0.7 rep3

description: Library name: d5464.S953_H_std_0.7

value: Sorbitol


title: MEC1 treated with UVI 5008 5 µM 24h rep2

description: Library name: RNAseq_MEC1_5008_rep2


title: MEC1 treated with UVI 5008 5 µM 24h rep1

description: Library name: RNAseq_MEC1_5008_rep1


title: S953_F_0.5_0.7 rep3

description: Library name: d5449.S953_F_0.5_0.7


title: Input_0hr.1

description:
Library name: Sample 1
column name in gene_count.AO.csv  Input_0hr.1

value: Ovary

value: in vivo labeling

value: follicle stem cell

value: wild type

value: Hour 0


title: GRANTA control rep2

description: Library name: RNAseq_GRANTA_CTR_rep2

value: GRANTA 519


title: WT Input #1

description: Library name: 13_Input_WT_1_S12

value: Ovary tissue

value: dissected 1-3 days post-eclosion


title: S953_F_0.5_0.7 rep2

description: Library name: d5448.S953_F_0.5_0.7


title: GRANTA control rep1

description: Library name: RNAseq_GRANTA_CTR_rep1

value: peripheral blood mononuclear cells


title: S953_F_std_0.7 rep3

description: Library name: d5446.S953_F_std_0.7


title: S953_F_std_0.7 rep1

description: Library name: d5444.S953_F_std_0.7


title: S953_F_std_0.7 rep2

description: Library name: d5445.S953_F_std_0.7


title: S953_E_0.1_0.7 rep3

description: Library name: d5442.S953_E_0.1_0.7

value: Sucrose


title: S953_E_0.5_0.7 rep3

description: Library name: d5439.S953_E_0.5_0.7


title: GRANTA treated with 5008 5 µM 24h rep1

description: Library name: RNAseq_GRANTA_5008_rep1

value: B cell lymphoma


title: S953_F_0.5_0.7 rep1

description: Library name: d5447.S953_F_0.5_0.7


title: Lung tissue, Mtb-infected Balb/c, 19 days, sample 4

city: Ribeirao Preto

first: Luiz Gustavo

middle: Araujo

last: Gardinassi

state: Sao Paulo

address: Av. dos Bandeirantes, 3900

institute: Ribeirao Preto Nursing School/ University of São Paulo

description: Library name: Lung_19_4

data_processing:
The data obtained through the SOLID platform was initially filtered by a structure designed for the efficient identification of errors within the sequencing of the platform. For this, the quality values (QV) informed by the SOLID primary analysis are used; the parameter used in our filtering was QV ≥20, and the objective of this filtering is to obtain data with a high-reliability index for functional applications. The raw data were processed using the the Rsubread package to align to the reference genome, GRMc38_p6, and to generate a read count table.
Assembly: GRMc38_p6
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: Lung

extract_protocol:
The right lung of the animals was collected and stored in 1.0 mL of Trizol Reagent (Invitrogen, Carlsbad, CA, USA). The RNA was analyzed for its integrity and concentration using the Agilent 2100 bioanalyzer using the RNA LabChip® Kit (Agilent Technologies, USA) to certify that it had the characteristics required to be used in RNA sequencing technology (RNAseq).
The RNAseq was performed using the SOLiD Total RNAseq kit (Applied Biosystems). The material was used for the construction of fragment-like libraries, for further sequencing using the kits and protocols recommended by the SOLID™ Platform. Mapping revealed that the coverage achieved by sequencing was 4.5 times the total mouse transcriptome, averaging approximately 7 million reads.

treatment_protocol: BALB/c adult female mice, weighing between 20 and 25 grams and about eight weeks old, coming from the Central Animal House of the University of São Paulo, Campus of Ribeirão Preto – USP were infected with H37Rv strain of Mtb, accordingly to the Committee on Animal Research and Ethics from the Medical School of Ribeirão Preto (protocol number 020/2012 CETEA, FMRP-USP). After anesthesia, the mice were inoculated intratracheally (i.t.) with a suspension of 1 x 105 bacilli/100 µL of Mtb. For the determination of the number of colony-forming units (CFU) kinetics, the animals were euthanized with anesthetic overdose at 1, 2, 3, 4, 5, 6, 10, 14, 19, 24, and 31 days after infection. At each time point, 5 animals were euthanized for the kinetics organ extraction. Then, the organs were processed, and the final solution was diluted and seeded in 7H11 solid culture medium and incubated for 28 days at 37°C. The mycobacterial colonies were counted with the aid of a magnifying glass. The number of colonies was corrected according to organ dilutions and weight and expressed as log10 per gram of organ. The lung suspension was diluted 102, 103, 104, and 105 times; the spleen and liver, 10, 102, 103, and 104 times.

value: Lung

value: WT

tag: infection

value: Mycobacterium tuberculosis infection

tag: day


title: WT Input #2

description: Library name: 14_Input_WT_2_S13

value: nos gal4; m/t

value: Adult


title: S953_E_0.1_0.7 rep1

city: Cambridge

description: Library name: d5440.S953_E_0.1_0.7

tag: co-feed


title: WTC11 iPSNs, untreated, rep3

city: Albuquerque

first: Kiran

last: Bhaskar

state: New Mexico

address: 915 Camino De Salud NE

department: Molecular Genetics and Microbiology

institute: University of New Mexico

description: Library name: WTCII_3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: WTC11 iPSNs

growth_protocol: Neural progenitor cells (NPCs) of WTC11 and sAD2.1 were first cultured in STEMdiff forebrain neuron differentiation kit (STEMCELL Tech # 08600) and then matured in BrainPhys neuronal medium with SM1 supplement (STEMCELL Tech # 05792) in humidified cell culture incubator with 5% CO2 at 37° C.

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: WTC11 iPSNs

value: iPSCs

value: Wild type (WT)

value: Untreated


title: Lung tissue, Mtb-infected Balb/c, 19 days, sample 5

description: Library name: Lung_19_5


title: Lung tissue, Mtb-infected Balb/c, 19 days, sample 3

description: Library name: Lung_19_3


title: S953_E_0.5_0.7 rep1

description: Library name: d5437.S953_E_0.5_0.7


title: S953_E_std_0.7 rep3

description: Library name: d5436.S953_E_std_0.7


title: S953_E_std_0.7 rep2

description: Library name: d5435.S953_E_std_0.7


title: Lung tissue, Mtb-infected Balb/c, 14 days, sample 5

description: Library name: Lung_14_5


title: WTC11 iPSNs, untreated, rep2

description: Library name: WTCII_2


title: Lung tissue, Mtb-infected Balb/c, 14 days, sample 3

description: Library name: Lung_14_3


title: S953_E_std_0.7 rep1

description: Library name: d5434.S953_E_std_0.7


title: WTC11 iPSNs, untreated, rep1

description: Library name: WTCII_1


title: GRANTA treated with 5008 5 µM 24h rep2

description: Library name: RNAseq_GRANTA_5008_rep2

value: wt


title: S953_D_std_0.7 rep3

description: Library name: d5433.S953_D_std_0.7

value: NoCofeed


title: S953_E_0.5_0.7 rep2

description: Library name: d5438.S953_E_0.5_0.7


title: sAD2.1 iPSNs, untreated, rep3

description: Library name: sAD_3

source_name: sAD2.1 iPSNs

value: sAD2.1 iPSNs

value: Sporadic Alzheimer's disease (sAD)


title: Lung tissue, Mtb-infected Balb/c, 14 days, sample 1

description: Library name: Lung_14_1


title: S953_D_std_0.7 rep1

description: Library name: d5431.S953_D_std_0.7


title: S953_D_std_0.7 rep2

description: Library name: d5432.S953_D_std_0.7


title: sAD2.1 iPSNs, untreated, rep2

description: Library name: sAD_2


title: Liver tissue, Mtb-infected Balb/c, 19 days, sample 5

description: Library name: Liver_19_5

source_name: Liver

value: Liver


title: S953_C_0.1_0.7 rep2

description: Library name: d5429.S953_C_0.1_0.7

value: Citrate


title: S953_E_0.1_0.7 rep2

description: Library name: d5441.S953_E_0.1_0.7

value: Sucrose


title: S953_C_0.1_0.7 rep3

description: Library name: d5430.S953_C_0.1_0.7


title: Liver tissue, Mtb-infected Balb/c, 19 days, sample 4

description: Library name: Liver_19_4


title: S953_C_0.5_0.7 rep3

description: Library name: d5427.S953_C_0.5_0.7


title: sAD2.1 iPSNs, untreated, rep1

description: Library name: sAD_1


title: S953_C_0.1_0.7 rep1

description: Library name: d5428.S953_C_0.1_0.7


title: S953_C_0.5_0.7 rep1

description: Library name: d5425.S953_C_0.5_0.7


title: S953_C_0.5_0.7 rep2

description: Library name: d5426.S953_C_0.5_0.7


title: Liver tissue, Mtb-infected Balb/c, 14 days, sample 5

description: Library name: Liver_14_5


title: Liver tissue, Mtb-infected Balb/c, 19 days, sample 3

description: Library name: Liver_19_3


title: CMK_ZNF217_2

city: Suzhou

description:
Library name: Sample 14
CUT&Tag DNA

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.2.5)
Peaks were identified using MACS3 (v3.0.1)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

value: CMK

value: AML cell line


title: CMK_ZNF217_1

description:
Library name: Sample 13
CUT&Tag DNA

value: WT


title: Liver tissue, Mtb-infected Balb/c, 14 days, sample 3

description: Library name: Liver_14_3

value: Mycobacterium tuberculosis infection


title: S953_C_std_0.7 rep2

description: Library name: d5423.S953_C_std_0.7


title: S953_C_std_0.7 rep1

description: Library name: d5422.S953_C_std_0.7


title: S953_B_0.1_0.7 rep3

description: Library name: d5421.S953_B_0.1_0.7

value: Galactose


title: S953_C_std_0.7 rep3

description: Library name: d5424.S953_C_std_0.7


title: S953_B_0.1_0.7 rep2

description: Library name: d5420.S953_B_0.1_0.7


title: CMK_TAL1_2

description:
Library name: Sample 12
CUT&Tag DNA

value: TAL1 (proteintech, #55317-1-AP)


title: Liver tissue, Mtb-infected Balb/c, 14 days, sample 1

description: Library name: Liver_14_1


title: S953_B_0.1_0.7 rep1

description: Library name: d5419.S953_B_0.1_0.7


title: CMK_TAL1_1

description:
Library name: Sample 11
CUT&Tag DNA


title: S953_B_0.5_0.7 rep3

description: Library name: d5418.S953_B_0.5_0.7


title: S953_B_0.5_0.7 rep2

description: Library name: d5417.S953_B_0.5_0.7


title: CMK_RUNX1_2

description:
Library name: Sample 10
CUT&Tag DNA

value: RUNX1 (Abcam, #ab272456)


title: S953_B_0.5_0.7 rep1

description: Library name: d5416.S953_B_0.5_0.7


title: CMK_RUNX1_1

description:
Library name: Sample 9
CUT&Tag DNA


title: Multiome_wt_120h_scATAC

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: Library name: Multiome_wt_120h_scATAC

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
scRNAseq: Mapping and demultiplexing of cell barcode were performed using RNA STARSolo v2.7.10b against the mouse reference genome mm10 and a motified gtf file based on Ensembl 102 (doi:zenodo.org/doi/10.5281/zenodo.10079672) with the following parameters --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 -- soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'GeneExpression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000  --limitSjdbInsertNsj 1000000.Then the matrices have been filtered with DropletUtils version 1.10 (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01).
For scATAC data processing, first, the I2 fastq was reverse complemented with seqtk seq version 1.3.3. Then cell barcodes were added to fastq reads using Sinto barcode v0.10.1. After adapters removal with cutadapt version 4.9, mapping was performed with BWA-MEM v0.7.18 against the mouse reference genome mm10. ATAC fragments with the associated cell barcode were retrieved with Sinto fragments version 0.9.0. The barcodes were translated to match the one from the gene expression. These translated fragment files were sorted and bgzipped to be used by Signac. On the other hand, the fragment file was duplicated and attributed to the + and - strand in order to use both extremities in the peak calling. This duplicated fragment file was used to call peaks with MACS2 v 2.2.9.1 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100. The peaks from wt and from Hox-/- samples were concatenated, sorted and merged with bedtools version 2.31.1 in order to create a single comprehensive peak list.
Downstream analysis was done in R with Signac. Individual chromatin assays were created using the ATAC fragment object and the comprehensive list of peaks, then added to the RNA Seurat object. wt and Hox-/- Seurat objects were then merged. The combined Seurat object was filtered to remove low quality cells using ATAC counts (below 1800 or above 100'000), RNA counts (below 1'000 and above 25'000), nucleosome signal (above 2) and TSS enrichment (below 1) values. RNA layer was normalized with SCTransform regressing the percentage of mitochondrial genes and the cell cycle. PCA was also performed on selected genes using the average expression, excluding Hox genes. For the ATAC layer, the all features with more than 5 counts were considered as top features and data normalized using the RunTFID function. The singular value decomposition (SVD) was computed with exclusion of genomic ranges spanning the deleted Hox regions. The joint neighbor graph using RNA and ATAC assays was performed with the FindMultiModalNeighbors function with the 50 first PC for SCT (RNA) and the second to fortieth for lsi (ATAC). The UMAP was computed using this 'weighted.nn' and clustering was computed using the grah 'wknn' with a resolution of 0.5. For motif analysis, chromVAR v1.26.0  was used with the JASPAR 2022 motif collection, the motifs from Berger et al. 2008, the ISMARA motif collection available at https://swissregulon.unibas.ch/data/mm10_f5/mm10_weight_matrices_v2 and the HOMER motifs.
For RNA velocity, velocyto v0.17.17 was used to pre-processes datasets and generate loom files. scVelo v1.10.2  was used to estimate and project RNA velocity and compute the pseudotime.
Assembly: mm10
Supplementary files format and content: .txt: fragment file for ATACseq generated by Sinto fragment and translated so the barcodes match the barcodes from RNAseq part
Supplementary files format and content: tar.gz: scRNAseq filtered matrix in 3 files (barcodes.tsv, genes.tsv, matrix.mtx)
Supplementary files format and content: loom: velocyto output
Supplementary files format and content: merged_peaks.bed.gz: comprehensive list of peaks
Supplementary files format and content: RDS: R seurat object with both samples

source_name: Gastruloid

growth_protocol: For gastruloid differentiation, 300 mES cells were resuspended in 40μl of prewarmed N2B27 medium (50% DMEM/F12 and 50% Neurobasal supplemented with 0.5x N2 and 0.5x B27), and seeded into each well of a low-attachment, rounded-bottom 96-well plate. After 48h, 150µl of N2B27 medium supplemented with 3μM of GSK-3 inhibitor was added to each well. Medium was then replaced every 24h.

extract_protocol:
Gastruloid at 96h and 120h were collected, pooled and dissociated. Nuclei isolation for the single-cell Multiome ATAC and gene expression procedure was per-formed following the manufacture’s instruction of the Chromium Nuclei Isolation Kit (10X Genomics). Dissociated cells were resuspended in cold lysis buffer and incubated for 10min on ice, then transferred to the nuclei isolation column and centrifuged at 16’000 rcf for 20sec at 4°C to re-move cellular debris. The Flowthrough was centrifuged to retrieve the nuclei pellet, then washed with cold Debris Removal Buffer and two rounds of centrifugation, and wash with cold Wash Buffer. Purified nuclei were resuspended in cold Resuspension Buffer, counted and their nuclear membrane assessed.
Samples were immediately processed according to 10X Genomics recommendations of the v1.0 Multiome ATAC + Gene Expression kit. The 10X ATAC and GEX libraries were sequenced

value: Gastruloid

value: whole gastruloid

tag: Stage


title: Multiome_BADC_120h_scRNA

description: Library name: Multiome_BADC_120h_scRNA

library_source: transcriptomic single cell

value: Hox-/-


title: S953_B_std_0.7 rep2

description: Library name: d5414.S953_B_std_0.7

source_name: K. phaffii S-953


title: S953_B_std_0.7 rep1

description: Library name: d5413.S953_B_std_0.7


title: S953_B_std_0.7 rep3

description: Library name: d5415.S953_B_std_0.7


title: Multiome_BADC_120h_scATAC

description: Library name: Multiome_BADC_120h_scATAC


title: CMK_IKZF1_1

description:
Library name: Sample 7
CUT&Tag DNA

value: IKZF1 (proteintech, #12016-1-AP)


title: S953_J_0.1_1 rep1

description: Library name: d5410.S953_J_0.1_1

value: Xylose


title: S953_J_0.1_1 rep2

description: Library name: d5411.S953_J_0.1_1


title: CMK_ETV6_2

description:
Library name: Sample 6
CUT&Tag DNA

value: ETV6 (Abclonal, #A1637)


title: S953_J_0.5_1 rep3

description: Library name: d5409.S953_J_0.5_1