title: mp34_niv_IL21_IL2_low_4

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

data_processing:
Sequencing reads were processed with MiXCR software (MiLaboratories) in order to extract TCRβ CDR3 clonotypes. MiXCR aligns reads to human V, D and J TCR gene segments.
VDJtools software was used for processing of MiXCR output TCR repertoire data, calculation of TCR repertoire diversity, and pre-processing of TCR repertoires (i.e., pooling of joined TCR repertoires and down-sampling of TCR repertoires)
Supplementary_files_format_and_content: Tab delimeted text files include the TCR clonotype tables in VDJtools output format

source_name: Bulk TILs cultivated with Nivolumab(20 μg/mL)+IL2+IL21 for 9 days

growth_protocol: TILs were expanded from the separate tumor fragments in different cultivation conditions. For patient mp26 conditions were - IL2(300IU/ml); IL2(200 IU/ml)+IL21(25ng/ml); Nivolumab(20 μg/mL)+IL2+IL21; Nivolumab+IL2+IL21+IFNγ(100 μg/ml). For patients mp34 and mp41 conditions were: IL2(300IU/ml); IL2(200 IU/ml; IL2(200 IU/ml)+IL21(25ng/ml); Nivolumab(20 μg/mL)+IL2+IL21).

extract_protocol:
RNA from fresh-frozen tumor fragments was isolated using TRIzol reagent(Invitrogen). RNA from RLT-lysed cells was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. RNA concentration was measured with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, US). No more than 500 ng of total RNA was used for cDNA synthesis.
cDNA libraries were generated using the Human RNA TCR Multiplex kit (MiLaboratories), according to the manufacturer's protocol.
other: targeted RNA-seq (TCR amplicon seq)

treatment_protocol: CD39+PD-1+ (double-positive, DP) and non-DP CD4+ and CD8+ T cells from TILs freshly isolated from lymph node metastases from 8 melanoma patients.

tag: subset

value: Bulk TILs

tag: patient

value: melanoma patient 34

tag: tcr chain

value: TCR beta


title: YCJQ_T

status: Public on Feb 14 2024

type: SRA

city: beijing

first: Chen

last: Tan

state: BEIJING

address: BEIJING DONGJIAOMIN NO 1

country: China

institute: Capital Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

molecule: total RNA

organism: Homo sapiens

source_name: larynx and hypopharynx

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: individual

value: Patient YCJQ

tag: disease state

value: laryngo-hypopharyngeal carcinoma

tag: tissue

value: larynx and hypopharynx

tag: tissue type

value: Tumor

tag: response to induction chemotherapy

value: non-response

tag: gender

value: male


title: lateral hypothalamus rostral, low workload, ZT13, rep1

city: La Jolla

first: Laura

last: van Rosmalen

state: California

address: 10010 N Torrey Pines Rd

department: RBIO-P

country: USA

institute: Salk Institute for Biological Studies

description:
LHr_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
TES_L_ZT21_X27 was removed from the analysis because it was an extreme outlier
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

organism: Mus musculus

source_name: lateral hypothalamus rostral

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 300ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

value: lateral hypothalamus rostral

tag: strain

value: CBA/CaJ

tag: Sex

tag: treatment

value: low workload

tag: zeitgeber time


title: lateral hypothalamus rostral, low workload, ZT09, rep2

description:
LHr_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ZZK_T

value: Patient ZZK

value: response


title: lateral hypothalamus rostral, low workload, ZT09, rep1

description:
LHr_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp34_niv_IL21_IL2_low_2


title: ZSQ_T

value: Patient ZSQ

value: female


title: mp34_niv_IL21_IL2_low_1


title: lateral hypothalamus rostral, low workload, ZT05, rep2

description:
LHr_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ZSQ_N

value: Normal


title: ZZK_N


title: mp34_IL21_IL2_low_4

source_name: Bulk TILs cultivated with IL2(200 IU/ml)+IL21(25ng/ml) for 9 days

value: Bulk TILs


title: lateral hypothalamus rostral, low workload, ZT01, rep2

description:
LHr_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp34_IL21_IL2_low_3

value: melanoma patient 34


title: HQCQ_T

value: Patient HQCQ


title: WQQ_T

value: Patient WQQ


title: WL_T

value: Patient WL

value: laryngo-hypopharyngeal carcinoma


title: lateral hypothalamus rostral, low workload, ZT01, rep1

description:
LHr_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: lateral hypothalamus caudal, high workload, ZT21, rep2

description:
LHc_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: lateral hypothalamus caudal

value: lateral hypothalamus caudal

value: high workload


title: mp34_IL21_IL2_low_2

value: TCR beta


title: S1_D3_18h, replicate 1, scRNAseq

city: London

first: Tiago

last: Rito

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: 10x Genomics Chromium Single-Cell 3′ mRNA V3.1

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the Homo sapiens GRCh38-3.0.0 reference genome using CellRanger (v4.0.0, 10X Genomics) and the analyses were performed using Scanpy67 (v1.7.0). Cells were filtered for a minimum of 200 genes, mitochondrial UMIs between 1-20%, total counts between 10,000-50,000 and doublet cells were filtered using Scrublet68 with a threshold of 0.2. Counts were normalized to a target sum of 10000 excluding highly expressed genes (3%). “Highly variable genes” were called using Scanpy’s function with default parameters.
Assembly: Homo sapiens GRCh38-3.0.0
Supplementary files format and content: mtx

source_name: differentiated hESCs

extract_protocol:
16 (day7) to 32 (day3) notoroids were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation and another incubation at 37°C. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The single-cell suspension was diluted to 1300 cells/uL and had a viability >95%.
The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs.

tag: cell line

value: differentiated hESCs

tag: cell type

tag: day

tag: hour


title: lateral hypothalamus caudal, high workload, ZT21, rep1

description:
LHc_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ

value: male


title: WGYQ_T

value: Patient WGYQ

value: larynx and hypopharynx

value: Tumor

value: non-response


title: mp34_niv_IL21_IL2_low_3

tag: subset


title: mp34_IL2_low_4

source_name: Bulk TILs cultivated with IL2(200 IU/ml) for 9 days

tag: patient


title: PXL_T

value: Patient PXL


title: mp34_IL2_low_3

value: Bulk TILs

tag: tcr chain


title: ZTS_N

tag: individual

value: Patient ZTS

value: Normal


title: PCS_T

value: Patient PCS

tag: disease state

value: response


title: lateral hypothalamus caudal, high workload, ZT17, rep1

description:
LHc_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: tissue


title: CBJ_N

value: Patient CBJ

value: laryngo-hypopharyngeal carcinoma

tag: tissue type


title: mp34_IL2_low_2

value: melanoma patient 34


title: lateral hypothalamus caudal, high workload, ZT13, rep2

description:
LHc_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus caudal

value: high workload


title: lateral hypothalamus caudal, high workload, ZT17, rep2

description:
LHc_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: lateral hypothalamus rostral, low workload, ZT05, rep1

description:
LHr_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus rostral

value: male

value: low workload


title: mp34_IL2_low_1

value: TCR beta


title: lateral hypothalamus caudal, high workload, ZT09, rep2

description:
LHc_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: WSYQ_T

value: Patient WSYQ

value: larynx and hypopharynx

value: Tumor

tag: response to induction chemotherapy

value: female


title: mp34_IL2_high_4

source_name: Bulk TILs cultivated with IL2 (3000 IU/ml) for 9 days

value: Bulk TILs


title: mp34_IL2_high_3


title: lateral hypothalamus caudal, high workload, ZT09, rep1

description:
LHc_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: lateral hypothalamus caudal, high workload, ZT13, rep1

description:
LHc_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ZTS_T

value: Patient ZTS

value: non-response

tag: gender


title: mp34_IL21_IL2_low_1


title: lateral hypothalamus caudal, high workload, ZT05, rep2

description:
LHc_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: strain


title: PCS_N

value: Patient PCS

value: Normal

value: response


title: mp34_IL2_high_2

value: melanoma patient 34


title: WL_N

value: Patient WL

value: laryngo-hypopharyngeal carcinoma


title: WQQ_N

value: Patient WQQ


title: mp34_IL2_high_1


title: lateral hypothalamus caudal, high workload, ZT05, rep1

description:
LHc_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus caudal

value: CBA/CaJ

tag: Sex

value: male

value: high workload


title: MCF7_ESR1Y537N_E2_3

city: Durham

first: Erika

last: Crosby

state: NC

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

library_source: genomic

data_processing:
STAR alignment (2.7.3a) to hg19 reference genome
Quantify samples with 100% read overlap with features, minimum number of reads = 10, and juntions reads requred to match introns.
TMM normalization
Identify differentially expressed genes using Partek Flow GSA algorithm
Genome_build: hg19
Supplementary_files_format_and_content: Normalized gene counts are listed with features in columns in a txt file

molecule: genomic DNA

source_name: Cell line

growth_protocol: MCF7 cells expressing ESR1-WT or ESR1-Y537N were cultured in media supplemented with charcoal-dextran treated FBS (Omega Scientific)

extract_protocol:
Total RNA was extracted using a RNeasy Kit (Qiagen)
libraries prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s protocol

treatment_protocol: with or without [20nM] estrogen for 24 hours

value: breast cancer cell line MCF7

tag: transfected with

tag: treatment


title: WGMQ_T

value: Patient WGMQ

value: larynx and hypopharynx

value: Tumor


title: MCF7_ESR1Y537N_E2_4

tag: cell line


title: lateral hypothalamus caudal, low workload, ZT21, rep2

description:
LHc_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload

tag: zeitgeber time


title: lateral hypothalamus caudal, high workload, ZT01, rep1

description:
LHc_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: PXL_N

value: Patient PXL

value: non-response


title: lateral hypothalamus caudal, low workload, ZT21, rep1

description:
LHc_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: lateral hypothalamus caudal, low workload, ZT17, rep2

description:
LHc_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: LRM_N

value: Patient LRM

value: Normal


title: ZLT_N

value: Patient ZLT

value: response


title: MCF7_ESR1Y537N_E2_2


title: MCF7_ESR1Y537N_E2_1


title: WY_T

value: Patient WY

value: laryngo-hypopharyngeal carcinoma


title: MCF7_ESR1Y537N_NoE2_4


title: lateral hypothalamus caudal, low workload, ZT13, rep2

description:
LHc_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus caudal


title: MCF7_ESR1Y537N_NoE2_3


title: MCF7_ESR1Y537N_NoE2_2


title: lateral hypothalamus caudal, low workload, ZT13, rep1

description:
LHc_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: MCF7_ESR1Y537N_NoE2_1


title: lateral hypothalamus caudal, low workload, ZT09, rep2

description:
LHc_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: MCF7_ESR1WT_E2_3


title: WY_N


title: MCF7_ESR1WT_E2_2


title: LJGQ_T

value: Patient LJGQ


title: LRM_T


title: LJG_N

value: Patient LJG


title: lateral hypothalamus caudal, low workload, ZT05, rep2

description:
LHc_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: MCF7_ESR1WT_NoE2_4

value: breast cancer cell line MCF7


title: lateral hypothalamus caudal, low workload, ZT17, rep1

description:
LHc_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: MCF7_ESR1WT_E2_1


title: lateral hypothalamus caudal, low workload, ZT05, rep1

description:
LHc_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CBJQ_T

value: Patient CBJQ

value: larynx and hypopharynx


title: WSY_N

value: Patient WSY

value: female


title: lateral hypothalamus caudal, low workload, ZT01, rep1

description:
LHc_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: hippocampus, high workload, ZT21, rep2

description:
HIP_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: hippocampus

value: hippocampus

value: high workload


title: ZLTQ_T

value: Patient ZLTQ

value: Tumor


title: MCF7_ESR1WT_NoE2_1


title: MCF7_ESR1WT_NoE2_2


title: hippocampus, high workload, ZT21, rep1

description:
HIP_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ZXZ_T

value: Patient ZXZ

value: response


title: MCF7_ESR1WT_NoE2_3


title: RNAseq_Atf7ip2-/-_PS_rep2

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: UC Davis

data_processing:
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) with the parameter ‘--paired’
Trimmed reads were aligned to the mouse (GRCm38/mm10) genome using STAR.
Raw read counts for each gene were generated by featurecounts, based on the UCSC mouse refGene annotation incorporated with ERCC spike-ins.
To perform ERCC spike-in normalization, we use the packages edgeR[19] and Limma[20] for analysis. First, normalization factors were calculated using the number of reads mapped to ERCC. Filtered raw reads (>2 at least in one sample) were assessed for library size using normalization factors and voom-transformed. The topTable function was used to identify the differentially expressed genes (DEGs: FDR<0.05; Log2FoldChange >2).
Assembly: mm10
Supplementary files format and content: Gene expression matrix: Spike-in normalized reads count with voom-transformed.

source_name: testis

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer's instructions.
RNA-seq libraries using the Smart-Seq2 method were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instructions.

value: testis

value: primary cells

tag: cell type

value: Pachytene spermatocytes

tag: genotype


title: YHJ_T

value: Patient YHJ

value: laryngo-hypopharyngeal carcinoma

value: male


title: hippocampus, high workload, ZT13, rep2

description:
HIP_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: RNAseq_Atf7ip2-/-_PS_rep3


title: hippocampus, high workload, ZT17, rep1

description:
HIP_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ZXZ_N

value: larynx and hypopharynx

value: Normal


title: lateral hypothalamus caudal, low workload, ZT09, rep1

description:
LHc_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: lateral hypothalamus caudal


title: YHJ_N


title: RNAseq_Atf7ip2-/-_PS_rep1


title: RNAseq_Atf7ip2+/+_PS_rep3


title: hippocampus, high workload, ZT09, rep2

description:
HIP_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CDMQ_T

value: Patient CDMQ

value: non-response


title: hippocampus, high workload, ZT13, rep1

description:
HIP_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: hippocampus

value: high workload


title: hippocampus, high workload, ZT09, rep1

description:
HIP_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: RNAseq_Atf7ip2+/+_PS_rep1


title: Alcoholic Cirrhosis Patient 3

city: Baltimore

first: Brandon

last: Peiffer

state: Maryland

address: 720 Rutland ave., Ross 771

department: Surgery

institute: Johns Hopkins

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic (v.0.36).
Trimmed reads were mapped to the Homo sapiens grch38 reference genome available on ENSEMBL using Hisat2 (v2.2.0).
Aligned reads were counted by FeatureCounts (v2.0.0).
Assembly: Homo sapiens grch38
Supplementary files format and content: .txt with raw counts

source_name: Liver

extract_protocol:
Qiagen RNeasy mini kit
RNA libraries were prepared using TRUseq library prep kit and manufacturers instructions.

value: Liver


title: Alcoholic Cirrhosis Patient 2


title: Alcoholic Cirrhosis Patient 4


title: hippocampus, high workload, ZT01, rep2

description:
HIP_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Alcoholic Hepatitis Patient 64


title: hippocampus, high workload, ZT05, rep2

description:
HIP_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Alcoholic Cirrhosis Patient 1


title: CutRun_Atf7ip2-/-_PS_H3K9me3_rep2

data_processing:
For CUT&RUN/Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) .
Trimmed reads were aligned mouse (GRCm38/mm10) genome using Bowtie2 (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Exogenous E. coli DNA added was used as spike-in DNA for CUT&RUN. For mapping E.coli spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).
Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli mapping files (the formula used for calculation of scale factors = 1,000,000 / spike-in reads).
For visualization using the Integrative Genomics Viewer55 (version 2.5.3), spike-in normalized genome coverage tracks were generated using the genomecov function of bedtools (version 2.29.2) with the ‘-bg -scale $scale_factor’ parameter.
SEACR (https://seacr.fredhutch.org/ ) was used for ATF7IP2 peak calling and HOMER (version 4.11) was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT& Run

extract_protocol:
CUT&Tag libraries of WT PS were prepared as previously described (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ). CUT&RUN libraries of Atf7ip2+/+ and Atf7ip2-/- or WT PS were conducted as previously described (a step-by-step protocol https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-14egnr4ql5dy/v3 ).
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ). CUT&RUN libraries were constructed using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

tag: chip antibody

tag: fraction

value: whole cell


title: RNAseq_Atf7ip2+/+_PS_rep2


title: hippocampus, high workload, ZT17, rep2

description:
HIP_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Alcoholic Cirrhosis Patient 5


title: Alcoholic Hepatitis Patient 63


title: CutRun_Atf7ip2+/+_PS_H3K9me3_rep2


title: CutRun_Atf7ip2+/+_PS_H3K9me3_rep1


title: hippocampus, high workload, ZT05, rep1

description:
HIP_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: hippocampus, high workload, ZT01, rep1

description:
HIP_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CutRun_Atf7ip2-/-_PS_H3K9me3_rep1


title: hippocampus, low workload, ZT21, rep2

description:
HIP_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: CutRun_WT_PS_H3K9me3_rep2

value: WT

value: testis


title: Alcoholic Hepatitis Patient 53


title: Alcoholic Hepatitis Patient 60


title: hippocampus, low workload, ZT21, rep1

description:
HIP_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CutRun_WT_PS_H3K9me3_rep1

value: primary cells

value: Pachytene spermatocytes


title: hippocampus, low workload, ZT17, rep2

description:
HIP_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Alcoholic Hepatitis Patient 51


title: hippocampus, low workload, ZT17, rep1

description:
HIP_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CutTag_WT_PS_ATF7IP2_rep1

description: CutTag_WT_PS_ATF7IP2_RPKM.bw; CutTag_WT_PS_ATF7IP2_peaks.bed

data_processing:
For CUT&RUN/Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) .
Trimmed reads were aligned mouse (GRCm38/mm10) genome using Bowtie2 (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Exogenous E. coli DNA added was used as spike-in DNA for CUT&RUN. For mapping E.coli spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).
Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli mapping files (the formula used for calculation of scale factors = 1,000,000 / spike-in reads).
For visualization using the Integrative Genomics Viewer55 (version 2.5.3), spike-in normalized genome coverage tracks were generated using the genomecov function of bedtools (version 2.29.2) with the ‘-bg -scale $scale_factor’ parameter.
SEACR (https://seacr.fredhutch.org/ ) was used for ATF7IP2 peak calling and HOMER (version 4.11) was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

value: nuclei


title: hippocampus, low workload, ZT13, rep2

description:
HIP_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: Alcoholic Hepatitis Patient 8


title: F6IS

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

data_processing:
The reads were first mapped to the Mouse genome (mm39) UCSD transcript set using Bowtie2 and the gene expression level was estimated using RSEM to generate TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with P < 0.05 and more than 1.5-fold changes were considered differentially expressed.
Assembly: Mouse genome (mm39) obtained from UCSD
Supplementary files format and content: Text file containing all detected genes (symbol, name) fold change, p-value, FDR, and TMM values for each of the individual samples.

source_name: primary cd31-positive cells

extract_protocol:
RNA was extracted using Trizol and Direct-Zol RNA isolation kit (Zymo)
PolyA enrichment and Kapa HyperPrep Library Construction Kit

treatment_protocol: Primary endothelial cells were isolated from the livers of male and female C57BL6J mice. Cells were cultured in standard conditions until undergoing treatment with indoxyl sulfate (100 micromolar) and hypoxia and nutrient deprivation (6 hours)

value: primary cd31-positive cells

value: Female

value: 100uM IS + Hypoxia


title: CutTag_WT_PS_ATF7IP2_rep2


title: Alcoholic Hepatitis Patient 6


title: hippocampus, low workload, ZT13, rep1

description:
HIP_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: F5IS


title: Donor Patient 8


title: Donor Patient 6


title: hippocampus, low workload, ZT09, rep1

description:
HIP_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: M6IS

value: Male


title: M5IS


title: hippocampus, low workload, ZT05, rep1

description:
HIP_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: rnaseT1_5

first: Taeyoung

last: Hwang

state: MD

address: 855 N. Wolfe St, 3rd floor, Suite 300

institute: Lieber Institute for Brain Development

description: R2 file contains UMI.

data_processing:
For ChIP-seq, Illumina sequencing adapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC was clipped by cutadapt. BWA was used for alignment with the following options: “-q 5 -l 32 -k 2”.  Samtools was used to keep only the primary alignments whose mapping score was greater than 30. Potential duplicates identified by Picard MarkDuplicates were removed. In case of sequencing with UMI (Unique Molecular Identifiers), the uniquely mapped reads were only used: the reads were flagged as duplicates if they had same UMI at the same positions in alignment. Coverage files (bigwig) were generated using bedtools and UCSC bedGraphToBigWig after pooling replicates for a given clone. Coverage is scaled as reads per million reads (RPM). Macs2 was used to call peaks with "--keep-dup all --nomodel --extsize X --bdg --broad" where X was found by SPP.
For fRIP-seq, STAR was used for alignment with GENCODE (v27) gene annotation. Samtools was used to keep only the primary alignments. Potential duplicates identified by Picard MarkDuplicates were removed. FeatureCounts were used to count reads in gene bodies (GENCODE v27) in a strand specific way.
For RNA-seq, STAR was used for alignment with GENCODE (v27) gene annotation. The number of reads were counted in a strand specific way for every gene annotated in GENCODE (v27) by featureCounts.
Assembly: hg38
Supplementary files format and content: For fRIP-seq, comma seperated file has the read counts for every gene in the GENCODE (v27) gene annotation.
Supplementary files format and content: For RNA-seq, comma seperated file has the transcripts per million reads (TPM) for every gene in the GENCODE (v27) gene annotation.
Supplementary files format and content: For ChIP-seq, bigwigs and Macs2 peaks were provided for biologically independent clones. For RNaseA and RNaseT1 samples, comma seperated file has the read counts for every gene in the GENCODE (v27) gene annotation.

source_name: iPSC

growth_protocol: Undifferentiated iPSCs were cultured in Essential 8 Flex medium on Vitronection-coated plates. Cardiomyocyte differentiation was induced using GSK3 inhibitor CHIR99021 and Wnt inhibitor IWP2 (GiWi protocol, Lian et al. Nature Protocol 2013)

extract_protocol:
Total RNA or RNA samples in fRIP-seq were extracted with Trizol following manufactuer's protocol. DNA samples in ChIP-seq was extracted using phenol-chloroform.
KAPA RNA Hyperprep kit with riboerase (RNA-seq and fRIP-seq), KAPA HyperPlus Kit (ChIP-seq) with or without IDT xGen UMI adapters.

treatment_protocol: For the RNase A treatment, 5 µg/mL of RNase A was added in pulldown step together with the primary antibody in the ChIP experiment; For the triptolide drug treatment, WT iPSC (two clones, two replicates each) grown to 80% confluency in Essential 8 flex media on vitronectin were treated with 10 µM triptolide (Sigma-Aldrich T3652) for 5 hours, after which cells were harvested and crosslinked for ChIP analysis.

value: iPSC

tag: antibody

tag: replicate

value: Replicate 2


title: F4IS


title: Alcoholic Hepatitis Patient 57


title: rnaseT1_4

description: R2 file contains UMI.

value: Replicate 1


title: hippocampus, low workload, ZT05, rep2

description:
HIP_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: hippocampus


title: rnaseT1_6

description: R2 file contains UMI.

value: Replicate 3


title: hippocampus, low workload, ZT01, rep2

description:
HIP_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: KO_3

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and overrepresented sequences have been removed using cutadapt software (https://cutadapt.readthedocs.io/ en/stable/).
Further reads preprocessing was performed by trim_galore with default parameters.
Mapping of RNA-seq reads was done using bowtie2 with default parameters for RNA-seq data.
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Assembly: mm10
Supplementary files format and content: txt format; raw counts for two experimental conditions with 3 replicates each.

source_name: Neural stem cells

growth_protocol: Primary mouse neural stem cells (mNSC) were isolated from the brain cortex of E13.5 embryos, and enriched using the neurosphere formation technique. The neurospheres were then expanded by culturing on laminin (5 µg/mL, overnight, 37°C) precoated dishes, in the presence of NeuroCult Proliferation mNSC media (05702, Stem Cell Technologies) that is supplemented with fibroblast growth factor (FGF) (F0291, Sigma) and epidermal growth factor (EGF) (E4127, Sigma) at 10 and 20 ng/mL, respectively.

extract_protocol: The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: Nestin-Cre (B6.Cg-Tg(Nes-cre)1Kln/J) mice (JAX stock #003771),Phf2 floxed mice, RIKEN BioResource Research Center (BRC).

value: Primary mouse neural stem cells

value: conditional KO (Nestin-Cre Tg, Phf2flox/flox) mutant


title: hippocampus, low workload, ZT01, rep1

description:
HIP_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: rnaseT1_2

description: R2 file contains UMI.

value: RNaseT1 negative


title: rnaseT1_3

description: R2 file contains UMI.


title: KO_2


title: habenula, high workload, ZT21, rep2

description:
HAB_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: habenula

value: habenula

value: high workload


title: KO_1


title: habenula, high workload, ZT21, rep1

description:
HAB_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: rnaseT1_1

description: R2 file contains UMI.


title: habenula, high workload, ZT17, rep2

description:
HAB_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: WT_2

value: Phf2 floxed mice, RIKEN BioResource Research Center (BRC).

value: wild type (Phf2flox/flox) control


title: hippocampus, low workload, ZT09, rep2

description:
HIP_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: WT_1


title: habenula, high workload, ZT17, rep1

description:
HAB_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: M4IS

value: primary cd31-positive cells

value: Male

value: 100uM IS + Hypoxia


title: rnaseA_28

value: iPSC

value: Replicate 1

value: RnaseA negative


title: habenula, high workload, ZT13, rep2

description:
HAB_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No_20%_N1E115_HiC_NcoI

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Mapped fastq files to reference genome using bowtie2
Cut the unmapped reads using dpnI and II cutsites
Mapped again using bowtie2
Merged global bam and local umapped bam using Samtools, and sorted.
Merged R1 and R2 using Samtools
Performed Hi-C filtering using mapped_2hic_fragments.py
validPairs files were merged into allValidPairs, and duplicates were removed.
Genome_build: mm10
Supplementary_files_format_and_content: AllValidPairs files were used to build .HiC files using Juicer (hicpro2juicebox.sh)

source_name: NOS1+ N1E115 mouse neuroblastoma cells

growth_protocol: NOS1+ N1E115 mouse neuroblastoma cells were cultured at high (20%) and low (4%) oxygen levels in the presence of 5% CO2 at ambient barometric pressure for 3 days.

extract_protocol:
Cells were cross-linked with 1% formaldehyde and quenched by 2.5 mol/L glycine and resuspended in lysis buffer provided with the Arima, Inc. HiC kit (Cat# A510008)
Libraries were prepared using KAPA Hyper Prep kit (Roche, Cat# KK8500)

value: brain

value: neuroblastoma

tag: agent

value: 20percent O2


title: rnaseA_26

value: Replicate 2

value: 2.3 ng/mL RNAseA dead mutant purified in-house


title: rnaseA_27

value: Replicate 3


title: habenula, high workload, ZT13, rep1

description:
HAB_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: tissue

value: habenula

value: high workload


title: Hy_4%_N1E115_HiC_NcoI

treatment_protocol: NOS1+ N1E115 mouse neuroblastoma cells were cultured at high (20%) and low (4%) oxygen levels in the presence of 5% CO2 at ambient barometric pressure for 3 days.

value: 4percent O2


title: rnaseA_25


title: habenula, high workload, ZT09, rep2

description:
HAB_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: N1E115_4%O2_H3K4me3_rep

data_processing:
Data were analyzed by the HiChIP pipeline developed by the Mayo Clinic Bioinformatics Core (PMCID: PMC4152589)
ChIP-seq reads were aligned to the mm10 genome assembly using BWA
Paired-end reads were aligned by BWA against the mm10 genome build. Duplicate reads were filtered out with Picard. Peak calling was performed with Sicer and MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak file is in bed format with column headers chr, peak_start, peak_end, peakname, pileup, peakCall, fold-change, -10logpvalue, -10logqvalue, peak_summit_position

extract_protocol:
Chromatin immunoprecipitation was performed on fixed and fragmented DNA isolated from N1E115 cells using anti-H3K27ac, anti-H3K27me3, anti-H3K36me3, anti-H3K4me1, and anti-H3K4me3 antibodies.
ThruPLEX DNA-seq Kit (Takara Bio USA)


title: habenula, high workload, ZT09, rep1

description:
HAB_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: rnaseA_24

value: 2.3 ng/mL RNAseA WT purified in-house


title: habenula, high workload, ZT05, rep2

description:
HAB_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: N1E115_4%O2_H3K36me3_rep


title: N1E115_4%O2_H3K4me1_rep


title: rnaseA_30


title: rnaseA_23


title: habenula, high workload, ZT01, rep2

description:
HAB_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: WT_3

value: Phf2 floxed mice, RIKEN BioResource Research Center (BRC).

value: Primary mouse neural stem cells

value: wild type (Phf2flox/flox) control


title: habenula, high workload, ZT05, rep1

description:
HAB_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: rnaseA_3

value: iPSC


title: rnaseA_22

value: Replicate 1


title: rnaseA_29

value: RnaseA negative


title: N1E115_4%O2 Input6

value: brain

value: neuroblastoma


title: habenula, high workload, ZT01, rep1

description:
HAB_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: habenula, low workload, ZT21, rep2

description:
HAB_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: N1E115_20%O2_H3K4me3_rep

value: 20percent O2


title: rnaseA_2

value: Replicate 2


title: rnaseA_1


title: habenula, low workload, ZT21, rep1

description:
HAB_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: habenula


title: N1E115_20%O2_H3K4me1_rep


title: habenula, low workload, ZT17, rep1

description:
HAB_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 769-P sh3

city: Guangzhou

first: Jiaxing

last: Zhang

state: China

address: 58 Zhongshan 2nd Road

institute: First Affiliated Hospital of Sun Yat-sen University

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DEseq/DESeq2/edgeR/DEGseq using read counts as input. The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05. All the differentially expressed genes were used for heat map analysis and KEGG ontology enrichment analyses. For KEGG enrichment analysis, a P-value < 0.05 was used as the threshold to determine significant enrichment of the gene sets.
Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Paired-end reads were aligned to the mouse reference genome mm10/hg19/rn6 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
Assembly: mm10/hg19/rn6

molecule: polyA RNA

source_name: kidney

extract_protocol:
Total RNA from tumor tissues or cell lines was extracted with TRIzol (Invitrogen). Total RNA was reverse transcribed using 4× Reverse Transcription Master Mix (EZBioscience, USA) according to the manufacturer’s instructions.
Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA).
The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: kidney

value: renal cell carcinoma

value: PABPC1L sh


title: MIBO, scRNAseq

city: Amherst

first: Narciso

last: Pavon

state: MA

address: Life Science Laboratories, 240 Thatcher Rd

department: Biochemistry and Molecular Biology

institute: University of Massachusetts

description: 10x Genomics

data_processing:
10x Could Analysis Cell Ranger Pipeline (Cell Ranger Count v7.0.1) was used for initial data processing including barcode processing, gene counting and aggregation.
Assembly: Reference genome (using 10x Cloud analysis): Human (GRCh38) 2020-A
Supplementary files format and content: H5

source_name: Forebrain organoid

extract_protocol:
Cell quality was performed using the Cellometer K2 cell counter (Nexcelom Bioscience). The single cell gene expression profiling was performed using the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) kit. Each sample (cell suspensions) were loaded onto a well of Chip G on the 10x Genomics Chromium Controller System following the manufacture’s user manual (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions. The qualitative analysis of cDNA was performed using the 2100 Agilent Bioanalyzer High Sensitivity assay. The cDNA libraries were constructed using the 10x Chromium Single cell 3’ Library Kit v3.1 (dual index) according to the manufacturer’s protocol.
The quality assessment of final Libraries was done on Qubit fluorometer using DNA High Sensitivity assay (Thermo Scientific), and 2100 Agilent Bioanalyzer High Sensitivity assay (Agilent Technologies). The libraries were sequenced on Illumina NextSeq 500 using NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles) sequencing kit, with following read length: 28 bp Read1 for 10x cell barcode and UMI, 90 bp Read 2 for insert, and 10 bp I7 and I5 for sample index. Phix (Illumina) was spiked in at 1% as per kit manual recommendation (10x Genomics).

value: Forebrain organoid

value: Neuronal

tag: age

value: 4 months old

value: Control

value: Purmorphamine Gradient


title: N1E115_20%O2_H3K36me3_rep


title: N1E115_20%O2_H3K27me3_rep


title: N1E115_4%O2_H3K27me3_rep

value: 4percent O2


title: 769-P sh2


title: N1E115_4%O2_H3K27ac_rep


title: habenula, low workload, ZT13, rep1

description:
HAB_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ

value: male


title: 769-P shnc3

value: PABPC1L shnc


title: N1E115_20%O2_H3K27ac_rep

value: brain

value: neuroblastoma


title: N1E115_20%O2 Input6

value: 20percent O2


title: 769-P sh1


title: N1E115_20%O2_input6

extract_protocol:
Chromatin immunoprecipitation was performed on fixed and fragmented DNA isolated from N1E115 cells using antibodies against CTCF, RAD21, H3K9ac, POLR2, POLR2S2p, and POLR2S5p.
ThruPLEX DNA-seq Kit (Takara Bio, USA)


title: 769-P shnc2


title: habenula, low workload, ZT09, rep1

description:
HAB_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: N1E115_4%O2_input6


title: habenula, low workload, ZT05, rep2

description:
HAB_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: habenula


title: 769-P shnc1

value: kidney


title: N1E115_20%O2_CTCF_rep

value: CTCF


title: buffered_rep3

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

description: rRNA depleted RNA

data_processing:
Kallisto software was used for quantifying transcript abundance from RNA-seq data against GRCh38 cDNA reference transcriptome from the Ensembl database, v96.
Assembly: GRCh38 cDNA reference transcriptome from the Ensembl database, v96.
Supplementary files format and content: xlsx

source_name: ATCC CCL-247

growth_protocol: HCT116 3D spheroids were initiated by seeding cell lines (750 cells/well) in ultra-low attachment 96-well plates in DMEM (GlutaMAX, 25mM D-glucose) supplemented with 10% heat-inactivated FBS and 1% P/S.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent, according to the manufacturer’s instructions. rRNA-depleted RNA was used for the library preparation.
The libraries were prepared with the NEBNext Ultra II Directional RNA library prep kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Libraries were paired-end sequenced (2*76 base pairs) on a NextSeq500 device (Illumina), with a read depth of 20 million.

treatment_protocol: No treatment

value: HCT116 cell line

value: KRAS G13D

value: colon carcinoma, adherent

tag: cell population

value: buffered


title: buffered_rep2

description: rRNA depleted RNA


title: habenula, low workload, ZT05, rep1

description:
HAB_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: habenula, low workload, ZT01, rep2

description:
HAB_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: habenula, low workload, ZT17, rep2

description:
HAB_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: habenula, low workload, ZT13, rep2

description:
HAB_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: buffered_rep1

description: rRNA depleted RNA


title: N1E115_4%O2_CTCF_rep


title: N1E115_20%O2_POLR2S2_rep


title: acidic_rep3

description: rRNA depleted RNA

value: acidic


title: dorsomedial hypothalamus, high workload, ZT21, rep2

description:
DMH_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: dorsomedial hypothalamus

value: dorsomedial hypothalamus

value: high workload


title: N1E115_20%O2_POLR2S5_rep


title: N1E115_20%O2_POLR2_rep


title: acidic_rep2

description: rRNA depleted RNA


title: habenula, low workload, ZT09, rep2

description:
HAB_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: N1E115_20%O2_RAD21_rep


title: dorsomedial hypothalamus, high workload, ZT17, rep2

description:
DMH_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: acidic_rep1

description: rRNA depleted RNA


title: N1E115_20%O2_H3K9ac_rep


title: dorsomedial hypothalamus, high workload, ZT17, rep1

description:
DMH_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: N1E115_4%O2_POLR2S5_rep

value: 4percent O2


title: mp41_niv_IL21_IL2_low_5

data_processing:
Sequencing reads were processed with MiXCR software (MiLaboratories) in order to extract TCRβ CDR3 clonotypes. MiXCR aligns reads to human V, D and J TCR gene segments.
VDJtools software was used for processing of MiXCR output TCR repertoire data, calculation of TCR repertoire diversity, and pre-processing of TCR repertoires (i.e., pooling of joined TCR repertoires and down-sampling of TCR repertoires)
Supplementary_files_format_and_content: Tab delimeted text files include the TCR clonotype tables in VDJtools output format

source_name: Bulk TILs cultivated with Nivolumab(20 μg/mL)+IL2+IL21 for 9 days

extract_protocol:
RNA from fresh-frozen tumor fragments was isolated using TRIzol reagent(Invitrogen). RNA from RLT-lysed cells was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. RNA concentration was measured with the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, US). No more than 500 ng of total RNA was used for cDNA synthesis.
cDNA libraries were generated using the Human RNA TCR Multiplex kit (MiLaboratories), according to the manufacturer's protocol.
other: targeted RNA-seq (TCR amplicon seq)

tag: subset

value: Bulk TILs

tag: patient

value: melanoma patient 41

tag: tcr chain

value: TCR beta


title: mp41_niv_IL21_IL2_low_4


title: N1E115_4%O2_POLR2_rep

value: brain

value: neuroblastoma


title: N1E115_4%O2_POLR2S2_rep


title: dorsomedial hypothalamus, high workload, ZT13, rep1

description:
DMH_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: strain

tag: Sex


title: dorsomedial hypothalamus, high workload, ZT09, rep2

description:
DMH_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: treatment


title: mp41_niv_IL21_IL2_low_2


title: N1E115_4%O2_RAD21_rep


title: habenula, low workload, ZT01, rep1

description:
HAB_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: habenula

value: low workload

tag: zeitgeber time


title: dorsomedial hypothalamus, high workload, ZT09, rep1

description:
DMH_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_niv_IL21_IL2_low_1


title: dorsomedial hypothalamus, high workload, ZT05, rep2

description:
DMH_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: N1E115_4%O2_H3K9ac_rep

tag: cell type


title: D-D-6

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

data_processing:
Reads were aligned to Mus musculus mm10 genome annotation (Ensembl) using STAR (2.5.3a)
Quality control of sequenced reads was performed using FastQC (Babraham Institute)
Gene count was performed using STAR (2.5.3a)
Differential gene expression analysis was performed with DESeq2 (1.22.1)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Adult neural stem cells

growth_protocol: NSCs were isolated from the SEZ and cultured as previously described in Belenguer et al, 2016

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Invitrogen, AM1560)
mRNA (stranded)

treatment_protocol: Differentiation was induced by culturing NSCs on an adhesive substrate in the absence of EGF

value: SEZ-isolated adult neural stem cells treateated to induce differentiation

tag: time

value: 6 hours


title: dorsomedial hypothalamus, high workload, ZT21, rep1

description:
DMH_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
TES_L_ZT21_X27 was removed from the analysis because it was an extreme outlier
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 300ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions


title: mp41_IL21_IL2_low_4

source_name: Bulk TILs cultivated with IL2(200 IU/ml)+IL21(25ng/ml) for 9 days


title: dorsomedial hypothalamus, high workload, ZT01, rep2

description:
DMH_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: D-D-1

value: 1 hour


title: mp41_IL21_IL2_low_5


title: mp41_IL21_IL2_low_3


title: mp41_IL21_IL2_low_2


title: D-C-6


title: mp41_niv_IL21_IL2_low_6


title: D-D-0

value: 0 hours


title: dorsomedial hypothalamus, low workload, ZT21, rep2

description:
DMH_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: dorsomedial hypothalamus, high workload, ZT13, rep2

description:
DMH_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: dorsomedial hypothalamus, high workload, ZT01, rep1

description:
DMH_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: D-C-1


title: D-C-0


title: mp41_niv_IL21_IL2_low_3


title: dorsomedial hypothalamus, low workload, ZT21, rep1

description:
DMH_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_IL21_IL2_low_1


title: D-B-6


title: mp41_IL2_low_6

source_name: Bulk TILs cultivated with IL2(200 IU/ml) for 9 days


title: dorsomedial hypothalamus, low workload, ZT17, rep1

description:
DMH_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: D-B-1


title: D-B-0


title: dorsomedial hypothalamus, high workload, ZT05, rep1

description:
DMH_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_IL2_low_3


title: mp41_IL2_low_4


title: dorsomedial hypothalamus, low workload, ZT13, rep2

description:
DMH_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Usp18f/f LysM-Cre

first: Sayuri

last: Miyauchi

address: 3855 Health Sciences Drive

institute: University of California, San Diego

description: L2_CKDL210001524-1a-SI_GA_A8_HFN7VBBXX_S1_L003

data_processing:
Samples were demultiplexed and reads were aligned using CellRanger (v3.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger matrix output. Contains matrix of genes, counts and cell barcodes.

source_name: B16F10 tumor

growth_protocol: B16F10 melanoma was subcutaneously injected into control (Usp18f/f)  or myeloid-specific Usp18 knockout (Usp18f/f LysM-Cre) mice. Tumors were harvested 14 days after tumor injection.

extract_protocol:
Single cell suspension was prepared from harvested tumors. 4 tumors per group were pooled. Live CD45+ cells were sorted on BD FACSAria.
Libraries were constructed with 10x Genomics Chromium Single Cell 3' Reagent Kits v3 following the manufacure's protocol. Libraries were sequenced on Illumina HiSeq 4000.

tag: host strain background

tag: mouse genotype

value: Usp18f/f LysM-Cre


title: mp41_IL2_low_2

value: melanoma patient 42


title: dorsomedial hypothalamus, low workload, ZT13, rep1

description:
DMH_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: dorsomedial hypothalamus


title: dorsomedial hypothalamus, low workload, ZT09, rep2

description:
DMH_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: dorsomedial hypothalamus, low workload, ZT05, rep2

description:
DMH_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: mp41_IL2_low_1


title: Usp18f/f

description: L1_CKDL210001523-1a-SI_GA_A7_HFN7VBBXX_S2_L003


title: dorsomedial hypothalamus, low workload, ZT09, rep1

description:
DMH_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Hy_4%_N1E115_HiC_NcoI rep2

data_processing:
Map fastq files to reference genome using bowtie2
Cut the unmapped reads using NcoI cutsites
Map again using bowtie2
Merge global bam and local umapped bam using Samtools, and sort.
Merge R1 and R2 using Samtools
Perform Hi-C filtering using mapped_2hic_fragments.py
validPairs files are merged into allValidPairs, and duplicates are removed.
Genome_build: mm10
Supplementary_files_format_and_content: AllValidPairs fils are used to build .HiC files using Juicer (hicpro2juicebox.sh)

growth_protocol: NOS1+ N1E115 mouse neuroblastoma cells were cultured under normoxia (20% O2) and hypoxia (4% O2) for 3 days

extract_protocol: Cells were  cross-linked with 1% formaldehyde, quenched with 2.5 mol/L glycine, lysed, digested by NcoI, labeld with biotin and ligated.

treatment_protocol: 4% and 20% oxygen

value: neuroblast


title: dorsomedial hypothalamus, low workload, ZT17, rep2

description:
DMH_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_IL2_high_6

source_name: Bulk TILs cultivated with IL2 (3000 IU/ml) for 9 days

value: Bulk TILs


title: No_20%_N1E115_HiC_NcoI rep2


title: mp41_IL2_high_5

value: melanoma patient 41


title: Nos1sc_H3K4me3

data_processing:
Data were analyzed by the HiChIP pipeline developed by the Mayo Clinic Bioinformatics Core (PMCID: PMC4152589).
ChIP-seq reads were aligned to the mm10 genome assembly using BWA
Paired-end reads were aligned by BWA against the mm10 genome build. Duplicate reads were filtered out with Picard. Peak calling was performed with MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak file is in bed format with column headers chr, peak_start, peak_end, peakname, pileup, peakCall, fold-change, -10logpvalue, -10logqvalue, peak_summit_position.

source_name: sorted NOS1+ mouse enteric neurons

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed on fixed and fragmented DNA isolated from sorted NOS1+ mouse enteric neurons using anti-H3K4me3 antibodies.
ThruPLEX DNA-seq Kit (Takara Bio, USA).

value: small intestinal NOS1+ enteric neurons

tag: antibody


title: dorsomedial hypothalamus, low workload, ZT01, rep2

description:
DMH_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: dorsomedial hypothalamus, low workload, ZT05, rep1

description:
DMH_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Nos1sc_input1


title: mp41_IL2_high_4

value: TCR beta


title: mp41_IL2_low_5


title: mp41_IL2_high_3


title: dorsomedial hypothalamus, low workload, ZT01, rep1

description:
DMH_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp41_IL2_high_2


title: cortex, high workload, ZT21, rep2

description:
COR_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: cortex

value: cortex

value: high workload


title: 37°C, rep2

first: Ben

last: Montpetit

address: One Shields Ave

department: Viticulture and Enology

institute: University of California, Davis

data_processing:
Unique sequence identifier (UMI) sequence was extracted and UMI, random primer seqence were trimed by UMI-tools (v1.0.1)
Adapter, poly A tail, low quality sequences at 3' end were trimed using bbduk (Bbmap v38.79)
Mapping of trimed reads on S. cerevisiae genome was performed by STAR (v2.7.10a)
PCR duplicates were removed by UMI-tools (v1.0.1)
Read count within the annotated genes was performed by htseq-counts (htseq v2.0.2)
Differentially expression analysis across the samples were performed using DESeq2 (v 1.38.2)
Assembly: GCF_000146045.2_R64
Supplementary files format and content: raw_readcounts_temp.xlsx file provides low read counts table. Each column has read count on every annotated genes in each samples.
Supplementary files format and content: Normalized_read_counts_temp.xlsx provides normalized read count generated by DESeq2. Each column has normalized read count on every annotated genes in each samples.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: For 25 and 30°C samples, yeast cells were grown in YPD at each temperature until OD around 1. For 37°C sample, cells grown at 25°C with OD around 1 was diluted by equal volume of pre-warmed media and initially incubated in the 37°C  water bath for 15 min. The cells were further cutured in 37°C shaker for totally 2 hours.

extract_protocol:
Cell lysate was generated by cryo-grinding and RNA was extracted using RNA extraction kit (Zymo research, R2014).
3'tag seq library was prepared using QuantSeq (Lexogen) kit.

tag: strain background

tag: genotype

value: CBP80-PPX-PrA, SNAPf-YRA1

value: Grown at 25°C followed by temperature shift to 37°C and culture for 2 hour


title: 37°C, rep1


title: mp41_IL2_high_1

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

institute: Russian National Research Medical University


title: cortex, high workload, ZT21, rep1

description:
COR_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

tag: tissue


title: mp26_FFT_LN2_2

source_name: Freshly frozen TILs (FFT)

value: melanoma patient 26


title: cortex, high workload, ZT17, rep2

description:
COR_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 30°C, rep2

value: Grown at 30°C


title: 30°C, rep1


title: cortex, high workload, ZT17, rep1

description:
COR_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 25°C, rep2

value: Grown at 25°C


title: mp26_FFT_LN2_1


title: mp26_FFT_LN1_1


title: mp26_FFT_LN1_2


title: cortex, high workload, ZT13, rep2

description:
COR_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: 25°C, rep1


title: Cbp80-PrA, tho2∆, Yra1 IP, rep2 - AVITI

description:
RNA from Cbp80-Yra1 two-step pulldown
AVITI
3771_YRA1IP_2

data_processing:
Unique sequence identifier (UMI) sequence was extracted and UMI, random primer seqence were trimed by UMI-tools (v1.0.1)
Adapter, poly A tail, low quality sequences at 3' end were trimed using bbduk (Bbmap v38.79)
rRNA reads were removed by bbsplit (Bbmap v38.79)
Mapping of trimed reads on S. cerevisiae genome was performed by STAR (v2.7.10a)
PCR duplicates were removed by UMI-tools (v1.0.1)
Read count within the annotated genes was performed by htseq-counts (htseq v2.0.2)
Differentially expression analysis across the samples were performed using DESeq2 (v 1.38.2)
Assembly: GCF_000146045.2_R64
Supplementary files format and content: raw_readcounts_conbined_Yra1.xlsx file provides low read counts table. In case of the samples which have two raw data FASTQ files, run the all processing steps individually and then summed read counts generated by htseq-counts. Each column has read count on every annotated genes in each samples.
Supplementary files format and content: Normalized_read_counts_Yra1.xlsx provides normalized read count generated by DESeq2. Each column has normalized read count on every annotated genes in each samples.

source_name: Cbp80-PrA, tho2∆, Yra1 IP, rep2

growth_protocol: Yeast cells were grown in YPD media at 30°C.

extract_protocol:
Cell lysate was generated by cryo-grinding and crosslnked by 0.2% formaldehyde. Immunoprecipitation was performed with IgG-beads to purify mRNPs via PrA tagged components. The mRNPs were eluted by HRV3C protease digestion and further purified by anti-Yra1 antibody conjugated with magnetic beads. The RNA was extracted from the two-step pulldown by phenol-chloroform extraction. Total RNA was prepared from 7.5% volume of crosslinked lysate.
3'tag seq library was prepared using QuantSeq (Lexogen) kit.

value: CBP80-PPX-PrA, SNAPf-YRA1, tho2{delta}


title: mp26_cult_IL21_niv_ifn_LN2_2

source_name: Bulk TILs cultivated with Nivolumab+IL2+IL21+IFNγ(100 μg/ml) for 9 days


title: cortex, high workload, ZT13, rep1

description:
COR_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_cult_IL21_niv_ifn_LN2_6


title: Cbp80-PrA, tho2∆, Yra1 IP, rep3 - AVITI

description:
RNA from Cbp80-Yra1 two-step pulldown
AVITI
3771_YRA1IP_3

source_name: Cbp80-PrA, tho2∆, Yra1 IP, rep3


title: cortex, high workload, ZT05, rep2

description:
COR_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_cult_IL21_niv_ifn_LN2_1


title: Cbp80-PrA, tho2∆, Yra1 IP, rep1 - AVITI

description:
RNA from Cbp80-Yra1 two-step pulldown
AVITI
3771_YRA1IP_1

source_name: Cbp80-PrA, tho2∆, Yra1 IP, rep1


title: Cbp80-PrA, tho2∆, INPUT, rep3 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3771_INPUT_3

source_name: Cbp80-PrA, tho2∆, INPUT, rep3


title: cortex, high workload, ZT05, rep1

description:
COR_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_cult_IL21_niv_ifn_LN1_6


title: Cbp80-PrA, tho2∆, INPUT, rep3 - AVITI

description:
Total RNA
AVITI
3771_INPUT_3


title: cortex, high workload, ZT01, rep1

description:
COR_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Cbp80-PrA, tho2∆, INPUT, rep2 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3771_INPUT_2

source_name: Cbp80-PrA, tho2∆, INPUT, rep2


title: cortex, low workload, ZT21, rep2

description:
COR_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: Cbp80-PrA, tho2∆, INPUT, rep1 - AVITI

description:
Total RNA
AVITI
3771_INPUT_1

source_name: Cbp80-PrA, tho2∆, INPUT, rep1


title: Cbp80-PrA, tho2∆, INPUT, rep2 - AVITI

description:
Total RNA
AVITI
3771_INPUT_2


title: mp26_cult_IL21_niv_ifn_LN1_3


title: cortex, low workload, ZT21, rep1

description:
COR_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cortex, high workload, ZT09, rep1

description:
COR_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cortex, low workload, ZT17, rep2

description:
COR_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_cult_IL21_niv_ifn_LN1_1


title: mp26_cult_IL21_LN2_4


title: mp26_cult_IL21_niv_ifn_LN1_4


title: mp26_cult_IL21_niv_ifn_LN1_2


title: cortex, high workload, ZT09, rep2

description:
COR_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No tag, tho2∆, Yra1 IP, rep1 - AVITI

description:
RNA from mock-Yra1 two-step pulldown
AVITI
3605_YRA1IP_1

source_name: No tag, tho2∆, Yra1 IP, rep1

value: SNAPf-YRA1, tho2{delta}


title: No tag, tho2∆, INPUT, rep3 - AVITI

description:
Total RNA
AVITI
3605_INPUT_3

source_name: No tag, tho2∆, INPUT, rep3


title: cortex, high workload, ZT01, rep2

description:
COR_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: mp26_cult_IL21_LN2_3

source_name: Bulk TILs cultivated with IL2(200 IU/ml)+IL21(25ng/ml) for 9 days


title: mp26_cult_IL21_niv_ifn_LN1_5


title: No tag, tho2∆, Yra1 IP, rep3 - AVITI

description:
RNA from mock-Yra1 two-step pulldown
AVITI
3605_YRA1IP_3

source_name: No tag, tho2∆, Yra1 IP, rep3


title: cortex, low workload, ZT13, rep1

description:
COR_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: mp26_cult_IL21_LN2_2


title: cortex, low workload, ZT17, rep1

description:
COR_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cortex, low workload, ZT09, rep1

description:
COR_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No tag, tho2∆, INPUT, rep1 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3605_INPUT_1

source_name: No tag, tho2∆, INPUT, rep1


title: mp26_cult_IL21_LN2_1


title: No tag, tho2∆, INPUT, rep2 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3605_INPUT_2

source_name: No tag, tho2∆, INPUT, rep2


title: cortex, low workload, ZT09, rep2

description:
COR_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_cult_IL21_LN1_6


title: No tag, tho2∆, INPUT, rep2 - AVITI

description:
Total RNA
AVITI
3605_INPUT_2


title: cortex, low workload, ZT05, rep2

description:
COR_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cortex, low workload, ZT05, rep1

description:
COR_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No tag, tho2∆, Yra1 IP, rep2 - AVITI

description:
RNA from mock-Yra1 two-step pulldown
AVITI
3605_YRA1IP_2

source_name: No tag, tho2∆, Yra1 IP, rep2


title: mp26_cult_IL21_LN1_3


title: mp26_cult_IL21_LN1_2


title: No tag, tho2∆, INPUT, rep1 - AVITI

description:
Total RNA
AVITI
3605_INPUT_1


title: mp26_cult_IL21_LN1_1


title: cortex, low workload, ZT01, rep2

description:
COR_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: cortex


title: cortex, low workload, ZT13, rep2

description:
COR_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Hpr1-PrA, wildtype, Yra1 IP, rep3 - AVITI

description:
RNA from Hpr1-Yra1 two-step pulldown
AVITI
3593_YRA1IP_3

source_name: Hpr1-PrA, wildtype, Yra1 IP, rep3

value: HPR1-PPX-PrA, SNAPf-YRA1


title: Hpr1-PrA, wildtype, Yra1 IP, rep1 - AVITI

description:
RNA from Hpr1-Yra1 two-step pulldown
AVITI
3593_YRA1IP_1

source_name: Hpr1-PrA, wildtype, Yra1 IP, rep1


title: mp26_cult_IL2_high_LN2_2

source_name: Bulk TILs cultivated with IL2 (3000 IU/ml) for 9 days

value: Bulk TILs


title: cortex, low workload, ZT01, rep1

description:
COR_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Hpr1-PrA, wildtype, INPUT, rep3 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3593_INPUT_3

source_name: Hpr1-PrA, wildtype, INPUT, rep3


title: mp26_cult_IL2_high_LN2_3


title: Hpr1-PrA, wildtype, Yra1 IP, rep2 - AVITI

description:
RNA from Hpr1-Yra1 two-step pulldown
AVITI
3593_YRA1IP_2

source_name: Hpr1-PrA, wildtype, Yra1 IP, rep2


title: cerebellum, high workload, ZT21, rep2

description:
CER_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: cerebellum

value: cerebellum


title: cerebellum, high workload, ZT21, rep1

description:
CER_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Hpr1-PrA, wildtype, INPUT, rep3 - AVITI

description:
Total RNA
AVITI
3593_INPUT_3


title: mp26_cult_IL2_high_LN2_1


title: mp26_cult_IL2_high_LN1_3


title: Hpr1-PrA, wildtype, INPUT, rep2 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3593_INPUT_2

source_name: Hpr1-PrA, wildtype, INPUT, rep2


title: Hpr1-PrA, wildtype, INPUT, rep1 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
3593_INPUT_1

source_name: Hpr1-PrA, wildtype, INPUT, rep1


title: mp26_cult_IL2_high_LN1_2


title: mp26_cult_IL2_high_LN1_1


title: cerebellum, high workload, ZT17, rep1

description:
CER_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_CD8_not-DP_CD137_TAA_restimulated

source_name: FACS-sorted and expanded on CD3/CD28 for 2 weeks CD39 PD-1 not-double-positive (not-DP) CD8+ melanoma TILs, upregulating CD137 upon stimulation with TAA-loaded APCs

value: CD8+ CD39 PD-1 not-DP CD137+


title: Hpr1-PrA, wildtype, INPUT, rep2 - AVITI

description:
Total RNA
AVITI
3593_INPUT_2


title: cerebellum, high workload, ZT13, rep2

description:
CER_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cerebellum, high workload, ZT13, rep1

description:
CER_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Cbp80-PrA, wildtype, Yra1 IP, rep3 - AVITI

description:
RNA from Cbp80-Yra1 two-step pulldown
AVITI
2527_YRA1IP_3

source_name: Cbp80-PrA, wildtype, Yra1 IP, rep3


title: cerebellum, high workload, ZT09, rep2

description:
CER_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_CD8_DP_CD137_TAA_restimulated

source_name: FACS-sorted and expanded on CD3/CD28 for 2 weeks CD39+ PD-1+ CD8+ melanoma TILs, upregulating CD137 upon stimulation with TAA-loaded APCs

value: TCR beta


title: Cbp80-PrA, wildtype, Yra1 IP, rep2 - Illumina NextSeq 500

description:
RNA from Cbp80-Yra1 two-step pulldown
Illumina NextSeq 500
2527_YRA1IP_2

source_name: Cbp80-PrA, wildtype, Yra1 IP, rep2


title: Hpr1-PrA, wildtype, INPUT, rep1 - AVITI

description:
Total RNA
AVITI
3593_INPUT_1


title: mp26_CD8_not-DP_CD137_control_restimulated

source_name: FACS-sorted and expanded on CD3/CD28 for 2 weeks CD39 PD-1 not-double-positive (not-DP) CD8+ melanoma TILs, upregulating CD137 upon stimulation with unloaded APCs


title: cerebellum, high workload, ZT09, rep1

description:
CER_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp26_CD8_DP_CD137_control_restimulated

source_name: FACS-sorted and expanded on CD3/CD28 for 2 weeks CD39+ PD-1+ CD8+ melanoma TILs, upregulating CD137 upon stimulation with unloaded APCs


title: Cbp80-PrA, wildtype, Yra1 IP, rep2 - AVITI

description:
RNA from Cbp80-Yra1 two-step pulldown
AVITI
2527_YRA1IP_2


title: Cbp80-PrA, wildtype, Yra1 IP, rep1 - AVITI

description:
RNA from Cbp80-Yra1 two-step pulldown
AVITI
2527_YRA1IP_1

source_name: Cbp80-PrA, wildtype, Yra1 IP, rep1


title: cerebellum, high workload, ZT05, rep2

description:
CER_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp44_CD8_nDP_2

source_name: CD39 PD-1 not-double-positive (not-DP) CD8+ melanoma TILs

value: CD8+ CD39 PD-1 not-DP

value: melanoma patient 44


title: cerebellum, high workload, ZT17, rep2

description:
CER_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: high workload


title: mp44_CD8_nDP_1


title: cerebellum, high workload, ZT01, rep2

description:
CER_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp44_CD8_DP_2

source_name: CD39+ PD-1+ CD8+ melanoma TILs


title: cerebellum, high workload, ZT01, rep1

description:
CER_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp44_CD8_DP_1


title: Cbp80-PrA, wildtype, INPUT, rep3 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
2527_INPUT_3

source_name: Cbp80-PrA, wildtype, INPUT, rep3

value: CBP80-PPX-PrA, SNAPf-YRA1


title: Cbp80-PrA, wildtype, INPUT, rep2 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
2527_INPUT_2

source_name: Cbp80-PrA, wildtype, INPUT, rep2


title: Cbp80-PrA, wildtype, INPUT, rep3 - AVITI

description:
Total RNA
AVITI
2527_INPUT_3


title: mp42_CD8_nDP_2

value: melanoma patient 42


title: Cbp80-PrA, wildtype, INPUT, rep2 - AVITI

description:
Total RNA
AVITI
2527_INPUT_2


title: cerebellum, low workload, ZT21, rep1

description:
CER_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Cbp80-PrA, wildtype, INPUT, rep1 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
2527_INPUT_1

source_name: Cbp80-PrA, wildtype, INPUT, rep1


title: mp42_CD8_nDP_1


title: mp42_CD8_DP_2


title: cerebellum, low workload, ZT17, rep2

description:
CER_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp42_CD8_DP_1


title: No tag, wildtype, Yra1 IP, rep3 - AVITI

description:
RNA from mock-Yra1 two-step pulldown
AVITI
2412_YRA1IP_3

source_name: No tag, wildtype, Yra1 IP, rep3


title: mp41_CD8_nDP_2

value: melanoma patient 41


title: cerebellum, low workload, ZT13, rep2

description:
CER_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: Cbp80-PrA, wildtype, INPUT, rep1 - AVITI

description:
Total RNA
AVITI
2527_INPUT_1


title: mp41_CD8_nDP_1


title: cerebellum, high workload, ZT05, rep1

description:
CER_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cerebellum, low workload, ZT09, rep2

description:
CER_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cerebellum, low workload, ZT13, rep1

description:
CER_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No tag, wildtype, INPUT, rep3 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
2412_INPUT_3

source_name: No tag, wildtype, INPUT, rep3


title: No tag, wildtype, Yra1 IP, rep2 - AVITI

description:
RNA from mock-Yra1 two-step pulldown
AVITI
2412_YRA1IP_2

source_name: No tag, wildtype, Yra1 IP, rep2


title: No tag, wildtype, Yra1 IP, rep1 - AVITI

description:
RNA from mock-Yra1 two-step pulldown
AVITI
2412_YRA1IP_1

source_name: No tag, wildtype, Yra1 IP, rep1


title: mp41_CD8_DP_2


title: cerebellum, low workload, ZT09, rep1

description:
CER_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: cerebellum


title: cerebellum, low workload, ZT21, rep2

description:
CER_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No tag, wildtype, INPUT, rep3 - AVITI

description:
Total RNA
AVITI
2412_INPUT_3


title: cerebellum, low workload, ZT05, rep2

description:
CER_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp34_CD8_not_DP_1

value: melanoma patient 34


title: cerebellum, low workload, ZT05, rep1

description:
CER_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: cerebellum, low workload, ZT01, rep2

description:
CER_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp34_CD8_not_DP_2


title: No tag, wildtype, INPUT, rep2 - AVITI

description:
Total RNA
AVITI
2412_INPUT_2

source_name: No tag, wildtype, INPUT, rep2


title: No tag, wildtype, INPUT, rep2 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
2412_INPUT_2


title: No tag, wildtype, INPUT, rep1 - Illumina NextSeq 500

description:
Total RNA
Illumina NextSeq 500
2412_INPUT_1

source_name: No tag, wildtype, INPUT, rep1


title: brainstem, high workload, ZT21, rep2

description:
BRS_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: brainstem

value: brainstem


title: cerebellum, low workload, ZT17, rep1

description:
CER_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: cerebellum, low workload, ZT01, rep1

description:
CER_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp34_CD8_DP_2


title: mp34_CD8_DP_1


title: mp41_CD8_DP_1


title: brainstem, high workload, ZT21, rep1

description:
BRS_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: No tag, wildtype, INPUT, rep1 - AVITI

description:
Total RNA
AVITI
2412_INPUT_1


title: mp26_notDP_LN1

value: melanoma patient 26


title: brainstem, high workload, ZT17, rep1

description:
BRS_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: Proc>GFP, control 5, scRNAseq

city: Bethesda

first: Mihaela

last: Serpe

address: 35 Convent Dr, Bldg 35, Room 1C-1016

department: NICHD

institute: NIH

description: 10X Genomics

data_processing:
Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was utilized to: (1) Generate a reference genome with optional addition of transgenes; (2) Demultiplex 10X run data from an Illumina sequencer; and (3) Align the data to the reference genome and generate read count matrices.
Starting to count matrices, until the genesis of single Seurat objects we used a multistage analysis pipeline that we described in Vicidomini et al., 2021 (PMID: 33600085). The read10xCounts function from the DropletUtils package was used to import the raw Cell Ranger output data into R as SingleCellExperiment (sce) objects. Empty droplets with low read counts were removed using the DropletUtils package. Barcodes with a profile significantly different from ambient RNA at a false discovery rate of 0.1% were retained. Next, low-quality barcodes/cells were removed based on specific criteria, including high mitochondrial fraction, high heat shock-related genes, low ribosomal fraction, low number of detected genes, and low log-transformed number of genes/UMI. Genes expressed in at least three cells across all samples were selected for further analysis. To address coverage differences between cells, normalization by deconvolution was performed using the scran package. Using Seurat V.3, the SingleCellExperiment (sce) objects were converted to Seurat objects.
Sample integration, dimensional reduction, and cell clustering were performed with Seurat. The same package has been used to generate t-distributes stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) plots for visualization of cell clusters. Differential gene expression analysis was performed using FindMarkers function with Wilcox rank-sum test as a default parameter. Cluster-specific marker genes were identified with a minimum log fold-change of 0.4 and a Bonferroni-adjusted p-value below 0.05.
For sub-clustering analysis,  all steps of the data processing workflow were repeated for specific groups of cells. First, we used the subset() function from Seurat package to isolate various groups of cells and remove contaminating cells identified by specific markers.  The groups of cells were next split based on the sample of origin and re-normalized, followed by integration, scaling, dimensionality reduction and sub-clustering using suitable parameters.
GFP-sorted populations of neurons were processed by generating count matrices from raw sequencing data and removing low-quality barcodes/cells as described. We then performed normalization, identified the most variable genes, scaled the data, and conducted dimensionality reduction. To ensure quality, we checked for marker genes that are not typically co-expressed together (e.g., Orcokinin, Capa, and Lk or glial markers with elav). Any identified doublets were removed.Next, we integrated the twit>GFP sorted cells with the unsorted twit+ cells from the initial dataset to enable downstream clustering and gene expression analysis. For the retained Proc>GFP sorted cells, they were directly analyzed for clustering and differentially expressed gene analysis.
Assembly: Drosophila melanogaster genome assembly BDGP6.28  (https://uswest.ensembl.org/Drosophila_melanogaster/Info/Index).
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz (cellranger raw_feature_bc_matrix)
Supplementary files format and content: rds (Seurat object)

organism: Drosophila melanogaster

source_name: Ventral cord

extract_protocol:
VNCs were manually dissected from wandering third instar larvae and gathered into iced Schneider’s medium supplemented with 0.1 µM TTX, 50 µM AP-5 and 20 µM CNQX, to inhibit neural activity. The collected VNCs were transferred to dissociation solution (1 mg/ml Collagenase/Dispase, 0.10 Wunsch units/ml Liberase in RNase/DNase-free water) and incubated for 1 h at 25°C. Samples were triturated by gently pipetting up and down ~200 times; the enzymatic activities were stopped by adding 1 volume of ice-cold Schneider’s medium followed by another ~100 cycles of trituration. The cell suspensions were filtered using 30 μm pre-separation filters to remove clumps and the proportion of viable cells was estimated using trypan blue. The detailed protocol is described in Nguyen et al., 2021 (PMID: 33620770). For the FACS sorted samples, before sorting, cells were passed through 40 mm cell strainer (Corning) and stained with 1 mg/ml DAPI  to label dead cells. The cells were then sampled using a MoFlo Astrios EQ high speed cell sorter (Beckman Coulter) equipped with standard UV (355 nm) and blue (488 nm) lasers and appropriate filter sets to detect GFP and DAPI emissions. Cell sorting was performed using Summit software V6.3.016900 (Beckman Coulter) with electronic gating strategy set to exclude dead cells and collect a vital population of GFP-expressing neurons. Sorted cells were immediately used for single-cell RNA-seq library preparation.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10X Genomics). For more detail also see Nguyen et al. 2021). Briefly, 9000-10000 cells per sample 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). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with DynaBead Myone Silance magnetic beads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequencet library contruction. During the library construction Ilumina R2 primer sequence, paired-end construct with P5 and P7 sequences and a sample index were added

value: Ventral cord

value: Third instar larvae


title: mp26_CD8_DP_LN1


title: mp26_notDP_LN2


title: FACS-enriched Proc>GFP, scRNAseq

description: 10X Genomics


title: mp26_CD8_DP_LN2


title: brainstem, high workload, ZT13, rep2

first: Laura

last: van Rosmalen

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description:
BRS_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: male


title: FACS-enriched twit>GFP, scRNAseq

description: 10X Genomics

value: UAS-GFP.nls/+; twit-Gal4/+


title: mp24_CD8_not_DP_2

value: melanoma patient 24


title: brainstem, high workload, ZT13, rep1

description:
BRS_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brainstem, high workload, ZT17, rep2

description:
BRS_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: brainstem, high workload, ZT09, rep1

description:
BRS_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: twit>GFP, control 2, scRNAseq

description: 10X Genomics


title: RN2>GFP, control 4, scRNAseq

description: 10X Genomics


title: brainstem, high workload, ZT09, rep2

description:
BRS_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp24_CD8_DP_2

value: TCR beta


title: w1118, control 1, scRNAseq

description: 10X Genomics


title: mp24_CD8_not_DP_1

value: CD8+ CD39 PD-1 not-DP


title: brainstem, high workload, ZT05, rep2

description:
BRS_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: mp44_CD4_nDP_2

source_name: CD39 PD-1 not-double-positive (not-DP) CD4+ melanoma TILs

value: CD4+ CD39 PD-1 not-DP

value: melanoma patient 44


title: CFP+YFP G2 ISCs batch 2

city: Canterbury

first: Jerome

last: Korzelius

state: Kent

address: Ingram Building, University of Kent

institute: University of Kent

data_processing:
Reads mapped to Drosophila genome using HISAT2 in the Galaxy user suite
Mapped reads were counted using the HTSeq count package in the Galaxy user suite
Differential expression analysis was done using DeSeq2 in the Galaxy user suite
Assembly: BDGP6

source_name: Intestine

growth_protocol: 3-5 day old adult female Drosophila were shifted from 25C to 29C for 2 days to induce expression of FlyFucci.

extract_protocol:
Total RNA was isolated using the Arcturus PicoPure kit. From this, we amplified mRNA using the Riboamp HS kit (ThermoFisher)
Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina) without the mRNA enrichment steps
50 bp single-end RNA-Seq

treatment_protocol: Guts were dissociated using Elastase as described previously. CFP and CFP+YFP cells were sorted using the FACSAria II system

value: Intestine

value: ISC

value: w; esg-Gal4, P{UAS-CFP.E2f.1-230}4 P{UAS-Venus.CycB.1-266}7;P{His2AV-mRFP1}/tub-Gal80ts, Su(H)-Gal80

value: 5-7 day old female adults shifted to 29C for 2 days to induce expression


title: CFP+YFP G2 ISCs batch 3


title: mp44_CD4_nDP_1


title: brainstem, high workload, ZT05, rep1

description:
BRS_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: brainstem

value: high workload


title: brainstem, high workload, ZT01, rep2

description:
BRS_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: CFP+YFP G2 ISCs batch 1


title: brainstem, low workload, ZT21, rep2

description:
BRS_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: mp44_CD4_DP_2

source_name: CD39+ PD-1+ CD4+ melanoma TILs


title: CFP_Fucci G1 ISCs batch 2


title: futsch-GFP, vGlut-RFP, control 3, scRNAseq

description: 10X Genomics

value: futsch-GFP, vGlut-RFP


title: brainstem, high workload, ZT01, rep1

description:
BRS_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: CBA/CaJ


title: CFP_Fucci G1 ISCs batch 3