title: YCTXD3, scRNAseq

city: Bunkyo-ku

first: Hiroyuki

last: Koike

state: Tokyo

address: 1-5-45 Yushima

department: Department of Medical Biochemistry

institute: Institute of Science Tokyo

description: 10X Genomics

data_processing:
The demultiplexing, barcoded ptocessing, gene counting, and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) v3.0.2 for samples 1 and 2, and v3.1.0 for samples 3 and 4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mouse tibialis anterior muscle was minced with scissors and digested with 2 μg/ml Collagenase type 2 (Worlington) in HBSS. Minced samples were incubated at 37°C for 1 hr with shaking, filtered through 70 μm and 40 μm filters, spun down, and resuspended in 2% FBS/PBS. 7AAD (BD Pharmingen, CA, USA) was added immediately before sorting. Sorting of viable cells (7AAD negative) was performed in BD FACSAria III using FACS DIVA software (BD Biosciences, CA, USA).
Single-cell capturing and library generation were performed using Chromium Single Cell 3’ Reagents Kits v3 (10x Genomics, CA, USA) as the manufacturer’s protocol. The sorted cells were resuspended at a concentration of approximately 1,000 cells/µL in PBS containing 0.04% BSA, and we targeted 10,000 cells per sample for capture. A single cell suspension was mixed with RT-PCR master mix and loaded with Single Cell 3’ v3 Gel Beads and Partitioning Oil onto Chromium Chip. The chip was then loaded onto a Chromium Controller for single-cell GEM generation. Immediately following GEM generation, the Gel Bead is dissolved, primers are released, and any co-partitioned cell is lysed. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA. After GEM disruption, full-length cDNA is amplified to generate sufficient mass library construction. Finally, amplified cDNAs were fragmented, and adapter and sample index were added into finished libraries.

value: Tibialis anterior muscle

value: 7-9 weeks old

value: Live cell

value: Cardiotoxin (CTX)


title: NCI-H441 NKX2-1

status: Public on Mar 25 2025

type: SRA

city: Boston

first: Matthew

last: Meyerson

state: MA

address: 44 Binney St

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
We trimmed paired end ChIP-seq reads using Trimmomatic (v. 0.36) for properly paired reads and to remove any TruSeq adapter sequences. We aligned to the hg38 reference genome (GRCh38_noalt_as) using bowtie2 (v. 2.2.9) with parameters “-k 1” and converted to a final BAM file with samtools (v. 1.9).
To generate genome-wide occupancy tracks, we used macs2 (v. 2.1.1) with parameters “-g hs -f BAM --nomodel -B --SPMR” to generate a per million normalized genome-wide track, and then converted to a bigwig file using bedGraphToBigWig.
Narrow ChIP-seq peaks were called using macs2 (v. 2.2.7.1) with parameters “g hs -q qe-3 -f BAMPE --nomodel” against an input control generated from sample cells. Peak calls were filtered against ENCODE hg38 blacklist regions using bedtools subtract with parameter “-A” to remove peaks with any overlap.
Assembly: GRCh38
Supplementary files format and content: bw - SPMR ChIP-seq occupancy tracks generated by MACS2
Supplementary files format and content: narrowPeak - Peak calls by MACS2 for ChIP-seq against input control.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cell lines were cultured in RPMI + 10% Fetal Bovine Serum + 1X PenStrep

extract_protocol:
Cells were prepared according to standard ChIP-seq protocols, see paper for full protocol. Briefly, thawed cells were rinsed twice, resuspended in Covaris Shearing Buffer, aliquoted to an 8 tube microTUBE strip (Covaris) at 5M cells (130µL) per tube, and sonicated on a Covaris LE220 at PIP 300/DF 15/CBP 200 for 20min total at 2min intervals. Sheared chromatin was incubated with ChIP antibody in ChIP buffer rotating overnight at 4°C. The next day, ChIP lysates were rotated with 30µL dynabeads for 2hr at 4°C, 12 total washed, 3 each of Wash Buffer 1, Wash Buffer 2, Wash Buffer 3, and Wash Buffer 4. Bead pellet was resuspended in elution buffer, and heated at 65°C for 1hr at 1000rpm, to eluted supernatnet added 1µL RNase (Roche) and incubated at 37°C for 30min at 1000rpm, then added 3µL of Proteinase K (Lifetech) and incubated at 65°C for 3hr at 1000rpm. ChIP DNA was purified using SPRISelect beads, eluted in 20µL of 10mM Tris-HCl pH 8. DNA concentration was quantified using Quant-IT dsDNA HS assay.
Libraries were prepared with eluted ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit. Final libraries were quantified using Qubit, pooled, and sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.

treatment_protocol: Cells were trypsinized, counted, and fixed in culture media at 1% formaldehyde at 37°C for 10min, quenched in 0.125M glycine for 5min at 37°C, PBS washed, pelleted, stored at -80°C.

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: chip antibody

value: NKX2-1 (Abcam Cat#ab137061 Lot#YJ050719CS)


title: CN 113691 [Cs030]

city: Saskatoon

first: Isobel

last: Parkin

address: 107 Science Pl

country: Canada

institute: Agriculture and Agri-Food Canada

library_source: transcriptomic

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to the C .sativa reference genome using STAR (version 2.7.10a) and gene expression levels were summarized by featureCounts (version 2.0.1).
Assembly: Camelina sative; GCF_000633955.1
Supplementary files format and content: raw_counts.txt, which contains the raw count number summarized by featureCounts

molecule: total RNA

organism: Camelina sativa

source_name: Leaves

extract_protocol:
We collected the fully expanded true leaves from the young seedlings of C .sativa to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide

tag: tissue

value: Leaves

value: plant cell

tag: genotype

tag: flower time_(days_to_50_%_flowering)


title: YCTXD0, scRNAseq

country: Japan

description: 10X Genomics

library_source: transcriptomic single cell

organism: Mus musculus

source_name: Tibialis anterior muscle

tag: strain

tag: age

value: WT


title: NCI-H358 Input

value: No antibody


title: tail dermis, White Leghorn, E9, rep 2

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

description:
Chuong-198
Chuong-198

data_processing:
The RNA-seq analysis was performed on Partek Flow platform (Partek Inc.). Default parameters were adopted except for those with specific annotations.
Pre-alignment QA/QC tasks were performed first.
Mapping: STAR - 2.7.3a (Genome: Ensembl galGal6) was used, followed by post-alignment QA/QC.
The aligned reads were quantified to annotation model (Ensembl release 103) using Partek E/M method.
The raw gene counts were normalized with TPM.
Assembly: emsemble GRCg6a for white leghorn samples; GRCg6a.polish.195-bp for Polish chicken samples
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample

organism: Gallus gallus

source_name: tail dermis

growth_protocol: White Leghorn chicken eggs were used. Eggs were incubated in a humidified egg incubator with an automatic egg turner.

extract_protocol:
Total RNAs of indicated tissues were isolated using the standard Trizol extraction protocol (Invitrogen, Cat.15596026).
Three different kits were used for RNA-seq library preparation. TruSeq RNA Prep Kit v2 (Illumina, RS-122-2001/-2002) was used for Chuong-191-198 and Chuong-207-208, SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, USA) was for Chuong-896/898/901/903, and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) was for the rest of samples.

treatment_protocol: No treatment

value: tail dermis

tag: developmental stage

value: wild-type

tag: treatment

value: no


title: CN 113691 [Cs019]


title: CD8-KO2(cKO2)

city: Beijing

first: Yujia

last: Wang

state: Beijing

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

country: China

institute: Peking university school of basic medical sciences

data_processing:
Quality control of Raw data: raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts.
Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene.
EdgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
GO and KEGG enrichment analysis of differentially expressed gene sets were implemented by the topG （http://www.bioconductor.org/packages/release/bioc/html/topGO.html） and KOBAS package, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD8+ T cells

extract_protocol:
On the day10 of LCMV Cl13 infection, 2×106 CD8+ T cells were sorted by flow cytometry and collected. RNA was purified and concentration were then examined using NanoDrop 2000, RNA integrity and quantity were measured using the Agilent 2100/4200 system.
The library was constructed using standard Illumina library construction process. After library construction, the concentration of library was measured by the Qubit fluorometer. The accurate concentration of cDNA library was again examined using qPCR. The size distribution of library was detected by agarose gel electrophoresis. After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.

value: CD8+ T cells


title: NCI-H358 H3K4me1


title: CN 113691 [Cs010]


title: NCI-H358 H3K27ac


title: CN 113690 [Cs145]


title: CN 113690 [Cs144]


title: 293T sgIL3i4 rep3 IL3i4

city: New York

first: Hina

last: Shah

state: NY

address: 430 East 67th Street

department: Molecular Biology

institute: Sloan Kettering Institute

description: Library name: 293T BFP 53bp1-/- sgIL3i4 biol rep 3 PCR IL3 intron 4

data_processing:
Paired-end sequencing data were analyzed using CRISPResso2. Each sample was aligned to either the reference sequence (with the intron intact) or the intron loss sequence (with the intron deleted).
For each sample, % WID was calculated by counting the number of "intron loss" reads  and dividing by the total aligned reads (reference+intronloss). Modified reads, containing insertions and/or deletions within a 6nt window of the exon-exon junction, were removed from the "intron loss" count but included in the total.
Assembly: GRCh38
Supplementary files format and content: text file includes number of unmodified and modified reads aligning to either the reference or intron loss sequence of interest

source_name: HEK 293T

growth_protocol: HEK293T cells were routinely grown with Dulbecco’s Modified Eagle’s Medium (DMEM) media supplemented with 10% bovine calf serum, 100 U/mL Penicillin-Streptomycin, 1% non-essential amino acids, 2mM L-glutamine. Cells were grown in a 37°C and 5% CO2 air incubator.

extract_protocol:
Cells were trypsinized and genomic DNA was harvested using the Zymo Research Miniprep Kit.
2µg of gDNA was used for library preparation. Locus-specific primers were used to amplify (35 cycle) target sequences of flanking exons. PCR products were subjected to a second round of PCR (11 cycle) with unique indexing sequences (i5 and i7). Samples were run by the MSK IGO core on the Illumina NovaSeq X instrument. Sequencing was performed using a 2x150 paired-end (PE) configuration.

treatment_protocol:
For knockdown experiments, 1.0x10^6 cells were reverse transfected using RNAi max (Invitrogen) according to the manufacturer’s instructions with 30 pmol of siRNAs for REV3L (Dharmacon) or scrambled nontarget siRNA (siCtrl) (Dharmacon). Cells were cultured for 48 hours.
To deliver Cas9 and the gRNA against CALR intron 2, GNAS intron 11, and IL3 intron 4, a CRISPR-Cas9 ribonucleoprotein was formed. The crRNA (IDT) and the tracrRNA (IDT) were resuspended to a final concentration of 100 mM in IDT buffer and mixed in an equimolar solution to a final concentration of 50 mM, heated at 95C for five minutes, and let cool at room temperature to form the crRNA:tracrRNA duplex. For each sample, 100 pmol of crRNA:tracrRNA duplex and 100 pmol of Cas9 enzyme (IDT) were diluted in PBS1X. The ribonucleoprotein formation reaction was incubated for 20 minutes at room temperature. 1.0x10^6 cells were electroporated using the Lonza buffer and 4D nucleofector machine. A chimera DNA/6RNA donor was included for some samples. Cells were cultured for 72 hours before DNA extraction.

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone


title: posterior dorsal dermis, White Leghorn, E9, rep 1

description:
Chuong-207
Chuong-207

source_name: posterior dorsal dermis

value: posterior dorsal dermis


title: NCI-H441 H3K4me1


title: NCI-H358 NKX2-1


title: 293T no break rep3 IL3i4

description: Library name: 293T BFP 53bp1-/- no break biol rep 3 PCR IL3 intron 4


title: posterior dorsal dermis, White Leghorn, E9, rep 2

description:
Chuong-208
Chuong-208


title: NCI-H2087 Input Rep2


title: CN 113690 [Cs106]


title: 293T sgIL3i4 rep2 IL3i4

description: Library name: 293T BFP 53bp1-/- sgIL3i4 biol rep 2 PCR IL3 intron 4


title: NCI-H2087 CTCF

value: CTCF (CST Cat#D31H2 Lot#4)


title: CN 113685 [S001370]


title: anterior dorsal dermis, White Leghorn, E9, rep 1

description:
Chuong-195
Chuong-195

source_name: anterior dorsal dermis

value: anterior dorsal dermis


title: NCI-H2087 SOX2

value: SOX2 (CST Cat#D9B8N Lot#1)


title: CN 113685 [S00136B]


title: tail dermis, White Leghorn, E9, rep 1

description:
Chuong-197
Chuong-197


title: neck dermis, White Leghorn, E9, rep 2

description:
Chuong-194
Chuong-194

source_name: neck dermis

value: neck dermis


title: 293T sgIL3i4 rep1 IL3i4

description: Library name: 293T BFP 53bp1-/- sgIL3i4 biol rep 1 PCR IL3 intron 4


title: CN 113685 [S001365]


title: 293T no break rep1 IL3i4

description: Library name: 293T BFP 53bp1-/- no break biol rep 1 PCR IL3 intron 4


title: CN 113683 [S00136A]


title: scalp dermis, White Leghorn, E9, rep 2

description:
Chuong-192
Chuong-192

source_name: scalp dermis

value: scalp dermis


title: neck dermis, White Leghorn, E9, rep 1

description:
Chuong-193
Chuong-193


title: NCI-H2087 FOXA1

value: lung adenocarcinoma

value: FOXA1 (CST Cat#E7E8W Lot#1)


title: NCI-H2087 c-Jun

value: c-Jun (CST Cat#60AB Lot#11)


title: 293T sgGNASi11 rep3 GNASi11

description: Library name: 293T BFP 53bp1-/- sgGNASi11 biol rep 3 PCR GNAS intron 11


title: anterior dorsal dermis, White Leghorn, E9, rep 2

description:
Chuong-196
Chuong-196


title: ΔpurA 90 min

city: xiamen

first: Weiwei

last: Zhu

address: 4221-117 South Xiang-An Road

institute: Xiamen University

description:
Library name: Sample 4
Sample of an independent experiment

data_processing:
DEGSeq R package (v1.20.0)
Assembly: NCBI Reference Sequence: NZ_CP009273.1
Supplementary files format and content: tab-delimited text file includes relative transcriptional differences among samples

organism: Escherichia coli

growth_protocol: Overnight cultures of the wild-type and ΔpurA strains were diluted 100-fold into fresh LB medium, and were grown to exponential phase (OD600 = 0.3) at 37 °C with shaking.

extract_protocol:
Total RNAs were prepared using an RNA extraction kit following the manufacturer protocol (Tiangen, China).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, rRNAs were removed by the Ribo-zero kit to enrich mRNAs, which were then digested into short fragments. The fragmented mRNAs were used as template to generate one-strand DNA using a six-base random primer and the corresponding double-stranded cDNA. After purification, the cDNA was firstly end-repaired, A-tailed and ligated to a sequencing linker. The size of fragments was selected using AMPure XP beads. PCR amplification was performed, and the amplified products were then purified using AMPure XP beads to obtain the final library.

treatment_protocol: These exponentially growing cultures were treated with 0.1 μg/ml (5 MIC) ciprofloxacin. After treatment for 90 min, cells were collected by centrifugation, frozen using liquid nitrogen, and then stored at -80 °C for subsequent total RNA extraction. The cultures immediately before ciprofloxacin treatment were used as a control (time 0).

value: strain 2131

value: bacterial cells

value: purA deletion

value: Treatment with 0.1 μg/ml ciprofloxacin for 90 min


title: CN 113683 [S00135F]

value: Leaves

value: plant cell


title: CN 113683 [S001360]


title: scalp dermis, White Leghorn, E9, rep 1

description:
Chuong-191
Chuong-191

value: wild-type

value: no


title: NCI-H2087 RNAPolII

value: RNAPolII (Diagenode Cat#C15200004 Lot#001-12)


title: NCI-H2087 H3K4me3

value: H3K4me3 (Millipore Cat#05-745R Lot#3158071)


title: 293T sgGNASi11 rep2 GNASi11

description: Library name: 293T BFP 53bp1-/- sgGNASi11 biol rep 2 PCR GNAS intron 11

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone


title: ΔpurA 0 min

description:
Library name: Sample 3
Sample of an independent experiment

value: No treatment


title: 293T no break rep2 GNASi11

description: Library name: 293T BFP 53bp1-/- no break biol rep 2 PCR GNAS intron 11


title: NCI-H2087 Input Rep1

value: lung adenocarcinoma

value: No antibody


title: CN 113682 [S001C33]


title: CN 113682 [S00136D]


title: 293T no break rep2 IL3i4

description: Library name: 293T BFP 53bp1-/- no break biol rep 2 PCR IL3 intron 4


title: NCI-H2087 FOXA2

value: FOXA2 (Abcam Cat#ab108422 Lot#GR3289185)


title: NCI-H2087 H3K4me1


title: 293T sgGNASi11 rep1 GNASi11

description: Library name: 293T BFP 53bp1-/- sgGNASi11 biol rep 1 PCR GNAS intron 11


title: 293T no break rep3 GNASi11

description: Library name: 293T BFP 53bp1-/- no break biol rep 3 PCR GNAS intron 11


title: CN 113682 [S001362]


title: WT 0 min

description:
Library name: Sample 1
Sample of an independent experiment

value: strain 685


title: 293T no break rep1 GNASi11

description: Library name: 293T BFP 53bp1-/- no break biol rep 1 PCR GNAS intron 11


title: CN 113672 [S001C24]


title: NCI-H2087 NKX2-1

value: NKX2-1 (Abcam Cat#ab137061 Lot#YJ050719CS)


title: ACTXD3, scRNAseq

description: 10X Genomics

value: Tibialis anterior muscle

value: 24 months old

value: WT

value: Live cell

value: Cardiotoxin (CTX)


title: 293T sgCALRi2 rep3 CALRi1

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 3 PCR CALR intron 1


title: PC9 hPGK-NKX2-1 Rep2

description:
JLP-A032
PC9_GFP-NKX2-1_ATAC_Cts.csv

data_processing:
We analyzed our ATAC-seq data using a pipeline modeled off PEPATAC (Smith et al., 2021). We used skewer (v. 0.2.2) to pair reads and remove any Nextera adapters from fastq files. We performed two rounds of read removal, mapping paired-end reads to the rCRSd (mtDNA) and human_rDNA reference genomes from refgenie (http://refgenomes.databio.org/index), using bowtie2 (v. 2.2.9) and mapping parameters (-k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --un-conc $dir), and retaining unmapped reads to either genome. We then mapped reads to the hg38 (GRCh38_noalt_as) bowtie2 reference genome using parameters (--very-sensitive -X 2000).
We filtered reads using samtools view (-f 2 -q 10 -@ 8 -b) for quality and then using picard (v. 2.27.4) (MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true). We also quantified insert metrics using picard (CollectInsertSizeMetrics, M=0.5).
We converted each ATAC-seq BAM file to a bed file using bedtools bamtobed. For each read, we corrected the Tn5 insertion bias for (-4/+5 for –/+ strand) in the bed tile using awk (awk 'BEGIN {OFS="\t"} {if ($6 =="+") print $1,$2-4,$2-4; else print $1,$3+5,$3+5 }'). We then sorted these Tn5 sites, and removed any sites that corrected to outside the hg38 reference genome.
We used bedtools makewindows (-w 100) (v. 2.26.0) to make 100bp windows of the chr1-22,X,Y for hg38. We used bedtools map (-c 2 -o count) to map the individual Tn5 cut sites to the 100bp genome-wide windows. We normalized this bedgraph file such that each 100bp window is the number of Tn5 cut sites per 10M Tn5 cut sites mapped to hg38. We converted this to a bigwig for visualization using bedGraphToBigWig.
For ATAC-seq differential analyses, we merged all ATAC-seq BAM files for a cell line assayed (NCI-H2087, NCI-H441, NCI-H1975, PC9), and called peaks on this merged BAM file using macs2 (v. 2.1.1) with parameters (-q 1e-3 -f BAMPE --nomodel). We used the summits generated by this peak calling, extended by 200bp on each side to generate 400bp windows, and filtered for peaks outside hg38. We mapped Tn5 corrected cut sites to these windows using bedtools map. These counts were used for DESeq2 differential analysis—differential peaks were called based on a Bonferroni-corrected p-value ≤ 1e-2 and a fold-change ≥ 1.5.
Assembly: GRCh38
Supplementary files format and content: bw - bigwig of Tn5 cut sites in 100bp windows genome-wide normalized per 10M insertions in called peaks by cell line
Supplementary files format and content: csv - raw counts mapped to each ATAC-seq peak called by cell line.

extract_protocol:
ATAC-seq samples were prepared according to the Omni-ATAC protocol (Corces et al., 2017). Cells were tagmented using Illumina Tn5 enzyme, purified using a Zymo DNA Clean and Concentrator-5 Kit.
ATAC-seq gDNA samples were PCR amplified for 5 cycles using NEBNext Ultra II Master Mix. Additional amplification was determined using qPCR on a QStudio 6 FLX real-Time PCR System, with the only modification being inclusion of ROX passive dye for qPCR. Samples were amplified for 2-3 additional cycles, column purified again using a post-ATAC-seq Zymo DNA Clean and Concentrator-5 Kit. Libraries were quantified by qPCR or Qubit and pooled. ATAC-seq libraries were sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.

treatment_protocol: Cells were spinfected with constructs at day 0, changed over to hard selection (1µg/mL puromycin) on day 1, then reduced to low selection (0.5µg/mL puromycin) on day 4. On day 7 or day 10 post-infection, cells were counted using a ViCell XR, and 50K fresh cells were harvested for ATAC-seq.


title: Setd8KD_ATAC_1

city: Ikoma

first: Taito

last: Matsuda

institute: Nara Institute of Science and Technology

data_processing:
RNA-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence. Processed reads were mapped to the mouse genome mm10 genome using STAR. DESeq2 package was used for differential gene expression analysis.
Sequence reads for ChIP-seq were trimmed based on read length and read quality using the Trimmomatic tool kit and aligned to the mouse genome (mm10) using Bowtie2 (v2.2.4). All redundant reads were removed from further analysis. SAM files were converted to the BAM format using SAMtools (v0.1.19)95.
Sequencing reads for ATAC-seq were mapped to the mouse reference genome (mm10) from the University of California, Santa Cruz (UCSC) Genome Browser using Bowtie2 (v2.2.4). Open chromatin regions were analyzed using MACS2 software (v2.1.0.20141030) against BAM data compiled by BEDTools.
Assembly: mm10
Supplementary files format and content: TPM (RNA-seq), biigWig (ChIP-seq)

source_name: Hippocampus

extract_protocol:
mRNAs were collected using a Dynabeads mRNA DIRECT Micro Kit (Invitrogen), and the purified mRNAs were subjected to cDNA library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocols. ATAC-seq was performed as previously described by Buenrostro, et al. (PMID:2559105). After transpisition reaction with transposase enzyme in Illumina Nextra DNA Preparetion Kit (#FC-121-1030). For H4K20me1 analysis, CUT&RUN (PMID: 28079019) was employed. Sequencing libraries for CUT&RUN were made using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs)
Llibraries were prepared for sequencing following standard Illumina protocols
RNA-seq, ATAC-seq, CUT&RUN

treatment_protocol: Lentiviruses were produced by transfecting HEK293T cells with the lentivirus constructs pCMV-VSV-G-RSV-Rev and pCAG-HIVgp using polyethylenimine. Samples were collected 3 days after viral infection with puromycin selection.

value: Hippocampus

value: Neural stem/progenitor cells


title: ACTXD0, scRNAseq

description: 10X Genomics


title: Setd8KD_ATAC_2


title: 293T no break rep3 CALRi1

description: Library name: 293T BFP 53bp1-/- no break biol rep 3 PCR CALR intron 1


title: 293T sgCALRi2 rep2 CALRi1

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 2 PCR CALR intron 1


title: WT 90 min

description:
Library name: Sample 2
Sample of an independent experiment

value: bacterial cells

value: Treatment with 0.1 μg/ml ciprofloxacin for 90 min


title: CN 113672 [Cs053]

value: Leaves

value: plant cell


title: PC9 EF1a-NKX2-1 Rep2

description:
JLP-A030
PC9_GFP-NKX2-1_ATAC_Cts.csv


title: 293T no break rep2 CALRi1

description: Library name: 293T BFP 53bp1-/- no break biol rep 2 PCR CALR intron 1

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone


title: CN 113669 [S001C26 ]


title: Ctrl_ATAC_2


title: PC9 hPGK-NKX2-1 Rep1

description:
JLP-A031
PC9_GFP-NKX2-1_ATAC_Cts.csv

value: lung adenocarcinoma


title: 293T sgCALRi2 rep1 CALRi1

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 1 PCR CALR intron 1


title: CN 113669 [S00136E]


title: Ctrl_ATAC_1


title: CN 113672 [S001C2D]


title: NCI-H2087 H3K27ac


title: PC9 EF1a-NKX2-1 Rep1

description:
JLP-A029
PC9_GFP-NKX2-1_ATAC_Cts.csv


title: NCI-H2087 EP300

value: EP300 (CST Cat#D2X6N Lot#1)


title: 293T no break rep1 CALRi1

description: Library name: 293T BFP 53bp1-/- no break biol rep 1 PCR CALR intron 1


title: CN 113669 [S001369]


title: CN 113672 [S001C1C ]


title: Setd8KD_H4k20me1_2


title: PC9 EF1a-GFP Rep2

description:
JLP-A028
PC9_GFP-NKX2-1_ATAC_Cts.csv


title: 293T sgCALRi2 rep5 CALRi2

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 5 PCR CALR intron 2


title: PC9 EF1a-GFP Rep1

description:
JLP-A027
PC9_GFP-NKX2-1_ATAC_Cts.csv


title: Setd8KD_H4k20me1_1


title: CN 113662 [Cs147]


title: NCI-H1975 hPGK-NKX2-1 Rep2

description:
JLP-A026
NCI-H1975_GFP-NKX2-1_ATAC_Cts.csv


title: Ctrl_H4k20me1_2


title: 293T no break rep5 CALRi2

description: Library name: 293T BFP 53bp1-/- no break biol rep 5 PCR CALR intron 2


title: CN 113662 [Cs040]


title: Ctrl_H4k20me1_1


title: NCI-H1975 hPGK-NKX2-1 Rep1

description:
JLP-A025
NCI-H1975_GFP-NKX2-1_ATAC_Cts.csv


title: CN 113662 [Cs035]


title: 293T no break rep4 CALRi2

description: Library name: 293T BFP 53bp1-/- no break biol rep 4 PCR CALR intron 2


title: 293T sgCALRi2 rep3 CALRi2 +6RNA

description: Library name: 293T BFP 53bp1-/- sgCALRi2 +6RNA donor biol rep 3 PCR CALR intron 2


title: cranial feather mesenchyme (Fm), Polish chicken, juvenile

data_processing:
From fastq to final valid pairs bam file: bwa mem -5SP -T0 -t<cores> <ref.fa> <MicroC.R1.fastq.gz> <MicroC.R2.fastq.gz>| \ pairtools parse --min-mapq 40 --walks-policy 5unique \ --max-inter-align-gap 30 --nproc-in <cores> --nproc-out <cores> --chroms-path <ref.genome> | \ pairtools sort --tmpdir=<full_path/to/tmpdir> --nproc <cores>|pairtools dedup --nproc-in <cores> \ --nproc-out <cores> --mark-dups --output-stats <stats.txt>|pairtools split --nproc-in <cores> \ --nproc-out <cores> --output-pairs <mapped.pairs> --output-sam -|samtools view -bS -@<cores> | \ samtools sort -@<cores> -o <mapped.PT.bam>;samtools index <mapped.PT.bam>
Generating cooler contact maps: cooler cload pairix -p <cores> <ref.genome>:<bin_size_in_bp> <mapped.pairs.gz> <matrix.cool>
Merge bins: use hicMergeMatrixBins merge adjacent 10 bins (1kb/bin)  from a Hi-C contact matrix to generate matrx at 10kb resolution
Correction of Hi-C matrix: use HiCExplore hicCorrectMatrix to correct the matrix counts using the Knights-Ruiz correction method and only chromosomes
TAD: (under conda mustache enviroment) java -jar juicertools.jar arrowhead java -jar juicertools.jar arrowhead  [-c chromosome(s)] [-m matrix size] [-r resolution] [-k normalization (NONE/VC/VC_SQRT/KR)] [--ignore-sparsity flag] <hicFile(s)> <output_file> [feature_list] [control_list]
Loops: (under conda mustache enviroment) mustache [-h] [-f F_PATH] [-d DISTFILTER] -o OUTDIR -r RESOLUTION [-bed BED] [-m MAT] [-b BIASFILE] [-cz CHRSIZE_FILE] [-norm NORM_METHOD] [-st ST] [-pt PT] [-sz S_Z] [-oc OCTAVES] [-i S] [-p NPROCESSES] [-ch CHROMOSOME [CHROMOSOME ...]] [-ch2 CHROMOSOME2 [CHROMOSOME2 ...]] [-v VERBOSE]
Assembly: emsemble GRCg6a for white leghorn samples; GRCg6a.polish.195-bp for Polish chicken samples (provided in this paper)
Supplementary files format and content: Loops: tab-delimited text files include chromatin contact pairs and FDR of each pair
Supplementary files format and content: TADs: tab-delimited text files include regions of significant topologically associated domains for each sample
Library strategy: Micro-C

source_name: cranial feather mesenchyme (Fm)

extract_protocol: Dovetails Micro-C Kit (Catalog #: 21006)

value: cranial feather mesenchyme (Fm)

value: juvemile

value: no


title: CN 113660 [Cs050]


title: tail dermis, White Leghorn, E9

value: tail dermis

value: wild-type


title: CN 113660 [Cs038]


title: NCI-H1975 EF1a-GFP Rep2

description:
JLP-A022
NCI-H1975_GFP-NKX2-1_ATAC_Cts.csv


title: NCI-H1975 EF1a-NKX2-1 Rep1

description:
JLP-A023
NCI-H1975_GFP-NKX2-1_ATAC_Cts.csv


title: 293T sgCALRi2 rep3 CALRi2

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 3 PCR CALR intron 2


title: CN 113669 [Cs052]


title: 293T no break rep3 CALRi2

description: Library name: 293T BFP 53bp1-/- no break biol rep 3 PCR CALR intron 2


title: CN 113660 [Cs034]


title: dorsal dermis, White Leghorn, E9

source_name: dorsal dermis

value: dorsal dermis


title: 293T sgCALRi2 rep4 CALRi2

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 4 PCR CALR intron 2


title: NCI-H1975 EF1a-GFP Rep1

description:
JLP-A021
NCI-H1975_GFP-NKX2-1_ATAC_Cts.csv


title: CN 113656 [S001C2C]


title: CN 113656 [S001C23 ]


title: 293T sgCALRi2 rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 2 PCR CALR intron 2


title: scalp dermis, White Leghorn, E9

value: scalp dermis


title: WT2disome

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description:
Disome footprints
Disome_5occupancy15.csv

data_processing:
*library strategy: Disome-seq
3’ adapter (NNNNNNCACTCGGGCACCAAGGA) was trimmed off using skewer, and 4 random nucleotides included in the RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed. Trimmed reads were aligned to human ribosomal and non-coding RNA sequences using STAR10. Unmapped reads were then mapped to an hg19 transcriptome file.
Assembly: hg19
Supplementary files format and content: Metagene analysis at translation start sites from all the datasets.

growth_protocol: Cells were grown in Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamin e and maintained in a 5% CO2 humidified incubator .

extract_protocol:
Cells were harvested in lysis buffer (20 mM Tris-Cl [pH 8], 150 mM KCl, 15 mM MgCl2, 1% Triton X100, 1 mM DTT, 0.1 mg/mL cycloheximide, supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail).
Footprints were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.

value: kidney embryonic

value: WT


title: NCI-H441 shNKX2-1(8) Rep1

description:
JLP-A019
NCI-H441_shLuc-shNKX2-1_ATAC_Cts.csv


title: CN 113656 [Cs148]


title: NCI-H1975 EF1a-NKX2-1 Rep2

description:
JLP-A024
NCI-H1975_GFP-NKX2-1_ATAC_Cts.csv


title: cranial feather mesenchyme (Fm), Polish chicken, juvenile, ATAC-Seq rep 1

data_processing:
The ATAC-seq analysis was conducted on Partek Flow platform (Partek Inc.). Default parameters were applied except for those with additional notes.
Pre-alignment QA/QC algorithms were run first.
Mapping: BWA-MEM algorithm v.0.7.17 (Genome: Ensembl galGal6) was adopted, and then analyzed by post-alignment QA/QC.
Filter alignment: Aligned reads were further filtered to remove duplicate alignments (defined as same start and same sequence).
Peak-calling: MACS2 - 2.1.1 (peak cutoff q-value <0.05; no shifting model; shift size 37; extension size 73) was used, and then narrowPeak and bedgraph files were generated.
Normalization: MACS2 bdgcmp deductd noise by using liner scale fold enrichment method to calculate a score in any bin by comparing treatment value and control value in bedGraph.
bigWig files were generated using the Wig/Bedgraph-to-bigWig converter (Galaxy Version 1.1.1).
Assembly: emsemble GRCg6a for white leghorn samples; GRCg6a.polish.195-bp for Polish chicken samples (provided in this paper)
Supplementary files format and content: bigWig is an indexed binary format showing linear scale fold enrichemnt
Supplementary files format and content: narrowPeak provides called peaks of signal enrichment based on normalized data

extract_protocol:
ATAC resuspension buffer (ARB) was comprised of 3mM MgCl2, 10mM NaCl, and 10mM Tris-HCl pH=7.4. 50,000 dissociated cells of indicated tissues were lysed in 50 μl of cold ATAC lysis buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin freshly added in ARB) for 5 min. 1 ml of ARB (with 0.1% Tween-20) was added and mixed well by inverting the tube. 50,000 nuclei were harvested for the Tn5 transposase reaction. The tagmented DNA was purified using a DNA Clean & Concentrator-5 kit (Zymo Research, Cat. D4014).
Nextera DNA Library Preparation Kit was used for ATAC-seq library preparation. The final libraries were purified utilizing 1X AMPure XP beads (Beckman, A63880).

value: juvenile


title: NCI-H441 shNKX2-1(8) Rep2

description:
JLP-A020
NCI-H441_shLuc-shNKX2-1_ATAC_Cts.csv


title: crest mesenchyme (Cm), Polish chicken, juvenile, ATAC-Seq rep 2

source_name: crest mesenchyme (Cm)

value: crest mesenchyme (Cm)


title: CN 111331 [S001C30]

value: Leaves

value: plant cell


title: 293T sgCALRi2 rep1 CALRi2 +6RNA

description: Library name: 293T BFP 53bp1-/- sgCALRi2 +6RNA donor biol rep 1 PCR CALR intron 2

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen


title: CN 113695 [S00135C]


title: crest mesenchyme (Cm), Polish chicken, juvenile, ATAC-Seq rep 1


title: NCI-H441 shNKX2-1(1) Rep1

description:
JLP-A017
NCI-H441_shLuc-shNKX2-1_ATAC_Cts.csv

value: lung adenocarcinoma


title: 293T sgCALRi2 rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- sgCALRi2 biol rep 1 PCR CALR intron 2

value: TP53BP1 knockout clone


title: CN 111331 [S001C22 ]


title: tail dermis, White Leghorn, E9, ATAC-Seq rep 2


title: 293T sgCALRi2 rep2 CALRi2 +6RNA

description: Library name: 293T BFP 53bp1-/- sgCALRi2 +6RNA donor biol rep 2 PCR CALR intron 2


title: NCI-H441 shLuc Rep2

description:
JLP-A016
NCI-H441_shLuc-shNKX2-1_ATAC_Cts.csv

value: shLuc


title: CN 111331 [Cs149]


title: 293T no break rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- no break biol rep 1 PCR CALR intron 2


title: NCI-H441 shLuc Rep1

description:
JLP-A015
NCI-H441_shLuc-shNKX2-1_ATAC_Cts.csv


title: 293T no break rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- no break biol rep 2 PCR CALR intron 2


title: tail dermis, White Leghorn, E9, ATAC-Seq rep 1


title: 293T siREV3L no break rep3 CALRi2

description: Library name: 293T BFP 53bp1-/- siREV3L no break biol rep 3 PCR CALR intron 2


title: anterior dorsal dermis, White Leghorn, E9, ATAC-Seq rep 2

value: anterior dorsal dermis


title: 293T siREV3L sgCALRi2 rep3 CALRi2

description: Library name: 293T BFP 53bp1-/- siREV3L sgCALRi2 biol rep 3 PCR CALR intron 2


title: cranial feather mesenchyme (Fm), Polish chicken, juvenile, ATAC-Seq rep 2

value: cranial feather mesenchyme (Fm)

value: no


title: NCI-H2087 shNKX2-1(1) Rep2

description:
JLP-A012
NCI-H2087_shLuc-shNKX2-1_ATAC_Cts.csv


title: CN 101990 [S001C25 ]


title: anterior dorsal dermis, White Leghorn, E9, ATAC-Seq rep 1

value: wild-type


title: NCI-H2087 shNKX2-1(8) Rep2

description:
JLP-A014
NCI-H2087_shLuc-shNKX2-1_ATAC_Cts.csv


title: NCI-H441 shNKX2-1(1) Rep2

description:
JLP-A018
NCI-H441_shLuc-shNKX2-1_ATAC_Cts.csv


title: CN 101990 [S001364]


title: CN 111331 [Cs046]


title: NCI-H2087 shNKX2-1(8) Rep1

description:
JLP-A013
NCI-H2087_shLuc-shNKX2-1_ATAC_Cts.csv


title: scalp dermis, White Leghorn, E9, ATAC-Seq rep 1


title: scalp dermis, White Leghorn, E9, ATAC-Seq rep 2


title: 293T siREV3L sgCALRi2 rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- siREV3L sgCALRi2 biol rep 2 PCR CALR intron 2


title: NCI-H2087 shLuc Rep2

description:
JLP-A010
NCI-H2087_shLuc-shNKX2-1_ATAC_Cts.csv


title: cranial feather mesenchyme (Fm), Polish chicken, juvenile, rep 2

description:
Chuong-903
Chuong-903


title: cranial feather mesenchyme (Fm), Polish chicken, juvenile, rep 1

description:
Chuong-901
Chuong-901


title: CN 101986 [S001C56]


title: 293T siCtrl sgCALRi2 rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- siCtrl sgCALRi2 biol rep 2 PCR CALR intron 2

value: siCtrl


title: NCI-H2087 shLuc Rep1

description:
JLP-A009
NCI-H2087_shLuc-shNKX2-1_ATAC_Cts.csv


title: CN 101990 [S001C31]


title: CN 101986 [S001C45]


title: crest mesenchyme (Cm), Polish chicken, juvenile, rep 2

description:
Chuong-898
Chuong-898


title: CN 101986 [Cs117]


title: 293T siCtrl no break rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- siCtrl no break biol rep 2 PCR CALR intron 2


title: crest mesenchyme (Cm), Polish chicken, juvenile, rep 1

description:
Chuong-896
Chuong-896


title: 293T siREV3L sgCALRi2 rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- siREV3L sgCALRi2 biol rep 1 PCR CALR intron 2


title: Bacterial cells, GroEL IP, knockout dnak,  rep1

city: SEVILLA

first: Carla

middle: Veronica

last: Galmozzi

state: SEVILLA

address: Avda. Manuel Siurot s/n

department: Genetics

country: Spain

institute: Instituto de Biomedicina de Sevilla

description: Library name: CV71

data_processing:
We first remove adapter sequences using cutadapt with the following parameter: “-u: 2, -nextseq-trim: 20, --discard-untrimmed, -m: 20 -M:45 -O:6 -a:NNNNNATCGTAGATCGGAAGAGCACACGTCTGAACTCCAG TCAC
Trimmed reads were first aligned against an rRNA/tRNA reference (HG738867.1) using bowtie1 with the following parameter: “-t, -n: 2, --best, --un: <outfile>”.
Unaligned reads from the previous step were aligned against the E. coli MC4100 reference genome (HG738867.1) using bowtie 1 with the following parameter: “-t, -n: 2, -m: 1, --best, --strata”
P-site positions were assigned using a fixed offset of 15 nucleotides from the 3’-end of reads
Assembly: Genome built HG738867.1
Supplementary files format and content: csv files include raw counts  for each Sample
Library strategy: Ribo-seq

source_name: E coli cells

growth_protocol: E. coli different strains were grown in EZ Rich Defined Medium (MOPS) at 30°C

extract_protocol:
Total RNA extraction and ribosome footprint isolation were conducted according to Ingolia et al. (2009)
Library preparation was conducted according to Ingolia et al. (2009)

value: E coli cells

value: MC4100 knockout dnak::cam

value: EZ Rich Defined Medium (MOPS), 30°C


title: Bacterial cells,  GroEL IP, knockout dnak,  rep2

description: Library name: CV72


title: comb skin, White Leghorn, E13, RCAS-HoxC8, rep 2

description:
Chuong-921
Chuong-921

source_name: comb skin

value: comb skin


title: CN 101985 [S001C2A]


title: NCI-H2087 shNKX2-1(1) Rep1

description:
JLP-A011
NCI-H2087_shLuc-shNKX2-1_ATAC_Cts.csv


title: 293T siREV3L no break rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- siREV3L no break biol rep 1 PCR CALR intron 2


title: CN 101985 [S001C20]


title: Bacterial cells, Total translatome, knockout dnak,  rep2 used for GroEL IP knockout dnak rep. 2

description:
Library name: CV70
Total translatome knockout dnak rep. 2 used for GroEL IP knockout dnak rep. 2


title: comb skin, White Leghorn, E13, RCAS-HoxC8, rep 1

description:
Chuong-920
Chuong-920


title: 293T siCtrl sgCALRi2 rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- siCtrl sgCALRi2 biol rep 1 PCR CALR intron 2


title: Bacterial cells, Total translatome, knockout dnak, rep1 used for GroEL IP knockout dnak rep. 1

description:
Library name: CV69
Total translatome knockout dnak rep. 1 used for GroEL IP knockout dnak rep. 1


title: CN 101985 [Cs150]


title: comb skin, White Leghorn, E13, Control, rep 2

description:
Chuong-919
Chuong-919


title: Bacterial cells, GroEL IP, knockout tig,  rep2

description: Library name: CV68

value: MC4100 knockout tig::kan


title: 293T siCtrl no break rep1 CALRi2

description: Library name: 293T BFP 53bp1-/- siCtrl no break biol rep 1 PCR CALR intron 2


title: comb skin, White Leghorn, E13, Control, rep 1

description:
Chuong-918
Chuong-918


title: CAM 276 [S001C49]

value: Leaves

value: CAM 276


title: Bacterial cells, GroEL IP, knockout tig,  rep1

description: Library name: CV67


title: CAM 276 [Cs126]

value: plant cell


title: tail feather follicle, White Leghorn, adult, rep 2

description:
Chuong-839
Chuong-839

source_name: tail feather follicle

value: tail feather follicle

value: adult


title: CAM 276 [Cs103]


title: tail feather follicle, White Leghorn, adult, rep 1

description:
Chuong-838
Chuong-838


title: Bacterial cells, Total translatome, knockout tig,  rep2  used for GroEL IP knockout tig rep. 2

description:
Library name: CV66
Total translatome knockout tig rep. 2 used for GroEL IP knockout tig rep. 2


title: Bacterial cells, Total translatome, knockout tig, rep1  used for GroEL IP knockout tig rep. 1

description:
Library name: CV65
Total translatome knockout tig rep. 1 used for GroEL IP knockout tig rep. 1


title: posterior dorsal feather follicle, White Leghorn, adult, rep 2

description:
Chuong-837
Chuong-837

source_name: posterior dorsal feather follicle

value: posterior dorsal feather follicle


title: CAM 275 [S001C5F]

source_name: Leaves

value: CAM 275


title: posterior dorsal feather follicle, White Leghorn, adult, rep 1

description:
Chuong-836
Chuong-836


title: CAM 275 [S001C50]


title: Bacterial cells, GroEL IP WT, rep2

description: Library name: CV64

value: MC4100 WT


title: anterior dorsal feather follicle, White Leghorn, adult, rep 2

description:
Chuong-835
Chuong-835

source_name: anterior dorsal feather follicle

value: anterior dorsal feather follicle


title: Bacterial cells, GroEL IP, WT, rep1

description: Library name: CV63


title: CAM 275 [Cs131]


title: CAM 262 [S001C58]

value: CAM 262


title: anterior dorsal feather follicle, White Leghorn, adult, rep 1

description:
Chuong-834
Chuong-834

value: wild-type

value: no


title: Bacterial cells,Total translatome, WT, rep2 used for GroEL IP WT rep. 2

description:
Library name: CV62
Total translatome WT rep. 2 used for GroEL IP WT rep. 2

value: E coli cells


title: Bacterial cells, Total translatome, WT, rep1  used for GroEL IP WT rep. 1

description:
Library name: CV61
Total translatome WT rep. 1 used for GroEL IP WT rep. 1


title: neck feather follicle, White Leghorn, adult, rep 2

description:
Chuong-833
Chuong-833

source_name: neck feather follicle

value: neck feather follicle


title: Bacterial cells, TF AP, knockout dnak,  rep2

description: Library name: CV48

value: MC4100 knockout dnak knockout tig::tig-TEV-AviTag

value: EZ Rich Defined Medium (MOPS), 30°C


title: CAM 262 [Cs140]


title: neck feather follicle, White Leghorn, adult, rep 1

description:
Chuong-832
Chuong-832


title: Bacterial cells, TF AP, knockout dnak,  rep1

description: Library name: CV47


title: genomic DNA from mESCs 205307790115_R06C01

type: genomic

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description:
genomic DNA from mESCs
KO_3_mESCs

hyb_protocol: Samples were bisulphite converted using EZ DNA Methylation-Gold™ Kit (Zymo Research, CA, USA) and were hybridized in the array following the manufacturer’s instructions.

scan_protocol: Raw signal intensities were obtained with GenomeStudio Software 2011.1 (Illumina) and DNA methylation beta values were computed from raw IDAT files

data_processing: The raw signal intensities for each array were assessed and analyzed with GenomeStudio Software 2011.1 (Illumina) using default normalization (control probes and background substraction). Raw signal intensity data were later QC’d and processed in R statistical environment (v4.0.3). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such removal of failed probes (probes with detection P value > 0.01),  genotyping probes and MFG probes.

label: Cy5 and Cy3

source_name: mouse embryonic stem cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA from frozen sample pellets was extracted using DNeasy Blood and Tissue Kit (Qiagen GmbH, Hilden, Germany). Purified genomic DNA was quantified with Qubit (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions

value: mouse embryonic stem cells

value: IkappBalpha-/-

value: knock-out

tag: timepoint

value: Timepoint 0h

tag: replicate


title: CAM 260 [S001C51]

value: Leaves

value: CAM 260

value: plant cell


title: CAM 262 [S001C4D]


title: Bacterial cells, Total translatome, knockout dnak,  rep2 used for TF AP knockout dnak, rep. 2

description:
Library name: CV46
Total translatome knockout dnak, rep. 2 used for TF AP knockout dnak, rep. 2


title: genomic DNA from mEBs 205307790115_R05C02

description:
genomic DNA from mEBs
KO_2_EBs_96h

source_name: mouse embryoid bodies

value: mouse embryonic bodies

value: Timepoint 96h


title: scalp feather follicle, White Leghorn, adult, rep 1

description:
Chuong-830
Chuong-830

source_name: scalp feather follicle

value: scalp feather follicle

value: adult


title: CAM 260 [Cs143]


title: genomic DNA from mEBs 205307790115_R04C02

description:
genomic DNA from mEBs
KO_1_EBs_96h


title: Bacterial cells, Total translatome, knockout dnak, rep1 used for TF AP knockout dnak, rep. 1

description:
Library name: CV45
Total translatome knockout dnak, rep. 1 used for TF AP knockout dnak, rep. 1


title: scalp feather follicle, White Leghorn, adult, rep 2

description:
Chuong-831
Chuong-831

value: wild-type


title: CAM 260 [Cs133]


title: RNA CRC ORG3 (3) Basal +EGF + 5ng/mL TGFbeta

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.14 package DESeq2 1.34.0, running under R 4.1.3.
Assembly: UCSC hg38 based on GRCh38
Supplementary files format and content: Per gene and sample raw (integer) alignment counts and DESeq2 normalization method of variance stabilizing transformation (VST) in comma-separated value (CSV) format.

molecule: polyA RNA

source_name: Colorectal cancer Patient derived tumoroids

extract_protocol:
RNA was isolated directly after treatment with RNeasy Kit (Qiagen, Cat. No. 74104) using the on-column DNA digestion protocol following the manufacturer’s instructions.
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

treatment_protocol: Single cells were seeded in a concentration of 2000 cells/ 10 µl in 50% Matrigel/ PBS domes. After 72 hours in ENAS + ROCK inhibitor, medium was replaced to different conditions: ENAS + solvent (0,2 mM HCL/PBS + BSA), ENAS + 5 ng/ml TGF-β1. Basal medium + solvent. Basal medium + 5 ng/ml TGF-β1. PDTs were treated for a time course of 10 days and medium was changed every other day.

value: Colorectal cancer

value: KRAS mut, APC mut

value: Basal +EGF + 5ng/mL TGFbeta


title: Bacterial cells, TF AP WT, rep2

description: Library name: CV44

value: E coli cells

value: MC4100 knockout tig::tig-TEV-AviTag


title: genomic DNA from mEBs 205307790115_R06C02

description:
genomic DNA from mEBs
KO_3_EBs_96h


title: CAM 229 [S001C63]

value: CAM 229


title: 293T siCtrl no break rep3 CALRi2

description: Library name: 293T BFP 53bp1-/- siCtrl no break biol rep 3 PCR CALR intron 2

source_name: HEK 293T

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone

value: siCtrl


title: RNA CRC ORG3 (3) Basal + EGF +solvent

value: Colorectal cancer Patient derived tumoroids

value: Basal + EGF +solvent


title: Bacterial cells, TF AP, WT, rep1

description: Library name: CV43

value: EZ Rich Defined Medium (MOPS), 30°C


title: EIS pig endometrium2

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

institute: Qingdao Agricultural University

description: Library name: Samples2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support 10xgenomics. com/single-cel-gene-expression/software/pipelines/latestwhat- is-cel-range)
Assembly: 10mm
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: endometrium

extract_protocol:
About 200 mg of endometrial tissue was clipped, washed twice with precooled phosphate-buffered saline (PBS) solution, placed in tissue protection solution (BioYou, 21903-10), and transferred to the laboratory on ice for follow-up treatment. After adding enzyme digestion solution (2 mg/mL collagenase II, 1 mg/mL dispersed protease, 30 μg/mL DNase I, 2.5 mM CaCl2, containing FBS 2% dissolved in basal medium), the samples were shaken in a 37 ℃ water bath shaker at 100 rpm/min for 20 min. The enzyme-digested suspension was filtered through a 30 µm cell filter and added to 15 mL PBS, centrifuged at 500 g for 5 min at 4 ℃. The supernatant was removed and the pellet resuspended with 1 ml of 0.04% BSA, added into 3 ml of 1X RBC to lyse erythrocytes, and left at room temperature for 5 min (the time can be adjusted according to the actual situation of erythrocyte lysis). The suspension was then washed twice with PBS and centrifuged at 4 ℃, 300 g for 5 min. The supernatant was removed and the pellet resuspended in 500 μl of 0.04% BSA. Cell parameters were then tested with a cell counter (CountessTM II FL Automated Cell Counter, Thermo Fisher Scientific, Waltham, MA, USA).
The 10X Genomics 3 'transcriptome uses short-read long sequencing and microfluidic techniques to enable simultaneous transcriptomic profiling of 500-10,000 cells per sample. We combine Gel Beads containing barcode information with a mixture of cells and enzymes, which are then coated with oil surfactant droplets located in a microfluidic "double cross" system to form GEMs (Gel Beads-InEmulsions). GEMs flow into a reservoir and are collected, the gel beads dissolve to release the Barcode sequence, reverse transcrib the cDNA fragment, and label the sample. The gel beads were broken and the oil droplets were broken, and PCR amplification was performed using cDNA as template. The standard sequencing library was constructed by mixing all GEMs products

value: endometrium

value: endometrium cell

tag: group

value: EIS


title: genomic DNA from mEBs 205307790115_R02C02

description:
genomic DNA from mEBs
WT_2_EBs_96h

value: mouse embryonic bodies

value: IkappBalpha+/+

value: wildtype

value: Timepoint 96h


title: genomic DNA from mESCs 205307790115_R04C01

description:
genomic DNA from mESCs
KO_1_mESCs

value: mouse embryonic stem cells

value: IkappBalpha-/-

value: knock-out

value: Timepoint 0h


title: genomic DNA from mESCs 205307790115_R03C01

description:
genomic DNA from mESCs
WT_3_mESCs


title: RNA CRC ORG3 (3) ENAS + 5ng/mL TGFbeta

value: Colorectal cancer

value: KRAS mut, APC mut

value: ENAS + 5ng/mL TGFbeta


title: genomic DNA from mEBs 205307790115_R03C02

description:
genomic DNA from mEBs
WT_3_EBs_96h


title: 293T siCtrl sgCALRi2 rep3 CALRi2

description: Library name: 293T BFP 53bp1-/- siCtrl sgCALRi2 biol rep 3 PCR CALR intron 2

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone

value: siCtrl


title: Bacterial cells,Total translatome, WT, rep2  used for TF AP WT rep. 2

description:
Library name: CV42
Total translatome WT rep. 2 used for TF AP WT rep. 2

value: E coli cells

value: MC4100 knockout tig::tig-TEV-AviTag

value: EZ Rich Defined Medium (MOPS), 30°C


title: EL pig endometrium1

description: Library name: Samples1

value: endometrium

value: endometrium cell

value: EL


title: CAM 229 [Cs123]

value: Leaves

value: CAM 229

value: plant cell


title: RNA CRC ORG3 (3) ENAS + solvent

value: Colorectal cancer Patient derived tumoroids

value: ENAS + solvent


title: genomic DNA from mESCs 205307790115_R02C01

description:
genomic DNA from mESCs
WT_2_mESCs

value: mouse embryonic stem cells

value: IkappBalpha+/+

value: wildtype

value: Timepoint 0h


title: Bacterial cells, Total translatome, WT, rep1  used for TF AP WT rep. 1

description:
Library name: CV41
Total translatome WT rep. 1 used for TF AP WT rep. 1


title: CAM 224 [S001C4E]

value: CAM 224


title: Bacterial cells, Dnak IP, knockout tig,  rep2

description: Library name: CV20

value: MC4100 knockout tig::kan


title: CAM 224 [Cs124]


title: S-LS-3

city: wuhan

first: yu

middle: kai

last: kaidi

address: shizishangjie

institute: Huazhong Agricultural University

description: Library name: Sample9

data_processing:
RNAseq_methods.pdf
Assembly: ASM1568090v1
Supplementary files format and content: The PDF file describes all the software and specific methods used for the analysis

organism: Coptis chinensis

source_name: leaf

extract_protocol:
Plant samples were extracted by ethanol precipitation and CTAB-PBIOZOL. Animal samples were extracted by Trizol method. After successful extraction, RNA was dissolved by adding 50 µL of DEPC-treated water. Subsequently, total RNA was identified and quantified using a Qubit fluorescence quantifier and a Qsep400 highthroughput biofragment analyzer.
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection，Finally, the effective concentration of the library was accurately quantified using Q-PCR;

value: leaf

tag: authority

value: Franch

value: susceptible


title: S-LS-2

description: Library name: Sample8


title: RNA CRC ORG3 (2) Basal + EGF +solvent

value: Colorectal cancer

value: KRAS mut, APC mut

value: Basal + EGF +solvent


title: RNA CRC ORG3 (2) Basal +EGF + 5ng/mL TGFbeta

value: Basal +EGF + 5ng/mL TGFbeta


title: S-LS-1

description: Library name: Sample7


title: genomic DNA from mEBs 205307790115_R01C02

description:
genomic DNA from mEBs
WT_1_EBs_96h

value: mouse embryonic bodies

value: Timepoint 96h


title: RNA CRC ORG3 (2) ENAS + 5ng/mL TGFbeta

value: Colorectal cancer Patient derived tumoroids

value: ENAS + 5ng/mL TGFbeta


title: Bacterial cells, Total translatome, knockout tig,  rep2 used for DnaK IP  knockout tig  rep. 2

description:
Library name: CV18
Total translatome knockout tig rep. 2 used for DnaK IP  knockout tig  rep. 2

value: E coli cells

value: EZ Rich Defined Medium (MOPS), 30°C


title: S-ES-3

description: Library name: Sample6


title: Bacterial cells, Total translatome, knockout tig, rep1 used for DnaK IP  knockout tig  rep. 1

description:
Library name: CV17
Total translatome knockout tig rep. 2 used for DnaK IP  knockout tig  rep. 2

value: MC4100 KOtig::kan


title: CAM 224 [Cs104]

value: Leaves

value: plant cell


title: CAM 223 [Cs132]

value: CAM 223


title: genomic DNA from mESCs 205307790115_R01C01

description:
genomic DNA from mESCs
WT_1_mESCs

value: mouse embryonic stem cells

value: IkappBalpha+/+

value: wildtype

value: Timepoint 0h


title: RNA CRC ORG3 (1) Basal +EGF + 5ng/mL TGFbeta

value: Colorectal cancer

value: KRAS mut, APC mut


title: S-ES-2

description: Library name: Sample5

value: leaf

value: Franch

value: susceptible


title: S-ES-1

description: Library name: Sample4


title: 293T siREV3L no break rep2 CALRi2

description: Library name: 293T BFP 53bp1-/- siREV3L no break biol rep 2 PCR CALR intron 2

value: HEK 293T

value: human embryonic kidneys transformed with large T antigen

value: TP53BP1 knockout clone


title: RNA CRC ORG3 (1) Basal + EGF +solvent

value: Colorectal cancer Patient derived tumoroids

value: Basal + EGF +solvent


title: RNA CRC ORG3 (2) ENAS + solvent

value: ENAS + solvent


title: Bacterial cells, Dnak IP, WT, rep1

description: Library name: CV15

value: E coli cells

value: MC4100 WT

value: EZ Rich Defined Medium (MOPS), 30°C


title: Bacterial cells, Dnak IP, knockout tig,  rep1

description: Library name: CV19

value: MC4100 knockout tig::kan


title: CAM 219 [S001C5C]

value: Leaves

value: CAM 219

value: plant cell


title: R-3

description: Library name: Sample3

value: resistance


title: RNA CRC ORG3 (1) ENAS + 5ng/mL TGFbeta

value: Colorectal cancer

value: KRAS mut, APC mut

value: ENAS + 5ng/mL TGFbeta


title: CAM 219 [Cs128]


title: CAM 223 [Cs120]

value: CAM 223


title: RNA CRC ORG3 (1) ENAS + solvent


title: CAM 219 [Cs082]


title: iHE_3

status: Public on Mar 24 2025

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

data_processing:
For the liver tissue and one primary LSEC sample, raw data obtained with the same RNA isolation and sequencing methods and deposited in GSE152447 of Gene Expression Omnibus were used for subsequent data processing and analysis. From the sequencing output, quality control, alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts and the normalization (reads per million, RPM) for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1.
Data scaling of AmpliSeq RPM count data were performed by converting into log2(RPM+1) or z-score.
Scaled dataset were first subjected to gene functional classification based on gene sets related to cytokines, growth factors, coagulation and complement system. The list of gene sets derived from the Gene Ontology (GO) (Gene Ontology Consortium) of Molecular Signatures Database (MSigDB, v7.0). Unsupervised clustering using Euclidean distance and average linkage method and visualization of heatmap and dendrogram were performed by R package heatmap.2.
For intercellular communication analysis and visualization, we applied scaled dataset of bulk RNA-seq to CellChat R package. The annotation of ligand-receptor pair was automatically assigned based on "Secreted Signaling" subset of CellChatDB.human database. The probability of intercellular communication and significantly enriched ligand-receptor pairs were inferred by the "timean" method with default parameters. Visualization was done using the functions implemented in CellChat.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include log2(RPM+1) values for each Sample

source_name: 1383D2 iPSC line

extract_protocol:
Total RNA was extracted from cultured cells and organoids using a PureLink RNA Mini Kit (Thermo Fisher Scientific).
A cDNA library was generated from 10 ng of total RNA, using a SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Amplification, primer digestion, and adapter ligation were performed using an Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). The cDNA library was purified using Agencourt AMPure XP Reagent (Beckman Coulter) and quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific), followed by dilution to 75 pM with water and pooled equally.

value: 1383D2 iPSC line

value: iPSC-derived hepatic endoderm (iHE)

tag: time

value: Day 10


title: Bacterial cells, Total translatome, WT, rep1  used for DnaK IP WT rep. 1

description:
Library name: CV13
Total translatome WT rep. 1 used for DnaK IP WT rep. 1


title: iHE_2


title: iHE_1


title: Bacterial cells, Dnak IP WT, rep2

description: Library name: CV16


title: iLSEP_HLBO_2

source_name: 1383D2 and 625-A4 iPSC line

value: 1383D2 and 625-A4 iPSC line

value: human liver bud organoid (HLBO)

value: Day 11


title: iLSEP_HLBO_1


title: iLSEP_HLBO_3


title: iAEC_HLBO_3


title: Bacterial cells,Total translatome, WT, rep2  used for DnaK IP WT rep. 2

description:
Library name: CV14
Total translatome WT rep. 2 used for DnaK IP WT rep. 2

value: E coli cells

value: MC4100 WT


title: iAEC_HLBO_2


title: iAEC_HLBO_1


title: iLSEC_+VEGF_2

source_name: 625-A4 iPSC line

value: 625-A4 iPSC line

value: iPSC-derived liver sinusoidal endothelial cell (iLSEC)

value: Day 14


title: iLSEC_+VEGF_1


title: iLSEC_+VEGF_3


title: iLSEC_+VEGF+OSM_3


title: CAM 223 [S001C53]

value: Leaves

value: plant cell


title: iLSEC_+VEGF+OSM_2


title: R-1

description: Library name: Sample1

value: leaf

value: Franch

value: resistance


title: iLSEP_3

value: iPSC-derived liver sinusoidal endothelial progenitor (iLSEP)


title: iAEC_3

value: 1383D2 iPSC line

value: iPSC-derived arterial endothelial cell (iAEC)


title: iLSEP_1

value: Day 10


title: Primary_LSEC_1

source_name: primary LSEC

value: primary LSEC

value: primary liver sinusoidal endothelial cell (LSEC)


title: iLSEP_2


title: iAEC_2


title: iSTM_2

value: iPSC-derived septum mesenchymal cell (iSTM)


title: iSTM_1


title: R-2

description: Library name: Sample2


title: iPSC_2

value: iPSC

value: Day 0


title: iPSC_1


title: CN 101990 [Cs048]


title: crypt_vko1

city: Shanghai

first: shuting

last: Yu

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

description: Library name: Sample4

data_processing:
Raw sequencing data were processed by removing low-quality reads, adapter contamination, and reads with excessive unknown bases (N), resulting in clean reads.
These clean reads were then aligned to the Mus musculus reference genome.
Gene expression was quantified, and differentially expressed genes (DEGs) were identified based on the criteria P-value < 0.05 and |Fold Change| > 2
Assembly: mm10
Supplementary files format and content: csv files include Read Counts for each Sample

source_name: small intestinal crypts

extract_protocol:
Small intestinal crypts were isolated from Fpr2f/f and Fpr2VKO mice, and total RNA was extracted using Ttizol (Invitrogen)
The library was constructed using the BGI Optimal dual-module mRNA library construction kit, followed by 50 bp single-end sequencing on the DNBSEQ platform at BGI Genomics Co. Ltd, Shenzhen, China.

value: small intestinal crypts

value: intestinal epithelil Fpr2 knockout


title: crypt_vko3

description: Library name: Sample6


title: crypt_flox2

description: Library name: Sample2

value: WT


title: crypt_flox3

description: Library name: Sample3


title: crypt_flox1

description: Library name: Sample1


title: KO16

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

institute: Nagoya University

description: Library name: Sample 12

data_processing:
Clean reads were mapped on the Oryzias latipes reference assembly using STAR (version 2.7.9a)
The Transcripts Per Million (TPM) was calculated using RSEM (version 1.3.1).
Assembly: Oryzias latipes reference assembly
Supplementary files format and content: Excel file include TPM for each sample.

organism: Oryzias latipes

source_name: Ventral part of telenchephalon, hypothalamus and pituitary

growth_protocol: Medaka were kept under short-day conditions or long-day conditions.

extract_protocol:
Total RNA of brain (ventral part of telenchephalon, hypothalamus and pituitary) were isolated with elimination of DNA contamination using DNase.
mRNA was first purified from the total RNA using poly-T oligo-attached magnetic beads and then fragmented, after which cDNA synthesis was performed. Then the synthesized cDNA was used for the preparation of PE150 strand specific sequencing libraries.

treatment_protocol: Medaka kept under short-day conditions were transferred to long-day conditions, and wild-type and pd1 knockout brains were collected at 12:00 before and 12 days after the transfer.

value: pd1 knockout

value: long-day conditions


title: WT15

description: Library name: Sample 9

value: Ventral part of telenchephalon, hypothalamus and pituitary

value: wild-type


title: KO14

description: Library name: Sample 11


title: WT14

description: Library name: Sample 8


title: KO13

description: Library name: Sample 10


title: KO4

description: Library name: Sample 6

value: short-day conditions


title: KO3

description: Library name: Sample 5


title: iLSEC_+VEGF+OSM_1

value: 625-A4 iPSC line

value: iPSC-derived liver sinusoidal endothelial cell (iLSEC)

value: Day 14


title: WT13

description: Library name: Sample 7


title: KO1

description: Library name: Sample 4


title: iAEC_1

value: 1383D2 iPSC line

value: iPSC-derived arterial endothelial cell (iAEC)

value: Day 10


title: WT3

description: Library name: Sample 3


title: WT2

description: Library name: Sample 2


title: mmtv_C3G

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: Library name: Sample 2

data_processing:
FastQC/MultiQC, Trimmomatic v0.38, mapping with HISHAT2 v2.1.0, quantification using featureCounts v2.0.0
Assembly: mm10
Supplementary files format and content: a csv file includes TPM values for each Sample

source_name: Mammary tumor

extract_protocol:
Mammary tumors arising from MMTV-PyVT were harvested, and RNA was extracted using RNeasy Plus Kits (QIAGEN)
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2

treatment_protocol: MMTV-PyVT mice

value: Mammary tumor


title: mmtv_DMSO

description: Library name: Sample 1

value: DMSO


title: crypt_vko2

description: Library name: Sample5


title: W-EGFP-SAG-1

city: Bunkyo-ku

first: Shogo

last: Yanai

institute: TMDU

description: Library name: Sample4

data_processing:
Sequence reads were trimmed for adaptor sequence using TrimGalore version 0.6.4.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR (Spliced transcripts Alignment to a Reference) version 2.7.3a.
Read count and downstream analysis were performed using FeatureCounts version 2.0.0 and edgeR version 2.2.1.
Assembly: mm10
Supplementary files format and content: CSV files include CPM values for each Sample.

source_name: testis

extract_protocol:
Total RNAs were prepared from W-EGFP cells (10,000 cells/sample) treated with 0.5 μM SAG or DMSO (vehicle) for 1 hour using the RNeasy Micro Kit (Qiagen).
RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs).

value: testis

value: SAG


title: W-EGFP-SAG-2

description: Library name: Sample5


title: W-EGFP-SAG-3

description: Library name: Sample6


title: W-EGFP-control-3

description: Library name: Sample3


title: Islet cells, remitter-rep4

city: New Haven

first: Ying

state: CT

address: 300 George St

institute: Yale University

description:
Library name: Remitter_NOD_4
10x Genomics

data_processing:
The demultiplexing, aligning reads, counting barcodes and UMIs, generating feature-barcode matrices, and performing clustering and gene expression analysis was performed using Cell Ranger software v7.1.0.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Islet

extract_protocol:
The isolated mouse islets were incubated in 2ml Accutase™ Cell Dissociation reagent at room temperature for 5 mins on a tube rotator. After incubation, islet cells were resuspened thoroughly by pipet up and down. Five-time volume of culture medium with 10% FBS was added to stop excessive dissociation reactions. Then dissociated islet cells were washed and resuspened in PBS with 0.04% BSA. Alive cells were counted using trypan blue and hemacytometer.
Library was constructed according to the manufacturer's protocols (Chromium Next GEM Single Cell 5' v2, Dual Index, 10X Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Gel bead primers contain an Illumina TruSeq Read 1 primer, a 10x Barcode, a unique molecular identifier (UMI), and template switch oligo (TSO). Then the poly-A mRNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which was amplified. The amplifiedd cDNA from poly-A mRNA and the amplified DNA from cell surface protein Feature Barcode are separated by size selection for generating V(D)J and/or 5' Gene Expression libraries and Cell Surface Protein (hashtag) libraries, respectively.

value: Islet

tag: Sex

value: female

value: Islet cells

value: NOD

value: anti-CD3 mAb


title: W-EGFP-control-1

description: Library name: Sample1


title: Multiplexed CD8ab+ IELs, Hashtag oligo

city: Chicago

first: Joseph

middle: Joy

last: Sifakis

state: IL

address: 900 East 57th Street

department: Chemistry

institute: The University of Chicago

description:
Library name: AB-ZE-2S-10X-ZAC-1-HT
CD8αβ+ IELs HT

library_source: other

data_processing:
cellranger multi' was run on raw sequencing data (HT/GET/TCR) based on a configuration file with specified CMO IDs.
‘bamtofastq' was used to convert each BAM file back into FASTQ format.
Assembly: The reference genome used is from CellRanger reference version 2020-A, which is based on the mm10 GENCODE v23 primary assembly for mice.
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns
Supplementary files format and content: Assembled contigs
Supplementary files format and content: the Feature_reference.csv file contains hashtag/mouse information from Cell Ranger
Library strategy: CITE-seq

molecule: protein

source_name: Jejunal intraepithelial CD8ab+ lymphocytes

extract_protocol:
CD8αβ+ IELs from three Ighasec+/‑ and Ighasec‑/‑ mice were isolated from the jejunal intraepithelial compartment. Isolated cells were stained with fluorochrome conjugated antibodies for fluorescence-activated cell sorting. For cell hash-tagging, TotalSeq-C hashtag antibodies were added to each sample individually during the cell surface staining. Cells were gated as follows: FSC, SSC, singlets, live, TCRβ+, CD4-, CD8α+, CD8β+. The samples were then sorted together directly into PBS supplemented with 2% FBS, spun down and reconstituted in 1X PBS (calcium- and magnesium-free) containing 0.04% BSA. Samples were loaded on 10x Chromium Controller (10x Genomics) immediately after sorting.
Libraries were constructed for gene expression data and TCR repertoire using Chromium Next GEM Single Cell 5’ Library kit (v1.1). Capture, library preparation and sequencing were performed at the University of Chicago Genomics Facility.

value: T cell

value: mixed sample, SPF, Ighasec+/- and Ighasec-/-

tag: library type

value: HTO

tag: hto

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody (mouse 637, Ighasec+/-), TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody (mouse 638, Ighasec-/-), TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody (mouse 644, Ighasec+/-), TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody (mouse 643, Ighasec-/-),TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody (mouse 651, Ighasec+/-), TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody (mouse 650, Ighasec-/-)


title: Intestinal Epithelial Cells, Ighasec-/-, anti_CD8b, Jejunum, 20J_Ep

description:
Library name: 20J_Ep
Epi_gene_counts.rds

data_processing:
Base calling was performed using the Illumina NovaSeq 6000 platform
Adapters were trimmed using Trim Galore! (0.6.7)
Trimmed sequences were aligned to the reference genome and projected to the transcriptome using STAR (2.7.9a)
Raw gene counts were quantified using Salmon (1.5.2)
Assembly: GRCm38, transcriptome mapped to Gencode Mouse V25 gene annotations
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns

source_name: Jejunal Intestinal Epithelial Cells

extract_protocol:
1 cm of tissue from the middle of the jejunum, the end of the ileum was excised and preserved in RNAprotect (Qiagen) overnight at 4°C. The preserved tissue was then stored at -80°C until processing. Tissue was thawed on ice and transferred to a screw-cap tube containing 450 μL of RLT Plus buffer supplemented with 2-mercaptoethanol and equal quantities of 1.0mm and 0.5 mm zirconium oxide beads (Next Advance). Tissue was homogenized three times for 30 sec at a speed of 6 m/s using Bead Ruptor Elite mill homogenizer (Omni), with 1 min incubation on ice between each cycle. RNA from the lysates was purified using RNeasy Plus Mini kit (Qiagen) with the optional on-column DNase I digest step according to manufacturer protocol. 50000 CD45-EpCAM+ IECs were sorted from the jejunum and the ileum of anti-CD8β, or isotype treated Ighasec+/- and Ighasec-/- mice. Two independent sorting experiments were performed. Cells were collected into RLT Plus buffer (Qiagen) supplemented with 2-mercaptoethanol. RNA was purified using RNeasy Micro kit (Qiagen) and quantified with Power SYBR™ Green RNA-to-CT 1-Step kit.
500 ng of tissue RNA was used as input in the TruSeq Stranded mRNA Library Prep (Illumina). For sorted epithelial cells, the SMART-Seq v4 Ultra Low input RNA kit (Takara) was used to generate cDNA from 10 ng of purified RNA. cDNA was amplified 9 cycles and purified according to manufacturer’s protocol. 200 pg of purified cDNA was the used to generate RNA-seq libraries with Nextera XT DNA Library preparation kit (Illumina) according to manufacturer’s specifications.

value: Jejunal Intestinal Epithelial Cells

value: Ighasec-/-


title: Multiplexed CD8ab+ IELs, TCR sequence

description:
Library name: AB-ZE-2S-10X-ZAC-1-TCR
CD8αβ+ IELs TCR

data_processing:
cellranger multi' was run on raw sequencing data (HT/GET/TCR) based on a configuration file with specified CMO IDs.
‘bamtofastq' was used to convert each BAM file back into FASTQ format.
Assembly: The reference genome used is from CellRanger reference version 2020-A, which is based on the mm10 GENCODE v23 primary assembly for mice.
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns
Supplementary files format and content: Assembled contigs
Supplementary files format and content: the Feature_reference.csv file contains hashtag/mouse information from Cell Ranger

value: Jejunal intraepithelial CD8ab+ lymphocytes

tag: cell type

value: VDJ


title: Multiplexed CD8ab+ IELs, Gene expression

description:
Library name: AB-ZE-2S-10X-ZAC-1-GE
CD8αβ+ IELs GE

value: GEX


title: Intestinal Epithelial Cells, Ighasec-/-, anti_CD8b, Jejunum, 19J_Ep

description:
Library name: 19J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, anti_CD8b, Jejunum, 18J_Ep

description:
Library name: 18J_Ep
Epi_gene_counts.rds

value: Ighasec+/-


title: Intestinal Epithelial Cells, Ighasec-/-, Isotype, Jejunum, 15J_Ep

description:
Library name: 15J_Ep
Epi_gene_counts.rds

value: Isotype


title: Intestinal Epithelial Cells, Ighasec+/-, Isotype, Jejunum, 14J_Ep

description:
Library name: 14J_Ep
Epi_gene_counts.rds


title: WT1

description: Library name: Sample 1

value: Ventral part of telenchephalon, hypothalamus and pituitary

value: wild-type

value: short-day conditions


title: Intestinal Epithelial Cells, Ighasec-/-, anti_CD8b, Jejunum, 11J_Ep

description:
Library name: 11J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, Isotype, Jejunum, 13J_Ep

description:
Library name: 13J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec-/-, anti_CD8b, Jejunum, 10J_Ep

description:
Library name: 10J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, anti_CD8b, Jejunum, 8J_Ep

description:
Library name: 8J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, anti_CD8b, Jejunum, 17J_Ep

description:
Library name: 17J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, anti_CD8b, Jejunum, 7J_Ep

description:
Library name: 7J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, anti_CD8b, Jejunum, 9J_Ep

description:
Library name: 9J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec-/-, Isotype, Jejunum, 6J_Ep

description:
Library name: 6J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec-/-, Isotype, Jejunum, 5J_Ep

description:
Library name: 5J_Ep
Epi_gene_counts.rds


title: W-EGFP-control-2

description: Library name: Sample2

value: testis

value: DMSO


title: Intestinal Epithelial Cells, Ighasec-/-, Isotype, Jejunum, 4J_Ep

description:
Library name: 4J_Ep
Epi_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Ileum, ZE40

description:
Library name: ZE40
Tissue_anti_cd8b_gene_counts.rds

source_name: Ileum

value: Ileum


title: Intestinal Epithelial Cells, Ighasec+/-, Isotype, Jejunum, 1J_Ep

description:
Library name: 1J_Ep
Epi_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Ileum, ZE38

description:
Library name: ZE38
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Ileum, ZE37

description:
Library name: ZE37
Tissue_anti_cd8b_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, Isotype, Jejunum, 2J_Ep

description:
Library name: 2J_Ep
Epi_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Ileum, ZE36

description:
Library name: ZE36
Tissue_anti_cd8b_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec-/-, anti_CD8b, Jejunum, 12J_Ep

description:
Library name: 12J_Ep
Epi_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec-/-, Isotype, Jejunum, 16J_Ep

description:
Library name: 16J_Ep
Epi_gene_counts.rds


title: CAM 229 [S001C59]

city: Saskatoon

first: Isobel

last: Parkin

institute: Agriculture and Agri-Food Canada

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to the C .sativa reference genome using STAR (version 2.7.10a) and gene expression levels were summarized by featureCounts (version 2.0.1).
Assembly: Camelina sative; GCF_000633955.1
Supplementary files format and content: raw_counts.txt, which contains the raw count number summarized by featureCounts

source_name: Leaves

extract_protocol:
We collected the fully expanded true leaves from the young seedlings of C .sativa to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide

value: Leaves

tag: cell line

value: CAM 229

value: plant cell


title: Tissue, Ighasec-/-, Isotype, Ileum, ZE35

description:
Library name: ZE35
Tissue_anti_cd8b_gene_counts.rds

tag: tissue


title: Tissue, Ighasec-/-, Isotype, Ileum, ZE34

description:
Library name: ZE34
Tissue_anti_cd8b_gene_counts.rds

tag: genotype


title: Tissue, Ighasec+/-, anti_CD8b, Ileum, ZE29

description:
Library name: ZE29
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Ileum, ZE31

description:
Library name: ZE31
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Ileum, ZE32

description:
Library name: ZE32
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Ileum, ZE33

description:
Library name: ZE33
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Ileum, ZE23

description:
Library name: ZE23
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Ileum, ZE22

description:
Library name: ZE22
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Ileum, ZE21

description:
Library name: ZE21
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, Isotype, Ileum, ZE24

description:
Library name: ZE24
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, Isotype, Ileum, ZE25

description:
Library name: ZE25
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Ileum, ZE27

description:
Library name: ZE27
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, Isotype, Ileum, ZE26

description:
Library name: ZE26
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Jejunum, ZE20

description:
Library name: ZE20
Tissue_anti_cd8b_gene_counts.rds

source_name: Jejunum

value: Jejunum


title: Tissue, Ighasec-/-, anti_CD8b, Jejunum, ZE19

description:
Library name: ZE19
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Jejunum, ZE18

description:
Library name: ZE18
Tissue_anti_cd8b_gene_counts.rds


title: Intestinal Epithelial Cells, Ighasec+/-, Isotype, Jejunum, 3J_Ep

description:
Library name: 3J_Ep
Epi_gene_counts.rds

value: Jejunal Intestinal Epithelial Cells


title: Tissue, Ighasec-/-, anti_CD8b, Ileum, ZE39

description:
Library name: ZE39
Tissue_anti_cd8b_gene_counts.rds

value: Ighasec-/-


title: Tissue, Ighasec+/-, anti_CD8b, Jejunum, ZE17

description:
Library name: ZE17
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Jejunum, ZE14

description:
Library name: ZE14
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Ileum, ZE28

description:
Library name: ZE28
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Ileum, ZE30

description:
Library name: ZE30
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Jejunum, ZE11

description:
Library name: ZE11
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Jejunum, ZE9

description:
Library name: ZE9
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, anti_CD8b, Jejunum, ZE8

description:
Library name: ZE8
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Jejunum, ZE13

description:
Library name: ZE13
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, anti_CD8b, Jejunum, ZE10

description:
Library name: ZE10
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, Isotype, Jejunum, ZE6

description:
Library name: ZE6
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, Isotype, Jejunum, ZE5

description:
Library name: ZE5
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Jejunum, ZE3

description:
Library name: ZE3
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, Isotype, Jejunum, ZE4

description:
Library name: ZE4
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Jejunum, ZE1

description:
Library name: ZE1
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, Isotype, Jejunum, ZE2

description:
Library name: ZE2
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, GF, Colon, ZE111

description: Library name: ZE111

source_name: Colon

extract_protocol:
1 cm of tissue from the beginning of the duodenum, the middle of the jejunum, the end of the ileum, and the middle of the colon was excised and preserved in RNAprotect (Qiagen) overnight at 4°C. The preserved tissue was then stored at -80°C until processing. Tissue was thawed on ice and transferred to a screw-cap tube containing 450 μL of RLT Plus buffer supplemented with 2-mercaptoethanol and equal quantities of 1.0mm and 0.5 mm zirconium oxide beads (Next Advance). Tissue was homogenized three times for 30 sec at a speed of 6 m/s using Bead Ruptor Elite mill homogenizer (Omni), with 1 min incubation on ice between each cycle. RNA from the lysates was purified using RNeasy Plus Mini kit (Qiagen) with the optional on-column DNase I digest step according to manufacturer protocol.
500 ng of RNA was used as input in the TruSeq Stranded mRNA Library Prep (Illumina) according to manufacturer’s specifications.

value: Colon

value: GF


title: Tissue, Ighasec-/-, GF, Colon, ZE110

description: Library name: ZE110


title: Tissue, Ighasec-/-, Isotype, Jejunum, ZE16

description:
Library name: ZE16
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, GF, Ileum, ZE107

description: Library name: ZE107


title: Tissue, Ighasec+/-, GF, Jejunum, ZE103

description: Library name: ZE103


title: Tissue, Ighasec+/-, GF, Colon, ZE109

description: Library name: ZE109


title: Tissue, Ighasec-/-, GF, Jejunum, ZE102

description: Library name: ZE102


title: Tissue, Ighasec+/-, GF, Jejunum, ZE101

description: Library name: ZE101


title: Tissue, Ighasec-/-, GF, Duodenum, ZE98

description: Library name: ZE98

source_name: Duodenum

value: Duodenum


title: Tissue, Ighasec-/-, Isotype, Jejunum, ZE15

description:
Library name: ZE15
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, GF, Duodenum, ZE99

description: Library name: ZE99

value: Ighasec+/-


title: Tissue, Ighasec-/-, anti_CD8b, Jejunum, ZE12

description:
Library name: ZE12
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec-/-, SPF, Colon, ZE92

description: Library name: ZE92

value: SPF


title: Tissue, Ighasec-/-, SPF, Colon, ZE91

description: Library name: ZE91


title: Tissue, Ighasec+/-, anti_CD8b, Jejunum, ZE7

description:
Library name: ZE7
Tissue_anti_cd8b_gene_counts.rds


title: Tissue, Ighasec+/-, SPF, Colon, ZE89

description: Library name: ZE89


title: Tissue, Ighasec-/-, SPF, Ileum, ZE84

description: Library name: ZE84


title: Tissue, Ighasec-/-, SPF, Ileum, ZE83

description: Library name: ZE83


title: Tissue, Ighasec+/-, SPF, Colon, ZE90

description: Library name: ZE90


title: Tissue, Ighasec-/-, SPF, Jejunum, ZE76

description: Library name: ZE76


title: Tissue, Ighasec-/-, SPF, Jejunum, ZE75

description: Library name: ZE75


title: Tissue, Ighasec-/-, GF, Ileum, ZE106

description: Library name: ZE106


title: Tissue, Ighasec+/-, SPF, Ileum, ZE81

description: Library name: ZE81


title: Tissue, Ighasec+/-, SPF, Ileum, ZE82

description: Library name: ZE82


title: Tissue, Ighasec+/-, SPF, Jejunum, ZE74

description: Library name: ZE74


title: Tissue, Ighasec+/-, GF, Ileum, ZE105

description: Library name: ZE105


title: Tissue, Ighasec-/-, SPF, Duodenum, ZE68

description: Library name: ZE68


title: Tissue, Ighasec-/-, SPF, Duodenum, ZE72

description: Library name: ZE72


title: Tissue, Ighasec+/-, SPF, Duodenum, ZE66

description: Library name: ZE66


title: Tissue, Ighasec+/-, SPF, Jejunum, ZE73

description: Library name: ZE73


title: Tissue, Ighasec-/-, GF, Colon, ZE63

description: Library name: ZE63


title: Tissue, Ighasec-/-, GF, Ileum, ZE56

description: Library name: ZE56


title: Tissue, Ighasec-/-, SPF, Colon, ZE60

description: Library name: ZE60


title: Tissue, Ighasec+/-, GF, Colon, ZE62

description: Library name: ZE62


title: genomic DNA from mESCs 205307790115_R05C01

description:
genomic DNA from mESCs
KO_2_mESCs

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: IkappBalpha-/-

value: knock-out

value: Timepoint 0h


title: Tissue, Ighasec+/-, SPF, Duodenum, ZE65

description: Library name: ZE65


title: Tissue, Ighasec+/-, SPF, Colon, ZE58

description: Library name: ZE58


title: Tissue, Ighasec-/-, GF, Ileum, ZE55

description: Library name: ZE55


title: Tissue, Ighasec+/-, SPF, Colon, ZE57

description: Library name: ZE57


title: Tissue, Ighasec-/-, SPF, Ileum, ZE52

description: Library name: ZE52


title: Tissue, Ighasec+/-, GF, Ileum, ZE54

description: Library name: ZE54


title: Tissue, Ighasec+/-, SPF, Ileum, ZE50

description: Library name: ZE50


title: Tissue, Ighasec+/-, SPF, Ileum, ZE49

description: Library name: ZE49


title: Tissue, Ighasec-/-, SPF, Duodenum, ZE67

description: Library name: ZE67


title: Tissue, Ighasec-/-, GF, Jejunum, ZE48

description: Library name: ZE48


title: Tissue, Ighasec-/-, GF, Colon, ZE64

description: Library name: ZE64


title: Tissue, Ighasec-/-, SPF, Colon, ZE59

description: Library name: ZE59


title: Tissue, Ighasec-/-, SPF, Jejunum, ZE43

description: Library name: ZE43


title: Tissue, Ighasec+/-, SPF, Jejunum, ZE42

description: Library name: ZE42


title: Tissue, Ighasec-/-, SPF, Jejunum, ZE44

description: Library name: ZE44


title: Tissue, Ighasec-/-, GF, Jejunum, ZE47

description: Library name: ZE47


title: Tissue, Ighasec+/-, SPF, Jejunum, ZE41

description: Library name: ZE41


title: Tissue, Ighasec-/-, GF, Duodenum, ZE39

description: Library name: ZE39


title: Tissue, Ighasec+/-, GF, Duodenum, ZE38

description: Library name: ZE38


title: Tissue, Ighasec-/-, SPF, Ileum, ZE51

description: Library name: ZE51


title: Tissue, Ighasec-/-, SPF, Duodenum, ZE35

description: Library name: ZE35


title: Tissue, Ighasec-/-, SPF, Colon, ZE27

description: Library name: ZE27


title: Tissue, Ighasec-/-, SPF, Colon, ZE28

description: Library name: ZE28


title: Tissue, Ighasec-/-, GF, Duodenum, ZE40

description: Library name: ZE40


title: Tissue, Ighasec+/-, SPF, Duodenum, ZE33

description: Library name: ZE33


title: Tissue, Ighasec+/-, SPF, Duodenum, ZE34

description: Library name: ZE34


title: Tissue, Ighasec+/-, GF, Colon, ZE30

description: Library name: ZE30


title: Tissue, Ighasec+/-, GF, Colon, ZE29

description: Library name: ZE29


title: Tissue, Ighasec+/-, SPF, Colon, ZE25

description: Library name: ZE25


title: Tissue, Ighasec+/-, GF, Jejunum, ZE46

description: Library name: ZE46


title: Tissue, Ighasec-/-, GF, Colon, ZE31

description: Library name: ZE31


title: Tissue, Ighasec-/-, GF, Colon, ZE32

description: Library name: ZE32


title: Tissue, Ighasec-/-, GF, Ileum, ZE23

description: Library name: ZE23


title: Tissue, Ighasec+/-, SPF, Colon, ZE26

description: Library name: ZE26


title: Tissue, Ighasec-/-, GF, Ileum, ZE24

description: Library name: ZE24


title: Tissue, Ighasec+/-, GF, Ileum, ZE21

description: Library name: ZE21


title: Tissue, Ighasec-/-, SPF, Ileum, ZE20

description: Library name: ZE20


title: Tissue, Ighasec+/-, GF, Ileum, ZE22

description: Library name: ZE22


title: Tissue, Ighasec-/-, SPF, Ileum, ZE19

description: Library name: ZE19


title: Tissue, Ighasec+/-, SPF, Ileum, ZE17

description: Library name: ZE17


title: Tissue, Ighasec+/-, SPF, Ileum, ZE18

description: Library name: ZE18


title: Tissue, Ighasec-/-, GF, Jejunum, ZE15

description: Library name: ZE15


title: Tissue, Ighasec-/-, GF, Jejunum, ZE16

description: Library name: ZE16


title: Tissue, Ighasec+/-, GF, Jejunum, ZE14

description: Library name: ZE14


title: Tissue, Ighasec+/-, GF, Jejunum, ZE13

description: Library name: ZE13


title: Tissue, Ighasec+/-, SPF, Jejunum, ZE9

description: Library name: ZE9


title: Tissue, Ighasec+/-, GF, Duodenum, ZE6

description: Library name: ZE6


title: Tissue, Ighasec-/-, GF, Duodenum, ZE8

description: Library name: ZE8


title: Tissue, Ighasec-/-, GF, Duodenum, ZE7

description: Library name: ZE7


title: Tissue, Ighasec+/-, SPF, Jejunum, ZE10

description: Library name: ZE10


title: Tissue, Ighasec+/-, GF, Duodenum, ZE5

description: Library name: ZE5


title: Tissue, Ighasec+/-, GF, Duodenum, ZE97

description: Library name: ZE97


title: Tissue, Ighasec-/-, SPF, Duodenum, ZE4

description: Library name: ZE4


title: Tissue, Ighasec-/-, SPF, Duodenum, ZE3

description: Library name: ZE3


title: Tissue, Ighasec+/-, SPF, Duodenum, ZE1

description: Library name: ZE1


title: Tissue, Ighasec+/-, SPF, Duodenum, ZE2

description: Library name: ZE2


title: UNTR+FTY (biol 2)

city: Zürich

first: Hakan

last: Köksal

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: control

data_processing:
read alignment, cell barcode demultiplexing, deduplication of reads, generation of expression matrices and quality report were done using the Rhapsody Sequence Analysis Pipeline v2.0 (https://www.bdbiosciences.com/en-us/products/software/rhapsody-sequence-analysis-pipeline)
Assembly: mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: tumor

extract_protocol:
Tumors were collected in RPMI with 10% FCS and digested with 1 mg/ml collagenase IV (Thermo Fisher Scientific) and 50 µg/ml DNase I (Roche) for 45 minutes at 37°C using a rotating device. The cells were then washed in PBS with 2 mM EDTA and passed through a 70-µm filter (Biologix). Red blood cells were lysed with a buffer (17 mM Tris pH 7.2, 144 mM NH4Cl) for 2 minutes, followed by a PBS wash.
Library amplification was carried out following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119 (02))

value: tumor

value: female

value: 12 weeks old

value: CD8+ T-cells


title: KO5

description: Library name: Sample 10

data_processing:
Reads were mapped on the Oryzias latipes reference assembly using BWA (v0.7.17-r1188).
The reads per million mapped reads (RPM) was calculated using Salmon (v1.4.0).
Assembly: Oryzias latipes reference assembly
Supplementary files format and content: Excel file include RPM for each sample.

source_name: Liver

growth_protocol: Medaka were kept under long-day conditions.

extract_protocol:
Total RNA of liver were isolated with elimination of DNA contamination using DNase.
Libraries were prepared using the Lasy-Seq v1.1 protocol for 3' RNA sequencing (Kamitani et al., 2019).

treatment_protocol: Liver of wild-type and pd1 knockout medaka kept under long-day conditions were sampled at 12:00.

value: Liver

value: pd1 knockout

value: long-day conditions


title: KO4

description: Library name: Sample 9


title: RT+FTY (biol 2)

description: irradiated